diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/clis/restraints/z_surface_restraints.py b/.venv_haddock/lib/python3.12/site-packages/haddock/clis/restraints/z_surface_restraints.py new file mode 100644 index 0000000000000000000000000000000000000000..e3e24afe81e89e5a5b903005ce7aab498978ada1 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/clis/restraints/z_surface_restraints.py @@ -0,0 +1,745 @@ +"""haddock3-restraints z-surface-restraints subcommand. + +Generate both z-restraints and corresponding z-surfaces based on +input pdb structure and residue selection. + +Usage: + haddock3-restraints z-surface-restraints + --pdb + --residues + --output + --spacing + --x-size + --y-size + --z-padding + +e.g: +haddock3-restraints z-surface-restraints + --pdb mystructure.pdb + --residues 1,2,3 7,8,9 + --spacing 20 + --x-size 200 + --y-size 200 + --z-padding 5 + --output myZrestaints +""" + +import logging +import os +from pathlib import Path + +from haddock.core.typing import Generator, Optional, Union +from haddock.libs.librestraints import read_structure, calc_euclidean + + +# As this script is a subcommand of the `haddock3-restraints` cli, +# it requires its own options and arguments that are managed here. +def add_z_surf_restraints_arguments(z_surf_restraints_subcommand): + """Add arguments to the z_plan subcommand.""" + z_surf_restraints_subcommand.add_argument( + "--pdb", "-p", + help="Path to a pdb file.", + required=True, + default='', + type=str, + ) + + z_surf_restraints_subcommand.add_argument( + "--residues", "-r", + help=( + "List of comma separated residues (can be multiple selections). " + "Example 1,2,3 7,8,9 for two selections." + ), + required=False, + default=[], + nargs='+', + type=str, + ) + + z_surf_restraints_subcommand.add_argument( + "--output", "-o", + help=( + "Base output path. This script will generate two files, " + "therefore no extention needed here" + ), + required=False, + default=None, + type=str, + ) + + z_surf_restraints_subcommand.add_argument( + "--spacing", "-s", + type=float, + help="Spacing between two beads (A)", + required=False, + default=20, + ) + + z_surf_restraints_subcommand.add_argument( + "--x-size", + "-x", + help="Size of the plan in X dimension (A)", + required=False, + default=100, + type=float, + ) + + z_surf_restraints_subcommand.add_argument( + "--y-size", + "-y", + help="Size of the plan in Y dimension", + required=False, + default=100, + type=float, + ) + + z_surf_restraints_subcommand.add_argument( + "--z-padding", + "-z", + help="Additional padding between two external plans.", + required=False, + default=5.0, + type=float, + ) + + z_surf_restraints_subcommand.add_argument( + "--log_level", + default='INFO', + choices=('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'), + help="Logging level", + required=False, + ) + + return z_surf_restraints_subcommand + + +def setup_logging(log_level: str = "INFO") -> None: + """Set log level and format.""" + logging.basicConfig( + level=log_level, + format='%(asctime)s L%(lineno)d %(levelname)s - %(message)s', + datefmt='%d/%m/%Y %H:%M:%S', + ) + + +############################ +# SET OF USEFULL FUNCTIONS # +############################ +def load_selected_resiudes_coords( + pdb_fpath: Union[str, Path], + selections: dict[str, list[int]], + ) -> tuple[dict[str, list[tuple[float, float, float]]], list[str], list[str]]: + """Load coordinates of selected residues. + + Parameters + ---------- + pdb_fpath : Union[str, Path] + Path to the PDB file to be parsed. + selections : dict[str, list[int]] + Dictionary holding the various residues indices for each selection. + + Returns + ------- + selection_coords: dict[str, list[tuple[float, float, float]]] + Dictionary holding the various Calpha coordinates for each selection. + """ + # Load structures atom coordinates + pdb_atoms = read_structure(pdb_fpath) + # Set paring variables + selection_coords: dict[str, list[tuple[float, float, float]]] = {} + selected_chains: list[str] = [] + selected_atoms: list[str] = [] + # Loop over atoms + for chain, resi, atname, coords in pdb_atoms: + # Simplify the probleme to Calpha/Phosphates/BackBone atoms only + # FIXME: maybe change P to C1 or C9 ? + if not atname in ("CA", "P", "BB", ): + continue + # Loop over selections + for selection, sele_resis in selections.items(): + # Check if residue of interest + if resi in sele_resis: + # Make sure the key is created + selection_coords.setdefault(selection, []) + # Hold this coordinates + selection_coords[selection].append(coords) + # Also add chain and atom type + selected_chains.append(chain) + selected_atoms.append(atname) + set_selected_chains = list(set(selected_chains)) + set_selected_atoms = list(set(selected_atoms)) + return selection_coords, set_selected_chains, set_selected_atoms + + +def compute_barycenter( + resi_coords: list[tuple[float, float, float]], + ) -> tuple[float, float, float]: + """Compute center of mass of multiple resiudes coordinates. + + Parameters + ---------- + resi_coords : list[tuple[float, float, float]] + List of Calpha coordinates. + + Returns + ------- + barycenter : tuple[float, float, float] + Corrdinates of the center of mass. + """ + # Combine coordinates + xs, ys, zs = [], [], [] + for coords in resi_coords: + xs.append(coords[0]) + ys.append(coords[1]) + zs.append(coords[2]) + # Compute average + x_avg = sum(xs) / len(xs) + y_avg = sum(ys) / len(ys) + z_avg = sum(zs) / len(zs) + # Return barycenter + barycenter = (x_avg, y_avg, z_avg) + return barycenter + + +def load_selections(residues_lists: list[str]) -> dict[str, list[int]]: + """Split and cast residues from an initial string to list. + + Parameters + ---------- + residues_lists : list[str] + List of strings containing coma separated resiudes indices. + + Returns + ------- + selections: dict[str, list[int]] + Dictionary of resiudes indices. + """ + selections: dict[str, list[int]] = {} + for listid, str_resiudes in enumerate(residues_lists, start=1): + resid_indices: list[int] = [] + selection_key = f"selection_{listid}" + for strresid in str_resiudes.split(','): + try: + resid = int(strresid) + except Exception as _e: + msg = f"Could not cast residue {strresid} from {selection_key}" + logging.warning(msg) + else: + resid_indices.append(resid) + if resid_indices == []: + err_msg = f"Not considering {selection_key} as it is empty !" + logging.error(err_msg) + else: + selections[selection_key] = resid_indices + return selections + + +def get_z_coords( + select_coords: dict[str, list[tuple[float, float, float]]], + padding: float = 5.0, + ) -> dict[str, float]: + """Generate z-coordinates from selection of residues. + + Here the idea is to find the most distant points between selections, + and project it on a Z axis to be able to later orient the protein. + + Parameters + ---------- + selection_coords: dict[str, list[tuple[float, float, float]]] + Dictionary holding the various Calpha coordinates for each selection. + padding : float, optional + Extra padding (in Angstrom) of z-coordinate, by default 10 + + Returns + ------- + selection_z : dict[str, float] + Z coodrinate for each selection. + """ + # Default when less than 1 selection was made + if select_coords == {}: + return {"z_1": 0} + elif len(select_coords.keys()) == 1: + return {s: 0 for s in select_coords.keys()} + + # Compute geometrical center + select_centers = { + select: compute_barycenter(select_resids_coords) + for select, select_resids_coords in select_coords.items() + } + # Compute distances + dists: dict[str, dict[str, float]] = {s: {} for s in select_centers.keys()} + max_dist: float = -1 + max_dist_keys: list[str] = [] + for select, center in select_centers.items(): + for select2, center2 in select_centers.items(): + if select == select2: + continue + # Compute dist + dist = calc_euclidean(center, center2) + # Hold data + dists[select][select2] = dist + dists[select2][select] = dist + # Define max + if max_dist < dist: + max_dist = dist + max_dist_keys = [select, select2] + # Initiate z-coords boundaries + max_z = (padding + max_dist) / 2 + # Compute Z coords for external surfaces + selection_z = { + max_dist_keys[0]: max_z, + max_dist_keys[1]: -max_z, + } + # Compute Z coords for internal surfaces (when nb. selections >= 3) + for select, dist in dists.items(): + # If the selection is part of the external surfaces + if select in max_dist_keys: + continue + # Compute location of z coordinate + dist_to_upper = max_z - dist[max_dist_keys[0]] + dist_to_lower = dist[max_dist_keys[1]] - max_z + select_z_coord = (dist_to_upper + dist_to_lower) / 2 + # Hold data + selection_z[select] = select_z_coord + + return selection_z + + +def gen_z_restraints( + res_select: dict[str, list[int]], + selection_z: dict[str, float], + rest_dist: float = 7.5, + segids: list[str] = ["A"], + atome_types: list[str] = ["CA"], + ) -> str: + """Generate set of z ambiguous restraints according to residue selections. + + Parameters + ---------- + res_select : dict[str, list[int]] + Dictionary holding the various residues indices for each selection. + selection_z : dict[str, float] + Z coodrinate for each selection. + rest_dist : float, optional + Upper boundary (in Angstrom) of satisfied restraints, by default 7.5 + + Returns + ------- + all_restraints : str + A string containing the AIR restraints. + """ + # Gather all coordinates + all_z_coords = [zcoord for zcoord in selection_z.values()] + # Point min and max values + minz = min(all_z_coords) + maxz = max(all_z_coords) + # Initiate restraints holder + restraints: list[str] = [] + # z_padding variable is used as a padding for the Z beads selection. + # This is meant for the CNS selection method using lt(lower than) + # and gt (geater than) rather than equal to. + z_padding: float = 0.1 + # Compile chain selection + chain_selection_string = _compile_multiple_cns_selections( + "segid", segids, + ) + # Compile atome selection + atom_selection_string = _compile_multiple_cns_selections( + "name", atome_types, + ) + # Loop over selections + for select in res_select.keys(): + # Point data + residues = res_select[select] + z_coord = selection_z[select] + # Add comment + list_residues = ",".join([str(r) for r in residues]) + restraints.append(f"! z restraints for {select}: {list_residues}") + # Loop over residues selection + for resid in residues: + # Compute lower/greater than z-coord + lt_coord = z_coord + z_padding + gt_coord = z_coord - z_padding + # If the lower Z coordinate plan + if z_coord == minz: + rest = ( + f"assign (resid {resid:>7d} and " + f"{atom_selection_string} and {chain_selection_string}) " + f"(name SHA and attr z lt {lt_coord:>-8.2f}) " + f"{rest_dist:.1f} {rest_dist:.1f} 0.0" + ) + # If the upper Z coordinate plan + elif z_coord == maxz: + rest = ( + f"assign (resid {resid:>7d} and " + f"{atom_selection_string} and {chain_selection_string}) " + f"(name SHA and attr z gt {gt_coord:>-8.2f}) " + f"{rest_dist:.1f} {rest_dist:.1f} 0.0" + ) + # If in between lower and upper plans (when nb. plans >= 3) + else: + rest = ( + f"assign (resid {resid:>7d} and " + f"{atom_selection_string} and {chain_selection_string}) " + f"(name SHA and attr z lt {lt_coord:>-8.2f} " + f"and attr z gt {gt_coord:>-8.2f}) " + f"{rest_dist:.1f} {rest_dist:.1f} 0.0" + ) + restraints.append(rest) + all_restraints = os.linesep.join(restraints) + return all_restraints + + +def _compile_multiple_cns_selections( + selection_key: str, + selections: list[str], + logical_operator: str = 'OR', + ) -> str: + """Generate a selection from multiple ones using logical operator. + + Parameters + ---------- + selection_key : str + Name of the selection key. (e.g.: segid, name, resid, ...) + selections : list[str] + List of selections. + + Returns + ------- + combined_selection : str + The combined selection. + """ + assert len(selections) >= 1 + if len(selections) == 1: + return f"{selection_key} {selections[0]}" + compiled_selections = [ + f"{selection_key} {select}" + for select in selections + ] + joined_selections = f" {logical_operator} ".join(compiled_selections) + combined_selection = f"({joined_selections})" + return combined_selection + + +def output_data( + restraints: str, + plans: str, + output: Optional[Union[str, Path]] = None, + ) -> tuple[str, str]: + """Write output files. + + Parameters + ---------- + restraints : str + String containing the ambiguous restraints. + plans : str + String containing shape beads coordinates as PDB file. + output : Optional[Union[str, Path]], optional + Base output path, by default None + + Returns + ------- + restraints_fpath: str + Path to the generated AIRs. + beadplans_fpath : str + Path to the generated PDB file containing beads. + """ + # Define base output path if not given + if not output: + output = 'Zrestraints' + # Write restraints + restraints_fpath = f"{output}.tbl" + with open(restraints_fpath, 'w') as filout: + filout.write(restraints) + # Write restraints + beadplans_fpath = f"{output}_beads.pdb" + with open(beadplans_fpath, 'w') as filout: + filout.write(plans) + # Return filepaths + return restraints_fpath, beadplans_fpath + + +def gen_bead_plans( + spacing: float = 40, + x_size: float = 200, + y_size: float = 200, + z_coords: Optional[list[float]] = None, + ) -> str: + """Generate multiple bead plans. + + Parameters + ---------- + spacing : float, optional + Spacing (in Angstrom) between beads in same dimension, by default 40 + x_size : float, optional + Width (in Angstrom) of the plan, by default 200 + y_size : float, optional + Height (in Angstrom) of the plan, by default 200 + z_coords : Optional[list[float]], optional + List of z-coordinates where to generate plans, by default None + + Returns + ------- + bead_plans : str + A PDB file containing multiple plans. + """ + # Presets + bead_plans: str = '' + resindex: int = 0 + if not z_coords: + z_coords = [0] + # Loop over z-coords + for z in z_coords: + plan, resindex = bead_plan( + spacing=spacing, + x_size=x_size, + y_size=y_size, + z_coord=z, + resindex=resindex, + ) + bead_plans += plan + return bead_plans + + +def bead_plan( + spacing: float = 40, + x_size: float = 200, + y_size: float = 200, + z_coord: float = 0, + resindex: int = 0, + ) -> tuple[str, int]: + """Generate a PDB plan made of beads. + + Parameters + ---------- + spacing : float, optional + Spacing (in Angstrom) between beads in same dimension, by default 40 + x_size : float, optional + Width (in Angstrom) of the plan, by default 200 + y_size : float, optional + Height (in Angstrom) of the plan, by default 200 + z_coord : float, optional + Z-coordinate where to generate the plan, by default 0 + resindex : int, optional + From which resiude to start the , by default 0 + + Returns + ------- + plan : str + The PDB plan made of beads. + resindex : int + Index of the last residue index added. + """ + plan_beads: list[str] = [] + # Loop over x coords + for x_coord in step_coords(x_size, spacing): + # Loop over y coords + for y_coord in step_coords(y_size, spacing): + resindex += 1 + # Generate new bead + bead = shape_bead(x_coord, y_coord, z_coord, resindex) + plan_beads.append(bead) + # Finalize plan + plan = ''.join(plan_beads) + return plan, resindex + + +def step_coords(_size: float, _spacing: float) -> Generator[float, None, None]: + """Generate set of evenly spaced coordinates between of defined size. + + Parameters + ---------- + size : float + Size (in Angstrom) to be sampled + spacing : float + Spacing between each coordinate + + Return + ------ + Generator[float, None, None] + 1D coodinate of current position. + """ + # Convert to absolute value + size = abs(_size) + spacing = abs(_spacing) + # Check if size is indeed greater than spacing + if spacing > size: + logging.error("Size must be greater than spacing!") + raise ValueError + return _step_coords(size, spacing) + + +def _step_coords(size: float, spacing: float) -> Generator[float, None, None]: + """Generate set of evenly spaced coordinates between of defined size. + + Parameters + ---------- + size : float + Size (in Angstrom) to be sampled + spacing : float + Spacing between each coordinate + + Yields + ------ + float + 1D coodinate of current position. + """ + # Define initial position + coord = - (size / 2) + # Define oversized position + oversized = (size + spacing) / 2 + # Loop until oversized + while coord <= oversized: + yield coord + coord += spacing + + +def shape_bead( + x: float, + y: float, + z: float, + resindex: int, + chain: str = "S", + atindex: int = 1, + bfactor: float = 1.00, + ) -> str: + """Generate a PDB shape bead. + + Parameters + ---------- + x : float + x coordinate of the bead + y : float + y coordinate of the bead + z : float + z coordinate of the bead + resindex : int + Residue index + chain : str, optional + Chain id, by default "S" + atindex : int, optional + Atome index, by default 1 + bfactor : float, optional + B-factor of the bead, by default 1.00 + + Returns + ------- + bead : str + A valid PDB shape bead. + """ + bead = f"ATOM {atindex:>5d} SHA SHA {chain}{resindex:>4d} {x:-8.3f}{y:-8.3f}{z:-8.3f} 1.00{bfactor:6.2f} SHA {os.linesep}" # noqa : E501 + return bead + + +def _get_ideal_restraint_dist(spacing: float) -> float: + """Computes ideal restraint distance based on spacing. + + Basically, want to return (spacing / 2) - 2 + + Parameters + ---------- + spacing : int + Spacing between beads. + + Returns + ------- + float + Effective distance restraint. + """ + # Compute de distance + effective_distance_restraint: float = (spacing / 2) - 2 + # Make sure it is not out of allowed boundaries + bounded_distance_restraint = max(effective_distance_restraint, 2.0) + return bounded_distance_restraint + + +def main( + pdb: Union[str, Path], + residues: Optional[list[str]] = None, + output: Optional[str] = None, + spacing: float = 40, + x_size: float = 200, + y_size: float = 200, + z_padding: float = 5.0, + log_level: str = "INFO", + ) -> tuple[str, str]: + """Generate both z-restraints and z-surface beads from residue selection. + + Parameters + ---------- + pdb : Union[str, Path] + Path to the PDB file to be parsed. + residues : list[str] + List of strings containing coma separated resids, by default None + spacing : float, optional + Spacing (in Angstrom) between beads in same dimension, by default 40 + x_size : float, optional + Width (in Angstrom) of the plan, by default 200 + y_size : float, optional + Height (in Angstrom) of the plan, by default 200 + + Returns + ------- + tuple[Union[str, Path], Union[str, Path]] + Paths to the Z_restraints.tbl and Z_surface.pdb + """ + # Load residue selection + res_select = load_selections(residues) + # Load corresponding coordinates + select_coords, chainids, atomtypes = load_selected_resiudes_coords( + pdb, res_select + ) + # Compute z-coordinates for each selection + selection_z = get_z_coords(select_coords, padding=z_padding) + # Generate corresponding z-surfaces + plans = gen_bead_plans( + spacing=spacing, + x_size=x_size, + y_size=y_size, + z_coords=[zcoord for zcoord in selection_z.values()], + ) + # Compute ideal restraint distance based on spacing + restraint_distance = _get_ideal_restraint_dist(spacing) + # Generate corresponding z-surface restraints + restraints = gen_z_restraints( + res_select, + selection_z, + rest_dist=restraint_distance, + segids=chainids, + atome_types=atomtypes, + ) + # Output data + restraints_tbl, plans_pdb = output_data(restraints, plans, output=output) + return restraints_tbl, plans_pdb + + +gen_z_surface_restraints = main + + +############################ +# COMMAND LINE ENTRY POINT # +############################ +if __name__ == "__main__": + import argparse + # Command line interface parser + ap = argparse.ArgumentParser( + prog="haddock3-restraints", + description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter, + ) + add_z_surf_restraints_arguments(ap) + args = vars(ap.parse_args()) + setup_logging(log_level=args['log_level']) + # Launch main + restraints_fpath, plan_s_fpath = gen_z_surface_restraints( + args['residues'], + residues=args['residues'], + output=args['output'], + spacing=args['spacing'], + x_size=args['x_size'], + y_size=args['y_size'], + z_padding=args['z_padding'], + log_level=args["log_level"], + ) + logging.info(restraints_fpath) + logging.info(plan_s_fpath) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/clis/wrapper_haddock_restraints.py b/.venv_haddock/lib/python3.12/site-packages/haddock/clis/wrapper_haddock_restraints.py new file mode 100644 index 0000000000000000000000000000000000000000..a7b4108372a4e4857dc4d638de75bb447ad5a9fe --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/clis/wrapper_haddock_restraints.py @@ -0,0 +1,20 @@ +#!/usr/bin/env python3 +import sys +from pathlib import Path + +from importlib.resources import files + + +def main(): + + binary = Path(files("haddock").joinpath("bin/haddock-restraints")) # type: ignore + sys.argv[0] = str(binary) # Replace argv[0] with actual binary path + + # Execute the binary + import subprocess + + sys.exit(subprocess.run([str(binary)] + sys.argv[1:]).returncode) + + +if __name__ == "__main__": + main() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/._bin b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/._bin new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/._bin differ diff --git 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b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/._top_axis_dani.pro differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/boxtyp20.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/boxtyp20.pdb new file mode 100644 index 0000000000000000000000000000000000000000..ad0b4c1d591d1dfcde102ce98df8b9a173b95882 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/boxtyp20.pdb @@ -0,0 +1,658 @@ +REMARKS ***** CHARMM water box from Charlie Brooks. ******** +REMARKS * This is a box of 216 3-site water molecules in the experimental +REMARKS * geometry. It was constructed from an equilibrated +REMARKS * configuration of TIP3P (3-site water model of Jorgenson) +REMARKS * waters at 1 atm pressure and a density of 0.0334 molecules/A**-3. +REMARKS * The box edgelength is 18.856 A. The minimum image periodic +REMARKS * boundary energy for this configuration using the TIP3P +REMARKS * potentials is -2150.6833 kcal/mol. +REMARKS +ATOM 1 OH2 WAT 1 2.531 0.596 -2.477 0.000 +ATOM 2 H1 WAT 1 2.620 1.540 -2.609 0.000 +ATOM 3 H2 WAT 1 1.892 0.321 -3.135 0.000 +ATOM 4 OH2 WAT 2 1.464 -0.149 0.942 0.000 +ATOM 5 H1 WAT 2 1.426 -0.795 1.647 0.000 +ATOM 6 H2 WAT 2 1.141 -0.615 0.171 0.000 +ATOM 7 OH2 WAT 3 -6.168 -0.534 2.535 0.000 +ATOM 8 H1 WAT 3 -6.126 -1.160 3.259 0.000 +ATOM 9 H2 WAT 3 -5.465 0.089 2.717 0.000 +ATOM 10 OH2 WAT 4 5.170 2.790 -0.756 0.000 +ATOM 11 H1 WAT 4 4.729 2.070 -0.306 0.000 +ATOM 12 H2 WAT 4 5.157 3.511 -0.126 0.000 +ATOM 13 OH2 WAT 5 -5.244 3.916 1.070 0.000 +ATOM 14 H1 WAT 5 -5.614 3.114 0.701 0.000 +ATOM 15 H2 WAT 5 -4.303 3.747 1.117 0.000 +ATOM 16 OH2 WAT 6 -8.634 -2.424 -3.537 0.000 +ATOM 17 H1 WAT 6 -9.082 -1.578 -3.555 0.000 +ATOM 18 H2 WAT 6 -9.195 -3.004 -4.052 0.000 +ATOM 19 OH2 WAT 7 -7.924 -0.262 -1.411 0.000 +ATOM 20 H1 WAT 7 -7.710 -1.032 -0.884 0.000 +ATOM 21 H2 WAT 7 -7.186 -0.173 -2.014 0.000 +ATOM 22 OH2 WAT 8 2.281 7.895 -0.544 0.000 +ATOM 23 H1 WAT 8 2.901 7.218 -0.817 0.000 +ATOM 24 H2 WAT 8 2.073 7.677 0.364 0.000 +ATOM 25 OH2 WAT 9 -0.147 2.284 1.348 0.000 +ATOM 26 H1 WAT 9 0.157 1.598 0.754 0.000 +ATOM 27 H2 WAT 9 0.575 2.402 1.966 0.000 +ATOM 28 OH2 WAT 10 8.516 -6.115 2.209 0.000 +ATOM 29 H1 WAT 10 8.565 -5.505 2.945 0.000 +ATOM 30 H2 WAT 10 8.942 -5.654 1.486 0.000 +ATOM 31 OH2 WAT 11 2.994 -3.322 1.676 0.000 +ATOM 32 H1 WAT 11 3.137 -4.269 1.696 0.000 +ATOM 33 H2 WAT 11 2.888 -3.115 0.747 0.000 +ATOM 34 OH2 WAT 12 -3.851 -5.221 -1.052 0.000 +ATOM 35 H1 WAT 12 -3.808 -4.361 -1.470 0.000 +ATOM 36 H2 WAT 12 -4.309 -5.773 -1.685 0.000 +ATOM 37 OH2 WAT 13 3.871 -5.090 -2.651 0.000 +ATOM 38 H1 WAT 13 4.517 -5.419 -2.026 0.000 +ATOM 39 H2 WAT 13 4.381 -4.572 -3.274 0.000 +ATOM 40 OH2 WAT 14 -7.231 -2.824 -0.290 0.000 +ATOM 41 H1 WAT 14 -6.577 -3.374 0.142 0.000 +ATOM 42 H2 WAT 14 -7.207 -3.098 -1.206 0.000 +ATOM 43 OH2 WAT 15 -2.075 -1.274 -1.074 0.000 +ATOM 44 H1 WAT 15 -1.459 -1.800 -0.565 0.000 +ATOM 45 H2 WAT 15 -2.661 -1.914 -1.478 0.000 +ATOM 46 OH2 WAT 16 8.908 -4.637 4.445 0.000 +ATOM 47 H1 WAT 16 8.219 -3.979 4.350 0.000 +ATOM 48 H2 WAT 16 8.923 -4.834 5.382 0.000 +ATOM 49 OH2 WAT 17 -5.041 -6.303 3.022 0.000 +ATOM 50 H1 WAT 17 -5.260 -5.773 2.256 0.000 +ATOM 51 H2 WAT 17 -5.709 -6.076 3.670 0.000 +ATOM 52 OH2 WAT 18 2.328 3.197 -3.434 0.000 +ATOM 53 H1 WAT 18 2.032 2.875 -4.285 0.000 +ATOM 54 H2 WAT 18 2.004 4.097 -3.392 0.000 +ATOM 55 OH2 WAT 19 -2.472 1.373 3.310 0.000 +ATOM 56 H1 WAT 19 -3.212 1.971 3.413 0.000 +ATOM 57 H2 WAT 19 -1.758 1.927 2.994 0.000 +ATOM 58 OH2 WAT 20 5.635 -5.799 -0.670 0.000 +ATOM 59 H1 WAT 20 5.420 -6.565 -0.138 0.000 +ATOM 60 H2 WAT 20 6.291 -5.327 -0.157 0.000 +ATOM 61 OH2 WAT 21 -5.447 -4.411 0.975 0.000 +ATOM 62 H1 WAT 21 -4.834 -3.778 1.348 0.000 +ATOM 63 H2 WAT 21 -4.935 -4.883 0.318 0.000 +ATOM 64 OH2 WAT 22 -4.064 3.337 4.097 0.000 +ATOM 65 H1 WAT 22 -4.070 4.216 3.719 0.000 +ATOM 66 H2 WAT 22 -4.918 3.254 4.522 0.000 +ATOM 67 OH2 WAT 23 -7.943 3.008 -5.121 0.000 +ATOM 68 H1 WAT 23 -8.215 3.237 -6.010 0.000 +ATOM 69 H2 WAT 23 -7.898 3.846 -4.661 0.000 +ATOM 70 OH2 WAT 24 5.682 4.630 1.592 0.000 +ATOM 71 H1 WAT 24 4.740 4.688 1.753 0.000 +ATOM 72 H2 WAT 24 5.958 5.536 1.455 0.000 +ATOM 73 OH2 WAT 25 5.982 -7.084 3.009 0.000 +ATOM 74 H1 WAT 25 5.246 -6.473 2.971 0.000 +ATOM 75 H2 WAT 25 6.666 -6.669 2.483 0.000 +ATOM 76 OH2 WAT 26 -1.015 -8.997 0.475 0.000 +ATOM 77 H1 WAT 26 -1.132 -9.946 0.421 0.000 +ATOM 78 H2 WAT 26 -1.870 -8.665 0.748 0.000 +ATOM 79 OH2 WAT 27 3.934 6.411 -1.783 0.000 +ATOM 80 H1 WAT 27 4.359 5.704 -2.268 0.000 +ATOM 81 H2 WAT 27 4.251 7.212 -2.200 0.000 +ATOM 82 OH2 WAT 28 5.093 4.312 -3.274 0.000 +ATOM 83 H1 WAT 28 4.836 3.622 -3.886 0.000 +ATOM 84 H2 WAT 28 5.164 3.869 -2.429 0.000 +ATOM 85 OH2 WAT 29 6.779 2.878 5.203 0.000 +ATOM 86 H1 WAT 29 6.919 2.287 4.464 0.000 +ATOM 87 H2 WAT 29 6.947 3.751 4.847 0.000 +ATOM 88 OH2 WAT 30 1.252 -0.160 -5.025 0.000 +ATOM 89 H1 WAT 30 0.540 0.375 -5.376 0.000 +ATOM 90 H2 WAT 30 1.943 -0.104 -5.685 0.000 +ATOM 91 OH2 WAT 31 1.306 -1.702 -7.986 0.000 +ATOM 92 H1 WAT 31 2.007 -1.680 -7.335 0.000 +ATOM 93 H2 WAT 31 1.608 -2.330 -8.642 0.000 +ATOM 94 OH2 WAT 32 8.621 -0.782 3.269 0.000 +ATOM 95 H1 WAT 32 7.969 -0.087 3.358 0.000 +ATOM 96 H2 WAT 32 9.086 -0.572 2.459 0.000 +ATOM 97 OH2 WAT 33 4.658 0.050 -4.073 0.000 +ATOM 98 H1 WAT 33 3.926 0.278 -3.500 0.000 +ATOM 99 H2 WAT 33 5.105 -0.664 -3.618 0.000 +ATOM 100 OH2 WAT 34 4.555 -1.776 4.995 0.000 +ATOM 101 H1 WAT 34 4.635 -1.013 5.567 0.000 +ATOM 102 H2 WAT 34 3.954 -1.497 4.304 0.000 +ATOM 103 OH2 WAT 35 -3.697 0.680 -2.190 0.000 +ATOM 104 H1 WAT 35 -4.027 0.310 -3.009 0.000 +ATOM 105 H2 WAT 35 -3.109 0.010 -1.844 0.000 +ATOM 106 OH2 WAT 36 -2.330 4.108 0.491 0.000 +ATOM 107 H1 WAT 36 -2.425 3.530 -0.266 0.000 +ATOM 108 H2 WAT 36 -1.601 3.737 0.987 0.000 +ATOM 109 OH2 WAT 37 -3.330 -0.551 1.443 0.000 +ATOM 110 H1 WAT 37 -2.765 -0.430 0.680 0.000 +ATOM 111 H2 WAT 37 -3.011 0.086 2.082 0.000 +ATOM 112 OH2 WAT 38 2.979 4.952 2.177 0.000 +ATOM 113 H1 WAT 38 2.738 5.614 2.825 0.000 +ATOM 114 H2 WAT 38 2.781 4.118 2.602 0.000 +ATOM 115 OH2 WAT 39 -2.450 3.848 6.160 0.000 +ATOM 116 H1 WAT 39 -2.762 4.630 6.616 0.000 +ATOM 117 H2 WAT 39 -3.100 3.695 5.474 0.000 +ATOM 118 OH2 WAT 40 3.529 -0.788 -6.388 0.000 +ATOM 119 H1 WAT 40 4.108 -0.638 -5.641 0.000 +ATOM 120 H2 WAT 40 3.943 -0.317 -7.111 0.000 +ATOM 121 OH2 WAT 41 -5.530 0.046 5.389 0.000 +ATOM 122 H1 WAT 41 -5.460 0.697 6.087 0.000 +ATOM 123 H2 WAT 41 -6.421 0.149 5.054 0.000 +ATOM 124 OH2 WAT 42 1.255 5.949 -2.953 0.000 +ATOM 125 H1 WAT 42 1.729 6.244 -2.175 0.000 +ATOM 126 H2 WAT 42 0.692 6.687 -3.186 0.000 +ATOM 127 OH2 WAT 43 -4.211 5.920 6.924 0.000 +ATOM 128 H1 WAT 43 -4.203 5.784 5.976 0.000 +ATOM 129 H2 WAT 43 -5.127 5.802 7.176 0.000 +ATOM 130 OH2 WAT 44 7.227 -9.038 -6.575 0.000 +ATOM 131 H1 WAT 44 6.328 -8.899 -6.280 0.000 +ATOM 132 H2 WAT 44 7.479 -8.207 -6.977 0.000 +ATOM 133 OH2 WAT 45 -4.707 -0.250 -4.601 0.000 +ATOM 134 H1 WAT 45 -4.999 0.518 -5.092 0.000 +ATOM 135 H2 WAT 45 -5.381 -0.910 -4.764 0.000 +ATOM 136 OH2 WAT 46 8.417 5.328 -8.198 0.000 +ATOM 137 H1 WAT 46 8.490 6.267 -8.028 0.000 +ATOM 138 H2 WAT 46 9.322 5.023 -8.255 0.000 +ATOM 139 OH2 WAT 47 -8.614 2.113 4.214 0.000 +ATOM 140 H1 WAT 47 -9.115 2.085 3.399 0.000 +ATOM 141 H2 WAT 47 -8.608 1.207 4.524 0.000 +ATOM 142 OH2 WAT 48 -8.863 4.893 1.098 0.000 +ATOM 143 H1 WAT 48 -7.917 4.749 1.079 0.000 +ATOM 144 H2 WAT 48 -8.976 5.677 1.635 0.000 +ATOM 145 OH2 WAT 49 9.334 5.559 6.780 0.000 +ATOM 146 H1 WAT 49 9.285 4.604 6.743 0.000 +ATOM 147 H2 WAT 49 8.508 5.827 7.182 0.000 +ATOM 148 OH2 WAT 50 0.313 5.133 5.656 0.000 +ATOM 149 H1 WAT 50 0.400 5.959 6.131 0.000 +ATOM 150 H2 WAT 50 -0.551 4.803 5.905 0.000 +ATOM 151 OH2 WAT 51 0.727 8.905 -4.538 0.000 +ATOM 152 H1 WAT 51 0.652 8.784 -5.484 0.000 +ATOM 153 H2 WAT 51 0.760 9.855 -4.419 0.000 +ATOM 154 OH2 WAT 52 -5.619 7.694 -2.757 0.000 +ATOM 155 H1 WAT 52 -5.467 7.346 -1.878 0.000 +ATOM 156 H2 WAT 52 -6.470 7.338 -3.012 0.000 +ATOM 157 OH2 WAT 53 3.829 8.059 -7.535 0.000 +ATOM 158 H1 WAT 53 4.204 7.315 -8.006 0.000 +ATOM 159 H2 WAT 53 3.833 7.789 -6.617 0.000 +ATOM 160 OH2 WAT 54 3.498 7.985 -4.786 0.000 +ATOM 161 H1 WAT 54 2.563 8.085 -4.607 0.000 +ATOM 162 H2 WAT 54 3.778 7.276 -4.208 0.000 +ATOM 163 OH2 WAT 55 6.486 -2.948 7.260 0.000 +ATOM 164 H1 WAT 55 6.079 -2.467 6.540 0.000 +ATOM 165 H2 WAT 55 6.527 -3.853 6.953 0.000 +ATOM 166 OH2 WAT 56 -6.365 3.436 5.257 0.000 +ATOM 167 H1 WAT 56 -6.148 3.075 6.117 0.000 +ATOM 168 H2 WAT 56 -7.220 3.062 5.047 0.000 +ATOM 169 OH2 WAT 57 -3.746 -8.094 1.253 0.000 +ATOM 170 H1 WAT 57 -4.607 -8.181 0.845 0.000 +ATOM 171 H2 WAT 57 -3.768 -7.238 1.680 0.000 +ATOM 172 OH2 WAT 58 0.917 -8.372 4.627 0.000 +ATOM 173 H1 WAT 58 1.337 -8.787 5.380 0.000 +ATOM 174 H2 WAT 58 -0.016 -8.550 4.744 0.000 +ATOM 175 OH2 WAT 59 4.243 -4.616 5.481 0.000 +ATOM 176 H1 WAT 59 3.729 -4.742 6.278 0.000 +ATOM 177 H2 WAT 59 4.088 -3.704 5.236 0.000 +ATOM 178 OH2 WAT 60 5.006 0.245 -8.758 0.000 +ATOM 179 H1 WAT 60 5.048 0.022 -9.688 0.000 +ATOM 180 H2 WAT 60 5.855 0.643 -8.568 0.000 +ATOM 181 OH2 WAT 61 0.579 -5.879 -8.088 0.000 +ATOM 182 H1 WAT 61 0.325 -5.860 -7.165 0.000 +ATOM 183 H2 WAT 61 0.322 -6.751 -8.389 0.000 +ATOM 184 OH2 WAT 62 -3.655 -3.128 2.348 0.000 +ATOM 185 H1 WAT 62 -4.297 -3.169 3.057 0.000 +ATOM 186 H2 WAT 62 -3.618 -2.202 2.110 0.000 +ATOM 187 OH2 WAT 63 -3.658 -2.907 -2.740 0.000 +ATOM 188 H1 WAT 63 -4.551 -3.248 -2.799 0.000 +ATOM 189 H2 WAT 63 -3.207 -3.284 -3.496 0.000 +ATOM 190 OH2 WAT 64 1.878 -2.491 -3.923 0.000 +ATOM 191 H1 WAT 64 1.469 -1.676 -4.215 0.000 +ATOM 192 H2 WAT 64 2.598 -2.631 -4.538 0.000 +ATOM 193 OH2 WAT 65 0.980 -2.316 7.565 0.000 +ATOM 194 H1 WAT 65 0.417 -3.020 7.885 0.000 +ATOM 195 H2 WAT 65 1.806 -2.436 8.032 0.000 +ATOM 196 OH2 WAT 66 2.882 -3.045 -1.109 0.000 +ATOM 197 H1 WAT 66 2.687 -2.440 -1.824 0.000 +ATOM 198 H2 WAT 66 3.064 -3.879 -1.544 0.000 +ATOM 199 OH2 WAT 67 -5.905 -2.808 4.215 0.000 +ATOM 200 H1 WAT 67 -5.943 -2.408 5.083 0.000 +ATOM 201 H2 WAT 67 -6.396 -3.625 4.305 0.000 +ATOM 202 OH2 WAT 68 -2.539 -5.434 -8.987 0.000 +ATOM 203 H1 WAT 68 -2.970 -5.879 -8.257 0.000 +ATOM 204 H2 WAT 68 -3.257 -5.062 -9.499 0.000 +ATOM 205 OH2 WAT 69 -9.297 -5.692 -1.935 0.000 +ATOM 206 H1 WAT 69 -8.666 -5.721 -1.215 0.000 +ATOM 207 H2 WAT 69 -8.847 -6.117 -2.665 0.000 +ATOM 208 OH2 WAT 70 -8.022 -4.946 -6.511 0.000 +ATOM 209 H1 WAT 70 -7.548 -4.355 -7.096 0.000 +ATOM 210 H2 WAT 70 -8.740 -4.415 -6.164 0.000 +ATOM 211 OH2 WAT 71 2.146 -1.407 3.562 0.000 +ATOM 212 H1 WAT 71 2.470 -2.038 2.919 0.000 +ATOM 213 H2 WAT 71 1.706 -1.942 4.223 0.000 +ATOM 214 OH2 WAT 72 -1.076 -5.480 -1.654 0.000 +ATOM 215 H1 WAT 72 -1.987 -5.423 -1.365 0.000 +ATOM 216 H2 WAT 72 -0.571 -5.540 -0.843 0.000 +ATOM 217 OH2 WAT 73 -6.248 -3.851 -2.827 0.000 +ATOM 218 H1 WAT 73 -7.137 -3.751 -3.167 0.000 +ATOM 219 H2 WAT 73 -5.952 -4.693 -3.173 0.000 +ATOM 220 OH2 WAT 74 -2.595 -3.851 -5.171 0.000 +ATOM 221 H1 WAT 74 -1.663 -3.722 -4.993 0.000 +ATOM 222 H2 WAT 74 -2.810 -3.181 -5.820 0.000 +ATOM 223 OH2 WAT 75 3.329 -6.245 1.610 0.000 +ATOM 224 H1 WAT 75 2.652 -6.114 2.274 0.000 +ATOM 225 H2 WAT 75 2.843 -6.400 0.800 0.000 +ATOM 226 OH2 WAT 76 -3.921 -2.656 -7.604 0.000 +ATOM 227 H1 WAT 76 -4.463 -3.036 -8.295 0.000 +ATOM 228 H2 WAT 76 -3.087 -2.462 -8.033 0.000 +ATOM 229 OH2 WAT 77 6.616 9.427 7.887 0.000 +ATOM 230 H1 WAT 77 6.816 9.851 7.052 0.000 +ATOM 231 H2 WAT 77 7.272 9.770 8.494 0.000 +ATOM 232 OH2 WAT 78 -5.786 1.901 7.495 0.000 +ATOM 233 H1 WAT 78 -5.053 2.155 8.056 0.000 +ATOM 234 H2 WAT 78 -6.566 2.105 8.010 0.000 +ATOM 235 OH2 WAT 79 0.244 -2.692 0.233 0.000 +ATOM 236 H1 WAT 79 0.808 -3.239 -0.314 0.000 +ATOM 237 H2 WAT 79 0.096 -3.214 1.022 0.000 +ATOM 238 OH2 WAT 80 -4.754 -6.556 -3.349 0.000 +ATOM 239 H1 WAT 80 -5.071 -7.458 -3.384 0.000 +ATOM 240 H2 WAT 80 -3.973 -6.554 -3.901 0.000 +ATOM 241 OH2 WAT 81 -1.130 -4.304 2.647 0.000 +ATOM 242 H1 WAT 81 -1.965 -3.850 2.757 0.000 +ATOM 243 H2 WAT 81 -0.606 -4.028 3.399 0.000 +ATOM 244 OH2 WAT 82 -0.586 1.909 -5.668 0.000 +ATOM 245 H1 WAT 82 -1.330 1.402 -5.991 0.000 +ATOM 246 H2 WAT 82 -0.720 1.958 -4.722 0.000 +ATOM 247 OH2 WAT 83 6.564 1.042 3.118 0.000 +ATOM 248 H1 WAT 83 7.206 1.499 2.575 0.000 +ATOM 249 H2 WAT 83 5.734 1.155 2.656 0.000 +ATOM 250 OH2 WAT 84 3.312 -5.277 -7.469 0.000 +ATOM 251 H1 WAT 84 2.374 -5.165 -7.620 0.000 +ATOM 252 H2 WAT 84 3.609 -4.420 -7.163 0.000 +ATOM 253 OH2 WAT 85 0.934 2.093 5.569 0.000 +ATOM 254 H1 WAT 85 0.588 1.712 6.375 0.000 +ATOM 255 H2 WAT 85 0.734 3.027 5.640 0.000 +ATOM 256 OH2 WAT 86 4.030 -3.410 -5.808 0.000 +ATOM 257 H1 WAT 86 4.922 -3.547 -5.489 0.000 +ATOM 258 H2 WAT 86 4.087 -2.619 -6.345 0.000 +ATOM 259 OH2 WAT 87 -5.461 1.204 0.101 0.000 +ATOM 260 H1 WAT 87 -4.716 1.202 -0.500 0.000 +ATOM 261 H2 WAT 87 -5.383 0.380 0.583 0.000 +ATOM 262 OH2 WAT 88 1.540 3.368 -6.643 0.000 +ATOM 263 H1 WAT 88 1.245 4.194 -6.261 0.000 +ATOM 264 H2 WAT 88 0.837 2.748 -6.447 0.000 +ATOM 265 OH2 WAT 89 -8.453 -0.335 5.416 0.000 +ATOM 266 H1 WAT 89 -8.230 -0.753 6.248 0.000 +ATOM 267 H2 WAT 89 -9.055 -0.948 4.994 0.000 +ATOM 268 OH2 WAT 90 -1.436 -0.818 7.629 0.000 +ATOM 269 H1 WAT 90 -1.732 -0.984 6.734 0.000 +ATOM 270 H2 WAT 90 -0.505 -1.038 7.619 0.000 +ATOM 271 OH2 WAT 91 3.184 4.555 5.519 0.000 +ATOM 272 H1 WAT 91 2.283 4.738 5.251 0.000 +ATOM 273 H2 WAT 91 3.218 4.814 6.440 0.000 +ATOM 274 OH2 WAT 92 8.915 -3.200 -6.114 0.000 +ATOM 275 H1 WAT 92 8.361 -3.596 -6.786 0.000 +ATOM 276 H2 WAT 92 9.016 -2.290 -6.391 0.000 +ATOM 277 OH2 WAT 93 8.879 2.600 6.723 0.000 +ATOM 278 H1 WAT 93 8.027 2.838 6.356 0.000 +ATOM 279 H2 WAT 93 9.469 2.583 5.970 0.000 +ATOM 280 OH2 WAT 94 7.211 5.586 -5.649 0.000 +ATOM 281 H1 WAT 94 6.838 4.760 -5.339 0.000 +ATOM 282 H2 WAT 94 7.488 5.403 -6.546 0.000 +ATOM 283 OH2 WAT 95 4.371 0.394 1.373 0.000 +ATOM 284 H1 WAT 95 3.443 0.162 1.346 0.000 +ATOM 285 H2 WAT 95 4.822 -0.383 1.043 0.000 +ATOM 286 OH2 WAT 96 -3.086 4.722 -2.494 0.000 +ATOM 287 H1 WAT 96 -2.559 5.495 -2.695 0.000 +ATOM 288 H2 WAT 96 -3.966 4.947 -2.796 0.000 +ATOM 289 OH2 WAT 97 -7.331 -0.416 -7.907 0.000 +ATOM 290 H1 WAT 97 -6.715 0.211 -7.528 0.000 +ATOM 291 H2 WAT 97 -8.193 -0.100 -7.636 0.000 +ATOM 292 OH2 WAT 98 -1.659 2.385 -2.918 0.000 +ATOM 293 H1 WAT 98 -1.900 3.310 -2.876 0.000 +ATOM 294 H2 WAT 98 -2.399 1.926 -2.522 0.000 +ATOM 295 OH2 WAT 99 -1.144 6.534 3.397 0.000 +ATOM 296 H1 WAT 99 -0.781 7.389 3.164 0.000 +ATOM 297 H2 WAT 99 -0.612 6.242 4.138 0.000 +ATOM 298 OH2 WAT 100 -2.975 7.407 -3.373 0.000 +ATOM 299 H1 WAT 100 -3.925 7.512 -3.321 0.000 +ATOM 300 H2 WAT 100 -2.624 8.227 -3.028 0.000 +ATOM 301 OH2 WAT 101 2.400 2.633 3.098 0.000 +ATOM 302 H1 WAT 101 1.974 2.406 3.924 0.000 +ATOM 303 H2 WAT 101 2.981 1.895 2.915 0.000 +ATOM 304 OH2 WAT 102 4.603 3.562 -7.828 0.000 +ATOM 305 H1 WAT 102 4.956 3.182 -7.024 0.000 +ATOM 306 H2 WAT 102 3.654 3.469 -7.742 0.000 +ATOM 307 OH2 WAT 103 5.059 7.185 5.567 0.000 +ATOM 308 H1 WAT 103 4.457 6.630 5.072 0.000 +ATOM 309 H2 WAT 103 5.340 7.852 4.941 0.000 +ATOM 310 OH2 WAT 104 9.107 8.042 -7.627 0.000 +ATOM 311 H1 WAT 104 9.850 8.628 -7.767 0.000 +ATOM 312 H2 WAT 104 8.412 8.610 -7.294 0.000 +ATOM 313 OH2 WAT 105 -6.819 -5.582 4.974 0.000 +ATOM 314 H1 WAT 105 -7.712 -5.243 4.907 0.000 +ATOM 315 H2 WAT 105 -6.918 -6.437 5.392 0.000 +ATOM 316 OH2 WAT 106 5.469 2.235 -5.602 0.000 +ATOM 317 H1 WAT 106 5.192 1.507 -5.046 0.000 +ATOM 318 H2 WAT 106 6.396 2.354 -5.396 0.000 +ATOM 319 OH2 WAT 107 -7.168 6.223 3.409 0.000 +ATOM 320 H1 WAT 107 -6.951 5.291 3.378 0.000 +ATOM 321 H2 WAT 107 -6.921 6.497 4.293 0.000 +ATOM 322 OH2 WAT 108 -1.306 4.674 -9.381 0.000 +ATOM 323 H1 WAT 108 -1.067 3.926 -9.929 0.000 +ATOM 324 H2 WAT 108 -1.575 4.286 -8.549 0.000 +ATOM 325 OH2 WAT 109 -2.369 4.244 -6.925 0.000 +ATOM 326 H1 WAT 109 -2.222 3.724 -6.135 0.000 +ATOM 327 H2 WAT 109 -2.372 5.151 -6.619 0.000 +ATOM 328 OH2 WAT 110 -5.916 1.497 -6.415 0.000 +ATOM 329 H1 WAT 110 -6.602 1.849 -5.848 0.000 +ATOM 330 H2 WAT 110 -5.393 2.260 -6.661 0.000 +ATOM 331 OH2 WAT 111 1.916 -5.841 3.864 0.000 +ATOM 332 H1 WAT 111 2.614 -5.767 4.514 0.000 +ATOM 333 H2 WAT 111 1.535 -6.705 4.019 0.000 +ATOM 334 OH2 WAT 112 2.700 -6.189 -5.039 0.000 +ATOM 335 H1 WAT 112 2.920 -5.717 -5.842 0.000 +ATOM 336 H2 WAT 112 3.258 -5.794 -4.368 0.000 +ATOM 337 OH2 WAT 113 0.369 5.942 -6.176 0.000 +ATOM 338 H1 WAT 113 -0.448 6.439 -6.123 0.000 +ATOM 339 H2 WAT 113 0.898 6.417 -6.816 0.000 +ATOM 340 OH2 WAT 114 -0.100 -4.461 -4.204 0.000 +ATOM 341 H1 WAT 114 0.712 -3.957 -4.158 0.000 +ATOM 342 H2 WAT 114 -0.345 -4.606 -3.290 0.000 +ATOM 343 OH2 WAT 115 0.436 -3.475 4.981 0.000 +ATOM 344 H1 WAT 115 0.555 -2.901 5.738 0.000 +ATOM 345 H2 WAT 115 1.091 -4.163 5.096 0.000 +ATOM 346 OH2 WAT 116 0.784 -7.380 -3.266 0.000 +ATOM 347 H1 WAT 116 0.437 -6.762 -2.621 0.000 +ATOM 348 H2 WAT 116 1.442 -6.879 -3.747 0.000 +ATOM 349 OH2 WAT 117 -2.293 6.985 -6.194 0.000 +ATOM 350 H1 WAT 117 -2.132 7.785 -6.695 0.000 +ATOM 351 H2 WAT 117 -2.490 7.292 -5.309 0.000 +ATOM 352 OH2 WAT 118 -3.559 -6.317 -6.578 0.000 +ATOM 353 H1 WAT 118 -3.642 -5.428 -6.232 0.000 +ATOM 354 H2 WAT 118 -2.669 -6.582 -6.347 0.000 +ATOM 355 OH2 WAT 119 6.640 -5.568 5.816 0.000 +ATOM 356 H1 WAT 119 5.724 -5.305 5.728 0.000 +ATOM 357 H2 WAT 119 6.976 -5.571 4.919 0.000 +ATOM 358 OH2 WAT 120 5.242 -1.817 -0.088 0.000 +ATOM 359 H1 WAT 120 4.445 -2.232 -0.417 0.000 +ATOM 360 H2 WAT 120 5.687 -2.508 0.403 0.000 +ATOM 361 OH2 WAT 121 -5.300 4.111 -7.518 0.000 +ATOM 362 H1 WAT 121 -4.708 4.810 -7.242 0.000 +ATOM 363 H2 WAT 121 -4.841 3.678 -8.237 0.000 +ATOM 364 OH2 WAT 122 -6.984 -3.225 -8.402 0.000 +ATOM 365 H1 WAT 122 -7.029 -2.286 -8.223 0.000 +ATOM 366 H2 WAT 122 -7.872 -3.461 -8.672 0.000 +ATOM 367 OH2 WAT 123 6.329 7.439 1.534 0.000 +ATOM 368 H1 WAT 123 6.173 8.117 0.877 0.000 +ATOM 369 H2 WAT 123 7.261 7.511 1.737 0.000 +ATOM 370 OH2 WAT 124 -6.176 -8.443 0.271 0.000 +ATOM 371 H1 WAT 124 -6.405 -8.384 -0.656 0.000 +ATOM 372 H2 WAT 124 -6.619 -9.235 0.578 0.000 +ATOM 373 OH2 WAT 125 -7.246 5.497 -3.568 0.000 +ATOM 374 H1 WAT 125 -8.078 5.970 -3.541 0.000 +ATOM 375 H2 WAT 125 -6.700 6.007 -4.167 0.000 +ATOM 376 OH2 WAT 126 -7.957 8.110 7.762 0.000 +ATOM 377 H1 WAT 126 -7.417 7.893 8.521 0.000 +ATOM 378 H2 WAT 126 -8.438 7.304 7.572 0.000 +ATOM 379 OH2 WAT 127 -3.360 7.029 9.382 0.000 +ATOM 380 H1 WAT 127 -2.592 6.570 9.723 0.000 +ATOM 381 H2 WAT 127 -3.381 6.803 8.452 0.000 +ATOM 382 OH2 WAT 128 0.732 6.537 -9.243 0.000 +ATOM 383 H1 WAT 128 0.088 5.906 -8.921 0.000 +ATOM 384 H2 WAT 128 1.494 6.006 -9.475 0.000 +ATOM 385 OH2 WAT 129 3.217 5.409 8.111 0.000 +ATOM 386 H1 WAT 129 2.866 4.553 8.354 0.000 +ATOM 387 H2 WAT 129 3.943 5.552 8.718 0.000 +ATOM 388 OH2 WAT 130 5.336 6.354 -9.009 0.000 +ATOM 389 H1 WAT 130 5.619 5.560 -8.556 0.000 +ATOM 390 H2 WAT 130 6.076 6.587 -9.570 0.000 +ATOM 391 OH2 WAT 131 -8.050 1.920 8.716 0.000 +ATOM 392 H1 WAT 131 -7.906 1.018 8.430 0.000 +ATOM 393 H2 WAT 131 -8.823 2.206 8.228 0.000 +ATOM 394 OH2 WAT 132 -3.709 2.264 -9.152 0.000 +ATOM 395 H1 WAT 132 -3.645 1.470 -8.621 0.000 +ATOM 396 H2 WAT 132 -3.056 2.145 -9.841 0.000 +ATOM 397 OH2 WAT 133 -1.395 1.890 8.149 0.000 +ATOM 398 H1 WAT 133 -1.723 2.161 7.291 0.000 +ATOM 399 H2 WAT 133 -1.243 0.949 8.061 0.000 +ATOM 400 OH2 WAT 134 1.643 3.311 -9.416 0.000 +ATOM 401 H1 WAT 134 1.375 3.491 -8.515 0.000 +ATOM 402 H2 WAT 134 1.437 2.385 -9.547 0.000 +ATOM 403 OH2 WAT 135 4.340 1.806 5.532 0.000 +ATOM 404 H1 WAT 135 5.085 2.394 5.412 0.000 +ATOM 405 H2 WAT 135 3.583 2.388 5.595 0.000 +ATOM 406 OH2 WAT 136 -7.218 -0.880 8.136 0.000 +ATOM 407 H1 WAT 136 -6.810 -1.737 8.015 0.000 +ATOM 408 H2 WAT 136 -7.478 -0.865 9.057 0.000 +ATOM 409 OH2 WAT 137 -2.560 0.236 -6.846 0.000 +ATOM 410 H1 WAT 137 -3.019 -0.248 -6.160 0.000 +ATOM 411 H2 WAT 137 -2.305 -0.432 -7.482 0.000 +ATOM 412 OH2 WAT 138 -3.271 -1.871 5.510 0.000 +ATOM 413 H1 WAT 138 -3.889 -1.196 5.791 0.000 +ATOM 414 H2 WAT 138 -2.927 -1.550 4.677 0.000 +ATOM 415 OH2 WAT 139 -1.489 -1.521 -8.583 0.000 +ATOM 416 H1 WAT 139 -1.669 -1.675 -9.511 0.000 +ATOM 417 H2 WAT 139 -0.538 -1.413 -8.539 0.000 +ATOM 418 OH2 WAT 140 1.749 0.600 8.788 0.000 +ATOM 419 H1 WAT 140 2.702 0.684 8.760 0.000 +ATOM 420 H2 WAT 140 1.589 -0.111 9.407 0.000 +ATOM 421 OH2 WAT 141 7.901 0.834 -9.138 0.000 +ATOM 422 H1 WAT 141 7.628 0.409 -9.951 0.000 +ATOM 423 H2 WAT 141 7.941 1.765 -9.355 0.000 +ATOM 424 OH2 WAT 142 -2.931 -4.516 6.593 0.000 +ATOM 425 H1 WAT 142 -2.781 -5.245 5.990 0.000 +ATOM 426 H2 WAT 142 -2.929 -3.739 6.034 0.000 +ATOM 427 OH2 WAT 143 -2.519 -6.146 4.085 0.000 +ATOM 428 H1 WAT 143 -1.983 -5.695 3.433 0.000 +ATOM 429 H2 WAT 143 -3.371 -6.254 3.663 0.000 +ATOM 430 OH2 WAT 144 -0.937 -0.707 4.325 0.000 +ATOM 431 H1 WAT 144 -0.186 -0.863 3.752 0.000 +ATOM 432 H2 WAT 144 -1.276 0.145 4.049 0.000 +ATOM 433 OH2 WAT 145 3.479 -2.892 9.353 0.000 +ATOM 434 H1 WAT 145 3.671 -3.823 9.242 0.000 +ATOM 435 H2 WAT 145 4.336 -2.467 9.343 0.000 +ATOM 436 OH2 WAT 146 4.795 -0.103 7.431 0.000 +ATOM 437 H1 WAT 146 4.514 0.606 6.853 0.000 +ATOM 438 H2 WAT 146 5.738 -0.176 7.280 0.000 +ATOM 439 OH2 WAT 147 -4.453 -3.318 8.504 0.000 +ATOM 440 H1 WAT 147 -5.220 -3.850 8.294 0.000 +ATOM 441 H2 WAT 147 -3.774 -3.628 7.905 0.000 +ATOM 442 OH2 WAT 148 -1.713 -8.690 4.517 0.000 +ATOM 443 H1 WAT 148 -1.811 -7.743 4.411 0.000 +ATOM 444 H2 WAT 148 -2.456 -9.062 4.041 0.000 +ATOM 445 OH2 WAT 149 -0.449 -4.368 8.080 0.000 +ATOM 446 H1 WAT 149 -0.685 -4.588 8.982 0.000 +ATOM 447 H2 WAT 149 -1.232 -4.575 7.571 0.000 +ATOM 448 OH2 WAT 150 2.267 -5.241 7.156 0.000 +ATOM 449 H1 WAT 150 1.319 -5.209 7.288 0.000 +ATOM 450 H2 WAT 150 2.579 -5.866 7.810 0.000 +ATOM 451 OH2 WAT 151 3.901 -6.607 9.161 0.000 +ATOM 452 H1 WAT 151 3.804 -7.559 9.155 0.000 +ATOM 453 H2 WAT 151 3.579 -6.338 10.022 0.000 +ATOM 454 OH2 WAT 152 -6.272 -5.397 8.209 0.000 +ATOM 455 H1 WAT 152 -6.061 -6.104 7.598 0.000 +ATOM 456 H2 WAT 152 -6.384 -5.835 9.053 0.000 +ATOM 457 OH2 WAT 153 -1.491 -9.396 7.188 0.000 +ATOM 458 H1 WAT 153 -0.779 -10.036 7.174 0.000 +ATOM 459 H2 WAT 153 -1.592 -9.129 6.274 0.000 +ATOM 460 OH2 WAT 154 -1.138 -7.713 9.242 0.000 +ATOM 461 H1 WAT 154 -1.269 -8.189 8.421 0.000 +ATOM 462 H2 WAT 154 -1.737 -6.969 9.186 0.000 +ATOM 463 OH2 WAT 155 -1.591 9.170 -7.582 0.000 +ATOM 464 H1 WAT 155 -0.658 9.328 -7.438 0.000 +ATOM 465 H2 WAT 155 -1.855 9.845 -8.207 0.000 +ATOM 466 OH2 WAT 156 -8.023 3.806 -8.099 0.000 +ATOM 467 H1 WAT 156 -7.109 3.885 -7.826 0.000 +ATOM 468 H2 WAT 156 -8.016 3.119 -8.766 0.000 +ATOM 469 OH2 WAT 157 -9.374 9.199 -3.022 0.000 +ATOM 470 H1 WAT 157 -10.021 8.737 -3.555 0.000 +ATOM 471 H2 WAT 157 -9.019 8.527 -2.439 0.000 +ATOM 472 OH2 WAT 158 -8.504 7.280 -1.217 0.000 +ATOM 473 H1 WAT 158 -8.838 6.399 -1.045 0.000 +ATOM 474 H2 WAT 158 -8.282 7.625 -0.353 0.000 +ATOM 475 OH2 WAT 159 9.045 8.089 1.763 0.000 +ATOM 476 H1 WAT 159 9.023 8.274 2.702 0.000 +ATOM 477 H2 WAT 159 9.735 8.658 1.422 0.000 +ATOM 478 OH2 WAT 160 8.608 7.656 4.685 0.000 +ATOM 479 H1 WAT 160 8.121 6.921 4.314 0.000 +ATOM 480 H2 WAT 160 9.157 7.263 5.363 0.000 +ATOM 481 OH2 WAT 161 7.059 3.446 9.323 0.000 +ATOM 482 H1 WAT 161 6.193 3.341 9.717 0.000 +ATOM 483 H2 WAT 161 7.435 4.205 9.770 0.000 +ATOM 484 OH2 WAT 162 8.360 1.703 -5.163 0.000 +ATOM 485 H1 WAT 162 9.210 2.124 -5.035 0.000 +ATOM 486 H2 WAT 162 8.365 0.963 -4.555 0.000 +ATOM 487 OH2 WAT 163 8.754 -0.244 -3.339 0.000 +ATOM 488 H1 WAT 163 8.028 -0.723 -2.941 0.000 +ATOM 489 H2 WAT 163 9.335 -0.038 -2.607 0.000 +ATOM 490 OH2 WAT 164 8.513 2.541 1.609 0.000 +ATOM 491 H1 WAT 164 9.347 2.163 1.328 0.000 +ATOM 492 H2 WAT 164 8.625 3.484 1.490 0.000 +ATOM 493 OH2 WAT 165 7.000 5.419 3.916 0.000 +ATOM 494 H1 WAT 165 6.352 5.744 4.541 0.000 +ATOM 495 H2 WAT 165 6.482 4.979 3.241 0.000 +ATOM 496 OH2 WAT 166 9.022 -0.343 -6.948 0.000 +ATOM 497 H1 WAT 166 8.501 0.014 -7.667 0.000 +ATOM 498 H2 WAT 166 8.989 0.332 -6.270 0.000 +ATOM 499 OH2 WAT 167 7.371 -3.103 -8.397 0.000 +ATOM 500 H1 WAT 167 7.468 -2.436 -9.077 0.000 +ATOM 501 H2 WAT 167 7.231 -3.919 -8.879 0.000 +ATOM 502 OH2 WAT 168 6.541 -1.723 -2.776 0.000 +ATOM 503 H1 WAT 168 6.391 -2.668 -2.796 0.000 +ATOM 504 H2 WAT 168 6.187 -1.442 -1.932 0.000 +ATOM 505 OH2 WAT 169 -8.424 0.355 1.234 0.000 +ATOM 506 H1 WAT 169 -8.240 0.273 0.299 0.000 +ATOM 507 H2 WAT 169 -7.575 0.231 1.658 0.000 +ATOM 508 OH2 WAT 170 7.397 0.247 6.863 0.000 +ATOM 509 H1 WAT 170 7.980 -0.487 7.054 0.000 +ATOM 510 H2 WAT 170 7.961 1.019 6.909 0.000 +ATOM 511 OH2 WAT 171 8.894 -1.850 7.547 0.000 +ATOM 512 H1 WAT 171 8.031 -2.229 7.382 0.000 +ATOM 513 H2 WAT 171 9.498 -2.589 7.473 0.000 +ATOM 514 OH2 WAT 172 6.619 -5.695 -9.280 0.000 +ATOM 515 H1 WAT 172 7.229 -6.067 -8.643 0.000 +ATOM 516 H2 WAT 172 5.782 -6.117 -9.084 0.000 +ATOM 517 OH2 WAT 173 6.251 -4.140 -4.314 0.000 +ATOM 518 H1 WAT 173 6.531 -5.047 -4.189 0.000 +ATOM 519 H2 WAT 173 7.010 -3.706 -4.703 0.000 +ATOM 520 OH2 WAT 174 6.863 -3.559 1.122 0.000 +ATOM 521 H1 WAT 174 7.796 -3.347 1.088 0.000 +ATOM 522 H2 WAT 174 6.628 -3.457 2.045 0.000 +ATOM 523 OH2 WAT 175 6.892 -2.822 3.898 0.000 +ATOM 524 H1 WAT 175 6.049 -2.554 4.264 0.000 +ATOM 525 H2 WAT 175 7.335 -2.000 3.687 0.000 +ATOM 526 OH2 WAT 176 -8.826 -4.374 7.375 0.000 +ATOM 527 H1 WAT 176 -7.907 -4.496 7.611 0.000 +ATOM 528 H2 WAT 176 -9.276 -5.124 7.764 0.000 +ATOM 529 OH2 WAT 177 9.175 -8.842 9.252 0.000 +ATOM 530 H1 WAT 177 9.525 -9.496 8.646 0.000 +ATOM 531 H2 WAT 177 9.322 -8.005 8.812 0.000 +ATOM 532 OH2 WAT 178 6.865 -6.877 -4.265 0.000 +ATOM 533 H1 WAT 178 7.047 -7.326 -3.440 0.000 +ATOM 534 H2 WAT 178 6.265 -7.462 -4.729 0.000 +ATOM 535 OH2 WAT 179 -7.605 -6.062 0.266 0.000 +ATOM 536 H1 WAT 179 -7.160 -6.854 0.568 0.000 +ATOM 537 H2 WAT 179 -7.139 -5.346 0.697 0.000 +ATOM 538 OH2 WAT 180 -9.301 -3.063 1.335 0.000 +ATOM 539 H1 WAT 180 -8.809 -3.284 0.545 0.000 +ATOM 540 H2 WAT 180 -8.939 -2.222 1.616 0.000 +ATOM 541 OH2 WAT 181 8.695 -6.733 7.601 0.000 +ATOM 542 H1 WAT 181 7.778 -6.462 7.565 0.000 +ATOM 543 H2 WAT 181 8.818 -7.268 6.817 0.000 +ATOM 544 OH2 WAT 182 8.731 -6.810 -7.737 0.000 +ATOM 545 H1 WAT 182 9.144 -7.531 -8.213 0.000 +ATOM 546 H2 WAT 182 9.413 -6.140 -7.679 0.000 +ATOM 547 OH2 WAT 183 -8.988 -6.805 -4.610 0.000 +ATOM 548 H1 WAT 183 -9.913 -6.596 -4.740 0.000 +ATOM 549 H2 WAT 183 -8.534 -6.321 -5.300 0.000 +ATOM 550 OH2 WAT 184 5.783 8.179 -2.665 0.000 +ATOM 551 H1 WAT 184 6.436 7.832 -3.273 0.000 +ATOM 552 H2 WAT 184 6.294 8.668 -2.019 0.000 +ATOM 553 OH2 WAT 185 -9.024 -8.067 3.734 0.000 +ATOM 554 H1 WAT 185 -9.689 -8.313 4.377 0.000 +ATOM 555 H2 WAT 185 -9.467 -7.445 3.157 0.000 +ATOM 556 OH2 WAT 186 -6.832 5.108 7.878 0.000 +ATOM 557 H1 WAT 186 -7.653 5.283 7.418 0.000 +ATOM 558 H2 WAT 186 -7.084 5.035 8.799 0.000 +ATOM 559 OH2 WAT 187 -3.878 6.083 4.137 0.000 +ATOM 560 H1 WAT 187 -4.303 6.892 3.854 0.000 +ATOM 561 H2 WAT 187 -2.973 6.168 3.835 0.000 +ATOM 562 OH2 WAT 188 0.433 7.482 7.096 0.000 +ATOM 563 H1 WAT 188 0.618 7.148 7.974 0.000 +ATOM 564 H2 WAT 188 1.280 7.791 6.774 0.000 +ATOM 565 OH2 WAT 189 2.778 8.767 6.340 0.000 +ATOM 566 H1 WAT 189 3.455 8.135 6.100 0.000 +ATOM 567 H2 WAT 189 3.100 9.169 7.148 0.000 +ATOM 568 OH2 WAT 190 7.696 -8.643 5.420 0.000 +ATOM 569 H1 WAT 190 6.883 -8.318 5.032 0.000 +ATOM 570 H2 WAT 190 7.929 -9.403 4.887 0.000 +ATOM 571 OH2 WAT 191 -6.476 9.339 4.184 0.000 +ATOM 572 H1 WAT 191 -7.196 9.779 3.733 0.000 +ATOM 573 H2 WAT 191 -6.842 9.088 5.033 0.000 +ATOM 574 OH2 WAT 192 -4.009 8.939 3.214 0.000 +ATOM 575 H1 WAT 192 -4.874 9.011 3.618 0.000 +ATOM 576 H2 WAT 192 -4.064 9.486 2.430 0.000 +ATOM 577 OH2 WAT 193 0.702 8.827 2.390 0.000 +ATOM 578 H1 WAT 193 0.245 9.356 1.736 0.000 +ATOM 579 H2 WAT 193 0.865 9.430 3.115 0.000 +ATOM 580 OH2 WAT 194 3.029 7.705 3.335 0.000 +ATOM 581 H1 WAT 194 2.125 7.870 3.069 0.000 +ATOM 582 H2 WAT 194 3.458 8.558 3.269 0.000 +ATOM 583 OH2 WAT 195 5.634 9.275 3.630 0.000 +ATOM 584 H1 WAT 195 5.452 10.191 3.419 0.000 +ATOM 585 H2 WAT 195 5.810 8.865 2.783 0.000 +ATOM 586 OH2 WAT 196 -7.061 7.962 1.095 0.000 +ATOM 587 H1 WAT 196 -7.080 7.537 1.952 0.000 +ATOM 588 H2 WAT 196 -6.256 7.644 0.686 0.000 +ATOM 589 OH2 WAT 197 -4.920 6.672 -0.250 0.000 +ATOM 590 H1 WAT 197 -5.139 5.756 -0.081 0.000 +ATOM 591 H2 WAT 197 -4.096 6.812 0.216 0.000 +ATOM 592 OH2 WAT 198 -2.383 7.142 0.598 0.000 +ATOM 593 H1 WAT 198 -2.170 6.254 0.311 0.000 +ATOM 594 H2 WAT 198 -2.318 7.108 1.553 0.000 +ATOM 595 OH2 WAT 199 1.126 -7.194 -0.257 0.000 +ATOM 596 H1 WAT 199 0.451 -7.823 -0.002 0.000 +ATOM 597 H2 WAT 199 1.690 -7.678 -0.860 0.000 +ATOM 598 OH2 WAT 200 6.268 -9.087 -0.145 0.000 +ATOM 599 H1 WAT 200 6.872 -8.539 -0.646 0.000 +ATOM 600 H2 WAT 200 5.399 -8.767 -0.385 0.000 +ATOM 601 OH2 WAT 201 7.995 -7.948 -1.811 0.000 +ATOM 602 H1 WAT 201 8.607 -8.462 -2.338 0.000 +ATOM 603 H2 WAT 201 8.378 -7.070 -1.788 0.000 +ATOM 604 OH2 WAT 202 -6.548 -8.560 -2.435 0.000 +ATOM 605 H1 WAT 202 -7.325 -8.794 -2.943 0.000 +ATOM 606 H2 WAT 202 -6.017 -9.357 -2.427 0.000 +ATOM 607 OH2 WAT 203 -7.711 -8.762 -6.632 0.000 +ATOM 608 H1 WAT 203 -7.272 -8.151 -7.223 0.000 +ATOM 609 H2 WAT 203 -8.345 -8.224 -6.158 0.000 +ATOM 610 OH2 WAT 204 -1.968 -8.633 -2.622 0.000 +ATOM 611 H1 WAT 204 -1.094 -8.245 -2.652 0.000 +ATOM 612 H2 WAT 204 -2.104 -8.848 -1.699 0.000 +ATOM 613 OH2 WAT 205 3.589 -8.603 -0.973 0.000 +ATOM 614 H1 WAT 205 3.665 -8.508 -1.922 0.000 +ATOM 615 H2 WAT 205 3.313 -9.511 -0.844 0.000 +ATOM 616 OH2 WAT 206 4.942 -8.577 -5.280 0.000 +ATOM 617 H1 WAT 206 4.239 -7.963 -5.490 0.000 +ATOM 618 H2 WAT 206 4.497 -9.415 -5.149 0.000 +ATOM 619 OH2 WAT 207 -7.810 7.186 -5.734 0.000 +ATOM 620 H1 WAT 207 -8.495 7.148 -6.402 0.000 +ATOM 621 H2 WAT 207 -7.807 8.099 -5.446 0.000 +ATOM 622 OH2 WAT 208 -5.850 -6.846 -8.189 0.000 +ATOM 623 H1 WAT 208 -5.359 -7.476 -8.717 0.000 +ATOM 624 H2 WAT 208 -5.227 -6.550 -7.526 0.000 +ATOM 625 OH2 WAT 209 -0.824 -6.553 -5.732 0.000 +ATOM 626 H1 WAT 209 -0.646 -7.199 -5.049 0.000 +ATOM 627 H2 WAT 209 -0.878 -5.719 -5.265 0.000 +ATOM 628 OH2 WAT 210 1.054 8.396 -7.337 0.000 +ATOM 629 H1 WAT 210 1.920 8.762 -7.515 0.000 +ATOM 630 H2 WAT 210 0.807 7.956 -8.150 0.000 +ATOM 631 OH2 WAT 211 7.763 7.959 -4.657 0.000 +ATOM 632 H1 WAT 211 7.569 7.211 -5.222 0.000 +ATOM 633 H2 WAT 211 7.724 8.717 -5.241 0.000 +ATOM 634 OH2 WAT 212 -6.590 -8.046 7.082 0.000 +ATOM 635 H1 WAT 212 -6.956 -8.811 7.525 0.000 +ATOM 636 H2 WAT 212 -5.677 -8.017 7.369 0.000 +ATOM 637 OH2 WAT 213 -4.617 -8.695 8.618 0.000 +ATOM 638 H1 WAT 213 -3.718 -8.969 8.433 0.000 +ATOM 639 H2 WAT 213 -5.003 -9.438 9.082 0.000 +ATOM 640 OH2 WAT 214 -5.992 8.106 -8.709 0.000 +ATOM 641 H1 WAT 214 -6.260 8.393 -7.836 0.000 +ATOM 642 H2 WAT 214 -5.221 7.560 -8.557 0.000 +ATOM 643 OH2 WAT 215 3.805 -9.363 8.800 0.000 +ATOM 644 H1 WAT 215 3.881 -9.789 9.654 0.000 +ATOM 645 H2 WAT 215 4.698 -9.349 8.458 0.000 +ATOM 646 OH2 WAT 216 6.981 6.710 7.493 0.000 +ATOM 647 H1 WAT 216 6.199 6.524 6.973 0.000 +ATOM 648 H2 WAT 216 6.909 7.639 7.710 0.000 +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.param new file mode 100644 index 0000000000000000000000000000000000000000..c4f65bbe8637318af40f471c16f5a5c3e9d8059d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.param @@ -0,0 +1,263 @@ +remarks file toppar/carbohydrate.param +REMARKS Parameter file for pyranose sugars +REMARKS Alexandre Bonvin - adapted to use unique atom types for sugar-specific atoms +REMARKS Joao Rodrigues 11-June-2020 +REMARKS Parameters updated to Feng, PLoS One, 2017 +REMARKS PMC 5726640 + +REMARKS Bill Weis 10-July-1988 +REMARKS Additions for atom type combinations not covered in PARAM19X.PRO. +REMARKS Needed additions are for ether oxygen and aliphatic carbon in all-atom +REMARKS representation used for sugars (type CC). Ditto for type HA. +REMARKS Values from J. Brady glucose parameters unless noted. +REMARKS These should be sufficient for refinement. + +REMARKS Additions 6-March-1992 Bill Weis +REMARKS New atom types CCA, CCE, OASfor the C1 & O1 positions to account +REMARKS for different BOND and ANGLe values due to the anomeric effect. +REMARKS More accurate equilibrium values for BOND ANGLe around this oxygen +REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for +REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA +REMARKS for linkages. +REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; +REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. + +REMARKS This set has been modified to be roughly consistent with +REMARKS the csd-derived protein parameters of Engh and Huber. +REMARKS New atom type CC6 for exocyclic 6 carbon +REMARKS Bill Weis 5/11/92 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +BOND CCS OES 1000.0 1.438 ! closer to crystal structures +BOND CCE OES 1000.0 1.428 +BOND CCA OES 1000.0 1.419 +BOND CCS CCS 1000.0 1.526 ! adjusted to Jeffries +BOND CCS CC6 1000.0 1.516 +BOND CCE CCS 1000.0 1.526 +BOND CCA CCS 1000.0 1.526 +BOND CCS HAS 1000.0 1.099 +BOND CC6 HAS 1000.0 1.099 +BOND CCE HAS 1000.0 1.099 +BOND CCA HAS 1000.0 1.099 +BOND CCS OH1 1000.0 1.420 +BOND CC6 OH1 1000.0 1.420 +BOND CCE OH1 1000.0 1.385 !force constant as for other exocylic OH +BOND CCA OH1 1000.0 1.398 ! " " " " " " " +BOND CCE OAS 1000.0 1.385 ! " " " " " " " +BOND CCA OAS 1000.0 1.398 ! " " " " " " " +BOND CCS OAS 1000.0 1.44 !force constant as for other exocylic OH +BOND CC6 OAS 1000.0 1.44 +BOND CCS NH1 1000.0 1.45 !as extended atom carbon-N +BOND CCE NH1 1000.0 1.45 !as extended atom carbon-N +BOND CCA NH1 1000.0 1.45 !as extended atom carbon-N +BOND CH1E OAS 1000.0 1.385 +BOND CCS C 1000.0 1.52 !" " " " -C +BOND CCE C 1000.0 1.52 +BOND CCA C 1000.0 1.52 +BOND CC6 OC 1000.0 1.25 ! standard CO bond (parm10) + + +ANGLe H OH1 CCS 500.0 109.35 +ANGLe H OH1 CC6 500.0 109.35 +ANGLe H OH1 CCE 500.0 109.35 +ANGLe H OH1 CCA 500.0 109.35 +ANGLe HAS CCS HAS 500.0 107.85 +ANGLe HAS CC6 HAS 500.0 107.85 +ANGLe HAS CCS CCS 500.0 108.72 +ANGLe HAS CC6 CCS 500.0 108.72 +ANGLe HAS CCS CC6 500.0 108.72 +ANGLe HAS CCS CCE 500.0 108.72 +ANGLe HAS CCS CCA 500.0 108.72 +ANGLe HAS CCE CCS 500.0 108.72 +ANGLe HAS CCA CCS 500.0 108.72 +ANGLe HAS CCS OH1 500.0 109.89 +ANGLe HAS CC6 OH1 500.0 109.89 +ANGLe HAS CCE OH1 500.0 109.89 +ANGLe HAS CCA OH1 500.0 109.89 +ANGLe HAS CCS OAS 500.0 109.89 +ANGLe HAS CC6 OAS 500.0 109.89 +ANGLe HAS CCE OAS 500.0 109.89 +ANGLe HAS CCA OAS 500.0 109.89 +ANGLe HAS CCS OES 500.0 107.24 +ANGLe HAS CCE OES 500.0 107.24 +ANGLe HAS CCA OES 500.0 107.24 +ANGLe CCS CCS CCS 500.0 110.40 +ANGLe CCS CCS CC6 500.0 112.50 +ANGLe CCE CCS CCS 500.0 110.40 +ANGLe CCA CCS CCS 500.0 110.40 +ANGLe CCS CC6 OH1 500.0 111.20 +ANGLe CCS CCE OH1 500.0 109.70 +ANGLe CCS CCA OH1 500.0 109.70 +ANGLe CCE CCS OH1 500.0 109.70 +ANGLe CCA CCS OH1 500.0 109.70 +ANGLe CCS CCS OH1 500.0 109.70 +ANGLe CCS CCS OES 500.0 110.00 +ANGLe CC6 CCS OES 500.0 107.20 +ANGLe CCS CCE OES 500.0 110.00 +ANGLe CCS CCA OES 500.0 110.00 +ANGLe CCS CCS OAS 500.0 109.70 +ANGLe CCS CC6 OAS 500.0 109.70 !guess for 1-6 links +ANGLe CCS CCE OAS 500.0 109.70 +ANGLe CCS CCA OAS 500.0 109.70 +ANGLe CCE CCS OAS 500.0 109.70 +ANGLe CCA CCS OAS 500.0 109.70 +ANGLe CCS OES CCE 500.0 112.0 +ANGLe CCS OES CCA 500.0 114.0 +ANGLe OES CCE OH1 500.0 108.0 +ANGLe OES CCE OAS 500.0 108.0 +ANGLe OES CCA OH1 500.0 112.1 +ANGLe OES CCA OAS 500.0 112.1 +ANGLe CCE OAS CCS 500.0 116.0 +ANGLe CCA OAS CCS 500.0 115.0 +ANGLe CCE OAS CC6 500.0 116.0 +ANGLe CCA OAS CCE 500.0 112.0 !alpha 1,1 link +ANGLe CH1E OAS CCE 500.0 112.0 !alpha 1,1 link +ANGLe CCA OAS CC6 500.0 111.5 !alpha 1,6 link +ANGLe O C CCS 500.0 120.0 !Mo & Jensen, Acta B, 31, 2867 (1975), 8/30/93 +ANGLe C CCS HAS 500.0 109.5 ! 8/30/93 +ANGLe CCS CCS NH1 500.0 110.0 +ANGLe CCE CCS NH1 500.0 110.0 +ANGLe CCA CCS NH1 500.0 110.0 +ANGLe CCS CCE NH1 500.0 110.0 +ANGLe CCS CCA NH1 500.0 110.0 +ANGLe HAS CCS NH1 500.0 109.5 +ANGLe HAS CCE NH1 500.0 109.5 +ANGLe HAS CCA NH1 500.0 109.5 +ANGLe CCS NH1 H 500.0 120.0 +ANGLe CCE NH1 H 500.0 120.0 +ANGLe CCA NH1 H 500.0 120.0 +ANGLe CCS NH1 C 500.0 120.0 +ANGLe CCE NH1 C 500.0 120.0 +ANGLe CCA NH1 C 500.0 120.0 +ANGLe NH1 CCS OES 500.0 110.7 !A complete guess +ANGLe NH1 CCE OES 500.0 110.7 !A complete guess +ANGLe NH1 CCA OES 500.0 110.7 !A complete guess +ANGLe NH1 C CCS 500.0 117.5 +ANGLe C CCE OH1 500.0 109.5 !A complete guess for SIA O2 +ANGLe C CCA OH1 500.0 109.5 !A complete guess for SIA O2 +ANGLe C CCE OAS 500.0 109.5 !A complete guess for SIA O2 +ANGLe C CCA OAS 500.0 109.5 !A complete guess for SIA O2 +ANGLe O C CCE 500.0 121.5 +ANGLe O C CCA 500.0 121.5 +ANGLe C CCE HAS 500.0 109.5 +ANGLe C CCA HAS 500.0 109.5 +ANGLe CCE C OC 500.0 118.75 +ANGLe CCA C OC 500.0 118.75 +ANGLe C CCE OES 500.0 107.24 +ANGLe C CCA OES 500.0 107.24 +ANGLe C CCE CCS 500.0 108.72 +ANGLe C CCA CCS 500.0 108.72 +! other angles +ANGLe OC CC6 OC 500.00 123.3548 +ANGLe CCS CC6 OC 500.0 109.70 ! guess from CCS-CC6-OAS (to check: experimental structures have 112-113) + + + +DIHEdral X CCS CCS X 2.0 3 0.0 +DIHEdral X CCS CC6 X 2.0 3 0.0 +DIHEdral X CCE CCS X 2.0 3 0.0 +DIHEdral X CCA CCS X 2.0 3 0.0 +DIHEdral X CCS OH1 X 2.0 3 0.0 +DIHEdral X CC6 OH1 X 2.0 3 0.0 +DIHEdral X CCE OH1 X 2.0 3 0.0 +DIHEdral X CCA OH1 X 2.0 3 0.0 +DIHEdral X CCS OAS X 2.0 3 0.0 +DIHEdral X CC6 OAS X 2.0 3 0.0 +DIHEdral X CCE OAS X 2.0 3 0.0 +DIHEdral X CCA OAS X 2.0 3 0.0 +DIHEdral X CCS OES X 2.0 3 0.0 +DIHEdral X CCE OES X 2.0 3 0.0 +DIHEdral X CCA OES X 2.0 3 0.0 +DIHEdral HAS CCS NH1 H 2.0 3 180.0 !for NAG and NANA +DIHEdral X CCS NH1 X 2.0 3 0.0 !beta link to Asn Nd1 +DIHEdral X CCE NH1 X 2.0 3 0.0 !beta link to Asn Nd1 +DIHEdral X CCA NH1 X 2.0 3 0.0 !beta link to Asn Nd1 +DIHEdral X C CCE X 2.0 3 0.0 +DIHEdral X C CCA X 2.0 3 0.0 +DIHEdral X C CCS X 2.0 3 0.0 ! N-acetyl in NAG, 8/30/93 +DIHEdral CCS NH1 C CCS 2.0 2 0.0 ! peptide plane in NAG + ! guess - PDA 8/99 +DIHEdral CCS OES CCE CCS 2.0 2 0.0 ! guessing for BDP + +IMPRoper CCS X X CCS 500.0 0 35.26439 +IMPRoper CCE X X CCS 500.0 0 35.26439 +IMPRoper CCA X X CCS 500.0 0 35.26439 +IMPRoper OH1 X X CCS 500.0 0 35.26439 +IMPRoper OH1 X X CCE 500.0 0 35.26439 +IMPRoper OH1 X X CCA 500.0 0 35.26439 +IMPRoper OAS X X CCS 500.0 0 35.26439 +IMPRoper OAS X X CCE 500.0 0 35.26439 +IMPRoper OAS X X CCA 500.0 0 35.26439 +IMPRoper CCS X X OES 500.0 0 35.26439 +IMPRoper CCE X X OES 500.0 0 35.26439 +IMPRoper CCA X X OES 500.0 0 35.26439 +IMPRoper C X X CCE 500.0 0 0.0 !NANA acid planarity +IMPRoper C X X CCA 500.0 0 0.0 !NANA acid planarity +IMPRoper HAS OES OH1 CCS 500.00 0 67.6 +IMPRoper HAS OH1 OES CCS 500.00 0 67.7 !beta-D C1 +IMPRoper C OH1 OES CCS 500.00 0 67.7 !SIA alpha-L C2 +IMPRoper C OH1 CCS OES 500.00 0 67.7 !SIA alpha-L C2 +IMPRoper OH1 C CCS OES 500.00 0 67.7 !SIA beta-L C2 +IMPRoper HAS OH1 CCA CCS 500.00 0 66.8 !MAN,FUC C2 +IMPRoper HAS OH1 CCE CCS 500.00 0 66.8 +IMPRoper HAS OAS CCA CCS 500.00 0 66.8 +IMPRoper HAS OAS CCE CCS 500.00 0 66.8 +IMPRoper HAS CCA OH1 CCS 500.00 0 66.8 !GLC,GLA,FCA,XYP C2 +IMPRoper HAS CCE OH1 CCS 500.00 0 66.8 +IMPRoper HAS CCA OAS CCS 500.00 0 66.8 +IMPRoper HAS CCE OAS CCS 500.00 0 66.8 +IMPRoper HAS HAS CCE CCS 500.00 0 70.3 !SIA C3 +IMPRoper HAS HAS CCS CCE 500.00 0 70.3 !SIA C3 +IMPRoper HAS HAS CCA CCS 500.00 0 70.3 +IMPRoper HAS HAS CCS CCS 500.00 0 70.3 !ABE C3 +IMPRoper HAS OH1 CCS CCS 500.00 0 66.9 !MAN,GLC,GLA,NAG,FCA,XYP C3 - A2G,FCA,SIA C4 - SIA C7,C8 +IMPRoper HAS OAS CCS CCS 500.00 0 66.9 +IMPRoper HAS CCS OH1 CCS 500.00 0 66.8 !FUC C3 MAN,GLC,GLA,NAG,FUC,XYP C4 +IMPRoper HAS CCS CCS OH1 500.00 0 66.8 !NGA C4 +IMPRoper HAS CCS OAS CCS 500.00 0 66.8 +IMPRoper HAS CCS OES CC6 500.00 0 66.8 !MAN,GLC,GLA,NAG,FCA C5 +IMPRoper HAS OES CCS CC6 500.00 0 66.8 !FUC C5 +IMPRoper HAS HAS OH1 CCS 500.00 0 70.3 !GLC,GLA,MAN,NAG,A2G C6 +IMPRoper HAS HAS OAS CCS 500.00 0 70.3 +IMPRoper HAS CCA NH1 CCS 500.00 0 66.8 !NAG,A2G C2 +IMPRoper HAS CCE NH1 CCS 500.00 0 66.8 +IMPRoper HAS CCS NH1 CCS 500.00 0 66.8 !SIA C5 +IMPRoper HAS CCS CCS OES 500.00 0 66.8 !SIA C6 +IMPRoper HAS CCS CCS OAS 500.00 0 66.8 !NGA C4 +IMPRoper HAS HAS CCS OH1 500.00 0 70.3 !SIA C9 +IMPRoper HAS HAS OES CCS 500.00 0 70.3 !XYP C5 +IMPRoper HAS CCS CCS NH1 500.00 0 66.8 !SIA C5 +IMPRoper HAS CCS OES CCS 500.00 0 66.8 !SIA C6 +IMPRoper HAS HAS OH1 CCS 500.00 0 70.3 !SIA C9 +IMPRoper HAS HAS OES CCS 500.00 0 70.3 !XYP C5 +IMPRoper NH1 CCE H C 500.00 0 0.0 !B1N +IMPRoper HAS NH1 OES CCS 500.00 0 67.7 !B1N beta-D C1 +IMPRoper HAS OAS OES CCS 500.00 0 67.7 !B12,B14,A12L,A13L,A14L,A16L beta-D C1 +IMPRoper HAS OES OAS CCS 500.00 0 67.6 !A12,A13,A14,A16,B12L,B14L alpha-D C1 +IMPRoper C CCS NH1 O 500.00 0 0.0 !NAG,SIA planar +IMPRoper NH1 C CCS H 500.00 0 0.0 !NAG,SIA planar +IMPRoper CCS NH1 C CCS 500.00 0 180.0 !NAG,SIA trans peptide +! new impropers +IMPRoper CC6 CCS OC OC 500.00 0 0.0 !BDP, angle taken from charmm + + +{Asn-NAG} +ANGLe CH2E C NH1 500.00 116.3225 {Asn CB-CG-ND2} +IMPRoper C CH2E O NH1 500.00 0 0.0124 {Asn CG-CB-OD1-ND2} + +! Values matching the OPLS one for proteins +NONBonded HAS 0.050 0.500 0.004 0.500 +NONBONDed CCS 0.105 3.750 0.013 3.750 +NONBONDed CC6 0.105 3.750 0.013 3.750 +NONBONDed CCE 0.105 3.750 0.013 3.750 +NONBONDed CCA 0.105 3.750 0.013 3.750 +NONBONDed OES 0.210 2.960 0.021 2.960 +NONBONDed OAS 0.210 2.960 0.021 2.960 + +set message=$old_message echo=$old_echo end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.top new file mode 100644 index 0000000000000000000000000000000000000000..41a363d95ad6eaf2ee57f53ce8c07185c23d227e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/carbohydrate.top @@ -0,0 +1,3095 @@ +REMARKS toppar/carbohydrate.top +REMARKS for use with carbohydrate.param for N-linked glycans +REMARKS ========================================================== +REMARKS Joao Rodrigues 11-June-2020 +REMARKS Topologies updated to Feng, PLoS One, 2017 +REMARKS PMC 5726640 +REMARKS Alexandre Bonvin July-2020 +REMARKS Patches added for GAL-SIA 2-3 and 2.6 linkages +REMARKS Marco Giulini November-2024 +REMARKS Topologies added for BDP-MMA-XYS-ABE +REMARKS ---------------------------------------------------------- +REMARKS Currently supported carbohydrates and their anomers: +REMARK (codes in parenthesis are commonly used alternatives - currently not recognized by CNS): +REMARKS GLC: alpha-D-glucopyranose +REMARKS BGC: beta -D-glucopyranose +REMARKS GLA: alpha-D-galactopyranose +REMARKS GAL (GLB): beta- D-galactopyranose +REMARKS MAN: alpha-D-mannopyranose +REMARKS BMA: beta -D-mannopyronose +REMARKS NDG: 2-N-acetyl-alpha-D-glucopyranose +REMARKS A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4 +REMARKS NAG: 2-N-acetyl-beta-D-glucopyranose +REMARKS NGA: 2-N-acetyl-beta-D-galactopyranose +REMARKS FUC: alpha-L-fucopyranose +REMARKS FUL: beta -L-fucopyranose +REMARKS FCA: alpha-D-fucopyranose +REMARKS FCB: beta -D-fucopyranose +REMARKS SIA: alpha-N-acetyl neuraminic acid +REMARKS SIB: beta-N-acetyl neuraminic acid - A. Bonvin +REMARKS XYP: beta-D-xylopyranose +REMARKS BDP: beta-D-glucoronic acid +REMARKS MMA: methyl alpha-D-mannopyranoside +REMARKS XYS: alpha-D-xylopyranose +REMARKS ABE: alpha-D-Abequopyranose +REMARKS ---------------------------------------------------------- +REMARKS Links +REMARKS B1N: N-linked glycan beta link from NAG and NDG to ASN (asparagine) +! note: PDB files with unusual NDG to ASN links are likely incorrect assignments +! they will be forced into the beta anomer by the B1N link. +REMARKS B12: beta(1,2) link from BGC, GAL, BMA, NAG, FCB, XYP to any +REMARKS B14: beta(1,4) link from BGC, GAL, BMA, NAG, FCB, XYP to any +REMARKS A12: alpha(1,2) link from GLC, GLA, MAN, NDG, A2G, FCA to any +REMARKS A13: alpha(1,3) link from GLC, GLA, MAN, NDG, A2G, FCA to any +REMARKS A14: alpha(1,4) link from GLC, GLA, MAN, NDG, A2G, FCA to any +REMARKS A16: alpha(1,6) link from GLC, GLA, MAN, NDG, A2G, FCA to any +REMARKS B12L: beta(1,2) link from FUL to any +REMARKS B14L: beta(1,4) link from FUL to any +REMARKS A12L: alpha(1,2) link from FUC to any +REMARKS A13L: alpha(1,3) link from FUC to any +REMARKS A14L: alpha(1,4) link from FUC to any +REMARKS A16L: alpha(1,6) link from FUC to any +REMARKS A23: alpha(2,3) link from GAL to SIA, SIB +REMARKS A23S: alpha(2,3) link from SIA to GAL +REMARKS A26: alpha(2,6) link from GAL to SIA, SIB +REMARKS A26S: alpha(2,6) link from SIA, SIB to GAL +REMARKS A28S: alpha(2,8) link from SIA, SIB to SIA, SIB +REMARKS RAM: alpha-L-rhamnose +REMARKS GXL: alpha-L-galactopyranose +REMARKS B13: beta(1,3) link from beta-D-sugar to any +REMARKS B13L: beta(1,3) link from beta-L-sugar to any +REMARKS B16: beta(1,6) link from beta-D-sugar to any +REMARKS B16L: beta(1,6) link from beta-L-sugar to any +REMARKS B1S: beta link from C1(D-) to Ser OG. +REMARKS A1S: alpha link from C1(D-) to Ser OG. +REMARKS B1T: beta link from C1(D-) to Thr OG1. +REMARKS A1T: alpha link from C1(D-) to Thr OG1. +REMARKS B1C: beta link from C1(D-) to Cys SG. +REMARKS A1C: alpha link from C1(D-) to Cys SG. +REMARKS B1SL: beta link from C1(L-) to Ser OG. +REMARKS A1SL: alpha link from C1(L-) to Ser OG. +REMARKS B1TL: beta link from C1(L-) to Thr OG1. +REMARKS A1TL: alpha link from C1(L-) to Thr OG1. +REMARKS B1CL: beta link from C1(L-) to Cys SG. +REMARKS A1CL: alpha link from C1(L-) to Cys SG. + +! History: +! Bill Weis 10-July-1988: +! Charges taken from John Brady's glucose topology file for ring, +! others from protein parameter file. +! Idealized values for impropers at ring carbons to allow simple +! construction of various anomers/epimers. +! Any other hexose or link can be easily constructed by analogy to these. + +! Additions 6-March-1992 Bill Weis for use with PARAM2.CHO +! New atom types CCA, CCE, OA for the C1 & O1 positions to account +! for different bond and angle values due to the anomeric effect. +! More accurate equilibrium values for bond angle around this oxygen +! in glycosidic linkages. CCE for equatorial O1, CCA for +! axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA +! for linkages. +! References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; +! K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. +! +! Additional CC6 atomtype for exocyclic carbon 5/11/92 +! New nomenclature, pairs of anomers for each pyranose sugar, generic links, ATB 12-Dec-2009 +! +! added impropers that define anomers using non-hydrogen atoms, ATB 12/06/09 +! +! added additional residues: FCA, FCB, A2G, ATB 12/07/09 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +AUTOGENERATE ANGLES=TRUE END +{*===========================*} + +{default masses -- only those not in the protein topology protein.top} +MASS CCS 12.01100! carbohydrate carbon +MASS CC6 12.01100! carbohydrate carbon, exocyclic C6 +MASS CCE 12.01100! carbohydrate carbon, equatorial C1 +MASS CCA 12.01100! carbohydrate carbon, axial C1 +MASS OES 15.99940! ether oxygen +MASS OAS 15.99940! ether oxygen in glycosidic bond +MASS HAS 1.00800! aliphatic hydrogen + +!------------------------------------------------------------------- + + +RESIdue GLC !alpha-D-glucopyranose ! alpha-anomer of BGC, ATB 12/06/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +RESIdue BGC !beta-D-glucopyranose ! (formerly called GLC) + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +!------------------------------------------------------------------- + +RESIdue GLA !alpha-D-galactopyranose ! alpha anomer form of GAL, ATB 12/06/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha anomer definition using non-hydrogen atoms + +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 O4 C3 C5 {Axial C4} +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +RESIdue GAL !beta-D-galactopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta anomer definition using non-hydrogen atoms + +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 O4 C3 C5 {Axial C4} +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +!------------------------------------------------------------------- + +RESIdue MAN !alpha-D-mannopyranose ! was formerly beta form, ATB 06/12/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 O2 C1 C3 {axial C2} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +RESIdue BMA !beta-D-mannopyranose ! formerly called MAN + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 O2 C1 C3 {axial C2} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +!------------------------------------------------------------------- + +RESIdue NDG !2-N-Acetyl-alpha-D-glucopyranose, ATB 12/06/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.000 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM N2 TYPE=NH1 CHARge=-0.350 END + ATOM HN2 TYPE=H CHARge= 0.250 END + ATOM C7 TYPE=C CHARge= 0.550 END + ATOM O7 TYPE=O CHARge=-0.550 END + ATOM C8 TYPE=CCS CHARge=-0.300 END + ATOM H81 TYPE=HAS CHARge= 0.100 END + ATOM H82 TYPE=HAS CHARge= 0.100 END + ATOM H83 TYPE=HAS CHARge= 0.100 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END ! is called O in PDB convention ! is renamed after topology generation in module mtfautogenerate ATB 12/07/09 + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 N2 + BOND N2 HN2 + BOND N2 C7 + BOND C7 O7 + BOND C7 C8 + BOND C8 H81 + BOND C8 H82 + BOND C8 H83 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 N2 HN2 + DIHEDRAL C2 N2 C7 C8 + DIHEDRAL N2 C7 C8 H81 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 N2 C3 + IMPRoper N2 C7 C2 HN2 {planar N} + IMPRoper C7 C8 N2 O7 {planar C} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 N2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + IMPRoper C2 N2 C7 C8 {trans peptide} + +END + +RESIdue NAG !2-N-Acetyl-beta-D-glucopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.000 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM N2 TYPE=NH1 CHARge=-0.350 END + ATOM HN2 TYPE=H CHARge= 0.250 END + ATOM C7 TYPE=C CHARge= 0.550 END + ATOM O7 TYPE=O CHARge=-0.550 END + ATOM C8 TYPE=CCS CHARge=-0.300 END + ATOM H81 TYPE=HAS CHARge= 0.100 END + ATOM H82 TYPE=HAS CHARge= 0.100 END + ATOM H83 TYPE=HAS CHARge= 0.100 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 N2 + BOND N2 HN2 + BOND N2 C7 + BOND C7 O7 + BOND C7 C8 + BOND C8 H81 + BOND C8 H82 + BOND C8 H83 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 N2 HN2 + DIHEDRAL C2 N2 C7 C8 + DIHEDRAL N2 C7 C8 H81 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 N2 C3 + IMPRoper N2 C7 C2 HN2 {planar N} + IMPRoper C7 C8 N2 O7 {planar C} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 N2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + IMPRoper C2 N2 C7 C8 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue NGA !2-N-Acetyl-beta-D-galactopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.000 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM N2 TYPE=NH1 CHARge=-0.350 END + ATOM HN2 TYPE=H CHARge= 0.250 END + ATOM C7 TYPE=C CHARge= 0.550 END + ATOM O7 TYPE=O CHARge=-0.550 END + ATOM C8 TYPE=CCS CHARge=-0.300 END + ATOM H81 TYPE=HAS CHARge= 0.100 END + ATOM H82 TYPE=HAS CHARge= 0.100 END + ATOM H83 TYPE=HAS CHARge= 0.100 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 N2 + BOND N2 HN2 + BOND N2 C7 + BOND C7 O7 + BOND C7 C8 + BOND C8 H81 + BOND C8 H82 + BOND C8 H83 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 N2 HN2 + DIHEDRAL C2 N2 C7 C8 + DIHEDRAL N2 C7 C8 H81 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 N2 C3 + IMPRoper N2 C7 C2 HN2 {planar N} + IMPRoper C7 C8 N2 O7 {planar C} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 N2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 C5 O4 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + IMPRoper C2 N2 C7 C8 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue MAG !2-N-Acetyl-beta-D-glucopyranose + Methyl at O1 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OAS CHARge=-0.400 END + ATOM CM TYPE=CCS CHARge=-0.150 END + ATOM HM1 TYPE=HAS CHARge= 0.100 END + ATOM HM2 TYPE=HAS CHARge= 0.100 END + ATOM HM3 TYPE=HAS CHARge= 0.100 END + ATOM C2 TYPE=CCS CHARge= 0.000 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM N2 TYPE=NH1 CHARge=-0.350 END + ATOM HN2 TYPE=H CHARge= 0.250 END + ATOM C7 TYPE=C CHARge= 0.550 END + ATOM O7 TYPE=O CHARge=-0.550 END + ATOM C8 TYPE=CCS CHARge=-0.300 END + ATOM H81 TYPE=HAS CHARge= 0.100 END + ATOM H82 TYPE=HAS CHARge= 0.100 END + ATOM H83 TYPE=HAS CHARge= 0.100 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 CM + BOND CM HM1 + BOND CM HM2 + BOND CM HM3 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 N2 + BOND N2 HN2 + BOND N2 C7 + BOND C7 O7 + BOND C7 C8 + BOND C8 H81 + BOND C8 H82 + BOND C8 H83 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 CM + DIHEDRAL H2 C2 N2 HN2 + DIHEDRAL C2 N2 C7 C8 + DIHEDRAL N2 C7 C8 H81 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 N2 C3 + IMPRoper N2 C7 C2 HN2 {planar N} + IMPRoper C7 C8 N2 O7 {planar C} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 N2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + IMPRoper C2 N2 C7 C8 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue A2G !2-N-Acetyl-alpha-D-galactopyranose, different stereochemistry at C4 ! new residue ATB 12/07/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.000 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM N2 TYPE=NH1 CHARge=-0.350 END + ATOM HN2 TYPE=H CHARge= 0.250 END + ATOM C7 TYPE=C CHARge= 0.550 END + ATOM O7 TYPE=O CHARge=-0.550 END + ATOM C8 TYPE=CCS CHARge=-0.300 END + ATOM H81 TYPE=HAS CHARge= 0.100 END + ATOM H82 TYPE=HAS CHARge= 0.100 END + ATOM H83 TYPE=HAS CHARge= 0.100 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END ! is called O in PDB convention ! is renamed after topology generation in module mtfautogenerate, ATB 12/07/09 + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 N2 + BOND N2 HN2 + BOND N2 C7 + BOND C7 O7 + BOND C7 C8 + BOND C8 H81 + BOND C8 H82 + BOND C8 H83 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 N2 HN2 + DIHEDRAL C2 N2 C7 C8 + DIHEDRAL N2 C7 C8 H81 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 C1 N2 C3 + IMPRoper N2 C7 C2 HN2 {planar N} + IMPRoper C7 C8 N2 O7 {planar C} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 O4 C3 C5 !!!<<<<< only difference to NDG !?? check!!! +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 N2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + IMPRoper C2 N2 C7 C8 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue FUC !alpha-L-fucopyranose, ! alpha anomer of FUL + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge=-0.300 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM H63 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 H61 + +{ This is an L-sugar, so impropers are reversed to maintain ring } +{ geometry equivalent to D-hexoses } +! IMPRoper C1 O5 H1 C2 ! alpha-anomer +! IMPRoper C1 O1 O5 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! L-form definition +! IMPRoper C2 O2 C1 C3 +! IMPRoper C3 C2 O3 C4 +! IMPRoper C4 C3 O4 C5 {Axial C4} +! IMPRoper C5 C4 C6 O5 + + IMPRoper H1 O1 O5 C2 {L alpha C1=D beta} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 C2 O3 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 O5 C4 C6 {C5} + +END + +RESIdue FUL !beta-L-fucopyranose (formerly called FUC), ATB 12/06/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge=-0.300 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM H63 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 H61 + +{ This is an L-sugar, so impropers are reversed to maintain ring } +{ geometry equivalent to D-hexoses } +! IMPRoper C1 H1 O5 C2 ! beta-anomer +! IMPRoper C1 O5 O1 C2 ! beta-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! L-form definition +! IMPRoper C2 O2 C1 C3 +! IMPRoper C3 C2 O3 C4 +! IMPRoper C4 C3 O4 C5 {Axial C4} +! IMPRoper C5 C4 C6 O5 + + IMPRoper H1 O5 O1 C2 {L beta C1=D alpha} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 C2 O3 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 O5 C4 C6 {C5} + +END + +!------------------------------------------------------------------- + +RESIdue FCA !alpha-D-fucopyranose, ! alpha anomer of FCB, ! new residue, ATB 12/07/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge=-0.300 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM H63 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 H61 + +{ anomer definition for D-sugars } +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms + +! D-form definition: +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 O4 C3 C5 {Axial C4} +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + +END + +RESIdue FCB !beta-D-fucopyranose ! new residue ATB 12/07/09 + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge=-0.300 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM H63 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 H61 + +{ anomer definition for D-sugar } +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer definition using non-hydrogen atoms + +! D-form definition: +! IMPRoper C2 C1 O2 C3 +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 O4 C3 C5 {Axial C4} +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + +END + + +!------------------------------------------------------------------- + +RESIdue SIA {alpha-N-acetyl neuraminic acid} + GROUP + ATOM C1 TYPE=C CHARge= 0.360 END + ATOM O1A TYPE=OC CHARge=-0.600 END + ATOM O1B TYPE=OC CHARge=-0.600 END + ATOM C2 TYPE=CCE CHARge= 0.290 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge=-0.200 END + ATOM H31 TYPE=HAS CHARge= 0.100 END + ATOM H32 TYPE=HAS CHARge= 0.100 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.000 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM N5 TYPE=NH1 CHARge=-0.350 END + ATOM HN5 TYPE=H CHARge= 0.250 END + ATOM C10 TYPE=C CHARge= 0.550 END + ATOM O10 TYPE=O CHARge=-0.550 END + ATOM C11 TYPE=CCS CHARge=-0.300 END + ATOM H111 TYPE=HAS CHARge= 0.100 END + ATOM H112 TYPE=HAS CHARge= 0.100 END + ATOM H113 TYPE=HAS CHARge= 0.100 END + ATOM C6 TYPE=CCS CHARge= 0.100 END + ATOM H6 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OES CHARge=-0.400 END + ATOM C7 TYPE=CCS CHARge= 0.150 END + ATOM H7 TYPE=HAS CHARge= 0.100 END + ATOM O7 TYPE=OH1 CHARge=-0.650 END + ATOM HO7 TYPE=H CHARge= 0.400 END + ATOM C8 TYPE=CCS CHARge= 0.150 END + ATOM H8 TYPE=HAS CHARge= 0.100 END + ATOM O8 TYPE=OH1 CHARge=-0.650 END + ATOM HO8 TYPE=H CHARge= 0.400 END + ATOM C9 TYPE=CCS CHARge= 0.050 END + ATOM H91 TYPE=HAS CHARge= 0.100 END + ATOM H92 TYPE=HAS CHARge= 0.100 END + ATOM O9 TYPE=OH1 CHARge=-0.650 END + ATOM HO9 TYPE=H CHARge= 0.400 END + + BOND C1 O1A + BOND C1 O1B + BOND C1 C2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 O6 + BOND C2 C3 + BOND C3 H31 + BOND C3 H32 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 N5 + BOND N5 HN5 + BOND N5 C10 + BOND C10 O10 + BOND C10 C11 + BOND C11 H111 + BOND C11 H112 + BOND C11 H113 + BOND C5 C6 + BOND C6 H6 + BOND C6 C7 + BOND C7 H7 + BOND C7 O7 + BOND O7 HO7 + BOND C7 C8 + BOND C8 H8 + BOND C8 O8 + BOND O8 HO8 + BOND C8 C9 + BOND C9 H91 + BOND C9 H92 + BOND C9 O9 + BOND O9 HO9 + BOND C6 O6 + + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 C6 + DIHEDRAL C4 C5 C6 O6 + DIHEDRAL C5 C6 O6 C2 + DIHEDRAL O6 C2 C3 C4 + DIHEDRAL C1 C2 O2 HO2 + DIHEDRAL O2 C2 C1 O1A + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 N5 HN5 + DIHEDRAL C5 N5 C10 C11 + DIHEDRAL N5 C10 C11 H111 + DIHEDRAL H6 C6 C7 C8 + DIHEDRAL H6 C6 C7 O7 + DIHEDRAL C6 C7 C8 C9 + DIHEDRAL C6 C7 C8 O8 + DIHEDRAL C7 C8 C9 O9 + DIHEDRAL C8 C9 O9 HO9 + +{ This is an L-sugar, so impropers are reversed to maintain ring } +{ geometry equivalent to D-hexoses } + + IMPRoper C1 O1A O1B C2 !planar acid +! IMPRoper C2 C1 O6 C3 {axial acid, i.e. alpha configuration} +! IMPRoper C2 O6 O2 C3 ! included improper using non-hydrogen atoms, ATB 12/06/09 +! IMPRoper C3 H31 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 N5 C4 C6 + IMPRoper N5 C10 C5 HN5 !planar N-acetyl N + IMPRoper C10 C11 N5 O10 !planar N-acetyl C +! IMPRoper C6 C5 C7 O6 +! IMPRoper C7 C6 O7 C8 +! IMPRoper C8 C7 O8 C9 + + IMPRoper C1 O2 C3 O6 {C2 L alpha=D beta} + IMPRoper H31 H32 C4 C2 {C3} + IMPRoper H4 O4 C5 C3 {C4} + IMPRoper H5 C4 C6 N5 {C5} + IMPRoper H6 C7 O6 C5 {C6} + IMPRoper H7 O7 C8 C6 {C7} + IMPRoper H8 O8 C9 C7 {C8} + IMPRoper H91 H92 O9 C8 {C9} + IMPRoper C5 N5 C10 C11 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue SIB {beta-N-acetyl neuraminic acid} + GROUP + ATOM C1 TYPE=C CHARge= 0.360 END + ATOM O1A TYPE=OC CHARge=-0.600 END + ATOM O1B TYPE=OC CHARge=-0.600 END + ATOM C2 TYPE=CCE CHARge= 0.290 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge=-0.200 END + ATOM H31 TYPE=HAS CHARge= 0.100 END + ATOM H32 TYPE=HAS CHARge= 0.100 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.000 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM N5 TYPE=NH1 CHARge=-0.350 END + ATOM HN5 TYPE=H CHARge= 0.250 END + ATOM C10 TYPE=C CHARge= 0.550 END + ATOM O10 TYPE=O CHARge=-0.550 END + ATOM C11 TYPE=CCS CHARge=-0.300 END + ATOM H111 TYPE=HAS CHARge= 0.100 END + ATOM H112 TYPE=HAS CHARge= 0.100 END + ATOM H113 TYPE=HAS CHARge= 0.100 END + ATOM C6 TYPE=CCS CHARge= 0.100 END + ATOM H6 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OES CHARge=-0.400 END + ATOM C7 TYPE=CCS CHARge= 0.150 END + ATOM H7 TYPE=HAS CHARge= 0.100 END + ATOM O7 TYPE=OH1 CHARge=-0.650 END + ATOM HO7 TYPE=H CHARge= 0.400 END + ATOM C8 TYPE=CCS CHARge= 0.150 END + ATOM H8 TYPE=HAS CHARge= 0.100 END + ATOM O8 TYPE=OH1 CHARge=-0.650 END + ATOM HO8 TYPE=H CHARge= 0.400 END + ATOM C9 TYPE=CCS CHARge= 0.050 END + ATOM H91 TYPE=HAS CHARge= 0.100 END + ATOM H92 TYPE=HAS CHARge= 0.100 END + ATOM O9 TYPE=OH1 CHARge=-0.650 END + ATOM HO9 TYPE=H CHARge= 0.400 END + + BOND C1 O1A + BOND C1 O1B + BOND C1 C2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 O6 + BOND C2 C3 + BOND C3 H31 + BOND C3 H32 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 N5 + BOND N5 HN5 + BOND N5 C10 + BOND C10 O10 + BOND C10 C11 + BOND C11 H111 + BOND C11 H112 + BOND C11 H113 + BOND C5 C6 + BOND C6 H6 + BOND C6 C7 + BOND C7 H7 + BOND C7 O7 + BOND O7 HO7 + BOND C7 C8 + BOND C8 H8 + BOND C8 O8 + BOND O8 HO8 + BOND C8 C9 + BOND C9 H91 + BOND C9 H92 + BOND C9 O9 + BOND O9 HO9 + BOND C6 O6 + + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 C6 + DIHEDRAL C4 C5 C6 O6 + DIHEDRAL C5 C6 O6 C2 + DIHEDRAL O6 C2 C3 C4 + DIHEDRAL C1 C2 O2 HO2 + DIHEDRAL O2 C2 C1 O1A + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 N5 HN5 + DIHEDRAL C5 N5 C10 C11 + DIHEDRAL N5 C10 C11 H111 + DIHEDRAL H6 C6 C7 C8 + DIHEDRAL H6 C6 C7 O7 + DIHEDRAL C6 C7 C8 C9 + DIHEDRAL C6 C7 C8 O8 + DIHEDRAL C7 C8 C9 O9 + DIHEDRAL C8 C9 O9 HO9 + +{ This is an L-sugar, so impropers are reversed to maintain ring } +{ geometry equivalent to D-hexoses } + + IMPRoper C1 O1A O1B C2 !planar acid +! IMPRoper C2 C1 O6 C3 {axial acid, i.e. alpha configuration} +! IMPRoper C2 O6 O2 C3 ! included improper using non-hydrogen atoms, ATB 12/06/09 +! IMPRoper C3 H31 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 N5 C4 C6 + IMPRoper N5 C10 C5 HN5 !planar N-acetyl N + IMPRoper C10 C11 N5 O10 !planar N-acetyl C +! IMPRoper C6 C5 C7 O6 +! IMPRoper C7 C6 O7 C8 +! IMPRoper C8 C7 O8 C9 + + IMPRoper O2 C1 C3 O6 {C2 beta} + IMPRoper H31 H32 C4 C2 {C3} + IMPRoper H4 O4 C5 C3 {C4} + IMPRoper H5 C4 C6 N5 {C5} + IMPRoper H6 C7 O6 C5 {C6} + IMPRoper H7 O7 C8 C6 {C7} + IMPRoper H8 O8 C9 C7 {C8} + IMPRoper H91 H92 O9 C8 {C9} + IMPRoper C5 N5 C10 C11 {trans peptide} + +END + +!------------------------------------------------------------------- + +RESIdue XYP !beta-D-xylopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM H51 TYPE=HAS CHARge= 0.100 END + ATOM H52 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H51 + BOND C5 H52 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + +! IMPRoper C1 O5 H1 C2 ! beta-anomer +! IMPRoper C1 O1 O5 C2 ! beta-anomer using non-hydrogen atoms + +! IMPRoper C2 C1 O2 C3 {equatorial C2} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 H51 C4 O5 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H51 H52 O5 C4 {C5} + +END + +!------------------------------------------------------------------- +RESIdue RAM !alpha-L-rhampyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge=-0.300 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM H63 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 H61 + + IMPRoper H1 O1 O5 C2 {L alpha C1=D beta} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 C2 O3 C4 {C3} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 O5 C4 C6 {C5} + +END + +!------------------------------------------------------------------- +RESIdue GXL !alpha-L-galactopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + + IMPRoper H1 O1 O5 C2 {alpha C1(L) = beta C1(D)} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 C2 O3 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 O5 C4 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + +END + +RESIdue BDP !beta-D-glucoronic acid +GROUP + +ATOM C1 TYPE=CCE CHARge= 0.340 END +ATOM H1 TYPE=HAS CHARge= 0.090 END +ATOM O1 TYPE=OH1 CHARge=-0.650 END +ATOM HO1 TYPE=H CHARge= 0.420 END +ATOM C5 TYPE=CCS CHARge= 0.110 END +ATOM H5 TYPE=HAS CHARge= 0.090 END +ATOM O5 TYPE=OES CHARge=-0.400 END +ATOM C2 TYPE=CCS CHARge= 0.140 END +ATOM H2 TYPE=HAS CHARge= 0.090 END +ATOM O2 TYPE=OH1 CHARge=-0.650 END +ATOM HO2 TYPE=H CHARge= 0.420 END +ATOM C3 TYPE=CCS CHARge= 0.140 END +ATOM H3 TYPE=HAS CHARge= 0.090 END +ATOM O3 TYPE=OH1 CHARge=-0.650 END +ATOM HO3 TYPE=H CHARge= 0.420 END +ATOM C4 TYPE=CCS CHARge= 0.140 END +ATOM H4 TYPE=HAS CHARge= 0.090 END +ATOM O4 TYPE=OH1 CHARge=-0.650 END +ATOM HO4 TYPE=H CHARge= 0.420 END +ATOM C6 TYPE=CC6 CHARge= 0.520 END +ATOM O61 TYPE=OC CHARge=-0.760 END +ATOM O62 TYPE=OC CHARge=-0.760 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 O61 + BOND C6 O62 + BOND C5 O5 + + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C4 C5 C6 O61 + DIHEDRAL O5 C1 O1 HO1 + DIHEDRAL C1 C2 O2 HO2 + DIHEDRAL C2 C3 O3 HO3 + DIHEDRAL C3 C4 O4 HO4 + DIHEDRAL C5 O5 C1 C2 ! the only one not defined in haddock + + IMPRoper C6 C5 O62 O61 + + IMPRoper H1 O1 O5 C2 {beta C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 +END + +RESIdue MMA ! methyl alpha-D-mannopyranoside ! axial O-methyl group added to C1 on mannose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.290 END ! lowered partial charge according to charmm36 + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OAS CHARge=-0.360 END ! lowered partial charge according to charmm36 and changed atom type as in MAG +! ATOM HO1 TYPE=H CHARge= 0.400 END ! deleted HO1 + ATOM C7 TYPE=CCS CHARge=-0.090 END ! C7 defined as CCS for consistency with MAG. + ATOM H71 TYPE=HAS CHARge= 0.090 END ! methyl hydrogens with charmm charges + ATOM H72 TYPE=HAS CHARge= 0.090 END + ATOM H73 TYPE=HAS CHARge= 0.090 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM H5 TYPE=HAS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM C6 TYPE=CC6 CHARge= 0.050 END + ATOM H61 TYPE=HAS CHARge= 0.100 END + ATOM H62 TYPE=HAS CHARge= 0.100 END + ATOM O6 TYPE=OH1 CHARge=-0.650 END + ATOM HO6 TYPE=H CHARge= 0.400 END + + BOND C1 O1 + BOND C1 H1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 O6 + BOND O6 HO6 + BOND C5 O5 + BOND O1 C7 + BOND C7 H71 + BOND C7 H72 + BOND C7 H73 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + DIHEDRAL H5 C5 C6 O6 + DIHEDRAL C5 C6 O6 H61 + DIHEDRAL O5 C1 O1 C7 ! the first not in HADDOCK: C7 dihedral +! DIHEDRAL C1 O1 C7 H71 ! the second not in HADDOCK. commented out in agreement with MAG + +! IMPRoper C1 H1 O5 C2 ! alpha-anomer +! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09 + +! IMPRoper C2 O2 C1 C3 {axial C2} +! IMPRoper C3 O3 C2 C4 +! IMPRoper C4 C3 O4 C5 +! IMPRoper C5 C6 C4 O5 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 O2 C1 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + IMPRoper H61 H62 O6 C5 !stereo C6 + + +END + +RESIdue XYS !alpha-D-xylopyranose + GROUP + ATOM C1 TYPE=CCE CHARge= 0.350 END + ATOM H1 TYPE=HAS CHARge= 0.100 END + ATOM O1 TYPE=OH1 CHARge=-0.650 END + ATOM HO1 TYPE=H CHARge= 0.400 END + ATOM C2 TYPE=CCS CHARge= 0.150 END + ATOM O2 TYPE=OH1 CHARge=-0.650 END + ATOM H2 TYPE=HAS CHARge= 0.100 END + ATOM HO2 TYPE=H CHARge= 0.400 END + ATOM C3 TYPE=CCS CHARge= 0.150 END + ATOM H3 TYPE=HAS CHARge= 0.100 END + ATOM O3 TYPE=OH1 CHARge=-0.650 END + ATOM HO3 TYPE=H CHARge= 0.400 END + ATOM C4 TYPE=CCS CHARge= 0.150 END + ATOM H4 TYPE=HAS CHARge= 0.100 END + ATOM O4 TYPE=OH1 CHARge=-0.650 END + ATOM HO4 TYPE=H CHARge= 0.400 END + ATOM C5 TYPE=CCS CHARge= 0.100 END + ATOM O5 TYPE=OES CHARge=-0.400 END + ATOM H51 TYPE=HAS CHARge= 0.100 END + ATOM H52 TYPE=HAS CHARge= 0.100 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H3 + BOND C3 O3 + BOND O3 HO3 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H51 + BOND C5 H52 + BOND C5 O5 + + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 + DIHEDRAL H3 C3 O3 HO3 + DIHEDRAL H4 C4 O4 HO4 + + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H3 O3 C2 C4 {C3} + IMPRoper H4 C3 O4 C5 {C4} + IMPRoper H51 H52 O5 C4 {C5} + +END + +RESIdue ABE !alpha-D-Abequopyranose +GROUP + +ATOM C1 TYPE=CCE CHARge= 0.340 END +ATOM H1 TYPE=HAS CHARge= 0.090 END +ATOM O1 TYPE=OH1 CHARge=-0.650 END +ATOM HO1 TYPE=H CHARge= 0.420 END +ATOM C5 TYPE=CCS CHARge= 0.110 END +ATOM H5 TYPE=HAS CHARge= 0.090 END +ATOM O5 TYPE=OES CHARge=-0.400 END +ATOM C2 TYPE=CCS CHARge= 0.140 END +ATOM H2 TYPE=HAS CHARge= 0.090 END +ATOM O2 TYPE=OH1 CHARge=-0.650 END +ATOM HO2 TYPE=H CHARge= 0.420 END +ATOM C3 TYPE=CCS CHARge=-0.180 END +ATOM H31 TYPE=HAS CHARge= 0.090 END +ATOM H32 TYPE=HAS CHARge= 0.090 END +ATOM C4 TYPE=CCS CHARge= 0.140 END +ATOM H4 TYPE=HAS CHARge= 0.090 END +ATOM O4 TYPE=OH1 CHARge=-0.650 END +ATOM HO4 TYPE=H CHARge= 0.420 END +ATOM C6 TYPE=CC6 CHARge=-0.270 END +ATOM H61 TYPE=HAS CHARge= 0.090 END +ATOM H62 TYPE=HAS CHARge= 0.090 END +ATOM H63 TYPE=HAS CHARge= 0.090 END + + BOND C1 O1 + BOND C1 H1 + BOND O1 HO1 + BOND C1 O5 + BOND C1 C2 + BOND C2 H2 + BOND C2 O2 + BOND O2 HO2 + BOND C2 C3 + BOND C3 H31 + BOND C3 H32 + BOND C3 C4 + BOND C4 H4 + BOND C4 O4 + BOND O4 HO4 + BOND C4 C5 + BOND C5 H5 + BOND C5 C6 + BOND C6 H61 + BOND C6 H62 + BOND C6 H63 + BOND C5 O5 + +! dihedrals taken from alpha mannose + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C4 C5 + DIHEDRAL C3 C4 C5 O5 + DIHEDRAL C4 C5 O5 C1 + DIHEDRAL C5 O5 C1 C2 + DIHEDRAL O5 C1 C2 C3 + DIHEDRAL H1 C1 O1 HO1 + DIHEDRAL H2 C2 O2 HO2 +! DIHEDRAL H3 C3 O3 HO3 ! not present anymore, substituted by the H31 H32 C4 C2 improper taken from SIA + DIHEDRAL H4 C4 O4 HO4 +! DIHEDRAL H5 C5 C6 O6 ! not present anymore (missing O6) +! DIHEDRAL C5 C6 O6 H61 ! not present anymore (missing O6) + DIHEDRAL H5 C5 C6 H61 ! taken from fucoses and RAM + + IMPRoper H31 H32 C4 C2 {C3} ! this improper is used in SIA but there the atom type of C2 is not CCS but CCE. + IMPRoper H1 O5 O1 C2 {alpha C1} + IMPRoper H2 C1 O2 C3 {C2} + IMPRoper H4 O4 C3 C5 {C4} + IMPRoper H5 C4 O5 C6 {C5} + +END + +!------------------------------------------------------------------- +!------------------------------------------------------------------- + +PRESidue B1N {beta link from NAG C1 to Asn Nd2} + MODIfy ATOM +ND2 TYPE=NH1 CHARge=-0.35 END + MODIfy ATOM +HD22 CHARge= 0.25 END + DELEte ATOM +HD21 END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +ND2 + + ADD ANGLe +CG +ND2 -C1 + ADD ANGLe +HD22 +ND2 -C1 + ADD ANGLe +ND2 -C1 -C2 + ADD ANGLe +ND2 -C1 -O5 + ADD ANGLe +ND2 -C1 -H1 + + !ADD DIHEdral +CB +CG +ND2 -C1 !trans peptide bond + !ADD DIHEdral +CG +ND2 -C1 -C2 + !ADD DIHEdral +CG +ND2 -C1 -O5 + ADD DIHEdral +CG +ND2 -C1 -H1 + + {respecify planar ND2 as removed HD21 above } + { Note that we take this from the protein parameter file NH1 X X C, which has } + { a stronger restraint on this (for peptide planes) than the Asn side chain } + ADD IMPRoper +ND2 -C1 +HD22 +CG + + {re-specify beta-anomer ATB 12/26/10} +! IMPRoper -C1 +ND2 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + IMPRoper -H1 +ND2 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + + +PRESidue B12 {beta(1,2) link} + MODIfy ATOM +O2 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C2 CHARge= 0.10 END + DELEte ATOM +HO2 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O2 + + ADD ANGle +C2 +O2 -C1 + ADD ANGle +O2 -C1 -H1 + ADD ANGle +O2 -C1 -O5 + ADD ANGle +O2 -C1 -C2 + + ADD DIHEdral +C2 +O2 -C1 -H1 + ADD DIHEdral +C2 +O2 -C1 -O5 + ADD DIHEdral +C2 +O2 -C1 -C2 + + {re-specify beta-anomer ATB 12/26/10 - except for FUL} +! IMPRoper -C1 +O2 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O2 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue B14 {beta(1,4) link} + MODIfy ATOM +O4 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C4 CHARge= 0.10 END + DELEte ATOM +HO4 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O4 + + ADD ANGle +C4 +O4 -C1 + ADD ANGle +O4 -C1 -H1 + ADD ANGle +O4 -C1 -O5 + ADD ANGle +O4 -C1 -C2 + + ADD DIHEdral +C4 +O4 -C1 -H1 + ADD DIHEdral +C4 +O4 -C1 -O5 + ADD DIHEdral +C4 +O4 -C1 -C2 + + {re-specify beta-anomer ATB 12/26/10 - except for FUL} +! IMPRoper -C1 +O4 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O4 -O5 -C2 ! beta-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A11 {alpha(1,1) link} + MODIfy ATOM +O1 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C1 CHARge= 0.10 END + DELEte ATOM +HO1 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O1 + + ADD ANGle +C1 +O1 -C1 + ADD ANGle +O1 -C1 -H1 + ADD ANGle +O1 -C1 -O5 + ADD ANGle +O1 -C1 -C2 + + ADD DIHEdral +C1 +O1 -C1 -H1 + ADD DIHEdral +C1 +O1 -C1 -O5 + ADD DIHEdral +C1 +O1 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O1 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O1 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A12 {alpha(1,2) link} + MODIfy ATOM +O2 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C2 CHARge= 0.10 END + DELEte ATOM +HO2 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O2 + + ADD ANGle +C2 +O2 -C1 + ADD ANGle +O2 -C1 -H1 + ADD ANGle +O2 -C1 -O5 + ADD ANGle +O2 -C1 -C2 + + ADD DIHEdral +C2 +O2 -C1 -H1 + ADD DIHEdral +C2 +O2 -C1 -O5 + ADD DIHEdral +C2 +O2 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O2 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O2 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + + +PRESidue A13 {alpha(1,3) link} + MODIfy ATOM +O3 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C3 CHARge= 0.10 END + DELEte ATOM +HO3 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O3 + + ADD ANGle +C3 +O3 -C1 + ADD ANGle +O3 -C1 -H1 + ADD ANGle +O3 -C1 -O5 + ADD ANGle +O3 -C1 -C2 + + ADD DIHEdral +C3 +O3 -C1 -H1 + ADD DIHEdral +C3 +O3 -C1 -O5 + ADD DIHEdral +C3 +O3 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O3 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O3 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A14 {alpha(1,4) link} + MODIfy ATOM +O4 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C4 CHARge= 0.10 END + DELEte ATOM +HO4 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O4 + + ADD ANGle +C4 +O4 -C1 + ADD ANGle +O4 -C1 -H1 + ADD ANGle +O4 -C1 -O5 + ADD ANGle +O4 -C1 -C2 + + ADD DIHEdral +C4 +O4 -C1 -H1 + ADD DIHEdral +C4 +O4 -C1 -O5 + ADD DIHEdral +C4 +O4 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O4 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O4 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A16 { alpha(1,6) link } + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O6 + + ADD ANGle +C6 +O6 -C1 + ADD ANGle +O6 -C1 -H1 + ADD ANGle +O6 -C1 -O5 + ADD ANGle +O6 -C1 -C2 + + ADD DIHEdral +C6 +O6 -C1 -H1 + ADD DIHEdral +C6 +O6 -C1 -O5 + ADD DIHEdral +C6 +O6 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O6 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O6 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue B12L {FUL beta(1,2) link} + MODIfy ATOM +O2 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C2 CHARge= 0.10 END + DELEte ATOM +HO2 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O2 + + ADD ANGle +C2 +O2 -C1 + ADD ANGle +O2 -C1 -H1 + ADD ANGle +O2 -C1 -O5 + ADD ANGle +O2 -C1 -C2 + + ADD DIHEdral +C2 +O2 -C1 -H1 + ADD DIHEdral +C2 +O2 -C1 -O5 + ADD DIHEdral +C2 +O2 -C1 -C2 + + {re-specify beta-anomer ATB 12/26/10 - for FUL} +! IMPRoper -C1 -O5 +O2 -C2 ! beta-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O2 -C2 ! beta-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue B14L {FUL beta(1,4) link} + MODIfy ATOM +O4 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C4 CHARge= 0.10 END + DELEte ATOM +HO4 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O4 + + ADD ANGle +C4 +O4 -C1 + ADD ANGle +O4 -C1 -H1 + ADD ANGle +O4 -C1 -O5 + ADD ANGle +O4 -C1 -C2 + + ADD DIHEdral +C4 +O4 -C1 -H1 + ADD DIHEdral +C4 +O4 -C1 -O5 + ADD DIHEdral +C4 +O4 -C1 -C2 + + {re-specify beta-anomer ATB 12/26/10 - for FUL} +! IMPRoper -C1 -O5 +O4 -C2 ! beta-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O4 -C2 ! beta-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A12L {FUC alpha(1,2) link} + MODIfy ATOM +O2 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C2 CHARge= 0.10 END + DELEte ATOM +HO2 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O2 + + ADD ANGle +C2 +O2 -C1 + ADD ANGle +O2 -C1 -H1 + ADD ANGle +O2 -C1 -O5 + ADD ANGle +O2 -C1 -C2 + + ADD DIHEdral +C2 +O2 -C1 -H1 + ADD DIHEdral +C2 +O2 -C1 -O5 + ADD DIHEdral +C2 +O2 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - FUC} +! IMPRoper -C1 +O2 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O2 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + + +PRESidue A13L {FUC alpha(1,3) link} + MODIfy ATOM +O3 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C3 CHARge= 0.10 END + DELEte ATOM +HO3 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O3 + + ADD ANGle +C3 +O3 -C1 + ADD ANGle +O3 -C1 -H1 + ADD ANGle +O3 -C1 -O5 + ADD ANGle +O3 -C1 -C2 + + ADD DIHEdral +C3 +O3 -C1 -H1 + ADD DIHEdral +C3 +O3 -C1 -O5 + ADD DIHEdral +C3 +O3 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - FUC} +! IMPRoper -C1 +O3 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O3 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A14L {FUC alpha(1,4) link} + MODIfy ATOM +O4 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C4 CHARge= 0.10 END + DELEte ATOM +HO4 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O4 + + ADD ANGle +C4 +O4 -C1 + ADD ANGle +O4 -C1 -H1 + ADD ANGle +O4 -C1 -O5 + ADD ANGle +O4 -C1 -C2 + + ADD DIHEdral +C4 +O4 -C1 -H1 + ADD DIHEdral +C4 +O4 -C1 -O5 + ADD DIHEdral +C4 +O4 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - FUC} +! IMPRoper -C1 +O4 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O4 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue A16L {FUC alpha(1,6) link } + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O6 + + ADD ANGle +C6 +O6 -C1 + ADD ANGle +O6 -C1 -H1 + ADD ANGle +O6 -C1 -O5 + ADD ANGle +O6 -C1 -C2 + + ADD DIHEdral +C6 +O6 -C1 -H1 + ADD DIHEdral +C6 +O6 -C1 -O5 + ADD DIHEdral +C6 +O6 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - FUC} +! IMPRoper -C1 +O6 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O6 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +{Links for SIA (sialic acid) -- input anomer is assumed ALPHA, i.e. glycosidic } +{ oxygen is equatorial to the NANA ring } + +PRESidue A23 {alpha(2,3) link for NANA} + + MODIfy ATOM +O3 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C3 CHARge= 0.10 END + DELEte ATOM +HO3 END + MODIfy ATOM -C2 CHARge= 0.24 END + DELEte ATOM -O2 END + DELEte ATOM -HO2 END + + ADD BOND -C2 +O3 + + ADD ANGle +C3 +O3 -C2 + ADD ANGle +O3 -C2 -C1 + ADD ANGle +O3 -C2 -O6 + ADD ANGle +O3 -C2 -C3 + + ADD DIHEdral +C3 +O3 -C2 -C1 + ADD DIHEdral +C3 +O3 -C2 -O6 + ADD DIHEdral +C3 +O3 -C2 -C3 + ADD DIHEdral +O3 -C2 -C1 -O1A + +END + +PRESidue A26 {alpha(2,6) link for NANA} + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C2 CHARge= 0.24 END + DELEte ATOM -O2 END + DELEte ATOM -HO2 END + + ADD BOND -C2 +O6 + + ADD ANGle +C6 +O6 -C2 + ADD ANGle +O6 -C2 -C1 + ADD ANGle +O6 -C2 -O6 + ADD ANGle +O6 -C2 -C3 + + ADD DIHEdral +C6 +O6 -C2 -C1 + ADD DIHEdral +C6 +O6 -C2 -O6 + ADD DIHEdral +C6 +O6 -C2 -C3 + ADD DIHEdral +O6 -C2 -C1 -O1A + + +END + +PRESidue A26S {alpha(2,6) link for SIA} + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C2 CHARge= 0.24 END + DELEte ATOM -O2 END + DELEte ATOM -HO2 END + + ADD BOND -C2 +O6 + + ADD ANGle +C6 +O6 -C2 + ADD ANGle +O6 -C2 -C1 + ADD ANGle +O6 -C2 -O6 + ADD ANGle +O6 -C2 -C3 + + ADD DIHEdral +C6 +O6 -C2 -C1 + ADD DIHEdral +C6 +O6 -C2 -O6 + ADD DIHEdral +C6 +O6 -C2 -C3 + ADD DIHEdral +O6 -C2 -C1 -O1A + + IMPRoper -C1 +O6 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + + +PRESidue A28S {alpha(2,8) link for SIA} + MODIfy ATOM +O8 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C8 CHARge= 0.00 END + DELEte ATOM +HO8 END + MODIfy ATOM -C2 CHARge= 0.24 END + DELEte ATOM -O2 END + DELEte ATOM -HO2 END + + ADD BOND -C2 +O8 + + ADD ANGle +C8 +O8 -C2 + ADD ANGle +O8 -C2 -C1 + ADD ANGle +O8 -C2 -O6 + ADD ANGle +O8 -C2 -C3 + + ADD DIHEdral +C8 +O8 -C2 -C1 + ADD DIHEdral +C8 +O8 -C2 -O6 + ADD DIHEdral +C8 +O8 -C2 -C3 + ADD DIHEdral +O8 -C2 -C1 -O1A + + IMPRoper -C1 +O8 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + + +!------------------------------------------------------------------- + +PRESidue A1S {alpha link from C1 to Ser OG} +! MODIfy ATOM +OG TYPE=OAS CHARge=-0.38 END {cns v1.2} + MODIfy ATOM +OG TYPE=OAS CHARge=-0.365 END {cns v1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG + + ADD ANGLe +CB +OG -C1 + ADD ANGLe +OG -C1 -C2 + ADD ANGLe +OG -C1 -O5 + ADD ANGLe +OG -C1 -H1 + + ADD DIHEdral +CA +CB +OG -C1 + ADD DIHEdral +CB +OG -C1 -H1 + + ADD IMPRoper -H1 -O5 +OG -C2 {alpha} + +END + +PRESidue B1S {beta link from C1 to Ser OG} +! MODIfy ATOM +OG TYPE=OAS CHARge=-0.38 END {cns1.2} + MODIfy ATOM +OG TYPE=OAS CHARge=-0.365 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG + + ADD ANGLe +CB +OG -C1 + ADD ANGLe +OG -C1 -C2 + ADD ANGLe +OG -C1 -O5 + ADD ANGLe +OG -C1 -H1 + + ADD DIHEdral +CA +CB +OG -C1 + ADD DIHEdral +CB +OG -C1 -H1 + + ADD IMPRoper -H1 +OG -O5 -C2 {beta} + +END + +PRESidue B1SL {beta link from L-C1 to Ser OG} +! MODIfy ATOM +OG TYPE=OAS CHARge=-0.38 END {cns v1.2} + MODIfy ATOM +OG TYPE=OAS CHARge=-0.365 END {cns v1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG + + ADD ANGLe +CB +OG -C1 + ADD ANGLe +OG -C1 -C2 + ADD ANGLe +OG -C1 -O5 + ADD ANGLe +OG -C1 -H1 + + ADD DIHEdral +CA +CB +OG -C1 + ADD DIHEdral +CB +OG -C1 -H1 + + ADD IMPRoper -H1 -O5 +OG -C2 {alpha} + +END + +PRESidue A1SL {alpha link from L-C1 to Ser OG} +! MODIfy ATOM +OG TYPE=OAS CHARge=-0.38 END {cns1.2} + MODIfy ATOM +OG TYPE=OAS CHARge=-0.365 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG + + ADD ANGLe +CB +OG -C1 + ADD ANGLe +OG -C1 -C2 + ADD ANGLe +OG -C1 -O5 + ADD ANGLe +OG -C1 -H1 + + ADD DIHEdral +CA +CB +OG -C1 + ADD DIHEdral +CB +OG -C1 -H1 + + ADD IMPRoper -H1 +OG -O5 -C2 {beta} + +END + +!------------------------------------------------------------------- + +PRESidue A1T {alpha link from C1 to Thr OG1} +! MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.38 END {cns 1.2} + MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.365 END {cns 1.3} +! MODIfy ATOM +CB TYPE=CH1E END {cns 1.2} + DELEte ATOM +HG1 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG1 + + ADD ANGLe +CB +OG1 -C1 + ADD ANGLe +OG1 -C1 -C2 + ADD ANGLe +OG1 -C1 -O5 + ADD ANGLe +OG1 -C1 -H1 + + ADD DIHEdral +CA +CB +OG1 -C1 + ADD DIHEdral +CB +OG1 -C1 -H1 + + ADD IMPRoper -H1 -O5 +OG1 -C2 {alpha} + +END + +PRESidue B1T {beta link from C1 to Thr OG1} +! MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.38 END {cns 1.2} + MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.365 END {cns 1.3} +! MODIfy ATOM +CB TYPE=CH1E END {cns 1.2} + DELEte ATOM +HG1 END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG1 + + ADD ANGLe +CB +OG1 -C1 + ADD ANGLe +OG1 -C1 -C2 + ADD ANGLe +OG1 -C1 -O5 + ADD ANGLe +OG1 -C1 -H1 + + ADD DIHEdral +CA +CB +OG1 -C1 + ADD DIHEdral +CB +OG1 -C1 -H1 + + ADD IMPRoper -H1 +OG1 -O5 -C2 {beta} + +END + +PRESidue B1TL {beta link from L-C1 to Thr OG1} +! MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.38 END {cns 1.2} + MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.365 END {cns 1.3} +! MODIfy ATOM +CB TYPE=CH1E END {cns 1.2} + DELEte ATOM +HG1 END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG1 + + ADD ANGLe +CB +OG1 -C1 + ADD ANGLe +OG1 -C1 -C2 + ADD ANGLe +OG1 -C1 -O5 + ADD ANGLe +OG1 -C1 -H1 + + ADD DIHEdral +CA +CB +OG1 -C1 + ADD DIHEdral +CB +OG1 -C1 -H1 + + ADD IMPRoper -H1 -O5 +OG1 -C2 {alpha} + +END + +PRESidue A1TL {alpha link from L-C1 to Thr OG1} +! MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.38 END {cns 1.2} + MODIfy ATOM +OG1 TYPE=OAS CHARge=-0.365 END {cns 1.3} +! MODIfy ATOM +CB TYPE=CH1E END {cns 1.2} + DELEte ATOM +HG1 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +OG1 + + ADD ANGLe +CB +OG1 -C1 + ADD ANGLe +OG1 -C1 -C2 + ADD ANGLe +OG1 -C1 -O5 + ADD ANGLe +OG1 -C1 -H1 + + ADD DIHEdral +CA +CB +OG1 -C1 + ADD DIHEdral +CB +OG1 -C1 -H1 + + ADD IMPRoper -H1 +OG1 -O5 -C2 {beta} + +END + +!------------------------------------------------------------------- + +PRESidue A1C {alpha link from C1 to Cys SG} +! MODIfy ATOM +SG TYPE=S CHARge=0.000 END {cns 1.2} + MODIfy ATOM +SG TYPE=S CHARge=-0.180 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +SG + + ADD ANGLe +CB +SG -C1 + ADD ANGLe +SG -C1 -C2 + ADD ANGLe +SG -C1 -O5 + ADD ANGLe +SG -C1 -H1 + + ADD DIHEdral +CA +CB +SG -C1 + ADD DIHEdral +CB +SG -C1 -H1 + + ADD IMPRoper -H1 -O5 +SG -C2 {alpha} + +END + +PRESidue B1C {beta link from C1 to Cys SG} +! MODIfy ATOM +SG TYPE=S CHARge=0.000 END {cns 1.2} + MODIfy ATOM +SG TYPE=S CHARge=-0.180 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +SG + + ADD ANGLe +CB +SG -C1 + ADD ANGLe +SG -C1 -C2 + ADD ANGLe +SG -C1 -O5 + ADD ANGLe +SG -C1 -H1 + + ADD DIHEdral +CA +CB +SG -C1 + ADD DIHEdral +CB +SG -C1 -H1 + + ADD IMPRoper -H1 +SG -O5 -C2 {beta} + +END + +PRESidue B1CL {beta link from L-C1 to Cys SG} +! MODIfy ATOM +SG TYPE=S CHARge=0.000 END {cns 1.2} + MODIfy ATOM +SG TYPE=S CHARge=-0.180 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +SG + + ADD ANGLe +CB +SG -C1 + ADD ANGLe +SG -C1 -C2 + ADD ANGLe +SG -C1 -O5 + ADD ANGLe +SG -C1 -H1 + + ADD DIHEdral +CA +CB +SG -C1 + ADD DIHEdral +CB +SG -C1 -H1 + + ADD IMPRoper -H1 -O5 +SG -C2 {alpha} + +END + +PRESidue A1CL {alpha link from L-C1 to Cys SG} +! MODIfy ATOM +SG TYPE=S CHARge=0.000 END {cns 1.2} + MODIfy ATOM +SG TYPE=S CHARge=-0.180 END {cns 1.3} + DELEte ATOM +HG END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.20 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +SG + + ADD ANGLe +CB +SG -C1 + ADD ANGLe +SG -C1 -C2 + ADD ANGLe +SG -C1 -O5 + ADD ANGLe +SG -C1 -H1 + + ADD DIHEdral +CA +CB +SG -C1 + ADD DIHEdral +CB +SG -C1 -H1 + + ADD IMPRoper -H1 +SG -O5 -C2 {beta} + +END + +!------------------------------------------------------------------- +PRESidue B13 {beta(1,3) link} + MODIfy ATOM +O3 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C3 CHARge= 0.10 END + DELEte ATOM +HO3 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O3 + + ADD ANGle +C3 +O3 -C1 + ADD ANGle +O3 -C1 -H1 + ADD ANGle +O3 -C1 -O5 + ADD ANGle +O3 -C1 -C2 + + ADD DIHEdral +C3 +O3 -C1 -H1 + ADD DIHEdral +C3 +O3 -C1 -O5 + ADD DIHEdral +C3 +O3 -C1 -C2 + + IMPRoper -H1 +O3 -O5 -C2 + +END + +!------------------------------------------------------------------- +PRESidue B13L {beta(1,3) link for L-sugar} + MODIfy ATOM +O3 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C3 CHARge= 0.10 END + DELEte ATOM +HO3 END + MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O3 + + ADD ANGle +C3 +O3 -C1 + ADD ANGle +O3 -C1 -H1 + ADD ANGle +O3 -C1 -O5 + ADD ANGle +O3 -C1 -C2 + + ADD DIHEdral +C3 +O3 -C1 -H1 + ADD DIHEdral +C3 +O3 -C1 -O5 + ADD DIHEdral +C3 +O3 -C1 -C2 + + IMPRoper -H1 -O5 +O3 -C2 + +END + +!------------------------------------------------------------------- + +PRESidue B16 { beta(1,6) link } + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O6 + + ADD ANGle +C6 +O6 -C1 + ADD ANGle +O6 -C1 -H1 + ADD ANGle +O6 -C1 -O5 + ADD ANGle +O6 -C1 -C2 + + ADD DIHEdral +C6 +O6 -C1 -H1 + ADD DIHEdral +C6 +O6 -C1 -O5 + ADD DIHEdral +C6 +O6 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - except FUC} +! IMPRoper -C1 -O5 +O6 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 +O6 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +PRESidue B16L {FUC alpha(1,6) link } + MODIfy ATOM +O6 TYPE=OAS CHARge=-0.40 END + MODIfy ATOM +C6 CHARge= 0.00 END + DELEte ATOM +HO6 END + MODIfy ATOM -C1 CHARge= 0.30 END + DELEte ATOM -O1 END + DELEte ATOM -HO1 END + + ADD BOND -C1 +O6 + + ADD ANGle +C6 +O6 -C1 + ADD ANGle +O6 -C1 -H1 + ADD ANGle +O6 -C1 -O5 + ADD ANGle +O6 -C1 -C2 + + ADD DIHEdral +C6 +O6 -C1 -H1 + ADD DIHEdral +C6 +O6 -C1 -O5 + ADD DIHEdral +C6 +O6 -C1 -C2 + + {re-specify alpha-anomer ATB 12/26/10 - FUC} +! IMPRoper -C1 +O6 -O5 -C2 ! alpha-anomer definition using non-hydrogen atoms + IMPRoper -H1 -O5 +O6 -C2 ! alpha-anomer definition using non-hydrogen atoms + +END + +!------------------------------------------------------------------- + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.param new file mode 100644 index 0000000000000000000000000000000000000000..a69a50e71961d010b9df936aaf52660023cac124 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.param @@ -0,0 +1,2449 @@ +REMARKS file toppar/cofactors.param +REMARKS Victor Reys - 19/03/2025 +REMARKS Parameters added for common co-factors +REMARKS ADN-ADP-AMP-ATP-CIT-FAD-FLC-GDP-GMP-GTP-NAD-NAP-NDP + +! History: +! Victor Reys - 19/03/2025 +! - Parameters taken from PRODRG version 070118.0614 +! - AtomType midfix for ADN: A0 +! - AtomType midfix for ADP: A2 +! - AtomType midfix for AMP: A1 +! - AtomType midfix for ATP: A3 +! - AtomType midfix for CIT: CI +! - AtomType midfix for FAD: F2 +! - AtomType midfix for FLC: CT +! - AtomType midfix for GDP: G2 +! - AtomType midfix for GMP: G1 +! - AtomType midfix for GTP: G3 +! - AtomType midfix for NAD: N2 +! - AtomType midfix for NAP: N3 +! - AtomType midfix for NDP: NP + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +! Set the pd_x var for all +evaluate ($pd_x = 1.0) + +! Adding parameter definition for residue ADN + +eval ($pd_v=$pd_x* 15000.0) BOND OA0L HA04 $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND OA0L CA00 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA00 CA0G $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CA00 CA0T $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CA0G OA0O $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA0G CA0N $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA0O HA0P $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CA0N CA0O $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CA0N OA0S $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA0O OA0M $pd_v 1.430 +eval ($pd_v=$pd_x* 15000.0) BOND OA0M HA0K $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND OA0S CA0T $pd_v 1.435 +eval ($pd_v=$pd_x* 12000.0) BOND CA0T NA0X $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NA0X CA0L $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA0X CA0D $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA0L NA0O $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA0O CA04 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA04 CA0D $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA04 CA0U $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA0D NA0E $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NA0E CA0E $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CA0E NA0N $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NA0N CA0U $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CA0U NA09 $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NA09 HA05 $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NA09 HA0O $pd_v 1.000 + +eval ($pd_v=$pd_x* 760.0) ANGLE HA04 OA0L CA00 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA0L CA00 CA0G $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA0L CA00 CA0T $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA0G CA00 CA0T $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA00 CA0G OA0O $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA00 CA0G CA0N $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA0O CA0G CA0N $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA0G OA0O HA0P $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CA0G CA0N CA0O $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA0G CA0N OA0S $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CA0O CA0N OA0S $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA0N CA0O OA0M $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA0O OA0M HA0K $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA0N OA0S CA0T $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA00 CA0T OA0S $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CA00 CA0T NA0X $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE OA0S CA0T NA0X $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0T NA0X CA0L $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0T NA0X CA0D $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0L NA0X CA0D $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0X CA0L NA0O $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0L NA0O CA04 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0O CA04 CA0D $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0O CA04 CA0U $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0D CA04 CA0U $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0X CA0D CA04 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0X CA0D NA0E $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA04 CA0D NA0E $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0D NA0E CA0E $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0E CA0E NA0N $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA0E NA0N CA0U $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA04 CA0U NA0N $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA04 CA0U NA09 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA0N CA0U NA09 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA0U NA09 HA05 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA0U NA09 HA0O $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HA05 NA09 HA0O $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NA0X CA0T CA0L CA0D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA04 CA0U CA0D NA0O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0D NA0E CA04 NA0X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0U CA04 NA0N NA09 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA09 CA0U HA05 HA0O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CA00 OA0L CA0G CA0T $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA0G CA00 OA0O CA0N $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA0N CA0G OA0S CA0O $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA0T CA00 NA0X OA0S $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NA0X CA0L NA0O CA04 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0L NA0O CA04 CA0D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA0O CA04 CA0D NA0X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA04 CA0D NA0X CA0L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0D NA0X CA0L NA0O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA04 CA0D NA0E CA0E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0D NA0E CA0E NA0N $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA0E CA0E NA0N CA0U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0E NA0N CA0U CA04 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA0N CA0U CA04 CA0D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA0U CA04 CA0D NA0E $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.9) DIHE CA0T CA00 OA0L HA04 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA0N CA0G CA00 OA0L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE OA0L CA00 CA0T NA0X $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA00 CA0G OA0O HA0P $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA00 CA0G CA0N OA0S $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA0G CA0N CA0O OA0M $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CA0G CA0N OA0S CA0T $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA0N CA0O OA0M HA0K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NA0X CA0T OA0S CA0N $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE CA00 CA0T NA0X CA0D $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CA04 CA0U NA09 HA0O $pd_v 2 180.000 + + +NONBONDED OA0L 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA04 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA00 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA0G 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA0O 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA0P 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA0N 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA0O 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA0M 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA0K 0.10000 1.42544 0.10000 1.15817 +NONBONDED OA0S 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA0T 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA0X 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA0L 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA0O 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA04 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA0D 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA0E 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA0E 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA0N 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA0U 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA09 0.10000 2.67270 0.10000 2.40543 +NONBONDED HA05 0.10000 1.42544 0.10000 1.15817 +NONBONDED HA0O 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue ADP + + +eval ($pd_v=$pd_x* 12000.0) BOND OA2J PA2N $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA2N OA2Z $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA2N OA2B $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA2N OA2L $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA2L PA22 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA22 OA2N $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA22 OA2D $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA22 OA2A $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA2A CA21 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CA21 CA2W $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CA2W OA2H $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA2W CA2K $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OA2H CA2Z $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA2K OA2Q $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA2K CA2X $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA2Q HA2Q $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CA2X OA2E $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA2X CA2Z $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA2E HA22 $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CA2Z NA2H $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NA2H CA2C $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA2H CA27 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA2C NA2B $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA2B CA2V $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA2V CA27 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA2V CA29 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA27 NA27 $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NA27 CA2T $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CA2T NA2G $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NA2G CA29 $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CA29 NA29 $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NA29 HA2I $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NA29 HA2C $pd_v 1.000 + +eval ($pd_v=$pd_x* 760.0) ANGLE OA2J PA2N OA2Z $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2J PA2N OA2B $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2J PA2N OA2L $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2Z PA2N OA2B $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2Z PA2N OA2L $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2B PA2N OA2L $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA2N OA2L PA22 $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2L PA22 OA2N $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2L PA22 OA2D $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2L PA22 OA2A $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2N PA22 OA2D $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2N PA22 OA2A $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA2D PA22 OA2A $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA22 OA2A CA21 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA2A CA21 CA2W $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CA21 CA2W OA2H $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CA21 CA2W CA2K $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA2H CA2W CA2K $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA2W OA2H CA2Z $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA2W CA2K OA2Q $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA2W CA2K CA2X $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA2Q CA2K CA2X $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA2K OA2Q HA2Q $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA2K CA2X OA2E $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA2K CA2X CA2Z $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA2E CA2X CA2Z $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA2X OA2E HA22 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA2H CA2Z CA2X $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OA2H CA2Z NA2H $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CA2X CA2Z NA2H $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2Z NA2H CA2C $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2Z NA2H CA27 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2C NA2H CA27 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2H CA2C NA2B $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2C NA2B CA2V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2B CA2V CA27 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2B CA2V CA29 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA27 CA2V CA29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2H CA27 CA2V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2H CA27 NA27 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2V CA27 NA27 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA27 NA27 CA2T $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA27 CA2T NA2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2T NA2G CA29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2V CA29 NA2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA2V CA29 NA29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA2G CA29 NA29 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA29 NA29 HA2I $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA29 NA29 HA2C $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HA2I NA29 HA2C $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NA2H CA2Z CA2C CA27 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA2V CA29 CA27 NA2B $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA27 NA27 CA2V NA2H $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA29 CA2V NA2G NA29 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA29 CA29 HA2I HA2C $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR PA2N OA2J OA2Z OA2B $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PA22 OA2L OA2N OA2D $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA2W CA21 CA2K OA2H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA2K CA2W CA2X OA2Q $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA2X CA2K CA2Z OA2E $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA2Z OA2H CA2X NA2H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NA2H CA2C NA2B CA2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA2C NA2B CA2V CA27 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA2B CA2V CA27 NA2H $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA2V CA27 NA2H CA2C $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA27 NA2H CA2C NA2B $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA2V CA27 NA27 CA2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA27 NA27 CA2T NA2G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA27 CA2T NA2G CA29 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA2T NA2G CA29 CA2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA2G CA29 CA2V CA27 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA29 CA2V CA27 NA27 $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.6) DIHE PA22 OA2L PA2N OA2J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA22 OA2L PA2N OA2J $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PA2N OA2L PA22 OA2A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA2N OA2L PA22 OA2A $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CA21 OA2A PA22 OA2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CA21 OA2A PA22 OA2L $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PA22 OA2A CA21 CA2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA2K CA2W CA21 OA2A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CA21 CA2W OA2H CA2Z $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA21 CA2W CA2K CA2X $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NA2H CA2Z OA2H CA2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA2W CA2K OA2Q HA2Q $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA2Z CA2X CA2K CA2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA2K CA2X OA2E HA22 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA2K CA2X CA2Z NA2H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OA2H CA2Z NA2H CA27 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CA2V CA29 NA29 HA2C $pd_v 2 180.000 + + +NONBONDED OA2J 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA2N 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA2Z 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA2B 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA2L 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA22 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA2N 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA2D 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA2A 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA21 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA2W 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA2H 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA2K 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA2Q 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA2Q 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA2X 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA2E 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA22 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA2Z 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA2H 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA2C 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA2B 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA2V 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA27 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA27 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA2T 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA2G 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA29 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA29 0.10000 2.67270 0.10000 2.40543 +NONBONDED HA2I 0.10000 1.42544 0.10000 1.15817 +NONBONDED HA2C 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue AMP + + +eval ($pd_v=$pd_x* 12000.0) BOND OA1Q PA1L $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA1L OA12 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA1L OA14 $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA1L OA1S $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA1S CA1H $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CA1H CA1J $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CA1J OA1H $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA1J CA1Y $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OA1H CA1F $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA1Y OA1C $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA1Y CA1K $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA1C HA1N $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CA1K OA16 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA1K CA1F $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA16 HA1H $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CA1F NA1V $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NA1V CA19 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA1V CA1U $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA19 NA17 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA17 CA1A $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA1A CA1U $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA1A CA1L $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA1U NA13 $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NA13 CA1C $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CA1C NA16 $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NA16 CA1L $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CA1L NA1G $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NA1G HA1W $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NA1G HA12 $pd_v 1.000 + +eval ($pd_v=$pd_x* 760.0) ANGLE OA1Q PA1L OA12 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA1Q PA1L OA14 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA1Q PA1L OA1S $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA12 PA1L OA14 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA12 PA1L OA1S $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA14 PA1L OA1S $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA1L OA1S CA1H $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA1S CA1H CA1J $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CA1H CA1J OA1H $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CA1H CA1J CA1Y $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA1H CA1J CA1Y $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA1J OA1H CA1F $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA1J CA1Y OA1C $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA1J CA1Y CA1K $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA1C CA1Y CA1K $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA1Y OA1C HA1N $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA1Y CA1K OA16 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA1Y CA1K CA1F $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA16 CA1K CA1F $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA1K OA16 HA1H $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA1H CA1F CA1K $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OA1H CA1F NA1V $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CA1K CA1F NA1V $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1F NA1V CA19 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1F NA1V CA1U $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA19 NA1V CA1U $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA1V CA19 NA17 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA19 NA17 CA1A $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA17 CA1A CA1U $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA17 CA1A CA1L $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1U CA1A CA1L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA1V CA1U CA1A $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA1V CA1U NA13 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1A CA1U NA13 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1U NA13 CA1C $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA13 CA1C NA16 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1C NA16 CA1L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1A CA1L NA16 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA1A CA1L NA1G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA16 CA1L NA1G $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA1L NA1G HA1W $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA1L NA1G HA12 $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HA1W NA1G HA12 $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NA1V CA1F CA19 CA1U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1A CA1L CA1U NA17 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1U NA13 CA1A NA1V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1L CA1A NA16 NA1G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA1G CA1L HA1W HA12 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR PA1L OA1Q OA14 OA12 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA1J CA1H CA1Y OA1H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA1Y CA1J CA1K OA1C $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA1K CA1Y CA1F OA16 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA1F OA1H CA1K NA1V $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NA1V CA19 NA17 CA1A $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA19 NA17 CA1A CA1U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA17 CA1A CA1U NA1V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1A CA1U NA1V CA19 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1U NA1V CA19 NA17 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1A CA1U NA13 CA1C $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1U NA13 CA1C NA16 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA13 CA1C NA16 CA1L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1C NA16 CA1L CA1A $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA16 CA1L CA1A CA1U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA1L CA1A CA1U NA13 $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.6) DIHE CA1H OA1S PA1L OA1Q $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CA1H OA1S PA1L OA1Q $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PA1L OA1S CA1H CA1J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA1Y CA1J CA1H OA1S $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CA1H CA1J OA1H CA1F $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA1H CA1J CA1Y CA1K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NA1V CA1F OA1H CA1J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA1J CA1Y OA1C HA1N $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA1F CA1K CA1Y CA1J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA1Y CA1K OA16 HA1H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA1Y CA1K CA1F NA1V $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OA1H CA1F NA1V CA1U $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CA1A CA1L NA1G HA12 $pd_v 2 180.000 + + +NONBONDED OA1Q 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA1L 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA12 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA14 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA1S 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA1H 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA1J 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA1H 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA1Y 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA1C 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA1N 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA1K 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA16 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA1H 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA1F 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA1V 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA19 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA17 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA1A 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA1U 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA13 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA1C 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA16 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA1L 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA1G 0.10000 2.67270 0.10000 2.40543 +NONBONDED HA1W 0.10000 1.42544 0.10000 1.15817 +NONBONDED HA12 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue ATP + + +eval ($pd_v=$pd_x* 12000.0) BOND OA3H PA3Q $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA3Q OA3D $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA3Q OA3S $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA3Q OA3U $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA3U PA38 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA38 OA3Z $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA38 OA3O $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA38 OA3H $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA3H PA3N $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PA3N OA39 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PA3N OA3T $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PA3N OA36 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OA36 CA31 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CA31 CA3K $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CA3K OA32 $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA3K CA3E $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OA32 CA37 $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CA3E OA34 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA3E CA33 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA34 HA37 $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CA33 OA3E $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CA33 CA37 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OA3E HA3W $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CA37 NA3X $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NA3X CA3P $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA3X CA3L $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA3P NA3U $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NA3U CA32 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CA32 CA3L $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA32 CA34 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CA3L NA3G $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NA3G CA3F $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CA3F NA3N $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NA3N CA34 $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CA34 NA3M $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NA3M HA3Q $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NA3M HA35 $pd_v 1.000 + +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3Q OA3D $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3Q OA3S $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3Q OA3U $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3D PA3Q OA3S $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3D PA3Q OA3U $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3S PA3Q OA3U $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA3Q OA3U PA38 $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3U PA38 OA3Z $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3U PA38 OA3O $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3U PA38 OA3H $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3Z PA38 OA3O $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3Z PA38 OA3H $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3O PA38 OA3H $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA38 OA3H PA3N $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3N OA39 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3N OA3T $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3H PA3N OA36 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA39 PA3N OA3T $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OA39 PA3N OA36 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OA3T PA3N OA36 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PA3N OA36 CA31 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA36 CA31 CA3K $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CA31 CA3K OA32 $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CA31 CA3K CA3E $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA32 CA3K CA3E $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA3K OA32 CA37 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CA3K CA3E OA34 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA3K CA3E CA33 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA34 CA3E CA33 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA3E OA34 HA37 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA3E CA33 OA3E $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CA3E CA33 CA37 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OA3E CA33 CA37 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CA33 OA3E HA3W $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OA32 CA37 CA33 $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OA32 CA37 NA3X $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CA33 CA37 NA3X $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CA37 NA3X CA3P $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA37 NA3X CA3L $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA3P NA3X CA3L $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3X CA3P NA3U $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA3P NA3U CA32 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3U CA32 CA3L $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3U CA32 CA34 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA3L CA32 CA34 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3X CA3L CA32 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3X CA3L NA3G $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA32 CA3L NA3G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA3L NA3G CA3F $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3G CA3F NA3N $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA3F NA3N CA34 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA32 CA34 NA3N $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CA32 CA34 NA3M $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NA3N CA34 NA3M $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA34 NA3M HA3Q $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CA34 NA3M HA35 $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HA3Q NA3M HA35 $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NA3X CA37 CA3P CA3L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA32 CA34 CA3L NA3U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA3L NA3G CA32 NA3X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA34 CA32 NA3N NA3M $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA3M CA34 HA3Q HA35 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR PA3Q OA3H OA3D OA3S $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PA38 OA3U OA3Z OA3O $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PA3N OA3H OA3T OA39 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA3K CA31 CA3E OA32 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA3E CA3K CA33 OA34 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA33 CA3E CA37 OA3E $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CA37 OA32 CA33 NA3X $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NA3X CA3P NA3U CA32 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA3P NA3U CA32 CA3L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA3U CA32 CA3L NA3X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA32 CA3L NA3X CA3P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA3L NA3X CA3P NA3U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA32 CA3L NA3G CA3F $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA3L NA3G CA3F NA3N $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA3G CA3F NA3N CA34 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA3F NA3N CA34 CA32 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NA3N CA34 CA32 CA3L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CA34 CA32 CA3L NA3G $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.6) DIHE PA38 OA3U PA3Q OA3H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA38 OA3U PA3Q OA3H $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PA3Q OA3U PA38 OA3H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA3Q OA3U PA38 OA3H $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PA3N OA3H PA38 OA3U $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA3N OA3H PA38 OA3U $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PA38 OA3H PA3N OA36 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PA38 OA3H PA3N OA36 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CA31 OA36 PA3N OA3H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CA31 OA36 PA3N OA3H $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PA3N OA36 CA31 CA3K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA3E CA3K CA31 OA36 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CA31 CA3K OA32 CA37 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA31 CA3K CA3E CA33 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NA3X CA37 OA32 CA3K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA3K CA3E OA34 HA37 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA37 CA33 CA3E CA3K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CA3E CA33 OA3E HA3W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CA3E CA33 CA37 NA3X $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OA32 CA37 NA3X CA3L $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CA32 CA34 NA3M HA35 $pd_v 2 180.000 + + +NONBONDED OA3H 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA3Q 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA3D 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA3S 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA3U 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA38 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA3Z 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA3O 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA3H 0.10000 2.58361 0.10000 2.31634 +NONBONDED PA3N 0.10000 3.38542 0.10000 3.11815 +NONBONDED OA39 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA3T 0.10000 2.58361 0.10000 2.31634 +NONBONDED OA36 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA31 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA3K 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA32 0.10000 2.58361 0.10000 2.31634 +NONBONDED CA3E 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA34 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA37 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA33 0.10000 3.29633 0.10000 3.02906 +NONBONDED OA3E 0.10000 2.58361 0.10000 2.31634 +NONBONDED HA3W 0.10000 1.42544 0.10000 1.15817 +NONBONDED CA37 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA3X 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA3P 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA3U 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA32 0.10000 3.29633 0.10000 3.02906 +NONBONDED CA3L 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA3G 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA3F 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA3N 0.10000 2.67270 0.10000 2.40543 +NONBONDED CA34 0.10000 3.29633 0.10000 3.02906 +NONBONDED NA3M 0.10000 2.67270 0.10000 2.40543 +NONBONDED HA3Q 0.10000 1.42544 0.10000 1.15817 +NONBONDED HA35 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue CIT + + +eval ($pd_v=$pd_x* 20000.0) BOND OCIM CCIV $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCIV OCIX $pd_v 1.250 +eval ($pd_v=$pd_x* 16000.0) BOND CCIV CCII $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCII CCIU $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCIU CCIY $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCIU OCIG $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CCIU CCIE $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CCIY OCIC $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCIY OCIT $pd_v 1.250 +eval ($pd_v=$pd_x* 15000.0) BOND OCIG HCIT $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CCIE CCIB $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CCIB OCI9 $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCIB OCID $pd_v 1.250 + +eval ($pd_v=$pd_x* 960.0) ANGLE OCIM CCIV OCIX $pd_v 126.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCIM CCIV CCII $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCIX CCIV CCII $pd_v 117.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CCIV CCII CCIU $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CCII CCIU CCIY $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCII CCIU OCIG $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCII CCIU CCIE $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CCIY CCIU OCIG $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCIY CCIU CCIE $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OCIG CCIU CCIE $pd_v 109.500 +eval ($pd_v=$pd_x* 960.0) ANGLE CCIU CCIY OCIC $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCIU CCIY OCIT $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCIC CCIY OCIT $pd_v 126.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CCIU OCIG HCIT $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCIU CCIE CCIB $pd_v 111.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCIE CCIB OCI9 $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCIE CCIB OCID $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCI9 CCIB OCID $pd_v 126.000 + +eval ($pd_v=$pd_x* 800.0) IMPR CCIV CCII OCIX OCIM $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CCIY CCIU OCIT OCIC $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CCIB CCIE OCID OCI9 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CCIU CCII OCIG CCIY $pd_v 0 35.264 + +eval ($pd_v=$pd_x* 0.1) DIHE CCIU CCII CCIV OCIM $pd_v 6 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CCIV CCII CCIU CCIE $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CCII CCIU CCIY OCIT $pd_v 6 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CCII CCIU OCIG HCIT $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CCIB CCIE CCIU CCII $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CCIU CCIE CCIB OCID $pd_v 6 0.000 + + +NONBONDED OCIM 0.10000 2.58361 0.10000 2.31634 +NONBONDED CCIV 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCIX 0.10000 2.58361 0.10000 2.31634 +NONBONDED CCII 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCIU 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCIY 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCIC 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCIT 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCIG 0.10000 2.58361 0.10000 2.31634 +NONBONDED HCIT 0.10000 1.42544 0.10000 1.15817 +NONBONDED CCIE 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCIB 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCI9 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCID 0.10000 2.58361 0.10000 2.31634 + + + +! Adding parameter definition for residue FAD + + +eval ($pd_v=$pd_x* 24000.0) BOND OF2N CF2T $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CF2T NF2Y $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CF2T CF2L $pd_v 1.390 +eval ($pd_v=$pd_x* 17900.0) BOND NF2Y HF2U $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NF2Y CF24 $pd_v 1.400 +eval ($pd_v=$pd_x* 24000.0) BOND CF24 OF2G $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CF24 NF2W $pd_v 1.400 +eval ($pd_v=$pd_x* 17900.0) BOND NF2W HF2N $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NF2W CF2V $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CF2V CF2L $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CF2V NF2G $pd_v 1.400 +eval ($pd_v=$pd_x* 16000.0) BOND CF2L NF2R $pd_v 1.400 +eval ($pd_v=$pd_x* 17900.0) BOND NF2R HF25 $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NF2R CF2E $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CF2E CF23 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CF2E CF2G $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CF23 CF2M $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CF2M CF29 $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CF2M CF27 $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CF27 CF2D $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CF27 CF21 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CF21 CF2G $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CF2G NF2G $pd_v 1.400 +eval ($pd_v=$pd_x* 16000.0) BOND NF2G CF2W $pd_v 1.480 +eval ($pd_v=$pd_x* 16000.0) BOND CF2W CF2N $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CF2N OF2M $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CF2N CF22 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OF2M HF2I $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CF22 OF22 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CF22 CF2Y $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OF22 HF2V $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CF2Y OF25 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CF2Y CF26 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OF25 HF27 $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CF26 OF2X $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND OF2X PF2N $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PF2N OF20 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PF2N OF21 $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PF2N OF2A $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OF2A PF2S $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PF2S OF2Y $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PF2S OF2Q $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PF2S OF2W $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OF2W CF2U $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CF2U CF2K $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CF2K OF2V $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CF2K CF2Q $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OF2V CF20 $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CF2Q OF2E $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CF2Q CF2R $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OF2E HF2X $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CF2R OF2C $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CF2R CF20 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OF2C HF2F $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CF20 NF2O $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NF2O CF2B $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NF2O CF25 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CF2B NF2X $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NF2X CF2S $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CF2S CF25 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CF2S CF2A $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CF25 NF2Z $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NF2Z CF2F $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CF2F NF21 $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NF21 CF2A $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CF2A NF29 $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NF29 HF2C $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NF29 HF2K $pd_v 1.000 + +eval ($pd_v=$pd_x* 800.0) ANGLE OF2N CF2T NF2Y $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE OF2N CF2T CF2L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2Y CF2T CF2L $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CF2T NF2Y HF2U $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2T NF2Y CF24 $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HF2U NF2Y CF24 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2Y CF24 OF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2Y CF24 NF2W $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE OF2G CF24 NF2W $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CF24 NF2W HF2N $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF24 NF2W CF2V $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HF2N NF2W CF2V $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2W CF2V CF2L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2W CF2V NF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2L CF2V NF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2T CF2L CF2V $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2T CF2L NF2R $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2V CF2L NF2R $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CF2L NF2R HF25 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2L NF2R CF2E $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HF25 NF2R CF2E $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2R CF2E CF23 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2R CF2E CF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF23 CF2E CF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2E CF23 CF2M $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF23 CF2M CF29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF23 CF2M CF27 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF29 CF2M CF27 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2M CF27 CF2D $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2M CF27 CF21 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2D CF27 CF21 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF27 CF21 CF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2E CF2G CF21 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2E CF2G NF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF21 CF2G NF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2V NF2G CF2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2V NF2G CF2W $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2G NF2G CF2W $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE NF2G CF2W CF2N $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2W CF2N OF2M $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2W CF2N CF22 $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2M CF2N CF22 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CF2N OF2M HF2I $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2N CF22 OF22 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2N CF22 CF2Y $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF22 CF22 CF2Y $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CF22 OF22 HF2V $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF22 CF2Y OF25 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF22 CF2Y CF26 $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF25 CF2Y CF26 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CF2Y OF25 HF27 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2Y CF26 OF2X $pd_v 111.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CF26 OF2X PF2N $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2X PF2N OF20 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2X PF2N OF21 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2X PF2N OF2A $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF20 PF2N OF21 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OF20 PF2N OF2A $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF21 PF2N OF2A $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PF2N OF2A PF2S $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2A PF2S OF2Y $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2A PF2S OF2Q $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2A PF2S OF2W $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2Y PF2S OF2Q $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2Y PF2S OF2W $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OF2Q PF2S OF2W $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PF2S OF2W CF2U $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2W CF2U CF2K $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CF2U CF2K OF2V $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CF2U CF2K CF2Q $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2V CF2K CF2Q $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2K OF2V CF20 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2K CF2Q OF2E $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2K CF2Q CF2R $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2E CF2Q CF2R $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CF2Q OF2E HF2X $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2Q CF2R OF2C $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CF2Q CF2R CF20 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2C CF2R CF20 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CF2R OF2C HF2F $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OF2V CF20 CF2R $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OF2V CF20 NF2O $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CF2R CF20 NF2O $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CF20 NF2O CF2B $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF20 NF2O CF25 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2B NF2O CF25 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2O CF2B NF2X $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2B NF2X CF2S $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2X CF2S CF25 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2X CF2S CF2A $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF25 CF2S CF2A $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2O CF25 CF2S $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2O CF25 NF2Z $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2S CF25 NF2Z $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF25 NF2Z CF2F $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF2Z CF2F NF21 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2F NF21 CF2A $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2S CF2A NF21 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CF2S CF2A NF29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NF21 CF2A NF29 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CF2A NF29 HF2C $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CF2A NF29 HF2K $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HF2C NF29 HF2K $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR CF2T CF2L NF2Y OF2N $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2Y CF24 HF2U CF2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF24 NF2Y NF2W OF2G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2W CF2V HF2N CF24 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2V NF2W NF2G CF2L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2L NF2R CF2V CF2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2R CF2E HF25 CF2L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2E NF2R CF2G CF23 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2M CF23 CF27 CF29 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF27 CF2M CF21 CF2D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2G CF2E NF2G CF21 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2G CF2V CF2G CF2W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2O CF20 CF2B CF25 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2S CF2A CF25 NF2X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF25 NF2Z CF2S NF2O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2A CF2S NF21 NF29 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF29 CF2A HF2C HF2K $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CF2N CF2W OF2M CF22 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF22 CF2N OF22 CF2Y $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF2Y CF22 OF25 CF26 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PF2N OF2X OF20 OF21 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PF2S OF2A OF2Q OF2Y $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF2K CF2U CF2Q OF2V $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF2Q CF2K CF2R OF2E $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF2R CF2Q CF20 OF2C $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CF20 OF2V CF2R NF2O $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NF2O CF2B NF2X CF2S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2B NF2X CF2S CF25 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2X CF2S CF25 NF2O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2S CF25 NF2O CF2B $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF25 NF2O CF2B NF2X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2E CF23 CF2M CF27 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF23 CF2M CF27 CF21 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2M CF27 CF21 CF2G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF27 CF21 CF2G CF2E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF21 CF2G CF2E CF23 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2G CF2E CF23 CF2M $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2T NF2Y CF24 NF2W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2Y CF24 NF2W CF2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF24 NF2W CF2V CF2L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2W CF2V CF2L CF2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2V CF2L CF2T NF2Y $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2L CF2T NF2Y CF24 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2S CF25 NF2Z CF2F $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF25 NF2Z CF2F NF21 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF2Z CF2F NF21 CF2A $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2F NF21 CF2A CF2S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NF21 CF2A CF2S CF25 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CF2A CF2S CF25 NF2Z $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 640.0) DIHE CF2W NF2G CF2V NF2W $pd_v 2 180.000 +eval ($pd_v=$pd_x* 640.0) DIHE CF2E NF2R CF2L CF2T $pd_v 2 180.000 +eval ($pd_v=$pd_x* 640.0) DIHE CF2L NF2R CF2E CF2G $pd_v 2 180.000 +eval ($pd_v=$pd_x* 640.0) DIHE CF2W NF2G CF2G CF2E $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.1) DIHE CF2V NF2G CF2W CF2N $pd_v 6 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE NF2G CF2W CF2N CF22 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CF2W CF2N OF2M HF2I $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF2Y CF22 CF2N CF2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CF2N CF22 OF22 HF2V $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF26 CF2Y CF22 CF2N $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CF22 CF2Y OF25 HF27 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE OF2X CF26 CF2Y CF22 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PF2N OF2X CF26 CF2Y $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CF26 OF2X PF2N OF2A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CF26 OF2X PF2N OF2A $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PF2S OF2A PF2N OF2X $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PF2S OF2A PF2N OF2X $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PF2N OF2A PF2S OF2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PF2N OF2A PF2S OF2W $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CF2U OF2W PF2S OF2A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CF2U OF2W PF2S OF2A $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PF2S OF2W CF2U CF2K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF2Q CF2K CF2U OF2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CF2U CF2K OF2V CF20 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF2U CF2K CF2Q CF2R $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NF2O CF20 OF2V CF2K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CF2K CF2Q OF2E HF2X $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF20 CF2R CF2Q CF2K $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CF2Q CF2R OF2C HF2F $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CF2Q CF2R CF20 NF2O $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OF2V CF20 NF2O CF25 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CF2S CF2A NF29 HF2K $pd_v 2 180.000 + + +NONBONDED OF2N 0.10000 2.58361 0.10000 2.31634 +NONBONDED CF2T 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2Y 0.10000 2.67270 0.10000 2.40543 +NONBONDED HF2U 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF24 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2G 0.10000 2.58361 0.10000 2.31634 +NONBONDED NF2W 0.10000 2.67270 0.10000 2.40543 +NONBONDED HF2N 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF2V 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2L 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2R 0.10000 2.67270 0.10000 2.40543 +NONBONDED HF25 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF2E 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF23 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2M 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF29 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF27 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2D 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF21 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2G 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2G 0.10000 2.67270 0.10000 2.40543 +NONBONDED CF2W 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2N 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2M 0.10000 2.58361 0.10000 2.31634 +NONBONDED HF2I 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF22 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF22 0.10000 2.58361 0.10000 2.31634 +NONBONDED HF2V 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF2Y 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF25 0.10000 2.58361 0.10000 2.31634 +NONBONDED HF27 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF26 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2X 0.10000 2.58361 0.10000 2.31634 +NONBONDED PF2N 0.10000 3.38542 0.10000 3.11815 +NONBONDED OF20 0.10000 2.58361 0.10000 2.31634 +NONBONDED OF21 0.10000 2.58361 0.10000 2.31634 +NONBONDED OF2A 0.10000 2.58361 0.10000 2.31634 +NONBONDED PF2S 0.10000 3.38542 0.10000 3.11815 +NONBONDED OF2Y 0.10000 2.58361 0.10000 2.31634 +NONBONDED OF2Q 0.10000 2.58361 0.10000 2.31634 +NONBONDED OF2W 0.10000 2.58361 0.10000 2.31634 +NONBONDED CF2U 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF2K 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2V 0.10000 2.58361 0.10000 2.31634 +NONBONDED CF2Q 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2E 0.10000 2.58361 0.10000 2.31634 +NONBONDED HF2X 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF2R 0.10000 3.29633 0.10000 3.02906 +NONBONDED OF2C 0.10000 2.58361 0.10000 2.31634 +NONBONDED HF2F 0.10000 1.42544 0.10000 1.15817 +NONBONDED CF20 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2O 0.10000 2.67270 0.10000 2.40543 +NONBONDED CF2B 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2X 0.10000 2.67270 0.10000 2.40543 +NONBONDED CF2S 0.10000 3.29633 0.10000 3.02906 +NONBONDED CF25 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF2Z 0.10000 2.67270 0.10000 2.40543 +NONBONDED CF2F 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF21 0.10000 2.67270 0.10000 2.40543 +NONBONDED CF2A 0.10000 3.29633 0.10000 3.02906 +NONBONDED NF29 0.10000 2.67270 0.10000 2.40543 +NONBONDED HF2C 0.10000 1.42544 0.10000 1.15817 +NONBONDED HF2K 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue FLC + + +eval ($pd_v=$pd_x* 20000.0) BOND OCTT CCT5 $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCT5 OCT7 $pd_v 1.250 +eval ($pd_v=$pd_x* 16000.0) BOND CCT5 CCTK $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCTK CCT2 $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCT2 CCTO $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CCT2 OCT6 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CCT2 CCTA $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CCTO OCTX $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCTO OCT9 $pd_v 1.250 +eval ($pd_v=$pd_x* 15000.0) BOND OCT6 HCTU $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CCTA CCTH $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CCTH OCTR $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CCTH OCT8 $pd_v 1.250 + +eval ($pd_v=$pd_x* 960.0) ANGLE OCTT CCT5 OCT7 $pd_v 126.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCTT CCT5 CCTK $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCT7 CCT5 CCTK $pd_v 117.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CCT5 CCTK CCT2 $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CCTK CCT2 CCTO $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCTK CCT2 OCT6 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCTK CCT2 CCTA $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CCTO CCT2 OCT6 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCTO CCT2 CCTA $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OCT6 CCT2 CCTA $pd_v 109.500 +eval ($pd_v=$pd_x* 960.0) ANGLE CCT2 CCTO OCTX $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCT2 CCTO OCT9 $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCTX CCTO OCT9 $pd_v 126.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CCT2 OCT6 HCTU $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CCT2 CCTA CCTH $pd_v 111.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCTA CCTH OCTR $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CCTA CCTH OCT8 $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OCTR CCTH OCT8 $pd_v 126.000 + +eval ($pd_v=$pd_x* 800.0) IMPR CCT5 CCTK OCT7 OCTT $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CCTO CCT2 OCT9 OCTX $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CCTH CCTA OCT8 OCTR $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CCT2 CCTK CCTO OCT6 $pd_v 0 35.264 + +eval ($pd_v=$pd_x* 0.1) DIHE CCT2 CCTK CCT5 OCTT $pd_v 6 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CCT5 CCTK CCT2 CCTA $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CCTK CCT2 CCTO OCT9 $pd_v 6 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CCTK CCT2 OCT6 HCTU $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CCTH CCTA CCT2 CCTK $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CCT2 CCTA CCTH OCT8 $pd_v 6 0.000 + + +NONBONDED OCTT 0.10000 2.58361 0.10000 2.31634 +NONBONDED CCT5 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCT7 0.10000 2.58361 0.10000 2.31634 +NONBONDED CCTK 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCT2 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCTO 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCTX 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCT9 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCT6 0.10000 2.58361 0.10000 2.31634 +NONBONDED HCTU 0.10000 1.42544 0.10000 1.15817 +NONBONDED CCTA 0.10000 3.29633 0.10000 3.02906 +NONBONDED CCTH 0.10000 3.29633 0.10000 3.02906 +NONBONDED OCTR 0.10000 2.58361 0.10000 2.31634 +NONBONDED OCT8 0.10000 2.58361 0.10000 2.31634 + + + +! Adding parameter definition for residue GDP + + +eval ($pd_v=$pd_x* 12000.0) BOND OG29 PG23 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PG23 OG2Y $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PG23 OG26 $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PG23 OG2J $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OG2J PG2T $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PG2T OG2O $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PG2T OG2V $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PG2T OG25 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OG25 CG26 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CG26 CG2B $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CG2B OG2C $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CG2B CG2G $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OG2C CG21 $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CG2G OG2H $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CG2G CG2R $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OG2H HG2V $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CG2R OG2F $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CG2R CG21 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OG2F HG25 $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CG21 NG2W $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NG2W CG2P $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NG2W CG2V $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG2P NG2Q $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NG2Q CG2Z $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG2Z CG2V $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CG2Z CG27 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CG2V NG2G $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NG2G CG2O $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CG2O NG2J $pd_v 1.330 +eval ($pd_v=$pd_x* 16000.0) BOND CG2O NG2K $pd_v 1.400 +eval ($pd_v=$pd_x* 17900.0) BOND NG2J HG2P $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NG2J HG2U $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NG2K HG2B $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NG2K CG27 $pd_v 1.400 +eval ($pd_v=$pd_x* 24000.0) BOND CG27 OG2E $pd_v 1.230 + +eval ($pd_v=$pd_x* 760.0) ANGLE OG29 PG23 OG2Y $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG29 PG23 OG26 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG29 PG23 OG2J $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2Y PG23 OG26 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2Y PG23 OG2J $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG26 PG23 OG2J $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PG23 OG2J PG2T $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2J PG2T OG2O $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2J PG2T OG2V $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2J PG2T OG25 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2O PG2T OG2V $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2O PG2T OG25 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG2V PG2T OG25 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PG2T OG25 CG26 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG25 CG26 CG2B $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CG26 CG2B OG2C $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CG26 CG2B CG2G $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG2C CG2B CG2G $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG2B OG2C CG21 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG2B CG2G OG2H $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG2B CG2G CG2R $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG2H CG2G CG2R $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG2G OG2H HG2V $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG2G CG2R OG2F $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG2G CG2R CG21 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG2F CG2R CG21 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG2R OG2F HG25 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG2C CG21 CG2R $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OG2C CG21 NG2W $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CG2R CG21 NG2W $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CG21 NG2W CG2P $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG21 NG2W CG2V $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2P NG2W CG2V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2W CG2P NG2Q $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2P NG2Q CG2Z $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2Q CG2Z CG2V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2Q CG2Z CG27 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2V CG2Z CG27 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2W CG2V CG2Z $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2W CG2V NG2G $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2Z CG2V NG2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2V NG2G CG2O $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2G CG2O NG2J $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2G CG2O NG2K $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2J CG2O NG2K $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG2O NG2J HG2P $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG2O NG2J HG2U $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HG2P NG2J HG2U $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CG2O NG2K HG2B $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2O NG2K CG27 $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HG2B NG2K CG27 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2Z CG27 NG2K $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG2Z CG27 OG2E $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG2K CG27 OG2E $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NG2W CG21 CG2P CG2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2Z CG27 CG2V NG2Q $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2V NG2G CG2Z NG2W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2O NG2G NG2K NG2J $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG2J CG2O HG2P HG2U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG2K CG27 HG2B CG2O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG27 CG2Z NG2K OG2E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR PG23 OG29 OG26 OG2Y $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PG2T OG2J OG2O OG2V $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG2B CG26 CG2G OG2C $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG2G CG2B CG2R OG2H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG2R CG2G CG21 OG2F $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG21 OG2C CG2R NG2W $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NG2W CG2P NG2Q CG2Z $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2P NG2Q CG2Z CG2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG2Q CG2Z CG2V NG2W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2Z CG2V NG2W CG2P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2V NG2W CG2P NG2Q $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2Z CG2V NG2G CG2O $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2V NG2G CG2O NG2K $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG2G CG2O NG2K CG27 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG2O NG2K CG27 CG2Z $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG2K CG27 CG2Z CG2V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG27 CG2Z CG2V NG2G $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.6) DIHE PG2T OG2J PG23 OG29 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG2T OG2J PG23 OG29 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PG23 OG2J PG2T OG25 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG23 OG2J PG2T OG25 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CG26 OG25 PG2T OG2J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CG26 OG25 PG2T OG2J $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PG2T OG25 CG26 CG2B $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG2G CG2B CG26 OG25 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CG26 CG2B OG2C CG21 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG26 CG2B CG2G CG2R $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NG2W CG21 OG2C CG2B $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG2B CG2G OG2H HG2V $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG21 CG2R CG2G CG2B $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG2G CG2R OG2F HG25 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG2G CG2R CG21 NG2W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OG2C CG21 NG2W CG2V $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE NG2G CG2O NG2J HG2U $pd_v 2 180.000 + + +NONBONDED OG29 0.10000 2.58361 0.10000 2.31634 +NONBONDED PG23 0.10000 3.38542 0.10000 3.11815 +NONBONDED OG2Y 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG26 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG2J 0.10000 2.58361 0.10000 2.31634 +NONBONDED PG2T 0.10000 3.38542 0.10000 3.11815 +NONBONDED OG2O 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG2V 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG25 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG26 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG2B 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG2C 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG2G 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG2H 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG2V 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG2R 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG2F 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG25 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG21 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG2W 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG2P 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG2Q 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG2Z 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG2V 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG2G 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG2O 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG2J 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG2P 0.10000 1.42544 0.10000 1.15817 +NONBONDED HG2U 0.10000 1.42544 0.10000 1.15817 +NONBONDED NG2K 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG2B 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG27 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG2E 0.10000 2.58361 0.10000 2.31634 + + + +! Adding parameter definition for residue GMP + + +eval ($pd_v=$pd_x* 24000.0) BOND OG1N CG17 $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CG17 NG1T $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CG17 CG1S $pd_v 1.390 +eval ($pd_v=$pd_x* 17900.0) BOND NG1T HG16 $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NG1T CG1O $pd_v 1.400 +eval ($pd_v=$pd_x* 18000.0) BOND CG1O NG14 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG1O NG1K $pd_v 1.340 +eval ($pd_v=$pd_x* 17900.0) BOND NG14 HG12 $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NG14 HG18 $pd_v 1.000 +eval ($pd_v=$pd_x* 20000.0) BOND NG1K CG14 $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND CG14 CG1S $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CG14 NG15 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG1S NG19 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NG19 CG1V $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG1V NG15 $pd_v 1.330 +eval ($pd_v=$pd_x* 12000.0) BOND NG15 CG1J $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CG1J OG1V $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CG1J CG1Q $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OG1V CG1A $pd_v 1.435 +eval ($pd_v=$pd_x* 12000.0) BOND CG1A CG1R $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CG1A CG16 $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CG1R OG1P $pd_v 1.430 +eval ($pd_v=$pd_x* 15000.0) BOND OG1P HG1N $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CG16 OG1R $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CG16 CG1Q $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OG1R HG1M $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CG1Q OG1O $pd_v 1.430 +eval ($pd_v=$pd_x* 15000.0) BOND OG1O HG1Z $pd_v 1.000 + +eval ($pd_v=$pd_x* 800.0) ANGLE OG1N CG17 NG1T $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE OG1N CG17 CG1S $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG1T CG17 CG1S $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CG17 NG1T HG16 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG17 NG1T CG1O $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HG16 NG1T CG1O $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG1T CG1O NG14 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG1T CG1O NG1K $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG14 CG1O NG1K $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG1O NG14 HG12 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG1O NG14 HG18 $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HG12 NG14 HG18 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG1O NG1K CG14 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG1K CG14 CG1S $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG1K CG14 NG15 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG1S CG14 NG15 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG17 CG1S CG14 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG17 CG1S NG19 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG14 CG1S NG19 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG1S NG19 CG1V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG19 CG1V NG15 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG14 NG15 CG1V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG14 NG15 CG1J $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG1V NG15 CG1J $pd_v 126.000 +eval ($pd_v=$pd_x* 544.0) ANGLE NG15 CG1J OG1V $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE NG15 CG1J CG1Q $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG1V CG1J CG1Q $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1J OG1V CG1A $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OG1V CG1A CG1R $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG1V CG1A CG16 $pd_v 104.000 +eval ($pd_v=$pd_x* 480.0) ANGLE CG1R CG1A CG16 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1A CG1R OG1P $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG1R OG1P HG1N $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1A CG16 OG1R $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1A CG16 CG1Q $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG1R CG16 CG1Q $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG16 OG1R HG1M $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1J CG1Q CG16 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG1J CG1Q OG1O $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG16 CG1Q OG1O $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG1Q OG1O HG1Z $pd_v 109.500 + +eval ($pd_v=$pd_x* 800.0) IMPR CG17 CG1S NG1T OG1N $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG1T CG1O HG16 CG17 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1O NG1T NG1K NG14 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG14 CG1O HG12 HG18 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG14 NG1K CG1S NG15 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1S CG17 CG14 NG19 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG15 CG14 CG1V CG1J $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CG1J NG15 OG1V CG1Q $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG1A OG1V CG1R CG16 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG16 CG1A CG1Q OG1R $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG1Q CG1J OG1O CG16 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR CG14 CG1S NG19 CG1V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1S NG19 CG1V NG15 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG19 CG1V NG15 CG14 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1V NG15 CG14 CG1S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG15 CG14 CG1S NG19 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG17 NG1T CG1O NG1K $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG1T CG1O NG1K CG14 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1O NG1K CG14 CG1S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG1K CG14 CG1S CG17 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG14 CG1S CG17 NG1T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG1S CG17 NG1T CG1O $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 640.0) DIHE NG1T CG1O NG14 HG18 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.0) DIHE CG1Q CG1J NG15 CG14 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NG15 CG1J OG1V CG1A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE NG15 CG1J CG1Q OG1O $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CG16 CG1A OG1V CG1J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE OG1V CG1A CG1R OG1P $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE OG1V CG1A CG16 CG1Q $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG1A CG1R OG1P HG1N $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG1A CG16 OG1R HG1M $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE OG1O CG1Q CG16 CG1A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG1J CG1Q OG1O HG1Z $pd_v 3 0.000 + + +NONBONDED OG1N 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG17 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG1T 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG16 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG1O 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG14 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG12 0.10000 1.42544 0.10000 1.15817 +NONBONDED HG18 0.10000 1.42544 0.10000 1.15817 +NONBONDED NG1K 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG14 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG1S 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG19 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG1V 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG15 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG1J 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG1V 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG1A 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG1R 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG1P 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG1N 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG16 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG1R 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG1M 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG1Q 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG1O 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG1Z 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue GTP + + +eval ($pd_v=$pd_x* 12000.0) BOND OG31 PG3E $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PG3E OG3D $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PG3E OG38 $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PG3E OG33 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OG33 PG3T $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PG3T OG3O $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PG3T OG3S $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PG3T OG3E $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OG3E PG3C $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PG3C OG3V $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PG3C OG3W $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PG3C OG3M $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND OG3M CG34 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CG34 CG37 $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CG37 OG3J $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CG37 CG3H $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND OG3J CG3J $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CG3H OG3X $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CG3H CG31 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OG3X HG3F $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CG31 OG3Y $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CG31 CG3J $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND OG3Y HG3L $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CG3J NG31 $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NG31 CG3U $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NG31 CG3E $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG3U NG3W $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NG3W CG3V $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CG3V CG3E $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CG3V CG3R $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CG3E NG3C $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NG3C CG3W $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CG3W NG3J $pd_v 1.330 +eval ($pd_v=$pd_x* 16000.0) BOND CG3W NG3D $pd_v 1.400 +eval ($pd_v=$pd_x* 17900.0) BOND NG3J HG35 $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NG3J HG3H $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NG3D HG3Q $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND NG3D CG3R $pd_v 1.400 +eval ($pd_v=$pd_x* 24000.0) BOND CG3R OG3F $pd_v 1.230 + +eval ($pd_v=$pd_x* 760.0) ANGLE OG31 PG3E OG3D $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG31 PG3E OG38 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG31 PG3E OG33 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3D PG3E OG38 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3D PG3E OG33 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG38 PG3E OG33 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PG3E OG33 PG3T $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG33 PG3T OG3O $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG33 PG3T OG3S $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG33 PG3T OG3E $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3O PG3T OG3S $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3O PG3T OG3E $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3S PG3T OG3E $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PG3T OG3E PG3C $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3E PG3C OG3V $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3E PG3C OG3W $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3E PG3C OG3M $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3V PG3C OG3W $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3V PG3C OG3M $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE OG3W PG3C OG3M $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PG3C OG3M CG34 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG3M CG34 CG37 $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CG34 CG37 OG3J $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CG34 CG37 CG3H $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG3J CG37 CG3H $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG37 OG3J CG3J $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CG37 CG3H OG3X $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG37 CG3H CG31 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG3X CG3H CG31 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG3H OG3X HG3F $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG3H CG31 OG3Y $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CG3H CG31 CG3J $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE OG3Y CG31 CG3J $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CG31 OG3Y HG3L $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE OG3J CG3J CG31 $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE OG3J CG3J NG31 $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CG31 CG3J NG31 $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3J NG31 CG3U $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3J NG31 CG3E $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3U NG31 CG3E $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG31 CG3U NG3W $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3U NG3W CG3V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3W CG3V CG3E $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3W CG3V CG3R $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3E CG3V CG3R $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG31 CG3E CG3V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG31 CG3E NG3C $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3V CG3E NG3C $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3E NG3C CG3W $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3C CG3W NG3J $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3C CG3W NG3D $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3J CG3W NG3D $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG3W NG3J HG35 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CG3W NG3J HG3H $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HG35 NG3J HG3H $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CG3W NG3D HG3Q $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3W NG3D CG3R $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HG3Q NG3D CG3R $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3V CG3R NG3D $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CG3V CG3R OG3F $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NG3D CG3R OG3F $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NG31 CG3J CG3U CG3E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3V CG3R CG3E NG3W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3E NG3C CG3V NG31 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3W NG3C NG3D NG3J $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG3J CG3W HG35 HG3H $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG3D CG3R HG3Q CG3W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3R CG3V NG3D OG3F $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR PG3E OG31 OG38 OG3D $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PG3T OG33 OG3O OG3S $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PG3C OG3E OG3V OG3W $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG37 CG34 CG3H OG3J $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG3H CG37 CG31 OG3X $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG31 CG3H CG3J OG3Y $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CG3J OG3J CG31 NG31 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NG31 CG3U NG3W CG3V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3U NG3W CG3V CG3E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG3W CG3V CG3E NG31 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3V CG3E NG31 CG3U $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3E NG31 CG3U NG3W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3V CG3E NG3C CG3W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3E NG3C CG3W NG3D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG3C CG3W NG3D CG3R $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3W NG3D CG3R CG3V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NG3D CG3R CG3V CG3E $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CG3R CG3V CG3E NG3C $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 0.6) DIHE PG3T OG33 PG3E OG31 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG3T OG33 PG3E OG31 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PG3E OG33 PG3T OG3E $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG3E OG33 PG3T OG3E $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PG3C OG3E PG3T OG33 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG3C OG3E PG3T OG33 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PG3T OG3E PG3C OG3M $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PG3T OG3E PG3C OG3M $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CG34 OG3M PG3C OG3E $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CG34 OG3M PG3C OG3E $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PG3C OG3M CG34 CG37 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG3H CG37 CG34 OG3M $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CG34 CG37 OG3J CG3J $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG34 CG37 CG3H CG31 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NG31 CG3J OG3J CG37 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG37 CG3H OG3X HG3F $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG3J CG31 CG3H CG37 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CG3H CG31 OG3Y HG3L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CG3H CG31 CG3J NG31 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE OG3J CG3J NG31 CG3E $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE NG3C CG3W NG3J HG3H $pd_v 2 180.000 + + +NONBONDED OG31 0.10000 2.58361 0.10000 2.31634 +NONBONDED PG3E 0.10000 3.38542 0.10000 3.11815 +NONBONDED OG3D 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG38 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG33 0.10000 2.58361 0.10000 2.31634 +NONBONDED PG3T 0.10000 3.38542 0.10000 3.11815 +NONBONDED OG3O 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG3S 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG3E 0.10000 2.58361 0.10000 2.31634 +NONBONDED PG3C 0.10000 3.38542 0.10000 3.11815 +NONBONDED OG3V 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG3W 0.10000 2.58361 0.10000 2.31634 +NONBONDED OG3M 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG34 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG37 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG3J 0.10000 2.58361 0.10000 2.31634 +NONBONDED CG3H 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG3X 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG3F 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG31 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG3Y 0.10000 2.58361 0.10000 2.31634 +NONBONDED HG3L 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG3J 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG31 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG3U 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG3W 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG3V 0.10000 3.29633 0.10000 3.02906 +NONBONDED CG3E 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG3C 0.10000 2.67270 0.10000 2.40543 +NONBONDED CG3W 0.10000 3.29633 0.10000 3.02906 +NONBONDED NG3J 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG35 0.10000 1.42544 0.10000 1.15817 +NONBONDED HG3H 0.10000 1.42544 0.10000 1.15817 +NONBONDED NG3D 0.10000 2.67270 0.10000 2.40543 +NONBONDED HG3Q 0.10000 1.42544 0.10000 1.15817 +NONBONDED CG3R 0.10000 3.29633 0.10000 3.02906 +NONBONDED OG3F 0.10000 2.58361 0.10000 2.31634 + + + +! Adding parameter definition for residue NAD + + +eval ($pd_v=$pd_x* 17900.0) BOND NN2Q HN27 $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NN2Q HN24 $pd_v 1.000 +eval ($pd_v=$pd_x* 18000.0) BOND NN2Q CN28 $pd_v 1.330 +eval ($pd_v=$pd_x* 24000.0) BOND CN28 ON2B $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CN28 CN2N $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CN2N CN24 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN2N CN29 $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CN24 NN20 $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CN29 CN2P $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN2P CN2G $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CN2G NN20 $pd_v 1.400 +eval ($pd_v=$pd_x* 16000.0) BOND NN20 CN2I $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CN2I ON2D $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN2I CN22 $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ON2D CN2O $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN22 ON27 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN22 CN2A $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON27 HN2M $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CN2A ON2N $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN2A CN2O $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON2N HN2Q $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CN2O CN27 $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CN27 ON2L $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND ON2L PN2D $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PN2D ON2U $pd_v 1.480 +eval ($pd_v=$pd_x* 18000.0) BOND PN2D ON2F $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PN2D ON2R $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ON2R PN21 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PN21 ON26 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PN21 ON2V $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PN21 ON24 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ON24 CN25 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CN25 CN2L $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CN2L ON2H $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN2L CN2U $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ON2H CN2E $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN2U ON29 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN2U CN2C $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON29 HN2B $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CN2C ON22 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN2C CN2E $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON22 HN2I $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CN2E NN2T $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NN2T CN2W $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NN2T CN2Q $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN2W NN25 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NN25 CN2S $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN2S CN2Q $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN2S CN2R $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN2Q NN2H $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NN2H CN2F $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CN2F NN2I $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NN2I CN2R $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CN2R NN24 $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NN24 HN2K $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NN24 HN26 $pd_v 1.000 + +eval ($pd_v=$pd_x* 640.0) ANGLE HN27 NN2Q HN24 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HN27 NN2Q CN28 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HN24 NN2Q CN28 $pd_v 120.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NN2Q CN28 ON2B $pd_v 124.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NN2Q CN28 CN2N $pd_v 115.000 +eval ($pd_v=$pd_x* 960.0) ANGLE ON2B CN28 CN2N $pd_v 121.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN28 CN2N CN24 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN28 CN2N CN29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN24 CN2N CN29 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2N CN24 NN20 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2N CN29 CN2P $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN29 CN2P CN2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2P CN2G NN20 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN24 NN20 CN2G $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN24 NN20 CN2I $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2G NN20 CN2I $pd_v 120.000 +eval ($pd_v=$pd_x* 544.0) ANGLE NN20 CN2I ON2D $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE NN20 CN2I CN22 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON2D CN2I CN22 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2I ON2D CN2O $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2I CN22 ON27 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2I CN22 CN2A $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON27 CN22 CN2A $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN22 ON27 HN2M $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN22 CN2A ON2N $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN22 CN2A CN2O $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON2N CN2A CN2O $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN2A ON2N HN2Q $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON2D CN2O CN2A $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ON2D CN2O CN27 $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CN2A CN2O CN27 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2O CN27 ON2L $pd_v 111.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CN27 ON2L PN2D $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2L PN2D ON2U $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2L PN2D ON2F $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2L PN2D ON2R $pd_v 103.000 +eval ($pd_v=$pd_x* 1120.0) ANGLE ON2U PN2D ON2F $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2U PN2D ON2R $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2F PN2D ON2R $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PN2D ON2R PN21 $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2R PN21 ON26 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2R PN21 ON2V $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2R PN21 ON24 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON26 PN21 ON2V $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON26 PN21 ON24 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON2V PN21 ON24 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PN21 ON24 CN25 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON24 CN25 CN2L $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CN25 CN2L ON2H $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CN25 CN2L CN2U $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON2H CN2L CN2U $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2L ON2H CN2E $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2L CN2U ON29 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2L CN2U CN2C $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON29 CN2U CN2C $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN2U ON29 HN2B $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2U CN2C ON22 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN2U CN2C CN2E $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON22 CN2C CN2E $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN2C ON22 HN2I $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON2H CN2E CN2C $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ON2H CN2E NN2T $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CN2C CN2E NN2T $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2E NN2T CN2W $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2E NN2T CN2Q $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2W NN2T CN2Q $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN2T CN2W NN25 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2W NN25 CN2S $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN25 CN2S CN2Q $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN25 CN2S CN2R $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2Q CN2S CN2R $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN2T CN2Q CN2S $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN2T CN2Q NN2H $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2S CN2Q NN2H $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2Q NN2H CN2F $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN2H CN2F NN2I $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2F NN2I CN2R $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2S CN2R NN2I $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2S CN2R NN24 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN2I CN2R NN24 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CN2R NN24 HN2K $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CN2R NN24 HN26 $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HN2K NN24 HN26 $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NN2Q HN27 HN24 CN28 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN28 NN2Q CN2N ON2B $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2N CN29 CN24 CN28 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN20 CN2I CN2G CN24 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN2T CN2E CN2W CN2Q $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2S CN2R CN2Q NN25 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2Q NN2H CN2S NN2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2R CN2S NN2I NN24 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN24 CN2R HN2K HN26 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CN2I NN20 ON2D CN22 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN22 CN2I ON27 CN2A $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2A CN22 ON2N CN2O $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2O ON2D CN27 CN2A $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PN2D ON2L ON2F ON2U $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PN21 ON2R ON26 ON2V $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2L CN25 CN2U ON2H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2U CN2L CN2C ON29 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2C CN2U CN2E ON22 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN2E ON2H CN2C NN2T $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NN2T CN2W NN25 CN2S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2W NN25 CN2S CN2Q $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN25 CN2S CN2Q NN2T $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2S CN2Q NN2T CN2W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2Q NN2T CN2W NN25 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2N CN24 NN20 CN2G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN24 NN20 CN2G CN2P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN20 CN2G CN2P CN29 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2G CN2P CN29 CN2N $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2P CN29 CN2N CN24 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN29 CN2N CN24 NN20 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2S CN2Q NN2H CN2F $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2Q NN2H CN2F NN2I $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN2H CN2F NN2I CN2R $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2F NN2I CN2R CN2S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN2I CN2R CN2S CN2Q $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2R CN2S CN2Q NN2H $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 640.0) DIHE CN2N CN28 NN2Q HN27 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN29 CN2N CN28 NN2Q $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.0) DIHE CN24 NN20 CN2I CN22 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NN20 CN2I ON2D CN2O $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE NN20 CN2I CN22 CN2A $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CN27 CN2O ON2D CN2I $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN2I CN22 ON27 HN2M $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN2O CN2A CN22 CN2I $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN22 CN2A ON2N HN2Q $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN22 CN2A CN2O CN27 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE ON2D CN2O CN27 ON2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PN2D ON2L CN27 CN2O $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CN27 ON2L PN2D ON2R $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CN27 ON2L PN2D ON2R $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PN21 ON2R PN2D ON2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PN21 ON2R PN2D ON2L $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PN2D ON2R PN21 ON24 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PN2D ON2R PN21 ON24 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CN25 ON24 PN21 ON2R $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CN25 ON24 PN21 ON2R $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PN21 ON24 CN25 CN2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN2U CN2L CN25 ON24 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CN25 CN2L ON2H CN2E $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN25 CN2L CN2U CN2C $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NN2T CN2E ON2H CN2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN2L CN2U ON29 HN2B $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN2E CN2C CN2U CN2L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN2U CN2C ON22 HN2I $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN2U CN2C CN2E NN2T $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE ON2H CN2E NN2T CN2Q $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CN2S CN2R NN24 HN26 $pd_v 2 180.000 + + +NONBONDED NN2Q 0.10000 2.67270 0.10000 2.40543 +NONBONDED HN27 0.10000 1.42544 0.10000 1.15817 +NONBONDED HN24 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN28 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON2B 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN2N 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN24 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN29 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN2P 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN2G 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN20 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN2I 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON2D 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN22 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON27 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN2M 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN2A 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON2N 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN2Q 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN2O 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN27 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON2L 0.10000 2.58361 0.10000 2.31634 +NONBONDED PN2D 0.10000 3.38542 0.10000 3.11815 +NONBONDED ON2U 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON2F 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON2R 0.10000 2.58361 0.10000 2.31634 +NONBONDED PN21 0.10000 3.38542 0.10000 3.11815 +NONBONDED ON26 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON2V 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON24 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN25 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN2L 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON2H 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN2U 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON29 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN2B 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN2C 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON22 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN2I 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN2E 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN2T 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN2W 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN25 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN2S 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN2Q 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN2H 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN2F 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN2I 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN2R 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN24 0.10000 2.67270 0.10000 2.40543 +NONBONDED HN2K 0.10000 1.42544 0.10000 1.15817 +NONBONDED HN26 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue NAP + + +eval ($pd_v=$pd_x* 17900.0) BOND NN36 HN3X $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NN36 HN3C $pd_v 1.000 +eval ($pd_v=$pd_x* 18000.0) BOND NN36 CN37 $pd_v 1.330 +eval ($pd_v=$pd_x* 24000.0) BOND CN37 ON34 $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CN37 CN3Y $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CN3Y CN35 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN3Y CN3X $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CN35 NN3L $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CN3X CN3S $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN3S CN3M $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CN3M NN3L $pd_v 1.400 +eval ($pd_v=$pd_x* 16000.0) BOND NN3L CN39 $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CN39 ON3U $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN39 CN34 $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ON3U CN3T $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN34 ON3N $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN34 CN3W $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON3N HN3S $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CN3W ON3C $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN3W CN3T $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON3C HN34 $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CN3T CN3G $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CN3G ON30 $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND ON30 PN3X $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PN3X ON35 $pd_v 1.480 +eval ($pd_v=$pd_x* 18000.0) BOND PN3X ON3B $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PN3X ON33 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ON33 PN3P $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PN3P ON3O $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PN3P ON3K $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PN3P ON3Y $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ON3Y CN3R $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CN3R CN3L $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CN3L ON3Z $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN3L CN3Z $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ON3Z CN3U $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CN3Z ON38 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN3Z CN32 $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ON38 HN3F $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CN32 ON3A $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CN32 CN3U $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ON3A PN3Q $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PN3Q ON3M $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PN3Q ON39 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PN3Q ON3W $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CN3U NN3H $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NN3H CN31 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NN3H CN3P $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN31 NN3G $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NN3G CN3V $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN3V CN3P $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN3V CN3B $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN3P NN3M $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NN3M CN3D $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CN3D NN34 $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NN34 CN3B $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CN3B NN3I $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NN3I HN31 $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NN3I HN3W $pd_v 1.000 + +eval ($pd_v=$pd_x* 640.0) ANGLE HN3X NN36 HN3C $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HN3X NN36 CN37 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HN3C NN36 CN37 $pd_v 120.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NN36 CN37 ON34 $pd_v 124.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NN36 CN37 CN3Y $pd_v 115.000 +eval ($pd_v=$pd_x* 960.0) ANGLE ON34 CN37 CN3Y $pd_v 121.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN37 CN3Y CN35 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN37 CN3Y CN3X $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN35 CN3Y CN3X $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3Y CN35 NN3L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3Y CN3X CN3S $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3X CN3S CN3M $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3S CN3M NN3L $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN35 NN3L CN3M $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN35 NN3L CN39 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3M NN3L CN39 $pd_v 120.000 +eval ($pd_v=$pd_x* 544.0) ANGLE NN3L CN39 ON3U $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE NN3L CN39 CN34 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3U CN39 CN34 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN39 ON3U CN3T $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN39 CN34 ON3N $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN39 CN34 CN3W $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3N CN34 CN3W $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN34 ON3N HN3S $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN34 CN3W ON3C $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN34 CN3W CN3T $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3C CN3W CN3T $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN3W ON3C HN34 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3U CN3T CN3W $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ON3U CN3T CN3G $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CN3W CN3T CN3G $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3T CN3G ON30 $pd_v 111.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CN3G ON30 PN3X $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON30 PN3X ON35 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON30 PN3X ON3B $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON30 PN3X ON33 $pd_v 103.000 +eval ($pd_v=$pd_x* 1120.0) ANGLE ON35 PN3X ON3B $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON35 PN3X ON33 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3B PN3X ON33 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PN3X ON33 PN3P $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON33 PN3P ON3O $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON33 PN3P ON3K $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON33 PN3P ON3Y $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3O PN3P ON3K $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3O PN3P ON3Y $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3K PN3P ON3Y $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PN3P ON3Y CN3R $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3Y CN3R CN3L $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CN3R CN3L ON3Z $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CN3R CN3L CN3Z $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3Z CN3L CN3Z $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3L ON3Z CN3U $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3L CN3Z ON38 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3L CN3Z CN32 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON38 CN3Z CN32 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN3Z ON38 HN3F $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3Z CN32 ON3A $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CN3Z CN32 CN3U $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3A CN32 CN3U $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CN32 ON3A PN3Q $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3A PN3Q ON3M $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3A PN3Q ON39 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3A PN3Q ON3W $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3M PN3Q ON39 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ON3M PN3Q ON3W $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ON39 PN3Q ON3W $pd_v 109.600 +eval ($pd_v=$pd_x* 880.0) ANGLE ON3Z CN3U CN32 $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ON3Z CN3U NN3H $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CN32 CN3U NN3H $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3U NN3H CN31 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3U NN3H CN3P $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN31 NN3H CN3P $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3H CN31 NN3G $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN31 NN3G CN3V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3G CN3V CN3P $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3G CN3V CN3B $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3P CN3V CN3B $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3H CN3P CN3V $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3H CN3P NN3M $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3V CN3P NN3M $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3P NN3M CN3D $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN3M CN3D NN34 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3D NN34 CN3B $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3V CN3B NN34 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN3V CN3B NN3I $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN34 CN3B NN3I $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CN3B NN3I HN31 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CN3B NN3I HN3W $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HN31 NN3I HN3W $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NN36 HN3X HN3C CN37 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN37 NN36 CN3Y ON34 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3Y CN3X CN35 CN37 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3L CN39 CN3M CN35 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3H CN3U CN31 CN3P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3V CN3B CN3P NN3G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3P NN3M CN3V NN3H $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3B CN3V NN34 NN3I $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3I CN3B HN31 HN3W $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CN39 NN3L ON3U CN34 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN34 CN39 ON3N CN3W $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN3W CN34 ON3C CN3T $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN3T ON3U CN3G CN3W $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PN3X ON30 ON3B ON35 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PN3P ON33 ON3K ON3O $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN3L CN3R CN3Z ON3Z $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN3Z CN3L CN32 ON38 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN32 CN3Z CN3U ON3A $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PN3Q ON3A ON39 ON3M $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CN3U ON3Z CN32 NN3H $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NN3H CN31 NN3G CN3V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN31 NN3G CN3V CN3P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3G CN3V CN3P NN3H $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3V CN3P NN3H CN31 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3P NN3H CN31 NN3G $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3Y CN35 NN3L CN3M $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN35 NN3L CN3M CN3S $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3L CN3M CN3S CN3X $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3M CN3S CN3X CN3Y $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3S CN3X CN3Y CN35 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3X CN3Y CN35 NN3L $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3V CN3P NN3M CN3D $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3P NN3M CN3D NN34 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3M CN3D NN34 CN3B $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3D NN34 CN3B CN3V $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN34 CN3B CN3V CN3P $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN3B CN3V CN3P NN3M $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 640.0) DIHE CN3Y CN37 NN36 HN3X $pd_v 2 180.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3X CN3Y CN37 NN36 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.0) DIHE CN35 NN3L CN39 CN34 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NN3L CN39 ON3U CN3T $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE NN3L CN39 CN34 CN3W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CN3G CN3T ON3U CN39 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN39 CN34 ON3N HN3S $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3T CN3W CN34 CN39 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN34 CN3W ON3C HN34 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN34 CN3W CN3T CN3G $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE ON3U CN3T CN3G ON30 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PN3X ON30 CN3G CN3T $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CN3G ON30 PN3X ON33 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CN3G ON30 PN3X ON33 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PN3P ON33 PN3X ON30 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PN3P ON33 PN3X ON30 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PN3X ON33 PN3P ON3Y $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PN3X ON33 PN3P ON3Y $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CN3R ON3Y PN3P ON33 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CN3R ON3Y PN3P ON33 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PN3P ON3Y CN3R CN3L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3Z CN3L CN3R ON3Y $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CN3R CN3L ON3Z CN3U $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3R CN3L CN3Z CN32 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NN3H CN3U ON3Z CN3L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN3L CN3Z ON38 HN3F $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3U CN32 CN3Z CN3L $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CN3Z CN32 ON3A PN3Q $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CN3Z CN32 CN3U NN3H $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CN32 ON3A PN3Q ON3W $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CN32 ON3A PN3Q ON3W $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE ON3Z CN3U NN3H CN3P $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CN3V CN3B NN3I HN3W $pd_v 2 180.000 + + +NONBONDED NN36 0.10000 2.67270 0.10000 2.40543 +NONBONDED HN3X 0.10000 1.42544 0.10000 1.15817 +NONBONDED HN3C 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN37 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON34 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN3Y 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN35 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3X 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3S 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3M 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3L 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN39 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON3U 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN34 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON3N 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN3S 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN3W 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON3C 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN34 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN3T 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3G 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON30 0.10000 2.58361 0.10000 2.31634 +NONBONDED PN3X 0.10000 3.38542 0.10000 3.11815 +NONBONDED ON35 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON3B 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON33 0.10000 2.58361 0.10000 2.31634 +NONBONDED PN3P 0.10000 3.38542 0.10000 3.11815 +NONBONDED ON3O 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON3K 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON3Y 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN3R 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3L 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON3Z 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN3Z 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON38 0.10000 2.58361 0.10000 2.31634 +NONBONDED HN3F 0.10000 1.42544 0.10000 1.15817 +NONBONDED CN32 0.10000 3.29633 0.10000 3.02906 +NONBONDED ON3A 0.10000 2.58361 0.10000 2.31634 +NONBONDED PN3Q 0.10000 3.38542 0.10000 3.11815 +NONBONDED ON3M 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON39 0.10000 2.58361 0.10000 2.31634 +NONBONDED ON3W 0.10000 2.58361 0.10000 2.31634 +NONBONDED CN3U 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3H 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN31 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3G 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN3V 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN3P 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3M 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN3D 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN34 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN3B 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3I 0.10000 2.67270 0.10000 2.40543 +NONBONDED HN31 0.10000 1.42544 0.10000 1.15817 +NONBONDED HN3W 0.10000 1.42544 0.10000 1.15817 + + + +! Adding parameter definition for residue NDP + + +eval ($pd_v=$pd_x* 17900.0) BOND NNPN HNPG $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NNPN HNPM $pd_v 1.000 +eval ($pd_v=$pd_x* 18000.0) BOND NNPN CNP1 $pd_v 1.330 +eval ($pd_v=$pd_x* 24000.0) BOND CNP1 ONPY $pd_v 1.230 +eval ($pd_v=$pd_x* 16000.0) BOND CNP1 CNP6 $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CNP6 CNP2 $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CNP6 CNPL $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CNP2 NNP7 $pd_v 1.400 +eval ($pd_v=$pd_x* 20000.0) BOND CNPL CNP9 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CNP9 CNP7 $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CNP7 NNP7 $pd_v 1.400 +eval ($pd_v=$pd_x* 16000.0) BOND NNP7 CNPI $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CNPI ONPA $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CNPI CNPC $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ONPA CNPO $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CNPC ONPN $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CNPC CNPE $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ONPN HNP5 $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CNPE ONP2 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CNPE CNPO $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ONP2 HNPA $pd_v 1.000 +eval ($pd_v=$pd_x* 12000.0) BOND CNPO CNPP $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CNPP ONPZ $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND ONPZ PNP4 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PNP4 ONPG $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PNP4 ONPM $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PNP4 ONPF $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ONPF PNPT $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PNPT ONP5 $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PNPT ONPB $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND PNPT ONP6 $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND ONP6 CNPU $pd_v 1.430 +eval ($pd_v=$pd_x* 12000.0) BOND CNPU CNPG $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND CNPG ONPU $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CNPG CNPY $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ONPU CNP0 $pd_v 1.435 +eval ($pd_v=$pd_x* 16000.0) BOND CNPY ONPW $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CNPY CNPF $pd_v 1.530 +eval ($pd_v=$pd_x* 15000.0) BOND ONPW HNPH $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CNPF ONP8 $pd_v 1.430 +eval ($pd_v=$pd_x* 16000.0) BOND CNPF CNP0 $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND ONP8 PNPL $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PNPL ONPO $pd_v 1.610 +eval ($pd_v=$pd_x* 12000.0) BOND PNPL ONPV $pd_v 1.610 +eval ($pd_v=$pd_x* 18000.0) BOND PNPL ONPX $pd_v 1.480 +eval ($pd_v=$pd_x* 12000.0) BOND CNP0 NNPK $pd_v 1.480 +eval ($pd_v=$pd_x* 20000.0) BOND NNPK CNPN $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NNPK CNP4 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CNPN NNPR $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NNPR CNPK $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CNPK CNP4 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CNPK CNP8 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CNP4 NNPG $pd_v 1.340 +eval ($pd_v=$pd_x* 20000.0) BOND NNPG CNPT $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND CNPT NNPF $pd_v 1.320 +eval ($pd_v=$pd_x* 20000.0) BOND NNPF CNP8 $pd_v 1.340 +eval ($pd_v=$pd_x* 18000.0) BOND CNP8 NNPW $pd_v 1.330 +eval ($pd_v=$pd_x* 17900.0) BOND NNPW HNPX $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NNPW HNPS $pd_v 1.000 + +eval ($pd_v=$pd_x* 640.0) ANGLE HNPG NNPN HNPM $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HNPG NNPN CNP1 $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE HNPM NNPN CNP1 $pd_v 120.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NNPN CNP1 ONPY $pd_v 124.000 +eval ($pd_v=$pd_x* 960.0) ANGLE NNPN CNP1 CNP6 $pd_v 115.000 +eval ($pd_v=$pd_x* 960.0) ANGLE ONPY CNP1 CNP6 $pd_v 121.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP1 CNP6 CNP2 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP1 CNP6 CNPL $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP2 CNP6 CNPL $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP6 CNP2 NNP7 $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CNP6 CNPL CNP9 $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPL CNP9 CNP7 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP9 CNP7 NNP7 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP2 NNP7 CNP7 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP2 NNP7 CNPI $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP7 NNP7 CNPI $pd_v 120.000 +eval ($pd_v=$pd_x* 544.0) ANGLE NNP7 CNPI ONPA $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE NNP7 CNPI CNPC $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPA CNPI CNPC $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPI ONPA CNPO $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPI CNPC ONPN $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPI CNPC CNPE $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPN CNPC CNPE $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CNPC ONPN HNP5 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPC CNPE ONP2 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPC CNPE CNPO $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ONP2 CNPE CNPO $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CNPE ONP2 HNPA $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPA CNPO CNPE $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ONPA CNPO CNPP $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CNPE CNPO CNPP $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPO CNPP ONPZ $pd_v 111.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CNPP ONPZ PNP4 $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPZ PNP4 ONPG $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPZ PNP4 ONPM $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPZ PNP4 ONPF $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPG PNP4 ONPM $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPG PNP4 ONPF $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPM PNP4 ONPF $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PNP4 ONPF PNPT $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPF PNPT ONP5 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPF PNPT ONPB $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPF PNPT ONP6 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONP5 PNPT ONPB $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONP5 PNPT ONP6 $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPB PNPT ONP6 $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE PNPT ONP6 CNPU $pd_v 120.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ONP6 CNPU CNPG $pd_v 111.000 +eval ($pd_v=$pd_x* 544.0) ANGLE CNPU CNPG ONPU $pd_v 109.500 +eval ($pd_v=$pd_x* 480.0) ANGLE CNPU CNPG CNPY $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPU CNPG CNPY $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPG ONPU CNP0 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPG CNPY ONPW $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPG CNPY CNPF $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPW CNPY CNPF $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CNPY ONPW HNPH $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPY CNPF ONP8 $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CNPY CNPF CNP0 $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE ONP8 CNPF CNP0 $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CNPF ONP8 PNPL $pd_v 120.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONP8 PNPL ONPO $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONP8 PNPL ONPV $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONP8 PNPL ONPX $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPO PNPL ONPV $pd_v 103.000 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPO PNPL ONPX $pd_v 109.600 +eval ($pd_v=$pd_x* 760.0) ANGLE ONPV PNPL ONPX $pd_v 109.600 +eval ($pd_v=$pd_x* 880.0) ANGLE ONPU CNP0 CNPF $pd_v 104.000 +eval ($pd_v=$pd_x* 544.0) ANGLE ONPU CNP0 NNPK $pd_v 109.500 +eval ($pd_v=$pd_x* 544.0) ANGLE CNPF CNP0 NNPK $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP0 NNPK CNPN $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP0 NNPK CNP4 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPN NNPK CNP4 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPK CNPN NNPR $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPN NNPR CNPK $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPR CNPK CNP4 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPR CNPK CNP8 $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP4 CNPK CNP8 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPK CNP4 CNPK $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPK CNP4 NNPG $pd_v 132.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPK CNP4 NNPG $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNP4 NNPG CNPT $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPG CNPT NNPF $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPT NNPF CNP8 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPK CNP8 NNPF $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNPK CNP8 NNPW $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NNPF CNP8 NNPW $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CNP8 NNPW HNPX $pd_v 120.000 +eval ($pd_v=$pd_x* 560.0) ANGLE CNP8 NNPW HNPS $pd_v 120.000 +eval ($pd_v=$pd_x* 640.0) ANGLE HNPX NNPW HNPS $pd_v 120.000 + +eval ($pd_v=$pd_x* 800.0) IMPR NNPN HNPG HNPM CNP1 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP1 NNPN CNP6 ONPY $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP6 CNPL CNP2 CNP1 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNP7 CNPI CNP7 CNP2 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNPK CNP0 CNPN CNP4 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNPK CNP8 CNP4 NNPR $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP4 NNPG CNPK NNPK $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP8 CNPK NNPF NNPW $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNPW CNP8 HNPX HNPS $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CNPI NNP7 ONPA CNPC $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPC CNPI ONPN CNPE $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPE CNPC ONP2 CNPO $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPO ONPA CNPP CNPE $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PNP4 ONPZ ONPM ONPG $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PNPT ONPF ONP5 ONPB $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPG CNPU CNPY ONPU $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPY CNPG CNPF ONPW $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNPF CNPY CNP0 ONP8 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR PNPL ONP8 ONPV ONPO $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CNP0 ONPU CNPF NNPK $pd_v 0 35.264 +eval ($pd_v=$pd_x* 800.0) IMPR NNPK CNPN NNPR CNPK $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNPN NNPR CNPK CNP4 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNPR CNPK CNP4 NNPK $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNPK CNP4 NNPK CNPN $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP4 NNPK CNPN NNPR $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNPK CNP4 NNPG CNPT $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP4 NNPG CNPT NNPF $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNPG CNPT NNPF CNP8 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNPT NNPF CNP8 CNPK $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NNPF CNP8 CNPK CNP4 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CNP8 CNPK CNP4 NNPG $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 640.0) DIHE CNP6 CNP1 NNPN HNPG $pd_v 2 180.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPL CNP6 CNP1 NNPN $pd_v 2 180.000 +eval ($pd_v=$pd_x* 1000.0) DIHE CNP1 CNP6 CNP2 NNP7 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.1) DIHE CNP1 CNP6 CNPL CNP9 $pd_v 6 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CNP6 CNP2 NNP7 CNPI $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.1) DIHE CNP6 CNPL CNP9 CNP7 $pd_v 6 0.000 +eval ($pd_v=$pd_x* 1000.0) DIHE CNPL CNP9 CNP7 NNP7 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 640.0) DIHE CNP9 CNP7 NNP7 CNPI $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.0) DIHE CNP2 NNP7 CNPI CNPC $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NNP7 CNPI ONPA CNPO $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE NNP7 CNPI CNPC CNPE $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CNPP CNPO ONPA CNPI $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CNPI CNPC ONPN HNP5 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPO CNPE CNPC CNPI $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CNPC CNPE ONP2 HNPA $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPC CNPE CNPO CNPP $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE ONPA CNPO CNPP ONPZ $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PNP4 ONPZ CNPP CNPO $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CNPP ONPZ PNP4 ONPF $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CNPP ONPZ PNP4 ONPF $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PNPT ONPF PNP4 ONPZ $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PNPT ONPF PNP4 ONPZ $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE PNP4 ONPF PNPT ONP6 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE PNP4 ONPF PNPT ONP6 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CNPU ONP6 PNPT ONPF $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CNPU ONP6 PNPT ONPF $pd_v 2 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE PNPT ONP6 CNPU CNPG $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPY CNPG CNPU ONP6 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CNPU CNPG ONPU CNP0 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPU CNPG CNPY CNPF $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE NNPK CNP0 ONPU CNPG $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CNPG CNPY ONPW HNPH $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNP0 CNPF CNPY CNPG $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CNPY CNPF ONP8 PNPL $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CNPY CNPF CNP0 NNPK $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CNPF ONP8 PNPL ONPX $pd_v 3 0.000 +eval ($pd_v=$pd_x* 5.6) DIHE CNPF ONP8 PNPL ONPX $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.0) DIHE ONPU CNP0 NNPK CNP4 $pd_v 2 0.000 +eval ($pd_v=$pd_x* 640.0) DIHE CNPK CNP8 NNPW HNPS $pd_v 2 180.000 + + +NONBONDED NNPN 0.10000 2.67270 0.10000 2.40543 +NONBONDED HNPG 0.10000 1.42544 0.10000 1.15817 +NONBONDED HNPM 0.10000 1.42544 0.10000 1.15817 +NONBONDED CNP1 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPY 0.10000 2.58361 0.10000 2.31634 +NONBONDED CNP6 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNP2 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNPL 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNP9 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNP7 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNP7 0.10000 2.67270 0.10000 2.40543 +NONBONDED CNPI 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPA 0.10000 2.58361 0.10000 2.31634 +NONBONDED CNPC 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPN 0.10000 2.58361 0.10000 2.31634 +NONBONDED HNP5 0.10000 1.42544 0.10000 1.15817 +NONBONDED CNPE 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONP2 0.10000 2.58361 0.10000 2.31634 +NONBONDED HNPA 0.10000 1.42544 0.10000 1.15817 +NONBONDED CNPO 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNPP 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPZ 0.10000 2.58361 0.10000 2.31634 +NONBONDED PNP4 0.10000 3.38542 0.10000 3.11815 +NONBONDED ONPG 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONPM 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONPF 0.10000 2.58361 0.10000 2.31634 +NONBONDED PNPT 0.10000 3.38542 0.10000 3.11815 +NONBONDED ONP5 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONPB 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONP6 0.10000 2.58361 0.10000 2.31634 +NONBONDED CNPU 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNPG 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPU 0.10000 2.58361 0.10000 2.31634 +NONBONDED CNPY 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONPW 0.10000 2.58361 0.10000 2.31634 +NONBONDED HNPH 0.10000 1.42544 0.10000 1.15817 +NONBONDED CNPF 0.10000 3.29633 0.10000 3.02906 +NONBONDED ONP8 0.10000 2.58361 0.10000 2.31634 +NONBONDED PNPL 0.10000 3.38542 0.10000 3.11815 +NONBONDED ONPO 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONPV 0.10000 2.58361 0.10000 2.31634 +NONBONDED ONPX 0.10000 2.58361 0.10000 2.31634 +NONBONDED CNP0 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNPK 0.10000 2.67270 0.10000 2.40543 +NONBONDED CNPN 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNPR 0.10000 2.67270 0.10000 2.40543 +NONBONDED CNPK 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNP4 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNPG 0.10000 2.67270 0.10000 2.40543 +NONBONDED CNPT 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNPF 0.10000 2.67270 0.10000 2.40543 +NONBONDED CNP8 0.10000 3.29633 0.10000 3.02906 +NONBONDED NNPW 0.10000 2.67270 0.10000 2.40543 +NONBONDED HNPX 0.10000 1.42544 0.10000 1.15817 +NONBONDED HNPS 0.10000 1.42544 0.10000 1.15817 + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.pep b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.pep new file mode 100644 index 0000000000000000000000000000000000000000..139597f9cb07c5d48bed18984ec4747f4b4f3438 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.pep @@ -0,0 +1,2 @@ + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.top new file mode 100644 index 0000000000000000000000000000000000000000..e6c4dc39d9419aa61f9c83c2421b1ed276f03a69 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/cofactors.top @@ -0,0 +1,2934 @@ +REMARKS file toppar/cofactors.top +REMARKS Victor Reys - 19/03/2025 +REMARKS Topologies added for common co-factors +REMARKS ADN-ADP-AMP-ATP-CIT-FAD-FLC-GDP-GMP-GTP-NAD-NAP-NDP + +! History: +! Victor Reys - 19/03/2025 +! - Topology taken from PRODRG version 070118.0614 +! - AtomType midfix for ADN: A0 +! - AtomType midfix for ADP: A2 +! - AtomType midfix for AMP: A1 +! - AtomType midfix for ATP: A3 +! - AtomType midfix for CIT: CI +! - AtomType midfix for FAD: F2 +! - AtomType midfix for FLC: CT +! - AtomType midfix for GDP: G2 +! - AtomType midfix for GMP: G1 +! - AtomType midfix for GTP: G3 +! - AtomType midfix for NAD: N2 +! - AtomType midfix for NAP: N3 +! - AtomType midfix for NDP: NP + + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +autogenerate + angles=true + dihedrals=false +end + + +! Adding topology definition for residue ADN + +MASS OA0L 15.9994 ! equivalent to OA +MASS HA04 1.0080 ! equivalent to HO +MASS CA00 13.0190 ! equivalent to CH1 +MASS CA0G 13.0190 ! equivalent to CH1 +MASS OA0O 15.9994 ! equivalent to OA +MASS HA0P 1.0080 ! equivalent to HO +MASS CA0N 13.0190 ! equivalent to CS1 +MASS CA0O 14.0270 ! equivalent to CH2 +MASS OA0M 15.9994 ! equivalent to OA +MASS HA0K 1.0080 ! equivalent to HO +MASS OA0S 15.9994 ! equivalent to OS +MASS CA0T 13.0190 ! equivalent to CS1 +MASS NA0X 14.0067 ! equivalent to NR5* +MASS CA0L 13.0190 ! equivalent to CR51 +MASS NA0O 14.0067 ! equivalent to NR5 +MASS CA04 12.0110 ! equivalent to CB +MASS CA0D 12.0110 ! equivalent to CB +MASS NA0E 14.0067 ! equivalent to NR6 +MASS CA0E 13.0190 ! equivalent to CR61 +MASS NA0N 14.0067 ! equivalent to NR6 +MASS CA0U 12.0110 ! equivalent to CB +MASS NA09 14.0067 ! equivalent to NT +MASS HA05 1.0080 ! equivalent to H +MASS HA0O 1.0080 ! equivalent to H + +RESIdue ADN +GROUP + ATOM O2' TYPE= OA0L CHARGE=-0.168 END + ATOM HO2' TYPE= HA04 CHARGE= 0.070 END + ATOM C2' TYPE= CA00 CHARGE= 0.148 END + ATOM C3' TYPE= CA0G CHARGE= 0.148 END + ATOM O3' TYPE= OA0O CHARGE=-0.168 END + ATOM HO3' TYPE= HA0P CHARGE= 0.070 END + ATOM C4' TYPE= CA0N CHARGE= 0.235 END + ATOM C5' TYPE= CA0O CHARGE= 0.085 END + ATOM O5' TYPE= OA0M CHARGE=-0.168 END + ATOM HO5' TYPE= HA0K CHARGE= 0.070 END + ATOM O4' TYPE= OA0S CHARGE=-0.159 END + ATOM C1' TYPE= CA0T CHARGE= 0.235 END + ATOM N9 TYPE= NA0X CHARGE= 0.255 END + ATOM C8 TYPE= CA0L CHARGE=-0.019 END + ATOM N7 TYPE= NA0O CHARGE=-0.484 END + ATOM C5 TYPE= CA04 CHARGE= 0.155 END + ATOM C4 TYPE= CA0D CHARGE= 0.292 END + ATOM N3 TYPE= NA0E CHARGE=-0.498 END + ATOM C2 TYPE= CA0E CHARGE=-0.019 END + ATOM N1 TYPE= NA0N CHARGE=-0.498 END + ATOM C6 TYPE= CA0U CHARGE= 0.291 END + ATOM N6 TYPE= NA09 CHARGE= 0.079 END + ATOM HN61 TYPE= HA05 CHARGE= 0.024 END + ATOM HN62 TYPE= HA0O CHARGE= 0.024 END + + BOND O2' HO2' + BOND O2' C2' + BOND C2' C3' + BOND C2' C1' + BOND C3' O3' + BOND C3' C4' + BOND O3' HO3' + BOND C4' C5' + BOND C4' O4' + BOND C5' O5' + BOND O5' HO5' + BOND O4' C1' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N1 + BOND N1 C6 + BOND C6 N6 + BOND N6 HN61 + BOND N6 HN62 + + ANGLE HO2' O2' C2' + ANGLE O2' C2' C3' + ANGLE O2' C2' C1' + ANGLE C3' C2' C1' + ANGLE C2' C3' O3' + ANGLE C2' C3' C4' + ANGLE O3' C3' C4' + ANGLE C3' O3' HO3' + ANGLE C3' C4' C5' + ANGLE C3' C4' O4' + ANGLE C5' C4' O4' + ANGLE C4' C5' O5' + ANGLE C5' O5' HO5' + ANGLE C4' O4' C1' + ANGLE C2' C1' O4' + ANGLE C2' C1' N9 + ANGLE O4' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N1 + ANGLE C2 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 N6 + ANGLE N1 C6 N6 + ANGLE C6 N6 HN61 + ANGLE C6 N6 HN62 + ANGLE HN61 N6 HN62 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C6 C5 N1 N6 + IMPROPER N6 C6 HN61 HN62 + IMPROPER C2' O2' C3' C1' + IMPROPER C3' C2' O3' C4' + IMPROPER C4' C3' O4' C5' + IMPROPER C1' C2' N9 O4' + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL C1' C2' O2' HO2' + DIHEDRAL C4' C3' C2' O2' + DIHEDRAL O2' C2' C1' N9 + DIHEDRAL C2' C3' O3' HO3' + DIHEDRAL C2' C3' C4' O4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C3' C4' O4' C1' + DIHEDRAL C4' C5' O5' HO5' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C2' C1' N9 C4 + DIHEDRAL C5 C6 N6 HN62 +END + + +! Adding topology definition for residue ADP + +MASS OA2J 15.9994 ! equivalent to OA +MASS PA2N 30.9738 ! equivalent to P +MASS OA2Z 15.9994 ! equivalent to OA +MASS OA2B 15.9994 ! equivalent to OM +MASS OA2L 15.9994 ! equivalent to OS +MASS PA22 30.9738 ! equivalent to P +MASS OA2N 15.9994 ! equivalent to OA +MASS OA2D 15.9994 ! equivalent to OM +MASS OA2A 15.9994 ! equivalent to OS +MASS CA21 14.0270 ! equivalent to CH2 +MASS CA2W 13.0190 ! equivalent to CS1 +MASS OA2H 15.9994 ! equivalent to OS +MASS CA2K 13.0190 ! equivalent to CH1 +MASS OA2Q 15.9994 ! equivalent to OA +MASS HA2Q 1.0080 ! equivalent to HO +MASS CA2X 13.0190 ! equivalent to CH1 +MASS OA2E 15.9994 ! equivalent to OA +MASS HA22 1.0080 ! equivalent to HO +MASS CA2Z 13.0190 ! equivalent to CS1 +MASS NA2H 14.0067 ! equivalent to NR5* +MASS CA2C 13.0190 ! equivalent to CR51 +MASS NA2B 14.0067 ! equivalent to NR5 +MASS CA2V 12.0110 ! equivalent to CB +MASS CA27 12.0110 ! equivalent to CB +MASS NA27 14.0067 ! equivalent to NR6 +MASS CA2T 13.0190 ! equivalent to CR61 +MASS NA2G 14.0067 ! equivalent to NR6 +MASS CA29 12.0110 ! equivalent to CB +MASS NA29 14.0067 ! equivalent to NT +MASS HA2I 1.0080 ! equivalent to H +MASS HA2C 1.0080 ! equivalent to H + +RESIdue ADP +GROUP + ATOM O2B TYPE= OA2J CHARGE=-1.064 END + ATOM PB TYPE= PA2N CHARGE= 1.206 END + ATOM O3B TYPE= OA2Z CHARGE=-1.064 END + ATOM O1B TYPE= OA2B CHARGE=-0.770 END + ATOM O3A TYPE= OA2L CHARGE=-0.192 END + ATOM PA TYPE= PA22 CHARGE= 1.206 END + ATOM O2A TYPE= OA2N CHARGE=-0.897 END + ATOM O1A TYPE= OA2D CHARGE=-0.604 END + ATOM O5' TYPE= OA2A CHARGE=-0.192 END + ATOM C5' TYPE= CA21 CHARGE= 0.052 END + ATOM C4' TYPE= CA2W CHARGE= 0.202 END + ATOM O4' TYPE= OA2H CHARGE=-0.192 END + ATOM C3' TYPE= CA2K CHARGE= 0.115 END + ATOM O3' TYPE= OA2Q CHARGE=-0.201 END + ATOM HAA TYPE= HA2Q CHARGE= 0.037 END + ATOM C2' TYPE= CA2X CHARGE= 0.115 END + ATOM O2' TYPE= OA2E CHARGE=-0.201 END + ATOM HO2' TYPE= HA22 CHARGE= 0.037 END + ATOM C1' TYPE= CA2Z CHARGE= 0.202 END + ATOM N9 TYPE= NA2H CHARGE= 0.222 END + ATOM C8 TYPE= CA2C CHARGE=-0.052 END + ATOM N7 TYPE= NA2B CHARGE=-0.517 END + ATOM C5 TYPE= CA2V CHARGE= 0.122 END + ATOM C4 TYPE= CA27 CHARGE= 0.258 END + ATOM N3 TYPE= NA27 CHARGE=-0.531 END + ATOM C2 TYPE= CA2T CHARGE=-0.052 END + ATOM N1 TYPE= NA2G CHARGE=-0.531 END + ATOM C6 TYPE= CA29 CHARGE= 0.258 END + ATOM N6 TYPE= NA29 CHARGE= 0.046 END + ATOM HN61 TYPE= HA2I CHARGE=-0.009 END + ATOM HN62 TYPE= HA2C CHARGE=-0.009 END + + BOND O2B PB + BOND PB O3B + BOND PB O1B + BOND PB O3A + BOND O3A PA + BOND PA O2A + BOND PA O1A + BOND PA O5' + BOND O5' C5' + BOND C5' C4' + BOND C4' O4' + BOND C4' C3' + BOND O4' C1' + BOND C3' O3' + BOND C3' C2' + BOND O3' HAA + BOND C2' O2' + BOND C2' C1' + BOND O2' HO2' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N1 + BOND N1 C6 + BOND C6 N6 + BOND N6 HN61 + BOND N6 HN62 + + ANGLE O2B PB O3B + ANGLE O2B PB O1B + ANGLE O2B PB O3A + ANGLE O3B PB O1B + ANGLE O3B PB O3A + ANGLE O1B PB O3A + ANGLE PB O3A PA + ANGLE O3A PA O2A + ANGLE O3A PA O1A + ANGLE O3A PA O5' + ANGLE O2A PA O1A + ANGLE O2A PA O5' + ANGLE O1A PA O5' + ANGLE PA O5' C5' + ANGLE O5' C5' C4' + ANGLE C5' C4' O4' + ANGLE C5' C4' C3' + ANGLE O4' C4' C3' + ANGLE C4' O4' C1' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HAA + ANGLE C3' C2' O2' + ANGLE C3' C2' C1' + ANGLE O2' C2' C1' + ANGLE C2' O2' HO2' + ANGLE O4' C1' C2' + ANGLE O4' C1' N9 + ANGLE C2' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N1 + ANGLE C2 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 N6 + ANGLE N1 C6 N6 + ANGLE C6 N6 HN61 + ANGLE C6 N6 HN62 + ANGLE HN61 N6 HN62 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C6 C5 N1 N6 + IMPROPER N6 C6 HN61 HN62 + IMPROPER PB O2B O3B O1B + IMPROPER PA O3A O2A O1A + IMPROPER C4' C5' C3' O4' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C3' C1' O2' + IMPROPER C1' O4' C2' N9 + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL PA O3A PB O2B + DIHEDRAL PA O3A PB O2B + DIHEDRAL PB O3A PA O5' + DIHEDRAL PB O3A PA O5' + DIHEDRAL C5' O5' PA O3A + DIHEDRAL C5' O5' PA O3A + DIHEDRAL PA O5' C5' C4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C5' C4' O4' C1' + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C4' C3' O3' HAA + DIHEDRAL C1' C2' C3' C4' + DIHEDRAL C3' C2' O2' HO2' + DIHEDRAL C3' C2' C1' N9 + DIHEDRAL O4' C1' N9 C4 + DIHEDRAL C5 C6 N6 HN62 +END + + +! Adding topology definition for residue AMP + +MASS OA1Q 15.9994 ! equivalent to OA +MASS PA1L 30.9738 ! equivalent to P +MASS OA12 15.9994 ! equivalent to OA +MASS OA14 15.9994 ! equivalent to OM +MASS OA1S 15.9994 ! equivalent to OS +MASS CA1H 14.0270 ! equivalent to CH2 +MASS CA1J 13.0190 ! equivalent to CS1 +MASS OA1H 15.9994 ! equivalent to OS +MASS CA1Y 13.0190 ! equivalent to CH1 +MASS OA1C 15.9994 ! equivalent to OA +MASS HA1N 1.0080 ! equivalent to HO +MASS CA1K 13.0190 ! equivalent to CH1 +MASS OA16 15.9994 ! equivalent to OA +MASS HA1H 1.0080 ! equivalent to HO +MASS CA1F 13.0190 ! equivalent to CS1 +MASS NA1V 14.0067 ! equivalent to NR5* +MASS CA19 13.0190 ! equivalent to CR51 +MASS NA17 14.0067 ! equivalent to NR5 +MASS CA1A 12.0110 ! equivalent to CB +MASS CA1U 12.0110 ! equivalent to CB +MASS NA13 14.0067 ! equivalent to NR6 +MASS CA1C 13.0190 ! equivalent to CR61 +MASS NA16 14.0067 ! equivalent to NR6 +MASS CA1L 12.0110 ! equivalent to CB +MASS NA1G 14.0067 ! equivalent to NT +MASS HA1W 1.0080 ! equivalent to H +MASS HA12 1.0080 ! equivalent to H + +RESIdue AMP +GROUP + ATOM O2P TYPE= OA1Q CHARGE=-1.045 END + ATOM P TYPE= PA1L CHARGE= 1.225 END + ATOM O3P TYPE= OA12 CHARGE=-1.045 END + ATOM O1P TYPE= OA14 CHARGE=-0.751 END + ATOM O5' TYPE= OA1S CHARGE=-0.173 END + ATOM C5' TYPE= CA1H CHARGE= 0.071 END + ATOM C4' TYPE= CA1J CHARGE= 0.221 END + ATOM O4' TYPE= OA1H CHARGE=-0.173 END + ATOM C3' TYPE= CA1Y CHARGE= 0.134 END + ATOM O3' TYPE= OA1C CHARGE=-0.182 END + ATOM HAA TYPE= HA1N CHARGE= 0.056 END + ATOM C2' TYPE= CA1K CHARGE= 0.134 END + ATOM O2' TYPE= OA16 CHARGE=-0.182 END + ATOM HO2' TYPE= HA1H CHARGE= 0.056 END + ATOM C1' TYPE= CA1F CHARGE= 0.221 END + ATOM N9 TYPE= NA1V CHARGE= 0.241 END + ATOM C8 TYPE= CA19 CHARGE=-0.033 END + ATOM N7 TYPE= NA17 CHARGE=-0.498 END + ATOM C5 TYPE= CA1A CHARGE= 0.141 END + ATOM C4 TYPE= CA1U CHARGE= 0.277 END + ATOM N3 TYPE= NA13 CHARGE=-0.512 END + ATOM C2 TYPE= CA1C CHARGE=-0.033 END + ATOM N1 TYPE= NA16 CHARGE=-0.512 END + ATOM C6 TYPE= CA1L CHARGE= 0.277 END + ATOM N6 TYPE= NA1G CHARGE= 0.065 END + ATOM HN62 TYPE= HA1W CHARGE= 0.010 END + ATOM HN61 TYPE= HA12 CHARGE= 0.010 END + + BOND O2P P + BOND P O3P + BOND P O1P + BOND P O5' + BOND O5' C5' + BOND C5' C4' + BOND C4' O4' + BOND C4' C3' + BOND O4' C1' + BOND C3' O3' + BOND C3' C2' + BOND O3' HAA + BOND C2' O2' + BOND C2' C1' + BOND O2' HO2' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N1 + BOND N1 C6 + BOND C6 N6 + BOND N6 HN62 + BOND N6 HN61 + + ANGLE O2P P O3P + ANGLE O2P P O1P + ANGLE O2P P O5' + ANGLE O3P P O1P + ANGLE O3P P O5' + ANGLE O1P P O5' + ANGLE P O5' C5' + ANGLE O5' C5' C4' + ANGLE C5' C4' O4' + ANGLE C5' C4' C3' + ANGLE O4' C4' C3' + ANGLE C4' O4' C1' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HAA + ANGLE C3' C2' O2' + ANGLE C3' C2' C1' + ANGLE O2' C2' C1' + ANGLE C2' O2' HO2' + ANGLE O4' C1' C2' + ANGLE O4' C1' N9 + ANGLE C2' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N1 + ANGLE C2 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 N6 + ANGLE N1 C6 N6 + ANGLE C6 N6 HN62 + ANGLE C6 N6 HN61 + ANGLE HN62 N6 HN61 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C6 C5 N1 N6 + IMPROPER N6 C6 HN62 HN61 + IMPROPER P O2P O1P O3P + IMPROPER C4' C5' C3' O4' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C3' C1' O2' + IMPROPER C1' O4' C2' N9 + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL C5' O5' P O2P + DIHEDRAL C5' O5' P O2P + DIHEDRAL P O5' C5' C4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C5' C4' O4' C1' + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C4' C3' O3' HAA + DIHEDRAL C1' C2' C3' C4' + DIHEDRAL C3' C2' O2' HO2' + DIHEDRAL C3' C2' C1' N9 + DIHEDRAL O4' C1' N9 C4 + DIHEDRAL C5 C6 N6 HN61 +END + + +! Adding topology definition for residue ATP + +MASS OA3H 15.9994 ! equivalent to OA +MASS PA3Q 30.9738 ! equivalent to P +MASS OA3D 15.9994 ! equivalent to OA +MASS OA3S 15.9994 ! equivalent to OM +MASS OA3U 15.9994 ! equivalent to OS +MASS PA38 30.9738 ! equivalent to P +MASS OA3Z 15.9994 ! equivalent to OA +MASS OA3O 15.9994 ! equivalent to OM +MASS OA3H 15.9994 ! equivalent to OS +MASS PA3N 30.9738 ! equivalent to P +MASS OA39 15.9994 ! equivalent to OA +MASS OA3T 15.9994 ! equivalent to OM +MASS OA36 15.9994 ! equivalent to OS +MASS CA31 14.0270 ! equivalent to CH2 +MASS CA3K 13.0190 ! equivalent to CS1 +MASS OA32 15.9994 ! equivalent to OS +MASS CA3E 13.0190 ! equivalent to CH1 +MASS OA34 15.9994 ! equivalent to OA +MASS HA37 1.0080 ! equivalent to HO +MASS CA33 13.0190 ! equivalent to CH1 +MASS OA3E 15.9994 ! equivalent to OA +MASS HA3W 1.0080 ! equivalent to HO +MASS CA37 13.0190 ! equivalent to CS1 +MASS NA3X 14.0067 ! equivalent to NR5* +MASS CA3P 13.0190 ! equivalent to CR51 +MASS NA3U 14.0067 ! equivalent to NR5 +MASS CA32 12.0110 ! equivalent to CB +MASS CA3L 12.0110 ! equivalent to CB +MASS NA3G 14.0067 ! equivalent to NR6 +MASS CA3F 13.0190 ! equivalent to CR61 +MASS NA3N 14.0067 ! equivalent to NR6 +MASS CA34 12.0110 ! equivalent to CB +MASS NA3M 14.0067 ! equivalent to NT +MASS HA3Q 1.0080 ! equivalent to H +MASS HA35 1.0080 ! equivalent to H + +RESIdue ATP +GROUP + ATOM O2G TYPE= OA3H CHARGE=-1.078 END + ATOM PG TYPE= PA3Q CHARGE= 1.191 END + ATOM O3G TYPE= OA3D CHARGE=-1.079 END + ATOM O1G TYPE= OA3S CHARGE=-0.785 END + ATOM O3B TYPE= OA3U CHARGE=-0.206 END + ATOM PB TYPE= PA38 CHARGE= 1.191 END + ATOM O2B TYPE= OA3Z CHARGE=-0.912 END + ATOM O1B TYPE= OA3O CHARGE=-0.618 END + ATOM O3A TYPE= OA3H CHARGE=-0.206 END + ATOM PA TYPE= PA3N CHARGE= 1.191 END + ATOM O2A TYPE= OA39 CHARGE=-0.912 END + ATOM O1A TYPE= OA3T CHARGE=-0.618 END + ATOM O5' TYPE= OA36 CHARGE=-0.206 END + ATOM C5' TYPE= CA31 CHARGE= 0.037 END + ATOM C4' TYPE= CA3K CHARGE= 0.187 END + ATOM O4' TYPE= OA32 CHARGE=-0.206 END + ATOM C3' TYPE= CA3E CHARGE= 0.100 END + ATOM O3' TYPE= OA34 CHARGE=-0.215 END + ATOM HAA TYPE= HA37 CHARGE= 0.022 END + ATOM C2' TYPE= CA33 CHARGE= 0.100 END + ATOM O2' TYPE= OA3E CHARGE=-0.215 END + ATOM HO2' TYPE= HA3W CHARGE= 0.022 END + ATOM C1' TYPE= CA37 CHARGE= 0.187 END + ATOM N9 TYPE= NA3X CHARGE= 0.208 END + ATOM C8 TYPE= CA3P CHARGE=-0.068 END + ATOM N7 TYPE= NA3U CHARGE=-0.532 END + ATOM C5 TYPE= CA32 CHARGE= 0.108 END + ATOM C4 TYPE= CA3L CHARGE= 0.244 END + ATOM N3 TYPE= NA3G CHARGE=-0.546 END + ATOM C2 TYPE= CA3F CHARGE=-0.067 END + ATOM N1 TYPE= NA3N CHARGE=-0.546 END + ATOM C6 TYPE= CA34 CHARGE= 0.244 END + ATOM N6 TYPE= NA3M CHARGE= 0.031 END + ATOM HN61 TYPE= HA3Q CHARGE=-0.024 END + ATOM HN62 TYPE= HA35 CHARGE=-0.024 END + + BOND O2G PG + BOND PG O3G + BOND PG O1G + BOND PG O3B + BOND O3B PB + BOND PB O2B + BOND PB O1B + BOND PB O3A + BOND O3A PA + BOND PA O2A + BOND PA O1A + BOND PA O5' + BOND O5' C5' + BOND C5' C4' + BOND C4' O4' + BOND C4' C3' + BOND O4' C1' + BOND C3' O3' + BOND C3' C2' + BOND O3' HAA + BOND C2' O2' + BOND C2' C1' + BOND O2' HO2' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N1 + BOND N1 C6 + BOND C6 N6 + BOND N6 HN61 + BOND N6 HN62 + + ANGLE O2G PG O3G + ANGLE O2G PG O1G + ANGLE O2G PG O3B + ANGLE O3G PG O1G + ANGLE O3G PG O3B + ANGLE O1G PG O3B + ANGLE PG O3B PB + ANGLE O3B PB O2B + ANGLE O3B PB O1B + ANGLE O3B PB O3A + ANGLE O2B PB O1B + ANGLE O2B PB O3A + ANGLE O1B PB O3A + ANGLE PB O3A PA + ANGLE O3A PA O2A + ANGLE O3A PA O1A + ANGLE O3A PA O5' + ANGLE O2A PA O1A + ANGLE O2A PA O5' + ANGLE O1A PA O5' + ANGLE PA O5' C5' + ANGLE O5' C5' C4' + ANGLE C5' C4' O4' + ANGLE C5' C4' C3' + ANGLE O4' C4' C3' + ANGLE C4' O4' C1' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HAA + ANGLE C3' C2' O2' + ANGLE C3' C2' C1' + ANGLE O2' C2' C1' + ANGLE C2' O2' HO2' + ANGLE O4' C1' C2' + ANGLE O4' C1' N9 + ANGLE C2' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N1 + ANGLE C2 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 N6 + ANGLE N1 C6 N6 + ANGLE C6 N6 HN61 + ANGLE C6 N6 HN62 + ANGLE HN61 N6 HN62 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C6 C5 N1 N6 + IMPROPER N6 C6 HN61 HN62 + IMPROPER PG O2G O3G O1G + IMPROPER PB O3B O2B O1B + IMPROPER PA O3A O1A O2A + IMPROPER C4' C5' C3' O4' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C3' C1' O2' + IMPROPER C1' O4' C2' N9 + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL PB O3B PG O2G + DIHEDRAL PB O3B PG O2G + DIHEDRAL PG O3B PB O3A + DIHEDRAL PG O3B PB O3A + DIHEDRAL PA O3A PB O3B + DIHEDRAL PA O3A PB O3B + DIHEDRAL PB O3A PA O5' + DIHEDRAL PB O3A PA O5' + DIHEDRAL C5' O5' PA O3A + DIHEDRAL C5' O5' PA O3A + DIHEDRAL PA O5' C5' C4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C5' C4' O4' C1' + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C4' C3' O3' HAA + DIHEDRAL C1' C2' C3' C4' + DIHEDRAL C3' C2' O2' HO2' + DIHEDRAL C3' C2' C1' N9 + DIHEDRAL O4' C1' N9 C4 + DIHEDRAL C5 C6 N6 HN62 +END + + +! Adding topology definition for residue CIT + +MASS OCIM 15.9994 ! equivalent to OM +MASS CCIV 12.0110 ! equivalent to C +MASS OCIX 15.9994 ! equivalent to OM +MASS CCII 14.0270 ! equivalent to CH2 +MASS CCIU 12.0110 ! equivalent to CH0 +MASS CCIY 12.0110 ! equivalent to C +MASS OCIC 15.9994 ! equivalent to OM +MASS OCIT 15.9994 ! equivalent to OM +MASS OCIG 15.9994 ! equivalent to OA +MASS HCIT 1.0080 ! equivalent to HO +MASS CCIE 14.0270 ! equivalent to CH2 +MASS CCIB 12.0110 ! equivalent to C +MASS OCI9 15.9994 ! equivalent to OM +MASS OCID 15.9994 ! equivalent to OM + +RESIdue CIT +GROUP + ATOM O1 TYPE= OCIM CHARGE=-0.734 END + ATOM C1 TYPE= CCIV CHARGE= 0.384 END + ATOM O2 TYPE= OCIX CHARGE=-0.733 END + ATOM C2 TYPE= CCII CHARGE= 0.084 END + ATOM C3 TYPE= CCIU CHARGE= 0.182 END + ATOM C6 TYPE= CCIY CHARGE= 0.384 END + ATOM O6 TYPE= OCIC CHARGE=-0.733 END + ATOM O5 TYPE= OCIT CHARGE=-0.734 END + ATOM O7 TYPE= OCIG CHARGE=-0.169 END + ATOM HO7 TYPE= HCIT CHARGE= 0.067 END + ATOM C4 TYPE= CCIE CHARGE= 0.084 END + ATOM C5 TYPE= CCIB CHARGE= 0.384 END + ATOM O4 TYPE= OCI9 CHARGE=-0.733 END + ATOM O3 TYPE= OCID CHARGE=-0.733 END + + BOND O1 C1 + BOND C1 O2 + BOND C1 C2 + BOND C2 C3 + BOND C3 C6 + BOND C3 O7 + BOND C3 C4 + BOND C6 O6 + BOND C6 O5 + BOND O7 HO7 + BOND C4 C5 + BOND C5 O4 + BOND C5 O3 + + ANGLE O1 C1 O2 + ANGLE O1 C1 C2 + ANGLE O2 C1 C2 + ANGLE C1 C2 C3 + ANGLE C2 C3 C6 + ANGLE C2 C3 O7 + ANGLE C2 C3 C4 + ANGLE C6 C3 O7 + ANGLE C6 C3 C4 + ANGLE O7 C3 C4 + ANGLE C3 C6 O6 + ANGLE C3 C6 O5 + ANGLE O6 C6 O5 + ANGLE C3 O7 HO7 + ANGLE C3 C4 C5 + ANGLE C4 C5 O4 + ANGLE C4 C5 O3 + ANGLE O4 C5 O3 + + IMPROPER C1 C2 O2 O1 + IMPROPER C6 C3 O5 O6 + IMPROPER C5 C4 O3 O4 + IMPROPER C3 C2 O7 C6 + + DIHEDRAL C3 C2 C1 O1 + DIHEDRAL C1 C2 C3 C4 + DIHEDRAL C2 C3 C6 O5 + DIHEDRAL C2 C3 O7 HO7 + DIHEDRAL C5 C4 C3 C2 + DIHEDRAL C3 C4 C5 O3 +END + + +! Adding topology definition for residue FAD + +MASS OF2N 15.9994 ! equivalent to O +MASS CF2T 12.0110 ! equivalent to CB +MASS NF2Y 14.0067 ! equivalent to NR6* +MASS HF2U 1.0080 ! equivalent to H +MASS CF24 12.0110 ! equivalent to CB +MASS OF2G 15.9994 ! equivalent to O +MASS NF2W 14.0067 ! equivalent to NR6* +MASS HF2N 1.0080 ! equivalent to H +MASS CF2V 12.0110 ! equivalent to CB +MASS CF2L 12.0110 ! equivalent to CB +MASS NF2R 14.0067 ! equivalent to NR6* +MASS HF25 1.0080 ! equivalent to H +MASS CF2E 12.0110 ! equivalent to CB +MASS CF23 13.0190 ! equivalent to CR61 +MASS CF2M 12.0110 ! equivalent to CB +MASS CF29 15.0350 ! equivalent to CH3 +MASS CF27 12.0110 ! equivalent to CB +MASS CF2D 15.0350 ! equivalent to CH3 +MASS CF21 13.0190 ! equivalent to CR61 +MASS CF2G 12.0110 ! equivalent to CB +MASS NF2G 14.0067 ! equivalent to NR6* +MASS CF2W 14.0270 ! equivalent to CH2 +MASS CF2N 13.0190 ! equivalent to CH1 +MASS OF2M 15.9994 ! equivalent to OA +MASS HF2I 1.0080 ! equivalent to HO +MASS CF22 13.0190 ! equivalent to CH1 +MASS OF22 15.9994 ! equivalent to OA +MASS HF2V 1.0080 ! equivalent to HO +MASS CF2Y 13.0190 ! equivalent to CH1 +MASS OF25 15.9994 ! equivalent to OA +MASS HF27 1.0080 ! equivalent to HO +MASS CF26 14.0270 ! equivalent to CH2 +MASS OF2X 15.9994 ! equivalent to OS +MASS PF2N 30.9738 ! equivalent to P +MASS OF20 15.9994 ! equivalent to OA +MASS OF21 15.9994 ! equivalent to OM +MASS OF2A 15.9994 ! equivalent to OS +MASS PF2S 30.9738 ! equivalent to P +MASS OF2Y 15.9994 ! equivalent to OA +MASS OF2Q 15.9994 ! equivalent to OM +MASS OF2W 15.9994 ! equivalent to OS +MASS CF2U 14.0270 ! equivalent to CH2 +MASS CF2K 13.0190 ! equivalent to CS1 +MASS OF2V 15.9994 ! equivalent to OS +MASS CF2Q 13.0190 ! equivalent to CH1 +MASS OF2E 15.9994 ! equivalent to OA +MASS HF2X 1.0080 ! equivalent to HO +MASS CF2R 13.0190 ! equivalent to CH1 +MASS OF2C 15.9994 ! equivalent to OA +MASS HF2F 1.0080 ! equivalent to HO +MASS CF20 13.0190 ! equivalent to CS1 +MASS NF2O 14.0067 ! equivalent to NR5* +MASS CF2B 13.0190 ! equivalent to CR51 +MASS NF2X 14.0067 ! equivalent to NR5 +MASS CF2S 12.0110 ! equivalent to CB +MASS CF25 12.0110 ! equivalent to CB +MASS NF2Z 14.0067 ! equivalent to NR6 +MASS CF2F 13.0190 ! equivalent to CR61 +MASS NF21 14.0067 ! equivalent to NR6 +MASS CF2A 12.0110 ! equivalent to CB +MASS NF29 14.0067 ! equivalent to NT +MASS HF2C 1.0080 ! equivalent to H +MASS HF2K 1.0080 ! equivalent to H + +RESIdue FAD +GROUP + ATOM O4 TYPE= OF2N CHARGE=-0.712 END + ATOM C4 TYPE= CF2T CHARGE= 0.260 END + ATOM N3 TYPE= NF2Y CHARGE= 0.026 END + ATOM HN3 TYPE= HF2U CHARGE=-0.008 END + ATOM C2 TYPE= CF24 CHARGE= 0.362 END + ATOM O2 TYPE= OF2G CHARGE=-0.712 END + ATOM N1 TYPE= NF2W CHARGE= 0.026 END + ATOM HAF TYPE= HF2N CHARGE=-0.008 END + ATOM C10 TYPE= CF2V CHARGE= 0.260 END + ATOM C4X TYPE= CF2L CHARGE= 0.124 END + ATOM N5 TYPE= NF2R CHARGE= 0.026 END + ATOM HAH TYPE= HF25 CHARGE=-0.008 END + ATOM C5X TYPE= CF2E CHARGE= 0.124 END + ATOM C6 TYPE= CF23 CHARGE=-0.051 END + ATOM C7 TYPE= CF2M CHARGE=-0.030 END + ATOM C7M TYPE= CF29 CHARGE= 0.016 END + ATOM C8 TYPE= CF27 CHARGE=-0.030 END + ATOM C8M TYPE= CF2D CHARGE= 0.016 END + ATOM C9 TYPE= CF21 CHARGE=-0.051 END + ATOM C9A TYPE= CF2G CHARGE= 0.124 END + ATOM N10 TYPE= NF2G CHARGE= 0.026 END + ATOM C1' TYPE= CF2W CHARGE= 0.053 END + ATOM C2' TYPE= CF2N CHARGE= 0.116 END + ATOM O2' TYPE= OF2M CHARGE=-0.199 END + ATOM HAC TYPE= HF2I CHARGE= 0.038 END + ATOM C3' TYPE= CF22 CHARGE= 0.116 END + ATOM O3' TYPE= OF22 CHARGE=-0.199 END + ATOM HAD TYPE= HF2V CHARGE= 0.038 END + ATOM C4' TYPE= CF2Y CHARGE= 0.116 END + ATOM O4' TYPE= OF25 CHARGE=-0.199 END + ATOM HAE TYPE= HF27 CHARGE= 0.038 END + ATOM C5' TYPE= CF26 CHARGE= 0.053 END + ATOM O5' TYPE= OF2X CHARGE=-0.190 END + ATOM P TYPE= PF2N CHARGE= 1.207 END + ATOM O2P TYPE= OF20 CHARGE=-0.896 END + ATOM O1P TYPE= OF21 CHARGE=-0.602 END + ATOM O3P TYPE= OF2A CHARGE=-0.190 END + ATOM PA TYPE= PF2S CHARGE= 1.207 END + ATOM O2A TYPE= OF2Y CHARGE=-0.896 END + ATOM O1A TYPE= OF2Q CHARGE=-0.602 END + ATOM O5B TYPE= OF2W CHARGE=-0.190 END + ATOM C5B TYPE= CF2U CHARGE= 0.053 END + ATOM C4B TYPE= CF2K CHARGE= 0.203 END + ATOM O4B TYPE= OF2V CHARGE=-0.189 END + ATOM C3B TYPE= CF2Q CHARGE= 0.116 END + ATOM O3B TYPE= OF2E CHARGE=-0.199 END + ATOM HAA TYPE= HF2X CHARGE= 0.038 END + ATOM C2B TYPE= CF2R CHARGE= 0.116 END + ATOM O2B TYPE= OF2C CHARGE=-0.199 END + ATOM HO2A TYPE= HF2F CHARGE= 0.038 END + ATOM C1B TYPE= CF20 CHARGE= 0.203 END + ATOM N9A TYPE= NF2O CHARGE= 0.224 END + ATOM C8A TYPE= CF2B CHARGE=-0.051 END + ATOM N7A TYPE= NF2X CHARGE=-0.516 END + ATOM C5A TYPE= CF2S CHARGE= 0.124 END + ATOM C4A TYPE= CF25 CHARGE= 0.260 END + ATOM N3A TYPE= NF2Z CHARGE=-0.530 END + ATOM C2A TYPE= CF2F CHARGE=-0.051 END + ATOM N1A TYPE= NF21 CHARGE=-0.530 END + ATOM C6A TYPE= CF2A CHARGE= 0.260 END + ATOM N6A TYPE= NF29 CHARGE= 0.047 END + ATOM H61A TYPE= HF2C CHARGE=-0.008 END + ATOM H62A TYPE= HF2K CHARGE=-0.008 END + + BOND O4 C4 + BOND C4 N3 + BOND C4 C4X + BOND N3 HN3 + BOND N3 C2 + BOND C2 O2 + BOND C2 N1 + BOND N1 HAF + BOND N1 C10 + BOND C10 C4X + BOND C10 N10 + BOND C4X N5 + BOND N5 HAH + BOND N5 C5X + BOND C5X C6 + BOND C5X C9A + BOND C6 C7 + BOND C7 C7M + BOND C7 C8 + BOND C8 C8M + BOND C8 C9 + BOND C9 C9A + BOND C9A N10 + BOND N10 C1' + BOND C1' C2' + BOND C2' O2' + BOND C2' C3' + BOND O2' HAC + BOND C3' O3' + BOND C3' C4' + BOND O3' HAD + BOND C4' O4' + BOND C4' C5' + BOND O4' HAE + BOND C5' O5' + BOND O5' P + BOND P O2P + BOND P O1P + BOND P O3P + BOND O3P PA + BOND PA O2A + BOND PA O1A + BOND PA O5B + BOND O5B C5B + BOND C5B C4B + BOND C4B O4B + BOND C4B C3B + BOND O4B C1B + BOND C3B O3B + BOND C3B C2B + BOND O3B HAA + BOND C2B O2B + BOND C2B C1B + BOND O2B HO2A + BOND C1B N9A + BOND N9A C8A + BOND N9A C4A + BOND C8A N7A + BOND N7A C5A + BOND C5A C4A + BOND C5A C6A + BOND C4A N3A + BOND N3A C2A + BOND C2A N1A + BOND N1A C6A + BOND C6A N6A + BOND N6A H61A + BOND N6A H62A + + ANGLE O4 C4 N3 + ANGLE O4 C4 C4X + ANGLE N3 C4 C4X + ANGLE C4 N3 HN3 + ANGLE C4 N3 C2 + ANGLE HN3 N3 C2 + ANGLE N3 C2 O2 + ANGLE N3 C2 N1 + ANGLE O2 C2 N1 + ANGLE C2 N1 HAF + ANGLE C2 N1 C10 + ANGLE HAF N1 C10 + ANGLE N1 C10 C4X + ANGLE N1 C10 N10 + ANGLE C4X C10 N10 + ANGLE C4 C4X C10 + ANGLE C4 C4X N5 + ANGLE C10 C4X N5 + ANGLE C4X N5 HAH + ANGLE C4X N5 C5X + ANGLE HAH N5 C5X + ANGLE N5 C5X C6 + ANGLE N5 C5X C9A + ANGLE C6 C5X C9A + ANGLE C5X C6 C7 + ANGLE C6 C7 C7M + ANGLE C6 C7 C8 + ANGLE C7M C7 C8 + ANGLE C7 C8 C8M + ANGLE C7 C8 C9 + ANGLE C8M C8 C9 + ANGLE C8 C9 C9A + ANGLE C5X C9A C9 + ANGLE C5X C9A N10 + ANGLE C9 C9A N10 + ANGLE C10 N10 C9A + ANGLE C10 N10 C1' + ANGLE C9A N10 C1' + ANGLE N10 C1' C2' + ANGLE C1' C2' O2' + ANGLE C1' C2' C3' + ANGLE O2' C2' C3' + ANGLE C2' O2' HAC + ANGLE C2' C3' O3' + ANGLE C2' C3' C4' + ANGLE O3' C3' C4' + ANGLE C3' O3' HAD + ANGLE C3' C4' O4' + ANGLE C3' C4' C5' + ANGLE O4' C4' C5' + ANGLE C4' O4' HAE + ANGLE C4' C5' O5' + ANGLE C5' O5' P + ANGLE O5' P O2P + ANGLE O5' P O1P + ANGLE O5' P O3P + ANGLE O2P P O1P + ANGLE O2P P O3P + ANGLE O1P P O3P + ANGLE P O3P PA + ANGLE O3P PA O2A + ANGLE O3P PA O1A + ANGLE O3P PA O5B + ANGLE O2A PA O1A + ANGLE O2A PA O5B + ANGLE O1A PA O5B + ANGLE PA O5B C5B + ANGLE O5B C5B C4B + ANGLE C5B C4B O4B + ANGLE C5B C4B C3B + ANGLE O4B C4B C3B + ANGLE C4B O4B C1B + ANGLE C4B C3B O3B + ANGLE C4B C3B C2B + ANGLE O3B C3B C2B + ANGLE C3B O3B HAA + ANGLE C3B C2B O2B + ANGLE C3B C2B C1B + ANGLE O2B C2B C1B + ANGLE C2B O2B HO2A + ANGLE O4B C1B C2B + ANGLE O4B C1B N9A + ANGLE C2B C1B N9A + ANGLE C1B N9A C8A + ANGLE C1B N9A C4A + ANGLE C8A N9A C4A + ANGLE N9A C8A N7A + ANGLE C8A N7A C5A + ANGLE N7A C5A C4A + ANGLE N7A C5A C6A + ANGLE C4A C5A C6A + ANGLE N9A C4A C5A + ANGLE N9A C4A N3A + ANGLE C5A C4A N3A + ANGLE C4A N3A C2A + ANGLE N3A C2A N1A + ANGLE C2A N1A C6A + ANGLE C5A C6A N1A + ANGLE C5A C6A N6A + ANGLE N1A C6A N6A + ANGLE C6A N6A H61A + ANGLE C6A N6A H62A + ANGLE H61A N6A H62A + + IMPROPER C4 C4X N3 O4 + IMPROPER N3 C2 HN3 C4 + IMPROPER C2 N3 N1 O2 + IMPROPER N1 C10 HAF C2 + IMPROPER C10 N1 N10 C4X + IMPROPER C4X N5 C10 C4 + IMPROPER N5 C5X HAH C4X + IMPROPER C5X N5 C9A C6 + IMPROPER C7 C6 C8 C7M + IMPROPER C8 C7 C9 C8M + IMPROPER C9A C5X N10 C9 + IMPROPER N10 C10 C9A C1' + IMPROPER N9A C1B C8A C4A + IMPROPER C5A C6A C4A N7A + IMPROPER C4A N3A C5A N9A + IMPROPER C6A C5A N1A N6A + IMPROPER N6A C6A H61A H62A + IMPROPER C2' C1' O2' C3' + IMPROPER C3' C2' O3' C4' + IMPROPER C4' C3' O4' C5' + IMPROPER P O5' O2P O1P + IMPROPER PA O3P O1A O2A + IMPROPER C4B C5B C3B O4B + IMPROPER C3B C4B C2B O3B + IMPROPER C2B C3B C1B O2B + IMPROPER C1B O4B C2B N9A + IMPROPER N9A C8A N7A C5A + IMPROPER C8A N7A C5A C4A + IMPROPER N7A C5A C4A N9A + IMPROPER C5A C4A N9A C8A + IMPROPER C4A N9A C8A N7A + IMPROPER C5X C6 C7 C8 + IMPROPER C6 C7 C8 C9 + IMPROPER C7 C8 C9 C9A + IMPROPER C8 C9 C9A C5X + IMPROPER C9 C9A C5X C6 + IMPROPER C9A C5X C6 C7 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C10 + IMPROPER C2 N1 C10 C4X + IMPROPER N1 C10 C4X C4 + IMPROPER C10 C4X C4 N3 + IMPROPER C4X C4 N3 C2 + IMPROPER C5A C4A N3A C2A + IMPROPER C4A N3A C2A N1A + IMPROPER N3A C2A N1A C6A + IMPROPER C2A N1A C6A C5A + IMPROPER N1A C6A C5A C4A + IMPROPER C6A C5A C4A N3A + + DIHEDRAL C1' N10 C10 N1 + DIHEDRAL C5X N5 C4X C4 + DIHEDRAL C4X N5 C5X C9A + DIHEDRAL C1' N10 C9A C5X + DIHEDRAL C10 N10 C1' C2' + DIHEDRAL N10 C1' C2' C3' + DIHEDRAL C1' C2' O2' HAC + DIHEDRAL C4' C3' C2' C1' + DIHEDRAL C2' C3' O3' HAD + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL C3' C4' O4' HAE + DIHEDRAL O5' C5' C4' C3' + DIHEDRAL P O5' C5' C4' + DIHEDRAL C5' O5' P O3P + DIHEDRAL C5' O5' P O3P + DIHEDRAL PA O3P P O5' + DIHEDRAL PA O3P P O5' + DIHEDRAL P O3P PA O5B + DIHEDRAL P O3P PA O5B + DIHEDRAL C5B O5B PA O3P + DIHEDRAL C5B O5B PA O3P + DIHEDRAL PA O5B C5B C4B + DIHEDRAL C3B C4B C5B O5B + DIHEDRAL C5B C4B O4B C1B + DIHEDRAL C5B C4B C3B C2B + DIHEDRAL N9A C1B O4B C4B + DIHEDRAL C4B C3B O3B HAA + DIHEDRAL C1B C2B C3B C4B + DIHEDRAL C3B C2B O2B HO2A + DIHEDRAL C3B C2B C1B N9A + DIHEDRAL O4B C1B N9A C4A + DIHEDRAL C5A C6A N6A H62A +END + + +! Adding topology definition for residue FLC + +MASS OCTT 15.9994 ! equivalent to OM +MASS CCT5 12.0110 ! equivalent to C +MASS OCT7 15.9994 ! equivalent to OM +MASS CCTK 14.0270 ! equivalent to CH2 +MASS CCT2 12.0110 ! equivalent to CH0 +MASS CCTO 12.0110 ! equivalent to C +MASS OCTX 15.9994 ! equivalent to OM +MASS OCT9 15.9994 ! equivalent to OM +MASS OCT6 15.9994 ! equivalent to OA +MASS HCTU 1.0080 ! equivalent to HO +MASS CCTA 14.0270 ! equivalent to CH2 +MASS CCTH 12.0110 ! equivalent to C +MASS OCTR 15.9994 ! equivalent to OM +MASS OCT8 15.9994 ! equivalent to OM + +RESIdue FLC +GROUP + ATOM OA1 TYPE= OCTT CHARGE=-0.734 END + ATOM CAC TYPE= CCT5 CHARGE= 0.384 END + ATOM OA2 TYPE= OCT7 CHARGE=-0.733 END + ATOM CA TYPE= CCTK CHARGE= 0.084 END + ATOM CB TYPE= CCT2 CHARGE= 0.182 END + ATOM CBC TYPE= CCTO CHARGE= 0.384 END + ATOM OB2 TYPE= OCTX CHARGE=-0.733 END + ATOM OB1 TYPE= OCT9 CHARGE=-0.734 END + ATOM OHB TYPE= OCT6 CHARGE=-0.169 END + ATOM HAA TYPE= HCTU CHARGE= 0.067 END + ATOM CG TYPE= CCTA CHARGE= 0.084 END + ATOM CGC TYPE= CCTH CHARGE= 0.384 END + ATOM OG2 TYPE= OCTR CHARGE=-0.733 END + ATOM OG1 TYPE= OCT8 CHARGE=-0.733 END + + BOND OA1 CAC + BOND CAC OA2 + BOND CAC CA + BOND CA CB + BOND CB CBC + BOND CB OHB + BOND CB CG + BOND CBC OB2 + BOND CBC OB1 + BOND OHB HAA + BOND CG CGC + BOND CGC OG2 + BOND CGC OG1 + + ANGLE OA1 CAC OA2 + ANGLE OA1 CAC CA + ANGLE OA2 CAC CA + ANGLE CAC CA CB + ANGLE CA CB CBC + ANGLE CA CB OHB + ANGLE CA CB CG + ANGLE CBC CB OHB + ANGLE CBC CB CG + ANGLE OHB CB CG + ANGLE CB CBC OB2 + ANGLE CB CBC OB1 + ANGLE OB2 CBC OB1 + ANGLE CB OHB HAA + ANGLE CB CG CGC + ANGLE CG CGC OG2 + ANGLE CG CGC OG1 + ANGLE OG2 CGC OG1 + + IMPROPER CAC CA OA2 OA1 + IMPROPER CBC CB OB1 OB2 + IMPROPER CGC CG OG1 OG2 + IMPROPER CB CA CBC OHB + + DIHEDRAL CB CA CAC OA1 + DIHEDRAL CAC CA CB CG + DIHEDRAL CA CB CBC OB1 + DIHEDRAL CA CB OHB HAA + DIHEDRAL CGC CG CB CA + DIHEDRAL CB CG CGC OG1 +END + + +! Adding topology definition for residue GDP + +MASS OG29 15.9994 ! equivalent to OA +MASS PG23 30.9738 ! equivalent to P +MASS OG2Y 15.9994 ! equivalent to OA +MASS OG26 15.9994 ! equivalent to OM +MASS OG2J 15.9994 ! equivalent to OS +MASS PG2T 30.9738 ! equivalent to P +MASS OG2O 15.9994 ! equivalent to OA +MASS OG2V 15.9994 ! equivalent to OM +MASS OG25 15.9994 ! equivalent to OS +MASS CG26 14.0270 ! equivalent to CH2 +MASS CG2B 13.0190 ! equivalent to CS1 +MASS OG2C 15.9994 ! equivalent to OS +MASS CG2G 13.0190 ! equivalent to CH1 +MASS OG2H 15.9994 ! equivalent to OA +MASS HG2V 1.0080 ! equivalent to HO +MASS CG2R 13.0190 ! equivalent to CH1 +MASS OG2F 15.9994 ! equivalent to OA +MASS HG25 1.0080 ! equivalent to HO +MASS CG21 13.0190 ! equivalent to CS1 +MASS NG2W 14.0067 ! equivalent to NR5* +MASS CG2P 13.0190 ! equivalent to CR51 +MASS NG2Q 14.0067 ! equivalent to NR5 +MASS CG2Z 12.0110 ! equivalent to CB +MASS CG2V 12.0110 ! equivalent to CB +MASS NG2G 14.0067 ! equivalent to NR6 +MASS CG2O 12.0110 ! equivalent to CB +MASS NG2J 14.0067 ! equivalent to NT +MASS HG2P 1.0080 ! equivalent to H +MASS HG2U 1.0080 ! equivalent to H +MASS NG2K 14.0067 ! equivalent to NR6* +MASS HG2B 1.0080 ! equivalent to H +MASS CG27 12.0110 ! equivalent to CB +MASS OG2E 15.9994 ! equivalent to O + +RESIdue GDP +GROUP + ATOM O2B TYPE= OG29 CHARGE=-1.071 END + ATOM PB TYPE= PG23 CHARGE= 1.198 END + ATOM O3B TYPE= OG2Y CHARGE=-1.071 END + ATOM O1B TYPE= OG26 CHARGE=-0.778 END + ATOM O3A TYPE= OG2J CHARGE=-0.199 END + ATOM PA TYPE= PG2T CHARGE= 1.198 END + ATOM O2A TYPE= OG2O CHARGE=-0.904 END + ATOM O1A TYPE= OG2V CHARGE=-0.611 END + ATOM O5' TYPE= OG25 CHARGE=-0.199 END + ATOM C5' TYPE= CG26 CHARGE= 0.044 END + ATOM C4' TYPE= CG2B CHARGE= 0.194 END + ATOM O4' TYPE= OG2C CHARGE=-0.199 END + ATOM C3' TYPE= CG2G CHARGE= 0.107 END + ATOM O3' TYPE= OG2H CHARGE=-0.208 END + ATOM HAA TYPE= HG2V CHARGE= 0.029 END + ATOM C2' TYPE= CG2R CHARGE= 0.107 END + ATOM O2' TYPE= OG2F CHARGE=-0.208 END + ATOM HO2' TYPE= HG25 CHARGE= 0.029 END + ATOM C1' TYPE= CG21 CHARGE= 0.194 END + ATOM N9 TYPE= NG2W CHARGE= 0.215 END + ATOM C8 TYPE= CG2P CHARGE=-0.060 END + ATOM N7 TYPE= NG2Q CHARGE=-0.524 END + ATOM C5 TYPE= CG2Z CHARGE= 0.115 END + ATOM C4 TYPE= CG2V CHARGE= 0.250 END + ATOM N3 TYPE= NG2G CHARGE=-0.538 END + ATOM C2 TYPE= CG2O CHARGE= 0.353 END + ATOM N2 TYPE= NG2J CHARGE= 0.038 END + ATOM HN22 TYPE= HG2P CHARGE=-0.016 END + ATOM HN21 TYPE= HG2U CHARGE=-0.016 END + ATOM N1 TYPE= NG2K CHARGE= 0.017 END + ATOM HN1 TYPE= HG2B CHARGE=-0.016 END + ATOM C6 TYPE= CG27 CHARGE= 0.251 END + ATOM O6 TYPE= OG2E CHARGE=-0.721 END + + BOND O2B PB + BOND PB O3B + BOND PB O1B + BOND PB O3A + BOND O3A PA + BOND PA O2A + BOND PA O1A + BOND PA O5' + BOND O5' C5' + BOND C5' C4' + BOND C4' O4' + BOND C4' C3' + BOND O4' C1' + BOND C3' O3' + BOND C3' C2' + BOND O3' HAA + BOND C2' O2' + BOND C2' C1' + BOND O2' HO2' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N2 + BOND C2 N1 + BOND N2 HN22 + BOND N2 HN21 + BOND N1 HN1 + BOND N1 C6 + BOND C6 O6 + + ANGLE O2B PB O3B + ANGLE O2B PB O1B + ANGLE O2B PB O3A + ANGLE O3B PB O1B + ANGLE O3B PB O3A + ANGLE O1B PB O3A + ANGLE PB O3A PA + ANGLE O3A PA O2A + ANGLE O3A PA O1A + ANGLE O3A PA O5' + ANGLE O2A PA O1A + ANGLE O2A PA O5' + ANGLE O1A PA O5' + ANGLE PA O5' C5' + ANGLE O5' C5' C4' + ANGLE C5' C4' O4' + ANGLE C5' C4' C3' + ANGLE O4' C4' C3' + ANGLE C4' O4' C1' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HAA + ANGLE C3' C2' O2' + ANGLE C3' C2' C1' + ANGLE O2' C2' C1' + ANGLE C2' O2' HO2' + ANGLE O4' C1' C2' + ANGLE O4' C1' N9 + ANGLE C2' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N2 + ANGLE N3 C2 N1 + ANGLE N2 C2 N1 + ANGLE C2 N2 HN22 + ANGLE C2 N2 HN21 + ANGLE HN22 N2 HN21 + ANGLE C2 N1 HN1 + ANGLE C2 N1 C6 + ANGLE HN1 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 O6 + ANGLE N1 C6 O6 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C2 N3 N1 N2 + IMPROPER N2 C2 HN22 HN21 + IMPROPER N1 C6 HN1 C2 + IMPROPER C6 C5 N1 O6 + IMPROPER PB O2B O1B O3B + IMPROPER PA O3A O2A O1A + IMPROPER C4' C5' C3' O4' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C3' C1' O2' + IMPROPER C1' O4' C2' N9 + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL PA O3A PB O2B + DIHEDRAL PA O3A PB O2B + DIHEDRAL PB O3A PA O5' + DIHEDRAL PB O3A PA O5' + DIHEDRAL C5' O5' PA O3A + DIHEDRAL C5' O5' PA O3A + DIHEDRAL PA O5' C5' C4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C5' C4' O4' C1' + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C4' C3' O3' HAA + DIHEDRAL C1' C2' C3' C4' + DIHEDRAL C3' C2' O2' HO2' + DIHEDRAL C3' C2' C1' N9 + DIHEDRAL O4' C1' N9 C4 + DIHEDRAL N3 C2 N2 HN21 +END + + +! Adding topology definition for residue GMP + +MASS OG1N 15.9994 ! equivalent to O +MASS CG17 12.0110 ! equivalent to CB +MASS NG1T 14.0067 ! equivalent to NR6* +MASS HG16 1.0080 ! equivalent to H +MASS CG1O 12.0110 ! equivalent to CB +MASS NG14 14.0067 ! equivalent to NT +MASS HG12 1.0080 ! equivalent to H +MASS HG18 1.0080 ! equivalent to H +MASS NG1K 14.0067 ! equivalent to NR6 +MASS CG14 12.0110 ! equivalent to CB +MASS CG1S 12.0110 ! equivalent to CB +MASS NG19 14.0067 ! equivalent to NR5 +MASS CG1V 13.0190 ! equivalent to CR51 +MASS NG15 14.0067 ! equivalent to NR5* +MASS CG1J 13.0190 ! equivalent to CS1 +MASS OG1V 15.9994 ! equivalent to OS +MASS CG1A 13.0190 ! equivalent to CS1 +MASS CG1R 14.0270 ! equivalent to CH2 +MASS OG1P 15.9994 ! equivalent to OA +MASS HG1N 1.0080 ! equivalent to HO +MASS CG16 13.0190 ! equivalent to CH1 +MASS OG1R 15.9994 ! equivalent to OA +MASS HG1M 1.0080 ! equivalent to HO +MASS CG1Q 13.0190 ! equivalent to CH1 +MASS OG1O 15.9994 ! equivalent to OA +MASS HG1Z 1.0080 ! equivalent to HO + +RESIdue GMP +GROUP + ATOM O6 TYPE= OG1N CHARGE=-0.692 END + ATOM C6 TYPE= CG17 CHARGE= 0.279 END + ATOM N1 TYPE= NG1T CHARGE= 0.046 END + ATOM HN1 TYPE= HG16 CHARGE= 0.012 END + ATOM C2 TYPE= CG1O CHARGE= 0.382 END + ATOM N2 TYPE= NG14 CHARGE= 0.067 END + ATOM HN22 TYPE= HG12 CHARGE= 0.012 END + ATOM HN21 TYPE= HG18 CHARGE= 0.012 END + ATOM N3 TYPE= NG1K CHARGE=-0.510 END + ATOM C4 TYPE= CG14 CHARGE= 0.279 END + ATOM C5 TYPE= CG1S CHARGE= 0.143 END + ATOM N7 TYPE= NG19 CHARGE=-0.496 END + ATOM C8 TYPE= CG1V CHARGE=-0.031 END + ATOM N9 TYPE= NG15 CHARGE= 0.243 END + ATOM C1' TYPE= CG1J CHARGE= 0.223 END + ATOM O4' TYPE= OG1V CHARGE=-0.171 END + ATOM C4' TYPE= CG1A CHARGE= 0.223 END + ATOM C5' TYPE= CG1R CHARGE= 0.073 END + ATOM O5' TYPE= OG1P CHARGE=-0.180 END + ATOM HO5' TYPE= HG1N CHARGE= 0.058 END + ATOM C3' TYPE= CG16 CHARGE= 0.136 END + ATOM O3' TYPE= OG1R CHARGE=-0.180 END + ATOM HO3' TYPE= HG1M CHARGE= 0.058 END + ATOM C2' TYPE= CG1Q CHARGE= 0.136 END + ATOM O2' TYPE= OG1O CHARGE=-0.180 END + ATOM HO2' TYPE= HG1Z CHARGE= 0.058 END + + BOND O6 C6 + BOND C6 N1 + BOND C6 C5 + BOND N1 HN1 + BOND N1 C2 + BOND C2 N2 + BOND C2 N3 + BOND N2 HN22 + BOND N2 HN21 + BOND N3 C4 + BOND C4 C5 + BOND C4 N9 + BOND C5 N7 + BOND N7 C8 + BOND C8 N9 + BOND N9 C1' + BOND C1' O4' + BOND C1' C2' + BOND O4' C4' + BOND C4' C5' + BOND C4' C3' + BOND C5' O5' + BOND O5' HO5' + BOND C3' O3' + BOND C3' C2' + BOND O3' HO3' + BOND C2' O2' + BOND O2' HO2' + + ANGLE O6 C6 N1 + ANGLE O6 C6 C5 + ANGLE N1 C6 C5 + ANGLE C6 N1 HN1 + ANGLE C6 N1 C2 + ANGLE HN1 N1 C2 + ANGLE N1 C2 N2 + ANGLE N1 C2 N3 + ANGLE N2 C2 N3 + ANGLE C2 N2 HN22 + ANGLE C2 N2 HN21 + ANGLE HN22 N2 HN21 + ANGLE C2 N3 C4 + ANGLE N3 C4 C5 + ANGLE N3 C4 N9 + ANGLE C5 C4 N9 + ANGLE C6 C5 C4 + ANGLE C6 C5 N7 + ANGLE C4 C5 N7 + ANGLE C5 N7 C8 + ANGLE N7 C8 N9 + ANGLE C4 N9 C8 + ANGLE C4 N9 C1' + ANGLE C8 N9 C1' + ANGLE N9 C1' O4' + ANGLE N9 C1' C2' + ANGLE O4' C1' C2' + ANGLE C1' O4' C4' + ANGLE O4' C4' C5' + ANGLE O4' C4' C3' + ANGLE C5' C4' C3' + ANGLE C4' C5' O5' + ANGLE C5' O5' HO5' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HO3' + ANGLE C1' C2' C3' + ANGLE C1' C2' O2' + ANGLE C3' C2' O2' + ANGLE C2' O2' HO2' + + IMPROPER C6 C5 N1 O6 + IMPROPER N1 C2 HN1 C6 + IMPROPER C2 N1 N3 N2 + IMPROPER N2 C2 HN22 HN21 + IMPROPER C4 N3 C5 N9 + IMPROPER C5 C6 C4 N7 + IMPROPER N9 C4 C8 C1' + IMPROPER C1' N9 O4' C2' + IMPROPER C4' O4' C5' C3' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C1' O2' C3' + IMPROPER C4 C5 N7 C8 + IMPROPER C5 N7 C8 N9 + IMPROPER N7 C8 N9 C4 + IMPROPER C8 N9 C4 C5 + IMPROPER N9 C4 C5 N7 + IMPROPER C6 N1 C2 N3 + IMPROPER N1 C2 N3 C4 + IMPROPER C2 N3 C4 C5 + IMPROPER N3 C4 C5 C6 + IMPROPER C4 C5 C6 N1 + IMPROPER C5 C6 N1 C2 + + DIHEDRAL N1 C2 N2 HN21 + DIHEDRAL C2' C1' N9 C4 + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL N9 C1' C2' O2' + DIHEDRAL C3' C4' O4' C1' + DIHEDRAL O4' C4' C5' O5' + DIHEDRAL O4' C4' C3' C2' + DIHEDRAL C4' C5' O5' HO5' + DIHEDRAL C4' C3' O3' HO3' + DIHEDRAL O2' C2' C3' C4' + DIHEDRAL C1' C2' O2' HO2' +END + + +! Adding topology definition for residue GTP + +MASS OG31 15.9994 ! equivalent to OA +MASS PG3E 30.9738 ! equivalent to P +MASS OG3D 15.9994 ! equivalent to OA +MASS OG38 15.9994 ! equivalent to OM +MASS OG33 15.9994 ! equivalent to OS +MASS PG3T 30.9738 ! equivalent to P +MASS OG3O 15.9994 ! equivalent to OA +MASS OG3S 15.9994 ! equivalent to OM +MASS OG3E 15.9994 ! equivalent to OS +MASS PG3C 30.9738 ! equivalent to P +MASS OG3V 15.9994 ! equivalent to OA +MASS OG3W 15.9994 ! equivalent to OM +MASS OG3M 15.9994 ! equivalent to OS +MASS CG34 14.0270 ! equivalent to CH2 +MASS CG37 13.0190 ! equivalent to CS1 +MASS OG3J 15.9994 ! equivalent to OS +MASS CG3H 13.0190 ! equivalent to CH1 +MASS OG3X 15.9994 ! equivalent to OA +MASS HG3F 1.0080 ! equivalent to HO +MASS CG31 13.0190 ! equivalent to CH1 +MASS OG3Y 15.9994 ! equivalent to OA +MASS HG3L 1.0080 ! equivalent to HO +MASS CG3J 13.0190 ! equivalent to CS1 +MASS NG31 14.0067 ! equivalent to NR5* +MASS CG3U 13.0190 ! equivalent to CR51 +MASS NG3W 14.0067 ! equivalent to NR5 +MASS CG3V 12.0110 ! equivalent to CB +MASS CG3E 12.0110 ! equivalent to CB +MASS NG3C 14.0067 ! equivalent to NR6 +MASS CG3W 12.0110 ! equivalent to CB +MASS NG3J 14.0067 ! equivalent to NT +MASS HG35 1.0080 ! equivalent to H +MASS HG3H 1.0080 ! equivalent to H +MASS NG3D 14.0067 ! equivalent to NR6* +MASS HG3Q 1.0080 ! equivalent to H +MASS CG3R 12.0110 ! equivalent to CB +MASS OG3F 15.9994 ! equivalent to O + +RESIdue GTP +GROUP + ATOM O2G TYPE= OG31 CHARGE=-1.084 END + ATOM PG TYPE= PG3E CHARGE= 1.185 END + ATOM O3G TYPE= OG3D CHARGE=-1.084 END + ATOM O1G TYPE= OG38 CHARGE=-0.791 END + ATOM O3B TYPE= OG33 CHARGE=-0.212 END + ATOM PB TYPE= PG3T CHARGE= 1.185 END + ATOM O2B TYPE= OG3O CHARGE=-0.918 END + ATOM O1B TYPE= OG3S CHARGE=-0.624 END + ATOM O3A TYPE= OG3E CHARGE=-0.212 END + ATOM PA TYPE= PG3C CHARGE= 1.185 END + ATOM O2A TYPE= OG3V CHARGE=-0.918 END + ATOM O1A TYPE= OG3W CHARGE=-0.624 END + ATOM O5' TYPE= OG3M CHARGE=-0.212 END + ATOM C5' TYPE= CG34 CHARGE= 0.031 END + ATOM C4' TYPE= CG37 CHARGE= 0.181 END + ATOM O4' TYPE= OG3J CHARGE=-0.212 END + ATOM C3' TYPE= CG3H CHARGE= 0.094 END + ATOM O3' TYPE= OG3X CHARGE=-0.221 END + ATOM HAA TYPE= HG3F CHARGE= 0.016 END + ATOM C2' TYPE= CG31 CHARGE= 0.094 END + ATOM O2' TYPE= OG3Y CHARGE=-0.221 END + ATOM HO2' TYPE= HG3L CHARGE= 0.016 END + ATOM C1' TYPE= CG3J CHARGE= 0.181 END + ATOM N9 TYPE= NG31 CHARGE= 0.202 END + ATOM C8 TYPE= CG3U CHARGE=-0.073 END + ATOM N7 TYPE= NG3W CHARGE=-0.538 END + ATOM C5 TYPE= CG3V CHARGE= 0.102 END + ATOM C4 TYPE= CG3E CHARGE= 0.238 END + ATOM N3 TYPE= NG3C CHARGE=-0.552 END + ATOM C2 TYPE= CG3W CHARGE= 0.340 END + ATOM N2 TYPE= NG3J CHARGE= 0.025 END + ATOM HN22 TYPE= HG35 CHARGE=-0.029 END + ATOM HN21 TYPE= HG3H CHARGE=-0.029 END + ATOM N1 TYPE= NG3D CHARGE= 0.004 END + ATOM HN1 TYPE= HG3Q CHARGE=-0.029 END + ATOM C6 TYPE= CG3R CHARGE= 0.238 END + ATOM O6 TYPE= OG3F CHARGE=-0.734 END + + BOND O2G PG + BOND PG O3G + BOND PG O1G + BOND PG O3B + BOND O3B PB + BOND PB O2B + BOND PB O1B + BOND PB O3A + BOND O3A PA + BOND PA O2A + BOND PA O1A + BOND PA O5' + BOND O5' C5' + BOND C5' C4' + BOND C4' O4' + BOND C4' C3' + BOND O4' C1' + BOND C3' O3' + BOND C3' C2' + BOND O3' HAA + BOND C2' O2' + BOND C2' C1' + BOND O2' HO2' + BOND C1' N9 + BOND N9 C8 + BOND N9 C4 + BOND C8 N7 + BOND N7 C5 + BOND C5 C4 + BOND C5 C6 + BOND C4 N3 + BOND N3 C2 + BOND C2 N2 + BOND C2 N1 + BOND N2 HN22 + BOND N2 HN21 + BOND N1 HN1 + BOND N1 C6 + BOND C6 O6 + + ANGLE O2G PG O3G + ANGLE O2G PG O1G + ANGLE O2G PG O3B + ANGLE O3G PG O1G + ANGLE O3G PG O3B + ANGLE O1G PG O3B + ANGLE PG O3B PB + ANGLE O3B PB O2B + ANGLE O3B PB O1B + ANGLE O3B PB O3A + ANGLE O2B PB O1B + ANGLE O2B PB O3A + ANGLE O1B PB O3A + ANGLE PB O3A PA + ANGLE O3A PA O2A + ANGLE O3A PA O1A + ANGLE O3A PA O5' + ANGLE O2A PA O1A + ANGLE O2A PA O5' + ANGLE O1A PA O5' + ANGLE PA O5' C5' + ANGLE O5' C5' C4' + ANGLE C5' C4' O4' + ANGLE C5' C4' C3' + ANGLE O4' C4' C3' + ANGLE C4' O4' C1' + ANGLE C4' C3' O3' + ANGLE C4' C3' C2' + ANGLE O3' C3' C2' + ANGLE C3' O3' HAA + ANGLE C3' C2' O2' + ANGLE C3' C2' C1' + ANGLE O2' C2' C1' + ANGLE C2' O2' HO2' + ANGLE O4' C1' C2' + ANGLE O4' C1' N9 + ANGLE C2' C1' N9 + ANGLE C1' N9 C8 + ANGLE C1' N9 C4 + ANGLE C8 N9 C4 + ANGLE N9 C8 N7 + ANGLE C8 N7 C5 + ANGLE N7 C5 C4 + ANGLE N7 C5 C6 + ANGLE C4 C5 C6 + ANGLE N9 C4 C5 + ANGLE N9 C4 N3 + ANGLE C5 C4 N3 + ANGLE C4 N3 C2 + ANGLE N3 C2 N2 + ANGLE N3 C2 N1 + ANGLE N2 C2 N1 + ANGLE C2 N2 HN22 + ANGLE C2 N2 HN21 + ANGLE HN22 N2 HN21 + ANGLE C2 N1 HN1 + ANGLE C2 N1 C6 + ANGLE HN1 N1 C6 + ANGLE C5 C6 N1 + ANGLE C5 C6 O6 + ANGLE N1 C6 O6 + + IMPROPER N9 C1' C8 C4 + IMPROPER C5 C6 C4 N7 + IMPROPER C4 N3 C5 N9 + IMPROPER C2 N3 N1 N2 + IMPROPER N2 C2 HN22 HN21 + IMPROPER N1 C6 HN1 C2 + IMPROPER C6 C5 N1 O6 + IMPROPER PG O2G O1G O3G + IMPROPER PB O3B O2B O1B + IMPROPER PA O3A O2A O1A + IMPROPER C4' C5' C3' O4' + IMPROPER C3' C4' C2' O3' + IMPROPER C2' C3' C1' O2' + IMPROPER C1' O4' C2' N9 + IMPROPER N9 C8 N7 C5 + IMPROPER C8 N7 C5 C4 + IMPROPER N7 C5 C4 N9 + IMPROPER C5 C4 N9 C8 + IMPROPER C4 N9 C8 N7 + IMPROPER C5 C4 N3 C2 + IMPROPER C4 N3 C2 N1 + IMPROPER N3 C2 N1 C6 + IMPROPER C2 N1 C6 C5 + IMPROPER N1 C6 C5 C4 + IMPROPER C6 C5 C4 N3 + + DIHEDRAL PB O3B PG O2G + DIHEDRAL PB O3B PG O2G + DIHEDRAL PG O3B PB O3A + DIHEDRAL PG O3B PB O3A + DIHEDRAL PA O3A PB O3B + DIHEDRAL PA O3A PB O3B + DIHEDRAL PB O3A PA O5' + DIHEDRAL PB O3A PA O5' + DIHEDRAL C5' O5' PA O3A + DIHEDRAL C5' O5' PA O3A + DIHEDRAL PA O5' C5' C4' + DIHEDRAL C3' C4' C5' O5' + DIHEDRAL C5' C4' O4' C1' + DIHEDRAL C5' C4' C3' C2' + DIHEDRAL N9 C1' O4' C4' + DIHEDRAL C4' C3' O3' HAA + DIHEDRAL C1' C2' C3' C4' + DIHEDRAL C3' C2' O2' HO2' + DIHEDRAL C3' C2' C1' N9 + DIHEDRAL O4' C1' N9 C4 + DIHEDRAL N3 C2 N2 HN21 +END + + +! Adding topology definition for residue NAD + +MASS NN2Q 14.0067 ! equivalent to NT +MASS HN27 1.0080 ! equivalent to H +MASS HN24 1.0080 ! equivalent to H +MASS CN28 12.0110 ! equivalent to C +MASS ON2B 15.9994 ! equivalent to O +MASS CN2N 12.0110 ! equivalent to CB +MASS CN24 13.0190 ! equivalent to CR61 +MASS CN29 13.0190 ! equivalent to CR61 +MASS CN2P 13.0190 ! equivalent to CR61 +MASS CN2G 13.0190 ! equivalent to CR61 +MASS NN20 14.0067 ! equivalent to NR6* +MASS CN2I 13.0190 ! equivalent to CS1 +MASS ON2D 15.9994 ! equivalent to OS +MASS CN22 13.0190 ! equivalent to CH1 +MASS ON27 15.9994 ! equivalent to OA +MASS HN2M 1.0080 ! equivalent to HO +MASS CN2A 13.0190 ! equivalent to CH1 +MASS ON2N 15.9994 ! equivalent to OA +MASS HN2Q 1.0080 ! equivalent to HO +MASS CN2O 13.0190 ! equivalent to CS1 +MASS CN27 14.0270 ! equivalent to CH2 +MASS ON2L 15.9994 ! equivalent to OS +MASS PN2D 30.9738 ! equivalent to P +MASS ON2U 15.9994 ! equivalent to OM +MASS ON2F 15.9994 ! equivalent to OM +MASS ON2R 15.9994 ! equivalent to OS +MASS PN21 30.9738 ! equivalent to P +MASS ON26 15.9994 ! equivalent to OA +MASS ON2V 15.9994 ! equivalent to OM +MASS ON24 15.9994 ! equivalent to OS +MASS CN25 14.0270 ! equivalent to CH2 +MASS CN2L 13.0190 ! equivalent to CS1 +MASS ON2H 15.9994 ! equivalent to OS +MASS CN2U 13.0190 ! equivalent to CH1 +MASS ON29 15.9994 ! equivalent to OA +MASS HN2B 1.0080 ! equivalent to HO +MASS CN2C 13.0190 ! equivalent to CH1 +MASS ON22 15.9994 ! equivalent to OA +MASS HN2I 1.0080 ! equivalent to HO +MASS CN2E 13.0190 ! equivalent to CS1 +MASS NN2T 14.0067 ! equivalent to NR5* +MASS CN2W 13.0190 ! equivalent to CR51 +MASS NN25 14.0067 ! equivalent to NR5 +MASS CN2S 12.0110 ! equivalent to CB +MASS CN2Q 12.0110 ! equivalent to CB +MASS NN2H 14.0067 ! equivalent to NR6 +MASS CN2F 13.0190 ! equivalent to CR61 +MASS NN2I 14.0067 ! equivalent to NR6 +MASS CN2R 12.0110 ! equivalent to CB +MASS NN24 14.0067 ! equivalent to NT +MASS HN2K 1.0080 ! equivalent to H +MASS HN26 1.0080 ! equivalent to H + +RESIdue NAD +GROUP + ATOM N7N TYPE= NN2Q CHARGE= 0.058 END + ATOM H72N TYPE= HN27 CHARGE= 0.003 END + ATOM H71N TYPE= HN24 CHARGE= 0.003 END + ATOM C7N TYPE= CN28 CHARGE= 0.365 END + ATOM O7N TYPE= ON2B CHARGE=-0.701 END + ATOM C3N TYPE= CN2N CHARGE=-0.019 END + ATOM C2N TYPE= CN24 CHARGE=-0.040 END + ATOM C4N TYPE= CN29 CHARGE=-0.040 END + ATOM C5N TYPE= CN2P CHARGE=-0.040 END + ATOM C6N TYPE= CN2G CHARGE=-0.040 END + ATOM N1N TYPE= NN20 CHARGE= 0.288 END + ATOM C1D TYPE= CN2I CHARGE= 0.214 END + ATOM O4D TYPE= ON2D CHARGE=-0.180 END + ATOM C2D TYPE= CN22 CHARGE= 0.127 END + ATOM O2D TYPE= ON27 CHARGE=-0.188 END + ATOM HO2N TYPE= HN2M CHARGE= 0.049 END + ATOM C3D TYPE= CN2A CHARGE= 0.127 END + ATOM O3D TYPE= ON2N CHARGE=-0.188 END + ATOM HAC TYPE= HN2Q CHARGE= 0.049 END + ATOM C4D TYPE= CN2O CHARGE= 0.214 END + ATOM C5D TYPE= CN27 CHARGE= 0.064 END + ATOM O5D TYPE= ON2L CHARGE=-0.180 END + ATOM PN TYPE= PN2D CHARGE= 1.218 END + ATOM O1N TYPE= ON2U CHARGE=-0.592 END + ATOM O2N TYPE= ON2F CHARGE=-0.592 END + ATOM O3 TYPE= ON2R CHARGE=-0.180 END + ATOM PA TYPE= PN21 CHARGE= 1.218 END + ATOM O2A TYPE= ON26 CHARGE=-0.884 END + ATOM O1A TYPE= ON2V CHARGE=-0.592 END + ATOM O5B TYPE= ON24 CHARGE=-0.180 END + ATOM C5B TYPE= CN25 CHARGE= 0.064 END + ATOM C4B TYPE= CN2L CHARGE= 0.214 END + ATOM O4B TYPE= ON2H CHARGE=-0.180 END + ATOM C3B TYPE= CN2U CHARGE= 0.127 END + ATOM O3B TYPE= ON29 CHARGE=-0.188 END + ATOM HAA TYPE= HN2B CHARGE= 0.049 END + ATOM C2B TYPE= CN2C CHARGE= 0.128 END + ATOM O2B TYPE= ON22 CHARGE=-0.188 END + ATOM HO2A TYPE= HN2I CHARGE= 0.049 END + ATOM C1B TYPE= CN2E CHARGE= 0.214 END + ATOM N9A TYPE= NN2T CHARGE= 0.235 END + ATOM C8A TYPE= CN2W CHARGE=-0.040 END + ATOM N7A TYPE= NN25 CHARGE=-0.505 END + ATOM C5A TYPE= CN2S CHARGE= 0.134 END + ATOM C4A TYPE= CN2Q CHARGE= 0.270 END + ATOM N3A TYPE= NN2H CHARGE=-0.519 END + ATOM C2A TYPE= CN2F CHARGE=-0.040 END + ATOM N1A TYPE= NN2I CHARGE=-0.519 END + ATOM C6A TYPE= CN2R CHARGE= 0.270 END + ATOM N6A TYPE= NN24 CHARGE= 0.058 END + ATOM H62A TYPE= HN2K CHARGE= 0.003 END + ATOM H61A TYPE= HN26 CHARGE= 0.003 END + + BOND N7N H72N + BOND N7N H71N + BOND N7N C7N + BOND C7N O7N + BOND C7N C3N + BOND C3N C2N + BOND C3N C4N + BOND C2N N1N + BOND C4N C5N + BOND C5N C6N + BOND C6N N1N + BOND N1N C1D + BOND C1D O4D + BOND C1D C2D + BOND O4D C4D + BOND C2D O2D + BOND C2D C3D + BOND O2D HO2N + BOND C3D O3D + BOND C3D C4D + BOND O3D HAC + BOND C4D C5D + BOND C5D O5D + BOND O5D PN + BOND PN O1N + BOND PN O2N + BOND PN O3 + BOND O3 PA + BOND PA O2A + BOND PA O1A + BOND PA O5B + BOND O5B C5B + BOND C5B C4B + BOND C4B O4B + BOND C4B C3B + BOND O4B C1B + BOND C3B O3B + BOND C3B C2B + BOND O3B HAA + BOND C2B O2B + BOND C2B C1B + BOND O2B HO2A + BOND C1B N9A + BOND N9A C8A + BOND N9A C4A + BOND C8A N7A + BOND N7A C5A + BOND C5A C4A + BOND C5A C6A + BOND C4A N3A + BOND N3A C2A + BOND C2A N1A + BOND N1A C6A + BOND C6A N6A + BOND N6A H62A + BOND N6A H61A + + ANGLE H72N N7N H71N + ANGLE H72N N7N C7N + ANGLE H71N N7N C7N + ANGLE N7N C7N O7N + ANGLE N7N C7N C3N + ANGLE O7N C7N C3N + ANGLE C7N C3N C2N + ANGLE C7N C3N C4N + ANGLE C2N C3N C4N + ANGLE C3N C2N N1N + ANGLE C3N C4N C5N + ANGLE C4N C5N C6N + ANGLE C5N C6N N1N + ANGLE C2N N1N C6N + ANGLE C2N N1N C1D + ANGLE C6N N1N C1D + ANGLE N1N C1D O4D + ANGLE N1N C1D C2D + ANGLE O4D C1D C2D + ANGLE C1D O4D C4D + ANGLE C1D C2D O2D + ANGLE C1D C2D C3D + ANGLE O2D C2D C3D + ANGLE C2D O2D HO2N + ANGLE C2D C3D O3D + ANGLE C2D C3D C4D + ANGLE O3D C3D C4D + ANGLE C3D O3D HAC + ANGLE O4D C4D C3D + ANGLE O4D C4D C5D + ANGLE C3D C4D C5D + ANGLE C4D C5D O5D + ANGLE C5D O5D PN + ANGLE O5D PN O1N + ANGLE O5D PN O2N + ANGLE O5D PN O3 + ANGLE O1N PN O2N + ANGLE O1N PN O3 + ANGLE O2N PN O3 + ANGLE PN O3 PA + ANGLE O3 PA O2A + ANGLE O3 PA O1A + ANGLE O3 PA O5B + ANGLE O2A PA O1A + ANGLE O2A PA O5B + ANGLE O1A PA O5B + ANGLE PA O5B C5B + ANGLE O5B C5B C4B + ANGLE C5B C4B O4B + ANGLE C5B C4B C3B + ANGLE O4B C4B C3B + ANGLE C4B O4B C1B + ANGLE C4B C3B O3B + ANGLE C4B C3B C2B + ANGLE O3B C3B C2B + ANGLE C3B O3B HAA + ANGLE C3B C2B O2B + ANGLE C3B C2B C1B + ANGLE O2B C2B C1B + ANGLE C2B O2B HO2A + ANGLE O4B C1B C2B + ANGLE O4B C1B N9A + ANGLE C2B C1B N9A + ANGLE C1B N9A C8A + ANGLE C1B N9A C4A + ANGLE C8A N9A C4A + ANGLE N9A C8A N7A + ANGLE C8A N7A C5A + ANGLE N7A C5A C4A + ANGLE N7A C5A C6A + ANGLE C4A C5A C6A + ANGLE N9A C4A C5A + ANGLE N9A C4A N3A + ANGLE C5A C4A N3A + ANGLE C4A N3A C2A + ANGLE N3A C2A N1A + ANGLE C2A N1A C6A + ANGLE C5A C6A N1A + ANGLE C5A C6A N6A + ANGLE N1A C6A N6A + ANGLE C6A N6A H62A + ANGLE C6A N6A H61A + ANGLE H62A N6A H61A + + IMPROPER N7N H72N H71N C7N + IMPROPER C7N N7N C3N O7N + IMPROPER C3N C4N C2N C7N + IMPROPER N1N C1D C6N C2N + IMPROPER N9A C1B C8A C4A + IMPROPER C5A C6A C4A N7A + IMPROPER C4A N3A C5A N9A + IMPROPER C6A C5A N1A N6A + IMPROPER N6A C6A H62A H61A + IMPROPER C1D N1N O4D C2D + IMPROPER C2D C1D O2D C3D + IMPROPER C3D C2D O3D C4D + IMPROPER C4D O4D C5D C3D + IMPROPER PN O5D O2N O1N + IMPROPER PA O3 O2A O1A + IMPROPER C4B C5B C3B O4B + IMPROPER C3B C4B C2B O3B + IMPROPER C2B C3B C1B O2B + IMPROPER C1B O4B C2B N9A + IMPROPER N9A C8A N7A C5A + IMPROPER C8A N7A C5A C4A + IMPROPER N7A C5A C4A N9A + IMPROPER C5A C4A N9A C8A + IMPROPER C4A N9A C8A N7A + IMPROPER C3N C2N N1N C6N + IMPROPER C2N N1N C6N C5N + IMPROPER N1N C6N C5N C4N + IMPROPER C6N C5N C4N C3N + IMPROPER C5N C4N C3N C2N + IMPROPER C4N C3N C2N N1N + IMPROPER C5A C4A N3A C2A + IMPROPER C4A N3A C2A N1A + IMPROPER N3A C2A N1A C6A + IMPROPER C2A N1A C6A C5A + IMPROPER N1A C6A C5A C4A + IMPROPER C6A C5A C4A N3A + + DIHEDRAL C3N C7N N7N H72N + DIHEDRAL C4N C3N C7N N7N + DIHEDRAL C2N N1N C1D C2D + DIHEDRAL N1N C1D O4D C4D + DIHEDRAL N1N C1D C2D C3D + DIHEDRAL C5D C4D O4D C1D + DIHEDRAL C1D C2D O2D HO2N + DIHEDRAL C4D C3D C2D C1D + DIHEDRAL C2D C3D O3D HAC + DIHEDRAL C2D C3D C4D C5D + DIHEDRAL O4D C4D C5D O5D + DIHEDRAL PN O5D C5D C4D + DIHEDRAL C5D O5D PN O3 + DIHEDRAL C5D O5D PN O3 + DIHEDRAL PA O3 PN O5D + DIHEDRAL PA O3 PN O5D + DIHEDRAL PN O3 PA O5B + DIHEDRAL PN O3 PA O5B + DIHEDRAL C5B O5B PA O3 + DIHEDRAL C5B O5B PA O3 + DIHEDRAL PA O5B C5B C4B + DIHEDRAL C3B C4B C5B O5B + DIHEDRAL C5B C4B O4B C1B + DIHEDRAL C5B C4B C3B C2B + DIHEDRAL N9A C1B O4B C4B + DIHEDRAL C4B C3B O3B HAA + DIHEDRAL C1B C2B C3B C4B + DIHEDRAL C3B C2B O2B HO2A + DIHEDRAL C3B C2B C1B N9A + DIHEDRAL O4B C1B N9A C4A + DIHEDRAL C5A C6A N6A H61A +END + + +! Adding topology definition for residue NAP + +MASS NN36 14.0067 ! equivalent to NT +MASS HN3X 1.0080 ! equivalent to H +MASS HN3C 1.0080 ! equivalent to H +MASS CN37 12.0110 ! equivalent to C +MASS ON34 15.9994 ! equivalent to O +MASS CN3Y 12.0110 ! equivalent to CB +MASS CN35 13.0190 ! equivalent to CR61 +MASS CN3X 13.0190 ! equivalent to CR61 +MASS CN3S 13.0190 ! equivalent to CR61 +MASS CN3M 13.0190 ! equivalent to CR61 +MASS NN3L 14.0067 ! equivalent to NR6* +MASS CN39 13.0190 ! equivalent to CS1 +MASS ON3U 15.9994 ! equivalent to OS +MASS CN34 13.0190 ! equivalent to CH1 +MASS ON3N 15.9994 ! equivalent to OA +MASS HN3S 1.0080 ! equivalent to HO +MASS CN3W 13.0190 ! equivalent to CH1 +MASS ON3C 15.9994 ! equivalent to OA +MASS HN34 1.0080 ! equivalent to HO +MASS CN3T 13.0190 ! equivalent to CS1 +MASS CN3G 14.0270 ! equivalent to CH2 +MASS ON30 15.9994 ! equivalent to OS +MASS PN3X 30.9738 ! equivalent to P +MASS ON35 15.9994 ! equivalent to OM +MASS ON3B 15.9994 ! equivalent to OM +MASS ON33 15.9994 ! equivalent to OS +MASS PN3P 30.9738 ! equivalent to P +MASS ON3O 15.9994 ! equivalent to OA +MASS ON3K 15.9994 ! equivalent to OM +MASS ON3Y 15.9994 ! equivalent to OS +MASS CN3R 14.0270 ! equivalent to CH2 +MASS CN3L 13.0190 ! equivalent to CS1 +MASS ON3Z 15.9994 ! equivalent to OS +MASS CN3Z 13.0190 ! equivalent to CH1 +MASS ON38 15.9994 ! equivalent to OA +MASS HN3F 1.0080 ! equivalent to HO +MASS CN32 13.0190 ! equivalent to CH1 +MASS ON3A 15.9994 ! equivalent to OS +MASS PN3Q 30.9738 ! equivalent to P +MASS ON3M 15.9994 ! equivalent to OA +MASS ON39 15.9994 ! equivalent to OA +MASS ON3W 15.9994 ! equivalent to OM +MASS CN3U 13.0190 ! equivalent to CS1 +MASS NN3H 14.0067 ! equivalent to NR5* +MASS CN31 13.0190 ! equivalent to CR51 +MASS NN3G 14.0067 ! equivalent to NR5 +MASS CN3V 12.0110 ! equivalent to CB +MASS CN3P 12.0110 ! equivalent to CB +MASS NN3M 14.0067 ! equivalent to NR6 +MASS CN3D 13.0190 ! equivalent to CR61 +MASS NN34 14.0067 ! equivalent to NR6 +MASS CN3B 12.0110 ! equivalent to CB +MASS NN3I 14.0067 ! equivalent to NT +MASS HN31 1.0080 ! equivalent to H +MASS HN3W 1.0080 ! equivalent to H + +RESIdue NAP +GROUP + ATOM N7N TYPE= NN36 CHARGE= 0.052 END + ATOM H72N TYPE= HN3X CHARGE=-0.002 END + ATOM H71N TYPE= HN3C CHARGE=-0.002 END + ATOM C7N TYPE= CN37 CHARGE= 0.358 END + ATOM O7N TYPE= ON34 CHARGE=-0.707 END + ATOM C3N TYPE= CN3Y CHARGE=-0.025 END + ATOM C2N TYPE= CN35 CHARGE=-0.046 END + ATOM C4N TYPE= CN3X CHARGE=-0.046 END + ATOM C5N TYPE= CN3S CHARGE=-0.046 END + ATOM C6N TYPE= CN3M CHARGE=-0.046 END + ATOM N1N TYPE= NN3L CHARGE= 0.282 END + ATOM C1D TYPE= CN39 CHARGE= 0.208 END + ATOM O4D TYPE= ON3U CHARGE=-0.185 END + ATOM C2D TYPE= CN34 CHARGE= 0.121 END + ATOM O2D TYPE= ON3N CHARGE=-0.194 END + ATOM HO2N TYPE= HN3S CHARGE= 0.043 END + ATOM C3D TYPE= CN3W CHARGE= 0.121 END + ATOM O3D TYPE= ON3C CHARGE=-0.194 END + ATOM HAB TYPE= HN34 CHARGE= 0.043 END + ATOM C4D TYPE= CN3T CHARGE= 0.208 END + ATOM C5D TYPE= CN3G CHARGE= 0.058 END + ATOM O5D TYPE= ON30 CHARGE=-0.185 END + ATOM PN TYPE= PN3X CHARGE= 1.212 END + ATOM O1N TYPE= ON35 CHARGE=-0.597 END + ATOM O2N TYPE= ON3B CHARGE=-0.597 END + ATOM O3 TYPE= ON33 CHARGE=-0.185 END + ATOM PA TYPE= PN3P CHARGE= 1.212 END + ATOM O2A TYPE= ON3O CHARGE=-0.891 END + ATOM O1A TYPE= ON3K CHARGE=-0.597 END + ATOM O5B TYPE= ON3Y CHARGE=-0.185 END + ATOM C5B TYPE= CN3R CHARGE= 0.058 END + ATOM C4B TYPE= CN3L CHARGE= 0.208 END + ATOM O4B TYPE= ON3Z CHARGE=-0.185 END + ATOM C3B TYPE= CN3Z CHARGE= 0.121 END + ATOM O3B TYPE= ON38 CHARGE=-0.194 END + ATOM HO3A TYPE= HN3F CHARGE= 0.043 END + ATOM C2B TYPE= CN32 CHARGE= 0.121 END + ATOM O2B TYPE= ON3A CHARGE=-0.185 END + ATOM P2B TYPE= PN3Q CHARGE= 1.211 END + ATOM O2X TYPE= ON3M CHARGE=-1.057 END + ATOM O3X TYPE= ON39 CHARGE=-1.057 END + ATOM O1X TYPE= ON3W CHARGE=-0.764 END + ATOM C1B TYPE= CN3U CHARGE= 0.208 END + ATOM N9A TYPE= NN3H CHARGE= 0.229 END + ATOM C8A TYPE= CN31 CHARGE=-0.046 END + ATOM N7A TYPE= NN3G CHARGE=-0.510 END + ATOM C5A TYPE= CN3V CHARGE= 0.129 END + ATOM C4A TYPE= CN3P CHARGE= 0.265 END + ATOM N3A TYPE= NN3M CHARGE=-0.525 END + ATOM C2A TYPE= CN3D CHARGE=-0.046 END + ATOM N1A TYPE= NN34 CHARGE=-0.525 END + ATOM C6A TYPE= CN3B CHARGE= 0.265 END + ATOM N6A TYPE= NN3I CHARGE= 0.052 END + ATOM H62A TYPE= HN31 CHARGE=-0.002 END + ATOM H61A TYPE= HN3W CHARGE=-0.002 END + + BOND N7N H72N + BOND N7N H71N + BOND N7N C7N + BOND C7N O7N + BOND C7N C3N + BOND C3N C2N + BOND C3N C4N + BOND C2N N1N + BOND C4N C5N + BOND C5N C6N + BOND C6N N1N + BOND N1N C1D + BOND C1D O4D + BOND C1D C2D + BOND O4D C4D + BOND C2D O2D + BOND C2D C3D + BOND O2D HO2N + BOND C3D O3D + BOND C3D C4D + BOND O3D HAB + BOND C4D C5D + BOND C5D O5D + BOND O5D PN + BOND PN O1N + BOND PN O2N + BOND PN O3 + BOND O3 PA + BOND PA O2A + BOND PA O1A + BOND PA O5B + BOND O5B C5B + BOND C5B C4B + BOND C4B O4B + BOND C4B C3B + BOND O4B C1B + BOND C3B O3B + BOND C3B C2B + BOND O3B HO3A + BOND C2B O2B + BOND C2B C1B + BOND O2B P2B + BOND P2B O2X + BOND P2B O3X + BOND P2B O1X + BOND C1B N9A + BOND N9A C8A + BOND N9A C4A + BOND C8A N7A + BOND N7A C5A + BOND C5A C4A + BOND C5A C6A + BOND C4A N3A + BOND N3A C2A + BOND C2A N1A + BOND N1A C6A + BOND C6A N6A + BOND N6A H62A + BOND N6A H61A + + ANGLE H72N N7N H71N + ANGLE H72N N7N C7N + ANGLE H71N N7N C7N + ANGLE N7N C7N O7N + ANGLE N7N C7N C3N + ANGLE O7N C7N C3N + ANGLE C7N C3N C2N + ANGLE C7N C3N C4N + ANGLE C2N C3N C4N + ANGLE C3N C2N N1N + ANGLE C3N C4N C5N + ANGLE C4N C5N C6N + ANGLE C5N C6N N1N + ANGLE C2N N1N C6N + ANGLE C2N N1N C1D + ANGLE C6N N1N C1D + ANGLE N1N C1D O4D + ANGLE N1N C1D C2D + ANGLE O4D C1D C2D + ANGLE C1D O4D C4D + ANGLE C1D C2D O2D + ANGLE C1D C2D C3D + ANGLE O2D C2D C3D + ANGLE C2D O2D HO2N + ANGLE C2D C3D O3D + ANGLE C2D C3D C4D + ANGLE O3D C3D C4D + ANGLE C3D O3D HAB + ANGLE O4D C4D C3D + ANGLE O4D C4D C5D + ANGLE C3D C4D C5D + ANGLE C4D C5D O5D + ANGLE C5D O5D PN + ANGLE O5D PN O1N + ANGLE O5D PN O2N + ANGLE O5D PN O3 + ANGLE O1N PN O2N + ANGLE O1N PN O3 + ANGLE O2N PN O3 + ANGLE PN O3 PA + ANGLE O3 PA O2A + ANGLE O3 PA O1A + ANGLE O3 PA O5B + ANGLE O2A PA O1A + ANGLE O2A PA O5B + ANGLE O1A PA O5B + ANGLE PA O5B C5B + ANGLE O5B C5B C4B + ANGLE C5B C4B O4B + ANGLE C5B C4B C3B + ANGLE O4B C4B C3B + ANGLE C4B O4B C1B + ANGLE C4B C3B O3B + ANGLE C4B C3B C2B + ANGLE O3B C3B C2B + ANGLE C3B O3B HO3A + ANGLE C3B C2B O2B + ANGLE C3B C2B C1B + ANGLE O2B C2B C1B + ANGLE C2B O2B P2B + ANGLE O2B P2B O2X + ANGLE O2B P2B O3X + ANGLE O2B P2B O1X + ANGLE O2X P2B O3X + ANGLE O2X P2B O1X + ANGLE O3X P2B O1X + ANGLE O4B C1B C2B + ANGLE O4B C1B N9A + ANGLE C2B C1B N9A + ANGLE C1B N9A C8A + ANGLE C1B N9A C4A + ANGLE C8A N9A C4A + ANGLE N9A C8A N7A + ANGLE C8A N7A C5A + ANGLE N7A C5A C4A + ANGLE N7A C5A C6A + ANGLE C4A C5A C6A + ANGLE N9A C4A C5A + ANGLE N9A C4A N3A + ANGLE C5A C4A N3A + ANGLE C4A N3A C2A + ANGLE N3A C2A N1A + ANGLE C2A N1A C6A + ANGLE C5A C6A N1A + ANGLE C5A C6A N6A + ANGLE N1A C6A N6A + ANGLE C6A N6A H62A + ANGLE C6A N6A H61A + ANGLE H62A N6A H61A + + IMPROPER N7N H72N H71N C7N + IMPROPER C7N N7N C3N O7N + IMPROPER C3N C4N C2N C7N + IMPROPER N1N C1D C6N C2N + IMPROPER N9A C1B C8A C4A + IMPROPER C5A C6A C4A N7A + IMPROPER C4A N3A C5A N9A + IMPROPER C6A C5A N1A N6A + IMPROPER N6A C6A H62A H61A + IMPROPER C1D N1N O4D C2D + IMPROPER C2D C1D O2D C3D + IMPROPER C3D C2D O3D C4D + IMPROPER C4D O4D C5D C3D + IMPROPER PN O5D O2N O1N + IMPROPER PA O3 O1A O2A + IMPROPER C4B C5B C3B O4B + IMPROPER C3B C4B C2B O3B + IMPROPER C2B C3B C1B O2B + IMPROPER P2B O2B O3X O2X + IMPROPER C1B O4B C2B N9A + IMPROPER N9A C8A N7A C5A + IMPROPER C8A N7A C5A C4A + IMPROPER N7A C5A C4A N9A + IMPROPER C5A C4A N9A C8A + IMPROPER C4A N9A C8A N7A + IMPROPER C3N C2N N1N C6N + IMPROPER C2N N1N C6N C5N + IMPROPER N1N C6N C5N C4N + IMPROPER C6N C5N C4N C3N + IMPROPER C5N C4N C3N C2N + IMPROPER C4N C3N C2N N1N + IMPROPER C5A C4A N3A C2A + IMPROPER C4A N3A C2A N1A + IMPROPER N3A C2A N1A C6A + IMPROPER C2A N1A C6A C5A + IMPROPER N1A C6A C5A C4A + IMPROPER C6A C5A C4A N3A + + DIHEDRAL C3N C7N N7N H72N + DIHEDRAL C4N C3N C7N N7N + DIHEDRAL C2N N1N C1D C2D + DIHEDRAL N1N C1D O4D C4D + DIHEDRAL N1N C1D C2D C3D + DIHEDRAL C5D C4D O4D C1D + DIHEDRAL C1D C2D O2D HO2N + DIHEDRAL C4D C3D C2D C1D + DIHEDRAL C2D C3D O3D HAB + DIHEDRAL C2D C3D C4D C5D + DIHEDRAL O4D C4D C5D O5D + DIHEDRAL PN O5D C5D C4D + DIHEDRAL C5D O5D PN O3 + DIHEDRAL C5D O5D PN O3 + DIHEDRAL PA O3 PN O5D + DIHEDRAL PA O3 PN O5D + DIHEDRAL PN O3 PA O5B + DIHEDRAL PN O3 PA O5B + DIHEDRAL C5B O5B PA O3 + DIHEDRAL C5B O5B PA O3 + DIHEDRAL PA O5B C5B C4B + DIHEDRAL C3B C4B C5B O5B + DIHEDRAL C5B C4B O4B C1B + DIHEDRAL C5B C4B C3B C2B + DIHEDRAL N9A C1B O4B C4B + DIHEDRAL C4B C3B O3B HO3A + DIHEDRAL C1B C2B C3B C4B + DIHEDRAL C3B C2B O2B P2B + DIHEDRAL C3B C2B C1B N9A + DIHEDRAL C2B O2B P2B O1X + DIHEDRAL C2B O2B P2B O1X + DIHEDRAL O4B C1B N9A C4A + DIHEDRAL C5A C6A N6A H61A +END + + +! Adding topology definition for residue NDP + +MASS NNPN 14.0067 ! equivalent to NT +MASS HNPG 1.0080 ! equivalent to H +MASS HNPM 1.0080 ! equivalent to H +MASS CNP1 12.0110 ! equivalent to C +MASS ONPY 15.9994 ! equivalent to O +MASS CNP6 12.0110 ! equivalent to CB +MASS CNP2 13.0190 ! equivalent to CR61 +MASS CNPL 14.0270 ! equivalent to CH2 +MASS CNP9 13.0190 ! equivalent to CR61 +MASS CNP7 13.0190 ! equivalent to CR61 +MASS NNP7 14.0067 ! equivalent to NR6* +MASS CNPI 13.0190 ! equivalent to CS1 +MASS ONPA 15.9994 ! equivalent to OS +MASS CNPC 13.0190 ! equivalent to CH1 +MASS ONPN 15.9994 ! equivalent to OA +MASS HNP5 1.0080 ! equivalent to HO +MASS CNPE 13.0190 ! equivalent to CH1 +MASS ONP2 15.9994 ! equivalent to OA +MASS HNPA 1.0080 ! equivalent to HO +MASS CNPO 13.0190 ! equivalent to CS1 +MASS CNPP 14.0270 ! equivalent to CH2 +MASS ONPZ 15.9994 ! equivalent to OS +MASS PNP4 30.9738 ! equivalent to P +MASS ONPG 15.9994 ! equivalent to OA +MASS ONPM 15.9994 ! equivalent to OM +MASS ONPF 15.9994 ! equivalent to OS +MASS PNPT 30.9738 ! equivalent to P +MASS ONP5 15.9994 ! equivalent to OA +MASS ONPB 15.9994 ! equivalent to OM +MASS ONP6 15.9994 ! equivalent to OS +MASS CNPU 14.0270 ! equivalent to CH2 +MASS CNPG 13.0190 ! equivalent to CS1 +MASS ONPU 15.9994 ! equivalent to OS +MASS CNPY 13.0190 ! equivalent to CH1 +MASS ONPW 15.9994 ! equivalent to OA +MASS HNPH 1.0080 ! equivalent to HO +MASS CNPF 13.0190 ! equivalent to CH1 +MASS ONP8 15.9994 ! equivalent to OS +MASS PNPL 30.9738 ! equivalent to P +MASS ONPO 15.9994 ! equivalent to OA +MASS ONPV 15.9994 ! equivalent to OA +MASS ONPX 15.9994 ! equivalent to OM +MASS CNP0 13.0190 ! equivalent to CS1 +MASS NNPK 14.0067 ! equivalent to NR5* +MASS CNPN 13.0190 ! equivalent to CR51 +MASS NNPR 14.0067 ! equivalent to NR5 +MASS CNPK 12.0110 ! equivalent to CB +MASS CNP4 12.0110 ! equivalent to CB +MASS NNPG 14.0067 ! equivalent to NR6 +MASS CNPT 13.0190 ! equivalent to CR61 +MASS NNPF 14.0067 ! equivalent to NR6 +MASS CNP8 12.0110 ! equivalent to CB +MASS NNPW 14.0067 ! equivalent to NT +MASS HNPX 1.0080 ! equivalent to H +MASS HNPS 1.0080 ! equivalent to H + +RESIdue NDP +GROUP + ATOM N7N TYPE= NNPN CHARGE= 0.054 END + ATOM H72N TYPE= HNPG CHARGE=-0.001 END + ATOM H71N TYPE= HNPM CHARGE=-0.001 END + ATOM C7N TYPE= CNP1 CHARGE= 0.360 END + ATOM O7N TYPE= ONPY CHARGE=-0.706 END + ATOM C3N TYPE= CNP6 CHARGE=-0.023 END + ATOM C2N TYPE= CNP2 CHARGE=-0.010 END + ATOM C4N TYPE= CNPL CHARGE= 0.060 END + ATOM C5N TYPE= CNP9 CHARGE=-0.010 END + ATOM C6N TYPE= CNP7 CHARGE=-0.010 END + ATOM N1N TYPE= NNP7 CHARGE= 0.284 END + ATOM C1D TYPE= CNPI CHARGE= 0.210 END + ATOM O4D TYPE= ONPA CHARGE=-0.184 END + ATOM C2D TYPE= CNPC CHARGE= 0.123 END + ATOM O2D TYPE= ONPN CHARGE=-0.193 END + ATOM HO2N TYPE= HNP5 CHARGE= 0.045 END + ATOM C3D TYPE= CNPE CHARGE= 0.123 END + ATOM O3D TYPE= ONP2 CHARGE=-0.193 END + ATOM HAB TYPE= HNPA CHARGE= 0.045 END + ATOM C4D TYPE= CNPO CHARGE= 0.210 END + ATOM C5D TYPE= CNPP CHARGE= 0.060 END + ATOM O5D TYPE= ONPZ CHARGE=-0.184 END + ATOM PN TYPE= PNP4 CHARGE= 1.214 END + ATOM O2N TYPE= ONPG CHARGE=-0.889 END + ATOM O1N TYPE= ONPM CHARGE=-0.596 END + ATOM O3 TYPE= ONPF CHARGE=-0.184 END + ATOM PA TYPE= PNPT CHARGE= 1.214 END + ATOM O2A TYPE= ONP5 CHARGE=-0.889 END + ATOM O1A TYPE= ONPB CHARGE=-0.596 END + ATOM O5B TYPE= ONP6 CHARGE=-0.184 END + ATOM C5B TYPE= CNPU CHARGE= 0.060 END + ATOM C4B TYPE= CNPG CHARGE= 0.210 END + ATOM O4B TYPE= ONPU CHARGE=-0.184 END + ATOM C3B TYPE= CNPY CHARGE= 0.123 END + ATOM O3B TYPE= ONPW CHARGE=-0.193 END + ATOM HO3A TYPE= HNPH CHARGE= 0.045 END + ATOM C2B TYPE= CNPF CHARGE= 0.123 END + ATOM O2B TYPE= ONP8 CHARGE=-0.184 END + ATOM P2B TYPE= PNPL CHARGE= 1.214 END + ATOM O2X TYPE= ONPO CHARGE=-1.056 END + ATOM O3X TYPE= ONPV CHARGE=-1.056 END + ATOM O1X TYPE= ONPX CHARGE=-0.762 END + ATOM C1B TYPE= CNP0 CHARGE= 0.210 END + ATOM N9A TYPE= NNPK CHARGE= 0.230 END + ATOM C8A TYPE= CNPN CHARGE=-0.044 END + ATOM N7A TYPE= NNPR CHARGE=-0.509 END + ATOM C5A TYPE= CNPK CHARGE= 0.130 END + ATOM C4A TYPE= CNP4 CHARGE= 0.266 END + ATOM N3A TYPE= NNPG CHARGE=-0.523 END + ATOM C2A TYPE= CNPT CHARGE=-0.044 END + ATOM N1A TYPE= NNPF CHARGE=-0.523 END + ATOM C6A TYPE= CNP8 CHARGE= 0.266 END + ATOM N6A TYPE= NNPW CHARGE= 0.054 END + ATOM H61A TYPE= HNPX CHARGE=-0.001 END + ATOM H62A TYPE= HNPS CHARGE=-0.001 END + + BOND N7N H72N + BOND N7N H71N + BOND N7N C7N + BOND C7N O7N + BOND C7N C3N + BOND C3N C2N + BOND C3N C4N + BOND C2N N1N + BOND C4N C5N + BOND C5N C6N + BOND C6N N1N + BOND N1N C1D + BOND C1D O4D + BOND C1D C2D + BOND O4D C4D + BOND C2D O2D + BOND C2D C3D + BOND O2D HO2N + BOND C3D O3D + BOND C3D C4D + BOND O3D HAB + BOND C4D C5D + BOND C5D O5D + BOND O5D PN + BOND PN O2N + BOND PN O1N + BOND PN O3 + BOND O3 PA + BOND PA O2A + BOND PA O1A + BOND PA O5B + BOND O5B C5B + BOND C5B C4B + BOND C4B O4B + BOND C4B C3B + BOND O4B C1B + BOND C3B O3B + BOND C3B C2B + BOND O3B HO3A + BOND C2B O2B + BOND C2B C1B + BOND O2B P2B + BOND P2B O2X + BOND P2B O3X + BOND P2B O1X + BOND C1B N9A + BOND N9A C8A + BOND N9A C4A + BOND C8A N7A + BOND N7A C5A + BOND C5A C4A + BOND C5A C6A + BOND C4A N3A + BOND N3A C2A + BOND C2A N1A + BOND N1A C6A + BOND C6A N6A + BOND N6A H61A + BOND N6A H62A + + ANGLE H72N N7N H71N + ANGLE H72N N7N C7N + ANGLE H71N N7N C7N + ANGLE N7N C7N O7N + ANGLE N7N C7N C3N + ANGLE O7N C7N C3N + ANGLE C7N C3N C2N + ANGLE C7N C3N C4N + ANGLE C2N C3N C4N + ANGLE C3N C2N N1N + ANGLE C3N C4N C5N + ANGLE C4N C5N C6N + ANGLE C5N C6N N1N + ANGLE C2N N1N C6N + ANGLE C2N N1N C1D + ANGLE C6N N1N C1D + ANGLE N1N C1D O4D + ANGLE N1N C1D C2D + ANGLE O4D C1D C2D + ANGLE C1D O4D C4D + ANGLE C1D C2D O2D + ANGLE C1D C2D C3D + ANGLE O2D C2D C3D + ANGLE C2D O2D HO2N + ANGLE C2D C3D O3D + ANGLE C2D C3D C4D + ANGLE O3D C3D C4D + ANGLE C3D O3D HAB + ANGLE O4D C4D C3D + ANGLE O4D C4D C5D + ANGLE C3D C4D C5D + ANGLE C4D C5D O5D + ANGLE C5D O5D PN + ANGLE O5D PN O2N + ANGLE O5D PN O1N + ANGLE O5D PN O3 + ANGLE O2N PN O1N + ANGLE O2N PN O3 + ANGLE O1N PN O3 + ANGLE PN O3 PA + ANGLE O3 PA O2A + ANGLE O3 PA O1A + ANGLE O3 PA O5B + ANGLE O2A PA O1A + ANGLE O2A PA O5B + ANGLE O1A PA O5B + ANGLE PA O5B C5B + ANGLE O5B C5B C4B + ANGLE C5B C4B O4B + ANGLE C5B C4B C3B + ANGLE O4B C4B C3B + ANGLE C4B O4B C1B + ANGLE C4B C3B O3B + ANGLE C4B C3B C2B + ANGLE O3B C3B C2B + ANGLE C3B O3B HO3A + ANGLE C3B C2B O2B + ANGLE C3B C2B C1B + ANGLE O2B C2B C1B + ANGLE C2B O2B P2B + ANGLE O2B P2B O2X + ANGLE O2B P2B O3X + ANGLE O2B P2B O1X + ANGLE O2X P2B O3X + ANGLE O2X P2B O1X + ANGLE O3X P2B O1X + ANGLE O4B C1B C2B + ANGLE O4B C1B N9A + ANGLE C2B C1B N9A + ANGLE C1B N9A C8A + ANGLE C1B N9A C4A + ANGLE C8A N9A C4A + ANGLE N9A C8A N7A + ANGLE C8A N7A C5A + ANGLE N7A C5A C4A + ANGLE N7A C5A C6A + ANGLE C4A C5A C6A + ANGLE N9A C4A C5A + ANGLE N9A C4A N3A + ANGLE C5A C4A N3A + ANGLE C4A N3A C2A + ANGLE N3A C2A N1A + ANGLE C2A N1A C6A + ANGLE C5A C6A N1A + ANGLE C5A C6A N6A + ANGLE N1A C6A N6A + ANGLE C6A N6A H61A + ANGLE C6A N6A H62A + ANGLE H61A N6A H62A + + IMPROPER N7N H72N H71N C7N + IMPROPER C7N N7N C3N O7N + IMPROPER C3N C4N C2N C7N + IMPROPER N1N C1D C6N C2N + IMPROPER N9A C1B C8A C4A + IMPROPER C5A C6A C4A N7A + IMPROPER C4A N3A C5A N9A + IMPROPER C6A C5A N1A N6A + IMPROPER N6A C6A H61A H62A + IMPROPER C1D N1N O4D C2D + IMPROPER C2D C1D O2D C3D + IMPROPER C3D C2D O3D C4D + IMPROPER C4D O4D C5D C3D + IMPROPER PN O5D O1N O2N + IMPROPER PA O3 O2A O1A + IMPROPER C4B C5B C3B O4B + IMPROPER C3B C4B C2B O3B + IMPROPER C2B C3B C1B O2B + IMPROPER P2B O2B O3X O2X + IMPROPER C1B O4B C2B N9A + IMPROPER N9A C8A N7A C5A + IMPROPER C8A N7A C5A C4A + IMPROPER N7A C5A C4A N9A + IMPROPER C5A C4A N9A C8A + IMPROPER C4A N9A C8A N7A + IMPROPER C5A C4A N3A C2A + IMPROPER C4A N3A C2A N1A + IMPROPER N3A C2A N1A C6A + IMPROPER C2A N1A C6A C5A + IMPROPER N1A C6A C5A C4A + IMPROPER C6A C5A C4A N3A + + DIHEDRAL C3N C7N N7N H72N + DIHEDRAL C4N C3N C7N N7N + DIHEDRAL C7N C3N C2N N1N + DIHEDRAL C7N C3N C4N C5N + DIHEDRAL C3N C2N N1N C1D + DIHEDRAL C3N C4N C5N C6N + DIHEDRAL C4N C5N C6N N1N + DIHEDRAL C5N C6N N1N C1D + DIHEDRAL C2N N1N C1D C2D + DIHEDRAL N1N C1D O4D C4D + DIHEDRAL N1N C1D C2D C3D + DIHEDRAL C5D C4D O4D C1D + DIHEDRAL C1D C2D O2D HO2N + DIHEDRAL C4D C3D C2D C1D + DIHEDRAL C2D C3D O3D HAB + DIHEDRAL C2D C3D C4D C5D + DIHEDRAL O4D C4D C5D O5D + DIHEDRAL PN O5D C5D C4D + DIHEDRAL C5D O5D PN O3 + DIHEDRAL C5D O5D PN O3 + DIHEDRAL PA O3 PN O5D + DIHEDRAL PA O3 PN O5D + DIHEDRAL PN O3 PA O5B + DIHEDRAL PN O3 PA O5B + DIHEDRAL C5B O5B PA O3 + DIHEDRAL C5B O5B PA O3 + DIHEDRAL PA O5B C5B C4B + DIHEDRAL C3B C4B C5B O5B + DIHEDRAL C5B C4B O4B C1B + DIHEDRAL C5B C4B C3B C2B + DIHEDRAL N9A C1B O4B C4B + DIHEDRAL C4B C3B O3B HO3A + DIHEDRAL C1B C2B C3B C4B + DIHEDRAL C3B C2B O2B P2B + DIHEDRAL C3B C2B C1B N9A + DIHEDRAL C2B O2B P2B O1X + DIHEDRAL C2B O2B P2B O1X + DIHEDRAL O4B C1B N9A C4A + DIHEDRAL C5A C6A N6A H62A +END + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dmso.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dmso.pdb new file mode 100644 index 0000000000000000000000000000000000000000..8a8c1e603067979fea846e7ed46349930d1e601d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dmso.pdb @@ -0,0 +1,852 @@ +! dmso.pdb +! +! *********************************************************************** +! * Copyright 2003-2018 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +REMARK DMSO Box, Alexandre Bonvin, Utrecht University, Jan. 2002 +REMARK This is a DMSO cubic box containing 208 molecules taken +REMARK from the GROMACS 3.0 distribution. +REMARK The box size is 29.096 A resulting in the proper +REMARK experimental density of 1.0955 g/cm**3 for DMSO at 298K. +REMARK This box was equilibrated for 1 ns at 300K under NVT +REMARK conditions using the DMSO parameters from Liu et al +REMARK JACS 117:4363 (1995). The total energy of the system is +REMARK -10197 kJ mol-1 +ATOM 1 SD DMS 1 13.280 17.430 7.870 1.00 0.000 +ATOM 2 CD1 DMS 1 14.750 16.810 6.750 1.00 0.000 +ATOM 3 OD DMS 1 13.790 18.670 8.600 1.00 0.000 +ATOM 4 CD2 DMS 1 12.130 17.950 6.380 1.00 0.000 +ATOM 5 SD DMS 2 9.010 10.650 6.690 1.00 0.000 +ATOM 6 CD1 DMS 2 10.220 9.560 7.770 1.00 0.000 +ATOM 7 OD DMS 2 8.480 11.860 7.450 1.00 0.000 +ATOM 8 CD2 DMS 2 10.320 11.160 5.340 1.00 0.000 +ATOM 9 SD DMS 3 21.660 13.440 9.220 1.00 0.000 +ATOM 10 CD1 DMS 3 21.240 12.090 7.870 1.00 0.000 +ATOM 11 OD DMS 3 21.620 12.660 10.530 1.00 0.000 +ATOM 12 CD2 DMS 3 23.500 13.760 8.650 1.00 0.000 +ATOM 13 SD DMS 4 4.640 13.540 9.630 1.00 0.000 +ATOM 14 CD1 DMS 4 5.880 13.380 8.140 1.00 0.000 +ATOM 15 OD DMS 4 5.130 12.610 10.750 1.00 0.000 +ATOM 16 CD2 DMS 4 5.320 15.280 10.190 1.00 0.000 +ATOM 17 SD DMS 5 3.110 18.030 23.680 1.00 0.000 +ATOM 18 CD1 DMS 5 4.070 19.520 22.870 1.00 0.000 +ATOM 19 OD DMS 5 1.650 18.290 24.070 1.00 0.000 +ATOM 20 CD2 DMS 5 3.120 16.730 22.230 1.00 0.000 +ATOM 21 SD DMS 6 0.390 27.450 12.750 1.00 0.000 +ATOM 22 CD1 DMS 6 -0.410 25.830 13.480 1.00 0.000 +ATOM 23 OD DMS 6 -0.670 28.490 12.380 1.00 0.000 +ATOM 24 CD2 DMS 6 1.160 27.840 14.500 1.00 0.000 +ATOM 25 SD DMS 7 9.910 5.240 13.400 1.00 0.000 +ATOM 26 CD1 DMS 7 9.930 7.160 13.750 1.00 0.000 +ATOM 27 OD DMS 7 10.430 5.110 11.970 1.00 0.000 +ATOM 28 CD2 DMS 7 11.470 4.750 14.450 1.00 0.000 +ATOM 29 SD DMS 8 -0.000 12.330 15.660 1.00 0.000 +ATOM 30 CD1 DMS 8 0.150 12.450 17.600 1.00 0.000 +ATOM 31 OD DMS 8 1.250 11.670 15.070 1.00 0.000 +ATOM 32 CD2 DMS 8 -1.390 10.960 15.580 1.00 0.000 +ATOM 33 SD DMS 9 15.760 8.050 22.200 1.00 0.000 +ATOM 34 CD1 DMS 9 17.430 7.650 21.280 1.00 0.000 +ATOM 35 OD DMS 9 15.120 6.700 22.490 1.00 0.000 +ATOM 36 CD2 DMS 9 16.620 8.600 23.870 1.00 0.000 +ATOM 37 SD DMS 10 9.720 0.760 10.370 1.00 0.000 +ATOM 38 CD1 DMS 10 8.910 2.510 10.080 1.00 0.000 +ATOM 39 OD DMS 10 9.040 -0.340 9.560 1.00 0.000 +ATOM 40 CD2 DMS 10 11.340 1.270 9.410 1.00 0.000 +ATOM 41 SD DMS 11 7.760 10.730 23.480 1.00 0.000 +ATOM 42 CD1 DMS 11 7.030 9.190 22.530 1.00 0.000 +ATOM 43 OD DMS 11 8.360 10.200 24.790 1.00 0.000 +ATOM 44 CD2 DMS 11 9.150 11.190 22.200 1.00 0.000 +ATOM 45 SD DMS 12 15.570 27.790 16.690 1.00 0.000 +ATOM 46 CD1 DMS 12 15.610 28.700 18.410 1.00 0.000 +ATOM 47 OD DMS 12 16.130 26.370 16.760 1.00 0.000 +ATOM 48 CD2 DMS 12 13.660 27.420 16.740 1.00 0.000 +ATOM 49 SD DMS 13 3.980 7.990 18.970 1.00 0.000 +ATOM 50 CD1 DMS 13 2.510 9.270 19.030 1.00 0.000 +ATOM 51 OD DMS 13 5.090 8.870 18.400 1.00 0.000 +ATOM 52 CD2 DMS 13 4.130 7.850 20.910 1.00 0.000 +ATOM 53 SD DMS 14 5.340 10.640 2.890 1.00 0.000 +ATOM 54 CD1 DMS 14 4.190 11.710 1.730 1.00 0.000 +ATOM 55 OD DMS 14 6.780 10.400 2.420 1.00 0.000 +ATOM 56 CD2 DMS 14 5.310 11.810 4.440 1.00 0.000 +ATOM 57 SD DMS 15 1.490 13.030 21.090 1.00 0.000 +ATOM 58 CD1 DMS 15 1.760 13.000 23.020 1.00 0.000 +ATOM 59 OD DMS 15 1.070 11.650 20.580 1.00 0.000 +ATOM 60 CD2 DMS 15 0.110 14.410 21.010 1.00 0.000 +ATOM 61 SD DMS 16 10.070 1.570 17.500 1.00 0.000 +ATOM 62 CD1 DMS 16 8.230 1.550 16.840 1.00 0.000 +ATOM 63 OD DMS 16 10.990 1.330 16.310 1.00 0.000 +ATOM 64 CD2 DMS 16 10.270 3.480 17.810 1.00 0.000 +ATOM 65 SD DMS 17 19.100 10.220 4.410 1.00 0.000 +ATOM 66 CD1 DMS 17 19.420 9.210 6.050 1.00 0.000 +ATOM 67 OD DMS 17 20.380 10.200 3.590 1.00 0.000 +ATOM 68 CD2 DMS 17 17.820 8.900 3.750 1.00 0.000 +ATOM 69 SD DMS 18 13.680 15.190 17.050 1.00 0.000 +ATOM 70 CD1 DMS 18 13.490 13.990 18.570 1.00 0.000 +ATOM 71 OD DMS 18 15.180 15.120 16.720 1.00 0.000 +ATOM 72 CD2 DMS 18 12.560 14.380 15.680 1.00 0.000 +ATOM 73 SD DMS 19 20.830 19.070 21.540 1.00 0.000 +ATOM 74 CD1 DMS 19 18.910 19.400 21.460 1.00 0.000 +ATOM 75 OD DMS 19 21.570 20.340 21.120 1.00 0.000 +ATOM 76 CD2 DMS 19 20.890 18.810 23.470 1.00 0.000 +ATOM 77 SD DMS 20 18.460 18.670 1.770 1.00 0.000 +ATOM 78 CD1 DMS 20 17.920 20.040 3.050 1.00 0.000 +ATOM 79 OD DMS 20 19.990 18.700 1.750 1.00 0.000 +ATOM 80 CD2 DMS 20 17.920 17.270 3.020 1.00 0.000 +ATOM 81 SD DMS 21 24.860 26.540 17.270 1.00 0.000 +ATOM 82 CD1 DMS 21 23.410 26.800 15.990 1.00 0.000 +ATOM 83 OD DMS 21 25.850 27.610 16.800 1.00 0.000 +ATOM 84 CD2 DMS 21 23.850 27.310 18.750 1.00 0.000 +ATOM 85 SD DMS 22 18.110 15.290 13.570 1.00 0.000 +ATOM 86 CD1 DMS 22 18.790 16.240 12.010 1.00 0.000 +ATOM 87 OD DMS 22 19.160 14.330 14.140 1.00 0.000 +ATOM 88 CD2 DMS 22 17.910 16.790 14.790 1.00 0.000 +ATOM 89 SD DMS 23 7.740 5.900 16.780 1.00 0.000 +ATOM 90 CD1 DMS 23 6.890 7.550 16.190 1.00 0.000 +ATOM 91 OD DMS 23 9.250 6.110 16.740 1.00 0.000 +ATOM 92 CD2 DMS 23 7.310 6.310 18.640 1.00 0.000 +ATOM 93 SD DMS 24 24.110 1.840 6.900 1.00 0.000 +ATOM 94 CD1 DMS 24 24.200 3.670 7.560 1.00 0.000 +ATOM 95 OD DMS 24 23.310 1.840 5.590 1.00 0.000 +ATOM 96 CD2 DMS 24 25.910 1.240 6.440 1.00 0.000 +ATOM 97 SD DMS 25 3.430 5.060 10.230 1.00 0.000 +ATOM 98 CD1 DMS 25 3.700 6.780 9.360 1.00 0.000 +ATOM 99 OD DMS 25 2.940 4.050 9.190 1.00 0.000 +ATOM 100 CD2 DMS 25 5.350 4.910 10.520 1.00 0.000 +ATOM 101 SD DMS 26 18.890 5.200 9.120 1.00 0.000 +ATOM 102 CD1 DMS 26 19.530 6.910 8.430 1.00 0.000 +ATOM 103 OD DMS 26 17.550 4.760 8.520 1.00 0.000 +ATOM 104 CD2 DMS 26 20.340 4.260 8.220 1.00 0.000 +ATOM 105 SD DMS 27 20.970 12.420 15.540 1.00 0.000 +ATOM 106 CD1 DMS 27 21.000 11.940 13.660 1.00 0.000 +ATOM 107 OD DMS 27 21.870 11.520 16.390 1.00 0.000 +ATOM 108 CD2 DMS 27 22.080 14.010 15.320 1.00 0.000 +ATOM 109 SD DMS 28 27.090 3.580 10.830 1.00 0.000 +ATOM 110 CD1 DMS 28 28.640 4.190 9.820 1.00 0.000 +ATOM 111 OD DMS 28 25.860 4.180 10.140 1.00 0.000 +ATOM 112 CD2 DMS 28 27.390 1.790 10.110 1.00 0.000 +ATOM 113 SD DMS 29 5.760 3.460 22.180 1.00 0.000 +ATOM 114 CD1 DMS 29 5.610 2.640 23.940 1.00 0.000 +ATOM 115 OD DMS 29 4.330 3.330 21.650 1.00 0.000 +ATOM 116 CD2 DMS 29 6.020 5.240 22.930 1.00 0.000 +ATOM 117 SD DMS 30 16.250 18.720 24.810 1.00 0.000 +ATOM 118 CD1 DMS 30 16.960 17.350 26.000 1.00 0.000 +ATOM 119 OD DMS 30 17.350 19.340 23.940 1.00 0.000 +ATOM 120 CD2 DMS 30 15.310 17.450 23.660 1.00 0.000 +ATOM 121 SD DMS 31 6.360 23.150 12.420 1.00 0.000 +ATOM 122 CD1 DMS 31 7.820 22.730 13.640 1.00 0.000 +ATOM 123 OD DMS 31 6.540 24.560 11.850 1.00 0.000 +ATOM 124 CD2 DMS 31 6.930 21.950 10.990 1.00 0.000 +ATOM 125 SD DMS 32 11.230 2.860 22.070 1.00 0.000 +ATOM 126 CD1 DMS 32 9.300 2.920 22.390 1.00 0.000 +ATOM 127 OD DMS 32 11.550 3.720 20.840 1.00 0.000 +ATOM 128 CD2 DMS 32 11.590 4.010 23.610 1.00 0.000 +ATOM 129 SD DMS 33 25.460 24.730 21.010 1.00 0.000 +ATOM 130 CD1 DMS 33 24.500 26.170 21.920 1.00 0.000 +ATOM 131 OD DMS 33 24.730 24.510 19.680 1.00 0.000 +ATOM 132 CD2 DMS 33 27.110 25.700 20.670 1.00 0.000 +ATOM 133 SD DMS 34 25.770 12.850 12.760 1.00 0.000 +ATOM 134 CD1 DMS 34 26.600 12.850 11.000 1.00 0.000 +ATOM 135 OD DMS 34 24.960 14.150 12.820 1.00 0.000 +ATOM 136 CD2 DMS 34 24.440 11.510 12.260 1.00 0.000 +ATOM 137 SD DMS 35 21.620 2.090 11.640 1.00 0.000 +ATOM 138 CD1 DMS 35 23.090 3.360 11.770 1.00 0.000 +ATOM 139 OD DMS 35 20.330 2.890 11.430 1.00 0.000 +ATOM 140 CD2 DMS 35 22.110 1.380 9.890 1.00 0.000 +ATOM 141 SD DMS 36 12.780 8.130 24.760 1.00 0.000 +ATOM 142 CD1 DMS 36 13.420 8.760 26.490 1.00 0.000 +ATOM 143 OD DMS 36 11.970 6.850 24.960 1.00 0.000 +ATOM 144 CD2 DMS 36 11.600 9.660 24.470 1.00 0.000 +ATOM 145 SD DMS 37 2.890 7.640 13.890 1.00 0.000 +ATOM 146 CD1 DMS 37 3.440 8.840 12.450 1.00 0.000 +ATOM 147 OD DMS 37 3.810 6.440 14.040 1.00 0.000 +ATOM 148 CD2 DMS 37 3.310 8.730 15.450 1.00 0.000 +ATOM 149 SD DMS 38 19.690 9.030 19.370 1.00 0.000 +ATOM 150 CD1 DMS 38 19.300 8.680 17.490 1.00 0.000 +ATOM 151 OD DMS 38 20.960 8.210 19.610 1.00 0.000 +ATOM 152 CD2 DMS 38 20.280 10.880 19.180 1.00 0.000 +ATOM 153 SD DMS 39 7.210 17.240 3.460 1.00 0.000 +ATOM 154 CD1 DMS 39 7.240 15.950 4.920 1.00 0.000 +ATOM 155 OD DMS 39 6.560 18.510 4.010 1.00 0.000 +ATOM 156 CD2 DMS 39 9.080 17.740 3.220 1.00 0.000 +ATOM 157 SD DMS 40 8.980 27.100 15.190 1.00 0.000 +ATOM 158 CD1 DMS 40 8.390 26.840 13.350 1.00 0.000 +ATOM 159 OD DMS 40 9.000 25.700 15.810 1.00 0.000 +ATOM 160 CD2 DMS 40 10.870 27.370 14.810 1.00 0.000 +ATOM 161 SD DMS 41 24.140 6.440 22.860 1.00 0.000 +ATOM 162 CD1 DMS 41 23.230 7.650 21.640 1.00 0.000 +ATOM 163 OD DMS 41 23.390 6.510 24.190 1.00 0.000 +ATOM 164 CD2 DMS 41 23.830 4.760 21.920 1.00 0.000 +ATOM 165 SD DMS 42 11.810 13.940 3.360 1.00 0.000 +ATOM 166 CD1 DMS 42 13.510 14.760 3.860 1.00 0.000 +ATOM 167 OD DMS 42 10.580 14.740 3.800 1.00 0.000 +ATOM 168 CD2 DMS 42 11.920 14.280 1.440 1.00 0.000 +ATOM 169 SD DMS 43 16.690 1.010 22.090 1.00 0.000 +ATOM 170 CD1 DMS 43 17.030 0.790 24.000 1.00 0.000 +ATOM 171 OD DMS 43 15.820 -0.170 21.670 1.00 0.000 +ATOM 172 CD2 DMS 43 15.550 2.590 22.090 1.00 0.000 +ATOM 173 SD DMS 44 26.910 19.520 19.630 1.00 0.000 +ATOM 174 CD1 DMS 44 24.990 19.790 19.880 1.00 0.000 +ATOM 175 OD DMS 44 27.210 20.060 18.240 1.00 0.000 +ATOM 176 CD2 DMS 44 27.520 20.690 21.060 1.00 0.000 +ATOM 177 SD DMS 45 5.380 27.050 3.380 1.00 0.000 +ATOM 178 CD1 DMS 45 5.340 28.130 5.000 1.00 0.000 +ATOM 179 OD DMS 45 6.490 25.990 3.420 1.00 0.000 +ATOM 180 CD2 DMS 45 3.760 26.070 3.850 1.00 0.000 +ATOM 181 SD DMS 46 14.580 15.870 10.810 1.00 0.000 +ATOM 182 CD1 DMS 46 15.670 17.490 10.710 1.00 0.000 +ATOM 183 OD DMS 46 15.590 14.770 10.480 1.00 0.000 +ATOM 184 CD2 DMS 46 14.210 15.830 12.720 1.00 0.000 +ATOM 185 SD DMS 47 13.090 12.000 12.720 1.00 0.000 +ATOM 186 CD1 DMS 47 14.930 11.600 12.210 1.00 0.000 +ATOM 187 OD DMS 47 12.380 12.770 11.610 1.00 0.000 +ATOM 188 CD2 DMS 47 12.310 10.220 12.860 1.00 0.000 +ATOM 189 SD DMS 48 23.710 17.200 10.150 1.00 0.000 +ATOM 190 CD1 DMS 48 25.530 16.520 10.110 1.00 0.000 +ATOM 191 OD DMS 48 23.110 16.640 8.860 1.00 0.000 +ATOM 192 CD2 DMS 48 22.920 16.230 11.650 1.00 0.000 +ATOM 193 SD DMS 49 15.520 24.690 22.260 1.00 0.000 +ATOM 194 CD1 DMS 49 16.500 25.910 23.420 1.00 0.000 +ATOM 195 OD DMS 49 14.050 24.660 22.680 1.00 0.000 +ATOM 196 CD2 DMS 49 15.660 25.670 20.580 1.00 0.000 +ATOM 197 SD DMS 50 20.200 7.150 12.830 1.00 0.000 +ATOM 198 CD1 DMS 50 22.020 6.670 12.340 1.00 0.000 +ATOM 199 OD DMS 50 19.560 7.540 11.490 1.00 0.000 +ATOM 200 CD2 DMS 50 19.390 5.430 13.270 1.00 0.000 +ATOM 201 SD DMS 51 26.250 11.530 19.550 1.00 0.000 +ATOM 202 CD1 DMS 51 24.340 11.140 19.550 1.00 0.000 +ATOM 203 OD DMS 51 26.400 12.900 18.900 1.00 0.000 +ATOM 204 CD2 DMS 51 26.540 11.860 21.450 1.00 0.000 +ATOM 205 SD DMS 52 26.590 13.840 26.850 1.00 0.000 +ATOM 206 CD1 DMS 52 27.870 14.020 28.300 1.00 0.000 +ATOM 207 OD DMS 52 26.620 15.260 26.290 1.00 0.000 +ATOM 208 CD2 DMS 52 27.840 12.740 25.850 1.00 0.000 +ATOM 209 SD DMS 53 14.710 19.000 14.330 1.00 0.000 +ATOM 210 CD1 DMS 53 13.360 18.670 15.690 1.00 0.000 +ATOM 211 OD DMS 53 13.990 19.610 13.120 1.00 0.000 +ATOM 212 CD2 DMS 53 15.470 20.380 15.470 1.00 0.000 +ATOM 213 SD DMS 54 22.690 19.420 15.950 1.00 0.000 +ATOM 214 CD1 DMS 54 24.440 19.950 16.630 1.00 0.000 +ATOM 215 OD DMS 54 22.000 20.700 15.470 1.00 0.000 +ATOM 216 CD2 DMS 54 23.460 18.450 14.440 1.00 0.000 +ATOM 217 SD DMS 55 2.200 14.990 13.270 1.00 0.000 +ATOM 218 CD1 DMS 55 2.330 13.310 12.280 1.00 0.000 +ATOM 219 OD DMS 55 2.900 16.100 12.480 1.00 0.000 +ATOM 220 CD2 DMS 55 0.310 15.400 13.110 1.00 0.000 +ATOM 221 SD DMS 56 17.140 21.830 19.150 1.00 0.000 +ATOM 222 CD1 DMS 56 16.550 23.310 18.030 1.00 0.000 +ATOM 223 OD DMS 56 16.070 20.740 19.300 1.00 0.000 +ATOM 224 CD2 DMS 56 18.470 21.200 17.870 1.00 0.000 +ATOM 225 SD DMS 57 15.190 3.210 10.880 1.00 0.000 +ATOM 226 CD1 DMS 57 14.810 3.340 8.970 1.00 0.000 +ATOM 227 OD DMS 57 14.120 2.290 11.490 1.00 0.000 +ATOM 228 CD2 DMS 57 16.790 2.110 10.840 1.00 0.000 +ATOM 229 SD DMS 58 14.280 9.980 2.480 1.00 0.000 +ATOM 230 CD1 DMS 58 15.390 10.090 0.880 1.00 0.000 +ATOM 231 OD DMS 58 14.770 10.950 3.560 1.00 0.000 +ATOM 232 CD2 DMS 58 12.780 10.930 1.690 1.00 0.000 +ATOM 233 SD DMS 59 2.220 2.320 0.300 1.00 0.000 +ATOM 234 CD1 DMS 59 0.640 3.390 0.690 1.00 0.000 +ATOM 235 OD DMS 59 3.080 3.150 -0.650 1.00 0.000 +ATOM 236 CD2 DMS 59 3.060 2.870 1.970 1.00 0.000 +ATOM 237 SD DMS 60 24.430 20.790 9.160 1.00 0.000 +ATOM 238 CD1 DMS 60 25.810 20.580 7.800 1.00 0.000 +ATOM 239 OD DMS 60 24.340 22.290 9.470 1.00 0.000 +ATOM 240 CD2 DMS 60 22.970 20.240 7.990 1.00 0.000 +ATOM 241 SD DMS 61 12.600 20.430 22.670 1.00 0.000 +ATOM 242 CD1 DMS 61 12.200 21.900 23.890 1.00 0.000 +ATOM 243 OD DMS 61 11.770 20.710 21.420 1.00 0.000 +ATOM 244 CD2 DMS 61 14.370 21.010 22.090 1.00 0.000 +ATOM 245 SD DMS 62 8.840 4.910 26.150 1.00 0.000 +ATOM 246 CD1 DMS 62 10.160 5.630 27.380 1.00 0.000 +ATOM 247 OD DMS 62 7.520 4.630 26.880 1.00 0.000 +ATOM 248 CD2 DMS 62 8.550 6.530 25.110 1.00 0.000 +ATOM 249 SD DMS 63 1.360 0.470 25.810 1.00 0.000 +ATOM 250 CD1 DMS 63 2.470 1.840 24.970 1.00 0.000 +ATOM 251 OD DMS 63 -0.050 1.020 25.990 1.00 0.000 +ATOM 252 CD2 DMS 63 1.310 -0.540 24.140 1.00 0.000 +ATOM 253 SD DMS 64 2.190 27.640 8.260 1.00 0.000 +ATOM 254 CD1 DMS 64 1.340 29.250 8.970 1.00 0.000 +ATOM 255 OD DMS 64 3.690 27.820 8.530 1.00 0.000 +ATOM 256 CD2 DMS 64 1.330 26.430 9.520 1.00 0.000 +ATOM 257 SD DMS 65 0.340 9.060 5.060 1.00 0.000 +ATOM 258 CD1 DMS 65 -0.990 8.790 3.660 1.00 0.000 +ATOM 259 OD DMS 65 1.250 7.830 5.090 1.00 0.000 +ATOM 260 CD2 DMS 65 1.520 10.320 4.170 1.00 0.000 +ATOM 261 SD DMS 66 17.950 23.840 13.490 1.00 0.000 +ATOM 262 CD1 DMS 66 16.800 25.400 13.330 1.00 0.000 +ATOM 263 OD DMS 66 18.610 23.600 12.130 1.00 0.000 +ATOM 264 CD2 DMS 66 19.330 24.640 14.610 1.00 0.000 +ATOM 265 SD DMS 67 10.270 20.470 5.250 1.00 0.000 +ATOM 266 CD1 DMS 67 8.370 20.880 5.040 1.00 0.000 +ATOM 267 OD DMS 67 10.810 20.280 3.830 1.00 0.000 +ATOM 268 CD2 DMS 67 10.760 22.260 5.850 1.00 0.000 +ATOM 269 SD DMS 68 17.290 12.350 21.410 1.00 0.000 +ATOM 270 CD1 DMS 68 17.250 14.230 21.940 1.00 0.000 +ATOM 271 OD DMS 68 17.680 11.460 22.600 1.00 0.000 +ATOM 272 CD2 DMS 68 15.390 12.160 21.020 1.00 0.000 +ATOM 273 SD DMS 69 3.710 0.860 17.270 1.00 0.000 +ATOM 274 CD1 DMS 69 4.730 -0.300 16.080 1.00 0.000 +ATOM 275 OD DMS 69 2.660 0.000 17.980 1.00 0.000 +ATOM 276 CD2 DMS 69 5.210 1.290 18.440 1.00 0.000 +ATOM 277 SD DMS 70 27.350 7.430 20.320 1.00 0.000 +ATOM 278 CD1 DMS 70 28.040 8.160 18.650 1.00 0.000 +ATOM 279 OD DMS 70 26.230 8.350 20.820 1.00 0.000 +ATOM 280 CD2 DMS 70 26.610 5.870 19.410 1.00 0.000 +ATOM 281 SD DMS 71 23.040 7.830 16.210 1.00 0.000 +ATOM 282 CD1 DMS 71 24.530 9.050 16.500 1.00 0.000 +ATOM 283 OD DMS 71 23.480 6.680 15.300 1.00 0.000 +ATOM 284 CD2 DMS 71 23.150 6.870 17.900 1.00 0.000 +ATOM 285 SD DMS 72 27.750 13.130 5.670 1.00 0.000 +ATOM 286 CD1 DMS 72 25.880 12.600 5.690 1.00 0.000 +ATOM 287 OD DMS 72 28.520 12.110 6.530 1.00 0.000 +ATOM 288 CD2 DMS 72 28.230 12.770 3.820 1.00 0.000 +ATOM 289 SD DMS 73 0.790 22.870 7.310 1.00 0.000 +ATOM 290 CD1 DMS 73 0.150 24.420 6.310 1.00 0.000 +ATOM 291 OD DMS 73 2.260 23.060 7.680 1.00 0.000 +ATOM 292 CD2 DMS 73 -0.300 23.390 8.840 1.00 0.000 +ATOM 293 SD DMS 74 21.180 1.920 26.770 1.00 0.000 +ATOM 294 CD1 DMS 74 22.070 3.640 27.080 1.00 0.000 +ATOM 295 OD DMS 74 21.660 0.960 27.860 1.00 0.000 +ATOM 296 CD2 DMS 74 19.290 2.230 27.120 1.00 0.000 +ATOM 297 SD DMS 75 26.720 16.330 22.080 1.00 0.000 +ATOM 298 CD1 DMS 75 25.810 15.030 23.210 1.00 0.000 +ATOM 299 OD DMS 75 25.710 17.390 21.640 1.00 0.000 +ATOM 300 CD2 DMS 75 27.820 17.090 23.500 1.00 0.000 +ATOM 301 SD DMS 76 13.630 25.280 4.030 1.00 0.000 +ATOM 302 CD1 DMS 76 14.210 27.030 4.660 1.00 0.000 +ATOM 303 OD DMS 76 13.110 24.420 5.180 1.00 0.000 +ATOM 304 CD2 DMS 76 12.090 25.890 3.010 1.00 0.000 +ATOM 305 SD DMS 77 19.610 7.000 28.440 1.00 0.000 +ATOM 306 CD1 DMS 77 17.720 6.660 28.770 1.00 0.000 +ATOM 307 OD DMS 77 19.890 7.790 27.160 1.00 0.000 +ATOM 308 CD2 DMS 77 20.000 8.180 29.940 1.00 0.000 +ATOM 309 SD DMS 78 25.940 6.430 28.610 1.00 0.000 +ATOM 310 CD1 DMS 78 26.460 7.250 26.930 1.00 0.000 +ATOM 311 OD DMS 78 26.600 7.140 29.800 1.00 0.000 +ATOM 312 CD2 DMS 78 24.130 7.160 28.730 1.00 0.000 +ATOM 313 SD DMS 79 7.310 9.970 12.160 1.00 0.000 +ATOM 314 CD1 DMS 79 7.270 8.230 11.280 1.00 0.000 +ATOM 315 OD DMS 79 8.410 10.070 13.230 1.00 0.000 +ATOM 316 CD2 DMS 79 8.140 10.790 10.600 1.00 0.000 +ATOM 317 SD DMS 80 21.710 20.250 27.700 1.00 0.000 +ATOM 318 CD1 DMS 80 20.430 18.780 27.700 1.00 0.000 +ATOM 319 OD DMS 80 21.030 21.470 28.330 1.00 0.000 +ATOM 320 CD2 DMS 80 22.940 19.490 29.000 1.00 0.000 +ATOM 321 SD DMS 81 22.880 8.340 5.200 1.00 0.000 +ATOM 322 CD1 DMS 81 23.770 7.350 3.770 1.00 0.000 +ATOM 323 OD DMS 81 22.590 7.510 6.450 1.00 0.000 +ATOM 324 CD2 DMS 81 24.360 9.560 5.570 1.00 0.000 +ATOM 325 SD DMS 82 5.470 18.890 28.080 1.00 0.000 +ATOM 326 CD1 DMS 82 6.660 17.580 28.890 1.00 0.000 +ATOM 327 OD DMS 82 4.430 18.140 27.240 1.00 0.000 +ATOM 328 CD2 DMS 82 4.810 19.400 29.840 1.00 0.000 +ATOM 329 SD DMS 83 23.610 16.760 5.610 1.00 0.000 +ATOM 330 CD1 DMS 83 21.780 16.360 6.150 1.00 0.000 +ATOM 331 OD DMS 83 24.020 15.550 4.760 1.00 0.000 +ATOM 332 CD2 DMS 83 23.070 18.250 4.480 1.00 0.000 +ATOM 333 SD DMS 84 4.310 19.060 13.250 1.00 0.000 +ATOM 334 CD1 DMS 84 4.830 19.380 15.100 1.00 0.000 +ATOM 335 OD DMS 84 3.870 20.430 12.730 1.00 0.000 +ATOM 336 CD2 DMS 84 6.110 18.770 12.560 1.00 0.000 +ATOM 337 SD DMS 85 3.170 26.650 0.600 1.00 0.000 +ATOM 338 CD1 DMS 85 1.970 26.810 -0.930 1.00 0.000 +ATOM 339 OD DMS 85 3.910 25.310 0.570 1.00 0.000 +ATOM 340 CD2 DMS 85 4.260 28.060 -0.190 1.00 0.000 +ATOM 341 SD DMS 86 25.340 28.960 28.930 1.00 0.000 +ATOM 342 CD1 DMS 86 25.010 30.230 27.500 1.00 0.000 +ATOM 343 OD DMS 86 25.110 27.540 28.400 1.00 0.000 +ATOM 344 CD2 DMS 86 27.280 29.120 29.010 1.00 0.000 +ATOM 345 SD DMS 87 21.530 23.230 3.980 1.00 0.000 +ATOM 346 CD1 DMS 87 20.620 22.620 5.590 1.00 0.000 +ATOM 347 OD DMS 87 22.890 23.810 4.400 1.00 0.000 +ATOM 348 CD2 DMS 87 21.890 21.630 2.930 1.00 0.000 +ATOM 349 SD DMS 88 1.070 22.880 26.730 1.00 0.000 +ATOM 350 CD1 DMS 88 -0.760 22.680 26.080 1.00 0.000 +ATOM 351 OD DMS 88 1.150 22.780 28.260 1.00 0.000 +ATOM 352 CD2 DMS 88 1.610 21.110 26.120 1.00 0.000 +ATOM 353 SD DMS 89 28.750 4.250 6.300 1.00 0.000 +ATOM 354 CD1 DMS 89 27.390 5.620 6.520 1.00 0.000 +ATOM 355 OD DMS 89 28.880 3.780 4.850 1.00 0.000 +ATOM 356 CD2 DMS 89 30.350 5.270 6.750 1.00 0.000 +ATOM 357 SD DMS 90 22.080 23.970 18.210 1.00 0.000 +ATOM 358 CD1 DMS 90 23.440 23.490 16.890 1.00 0.000 +ATOM 359 OD DMS 90 21.020 24.680 17.380 1.00 0.000 +ATOM 360 CD2 DMS 90 21.530 22.130 18.570 1.00 0.000 +ATOM 361 SD DMS 91 3.530 27.590 20.760 1.00 0.000 +ATOM 362 CD1 DMS 91 3.240 29.460 21.210 1.00 0.000 +ATOM 363 OD DMS 91 3.990 26.810 21.990 1.00 0.000 +ATOM 364 CD2 DMS 91 1.670 27.060 20.490 1.00 0.000 +ATOM 365 SD DMS 92 20.260 19.920 10.810 1.00 0.000 +ATOM 366 CD1 DMS 92 19.960 20.300 12.700 1.00 0.000 +ATOM 367 OD DMS 92 19.110 19.010 10.380 1.00 0.000 +ATOM 368 CD2 DMS 92 20.260 21.730 10.080 1.00 0.000 +ATOM 369 SD DMS 93 14.700 12.510 26.580 1.00 0.000 +ATOM 370 CD1 DMS 93 16.350 11.890 25.740 1.00 0.000 +ATOM 371 OD DMS 93 14.910 12.390 28.090 1.00 0.000 +ATOM 372 CD2 DMS 93 14.470 14.360 26.020 1.00 0.000 +ATOM 373 SD DMS 94 28.180 18.400 15.290 1.00 0.000 +ATOM 374 CD1 DMS 94 27.120 18.620 13.670 1.00 0.000 +ATOM 375 OD DMS 94 28.470 16.900 15.450 1.00 0.000 +ATOM 376 CD2 DMS 94 29.810 19.090 14.470 1.00 0.000 +ATOM 377 SD DMS 95 7.410 14.110 1.110 1.00 0.000 +ATOM 378 CD1 DMS 95 7.170 12.540 -0.030 1.00 0.000 +ATOM 379 OD DMS 95 6.090 14.780 1.490 1.00 0.000 +ATOM 380 CD2 DMS 95 8.000 13.310 2.790 1.00 0.000 +ATOM 381 SD DMS 96 3.360 14.650 4.130 1.00 0.000 +ATOM 382 CD1 DMS 96 2.020 15.400 5.340 1.00 0.000 +ATOM 383 OD DMS 96 2.870 13.220 3.910 1.00 0.000 +ATOM 384 CD2 DMS 96 2.660 15.790 2.710 1.00 0.000 +ATOM 385 SD DMS 97 10.950 1.470 26.940 1.00 0.000 +ATOM 386 CD1 DMS 97 12.330 0.380 26.110 1.00 0.000 +ATOM 387 OD DMS 97 10.590 2.640 26.020 1.00 0.000 +ATOM 388 CD2 DMS 97 9.480 0.220 26.640 1.00 0.000 +ATOM 389 SD DMS 98 19.850 23.140 21.910 1.00 0.000 +ATOM 390 CD1 DMS 98 20.310 22.290 23.600 1.00 0.000 +ATOM 391 OD DMS 98 18.760 24.180 22.150 1.00 0.000 +ATOM 392 CD2 DMS 98 21.520 24.160 21.890 1.00 0.000 +ATOM 393 SD DMS 99 26.600 27.250 9.690 1.00 0.000 +ATOM 394 CD1 DMS 99 26.110 25.390 10.000 1.00 0.000 +ATOM 395 OD DMS 99 27.550 27.140 8.500 1.00 0.000 +ATOM 396 CD2 DMS 99 24.840 27.890 9.130 1.00 0.000 +ATOM 397 SD DMS 100 7.060 1.920 0.330 1.00 0.000 +ATOM 398 CD1 DMS 100 7.500 3.790 0.680 1.00 0.000 +ATOM 399 OD DMS 100 5.980 1.350 1.250 1.00 0.000 +ATOM 400 CD2 DMS 100 6.300 1.860 -1.460 1.00 0.000 +ATOM 401 SD DMS 101 2.750 5.840 25.570 1.00 0.000 +ATOM 402 CD1 DMS 101 4.300 5.420 26.680 1.00 0.000 +ATOM 403 OD DMS 101 2.880 4.800 24.450 1.00 0.000 +ATOM 404 CD2 DMS 101 1.350 5.450 26.860 1.00 0.000 +ATOM 405 SD DMS 102 15.380 4.430 27.130 1.00 0.000 +ATOM 406 CD1 DMS 102 13.800 3.360 27.530 1.00 0.000 +ATOM 407 OD DMS 102 16.580 3.540 26.800 1.00 0.000 +ATOM 408 CD2 DMS 102 14.870 5.290 25.450 1.00 0.000 +ATOM 409 SD DMS 103 9.750 19.350 11.120 1.00 0.000 +ATOM 410 CD1 DMS 103 11.320 18.500 11.900 1.00 0.000 +ATOM 411 OD DMS 103 9.970 20.850 11.280 1.00 0.000 +ATOM 412 CD2 DMS 103 10.070 19.010 9.230 1.00 0.000 +ATOM 413 SD DMS 104 4.780 5.300 5.480 1.00 0.000 +ATOM 414 CD1 DMS 104 6.030 5.590 6.950 1.00 0.000 +ATOM 415 OD DMS 104 5.350 5.530 4.070 1.00 0.000 +ATOM 416 CD2 DMS 104 4.690 3.360 5.680 1.00 0.000 +ATOM 417 SD DMS 105 21.470 26.230 7.860 1.00 0.000 +ATOM 418 CD1 DMS 105 22.760 24.830 8.290 1.00 0.000 +ATOM 419 OD DMS 105 21.830 27.370 8.820 1.00 0.000 +ATOM 420 CD2 DMS 105 22.010 26.750 6.070 1.00 0.000 +ATOM 421 SD DMS 106 19.920 27.740 20.960 1.00 0.000 +ATOM 422 CD1 DMS 106 19.150 26.310 19.870 1.00 0.000 +ATOM 423 OD DMS 106 21.440 27.590 20.990 1.00 0.000 +ATOM 424 CD2 DMS 106 19.530 29.310 19.880 1.00 0.000 +ATOM 425 SD DMS 107 18.520 4.460 23.450 1.00 0.000 +ATOM 426 CD1 DMS 107 20.040 5.380 22.640 1.00 0.000 +ATOM 427 OD DMS 107 19.070 3.080 23.830 1.00 0.000 +ATOM 428 CD2 DMS 107 18.550 5.490 25.110 1.00 0.000 +ATOM 429 SD DMS 108 1.440 19.730 4.900 1.00 0.000 +ATOM 430 CD1 DMS 108 0.760 19.690 3.070 1.00 0.000 +ATOM 431 OD DMS 108 1.440 18.300 5.450 1.00 0.000 +ATOM 432 CD2 DMS 108 3.230 20.120 4.230 1.00 0.000 +ATOM 433 SD DMS 109 23.130 0.640 23.000 1.00 0.000 +ATOM 434 CD1 DMS 109 23.650 0.930 21.140 1.00 0.000 +ATOM 435 OD DMS 109 24.000 1.540 23.870 1.00 0.000 +ATOM 436 CD2 DMS 109 21.330 1.390 22.920 1.00 0.000 +ATOM 437 SD DMS 110 3.710 7.530 1.150 1.00 0.000 +ATOM 438 CD1 DMS 110 4.840 5.940 1.100 1.00 0.000 +ATOM 439 OD DMS 110 3.150 7.960 -0.200 1.00 0.000 +ATOM 440 CD2 DMS 110 2.220 6.710 2.110 1.00 0.000 +ATOM 441 SD DMS 111 9.580 15.850 17.440 1.00 0.000 +ATOM 442 CD1 DMS 111 7.860 16.750 17.260 1.00 0.000 +ATOM 443 OD DMS 111 10.560 16.740 18.210 1.00 0.000 +ATOM 444 CD2 DMS 111 8.850 14.620 18.760 1.00 0.000 +ATOM 445 SD DMS 112 14.960 6.550 6.190 1.00 0.000 +ATOM 446 CD1 DMS 112 13.370 7.600 5.790 1.00 0.000 +ATOM 447 OD DMS 112 15.630 6.240 4.840 1.00 0.000 +ATOM 448 CD2 DMS 112 15.970 7.910 7.150 1.00 0.000 +ATOM 449 SD DMS 113 26.750 7.970 12.190 1.00 0.000 +ATOM 450 CD1 DMS 113 27.000 7.260 13.990 1.00 0.000 +ATOM 451 OD DMS 113 27.280 9.400 12.320 1.00 0.000 +ATOM 452 CD2 DMS 113 28.170 6.860 11.440 1.00 0.000 +ATOM 453 SD DMS 114 17.850 24.160 2.080 1.00 0.000 +ATOM 454 CD1 DMS 114 18.480 25.380 3.470 1.00 0.000 +ATOM 455 OD DMS 114 16.320 24.120 2.080 1.00 0.000 +ATOM 456 CD2 DMS 114 18.360 25.330 0.610 1.00 0.000 +ATOM 457 SD DMS 115 26.120 23.190 13.680 1.00 0.000 +ATOM 458 CD1 DMS 115 24.570 22.010 13.740 1.00 0.000 +ATOM 459 OD DMS 115 27.110 22.600 14.690 1.00 0.000 +ATOM 460 CD2 DMS 115 26.850 22.520 12.000 1.00 0.000 +ATOM 461 SD DMS 116 8.980 21.020 28.500 1.00 0.000 +ATOM 462 CD1 DMS 116 10.780 21.680 28.170 1.00 0.000 +ATOM 463 OD DMS 116 8.900 19.690 27.760 1.00 0.000 +ATOM 464 CD2 DMS 116 9.170 20.930 30.440 1.00 0.000 +ATOM 465 SD DMS 117 1.180 4.650 19.390 1.00 0.000 +ATOM 466 CD1 DMS 117 1.490 4.370 21.290 1.00 0.000 +ATOM 467 OD DMS 117 1.020 6.150 19.100 1.00 0.000 +ATOM 468 CD2 DMS 117 2.950 4.090 18.790 1.00 0.000 +ATOM 469 SD DMS 118 27.170 17.250 2.480 1.00 0.000 +ATOM 470 CD1 DMS 118 25.570 16.260 1.960 1.00 0.000 +ATOM 471 OD DMS 118 26.980 18.700 2.050 1.00 0.000 +ATOM 472 CD2 DMS 118 27.240 17.160 4.430 1.00 0.000 +ATOM 473 SD DMS 119 -0.220 10.760 28.860 1.00 0.000 +ATOM 474 CD1 DMS 119 0.350 8.910 28.620 1.00 0.000 +ATOM 475 OD DMS 119 -0.150 11.000 30.370 1.00 0.000 +ATOM 476 CD2 DMS 119 1.530 11.390 28.260 1.00 0.000 +ATOM 477 SD DMS 120 14.030 17.520 0.830 1.00 0.000 +ATOM 478 CD1 DMS 120 12.490 18.440 1.600 1.00 0.000 +ATOM 479 OD DMS 120 13.490 16.430 -0.100 1.00 0.000 +ATOM 480 CD2 DMS 120 14.700 19.050 -0.170 1.00 0.000 +ATOM 481 SD DMS 121 5.030 13.660 15.480 1.00 0.000 +ATOM 482 CD1 DMS 121 4.500 12.160 16.600 1.00 0.000 +ATOM 483 OD DMS 121 6.250 14.320 16.120 1.00 0.000 +ATOM 484 CD2 DMS 121 5.500 12.640 13.880 1.00 0.000 +ATOM 485 SD DMS 122 5.400 9.580 7.500 1.00 0.000 +ATOM 486 CD1 DMS 122 3.920 10.410 8.460 1.00 0.000 +ATOM 487 OD DMS 122 6.140 8.480 8.260 1.00 0.000 +ATOM 488 CD2 DMS 122 4.310 8.840 6.070 1.00 0.000 +ATOM 489 SD DMS 123 20.890 0.480 16.120 1.00 0.000 +ATOM 490 CD1 DMS 123 19.750 1.080 14.660 1.00 0.000 +ATOM 491 OD DMS 123 20.970 1.750 16.970 1.00 0.000 +ATOM 492 CD2 DMS 123 19.450 -0.670 16.730 1.00 0.000 +ATOM 493 SD DMS 124 11.630 18.410 25.560 1.00 0.000 +ATOM 494 CD1 DMS 124 9.890 18.980 24.890 1.00 0.000 +ATOM 495 OD DMS 124 12.410 19.640 26.040 1.00 0.000 +ATOM 496 CD2 DMS 124 11.160 17.480 27.200 1.00 0.000 +ATOM 497 SD DMS 125 11.730 23.940 19.710 1.00 0.000 +ATOM 498 CD1 DMS 125 12.790 22.430 19.080 1.00 0.000 +ATOM 499 OD DMS 125 12.430 25.230 19.280 1.00 0.000 +ATOM 500 CD2 DMS 125 10.250 23.480 18.530 1.00 0.000 +ATOM 501 SD DMS 126 3.660 9.780 25.030 1.00 0.000 +ATOM 502 CD1 DMS 126 4.380 11.450 25.720 1.00 0.000 +ATOM 503 OD DMS 126 3.740 9.980 23.520 1.00 0.000 +ATOM 504 CD2 DMS 126 5.020 8.510 25.610 1.00 0.000 +ATOM 505 SD DMS 127 23.220 11.130 25.840 1.00 0.000 +ATOM 506 CD1 DMS 127 22.240 9.540 26.390 1.00 0.000 +ATOM 507 OD DMS 127 23.740 11.830 27.100 1.00 0.000 +ATOM 508 CD2 DMS 127 24.790 10.460 24.890 1.00 0.000 +ATOM 509 SD DMS 128 23.990 9.180 9.870 1.00 0.000 +ATOM 510 CD1 DMS 128 24.480 7.420 9.170 1.00 0.000 +ATOM 511 OD DMS 128 24.610 10.220 8.940 1.00 0.000 +ATOM 512 CD2 DMS 128 22.140 9.080 9.250 1.00 0.000 +ATOM 513 SD DMS 129 14.870 26.790 10.570 1.00 0.000 +ATOM 514 CD1 DMS 129 14.330 28.300 9.450 1.00 0.000 +ATOM 515 OD DMS 129 16.340 27.080 10.880 1.00 0.000 +ATOM 516 CD2 DMS 129 13.770 27.340 12.090 1.00 0.000 +ATOM 517 SD DMS 130 26.240 20.510 28.770 1.00 0.000 +ATOM 518 CD1 DMS 130 27.700 21.500 29.590 1.00 0.000 +ATOM 519 OD DMS 130 25.650 21.300 27.600 1.00 0.000 +ATOM 520 CD2 DMS 130 27.450 19.170 28.050 1.00 0.000 +ATOM 521 SD DMS 131 10.980 27.040 22.930 1.00 0.000 +ATOM 522 CD1 DMS 131 11.670 25.830 24.300 1.00 0.000 +ATOM 523 OD DMS 131 10.690 28.350 23.660 1.00 0.000 +ATOM 524 CD2 DMS 131 12.630 27.210 21.900 1.00 0.000 +ATOM 525 SD DMS 132 8.000 24.160 21.630 1.00 0.000 +ATOM 526 CD1 DMS 132 6.120 23.990 22.140 1.00 0.000 +ATOM 527 OD DMS 132 8.370 25.560 22.110 1.00 0.000 +ATOM 528 CD2 DMS 132 8.700 22.880 22.920 1.00 0.000 +ATOM 529 SD DMS 133 14.310 4.760 18.220 1.00 0.000 +ATOM 530 CD1 DMS 133 13.600 2.950 18.350 1.00 0.000 +ATOM 531 OD DMS 133 13.320 5.440 17.280 1.00 0.000 +ATOM 532 CD2 DMS 133 14.100 5.430 20.050 1.00 0.000 +ATOM 533 SD DMS 134 20.420 14.410 2.930 1.00 0.000 +ATOM 534 CD1 DMS 134 21.890 13.480 3.820 1.00 0.000 +ATOM 535 OD DMS 134 19.680 15.060 4.110 1.00 0.000 +ATOM 536 CD2 DMS 134 21.330 15.820 1.940 1.00 0.000 +ATOM 537 SD DMS 135 6.440 22.750 26.550 1.00 0.000 +ATOM 538 CD1 DMS 135 5.900 21.510 25.140 1.00 0.000 +ATOM 539 OD DMS 135 7.490 23.670 25.920 1.00 0.000 +ATOM 540 CD2 DMS 135 4.830 23.770 26.990 1.00 0.000 +ATOM 541 SD DMS 136 7.250 15.830 25.900 1.00 0.000 +ATOM 542 CD1 DMS 136 6.520 14.200 25.120 1.00 0.000 +ATOM 543 OD DMS 136 8.750 15.540 25.960 1.00 0.000 +ATOM 544 CD2 DMS 136 6.950 17.220 24.560 1.00 0.000 +ATOM 545 SD DMS 137 17.570 14.520 28.330 1.00 0.000 +ATOM 546 CD1 DMS 137 16.440 14.440 29.910 1.00 0.000 +ATOM 547 OD DMS 137 18.510 15.710 28.580 1.00 0.000 +ATOM 548 CD2 DMS 137 18.540 12.830 28.520 1.00 0.000 +ATOM 549 SD DMS 138 8.950 20.590 16.470 1.00 0.000 +ATOM 550 CD1 DMS 138 9.810 19.760 14.920 1.00 0.000 +ATOM 551 OD DMS 138 7.540 20.020 16.560 1.00 0.000 +ATOM 552 CD2 DMS 138 10.030 19.790 17.880 1.00 0.000 +ATOM 553 SD DMS 139 9.930 28.580 6.040 1.00 0.000 +ATOM 554 CD1 DMS 139 9.500 28.120 4.190 1.00 0.000 +ATOM 555 OD DMS 139 11.140 29.520 6.030 1.00 0.000 +ATOM 556 CD2 DMS 139 8.380 29.660 6.540 1.00 0.000 +ATOM 557 SD DMS 140 29.300 9.060 8.360 1.00 0.000 +ATOM 558 CD1 DMS 140 29.630 10.000 10.040 1.00 0.000 +ATOM 559 OD DMS 140 29.460 7.570 8.670 1.00 0.000 +ATOM 560 CD2 DMS 140 27.390 9.430 8.210 1.00 0.000 +ATOM 561 SD DMS 141 15.250 2.100 14.930 1.00 0.000 +ATOM 562 CD1 DMS 141 14.960 4.030 14.930 1.00 0.000 +ATOM 563 OD DMS 141 15.760 1.920 16.360 1.00 0.000 +ATOM 564 CD2 DMS 141 13.480 1.350 14.620 1.00 0.000 +ATOM 565 SD DMS 142 3.880 18.610 7.890 1.00 0.000 +ATOM 566 CD1 DMS 142 5.780 18.240 7.650 1.00 0.000 +ATOM 567 OD DMS 142 3.390 17.510 8.830 1.00 0.000 +ATOM 568 CD2 DMS 142 3.850 20.330 8.800 1.00 0.000 +ATOM 569 SD DMS 143 17.380 25.050 7.200 1.00 0.000 +ATOM 570 CD1 DMS 143 17.280 26.940 7.690 1.00 0.000 +ATOM 571 OD DMS 143 18.700 24.790 6.470 1.00 0.000 +ATOM 572 CD2 DMS 143 17.820 24.500 9.020 1.00 0.000 +ATOM 573 SD DMS 144 19.970 0.000 1.140 1.00 0.000 +ATOM 574 CD1 DMS 144 21.840 -0.490 1.430 1.00 0.000 +ATOM 575 OD DMS 144 19.130 -0.490 2.310 1.00 0.000 +ATOM 576 CD2 DMS 144 20.170 1.920 1.430 1.00 0.000 +ATOM 577 SD DMS 145 16.790 12.440 17.390 1.00 0.000 +ATOM 578 CD1 DMS 145 16.490 12.110 15.490 1.00 0.000 +ATOM 579 OD DMS 145 17.030 11.050 17.980 1.00 0.000 +ATOM 580 CD2 DMS 145 18.350 13.610 17.300 1.00 0.000 +ATOM 581 SD DMS 146 9.360 7.470 3.250 1.00 0.000 +ATOM 582 CD1 DMS 146 9.210 8.810 1.840 1.00 0.000 +ATOM 583 OD DMS 146 10.470 7.830 4.240 1.00 0.000 +ATOM 584 CD2 DMS 146 7.790 7.880 4.330 1.00 0.000 +ATOM 585 SD DMS 147 10.580 25.810 10.430 1.00 0.000 +ATOM 586 CD1 DMS 147 9.330 24.440 9.830 1.00 0.000 +ATOM 587 OD DMS 147 11.380 25.450 11.690 1.00 0.000 +ATOM 588 CD2 DMS 147 11.750 25.200 8.990 1.00 0.000 +ATOM 589 SD DMS 148 11.750 2.190 1.490 1.00 0.000 +ATOM 590 CD1 DMS 148 11.660 0.270 1.140 1.00 0.000 +ATOM 591 OD DMS 148 10.290 2.650 1.520 1.00 0.000 +ATOM 592 CD2 DMS 148 12.240 1.790 3.330 1.00 0.000 +ATOM 593 SD DMS 149 4.250 20.830 18.460 1.00 0.000 +ATOM 594 CD1 DMS 149 5.920 21.700 18.960 1.00 0.000 +ATOM 595 OD DMS 149 4.360 19.350 18.830 1.00 0.000 +ATOM 596 CD2 DMS 149 3.190 21.670 19.870 1.00 0.000 +ATOM 597 SD DMS 150 27.620 3.270 23.310 1.00 0.000 +ATOM 598 CD1 DMS 150 27.390 1.340 23.080 1.00 0.000 +ATOM 599 OD DMS 150 27.010 4.010 22.120 1.00 0.000 +ATOM 600 CD2 DMS 150 26.470 3.650 24.840 1.00 0.000 +ATOM 601 SD DMS 151 1.530 16.220 17.470 1.00 0.000 +ATOM 602 CD1 DMS 151 3.150 16.770 16.540 1.00 0.000 +ATOM 603 OD DMS 151 1.820 15.060 18.410 1.00 0.000 +ATOM 604 CD2 DMS 151 1.390 17.770 18.650 1.00 0.000 +ATOM 605 SD DMS 152 0.800 -0.400 3.600 1.00 0.000 +ATOM 606 CD1 DMS 152 -0.440 1.090 3.360 1.00 0.000 +ATOM 607 OD DMS 152 1.850 -0.390 2.490 1.00 0.000 +ATOM 608 CD2 DMS 152 1.670 0.420 5.140 1.00 0.000 +ATOM 609 SD DMS 153 5.070 24.370 16.680 1.00 0.000 +ATOM 610 CD1 DMS 153 3.750 25.710 17.220 1.00 0.000 +ATOM 611 OD DMS 153 4.190 23.190 16.270 1.00 0.000 +ATOM 612 CD2 DMS 153 5.590 25.300 15.040 1.00 0.000 +ATOM 613 SD DMS 154 21.920 25.710 26.150 1.00 0.000 +ATOM 614 CD1 DMS 154 20.090 26.320 25.870 1.00 0.000 +ATOM 615 OD DMS 154 22.450 24.970 24.910 1.00 0.000 +ATOM 616 CD2 DMS 154 22.630 27.520 25.970 1.00 0.000 +ATOM 617 SD DMS 155 8.620 28.100 19.910 1.00 0.000 +ATOM 618 CD1 DMS 155 10.100 27.510 18.780 1.00 0.000 +ATOM 619 OD DMS 155 8.470 29.620 19.830 1.00 0.000 +ATOM 620 CD2 DMS 155 7.210 27.400 18.760 1.00 0.000 +ATOM 621 SD DMS 156 8.550 15.100 14.100 1.00 0.000 +ATOM 622 CD1 DMS 156 9.450 13.390 13.850 1.00 0.000 +ATOM 623 OD DMS 156 9.630 16.160 14.320 1.00 0.000 +ATOM 624 CD2 DMS 156 7.920 15.300 12.260 1.00 0.000 +ATOM 625 SD DMS 157 24.790 3.360 1.670 1.00 0.000 +ATOM 626 CD1 DMS 157 23.450 2.460 2.770 1.00 0.000 +ATOM 627 OD DMS 157 24.220 4.650 1.090 1.00 0.000 +ATOM 628 CD2 DMS 157 25.890 3.960 3.170 1.00 0.000 +ATOM 629 SD DMS 158 14.070 8.740 16.030 1.00 0.000 +ATOM 630 CD1 DMS 158 14.060 10.160 17.360 1.00 0.000 +ATOM 631 OD DMS 158 14.720 9.160 14.710 1.00 0.000 +ATOM 632 CD2 DMS 158 15.490 7.670 16.830 1.00 0.000 +ATOM 633 SD DMS 159 19.940 5.890 4.200 1.00 0.000 +ATOM 634 CD1 DMS 159 21.490 4.800 4.660 1.00 0.000 +ATOM 635 OD DMS 159 19.570 5.710 2.730 1.00 0.000 +ATOM 636 CD2 DMS 159 18.540 5.010 5.240 1.00 0.000 +ATOM 637 SD DMS 160 18.850 4.650 18.680 1.00 0.000 +ATOM 638 CD1 DMS 160 18.400 3.720 17.020 1.00 0.000 +ATOM 639 OD DMS 160 18.000 4.080 19.820 1.00 0.000 +ATOM 640 CD2 DMS 160 20.710 4.220 19.070 1.00 0.000 +ATOM 641 SD DMS 161 27.970 0.010 20.000 1.00 0.000 +ATOM 642 CD1 DMS 161 27.830 1.910 19.570 1.00 0.000 +ATOM 643 OD DMS 161 26.500 -0.370 20.210 1.00 0.000 +ATOM 644 CD2 DMS 161 28.620 -0.830 18.370 1.00 0.000 +ATOM 645 SD DMS 162 12.550 22.660 14.580 1.00 0.000 +ATOM 646 CD1 DMS 162 13.510 24.280 15.090 1.00 0.000 +ATOM 647 OD DMS 162 12.200 21.800 15.790 1.00 0.000 +ATOM 648 CD2 DMS 162 10.970 23.730 14.170 1.00 0.000 +ATOM 649 SD DMS 163 24.320 11.960 1.420 1.00 0.000 +ATOM 650 CD1 DMS 163 22.600 11.070 1.150 1.00 0.000 +ATOM 651 OD DMS 163 24.750 11.820 2.880 1.00 0.000 +ATOM 652 CD2 DMS 163 25.410 10.510 0.690 1.00 0.000 +ATOM 653 SD DMS 164 14.030 8.180 10.640 1.00 0.000 +ATOM 654 CD1 DMS 164 15.740 7.240 10.640 1.00 0.000 +ATOM 655 OD DMS 164 13.540 8.020 9.200 1.00 0.000 +ATOM 656 CD2 DMS 164 13.130 6.870 11.770 1.00 0.000 +ATOM 657 SD DMS 165 5.990 13.650 20.740 1.00 0.000 +ATOM 658 CD1 DMS 165 4.830 14.490 19.410 1.00 0.000 +ATOM 659 OD DMS 165 5.710 14.380 22.060 1.00 0.000 +ATOM 660 CD2 DMS 165 4.990 11.980 20.590 1.00 0.000 +ATOM 661 SD DMS 166 23.610 23.130 0.300 1.00 0.000 +ATOM 662 CD1 DMS 166 24.930 24.190 -0.670 1.00 0.000 +ATOM 663 OD DMS 166 24.120 23.140 1.740 1.00 0.000 +ATOM 664 CD2 DMS 166 22.100 24.370 0.250 1.00 0.000 +ATOM 665 SD DMS 167 10.020 6.350 20.940 1.00 0.000 +ATOM 666 CD1 DMS 167 11.450 7.210 21.960 1.00 0.000 +ATOM 667 OD DMS 167 8.800 7.250 21.140 1.00 0.000 +ATOM 668 CD2 DMS 167 10.830 6.720 19.210 1.00 0.000 +ATOM 669 SD DMS 168 16.540 22.610 26.730 1.00 0.000 +ATOM 670 CD1 DMS 168 18.220 21.630 26.540 1.00 0.000 +ATOM 671 OD DMS 168 16.810 24.110 26.630 1.00 0.000 +ATOM 672 CD2 DMS 168 16.170 22.370 24.830 1.00 0.000 +ATOM 673 SD DMS 169 24.360 3.530 17.090 1.00 0.000 +ATOM 674 CD1 DMS 169 24.680 1.610 17.110 1.00 0.000 +ATOM 675 OD DMS 169 25.660 4.300 16.840 1.00 0.000 +ATOM 676 CD2 DMS 169 23.300 3.530 15.450 1.00 0.000 +ATOM 677 SD DMS 170 4.770 29.090 11.680 1.00 0.000 +ATOM 678 CD1 DMS 170 5.350 27.380 10.950 1.00 0.000 +ATOM 679 OD DMS 170 5.910 29.190 12.700 1.00 0.000 +ATOM 680 CD2 DMS 170 5.180 30.260 10.170 1.00 0.000 +ATOM 681 SD DMS 171 13.960 13.120 7.990 1.00 0.000 +ATOM 682 CD1 DMS 171 14.630 12.410 6.300 1.00 0.000 +ATOM 683 OD DMS 171 12.870 14.120 7.600 1.00 0.000 +ATOM 684 CD2 DMS 171 13.110 11.440 8.510 1.00 0.000 +ATOM 685 SD DMS 172 9.020 15.070 8.760 1.00 0.000 +ATOM 686 CD1 DMS 172 10.550 15.050 9.970 1.00 0.000 +ATOM 687 OD DMS 172 8.330 16.430 8.830 1.00 0.000 +ATOM 688 CD2 DMS 172 10.040 14.950 7.100 1.00 0.000 +ATOM 689 SD DMS 173 21.830 12.510 22.250 1.00 0.000 +ATOM 690 CD1 DMS 173 20.510 13.540 23.250 1.00 0.000 +ATOM 691 OD DMS 173 23.150 12.700 23.000 1.00 0.000 +ATOM 692 CD2 DMS 173 21.360 10.740 22.910 1.00 0.000 +ATOM 693 SD DMS 174 27.060 22.100 4.190 1.00 0.000 +ATOM 694 CD1 DMS 174 25.960 23.240 5.320 1.00 0.000 +ATOM 695 OD DMS 174 27.880 21.370 5.260 1.00 0.000 +ATOM 696 CD2 DMS 174 25.580 20.920 3.730 1.00 0.000 +ATOM 697 SD DMS 175 13.040 26.020 27.840 1.00 0.000 +ATOM 698 CD1 DMS 175 13.500 24.210 28.400 1.00 0.000 +ATOM 699 OD DMS 175 12.900 27.050 28.960 1.00 0.000 +ATOM 700 CD2 DMS 175 14.670 26.470 26.860 1.00 0.000 +ATOM 701 SD DMS 176 17.370 12.350 9.350 1.00 0.000 +ATOM 702 CD1 DMS 176 18.180 14.050 8.870 1.00 0.000 +ATOM 703 OD DMS 176 17.850 11.250 8.400 1.00 0.000 +ATOM 704 CD2 DMS 176 18.570 12.240 10.890 1.00 0.000 +ATOM 705 SD DMS 177 6.150 27.460 24.290 1.00 0.000 +ATOM 706 CD1 DMS 177 7.570 26.600 25.300 1.00 0.000 +ATOM 707 OD DMS 177 5.310 28.300 25.260 1.00 0.000 +ATOM 708 CD2 DMS 177 7.450 28.610 23.390 1.00 0.000 +ATOM 709 SD DMS 178 28.990 25.130 2.320 1.00 0.000 +ATOM 710 CD1 DMS 178 28.420 25.140 0.460 1.00 0.000 +ATOM 711 OD DMS 178 27.760 24.810 3.180 1.00 0.000 +ATOM 712 CD2 DMS 178 30.230 23.640 2.200 1.00 0.000 +ATOM 713 SD DMS 179 28.080 8.860 23.950 1.00 0.000 +ATOM 714 CD1 DMS 179 28.680 7.020 24.190 1.00 0.000 +ATOM 715 OD DMS 179 28.230 9.600 25.280 1.00 0.000 +ATOM 716 CD2 DMS 179 29.630 9.140 22.810 1.00 0.000 +ATOM 717 SD DMS 180 5.500 3.900 14.520 1.00 0.000 +ATOM 718 CD1 DMS 180 4.120 3.200 13.340 1.00 0.000 +ATOM 719 OD DMS 180 5.520 3.260 15.910 1.00 0.000 +ATOM 720 CD2 DMS 180 7.010 3.150 13.530 1.00 0.000 +ATOM 721 SD DMS 181 10.070 5.480 6.870 1.00 0.000 +ATOM 722 CD1 DMS 181 11.230 4.640 5.550 1.00 0.000 +ATOM 723 OD DMS 181 9.010 4.470 7.330 1.00 0.000 +ATOM 724 CD2 DMS 181 11.480 5.670 8.200 1.00 0.000 +ATOM 725 SD DMS 182 0.690 23.800 17.560 1.00 0.000 +ATOM 726 CD1 DMS 182 -1.240 23.950 17.440 1.00 0.000 +ATOM 727 OD DMS 182 1.110 24.220 18.970 1.00 0.000 +ATOM 728 CD2 DMS 182 0.860 21.880 17.280 1.00 0.000 +ATOM 729 SD DMS 183 7.270 25.090 6.300 1.00 0.000 +ATOM 730 CD1 DMS 183 7.050 26.490 7.630 1.00 0.000 +ATOM 731 OD DMS 183 8.280 24.010 6.720 1.00 0.000 +ATOM 732 CD2 DMS 183 5.470 24.380 6.530 1.00 0.000 +ATOM 733 SD DMS 184 2.170 24.050 12.280 1.00 0.000 +ATOM 734 CD1 DMS 184 2.840 23.170 13.890 1.00 0.000 +ATOM 735 OD DMS 184 2.700 25.480 12.370 1.00 0.000 +ATOM 736 CD2 DMS 184 3.190 23.170 10.870 1.00 0.000 +ATOM 737 SD DMS 185 28.780 19.570 10.110 1.00 0.000 +ATOM 738 CD1 DMS 185 29.400 19.520 8.260 1.00 0.000 +ATOM 739 OD DMS 185 27.290 19.200 10.140 1.00 0.000 +ATOM 740 CD2 DMS 185 29.830 18.030 10.710 1.00 0.000 +ATOM 741 SD DMS 186 13.630 6.790 1.340 1.00 0.000 +ATOM 742 CD1 DMS 186 14.790 5.430 2.130 1.00 0.000 +ATOM 743 OD DMS 186 14.150 7.170 -0.050 1.00 0.000 +ATOM 744 CD2 DMS 186 12.050 5.670 1.150 1.00 0.000 +ATOM 745 SD DMS 187 26.240 27.580 3.620 1.00 0.000 +ATOM 746 CD1 DMS 187 24.940 26.200 3.190 1.00 0.000 +ATOM 747 OD DMS 187 25.400 28.860 3.670 1.00 0.000 +ATOM 748 CD2 DMS 187 26.710 27.020 5.430 1.00 0.000 +ATOM 749 SD DMS 188 19.590 19.130 7.310 1.00 0.000 +ATOM 750 CD1 DMS 188 18.380 17.690 6.810 1.00 0.000 +ATOM 751 OD DMS 188 20.530 19.240 6.110 1.00 0.000 +ATOM 752 CD2 DMS 188 18.200 20.500 7.320 1.00 0.000 +ATOM 753 SD DMS 189 25.580 16.620 16.920 1.00 0.000 +ATOM 754 CD1 DMS 189 26.140 14.990 16.020 1.00 0.000 +ATOM 755 OD DMS 189 24.050 16.590 16.990 1.00 0.000 +ATOM 756 CD2 DMS 189 26.020 16.010 18.720 1.00 0.000 +ATOM 757 SD DMS 190 27.150 26.320 24.440 1.00 0.000 +ATOM 758 CD1 DMS 190 26.800 27.650 25.810 1.00 0.000 +ATOM 759 OD DMS 190 28.460 25.600 24.760 1.00 0.000 +ATOM 760 CD2 DMS 190 25.620 25.160 24.730 1.00 0.000 +ATOM 761 SD DMS 191 2.810 14.960 26.650 1.00 0.000 +ATOM 762 CD1 DMS 191 3.760 14.720 28.330 1.00 0.000 +ATOM 763 OD DMS 191 1.870 13.760 26.480 1.00 0.000 +ATOM 764 CD2 DMS 191 1.950 16.650 27.090 1.00 0.000 +ATOM 765 SD DMS 192 24.730 29.020 13.050 1.00 0.000 +ATOM 766 CD1 DMS 192 26.060 30.100 13.990 1.00 0.000 +ATOM 767 OD DMS 192 24.520 29.540 11.630 1.00 0.000 +ATOM 768 CD2 DMS 192 25.440 27.200 12.920 1.00 0.000 +ATOM 769 SD DMS 193 2.730 23.830 22.880 1.00 0.000 +ATOM 770 CD1 DMS 193 2.620 25.230 24.230 1.00 0.000 +ATOM 771 OD DMS 193 2.980 22.560 23.690 1.00 0.000 +ATOM 772 CD2 DMS 193 0.830 23.920 22.430 1.00 0.000 +ATOM 773 SD DMS 194 15.940 0.350 1.560 1.00 0.000 +ATOM 774 CD1 DMS 194 16.700 0.270 -0.240 1.00 0.000 +ATOM 775 OD DMS 194 14.610 1.040 1.240 1.00 0.000 +ATOM 776 CD2 DMS 194 15.540 -1.550 1.670 1.00 0.000 +ATOM 777 SD DMS 195 14.840 17.810 20.270 1.00 0.000 +ATOM 778 CD1 DMS 195 13.320 18.000 19.060 1.00 0.000 +ATOM 779 OD DMS 195 14.810 16.360 20.750 1.00 0.000 +ATOM 780 CD2 DMS 195 16.170 17.810 18.850 1.00 0.000 +ATOM 781 SD DMS 196 12.000 14.320 23.190 1.00 0.000 +ATOM 782 CD1 DMS 196 10.090 14.650 23.400 1.00 0.000 +ATOM 783 OD DMS 196 12.310 12.860 22.880 1.00 0.000 +ATOM 784 CD2 DMS 196 11.940 15.330 21.520 1.00 0.000 +ATOM 785 SD DMS 197 21.740 15.070 18.890 1.00 0.000 +ATOM 786 CD1 DMS 197 22.760 15.980 20.280 1.00 0.000 +ATOM 787 OD DMS 197 20.790 14.080 19.550 1.00 0.000 +ATOM 788 CD2 DMS 197 20.770 16.670 18.330 1.00 0.000 +ATOM 789 SD DMS 198 14.250 20.290 4.650 1.00 0.000 +ATOM 790 CD1 DMS 198 14.790 21.890 3.670 1.00 0.000 +ATOM 791 OD DMS 198 15.350 19.240 4.760 1.00 0.000 +ATOM 792 CD2 DMS 198 14.190 21.120 6.420 1.00 0.000 +ATOM 793 SD DMS 199 7.880 19.220 21.150 1.00 0.000 +ATOM 794 CD1 DMS 199 6.680 17.780 20.620 1.00 0.000 +ATOM 795 OD DMS 199 7.780 19.510 22.650 1.00 0.000 +ATOM 796 CD2 DMS 199 9.500 18.130 21.110 1.00 0.000 +ATOM 797 SD DMS 200 8.770 25.220 1.040 1.00 0.000 +ATOM 798 CD1 DMS 200 7.260 23.990 1.080 1.00 0.000 +ATOM 799 OD DMS 200 9.700 24.610 -0.010 1.00 0.000 +ATOM 800 CD2 DMS 200 7.870 26.710 0.140 1.00 0.000 +ATOM 801 SD DMS 201 9.180 11.240 17.330 1.00 0.000 +ATOM 802 CD1 DMS 201 8.800 9.810 18.610 1.00 0.000 +ATOM 803 OD DMS 201 10.440 12.040 17.650 1.00 0.000 +ATOM 804 CD2 DMS 201 9.840 9.810 16.180 1.00 0.000 +ATOM 805 SD DMS 202 24.030 21.660 23.550 1.00 0.000 +ATOM 806 CD1 DMS 202 23.930 22.130 25.440 1.00 0.000 +ATOM 807 OD DMS 202 25.240 22.470 23.090 1.00 0.000 +ATOM 808 CD2 DMS 202 24.560 19.790 23.760 1.00 0.000 +ATOM 809 SD DMS 203 21.280 27.100 11.880 1.00 0.000 +ATOM 810 CD1 DMS 203 19.390 27.100 11.390 1.00 0.000 +ATOM 811 OD DMS 203 21.280 27.120 13.410 1.00 0.000 +ATOM 812 CD2 DMS 203 21.800 25.260 11.520 1.00 0.000 +ATOM 813 SD DMS 204 10.760 11.290 27.890 1.00 0.000 +ATOM 814 CD1 DMS 204 10.000 12.400 26.480 1.00 0.000 +ATOM 815 OD DMS 204 10.330 11.690 29.300 1.00 0.000 +ATOM 816 CD2 DMS 204 9.600 9.770 27.480 1.00 0.000 +ATOM 817 SD DMS 205 22.110 14.990 25.730 1.00 0.000 +ATOM 818 CD1 DMS 205 21.910 14.390 27.570 1.00 0.000 +ATOM 819 OD DMS 205 20.810 15.760 25.450 1.00 0.000 +ATOM 820 CD2 DMS 205 23.510 16.300 26.060 1.00 0.000 +ATOM 821 SD DMS 206 14.500 22.950 9.860 1.00 0.000 +ATOM 822 CD1 DMS 206 15.560 21.400 10.410 1.00 0.000 +ATOM 823 OD DMS 206 14.970 23.270 8.440 1.00 0.000 +ATOM 824 CD2 DMS 206 12.900 21.840 9.840 1.00 0.000 +ATOM 825 SD DMS 207 0.660 4.580 14.780 1.00 0.000 +ATOM 826 CD1 DMS 207 1.220 2.840 15.460 1.00 0.000 +ATOM 827 OD DMS 207 -0.160 4.600 13.490 1.00 0.000 +ATOM 828 CD2 DMS 207 -0.440 5.150 16.280 1.00 0.000 +ATOM 829 SD DMS 208 16.990 1.820 6.160 1.00 0.000 +ATOM 830 CD1 DMS 208 15.530 2.540 5.080 1.00 0.000 +ATOM 831 OD DMS 208 16.310 0.900 7.170 1.00 0.000 +ATOM 832 CD2 DMS 208 17.900 0.770 4.780 1.00 0.000 +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-1.3.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-1.3.link new file mode 100644 index 0000000000000000000000000000000000000000..8b2cc9d6ed1ac80b48941c737c184d85b07bdd65 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-1.3.link @@ -0,0 +1,88 @@ +remarks file toppar/dna-rna.link +remarks macro to define standard nucleic acid links and termini +remarks this file has both 3' and 5' terminii without phosphate groups +remarks + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link nuc head - DA tail + DA end +link nuc head - DA tail + DC end +link nuc head - DA tail + DG end +link nuc head - DA tail + DT end +link nuc head - DA tail + DJ end + +link nuc head - DC tail + DA end +link nuc head - DC tail + DC end +link nuc head - DC tail + DG end +link nuc head - DC tail + DT end +link nuc head - DC tail + DJ end + +link nuc head - DG tail + DA end +link nuc head - DG tail + DC end +link nuc head - DG tail + DG end +link nuc head - DG tail + DT end +link nuc head - DG tail + DJ end + +link nuc head - DT tail + DA end +link nuc head - DT tail + DC end +link nuc head - DT tail + DG end +link nuc head - DT tail + DT end +link nuc head - DT tail + DJ end + +link nuc head - DJ tail + DA end +link nuc head - DJ tail + DC end +link nuc head - DJ tail + DG end +link nuc head - DJ tail + DT end +link nuc head - DJ tail + DJ end + + +link nuc head - A tail + A end +link nuc head - A tail + C end +link nuc head - A tail + G end +link nuc head - A tail + U end + +link nuc head - C tail + A end +link nuc head - C tail + C end +link nuc head - C tail + G end +link nuc head - C tail + U end + +link nuc head - G tail + A end +link nuc head - G tail + C end +link nuc head - G tail + G end +link nuc head - G tail + U end + +link nuc head - U tail + A end +link nuc head - U tail + C end +link nuc head - U tail + G end +link nuc head - U tail + U end + + + +first 5ter tail + a end +first 5ter tail + c end +first 5ter tail + g end +first 5ter tail + u end + +first 5ter tail + da end +first 5ter tail + dc end +first 5ter tail + dg end +first 5ter tail + dt end +first 5ter tail + dj end + + +last 3ter head - a end +last 3ter head - c end +last 3ter head - g end +last 3ter head - u end + +last 3ter head - da end +last 3ter head - dc end +last 3ter head - dg end +last 3ter head - dt end +last 3ter head - dj end + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p-break.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p-break.top new file mode 100644 index 0000000000000000000000000000000000000000..c1a2cb341d1ceae02a2856f508598b6dae4776b7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p-break.top @@ -0,0 +1,19 @@ +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + + +PRESidue DNCG + ! patch for deletion of nucleic acid linkage + ! that are too long to exist + + DELETE BOND +BB3 -BB1 + DELETE ANGLE -BB2 -BB3 +BB1 + DELETE ANGLE -BB3 +BB1 +BB2 + DELETE DIHEdral -BB1 -BB2 -BB3 +BB1 + DELETE DIHEdral -BB2 -BB3 +BB1 +BB2 + DELETE DIHEdral -BB3 +BB1 +BB2 +BB3 + DELETE ANGLE -SC1 -BB3 +BB1 + +END {DNCG} + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.link new file mode 100644 index 0000000000000000000000000000000000000000..1f477d3faf7e52987886196dd7c299ecacf095e8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.link @@ -0,0 +1,48 @@ +remarks this is a macro to define cg nucleid acid links + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link nuc head - DA tail + DA end +link nuc head - DA tail + DC end +link nuc head - DA tail + DG end +link nuc head - DA tail + DT end + +link nuc head - DC tail + DA end +link nuc head - DC tail + DC end +link nuc head - DC tail + DG end +link nuc head - DC tail + DT end + +link nuc head - DG tail + DA end +link nuc head - DG tail + DC end +link nuc head - DG tail + DG end +link nuc head - DG tail + DT end + +link nuc head - DT tail + DA end +link nuc head - DT tail + DC end +link nuc head - DT tail + DG end +link nuc head - DT tail + DT end + +link nuc head - A tail + A end +link nuc head - A tail + C end +link nuc head - A tail + G end +link nuc head - A tail + U end + +link nuc head - C tail + A end +link nuc head - C tail + C end +link nuc head - C tail + G end +link nuc head - C tail + U end + +link nuc head - G tail + A end +link nuc head - G tail + C end +link nuc head - G tail + G end +link nuc head - G tail + U end + +link nuc head - U tail + A end +link nuc head - U tail + C end +link nuc head - U tail + G end +link nuc head - U tail + U end + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.param new file mode 100644 index 0000000000000000000000000000000000000000..04991b4571eb77c6983dc8a04cfb5d4acfacf5b6 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.param @@ -0,0 +1,1467 @@ +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + + +BOND TNS4 TNS2 500.000 3.220 +BOND TNS4 NH6 500.000 3.220 +BOND NH5 TNS2 500.000 3.220 +BOND NH5 NH6 500.000 3.220 +BOND GNS3 GNS4 500.000 2.950 +BOND GNS3 NH4 500.000 2.950 +BOND NH3 GNS4 500.000 2.950 +BOND NH3 NH4 500.000 2.950 +BOND NB1 NB2 47.870 3.600 +BOND ANS1 ANS3 500.000 2.660 +BOND ANS1 NH2 500.000 2.660 +BOND NH1 ANS3 500.000 2.660 +BOND NH1 NH2 500.000 2.660 +BOND CNS4 CNS3 500.000 2.850 +BOND CNS4 NH8 500.000 2.850 +BOND NH7 CNS3 500.000 2.850 +BOND NH7 NH8 500.000 2.850 +BOND NB3 ANS1 71.805 3.000 +BOND NB3 GNS1 71.805 3.000 +BOND NB3 CNS1 71.805 2.700 +BOND TNS2 TNS1 500.000 2.650 +BOND NH6 TNS1 500.000 2.650 +BOND GNS2 GNS1 500.000 1.610 +BOND ANS1 ANS2 47.870 3.260 +BOND NH1 ANS2 47.870 3.260 +BOND CNS3 CNS1 500.000 2.680 +BOND NH8 CNS1 500.000 2.680 +BOND NB2 NB3 191.479 1.980 +BOND ANS1 ANS1 500.000 2.290 +BOND ANS1 NH1 500.000 2.290 +BOND CNS1 CNS4 500.000 2.200 +BOND CNS1 NH7 500.000 2.200 +BOND ANS3 ANS2 500.000 2.880 +BOND NH2 ANS2 500.000 2.880 +BOND GNS1 GNS3 500.000 2.950 +BOND GNS1 NH3 500.000 2.950 +BOND GNS3 GNS2 47.870 3.890 +BOND NH3 GNS2 47.870 3.890 +BOND TNS1 TNS4 500.000 2.170 +BOND TNS1 NH5 500.000 2.170 +BOND NB3 TNS1 71.805 2.700 +BOND NB3 NB1 23.935 3.530 +BOND GNS4 GNS2 500.000 2.850 +BOND NH4 GNS2 500.000 2.850 +BOND ANS2 ANS1 500.000 1.620 +BOND URS4 URS2 500.000 2.890 +BOND URS4 RH6 500.000 2.890 +BOND RH5 URS2 500.000 2.890 +BOND RH5 RH6 500.000 2.890 +BOND GRS3 GRS4 500.000 2.910 +BOND GRS3 RH4 500.000 2.910 +BOND RH3 GRS4 500.000 2.910 +BOND RH3 RH4 500.000 2.910 +BOND RNB1 RNB2 47.870 3.630 +BOND ARS1 ARS2 500.000 2.630 +BOND ARS1 RH2 500.000 2.630 +BOND RH1 ARS2 500.000 2.630 +BOND RH1 RH2 500.000 2.630 +BOND CRS4 CRS3 500.000 2.810 +BOND CRS4 RH8 500.000 2.810 +BOND RH7 CRS3 500.000 2.810 +BOND RH7 RH8 500.000 2.810 +BOND RNB3 ARS1 67.018 2.930 +BOND RNB3 GRS1 47.870 2.920 +BOND RNB3 CRS1 26.328 2.800 +BOND URS2 URS1 500.000 2.760 +BOND RH6 URS1 500.000 2.760 +BOND GRS2 GRS1 500.000 1.620 +BOND ARS1 ARS3 95.740 3.350 +BOND RH1 ARS3 95.740 3.350 +BOND CRS3 CRS1 500.000 2.670 +BOND RH8 CRS1 500.000 2.670 +BOND RNB2 RNB3 95.740 2.020 +BOND CRS1 CRS4 500.000 2.240 +BOND CRS1 RH7 500.000 2.240 +BOND ARS2 ARS3 500.000 2.990 +BOND RH2 ARS3 500.000 2.990 +BOND URS1 URS4 500.000 2.240 +BOND URS1 RH5 500.000 2.240 +BOND GRS1 GRS3 500.000 2.960 +BOND GRS1 RH3 500.000 2.960 +BOND GRS3 GRS2 95.740 3.850 +BOND RH3 GRS2 95.740 3.850 +BOND ARS1 ARS1 500.000 2.340 +BOND ARS1 RH1 500.000 2.340 +BOND RNB3 RNB1 23.935 3.540 +BOND GRS4 GRS2 500.000 2.960 +BOND RH4 GRS2 500.000 2.960 +BOND RNB3 URS1 43.083 2.860 +BOND ARS3 ARS1 500.000 1.620 +ANGLE NB2 TNS1 TNS2 95.74 145 +ANGLE NB2 TNS1 NH6 95.74 145 +ANGLE NB2 NB3 CNS1 50.26 95 +ANGLE TNS4 TNS2 TNS1 23.93 42 +ANGLE TNS4 NH6 TNS1 23.93 42 +ANGLE NH5 TNS2 TNS1 23.93 42 +ANGLE NH5 NH6 TNS1 23.93 42 +ANGLE NB3 TNS1 TNS4 71.80 107 +ANGLE NB3 TNS1 NH5 71.80 107 +ANGLE NB3 CNS1 CNS4 71.80 95 +ANGLE NB3 CNS1 NH7 71.80 95 +ANGLE ANS1 ANS1 ANS3 47.87 85 +ANGLE ANS1 ANS1 NH2 47.87 85 +ANGLE ANS1 NH1 ANS3 47.87 85 +ANGLE ANS1 NH1 NH2 47.87 85 +ANGLE GNS3 GNS1 GNS2 47.87 125 +ANGLE NH3 GNS1 GNS2 47.87 125 +ANGLE NB3 GNS1 GNS2 59.84 130 +ANGLE ANS1 NB3 NB1 47.87 158 +ANGLE ANS3 ANS2 ANS1 47.87 98 +ANGLE NH2 ANS2 ANS1 47.87 98 +ANGLE NB2 NB3 GNS1 59.84 94 +ANGLE TNS1 NB3 NB1 7.18 180 +ANGLE NB3 ANS1 ANS1 47.87 160 +ANGLE NB3 ANS1 NH1 47.87 160 +ANGLE CNS1 CNS4 CNS3 47.87 61 +ANGLE CNS1 CNS4 NH8 47.87 61 +ANGLE CNS1 NH7 CNS3 47.87 61 +ANGLE CNS1 NH7 NH8 47.87 61 +ANGLE TNS1 TNS4 TNS2 23.93 55 +ANGLE TNS1 TNS4 NH6 23.93 55 +ANGLE TNS1 NH5 TNS2 23.93 55 +ANGLE TNS1 NH5 NH6 23.93 55 +ANGLE NB3 NB1 NB2 17.95 106 +ANGLE NB3 GNS1 GNS3 71.80 137 +ANGLE NB3 GNS1 NH3 71.80 137 +ANGLE NB2 NB3 TNS1 52.66 92 +ANGLE GNS1 NB3 NB1 35.90 157 +ANGLE NB1 NB2 NB3 47.87 110 +ANGLE ANS1 ANS1 ANS2 47.87 125 +ANGLE NH1 ANS1 ANS2 47.87 125 +ANGLE CNS4 CNS1 CNS3 47.87 71 +ANGLE CNS4 CNS1 NH8 47.87 71 +ANGLE NH7 CNS1 CNS3 47.87 71 +ANGLE NH7 CNS1 NH8 47.87 71 +ANGLE TNS4 TNS1 TNS2 23.93 83 +ANGLE TNS4 TNS1 NH6 23.93 83 +ANGLE NH5 TNS1 TNS2 23.93 83 +ANGLE NH5 TNS1 NH6 23.93 83 +ANGLE GNS4 GNS2 GNS1 47.87 94 +ANGLE NH4 GNS2 GNS1 47.87 94 +ANGLE NB2 NB3 ANS1 59.84 94 +ANGLE NB2 CNS1 CNS3 119.67 150 +ANGLE NB2 CNS1 NH8 119.67 150 +ANGLE NB2 NB3 NB1 35.90 102 +ANGLE ANS1 ANS3 ANS2 47.87 74 +ANGLE ANS1 NH2 ANS2 47.87 74 +ANGLE NH1 ANS3 ANS2 47.87 74 +ANGLE NH1 NH2 ANS2 47.87 74 +ANGLE GNS1 GNS3 GNS4 47.87 69 +ANGLE GNS1 GNS3 NH4 47.87 69 +ANGLE GNS1 NH3 GNS4 47.87 69 +ANGLE GNS1 NH3 NH4 47.87 69 +ANGLE GNS3 GNS4 GNS2 47.87 84 +ANGLE GNS3 NH4 GNS2 47.87 84 +ANGLE NH3 GNS4 GNS2 47.87 84 +ANGLE NH3 NH4 GNS2 47.87 84 +ANGLE CNS1 NB3 NB1 7.18 180 +ANGLE NB3 ANS1 ANS2 47.87 140 +ANGLE CNS4 CNS3 CNS1 47.87 47 +ANGLE CNS4 NH8 CNS1 47.87 47 +ANGLE NH7 CNS3 CNS1 47.87 47 +ANGLE NH7 NH8 CNS1 47.87 47 +ANGLE RNB2 RNB3 URS1 53.85 95 +ANGLE RNB2 RNB3 CRS1 55.05 94 +ANGLE RNB3 CRS1 CRS4 40.69 103 +ANGLE RNB3 CRS1 RH7 40.69 103 +ANGLE ARS1 ARS1 ARS2 47.87 87 +ANGLE ARS1 ARS1 RH2 47.87 87 +ANGLE ARS1 RH1 ARS2 47.87 87 +ANGLE ARS1 RH1 RH2 47.87 87 +ANGLE GRS3 GRS1 GRS2 47.87 117 +ANGLE RH3 GRS1 GRS2 47.87 117 +ANGLE RNB3 GRS1 GRS2 28.72 137 +ANGLE ARS1 RNB3 RNB1 3.59 160 +ANGLE ARS2 ARS3 ARS1 47.87 92 +ANGLE RH2 ARS3 ARS1 47.87 92 +ANGLE RNB2 RNB3 GRS1 62.23 103 +ANGLE URS4 URS1 URS2 23.93 83 +ANGLE URS4 URS1 RH6 23.93 83 +ANGLE RH5 URS1 URS2 23.93 83 +ANGLE RH5 URS1 RH6 23.93 83 +ANGLE RNB3 ARS1 ARS1 21.54 153 +ANGLE RNB3 ARS1 RH1 21.54 153 +ANGLE CRS1 CRS4 CRS3 47.87 61 +ANGLE CRS1 CRS4 RH8 47.87 61 +ANGLE CRS1 RH7 CRS3 47.87 61 +ANGLE CRS1 RH7 RH8 47.87 61 +ANGLE RNB3 RNB1 RNB2 17.95 93 +ANGLE URS1 URS4 URS2 23.93 55 +ANGLE URS1 URS4 RH6 23.93 55 +ANGLE URS1 RH5 URS2 23.93 55 +ANGLE URS1 RH5 RH6 23.93 55 +ANGLE RNB3 GRS1 GRS3 19.15 129 +ANGLE RNB3 GRS1 RH3 19.15 129 +ANGLE URS1 RNB3 RNB1 1.20 180 +ANGLE GRS1 RNB3 RNB1 4.79 170 +ANGLE RNB1 RNB2 RNB3 41.89 117 +ANGLE ARS1 ARS1 ARS3 47.87 115 +ANGLE RH1 ARS1 ARS3 47.87 115 +ANGLE CRS4 CRS1 CRS3 47.87 71 +ANGLE CRS4 CRS1 RH8 47.87 71 +ANGLE RH7 CRS1 CRS3 47.87 71 +ANGLE RH7 CRS1 RH8 47.87 71 +ANGLE RNB2 URS1 URS2 23.93 155 +ANGLE RNB2 URS1 RH6 23.93 155 +ANGLE GRS4 GRS2 GRS1 47.87 96 +ANGLE RH4 GRS2 GRS1 47.87 96 +ANGLE URS4 URS2 URS1 23.93 42 +ANGLE URS4 RH6 URS1 23.93 42 +ANGLE RH5 URS2 URS1 23.93 42 +ANGLE RH5 RH6 URS1 23.93 42 +ANGLE RNB2 RNB3 ARS1 62.23 101 +ANGLE RNB2 CRS1 CRS3 23.93 155 +ANGLE RNB2 CRS1 RH8 23.93 155 +ANGLE RNB2 RNB3 RNB1 25.13 95 +ANGLE ARS1 ARS2 ARS3 47.87 74 +ANGLE ARS1 RH2 ARS3 47.87 74 +ANGLE RH1 ARS2 ARS3 47.87 74 +ANGLE RH1 RH2 ARS3 47.87 74 +ANGLE GRS1 GRS3 GRS4 47.87 72 +ANGLE GRS1 GRS3 RH4 47.87 72 +ANGLE GRS1 RH3 GRS4 47.87 72 +ANGLE GRS1 RH3 RH4 47.87 72 +ANGLE GRS3 GRS4 GRS2 47.87 84 +ANGLE GRS3 RH4 GRS2 47.87 84 +ANGLE RH3 GRS4 GRS2 47.87 84 +ANGLE RH3 RH4 GRS2 47.87 84 +ANGLE RNB3 URS1 URS4 47.87 99 +ANGLE RNB3 URS1 RH5 47.87 99 +ANGLE CRS1 RNB3 RNB1 0.12 130 +ANGLE RNB3 ARS1 ARS3 44.28 135 +ANGLE CRS4 CRS3 CRS1 47.87 47 +ANGLE CRS4 RH8 CRS1 47.87 47 +ANGLE RH7 CRS3 CRS1 47.87 47 +ANGLE RH7 RH8 CRS1 47.87 47 +DIHEdral NB2 NB3 ANS1 ANS2 0.04 2 98 +DIHEdral NB1 NB2 NB3 TNS1 0.10 2 -75 +DIHEdral NB2 NB3 CNS1 CNS3 0.12 2 -142 +DIHEdral NB2 NB3 CNS1 NH8 0.12 2 -142 +DIHEdral NB2 NB3 GNS1 GNS2 0.04 2 92 +DIHEdral NB2 NB3 GNS1 GNS3 0.00 2 -117 +DIHEdral NB2 NB3 GNS1 NH3 0.00 2 -117 +DIHEdral NB2 NB3 TNS1 TNS2 0.16 2 -145 +DIHEdral NB2 NB3 TNS1 NH6 0.16 2 -145 +DIHEdral NB2 NB3 ANS1 ANS1 0.00 2 -116 +DIHEdral NB2 NB3 ANS1 NH1 0.00 2 -116 +DIHEdral NB1 NB2 NB3 GNS1 0.05 2 -90 +DIHEdral NB3 NB1 NB2 NB3 0.00 9 160 +DIHEdral NB2 NB3 NB1 NB2 0.00 1 1803 +DIHEdral NB1 NB2 NB3 ANS1 0.05 2 -90 +DIHEdral NB2 NB3 TNS1 TNS4 0.04 2 -110 +DIHEdral NB2 NB3 TNS1 NH5 0.04 2 -110 +DIHEdral NB1 NB2 NB3 NB1 0.06 2 95 +DIHEdral NB2 NB3 CNS1 CNS4 0.05 2 -90 +DIHEdral NB2 NB3 CNS1 NH7 0.05 2 -90 +DIHEdral NB1 NB2 NB3 CNS1 0.06 2 -78 +DIHEdral RNB2 RNB3 ARS1 ARS3 0.00 2 80 +DIHEdral ARS1 ARS1 ARS2 ARS3 0.02 2 0 +DIHEdral ARS1 ARS1 RH2 ARS3 0.02 2 0 +DIHEdral ARS1 RH1 ARS2 ARS3 0.02 2 0 +DIHEdral ARS1 RH1 RH2 ARS3 0.02 2 0 +DIHEdral RNB2 RNB3 URS1 URS4 0.01 2 180 +DIHEdral RNB2 RNB3 URS1 RH5 0.01 2 180 +DIHEdral RNB2 RNB3 GRS1 GRS2 0.01 1 0 +DIHEdral RNB2 RNB3 GRS1 GRS3 0.01 2 180 +DIHEdral RNB2 RNB3 GRS1 RH3 0.01 2 180 +DIHEdral RNB2 RNB3 URS1 URS2 0.00 1 0 +DIHEdral RNB2 RNB3 URS1 RH6 0.00 1 0 +DIHEdral RNB2 RNB3 ARS1 ARS1 0.00 2 180 +DIHEdral RNB2 RNB3 ARS1 RH1 0.00 2 180 +DIHEdral RNB1 RNB2 RNB3 GRS1 0.00 1 -20 +DIHEdral RNB3 RNB1 RNB2 RNB3 0.00 9 10 +DIHEdral GRS1 GRS3 GRS4 GRS2 0.02 2 0 +DIHEdral GRS1 GRS3 RH4 GRS2 0.02 2 0 +DIHEdral GRS1 RH3 GRS4 GRS2 0.02 2 0 +DIHEdral GRS1 RH3 RH4 GRS2 0.02 2 0 +DIHEdral RNB2 RNB3 RNB1 RNB2 0.00 1 0 +DIHEdral RNB1 RNB2 RNB3 ARS1 0.00 2 180 +DIHEdral RNB1 RNB2 RNB3 RNB1 0.01 2 0 +DIHEdral RNB2 RNB3 CRS1 CRS4 0.00 1 0 +DIHEdral RNB2 RNB3 CRS1 RH7 0.00 1 0 +DIHEdral RNB1 RNB2 RNB3 URS1 0.00 1 0 +DIHEdral RNB1 RNB2 RNB3 CRS1 0.00 2 -130 +NONBONded RH8 3.200 0.8 3.200 0.8 +NONBONded GRS1 3.200 0.6 3.200 0.6 +NONBONded RH1 3.200 0.6 3.200 0.6 +NONBONded RNB3 4.300 0.8 4.300 0.8 +NONBONded RH3 3.200 0.5 3.200 0.5 +NONBONded RH2 3.200 0.6 3.200 0.6 +NONBONded RH5 3.200 1.1 3.200 1.1 +NONBONded RH4 3.200 0.5 3.200 0.5 +NONBONded RH7 3.200 0.8 3.200 0.8 +NONBONded RH6 3.200 1.0 3.200 1.0 +NONBONded CRS1 3.200 0.6 3.200 0.6 +NONBONded ARS1 3.200 0.6 3.200 0.6 +NONBONded ARS2 3.200 0.8 3.200 0.8 +NONBONded ARS3 3.200 0.7 3.200 0.7 +NONBONded RNB2 4.300 0.6 4.300 0.6 +NONBONded CRS3 3.200 0.8 3.200 0.8 +NONBONded GNS2 3.200 0.7 3.200 0.7 +NONBONded GNS3 3.200 0.8 3.200 0.8 +NONBONded GNS1 3.200 0.6 3.200 0.6 +NONBONded GNS4 3.200 0.8 3.200 0.8 +NONBONded URS1 3.200 0.6 3.200 0.6 +NONBONded TNS2 3.200 0.7 3.200 0.7 +NONBONded TNS1 3.200 0.6 3.200 0.6 +NONBONded URS2 3.200 0.7 3.200 0.7 +NONBONded TNS4 3.200 0.8 3.200 0.8 +NONBONded RNB1 4.700 0.8 4.700 0.8 +NONBONded CRS4 3.200 0.8 3.200 0.8 +NONBONded NB3 4.300 0.6 4.300 0.6 +NONBONded NB2 4.300 0.6 4.300 0.6 +NONBONded NB1 4.700 0.8 4.700 0.8 +NONBONded URS4 3.200 0.8 3.200 0.8 +NONBONded GRS4 3.200 0.8 3.200 0.8 +NONBONded NH5 3.200 1.1 3.200 1.1 +NONBONded NH4 3.200 0.5 3.200 0.5 +NONBONded NH7 3.200 0.8 3.200 0.8 +NONBONded NH6 3.200 1.0 3.200 1.0 +NONBONded NH1 3.200 0.6 3.200 0.6 +NONBONded NH3 3.200 0.5 3.200 0.5 +NONBONded NH2 3.200 0.6 3.200 0.6 +NONBONded NH8 3.200 0.8 3.200 0.8 +NONBONded GRS3 3.200 0.8 3.200 0.8 +NONBONded CNS4 3.200 0.8 3.200 0.8 +NONBONded GRS2 3.200 0.7 3.200 0.7 +NONBONded CNS3 3.200 0.8 3.200 0.8 +NONBONded CNS1 3.200 0.6 3.200 0.6 +NONBONded ANS1 3.200 0.6 3.200 0.6 +NONBONded ANS2 3.200 0.7 3.200 0.7 +NONBONded ANS3 3.200 0.8 3.200 0.8 +NBFIx RH8 GRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 RH1 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH8 RNB3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RH8 RH3 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH8 RH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH8 RH5 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH8 RH4 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH8 RH7 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH8 RH6 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH8 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH8 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH8 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx RH8 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH8 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH8 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 NH5 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH8 NH4 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH8 NH7 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH8 NH6 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH8 NH1 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH8 NH3 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH8 NH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH8 NH8 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH8 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH8 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH8 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS1 RH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 RNB3 100425113.301 15886.623 100425113.301 15886.623 +NBFIx GRS1 RH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 CRS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 ARS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 ARS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 ARS3 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx GRS1 CRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 GNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 GNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 GNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx GRS1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx GRS1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx GRS1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx GRS1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 NH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 NH8 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 RNB3 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RH1 RH3 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 RH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH1 RH5 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH1 RH4 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 RH7 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH1 RH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 CRS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 ARS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 ARS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 ARS3 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RH1 CRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 GNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 GNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 GNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RH1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx RH1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RH1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RH1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 NH5 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH1 NH4 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 NH7 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH1 NH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 NH1 2538745.295 2364.391 2538745.295 2364.391 +NBFIx RH1 NH3 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH1 NH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH1 NH8 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RNB3 RH3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RH2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RH5 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RH4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RH7 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RH6 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 CRS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 ARS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 ARS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 ARS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 CRS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GNS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GNS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 GNS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 URS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 TNS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 TNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 URS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 TNS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB3 CRS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx RNB3 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB3 URS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GRS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH5 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH7 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH6 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 NH3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 NH8 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GRS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 CNS4 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 GRS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 CNS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 CNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 ANS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB3 ANS2 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RNB3 ANS3 129118002.815 20425.658 129118002.815 20425.658 +NBFIx RH3 RH2 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH3 RH5 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH3 RH4 2207604.604 2055.992 2207604.604 2055.992 +NBFIx RH3 RH7 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH3 RH6 3421787.137 3186.788 3421787.137 3186.788 +NBFIx RH3 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH3 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH3 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx RH3 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH3 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH3 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 NH5 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH3 NH4 2207604.604 2055.992 2207604.604 2055.992 +NBFIx RH3 NH7 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH3 NH6 3421787.137 3186.788 3421787.137 3186.788 +NBFIx RH3 NH1 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH3 NH3 2207604.604 2055.992 2207604.604 2055.992 +NBFIx RH3 NH2 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH3 NH8 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH3 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 RH5 4967110.360 4625.982 4967110.360 4625.982 +NBFIx RH2 RH4 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH2 RH7 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH2 RH6 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH2 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH2 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH2 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx RH2 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH2 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RH2 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 NH5 4967110.360 4625.982 4967110.360 4625.982 +NBFIx RH2 NH4 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH2 NH7 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH2 NH6 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH2 NH1 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH2 NH3 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH2 NH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH2 NH8 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH2 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 RH4 3421787.137 3186.788 3421787.137 3186.788 +NBFIx RH5 RH7 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH5 RH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH5 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH5 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 RNB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH5 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx RH5 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH5 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH5 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 NH5 4967110.360 4625.982 4967110.360 4625.982 +NBFIx RH5 NH4 3421787.137 3186.788 3421787.137 3186.788 +NBFIx RH5 NH7 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH5 NH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH5 NH1 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH5 NH3 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH5 NH2 4967110.360 4625.982 4967110.360 4625.982 +NBFIx RH5 NH8 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH5 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH5 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH5 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 RH7 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH4 RH6 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH4 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH4 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 RNB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH4 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx RH4 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH4 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH4 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 NH5 3421787.137 3186.788 3421787.137 3186.788 +NBFIx RH4 NH4 2207604.604 2055.992 2207604.604 2055.992 +NBFIx RH4 NH7 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH4 NH6 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH4 NH1 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH4 NH3 2207604.604 2055.992 2207604.604 2055.992 +NBFIx RH4 NH2 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH4 NH8 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 RH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH7 CRS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 ARS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 ARS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH7 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 RNB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH7 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx RH7 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RH7 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RH7 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 NH5 5519011.511 5139.980 5519011.511 5139.980 +NBFIx RH7 NH4 6843574.273 6373.575 6843574.273 6373.575 +NBFIx RH7 NH7 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH7 NH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx RH7 NH1 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH7 NH3 7174714.964 6681.974 7174714.964 6681.974 +NBFIx RH7 NH2 3863308.058 3597.986 3863308.058 3597.986 +NBFIx RH7 NH8 2980266.216 2775.589 2980266.216 2775.589 +NBFIx RH7 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH7 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH7 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RH6 CRS1 2897481.043 2698.490 2897481.043 2698.490 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ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx RH6 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx RH6 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS1 ARS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 ARS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS1 ARS3 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx CRS1 CRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS1 GNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 GNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS1 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 GNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS1 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 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3311406.906 3083.988 +NBFIx CRS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CRS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 ARS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 ARS3 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx ARS1 CRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 GNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 GNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 GNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx ARS1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx ARS1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx ARS1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx ARS1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 NH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 NH8 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 ARS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 RNB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx ARS2 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx ARS2 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx ARS2 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx ARS2 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx ARS2 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS2 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 RNB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx ARS3 CRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 GNS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 TNS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 URS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx ARS3 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx ARS3 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx ARS3 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx ARS3 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH6 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 GRS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx ARS3 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ARS3 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ARS3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RNB2 CRS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 GNS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 GNS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 GNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 GNS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 URS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 TNS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 TNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 URS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 TNS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB2 CRS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx RNB2 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB2 URS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 GRS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH5 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH7 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH6 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 NH1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 NH3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 NH8 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 GRS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 CNS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 GRS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 CNS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx RNB2 CNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 ANS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 ANS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx RNB2 ANS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx CRS3 GNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx CRS3 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx CRS3 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx CRS3 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx CRS3 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 GNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 GNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 TNS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS2 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 URS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS2 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx GNS2 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx GNS2 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx GNS2 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx GNS2 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH6 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS2 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 GRS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS2 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS2 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 GNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 GNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx GNS3 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx GNS3 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx GNS3 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx GNS3 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS1 GNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 URS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx GNS1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx GNS1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx GNS1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx GNS1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 NH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 NH8 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GNS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 URS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 TNS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 TNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 URS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 RNB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx GNS4 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx GNS4 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx GNS4 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx GNS4 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GNS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GNS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS1 TNS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx URS1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx URS1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx URS1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx URS1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 NH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 NH8 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS2 TNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS2 URS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS2 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx TNS2 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx TNS2 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx TNS2 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx TNS2 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH6 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS2 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS2 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 GRS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS2 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS2 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS2 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS1 URS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 TNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 RNB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx TNS1 CRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NB3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx TNS1 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx TNS1 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx TNS1 URS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 GRS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH5 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH7 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH6 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 NH3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 NH8 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx TNS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS2 TNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 RNB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx URS2 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx URS2 NB2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx URS2 NB1 500585614.160 46439.894 500585614.160 46439.894 +NBFIx URS2 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH6 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS2 NH1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS2 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 GRS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS2 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS2 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx URS2 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 RNB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx TNS4 CRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx TNS4 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx TNS4 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx TNS4 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS4 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx TNS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx TNS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx RNB1 CRS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 NB3 255854869.460 23735.946 255854869.460 23735.946 +NBFIx RNB1 NB2 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB1 NB1 389344366.569 36119.917 389344366.569 36119.917 +NBFIx RNB1 URS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 GRS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 NH5 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 NH4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 NH7 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 NH6 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 NH1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB1 NH3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 NH2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 NH8 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 GRS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 CNS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx RNB1 GRS2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 CNS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 CNS1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB1 ANS1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx RNB1 ANS2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx RNB1 ANS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx CRS4 NB3 77470801.689 12255.395 77470801.689 12255.395 +NBFIx CRS4 NB2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx CRS4 NB1 556206237.956 51599.882 556206237.956 51599.882 +NBFIx CRS4 URS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS4 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CRS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CRS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NB3 NB2 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 NB1 255854869.460 23735.946 255854869.460 23735.946 +NBFIx NB3 URS4 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 GRS4 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 NH5 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 NH4 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 NH7 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 NH6 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 NH1 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 NH3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 NH2 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 NH8 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 GRS3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 CNS4 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 GRS2 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 CNS3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 CNS1 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 ANS1 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB3 ANS2 77470801.689 12255.395 77470801.689 12255.395 +NBFIx NB3 ANS3 88947957.495 14071.009 88947957.495 14071.009 +NBFIx NB2 NB1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx NB2 URS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 GRS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH5 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH7 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH6 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 NH1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 NH3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH2 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 NH8 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 GRS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 CNS4 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 GRS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 CNS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB2 CNS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 ANS1 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 ANS2 100425113.301 15886.623 100425113.301 15886.623 +NBFIx NB2 ANS3 114771558.058 18156.141 114771558.058 18156.141 +NBFIx NB1 URS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 GRS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 NH5 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 NH4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 NH7 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 NH6 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 NH1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx NB1 NH3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 NH2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 NH8 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 GRS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 CNS4 556206237.956 51599.882 556206237.956 51599.882 +NBFIx NB1 GRS2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 CNS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 CNS1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx NB1 ANS1 444964990.365 41279.906 444964990.365 41279.906 +NBFIx NB1 ANS2 500585614.160 46439.894 500585614.160 46439.894 +NBFIx NB1 ANS3 500585614.160 46439.894 500585614.160 46439.894 +NBFIx URS4 GRS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS4 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx URS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx URS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH5 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH7 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH6 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS4 NH3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 NH8 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 NH4 3421787.137 3186.788 3421787.137 3186.788 +NBFIx NH5 NH7 5519011.511 5139.980 5519011.511 5139.980 +NBFIx NH5 NH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH5 NH1 5519011.511 5139.980 5519011.511 5139.980 +NBFIx NH5 NH3 3863308.058 3597.986 3863308.058 3597.986 +NBFIx NH5 NH2 4967110.360 4625.982 4967110.360 4625.982 +NBFIx NH5 NH8 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH5 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH5 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH5 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH5 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 NH7 6843574.273 6373.575 6843574.273 6373.575 +NBFIx NH4 NH6 3863308.058 3597.986 3863308.058 3597.986 +NBFIx NH4 NH1 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH4 NH3 2207604.604 2055.992 2207604.604 2055.992 +NBFIx NH4 NH2 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH4 NH8 7174714.964 6681.974 7174714.964 6681.974 +NBFIx NH4 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 NH6 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH7 NH1 2980266.216 2775.589 2980266.216 2775.589 +NBFIx NH7 NH3 7174714.964 6681.974 7174714.964 6681.974 +NBFIx NH7 NH2 3863308.058 3597.986 3863308.058 3597.986 +NBFIx NH7 NH8 2980266.216 2775.589 2980266.216 2775.589 +NBFIx NH7 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH7 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH7 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH7 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH6 NH1 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH6 NH3 3421787.137 3186.788 3421787.137 3186.788 +NBFIx NH6 NH2 5519011.511 5139.980 5519011.511 5139.980 +NBFIx NH6 NH8 5519011.511 5139.980 5519011.511 5139.980 +NBFIx NH6 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH6 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH6 GRS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH6 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH6 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH6 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH6 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH6 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH1 NH3 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH1 NH2 2980266.216 2775.589 2980266.216 2775.589 +NBFIx NH1 NH8 3863308.058 3597.986 3863308.058 3597.986 +NBFIx NH1 GRS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH1 CNS4 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH1 GRS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH1 CNS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH1 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx NH1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH3 NH2 4415209.209 4111.984 4415209.209 4111.984 +NBFIx NH3 NH8 6843574.273 6373.575 6843574.273 6373.575 +NBFIx NH3 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH3 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 NH8 2980266.216 2775.589 2980266.216 2775.589 +NBFIx NH2 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH2 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH2 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 GRS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH8 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx NH8 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx NH8 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS3 CNS4 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS3 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS3 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS4 GRS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS4 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS4 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CNS4 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CNS4 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS4 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS2 CNS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx GRS2 CNS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS2 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx GRS2 ANS2 3311406.906 3083.988 3311406.906 3083.988 +NBFIx GRS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS3 CNS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CNS3 ANS1 3311406.906 3083.988 3311406.906 3083.988 +NBFIx CNS3 ANS2 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS3 ANS3 3725332.770 3469.487 3725332.770 3469.487 +NBFIx CNS1 ANS1 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CNS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx CNS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ANS1 ANS2 2897481.043 2698.490 2897481.043 2698.490 +NBFIx ANS1 ANS3 3311406.906 3083.988 3311406.906 3083.988 +NBFIx ANS2 ANS3 3725332.770 3469.487 3725332.770 3469.487 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.top new file mode 100644 index 0000000000000000000000000000000000000000..5d5ca5eac81a58b6efc60a680b722d5f0c9dd44b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.top @@ -0,0 +1,448 @@ +!-----------------------------------------------------------------------------! +! Topology file for CG nucleic acid based on martinize script and parameters ! +! Authors: Rodrigo Honorato & Jorge Roel, MAY-2018 ! +!-----------------------------------------------------------------------------! + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +!------------! +! Backbone ! +!------------! +! DNA +MASS NB1 72.00 +MASS NB2 45.00 +MASS NB3 45.00 + +! RNA +MASS RNB1 72.00 +MASS RNB2 45.00 +MASS RNB3 45.00 ! MARTINI bead SNda + +!------------! +! Sidechains ! +!------------! + +! DA +MASS ANS1 45.00 +MASS ANS2 45.00 +MASS ANS3 45.00 + +! A +MASS ARS1 45.00 +MASS ARS2 45.00 +MASS ARS3 45.00 + +! DC +MASS CNS4 45.00 +MASS CNS3 45.00 +MASS CNS1 45.00 + +! C +MASS CRS1 45.00 +MASS CRS4 45.00 +MASS CRS3 45.00 + +! DG +MASS GNS2 45.00 +MASS GNS3 45.00 +MASS GNS1 45.00 +MASS GNS4 45.00 + +! G +MASS GRS1 45.00 +MASS GRS3 45.00 +MASS GRS4 45.00 +MASS GRS2 45.00 + +! DT +MASS TNS2 45.00 +MASS TNS1 45.00 +MASS TNS4 45.00 + +! U +MASS URS1 45.00 +MASS URS4 45.00 +MASS URS2 45.00 + + + +! SPECIAL HBONDing +! DNA +MASS NH1 45.00 +MASS NH2 45.00 +MASS NH3 45.00 +MASS NH4 45.00 +MASS NH5 45.00 +MASS NH6 45.00 +MASS NH7 45.00 +MASS NH8 45.00 +! RNA +MASS RH1 45.00 +MASS RH2 45.00 +MASS RH3 45.00 +MASS RH4 45.00 +MASS RH5 45.00 +MASS RH6 45.00 +MASS RH7 45.00 +MASS RH8 45.00 + +!------------------------------! +! Nucleic Acid Topology ! +!------------------------------! + +!------------------------------! +! DNA ! +!------------------------------! + +RESIdue DA + GROUp + ATOM BB1 type=NB1 charge=0.000 end + ATOM BB2 type=NB2 charge=0.000 end + ATOM BB3 type=NB3 charge=0.000 end + ATOM SC1 type=ANS1 charge=0.000 end + ATOM SC2 type=ANS1 charge=0.000 end + ATOM SC3 type=ANS3 charge=0.000 end + ATOM SC4 type=ANS2 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC2 SC4 + BOND SC3 SC4 + BOND SC4 SC1 + + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB3 SC1 SC4 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC4 + ANGLE SC2 SC3 SC4 + ANGLE SC3 SC4 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC4 +END + +!----------------------------------------------------------------! + +RESIdue DC + GROUp + ATOM BB1 type=NB1 charge=0.000 end + ATOM BB2 type=NB2 charge=0.000 end + ATOM BB3 type=NB3 charge=0.000 end + ATOM SC1 type=CNS1 charge=0.000 end + ATOM SC2 type=CNS4 charge=0.000 end + ATOM SC3 type=CNS3 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC3 SC1 + + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB2 SC1 SC3 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC3 + ANGLE SC2 SC3 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC3 + +END + +!----------------------------------------------------------------! + +RESIdue DG + GROUp + ATOM BB1 type=NB1 charge=0.000 end + ATOM BB2 type=NB2 charge=0.000 end + ATOM BB3 type=NB3 charge=0.000 end + ATOM SC1 type=GNS1 charge=0.000 end + ATOM SC2 type=GNS3 charge=0.000 end + ATOM SC3 type=GNS4 charge=0.000 end + ATOM SC4 type=GNS2 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC3 SC4 + BOND SC4 SC1 + + ANGLE BB1 BB2 BB3 + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB3 SC1 SC4 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC4 + ANGLE SC2 SC3 SC4 + ANGLE SC3 SC4 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC4 + +END + +!----------------------------------------------------------------! + +RESIdue DT + GROUp + ATOM BB1 type=NB1 charge=0.000 end + ATOM BB2 type=NB2 charge=0.000 end + ATOM BB3 type=NB3 charge=0.000 end + ATOM SC1 type=TNS1 charge=0.000 end + ATOM SC2 type=TNS4 charge=0.000 end + ATOM SC3 type=TNS2 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC3 SC1 + + ANGLE BB1 BB2 BB3 + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB2 SC1 SC3 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC3 + ANGLE SC2 SC3 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC3 + +END + +!------------------------------! +! RNA ! +!------------------------------! + +RESIdue A + GROUp + ATOM BB1 type=RNB1 charge=0.000 end + ATOM BB2 type=RNB2 charge=0.000 end + ATOM BB3 type=RNB3 charge=0.000 end + ATOM SC1 type=ARS1 charge=0.000 end + ATOM SC2 type=ARS1 charge=0.000 end + ATOM SC3 type=ARS2 charge=0.000 end + ATOM SC4 type=ARS3 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC2 SC4 + BOND SC3 SC4 + BOND SC4 SC1 + + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB3 SC1 SC4 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC4 + ANGLE SC2 SC3 SC4 + ANGLE SC3 SC4 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC4 + DIHEdral SC1 SC2 SC3 SC4 +END + +!----------------------------------------------------------------! + +RESIdue C + GROUp + ATOM BB1 type=RNB1 charge=0.000 end + ATOM BB2 type=RNB2 charge=0.000 end + ATOM BB3 type=RNB3 charge=0.000 end + ATOM SC1 type=CRS1 charge=0.000 end + ATOM SC2 type=CRS4 charge=0.000 end + ATOM SC3 type=CRS3 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC3 SC1 + + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB2 SC1 SC3 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC3 + ANGLE SC2 SC3 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + +END + +!----------------------------------------------------------------! + +RESIdue G + GROUp + ATOM BB1 type=RNB1 charge=0.000 end + ATOM BB2 type=RNB2 charge=0.000 end + ATOM BB3 type=RNB3 charge=0.000 end + ATOM SC1 type=GRS1 charge=0.000 end + ATOM SC2 type=GRS3 charge=0.000 end + ATOM SC3 type=GRS4 charge=0.000 end + ATOM SC4 type=GRS2 charge=0.000 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC3 SC4 + BOND SC4 SC1 + + ANGLE BB1 BB2 BB3 + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB3 SC1 SC4 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC4 + ANGLE SC2 SC3 SC4 + ANGLE SC3 SC4 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC4 + DIHEdral SC1 SC2 SC3 SC4 + +END + +!----------------------------------------------------------------! + +RESIdue U + + GROUp + ATOM BB1 type=RNB1 charge=0.00 end + ATOM BB2 type=RNB2 charge=0.00 end + ATOM BB3 type=RNB3 charge=0.00 end + ATOM SC1 type=URS1 charge=0.00 end + ATOM SC2 type=URS4 charge=0.00 end + ATOM SC3 type=URS2 charge=0.00 end + + BOND BB1 BB2 + BOND BB2 BB3 + BOND BB3 SC1 + BOND SC1 SC2 + BOND SC2 SC3 + BOND SC3 SC1 + + ANGLE BB1 BB2 BB3 + ANGLE BB2 BB3 SC1 + ANGLE BB3 SC1 SC2 + ANGLE BB2 SC1 SC3 + ANGLE SC1 SC2 SC3 + ANGLE SC2 SC1 SC3 + ANGLE SC2 SC3 SC1 + + DIHEdral BB1 BB2 BB3 SC1 + DIHEdral BB2 BB3 SC1 SC2 + DIHEdral BB2 BB3 SC1 SC3 + +END +!----------------------------------------------------------------! + + +!--------------------------------! +! Hydrogen Bonding nucleic acids ! +!--------------------------------! + +! DNA + +PRESidue DA1 + MODIFY ATOM SC2 TYPE=NH1 END + MODIFY ATOM SC3 TYPE=NH2 END +END + +PRESidue DC1 + MODIFY ATOM SC2 TYPE=NH7 END + MODIFY ATOM SC3 TYPE=NH8 END +END + +PRESidue DG1 + MODIFY ATOM SC2 TYPE=NH3 END + MODIFY ATOM SC3 TYPE=NH4 END +END + +PRESidue DT1 + MODIFY ATOM SC2 TYPE=NH5 END + MODIFY ATOM SC3 TYPE=NH6 END +END + +! RNA + +PRESidue A1 + MODIFY ATOM SC2 TYPE=RH1 END + MODIFY ATOM SC3 TYPE=RH2 END +END + +PRESidue C1 + MODIFY ATOM SC2 TYPE=RH7 END + MODIFY ATOM SC3 TYPE=RH8 END +END + +PRESidue G1 + MODIFY ATOM SC2 TYPE=RH3 END + MODIFY ATOM SC3 TYPE=RH4 END +END + +PRESidue U1 + MODIFY ATOM SC2 TYPE=RH5 END + MODIFY ATOM SC3 TYPE=RH6 END +END + +!----------------------------------------------------------------! + +!------------------------------! +! Patch to create connectivity ! +! *same for DNA and RNA* ! +!------------------------------! + +PRESidue NUC + ! patch for CG nucleic acid + ! (-) previous atom + ! (+) current atom + + ! BB + ADD BOND -BB3 +BB1 + + ADD ANGLE -BB2 -BB3 +BB1 + ADD ANGLE -BB3 +BB1 +BB2 + + ADD DIHEdral -BB1 -BB2 -BB3 +BB1 + ADD DIHEdral -BB2 -BB3 +BB1 +BB2 + ADD DIHEdral -BB3 +BB1 +BB2 +BB3 + + ! SC + ADD ANGLE -SC1 -BB3 +BB1 + +END + +!---------------------------------------------------------------- + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.param new file mode 100644 index 0000000000000000000000000000000000000000..782303b7a76b2ce22044c9dbe2a59f3bc405a41b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.param @@ -0,0 +1,1244 @@ +remarks file toppar/dna-rna-allatom.top +remarks dna-rna-allatom-hj-opls-1.3.param +remarks all-hydrogen dna/rna parameters using the OPLS force field + +!RNA PARAMETER FILE 'FRAMEWORK' FROM PARALLHDG.DNA AND ATOM NAMES +! AND HEAVY ATOM PARAMETERS FROM DNA-RNA.PARAM +!INCLUDES ALL NONEXCHANGEABLE HYDROGEN TERMS FOR BOND, ANGLE, AND +!IMPROPERS WITH ENERGY CONSTANT VARIABLES: $kchbond, $kchangle, AND $kchimpr. +!BOND, ANGLE, AND IMPROPERS WERE ESTIMATED FROM VALUES FROM THE STANDARD +!NUCLEOTIDES OF INSIGHTII 95.0 (BIOSYM/MOLECULAR SIMULATIONS). +!CREATED 2/24/96 -- JASON P. RIFE AND PETER B. MOORE +!ADDED OPLSX SECTION 6/2/07 -- HENRY JONKER +!ADAPTED/CLEANED FOR HADDOCK -- ALEXANDRE BONVIN + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + + +if ( $exist_par_nonbonded = false ) then + evaluate ($par_nonbonded = "OPLSX") +end if + +checkversion 1.3 + + +evaluate ($kchbond = 2000) +evaluate ($kchangle = 1000) +evaluate ($kchimpr = 1000) + + +!the generic bonds were taken from param11.dna with 3*kq +BOND C5R OH 876.000 1.4300 ! 5' end +BOND C5D OH 876.000 1.4300 ! 5' end +BOND C3R OH 876.000 1.4300 ! 3' end +BOND C3D OH 876.000 1.4300 ! 3' end +BOND O2R HO 1350.000 0.9572 + +!Phos. - combined RNA/DNA statistics used +! kq x_eq sigma +BOND P OP1 1489.209 1.485 ! 0.015 Phos +BOND P OP2 1489.209 1.485 ! 0.015 P +BOND P O5R 3350.720 1.593 ! 0.010 P +BOND P OH 3350.720 1.593 ! 0.010 P ! For 5pho patch +BOND P O3R 2326.889 1.607 ! 0.012 P + +!Sugars +!RNA statistics +BOND O5R C5R 1709.551 1.425 ! 0.014 Sugar +BOND C5R C4R 1982.674 1.510 ! 0.013 S +BOND C4R C3R 2769.190 1.524 ! 0.011 S +BOND C3R C2R 2769.190 1.525 ! 0.011 S +BOND C2R C1R 3350.720 1.528 ! 0.010 S +BOND O4R C1R 2326.888 1.414 ! 0.012 S +BOND O4R C4R 2326.888 1.453 ! 0.012 S +BOND O3R C3R 1982.674 1.423 ! 0.013 S +BOND C2R O2R 1982.674 1.413 ! 0.013 S + +!DNA statistics +BOND O5R C5D 1709.551 1.427 ! 0.014 Sugar +BOND C5R C4D 5235.500 1.511 ! 0.008 S +BOND C5D C4D 5235.500 1.511 ! 0.008 S +BOND C4D C3D 3350.720 1.528 ! 0.010 S +BOND C3D C2D 3350.720 1.518 ! 0.010 S +BOND C2D C1D 1709.551 1.521 ! 0.014 S +BOND O4D C1D 1982.674 1.420 ! 0.013 S +BOND O4D C4D 2769.190 1.446 ! 0.011 S +BOND O3R C3D 1982.674 1.431 ! 0.013 S +BOND C4D C3R 3350.720 1.528 ! 0.010 S ! for 3ter terminus +BOND C3R C2D 3350.720 1.518 ! 0.010 S ! for 3ter terminus + +!hydrogen/carbon +BOND C4R HR $kchbond 1.09 +BOND C3R HR $kchbond 1.09 +BOND C2R HR $kchbond 1.09 +BOND C1R HR $kchbond 1.09 +BOND C5R HR $kchbond 1.09 + +BOND C4D HR $kchbond 1.09 +BOND C3D HR $kchbond 1.09 +BOND C2D HR $kchbond 1.09 +BOND C1D HR $kchbond 1.09 +BOND C5D HR $kchbond 1.09 + +!Bases +!base specific bonds taken from param11.dna , 3*kq +BOND O2U HO 1350.000 0.957 ! UR +BOND HN NNA 1416.000 1.010 ! URA +BOND HN N1T 1416.000 1.010 ! Infer. +BOND HN N1C 1416.000 1.010 +BOND HN N9G 1416.000 1.010 +BOND HN N9A 1416.000 1.010 +BOND HN N9P 1416.000 1.010 +BOND HN N3U 1416.000 1.010 +BOND HN N3T 1416.000 1.010 +BOND H2 N2 1416.000 1.010 +BOND H2 N4C 1416.000 1.010 +BOND H2 N2G 1416.000 1.010 +BOND H2 N6A 1416.000 1.010 + +BOND HO OH 1350.000 0.960 ! PARAM7 (IR stretch 3400 cm-1) + +!Base sugar joint bonds (scale from sugar) +! kq x_eq sigma +BOND C1R N1T 1709.551 1.473 ! 0.014 Base +BOND C1R N1U 4136.691 1.469 ! 0.009 B +BOND C1R N1C 2326.889 1.470 ! 0.012 B +BOND C1R N9G 4136.691 1.459 ! 0.009 B +BOND C1R N9A 3350.720 1.462 ! 0.010 B +BOND C1R N9P 3350.720 1.462 ! 0.010 B + +BOND C1D N1T 1709.551 1.473 ! 0.014 B !DNA +BOND C1D N1U 4136.691 1.469 ! 0.009 B +BOND C1D N1C 2326.889 1.470 ! 0.012 B +BOND C1D N9G 4136.691 1.459 ! 0.009 B +BOND C1D N9A 3350.720 1.462 ! 0.010 B +BOND C1D N9P 3350.720 1.462 ! 0.010 B + +!cytosine kq x_eq sigma +BOND C2C ON 1370.370 1.240 !0.009 B +BOND C4C N4C 1370.370 1.335 !0.009 B +BOND N1C C2C 1110.000 1.397 !0.010 B +BOND N1C C6C 3083.333 1.367 !0.006 B +BOND C2C NC 1734.375 1.353 !0.008 B +BOND NC C4C 2265.306 1.335 !0.007 B +BOND C4C C5C 1734.375 1.425 !0.008 B +BOND C5C C6C 1734.375 1.339 !0.008 B +BOND C5C HR $kchbond 1.09 +BOND C6C HR $kchbond 1.09 + +!baseJ kq x_eq sigma +BOND C5T C3J 1734.375 1.339 !0.008 B +BOND OH H4J 1350.000 0.9572 + +!thymine +BOND N1T C2T 1734.375 1.376 !0.008 B +BOND C2T N3T 1734.375 1.373 !0.008 B +BOND N3T C4T 1734.375 1.382 !0.008 B +BOND C4T C5T 1370.370 1.445 !0.009 B +BOND C5T C6T 2265.306 1.339 !0.007 B +BOND C6T N1T 2265.306 1.378 !0.007 B +BOND C2T ON 1734.375 1.220 !0.008 B +BOND C4T ON 1370.370 1.228 !0.009 B +BOND C5T CC3E 3083.333 1.496 !0.006 B +BOND C6T HR $kchbond 1.09 +BOND CC3E HR $kchbond 1.09 + +!basej +BOND C3J H1J $kchbond 1.0969 +BOND C3J H2J $kchbond 1.0961 +BOND NJ HN 403.2 1.0129 +BOND CDJ H4J $kchbond 1.0817 +BOND C3J HCJ 330.6 1.0969 +BOND OH C3J 316.7 1.4233 +BOND C3J C3J 300.9 1.5375 +BOND C3J OSJ 308.6 1.4316 +BOND C3J CCJ 334.8 1.5015 +BOND CCJ CJ 371.0 1.4676 +BOND CCJ CDJ 500.9 1.3729 +BOND CJ NJ 427.6 1.3789 +BOND CJ OJ 637.7 1.2183 +BOND CDJ NJ 425.1 1.3807 +BOND NJ C3J 328.7 1.4619 + +!adenine +BOND NC C2A 1370.370 1.339 !0.009 B +BOND C2A N3A 1370.370 1.331 !0.009 B +BOND N3A C4A 3083.333 1.344 !0.006 B +BOND C4A C5A 2265.306 1.383 !0.007 B +BOND C5A C6A 1370.370 1.406 !0.009 B +BOND C6A NC 2265.306 1.351 !0.007 B +BOND C5A N7A 3083.333 1.388 !0.006 B +BOND N7A C8A 2265.306 1.311 !0.007 B +BOND C8A N9A 1734.375 1.373 !0.008 B +BOND N9A C4A 3083.333 1.374 !0.006 B +BOND C6A N6A 1734.375 1.335 !0.008 B +BOND C8A HR $kchbond 1.08 +BOND C2A HR $kchbond 1.09 + +!purine +BOND NC C2P 1370.370 1.339 !0.009 B +BOND C2P N3P 1370.370 1.331 !0.009 B +BOND N3P C4P 3083.333 1.344 !0.006 B +BOND C4P C5P 2265.306 1.383 !0.007 B +BOND C5P C6P 1370.370 1.406 !0.009 B +BOND C6P NC 2265.306 1.351 !0.007 B +BOND C5P N7P 3083.333 1.388 !0.006 B +BOND N7P C8P 2265.306 1.311 !0.007 B +BOND C8P N9P 1734.375 1.373 !0.008 B +BOND N9P C4P 3083.333 1.374 !0.006 B +BOND C6P HR $kchbond 1.09 !0.008 B +BOND C8P HR $kchbond 1.08 +BOND C2P HR $kchbond 1.09 + +!guanine +BOND NNA C2G 1734.375 1.373 !0.008 B +BOND C2G N3G 1734.375 1.323 !0.008 B +BOND N3G C4G 2265.306 1.350 !0.007 B +BOND C4G C5G 2265.306 1.379 !0.007 B +BOND C5G C6G 1110.000 1.419 !0.010 B +BOND C6G NNA 2265.306 1.391 !0.007 B +BOND C5G N7G 3083.333 1.388 !0.006 B +BOND N7G C8G 3083.333 1.305 !0.006 B +BOND C8G N9G 2265.306 1.374 !0.007 B +BOND N9G C4G 1734.375 1.375 !0.008 B +BOND C2G N2G 1110.000 1.341 !0.010 B +BOND C6G O6G 1370.370 1.237 !0.009 B +BOND C8G HR $kchbond 1.08 + +!uracil +BOND C2U ON 1370.370 1.219 !0.009 B +BOND C4U ON 1734.375 1.232 !0.008 B +BOND N1U C2U 1370.370 1.381 !0.009 B +BOND N1U C6U 1370.370 1.375 !0.009 B +BOND C2U N3U 2265.306 1.373 !0.007 B +BOND N3U C4U 1370.370 1.380 !0.009 B +BOND C4U C5U 1370.370 1.431 !0.009 B +BOND C5U C6U 1370.370 1.337 !0.009 B +BOND C5U HR $kchbond 1.09 +BOND C6U HR $kchbond 1.09 + +!Phos. +!the ANGLe s were taken from param11.dna with 3*kq +ANGLe HO OH C5R 139.500 107.300 +ANGLe HO O5R C5R 139.500 107.300 +ANGLe HO OH C5D 139.500 107.300 +ANGLe HO O5R C5D 139.500 107.300 +ANGLe HO O3R P 139.500 107.300 +ANGLe HO OH P 139.500 107.300 ! For 5pho patch +ANGLe HO O2R C2R 139.500 107.300 +ANGLe OH P O3R 144.300 102.600 ! +ANGLe OH P O5R 144.300 102.600 ! +ANGLe OH P OP1 296.700 108.230 ! +ANGLe OH P OP2 296.700 108.230 ! +ANGLe OH C5R C4R 210.000 112.000 ! +ANGLe OH C5D C4D 210.000 112.000 ! +ANGLe OH C5R C4D 210.000 112.000 ! +ANGLe C4D C3D OH 139.500 111.000 ! +ANGLe C4R C3R OH 139.500 111.000 ! +ANGLe C2D C3D OH 139.500 111.000 ! +ANGLe C2R C3R OH 139.500 111.000 ! +ANGLe C3R OH HO 139.500 107.300 ! +ANGLe C3D OH HO 139.500 107.300 ! +ANGLe C4D C3R OH 139.500 111.000 ! for 3ter terminus +ANGLe C2D C3R OH 139.500 111.000 ! for 3ter terminus + +!Phos. - combined RNA/DNA statistics used +! kq x_eq sigma +ANGLe OP1 P OP2 1337.074 119.600 !1.5 P +ANGLe O5R P OP1 357.719 108.100 !2.9 P +ANGLe O5R P OP2 412.677 108.300 !2.7 P +ANGLe O3R P O5R 833.356 104.000 !1.9 P +ANGLe OP2 P O3R 293.791 108.300 !3.2 P +ANGLe OP1 P O3R 293.791 107.400 !3.2 P + +ANGLe O5R C5R C4R 1534.906 110.200 !1.4 P +ANGLe P O5R C5R 1175.163 120.900 !1.6 P +ANGLe P O3R C3R 2089.178 119.700 !1.2 P + +ANGLe O5R C5R C4D 1534.906 110.200 !1.4 P !DNA +ANGLe O5R C5D C4D 1534.906 110.200 !1.4 P !DNA +ANGLe P O5R C5D 1175.163 120.900 !1.6 P +ANGLe P O3R C3D 2089.178 119.700 !1.2 P + +!Sugars +!RNA statistics +! kq x_eq sigma +ANGLe O4R C4R C3R 561.212 105.500 !1.4 S +ANGLe C5R C4R C3R 488.878 115.500 !1.5 S +ANGLe C5R C4R O4R 561.212 109.200 !1.4 S +ANGLe C1R O4R C4R 1357.996 109.600 !0.9 S +ANGLe C4R C3R C2R 1099.976 102.700 !1.0 S +ANGLe C3R C2R C1R 1357.996 101.500 !0.9 S +ANGLe O4R C1R C2R 561.212 106.400 !1.4 S +ANGLe N1T C1R C2R 429.678 113.400 !1.6 S +ANGLe N1C C1R C2R 429.678 113.400 !1.6 S +ANGLe N1U C1R C2R 429.678 113.400 !1.6 S +ANGLe N9G C1R C2R 429.678 113.400 !1.6 S +ANGLe N9A C1R C2R 429.678 113.400 !1.6 S +ANGLe N9P C1R C2R 429.678 113.400 !1.6 S +ANGLe O4R C1R N1T 1099.976 108.200 !1.0 S +ANGLe O4R C1R N1C 1099.976 108.200 !1.0 S +ANGLe O4R C1R N1U 1099.976 108.200 !1.0 S +ANGLe O4R C1R N9A 1099.976 108.200 !1.0 S +ANGLe O4R C1R N9P 1099.976 108.200 !1.0 S +ANGLe O4R C1R N9G 1099.976 108.200 !1.0 S +ANGLe C1R C2R O2R 357.719 110.600 !2.9 S scale from phos. +ANGLe C3R C2R O2R 357.719 113.300 !2.9 S scale from phos. +ANGLe C4R C3R O3R 445.032 110.500 !2.6 S scale from phos. +ANGLe C2R C3R O3R 383.726 111.000 !2.8 S scale from phos. + +!DNA statistics +ANGLe O4D C4D C3D 1099.976 105.600 !1.0 S +ANGLe C5D C4D C3D 488.878 114.700 !1.5 S +ANGLe C5R C4D C3D 488.878 114.700 !1.5 S +ANGLe C5D C4D O4D 429.678 109.400 !1.6 S +ANGLe C5R C4D O4D 429.678 109.400 !1.6 S +ANGLe C1D O4D C4D 650.874 109.700 !1.3 S +ANGLe C4D C3D C2D 1099.976 103.200 !1.0 S +ANGLe C3D C2D C1D 650.874 102.700 !1.3 S +ANGLe O4D C1D C2D 909.071 106.100 !1.1 S +ANGLe N1T C1D C2D 488.878 114.200 !1.5 S +ANGLe N1C C1D C2D 488.878 114.200 !1.5 S +ANGLe N1U C1D C2D 488.878 114.200 !1.5 S +ANGLe N9G C1D C2D 488.878 114.200 !1.5 S +ANGLe N9A C1D C2D 488.878 114.200 !1.5 S +ANGLe N9P C1D C2D 488.878 114.200 !1.5 S +ANGLe O4D C1D N1T 1357.996 107.800 !0.9 S +ANGLe O4D C1D N1C 1357.996 107.800 !0.9 S +ANGLe O4D C1D N1U 1357.996 107.800 !0.9 S +ANGLe O4D C1D N9A 1357.996 107.800 !0.9 S +ANGLe O4D C1D N9P 1357.996 107.800 !0.9 S +ANGLe O4D C1D N9G 1357.996 107.800 !0.9 S +ANGLe C4D C3D O3R 621.574 110.300 !2.2 S scale from phos. +ANGLe C2D C3D O3R 412.677 110.600 !2.7 S scale from phos. +ANGLe O4D C4D C3R 1099.976 105.600 !1.0 S ! for 3ter terminus +ANGLe C5R C4D C3R 488.878 114.700 !1.5 S ! for 3ter terminus +ANGLe C5D C4D C3R 488.878 114.700 !1.5 S ! for 3ter terminus +ANGLe C4D C3R C2D 1099.976 103.200 !1.0 S ! for 3ter terminus +ANGLe C3R C2D C1D 650.874 102.700 !1.3 S ! for 3ter terminus +ANGLe C4D C3R O3R 621.574 110.300 !2.2 S ! for 3ter terminus +ANGLe C2D C3R O3R 412.677 110.600 !2.7 S ! for 3ter terminus + + +!Ribose terms involving non-exchageables +ANGLe OH C5R HR $kchangle 109.83 +ANGLe O5R C5R HR $kchangle 109.83 +ANGLe HR C5R HR $kchangle 109.11 +ANGLe C4R C5R HR $kchangle 109.11 +ANGLe C5R C4R HR $kchangle 107.93 +ANGLe HR C4R C3R $kchangle 107.13 +ANGLe HR C4R O4R $kchangle 113.74 +ANGLe HR C3R C4R $kchangle 111.35 +ANGLe HR C3R O3R $kchangle 105.87 +ANGLe HR C3R OH $kchangle 105.87 +ANGLe HR C3R C2R $kchangle 112.27 +ANGLe HR C2R C3R $kchangle 111.41 +ANGLe HR C2R O2R $kchangle 113.07 +ANGLe HR C2R C1R $kchangle 112.38 +ANGLe HR C1R C2R $kchangle 111.95 +ANGLe HR C1R N1C $kchangle 107.70 +ANGLe HR C1R N1U $kchangle 107.70 +ANGLe HR C1R N1T $kchangle 107.70 +ANGLe HR C1R N9A $kchangle 107.70 +ANGLe HR C1R N9P $kchangle 107.70 +ANGLe HR C1R N9G $kchangle 107.70 +ANGLe HR C1R O4R $kchangle 106.86 + +!Deoxyribose terms involving non-exchageables +! +ANGLe OH C5D HR $kchangle 109.70 +ANGLe O5R C5D HR $kchangle 109.70 +ANGLe HR C5D HR $kchangle 109.17 +ANGLe C4D C5D HR $kchangle 109.17 +ANGLe C4D C5R HR $kchangle 109.17 +ANGLe C5D C4D HR $kchangle 107.78 +ANGLe C5R C4D HR $kchangle 107.78 +ANGLe HR C4D C3D $kchangle 106.91 +ANGLe HR C4D C3R $kchangle 106.91 ! for 3ter terminus +ANGLe HR C4D O4D $kchangle 112.98 +ANGLe HR C3D C4D $kchangle 111.16 +ANGLe HR C3R C4D $kchangle 111.16 +ANGLe HR C3D O3R $kchangle 109.34 +ANGLe HR C3D OH $kchangle 109.34 +ANGLe HR C3D C2D $kchangle 111.98 +ANGLe HR C3R C2D $kchangle 111.98 ! for 3ter terminus +ANGLe HR C2D C3D $kchangle 111.36 +ANGLe HR C2D C3R $kchangle 111.36 ! for 3ter terminus +ANGLe HR C2D HR $kchangle 107.52 +ANGLe HR C2D C1D $kchangle 112.29 +ANGLe HR C1D C2D $kchangle 110.94 +ANGLe HR C1D N1C $kchangle 108.25 +ANGLe HR C1D N1U $kchangle 108.25 +ANGLe HR C1D N1T $kchangle 108.25 +ANGLe HR C1D N9A $kchangle 108.25 +ANGLe HR C1D N9P $kchangle 108.25 +ANGLe HR C1D N9G $kchangle 108.25 +ANGLe HR C1D O4D $kchangle 107.95 + +!Bases +!cytosine kq x_eq sigma +ANGLe C6C N1C C2C 2277.447 120.300 !0.40 B +ANGLe N1C C2C NC 743.656 119.200 !0.70 B +ANGLe C2C NC C4C 1457.566 119.900 !0.50 B +ANGLe NC C4C C5C 2277.447 121.900 !0.40 B +ANGLe C4C C5C C6C 1457.566 117.400 !0.50 B +ANGLe C5C C6C N1C 1457.566 121.000 !0.50 B +ANGLe N1C C2C ON 1012.199 118.900 !0.60 B +ANGLe NC C2C ON 743.656 121.900 !0.70 B +ANGLe NC C4C N4C 743.656 118.000 !0.70 B +ANGLe C5C C4C N4C 743.656 120.200 !0.70 B +ANGLe C6C N1C C1R 763.873 120.800 !1.20 B scale from sugar +ANGLe C2C N1C C1R 909.071 118.800 !1.10 B scale from sugar +ANGLe C6C N1C C1D 763.873 120.800 !1.20 B !DNA +ANGLe C2C N1C C1D 909.071 118.800 !1.10 B +ANGLe C4C N4C H2 $kchangle 120.000 !from param11.dna, 3*keq +ANGLe H2 N4C H2 $kchangle 120.000 +ANGLe N1C C6C HR $kchangle 119.63 +ANGLe C5C C6C HR $kchangle 119.36 +ANGLe C4C C5C HR $kchangle 121.54 +ANGLe C6C C5C HR $kchangle 121.54 + +!thymine kq x_eq sigma +ANGLe C6T N1T C2T 1457.566 121.300 !0.50 B +ANGLe N1T C2T N3T 1012.199 114.600 !0.60 B +ANGLe C2T N3T C4T 1012.199 127.200 !0.60 B +ANGLe N3T C4T C5T 1012.199 115.200 !0.60 B +ANGLe C4T C5T C6T 1012.199 118.000 !0.60 B +ANGLe C5T C6T N1T 1012.199 123.700 !0.60 B +ANGLe N1T C2T ON 569.362 123.100 !0.80 B +ANGLe N3T C2T ON 1012.199 122.300 !0.60 B +ANGLe N3T C4T ON 1012.199 119.900 !0.60 B +ANGLe C5T C4T ON 743.656 124.900 !0.70 B +ANGLe C4T C5T CC3E 1012.199 119.000 !0.60 B +ANGLe C6T C5T CC3E 1012.199 122.900 !0.60 B +ANGLe C6T N1T C1R 488.878 120.400 !1.50 B scale from sugar +ANGLe C2T N1T C1R 429.678 118.200 !1.60 B scale from sugar +ANGLe C6T N1T C1D 488.878 120.400 !1.50 B !DNA +ANGLe C2T N1T C1D 429.678 118.200 !1.60 B +ANGLe C2T N3T HN $kchangle 116.500 !from param11.dna, 3*keq +ANGLe C4T N3T HN $kchangle 116.500 +ANGLe C5T CC3E HR $kchangle 109.50 +ANGLe HR CC3E HR $kchangle 109.44 +ANGLe N1T C6T HR $kchangle 119.52 +ANGLe C5T C6T HR $kchangle 119.52 + +!baseJ +ANGLe C6T C5T C3J 1457.566 117.400 +ANGLe C4T C5T C3J 1457.566 117.400 +ANGLe C5T C3J OSJ 743.656 124.900 +ANGLe C5T C3J H1J $kchangle 121.54 +ANGLe OH C3J H1J $kchangle 110.26 +ANGLe C3J C3J H1J $kchangle 109.56 +ANGLe C3J C3J H2J $kchangle 110.22 +ANGLe OSJ C3J H2J $kchangle 109.58 +ANGLe OSJ C3J H1J $kchangle 109.78 +ANGLe H1J C3J H1J $kchangle 109.58 +ANGLe CCJ C3J H1J $kchangle 109.64 +ANGLe CCJ CDJ H4J $kchangle 128.48 +ANGLe CJ NJ HN $kchangle 117.55 +ANGLe OH C3J C3J $kchangle 110.19 +ANGLe C3J C3J C3J $kchangle 111.51 +ANGLe C3J C3J OSJ $kchangle 107.97 +ANGLe C3J OSJ C3J $kchangle 112.48 +ANGLe C3J OH HO $kchangle 107.30 +ANGLe OSJ C3J OSJ $kchangle 108.29 +ANGLe OSJ C3J CCJ $kchangle 108.90 +ANGLe C3J CCJ CJ $kchangle 117.76 +ANGLe C3J CCJ CDJ $kchangle 119.45 +ANGLe CCJ CJ NJ $kchangle 112.70 +ANGLe CCJ CJ OJ $kchangle 123.93 +ANGLe CCJ CDJ NJ $kchangle 121.33 +ANGLe CJ CCJ CDJ $kchangle 121.35 +ANGLe CJ NJ CJ $kchangle 127.08 +ANGLe NJ CJ OJ $kchangle 123.05 +ANGLe NJ CJ NJ $kchangle 113.56 +ANGLe CDJ NJ C3J $kchangle 120.85 +ANGLe CDJ NJ CJ $kchangle 123.27 +ANGLe NJ C3J C3J $kchangle 111.61 +ANGLe NJ C3J OSJ $kchangle 109.13 +ANGLe C3J NJ CJ $kchangle 120.69 + + +!adenine kq x_eq sigma +ANGLe C6A NC C2A 1012.199 118.600 !0.60 B +ANGLe NC C2A N3A 1457.566 129.300 !0.50 B +ANGLe C2A N3A C4A 1457.566 110.600 !0.50 B +ANGLe N3A C4A C5A 743.656 126.800 !0.70 B +ANGLe C4A C5A C6A 1457.566 117.000 !0.50 B +ANGLe C5A C6A NC 1457.566 117.700 !0.50 B +ANGLe C4A C5A N7A 1457.566 110.700 !0.50 B +ANGLe C5A N7A C8A 1457.566 103.900 !0.50 B +ANGLe N7A C8A N9A 1457.566 113.800 !0.50 B +ANGLe C8A N9A C4A 2277.447 105.800 !0.40 B +ANGLe N9A C4A C5A 2277.447 105.800 !0.40 B +ANGLe N3A C4A N9A 569.362 127.400 !0.80 B +ANGLe C6A C5A N7A 743.656 132.300 !0.70 B +ANGLe NC C6A N6A 1012.199 118.600 !0.60 B +ANGLe C5A C6A N6A 569.362 123.700 !0.80 B +ANGLe C8A N9A C1R 339.499 127.700 !1.80 B scale from sugar +ANGLe C4A N9A C1R 339.499 126.300 !1.80 B scale from sugar +ANGLe C8A N9A C1D 339.499 127.700 !1.80 B !DNA +ANGLe C4A N9A C1D 339.499 126.300 !1.80 B +ANGLe C6A N6A H2 105.000 120.000 !from param11.dna, 3*keq +ANGLe H2 N6A H2 105.000 120.000 +ANGLe N7A C8A HR $kchangle 123.16 +ANGLe N9A C8A HR $kchangle 123.16 +ANGLe NC C2A HR $kchangle 115.54 +ANGLe N3A C2A HR $kchangle 115.54 + +!purine kq x_eq sigma +ANGLe C6P NC C2P 1012.199 118.600 !0.60 B +ANGLe NC C2P N3P 1457.566 129.300 !0.50 B +ANGLe C2P N3P C4P 1457.566 110.600 !0.50 B +ANGLe N3P C4P C5P 743.656 126.800 !0.70 B +ANGLe C4P C5P C6P 1457.566 117.000 !0.50 B +ANGLe C5P C6P NC 1457.566 117.700 !0.50 B +ANGLe C4P C5P N7P 1457.566 110.700 !0.50 B +ANGLe C5P N7P C8P 1457.566 103.900 !0.50 B +ANGLe N7P C8P N9P 1457.566 113.800 !0.50 B +ANGLe C8P N9P C4P 2277.447 105.800 !0.40 B +ANGLe N9P C4P C5P 2277.447 105.800 !0.40 B +ANGLe N3P C4P N9P 569.362 127.400 !0.80 B +ANGLe C6P C5P N7P 743.656 132.300 !0.70 B +ANGLe NC C6P HR $kchangle 115.54 !0.60 B +ANGLe C5P C6P HR $kchangle 115.54 !0.80 B +ANGLe C8P N9P C1R 339.499 127.700 !1.80 B scale from sugar +ANGLe C4P N9P C1R 339.499 126.300 !1.80 B scale from sugar +ANGLe C8P N9P C1D 339.499 127.700 !1.80 B !DNA +ANGLe C4P N9P C1D 339.499 126.300 !1.80 B +ANGLe N7P C8P HR $kchangle 123.16 +ANGLe N9P C8P HR $kchangle 123.16 +ANGLe NC C2P HR $kchangle 115.54 +ANGLe N3P C2P HR $kchangle 115.54 + +!guanine kq x_eq sigma +ANGLe C6G NNA C2G 1012.199 125.100 !0.60 B +ANGLe NNA C2G N3G 1012.199 123.900 !0.60 B +ANGLe C2G N3G C4G 1457.566 111.900 !0.50 B +ANGLe N3G C4G C5G 1457.566 128.600 !0.50 B +ANGLe C4G C5G C6G 1012.199 118.800 !0.60 B +ANGLe C5G C6G NNA 1457.566 111.500 !0.50 B +ANGLe C4G C5G N7G 2277.447 110.800 !0.40 B +ANGLe C5G N7G C8G 1457.566 104.300 !0.50 B +ANGLe N7G C8G N9G 1457.566 113.100 !0.50 B +ANGLe C8G N9G C4G 2277.447 106.400 !0.40 B +ANGLe N9G C4G C5G 2277.447 105.400 !0.40 B +ANGLe N3G C4G N9G 1012.199 126.000 !0.60 B +ANGLe C6G C5G N7G 1012.199 130.400 !0.60 B +ANGLe NNA C2G N2G 449.866 116.20 !0.90 B +ANGLe N3G C2G N2G 743.656 119.900 !0.70 B +ANGLe NNA C6G O6G 1012.199 119.900 !0.60 B +ANGLe C5G C6G O6G 1012.199 128.600 !0.60 B +ANGLe C8G N9G C1R 650.874 127.000 !1.30 B scale from sugar +ANGLe C4G N9G C1R 650.874 126.500 !1.30 B scale from sugar +ANGLe C8G N9G C1D 650.874 127.000 !1.30 B !DNA +ANGLe C4G N9G C1D 650.874 126.500 !1.30 B +ANGLe C2G N2G H2 105.000 120.000 !from param11.dna, 3*keq +ANGLe H2 N2G H2 105.000 120.000 +ANGLe C2G NNA HN 105.000 119.300 +ANGLe C6G NNA HN 105.000 119.300 +ANGLe N7G C8G HR $kchangle 122.91 +ANGLe N9G C8G HR $kchangle 122.91 + +!uracile kq x_eq sigma +ANGLe C6U N1U C2U 1012.199 121.000 !0.60 B +ANGLe N1U C2U N3U 1012.199 114.900 !0.60 B +ANGLe C2U N3U C4U 1012.199 127.000 !0.60 B +ANGLe N3U C4U C5U 1012.199 114.600 !0.60 B +ANGLe C4U C5U C6U 1012.199 119.700 !0.60 B +ANGLe C5U C6U N1U 1457.566 122.700 !0.50 B +ANGLe N1U C2U ON 743.656 122.800 !0.70 B +ANGLe N3U C2U ON 743.656 122.200 !0.70 B +ANGLe N3U C4U ON 743.656 119.400 !0.70 B +ANGLe C5U C4U ON 1012.199 125.900 !0.60 B +ANGLe C6U N1U C1R 561.212 121.200 !1.40 B +ANGLe C2U N1U C1R 763.872 117.700 !1.20 B +ANGLe C6U N1U C1D 561.212 121.200 !1.40 B !DNA +ANGLe C2U N1U C1D 763.872 117.700 !1.20 B +ANGLe C4U ON HO 105.000 120.000 !from param11.dna, 3*keq +ANGLe C2U N3U HN 105.000 116.500 +ANGLe C4U N3U HN 105.000 116.500 +ANGLe N1U C6U HR $kchangle 119.38 +ANGLe C5U C6U HR $kchangle 119.38 +ANGLe C4U C5U HR $kchangle 119.56 +ANGLe C6U C5U HR $kchangle 119.56 + + +!IMPRopers to keep the two purine rings parallel: +!guanine +IMPRoper C8G C4G C5G NNA 250.0 2 180.000 +IMPRoper C8G C5G C4G C2G 250.0 2 180.000 +IMPRoper N3G C4G C5G N7G 250.0 2 180.000 +IMPRoper C6G C5G C4G N9G 250.0 2 180.000 +!adenine +IMPRoper C8A C4A C5A N9A 250.0 2 180.000 ! WYE AND PATCHED RESIDUES +IMPRoper C8A C5A C4A C2A 250.0 2 180.000 +IMPRoper C8A C4A C5A NC 250.0 2 180.000 +IMPRoper N3A C4A C5A N7A 250.0 2 180.000 +IMPRoper C6A C5A C4A N9A 250.0 2 180.000 +!purine +IMPRoper C8P C4P C5P N9P 250.0 2 180.000 ! WYE AND PATCHED RESIDUES +IMPRoper C8P C5P C4P C2P 250.0 2 180.000 +IMPRoper C8P C4P C5P NC 250.0 2 180.000 +IMPRoper N3P C4P C5P N7P 250.0 2 180.000 +IMPRoper C6P C5P C4P N9P 250.0 2 180.000 + + +!other base specific non-exch hydrogen IMPRopers +IMPRoper HR C4C C6C C5C $kchimpr 0 0.000 +IMPRoper HR N1C C5C C6C $kchimpr 0 0.000 +IMPRoper HR C4U C6U C5U $kchimpr 0 0.000 +IMPRoper HR N1U C5U C6U $kchimpr 0 0.000 +IMPRoper HR N1T C5T C6T $kchimpr 0 0.000 +IMPRoper HR N7A N9A C8A $kchimpr 0 0.000 +IMPRoper HR NC N3A C2A $kchimpr 0 0.000 +IMPRoper HR N7P N9P C8P $kchimpr 0 0.000 +IMPRoper HR NC N3P C2P $kchimpr 0 0.000 +IMPRoper HR NC C5P C6P $kchimpr 0 0.000 +IMPRoper HR N7G N9G C8G $kchimpr 0 0.000 + +!Impropers for ribose chirality +IMPRoper HR C2R O4R N9A $kchimpr 0 -65.000!C1R +IMPRoper HR C2R O4R N9P $kchimpr 0 -65.000!C1R +IMPRoper HR C2R O4R N9G $kchimpr 0 -65.000!C1R +IMPRoper HR C2R O4R N1C $kchimpr 0 -65.000!C1R +IMPRoper HR C2R O4R N1U $kchimpr 0 -65.000!C1R +IMPRoper HR C2R O4R N1T $kchimpr 0 -65.000!C1R + +IMPRoper HR C3R C1R O2R $kchimpr 0 65.000!C2R +IMPRoper HR C4R C2R O3R $kchimpr 0 60.300!C3R +IMPRoper HR C4R C2R OH $kchimpr 0 60.300!C3R; TERMINAL RES +IMPRoper HR C5R C3R O4R $kchimpr 0 70.300!C4R +IMPRoper HR O5R HR C4R $kchimpr 0 72.000!C5R; +IMPRoper HR OH HR C4R $kchimpr 0 72.000!C5R; TERMINAL RES + +!Impropers for deoxyribose chirality +IMPRoper HR C2D O4D N9A $kchimpr 0 -65.280!C1D +IMPRoper HR C2D O4D N9P $kchimpr 0 -65.280!C1D +IMPRoper HR C2D O4D N9G $kchimpr 0 -65.280!C1D +IMPRoper HR C2D O4D N1C $kchimpr 0 -65.280!C1D +IMPRoper HR C2D O4D N1T $kchimpr 0 -65.280!C1D +IMPRoper HR C2D O4D N1U $kchimpr 0 -65.280!C1D + +IMPRoper HR C3D HR C1D $kchimpr 0 -73.500!C2D +IMPRoper HR C3R HR C1D $kchimpr 0 -73.500!C2D ! for 3ter terminus +IMPRoper HR C4D C2D O3R $kchimpr 0 62.660!C3D +IMPRoper HR C4D C2D OH $kchimpr 0 62.660!C3D; TERMINAL RES +IMPRoper HR C5R C3D O4D $kchimpr 0 70.220!C4D +IMPRoper HR C5R C3R O4D $kchimpr 0 70.220!C4D +IMPRoper HR C5D C3D O4D $kchimpr 0 70.220!C4D +IMPRoper HR C5D C3R O4D $kchimpr 0 70.220!C4D ! for 3ter terminus +IMPRoper HR O5R HR C4D $kchimpr 0 71.430!C5D; +IMPRoper HR OH HR C4D $kchimpr 0 71.430!C5D; TERMINAL RES + +!Impropers taken from param11.dna , 3*kq +IMPRoper C5R X X C2R 94.5 0 35.260 +IMPRoper C5R X X C1R 94.5 0 35.260 +IMPRoper OH X X C3R 94.5 0 35.260 +IMPRoper OH X X C4R 94.5 0 35.260 +IMPRoper OH X X C1R 94.5 0 35.260 +IMPRoper O3R X X C3R 94.5 0 35.260 +IMPRoper O5R X X C1R 94.5 0 35.260 +IMPRoper O2R X X C2R 94.5 0 35.260 +IMPRoper C4R O5R C1R N1T 94.5 0 35.260 +IMPRoper C4R O5R C1R N1C 94.5 0 35.260 +IMPRoper C4R O5R C1R N9G 94.5 0 35.260 +IMPRoper C4R O5R C1R N9A 94.5 0 35.260 +IMPRoper C4R O5R C1R N9P 94.5 0 35.260 +IMPRoper C5R O4R C3R C4R 94.5 0 35.260 +IMPRoper N1T C2R O4R C1R 94.5 0 35.260 +IMPRoper N1C C2R O4R C1R 94.5 0 35.260 +IMPRoper N9A C2R O4R C1R 94.5 0 35.260 +IMPRoper N9P C2R O4R C1R 94.5 0 35.260 +IMPRoper N9G C2R O4R C1R 94.5 0 35.260 +IMPRoper C4R O5R C1R N1U 94.5 0 35.260 +IMPRoper N1U C2R O4R C1R 94.5 0 35.260 + +IMPRoper C5D X X C2D 94.5 0 35.260 !DNA +IMPRoper C5D X X C1D 94.5 0 35.260 +IMPRoper OH X X C3D 94.5 0 35.260 +IMPRoper OH X X C3R 94.5 0 35.260 ! for 3ter terminus +IMPRoper OH X X C4D 94.5 0 35.260 +IMPRoper OH X X C1D 94.5 0 35.260 +IMPRoper O3R X X C3D 94.5 0 35.260 +IMPRoper O3R X X C3R 94.5 0 35.260 ! for 3ter terminus +IMPRoper O5R X X C1D 94.5 0 35.260 +IMPRoper C4D O5R C1D N1T 94.5 0 35.260 +IMPRoper C4D O5R C1D N1C 94.5 0 35.260 +IMPRoper C4D O5R C1D N9G 94.5 0 35.260 +IMPRoper C4D O5R C1D N9A 94.5 0 35.260 +IMPRoper C4D O5R C1D N9P 94.5 0 35.260 +IMPRoper C5D O4D C3D C4D 94.5 0 35.260 +IMPRoper C5D O4D C3R C4D 94.5 0 35.260 ! for 3ter terminus +IMPRoper N1T C2D O4D C1D 94.5 0 35.260 +IMPRoper N1C C2D O4D C1D 94.5 0 35.260 +IMPRoper N9A C2D O4D C1D 94.5 0 35.260 +IMPRoper N9P C2D O4D C1D 94.5 0 35.260 +IMPRoper N9G C2D O4D C1D 94.5 0 35.260 +IMPRoper C4D O5R C1D N1U 94.5 0 35.260 +IMPRoper N1U C2D O4D C1D 94.5 0 35.260 + +!the following impropers were taken from param11x.dna +!the higher kq was used to enforce the ring planarity +!cytosine +IMPRoper C4C X X ON 2400.0 0 0.000 +IMPRoper C4C X X N1C 250.0 0 0.000 +IMPRoper C6C X X NC 250.0 0 0.000 +IMPRoper C4C X X N2 2400.0 0 0.000 +IMPRoper C2C X X ON 2400.0 0 0.000 +!infer +IMPRoper C1R C2C C6C N1C 2400.0 0 0.000 +IMPRoper C1D C2C C6C N1C 2400.0 0 0.000 +IMPRoper N4C NC C5C C4C 2400.0 0 0.000 +IMPRoper C2C NC C4C C5C 250.0 0 0.000 +IMPRoper C5C C6C N1C C2C 250.0 0 0.000 +IMPRoper H2 C4C H2 N4C 250.0 0 0.000 +IMPRoper C5C C4C N4C H2 2000.0 0 0.000 + +!uracil +IMPRoper C4U X X ON 2400.0 0 0.000 +IMPRoper C4U X X N1U 250.0 0 0.000 +IMPRoper C6U X X N3U 250.0 0 0.000 +IMPRoper C4U X X N2 2400.0 0 0.000 +IMPRoper C2U X X ON 2400.0 0 0.000 +IMPRoper C1R C2U C6U N1U 2400.0 0 0.000 +IMPRoper C1D C2U C6U N1U 2400.0 0 0.000 +IMPRoper ON N3U C5U C4U 250.0 0 0.000 +IMPRoper C2U N3U C4U C5U 250.0 0 0.000 +IMPRoper C5U C6U N1U C2U 250.0 0 0.000 +IMPRoper H2 C4U H2 ON 250.0 0 0.000 +IMPRoper HN C2U C4U N3U 250.0 0 0.000 + +!thymidine +IMPRoper C4T X X ON 2400.0 0 0.000 +IMPRoper C4T X X N1T 250.0 0 0.000 +IMPRoper C6T X X N3T 250.0 0 0.000 +IMPRoper C4T X X N2 2400.0 0 0.000 +IMPRoper C2T X X ON 2400.0 0 0.000 +IMPRoper C1R C2T C6T N1T 2400.0 0 0.000 +IMPRoper C1D C2T C6T N1T 2400.0 0 0.000 +IMPRoper ON N3T C5T C4T 250.0 0 0.000 +IMPRoper C2T N3T C4T C5T 250.0 0 0.000 +IMPRoper C5T C6T N1T C2T 250.0 0 0.000 +IMPRoper H2 C4T H2 ON 250.0 0 0.000 +IMPRoper CC3E C4T C6T C5T 250.0 0 0.000 + +!basej +IMPRoper HR C6T C5T N1T 250.0 0 180.00 +IMPRoper HN C2T C4T NC 250.0 0 180.00 +IMPRoper HN N3T C2T C4T 250.0 0 180.00 +IMPRoper C4T C3J C5T C3J 250.0 0 180.00 +IMPRoper C3J C5T C4T C6T 250.0 0 180.00 +IMPRoper C5T N5Y C4T ON 250.0 0 180.00 +IMPRoper C2T C1D N1T C3J 250.0 0 180.00 +IMPRoper C5T HR C3J N1T 250.0 0 180.00 +IMPRoper NC N1T C2T ON 250.0 0 180.00 +IMPRoper H1J C3J OSJ C3J 500.0 0 66.8 +IMPRoper H1J OH C3J C3J 500.0 0 66.9 +IMPRoper H1J C3J OH C3J 500.0 0 66.8 +IMPRoper H1J H1J OH C3J 500.0 0 70.3 +IMPRoper H2J OSJ OSJ C3J 500.0 0 -67.6 + + +!infer +IMPRoper HN C2T C4T N3T 250.0 0 0.000 + +! The ring-spanning impropers have been left out. +!adenine +IMPRoper N2A N3A NC C2A 250.0 0 0.000 +IMPRoper H2 C2A H2 N2A 250.0 0 0.000 +IMPRoper C4A C5A N7A C8A 250.0 0 0.000 +IMPRoper C5A C4A N9A C8A 250.0 0 0.000 +IMPRoper C4A X X NC 250.0 0 0.000 +IMPRoper C2A X X N9A 250.0 0 0.000 +IMPRoper C2A X X C5A 250.0 0 0.000 +IMPRoper C6A C5A C4A N3A 250.0 0 0.000 +IMPRoper C5A X X N9A 250.0 0 0.000 +IMPRoper C6A X X N6A 2400.0 0 0.000 +IMPRoper H2 X X N6A 250.0 0 0.000 + +!infer +IMPRoper C1R C4A C8A N9A 2400.0 0 0.000 +IMPRoper C1D C4A C8A N9A 2400.0 0 0.000 +IMPRoper N9A C4A C5A N7A 250.0 0 0.000 +IMPRoper N7A C8A N9A C4A 250.0 0 0.000 +IMPRoper N3A C2A NC C6A 250.0 0 0.000 +IMPRoper C5A C6A N6A H2 2000.0 0 0.000 + +! The ring-spanning impropers have been left out. +!purine +IMPRoper N2P N3P NC C2P 250.0 0 0.000 +IMPRoper C4P C5P N7P C8P 250.0 0 0.000 +IMPRoper C5P C4P N9P C8P 250.0 0 0.000 +IMPRoper C4P X X NC 250.0 0 0.000 +IMPRoper C2P X X N9P 250.0 0 0.000 +IMPRoper C2P X X C5P 250.0 0 0.000 +IMPRoper C6P C5P C4P N3P 250.0 0 0.000 +IMPRoper C5P X X N9P 250.0 0 0.000 + +!infer +IMPRoper C1R C4P C8P N9P 2400.0 0 0.000 +IMPRoper C1D C4P C8P N9P 2400.0 0 0.000 +IMPRoper N9P C4P C5P N7P 250.0 0 0.000 +IMPRoper N7P C8P N9P C4P 250.0 0 0.000 +IMPRoper N3P C2P NC C6P 250.0 0 0.000 + +! The ring-spanning impropers have been left out. +!guanine +IMPRoper C4G C5G N7G C8G 250.0 0 0.000 +IMPRoper C5G C4G N9G C8G 250.0 0 0.000 +IMPRoper C4G X X NNA 250.0 0 0.000 +IMPRoper C2G X X N9G 250.0 0 0.000 +IMPRoper C2G X X C5G 250.0 0 0.000 +IMPRoper C6G C5G C4G N3G 250.0 0 0.000 +IMPRoper C5G X X N9G 250.0 0 0.000 +IMPRoper C6G X X O6G 2400.0 0 0.000 +IMPRoper C2G X X N2G 2400.0 0 0.000 + +!infer +IMPRoper C1R C4G C8G N9G 2400.0 0 0.000 +IMPRoper C1D C4G C8G N9G 2400.0 0 0.000 +IMPRoper N9G C4G C5G N7G 250.0 0 0.000 +IMPRoper N7G C8G N9G C4G 250.0 0 0.000 +IMPRoper N3G C2G NNA C6G 250.0 0 0.000 +IMPRoper H2 H2 C2G N2G 250.0 0 0.000 +IMPRoper HN C2G C6G NNA 2000.0 0 0.000 +IMPRoper N3G C2G N2G H2 2000.0 0 0.000 + +!dihedrals baseJ +DIHEdral X C3J OSJ X 2.0 3 0.0 + + +if ($par_nonbonded eq "PROLSQ") then +! type 2 x van der Waals radius correction applied for hbond +evaluate ($vdw_radius_C= 3.7) +evaluate ($vdw_radius_N= 3.0) {-0.1} +evaluate ($vdw_radius_O= 2.9) {-0.1} +evaluate ($vdw_radius_S= 3.6) +evaluate ($vdw_radius_FE= 2.4) +evaluate ($vdw_radius_H= 1.6) {!!!-0.8 MN} +evaluate ($vdw_radius_HH= 1.6) {-0.8} +evaluate ($vdw_radius_P= 3.8) +evaluate ($vdw_radius_I= 4.3) +evaluate ($vdw_radius_C_SP2= 3.4) + + +{ convert radii into sigmas } +evaluate ($vdw_radius_C = $vdw_radius_C / 2^(1/6)) +evaluate ($vdw_radius_N = $vdw_radius_N / 2^(1/6)) +evaluate ($vdw_radius_O = $vdw_radius_O / 2^(1/6)) +evaluate ($vdw_radius_S = $vdw_radius_S / 2^(1/6)) +evaluate ($vdw_radius_FE = $vdw_radius_FE / 2^(1/6)) +evaluate ($vdw_radius_H = $vdw_radius_H / 2^(1/6)) +evaluate ($vdw_radius_HH = $vdw_radius_HH / 2^(1/6)) +evaluate ($vdw_radius_P = $vdw_radius_P / 2^(1/6)) +evaluate ($vdw_radius_I = $vdw_radius_I / 2^(1/6)) +evaluate ($vdw_radius_C_SP2=$vdw_radius_C_SP2/ 2^(1/6)) + +{ compute 1-4 sigmas } +evaluate ($vdw_radius14_C = $vdw_radius_C -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_N = $vdw_radius_N -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_O = $vdw_radius_O -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_S = $vdw_radius_S -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_FE = $vdw_radius_FE -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_H = $vdw_radius_H -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_HH = $vdw_radius_HH -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_P = $vdw_radius_P -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_I = $vdw_radius_I -0.3/ 2^(1/6)) +evaluate ($vdw_radius14_C_SP2=$vdw_radius_C_SP2-0.3/ 2^(1/6)) + +evaluate ($vdw_eps=0.1) + +! +! eps sigma eps(1:4) sigma(1:4) +NONBonded C5R $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C1R $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2R $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C3R $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4R $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C + +NONBonded C5D $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C1D $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2D $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C3D $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4D $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C + +NONBonded HN $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH +NONBonded H2 $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH +NONBonded HO $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH +NONBonded HR $vdw_eps $vdw_radius_H $vdw_eps $vdw_radius14_H +! +NONBonded O3R $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded O4R $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded O4D $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded O5R $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded OP1 $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded OP2 $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded OP1H $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded OP2H $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O + +NONBonded P $vdw_eps $vdw_radius_P $vdw_eps $vdw_radius14_P + +NONBonded C2 $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C3 $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded CB $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded CE $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded CH $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C + +NONBonded N2 $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N3U $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded NNA $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded NB $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded NC $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N + +NONBonded NH2E $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded NS $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N1T $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N3T $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N1C $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N9A $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N9G $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N1U $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N + +NONBonded ON $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded O2R $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded OH $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded O5H $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O + +NONBonded SD $vdw_eps $vdw_radius_S $vdw_eps $vdw_radius14_S + +NONBonded C6C $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C5C $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4C $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2C $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C6U $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C5U $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4U $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2U $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C8A $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C6A $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C5A $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4A $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2A $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C8G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C6G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C5G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C6T $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C5T $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C4T $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded C2T $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C + +NONBonded N4C $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded O4U $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded N7G $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N3G $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N2G $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N3A $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N7A $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded N6A $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N +NONBonded O6G $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O +NONBonded CC3E $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C +NONBonded N2A $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N + +NONBonded I5U $vdw_eps $vdw_radius_I $vdw_eps $vdw_radius14_I + + +elseif ($par_nonbonded eq "OPLSX") then +! these are OPLS values derived from W.L. Jorgensen. 2/92 +! included in 2007 by Henry Jonker +{ suggested values for refinement in H2O + NBONds + CUTNB=12 WMIN=1.5 + REPEl = 0.0 cdie shift + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=11.0 + END +} +evaluate ($repel_radius = 0.0) + +NONBonded C5R 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C1R 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C2R 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C3R 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C4R 0.050 3.800 0.006 3.800 ! opls CT + +NONBonded C5D 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C1D 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C2D 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C3D 0.050 3.800 0.006 3.800 ! opls CT +NONBonded C4D 0.050 3.800 0.006 3.800 ! opls CT + +NONBonded H 0.050 0.500 0.004 0.500 +NONBonded HA 0.050 0.500 0.004 0.500 +NONBonded HR 0.050 0.500 0.004 0.500 +NONBonded HC 0.050 0.500 0.004 0.500 +NONBonded HN 0.050 0.500 0.004 0.500 +NONBonded H2 0.050 0.500 0.004 0.500 +NONBonded HO 0.050 0.500 0.004 0.500 + +NONBonded O3R 0.170 3.000 0.021 3.000 ! opls OS +NONBonded O4R 0.170 3.000 0.021 3.000 ! opls OS +NONBonded O4D 0.170 3.000 0.021 3.000 ! opls OS +NONBonded O5R 0.170 3.000 0.021 3.000 ! opls OS +NONBonded OP1 0.210 2.960 0.026 2.960 ! opls O2 +NONBonded OP2 0.210 2.960 0.026 2.960 ! opls O2 +NONBonded O2R 0.170 3.070 0.021 3.070 ! opls OH +NONBonded ON 0.210 2.960 0.026 2.960 ! opls O +NONBonded O6G 0.210 2.960 0.026 2.960 ! opls O + +NONBonded P 0.200 3.740 0.025 3.740 ! opls P + +NONBonded N2 0.170 3.250 0.021 3.250 ! opls N2 +NONBonded N4C 0.170 3.250 0.021 3.250 ! opls N2 +NONBonded N2G 0.170 3.250 0.021 3.250 ! opls N2 +NONBonded N6A 0.170 3.250 0.021 3.250 ! opls N2 + +NONBonded N3U 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N3T 0.170 3.250 0.021 3.250 ! opls NA +NONBonded NNA 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N1C 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N9A 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N9G 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N1U 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N1T 0.170 3.250 0.021 3.250 ! opls NA + +NONBonded N7G 0.170 3.250 0.021 3.250 ! opls NB +NONBonded N7A 0.170 3.250 0.021 3.250 ! opls NB + +NONBonded NC 0.170 3.250 0.021 3.250 ! opls NC +NONBonded N3G 0.170 3.250 0.021 3.250 ! opls NC +NONBonded N3A 0.170 3.250 0.021 3.250 ! opls NC + +NONBonded C6C 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C5C 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C4C 0.080 3.500 0.010 3.500 ! opls CA +NONBonded C2C 0.105 3.750 0.013 3.750 ! opls C +NONBonded C6U 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C5U 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C4U 0.105 3.750 0.013 3.750 ! opls C +NONBonded C2U 0.105 3.750 0.013 3.750 ! opls C +NONBonded C8A 0.080 3.500 0.010 3.500 ! opls CK +NONBonded C6A 0.080 3.500 0.010 3.500 ! opls CA +NONBonded C5A 0.080 3.500 0.010 3.500 ! opls CB +NONBonded C4A 0.080 3.500 0.010 3.500 ! opls CB +NONBonded C2A 0.080 3.500 0.010 3.500 ! opls CA +NONBonded C8G 0.080 3.500 0.010 3.500 ! opls CK +NONBonded C6G 0.105 3.750 0.013 3.750 ! opls C +NONBonded C5G 0.080 3.500 0.010 3.500 ! opls CB +NONBonded C4G 0.080 3.500 0.010 3.500 ! opls CB +NONBonded C2G 0.080 3.500 0.010 3.500 ! opls CA +NONBonded C6T 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C5T 0.080 3.500 0.010 3.500 ! opls CM +NONBonded C4T 0.105 3.750 0.013 3.750 ! opls C +NONBonded C2T 0.105 3.750 0.013 3.750 ! opls C +NONBonded CC3E 0.080 3.500 0.010 3.500 ! opls CT + +! I don't know why the next ones are there; probably old parameters HJ +NONBonded C2 0.118 3.800 0.015 3.800 ! opls C2 +NONBonded C3 0.160 3.910 0.020 3.910 ! opls C3 +NONBonded CB 0.145 3.750 0.018 3.750 ! opls CB +NONBonded CE 0.080 3.500 0.010 3.500 ! opls CA +NONBonded CH 0.080 3.800 0.010 3.800 ! opls CH +NONBonded NB 0.170 3.250 0.021 3.250 ! opls NB +NONBonded NH2E 0.170 3.250 0.021 3.250 ! opls N2 +NONBonded NS 0.170 3.250 0.021 3.250 ! opls NA +NONBonded N2A 0.170 3.250 0.021 3.250 ! opls N2 +NONBonded OH 0.170 3.070 0.021 3.070 ! opls OH +NONBonded O5H 0.170 3.070 0.021 3.070 ! opls OH +NONBonded O4U 0.210 2.960 0.026 2.960 ! opls O +NONBonded OP1H 0.170 3.070 0.021 3.070 ! opls OH +NONBonded OP2H 0.170 3.070 0.021 3.070 ! opls OH +NONBonded SD 0.250 3.550 0.031 3.550 ! opls S + +!basej +NONBonded C3J 0.109 3.400 0.055 3.400 +NONBonded OSJ 0.170 3.000 0.085 3.000 +NONBonded CCJ 0.086 3.400 0.043 3.400 +NONBonded CJ 0.086 3.400 0.043 3.400 +NONBonded NJ 0.170 3.250 0.085 3.250 +NONBonded OJ 0.210 2.960 0.105 2.960 +NONBonded CDJ 0.086 3.400 0.043 3.400 +NONBonded HO 0.000 0.000 0.000 0.000 +NONBonded H1J 0.016 2.471 0.008 2.471 +NONBonded H2J 0.016 2.293 0.008 2.293 +NONBonded HN 0.016 1.069 0.008 1.069 +NONBonded H4J 0.016 2.511 0.008 2.511 +NONBonded HCJ 0.016 2.650 0.008 2.650 + + +else +! Lennard-Jones parameters +! ------1-4------- +! epsilon sigma epsilon sigma +! (Kcal/mol) (A) (Kcal/mol) (A) +! Taken from Rossky Karplus and Rahman BIOPOLY (1979) +! 0.05 ADDED TO RADII TO IMPRoperOVE ON NUCL.ACID STACKING/LN +! +! eps sigma eps(1:4) sigma(1:4) +NONBonded C5R 0.0900 3.2970 0.0900 3.2970 +NONBonded C1R 0.0900 3.2970 0.0900 3.2970 +NONBonded C2R 0.0900 3.2970 0.0900 3.2970 +NONBonded C3R 0.0900 3.2970 0.0900 3.2970 +NONBonded C4R 0.0900 3.2970 0.0900 3.2970 + +NONBonded C5D 0.0900 3.2970 0.0900 3.2970 !DNA +NONBonded C1D 0.0900 3.2970 0.0900 3.2970 +NONBonded C2D 0.0900 3.2970 0.0900 3.2970 +NONBonded C3D 0.0900 3.2970 0.0900 3.2970 +NONBonded C4D 0.0900 3.2970 0.0900 3.2970 + +NONBonded HN 0.0045 1.6040 0.0045 1.6040 +NONBonded H2 0.0045 1.6040 0.0045 1.6040 +NONBonded HR 0.0045 1.6040 0.0045 1.6040 +! +! give it the same as th Hn from RKR +NONBonded HO 0.0045 1.6040 0.0045 1.6040 + +! +! THIS STILL IS AN EXTENDED ATOM +NONBonded O3R 0.2304 2.7290 0.2304 2.7290 +NONBonded O4R 0.2304 2.7290 0.2304 2.7290 +NONBonded O4D 0.2304 2.7290 0.2304 2.7290 +NONBonded O5R 0.2304 2.7290 0.2304 2.7290 +NONBonded OP1 0.2304 2.7290 0.2304 2.7290 +NONBonded OP2 0.2304 2.7290 0.2304 2.7290 +NONBonded P 0.5849 3.3854 0.5849 3.3854 + +!bases +NONBonded C2 0.0900 3.2970 0.0900 3.2970 +NONBonded C3 0.0900 3.2970 0.0900 3.2970 +NONBonded CB 0.0900 3.2970 0.0900 3.2970 +NONBonded CE 0.0900 3.2970 0.0900 3.2970 +NONBonded CH 0.0900 3.2970 0.0900 3.2970 + +NONBonded N2 0.1600 2.8591 0.1600 2.8591 +NONBonded N3U 0.1600 2.8591 0.1600 2.8591 +NONBonded N3T 0.1600 2.8591 0.1600 2.8591 +NONBonded NNA 0.1600 2.8591 0.1600 2.8591 +NONBonded NB 0.1600 2.8591 0.1600 2.8591 +NONBonded NC 0.1600 2.8591 0.1600 2.8591 + +NONBonded NH2E 0.1600 3.0291 0.1600 3.0291 +NONBonded NS 0.1600 2.8591 0.1600 2.8591 +NONBonded N1T 0.1600 2.8591 0.1600 2.8591 +NONBonded N1C 0.1600 2.8591 0.1600 2.8591 +NONBonded N9A 0.1600 2.8591 0.1600 2.8591 +NONBonded N9P 0.1600 2.8591 0.1600 2.8591 +NONBonded N9G 0.1600 2.8591 0.1600 2.8591 +NONBonded N1U 0.1600 2.8591 0.1600 2.8591 +NONBonded ON 0.2304 2.7290 0.2304 2.7290 +NONBonded O2R 0.2304 2.7290 0.2304 2.7290 +NONBonded OH 0.2304 2.5508 0.2304 2.5508 +NONBonded SD 0.3515 2.6727 0.3515 2.6727 ! G U E S S +NONBonded O2 0.2304 2.7290 0.2304 2.7290 + +! NEW +NONBonded C6C 0.0900 3.2970 0.0900 3.2970 +NONBonded C5C 0.0900 3.2970 0.0900 3.2970 +NONBonded C4C 0.0900 3.2970 0.0900 3.2970 +NONBonded C2C 0.0900 3.2970 0.0900 3.2970 +NONBonded C6U 0.0900 3.2970 0.0900 3.2970 +NONBonded C5U 0.0900 3.2970 0.0900 3.2970 +NONBonded C4U 0.0900 3.2970 0.0900 3.2970 +NONBonded C2U 0.0900 3.2970 0.0900 3.2970 +NONBonded C8A 0.0900 3.2970 0.0900 3.2970 +NONBonded C6A 0.0900 3.2970 0.0900 3.2970 +NONBonded C5A 0.0900 3.2970 0.0900 3.2970 +NONBonded C4A 0.0900 3.2970 0.0900 3.2970 +NONBonded C2A 0.0900 3.2970 0.0900 3.2970 +NONBonded C8P 0.0900 3.2970 0.0900 3.2970 +NONBonded C6P 0.0900 3.2970 0.0900 3.2970 +NONBonded C5P 0.0900 3.2970 0.0900 3.2970 +NONBonded C4P 0.0900 3.2970 0.0900 3.2970 +NONBonded C2P 0.0900 3.2970 0.0900 3.2970 +NONBonded C8G 0.0900 3.2970 0.0900 3.2970 +NONBonded C6G 0.0900 3.2970 0.0900 3.2970 +NONBonded C5G 0.0900 3.2970 0.0900 3.2970 +NONBonded C4G 0.0900 3.2970 0.0900 3.2970 +NONBonded C2G 0.0900 3.2970 0.0900 3.2970 +NONBonded C6T 0.0900 3.2970 0.0900 3.2970 +NONBonded C5T 0.0900 3.2970 0.0900 3.2970 +NONBonded C4T 0.0900 3.2970 0.0900 3.2970 +NONBonded C2T 0.0900 3.2970 0.0900 3.2970 +NONBonded N4C 0.1600 2.8591 0.1600 2.8591 +NONBonded O4U 0.2304 2.7290 0.2304 2.7290 +NONBonded N7G 0.1600 2.8591 0.1600 2.8591 +NONBonded N3G 0.1600 2.8591 0.1600 2.8591 +NONBonded N2G 0.1600 2.8591 0.1600 2.8591 +NONBonded N3A 0.1600 2.8591 0.1600 2.8591 +NONBonded N7A 0.1600 2.8591 0.1600 2.8591 +NONBonded N6A 0.1600 2.8591 0.1600 2.8591 +NONBonded O6G 0.2304 2.7290 0.2304 2.7290 +NONBonded CC3E 0.0900 3.2970 0.0900 3.2970 +NONBonded N2A 0.1600 2.8591 0.1600 2.8591 +NONBonded N2P 0.1600 2.8591 0.1600 2.8591 +NONBonded N3P 0.1600 2.8591 0.1600 2.8591 +NONBonded N7P 0.1600 2.8591 0.1600 2.8591 + +! special solute-solute hydrogen bonding potential parameters +!AEXP 4 +!REXP 6 + +!HAEX 4 + +!AAEX 2 +! "all" possible combinations of HB-pairs in nucleic acids: +! WELL DEPTHS DEEPENED BY 0.5 KCAL TO IMPROVE BASEPAIR ENERGIES /LN +! AND DISTANCES INCREASED BY 0.05 +! Emin Rmin +! (Kcal/mol) (A) +!hbond N* O* -14.0 2.95 +!hbond N* N* -14.5 3.05 +!hbond O* O* -15.75 2.80 +!hbond O* N* -15.50 2.90 + +! the following NBFIXes are for DNA-DNA hydrogen bonding + +! terms +! ------1-4------ +! A B A B +! [Kcal/(mol A^12)] [Kcal/(mol A^6)] +! +nbfix HO ON 0.05 0.1 0.05 0.1 +nbfix HO O3R 0.05 0.1 0.05 0.1 +nbfix HO O5R 0.05 0.1 0.05 0.1 +nbfix HO OH 0.05 0.1 0.05 0.1 +nbfix HO O2R 0.05 0.1 0.05 0.1 +nbfix HO NC 0.05 0.1 0.05 0.1 + + +nbfix HR ON 0.05 0.1 0.05 0.1 +nbfix HR O2 0.05 0.1 0.05 0.1 +nbfix HR O5R 0.05 0.1 0.05 0.1 +nbfix HR O4R 0.05 0.1 0.05 0.1 +nbfix HR O4D 0.05 0.1 0.05 0.1 +nbfix HR O3R 0.05 0.1 0.05 0.1 +nbfix HR O2R 0.05 0.1 0.05 0.1 +nbfix HR OH 0.05 0.1 0.05 0.1 +nbfix HR N7A 0.05 0.1 0.05 0.1 +nbfix HR N7P 0.05 0.1 0.05 0.1 +nbfix HR N7G 0.05 0.1 0.05 0.1 +nbfix HR N3A 0.05 0.1 0.05 0.1 +nbfix HR N3P 0.05 0.1 0.05 0.1 +nbfix HR N3G 0.05 0.1 0.05 0.1 + + +nbfix HN ON 0.05 0.1 0.05 0.1 +nbfix HN O2R 0.05 0.1 0.05 0.1 +nbfix HN OH 0.05 0.1 0.05 0.1 +nbfix HN NC 0.05 0.1 0.05 0.1 + +nbfix H2 ON 0.05 0.1 0.05 0.1 +nbfix H2 O2R 0.05 0.1 0.05 0.1 +nbfix H2 OH 0.05 0.1 0.05 0.1 + +nbfix H2 NC 0.05 0.1 0.05 0.1 + +end if + + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.top new file mode 100644 index 0000000000000000000000000000000000000000..48dfc43f130eb0e1d1c9ab2a682b1596926a6996 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-allatom-hj-opls-1.3.top @@ -0,0 +1,1086 @@ +remarks file toppar/dna-rna-allatom-hj-opls-1.3 +remarks all-hydrogen dna/rna topology using the OPLS force field + +!RNA TOPOLOGY FILE 'FRAMEWORK' FROM TOPALLHDG.DNA AND ATOM NAMES +! FROM DNA-RNA.PARAM +!INCLUDES ALL NONEXCHANGEABLE HYDROGENS AND TERMS FOR BOND, ANGLE, AND +!IMPROPERS. NONEXCHANGEABLE HYDROGEN CHARGES WERE ASSIGNED 0.035. +!CARBON CHARGES WERE REDUCED 0.035 FOR EACH ATTACHED HYDROGEN. +!CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE +!CHANGED TO OPLSX CHARGES 6/2/07 -- HENRY JONKER +!ADAPTED/CLEANED FOR HADDOCK - ALEXANDRE BONVIN + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + + +AUTOGENERATE ANGLES=TRUE END +{*==========================*} + +{* DNA/RNA default masses *} + +MASS P 30.97400! phosphorus +MASS OP1 15.99940! O in phosphate +MASS OP2 15.99940! O in phosphate +MASS O5R 15.99940! ester -P-O-C- +MASS C5R 12.011! corresp. to CH2E +MASS C4R 12.011! corresp. to CH1E +MASS C3R 12.011! corresp. to CH1E +MASS C2R 12.011! corresp. to CH1E +MASS C1R 12.011! corresp. to CH1E +MASS O4R 15.99940! ester -P-O-C- +MASS O3R 15.99940! ester -P-O-C- +MASS O2R 15.99940! ester -P-O-C- +MASS OH 15.99940! corresp. to OH1 + +!DEOXY SUGAR +MASS C5D 14.02700! corresp. to CH2E +MASS C4D 13.01900! corresp. to CH1E +MASS C3D 13.01900! corresp. to CH1E +MASS C2D 13.01900! corresp. to CH1E +MASS C1D 13.01900! corresp. to CH1E +MASS O4D 15.99940! ester -P-O-C- +MASS O5D 15.99940! +MASS O3D 15.99940! + +! Insert Bases +! Generic + +MASS N2 14.00670! nitrogen in -NH2 +MASS NNA 14.00670! corresp. to NH1 +MASS ON 15.99940! corresp. to O +MASS NC 14.00670! corresp. to NR +MASS NS 14.00670! nitrogen in ring >N- + +! Insert 4 Bases +! GUA +MASS N9G 14.00670! nitrogen in ring >N- +MASS C2G 12.011! (prev CE) +MASS N3G 14.00670! (prev NC) +MASS C4G 12.01100! (prev CB) +MASS C5G 12.01100! (prev CB) +MASS C6G 12.01100! (prev CN) +MASS N7G 14.00670! (prev NB) +MASS C8G 12.011! (prev CE) +MASS O6G 15.99940! (prev CE) +MASS N2G 14.00670! nitrogen in -NH2 + +! ADE +MASS N9A 14.00670! nitrogen in ring >N- +MASS C2A 12.011! (prev CE) +MASS N3A 14.00670! (prev NC) +MASS C4A 12.01100! (prev CB) +MASS C5A 12.01100! (prev CB) +MASS C6A 12.01100! (prev CA) +MASS N7A 14.00670! (prev NB) +MASS C8A 12.011! (prev CE) +MASS N6A 14.00670! nitrogen in -NH2 + +! PUR +MASS N9P 14.00670! nitrogen in ring >N- +MASS C2P 12.011! (prev CE) +MASS N3P 14.00670! (prev NC) +MASS C4P 12.01100! (prev CB) +MASS C5P 12.01100! (prev CB) +MASS C6P 12.01100! (prev CA) +MASS N7P 14.00670! (prev NB) +MASS C8P 12.011! (prev CE) + +! CYT +MASS N1C 14.00670! nitrogen in ring >N- +MASS C2C 12.01100! (prev CN) +MASS C4C 12.01100! (prev CA) +MASS C5C 12.011! (prev CF) +MASS C6C 12.011! (prev CF) +MASS N4C 14.00670! nitrogen in -NH2 + +! THY +MASS N1T 14.00670! nitrogen in ring >N- +MASS N3T 14.00670! nitrogen in ring >N- +MASS C2T 12.01100! (prev CN) +MASS C4T 12.01100! (prev CN) +MASS C5T 12.011! (prev CS) +MASS C6T 12.011! (prev CF) +MASS CC3E 12.01100! (prev CF) + +! basej +MASS C3J 12.010 +MASS OSJ 16.000 +MASS CCJ 12.010 +MASS CJ 12.010 +MASS NJ 14.010 +MASS OJ 16.000 +MASS CDJ 12.010 +MASS H1J 1.0080 +MASS H2J 1.0080 +MASS H4J 1.0080 +MASS HCJ 1.0080 + +! END + +MASS HR 1.00800! non-exchangeable Hydrogens +MASS HN 1.00800! corresp. to H +MASS H2 1.00800! hydrogen in -NH2 +MASS HO 1.00800! hydroxy hydrogen + +! URI +MASS N1U 14.00670! nitrogen in ring >N- +MASS C2U 12.01100! (prev CN) +MASS C4U 12.01100! (prev CA) +MASS C5U 12.011! (prev CF) +MASS C6U 12.011! (prev CF) +MASS N3U 14.00670! + +! --------------------------------------------------------------------- + + +RESIdue G ! RNA GUA + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5R CHARGE=0.00 END + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4R CHARGE=0.15 END + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4R CHARGE=-0.50 END + ATOM C1' TYPE=C1R CHARGE=0.50 END + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N9 TYPE=N9G CHARGE=-0.50 END + ATOM C4 TYPE=C4G CHARGE=0.34 EXCLusion=( N1 ) END + GROUp + ATOM N3 TYPE=N3G CHARGE=-0.51 EXCLusion=( C6 ) END + ATOM C2 TYPE=C2G CHARGE=0.46 EXCLusion=( C5 ) END + GROUp + ATOM N2 TYPE=N2G CHARGE=-0.80 END + ATOM H21 TYPE=H2 CHARGE=0.40 END + ATOM H22 TYPE=H2 CHARGE=0.40 END + GROUp + ATOM N1 TYPE=NNA CHARGE=-0.56 END + ATOM H1 TYPE=HN CHARGE=0.38 END + GROUp + ATOM C6 TYPE=C6G CHARGE=0.52 END + ATOM O6 TYPE=O6G CHARGE=-0.51 END + GROUp + ATOM C5 TYPE=C5G CHARGE=0.12 END + ATOM N7 TYPE=N7G CHARGE=-0.49 END + ATOM C8 TYPE=C8G CHARGE=0.20 END + ATOM H8 TYPE=HR CHARGE=0.20 END + + GROUP + ATOM C2' TYPE=C2R CHARGE=0.165 END + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM O2' TYPE=O2R CHARGE=-0.70 END + ATOM HO2' type=HO CHARGE=0.435 END + GROUP + ATOM C3' TYPE=C3R CHARGE=0.10 END + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N9 + BOND C1' C2' BOND N9 C4 BOND N9 C8 + BOND C4 N3 BOND C4 C5 BOND N3 C2 + BOND C2 N2 BOND C2 N1 BOND N2 H21 + + BOND N2 H22 BOND N1 H1 BOND N1 C6 + BOND C6 O6 BOND C6 C5 BOND C5 N7 + BOND N7 C8 BOND C2' C3' BOND C3' O3' + BOND C2' O2' BOND C8 H8 + + BOND O2' HO2' + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + ! + IMPRoper N3 C2 N2 H21 IMPRoper C1' C4 C8 N9 + IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 + IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 + IMPRoper C8 N9 C4 C5 IMPRoper N2 N3 N1 C2 + + IMPRoper H1 C2 C6 N1 IMPRoper O6 N1 C5 C6 + IMPRoper C4 N3 C2 N1 IMPRoper N3 C2 N1 C6 + IMPRoper C2 N1 C6 C5 IMPRoper N1 C6 C5 C4 + + IMPRoper C6 C5 C4 N3 IMPRoper C5 C4 N3 C2 + IMPRoper H22 H21 C2 N2 + IMPRoper H8 N7 N9 C8 + + !IMPRoper to keep the two purine rings parallel: + IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 + IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N9 !C1' + IMPRoper H2' C3' C1' O2' !C2' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + +END {G} + +! --------------------------------------------------------------------- + +RESIdue DG ! deoxy form of GUA + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy + ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N9 TYPE=N9G CHARGE=-0.50 END + ATOM C4 TYPE=C4G CHARGE=0.34 EXCLusion=( N1 ) END + GROUp + ATOM N3 TYPE=N3G CHARGE=-0.51 EXCLusion=( C6 ) END + ATOM C2 TYPE=C2G CHARGE=0.46 EXCLusion=( C5 ) END + GROUp + ATOM N2 TYPE=N2G CHARGE=-0.80 END + ATOM H21 TYPE=H2 CHARGE=0.40 END + ATOM H22 TYPE=H2 CHARGE=0.40 END + GROUp + ATOM N1 TYPE=NNA CHARGE=-0.56 END + ATOM H1 TYPE=HN CHARGE=0.38 END + GROUp + ATOM C6 TYPE=C6G CHARGE=0.52 END + ATOM O6 TYPE=O6G CHARGE=-0.51 END + GROUp + ATOM C5 TYPE=C5G CHARGE=0.12 END + ATOM N7 TYPE=N7G CHARGE=-0.49 END + ATOM C8 TYPE=C8G CHARGE=0.20 END + ATOM H8 TYPE=HR CHARGE=0.20 END + + GROUP + ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy + GROUP + ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N9 + BOND C1' C2' BOND N9 C4 BOND N9 C8 + BOND C4 N3 BOND C4 C5 BOND N3 C2 + BOND C2 N2 BOND C2 N1 BOND N2 H21 + + BOND N2 H22 BOND N1 H1 BOND N1 C6 + BOND C6 O6 BOND C6 C5 BOND C5 N7 + BOND N7 C8 BOND C2' C3' BOND C3' O3' + BOND C8 H8 + + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + BOND C2' H2'' ! deoxy + + ! + IMPRoper N3 C2 N2 H21 IMPRoper C1' C4 C8 N9 + IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 + IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 + IMPRoper C8 N9 C4 C5 IMPRoper N2 N3 N1 C2 + + IMPRoper H1 C2 C6 N1 IMPRoper O6 N1 C5 C6 + IMPRoper C4 N3 C2 N1 IMPRoper N3 C2 N1 C6 + IMPRoper C2 N1 C6 C5 IMPRoper N1 C6 C5 C4 + + IMPRoper C6 C5 C4 N3 IMPRoper C5 C4 N3 C2 + IMPRoper H22 H21 C2 N2 + IMPRoper H8 N7 N9 C8 + + !IMPRoper to keep the two purine rings parallel: + IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 + IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 + + IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N9 !C1' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + +END {DG} + +! --------------------------------------------------------------------- + +RESIdue A ! RNA ADE + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5R CHARGE=0.00 END + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4R CHARGE=0.15 END + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4R CHARGE=-0.50 END + ATOM C1' TYPE=C1R CHARGE=0.50 END + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N9 TYPE=N9A CHARGE=-0.50 END + ATOM C4 TYPE=C4A CHARGE=0.38 EXCLusion=( N1 ) END + GROUp + ATOM N3 TYPE=N3A CHARGE=-0.55 EXCLusion=( C6 ) END + ATOM C2 TYPE=C2A CHARGE=0.22 EXCLusion=( C5 ) END + ATOM H2 TYPE=HR CHARGE=0.20 END + GROUp + ATOM N1 TYPE=NC CHARGE=-0.53 END + ATOM C6 TYPE=C6A CHARGE=0.44 END + GROUp + ATOM N6 TYPE=N6A CHARGE=-0.81 END + ATOM H61 TYPE=H2 CHARGE=0.355 END + ATOM H62 TYPE=H2 CHARGE=0.385 END + GROUp + ATOM C5 TYPE=C5A CHARGE=0.15 END + ATOM N7 TYPE=N7A CHARGE=-0.49 END + ATOM C8 TYPE=C8A CHARGE=0.20 END + ATOM H8 TYPE=HR CHARGE=0.20 END + + GROUP + ATOM C2' TYPE=C2R CHARGE=0.165 END + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM O2' TYPE=O2R CHARGE=-0.70 END + ATOM HO2' TYPE=HO CHARGE=0.435 END + GROUP + ATOM C3' TYPE=C3R CHARGE=0.10 END + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N9 + BOND C1' C2' BOND N9 C4 BOND N9 C8 + BOND C4 N3 BOND C4 C5 BOND N3 C2 + BOND C2 N1 BOND N1 C6 BOND C6 N6 + + BOND N6 H61 BOND N6 H62 BOND C6 C5 + + BOND C5 N7 BOND N7 C8 BOND C2' C3' + BOND C2' O2' BOND C3' O3' + BOND C8 H8 BOND C2 H2 + BOND O2' HO2' + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + ! + IMPRoper C5 C6 N6 H61 IMPRoper C1' C4 C8 N9 + IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 + IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 + IMPRoper C8 N9 C4 C5 IMPRoper N6 N1 C5 C6 + IMPRoper H62 C6 H61 N6 IMPRoper C4 N3 C2 N1 + IMPRoper N3 C2 N1 C6 IMPRoper C2 N1 C6 C5 + IMPRoper N1 C6 C5 C4 IMPRoper C6 C5 C4 N3 + IMPRoper C5 C4 N3 C2 + IMPRoper H2 N1 N3 C2 IMPRoper H8 N7 N9 C8 + ! IMPRoper to keep the two purine rings parallel: + IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 + IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 + + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N9 !C1' + IMPRoper H2' C3' C1' O2' !C2' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + +END {A} + +! --------------------------------------------------------------------- + +RESIdue DA ! deoxy form at ADE + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy + ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N9 TYPE=N9A CHARGE=-0.50 END + ATOM C4 TYPE=C4A CHARGE=0.38 EXCLusion=( N1 ) END + GROUp + ATOM N3 TYPE=N3A CHARGE=-0.55 EXCLusion=( C6 ) END + ATOM C2 TYPE=C2A CHARGE=0.22 EXCLusion=( C5 ) END + ATOM H2 TYPE=HR CHARGE=0.20 END + GROUp + ATOM N1 TYPE=NC CHARGE=-0.53 END + ATOM C6 TYPE=C6A CHARGE=0.44 END + GROUp + ATOM N6 TYPE=N6A CHARGE=-0.81 END + ATOM H61 TYPE=H2 CHARGE=0.355 END + ATOM H62 TYPE=H2 CHARGE=0.385 END + GROUp + ATOM C5 TYPE=C5A CHARGE=0.15 END + ATOM N7 TYPE=N7A CHARGE=-0.49 END + ATOM C8 TYPE=C8A CHARGE=0.20 END + ATOM H8 TYPE=HR CHARGE=0.20 END + + GROUP + ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy + GROUP + ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N9 + BOND C1' C2' BOND N9 C4 BOND N9 C8 + BOND C4 N3 BOND C4 C5 BOND N3 C2 + BOND C2 N1 BOND N1 C6 BOND C6 N6 + + BOND N6 H61 BOND N6 H62 BOND C6 C5 + + BOND C5 N7 BOND N7 C8 BOND C2' C3' + BOND C3' O3' + BOND C8 H8 BOND C2 H2 + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + BOND C2' H2'' ! deoxy + + ! + IMPRoper C5 C6 N6 H61 IMPRoper C1' C4 C8 N9 + IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 + IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 + IMPRoper C8 N9 C4 C5 IMPRoper N6 N1 C5 C6 + IMPRoper H62 C6 H61 N6 IMPRoper C4 N3 C2 N1 + IMPRoper N3 C2 N1 C6 IMPRoper C2 N1 C6 C5 + IMPRoper N1 C6 C5 C4 IMPRoper C6 C5 C4 N3 + IMPRoper C5 C4 N3 C2 + IMPRoper H2 N1 N3 C2 IMPRoper H8 N7 N9 C8 + ! IMPRoper to keep the two purine rings parallel: + IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 + IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 + + IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N9 !C1' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + + END {DA} + + +! --------------------------------------------------------------------- + +RESIdue C ! RNA CYT + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5R CHARGE=0.00 END + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4R CHARGE=0.15 END + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4R CHARGE=-0.50 END + ATOM C1' TYPE=C1R CHARGE=0.53 END + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N1 TYPE=N1C CHARGE=-0.56 EXCLUSION=( C4 ) END + ATOM C6 TYPE=C6C CHARGE=0.10 EXCLUSION=( N3 ) END + ATOM H6 TYPE=HR CHARGE=0.10 END + GROUp + ATOM C2 TYPE=C2C CHARGE=0.55 EXCLUSION=( C5 ) END + ATOM O2 TYPE=ON CHARGE=-0.48 END + GROUp + ATOM N3 TYPE=NC CHARGE=-0.54 END + ATOM C4 TYPE=C4C CHARGE=0.46 END + GROUp + ATOM N4 TYPE=N4C CHARGE=-0.79 END + ATOM H41 TYPE=H2 CHARGE=0.355 END + ATOM H42 TYPE=H2 CHARGE=0.385 END + GROUp + ATOM C5 TYPE=C5C CHARGE=-0.06 END + ATOM H5 TYPE=HR CHARGE=0.10 END + + GROUP + ATOM C2' TYPE=C2R CHARGE=0.165 END + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM O2' TYPE=O2R CHARGE=-0.70 END + ATOM HO2' TYPE=HO CHARGE=0.435 END + GROUP + ATOM C3' TYPE=C3R CHARGE=0.10 END + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N1 + BOND C1' C2' BOND N1 C2 BOND N1 C6 + BOND C2 N3 BOND N3 C4 + BOND C4 N4 BOND N4 H41 BOND N4 H42 + BOND C2 O2 + BOND C4 C5 BOND C5 C6 BOND C2' C3' + BOND C3' O3' BOND C2' O2' + BOND C6 H6 BOND C5 H5 + BOND O2' HO2' + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + IMPRoper C5 C4 N4 H41 IMPRoper C1' C2 C6 N1 + IMPRoper O2 N1 N3 C2 IMPRoper N4 N3 C5 C4 + IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 + IMPRoper N3 C4 C5 C6 IMPRoper C4 C5 C6 N1 + IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 + IMPRoper H42 C4 H41 N4 + IMPRoper H5 C4 C6 C5 IMPRoper H6 N1 C5 C6 + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N1 !C1' + IMPRoper H2' C3' C1' O2' !C2' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + + END {C} + +! --------------------------------------------------------------------- + +RESIdue DC ! deoxy form of CYT + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy + ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N1 TYPE=N1C CHARGE=-0.56 EXCLUSION=( C4 ) END + ATOM C6 TYPE=C6C CHARGE=0.10 EXCLUSION=( N3 ) END + ATOM H6 TYPE=HR CHARGE=0.10 END + GROUp + ATOM C2 TYPE=C2C CHARGE=0.55 EXCLUSION=( C5 ) END + ATOM O2 TYPE=ON CHARGE=-0.48 END + GROUp + ATOM N3 TYPE=NC CHARGE=-0.54 END + ATOM C4 TYPE=C4C CHARGE=0.46 END + GROUp + ATOM N4 TYPE=N4C CHARGE=-0.79 END + ATOM H41 TYPE=H2 CHARGE=0.355 END + ATOM H42 TYPE=H2 CHARGE=0.385 END + GROUp + ATOM C5 TYPE=C5C CHARGE=-0.06 END + ATOM H5 TYPE=HR CHARGE=0.10 END + + GROUp + ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy + GROUP + ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N1 + BOND C1' C2' BOND N1 C2 BOND N1 C6 + BOND C2 N3 BOND N3 C4 + BOND C4 N4 BOND N4 H41 BOND N4 H42 + BOND C2 O2 + BOND C4 C5 BOND C5 C6 BOND C2' C3' + BOND C3' O3' + BOND C6 H6 BOND C5 H5 + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + BOND C2' H2'' ! deoxy + + + IMPRoper C5 C4 N4 H41 IMPRoper C1' C2 C6 N1 + IMPRoper O2 N1 N3 C2 IMPRoper N4 N3 C5 C4 + IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 + IMPRoper N3 C4 C5 C6 IMPRoper C4 C5 C6 N1 + IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 + IMPRoper H42 C4 H41 N4 + IMPRoper H5 C4 C6 C5 IMPRoper H6 N1 C5 C6 + + IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy + + !RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N1 !C1' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + + END {DC} + + +!------------------------------------------------------------------ + +RESIdue DT ! deoxy form of THY + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy + ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N1 TYPE=N1T CHARGE=-0.60 EXCLUSION=( C4 ) END + ATOM C6 TYPE=C6T CHARGE=0.08 EXCLUSION=( N3 ) END + ATOM H6 TYPE=HR CHARGE=0.10 END + GROUp + ATOM C2 TYPE=C2T CHARGE=0.50 EXCLUSION=( C5 ) END + ATOM O2 TYPE=ON CHARGE=-0.40 END + GROUp + ATOM N3 TYPE=N3T CHARGE=-0.51 END + ATOM H3 TYPE=HN CHARGE=0.36 END + GROUp + ATOM C4 TYPE=C4T CHARGE=0.45 END + ATOM O4 TYPE=ON CHARGE=-0.42 END + GROUp + ATOM C5 TYPE=C5T CHARGE=-0.07 END + ATOM C7 TYPE=CC3E CHARGE=-0.14 END ! name per IUPAC-IUB recomm. + ATOM H71 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. + ATOM H72 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. + ATOM H73 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. + + GROUP + ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy + GROUP + ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N1 + BOND C1' C2' BOND N1 C2 BOND N1 C6 + BOND C2 O2 BOND C2 N3 BOND N3 H3 + BOND N3 C4 BOND C4 O4 BOND C4 C5 + BOND C5 C7 BOND C5 C6 BOND C2' C3' + BOND C3' O3' + BOND C5' H5' BOND C5' H5'' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + BOND C4' H4' BOND C7 H71 BOND C7 H72 + BOND C7 H73 BOND C6 H6 + + BOND C2' H2'' ! deoxy + + + IMPRoper O4 N3 C5 C4 IMPRoper C1' C2 C6 N1 + IMPRoper O2 N1 N3 C2 IMPRoper C4 C5 C6 N1 + IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 + IMPRoper N3 C4 C5 C6 + IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 + IMPRoper H3 C2 C4 N3 + IMPRoper C7 C4 C6 C5 IMPRoper H6 N1 C5 C6 + + IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy + +!RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N1 ! C1' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + + + + END {DT} + +!------------------------------------------------------------------ + +RESIdue DJ ! baseJ implemented based on DT and acpype output + + GROUp + ATOM P TYPE=P CHARGE= 0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5D CHARGE= 0.00 END ! deoxy + ATOM H5' TYPE=HR CHARGE= 0.10 END + ATOM H5'' TYPE=HR CHARGE= 0.10 END + GROUp + ATOM C4' TYPE=C4D CHARGE= 0.15 END ! deoxy + ATOM H4' TYPE=HR CHARGE= 0.10 END + ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy + ATOM C1' TYPE=C1D CHARGE= 0.53 END ! deoxy + ATOM H1' TYPE=HR CHARGE= 0.10 END + + GROUp + ATOM N1 TYPE=N1T CHARGE=-0.60 EXCLUSION=( C4 ) END + ATOM C6 TYPE=C6T CHARGE=0.08 EXCLUSION=( N3 ) END + ATOM H6 TYPE=HR CHARGE=0.10 END + GROUp + ATOM C2 TYPE=C2T CHARGE= 0.50 EXCLUSION=( C5 ) END + ATOM O2 TYPE=ON CHARGE=-0.4 END + GROUp + ATOM N3 TYPE=N3T CHARGE=-0.51 END + ATOM H3 TYPE=HN CHARGE= 0.36 END + GROUp + ATOM C4 TYPE=C4T CHARGE= 0.45 END + ATOM O4 TYPE=ON CHARGE=-0.45 END + GROUp + ATOM C5 TYPE= C5T CHARGE= 0.100 END + ATOM C5M TYPE= C3J CHARGE= 0.100 END + ATOM H5M2 TYPE= H1J CHARGE= 0.100 END + ATOM H5M1 TYPE= H1J CHARGE= 0.100 END + ATOM O1S TYPE= OSJ CHARGE=-0.400 END + GROUp + ATOM C2S TYPE= C3J CHARGE= 0.150 END + ATOM H2S TYPE= H1J CHARGE= 0.100 END + ATOM O2S TYPE= OH CHARGE=-0.650 END + ATOM HO2 TYPE= HO CHARGE= 0.400 END + GROUp + ATOM C3S TYPE= C3J CHARGE= 0.150 END + ATOM H3S TYPE= H1J CHARGE= 0.100 END + ATOM O3S TYPE= OH CHARGE=-0.650 END + ATOM HO3 TYPE= HO CHARGE= 0.400 END + GROUp + ATOM C4S TYPE= C3J CHARGE= 0.150 END + ATOM H4S TYPE= H1J CHARGE= 0.100 END + ATOM O4S TYPE= OH CHARGE=-0.650 END + ATOM HO4 TYPE= HO CHARGE= 0.400 END + GROUp + ATOM C5S TYPE= C3J CHARGE= 0.100 END + ATOM H5S TYPE= H1J CHARGE= 0.100 END + ATOM O5S TYPE= OSJ CHARGE=-0.400 END + ATOM C1S TYPE= C3J CHARGE= 0.100 END + ATOM H1S TYPE= H2J CHARGE= 0.100 END + GROUp + ATOM C6S TYPE= C3J CHARGE= 0.080 END + ATOM H6S2 TYPE= H1J CHARGE= 0.100 END + ATOM H6S1 TYPE= H1J CHARGE= 0.100 END + ATOM O6S TYPE= OH CHARGE=-0.650 END + ATOM HO6 TYPE= HO CHARGE= 0.400 END + GROUP + ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy + ATOM H2' TYPE=HR CHARGE= 0.10 END + ATOM H2'' TYPE=HR CHARGE= 0.10 END ! deoxy + GROUP + ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy + ATOM H3' TYPE=HR CHARGE= 0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N1 + BOND C1' C2' BOND N1 C2 BOND N1 C6 + BOND C2' C3' BOND C3' O3' BOND C6 C5 + BOND C2 N3 BOND C2 O2 BOND N3 C4 + BOND C4 O4 BOND C4 C5 BOND C5 C5M + BOND C5M O1S BOND O1S C1S BOND C1S C2S + BOND C2S C3S BOND C2S O2S BOND C3S C4S + BOND C3S O3S BOND C4S O4S BOND C4S C5S + BOND C5S O5S BOND C5S C6S BOND C6S O6S + BOND O5S C1S + BOND C5' H5' BOND C5' H5'' + BOND C3' H3' BOND C2' H2' BOND C2' H2'' + BOND C1' H1' BOND C4' H4' + BOND N3 H3 BOND C6 H6 + BOND C5M H5M2 BOND C5M H5M1 + BOND C1S H1S BOND C2S H2S BOND C3S H3S + BOND C4S H4S BOND C5S H5S + BOND C6S H6S2 BOND C6S H6S1 + BOND O2S HO2 BOND O3S HO3 BOND O4S HO4 + BOND O6S HO6 + + + IMPRoper O4 N3 C5 C4 IMPRoper C1' C2 C6 N1 + IMPRoper O2 N1 N3 C2 IMPRoper C4 C5 C6 N1 + IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 + IMPRoper N3 C4 C5 C6 + IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 + IMPRoper H3 N3 C2 C4 + IMPRoper C5M C5 C4 C6 IMPRoper H6 N1 C5 C6 + + IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy + + +!RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N1 !C1'thymine + IMPRoper H3' C4' C2' O3' !C3'thymine + IMPRoper H4' C5' C3' O4' !C4'thymine + IMPRoper H5' O5' H5'' C4' !C5'thymine + +!Sugar impropers + IMPRoper H1S O5S O1S C2S {alpha C1} + IMPRoper H2S O2S C3S C2S {C2} + IMPRoper H3S O3S C2S C4S {C3} + IMPRoper H4S C3S O4S C5S {C4} + IMPRoper H5S C4S O5S C6S {C5} + IMPRoper H6S2 H6S1 O6S C5S !stereo C6 + + DIHEdral C5 C5M O1S C1S + DIHEdral C5M O1S C1S C2S + + END {DJ} + +!------------------------------------------------------------------ + +RESIdue U ! URI + + GROUp + ATOM P TYPE=P CHARGE=0.78 END + ATOM OP1 TYPE=OP1 CHARGE=-0.66 END + ATOM OP2 TYPE=OP2 CHARGE=-0.66 END + ATOM O5' TYPE=O5R CHARGE=-0.43 END + GROUp + ATOM C5' TYPE=C5R CHARGE=0.00 END + ATOM H5' TYPE=HR CHARGE=0.10 END + ATOM H5'' TYPE=HR CHARGE=0.10 END + GROUp + ATOM C4' TYPE=C4R CHARGE=0.15 END + ATOM H4' TYPE=HR CHARGE=0.10 END + ATOM O4' TYPE=O4R CHARGE=-0.50 END + ATOM C1' TYPE=C1R CHARGE=0.56 END + ATOM H1' TYPE=HR CHARGE=0.10 END + + GROUp + ATOM N1 TYPE=N1U CHARGE=-0.60 EXCLUSION=( C4 ) END + ATOM C6 TYPE=C6U CHARGE=0.08 EXCLUSION=( N3 ) END + ATOM H6 TYPE=HR CHARGE=0.10 END + GROUp + ATOM C2 TYPE=C2U CHARGE=0.50 EXCLUSION=( C5 ) END + ATOM O2 TYPE=ON CHARGE=-0.40 END + GROUp + ATOM N3 TYPE=N3U CHARGE=-0.51 END + ATOM H3 TYPE=HN CHARGE=0.36 END + GROUp + ATOM C4 TYPE=C4U CHARGE=0.45 END + ATOM O4 TYPE=ON CHARGE=-0.42 END + GROUp + ATOM C5 TYPE=C5U CHARGE=-0.07 END + ATOM H5 TYPE=HR CHARGE=0.10 END + + GROUP + ATOM C2' TYPE=C2R CHARGE=0.165 END + ATOM H2' TYPE=HR CHARGE=0.10 END + ATOM O2' TYPE=O2R CHARGE=-0.70 END + ATOM HO2' TYPE=HO CHARGE=0.435 END + GROUP + ATOM C3' TYPE=C3R CHARGE=0.10 END + ATOM H3' TYPE=HR CHARGE=0.10 END + GROUP + ATOM O3' TYPE=O3R CHARGE=-0.43 END + + BOND P OP1 BOND P OP2 BOND P O5' + BOND O5' C5' BOND C5' C4' BOND C4' O4' + BOND C4' C3' BOND O4' C1' BOND C1' N1 + BOND C1' C2' BOND N1 C2 BOND N1 C6 + BOND C2 O2 BOND C2 N3 BOND N3 H3 + BOND N3 C4 BOND C4 O4 BOND C4 C5 + + BOND C5 C6 BOND C2' C3' BOND C3' O3' + BOND C2' O2' + BOND C5 H5 BOND C6 H6 + + BOND O2' HO2' + BOND C5' H5' BOND C5' H5'' BOND C4' H4' + BOND C3' H3' BOND C2' H2' BOND C1' H1' + + IMPRoper C1' C2 C6 N1 + IMPRoper O2 N1 N3 C2 IMPRoper H3 C2 C4 N3 + IMPRoper O4 N3 C5 C4 IMPRoper N1 C2 N3 C4 + IMPRoper C2 N3 C4 C5 IMPRoper N3 C4 C5 C6 + IMPRoper C4 C5 C6 N1 IMPRoper C5 C6 N1 C2 + IMPRoper C6 N1 C2 N3 + IMPRoper H5 C4 C6 C5 IMPRoper H6 N1 C5 C6 + + !GENERAL RIBOSE IMPROPERS + IMPRoper H1' C2' O4' N1 !C1' + IMPRoper H2' C3' C1' O2' !C2' + IMPRoper H3' C4' C2' O3' !C3' + IMPRoper H4' C5' C3' O4' !C4' + IMPRoper H5' O5' H5'' C4' !C5' + +END {U} + +!------------------------------------------------------------------ +!------------------------------------------------------------------ +!note: O3' and O5' will remain O3R and O5R for DNA molecules +!this is consistent with values in parameter files + +PRESidue DEOX ! Patch to make DEOXYribose of the ribose + DELETE ATOM O2' END + DELETE ATOM HO2' END + +GROUP + + MODIFY ATOM C2' TYPE=C2D CHARGE=-0.20 END + MODIFY ATOM C5' TYPE=C5D CHARGE=0.00 END + MODIFY ATOM C4' TYPE=C4D CHARGE=0.15 END + MODIFY ATOM O4' TYPE=O4D CHARGE=-0.50 END + MODIFY ATOM C1' TYPE=C1D CHARGE=0.53 END + MODIFY ATOM C3' TYPE=C3D CHARGE=-0.10 END + ADD ATOM H2'' TYPE=HR CHARGE=0.10 END + + ADD BOND C2' H2'' + ADD ANGLE C1' C2' H2' + ADD ANGLE C3' C2' H2'' + ADD ANGLE H2' C2' H2'' + ADD IMPRoper H2' C3' H2'' C1'! C2' chirality term + +END {DEOX} + +!------------------------------------------------------------------ +!------------------------------------------------------------------ + + +PRESidue 5PHO ! 5-terminus (with phosphate) + ! ! should be used as "FIRST 5PHO TAIL + * END" + GROUp ! i.e. to be patched to the first RNA/DNA residue + ADD ATOM +H5T TYPE=HO CHARGE=0.50 END + ADD ATOM +O5T TYPE=OH CHARGE=-0.70 END + + ADD BOND +H5T +O5T + ADD BOND +O5T +P + ADD ANGLe +H5T +O5T +P + ADD ANGLe +O5' +P +O5T + ADD ANGLe +O5T +P +OP1 + ADD ANGLe +O5T +P +OP2 + +END {5PHO} + +!------------------------------------------------------------------ + + +PRESidue 3TER ! 3-terminus (without phosphate) + ! should be used as "LAST 3TER HEAD - * END" + GROUp ! i.e. to be patched to the last RMA/DNA residue + MODIFY ATOM -C3' TYPE=C3R CHARGE=0.10 END + MODIFY ATOM -O3' TYPE=OH CHARGE=-0.70 END + ADD ATOM -H3T TYPE=HO CHARGE=0.50 END + ! + ADD BOND -O3' -H3T + ADD ANGLe -C3' -O3' -H3T +! ADD DIHEdral -C4' -C3' -O3' -H3T +END {3TER} + +!------------------------------------------------------------------ + + +PRESidue 5TER ! 5-terminus (without phosphate) + ! ! should be used as "FIRST 5TER TAIL + * END" + GROUp ! i.e. to be patched to the first RNA/DNA residue + ADD ATOM +H5T TYPE=HO CHARGE=0.50 END + MODIFY ATOM +O5' TYPE=OH CHARGE=-0.70 END + MODIFY ATOM +C5' TYPE=C5R CHARGE=0.00 END + DELETE ATOM +P END + DELETE ATOM +OP1 END + DELETE ATOM +OP2 END + ! + ADD BOND +H5T +O5' + ADD ANGLe +H5T +O5' +C5' +! ADD DIHEdral +H5T +O5' +C5' +C4' +END {5TER} + +! --------------------------------------------------------------------- +!------------------------------------------------------------------ + +PRESidue NUC ! patch for nucleic acid backbone + ! should be used as "LINK NUC HEAD - * TAIL + * END" + ! i.e. it links the previous RNA/DNA residue (-) with + ! the current one (+) + GROUp + + MODIFY ATOM -O3' END ! + MODIFY ATOM +P END ! + MODIFY ATOM +OP1 END ! this should correctly define the electrostatic + + MODIFY ATOM +OP2 END ! group boundary + + MODIFY ATOM +O5' END ! + ADD BOND -O3' +P + ADD ANGLE -C3' -O3' +P + ADD ANGLE -O3' +P +OP1 + ADD ANGLE -O3' +P +OP2 + ADD ANGLE -O3' +P +O5' +!ADD DIHEdral -O3' +P +O5' +C5' + +! ADD DIHEdral -C4' -C3' -O3' +P +! ADD DIHEdral -C3' -O3' +P +O5' + +END {NUC} + +!------------------------------------------------------------------ + +set message=$old_message echo=$old_echo end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-pho-1.3.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-pho-1.3.link new file mode 100644 index 0000000000000000000000000000000000000000..c7934d3efbe0a56bb720517d04eecfa2b7eb402a --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna-rna-pho-1.3.link @@ -0,0 +1,87 @@ +remarks file toppar/dna-rna-pho.link +remarks macro to define nucleic acid links and terminii +remarks this file uses a 5' phosphate group +remarks + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link nuc head - DA tail + DA end +link nuc head - DA tail + DC end +link nuc head - DA tail + DG end +link nuc head - DA tail + DT end +link nuc head - DA tail + DJ end + +link nuc head - DC tail + DA end +link nuc head - DC tail + DC end +link nuc head - DC tail + DG end +link nuc head - DC tail + DT end +link nuc head - DC tail + DJ end + +link nuc head - DG tail + DA end +link nuc head - DG tail + DC end +link nuc head - DG tail + DG end +link nuc head - DG tail + DT end +link nuc head - DG tail + DJ end + +link nuc head - DT tail + DA end +link nuc head - DT tail + DC end +link nuc head - DT tail + DG end +link nuc head - DT tail + DT end +link nuc head - DT tail + DJ end + +link nuc head - DJ tail + DA end +link nuc head - DJ tail + DC end +link nuc head - DJ tail + DG end +link nuc head - DJ tail + DT end +link nuc head - DJ tail + DJ end + + +link nuc head - A tail + A end +link nuc head - A tail + C end +link nuc head - A tail + G end +link nuc head - A tail + U end + +link nuc head - C tail + A end +link nuc head - C tail + C end +link nuc head - C tail + G end +link nuc head - C tail + U end + +link nuc head - G tail + A end +link nuc head - G tail + C end +link nuc head - G tail + G end +link nuc head - G tail + U end + +link nuc head - U tail + A end +link nuc head - U tail + C end +link nuc head - U tail + G end +link nuc head - U tail + U end + + +first 5pho tail + A end +first 5pho tail + C end +first 5pho tail + G end +first 5pho tail + U end + +first 5pho tail + DA end +first 5pho tail + DC end +first 5pho tail + DG end +first 5pho tail + DT end +first 5pho tail + DJ end + + +last 3ter head - A end +last 3ter head - C end +last 3ter head - G end +last 3ter head - U end + +last 3ter head - DA end +last 3ter head - DC end +last 3ter head - DG end +last 3ter head - DT end +last 3ter head - DJ end + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna_break.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna_break.top new file mode 100644 index 0000000000000000000000000000000000000000..aa2fd969eda1c8b09dfa608a4d4556a697fa4374 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/dna_break.top @@ -0,0 +1,18 @@ +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +PRESidue DNUC ! patch for deletion of nucleic acid linkage + ! i.e. it deletes the link the previous RNA residue (-) with + ! the current one (+) + DELETE BOND -O3' +P + DELETE ANGLE -C3' -O3' +P + DELETE ANGLE -O3' +P +OP1 + DELETE ANGLE -O3' +P +O1P + DELETE ANGLE -O3' +P +OP2 + DELETE ANGLE -O3' +P +O2P + DELETE ANGLE -O3' +P +O5' + +END {DNUC} + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.param new file mode 100644 index 0000000000000000000000000000000000000000..8fcfc4437c3e96d4488ff45fd740a640e66ed992 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.param @@ -0,0 +1,519 @@ +Remarks Parameters for Fragment-based Ligand Binding Site Mapping +Remarks created by acpype (Rev: 7268) on Mon Apr 13 10:01:53 2015 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +{ Bonds: atomType1 atomType2 kb r0 } +BOND c__ n__ 478.2 1.3450 +BOND c__ o__ 648.0 1.2140 +BOND c__ c3__ 328.3 1.5080 +BOND c__ ca__ 349.7 1.4870 +BOND c__ h4__ 310.5 1.1123 +BOND c__ h5__ 319.4 1.1053 +BOND n__ hn__ 410.2 1.0090 +BOND c1__ c3__ 368.3 1.4700 +BOND c3__ n__ 330.6 1.4600 +BOND c3__ c3__ 303.1 1.5350 +BOND c3__ h1__ 335.9 1.0930 +BOND c3__ hc__ 337.3 1.0920 +BOND c3__ oh__ 314.1 1.4260 +BOND c3__ os__ 301.5 1.4390 +BOND ca__ ca__ 478.4 1.3870 +BOND ca__ ha__ 344.3 1.0870 +BOND ca__ oh__ 386.1 1.3620 +BOND n1__ c1__ 1014.5 1.1380 +BOND n3__ c3__ 320.6 1.4700 +BOND n3__ hn__ 394.1 1.0180 +BOND oh__ ho__ 369.6 0.9740 +{ Bonds: from Cagliari } +BOND C_ O_ 648.0 1.2140 +BOND C_ CT_ 328.3 1.5080 +BOND C_ O2_ 648.0 1.2140 +BOND S_ CM_ 280.0 1.7360 +BOND CD_ C_ 449.9 1.4060 +BOND CD_ N_ 390.5 1.4070 +BOND CM_ CD_ 549.0 1.3500 +BOND CM_ CT_ 317.0 1.5100 +BOND CM_ HA_ 367.0 1.0800 +BOND CT_ N_ 330.6 1.4600 +BOND CT_ S_ 227.0 1.8100 +BOND CT_ CT_ 303.1 1.5350 +BOND CT_ H1_ 335.9 1.0930 +BOND CT_ HC_ 337.3 1.0920 +BOND CT_ HP_ 340.0 1.0900 +BOND CT_ N3_ 367.0 1.4710 +BOND CT_ OH_ 314.1 1.4260 +BOND N3_ H_ 434.0 1.0100 +BOND NT_ H_ 434.0 1.0100 +BOND NT_ CM_ 486.3 1.3400 +BOND NT_ CT_ 367.0 1.4710 +BOND OH_ HO_ 369.6 0.9740 +BOND N_ H_ 410.2 1.0090 +BOND CA_ HA_ 344.3 1.0870 +BOND C_ N_ 478.2 1.3450 +BOND CM_ OH_ 425.4 1.3330 +BOND CD_ CT_ 317.0 1.5100 +BOND C_ CA_ 349.7 1.4870 +BOND CT_ CA_ 317.0 1.5100 +BOND CA_ CA_ 478.4 1.3870 +BOND CA_ OH_ 386.1 1.3620 +BOND CA_ N2_ 481.0 1.3400 +BOND N2_ CT_ 337.0 1.4630 + +{ Angles: aType1 aType2 aType3 kt t0 } +ANGLe c__ n__ hn__ 49.2 118.46 +ANGLe c__ c3__ hc__ 47.2 109.68 +ANGLe c__ ca__ ca__ 64.6 120.14 +ANGLe n__ c__ n__ 74.8 113.38 +ANGLe n__ c__ c3__ 67.9 115.15 +ANGLe n__ c__ h5__ 52.4 112.19 +ANGLe n__ c3__ h1__ 49.8 109.32 +ANGLe o__ c__ n__ 75.8 122.03 +ANGLe o__ c__ c3__ 68.0 123.11 +ANGLe o__ c__ ca__ 68.7 123.44 +ANGLe o__ c__ h4__ 54.3 120.93 +ANGLe o__ c__ h5__ 53.9 123.26 +ANGLe c1__ c3__ hc__ 48.2 109.75 +ANGLe c3__ c__ c3__ 62.8 116.05 +ANGLe c3__ c__ h4__ 46.1 114.40 +ANGLe c3__ n__ c__ 63.9 121.35 +ANGLe c3__ n__ c3__ 63.1 115.56 +ANGLe c3__ c3__ c3__ 63.2 110.63 +ANGLe c3__ c3__ h1__ 46.4 110.07 +ANGLe c3__ c3__ hc__ 46.4 110.05 +ANGLe c3__ c3__ oh__ 67.7 109.43 +ANGLe c3__ n3__ hn__ 47.1 109.92 +ANGLe c3__ oh__ ho__ 47.1 108.16 +ANGLe c3__ os__ c3__ 62.4 112.45 +ANGLe ca__ c__ h4__ 46.5 115.14 +ANGLe ca__ ca__ ca__ 67.2 119.97 +ANGLe ca__ ca__ ha__ 48.5 120.01 +ANGLe ca__ ca__ oh__ 69.8 119.94 +ANGLe ca__ oh__ ho__ 48.9 109.47 +ANGLe h1__ c3__ h1__ 39.2 109.55 +ANGLe h1__ c3__ oh__ 51.0 109.88 +ANGLe hc__ c3__ hc__ 39.4 108.35 +ANGLe hn__ n__ hn__ 39.7 117.85 +ANGLe hn__ n3__ hn__ 41.3 107.13 +ANGLe n1__ c1__ c3__ 58.1 178.50 +ANGLe n3__ c3__ h1__ 49.4 109.92 +ANGLe os__ c3__ h1__ 50.8 108.82 +{ Angles: from Cagliari } +ANGLe C_ CD_ N_ 69.0 116.06 +ANGLe C_ CT_ CT_ 63.0 111.10 +ANGLe C_ CT_ HC_ 47.2 109.68 +ANGLe C_ CT_ HP_ 50.0 109.50 +ANGLe C_ CT_ N3_ 80.0 111.20 +ANGLe H_ N3_ H_ 35.0 109.50 +ANGLe H_ NT_ H_ 35.0 109.50 +ANGLe H_ NT_ CM_ 49.1 119.38 +ANGLe H_ NT_ CT_ 50.0 109.50 +ANGLe N_ C_ CT_ 67.9 115.15 +ANGLe O_ C_ CT_ 68.0 123.11 +ANGLe S_ CM_ CD_ 62.8 122.86 +ANGLe S_ CM_ CT_ 61.6 119.66 +ANGLe CD_ C_ O2_ 72.8 119.12 +ANGLe CD_ N_ C_ 65.1 122.15 +ANGLe CD_ N_ CT_ 63.1 119.98 +ANGLe CD_ CM_ CT_ 64.3 123.42 +ANGLe CM_ CD_ C_ 67.9 120.70 +ANGLe CM_ CD_ N_ 68.9 123.20 +ANGLe CM_ CT_ CT_ 63.0 111.00 +ANGLe CM_ CT_ HC_ 50.0 109.50 +ANGLe CM_ NT_ CT_ 64.7 117.79 +ANGLe CT_ N_ C_ 63.9 121.35 +ANGLe CT_ N_ CT_ 63.1 115.56 +ANGLe CT_ S_ CM_ 61.9 100.37 +ANGLe CT_ CT_ N_ 80.0 109.70 +ANGLe CT_ CT_ S_ 50.0 114.70 +ANGLe CT_ CT_ CT_ 63.2 110.63 +ANGLe CT_ CT_ H1_ 46.4 110.07 +ANGLe CT_ CT_ HC_ 46.4 110.05 +ANGLe CT_ CT_ HP_ 50.0 109.50 +ANGLe CT_ CT_ N3_ 80.0 111.20 +ANGLe CT_ CT_ OH_ 67.7 109.43 +ANGLe CT_ N3_ H_ 50.0 109.50 +ANGLe CT_ N3_ CT_ 50.0 109.50 +ANGLe CT_ OH_ HO_ 47.1 108.16 +ANGLe H1_ CT_ N_ 49.8 109.32 +ANGLe H1_ CT_ S_ 50.0 109.50 +ANGLe H1_ CT_ H1_ 39.2 109.55 +ANGLe H1_ CT_ OH_ 51.0 109.88 +ANGLe HC_ CT_ HC_ 39.4 108.35 +ANGLe HP_ CT_ HP_ 35.0 109.50 +ANGLe HP_ CT_ N3_ 50.0 109.50 +ANGLe NT_ CM_ HA_ 51.3 118.70 +ANGLe NT_ CM_ NT_ 73.5 118.47 +ANGLe NT_ CT_ CT_ 80.0 111.20 +ANGLe NT_ CT_ H1_ 50.0 109.50 +ANGLe O2_ C_ O2_ 80.0 126.00 +ANGLe C_ N_ H_ 49.2 118.46 +ANGLe H_ N_ H_ 39.7 117.85 +ANGLe CM_ OH_ HO_ 49.9 108.98 +ANGLe CD_ CT_ HC_ 50.0 109.50 +ANGLe HC_ CT_ CA_ 50.0 109.50 +ANGLe CA_ OH_ HO_ 48.9 109.47 +ANGLe CA_ CA_ HA_ 48.5 120.01 +ANGLe N2_ CT_ H1_ 50.0 109.50 +ANGLe O_ C_ CD_ 72.8 119.12 +ANGLe C_ CD_ C_ 66.6 118.88 +ANGLe CD_ C_ CT_ 64.8 116.42 +ANGLe CD_ C_ N_ 70.8 115.08 +ANGLe C_ CT_ OH_ 68.7 108.70 +ANGLe C_ CT_ CM_ 64.1 111.32 +ANGLe O_ C_ N_ 75.8 122.03 +ANGLe CT_ CT_ CD_ 63.5 111.44 +ANGLe CT_ CM_ OH_ 68.5 115.04 +ANGLe OH_ CT_ CM_ 68.2 110.21 +ANGLe CM_ CD_ CT_ 70.0 120.00 +ANGLe OH_ CM_ CD_ 71.6 122.07 +ANGLe CD_ C_ CA_ 67.2 116.78 +ANGLe C_ CA_ CA_ 64.6 120.14 +ANGLe C_ CD_ CT_ 63.9 119.70 +ANGLe O_ C_ CA_ 68.7 123.44 +ANGLe CT_ CT_ CA_ 63.0 114.00 +ANGLe CT_ CA_ CA_ 70.0 120.00 +ANGLe CA_ CA_ CA_ 67.2 119.97 +ANGLe CA_ CA_ N2_ 69.6 120.00 +ANGLe CA_ CA_ OH_ 69.8 119.94 +ANGLe CA_ N2_ CT_ 50.0 123.20 +ANGLe CT_ N2_ CT_ 64.0 110.90 + + + + +{ Proper Dihedrals: aType1 aType2 aType3 aType4 kt period phase } +DIHEdral c__ n__ c3__ h1__ 0.000 0 0.00 +DIHEdral c__ ca__ ca__ ca__ 3.625 2 180.00 +DIHEdral c__ ca__ ca__ ha__ 3.625 2 180.00 +DIHEdral n__ c__ n__ hn__ 2.500 2 180.00 +DIHEdral n__ c__ c3__ hc__ 0.000 2 180.00 +DIHEdral o__ c__ ca__ ca__ 1.000 2 180.00 +DIHEdral c3__ c__ n__ hn__ 2.500 2 180.00 +DIHEdral c3__ c__ c3__ hc__ 0.000 2 180.00 +DIHEdral c3__ n__ c__ o__ 2.500 2 180.00 +DIHEdral c3__ n__ c__ h5__ 2.500 2 180.00 +DIHEdral c3__ n__ c3__ h1__ 0.000 0 0.00 +DIHEdral c3__ c3__ c3__ hc__ 0.160 3 0.00 +DIHEdral c3__ os__ c3__ h1__ 0.383 3 0.00 +DIHEdral ca__ ca__ ca__ ca__ 3.625 2 180.00 +DIHEdral ca__ ca__ ca__ ha__ 3.625 2 180.00 +DIHEdral ca__ ca__ oh__ ho__ 0.900 2 180.00 +DIHEdral h1__ c3__ n__ c__ 0.000 0 0.00 +DIHEdral h1__ c3__ n__ c3__ 0.000 0 0.00 +DIHEdral h1__ c3__ c3__ c3__ 0.156 3 0.00 +DIHEdral h1__ c3__ c3__ hc__ 0.156 3 0.00 +DIHEdral h1__ c3__ oh__ ho__ 0.167 3 0.00 +DIHEdral h1__ c3__ os__ c3__ 0.383 3 0.00 +DIHEdral h4__ c__ c3__ hc__ 0.000 2 180.00 +DIHEdral h4__ c__ ca__ ca__ 1.000 2 180.00 +DIHEdral ha__ ca__ ca__ ca__ 3.625 2 180.00 +DIHEdral ha__ ca__ ca__ ha__ 3.625 2 180.00 +DIHEdral hc__ c3__ c3__ c3__ 0.160 3 0.00 +DIHEdral hc__ c3__ c3__ h1__ 0.156 3 0.00 +DIHEdral hc__ c3__ c3__ hc__ 0.150 3 0.00 +DIHEdral hn__ n3__ c3__ h1__ 0.300 3 0.00 +DIHEdral n1__ c1__ c3__ hc__ 0.000 2 180.00 +DIHEdral oh__ c3__ c3__ c3__ 0.156 3 0.00 +DIHEdral oh__ ca__ ca__ ca__ 3.625 2 180.00 +DIHEdral oh__ ca__ ca__ ha__ 3.625 2 180.00 +DIHEdral o__ c__ n__ hn__ MULT 2 2.000 1 0.00 + 2.500 2 180.00 +DIHEdral o__ c__ c3__ hc__ MULT 2 0.800 1 0.00 + 0.080 3 180.00 +DIHEdral c3__ c3__ c3__ c3__ MULT 3 0.200 1 180.00 + 0.250 2 180.00 + 0.180 3 0.00 +DIHEdral oh__ c3__ c3__ hc__ MULT 2 0.250 1 0.00 + 0.000 0 0.00 +DIHEdral c3__ c3__ oh__ ho__ MULT 2 0.250 1 0.00 + 0.160 3 0.00 +DIHEdral ho__ oh__ c3__ c3__ MULT 2 0.250 1 0.00 + 0.160 3 0.00 +DIHEdral hc__ c3__ c3__ oh__ MULT 2 0.250 1 0.00 + 0.000 0 0.00 + +{ Proper Dihedrals: from Cagliari } +DIHEdral C_ CD_ N_ C_ 0.650 2 180.00 +DIHEdral C_ CD_ N_ CT_ 0.650 2 180.00 +DIHEdral C_ CD_ CM_ CT_ 6.650 2 180.00 +DIHEdral C_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral C_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral C_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral C_ CT_ CT_ OH_ 0.156 3 0.00 +DIHEdral C_ CT_ N3_ H_ 0.156 3 0.00 +DIHEdral C_ CT_ N3_ CT_ 0.156 3 0.00 +DIHEdral H_ N3_ CT_ CT_ 0.156 3 0.00 +DIHEdral H_ N3_ CT_ HP_ 0.156 3 0.00 +DIHEdral H_ NT_ CM_ HA_ 0.300 2 180.00 +DIHEdral H_ NT_ CM_ NT_ 0.300 2 180.00 +DIHEdral H_ NT_ CT_ CT_ 0.300 3 0.00 +DIHEdral H_ NT_ CT_ H1_ 0.300 3 0.00 +DIHEdral N_ C_ CT_ HC_ 0.000 2 180.00 +DIHEdral N_ C_ CT_ HP_ 0.000 0 0.00 +DIHEdral N_ C_ CT_ N3_ 0.000 0 0.00 +DIHEdral N_ CT_ CT_ C_ 0.156 3 0.00 +DIHEdral N_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral N_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral O_ C_ CT_ CT_ 0.000 0 0.00 +DIHEdral O_ C_ CT_ HP_ 0.000 0 0.00 +DIHEdral O_ C_ CT_ N3_ 0.000 0 0.00 +DIHEdral S_ CM_ CD_ C_ 6.650 2 180.00 +DIHEdral S_ CM_ CD_ N_ 6.650 2 180.00 +DIHEdral S_ CM_ CT_ CT_ 0.000 0 0.00 +DIHEdral S_ CM_ CT_ HC_ 0.000 0 0.00 +DIHEdral CD_ N_ C_ O_ 2.500 2 180.00 +DIHEdral CD_ N_ C_ CT_ 2.500 2 180.00 +DIHEdral CD_ N_ CT_ CT_ 0.000 0 0.00 +DIHEdral CD_ N_ CT_ H1_ 0.000 0 0.00 +DIHEdral CD_ CM_ CT_ CT_ 0.000 0 0.00 +DIHEdral CD_ CM_ CT_ HC_ 0.000 0 0.00 +DIHEdral CM_ CD_ N_ CT_ 0.650 2 180.00 +DIHEdral CM_ CT_ CT_ N_ 0.156 3 0.00 +DIHEdral CM_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral CM_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral CM_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral CM_ NT_ CT_ CT_ 0.300 3 0.00 +DIHEdral CM_ NT_ CT_ H1_ 0.300 3 0.00 +DIHEdral CT_ N_ C_ O_ 2.500 2 180.00 +DIHEdral CT_ N_ C_ CT_ 2.500 2 180.00 +DIHEdral CT_ N_ CT_ H1_ 0.000 0 0.00 +DIHEdral CT_ S_ CM_ CT_ 1.100 2 180.00 +DIHEdral CT_ CM_ CD_ N_ 6.650 2 180.00 +DIHEdral CT_ CT_ C_ O_ 0.000 0 0.00 +DIHEdral CT_ CT_ S_ CM_ 0.333 3 0.00 +DIHEdral CT_ CT_ CT_ C_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ N_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ HC_ 0.160 3 0.00 +DIHEdral CT_ CT_ CT_ HP_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ N3_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ OH_ 0.156 3 0.00 +DIHEdral CT_ CT_ N3_ H_ 0.156 3 0.00 +DIHEdral CT_ CT_ N3_ CT_ 0.156 3 0.00 +DIHEdral CT_ N3_ CT_ CT_ 0.156 3 0.00 +DIHEdral CT_ N3_ CT_ HP_ 0.156 3 0.00 +DIHEdral H1_ CT_ N_ C_ 0.000 0 0.00 +DIHEdral H1_ CT_ N_ CT_ 0.000 0 0.00 +DIHEdral H1_ CT_ S_ CM_ 0.333 3 0.00 +DIHEdral H1_ CT_ CT_ C_ 0.156 3 0.00 +DIHEdral H1_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral H1_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral H1_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral H1_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral H1_ CT_ OH_ HO_ 0.167 3 0.00 +DIHEdral HA_ CM_ NT_ H_ 0.300 2 180.00 +DIHEdral HA_ CM_ NT_ CT_ 0.300 2 180.00 +DIHEdral HC_ CT_ CT_ N_ 0.156 3 0.00 +DIHEdral HC_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral HC_ CT_ CT_ CT_ 0.160 3 0.00 +DIHEdral HC_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral HC_ CT_ CT_ HC_ 0.150 3 0.00 +DIHEdral HC_ CT_ CT_ HP_ 0.156 3 0.00 +DIHEdral HC_ CT_ CT_ N3_ 0.156 3 0.00 +DIHEdral HP_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral HP_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral HP_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral HP_ CT_ N3_ H_ 0.156 3 0.00 +DIHEdral HP_ CT_ N3_ CT_ 0.156 3 0.00 +DIHEdral N3_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral N3_ CT_ CT_ CT_ 0.156 3 0.00 +DIHEdral N3_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral NT_ CM_ NT_ H_ 0.300 2 180.00 +DIHEdral NT_ CM_ NT_ CT_ 0.300 2 180.00 +DIHEdral NT_ CT_ CT_ S_ 0.156 3 0.00 +DIHEdral NT_ CT_ CT_ H1_ 0.156 3 0.00 +DIHEdral O2_ C_ CD_ N_ 2.175 2 180.00 +DIHEdral C_ N_ CT_ CT_ MULT 4 2.000 1 0.00 + 2.000 2 0.00 + 0.400 3 0.00 + 0.000 0 0.00 +DIHEdral CT_ CT_ C_ N_ MULT 4 0.200 1 0.00 + 0.200 2 0.00 + 0.400 3 0.00 + 0.000 0 0.00 +DIHEdral O_ C_ CT_ HC_ MULT 2 0.800 1 0.00 + 0.080 3 180.00 +DIHEdral HC_ CT_ CT_ OH_ MULT 2 0.250 1 0.00 + 0.000 0 0.00 +DIHEdral N_ C_ CT_ CT_ MULT 4 0.200 1 0.00 + 0.200 2 0.00 + 0.400 3 0.00 + 0.000 0 0.00 +DIHEdral CM_ CD_ N_ C_ MULT 2 1.200 1 180.00 + 0.650 2 180.00 +DIHEdral CM_ CD_ C_ O2_ MULT 2 2.175 2 180.00 + 0.300 3 0.00 +DIHEdral CT_ CT_ OH_ HO_ MULT 2 0.250 1 0.00 + 0.160 3 0.00 +DIHEdral CT_ S_ CM_ CD_ MULT 2 1.100 2 180.00 + 0.700 3 180.00 +DIHEdral CT_ CT_ N_ C_ MULT 4 2.000 1 0.00 + 2.000 2 0.00 + 0.400 3 0.00 + 0.000 0 0.00 +DIHEdral CT_ CT_ CT_ CT_ MULT 3 0.200 1 180.00 + 0.250 2 180.00 + 0.180 3 0.00 +DIHEdral C_ CD_ CT_ HC_ 0.000 0 0.00 +DIHEdral C_ CA_ CA_ CA_ 3.625 2 180.00 +DIHEdral CA_ CA_ CA_ CA_ 3.625 2 180.00 +DIHEdral CT_ CA_ CA_ CA_ 3.625 2 180.00 +DIHEdral OH_ CT_ CM_ CD_ 0.000 0 0.00 +DIHEdral CT_ CT_ CM_ OH_ 0.000 0 0.00 +DIHEdral CA_ CA_ CA_ N2_ 3.625 2 180.00 +DIHEdral O_ C_ CT_ CM_ 0.000 0 0.00 +DIHEdral O_ C_ CD_ CT_ 2.175 2 180.00 +DIHEdral HA_ CA_ CA_ N2_ 3.625 2 180.00 +DIHEdral HC_ CT_ CT_ CA_ 0.156 3 0.00 +DIHEdral CT_ CD_ C_ CA_ 2.175 2 180.00 +DIHEdral CD_ CT_ CT_ CA_ 0.156 3 0.00 +DIHEdral CM_ CD_ C_ O_ MULT 2 2.175 2 180.00 + 0.300 3 0.00 +DIHEdral HP_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral O_ C_ CD_ C_ 2.175 2 180.00 +DIHEdral CA_ CA_ CA_ OH_ 3.625 2 180.00 +DIHEdral C_ CA_ CA_ OH_ 3.625 2 180.00 +DIHEdral CT_ CM_ OH_ HO_ 1.050 2 180.00 +DIHEdral HC_ CT_ CT_ CD_ 0.156 3 0.00 +DIHEdral C_ CT_ CM_ CD_ 0.000 0 0.00 +DIHEdral O_ C_ N_ H_ MULT 2 2.000 1 0.00 + 2.500 2 180.00 +DIHEdral HC_ CT_ CA_ CA_ 0.000 0 0.00 +DIHEdral CM_ CD_ CT_ CT_ 0.000 0 0.00 +DIHEdral CM_ CD_ C_ CA_ 2.175 2 180.00 +DIHEdral C_ CT_ CM_ OH_ 0.000 0 0.00 +DIHEdral CM_ CD_ CT_ HC_ 0.000 0 0.00 +DIHEdral O_ C_ CT_ OH_ 0.000 0 0.00 +DIHEdral CT_ N2_ CT_ H1_ 0.000 0 0.00 +DIHEdral OH_ CM_ CD_ CT_ 6.650 2 180.00 +DIHEdral CD_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ CM_ 0.156 3 0.00 +DIHEdral CD_ C_ CT_ CT_ 0.000 0 0.00 +DIHEdral CT_ CT_ CD_ C_ 0.000 0 0.00 +DIHEdral C_ CT_ OH_ HO_ 0.167 3 0.00 +DIHEdral CA_ CA_ N2_ CT_ 2.400 2 180.00 +DIHEdral C_ CD_ C_ N_ 2.175 2 180.00 +DIHEdral CA_ CA_ OH_ HO_ 0.900 2 180.00 +DIHEdral CT_ CM_ CD_ C_ 6.650 2 180.00 +DIHEdral C_ CD_ C_ O_ 2.175 2 180.00 +DIHEdral CT_ CT_ CD_ CM_ 0.000 0 0.00 +DIHEdral HO_ OH_ CA_ CA_ 0.900 2 180.00 +DIHEdral C_ CA_ CA_ CT_ 3.625 2 180.00 +DIHEdral HO_ OH_ CT_ CM_ 0.167 3 0.00 +DIHEdral OH_ CA_ CA_ HA_ 3.625 2 180.00 +DIHEdral C_ CD_ C_ CT_ 2.175 2 180.00 +DIHEdral CT_ CM_ CD_ CT_ 6.650 2 180.00 +DIHEdral CD_ C_ CT_ OH_ 0.000 0 0.00 +DIHEdral OH_ CM_ CD_ C_ 6.650 2 180.00 +DIHEdral CD_ C_ CT_ CM_ 0.000 0 0.00 +DIHEdral CD_ C_ CT_ HP_ 0.000 0 0.00 +DIHEdral N3_ CT_ CT_ HC_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ CA_ 0.156 3 0.00 +DIHEdral OH_ CA_ CA_ CA_ 3.625 2 180.00 +DIHEdral HO_ OH_ CM_ CD_ 1.050 2 180.00 +DIHEdral CA_ CA_ CA_ HA_ 3.625 2 180.00 +DIHEdral HA_ CA_ CA_ HA_ 3.625 2 180.00 +DIHEdral CT_ CT_ CM_ CD_ 0.000 0 0.00 +DIHEdral HC_ CT_ CT_ CM_ 0.156 3 0.00 +DIHEdral CT_ CT_ CT_ CD_ 0.156 3 0.00 +DIHEdral CA_ N2_ CT_ H1_ 0.000 0 0.00 +DIHEdral O_ C_ CA_ CA_ 1.000 2 180.00 +DIHEdral HA_ CA_ CA_ CA_ 3.625 2 180.00 +DIHEdral CT_ CA_ CA_ N2_ 3.625 2 180.00 +DIHEdral CT_ CT_ CA_ CA_ 0.000 0 0.00 +DIHEdral CD_ C_ CT_ N3_ 0.000 0 0.00 +DIHEdral CD_ C_ CA_ CA_ 3.625 2 180.00 +DIHEdral OH_ CT_ CM_ OH_ 0.000 0 0.00 +DIHEdral CD_ C_ N_ H_ 2.500 2 180.00 +DIHEdral C_ CD_ CT_ CT_ 0.000 0 0.00 +DIHEdral H1_ CT_ N2_ CT_ 0.000 0 0.00 + + + + +{ Improper Dihedrals: aType1 aType2 aType3 aType4 kt period phase } +IMPRoper c__ c3__ n__ c3__ 1.1 2 180.00 +IMPRoper c__ ca__ ca__ ca__ 1.1 2 180.00 +IMPRoper c__ hn__ n__ hn__ 1.1 2 180.00 +IMPRoper o__ c__ n__ n__ 10.5 2 180.00 +IMPRoper o__ c__ n__ c3__ 10.5 2 180.00 +IMPRoper o__ c__ c3__ c3__ 10.5 2 180.00 +IMPRoper o__ c__ h4__ c3__ 10.5 2 180.00 +IMPRoper o__ c__ h4__ ca__ 10.5 2 180.00 +IMPRoper ca__ ca__ ca__ ha__ 1.1 2 180.00 +IMPRoper h5__ n__ c__ o__ 10.5 2 180.00 +IMPRoper ha__ ca__ ca__ ca__ 1.1 2 180.00 +IMPRoper oh__ ca__ ca__ ca__ 1.1 2 180.00 + +{ Improper Dihedrals: from Cagliari } + +IMPRoper C_ CD_ N_ CT_ 1.1 2 180.00 +IMPRoper C_ CM_ CD_ N_ 1.1 2 180.00 +IMPRoper C_ CT_ N_ CT_ 1.1 2 180.00 +IMPRoper CD_ CT_ CM_ S_ 1.1 2 180.00 +IMPRoper CD_ O2_ C_ O2_ 10.5 2 180.00 +IMPRoper CT_ N_ C_ O_ 10.5 2 180.00 +IMPRoper HA_ NT_ CM_ NT_ 1.1 2 180.00 +IMPRoper CA_ CA_ CA_ CT_ 1.1 2 180.00 +IMPRoper O_ C_ CT_ CD_ 10.5 2 180.00 +IMPRoper CA_ CT_ N2_ CT_ 1.1 2 180.00 +IMPRoper CA_ CD_ C_ O_ 10.5 2 180.00 +IMPRoper CA_ CA_ CA_ N2_ 1.1 2 180.00 +IMPRoper C_ C_ CD_ C_ 1.1 2 180.00 +IMPRoper C_ CA_ CA_ CA_ 1.1 2 180.00 +IMPRoper CA_ CA_ CA_ HA_ 1.1 2 180.00 +IMPRoper C_ H_ N_ H_ 1.1 2 180.00 +IMPRoper C_ CM_ CD_ CT_ 1.1 2 180.00 +IMPRoper CD_ N_ C_ O_ 10.5 2 180.00 +IMPRoper CD_ CT_ C_ O_ 10.5 2 180.00 +IMPRoper CD_ CT_ CM_ OH_ 1.1 2 180.00 +IMPRoper CA_ CA_ CA_ OH_ 1.1 2 180.00 + + + + +{ Nonbonded: Type Emin sigma; (1-4): Emin/2 sigma } +NONBonded c__ 0.086000 3.399670 0.043000 3.399670 +NONBonded n__ 0.170000 3.249999 0.085000 3.249999 +NONBonded o__ 0.210000 2.959922 0.105000 2.959922 +NONBonded c1__ 0.210000 3.399670 0.105000 3.399670 +NONBonded c3__ 0.109400 3.399670 0.054700 3.399670 +NONBonded ca__ 0.086000 3.399670 0.043000 3.399670 +NONBonded h1__ 0.015700 2.471353 0.007850 2.471353 +NONBonded h4__ 0.015000 2.510553 0.007500 2.510553 +NONBonded h5__ 0.015000 2.421463 0.007500 2.421463 +NONBonded ha__ 0.015000 2.599642 0.007500 2.599642 +NONBonded hc__ 0.015700 2.649533 0.007850 2.649533 +NONBonded hn__ 0.015700 1.069078 0.007850 1.069078 +NONBonded ho__ 0.000000 0.000000 0.000000 0.000000 +NONBonded n1__ 0.170000 3.249999 0.085000 3.249999 +NONBonded n3__ 0.170000 3.249999 0.085000 3.249999 +NONBonded oh__ 0.210400 3.066473 0.105200 3.066473 +NONBonded os__ 0.170000 3.000012 0.085000 3.000012 + +{ Nonbonded: Type Emin sigma; (1-4): Emin/2 sigma - from Cagliari } +NONBonded C_ 0.086000 3.399670 0.043000 3.399670 +NONBonded H_ 0.015700 1.069078 0.007850 1.069078 +NONBonded N_ 0.170000 3.249999 0.085000 3.249999 +NONBonded O_ 0.210000 2.959922 0.105000 2.959922 +NONBonded S_ 0.250000 3.563595 0.125000 3.563595 +NONBonded CD_ 0.086000 3.399670 0.043000 3.399670 +NONBonded CM_ 0.086000 3.399670 0.043000 3.399670 +NONBonded CT_ 0.109400 3.399670 0.054700 3.399670 +NONBonded H1_ 0.015700 2.471353 0.007850 2.471353 +NONBonded HA_ 0.015000 2.599642 0.007500 2.599642 +NONBonded HC_ 0.015700 2.649533 0.007850 2.649533 +NONBonded HO_ 0.000000 0.000000 0.000000 0.000000 +NONBonded HP_ 0.015700 1.959977 0.007850 1.959977 +NONBonded N3_ 0.170000 3.249999 0.085000 3.249999 +NONBonded NT_ 0.170000 3.249999 0.085000 3.249999 +NONBonded O2_ 0.210000 2.959922 0.105000 2.959922 +NONBonded OH_ 0.210400 3.066473 0.105200 3.066473 +NONBonded CA_ 0.086000 3.399670 0.043000 3.399670 +NONBonded N2_ 0.170000 3.249999 0.085000 3.249999 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.top new file mode 100644 index 0000000000000000000000000000000000000000..64c01f74a42e2001be013b0d0875b07a2c79285b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/fragment_probes.top @@ -0,0 +1,2208 @@ +Remarks Parameters for Fragment-based Ligand Binding Site Mapping +Remarks created by acpype (Rev: 7268) on Mon Apr 13 10:01:53 2015 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +MASS c1__ 12.010 +MASS c3__ 12.010 +MASS c__ 12.010 +MASS ca__ 12.010 +MASS h1__ 1.008 +MASS h4__ 1.008 +MASS h5__ 1.008 +MASS ha__ 1.008 +MASS hc__ 1.008 +MASS hn__ 1.008 +MASS ho__ 1.008 +MASS n1__ 14.010 +MASS n3__ 14.010 +MASS n__ 14.010 +MASS o__ 16.000 +MASS oh__ 16.000 +MASS os__ 16.000 + +{ atomType mass } +MASS NT_ 14.010 +MASS H_ 1.008 +MASS CM_ 12.010 +MASS HA_ 1.008 +MASS CT_ 12.010 +MASS H1_ 1.008 +MASS S_ 32.060 +MASS CD_ 12.010 +MASS C_ 12.010 +MASS O2_ 16.000 +MASS HC_ 1.008 +MASS N_ 14.010 +MASS O_ 16.000 +MASS OH_ 16.000 +MASS HO_ 1.008 +MASS HP_ 1.008 +MASS N3_ 14.010 +MASS CA_ 12.010 +MASS N2_ 14.010 + + +! N,N-dimethylformamide +RESIdue DFO + +GROUP +ATOM C1 TYPE= c3__ CHARGE= 0.0793 END +ATOM C2 TYPE= c3__ CHARGE= 0.0793 END +ATOM C TYPE= c__ CHARGE= 0.6619 END +ATOM O TYPE= o__ CHARGE= -0.6041 END +ATOM N TYPE= n__ CHARGE= -0.4948 END +ATOM H11 TYPE= h1__ CHARGE= 0.0417 END +ATOM H12 TYPE= h1__ CHARGE= 0.0417 END +ATOM H13 TYPE= h1__ CHARGE= 0.0417 END +ATOM H21 TYPE= h1__ CHARGE= 0.0417 END +ATOM H22 TYPE= h1__ CHARGE= 0.0417 END +ATOM H23 TYPE= h1__ CHARGE= 0.0417 END +ATOM HC TYPE= h5__ CHARGE= 0.0282 END + +BOND C1 H11 +BOND C1 H12 +BOND C1 H13 +BOND C2 H21 +BOND C2 H22 +BOND C2 H23 +BOND C HC +BOND C1 N +BOND C2 N +BOND C N +BOND C O + +ANGLe O C HC +ANGLe N C1 H11 +ANGLe N C1 H12 +ANGLe N C1 H13 +ANGLe N C2 H21 +ANGLe N C2 H22 +ANGLe N C2 H23 +ANGLe N C HC +ANGLe H11 C1 H12 +ANGLe H11 C1 H13 +ANGLe H12 C1 H13 +ANGLe H21 C2 H22 +ANGLe H21 C2 H23 +ANGLe H22 C2 H23 +ANGLe C1 N C2 +ANGLe C1 N C +ANGLe C2 N C +ANGLe O C N + +DIHEdral C1 N C2 H21 +DIHEdral C1 N C2 H22 +DIHEdral C1 N C2 H23 +DIHEdral C1 N C HC +DIHEdral H11 C1 N C2 +DIHEdral H12 C1 N C2 +DIHEdral H13 C1 N C2 +DIHEdral C2 N C HC +DIHEdral H11 C1 N C +DIHEdral H12 C1 N C +DIHEdral H13 C1 N C +DIHEdral C N C2 H21 +DIHEdral C N C2 H22 +DIHEdral C N C2 H23 +DIHEdral C1 N C O +DIHEdral C2 N C O + +IMPRoper HC N C O +IMPRoper C C1 N C2 + +END {RESIdue DFO} + +! acetaldehyde +RESIdue ADY + +GROUP +ATOM C TYPE= c__ CHARGE= 0.5619 END +ATOM O TYPE= o__ CHARGE= -0.5261 END +ATOM CH3 TYPE= c3__ CHARGE= -0.2211 END +ATOM H TYPE= h4__ CHARGE= -0.0098 END +ATOM H1 TYPE= hc__ CHARGE= 0.0650 END +ATOM H2 TYPE= hc__ CHARGE= 0.0650 END +ATOM H3 TYPE= hc__ CHARGE= 0.0650 END + +BOND C H +BOND CH3 H1 +BOND CH3 H2 +BOND CH3 H3 +BOND C CH3 +BOND C O + +ANGLe C CH3 H1 +ANGLe C CH3 H2 +ANGLe C CH3 H3 +ANGLe O C H +ANGLe CH3 C H +ANGLe H1 CH3 H2 +ANGLe H1 CH3 H3 +ANGLe H2 CH3 H3 +ANGLe O C CH3 + +DIHEdral O C CH3 H1 +DIHEdral O C CH3 H2 +DIHEdral O C CH3 H3 +DIHEdral H C CH3 H1 +DIHEdral H C CH3 H2 +DIHEdral H C CH3 H3 + +IMPRoper O C H CH3 + +END {RESIdue ADY} + +! acetamide +RESIdue ACD + +GROUP + +ATOM C1 TYPE= c__ CHARGE= 0.6561 END +ATOM O TYPE= o__ CHARGE= -0.6131 END +ATOM N TYPE= n__ CHARGE= -0.6850 END +ATOM C2 TYPE= c3__ CHARGE= -0.1741 END +ATOM HN1 TYPE= hn__ CHARGE= 0.3100 END +ATOM HN2 TYPE= hn__ CHARGE= 0.3100 END +ATOM H21 TYPE= hc__ CHARGE= 0.0654 END +ATOM H22 TYPE= hc__ CHARGE= 0.0654 END +ATOM H23 TYPE= hc__ CHARGE= 0.0654 END + +BOND N HN1 +BOND N HN2 +BOND C2 H21 +BOND C2 H22 +BOND C2 H23 +BOND C1 C2 +BOND C1 N +BOND C1 O + +ANGLe C1 C2 H21 +ANGLe C1 C2 H22 +ANGLe C1 C2 H23 +ANGLe C1 N HN1 +ANGLe C1 N HN2 +ANGLe HN1 N HN2 +ANGLe H21 C2 H22 +ANGLe H21 C2 H23 +ANGLe H22 C2 H23 +ANGLe O C1 C2 +ANGLe O C1 N +ANGLe N C1 C2 + +DIHEdral O C1 C2 H21 +DIHEdral O C1 C2 H22 +DIHEdral O C1 C2 H23 +DIHEdral O C1 N HN1 +DIHEdral O C1 N HN2 +DIHEdral N C1 C2 H21 +DIHEdral N C1 C2 H22 +DIHEdral N C1 C2 H23 +DIHEdral C2 C1 N HN1 +DIHEdral C2 C1 N HN2 + +IMPRoper C1 HN1 N HN2 +IMPRoper O C1 N C2 + +END {RESIdue ACD} + +! acetone +RESIdue ACT + +GROUP + +ATOM C TYPE= c__ CHARGE= 0.5631 END +ATOM O TYPE= o__ CHARGE= -0.5311 END +ATOM C1 TYPE= c3__ CHARGE= -0.2041 END +ATOM C2 TYPE= c3__ CHARGE= -0.2041 END +ATOM H11 TYPE= hc__ CHARGE= 0.0627 END +ATOM H12 TYPE= hc__ CHARGE= 0.0627 END +ATOM H13 TYPE= hc__ CHARGE= 0.0627 END +ATOM H21 TYPE= hc__ CHARGE= 0.0627 END +ATOM H22 TYPE= hc__ CHARGE= 0.0627 END +ATOM H23 TYPE= hc__ CHARGE= 0.0627 END + +BOND C1 H11 +BOND C1 H12 +BOND C1 H13 +BOND C2 H21 +BOND C2 H22 +BOND C2 H23 +BOND C C1 +BOND C C2 +BOND C O + +ANGLe C C1 H11 +ANGLe C C1 H12 +ANGLe C C1 H13 +ANGLe C C2 H21 +ANGLe C C2 H22 +ANGLe C C2 H23 +ANGLe H11 C1 H12 +ANGLe H11 C1 H13 +ANGLe H12 C1 H13 +ANGLe H21 C2 H22 +ANGLe H21 C2 H23 +ANGLe H22 C2 H23 +ANGLe O C C1 +ANGLe O C C2 +ANGLe C1 C C2 + +DIHEdral O C C1 H11 +DIHEdral O C C1 H12 +DIHEdral O C C1 H13 +DIHEdral O C C2 H21 +DIHEdral O C C2 H22 +DIHEdral O C C2 H23 +DIHEdral C1 C C2 H21 +DIHEdral C1 C C2 H22 +DIHEdral C1 C C2 H23 +DIHEdral C2 C C1 H11 +DIHEdral C2 C C1 H12 +DIHEdral C2 C C1 H13 + +IMPRoper O C C2 C1 + +END {RESIdue ACT} + +! acetonitrile +RESIdue ACN + +GROUP + +ATOM N TYPE= n1__ CHARGE= -0.3758 END +ATOM C1 TYPE= c1__ CHARGE= 0.2087 END +ATOM C2 TYPE= c3__ CHARGE= -0.0450 END +ATOM H21 TYPE= hc__ CHARGE= 0.0707 END +ATOM H22 TYPE= hc__ CHARGE= 0.0707 END +ATOM H23 TYPE= hc__ CHARGE= 0.0707 END + +BOND C2 H21 +BOND C2 H22 +BOND C2 H23 +BOND N C1 +BOND C1 C2 + +ANGLe C1 C2 H21 +ANGLe C1 C2 H22 +ANGLe C1 C2 H23 +ANGLe H21 C2 H22 +ANGLe H21 C2 H23 +ANGLe H22 C2 H23 +ANGLe N C1 C2 + +DIHEdral N C1 C2 H21 +DIHEdral N C1 C2 H22 +DIHEdral N C1 C2 H23 + +END {RESIdue ACN} + +! benzaldehyde +RESIdue BDY + +GROUP + +ATOM C1 TYPE= c__ CHARGE= 0.5745 END +ATOM O1 TYPE= o__ CHARGE= -0.5281 END +ATOM C2 TYPE= ca__ CHARGE= -0.1976 END +ATOM C3 TYPE= ca__ CHARGE= -0.0780 END +ATOM C4 TYPE= ca__ CHARGE= -0.1450 END +ATOM C5 TYPE= ca__ CHARGE= -0.0980 END +ATOM C6 TYPE= ca__ CHARGE= -0.1450 END +ATOM C7 TYPE= ca__ CHARGE= -0.0780 END +ATOM H1 TYPE= h4__ CHARGE= -0.0028 END +ATOM H2 TYPE= ha__ CHARGE= 0.1440 END +ATOM H3 TYPE= ha__ CHARGE= 0.1375 END +ATOM H4 TYPE= ha__ CHARGE= 0.1350 END +ATOM H5 TYPE= ha__ CHARGE= 0.1375 END +ATOM H6 TYPE= ha__ CHARGE= 0.1440 END + +BOND C1 H1 +BOND C3 H2 +BOND C4 H3 +BOND C5 H4 +BOND C6 H5 +BOND C7 H6 +BOND C1 C2 +BOND C1 O1 +BOND C2 C3 +BOND C2 C7 +BOND C3 C4 +BOND C4 C5 +BOND C5 C6 +BOND C6 C7 + +ANGLe O1 C1 H1 +ANGLe C2 C1 H1 +ANGLe C2 C3 H2 +ANGLe C2 C7 H6 +ANGLe C3 C4 H3 +ANGLe C4 C3 H2 +ANGLe C4 C5 H4 +ANGLe C5 C4 H3 +ANGLe C5 C6 H5 +ANGLe C6 C5 H4 +ANGLe C6 C7 H6 +ANGLe C7 C6 H5 +ANGLe C1 C2 C3 +ANGLe C1 C2 C7 +ANGLe O1 C1 C2 +ANGLe C2 C3 C4 +ANGLe C2 C7 C6 +ANGLe C3 C2 C7 +ANGLe C3 C4 C5 +ANGLe C4 C5 C6 +ANGLe C5 C6 C7 + +DIHEdral C1 C2 C3 H2 +DIHEdral C1 C2 C7 H6 +DIHEdral C2 C3 C4 H3 +DIHEdral C2 C7 C6 H5 +DIHEdral H1 C1 C2 C3 +DIHEdral C3 C2 C7 H6 +DIHEdral C3 C4 C5 H4 +DIHEdral C4 C5 C6 H5 +DIHEdral C5 C4 C3 H2 +DIHEdral C5 C6 C7 H6 +DIHEdral C6 C5 C4 H3 +DIHEdral H1 C1 C2 C7 +DIHEdral C7 C2 C3 H2 +DIHEdral C7 C6 C5 H4 +DIHEdral H2 C3 C4 H3 +DIHEdral H3 C4 C5 H4 +DIHEdral H4 C5 C6 H5 +DIHEdral H5 C6 C7 H6 +DIHEdral C1 C2 C3 C4 +DIHEdral C1 C2 C7 C6 +DIHEdral O1 C1 C2 C3 +DIHEdral O1 C1 C2 C7 +DIHEdral C2 C3 C4 C5 +DIHEdral C2 C7 C6 C5 +DIHEdral C3 C2 C7 C6 +DIHEdral C3 C4 C5 C6 +DIHEdral C4 C3 C2 C7 +DIHEdral C4 C5 C6 C7 + +IMPRoper O1 C1 H1 C2 +IMPRoper C2 C4 C3 H2 +IMPRoper C3 C5 C4 H3 +IMPRoper C4 C6 C5 H4 +IMPRoper C5 C7 C6 H5 +IMPRoper C2 C6 C7 H6 +IMPRoper C1 C3 C2 C7 + +END {RESIdue BDY} + +! benzene +RESIdue BEN + +GROUP + +ATOM C1 TYPE= ca__ CHARGE= -0.1300 END +ATOM C2 TYPE= ca__ CHARGE= -0.1300 END +ATOM C3 TYPE= ca__ CHARGE= -0.1300 END +ATOM C4 TYPE= ca__ CHARGE= -0.1300 END +ATOM C5 TYPE= ca__ CHARGE= -0.1300 END +ATOM C6 TYPE= ca__ CHARGE= -0.1300 END +ATOM H1 TYPE= ha__ CHARGE= 0.1300 END +ATOM H2 TYPE= ha__ CHARGE= 0.1300 END +ATOM H3 TYPE= ha__ CHARGE= 0.1300 END +ATOM H4 TYPE= ha__ CHARGE= 0.1300 END +ATOM H5 TYPE= ha__ CHARGE= 0.1300 END +ATOM H6 TYPE= ha__ CHARGE= 0.1300 END + +BOND C1 H1 +BOND C2 H2 +BOND C3 H3 +BOND C4 H4 +BOND C5 H5 +BOND C6 H6 +BOND C1 C2 +BOND C1 C6 +BOND C2 C3 +BOND C3 C4 +BOND C4 C5 +BOND C5 C6 + +ANGLe C1 C2 H2 +ANGLe C1 C6 H6 +ANGLe C2 C1 H1 +ANGLe C2 C3 H3 +ANGLe C3 C2 H2 +ANGLe C3 C4 H4 +ANGLe C4 C3 H3 +ANGLe C4 C5 H5 +ANGLe C5 C4 H4 +ANGLe C5 C6 H6 +ANGLe C6 C1 H1 +ANGLe C6 C5 H5 +ANGLe C1 C2 C3 +ANGLe C1 C6 C5 +ANGLe C2 C1 C6 +ANGLe C2 C3 C4 +ANGLe C3 C4 C5 +ANGLe C4 C5 C6 + +DIHEdral C1 C2 C3 H3 +DIHEdral C1 C6 C5 H5 +DIHEdral C2 C1 C6 H6 +DIHEdral C2 C3 C4 H4 +DIHEdral H1 C1 C2 C3 +DIHEdral C3 C4 C5 H5 +DIHEdral C4 C3 C2 H2 +DIHEdral C4 C5 C6 H6 +DIHEdral C5 C4 C3 H3 +DIHEdral H1 C1 C6 C5 +DIHEdral C6 C1 C2 H2 +DIHEdral C6 C5 C4 H4 +DIHEdral H1 C1 C2 H2 +DIHEdral H1 C1 C6 H6 +DIHEdral H2 C2 C3 H3 +DIHEdral H3 C3 C4 H4 +DIHEdral H4 C4 C5 H5 +DIHEdral H5 C5 C6 H6 +DIHEdral C1 C2 C3 C4 +DIHEdral C1 C6 C5 C4 +DIHEdral C2 C1 C6 C5 +DIHEdral C2 C3 C4 C5 +DIHEdral C6 C1 C2 C3 +DIHEdral C3 C4 C5 C6 + +IMPRoper H1 C1 C6 C2 +IMPRoper C1 C3 C2 H2 +IMPRoper C2 C4 C3 H3 +IMPRoper C3 C5 C4 H4 +IMPRoper C4 C6 C5 H5 +IMPRoper C1 C5 C6 H6 + +END {RESIdue BEN} + +! cyclohexane +RESIdue CHE + +GROUP + +ATOM C1 TYPE= c3__ CHARGE= -0.0764 END +ATOM C2 TYPE= c3__ CHARGE= -0.0764 END +ATOM C3 TYPE= c3__ CHARGE= -0.0764 END +ATOM C4 TYPE= c3__ CHARGE= -0.0764 END +ATOM C5 TYPE= c3__ CHARGE= -0.0764 END +ATOM C6 TYPE= c3__ CHARGE= -0.0764 END +ATOM H11 TYPE= hc__ CHARGE= 0.0382 END +ATOM H12 TYPE= hc__ CHARGE= 0.0382 END +ATOM H21 TYPE= hc__ CHARGE= 0.0382 END +ATOM H22 TYPE= hc__ CHARGE= 0.0382 END +ATOM H31 TYPE= hc__ CHARGE= 0.0382 END +ATOM H32 TYPE= hc__ CHARGE= 0.0382 END +ATOM H41 TYPE= hc__ CHARGE= 0.0382 END +ATOM H42 TYPE= hc__ CHARGE= 0.0382 END +ATOM H51 TYPE= hc__ CHARGE= 0.0382 END +ATOM H52 TYPE= hc__ CHARGE= 0.0382 END +ATOM H61 TYPE= hc__ CHARGE= 0.0382 END +ATOM H62 TYPE= hc__ CHARGE= 0.0382 END + +BOND C1 H11 +BOND C1 H12 +BOND C2 H21 +BOND C2 H22 +BOND C3 H31 +BOND C3 H32 +BOND C4 H41 +BOND C4 H42 +BOND C5 H51 +BOND C5 H52 +BOND C6 H61 +BOND C6 H62 +BOND C1 C2 +BOND C1 C6 +BOND C2 C3 +BOND C3 C4 +BOND C4 C5 +BOND C5 C6 + +ANGLe C1 C2 H21 +ANGLe C1 C2 H22 +ANGLe C1 C6 H61 +ANGLe C1 C6 H62 +ANGLe C2 C1 H11 +ANGLe C2 C1 H12 +ANGLe C2 C3 H31 +ANGLe C2 C3 H32 +ANGLe C3 C2 H21 +ANGLe C3 C2 H22 +ANGLe C3 C4 H41 +ANGLe C3 C4 H42 +ANGLe C4 C3 H31 +ANGLe C4 C3 H32 +ANGLe C4 C5 H51 +ANGLe C4 C5 H52 +ANGLe C5 C4 H41 +ANGLe C5 C4 H42 +ANGLe C5 C6 H61 +ANGLe C5 C6 H62 +ANGLe C6 C1 H11 +ANGLe C6 C1 H12 +ANGLe C6 C5 H51 +ANGLe C6 C5 H52 +ANGLe H11 C1 H12 +ANGLe H21 C2 H22 +ANGLe H31 C3 H32 +ANGLe H41 C4 H42 +ANGLe H51 C5 H52 +ANGLe H61 C6 H62 +ANGLe C1 C2 C3 +ANGLe C1 C6 C5 +ANGLe C2 C1 C6 +ANGLe C2 C3 C4 +ANGLe C3 C4 C5 +ANGLe C4 C5 C6 + +DIHEdral C1 C2 C3 H31 +DIHEdral C1 C2 C3 H32 +DIHEdral C1 C6 C5 H51 +DIHEdral C1 C6 C5 H52 +DIHEdral C2 C1 C6 H61 +DIHEdral C2 C1 C6 H62 +DIHEdral C2 C3 C4 H41 +DIHEdral C2 C3 C4 H42 +DIHEdral H11 C1 C2 C3 +DIHEdral H12 C1 C2 C3 +DIHEdral C3 C4 C5 H51 +DIHEdral C3 C4 C5 H52 +DIHEdral C4 C3 C2 H21 +DIHEdral C4 C3 C2 H22 +DIHEdral C4 C5 C6 H61 +DIHEdral C4 C5 C6 H62 +DIHEdral C5 C4 C3 H31 +DIHEdral C5 C4 C3 H32 +DIHEdral H11 C1 C6 C5 +DIHEdral H12 C1 C6 C5 +DIHEdral C6 C1 C2 H21 +DIHEdral C6 C1 C2 H22 +DIHEdral C6 C5 C4 H41 +DIHEdral C6 C5 C4 H42 +DIHEdral H11 C1 C2 H21 +DIHEdral H11 C1 C2 H22 +DIHEdral H11 C1 C6 H61 +DIHEdral H11 C1 C6 H62 +DIHEdral H12 C1 C2 H21 +DIHEdral H12 C1 C2 H22 +DIHEdral H12 C1 C6 H61 +DIHEdral H12 C1 C6 H62 +DIHEdral H21 C2 C3 H31 +DIHEdral H21 C2 C3 H32 +DIHEdral H22 C2 C3 H31 +DIHEdral H22 C2 C3 H32 +DIHEdral H31 C3 C4 H41 +DIHEdral H31 C3 C4 H42 +DIHEdral H32 C3 C4 H41 +DIHEdral H32 C3 C4 H42 +DIHEdral H41 C4 C5 H51 +DIHEdral H41 C4 C5 H52 +DIHEdral H42 C4 C5 H51 +DIHEdral H42 C4 C5 H52 +DIHEdral H51 C5 C6 H61 +DIHEdral H51 C5 C6 H62 +DIHEdral H52 C5 C6 H61 +DIHEdral H52 C5 C6 H62 +DIHEdral C1 C2 C3 C4 +DIHEdral C1 C6 C5 C4 +DIHEdral C2 C1 C6 C5 +DIHEdral C2 C3 C4 C5 +DIHEdral C6 C1 C2 C3 +DIHEdral C3 C4 C5 C6 + +END {RESIdue CHE} + +! dimethylether +RESIdue DME + +GROUP + +ATOM C1 TYPE= c3__ CHARGE= 0.1137 END +ATOM O TYPE= os__ CHARGE= -0.4196 END +ATOM C TYPE= c3__ CHARGE= 0.1137 END +ATOM H1 TYPE= h1__ CHARGE= 0.0320 END +ATOM H2 TYPE= h1__ CHARGE= 0.0320 END +ATOM H3 TYPE= h1__ CHARGE= 0.0320 END +ATOM H4 TYPE= h1__ CHARGE= 0.0320 END +ATOM H5 TYPE= h1__ CHARGE= 0.0320 END +ATOM H6 TYPE= h1__ CHARGE= 0.0320 END + +BOND C1 H1 +BOND C1 H2 +BOND C1 H3 +BOND C H4 +BOND C H5 +BOND C H6 +BOND C1 O +BOND O C + +ANGLe O C1 H1 +ANGLe O C1 H2 +ANGLe O C1 H3 +ANGLe O C H4 +ANGLe O C H5 +ANGLe O C H6 +ANGLe H1 C1 H2 +ANGLe H1 C1 H3 +ANGLe H2 C1 H3 +ANGLe H4 C H5 +ANGLe H4 C H6 +ANGLe H5 C H6 +ANGLe C1 O C + +DIHEdral C1 O C H4 +DIHEdral C1 O C H5 +DIHEdral C1 O C H6 +DIHEdral H1 C1 O C +DIHEdral H2 C1 O C +DIHEdral H3 C1 O C + +END {RESIdue DME} + +! ethane +RESIdue ETA + +GROUP + +ATOM C1 TYPE= c3__ CHARGE= -0.0951 END +ATOM C2 TYPE= c3__ CHARGE= -0.0951 END +ATOM H1 TYPE= hc__ CHARGE= 0.0317 END +ATOM H2 TYPE= hc__ CHARGE= 0.0317 END +ATOM H3 TYPE= hc__ CHARGE= 0.0317 END +ATOM H4 TYPE= hc__ CHARGE= 0.0317 END +ATOM H5 TYPE= hc__ CHARGE= 0.0317 END +ATOM H6 TYPE= hc__ CHARGE= 0.0317 END + +BOND C1 H1 +BOND C1 H2 +BOND C1 H3 +BOND C2 H4 +BOND C2 H5 +BOND C2 H6 +BOND C1 C2 + +ANGLe C1 C2 H4 +ANGLe C1 C2 H5 +ANGLe C1 C2 H6 +ANGLe C2 C1 H1 +ANGLe C2 C1 H2 +ANGLe C2 C1 H3 +ANGLe H1 C1 H2 +ANGLe H1 C1 H3 +ANGLe H2 C1 H3 +ANGLe H4 C2 H5 +ANGLe H4 C2 H6 +ANGLe H5 C2 H6 + +DIHEdral H1 C1 C2 H4 +DIHEdral H1 C1 C2 H5 +DIHEdral H1 C1 C2 H6 +DIHEdral H2 C1 C2 H4 +DIHEdral H2 C1 C2 H5 +DIHEdral H2 C1 C2 H6 +DIHEdral H3 C1 C2 H4 +DIHEdral H3 C1 C2 H5 +DIHEdral H3 C1 C2 H6 + +END {RESIdue ETH} + +! ethanol +RESIdue EOL + +GROUP + +ATOM C1 TYPE= c3__ CHARGE= 0.1314 END +ATOM C2 TYPE= c3__ CHARGE= -0.0971 END +ATOM O TYPE= oh__ CHARGE= -0.6028 END +ATOM H11 TYPE= h1__ CHARGE= 0.0187 END +ATOM H12 TYPE= h1__ CHARGE= 0.0187 END +ATOM H21 TYPE= hc__ CHARGE= 0.0444 END +ATOM H22 TYPE= hc__ CHARGE= 0.0444 END +ATOM H23 TYPE= hc__ CHARGE= 0.0444 END +ATOM HO TYPE= ho__ CHARGE= 0.3980 END + +BOND C1 H11 +BOND C1 H12 +BOND C2 H21 +BOND C2 H22 +BOND C2 H23 +BOND O HO +BOND C1 C2 +BOND C1 O + +ANGLe C1 C2 H21 +ANGLe C1 C2 H22 +ANGLe C1 C2 H23 +ANGLe C1 O HO +ANGLe C2 C1 H11 +ANGLe C2 C1 H12 +ANGLe O C1 H11 +ANGLe O C1 H12 +ANGLe H11 C1 H12 +ANGLe H21 C2 H22 +ANGLe H21 C2 H23 +ANGLe H22 C2 H23 +ANGLe C2 C1 O + +DIHEdral C2 C1 O HO +DIHEdral O C1 C2 H21 +DIHEdral O C1 C2 H22 +DIHEdral O C1 C2 H23 +DIHEdral H11 C1 C2 H21 +DIHEdral H11 C1 C2 H22 +DIHEdral H11 C1 C2 H23 +DIHEdral H11 C1 O HO +DIHEdral H12 C1 C2 H21 +DIHEdral H12 C1 C2 H22 +DIHEdral H12 C1 C2 H23 +DIHEdral H12 C1 O HO + +END {RESIdue EOL} + +! isobutanol +RESIdue BUT + +GROUP + +ATOM CAB TYPE= c3__ CHARGE= -0.0921 END +ATOM HAD TYPE= hc__ CHARGE= 0.0444 END +ATOM HAE TYPE= hc__ CHARGE= 0.0444 END +ATOM HAF TYPE= hc__ CHARGE= 0.0444 END +ATOM CAE TYPE= c3__ CHARGE= 0.1401 END +ATOM HAI TYPE= h1__ CHARGE= 0.0297 END +ATOM OAC TYPE= oh__ CHARGE= -0.5998 END +ATOM HAJ TYPE= ho__ CHARGE= 0.3980 END +ATOM CAD TYPE= c3__ CHARGE= -0.1204 END +ATOM HAG TYPE= hc__ CHARGE= 0.0527 END +ATOM HAH TYPE= hc__ CHARGE= 0.0527 END +ATOM CAA TYPE= c3__ CHARGE= -0.0971 END +ATOM HAB TYPE= hc__ CHARGE= 0.0344 END +ATOM HAC TYPE= hc__ CHARGE= 0.0344 END +ATOM HAA TYPE= hc__ CHARGE= 0.0344 END + +BOND CAB HAD +BOND CAB HAE +BOND CAB HAF +BOND CAE HAI +BOND OAC HAJ +BOND CAD HAG +BOND CAD HAH +BOND CAA HAB +BOND CAA HAC +BOND CAA HAA +BOND CAB CAE +BOND CAE OAC +BOND CAE CAD +BOND CAD CAA + +ANGLe CAB CAE HAI +ANGLe HAD CAB HAE +ANGLe HAD CAB HAF +ANGLe HAD CAB CAE +ANGLe HAE CAB HAF +ANGLe HAE CAB CAE +ANGLe HAF CAB CAE +ANGLe CAE OAC HAJ +ANGLe CAE CAD HAG +ANGLe CAE CAD HAH +ANGLe HAI CAE OAC +ANGLe HAI CAE CAD +ANGLe CAD CAA HAB +ANGLe CAD CAA HAC +ANGLe CAD CAA HAA +ANGLe HAG CAD HAH +ANGLe HAG CAD CAA +ANGLe HAH CAD CAA +ANGLe HAB CAA HAC +ANGLe HAB CAA HAA +ANGLe HAC CAA HAA +ANGLe CAB CAE OAC +ANGLe CAB CAE CAD +ANGLe CAE CAD CAA +ANGLe OAC CAE CAD + +DIHEdral CAB CAE OAC HAJ +DIHEdral CAB CAE CAD HAG +DIHEdral CAB CAE CAD HAH +DIHEdral HAD CAB CAE HAI +DIHEdral HAD CAB CAE OAC +DIHEdral HAD CAB CAE CAD +DIHEdral HAE CAB CAE HAI +DIHEdral HAE CAB CAE OAC +DIHEdral HAE CAB CAE CAD +DIHEdral HAF CAB CAE HAI +DIHEdral HAF CAB CAE OAC +DIHEdral HAF CAB CAE CAD +DIHEdral CAE CAD CAA HAB +DIHEdral CAE CAD CAA HAC +DIHEdral CAE CAD CAA HAA +DIHEdral HAI CAE OAC HAJ +DIHEdral HAI CAE CAD HAG +DIHEdral HAI CAE CAD HAH +DIHEdral HAI CAE CAD CAA +DIHEdral OAC CAE CAD HAG +DIHEdral OAC CAE CAD HAH +DIHEdral HAJ OAC CAE CAD +DIHEdral HAG CAD CAA HAB +DIHEdral HAG CAD CAA HAC +DIHEdral HAG CAD CAA HAA +DIHEdral HAH CAD CAA HAB +DIHEdral HAH CAD CAA HAC +DIHEdral HAH CAD CAA HAA +DIHEdral CAB CAE CAD CAA +DIHEdral OAC CAE CAD CAA + +END {RESIdue BUT} + +! isopropanol +RESIdue THS + +GROUP + +ATOM CAA TYPE= c3__ CHARGE= -0.1116 END +ATOM HAA TYPE= hc__ CHARGE= 0.0434 END +ATOM HAB TYPE= hc__ CHARGE= 0.0434 END +ATOM HAC TYPE= hc__ CHARGE= 0.0434 END +ATOM CAD TYPE= c3__ CHARGE= 0.1391 END +ATOM HAG TYPE= h1__ CHARGE= 0.0287 END +ATOM CAB TYPE= c3__ CHARGE= -0.1116 END +ATOM HAE TYPE= hc__ CHARGE= 0.0434 END +ATOM HAF TYPE= hc__ CHARGE= 0.0434 END +ATOM HAD TYPE= hc__ CHARGE= 0.0434 END +ATOM OAC TYPE= oh__ CHARGE= -0.6018 END +ATOM HAH TYPE= ho__ CHARGE= 0.3970 END + +BOND CAA HAA +BOND CAA HAB +BOND CAA HAC +BOND CAD HAG +BOND CAB HAE +BOND CAB HAF +BOND CAB HAD +BOND OAC HAH +BOND CAA CAD +BOND CAD CAB +BOND CAD OAC + +ANGLe CAA CAD HAG +ANGLe HAA CAA HAB +ANGLe HAA CAA HAC +ANGLe HAA CAA CAD +ANGLe HAB CAA HAC +ANGLe HAB CAA CAD +ANGLe HAC CAA CAD +ANGLe CAD CAB HAE +ANGLe CAD CAB HAF +ANGLe CAD CAB HAD +ANGLe CAD OAC HAH +ANGLe HAG CAD CAB +ANGLe HAG CAD OAC +ANGLe HAE CAB HAF +ANGLe HAE CAB HAD +ANGLe HAF CAB HAD +ANGLe CAA CAD CAB +ANGLe CAA CAD OAC +ANGLe CAB CAD OAC + +DIHEdral CAA CAD CAB HAE +DIHEdral CAA CAD CAB HAF +DIHEdral CAA CAD CAB HAD +DIHEdral CAA CAD OAC HAH +DIHEdral HAA CAA CAD HAG +DIHEdral HAA CAA CAD CAB +DIHEdral HAA CAA CAD OAC +DIHEdral HAB CAA CAD HAG +DIHEdral HAB CAA CAD CAB +DIHEdral HAB CAA CAD OAC +DIHEdral HAC CAA CAD HAG +DIHEdral HAC CAA CAD CAB +DIHEdral HAC CAA CAD OAC +DIHEdral HAG CAD CAB HAE +DIHEdral HAG CAD CAB HAF +DIHEdral HAG CAD CAB HAD +DIHEdral HAG CAD OAC HAH +DIHEdral CAB CAD OAC HAH +DIHEdral HAE CAB CAD OAC +DIHEdral HAF CAB CAD OAC +DIHEdral HAD CAB CAD OAC + +END {RESIdue THS} + +! Methylamine +RESIdue AMN + +GROUP + +ATOM N TYPE= n3__ CHARGE= -0.9198 END +ATOM C TYPE= c3__ CHARGE= 0.1471 END +ATOM HN1 TYPE= hn__ CHARGE= 0.3478 END +ATOM HN2 TYPE= hn__ CHARGE= 0.3478 END +ATOM H1 TYPE= h1__ CHARGE= 0.0257 END +ATOM H2 TYPE= h1__ CHARGE= 0.0257 END +ATOM H3 TYPE= h1__ CHARGE= 0.0257 END + +BOND N HN1 +BOND N HN2 +BOND C H1 +BOND C H2 +BOND C H3 +BOND N C + +ANGLe N C H1 +ANGLe N C H2 +ANGLe N C H3 +ANGLe C N HN1 +ANGLe C N HN2 +ANGLe HN1 N HN2 +ANGLe H1 C H2 +ANGLe H1 C H3 +ANGLe H2 C H3 + +DIHEdral HN1 N C H1 +DIHEdral HN1 N C H2 +DIHEdral HN1 N C H3 +DIHEdral HN2 N C H1 +DIHEdral HN2 N C H2 +DIHEdral HN2 N C H3 + +END {RESIdue AMN} + +! Phenol +RESIdue PHN + +GROUP + +ATOM C1 TYPE= ca__ CHARGE= 0.1231 END +ATOM C2 TYPE= ca__ CHARGE= -0.1850 END +ATOM C3 TYPE= ca__ CHARGE= -0.0945 END +ATOM C4 TYPE= ca__ CHARGE= -0.1660 END +ATOM C5 TYPE= ca__ CHARGE= -0.0945 END +ATOM C6 TYPE= ca__ CHARGE= -0.1850 END +ATOM O1 TYPE= oh__ CHARGE= -0.4981 END +ATOM H2 TYPE= ha__ CHARGE= 0.1415 END +ATOM H3 TYPE= ha__ CHARGE= 0.1330 END +ATOM H4 TYPE= ha__ CHARGE= 0.1330 END +ATOM H5 TYPE= ha__ CHARGE= 0.1330 END +ATOM H6 TYPE= ha__ CHARGE= 0.1415 END +ATOM HO1 TYPE= ho__ CHARGE= 0.4180 END + +BOND C2 H2 +BOND C3 H3 +BOND C4 H4 +BOND C5 H5 +BOND C6 H6 +BOND O1 HO1 +BOND C1 C2 +BOND C1 C6 +BOND C1 O1 +BOND C2 C3 +BOND C3 C4 +BOND C4 C5 +BOND C5 C6 + +ANGLe C1 C2 H2 +ANGLe C1 C6 H6 +ANGLe C1 O1 HO1 +ANGLe C2 C3 H3 +ANGLe C3 C2 H2 +ANGLe C3 C4 H4 +ANGLe C4 C3 H3 +ANGLe C4 C5 H5 +ANGLe C5 C4 H4 +ANGLe C5 C6 H6 +ANGLe C6 C5 H5 +ANGLe C1 C2 C3 +ANGLe C1 C6 C5 +ANGLe C2 C1 C6 +ANGLe C2 C1 O1 +ANGLe C2 C3 C4 +ANGLe C3 C4 C5 +ANGLe C4 C5 C6 +ANGLe C6 C1 O1 + +DIHEdral C1 C2 C3 H3 +DIHEdral C1 C6 C5 H5 +DIHEdral C2 C1 C6 H6 +DIHEdral C2 C1 O1 HO1 +DIHEdral C2 C3 C4 H4 +DIHEdral C3 C4 C5 H5 +DIHEdral C4 C3 C2 H2 +DIHEdral C4 C5 C6 H6 +DIHEdral C5 C4 C3 H3 +DIHEdral C6 C1 C2 H2 +DIHEdral C6 C1 O1 HO1 +DIHEdral C6 C5 C4 H4 +DIHEdral O1 C1 C2 H2 +DIHEdral O1 C1 C6 H6 +DIHEdral H2 C2 C3 H3 +DIHEdral H3 C3 C4 H4 +DIHEdral H4 C4 C5 H5 +DIHEdral H5 C5 C6 H6 +DIHEdral C1 C2 C3 C4 +DIHEdral C1 C6 C5 C4 +DIHEdral C2 C1 C6 C5 +DIHEdral C2 C3 C4 C5 +DIHEdral C6 C1 C2 C3 +DIHEdral O1 C1 C2 C3 +DIHEdral C3 C4 C5 C6 +DIHEdral O1 C1 C6 C5 + +IMPRoper C1 C3 C2 H2 +IMPRoper C2 C4 C3 H3 +IMPRoper C3 C5 C4 H4 +IMPRoper C4 C6 C5 H5 +IMPRoper C1 C5 C6 H6 +IMPRoper O1 C1 C6 C2 + +END {RESIdue PHN} + +! Urea +RESIdue URE + +GROUP + +ATOM C TYPE= c__ CHARGE= 0.7271 END +ATOM O TYPE= o__ CHARGE= -0.6391 END +ATOM N1 TYPE= n__ CHARGE= -0.6420 END +ATOM N2 TYPE= n__ CHARGE= -0.6420 END +ATOM HN11 TYPE= hn__ CHARGE= 0.2990 END +ATOM HN12 TYPE= hn__ CHARGE= 0.2990 END +ATOM HN21 TYPE= hn__ CHARGE= 0.2990 END +ATOM HN22 TYPE= hn__ CHARGE= 0.2990 END + +BOND N1 HN11 +BOND N1 HN12 +BOND N2 HN21 +BOND N2 HN22 +BOND C N1 +BOND C N2 +BOND C O + +ANGLe C N1 HN11 +ANGLe C N1 HN12 +ANGLe C N2 HN21 +ANGLe C N2 HN22 +ANGLe HN11 N1 HN12 +ANGLe HN21 N2 HN22 +ANGLe O C N1 +ANGLe O C N2 +ANGLe N1 C N2 + +DIHEdral O C N1 HN11 +DIHEdral O C N1 HN12 +DIHEdral O C N2 HN21 +DIHEdral O C N2 HN22 +DIHEdral N1 C N2 HN21 +DIHEdral N1 C N2 HN22 +DIHEdral N2 C N1 HN11 +DIHEdral N2 C N1 HN12 + +IMPRoper C HN11 N1 HN12 +IMPRoper C HN21 N2 HN22 +IMPRoper O C N2 N1 + +END {RESIdue URE} + +! From Cagliari +! Imipenem +RESIdue IMI + +GROUP + +{ atomName atomType Charge } +ATOM N3 TYPE= NT_ CHARGE= -0.6188 END +ATOM H3 TYPE= H_ CHARGE= 0.3782 END +ATOM H4 TYPE= H_ CHARGE= 0.3782 END +ATOM C12 TYPE= CM_ CHARGE= 0.1731 END +ATOM H17 TYPE= HA_ CHARGE= 0.1645 END +ATOM N2 TYPE= NT_ CHARGE= -0.0943 END +ATOM H2 TYPE= H_ CHARGE= 0.1320 END +ATOM C11 TYPE= CT_ CHARGE= -0.1381 END +ATOM H15 TYPE= H1_ CHARGE= 0.0932 END +ATOM H16 TYPE= H1_ CHARGE= 0.0932 END +ATOM C10 TYPE= CT_ CHARGE= 0.2413 END +ATOM H13 TYPE= H1_ CHARGE= -0.0139 END +ATOM H14 TYPE= H1_ CHARGE= -0.0139 END +ATOM S1 TYPE= S_ CHARGE= -0.2425 END +ATOM C7 TYPE= CM_ CHARGE= 0.0949 END +ATOM C6 TYPE= CD_ CHARGE= 0.1967 END +ATOM C9 TYPE= C_ CHARGE= 0.5283 END +ATOM O3 TYPE= O2_ CHARGE= -0.5432 END +ATOM O4 TYPE= O2_ CHARGE= -0.5432 END +ATOM C3 TYPE= CT_ CHARGE= -0.3383 END +ATOM H7 TYPE= HC_ CHARGE= 0.0921 END +ATOM H8 TYPE= HC_ CHARGE= 0.0921 END +ATOM C1 TYPE= CT_ CHARGE= 0.3569 END +ATOM H5 TYPE= H1_ CHARGE= 0.0557 END +ATOM N1 TYPE= N_ CHARGE= -0.4585 END +ATOM C4 TYPE= C_ CHARGE= 0.6593 END +ATOM O2 TYPE= O_ CHARGE= -0.4751 END +ATOM C2 TYPE= CT_ CHARGE= -0.6220 END +ATOM H6 TYPE= HC_ CHARGE= 0.1703 END +ATOM C5 TYPE= CT_ CHARGE= 0.4740 END +ATOM C8 TYPE= CT_ CHARGE= -0.4200 END +ATOM H10 TYPE= HC_ CHARGE= 0.1065 END +ATOM H11 TYPE= HC_ CHARGE= 0.1065 END +ATOM H12 TYPE= HC_ CHARGE= 0.1065 END +ATOM H9 TYPE= H1_ CHARGE= 0.0691 END +ATOM O1 TYPE= OH_ CHARGE= -0.6451 END +ATOM H1 TYPE= HO_ CHARGE= 0.4046 END + +{ Bonds: atomName1 atomName2 } +BOND N3 H3 +BOND N3 H4 +BOND C12 H17 +BOND N2 H2 +BOND C11 H15 +BOND C11 H16 +BOND C10 H13 +BOND C10 H14 +BOND C3 H7 +BOND C3 H8 +BOND C1 H5 +BOND C2 H6 +BOND C5 H9 +BOND C8 H10 +BOND C8 H11 +BOND C8 H12 +BOND O1 H1 +BOND N3 C12 +BOND C12 N2 +BOND N2 C11 +BOND C11 C10 +BOND C10 S1 +BOND S1 C7 +BOND C7 C6 +BOND C7 C3 +BOND C6 C9 +BOND C6 N1 +BOND C9 O3 +BOND C9 O4 +BOND C3 C1 +BOND C1 N1 +BOND C1 C2 +BOND N1 C4 +BOND C4 O2 +BOND C4 C2 +BOND C2 C5 +BOND C5 C8 +BOND C5 O1 + +{ Angles: atomName1 atomName2 atomName3} +ANGLe N3 C12 H17 +ANGLe H3 N3 H4 +ANGLe H3 N3 C12 +ANGLe H4 N3 C12 +ANGLe C12 N2 H2 +ANGLe H17 C12 N2 +ANGLe N2 C11 H15 +ANGLe N2 C11 H16 +ANGLe H2 N2 C11 +ANGLe C11 C10 H13 +ANGLe C11 C10 H14 +ANGLe H15 C11 H16 +ANGLe H15 C11 C10 +ANGLe H16 C11 C10 +ANGLe H13 C10 H14 +ANGLe H13 C10 S1 +ANGLe H14 C10 S1 +ANGLe C7 C3 H7 +ANGLe C7 C3 H8 +ANGLe C3 C1 H5 +ANGLe H7 C3 H8 +ANGLe H7 C3 C1 +ANGLe H8 C3 C1 +ANGLe C1 C2 H6 +ANGLe H5 C1 N1 +ANGLe H5 C1 C2 +ANGLe C4 C2 H6 +ANGLe C2 C5 H9 +ANGLe H6 C2 C5 +ANGLe C5 C8 H10 +ANGLe C5 C8 H11 +ANGLe C5 C8 H12 +ANGLe C5 O1 H1 +ANGLe C8 C5 H9 +ANGLe H10 C8 H11 +ANGLe H10 C8 H12 +ANGLe H11 C8 H12 +ANGLe H9 C5 O1 +ANGLe N3 C12 N2 +ANGLe C12 N2 C11 +ANGLe N2 C11 C10 +ANGLe C11 C10 S1 +ANGLe C10 S1 C7 +ANGLe S1 C7 C6 +ANGLe S1 C7 C3 +ANGLe C7 C6 C9 +ANGLe C7 C6 N1 +ANGLe C7 C3 C1 +ANGLe C6 C7 C3 +ANGLe C6 C9 O3 +ANGLe C6 C9 O4 +ANGLe C6 N1 C1 +ANGLe C6 N1 C4 +ANGLe C9 C6 N1 +ANGLe O3 C9 O4 +ANGLe C3 C1 N1 +ANGLe C3 C1 C2 +ANGLe C1 N1 C4 +ANGLe C1 C2 C4 +ANGLe C1 C2 C5 +ANGLe N1 C1 C2 +ANGLe N1 C4 O2 +ANGLe N1 C4 C2 +ANGLe C4 C2 C5 +ANGLe O2 C4 C2 +ANGLe C2 C5 C8 +ANGLe C2 C5 O1 +ANGLe C8 C5 O1 + +{ Proper Dihedrals: name1 name2 name3 name4 } +DIHEdral N3 C12 N2 H2 +DIHEdral H3 N3 C12 H17 +DIHEdral H3 N3 C12 N2 +DIHEdral H4 N3 C12 H17 +DIHEdral H4 N3 C12 N2 +DIHEdral C12 N2 C11 H15 +DIHEdral C12 N2 C11 H16 +DIHEdral H17 C12 N2 H2 +DIHEdral H17 C12 N2 C11 +DIHEdral N2 C11 C10 H13 +DIHEdral N2 C11 C10 H14 +DIHEdral H2 N2 C11 H15 +DIHEdral H2 N2 C11 H16 +DIHEdral H2 N2 C11 C10 +DIHEdral H15 C11 C10 H13 +DIHEdral H15 C11 C10 H14 +DIHEdral H15 C11 C10 S1 +DIHEdral H16 C11 C10 H13 +DIHEdral H16 C11 C10 H14 +DIHEdral H16 C11 C10 S1 +DIHEdral H13 C10 S1 C7 +DIHEdral H14 C10 S1 C7 +DIHEdral S1 C7 C3 H7 +DIHEdral S1 C7 C3 H8 +DIHEdral C7 C3 C1 H5 +DIHEdral C6 C7 C3 H7 +DIHEdral C6 C7 C3 H8 +DIHEdral C6 N1 C1 H5 +DIHEdral C3 C1 C2 H6 +DIHEdral H7 C3 C1 H5 +DIHEdral H7 C3 C1 N1 +DIHEdral H7 C3 C1 C2 +DIHEdral H8 C3 C1 H5 +DIHEdral H8 C3 C1 N1 +DIHEdral H8 C3 C1 C2 +DIHEdral C1 C2 C5 H9 +DIHEdral H5 C1 N1 C4 +DIHEdral H5 C1 C2 C4 +DIHEdral H5 C1 C2 H6 +DIHEdral H5 C1 C2 C5 +DIHEdral N1 C1 C2 H6 +DIHEdral N1 C4 C2 H6 +DIHEdral C4 C2 C5 H9 +DIHEdral O2 C4 C2 H6 +DIHEdral C2 C5 C8 H10 +DIHEdral C2 C5 C8 H11 +DIHEdral C2 C5 C8 H12 +DIHEdral C2 C5 O1 H1 +DIHEdral H6 C2 C5 C8 +DIHEdral H6 C2 C5 H9 +DIHEdral H6 C2 C5 O1 +DIHEdral C8 C5 O1 H1 +DIHEdral H10 C8 C5 H9 +DIHEdral H10 C8 C5 O1 +DIHEdral H11 C8 C5 H9 +DIHEdral H11 C8 C5 O1 +DIHEdral H12 C8 C5 H9 +DIHEdral H12 C8 C5 O1 +DIHEdral H9 C5 O1 H1 +DIHEdral N3 C12 N2 C11 +DIHEdral C12 N2 C11 C10 +DIHEdral N2 C11 C10 S1 +DIHEdral C11 C10 S1 C7 +DIHEdral C10 S1 C7 C6 +DIHEdral C10 S1 C7 C3 +DIHEdral S1 C7 C6 C9 +DIHEdral S1 C7 C6 N1 +DIHEdral S1 C7 C3 C1 +DIHEdral C7 C6 C9 O3 +DIHEdral C7 C6 C9 O4 +DIHEdral C7 C6 N1 C1 +DIHEdral C7 C6 N1 C4 +DIHEdral C7 C3 C1 N1 +DIHEdral C7 C3 C1 C2 +DIHEdral C6 C7 C3 C1 +DIHEdral C6 N1 C1 C3 +DIHEdral C6 N1 C1 C2 +DIHEdral C6 N1 C4 O2 +DIHEdral C6 N1 C4 C2 +DIHEdral C9 C6 C7 C3 +DIHEdral C9 C6 N1 C1 +DIHEdral C9 C6 N1 C4 +DIHEdral O3 C9 C6 N1 +DIHEdral O4 C9 C6 N1 +DIHEdral C3 C7 C6 N1 +DIHEdral C3 C1 N1 C4 +DIHEdral C3 C1 C2 C4 +DIHEdral C3 C1 C2 C5 +DIHEdral C1 N1 C4 O2 +DIHEdral C1 N1 C4 C2 +DIHEdral C1 C2 C4 N1 +DIHEdral C1 C2 C4 O2 +DIHEdral C1 C2 C5 C8 +DIHEdral C1 C2 C5 O1 +DIHEdral N1 C1 C2 C4 +DIHEdral N1 C1 C2 C5 +DIHEdral N1 C4 C2 C5 +DIHEdral C4 N1 C1 C2 +DIHEdral C4 C2 C5 C8 +DIHEdral C4 C2 C5 O1 +DIHEdral O2 C4 C2 C5 + +{ Improper Dihedrals: aName1 aName2 aName3 aName4 } +IMPRoper H17 N3 C12 N2 +IMPRoper C6 C3 C7 S1 +IMPRoper C9 C7 C6 N1 +IMPRoper C6 O3 C9 O4 +IMPRoper C4 C6 N1 C1 +IMPRoper C2 N1 C4 O2 + +END {RESIdue IMI} + + +! Meropenem +RESIdue MER + +GROUP + +{ atomName atomType Charge } +ATOM C16 TYPE= CT_ CHARGE= -0.1733 END +ATOM H20 TYPE= H1_ CHARGE= 0.1001 END +ATOM H21 TYPE= H1_ CHARGE= 0.1001 END +ATOM H22 TYPE= H1_ CHARGE= 0.1001 END +ATOM N3 TYPE= N_ CHARGE= 0.0103 END +ATOM C17 TYPE= CT_ CHARGE= -0.1733 END +ATOM H23 TYPE= H1_ CHARGE= 0.1001 END +ATOM H24 TYPE= H1_ CHARGE= 0.1001 END +ATOM H25 TYPE= H1_ CHARGE= 0.1001 END +ATOM C15 TYPE= C_ CHARGE= 0.2610 END +ATOM O5 TYPE= O_ CHARGE= -0.4455 END +ATOM C13 TYPE= CT_ CHARGE= 0.1154 END +ATOM C10 TYPE= CT_ CHARGE= -0.3904 END +ATOM H12 TYPE= HC_ CHARGE= 0.1858 END +ATOM H13 TYPE= HC_ CHARGE= 0.1858 END +ATOM H19 TYPE= HP_ CHARGE= 0.0525 END +ATOM N2 TYPE= N3_ CHARGE= -0.1133 END +ATOM H2 TYPE= H_ CHARGE= 0.2503 END +ATOM H3 TYPE= H_ CHARGE= 0.2503 END +ATOM C12 TYPE= CT_ CHARGE= -0.0301 END +ATOM H17 TYPE= HP_ CHARGE= 0.1087 END +ATOM H18 TYPE= HP_ CHARGE= 0.1087 END +ATOM C9 TYPE= CT_ CHARGE= 0.0454 END +ATOM H11 TYPE= H1_ CHARGE= 0.0742 END +ATOM S1 TYPE= S_ CHARGE= -0.1883 END +ATOM C5 TYPE= CM_ CHARGE= -0.2617 END +ATOM C6 TYPE= CD_ CHARGE= 0.2965 END +ATOM C14 TYPE= C_ CHARGE= 0.5435 END +ATOM O3 TYPE= O2_ CHARGE= -0.5942 END +ATOM O4 TYPE= O2_ CHARGE= -0.5942 END +ATOM C3 TYPE= CT_ CHARGE= 0.3477 END +ATOM C8 TYPE= CT_ CHARGE= -0.2817 END +ATOM H8 TYPE= HC_ CHARGE= 0.0690 END +ATOM H9 TYPE= HC_ CHARGE= 0.0690 END +ATOM H10 TYPE= HC_ CHARGE= 0.0690 END +ATOM H6 TYPE= HC_ CHARGE= -0.0770 END +ATOM C1 TYPE= CT_ CHARGE= 0.0477 END +ATOM H4 TYPE= H1_ CHARGE= 0.0884 END +ATOM N1 TYPE= N_ CHARGE= -0.4733 END +ATOM C4 TYPE= C_ CHARGE= 0.7164 END +ATOM O1 TYPE= O_ CHARGE= -0.4923 END +ATOM C2 TYPE= CT_ CHARGE= -0.5145 END +ATOM H5 TYPE= HC_ CHARGE= 0.1449 END +ATOM C7 TYPE= CT_ CHARGE= 0.4340 END +ATOM C11 TYPE= CT_ CHARGE= -0.1504 END +ATOM H14 TYPE= HC_ CHARGE= 0.0378 END +ATOM H15 TYPE= HC_ CHARGE= 0.0378 END +ATOM H16 TYPE= HC_ CHARGE= 0.0378 END +ATOM H7 TYPE= H1_ CHARGE= -0.0234 END +ATOM O2 TYPE= OH_ CHARGE= -0.6063 END +ATOM H1 TYPE= HO_ CHARGE= 0.3948 END + +{ Bonds: atomName1 atomName2 } +BOND C16 H20 +BOND C16 H21 +BOND C16 H22 +BOND C17 H23 +BOND C17 H24 +BOND C17 H25 +BOND C13 H19 +BOND C10 H12 +BOND C10 H13 +BOND N2 H2 +BOND N2 H3 +BOND C12 H17 +BOND C12 H18 +BOND C9 H11 +BOND C3 H6 +BOND C8 H8 +BOND C8 H9 +BOND C8 H10 +BOND C1 H4 +BOND C2 H5 +BOND C7 H7 +BOND C11 H14 +BOND C11 H15 +BOND C11 H16 +BOND O2 H1 +BOND C16 N3 +BOND N3 C17 +BOND N3 C15 +BOND C15 O5 +BOND C15 C13 +BOND C13 C10 +BOND C13 N2 +BOND C10 C9 +BOND N2 C12 +BOND C12 C9 +BOND C9 S1 +BOND S1 C5 +BOND C5 C6 +BOND C5 C3 +BOND C6 C14 +BOND C6 N1 +BOND C14 O3 +BOND C14 O4 +BOND C3 C8 +BOND C3 C1 +BOND C1 N1 +BOND C1 C2 +BOND N1 C4 +BOND C4 O1 +BOND C4 C2 +BOND C2 C7 +BOND C7 C11 +BOND C7 O2 + +{ Angles: atomName1 atomName2 atomName3} +ANGLe H20 C16 H21 +ANGLe H20 C16 H22 +ANGLe H20 C16 N3 +ANGLe H21 C16 H22 +ANGLe H21 C16 N3 +ANGLe H22 C16 N3 +ANGLe N3 C17 H23 +ANGLe N3 C17 H24 +ANGLe N3 C17 H25 +ANGLe H23 C17 H24 +ANGLe H23 C17 H25 +ANGLe H24 C17 H25 +ANGLe C15 C13 H19 +ANGLe C13 C10 H12 +ANGLe C13 C10 H13 +ANGLe C13 N2 H2 +ANGLe C13 N2 H3 +ANGLe C10 C13 H19 +ANGLe C10 C9 H11 +ANGLe H12 C10 H13 +ANGLe H12 C10 C9 +ANGLe H13 C10 C9 +ANGLe H19 C13 N2 +ANGLe N2 C12 H17 +ANGLe N2 C12 H18 +ANGLe H2 N2 H3 +ANGLe H2 N2 C12 +ANGLe H3 N2 C12 +ANGLe C12 C9 H11 +ANGLe H17 C12 H18 +ANGLe H17 C12 C9 +ANGLe H18 C12 C9 +ANGLe H11 C9 S1 +ANGLe C5 C3 H6 +ANGLe C3 C8 H8 +ANGLe C3 C8 H9 +ANGLe C3 C8 H10 +ANGLe C3 C1 H4 +ANGLe C8 C3 H6 +ANGLe H8 C8 H9 +ANGLe H8 C8 H10 +ANGLe H9 C8 H10 +ANGLe H6 C3 C1 +ANGLe C1 C2 H5 +ANGLe H4 C1 N1 +ANGLe H4 C1 C2 +ANGLe C4 C2 H5 +ANGLe C2 C7 H7 +ANGLe H5 C2 C7 +ANGLe C7 C11 H14 +ANGLe C7 C11 H15 +ANGLe C7 C11 H16 +ANGLe C7 O2 H1 +ANGLe C11 C7 H7 +ANGLe H14 C11 H15 +ANGLe H14 C11 H16 +ANGLe H15 C11 H16 +ANGLe H7 C7 O2 +ANGLe C16 N3 C17 +ANGLe C16 N3 C15 +ANGLe N3 C15 O5 +ANGLe N3 C15 C13 +ANGLe C17 N3 C15 +ANGLe C15 C13 C10 +ANGLe C15 C13 N2 +ANGLe O5 C15 C13 +ANGLe C13 C10 C9 +ANGLe C13 N2 C12 +ANGLe C10 C13 N2 +ANGLe C10 C9 C12 +ANGLe C10 C9 S1 +ANGLe N2 C12 C9 +ANGLe C12 C9 S1 +ANGLe C9 S1 C5 +ANGLe S1 C5 C6 +ANGLe S1 C5 C3 +ANGLe C5 C6 C14 +ANGLe C5 C6 N1 +ANGLe C5 C3 C8 +ANGLe C5 C3 C1 +ANGLe C6 C5 C3 +ANGLe C6 C14 O3 +ANGLe C6 C14 O4 +ANGLe C6 N1 C1 +ANGLe C6 N1 C4 +ANGLe C14 C6 N1 +ANGLe O3 C14 O4 +ANGLe C3 C1 N1 +ANGLe C3 C1 C2 +ANGLe C8 C3 C1 +ANGLe C1 N1 C4 +ANGLe C1 C2 C4 +ANGLe C1 C2 C7 +ANGLe N1 C1 C2 +ANGLe N1 C4 O1 +ANGLe N1 C4 C2 +ANGLe C4 C2 C7 +ANGLe O1 C4 C2 +ANGLe C2 C7 C11 +ANGLe C2 C7 O2 +ANGLe C11 C7 O2 + +{ Proper Dihedrals: name1 name2 name3 name4 } +DIHEdral C16 N3 C17 H23 +DIHEdral C16 N3 C17 H24 +DIHEdral C16 N3 C17 H25 +DIHEdral H20 C16 N3 C17 +DIHEdral H20 C16 N3 C15 +DIHEdral H21 C16 N3 C17 +DIHEdral H21 C16 N3 C15 +DIHEdral H22 C16 N3 C17 +DIHEdral H22 C16 N3 C15 +DIHEdral N3 C15 C13 H19 +DIHEdral H23 C17 N3 C15 +DIHEdral H24 C17 N3 C15 +DIHEdral H25 C17 N3 C15 +DIHEdral C15 C13 C10 H12 +DIHEdral C15 C13 C10 H13 +DIHEdral C15 C13 N2 H2 +DIHEdral C15 C13 N2 H3 +DIHEdral O5 C15 C13 H19 +DIHEdral C13 C10 C9 H11 +DIHEdral C13 N2 C12 H17 +DIHEdral C13 N2 C12 H18 +DIHEdral C10 C13 N2 H2 +DIHEdral C10 C13 N2 H3 +DIHEdral C10 C9 C12 H17 +DIHEdral C10 C9 C12 H18 +DIHEdral H12 C10 C13 H19 +DIHEdral H12 C10 C13 N2 +DIHEdral H12 C10 C9 C12 +DIHEdral H12 C10 C9 H11 +DIHEdral H12 C10 C9 S1 +DIHEdral H13 C10 C13 H19 +DIHEdral H13 C10 C13 N2 +DIHEdral H13 C10 C9 C12 +DIHEdral H13 C10 C9 H11 +DIHEdral H13 C10 C9 S1 +DIHEdral H19 C13 C10 C9 +DIHEdral H19 C13 N2 H2 +DIHEdral H19 C13 N2 H3 +DIHEdral H19 C13 N2 C12 +DIHEdral N2 C12 C9 H11 +DIHEdral H2 N2 C12 H17 +DIHEdral H2 N2 C12 H18 +DIHEdral H2 N2 C12 C9 +DIHEdral H3 N2 C12 H17 +DIHEdral H3 N2 C12 H18 +DIHEdral H3 N2 C12 C9 +DIHEdral H17 C12 C9 H11 +DIHEdral H17 C12 C9 S1 +DIHEdral H18 C12 C9 H11 +DIHEdral H18 C12 C9 S1 +DIHEdral H11 C9 S1 C5 +DIHEdral S1 C5 C3 H6 +DIHEdral C5 C3 C8 H8 +DIHEdral C5 C3 C8 H9 +DIHEdral C5 C3 C8 H10 +DIHEdral C5 C3 C1 H4 +DIHEdral C6 C5 C3 H6 +DIHEdral C6 N1 C1 H4 +DIHEdral C3 C1 C2 H5 +DIHEdral C8 C3 C1 H4 +DIHEdral H8 C8 C3 H6 +DIHEdral H8 C8 C3 C1 +DIHEdral H9 C8 C3 H6 +DIHEdral H9 C8 C3 C1 +DIHEdral H10 C8 C3 H6 +DIHEdral H10 C8 C3 C1 +DIHEdral H6 C3 C1 H4 +DIHEdral H6 C3 C1 N1 +DIHEdral H6 C3 C1 C2 +DIHEdral C1 C2 C7 H7 +DIHEdral H4 C1 N1 C4 +DIHEdral H4 C1 C2 C4 +DIHEdral H4 C1 C2 H5 +DIHEdral H4 C1 C2 C7 +DIHEdral N1 C1 C2 H5 +DIHEdral N1 C4 C2 H5 +DIHEdral C4 C2 C7 H7 +DIHEdral O1 C4 C2 H5 +DIHEdral C2 C7 C11 H14 +DIHEdral C2 C7 C11 H15 +DIHEdral C2 C7 C11 H16 +DIHEdral C2 C7 O2 H1 +DIHEdral H5 C2 C7 C11 +DIHEdral H5 C2 C7 H7 +DIHEdral H5 C2 C7 O2 +DIHEdral C11 C7 O2 H1 +DIHEdral H14 C11 C7 H7 +DIHEdral H14 C11 C7 O2 +DIHEdral H15 C11 C7 H7 +DIHEdral H15 C11 C7 O2 +DIHEdral H16 C11 C7 H7 +DIHEdral H16 C11 C7 O2 +DIHEdral H7 C7 O2 H1 +DIHEdral C16 N3 C15 O5 +DIHEdral C16 N3 C15 C13 +DIHEdral N3 C15 C13 C10 +DIHEdral N3 C15 C13 N2 +DIHEdral C17 N3 C15 O5 +DIHEdral C17 N3 C15 C13 +DIHEdral C15 C13 C10 C9 +DIHEdral C15 C13 N2 C12 +DIHEdral O5 C15 C13 C10 +DIHEdral O5 C15 C13 N2 +DIHEdral C13 C10 C9 C12 +DIHEdral C13 C10 C9 S1 +DIHEdral C13 N2 C12 C9 +DIHEdral C10 C13 N2 C12 +DIHEdral C10 C9 C12 N2 +DIHEdral C10 C9 S1 C5 +DIHEdral N2 C13 C10 C9 +DIHEdral N2 C12 C9 S1 +DIHEdral C12 C9 S1 C5 +DIHEdral C9 S1 C5 C6 +DIHEdral C9 S1 C5 C3 +DIHEdral S1 C5 C6 C14 +DIHEdral S1 C5 C6 N1 +DIHEdral S1 C5 C3 C8 +DIHEdral S1 C5 C3 C1 +DIHEdral C5 C6 C14 O3 +DIHEdral C5 C6 C14 O4 +DIHEdral C5 C6 N1 C1 +DIHEdral C5 C6 N1 C4 +DIHEdral C5 C3 C1 N1 +DIHEdral C5 C3 C1 C2 +DIHEdral C6 C5 C3 C8 +DIHEdral C6 C5 C3 C1 +DIHEdral C6 N1 C1 C3 +DIHEdral C6 N1 C1 C2 +DIHEdral C6 N1 C4 O1 +DIHEdral C6 N1 C4 C2 +DIHEdral C14 C6 C5 C3 +DIHEdral C14 C6 N1 C1 +DIHEdral C14 C6 N1 C4 +DIHEdral O3 C14 C6 N1 +DIHEdral O4 C14 C6 N1 +DIHEdral C3 C5 C6 N1 +DIHEdral C3 C1 N1 C4 +DIHEdral C3 C1 C2 C4 +DIHEdral C3 C1 C2 C7 +DIHEdral C8 C3 C1 N1 +DIHEdral C8 C3 C1 C2 +DIHEdral C1 N1 C4 O1 +DIHEdral C1 N1 C4 C2 +DIHEdral C1 C2 C4 N1 +DIHEdral C1 C2 C4 O1 +DIHEdral C1 C2 C7 C11 +DIHEdral C1 C2 C7 O2 +DIHEdral N1 C1 C2 C4 +DIHEdral N1 C1 C2 C7 +DIHEdral N1 C4 C2 C7 +DIHEdral C4 N1 C1 C2 +DIHEdral C4 C2 C7 C11 +DIHEdral C4 C2 C7 O2 +DIHEdral O1 C4 C2 C7 + +{ Improper Dihedrals: aName1 aName2 aName3 aName4 } +IMPRoper C15 C16 N3 C17 +IMPRoper C13 N3 C15 O5 +IMPRoper C6 C3 C5 S1 +IMPRoper C14 C5 C6 N1 +IMPRoper C6 O3 C14 O4 +IMPRoper C4 C6 N1 C1 +IMPRoper C2 N1 C4 O1 + +END {RESIdue MER} + +! Minocycline +RESIdue MIY + +GROUP + +{ atomName atomType Charge } +ATOM O5 TYPE= O_ CHARGE= -0.5039 END +ATOM C10 TYPE= C_ CHARGE= 0.5574 END +ATOM C13 TYPE= CD_ CHARGE= -0.4821 END +ATOM C9 TYPE= C_ CHARGE= 0.3941 END +ATOM O3 TYPE= O_ CHARGE= -0.4945 END +ATOM C19 TYPE= C_ CHARGE= 0.7099 END +ATOM O7 TYPE= O_ CHARGE= -0.5545 END +ATOM N3 TYPE= N_ CHARGE= -0.8805 END +ATOM H18 TYPE= H_ CHARGE= 0.3708 END +ATOM H19 TYPE= H_ CHARGE= 0.3708 END +ATOM C5 TYPE= CT_ CHARGE= -0.3682 END +ATOM N1 TYPE= N3_ CHARGE= 0.1152 END +ATOM C16 TYPE= CT_ CHARGE= -0.2798 END +ATOM H9 TYPE= HP_ CHARGE= 0.1415 END +ATOM H10 TYPE= HP_ CHARGE= 0.1415 END +ATOM H11 TYPE= HP_ CHARGE= 0.1415 END +ATOM C17 TYPE= CT_ CHARGE= -0.2798 END +ATOM H12 TYPE= HP_ CHARGE= 0.1415 END +ATOM H13 TYPE= HP_ CHARGE= 0.1415 END +ATOM H14 TYPE= HP_ CHARGE= 0.1415 END +ATOM H27 TYPE= H_ CHARGE= 0.2734 END +ATOM H5 TYPE= HP_ CHARGE= 0.1654 END +ATOM C1 TYPE= CT_ CHARGE= 0.0375 END +ATOM C3 TYPE= CT_ CHARGE= -0.1602 END +ATOM H2 TYPE= HC_ CHARGE= 0.0767 END +ATOM H3 TYPE= HC_ CHARGE= 0.0767 END +ATOM H1 TYPE= HC_ CHARGE= 0.0819 END +ATOM C2 TYPE= CT_ CHARGE= 0.0453 END +ATOM O1 TYPE= OH_ CHARGE= -0.5877 END +ATOM H8 TYPE= HO_ CHARGE= 0.4321 END +ATOM C7 TYPE= CM_ CHARGE= 0.4169 END +ATOM O2 TYPE= OH_ CHARGE= -0.5247 END +ATOM H15 TYPE= HO_ CHARGE= 0.4418 END +ATOM C6 TYPE= CD_ CHARGE= -0.3888 END +ATOM C12 TYPE= C_ CHARGE= 0.5118 END +ATOM O4 TYPE= O_ CHARGE= -0.5544 END +ATOM C4 TYPE= CT_ CHARGE= 0.0534 END +ATOM H4 TYPE= HC_ CHARGE= 0.0308 END +ATOM C8 TYPE= CT_ CHARGE= 0.0438 END +ATOM H6 TYPE= HC_ CHARGE= 0.0398 END +ATOM H7 TYPE= HC_ CHARGE= 0.0398 END +ATOM C11 TYPE= CA_ CHARGE= -0.0429 END +ATOM C14 TYPE= CA_ CHARGE= -0.2639 END +ATOM C18 TYPE= CA_ CHARGE= 0.4048 END +ATOM O6 TYPE= OH_ CHARGE= -0.5374 END +ATOM H20 TYPE= HO_ CHARGE= 0.4171 END +ATOM C21 TYPE= CA_ CHARGE= -0.3197 END +ATOM H17 TYPE= HA_ CHARGE= 0.1786 END +ATOM C20 TYPE= CA_ CHARGE= -0.1119 END +ATOM H16 TYPE= HA_ CHARGE= 0.1345 END +ATOM C15 TYPE= CA_ CHARGE= 0.1444 END +ATOM N2 TYPE= N2_ CHARGE= -0.1576 END +ATOM C23 TYPE= CT_ CHARGE= -0.3869 END +ATOM H24 TYPE= H1_ CHARGE= 0.1421 END +ATOM H25 TYPE= H1_ CHARGE= 0.1421 END +ATOM H26 TYPE= H1_ CHARGE= 0.1421 END +ATOM C22 TYPE= CT_ CHARGE= -0.3869 END +ATOM H21 TYPE= H1_ CHARGE= 0.1421 END +ATOM H22 TYPE= H1_ CHARGE= 0.1421 END +ATOM H23 TYPE= H1_ CHARGE= 0.1421 END + +{ Bonds: atomName1 atomName2 } +BOND N3 H18 +BOND N3 H19 +BOND C5 H5 +BOND N1 H27 +BOND C16 H9 +BOND C16 H10 +BOND C16 H11 +BOND C17 H12 +BOND C17 H13 +BOND C17 H14 +BOND C1 H1 +BOND C3 H2 +BOND C3 H3 +BOND O1 H8 +BOND O2 H15 +BOND C4 H4 +BOND C8 H6 +BOND C8 H7 +BOND O6 H20 +BOND C21 H17 +BOND C20 H16 +BOND C23 H24 +BOND C23 H25 +BOND C23 H26 +BOND C22 H21 +BOND C22 H22 +BOND C22 H23 +BOND O5 C10 +BOND C10 C13 +BOND C10 C5 +BOND C13 C9 +BOND C13 C19 +BOND C9 O3 +BOND C9 C2 +BOND C19 O7 +BOND C19 N3 +BOND C5 N1 +BOND C5 C1 +BOND N1 C16 +BOND N1 C17 +BOND C1 C3 +BOND C1 C2 +BOND C3 C4 +BOND C2 O1 +BOND C2 C7 +BOND C7 O2 +BOND C7 C6 +BOND C6 C12 +BOND C6 C4 +BOND C12 O4 +BOND C12 C14 +BOND C4 C8 +BOND C8 C11 +BOND C11 C14 +BOND C11 C15 +BOND C14 C18 +BOND C18 O6 +BOND C18 C21 +BOND C21 C20 +BOND C20 C15 +BOND C15 N2 +BOND N2 C23 +BOND N2 C22 + +{ Angles: atomName1 atomName2 atomName3} +ANGLe C10 C5 H5 +ANGLe C19 N3 H18 +ANGLe C19 N3 H19 +ANGLe H18 N3 H19 +ANGLe C5 N1 H27 +ANGLe C5 C1 H1 +ANGLe N1 C16 H9 +ANGLe N1 C16 H10 +ANGLe N1 C16 H11 +ANGLe N1 C17 H12 +ANGLe N1 C17 H13 +ANGLe N1 C17 H14 +ANGLe N1 C5 H5 +ANGLe C16 N1 H27 +ANGLe H9 C16 H10 +ANGLe H9 C16 H11 +ANGLe H10 C16 H11 +ANGLe C17 N1 H27 +ANGLe H12 C17 H13 +ANGLe H12 C17 H14 +ANGLe H13 C17 H14 +ANGLe H5 C5 C1 +ANGLe C1 C3 H2 +ANGLe C1 C3 H3 +ANGLe C3 C4 H4 +ANGLe C3 C1 H1 +ANGLe H2 C3 H3 +ANGLe H2 C3 C4 +ANGLe H3 C3 C4 +ANGLe H1 C1 C2 +ANGLe C2 O1 H8 +ANGLe C7 O2 H15 +ANGLe C6 C4 H4 +ANGLe C4 C8 H6 +ANGLe C4 C8 H7 +ANGLe H4 C4 C8 +ANGLe H6 C8 H7 +ANGLe H6 C8 C11 +ANGLe H7 C8 C11 +ANGLe C18 O6 H20 +ANGLe C18 C21 H17 +ANGLe C21 C20 H16 +ANGLe H17 C21 C20 +ANGLe H16 C20 C15 +ANGLe N2 C23 H24 +ANGLe N2 C23 H25 +ANGLe N2 C23 H26 +ANGLe N2 C22 H21 +ANGLe N2 C22 H22 +ANGLe N2 C22 H23 +ANGLe H24 C23 H25 +ANGLe H24 C23 H26 +ANGLe H25 C23 H26 +ANGLe H21 C22 H22 +ANGLe H21 C22 H23 +ANGLe H22 C22 H23 +ANGLe O5 C10 C13 +ANGLe O5 C10 C5 +ANGLe C10 C13 C9 +ANGLe C10 C13 C19 +ANGLe C10 C5 N1 +ANGLe C10 C5 C1 +ANGLe C13 C9 O3 +ANGLe C13 C9 C2 +ANGLe C13 C19 O7 +ANGLe C13 C19 N3 +ANGLe C13 C10 C5 +ANGLe C9 C2 O1 +ANGLe C9 C2 C7 +ANGLe C9 C2 C1 +ANGLe C9 C13 C19 +ANGLe O3 C9 C2 +ANGLe O7 C19 N3 +ANGLe C5 N1 C16 +ANGLe C5 N1 C17 +ANGLe C5 C1 C3 +ANGLe C5 C1 C2 +ANGLe N1 C5 C1 +ANGLe C16 N1 C17 +ANGLe C1 C3 C4 +ANGLe C1 C2 O1 +ANGLe C1 C2 C7 +ANGLe C3 C4 C8 +ANGLe C3 C4 C6 +ANGLe C3 C1 C2 +ANGLe C2 C7 O2 +ANGLe C2 C7 C6 +ANGLe O1 C2 C7 +ANGLe C7 C6 C12 +ANGLe C7 C6 C4 +ANGLe O2 C7 C6 +ANGLe C6 C12 O4 +ANGLe C6 C12 C14 +ANGLe C6 C4 C8 +ANGLe C12 C14 C18 +ANGLe C12 C14 C11 +ANGLe C12 C6 C4 +ANGLe O4 C12 C14 +ANGLe C4 C8 C11 +ANGLe C8 C11 C14 +ANGLe C8 C11 C15 +ANGLe C11 C14 C18 +ANGLe C11 C15 N2 +ANGLe C11 C15 C20 +ANGLe C14 C18 O6 +ANGLe C14 C18 C21 +ANGLe C14 C11 C15 +ANGLe C18 C21 C20 +ANGLe O6 C18 C21 +ANGLe C21 C20 C15 +ANGLe C20 C15 N2 +ANGLe C15 N2 C23 +ANGLe C15 N2 C22 +ANGLe C23 N2 C22 + +{ Proper Dihedrals: name1 name2 name3 name4 } +DIHEdral O5 C10 C5 H5 +DIHEdral C10 C5 N1 H27 +DIHEdral C10 C5 C1 H1 +DIHEdral C13 C19 N3 H18 +DIHEdral C13 C19 N3 H19 +DIHEdral C13 C10 C5 H5 +DIHEdral C9 C2 O1 H8 +DIHEdral C9 C2 C1 H1 +DIHEdral O7 C19 N3 H18 +DIHEdral O7 C19 N3 H19 +DIHEdral C5 N1 C16 H9 +DIHEdral C5 N1 C16 H10 +DIHEdral C5 N1 C16 H11 +DIHEdral C5 N1 C17 H12 +DIHEdral C5 N1 C17 H13 +DIHEdral C5 N1 C17 H14 +DIHEdral C5 C1 C3 H2 +DIHEdral C5 C1 C3 H3 +DIHEdral N1 C5 C1 H1 +DIHEdral C16 N1 C17 H12 +DIHEdral C16 N1 C17 H13 +DIHEdral C16 N1 C17 H14 +DIHEdral C16 N1 C5 H5 +DIHEdral H9 C16 N1 C17 +DIHEdral H9 C16 N1 H27 +DIHEdral H10 C16 N1 C17 +DIHEdral H10 C16 N1 H27 +DIHEdral H11 C16 N1 C17 +DIHEdral H11 C16 N1 H27 +DIHEdral C17 N1 C5 H5 +DIHEdral H12 C17 N1 H27 +DIHEdral H13 C17 N1 H27 +DIHEdral H14 C17 N1 H27 +DIHEdral H27 N1 C5 H5 +DIHEdral H27 N1 C5 C1 +DIHEdral H5 C5 C1 C3 +DIHEdral H5 C5 C1 H1 +DIHEdral H5 C5 C1 C2 +DIHEdral C1 C3 C4 H4 +DIHEdral C1 C2 O1 H8 +DIHEdral C3 C4 C8 H6 +DIHEdral C3 C4 C8 H7 +DIHEdral H2 C3 C4 H4 +DIHEdral H2 C3 C4 C8 +DIHEdral H2 C3 C4 C6 +DIHEdral H2 C3 C1 H1 +DIHEdral H2 C3 C1 C2 +DIHEdral H3 C3 C4 H4 +DIHEdral H3 C3 C4 C8 +DIHEdral H3 C3 C4 C6 +DIHEdral H3 C3 C1 H1 +DIHEdral H3 C3 C1 C2 +DIHEdral H1 C1 C3 C4 +DIHEdral H1 C1 C2 O1 +DIHEdral H1 C1 C2 C7 +DIHEdral C2 C7 O2 H15 +DIHEdral H8 O1 C2 C7 +DIHEdral C7 C6 C4 H4 +DIHEdral H15 O2 C7 C6 +DIHEdral C6 C4 C8 H6 +DIHEdral C6 C4 C8 H7 +DIHEdral C12 C6 C4 H4 +DIHEdral H4 C4 C8 H6 +DIHEdral H4 C4 C8 H7 +DIHEdral H4 C4 C8 C11 +DIHEdral H6 C8 C11 C14 +DIHEdral H6 C8 C11 C15 +DIHEdral H7 C8 C11 C14 +DIHEdral H7 C8 C11 C15 +DIHEdral C11 C15 C20 H16 +DIHEdral C14 C18 O6 H20 +DIHEdral C14 C18 C21 H17 +DIHEdral C18 C21 C20 H16 +DIHEdral O6 C18 C21 H17 +DIHEdral H20 O6 C18 C21 +DIHEdral H17 C21 C20 H16 +DIHEdral H17 C21 C20 C15 +DIHEdral H16 C20 C15 N2 +DIHEdral C15 N2 C23 H24 +DIHEdral C15 N2 C23 H25 +DIHEdral C15 N2 C23 H26 +DIHEdral C15 N2 C22 H21 +DIHEdral C15 N2 C22 H22 +DIHEdral C15 N2 C22 H23 +DIHEdral C23 N2 C22 H21 +DIHEdral C23 N2 C22 H22 +DIHEdral C23 N2 C22 H23 +DIHEdral H24 C23 N2 C22 +DIHEdral H25 C23 N2 C22 +DIHEdral H26 C23 N2 C22 +DIHEdral O5 C10 C13 C9 +DIHEdral O5 C10 C13 C19 +DIHEdral O5 C10 C5 N1 +DIHEdral O5 C10 C5 C1 +DIHEdral C10 C13 C9 O3 +DIHEdral C10 C13 C9 C2 +DIHEdral C10 C13 C19 O7 +DIHEdral C10 C13 C19 N3 +DIHEdral C10 C5 N1 C16 +DIHEdral C10 C5 N1 C17 +DIHEdral C10 C5 C1 C3 +DIHEdral C10 C5 C1 C2 +DIHEdral C13 C9 C2 O1 +DIHEdral C13 C9 C2 C7 +DIHEdral C13 C9 C2 C1 +DIHEdral C13 C10 C5 N1 +DIHEdral C13 C10 C5 C1 +DIHEdral C9 C2 C7 O2 +DIHEdral C9 C2 C7 C6 +DIHEdral C9 C2 C1 C3 +DIHEdral C9 C2 C1 C5 +DIHEdral C9 C13 C19 O7 +DIHEdral C9 C13 C19 N3 +DIHEdral C9 C13 C10 C5 +DIHEdral O3 C9 C2 O1 +DIHEdral O3 C9 C2 C7 +DIHEdral O3 C9 C2 C1 +DIHEdral O3 C9 C13 C19 +DIHEdral C19 C13 C9 C2 +DIHEdral C19 C13 C10 C5 +DIHEdral C5 C1 C3 C4 +DIHEdral C5 C1 C2 O1 +DIHEdral C5 C1 C2 C7 +DIHEdral N1 C5 C1 C3 +DIHEdral N1 C5 C1 C2 +DIHEdral C16 N1 C5 C1 +DIHEdral C17 N1 C5 C1 +DIHEdral C1 C3 C4 C8 +DIHEdral C1 C3 C4 C6 +DIHEdral C1 C2 C7 O2 +DIHEdral C1 C2 C7 C6 +DIHEdral C3 C4 C8 C11 +DIHEdral C3 C4 C6 C12 +DIHEdral C3 C4 C6 C7 +DIHEdral C3 C1 C2 O1 +DIHEdral C3 C1 C2 C7 +DIHEdral C2 C7 C6 C12 +DIHEdral C2 C7 C6 C4 +DIHEdral C2 C1 C3 C4 +DIHEdral O1 C2 C7 O2 +DIHEdral O1 C2 C7 C6 +DIHEdral C7 C6 C12 O4 +DIHEdral C7 C6 C12 C14 +DIHEdral C7 C6 C4 C8 +DIHEdral O2 C7 C6 C12 +DIHEdral O2 C7 C6 C4 +DIHEdral C6 C12 C14 C18 +DIHEdral C6 C12 C14 C11 +DIHEdral C6 C4 C8 C11 +DIHEdral C12 C14 C18 O6 +DIHEdral C12 C14 C18 C21 +DIHEdral C12 C14 C11 C15 +DIHEdral C12 C14 C11 C8 +DIHEdral C12 C6 C4 C8 +DIHEdral O4 C12 C14 C18 +DIHEdral O4 C12 C14 C11 +DIHEdral O4 C12 C6 C4 +DIHEdral C4 C8 C11 C14 +DIHEdral C4 C8 C11 C15 +DIHEdral C4 C6 C12 C14 +DIHEdral C8 C11 C14 C18 +DIHEdral C8 C11 C15 N2 +DIHEdral C8 C11 C15 C20 +DIHEdral C11 C14 C18 O6 +DIHEdral C11 C14 C18 C21 +DIHEdral C11 C15 N2 C23 +DIHEdral C11 C15 N2 C22 +DIHEdral C11 C15 C20 C21 +DIHEdral C14 C18 C21 C20 +DIHEdral C14 C11 C15 N2 +DIHEdral C14 C11 C15 C20 +DIHEdral C18 C21 C20 C15 +DIHEdral C18 C14 C11 C15 +DIHEdral O6 C18 C21 C20 +DIHEdral C21 C20 C15 N2 +DIHEdral C20 C15 N2 C23 +DIHEdral C20 C15 N2 C22 + +{ Improper Dihedrals: aName1 aName2 aName3 aName4 } +IMPRoper C19 H18 N3 H19 +IMPRoper C18 C20 C21 H17 +IMPRoper C21 C15 C20 H16 +IMPRoper O5 C10 C5 C13 +IMPRoper C10 C9 C13 C19 +IMPRoper C13 C2 C9 O3 +IMPRoper C13 N3 C19 O7 +IMPRoper C6 C2 C7 O2 +IMPRoper C12 C7 C6 C4 +IMPRoper C14 C6 C12 O4 +IMPRoper C14 C15 C11 C8 +IMPRoper C12 C11 C14 C18 +IMPRoper C14 C21 C18 O6 +IMPRoper C11 C20 C15 N2 +IMPRoper C15 C23 N2 C22 + +END {RESIdue MIY} + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.pdb new file mode 100644 index 0000000000000000000000000000000000000000..260060607660d62533276279c634bdac945acda0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.pdb @@ -0,0 +1,87 @@ +REMARK FILENAME="test.pdb" +REMARK ================================================================ +REMARK overall,bonds,angles,impropers,vdw +REMARK energies: 0.813309, 6.626787E-02, 0.747041, 4.099165E-09, 7.625618E-11 +REMARK ================================================================ +REMARK bonds,angles,impropers +REMARK rms-d: 8.989687E-04,0.182045,2.320066E-05 +REMARK ================================================================ +REMARK produced by nmr/generate_template.inp +REMARK DATE:24-May-2004 15:58:37 created by user: abonvin +REMARK VERSION:1.1 +ATOM 1 FE HEC 400 3.565 0.487 0.949 1.00 0.00 +ATOM 2 NA HEC 400 2.428 0.067 -0.589 1.00 0.00 +ATOM 3 NB HEC 400 2.047 1.349 1.835 1.00 0.00 +ATOM 4 NC HEC 400 4.701 0.907 2.487 1.00 0.00 +ATOM 5 ND HEC 400 5.083 -0.375 0.062 1.00 0.00 +ATOM 6 C1A HEC 400 2.777 -0.593 -1.748 1.00 0.00 +ATOM 7 CHA HEC 400 4.031 -1.080 -2.015 1.00 0.00 +ATOM 8 HA HEC 400 4.181 -1.584 -2.970 1.00 0.00 +ATOM 9 C4D HEC 400 5.111 -0.982 -1.176 1.00 0.00 +ATOM 10 C1B HEC 400 0.758 1.490 1.367 1.00 0.00 +ATOM 11 CHB HEC 400 0.320 1.028 0.153 1.00 0.00 +ATOM 12 HB HEC 400 -0.725 1.202 -0.104 1.00 0.00 +ATOM 13 C4A HEC 400 1.093 0.363 -0.765 1.00 0.00 +ATOM 14 C1C HEC 400 4.353 1.567 3.646 1.00 0.00 +ATOM 15 CHC HEC 400 3.099 2.054 3.913 1.00 0.00 +ATOM 16 HC HEC 400 2.949 2.558 4.867 1.00 0.00 +ATOM 17 C4B HEC 400 2.019 1.956 3.073 1.00 0.00 +ATOM 18 C1D HEC 400 6.372 -0.516 0.530 1.00 0.00 +ATOM 19 CHD HEC 400 6.810 -0.054 1.745 1.00 0.00 +ATOM 20 HD HEC 400 7.855 -0.228 2.001 1.00 0.00 +ATOM 21 C4C HEC 400 6.037 0.611 2.662 1.00 0.00 +ATOM 22 C2A HEC 400 1.657 -0.708 -2.647 1.00 0.00 +ATOM 23 CAA HEC 400 1.655 -1.356 -3.989 1.00 0.00 +ATOM 24 HAA1 HEC 400 0.763 -1.959 -4.084 1.00 0.00 +ATOM 25 HAA2 HEC 400 2.520 -1.997 -4.069 1.00 0.00 +ATOM 26 CBA HEC 400 1.688 -0.336 -5.128 1.00 0.00 +ATOM 27 HBA1 HEC 400 0.817 0.300 -5.068 1.00 0.00 +ATOM 28 HBA2 HEC 400 1.689 -0.855 -6.076 1.00 0.00 +ATOM 29 CGA HEC 400 2.952 0.518 -5.012 1.00 0.00 +ATOM 30 O1A HEC 400 3.380 1.048 -6.024 1.00 0.00 +ATOM 31 O2A HEC 400 3.469 0.628 -3.913 1.00 0.00 +ATOM 32 C3A HEC 400 0.609 -0.113 -2.035 1.00 0.00 +ATOM 33 CMA HEC 400 -0.775 0.023 -2.569 1.00 0.00 +ATOM 34 HMA1 HEC 400 -0.815 -0.376 -3.572 1.00 0.00 +ATOM 35 HMA2 HEC 400 -1.053 1.067 -2.586 1.00 0.00 +ATOM 36 HMA3 HEC 400 -1.460 -0.522 -1.937 1.00 0.00 +ATOM 37 C2B HEC 400 -0.075 2.186 2.315 1.00 0.00 +ATOM 38 CMB HEC 400 -1.518 2.521 2.156 1.00 0.00 +ATOM 39 HMB1 HEC 400 -1.899 2.055 1.259 1.00 0.00 +ATOM 40 HMB2 HEC 400 -1.633 3.592 2.081 1.00 0.00 +ATOM 41 HMB3 HEC 400 -2.068 2.158 3.011 1.00 0.00 +ATOM 42 C3B HEC 400 0.710 2.476 3.377 1.00 0.00 +ATOM 43 CAB HEC 400 0.302 3.192 4.617 1.00 0.00 +ATOM 44 HAB HEC 400 0.638 4.217 4.569 1.00 0.00 +ATOM 45 CBB HEC 400 0.841 2.537 5.891 1.00 0.00 +ATOM 46 HBB1 HEC 400 1.196 1.544 5.662 1.00 0.00 +ATOM 47 HBB2 HEC 400 0.052 2.477 6.626 1.00 0.00 +ATOM 48 HBB3 HEC 400 1.654 3.129 6.283 1.00 0.00 +ATOM 49 C2C HEC 400 5.472 1.682 4.545 1.00 0.00 +ATOM 50 CMC HEC 400 5.475 2.330 5.886 1.00 0.00 +ATOM 51 HMC1 HEC 400 4.622 2.987 5.970 1.00 0.00 +ATOM 52 HMC2 HEC 400 6.383 2.902 6.008 1.00 0.00 +ATOM 53 HMC3 HEC 400 5.421 1.571 6.653 1.00 0.00 +ATOM 54 C3C HEC 400 6.520 1.087 3.932 1.00 0.00 +ATOM 55 CAC HEC 400 7.905 0.951 4.467 1.00 0.00 +ATOM 56 HAC HEC 400 8.472 1.838 4.228 1.00 0.00 +ATOM 57 CBC HEC 400 7.941 0.712 5.978 1.00 0.00 +ATOM 58 HBC1 HEC 400 6.953 0.450 6.325 1.00 0.00 +ATOM 59 HBC2 HEC 400 8.271 1.611 6.476 1.00 0.00 +ATOM 60 HBC3 HEC 400 8.626 -0.094 6.198 1.00 0.00 +ATOM 61 C2D HEC 400 7.204 -1.212 -0.417 1.00 0.00 +ATOM 62 CMD HEC 400 8.647 -1.547 -0.258 1.00 0.00 +ATOM 63 HMD1 HEC 400 8.984 -1.233 0.719 1.00 0.00 +ATOM 64 HMD2 HEC 400 9.221 -1.036 -1.017 1.00 0.00 +ATOM 65 HMD3 HEC 400 8.783 -2.613 -0.360 1.00 0.00 +ATOM 66 C3D HEC 400 6.419 -1.502 -1.479 1.00 0.00 +ATOM 67 CAD HEC 400 6.828 -2.218 -2.720 1.00 0.00 +ATOM 68 HAD1 HEC 400 5.945 -2.603 -3.208 1.00 0.00 +ATOM 69 HAD2 HEC 400 7.468 -3.046 -2.451 1.00 0.00 +ATOM 70 CBD HEC 400 7.577 -1.310 -3.697 1.00 0.00 +ATOM 71 HBD1 HEC 400 8.323 -1.887 -4.225 1.00 0.00 +ATOM 72 HBD2 HEC 400 8.059 -0.513 -3.150 1.00 0.00 +ATOM 73 CGD HEC 400 6.588 -0.715 -4.701 1.00 0.00 +ATOM 74 O1D HEC 400 6.218 -1.418 -5.626 1.00 0.00 +ATOM 75 O2D HEC 400 6.218 0.435 -4.527 1.00 0.00 +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.psf b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.psf new file mode 100644 index 0000000000000000000000000000000000000000..0c7fad7f53bc03837e13e8807f62dea43d8cb1f8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/heme.psf @@ -0,0 +1,525 @@ +data_cns_mtf + +_cns_mtf.title +; FILENAME="test.psf" + ================================================================ + overall,bonds,angles,impropers,vdw + energies: 0.813309, 6.626787E-02, 0.747041, 4.099165E-09, 7.625618E-11 + ================================================================ + bonds,angles,impropers + rms-d: 8.989687E-04,0.182045,2.320066E-05 + ================================================================ + produced by nmr/generate_template.inp + DATE:24-May-2004 15:58:44 created by user: abonvin + VERSION:1.1 +; + +loop_ +_cns_mtf_atom.id +_cns_mtf_atom.segment_id +_cns_mtf_atom.residue_id +_cns_mtf_atom.residue_name +_cns_mtf_atom.atom_name +_cns_mtf_atom.chemical_type +_cns_mtf_atom.charge +_cns_mtf_atom.atom_mass +1 ' ' '400' 'HEC' 'FE' 'FE' 0.240000 55.8470 +2 ' ' '400' 'HEC' 'NA' 'NPH' -0.180000 14.0070 +3 ' ' '400' 'HEC' 'NB' 'NPH' -0.180000 14.0070 +4 ' ' '400' 'HEC' 'NC' 'NPH' -0.180000 14.0070 +5 ' ' '400' 'HEC' 'ND' 'NPH' -0.180000 14.0070 +6 ' ' '400' 'HEC' 'C1A' 'CPA' 0.120000 12.0110 +7 ' ' '400' 'HEC' 'CHA' 'CPM' -0.100000 12.0110 +8 ' ' '400' 'HEC' 'HA' 'HA' 0.100000 9999.00 +9 ' ' '400' 'HEC' 'C4D' 'CPA' 0.120000 12.0110 +10 ' ' '400' 'HEC' 'C1B' 'CPA' 0.120000 12.0110 +11 ' ' '400' 'HEC' 'CHB' 'CPM' -0.100000 12.0110 +12 ' ' '400' 'HEC' 'HB' 'HA' 0.100000 9999.00 +13 ' ' '400' 'HEC' 'C4A' 'CPA' 0.120000 12.0110 +14 ' ' '400' 'HEC' 'C1C' 'CPA' 0.120000 12.0110 +15 ' ' '400' 'HEC' 'CHC' 'CPM' -0.100000 12.0110 +16 ' ' '400' 'HEC' 'HC' 'HA' 0.100000 9999.00 +17 ' ' '400' 'HEC' 'C4B' 'CPA' 0.120000 12.0110 +18 ' ' '400' 'HEC' 'C1D' 'CPA' 0.120000 12.0110 +19 ' ' '400' 'HEC' 'CHD' 'CPM' -0.100000 12.0110 +20 ' ' '400' 'HEC' 'HD' 'HA' 0.100000 9999.00 +21 ' ' '400' 'HEC' 'C4C' 'CPA' 0.120000 12.0110 +22 ' ' '400' 'HEC' 'C2A' 'CPB' -0.600000E-01 12.0110 +23 ' ' '400' 'HEC' 'CAA' 'CT' -0.180000 9999.00 +24 ' ' '400' 'HEC' 'HAA1' 'HA' 0.900000E-01 9999.00 +25 ' ' '400' 'HEC' 'HAA2' 'HA' 0.900000E-01 9999.00 +26 ' ' '400' 'HEC' 'CBA' 'CT' -0.280000 9999.00 +27 ' ' '400' 'HEC' 'HBA1' 'HA' 0.900000E-01 9999.00 +28 ' ' '400' 'HEC' 'HBA2' 'HA' 0.900000E-01 9999.00 +29 ' ' '400' 'HEC' 'CGA' 'C' 0.620000 9999.00 +30 ' ' '400' 'HEC' 'O1A' 'OC' -0.760000 9999.00 +31 ' ' '400' 'HEC' 'O2A' 'OC' -0.760000 9999.00 +32 ' ' '400' 'HEC' 'C3A' 'CPB' -0.600000E-01 12.0110 +33 ' ' '400' 'HEC' 'CMA' 'CT' -0.270000 9999.00 +34 ' ' '400' 'HEC' 'HMA1' 'HA' 0.900000E-01 9999.00 +35 ' ' '400' 'HEC' 'HMA2' 'HA' 0.900000E-01 9999.00 +36 ' ' '400' 'HEC' 'HMA3' 'HA' 0.900000E-01 9999.00 +37 ' ' '400' 'HEC' 'C2B' 'CPB' -0.600000E-01 12.0110 +38 ' ' '400' 'HEC' 'CMB' 'CT' -0.270000 9999.00 +39 ' ' '400' 'HEC' 'HMB1' 'HA' 0.900000E-01 9999.00 +40 ' ' '400' 'HEC' 'HMB2' 'HA' 0.900000E-01 9999.00 +41 ' ' '400' 'HEC' 'HMB3' 'HA' 0.900000E-01 9999.00 +42 ' ' '400' 'HEC' 'C3B' 'CPB' -0.600000E-01 12.0110 +43 ' ' '400' 'HEC' 'CAB' 'CT' -0.200000 9999.00 +44 ' ' '400' 'HEC' 'HAB' 'HA' 0.200000 9999.00 +45 ' ' '400' 'HEC' 'CBB' 'CT' -0.270000 9999.00 +46 ' ' '400' 'HEC' 'HBB1' 'HA' 0.900000E-01 9999.00 +47 ' ' '400' 'HEC' 'HBB2' 'HA' 0.900000E-01 9999.00 +48 ' ' '400' 'HEC' 'HBB3' 'HA' 0.900000E-01 9999.00 +49 ' ' '400' 'HEC' 'C2C' 'CPB' -0.600000E-01 12.0110 +50 ' ' '400' 'HEC' 'CMC' 'CT' -0.270000 9999.00 +51 ' ' '400' 'HEC' 'HMC1' 'HA' 0.900000E-01 9999.00 +52 ' ' '400' 'HEC' 'HMC2' 'HA' 0.900000E-01 9999.00 +53 ' ' '400' 'HEC' 'HMC3' 'HA' 0.900000E-01 9999.00 +54 ' ' '400' 'HEC' 'C3C' 'CPB' -0.600000E-01 12.0110 +55 ' ' '400' 'HEC' 'CAC' 'CT' -0.200000 9999.00 +56 ' ' '400' 'HEC' 'HAC' 'HA' 0.200000 9999.00 +57 ' ' '400' 'HEC' 'CBC' 'CT' -0.270000 9999.00 +58 ' ' '400' 'HEC' 'HBC1' 'HA' 0.900000E-01 9999.00 +59 ' ' '400' 'HEC' 'HBC2' 'HA' 0.900000E-01 9999.00 +60 ' ' '400' 'HEC' 'HBC3' 'HA' 0.900000E-01 9999.00 +61 ' ' '400' 'HEC' 'C2D' 'CPB' -0.600000E-01 12.0110 +62 ' ' '400' 'HEC' 'CMD' 'CT' -0.270000 9999.00 +63 ' ' '400' 'HEC' 'HMD1' 'HA' 0.900000E-01 9999.00 +64 ' ' '400' 'HEC' 'HMD2' 'HA' 0.900000E-01 9999.00 +65 ' ' '400' 'HEC' 'HMD3' 'HA' 0.900000E-01 9999.00 +66 ' ' '400' 'HEC' 'C3D' 'CPB' -0.600000E-01 12.0110 +67 ' ' '400' 'HEC' 'CAD' 'CT' -0.180000 9999.00 +68 ' ' '400' 'HEC' 'HAD1' 'HA' 0.900000E-01 9999.00 +69 ' ' '400' 'HEC' 'HAD2' 'HA' 0.900000E-01 9999.00 +70 ' ' '400' 'HEC' 'CBD' 'CT' -0.280000 9999.00 +71 ' ' '400' 'HEC' 'HBD1' 'HA' 0.900000E-01 9999.00 +72 ' ' '400' 'HEC' 'HBD2' 'HA' 0.900000E-01 9999.00 +73 ' ' '400' 'HEC' 'CGD' 'C' 0.620000 9999.00 +74 ' ' '400' 'HEC' 'O1D' 'OC' -0.760000 9999.00 +75 ' ' '400' 'HEC' 'O2D' 'OC' -0.760000 9999.00 +-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000 + +loop_ +_cns_mtf_bond.id[1] +_cns_mtf_bond.id[2] +1 2 +1 3 +1 4 +1 5 +2 6 +6 22 +22 32 +32 13 +2 13 +22 23 +23 26 +26 29 +29 30 +29 31 +32 33 +11 13 +11 10 +3 10 +10 37 +37 42 +42 17 +3 17 +37 38 +42 43 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+_cns_mtf_dihedral.id[4] +6 22 23 26 +22 23 26 29 +23 26 29 30 +61 66 67 70 +66 67 70 73 +67 70 73 74 +37 42 43 45 +42 43 45 46 +49 54 55 57 +54 55 57 58 +22 32 33 34 +10 37 38 39 +14 49 50 51 +18 61 62 63 +-1 -1 -1 -1 + +loop_ +_cns_mtf_improper.id[1] +_cns_mtf_improper.id[2] +_cns_mtf_improper.id[3] +_cns_mtf_improper.id[4] +22 6 32 23 +32 22 13 33 +37 10 42 38 +42 37 17 43 +49 14 54 50 +54 49 21 55 +61 18 66 62 +66 61 9 67 +29 26 31 30 +73 70 75 74 +13 2 6 22 +6 2 13 32 +17 3 10 37 +10 3 17 42 +21 4 14 49 +14 4 21 54 +9 5 18 61 +18 5 9 66 +2 6 22 32 +2 13 32 22 +3 10 37 42 +3 17 42 37 +4 14 49 54 +4 21 54 49 +5 18 61 66 +5 9 66 61 +2 6 7 9 +2 13 11 10 +3 10 11 13 +3 17 15 14 +4 14 15 17 +4 21 19 18 +5 18 19 21 +5 9 7 6 +7 6 9 8 +11 10 13 12 +15 14 17 16 +19 18 21 20 +6 22 7 2 +13 32 11 2 +10 37 11 3 +17 42 15 3 +14 49 15 4 +21 54 19 4 +18 61 19 5 +9 66 7 5 +2 6 13 1 +3 10 17 1 +4 14 21 1 +5 18 9 1 +-1 -1 -1 -1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.inb +-1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.iblo +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-1 + +loop_ +_cns_mtf_group_linked_list.first_atom_id +0 +5 +9 +13 +17 +21 +25 +31 +36 +41 +44 +48 +53 +56 +60 +65 +69 +-1 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.pdb new file mode 100644 index 0000000000000000000000000000000000000000..8276df49326e073709728e56299b7bf6d9a2173b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.pdb @@ -0,0 +1,77 @@ +REMARK FILENAME=".//begin/hemeB.pdb" +REMARK DATE:14-May-2010 11:45:28 created by user: abonvin +REMARK VERSION:1.2 +ATOM 1 FE HEB 500 3.565 0.487 0.949 1.00 15.00 +ATOM 2 NA HEB 500 2.428 0.067 -0.589 1.00 15.00 +ATOM 3 NB HEB 500 2.047 1.349 1.835 1.00 15.00 +ATOM 4 NC HEB 500 4.701 0.907 2.487 1.00 15.00 +ATOM 5 ND HEB 500 5.083 -0.375 0.062 1.00 15.00 +ATOM 6 C1A HEB 500 2.777 -0.593 -1.748 1.00 15.00 +ATOM 7 CHA HEB 500 4.031 -1.080 -2.015 1.00 15.00 +ATOM 8 HA HEB 500 4.181 -1.585 -2.969 1.00 15.00 +ATOM 9 C4D HEB 500 5.111 -0.982 -1.176 1.00 15.00 +ATOM 10 C1B HEB 500 0.758 1.490 1.367 1.00 15.00 +ATOM 11 CHB HEB 500 0.320 1.028 0.153 1.00 15.00 +ATOM 12 HB HEB 500 -0.725 1.203 -0.103 1.00 15.00 +ATOM 13 C4A HEB 500 1.093 0.363 -0.765 1.00 15.00 +ATOM 14 C1C HEB 500 4.353 1.567 3.646 1.00 15.00 +ATOM 15 CHC HEB 500 3.099 2.054 3.913 1.00 15.00 +ATOM 16 HC HEB 500 2.949 2.558 4.867 1.00 15.00 +ATOM 17 C4B HEB 500 2.019 1.956 3.073 1.00 15.00 +ATOM 18 C1D HEB 500 6.372 -0.516 0.530 1.00 15.00 +ATOM 19 CHD HEB 500 6.810 -0.054 1.745 1.00 15.00 +ATOM 20 HD HEB 500 7.855 -0.229 2.002 1.00 15.00 +ATOM 21 C4C HEB 500 6.037 0.611 2.662 1.00 15.00 +ATOM 22 C2A HEB 500 1.657 -0.708 -2.647 1.00 15.00 +ATOM 23 CAA HEB 500 1.655 -1.356 -3.989 1.00 15.00 +ATOM 24 HAA1 HEB 500 2.521 -1.997 -4.069 1.00 15.00 +ATOM 25 HAA2 HEB 500 0.764 -1.958 -4.085 1.00 15.00 +ATOM 26 CBA HEB 500 1.688 -0.336 -5.128 1.00 15.00 +ATOM 27 HBA1 HEB 500 0.817 0.300 -5.067 1.00 15.00 +ATOM 28 HBA2 HEB 500 1.690 -0.854 -6.075 1.00 15.00 +ATOM 29 CGA HEB 500 2.952 0.518 -5.012 1.00 15.00 +ATOM 30 O1A HEB 500 3.380 1.048 -6.024 1.00 15.00 +ATOM 31 O2A HEB 500 3.469 0.628 -3.913 1.00 15.00 +ATOM 32 C3A HEB 500 0.609 -0.113 -2.035 1.00 15.00 +ATOM 33 CMA HEB 500 -0.775 0.023 -2.569 1.00 15.00 +ATOM 34 HMA1 HEB 500 -1.005 1.069 -2.712 1.00 15.00 +ATOM 35 HMA2 HEB 500 -1.475 -0.407 -1.868 1.00 15.00 +ATOM 36 HMA3 HEB 500 -0.849 -0.494 -3.514 1.00 15.00 +ATOM 37 C2B HEB 500 -0.075 2.186 2.315 1.00 15.00 +ATOM 38 CMB HEB 500 -1.518 2.521 2.156 1.00 15.00 +ATOM 39 HMB1 HEB 500 -1.867 2.172 1.198 1.00 15.00 +ATOM 40 HMB2 HEB 500 -1.645 3.595 2.222 1.00 15.00 +ATOM 41 HMB3 HEB 500 -2.089 2.039 2.932 1.00 15.00 +ATOM 42 C3B HEB 500 0.710 2.476 3.377 1.00 15.00 +ATOM 43 CAB HEB 500 0.302 3.192 4.617 1.00 15.00 +ATOM 44 HAB HEB 500 -0.304 4.081 4.716 1.00 15.00 +ATOM 45 CBB HEB 500 0.841 2.537 5.891 1.00 15.00 +ATOM 46 HBB1 HEB 500 1.444 1.649 5.772 1.00 15.00 +ATOM 47 HBB2 HEB 500 0.585 3.003 6.831 1.00 15.00 +ATOM 48 C2C HEB 500 5.472 1.682 4.545 1.00 15.00 +ATOM 49 CMC HEB 500 5.475 2.330 5.886 1.00 15.00 +ATOM 50 HMC1 HEB 500 5.318 1.585 6.649 1.00 15.00 +ATOM 51 HMC2 HEB 500 4.683 3.068 5.928 1.00 15.00 +ATOM 52 HMC3 HEB 500 6.426 2.808 6.055 1.00 15.00 +ATOM 53 C3C HEB 500 6.520 1.087 3.932 1.00 15.00 +ATOM 54 CAC HEB 500 7.905 0.951 4.467 1.00 15.00 +ATOM 55 HAC HEB 500 8.843 1.000 3.934 1.00 15.00 +ATOM 56 CBC HEB 500 7.941 0.712 5.978 1.00 15.00 +ATOM 57 HBC1 HEB 500 6.993 0.667 6.493 1.00 15.00 +ATOM 58 HBC2 HEB 500 8.913 0.603 6.437 1.00 15.00 +ATOM 59 C2D HEB 500 7.204 -1.212 -0.417 1.00 15.00 +ATOM 60 CMD HEB 500 8.647 -1.547 -0.258 1.00 15.00 +ATOM 61 HMD1 HEB 500 9.217 -0.642 -0.129 1.00 15.00 +ATOM 62 HMD2 HEB 500 8.991 -2.073 -1.140 1.00 15.00 +ATOM 63 HMD3 HEB 500 8.781 -2.170 0.611 1.00 15.00 +ATOM 64 C3D HEB 500 6.419 -1.502 -1.479 1.00 15.00 +ATOM 65 CAD HEB 500 6.828 -2.218 -2.720 1.00 15.00 +ATOM 66 HAD1 HEB 500 5.945 -2.603 -3.208 1.00 15.00 +ATOM 67 HAD2 HEB 500 7.468 -3.045 -2.451 1.00 15.00 +ATOM 68 CBD HEB 500 7.577 -1.310 -3.697 1.00 15.00 +ATOM 69 HBD1 HEB 500 8.059 -0.513 -3.150 1.00 15.00 +ATOM 70 HBD2 HEB 500 8.323 -1.886 -4.225 1.00 15.00 +ATOM 71 CGD HEB 500 6.588 -0.715 -4.701 1.00 15.00 +ATOM 72 O1D HEB 500 6.218 -1.418 -5.626 1.00 15.00 +ATOM 73 O2D HEB 500 6.218 0.435 -4.527 1.00 15.00 +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.psf b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.psf new file mode 100644 index 0000000000000000000000000000000000000000..9d0c7af884b204f5abf932fc5d9bcecdf5e19e90 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemeB.psf @@ -0,0 +1,1013 @@ +data_cns_mtf + +_cns_mtf.title +; FILENAME=".//begin/hemeB.psf" + DATE:14-May-2010 11:45:28 created by user: abonvin + VERSION:1.2 +; + +loop_ +_cns_mtf_atom.id +_cns_mtf_atom.segment_id +_cns_mtf_atom.residue_id +_cns_mtf_atom.residue_name +_cns_mtf_atom.atom_name +_cns_mtf_atom.chemical_type +_cns_mtf_atom.charge +_cns_mtf_atom.atom_mass +1 'A' '500' 'HEB' 'FE' 'FEH' +3.00000 55.8470 +2 'A' '500' 'HEB' 'NA' 'NPH1' -0.180000 14.0070 +3 'A' '500' 'HEB' 'NB' 'NPH2' -0.180000 14.0070 +4 'A' '500' 'HEB' 'NC' 'NPH1' -0.180000 14.0070 +5 'A' '500' 'HEB' 'ND' 'NPH2' -0.180000 14.0070 +6 'A' '500' 'HEB' 'C1A' 'CPA' 0.120000 12.0110 +7 'A' '500' 'HEB' 'CHA' 'CPM' -0.100000 12.0110 +8 'A' '500' 'HEB' 'HA' 'HA' 0.100000 1.00800 +9 'A' '500' 'HEB' 'C4D' 'CPA' 0.120000 12.0110 +10 'A' '500' 'HEB' 'C1B' 'CPA' 0.120000 12.0110 +11 'A' '500' 'HEB' 'CHB' 'CPM' -0.100000 12.0110 +12 'A' '500' 'HEB' 'HB' 'HA' 0.100000 1.00800 +13 'A' '500' 'HEB' 'C4A' 'CPA' 0.120000 12.0110 +14 'A' '500' 'HEB' 'C1C' 'CPA' 0.120000 12.0110 +15 'A' '500' 'HEB' 'CHC' 'CPM' -0.100000 12.0110 +16 'A' '500' 'HEB' 'HC' 'HA' 0.100000 1.00800 +17 'A' '500' 'HEB' 'C4B' 'CPA' 0.120000 12.0110 +18 'A' '500' 'HEB' 'C1D' 'CPA' 0.120000 12.0110 +19 'A' '500' 'HEB' 'CHD' 'CPM' -0.100000 12.0110 +20 'A' '500' 'HEB' 'HD' 'HA' 0.100000 1.00800 +21 'A' '500' 'HEB' 'C4C' 'CPA' 0.120000 12.0110 +22 'A' '500' 'HEB' 'C2A' 'CPB' -0.600000E-01 12.0110 +23 'A' '500' 'HEB' 'CAA' 'CT' -0.180000 12.0110 +24 'A' '500' 'HEB' 'HAA1' 'HA' 0.900000E-01 1.00800 +25 'A' '500' 'HEB' 'HAA2' 'HA' 0.900000E-01 1.00800 +26 'A' '500' 'HEB' 'CBA' 'CT' -0.280000 12.0110 +27 'A' '500' 'HEB' 'HBA1' 'HA' 0.900000E-01 1.00800 +28 'A' '500' 'HEB' 'HBA2' 'HA' 0.900000E-01 1.00800 +29 'A' '500' 'HEB' 'CGA' 'C' 0.620000 12.0110 +30 'A' '500' 'HEB' 'O1A' 'OC' -0.760000 15.9994 +31 'A' '500' 'HEB' 'O2A' 'OC' -0.760000 15.9994 +32 'A' '500' 'HEB' 'C3A' 'CPB' -0.600000E-01 12.0110 +33 'A' '500' 'HEB' 'CMA' 'CT' -0.270000 12.0110 +34 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54 +53 21 19 +4 21 19 +48 49 50 +48 49 51 +48 49 52 +53 54 56 +53 54 55 +56 54 55 +54 56 57 +54 56 58 +21 19 18 +21 19 20 +19 18 5 +19 18 59 +18 19 20 +5 18 59 +18 5 9 +18 59 64 +18 59 60 +59 64 9 +64 59 60 +59 64 65 +64 9 5 +9 64 65 +64 9 7 +5 9 7 +59 60 61 +59 60 62 +59 60 63 +64 65 68 +64 65 66 +64 65 67 +65 68 71 +68 65 66 +68 65 67 +65 68 69 +65 68 70 +68 71 72 +68 71 73 +71 68 69 +71 68 70 +72 71 73 +9 7 6 +9 7 8 +6 7 8 +24 23 25 +27 26 28 +34 33 35 +34 33 36 +35 33 36 +39 38 40 +39 38 41 +40 38 41 +46 45 47 +50 49 51 +50 49 52 +51 49 52 +57 56 58 +61 60 62 +61 60 63 +62 60 63 +66 65 67 +69 68 70 +-1 -1 -1 + +loop_ +_cns_mtf_dihedral.id[1] +_cns_mtf_dihedral.id[2] +_cns_mtf_dihedral.id[3] +_cns_mtf_dihedral.id[4] +6 22 23 26 +22 23 26 29 +23 26 29 30 +59 64 65 68 +64 65 68 71 +65 68 71 72 +37 42 43 45 +48 53 54 56 +22 32 33 34 +10 37 38 39 +14 48 49 50 +18 59 60 61 +-1 -1 -1 -1 + +loop_ +_cns_mtf_improper.id[1] +_cns_mtf_improper.id[2] +_cns_mtf_improper.id[3] +_cns_mtf_improper.id[4] +22 6 32 23 +32 22 13 33 +37 10 42 38 +42 37 17 43 +48 14 53 49 +53 48 21 54 +59 18 64 60 +64 59 9 65 +29 26 31 30 +71 68 73 72 +13 2 6 22 +6 2 13 32 +17 3 10 37 +10 3 17 42 +21 4 14 48 +14 4 21 53 +9 5 18 59 +18 5 9 64 +2 6 22 32 +2 13 32 22 +3 10 37 42 +3 17 42 37 +4 14 48 53 +4 21 53 48 +5 18 59 64 +5 9 64 59 +2 6 7 9 +2 13 11 10 +3 10 11 13 +3 17 15 14 +4 14 15 17 +4 21 19 18 +5 18 19 21 +5 9 7 6 +7 6 9 8 +11 10 13 12 +15 14 17 16 +19 18 21 20 +6 22 7 2 +13 32 11 2 +10 37 11 3 +17 42 15 3 +14 48 15 4 +21 53 19 4 +18 59 19 5 +9 64 7 5 +2 6 13 1 +3 10 17 1 +4 14 21 1 +5 18 9 1 +43 45 42 44 +44 43 45 47 +45 43 47 46 +54 56 53 55 +55 54 56 58 +56 54 58 57 +34 35 22 36 +39 40 37 41 +50 51 48 52 +61 62 59 63 +-1 -1 -1 -1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.inb +-1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.iblo +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-1 + +loop_ +_cns_mtf_group_linked_list.first_atom_id +0 +5 +9 +13 +17 +21 +25 +31 +36 +41 +47 +52 +58 +63 +67 +-1 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.param new file mode 100644 index 0000000000000000000000000000000000000000..6130df1629f05b3243b3d0387e5b63914ce5f656 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.param @@ -0,0 +1,223 @@ +remark file parallhdg.hemes + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +evaluate ($kbon = 1000) +evaluate ($kang = 500) +evaluate ($kchi = 500) +evaluate ($kpla = 500) +evaluate ($kdih = 0) + + bond FEH NPH $kbon 1.96 + bond CPA NPH $kbon 1.38 + bond FEH NPH1 $kbon 1.96 + bond FEH NPH2 $kbon 1.96 + bond CPA NPH1 $kbon 1.38 + bond CPA NPH2 $kbon 1.38 + bond CPA CPB $kbon 1.44 + bond CPA CPM $kbon 1.37 + bond CPB CPB $kbon 1.35 + bond CPB CT $kbon 1.49 + bond CPB CHH $kbon 1.38 + bond CPM HA $kbon 1.09 + bond CHH CHH $kbon 1.53 + bond CHH OCH $kbon 1.25 + bond CT CHH $kbon 1.53 + bond CT CT $kbon 1.53 + bond CHH HA $kbon 1.08 + bond CT HA $kbon 1.08 + bond CT S $kbon 1.81 + bond CT SH1E $kbon 1.81 + bond FEH NB $kbon 2.10 ! Histidine ligand + bond FEH CYC $kbon 1.85 ! Cyanide ligand + bond CYC CYN $kbon 1.26 ! Cyanide ion + bond FEH S $kbon 2.30 ! Cystein ligand + + angle NPH FEH NPH $kang 90.0 + angle FEH NPH CPA $kang 128.0 + angle NPH CPA CPB $kang 111.6 + angle NPH CPA CPM $kang 124.4 + angle NPH1 FEH NPH2 $kang 90.0 + angle NPH1 FEH NPH1 $kang 180.0 !add angle + angle NPH2 FEH NPH2 $kang 180.0 !add angle + angle FEH NPH1 CPA $kang 128.0 + angle FEH NPH2 CPA $kang 128.0 + angle NPH1 CPA CPB $kang 111.6 + angle NPH1 CPA CPM $kang 124.4 + angle NPH2 CPA CPB $kang 111.6 + angle NPH2 CPA CPM $kang 124.4 + angle CHH CHH HA $kang 109.5 + angle CHH CHH CT $kang 109.5 + angle CHH CT CT $kang 109.5 + angle CHH CT HA $kang 109.5 + angle CH2E SH1E CT $kang 97.2 + angle CPA NPH CPA $kang 103.9 + angle CPA NPH1 CPA $kang 103.9 + angle CPA NPH2 CPA $kang 103.9 + angle CPA CPB CPB $kang 106.5 + angle CPA CPB CT $kang 126.8 + angle CPA CPB CHH $kang 126.8 + angle CPA CPM CPA $kang 125.1 + angle CPA CPM HA $kang 117.4 + angle CPB CPA CPM $kang 124.0 + angle CPB CPB CT $kang 126.8 + angle CPB CPB CHH $kang 126.8 + angle CPB CT CT $kang 113.0 + angle CPB CHH CHH $kang 121.5 + angle CPB CT HA $kang 109.5 + angle CPB CHH HA $kang 120.0 + angle CT CT HA $kang 109.5 + angle CT CT S $kang 109.5 + angle CT CT SH1E $kang 109.5 + angle CT CHH OCH $kang 118.0 + angle HA CT HA $kang 109.5 + angle HA CT S $kang 109.5 + angle HA CT SH1E $kang 109.5 + angle HA CHH HA $kang 118.0 + angle CV NB FEH 0.0 120.0 ! Histidine ligand, allow bending + angle CR NB FEH 0.0 130.0 ! Histidine ligand, allow bending + angle NB FEH NPH $kang 90.0 ! Histidine ligand + angle CYC FEH NPH $kang 90.0 ! Cyanide ligand + angle NB FEH NPH1 $kang 90.0 ! Histidine ligand + angle CYC FEH NPH1 $kang 90.0 ! Cyanide ligand + angle NB FEH NPH2 $kang 90.0 ! Histidine ligand + angle CYC FEH NPH2 $kang 90.0 ! Cyanide ligand + angle CYN CYC FEH $kang 180.0 ! Cyanide ligand + angle S CT CPB $kang 106.0 ! Heme CHthioether linkage + angle SH1E CT CPB $kang 106.0 ! Heme CHthioether linkage + angle OCH CHH OCH $kang 123.4 + angle CB S FEH $kang 109.7 ! Cystein ligand + angle S FEH NPH1 $kang 90.0 ! Cystein ligand + angle S FEH NPH2 $kang 90.0 ! Cystein ligand + + + improper CPA NPH CPA CPB $kpla 0 0.0 + improper NPH CPA CPB CPB $kpla 0 0.0 + improper NPH CPA CPM CPA $kpla 0 0.0 + improper CPA NPH1 CPA CPB $kpla 0 0.0 + improper NPH1 CPA CPB CPB $kpla 0 0.0 + improper NPH1 CPA CPM CPA $kpla 0 0.0 + improper CPA NPH2 CPA CPB $kpla 0 0.0 + improper NPH2 CPA CPB CPB $kpla 0 0.0 + improper NPH2 CPA CPM CPA $kpla 0 0.0 + improper HA CHH CHH HA $kpla 0 0.0 + improper HA HA CHH CHH $kpla 0 0.0 + improper HA CPB CHH CHH $kpla 0 0.0 + improper HA CT HA HA $kpla 0 -65.0 + improper HA CPB HA HA $kpla 0 -65.0 + + improper CPB CPA CPB CT $kchi 0 0.0 + improper CPB CPB CPA CT $kchi 0 0.0 + improper CPB CPB CPA CHH $kchi 0 0.0 + improper CPM CPA CPA HA $kchi 0 0.0 + improper CPA CPB CPM NPH1 $kchi 0 0.0 + improper NPH1 CPA CPA FEH $kchi 0 0.0 + improper CPA CPB CPM NPH2 $kchi 0 0.0 + improper NPH2 CPA CPA FEH $kchi 0 0.0 + improper CPA CPB CPM NPH $kchi 0 0.0 + improper NPH CPA CPA FEH $kchi 0 0.0 + improper CHH X X OCH $kchi 0 0.0 + + + improper S CT CPB HA $kchi 0 69.7 + improper SH1E CT CPB HA $kchi 0 69.7 + + dihedral CPA CPA CT CT $kdih 3 0.0 + dihedral CPB CT CT CHH $kdih 3 0.0 + dihedral CT CT CHH OCH $kdih 3 0.0 + dihedral CPB CPB CHH CHH $kdih 2 180.0 + dihedral X CT CT X $kdih 3 0.0 + dihedral X CT S X $kdih 2 0.0 + dihedral X CT SH1E X $kdih 2 0.0 + dihedral X CH2E SH1E X $kdih 2 0.0 + dihedral X CPA CT X $kdih 3 0.0 + dihedral X CPB CT X $kdih 3 0.0 + + + + nonbonded FEH 0.0001 1.0565 0.0001 1.0565 + nonbonded NPH 0.1592 3.0068 0.1592 3.0068 + nonbonded NPH1 0.1592 3.0068 0.1592 3.0068 + nonbonded NPH2 0.1592 3.0068 0.1592 3.0068 + nonbonded CYN 0.1592 3.0068 0.1592 3.0068 + nonbonded CPA 0.1200 3.3409 0.1200 3.3409 + nonbonded CPB 0.1200 3.3409 0.1200 3.3409 + nonbonded CPM 0.1200 3.3409 0.1200 3.3409 + nonbonded CYC 0.1200 3.3409 0.1200 3.3409 + nonbonded CT 0.1200 3.3409 0.1200 3.3409 + nonbonded HA 0.05 0.50 0.004 0.50 + nonbonded OCH 0.210 2.960 0.021 2.960 + NONBonded CHH 0.105 3.750 0.013 3.750 + +evaluate ($pd_x = 1.0) + +eval ($pd_v=$pd_x* 20000.0) BOND CN11 CN10 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN11 CN6 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN10 CN9 $pd_v 1.390 +eval ($pd_v=$pd_x* 16000.0) BOND CN9 CNL $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CN9 CN8 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN8 CN7 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN7 CN6 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN6 CN4 $pd_v 1.390 +eval ($pd_v=$pd_x* 20000.0) BOND CN4 CN2 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN4 NN3 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN2 NN1 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND NN1 CN5 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND CN5 NN3 $pd_v 1.330 +eval ($pd_v=$pd_x* 20000.0) BOND FEH NN1 $pd_v 2.300 + +eval ($pd_v=$pd_x* 800.0) ANGLE CN10 CN11 CN6 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN11 CN10 CN9 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN10 CN9 CNL $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN10 CN9 CN8 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CNL CN9 CN8 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN9 CN8 CN7 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN8 CN7 CN6 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN11 CN6 CN7 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN11 CN6 CN4 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN7 CN6 CN4 $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN6 CN4 CN2 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN6 CN4 NN3 $pd_v 126.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2 CN4 NN3 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN4 CN2 NN1 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2 NN1 CN5 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN1 CN5 NN3 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN4 NN3 CN5 $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN1 FEH NPH1 $pd_v 90.000 +eval ($pd_v=$pd_x* 800.0) ANGLE NN1 FEH NPH2 $pd_v 90.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CN2 NN1 FEH $pd_v 125.100 + +eval ($pd_v=$pd_x* 800.0) IMPR CN9 CN10 CN8 CNL $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN6 CN4 CN7 CN11 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN4 CN6 CN2 NN3 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN4 CN2 NN1 CN5 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN2 NN1 CN5 NN3 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN1 CN5 NN3 CN4 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN5 NN3 CN4 CN2 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR NN3 CN4 CN2 NN1 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN11 CN10 CN9 CN8 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN10 CN9 CN8 CN7 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN9 CN8 CN7 CN6 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN8 CN7 CN6 CN11 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN7 CN6 CN11 CN10 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CN6 CN11 CN10 CN9 $pd_v 0 0.000 + +eval ($pd_v=$pd_x* 19.6) DIHE CN11 CN6 CN4 NN3 $pd_v 2 180.000 + + +NONBONDED CN11 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN10 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN9 0.10000 3.29633 0.10000 3.02906 +NONBONDED CNL 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN8 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN7 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN6 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN4 0.10000 3.29633 0.10000 3.02906 +NONBONDED CN2 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN1 0.10000 2.67270 0.10000 2.40543 +NONBONDED CN5 0.10000 3.29633 0.10000 3.02906 +NONBONDED NN3 0.10000 2.67270 0.10000 2.40543 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.top new file mode 100644 index 0000000000000000000000000000000000000000..4de621ddcb8cb0666cd77ecb4c43e82c1653a979 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes-allhdg.top @@ -0,0 +1,708 @@ +remark file topallhdg.hemes + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +autogenerate + angles=true + dihedrals=false +end + +mass CPA 12.011 +mass CPB 12.011 +mass CPM 12.011 +mass CYC 12.011 +mass CT 12.011 +mass CHH 12.011 +mass NPH 14.007 +mass NPH1 14.007 +mass NPH2 14.007 +mass CYN 14.007 +mass OCH 15.9994 +mass FEH 55.847 +mass HA 1.008 + + +residue HEB ! Heme b + group + atom FE type=FEH charge= 0.24 end + atom NA type=NPH charge=-0.18 end + atom NB type=NPH charge=-0.18 end + atom NC type=NPH charge=-0.18 end + atom ND type=NPH charge=-0.18 end + group + atom C1A type=CPA charge= 0.12 end + atom CHA type=CPM charge=-0.10 end + atom HA type=HA charge= 0.10 end + atom C4D type=CPA charge= 0.12 end + group + atom C1B type=CPA charge= 0.12 end + atom CHB type=CPM charge=-0.10 end + atom HB type=HA charge= 0.10 end + atom C4A type=CPA charge= 0.12 end + group + atom C1C type=CPA charge= 0.12 end + atom CHC type=CPM charge=-0.10 end + atom HC type=HA charge= 0.10 end + atom C4B type=CPA charge= 0.12 end + group + atom C1D type=CPA charge= 0.12 end + atom CHD type=CPM charge=-0.10 end + atom HD type=HA charge= 0.10 end + atom C4C type=CPA charge= 0.12 end + group + atom C2A type=CPB charge=-0.06 end + atom CAA type=CT charge=-0.18 end + atom HAA1 type=HA charge= 0.09 end + atom HAA2 type=HA charge= 0.09 end + group + atom CBA type=CT charge=-0.28 end + atom HBA1 type=HA charge= 0.09 end + atom HBA2 type=HA charge= 0.09 end + atom CGA type=CHH charge= 0.62 end + atom O1A type=OCH charge=-0.76 end + atom O2A type=OCH charge=-0.76 end + group + atom C3A type=CPB charge=-0.06 end + atom CMA type=CT charge=-0.27 end + atom HMA1 type=HA charge= 0.09 end + atom HMA2 type=HA charge= 0.09 end + atom HMA3 type=HA charge= 0.09 end + group + atom C2B type=CPB charge=-0.06 end + atom CMB type=CT charge=-0.27 end + atom HMB1 type=HA charge= 0.09 end + atom HMB2 type=HA charge= 0.09 end + atom HMB3 type=HA charge= 0.09 end + group + atom C3B type=CPB charge=-0.06 end + atom CAB type=CHH charge=-0.20 end + atom HAB type=HA charge= 0.20 end + atom CBB type=CHH charge=-0.20 end + atom HBB1 type=HA charge= 0.10 end + atom HBB2 type=HA charge= 0.10 end + group + atom C2C type=CPB charge=-0.06 end + atom CMC type=CT charge=-0.27 end + atom HMC1 type=HA charge= 0.09 end + atom HMC2 type=HA charge= 0.09 end + atom HMC3 type=HA charge= 0.09 end + group + atom C3C type=CPB charge=-0.06 end + atom CAC type=CHH charge=-0.20 end + atom HAC type=HA charge= 0.20 end + atom CBC type=CHH charge=-0.20 end + atom HBC1 type=HA charge= 0.10 end + atom HBC2 type=HA charge= 0.10 end + group + atom C2D type=CPB charge=-0.06 end + atom CMD type=CT charge=-0.27 end + atom HMD1 type=HA charge= 0.09 end + atom HMD2 type=HA charge= 0.09 end + atom HMD3 type=HA charge= 0.09 end + group + atom C3D type=CPB charge=-0.06 end + atom CAD type=CT charge=-0.18 end + atom HAD1 type=HA charge= 0.09 end + atom HAD2 type=HA charge= 0.09 end + group + atom CBD type=CT charge=-0.28 end + atom HBD1 type=HA charge= 0.09 end + atom HBD2 type=HA charge= 0.09 end + atom CGD type=CHH charge= 0.62 end + atom O1D type=OCH charge=-0.76 end + atom O2D type=OCH charge=-0.76 end + + bond FE NA + bond FE NB + bond FE NC + bond FE ND + bond NA C1A + bond C1A C2A + bond C2A C3A + bond C3A C4A + bond NA C4A + bond C2A CAA + bond CAA CBA + bond CBA CGA + bond CGA O1A + bond CGA O2A + bond C3A CMA + bond CHB C4A + bond CHB C1B + bond NB C1B + bond C1B C2B + bond C2B C3B + bond C3B C4B + bond NB C4B + bond C2B CMB + bond C3B CAB + bond CAB CBB + bond CHC C4B + bond CHC C1C + bond NC C1C + bond C1C C2C + bond C2C C3C + bond C3C C4C + bond NC C4C + bond C2C CMC + bond C3C CAC + bond CAC CBC + bond CHD C4C + bond CHD C1D + bond ND C1D + bond C1D C2D + bond C2D C3D + bond C3D C4D + bond ND C4D + bond C2D CMD + bond C3D CAD + bond CAD CBD + bond CBD CGD + bond CGD O1D + bond CGD O2D + bond CHA C4D + bond CHA C1A + bond CHA HA + bond CHB HB + bond CHC HC + bond CHD HD + bond CAA HAA1 + bond CAA HAA2 + bond CBA HBA1 + bond CBA HBA2 + bond CMA HMA1 + bond CMA HMA2 + bond CMA HMA3 + bond CMB HMB1 + bond CMB HMB2 + bond CMB HMB3 + bond CAB HAB + bond CBB HBB1 + bond CBB HBB2 + bond CMC HMC1 + bond CMC HMC2 + bond CMC HMC3 + bond CAC HAC + bond CBC HBC1 + bond CBC HBC2 + bond CMD HMD1 + bond CMD HMD2 + bond CMD HMD3 + bond CAD HAD1 + bond CAD HAD2 + bond CBD HBD1 + bond CBD HBD2 + + omit angle NA FE NC + omit angle NB FE ND + + improper C2A C1A C3A CAA + improper C3A C2A C4A CMA + improper C2B C1B C3B CMB + improper C3B C2B C4B CAB + improper C2C C1C C3C CMC + improper C3C C2C C4C CAC + improper C2D C1D C3D CMD + improper C3D C2D C4D CAD + improper CGA CBA O2A O1A + improper CGD CBD O2D O1D + improper C4A NA C1A C2A + improper C1A NA C4A C3A + improper C4B NB C1B C2B + improper C1B NB C4B C3B + improper C4C NC C1C C2C + improper C1C NC C4C C3C + improper C4D ND C1D C2D + improper C1D ND C4D C3D + improper NA C1A C2A C3A + improper NA C4A C3A C2A + improper NB C1B C2B C3B + improper NB C4B C3B C2B + improper NC C1C C2C C3C + improper NC C4C C3C C2C + improper ND C1D C2D C3D + improper ND C4D C3D C2D + improper NA C1A CHA C4D + improper NA C4A CHB C1B + improper NB C1B CHB C4A + improper NB C4B CHC C1C + improper NC C1C CHC C4B + improper NC C4C CHD C1D + improper ND C1D CHD C4C + improper ND C4D CHA C1A + improper CHA C1A C4D HA + improper CHB C1B C4A HB + improper CHC C1C C4B HC + improper CHD C1D C4C HD + improper C1A C2A CHA NA + improper C4A C3A CHB NA + improper C1B C2B CHB NB + improper C4B C3B CHC NB + improper C1C C2C CHC NC + improper C4C C3C CHD NC + improper C1D C2D CHD ND + improper C4D C3D CHA ND + improper NA C1A C4A FE + improper NB C1B C4B FE + improper NC C1C C4C FE + improper ND C1D C4D FE + improper CAB CBB C3B HAB + improper HAB CAB CBB HBB2 + improper CBB CAB HBB2 HBB1 + improper CAC CBC C3C HAC + improper HAC CAC CBC HBC2 + improper CBC CAC HBC2 HBC1 + improper HMA1 HMA2 C2A HMA3 + improper HMB1 HMB2 C2B HMB3 + improper HMC1 HMC2 C2C HMC3 + improper HMD1 HMD2 C2D HMD3 + + dihedral C1A C2A CAA CBA + dihedral C2A CAA CBA CGA + dihedral CAA CBA CGA O1A + dihedral C2D C3D CAD CBD + dihedral C3D CAD CBD CGD + dihedral CAD CBD CGD O1D + dihedral C2B C3B CAB CBB + dihedral C2C C3C CAC CBC + dihedral C2A C3A CMA HMA1 + dihedral C1B C2B CMB HMB1 + dihedral C1C C2C CMC HMC1 + dihedral C1D C2D CMD HMD1 + +end + +residue HEC ! Heme c + group + atom FE type=FEH charge= 0.24 end + atom NA type=NPH charge=-0.18 end + atom NB type=NPH charge=-0.18 end + atom NC type=NPH charge=-0.18 end + atom ND type=NPH charge=-0.18 end + group + atom C1A type=CPA charge= 0.12 end + atom CHA type=CPM charge=-0.10 end + atom HA type=HA charge= 0.10 end + atom C4D type=CPA charge= 0.12 end + group + atom C1B type=CPA charge= 0.12 end + atom CHB type=CPM charge=-0.10 end + atom HB type=HA charge= 0.10 end + atom C4A type=CPA charge= 0.12 end + group + atom C1C type=CPA charge= 0.12 end + atom CHC type=CPM charge=-0.10 end + atom HC type=HA charge= 0.10 end + atom C4B type=CPA charge= 0.12 end + group + atom C1D type=CPA charge= 0.12 end + atom CHD type=CPM charge=-0.10 end + atom HD type=HA charge= 0.10 end + atom C4C type=CPA charge= 0.12 end + group + atom C2A type=CPB charge=-0.06 end + atom CAA type=CT charge=-0.18 end + atom HAA1 type=HA charge= 0.09 end + atom HAA2 type=HA charge= 0.09 end + group + atom CBA type=CT charge=-0.28 end + atom HBA1 type=HA charge= 0.09 end + atom HBA2 type=HA charge= 0.09 end + atom CGA type=CHH charge= 0.62 end + atom O1A type=OCH charge=-0.76 end + atom O2A type=OCH charge=-0.76 end + group + atom C3A type=CPB charge=-0.06 end + atom CMA type=CT charge=-0.27 end + atom HMA1 type=HA charge= 0.09 end + atom HMA2 type=HA charge= 0.09 end + atom HMA3 type=HA charge= 0.09 end + group + atom C2B type=CPB charge=-0.06 end + atom CMB type=CT charge=-0.27 end + atom HMB1 type=HA charge= 0.09 end + atom HMB2 type=HA charge= 0.09 end + atom HMB3 type=HA charge= 0.09 end + group + atom C3B type=CPB charge=-0.06 end + atom CAB type=CT charge=-0.20 end + atom HAB type=HA charge= 0.20 end + group + atom CBB type=CT charge=-0.27 end + atom HBB1 type=HA charge= 0.09 end + atom HBB2 type=HA charge= 0.09 end + atom HBB3 type=HA charge= 0.09 end + group + atom C2C type=CPB charge=-0.06 end + atom CMC type=CT charge=-0.27 end + atom HMC1 type=HA charge= 0.09 end + atom HMC2 type=HA charge= 0.09 end + atom HMC3 type=HA charge= 0.09 end + group + atom C3C type=CPB charge=-0.06 end + atom CAC type=CT charge=-0.20 end + atom HAC type=HA charge= 0.20 end + group + atom CBC type=CT charge=-0.27 end + atom HBC1 type=HA charge= 0.09 end + atom HBC2 type=HA charge= 0.09 end + atom HBC3 type=HA charge= 0.09 end + group + atom C2D type=CPB charge=-0.06 end + atom CMD type=CT charge=-0.27 end + atom HMD1 type=HA charge= 0.09 end + atom HMD2 type=HA charge= 0.09 end + atom HMD3 type=HA charge= 0.09 end + group + atom C3D type=CPB charge=-0.06 end + atom CAD type=CT charge=-0.18 end + atom HAD1 type=HA charge= 0.09 end + atom HAD2 type=HA charge= 0.09 end + group + atom CBD type=CT charge=-0.28 end + atom HBD1 type=HA charge= 0.09 end + atom HBD2 type=HA charge= 0.09 end + atom CGD type=CHH charge= 0.62 end + atom O1D type=OCH charge=-0.76 end + atom O2D type=OCH charge=-0.76 end + + bond FE NA + bond FE NB + bond FE NC + bond FE ND + bond NA C1A + bond C1A C2A + bond C2A C3A + bond C3A C4A + bond NA C4A + bond C2A CAA + bond CAA CBA + bond CBA CGA + bond CGA O1A + bond CGA O2A + bond C3A CMA + bond CHB C4A + bond CHB C1B + bond NB C1B + bond C1B C2B + bond C2B C3B + bond C3B C4B + bond NB C4B + bond C2B CMB + bond C3B CAB + bond CAB CBB + bond CHC C4B + bond CHC C1C + bond NC C1C + bond C1C C2C + bond C2C C3C + bond C3C C4C + bond NC C4C + bond C2C CMC + bond C3C CAC + bond CAC CBC + bond CHD C4C + bond CHD C1D + bond ND C1D + bond C1D C2D + bond C2D C3D + bond C3D C4D + bond ND C4D + bond C2D CMD + bond C3D CAD + bond CAD CBD + bond CBD CGD + bond CGD O1D + bond CGD O2D + bond CHA C4D + bond CHA C1A + bond CHA HA + bond CHB HB + bond CHC HC + bond CHD HD + bond CAA HAA1 + bond CAA HAA2 + bond CBA HBA1 + bond CBA HBA2 + bond CMA HMA1 + bond CMA HMA2 + bond CMA HMA3 + bond CMB HMB1 + bond CMB HMB2 + bond CMB HMB3 + bond CAB HAB + bond CBB HBB1 + bond CBB HBB2 + bond CBB HBB3 + bond CMC HMC1 + bond CMC HMC2 + bond CMC HMC3 + bond CAC HAC + bond CBC HBC1 + bond CBC HBC2 + bond CBC HBC3 + bond CMD HMD1 + bond CMD HMD2 + bond CMD HMD3 + bond CAD HAD1 + bond CAD HAD2 + bond CBD HBD1 + bond CBD HBD2 + + omit angle NA FE NC + omit angle NB FE ND + + improper C2A C1A C3A CAA + improper C3A C2A C4A CMA + improper C2B C1B C3B CMB + improper C3B C2B C4B CAB + improper C2C C1C C3C CMC + improper C3C C2C C4C CAC + improper C2D C1D C3D CMD + improper C3D C2D C4D CAD + improper CGA CBA O2A O1A + improper CGD CBD O2D O1D + improper C4A NA C1A C2A + improper C1A NA C4A C3A + improper C4B NB C1B C2B + improper C1B NB C4B C3B + improper C4C NC C1C C2C + improper C1C NC C4C C3C + improper C4D ND C1D C2D + improper C1D ND C4D C3D + improper NA C1A C2A C3A + improper NA C4A C3A C2A + improper NB C1B C2B C3B + improper NB C4B C3B C2B + improper NC C1C C2C C3C + improper NC C4C C3C C2C + improper ND C1D C2D C3D + improper ND C4D C3D C2D + improper NA C1A CHA C4D + improper NA C4A CHB C1B + improper NB C1B CHB C4A + improper NB C4B CHC C1C + improper NC C1C CHC C4B + improper NC C4C CHD C1D + improper ND C1D CHD C4C + improper ND C4D CHA C1A + improper CHA C1A C4D HA + improper CHB C1B C4A HB + improper CHC C1C C4B HC + improper CHD C1D C4C HD + improper C1A C2A CHA NA + improper C4A C3A CHB NA + improper C1B C2B CHB NB + improper C4B C3B CHC NB + improper C1C C2C CHC NC + improper C4C C3C CHD NC + improper C1D C2D CHD ND + improper C4D C3D CHA ND + improper NA C1A C4A FE + improper NB C1B C4B FE + improper NC C1C C4C FE + improper ND C1D C4D FE + improper HBB1 HBB2 CAB HBB3 + improper HBC1 HBC2 CAC HBC3 + improper HMA1 HMA2 C3A HMCA + improper HMC1 HMC2 C2C HMC3 + improper HMD1 HMD2 C2D HMD3 + + dihedral C1A C2A CAA CBA + dihedral C2A CAA CBA CGA + dihedral CAA CBA CGA O1A + dihedral C2D C3D CAD CBD + dihedral C3D CAD CBD CGD + dihedral CAD CBD CGD O1D + dihedral C2B C3B CAB CBB + dihedral C3B CAB CBB HBB1 + dihedral C2C C3C CAC CBC + dihedral C3C CAC CBC HBC1 + dihedral C2A C3A CMA HMA1 + dihedral C1B C2B CMB HMB1 + dihedral C1C C2C CMC HMC1 + dihedral C1D C2D CMD HMD1 + +end + +residue CYA ! Cyanide ion + group + atom C type=CYC charge= 0.00 end + atom N type=CYN charge= 0.00 end + + bond C N +end + +presidue PCYA ! Patch residue for 1=CYA and 2=HEC + add bond 1C 2FE + + add angle 1N 1C 2FE + add angle 1C 2FE 2NA + add angle 1C 2FE 2NB + add angle 1C 2FE 2NC + add angle 1C 2FE 2ND +end + +presidue PHEM ! Patch residue for 1=HIS and 2=HEB, or 2=HEC + add bond 1NE2 2FE + + add angle 1CD2 1NE2 2FE + add angle 1CE1 1NE2 2FE + add angle 1NE2 2FE 2NA + add angle 1NE2 2FE 2NB + add angle 1NE2 2FE 2NC + add angle 1NE2 2FE 2ND +end + +presidue PHCB ! Patch residue for 1=CYS and 2=HEC (CAB carbon) + delete atom 1HG end + + modify atom 1SG charge= 0.00 end + + add bond 1SG 2CAB + + add angle 1CB 1SG 2CAB + add angle 1SG 2CAB 2C3B + add angle 1SG 2CAB 2HAB + add angle 1SG 2CAB 2CBB + + add dihedral 1CA 1CB 1SG 2CAB + add dihedral 1CB 1SG 2CAB 2C3B + add dihedral 1SG 2CAB 2C3B 2C2B + + add improper 1SG 2CBB 2C3B 2HAB +end + +presidue PHEB ! Patch residue for 1=CYS and 2=HEB (FE) + delete atom 1HG end + + modify atom 1SG charge= 0.00 end + + add bond 1SG 2FE + + add angle 1CB 1SG 2FE + add angle 1SG 2FE 2NA + add angle 1SG 2FE 2NB + add angle 1SG 2FE 2NC + add angle 1SG 2FE 2ND +end + +presidue PHCH ! Patch residue for 1=CPZ and 2=HEB (FE) + add bond 1N1 2FE + + modify atom 1N1 charge= 0.00 end + + add angle 1C2 1N1 2FE + add angle 1N1 2FE 2NA + add angle 1N1 2FE 2NB + add angle 1N1 2FE 2NC + add angle 1N1 2FE 2ND +end + +presidue PHCC ! Patch residue for 1=CYS and 2=HEC (CAC carbon) + delete atom 1HG end + + modify atom 1SG charge= 0.00 end + + add bond 1SG 2CAC + + add angle 1CB 1SG 2CAC + add angle 1SG 2CAC 2C3C + add angle 1SG 2CAC 2HAC + add angle 1SG 2CAC 2CBC + + add dihedral 1CA 1CB 1SG 2CAC + add dihedral 1CB 1SG 2CAC 2C3C + add dihedral 1SG 2CAC 2C3C 2C2C + + add improper 1SG 2CBC 2C3C 2HAC +end + +AUTOGENERATE ANGLES=FALSE END +MASS CN11 13.0190 ! equivalent to CR61 +MASS CN10 13.0190 ! equivalent to CR61 +MASS CN9 12.0110 ! equivalent to CB +MASS CNL 15.0350 ! equivalent to CH3 +MASS CN8 13.0190 ! equivalent to CR61 +MASS CN7 13.0190 ! equivalent to CR61 +MASS CN6 12.0110 ! equivalent to CB +MASS CN4 12.0110 ! equivalent to CB +MASS CN2 13.0190 ! equivalent to CR51 +MASS NN1 14.0067 ! equivalent to NR5* +MASS CN5 13.0190 ! equivalent to CR51 +MASS NN3 14.0067 ! equivalent to NR5 + +Residue CPH +GROUP + ATOM C11 TYPE= CN11 CHARGE=-0.007 END + ATOM C10 TYPE= CN10 CHARGE=-0.007 END + ATOM C9 TYPE= CN9 CHARGE= 0.007 END + ATOM CL TYPE= CNL CHARGE= 0.034 END + ATOM C8 TYPE= CN8 CHARGE=-0.007 END + ATOM C7 TYPE= CN7 CHARGE=-0.007 END + ATOM C6 TYPE= CN6 CHARGE= 0.007 END + ATOM C4 TYPE= CN4 CHARGE= 0.099 END + ATOM C2 TYPE= CN2 CHARGE=-0.007 END + ATOM N1 TYPE= NN1 CHARGE= 0.159 END + ATOM C5 TYPE= CN5 CHARGE=-0.007 END + ATOM N3 TYPE= NN3 CHARGE=-0.284 END + + BOND C11 C10 + BOND C11 C6 + BOND C10 C9 + BOND C9 CL + BOND C9 C8 + BOND C8 C7 + BOND C7 C6 + BOND C6 C4 + BOND C4 C2 + BOND C4 N3 + BOND C2 N1 + BOND N1 C5 + BOND C5 N3 + BOND FE N1 + + ANGLE C10 C11 C6 + ANGLE C11 C10 C9 + ANGLE C10 C9 CL + ANGLE C10 C9 C8 + ANGLE CL C9 C8 + ANGLE C9 C8 C7 + ANGLE C8 C7 C6 + ANGLE C11 C6 C7 + ANGLE C11 C6 C4 + ANGLE C7 C6 C4 + ANGLE C6 C4 C2 + ANGLE C6 C4 N3 + ANGLE C2 C4 N3 + ANGLE C4 C2 N1 + ANGLE C2 N1 C5 + ANGLE N1 C5 N3 + ANGLE C4 N3 C5 + ANGLE N1 FE NA + ANGLE N1 FE NB + ANGLE N1 FE NC + ANGLE N1 FE ND + ANGLE C2 N1 FE + + IMPROPER C9 C10 C8 CL + IMPROPER C6 C4 C7 C11 + IMPROPER C4 C6 C2 N3 + IMPROPER C4 C2 N1 C5 + IMPROPER C2 N1 C5 N3 + IMPROPER N1 C5 N3 C4 + IMPROPER C5 N3 C4 C2 + IMPROPER N3 C4 C2 N1 + IMPROPER C11 C10 C9 C8 + IMPROPER C10 C9 C8 C7 + IMPROPER C9 C8 C7 C6 + IMPROPER C8 C7 C6 C11 + IMPROPER C7 C6 C11 C10 + IMPROPER C6 C11 C10 C9 + + DIHEDRAL C11 C6 C4 N3 +END + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes.pep b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/hemes.pep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/._trans_vector_0 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/._trans_vector_0 new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and 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b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/._trans_vector_9 differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_0 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_0 new file mode 100644 index 0000000000000000000000000000000000000000..afb4c09eeb639cdfc018fd9fdaee303799d89299 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_0 @@ -0,0 +1,3 @@ +evaluate($x_1 = $spacing * 0.000000 ) +evaluate($y_1 = $spacing * 0.000000 ) +evaluate($z_1 = $spacing * 0.000000 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_1 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_1 new file mode 100644 index 0000000000000000000000000000000000000000..819b54aaf9a5d7855e4b1b3a26534b2fd22bb59e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_1 @@ -0,0 +1,3 @@ +evaluate ($x_1 = $spacing * 1.000000 ) +evaluate($y_1 = $spacing * 0.000000 ) +evaluate($z_1 = $spacing * 0.000000 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_10 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_10 new file mode 100644 index 0000000000000000000000000000000000000000..205b2be91284643327ff2a320d15f956d9fa512c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_10 @@ -0,0 +1,30 @@ +evaluate ($x_1 = $spacing * 0.476658 ) +evaluate($y_1 = $spacing * -0.874002 ) +evaluate($z_1 = $spacing * -0.094435 ) +evaluate ($x_2 = $spacing * -0.448934 ) +evaluate($y_2 = $spacing * -0.776287 ) +evaluate($z_2 = $spacing * 0.442534 ) +evaluate ($x_3 = $spacing * -0.258662 ) +evaluate($y_3 = $spacing * -0.537976 ) +evaluate($z_3 = $spacing * -0.802294 ) +evaluate ($x_4 = $spacing * 0.661654 ) +evaluate($y_4 = $spacing * -0.200856 ) +evaluate($z_4 = $spacing * 0.722406 ) +evaluate ($x_5 = $spacing * -0.986736 ) +evaluate($y_5 = $spacing * -0.037401 ) +evaluate($z_5 = $spacing * -0.157968 ) +evaluate ($x_6 = $spacing * 0.851811 ) +evaluate($y_6 = $spacing * 0.037401 ) +evaluate($z_6 = $spacing * -0.522512 ) +evaluate ($x_7 = $spacing * -0.335959 ) +evaluate($y_7 = $spacing * 0.200856 ) +evaluate($z_7 = $spacing * 0.920211 ) +evaluate ($x_8 = $spacing * -0.067028 ) +evaluate($y_8 = $spacing * 0.537976 ) +evaluate($z_8 = $spacing * -0.840291 ) +evaluate ($x_9 = $spacing * 0.583822 ) +evaluate($y_9 = $spacing * 0.776287 ) +evaluate($z_9 = $spacing * 0.237761 ) +evaluate ($x_10 = $spacing * -0.476629 ) +evaluate($y_10 = $spacing * 0.874002 ) +evaluate($z_10 = $spacing * 0.094582 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_11 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_11 new file mode 100644 index 0000000000000000000000000000000000000000..269d94aab7cd569bb88e5d66d9552faaa31eb58d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_11 @@ -0,0 +1,33 @@ +evaluate ($x_1 = $spacing * 0.520608 ) +evaluate($y_1 = $spacing * -0.841959 ) +evaluate($z_1 = $spacing * -0.141676 ) +evaluate ($x_2 = $spacing * -0.382941 ) +evaluate($y_2 = $spacing * -0.818783 ) +evaluate($z_2 = $spacing * 0.427727 ) +evaluate ($x_3 = $spacing * -0.260271 ) +evaluate($y_3 = $spacing * -0.639964 ) +evaluate($z_3 = $spacing * -0.722984 ) +evaluate ($x_4 = $spacing * 0.642273 ) +evaluate($y_4 = $spacing * -0.320721 ) +evaluate($z_4 = $spacing * 0.696149 ) +evaluate ($x_5 = $spacing * -0.992186 ) +evaluate($y_5 = $spacing * -0.110396 ) +evaluate($z_5 = $spacing * -0.058143 ) +evaluate ($x_6 = $spacing * 0.843755 ) +evaluate($y_6 = $spacing * 0.000000 ) +evaluate($z_6 = $spacing * -0.536728 ) +evaluate ($x_7 = $spacing * -0.367872 ) +evaluate($y_7 = $spacing * 0.110396 ) +evaluate($z_7 = $spacing * 0.923300 ) +evaluate ($x_8 = $spacing * -0.358301 ) +evaluate($y_8 = $spacing * 0.320721 ) +evaluate($z_8 = $spacing * -0.876789 ) +evaluate ($x_9 = $spacing * 0.544516 ) +evaluate($y_9 = $spacing * 0.639964 ) +evaluate($z_9 = $spacing * 0.542170 ) +evaluate ($x_10 = $spacing * -0.549715 ) +evaluate($y_10 = $spacing * 0.818783 ) +evaluate($z_10 = $spacing * 0.165553 ) +evaluate ($x_11 = $spacing * 0.348978 ) +evaluate($y_11 = $spacing * 0.841959 ) +evaluate($z_11 = $spacing * -0.411484 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_12 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_12 new file mode 100644 index 0000000000000000000000000000000000000000..8f3be22979a0fb07ad8303eab79597a8882933f8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_12 @@ -0,0 +1,36 @@ +evaluate ($x_1 = $spacing * 0.660320 ) +evaluate($y_1 = $spacing * -0.750904 ) +evaluate($z_1 = $spacing * -0.010970 ) +evaluate ($x_2 = $spacing * -0.298250 ) +evaluate($y_2 = $spacing * -0.863777 ) +evaluate($z_2 = $spacing * 0.406123 ) +evaluate ($x_3 = $spacing * -0.187157 ) +evaluate($y_3 = $spacing * -0.750895 ) +evaluate($z_3 = $spacing * -0.633347 ) +evaluate ($x_4 = $spacing * 0.410935 ) +evaluate($y_4 = $spacing * -0.247024 ) +evaluate($z_4 = $spacing * 0.877560 ) +evaluate ($x_5 = $spacing * -0.960322 ) +evaluate($y_5 = $spacing * -0.247027 ) +evaluate($z_5 = $spacing * -0.129456 ) +evaluate ($x_6 = $spacing * 0.590688 ) +evaluate($y_6 = $spacing * -0.064385 ) +evaluate($z_6 = $spacing * -0.804327 ) +evaluate ($x_7 = $spacing * -0.590677 ) +evaluate($y_7 = $spacing * 0.064385 ) +evaluate($z_7 = $spacing * 0.804335 ) +evaluate ($x_8 = $spacing * -0.410931 ) +evaluate($y_8 = $spacing * 0.247027 ) +evaluate($z_8 = $spacing * -0.877561 ) +evaluate ($x_9 = $spacing * 0.960322 ) +evaluate($y_9 = $spacing * 0.247024 ) +evaluate($z_9 = $spacing * 0.129460 ) +evaluate ($x_10 = $spacing * -0.660330 ) +evaluate($y_10 = $spacing * 0.750895 ) +evaluate($z_10 = $spacing * 0.010972 ) +evaluate ($x_11 = $spacing * 0.298246 ) +evaluate($y_11 = $spacing * 0.863777 ) +evaluate($z_11 = $spacing * -0.406126 ) +evaluate ($x_12 = $spacing * 0.187157 ) +evaluate($y_12 = $spacing * 0.750904 ) +evaluate($z_12 = $spacing * 0.633337 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_13 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_13 new file mode 100644 index 0000000000000000000000000000000000000000..e9a52f92456763bce01c52c0251fdc24a3c703b7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_13 @@ -0,0 +1,39 @@ +evaluate ($x_1 = $spacing * 0.227928 ) +evaluate($y_1 = $spacing * -0.972553 ) +evaluate($z_1 = $spacing * -0.046792 ) +evaluate ($x_2 = $spacing * -0.464839 ) +evaluate($y_2 = $spacing * -0.725134 ) +evaluate($z_2 = $spacing * 0.508041 ) +evaluate ($x_3 = $spacing * 0.028573 ) +evaluate($y_3 = $spacing * -0.462931 ) +evaluate($z_3 = $spacing * -0.885934 ) +evaluate ($x_4 = $spacing * 0.636022 ) +evaluate($y_4 = $spacing * -0.346780 ) +evaluate($z_4 = $spacing * 0.689361 ) +evaluate ($x_5 = $spacing * -0.798751 ) +evaluate($y_5 = $spacing * -0.507757 ) +evaluate($z_5 = $spacing * -0.322769 ) +evaluate ($x_6 = $spacing * 0.883485 ) +evaluate($y_6 = $spacing * -0.335966 ) +evaluate($z_6 = $spacing * -0.326467 ) +evaluate ($x_7 = $spacing * -0.259628 ) +evaluate($y_7 = $spacing * 0.000004 ) +evaluate($z_7 = $spacing * 0.965709 ) +evaluate ($x_8 = $spacing * -0.600709 ) +evaluate($y_8 = $spacing * 0.335964 ) +evaluate($z_8 = $spacing * -0.725450 ) +evaluate ($x_9 = $spacing * 0.852930 ) +evaluate($y_9 = $spacing * 0.507755 ) +evaluate($z_9 = $spacing * 0.121224 ) +evaluate ($x_10 = $spacing * -0.895949 ) +evaluate($y_10 = $spacing * 0.346782 ) +evaluate($z_10 = $spacing * 0.277520 ) +evaluate ($x_11 = $spacing * 0.419485 ) +evaluate($y_11 = $spacing * 0.462935 ) +evaluate($z_11 = $spacing * -0.780848 ) +evaluate ($x_12 = $spacing * 0.147481 ) +evaluate($y_12 = $spacing * 0.725126 ) +evaluate($z_12 = $spacing * 0.672638 ) +evaluate ($x_13 = $spacing * -0.173741 ) +evaluate($y_13 = $spacing * 0.972556 ) +evaluate($z_13 = $spacing * -0.154752 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_14 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_14 new file mode 100644 index 0000000000000000000000000000000000000000..70cb3c907f361475e4ed5b6da72374b3bf9fb89f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_14 @@ -0,0 +1,42 @@ +evaluate ($x_1 = $spacing * 0.634292 ) +evaluate($y_1 = $spacing * -0.773026 ) +evaluate($z_1 = $spacing * 0.010217 ) +evaluate ($x_2 = $spacing * -0.204241 ) +evaluate($y_2 = $spacing * -0.944871 ) +evaluate($z_2 = $spacing * 0.255937 ) +evaluate ($x_3 = $spacing * -0.080616 ) +evaluate($y_3 = $spacing * -0.665380 ) +evaluate($z_3 = $spacing * -0.742140 ) +evaluate ($x_4 = $spacing * 0.327610 ) +evaluate($y_4 = $spacing * -0.339084 ) +evaluate($z_4 = $spacing * 0.881869 ) +evaluate ($x_5 = $spacing * -0.875092 ) +evaluate($y_5 = $spacing * -0.475038 ) +evaluate($z_5 = $spacing * -0.092481 ) +evaluate ($x_6 = $spacing * 0.801786 ) +evaluate($y_6 = $spacing * -0.130940 ) +evaluate($z_6 = $spacing * -0.583091 ) +evaluate ($x_7 = $spacing * -0.543684 ) +evaluate($y_7 = $spacing * -0.166836 ) +evaluate($z_7 = $spacing * 0.822541 ) +evaluate ($x_8 = $spacing * -0.707618 ) +evaluate($y_8 = $spacing * 0.166836 ) +evaluate($z_8 = $spacing * -0.686616 ) +evaluate ($x_9 = $spacing * 0.908285 ) +evaluate($y_9 = $spacing * 0.130940 ) +evaluate($z_9 = $spacing * 0.397331 ) +evaluate ($x_10 = $spacing * -0.834824 ) +evaluate($y_10 = $spacing * 0.475038 ) +evaluate($z_10 = $spacing * 0.278223 ) +evaluate ($x_11 = $spacing * 0.130614 ) +evaluate($y_11 = $spacing * 0.339084 ) +evaluate($z_11 = $spacing * -0.931645 ) +evaluate ($x_12 = $spacing * 0.080616 ) +evaluate($y_12 = $spacing * 0.665380 ) +evaluate($z_12 = $spacing * 0.742140 ) +evaluate ($x_13 = $spacing * -0.254432 ) +evaluate($y_13 = $spacing * 0.944871 ) +evaluate($z_13 = $spacing * -0.206113 ) +evaluate ($x_14 = $spacing * 0.617304 ) +evaluate($y_14 = $spacing * 0.773026 ) +evaluate($z_14 = $spacing * -0.146173 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_15 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_15 new file mode 100644 index 0000000000000000000000000000000000000000..2636bb858ad5f08c65bc3965f80532feb540376c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_15 @@ -0,0 +1,45 @@ +evaluate ($x_1 = $spacing * 0.618895 ) +evaluate($y_1 = $spacing * -0.783251 ) +evaluate($z_1 = $spacing * 0.059052 ) +evaluate ($x_2 = $spacing * -0.289241 ) +evaluate($y_2 = $spacing * -0.870627 ) +evaluate($z_2 = $spacing * 0.397931 ) +evaluate ($x_3 = $spacing * -0.130128 ) +evaluate($y_3 = $spacing * -0.817567 ) +evaluate($z_3 = $spacing * -0.560938 ) +evaluate ($x_4 = $spacing * 0.372860 ) +evaluate($y_4 = $spacing * -0.413223 ) +evaluate($z_4 = $spacing * 0.830797 ) +evaluate ($x_5 = $spacing * -0.868720 ) +evaluate($y_5 = $spacing * -0.472512 ) +evaluate($z_5 = $spacing * -0.148517 ) +evaluate ($x_6 = $spacing * 0.594599 ) +evaluate($y_6 = $spacing * -0.329397 ) +evaluate($z_6 = $spacing * -0.733450 ) +evaluate ($x_7 = $spacing * -0.534744 ) +evaluate($y_7 = $spacing * -0.078449 ) +evaluate($z_7 = $spacing * 0.841365 ) +evaluate ($x_8 = $spacing * -0.460907 ) +evaluate($y_8 = $spacing * 0.000000 ) +evaluate($z_8 = $spacing * -0.887448 ) +evaluate ($x_9 = $spacing * 0.995836 ) +evaluate($y_9 = $spacing * 0.078449 ) +evaluate($z_9 = $spacing * 0.046439 ) +evaluate ($x_10 = $spacing * -0.941980 ) +evaluate($y_10 = $spacing * 0.329397 ) +evaluate($z_10 = $spacing * 0.064591 ) +evaluate ($x_11 = $spacing * 0.378131 ) +evaluate($y_11 = $spacing * 0.472512 ) +evaluate($z_11 = $spacing * -0.796084 ) +evaluate ($x_12 = $spacing * 0.465201 ) +evaluate($y_12 = $spacing * 0.413223 ) +evaluate($z_12 = $spacing * 0.782838 ) +evaluate ($x_13 = $spacing * -0.384042 ) +evaluate($y_13 = $spacing * 0.817567 ) +evaluate($z_13 = $spacing * -0.429065 ) +evaluate ($x_14 = $spacing * 0.491883 ) +evaluate($y_14 = $spacing * 0.870627 ) +evaluate($z_14 = $spacing * -0.007755 ) +evaluate ($x_15 = $spacing * -0.307637 ) +evaluate($y_15 = $spacing * 0.783251 ) +evaluate($z_15 = $spacing * 0.540257 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_16 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_16 new file mode 100644 index 0000000000000000000000000000000000000000..6aef3448d0be78b2583dc83c8f68b73a3a3cdb9b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_16 @@ -0,0 +1,48 @@ +evaluate ($x_1 = $spacing * 0.358373 ) +evaluate($y_1 = $spacing * -0.933578 ) +evaluate($z_1 = $spacing * -0.000803 ) +evaluate ($x_2 = $spacing * -0.413099 ) +evaluate($y_2 = $spacing * -0.818264 ) +evaluate($z_2 = $spacing * 0.399741 ) +evaluate ($x_3 = $spacing * 0.008328 ) +evaluate($y_3 = $spacing * -0.655629 ) +evaluate($z_3 = $spacing * -0.755037 ) +evaluate ($x_4 = $spacing * 0.341022 ) +evaluate($y_4 = $spacing * -0.495569 ) +evaluate($z_4 = $spacing * 0.798821 ) +evaluate ($x_5 = $spacing * -0.763142 ) +evaluate($y_5 = $spacing * -0.540279 ) +evaluate($z_5 = $spacing * -0.354560 ) +evaluate ($x_6 = $spacing * 0.811829 ) +evaluate($y_6 = $spacing * -0.313665 ) +evaluate($z_6 = $spacing * -0.492492 ) +evaluate ($x_7 = $spacing * -0.282470 ) +evaluate($y_7 = $spacing * 0.055696 ) +evaluate($z_7 = $spacing * 0.957658 ) +evaluate ($x_8 = $spacing * -0.441881 ) +evaluate($y_8 = $spacing * 0.126105 ) +evaluate($z_8 = $spacing * -0.888166 ) +evaluate ($x_9 = $spacing * 0.937588 ) +evaluate($y_9 = $spacing * -0.126105 ) +evaluate($z_9 = $spacing * 0.324078 ) +evaluate ($x_10 = $spacing * -0.913417 ) +evaluate($y_10 = $spacing * -0.055696 ) +evaluate($z_10 = $spacing * 0.403197 ) +evaluate ($x_11 = $spacing * 0.384079 ) +evaluate($y_11 = $spacing * 0.313665 ) +evaluate($z_11 = $spacing * -0.868388 ) +evaluate ($x_12 = $spacing * 0.449692 ) +evaluate($y_12 = $spacing * 0.540279 ) +evaluate($z_12 = $spacing * 0.711250 ) +evaluate ($x_13 = $spacing * -0.836022 ) +evaluate($y_13 = $spacing * 0.495569 ) +evaluate($z_13 = $spacing * -0.235537 ) +evaluate ($x_14 = $spacing * 0.747706 ) +evaluate($y_14 = $spacing * 0.655629 ) +evaluate($z_14 = $spacing * -0.105289 ) +evaluate ($x_15 = $spacing * -0.343339 ) +evaluate($y_15 = $spacing * 0.818264 ) +evaluate($z_15 = $spacing * 0.461045 ) +evaluate ($x_16 = $spacing * -0.045259 ) +evaluate($y_16 = $spacing * 0.933578 ) +evaluate($z_16 = $spacing * -0.355505 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_17 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_17 new file mode 100644 index 0000000000000000000000000000000000000000..f1f7681e7cf2f6451ca3d35fa4c4143a8dbf94fd --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_17 @@ -0,0 +1,51 @@ +evaluate ($x_1 = $spacing * 0.329792 ) +evaluate($y_1 = $spacing * -0.944052 ) +evaluate($z_1 = $spacing * -0.001540 ) +evaluate ($x_2 = $spacing * -0.406538 ) +evaluate($y_2 = $spacing * -0.822071 ) +evaluate($z_2 = $spacing * 0.398655 ) +evaluate ($x_3 = $spacing * 0.008419 ) +evaluate($y_3 = $spacing * -0.675302 ) +evaluate($z_3 = $spacing * -0.737493 ) +evaluate ($x_4 = $spacing * 0.414026 ) +evaluate($y_4 = $spacing * -0.535998 ) +evaluate($z_4 = $spacing * 0.735724 ) +evaluate ($x_5 = $spacing * -0.736090 ) +evaluate($y_5 = $spacing * -0.582898 ) +evaluate($z_5 = $spacing * -0.344096 ) +evaluate ($x_6 = $spacing * 0.829223 ) +evaluate($y_6 = $spacing * -0.389130 ) +evaluate($z_6 = $spacing * -0.401208 ) +evaluate ($x_7 = $spacing * -0.340389 ) +evaluate($y_7 = $spacing * -0.120467 ) +evaluate($z_7 = $spacing * 0.932536 ) +evaluate ($x_8 = $spacing * -0.536474 ) +evaluate($y_8 = $spacing * 0.073521 ) +evaluate($z_8 = $spacing * -0.840708 ) +evaluate ($x_9 = $spacing * 0.939321 ) +evaluate($y_9 = $spacing * 0.000000 ) +evaluate($z_9 = $spacing * 0.343039 ) +evaluate ($x_10 = $spacing * -0.952006 ) +evaluate($y_10 = $spacing * -0.073521 ) +evaluate($z_10 = $spacing * 0.297118 ) +evaluate ($x_11 = $spacing * 0.340692 ) +evaluate($y_11 = $spacing * 0.120467 ) +evaluate($z_11 = $spacing * -0.932425 ) +evaluate ($x_12 = $spacing * 0.375507 ) +evaluate($y_12 = $spacing * 0.389130 ) +evaluate($z_12 = $spacing * 0.841173 ) +evaluate ($x_13 = $spacing * -0.784602 ) +evaluate($y_13 = $spacing * 0.582898 ) +evaluate($z_13 = $spacing * -0.211258 ) +evaluate ($x_14 = $spacing * 0.790719 ) +evaluate($y_14 = $spacing * 0.535998 ) +evaluate($z_14 = $spacing * -0.295753 ) +evaluate ($x_15 = $spacing * -0.468838 ) +evaluate($y_15 = $spacing * 0.675302 ) +evaluate($z_15 = $spacing * 0.569349 ) +evaluate ($x_16 = $spacing * -0.053947 ) +evaluate($y_16 = $spacing * 0.822071 ) +evaluate($z_16 = $spacing * -0.566823 ) +evaluate ($x_17 = $spacing * 0.251182 ) +evaluate($y_17 = $spacing * 0.944052 ) +evaluate($z_17 = $spacing * 0.213711 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_18 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_18 new file mode 100644 index 0000000000000000000000000000000000000000..4278f3818f6a800535699c7f5ceff81266ddeeb1 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_18 @@ -0,0 +1,54 @@ +evaluate ($x_1 = $spacing * 0.319340 ) +evaluate($y_1 = $spacing * -0.947619 ) +evaluate($z_1 = $spacing * -0.006295 ) +evaluate ($x_2 = $spacing * -0.424438 ) +evaluate($y_2 = $spacing * -0.857399 ) +evaluate($z_2 = $spacing * 0.291066 ) +evaluate ($x_3 = $spacing * -0.065760 ) +evaluate($y_3 = $spacing * -0.730071 ) +evaluate($z_3 = $spacing * -0.680200 ) +evaluate ($x_4 = $spacing * 0.497169 ) +evaluate($y_4 = $spacing * -0.549432 ) +evaluate($z_4 = $spacing * 0.671527 ) +evaluate ($x_5 = $spacing * -0.799747 ) +evaluate($y_5 = $spacing * -0.481645 ) +evaluate($z_5 = $spacing * -0.358361 ) +evaluate ($x_6 = $spacing * 0.855345 ) +evaluate($y_6 = $spacing * -0.422253 ) +evaluate($z_6 = $spacing * -0.300145 ) +evaluate ($x_7 = $spacing * -0.271429 ) +evaluate($y_7 = $spacing * -0.312474 ) +evaluate($z_7 = $spacing * 0.910322 ) +evaluate ($x_8 = $spacing * -0.438539 ) +evaluate($y_8 = $spacing * 0.073036 ) +evaluate($z_8 = $spacing * -0.895740 ) +evaluate ($x_9 = $spacing * 0.929765 ) +evaluate($y_9 = $spacing * 0.096109 ) +evaluate($z_9 = $spacing * 0.355388 ) +evaluate ($x_10 = $spacing * -0.914287 ) +evaluate($y_10 = $spacing * -0.096109 ) +evaluate($z_10 = $spacing * 0.393500 ) +evaluate ($x_11 = $spacing * 0.401154 ) +evaluate($y_11 = $spacing * -0.073036 ) +evaluate($z_11 = $spacing * -0.913094 ) +evaluate ($x_12 = $spacing * 0.308810 ) +evaluate($y_12 = $spacing * 0.312474 ) +evaluate($z_12 = $spacing * 0.898330 ) +evaluate ($x_13 = $spacing * -0.867016 ) +evaluate($y_13 = $spacing * 0.422253 ) +evaluate($z_13 = $spacing * -0.264548 ) +evaluate ($x_14 = $spacing * 0.784257 ) +evaluate($y_14 = $spacing * 0.481645 ) +evaluate($z_14 = $spacing * -0.391099 ) +evaluate ($x_15 = $spacing * -0.468998 ) +evaluate($y_15 = $spacing * 0.549432 ) +evaluate($z_15 = $spacing * 0.691495 ) +evaluate ($x_16 = $spacing * 0.037599 ) +evaluate($y_16 = $spacing * 0.730071 ) +evaluate($z_16 = $spacing * -0.682336 ) +evaluate ($x_17 = $spacing * 0.436102 ) +evaluate($y_17 = $spacing * 0.857399 ) +evaluate($z_17 = $spacing * 0.273280 ) +evaluate ($x_18 = $spacing * -0.319327 ) +evaluate($y_18 = $spacing * 0.947619 ) +evaluate($z_18 = $spacing * 0.006905 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_19 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_19 new file mode 100644 index 0000000000000000000000000000000000000000..0677e92413329b0e88433e47f85c700c172bf85f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_19 @@ -0,0 +1,57 @@ +evaluate ($x_1 = $spacing * 0.481833 ) +evaluate($y_1 = $spacing * -0.875674 ) +evaluate($z_1 = $spacing * 0.032123 ) +evaluate ($x_2 = $spacing * -0.345485 ) +evaluate($y_2 = $spacing * -0.908778 ) +evaluate($z_2 = $spacing * 0.234013 ) +evaluate ($x_3 = $spacing * 0.006781 ) +evaluate($y_3 = $spacing * -0.787268 ) +evaluate($z_3 = $spacing * -0.616573 ) +evaluate ($x_4 = $spacing * 0.324436 ) +evaluate($y_4 = $spacing * -0.596484 ) +evaluate($z_4 = $spacing * 0.734131 ) +evaluate ($x_5 = $spacing * -0.805119 ) +evaluate($y_5 = $spacing * -0.534403 ) +evaluate($z_5 = $spacing * -0.257287 ) +evaluate ($x_6 = $spacing * 0.785858 ) +evaluate($y_6 = $spacing * -0.384106 ) +evaluate($z_6 = $spacing * -0.484653 ) +evaluate ($x_7 = $spacing * -0.413826 ) +evaluate($y_7 = $spacing * -0.330734 ) +evaluate($z_7 = $spacing * 0.848153 ) +evaluate ($x_8 = $spacing * -0.414171 ) +evaluate($y_8 = $spacing * -0.192101 ) +evaluate($z_8 = $spacing * -0.889696 ) +evaluate ($x_9 = $spacing * 0.915180 ) +evaluate($y_9 = $spacing * -0.114995 ) +evaluate($z_9 = $spacing * 0.386291 ) +evaluate ($x_10 = $spacing * -0.924346 ) +evaluate($y_10 = $spacing * -0.000000 ) +evaluate($z_10 = $spacing * 0.381556 ) +evaluate ($x_11 = $spacing * 0.376225 ) +evaluate($y_11 = $spacing * 0.114995 ) +evaluate($z_11 = $spacing * -0.919365 ) +evaluate ($x_12 = $spacing * 0.333997 ) +evaluate($y_12 = $spacing * 0.192101 ) +evaluate($z_12 = $spacing * 0.922791 ) +evaluate ($x_13 = $spacing * -0.891602 ) +evaluate($y_13 = $spacing * 0.330734 ) +evaluate($z_13 = $spacing * -0.309291 ) +evaluate ($x_14 = $spacing * 0.898904 ) +evaluate($y_14 = $spacing * 0.384106 ) +evaluate($z_14 = $spacing * -0.210792 ) +evaluate ($x_15 = $spacing * -0.389207 ) +evaluate($y_15 = $spacing * 0.534403 ) +evaluate($z_15 = $spacing * 0.750287 ) +evaluate ($x_16 = $spacing * -0.287872 ) +evaluate($y_16 = $spacing * 0.596484 ) +evaluate($z_16 = $spacing * -0.749224 ) +evaluate ($x_17 = $spacing * 0.439725 ) +evaluate($y_17 = $spacing * 0.787268 ) +evaluate($z_17 = $spacing * 0.432262 ) +evaluate ($x_18 = $spacing * -0.409958 ) +evaluate($y_18 = $spacing * 0.908778 ) +evaluate($z_18 = $spacing * 0.077823 ) +evaluate ($x_19 = $spacing * 0.318879 ) +evaluate($y_19 = $spacing * 0.875674 ) +evaluate($z_19 = $spacing * -0.362645 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_2 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_2 new file mode 100644 index 0000000000000000000000000000000000000000..d7e05cc2940b69fc55ccd38f0114a2f70d625938 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_2 @@ -0,0 +1,6 @@ +evaluate ($x_1 = $spacing * 0.792331 ) +evaluate($y_1 = $spacing * -0.526604 ) +evaluate($z_1 = $spacing * -0.308059 ) +evaluate ($x_2 = $spacing * -0.792331 ) +evaluate($y_2 = $spacing * 0.526604 ) +evaluate($z_2 = $spacing * 0.308059 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_20 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_20 new file mode 100644 index 0000000000000000000000000000000000000000..2d301a260a07d77d525e4530f8e6d6f5ef96829e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_20 @@ -0,0 +1,60 @@ +evaluate ($x_1 = $spacing * 0.415876 ) +evaluate($y_1 = $spacing * -0.903810 ) +evaluate($z_1 = $spacing * 0.100867 ) +evaluate ($x_2 = $spacing * -0.335550 ) +evaluate($y_2 = $spacing * -0.885879 ) +evaluate($z_2 = $spacing * 0.320349 ) +evaluate ($x_3 = $spacing * -0.005787 ) +evaluate($y_3 = $spacing * -0.817798 ) +evaluate($z_3 = $spacing * -0.575476 ) +evaluate ($x_4 = $spacing * 0.398064 ) +evaluate($y_4 = $spacing * -0.480671 ) +evaluate($z_4 = $spacing * 0.781346 ) +evaluate ($x_5 = $spacing * -0.730185 ) +evaluate($y_5 = $spacing * -0.614431 ) +evaluate($z_5 = $spacing * -0.298839 ) +evaluate ($x_6 = $spacing * 0.698588 ) +evaluate($y_6 = $spacing * -0.462123 ) +evaluate($z_6 = $spacing * -0.546277 ) +evaluate ($x_7 = $spacing * -0.383837 ) +evaluate($y_7 = $spacing * -0.324793 ) +evaluate($z_7 = $spacing * 0.864395 ) +evaluate ($x_8 = $spacing * -0.355085 ) +evaluate($y_8 = $spacing * -0.196091 ) +evaluate($z_8 = $spacing * -0.914037 ) +evaluate ($x_9 = $spacing * 0.933107 ) +evaluate($y_9 = $spacing * -0.265886 ) +evaluate($z_9 = $spacing * 0.242108 ) +evaluate ($x_10 = $spacing * -0.938322 ) +evaluate($y_10 = $spacing * -0.142563 ) +evaluate($z_10 = $spacing * 0.315004 ) +evaluate ($x_11 = $spacing * 0.358010 ) +evaluate($y_11 = $spacing * 0.142563 ) +evaluate($z_11 = $spacing * -0.922770 ) +evaluate ($x_12 = $spacing * 0.198748 ) +evaluate($y_12 = $spacing * 0.265886 ) +evaluate($z_12 = $spacing * 0.943294 ) +evaluate ($x_13 = $spacing * -0.896659 ) +evaluate($y_13 = $spacing * 0.196091 ) +evaluate($z_13 = $spacing * -0.396927 ) +evaluate ($x_14 = $spacing * 0.881202 ) +evaluate($y_14 = $spacing * 0.324793 ) +evaluate($z_14 = $spacing * -0.343500 ) +evaluate ($x_15 = $spacing * -0.577962 ) +evaluate($y_15 = $spacing * 0.462123 ) +evaluate($z_15 = $spacing * 0.672609 ) +evaluate ($x_16 = $spacing * -0.264792 ) +evaluate($y_16 = $spacing * 0.614431 ) +evaluate($z_16 = $spacing * -0.743209 ) +evaluate ($x_17 = $spacing * 0.762125 ) +evaluate($y_17 = $spacing * 0.480671 ) +evaluate($z_17 = $spacing * 0.433730 ) +evaluate ($x_18 = $spacing * -0.574595 ) +evaluate($y_18 = $spacing * 0.817798 ) +evaluate($z_18 = $spacing * -0.032363 ) +evaluate ($x_19 = $spacing * 0.335507 ) +evaluate($y_19 = $spacing * 0.885879 ) +evaluate($z_19 = $spacing * -0.320395 ) +evaluate ($x_20 = $spacing * 0.081549 ) +evaluate($y_20 = $spacing * 0.903810 ) +evaluate($z_20 = $spacing * 0.420091 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_21 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_21 new file mode 100644 index 0000000000000000000000000000000000000000..006c95150dc69316d9c7633aca36b67a7b385c13 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_21 @@ -0,0 +1,63 @@ +evaluate ($x_1 = $spacing * 0.399036 ) +evaluate($y_1 = $spacing * -0.904024 ) +evaluate($z_1 = $spacing * 0.153332 ) +evaluate ($x_2 = $spacing * -0.371076 ) +evaluate($y_2 = $spacing * -0.899330 ) +evaluate($z_2 = $spacing * 0.231320 ) +evaluate ($x_3 = $spacing * 0.021520 ) +evaluate($y_3 = $spacing * -0.826316 ) +evaluate($z_3 = $spacing * -0.562796 ) +evaluate ($x_4 = $spacing * 0.253227 ) +evaluate($y_4 = $spacing * -0.542500 ) +evaluate($z_4 = $spacing * 0.800981 ) +evaluate ($x_5 = $spacing * -0.728555 ) +evaluate($y_5 = $spacing * -0.574221 ) +evaluate($z_5 = $spacing * -0.373466 ) +evaluate ($x_6 = $spacing * 0.734254 ) +evaluate($y_6 = $spacing * -0.530089 ) +evaluate($z_6 = $spacing * -0.424118 ) +evaluate ($x_7 = $spacing * -0.478534 ) +evaluate($y_7 = $spacing * -0.362125 ) +evaluate($z_7 = $spacing * 0.799920 ) +evaluate ($x_8 = $spacing * -0.324956 ) +evaluate($y_8 = $spacing * -0.220739 ) +evaluate($z_8 = $spacing * -0.919607 ) +evaluate ($x_9 = $spacing * 0.900874 ) +evaluate($y_9 = $spacing * -0.255075 ) +evaluate($z_9 = $spacing * 0.351230 ) +evaluate ($x_10 = $spacing * -0.952172 ) +evaluate($y_10 = $spacing * -0.190671 ) +evaluate($z_10 = $spacing * 0.238773 ) +evaluate ($x_11 = $spacing * 0.423872 ) +evaluate($y_11 = $spacing * -0.000008 ) +evaluate($z_11 = $spacing * -0.905722 ) +evaluate ($x_12 = $spacing * 0.426746 ) +evaluate($y_12 = $spacing * 0.190683 ) +evaluate($z_12 = $spacing * 0.884041 ) +evaluate ($x_13 = $spacing * -0.846867 ) +evaluate($y_13 = $spacing * 0.255075 ) +evaluate($z_13 = $spacing * -0.466640 ) +evaluate ($x_14 = $spacing * 0.914261 ) +evaluate($y_14 = $spacing * 0.220695 ) +evaluate($z_14 = $spacing * -0.339736 ) +evaluate ($x_15 = $spacing * -0.307566 ) +evaluate($y_15 = $spacing * 0.362125 ) +evaluate($z_15 = $spacing * 0.879925 ) +evaluate ($x_16 = $spacing * -0.144816 ) +evaluate($y_16 = $spacing * 0.530134 ) +evaluate($z_16 = $spacing * -0.835456 ) +evaluate ($x_17 = $spacing * 0.753521 ) +evaluate($y_17 = $spacing * 0.574221 ) +evaluate($z_17 = $spacing * 0.320120 ) +evaluate ($x_18 = $spacing * -0.777231 ) +evaluate($y_18 = $spacing * 0.542487 ) +evaluate($z_18 = $spacing * 0.318778 ) +evaluate ($x_19 = $spacing * 0.418285 ) +evaluate($y_19 = $spacing * 0.826325 ) +evaluate($z_19 = $spacing * -0.377126 ) +evaluate ($x_20 = $spacing * 0.060158 ) +evaluate($y_20 = $spacing * 0.899327 ) +evaluate($z_20 = $spacing * 0.433120 ) +evaluate ($x_21 = $spacing * -0.373377 ) +evaluate($y_21 = $spacing * 0.904024 ) +evaluate($z_21 = $spacing * -0.208160 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_22 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_22 new file mode 100644 index 0000000000000000000000000000000000000000..49badd8ac15b80991ec1794abddc3b18ead7326c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_22 @@ -0,0 +1,66 @@ +evaluate ($x_1 = $spacing * 0.495928 ) +evaluate($y_1 = $spacing * -0.866742 ) +evaluate($z_1 = $spacing * 0.053042 ) +evaluate ($x_2 = $spacing * -0.238113 ) +evaluate($y_2 = $spacing * -0.944397 ) +evaluate($z_2 = $spacing * 0.226750 ) +evaluate ($x_3 = $spacing * 0.037659 ) +evaluate($y_3 = $spacing * -0.825858 ) +evaluate($z_3 = $spacing * -0.562620 ) +evaluate ($x_4 = $spacing * 0.331397 ) +evaluate($y_4 = $spacing * -0.569223 ) +evaluate($z_4 = $spacing * 0.752437 ) +evaluate ($x_5 = $spacing * -0.721444 ) +evaluate($y_5 = $spacing * -0.650745 ) +evaluate($z_5 = $spacing * -0.236749 ) +evaluate ($x_6 = $spacing * 0.769906 ) +evaluate($y_6 = $spacing * -0.412028 ) +evaluate($z_6 = $spacing * -0.487317 ) +evaluate ($x_7 = $spacing * -0.433195 ) +evaluate($y_7 = $spacing * -0.471383 ) +evaluate($z_7 = $spacing * 0.768206 ) +evaluate ($x_8 = $spacing * -0.442836 ) +evaluate($y_8 = $spacing * -0.297284 ) +evaluate($z_8 = $spacing * -0.845883 ) +evaluate ($x_9 = $spacing * 0.900766 ) +evaluate($y_9 = $spacing * -0.263869 ) +evaluate($z_9 = $spacing * 0.344955 ) +evaluate ($x_10 = $spacing * -0.943111 ) +evaluate($y_10 = $spacing * -0.168365 ) +evaluate($z_10 = $spacing * 0.286696 ) +evaluate ($x_11 = $spacing * 0.286655 ) +evaluate($y_11 = $spacing * -0.118411 ) +evaluate($z_11 = $spacing * -0.950688 ) +evaluate ($x_12 = $spacing * 0.157324 ) +evaluate($y_12 = $spacing * 0.118411 ) +evaluate($z_12 = $spacing * 0.980422 ) +evaluate ($x_13 = $spacing * -0.896459 ) +evaluate($y_13 = $spacing * 0.168365 ) +evaluate($z_13 = $spacing * -0.409896 ) +evaluate ($x_14 = $spacing * 0.938720 ) +evaluate($y_14 = $spacing * 0.263869 ) +evaluate($z_14 = $spacing * -0.221759 ) +evaluate ($x_15 = $spacing * -0.551677 ) +evaluate($y_15 = $spacing * 0.297284 ) +evaluate($z_15 = $spacing * 0.779278 ) +evaluate ($x_16 = $spacing * -0.326888 ) +evaluate($y_16 = $spacing * 0.471383 ) +evaluate($z_16 = $spacing * -0.819110 ) +evaluate ($x_17 = $spacing * 0.698048 ) +evaluate($y_17 = $spacing * 0.412028 ) +evaluate($z_17 = $spacing * 0.585630 ) +evaluate ($x_18 = $spacing * -0.746571 ) +evaluate($y_18 = $spacing * 0.650745 ) +evaluate($z_18 = $spacing * 0.138433 ) +evaluate ($x_19 = $spacing * 0.428772 ) +evaluate($y_19 = $spacing * 0.569223 ) +evaluate($z_19 = $spacing * -0.701526 ) +evaluate ($x_20 = $spacing * -0.037701 ) +evaluate($y_20 = $spacing * 0.825858 ) +evaluate($z_20 = $spacing * 0.562617 ) +evaluate ($x_21 = $spacing * -0.205750 ) +evaluate($y_21 = $spacing * 0.944397 ) +evaluate($z_21 = $spacing * -0.256477 ) +evaluate ($x_22 = $spacing * 0.498572 ) +evaluate($y_22 = $spacing * 0.866742 ) +evaluate($z_22 = $spacing * 0.013562 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_23 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_23 new file mode 100644 index 0000000000000000000000000000000000000000..c5de1bccde45c530ec05ba1f80a79d5224ad37ec --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_23 @@ -0,0 +1,69 @@ +evaluate ($x_1 = $spacing * 0.408148 ) +evaluate($y_1 = $spacing * -0.910470 ) +evaluate($z_1 = $spacing * 0.066775 ) +evaluate ($x_2 = $spacing * -0.358050 ) +evaluate($y_2 = $spacing * -0.906696 ) +evaluate($z_2 = $spacing * 0.222941 ) +evaluate ($x_3 = $spacing * 0.048085 ) +evaluate($y_3 = $spacing * -0.840855 ) +evaluate($z_3 = $spacing * -0.539120 ) +evaluate ($x_4 = $spacing * 0.241995 ) +evaluate($y_4 = $spacing * -0.662114 ) +evaluate($z_4 = $spacing * 0.709255 ) +evaluate ($x_5 = $spacing * -0.730677 ) +evaluate($y_5 = $spacing * -0.606646 ) +evaluate($z_5 = $spacing * -0.313195 ) +evaluate ($x_6 = $spacing * 0.792598 ) +evaluate($y_6 = $spacing * -0.476030 ) +evaluate($z_6 = $spacing * -0.381029 ) +evaluate ($x_7 = $spacing * -0.432745 ) +evaluate($y_7 = $spacing * -0.394515 ) +evaluate($z_7 = $spacing * 0.810611 ) +evaluate ($x_8 = $spacing * -0.335988 ) +evaluate($y_8 = $spacing * -0.349372 ) +evaluate($z_8 = $spacing * -0.874672 ) +evaluate ($x_9 = $spacing * 0.865819 ) +evaluate($y_9 = $spacing * -0.321629 ) +evaluate($z_9 = $spacing * 0.383291 ) +evaluate ($x_10 = $spacing * -0.926371 ) +evaluate($y_10 = $spacing * -0.239421 ) +evaluate($z_10 = $spacing * 0.290714 ) +evaluate ($x_11 = $spacing * 0.418273 ) +evaluate($y_11 = $spacing * -0.144275 ) +evaluate($z_11 = $spacing * -0.896790 ) +evaluate ($x_12 = $spacing * 0.299284 ) +evaluate($y_12 = $spacing * 0.000000 ) +evaluate($z_12 = $spacing * 0.954164 ) +evaluate ($x_13 = $spacing * -0.855528 ) +evaluate($y_13 = $spacing * 0.144275 ) +evaluate($z_13 = $spacing * -0.497249 ) +evaluate ($x_14 = $spacing * 0.926455 ) +evaluate($y_14 = $spacing * 0.239421 ) +evaluate($z_14 = $spacing * -0.290445 ) +evaluate ($x_15 = $spacing * -0.491805 ) +evaluate($y_15 = $spacing * 0.321629 ) +evaluate($z_15 = $spacing * 0.809124 ) +evaluate ($x_16 = $spacing * -0.223755 ) +evaluate($y_16 = $spacing * 0.349372 ) +evaluate($z_16 = $spacing * -0.909876 ) +evaluate ($x_17 = $spacing * 0.818188 ) +evaluate($y_17 = $spacing * 0.394515 ) +evaluate($z_17 = $spacing * 0.418242 ) +evaluate ($x_18 = $spacing * -0.868229 ) +evaluate($y_18 = $spacing * 0.476030 ) +evaluate($z_18 = $spacing * 0.139907 ) +evaluate ($x_19 = $spacing * 0.420906 ) +evaluate($y_19 = $spacing * 0.606646 ) +evaluate($z_19 = $spacing * -0.674402 ) +evaluate ($x_20 = $spacing * 0.206435 ) +evaluate($y_20 = $spacing * 0.662114 ) +evaluate($z_20 = $spacing * 0.720409 ) +evaluate ($x_21 = $spacing * -0.347380 ) +evaluate($y_21 = $spacing * 0.840855 ) +evaluate($z_21 = $spacing * -0.415078 ) +evaluate ($x_22 = $spacing * 0.421237 ) +evaluate($y_22 = $spacing * 0.906696 ) +evaluate($z_22 = $spacing * -0.021491 ) +evaluate ($x_23 = $spacing * -0.296895 ) +evaluate($y_23 = $spacing * 0.910470 ) +evaluate($z_23 = $spacing * 0.287919 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_24 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_24 new file mode 100644 index 0000000000000000000000000000000000000000..35cb3e0b878f5c613293d3e7ffa0b9031a997aaf --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_24 @@ -0,0 +1,72 @@ +evaluate ($x_1 = $spacing * 0.337600 ) +evaluate($y_1 = $spacing * -0.941051 ) +evaluate($z_1 = $spacing * 0.021205 ) +evaluate ($x_2 = $spacing * -0.318885 ) +evaluate($y_2 = $spacing * -0.896311 ) +evaluate($z_2 = $spacing * 0.308122 ) +evaluate ($x_3 = $spacing * 0.066659 ) +evaluate($y_3 = $spacing * -0.779061 ) +evaluate($z_3 = $spacing * -0.623394 ) +evaluate ($x_4 = $spacing * 0.263254 ) +evaluate($y_4 = $spacing * -0.631178 ) +evaluate($z_4 = $spacing * 0.729597 ) +evaluate ($x_5 = $spacing * -0.589797 ) +evaluate($y_5 = $spacing * -0.734130 ) +evaluate($z_5 = $spacing * -0.336441 ) +evaluate ($x_6 = $spacing * 0.760203 ) +evaluate($y_6 = $spacing * -0.487832 ) +evaluate($z_6 = $spacing * -0.429082 ) +evaluate ($x_7 = $spacing * -0.441210 ) +evaluate($y_7 = $spacing * -0.346859 ) +evaluate($z_7 = $spacing * 0.827661 ) +evaluate ($x_8 = $spacing * -0.392520 ) +evaluate($y_8 = $spacing * -0.227454 ) +evaluate($z_8 = $spacing * -0.891175 ) +evaluate ($x_9 = $spacing * 0.831496 ) +evaluate($y_9 = $spacing * -0.445093 ) +evaluate($z_9 = $spacing * 0.332426 ) +evaluate ($x_10 = $spacing * -0.889435 ) +evaluate($y_10 = $spacing * -0.370573 ) +evaluate($z_10 = $spacing * 0.267547 ) +evaluate ($x_11 = $spacing * 0.367924 ) +evaluate($y_11 = $spacing * -0.139936 ) +evaluate($z_11 = $spacing * -0.919266 ) +evaluate ($x_12 = $spacing * 0.215058 ) +evaluate($y_12 = $spacing * 0.041367 ) +evaluate($z_12 = $spacing * 0.975725 ) +evaluate ($x_13 = $spacing * -0.904732 ) +evaluate($y_13 = $spacing * -0.041367 ) +evaluate($z_13 = $spacing * -0.423968 ) +evaluate ($x_14 = $spacing * 0.977604 ) +evaluate($y_14 = $spacing * 0.139936 ) +evaluate($z_14 = $spacing * -0.157191 ) +evaluate ($x_15 = $spacing * -0.456238 ) +evaluate($y_15 = $spacing * 0.370573 ) +evaluate($z_15 = $spacing * 0.809026 ) +evaluate ($x_16 = $spacing * -0.141822 ) +evaluate($y_16 = $spacing * 0.445093 ) +evaluate($z_16 = $spacing * -0.884182 ) +evaluate ($x_17 = $spacing * 0.783294 ) +evaluate($y_17 = $spacing * 0.227454 ) +evaluate($z_17 = $spacing * 0.578546 ) +evaluate ($x_18 = $spacing * -0.904317 ) +evaluate($y_18 = $spacing * 0.346859 ) +evaluate($z_18 = $spacing * 0.248796 ) +evaluate ($x_19 = $spacing * 0.585470 ) +evaluate($y_19 = $spacing * 0.487832 ) +evaluate($z_19 = $spacing * -0.647491 ) +evaluate ($x_20 = $spacing * 0.198788 ) +evaluate($y_20 = $spacing * 0.734130 ) +evaluate($z_20 = $spacing * 0.649258 ) +evaluate ($x_21 = $spacing * -0.654028 ) +evaluate($y_21 = $spacing * 0.631178 ) +evaluate($z_21 = $spacing * -0.416968 ) +evaluate ($x_22 = $spacing * 0.622824 ) +evaluate($y_22 = $spacing * 0.779061 ) +evaluate($z_22 = $spacing * 0.071790 ) +evaluate ($x_23 = $spacing * -0.370599 ) +evaluate($y_23 = $spacing * 0.896311 ) +evaluate($z_23 = $spacing * 0.243482 ) +evaluate ($x_24 = $spacing * 0.053409 ) +evaluate($y_24 = $spacing * 0.941051 ) +evaluate($z_24 = $spacing * -0.334022 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_25 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_25 new file mode 100644 index 0000000000000000000000000000000000000000..8d959242b4d4fe6b938b022babb81eee067262b9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_25 @@ -0,0 +1,75 @@ +evaluate ($x_1 = $spacing * 0.409713 ) +evaluate($y_1 = $spacing * -0.911797 ) +evaluate($z_1 = $spacing * 0.027589 ) +evaluate ($x_2 = $spacing * -0.322498 ) +evaluate($y_2 = $spacing * -0.912413 ) +evaluate($z_2 = $spacing * 0.251989 ) +evaluate ($x_3 = $spacing * -0.003543 ) +evaluate($y_3 = $spacing * -0.848968 ) +evaluate($z_3 = $spacing * -0.528432 ) +evaluate ($x_4 = $spacing * 0.237969 ) +evaluate($y_4 = $spacing * -0.706768 ) +evaluate($z_4 = $spacing * 0.666221 ) +evaluate ($x_5 = $spacing * -0.679040 ) +evaluate($y_5 = $spacing * -0.666804 ) +evaluate($z_5 = $spacing * -0.307047 ) +evaluate ($x_6 = $spacing * 0.751278 ) +evaluate($y_6 = $spacing * -0.509056 ) +evaluate($z_6 = $spacing * -0.420052 ) +evaluate ($x_7 = $spacing * -0.357028 ) +evaluate($y_7 = $spacing * -0.368763 ) +evaluate($z_7 = $spacing * 0.858222 ) +evaluate ($x_8 = $spacing * -0.364017 ) +evaluate($y_8 = $spacing * -0.296855 ) +evaluate($z_8 = $spacing * -0.882818 ) +evaluate ($x_9 = $spacing * 0.843960 ) +evaluate($y_9 = $spacing * -0.370368 ) +evaluate($z_9 = $spacing * 0.388020 ) +evaluate ($x_10 = $spacing * -0.864066 ) +evaluate($y_10 = $spacing * -0.383560 ) +evaluate($z_10 = $spacing * 0.325994 ) +evaluate ($x_11 = $spacing * 0.336977 ) +evaluate($y_11 = $spacing * -0.263612 ) +evaluate($z_11 = $spacing * -0.903856 ) +evaluate ($x_12 = $spacing * 0.350826 ) +evaluate($y_12 = $spacing * -0.074508 ) +evaluate($z_12 = $spacing * 0.933472 ) +evaluate ($x_13 = $spacing * -0.865211 ) +evaluate($y_13 = $spacing * -0.000000 ) +evaluate($z_13 = $spacing * -0.501408 ) +evaluate ($x_14 = $spacing * 0.984348 ) +evaluate($y_14 = $spacing * 0.074508 ) +evaluate($z_14 = $spacing * -0.159711 ) +evaluate ($x_15 = $spacing * -0.616689 ) +evaluate($y_15 = $spacing * 0.263612 ) +evaluate($z_15 = $spacing * 0.741757 ) +evaluate ($x_16 = $spacing * -0.146749 ) +evaluate($y_16 = $spacing * 0.383560 ) +evaluate($z_16 = $spacing * -0.911782 ) +evaluate ($x_17 = $spacing * 0.756265 ) +evaluate($y_17 = $spacing * 0.370368 ) +evaluate($z_17 = $spacing * 0.539343 ) +evaluate ($x_18 = $spacing * -0.946957 ) +evaluate($y_18 = $spacing * 0.296855 ) +evaluate($z_18 = $spacing * 0.123082 ) +evaluate ($x_19 = $spacing * 0.567126 ) +evaluate($y_19 = $spacing * 0.368763 ) +evaluate($z_19 = $spacing * -0.736466 ) +evaluate ($x_20 = $spacing * 0.009064 ) +evaluate($y_20 = $spacing * 0.509056 ) +evaluate($z_20 = $spacing * 0.860686 ) +evaluate ($x_21 = $spacing * -0.604014 ) +evaluate($y_21 = $spacing * 0.666804 ) +evaluate($z_21 = $spacing * -0.436509 ) +evaluate ($x_22 = $spacing * 0.696358 ) +evaluate($y_22 = $spacing * 0.706768 ) +evaluate($z_22 = $spacing * -0.124759 ) +evaluate ($x_23 = $spacing * -0.460254 ) +evaluate($y_23 = $spacing * 0.848968 ) +evaluate($z_23 = $spacing * 0.259653 ) +evaluate ($x_24 = $spacing * 0.058298 ) +evaluate($y_24 = $spacing * 0.912413 ) +evaluate($z_24 = $spacing * -0.405098 ) +evaluate ($x_25 = $spacing * 0.227639 ) +evaluate($y_25 = $spacing * 0.911797 ) +evaluate($z_25 = $spacing * 0.341770 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_26 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_26 new file mode 100644 index 0000000000000000000000000000000000000000..353a31415fbbb0848507d2081bb43d7589d3a078 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_26 @@ -0,0 +1,78 @@ +evaluate ($x_1 = $spacing * 0.392532 ) +evaluate($y_1 = $spacing * -0.919072 ) +evaluate($z_1 = $spacing * -0.034992 ) +evaluate ($x_2 = $spacing * -0.334206 ) +evaluate($y_2 = $spacing * -0.905665 ) +evaluate($z_2 = $spacing * 0.260916 ) +evaluate ($x_3 = $spacing * -0.015847 ) +evaluate($y_3 = $spacing * -0.833155 ) +evaluate($z_3 = $spacing * -0.552812 ) +evaluate ($x_4 = $spacing * 0.238974 ) +evaluate($y_4 = $spacing * -0.754691 ) +evaluate($z_4 = $spacing * 0.611010 ) +evaluate ($x_5 = $spacing * -0.636853 ) +evaluate($y_5 = $spacing * -0.705533 ) +evaluate($z_5 = $spacing * -0.310873 ) +evaluate ($x_6 = $spacing * 0.772475 ) +evaluate($y_6 = $spacing * -0.479524 ) +evaluate($z_6 = $spacing * -0.416339 ) +evaluate ($x_7 = $spacing * -0.304124 ) +evaluate($y_7 = $spacing * -0.396745 ) +evaluate($z_7 = $spacing * 0.866085 ) +evaluate ($x_8 = $spacing * -0.440573 ) +evaluate($y_8 = $spacing * -0.249698 ) +evaluate($z_8 = $spacing * -0.862291 ) +evaluate ($x_9 = $spacing * 0.830599 ) +evaluate($y_9 = $spacing * -0.421026 ) +evaluate($z_9 = $spacing * 0.364477 ) +evaluate ($x_10 = $spacing * -0.862334 ) +evaluate($y_10 = $spacing * -0.386041 ) +evaluate($z_10 = $spacing * 0.327647 ) +evaluate ($x_11 = $spacing * 0.293635 ) +evaluate($y_11 = $spacing * -0.324167 ) +evaluate($z_11 = $spacing * -0.899274 ) +evaluate ($x_12 = $spacing * 0.411924 ) +evaluate($y_12 = $spacing * -0.147812 ) +evaluate($z_12 = $spacing * 0.899150 ) +evaluate ($x_13 = $spacing * -0.934605 ) +evaluate($y_13 = $spacing * -0.085510 ) +evaluate($z_13 = $spacing * -0.345257 ) +evaluate ($x_14 = $spacing * 0.995327 ) +evaluate($y_14 = $spacing * 0.085510 ) +evaluate($z_14 = $spacing * -0.044865 ) +evaluate ($x_15 = $spacing * -0.665720 ) +evaluate($y_15 = $spacing * 0.147812 ) +evaluate($z_15 = $spacing * 0.731415 ) +evaluate ($x_16 = $spacing * -0.006423 ) +evaluate($y_16 = $spacing * 0.324167 ) +evaluate($z_16 = $spacing * -0.945978 ) +evaluate ($x_17 = $spacing * 0.721956 ) +evaluate($y_17 = $spacing * 0.386041 ) +evaluate($z_17 = $spacing * 0.574240 ) +evaluate ($x_18 = $spacing * -0.902083 ) +evaluate($y_18 = $spacing * 0.421026 ) +evaluate($z_18 = $spacing * 0.094787 ) +evaluate ($x_19 = $spacing * 0.681811 ) +evaluate($y_19 = $spacing * 0.249698 ) +evaluate($z_19 = $spacing * -0.687593 ) +evaluate ($x_20 = $spacing * 0.026503 ) +evaluate($y_20 = $spacing * 0.396745 ) +evaluate($z_20 = $spacing * 0.917546 ) +evaluate ($x_21 = $spacing * -0.609392 ) +evaluate($y_21 = $spacing * 0.479524 ) +evaluate($z_21 = $spacing * -0.631426 ) +evaluate ($x_22 = $spacing * 0.701210 ) +evaluate($y_22 = $spacing * 0.705533 ) +evaluate($z_22 = $spacing * -0.102604 ) +evaluate ($x_23 = $spacing * -0.413376 ) +evaluate($y_23 = $spacing * 0.754691 ) +evaluate($z_23 = $spacing * 0.509472 ) +evaluate ($x_24 = $spacing * 0.183116 ) +evaluate($y_24 = $spacing * 0.833155 ) +evaluate($z_24 = $spacing * -0.521844 ) +evaluate ($x_25 = $spacing * 0.239095 ) +evaluate($y_25 = $spacing * 0.905665 ) +evaluate($z_25 = $spacing * 0.350149 ) +evaluate ($x_26 = $spacing * -0.363327 ) +evaluate($y_26 = $spacing * 0.919072 ) +evaluate($z_26 = $spacing * -0.152641 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_27 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_27 new file mode 100644 index 0000000000000000000000000000000000000000..a16c6ed0a9efea3c55d138883678370b33d25b94 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_27 @@ -0,0 +1,81 @@ +evaluate ($x_1 = $spacing * 0.130082 ) +evaluate($y_1 = $spacing * -0.990069 ) +evaluate($z_1 = $spacing * -0.053305 ) +evaluate ($x_2 = $spacing * -0.396994 ) +evaluate($y_2 = $spacing * -0.831810 ) +evaluate($z_2 = $spacing * 0.387927 ) +evaluate ($x_3 = $spacing * 0.079525 ) +evaluate($y_3 = $spacing * -0.707119 ) +evaluate($z_3 = $spacing * -0.702608 ) +evaluate ($x_4 = $spacing * 0.274326 ) +evaluate($y_4 = $spacing * -0.756757 ) +evaluate($z_4 = $spacing * 0.593350 ) +evaluate ($x_5 = $spacing * -0.542926 ) +evaluate($y_5 = $spacing * -0.788371 ) +evaluate($z_5 = $spacing * -0.289314 ) +evaluate ($x_6 = $spacing * 0.686681 ) +evaluate($y_6 = $spacing * -0.675796 ) +evaluate($z_6 = $spacing * -0.267897 ) +evaluate ($x_7 = $spacing * -0.282271 ) +evaluate($y_7 = $spacing * -0.364969 ) +evaluate($z_7 = $spacing * 0.887198 ) +evaluate ($x_8 = $spacing * -0.453525 ) +evaluate($y_8 = $spacing * -0.320411 ) +evaluate($z_8 = $spacing * -0.831656 ) +evaluate ($x_9 = $spacing * 0.822339 ) +evaluate($y_9 = $spacing * -0.452629 ) +evaluate($z_9 = $spacing * 0.344797 ) +evaluate ($x_10 = $spacing * -0.872472 ) +evaluate($y_10 = $spacing * -0.366505 ) +evaluate($z_10 = $spacing * 0.323214 ) +evaluate ($x_11 = $spacing * 0.570665 ) +evaluate($y_11 = $spacing * -0.229588 ) +evaluate($z_11 = $spacing * -0.788436 ) +evaluate ($x_12 = $spacing * 0.431172 ) +evaluate($y_12 = $spacing * -0.131039 ) +evaluate($z_12 = $spacing * 0.892703 ) +evaluate ($x_13 = $spacing * -0.923628 ) +evaluate($y_13 = $spacing * -0.183977 ) +evaluate($z_13 = $spacing * -0.336249 ) +evaluate ($x_14 = $spacing * 0.976676 ) +evaluate($y_14 = $spacing * 0.000000 ) +evaluate($z_14 = $spacing * -0.214719 ) +evaluate ($x_15 = $spacing * -0.697431 ) +evaluate($y_15 = $spacing * 0.183977 ) +evaluate($z_15 = $spacing * 0.692635 ) +evaluate ($x_16 = $spacing * 0.016995 ) +evaluate($y_16 = $spacing * 0.131039 ) +evaluate($z_16 = $spacing * -0.991232 ) +evaluate ($x_17 = $spacing * 0.848732 ) +evaluate($y_17 = $spacing * 0.229588 ) +evaluate($z_17 = $spacing * 0.476385 ) +evaluate ($x_18 = $spacing * -0.927585 ) +evaluate($y_18 = $spacing * 0.366505 ) +evaluate($z_18 = $spacing * 0.072523 ) +evaluate ($x_19 = $spacing * 0.601897 ) +evaluate($y_19 = $spacing * 0.452629 ) +evaluate($z_19 = $spacing * -0.657911 ) +evaluate ($x_20 = $spacing * -0.062891 ) +evaluate($y_20 = $spacing * 0.320411 ) +evaluate($z_20 = $spacing * 0.945189 ) +evaluate ($x_21 = $spacing * -0.628354 ) +evaluate($y_21 = $spacing * 0.364969 ) +evaluate($z_21 = $spacing * -0.687000 ) +evaluate ($x_22 = $spacing * 0.735725 ) +evaluate($y_22 = $spacing * 0.675796 ) +evaluate($z_22 = $spacing * -0.044815 ) +evaluate ($x_23 = $spacing * -0.371519 ) +evaluate($y_23 = $spacing * 0.788371 ) +evaluate($z_23 = $spacing * 0.490352 ) +evaluate ($x_24 = $spacing * 0.000166 ) +evaluate($y_24 = $spacing * 0.756757 ) +evaluate($z_24 = $spacing * -0.653697 ) +evaluate ($x_25 = $spacing * 0.366882 ) +evaluate($y_25 = $spacing * 0.707119 ) +evaluate($z_25 = $spacing * 0.604467 ) +evaluate ($x_26 = $spacing * -0.523093 ) +evaluate($y_26 = $spacing * 0.831810 ) +evaluate($z_26 = $spacing * -0.185649 ) +evaluate ($x_27 = $spacing * 0.140444 ) +evaluate($y_27 = $spacing * 0.990069 ) +evaluate($z_27 = $spacing * -0.006170 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_28 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_28 new file mode 100644 index 0000000000000000000000000000000000000000..0131a1d85df2831ac0c78d38f19cbc9a8be068c7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_28 @@ -0,0 +1,84 @@ +evaluate ($x_1 = $spacing * 0.271423 ) +evaluate($y_1 = $spacing * -0.959995 ) +evaluate($z_1 = $spacing * 0.068850 ) +evaluate ($x_2 = $spacing * -0.239004 ) +evaluate($y_2 = $spacing * -0.808385 ) +evaluate($z_2 = $spacing * 0.537950 ) +evaluate ($x_3 = $spacing * -0.086378 ) +evaluate($y_3 = $spacing * -0.766909 ) +evaluate($z_3 = $spacing * -0.635917 ) +evaluate ($x_4 = $spacing * 0.393393 ) +evaluate($y_4 = $spacing * -0.609055 ) +evaluate($z_4 = $spacing * 0.688690 ) +evaluate ($x_5 = $spacing * -0.422667 ) +evaluate($y_5 = $spacing * -0.900946 ) +evaluate($z_5 = $spacing * -0.098229 ) +evaluate ($x_6 = $spacing * 0.540001 ) +evaluate($y_6 = $spacing * -0.683412 ) +evaluate($z_6 = $spacing * -0.491271 ) +evaluate ($x_7 = $spacing * -0.318372 ) +evaluate($y_7 = $spacing * -0.280370 ) +evaluate($z_7 = $spacing * 0.905556 ) +evaluate ($x_8 = $spacing * -0.322482 ) +evaluate($y_8 = $spacing * -0.232921 ) +evaluate($z_8 = $spacing * -0.917471 ) +evaluate ($x_9 = $spacing * 0.843046 ) +evaluate($y_9 = $spacing * -0.521974 ) +evaluate($z_9 = $spacing * 0.129679 ) +evaluate ($x_10 = $spacing * -0.826894 ) +evaluate($y_10 = $spacing * -0.475235 ) +evaluate($z_10 = $spacing * 0.300661 ) +evaluate ($x_11 = $spacing * 0.351831 ) +evaluate($y_11 = $spacing * -0.145224 ) +evaluate($z_11 = $spacing * -0.924730 ) +evaluate ($x_12 = $spacing * 0.245304 ) +evaluate($y_12 = $spacing * 0.033392 ) +evaluate($z_12 = $spacing * 0.968871 ) +evaluate ($x_13 = $spacing * -0.797100 ) +evaluate($y_13 = $spacing * -0.433690 ) +evaluate($z_13 = $spacing * -0.420172 ) +evaluate ($x_14 = $spacing * 0.883312 ) +evaluate($y_14 = $spacing * -0.110845 ) +evaluate($z_14 = $spacing * -0.455492 ) +evaluate ($x_15 = $spacing * -0.761191 ) +evaluate($y_15 = $spacing * 0.110845 ) +evaluate($z_15 = $spacing * 0.638984 ) +evaluate ($x_16 = $spacing * -0.079868 ) +evaluate($y_16 = $spacing * 0.433690 ) +evaluate($z_16 = $spacing * -0.897516 ) +evaluate ($x_17 = $spacing * 0.799055 ) +evaluate($y_17 = $spacing * -0.033392 ) +evaluate($z_17 = $spacing * 0.600330 ) +evaluate ($x_18 = $spacing * -0.988867 ) +evaluate($y_18 = $spacing * 0.145224 ) +evaluate($z_18 = $spacing * -0.032448 ) +evaluate ($x_19 = $spacing * 0.596584 ) +evaluate($y_19 = $spacing * 0.475235 ) +evaluate($z_19 = $spacing * -0.646714 ) +evaluate ($x_20 = $spacing * -0.205842 ) +evaluate($y_20 = $spacing * 0.521974 ) +evaluate($z_20 = $spacing * 0.827751 ) +evaluate ($x_21 = $spacing * -0.721845 ) +evaluate($y_21 = $spacing * 0.232921 ) +evaluate($z_21 = $spacing * -0.651681 ) +evaluate ($x_22 = $spacing * 0.958262 ) +evaluate($y_22 = $spacing * 0.280370 ) +evaluate($z_22 = $spacing * 0.055911 ) +evaluate ($x_23 = $spacing * -0.661658 ) +evaluate($y_23 = $spacing * 0.683412 ) +evaluate($z_23 = $spacing * 0.308476 ) +evaluate ($x_24 = $spacing * 0.072562 ) +evaluate($y_24 = $spacing * 0.900946 ) +evaluate($z_24 = $spacing * -0.427821 ) +evaluate ($x_25 = $spacing * 0.483424 ) +evaluate($y_25 = $spacing * 0.609055 ) +evaluate($z_25 = $spacing * 0.628771 ) +evaluate ($x_26 = $spacing * -0.553269 ) +evaluate($y_26 = $spacing * 0.766909 ) +evaluate($z_26 = $spacing * -0.325184 ) +evaluate ($x_27 = $spacing * 0.588515 ) +evaluate($y_27 = $spacing * 0.808385 ) +evaluate($z_27 = $spacing * -0.012794 ) +evaluate ($x_28 = $spacing * -0.041274 ) +evaluate($y_28 = $spacing * 0.959995 ) +evaluate($z_28 = $spacing * 0.276960 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_29 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_29 new file mode 100644 index 0000000000000000000000000000000000000000..d2244b416b1ae290b0cc782847843f182ad83003 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_29 @@ -0,0 +1,87 @@ +evaluate ($x_1 = $spacing * 0.303229 ) +evaluate($y_1 = $spacing * -0.928833 ) +evaluate($z_1 = $spacing * 0.212886 ) +evaluate ($x_2 = $spacing * -0.313997 ) +evaluate($y_2 = $spacing * -0.941898 ) +evaluate($z_2 = $spacing * 0.119304 ) +evaluate ($x_3 = $spacing * -0.043277 ) +evaluate($y_3 = $spacing * -0.851351 ) +evaluate($z_3 = $spacing * -0.522808 ) +evaluate ($x_4 = $spacing * 0.445021 ) +evaluate($y_4 = $spacing * -0.561368 ) +evaluate($z_4 = $spacing * 0.697726 ) +evaluate ($x_5 = $spacing * -0.679240 ) +evaluate($y_5 = $spacing * -0.646116 ) +evaluate($z_5 = $spacing * -0.348092 ) +evaluate ($x_6 = $spacing * 0.598463 ) +evaluate($y_6 = $spacing * -0.741069 ) +evaluate($z_6 = $spacing * -0.304399 ) +evaluate ($x_7 = $spacing * -0.252470 ) +evaluate($y_7 = $spacing * -0.633474 ) +evaluate($z_7 = $spacing * 0.731416 ) +evaluate ($x_8 = $spacing * -0.371108 ) +evaluate($y_8 = $spacing * -0.319647 ) +evaluate($z_8 = $spacing * -0.871840 ) +evaluate ($x_9 = $spacing * 0.900525 ) +evaluate($y_9 = $spacing * -0.377019 ) +evaluate($z_9 = $spacing * 0.216590 ) +evaluate ($x_10 = $spacing * -0.796062 ) +evaluate($y_10 = $spacing * -0.510051 ) +evaluate($z_10 = $spacing * 0.325781 ) +evaluate ($x_11 = $spacing * 0.367033 ) +evaluate($y_11 = $spacing * -0.396314 ) +evaluate($z_11 = $spacing * -0.841559 ) +evaluate ($x_12 = $spacing * 0.085527 ) +evaluate($y_12 = $spacing * -0.089404 ) +evaluate($z_12 = $spacing * 0.992317 ) +evaluate ($x_13 = $spacing * -0.903881 ) +evaluate($y_13 = $spacing * -0.066304 ) +evaluate($z_13 = $spacing * -0.422613 ) +evaluate ($x_14 = $spacing * 0.884869 ) +evaluate($y_14 = $spacing * -0.158667 ) +evaluate($z_14 = $spacing * -0.437986 ) +evaluate ($x_15 = $spacing * -0.575129 ) +evaluate($y_15 = $spacing * -0.000000 ) +evaluate($z_15 = $spacing * 0.818062 ) +evaluate ($x_16 = $spacing * 0.112652 ) +evaluate($y_16 = $spacing * 0.158667 ) +evaluate($z_16 = $spacing * -0.980884 ) +evaluate ($x_17 = $spacing * 0.703593 ) +evaluate($y_17 = $spacing * 0.066304 ) +evaluate($z_17 = $spacing * 0.707503 ) +evaluate ($x_18 = $spacing * -0.962700 ) +evaluate($y_18 = $spacing * 0.089404 ) +evaluate($z_18 = $spacing * 0.255372 ) +evaluate ($x_19 = $spacing * 0.667671 ) +evaluate($y_19 = $spacing * 0.396314 ) +evaluate($z_19 = $spacing * -0.630199 ) +evaluate ($x_20 = $spacing * -0.037126 ) +evaluate($y_20 = $spacing * 0.510051 ) +evaluate($z_20 = $spacing * 0.859342 ) +evaluate ($x_21 = $spacing * -0.508592 ) +evaluate($y_21 = $spacing * 0.377019 ) +evaluate($z_21 = $spacing * -0.774074 ) +evaluate ($x_22 = $spacing * 0.945989 ) +evaluate($y_22 = $spacing * 0.319647 ) +evaluate($z_22 = $spacing * 0.054130 ) +evaluate ($x_23 = $spacing * -0.602801 ) +evaluate($y_23 = $spacing * 0.633474 ) +evaluate($z_23 = $spacing * 0.485120 ) +evaluate ($x_24 = $spacing * 0.083883 ) +evaluate($y_24 = $spacing * 0.741069 ) +evaluate($z_24 = $spacing * -0.666169 ) +evaluate ($x_25 = $spacing * 0.557439 ) +evaluate($y_25 = $spacing * 0.646116 ) +evaluate($z_25 = $spacing * 0.521341 ) +evaluate ($x_26 = $spacing * -0.807167 ) +evaluate($y_26 = $spacing * 0.561368 ) +evaluate($z_26 = $spacing * -0.182611 ) +evaluate ($x_27 = $spacing * 0.506601 ) +evaluate($y_27 = $spacing * 0.851351 ) +evaluate($z_27 = $spacing * -0.136222 ) +evaluate ($x_28 = $spacing * -0.005990 ) +evaluate($y_28 = $spacing * 0.941898 ) +evaluate($z_28 = $spacing * 0.335845 ) +evaluate ($x_29 = $spacing * -0.302951 ) +evaluate($y_29 = $spacing * 0.928833 ) +evaluate($z_29 = $spacing * -0.213282 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_3 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_3 new file mode 100644 index 0000000000000000000000000000000000000000..440220478a41a7e45a9576b168f541bfc638d647 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_3 @@ -0,0 +1,9 @@ +evaluate ($x_1 = $spacing * 0.721237 ) +evaluate($y_1 = $spacing * -0.691085 ) +evaluate($z_1 = $spacing * 0.047104 ) +evaluate ($x_2 = $spacing * -0.737369 ) +evaluate($y_2 = $spacing * 0.000000 ) +evaluate($z_2 = $spacing * 0.675490 ) +evaluate ($x_3 = $spacing * 0.016131 ) +evaluate($y_3 = $spacing * 0.691085 ) +evaluate($z_3 = $spacing * -0.722594 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_30 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_30 new file mode 100644 index 0000000000000000000000000000000000000000..1994c92eec64040a64ab85d5679aa6f776d7f87f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_30 @@ -0,0 +1,90 @@ +evaluate ($x_1 = $spacing * 0.401381 ) +evaluate($y_1 = $spacing * -0.914426 ) +evaluate($z_1 = $spacing * 0.052134 ) +evaluate ($x_2 = $spacing * -0.248643 ) +evaluate($y_2 = $spacing * -0.949613 ) +evaluate($z_2 = $spacing * 0.190817 ) +evaluate ($x_3 = $spacing * -0.066822 ) +evaluate($y_3 = $spacing * -0.898055 ) +evaluate($z_3 = $spacing * -0.434777 ) +evaluate ($x_4 = $spacing * 0.434792 ) +evaluate($y_4 = $spacing * -0.640026 ) +evaluate($z_4 = $spacing * 0.633500 ) +evaluate ($x_5 = $spacing * -0.726964 ) +evaluate($y_5 = $spacing * -0.643466 ) +evaluate($z_5 = $spacing * -0.239738 ) +evaluate ($x_6 = $spacing * 0.686416 ) +evaluate($y_6 = $spacing * -0.587029 ) +evaluate($z_6 = $spacing * -0.429220 ) +evaluate ($x_7 = $spacing * -0.182762 ) +evaluate($y_7 = $spacing * -0.632834 ) +evaluate($z_7 = $spacing * 0.752409 ) +evaluate ($x_8 = $spacing * -0.450598 ) +evaluate($y_8 = $spacing * -0.435249 ) +evaluate($z_8 = $spacing * -0.779436 ) +evaluate ($x_9 = $spacing * 0.895143 ) +evaluate($y_9 = $spacing * -0.398818 ) +evaluate($z_9 = $spacing * 0.199158 ) +evaluate ($x_10 = $spacing * -0.756520 ) +evaluate($y_10 = $spacing * -0.523698 ) +evaluate($z_10 = $spacing * 0.391686 ) +evaluate ($x_11 = $spacing * 0.225570 ) +evaluate($y_11 = $spacing * -0.483604 ) +evaluate($z_11 = $spacing * -0.845722 ) +evaluate ($x_12 = $spacing * 0.128549 ) +evaluate($y_12 = $spacing * -0.076955 ) +evaluate($z_12 = $spacing * 0.988713 ) +evaluate ($x_13 = $spacing * -0.845371 ) +evaluate($y_13 = $spacing * 0.016604 ) +evaluate($z_13 = $spacing * -0.533921 ) +evaluate ($x_14 = $spacing * 0.955181 ) +evaluate($y_14 = $spacing * 0.018603 ) +evaluate($z_14 = $spacing * -0.295438 ) +evaluate ($x_15 = $spacing * -0.565123 ) +evaluate($y_15 = $spacing * -0.080517 ) +evaluate($z_15 = $spacing * 0.821068 ) +evaluate ($x_16 = $spacing * -0.118255 ) +evaluate($y_16 = $spacing * 0.080517 ) +evaluate($z_16 = $spacing * -0.989713 ) +evaluate ($x_17 = $spacing * 0.708069 ) +evaluate($y_17 = $spacing * -0.018603 ) +evaluate($z_17 = $spacing * 0.705898 ) +evaluate ($x_18 = $spacing * -0.996710 ) +evaluate($y_18 = $spacing * -0.016604 ) +evaluate($z_18 = $spacing * 0.079329 ) +evaluate ($x_19 = $spacing * 0.573770 ) +evaluate($y_19 = $spacing * 0.076955 ) +evaluate($z_19 = $spacing * -0.815393 ) +evaluate ($x_20 = $spacing * -0.193784 ) +evaluate($y_20 = $spacing * 0.483604 ) +evaluate($z_20 = $spacing * 0.853566 ) +evaluate ($x_21 = $spacing * -0.487439 ) +evaluate($y_21 = $spacing * 0.523698 ) +evaluate($z_21 = $spacing * -0.698673 ) +evaluate ($x_22 = $spacing * 0.885025 ) +evaluate($y_22 = $spacing * 0.398818 ) +evaluate($z_22 = $spacing * 0.240155 ) +evaluate ($x_23 = $spacing * -0.761482 ) +evaluate($y_23 = $spacing * 0.435249 ) +evaluate($z_23 = $spacing * 0.480316 ) +evaluate ($x_24 = $spacing * 0.188265 ) +evaluate($y_24 = $spacing * 0.632834 ) +evaluate($z_24 = $spacing * -0.751051 ) +evaluate ($x_25 = $spacing * 0.407922 ) +evaluate($y_25 = $spacing * 0.587029 ) +evaluate($z_25 = $spacing * 0.699283 ) +evaluate ($x_26 = $spacing * -0.755035 ) +evaluate($y_26 = $spacing * 0.643466 ) +evaluate($z_26 = $spacing * -0.125992 ) +evaluate ($x_27 = $spacing * 0.679597 ) +evaluate($y_27 = $spacing * 0.640026 ) +evaluate($z_27 = $spacing * -0.358490 ) +evaluate ($x_28 = $spacing * -0.261422 ) +evaluate($y_28 = $spacing * 0.898055 ) +evaluate($z_28 = $spacing * 0.353773 ) +evaluate ($x_29 = $spacing * -0.131322 ) +evaluate($y_29 = $spacing * 0.949613 ) +evaluate($z_29 = $spacing * -0.284586 ) +evaluate ($x_30 = $spacing * 0.379552 ) +evaluate($y_30 = $spacing * 0.914426 ) +evaluate($z_30 = $spacing * 0.140586 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_31 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_31 new file mode 100644 index 0000000000000000000000000000000000000000..4b85580d08a9ca6052399f0ed1554a48f760946c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_31 @@ -0,0 +1,93 @@ +evaluate ($x_1 = $spacing * 0.376501 ) +evaluate($y_1 = $spacing * -0.921111 ) +evaluate($z_1 = $spacing * -0.098998 ) +evaluate ($x_2 = $spacing * -0.194173 ) +evaluate($y_2 = $spacing * -0.933294 ) +evaluate($z_2 = $spacing * 0.302092 ) +evaluate ($x_3 = $spacing * -0.217343 ) +evaluate($y_3 = $spacing * -0.918744 ) +evaluate($z_3 = $spacing * -0.329653 ) +evaluate ($x_4 = $spacing * 0.360192 ) +evaluate($y_4 = $spacing * -0.736259 ) +evaluate($z_4 = $spacing * 0.572873 ) +evaluate ($x_5 = $spacing * -0.784427 ) +evaluate($y_5 = $spacing * -0.573071 ) +evaluate($z_5 = $spacing * -0.237201 ) +evaluate ($x_6 = $spacing * 0.750257 ) +evaluate($y_6 = $spacing * -0.509272 ) +evaluate($z_6 = $spacing * -0.421611 ) +evaluate ($x_7 = $spacing * -0.205202 ) +evaluate($y_7 = $spacing * -0.491663 ) +evaluate($z_7 = $spacing * 0.846262 ) +evaluate ($x_8 = $spacing * -0.419227 ) +evaluate($y_8 = $spacing * -0.490810 ) +evaluate($z_8 = $spacing * -0.763777 ) +evaluate ($x_9 = $spacing * 0.830785 ) +evaluate($y_9 = $spacing * -0.507667 ) +evaluate($z_9 = $spacing * 0.228190 ) +evaluate ($x_10 = $spacing * -0.708161 ) +evaluate($y_10 = $spacing * -0.590912 ) +evaluate($z_10 = $spacing * 0.386435 ) +evaluate ($x_11 = $spacing * 0.221707 ) +evaluate($y_11 = $spacing * -0.594843 ) +evaluate($z_11 = $spacing * -0.772663 ) +evaluate ($x_12 = $spacing * 0.398099 ) +evaluate($y_12 = $spacing * -0.181958 ) +evaluate($z_12 = $spacing * 0.899115 ) +evaluate ($x_13 = $spacing * -0.777060 ) +evaluate($y_13 = $spacing * 0.021117 ) +evaluate($z_13 = $spacing * -0.629072 ) +evaluate ($x_14 = $spacing * 0.982466 ) +evaluate($y_14 = $spacing * 0.044577 ) +evaluate($z_14 = $spacing * -0.181033 ) +evaluate ($x_15 = $spacing * -0.697787 ) +evaluate($y_15 = $spacing * -0.041081 ) +evaluate($z_15 = $spacing * 0.715126 ) +evaluate ($x_16 = $spacing * -0.128511 ) +evaluate($y_16 = $spacing * -0.000000 ) +evaluate($z_16 = $spacing * -0.991708 ) +evaluate ($x_17 = $spacing * 0.857018 ) +evaluate($y_17 = $spacing * 0.041081 ) +evaluate($z_17 = $spacing * 0.513647 ) +evaluate ($x_18 = $spacing * -0.996159 ) +evaluate($y_18 = $spacing * -0.044577 ) +evaluate($z_18 = $spacing * 0.075367 ) +evaluate ($x_19 = $spacing * 0.591049 ) +evaluate($y_19 = $spacing * -0.021117 ) +evaluate($z_19 = $spacing * -0.806359 ) +evaluate ($x_20 = $spacing * -0.155774 ) +evaluate($y_20 = $spacing * 0.181958 ) +evaluate($z_20 = $spacing * 0.970889 ) +evaluate ($x_21 = $spacing * -0.411329 ) +evaluate($y_21 = $spacing * 0.594843 ) +evaluate($z_21 = $spacing * -0.690630 ) +evaluate ($x_22 = $spacing * 0.783269 ) +evaluate($y_22 = $spacing * 0.590912 ) +evaluate($z_22 = $spacing * 0.193168 ) +evaluate ($x_23 = $spacing * -0.745181 ) +evaluate($y_23 = $spacing * 0.507667 ) +evaluate($z_23 = $spacing * 0.432412 ) +evaluate ($x_24 = $spacing * 0.210701 ) +evaluate($y_24 = $spacing * 0.490810 ) +evaluate($z_24 = $spacing * -0.845406 ) +evaluate ($x_25 = $spacing * 0.414128 ) +evaluate($y_25 = $spacing * 0.491663 ) +evaluate($z_25 = $spacing * 0.766006 ) +evaluate ($x_26 = $spacing * -0.832941 ) +evaluate($y_26 = $spacing * 0.509272 ) +evaluate($z_26 = $spacing * -0.216452 ) +evaluate ($x_27 = $spacing * 0.698057 ) +evaluate($y_27 = $spacing * 0.573071 ) +evaluate($z_27 = $spacing * -0.429309 ) +evaluate ($x_28 = $spacing * -0.202275 ) +evaluate($y_28 = $spacing * 0.736259 ) +evaluate($z_28 = $spacing * 0.645761 ) +evaluate ($x_29 = $spacing * 0.126139 ) +evaluate($y_29 = $spacing * 0.918744 ) +evaluate($z_29 = $spacing * -0.374163 ) +evaluate ($x_30 = $spacing * 0.264760 ) +evaluate($y_30 = $spacing * 0.933294 ) +evaluate($z_30 = $spacing * 0.242622 ) +evaluate ($x_31 = $spacing * -0.389299 ) +evaluate($y_31 = $spacing * 0.921111 ) +evaluate($z_31 = $spacing * 0.000239 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_32 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_32 new file mode 100644 index 0000000000000000000000000000000000000000..a685eaa74ed8fe0b865e12f6563913f2cb09c78d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_32 @@ -0,0 +1,96 @@ +evaluate ($x_1 = $spacing * 0.346982 ) +evaluate($y_1 = $spacing * -0.937755 ) +evaluate($z_1 = $spacing * -0.014818 ) +evaluate ($x_2 = $spacing * -0.200178 ) +evaluate($y_2 = $spacing * -0.937746 ) +evaluate($z_2 = $spacing * 0.283834 ) +evaluate ($x_3 = $spacing * 0.052674 ) +evaluate($y_3 = $spacing * -0.830957 ) +evaluate($z_3 = $spacing * -0.553838 ) +evaluate ($x_4 = $spacing * 0.338038 ) +evaluate($y_4 = $spacing * -0.708748 ) +evaluate($z_4 = $spacing * 0.619198 ) +evaluate ($x_5 = $spacing * -0.494496 ) +evaluate($y_5 = $spacing * -0.830868 ) 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-0.311081 ) +evaluate ($x_14 = $spacing * 0.983168 ) +evaluate($y_14 = $spacing * -0.055340 ) +evaluate($z_14 = $spacing * -0.174120 ) +evaluate ($x_15 = $spacing * -0.678196 ) +evaluate($y_15 = $spacing * -0.055389 ) +evaluate($z_15 = $spacing * 0.732790 ) +evaluate ($x_16 = $spacing * -0.163129 ) +evaluate($y_16 = $spacing * 0.162168 ) +evaluate($z_16 = $spacing * -0.973186 ) +evaluate ($x_17 = $spacing * 0.730346 ) +evaluate($y_17 = $spacing * -0.162168 ) +evaluate($z_17 = $spacing * 0.663548 ) +evaluate ($x_18 = $spacing * -0.983164 ) +evaluate($y_18 = $spacing * 0.055389 ) +evaluate($z_18 = $spacing * 0.174129 ) +evaluate ($x_19 = $spacing * 0.678192 ) +evaluate($y_19 = $spacing * 0.055340 ) +evaluate($z_19 = $spacing * -0.732798 ) +evaluate ($x_20 = $spacing * -0.221279 ) +evaluate($y_20 = $spacing * 0.325394 ) +evaluate($z_20 = $spacing * 0.919323 ) +evaluate ($x_21 = $spacing * -0.730218 ) +evaluate($y_21 = $spacing * 0.162227 ) +evaluate($z_21 = $spacing * -0.663675 ) +evaluate ($x_22 = $spacing * 0.892898 ) +evaluate($y_22 = $spacing * 0.325566 ) +evaluate($z_22 = $spacing * 0.311032 ) +evaluate ($x_23 = $spacing * -0.669265 ) +evaluate($y_23 = $spacing * 0.568788 ) +evaluate($z_23 = $spacing * 0.478085 ) +evaluate ($x_24 = $spacing * 0.293712 ) +evaluate($y_24 = $spacing * 0.543045 ) +evaluate($z_24 = $spacing * -0.786661 ) +evaluate ($x_25 = $spacing * 0.432845 ) +evaluate($y_25 = $spacing * 0.428871 ) +evaluate($z_25 = $spacing * 0.792916 ) +evaluate ($x_26 = $spacing * -0.820521 ) +evaluate($y_26 = $spacing * 0.543045 ) +evaluate($z_26 = $spacing * -0.178461 ) +evaluate ($x_27 = $spacing * 0.764066 ) +evaluate($y_27 = $spacing * 0.568823 ) +evaluate($z_27 = $spacing * -0.304373 ) +evaluate ($x_28 = $spacing * -0.052777 ) +evaluate($y_28 = $spacing * 0.830868 ) +evaluate($z_28 = $spacing * 0.553961 ) +evaluate ($x_29 = $spacing * -0.338000 ) +evaluate($y_29 = $spacing * 0.708748 ) +evaluate($z_29 = $spacing * -0.619219 ) +evaluate ($x_30 = $spacing * 0.494336 ) +evaluate($y_30 = $spacing * 0.830957 ) +evaluate($z_30 = $spacing * 0.255231 ) +evaluate ($x_31 = $spacing * -0.347004 ) +evaluate($y_31 = $spacing * 0.937746 ) +evaluate($z_31 = $spacing * 0.014867 ) +evaluate ($x_32 = $spacing * 0.200125 ) +evaluate($y_32 = $spacing * 0.937755 ) +evaluate($z_32 = $spacing * -0.283842 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_33 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_33 new file mode 100644 index 0000000000000000000000000000000000000000..f82429c87d49009e2a206f0bb9dbe4b9814329a9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_33 @@ -0,0 +1,99 @@ +evaluate ($x_1 = $spacing * 0.380780 ) +evaluate($y_1 = $spacing * -0.924063 ) +evaluate($z_1 = $spacing * 0.033372 ) +evaluate ($x_2 = $spacing * -0.201792 ) +evaluate($y_2 = $spacing * -0.941484 ) +evaluate($z_2 = $spacing * 0.269977 ) +evaluate ($x_3 = $spacing * -0.056690 ) +evaluate($y_3 = $spacing * -0.906534 ) +evaluate($z_3 = $spacing * -0.418309 ) +evaluate ($x_4 = $spacing * 0.363484 ) +evaluate($y_4 = $spacing * -0.710202 ) +evaluate($z_4 = $spacing * 0.602903 ) +evaluate ($x_5 = $spacing * -0.627331 ) +evaluate($y_5 = $spacing * -0.748186 ) +evaluate($z_5 = $spacing * -0.216038 ) +evaluate ($x_6 = $spacing * 0.631864 ) +evaluate($y_6 = $spacing * -0.642822 ) +evaluate($z_6 = $spacing * -0.433044 ) +evaluate ($x_7 = $spacing * -0.254324 ) +evaluate($y_7 = $spacing * -0.543042 ) +evaluate($z_7 = $spacing * 0.800266 ) +evaluate ($x_8 = $spacing * -0.412816 ) +evaluate($y_8 = $spacing * -0.461476 ) +evaluate($z_8 = $spacing * -0.785253 ) +evaluate ($x_9 = $spacing * 0.846053 ) +evaluate($y_9 = $spacing * -0.482882 ) +evaluate($z_9 = $spacing * 0.225875 ) +evaluate ($x_10 = $spacing * -0.724868 ) +evaluate($y_10 = $spacing * -0.582037 ) +evaluate($z_10 = $spacing * 0.368509 ) +evaluate ($x_11 = $spacing * 0.213070 ) +evaluate($y_11 = $spacing * -0.496366 ) +evaluate($z_11 = $spacing * -0.841559 ) +evaluate ($x_12 = $spacing * 0.300437 ) +evaluate($y_12 = $spacing * -0.213506 ) +evaluate($z_12 = $spacing * 0.929598 ) +evaluate ($x_13 = $spacing * -0.876045 ) +evaluate($y_13 = $spacing * -0.212524 ) +evaluate($z_13 = $spacing * -0.432872 ) +evaluate ($x_14 = $spacing * 0.931649 ) +evaluate($y_14 = $spacing * -0.132049 ) +evaluate($z_14 = $spacing * -0.338517 ) +evaluate ($x_15 = $spacing * -0.697304 ) +evaluate($y_15 = $spacing * -0.032475 ) +evaluate($z_15 = $spacing * 0.716039 ) +evaluate ($x_16 = $spacing * -0.037308 ) +evaluate($y_16 = $spacing * 0.070799 ) +evaluate($z_16 = $spacing * -0.996793 ) +evaluate ($x_17 = $spacing * 0.764646 ) +evaluate($y_17 = $spacing * 0.000002 ) +evaluate($z_17 = $spacing * 0.644450 ) +evaluate ($x_18 = $spacing * -0.988709 ) +evaluate($y_18 = $spacing * -0.070799 ) +evaluate($z_18 = $spacing * 0.132069 ) +evaluate ($x_19 = $spacing * 0.587592 ) +evaluate($y_19 = $spacing * 0.032470 ) +evaluate($z_19 = $spacing * -0.808506 ) +evaluate ($x_20 = $spacing * -0.175817 ) +evaluate($y_20 = $spacing * 0.132047 ) +evaluate($z_20 = $spacing * 0.975526 ) +evaluate ($x_21 = $spacing * -0.574997 ) +evaluate($y_21 = $spacing * 0.212521 ) +evaluate($z_21 = $spacing * -0.790072 ) +evaluate ($x_22 = $spacing * 0.967051 ) +evaluate($y_22 = $spacing * 0.213517 ) +evaluate($z_22 = $spacing * 0.138645 ) +evaluate ($x_23 = $spacing * -0.793312 ) +evaluate($y_23 = $spacing * 0.496366 ) +evaluate($z_23 = $spacing * 0.352529 ) +evaluate ($x_24 = $spacing * 0.240406 ) +evaluate($y_24 = $spacing * 0.582042 ) +evaluate($z_24 = $spacing * -0.776809 ) +evaluate ($x_25 = $spacing * 0.365914 ) +evaluate($y_25 = $spacing * 0.482874 ) +evaluate($z_25 = $spacing * 0.795575 ) +evaluate ($x_26 = $spacing * -0.843829 ) +evaluate($y_26 = $spacing * 0.461477 ) +evaluate($z_26 = $spacing * -0.273845 ) +evaluate ($x_27 = $spacing * 0.745628 ) 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b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_34 new file mode 100644 index 0000000000000000000000000000000000000000..ca5f072c90a56cae7c84842ac455917371d67d27 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_34 @@ -0,0 +1,102 @@ +evaluate ($x_1 = $spacing * 0.490913 ) +evaluate($y_1 = $spacing * -0.871208 ) +evaluate($z_1 = $spacing * 0.001132 ) +evaluate ($x_2 = $spacing * -0.104394 ) +evaluate($y_2 = $spacing * -0.985971 ) +evaluate($z_2 = $spacing * 0.130242 ) +evaluate ($x_3 = $spacing * 0.008482 ) +evaluate($y_3 = $spacing * -0.885782 ) +evaluate($z_3 = $spacing * -0.464024 ) +evaluate ($x_4 = $spacing * 0.332888 ) +evaluate($y_4 = $spacing * -0.743926 ) +evaluate($z_4 = $spacing * 0.579448 ) +evaluate ($x_5 = $spacing * -0.597734 ) +evaluate($y_5 = $spacing * -0.775881 ) +evaluate($z_5 = $spacing * -0.201798 ) +evaluate ($x_6 = $spacing * 0.679368 ) +evaluate($y_6 = 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$spacing * 0.895695 ) +evaluate($z_37 = $spacing * -0.441627 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_38 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_38 new file mode 100644 index 0000000000000000000000000000000000000000..79139986c4dc3c8df281c05ad3e24f332f895841 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_38 @@ -0,0 +1,114 @@ +evaluate ($x_1 = $spacing * 0.327993 ) +evaluate($y_1 = $spacing * -0.938963 ) +evaluate($z_1 = $spacing * 0.103775 ) +evaluate ($x_2 = $spacing * -0.240019 ) +evaluate($y_2 = $spacing * -0.954811 ) +evaluate($z_2 = $spacing * 0.175291 ) +evaluate ($x_3 = $spacing * -0.014305 ) +evaluate($y_3 = $spacing * -0.916111 ) +evaluate($z_3 = $spacing * -0.400670 ) +evaluate ($x_4 = $spacing * 0.424742 ) +evaluate($y_4 = $spacing * -0.672475 ) +evaluate($z_4 = $spacing * 0.606112 ) 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/dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_41 @@ -0,0 +1,123 @@ +evaluate ($x_1 = $spacing * 0.367038 ) +evaluate($y_1 = $spacing * -0.929580 ) +evaluate($z_1 = $spacing * 0.034114 ) +evaluate ($x_2 = $spacing * -0.126528 ) +evaluate($y_2 = $spacing * -0.948835 ) +evaluate($z_2 = $spacing * 0.289314 ) +evaluate ($x_3 = $spacing * -0.074956 ) +evaluate($y_3 = $spacing * -0.938250 ) +evaluate($z_3 = $spacing * -0.337739 ) +evaluate ($x_4 = $spacing * 0.385302 ) +evaluate($y_4 = $spacing * -0.736964 ) +evaluate($z_4 = $spacing * 0.555362 ) +evaluate ($x_5 = $spacing * -0.569638 ) +evaluate($y_5 = $spacing * -0.810598 ) +evaluate($z_5 = $spacing * -0.135808 ) +evaluate ($x_6 = $spacing * 0.529565 ) +evaluate($y_6 = $spacing * -0.724071 ) +evaluate($z_6 = $spacing * -0.441907 ) +evaluate ($x_7 = $spacing * -0.161108 ) +evaluate($y_7 = $spacing * -0.597315 ) +evaluate($z_7 = $spacing * 0.785658 ) +evaluate ($x_8 = $spacing * 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0000000000000000000000000000000000000000..48401689c9fe1f8b1fec391809778f0cd1abda57 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_43 @@ -0,0 +1,129 @@ +evaluate ($x_1 = $spacing * 0.349433 ) +evaluate($y_1 = $spacing * -0.936691 ) +evaluate($z_1 = $spacing * -0.022492 ) +evaluate ($x_2 = $spacing * -0.065468 ) +evaluate($y_2 = $spacing * -0.884783 ) +evaluate($z_2 = $spacing * 0.461381 ) +evaluate ($x_3 = $spacing * 0.066142 ) +evaluate($y_3 = $spacing * -0.867856 ) +evaluate($z_3 = $spacing * -0.492394 ) +evaluate ($x_4 = $spacing * 0.458923 ) +evaluate($y_4 = $spacing * -0.753265 ) +evaluate($z_4 = $spacing * 0.471149 ) +evaluate ($x_5 = $spacing * -0.241934 ) +evaluate($y_5 = $spacing * -0.968549 ) +evaluate($z_5 = $spacing * -0.058146 ) +evaluate ($x_6 = $spacing * 0.581628 ) +evaluate($y_6 = $spacing * -0.653936 ) +evaluate($z_6 = $spacing * -0.483814 ) +evaluate ($x_7 = $spacing * -0.343962 ) +evaluate($y_7 = 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b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_49 new file mode 100644 index 0000000000000000000000000000000000000000..cca5a130ce1849f772fb690c3647526dbf4cd99e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_49 @@ -0,0 +1,147 @@ +evaluate ($x_1 = $spacing * 0.293897 ) +evaluate($y_1 = $spacing * -0.955739 ) +evaluate($z_1 = $spacing * -0.013701 ) +evaluate ($x_2 = $spacing * -0.165744 ) +evaluate($y_2 = $spacing * -0.958249 ) +evaluate($z_2 = $spacing * 0.233000 ) +evaluate ($x_3 = $spacing * -0.061716 ) +evaluate($y_3 = $spacing * -0.929284 ) +evaluate($z_3 = $spacing * -0.364173 ) +evaluate ($x_4 = $spacing * 0.351055 ) +evaluate($y_4 = $spacing * -0.813035 ) +evaluate($z_4 = $spacing * 0.464472 ) +evaluate ($x_5 = $spacing * -0.533868 ) +evaluate($y_5 = $spacing * -0.841248 ) +evaluate($z_5 = $spacing * -0.085363 ) +evaluate ($x_6 = $spacing * 0.492202 ) +evaluate($y_6 = 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+evaluate($y_47 = $spacing * 0.929284 ) +evaluate($z_47 = $spacing * -0.237379 ) +evaluate ($x_48 = $spacing * 0.284825 ) +evaluate($y_48 = $spacing * 0.958249 ) +evaluate($z_48 = $spacing * -0.025186 ) +evaluate ($x_49 = $spacing * -0.160421 ) +evaluate($y_49 = $spacing * 0.955739 ) +evaluate($z_49 = $spacing * 0.246633 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_5 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_5 new file mode 100644 index 0000000000000000000000000000000000000000..99db8175d69b956253718df1f3026b26a30dcbaa --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_5 @@ -0,0 +1,15 @@ +evaluate ($x_1 = $spacing * 0.575654 ) +evaluate($y_1 = $spacing * -0.816133 ) +evaluate($z_1 = $spacing * 0.050504 ) +evaluate ($x_2 = $spacing * -0.747791 ) +evaluate($y_2 = $spacing * -0.500440 ) +evaluate($z_2 = $spacing * 0.436312 ) +evaluate ($x_3 = $spacing * 0.087426 ) +evaluate($y_3 = $spacing * -0.000000 ) +evaluate($z_3 = $spacing * -0.996171 ) +evaluate ($x_4 = $spacing * 0.660362 ) +evaluate($y_4 = $spacing * 0.500440 ) +evaluate($z_4 = $spacing * 0.559894 ) +evaluate ($x_5 = $spacing * -0.575651 ) +evaluate($y_5 = $spacing * 0.816133 ) +evaluate($z_5 = $spacing * -0.050536 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_50 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_50 new file mode 100644 index 0000000000000000000000000000000000000000..ff8a1e0809d870a8315594bcda45143e5cdae581 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_50 @@ -0,0 +1,150 @@ +evaluate ($x_1 = $spacing * 0.299090 ) +evaluate($y_1 = $spacing * -0.953812 ) +evaluate($z_1 = $spacing * -0.028053 ) +evaluate ($x_2 = $spacing * -0.161990 ) +evaluate($y_2 = $spacing * -0.970894 ) +evaluate($z_2 = $spacing * 0.176418 ) +evaluate ($x_3 = $spacing * -0.066782 ) +evaluate($y_3 = $spacing * -0.920579 ) +evaluate($z_3 = $spacing * -0.384804 ) +evaluate ($x_4 = $spacing * 0.358091 ) +evaluate($y_4 = $spacing * -0.810318 ) +evaluate($z_4 = $spacing * 0.463848 ) +evaluate ($x_5 = $spacing * -0.543554 ) +evaluate($y_5 = $spacing * -0.832348 ) +evaluate($z_5 = $spacing * -0.108383 ) +evaluate ($x_6 = $spacing * 0.474831 ) +evaluate($y_6 = $spacing * -0.752609 ) +evaluate($z_6 = $spacing * -0.456197 ) +evaluate ($x_7 = $spacing * -0.126244 ) +evaluate($y_7 = $spacing * -0.762443 ) +evaluate($z_7 = $spacing * 0.634620 ) +evaluate ($x_8 = $spacing * -0.405165 ) +evaluate($y_8 = $spacing * -0.658011 ) +evaluate($z_8 = $spacing * -0.634714 ) +evaluate ($x_9 = $spacing * 0.719693 ) +evaluate($y_9 = $spacing * -0.686362 ) +evaluate($z_9 = $spacing * 0.104640 ) +evaluate ($x_10 = $spacing * -0.588569 ) +evaluate($y_10 = $spacing * -0.685750 ) +evaluate($z_10 = $spacing * 0.428176 ) +evaluate ($x_11 = $spacing * 0.141756 ) +evaluate($y_11 = $spacing * -0.597518 ) +evaluate($z_11 = $spacing * -0.789226 ) +evaluate ($x_12 = $spacing * 0.242813 ) +evaluate($y_12 = $spacing * -0.471815 ) +evaluate($z_12 = $spacing * 0.847604 ) +evaluate ($x_13 = $spacing * -0.796579 ) +evaluate($y_13 = $spacing * -0.474999 ) +evaluate($z_13 = $spacing * -0.373948 ) +evaluate ($x_14 = $spacing * 0.841312 ) +evaluate($y_14 = $spacing * -0.430775 ) +evaluate($z_14 = $spacing * -0.326538 ) +evaluate ($x_15 = $spacing * -0.365000 ) +evaluate($y_15 = $spacing * -0.374727 ) +evaluate($z_15 = $spacing * 0.852265 ) +evaluate ($x_16 = $spacing * -0.237977 ) +evaluate($y_16 = $spacing * -0.283634 ) +evaluate($z_16 = $spacing * -0.928934 ) +evaluate ($x_17 = $spacing * 0.709918 ) +evaluate($y_17 = $spacing * -0.408579 ) +evaluate($z_17 = $spacing * 0.573655 ) +evaluate ($x_18 = $spacing * -0.889980 ) +evaluate($y_18 = $spacing * -0.439725 ) +evaluate($z_18 = $spacing * 0.120735 ) +evaluate ($x_19 = $spacing * 0.598437 ) +evaluate($y_19 = $spacing * -0.278944 ) +evaluate($z_19 = $spacing * -0.751042 ) +evaluate ($x_20 = $spacing * -0.009366 ) +evaluate($y_20 = $spacing * -0.048036 ) +evaluate($z_20 = $spacing * 0.998802 ) +evaluate ($x_21 = $spacing * -0.680136 ) +evaluate($y_21 = $spacing * -0.114605 ) +evaluate($z_21 = $spacing * -0.724073 ) +evaluate ($x_22 = $spacing * 0.966010 ) +evaluate($y_22 = $spacing * -0.223905 ) +evaluate($z_22 = $spacing * 0.129194 ) +evaluate ($x_23 = $spacing * -0.761964 ) +evaluate($y_23 = $spacing * -0.190712 ) +evaluate($z_23 = $spacing * 0.618902 ) +evaluate ($x_24 = $spacing * 0.212994 ) +evaluate($y_24 = $spacing * -0.061846 ) +evaluate($z_24 = $spacing * -0.975094 ) +evaluate ($x_25 = $spacing * 0.489135 ) +evaluate($y_25 = $spacing * -0.009350 ) +evaluate($z_25 = $spacing * 0.872158 ) +evaluate ($x_26 = $spacing * -0.955414 ) +evaluate($y_26 = $spacing * 0.009350 ) +evaluate($z_26 = $spacing * -0.295121 ) +evaluate ($x_27 = $spacing * 0.908642 ) +evaluate($y_27 = $spacing * 0.061846 ) +evaluate($z_27 = $spacing * -0.412970 ) +evaluate ($x_28 = $spacing * -0.445131 ) +evaluate($y_28 = $spacing * 0.190712 ) +evaluate($z_28 = $spacing * 0.874921 ) +evaluate ($x_29 = $spacing * -0.329130 ) +evaluate($y_29 = $spacing * 0.223905 ) +evaluate($z_29 = $spacing * -0.917355 ) +evaluate ($x_30 = $spacing * 0.850730 ) +evaluate($y_30 = $spacing * 0.114605 ) +evaluate($z_30 = $spacing * 0.512956 ) +evaluate ($x_31 = $spacing * -0.974574 ) +evaluate($y_31 = $spacing * 0.048036 ) +evaluate($z_31 = $spacing * 0.218858 ) +evaluate ($x_32 = $spacing * 0.608659 ) +evaluate($y_32 = $spacing * 0.278944 ) +evaluate($z_32 = $spacing * -0.742781 ) +evaluate ($x_33 = $spacing * 0.068810 ) +evaluate($y_33 = $spacing * 0.439725 ) +evaluate($z_33 = $spacing * 0.895493 ) +evaluate ($x_34 = $spacing * -0.709918 ) +evaluate($y_34 = $spacing * 0.408579 ) +evaluate($z_34 = $spacing * -0.573655 ) +evaluate ($x_35 = $spacing * 0.958194 ) +evaluate($y_35 = $spacing * 0.283634 ) +evaluate($z_35 = $spacing * 0.037641 ) +evaluate ($x_36 = $spacing * -0.756636 ) +evaluate($y_36 = $spacing * 0.374727 ) +evaluate($z_36 = $spacing * 0.535800 ) +evaluate ($x_37 = $spacing * 0.142624 ) +evaluate($y_37 = $spacing * 0.430775 ) +evaluate($z_37 = $spacing * -0.891118 ) +evaluate ($x_38 = $spacing * 0.532857 ) +evaluate($y_38 = $spacing * 0.474999 ) +evaluate($z_38 = $spacing * 0.700313 ) +evaluate ($x_39 = $spacing * -0.879691 ) +evaluate($y_39 = $spacing * 0.471815 ) +evaluate($z_39 = $spacing * -0.059445 ) +evaluate ($x_40 = $spacing * 0.741874 ) +evaluate($y_40 = $spacing * 0.597518 ) +evaluate($z_40 = $spacing * -0.304296 ) +evaluate ($x_41 = $spacing * -0.295061 ) +evaluate($y_41 = $spacing * 0.685750 ) +evaluate($z_41 = $spacing * 0.665347 ) +evaluate ($x_42 = $spacing * -0.253409 ) +evaluate($y_42 = $spacing * 0.686362 ) +evaluate($z_42 = $spacing * -0.681683 ) +evaluate ($x_43 = $spacing * 0.705633 ) +evaluate($y_43 = $spacing * 0.658011 ) +evaluate($z_43 = $spacing * 0.262875 ) +evaluate ($x_44 = $spacing * -0.593970 ) +evaluate($y_44 = $spacing * 0.762443 ) +evaluate($z_44 = $spacing * 0.256670 ) +evaluate ($x_45 = $spacing * 0.346338 ) +evaluate($y_45 = $spacing * 0.752609 ) +evaluate($z_45 = $spacing * -0.560027 ) +evaluate ($x_46 = $spacing * 0.220087 ) +evaluate($y_46 = $spacing * 0.832348 ) +evaluate($z_46 = $spacing * 0.508684 ) +evaluate ($x_47 = $spacing * -0.528692 ) +evaluate($y_47 = $spacing * 0.810318 ) +evaluate($z_47 = $spacing * -0.252724 ) +evaluate ($x_48 = $spacing * 0.390248 ) +evaluate($y_48 = $spacing * 0.920579 ) +evaluate($z_48 = $spacing * -0.015497 ) +evaluate ($x_49 = $spacing * -0.138475 ) +evaluate($y_49 = $spacing * 0.970894 ) +evaluate($z_49 = $spacing * 0.195419 ) +evaluate ($x_50 = $spacing * -0.035367 ) +evaluate($y_50 = $spacing * 0.953812 ) +evaluate($z_50 = $spacing * -0.298314 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_6 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_6 new file mode 100644 index 0000000000000000000000000000000000000000..01a8663b52edf6633f92c785dc7e4cdafbe3c409 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_6 @@ -0,0 +1,18 @@ +evaluate ($x_1 = $spacing * 0.734901 ) +evaluate($y_1 = $spacing * -0.678154 ) +evaluate($z_1 = $spacing * -0.005343 ) +evaluate ($x_2 = $spacing * -0.622947 ) +evaluate($y_2 = $spacing * -0.678147 ) +evaluate($z_2 = $spacing * 0.389940 ) +evaluate ($x_3 = $spacing * -0.268053 ) +evaluate($y_3 = $spacing * -0.283239 ) +evaluate($z_3 = $spacing * -0.920827 ) +evaluate ($x_4 = $spacing * 0.268063 ) +evaluate($y_4 = $spacing * 0.283239 ) +evaluate($z_4 = $spacing * 0.920825 ) +evaluate ($x_5 = $spacing * -0.734907 ) +evaluate($y_5 = $spacing * 0.678147 ) +evaluate($z_5 = $spacing * 0.005339 ) +evaluate ($x_6 = $spacing * 0.622944 ) +evaluate($y_6 = $spacing * 0.678154 ) +evaluate($z_6 = $spacing * -0.389934 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_7 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_7 new file mode 100644 index 0000000000000000000000000000000000000000..13448c7a9e7753f8109df729102a046e3821b334 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_7 @@ -0,0 +1,21 @@ +evaluate ($x_1 = $spacing * 0.630545 ) +evaluate($y_1 = $spacing * -0.770433 ) +evaluate($z_1 = $spacing * -0.094055 ) +evaluate ($x_2 = $spacing * -0.641872 ) +evaluate($y_2 = $spacing * -0.588059 ) +evaluate($z_2 = $spacing * 0.492125 ) +evaluate ($x_3 = $spacing * -0.215812 ) +evaluate($y_3 = $spacing * -0.473463 ) +evaluate($z_3 = $spacing * -0.853966 ) +evaluate ($x_4 = $spacing * 0.608439 ) +evaluate($y_4 = $spacing * -0.000000 ) +evaluate($z_4 = $spacing * 0.793601 ) +evaluate ($x_5 = $spacing * -0.768662 ) +evaluate($y_5 = $spacing * 0.473463 ) +evaluate($z_5 = $spacing * -0.430106 ) +evaluate ($x_6 = $spacing * 0.641885 ) +evaluate($y_6 = $spacing * 0.588059 ) +evaluate($z_6 = $spacing * -0.492108 ) +evaluate ($x_7 = $spacing * -0.254522 ) +evaluate($y_7 = $spacing * 0.770433 ) +evaluate($z_7 = $spacing * 0.584510 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_8 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_8 new file mode 100644 index 0000000000000000000000000000000000000000..6616657efe3fe187ddc0da16c01874e98c23acc3 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_8 @@ -0,0 +1,24 @@ +evaluate ($x_1 = $spacing * 0.418929 ) +evaluate($y_1 = $spacing * -0.900532 ) +evaluate($z_1 = $spacing * -0.116362 ) +evaluate ($x_2 = $spacing * -0.454808 ) +evaluate($y_2 = $spacing * -0.640327 ) +evaluate($z_2 = $spacing * 0.618976 ) +evaluate ($x_3 = $spacing * -0.101394 ) +evaluate($y_3 = $spacing * -0.272325 ) +evaluate($z_3 = $spacing * -0.956848 ) +evaluate ($x_4 = $spacing * 0.645983 ) +evaluate($y_4 = $spacing * 0.012051 ) +evaluate($z_4 = $spacing * 0.763257 ) +evaluate ($x_5 = $spacing * -0.975089 ) +evaluate($y_5 = $spacing * -0.012051 ) +evaluate($z_5 = $spacing * -0.221486 ) +evaluate ($x_6 = $spacing * 0.895887 ) +evaluate($y_6 = $spacing * 0.272325 ) +evaluate($z_6 = $spacing * -0.351036 ) +evaluate ($x_7 = $spacing * -0.339685 ) +evaluate($y_7 = $spacing * 0.640327 ) +evaluate($z_7 = $spacing * 0.688909 ) +evaluate ($x_8 = $spacing * -0.089822 ) +evaluate($y_8 = $spacing * 0.900532 ) +evaluate($z_8 = $spacing * -0.425410 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_9 b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_9 new file mode 100644 index 0000000000000000000000000000000000000000..6d1a70b1f66bb3e13a0bbeddb9450ed86c7080a9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/initial_positions/trans_vector_9 @@ -0,0 +1,27 @@ +evaluate ($x_1 = $spacing * 0.520089 ) +evaluate($y_1 = $spacing * -0.851243 ) +evaluate($z_1 = $spacing * -0.069943 ) +evaluate ($x_2 = $spacing * -0.450573 ) +evaluate($y_2 = $spacing * -0.734380 ) +evaluate($z_2 = $spacing * 0.507612 ) +evaluate ($x_3 = $spacing * -0.209633 ) +evaluate($y_3 = $spacing * -0.475251 ) +evaluate($z_3 = $spacing * -0.854512 ) +evaluate ($x_4 = $spacing * 0.579259 ) +evaluate($y_4 = $spacing * -0.129555 ) +evaluate($z_4 = $spacing * 0.804782 ) +evaluate ($x_5 = $spacing * -0.984713 ) +evaluate($y_5 = $spacing * 0.000000 ) +evaluate($z_5 = $spacing * -0.174182 ) +evaluate ($x_6 = $spacing * 0.820182 ) +evaluate($y_6 = $spacing * 0.129555 ) +evaluate($z_6 = $spacing * -0.557241 ) +evaluate ($x_7 = $spacing * -0.490043 ) +evaluate($y_7 = $spacing * 0.475251 ) +evaluate($z_7 = $spacing * 0.730749 ) +evaluate ($x_8 = $spacing * -0.249103 ) +evaluate($y_8 = $spacing * 0.734380 ) +evaluate($z_8 = $spacing * -0.631375 ) +evaluate ($x_9 = $spacing * 0.464538 ) +evaluate($y_9 = $spacing * 0.851243 ) +evaluate($z_9 = $spacing * 0.244110 ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.param new file mode 100644 index 0000000000000000000000000000000000000000..1854ec195789664334feaf3d0db1e33866085586 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.param @@ -0,0 +1,124 @@ +remarks file toppar/ion.param +remarks nonbonded parameters for common ions +remarks new parameters derived from literature for single atom species +remarks PDA 02/09/99 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +! checkversion 1.1 + +BOND OLF SLF 1480.000 1.475 +BOND OHF PHF 1489.209 1.485 +BOND OWF W 1489.209 1.730 + +ANGLE OLF SLF OLF 337.400 109.400 +ANGLE OHF PHF OHF 1337.074 119.600 +ANGLE OWF W OWF 1337.074 119.600 + +! eps sigma eps(1:4) sigma(1:4) +! (kcal/mol) (A) (kcal/mol) (A) +! -------------------------------------- + +{- neutral radii -} +{- from: Teatum, Gschneider & Waber. (1960) Compilation of calculated data + useful in predicting metallurgical behaviour of the elements in + binary alloy systems, LE-2345, Los Alamos Scientific Laboratory -} + +NONBonded LI 0.01 2.783 0.01 2.783 +NONBonded F 0.01 2.619 0.01 2.619 +NONBonded NA 0.01 3.405 0.01 3.405 +NONBonded MG 0.01 2.854 0.01 2.854 +NONBonded AL 0.01 2.552 0.01 2.552 +NONBonded CL 0.01 3.118 0.01 3.118 +NONBonded K 0.01 4.234 0.01 4.234 +NONBonded AR 0.01 3.200 0.01 3.200 +NONBonded CA 0.01 3.517 0.01 3.517 +NONBonded V 0.01 2.398 0.01 2.398 +NONBonded CR 0.01 2.284 0.01 2.284 +NONBonded MN 0.01 2.252 0.01 2.252 +NONBonded FE 0.01 2.270 0.01 2.270 +NONBonded NI 0.01 2.220 0.01 2.220 +NONBonded CO 0.01 2.231 0.01 2.231 +NONBonded CU 0.01 2.277 0.01 2.277 +NONBonded ZN 0.01 2.484 0.01 2.484 +NONBonded AS 0.01 3.296 0.01 3.296 +NONBonded BR 0.01 3.296 0.01 3.296 +NONBonded KR 0.01 3.400 0.01 3.400 +NONBonded SR 0.01 3.833 0.01 3.833 +NONBonded MO 0.01 2.495 0.01 2.495 +NONBonded AG 0.01 2.575 0.01 2.575 +NONBonded CD 0.01 2.794 0.01 2.794 +NONBonded I 0.01 3.528 0.01 3.528 +NONBonded XE 0.01 3.564 0.01 3.564 +NONBonded CS 0.01 4.866 0.01 4.866 +NONBonded HO 0.01 3.147 0.01 3.147 +NONBonded YB 0.01 3.100 0.01 3.100 +NONBonded OS 0.01 2.411 0.01 2.411 +NONBonded IR 0.01 2.418 0.01 2.418 +NONBonded PT 0.01 2.471 0.01 2.471 +NONBonded AU 0.01 2.569 0.01 2.569 +NONBonded HG 0.01 2.803 0.01 2.803 +NONBonded PB 0.01 3.118 0.01 3.118 +NONBonded U 0.01 2.780 0.01 2.780 + +{- ionic radii -} +{- from: Shannon (1976) Revised effective ionic radii in halides and + chalcogenides, Acta Cryst. A32, 751. -} + +NONBonded LI+1 0.01 1.604 0.01 1.604 +NONBonded F-1 0.01 2.120 0.01 2.120 +NONBonded NA+1 0.01 2.067 0.01 2.067 +NONBonded MG+2 0.01 1.532 0.01 1.532 +NONBonded AL+3 0.01 1.203 0.01 1.203 +NONBonded CL-1 0.01 2.976 0.01 2.976 +NONBonded K+1 0.01 2.708 0.01 2.708 +NONBonded CA+2 0.41 2.440 0.41 2.440 ! added 13-06-2012 AB +!NONBonded CA+2 0.01 2.031 0.01 2.031 +NONBonded V+2 0.01 1.657 0.01 1.657 +NONBonded V+3 0.01 1.390 0.01 1.390 +NONBonded CR+2 0.01 1.550 0.01 1.550 +NONBonded CR+3 0.01 1.345 0.01 1.345 +NONBonded MN+2 0.01 1.443 0.01 1.443 +NONBonded MN+3 0.01 1.283 0.01 1.283 +NONBonded FE+2 0.01 1.336 0.01 1.336 +NONBonded FE+3 0.01 1.229 0.01 1.229 +NONBonded NI+2 0.01 1.479 0.01 1.479 +NONBonded CO+2 0.01 1.408 0.01 1.408 +NONBonded CO+3 0.01 1.221 0.01 1.221 +NONBonded CU+1 0.01 1.621 0.01 1.621 +NONBonded CU+2 0.01 1.550 0.01 1.550 +NONBonded ZN+2 0.01 1.568 0.01 1.568 +NONBonded BR-1 0.01 3.243 0.01 3.243 +NONBonded SR+2 0.01 2.352 0.01 2.352 +NONBonded MO+3 0.01 1.479 0.01 1.479 +NONBonded AG+1 0.01 2.299 0.01 2.299 +NONBonded CD+2 0.01 1.942 0.01 1.942 +NONBonded I-1 0.01 3.671 0.01 3.671 +NONBonded CS+1 0.01 3.225 0.01 3.225 +NONBonded HO+3 0.01 1.855 0.01 1.855 +NONBonded YB+2 0.01 2.067 0.01 2.067 +NONBonded YB+3 0.01 1.796 0.01 1.796 +NONBonded OS+4 0.01 1.372 0.01 1.372 +NONBonded IR+3 0.01 1.461 0.01 1.461 +NONBonded PT+2 0.01 1.675 0.01 1.675 +NONBonded AU+1 0.01 2.691 0.01 2.691 +NONBonded AU+3 0.01 1.764 0.01 1.764 +NONBonded HG+1 0.01 2.370 0.01 2.370 +NONBonded HG+2 0.01 2.067 0.01 2.067 +NONBonded PB+2 0.01 2.370 0.01 2.370 +NONBonded U+3 0.01 2.076 0.01 2.076 +NONBonded U+4 0.01 1.835 0.01 1.835 + +{- multi-atom species -} +{- source of parameters unknown, therefore possibly in error -} + +NONBonded SLF 0.01 3.368 0.01 3.368 +NONBonded OLF 0.01 2.851 0.01 2.851 +NONBonded PHF 0.01 3.385 0.01 3.385 +NONBonded OHF 0.01 2.729 0.01 2.729 +NONBonded W 0.01 2.305 0.01 2.305 +NONBonded OWF 0.01 2.729 0.01 2.729 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.top new file mode 100644 index 0000000000000000000000000000000000000000..b8e9b4243678ac78266d8fe38254c3cbd9455e3d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/ion.top @@ -0,0 +1,543 @@ +remarks file toppar/ion.top +remarks topology and masses for common ions +remarks Dingle atom ion residues are given the name of the element. +remarks By default the atom will be uncharged (eg. the residue MG will +remarks contain the atom called MG with zero charge). +remarks To use the charged species the charge state is appended to +remarks the atom name (eg to use MG2+ the residue name is MG2, and the +remarks atom name is MG+2 and has charge +2.0). +remarks NOTE: not all ionic species are represented +remarks PDA 02/09/99 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +! checkversion 1.1 + +autogenerate angles=true end + +MASS LI 6.9410 ! lithium +MASS F 18.9984 ! fluorine +MASS NA 22.9898 ! sodium +MASS MG 24.3050 ! magnesium +MASS AL 26.9815 ! aluminum +MASS CL 35.4530 ! chlorine +MASS K 39.0980 ! potassium +MASS AR 39.9480 ! argon +MASS CA 40.0800 ! calcium +MASS V 50.9415 ! vanadium +MASS CR 51.9960 ! chromium +MASS MN 54.9380 ! manganese +MASS FE 55.8470 ! iron +MASS NI 58.6900 ! nickel +MASS CO 58.9332 ! cobalt +MASS CU 63.5460 ! copper +MASS ZN 65.3700 ! zinc +MASS AS 74.9216 ! arsenic +MASS BR 79.9040 ! bromine +MASS KR 83.8000 ! krypton +MASS SR 87.6200 ! strontium +MASS MO 95.9400 ! molybdenum +MASS AG 107.8680 ! silver +MASS CD 112.4100 ! cadmium +MASS I 126.9045 ! iodine +MASS XE 131.2900 ! xenon +MASS CS 132.9054 ! cesium +MASS HO 164.9304 ! holmium +MASS YB 173.0400 ! ytterbium +MASS OS 190.2000 ! osmium +MASS IR 192.2200 ! iridium +MASS PT 195.0800 ! platinum +MASS AU 196.9665 ! gold +MASS HG 200.5900 ! mercury +MASS PB 207.2000 ! lead +MASS U 238.0289 ! uranium + +MASS LI+1 6.9410 ! lithium 1+ +MASS F-1 18.9984 ! fluorine 1- +MASS NA+1 22.9898 ! sodium 1+ +MASS MG+2 24.3050 ! magnesium 2+ +MASS AL+3 26.9815 ! aluminum 3+ +MASS CL-1 35.4530 ! chloride 1- +MASS K+1 39.0980 ! potassium 1+ +MASS CA+2 40.0800 ! calcium 2+ +MASS V+2 50.9415 ! vanadium 2+ +MASS V+3 50.9415 ! vanadium 3+ +MASS CR+2 51.9960 ! chromium 2+ +MASS CR+3 51.9960 ! chromium 3+ +MASS MN+2 54.9380 ! manganese 2+ +MASS MN+3 54.9380 ! manganese 3+ +MASS FE+2 55.8470 ! iron 2+ +MASS FE+3 55.8470 ! iron 3+ +MASS NI+2 58.6900 ! nickel 2+ +MASS CO+2 58.9332 ! cobalt 2+ +MASS CO+3 58.9332 ! cobalt 3+ +MASS CU+1 63.5460 ! copper 1+ +MASS CU+2 63.5460 ! copper 2+ +MASS ZN+2 65.3700 ! zinc 2+ +MASS BR-1 79.9040 ! bromine 1- +MASS SR+2 87.6200 ! strontium 2+ +MASS MO+3 95.9400 ! molybdenum 3+ +MASS AG+1 107.8680 ! silver 1+ +MASS CD+2 112.4100 ! cadmium 2+ +MASS I-1 126.9045 ! iodine 1- +MASS CS+1 132.9054 ! cesium 1+ +MASS HO+3 164.9304 ! holmium 3+ +MASS YB+2 173.0400 ! ytterbium 2+ +MASS YB+3 173.0400 ! ytterbium 3+ +MASS OS+4 190.2000 ! osmium 4+ +MASS IR+3 192.2200 ! iridium 3+ +MASS PT+2 195.0800 ! platinum 2+ +MASS AU+1 196.9665 ! gold 1+ +MASS AU+3 196.9665 ! gold 3+ +MASS HG+1 200.5900 ! mercury 1+ +MASS HG+2 200.5900 ! mercury 2+ +MASS PB+2 207.2000 ! lead 2+ +MASS U+3 238.0289 ! uranium 3+ +MASS U+4 238.0289 ! uranium 4+ + +MASS SUF 32.0600 ! sulphate anion sulphur +MASS OUF 15.9994 ! sulphate anion oxygen +MASS PHF 30.9740 ! phosphate anion phosphorus +MASS OHF 15.9994 ! phosphate anion oxygen +MASS W 184.0000 ! tungstate anion tungsten +MASS OWF 15.9994 ! tungstate anion oxygen + +{- ========================== uncharged states ============================ -} + +RESIdue F {fluorine} + GROUp + ATOM F TYPE=F CHARge=0.0 END +END {F} + +RESIdue NA {sodium} + GROUp + ATOM NA TYPE=NA CHARge=0.0 END +END {NA} + +RESIdue MG {magnesium} + GROUp + ATOM MG TYPE=MG CHARge=0.0 END +END {MG} + +RESIdue AL {aluminum} + GROUp + ATOM AL TYPE=AL CHARge=0.0 END +END {AL} + +RESIdue CL {chlorine} + GROUp + ATOM CL TYPE=CL CHARge=0.0 END +END {CL} + +RESIdue K {potassium} + GROUp + ATOM K TYPE=K CHARge=0.0 END +END {K} + +RESIdue AR {argon} + GROUp + ATOM AR TYPE=AR CHARge=0.0 END +END {AR} + +RESIdue CA {calcium} + GROUp + ATOM CA TYPE=CA CHARge=0.0 END +END {CA} + +RESIdue V {vanadium} + GROUp + ATOM V TYPE=V CHARge=0.0 END +END {V} + +RESIdue CR {chromium} + GROUp + ATOM CR TYPE=CR CHARge=0.0 END +END {CR} + +RESIdue MN {manganese} + GROUp + ATOM MN TYPE=MN CHARge=0.0 END +END {MN} + +RESIdue FE {iron} + GROUp + ATOM FE TYPE=FE CHARge=0.0 END +END {FE} + +RESIdue NI {nickel} + GROUp + ATOM NI TYPE=NI CHARge=0.0 END +END {NI} + +RESIdue CO {cobalt} + GROUp + ATOM CO TYPE=CO CHARge=0.0 END +END {CO} + +RESIdue CU {copper} + GROUp + ATOM CU TYPE=CU CHARge=0.0 END +END {CU} + +RESIdue ZN {zinc} + GROUp + ATOM ZN TYPE=ZN CHARge=0.0 END +END {ZN} + +RESIdue AS {arsenic} + GROUp + ATOM AS TYPE=AS CHARge=0.0 END +END {AS} + +RESIdue BR {bromine} + GROUp + ATOM BR TYPE=BR CHARge=0.0 END +END {BR} + +RESIdue KR {krypton} + GROUp + ATOM KR TYPE=KR CHARge=0.0 END +END {KR} + +RESIdue SR {strontium} + GROUp + ATOM SR TYPE=SR CHARge=0.0 END +END {SR} + +RESIdue MO {molybdenum} + GROUp + ATOM MO TYPE=MO CHARge=0.0 END +END {MO} + +RESIdue AG {silver} + GROUp + ATOM AG TYPE=AG CHARge=0.0 END +END {AG} + +RESIdue CD {cadmium} + GROUp + ATOM CD TYPE=CD CHARge=0.0 END +END {CD} + +RESIdue I {iodine} + GROUp + ATOM I TYPE=I CHARge=0.0 END +END {I} + +RESIdue XE {xenon} + GROUp + ATOM XE TYPE=XE CHARge=0.0 END +END {XE} + +RESIdue CS {cesium} + GROUp + ATOM CS TYPE=CS CHARge=0.0 END +END {CS} + +RESIdue HO {holmium} + GROUp + ATOM HO TYPE=HO CHARge=0.0 END +END {HO} + +RESIdue YB {ytterbium} + GROUp + ATOM YB TYPE=YB CHARge=0.0 END +END {YB} + +RESIdue OS {osmium} + GROUp + ATOM OS TYPE=OS CHARge=0.0 END +END {OS} + +RESIdue IR {iridium} + GROUp + ATOM IR TYPE=IR CHARge=0.0 END +END {IR} + +RESIdue PT {platinum} + GROUp + ATOM PT TYPE=PT CHARge=0.0 END +END {PT} + +RESIdue AU {gold} + GROUp + ATOM AU TYPE=AU CHARge=0.0 END +END {AU} + +RESIdue HG {mercury} + GROUp + ATOM HG TYPE=HG CHARge=0.0 END +END {HG} + +RESIdue PB {lead} + GROUp + ATOM PB TYPE=PB CHARge=0.0 END +END {PB} + +!RESIdue U {uranium} +! GROUp +! ATOM U TYPE=U CHARge=0.0 END +!END {U} + +{- ============================ ionic states ============================== -} + +RESIdue LI1 {lithium 1+} + GROUp + ATOM LI+1 TYPE=LI+1 CHARge=+1.0 END +END {LI1} + +RESIdue F1 {fluorine 1-} + GROUp + ATOM F-1 TYPE=F-1 CHARge=-1.0 END +END {F1} + +RESIdue NA1 {sodium 1+} + GROUp + ATOM NA+1 TYPE=NA+1 CHARge=+1.0 END +END {NA1} + +RESIdue MG2 {magnesium 2+} + GROUp + ATOM MG+2 TYPE=MG+2 CHARge=+2.0 END +END {MG2} + +RESIdue AL3 {aluminum 3+} + GROUp + ATOM AL+3 TYPE=AL+3 CHARge=+3.0 END +END {AL3} + +RESIdue CL1 {chloride 1-} + GROUp + ATOM CL-1 TYPE=CL-1 CHARge=-1.0 END +END {CL1} + +RESIdue K1 {potassium 1+} + GROUp + ATOM K+1 TYPE=K+1 CHARge=+1.0 END +END {K1} + +RESIdue CA2 {calcium 2+} + GROUp + ATOM CA+2 TYPE=CA+2 CHARge=+2.0 END +END {CA2} + +RESIdue V2 {vanadium 2+} + GROUp + ATOM V+2 TYPE=V+2 CHARge=+2.0 END +END {V2} + +RESIdue V3 {vanadium 3+} + GROUp + ATOM V+3 TYPE=V+3 CHARge=+3.0 END +END {V3} + +RESIdue CR2 {chromium 2+} + GROUp + ATOM CR+2 TYPE=CR+2 CHARge=+2.0 END +END {CR2} + +RESIdue CR3 {chromium 3+} + GROUp + ATOM CR+3 TYPE=CR+3 CHARge=+3.0 END +END {CR3} + +RESIdue MN2 {manganese 2+} + GROUp + ATOM MN+2 TYPE=MN+2 CHARge=+2.0 END +END {MN2} + +RESIdue MN3 {manganese 3+} + GROUp + ATOM MN+3 TYPE=MN+3 CHARge=+3.0 END +END {MN3} + +RESIdue FE2 {iron 2+} + GROUp + ATOM FE+2 TYPE=FE+2 CHARge=+2.0 END +END {FE2} + +RESIdue FE3 {iron 3+} + GROUp + ATOM FE+3 TYPE=FE+3 CHARge=+3.0 END +END {FE3} + +RESIdue NI2 {nickel 2+} + GROUp + ATOM NI+2 TYPE=NI+2 CHARge=+2.0 END +END {NI2} + +RESIdue CO2 {cobalt 2+} + GROUp + ATOM CO+2 TYPE=CO+2 CHARge=+2.0 END +END {CO2} + +RESIdue CO3 {cobalt 3+} + GROUp + ATOM CO+3 TYPE=CO+3 CHARge=+3.0 END +END {CO3} + +RESIdue CU1 {copper 1+} + GROUp + ATOM CU+1 TYPE=CU+1 CHARge=+1.0 END +END {CU1} + +RESIdue CU2 {copper 2+} + GROUp + ATOM CU+2 TYPE=CU+2 CHARge=+2.0 END +END {CU2} + +RESIdue ZN2 {zinc 2+} + GROUp + ATOM ZN+2 TYPE=ZN+2 CHARge=+0.96 END ! changed AB for better ZN coordination by CYF +END {ZN2} + +RESIdue BR1 {bromine 1-} + GROUp + ATOM BR-1 TYPE=BR-1 CHARge=-1.0 END +END {BR1} + +RESIdue SR2 {strontium 2+} + GROUp + ATOM SR+2 TYPE=SR+2 CHARge=+2.0 END +END {SR2} + +RESIdue MO3 {molybdenum 3+} + GROUp + ATOM MO+3 TYPE=MO+3 CHARge=+3.0 END +END {MO3} + +RESIdue AG1 {silver 1+} + GROUp + ATOM AG+1 TYPE=AG+1 CHARge=+1.0 END +END {AG1} + +RESIdue CD2 {cadmium 2+} + GROUp + ATOM CD+2 TYPE=CD+2 CHARge=+2.0 END +END {CD2} + +RESIdue I1 {iodine 1-} + GROUp + ATOM I-1 TYPE=I-1 CHARge=-1.0 END +END {I1} + +RESIdue CS1 {cesium 1+} + GROUp + ATOM CS+1 TYPE=CS+1 CHARge=+1.0 END +END {CS1} + +RESIdue HO3 {holmium 3+} + GROUp + ATOM HO+3 TYPE=HO+3 CHARge=+3.0 END +END {HO3} + +RESIdue YB2 {ytterbium 2+} + GROUp + ATOM YB+2 TYPE=YB+2 CHARge=+2.0 END +END {YB2} + +RESIdue YB3 {ytterbium 3+} + GROUp + ATOM YB+3 TYPE=YB+3 CHARge=+3.0 END +END {YB3} + +RESIdue OS4 {osmium 4+} + GROUp + ATOM OS+4 TYPE=OS+4 CHARge=+4.0 END +END {OS4} + +RESIdue IR3 {iridium 3+} + GROUp + ATOM IR+3 TYPE=IR+3 CHARge=+3.0 END +END {IR3} + +RESIdue PT2 {platinum 2+} + GROUp + ATOM PT+2 TYPE=PT+2 CHARge=+2.0 END +END {PT2} + +RESIdue AU1 {gold 1+} + GROUp + ATOM AU+1 TYPE=AU+1 CHARge=+1.0 END +END {AU1} + +RESIdue AU3 {gold 3+} + GROUp + ATOM AU+3 TYPE=AU+3 CHARge=+3.0 END +END {AU3} + +RESIdue HG1 {mercury 1+} + GROUp + ATOM HG+1 TYPE=HG+1 CHARge=+1.0 END +END {HG1} + +RESIdue HG2 {mercury 2+} + GROUp + ATOM HG+2 TYPE=HG+2 CHARge=+2.0 END +END {HG2} + +RESIdue PB2 {lead 2+} + GROUp + ATOM PB+2 TYPE=PB+2 CHARge=+2.0 END +END {PB2} + +RESIdue U3 {uranium 3+} + GROUp + ATOM U+3 TYPE=U+3 CHARge=+3.0 END +END {U3} + +RESIdue U4 {uranium 4+} + GROUp + ATOM U+4 TYPE=U+4 CHARge=+4.0 END +END {U4} + +{- ========================= multi-atom species =========================== -} + +RESIdue SO4 {Sulphate} + GROUP + ATOM S TYPE=SUF CHARGE=+2.0 END + ATOM O1 TYPE=OUF CHARGE=-1.0 END + ATOM O2 TYPE=OUF CHARGE=-1.0 END + ATOM O3 TYPE=OUF CHARGE=-1.0 END + ATOM O4 TYPE=OUF CHARGE=-1.0 END + + BOND S O1 + BOND S O2 + BOND S O3 + BOND S O4 + +END {SO4} + +RESIdue PO4 {Phosphate} + GROUP + ATOM P TYPE=PHF CHARGE=+2.0 END + ATOM O1 TYPE=OHF CHARGE=-1.0 END + ATOM O2 TYPE=OHF CHARGE=-1.0 END + ATOM O3 TYPE=OHF CHARGE=-1.0 END + ATOM O4 TYPE=OHF CHARGE=-1.0 END + + BOND P O1 + BOND P O2 + BOND P O3 + BOND P O4 + +END {PO4} + +RESIdue WO4 {Tungstate} + GROUP + ATOM W TYPE=W CHARGE=+2.0 END + ATOM O1 TYPE=OWF CHARGE=-1.0 END + ATOM O2 TYPE=OWF CHARGE=-1.0 END + ATOM O3 TYPE=OWF CHARGE=-1.0 END + ATOM O4 TYPE=OWF CHARGE=-1.0 END + + BOND W O1 + BOND W O2 + BOND W O3 + BOND W O4 + +END {WO4} + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/metalcenter.tbl b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/metalcenter.tbl new file mode 100644 index 0000000000000000000000000000000000000000..2dd671fe62bf81094e8596c15258b63328dc65cc --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/metalcenter.tbl @@ -0,0 +1,2 @@ + assign (resid 400 and name FE ) (resid 15 and name NE2 ) 1.99 0.05 0.05 + assign (resid 400 and name FE ) (resid 50 and name SD ) 2.33 0.05 0.05 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis.pro b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis.pro new file mode 100644 index 0000000000000000000000000000000000000000..918000dcc7a6a5ecf3be462418aacc65952f519f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis.pro @@ -0,0 +1,21 @@ +remark parameter file for dipolar coupling calculations + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +bonds OO XX 1000.0 3.00 +bonds OO YY 1000.0 3.00 +bonds OO ZZ 1000.0 3.00 + +angle XX OO YY 1000.0 90.0 +angle XX OO ZZ 1000.0 90.0 +angle YY OO ZZ 1000.0 90.0 + +NONBonded XX 0.01 0.01 0.01 0.01 +NONBonded YY 0.01 0.01 0.01 0.01 +NONBonded ZZ 0.01 0.01 0.01 0.01 +NONBonded OO 0.01 0.01 0.01 0.01 + +IMPROPER XX YY OO ZZ 500.0 0 90.0 + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis_dani.pro b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis_dani.pro new file mode 100644 index 0000000000000000000000000000000000000000..6950f4c52891cea0c9a917de18b1621db32b07de --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/par_axis_dani.pro @@ -0,0 +1,19 @@ +remark parameter file for dipolar coupling calculations + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +bonds OO XX 1000.0 3.00 +bonds OO YY 1000.0 3.00 +bonds OO ZZ 1000.0 3.00 + +angle XX OO YY 1000.0 90.0 +angle XX OO ZZ 1000.0 90.0 +angle YY OO ZZ 1000.0 90.0 + +NONBonded XX 0.01 0.01 0.01 0.01 +NONBonded YY 0.01 0.01 0.01 0.01 +NONBonded ZZ 0.01 0.01 0.01 0.01 +NONBonded OO 0.01 0.01 0.01 0.01 + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.link new file mode 100644 index 0000000000000000000000000000000000000000..05853e43e8d962be87a17f9096db0b08d91a5102 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.link @@ -0,0 +1,1615 @@ +remarks file toppar/protein-CG-Martin.link +remarks +remarks this is a macro to define standard protein peptide bonds + + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link pept head - GLY tail + PRO end +link pept head - GLY tail + HYP end +link pept head - GLY tail + GLY end + +{ special link to GLY} +link pept head - ACE tail + GLY end +link pept head - ALA tail + GLY end +link pept head - CYS tail + GLY end +link pept head - CYM tail + GLY end +link pept head - CYF tail + GLY end +link pept head - CSP tail + GLY end +link pept head - ASP tail + GLY end +link pept head - ASH tail + GLY end +link pept head - GLU tail + GLY end +link pept head - GLH tail + GLY end +link pept head - PHE tail + GLY end +link pept head - HIS tail + GLY end +link pept head - NEP tail + GLY end +link pept head - ILE tail + GLY end +link pept head - LYS tail + GLY end +link pept head - ALY tail + GLY end +link pept head - MLY tail + GLY end +link pept head - MLZ tail + GLY end +link pept head - M3L tail + GLY end +link pept head - LEU tail + GLY end +link pept head - MET tail + GLY end +link pept head - MSE tail + GLY end ! +link pept head - ASN tail + GLY end +link pept head - PRO tail + GLY end +link pept head - GLN tail + GLY end +link pept head - ARG tail + GLY end +link pept head - SER tail + GLY end +link pept head - SEP tail + GLY end +link pept head - THR tail + GLY end +link pept head - THP tail + GLY end +link pept head - TOP tail + GLY end +link pept head - VAL tail + GLY end +link pept head - TRP tail + GLY end +link pept head - TYR tail + GLY end +link pept head - TYP tail + GLY end +link pept head - TYS tail + GLY end +link pept head - HYP tail + GLY end + +{ special link from GLY} +link pept head - GLY tail + ALA end +link pept head - GLY tail + CYS end +link pept head - GLY tail + CYM end +link pept head - GLY tail + CYF end +link pept head - GLY tail + CSP end +link pept head - GLY tail + ASP end +link pept head - GLY tail + ASH end +link pept head - GLY tail + GLU end +link pept head - GLY tail + GLH end +link pept head - GLY tail + PHE end +link pept head - GLY tail + HIS end +link pept head - GLY tail + NEP end +link pept head - GLY tail + ILE end +link pept head - GLY tail + LYS end +link pept head - GLY tail + ALY end +link pept head - GLY tail + MLY end +link pept head - GLY tail + MLZ end +link pept head - GLY tail + M3L end +link pept head - GLY tail + LEU end +link pept head - GLY tail + MET end +link pept head - GLY tail + MSE end +link pept head - GLY tail + ASN end +link pept head - GLY tail + PRO end +link pept head - GLY tail + GLN end +link pept head - GLY tail + ARG end +link pept head - GLY tail + SER end +link pept head - GLY tail + SEP end +link pept head - GLY tail + THR end +link pept head - GLY tail + THP end +link pept head - GLY tail + TOP end +link pept head - GLY tail + VAL end +link pept head - GLY tail + TRP end +link pept head - GLY tail + TYR end +link pept head - GLY tail + TYP end +link pept head - GLY tail + TYS end +link pept head - GLY tail + HYP end +link pept head - GLY tail + CTN end + +{ special link to PRO and HYP} +link pept head - ACE tail + PRO end +link pept head - ALA tail + PRO end +link pept head - CYS tail + PRO end +link pept head - CYM tail + PRO end +link pept head - CYF tail + PRO end +link pept head - CSP tail + PRO end +link pept head - ASP tail + PRO end +link pept head - ASH tail + PRO end +link pept head - GLU tail + PRO end +link pept head - GLH tail + PRO end +link pept head - PHE tail + PRO end +link pept head - HIS tail + PRO end +link pept head - NEP tail + PRO end +link pept head - ILE tail + PRO end +link pept head - LYS tail + PRO end +link pept head - ALY tail + PRO end +link pept head - MLY tail + PRO end +link pept head - MLZ tail + PRO end +link pept head - M3L tail + PRO end +link pept head - LEU tail + PRO end +link pept head - MET tail + PRO end +link pept head - MSE tail + PRO end +link pept head - ASN tail + PRO end +link pept head - PRO tail + PRO end +link pept head - GLN tail + PRO end +link pept head - ARG tail + PRO end +link pept head - SER tail + PRO end +link pept head - SEP tail + PRO end +link pept head - THR tail + PRO end +link pept head - THP tail + PRO end +link pept head - TOP tail + PRO end +link pept head - VAL tail + PRO end +link pept head - TRP tail + PRO end +link pept head - TYR tail + PRO end +link pept head - TYP tail + PRO end +link pept head - TYS tail + PRO end +link pept head - HYP tail + PRO end + +{ special link to PRO and HYP} +link pept head - ACE tail + HYP end +link pept head - ALA tail + HYP end +link pept head - CYS tail + HYP end +link pept head - CYM tail + HYP end +link pept head - CYF tail + HYP end +link pept head - CSP tail + HYP end +link pept head - ASP tail + HYP end +link pept head - ASH tail + HYP end +link pept head - GLU tail + HYP end +link pept head - GLH tail + HYP end +link pept head - PHE tail + HYP end +link pept head - HIS tail + HYP end +link pept head - NEP tail + HYP end +link pept head - ILE tail + HYP end +link pept head - LYS tail + HYP end +link pept head - ALY tail + HYP end +link pept head - MLY tail + HYP end +link pept head - MLZ tail + HYP end +link pept head - M3L tail + HYP end +link pept head - LEU tail + HYP end +link pept head - MET tail + HYP end +link pept head - MSE tail + HYP end +link pept head - ASN tail + HYP end +link pept head - PRO tail + HYP end +link pept head - GLN tail + HYP end +link pept head - ARG tail + HYP end +link pept head - SER tail + HYP end +link pept head - SEP tail + HYP end +link pept head - THR tail + HYP end +link pept head - THP tail + HYP end +link pept head - TOP tail + HYP end +link pept head - VAL tail + HYP end +link pept head - TRP tail + HYP end +link pept head - TYR tail + HYP end +link pept head - TYP tail + HYP end +link pept head - TYS tail + HYP end +link pept head - HYP tail + HYP end + +{ peptide linkages for ACE } +link pept head - ACE tail + ALA end +link pept head - ACE tail + CYS end +link pept head - ACE tail + CYM end +link pept head - ACE tail + CYF end +link pept head - ACE tail + CSP end +link pept head - ACE tail + ASP end +link pept head - ACE tail + ASH end +link pept head - ACE tail + GLU end +link pept head - ACE tail + GLH end +link pept head - ACE tail + PHE end +link pept head - ACE tail + HIS end +link pept head - ACE tail + NEP end +link pept head - ACE tail + ILE end +link pept head - ACE tail + LYS end +link pept head - ACE tail + ALY end +link pept head - ACE tail + MLY end +link pept head - ACE tail + MLZ end +link pept head - ACE tail + M3L end +link pept head - ACE tail + LEU end +link pept head - ACE tail + MET end +link pept head - ACE tail + MSE end +link pept head - ACE tail + ASN end +link pept head - ACE tail + PRO end +link pept head - ACE tail + GLN end +link pept head - ACE tail + ARG end +link pept head - ACE tail + SER end +link pept head - ACE tail + SEP end +link pept head - ACE tail + THR end +link pept head - ACE tail + THP end +link pept head - ACE tail + TOP end +link pept head - ACE tail + VAL end +link pept head - ACE tail + TRP end +link pept head - ACE tail + TYR end +link pept head - ACE tail + TYP end +link pept head - ACE tail + TYS end +link pept head - ACE tail + HYP end +link pept head - ACE tail + CTN end + +{ peptide linkages for ALA } +link pept head - ALA tail + ALA end +link pept head - ALA tail + CYS end +link pept head - ALA tail + CYM end +link pept head - ALA tail + CYF end +link pept head - ALA tail + CSP end +link pept head - ALA tail + ASP end +link pept head - ALA tail + ASH end +link pept head - ALA tail + GLU end +link pept head - ALA tail + GLH end +link pept head - ALA tail + PHE end +link pept head - ALA tail + HIS end +link pept head - ALA tail + NEP end +link pept head - ALA tail + ILE end +link pept head - ALA tail + LYS end +link pept head - ALA tail + ALY end +link pept head - ALA tail + MLY end +link pept head - ALA tail + MLZ end +link pept head - ALA tail + M3L end +link pept head - ALA tail + LEU end +link pept head - ALA tail + MET end +link pept head - ALA tail + MSE end +link pept head - ALA tail + ASN end +link pept head - ALA tail + PRO end +link pept head - ALA tail + GLN end +link pept head - ALA tail + ARG end +link pept head - ALA tail + SER end +link pept head - ALA tail + SEP end +link pept head - ALA tail + THR end +link pept head - ALA tail + THP end +link pept head - ALA tail + TOP end +link pept head - ALA tail + VAL end +link pept head - ALA tail + TRP end +link pept head - ALA tail + TYR end +link pept head - ALA tail + TYP end +link pept head - ALA tail + TYS end +link pept head - ALA tail + HYP end +link pept head - ALA tail + CTN end + +{ peptide linkages for CYS } +link pept head - CYS tail + ALA end +link pept head - CYS tail + CYS end +link pept head - CYS tail + CYM end +link pept head - CYS tail + CYF end +link pept head - CYS tail + CSP end +link pept head - CYS tail + ASP end +link pept head - CYS tail + ASH end +link pept head - CYS tail + GLU end +link pept head - CYS tail + GLH end +link pept head - CYS tail + PHE end +link pept head - CYS tail + HIS end +link pept head - CYS tail + NEP end +link pept head - CYS tail + ILE end +link pept head - CYS tail + LYS end +link pept head - CYS tail + ALY end +link pept head - CYS tail + MLY end +link pept head - CYS tail + MLZ end +link pept head - CYS tail + M3L end +link pept head - CYS tail + LEU end +link pept head - CYS tail + MET end +link pept head - CYS tail + MSE end +link pept head - CYS tail + ASN end +link pept head - CYS tail + PRO end +link pept head - CYS tail + GLN end +link pept head - CYS tail + ARG end +link pept head - CYS tail + SER end +link pept head - CYS tail + SEP end +link pept head - CYS tail + THR end +link pept head - CYS tail + THP end +link pept head - CYS tail + TOP end +link pept head - CYS tail + VAL end +link pept head - CYS tail + TRP end +link pept head - CYS tail + TYR end +link pept head - CYS tail + TYP end +link pept head - CYS tail + TYS end +link pept head - CYS tail + HYP end +link pept head - CYS tail + CTN end + +{ peptide linkages for CYM } +link pept head - CYM tail + ALA end +link pept head - CYM tail + CYS end +link pept head - CYM tail + CYM end +link pept head - CYM tail + CYF end +link pept head - CYM tail + CSP end +link pept head - CYM tail + ASP end +link pept head - CYM tail + ASH end +link pept head - CYM tail + GLU end +link pept head - CYM tail + GLH end +link pept head - CYM tail + PHE end +link pept head - CYM tail + HIS end +link pept head - CYM tail + NEP end +link pept head - CYM tail + ILE end +link pept head - CYM tail + LYS end +link pept head - CYM tail + ALY end +link pept head - CYM tail + MLY end +link pept head - CYM tail + MLZ end +link pept head - CYM tail + M3L end +link pept head - CYM tail + LEU end +link pept head - CYM tail + MET end +link pept head - CYM tail + MSE end +link pept head - CYM tail + ASN end +link pept head - CYM tail + PRO end +link pept head - CYM tail + GLN end +link pept head - CYM tail + ARG end +link pept head - CYM tail + SER end +link pept head - CYM tail + SEP end +link pept head - CYM tail + THR end +link pept head - CYM tail + THP end +link pept head - CYM tail + TOP end +link pept head - CYM tail + VAL end +link pept head - CYM tail + TRP end +link pept head - CYM tail + TYR end +link pept head - CYM tail + TYP end +link pept head - CYM tail + TYS end +link pept head - CYM tail + HYP end +link pept head - CYM tail + CTN end + +{ peptide linkages for CYF } +link pept head - CYF tail + ALA end +link pept head - CYF tail + CYS end +link pept head - CYF tail + CYM end +link pept head - CYF tail + CYF end +link pept head - CYF tail + CSP end +link pept head - CYF tail + ASP end +link pept head - CYF tail + ASH end +link pept head - CYF tail + GLU end +link pept head - CYF tail + GLH end +link pept head - CYF tail + PHE end +link pept head - CYF tail + HIS end +link pept head - CYF tail + NEP end +link pept head - CYF tail + ILE end +link pept head - CYF tail + LYS end +link pept head - CYF tail + ALY end +link pept head - CYF tail + MLY end +link pept head - CYF tail + MLZ end +link pept head - CYF tail + M3L end +link pept head - CYF tail + LEU end +link pept head - CYF tail + MET end +link pept head - CYF tail + MSE end +link pept head - CYF tail + ASN end +link pept head - CYF tail + PRO end +link pept head - CYF tail + GLN end +link pept head - CYF tail + ARG end +link pept head - CYF tail + SER end +link pept head - CYF tail + SEP end +link pept head - CYF tail + THR end +link pept head - CYF tail + THP end +link pept head - CYF tail + TOP end +link pept head - CYF tail + VAL end +link pept head - CYF tail + TRP end +link pept head - CYF tail + TYR end +link pept head - CYF tail + TYP end +link pept head - CYF tail + TYS end +link pept head - CYF tail + HYP end +link pept head - CYF tail + CTN end + +{ peptide linkages for CSP } +link pept head - CSP tail + ALA end +link pept head - CSP tail + CYS end +link pept head - CSP tail + CYM end +link pept head - CSP tail + CYF end +link pept head - CSP tail + CSP end +link pept head - CSP tail + ASP end +link pept head - CSP tail + ASH end +link pept head - CSP tail + GLU end +link pept head - CSP tail + GLH end +link pept head - CSP tail + PHE end +link pept head - CSP tail + HIS end +link pept head - CSP tail + NEP end +link pept head - CSP tail + ILE end +link pept head - CSP tail + LYS end +link pept head - CSP tail + ALY end +link pept head - CSP tail + MLY end +link pept head - CSP tail + MLZ end +link pept head - CSP tail + M3L end +link pept head - CSP tail + LEU end +link pept head - CSP tail + MET end +link pept head - CSP tail + MSE end +link pept head - CSP tail + ASN end +link pept head - CSP tail + PRO end +link pept head - CSP tail + GLN end +link pept head - CSP tail + ARG end +link pept head - CSP tail + SER end +link pept head - CSP tail + SEP end +link pept head - CSP tail + THR end +link pept head - CSP tail + THP end +link pept head - CSP tail + TOP end +link pept head - CSP tail + VAL end +link pept head - CSP tail + TRP end +link pept head - CSP tail + TYR end +link pept head - CSP tail + TYP end +link pept head - CSP tail + TYS end +link pept head - CSP tail + HYP end +link pept head - CSP tail + CTN end + +{ peptide linkages for ASP } +link pept head - ASP tail + ALA end +link pept head - ASP tail + CYS end +link pept head - ASP tail + CYM end +link pept head - ASP tail + CYF end +link pept head - ASP tail + CSP end +link pept head - ASP tail + ASP end +link pept head - ASP tail + ASH end +link pept head - ASP tail + GLU end +link pept head - ASP tail + GLH end +link pept head - ASP tail + PHE end +link pept head - ASP tail + HIS end +link pept head - ASP tail + NEP end +link pept head - ASP tail + ILE end +link pept head - ASP tail + LYS end +link pept head - ASP tail + ALY end +link pept head - ASP tail + MLY end +link pept head - ASP tail + MLZ end +link pept head - ASP tail + M3L end +link pept head - ASP tail + LEU end +link pept head - ASP tail + MET end +link pept head - ASP tail + MSE end +link pept head - ASP tail + ASN end +link pept head - ASP tail + PRO end +link pept head - ASP tail + GLN end +link pept head - ASP tail + ARG end +link pept head - ASP tail + SER end +link pept head - ASP tail + SEP end +link pept head - ASP tail + THR end +link pept head - ASP tail + THP end +link pept head - ASP tail + TOP end +link pept head - ASP tail + VAL end +link pept head - ASP tail + TRP end +link pept head - ASP tail + TYR end +link pept head - ASP tail + TYP end +link pept head - ASP tail + TYS end +link pept head - ASP tail + HYP end +link pept head - ASP tail + CTN end + +{ peptide linkages for ASH } +link pept head - ASH tail + ALA end +link pept head - ASH tail + CYS end +link pept head - ASH tail + CYM end +link pept head - ASH tail + CYF end +link pept head - ASH tail + CSP end +link pept head - ASH tail + ASP end +link pept head - ASH tail + ASH end +link pept head - ASH tail + GLU end +link pept head - ASH tail + GLH end +link pept head - ASH tail + PHE end +link pept head - ASH tail + HIS end +link pept head - ASH tail + NEP end +link pept head - ASH tail + ILE end +link pept head - ASH tail + LYS end +link pept head - ASH tail + ALY end +link pept head - ASH tail + MLY end +link pept head - ASH tail + MLZ end +link pept head - ASH tail + M3L end +link pept head - ASH tail + LEU end +link pept head - ASH tail + MET end +link pept head - ASH tail + MSE end +link pept head - ASH tail + ASN end +link pept head - ASH tail + PRO end +link pept head - ASH tail + GLN end +link pept head - ASH tail + ARG end +link pept head - ASH tail + SER end +link pept head - ASH tail + SEP end +link pept head - ASH tail + THR end +link pept head - ASH tail + THP end +link pept head - ASH tail + TOP end +link pept head - ASH tail + VAL end +link pept head - ASH tail + TRP end +link pept head - ASH tail + TYR end +link pept head - ASH tail + TYP end +link pept head - ASH tail + TYS end +link pept head - ASH tail + HYP end +link pept head - ASH tail + CTN end + +{ peptide linkages for GLU } +link pept head - GLU tail + ALA end +link pept head - GLU tail + CYS end +link pept head - GLU tail + CYM end +link pept head - GLU tail + CYF end +link pept head - GLU tail + CSP end +link pept head - GLU tail + ASP end +link pept head - GLU tail + ASH end +link pept head - GLU tail + GLU end +link pept head - GLU tail + GLH end +link pept head - GLU tail + PHE end +link pept head - GLU tail + HIS end +link pept head - GLU tail + NEP end +link pept head - GLU tail + ILE end +link pept head - GLU tail + LYS end +link pept head - GLU tail + ALY end +link pept head - GLU tail + MLY end +link pept head - GLU tail + MLZ end +link pept head - GLU tail + M3L end +link pept head - GLU tail + LEU end +link pept head - GLU tail + MET end +link pept head - GLU tail + MSE end +link pept head - GLU tail + ASN end +link pept head - GLU tail + PRO end +link pept head - GLU tail + GLN end +link pept head - GLU tail + ARG end +link pept head - GLU tail + SER end +link pept head - GLU tail + SEP end +link pept head - GLU tail + THR end +link pept head - GLU tail + THP end +link pept head - GLU tail + TOP end +link pept head - GLU tail + VAL end +link pept head - GLU tail + TRP end +link pept head - GLU tail + TYR end +link pept head - GLU tail + TYP end +link pept head - GLU tail + TYS end +link pept head - GLU tail + HYP end +link pept head - GLU tail + CTN end + +{ peptide linkages for GLH } +link pept head - GLH tail + ALA end +link pept head - GLH tail + CYS end +link pept head - GLH tail + CYM end +link pept head - GLH tail + CYF end +link pept head - GLH tail + CSP end +link pept head - GLH tail + ASP end +link pept head - GLH tail + ASH end +link pept head - GLH tail + GLU end +link pept head - GLH tail + GLH end +link pept head - GLH tail + PHE end +link pept head - GLH tail + HIS end +link pept head - GLH tail + NEP end +link pept head - GLH tail + ILE end +link pept head - GLH tail + LYS end +link pept head - GLH tail + ALY end +link pept head - GLH tail + MLY end +link pept head - GLH tail + MLZ end +link pept head - GLH tail + M3L end +link pept head - GLH tail + LEU end +link pept head - GLH tail + MET end +link pept head - GLH tail + MSE end +link pept head - GLH tail + ASN end +link pept head - GLH tail + PRO end +link pept head - GLH tail + GLN end +link pept head - GLH tail + ARG end +link pept head - GLH tail + SER end +link pept head - GLH tail + SEP end +link pept head - GLH tail + THR end +link pept head - GLH tail + THP end +link pept head - GLH tail + TOP end +link pept head - GLH tail + VAL end +link pept head - GLH tail + TRP end +link pept head - GLH tail + TYR end +link pept head - GLH tail + TYP end +link pept head - GLH tail + TYS end +link pept head - GLH tail + HYP end +link pept head - GLH tail + CTN end + +{ peptide linkages for PHE } +link pept head - PHE tail + ALA end +link pept head - PHE tail + CYS end +link pept head - PHE tail + CYM end +link pept head - PHE tail + CYF end +link pept head - PHE tail + CSP end +link pept head - PHE tail + ASP end +link pept head - PHE tail + ASH end +link pept head - PHE tail + GLU end +link pept head - PHE tail + GLH end +link pept head - PHE tail + PHE end +link pept head - PHE tail + HIS end +link pept head - PHE tail + NEP end +link pept head - PHE tail + ILE end +link pept head - PHE tail + LYS end +link pept head - PHE tail + ALY end +link pept head - PHE tail + MLY end +link pept head - PHE tail + MLZ end +link pept head - PHE tail + M3L end +link pept head - PHE tail + LEU end +link pept head - PHE tail + MET end +link pept head - PHE tail + MSE end +link pept head - PHE tail + ASN end +link pept head - PHE tail + PRO end +link pept head - PHE tail + GLN end +link pept head - PHE tail + ARG end +link pept head - PHE tail + SER end +link pept head - PHE tail + SEP end +link pept head - PHE tail + THR end +link pept head - PHE tail + THP end +link pept head - PHE tail + TOP end +link pept head - PHE tail + VAL end +link pept head - PHE tail + TRP end +link pept head - PHE tail + TYR end +link pept head - PHE tail + TYP end +link pept head - PHE tail + TYS end +link pept head - PHE tail + HYP end +link pept head - PHE tail + CTN end + +{ peptide linkages for HIS } +link pept head - HIS tail + ALA end +link pept head - HIS tail + CYS end +link pept head - HIS tail + CYM end +link pept head - HIS tail + CYF end +link pept head - HIS tail + CSP end +link pept head - HIS tail + ASP end +link pept head - HIS tail + ASH end +link pept head - HIS tail + GLU end +link pept head - HIS tail + GLH end +link pept head - HIS tail + PHE end +link pept head - HIS tail + HIS end +link pept head - HIS tail + NEP end +link pept head - HIS tail + ILE end +link pept head - HIS tail + LYS end +link pept head - HIS tail + ALY end +link pept head - HIS tail + MLY end +link pept head - HIS tail + MLZ end +link pept head - HIS tail + M3L end +link pept head - HIS tail + LEU end +link pept head - HIS tail + MET end +link pept head - HIS tail + MSE end +link pept head - HIS tail + ASN end +link pept head - HIS tail + PRO end +link pept head - HIS tail + GLN end +link pept head - HIS tail + ARG end +link pept head - HIS tail + SER end +link pept head - HIS tail + SEP end +link pept head - HIS 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end +link pept head - SEP tail + M3L end +link pept head - SEP tail + LEU end +link pept head - SEP tail + MET end +link pept head - SEP tail + MSE end +link pept head - SEP tail + ASN end +link pept head - SEP tail + PRO end +link pept head - SEP tail + GLN end +link pept head - SEP tail + ARG end +link pept head - SEP tail + SER end +link pept head - SEP tail + SEP end +link pept head - SEP tail + THR end +link pept head - SEP tail + THP end +link pept head - SEP tail + TOP end +link pept head - SEP tail + VAL end +link pept head - SEP tail + TRP end +link pept head - SEP tail + TYR end +link pept head - SEP tail + TYP end +link pept head - SEP tail + TYS end +link pept head - SEP tail + HYP end +link pept head - SEP tail + CTN end + +{ peptide linkages for THR } +link pept head - THR tail + ALA end +link pept head - THR tail + CYS end +link pept head - THR tail + CYM end +link pept head - THR tail + CYF end +link pept head - THR tail + CSP end +link pept head - THR tail + ASP end +link pept head - THR tail + ASH end +link pept head - THR tail + GLU end +link pept head - THR tail + GLH end +link pept head - THR tail + PHE end +link pept head - THR tail + HIS end +link pept head - THR tail + NEP end +link pept head - THR tail + ILE end +link pept head - THR tail + LYS end +link pept head - THR tail + ALY end +link pept head - THR tail + MLY end +link pept head - THR tail + MLZ end +link pept head - THR tail + M3L end +link pept head - THR tail + LEU end +link pept head - THR tail + MET end +link pept head - THR tail + MSE end +link pept head - THR tail + ASN end +link pept head - THR tail + PRO end +link pept head - THR tail + GLN end +link pept head - THR tail + ARG end +link pept head - THR tail + SER end +link pept head - THR tail + SEP end +link pept head - THR tail + THR end +link pept head - THR tail + THP end +link pept head - THR tail + TOP end +link pept head - THR tail + VAL end +link pept head - THR tail + TRP end +link pept head - THR tail + TYR end +link pept head - THR tail + TYP end +link pept head - THR tail + TYS end +link pept head - THR tail + HYP end +link pept head - THR tail + CTN end + +{ peptide linkages for THP } +link pept head - THP tail + ALA end +link pept head - THP tail + CYS end +link pept head - THP tail + CYM end +link pept head - THP tail + CYF end +link pept head - THP tail + CSP end +link pept head - THP tail + ASP end +link pept head - THP tail + ASH end +link pept head - THP tail + GLU end +link pept head - THP tail + GLH end +link pept head - THP tail + PHE end +link pept head - THP tail + HIS end +link pept head - THP tail + NEP end +link pept head - THP tail + ILE end +link pept head - THP tail + LYS end +link pept head - THP tail + ALY end +link pept head - THP tail + MLY end +link pept head - THP tail + MLZ end +link pept head - THP tail + M3L end +link pept head - THP tail + LEU end +link pept head - THP tail + MET end +link pept head - THP tail + MSE end +link pept head - THP tail + ASN end +link pept head - THP tail + PRO end +link pept head - THP tail + GLN end +link pept head - THP tail + ARG end +link pept head - THP tail + SER end +link pept head - THP tail + SEP end +link pept head - THP tail + THR end +link pept head - THP tail + THP end +link pept head - THP tail + TOP end +link pept head - THP tail + VAL end +link pept head - THP tail + TRP end +link pept head - THP tail + TYR end +link pept head - THP tail + TYP end +link pept head - THP tail + TYS end +link pept head - THP tail + HYP end +link pept head - THP tail + CTN end + +{ peptide linkages for TOP } +link pept head - TOP tail + ALA end +link pept head - TOP tail + CYS end +link pept head - TOP tail + CYM end +link pept head - TOP tail + CYF end +link pept head - TOP tail + CSP end +link pept head - TOP tail + ASP end +link pept head - TOP tail + ASH end +link pept head - TOP tail + GLU end +link pept head - TOP tail + GLH end +link pept head - TOP tail + PHE end +link pept head - TOP tail + HIS end +link pept head - TOP tail + NEP end +link pept head - TOP tail + ILE end +link pept head - TOP tail + LYS end +link pept head - TOP tail + ALY end +link pept head - TOP tail + MLY end +link pept head - TOP tail + MLZ end +link pept head - TOP tail + M3L end +link pept head - TOP tail + LEU end +link pept head - TOP tail + MET end +link pept head - TOP tail + MSE end +link pept head - TOP tail + ASN end +link pept head - TOP tail + PRO end +link pept head - TOP tail + GLN end +link pept head - TOP tail + ARG end +link pept head - TOP tail + SER end +link pept head - TOP tail + SEP end +link pept head - TOP tail + THR end +link pept head - TOP tail + THP end +link pept head - TOP tail + TOP end +link pept head - TOP tail + VAL end +link pept head - TOP tail + TRP end +link pept head - TOP tail + TYR end +link pept head - TOP tail + TYP end +link pept head - TOP tail + TYS end +link pept head - TOP tail + HYP end +link pept head - TOP tail + CTN end + +{ peptide linkages for VAL } +link pept head - VAL tail + ALA end +link pept head - VAL tail + CYS end +link pept head - VAL tail + CYM end +link pept head - VAL tail + CYF end +link pept head - VAL tail + CSP end +link pept head - VAL tail + ASP end +link pept head - VAL tail + ASH end +link pept head - VAL tail + GLU end +link pept head - VAL tail + GLH end +link pept head - VAL tail + PHE end +link pept head - VAL tail + HIS end +link pept head - VAL tail + NEP end +link pept head - VAL tail + ILE end +link pept head - VAL tail + LYS end +link pept head - VAL tail + ALY end +link pept head - VAL tail + MLY end +link pept head - VAL tail + MLZ end +link pept head - VAL tail + M3L end +link pept head - VAL tail + LEU end +link pept head - VAL tail + MET end +link pept head - VAL tail + MSE end +link pept head - VAL tail + ASN end +link pept head - VAL tail + PRO end +link pept head - VAL tail + GLN end +link pept head - VAL tail + ARG end +link pept head - VAL tail + SER end +link pept head - VAL tail + SEP end +link pept head - VAL tail + THR end +link pept head - VAL tail + THP end +link pept head - VAL tail + TOP end +link pept head - VAL tail + VAL end +link pept head - VAL tail + TRP end +link pept head - VAL tail + TYR end +link pept head - VAL tail + TYP end +link pept head - VAL tail + TYS end +link pept head - VAL tail + HYP end +link pept head - VAL tail + CTN end + +{ peptide linkages for TRP } +link pept head - TRP tail + ALA end +link pept head - TRP tail + CYS end +link pept head - TRP tail + CYM end +link pept head - TRP tail + CYF end +link pept head - TRP tail + CSP end +link pept head - TRP tail + ASP end +link pept head - TRP tail + ASH end +link pept head - TRP tail + GLU end +link pept head - TRP tail + GLH end +link pept head - TRP tail + PHE end +link pept head - TRP tail + HIS end +link pept head - TRP tail + NEP end +link pept head - TRP tail + ILE end +link pept head - TRP tail + LYS end +link pept head - TRP tail + ALY end +link pept head - TRP tail + MLY end +link pept head - TRP tail + MLZ end +link pept head - TRP tail + M3L end +link pept head - TRP tail + LEU end +link pept head - TRP tail + MET end +link pept head - TRP tail + MSE end +link pept head - TRP tail + ASN end +link pept head - TRP tail + PRO end +link pept head - TRP tail + GLN end +link pept head - TRP tail + ARG end +link pept head - TRP tail + SER end +link pept head - TRP tail + SEP end +link pept head - TRP tail + THR end +link pept head - TRP tail + THP end +link pept head - TRP tail + TOP end +link pept head - TRP tail + VAL end +link pept head - TRP tail + TRP end +link pept head - TRP tail + TYR end +link pept head - TRP tail + TYP end +link pept head - TRP tail + TYS end +link pept head - TRP tail + HYP end +link pept head - TRP tail + CTN end + +{ peptide linkages for TYR } +link pept head - TYR tail + ALA end +link pept head - TYR tail + CYS end +link pept head - TYR tail + CYM end +link pept head - TYR tail + CYF end +link pept head - TYR tail + CSP end +link pept head - TYR tail + ASP end +link pept head - TYR tail + ASH end +link pept head - TYR tail + GLU end +link pept head - TYR tail + GLH end +link pept head - TYR tail + PHE end +link pept head - TYR tail + HIS end +link pept head - TYR tail + NEP end +link pept head - TYR tail + ILE end +link pept head - TYR tail + LYS end +link pept head - TYR tail + ALY end +link pept head - TYR tail + MLY end +link pept head - TYR tail + MLZ end +link pept head - TYR tail + M3L end +link pept head - TYR tail + LEU end +link pept head - TYR tail + MET end +link pept head - TYR tail + MSE end +link pept head - TYR tail + ASN end +link pept head - TYR tail + PRO end +link pept head - TYR tail + GLN end +link pept head - TYR tail + ARG end +link pept head - TYR tail + SER end +link pept head - TYR tail + SEP end +link pept head - TYR tail + THR end +link pept head - TYR tail + THP end +link pept head - TYR tail + TOP end +link pept head - TYR tail + VAL end +link pept head - TYR tail + TRP end +link pept head - TYR tail + TYR end +link pept head - TYR tail + TYP end +link pept head - TYR tail + TYS end +link pept head - TYR tail + HYP end +link pept head - TYR tail + CTN end + +{ peptide linkages for TYP } +link pept head - TYP tail + ALA end +link pept head - TYP tail + CYS end +link pept head - TYP tail + CYM end +link pept head - TYP tail + CYF end +link pept head - TYP tail + CSP end +link pept head - TYP tail + ASP end +link pept head - TYP tail + ASH end +link pept head - TYP tail + GLU end +link pept head - TYP tail + GLH end +link pept head - TYP tail + PHE end +link pept head - TYP tail + HIS end +link pept head - TYP tail + NEP end +link pept head - TYP tail + ILE end +link pept head - TYP tail + LYS end +link pept head - TYP tail + ALY end +link pept head - TYP tail + MLY end +link pept head - TYP tail + MLZ end +link pept head - TYP tail + M3L end +link pept head - TYP tail + LEU end +link pept head - TYP tail + MET end +link pept head - TYP tail + MSE end +link pept head - TYP tail + ASN end +link pept head - TYP tail + PRO end +link pept head - TYP tail + GLN end +link pept head - TYP tail + ARG end +link pept head - TYP tail + SER end +link pept head - TYP tail + SEP end +link pept head - TYP tail + THR end +link pept head - TYP tail + THP end +link pept head - TYP tail + TOP end +link pept head - TYP tail + VAL end +link pept head - TYP tail + TRP end +link pept head - TYP tail + TYR end +link pept head - TYP tail + TYP end +link pept head - TYP tail + TYS end +link pept head - TYP tail + HYP end +link pept head - TYP tail + CTN end + +{ peptide linkages for TYS } +link pept head - TYS tail + ALA end +link pept head - TYS tail + CYS end +link pept head - TYS tail + CYM end +link pept head - TYS tail + CYF end +link pept head - TYS tail + CSP end +link pept head - TYS tail + ASP end +link pept head - TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + CTN end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + CTN end + + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.param new file mode 100644 index 0000000000000000000000000000000000000000..5a839ddd90ac91d4ce18eb75cfc7502c55ac4166 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.param @@ -0,0 +1,47164 @@ +! Parameter file based on Martinize.py CG script version 2.2p +! Author: Jorge Roel, OCT-2017 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +!evaluate ($kbon = 500) + +{* backbone bonds *} +! Same Secondary Structure. Self Terms (14) +BOND B0 B0 12.50 3.500 +BOND Bda Bda 12.50 3.500 +BOND F4 F4 12.50 3.500 +BOND F5 F5 12.50 3.500 +BOND H0 H0 12.50 3.100 +BOND H5 H5 12.50 3.100 +BOND Ha Ha 12.50 3.100 +BOND Hd Hd 12.50 3.100 +BOND Hda Hda 12.50 3.100 +BOND HP0 HP0 12.50 3.100 +BOND HP5 HP5 12.50 3.100 +BOND HPa HPa 12.50 3.100 +BOND T0 T0 12.50 3.500 +BOND Tda Tda 12.50 3.500 +! Same Secondary Structure. Cross Terms (26) +BOND Bda B0 12.50 3.500 +BOND F5 F4 12.50 3.500 +BOND H0 H5 12.50 3.100 +BOND H0 Hd 12.50 3.100 +BOND H0 HP0 12.50 3.100 +BOND H0 HPa 12.50 3.100 +BOND H0 HP5 12.50 3.100 +BOND H0 Hda 12.50 3.100 +BOND H5 HP5 12.50 3.100 +BOND H5 HPa 12.50 3.100 +BOND H5 HP0 12.50 3.100 +BOND Ha H0 12.50 3.100 +BOND Ha HPa 12.50 3.100 +BOND Ha HP5 12.50 3.100 +BOND Hda Ha 12.50 3.100 +BOND Ha H5 12.50 3.100 +BOND Hd Ha 12.50 3.100 +BOND Hd HP0 12.50 3.100 +BOND Hd H5 12.50 3.100 +BOND Hd Hda 12.50 3.100 +BOND Hd HP5 12.50 3.100 +BOND Hd HPa 12.50 3.100 +BOND Hda HP0 12.50 3.100 +BOND Hda H5 12.50 3.100 +BOND Hda HPa 12.50 3.100 +BOND Tda T0 12.50 3.500 +! Different Secondary Structure. Helix-like (48) +BOND B0 H0 12.50 3.100 +BOND B0 H5 12.50 3.100 +BOND B0 Hd 12.50 3.100 +BOND B0 Ha 12.50 3.100 +BOND B0 HPa 12.50 3.100 +BOND B0 HP0 12.50 3.100 +BOND B0 HP5 12.50 3.100 +BOND B0 Hda 12.50 3.100 +BOND Bda H0 12.50 3.100 +BOND Bda H5 12.50 3.100 +BOND Bda Hd 12.50 3.100 +BOND Bda Ha 12.50 3.100 +BOND Bda HPa 12.50 3.100 +BOND Bda HP0 12.50 3.100 +BOND Bda HP5 12.50 3.100 +BOND Bda Hda 12.50 3.100 +BOND F4 H0 12.50 3.100 +BOND F4 H5 12.50 3.100 +BOND F4 Hd 12.50 3.100 +BOND F4 Ha 12.50 3.100 +BOND F4 HPa 12.50 3.100 +BOND F4 HP0 12.50 3.100 +BOND F4 HP5 12.50 3.100 +BOND F4 Hda 12.50 3.100 +BOND F5 H0 12.50 3.100 +BOND F5 H5 12.50 3.100 +BOND F5 Hd 12.50 3.100 +BOND F5 Ha 12.50 3.100 +BOND F5 HPa 12.50 3.100 +BOND F5 HP0 12.50 3.100 +BOND F5 HP5 12.50 3.100 +BOND F5 Hda 12.50 3.100 +BOND T0 H0 12.50 3.100 +BOND T0 H5 12.50 3.100 +BOND T0 Hd 12.50 3.100 +BOND T0 Ha 12.50 3.100 +BOND T0 HPa 12.50 3.100 +BOND T0 HP0 12.50 3.100 +BOND T0 HP5 12.50 3.100 +BOND T0 Hda 12.50 3.100 +BOND Tda H0 12.50 3.100 +BOND Tda H5 12.50 3.100 +BOND Tda Hd 12.50 3.100 +BOND Tda Ha 12.50 3.100 +BOND Tda HPa 12.50 3.100 +BOND Tda HP0 12.50 3.100 +BOND Tda HP5 12.50 3.100 +BOND Tda Hda 12.50 3.100 +! Different Secondary Structure. No Helix-like (12) +BOND B0 F4 12.50 3.500 +BOND B0 F5 12.50 3.500 +BOND B0 Tda 12.50 3.500 +BOND B0 T0 12.50 3.500 +BOND Bda F4 12.50 3.500 +BOND Bda F5 12.50 3.500 +BOND Bda Tda 12.50 3.500 +BOND Bda T0 12.50 3.500 +BOND F4 Tda 12.50 3.500 +BOND F4 T0 12.50 3.500 +BOND F5 Tda 12.50 3.500 +BOND F5 T0 12.50 3.500 + +{* BS, backbone sidechain bonds *} +BOND F5 RN0 50.00 3.300 +BOND F5 Nda 50.00 3.200 +BOND F5 DQa 75.00 3.200 +BOND F5 C5 75.00 3.100 +BOND F5 QNda 50.00 4.000 +BOND F5 Qa 50.00 4.000 +BOND F5 HC4 75.00 3.200 +BOND F5 LC1 75.00 3.300 +BOND F5 KC3 50.00 3.300 +BOND F5 MC5 25.00 4.000 +BOND F5 FC5 75.00 3.100 +BOND F5 SN0 75.00 2.500 +BOND F5 TNda 75.00 2.500 +BOND F5 WC4 50.00 3.000 +BOND F5 YC4 50.00 3.200 +BOND F5 AC1 12.50 3.100 +BOND F5 AC2 12.50 2.650 +! +BOND H0 RN0 50.00 3.300 +BOND H0 Nda 50.00 3.200 +BOND H0 DQa 75.00 3.200 +BOND H0 C5 75.00 3.100 +BOND H0 QNda 50.00 4.000 +BOND H0 Qa 50.00 4.000 +BOND H0 HC4 75.00 3.200 +BOND H0 LC1 75.00 3.300 +BOND H0 KC3 50.00 3.300 +BOND H0 MC5 25.00 4.000 +BOND H0 FC5 75.00 3.100 +BOND H0 SN0 75.00 2.500 +BOND H0 TNda 75.00 2.500 +BOND H0 WC4 50.00 3.000 +BOND H0 YC4 50.00 3.200 +BOND H0 AC1 12.50 3.100 +BOND H0 AC2 12.50 2.650 +! +BOND Ha RN0 50.00 3.300 +BOND Ha Nda 50.00 3.200 +BOND Ha DQa 75.00 3.200 +BOND Ha C5 75.00 3.100 +BOND Ha QNda 50.00 4.000 +BOND Ha Qa 50.00 4.000 +BOND Ha HC4 75.00 3.200 +BOND Ha LC1 75.00 3.300 +BOND Ha KC3 50.00 3.300 +BOND Ha MC5 25.00 4.000 +BOND Ha FC5 75.00 3.100 +BOND Ha SN0 75.00 2.500 +BOND Ha TNda 75.00 2.500 +BOND Ha WC4 50.00 3.000 +BOND Ha YC4 50.00 3.200 +BOND Ha AC1 12.50 3.100 +BOND Ha AC2 12.50 2.650 +! +BOND Hd RN0 50.00 3.300 +BOND Hd Nda 50.00 3.200 +BOND Hd DQa 75.00 3.200 +BOND Hd C5 75.00 3.100 +BOND Hd QNda 50.00 4.000 +BOND Hd Qa 50.00 4.000 +BOND Hd HC4 75.00 3.200 +BOND Hd LC1 75.00 3.300 +BOND Hd KC3 50.00 3.300 +BOND Hd MC5 25.00 4.000 +BOND Hd FC5 75.00 3.100 +BOND Hd SN0 75.00 2.500 +BOND Hd TNda 75.00 2.500 +BOND Hd WC4 50.00 3.000 +BOND Hd YC4 50.00 3.200 +BOND Hd AC1 12.50 3.100 +BOND Hd AC2 12.50 2.650 +! +BOND Hda RN0 50.00 3.300 +BOND Hda Nda 50.00 3.200 +BOND Hda DQa 75.00 3.200 +BOND Hda C5 75.00 3.100 +BOND Hda QNda 50.00 4.000 +BOND Hda Qa 50.00 4.000 +BOND Hda HC4 75.00 3.200 +BOND Hda LC1 75.00 3.300 +BOND Hda KC3 50.00 3.300 +BOND Hda MC5 25.00 4.000 +BOND Hda FC5 75.00 3.100 +BOND Hda SN0 75.00 2.500 +BOND Hda TNda 75.00 2.500 +BOND Hda WC4 50.00 3.000 +BOND Hda YC4 50.00 3.200 +BOND Hda AC1 12.50 3.100 +BOND Hda AC2 12.50 2.650 +! +BOND Bda RN0 50.00 3.300 +BOND Bda Nda 50.00 3.200 +BOND Bda DQa 75.00 3.200 +BOND Bda C5 75.00 3.100 +BOND Bda QNda 50.00 4.000 +BOND Bda Qa 50.00 4.000 +BOND Bda HC4 75.00 3.200 +BOND Bda LC1 75.00 3.300 +BOND Bda KC3 50.00 3.300 +BOND Bda MC5 25.00 4.000 +BOND Bda FC5 75.00 3.100 +BOND Bda SN0 75.00 2.500 +BOND Bda TNda 75.00 2.500 +BOND Bda WC4 50.00 3.000 +BOND Bda YC4 50.00 3.200 +BOND Bda AC1 12.50 3.100 +BOND Bda AC2 12.50 2.650 +! +BOND Tda RN0 50.00 3.300 +BOND Tda Nda 50.00 3.200 +BOND Tda DQa 75.00 3.200 +BOND Tda C5 75.00 3.100 +BOND Tda QNda 50.00 4.000 +BOND Tda Qa 50.00 4.000 +BOND Tda HC4 75.00 3.200 +BOND Tda LC1 75.00 3.300 +BOND Tda KC3 50.00 3.300 +BOND Tda MC5 25.00 4.000 +BOND Tda FC5 75.00 3.100 +BOND Tda SN0 75.00 2.500 +BOND Tda TNda 75.00 2.500 +BOND Tda WC4 50.00 3.000 +BOND Tda YC4 50.00 3.200 +BOND Tda AC1 12.50 3.100 +BOND Tda AC2 12.50 2.650 +! Pro specific +BOND F4 PC3 75.00 3.000 +BOND B0 PC3 75.00 3.000 +BOND HP5 PC3 75.00 3.000 +BOND HP0 PC3 75.00 3.000 +BOND HPa PC3 75.00 3.000 +BOND T0 PC3 75.00 3.000 + +{* SS, sidechain bonds *} +BOND QNda SCd 500 1.100 ! fake bond GLN +BOND Nda SCd 500 1.100 ! fake bond ASN +BOND SN0 SCd 500 1.100 ! fake bond SER +BOND TNda SCd 500 1.100 ! fake bond THR +BOND AQd SCd 500 1.100 ! constraints ARG +BOND DQa SCd 500 1.100 ! constraints ASP +BOND Qa SCd 500 1.100 ! constraints GLU +BOND KQd SCd 500 1.100 ! constraints LYS +BOND HC4 SP1 500 2.700 ! constraints +BOND SP1 SP1 500 2.700 ! constraints +BOND FC5 SC5 500 2.700 ! constraints +BOND SC5 SC5 500 2.700 ! constraints +BOND WC4 SC5 500 2.700 ! constraints +BOND WC4 SNd 500 2.700 ! constraints +BOND SC4 SC5 500 2.700 ! constraints +BOND SNd SC5 500 2.700 ! constraints +BOND YC4 SC4 500 2.700 ! constraints +BOND YC4 SP1 500 2.700 ! constraints +BOND SC4 SP1 500 2.700 ! constraints +BOND SCd SCd 500 2.800 ! constraints +BOND RN0 AQd 50.00 3.400 +BOND KC3 KQd 50.00 2.800 + +{* BBB, backbone angles *} +ANGLe F4 F4 F4 5.971 127 +ANGLe F4 F4 F5 5.971 127 +ANGLe F4 F4 H0 5.971 127 +ANGLe F4 F4 H5 5.971 127 +ANGLe F4 F4 Hd 5.971 127 +ANGLe F4 F4 Ha 5.971 127 +ANGLe F4 F4 Hda 5.971 127 +ANGLe F4 F4 Bda 5.971 127 +ANGLe F4 F4 B0 5.971 127 +ANGLe F4 F4 Tda 5.971 127 +ANGLe F4 F4 T0 5.971 127 +ANGLe F4 F4 HP5 5.971 127 +ANGLe F4 F4 HP0 5.971 127 +ANGLe F4 F4 HPa 5.971 127 +ANGLe F4 F5 F4 5.971 127 +ANGLe F4 F5 F5 5.971 127 +ANGLe F4 F5 H0 5.971 127 +ANGLe F4 F5 H5 5.971 127 +ANGLe F4 F5 Hd 5.971 127 +ANGLe F4 F5 Ha 5.971 127 +ANGLe F4 F5 Hda 5.971 127 +ANGLe F4 F5 Bda 5.971 127 +ANGLe F4 F5 B0 5.971 127 +ANGLe F4 F5 Tda 5.971 127 +ANGLe F4 F5 T0 5.971 127 +ANGLe F4 F5 HP5 5.971 127 +ANGLe F4 F5 HP0 5.971 127 +ANGLe F4 F5 HPa 5.971 127 +ANGLe F4 H0 F4 5.971 127 +ANGLe F4 H0 F5 5.971 127 +ANGLe F4 H0 H0 5.971 127 +ANGLe F4 H0 H5 5.971 127 +ANGLe F4 H0 Hd 5.971 127 +ANGLe F4 H0 Ha 5.971 127 +ANGLe F4 H0 Hda 5.971 127 +ANGLe F4 H0 Bda 5.971 127 +ANGLe F4 H0 B0 5.971 127 +ANGLe F4 H0 Tda 5.971 127 +ANGLe F4 H0 T0 5.971 127 +ANGLe F4 H0 HP5 5.971 127 +ANGLe F4 H0 HP0 5.971 127 +ANGLe F4 H0 HPa 5.971 127 +ANGLe F4 H5 F4 5.971 127 +ANGLe F4 H5 F5 5.971 127 +ANGLe F4 H5 H0 5.971 127 +ANGLe F4 H5 H5 5.971 127 +ANGLe F4 H5 Hd 5.971 127 +ANGLe F4 H5 Ha 5.971 127 +ANGLe F4 H5 Hda 5.971 127 +ANGLe F4 H5 Bda 5.971 127 +ANGLe F4 H5 B0 5.971 127 +ANGLe F4 H5 Tda 5.971 127 +ANGLe F4 H5 T0 5.971 127 +ANGLe F4 H5 HP5 5.971 127 +ANGLe F4 H5 HP0 5.971 127 +ANGLe F4 H5 HPa 5.971 127 +ANGLe F4 Hd F4 5.971 127 +ANGLe F4 Hd F5 5.971 127 +ANGLe F4 Hd H0 5.971 127 +ANGLe F4 Hd H5 5.971 127 +ANGLe F4 Hd Hd 5.971 127 +ANGLe F4 Hd Ha 5.971 127 +ANGLe F4 Hd Hda 5.971 127 +ANGLe F4 Hd Bda 5.971 127 +ANGLe F4 Hd B0 5.971 127 +ANGLe F4 Hd Tda 5.971 127 +ANGLe F4 Hd T0 5.971 127 +ANGLe F4 Hd HP5 5.971 127 +ANGLe F4 Hd HP0 5.971 127 +ANGLe F4 Hd HPa 5.971 127 +ANGLe F4 Ha F4 5.971 127 +ANGLe F4 Ha F5 5.971 127 +ANGLe F4 Ha H0 5.971 127 +ANGLe F4 Ha H5 5.971 127 +ANGLe F4 Ha Hd 5.971 127 +ANGLe F4 Ha Ha 5.971 127 +ANGLe F4 Ha Hda 5.971 127 +ANGLe F4 Ha Bda 5.971 127 +ANGLe F4 Ha B0 5.971 127 +ANGLe F4 Ha Tda 5.971 127 +ANGLe F4 Ha T0 5.971 127 +ANGLe F4 Ha HP5 5.971 127 +ANGLe F4 Ha HP0 5.971 127 +ANGLe F4 Ha HPa 5.971 127 +ANGLe F4 Hda F4 5.971 127 +ANGLe F4 Hda F5 5.971 127 +ANGLe F4 Hda H0 5.971 127 +ANGLe F4 Hda H5 5.971 127 +ANGLe F4 Hda Hd 5.971 127 +ANGLe F4 Hda Ha 5.971 127 +ANGLe F4 Hda Hda 5.971 127 +ANGLe F4 Hda Bda 5.971 127 +ANGLe F4 Hda B0 5.971 127 +ANGLe F4 Hda Tda 5.971 127 +ANGLe F4 Hda T0 5.971 127 +ANGLe F4 Hda HP5 5.971 127 +ANGLe F4 Hda HP0 5.971 127 +ANGLe F4 Hda HPa 5.971 127 +ANGLe F4 Bda F4 5.971 127 +ANGLe F4 Bda F5 5.971 127 +ANGLe F4 Bda H0 5.971 127 +ANGLe F4 Bda H5 5.971 127 +ANGLe F4 Bda Hd 5.971 127 +ANGLe F4 Bda Ha 5.971 127 +ANGLe F4 Bda Hda 5.971 127 +ANGLe F4 Bda Bda 5.971 127 +ANGLe F4 Bda B0 5.971 127 +ANGLe F4 Bda Tda 5.971 127 +ANGLe F4 Bda T0 5.971 127 +ANGLe F4 Bda HP5 5.971 127 +ANGLe F4 Bda HP0 5.971 127 +ANGLe F4 Bda HPa 5.971 127 +ANGLe F4 B0 F4 5.971 127 +ANGLe F4 B0 F5 5.971 127 +ANGLe F4 B0 H0 5.971 127 +ANGLe F4 B0 H5 5.971 127 +ANGLe F4 B0 Hd 5.971 127 +ANGLe F4 B0 Ha 5.971 127 +ANGLe F4 B0 Hda 5.971 127 +ANGLe F4 B0 Bda 5.971 127 +ANGLe F4 B0 B0 5.971 127 +ANGLe F4 B0 Tda 5.971 127 +ANGLe F4 B0 T0 5.971 127 +ANGLe F4 B0 HP5 5.971 127 +ANGLe F4 B0 HP0 5.971 127 +ANGLe F4 B0 HPa 5.971 127 +ANGLe F4 Tda F4 5.971 127 +ANGLe F4 Tda F5 5.971 127 +ANGLe F4 Tda H0 5.971 127 +ANGLe F4 Tda H5 5.971 127 +ANGLe F4 Tda Hd 5.971 127 +ANGLe F4 Tda Ha 5.971 127 +ANGLe F4 Tda Hda 5.971 127 +ANGLe F4 Tda Bda 5.971 127 +ANGLe F4 Tda B0 5.971 127 +ANGLe F4 Tda Tda 5.971 127 +ANGLe F4 Tda T0 5.971 127 +ANGLe F4 Tda HP5 5.971 127 +ANGLe F4 Tda HP0 5.971 127 +ANGLe F4 Tda HPa 5.971 127 +ANGLe F4 T0 F4 5.971 127 +ANGLe F4 T0 F5 5.971 127 +ANGLe F4 T0 H0 5.971 127 +ANGLe F4 T0 H5 5.971 127 +ANGLe F4 T0 Hd 5.971 127 +ANGLe F4 T0 Ha 5.971 127 +ANGLe F4 T0 Hda 5.971 127 +ANGLe F4 T0 Bda 5.971 127 +ANGLe F4 T0 B0 5.971 127 +ANGLe F4 T0 Tda 5.971 127 +ANGLe F4 T0 T0 5.971 127 +ANGLe F4 T0 HP5 5.971 127 +ANGLe F4 T0 HP0 5.971 127 +ANGLe F4 T0 HPa 5.971 127 +ANGLe F4 HP5 F4 5.971 127 +ANGLe F4 HP5 F5 5.971 127 +ANGLe F4 HP5 H0 5.971 127 +ANGLe F4 HP5 H5 5.971 127 +ANGLe F4 HP5 Hd 5.971 127 +ANGLe F4 HP5 Ha 5.971 127 +ANGLe F4 HP5 Hda 5.971 127 +ANGLe F4 HP5 Bda 5.971 127 +ANGLe F4 HP5 B0 5.971 127 +ANGLe F4 HP5 Tda 5.971 127 +ANGLe F4 HP5 T0 5.971 127 +ANGLe F4 HP5 HP5 5.971 127 +ANGLe F4 HP5 HP0 5.971 127 +ANGLe F4 HP5 HPa 5.971 127 +ANGLe F4 HP0 F4 5.971 127 +ANGLe F4 HP0 F5 5.971 127 +ANGLe F4 HP0 H0 5.971 127 +ANGLe F4 HP0 H5 5.971 127 +ANGLe F4 HP0 Hd 5.971 127 +ANGLe F4 HP0 Ha 5.971 127 +ANGLe F4 HP0 Hda 5.971 127 +ANGLe F4 HP0 Bda 5.971 127 +ANGLe F4 HP0 B0 5.971 127 +ANGLe F4 HP0 Tda 5.971 127 +ANGLe F4 HP0 T0 5.971 127 +ANGLe F4 HP0 HP5 5.971 127 +ANGLe F4 HP0 HP0 5.971 127 +ANGLe F4 HP0 HPa 5.971 127 +ANGLe F4 HPa F4 5.971 127 +ANGLe F4 HPa F5 5.971 127 +ANGLe F4 HPa H0 5.971 127 +ANGLe F4 HPa H5 5.971 127 +ANGLe F4 HPa Hd 5.971 127 +ANGLe F4 HPa Ha 5.971 127 +ANGLe F4 HPa Hda 5.971 127 +ANGLe F4 HPa Bda 5.971 127 +ANGLe F4 HPa B0 5.971 127 +ANGLe F4 HPa Tda 5.971 127 +ANGLe F4 HPa T0 5.971 127 +ANGLe F4 HPa HP5 5.971 127 +ANGLe F4 HPa HP0 5.971 127 +ANGLe F4 HPa HPa 5.971 127 +ANGLe F5 F4 F4 5.971 127 +ANGLe F5 F4 F5 5.971 127 +ANGLe F5 F4 H0 5.971 127 +ANGLe F5 F4 H5 5.971 127 +ANGLe F5 F4 Hd 5.971 127 +ANGLe F5 F4 Ha 5.971 127 +ANGLe F5 F4 Hda 5.971 127 +ANGLe F5 F4 Bda 5.971 127 +ANGLe F5 F4 B0 5.971 127 +ANGLe F5 F4 Tda 5.971 127 +ANGLe F5 F4 T0 5.971 127 +ANGLe F5 F4 HP5 5.971 127 +ANGLe F5 F4 HP0 5.971 127 +ANGLe F5 F4 HPa 5.971 127 +ANGLe F5 F5 F4 5.971 127 +ANGLe F5 F5 F5 5.971 127 +ANGLe F5 F5 H0 5.971 127 +ANGLe F5 F5 H5 5.971 127 +ANGLe F5 F5 Hd 5.971 127 +ANGLe F5 F5 Ha 5.971 127 +ANGLe F5 F5 Hda 5.971 127 +ANGLe F5 F5 Bda 5.971 127 +ANGLe F5 F5 B0 5.971 127 +ANGLe F5 F5 Tda 5.971 127 +ANGLe F5 F5 T0 5.971 127 +ANGLe F5 F5 HP5 5.971 127 +ANGLe F5 F5 HP0 5.971 127 +ANGLe F5 F5 HPa 5.971 127 +ANGLe F5 H0 F4 5.971 127 +ANGLe F5 H0 F5 5.971 127 +ANGLe F5 H0 H0 5.971 127 +ANGLe F5 H0 H5 5.971 127 +ANGLe F5 H0 Hd 5.971 127 +ANGLe F5 H0 Ha 5.971 127 +ANGLe F5 H0 Hda 5.971 127 +ANGLe F5 H0 Bda 5.971 127 +ANGLe F5 H0 B0 5.971 127 +ANGLe F5 H0 Tda 5.971 127 +ANGLe F5 H0 T0 5.971 127 +ANGLe F5 H0 HP5 5.971 127 +ANGLe F5 H0 HP0 5.971 127 +ANGLe F5 H0 HPa 5.971 127 +ANGLe F5 H5 F4 5.971 127 +ANGLe F5 H5 F5 5.971 127 +ANGLe F5 H5 H0 5.971 127 +ANGLe F5 H5 H5 5.971 127 +ANGLe F5 H5 Hd 5.971 127 +ANGLe F5 H5 Ha 5.971 127 +ANGLe F5 H5 Hda 5.971 127 +ANGLe F5 H5 Bda 5.971 127 +ANGLe F5 H5 B0 5.971 127 +ANGLe F5 H5 Tda 5.971 127 +ANGLe F5 H5 T0 5.971 127 +ANGLe F5 H5 HP5 5.971 127 +ANGLe F5 H5 HP0 5.971 127 +ANGLe F5 H5 HPa 5.971 127 +ANGLe F5 Hd F4 5.971 127 +ANGLe F5 Hd F5 5.971 127 +ANGLe F5 Hd H0 5.971 127 +ANGLe F5 Hd H5 5.971 127 +ANGLe F5 Hd Hd 5.971 127 +ANGLe F5 Hd Ha 5.971 127 +ANGLe F5 Hd Hda 5.971 127 +ANGLe F5 Hd Bda 5.971 127 +ANGLe F5 Hd B0 5.971 127 +ANGLe F5 Hd Tda 5.971 127 +ANGLe F5 Hd T0 5.971 127 +ANGLe F5 Hd HP5 5.971 127 +ANGLe F5 Hd HP0 5.971 127 +ANGLe F5 Hd HPa 5.971 127 +ANGLe F5 Ha F4 5.971 127 +ANGLe F5 Ha F5 5.971 127 +ANGLe F5 Ha H0 5.971 127 +ANGLe F5 Ha H5 5.971 127 +ANGLe F5 Ha Hd 5.971 127 +ANGLe F5 Ha Ha 5.971 127 +ANGLe F5 Ha Hda 5.971 127 +ANGLe F5 Ha Bda 5.971 127 +ANGLe F5 Ha B0 5.971 127 +ANGLe F5 Ha Tda 5.971 127 +ANGLe F5 Ha T0 5.971 127 +ANGLe F5 Ha HP5 5.971 127 +ANGLe F5 Ha HP0 5.971 127 +ANGLe F5 Ha HPa 5.971 127 +ANGLe F5 Hda F4 5.971 127 +ANGLe F5 Hda F5 5.971 127 +ANGLe F5 Hda H0 5.971 127 +ANGLe F5 Hda H5 5.971 127 +ANGLe F5 Hda Hd 5.971 127 +ANGLe F5 Hda Ha 5.971 127 +ANGLe F5 Hda Hda 5.971 127 +ANGLe F5 Hda Bda 5.971 127 +ANGLe F5 Hda B0 5.971 127 +ANGLe F5 Hda Tda 5.971 127 +ANGLe F5 Hda T0 5.971 127 +ANGLe F5 Hda HP5 5.971 127 +ANGLe F5 Hda HP0 5.971 127 +ANGLe F5 Hda HPa 5.971 127 +ANGLe F5 Bda F4 5.971 127 +ANGLe F5 Bda F5 5.971 127 +ANGLe F5 Bda H0 5.971 127 +ANGLe F5 Bda H5 5.971 127 +ANGLe F5 Bda Hd 5.971 127 +ANGLe F5 Bda Ha 5.971 127 +ANGLe F5 Bda Hda 5.971 127 +ANGLe F5 Bda Bda 5.971 127 +ANGLe F5 Bda B0 5.971 127 +ANGLe F5 Bda Tda 5.971 127 +ANGLe F5 Bda T0 5.971 127 +ANGLe F5 Bda HP5 5.971 127 +ANGLe F5 Bda HP0 5.971 127 +ANGLe F5 Bda HPa 5.971 127 +ANGLe F5 B0 F4 5.971 127 +ANGLe F5 B0 F5 5.971 127 +ANGLe F5 B0 H0 5.971 127 +ANGLe F5 B0 H5 5.971 127 +ANGLe F5 B0 Hd 5.971 127 +ANGLe F5 B0 Ha 5.971 127 +ANGLe F5 B0 Hda 5.971 127 +ANGLe F5 B0 Bda 5.971 127 +ANGLe F5 B0 B0 5.971 127 +ANGLe F5 B0 Tda 5.971 127 +ANGLe F5 B0 T0 5.971 127 +ANGLe F5 B0 HP5 5.971 127 +ANGLe F5 B0 HP0 5.971 127 +ANGLe F5 B0 HPa 5.971 127 +ANGLe F5 Tda F4 5.971 127 +ANGLe F5 Tda F5 5.971 127 +ANGLe F5 Tda H0 5.971 127 +ANGLe F5 Tda H5 5.971 127 +ANGLe F5 Tda Hd 5.971 127 +ANGLe F5 Tda Ha 5.971 127 +ANGLe F5 Tda Hda 5.971 127 +ANGLe F5 Tda Bda 5.971 127 +ANGLe F5 Tda B0 5.971 127 +ANGLe F5 Tda Tda 5.971 127 +ANGLe F5 Tda T0 5.971 127 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+ANGLe T0 Tda T0 5.971 100 +ANGLe T0 Tda HP5 5.971 100 +ANGLe T0 Tda HP0 5.971 100 +ANGLe T0 Tda HPa 5.971 100 +ANGLe T0 T0 F4 5.971 100 +ANGLe T0 T0 F5 5.971 100 +ANGLe T0 T0 H0 5.971 100 +ANGLe T0 T0 H5 5.971 100 +ANGLe T0 T0 Hd 5.971 100 +ANGLe T0 T0 Ha 5.971 100 +ANGLe T0 T0 Hda 5.971 100 +ANGLe T0 T0 Bda 5.971 100 +ANGLe T0 T0 B0 5.971 100 +ANGLe T0 T0 Tda 5.971 100 +ANGLe T0 T0 T0 5.971 100 +ANGLe T0 T0 HP5 5.971 100 +ANGLe T0 T0 HP0 5.971 100 +ANGLe T0 T0 HPa 5.971 100 +ANGLe T0 HP5 F4 5.971 100 +ANGLe T0 HP5 F5 5.971 100 +ANGLe T0 HP5 H0 5.971 100 +ANGLe T0 HP5 H5 5.971 100 +ANGLe T0 HP5 Hd 5.971 100 +ANGLe T0 HP5 Ha 5.971 100 +ANGLe T0 HP5 Hda 5.971 100 +ANGLe T0 HP5 Bda 5.971 100 +ANGLe T0 HP5 B0 5.971 100 +ANGLe T0 HP5 Tda 5.971 100 +ANGLe T0 HP5 T0 5.971 100 +ANGLe T0 HP5 HP5 5.971 100 +ANGLe T0 HP5 HP0 5.971 100 +ANGLe T0 HP5 HPa 5.971 100 +ANGLe T0 HP0 F4 5.971 100 +ANGLe T0 HP0 F5 5.971 100 +ANGLe T0 HP0 H0 5.971 100 +ANGLe T0 HP0 H5 5.971 100 +ANGLe T0 HP0 Hd 5.971 100 +ANGLe T0 HP0 Ha 5.971 100 +ANGLe T0 HP0 Hda 5.971 100 +ANGLe T0 HP0 Bda 5.971 100 +ANGLe T0 HP0 B0 5.971 100 +ANGLe T0 HP0 Tda 5.971 100 +ANGLe T0 HP0 T0 5.971 100 +ANGLe T0 HP0 HP5 5.971 100 +ANGLe T0 HP0 HP0 5.971 100 +ANGLe T0 HP0 HPa 5.971 100 +ANGLe T0 HPa F4 5.971 100 +ANGLe T0 HPa F5 5.971 100 +ANGLe T0 HPa H0 5.971 100 +ANGLe T0 HPa H5 5.971 100 +ANGLe T0 HPa Hd 5.971 100 +ANGLe T0 HPa Ha 5.971 100 +ANGLe T0 HPa Hda 5.971 100 +ANGLe T0 HPa Bda 5.971 100 +ANGLe T0 HPa B0 5.971 100 +ANGLe T0 HPa Tda 5.971 100 +ANGLe T0 HPa T0 5.971 100 +ANGLe T0 HPa HP5 5.971 100 +ANGLe T0 HPa HP0 5.971 100 +ANGLe T0 HPa HPa 5.971 100 +ANGLe HP5 F4 F4 23.883 98 +ANGLe HP5 F4 F5 23.883 98 +ANGLe HP5 F4 H0 23.883 98 +ANGLe HP5 F4 H5 23.883 98 +ANGLe HP5 F4 Hd 23.883 98 +ANGLe HP5 F4 Ha 23.883 98 +ANGLe HP5 F4 Hda 23.883 98 +ANGLe HP5 F4 Bda 23.883 98 +ANGLe HP5 F4 B0 23.883 98 +ANGLe HP5 F4 Tda 23.883 98 +ANGLe HP5 F4 T0 23.883 98 +ANGLe HP5 F4 HP5 23.883 98 +ANGLe HP5 F4 HP0 23.883 98 +ANGLe HP5 F4 HPa 23.883 98 +ANGLe HP5 F5 F4 23.883 98 +ANGLe HP5 F5 F5 23.883 98 +ANGLe HP5 F5 H0 23.883 98 +ANGLe HP5 F5 H5 23.883 98 +ANGLe HP5 F5 Hd 23.883 98 +ANGLe HP5 F5 Ha 23.883 98 +ANGLe HP5 F5 Hda 23.883 98 +ANGLe HP5 F5 Bda 23.883 98 +ANGLe HP5 F5 B0 23.883 98 +ANGLe HP5 F5 Tda 23.883 98 +ANGLe HP5 F5 T0 23.883 98 +ANGLe HP5 F5 HP5 23.883 98 +ANGLe HP5 F5 HP0 23.883 98 +ANGLe HP5 F5 HPa 23.883 98 +ANGLe HP5 H0 F4 23.883 98 +ANGLe HP5 H0 F5 23.883 98 +ANGLe HP5 H0 H0 23.883 98 +ANGLe HP5 H0 H5 23.883 98 +ANGLe HP5 H0 Hd 23.883 98 +ANGLe HP5 H0 Ha 23.883 98 +ANGLe HP5 H0 Hda 23.883 98 +ANGLe HP5 H0 Bda 23.883 98 +ANGLe HP5 H0 B0 23.883 98 +ANGLe HP5 H0 Tda 23.883 98 +ANGLe HP5 H0 T0 23.883 98 +ANGLe HP5 H0 HP5 23.883 98 +ANGLe HP5 H0 HP0 23.883 98 +ANGLe HP5 H0 HPa 23.883 98 +ANGLe HP5 H5 F4 23.883 98 +ANGLe HP5 H5 F5 23.883 98 +ANGLe HP5 H5 H0 23.883 98 +ANGLe HP5 H5 H5 23.883 98 +ANGLe HP5 H5 Hd 23.883 98 +ANGLe HP5 H5 Ha 23.883 98 +ANGLe HP5 H5 Hda 23.883 98 +ANGLe HP5 H5 Bda 23.883 98 +ANGLe HP5 H5 B0 23.883 98 +ANGLe HP5 H5 Tda 23.883 98 +ANGLe HP5 H5 T0 23.883 98 +ANGLe HP5 H5 HP5 23.883 98 +ANGLe HP5 H5 HP0 23.883 98 +ANGLe HP5 H5 HPa 23.883 98 +ANGLe HP5 Hd F4 23.883 98 +ANGLe HP5 Hd F5 23.883 98 +ANGLe HP5 Hd H0 23.883 98 +ANGLe HP5 Hd H5 23.883 98 +ANGLe HP5 Hd Hd 23.883 98 +ANGLe HP5 Hd Ha 23.883 98 +ANGLe HP5 Hd Hda 23.883 98 +ANGLe HP5 Hd Bda 23.883 98 +ANGLe HP5 Hd B0 23.883 98 +ANGLe HP5 Hd Tda 23.883 98 +ANGLe HP5 Hd T0 23.883 98 +ANGLe HP5 Hd HP5 23.883 98 +ANGLe HP5 Hd HP0 23.883 98 +ANGLe HP5 Hd HPa 23.883 98 +ANGLe HP5 Ha F4 23.883 98 +ANGLe HP5 Ha F5 23.883 98 +ANGLe HP5 Ha H0 23.883 98 +ANGLe HP5 Ha H5 23.883 98 +ANGLe HP5 Ha Hd 23.883 98 +ANGLe HP5 Ha Ha 23.883 98 +ANGLe HP5 Ha Hda 23.883 98 +ANGLe HP5 Ha Bda 23.883 98 +ANGLe HP5 Ha B0 23.883 98 +ANGLe HP5 Ha Tda 23.883 98 +ANGLe HP5 Ha T0 23.883 98 +ANGLe HP5 Ha HP5 23.883 98 +ANGLe HP5 Ha HP0 23.883 98 +ANGLe HP5 Ha HPa 23.883 98 +ANGLe HP5 Hda F4 23.883 98 +ANGLe HP5 Hda F5 23.883 98 +ANGLe HP5 Hda H0 23.883 98 +ANGLe HP5 Hda H5 23.883 98 +ANGLe HP5 Hda Hd 23.883 98 +ANGLe HP5 Hda Ha 23.883 98 +ANGLe HP5 Hda Hda 23.883 98 +ANGLe HP5 Hda Bda 23.883 98 +ANGLe HP5 Hda B0 23.883 98 +ANGLe HP5 Hda Tda 23.883 98 +ANGLe HP5 Hda T0 23.883 98 +ANGLe HP5 Hda HP5 23.883 98 +ANGLe HP5 Hda HP0 23.883 98 +ANGLe HP5 Hda HPa 23.883 98 +ANGLe HP5 Bda F4 23.883 98 +ANGLe HP5 Bda F5 23.883 98 +ANGLe HP5 Bda H0 23.883 98 +ANGLe HP5 Bda H5 23.883 98 +ANGLe HP5 Bda Hd 23.883 98 +ANGLe HP5 Bda Ha 23.883 98 +ANGLe HP5 Bda Hda 23.883 98 +ANGLe HP5 Bda Bda 23.883 98 +ANGLe HP5 Bda B0 23.883 98 +ANGLe HP5 Bda Tda 23.883 98 +ANGLe HP5 Bda T0 23.883 98 +ANGLe HP5 Bda HP5 23.883 98 +ANGLe HP5 Bda HP0 23.883 98 +ANGLe HP5 Bda HPa 23.883 98 +ANGLe HP5 B0 F4 23.883 98 +ANGLe HP5 B0 F5 23.883 98 +ANGLe HP5 B0 H0 23.883 98 +ANGLe HP5 B0 H5 23.883 98 +ANGLe HP5 B0 Hd 23.883 98 +ANGLe HP5 B0 Ha 23.883 98 +ANGLe HP5 B0 Hda 23.883 98 +ANGLe HP5 B0 Bda 23.883 98 +ANGLe HP5 B0 B0 23.883 98 +ANGLe HP5 B0 Tda 23.883 98 +ANGLe HP5 B0 T0 23.883 98 +ANGLe HP5 B0 HP5 23.883 98 +ANGLe HP5 B0 HP0 23.883 98 +ANGLe HP5 B0 HPa 23.883 98 +ANGLe HP5 Tda F4 23.883 98 +ANGLe HP5 Tda F5 23.883 98 +ANGLe HP5 Tda H0 23.883 98 +ANGLe HP5 Tda H5 23.883 98 +ANGLe HP5 Tda Hd 23.883 98 +ANGLe HP5 Tda Ha 23.883 98 +ANGLe HP5 Tda Hda 23.883 98 +ANGLe HP5 Tda Bda 23.883 98 +ANGLe HP5 Tda B0 23.883 98 +ANGLe HP5 Tda Tda 23.883 98 +ANGLe HP5 Tda T0 23.883 98 +ANGLe HP5 Tda HP5 23.883 98 +ANGLe HP5 Tda HP0 23.883 98 +ANGLe HP5 Tda HPa 23.883 98 +ANGLe HP5 T0 F4 23.883 98 +ANGLe HP5 T0 F5 23.883 98 +ANGLe HP5 T0 H0 23.883 98 +ANGLe HP5 T0 H5 23.883 98 +ANGLe HP5 T0 Hd 23.883 98 +ANGLe HP5 T0 Ha 23.883 98 +ANGLe HP5 T0 Hda 23.883 98 +ANGLe HP5 T0 Bda 23.883 98 +ANGLe HP5 T0 B0 23.883 98 +ANGLe HP5 T0 Tda 23.883 98 +ANGLe HP5 T0 T0 23.883 98 +ANGLe HP5 T0 HP5 23.883 98 +ANGLe HP5 T0 HP0 23.883 98 +ANGLe HP5 T0 HPa 23.883 98 +ANGLe HP5 HP5 F4 23.883 98 +ANGLe HP5 HP5 F5 23.883 98 +ANGLe HP5 HP5 H0 23.883 98 +ANGLe HP5 HP5 H5 23.883 98 +ANGLe HP5 HP5 Hd 23.883 98 +ANGLe HP5 HP5 Ha 23.883 98 +ANGLe HP5 HP5 Hda 23.883 98 +ANGLe HP5 HP5 Bda 23.883 98 +ANGLe HP5 HP5 B0 23.883 98 +ANGLe HP5 HP5 Tda 23.883 98 +ANGLe HP5 HP5 T0 23.883 98 +ANGLe HP5 HP5 HP5 23.883 98 +ANGLe HP5 HP5 HP0 23.883 98 +ANGLe HP5 HP5 HPa 23.883 98 +ANGLe HP5 HP0 F4 23.883 98 +ANGLe HP5 HP0 F5 23.883 98 +ANGLe HP5 HP0 H0 23.883 98 +ANGLe HP5 HP0 H5 23.883 98 +ANGLe HP5 HP0 Hd 23.883 98 +ANGLe HP5 HP0 Ha 23.883 98 +ANGLe HP5 HP0 Hda 23.883 98 +ANGLe HP5 HP0 Bda 23.883 98 +ANGLe HP5 HP0 B0 23.883 98 +ANGLe HP5 HP0 Tda 23.883 98 +ANGLe HP5 HP0 T0 23.883 98 +ANGLe HP5 HP0 HP5 23.883 98 +ANGLe HP5 HP0 HP0 23.883 98 +ANGLe HP5 HP0 HPa 23.883 98 +ANGLe HP5 HPa F4 23.883 98 +ANGLe HP5 HPa F5 23.883 98 +ANGLe HP5 HPa H0 23.883 98 +ANGLe HP5 HPa H5 23.883 98 +ANGLe HP5 HPa Hd 23.883 98 +ANGLe HP5 HPa Ha 23.883 98 +ANGLe HP5 HPa Hda 23.883 98 +ANGLe HP5 HPa Bda 23.883 98 +ANGLe HP5 HPa B0 23.883 98 +ANGLe HP5 HPa Tda 23.883 98 +ANGLe HP5 HPa T0 23.883 98 +ANGLe HP5 HPa HP5 23.883 98 +ANGLe HP5 HPa HP0 23.883 98 +ANGLe HP5 HPa HPa 23.883 98 +ANGLe HP0 F4 F4 23.883 98 +ANGLe HP0 F4 F5 23.883 98 +ANGLe HP0 F4 H0 23.883 98 +ANGLe HP0 F4 H5 23.883 98 +ANGLe HP0 F4 Hd 23.883 98 +ANGLe HP0 F4 Ha 23.883 98 +ANGLe HP0 F4 Hda 23.883 98 +ANGLe HP0 F4 Bda 23.883 98 +ANGLe HP0 F4 B0 23.883 98 +ANGLe HP0 F4 Tda 23.883 98 +ANGLe HP0 F4 T0 23.883 98 +ANGLe HP0 F4 HP5 23.883 98 +ANGLe HP0 F4 HP0 23.883 98 +ANGLe HP0 F4 HPa 23.883 98 +ANGLe HP0 F5 F4 23.883 98 +ANGLe HP0 F5 F5 23.883 98 +ANGLe HP0 F5 H0 23.883 98 +ANGLe HP0 F5 H5 23.883 98 +ANGLe HP0 F5 Hd 23.883 98 +ANGLe HP0 F5 Ha 23.883 98 +ANGLe HP0 F5 Hda 23.883 98 +ANGLe HP0 F5 Bda 23.883 98 +ANGLe HP0 F5 B0 23.883 98 +ANGLe HP0 F5 Tda 23.883 98 +ANGLe HP0 F5 T0 23.883 98 +ANGLe HP0 F5 HP5 23.883 98 +ANGLe HP0 F5 HP0 23.883 98 +ANGLe HP0 F5 HPa 23.883 98 +ANGLe HP0 H0 F4 23.883 98 +ANGLe HP0 H0 F5 23.883 98 +ANGLe HP0 H0 H0 23.883 98 +ANGLe HP0 H0 H5 23.883 98 +ANGLe HP0 H0 Hd 23.883 98 +ANGLe HP0 H0 Ha 23.883 98 +ANGLe HP0 H0 Hda 23.883 98 +ANGLe HP0 H0 Bda 23.883 98 +ANGLe HP0 H0 B0 23.883 98 +ANGLe HP0 H0 Tda 23.883 98 +ANGLe HP0 H0 T0 23.883 98 +ANGLe HP0 H0 HP5 23.883 98 +ANGLe HP0 H0 HP0 23.883 98 +ANGLe HP0 H0 HPa 23.883 98 +ANGLe HP0 H5 F4 23.883 98 +ANGLe HP0 H5 F5 23.883 98 +ANGLe HP0 H5 H0 23.883 98 +ANGLe HP0 H5 H5 23.883 98 +ANGLe HP0 H5 Hd 23.883 98 +ANGLe HP0 H5 Ha 23.883 98 +ANGLe HP0 H5 Hda 23.883 98 +ANGLe HP0 H5 Bda 23.883 98 +ANGLe HP0 H5 B0 23.883 98 +ANGLe HP0 H5 Tda 23.883 98 +ANGLe HP0 H5 T0 23.883 98 +ANGLe HP0 H5 HP5 23.883 98 +ANGLe HP0 H5 HP0 23.883 98 +ANGLe HP0 H5 HPa 23.883 98 +ANGLe HP0 Hd F4 23.883 98 +ANGLe HP0 Hd F5 23.883 98 +ANGLe HP0 Hd H0 23.883 98 +ANGLe HP0 Hd H5 23.883 98 +ANGLe HP0 Hd Hd 23.883 98 +ANGLe HP0 Hd Ha 23.883 98 +ANGLe HP0 Hd Hda 23.883 98 +ANGLe HP0 Hd Bda 23.883 98 +ANGLe HP0 Hd B0 23.883 98 +ANGLe HP0 Hd Tda 23.883 98 +ANGLe HP0 Hd T0 23.883 98 +ANGLe HP0 Hd HP5 23.883 98 +ANGLe HP0 Hd HP0 23.883 98 +ANGLe HP0 Hd HPa 23.883 98 +ANGLe HP0 Ha F4 23.883 98 +ANGLe HP0 Ha F5 23.883 98 +ANGLe HP0 Ha H0 23.883 98 +ANGLe HP0 Ha H5 23.883 98 +ANGLe HP0 Ha Hd 23.883 98 +ANGLe HP0 Ha Ha 23.883 98 +ANGLe HP0 Ha Hda 23.883 98 +ANGLe HP0 Ha Bda 23.883 98 +ANGLe HP0 Ha B0 23.883 98 +ANGLe HP0 Ha Tda 23.883 98 +ANGLe HP0 Ha T0 23.883 98 +ANGLe HP0 Ha HP5 23.883 98 +ANGLe HP0 Ha HP0 23.883 98 +ANGLe HP0 Ha HPa 23.883 98 +ANGLe HP0 Hda F4 23.883 98 +ANGLe HP0 Hda F5 23.883 98 +ANGLe HP0 Hda H0 23.883 98 +ANGLe HP0 Hda H5 23.883 98 +ANGLe HP0 Hda Hd 23.883 98 +ANGLe HP0 Hda Ha 23.883 98 +ANGLe HP0 Hda Hda 23.883 98 +ANGLe HP0 Hda Bda 23.883 98 +ANGLe HP0 Hda B0 23.883 98 +ANGLe HP0 Hda Tda 23.883 98 +ANGLe HP0 Hda T0 23.883 98 +ANGLe HP0 Hda HP5 23.883 98 +ANGLe HP0 Hda HP0 23.883 98 +ANGLe HP0 Hda HPa 23.883 98 +ANGLe HP0 Bda F4 23.883 98 +ANGLe HP0 Bda F5 23.883 98 +ANGLe HP0 Bda H0 23.883 98 +ANGLe HP0 Bda H5 23.883 98 +ANGLe HP0 Bda Hd 23.883 98 +ANGLe HP0 Bda Ha 23.883 98 +ANGLe HP0 Bda Hda 23.883 98 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23.883 98 +ANGLe HP0 T0 F5 23.883 98 +ANGLe HP0 T0 H0 23.883 98 +ANGLe HP0 T0 H5 23.883 98 +ANGLe HP0 T0 Hd 23.883 98 +ANGLe HP0 T0 Ha 23.883 98 +ANGLe HP0 T0 Hda 23.883 98 +ANGLe HP0 T0 Bda 23.883 98 +ANGLe HP0 T0 B0 23.883 98 +ANGLe HP0 T0 Tda 23.883 98 +ANGLe HP0 T0 T0 23.883 98 +ANGLe HP0 T0 HP5 23.883 98 +ANGLe HP0 T0 HP0 23.883 98 +ANGLe HP0 T0 HPa 23.883 98 +ANGLe HP0 HP5 F4 23.883 98 +ANGLe HP0 HP5 F5 23.883 98 +ANGLe HP0 HP5 H0 23.883 98 +ANGLe HP0 HP5 H5 23.883 98 +ANGLe HP0 HP5 Hd 23.883 98 +ANGLe HP0 HP5 Ha 23.883 98 +ANGLe HP0 HP5 Hda 23.883 98 +ANGLe HP0 HP5 Bda 23.883 98 +ANGLe HP0 HP5 B0 23.883 98 +ANGLe HP0 HP5 Tda 23.883 98 +ANGLe HP0 HP5 T0 23.883 98 +ANGLe HP0 HP5 HP5 23.883 98 +ANGLe HP0 HP5 HP0 23.883 98 +ANGLe HP0 HP5 HPa 23.883 98 +ANGLe HP0 HP0 F4 23.883 98 +ANGLe HP0 HP0 F5 23.883 98 +ANGLe HP0 HP0 H0 23.883 98 +ANGLe HP0 HP0 H5 23.883 98 +ANGLe HP0 HP0 Hd 23.883 98 +ANGLe HP0 HP0 Ha 23.883 98 +ANGLe HP0 HP0 Hda 23.883 98 +ANGLe HP0 HP0 Bda 23.883 98 +ANGLe HP0 HP0 B0 23.883 98 +ANGLe HP0 HP0 Tda 23.883 98 +ANGLe HP0 HP0 T0 23.883 98 +ANGLe HP0 HP0 HP5 23.883 98 +ANGLe HP0 HP0 HP0 23.883 98 +ANGLe HP0 HP0 HPa 23.883 98 +ANGLe HP0 HPa F4 23.883 98 +ANGLe HP0 HPa F5 23.883 98 +ANGLe HP0 HPa H0 23.883 98 +ANGLe HP0 HPa H5 23.883 98 +ANGLe HP0 HPa Hd 23.883 98 +ANGLe HP0 HPa Ha 23.883 98 +ANGLe HP0 HPa Hda 23.883 98 +ANGLe HP0 HPa Bda 23.883 98 +ANGLe HP0 HPa B0 23.883 98 +ANGLe HP0 HPa Tda 23.883 98 +ANGLe HP0 HPa T0 23.883 98 +ANGLe HP0 HPa HP5 23.883 98 +ANGLe HP0 HPa HP0 23.883 98 +ANGLe HP0 HPa HPa 23.883 98 +ANGLe HPa F4 F4 23.883 98 +ANGLe HPa F4 F5 23.883 98 +ANGLe HPa F4 H0 23.883 98 +ANGLe HPa F4 H5 23.883 98 +ANGLe HPa F4 Hd 23.883 98 +ANGLe HPa F4 Ha 23.883 98 +ANGLe HPa F4 Hda 23.883 98 +ANGLe HPa F4 Bda 23.883 98 +ANGLe HPa F4 B0 23.883 98 +ANGLe HPa F4 Tda 23.883 98 +ANGLe HPa F4 T0 23.883 98 +ANGLe HPa F4 HP5 23.883 98 +ANGLe HPa F4 HP0 23.883 98 +ANGLe HPa F4 HPa 23.883 98 +ANGLe HPa F5 F4 23.883 98 +ANGLe HPa F5 F5 23.883 98 +ANGLe HPa F5 H0 23.883 98 +ANGLe HPa F5 H5 23.883 98 +ANGLe HPa F5 Hd 23.883 98 +ANGLe HPa F5 Ha 23.883 98 +ANGLe HPa F5 Hda 23.883 98 +ANGLe HPa F5 Bda 23.883 98 +ANGLe HPa F5 B0 23.883 98 +ANGLe HPa F5 Tda 23.883 98 +ANGLe HPa F5 T0 23.883 98 +ANGLe HPa F5 HP5 23.883 98 +ANGLe HPa F5 HP0 23.883 98 +ANGLe HPa F5 HPa 23.883 98 +ANGLe HPa H0 F4 23.883 98 +ANGLe HPa H0 F5 23.883 98 +ANGLe HPa H0 H0 23.883 98 +ANGLe HPa H0 H5 23.883 98 +ANGLe HPa H0 Hd 23.883 98 +ANGLe HPa H0 Ha 23.883 98 +ANGLe HPa H0 Hda 23.883 98 +ANGLe HPa H0 Bda 23.883 98 +ANGLe HPa H0 B0 23.883 98 +ANGLe HPa H0 Tda 23.883 98 +ANGLe HPa H0 T0 23.883 98 +ANGLe HPa H0 HP5 23.883 98 +ANGLe HPa H0 HP0 23.883 98 +ANGLe HPa H0 HPa 23.883 98 +ANGLe HPa H5 F4 23.883 98 +ANGLe HPa H5 F5 23.883 98 +ANGLe HPa H5 H0 23.883 98 +ANGLe HPa H5 H5 23.883 98 +ANGLe HPa H5 Hd 23.883 98 +ANGLe HPa H5 Ha 23.883 98 +ANGLe HPa H5 Hda 23.883 98 +ANGLe HPa H5 Bda 23.883 98 +ANGLe HPa H5 B0 23.883 98 +ANGLe HPa H5 Tda 23.883 98 +ANGLe HPa H5 T0 23.883 98 +ANGLe HPa H5 HP5 23.883 98 +ANGLe HPa H5 HP0 23.883 98 +ANGLe HPa H5 HPa 23.883 98 +ANGLe HPa Hd F4 23.883 98 +ANGLe HPa Hd F5 23.883 98 +ANGLe HPa Hd H0 23.883 98 +ANGLe HPa Hd H5 23.883 98 +ANGLe HPa Hd Hd 23.883 98 +ANGLe HPa Hd Ha 23.883 98 +ANGLe HPa Hd Hda 23.883 98 +ANGLe HPa Hd Bda 23.883 98 +ANGLe HPa Hd B0 23.883 98 +ANGLe HPa Hd Tda 23.883 98 +ANGLe HPa Hd T0 23.883 98 +ANGLe HPa Hd HP5 23.883 98 +ANGLe HPa Hd HP0 23.883 98 +ANGLe HPa Hd HPa 23.883 98 +ANGLe HPa Ha F4 23.883 98 +ANGLe HPa Ha F5 23.883 98 +ANGLe HPa Ha H0 23.883 98 +ANGLe HPa Ha H5 23.883 98 +ANGLe HPa Ha Hd 23.883 98 +ANGLe HPa Ha Ha 23.883 98 +ANGLe HPa Ha Hda 23.883 98 +ANGLe HPa Ha Bda 23.883 98 +ANGLe HPa Ha B0 23.883 98 +ANGLe HPa Ha Tda 23.883 98 +ANGLe HPa Ha T0 23.883 98 +ANGLe HPa Ha HP5 23.883 98 +ANGLe HPa Ha HP0 23.883 98 +ANGLe HPa Ha HPa 23.883 98 +ANGLe HPa Hda F4 23.883 98 +ANGLe HPa Hda F5 23.883 98 +ANGLe HPa Hda H0 23.883 98 +ANGLe HPa Hda H5 23.883 98 +ANGLe HPa Hda Hd 23.883 98 +ANGLe HPa Hda Ha 23.883 98 +ANGLe HPa Hda Hda 23.883 98 +ANGLe HPa Hda Bda 23.883 98 +ANGLe HPa Hda B0 23.883 98 +ANGLe HPa Hda Tda 23.883 98 +ANGLe HPa Hda T0 23.883 98 +ANGLe HPa Hda HP5 23.883 98 +ANGLe HPa Hda HP0 23.883 98 +ANGLe HPa Hda HPa 23.883 98 +ANGLe HPa Bda F4 23.883 98 +ANGLe HPa Bda F5 23.883 98 +ANGLe HPa Bda H0 23.883 98 +ANGLe HPa Bda H5 23.883 98 +ANGLe HPa Bda Hd 23.883 98 +ANGLe HPa Bda Ha 23.883 98 +ANGLe HPa Bda Hda 23.883 98 +ANGLe HPa Bda Bda 23.883 98 +ANGLe HPa Bda B0 23.883 98 +ANGLe HPa Bda Tda 23.883 98 +ANGLe HPa Bda T0 23.883 98 +ANGLe HPa Bda HP5 23.883 98 +ANGLe HPa Bda HP0 23.883 98 +ANGLe HPa Bda HPa 23.883 98 +ANGLe HPa B0 F4 23.883 98 +ANGLe HPa B0 F5 23.883 98 +ANGLe HPa B0 H0 23.883 98 +ANGLe HPa B0 H5 23.883 98 +ANGLe HPa B0 Hd 23.883 98 +ANGLe HPa B0 Ha 23.883 98 +ANGLe HPa B0 Hda 23.883 98 +ANGLe HPa B0 Bda 23.883 98 +ANGLe HPa B0 B0 23.883 98 +ANGLe HPa B0 Tda 23.883 98 +ANGLe HPa B0 T0 23.883 98 +ANGLe HPa B0 HP5 23.883 98 +ANGLe HPa B0 HP0 23.883 98 +ANGLe HPa B0 HPa 23.883 98 +ANGLe HPa Tda F4 23.883 98 +ANGLe HPa Tda F5 23.883 98 +ANGLe HPa Tda H0 23.883 98 +ANGLe HPa Tda H5 23.883 98 +ANGLe HPa Tda Hd 23.883 98 +ANGLe HPa Tda Ha 23.883 98 +ANGLe HPa Tda Hda 23.883 98 +ANGLe HPa Tda Bda 23.883 98 +ANGLe HPa Tda B0 23.883 98 +ANGLe HPa Tda Tda 23.883 98 +ANGLe HPa Tda T0 23.883 98 +ANGLe HPa Tda HP5 23.883 98 +ANGLe HPa Tda HP0 23.883 98 +ANGLe HPa Tda HPa 23.883 98 +ANGLe HPa T0 F4 23.883 98 +ANGLe HPa T0 F5 23.883 98 +ANGLe HPa T0 H0 23.883 98 +ANGLe HPa T0 H5 23.883 98 +ANGLe HPa T0 Hd 23.883 98 +ANGLe HPa T0 Ha 23.883 98 +ANGLe HPa T0 Hda 23.883 98 +ANGLe HPa T0 Bda 23.883 98 +ANGLe HPa T0 B0 23.883 98 +ANGLe HPa T0 Tda 23.883 98 +ANGLe HPa T0 T0 23.883 98 +ANGLe HPa T0 HP5 23.883 98 +ANGLe HPa T0 HP0 23.883 98 +ANGLe HPa T0 HPa 23.883 98 +ANGLe HPa HP5 F4 23.883 98 +ANGLe HPa HP5 F5 23.883 98 +ANGLe HPa HP5 H0 23.883 98 +ANGLe HPa HP5 H5 23.883 98 +ANGLe HPa HP5 Hd 23.883 98 +ANGLe HPa HP5 Ha 23.883 98 +ANGLe HPa HP5 Hda 23.883 98 +ANGLe HPa HP5 Bda 23.883 98 +ANGLe HPa HP5 B0 23.883 98 +ANGLe HPa HP5 Tda 23.883 98 +ANGLe HPa HP5 T0 23.883 98 +ANGLe HPa HP5 HP5 23.883 98 +ANGLe HPa HP5 HP0 23.883 98 +ANGLe HPa HP5 HPa 23.883 98 +ANGLe HPa HP0 F4 23.883 98 +ANGLe HPa HP0 F5 23.883 98 +ANGLe HPa HP0 H0 23.883 98 +ANGLe HPa HP0 H5 23.883 98 +ANGLe HPa HP0 Hd 23.883 98 +ANGLe HPa HP0 Ha 23.883 98 +ANGLe HPa HP0 Hda 23.883 98 +ANGLe HPa HP0 Bda 23.883 98 +ANGLe HPa HP0 B0 23.883 98 +ANGLe HPa HP0 Tda 23.883 98 +ANGLe HPa HP0 T0 23.883 98 +ANGLe HPa HP0 HP5 23.883 98 +ANGLe HPa HP0 HP0 23.883 98 +ANGLe HPa HP0 HPa 23.883 98 +ANGLe HPa HPa F4 23.883 98 +ANGLe HPa HPa F5 23.883 98 +ANGLe HPa HPa H0 23.883 98 +ANGLe HPa HPa H5 23.883 98 +ANGLe HPa HPa Hd 23.883 98 +ANGLe HPa HPa Ha 23.883 98 +ANGLe HPa HPa Hda 23.883 98 +ANGLe HPa HPa Bda 23.883 98 +ANGLe HPa HPa B0 23.883 98 +ANGLe HPa HPa Tda 23.883 98 +ANGLe HPa HPa T0 23.883 98 +ANGLe HPa HPa HP5 23.883 98 +ANGLe HPa HPa HP0 23.883 98 +ANGLe HPa HPa HPa 23.883 98 + +{* BBS angles *} +ANGLe F4 F4 AC1 5.971 100 +ANGLe F4 F5 AC1 5.971 100 +ANGLe F4 H0 AC1 5.971 100 +ANGLe F4 H5 AC1 5.971 100 +ANGLe F4 Hd AC1 5.971 100 +ANGLe F4 Ha AC1 5.971 100 +ANGLe F4 Hda AC1 5.971 100 +ANGLe F4 Bda AC1 5.971 100 +ANGLe F4 B0 AC1 5.971 100 +ANGLe F4 Tda AC1 5.971 100 +ANGLe F4 T0 AC1 5.971 100 +ANGLe F4 HP5 AC1 5.971 100 +ANGLe F4 HP0 AC1 5.971 100 +ANGLe F4 HPa AC1 5.971 100 +ANGLe F5 F4 AC1 5.971 100 +ANGLe F5 F5 AC1 5.971 100 +ANGLe F5 H0 AC1 5.971 100 +ANGLe F5 H5 AC1 5.971 100 +ANGLe F5 Hd AC1 5.971 100 +ANGLe F5 Ha AC1 5.971 100 +ANGLe F5 Hda AC1 5.971 100 +ANGLe F5 Bda AC1 5.971 100 +ANGLe F5 B0 AC1 5.971 100 +ANGLe F5 Tda AC1 5.971 100 +ANGLe F5 T0 AC1 5.971 100 +ANGLe F5 HP5 AC1 5.971 100 +ANGLe F5 HP0 AC1 5.971 100 +ANGLe F5 HPa AC1 5.971 100 +ANGLe H0 F4 AC1 5.971 100 +ANGLe H0 F5 AC1 5.971 100 +ANGLe H0 H0 AC1 5.971 100 +ANGLe H0 H5 AC1 5.971 100 +ANGLe H0 Hd AC1 5.971 100 +ANGLe H0 Ha AC1 5.971 100 +ANGLe H0 Hda AC1 5.971 100 +ANGLe H0 Bda AC1 5.971 100 +ANGLe H0 B0 AC1 5.971 100 +ANGLe H0 Tda AC1 5.971 100 +ANGLe H0 T0 AC1 5.971 100 +ANGLe H0 HP5 AC1 5.971 100 +ANGLe H0 HP0 AC1 5.971 100 +ANGLe H0 HPa AC1 5.971 100 +ANGLe H5 F4 AC1 5.971 100 +ANGLe H5 F5 AC1 5.971 100 +ANGLe H5 H0 AC1 5.971 100 +ANGLe H5 H5 AC1 5.971 100 +ANGLe H5 Hd AC1 5.971 100 +ANGLe H5 Ha AC1 5.971 100 +ANGLe H5 Hda AC1 5.971 100 +ANGLe H5 Bda AC1 5.971 100 +ANGLe H5 B0 AC1 5.971 100 +ANGLe H5 Tda AC1 5.971 100 +ANGLe H5 T0 AC1 5.971 100 +ANGLe H5 HP5 AC1 5.971 100 +ANGLe H5 HP0 AC1 5.971 100 +ANGLe H5 HPa AC1 5.971 100 +ANGLe Hd F4 AC1 5.971 100 +ANGLe Hd F5 AC1 5.971 100 +ANGLe Hd H0 AC1 5.971 100 +ANGLe Hd H5 AC1 5.971 100 +ANGLe Hd Hd AC1 5.971 100 +ANGLe Hd Ha AC1 5.971 100 +ANGLe Hd Hda AC1 5.971 100 +ANGLe Hd Bda AC1 5.971 100 +ANGLe Hd B0 AC1 5.971 100 +ANGLe Hd Tda AC1 5.971 100 +ANGLe Hd T0 AC1 5.971 100 +ANGLe Hd HP5 AC1 5.971 100 +ANGLe Hd HP0 AC1 5.971 100 +ANGLe Hd HPa AC1 5.971 100 +ANGLe Ha F4 AC1 5.971 100 +ANGLe Ha F5 AC1 5.971 100 +ANGLe Ha H0 AC1 5.971 100 +ANGLe Ha H5 AC1 5.971 100 +ANGLe Ha Hd AC1 5.971 100 +ANGLe Ha Ha AC1 5.971 100 +ANGLe Ha Hda AC1 5.971 100 +ANGLe Ha Bda AC1 5.971 100 +ANGLe Ha B0 AC1 5.971 100 +ANGLe Ha Tda AC1 5.971 100 +ANGLe Ha T0 AC1 5.971 100 +ANGLe Ha HP5 AC1 5.971 100 +ANGLe Ha HP0 AC1 5.971 100 +ANGLe Ha HPa AC1 5.971 100 +ANGLe Hda F4 AC1 5.971 100 +ANGLe Hda F5 AC1 5.971 100 +ANGLe Hda H0 AC1 5.971 100 +ANGLe Hda H5 AC1 5.971 100 +ANGLe Hda Hd AC1 5.971 100 +ANGLe Hda Ha AC1 5.971 100 +ANGLe Hda Hda AC1 5.971 100 +ANGLe Hda Bda AC1 5.971 100 +ANGLe Hda B0 AC1 5.971 100 +ANGLe Hda Tda AC1 5.971 100 +ANGLe Hda T0 AC1 5.971 100 +ANGLe Hda HP5 AC1 5.971 100 +ANGLe Hda HP0 AC1 5.971 100 +ANGLe Hda HPa AC1 5.971 100 +ANGLe Bda F4 AC1 5.971 100 +ANGLe Bda F5 AC1 5.971 100 +ANGLe Bda H0 AC1 5.971 100 +ANGLe Bda H5 AC1 5.971 100 +ANGLe Bda Hd AC1 5.971 100 +ANGLe Bda Ha AC1 5.971 100 +ANGLe Bda Hda AC1 5.971 100 +ANGLe Bda Bda AC1 5.971 100 +ANGLe Bda B0 AC1 5.971 100 +ANGLe Bda Tda AC1 5.971 100 +ANGLe Bda T0 AC1 5.971 100 +ANGLe Bda HP5 AC1 5.971 100 +ANGLe Bda HP0 AC1 5.971 100 +ANGLe Bda HPa AC1 5.971 100 +ANGLe B0 F4 AC1 5.971 100 +ANGLe B0 F5 AC1 5.971 100 +ANGLe B0 H0 AC1 5.971 100 +ANGLe B0 H5 AC1 5.971 100 +ANGLe B0 Hd AC1 5.971 100 +ANGLe B0 Ha AC1 5.971 100 +ANGLe B0 Hda AC1 5.971 100 +ANGLe B0 Bda AC1 5.971 100 +ANGLe B0 B0 AC1 5.971 100 +ANGLe B0 Tda AC1 5.971 100 +ANGLe B0 T0 AC1 5.971 100 +ANGLe B0 HP5 AC1 5.971 100 +ANGLe B0 HP0 AC1 5.971 100 +ANGLe B0 HPa AC1 5.971 100 +ANGLe Tda F4 AC1 5.971 100 +ANGLe Tda F5 AC1 5.971 100 +ANGLe Tda H0 AC1 5.971 100 +ANGLe Tda H5 AC1 5.971 100 +ANGLe Tda Hd AC1 5.971 100 +ANGLe Tda Ha AC1 5.971 100 +ANGLe Tda Hda AC1 5.971 100 +ANGLe Tda Bda AC1 5.971 100 +ANGLe Tda B0 AC1 5.971 100 +ANGLe Tda Tda AC1 5.971 100 +ANGLe Tda T0 AC1 5.971 100 +ANGLe Tda HP5 AC1 5.971 100 +ANGLe Tda HP0 AC1 5.971 100 +ANGLe Tda HPa AC1 5.971 100 +ANGLe T0 F4 AC1 5.971 100 +ANGLe T0 F5 AC1 5.971 100 +ANGLe T0 H0 AC1 5.971 100 +ANGLe T0 H5 AC1 5.971 100 +ANGLe T0 Hd AC1 5.971 100 +ANGLe T0 Ha AC1 5.971 100 +ANGLe T0 Hda AC1 5.971 100 +ANGLe T0 Bda AC1 5.971 100 +ANGLe T0 B0 AC1 5.971 100 +ANGLe T0 Tda AC1 5.971 100 +ANGLe T0 T0 AC1 5.971 100 +ANGLe T0 HP5 AC1 5.971 100 +ANGLe T0 HP0 AC1 5.971 100 +ANGLe T0 HPa AC1 5.971 100 +ANGLe HP5 F4 AC1 5.971 100 +ANGLe HP5 F5 AC1 5.971 100 +ANGLe HP5 H0 AC1 5.971 100 +ANGLe HP5 H5 AC1 5.971 100 +ANGLe HP5 Hd AC1 5.971 100 +ANGLe HP5 Ha AC1 5.971 100 +ANGLe HP5 Hda AC1 5.971 100 +ANGLe HP5 Bda AC1 5.971 100 +ANGLe HP5 B0 AC1 5.971 100 +ANGLe HP5 Tda AC1 5.971 100 +ANGLe HP5 T0 AC1 5.971 100 +ANGLe HP5 HP5 AC1 5.971 100 +ANGLe HP5 HP0 AC1 5.971 100 +ANGLe HP5 HPa AC1 5.971 100 +ANGLe HP0 F4 AC1 5.971 100 +ANGLe HP0 F5 AC1 5.971 100 +ANGLe HP0 H0 AC1 5.971 100 +ANGLe HP0 H5 AC1 5.971 100 +ANGLe HP0 Hd AC1 5.971 100 +ANGLe HP0 Ha AC1 5.971 100 +ANGLe HP0 Hda AC1 5.971 100 +ANGLe HP0 Bda AC1 5.971 100 +ANGLe HP0 B0 AC1 5.971 100 +ANGLe HP0 Tda AC1 5.971 100 +ANGLe HP0 T0 AC1 5.971 100 +ANGLe HP0 HP5 AC1 5.971 100 +ANGLe HP0 HP0 AC1 5.971 100 +ANGLe HP0 HPa AC1 5.971 100 +ANGLe HPa F4 AC1 5.971 100 +ANGLe HPa F5 AC1 5.971 100 +ANGLe HPa H0 AC1 5.971 100 +ANGLe HPa H5 AC1 5.971 100 +ANGLe HPa Hd AC1 5.971 100 +ANGLe HPa Ha AC1 5.971 100 +ANGLe HPa Hda AC1 5.971 100 +ANGLe HPa Bda AC1 5.971 100 +ANGLe HPa B0 AC1 5.971 100 +ANGLe HPa Tda AC1 5.971 100 +ANGLe HPa T0 AC1 5.971 100 +ANGLe HPa HP5 AC1 5.971 100 +ANGLe HPa HP0 AC1 5.971 100 +ANGLe HPa HPa AC1 5.971 100 +ANGLe F4 F4 AC2 5.971 100 +ANGLe F4 F5 AC2 5.971 100 +ANGLe F4 H0 AC2 5.971 100 +ANGLe F4 H5 AC2 5.971 100 +ANGLe F4 Hd AC2 5.971 100 +ANGLe F4 Ha AC2 5.971 100 +ANGLe F4 Hda AC2 5.971 100 +ANGLe F4 Bda AC2 5.971 100 +ANGLe F4 B0 AC2 5.971 100 +ANGLe F4 Tda AC2 5.971 100 +ANGLe F4 T0 AC2 5.971 100 +ANGLe F4 HP5 AC2 5.971 100 +ANGLe F4 HP0 AC2 5.971 100 +ANGLe F4 HPa AC2 5.971 100 +ANGLe F5 F4 AC2 5.971 100 +ANGLe F5 F5 AC2 5.971 100 +ANGLe F5 H0 AC2 5.971 100 +ANGLe F5 H5 AC2 5.971 100 +ANGLe F5 Hd AC2 5.971 100 +ANGLe F5 Ha AC2 5.971 100 +ANGLe F5 Hda AC2 5.971 100 +ANGLe F5 Bda AC2 5.971 100 +ANGLe F5 B0 AC2 5.971 100 +ANGLe F5 Tda AC2 5.971 100 +ANGLe F5 T0 AC2 5.971 100 +ANGLe F5 HP5 AC2 5.971 100 +ANGLe F5 HP0 AC2 5.971 100 +ANGLe F5 HPa AC2 5.971 100 +ANGLe H0 F4 AC2 5.971 100 +ANGLe H0 F5 AC2 5.971 100 +ANGLe H0 H0 AC2 5.971 100 +ANGLe H0 H5 AC2 5.971 100 +ANGLe H0 Hd AC2 5.971 100 +ANGLe H0 Ha AC2 5.971 100 +ANGLe H0 Hda AC2 5.971 100 +ANGLe H0 Bda AC2 5.971 100 +ANGLe H0 B0 AC2 5.971 100 +ANGLe H0 Tda AC2 5.971 100 +ANGLe H0 T0 AC2 5.971 100 +ANGLe H0 HP5 AC2 5.971 100 +ANGLe H0 HP0 AC2 5.971 100 +ANGLe H0 HPa AC2 5.971 100 +ANGLe H5 F4 AC2 5.971 100 +ANGLe H5 F5 AC2 5.971 100 +ANGLe H5 H0 AC2 5.971 100 +ANGLe H5 H5 AC2 5.971 100 +ANGLe H5 Hd AC2 5.971 100 +ANGLe H5 Ha AC2 5.971 100 +ANGLe H5 Hda AC2 5.971 100 +ANGLe H5 Bda AC2 5.971 100 +ANGLe H5 B0 AC2 5.971 100 +ANGLe H5 Tda AC2 5.971 100 +ANGLe H5 T0 AC2 5.971 100 +ANGLe H5 HP5 AC2 5.971 100 +ANGLe H5 HP0 AC2 5.971 100 +ANGLe H5 HPa AC2 5.971 100 +ANGLe Hd F4 AC2 5.971 100 +ANGLe Hd F5 AC2 5.971 100 +ANGLe Hd H0 AC2 5.971 100 +ANGLe Hd H5 AC2 5.971 100 +ANGLe Hd Hd AC2 5.971 100 +ANGLe Hd Ha AC2 5.971 100 +ANGLe Hd Hda AC2 5.971 100 +ANGLe Hd Bda AC2 5.971 100 +ANGLe Hd B0 AC2 5.971 100 +ANGLe Hd Tda AC2 5.971 100 +ANGLe Hd T0 AC2 5.971 100 +ANGLe Hd HP5 AC2 5.971 100 +ANGLe Hd HP0 AC2 5.971 100 +ANGLe Hd HPa AC2 5.971 100 +ANGLe Ha F4 AC2 5.971 100 +ANGLe Ha F5 AC2 5.971 100 +ANGLe Ha H0 AC2 5.971 100 +ANGLe Ha H5 AC2 5.971 100 +ANGLe Ha Hd AC2 5.971 100 +ANGLe Ha Ha AC2 5.971 100 +ANGLe Ha Hda AC2 5.971 100 +ANGLe Ha Bda AC2 5.971 100 +ANGLe Ha B0 AC2 5.971 100 +ANGLe Ha Tda AC2 5.971 100 +ANGLe Ha T0 AC2 5.971 100 +ANGLe Ha HP5 AC2 5.971 100 +ANGLe Ha HP0 AC2 5.971 100 +ANGLe Ha HPa AC2 5.971 100 +ANGLe Hda F4 AC2 5.971 100 +ANGLe Hda F5 AC2 5.971 100 +ANGLe Hda H0 AC2 5.971 100 +ANGLe Hda H5 AC2 5.971 100 +ANGLe Hda Hd AC2 5.971 100 +ANGLe Hda Ha AC2 5.971 100 +ANGLe Hda Hda AC2 5.971 100 +ANGLe Hda Bda AC2 5.971 100 +ANGLe Hda B0 AC2 5.971 100 +ANGLe Hda Tda AC2 5.971 100 +ANGLe Hda T0 AC2 5.971 100 +ANGLe Hda HP5 AC2 5.971 100 +ANGLe Hda HP0 AC2 5.971 100 +ANGLe Hda HPa AC2 5.971 100 +ANGLe Bda F4 AC2 5.971 100 +ANGLe Bda F5 AC2 5.971 100 +ANGLe Bda H0 AC2 5.971 100 +ANGLe Bda H5 AC2 5.971 100 +ANGLe Bda Hd AC2 5.971 100 +ANGLe Bda Ha AC2 5.971 100 +ANGLe Bda Hda AC2 5.971 100 +ANGLe Bda Bda AC2 5.971 100 +ANGLe Bda B0 AC2 5.971 100 +ANGLe Bda Tda AC2 5.971 100 +ANGLe Bda T0 AC2 5.971 100 +ANGLe Bda HP5 AC2 5.971 100 +ANGLe Bda HP0 AC2 5.971 100 +ANGLe Bda HPa AC2 5.971 100 +ANGLe B0 F4 AC2 5.971 100 +ANGLe B0 F5 AC2 5.971 100 +ANGLe B0 H0 AC2 5.971 100 +ANGLe B0 H5 AC2 5.971 100 +ANGLe B0 Hd AC2 5.971 100 +ANGLe B0 Ha AC2 5.971 100 +ANGLe B0 Hda AC2 5.971 100 +ANGLe B0 Bda AC2 5.971 100 +ANGLe B0 B0 AC2 5.971 100 +ANGLe B0 Tda AC2 5.971 100 +ANGLe B0 T0 AC2 5.971 100 +ANGLe B0 HP5 AC2 5.971 100 +ANGLe B0 HP0 AC2 5.971 100 +ANGLe B0 HPa AC2 5.971 100 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HPa 95.524 1 -120 +DIHEdral HPa HP5 Ha H0 95.524 1 -120 +DIHEdral HPa HP5 Ha H5 95.524 1 -120 +DIHEdral HPa HP5 Ha Hd 95.524 1 -120 +DIHEdral HPa HP5 Ha Ha 95.524 1 -120 +DIHEdral HPa HP5 Ha Hda 95.524 1 -120 +DIHEdral HPa HP5 Ha HP5 95.524 1 -120 +DIHEdral HPa HP5 Ha HP0 95.524 1 -120 +DIHEdral HPa HP5 Ha HPa 95.524 1 -120 +DIHEdral HPa HP5 Hda H0 95.524 1 -120 +DIHEdral HPa HP5 Hda H5 95.524 1 -120 +DIHEdral HPa HP5 Hda Hd 95.524 1 -120 +DIHEdral HPa HP5 Hda Ha 95.524 1 -120 +DIHEdral HPa HP5 Hda Hda 95.524 1 -120 +DIHEdral HPa HP5 Hda HP5 95.524 1 -120 +DIHEdral HPa HP5 Hda HP0 95.524 1 -120 +DIHEdral HPa HP5 Hda HPa 95.524 1 -120 +DIHEdral HPa HP5 HP5 H0 95.524 1 -120 +DIHEdral HPa HP5 HP5 H5 95.524 1 -120 +DIHEdral HPa HP5 HP5 Hd 95.524 1 -120 +DIHEdral HPa HP5 HP5 Ha 95.524 1 -120 +DIHEdral HPa HP5 HP5 Hda 95.524 1 -120 +DIHEdral HPa HP5 HP5 HP5 95.524 1 -120 +DIHEdral HPa HP5 HP5 HP0 95.524 1 -120 +DIHEdral HPa HP5 HP5 HPa 95.524 1 -120 +DIHEdral HPa HP5 HP0 H0 95.524 1 -120 +DIHEdral HPa HP5 HP0 H5 95.524 1 -120 +DIHEdral HPa HP5 HP0 Hd 95.524 1 -120 +DIHEdral HPa HP5 HP0 Ha 95.524 1 -120 +DIHEdral HPa HP5 HP0 Hda 95.524 1 -120 +DIHEdral HPa HP5 HP0 HP5 95.524 1 -120 +DIHEdral HPa HP5 HP0 HP0 95.524 1 -120 +DIHEdral HPa HP5 HP0 HPa 95.524 1 -120 +DIHEdral HPa HP5 HPa H0 95.524 1 -120 +DIHEdral HPa HP5 HPa H5 95.524 1 -120 +DIHEdral HPa HP5 HPa Hd 95.524 1 -120 +DIHEdral HPa HP5 HPa Ha 95.524 1 -120 +DIHEdral HPa HP5 HPa Hda 95.524 1 -120 +DIHEdral HPa HP5 HPa HP5 95.524 1 -120 +DIHEdral HPa HP5 HPa HP0 95.524 1 -120 +DIHEdral HPa HP5 HPa HPa 95.524 1 -120 +DIHEdral HPa HP0 H0 H0 95.524 1 -120 +DIHEdral HPa HP0 H0 H5 95.524 1 -120 +DIHEdral HPa HP0 H0 Hd 95.524 1 -120 +DIHEdral HPa HP0 H0 Ha 95.524 1 -120 +DIHEdral HPa HP0 H0 Hda 95.524 1 -120 +DIHEdral HPa HP0 H0 HP5 95.524 1 -120 +DIHEdral HPa HP0 H0 HP0 95.524 1 -120 +DIHEdral HPa HP0 H0 HPa 95.524 1 -120 +DIHEdral HPa HP0 H5 H0 95.524 1 -120 +DIHEdral HPa HP0 H5 H5 95.524 1 -120 +DIHEdral HPa HP0 H5 Hd 95.524 1 -120 +DIHEdral HPa HP0 H5 Ha 95.524 1 -120 +DIHEdral HPa HP0 H5 Hda 95.524 1 -120 +DIHEdral HPa HP0 H5 HP5 95.524 1 -120 +DIHEdral HPa HP0 H5 HP0 95.524 1 -120 +DIHEdral HPa HP0 H5 HPa 95.524 1 -120 +DIHEdral HPa HP0 Hd H0 95.524 1 -120 +DIHEdral HPa HP0 Hd H5 95.524 1 -120 +DIHEdral HPa HP0 Hd Hd 95.524 1 -120 +DIHEdral HPa HP0 Hd Ha 95.524 1 -120 +DIHEdral HPa HP0 Hd Hda 95.524 1 -120 +DIHEdral HPa HP0 Hd HP5 95.524 1 -120 +DIHEdral HPa HP0 Hd HP0 95.524 1 -120 +DIHEdral HPa HP0 Hd HPa 95.524 1 -120 +DIHEdral HPa HP0 Ha H0 95.524 1 -120 +DIHEdral HPa HP0 Ha H5 95.524 1 -120 +DIHEdral HPa HP0 Ha Hd 95.524 1 -120 +DIHEdral HPa HP0 Ha Ha 95.524 1 -120 +DIHEdral HPa HP0 Ha Hda 95.524 1 -120 +DIHEdral HPa HP0 Ha HP5 95.524 1 -120 +DIHEdral HPa HP0 Ha HP0 95.524 1 -120 +DIHEdral HPa HP0 Ha HPa 95.524 1 -120 +DIHEdral HPa HP0 Hda H0 95.524 1 -120 +DIHEdral HPa HP0 Hda H5 95.524 1 -120 +DIHEdral HPa HP0 Hda Hd 95.524 1 -120 +DIHEdral HPa HP0 Hda Ha 95.524 1 -120 +DIHEdral HPa HP0 Hda Hda 95.524 1 -120 +DIHEdral HPa HP0 Hda HP5 95.524 1 -120 +DIHEdral HPa HP0 Hda HP0 95.524 1 -120 +DIHEdral HPa HP0 Hda HPa 95.524 1 -120 +DIHEdral HPa HP0 HP5 H0 95.524 1 -120 +DIHEdral HPa HP0 HP5 H5 95.524 1 -120 +DIHEdral HPa HP0 HP5 Hd 95.524 1 -120 +DIHEdral HPa HP0 HP5 Ha 95.524 1 -120 +DIHEdral HPa HP0 HP5 Hda 95.524 1 -120 +DIHEdral HPa HP0 HP5 HP5 95.524 1 -120 +DIHEdral HPa HP0 HP5 HP0 95.524 1 -120 +DIHEdral HPa HP0 HP5 HPa 95.524 1 -120 +DIHEdral HPa HP0 HP0 H0 95.524 1 -120 +DIHEdral HPa HP0 HP0 H5 95.524 1 -120 +DIHEdral HPa HP0 HP0 Hd 95.524 1 -120 +DIHEdral HPa HP0 HP0 Ha 95.524 1 -120 +DIHEdral HPa HP0 HP0 Hda 95.524 1 -120 +DIHEdral HPa HP0 HP0 HP5 95.524 1 -120 +DIHEdral HPa HP0 HP0 HP0 95.524 1 -120 +DIHEdral HPa HP0 HP0 HPa 95.524 1 -120 +DIHEdral HPa HP0 HPa H0 95.524 1 -120 +DIHEdral HPa HP0 HPa H5 95.524 1 -120 +DIHEdral HPa HP0 HPa Hd 95.524 1 -120 +DIHEdral HPa HP0 HPa Ha 95.524 1 -120 +DIHEdral HPa HP0 HPa Hda 95.524 1 -120 +DIHEdral HPa HP0 HPa HP5 95.524 1 -120 +DIHEdral HPa HP0 HPa HP0 95.524 1 -120 +DIHEdral HPa HP0 HPa HPa 95.524 1 -120 +DIHEdral HPa HPa H0 H0 95.524 1 -120 +DIHEdral HPa HPa H0 H5 95.524 1 -120 +DIHEdral HPa HPa H0 Hd 95.524 1 -120 +DIHEdral HPa HPa H0 Ha 95.524 1 -120 +DIHEdral HPa HPa H0 Hda 95.524 1 -120 +DIHEdral HPa HPa H0 HP5 95.524 1 -120 +DIHEdral HPa HPa H0 HP0 95.524 1 -120 +DIHEdral HPa HPa H0 HPa 95.524 1 -120 +DIHEdral HPa HPa H5 H0 95.524 1 -120 +DIHEdral HPa HPa H5 H5 95.524 1 -120 +DIHEdral HPa HPa H5 Hd 95.524 1 -120 +DIHEdral HPa HPa H5 Ha 95.524 1 -120 +DIHEdral HPa HPa H5 Hda 95.524 1 -120 +DIHEdral HPa HPa H5 HP5 95.524 1 -120 +DIHEdral HPa HPa H5 HP0 95.524 1 -120 +DIHEdral HPa HPa H5 HPa 95.524 1 -120 +DIHEdral HPa HPa Hd H0 95.524 1 -120 +DIHEdral HPa HPa Hd H5 95.524 1 -120 +DIHEdral HPa HPa Hd Hd 95.524 1 -120 +DIHEdral HPa HPa Hd Ha 95.524 1 -120 +DIHEdral HPa HPa Hd Hda 95.524 1 -120 +DIHEdral HPa HPa Hd HP5 95.524 1 -120 +DIHEdral HPa HPa Hd HP0 95.524 1 -120 +DIHEdral HPa HPa Hd HPa 95.524 1 -120 +DIHEdral HPa HPa Ha H0 95.524 1 -120 +DIHEdral HPa HPa Ha H5 95.524 1 -120 +DIHEdral HPa HPa Ha Hd 95.524 1 -120 +DIHEdral HPa HPa Ha Ha 95.524 1 -120 +DIHEdral HPa HPa Ha Hda 95.524 1 -120 +DIHEdral HPa HPa Ha HP5 95.524 1 -120 +DIHEdral HPa HPa Ha HP0 95.524 1 -120 +DIHEdral HPa HPa Ha HPa 95.524 1 -120 +DIHEdral HPa HPa Hda H0 95.524 1 -120 +DIHEdral HPa HPa Hda H5 95.524 1 -120 +DIHEdral HPa HPa Hda Hd 95.524 1 -120 +DIHEdral HPa HPa Hda Ha 95.524 1 -120 +DIHEdral HPa HPa Hda Hda 95.524 1 -120 +DIHEdral HPa HPa Hda HP5 95.524 1 -120 +DIHEdral HPa HPa Hda HP0 95.524 1 -120 +DIHEdral HPa HPa Hda HPa 95.524 1 -120 +DIHEdral HPa HPa HP5 H0 95.524 1 -120 +DIHEdral HPa HPa HP5 H5 95.524 1 -120 +DIHEdral HPa HPa HP5 Hd 95.524 1 -120 +DIHEdral HPa HPa HP5 Ha 95.524 1 -120 +DIHEdral HPa HPa HP5 Hda 95.524 1 -120 +DIHEdral HPa HPa HP5 HP5 95.524 1 -120 +DIHEdral HPa HPa HP5 HP0 95.524 1 -120 +DIHEdral HPa HPa HP5 HPa 95.524 1 -120 +DIHEdral HPa HPa HP0 H0 95.524 1 -120 +DIHEdral HPa HPa HP0 H5 95.524 1 -120 +DIHEdral HPa HPa HP0 Hd 95.524 1 -120 +DIHEdral HPa HPa HP0 Ha 95.524 1 -120 +DIHEdral HPa HPa HP0 Hda 95.524 1 -120 +DIHEdral HPa HPa HP0 HP5 95.524 1 -120 +DIHEdral HPa HPa HP0 HP0 95.524 1 -120 +DIHEdral HPa HPa HP0 HPa 95.524 1 -120 +DIHEdral HPa HPa HPa H0 95.524 1 -120 +DIHEdral HPa HPa HPa H5 95.524 1 -120 +DIHEdral HPa HPa HPa Hd 95.524 1 -120 +DIHEdral HPa HPa HPa Ha 95.524 1 -120 +DIHEdral HPa HPa HPa Hda 95.524 1 -120 +DIHEdral HPa HPa HPa HP5 95.524 1 -120 +DIHEdral HPa HPa HPa HP0 95.524 1 -120 +DIHEdral HPa HPa HPa HPa 95.524 1 -120 + +DIHEdral Bda Bda Bda Bda 0.570 1 0 +DIHEdral Bda Bda Bda B0 0.570 1 0 +DIHEdral Bda Bda B0 Bda 0.570 1 0 +DIHEdral Bda Bda B0 B0 0.570 1 0 +DIHEdral Bda B0 Bda Bda 0.570 1 0 +DIHEdral Bda B0 Bda B0 0.570 1 0 +DIHEdral Bda B0 B0 Bda 0.570 1 0 +DIHEdral Bda B0 B0 B0 0.570 1 0 +DIHEdral B0 Bda Bda Bda 0.570 1 0 +DIHEdral B0 Bda Bda B0 0.570 1 0 +DIHEdral B0 Bda B0 Bda 0.570 1 0 +DIHEdral B0 Bda B0 B0 0.570 1 0 +DIHEdral B0 B0 Bda Bda 0.570 1 0 +DIHEdral B0 B0 Bda B0 0.570 1 0 +DIHEdral B0 B0 B0 Bda 0.570 1 0 +DIHEdral B0 B0 B0 B0 0.570 1 0 + + +{*BSSS, backbone sidechain dihedrals & impropers *} + +DIHEdral F5 SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral F5 SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral F5 SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral F5 SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Bda SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral Bda SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral Bda SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral Bda SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral H0 SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral H0 SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral H0 SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral H0 SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Hd SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral Hd SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral Hd SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral Hd SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Ha SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral Ha SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral Ha SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral Ha SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Hda SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral Hda SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral Hda SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral Hda SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Tda SNd SC5 WC4 11.942 0 0.000 ! TRP +DIHEdral Tda SC4 SP1 YC4 11.942 0 0.000 ! TYR +DIHEdral Tda SC5 SC5 FC5 11.942 0 0.000 ! PHE +DIHEdral Tda SP1 SP1 HC4 11.942 0 0.000 ! HIS + + +{* SSSS, sidechain impropers *} +DIHEdral WC4 SNd SC5 SC5 47.767 0 0 ! TRP + +{*BBBB,Not to be defined backbone dihedrals & impropers *} + +DIHEdral F4 F4 F4 F4 0 6 0 +DIHEdral F4 F4 F4 F5 0 6 0 +DIHEdral F4 F4 F4 H0 0 6 0 +DIHEdral F4 F4 F4 H5 0 6 0 +DIHEdral F4 F4 F4 Hd 0 6 0 +DIHEdral F4 F4 F4 Ha 0 6 0 +DIHEdral F4 F4 F4 Hda 0 6 0 +DIHEdral F4 F4 F4 Bda 0 6 0 +DIHEdral F4 F4 F4 B0 0 6 0 +DIHEdral F4 F4 F4 Tda 0 6 0 +DIHEdral F4 F4 F4 T0 0 6 0 +DIHEdral F4 F4 F4 HP5 0 6 0 +DIHEdral F4 F4 F4 HP0 0 6 0 +DIHEdral F4 F4 F4 HPa 0 6 0 +DIHEdral F4 F4 F5 F4 0 6 0 +DIHEdral F4 F4 F5 F5 0 6 0 +DIHEdral F4 F4 F5 H0 0 6 0 +DIHEdral F4 F4 F5 H5 0 6 0 +DIHEdral F4 F4 F5 Hd 0 6 0 +DIHEdral F4 F4 F5 Ha 0 6 0 +DIHEdral F4 F4 F5 Hda 0 6 0 +DIHEdral F4 F4 F5 Bda 0 6 0 +DIHEdral F4 F4 F5 B0 0 6 0 +DIHEdral F4 F4 F5 Tda 0 6 0 +DIHEdral F4 F4 F5 T0 0 6 0 +DIHEdral F4 F4 F5 HP5 0 6 0 +DIHEdral F4 F4 F5 HP0 0 6 0 +DIHEdral F4 F4 F5 HPa 0 6 0 +DIHEdral F4 F4 H0 F4 0 6 0 +DIHEdral F4 F4 H0 F5 0 6 0 +DIHEdral F4 F4 H0 H0 0 6 0 +DIHEdral F4 F4 H0 H5 0 6 0 +DIHEdral F4 F4 H0 Hd 0 6 0 +DIHEdral F4 F4 H0 Ha 0 6 0 +DIHEdral F4 F4 H0 Hda 0 6 0 +DIHEdral F4 F4 H0 Bda 0 6 0 +DIHEdral F4 F4 H0 B0 0 6 0 +DIHEdral F4 F4 H0 Tda 0 6 0 +DIHEdral F4 F4 H0 T0 0 6 0 +DIHEdral F4 F4 H0 HP5 0 6 0 +DIHEdral F4 F4 H0 HP0 0 6 0 +DIHEdral F4 F4 H0 HPa 0 6 0 +DIHEdral F4 F4 H5 F4 0 6 0 +DIHEdral F4 F4 H5 F5 0 6 0 +DIHEdral F4 F4 H5 H0 0 6 0 +DIHEdral F4 F4 H5 H5 0 6 0 +DIHEdral F4 F4 H5 Hd 0 6 0 +DIHEdral F4 F4 H5 Ha 0 6 0 +DIHEdral F4 F4 H5 Hda 0 6 0 +DIHEdral F4 F4 H5 Bda 0 6 0 +DIHEdral F4 F4 H5 B0 0 6 0 +DIHEdral F4 F4 H5 Tda 0 6 0 +DIHEdral F4 F4 H5 T0 0 6 0 +DIHEdral F4 F4 H5 HP5 0 6 0 +DIHEdral F4 F4 H5 HP0 0 6 0 +DIHEdral F4 F4 H5 HPa 0 6 0 +DIHEdral F4 F4 Hd F4 0 6 0 +DIHEdral F4 F4 Hd F5 0 6 0 +DIHEdral F4 F4 Hd H0 0 6 0 +DIHEdral F4 F4 Hd H5 0 6 0 +DIHEdral F4 F4 Hd Hd 0 6 0 +DIHEdral F4 F4 Hd Ha 0 6 0 +DIHEdral F4 F4 Hd Hda 0 6 0 +DIHEdral F4 F4 Hd Bda 0 6 0 +DIHEdral F4 F4 Hd B0 0 6 0 +DIHEdral F4 F4 Hd Tda 0 6 0 +DIHEdral F4 F4 Hd T0 0 6 0 +DIHEdral F4 F4 Hd HP5 0 6 0 +DIHEdral F4 F4 Hd HP0 0 6 0 +DIHEdral F4 F4 Hd HPa 0 6 0 +DIHEdral F4 F4 Ha F4 0 6 0 +DIHEdral F4 F4 Ha F5 0 6 0 +DIHEdral F4 F4 Ha H0 0 6 0 +DIHEdral F4 F4 Ha H5 0 6 0 +DIHEdral F4 F4 Ha Hd 0 6 0 +DIHEdral F4 F4 Ha Ha 0 6 0 +DIHEdral F4 F4 Ha Hda 0 6 0 +DIHEdral F4 F4 Ha Bda 0 6 0 +DIHEdral F4 F4 Ha B0 0 6 0 +DIHEdral F4 F4 Ha Tda 0 6 0 +DIHEdral F4 F4 Ha T0 0 6 0 +DIHEdral F4 F4 Ha HP5 0 6 0 +DIHEdral F4 F4 Ha HP0 0 6 0 +DIHEdral F4 F4 Ha HPa 0 6 0 +DIHEdral F4 F4 Hda F4 0 6 0 +DIHEdral F4 F4 Hda F5 0 6 0 +DIHEdral F4 F4 Hda H0 0 6 0 +DIHEdral F4 F4 Hda H5 0 6 0 +DIHEdral F4 F4 Hda Hd 0 6 0 +DIHEdral F4 F4 Hda Ha 0 6 0 +DIHEdral F4 F4 Hda Hda 0 6 0 +DIHEdral F4 F4 Hda Bda 0 6 0 +DIHEdral F4 F4 Hda B0 0 6 0 +DIHEdral F4 F4 Hda Tda 0 6 0 +DIHEdral F4 F4 Hda T0 0 6 0 +DIHEdral F4 F4 Hda HP5 0 6 0 +DIHEdral F4 F4 Hda HP0 0 6 0 +DIHEdral F4 F4 Hda HPa 0 6 0 +DIHEdral F4 F4 Bda F4 0 6 0 +DIHEdral F4 F4 Bda F5 0 6 0 +DIHEdral F4 F4 Bda H0 0 6 0 +DIHEdral F4 F4 Bda H5 0 6 0 +DIHEdral F4 F4 Bda Hd 0 6 0 +DIHEdral F4 F4 Bda Ha 0 6 0 +DIHEdral F4 F4 Bda Hda 0 6 0 +DIHEdral F4 F4 Bda Bda 0 6 0 +DIHEdral F4 F4 Bda B0 0 6 0 +DIHEdral F4 F4 Bda Tda 0 6 0 +DIHEdral F4 F4 Bda T0 0 6 0 +DIHEdral F4 F4 Bda HP5 0 6 0 +DIHEdral F4 F4 Bda HP0 0 6 0 +DIHEdral F4 F4 Bda HPa 0 6 0 +DIHEdral F4 F4 B0 F4 0 6 0 +DIHEdral F4 F4 B0 F5 0 6 0 +DIHEdral F4 F4 B0 H0 0 6 0 +DIHEdral F4 F4 B0 H5 0 6 0 +DIHEdral F4 F4 B0 Hd 0 6 0 +DIHEdral F4 F4 B0 Ha 0 6 0 +DIHEdral F4 F4 B0 Hda 0 6 0 +DIHEdral F4 F4 B0 Bda 0 6 0 +DIHEdral F4 F4 B0 B0 0 6 0 +DIHEdral F4 F4 B0 Tda 0 6 0 +DIHEdral F4 F4 B0 T0 0 6 0 +DIHEdral F4 F4 B0 HP5 0 6 0 +DIHEdral F4 F4 B0 HP0 0 6 0 +DIHEdral F4 F4 B0 HPa 0 6 0 +DIHEdral F4 F4 Tda F4 0 6 0 +DIHEdral F4 F4 Tda F5 0 6 0 +DIHEdral F4 F4 Tda H0 0 6 0 +DIHEdral F4 F4 Tda H5 0 6 0 +DIHEdral F4 F4 Tda Hd 0 6 0 +DIHEdral F4 F4 Tda Ha 0 6 0 +DIHEdral F4 F4 Tda Hda 0 6 0 +DIHEdral F4 F4 Tda Bda 0 6 0 +DIHEdral F4 F4 Tda B0 0 6 0 +DIHEdral F4 F4 Tda Tda 0 6 0 +DIHEdral F4 F4 Tda T0 0 6 0 +DIHEdral F4 F4 Tda HP5 0 6 0 +DIHEdral F4 F4 Tda HP0 0 6 0 +DIHEdral F4 F4 Tda HPa 0 6 0 +DIHEdral F4 F4 T0 F4 0 6 0 +DIHEdral F4 F4 T0 F5 0 6 0 +DIHEdral F4 F4 T0 H0 0 6 0 +DIHEdral F4 F4 T0 H5 0 6 0 +DIHEdral F4 F4 T0 Hd 0 6 0 +DIHEdral F4 F4 T0 Ha 0 6 0 +DIHEdral F4 F4 T0 Hda 0 6 0 +DIHEdral F4 F4 T0 Bda 0 6 0 +DIHEdral F4 F4 T0 B0 0 6 0 +DIHEdral F4 F4 T0 Tda 0 6 0 +DIHEdral F4 F4 T0 T0 0 6 0 +DIHEdral F4 F4 T0 HP5 0 6 0 +DIHEdral F4 F4 T0 HP0 0 6 0 +DIHEdral F4 F4 T0 HPa 0 6 0 +DIHEdral F4 F4 HP5 F4 0 6 0 +DIHEdral F4 F4 HP5 F5 0 6 0 +DIHEdral F4 F4 HP5 H0 0 6 0 +DIHEdral F4 F4 HP5 H5 0 6 0 +DIHEdral F4 F4 HP5 Hd 0 6 0 +DIHEdral F4 F4 HP5 Ha 0 6 0 +DIHEdral F4 F4 HP5 Hda 0 6 0 +DIHEdral F4 F4 HP5 Bda 0 6 0 +DIHEdral F4 F4 HP5 B0 0 6 0 +DIHEdral F4 F4 HP5 Tda 0 6 0 +DIHEdral F4 F4 HP5 T0 0 6 0 +DIHEdral F4 F4 HP5 HP5 0 6 0 +DIHEdral F4 F4 HP5 HP0 0 6 0 +DIHEdral F4 F4 HP5 HPa 0 6 0 +DIHEdral F4 F4 HP0 F4 0 6 0 +DIHEdral F4 F4 HP0 F5 0 6 0 +DIHEdral F4 F4 HP0 H0 0 6 0 +DIHEdral F4 F4 HP0 H5 0 6 0 +DIHEdral F4 F4 HP0 Hd 0 6 0 +DIHEdral F4 F4 HP0 Ha 0 6 0 +DIHEdral F4 F4 HP0 Hda 0 6 0 +DIHEdral F4 F4 HP0 Bda 0 6 0 +DIHEdral F4 F4 HP0 B0 0 6 0 +DIHEdral F4 F4 HP0 Tda 0 6 0 +DIHEdral F4 F4 HP0 T0 0 6 0 +DIHEdral F4 F4 HP0 HP5 0 6 0 +DIHEdral F4 F4 HP0 HP0 0 6 0 +DIHEdral F4 F4 HP0 HPa 0 6 0 +DIHEdral F4 F4 HPa F4 0 6 0 +DIHEdral F4 F4 HPa F5 0 6 0 +DIHEdral F4 F4 HPa H0 0 6 0 +DIHEdral F4 F4 HPa H5 0 6 0 +DIHEdral F4 F4 HPa Hd 0 6 0 +DIHEdral F4 F4 HPa Ha 0 6 0 +DIHEdral F4 F4 HPa Hda 0 6 0 +DIHEdral F4 F4 HPa Bda 0 6 0 +DIHEdral F4 F4 HPa B0 0 6 0 +DIHEdral F4 F4 HPa Tda 0 6 0 +DIHEdral F4 F4 HPa T0 0 6 0 +DIHEdral F4 F4 HPa HP5 0 6 0 +DIHEdral F4 F4 HPa HP0 0 6 0 +DIHEdral F4 F4 HPa HPa 0 6 0 +DIHEdral F4 F5 F4 F4 0 6 0 +DIHEdral F4 F5 F4 F5 0 6 0 +DIHEdral F4 F5 F4 H0 0 6 0 +DIHEdral F4 F5 F4 H5 0 6 0 +DIHEdral F4 F5 F4 Hd 0 6 0 +DIHEdral F4 F5 F4 Ha 0 6 0 +DIHEdral F4 F5 F4 Hda 0 6 0 +DIHEdral F4 F5 F4 Bda 0 6 0 +DIHEdral F4 F5 F4 B0 0 6 0 +DIHEdral F4 F5 F4 Tda 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F4 B0 0 6 0 +DIHEdral H0 Ha F4 Tda 0 6 0 +DIHEdral H0 Ha F4 T0 0 6 0 +DIHEdral H0 Ha F4 HP5 0 6 0 +DIHEdral H0 Ha F4 HP0 0 6 0 +DIHEdral H0 Ha F4 HPa 0 6 0 +DIHEdral H0 Ha F5 F4 0 6 0 +DIHEdral H0 Ha F5 F5 0 6 0 +DIHEdral H0 Ha F5 H0 0 6 0 +DIHEdral H0 Ha F5 H5 0 6 0 +DIHEdral H0 Ha F5 Hd 0 6 0 +DIHEdral H0 Ha F5 Ha 0 6 0 +DIHEdral H0 Ha F5 Hda 0 6 0 +DIHEdral H0 Ha F5 Bda 0 6 0 +DIHEdral H0 Ha F5 B0 0 6 0 +DIHEdral H0 Ha F5 Tda 0 6 0 +DIHEdral H0 Ha F5 T0 0 6 0 +DIHEdral H0 Ha F5 HP5 0 6 0 +DIHEdral H0 Ha F5 HP0 0 6 0 +DIHEdral H0 Ha F5 HPa 0 6 0 +DIHEdral H0 Ha H0 F4 0 6 0 +DIHEdral H0 Ha H0 F5 0 6 0 +DIHEdral H0 Ha H0 Bda 0 6 0 +DIHEdral H0 Ha H0 B0 0 6 0 +DIHEdral H0 Ha H0 Tda 0 6 0 +DIHEdral H0 Ha H0 T0 0 6 0 +DIHEdral H0 Ha H5 F4 0 6 0 +DIHEdral H0 Ha H5 F5 0 6 0 +DIHEdral H0 Ha H5 Bda 0 6 0 +DIHEdral H0 Ha H5 B0 0 6 0 +DIHEdral H0 Ha H5 Tda 0 6 0 +DIHEdral H0 Ha H5 T0 0 6 0 +DIHEdral H0 Ha Hd F4 0 6 0 +DIHEdral H0 Ha Hd F5 0 6 0 +DIHEdral H0 Ha Hd Bda 0 6 0 +DIHEdral H0 Ha Hd B0 0 6 0 +DIHEdral H0 Ha Hd Tda 0 6 0 +DIHEdral H0 Ha Hd T0 0 6 0 +DIHEdral H0 Ha Ha F4 0 6 0 +DIHEdral H0 Ha Ha F5 0 6 0 +DIHEdral H0 Ha Ha Bda 0 6 0 +DIHEdral H0 Ha Ha B0 0 6 0 +DIHEdral H0 Ha Ha Tda 0 6 0 +DIHEdral H0 Ha Ha T0 0 6 0 +DIHEdral H0 Ha Hda F4 0 6 0 +DIHEdral H0 Ha Hda F5 0 6 0 +DIHEdral H0 Ha Hda Bda 0 6 0 +DIHEdral H0 Ha Hda B0 0 6 0 +DIHEdral H0 Ha Hda Tda 0 6 0 +DIHEdral H0 Ha Hda T0 0 6 0 +DIHEdral H0 Ha Bda F4 0 6 0 +DIHEdral H0 Ha Bda F5 0 6 0 +DIHEdral H0 Ha Bda H0 0 6 0 +DIHEdral H0 Ha Bda H5 0 6 0 +DIHEdral H0 Ha Bda Hd 0 6 0 +DIHEdral H0 Ha Bda Ha 0 6 0 +DIHEdral H0 Ha Bda Hda 0 6 0 +DIHEdral H0 Ha Bda Bda 0 6 0 +DIHEdral H0 Ha Bda B0 0 6 0 +DIHEdral H0 Ha Bda Tda 0 6 0 +DIHEdral H0 Ha Bda T0 0 6 0 +DIHEdral H0 Ha Bda HP5 0 6 0 +DIHEdral H0 Ha Bda HP0 0 6 0 +DIHEdral H0 Ha Bda HPa 0 6 0 +DIHEdral H0 Ha B0 F4 0 6 0 +DIHEdral H0 Ha B0 F5 0 6 0 +DIHEdral H0 Ha B0 H0 0 6 0 +DIHEdral H0 Ha B0 H5 0 6 0 +DIHEdral H0 Ha B0 Hd 0 6 0 +DIHEdral H0 Ha B0 Ha 0 6 0 +DIHEdral 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H0 Hda B0 T0 0 6 0 +DIHEdral H0 Hda B0 HP5 0 6 0 +DIHEdral H0 Hda B0 HP0 0 6 0 +DIHEdral H0 Hda B0 HPa 0 6 0 +DIHEdral H0 Hda Tda F4 0 6 0 +DIHEdral H0 Hda Tda F5 0 6 0 +DIHEdral H0 Hda Tda H0 0 6 0 +DIHEdral H0 Hda Tda H5 0 6 0 +DIHEdral H0 Hda Tda Hd 0 6 0 +DIHEdral H0 Hda Tda Ha 0 6 0 +DIHEdral H0 Hda Tda Hda 0 6 0 +DIHEdral H0 Hda Tda Bda 0 6 0 +DIHEdral H0 Hda Tda B0 0 6 0 +DIHEdral H0 Hda Tda Tda 0 6 0 +DIHEdral H0 Hda Tda T0 0 6 0 +DIHEdral H0 Hda Tda HP5 0 6 0 +DIHEdral H0 Hda Tda HP0 0 6 0 +DIHEdral H0 Hda Tda HPa 0 6 0 +DIHEdral H0 Hda T0 F4 0 6 0 +DIHEdral H0 Hda T0 F5 0 6 0 +DIHEdral H0 Hda T0 H0 0 6 0 +DIHEdral H0 Hda T0 H5 0 6 0 +DIHEdral H0 Hda T0 Hd 0 6 0 +DIHEdral H0 Hda T0 Ha 0 6 0 +DIHEdral H0 Hda T0 Hda 0 6 0 +DIHEdral H0 Hda T0 Bda 0 6 0 +DIHEdral H0 Hda T0 B0 0 6 0 +DIHEdral H0 Hda T0 Tda 0 6 0 +DIHEdral H0 Hda T0 T0 0 6 0 +DIHEdral H0 Hda T0 HP5 0 6 0 +DIHEdral H0 Hda T0 HP0 0 6 0 +DIHEdral H0 Hda T0 HPa 0 6 0 +DIHEdral H0 Hda HP5 F4 0 6 0 +DIHEdral H0 Hda HP5 F5 0 6 0 +DIHEdral H0 Hda HP5 Bda 0 6 0 +DIHEdral H0 Hda HP5 B0 0 6 0 +DIHEdral H0 Hda HP5 Tda 0 6 0 +DIHEdral H0 Hda HP5 T0 0 6 0 +DIHEdral H0 Hda HP0 F4 0 6 0 +DIHEdral H0 Hda HP0 F5 0 6 0 +DIHEdral H0 Hda HP0 Bda 0 6 0 +DIHEdral H0 Hda HP0 B0 0 6 0 +DIHEdral H0 Hda HP0 Tda 0 6 0 +DIHEdral H0 Hda HP0 T0 0 6 0 +DIHEdral H0 Hda HPa F4 0 6 0 +DIHEdral H0 Hda HPa F5 0 6 0 +DIHEdral H0 Hda HPa Bda 0 6 0 +DIHEdral H0 Hda HPa B0 0 6 0 +DIHEdral H0 Hda HPa Tda 0 6 0 +DIHEdral H0 Hda HPa T0 0 6 0 +DIHEdral H0 Bda F4 F4 0 6 0 +DIHEdral H0 Bda F4 F5 0 6 0 +DIHEdral H0 Bda F4 H0 0 6 0 +DIHEdral H0 Bda F4 H5 0 6 0 +DIHEdral H0 Bda F4 Hd 0 6 0 +DIHEdral H0 Bda F4 Ha 0 6 0 +DIHEdral H0 Bda F4 Hda 0 6 0 +DIHEdral H0 Bda F4 Bda 0 6 0 +DIHEdral H0 Bda F4 B0 0 6 0 +DIHEdral H0 Bda F4 Tda 0 6 0 +DIHEdral H0 Bda F4 T0 0 6 0 +DIHEdral H0 Bda F4 HP5 0 6 0 +DIHEdral H0 Bda F4 HP0 0 6 0 +DIHEdral H0 Bda F4 HPa 0 6 0 +DIHEdral H0 Bda F5 F4 0 6 0 +DIHEdral H0 Bda F5 F5 0 6 0 +DIHEdral H0 Bda F5 H0 0 6 0 +DIHEdral H0 Bda F5 H5 0 6 0 +DIHEdral H0 Bda F5 Hd 0 6 0 +DIHEdral H0 Bda F5 Ha 0 6 0 +DIHEdral H0 Bda F5 Hda 0 6 0 +DIHEdral H0 Bda F5 Bda 0 6 0 +DIHEdral H0 Bda F5 B0 0 6 0 +DIHEdral H0 Bda F5 Tda 0 6 0 +DIHEdral H0 Bda F5 T0 0 6 0 +DIHEdral H0 Bda F5 HP5 0 6 0 +DIHEdral H0 Bda F5 HP0 0 6 0 +DIHEdral H0 Bda F5 HPa 0 6 0 +DIHEdral H0 Bda H0 F4 0 6 0 +DIHEdral H0 Bda H0 F5 0 6 0 +DIHEdral H0 Bda H0 H0 0 6 0 +DIHEdral H0 Bda H0 H5 0 6 0 +DIHEdral H0 Bda H0 Hd 0 6 0 +DIHEdral H0 Bda H0 Ha 0 6 0 +DIHEdral H0 Bda H0 Hda 0 6 0 +DIHEdral H0 Bda H0 Bda 0 6 0 +DIHEdral H0 Bda H0 B0 0 6 0 +DIHEdral H0 Bda H0 Tda 0 6 0 +DIHEdral H0 Bda H0 T0 0 6 0 +DIHEdral H0 Bda H0 HP5 0 6 0 +DIHEdral H0 Bda H0 HP0 0 6 0 +DIHEdral H0 Bda H0 HPa 0 6 0 +DIHEdral H0 Bda H5 F4 0 6 0 +DIHEdral H0 Bda H5 F5 0 6 0 +DIHEdral H0 Bda H5 H0 0 6 0 +DIHEdral H0 Bda H5 H5 0 6 0 +DIHEdral H0 Bda H5 Hd 0 6 0 +DIHEdral H0 Bda H5 Ha 0 6 0 +DIHEdral H0 Bda H5 Hda 0 6 0 +DIHEdral H0 Bda H5 Bda 0 6 0 +DIHEdral H0 Bda H5 B0 0 6 0 +DIHEdral H0 Bda H5 Tda 0 6 0 +DIHEdral H0 Bda H5 T0 0 6 0 +DIHEdral H0 Bda H5 HP5 0 6 0 +DIHEdral H0 Bda H5 HP0 0 6 0 +DIHEdral H0 Bda H5 HPa 0 6 0 +DIHEdral H0 Bda Hd F4 0 6 0 +DIHEdral H0 Bda Hd F5 0 6 0 +DIHEdral H0 Bda Hd H0 0 6 0 +DIHEdral H0 Bda Hd H5 0 6 0 +DIHEdral H0 Bda Hd Hd 0 6 0 +DIHEdral H0 Bda Hd Ha 0 6 0 +DIHEdral H0 Bda Hd Hda 0 6 0 +DIHEdral H0 Bda Hd Bda 0 6 0 +DIHEdral H0 Bda Hd B0 0 6 0 +DIHEdral H0 Bda Hd Tda 0 6 0 +DIHEdral H0 Bda Hd T0 0 6 0 +DIHEdral H0 Bda Hd HP5 0 6 0 +DIHEdral H0 Bda Hd HP0 0 6 0 +DIHEdral H0 Bda Hd HPa 0 6 0 +DIHEdral H0 Bda Ha F4 0 6 0 +DIHEdral H0 Bda Ha F5 0 6 0 +DIHEdral H0 Bda Ha H0 0 6 0 +DIHEdral H0 Bda Ha H5 0 6 0 +DIHEdral H0 Bda Ha Hd 0 6 0 +DIHEdral H0 Bda Ha Ha 0 6 0 +DIHEdral H0 Bda Ha Hda 0 6 0 +DIHEdral H0 Bda Ha Bda 0 6 0 +DIHEdral H0 Bda Ha B0 0 6 0 +DIHEdral H0 Bda Ha Tda 0 6 0 +DIHEdral H0 Bda Ha T0 0 6 0 +DIHEdral H0 Bda Ha HP5 0 6 0 +DIHEdral H0 Bda Ha HP0 0 6 0 +DIHEdral H0 Bda Ha HPa 0 6 0 +DIHEdral H0 Bda Hda F4 0 6 0 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6 0 +DIHEdral H0 T0 Ha Ha 0 6 0 +DIHEdral H0 T0 Ha Hda 0 6 0 +DIHEdral H0 T0 Ha Bda 0 6 0 +DIHEdral H0 T0 Ha B0 0 6 0 +DIHEdral H0 T0 Ha Tda 0 6 0 +DIHEdral H0 T0 Ha T0 0 6 0 +DIHEdral H0 T0 Ha HP5 0 6 0 +DIHEdral H0 T0 Ha HP0 0 6 0 +DIHEdral H0 T0 Ha HPa 0 6 0 +DIHEdral H0 T0 Hda F4 0 6 0 +DIHEdral H0 T0 Hda F5 0 6 0 +DIHEdral H0 T0 Hda H0 0 6 0 +DIHEdral H0 T0 Hda H5 0 6 0 +DIHEdral H0 T0 Hda Hd 0 6 0 +DIHEdral H0 T0 Hda Ha 0 6 0 +DIHEdral H0 T0 Hda Hda 0 6 0 +DIHEdral H0 T0 Hda Bda 0 6 0 +DIHEdral H0 T0 Hda B0 0 6 0 +DIHEdral H0 T0 Hda Tda 0 6 0 +DIHEdral H0 T0 Hda T0 0 6 0 +DIHEdral H0 T0 Hda HP5 0 6 0 +DIHEdral H0 T0 Hda HP0 0 6 0 +DIHEdral H0 T0 Hda HPa 0 6 0 +DIHEdral H0 T0 Bda F4 0 6 0 +DIHEdral H0 T0 Bda F5 0 6 0 +DIHEdral H0 T0 Bda H0 0 6 0 +DIHEdral H0 T0 Bda H5 0 6 0 +DIHEdral H0 T0 Bda Hd 0 6 0 +DIHEdral H0 T0 Bda Ha 0 6 0 +DIHEdral H0 T0 Bda Hda 0 6 0 +DIHEdral H0 T0 Bda Bda 0 6 0 +DIHEdral H0 T0 Bda B0 0 6 0 +DIHEdral H0 T0 Bda Tda 0 6 0 +DIHEdral H0 T0 Bda T0 0 6 0 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0 +DIHEdral H0 T0 HP0 T0 0 6 0 +DIHEdral H0 T0 HP0 HP5 0 6 0 +DIHEdral H0 T0 HP0 HP0 0 6 0 +DIHEdral H0 T0 HP0 HPa 0 6 0 +DIHEdral H0 T0 HPa F4 0 6 0 +DIHEdral H0 T0 HPa F5 0 6 0 +DIHEdral H0 T0 HPa H0 0 6 0 +DIHEdral H0 T0 HPa H5 0 6 0 +DIHEdral H0 T0 HPa Hd 0 6 0 +DIHEdral H0 T0 HPa Ha 0 6 0 +DIHEdral H0 T0 HPa Hda 0 6 0 +DIHEdral H0 T0 HPa Bda 0 6 0 +DIHEdral H0 T0 HPa B0 0 6 0 +DIHEdral H0 T0 HPa Tda 0 6 0 +DIHEdral H0 T0 HPa T0 0 6 0 +DIHEdral H0 T0 HPa HP5 0 6 0 +DIHEdral H0 T0 HPa HP0 0 6 0 +DIHEdral H0 T0 HPa HPa 0 6 0 +DIHEdral H0 HP5 F4 F4 0 6 0 +DIHEdral H0 HP5 F4 F5 0 6 0 +DIHEdral H0 HP5 F4 H0 0 6 0 +DIHEdral H0 HP5 F4 H5 0 6 0 +DIHEdral H0 HP5 F4 Hd 0 6 0 +DIHEdral H0 HP5 F4 Ha 0 6 0 +DIHEdral H0 HP5 F4 Hda 0 6 0 +DIHEdral H0 HP5 F4 Bda 0 6 0 +DIHEdral H0 HP5 F4 B0 0 6 0 +DIHEdral H0 HP5 F4 Tda 0 6 0 +DIHEdral H0 HP5 F4 T0 0 6 0 +DIHEdral H0 HP5 F4 HP5 0 6 0 +DIHEdral H0 HP5 F4 HP0 0 6 0 +DIHEdral H0 HP5 F4 HPa 0 6 0 +DIHEdral H0 HP5 F5 F4 0 6 0 +DIHEdral H0 HP5 F5 F5 0 6 0 +DIHEdral H0 HP5 F5 H0 0 6 0 +DIHEdral H0 HP5 F5 H5 0 6 0 +DIHEdral H0 HP5 F5 Hd 0 6 0 +DIHEdral H0 HP5 F5 Ha 0 6 0 +DIHEdral H0 HP5 F5 Hda 0 6 0 +DIHEdral H0 HP5 F5 Bda 0 6 0 +DIHEdral H0 HP5 F5 B0 0 6 0 +DIHEdral H0 HP5 F5 Tda 0 6 0 +DIHEdral H0 HP5 F5 T0 0 6 0 +DIHEdral H0 HP5 F5 HP5 0 6 0 +DIHEdral H0 HP5 F5 HP0 0 6 0 +DIHEdral H0 HP5 F5 HPa 0 6 0 +DIHEdral H0 HP5 H0 F4 0 6 0 +DIHEdral H0 HP5 H0 F5 0 6 0 +DIHEdral H0 HP5 H0 Bda 0 6 0 +DIHEdral H0 HP5 H0 B0 0 6 0 +DIHEdral H0 HP5 H0 Tda 0 6 0 +DIHEdral H0 HP5 H0 T0 0 6 0 +DIHEdral H0 HP5 H5 F4 0 6 0 +DIHEdral H0 HP5 H5 F5 0 6 0 +DIHEdral H0 HP5 H5 Bda 0 6 0 +DIHEdral H0 HP5 H5 B0 0 6 0 +DIHEdral H0 HP5 H5 Tda 0 6 0 +DIHEdral H0 HP5 H5 T0 0 6 0 +DIHEdral H0 HP5 Hd F4 0 6 0 +DIHEdral H0 HP5 Hd F5 0 6 0 +DIHEdral H0 HP5 Hd Bda 0 6 0 +DIHEdral H0 HP5 Hd B0 0 6 0 +DIHEdral H0 HP5 Hd Tda 0 6 0 +DIHEdral H0 HP5 Hd T0 0 6 0 +DIHEdral H0 HP5 Ha F4 0 6 0 +DIHEdral H0 HP5 Ha F5 0 6 0 +DIHEdral H0 HP5 Ha Bda 0 6 0 +DIHEdral H0 HP5 Ha B0 0 6 0 +DIHEdral H0 HP5 Ha Tda 0 6 0 +DIHEdral H0 HP5 Ha T0 0 6 0 +DIHEdral H0 HP5 Hda F4 0 6 0 +DIHEdral H0 HP5 Hda F5 0 6 0 +DIHEdral H0 HP5 Hda Bda 0 6 0 +DIHEdral H0 HP5 Hda B0 0 6 0 +DIHEdral H0 HP5 Hda Tda 0 6 0 +DIHEdral H0 HP5 Hda T0 0 6 0 +DIHEdral H0 HP5 Bda F4 0 6 0 +DIHEdral H0 HP5 Bda F5 0 6 0 +DIHEdral H0 HP5 Bda H0 0 6 0 +DIHEdral H0 HP5 Bda H5 0 6 0 +DIHEdral H0 HP5 Bda Hd 0 6 0 +DIHEdral H0 HP5 Bda Ha 0 6 0 +DIHEdral H0 HP5 Bda Hda 0 6 0 +DIHEdral H0 HP5 Bda Bda 0 6 0 +DIHEdral H0 HP5 Bda B0 0 6 0 +DIHEdral H0 HP5 Bda Tda 0 6 0 +DIHEdral H0 HP5 Bda T0 0 6 0 +DIHEdral H0 HP5 Bda HP5 0 6 0 +DIHEdral H0 HP5 Bda HP0 0 6 0 +DIHEdral H0 HP5 Bda HPa 0 6 0 +DIHEdral H0 HP5 B0 F4 0 6 0 +DIHEdral H0 HP5 B0 F5 0 6 0 +DIHEdral H0 HP5 B0 H0 0 6 0 +DIHEdral H0 HP5 B0 H5 0 6 0 +DIHEdral H0 HP5 B0 Hd 0 6 0 +DIHEdral H0 HP5 B0 Ha 0 6 0 +DIHEdral H0 HP5 B0 Hda 0 6 0 +DIHEdral H0 HP5 B0 Bda 0 6 0 +DIHEdral H0 HP5 B0 B0 0 6 0 +DIHEdral H0 HP5 B0 Tda 0 6 0 +DIHEdral H0 HP5 B0 T0 0 6 0 +DIHEdral 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6 0 +DIHEdral Hd Hd HP5 Tda 0 6 0 +DIHEdral Hd Hd HP5 T0 0 6 0 +DIHEdral Hd Hd HP0 F4 0 6 0 +DIHEdral Hd Hd HP0 F5 0 6 0 +DIHEdral Hd Hd HP0 Bda 0 6 0 +DIHEdral Hd Hd HP0 B0 0 6 0 +DIHEdral Hd Hd HP0 Tda 0 6 0 +DIHEdral Hd Hd HP0 T0 0 6 0 +DIHEdral Hd Hd HPa F4 0 6 0 +DIHEdral Hd Hd HPa F5 0 6 0 +DIHEdral Hd Hd HPa Bda 0 6 0 +DIHEdral Hd Hd HPa B0 0 6 0 +DIHEdral Hd Hd HPa Tda 0 6 0 +DIHEdral Hd Hd HPa T0 0 6 0 +DIHEdral Hd Ha F4 F4 0 6 0 +DIHEdral Hd Ha F4 F5 0 6 0 +DIHEdral Hd Ha F4 H0 0 6 0 +DIHEdral Hd Ha F4 H5 0 6 0 +DIHEdral Hd Ha F4 Hd 0 6 0 +DIHEdral Hd Ha F4 Ha 0 6 0 +DIHEdral Hd Ha F4 Hda 0 6 0 +DIHEdral Hd Ha F4 Bda 0 6 0 +DIHEdral Hd Ha F4 B0 0 6 0 +DIHEdral Hd Ha F4 Tda 0 6 0 +DIHEdral Hd Ha F4 T0 0 6 0 +DIHEdral Hd Ha F4 HP5 0 6 0 +DIHEdral Hd Ha F4 HP0 0 6 0 +DIHEdral Hd Ha F4 HPa 0 6 0 +DIHEdral Hd Ha F5 F4 0 6 0 +DIHEdral Hd Ha F5 F5 0 6 0 +DIHEdral Hd Ha F5 H0 0 6 0 +DIHEdral Hd Ha F5 H5 0 6 0 +DIHEdral Hd Ha F5 Hd 0 6 0 +DIHEdral Hd Ha F5 Ha 0 6 0 +DIHEdral Hd Ha F5 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B0 0 6 0 +DIHEdral Hd Ha Hda Tda 0 6 0 +DIHEdral Hd Ha Hda T0 0 6 0 +DIHEdral Hd Ha Bda F4 0 6 0 +DIHEdral Hd Ha Bda F5 0 6 0 +DIHEdral Hd Ha Bda H0 0 6 0 +DIHEdral Hd Ha Bda H5 0 6 0 +DIHEdral Hd Ha Bda Hd 0 6 0 +DIHEdral Hd Ha Bda Ha 0 6 0 +DIHEdral Hd Ha Bda Hda 0 6 0 +DIHEdral Hd Ha Bda Bda 0 6 0 +DIHEdral Hd Ha Bda B0 0 6 0 +DIHEdral Hd Ha Bda Tda 0 6 0 +DIHEdral Hd Ha Bda T0 0 6 0 +DIHEdral Hd Ha Bda HP5 0 6 0 +DIHEdral Hd Ha Bda HP0 0 6 0 +DIHEdral Hd Ha Bda HPa 0 6 0 +DIHEdral Hd Ha B0 F4 0 6 0 +DIHEdral Hd Ha B0 F5 0 6 0 +DIHEdral Hd Ha B0 H0 0 6 0 +DIHEdral Hd Ha B0 H5 0 6 0 +DIHEdral Hd Ha B0 Hd 0 6 0 +DIHEdral Hd Ha B0 Ha 0 6 0 +DIHEdral Hd Ha B0 Hda 0 6 0 +DIHEdral Hd Ha B0 Bda 0 6 0 +DIHEdral Hd Ha B0 B0 0 6 0 +DIHEdral Hd Ha B0 Tda 0 6 0 +DIHEdral Hd Ha B0 T0 0 6 0 +DIHEdral Hd Ha B0 HP5 0 6 0 +DIHEdral Hd Ha B0 HP0 0 6 0 +DIHEdral Hd Ha B0 HPa 0 6 0 +DIHEdral Hd Ha Tda F4 0 6 0 +DIHEdral Hd Ha Tda F5 0 6 0 +DIHEdral Hd Ha Tda H0 0 6 0 +DIHEdral Hd Ha Tda H5 0 6 0 +DIHEdral Hd Ha Tda Hd 0 6 0 +DIHEdral Hd Ha Tda Ha 0 6 0 +DIHEdral Hd Ha Tda Hda 0 6 0 +DIHEdral Hd Ha Tda Bda 0 6 0 +DIHEdral Hd Ha Tda B0 0 6 0 +DIHEdral Hd Ha Tda Tda 0 6 0 +DIHEdral Hd Ha Tda T0 0 6 0 +DIHEdral Hd Ha Tda HP5 0 6 0 +DIHEdral Hd Ha Tda HP0 0 6 0 +DIHEdral Hd Ha Tda HPa 0 6 0 +DIHEdral Hd Ha T0 F4 0 6 0 +DIHEdral Hd Ha T0 F5 0 6 0 +DIHEdral Hd Ha T0 H0 0 6 0 +DIHEdral Hd Ha T0 H5 0 6 0 +DIHEdral Hd Ha T0 Hd 0 6 0 +DIHEdral Hd Ha T0 Ha 0 6 0 +DIHEdral Hd Ha T0 Hda 0 6 0 +DIHEdral Hd Ha T0 Bda 0 6 0 +DIHEdral Hd Ha T0 B0 0 6 0 +DIHEdral Hd Ha T0 Tda 0 6 0 +DIHEdral Hd Ha T0 T0 0 6 0 +DIHEdral Hd Ha T0 HP5 0 6 0 +DIHEdral Hd Ha T0 HP0 0 6 0 +DIHEdral Hd Ha T0 HPa 0 6 0 +DIHEdral Hd Ha HP5 F4 0 6 0 +DIHEdral Hd Ha HP5 F5 0 6 0 +DIHEdral Hd Ha HP5 Bda 0 6 0 +DIHEdral Hd Ha HP5 B0 0 6 0 +DIHEdral Hd Ha HP5 Tda 0 6 0 +DIHEdral Hd Ha HP5 T0 0 6 0 +DIHEdral Hd Ha HP0 F4 0 6 0 +DIHEdral Hd Ha HP0 F5 0 6 0 +DIHEdral Hd Ha HP0 Bda 0 6 0 +DIHEdral Hd Ha HP0 B0 0 6 0 +DIHEdral Hd Ha HP0 Tda 0 6 0 +DIHEdral Hd Ha HP0 T0 0 6 0 +DIHEdral Hd Ha HPa F4 0 6 0 +DIHEdral Hd Ha HPa F5 0 6 0 +DIHEdral Hd Ha HPa Bda 0 6 0 +DIHEdral Hd Ha HPa B0 0 6 0 +DIHEdral Hd Ha HPa Tda 0 6 0 +DIHEdral Hd Ha HPa T0 0 6 0 +DIHEdral Hd Hda F4 F4 0 6 0 +DIHEdral Hd Hda F4 F5 0 6 0 +DIHEdral Hd Hda F4 H0 0 6 0 +DIHEdral Hd Hda F4 H5 0 6 0 +DIHEdral Hd Hda F4 Hd 0 6 0 +DIHEdral Hd Hda F4 Ha 0 6 0 +DIHEdral Hd Hda F4 Hda 0 6 0 +DIHEdral Hd Hda F4 Bda 0 6 0 +DIHEdral Hd Hda F4 B0 0 6 0 +DIHEdral Hd Hda F4 Tda 0 6 0 +DIHEdral Hd Hda F4 T0 0 6 0 +DIHEdral Hd Hda F4 HP5 0 6 0 +DIHEdral Hd Hda F4 HP0 0 6 0 +DIHEdral Hd Hda F4 HPa 0 6 0 +DIHEdral Hd Hda F5 F4 0 6 0 +DIHEdral Hd Hda F5 F5 0 6 0 +DIHEdral Hd Hda F5 H0 0 6 0 +DIHEdral Hd Hda F5 H5 0 6 0 +DIHEdral Hd Hda F5 Hd 0 6 0 +DIHEdral Hd Hda F5 Ha 0 6 0 +DIHEdral Hd Hda F5 Hda 0 6 0 +DIHEdral Hd Hda F5 Bda 0 6 0 +DIHEdral Hd Hda F5 B0 0 6 0 +DIHEdral Hd Hda F5 Tda 0 6 0 +DIHEdral Hd Hda F5 T0 0 6 0 +DIHEdral Hd Hda F5 HP5 0 6 0 +DIHEdral Hd Hda F5 HP0 0 6 0 +DIHEdral Hd Hda F5 HPa 0 6 0 +DIHEdral Hd Hda H0 F4 0 6 0 +DIHEdral Hd Hda H0 F5 0 6 0 +DIHEdral Hd Hda H0 Bda 0 6 0 +DIHEdral Hd Hda H0 B0 0 6 0 +DIHEdral Hd Hda H0 Tda 0 6 0 +DIHEdral Hd Hda H0 T0 0 6 0 +DIHEdral Hd Hda H5 F4 0 6 0 +DIHEdral Hd Hda H5 F5 0 6 0 +DIHEdral Hd Hda H5 Bda 0 6 0 +DIHEdral Hd Hda H5 B0 0 6 0 +DIHEdral Hd Hda H5 Tda 0 6 0 +DIHEdral Hd Hda H5 T0 0 6 0 +DIHEdral Hd Hda Hd F4 0 6 0 +DIHEdral Hd Hda Hd F5 0 6 0 +DIHEdral Hd Hda Hd Bda 0 6 0 +DIHEdral Hd Hda Hd B0 0 6 0 +DIHEdral Hd Hda Hd Tda 0 6 0 +DIHEdral Hd Hda Hd T0 0 6 0 +DIHEdral Hd Hda Ha F4 0 6 0 +DIHEdral Hd Hda Ha F5 0 6 0 +DIHEdral Hd Hda Ha Bda 0 6 0 +DIHEdral Hd Hda Ha B0 0 6 0 +DIHEdral Hd Hda Ha Tda 0 6 0 +DIHEdral Hd Hda Ha T0 0 6 0 +DIHEdral Hd Hda Hda F4 0 6 0 +DIHEdral Hd Hda Hda F5 0 6 0 +DIHEdral Hd Hda Hda Bda 0 6 0 +DIHEdral Hd Hda Hda B0 0 6 0 +DIHEdral Hd Hda Hda Tda 0 6 0 +DIHEdral Hd Hda Hda T0 0 6 0 +DIHEdral Hd Hda Bda F4 0 6 0 +DIHEdral Hd Hda Bda F5 0 6 0 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HPa F4 0 6 0 +DIHEdral Hd Hda HPa F5 0 6 0 +DIHEdral Hd Hda HPa Bda 0 6 0 +DIHEdral Hd Hda HPa B0 0 6 0 +DIHEdral Hd Hda HPa Tda 0 6 0 +DIHEdral Hd Hda HPa T0 0 6 0 +DIHEdral Hd Bda F4 F4 0 6 0 +DIHEdral Hd Bda F4 F5 0 6 0 +DIHEdral Hd Bda F4 H0 0 6 0 +DIHEdral Hd Bda F4 H5 0 6 0 +DIHEdral Hd Bda F4 Hd 0 6 0 +DIHEdral Hd Bda F4 Ha 0 6 0 +DIHEdral Hd Bda F4 Hda 0 6 0 +DIHEdral Hd Bda F4 Bda 0 6 0 +DIHEdral Hd Bda F4 B0 0 6 0 +DIHEdral Hd Bda F4 Tda 0 6 0 +DIHEdral Hd Bda F4 T0 0 6 0 +DIHEdral Hd Bda F4 HP5 0 6 0 +DIHEdral Hd Bda F4 HP0 0 6 0 +DIHEdral Hd Bda F4 HPa 0 6 0 +DIHEdral Hd Bda F5 F4 0 6 0 +DIHEdral Hd Bda F5 F5 0 6 0 +DIHEdral Hd Bda F5 H0 0 6 0 +DIHEdral Hd Bda F5 H5 0 6 0 +DIHEdral Hd Bda F5 Hd 0 6 0 +DIHEdral Hd Bda F5 Ha 0 6 0 +DIHEdral Hd Bda F5 Hda 0 6 0 +DIHEdral Hd Bda F5 Bda 0 6 0 +DIHEdral Hd Bda F5 B0 0 6 0 +DIHEdral Hd Bda F5 Tda 0 6 0 +DIHEdral Hd Bda F5 T0 0 6 0 +DIHEdral Hd Bda F5 HP5 0 6 0 +DIHEdral Hd Bda F5 HP0 0 6 0 +DIHEdral Hd Bda F5 HPa 0 6 0 +DIHEdral 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Bda Hd HP5 Hd 0 6 0 +DIHEdral Bda Hd HP5 Ha 0 6 0 +DIHEdral Bda Hd HP5 Hda 0 6 0 +DIHEdral Bda Hd HP5 Bda 0 6 0 +DIHEdral Bda Hd HP5 B0 0 6 0 +DIHEdral Bda Hd HP5 Tda 0 6 0 +DIHEdral Bda Hd HP5 T0 0 6 0 +DIHEdral Bda Hd HP5 HP5 0 6 0 +DIHEdral Bda Hd HP5 HP0 0 6 0 +DIHEdral Bda Hd HP5 HPa 0 6 0 +DIHEdral Bda Hd HP0 F4 0 6 0 +DIHEdral Bda Hd HP0 F5 0 6 0 +DIHEdral Bda Hd HP0 H0 0 6 0 +DIHEdral Bda Hd HP0 H5 0 6 0 +DIHEdral Bda Hd HP0 Hd 0 6 0 +DIHEdral Bda Hd HP0 Ha 0 6 0 +DIHEdral Bda Hd HP0 Hda 0 6 0 +DIHEdral Bda Hd HP0 Bda 0 6 0 +DIHEdral Bda Hd HP0 B0 0 6 0 +DIHEdral Bda Hd HP0 Tda 0 6 0 +DIHEdral Bda Hd HP0 T0 0 6 0 +DIHEdral Bda Hd HP0 HP5 0 6 0 +DIHEdral Bda Hd HP0 HP0 0 6 0 +DIHEdral Bda Hd HP0 HPa 0 6 0 +DIHEdral Bda Hd HPa F4 0 6 0 +DIHEdral Bda Hd HPa F5 0 6 0 +DIHEdral Bda Hd HPa H0 0 6 0 +DIHEdral Bda Hd HPa H5 0 6 0 +DIHEdral Bda Hd HPa Hd 0 6 0 +DIHEdral Bda Hd HPa Ha 0 6 0 +DIHEdral Bda Hd HPa Hda 0 6 0 +DIHEdral Bda Hd HPa Bda 0 6 0 +DIHEdral Bda Hd HPa B0 0 6 0 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0 6 0 +DIHEdral Bda Ha H0 F5 0 6 0 +DIHEdral Bda Ha H0 H0 0 6 0 +DIHEdral Bda Ha H0 H5 0 6 0 +DIHEdral Bda Ha H0 Hd 0 6 0 +DIHEdral Bda Ha H0 Ha 0 6 0 +DIHEdral Bda Ha H0 Hda 0 6 0 +DIHEdral Bda Ha H0 Bda 0 6 0 +DIHEdral Bda Ha H0 B0 0 6 0 +DIHEdral Bda Ha H0 Tda 0 6 0 +DIHEdral Bda Ha H0 T0 0 6 0 +DIHEdral Bda Ha H0 HP5 0 6 0 +DIHEdral Bda Ha H0 HP0 0 6 0 +DIHEdral Bda Ha H0 HPa 0 6 0 +DIHEdral Bda Ha H5 F4 0 6 0 +DIHEdral Bda Ha H5 F5 0 6 0 +DIHEdral Bda Ha H5 H0 0 6 0 +DIHEdral Bda Ha H5 H5 0 6 0 +DIHEdral Bda Ha H5 Hd 0 6 0 +DIHEdral Bda Ha H5 Ha 0 6 0 +DIHEdral Bda Ha H5 Hda 0 6 0 +DIHEdral Bda Ha H5 Bda 0 6 0 +DIHEdral Bda Ha H5 B0 0 6 0 +DIHEdral Bda Ha H5 Tda 0 6 0 +DIHEdral Bda Ha H5 T0 0 6 0 +DIHEdral Bda Ha H5 HP5 0 6 0 +DIHEdral Bda Ha H5 HP0 0 6 0 +DIHEdral Bda Ha H5 HPa 0 6 0 +DIHEdral Bda Ha Hd F4 0 6 0 +DIHEdral Bda Ha Hd F5 0 6 0 +DIHEdral Bda Ha Hd H0 0 6 0 +DIHEdral Bda Ha Hd H5 0 6 0 +DIHEdral Bda Ha Hd Hd 0 6 0 +DIHEdral Bda Ha Hd Ha 0 6 0 +DIHEdral Bda Ha Hd Hda 0 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6 0 +DIHEdral HPa F4 F4 Ha 0 6 0 +DIHEdral HPa F4 F4 Hda 0 6 0 +DIHEdral HPa F4 F4 Bda 0 6 0 +DIHEdral HPa F4 F4 B0 0 6 0 +DIHEdral HPa F4 F4 Tda 0 6 0 +DIHEdral HPa F4 F4 T0 0 6 0 +DIHEdral HPa F4 F4 HP5 0 6 0 +DIHEdral HPa F4 F4 HP0 0 6 0 +DIHEdral HPa F4 F4 HPa 0 6 0 +DIHEdral HPa F4 F5 F4 0 6 0 +DIHEdral HPa F4 F5 F5 0 6 0 +DIHEdral HPa F4 F5 H0 0 6 0 +DIHEdral HPa F4 F5 H5 0 6 0 +DIHEdral HPa F4 F5 Hd 0 6 0 +DIHEdral HPa F4 F5 Ha 0 6 0 +DIHEdral HPa F4 F5 Hda 0 6 0 +DIHEdral HPa F4 F5 Bda 0 6 0 +DIHEdral HPa F4 F5 B0 0 6 0 +DIHEdral HPa F4 F5 Tda 0 6 0 +DIHEdral HPa F4 F5 T0 0 6 0 +DIHEdral HPa F4 F5 HP5 0 6 0 +DIHEdral HPa F4 F5 HP0 0 6 0 +DIHEdral HPa F4 F5 HPa 0 6 0 +DIHEdral HPa F4 H0 F4 0 6 0 +DIHEdral HPa F4 H0 F5 0 6 0 +DIHEdral HPa F4 H0 H0 0 6 0 +DIHEdral HPa F4 H0 H5 0 6 0 +DIHEdral HPa F4 H0 Hd 0 6 0 +DIHEdral HPa F4 H0 Ha 0 6 0 +DIHEdral HPa F4 H0 Hda 0 6 0 +DIHEdral HPa F4 H0 Bda 0 6 0 +DIHEdral HPa F4 H0 B0 0 6 0 +DIHEdral HPa F4 H0 Tda 0 6 0 +DIHEdral HPa F4 H0 T0 0 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6 0 +DIHEdral HPa F4 Ha H5 0 6 0 +DIHEdral HPa F4 Ha Hd 0 6 0 +DIHEdral HPa F4 Ha Ha 0 6 0 +DIHEdral HPa F4 Ha Hda 0 6 0 +DIHEdral HPa F4 Ha Bda 0 6 0 +DIHEdral HPa F4 Ha B0 0 6 0 +DIHEdral HPa F4 Ha Tda 0 6 0 +DIHEdral HPa F4 Ha T0 0 6 0 +DIHEdral HPa F4 Ha HP5 0 6 0 +DIHEdral HPa F4 Ha HP0 0 6 0 +DIHEdral HPa F4 Ha HPa 0 6 0 +DIHEdral HPa F4 Hda F4 0 6 0 +DIHEdral HPa F4 Hda F5 0 6 0 +DIHEdral HPa F4 Hda H0 0 6 0 +DIHEdral HPa F4 Hda H5 0 6 0 +DIHEdral HPa F4 Hda Hd 0 6 0 +DIHEdral HPa F4 Hda Ha 0 6 0 +DIHEdral HPa F4 Hda Hda 0 6 0 +DIHEdral HPa F4 Hda Bda 0 6 0 +DIHEdral HPa F4 Hda B0 0 6 0 +DIHEdral HPa F4 Hda Tda 0 6 0 +DIHEdral HPa F4 Hda T0 0 6 0 +DIHEdral HPa F4 Hda HP5 0 6 0 +DIHEdral HPa F4 Hda HP0 0 6 0 +DIHEdral HPa F4 Hda HPa 0 6 0 +DIHEdral HPa F4 Bda F4 0 6 0 +DIHEdral HPa F4 Bda F5 0 6 0 +DIHEdral HPa F4 Bda H0 0 6 0 +DIHEdral HPa F4 Bda H5 0 6 0 +DIHEdral HPa F4 Bda Hd 0 6 0 +DIHEdral HPa F4 Bda Ha 0 6 0 +DIHEdral HPa F4 Bda Hda 0 6 0 +DIHEdral HPa F4 Bda Bda 0 6 0 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6 0 +DIHEdral HPa F5 H5 H0 0 6 0 +DIHEdral HPa F5 H5 H5 0 6 0 +DIHEdral HPa F5 H5 Hd 0 6 0 +DIHEdral HPa F5 H5 Ha 0 6 0 +DIHEdral HPa F5 H5 Hda 0 6 0 +DIHEdral HPa F5 H5 Bda 0 6 0 +DIHEdral HPa F5 H5 B0 0 6 0 +DIHEdral HPa F5 H5 Tda 0 6 0 +DIHEdral HPa F5 H5 T0 0 6 0 +DIHEdral HPa F5 H5 HP5 0 6 0 +DIHEdral HPa F5 H5 HP0 0 6 0 +DIHEdral HPa F5 H5 HPa 0 6 0 +DIHEdral HPa F5 Hd F4 0 6 0 +DIHEdral HPa F5 Hd F5 0 6 0 +DIHEdral HPa F5 Hd H0 0 6 0 +DIHEdral HPa F5 Hd H5 0 6 0 +DIHEdral HPa F5 Hd Hd 0 6 0 +DIHEdral HPa F5 Hd Ha 0 6 0 +DIHEdral HPa F5 Hd Hda 0 6 0 +DIHEdral HPa F5 Hd Bda 0 6 0 +DIHEdral HPa F5 Hd B0 0 6 0 +DIHEdral HPa F5 Hd Tda 0 6 0 +DIHEdral HPa F5 Hd T0 0 6 0 +DIHEdral HPa F5 Hd HP5 0 6 0 +DIHEdral HPa F5 Hd HP0 0 6 0 +DIHEdral HPa F5 Hd HPa 0 6 0 +DIHEdral HPa F5 Ha F4 0 6 0 +DIHEdral HPa F5 Ha F5 0 6 0 +DIHEdral HPa F5 Ha H0 0 6 0 +DIHEdral HPa F5 Ha H5 0 6 0 +DIHEdral HPa F5 Ha Hd 0 6 0 +DIHEdral HPa F5 Ha Ha 0 6 0 +DIHEdral HPa F5 Ha Hda 0 6 0 +DIHEdral HPa F5 Ha Bda 0 6 0 +DIHEdral HPa F5 Ha B0 0 6 0 +DIHEdral HPa F5 Ha Tda 0 6 0 +DIHEdral HPa F5 Ha T0 0 6 0 +DIHEdral HPa F5 Ha HP5 0 6 0 +DIHEdral HPa F5 Ha HP0 0 6 0 +DIHEdral HPa F5 Ha HPa 0 6 0 +DIHEdral HPa F5 Hda F4 0 6 0 +DIHEdral HPa F5 Hda F5 0 6 0 +DIHEdral HPa F5 Hda H0 0 6 0 +DIHEdral HPa F5 Hda H5 0 6 0 +DIHEdral HPa F5 Hda Hd 0 6 0 +DIHEdral HPa F5 Hda Ha 0 6 0 +DIHEdral HPa F5 Hda Hda 0 6 0 +DIHEdral HPa F5 Hda Bda 0 6 0 +DIHEdral HPa F5 Hda B0 0 6 0 +DIHEdral HPa F5 Hda Tda 0 6 0 +DIHEdral HPa F5 Hda T0 0 6 0 +DIHEdral HPa F5 Hda HP5 0 6 0 +DIHEdral HPa F5 Hda HP0 0 6 0 +DIHEdral HPa F5 Hda HPa 0 6 0 +DIHEdral HPa F5 Bda F4 0 6 0 +DIHEdral HPa F5 Bda F5 0 6 0 +DIHEdral HPa F5 Bda H0 0 6 0 +DIHEdral HPa F5 Bda H5 0 6 0 +DIHEdral HPa F5 Bda Hd 0 6 0 +DIHEdral HPa F5 Bda Ha 0 6 0 +DIHEdral HPa F5 Bda Hda 0 6 0 +DIHEdral HPa F5 Bda Bda 0 6 0 +DIHEdral HPa F5 Bda B0 0 6 0 +DIHEdral HPa F5 Bda Tda 0 6 0 +DIHEdral HPa F5 Bda T0 0 6 0 +DIHEdral HPa F5 Bda HP5 0 6 0 +DIHEdral HPa F5 Bda HP0 0 6 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HP0 Hda Tda 0 6 0 +DIHEdral HPa HP0 Hda T0 0 6 0 +DIHEdral HPa HP0 Bda F4 0 6 0 +DIHEdral HPa HP0 Bda F5 0 6 0 +DIHEdral HPa HP0 Bda H0 0 6 0 +DIHEdral HPa HP0 Bda H5 0 6 0 +DIHEdral HPa HP0 Bda Hd 0 6 0 +DIHEdral HPa HP0 Bda Ha 0 6 0 +DIHEdral HPa HP0 Bda Hda 0 6 0 +DIHEdral HPa HP0 Bda Bda 0 6 0 +DIHEdral HPa HP0 Bda B0 0 6 0 +DIHEdral HPa HP0 Bda Tda 0 6 0 +DIHEdral HPa HP0 Bda T0 0 6 0 +DIHEdral HPa HP0 Bda HP5 0 6 0 +DIHEdral HPa HP0 Bda HP0 0 6 0 +DIHEdral HPa HP0 Bda HPa 0 6 0 +DIHEdral HPa HP0 B0 F4 0 6 0 +DIHEdral HPa HP0 B0 F5 0 6 0 +DIHEdral HPa HP0 B0 H0 0 6 0 +DIHEdral HPa HP0 B0 H5 0 6 0 +DIHEdral HPa HP0 B0 Hd 0 6 0 +DIHEdral HPa HP0 B0 Ha 0 6 0 +DIHEdral HPa HP0 B0 Hda 0 6 0 +DIHEdral HPa HP0 B0 Bda 0 6 0 +DIHEdral HPa HP0 B0 B0 0 6 0 +DIHEdral HPa HP0 B0 Tda 0 6 0 +DIHEdral HPa HP0 B0 T0 0 6 0 +DIHEdral HPa HP0 B0 HP5 0 6 0 +DIHEdral HPa HP0 B0 HP0 0 6 0 +DIHEdral HPa HP0 B0 HPa 0 6 0 +DIHEdral HPa HP0 Tda F4 0 6 0 +DIHEdral HPa HP0 Tda F5 0 6 0 +DIHEdral HPa HP0 Tda H0 0 6 0 +DIHEdral HPa HP0 Tda H5 0 6 0 +DIHEdral HPa HP0 Tda Hd 0 6 0 +DIHEdral HPa HP0 Tda Ha 0 6 0 +DIHEdral HPa HP0 Tda Hda 0 6 0 +DIHEdral HPa HP0 Tda Bda 0 6 0 +DIHEdral HPa HP0 Tda B0 0 6 0 +DIHEdral HPa HP0 Tda Tda 0 6 0 +DIHEdral HPa HP0 Tda T0 0 6 0 +DIHEdral HPa HP0 Tda HP5 0 6 0 +DIHEdral HPa HP0 Tda HP0 0 6 0 +DIHEdral HPa HP0 Tda HPa 0 6 0 +DIHEdral HPa HP0 T0 F4 0 6 0 +DIHEdral HPa HP0 T0 F5 0 6 0 +DIHEdral HPa HP0 T0 H0 0 6 0 +DIHEdral HPa HP0 T0 H5 0 6 0 +DIHEdral HPa HP0 T0 Hd 0 6 0 +DIHEdral HPa HP0 T0 Ha 0 6 0 +DIHEdral HPa HP0 T0 Hda 0 6 0 +DIHEdral HPa HP0 T0 Bda 0 6 0 +DIHEdral HPa HP0 T0 B0 0 6 0 +DIHEdral HPa HP0 T0 Tda 0 6 0 +DIHEdral HPa HP0 T0 T0 0 6 0 +DIHEdral HPa HP0 T0 HP5 0 6 0 +DIHEdral HPa HP0 T0 HP0 0 6 0 +DIHEdral HPa HP0 T0 HPa 0 6 0 +DIHEdral HPa HP0 HP5 F4 0 6 0 +DIHEdral HPa HP0 HP5 F5 0 6 0 +DIHEdral HPa HP0 HP5 Bda 0 6 0 +DIHEdral HPa HP0 HP5 B0 0 6 0 +DIHEdral HPa HP0 HP5 Tda 0 6 0 +DIHEdral HPa HP0 HP5 T0 0 6 0 +DIHEdral HPa HP0 HP0 F4 0 6 0 +DIHEdral HPa HP0 HP0 F5 0 6 0 +DIHEdral HPa HP0 HP0 Bda 0 6 0 +DIHEdral HPa HP0 HP0 B0 0 6 0 +DIHEdral HPa HP0 HP0 Tda 0 6 0 +DIHEdral HPa HP0 HP0 T0 0 6 0 +DIHEdral HPa HP0 HPa F4 0 6 0 +DIHEdral HPa HP0 HPa F5 0 6 0 +DIHEdral HPa HP0 HPa Bda 0 6 0 +DIHEdral HPa HP0 HPa B0 0 6 0 +DIHEdral HPa HP0 HPa Tda 0 6 0 +DIHEdral HPa HP0 HPa T0 0 6 0 +DIHEdral HPa HPa F4 F4 0 6 0 +DIHEdral HPa HPa F4 F5 0 6 0 +DIHEdral HPa HPa F4 H0 0 6 0 +DIHEdral HPa HPa F4 H5 0 6 0 +DIHEdral HPa HPa F4 Hd 0 6 0 +DIHEdral HPa HPa F4 Ha 0 6 0 +DIHEdral HPa HPa F4 Hda 0 6 0 +DIHEdral HPa HPa F4 Bda 0 6 0 +DIHEdral HPa HPa F4 B0 0 6 0 +DIHEdral HPa HPa F4 Tda 0 6 0 +DIHEdral HPa HPa F4 T0 0 6 0 +DIHEdral HPa HPa F4 HP5 0 6 0 +DIHEdral HPa HPa F4 HP0 0 6 0 +DIHEdral HPa HPa F4 HPa 0 6 0 +DIHEdral HPa HPa F5 F4 0 6 0 +DIHEdral HPa HPa F5 F5 0 6 0 +DIHEdral HPa HPa F5 H0 0 6 0 +DIHEdral HPa HPa F5 H5 0 6 0 +DIHEdral HPa HPa F5 Hd 0 6 0 +DIHEdral HPa HPa F5 Ha 0 6 0 +DIHEdral HPa HPa F5 Hda 0 6 0 +DIHEdral HPa HPa F5 Bda 0 6 0 +DIHEdral HPa HPa F5 B0 0 6 0 +DIHEdral HPa HPa F5 Tda 0 6 0 +DIHEdral HPa HPa F5 T0 0 6 0 +DIHEdral HPa HPa F5 HP5 0 6 0 +DIHEdral HPa HPa F5 HP0 0 6 0 +DIHEdral HPa HPa F5 HPa 0 6 0 +DIHEdral HPa HPa H0 F4 0 6 0 +DIHEdral HPa HPa H0 F5 0 6 0 +DIHEdral HPa HPa H0 Bda 0 6 0 +DIHEdral HPa HPa H0 B0 0 6 0 +DIHEdral HPa HPa H0 Tda 0 6 0 +DIHEdral HPa HPa H0 T0 0 6 0 +DIHEdral HPa HPa H5 F4 0 6 0 +DIHEdral HPa HPa H5 F5 0 6 0 +DIHEdral HPa HPa H5 Bda 0 6 0 +DIHEdral HPa HPa H5 B0 0 6 0 +DIHEdral HPa HPa H5 Tda 0 6 0 +DIHEdral HPa HPa H5 T0 0 6 0 +DIHEdral HPa HPa Hd F4 0 6 0 +DIHEdral HPa HPa Hd F5 0 6 0 +DIHEdral HPa HPa Hd Bda 0 6 0 +DIHEdral HPa HPa Hd B0 0 6 0 +DIHEdral HPa HPa Hd Tda 0 6 0 +DIHEdral HPa HPa Hd T0 0 6 0 +DIHEdral HPa HPa Ha F4 0 6 0 +DIHEdral HPa HPa Ha F5 0 6 0 +DIHEdral HPa HPa Ha Bda 0 6 0 +DIHEdral HPa HPa Ha B0 0 6 0 +DIHEdral HPa HPa Ha Tda 0 6 0 +DIHEdral HPa HPa Ha T0 0 6 0 +DIHEdral HPa HPa Hda F4 0 6 0 +DIHEdral HPa HPa Hda F5 0 6 0 +DIHEdral HPa HPa Hda Bda 0 6 0 +DIHEdral HPa HPa Hda B0 0 6 0 +DIHEdral HPa HPa Hda Tda 0 6 0 +DIHEdral HPa HPa Hda T0 0 6 0 +DIHEdral HPa HPa Bda F4 0 6 0 +DIHEdral HPa HPa Bda F5 0 6 0 +DIHEdral HPa HPa Bda H0 0 6 0 +DIHEdral HPa HPa Bda H5 0 6 0 +DIHEdral HPa HPa Bda Hd 0 6 0 +DIHEdral HPa HPa Bda Ha 0 6 0 +DIHEdral HPa HPa Bda Hda 0 6 0 +DIHEdral HPa HPa Bda Bda 0 6 0 +DIHEdral HPa HPa Bda B0 0 6 0 +DIHEdral HPa HPa Bda Tda 0 6 0 +DIHEdral HPa HPa Bda T0 0 6 0 +DIHEdral HPa HPa Bda HP5 0 6 0 +DIHEdral HPa HPa Bda HP0 0 6 0 +DIHEdral HPa HPa Bda HPa 0 6 0 +DIHEdral HPa HPa B0 F4 0 6 0 +DIHEdral HPa HPa B0 F5 0 6 0 +DIHEdral HPa HPa B0 H0 0 6 0 +DIHEdral HPa HPa B0 H5 0 6 0 +DIHEdral HPa HPa B0 Hd 0 6 0 +DIHEdral HPa HPa B0 Ha 0 6 0 +DIHEdral HPa HPa B0 Hda 0 6 0 +DIHEdral HPa HPa B0 Bda 0 6 0 +DIHEdral HPa HPa B0 B0 0 6 0 +DIHEdral HPa HPa B0 Tda 0 6 0 +DIHEdral HPa HPa B0 T0 0 6 0 +DIHEdral HPa HPa B0 HP5 0 6 0 +DIHEdral HPa HPa B0 HP0 0 6 0 +DIHEdral HPa HPa B0 HPa 0 6 0 +DIHEdral HPa HPa Tda F4 0 6 0 +DIHEdral HPa HPa Tda F5 0 6 0 +DIHEdral HPa HPa Tda H0 0 6 0 +DIHEdral HPa HPa Tda H5 0 6 0 +DIHEdral HPa HPa Tda Hd 0 6 0 +DIHEdral HPa HPa Tda Ha 0 6 0 +DIHEdral HPa HPa Tda Hda 0 6 0 +DIHEdral HPa HPa Tda Bda 0 6 0 +DIHEdral HPa HPa Tda B0 0 6 0 +DIHEdral HPa HPa Tda Tda 0 6 0 +DIHEdral HPa HPa Tda T0 0 6 0 +DIHEdral HPa HPa Tda HP5 0 6 0 +DIHEdral HPa HPa Tda HP0 0 6 0 +DIHEdral HPa HPa Tda HPa 0 6 0 +DIHEdral HPa HPa T0 F4 0 6 0 +DIHEdral HPa HPa T0 F5 0 6 0 +DIHEdral HPa HPa T0 H0 0 6 0 +DIHEdral HPa HPa T0 H5 0 6 0 +DIHEdral HPa HPa T0 Hd 0 6 0 +DIHEdral HPa HPa T0 Ha 0 6 0 +DIHEdral HPa HPa T0 Hda 0 6 0 +DIHEdral HPa HPa T0 Bda 0 6 0 +DIHEdral HPa HPa T0 B0 0 6 0 +DIHEdral HPa HPa T0 Tda 0 6 0 +DIHEdral HPa HPa T0 T0 0 6 0 +DIHEdral HPa HPa T0 HP5 0 6 0 +DIHEdral HPa HPa T0 HP0 0 6 0 +DIHEdral HPa HPa T0 HPa 0 6 0 +DIHEdral HPa HPa HP5 F4 0 6 0 +DIHEdral HPa HPa HP5 F5 0 6 0 +DIHEdral HPa HPa HP5 Bda 0 6 0 +DIHEdral HPa HPa HP5 B0 0 6 0 +DIHEdral HPa HPa HP5 Tda 0 6 0 +DIHEdral HPa HPa HP5 T0 0 6 0 +DIHEdral HPa HPa HP0 F4 0 6 0 +DIHEdral HPa HPa HP0 F5 0 6 0 +DIHEdral HPa HPa HP0 Bda 0 6 0 +DIHEdral HPa HPa HP0 B0 0 6 0 +DIHEdral HPa HPa HP0 Tda 0 6 0 +DIHEdral HPa HPa HP0 T0 0 6 0 +DIHEdral HPa HPa HPa F4 0 6 0 +DIHEdral HPa HPa HPa F5 0 6 0 +DIHEdral HPa HPa HPa Bda 0 6 0 +DIHEdral HPa HPa HPa B0 0 6 0 +DIHEdral HPa HPa HPa Tda 0 6 0 +DIHEdral HPa HPa HPa T0 0 6 0 + +{* non-bonded parameters *} +! Adapted MARTINI Info +! +! levels of LJ interaction: +! kJ to kCal: mult by (1/4.178) +! +! (Kcal/mol) (a) +! O - supra attractive: (eps=1.340), s=4.7) +! I - attractive: (eps=1.197), s=4.7) +! II - almost attractive: (eps=1.077), s=4.7) +! III - semi attractive: (eps=0.957), s=4.7) +! IV - intermediate: (eps=0.838), s=4.7) +! V - almost intermediate: (eps=0.742), s=4.7) +! VI - semi repulsive: (eps=0.646), s=4.7) +! VII - almost repulsive: (eps=0.551), s=4.7) +! VIII - repulsive: (eps=0.479), s=4.7) +! IX - super repulsive: (eps=0.479), s=6.2) +! +! RINGS: for ring-ring interactions eps is reduced to 75%, sigma=4.3 +! +! eps sigma eps(1:4) sigma(1:4) +! (kcal/mol) (A) (kcal/mol) (A) +! ---------------------------------------------- +! Self-terms BACKBONE (14) +NONBonded F5 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded H0 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded Hd 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded Ha 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded Hda 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded Bda 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded Tda 1.340 4.7 1.340 4.7 ! supra attractive +NONBONded F4 1.197 4.7 1.197 4.7 ! attractive +NONBONded H5 1.197 4.7 1.197 4.7 ! attractive +NONBONded HP5 1.197 4.7 1.197 4.7 ! attractive +NONBONded HP0 1.197 4.7 1.197 4.7 ! attractive +NONBONded HPa 1.197 4.7 1.197 4.7 ! attractive +NONBONded B0 1.197 4.7 1.197 4.7 ! attractive +NONBONded T0 1.197 4.7 1.197 4.7 ! attractive +! +! Self-terms SIDECHAIN ring-ring (8) +NONBONded FC5 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded SC5 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded YC4 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded SC4 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded HC4 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded WC4 0.628 4.3 0.628 4.3 ! intermediate (ring) +NONBONded SP1 0.807 4.3 0.807 4.3 ! almost attractive (ring) +NONBONded SNd 0.717 4.3 0.717 4.3 ! semi attractive (ring) +! +! self-terms SIDECHAIN (17) +NONBONded RN0 0.838 4.7 0.838 4.7 ! intermediate +NONBONded AQd 0.838 4.7 0.838 4.7 ! intermediate +NONBONded Nda 1.077 4.7 1.077 4.7 ! almost attractive +NONBONded DQa 0.838 4.7 0.838 4.7 ! intermediate +NONBONded C5 0.838 4.7 0.838 4.7 ! intermediate +NONBONded QNda 1.077 4.7 1.077 4.7 ! almost attractive +NONBONded Qa 0.838 4.7 0.838 4.7 ! intermediate +NONBONded AC1 0.838 4.7 0.838 4.7 ! intermediate +NONBONded LC1 0.838 4.7 0.838 4.7 ! intermediate +NONBONded KC3 0.838 4.7 0.838 4.7 ! intermediate +NONBONded KQd 0.838 4.7 0.838 4.7 ! intermediate +NONBONded MC5 0.838 4.7 0.838 4.7 ! intermediate +NONBONded PC3 0.838 4.7 0.838 4.7 ! intermediate +NONBONded SN0 0.838 4.7 0.838 4.7 ! intermediate +NONBONded TNda 1.077 4.7 1.077 4.7 ! almost attractive +NONBONded AC2 0.838 4.7 0.838 4.7 ! intermediate +NONBONded SCd 0.000 0.0 0.000 0.0 ! no LJ interaction (fake bead) + +! cross-terms: important at least for ring particles +! Not sigma and eps anymore, but A & B +! A = 4 * sigma^12 * eps +! B = 4 * sigma^6 * eps +! (A) (B) +! O - supra attractive: (622786349.464) (57776.594) +! I - attractive: (556324821.126) (51610.882) +! II - almost attractive: (500552909.233) (46436.859) +! III - semi attractive: (444780997.341) (41262.836) +! IV - intermediate: (389473851.381) (36131.929) +! V - almost intermediate: (344856321.867) (31992.711) +! VI - semi repulsive: (300238792.354) (27853.492) +! VII - almost repulsive: (256086028.772) (23886.741) +! VIII - repulsive: (222622881.637) (20652.976) +! +! RINGS: for ring-ring interactions eps is reduced to 75%, sigma=4.3 +! +! O r - supra attractive: (160637715.805) (25411.879) ! ring +! I r - attractive: (143495034.193) (22700.014) ! ring +! II r - almost attractive: (129109567.106) (20424.324) ! ring +! III r - semi attractive: (114724100.019) (18148.633) ! ring +! IV r - intermediate: (100458511.824) (15891.906) ! ring +! V r - almost intermediate: (88950138.154) (14071.354) ! ring +! VI r - semi repulsive: (77441764.485) (12250.801) ! ring +! VII r - almost repulsive: (66053269.707) (10449.213) ! ring +! VIIIr - repulsive: (57421989.455) (9026.906) ! ring +! -------------------------------------------------------------------- +! +! BACKBONE BEADS +! +NBFIx F5 H0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Hd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Ha 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Hda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Bda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F5 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F5 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F5 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx F5 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F5 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F5 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F5 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx F5 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx F5 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F5 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F5 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F5 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx F5 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F5 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx H0 Hd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 Ha 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 Hda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 Bda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H0 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H0 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H0 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx H0 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H0 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H0 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H0 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx H0 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx H0 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H0 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H0 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H0 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx H0 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H0 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Hd Ha 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd Hda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd Bda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hd SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hd YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hd RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Hd AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hd DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hd QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hd Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Hd LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Hd KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hd MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hd PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hd SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Hd TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hd AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Ha Hda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha Bda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Ha SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Ha YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Ha RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Ha AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Ha DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Ha QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Ha Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Ha LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Ha KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Ha MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Ha PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Ha SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Ha TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Ha AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Hda Bda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hda SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hda YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hda RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Hda AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hda DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hda QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hda Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Hda LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Hda KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Hda MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Hda PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Hda SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Hda TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Hda AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Bda Tda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Bda SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Bda YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Bda RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Bda AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Bda DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Bda QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Bda Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Bda LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Bda KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Bda MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Bda PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Bda SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Bda TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Bda AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Tda F4 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Tda SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Tda YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Tda RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Tda AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Tda DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Tda QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Tda Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Tda LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx Tda KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Tda MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Tda PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Tda SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Tda TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx Tda AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx F4 H5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F4 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F4 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F4 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx F4 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F4 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F4 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F4 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx F4 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx F4 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx F4 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx F4 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx F4 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx F4 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx F4 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx H5 HP5 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H5 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H5 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H5 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx H5 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H5 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H5 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H5 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx H5 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx H5 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx H5 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx H5 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx H5 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx H5 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx H5 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx HP5 HP0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP5 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP5 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP5 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HP5 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP5 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP5 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP5 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HP5 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HP5 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP5 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP5 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP5 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HP5 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP5 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx HP0 HPa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP0 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP0 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP0 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HP0 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP0 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP0 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP0 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HP0 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HP0 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HP0 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HP0 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HP0 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HP0 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HP0 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx HPa B0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HPa SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HPa YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HPa RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HPa AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HPa DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HPa QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HPa Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HPa LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx HPa KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx HPa MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx HPa PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx HPa SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx HPa TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx HPa AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx B0 T0 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx B0 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx B0 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx B0 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx B0 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx B0 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx B0 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx B0 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx B0 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx B0 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx B0 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx B0 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx B0 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx B0 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx B0 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx T0 FC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx T0 SC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx T0 YC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 SC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 HC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 WC4 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 SP1 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx T0 SNd 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx T0 RN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx T0 AQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx T0 Nda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx T0 DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx T0 C5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx T0 QNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx T0 Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx T0 AC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx T0 LC1 222622881.637 20652.976 222622881.637 20652.976 ! repulsive +NBFIx T0 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx T0 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx T0 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx T0 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx T0 TNda 556324821.126 51610.882 556324821.126 51610.882 ! attractive +NBFIx T0 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +! SIDE CHAIN BEADS. NO RING-RING +! +NBFIx RN0 AQd 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx RN0 Nda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 DQa 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx RN0 C5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 QNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 Qa 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx RN0 AC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx RN0 LC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx RN0 KC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 KQd 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx RN0 MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 PC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 TNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx RN0 AC2 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +! +NBFIx AQd Nda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx AQd DQa 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx AQd C5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AQd QNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx AQd Qa 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx AQd AC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx AQd LC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx AQd KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx AQd KQd 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AQd MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AQd PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx AQd SN0 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx AQd TNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx AQd AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx Nda DQa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Nda C5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Nda QNda 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Nda Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Nda AC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Nda LC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Nda KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Nda KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Nda MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Nda PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Nda SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Nda TNda 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx Nda AC2 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +! +NBFIx DQa C5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx DQa QNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx DQa Qa 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx DQa AC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx DQa LC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx DQa KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx DQa KQd 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx DQa MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx DQa PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx DQa SN0 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx DQa TNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx DQa AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx C5 QNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 Qa 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 AC1 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx C5 LC1 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx C5 KC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 KQd 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 PC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 TNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx C5 AC2 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +! +NBFIx QNda Qa 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx QNda AC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx QNda LC1 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx QNda KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx QNda KQd 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx QNda MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx QNda PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx QNda SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx QNda TNda 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx QNda AC2 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +! +NBFIx Qa AC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx Qa LC1 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx Qa KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Qa KQd 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx Qa MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx Qa PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx Qa SN0 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx Qa TNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx Qa AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx AC1 LC1 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AC1 KC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AC1 KQd 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +NBFIx AC1 MC5 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +NBFIx AC1 PC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx AC1 SN0 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx AC1 TNda 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx AC1 AC2 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +! +NBFIx LC1 KC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx LC1 KQd 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx LC1 MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx LC1 PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx LC1 SN0 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx LC1 TNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx LC1 AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx KC3 KQd 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx KC3 MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx KC3 PC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx KC3 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx KC3 TNda 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx KC3 AC2 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +! +NBFIx KQd MC5 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx KQd PC3 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx KQd SN0 444780997.341 41262.836 444780997.341 41262.836 ! semi attractive +NBFIx KQd TNda 622786349.464 57776.594 622786349.464 57776.594 ! supra attractive +NBFIx KQd AC2 256086028.772 23886.741 256086028.772 23886.741 ! almost repulsive +! +NBFIx MC5 PC3 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx MC5 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx MC5 TNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx MC5 AC2 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +! +NBFIx PC3 SN0 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx PC3 TNda 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +NBFIx PC3 AC2 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +! +NBFIx SN0 TNda 389473851.381 36131.929 389473851.381 36131.929 ! intermediate +NBFIx SN0 AC2 344856321.867 31992.711 344856321.867 31992.711 ! almost intermediate +! +NBFIx TNda AC2 300238792.354 27853.492 300238792.354 27853.492 ! semi repulsive +! +! SIDE CHAIN BEADS. RING-RING +! +NBFIx FC5 SC5 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 YC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 SC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 SP1 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 HC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx FC5 SNd 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +! +NBFIx SC5 YC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC5 SC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC5 SP1 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC5 HC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC5 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC5 SNd 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +! +NBFIx YC4 SC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx YC4 SP1 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx YC4 HC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx YC4 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx YC4 SNd 88950138.154 14071.354 88950138.154 14071.354 ! almost intermediate (ring) +! +NBFIx SC4 SP1 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC4 HC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC4 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SC4 SNd 88950138.154 14071.354 88950138.154 14071.354 ! almost intermediate (ring) +! +NBFIx SP1 HC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SP1 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx SP1 SNd 129109567.106 20424.324 129109567.106 20424.324 ! almost attractive (ring) +! +NBFIx HC4 WC4 100458511.824 15891.906 100458511.824 15891.906 ! intermediate (ring) +NBFIx HC4 SNd 88950138.154 14071.354 88950138.154 14071.354 ! almost intermediate (ring) +! +NBFIx WC4 SNd 88950138.154 14071.354 88950138.154 14071.354 ! almost intermediate (ring) +! +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.top new file mode 100644 index 0000000000000000000000000000000000000000..7199f1eeec8ab0d8c196dc66edd8fb774e1eae52 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini-2-2.top @@ -0,0 +1,520 @@ +! Topology file based on Martinize.py CG script version 2.2p +! Author: Jorge Roel, OCT-2017 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +autogenerate + angles=false + dihedrals=false +end + +{* PROTEIN default masses *} +! Backbone types +MASS F4 72.00 +MASS F5 72.00 +MASS Tda 72.00 +MASS T0 72.00 +MASS Bda 72.00 +MASS B0 72.00 +MASS H0 72.00 +MASS H5 72.00 +MASS Hd 72.00 +MASS Ha 72.00 +MASS HPa 72.00 +MASS HP0 72.00 +MASS HP5 72.00 +MASS Hda 72.00 +! Side chain types +MASS AQd 45.00 +MASS DQa 45.00 +MASS C5 45.00 +MASS Qa 45.00 +MASS HC4 45.00 +MASS SP1 45.00 +MASS LC1 45.00 +MASS KQd 45.00 +MASS MC5 45.00 +MASS FC5 45.00 +MASS SC5 45.00 +MASS WC4 45.00 +MASS SNd 45.00 +MASS YC4 45.00 +MASS SC4 45.00 +MASS HC4 45.00 +MASS PC3 45.00 +MASS AC1 45.00 +MASS AC2 45.00 +! Special side chain beads +MASS RN0 72.00 +MASS Nda 45.00 +MASS QNda 45.00 +MASS KC3 72.00 +MASS SN0 45.00 +MASS TNda 45.00 +! Polarizable artificial bead +MASS SCd 36.00 + +RESIdue ALA + GROUp + ATOM BB type=F4 charge=0.000 end +END + + +RESIdue ARG + GROUPp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=RN0 charge=0.00 end + ATOM SC2 type=AQd charge=0.00 end + ATOM SCD1 type=SCd charge=1.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC2 SCD1 + + ANGLE BB SC1 SC2 +END + + +RESIdue ASN + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=Nda charge=0.00 end + ATOM SCD1 type=SCd charge=+0.46 end + ATOM SCD2 type=SCd charge=-0.46 end + + BOND BB SC1 + BOND SC1 SCD1 + BOND SC1 SCD2 + BOND SCD1 SCD2 +END + + +RESIdue ASP + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=DQa charge=0.00 end + ATOM SCD1 type=SCd charge=-1.00 end + + BOND BB SC1 + BOND SC1 SCD1 +END + + +RESIdue CYS + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=C5 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue GLN + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=QNda charge=0.00 end + ATOM SCD1 type=SCd charge=+0.46 end + ATOM SCD2 type=SCd charge=-0.46 end + + BOND BB SC1 + BOND SC1 SCD1 + BOND SC1 SCD2 + BOND SCD1 SCD2 +END + +RESIdue GLU + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=Qa charge=0.00 end + ATOM SCD1 type=SCd charge=-1.00 end + + BOND BB SC1 + BOND SC1 SCD1 +END + + +RESIdue GLY + GROUp + ATOM BB type=F5 charge=0.00 end +END + + +RESIdue NEP + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=HC4 charge=0.000 end + ATOM SC2 type=SP1 charge=-0.500 end + ATOM SC3 type=SP1 charge=-0.500 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue HIS + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=HC4 charge=0.00 end + ATOM SC2 type=SP1 charge=0.00 end + ATOM SC3 type=SP1 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue ILE + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=AC1 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue LEU + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=LC1 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue LYS + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=KC3 charge=0.00 end + ATOM SC2 type=KQd charge=0.00 end + ATOM SCD1 type=SCd charge=1.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC2 SCD1 + + ANGLE BB SC1 SC2 +END + +RESIdue MET + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=MC5 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue PHE + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=FC5 charge=0.00 end + ATOM SC2 type=SC5 charge=0.00 end + ATOM SC3 type=SC5 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue PRO + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=PC3 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue SER + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=SN0 charge=0.00 end + ATOM SCD1 type=SCd charge=+0.40 end + ATOM SCD2 type=SCd charge=-0.40 end + + BOND BB SC1 + BOND SC1 SCD1 + BOND SC1 SCD2 + BOND SCD1 SCD2 +END + +RESIdue THR + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=TNda charge=0.00 end + ATOM SCD1 type=SCd charge=+0.31 end + ATOM SCD2 type=SCd charge=-0.31 end + + BOND BB SC1 + BOND SC1 SCD1 + BOND SC1 SCD2 + BOND SCD1 SCD2 +END + + +RESIdue TRP + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=WC4 charge=0.00 end + ATOM SC2 type=SNd charge=0.00 end + ATOM SC3 type=SC5 charge=0.00 end + ATOM SC4 type SC5 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC3 SC4 + + DIHEdral BB SC2 SC3 SC1 + DIHEdral SC1 SC2 SC4 SC3 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue TYR + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=YC4 charge=0.00 end + ATOM SC2 type=SC4 charge=0.00 end + ATOM SC3 type=SP1 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue VAL + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=AC2 charge=0.00 end + + BOND BB SC1 +END + + +!------------------------------------------------------------------ + +PRESidue PTY1 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA1 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP1 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTH1 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTY2 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA2 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP2 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTH2 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTY3 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTA3 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTP3 + MODIFY ATOM BB TYPE=HP5 END +END + + +PRESidue PTH3 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY4 + MODIFY ATOM BB TYPE=Hd END +END + + +PRESidue PTA4 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP4 + MODIFY ATOM BB TYPE=HP0 END +END + + +PRESidue PTH4 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY5 + MODIFY ATOM BB TYPE=Ha END +END + + +PRESidue PTA5 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP5 + MODIFY ATOM BB TYPE=HPa END +END + + +PRESidue PTH5 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY6 + MODIFY ATOM BB TYPE=Hda END +END + + +PRESidue PTA6 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP6 + MODIFY ATOM BB TYPE=HP0 END +END + + +PRESidue PTH6 + MODIFY ATOM BB TYPE=H5 END +END + +PRESidue PTY7 + MODIFY ATOM BB TYPE=Bda END +END + + +PRESidue PTA7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTP7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTH7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTY8 + MODIFY ATOM BB TYPE=Tda END +END + + +PRESidue PTA8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTP8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTH8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTY9 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA9 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP9 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTH9 + MODIFY ATOM BB TYPE=F4 END +END + +PRESidue PEPT ! PEPTide bond link, for all + ! "*(-) - PEPT - (+)*: + add bond -BB +BB +END + +PRESidue DCGP + ! Delete bonds that are too long to exist + DELETE BOND -BB +BB +END {DCGP} + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.link new file mode 100644 index 0000000000000000000000000000000000000000..05853e43e8d962be87a17f9096db0b08d91a5102 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.link @@ -0,0 +1,1615 @@ +remarks file toppar/protein-CG-Martin.link +remarks +remarks this is a macro to define standard protein peptide bonds + + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link pept head - GLY tail + PRO end +link pept head - GLY tail + HYP end +link pept head - GLY tail + GLY end + +{ special link to GLY} +link pept head - ACE tail + GLY end +link pept head - ALA tail + GLY end +link pept head - CYS tail + GLY end +link pept head - CYM tail + GLY end +link pept head - CYF tail + GLY end +link pept head - CSP tail + GLY end +link pept head - ASP tail + GLY end +link pept head - ASH tail + GLY end +link pept head - GLU tail + GLY end +link pept head - GLH tail + GLY end +link pept head - PHE tail + GLY end +link pept head - HIS tail + GLY end +link pept head - NEP tail + GLY end +link pept head - ILE tail + GLY end +link pept head - LYS tail + GLY end +link pept head - ALY tail + GLY end +link pept head - MLY tail + GLY end +link pept head - MLZ tail + GLY end +link pept head - M3L tail + GLY end +link pept head - LEU tail + GLY end +link pept head - MET tail + GLY end +link pept head - MSE tail + GLY end ! +link pept head - ASN tail + GLY end +link pept head - PRO tail + GLY end +link pept head - GLN tail + GLY end +link pept head - ARG tail + GLY end +link pept head - SER tail + GLY end +link pept head - SEP tail + GLY end +link pept head - THR tail + GLY end +link pept head - THP tail + GLY end +link pept head - TOP tail + GLY end +link pept head - VAL tail + GLY end +link pept head - TRP tail + GLY end +link pept head - TYR tail + GLY end +link pept head - TYP tail + GLY end +link pept head - TYS tail + GLY end +link pept head - HYP tail + GLY end + +{ special link from GLY} +link pept head - GLY tail + ALA end +link pept head - GLY tail + CYS end +link pept head - GLY tail + CYM end +link pept head - GLY tail + CYF end +link pept head - GLY tail + CSP end +link pept head - GLY tail + ASP end +link pept head - GLY tail + ASH end +link pept head - GLY tail + GLU end +link pept head - GLY tail + GLH end +link pept head - GLY tail + PHE end +link pept head - GLY tail + HIS end +link pept head - GLY tail + NEP end +link pept head - GLY tail + ILE end +link pept head - GLY tail + LYS end +link pept head - GLY tail + ALY end +link pept head - GLY tail + MLY end +link pept head - GLY tail + MLZ end +link pept head - GLY tail + M3L end +link pept head - GLY tail + LEU end +link pept head - GLY tail + MET end +link pept head - GLY tail + MSE end +link pept head - GLY tail + ASN end +link pept head - GLY tail + PRO end +link pept head - GLY tail + GLN end +link pept head - GLY tail + ARG end +link pept head - GLY tail + SER end +link pept head - GLY tail + SEP end +link pept head - GLY tail + THR end +link pept head - GLY tail + THP end +link pept head - GLY tail + TOP end +link pept head - GLY tail + VAL end +link pept head - GLY tail + TRP end +link pept head - GLY tail + TYR end +link pept head - GLY tail + TYP end +link pept head - GLY tail + TYS end +link pept head - GLY tail + HYP end +link pept head - GLY tail + CTN end + +{ special link to PRO and HYP} +link pept head - ACE tail + PRO end +link pept head - ALA tail + PRO end +link pept head - CYS tail + PRO end +link pept head - CYM tail + PRO end +link pept head - CYF tail + PRO end +link pept head - CSP tail + PRO end +link pept head - ASP tail + PRO end +link pept head - ASH tail + PRO end +link pept head - GLU tail + PRO end +link pept head - GLH tail + PRO end +link pept head - PHE tail + PRO end +link pept head - HIS tail + PRO end +link pept head - NEP tail + PRO end +link pept head - ILE tail + PRO end +link pept head - LYS tail + PRO end +link pept head - ALY tail + PRO end +link pept head - MLY tail + PRO end +link pept head - MLZ tail + PRO end +link pept head - M3L tail + PRO end +link pept head - LEU tail + PRO end +link pept head - MET tail + PRO end +link pept head - MSE tail + PRO end +link pept head - ASN tail + PRO end +link pept head - PRO tail + PRO end +link pept head - GLN tail + PRO end +link pept head - ARG tail + PRO end +link pept head - SER tail + PRO end +link pept head - SEP tail + PRO end +link pept head - THR tail + PRO end +link pept head - THP tail + PRO end +link pept head - TOP tail + PRO end +link pept head - VAL tail + PRO end +link pept head - TRP tail + PRO end +link pept head - TYR tail + PRO end +link pept head - TYP tail + PRO end +link pept head - TYS tail + PRO end +link pept head - HYP tail + PRO end + +{ special link to PRO and HYP} +link pept head - ACE tail + HYP end +link pept head - ALA tail + HYP end +link pept head - CYS tail + HYP end +link pept head - CYM tail + HYP end +link pept head - CYF tail + HYP end +link pept head - CSP tail + HYP end +link pept head - ASP tail + HYP end +link pept head - ASH tail + HYP end +link pept head - GLU tail + HYP end +link pept head - GLH tail + HYP end +link pept head - PHE tail + HYP end +link pept head - HIS tail + HYP end +link pept head - NEP tail + HYP end +link pept head - ILE tail + HYP end +link pept head - LYS tail + HYP end +link pept head - ALY tail + HYP end +link pept head - MLY tail + HYP end +link pept head - MLZ tail + HYP end +link pept head - M3L tail + HYP end +link pept head - LEU tail + HYP end +link pept head - MET tail + HYP end +link pept head - MSE tail + HYP end +link pept head - ASN tail + HYP end +link pept head - PRO tail + HYP end +link pept head - GLN tail + HYP end +link pept head - ARG tail + HYP end +link pept head - SER tail + HYP end +link pept head - SEP tail + HYP end +link pept head - THR tail + HYP end +link pept head - THP tail + HYP end +link pept head - TOP tail + HYP end +link pept head - VAL tail + HYP end +link pept head - TRP tail + HYP end +link pept head - TYR tail + HYP end +link pept head - TYP tail + HYP end +link pept head - TYS tail + HYP end +link pept head - HYP tail + HYP end + +{ peptide linkages for ACE } +link pept head - ACE tail + ALA end +link pept head - ACE tail + CYS end +link pept head - ACE tail + CYM end +link pept head - ACE tail + CYF end +link pept head - ACE tail + CSP end +link pept head - ACE tail + ASP end +link pept head - ACE tail + ASH end +link pept head - ACE tail + GLU end +link pept head - ACE tail + GLH end +link pept head - ACE tail + PHE end +link pept head - ACE tail + HIS end +link pept head - ACE tail + NEP end +link pept head - ACE tail + ILE end +link pept head - ACE tail + LYS end +link pept head - ACE tail + ALY end +link pept head - ACE tail + MLY end +link pept head - ACE tail + MLZ end +link pept head - ACE tail + M3L end +link pept head - ACE tail + LEU end +link pept head - ACE tail + MET end +link pept head - ACE tail + MSE end +link pept head - ACE tail + ASN end +link pept head - ACE tail + PRO end +link pept head - ACE tail + GLN end +link pept head - ACE tail + ARG end +link pept head - ACE tail + SER end +link pept head - ACE tail + SEP end +link pept head - ACE tail + THR end +link pept head - ACE tail + THP end +link pept head - ACE tail + TOP end +link pept head - ACE tail + VAL end +link pept head - ACE tail + TRP end +link pept head - ACE tail + TYR end +link pept head - ACE tail + TYP end +link pept head - ACE tail + TYS end +link pept head - ACE tail + HYP end +link pept head - ACE tail + CTN end + +{ peptide linkages for ALA } +link pept head - ALA tail + ALA end +link pept head - ALA tail + CYS end +link pept head - ALA tail + CYM end +link pept head - ALA tail + CYF end +link pept head - ALA tail + CSP end +link pept head - ALA tail + ASP end +link pept head - ALA tail + ASH end +link pept head - ALA tail + GLU end +link pept head - ALA tail + GLH end +link pept head - ALA tail + PHE end +link pept head - ALA tail + HIS end +link pept head - ALA tail + NEP end +link pept head - ALA tail + ILE end +link pept head - ALA tail + LYS end +link pept head - ALA tail + ALY end +link pept head - ALA tail + MLY end +link pept head - ALA tail + MLZ end +link pept head - ALA tail + M3L end +link pept head - ALA tail + LEU end +link pept head - ALA tail + MET end +link pept head - ALA tail + MSE end +link pept head - ALA tail + ASN end +link pept head - ALA tail + PRO end +link pept head - ALA tail + GLN end +link pept head - ALA tail + ARG end +link pept head - ALA tail + SER end +link pept head - ALA tail + SEP end +link pept head - ALA tail + THR end +link pept head - ALA tail + THP end +link pept head - ALA tail + TOP end +link pept head - ALA tail + VAL end +link pept head - ALA tail + TRP end +link pept head - ALA tail + TYR end +link pept head - ALA tail + TYP end +link pept head - ALA tail + TYS end +link pept head - ALA tail + HYP end +link pept head - ALA tail + CTN end + +{ peptide linkages for CYS } +link pept head - CYS tail + ALA end +link pept head - CYS tail + CYS end +link pept head - CYS tail + CYM end +link pept head - CYS tail + CYF end +link pept head - CYS tail + CSP end +link pept head - CYS tail + ASP end +link pept head - CYS tail + ASH end +link pept head - CYS tail + GLU end +link pept head - CYS tail + GLH end +link pept head - CYS tail + PHE end +link pept head - CYS tail + HIS end +link pept head - CYS tail + NEP end +link pept head - CYS tail + ILE end +link pept head - CYS tail + LYS end +link pept head - CYS tail + ALY end +link pept head - CYS tail + MLY end +link pept head - CYS tail + MLZ end +link pept head - CYS tail + M3L end +link pept head - CYS tail + LEU end +link pept head - CYS tail + MET end +link pept head - CYS tail + MSE end +link pept head - CYS tail + ASN end +link pept head - CYS tail + PRO end +link pept head - CYS tail + GLN end +link pept head - CYS tail + ARG end +link pept head - CYS tail + SER end +link pept head - CYS tail + SEP end +link pept head - CYS tail + THR end +link pept head - CYS tail + THP end +link pept head - CYS tail + TOP end +link pept head - CYS tail + VAL end +link pept head - CYS tail + TRP end +link pept head - CYS tail + TYR end +link pept head - CYS tail + TYP end +link pept head - CYS tail + TYS end +link pept head - CYS tail + HYP end +link pept head - CYS tail + CTN end + +{ peptide linkages for CYM } +link pept head - CYM tail + ALA end +link pept head - CYM tail + CYS end +link pept head - CYM tail + CYM end +link pept head - CYM tail + CYF end +link pept head - CYM tail + CSP end +link pept head - CYM tail + ASP end +link pept head - CYM tail + ASH end +link pept head - CYM tail + GLU end +link pept head - CYM tail + GLH end +link pept head - CYM tail + PHE end +link pept head - CYM tail + HIS end +link pept head - CYM tail + NEP end +link pept head - CYM tail + ILE end +link pept head - CYM tail + LYS end +link pept head - CYM tail + ALY end +link pept head - CYM tail + MLY end +link pept head - 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TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + CTN end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + CTN end + + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.param new file mode 100644 index 0000000000000000000000000000000000000000..a20859dc5edf1161a0f99bd1b424ff076fd485e2 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.param @@ -0,0 +1,60603 @@ +! Parameter file based on Martinize.py CG script +! Author: Charleen Don, MAR-12 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +!evaluate ($kbon = 500) + +{* backbone bonds *} +BOND F4 F4 500 3.500 +BOND F4 F5 500 3.500 +BOND F4 Fa 500 3.500 +BOND F4 H0 500 3.500 +BOND F4 H5 500 3.500 +BOND F4 Hd 500 3.500 +BOND F4 Ha 500 3.500 +BOND F4 Hda 500 3.500 +BOND F4 Bda 500 3.500 +BOND F4 B0 500 3.500 +BOND F4 Tda 500 3.500 +BOND F4 T0 500 3.500 +BOND F4 HP5 500 3.500 +BOND F4 HP0 500 3.500 +BOND F4 HPa 500 3.500 +BOND F5 F5 500 3.500 +BOND F5 Fa 500 3.500 +BOND F5 H0 500 3.500 +BOND F5 H5 500 3.500 +BOND F5 Hd 500 3.500 +BOND F5 Ha 500 3.500 +BOND F5 Hda 500 3.500 +BOND F5 Bda 500 3.500 +BOND F5 B0 500 3.500 +BOND F5 Tda 500 3.500 +BOND F5 T0 500 3.500 +BOND F5 HP5 500 3.500 +BOND F5 HP0 500 3.500 +BOND F5 HPa 500 3.500 +BOND Fa Fa 500 3.500 +BOND Fa H0 500 3.500 +BOND Fa H5 500 3.500 +BOND Fa Hd 500 3.500 +BOND Fa Ha 500 3.500 +BOND Fa Hda 500 3.500 +BOND Fa Bda 500 3.500 +BOND Fa B0 500 3.500 +BOND Fa Tda 500 3.500 +BOND Fa T0 500 3.500 +BOND Fa HP5 500 3.500 +BOND Fa HP0 500 3.500 +BOND Fa HPa 500 3.500 +BOND H0 H0 500 3.500 +BOND H0 H5 500 3.500 +BOND H0 Hd 500 3.500 +BOND H0 Ha 500 3.500 +BOND H0 Hda 500 3.500 +BOND H0 Bda 500 3.500 +BOND H0 B0 500 3.500 +BOND H0 Tda 500 3.500 +BOND H0 T0 500 3.500 +BOND H0 HP5 500 3.500 +BOND H0 HP0 500 3.500 +BOND H0 HPa 500 3.500 +BOND H5 H5 500 3.500 +BOND H5 Hd 500 3.500 +BOND H5 Ha 500 3.500 +BOND H5 Hda 500 3.500 +BOND H5 Bda 500 3.500 +BOND H5 B0 500 3.500 +BOND H5 Tda 500 3.500 +BOND H5 T0 500 3.500 +BOND H5 HP5 500 3.500 +BOND H5 HP0 500 3.500 +BOND H5 HPa 500 3.500 +BOND Hd Hd 500 3.500 +BOND Hd Ha 500 3.500 +BOND Hd Hda 500 3.500 +BOND Hd Bda 500 3.500 +BOND Hd B0 500 3.500 +BOND Hd Tda 500 3.500 +BOND Hd T0 500 3.500 +BOND Hd HP5 500 3.500 +BOND Hd HP0 500 3.500 +BOND Hd HPa 500 3.500 +BOND Ha Ha 500 3.500 +BOND Ha Hda 500 3.500 +BOND Ha Bda 500 3.500 +BOND Ha B0 500 3.500 +BOND Ha Tda 500 3.500 +BOND Ha T0 500 3.500 +BOND Ha HP5 500 3.500 +BOND Ha HP0 500 3.500 +BOND Ha HPa 500 3.500 +BOND Hda Hda 500 3.500 +BOND Hda Bda 500 3.500 +BOND Hda B0 500 3.500 +BOND Hda Tda 500 3.500 +BOND Hda T0 500 3.500 +BOND Hda HP5 500 3.500 +BOND Hda HP0 500 3.500 +BOND Hda HPa 500 3.500 +BOND Bda Bda 500 3.500 +BOND Bda B0 500 3.500 +BOND Bda Tda 500 3.500 +BOND Bda T0 500 3.500 +BOND Bda HP5 500 3.500 +BOND Bda HP0 500 3.500 +BOND Bda HPa 500 3.500 +BOND B0 B0 500 3.500 +BOND B0 Tda 500 3.500 +BOND B0 T0 500 3.500 +BOND B0 HP5 500 3.500 +BOND B0 HP0 500 3.500 +BOND B0 HPa 500 3.500 +BOND Tda Tda 500 3.500 +BOND Tda T0 500 3.500 +BOND Tda HP5 500 3.500 +BOND Tda HP0 500 3.500 +BOND Tda HPa 500 3.500 +BOND T0 T0 500 3.500 +BOND T0 HP5 500 3.500 +BOND T0 HP0 500 3.500 +BOND T0 HPa 500 3.500 +BOND HP5 HP5 500 3.500 +BOND HP5 HP0 500 3.500 +BOND HP5 HPa 500 3.500 +BOND HP0 HP0 500 3.500 +BOND HP0 HPa 500 3.500 +BOND HPa HPa 500 3.500 + + +{* BS, backbone sidechain bonds *} +BOND F5 N0 500 3.300 +BOND F5 AP5 500 3.200 +BOND F5 Qa 500 3.200 +BOND F5 C5 500 3.100 +BOND F5 GP4 500 4.000 +BOND F5 GQa 500 4.000 +BOND F5 HC4 500 3.200 +BOND F5 AC1 500 3.100 +BOND F5 LC1 500 3.300 +BOND F5 C3 500 3.300 +BOND F5 MC5 500 4.000 +BOND F5 PC4 500 3.100 +BOND F5 AC2 500 3.000 +BOND F5 P1 500 2.500 +BOND F5 TP1 500 2.600 +BOND F5 SC4 500 3.000 +BOND F5 AC2 500 2.650 +BOND F5 TC4 500 3.200 + +BOND Bda N0 500 3.300 +BOND Bda AP5 500 3.200 +BOND Bda Qa 500 3.200 +BOND Bda C5 500 3.100 +BOND Bda GP4 500 4.000 +BOND Bda GQa 500 4.000 +BOND Bda HC4 500 3.200 +BOND Bda AC1 500 3.100 +BOND Bda LC1 500 3.300 +BOND Bda C3 500 3.300 +BOND Bda MC5 500 4.000 +BOND Bda PC4 500 3.100 +BOND Bda AC2 500 3.000 +BOND Bda P1 500 2.500 +BOND Bda TP1 500 2.600 +BOND Bda SC4 500 3.000 +BOND Bda AC2 500 2.650 +BOND Bda TC4 500 3.200 + +BOND H0 N0 500 3.300 +BOND H0 AP5 500 3.200 +BOND H0 Qa 500 3.200 +BOND H0 C5 500 3.100 +BOND H0 GP4 500 4.000 +BOND H0 GQa 500 4.000 +BOND H0 HC4 500 3.200 +BOND H0 AC1 500 3.100 +BOND H0 LC1 500 3.300 +BOND H0 C3 500 3.300 +BOND H0 MC5 500 4.000 +BOND H0 PC4 500 3.100 +BOND H0 AC2 500 3.000 +BOND H0 P1 500 2.500 +BOND H0 TP1 500 2.600 +BOND H0 SC4 500 3.000 +BOND H0 AC2 500 2.650 +BOND H0 TC4 500 3.200 +! +BOND Hd N0 500 3.300 +BOND Hd AP5 500 3.200 +BOND Hd Qa 500 3.200 +BOND Hd C5 500 3.100 +BOND Hd GP4 500 4.000 +BOND Hd GQa 500 4.000 +BOND Hd HC4 500 3.200 +BOND Hd AC1 500 3.100 +BOND Hd LC1 500 3.300 +BOND Hd C3 500 3.300 +BOND Hd MC5 500 4.000 +BOND Hd PC4 500 3.100 +BOND Hd AC2 500 3.000 +BOND Hd P1 500 2.500 +BOND Hd TP1 500 2.600 +BOND Hd SC4 500 3.000 +BOND Hd AC2 500 2.650 +BOND Hd TC4 500 3.200 +! +BOND Ha N0 500 3.300 +BOND Ha AP5 500 3.200 +BOND Ha Qa 500 3.200 +BOND Ha C5 500 3.100 +BOND Ha GP4 500 4.000 +BOND Ha GQa 500 4.000 +BOND Ha HC4 500 3.200 +BOND Ha AC1 500 3.100 +BOND Ha LC1 500 3.300 +BOND Ha C3 500 3.300 +BOND Ha MC5 500 4.000 +BOND Ha PC4 500 3.100 +BOND Ha AC2 500 3.000 +BOND Ha P1 500 2.500 +BOND Ha TP1 500 2.600 +BOND Ha SC4 500 3.000 +BOND Ha AC2 500 2.650 +BOND Ha TC4 500 3.200 +! +BOND Hda N0 500 3.300 +BOND Hda AP5 500 3.200 +BOND Hda Qa 500 3.200 +BOND Hda C5 500 3.100 +BOND Hda GP4 500 4.000 +BOND Hda GQa 500 4.000 +BOND Hda HC4 500 3.200 +BOND Hda AC1 500 3.100 +BOND Hda LC1 500 3.300 +BOND Hda C3 500 3.300 +BOND Hda MC5 500 4.000 +BOND Hda PC4 500 3.100 +BOND Hda AC2 500 3.000 +BOND Hda P1 500 2.500 +BOND Hda TP1 500 2.600 +BOND Hda SC4 500 3.000 +BOND Hda AC2 500 2.650 +BOND Hda TC4 500 3.200 +! +BOND Tda N0 500 3.300 +BOND Tda AP5 500 3.200 +BOND Tda Qa 500 3.200 +BOND Tda C5 500 3.100 +BOND Tda GP4 500 4.000 +BOND Tda GQa 500 4.000 +BOND Tda HC4 500 3.200 +BOND Tda AC1 500 3.100 +BOND Tda LC1 500 3.300 +BOND Tda C3 500 3.300 +BOND Tda MC5 500 4.000 +BOND Tda PC4 500 3.100 +BOND Tda AC2 500 3.000 +BOND Tda P1 500 2.500 +BOND Tda TP1 500 2.600 +BOND Tda SC4 500 3.000 +BOND Tda AC2 500 2.650 +BOND Tda TC4 500 3.200 +! Pro specific +BOND Fa AC2 500 3.000 +BOND B0 AC2 500 3.000 +BOND HP5 AC2 500 3.000 +BOND HP0 AC2 500 3.000 +BOND HPa AC2 500 3.000 +BOND T0 AC2 500 3.000 + + +{* SS, sidechain bonds *} +BOND N0 Qd 500 3.400 +BOND HC4 SC4 500 2.700 ! constraint +BOND HC4 SP1 500 2.700 ! constraint +BOND SP1 SP1 500 2.700 ! constraint +BOND C3 Qd 500 2.800 +BOND PC4 SC4 500 3.200 ! constraint +BOND SC4 SP1 500 2.700 ! constraint +BOND SC4 SC4 500 2.700 ! constraint +BOND TC4 SC4 500 2.700 ! constraint +BOND TC4 SP1 500 2.700 ! constraint + + +{* BBB, backbone angles *} +ANGLe F4 F4 F4 5.971 127 +ANGLe F4 F4 F5 5.971 127 +ANGLe F4 F4 Fa 5.971 127 +ANGLe F4 F4 H0 5.971 127 +ANGLe F4 F4 H5 5.971 127 +ANGLe F4 F4 Hd 5.971 127 +ANGLe F4 F4 Ha 5.971 127 +ANGLe F4 F4 Hda 5.971 127 +ANGLe F4 F4 Bda 5.971 127 +ANGLe F4 F4 B0 5.971 127 +ANGLe F4 F4 Tda 5.971 127 +ANGLe F4 F4 T0 5.971 127 +ANGLe F4 F4 HP5 5.971 127 +ANGLe F4 F4 HP0 5.971 127 +ANGLe F4 F4 HPa 5.971 127 +ANGLe F4 F5 F4 5.971 127 +ANGLe F4 F5 F5 5.971 127 +ANGLe F4 F5 Fa 5.971 127 +ANGLe F4 F5 H0 5.971 127 +ANGLe F4 F5 H5 5.971 127 +ANGLe F4 F5 Hd 5.971 127 +ANGLe F4 F5 Ha 5.971 127 +ANGLe F4 F5 Hda 5.971 127 +ANGLe F4 F5 Bda 5.971 127 +ANGLe F4 F5 B0 5.971 127 +ANGLe F4 F5 Tda 5.971 127 +ANGLe F4 F5 T0 5.971 127 +ANGLe F4 F5 HP5 5.971 127 +ANGLe F4 F5 HP0 5.971 127 +ANGLe F4 F5 HPa 5.971 127 +ANGLe F4 Fa F4 5.971 127 +ANGLe F4 Fa F5 5.971 127 +ANGLe F4 Fa Fa 5.971 127 +ANGLe F4 Fa H0 5.971 127 +ANGLe F4 Fa H5 5.971 127 +ANGLe F4 Fa Hd 5.971 127 +ANGLe F4 Fa Ha 5.971 127 +ANGLe F4 Fa Hda 5.971 127 +ANGLe F4 Fa Bda 5.971 127 +ANGLe F4 Fa B0 5.971 127 +ANGLe F4 Fa Tda 5.971 127 +ANGLe F4 Fa T0 5.971 127 +ANGLe F4 Fa HP5 5.971 127 +ANGLe F4 Fa HP0 5.971 127 +ANGLe F4 Fa HPa 5.971 127 +ANGLe F4 H0 F4 5.971 127 +ANGLe F4 H0 F5 5.971 127 +ANGLe F4 H0 Fa 5.971 127 +ANGLe F4 H0 H0 5.971 127 +ANGLe F4 H0 H5 5.971 127 +ANGLe F4 H0 Hd 5.971 127 +ANGLe F4 H0 Ha 5.971 127 +ANGLe F4 H0 Hda 5.971 127 +ANGLe F4 H0 Bda 5.971 127 +ANGLe F4 H0 B0 5.971 127 +ANGLe F4 H0 Tda 5.971 127 +ANGLe F4 H0 T0 5.971 127 +ANGLe F4 H0 HP5 5.971 127 +ANGLe F4 H0 HP0 5.971 127 +ANGLe F4 H0 HPa 5.971 127 +ANGLe F4 H5 F4 5.971 127 +ANGLe F4 H5 F5 5.971 127 +ANGLe F4 H5 Fa 5.971 127 +ANGLe F4 H5 H0 5.971 127 +ANGLe F4 H5 H5 5.971 127 +ANGLe F4 H5 Hd 5.971 127 +ANGLe F4 H5 Ha 5.971 127 +ANGLe F4 H5 Hda 5.971 127 +ANGLe F4 H5 Bda 5.971 127 +ANGLe F4 H5 B0 5.971 127 +ANGLe F4 H5 Tda 5.971 127 +ANGLe F4 H5 T0 5.971 127 +ANGLe F4 H5 HP5 5.971 127 +ANGLe F4 H5 HP0 5.971 127 +ANGLe F4 H5 HPa 5.971 127 +ANGLe F4 Hd F4 5.971 127 +ANGLe F4 Hd F5 5.971 127 +ANGLe F4 Hd Fa 5.971 127 +ANGLe F4 Hd H0 5.971 127 +ANGLe F4 Hd H5 5.971 127 +ANGLe F4 Hd Hd 5.971 127 +ANGLe F4 Hd Ha 5.971 127 +ANGLe F4 Hd Hda 5.971 127 +ANGLe F4 Hd Bda 5.971 127 +ANGLe F4 Hd B0 5.971 127 +ANGLe F4 Hd Tda 5.971 127 +ANGLe F4 Hd T0 5.971 127 +ANGLe F4 Hd HP5 5.971 127 +ANGLe F4 Hd HP0 5.971 127 +ANGLe F4 Hd HPa 5.971 127 +ANGLe F4 Ha F4 5.971 127 +ANGLe F4 Ha F5 5.971 127 +ANGLe F4 Ha Fa 5.971 127 +ANGLe F4 Ha H0 5.971 127 +ANGLe F4 Ha H5 5.971 127 +ANGLe F4 Ha Hd 5.971 127 +ANGLe F4 Ha Ha 5.971 127 +ANGLe F4 Ha Hda 5.971 127 +ANGLe F4 Ha Bda 5.971 127 +ANGLe F4 Ha B0 5.971 127 +ANGLe F4 Ha Tda 5.971 127 +ANGLe F4 Ha T0 5.971 127 +ANGLe F4 Ha HP5 5.971 127 +ANGLe F4 Ha HP0 5.971 127 +ANGLe F4 Ha HPa 5.971 127 +ANGLe F4 Hda F4 5.971 127 +ANGLe F4 Hda F5 5.971 127 +ANGLe F4 Hda Fa 5.971 127 +ANGLe F4 Hda H0 5.971 127 +ANGLe F4 Hda H5 5.971 127 +ANGLe F4 Hda Hd 5.971 127 +ANGLe F4 Hda Ha 5.971 127 +ANGLe F4 Hda Hda 5.971 127 +ANGLe F4 Hda Bda 5.971 127 +ANGLe F4 Hda B0 5.971 127 +ANGLe F4 Hda Tda 5.971 127 +ANGLe F4 Hda T0 5.971 127 +ANGLe F4 Hda HP5 5.971 127 +ANGLe F4 Hda HP0 5.971 127 +ANGLe F4 Hda HPa 5.971 127 +ANGLe F4 Bda F4 5.971 127 +ANGLe F4 Bda F5 5.971 127 +ANGLe F4 Bda Fa 5.971 127 +ANGLe F4 Bda H0 5.971 127 +ANGLe F4 Bda H5 5.971 127 +ANGLe F4 Bda Hd 5.971 127 +ANGLe F4 Bda Ha 5.971 127 +ANGLe F4 Bda Hda 5.971 127 +ANGLe F4 Bda Bda 5.971 127 +ANGLe F4 Bda B0 5.971 127 +ANGLe F4 Bda Tda 5.971 127 +ANGLe F4 Bda T0 5.971 127 +ANGLe F4 Bda HP5 5.971 127 +ANGLe F4 Bda HP0 5.971 127 +ANGLe F4 Bda HPa 5.971 127 +ANGLe F4 B0 F4 5.971 127 +ANGLe F4 B0 F5 5.971 127 +ANGLe F4 B0 Fa 5.971 127 +ANGLe F4 B0 H0 5.971 127 +ANGLe F4 B0 H5 5.971 127 +ANGLe F4 B0 Hd 5.971 127 +ANGLe F4 B0 Ha 5.971 127 +ANGLe F4 B0 Hda 5.971 127 +ANGLe F4 B0 Bda 5.971 127 +ANGLe F4 B0 B0 5.971 127 +ANGLe F4 B0 Tda 5.971 127 +ANGLe F4 B0 T0 5.971 127 +ANGLe F4 B0 HP5 5.971 127 +ANGLe F4 B0 HP0 5.971 127 +ANGLe F4 B0 HPa 5.971 127 +ANGLe F4 Tda F4 5.971 127 +ANGLe F4 Tda F5 5.971 127 +ANGLe F4 Tda Fa 5.971 127 +ANGLe F4 Tda H0 5.971 127 +ANGLe F4 Tda H5 5.971 127 +ANGLe F4 Tda Hd 5.971 127 +ANGLe F4 Tda Ha 5.971 127 +ANGLe F4 Tda Hda 5.971 127 +ANGLe F4 Tda Bda 5.971 127 +ANGLe F4 Tda B0 5.971 127 +ANGLe F4 Tda Tda 5.971 127 +ANGLe F4 Tda T0 5.971 127 +ANGLe F4 Tda HP5 5.971 127 +ANGLe F4 Tda HP0 5.971 127 +ANGLe F4 Tda HPa 5.971 127 +ANGLe F4 T0 F4 5.971 127 +ANGLe F4 T0 F5 5.971 127 +ANGLe F4 T0 Fa 5.971 127 +ANGLe F4 T0 H0 5.971 127 +ANGLe F4 T0 H5 5.971 127 +ANGLe F4 T0 Hd 5.971 127 +ANGLe F4 T0 Ha 5.971 127 +ANGLe F4 T0 Hda 5.971 127 +ANGLe F4 T0 Bda 5.971 127 +ANGLe F4 T0 B0 5.971 127 +ANGLe F4 T0 Tda 5.971 127 +ANGLe F4 T0 T0 5.971 127 +ANGLe F4 T0 HP5 5.971 127 +ANGLe F4 T0 HP0 5.971 127 +ANGLe F4 T0 HPa 5.971 127 +ANGLe F4 HP5 F4 5.971 127 +ANGLe F4 HP5 F5 5.971 127 +ANGLe F4 HP5 Fa 5.971 127 +ANGLe F4 HP5 H0 5.971 127 +ANGLe F4 HP5 H5 5.971 127 +ANGLe F4 HP5 Hd 5.971 127 +ANGLe F4 HP5 Ha 5.971 127 +ANGLe F4 HP5 Hda 5.971 127 +ANGLe F4 HP5 Bda 5.971 127 +ANGLe F4 HP5 B0 5.971 127 +ANGLe F4 HP5 Tda 5.971 127 +ANGLe F4 HP5 T0 5.971 127 +ANGLe F4 HP5 HP5 5.971 127 +ANGLe F4 HP5 HP0 5.971 127 +ANGLe F4 HP5 HPa 5.971 127 +ANGLe F4 HP0 F4 5.971 127 +ANGLe F4 HP0 F5 5.971 127 +ANGLe F4 HP0 Fa 5.971 127 +ANGLe F4 HP0 H0 5.971 127 +ANGLe F4 HP0 H5 5.971 127 +ANGLe F4 HP0 Hd 5.971 127 +ANGLe F4 HP0 Ha 5.971 127 +ANGLe F4 HP0 Hda 5.971 127 +ANGLe F4 HP0 Bda 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23.883 98 +ANGLe HP5 Tda H5 23.883 98 +ANGLe HP5 Tda Hd 23.883 98 +ANGLe HP5 Tda Ha 23.883 98 +ANGLe HP5 Tda Hda 23.883 98 +ANGLe HP5 Tda Bda 23.883 98 +ANGLe HP5 Tda B0 23.883 98 +ANGLe HP5 Tda Tda 23.883 98 +ANGLe HP5 Tda T0 23.883 98 +ANGLe HP5 Tda HP5 23.883 98 +ANGLe HP5 Tda HP0 23.883 98 +ANGLe HP5 Tda HPa 23.883 98 +ANGLe HP5 T0 F4 23.883 98 +ANGLe HP5 T0 F5 23.883 98 +ANGLe HP5 T0 Fa 23.883 98 +ANGLe HP5 T0 H0 23.883 98 +ANGLe HP5 T0 H5 23.883 98 +ANGLe HP5 T0 Hd 23.883 98 +ANGLe HP5 T0 Ha 23.883 98 +ANGLe HP5 T0 Hda 23.883 98 +ANGLe HP5 T0 Bda 23.883 98 +ANGLe HP5 T0 B0 23.883 98 +ANGLe HP5 T0 Tda 23.883 98 +ANGLe HP5 T0 T0 23.883 98 +ANGLe HP5 T0 HP5 23.883 98 +ANGLe HP5 T0 HP0 23.883 98 +ANGLe HP5 T0 HPa 23.883 98 +ANGLe HP5 HP5 F4 23.883 98 +ANGLe HP5 HP5 F5 23.883 98 +ANGLe HP5 HP5 Fa 23.883 98 +ANGLe HP5 HP5 H0 23.883 98 +ANGLe HP5 HP5 H5 23.883 98 +ANGLe HP5 HP5 Hd 23.883 98 +ANGLe HP5 HP5 Ha 23.883 98 +ANGLe HP5 HP5 Hda 23.883 98 +ANGLe HP5 HP5 Bda 23.883 98 +ANGLe HP5 HP5 B0 23.883 98 +ANGLe HP5 HP5 Tda 23.883 98 +ANGLe HP5 HP5 T0 23.883 98 +ANGLe HP5 HP5 HP5 23.883 98 +ANGLe HP5 HP5 HP0 23.883 98 +ANGLe HP5 HP5 HPa 23.883 98 +ANGLe HP5 HP0 F4 23.883 98 +ANGLe HP5 HP0 F5 23.883 98 +ANGLe HP5 HP0 Fa 23.883 98 +ANGLe HP5 HP0 H0 23.883 98 +ANGLe HP5 HP0 H5 23.883 98 +ANGLe HP5 HP0 Hd 23.883 98 +ANGLe HP5 HP0 Ha 23.883 98 +ANGLe HP5 HP0 Hda 23.883 98 +ANGLe HP5 HP0 Bda 23.883 98 +ANGLe HP5 HP0 B0 23.883 98 +ANGLe HP5 HP0 Tda 23.883 98 +ANGLe HP5 HP0 T0 23.883 98 +ANGLe HP5 HP0 HP5 23.883 98 +ANGLe HP5 HP0 HP0 23.883 98 +ANGLe HP5 HP0 HPa 23.883 98 +ANGLe HP5 HPa F4 23.883 98 +ANGLe HP5 HPa F5 23.883 98 +ANGLe HP5 HPa Fa 23.883 98 +ANGLe HP5 HPa H0 23.883 98 +ANGLe HP5 HPa H5 23.883 98 +ANGLe HP5 HPa Hd 23.883 98 +ANGLe HP5 HPa Ha 23.883 98 +ANGLe HP5 HPa Hda 23.883 98 +ANGLe HP5 HPa Bda 23.883 98 +ANGLe HP5 HPa B0 23.883 98 +ANGLe HP5 HPa Tda 23.883 98 +ANGLe HP5 HPa T0 23.883 98 +ANGLe HP5 HPa HP5 23.883 98 +ANGLe HP5 HPa HP0 23.883 98 +ANGLe HP5 HPa HPa 23.883 98 +ANGLe HP0 F4 F4 23.883 98 +ANGLe HP0 F4 F5 23.883 98 +ANGLe HP0 F4 Fa 23.883 98 +ANGLe HP0 F4 H0 23.883 98 +ANGLe HP0 F4 H5 23.883 98 +ANGLe HP0 F4 Hd 23.883 98 +ANGLe HP0 F4 Ha 23.883 98 +ANGLe HP0 F4 Hda 23.883 98 +ANGLe HP0 F4 Bda 23.883 98 +ANGLe HP0 F4 B0 23.883 98 +ANGLe HP0 F4 Tda 23.883 98 +ANGLe HP0 F4 T0 23.883 98 +ANGLe HP0 F4 HP5 23.883 98 +ANGLe HP0 F4 HP0 23.883 98 +ANGLe HP0 F4 HPa 23.883 98 +ANGLe HP0 F5 F4 23.883 98 +ANGLe HP0 F5 F5 23.883 98 +ANGLe HP0 F5 Fa 23.883 98 +ANGLe HP0 F5 H0 23.883 98 +ANGLe HP0 F5 H5 23.883 98 +ANGLe HP0 F5 Hd 23.883 98 +ANGLe HP0 F5 Ha 23.883 98 +ANGLe HP0 F5 Hda 23.883 98 +ANGLe HP0 F5 Bda 23.883 98 +ANGLe HP0 F5 B0 23.883 98 +ANGLe HP0 F5 Tda 23.883 98 +ANGLe HP0 F5 T0 23.883 98 +ANGLe HP0 F5 HP5 23.883 98 +ANGLe HP0 F5 HP0 23.883 98 +ANGLe HP0 F5 HPa 23.883 98 +ANGLe HP0 Fa F4 23.883 98 +ANGLe HP0 Fa F5 23.883 98 +ANGLe HP0 Fa Fa 23.883 98 +ANGLe HP0 Fa H0 23.883 98 +ANGLe HP0 Fa H5 23.883 98 +ANGLe HP0 Fa Hd 23.883 98 +ANGLe HP0 Fa Ha 23.883 98 +ANGLe HP0 Fa Hda 23.883 98 +ANGLe HP0 Fa Bda 23.883 98 +ANGLe HP0 Fa B0 23.883 98 +ANGLe HP0 Fa Tda 23.883 98 +ANGLe HP0 Fa T0 23.883 98 +ANGLe HP0 Fa HP5 23.883 98 +ANGLe HP0 Fa HP0 23.883 98 +ANGLe HP0 Fa HPa 23.883 98 +ANGLe HP0 H0 F4 23.883 98 +ANGLe HP0 H0 F5 23.883 98 +ANGLe HP0 H0 Fa 23.883 98 +ANGLe HP0 H0 H0 23.883 98 +ANGLe HP0 H0 H5 23.883 98 +ANGLe HP0 H0 Hd 23.883 98 +ANGLe HP0 H0 Ha 23.883 98 +ANGLe HP0 H0 Hda 23.883 98 +ANGLe HP0 H0 Bda 23.883 98 +ANGLe HP0 H0 B0 23.883 98 +ANGLe HP0 H0 Tda 23.883 98 +ANGLe HP0 H0 T0 23.883 98 +ANGLe HP0 H0 HP5 23.883 98 +ANGLe HP0 H0 HP0 23.883 98 +ANGLe HP0 H0 HPa 23.883 98 +ANGLe HP0 H5 F4 23.883 98 +ANGLe HP0 H5 F5 23.883 98 +ANGLe HP0 H5 Fa 23.883 98 +ANGLe HP0 H5 H0 23.883 98 +ANGLe HP0 H5 H5 23.883 98 +ANGLe HP0 H5 Hd 23.883 98 +ANGLe HP0 H5 Ha 23.883 98 +ANGLe HP0 H5 Hda 23.883 98 +ANGLe HP0 H5 Bda 23.883 98 +ANGLe HP0 H5 B0 23.883 98 +ANGLe HP0 H5 Tda 23.883 98 +ANGLe HP0 H5 T0 23.883 98 +ANGLe HP0 H5 HP5 23.883 98 +ANGLe HP0 H5 HP0 23.883 98 +ANGLe HP0 H5 HPa 23.883 98 +ANGLe HP0 Hd F4 23.883 98 +ANGLe HP0 Hd F5 23.883 98 +ANGLe HP0 Hd Fa 23.883 98 +ANGLe HP0 Hd H0 23.883 98 +ANGLe HP0 Hd H5 23.883 98 +ANGLe HP0 Hd Hd 23.883 98 +ANGLe HP0 Hd Ha 23.883 98 +ANGLe HP0 Hd Hda 23.883 98 +ANGLe HP0 Hd Bda 23.883 98 +ANGLe HP0 Hd B0 23.883 98 +ANGLe HP0 Hd Tda 23.883 98 +ANGLe HP0 Hd T0 23.883 98 +ANGLe HP0 Hd HP5 23.883 98 +ANGLe HP0 Hd HP0 23.883 98 +ANGLe HP0 Hd HPa 23.883 98 +ANGLe HP0 Ha F4 23.883 98 +ANGLe HP0 Ha F5 23.883 98 +ANGLe HP0 Ha Fa 23.883 98 +ANGLe HP0 Ha H0 23.883 98 +ANGLe HP0 Ha H5 23.883 98 +ANGLe HP0 Ha Hd 23.883 98 +ANGLe HP0 Ha Ha 23.883 98 +ANGLe HP0 Ha Hda 23.883 98 +ANGLe HP0 Ha Bda 23.883 98 +ANGLe HP0 Ha B0 23.883 98 +ANGLe HP0 Ha Tda 23.883 98 +ANGLe HP0 Ha T0 23.883 98 +ANGLe HP0 Ha HP5 23.883 98 +ANGLe HP0 Ha HP0 23.883 98 +ANGLe HP0 Ha HPa 23.883 98 +ANGLe HP0 Hda F4 23.883 98 +ANGLe HP0 Hda F5 23.883 98 +ANGLe HP0 Hda Fa 23.883 98 +ANGLe HP0 Hda H0 23.883 98 +ANGLe HP0 Hda H5 23.883 98 +ANGLe HP0 Hda Hd 23.883 98 +ANGLe HP0 Hda Ha 23.883 98 +ANGLe HP0 Hda Hda 23.883 98 +ANGLe HP0 Hda Bda 23.883 98 +ANGLe HP0 Hda B0 23.883 98 +ANGLe HP0 Hda Tda 23.883 98 +ANGLe HP0 Hda T0 23.883 98 +ANGLe HP0 Hda HP5 23.883 98 +ANGLe HP0 Hda HP0 23.883 98 +ANGLe HP0 Hda HPa 23.883 98 +ANGLe HP0 Bda F4 23.883 98 +ANGLe HP0 Bda F5 23.883 98 +ANGLe HP0 Bda Fa 23.883 98 +ANGLe HP0 Bda H0 23.883 98 +ANGLe HP0 Bda H5 23.883 98 +ANGLe HP0 Bda Hd 23.883 98 +ANGLe HP0 Bda Ha 23.883 98 +ANGLe HP0 Bda Hda 23.883 98 +ANGLe HP0 Bda Bda 23.883 98 +ANGLe HP0 Bda B0 23.883 98 +ANGLe HP0 Bda Tda 23.883 98 +ANGLe HP0 Bda T0 23.883 98 +ANGLe HP0 Bda HP5 23.883 98 +ANGLe HP0 Bda HP0 23.883 98 +ANGLe HP0 Bda HPa 23.883 98 +ANGLe HP0 B0 F4 23.883 98 +ANGLe HP0 B0 F5 23.883 98 +ANGLe HP0 B0 Fa 23.883 98 +ANGLe HP0 B0 H0 23.883 98 +ANGLe HP0 B0 H5 23.883 98 +ANGLe HP0 B0 Hd 23.883 98 +ANGLe HP0 B0 Ha 23.883 98 +ANGLe HP0 B0 Hda 23.883 98 +ANGLe HP0 B0 Bda 23.883 98 +ANGLe HP0 B0 B0 23.883 98 +ANGLe HP0 B0 Tda 23.883 98 +ANGLe HP0 B0 T0 23.883 98 +ANGLe HP0 B0 HP5 23.883 98 +ANGLe HP0 B0 HP0 23.883 98 +ANGLe HP0 B0 HPa 23.883 98 +ANGLe HP0 Tda F4 23.883 98 +ANGLe HP0 Tda F5 23.883 98 +ANGLe HP0 Tda Fa 23.883 98 +ANGLe HP0 Tda H0 23.883 98 +ANGLe HP0 Tda H5 23.883 98 +ANGLe HP0 Tda Hd 23.883 98 +ANGLe HP0 Tda Ha 23.883 98 +ANGLe HP0 Tda Hda 23.883 98 +ANGLe HP0 Tda Bda 23.883 98 +ANGLe HP0 Tda B0 23.883 98 +ANGLe HP0 Tda Tda 23.883 98 +ANGLe HP0 Tda T0 23.883 98 +ANGLe HP0 Tda HP5 23.883 98 +ANGLe HP0 Tda HP0 23.883 98 +ANGLe HP0 Tda HPa 23.883 98 +ANGLe HP0 T0 F4 23.883 98 +ANGLe HP0 T0 F5 23.883 98 +ANGLe HP0 T0 Fa 23.883 98 +ANGLe HP0 T0 H0 23.883 98 +ANGLe HP0 T0 H5 23.883 98 +ANGLe HP0 T0 Hd 23.883 98 +ANGLe HP0 T0 Ha 23.883 98 +ANGLe HP0 T0 Hda 23.883 98 +ANGLe HP0 T0 Bda 23.883 98 +ANGLe HP0 T0 B0 23.883 98 +ANGLe HP0 T0 Tda 23.883 98 +ANGLe HP0 T0 T0 23.883 98 +ANGLe HP0 T0 HP5 23.883 98 +ANGLe HP0 T0 HP0 23.883 98 +ANGLe HP0 T0 HPa 23.883 98 +ANGLe HP0 HP5 F4 23.883 98 +ANGLe HP0 HP5 F5 23.883 98 +ANGLe HP0 HP5 Fa 23.883 98 +ANGLe HP0 HP5 H0 23.883 98 +ANGLe HP0 HP5 H5 23.883 98 +ANGLe HP0 HP5 Hd 23.883 98 +ANGLe HP0 HP5 Ha 23.883 98 +ANGLe HP0 HP5 Hda 23.883 98 +ANGLe HP0 HP5 Bda 23.883 98 +ANGLe HP0 HP5 B0 23.883 98 +ANGLe HP0 HP5 Tda 23.883 98 +ANGLe HP0 HP5 T0 23.883 98 +ANGLe HP0 HP5 HP5 23.883 98 +ANGLe HP0 HP5 HP0 23.883 98 +ANGLe HP0 HP5 HPa 23.883 98 +ANGLe HP0 HP0 F4 23.883 98 +ANGLe HP0 HP0 F5 23.883 98 +ANGLe HP0 HP0 Fa 23.883 98 +ANGLe HP0 HP0 H0 23.883 98 +ANGLe HP0 HP0 H5 23.883 98 +ANGLe HP0 HP0 Hd 23.883 98 +ANGLe HP0 HP0 Ha 23.883 98 +ANGLe HP0 HP0 Hda 23.883 98 +ANGLe HP0 HP0 Bda 23.883 98 +ANGLe HP0 HP0 B0 23.883 98 +ANGLe HP0 HP0 Tda 23.883 98 +ANGLe HP0 HP0 T0 23.883 98 +ANGLe HP0 HP0 HP5 23.883 98 +ANGLe HP0 HP0 HP0 23.883 98 +ANGLe HP0 HP0 HPa 23.883 98 +ANGLe HP0 HPa F4 23.883 98 +ANGLe HP0 HPa F5 23.883 98 +ANGLe HP0 HPa Fa 23.883 98 +ANGLe HP0 HPa H0 23.883 98 +ANGLe HP0 HPa H5 23.883 98 +ANGLe HP0 HPa Hd 23.883 98 +ANGLe HP0 HPa Ha 23.883 98 +ANGLe HP0 HPa Hda 23.883 98 +ANGLe HP0 HPa Bda 23.883 98 +ANGLe HP0 HPa B0 23.883 98 +ANGLe HP0 HPa Tda 23.883 98 +ANGLe HP0 HPa T0 23.883 98 +ANGLe HP0 HPa HP5 23.883 98 +ANGLe HP0 HPa HP0 23.883 98 +ANGLe HP0 HPa HPa 23.883 98 +ANGLe HPa F4 F4 23.883 98 +ANGLe HPa F4 F5 23.883 98 +ANGLe HPa F4 Fa 23.883 98 +ANGLe HPa F4 H0 23.883 98 +ANGLe HPa F4 H5 23.883 98 +ANGLe HPa F4 Hd 23.883 98 +ANGLe HPa F4 Ha 23.883 98 +ANGLe HPa F4 Hda 23.883 98 +ANGLe HPa F4 Bda 23.883 98 +ANGLe HPa F4 B0 23.883 98 +ANGLe HPa F4 Tda 23.883 98 +ANGLe HPa F4 T0 23.883 98 +ANGLe HPa F4 HP5 23.883 98 +ANGLe HPa F4 HP0 23.883 98 +ANGLe HPa F4 HPa 23.883 98 +ANGLe HPa F5 F4 23.883 98 +ANGLe HPa F5 F5 23.883 98 +ANGLe HPa F5 Fa 23.883 98 +ANGLe HPa F5 H0 23.883 98 +ANGLe HPa F5 H5 23.883 98 +ANGLe HPa F5 Hd 23.883 98 +ANGLe HPa F5 Ha 23.883 98 +ANGLe HPa F5 Hda 23.883 98 +ANGLe HPa F5 Bda 23.883 98 +ANGLe HPa F5 B0 23.883 98 +ANGLe HPa F5 Tda 23.883 98 +ANGLe HPa F5 T0 23.883 98 +ANGLe HPa F5 HP5 23.883 98 +ANGLe HPa F5 HP0 23.883 98 +ANGLe HPa F5 HPa 23.883 98 +ANGLe HPa Fa F4 23.883 98 +ANGLe HPa Fa F5 23.883 98 +ANGLe HPa Fa Fa 23.883 98 +ANGLe HPa Fa H0 23.883 98 +ANGLe HPa Fa H5 23.883 98 +ANGLe HPa Fa Hd 23.883 98 +ANGLe HPa Fa Ha 23.883 98 +ANGLe HPa Fa Hda 23.883 98 +ANGLe HPa Fa Bda 23.883 98 +ANGLe HPa Fa B0 23.883 98 +ANGLe HPa Fa Tda 23.883 98 +ANGLe HPa Fa T0 23.883 98 +ANGLe HPa Fa HP5 23.883 98 +ANGLe HPa Fa HP0 23.883 98 +ANGLe HPa Fa HPa 23.883 98 +ANGLe HPa H0 F4 23.883 98 +ANGLe HPa H0 F5 23.883 98 +ANGLe HPa H0 Fa 23.883 98 +ANGLe HPa H0 H0 23.883 98 +ANGLe HPa H0 H5 23.883 98 +ANGLe HPa H0 Hd 23.883 98 +ANGLe HPa H0 Ha 23.883 98 +ANGLe HPa H0 Hda 23.883 98 +ANGLe HPa H0 Bda 23.883 98 +ANGLe HPa H0 B0 23.883 98 +ANGLe HPa H0 Tda 23.883 98 +ANGLe HPa H0 T0 23.883 98 +ANGLe HPa H0 HP5 23.883 98 +ANGLe HPa H0 HP0 23.883 98 +ANGLe HPa H0 HPa 23.883 98 +ANGLe HPa H5 F4 23.883 98 +ANGLe HPa H5 F5 23.883 98 +ANGLe HPa H5 Fa 23.883 98 +ANGLe HPa H5 H0 23.883 98 +ANGLe HPa H5 H5 23.883 98 +ANGLe HPa H5 Hd 23.883 98 +ANGLe HPa H5 Ha 23.883 98 +ANGLe HPa H5 Hda 23.883 98 +ANGLe HPa H5 Bda 23.883 98 +ANGLe HPa H5 B0 23.883 98 +ANGLe HPa H5 Tda 23.883 98 +ANGLe HPa H5 T0 23.883 98 +ANGLe HPa H5 HP5 23.883 98 +ANGLe HPa H5 HP0 23.883 98 +ANGLe HPa H5 HPa 23.883 98 +ANGLe HPa Hd F4 23.883 98 +ANGLe HPa Hd F5 23.883 98 +ANGLe HPa Hd Fa 23.883 98 +ANGLe HPa Hd H0 23.883 98 +ANGLe HPa Hd H5 23.883 98 +ANGLe HPa Hd Hd 23.883 98 +ANGLe HPa Hd Ha 23.883 98 +ANGLe HPa Hd Hda 23.883 98 +ANGLe HPa Hd Bda 23.883 98 +ANGLe HPa Hd B0 23.883 98 +ANGLe HPa Hd Tda 23.883 98 +ANGLe HPa Hd T0 23.883 98 +ANGLe HPa Hd HP5 23.883 98 +ANGLe HPa Hd HP0 23.883 98 +ANGLe HPa Hd HPa 23.883 98 +ANGLe HPa Ha F4 23.883 98 +ANGLe HPa Ha F5 23.883 98 +ANGLe HPa Ha Fa 23.883 98 +ANGLe HPa Ha H0 23.883 98 +ANGLe HPa Ha H5 23.883 98 +ANGLe HPa Ha Hd 23.883 98 +ANGLe HPa Ha Ha 23.883 98 +ANGLe HPa Ha Hda 23.883 98 +ANGLe HPa Ha Bda 23.883 98 +ANGLe HPa Ha B0 23.883 98 +ANGLe HPa Ha Tda 23.883 98 +ANGLe HPa Ha T0 23.883 98 +ANGLe HPa Ha HP5 23.883 98 +ANGLe HPa Ha HP0 23.883 98 +ANGLe HPa Ha HPa 23.883 98 +ANGLe HPa Hda F4 23.883 98 +ANGLe HPa Hda F5 23.883 98 +ANGLe HPa Hda Fa 23.883 98 +ANGLe HPa Hda H0 23.883 98 +ANGLe HPa Hda H5 23.883 98 +ANGLe HPa Hda Hd 23.883 98 +ANGLe HPa Hda Ha 23.883 98 +ANGLe HPa Hda Hda 23.883 98 +ANGLe HPa Hda Bda 23.883 98 +ANGLe HPa Hda B0 23.883 98 +ANGLe HPa Hda Tda 23.883 98 +ANGLe HPa Hda T0 23.883 98 +ANGLe HPa Hda HP5 23.883 98 +ANGLe HPa Hda HP0 23.883 98 +ANGLe HPa Hda HPa 23.883 98 +ANGLe HPa Bda F4 23.883 98 +ANGLe HPa Bda F5 23.883 98 +ANGLe HPa Bda Fa 23.883 98 +ANGLe HPa Bda H0 23.883 98 +ANGLe HPa Bda H5 23.883 98 +ANGLe HPa Bda Hd 23.883 98 +ANGLe HPa Bda Ha 23.883 98 +ANGLe HPa Bda Hda 23.883 98 +ANGLe HPa Bda Bda 23.883 98 +ANGLe HPa Bda B0 23.883 98 +ANGLe HPa Bda Tda 23.883 98 +ANGLe HPa Bda T0 23.883 98 +ANGLe HPa Bda HP5 23.883 98 +ANGLe HPa Bda HP0 23.883 98 +ANGLe HPa Bda HPa 23.883 98 +ANGLe HPa B0 F4 23.883 98 +ANGLe HPa B0 F5 23.883 98 +ANGLe HPa B0 Fa 23.883 98 +ANGLe HPa B0 H0 23.883 98 +ANGLe HPa B0 H5 23.883 98 +ANGLe HPa B0 Hd 23.883 98 +ANGLe HPa B0 Ha 23.883 98 +ANGLe HPa B0 Hda 23.883 98 +ANGLe HPa B0 Bda 23.883 98 +ANGLe HPa B0 B0 23.883 98 +ANGLe HPa B0 Tda 23.883 98 +ANGLe HPa B0 T0 23.883 98 +ANGLe HPa B0 HP5 23.883 98 +ANGLe HPa B0 HP0 23.883 98 +ANGLe HPa B0 HPa 23.883 98 +ANGLe HPa Tda F4 23.883 98 +ANGLe HPa Tda F5 23.883 98 +ANGLe HPa Tda Fa 23.883 98 +ANGLe HPa Tda H0 23.883 98 +ANGLe HPa Tda H5 23.883 98 +ANGLe HPa Tda Hd 23.883 98 +ANGLe HPa Tda Ha 23.883 98 +ANGLe HPa Tda Hda 23.883 98 +ANGLe HPa Tda Bda 23.883 98 +ANGLe HPa Tda B0 23.883 98 +ANGLe HPa Tda Tda 23.883 98 +ANGLe HPa Tda T0 23.883 98 +ANGLe HPa Tda HP5 23.883 98 +ANGLe HPa Tda HP0 23.883 98 +ANGLe HPa Tda HPa 23.883 98 +ANGLe HPa T0 F4 23.883 98 +ANGLe HPa T0 F5 23.883 98 +ANGLe HPa T0 Fa 23.883 98 +ANGLe HPa T0 H0 23.883 98 +ANGLe HPa T0 H5 23.883 98 +ANGLe HPa T0 Hd 23.883 98 +ANGLe HPa T0 Ha 23.883 98 +ANGLe HPa T0 Hda 23.883 98 +ANGLe HPa T0 Bda 23.883 98 +ANGLe HPa T0 B0 23.883 98 +ANGLe HPa T0 Tda 23.883 98 +ANGLe HPa T0 T0 23.883 98 +ANGLe HPa T0 HP5 23.883 98 +ANGLe HPa T0 HP0 23.883 98 +ANGLe HPa T0 HPa 23.883 98 +ANGLe HPa HP5 F4 23.883 98 +ANGLe HPa HP5 F5 23.883 98 +ANGLe HPa HP5 Fa 23.883 98 +ANGLe HPa HP5 H0 23.883 98 +ANGLe HPa HP5 H5 23.883 98 +ANGLe HPa HP5 Hd 23.883 98 +ANGLe HPa HP5 Ha 23.883 98 +ANGLe HPa HP5 Hda 23.883 98 +ANGLe HPa HP5 Bda 23.883 98 +ANGLe HPa HP5 B0 23.883 98 +ANGLe HPa HP5 Tda 23.883 98 +ANGLe HPa HP5 T0 23.883 98 +ANGLe HPa HP5 HP5 23.883 98 +ANGLe HPa HP5 HP0 23.883 98 +ANGLe HPa HP5 HPa 23.883 98 +ANGLe HPa HP0 F4 23.883 98 +ANGLe HPa HP0 F5 23.883 98 +ANGLe HPa HP0 Fa 23.883 98 +ANGLe HPa HP0 H0 23.883 98 +ANGLe HPa HP0 H5 23.883 98 +ANGLe HPa HP0 Hd 23.883 98 +ANGLe HPa HP0 Ha 23.883 98 +ANGLe HPa HP0 Hda 23.883 98 +ANGLe HPa HP0 Bda 23.883 98 +ANGLe HPa HP0 B0 23.883 98 +ANGLe HPa HP0 Tda 23.883 98 +ANGLe HPa HP0 T0 23.883 98 +ANGLe HPa HP0 HP5 23.883 98 +ANGLe HPa HP0 HP0 23.883 98 +ANGLe HPa HP0 HPa 23.883 98 +ANGLe HPa HPa F4 23.883 98 +ANGLe HPa HPa F5 23.883 98 +ANGLe HPa HPa Fa 23.883 98 +ANGLe HPa HPa H0 23.883 98 +ANGLe HPa HPa H5 23.883 98 +ANGLe HPa HPa Hd 23.883 98 +ANGLe HPa HPa Ha 23.883 98 +ANGLe HPa HPa Hda 23.883 98 +ANGLe HPa HPa Bda 23.883 98 +ANGLe HPa HPa B0 23.883 98 +ANGLe HPa HPa Tda 23.883 98 +ANGLe HPa HPa T0 23.883 98 +ANGLe HPa HPa HP5 23.883 98 +ANGLe HPa HPa HP0 23.883 98 +ANGLe HPa HPa HPa 23.883 98 + + +{* BBS angles *} +ANGLe F4 F4 AC1 5.971 100 +ANGLe F4 F5 AC1 5.971 100 +ANGLe F4 Fa AC1 5.971 100 +ANGLe F4 H0 AC1 5.971 100 +ANGLe F4 H5 AC1 5.971 100 +ANGLe F4 Hd AC1 5.971 100 +ANGLe F4 Ha AC1 5.971 100 +ANGLe F4 Hda AC1 5.971 100 +ANGLe F4 Bda AC1 5.971 100 +ANGLe F4 B0 AC1 5.971 100 +ANGLe F4 Tda AC1 5.971 100 +ANGLe F4 T0 AC1 5.971 100 +ANGLe F4 HP5 AC1 5.971 100 +ANGLe F4 HP0 AC1 5.971 100 +ANGLe F4 HPa AC1 5.971 100 +ANGLe F5 F4 AC1 5.971 100 +ANGLe F5 F5 AC1 5.971 100 +ANGLe F5 Fa AC1 5.971 100 +ANGLe F5 H0 AC1 5.971 100 +ANGLe F5 H5 AC1 5.971 100 +ANGLe F5 Hd AC1 5.971 100 +ANGLe F5 Ha AC1 5.971 100 +ANGLe F5 Hda AC1 5.971 100 +ANGLe F5 Bda AC1 5.971 100 +ANGLe F5 B0 AC1 5.971 100 +ANGLe F5 Tda AC1 5.971 100 +ANGLe F5 T0 AC1 5.971 100 +ANGLe F5 HP5 AC1 5.971 100 +ANGLe F5 HP0 AC1 5.971 100 +ANGLe F5 HPa AC1 5.971 100 +ANGLe Fa F4 AC1 5.971 100 +ANGLe Fa F5 AC1 5.971 100 +ANGLe Fa Fa AC1 5.971 100 +ANGLe Fa H0 AC1 5.971 100 +ANGLe Fa H5 AC1 5.971 100 +ANGLe Fa Hd AC1 5.971 100 +ANGLe Fa Ha AC1 5.971 100 +ANGLe Fa Hda AC1 5.971 100 +ANGLe Fa Bda AC1 5.971 100 +ANGLe Fa B0 AC1 5.971 100 +ANGLe Fa Tda AC1 5.971 100 +ANGLe Fa T0 AC1 5.971 100 +ANGLe Fa HP5 AC1 5.971 100 +ANGLe Fa HP0 AC1 5.971 100 +ANGLe Fa HPa AC1 5.971 100 +ANGLe H0 F4 AC1 5.971 100 +ANGLe H0 F5 AC1 5.971 100 +ANGLe H0 Fa AC1 5.971 100 +ANGLe H0 H0 AC1 5.971 100 +ANGLe H0 H5 AC1 5.971 100 +ANGLe H0 Hd AC1 5.971 100 +ANGLe H0 Ha AC1 5.971 100 +ANGLe H0 Hda AC1 5.971 100 +ANGLe H0 Bda AC1 5.971 100 +ANGLe H0 B0 AC1 5.971 100 +ANGLe H0 Tda AC1 5.971 100 +ANGLe H0 T0 AC1 5.971 100 +ANGLe H0 HP5 AC1 5.971 100 +ANGLe H0 HP0 AC1 5.971 100 +ANGLe H0 HPa AC1 5.971 100 +ANGLe H5 F4 AC1 5.971 100 +ANGLe H5 F5 AC1 5.971 100 +ANGLe H5 Fa AC1 5.971 100 +ANGLe H5 H0 AC1 5.971 100 +ANGLe H5 H5 AC1 5.971 100 +ANGLe H5 Hd AC1 5.971 100 +ANGLe H5 Ha AC1 5.971 100 +ANGLe H5 Hda AC1 5.971 100 +ANGLe H5 Bda AC1 5.971 100 +ANGLe H5 B0 AC1 5.971 100 +ANGLe H5 Tda AC1 5.971 100 +ANGLe H5 T0 AC1 5.971 100 +ANGLe H5 HP5 AC1 5.971 100 +ANGLe H5 HP0 AC1 5.971 100 +ANGLe H5 HPa AC1 5.971 100 +ANGLe Hd F4 AC1 5.971 100 +ANGLe Hd F5 AC1 5.971 100 +ANGLe Hd Fa AC1 5.971 100 +ANGLe Hd H0 AC1 5.971 100 +ANGLe Hd H5 AC1 5.971 100 +ANGLe Hd Hd AC1 5.971 100 +ANGLe Hd Ha AC1 5.971 100 +ANGLe Hd Hda AC1 5.971 100 +ANGLe Hd Bda AC1 5.971 100 +ANGLe Hd B0 AC1 5.971 100 +ANGLe Hd Tda AC1 5.971 100 +ANGLe Hd T0 AC1 5.971 100 +ANGLe Hd HP5 AC1 5.971 100 +ANGLe Hd HP0 AC1 5.971 100 +ANGLe 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5.971 100 +ANGLe Tda T0 AC1 5.971 100 +ANGLe Tda HP5 AC1 5.971 100 +ANGLe Tda HP0 AC1 5.971 100 +ANGLe Tda HPa AC1 5.971 100 +ANGLe T0 F4 AC1 5.971 100 +ANGLe T0 F5 AC1 5.971 100 +ANGLe T0 Fa AC1 5.971 100 +ANGLe T0 H0 AC1 5.971 100 +ANGLe T0 H5 AC1 5.971 100 +ANGLe T0 Hd AC1 5.971 100 +ANGLe T0 Ha AC1 5.971 100 +ANGLe T0 Hda AC1 5.971 100 +ANGLe T0 Bda AC1 5.971 100 +ANGLe T0 B0 AC1 5.971 100 +ANGLe T0 Tda AC1 5.971 100 +ANGLe T0 T0 AC1 5.971 100 +ANGLe T0 HP5 AC1 5.971 100 +ANGLe T0 HP0 AC1 5.971 100 +ANGLe T0 HPa AC1 5.971 100 +ANGLe HP5 F4 AC1 5.971 100 +ANGLe HP5 F5 AC1 5.971 100 +ANGLe HP5 Fa AC1 5.971 100 +ANGLe HP5 H0 AC1 5.971 100 +ANGLe HP5 H5 AC1 5.971 100 +ANGLe HP5 Hd AC1 5.971 100 +ANGLe HP5 Ha AC1 5.971 100 +ANGLe HP5 Hda AC1 5.971 100 +ANGLe HP5 Bda AC1 5.971 100 +ANGLe HP5 B0 AC1 5.971 100 +ANGLe HP5 Tda AC1 5.971 100 +ANGLe HP5 T0 AC1 5.971 100 +ANGLe HP5 HP5 AC1 5.971 100 +ANGLe HP5 HP0 AC1 5.971 100 +ANGLe HP5 HPa AC1 5.971 100 +ANGLe HP0 F4 AC1 5.971 100 +ANGLe HP0 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100 +ANGLe F4 Hda AC2 5.971 100 +ANGLe F4 Bda AC2 5.971 100 +ANGLe F4 B0 AC2 5.971 100 +ANGLe F4 Tda AC2 5.971 100 +ANGLe F4 T0 AC2 5.971 100 +ANGLe F4 HP5 AC2 5.971 100 +ANGLe F4 HP0 AC2 5.971 100 +ANGLe F4 HPa AC2 5.971 100 +ANGLe F5 F4 AC2 5.971 100 +ANGLe F5 F5 AC2 5.971 100 +ANGLe F5 Fa AC2 5.971 100 +ANGLe F5 H0 AC2 5.971 100 +ANGLe F5 H5 AC2 5.971 100 +ANGLe F5 Hd AC2 5.971 100 +ANGLe F5 Ha AC2 5.971 100 +ANGLe F5 Hda AC2 5.971 100 +ANGLe F5 Bda AC2 5.971 100 +ANGLe F5 B0 AC2 5.971 100 +ANGLe F5 Tda AC2 5.971 100 +ANGLe F5 T0 AC2 5.971 100 +ANGLe F5 HP5 AC2 5.971 100 +ANGLe F5 HP0 AC2 5.971 100 +ANGLe F5 HPa AC2 5.971 100 +ANGLe Fa F4 AC2 5.971 100 +ANGLe Fa F5 AC2 5.971 100 +ANGLe Fa Fa AC2 5.971 100 +ANGLe Fa H0 AC2 5.971 100 +ANGLe Fa H5 AC2 5.971 100 +ANGLe Fa Hd AC2 5.971 100 +ANGLe Fa Ha AC2 5.971 100 +ANGLe Fa Hda AC2 5.971 100 +ANGLe Fa Bda AC2 5.971 100 +ANGLe Fa B0 AC2 5.971 100 +ANGLe Fa Tda AC2 5.971 100 +ANGLe Fa T0 AC2 5.971 100 +ANGLe Fa HP5 AC2 5.971 100 +ANGLe 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5.971 100 +ANGLe F4 H0 HC4 5.971 100 +ANGLe F4 H5 HC4 5.971 100 +ANGLe F4 Hd HC4 5.971 100 +ANGLe F4 Ha HC4 5.971 100 +ANGLe F4 Hda HC4 5.971 100 +ANGLe F4 Bda HC4 5.971 100 +ANGLe F4 B0 HC4 5.971 100 +ANGLe F4 Tda HC4 5.971 100 +ANGLe F4 T0 HC4 5.971 100 +ANGLe F4 HP5 HC4 5.971 100 +ANGLe F4 HP0 HC4 5.971 100 +ANGLe F4 HPa HC4 5.971 100 +ANGLe F5 F4 HC4 5.971 100 +ANGLe F5 F5 HC4 5.971 100 +ANGLe F5 Fa HC4 5.971 100 +ANGLe F5 H0 HC4 5.971 100 +ANGLe F5 H5 HC4 5.971 100 +ANGLe F5 Hd HC4 5.971 100 +ANGLe F5 Ha HC4 5.971 100 +ANGLe F5 Hda HC4 5.971 100 +ANGLe F5 Bda HC4 5.971 100 +ANGLe F5 B0 HC4 5.971 100 +ANGLe F5 Tda HC4 5.971 100 +ANGLe F5 T0 HC4 5.971 100 +ANGLe F5 HP5 HC4 5.971 100 +ANGLe F5 HP0 HC4 5.971 100 +ANGLe F5 HPa HC4 5.971 100 +ANGLe Fa F4 HC4 5.971 100 +ANGLe Fa F5 HC4 5.971 100 +ANGLe Fa Fa HC4 5.971 100 +ANGLe Fa H0 HC4 5.971 100 +ANGLe Fa H5 HC4 5.971 100 +ANGLe Fa Hd HC4 5.971 100 +ANGLe Fa Ha HC4 5.971 100 +ANGLe Fa Hda HC4 5.971 100 +ANGLe Fa Bda HC4 5.971 100 +ANGLe Fa B0 HC4 5.971 100 +ANGLe Fa Tda HC4 5.971 100 +ANGLe Fa T0 HC4 5.971 100 +ANGLe Fa HP5 HC4 5.971 100 +ANGLe Fa HP0 HC4 5.971 100 +ANGLe Fa HPa HC4 5.971 100 +ANGLe H0 F4 HC4 5.971 100 +ANGLe H0 F5 HC4 5.971 100 +ANGLe H0 Fa HC4 5.971 100 +ANGLe H0 H0 HC4 5.971 100 +ANGLe H0 H5 HC4 5.971 100 +ANGLe H0 Hd HC4 5.971 100 +ANGLe H0 Ha HC4 5.971 100 +ANGLe H0 Hda HC4 5.971 100 +ANGLe H0 Bda HC4 5.971 100 +ANGLe H0 B0 HC4 5.971 100 +ANGLe H0 Tda HC4 5.971 100 +ANGLe H0 T0 HC4 5.971 100 +ANGLe H0 HP5 HC4 5.971 100 +ANGLe H0 HP0 HC4 5.971 100 +ANGLe H0 HPa HC4 5.971 100 +ANGLe H5 F4 HC4 5.971 100 +ANGLe H5 F5 HC4 5.971 100 +ANGLe H5 Fa HC4 5.971 100 +ANGLe H5 H0 HC4 5.971 100 +ANGLe H5 H5 HC4 5.971 100 +ANGLe H5 Hd HC4 5.971 100 +ANGLe H5 Ha HC4 5.971 100 +ANGLe H5 Hda HC4 5.971 100 +ANGLe H5 Bda HC4 5.971 100 +ANGLe H5 B0 HC4 5.971 100 +ANGLe H5 Tda HC4 5.971 100 +ANGLe H5 T0 HC4 5.971 100 +ANGLe H5 HP5 HC4 5.971 100 +ANGLe H5 HP0 HC4 5.971 100 +ANGLe H5 HPa HC4 5.971 100 +ANGLe Hd F4 HC4 5.971 100 +ANGLe Hd F5 HC4 5.971 100 +ANGLe Hd Fa HC4 5.971 100 +ANGLe Hd H0 HC4 5.971 100 +ANGLe Hd H5 HC4 5.971 100 +ANGLe Hd Hd HC4 5.971 100 +ANGLe Hd Ha HC4 5.971 100 +ANGLe Hd Hda HC4 5.971 100 +ANGLe Hd Bda HC4 5.971 100 +ANGLe Hd B0 HC4 5.971 100 +ANGLe Hd Tda HC4 5.971 100 +ANGLe Hd T0 HC4 5.971 100 +ANGLe Hd HP5 HC4 5.971 100 +ANGLe Hd HP0 HC4 5.971 100 +ANGLe Hd HPa HC4 5.971 100 +ANGLe Ha F4 HC4 5.971 100 +ANGLe Ha F5 HC4 5.971 100 +ANGLe Ha Fa HC4 5.971 100 +ANGLe Ha H0 HC4 5.971 100 +ANGLe Ha H5 HC4 5.971 100 +ANGLe Ha Hd HC4 5.971 100 +ANGLe Ha Ha HC4 5.971 100 +ANGLe Ha Hda HC4 5.971 100 +ANGLe Ha Bda HC4 5.971 100 +ANGLe Ha B0 HC4 5.971 100 +ANGLe Ha Tda HC4 5.971 100 +ANGLe Ha T0 HC4 5.971 100 +ANGLe Ha HP5 HC4 5.971 100 +ANGLe Ha HP0 HC4 5.971 100 +ANGLe Ha HPa HC4 5.971 100 +ANGLe Hda F4 HC4 5.971 100 +ANGLe Hda F5 HC4 5.971 100 +ANGLe Hda Fa HC4 5.971 100 +ANGLe Hda H0 HC4 5.971 100 +ANGLe Hda H5 HC4 5.971 100 +ANGLe Hda Hd HC4 5.971 100 +ANGLe Hda Ha HC4 5.971 100 +ANGLe Hda Hda HC4 5.971 100 +ANGLe Hda Bda HC4 5.971 100 +ANGLe Hda B0 HC4 5.971 100 +ANGLe Hda Tda HC4 5.971 100 +ANGLe Hda T0 HC4 5.971 100 +ANGLe Hda HP5 HC4 5.971 100 +ANGLe Hda HP0 HC4 5.971 100 +ANGLe Hda HPa HC4 5.971 100 +ANGLe Bda F4 HC4 5.971 100 +ANGLe Bda F5 HC4 5.971 100 +ANGLe Bda Fa HC4 5.971 100 +ANGLe Bda H0 HC4 5.971 100 +ANGLe Bda H5 HC4 5.971 100 +ANGLe Bda Hd HC4 5.971 100 +ANGLe Bda Ha HC4 5.971 100 +ANGLe Bda Hda HC4 5.971 100 +ANGLe Bda Bda HC4 5.971 100 +ANGLe Bda B0 HC4 5.971 100 +ANGLe Bda Tda HC4 5.971 100 +ANGLe Bda T0 HC4 5.971 100 +ANGLe Bda HP5 HC4 5.971 100 +ANGLe Bda HP0 HC4 5.971 100 +ANGLe Bda HPa HC4 5.971 100 +ANGLe B0 F4 HC4 5.971 100 +ANGLe B0 F5 HC4 5.971 100 +ANGLe B0 Fa HC4 5.971 100 +ANGLe B0 H0 HC4 5.971 100 +ANGLe B0 H5 HC4 5.971 100 +ANGLe B0 Hd HC4 5.971 100 +ANGLe B0 Ha HC4 5.971 100 +ANGLe B0 Hda HC4 5.971 100 +ANGLe B0 Bda HC4 5.971 100 +ANGLe B0 B0 HC4 5.971 100 +ANGLe B0 Tda HC4 5.971 100 +ANGLe B0 T0 HC4 5.971 100 +ANGLe B0 HP5 HC4 5.971 100 +ANGLe B0 HP0 HC4 5.971 100 +ANGLe B0 HPa HC4 5.971 100 +ANGLe Tda F4 HC4 5.971 100 +ANGLe Tda F5 HC4 5.971 100 +ANGLe Tda Fa HC4 5.971 100 +ANGLe Tda H0 HC4 5.971 100 +ANGLe Tda H5 HC4 5.971 100 +ANGLe Tda Hd HC4 5.971 100 +ANGLe Tda Ha HC4 5.971 100 +ANGLe Tda Hda HC4 5.971 100 +ANGLe Tda Bda HC4 5.971 100 +ANGLe Tda B0 HC4 5.971 100 +ANGLe Tda Tda HC4 5.971 100 +ANGLe Tda T0 HC4 5.971 100 +ANGLe Tda HP5 HC4 5.971 100 +ANGLe Tda HP0 HC4 5.971 100 +ANGLe Tda HPa HC4 5.971 100 +ANGLe T0 F4 HC4 5.971 100 +ANGLe T0 F5 HC4 5.971 100 +ANGLe T0 Fa HC4 5.971 100 +ANGLe T0 H0 HC4 5.971 100 +ANGLe T0 H5 HC4 5.971 100 +ANGLe T0 Hd HC4 5.971 100 +ANGLe T0 Ha HC4 5.971 100 +ANGLe T0 Hda HC4 5.971 100 +ANGLe T0 Bda HC4 5.971 100 +ANGLe T0 B0 HC4 5.971 100 +ANGLe T0 Tda HC4 5.971 100 +ANGLe T0 T0 HC4 5.971 100 +ANGLe T0 HP5 HC4 5.971 100 +ANGLe T0 HP0 HC4 5.971 100 +ANGLe T0 HPa HC4 5.971 100 +ANGLe HP5 F4 HC4 5.971 100 +ANGLe HP5 F5 HC4 5.971 100 +ANGLe HP5 Fa HC4 5.971 100 +ANGLe HP5 H0 HC4 5.971 100 +ANGLe HP5 H5 HC4 5.971 100 +ANGLe HP5 Hd HC4 5.971 100 +ANGLe HP5 Ha HC4 5.971 100 +ANGLe HP5 Hda HC4 5.971 100 +ANGLe HP5 Bda HC4 5.971 100 +ANGLe HP5 B0 HC4 5.971 100 +ANGLe HP5 Tda HC4 5.971 100 +ANGLe HP5 T0 HC4 5.971 100 +ANGLe HP5 HP5 HC4 5.971 100 +ANGLe HP5 HP0 HC4 5.971 100 +ANGLe HP5 HPa HC4 5.971 100 +ANGLe HP0 F4 HC4 5.971 100 +ANGLe HP0 F5 HC4 5.971 100 +ANGLe HP0 Fa HC4 5.971 100 +ANGLe HP0 H0 HC4 5.971 100 +ANGLe HP0 H5 HC4 5.971 100 +ANGLe HP0 Hd HC4 5.971 100 +ANGLe HP0 Ha HC4 5.971 100 +ANGLe HP0 Hda HC4 5.971 100 +ANGLe HP0 Bda HC4 5.971 100 +ANGLe HP0 B0 HC4 5.971 100 +ANGLe HP0 Tda HC4 5.971 100 +ANGLe HP0 T0 HC4 5.971 100 +ANGLe HP0 HP5 HC4 5.971 100 +ANGLe HP0 HP0 HC4 5.971 100 +ANGLe HP0 HPa HC4 5.971 100 +ANGLe HPa F4 HC4 5.971 100 +ANGLe HPa F5 HC4 5.971 100 +ANGLe HPa Fa HC4 5.971 100 +ANGLe HPa H0 HC4 5.971 100 +ANGLe HPa H5 HC4 5.971 100 +ANGLe HPa Hd HC4 5.971 100 +ANGLe HPa Ha HC4 5.971 100 +ANGLe HPa Hda HC4 5.971 100 +ANGLe HPa Bda HC4 5.971 100 +ANGLe HPa B0 HC4 5.971 100 +ANGLe HPa Tda HC4 5.971 100 +ANGLe HPa T0 HC4 5.971 100 +ANGLe HPa HP5 HC4 5.971 100 +ANGLe HPa HP0 HC4 5.971 100 +ANGLe HPa HPa HC4 5.971 100 +ANGLe F4 F4 LC1 5.971 100 +ANGLe F4 F5 LC1 5.971 100 +ANGLe F4 Fa LC1 5.971 100 +ANGLe F4 H0 LC1 5.971 100 +ANGLe F4 H5 LC1 5.971 100 +ANGLe F4 Hd LC1 5.971 100 +ANGLe F4 Ha LC1 5.971 100 +ANGLe F4 Hda LC1 5.971 100 +ANGLe F4 Bda LC1 5.971 100 +ANGLe F4 B0 LC1 5.971 100 +ANGLe F4 Tda LC1 5.971 100 +ANGLe F4 T0 LC1 5.971 100 +ANGLe F4 HP5 LC1 5.971 100 +ANGLe F4 HP0 LC1 5.971 100 +ANGLe F4 HPa LC1 5.971 100 +ANGLe F5 F4 LC1 5.971 100 +ANGLe F5 F5 LC1 5.971 100 +ANGLe F5 Fa LC1 5.971 100 +ANGLe F5 H0 LC1 5.971 100 +ANGLe F5 H5 LC1 5.971 100 +ANGLe F5 Hd LC1 5.971 100 +ANGLe F5 Ha LC1 5.971 100 +ANGLe F5 Hda LC1 5.971 100 +ANGLe F5 Bda LC1 5.971 100 +ANGLe F5 B0 LC1 5.971 100 +ANGLe F5 Tda LC1 5.971 100 +ANGLe F5 T0 LC1 5.971 100 +ANGLe F5 HP5 LC1 5.971 100 +ANGLe F5 HP0 LC1 5.971 100 +ANGLe F5 HPa LC1 5.971 100 +ANGLe Fa F4 LC1 5.971 100 +ANGLe Fa F5 LC1 5.971 100 +ANGLe Fa Fa LC1 5.971 100 +ANGLe Fa H0 LC1 5.971 100 +ANGLe Fa H5 LC1 5.971 100 +ANGLe Fa Hd LC1 5.971 100 +ANGLe Fa Ha LC1 5.971 100 +ANGLe Fa Hda LC1 5.971 100 +ANGLe Fa Bda LC1 5.971 100 +ANGLe Fa B0 LC1 5.971 100 +ANGLe Fa Tda LC1 5.971 100 +ANGLe Fa T0 LC1 5.971 100 +ANGLe Fa HP5 LC1 5.971 100 +ANGLe Fa HP0 LC1 5.971 100 +ANGLe Fa HPa LC1 5.971 100 +ANGLe H0 F4 LC1 5.971 100 +ANGLe H0 F5 LC1 5.971 100 +ANGLe H0 Fa LC1 5.971 100 +ANGLe H0 H0 LC1 5.971 100 +ANGLe H0 H5 LC1 5.971 100 +ANGLe H0 Hd LC1 5.971 100 +ANGLe H0 Ha LC1 5.971 100 +ANGLe H0 Hda LC1 5.971 100 +ANGLe H0 Bda LC1 5.971 100 +ANGLe H0 B0 LC1 5.971 100 +ANGLe H0 Tda LC1 5.971 100 +ANGLe H0 T0 LC1 5.971 100 +ANGLe H0 HP5 LC1 5.971 100 +ANGLe H0 HP0 LC1 5.971 100 +ANGLe H0 HPa LC1 5.971 100 +ANGLe H5 F4 LC1 5.971 100 +ANGLe H5 F5 LC1 5.971 100 +ANGLe H5 Fa LC1 5.971 100 +ANGLe H5 H0 LC1 5.971 100 +ANGLe H5 H5 LC1 5.971 100 +ANGLe H5 Hd LC1 5.971 100 +ANGLe H5 Ha LC1 5.971 100 +ANGLe H5 Hda LC1 5.971 100 +ANGLe H5 Bda LC1 5.971 100 +ANGLe H5 B0 LC1 5.971 100 +ANGLe H5 Tda LC1 5.971 100 +ANGLe H5 T0 LC1 5.971 100 +ANGLe H5 HP5 LC1 5.971 100 +ANGLe H5 HP0 LC1 5.971 100 +ANGLe H5 HPa LC1 5.971 100 +ANGLe Hd F4 LC1 5.971 100 +ANGLe Hd F5 LC1 5.971 100 +ANGLe Hd Fa LC1 5.971 100 +ANGLe Hd H0 LC1 5.971 100 +ANGLe Hd H5 LC1 5.971 100 +ANGLe Hd Hd LC1 5.971 100 +ANGLe Hd Ha LC1 5.971 100 +ANGLe Hd Hda LC1 5.971 100 +ANGLe Hd Bda LC1 5.971 100 +ANGLe Hd B0 LC1 5.971 100 +ANGLe Hd Tda LC1 5.971 100 +ANGLe Hd T0 LC1 5.971 100 +ANGLe Hd HP5 LC1 5.971 100 +ANGLe Hd HP0 LC1 5.971 100 +ANGLe Hd HPa LC1 5.971 100 +ANGLe Ha F4 LC1 5.971 100 +ANGLe Ha F5 LC1 5.971 100 +ANGLe Ha Fa LC1 5.971 100 +ANGLe Ha H0 LC1 5.971 100 +ANGLe Ha H5 LC1 5.971 100 +ANGLe Ha Hd LC1 5.971 100 +ANGLe Ha Ha LC1 5.971 100 +ANGLe Ha Hda LC1 5.971 100 +ANGLe Ha Bda LC1 5.971 100 +ANGLe Ha B0 LC1 5.971 100 +ANGLe Ha Tda LC1 5.971 100 +ANGLe Ha T0 LC1 5.971 100 +ANGLe Ha HP5 LC1 5.971 100 +ANGLe Ha HP0 LC1 5.971 100 +ANGLe Ha HPa LC1 5.971 100 +ANGLe Hda F4 LC1 5.971 100 +ANGLe Hda F5 LC1 5.971 100 +ANGLe Hda Fa LC1 5.971 100 +ANGLe Hda H0 LC1 5.971 100 +ANGLe Hda H5 LC1 5.971 100 +ANGLe Hda Hd LC1 5.971 100 +ANGLe Hda Ha LC1 5.971 100 +ANGLe Hda Hda LC1 5.971 100 +ANGLe Hda Bda LC1 5.971 100 +ANGLe Hda B0 LC1 5.971 100 +ANGLe Hda Tda LC1 5.971 100 +ANGLe Hda T0 LC1 5.971 100 +ANGLe Hda HP5 LC1 5.971 100 +ANGLe Hda HP0 LC1 5.971 100 +ANGLe Hda HPa LC1 5.971 100 +ANGLe Bda F4 LC1 5.971 100 +ANGLe Bda F5 LC1 5.971 100 +ANGLe Bda Fa LC1 5.971 100 +ANGLe Bda H0 LC1 5.971 100 +ANGLe Bda H5 LC1 5.971 100 +ANGLe Bda Hd LC1 5.971 100 +ANGLe Bda Ha LC1 5.971 100 +ANGLe Bda Hda LC1 5.971 100 +ANGLe Bda Bda LC1 5.971 100 +ANGLe Bda B0 LC1 5.971 100 +ANGLe Bda Tda LC1 5.971 100 +ANGLe Bda T0 LC1 5.971 100 +ANGLe Bda HP5 LC1 5.971 100 +ANGLe Bda HP0 LC1 5.971 100 +ANGLe Bda HPa LC1 5.971 100 +ANGLe B0 F4 LC1 5.971 100 +ANGLe B0 F5 LC1 5.971 100 +ANGLe B0 Fa LC1 5.971 100 +ANGLe B0 H0 LC1 5.971 100 +ANGLe B0 H5 LC1 5.971 100 +ANGLe B0 Hd LC1 5.971 100 +ANGLe B0 Ha LC1 5.971 100 +ANGLe B0 Hda LC1 5.971 100 +ANGLe B0 Bda LC1 5.971 100 +ANGLe B0 B0 LC1 5.971 100 +ANGLe B0 Tda LC1 5.971 100 +ANGLe B0 T0 LC1 5.971 100 +ANGLe B0 HP5 LC1 5.971 100 +ANGLe B0 HP0 LC1 5.971 100 +ANGLe B0 HPa LC1 5.971 100 +ANGLe Tda F4 LC1 5.971 100 +ANGLe Tda F5 LC1 5.971 100 +ANGLe Tda Fa LC1 5.971 100 +ANGLe Tda H0 LC1 5.971 100 +ANGLe Tda H5 LC1 5.971 100 +ANGLe Tda Hd LC1 5.971 100 +ANGLe Tda Ha LC1 5.971 100 +ANGLe Tda Hda LC1 5.971 100 +ANGLe Tda Bda LC1 5.971 100 +ANGLe Tda B0 LC1 5.971 100 +ANGLe Tda Tda LC1 5.971 100 +ANGLe Tda T0 LC1 5.971 100 +ANGLe Tda HP5 LC1 5.971 100 +ANGLe Tda HP0 LC1 5.971 100 +ANGLe Tda HPa LC1 5.971 100 +ANGLe T0 F4 LC1 5.971 100 +ANGLe T0 F5 LC1 5.971 100 +ANGLe T0 Fa LC1 5.971 100 +ANGLe T0 H0 LC1 5.971 100 +ANGLe T0 H5 LC1 5.971 100 +ANGLe T0 Hd LC1 5.971 100 +ANGLe T0 Ha LC1 5.971 100 +ANGLe T0 Hda LC1 5.971 100 +ANGLe T0 Bda LC1 5.971 100 +ANGLe T0 B0 LC1 5.971 100 +ANGLe T0 Tda LC1 5.971 100 +ANGLe T0 T0 LC1 5.971 100 +ANGLe T0 HP5 LC1 5.971 100 +ANGLe T0 HP0 LC1 5.971 100 +ANGLe T0 HPa LC1 5.971 100 +ANGLe HP5 F4 LC1 5.971 100 +ANGLe HP5 F5 LC1 5.971 100 +ANGLe HP5 Fa LC1 5.971 100 +ANGLe HP5 H0 LC1 5.971 100 +ANGLe HP5 H5 LC1 5.971 100 +ANGLe HP5 Hd LC1 5.971 100 +ANGLe HP5 Ha LC1 5.971 100 +ANGLe HP5 Hda LC1 5.971 100 +ANGLe HP5 Bda LC1 5.971 100 +ANGLe HP5 B0 LC1 5.971 100 +ANGLe HP5 Tda LC1 5.971 100 +ANGLe HP5 T0 LC1 5.971 100 +ANGLe HP5 HP5 LC1 5.971 100 +ANGLe HP5 HP0 LC1 5.971 100 +ANGLe HP5 HPa LC1 5.971 100 +ANGLe HP0 F4 LC1 5.971 100 +ANGLe HP0 F5 LC1 5.971 100 +ANGLe HP0 Fa LC1 5.971 100 +ANGLe HP0 H0 LC1 5.971 100 +ANGLe HP0 H5 LC1 5.971 100 +ANGLe HP0 Hd LC1 5.971 100 +ANGLe HP0 Ha LC1 5.971 100 +ANGLe HP0 Hda LC1 5.971 100 +ANGLe HP0 Bda LC1 5.971 100 +ANGLe HP0 B0 LC1 5.971 100 +ANGLe HP0 Tda LC1 5.971 100 +ANGLe HP0 T0 LC1 5.971 100 +ANGLe HP0 HP5 LC1 5.971 100 +ANGLe HP0 HP0 LC1 5.971 100 +ANGLe HP0 HPa LC1 5.971 100 +ANGLe HPa F4 LC1 5.971 100 +ANGLe HPa F5 LC1 5.971 100 +ANGLe HPa Fa LC1 5.971 100 +ANGLe HPa H0 LC1 5.971 100 +ANGLe HPa H5 LC1 5.971 100 +ANGLe HPa Hd LC1 5.971 100 +ANGLe HPa Ha LC1 5.971 100 +ANGLe HPa Hda LC1 5.971 100 +ANGLe HPa Bda LC1 5.971 100 +ANGLe HPa B0 LC1 5.971 100 +ANGLe HPa Tda LC1 5.971 100 +ANGLe HPa T0 LC1 5.971 100 +ANGLe HPa HP5 LC1 5.971 100 +ANGLe HPa HP0 LC1 5.971 100 +ANGLe HPa HPa LC1 5.971 100 +ANGLe F4 F4 MC5 5.971 100 +ANGLe F4 F5 MC5 5.971 100 +ANGLe F4 Fa MC5 5.971 100 +ANGLe F4 H0 MC5 5.971 100 +ANGLe F4 H5 MC5 5.971 100 +ANGLe F4 Hd MC5 5.971 100 +ANGLe F4 Ha MC5 5.971 100 +ANGLe F4 Hda MC5 5.971 100 +ANGLe F4 Bda MC5 5.971 100 +ANGLe F4 B0 MC5 5.971 100 +ANGLe F4 Tda MC5 5.971 100 +ANGLe F4 T0 MC5 5.971 100 +ANGLe F4 HP5 MC5 5.971 100 +ANGLe F4 HP0 MC5 5.971 100 +ANGLe F4 HPa MC5 5.971 100 +ANGLe F5 F4 MC5 5.971 100 +ANGLe F5 F5 MC5 5.971 100 +ANGLe F5 Fa MC5 5.971 100 +ANGLe F5 H0 MC5 5.971 100 +ANGLe F5 H5 MC5 5.971 100 +ANGLe F5 Hd MC5 5.971 100 +ANGLe F5 Ha MC5 5.971 100 +ANGLe F5 Hda MC5 5.971 100 +ANGLe F5 Bda MC5 5.971 100 +ANGLe F5 B0 MC5 5.971 100 +ANGLe F5 Tda MC5 5.971 100 +ANGLe F5 T0 MC5 5.971 100 +ANGLe F5 HP5 MC5 5.971 100 +ANGLe F5 HP0 MC5 5.971 100 +ANGLe F5 HPa MC5 5.971 100 +ANGLe Fa F4 MC5 5.971 100 +ANGLe Fa F5 MC5 5.971 100 +ANGLe Fa Fa MC5 5.971 100 +ANGLe Fa H0 MC5 5.971 100 +ANGLe Fa H5 MC5 5.971 100 +ANGLe Fa Hd MC5 5.971 100 +ANGLe Fa Ha MC5 5.971 100 +ANGLe Fa Hda MC5 5.971 100 +ANGLe Fa Bda MC5 5.971 100 +ANGLe Fa B0 MC5 5.971 100 +ANGLe Fa Tda MC5 5.971 100 +ANGLe Fa T0 MC5 5.971 100 +ANGLe Fa HP5 MC5 5.971 100 +ANGLe Fa HP0 MC5 5.971 100 +ANGLe Fa HPa MC5 5.971 100 +ANGLe H0 F4 MC5 5.971 100 +ANGLe H0 F5 MC5 5.971 100 +ANGLe H0 Fa MC5 5.971 100 +ANGLe H0 H0 MC5 5.971 100 +ANGLe H0 H5 MC5 5.971 100 +ANGLe H0 Hd MC5 5.971 100 +ANGLe H0 Ha MC5 5.971 100 +ANGLe H0 Hda MC5 5.971 100 +ANGLe H0 Bda MC5 5.971 100 +ANGLe H0 B0 MC5 5.971 100 +ANGLe H0 Tda MC5 5.971 100 +ANGLe H0 T0 MC5 5.971 100 +ANGLe H0 HP5 MC5 5.971 100 +ANGLe H0 HP0 MC5 5.971 100 +ANGLe H0 HPa MC5 5.971 100 +ANGLe H5 F4 MC5 5.971 100 +ANGLe H5 F5 MC5 5.971 100 +ANGLe H5 Fa MC5 5.971 100 +ANGLe H5 H0 MC5 5.971 100 +ANGLe H5 H5 MC5 5.971 100 +ANGLe H5 Hd MC5 5.971 100 +ANGLe H5 Ha MC5 5.971 100 +ANGLe H5 Hda MC5 5.971 100 +ANGLe H5 Bda MC5 5.971 100 +ANGLe H5 B0 MC5 5.971 100 +ANGLe H5 Tda MC5 5.971 100 +ANGLe H5 T0 MC5 5.971 100 +ANGLe H5 HP5 MC5 5.971 100 +ANGLe H5 HP0 MC5 5.971 100 +ANGLe H5 HPa MC5 5.971 100 +ANGLe Hd F4 MC5 5.971 100 +ANGLe Hd F5 MC5 5.971 100 +ANGLe Hd Fa MC5 5.971 100 +ANGLe Hd H0 MC5 5.971 100 +ANGLe Hd H5 MC5 5.971 100 +ANGLe Hd Hd MC5 5.971 100 +ANGLe Hd Ha MC5 5.971 100 +ANGLe Hd Hda MC5 5.971 100 +ANGLe Hd Bda MC5 5.971 100 +ANGLe Hd B0 MC5 5.971 100 +ANGLe Hd Tda MC5 5.971 100 +ANGLe Hd T0 MC5 5.971 100 +ANGLe Hd HP5 MC5 5.971 100 +ANGLe Hd HP0 MC5 5.971 100 +ANGLe Hd HPa MC5 5.971 100 +ANGLe Ha F4 MC5 5.971 100 +ANGLe Ha F5 MC5 5.971 100 +ANGLe Ha Fa MC5 5.971 100 +ANGLe Ha H0 MC5 5.971 100 +ANGLe Ha H5 MC5 5.971 100 +ANGLe Ha Hd MC5 5.971 100 +ANGLe Ha Ha MC5 5.971 100 +ANGLe Ha Hda MC5 5.971 100 +ANGLe Ha Bda MC5 5.971 100 +ANGLe Ha B0 MC5 5.971 100 +ANGLe Ha Tda MC5 5.971 100 +ANGLe Ha T0 MC5 5.971 100 +ANGLe Ha HP5 MC5 5.971 100 +ANGLe Ha HP0 MC5 5.971 100 +ANGLe Ha HPa MC5 5.971 100 +ANGLe Hda F4 MC5 5.971 100 +ANGLe Hda F5 MC5 5.971 100 +ANGLe Hda Fa MC5 5.971 100 +ANGLe Hda H0 MC5 5.971 100 +ANGLe Hda H5 MC5 5.971 100 +ANGLe Hda Hd MC5 5.971 100 +ANGLe Hda Ha MC5 5.971 100 +ANGLe Hda Hda MC5 5.971 100 +ANGLe Hda Bda MC5 5.971 100 +ANGLe Hda B0 MC5 5.971 100 +ANGLe Hda Tda MC5 5.971 100 +ANGLe Hda T0 MC5 5.971 100 +ANGLe Hda HP5 MC5 5.971 100 +ANGLe Hda HP0 MC5 5.971 100 +ANGLe Hda HPa MC5 5.971 100 +ANGLe Bda F4 MC5 5.971 100 +ANGLe Bda F5 MC5 5.971 100 +ANGLe Bda Fa MC5 5.971 100 +ANGLe Bda H0 MC5 5.971 100 +ANGLe Bda H5 MC5 5.971 100 +ANGLe Bda Hd MC5 5.971 100 +ANGLe Bda Ha MC5 5.971 100 +ANGLe Bda Hda MC5 5.971 100 +ANGLe Bda Bda MC5 5.971 100 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5.971 100 +ANGLe T0 F4 MC5 5.971 100 +ANGLe T0 F5 MC5 5.971 100 +ANGLe T0 Fa MC5 5.971 100 +ANGLe T0 H0 MC5 5.971 100 +ANGLe T0 H5 MC5 5.971 100 +ANGLe T0 Hd MC5 5.971 100 +ANGLe T0 Ha MC5 5.971 100 +ANGLe T0 Hda MC5 5.971 100 +ANGLe T0 Bda MC5 5.971 100 +ANGLe T0 B0 MC5 5.971 100 +ANGLe T0 Tda MC5 5.971 100 +ANGLe T0 T0 MC5 5.971 100 +ANGLe T0 HP5 MC5 5.971 100 +ANGLe T0 HP0 MC5 5.971 100 +ANGLe T0 HPa MC5 5.971 100 +ANGLe HP5 F4 MC5 5.971 100 +ANGLe HP5 F5 MC5 5.971 100 +ANGLe HP5 Fa MC5 5.971 100 +ANGLe HP5 H0 MC5 5.971 100 +ANGLe HP5 H5 MC5 5.971 100 +ANGLe HP5 Hd MC5 5.971 100 +ANGLe HP5 Ha MC5 5.971 100 +ANGLe HP5 Hda MC5 5.971 100 +ANGLe HP5 Bda MC5 5.971 100 +ANGLe HP5 B0 MC5 5.971 100 +ANGLe HP5 Tda MC5 5.971 100 +ANGLe HP5 T0 MC5 5.971 100 +ANGLe HP5 HP5 MC5 5.971 100 +ANGLe HP5 HP0 MC5 5.971 100 +ANGLe HP5 HPa MC5 5.971 100 +ANGLe HP0 F4 MC5 5.971 100 +ANGLe HP0 F5 MC5 5.971 100 +ANGLe HP0 Fa MC5 5.971 100 +ANGLe HP0 H0 MC5 5.971 100 +ANGLe HP0 H5 MC5 5.971 100 +ANGLe HP0 Hd MC5 5.971 100 +ANGLe HP0 Ha MC5 5.971 100 +ANGLe HP0 Hda MC5 5.971 100 +ANGLe HP0 Bda MC5 5.971 100 +ANGLe HP0 B0 MC5 5.971 100 +ANGLe HP0 Tda MC5 5.971 100 +ANGLe HP0 T0 MC5 5.971 100 +ANGLe HP0 HP5 MC5 5.971 100 +ANGLe HP0 HP0 MC5 5.971 100 +ANGLe HP0 HPa MC5 5.971 100 +ANGLe HPa F4 MC5 5.971 100 +ANGLe HPa F5 MC5 5.971 100 +ANGLe HPa Fa MC5 5.971 100 +ANGLe HPa H0 MC5 5.971 100 +ANGLe HPa H5 MC5 5.971 100 +ANGLe HPa Hd MC5 5.971 100 +ANGLe HPa Ha MC5 5.971 100 +ANGLe HPa Hda MC5 5.971 100 +ANGLe HPa Bda MC5 5.971 100 +ANGLe HPa B0 MC5 5.971 100 +ANGLe HPa Tda MC5 5.971 100 +ANGLe HPa T0 MC5 5.971 100 +ANGLe HPa HP5 MC5 5.971 100 +ANGLe HPa HP0 MC5 5.971 100 +ANGLe HPa HPa MC5 5.971 100 +ANGLe F4 F4 N0 5.971 100 +ANGLe F4 F5 N0 5.971 100 +ANGLe F4 Fa N0 5.971 100 +ANGLe F4 H0 N0 5.971 100 +ANGLe F4 H5 N0 5.971 100 +ANGLe F4 Hd N0 5.971 100 +ANGLe F4 Ha N0 5.971 100 +ANGLe F4 Hda N0 5.971 100 +ANGLe F4 Bda N0 5.971 100 +ANGLe F4 B0 N0 5.971 100 +ANGLe F4 Tda N0 5.971 100 +ANGLe F4 T0 N0 5.971 100 +ANGLe F4 HP5 N0 5.971 100 +ANGLe F4 HP0 N0 5.971 100 +ANGLe F4 HPa N0 5.971 100 +ANGLe F5 F4 N0 5.971 100 +ANGLe F5 F5 N0 5.971 100 +ANGLe F5 Fa N0 5.971 100 +ANGLe F5 H0 N0 5.971 100 +ANGLe F5 H5 N0 5.971 100 +ANGLe F5 Hd N0 5.971 100 +ANGLe F5 Ha N0 5.971 100 +ANGLe F5 Hda N0 5.971 100 +ANGLe F5 Bda N0 5.971 100 +ANGLe F5 B0 N0 5.971 100 +ANGLe F5 Tda N0 5.971 100 +ANGLe F5 T0 N0 5.971 100 +ANGLe F5 HP5 N0 5.971 100 +ANGLe F5 HP0 N0 5.971 100 +ANGLe F5 HPa N0 5.971 100 +ANGLe Fa F4 N0 5.971 100 +ANGLe Fa F5 N0 5.971 100 +ANGLe Fa Fa N0 5.971 100 +ANGLe Fa H0 N0 5.971 100 +ANGLe Fa H5 N0 5.971 100 +ANGLe Fa Hd N0 5.971 100 +ANGLe Fa Ha N0 5.971 100 +ANGLe Fa Hda N0 5.971 100 +ANGLe Fa Bda N0 5.971 100 +ANGLe Fa B0 N0 5.971 100 +ANGLe Fa Tda N0 5.971 100 +ANGLe Fa T0 N0 5.971 100 +ANGLe Fa HP5 N0 5.971 100 +ANGLe Fa HP0 N0 5.971 100 +ANGLe Fa HPa N0 5.971 100 +ANGLe H0 F4 N0 5.971 100 +ANGLe H0 F5 N0 5.971 100 +ANGLe H0 Fa N0 5.971 100 +ANGLe H0 H0 N0 5.971 100 +ANGLe H0 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Hd HP5 N0 5.971 100 +ANGLe Hd HP0 N0 5.971 100 +ANGLe Hd HPa N0 5.971 100 +ANGLe Ha F4 N0 5.971 100 +ANGLe Ha F5 N0 5.971 100 +ANGLe Ha Fa N0 5.971 100 +ANGLe Ha H0 N0 5.971 100 +ANGLe Ha H5 N0 5.971 100 +ANGLe Ha Hd N0 5.971 100 +ANGLe Ha Ha N0 5.971 100 +ANGLe Ha Hda N0 5.971 100 +ANGLe Ha Bda N0 5.971 100 +ANGLe Ha B0 N0 5.971 100 +ANGLe Ha Tda N0 5.971 100 +ANGLe Ha T0 N0 5.971 100 +ANGLe Ha HP5 N0 5.971 100 +ANGLe Ha HP0 N0 5.971 100 +ANGLe Ha HPa N0 5.971 100 +ANGLe Hda F4 N0 5.971 100 +ANGLe Hda F5 N0 5.971 100 +ANGLe Hda Fa N0 5.971 100 +ANGLe Hda H0 N0 5.971 100 +ANGLe Hda H5 N0 5.971 100 +ANGLe Hda Hd N0 5.971 100 +ANGLe Hda Ha N0 5.971 100 +ANGLe Hda Hda N0 5.971 100 +ANGLe Hda Bda N0 5.971 100 +ANGLe Hda B0 N0 5.971 100 +ANGLe Hda Tda N0 5.971 100 +ANGLe Hda T0 N0 5.971 100 +ANGLe Hda HP5 N0 5.971 100 +ANGLe Hda HP0 N0 5.971 100 +ANGLe Hda HPa N0 5.971 100 +ANGLe Bda F4 N0 5.971 100 +ANGLe Bda F5 N0 5.971 100 +ANGLe Bda Fa N0 5.971 100 +ANGLe Bda H0 N0 5.971 100 +ANGLe Bda 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5.971 100 +ANGLe T0 Fa AP5 5.971 100 +ANGLe T0 H0 AP5 5.971 100 +ANGLe T0 H5 AP5 5.971 100 +ANGLe T0 Hd AP5 5.971 100 +ANGLe T0 Ha AP5 5.971 100 +ANGLe T0 Hda AP5 5.971 100 +ANGLe T0 Bda AP5 5.971 100 +ANGLe T0 B0 AP5 5.971 100 +ANGLe T0 Tda AP5 5.971 100 +ANGLe T0 T0 AP5 5.971 100 +ANGLe T0 HP5 AP5 5.971 100 +ANGLe T0 HP0 AP5 5.971 100 +ANGLe T0 HPa AP5 5.971 100 +ANGLe HP5 F4 AP5 5.971 100 +ANGLe HP5 F5 AP5 5.971 100 +ANGLe HP5 Fa AP5 5.971 100 +ANGLe HP5 H0 AP5 5.971 100 +ANGLe HP5 H5 AP5 5.971 100 +ANGLe HP5 Hd AP5 5.971 100 +ANGLe HP5 Ha AP5 5.971 100 +ANGLe HP5 Hda AP5 5.971 100 +ANGLe HP5 Bda AP5 5.971 100 +ANGLe HP5 B0 AP5 5.971 100 +ANGLe HP5 Tda AP5 5.971 100 +ANGLe HP5 T0 AP5 5.971 100 +ANGLe HP5 HP5 AP5 5.971 100 +ANGLe HP5 HP0 AP5 5.971 100 +ANGLe HP5 HPa AP5 5.971 100 +ANGLe HP0 F4 AP5 5.971 100 +ANGLe HP0 F5 AP5 5.971 100 +ANGLe HP0 Fa AP5 5.971 100 +ANGLe HP0 H0 AP5 5.971 100 +ANGLe HP0 H5 AP5 5.971 100 +ANGLe HP0 Hd AP5 5.971 100 +ANGLe HP0 Ha AP5 5.971 100 +ANGLe HP0 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HP0 HP5 H5 HP5 95.524 1 -120 +DIHEdral HP0 HP5 H5 HP0 95.524 1 -120 +DIHEdral HP0 HP5 H5 HPa 95.524 1 -120 +DIHEdral HP0 HP5 Hd H0 95.524 1 -120 +DIHEdral HP0 HP5 Hd H5 95.524 1 -120 +DIHEdral HP0 HP5 Hd Hd 95.524 1 -120 +DIHEdral HP0 HP5 Hd Ha 95.524 1 -120 +DIHEdral HP0 HP5 Hd Hda 95.524 1 -120 +DIHEdral HP0 HP5 Hd HP5 95.524 1 -120 +DIHEdral HP0 HP5 Hd HP0 95.524 1 -120 +DIHEdral HP0 HP5 Hd HPa 95.524 1 -120 +DIHEdral HP0 HP5 Ha H0 95.524 1 -120 +DIHEdral HP0 HP5 Ha H5 95.524 1 -120 +DIHEdral HP0 HP5 Ha Hd 95.524 1 -120 +DIHEdral HP0 HP5 Ha Ha 95.524 1 -120 +DIHEdral HP0 HP5 Ha Hda 95.524 1 -120 +DIHEdral HP0 HP5 Ha HP5 95.524 1 -120 +DIHEdral HP0 HP5 Ha HP0 95.524 1 -120 +DIHEdral HP0 HP5 Ha HPa 95.524 1 -120 +DIHEdral HP0 HP5 Hda H0 95.524 1 -120 +DIHEdral HP0 HP5 Hda H5 95.524 1 -120 +DIHEdral HP0 HP5 Hda Hd 95.524 1 -120 +DIHEdral HP0 HP5 Hda Ha 95.524 1 -120 +DIHEdral HP0 HP5 Hda Hda 95.524 1 -120 +DIHEdral HP0 HP5 Hda HP5 95.524 1 -120 +DIHEdral HP0 HP5 Hda HP0 95.524 1 -120 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HP0 HP0 H0 H0 95.524 1 -120 +DIHEdral HP0 HP0 H0 H5 95.524 1 -120 +DIHEdral HP0 HP0 H0 Hd 95.524 1 -120 +DIHEdral HP0 HP0 H0 Ha 95.524 1 -120 +DIHEdral HP0 HP0 H0 Hda 95.524 1 -120 +DIHEdral HP0 HP0 H0 HP5 95.524 1 -120 +DIHEdral HP0 HP0 H0 HP0 95.524 1 -120 +DIHEdral HP0 HP0 H0 HPa 95.524 1 -120 +DIHEdral HP0 HP0 H5 H0 95.524 1 -120 +DIHEdral HP0 HP0 H5 H5 95.524 1 -120 +DIHEdral HP0 HP0 H5 Hd 95.524 1 -120 +DIHEdral HP0 HP0 H5 Ha 95.524 1 -120 +DIHEdral HP0 HP0 H5 Hda 95.524 1 -120 +DIHEdral HP0 HP0 H5 HP5 95.524 1 -120 +DIHEdral HP0 HP0 H5 HP0 95.524 1 -120 +DIHEdral HP0 HP0 H5 HPa 95.524 1 -120 +DIHEdral HP0 HP0 Hd H0 95.524 1 -120 +DIHEdral HP0 HP0 Hd H5 95.524 1 -120 +DIHEdral HP0 HP0 Hd Hd 95.524 1 -120 +DIHEdral HP0 HP0 Hd Ha 95.524 1 -120 +DIHEdral HP0 HP0 Hd Hda 95.524 1 -120 +DIHEdral HP0 HP0 Hd HP5 95.524 1 -120 +DIHEdral HP0 HP0 Hd HP0 95.524 1 -120 +DIHEdral HP0 HP0 Hd HPa 95.524 1 -120 +DIHEdral HP0 HP0 Ha H0 95.524 1 -120 +DIHEdral HP0 HP0 Ha H5 95.524 1 -120 +DIHEdral HP0 HP0 Ha Hd 95.524 1 -120 +DIHEdral HP0 HP0 Ha Ha 95.524 1 -120 +DIHEdral HP0 HP0 Ha Hda 95.524 1 -120 +DIHEdral HP0 HP0 Ha HP5 95.524 1 -120 +DIHEdral HP0 HP0 Ha HP0 95.524 1 -120 +DIHEdral HP0 HP0 Ha HPa 95.524 1 -120 +DIHEdral HP0 HP0 Hda H0 95.524 1 -120 +DIHEdral HP0 HP0 Hda H5 95.524 1 -120 +DIHEdral HP0 HP0 Hda Hd 95.524 1 -120 +DIHEdral HP0 HP0 Hda Ha 95.524 1 -120 +DIHEdral HP0 HP0 Hda Hda 95.524 1 -120 +DIHEdral HP0 HP0 Hda HP5 95.524 1 -120 +DIHEdral HP0 HP0 Hda HP0 95.524 1 -120 +DIHEdral HP0 HP0 Hda HPa 95.524 1 -120 +DIHEdral HP0 HP0 HP5 H0 95.524 1 -120 +DIHEdral HP0 HP0 HP5 H5 95.524 1 -120 +DIHEdral HP0 HP0 HP5 Hd 95.524 1 -120 +DIHEdral HP0 HP0 HP5 Ha 95.524 1 -120 +DIHEdral HP0 HP0 HP5 Hda 95.524 1 -120 +DIHEdral HP0 HP0 HP5 HP5 95.524 1 -120 +DIHEdral HP0 HP0 HP5 HP0 95.524 1 -120 +DIHEdral HP0 HP0 HP5 HPa 95.524 1 -120 +DIHEdral HP0 HP0 HP0 H0 95.524 1 -120 +DIHEdral HP0 HP0 HP0 H5 95.524 1 -120 +DIHEdral HP0 HP0 HP0 Hd 95.524 1 -120 +DIHEdral HP0 HP0 HP0 Ha 95.524 1 -120 +DIHEdral HP0 HP0 HP0 Hda 95.524 1 -120 +DIHEdral HP0 HP0 HP0 HP5 95.524 1 -120 +DIHEdral HP0 HP0 HP0 HP0 95.524 1 -120 +DIHEdral HP0 HP0 HP0 HPa 95.524 1 -120 +DIHEdral HP0 HP0 HPa H0 95.524 1 -120 +DIHEdral HP0 HP0 HPa H5 95.524 1 -120 +DIHEdral HP0 HP0 HPa Hd 95.524 1 -120 +DIHEdral HP0 HP0 HPa Ha 95.524 1 -120 +DIHEdral HP0 HP0 HPa Hda 95.524 1 -120 +DIHEdral HP0 HP0 HPa HP5 95.524 1 -120 +DIHEdral HP0 HP0 HPa HP0 95.524 1 -120 +DIHEdral HP0 HP0 HPa HPa 95.524 1 -120 +DIHEdral HP0 HPa H0 H0 95.524 1 -120 +DIHEdral HP0 HPa H0 H5 95.524 1 -120 +DIHEdral HP0 HPa H0 Hd 95.524 1 -120 +DIHEdral HP0 HPa H0 Ha 95.524 1 -120 +DIHEdral HP0 HPa H0 Hda 95.524 1 -120 +DIHEdral HP0 HPa H0 HP5 95.524 1 -120 +DIHEdral HP0 HPa H0 HP0 95.524 1 -120 +DIHEdral HP0 HPa H0 HPa 95.524 1 -120 +DIHEdral HP0 HPa H5 H0 95.524 1 -120 +DIHEdral HP0 HPa H5 H5 95.524 1 -120 +DIHEdral HP0 HPa H5 Hd 95.524 1 -120 +DIHEdral HP0 HPa H5 Ha 95.524 1 -120 +DIHEdral HP0 HPa H5 Hda 95.524 1 -120 +DIHEdral HP0 HPa H5 HP5 95.524 1 -120 +DIHEdral HP0 HPa H5 HP0 95.524 1 -120 +DIHEdral HP0 HPa H5 HPa 95.524 1 -120 +DIHEdral HP0 HPa Hd H0 95.524 1 -120 +DIHEdral HP0 HPa Hd H5 95.524 1 -120 +DIHEdral HP0 HPa Hd Hd 95.524 1 -120 +DIHEdral HP0 HPa Hd Ha 95.524 1 -120 +DIHEdral HP0 HPa Hd Hda 95.524 1 -120 +DIHEdral HP0 HPa Hd HP5 95.524 1 -120 +DIHEdral HP0 HPa Hd HP0 95.524 1 -120 +DIHEdral HP0 HPa Hd HPa 95.524 1 -120 +DIHEdral HP0 HPa Ha H0 95.524 1 -120 +DIHEdral HP0 HPa Ha H5 95.524 1 -120 +DIHEdral HP0 HPa Ha Hd 95.524 1 -120 +DIHEdral HP0 HPa Ha Ha 95.524 1 -120 +DIHEdral HP0 HPa Ha Hda 95.524 1 -120 +DIHEdral HP0 HPa Ha HP5 95.524 1 -120 +DIHEdral HP0 HPa Ha HP0 95.524 1 -120 +DIHEdral HP0 HPa Ha HPa 95.524 1 -120 +DIHEdral HP0 HPa Hda H0 95.524 1 -120 +DIHEdral HP0 HPa Hda H5 95.524 1 -120 +DIHEdral HP0 HPa Hda Hd 95.524 1 -120 +DIHEdral HP0 HPa Hda Ha 95.524 1 -120 +DIHEdral HP0 HPa Hda Hda 95.524 1 -120 +DIHEdral HP0 HPa Hda HP5 95.524 1 -120 +DIHEdral HP0 HPa Hda HP0 95.524 1 -120 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HPa H0 H0 H0 95.524 1 -120 +DIHEdral HPa H0 H0 H5 95.524 1 -120 +DIHEdral HPa H0 H0 Hd 95.524 1 -120 +DIHEdral HPa H0 H0 Ha 95.524 1 -120 +DIHEdral HPa H0 H0 Hda 95.524 1 -120 +DIHEdral HPa H0 H0 HP5 95.524 1 -120 +DIHEdral HPa H0 H0 HP0 95.524 1 -120 +DIHEdral HPa H0 H0 HPa 95.524 1 -120 +DIHEdral HPa H0 H5 H0 95.524 1 -120 +DIHEdral HPa H0 H5 H5 95.524 1 -120 +DIHEdral HPa H0 H5 Hd 95.524 1 -120 +DIHEdral HPa H0 H5 Ha 95.524 1 -120 +DIHEdral HPa H0 H5 Hda 95.524 1 -120 +DIHEdral HPa H0 H5 HP5 95.524 1 -120 +DIHEdral HPa H0 H5 HP0 95.524 1 -120 +DIHEdral HPa H0 H5 HPa 95.524 1 -120 +DIHEdral HPa H0 Hd H0 95.524 1 -120 +DIHEdral HPa H0 Hd H5 95.524 1 -120 +DIHEdral HPa H0 Hd Hd 95.524 1 -120 +DIHEdral HPa H0 Hd Ha 95.524 1 -120 +DIHEdral HPa H0 Hd Hda 95.524 1 -120 +DIHEdral HPa H0 Hd HP5 95.524 1 -120 +DIHEdral HPa H0 Hd HP0 95.524 1 -120 +DIHEdral HPa H0 Hd HPa 95.524 1 -120 +DIHEdral HPa H0 Ha H0 95.524 1 -120 +DIHEdral HPa H0 Ha H5 95.524 1 -120 +DIHEdral HPa H0 Ha Hd 95.524 1 -120 +DIHEdral HPa H0 Ha Ha 95.524 1 -120 +DIHEdral HPa H0 Ha Hda 95.524 1 -120 +DIHEdral HPa H0 Ha HP5 95.524 1 -120 +DIHEdral HPa H0 Ha HP0 95.524 1 -120 +DIHEdral HPa H0 Ha HPa 95.524 1 -120 +DIHEdral HPa H0 Hda H0 95.524 1 -120 +DIHEdral HPa H0 Hda H5 95.524 1 -120 +DIHEdral HPa H0 Hda Hd 95.524 1 -120 +DIHEdral HPa H0 Hda Ha 95.524 1 -120 +DIHEdral HPa H0 Hda Hda 95.524 1 -120 +DIHEdral HPa H0 Hda HP5 95.524 1 -120 +DIHEdral HPa H0 Hda HP0 95.524 1 -120 +DIHEdral HPa H0 Hda HPa 95.524 1 -120 +DIHEdral HPa H0 HP5 H0 95.524 1 -120 +DIHEdral HPa H0 HP5 H5 95.524 1 -120 +DIHEdral HPa H0 HP5 Hd 95.524 1 -120 +DIHEdral HPa H0 HP5 Ha 95.524 1 -120 +DIHEdral HPa H0 HP5 Hda 95.524 1 -120 +DIHEdral HPa H0 HP5 HP5 95.524 1 -120 +DIHEdral HPa H0 HP5 HP0 95.524 1 -120 +DIHEdral HPa H0 HP5 HPa 95.524 1 -120 +DIHEdral HPa H0 HP0 H0 95.524 1 -120 +DIHEdral HPa H0 HP0 H5 95.524 1 -120 +DIHEdral HPa H0 HP0 Hd 95.524 1 -120 +DIHEdral HPa H0 HP0 Ha 95.524 1 -120 +DIHEdral HPa H0 HP0 Hda 95.524 1 -120 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H5 H5 HPa 95.524 1 -120 +DIHEdral HPa H5 Hd H0 95.524 1 -120 +DIHEdral HPa H5 Hd H5 95.524 1 -120 +DIHEdral HPa H5 Hd Hd 95.524 1 -120 +DIHEdral HPa H5 Hd Ha 95.524 1 -120 +DIHEdral HPa H5 Hd Hda 95.524 1 -120 +DIHEdral HPa H5 Hd HP5 95.524 1 -120 +DIHEdral HPa H5 Hd HP0 95.524 1 -120 +DIHEdral HPa H5 Hd HPa 95.524 1 -120 +DIHEdral HPa H5 Ha H0 95.524 1 -120 +DIHEdral HPa H5 Ha H5 95.524 1 -120 +DIHEdral HPa H5 Ha Hd 95.524 1 -120 +DIHEdral HPa H5 Ha Ha 95.524 1 -120 +DIHEdral HPa H5 Ha Hda 95.524 1 -120 +DIHEdral HPa H5 Ha HP5 95.524 1 -120 +DIHEdral HPa H5 Ha HP0 95.524 1 -120 +DIHEdral HPa H5 Ha HPa 95.524 1 -120 +DIHEdral HPa H5 Hda H0 95.524 1 -120 +DIHEdral HPa H5 Hda H5 95.524 1 -120 +DIHEdral HPa H5 Hda Hd 95.524 1 -120 +DIHEdral HPa H5 Hda Ha 95.524 1 -120 +DIHEdral HPa H5 Hda Hda 95.524 1 -120 +DIHEdral HPa H5 Hda HP5 95.524 1 -120 +DIHEdral HPa H5 Hda HP0 95.524 1 -120 +DIHEdral HPa H5 Hda HPa 95.524 1 -120 +DIHEdral HPa H5 HP5 H0 95.524 1 -120 +DIHEdral HPa H5 HP5 H5 95.524 1 -120 +DIHEdral HPa H5 HP5 Hd 95.524 1 -120 +DIHEdral HPa H5 HP5 Ha 95.524 1 -120 +DIHEdral HPa H5 HP5 Hda 95.524 1 -120 +DIHEdral HPa H5 HP5 HP5 95.524 1 -120 +DIHEdral HPa H5 HP5 HP0 95.524 1 -120 +DIHEdral HPa H5 HP5 HPa 95.524 1 -120 +DIHEdral HPa H5 HP0 H0 95.524 1 -120 +DIHEdral HPa H5 HP0 H5 95.524 1 -120 +DIHEdral HPa H5 HP0 Hd 95.524 1 -120 +DIHEdral HPa H5 HP0 Ha 95.524 1 -120 +DIHEdral HPa H5 HP0 Hda 95.524 1 -120 +DIHEdral HPa H5 HP0 HP5 95.524 1 -120 +DIHEdral HPa H5 HP0 HP0 95.524 1 -120 +DIHEdral HPa H5 HP0 HPa 95.524 1 -120 +DIHEdral HPa H5 HPa H0 95.524 1 -120 +DIHEdral HPa H5 HPa H5 95.524 1 -120 +DIHEdral HPa H5 HPa Hd 95.524 1 -120 +DIHEdral HPa H5 HPa Ha 95.524 1 -120 +DIHEdral HPa H5 HPa Hda 95.524 1 -120 +DIHEdral HPa H5 HPa HP5 95.524 1 -120 +DIHEdral HPa H5 HPa HP0 95.524 1 -120 +DIHEdral HPa H5 HPa HPa 95.524 1 -120 +DIHEdral HPa Hd H0 H0 95.524 1 -120 +DIHEdral HPa Hd H0 H5 95.524 1 -120 +DIHEdral HPa Hd H0 Hd 95.524 1 -120 +DIHEdral HPa Hd H0 Ha 95.524 1 -120 +DIHEdral HPa Hd H0 Hda 95.524 1 -120 +DIHEdral HPa Hd H0 HP5 95.524 1 -120 +DIHEdral HPa Hd H0 HP0 95.524 1 -120 +DIHEdral HPa Hd H0 HPa 95.524 1 -120 +DIHEdral HPa Hd H5 H0 95.524 1 -120 +DIHEdral HPa Hd H5 H5 95.524 1 -120 +DIHEdral HPa Hd H5 Hd 95.524 1 -120 +DIHEdral HPa Hd H5 Ha 95.524 1 -120 +DIHEdral HPa Hd H5 Hda 95.524 1 -120 +DIHEdral HPa Hd H5 HP5 95.524 1 -120 +DIHEdral HPa Hd H5 HP0 95.524 1 -120 +DIHEdral HPa Hd H5 HPa 95.524 1 -120 +DIHEdral HPa Hd Hd H0 95.524 1 -120 +DIHEdral HPa Hd Hd H5 95.524 1 -120 +DIHEdral HPa Hd Hd Hd 95.524 1 -120 +DIHEdral HPa Hd Hd Ha 95.524 1 -120 +DIHEdral HPa Hd Hd Hda 95.524 1 -120 +DIHEdral HPa Hd Hd HP5 95.524 1 -120 +DIHEdral HPa Hd Hd HP0 95.524 1 -120 +DIHEdral HPa Hd Hd HPa 95.524 1 -120 +DIHEdral HPa Hd Ha H0 95.524 1 -120 +DIHEdral HPa Hd Ha H5 95.524 1 -120 +DIHEdral HPa Hd Ha Hd 95.524 1 -120 +DIHEdral HPa Hd Ha Ha 95.524 1 -120 +DIHEdral HPa Hd Ha Hda 95.524 1 -120 +DIHEdral HPa Hd Ha HP5 95.524 1 -120 +DIHEdral HPa Hd Ha HP0 95.524 1 -120 +DIHEdral HPa Hd Ha HPa 95.524 1 -120 +DIHEdral HPa Hd Hda H0 95.524 1 -120 +DIHEdral HPa Hd Hda H5 95.524 1 -120 +DIHEdral HPa Hd Hda Hd 95.524 1 -120 +DIHEdral HPa Hd Hda Ha 95.524 1 -120 +DIHEdral HPa Hd Hda Hda 95.524 1 -120 +DIHEdral HPa Hd Hda HP5 95.524 1 -120 +DIHEdral HPa Hd Hda HP0 95.524 1 -120 +DIHEdral HPa Hd Hda HPa 95.524 1 -120 +DIHEdral HPa Hd HP5 H0 95.524 1 -120 +DIHEdral HPa Hd HP5 H5 95.524 1 -120 +DIHEdral HPa Hd HP5 Hd 95.524 1 -120 +DIHEdral HPa Hd HP5 Ha 95.524 1 -120 +DIHEdral HPa Hd HP5 Hda 95.524 1 -120 +DIHEdral HPa Hd HP5 HP5 95.524 1 -120 +DIHEdral HPa Hd HP5 HP0 95.524 1 -120 +DIHEdral HPa Hd HP5 HPa 95.524 1 -120 +DIHEdral HPa Hd HP0 H0 95.524 1 -120 +DIHEdral HPa Hd HP0 H5 95.524 1 -120 +DIHEdral HPa Hd HP0 Hd 95.524 1 -120 +DIHEdral HPa Hd HP0 Ha 95.524 1 -120 +DIHEdral HPa Hd HP0 Hda 95.524 1 -120 +DIHEdral HPa Hd HP0 HP5 95.524 1 -120 +DIHEdral HPa Hd HP0 HP0 95.524 1 -120 +DIHEdral HPa Hd HP0 HPa 95.524 1 -120 +DIHEdral HPa Hd HPa H0 95.524 1 -120 +DIHEdral HPa Hd HPa H5 95.524 1 -120 +DIHEdral HPa Hd HPa Hd 95.524 1 -120 +DIHEdral HPa Hd HPa Ha 95.524 1 -120 +DIHEdral HPa Hd HPa Hda 95.524 1 -120 +DIHEdral HPa Hd HPa HP5 95.524 1 -120 +DIHEdral HPa Hd HPa HP0 95.524 1 -120 +DIHEdral HPa Hd HPa HPa 95.524 1 -120 +DIHEdral HPa Ha H0 H0 95.524 1 -120 +DIHEdral HPa Ha H0 H5 95.524 1 -120 +DIHEdral HPa Ha H0 Hd 95.524 1 -120 +DIHEdral HPa Ha H0 Ha 95.524 1 -120 +DIHEdral HPa Ha H0 Hda 95.524 1 -120 +DIHEdral HPa Ha H0 HP5 95.524 1 -120 +DIHEdral HPa Ha H0 HP0 95.524 1 -120 +DIHEdral HPa Ha H0 HPa 95.524 1 -120 +DIHEdral HPa Ha H5 H0 95.524 1 -120 +DIHEdral HPa Ha H5 H5 95.524 1 -120 +DIHEdral HPa Ha H5 Hd 95.524 1 -120 +DIHEdral HPa Ha H5 Ha 95.524 1 -120 +DIHEdral HPa Ha H5 Hda 95.524 1 -120 +DIHEdral HPa Ha H5 HP5 95.524 1 -120 +DIHEdral HPa Ha H5 HP0 95.524 1 -120 +DIHEdral HPa Ha H5 HPa 95.524 1 -120 +DIHEdral HPa Ha Hd H0 95.524 1 -120 +DIHEdral HPa Ha Hd H5 95.524 1 -120 +DIHEdral HPa Ha Hd Hd 95.524 1 -120 +DIHEdral HPa Ha Hd Ha 95.524 1 -120 +DIHEdral HPa Ha Hd Hda 95.524 1 -120 +DIHEdral HPa Ha Hd HP5 95.524 1 -120 +DIHEdral HPa Ha Hd HP0 95.524 1 -120 +DIHEdral HPa Ha Hd HPa 95.524 1 -120 +DIHEdral HPa Ha Ha H0 95.524 1 -120 +DIHEdral HPa Ha Ha H5 95.524 1 -120 +DIHEdral HPa Ha Ha Hd 95.524 1 -120 +DIHEdral HPa Ha Ha Ha 95.524 1 -120 +DIHEdral HPa Ha Ha Hda 95.524 1 -120 +DIHEdral HPa Ha Ha HP5 95.524 1 -120 +DIHEdral HPa Ha Ha HP0 95.524 1 -120 +DIHEdral HPa Ha Ha HPa 95.524 1 -120 +DIHEdral HPa Ha Hda H0 95.524 1 -120 +DIHEdral HPa Ha Hda H5 95.524 1 -120 +DIHEdral HPa Ha Hda Hd 95.524 1 -120 +DIHEdral HPa Ha Hda Ha 95.524 1 -120 +DIHEdral HPa Ha Hda Hda 95.524 1 -120 +DIHEdral HPa Ha Hda HP5 95.524 1 -120 +DIHEdral HPa Ha Hda HP0 95.524 1 -120 +DIHEdral HPa Ha Hda HPa 95.524 1 -120 +DIHEdral HPa Ha HP5 H0 95.524 1 -120 +DIHEdral HPa Ha HP5 H5 95.524 1 -120 +DIHEdral HPa Ha HP5 Hd 95.524 1 -120 +DIHEdral HPa Ha HP5 Ha 95.524 1 -120 +DIHEdral HPa Ha HP5 Hda 95.524 1 -120 +DIHEdral HPa Ha HP5 HP5 95.524 1 -120 +DIHEdral HPa Ha HP5 HP0 95.524 1 -120 +DIHEdral HPa Ha HP5 HPa 95.524 1 -120 +DIHEdral HPa Ha HP0 H0 95.524 1 -120 +DIHEdral HPa Ha HP0 H5 95.524 1 -120 +DIHEdral HPa Ha HP0 Hd 95.524 1 -120 +DIHEdral HPa Ha HP0 Ha 95.524 1 -120 +DIHEdral HPa Ha HP0 Hda 95.524 1 -120 +DIHEdral HPa Ha HP0 HP5 95.524 1 -120 +DIHEdral HPa Ha HP0 HP0 95.524 1 -120 +DIHEdral HPa Ha HP0 HPa 95.524 1 -120 +DIHEdral HPa Ha HPa H0 95.524 1 -120 +DIHEdral HPa Ha HPa H5 95.524 1 -120 +DIHEdral HPa Ha HPa Hd 95.524 1 -120 +DIHEdral HPa Ha HPa Ha 95.524 1 -120 +DIHEdral HPa Ha HPa Hda 95.524 1 -120 +DIHEdral HPa Ha HPa HP5 95.524 1 -120 +DIHEdral HPa Ha HPa HP0 95.524 1 -120 +DIHEdral HPa Ha HPa HPa 95.524 1 -120 +DIHEdral HPa Hda H0 H0 95.524 1 -120 +DIHEdral HPa Hda H0 H5 95.524 1 -120 +DIHEdral HPa Hda H0 Hd 95.524 1 -120 +DIHEdral HPa Hda H0 Ha 95.524 1 -120 +DIHEdral HPa Hda H0 Hda 95.524 1 -120 +DIHEdral HPa Hda H0 HP5 95.524 1 -120 +DIHEdral HPa Hda H0 HP0 95.524 1 -120 +DIHEdral HPa Hda H0 HPa 95.524 1 -120 +DIHEdral HPa Hda H5 H0 95.524 1 -120 +DIHEdral HPa Hda H5 H5 95.524 1 -120 +DIHEdral HPa Hda H5 Hd 95.524 1 -120 +DIHEdral HPa Hda H5 Ha 95.524 1 -120 +DIHEdral HPa Hda H5 Hda 95.524 1 -120 +DIHEdral HPa Hda H5 HP5 95.524 1 -120 +DIHEdral HPa Hda H5 HP0 95.524 1 -120 +DIHEdral HPa Hda H5 HPa 95.524 1 -120 +DIHEdral HPa Hda Hd H0 95.524 1 -120 +DIHEdral HPa Hda Hd H5 95.524 1 -120 +DIHEdral HPa Hda Hd Hd 95.524 1 -120 +DIHEdral HPa Hda Hd Ha 95.524 1 -120 +DIHEdral HPa Hda Hd Hda 95.524 1 -120 +DIHEdral HPa Hda Hd HP5 95.524 1 -120 +DIHEdral HPa Hda Hd HP0 95.524 1 -120 +DIHEdral HPa Hda Hd HPa 95.524 1 -120 +DIHEdral HPa Hda Ha H0 95.524 1 -120 +DIHEdral HPa Hda Ha H5 95.524 1 -120 +DIHEdral HPa Hda Ha Hd 95.524 1 -120 +DIHEdral HPa Hda Ha Ha 95.524 1 -120 +DIHEdral HPa Hda Ha Hda 95.524 1 -120 +DIHEdral HPa Hda Ha HP5 95.524 1 -120 +DIHEdral HPa Hda Ha HP0 95.524 1 -120 +DIHEdral HPa Hda Ha HPa 95.524 1 -120 +DIHEdral HPa Hda Hda H0 95.524 1 -120 +DIHEdral HPa Hda Hda H5 95.524 1 -120 +DIHEdral HPa Hda Hda Hd 95.524 1 -120 +DIHEdral HPa Hda Hda Ha 95.524 1 -120 +DIHEdral HPa Hda Hda Hda 95.524 1 -120 +DIHEdral HPa Hda Hda HP5 95.524 1 -120 +DIHEdral HPa Hda Hda HP0 95.524 1 -120 +DIHEdral HPa Hda Hda HPa 95.524 1 -120 +DIHEdral HPa Hda HP5 H0 95.524 1 -120 +DIHEdral HPa Hda HP5 H5 95.524 1 -120 +DIHEdral HPa Hda HP5 Hd 95.524 1 -120 +DIHEdral HPa Hda HP5 Ha 95.524 1 -120 +DIHEdral HPa Hda HP5 Hda 95.524 1 -120 +DIHEdral HPa Hda HP5 HP5 95.524 1 -120 +DIHEdral HPa Hda HP5 HP0 95.524 1 -120 +DIHEdral HPa Hda HP5 HPa 95.524 1 -120 +DIHEdral HPa Hda HP0 H0 95.524 1 -120 +DIHEdral HPa Hda HP0 H5 95.524 1 -120 +DIHEdral HPa Hda HP0 Hd 95.524 1 -120 +DIHEdral HPa Hda HP0 Ha 95.524 1 -120 +DIHEdral HPa Hda HP0 Hda 95.524 1 -120 +DIHEdral HPa Hda HP0 HP5 95.524 1 -120 +DIHEdral HPa Hda HP0 HP0 95.524 1 -120 +DIHEdral HPa Hda HP0 HPa 95.524 1 -120 +DIHEdral HPa Hda HPa H0 95.524 1 -120 +DIHEdral HPa Hda HPa H5 95.524 1 -120 +DIHEdral HPa Hda HPa Hd 95.524 1 -120 +DIHEdral HPa Hda HPa Ha 95.524 1 -120 +DIHEdral HPa Hda HPa Hda 95.524 1 -120 +DIHEdral HPa Hda HPa HP5 95.524 1 -120 +DIHEdral HPa Hda HPa HP0 95.524 1 -120 +DIHEdral HPa Hda HPa HPa 95.524 1 -120 +DIHEdral HPa HP5 H0 H0 95.524 1 -120 +DIHEdral HPa HP5 H0 H5 95.524 1 -120 +DIHEdral HPa HP5 H0 Hd 95.524 1 -120 +DIHEdral HPa HP5 H0 Ha 95.524 1 -120 +DIHEdral HPa HP5 H0 Hda 95.524 1 -120 +DIHEdral HPa HP5 H0 HP5 95.524 1 -120 +DIHEdral HPa HP5 H0 HP0 95.524 1 -120 +DIHEdral HPa HP5 H0 HPa 95.524 1 -120 +DIHEdral HPa HP5 H5 H0 95.524 1 -120 +DIHEdral HPa HP5 H5 H5 95.524 1 -120 +DIHEdral HPa HP5 H5 Hd 95.524 1 -120 +DIHEdral HPa HP5 H5 Ha 95.524 1 -120 +DIHEdral HPa HP5 H5 Hda 95.524 1 -120 +DIHEdral HPa HP5 H5 HP5 95.524 1 -120 +DIHEdral HPa HP5 H5 HP0 95.524 1 -120 +DIHEdral HPa HP5 H5 HPa 95.524 1 -120 +DIHEdral HPa HP5 Hd H0 95.524 1 -120 +DIHEdral HPa HP5 Hd H5 95.524 1 -120 +DIHEdral HPa HP5 Hd Hd 95.524 1 -120 +DIHEdral HPa HP5 Hd Ha 95.524 1 -120 +DIHEdral HPa HP5 Hd Hda 95.524 1 -120 +DIHEdral HPa HP5 Hd HP5 95.524 1 -120 +DIHEdral HPa HP5 Hd HP0 95.524 1 -120 +DIHEdral HPa HP5 Hd HPa 95.524 1 -120 +DIHEdral HPa HP5 Ha H0 95.524 1 -120 +DIHEdral HPa HP5 Ha H5 95.524 1 -120 +DIHEdral HPa HP5 Ha Hd 95.524 1 -120 +DIHEdral HPa HP5 Ha Ha 95.524 1 -120 +DIHEdral HPa HP5 Ha Hda 95.524 1 -120 +DIHEdral HPa HP5 Ha HP5 95.524 1 -120 +DIHEdral HPa HP5 Ha HP0 95.524 1 -120 +DIHEdral HPa HP5 Ha HPa 95.524 1 -120 +DIHEdral HPa HP5 Hda H0 95.524 1 -120 +DIHEdral HPa HP5 Hda H5 95.524 1 -120 +DIHEdral HPa HP5 Hda Hd 95.524 1 -120 +DIHEdral HPa HP5 Hda Ha 95.524 1 -120 +DIHEdral HPa HP5 Hda Hda 95.524 1 -120 +DIHEdral HPa HP5 Hda HP5 95.524 1 -120 +DIHEdral HPa HP5 Hda HP0 95.524 1 -120 +DIHEdral HPa HP5 Hda HPa 95.524 1 -120 +DIHEdral HPa HP5 HP5 H0 95.524 1 -120 +DIHEdral HPa HP5 HP5 H5 95.524 1 -120 +DIHEdral HPa HP5 HP5 Hd 95.524 1 -120 +DIHEdral HPa HP5 HP5 Ha 95.524 1 -120 +DIHEdral HPa HP5 HP5 Hda 95.524 1 -120 +DIHEdral HPa HP5 HP5 HP5 95.524 1 -120 +DIHEdral HPa HP5 HP5 HP0 95.524 1 -120 +DIHEdral HPa HP5 HP5 HPa 95.524 1 -120 +DIHEdral HPa HP5 HP0 H0 95.524 1 -120 +DIHEdral HPa HP5 HP0 H5 95.524 1 -120 +DIHEdral HPa HP5 HP0 Hd 95.524 1 -120 +DIHEdral HPa HP5 HP0 Ha 95.524 1 -120 +DIHEdral HPa HP5 HP0 Hda 95.524 1 -120 +DIHEdral HPa HP5 HP0 HP5 95.524 1 -120 +DIHEdral HPa HP5 HP0 HP0 95.524 1 -120 +DIHEdral HPa HP5 HP0 HPa 95.524 1 -120 +DIHEdral HPa HP5 HPa H0 95.524 1 -120 +DIHEdral HPa HP5 HPa H5 95.524 1 -120 +DIHEdral HPa HP5 HPa Hd 95.524 1 -120 +DIHEdral HPa HP5 HPa Ha 95.524 1 -120 +DIHEdral HPa HP5 HPa Hda 95.524 1 -120 +DIHEdral HPa HP5 HPa HP5 95.524 1 -120 +DIHEdral HPa HP5 HPa HP0 95.524 1 -120 +DIHEdral HPa HP5 HPa HPa 95.524 1 -120 +DIHEdral HPa HP0 H0 H0 95.524 1 -120 +DIHEdral HPa HP0 H0 H5 95.524 1 -120 +DIHEdral HPa HP0 H0 Hd 95.524 1 -120 +DIHEdral HPa HP0 H0 Ha 95.524 1 -120 +DIHEdral HPa HP0 H0 Hda 95.524 1 -120 +DIHEdral HPa HP0 H0 HP5 95.524 1 -120 +DIHEdral HPa HP0 H0 HP0 95.524 1 -120 +DIHEdral HPa HP0 H0 HPa 95.524 1 -120 +DIHEdral HPa HP0 H5 H0 95.524 1 -120 +DIHEdral HPa HP0 H5 H5 95.524 1 -120 +DIHEdral HPa HP0 H5 Hd 95.524 1 -120 +DIHEdral HPa HP0 H5 Ha 95.524 1 -120 +DIHEdral HPa HP0 H5 Hda 95.524 1 -120 +DIHEdral HPa HP0 H5 HP5 95.524 1 -120 +DIHEdral HPa HP0 H5 HP0 95.524 1 -120 +DIHEdral HPa HP0 H5 HPa 95.524 1 -120 +DIHEdral HPa HP0 Hd H0 95.524 1 -120 +DIHEdral HPa HP0 Hd H5 95.524 1 -120 +DIHEdral HPa HP0 Hd Hd 95.524 1 -120 +DIHEdral HPa HP0 Hd Ha 95.524 1 -120 +DIHEdral HPa HP0 Hd Hda 95.524 1 -120 +DIHEdral HPa HP0 Hd HP5 95.524 1 -120 +DIHEdral HPa HP0 Hd HP0 95.524 1 -120 +DIHEdral HPa HP0 Hd HPa 95.524 1 -120 +DIHEdral HPa HP0 Ha H0 95.524 1 -120 +DIHEdral HPa HP0 Ha H5 95.524 1 -120 +DIHEdral HPa HP0 Ha Hd 95.524 1 -120 +DIHEdral HPa HP0 Ha Ha 95.524 1 -120 +DIHEdral HPa HP0 Ha Hda 95.524 1 -120 +DIHEdral HPa HP0 Ha HP5 95.524 1 -120 +DIHEdral HPa HP0 Ha HP0 95.524 1 -120 +DIHEdral HPa HP0 Ha HPa 95.524 1 -120 +DIHEdral HPa HP0 Hda H0 95.524 1 -120 +DIHEdral HPa HP0 Hda H5 95.524 1 -120 +DIHEdral HPa HP0 Hda Hd 95.524 1 -120 +DIHEdral HPa HP0 Hda Ha 95.524 1 -120 +DIHEdral HPa HP0 Hda Hda 95.524 1 -120 +DIHEdral HPa HP0 Hda HP5 95.524 1 -120 +DIHEdral HPa HP0 Hda HP0 95.524 1 -120 +DIHEdral HPa HP0 Hda HPa 95.524 1 -120 +DIHEdral HPa HP0 HP5 H0 95.524 1 -120 +DIHEdral HPa HP0 HP5 H5 95.524 1 -120 +DIHEdral HPa HP0 HP5 Hd 95.524 1 -120 +DIHEdral HPa HP0 HP5 Ha 95.524 1 -120 +DIHEdral HPa HP0 HP5 Hda 95.524 1 -120 +DIHEdral HPa HP0 HP5 HP5 95.524 1 -120 +DIHEdral HPa HP0 HP5 HP0 95.524 1 -120 +DIHEdral HPa HP0 HP5 HPa 95.524 1 -120 +DIHEdral HPa HP0 HP0 H0 95.524 1 -120 +DIHEdral HPa HP0 HP0 H5 95.524 1 -120 +DIHEdral HPa HP0 HP0 Hd 95.524 1 -120 +DIHEdral HPa HP0 HP0 Ha 95.524 1 -120 +DIHEdral HPa HP0 HP0 Hda 95.524 1 -120 +DIHEdral HPa HP0 HP0 HP5 95.524 1 -120 +DIHEdral HPa HP0 HP0 HP0 95.524 1 -120 +DIHEdral HPa HP0 HP0 HPa 95.524 1 -120 +DIHEdral HPa HP0 HPa H0 95.524 1 -120 +DIHEdral HPa HP0 HPa H5 95.524 1 -120 +DIHEdral HPa HP0 HPa Hd 95.524 1 -120 +DIHEdral HPa HP0 HPa Ha 95.524 1 -120 +DIHEdral HPa HP0 HPa Hda 95.524 1 -120 +DIHEdral HPa HP0 HPa HP5 95.524 1 -120 +DIHEdral HPa HP0 HPa HP0 95.524 1 -120 +DIHEdral HPa HP0 HPa HPa 95.524 1 -120 +DIHEdral HPa HPa H0 H0 95.524 1 -120 +DIHEdral HPa HPa H0 H5 95.524 1 -120 +DIHEdral HPa HPa H0 Hd 95.524 1 -120 +DIHEdral HPa HPa H0 Ha 95.524 1 -120 +DIHEdral HPa HPa H0 Hda 95.524 1 -120 +DIHEdral HPa HPa H0 HP5 95.524 1 -120 +DIHEdral HPa HPa H0 HP0 95.524 1 -120 +DIHEdral HPa HPa H0 HPa 95.524 1 -120 +DIHEdral HPa HPa H5 H0 95.524 1 -120 +DIHEdral HPa HPa H5 H5 95.524 1 -120 +DIHEdral HPa HPa H5 Hd 95.524 1 -120 +DIHEdral HPa HPa H5 Ha 95.524 1 -120 +DIHEdral HPa HPa H5 Hda 95.524 1 -120 +DIHEdral HPa HPa H5 HP5 95.524 1 -120 +DIHEdral HPa HPa H5 HP0 95.524 1 -120 +DIHEdral HPa HPa H5 HPa 95.524 1 -120 +DIHEdral HPa HPa Hd H0 95.524 1 -120 +DIHEdral HPa HPa Hd H5 95.524 1 -120 +DIHEdral HPa HPa Hd Hd 95.524 1 -120 +DIHEdral HPa HPa Hd Ha 95.524 1 -120 +DIHEdral HPa HPa Hd Hda 95.524 1 -120 +DIHEdral HPa HPa Hd HP5 95.524 1 -120 +DIHEdral HPa HPa Hd HP0 95.524 1 -120 +DIHEdral HPa HPa Hd HPa 95.524 1 -120 +DIHEdral HPa HPa Ha H0 95.524 1 -120 +DIHEdral HPa HPa Ha H5 95.524 1 -120 +DIHEdral HPa HPa Ha Hd 95.524 1 -120 +DIHEdral HPa HPa Ha Ha 95.524 1 -120 +DIHEdral HPa HPa Ha Hda 95.524 1 -120 +DIHEdral HPa HPa Ha HP5 95.524 1 -120 +DIHEdral HPa HPa Ha HP0 95.524 1 -120 +DIHEdral HPa HPa Ha HPa 95.524 1 -120 +DIHEdral HPa HPa Hda H0 95.524 1 -120 +DIHEdral HPa HPa Hda H5 95.524 1 -120 +DIHEdral HPa HPa Hda Hd 95.524 1 -120 +DIHEdral HPa HPa Hda Ha 95.524 1 -120 +DIHEdral HPa HPa Hda Hda 95.524 1 -120 +DIHEdral HPa HPa Hda HP5 95.524 1 -120 +DIHEdral HPa HPa Hda HP0 95.524 1 -120 +DIHEdral HPa HPa Hda HPa 95.524 1 -120 +DIHEdral HPa HPa HP5 H0 95.524 1 -120 +DIHEdral HPa HPa HP5 H5 95.524 1 -120 +DIHEdral HPa HPa HP5 Hd 95.524 1 -120 +DIHEdral HPa HPa HP5 Ha 95.524 1 -120 +DIHEdral HPa HPa HP5 Hda 95.524 1 -120 +DIHEdral HPa HPa HP5 HP5 95.524 1 -120 +DIHEdral HPa HPa HP5 HP0 95.524 1 -120 +DIHEdral HPa HPa HP5 HPa 95.524 1 -120 +DIHEdral HPa HPa HP0 H0 95.524 1 -120 +DIHEdral HPa HPa HP0 H5 95.524 1 -120 +DIHEdral HPa HPa HP0 Hd 95.524 1 -120 +DIHEdral HPa HPa HP0 Ha 95.524 1 -120 +DIHEdral HPa HPa HP0 Hda 95.524 1 -120 +DIHEdral HPa HPa HP0 HP5 95.524 1 -120 +DIHEdral HPa HPa HP0 HP0 95.524 1 -120 +DIHEdral HPa HPa HP0 HPa 95.524 1 -120 +DIHEdral HPa HPa HPa H0 95.524 1 -120 +DIHEdral HPa HPa HPa H5 95.524 1 -120 +DIHEdral HPa HPa HPa Hd 95.524 1 -120 +DIHEdral HPa HPa HPa Ha 95.524 1 -120 +DIHEdral HPa HPa HPa Hda 95.524 1 -120 +DIHEdral HPa HPa HPa HP5 95.524 1 -120 +DIHEdral HPa HPa HPa HP0 95.524 1 -120 +DIHEdral HPa HPa HPa HPa 95.524 1 -120 + +DIHEdral Bda Bda Bda Bda 0.570 1 0 +DIHEdral Bda Bda Bda B0 0.570 1 0 +DIHEdral Bda Bda B0 Bda 0.570 1 0 +DIHEdral Bda Bda B0 B0 0.570 1 0 +DIHEdral Bda B0 Bda Bda 0.570 1 0 +DIHEdral Bda B0 Bda B0 0.570 1 0 +DIHEdral Bda B0 B0 Bda 0.570 1 0 +DIHEdral Bda B0 B0 B0 0.570 1 0 +DIHEdral B0 Bda Bda Bda 0.570 1 0 +DIHEdral B0 Bda Bda B0 0.570 1 0 +DIHEdral B0 Bda B0 Bda 0.570 1 0 +DIHEdral B0 Bda B0 B0 0.570 1 0 +DIHEdral B0 B0 Bda Bda 0.570 1 0 +DIHEdral B0 B0 Bda B0 0.570 1 0 +DIHEdral B0 B0 B0 Bda 0.570 1 0 +DIHEdral B0 B0 B0 B0 0.570 1 0 + + +{*BSSS, backbone sidechain dihedrals & impropers *} + +DIHEdral F5 SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral F5 SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral F5 SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral F5 SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Bda SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral Bda SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral Bda SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral Bda SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral H0 SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral H0 SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral H0 SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral H0 SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Hd SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral Hd SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral Hd SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral Hd SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Ha SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral Ha SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral Ha SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral Ha SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Hda SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral Hda SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral Hda SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral Hda SP1 SP1 HC4 11.942 0 0.000 ! HIS +DIHEdral Tda SP1 SC4 SC4 11.942 0 0.000 ! TRP +DIHEdral Tda SC4 SP1 TC4 11.942 0 0.000 ! TYR +DIHEdral Tda SC4 SC4 PC4 11.942 0 0.000 ! PHE +DIHEdral Tda SP1 SP1 HC4 11.942 0 0.000 ! HIS + + +{* SSSS, sidechain impropers *} +DIHEdral SC4 SP1 SC4 SC4 47.767 0 0 ! TRP + +{*BBBB,Not to be defined backbone dihedrals & impropers *} + +DIHEdral F4 F4 F4 F4 0 6 0 +DIHEdral F4 F4 F4 F5 0 6 0 +DIHEdral F4 F4 F4 Fa 0 6 0 +DIHEdral F4 F4 F4 H0 0 6 0 +DIHEdral F4 F4 F4 H5 0 6 0 +DIHEdral F4 F4 F4 Hd 0 6 0 +DIHEdral F4 F4 F4 Ha 0 6 0 +DIHEdral F4 F4 F4 Hda 0 6 0 +DIHEdral F4 F4 F4 Bda 0 6 0 +DIHEdral F4 F4 F4 B0 0 6 0 +DIHEdral F4 F4 F4 Tda 0 6 0 +DIHEdral F4 F4 F4 T0 0 6 0 +DIHEdral F4 F4 F4 HP5 0 6 0 +DIHEdral F4 F4 F4 HP0 0 6 0 +DIHEdral F4 F4 F4 HPa 0 6 0 +DIHEdral F4 F4 F5 F4 0 6 0 +DIHEdral F4 F4 F5 F5 0 6 0 +DIHEdral F4 F4 F5 Fa 0 6 0 +DIHEdral F4 F4 F5 H0 0 6 0 +DIHEdral F4 F4 F5 H5 0 6 0 +DIHEdral F4 F4 F5 Hd 0 6 0 +DIHEdral F4 F4 F5 Ha 0 6 0 +DIHEdral F4 F4 F5 Hda 0 6 0 +DIHEdral F4 F4 F5 Bda 0 6 0 +DIHEdral F4 F4 F5 B0 0 6 0 +DIHEdral F4 F4 F5 Tda 0 6 0 +DIHEdral F4 F4 F5 T0 0 6 0 +DIHEdral F4 F4 F5 HP5 0 6 0 +DIHEdral F4 F4 F5 HP0 0 6 0 +DIHEdral F4 F4 F5 HPa 0 6 0 +DIHEdral F4 F4 Fa F4 0 6 0 +DIHEdral F4 F4 Fa F5 0 6 0 +DIHEdral F4 F4 Fa Fa 0 6 0 +DIHEdral F4 F4 Fa H0 0 6 0 +DIHEdral F4 F4 Fa H5 0 6 0 +DIHEdral F4 F4 Fa Hd 0 6 0 +DIHEdral F4 F4 Fa Ha 0 6 0 +DIHEdral F4 F4 Fa Hda 0 6 0 +DIHEdral F4 F4 Fa Bda 0 6 0 +DIHEdral F4 F4 Fa B0 0 6 0 +DIHEdral F4 F4 Fa Tda 0 6 0 +DIHEdral F4 F4 Fa T0 0 6 0 +DIHEdral F4 F4 Fa HP5 0 6 0 +DIHEdral F4 F4 Fa HP0 0 6 0 +DIHEdral F4 F4 Fa HPa 0 6 0 +DIHEdral F4 F4 H0 F4 0 6 0 +DIHEdral F4 F4 H0 F5 0 6 0 +DIHEdral F4 F4 H0 Fa 0 6 0 +DIHEdral F4 F4 H0 H0 0 6 0 +DIHEdral F4 F4 H0 H5 0 6 0 +DIHEdral F4 F4 H0 Hd 0 6 0 +DIHEdral F4 F4 H0 Ha 0 6 0 +DIHEdral F4 F4 H0 Hda 0 6 0 +DIHEdral F4 F4 H0 Bda 0 6 0 +DIHEdral F4 F4 H0 B0 0 6 0 +DIHEdral F4 F4 H0 Tda 0 6 0 +DIHEdral F4 F4 H0 T0 0 6 0 +DIHEdral F4 F4 H0 HP5 0 6 0 +DIHEdral F4 F4 H0 HP0 0 6 0 +DIHEdral F4 F4 H0 HPa 0 6 0 +DIHEdral F4 F4 H5 F4 0 6 0 +DIHEdral F4 F4 H5 F5 0 6 0 +DIHEdral F4 F4 H5 Fa 0 6 0 +DIHEdral F4 F4 H5 H0 0 6 0 +DIHEdral F4 F4 H5 H5 0 6 0 +DIHEdral F4 F4 H5 Hd 0 6 0 +DIHEdral F4 F4 H5 Ha 0 6 0 +DIHEdral F4 F4 H5 Hda 0 6 0 +DIHEdral F4 F4 H5 Bda 0 6 0 +DIHEdral F4 F4 H5 B0 0 6 0 +DIHEdral F4 F4 H5 Tda 0 6 0 +DIHEdral F4 F4 H5 T0 0 6 0 +DIHEdral F4 F4 H5 HP5 0 6 0 +DIHEdral F4 F4 H5 HP0 0 6 0 +DIHEdral F4 F4 H5 HPa 0 6 0 +DIHEdral F4 F4 Hd F4 0 6 0 +DIHEdral F4 F4 Hd F5 0 6 0 +DIHEdral F4 F4 Hd Fa 0 6 0 +DIHEdral F4 F4 Hd H0 0 6 0 +DIHEdral F4 F4 Hd H5 0 6 0 +DIHEdral F4 F4 Hd Hd 0 6 0 +DIHEdral F4 F4 Hd Ha 0 6 0 +DIHEdral F4 F4 Hd Hda 0 6 0 +DIHEdral F4 F4 Hd Bda 0 6 0 +DIHEdral F4 F4 Hd B0 0 6 0 +DIHEdral F4 F4 Hd Tda 0 6 0 +DIHEdral F4 F4 Hd T0 0 6 0 +DIHEdral F4 F4 Hd HP5 0 6 0 +DIHEdral F4 F4 Hd HP0 0 6 0 +DIHEdral F4 F4 Hd HPa 0 6 0 +DIHEdral F4 F4 Ha F4 0 6 0 +DIHEdral F4 F4 Ha F5 0 6 0 +DIHEdral F4 F4 Ha Fa 0 6 0 +DIHEdral F4 F4 Ha H0 0 6 0 +DIHEdral F4 F4 Ha H5 0 6 0 +DIHEdral F4 F4 Ha Hd 0 6 0 +DIHEdral F4 F4 Ha Ha 0 6 0 +DIHEdral F4 F4 Ha Hda 0 6 0 +DIHEdral F4 F4 Ha Bda 0 6 0 +DIHEdral F4 F4 Ha B0 0 6 0 +DIHEdral F4 F4 Ha Tda 0 6 0 +DIHEdral F4 F4 Ha T0 0 6 0 +DIHEdral F4 F4 Ha HP5 0 6 0 +DIHEdral F4 F4 Ha HP0 0 6 0 +DIHEdral F4 F4 Ha HPa 0 6 0 +DIHEdral F4 F4 Hda F4 0 6 0 +DIHEdral F4 F4 Hda F5 0 6 0 +DIHEdral F4 F4 Hda Fa 0 6 0 +DIHEdral F4 F4 Hda H0 0 6 0 +DIHEdral F4 F4 Hda H5 0 6 0 +DIHEdral F4 F4 Hda Hd 0 6 0 +DIHEdral F4 F4 Hda Ha 0 6 0 +DIHEdral F4 F4 Hda Hda 0 6 0 +DIHEdral F4 F4 Hda Bda 0 6 0 +DIHEdral F4 F4 Hda B0 0 6 0 +DIHEdral F4 F4 Hda Tda 0 6 0 +DIHEdral F4 F4 Hda T0 0 6 0 +DIHEdral F4 F4 Hda HP5 0 6 0 +DIHEdral F4 F4 Hda HP0 0 6 0 +DIHEdral F4 F4 Hda HPa 0 6 0 +DIHEdral F4 F4 Bda F4 0 6 0 +DIHEdral F4 F4 Bda F5 0 6 0 +DIHEdral F4 F4 Bda Fa 0 6 0 +DIHEdral F4 F4 Bda H0 0 6 0 +DIHEdral F4 F4 Bda H5 0 6 0 +DIHEdral F4 F4 Bda Hd 0 6 0 +DIHEdral F4 F4 Bda Ha 0 6 0 +DIHEdral F4 F4 Bda Hda 0 6 0 +DIHEdral F4 F4 Bda Bda 0 6 0 +DIHEdral F4 F4 Bda B0 0 6 0 +DIHEdral F4 F4 Bda Tda 0 6 0 +DIHEdral F4 F4 Bda T0 0 6 0 +DIHEdral F4 F4 Bda HP5 0 6 0 +DIHEdral F4 F4 Bda HP0 0 6 0 +DIHEdral F4 F4 Bda HPa 0 6 0 +DIHEdral F4 F4 B0 F4 0 6 0 +DIHEdral F4 F4 B0 F5 0 6 0 +DIHEdral F4 F4 B0 Fa 0 6 0 +DIHEdral F4 F4 B0 H0 0 6 0 +DIHEdral F4 F4 B0 H5 0 6 0 +DIHEdral F4 F4 B0 Hd 0 6 0 +DIHEdral F4 F4 B0 Ha 0 6 0 +DIHEdral F4 F4 B0 Hda 0 6 0 +DIHEdral F4 F4 B0 Bda 0 6 0 +DIHEdral F4 F4 B0 B0 0 6 0 +DIHEdral F4 F4 B0 Tda 0 6 0 +DIHEdral F4 F4 B0 T0 0 6 0 +DIHEdral F4 F4 B0 HP5 0 6 0 +DIHEdral F4 F4 B0 HP0 0 6 0 +DIHEdral F4 F4 B0 HPa 0 6 0 +DIHEdral F4 F4 Tda F4 0 6 0 +DIHEdral F4 F4 Tda F5 0 6 0 +DIHEdral F4 F4 Tda Fa 0 6 0 +DIHEdral F4 F4 Tda H0 0 6 0 +DIHEdral F4 F4 Tda H5 0 6 0 +DIHEdral F4 F4 Tda Hd 0 6 0 +DIHEdral F4 F4 Tda Ha 0 6 0 +DIHEdral F4 F4 Tda Hda 0 6 0 +DIHEdral F4 F4 Tda Bda 0 6 0 +DIHEdral F4 F4 Tda B0 0 6 0 +DIHEdral F4 F4 Tda Tda 0 6 0 +DIHEdral F4 F4 Tda T0 0 6 0 +DIHEdral F4 F4 Tda HP5 0 6 0 +DIHEdral F4 F4 Tda HP0 0 6 0 +DIHEdral F4 F4 Tda HPa 0 6 0 +DIHEdral F4 F4 T0 F4 0 6 0 +DIHEdral F4 F4 T0 F5 0 6 0 +DIHEdral F4 F4 T0 Fa 0 6 0 +DIHEdral F4 F4 T0 H0 0 6 0 +DIHEdral F4 F4 T0 H5 0 6 0 +DIHEdral F4 F4 T0 Hd 0 6 0 +DIHEdral F4 F4 T0 Ha 0 6 0 +DIHEdral F4 F4 T0 Hda 0 6 0 +DIHEdral F4 F4 T0 Bda 0 6 0 +DIHEdral F4 F4 T0 B0 0 6 0 +DIHEdral F4 F4 T0 Tda 0 6 0 +DIHEdral F4 F4 T0 T0 0 6 0 +DIHEdral F4 F4 T0 HP5 0 6 0 +DIHEdral F4 F4 T0 HP0 0 6 0 +DIHEdral F4 F4 T0 HPa 0 6 0 +DIHEdral F4 F4 HP5 F4 0 6 0 +DIHEdral F4 F4 HP5 F5 0 6 0 +DIHEdral F4 F4 HP5 Fa 0 6 0 +DIHEdral F4 F4 HP5 H0 0 6 0 +DIHEdral F4 F4 HP5 H5 0 6 0 +DIHEdral F4 F4 HP5 Hd 0 6 0 +DIHEdral F4 F4 HP5 Ha 0 6 0 +DIHEdral F4 F4 HP5 Hda 0 6 0 +DIHEdral F4 F4 HP5 Bda 0 6 0 +DIHEdral F4 F4 HP5 B0 0 6 0 +DIHEdral F4 F4 HP5 Tda 0 6 0 +DIHEdral F4 F4 HP5 T0 0 6 0 +DIHEdral F4 F4 HP5 HP5 0 6 0 +DIHEdral F4 F4 HP5 HP0 0 6 0 +DIHEdral F4 F4 HP5 HPa 0 6 0 +DIHEdral F4 F4 HP0 F4 0 6 0 +DIHEdral F4 F4 HP0 F5 0 6 0 +DIHEdral F4 F4 HP0 Fa 0 6 0 +DIHEdral F4 F4 HP0 H0 0 6 0 +DIHEdral F4 F4 HP0 H5 0 6 0 +DIHEdral F4 F4 HP0 Hd 0 6 0 +DIHEdral F4 F4 HP0 Ha 0 6 0 +DIHEdral F4 F4 HP0 Hda 0 6 0 +DIHEdral F4 F4 HP0 Bda 0 6 0 +DIHEdral F4 F4 HP0 B0 0 6 0 +DIHEdral F4 F4 HP0 Tda 0 6 0 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F5 F5 F4 0 6 0 +DIHEdral F4 F5 F5 F5 0 6 0 +DIHEdral F4 F5 F5 Fa 0 6 0 +DIHEdral F4 F5 F5 H0 0 6 0 +DIHEdral F4 F5 F5 H5 0 6 0 +DIHEdral F4 F5 F5 Hd 0 6 0 +DIHEdral F4 F5 F5 Ha 0 6 0 +DIHEdral F4 F5 F5 Hda 0 6 0 +DIHEdral F4 F5 F5 Bda 0 6 0 +DIHEdral F4 F5 F5 B0 0 6 0 +DIHEdral F4 F5 F5 Tda 0 6 0 +DIHEdral F4 F5 F5 T0 0 6 0 +DIHEdral F4 F5 F5 HP5 0 6 0 +DIHEdral F4 F5 F5 HP0 0 6 0 +DIHEdral F4 F5 F5 HPa 0 6 0 +DIHEdral F4 F5 Fa F4 0 6 0 +DIHEdral F4 F5 Fa F5 0 6 0 +DIHEdral F4 F5 Fa Fa 0 6 0 +DIHEdral F4 F5 Fa H0 0 6 0 +DIHEdral F4 F5 Fa H5 0 6 0 +DIHEdral F4 F5 Fa Hd 0 6 0 +DIHEdral F4 F5 Fa Ha 0 6 0 +DIHEdral F4 F5 Fa Hda 0 6 0 +DIHEdral F4 F5 Fa Bda 0 6 0 +DIHEdral F4 F5 Fa B0 0 6 0 +DIHEdral F4 F5 Fa Tda 0 6 0 +DIHEdral F4 F5 Fa T0 0 6 0 +DIHEdral F4 F5 Fa HP5 0 6 0 +DIHEdral F4 F5 Fa HP0 0 6 0 +DIHEdral F4 F5 Fa HPa 0 6 0 +DIHEdral F4 F5 H0 F4 0 6 0 +DIHEdral F4 F5 H0 F5 0 6 0 +DIHEdral F4 F5 H0 Fa 0 6 0 +DIHEdral F4 F5 H0 H0 0 6 0 +DIHEdral F4 F5 H0 H5 0 6 0 +DIHEdral F4 F5 H0 Hd 0 6 0 +DIHEdral F4 F5 H0 Ha 0 6 0 +DIHEdral F4 F5 H0 Hda 0 6 0 +DIHEdral F4 F5 H0 Bda 0 6 0 +DIHEdral F4 F5 H0 B0 0 6 0 +DIHEdral F4 F5 H0 Tda 0 6 0 +DIHEdral F4 F5 H0 T0 0 6 0 +DIHEdral F4 F5 H0 HP5 0 6 0 +DIHEdral F4 F5 H0 HP0 0 6 0 +DIHEdral F4 F5 H0 HPa 0 6 0 +DIHEdral F4 F5 H5 F4 0 6 0 +DIHEdral F4 F5 H5 F5 0 6 0 +DIHEdral F4 F5 H5 Fa 0 6 0 +DIHEdral F4 F5 H5 H0 0 6 0 +DIHEdral F4 F5 H5 H5 0 6 0 +DIHEdral F4 F5 H5 Hd 0 6 0 +DIHEdral F4 F5 H5 Ha 0 6 0 +DIHEdral F4 F5 H5 Hda 0 6 0 +DIHEdral F4 F5 H5 Bda 0 6 0 +DIHEdral F4 F5 H5 B0 0 6 0 +DIHEdral F4 F5 H5 Tda 0 6 0 +DIHEdral F4 F5 H5 T0 0 6 0 +DIHEdral F4 F5 H5 HP5 0 6 0 +DIHEdral F4 F5 H5 HP0 0 6 0 +DIHEdral F4 F5 H5 HPa 0 6 0 +DIHEdral F4 F5 Hd F4 0 6 0 +DIHEdral F4 F5 Hd F5 0 6 0 +DIHEdral F4 F5 Hd Fa 0 6 0 +DIHEdral F4 F5 Hd H0 0 6 0 +DIHEdral F4 F5 Hd H5 0 6 0 +DIHEdral F4 F5 Hd Hd 0 6 0 +DIHEdral F4 F5 Hd Ha 0 6 0 +DIHEdral F4 F5 Hd Hda 0 6 0 +DIHEdral F4 F5 Hd Bda 0 6 0 +DIHEdral F4 F5 Hd B0 0 6 0 +DIHEdral F4 F5 Hd Tda 0 6 0 +DIHEdral F4 F5 Hd T0 0 6 0 +DIHEdral F4 F5 Hd HP5 0 6 0 +DIHEdral F4 F5 Hd HP0 0 6 0 +DIHEdral F4 F5 Hd HPa 0 6 0 +DIHEdral F4 F5 Ha F4 0 6 0 +DIHEdral F4 F5 Ha F5 0 6 0 +DIHEdral F4 F5 Ha Fa 0 6 0 +DIHEdral F4 F5 Ha H0 0 6 0 +DIHEdral F4 F5 Ha H5 0 6 0 +DIHEdral F4 F5 Ha Hd 0 6 0 +DIHEdral F4 F5 Ha Ha 0 6 0 +DIHEdral F4 F5 Ha Hda 0 6 0 +DIHEdral F4 F5 Ha Bda 0 6 0 +DIHEdral F4 F5 Ha B0 0 6 0 +DIHEdral F4 F5 Ha Tda 0 6 0 +DIHEdral F4 F5 Ha T0 0 6 0 +DIHEdral F4 F5 Ha HP5 0 6 0 +DIHEdral F4 F5 Ha HP0 0 6 0 +DIHEdral F4 F5 Ha HPa 0 6 0 +DIHEdral F4 F5 Hda F4 0 6 0 +DIHEdral F4 F5 Hda F5 0 6 0 +DIHEdral F4 F5 Hda Fa 0 6 0 +DIHEdral F4 F5 Hda H0 0 6 0 +DIHEdral F4 F5 Hda H5 0 6 0 +DIHEdral F4 F5 Hda Hd 0 6 0 +DIHEdral F4 F5 Hda Ha 0 6 0 +DIHEdral F4 F5 Hda Hda 0 6 0 +DIHEdral F4 F5 Hda Bda 0 6 0 +DIHEdral F4 F5 Hda B0 0 6 0 +DIHEdral F4 F5 Hda Tda 0 6 0 +DIHEdral F4 F5 Hda T0 0 6 0 +DIHEdral F4 F5 Hda HP5 0 6 0 +DIHEdral F4 F5 Hda HP0 0 6 0 +DIHEdral F4 F5 Hda HPa 0 6 0 +DIHEdral F4 F5 Bda F4 0 6 0 +DIHEdral F4 F5 Bda F5 0 6 0 +DIHEdral F4 F5 Bda Fa 0 6 0 +DIHEdral F4 F5 Bda H0 0 6 0 +DIHEdral F4 F5 Bda H5 0 6 0 +DIHEdral F4 F5 Bda Hd 0 6 0 +DIHEdral F4 F5 Bda Ha 0 6 0 +DIHEdral F4 F5 Bda Hda 0 6 0 +DIHEdral F4 F5 Bda Bda 0 6 0 +DIHEdral F4 F5 Bda B0 0 6 0 +DIHEdral F4 F5 Bda Tda 0 6 0 +DIHEdral F4 F5 Bda T0 0 6 0 +DIHEdral F4 F5 Bda HP5 0 6 0 +DIHEdral F4 F5 Bda HP0 0 6 0 +DIHEdral F4 F5 Bda HPa 0 6 0 +DIHEdral F4 F5 B0 F4 0 6 0 +DIHEdral F4 F5 B0 F5 0 6 0 +DIHEdral F4 F5 B0 Fa 0 6 0 +DIHEdral F4 F5 B0 H0 0 6 0 +DIHEdral F4 F5 B0 H5 0 6 0 +DIHEdral F4 F5 B0 Hd 0 6 0 +DIHEdral F4 F5 B0 Ha 0 6 0 +DIHEdral F4 F5 B0 Hda 0 6 0 +DIHEdral F4 F5 B0 Bda 0 6 0 +DIHEdral F4 F5 B0 B0 0 6 0 +DIHEdral F4 F5 B0 Tda 0 6 0 +DIHEdral F4 F5 B0 T0 0 6 0 +DIHEdral F4 F5 B0 HP5 0 6 0 +DIHEdral F4 F5 B0 HP0 0 6 0 +DIHEdral F4 F5 B0 HPa 0 6 0 +DIHEdral F4 F5 Tda F4 0 6 0 +DIHEdral F4 F5 Tda F5 0 6 0 +DIHEdral F4 F5 Tda Fa 0 6 0 +DIHEdral F4 F5 Tda H0 0 6 0 +DIHEdral F4 F5 Tda H5 0 6 0 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6 0 +DIHEdral Bda Hd Fa F5 0 6 0 +DIHEdral Bda Hd Fa Fa 0 6 0 +DIHEdral Bda Hd Fa H0 0 6 0 +DIHEdral Bda Hd Fa H5 0 6 0 +DIHEdral Bda Hd Fa Hd 0 6 0 +DIHEdral Bda Hd Fa Ha 0 6 0 +DIHEdral Bda Hd Fa Hda 0 6 0 +DIHEdral Bda Hd Fa Bda 0 6 0 +DIHEdral Bda Hd Fa B0 0 6 0 +DIHEdral Bda Hd Fa Tda 0 6 0 +DIHEdral Bda Hd Fa T0 0 6 0 +DIHEdral Bda Hd Fa HP5 0 6 0 +DIHEdral Bda Hd Fa HP0 0 6 0 +DIHEdral Bda Hd Fa HPa 0 6 0 +DIHEdral Bda Hd H0 F4 0 6 0 +DIHEdral Bda Hd H0 F5 0 6 0 +DIHEdral Bda Hd H0 Fa 0 6 0 +DIHEdral Bda Hd H0 H0 0 6 0 +DIHEdral Bda Hd H0 H5 0 6 0 +DIHEdral Bda Hd H0 Hd 0 6 0 +DIHEdral Bda Hd H0 Ha 0 6 0 +DIHEdral Bda Hd H0 Hda 0 6 0 +DIHEdral Bda Hd H0 Bda 0 6 0 +DIHEdral Bda Hd H0 B0 0 6 0 +DIHEdral Bda Hd H0 Tda 0 6 0 +DIHEdral Bda Hd H0 T0 0 6 0 +DIHEdral Bda Hd H0 HP5 0 6 0 +DIHEdral Bda Hd H0 HP0 0 6 0 +DIHEdral Bda Hd H0 HPa 0 6 0 +DIHEdral Bda Hd H5 F4 0 6 0 +DIHEdral Bda Hd H5 F5 0 6 0 +DIHEdral Bda Hd H5 Fa 0 6 0 +DIHEdral Bda Hd H5 H0 0 6 0 +DIHEdral Bda Hd H5 H5 0 6 0 +DIHEdral Bda Hd H5 Hd 0 6 0 +DIHEdral Bda Hd H5 Ha 0 6 0 +DIHEdral Bda Hd H5 Hda 0 6 0 +DIHEdral Bda Hd H5 Bda 0 6 0 +DIHEdral Bda Hd H5 B0 0 6 0 +DIHEdral Bda Hd H5 Tda 0 6 0 +DIHEdral Bda Hd H5 T0 0 6 0 +DIHEdral Bda Hd H5 HP5 0 6 0 +DIHEdral Bda Hd H5 HP0 0 6 0 +DIHEdral Bda Hd H5 HPa 0 6 0 +DIHEdral Bda Hd Hd F4 0 6 0 +DIHEdral Bda Hd Hd F5 0 6 0 +DIHEdral Bda Hd Hd Fa 0 6 0 +DIHEdral Bda Hd Hd H0 0 6 0 +DIHEdral Bda Hd Hd H5 0 6 0 +DIHEdral Bda Hd Hd Hd 0 6 0 +DIHEdral Bda Hd Hd Ha 0 6 0 +DIHEdral Bda Hd Hd Hda 0 6 0 +DIHEdral Bda Hd Hd Bda 0 6 0 +DIHEdral Bda Hd Hd B0 0 6 0 +DIHEdral Bda Hd Hd Tda 0 6 0 +DIHEdral Bda Hd Hd T0 0 6 0 +DIHEdral Bda Hd Hd HP5 0 6 0 +DIHEdral Bda Hd Hd HP0 0 6 0 +DIHEdral Bda Hd Hd HPa 0 6 0 +DIHEdral Bda Hd Ha F4 0 6 0 +DIHEdral Bda Hd Ha F5 0 6 0 +DIHEdral Bda Hd Ha Fa 0 6 0 +DIHEdral Bda Hd Ha H0 0 6 0 +DIHEdral Bda Hd Ha H5 0 6 0 +DIHEdral Bda Hd Ha Hd 0 6 0 +DIHEdral Bda Hd Ha Ha 0 6 0 +DIHEdral Bda Hd Ha Hda 0 6 0 +DIHEdral Bda Hd Ha Bda 0 6 0 +DIHEdral Bda Hd Ha B0 0 6 0 +DIHEdral Bda Hd Ha Tda 0 6 0 +DIHEdral Bda Hd Ha T0 0 6 0 +DIHEdral Bda Hd Ha HP5 0 6 0 +DIHEdral Bda Hd Ha HP0 0 6 0 +DIHEdral Bda Hd Ha HPa 0 6 0 +DIHEdral Bda Hd Hda F4 0 6 0 +DIHEdral Bda Hd Hda F5 0 6 0 +DIHEdral Bda Hd Hda Fa 0 6 0 +DIHEdral Bda Hd Hda H0 0 6 0 +DIHEdral Bda Hd Hda H5 0 6 0 +DIHEdral Bda Hd Hda Hd 0 6 0 +DIHEdral Bda Hd Hda Ha 0 6 0 +DIHEdral Bda Hd Hda Hda 0 6 0 +DIHEdral Bda Hd Hda Bda 0 6 0 +DIHEdral Bda Hd Hda B0 0 6 0 +DIHEdral Bda Hd Hda Tda 0 6 0 +DIHEdral Bda Hd Hda T0 0 6 0 +DIHEdral Bda Hd Hda HP5 0 6 0 +DIHEdral Bda Hd Hda HP0 0 6 0 +DIHEdral Bda Hd Hda HPa 0 6 0 +DIHEdral Bda Hd Bda F4 0 6 0 +DIHEdral Bda Hd Bda F5 0 6 0 +DIHEdral Bda Hd Bda Fa 0 6 0 +DIHEdral Bda Hd Bda H0 0 6 0 +DIHEdral Bda Hd Bda H5 0 6 0 +DIHEdral Bda Hd Bda Hd 0 6 0 +DIHEdral Bda Hd Bda Ha 0 6 0 +DIHEdral Bda Hd Bda Hda 0 6 0 +DIHEdral Bda Hd Bda Bda 0 6 0 +DIHEdral Bda Hd Bda B0 0 6 0 +DIHEdral Bda Hd Bda Tda 0 6 0 +DIHEdral Bda Hd Bda T0 0 6 0 +DIHEdral Bda Hd Bda HP5 0 6 0 +DIHEdral Bda Hd Bda HP0 0 6 0 +DIHEdral Bda Hd Bda HPa 0 6 0 +DIHEdral Bda Hd B0 F4 0 6 0 +DIHEdral Bda Hd B0 F5 0 6 0 +DIHEdral Bda Hd B0 Fa 0 6 0 +DIHEdral Bda Hd B0 H0 0 6 0 +DIHEdral Bda Hd B0 H5 0 6 0 +DIHEdral Bda Hd B0 Hd 0 6 0 +DIHEdral Bda Hd B0 Ha 0 6 0 +DIHEdral Bda Hd B0 Hda 0 6 0 +DIHEdral Bda Hd B0 Bda 0 6 0 +DIHEdral Bda Hd B0 B0 0 6 0 +DIHEdral Bda Hd B0 Tda 0 6 0 +DIHEdral Bda Hd B0 T0 0 6 0 +DIHEdral Bda Hd B0 HP5 0 6 0 +DIHEdral Bda Hd B0 HP0 0 6 0 +DIHEdral Bda Hd B0 HPa 0 6 0 +DIHEdral Bda Hd Tda F4 0 6 0 +DIHEdral Bda Hd Tda F5 0 6 0 +DIHEdral Bda Hd Tda Fa 0 6 0 +DIHEdral Bda Hd Tda H0 0 6 0 +DIHEdral Bda Hd Tda H5 0 6 0 +DIHEdral Bda Hd Tda Hd 0 6 0 +DIHEdral Bda Hd Tda Ha 0 6 0 +DIHEdral Bda Hd Tda Hda 0 6 0 +DIHEdral Bda Hd Tda Bda 0 6 0 +DIHEdral Bda Hd Tda B0 0 6 0 +DIHEdral Bda Hd Tda Tda 0 6 0 +DIHEdral Bda Hd Tda T0 0 6 0 +DIHEdral Bda Hd Tda HP5 0 6 0 +DIHEdral Bda Hd Tda HP0 0 6 0 +DIHEdral Bda Hd Tda HPa 0 6 0 +DIHEdral Bda Hd T0 F4 0 6 0 +DIHEdral Bda Hd T0 F5 0 6 0 +DIHEdral Bda Hd T0 Fa 0 6 0 +DIHEdral Bda Hd T0 H0 0 6 0 +DIHEdral Bda Hd T0 H5 0 6 0 +DIHEdral Bda Hd T0 Hd 0 6 0 +DIHEdral Bda Hd T0 Ha 0 6 0 +DIHEdral Bda Hd T0 Hda 0 6 0 +DIHEdral Bda Hd T0 Bda 0 6 0 +DIHEdral Bda Hd T0 B0 0 6 0 +DIHEdral Bda Hd T0 Tda 0 6 0 +DIHEdral Bda Hd T0 T0 0 6 0 +DIHEdral Bda Hd T0 HP5 0 6 0 +DIHEdral Bda Hd T0 HP0 0 6 0 +DIHEdral Bda Hd T0 HPa 0 6 0 +DIHEdral Bda Hd HP5 F4 0 6 0 +DIHEdral Bda Hd HP5 F5 0 6 0 +DIHEdral Bda Hd HP5 Fa 0 6 0 +DIHEdral Bda Hd HP5 H0 0 6 0 +DIHEdral Bda Hd HP5 H5 0 6 0 +DIHEdral Bda Hd HP5 Hd 0 6 0 +DIHEdral Bda Hd HP5 Ha 0 6 0 +DIHEdral Bda Hd HP5 Hda 0 6 0 +DIHEdral Bda Hd HP5 Bda 0 6 0 +DIHEdral Bda Hd HP5 B0 0 6 0 +DIHEdral Bda Hd HP5 Tda 0 6 0 +DIHEdral Bda Hd HP5 T0 0 6 0 +DIHEdral Bda Hd HP5 HP5 0 6 0 +DIHEdral Bda Hd HP5 HP0 0 6 0 +DIHEdral Bda Hd HP5 HPa 0 6 0 +DIHEdral Bda Hd HP0 F4 0 6 0 +DIHEdral Bda Hd HP0 F5 0 6 0 +DIHEdral Bda Hd HP0 Fa 0 6 0 +DIHEdral Bda Hd HP0 H0 0 6 0 +DIHEdral Bda Hd HP0 H5 0 6 0 +DIHEdral Bda Hd HP0 Hd 0 6 0 +DIHEdral Bda Hd HP0 Ha 0 6 0 +DIHEdral Bda Hd HP0 Hda 0 6 0 +DIHEdral Bda Hd HP0 Bda 0 6 0 +DIHEdral Bda Hd HP0 B0 0 6 0 +DIHEdral Bda Hd HP0 Tda 0 6 0 +DIHEdral Bda Hd HP0 T0 0 6 0 +DIHEdral Bda Hd HP0 HP5 0 6 0 +DIHEdral Bda Hd HP0 HP0 0 6 0 +DIHEdral Bda Hd HP0 HPa 0 6 0 +DIHEdral Bda Hd HPa F4 0 6 0 +DIHEdral Bda Hd HPa F5 0 6 0 +DIHEdral Bda Hd HPa Fa 0 6 0 +DIHEdral Bda Hd HPa H0 0 6 0 +DIHEdral Bda Hd HPa H5 0 6 0 +DIHEdral Bda Hd HPa Hd 0 6 0 +DIHEdral Bda Hd HPa Ha 0 6 0 +DIHEdral Bda Hd HPa Hda 0 6 0 +DIHEdral Bda Hd HPa Bda 0 6 0 +DIHEdral Bda Hd HPa B0 0 6 0 +DIHEdral Bda Hd HPa Tda 0 6 0 +DIHEdral Bda Hd HPa T0 0 6 0 +DIHEdral Bda Hd HPa HP5 0 6 0 +DIHEdral Bda Hd HPa HP0 0 6 0 +DIHEdral Bda Hd HPa HPa 0 6 0 +DIHEdral Bda Ha F4 F4 0 6 0 +DIHEdral Bda Ha F4 F5 0 6 0 +DIHEdral Bda Ha F4 Fa 0 6 0 +DIHEdral Bda Ha F4 H0 0 6 0 +DIHEdral Bda Ha F4 H5 0 6 0 +DIHEdral Bda Ha F4 Hd 0 6 0 +DIHEdral Bda Ha F4 Ha 0 6 0 +DIHEdral Bda Ha F4 Hda 0 6 0 +DIHEdral Bda Ha F4 Bda 0 6 0 +DIHEdral Bda Ha F4 B0 0 6 0 +DIHEdral Bda Ha F4 Tda 0 6 0 +DIHEdral Bda Ha F4 T0 0 6 0 +DIHEdral Bda Ha F4 HP5 0 6 0 +DIHEdral Bda Ha F4 HP0 0 6 0 +DIHEdral Bda Ha F4 HPa 0 6 0 +DIHEdral Bda Ha F5 F4 0 6 0 +DIHEdral Bda Ha F5 F5 0 6 0 +DIHEdral Bda Ha F5 Fa 0 6 0 +DIHEdral Bda Ha F5 H0 0 6 0 +DIHEdral Bda Ha F5 H5 0 6 0 +DIHEdral Bda Ha F5 Hd 0 6 0 +DIHEdral Bda Ha F5 Ha 0 6 0 +DIHEdral Bda Ha F5 Hda 0 6 0 +DIHEdral Bda Ha F5 Bda 0 6 0 +DIHEdral Bda Ha F5 B0 0 6 0 +DIHEdral Bda Ha F5 Tda 0 6 0 +DIHEdral Bda Ha F5 T0 0 6 0 +DIHEdral Bda Ha F5 HP5 0 6 0 +DIHEdral Bda Ha F5 HP0 0 6 0 +DIHEdral Bda Ha F5 HPa 0 6 0 +DIHEdral Bda Ha Fa F4 0 6 0 +DIHEdral Bda Ha Fa F5 0 6 0 +DIHEdral Bda Ha Fa Fa 0 6 0 +DIHEdral Bda Ha Fa H0 0 6 0 +DIHEdral Bda Ha Fa H5 0 6 0 +DIHEdral Bda Ha Fa Hd 0 6 0 +DIHEdral Bda Ha Fa Ha 0 6 0 +DIHEdral Bda Ha Fa Hda 0 6 0 +DIHEdral Bda Ha Fa Bda 0 6 0 +DIHEdral Bda Ha Fa B0 0 6 0 +DIHEdral Bda Ha Fa Tda 0 6 0 +DIHEdral Bda Ha Fa T0 0 6 0 +DIHEdral Bda Ha Fa HP5 0 6 0 +DIHEdral Bda Ha Fa HP0 0 6 0 +DIHEdral Bda Ha Fa HPa 0 6 0 +DIHEdral Bda Ha H0 F4 0 6 0 +DIHEdral Bda Ha H0 F5 0 6 0 +DIHEdral Bda Ha H0 Fa 0 6 0 +DIHEdral Bda Ha H0 H0 0 6 0 +DIHEdral Bda Ha H0 H5 0 6 0 +DIHEdral Bda Ha H0 Hd 0 6 0 +DIHEdral Bda Ha H0 Ha 0 6 0 +DIHEdral Bda Ha H0 Hda 0 6 0 +DIHEdral Bda Ha H0 Bda 0 6 0 +DIHEdral Bda Ha H0 B0 0 6 0 +DIHEdral Bda Ha H0 Tda 0 6 0 +DIHEdral Bda Ha H0 T0 0 6 0 +DIHEdral Bda Ha H0 HP5 0 6 0 +DIHEdral Bda Ha H0 HP0 0 6 0 +DIHEdral Bda Ha H0 HPa 0 6 0 +DIHEdral Bda Ha H5 F4 0 6 0 +DIHEdral Bda Ha H5 F5 0 6 0 +DIHEdral Bda Ha H5 Fa 0 6 0 +DIHEdral Bda Ha H5 H0 0 6 0 +DIHEdral Bda Ha H5 H5 0 6 0 +DIHEdral Bda Ha H5 Hd 0 6 0 +DIHEdral Bda Ha H5 Ha 0 6 0 +DIHEdral Bda Ha H5 Hda 0 6 0 +DIHEdral Bda Ha H5 Bda 0 6 0 +DIHEdral Bda Ha H5 B0 0 6 0 +DIHEdral Bda Ha H5 Tda 0 6 0 +DIHEdral Bda Ha H5 T0 0 6 0 +DIHEdral Bda Ha H5 HP5 0 6 0 +DIHEdral Bda Ha H5 HP0 0 6 0 +DIHEdral Bda Ha H5 HPa 0 6 0 +DIHEdral Bda Ha Hd F4 0 6 0 +DIHEdral Bda Ha Hd F5 0 6 0 +DIHEdral Bda Ha Hd Fa 0 6 0 +DIHEdral Bda Ha Hd H0 0 6 0 +DIHEdral Bda Ha Hd H5 0 6 0 +DIHEdral Bda Ha Hd Hd 0 6 0 +DIHEdral Bda Ha Hd Ha 0 6 0 +DIHEdral Bda Ha Hd Hda 0 6 0 +DIHEdral Bda Ha Hd Bda 0 6 0 +DIHEdral Bda Ha Hd B0 0 6 0 +DIHEdral Bda Ha Hd Tda 0 6 0 +DIHEdral Bda Ha Hd T0 0 6 0 +DIHEdral Bda Ha Hd HP5 0 6 0 +DIHEdral Bda Ha Hd HP0 0 6 0 +DIHEdral Bda Ha Hd HPa 0 6 0 +DIHEdral Bda Ha Ha F4 0 6 0 +DIHEdral Bda Ha Ha F5 0 6 0 +DIHEdral Bda Ha Ha Fa 0 6 0 +DIHEdral Bda Ha Ha H0 0 6 0 +DIHEdral Bda Ha Ha H5 0 6 0 +DIHEdral Bda Ha Ha Hd 0 6 0 +DIHEdral Bda Ha Ha Ha 0 6 0 +DIHEdral Bda Ha Ha Hda 0 6 0 +DIHEdral Bda Ha Ha Bda 0 6 0 +DIHEdral Bda Ha Ha B0 0 6 0 +DIHEdral Bda Ha Ha Tda 0 6 0 +DIHEdral Bda Ha Ha T0 0 6 0 +DIHEdral Bda Ha Ha HP5 0 6 0 +DIHEdral Bda Ha Ha HP0 0 6 0 +DIHEdral Bda Ha Ha HPa 0 6 0 +DIHEdral Bda Ha Hda F4 0 6 0 +DIHEdral Bda Ha Hda F5 0 6 0 +DIHEdral Bda Ha Hda Fa 0 6 0 +DIHEdral Bda Ha Hda H0 0 6 0 +DIHEdral Bda Ha Hda H5 0 6 0 +DIHEdral Bda Ha Hda Hd 0 6 0 +DIHEdral Bda Ha Hda Ha 0 6 0 +DIHEdral Bda Ha Hda Hda 0 6 0 +DIHEdral Bda Ha Hda Bda 0 6 0 +DIHEdral Bda Ha Hda B0 0 6 0 +DIHEdral Bda Ha Hda Tda 0 6 0 +DIHEdral Bda Ha Hda T0 0 6 0 +DIHEdral Bda Ha Hda HP5 0 6 0 +DIHEdral Bda Ha Hda HP0 0 6 0 +DIHEdral Bda Ha Hda HPa 0 6 0 +DIHEdral Bda Ha Bda F4 0 6 0 +DIHEdral Bda Ha Bda F5 0 6 0 +DIHEdral Bda Ha Bda Fa 0 6 0 +DIHEdral Bda Ha Bda H0 0 6 0 +DIHEdral Bda Ha Bda H5 0 6 0 +DIHEdral Bda Ha Bda Hd 0 6 0 +DIHEdral Bda Ha Bda Ha 0 6 0 +DIHEdral Bda Ha Bda Hda 0 6 0 +DIHEdral Bda Ha Bda Bda 0 6 0 +DIHEdral Bda Ha Bda B0 0 6 0 +DIHEdral Bda Ha Bda Tda 0 6 0 +DIHEdral Bda Ha Bda T0 0 6 0 +DIHEdral Bda Ha Bda HP5 0 6 0 +DIHEdral Bda Ha Bda HP0 0 6 0 +DIHEdral Bda Ha Bda HPa 0 6 0 +DIHEdral Bda Ha B0 F4 0 6 0 +DIHEdral Bda Ha B0 F5 0 6 0 +DIHEdral Bda Ha B0 Fa 0 6 0 +DIHEdral Bda Ha B0 H0 0 6 0 +DIHEdral Bda Ha B0 H5 0 6 0 +DIHEdral Bda Ha B0 Hd 0 6 0 +DIHEdral Bda Ha B0 Ha 0 6 0 +DIHEdral Bda Ha B0 Hda 0 6 0 +DIHEdral Bda Ha B0 Bda 0 6 0 +DIHEdral Bda Ha B0 B0 0 6 0 +DIHEdral Bda Ha B0 Tda 0 6 0 +DIHEdral Bda Ha B0 T0 0 6 0 +DIHEdral Bda Ha B0 HP5 0 6 0 +DIHEdral Bda Ha B0 HP0 0 6 0 +DIHEdral Bda Ha B0 HPa 0 6 0 +DIHEdral Bda Ha Tda F4 0 6 0 +DIHEdral Bda Ha Tda F5 0 6 0 +DIHEdral Bda Ha Tda Fa 0 6 0 +DIHEdral Bda Ha Tda H0 0 6 0 +DIHEdral Bda Ha Tda H5 0 6 0 +DIHEdral Bda Ha Tda Hd 0 6 0 +DIHEdral Bda Ha Tda Ha 0 6 0 +DIHEdral Bda Ha Tda Hda 0 6 0 +DIHEdral Bda Ha Tda Bda 0 6 0 +DIHEdral Bda Ha Tda B0 0 6 0 +DIHEdral Bda Ha Tda Tda 0 6 0 +DIHEdral Bda Ha Tda T0 0 6 0 +DIHEdral Bda Ha Tda HP5 0 6 0 +DIHEdral Bda Ha Tda HP0 0 6 0 +DIHEdral Bda Ha Tda HPa 0 6 0 +DIHEdral Bda Ha T0 F4 0 6 0 +DIHEdral Bda Ha T0 F5 0 6 0 +DIHEdral Bda Ha T0 Fa 0 6 0 +DIHEdral Bda Ha T0 H0 0 6 0 +DIHEdral Bda Ha T0 H5 0 6 0 +DIHEdral Bda Ha T0 Hd 0 6 0 +DIHEdral Bda Ha T0 Ha 0 6 0 +DIHEdral Bda Ha T0 Hda 0 6 0 +DIHEdral Bda Ha T0 Bda 0 6 0 +DIHEdral Bda Ha T0 B0 0 6 0 +DIHEdral Bda 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Fa HP5 0 6 0 +DIHEdral HPa HP5 Fa HP0 0 6 0 +DIHEdral HPa HP5 Fa HPa 0 6 0 +DIHEdral HPa HP5 H0 F4 0 6 0 +DIHEdral HPa HP5 H0 F5 0 6 0 +DIHEdral HPa HP5 H0 Fa 0 6 0 +DIHEdral HPa HP5 H0 Bda 0 6 0 +DIHEdral HPa HP5 H0 B0 0 6 0 +DIHEdral HPa HP5 H0 Tda 0 6 0 +DIHEdral HPa HP5 H0 T0 0 6 0 +DIHEdral HPa HP5 H5 F4 0 6 0 +DIHEdral HPa HP5 H5 F5 0 6 0 +DIHEdral HPa HP5 H5 Fa 0 6 0 +DIHEdral HPa HP5 H5 Bda 0 6 0 +DIHEdral HPa HP5 H5 B0 0 6 0 +DIHEdral HPa HP5 H5 Tda 0 6 0 +DIHEdral HPa HP5 H5 T0 0 6 0 +DIHEdral HPa HP5 Hd F4 0 6 0 +DIHEdral HPa HP5 Hd F5 0 6 0 +DIHEdral HPa HP5 Hd Fa 0 6 0 +DIHEdral HPa HP5 Hd Bda 0 6 0 +DIHEdral HPa HP5 Hd B0 0 6 0 +DIHEdral HPa HP5 Hd Tda 0 6 0 +DIHEdral HPa HP5 Hd T0 0 6 0 +DIHEdral HPa HP5 Ha F4 0 6 0 +DIHEdral HPa HP5 Ha F5 0 6 0 +DIHEdral HPa HP5 Ha Fa 0 6 0 +DIHEdral HPa HP5 Ha Bda 0 6 0 +DIHEdral HPa HP5 Ha B0 0 6 0 +DIHEdral HPa HP5 Ha Tda 0 6 0 +DIHEdral HPa HP5 Ha T0 0 6 0 +DIHEdral HPa HP5 Hda F4 0 6 0 +DIHEdral HPa HP5 Hda F5 0 6 0 +DIHEdral HPa HP5 Hda Fa 0 6 0 +DIHEdral HPa HP5 Hda Bda 0 6 0 +DIHEdral HPa HP5 Hda B0 0 6 0 +DIHEdral HPa HP5 Hda Tda 0 6 0 +DIHEdral HPa HP5 Hda T0 0 6 0 +DIHEdral HPa HP5 Bda F4 0 6 0 +DIHEdral HPa HP5 Bda F5 0 6 0 +DIHEdral HPa HP5 Bda Fa 0 6 0 +DIHEdral HPa HP5 Bda H0 0 6 0 +DIHEdral HPa HP5 Bda H5 0 6 0 +DIHEdral HPa HP5 Bda Hd 0 6 0 +DIHEdral HPa HP5 Bda Ha 0 6 0 +DIHEdral HPa HP5 Bda Hda 0 6 0 +DIHEdral HPa HP5 Bda Bda 0 6 0 +DIHEdral HPa HP5 Bda B0 0 6 0 +DIHEdral HPa HP5 Bda Tda 0 6 0 +DIHEdral HPa HP5 Bda T0 0 6 0 +DIHEdral HPa HP5 Bda HP5 0 6 0 +DIHEdral HPa HP5 Bda HP0 0 6 0 +DIHEdral HPa HP5 Bda HPa 0 6 0 +DIHEdral HPa HP5 B0 F4 0 6 0 +DIHEdral HPa HP5 B0 F5 0 6 0 +DIHEdral HPa HP5 B0 Fa 0 6 0 +DIHEdral HPa HP5 B0 H0 0 6 0 +DIHEdral HPa HP5 B0 H5 0 6 0 +DIHEdral HPa HP5 B0 Hd 0 6 0 +DIHEdral HPa HP5 B0 Ha 0 6 0 +DIHEdral HPa HP5 B0 Hda 0 6 0 +DIHEdral HPa HP5 B0 Bda 0 6 0 +DIHEdral HPa HP5 B0 B0 0 6 0 +DIHEdral HPa HP5 B0 Tda 0 6 0 +DIHEdral HPa HP5 B0 T0 0 6 0 +DIHEdral HPa HP5 B0 HP5 0 6 0 +DIHEdral HPa HP5 B0 HP0 0 6 0 +DIHEdral HPa HP5 B0 HPa 0 6 0 +DIHEdral HPa HP5 Tda F4 0 6 0 +DIHEdral HPa HP5 Tda F5 0 6 0 +DIHEdral HPa HP5 Tda Fa 0 6 0 +DIHEdral HPa HP5 Tda H0 0 6 0 +DIHEdral HPa HP5 Tda H5 0 6 0 +DIHEdral HPa HP5 Tda Hd 0 6 0 +DIHEdral HPa HP5 Tda Ha 0 6 0 +DIHEdral HPa HP5 Tda Hda 0 6 0 +DIHEdral HPa HP5 Tda Bda 0 6 0 +DIHEdral HPa HP5 Tda B0 0 6 0 +DIHEdral HPa HP5 Tda Tda 0 6 0 +DIHEdral HPa HP5 Tda T0 0 6 0 +DIHEdral HPa HP5 Tda HP5 0 6 0 +DIHEdral HPa HP5 Tda HP0 0 6 0 +DIHEdral HPa HP5 Tda HPa 0 6 0 +DIHEdral HPa HP5 T0 F4 0 6 0 +DIHEdral HPa HP5 T0 F5 0 6 0 +DIHEdral HPa HP5 T0 Fa 0 6 0 +DIHEdral HPa HP5 T0 H0 0 6 0 +DIHEdral HPa HP5 T0 H5 0 6 0 +DIHEdral HPa HP5 T0 Hd 0 6 0 +DIHEdral HPa HP5 T0 Ha 0 6 0 +DIHEdral HPa HP5 T0 Hda 0 6 0 +DIHEdral HPa HP5 T0 Bda 0 6 0 +DIHEdral HPa HP5 T0 B0 0 6 0 +DIHEdral HPa HP5 T0 Tda 0 6 0 +DIHEdral HPa HP5 T0 T0 0 6 0 +DIHEdral HPa HP5 T0 HP5 0 6 0 +DIHEdral HPa HP5 T0 HP0 0 6 0 +DIHEdral HPa HP5 T0 HPa 0 6 0 +DIHEdral HPa HP5 HP5 F4 0 6 0 +DIHEdral HPa HP5 HP5 F5 0 6 0 +DIHEdral HPa HP5 HP5 Fa 0 6 0 +DIHEdral HPa HP5 HP5 Bda 0 6 0 +DIHEdral HPa HP5 HP5 B0 0 6 0 +DIHEdral HPa HP5 HP5 Tda 0 6 0 +DIHEdral HPa HP5 HP5 T0 0 6 0 +DIHEdral HPa HP5 HP0 F4 0 6 0 +DIHEdral HPa HP5 HP0 F5 0 6 0 +DIHEdral HPa HP5 HP0 Fa 0 6 0 +DIHEdral HPa HP5 HP0 Bda 0 6 0 +DIHEdral HPa HP5 HP0 B0 0 6 0 +DIHEdral HPa HP5 HP0 Tda 0 6 0 +DIHEdral HPa HP5 HP0 T0 0 6 0 +DIHEdral HPa HP5 HPa F4 0 6 0 +DIHEdral HPa HP5 HPa F5 0 6 0 +DIHEdral HPa HP5 HPa Fa 0 6 0 +DIHEdral HPa HP5 HPa Bda 0 6 0 +DIHEdral HPa HP5 HPa B0 0 6 0 +DIHEdral HPa HP5 HPa Tda 0 6 0 +DIHEdral HPa HP5 HPa T0 0 6 0 +DIHEdral HPa HP0 F4 F4 0 6 0 +DIHEdral HPa HP0 F4 F5 0 6 0 +DIHEdral HPa HP0 F4 Fa 0 6 0 +DIHEdral HPa HP0 F4 H0 0 6 0 +DIHEdral HPa HP0 F4 H5 0 6 0 +DIHEdral HPa HP0 F4 Hd 0 6 0 +DIHEdral HPa HP0 F4 Ha 0 6 0 +DIHEdral HPa HP0 F4 Hda 0 6 0 +DIHEdral HPa HP0 F4 Bda 0 6 0 +DIHEdral HPa HP0 F4 B0 0 6 0 +DIHEdral HPa HP0 F4 Tda 0 6 0 +DIHEdral HPa HP0 F4 T0 0 6 0 +DIHEdral HPa HP0 F4 HP5 0 6 0 +DIHEdral HPa HP0 F4 HP0 0 6 0 +DIHEdral HPa HP0 F4 HPa 0 6 0 +DIHEdral HPa HP0 F5 F4 0 6 0 +DIHEdral HPa HP0 F5 F5 0 6 0 +DIHEdral HPa HP0 F5 Fa 0 6 0 +DIHEdral HPa HP0 F5 H0 0 6 0 +DIHEdral HPa HP0 F5 H5 0 6 0 +DIHEdral HPa HP0 F5 Hd 0 6 0 +DIHEdral HPa HP0 F5 Ha 0 6 0 +DIHEdral HPa HP0 F5 Hda 0 6 0 +DIHEdral HPa HP0 F5 Bda 0 6 0 +DIHEdral HPa HP0 F5 B0 0 6 0 +DIHEdral HPa HP0 F5 Tda 0 6 0 +DIHEdral HPa HP0 F5 T0 0 6 0 +DIHEdral HPa HP0 F5 HP5 0 6 0 +DIHEdral HPa HP0 F5 HP0 0 6 0 +DIHEdral HPa HP0 F5 HPa 0 6 0 +DIHEdral HPa HP0 Fa F4 0 6 0 +DIHEdral HPa HP0 Fa F5 0 6 0 +DIHEdral HPa HP0 Fa Fa 0 6 0 +DIHEdral HPa HP0 Fa H0 0 6 0 +DIHEdral HPa HP0 Fa H5 0 6 0 +DIHEdral HPa HP0 Fa Hd 0 6 0 +DIHEdral HPa HP0 Fa Ha 0 6 0 +DIHEdral HPa HP0 Fa Hda 0 6 0 +DIHEdral HPa HP0 Fa Bda 0 6 0 +DIHEdral HPa HP0 Fa B0 0 6 0 +DIHEdral HPa HP0 Fa Tda 0 6 0 +DIHEdral HPa HP0 Fa T0 0 6 0 +DIHEdral HPa HP0 Fa HP5 0 6 0 +DIHEdral HPa HP0 Fa HP0 0 6 0 +DIHEdral HPa HP0 Fa HPa 0 6 0 +DIHEdral HPa HP0 H0 F4 0 6 0 +DIHEdral HPa HP0 H0 F5 0 6 0 +DIHEdral HPa HP0 H0 Fa 0 6 0 +DIHEdral HPa HP0 H0 Bda 0 6 0 +DIHEdral HPa HP0 H0 B0 0 6 0 +DIHEdral HPa HP0 H0 Tda 0 6 0 +DIHEdral HPa HP0 H0 T0 0 6 0 +DIHEdral HPa HP0 H5 F4 0 6 0 +DIHEdral HPa HP0 H5 F5 0 6 0 +DIHEdral HPa HP0 H5 Fa 0 6 0 +DIHEdral HPa HP0 H5 Bda 0 6 0 +DIHEdral HPa HP0 H5 B0 0 6 0 +DIHEdral HPa HP0 H5 Tda 0 6 0 +DIHEdral HPa HP0 H5 T0 0 6 0 +DIHEdral HPa HP0 Hd F4 0 6 0 +DIHEdral HPa HP0 Hd F5 0 6 0 +DIHEdral HPa HP0 Hd Fa 0 6 0 +DIHEdral HPa HP0 Hd Bda 0 6 0 +DIHEdral HPa HP0 Hd B0 0 6 0 +DIHEdral HPa HP0 Hd Tda 0 6 0 +DIHEdral HPa HP0 Hd T0 0 6 0 +DIHEdral HPa HP0 Ha F4 0 6 0 +DIHEdral HPa HP0 Ha F5 0 6 0 +DIHEdral HPa HP0 Ha Fa 0 6 0 +DIHEdral HPa HP0 Ha Bda 0 6 0 +DIHEdral HPa HP0 Ha B0 0 6 0 +DIHEdral HPa HP0 Ha Tda 0 6 0 +DIHEdral HPa HP0 Ha T0 0 6 0 +DIHEdral HPa HP0 Hda F4 0 6 0 +DIHEdral HPa HP0 Hda F5 0 6 0 +DIHEdral HPa HP0 Hda Fa 0 6 0 +DIHEdral HPa HP0 Hda Bda 0 6 0 +DIHEdral HPa HP0 Hda B0 0 6 0 +DIHEdral HPa HP0 Hda Tda 0 6 0 +DIHEdral HPa HP0 Hda T0 0 6 0 +DIHEdral HPa HP0 Bda F4 0 6 0 +DIHEdral HPa HP0 Bda F5 0 6 0 +DIHEdral HPa HP0 Bda Fa 0 6 0 +DIHEdral HPa HP0 Bda H0 0 6 0 +DIHEdral HPa HP0 Bda H5 0 6 0 +DIHEdral HPa HP0 Bda Hd 0 6 0 +DIHEdral HPa HP0 Bda Ha 0 6 0 +DIHEdral HPa HP0 Bda Hda 0 6 0 +DIHEdral HPa HP0 Bda Bda 0 6 0 +DIHEdral HPa HP0 Bda B0 0 6 0 +DIHEdral HPa HP0 Bda Tda 0 6 0 +DIHEdral HPa HP0 Bda T0 0 6 0 +DIHEdral HPa HP0 Bda HP5 0 6 0 +DIHEdral HPa HP0 Bda HP0 0 6 0 +DIHEdral HPa HP0 Bda HPa 0 6 0 +DIHEdral HPa HP0 B0 F4 0 6 0 +DIHEdral HPa HP0 B0 F5 0 6 0 +DIHEdral HPa HP0 B0 Fa 0 6 0 +DIHEdral HPa HP0 B0 H0 0 6 0 +DIHEdral HPa HP0 B0 H5 0 6 0 +DIHEdral HPa HP0 B0 Hd 0 6 0 +DIHEdral HPa HP0 B0 Ha 0 6 0 +DIHEdral HPa HP0 B0 Hda 0 6 0 +DIHEdral HPa HP0 B0 Bda 0 6 0 +DIHEdral HPa HP0 B0 B0 0 6 0 +DIHEdral HPa HP0 B0 Tda 0 6 0 +DIHEdral HPa HP0 B0 T0 0 6 0 +DIHEdral HPa HP0 B0 HP5 0 6 0 +DIHEdral HPa HP0 B0 HP0 0 6 0 +DIHEdral HPa HP0 B0 HPa 0 6 0 +DIHEdral HPa HP0 Tda F4 0 6 0 +DIHEdral HPa HP0 Tda F5 0 6 0 +DIHEdral HPa HP0 Tda Fa 0 6 0 +DIHEdral HPa HP0 Tda H0 0 6 0 +DIHEdral HPa HP0 Tda H5 0 6 0 +DIHEdral HPa HP0 Tda Hd 0 6 0 +DIHEdral HPa HP0 Tda Ha 0 6 0 +DIHEdral HPa HP0 Tda Hda 0 6 0 +DIHEdral HPa HP0 Tda Bda 0 6 0 +DIHEdral HPa HP0 Tda B0 0 6 0 +DIHEdral HPa HP0 Tda Tda 0 6 0 +DIHEdral HPa HP0 Tda T0 0 6 0 +DIHEdral HPa HP0 Tda HP5 0 6 0 +DIHEdral HPa HP0 Tda HP0 0 6 0 +DIHEdral HPa HP0 Tda HPa 0 6 0 +DIHEdral HPa HP0 T0 F4 0 6 0 +DIHEdral HPa HP0 T0 F5 0 6 0 +DIHEdral HPa HP0 T0 Fa 0 6 0 +DIHEdral HPa HP0 T0 H0 0 6 0 +DIHEdral HPa HP0 T0 H5 0 6 0 +DIHEdral HPa HP0 T0 Hd 0 6 0 +DIHEdral HPa HP0 T0 Ha 0 6 0 +DIHEdral HPa HP0 T0 Hda 0 6 0 +DIHEdral HPa HP0 T0 Bda 0 6 0 +DIHEdral HPa HP0 T0 B0 0 6 0 +DIHEdral HPa HP0 T0 Tda 0 6 0 +DIHEdral HPa HP0 T0 T0 0 6 0 +DIHEdral HPa HP0 T0 HP5 0 6 0 +DIHEdral HPa HP0 T0 HP0 0 6 0 +DIHEdral HPa HP0 T0 HPa 0 6 0 +DIHEdral HPa HP0 HP5 F4 0 6 0 +DIHEdral HPa HP0 HP5 F5 0 6 0 +DIHEdral HPa HP0 HP5 Fa 0 6 0 +DIHEdral HPa HP0 HP5 Bda 0 6 0 +DIHEdral HPa HP0 HP5 B0 0 6 0 +DIHEdral HPa HP0 HP5 Tda 0 6 0 +DIHEdral HPa HP0 HP5 T0 0 6 0 +DIHEdral HPa HP0 HP0 F4 0 6 0 +DIHEdral HPa HP0 HP0 F5 0 6 0 +DIHEdral HPa HP0 HP0 Fa 0 6 0 +DIHEdral HPa HP0 HP0 Bda 0 6 0 +DIHEdral HPa HP0 HP0 B0 0 6 0 +DIHEdral HPa HP0 HP0 Tda 0 6 0 +DIHEdral HPa HP0 HP0 T0 0 6 0 +DIHEdral HPa HP0 HPa F4 0 6 0 +DIHEdral HPa HP0 HPa F5 0 6 0 +DIHEdral HPa HP0 HPa Fa 0 6 0 +DIHEdral HPa HP0 HPa Bda 0 6 0 +DIHEdral HPa HP0 HPa B0 0 6 0 +DIHEdral HPa HP0 HPa Tda 0 6 0 +DIHEdral HPa HP0 HPa T0 0 6 0 +DIHEdral HPa HPa F4 F4 0 6 0 +DIHEdral HPa HPa F4 F5 0 6 0 +DIHEdral HPa HPa F4 Fa 0 6 0 +DIHEdral HPa HPa F4 H0 0 6 0 +DIHEdral HPa HPa F4 H5 0 6 0 +DIHEdral HPa HPa F4 Hd 0 6 0 +DIHEdral HPa HPa F4 Ha 0 6 0 +DIHEdral HPa HPa F4 Hda 0 6 0 +DIHEdral HPa HPa F4 Bda 0 6 0 +DIHEdral HPa HPa F4 B0 0 6 0 +DIHEdral HPa HPa F4 Tda 0 6 0 +DIHEdral HPa HPa F4 T0 0 6 0 +DIHEdral HPa HPa F4 HP5 0 6 0 +DIHEdral HPa HPa F4 HP0 0 6 0 +DIHEdral HPa HPa F4 HPa 0 6 0 +DIHEdral HPa HPa F5 F4 0 6 0 +DIHEdral HPa HPa F5 F5 0 6 0 +DIHEdral HPa HPa F5 Fa 0 6 0 +DIHEdral HPa HPa F5 H0 0 6 0 +DIHEdral HPa HPa F5 H5 0 6 0 +DIHEdral HPa HPa F5 Hd 0 6 0 +DIHEdral HPa HPa F5 Ha 0 6 0 +DIHEdral HPa HPa F5 Hda 0 6 0 +DIHEdral HPa HPa F5 Bda 0 6 0 +DIHEdral HPa HPa F5 B0 0 6 0 +DIHEdral HPa HPa F5 Tda 0 6 0 +DIHEdral HPa HPa F5 T0 0 6 0 +DIHEdral HPa HPa F5 HP5 0 6 0 +DIHEdral HPa HPa F5 HP0 0 6 0 +DIHEdral HPa HPa F5 HPa 0 6 0 +DIHEdral HPa HPa Fa F4 0 6 0 +DIHEdral HPa HPa Fa F5 0 6 0 +DIHEdral HPa HPa Fa Fa 0 6 0 +DIHEdral HPa HPa Fa H0 0 6 0 +DIHEdral HPa HPa Fa H5 0 6 0 +DIHEdral HPa HPa Fa Hd 0 6 0 +DIHEdral HPa HPa Fa Ha 0 6 0 +DIHEdral HPa HPa Fa Hda 0 6 0 +DIHEdral HPa HPa Fa Bda 0 6 0 +DIHEdral HPa HPa Fa B0 0 6 0 +DIHEdral HPa HPa Fa Tda 0 6 0 +DIHEdral HPa HPa Fa T0 0 6 0 +DIHEdral HPa HPa Fa HP5 0 6 0 +DIHEdral HPa HPa Fa HP0 0 6 0 +DIHEdral HPa HPa Fa HPa 0 6 0 +DIHEdral HPa HPa H0 F4 0 6 0 +DIHEdral HPa HPa H0 F5 0 6 0 +DIHEdral HPa HPa H0 Fa 0 6 0 +DIHEdral HPa HPa H0 Bda 0 6 0 +DIHEdral HPa HPa H0 B0 0 6 0 +DIHEdral HPa HPa H0 Tda 0 6 0 +DIHEdral HPa HPa H0 T0 0 6 0 +DIHEdral HPa HPa H5 F4 0 6 0 +DIHEdral HPa HPa H5 F5 0 6 0 +DIHEdral HPa HPa H5 Fa 0 6 0 +DIHEdral HPa HPa H5 Bda 0 6 0 +DIHEdral HPa HPa H5 B0 0 6 0 +DIHEdral HPa HPa H5 Tda 0 6 0 +DIHEdral HPa HPa H5 T0 0 6 0 +DIHEdral HPa HPa Hd F4 0 6 0 +DIHEdral HPa HPa Hd F5 0 6 0 +DIHEdral HPa HPa Hd Fa 0 6 0 +DIHEdral HPa HPa Hd Bda 0 6 0 +DIHEdral HPa HPa Hd B0 0 6 0 +DIHEdral HPa HPa Hd Tda 0 6 0 +DIHEdral HPa HPa Hd T0 0 6 0 +DIHEdral HPa HPa Ha F4 0 6 0 +DIHEdral HPa HPa Ha F5 0 6 0 +DIHEdral HPa HPa Ha Fa 0 6 0 +DIHEdral HPa HPa Ha Bda 0 6 0 +DIHEdral HPa HPa Ha B0 0 6 0 +DIHEdral HPa HPa Ha Tda 0 6 0 +DIHEdral HPa HPa Ha T0 0 6 0 +DIHEdral HPa HPa Hda F4 0 6 0 +DIHEdral HPa HPa Hda F5 0 6 0 +DIHEdral HPa HPa Hda Fa 0 6 0 +DIHEdral HPa HPa Hda Bda 0 6 0 +DIHEdral HPa HPa Hda B0 0 6 0 +DIHEdral HPa HPa Hda Tda 0 6 0 +DIHEdral HPa HPa Hda T0 0 6 0 +DIHEdral HPa HPa Bda F4 0 6 0 +DIHEdral HPa HPa Bda F5 0 6 0 +DIHEdral HPa HPa Bda Fa 0 6 0 +DIHEdral HPa HPa Bda H0 0 6 0 +DIHEdral HPa HPa Bda H5 0 6 0 +DIHEdral HPa HPa Bda Hd 0 6 0 +DIHEdral HPa HPa Bda Ha 0 6 0 +DIHEdral HPa HPa Bda Hda 0 6 0 +DIHEdral HPa HPa Bda Bda 0 6 0 +DIHEdral HPa HPa Bda B0 0 6 0 +DIHEdral HPa HPa Bda Tda 0 6 0 +DIHEdral HPa HPa Bda T0 0 6 0 +DIHEdral HPa HPa Bda HP5 0 6 0 +DIHEdral HPa HPa Bda HP0 0 6 0 +DIHEdral HPa HPa Bda HPa 0 6 0 +DIHEdral HPa HPa B0 F4 0 6 0 +DIHEdral HPa HPa B0 F5 0 6 0 +DIHEdral HPa HPa B0 Fa 0 6 0 +DIHEdral HPa HPa B0 H0 0 6 0 +DIHEdral HPa HPa B0 H5 0 6 0 +DIHEdral HPa HPa B0 Hd 0 6 0 +DIHEdral HPa HPa B0 Ha 0 6 0 +DIHEdral HPa HPa B0 Hda 0 6 0 +DIHEdral HPa HPa B0 Bda 0 6 0 +DIHEdral HPa HPa B0 B0 0 6 0 +DIHEdral HPa HPa B0 Tda 0 6 0 +DIHEdral HPa HPa B0 T0 0 6 0 +DIHEdral HPa HPa B0 HP5 0 6 0 +DIHEdral HPa HPa B0 HP0 0 6 0 +DIHEdral HPa HPa B0 HPa 0 6 0 +DIHEdral HPa HPa Tda F4 0 6 0 +DIHEdral HPa HPa Tda F5 0 6 0 +DIHEdral HPa HPa Tda Fa 0 6 0 +DIHEdral HPa HPa Tda H0 0 6 0 +DIHEdral HPa HPa Tda H5 0 6 0 +DIHEdral HPa HPa Tda Hd 0 6 0 +DIHEdral HPa HPa Tda Ha 0 6 0 +DIHEdral HPa HPa Tda Hda 0 6 0 +DIHEdral HPa HPa Tda Bda 0 6 0 +DIHEdral HPa HPa Tda B0 0 6 0 +DIHEdral HPa HPa Tda Tda 0 6 0 +DIHEdral HPa HPa Tda T0 0 6 0 +DIHEdral HPa HPa Tda HP5 0 6 0 +DIHEdral HPa HPa Tda HP0 0 6 0 +DIHEdral HPa HPa Tda HPa 0 6 0 +DIHEdral HPa HPa T0 F4 0 6 0 +DIHEdral HPa HPa T0 F5 0 6 0 +DIHEdral HPa HPa T0 Fa 0 6 0 +DIHEdral HPa HPa T0 H0 0 6 0 +DIHEdral HPa HPa T0 H5 0 6 0 +DIHEdral HPa HPa T0 Hd 0 6 0 +DIHEdral HPa HPa T0 Ha 0 6 0 +DIHEdral HPa HPa T0 Hda 0 6 0 +DIHEdral HPa HPa T0 Bda 0 6 0 +DIHEdral HPa HPa T0 B0 0 6 0 +DIHEdral HPa HPa T0 Tda 0 6 0 +DIHEdral HPa HPa T0 T0 0 6 0 +DIHEdral HPa HPa T0 HP5 0 6 0 +DIHEdral HPa HPa T0 HP0 0 6 0 +DIHEdral HPa HPa T0 HPa 0 6 0 +DIHEdral HPa HPa HP5 F4 0 6 0 +DIHEdral HPa HPa HP5 F5 0 6 0 +DIHEdral HPa HPa HP5 Fa 0 6 0 +DIHEdral HPa HPa HP5 Bda 0 6 0 +DIHEdral HPa HPa HP5 B0 0 6 0 +DIHEdral HPa HPa HP5 Tda 0 6 0 +DIHEdral HPa HPa HP5 T0 0 6 0 +DIHEdral HPa HPa HP0 F4 0 6 0 +DIHEdral HPa HPa HP0 F5 0 6 0 +DIHEdral HPa HPa HP0 Fa 0 6 0 +DIHEdral HPa HPa HP0 Bda 0 6 0 +DIHEdral HPa HPa HP0 B0 0 6 0 +DIHEdral HPa HPa HP0 Tda 0 6 0 +DIHEdral HPa HPa HP0 T0 0 6 0 +DIHEdral HPa HPa HPa F4 0 6 0 +DIHEdral HPa HPa HPa F5 0 6 0 +DIHEdral HPa HPa HPa Fa 0 6 0 +DIHEdral HPa HPa HPa Bda 0 6 0 +DIHEdral HPa HPa HPa B0 0 6 0 +DIHEdral HPa HPa HPa Tda 0 6 0 +DIHEdral HPa HPa HPa T0 0 6 0 + + + + + +{* non-bonded parameters *} +! Adapted MARTINI Info +! +! levels of LJ interaction: +! kJ to kCal: mult by (1/4.178) +! +! (Kj/mol) (a) +! O - supra attractive: (eps=1.337), s=4.7) +! I - attractive: (eps=1.194), s=4.7) +! II - almost attractive: (eps=1.075), s=4.7) +! III - semi attractive: (eps=0.955), s=4.7) +! IV - intermediate: (eps=0.836), s=4.7) +! V - almost intermediate: (eps=0.740), s=4.7) +! VI - semi repulsive: (eps=0.645), s=4.7) +! VII - almost repulsive: (eps=0.549), s=4.7) +! VIII - repulsive: (eps=0.478), s=4.7) +! IX - super repulsive: (eps=0.478), s=6.2) +! +! RINGS: for ring-ring interactions eps is reduced to 75%, sigma=4.3 +! +! eps sigma eps(1:4) sigma(1:4) +! (kcal/mol) (A) (kcal/mol) (A) +! ---------------------------------------------- +! Self-terms BACKBONE (15) +NONBONded Hda 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded H0 0.836 4.7 0.836 4.7 ! intermediate +NONBONded H5 0.836 4.7 0.836 4.7 ! intermediate +NONBONded HP5 0.836 4.7 0.836 4.7 ! intermediate +NONBONded Hd 0.955 4.7 0.955 4.7 ! semi attractive +NONBONded Ha 0.955 4.7 0.955 4.7 ! semi attractive +NONBONded HPa 0.955 4.7 0.955 4.7 ! semi attractive +NONBONded HP0 0.836 4.7 0.836 4.7 ! intermediate +NONBONded Bda 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded B0 0.836 4.7 0.836 4.7 ! intermediate +NONBONded Tda 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded T0 0.836 4.7 0.836 4.7 ! intermediate +NONBonded F5 1.337 4.7 1.337 4.7 ! supra attractive +NONBONded F4 1.194 4.7 1.194 4.7 ! attractive +NONBONded Fa 0.955 4.7 0.955 4.7 ! semi attractive + +! Self-terms SIDECHAIN (45) +NONBonded P5 1.337 4.7 1.337 4.7 ! supra attractive +NONBonded AP5 1.337 4.7 1.337 4.7 ! supra attractive +NONBONded P4 1.194 4.7 1.194 4.7 ! attractive +NONBONded GP4 1.194 4.7 1.194 4.7 ! attractive +NONBONded P3 1.194 4.7 1.194 4.7 ! attractive +NONBONded P2 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded P1 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded TP1 1.075 4.7 1.075 4.7 ! almost attractive +NONBONded N0 0.836 4.7 0.836 4.7 ! intermediate +NONBONded C5 0.836 4.7 0.836 4.7 ! intermediate +NONBONded MC5 0.836 4.7 0.836 4.7 ! intermediate +NONBONded C4 0.836 4.7 0.836 4.7 ! intermediate +NONBONded C3 0.836 4.7 0.836 4.7 ! intermediate +NONBONded C2 0.836 4.7 0.836 4.7 ! intermediate +NONBONded C1 0.836 4.7 0.836 4.7 ! intermediate +NONBONded Qda 1.337 4.7 1.337 4.7 ! supra attractive +NONBONded Qd 1.194 4.7 1.194 4.7 ! attractive +NONBONded Qa 1.194 4.7 1.194 4.7 ! attractive +NONBONded GQa 1.194 4.7 1.194 4.7 ! attractive +NONBONded Q0 0.836 4.7 0.836 4.7 ! intermediate +NONBONded SP5 1.003 4.3 1.003 4.3 ! supra attractive (ring) +NONBONded SP4 0.895 4.3 0.895 4.3 ! attractive (ring) +NONBONded SP3 0.895 4.3 0.895 4.3 ! attractive (ring) +NONBONded SP2 0.806 4.3 0.806 4.3 ! almost attractive (ring) +NONBONded SP1 0.806 4.3 0.806 4.3 ! almost attractive (ring) +NONBONded SNda 0.806 4.3 0.806 4.3 ! almost attractive (ring) +NONBONded SNd 0.716 4.3 0.716 4.3 ! semi attractive (ring) +NONBONded SNa 0.716 4.3 0.716 4.3 ! semi attractive (ring) +NONBONded SN0 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SC5 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SC4 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded PC4 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded HC4 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded TC4 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SC3 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SC2 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SC1 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded SQda 1.003 4.3 1.003 4.3 ! supra attractive (ring) +NONBONded SQd 0.895 4.3 0.895 4.3 ! attractive (ring) +NONBONded SQa 0.895 4.3 0.895 4.3 ! attractive (ring) +NONBONded SQ0 0.627 4.3 0.627 4.3 ! intermediate (ring) +NONBONded AC2 0.836 4.7 0.836 4.7 ! intermediate +NONBONded AC1 0.836 4.7 0.836 4.7 ! intermediate +NONBONded LC1 0.836 4.7 0.836 4.7 ! intermediate +NONBONded BP4 1.194 4.7 1.194 4.7 ! attractive + + +! cross-terms: important at least for ring particles +! Not sigma and eps anymore, but A & B +! A = 4 * sigma^12 * eps +! B = 4 * sigma^6 * eps +! -------------------------------------------------------------------- + +NBFIx P5 SP5 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 P4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 GP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 F4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 BP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 P3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SP3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 P2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SP2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 P1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 TP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 Bda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 Tda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 SNda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 Hd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 SNd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 Fa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 HPa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 Ha 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 SNa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P5 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P5 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P5 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P5 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P5 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P5 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P5 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P5 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P5 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P5 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P5 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P5 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P5 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P5 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P5 SQ0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +! +NBFIx F5 SP5 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 P4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 GP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 F4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 BP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 P3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SP3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 P2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SP2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 P1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 TP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 Bda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 Tda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 SNda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 Hd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 SNd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 Fa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 HPa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 Ha 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 SNa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F5 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F5 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F5 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F5 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F5 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F5 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F5 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F5 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F5 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F5 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F5 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F5 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F5 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F5 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F5 SQ0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +! +NBFIx AP5 SP5 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 P4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 GP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 F4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 BP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 P3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SP3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 P2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SP2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 P1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 TP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 Bda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 Tda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 SNda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 Hd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 SNd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 Fa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 HPa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 Ha 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 SNa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AP5 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx AP5 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx AP5 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx AP5 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx AP5 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx AP5 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx AP5 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx AP5 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx AP5 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AP5 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AP5 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AP5 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AP5 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx AP5 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx AP5 SQ0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +! +NBFIx SP5 P4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 F4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 GP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 BP4 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 P3 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 P2 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 P1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 TP1 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 Bda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 Tda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 Hd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 Ha 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 HPa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 Fa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP5 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP5 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP5 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP5 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP5 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP5 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP5 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP5 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP5 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP5 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP5 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP5 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP5 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SP5 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SP5 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP5 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +! +NBFIx P4 BP4 6290565179.796 183417.400 6290565179.796 183417.400 ! supra attractive (s=5.7) +NBFIx P4 SP4 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P4 P3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P4 SP3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P4 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P4 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P4 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P4 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P4 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P4 Bda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 Tda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 SNda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 Hd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 SNd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 Ha 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 HPa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 Fa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P4 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P4 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P4 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P4 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P4 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P4 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P4 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P4 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P4 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P4 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P4 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P4 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P4 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx P4 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 Q0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P4 SQ0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +! +NBFIx F4 BP4 6290565179.796 183417.400 6290565179.796 183417.400 ! supra attractive (s=5.7) +NBFIx F4 SP4 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F4 P3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F4 SP3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx F4 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx F4 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx F4 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx F4 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx F4 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx F4 Bda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 Tda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 SNda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 Hd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 SNd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 Ha 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 HPa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 Fa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx F4 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx F4 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F4 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F4 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F4 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx F4 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx F4 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F4 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F4 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx F4 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F4 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F4 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F4 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx F4 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 Q0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx F4 SQ0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +! +NBFIx GP4 BP4 6290565179.796 183417.400 6290565179.796 183417.400 ! supra attractive (s=5.7) +NBFIx GP4 SP4 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx GP4 P3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx GP4 SP3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx GP4 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GP4 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GP4 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GP4 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GP4 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GP4 Bda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 Tda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 SNda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 Hd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 SNd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 Ha 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 HPa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 Fa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx GP4 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx GP4 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx GP4 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx GP4 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx GP4 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx GP4 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx GP4 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx GP4 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx GP4 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx GP4 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx GP4 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx GP4 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx GP4 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx GP4 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 Q0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx GP4 SQ0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +! +NBFIx BP4 SP4 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx BP4 P3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx BP4 SP3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx BP4 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx BP4 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx BP4 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx BP4 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx BP4 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx BP4 Tda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 Bda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 SNda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 Hd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 SNd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 Ha 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 HPa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 Fa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx BP4 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx BP4 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx BP4 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx BP4 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx BP4 SC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx BP4 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 SC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 HC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 PC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 TC4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx BP4 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx BP4 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx BP4 SC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx BP4 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx BP4 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx BP4 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx BP4 SC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx BP4 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 Q0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx BP4 SQ0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +! +NBFIx SP4 P3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP4 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP4 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP4 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP4 Bda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 Tda 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 Ha 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 HPa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 Fa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP4 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP4 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP4 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP4 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP4 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP4 C5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP4 H5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP4 MC5 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP4 C4 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP4 C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP4 C2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP4 AC2 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP4 C1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SP4 AC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SP4 LC1 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SP4 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP4 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP4 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP4 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP4 Q0 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 SP3 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P3 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P3 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P3 C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 C3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 SC3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P3 C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P3 AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P3 SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P3 C1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P3 AC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P3 LC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P3 SC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P3 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx P3 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P3 SQ0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP3 P2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP3 N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP3 C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP3 C3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP3 C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP3 AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP3 C1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP3 AC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP3 LC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP3 Qda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP3 Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP3 Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP3 GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SP3 Q0 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 SP2 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 N0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 HP0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 T0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 H0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 SN0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P2 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P2 C3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P2 SC3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P2 C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P2 AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P2 SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P2 C1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P2 AC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P2 LC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P2 SC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx P2 Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P2 Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P2 SQ0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 P1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 TP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP2 N0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP2 HP0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP2 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP2 T0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP2 H0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP2 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP2 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP2 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP2 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP2 C3 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP2 C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP2 AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP2 C1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP2 AC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP2 LC1 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SP2 Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP2 Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP2 Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP2 GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP2 Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +! +NBFIx P1 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx P1 N0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 HP0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 T0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 H0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 SN0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx P1 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P1 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P1 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx P1 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P1 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P1 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P1 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx P1 Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx P1 Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx P1 SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx TP1 SP1 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx TP1 N0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 HP0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 T0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 H0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 SN0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TP1 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TP1 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TP1 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TP1 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TP1 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TP1 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TP1 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TP1 Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx TP1 Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx TP1 SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx SP1 Bda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 Tda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 B0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 T0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SP1 N0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP1 HP0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP1 B0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP1 T0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP1 H0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SP1 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP1 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP1 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP1 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP1 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SP1 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP1 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SP1 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP1 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP1 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SP1 Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP1 Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP1 Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP1 GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SP1 Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx Bda SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Bda N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Bda C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Bda SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Bda HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Bda TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Bda PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Bda C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Bda Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Bda Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Bda SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx Tda SNda 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda Hd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda SNd 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Tda N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Tda C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Tda SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Tda HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Tda TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Tda PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Tda C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Tda Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Tda Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Tda SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx Hd SNd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Hd Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Hd HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Hd Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Hd SNa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Hd N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Hd C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Hd SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Hd HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Hd TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Hd PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Hd C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Hd Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Hd SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Hd Qd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Hd SQd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Hd Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Hd GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Hd SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Hd Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Hd SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx SNd HPa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SNd Ha 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SNd Fa 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SNd N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNd C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SNd C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNd Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SNd Qd 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SNd Qa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SNd GQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SNd Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx Ha SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Ha C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Ha SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Ha HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Ha TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Ha PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Ha C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Ha Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Ha SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Ha Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Ha SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Ha Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha GQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha SQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Ha Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx HPa SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HPa C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HPa SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HPa HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HPa TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HPa PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HPa C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HPa Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx HPa SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx HPa Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx HPa SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx HPa Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa GQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa SQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx HPa Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx Fa SNa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx Fa C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Fa SC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Fa HC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Fa TC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Fa PC4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx Fa C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa SC3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa SC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx Fa Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Fa SQda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Fa Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Fa SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Fa Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa GQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa SQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa SQ0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx Fa Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx SNa HP0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa B0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa T0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa H0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa N0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SNa C4 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SNa C3 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa C2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa AC2 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SNa Qda 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SNa Qd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx SNa Qa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SNa GQa 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +NBFIx SNa Q0 443851465.476 41176.603 443851465.476 41176.603 ! semi attractive +! +NBFIx HP0 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HP0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HP0 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HP0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HP0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HP0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HP0 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HP0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SQda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SQd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HP0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx B0 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx B0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx B0 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx B0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx B0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx B0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx B0 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx B0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SQda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SQd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx B0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx T0 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx T0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx T0 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx T0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx T0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx T0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx T0 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx T0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SQda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SQd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx T0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx H0 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H0 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx H0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx H0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx H0 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx H0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SQda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SQd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx N0 SN0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx N0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx N0 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx N0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx N0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx N0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx N0 SC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx N0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SQda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SQd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx N0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx SN0 C5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 MC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 H5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SN0 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SN0 C1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SN0 AC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SN0 LC1 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SN0 Qda 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 Qd 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 Qa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 GQa 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SN0 Q0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +NBFIx C5 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C5 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 Qda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SQda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 Qd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SQd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 Qa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 GQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 Q0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C5 SQ0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +! +NBFIx MC5 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx MC5 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 Qda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SQda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 Qd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SQd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 Qa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 GQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 Q0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx MC5 SQ0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +! +NBFIx H5 SC5 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx H5 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 Qda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SQda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 Qd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SQd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 Qa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 GQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 Q0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx H5 SQ0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +! +NBFIx SC5 C4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC5 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC5 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 Qda 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 Qd 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 Qa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 GQa 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC5 Q0 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 SC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 HC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 TC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 PC4 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C4 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 SC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 SC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx C4 Qda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 SQda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 Qd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 SQd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 Qa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 GQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 SQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 Q0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx C4 SQ0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +! +NBFIx SC4 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC4 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC4 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC4 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC4 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC4 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx SC4 Qda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SC4 Qd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SC4 Qa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SC4 GQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx SC4 Q0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +! +NBFIx TC4 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx TC4 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TC4 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TC4 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TC4 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TC4 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx TC4 Qda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TC4 Qd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TC4 Qa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TC4 GQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx TC4 Q0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +! +NBFIx PC4 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx PC4 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx PC4 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx PC4 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx PC4 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx PC4 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx PC4 Qda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx PC4 Qd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx PC4 Qa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx PC4 GQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx PC4 Q0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +! +NBFIx HC4 C3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx HC4 C2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HC4 AC2 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HC4 C1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HC4 AC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HC4 LC1 343926790.002 31906.477 343926790.002 31906.477 ! almost intermediate +NBFIx HC4 Qda 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HC4 Qd 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HC4 Qa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HC4 GQa 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +NBFIx HC4 Q0 299774026.421 27810.376 299774026.421 27810.376 ! semi repulsive +! +NBFIx C3 SC3 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 C2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 AC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 SC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 C1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 LC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C3 Qda 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 SQda 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 Qd 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 SQd 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 Qa 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 GQa 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 SQa 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 Q0 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C3 SQ0 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SC3 C2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC3 AC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC3 C1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC3 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC3 LC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC3 Qda 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SC3 Qd 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SC3 Qa 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SC3 GQa 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx SC3 Q0 255156496.907 23671.157 255156496.907 23671.157 ! almost repulsive +NBFIx C2 AC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 SC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 C1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 LC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C2 Qda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 SQda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 Qd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 SQd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 Qa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 GQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 SQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 Q0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C2 SQ0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx AC2 SC2 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC2 C1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC2 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC2 LC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC2 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC2 Qda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 SQda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 Qd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 SQd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 Qa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 GQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 SQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 Q0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC2 SQ0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx SC2 C1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC2 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx SC2 Qda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 SQda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 Qd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 SQd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 Qa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 SQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 Q0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC2 SQ0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 AC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C1 LC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C1 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx C1 Qda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 SQda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 Qd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 SQd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 Qa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 GQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 SQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 Q0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx C1 SQ0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +! +NBFIx AC1 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx AC1 Qda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 SQda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 Qd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 SQd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 Qa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 GQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 SQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 Q0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx AC1 SQ0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +! +NBFIx LC1 SC1 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +NBFIx LC1 Qda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 SQda 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 Qd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 SQd 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 Qa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 GQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 SQa 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 Q0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +NBFIx LC1 SQ0 222158115.704 20609.860 222158115.704 20609.860 ! repulsive +! +NBFIx SC1 Qda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 SQda 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 Qd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 SQd 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 Qa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 GQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 SQa 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 Q0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx SC1 SQ0 6168622049.705 108602.050 6168622049.705 108602.050 ! super repulsive (s=6.2) +NBFIx Qda SQda 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda SQd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qda Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Qda SQ0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SQda Qd 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SQda Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SQda GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SQda Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Qd SQd 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Qd Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qd GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qd SQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx Qd Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Qd SQ0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx SQd Qa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SQd GQa 621392051.667 57647.244 621392051.667 57647.244 ! supra attractive +NBFIx SQd Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +! +NBFIx Qa SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx Qa Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Qa SQ0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +! +NBFIx GQa SQa 554930523.328 51481.532 554930523.328 51481.532 ! attractive +NBFIx GQa Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx GQa SQ0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +! +NBFIx SQa Q0 499623377.368 46350.626 499623377.368 46350.626 ! almost attractive +NBFIx Q0 SQ0 388544319.516 36045.696 388544319.516 36045.696 ! intermediate +! +!RING-RING +NBFIx SP5 SP4 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SP3 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SP2 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SP1 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SNda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP5 SNd 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP5 SNa 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP5 SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP5 SC5 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP5 SC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP5 TC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP5 PC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP5 HC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP5 SC3 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP5 SC2 65853471.554 10417.606 65853471.554 10417.606 ! almost repulsive (ring) +NBFIx SP5 SC1 57382029.825 9077.477 57382029.825 9077.477 ! repulsive (ring) +NBFIx SP5 SQda 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SQd 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SQa 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP5 SQ0 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP4 SP3 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP4 SP2 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP4 SP1 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP4 SNda 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SP4 SNd 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SP4 SNa 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SP4 SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP4 SC5 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP4 SC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP4 HC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP4 PC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP4 TC4 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP4 SC3 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP4 SC2 65853471.554 10417.606 65853471.554 10417.606 ! almost repulsive (ring) +NBFIx SP4 SC1 57382029.825 9077.477 57382029.825 9077.477 ! repulsive (ring) +NBFIx SP4 SQda 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP4 SQd 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP4 SQa 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP4 SQ0 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP3 SP2 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP3 SP1 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP3 SNda 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP3 SNd 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP3 SNa 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP3 SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP3 SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP3 SC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP3 HC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP3 TC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP3 PC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP3 SC3 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP3 SC2 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP3 SC1 65853471.554 10417.606 65853471.554 10417.606 ! almost repulsive (ring) +NBFIx SP3 SQda 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP3 SQd 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP3 SQa 160318038.759 25361.309 160318038.759 25361.309 ! supra attractive (ring) +NBFIx SP3 SQ0 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP2 SP1 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP2 SNda 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP2 SNd 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP2 SNa 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP2 SN0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SP2 SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP2 SC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP2 HC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP2 TC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP2 PC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP2 SC3 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP2 SC2 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP2 SC1 65853471.554 10417.606 65853471.554 10417.606 ! almost repulsive (ring) +NBFIx SP2 SQda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP2 SQd 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP2 SQa 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP2 SQ0 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP1 SNda 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP1 SNd 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP1 SNa 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SP1 SN0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SP1 SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 SC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 HC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 TC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 PC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 SC3 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SP1 SC2 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SP1 SC1 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SP1 SQda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP1 SQd 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP1 SQa 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SP1 SQ0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SNda SNd 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SNda SNa 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SNda SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNda SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNda SC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNda HC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNda TC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNda PC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNda SC3 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNda SC2 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNda SC1 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNda SQda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNda SQd 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNda SQa 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNda SQ0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SNd SNa 128829849.690 20380.074 128829849.690 20380.074 ! almost attractive (ring) +NBFIx SNd SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNd SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNd SC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNd HC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNd TC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNd PC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNd SC3 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNd SC2 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNd SC1 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNd SQda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNd SQd 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SNd SQa 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNd SQ0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SNa SN0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNa SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SNa SC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNa HC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNa TC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNa PC4 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SNa SC3 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNa SC2 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNa SC1 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SNa SQda 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNa SQd 143055478.254 22630.480 143055478.254 22630.480 ! attractive (ring) +NBFIx SNa SQa 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SNa SQ0 114444382.603 18104.384 114444382.603 18104.384 ! semi attractive (ring) +NBFIx SN0 SC5 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 HC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 TC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 PC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SC3 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SC2 88710380.370 14033.426 88710380.370 14033.426 ! almost intermediate (ring) +NBFIx SN0 SC1 77361845.224 12238.159 77361845.224 12238.159 ! semi repulsive (ring) +NBFIx SN0 SQda 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SQd 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SQa 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SN0 SQ0 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SC5 SC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SC5 HC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SC5 TC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) +NBFIx SC5 PC4 100218754.040 15853.979 100218754.040 15853.979 ! intermediate (ring) + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.top new file mode 100644 index 0000000000000000000000000000000000000000..c967911b417484ed22eb44581b4dcbc9bf888800 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-CG-Martini.top @@ -0,0 +1,506 @@ +! Topology file based on Martinize.py CG script +! Author: Charleen Don, MAR-12 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +autogenerate + angles=false + dihedrals=false +end + +{* PROTEIN default masses *} +! Backbone types +MASS F4 72.00 +MASS F5 72.00 +MASS Fa 72.00 +MASS Tda 72.00 +MASS T0 72.00 +MASS Bda 72.00 +MASS B0 72.00 +MASS H0 72.00 +MASS H5 72.00 +MASS Hd 72.00 +MASS Ha 72.00 +MASS HPa 72.00 +MASS HP0 72.00 +MASS HP5 72.00 +MASS Hda 72.00 + +! Side chain types +MASS AP5 72.00 +MASS P4 72.00 +MASS GP4 72.00 +MASS P3 72.00 +MASS P2 72.00 +MASS P1 72.00 +MASS TP1 72.00 +MASS N0 72.00 +MASS C5 72.00 +MASS MC5 72.00 +MASS C4 72.00 +MASS C3 72.00 +MASS C2 72.00 +MASS C1 72.00 +MASS Qda 72.00 +MASS Qd 72.00 +MASS Qa 72.00 +MASS Q0 72.00 +MASS GQa 72.00 +MASS SP5 45.00 +MASS SP4 45.00 +MASS SP3 45.00 +MASS SP2 45.00 +MASS SP1 45.00 +MASS SC5 45.00 +MASS SC4 45.00 +MASS PC4 45.00 +MASS HC4 45.00 +MASS TC4 45.00 +MASS SC3 45.00 +MASS SC2 45.00 +MASS SC1 45.00 +MASS SQda 45.00 +MASS SQd 45.00 +MASS SQa 45.00 +MASS SQ0 45.00 +MASS SNda 45.00 +MASS SNd 45.00 +MASS SNa 45.00 +MASS SN0 45.00 +MASS AC1 72.00 +MASS LC1 72.00 +MASS AC2 72.00 +MASS BP4 72.00 + +RESIdue ALA + GROUp + ATOM BB type=F4 charge=0.000 end +END + + +RESIdue ARG + GROUPp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=N0 charge=0.00 end + ATOM SC2 type=Qd charge=1.00 end + + BOND BB SC1 + BOND SC1 SC2 + + ANGLE BB SC1 SC2 +END + + +RESIdue ASN + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=AP5 charge=0.00 end + + BOND BB SC1 +END + + +RESIdue ASP + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=Qa charge=-1.000 end + + BOND BB SC1 +END + + +RESIdue CYS + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=C5 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue GLN + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=GP4 charge=0.000 end + + BOND BB SC1 +END + +RESIdue GLU + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=Qa charge=-1.000 end + + BOND BB SC1 +END + + +RESIdue GLY + GROUp + ATOM BB type=F5 charge=0.00 end +END + + +RESIdue NEP + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=HC4 charge=0.000 end + ATOM SC2 type=SP1 charge=-0.500 end + ATOM SC3 type=SP1 charge=-0.500 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue HIS + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=HC4 charge=0.000 end + ATOM SC2 type=SP1 charge=0.000 end + ATOM SC3 type=SP1 charge=0.000 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue ILE + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=AC1 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue LEU + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=LC1 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue LYS + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=C3 charge=0.000 end + ATOM SC2 type=Qd charge=1.000 end + + BOND BB SC1 + BOND SC1 SC2 + + ANGLE BB SC1 SC2 +END + +RESIdue MET + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=MC5 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue PHE + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=PC4 charge=0.00 end + ATOM SC2 type=SC4 charge=0.00 end + ATOM SC3 type=SC4 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue PRO + GROUp + ATOM BB type=Fa charge=0.000 end + ATOM SC1 type=AC2 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue SER + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=P1 charge=0.000 end + + BOND BB SC1 +END + +RESIdue THR + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=TP1 charge=0.000 end + + BOND BB SC1 +END + + +RESIdue TRP + GROUp + ATOM BB type=F5 charge=0.000 end + ATOM SC1 type=SC4 charge=0.000 end + ATOM SC2 type=SP1 charge=0.000 end + ATOM SC3 type=SC4 charge=0.000 end + ATOM SC4 type SC4 charge=0.000 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + BOND SC2 SC4 + BOND SC3 SC4 + + DIHEdral BB SC2 SC3 SC1 + DIHEdral SC1 SC2 SC4 SC3 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue TYR + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=TC4 charge=0.00 end + ATOM SC2 type=SC4 charge=0.00 end + ATOM SC3 type=SP1 charge=0.00 end + + BOND BB SC1 + BOND SC1 SC2 + BOND SC1 SC3 + BOND SC2 SC3 + + DIHEdral BB SC2 SC3 SC1 + + ANGLE BB SC1 SC2 + ANGLE BB SC1 SC3 +END + + +RESIdue VAL + GROUp + ATOM BB type=F5 charge=0.00 end + ATOM SC1 type=AC2 charge=0.00 end + + BOND BB SC1 +END + + +!------------------------------------------------------------------ + +PRESidue PTY1 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA1 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP1 + MODIFY ATOM BB TYPE=Fa END +END + + +PRESidue PTH1 + MODIFY ATOM BB TYPE=Fa END +END + + +PRESidue PTY2 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA2 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP2 + MODIFY ATOM BB TYPE=Fa END +END + + +PRESidue PTH2 + MODIFY ATOM BB TYPE=Fa END +END + + +PRESidue PTY3 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTA3 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTP3 + MODIFY ATOM BB TYPE=HP5 END +END + + +PRESidue PTH3 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY4 + MODIFY ATOM BB TYPE=Hd END +END + + +PRESidue PTA4 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP4 + MODIFY ATOM BB TYPE=HP0 END +END + + +PRESidue PTH4 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY5 + MODIFY ATOM BB TYPE=Ha END +END + + +PRESidue PTA5 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP5 + MODIFY ATOM BB TYPE=HPa END +END + + +PRESidue PTH5 + MODIFY ATOM BB TYPE=H5 END +END + + +PRESidue PTY6 + MODIFY ATOM BB TYPE=Hda END +END + + +PRESidue PTA6 + MODIFY ATOM BB TYPE=H0 END +END + + +PRESidue PTP6 + MODIFY ATOM BB TYPE=HP0 END +END + + +PRESidue PTH6 + MODIFY ATOM BB TYPE=H5 END +END + +PRESidue PTY7 + MODIFY ATOM BB TYPE=Bda END +END + + +PRESidue PTA7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTP7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTH7 + MODIFY ATOM BB TYPE=B0 END +END + + +PRESidue PTY8 + MODIFY ATOM BB TYPE=Tda END +END + + +PRESidue PTA8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTP8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTH8 + MODIFY ATOM BB TYPE=T0 END +END + + +PRESidue PTY9 + MODIFY ATOM BB TYPE=F5 END +END + + +PRESidue PTA9 + MODIFY ATOM BB TYPE=F4 END +END + + +PRESidue PTP9 + MODIFY ATOM BB TYPE=Fa END +END + + +PRESidue PTH9 + MODIFY ATOM BB TYPE=Fa END +END + +PRESidue PEPT ! PEPTide bond link, for all + ! "*(-) - PEPT - (+)*: + add bond -BB +BB +END + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noCter.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noCter.link new file mode 100644 index 0000000000000000000000000000000000000000..a1e3d321a64e013d7f9a32861b53f56522936034 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noCter.link @@ -0,0 +1,2712 @@ +remarks file toppar/protein-allhdg5-4.link +remarks +remarks this is a macro to define standard protein peptide bonds +remarks and termini to generate a protein sequence. + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link ppgp head - GLY tail + PRO end +link ppgp head - GLY tail + HYP end +link ppgp head - GLY tail + HY3 end +link ppgg head - GLY tail + GLY end + +{ special link to GLY} +link ppg1 head - ACE tail + GLY end +link ppg1 head - ALA tail + GLY end +link ppg1 head - CYS tail + GLY end +link ppg1 head - CFE tail + GLY end +link ppg1 head - CYM tail + GLY end +link ppg1 head - CYF tail + GLY end +link ppg1 head - CYC tail + GLY end +link ppg1 head - CSP tail + GLY end +link ppg1 head - ASP tail + GLY end +link ppg1 head - ASH tail + GLY end +link ppg1 head - GLU tail + GLY end +link ppg1 head - GLH tail + GLY end +link ppg1 head - PCA tail + GLY end +link ppg1 head - PHE tail + GLY end +link ppg1 head - HIS tail + GLY end +link ppg1 head - NEP tail + GLY end +link ppg1 head - ILE tail + GLY end +link ppg1 head - LYS tail + GLY end +link ppg1 head - ALY tail + GLY end +link ppg1 head - HLY tail + GLY end +link ppg1 head - MLY tail + GLY end +link ppg1 head - MLZ tail + GLY end +link ppg1 head - M3L tail + GLY end +link ppg1 head - LEU tail + GLY end +link ppg1 head - MET tail + GLY end +link ppg1 head - MSE tail + GLY end ! +link ppg1 head - ASN tail + GLY end +link ppg1 head - PRO tail + GLY end +link ppg1 head - GLN tail + GLY end +link ppg1 head - ARG tail + GLY end +link ppg1 head - SER tail + GLY end +link ppg1 head - SEC tail + GLY end +link ppg1 head - SEP tail + GLY end +link ppg1 head - THR tail + GLY end +link ppg1 head - THP tail + GLY end +link ppg1 head - TOP tail + GLY end +link ppg1 head - VAL tail + GLY end +link ppg1 head - TRP tail + GLY end +link ppg1 head - TYR tail + GLY end +link ppg1 head - TYP tail + GLY end +link ppg1 head - PTR tail + GLY end +link ppg1 head - TYS tail + GLY end +link ppg1 head - HYP tail + GLY end +link ppg1 head - HY3 tail + GLY end +link ppg1 head - DDZ tail + GLY end +link ppg1 head - QSR tail + GLY end +link ppg1 head - PNS tail + GLY end +link ppg1 head - CIR tail + GLY end + +{ special link from GLY} +link ppg2 head - GLY tail + ALA end +link ppg2 head - GLY tail + CYS end +link ppg2 head - GLY tail + CFE end +link ppg2 head - GLY tail + CYM end +link ppg2 head - GLY tail + CYF end +link ppg2 head - GLY tail + CYC end +link ppg2 head - GLY tail + CSP end +link ppg2 head - GLY tail + ASP end +link ppg2 head - GLY tail + ASH end +link ppg2 head - GLY tail + GLU end +link ppg2 head - GLY tail + GLH end +link ppg2 head - GLY tail + PHE end +link ppg2 head - GLY tail + HIS end +link ppg2 head - GLY tail + NEP end +link ppg2 head - GLY tail + ILE end +link ppg2 head - GLY tail + LYS end +link ppg2 head - GLY tail + ALY end +link ppg2 head - GLY tail + HLY end +link ppg2 head - GLY tail + MLY end +link ppg2 head - GLY tail + MLZ end +link ppg2 head - GLY tail + M3L end +link ppg2 head - GLY tail + LEU end +link ppg2 head - GLY tail + MET end +link ppg2 head - GLY tail + MSE end +link ppg2 head - GLY tail + ASN end +link ppg2 head - GLY tail + PRO end +link ppg2 head - GLY tail + GLN end +link ppg2 head - GLY tail + ARG end +link ppg2 head - GLY tail + SER end +link ppg2 head - GLY tail + SEC end +link ppg2 head - GLY tail + SEP end +link ppg2 head - GLY tail + THR end +link ppg2 head - GLY tail + THP end +link ppg2 head - GLY tail + TOP end +link ppg2 head - GLY tail + VAL end +link ppg2 head - GLY tail + TRP end +link ppg2 head - GLY tail + TYR end +link ppg2 head - GLY tail + TYP end +link ppg2 head - GLY tail + PTR end +link ppg2 head - GLY tail + TYS end +link ppg2 head - GLY tail + HYP end +link ppg2 head - GLY tail + HY3 end +link ppg2 head - GLY tail + DDZ end +link ppg2 head - GLY tail + PNS end +link ppg2 head - GLY tail + QSR end +link ppg2 head - CIR tail + GLY end +link pctn head - GLY tail + CTN end +link pept head - GLY tail + NME end + +{ special link to PRO} +link pepp head - ACE tail + PRO end +link pepp head - ALA tail + PRO end +link pepp head - CYS tail + PRO end +link pepp head - CFE tail + PRO end +link pepp head - CYM tail + PRO end +link pepp head - CYF tail + PRO end +link pepp head - CYC tail + PRO end +link pepp head - CSP tail + PRO end +link pepp head - ASP tail + PRO end +link pepp head - ASH tail + PRO end +link pepp head - GLU tail + PRO end +link pepp head - GLH tail + PRO end +link pepp head - PCA tail + PRO end +link pepp head - PHE tail + PRO end +link pepp head - HIS tail + PRO end +link pepp head - NEP tail + PRO end +link pepp head - ILE tail + PRO end +link pepp head - LYS tail + PRO end +link pepp head - ALY tail + PRO end +link pepp head - HLY tail + PRO end +link pepp head - MLY tail + PRO end +link pepp head - MLZ tail + PRO end +link pepp head - M3L tail + PRO end +link pepp head - LEU tail + PRO end +link pepp head - MET tail + PRO end +link pepp head - MSE tail + PRO end +link pepp head - ASN tail + PRO end +link pepp head - PRO tail + PRO end +link pepp head - GLN tail + PRO end +link pepp head - ARG tail + PRO end +link pepp head - SER tail + PRO end +link pepp head - SEC tail + PRO end +link pepp head - SEP tail + PRO end +link pepp head - THR tail + PRO end +link pepp head - THP tail + PRO end +link pepp head - TOP tail + PRO end +link pepp head - VAL tail + PRO end +link pepp head - TRP tail + PRO end +link pepp head - TYR tail + PRO end +link pepp head - TYP tail + PRO end +link pepp head - PTR tail + PRO end +link pepp head - TYS tail + PRO end +link pepp head - HYP tail + PRO end +link pepp head - HY3 tail + PRO end +link pepp head - QSR tail + PRO end +link pepp head - CIR tail + PRO end + +{ special link to HYP} +link pepp head - ACE tail + HYP end +link pepp head - ALA tail + HYP end +link pepp head - CYS tail + HYP end +link pepp head - CFE tail + HYP end +link pepp head - CYM tail + HYP end +link pepp head - CYF tail + HYP end +link pepp head - CYC tail + HYP end +link pepp head - CSP tail + HYP end +link pepp head - ASP tail + HYP end +link pepp head - ASH tail + HYP end +link pepp head - GLU tail + HYP end +link pepp head - GLH tail + HYP end +link pepp head - PCA tail + HYP end +link pepp head - PHE tail + HYP end +link pepp head - HIS tail + HYP end +link pepp head - NEP tail + HYP end +link pepp head - ILE tail + HYP end +link pepp head - LYS tail + HYP end +link pepp head - ALY tail + HYP end +link pepp head - HLY tail + HYP end +link pepp head - MLY tail + HYP end +link pepp head - MLZ tail + HYP end +link pepp head - M3L tail + HYP end +link pepp head - LEU tail + HYP end +link pepp head - MET tail + HYP end +link pepp head - MSE tail + HYP end +link pepp head - ASN tail + HYP end +link pepp head - PRO tail + HYP end +link pepp head - GLN tail + HYP end +link pepp head - ARG tail + HYP end +link pepp head - SER tail + HYP end +link pepp head - SEC tail + HYP end +link pepp head - SEP tail + HYP end +link pepp head - THR tail + HYP end +link pepp head - THP tail + HYP end +link pepp head - TOP tail + HYP end +link pepp head - VAL tail + HYP end +link pepp head - TRP tail + HYP end +link pepp head - TYR tail + HYP end +link pepp head - TYP tail + HYP end +link pepp head - PTR tail + HYP end +link pepp head - TYS tail + HYP end +link pepp head - HYP tail + HYP end +link pepp head - HY3 tail + HYP end +link pepp head - DDZ tail + HYP end +link pepp head - PNS tail + HYP end +link pepp head - QSR tail + HYP end +link pepp head - CIR tail + HYP end + +{ special link to HYP} +link pepp head - ACE tail + HY3 end +link pepp head - ALA tail + HY3 end +link pepp head - CYS tail + HY3 end +link pepp head - CFE tail + HY3 end +link pepp head - CYM tail + HY3 end +link pepp head - CYF tail + HY3 end +link pepp head - CYC tail + HY3 end +link pepp head - CSP tail + HY3 end +link pepp head - ASP tail + HY3 end +link pepp head - ASH tail + HY3 end +link pepp head - GLU tail + HY3 end +link pepp head - GLH tail + HY3 end +link pepp head - PCA tail + HY3 end +link pepp head - PHE tail + HY3 end +link pepp head - HIS tail + HY3 end +link pepp head - NEP tail + HY3 end +link pepp head - ILE tail + HY3 end +link pepp head - LYS tail + HY3 end +link pepp head - ALY tail + HY3 end +link pepp head - HLY tail + HY3 end +link pepp head - MLY tail + HY3 end +link pepp head - MLZ tail + HY3 end +link pepp head - M3L tail + HY3 end +link pepp head - LEU tail + HY3 end +link pepp head - MET tail + HY3 end +link pepp head - MSE tail + HY3 end +link pepp head - ASN tail + HY3 end +link pepp head - PRO tail + HY3 end +link pepp head - GLN tail + HY3 end +link pepp head - ARG tail + HY3 end +link pepp head - SER tail + HY3 end +link pepp head - SEC tail + HY3 end +link pepp head - SEP tail + HY3 end +link pepp head - THR tail + HY3 end +link pepp head - THP tail + HY3 end +link pepp head - TOP tail + HY3 end +link pepp head - VAL tail + HY3 end +link pepp head - TRP tail + HY3 end +link pepp head - TYR tail + HY3 end +link pepp head - TYP tail + HY3 end +link pepp head - PTR tail + HY3 end +link pepp head - TYS tail + HY3 end +link pepp head - HYP tail + HY3 end +link pepp head - HY3 tail + HY3 end +link pepp head - DDZ tail + HY3 end +link pepp head - PNS tail + HY3 end +link pepp head - QSR tail + HY3 end +link pepp head - CIR tail + HY3 end + +{ peptide linkages for ACE } +link pept head - ACE tail + ALA end +link pept head - ACE tail + CYS end +link pept head - ACE tail + CFE end +link pept head - ACE tail + CYM end +link pept head - ACE tail + CYF end +link pept head - ACE tail + CYC end +link pept head - ACE tail + CSP end +link pept head - ACE tail + ASP end +link pept head - ACE tail + ASH end +link pept head - ACE tail + GLU end +link pept head - ACE tail + GLH end +link pept head - ACE tail + PHE end +link pept head - ACE tail + HIS end +link pept head - ACE tail + NEP end +link pept head - ACE tail + ILE end +link pept head - ACE tail + LYS end +link pept head - ACE tail + ALY end +link pept head - ACE tail + HLY end +link pept head - ACE tail + MLY end +link pept head - ACE tail + MLZ end +link pept head - ACE tail + M3L end +link pept head - ACE tail + LEU end +link pept head - ACE tail + MET end +link pept head - ACE tail + MSE end +link pept head - ACE tail + ASN end +link pept head - ACE tail + PRO end +link pept head - ACE tail + GLN end +link pept head - ACE tail + ARG end +link pept head - ACE tail + SER end +link pept head - ACE tail + SEC end +link pept head - ACE tail + SEP end +link pept head - ACE tail + THR end +link pept head - ACE tail + THP end +link pept head - ACE tail + TOP end +link pept head - ACE tail + VAL end +link pept head - ACE tail + TRP end +link pept head - ACE tail + TYR end +link pept head - ACE tail + TYP end +link pept head - ACE tail + PTR end +link pept head - ACE tail + TYS end +link pept head - ACE tail + HYP end +link pept head - ACE tail + HY3 end +link pept head - ACE tail + DDZ end +link pept head - ACE tail + PNS end +link pept head - ACE tail + QSR end +link pctn head - ACE tail + CTN end +link pept head - ACE tail + NME end +link pept head - ACE tail + CIR end + +{ peptide linkages for ALA } +link pept head - ALA tail + ALA end +link pept head - ALA tail + CYS end +link pept head - ALA tail + CFE end +link pept head - ALA tail + CYM end +link pept head - ALA tail + CYF end +link pept head - ALA tail + CYC end +link pept head - ALA tail + CSP end +link pept head - ALA tail + ASP end +link pept head - ALA tail + ASH end +link pept head - ALA tail + GLU end +link pept head - ALA tail + GLH end +link pept head - ALA tail + PHE end +link pept head - ALA tail + HIS end +link pept head - ALA tail + NEP end +link pept head - ALA tail + ILE end +link pept head - ALA tail + LYS end +link pept head - ALA tail + ALY end +link pept head - ALA tail + HLY end +link pept head - ALA tail + MLY end +link pept head - ALA tail + MLZ end +link pept head - ALA tail + M3L end +link pept head - ALA tail + LEU end +link pept head - ALA tail + MET end +link pept head - ALA tail + MSE end +link pept head - ALA tail + ASN end +link pept head - ALA tail + PRO end +link pept head - ALA tail + GLN end +link pept head - ALA tail + ARG end +link pept head - ALA tail + SER end +link pept head - ALA tail + SEC end +link pept head - ALA tail + SEP end +link pept head - ALA tail + THR end +link pept head - ALA tail + THP end +link pept head - ALA tail + TOP end +link pept head - ALA tail + VAL end +link pept head - ALA tail + TRP end +link pept head - ALA tail + TYR end +link pept head - ALA tail + TYP end +link pept head - ALA tail + PTR end +link pept head - ALA tail + TYS end +link pept head - ALA tail + HYP end +link pept head - ALA tail + HY3 end +link pept head - ALA tail + DDZ end +link pept head - ALA tail + PNS end +link pept head - ALA tail + QSR end +link pctn head - ALA tail + CTN end +link pept head - ALA tail + NME end +link pept head - ALA tail + CIR end + +{ peptide linkages for CYS } +link pept head - CYS tail + ALA end +link pept head - CYS tail + CYS end +link pept head - CYS tail + CFE end +link pept head - CYS tail + CYM end +link pept head - CYS tail + CYF end +link pept head - CYS tail + CYC end +link pept head - CYS tail + CSP end +link pept head - CYS tail + ASP end +link pept head - CYS tail + ASH end +link pept head - CYS tail + GLU end +link pept head - CYS tail + GLH end +link pept head - CYS tail + PHE end +link pept head - CYS tail + HIS end +link pept head - CYS tail + NEP end +link pept head - CYS tail + ILE end +link pept head - CYS tail + LYS end +link pept head - CYS tail + ALY end +link pept head - CYS tail + HLY end +link pept head - CYS tail + MLY end +link pept head - CYS tail + MLZ end +link pept head - CYS tail + M3L end +link pept head - CYS tail + LEU end +link pept head - CYS tail + MET end +link pept head - CYS tail + MSE end +link pept head - CYS tail + ASN end +link pept head - CYS tail + PRO end +link pept head - CYS tail + GLN end +link pept head - CYS tail + ARG end +link pept head - CYS tail + SER end +link pept head - CYS tail + SEC end +link pept head - CYS tail + SEP end +link pept head - CYS tail + THR end +link pept head - CYS tail + THP end +link pept head - CYS tail + TOP end +link pept head - CYS tail + VAL end +link pept head - CYS tail + TRP end +link pept head - CYS tail + TYR end +link pept head - CYS tail + TYP end +link pept head - CYS tail + PTR end +link pept head - CYS tail + TYS end +link pept head - CYS tail + HYP end +link pept head - CYS tail + HY3 end +link pept head - CYS tail + DDZ end +link pept head - CYS tail + PNS end +link pept head - CYS tail + QSR end +link pctn head - CYS tail + CTN end +link pept head - CYS tail + NME end +link pept head - CYS tail + CIR end + +{ peptide linkages for CFE } +link pept head - CFE tail + ALA end +link pept head - 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GLN tail + GLU end +link pept head - GLN tail + GLH end +link pept head - GLN tail + PHE end +link pept head - GLN tail + HIS end +link pept head - GLN tail + NEP end +link pept head - GLN tail + ILE end +link pept head - GLN tail + LYS end +link pept head - GLN tail + ALY end +link pept head - GLN tail + HLY end +link pept head - GLN tail + MLY end +link pept head - GLN tail + MLZ end +link pept head - GLN tail + M3L end +link pept head - GLN tail + LEU end +link pept head - GLN tail + MET end +link pept head - GLN tail + MSE end +link pept head - GLN tail + ASN end +link pept head - GLN tail + PRO end +link pept head - GLN tail + GLN end +link pept head - GLN tail + ARG end +link pept head - GLN tail + SER end +link pept head - GLN tail + SEC end +link pept head - GLN tail + SEP end +link pept head - GLN tail + THR end +link pept head - GLN tail + THP end +link pept head - GLN tail + TOP end +link pept head - GLN tail + VAL end +link pept head - GLN tail + TRP end +link pept head - GLN tail + TYR end +link pept head - GLN tail + TYP end +link pept head - GLN tail + PTR end +link pept head - GLN tail + TYS end +link pept head - GLN tail + HYP end +link pept head - GLN tail + HY3 end +link pept head - GLN tail + DDZ end +link pept head - GLN tail + PNS end +link pept head - GLN tail + QSR end +link pctn head - GLN tail + CTN end +link pept head - GLN tail + NME end +link pept head - GLN tail + CIR end + +{ peptide linkages for ARG } +link pept head - ARG tail + ALA end +link pept head - ARG tail + CYS end +link pept head - ARG tail + CFE end +link pept head - ARG tail + CYM end +link pept head - ARG tail + CYF end +link pept head - ARG tail + CYC end +link pept head - ARG tail + CSP end +link pept head - ARG tail + ASP end +link pept head - ARG tail + ASH end +link pept head - ARG tail + GLU end +link pept head - ARG tail + GLH end +link pept head - ARG tail + PHE end +link pept head - ARG tail + HIS end +link pept head - ARG tail + NEP end +link pept head - ARG tail + ILE end +link pept head - ARG tail + LYS end +link pept head - ARG tail + ALY end +link pept head - ARG tail + HLY end +link pept head - ARG tail + MLY end +link pept head - ARG tail + MLZ end +link pept head - ARG tail + M3L end +link pept head - ARG tail + LEU end +link pept head - ARG tail + MET end +link pept head - ARG tail + MSE end +link pept head - ARG tail + ASN end +link pept head - ARG tail + PRO end +link pept head - ARG tail + GLN end +link pept head - ARG tail + ARG end +link pept head - ARG tail + SER end +link pept head - ARG tail + SEC end +link pept head - ARG tail + SEP end +link pept head - ARG tail + THR end +link pept head - ARG tail + THP end +link pept head - ARG tail + TOP end +link pept head - ARG tail + VAL end +link pept head - ARG tail + TRP end +link pept head - ARG tail + TYR end +link pept head - ARG tail + TYP end +link pept head - ARG tail + PTR end +link pept head - ARG tail + TYS end +link pept head - ARG tail + HYP end +link pept head - ARG tail + HY3 end +link pept head - ARG tail + DDZ end +link pept head - ARG tail + PNS end +link pept head - ARG tail + QSR end +link pctn head - ARG tail + CTN end +link pept head - ARG tail + NME end +link pept head - ARG tail + CIR end + +{ peptide linkages for SER } +link pept head - SER tail + ALA end +link pept head - SER tail + CYS end +link pept head - SER tail + CFE end +link pept head - SER tail + CYM end +link pept head - SER tail + CYF end +link pept head - SER tail + CYC end +link pept head - SER tail + CSP end +link pept head - SER tail + ASP end +link pept head - SER tail + ASH end +link pept head - SER tail + GLU end +link pept head - SER tail + GLH end +link pept head - SER tail + PHE end +link pept head - SER tail + HIS end +link pept head - SER tail + NEP end +link pept head - SER tail + ILE end +link pept head - SER tail + LYS end +link pept head - SER tail + ALY end +link pept head - SER tail + HLY end +link pept head - SER tail + MLY end +link pept head - SER tail + MLZ end +link pept head - SER tail + M3L end +link pept head - SER tail + LEU end +link pept head - SER tail + MET end +link pept head - SER tail + MSE end +link pept head - SER tail + ASN end +link pept head - SER tail + PRO end +link pept head - SER tail + GLN end +link pept head - SER tail + ARG end +link pept head - SER tail + SER end +link pept head - SER tail + SEP end +link pept head - SER tail + THR end +link pept head - SER tail + THP end +link pept head - SER tail + TOP end +link pept head - SER tail + VAL end +link pept head - SER tail + TRP end +link pept head - SER tail + TYR end +link pept head - SER tail + TYP end +link pept head - SER tail + PTR end +link pept head - SER tail + TYS end +link pept head - SER tail + HYP end +link pept head - SER tail + HY3 end +link pept head - SER tail + DDZ end +link pept head - SER tail + PNS end +link pept head - SER tail + QSR end +link pctn head - SER tail + CTN end +link pept head - SER tail + NME end +link pept head - SER tail + CIR end + +{ peptide linkages for SEC } +link pept head - SEC tail + ALA end +link pept head - SEC tail + CYS end +link pept head - SEC tail + CFE end +link pept head - SEC tail + CYM end +link pept head - SEC tail + CYF end +link pept head - SEC tail + CYC end +link pept head - SEC tail + CSP end +link pept head - SEC tail + ASP end +link pept head - SEC tail + ASH end +link pept head - SEC tail + GLU end +link pept head - SEC tail + GLH end +link pept head - SEC tail + PHE end +link pept head - SEC tail + HIS end +link pept head - SEC tail + NEP end +link pept head - SEC tail + ILE end +link pept head - SEC tail + LYS end +link pept head - SEC tail + ALY end +link pept head - SEC tail + HLY end +link pept head - SEC tail + MLY end +link pept head - SEC tail + MLZ end +link pept head - SEC tail + M3L end +link pept head - SEC tail + LEU end +link pept head - SEC tail + MET end +link pept head - SEC tail + MSE end +link pept head - SEC tail + ASN end +link pept head - SEC tail + PRO end +link pept head - SEC tail + GLN end +link pept head - SEC tail + ARG end +link pept head - SEC tail + SER end +link pept head - SEC tail + SEC end +link pept head - SEC tail + SEP end +link pept head - SEC tail + THR end +link pept head - SEC tail + THP end +link pept head - SEC tail + TOP end +link pept head - SEC tail + VAL end +link pept head - SEC tail + TRP end +link pept head - SEC tail + TYR end +link pept head - SEC tail + TYP end +link pept head - SEC tail + PTR end +link pept head - SEC tail + TYS end +link pept head - SEC tail + HYP end +link pept head - SEC tail + HY3 end +link pept head - SEC tail + DDZ end +link pept head - SEC tail + PNS end +link pept head - SEC tail + QSR end +link pctn head - SEC tail + CTN end +link pept head - SEC tail + NME end +link pept head - SEC tail + CIR end + +{ peptide linkages for SEP } +link pept head - SEP tail + ALA end +link pept head - SEP tail + CYS end +link pept head - SEP tail + CFE end +link pept head - SEP tail + CYM end +link pept head - SEP tail + CYF end +link pept head - SEP tail + CYC end +link pept head - SEP tail + CSP end +link pept head - SEP tail + ASP end +link pept head - SEP tail + ASH end +link pept head - SEP tail + GLU end +link pept head - SEP tail + GLH end +link pept head - SEP tail + PHE end +link pept head - SEP tail + HIS end +link pept head - SEP tail + NEP end +link pept head - SEP tail + ILE end +link pept head - SEP tail + LYS end +link pept head - SEP tail + ALY end +link pept head - SEP tail + HLY end +link pept head - SEP tail + MLY end +link pept head - SEP tail + MLZ end +link pept head - SEP tail + M3L end +link pept head - SEP tail + LEU end +link pept head - SEP tail + MET end +link pept head - SEP tail + MSE end +link pept head - SEP tail + ASN end +link pept head - SEP tail + PRO end +link pept head - SEP tail + GLN end +link pept head - SEP tail + ARG end +link pept head - SEP tail + SER end +link pept head - SEP tail + SEC end +link pept head - SEP tail + SEP end +link pept head - SEP tail + THR end +link pept head - SEP tail + THP end +link pept head - SEP tail + TOP end +link pept head - SEP tail + VAL end +link pept head - SEP tail + TRP end +link pept head - SEP tail + TYR end +link pept head - SEP tail + TYP end +link pept head - SEP tail + PTR end +link pept head - SEP tail + TYS end +link pept head - SEP tail + HYP end +link pept head - SEP tail + HY3 end +link pept head - SEP tail + DDZ end +link pept head - SEP tail + PNS end +link pept head - SEP tail + QSR end +link pctn head - SEP tail + CTN end +link pept head - SEP tail + NME end +link pept head - SEP tail + CIR end + +{ peptide linkages for THR } +link pept head - THR tail + ALA end +link pept head - THR tail + CYS end +link pept head - THR tail + CFE end +link pept head - THR tail + CYM end +link pept head - THR tail + CYF end +link pept head - THR tail + CYC end +link pept head - THR tail + CSP end +link pept head - THR tail + ASP end +link pept head - THR tail + ASH end +link pept head - THR tail + GLU end +link pept head - THR tail + GLH end +link pept head - THR tail + PHE end +link pept head - THR tail + HIS end +link pept head - THR tail + NEP end +link pept head - THR tail + ILE end +link pept head - THR tail + LYS end +link pept head - THR tail + ALY end +link pept head - THR tail + HLY end +link pept head - THR tail + MLY end +link pept head - THR tail + MLZ end +link pept head - THR tail + M3L end +link pept head - THR tail + LEU end +link pept head - THR tail + MET end +link pept head - THR tail + MSE end +link pept head - THR tail + ASN end +link pept head - THR tail + PRO end +link pept head - THR tail + GLN end +link pept head - THR tail + ARG end +link pept head - THR tail + SER end +link pept head - THR tail + SEC end +link pept head - THR tail + SEP end +link pept head - THR tail + THR end +link pept head - THR tail + THP end +link pept head - THR tail + TOP end +link pept head - THR tail + VAL end +link pept head - THR tail + TRP end +link pept head - THR tail + TYR end +link pept head - THR tail + TYP end +link pept head - THR tail + PTR end +link pept head - THR tail + TYS end +link pept head - THR tail + HYP end +link pept head - THR tail + HY3 end +link pept head - THR tail + DDZ end +link pept head - THR tail + PNS end +link pept head - THR tail + QSR end +link pctn head - THR tail + CTN end +link pept head - THR tail + NME end +link pept head - THR tail + CIR end + +{ peptide linkages for THP } +link pept head - THP tail + ALA end +link pept head - THP tail + CYS end +link pept head - THP tail + CFE end +link pept head - THP tail + CYM end +link pept head - THP tail + CYF end +link pept head - THP tail + CYC end +link pept head - THP tail + CSP end +link pept head - THP tail + ASP end +link pept head - THP tail + ASH end +link pept head - THP tail + GLU end +link pept head - THP tail + GLH end +link pept head - THP tail + PHE end +link pept head - THP tail + HIS end +link pept head - THP tail + NEP end +link pept head - THP tail + ILE end +link pept head - THP tail + LYS end +link pept head - THP tail + ALY end +link pept head - THP tail + HLY end +link pept head - THP tail + MLY end +link pept head - THP tail + MLZ end +link pept head - THP tail + M3L end +link pept head - THP tail + LEU end +link pept head - THP tail + MET end +link pept head - THP tail + MSE end +link pept head - THP tail + ASN end +link pept head - THP tail + PRO end +link pept head - THP tail + GLN end +link pept head - THP tail + ARG end +link pept head - THP tail + SER end +link pept head - THP tail + SEC end +link pept head - THP tail + SEP end +link pept head - THP tail + THR end +link pept head - THP tail + THP end +link pept head - THP tail + TOP end +link pept head - THP tail + VAL end +link pept head - THP tail + TRP end +link pept head - THP tail + TYR end +link pept head - THP tail + TYP end +link pept head - THP tail + PTR end +link pept head - THP tail + TYS end +link pept head - THP tail + HYP end +link pept head - THP tail + HY3 end +link pept head - THP tail + DDZ end +link pept head - THP tail + PNS end +link pept head - THP tail + QSR end +link pctn head - THP tail + CTN end +link pept head - THP tail + NME end +link pept head - THP tail + CIR end + +{ peptide linkages for TOP } +link pept head - TOP tail + ALA end +link pept head - TOP tail + CYS end +link pept head - TOP tail + CFE end +link pept head - TOP tail + CYM end +link pept head - TOP tail + CYF end +link pept head - TOP tail + CYC end +link pept head - TOP tail + CSP end +link pept head - TOP tail + ASP end +link pept head - TOP tail + ASH end +link pept head - TOP tail + GLU end +link pept head - TOP tail + GLH end +link pept head - TOP tail + PHE end +link pept head - TOP tail + HIS end +link pept head - TOP tail + NEP end +link pept head - TOP tail + ILE end +link pept head - TOP tail + LYS end +link pept head - TOP tail + ALY end +link pept head - TOP tail + HLY end +link pept head - TOP tail + MLY end +link pept head - TOP tail + MLZ end +link pept head - TOP tail + M3L end +link pept head - TOP tail + LEU end +link pept head - TOP tail + MET end +link pept head - TOP tail + MSE end +link pept head - TOP tail + ASN end +link pept head - TOP tail + PRO end +link pept head - TOP tail + GLN end +link pept head - TOP tail + ARG end +link pept head - TOP tail + SER end +link pept head - TOP tail + SEC end +link pept head - TOP tail + SEP end +link pept head - TOP tail + THR end +link pept head - TOP tail + THP end +link pept head - TOP tail + TOP end +link pept head - TOP tail + VAL end +link pept head - TOP tail + TRP end +link pept head - TOP tail + TYR end +link pept head - TOP tail + TYP end +link pept head - TOP tail + PTR end +link pept head - TOP tail + TYS end +link pept head - TOP tail + HYP end +link pept head - TOP tail + HY3 end +link pept head - TOP tail + DDZ end +link pept head - TOP tail + PNS end +link pept head - TOP tail + QSR end +link pctn head - TOP tail + CTN end +link pept head - TOP tail + NME end +link pept head - TOP tail + CIR end + +{ peptide linkages for VAL } +link pept head - VAL tail + ALA end +link pept head - VAL tail + CYS end +link pept head - VAL tail + CFE end +link pept head - VAL tail + CYM end +link pept head - VAL tail + CYF end +link pept head - VAL tail + CYC end +link pept head - VAL tail + CSP end +link pept head - VAL tail + ASP end +link pept head - VAL tail + ASH end +link pept head - VAL tail + GLU end +link pept head - VAL tail + GLH end +link pept head - VAL tail + PHE end +link pept head - VAL tail + HIS end +link pept head - VAL tail + NEP end +link pept head - VAL tail + ILE end +link pept head - VAL tail + LYS end +link pept head - VAL tail + ALY end +link pept head - VAL tail + HLY end +link pept head - VAL tail + MLY end +link pept head - VAL tail + MLZ end +link pept head - VAL tail + M3L end +link pept head - VAL tail + LEU end +link pept head - VAL tail + MET end +link pept head - VAL tail + MSE end +link pept head - VAL tail + ASN end +link pept head - VAL tail + PRO end +link pept head - VAL tail + GLN end +link pept head - VAL tail + ARG end +link pept head - VAL tail + SER end +link pept head - VAL tail + SEC end +link pept head - VAL tail + SEP end +link pept head - VAL tail + THR end +link pept head - VAL tail + THP end +link pept head - VAL tail + TOP end +link pept head - VAL tail + VAL end +link pept head - VAL tail + TRP end +link pept head - VAL tail + TYR end +link pept head - VAL tail + TYP end +link pept head - VAL tail + PTR end +link pept head - VAL tail + TYS end +link pept head - VAL tail + HYP end +link pept head - VAL tail + HY3 end +link pept head - VAL tail + DDZ end +link pept head - VAL tail + PNS end +link pept head - VAL tail + QSR end +link pctn head - VAL tail + CTN end +link pept head - VAL tail + NME end +link pept head - VAL tail + CIR end + +{ peptide linkages for TRP } +link pept head - TRP tail + ALA end +link pept head - TRP tail + CYS end +link pept head - TRP tail + CFE end +link pept head - TRP tail + CYM end +link pept head - TRP tail + CYF end +link pept head - TRP tail + CYC end +link pept head - TRP tail + CSP end +link pept head - TRP tail + ASP end +link pept head - TRP tail + ASH end +link pept head - TRP tail + GLU end +link pept head - TRP tail + GLH end +link pept head - TRP tail + PHE end +link pept head - TRP tail + HIS end +link pept head - TRP tail + NEP end +link pept head - TRP tail + ILE end +link pept head - TRP tail + LYS end +link pept head - TRP tail + ALY end +link pept head - TRP tail + HLY end +link pept head - TRP tail + MLY end +link pept head - TRP tail + MLZ end +link pept head - TRP tail + M3L end +link pept head - TRP tail + LEU end +link pept head - TRP tail + MET end +link pept head - TRP tail + MSE end +link pept head - TRP tail + ASN end +link pept head - TRP tail + PRO end +link pept head - TRP tail + GLN end +link pept head - TRP tail + ARG end +link pept head - TRP tail + SER end +link pept head - TRP tail + SEC end +link pept head - TRP tail + SEP end +link pept head - TRP tail + THR end +link pept head - TRP tail + THP end +link pept head - TRP tail + TOP end +link pept head - TRP tail + VAL end +link pept head - TRP tail + TRP end +link pept head - TRP tail + TYR end +link pept head - TRP tail + TYP end +link pept head - TRP tail + PTR end +link pept head - TRP tail + TYS end +link pept head - TRP tail + HYP end +link pept head - TRP tail + HY3 end +link pept head - TRP tail + DDZ end +link pept head - TRP tail + PNS end +link pept head - TRP tail + QSR end +link pctn head - TRP tail + CTN end +link pept head - TRP tail + NME end +link pept head - TRP tail + CIR end + +{ peptide linkages for TYR } +link pept head - TYR tail + ALA end +link pept head - TYR tail + CYS end +link pept head - TYR tail + CFE end +link pept head - TYR tail + CYM end +link pept head - TYR tail + CYF end +link pept head - TYR tail + CYC end +link pept head - TYR tail + CSP end +link pept head - TYR tail + ASP end +link pept head - TYR tail + ASH end +link pept head - TYR tail + GLU end +link pept head - TYR tail + GLH end +link pept head - TYR tail + PHE end +link pept head - TYR tail + HIS end +link pept head - TYR tail + NEP end +link pept head - TYR tail + ILE end +link pept head - TYR tail + LYS end +link pept head - TYR tail + ALY end +link pept head - TYR tail + HLY end +link pept head - TYR tail + MLY end +link pept head - TYR tail + MLZ end +link pept head - TYR tail + M3L end +link pept head - TYR tail + LEU end +link pept head - TYR tail + MET end +link pept head - TYR tail + MSE end +link pept head - TYR tail + ASN end +link pept head - TYR tail + PRO end +link pept head - TYR tail + GLN end +link pept head - TYR tail + ARG end +link pept head - TYR tail + SER end +link pept head - TYR tail + SEC end +link pept head - TYR tail + SEP end +link pept head - TYR tail + THR end +link pept head - TYR tail + THP end +link pept head - TYR tail + TOP end +link pept head - TYR tail + VAL end +link pept head - TYR tail + TRP end +link pept head - TYR tail + TYR end +link pept head - TYR tail + TYP end +link pept head - TYR tail + PTR end +link pept head - TYR tail + TYS end +link pept head - TYR tail + HYP end +link pept head - TYR tail + HY3 end +link pept head - TYR tail + DDZ end +link pept head - TYR tail + PNS end +link pept head - TYR tail + QSR end +link pctn head - TYR tail + CTN end +link pept head - TYR tail + NME end +link pept head - TYR tail + CIR end + +{ peptide linkages for TYP } +link pept head - TYP tail + ALA end +link pept head - TYP tail + CYS end +link pept head - TYP tail + CFE end +link pept head - TYP tail + CYM end +link pept head - TYP tail + CYF end +link pept head - TYP tail + CYC end +link pept head - TYP tail + CSP end +link pept head - TYP tail + ASP end +link pept head - TYP tail + ASH end +link pept head - TYP tail + GLU end +link pept head - TYP tail + GLH end +link pept head - TYP tail + PHE end +link pept head - TYP tail + HIS end +link pept head - TYP tail + NEP end +link pept head - TYP tail + ILE end +link pept head - TYP tail + LYS end +link pept head - TYP tail + ALY end +link pept head - TYP tail + HLY end +link pept head - TYP tail + MLY end +link pept head - TYP tail + MLZ end +link pept head - TYP tail + M3L end +link pept head - TYP tail + LEU end +link pept head - TYP tail + MET end +link pept head - TYP tail + MSE end +link pept head - TYP tail + ASN end +link pept head - TYP tail + PRO end +link pept head - TYP tail + GLN end +link pept head - TYP tail + ARG end +link pept head - TYP tail + SER end +link pept head - TYP tail + SEC end +link pept head - TYP tail + SEP end +link pept head - TYP tail + THR end +link pept head - TYP tail + THP end +link pept head - TYP tail + TOP end +link pept head - TYP tail + VAL end +link pept head - TYP tail + TRP end +link pept head - TYP tail + TYR end +link pept head - TYP tail + TYP end +link pept head - TYP tail + PTR end +link pept head - TYP tail + TYS end +link pept head - TYP tail + HYP end +link pept head - TYP tail + HY3 end +link pept head - TYP tail + DDZ end +link pept head - TYP tail + PNS end +link pept head - TYP tail + QSR end +link pctn head - TYP tail + CTN end +link pept head - TYP tail + NME end +link pept head - TYP tail + CIR end + +{ peptide linkages for PTR - same as TYP } +link pept head - PTR tail + ALA end +link pept head - PTR tail + CYS end +link pept head - PTR tail + CFE end +link pept head - PTR tail + CYM end +link pept head - PTR tail + CYF end +link pept head - PTR tail + CYC end +link pept head - PTR tail + CSP end +link pept head - PTR tail + ASP end +link pept head - PTR tail + ASH end +link pept head - PTR tail + GLU end +link pept head - PTR tail + GLH end +link pept head - PTR tail + PHE end +link pept head - PTR tail + HIS end +link pept head - PTR tail + NEP end +link pept head - PTR tail + ILE end +link pept head - PTR tail + LYS end +link pept head - PTR tail + ALY end +link pept head - PTR tail + HLY end +link pept head - PTR tail + MLY end +link pept head - PTR tail + MLZ end +link pept head - PTR tail + M3L end +link pept head - PTR tail + LEU end +link pept head - PTR tail + MET end +link pept head - PTR tail + MSE end +link pept head - PTR tail + ASN end +link pept head - PTR tail + PRO end +link pept head - PTR tail + GLN end +link pept head - PTR tail + ARG end +link pept head - PTR tail + SER end +link pept head - PTR tail + SEC end +link pept head - PTR tail + SEP end +link pept head - PTR tail + THR end +link pept head - PTR tail + THP end +link pept head - PTR tail + TOP end +link pept head - PTR tail + VAL end +link pept head - PTR tail + TRP end +link pept head - PTR tail + TYR end +link pept head - PTR tail + TYP end +link pept head - PTR tail + PTR end +link pept head - PTR tail + TYS end +link pept head - PTR tail + HYP end +link pept head - PTR tail + HY3 end +link pept head - PTR tail + DDZ end +link pept head - PTR tail + PNS end +link pept head - PTR tail + QSR end +link pctn head - PTR tail + CTN end +link pept head - PTR tail + NME end +link pept head - PTR tail + CIR end + +{ peptide linkages for TYS } +link pept head - TYS tail + ALA end +link pept head - TYS tail + CYS end +link pept head - TYS tail + CFE end +link pept head - TYS tail + CYM end +link pept head - TYS tail + CYF end +link pept head - TYS tail + CYC end +link pept head - TYS tail + CSP end +link pept head - TYS tail + ASP end +link pept head - TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + HLY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEC end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + PTR end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + HY3 end +link pept head - TYS tail + DDZ end +link pept head - TYS tail + PNS end +link pept head - TYS tail + QSR end +link pctn head - TYS tail + CTN end +link pept head - TYS tail + NME end +link pept head - TYS tail + CIR end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CFE end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CYC end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + HLY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEC end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + PTR end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + HY3 end +link pept head - HYP tail + DDZ end +link pept head - HYP tail + QSR end +link pept head - HYP tail + PNS end +link pept head - HYP tail + CIR end + +{ peptide linkages for HY3 } +link pept head - HY3 tail + ALA end +link pept head - HY3 tail + CYS end +link pept head - HY3 tail + CFE end +link pept head - HY3 tail + CYM end +link pept head - HY3 tail + CYF end +link pept head - HY3 tail + CYC end +link pept head - HY3 tail + CSP end +link pept head - HY3 tail + ASP end +link pept head - HY3 tail + ASH end +link pept head - HY3 tail + GLU end +link pept head - HY3 tail + GLH end +link pept head - HY3 tail + PHE end +link pept head - HY3 tail + HIS end +link pept head - HY3 tail + NEP end +link pept head - HY3 tail + ILE end +link pept head - HY3 tail + LYS end +link pept head - HY3 tail + ALY end +link pept head - HY3 tail + HLY end +link pept head - HY3 tail + MLY end +link pept head - HY3 tail + MLZ end +link pept head - HY3 tail + M3L end +link pept head - HY3 tail + LEU end +link pept head - HY3 tail + MET end +link pept head - HY3 tail + MSE end +link pept head - HY3 tail + ASN end +link pept head - HY3 tail + PRO end +link pept head - HY3 tail + GLN end +link pept head - HY3 tail + ARG end +link pept head - HY3 tail + SER end +link pept head - HY3 tail + SEC end +link pept head - HY3 tail + SEP end +link pept head - HY3 tail + THR end +link pept head - HY3 tail + THP end +link pept head - HY3 tail + TOP end +link pept head - HY3 tail + VAL end +link pept head - HY3 tail + TRP end +link pept head - HY3 tail + TYR end +link pept head - HY3 tail + TYP end +link pept head - HY3 tail + PTR end +link pept head - HY3 tail + TYS end +link pept head - HY3 tail + HYP end +link pept head - HY3 tail + HY3 end +link pept head - HY3 tail + DDZ end +link pept head - HY3 tail + QSR end +link pept head - HY3 tail + PNS end +link pept head - HY3 tail + CIR end + +{ peptide linkages for DDZ } +link pept head - DDZ tail + ALA end +link pept head - DDZ tail + CYS end +link pept head - DDZ tail + CFE end +link pept head - DDZ tail + CYM end +link pept head - DDZ tail + CYF end +link pept head - DDZ tail + CYC end +link pept head - DDZ tail + CSP end +link pept head - DDZ tail + ASP end +link pept head - DDZ tail + ASH end +link pept head - DDZ tail + GLU end +link pept head - DDZ tail + GLH end +link pept head - DDZ tail + PHE end +link pept head - DDZ tail + HIS end +link pept head - DDZ tail + NEP end +link pept head - DDZ tail + ILE end +link pept head - DDZ tail + LYS end +link pept head - DDZ tail + ALY end +link pept head - DDZ tail + HLY end +link pept head - DDZ tail + MLY end +link pept head - DDZ tail + MLZ end +link pept head - DDZ tail + M3L end +link pept head - DDZ tail + LEU end +link pept head - DDZ tail + MET end +link pept head - DDZ tail + MSE end +link pept head - DDZ tail + ASN end +link pept head - DDZ tail + PRO end +link pept head - DDZ tail + GLN end +link pept head - DDZ tail + ARG end +link pept head - DDZ tail + SER end +link pept head - DDZ tail + SEC end +link pept head - DDZ tail + SEP end +link pept head - DDZ tail + THR end +link pept head - DDZ tail + THP end +link pept head - DDZ tail + TOP end +link pept head - DDZ tail + VAL end +link pept head - DDZ tail + TRP end +link pept head - DDZ tail + TYR end +link pept head - DDZ tail + TYP end +link pept head - DDZ tail + PTR end +link pept head - DDZ tail + TYS end +link pept head - DDZ tail + HYP end +link pept head - DDZ tail + DDZ end +link pept head - DDZ tail + PNS end +link pept head - DDZ tail + QSR end +link pctn head - DDZ tail + CTN end +link pept head - DDZ tail + NME end +link pept head - DDZ tail + CIR end + +{ peptide linkages for PNS } +link pept head - PNS tail + ALA end +link pept head - PNS tail + CYS end +link pept head - PNS tail + CFE end +link pept head - PNS tail + CYM end +link pept head - PNS tail + CYF end +link pept head - PNS tail + CYC end +link pept head - PNS tail + CSP end +link pept head - PNS tail + ASP end +link pept head - PNS tail + ASH end +link pept head - PNS tail + GLU end +link pept head - PNS tail + GLH end +link pept head - PNS tail + PHE end +link pept head - PNS tail + HIS end +link pept head - PNS tail + NEP end +link pept head - PNS tail + ILE end +link pept head - PNS tail + LYS end +link pept head - PNS tail + ALY end +link pept head - PNS tail + HLY end +link pept head - PNS tail + MLY end +link pept head - PNS tail + MLZ end +link pept head - PNS tail + M3L end +link pept head - PNS tail + LEU end +link pept head - PNS tail + MET end +link pept head - PNS tail + MSE end +link pept head - PNS tail + ASN end +link pept head - PNS tail + PRO end +link pept head - PNS tail + GLN end +link pept head - PNS tail + ARG end +link pept head - PNS tail + SER end +link pept head - PNS tail + SEC end +link pept head - PNS tail + SEP end +link pept head - PNS tail + THR end +link pept head - PNS tail + THP end +link pept head - PNS tail + TOP end +link pept head - PNS tail + VAL end +link pept head - PNS tail + TRP end +link pept head - PNS tail + TYR end +link pept head - PNS tail + TYP end +link pept head - PNS tail + PTR end +link pept head - PNS tail + TYS end +link pept head - PNS tail + HYP end +link pept head - PNS tail + HY3 end +link pept head - PNS tail + DDZ end +link pept head - PNS tail + PNS end +link pept head - PNS tail + QSR end +link pctn head - PNS tail + CTN end +link pept head - PNS tail + NME end +link pept head - PNS tail + CIR end + +{ peptide linkages for QSR } +link pept head - QSR tail + ALA end +link pept head - QSR tail + CYS end +link pept head - QSR tail + CFE end +link pept head - QSR tail + CYM end +link pept head - QSR tail + CYF end +link pept head - QSR tail + CYC end +link pept head - QSR tail + CSP end +link pept head - QSR tail + ASP end +link pept head - QSR tail + ASH end +link pept head - QSR tail + GLU end +link pept head - QSR tail + GLH end +link pept head - QSR tail + PHE end +link pept head - QSR tail + HIS end +link pept head - QSR tail + NEP end +link pept head - QSR tail + ILE end +link pept head - QSR tail + LYS end +link pept head - QSR tail + ALY end +link pept head - QSR tail + HLY end +link pept head - QSR tail + MLY end +link pept head - QSR tail + MLZ end +link pept head - QSR tail + M3L end +link pept head - QSR tail + LEU end +link pept head - QSR tail + MET end +link pept head - QSR tail + MSE end +link pept head - QSR tail + ASN end +link pept head - QSR tail + PRO end +link pept head - QSR tail + GLN end +link pept head - QSR tail + ARG end +link pept head - QSR tail + SER end +link pept head - QSR tail + SEC end +link pept head - QSR tail + SEP end +link pept head - QSR tail + THR end +link pept head - QSR tail + THP end +link pept head - QSR tail + TOP end +link pept head - QSR tail + VAL end +link pept head - QSR tail + TRP end +link pept head - QSR tail + TYR end +link pept head - QSR tail + TYP end +link pept head - QSR tail + PTR end +link pept head - QSR tail + TYS end +link pept head - QSR tail + HYP end +link pept head - QSR tail + HY3 end +link pept head - QSR tail + DDZ end +link pept head - QSR tail + PNS end +link pept head - QSR tail + QSR end +link pctn head - QSR tail + CTN end +link pept head - QSR tail + NME end +link pept head - QSR tail + CIR end + +{ peptide linkages for CIR } +link pept head - CIR tail + ALA end +link pept head - CIR tail + CYS end +link pept head - CIR tail + CFE end +link pept head - CIR tail + CYM end +link pept head - CIR tail + CYF end +link pept head - CIR tail + CYC end +link pept head - CIR tail + CSP end +link pept head - CIR tail + ASP end +link pept head - CIR tail + ASH end +link pept head - CIR tail + GLU end +link pept head - CIR tail + GLH end +link pept head - CIR tail + PHE end +link pept head - CIR tail + HIS end +link pept head - CIR tail + NEP end +link pept head - CIR tail + ILE end +link pept head - CIR tail + LYS end +link pept head - CIR tail + ALY end +link pept head - CIR tail + HLY end +link pept head - CIR tail + MLY end +link pept head - CIR tail + MLZ end +link pept head - CIR tail + M3L end +link pept head - CIR tail + LEU end +link pept head - CIR tail + MET end +link pept head - CIR tail + MSE end +link pept head - CIR tail + ASN end +link pept head - CIR tail + PRO end +link pept head - CIR tail + GLN end +link pept head - CIR tail + ARG end +link pept head - CIR tail + SER end +link pept head - CIR tail + SEC end +link pept head - CIR tail + SEP end +link pept head - CIR tail + THR end +link pept head - CIR tail + THP end +link pept head - CIR tail + TOP end +link pept head - CIR tail + VAL end +link pept head - CIR tail + TRP end +link pept head - CIR tail + TYR end +link pept head - CIR tail + TYP end +link pept head - CIR tail + PTR end +link pept head - CIR tail + TYS end +link pept head - CIR tail + HYP end +link pept head - CIR tail + HY3 end +link pept head - CIR tail + DDZ end +link pept head - CIR tail + PNS end +link pept head - CIR tail + QSR end +link pctn head - CIR tail + CTN end +link pept head - CIR tail + NME end +link pept head - CIR tail + CIR end + +first PROP tail + PRO end +first PROP tail + HYP end +first PROP tail + HY3 end + +first ACET tail + ACE end + +first NTER tail + ALA end +first NTER tail + CYS end +first NTER tail + CFE end +first NTER tail + CYM end +first NTER tail + CYF end +first NTER tail + CYC end +first NTER tail + CSP end +first NTER tail + ASP end +first NTER tail + ASH end +first NTER tail + GLU end +first NTER tail + GLH end +first NTER tail + GLY end +first NTER tail + PHE end +first NTER tail + HIS end +first NTER tail + NEP end +first NTER tail + ILE end +first NTER tail + LYS end +first NTER tail + ALY end +first NTER tail + HLY end +first NTER tail + MLY end +first NTER tail + MLZ end +first NTER tail + M3L end +first NTER tail + LEU end +first NTER tail + MET end +first NTER tail + MSE end +first NTER tail + ASN end +first NTER tail + PRO end +first NTER tail + GLN end +first NTER tail + ARG end +first NTER tail + SER end +first NTER tail + SEC end +first NTER tail + SEP end +first NTER tail + THR end +first NTER tail + THP end +first NTER tail + TOP end +first NTER tail + VAL end +first NTER tail + TRP end +first NTER tail + TYR end +first NTER tail + TYP end +first NTER tail + PTR end +first NTER tail + TYS end +first NTER tail + HYP end +first NTER tail + HY3 end +first NTER tail + DDZ end +first NTER tail + PNS end +first NTER tail + QSR end +first NTER tail + CIR end + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noNter.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noNter.link new file mode 100644 index 0000000000000000000000000000000000000000..67557e141f978b04ab90e703499100b2c85951a1 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noNter.link @@ -0,0 +1,2709 @@ +remarks file toppar/protein-allhdg5-4.link +remarks +remarks this is a macro to define standard protein peptide bonds +remarks and termini to generate a protein sequence. + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link ppgp head - GLY tail + PRO end +link ppgp head - GLY tail + HYP end +link ppgp head - GLY tail + HY3 end +link ppgg head - GLY tail + GLY end + +{ special link to GLY} +link ppg1 head - ACE tail + GLY end +link ppg1 head - ALA tail + GLY end +link ppg1 head - CYS tail + GLY end +link ppg1 head - CFE tail + GLY end +link ppg1 head - CYM tail + GLY end +link ppg1 head - CYF tail + GLY end +link ppg1 head - CYC tail + GLY end +link ppg1 head - CSP tail + GLY end +link ppg1 head - ASP tail + GLY end +link ppg1 head - ASH tail + GLY end +link ppg1 head - GLU tail + GLY end +link ppg1 head - GLH tail + GLY end +link ppg1 head - PCA tail + GLY end +link ppg1 head - PHE tail + GLY end +link ppg1 head - HIS tail + GLY end +link ppg1 head - NEP tail + GLY end +link ppg1 head - ILE tail + GLY end +link ppg1 head - LYS tail + GLY end +link ppg1 head - ALY tail + GLY end +link ppg1 head - HLY tail + GLY end +link ppg1 head - MLY tail + GLY end +link ppg1 head - MLZ tail + GLY end +link ppg1 head - M3L tail + GLY end +link ppg1 head - LEU tail + GLY end +link ppg1 head - MET tail + GLY end +link ppg1 head - MSE tail + GLY end ! +link ppg1 head - ASN tail + GLY end +link ppg1 head - PRO tail + GLY end +link ppg1 head - GLN tail + GLY end +link ppg1 head - ARG tail + GLY end +link ppg1 head - SER tail + GLY end +link ppg1 head - SEC tail + GLY end +link ppg1 head - SEP tail + GLY end +link ppg1 head - THR tail + GLY end +link ppg1 head - THP tail + GLY end +link ppg1 head - TOP tail + GLY end +link ppg1 head - VAL tail + GLY end +link ppg1 head - TRP tail + GLY end +link ppg1 head - TYR tail + GLY end +link ppg1 head - TYP tail + GLY end +link ppg1 head - PTR tail + GLY end +link ppg1 head - TYS tail + GLY end +link ppg1 head - HYP tail + GLY end +link ppg1 head - HY3 tail + GLY end +link ppg1 head - DDZ tail + GLY end +link ppg1 head - QSR tail + GLY end +link ppg1 head - PNS tail + GLY end +link ppg1 head - CIR tail + GLY end + +{ special link from GLY} +link ppg2 head - GLY tail + ALA end +link ppg2 head - GLY tail + CYS end +link ppg2 head - GLY tail + CFE end +link ppg2 head - GLY tail + CYM end +link ppg2 head - GLY tail + CYF end +link ppg2 head - GLY tail + CYC end +link ppg2 head - GLY tail + CSP end +link ppg2 head - GLY tail + ASP end +link ppg2 head - GLY tail + ASH end +link ppg2 head - GLY tail + GLU end +link ppg2 head - GLY tail + GLH end +link ppg2 head - GLY tail + PHE end +link ppg2 head - GLY tail + HIS end +link ppg2 head - GLY tail + NEP end +link ppg2 head - GLY tail + ILE end +link ppg2 head - GLY tail + LYS end +link ppg2 head - GLY tail + ALY end +link ppg2 head - GLY tail + HLY end +link ppg2 head - GLY tail + MLY end +link ppg2 head - GLY tail + MLZ end +link ppg2 head - GLY tail + M3L end +link ppg2 head - GLY tail + LEU end +link ppg2 head - GLY tail + MET end +link ppg2 head - GLY tail + MSE end +link ppg2 head - GLY tail + ASN end +link ppg2 head - GLY tail + PRO end +link ppg2 head - GLY tail + GLN end +link ppg2 head - GLY tail + ARG end +link ppg2 head - GLY tail + SER end +link ppg2 head - GLY tail + SEC end +link ppg2 head - GLY tail + SEP end +link ppg2 head - GLY tail + THR end +link ppg2 head - GLY tail + THP end +link ppg2 head - GLY tail + TOP end +link ppg2 head - GLY tail + VAL end +link ppg2 head - GLY tail + TRP end +link ppg2 head - GLY tail + TYR end +link ppg2 head - GLY tail + TYP end +link ppg2 head - GLY tail + PTR end +link ppg2 head - GLY tail + TYS end +link ppg2 head - GLY tail + HYP end +link ppg2 head - GLY tail + HY3 end +link ppg2 head - GLY tail + DDZ end +link ppg2 head - GLY tail + PNS end +link ppg2 head - GLY tail + QSR end +link ppg2 head - CIR tail + GLY end +link pctn head - GLY tail + CTN end +link pept head - GLY tail + NME end + +{ special link to PRO} +link pepp head - ACE tail + PRO end +link pepp head - ALA tail + PRO end +link pepp head - CYS tail + PRO end +link pepp head - CFE tail + PRO end +link pepp head - CYM tail + PRO end +link pepp head - CYF tail + PRO end +link pepp head - CYC tail + PRO end +link pepp head - CSP tail + PRO end +link pepp head - ASP tail + PRO end +link pepp head - ASH tail + PRO end +link pepp head - GLU tail + PRO end +link pepp head - GLH tail + PRO end +link pepp head - PCA tail + PRO end +link pepp head - PHE tail + PRO end +link pepp head - HIS tail + PRO end +link pepp head - NEP tail + PRO end +link pepp head - ILE tail + PRO end +link pepp head - LYS tail + PRO end +link pepp head - ALY tail + PRO end +link pepp head - HLY tail + PRO end +link pepp head - MLY tail + PRO end +link pepp head - MLZ tail + PRO end +link pepp head - M3L tail + PRO end +link pepp head - LEU tail + PRO end +link pepp head - MET tail + PRO end +link pepp head - MSE tail + PRO end +link pepp head - ASN tail + PRO end +link pepp head - PRO tail + PRO end +link pepp head - GLN tail + PRO end +link pepp head - ARG tail + PRO end +link pepp head - SER tail + PRO end +link pepp head - SEC tail + PRO end +link pepp head - SEP tail + PRO end +link pepp head - THR tail + PRO end +link pepp head - THP tail + PRO end +link pepp head - TOP tail + PRO end +link pepp head - VAL tail + PRO end +link pepp head - TRP tail + PRO end +link pepp head - TYR tail + PRO end +link pepp head - TYP tail + PRO end +link pepp head - PTR tail + PRO end +link pepp head - TYS tail + PRO end +link pepp head - HYP tail + PRO end +link pepp head - HY3 tail + PRO end +link pepp head - QSR tail + PRO end +link pepp head - CIR tail + PRO end + +{ special link to HYP} +link pepp head - ACE tail + HYP end +link pepp head - ALA tail + HYP end +link pepp head - CYS tail + HYP end +link pepp head - CFE tail + HYP end +link pepp head - CYM tail + HYP end +link pepp head - CYF tail + HYP end +link pepp head - CYC tail + HYP end +link pepp head - CSP tail + HYP end +link pepp head - ASP tail + HYP end +link pepp head - ASH tail + HYP end +link pepp head - GLU tail + HYP end +link pepp head - GLH tail + HYP end +link pepp head - PCA tail + HYP end +link pepp head - PHE tail + HYP end +link pepp head - HIS tail + HYP end +link pepp head - NEP tail + HYP end +link pepp head - ILE tail + HYP end +link pepp head - LYS tail + HYP end +link pepp head - ALY tail + HYP end +link pepp head - HLY tail + HYP end +link pepp head - MLY tail + HYP end +link pepp head - MLZ tail + HYP end +link pepp head - M3L tail + HYP end +link pepp head - LEU tail + HYP end +link pepp head - MET tail + HYP end +link pepp head - MSE tail + HYP end +link pepp head - ASN tail + HYP end +link pepp head - PRO tail + HYP end +link pepp head - GLN tail + HYP end +link pepp head - ARG tail + HYP end +link pepp head - SER tail + HYP end +link pepp head - SEC tail + HYP end +link pepp head - SEP tail + HYP end +link pepp head - THR tail + HYP end +link pepp head - THP tail + HYP end +link pepp head - TOP tail + HYP end +link pepp head - VAL tail + HYP end +link pepp head - TRP tail + HYP end +link pepp head - TYR tail + HYP end +link pepp head - TYP tail + HYP end +link pepp head - PTR tail + HYP end +link pepp head - TYS tail + HYP end +link pepp head - HYP tail + HYP end +link pepp head - HY3 tail + HYP end +link pepp head - DDZ tail + HYP end +link pepp head - PNS tail + HYP end +link pepp head - QSR tail + HYP end +link pepp head - CIR tail + HYP end + +{ special link to HYP} +link pepp head - ACE tail + HY3 end +link pepp head - ALA tail + HY3 end +link pepp head - CYS tail + HY3 end +link pepp head - CFE tail + HY3 end +link pepp head - CYM tail + HY3 end +link pepp head - CYF tail + HY3 end +link pepp head - CYC tail + HY3 end +link pepp head - CSP tail + HY3 end +link pepp head - ASP tail + HY3 end +link pepp head - ASH tail + HY3 end +link pepp head - GLU tail + HY3 end +link pepp head - GLH tail + HY3 end +link pepp head - PCA tail + HY3 end +link pepp head - PHE tail + HY3 end +link pepp head - HIS tail + HY3 end +link pepp head - NEP tail + HY3 end +link pepp head - ILE tail + HY3 end +link pepp head - LYS tail + HY3 end +link pepp head - ALY tail + HY3 end +link pepp head - HLY tail + HY3 end +link pepp head - MLY tail + HY3 end +link pepp head - MLZ tail + HY3 end +link pepp head - M3L tail + HY3 end +link pepp head - LEU tail + HY3 end +link pepp head - MET tail + HY3 end +link pepp head - 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MSE tail + TOP end +link pept head - MSE tail + VAL end +link pept head - MSE tail + TRP end +link pept head - MSE tail + TYR end +link pept head - MSE tail + TYP end +link pept head - MSE tail + PTR end +link pept head - MSE tail + TYS end +link pept head - MSE tail + HYP end +link pept head - MSE tail + HY3 end +link pept head - MSE tail + DDZ end +link pept head - MSE tail + PNS end +link pept head - MSE tail + QSR end +link pctn head - MSE tail + CTN end +link pept head - MSE tail + NME end +link pept head - MSE tail + CIR end + +{ peptide linkages for ASN } +link pept head - ASN tail + ALA end +link pept head - ASN tail + CYS end +link pept head - ASN tail + CFE end +link pept head - ASN tail + CYM end +link pept head - ASN tail + CYF end +link pept head - ASN tail + CYC end +link pept head - ASN tail + CSP end +link pept head - ASN tail + ASP end +link pept head - ASN tail + ASH end +link pept head - ASN tail + GLU end +link pept head - ASN tail + GLH end +link pept head - ASN tail + PHE end +link pept head - ASN tail + HIS end +link pept head - ASN tail + NEP end +link pept head - ASN tail + ILE end +link pept head - ASN tail + LYS end +link pept head - ASN tail + ALY end +link pept head - ASN tail + HLY end +link pept head - ASN tail + MLY end +link pept head - ASN tail + MLZ end +link pept head - ASN tail + M3L end +link pept head - ASN tail + LEU end +link pept head - ASN tail + MET end +link pept head - ASN tail + MSE end +link pept head - ASN tail + ASN end +link pept head - ASN tail + PRO end +link pept head - ASN tail + GLN end +link pept head - ASN tail + ARG end +link pept head - ASN tail + SER end +link pept head - ASN tail + SEC end +link pept head - ASN tail + SEP end +link pept head - ASN tail + THR end +link pept head - ASN tail + THP end +link pept head - ASN tail + TOP end +link pept head - ASN tail + VAL end +link pept head - ASN tail + TRP end +link pept head - ASN tail + TYR end +link pept head - ASN tail + TYP end +link pept head - ASN tail + PTR end +link pept head - ASN tail + TYS end +link pept head - ASN tail + HYP end +link pept head - ASN tail + HY3 end +link pept head - ASN tail + DDZ end +link pept head - ASN tail + PNS end +link pept head - ASN tail + QSR end +link pctn head - ASN tail + CTN end +link pept head - ASN tail + NME end +link pept head - ASN tail + CIR end + +{ peptide linkages for PCA} +link pept head - PCA tail + ALA end +link pept head - PCA tail + CYS end +link pept head - PCA tail + CFE end +link pept head - PCA tail + CYM end +link pept head - PCA tail + CYF end +link pept head - PCA tail + CYC end +link pept head - PCA tail + CSP end +link pept head - PCA tail + ASP end +link pept head - PCA tail + ASH end +link pept head - PCA tail + GLU end +link pept head - PCA tail + GLH end +link pept head - PCA tail + PHE end +link pept head - PCA tail + HIS end +link pept head - PCA tail + NEP end +link pept head - PCA tail + ILE end +link pept head - PCA tail + LYS end +link pept head - PCA tail + ALY end +link pept head - PCA tail + HLY end +link pept head - PCA tail + MLY end +link pept head - 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GLN tail + TOP end +link pept head - GLN tail + VAL end +link pept head - GLN tail + TRP end +link pept head - GLN tail + TYR end +link pept head - GLN tail + TYP end +link pept head - GLN tail + PTR end +link pept head - GLN tail + TYS end +link pept head - GLN tail + HYP end +link pept head - GLN tail + HY3 end +link pept head - GLN tail + DDZ end +link pept head - GLN tail + PNS end +link pept head - GLN tail + QSR end +link pctn head - GLN tail + CTN end +link pept head - GLN tail + NME end +link pept head - GLN tail + CIR end + +{ peptide linkages for ARG } +link pept head - ARG tail + ALA end +link pept head - ARG tail + CYS end +link pept head - ARG tail + CFE end +link pept head - ARG tail + CYM end +link pept head - ARG tail + CYF end +link pept head - ARG tail + CYC end +link pept head - ARG tail + CSP end +link pept head - ARG tail + ASP end +link pept head - ARG tail + ASH end +link pept head - ARG tail + GLU end +link pept head - ARG tail + GLH end +link pept head - ARG tail + PHE end +link pept head - 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SER tail + MLZ end +link pept head - SER tail + M3L end +link pept head - SER tail + LEU end +link pept head - SER tail + MET end +link pept head - SER tail + MSE end +link pept head - SER tail + ASN end +link pept head - SER tail + PRO end +link pept head - SER tail + GLN end +link pept head - SER tail + ARG end +link pept head - SER tail + SER end +link pept head - SER tail + SEP end +link pept head - SER tail + THR end +link pept head - SER tail + THP end +link pept head - SER tail + TOP end +link pept head - SER tail + VAL end +link pept head - SER tail + TRP end +link pept head - SER tail + TYR end +link pept head - SER tail + TYP end +link pept head - SER tail + PTR end +link pept head - SER tail + TYS end +link pept head - SER tail + HYP end +link pept head - SER tail + HY3 end +link pept head - SER tail + DDZ end +link pept head - SER tail + PNS end +link pept head - SER tail + QSR end +link pctn head - SER tail + CTN end +link pept head - SER tail + NME end +link pept head - SER tail + CIR end + +{ peptide linkages for SEC } +link pept head - 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SEP tail + ASP end +link pept head - SEP tail + ASH end +link pept head - SEP tail + GLU end +link pept head - SEP tail + GLH end +link pept head - SEP tail + PHE end +link pept head - SEP tail + HIS end +link pept head - SEP tail + NEP end +link pept head - SEP tail + ILE end +link pept head - SEP tail + LYS end +link pept head - SEP tail + ALY end +link pept head - SEP tail + HLY end +link pept head - SEP tail + MLY end +link pept head - SEP tail + MLZ end +link pept head - SEP tail + M3L end +link pept head - SEP tail + LEU end +link pept head - SEP tail + MET end +link pept head - SEP tail + MSE end +link pept head - SEP tail + ASN end +link pept head - SEP tail + PRO end +link pept head - SEP tail + GLN end +link pept head - SEP tail + ARG end +link pept head - SEP tail + SER end +link pept head - SEP tail + SEC end +link pept head - SEP tail + SEP end +link pept head - SEP tail + THR end +link pept head - SEP tail + THP end +link pept head - SEP tail + TOP end +link pept head - SEP tail + VAL end +link pept head - SEP tail + TRP end +link pept head - SEP tail + TYR end +link pept head - SEP tail + TYP end +link pept head - SEP tail + PTR end +link pept head - SEP tail + TYS end +link pept head - SEP tail + HYP end +link pept head - SEP tail + HY3 end +link pept head - SEP tail + DDZ end +link pept head - SEP tail + PNS end +link pept head - SEP tail + QSR end +link pctn head - SEP tail + CTN end +link pept head - SEP tail + NME end +link pept head - SEP tail + CIR end + +{ peptide linkages for THR } +link pept head - THR tail + ALA end +link pept head - THR tail + CYS end +link pept head - THR tail + CFE end +link pept head - THR tail + CYM end +link pept head - THR tail + CYF end +link pept head - THR tail + CYC end +link pept head - THR tail + CSP end +link pept head - THR tail + ASP end +link pept head - THR tail + ASH end +link pept head - THR tail + GLU end +link pept head - THR tail + GLH end +link pept head - THR tail + PHE end +link pept head - THR tail + HIS end +link pept head - THR tail + NEP end +link pept head - THR tail + ILE end +link pept head - THR tail + LYS end +link pept head - THR tail + ALY end +link pept head - THR tail + HLY end +link pept head - THR tail + MLY end +link pept head - THR tail + MLZ end +link pept head - THR tail + M3L end +link pept head - THR tail + LEU end +link pept head - THR tail + MET end +link pept head - THR tail + MSE end +link pept head - THR tail + ASN end +link pept head - THR tail + PRO end +link pept head - THR tail + GLN end +link pept head - THR tail + ARG end +link pept head - THR tail + SER end +link pept head - THR tail + SEC end +link pept head - THR tail + SEP end +link pept head - THR tail + THR end +link pept head - THR tail + THP end +link pept head - THR tail + TOP end +link pept head - THR tail + VAL end +link pept head - THR tail + TRP end +link pept head - THR tail + TYR end +link pept head - THR tail + TYP end +link pept head - THR tail + PTR end +link pept head - THR tail + TYS end +link pept head - THR tail + HYP end +link pept head - THR tail + HY3 end +link pept head - 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VAL tail + TRP end +link pept head - VAL tail + TYR end +link pept head - VAL tail + TYP end +link pept head - VAL tail + PTR end +link pept head - VAL tail + TYS end +link pept head - VAL tail + HYP end +link pept head - VAL tail + HY3 end +link pept head - VAL tail + DDZ end +link pept head - VAL tail + PNS end +link pept head - VAL tail + QSR end +link pctn head - VAL tail + CTN end +link pept head - VAL tail + NME end +link pept head - VAL tail + CIR end + +{ peptide linkages for TRP } +link pept head - TRP tail + ALA end +link pept head - TRP tail + CYS end +link pept head - TRP tail + CFE end +link pept head - TRP tail + CYM end +link pept head - TRP tail + CYF end +link pept head - TRP tail + CYC end +link pept head - TRP tail + CSP end +link pept head - TRP tail + ASP end +link pept head - TRP tail + ASH end +link pept head - TRP tail + GLU end +link pept head - TRP tail + GLH end +link pept head - TRP tail + PHE end +link pept head - TRP tail + HIS end +link pept head - TRP tail + NEP end +link pept head - TRP tail + ILE end +link pept head - TRP tail + LYS end +link pept head - TRP tail + ALY end +link pept head - TRP tail + HLY end +link pept head - TRP tail + MLY end +link pept head - TRP tail + MLZ end +link pept head - TRP tail + M3L end +link pept head - TRP tail + LEU end +link pept head - TRP tail + MET end +link pept head - TRP tail + MSE end +link pept head - TRP tail + ASN end +link pept head - TRP tail + PRO end +link pept head - TRP tail + GLN end +link pept head - TRP tail + ARG end +link pept head - TRP tail + SER end +link pept head - TRP tail + SEC end +link pept head - TRP tail + SEP end +link pept head - TRP tail + THR end +link pept head - TRP tail + THP end +link pept head - TRP tail + TOP end +link pept head - TRP tail + VAL end +link pept head - TRP tail + TRP end +link pept head - TRP tail + TYR end +link pept head - TRP tail + TYP end +link pept head - TRP tail + PTR end +link pept head - TRP tail + TYS end +link pept head - TRP tail + HYP end +link pept head - TRP tail + HY3 end +link pept head - TRP tail + DDZ end +link pept head - TRP tail + PNS end +link pept head - TRP tail + QSR end +link pctn head - TRP tail + CTN end +link pept head - TRP tail + NME end +link pept head - TRP tail + CIR end + +{ peptide linkages for TYR } +link pept head - TYR tail + ALA end +link pept head - TYR tail + CYS end +link pept head - TYR tail + CFE end +link pept head - TYR tail + CYM end +link pept head - TYR tail + CYF end +link pept head - TYR tail + CYC end +link pept head - TYR tail + CSP end +link pept head - TYR tail + ASP end +link pept head - TYR tail + ASH end +link pept head - TYR tail + GLU end +link pept head - TYR tail + GLH end +link pept head - TYR tail + PHE end +link pept head - TYR tail + HIS end +link pept head - TYR tail + NEP end +link pept head - TYR tail + ILE end +link pept head - TYR tail + LYS end +link pept head - TYR tail + ALY end +link pept head - TYR tail + HLY end +link pept head - TYR tail + MLY end +link pept head - TYR tail + MLZ end +link pept head - TYR tail + M3L end +link pept head - TYR tail + LEU end +link pept head - TYR tail + MET end +link pept head - TYR tail + MSE end +link pept head - TYR tail + ASN end +link pept head - TYR tail + PRO end +link pept head - TYR tail + GLN end +link pept head - TYR tail + ARG end +link pept head - TYR tail + SER end +link pept head - TYR tail + SEC end +link pept head - TYR tail + SEP end +link pept head - TYR tail + THR end +link pept head - TYR tail + THP end +link pept head - TYR tail + TOP end +link pept head - TYR tail + VAL end +link pept head - TYR tail + TRP end +link pept head - TYR tail + TYR end +link pept head - TYR tail + TYP end +link pept head - TYR tail + PTR end +link pept head - TYR tail + TYS end +link pept head - TYR tail + HYP end +link pept head - TYR tail + HY3 end +link pept head - TYR tail + DDZ end +link pept head - TYR tail + PNS end +link pept head - TYR tail + QSR end +link pctn head - TYR tail + CTN end +link pept head - TYR tail + NME end +link pept head - TYR tail + CIR end + +{ peptide linkages for TYP } +link pept head - TYP tail + ALA end +link pept head - TYP tail + CYS end +link pept head - TYP tail + CFE end +link pept head - TYP tail + CYM end +link pept head - TYP tail + CYF end +link pept head - TYP tail + CYC end +link pept head - TYP tail + CSP end +link pept head - TYP tail + ASP end +link pept head - TYP tail + ASH end +link pept head - TYP tail + GLU end +link pept head - TYP tail + GLH end +link pept head - TYP tail + PHE end +link pept head - TYP tail + HIS end +link pept head - TYP tail + NEP end +link pept head - TYP tail + ILE end +link pept head - TYP tail + LYS end +link pept head - TYP tail + ALY end +link pept head - TYP tail + HLY end +link pept head - TYP tail + MLY end +link pept head - TYP tail + MLZ end +link pept head - TYP tail + M3L end +link pept head - TYP tail + LEU end +link pept head - TYP tail + MET end +link pept head - TYP tail + MSE end +link pept head - TYP tail + ASN end +link pept head - TYP tail + PRO end +link pept head - TYP tail + GLN end +link pept head - TYP tail + ARG end +link pept head - TYP tail + SER end +link pept head - TYP tail + SEC end +link pept head - TYP tail + SEP end +link pept head - TYP tail + THR end +link pept head - TYP tail + THP end +link pept head - TYP tail + TOP end +link pept head - TYP tail + VAL end +link pept head - TYP tail + TRP end +link pept head - TYP tail + TYR end +link pept head - TYP tail + TYP end +link pept head - TYP tail + PTR end +link pept head - TYP tail + TYS end +link pept head - TYP tail + HYP end +link pept head - TYP tail + HY3 end +link pept head - TYP tail + DDZ end +link pept head - TYP tail + PNS end +link pept head - TYP tail + QSR end +link pctn head - TYP tail + CTN end +link pept head - TYP tail + NME end +link pept head - TYP tail + CIR end + +{ peptide linkages for PTR - same as TYP } +link pept head - PTR tail + ALA end +link pept head - PTR tail + CYS end +link pept head - PTR tail + CFE end +link pept head - PTR tail + CYM end +link pept head - PTR tail + CYF end +link pept head - PTR tail + CYC end +link pept head - PTR tail + CSP end +link pept head - PTR tail + ASP end +link pept head - PTR tail + ASH end +link pept head - PTR tail + GLU end +link pept head - PTR tail + GLH end +link pept head - PTR tail + PHE end +link pept head - PTR tail + HIS end +link pept head - PTR tail + NEP end +link pept head - PTR tail + ILE end +link pept head - PTR tail + LYS end +link pept head - PTR tail + ALY end +link pept head - PTR tail + HLY end +link pept head - PTR tail + MLY end +link pept head - PTR tail + MLZ end +link pept head - PTR tail + M3L end +link pept head - PTR tail + LEU end +link pept head - PTR tail + MET end +link pept head - PTR tail + MSE end +link pept head - PTR tail + ASN end +link pept head - PTR tail + PRO end +link pept head - PTR tail + GLN end +link pept head - PTR tail + ARG end +link pept head - PTR tail + SER end +link pept head - PTR tail + SEC end +link pept head - PTR tail + SEP end +link pept head - PTR tail + THR end +link pept head - PTR tail + THP end +link pept head - PTR tail + TOP end +link pept head - PTR tail + VAL end +link pept head - PTR tail + TRP end +link pept head - PTR tail + TYR end +link pept head - PTR tail + TYP end +link pept head - PTR tail + PTR end +link pept head - PTR tail + TYS end +link pept head - PTR tail + HYP end +link pept head - PTR tail + HY3 end +link pept head - PTR tail + DDZ end +link pept head - PTR tail + PNS end +link pept head - PTR tail + QSR end +link pctn head - PTR tail + CTN end +link pept head - PTR tail + NME end +link pept head - PTR tail + CIR end + +{ peptide linkages for TYS } +link pept head - TYS tail + ALA end +link pept head - TYS tail + CYS end +link pept head - TYS tail + CFE end +link pept head - TYS tail + CYM end +link pept head - TYS tail + CYF end +link pept head - TYS tail + CYC end +link pept head - TYS tail + CSP end +link pept head - TYS tail + ASP end +link pept head - TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + HLY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEC end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + PTR end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + HY3 end +link pept head - TYS tail + DDZ end +link pept head - TYS tail + PNS end +link pept head - TYS tail + QSR end +link pctn head - TYS tail + CTN end +link pept head - TYS tail + NME end +link pept head - TYS tail + CIR end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CFE end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CYC end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + HLY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEC end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + PTR end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + HY3 end +link pept head - HYP tail + DDZ end +link pept head - HYP tail + QSR end +link pept head - HYP tail + PNS end +link pept head - HYP tail + CIR end + +{ peptide linkages for HY3 } +link pept head - HY3 tail + ALA end +link pept head - HY3 tail + CYS end +link pept head - HY3 tail + CFE end +link pept head - HY3 tail + CYM end +link pept head - HY3 tail + CYF end +link pept head - HY3 tail + CYC end +link pept head - HY3 tail + CSP end +link pept head - HY3 tail + ASP end +link pept head - HY3 tail + ASH end +link pept head - HY3 tail + GLU end +link pept head - HY3 tail + GLH end +link pept head - HY3 tail + PHE end +link pept head - HY3 tail + HIS end +link pept head - HY3 tail + NEP end +link pept head - HY3 tail + ILE end +link pept head - HY3 tail + LYS end +link pept head - HY3 tail + ALY end +link pept head - HY3 tail + HLY end +link pept head - HY3 tail + MLY end +link pept head - HY3 tail + MLZ end +link pept head - HY3 tail + M3L end +link pept head - HY3 tail + LEU end +link pept head - HY3 tail + MET end +link pept head - HY3 tail + MSE end +link pept head - HY3 tail + ASN end +link pept head - HY3 tail + PRO end +link pept head - HY3 tail + GLN end +link pept head - HY3 tail + ARG end +link pept head - HY3 tail + SER end +link pept head - HY3 tail + SEC end +link pept head - HY3 tail + SEP end +link pept head - HY3 tail + THR end +link pept head - HY3 tail + THP end +link pept head - HY3 tail + TOP end +link pept head - HY3 tail + VAL end +link pept head - HY3 tail + TRP end +link pept head - HY3 tail + TYR end +link pept head - HY3 tail + TYP end +link pept head - HY3 tail + PTR end +link pept head - HY3 tail + TYS end +link pept head - HY3 tail + HYP end +link pept head - HY3 tail + HY3 end +link pept head - HY3 tail + DDZ end +link pept head - HY3 tail + QSR end +link pept head - HY3 tail + PNS end +link pept head - HY3 tail + CIR end + +{ peptide linkages for DDZ } +link pept head - DDZ tail + ALA end +link pept head - DDZ tail + CYS end +link pept head - DDZ tail + CFE end +link pept head - DDZ tail + CYM end +link pept head - DDZ tail + CYF end +link pept head - DDZ tail + CYC end +link pept head - DDZ tail + CSP end +link pept head - DDZ tail + ASP end +link pept head - DDZ tail + ASH end +link pept head - DDZ tail + GLU end +link pept head - DDZ tail + GLH end +link pept head - DDZ tail + PHE end +link pept head - DDZ tail + HIS end +link pept head - DDZ tail + NEP end +link pept head - DDZ tail + ILE end +link pept head - DDZ tail + LYS end +link pept head - DDZ tail + ALY end +link pept head - DDZ tail + HLY end +link pept head - DDZ tail + MLY end +link pept head - DDZ tail + MLZ end +link pept head - DDZ tail + M3L end +link pept head - DDZ tail + LEU end +link pept head - DDZ tail + MET end +link pept head - DDZ tail + MSE end +link pept head - DDZ tail + ASN end +link pept head - DDZ tail + PRO end +link pept head - DDZ tail + GLN end +link pept head - DDZ tail + ARG end +link pept head - DDZ tail + SER end +link pept head - DDZ tail + SEC end +link pept head - DDZ tail + SEP end +link pept head - DDZ tail + THR end +link pept head - DDZ tail + THP end +link pept head - DDZ tail + TOP end +link pept head - DDZ tail + VAL end +link pept head - DDZ tail + TRP end +link pept head - DDZ tail + TYR end +link pept head - DDZ tail + TYP end +link pept head - DDZ tail + PTR end +link pept head - DDZ tail + TYS end +link pept head - DDZ tail + HYP end +link pept head - DDZ tail + DDZ end +link pept head - DDZ tail + PNS end +link pept head - DDZ tail + QSR end +link pctn head - DDZ tail + CTN end +link pept head - DDZ tail + NME end +link pept head - DDZ tail + CIR end + +{ peptide linkages for PNS } +link pept head - PNS tail + ALA end +link pept head - PNS tail + CYS end +link pept head - PNS tail + CFE end +link pept head - PNS tail + CYM end +link pept head - PNS tail + CYF end +link pept head - PNS tail + CYC end +link pept head - PNS tail + CSP end +link pept head - PNS tail + ASP end +link pept head - PNS tail + ASH end +link pept head - PNS tail + GLU end +link pept head - PNS tail + GLH end +link pept head - PNS tail + PHE end +link pept head - PNS tail + HIS end +link pept head - PNS tail + NEP end +link pept head - PNS tail + ILE end +link pept head - PNS tail + LYS end +link pept head - PNS tail + ALY end +link pept head - PNS tail + HLY end +link pept head - PNS tail + MLY end +link pept head - PNS tail + MLZ end +link pept head - PNS tail + M3L end +link pept head - PNS tail + LEU end +link pept head - PNS tail + MET end +link pept head - PNS tail + MSE end +link pept head - PNS tail + ASN end +link pept head - PNS tail + PRO end +link pept head - PNS tail + GLN end +link pept head - PNS tail + ARG end +link pept head - PNS tail + SER end +link pept head - PNS tail + SEC end +link pept head - PNS tail + SEP end +link pept head - PNS tail + THR end +link pept head - PNS tail + THP end +link pept head - PNS tail + TOP end +link pept head - PNS tail + VAL end +link pept head - PNS tail + TRP end +link pept head - PNS tail + TYR end +link pept head - PNS tail + TYP end +link pept head - PNS tail + PTR end +link pept head - PNS tail + TYS end +link pept head - PNS tail + HYP end +link pept head - PNS tail + HY3 end +link pept head - PNS tail + DDZ end +link pept head - PNS tail + PNS end +link pept head - PNS tail + QSR end +link pctn head - PNS tail + CTN end +link pept head - PNS tail + NME end +link pept head - PNS tail + CIR end + +{ peptide linkages for QSR } +link pept head - QSR tail + ALA end +link pept head - QSR tail + CYS end +link pept head - QSR tail + CFE end +link pept head - QSR tail + CYM end +link pept head - QSR tail + CYF end +link pept head - QSR tail + CYC end +link pept head - QSR tail + CSP end +link pept head - QSR tail + ASP end +link pept head - QSR tail + ASH end +link pept head - QSR tail + GLU end +link pept head - QSR tail + GLH end +link pept head - QSR tail + PHE end +link pept head - QSR tail + HIS end +link pept head - QSR tail + NEP end +link pept head - QSR tail + ILE end +link pept head - QSR tail + LYS end +link pept head - QSR tail + ALY end +link pept head - QSR tail + HLY end +link pept head - QSR tail + MLY end +link pept head - QSR tail + MLZ end +link pept head - QSR tail + M3L end +link pept head - QSR tail + LEU end +link pept head - QSR tail + MET end +link pept head - QSR tail + MSE end +link pept head - QSR tail + ASN end +link pept head - QSR tail + PRO end +link pept head - QSR tail + GLN end +link pept head - QSR tail + ARG end +link pept head - QSR tail + SER end +link pept head - QSR tail + SEC end +link pept head - QSR tail + SEP end +link pept head - QSR tail + THR end +link pept head - QSR tail + THP end +link pept head - QSR tail + TOP end +link pept head - QSR tail + VAL end +link pept head - QSR tail + TRP end +link pept head - QSR tail + TYR end +link pept head - QSR tail + TYP end +link pept head - QSR tail + PTR end +link pept head - QSR tail + TYS end +link pept head - QSR tail + HYP end +link pept head - QSR tail + HY3 end +link pept head - QSR tail + DDZ end +link pept head - QSR tail + PNS end +link pept head - QSR tail + QSR end +link pctn head - QSR tail + CTN end +link pept head - QSR tail + NME end +link pept head - QSR tail + CIR end + +{ peptide linkages for CIR } +link pept head - CIR tail + ALA end +link pept head - CIR tail + CYS end +link pept head - CIR tail + CFE end +link pept head - CIR tail + CYM end +link pept head - CIR tail + CYF end +link pept head - CIR tail + CYC end +link pept head - CIR tail + CSP end +link pept head - CIR tail + ASP end +link pept head - CIR tail + ASH end +link pept head - CIR tail + GLU end +link pept head - CIR tail + GLH end +link pept head - CIR tail + PHE end +link pept head - CIR tail + HIS end +link pept head - CIR tail + NEP end +link pept head - CIR tail + ILE end +link pept head - CIR tail + LYS end +link pept head - CIR tail + ALY end +link pept head - CIR tail + HLY end +link pept head - CIR tail + MLY end +link pept head - CIR tail + MLZ end +link pept head - CIR tail + M3L end +link pept head - CIR tail + LEU end +link pept head - CIR tail + MET end +link pept head - CIR tail + MSE end +link pept head - CIR tail + ASN end +link pept head - CIR tail + PRO end +link pept head - CIR tail + GLN end +link pept head - CIR tail + ARG end +link pept head - CIR tail + SER end +link pept head - CIR tail + SEC end +link pept head - CIR tail + SEP end +link pept head - CIR tail + THR end +link pept head - CIR tail + THP end +link pept head - CIR tail + TOP end +link pept head - CIR tail + VAL end +link pept head - CIR tail + TRP end +link pept head - CIR tail + TYR end +link pept head - CIR tail + TYP end +link pept head - CIR tail + PTR end +link pept head - CIR tail + TYS end +link pept head - CIR tail + HYP end +link pept head - CIR tail + HY3 end +link pept head - CIR tail + DDZ end +link pept head - CIR tail + PNS end +link pept head - CIR tail + QSR end +link pctn head - CIR tail + CTN end +link pept head - CIR tail + NME end +link pept head - CIR tail + CIR end + +first ACET tail + ACE end + +last CTER head - ALA end +last CTER head - CYS end +last CTER head - CFE end +last CTER head - CYM end +last CTER head - CYC end +last CTER head - CYF end +last CTER head - CSP end +last CTER head - ASP end +last CTER head - ASH end +last CTER head - GLU end +last CTER head - GLH end +last CTER head - GLY end +last CTER head - PHE end +last CTER head - HIS end +last CTER head - NEP end +last CTER head - ILE end +last CTER head - LYS end +last CTER head - ALY end +last CTER head - HLY end +last CTER head - MLY end +last CTER head - MLZ end +last CTER head - M3L end +last CTER head - LEU end +last CTER head - MET end +last CTER head - MSE end +last CTER head - ASN end +last CTER head - PCA end +last CTER head - PRO end +last CTER head - GLN end +last CTER head - ARG end +last CTER head - SER end +last CTER head - SEC end +last CTER head - SEP end +last CTER head - THR end +last CTER head - THP end +last CTER head - TOP end +last CTER head - VAL end +last CTER head - TRP end +last CTER head - TYR end +last CTER head - TYP end +last CTER head - PTR end +last CTER head - TYS end +last CTER head - HYP end +last CTER head - HY3 end +last CTER head - DDZ end +last CTER head - PNS end +last CTER head - QSR end +last CTER head - CIR end + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noter.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noter.link new file mode 100644 index 0000000000000000000000000000000000000000..8ee003fbde573cfde2f8794c95e31110a524c760 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4-noter.link @@ -0,0 +1,2659 @@ +remarks file toppar/protein-allhdg5-4.link +remarks +remarks this is a macro to define standard protein peptide bonds +remarks and termini to generate a protein sequence. + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link ppgp head - GLY tail + PRO end +link ppgp head - GLY tail + HYP end +link ppgp head - GLY tail + HY3 end +link ppgg head - GLY tail + GLY end + +{ special link to GLY} +link ppg1 head - ACE tail + GLY end +link ppg1 head - ALA tail + GLY end +link ppg1 head - CYS tail + GLY end +link ppg1 head - CFE tail + GLY end +link ppg1 head - CYM tail + GLY end +link ppg1 head - CYF tail + GLY end +link ppg1 head - CYC tail + GLY end +link ppg1 head - CSP tail + GLY end +link ppg1 head - ASP tail + GLY end +link ppg1 head - ASH tail + GLY end +link ppg1 head - GLU tail + GLY end +link ppg1 head - GLH tail + GLY end +link ppg1 head - PCA tail + GLY end +link ppg1 head - PHE tail + GLY end +link ppg1 head - HIS tail + GLY end +link ppg1 head - NEP tail + GLY end +link ppg1 head - ILE tail + GLY end +link ppg1 head - LYS tail + GLY end +link ppg1 head - ALY tail + GLY end +link ppg1 head - HLY tail + GLY end +link ppg1 head - MLY tail + GLY end +link ppg1 head - MLZ tail + GLY end +link ppg1 head - M3L tail + GLY end +link ppg1 head - LEU tail + GLY end +link ppg1 head - MET tail + GLY end +link ppg1 head - MSE tail + GLY end ! +link ppg1 head - ASN tail + GLY end +link ppg1 head - PRO tail + GLY end +link ppg1 head - GLN tail + GLY end +link ppg1 head - ARG tail + GLY end +link ppg1 head - SER tail + GLY end +link ppg1 head - SEC tail + GLY end +link ppg1 head - SEP tail + GLY end +link ppg1 head - THR tail + GLY end +link ppg1 head - THP tail + GLY end +link ppg1 head - TOP tail + GLY end +link ppg1 head - VAL tail + GLY end +link ppg1 head - TRP tail + GLY end +link ppg1 head - TYR tail + GLY end +link ppg1 head - TYP tail + GLY end +link ppg1 head - PTR tail + GLY end +link ppg1 head - TYS tail + GLY end +link ppg1 head - HYP tail + GLY end +link ppg1 head - HY3 tail + GLY end +link ppg1 head - DDZ tail + GLY end +link ppg1 head - QSR tail + GLY end +link ppg1 head - PNS tail + GLY end +link ppg1 head - CIR tail + GLY end + +{ special link from GLY} +link ppg2 head - GLY tail + ALA end +link ppg2 head - GLY tail + CYS end +link ppg2 head - 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THR tail + ILE end +link pept head - THR tail + LYS end +link pept head - THR tail + ALY end +link pept head - THR tail + HLY end +link pept head - THR tail + MLY end +link pept head - THR tail + MLZ end +link pept head - THR tail + M3L end +link pept head - THR tail + LEU end +link pept head - THR tail + MET end +link pept head - THR tail + MSE end +link pept head - THR tail + ASN end +link pept head - THR tail + PRO end +link pept head - THR tail + GLN end +link pept head - THR tail + ARG end +link pept head - THR tail + SER end +link pept head - THR tail + SEC end +link pept head - THR tail + SEP end +link pept head - THR tail + THR end +link pept head - THR tail + THP end +link pept head - THR tail + TOP end +link pept head - THR tail + VAL end +link pept head - THR tail + TRP end +link pept head - THR tail + TYR end +link pept head - THR tail + TYP end +link pept head - THR tail + PTR end +link pept head - THR tail + TYS end +link pept head - THR tail + HYP end +link pept head - THR tail + HY3 end +link pept head - 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THP tail + LEU end +link pept head - THP tail + MET end +link pept head - THP tail + MSE end +link pept head - THP tail + ASN end +link pept head - THP tail + PRO end +link pept head - THP tail + GLN end +link pept head - THP tail + ARG end +link pept head - THP tail + SER end +link pept head - THP tail + SEC end +link pept head - THP tail + SEP end +link pept head - THP tail + THR end +link pept head - THP tail + THP end +link pept head - THP tail + TOP end +link pept head - THP tail + VAL end +link pept head - THP tail + TRP end +link pept head - THP tail + TYR end +link pept head - THP tail + TYP end +link pept head - THP tail + PTR end +link pept head - THP tail + TYS end +link pept head - THP tail + HYP end +link pept head - THP tail + HY3 end +link pept head - THP tail + DDZ end +link pept head - THP tail + PNS end +link pept head - THP tail + QSR end +link pctn head - THP tail + CTN end +link pept head - THP tail + NME end +link pept head - THP tail + CIR end + +{ peptide linkages for TOP } +link pept head - TOP tail + ALA end +link pept head - TOP tail + CYS end +link pept head - TOP tail + CFE end +link pept head - TOP tail + CYM end +link pept head - TOP tail + CYF end +link pept head - TOP tail + CYC end +link pept head - TOP tail + CSP end +link pept head - TOP tail + ASP end +link pept head - TOP tail + ASH end +link pept head - TOP tail + GLU end +link pept head - TOP tail + GLH end +link pept head - TOP tail + PHE end +link pept head - TOP tail + HIS end +link pept head - TOP tail + NEP end +link pept head - TOP tail + ILE end +link pept head - TOP tail + LYS end +link pept head - TOP tail + ALY end +link pept head - TOP tail + HLY end +link pept head - TOP tail + MLY end +link pept head - TOP tail + MLZ end +link pept head - TOP tail + M3L end +link pept head - TOP tail + LEU end +link pept head - TOP tail + MET end +link pept head - TOP tail + MSE end +link pept head - TOP tail + ASN end +link pept head - TOP tail + PRO end +link pept head - TOP tail + GLN end +link pept head - TOP tail + ARG end +link pept head - TOP tail + SER end +link pept head - TOP tail + SEC end +link pept head - TOP tail + SEP end +link pept head - TOP tail + THR end +link pept head - TOP tail + THP end +link pept head - TOP tail + TOP end +link pept head - TOP tail + VAL end +link pept head - TOP tail + TRP end +link pept head - TOP tail + TYR end +link pept head - TOP tail + TYP end +link pept head - TOP tail + PTR end +link pept head - TOP tail + TYS end +link pept head - TOP tail + HYP end +link pept head - TOP tail + HY3 end +link pept head - TOP tail + DDZ end +link pept head - TOP tail + PNS end +link pept head - TOP tail + QSR end +link pctn head - TOP tail + CTN end +link pept head - TOP tail + NME end +link pept head - TOP tail + CIR end + +{ peptide linkages for VAL } +link pept head - VAL tail + ALA end +link pept head - VAL tail + CYS end +link pept head - VAL tail + CFE end +link pept head - VAL tail + CYM end +link pept head - VAL tail + CYF end +link pept head - VAL tail + CYC end +link pept head - VAL tail + CSP end +link pept head - VAL tail + ASP end +link pept head - VAL tail + ASH end +link pept head - VAL tail + GLU end +link pept head - VAL tail + GLH end +link pept head - VAL tail + PHE end +link pept head - VAL tail + HIS end +link pept head - VAL tail + NEP end +link pept head - VAL tail + ILE end +link pept head - VAL tail + LYS end +link pept head - VAL tail + ALY end +link pept head - VAL tail + HLY end +link pept head - VAL tail + MLY end +link pept head - VAL tail + MLZ end +link pept head - VAL tail + M3L end +link pept head - VAL tail + LEU end +link pept head - VAL tail + MET end +link pept head - VAL tail + MSE end +link pept head - VAL tail + ASN end +link pept head - VAL tail + PRO end +link pept head - VAL tail + GLN end +link pept head - VAL tail + ARG end +link pept head - VAL tail + SER end +link pept head - VAL tail + SEC end +link pept head - VAL tail + SEP end +link pept head - VAL tail + THR end +link pept head - VAL tail + THP end +link pept head - VAL tail + TOP end +link pept head - VAL tail + VAL end +link pept head - VAL tail + TRP end +link pept head - VAL tail + TYR end +link pept head - VAL tail + TYP end +link pept head - VAL tail + PTR end +link pept head - VAL tail + TYS end +link pept head - VAL tail + HYP end +link pept head - VAL tail + HY3 end +link pept head - VAL tail + DDZ end +link pept head - VAL tail + PNS end +link pept head - VAL tail + QSR end +link pctn head - VAL tail + CTN end +link pept head - VAL tail + NME end +link pept head - VAL tail + CIR end + +{ peptide linkages for TRP } +link pept head - TRP tail + ALA end +link pept head - TRP tail + CYS end +link pept head - TRP tail + CFE end +link pept head - TRP tail + CYM end +link pept head - TRP tail + CYF end +link pept head - TRP tail + CYC end +link pept head - TRP tail + CSP end +link pept head - TRP tail + ASP end +link pept head - TRP tail + ASH end +link pept head - TRP tail + GLU end +link pept head - TRP tail + GLH end +link pept head - TRP tail + PHE end +link pept head - TRP tail + HIS end +link pept head - TRP tail + NEP end +link pept head - TRP tail + ILE end +link pept head - TRP tail + LYS end +link pept head - TRP tail + ALY end +link pept head - TRP tail + HLY end +link pept head - TRP tail + MLY end +link pept head - TRP tail + MLZ end +link pept head - TRP tail + M3L end +link pept head - TRP tail + LEU end +link pept head - TRP tail + MET end +link pept head - TRP tail + MSE end +link pept head - TRP tail + ASN end +link pept head - TRP tail + PRO end +link pept head - TRP tail + GLN end +link pept head - TRP tail + ARG end +link pept head - TRP tail + SER end +link pept head - TRP tail + SEC end +link pept head - TRP tail + SEP end +link pept head - TRP tail + THR end +link pept head - TRP tail + THP end +link pept head - TRP tail + TOP end +link pept head - TRP tail + VAL end +link pept head - TRP tail + TRP end +link pept head - TRP tail + TYR end +link pept head - TRP tail + TYP end +link pept head - TRP tail + PTR end +link pept head - TRP tail + TYS end +link pept head - TRP tail + HYP end +link pept head - TRP tail + HY3 end +link pept head - TRP tail + DDZ end +link pept head - TRP tail + PNS end +link pept head - TRP tail + QSR end +link pctn head - TRP tail + CTN end +link pept head - TRP tail + NME end +link pept head - TRP tail + CIR end + +{ peptide linkages for TYR } +link pept head - TYR tail + ALA end +link pept head - TYR tail + CYS end +link pept head - TYR tail + CFE end +link pept head - TYR tail + CYM end +link pept head - TYR tail + CYF end +link pept head - TYR tail + CYC end +link pept head - TYR tail + CSP end +link pept head - TYR tail + ASP end +link pept head - TYR tail + ASH end +link pept head - TYR tail + GLU end +link pept head - TYR tail + GLH end +link pept head - TYR tail + PHE end +link pept head - TYR tail + HIS end +link pept head - TYR tail + NEP end +link pept head - TYR tail + ILE end +link pept head - TYR tail + LYS end +link pept head - TYR tail + ALY end +link pept head - TYR tail + HLY end +link pept head - TYR tail + MLY end +link pept head - TYR tail + MLZ end +link pept head - TYR tail + M3L end +link pept head - TYR tail + LEU end +link pept head - TYR tail + MET end +link pept head - TYR tail + MSE end +link pept head - TYR tail + ASN end +link pept head - TYR tail + PRO end +link pept head - TYR tail + GLN end +link pept head - TYR tail + ARG end +link pept head - TYR tail + SER end +link pept head - TYR tail + SEC end +link pept head - TYR tail + SEP end +link pept head - TYR tail + THR end +link pept head - TYR tail + THP end +link pept head - TYR tail + TOP end +link pept head - TYR tail + VAL end +link pept head - TYR tail + TRP end +link pept head - TYR tail + TYR end +link pept head - TYR tail + TYP end +link pept head - TYR tail + PTR end +link pept head - TYR tail + TYS end +link pept head - TYR tail + HYP end +link pept head - TYR tail + HY3 end +link pept head - TYR tail + DDZ end +link pept head - TYR tail + PNS end +link pept head - TYR tail + QSR end +link pctn head - TYR tail + CTN end +link pept head - TYR tail + NME end +link pept head - TYR tail + CIR end + +{ peptide linkages for TYP } +link pept head - TYP tail + ALA end +link pept head - TYP tail + CYS end +link pept head - TYP tail + CFE end +link pept head - TYP tail + CYM end +link pept head - TYP tail + CYF end +link pept head - TYP tail + CYC end +link pept head - TYP tail + CSP end +link pept head - TYP tail + ASP end +link pept head - TYP tail + ASH end +link pept head - TYP tail + GLU end +link pept head - TYP tail + GLH end +link pept head - TYP tail + PHE end +link pept head - TYP tail + HIS end +link pept head - TYP tail + NEP end +link pept head - TYP tail + ILE end +link pept head - TYP tail + LYS end +link pept head - TYP tail + ALY end +link pept head - TYP tail + HLY end +link pept head - TYP tail + MLY end +link pept head - TYP tail + MLZ end +link pept head - TYP tail + M3L end +link pept head - TYP tail + LEU end +link pept head - TYP tail + MET end +link pept head - TYP tail + MSE end +link pept head - TYP tail + ASN end +link pept head - TYP tail + PRO end +link pept head - TYP tail + GLN end +link pept head - TYP tail + ARG end +link pept head - TYP tail + SER end +link pept head - TYP tail + SEC end +link pept head - TYP tail + SEP end +link pept head - TYP tail + THR end +link pept head - TYP tail + THP end +link pept head - TYP tail + TOP end +link pept head - TYP tail + VAL end +link pept head - TYP tail + TRP end +link pept head - TYP tail + TYR end +link pept head - TYP tail + TYP end +link pept head - TYP tail + PTR end +link pept head - TYP tail + TYS end +link pept head - TYP tail + HYP end +link pept head - TYP tail + HY3 end +link pept head - TYP tail + DDZ end +link pept head - TYP tail + PNS end +link pept head - TYP tail + QSR end +link pctn head - TYP tail + CTN end +link pept head - TYP tail + NME end +link pept head - TYP tail + CIR end + +{ peptide linkages for PTR - same as TYP } +link pept head - PTR tail + ALA end +link pept head - PTR tail + CYS end +link pept head - PTR tail + CFE end +link pept head - PTR tail + CYM end +link pept head - PTR tail + CYF end +link pept head - PTR tail + CYC end +link pept head - PTR tail + CSP end +link pept head - PTR tail + ASP end +link pept head - PTR tail + ASH end +link pept head - PTR tail + GLU end +link pept head - PTR tail + GLH end +link pept head - PTR tail + PHE end +link pept head - PTR tail + HIS end +link pept head - PTR tail + NEP end +link pept head - PTR tail + ILE end +link pept head - PTR tail + LYS end +link pept head - PTR tail + ALY end +link pept head - PTR tail + HLY end +link pept head - PTR tail + MLY end +link pept head - PTR tail + MLZ end +link pept head - PTR tail + M3L end +link pept head - PTR tail + LEU end +link pept head - PTR tail + MET end +link pept head - PTR tail + MSE end +link pept head - PTR tail + ASN end +link pept head - PTR tail + PRO end +link pept head - PTR tail + GLN end +link pept head - PTR tail + ARG end +link pept head - PTR tail + SER end +link pept head - PTR tail + SEC end +link pept head - PTR tail + SEP end +link pept head - PTR tail + THR end +link pept head - PTR tail + THP end +link pept head - PTR tail + TOP end +link pept head - PTR tail + VAL end +link pept head - PTR tail + TRP end +link pept head - PTR tail + TYR end +link pept head - PTR tail + TYP end +link pept head - PTR tail + PTR end +link pept head - PTR tail + TYS end +link pept head - PTR tail + HYP end +link pept head - PTR tail + HY3 end +link pept head - PTR tail + DDZ end +link pept head - PTR tail + PNS end +link pept head - PTR tail + QSR end +link pctn head - PTR tail + CTN end +link pept head - PTR tail + NME end +link pept head - PTR tail + CIR end + +{ peptide linkages for TYS } +link pept head - TYS tail + ALA end +link pept head - TYS tail + CYS end +link pept head - TYS tail + CFE end +link pept head - TYS tail + CYM end +link pept head - TYS tail + CYF end +link pept head - TYS tail + CYC end +link pept head - TYS tail + CSP end +link pept head - TYS tail + ASP end +link pept head - TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + HLY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEC end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + PTR end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + HY3 end +link pept head - TYS tail + DDZ end +link pept head - TYS tail + PNS end +link pept head - TYS tail + QSR end +link pctn head - TYS tail + CTN end +link pept head - TYS tail + NME end +link pept head - TYS tail + CIR end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CFE end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CYC end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + HLY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEC end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + PTR end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + HY3 end +link pept head - HYP tail + DDZ end +link pept head - HYP tail + QSR end +link pept head - HYP tail + PNS end +link pept head - HYP tail + CIR end + +{ peptide linkages for HY3 } +link pept head - HY3 tail + ALA end +link pept head - HY3 tail + CYS end +link pept head - HY3 tail + CFE end +link pept head - HY3 tail + CYM end +link pept head - HY3 tail + CYF end +link pept head - HY3 tail + CYC end +link pept head - HY3 tail + CSP end +link pept head - HY3 tail + ASP end +link pept head - HY3 tail + ASH end +link pept head - HY3 tail + GLU end +link pept head - HY3 tail + GLH end +link pept head - HY3 tail + PHE end +link pept head - HY3 tail + HIS end +link pept head - HY3 tail + NEP end +link pept head - HY3 tail + ILE end +link pept head - HY3 tail + LYS end +link pept head - HY3 tail + ALY end +link pept head - HY3 tail + HLY end +link pept head - HY3 tail + MLY end +link pept head - HY3 tail + MLZ end +link pept head - HY3 tail + M3L end +link pept head - HY3 tail + LEU end +link pept head - HY3 tail + MET end +link pept head - HY3 tail + MSE end +link pept head - HY3 tail + ASN end +link pept head - HY3 tail + PRO end +link pept head - HY3 tail + GLN end +link pept head - HY3 tail + ARG end +link pept head - HY3 tail + SER end +link pept head - HY3 tail + SEC end +link pept head - HY3 tail + SEP end +link pept head - HY3 tail + THR end +link pept head - HY3 tail + THP end +link pept head - HY3 tail + TOP end +link pept head - HY3 tail + VAL end +link pept head - HY3 tail + TRP end +link pept head - HY3 tail + TYR end +link pept head - HY3 tail + TYP end +link pept head - HY3 tail + PTR end +link pept head - HY3 tail + TYS end +link pept head - HY3 tail + HYP end +link pept head - HY3 tail + HY3 end +link pept head - HY3 tail + DDZ end +link pept head - HY3 tail + QSR end +link pept head - HY3 tail + PNS end +link pept head - HY3 tail + CIR end + +{ peptide linkages for DDZ } +link pept head - DDZ tail + ALA end +link pept head - DDZ tail + CYS end +link pept head - DDZ tail + CFE end +link pept head - DDZ tail + CYM end +link pept head - DDZ tail + CYF end +link pept head - DDZ tail + CYC end +link pept head - DDZ tail + CSP end +link pept head - DDZ tail + ASP end +link pept head - DDZ tail + ASH end +link pept head - DDZ tail + GLU end +link pept head - DDZ tail + GLH end +link pept head - DDZ tail + PHE end +link pept head - DDZ tail + HIS end +link pept head - DDZ tail + NEP end +link pept head - DDZ tail + ILE end +link pept head - DDZ tail + LYS end +link pept head - DDZ tail + ALY end +link pept head - DDZ tail + HLY end +link pept head - DDZ tail + MLY end +link pept head - DDZ tail + MLZ end +link pept head - DDZ tail + M3L end +link pept head - DDZ tail + LEU end +link pept head - DDZ tail + MET end +link pept head - DDZ tail + MSE end +link pept head - DDZ tail + ASN end +link pept head - DDZ tail + PRO end +link pept head - DDZ tail + GLN end +link pept head - DDZ tail + ARG end +link pept head - DDZ tail + SER end +link pept head - DDZ tail + SEC end +link pept head - DDZ tail + SEP end +link pept head - DDZ tail + THR end +link pept head - DDZ tail + THP end +link pept head - DDZ tail + TOP end +link pept head - DDZ tail + VAL end +link pept head - DDZ tail + TRP end +link pept head - DDZ tail + TYR end +link pept head - DDZ tail + TYP end +link pept head - DDZ tail + PTR end +link pept head - DDZ tail + TYS end +link pept head - DDZ tail + HYP end +link pept head - DDZ tail + DDZ end +link pept head - DDZ tail + PNS end +link pept head - DDZ tail + QSR end +link pctn head - DDZ tail + CTN end +link pept head - DDZ tail + NME end +link pept head - DDZ tail + CIR end + +{ peptide linkages for PNS } +link pept head - PNS tail + ALA end +link pept head - PNS tail + CYS end +link pept head - PNS tail + CFE end +link pept head - PNS tail + CYM end +link pept head - PNS tail + CYF end +link pept head - PNS tail + CYC end +link pept head - PNS tail + CSP end +link pept head - PNS tail + ASP end +link pept head - PNS tail + ASH end +link pept head - PNS tail + GLU end +link pept head - PNS tail + GLH end +link pept head - PNS tail + PHE end +link pept head - PNS tail + HIS end +link pept head - PNS tail + NEP end +link pept head - PNS tail + ILE end +link pept head - PNS tail + LYS end +link pept head - PNS tail + ALY end +link pept head - PNS tail + HLY end +link pept head - PNS tail + MLY end +link pept head - PNS tail + MLZ end +link pept head - PNS tail + M3L end +link pept head - PNS tail + LEU end +link pept head - PNS tail + MET end +link pept head - PNS tail + MSE end +link pept head - PNS tail + ASN end +link pept head - PNS tail + PRO end +link pept head - PNS tail + GLN end +link pept head - PNS tail + ARG end +link pept head - PNS tail + SER end +link pept head - PNS tail + SEC end +link pept head - PNS tail + SEP end +link pept head - PNS tail + THR end +link pept head - PNS tail + THP end +link pept head - PNS tail + TOP end +link pept head - PNS tail + VAL end +link pept head - PNS tail + TRP end +link pept head - PNS tail + TYR end +link pept head - PNS tail + TYP end +link pept head - PNS tail + PTR end +link pept head - PNS tail + TYS end +link pept head - PNS tail + HYP end +link pept head - PNS tail + HY3 end +link pept head - PNS tail + DDZ end +link pept head - PNS tail + PNS end +link pept head - PNS tail + QSR end +link pctn head - PNS tail + CTN end +link pept head - PNS tail + NME end +link pept head - PNS tail + CIR end + +{ peptide linkages for QSR } +link pept head - QSR tail + ALA end +link pept head - QSR tail + CYS end +link pept head - QSR tail + CFE end +link pept head - QSR tail + CYM end +link pept head - QSR tail + CYF end +link pept head - QSR tail + CYC end +link pept head - QSR tail + CSP end +link pept head - QSR tail + ASP end +link pept head - QSR tail + ASH end +link pept head - QSR tail + GLU end +link pept head - QSR tail + GLH end +link pept head - QSR tail + PHE end +link pept head - QSR tail + HIS end +link pept head - QSR tail + NEP end +link pept head - QSR tail + ILE end +link pept head - QSR tail + LYS end +link pept head - QSR tail + ALY end +link pept head - QSR tail + HLY end +link pept head - QSR tail + MLY end +link pept head - QSR tail + MLZ end +link pept head - QSR tail + M3L end +link pept head - QSR tail + LEU end +link pept head - QSR tail + MET end +link pept head - QSR tail + MSE end +link pept head - QSR tail + ASN end +link pept head - QSR tail + PRO end +link pept head - QSR tail + GLN end +link pept head - QSR tail + ARG end +link pept head - QSR tail + SER end +link pept head - QSR tail + SEC end +link pept head - QSR tail + SEP end +link pept head - QSR tail + THR end +link pept head - QSR tail + THP end +link pept head - QSR tail + TOP end +link pept head - QSR tail + VAL end +link pept head - QSR tail + TRP end +link pept head - QSR tail + TYR end +link pept head - QSR tail + TYP end +link pept head - QSR tail + PTR end +link pept head - QSR tail + TYS end +link pept head - QSR tail + HYP end +link pept head - QSR tail + HY3 end +link pept head - QSR tail + DDZ end +link pept head - QSR tail + PNS end +link pept head - QSR tail + QSR end +link pctn head - QSR tail + CTN end +link pept head - QSR tail + NME end +link pept head - QSR tail + CIR end + +{ peptide linkages for CIR } +link pept head - CIR tail + ALA end +link pept head - CIR tail + CYS end +link pept head - CIR tail + CFE end +link pept head - CIR tail + CYM end +link pept head - CIR tail + CYF end +link pept head - CIR tail + CYC end +link pept head - CIR tail + CSP end +link pept head - CIR tail + ASP end +link pept head - CIR tail + ASH end +link pept head - CIR tail + GLU end +link pept head - CIR tail + GLH end +link pept head - CIR tail + PHE end +link pept head - CIR tail + HIS end +link pept head - CIR tail + NEP end +link pept head - CIR tail + ILE end +link pept head - CIR tail + LYS end +link pept head - CIR tail + ALY end +link pept head - CIR tail + HLY end +link pept head - CIR tail + MLY end +link pept head - CIR tail + MLZ end +link pept head - CIR tail + M3L end +link pept head - CIR tail + LEU end +link pept head - CIR tail + MET end +link pept head - CIR tail + MSE end +link pept head - CIR tail + ASN end +link pept head - CIR tail + PRO end +link pept head - CIR tail + GLN end +link pept head - CIR tail + ARG end +link pept head - CIR tail + SER end +link pept head - CIR tail + SEC end +link pept head - CIR tail + SEP end +link pept head - CIR tail + THR end +link pept head - CIR tail + THP end +link pept head - CIR tail + TOP end +link pept head - CIR tail + VAL end +link pept head - CIR tail + TRP end +link pept head - CIR tail + TYR end +link pept head - CIR tail + TYP end +link pept head - CIR tail + PTR end +link pept head - CIR tail + TYS end +link pept head - CIR tail + HYP end +link pept head - CIR tail + HY3 end +link pept head - CIR tail + DDZ end +link pept head - CIR tail + PNS end +link pept head - CIR tail + QSR end +link pctn head - CIR tail + CTN end +link pept head - CIR tail + NME end +link pept head - CIR tail + CIR end + +first ACET tail + ACE end + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.link b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.link new file mode 100644 index 0000000000000000000000000000000000000000..06268b52324ebbb6c4a10fa6efb795663301f345 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.link @@ -0,0 +1,2761 @@ +remarks file toppar/protein-allhdg5-4.link +remarks +remarks this is a macro to define standard protein peptide bonds +remarks and termini to generate a protein sequence. + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +link ppgp head - GLY tail + PRO end +link ppgp head - GLY tail + HYP end +link ppgp head - GLY tail + HY3 end +link ppgg head - GLY tail + GLY end + +{ special link to GLY} +link ppg1 head - ACE tail + GLY end +link ppg1 head - ALA tail + GLY end +link ppg1 head - CYS tail + GLY end +link ppg1 head - CFE tail + GLY end +link ppg1 head - CYM tail + GLY end +link ppg1 head - CYF tail + GLY end +link ppg1 head - CYC tail + GLY end +link ppg1 head - CSP tail + GLY end +link ppg1 head - ASP tail + GLY end +link ppg1 head - ASH tail + GLY end +link ppg1 head - GLU tail + GLY end +link ppg1 head - GLH tail + GLY end +link ppg1 head - PCA tail + GLY end +link ppg1 head - PHE tail + GLY end +link ppg1 head - HIS tail + GLY end +link ppg1 head - NEP tail + GLY end +link ppg1 head - ILE tail + GLY end +link ppg1 head - LYS tail + GLY end +link ppg1 head - ALY tail + GLY end +link ppg1 head - HLY tail + GLY end +link ppg1 head - MLY tail + GLY end +link ppg1 head - MLZ tail + GLY end +link ppg1 head - M3L tail + GLY end +link ppg1 head - LEU tail + GLY end +link ppg1 head - MET tail + GLY end +link ppg1 head - MSE tail + GLY end ! +link ppg1 head - ASN tail + GLY end +link ppg1 head - PRO tail + GLY end +link ppg1 head - GLN tail + GLY end +link ppg1 head - ARG tail + GLY end +link ppg1 head - SER tail + GLY end +link ppg1 head - SEC tail + GLY end +link ppg1 head - SEP tail + GLY end +link ppg1 head - THR tail + GLY end +link ppg1 head - THP tail + GLY end +link ppg1 head - TOP tail + GLY end +link ppg1 head - VAL tail + GLY end +link ppg1 head - TRP tail + GLY end +link ppg1 head - TYR tail + GLY end +link ppg1 head - TYP tail + GLY end +link ppg1 head - PTR tail + GLY end +link ppg1 head - TYS tail + GLY end +link ppg1 head - HYP tail + GLY end +link ppg1 head - HY3 tail + GLY end +link ppg1 head - DDZ tail + GLY end +link ppg1 head - QSR tail + GLY end +link ppg1 head - PNS tail + GLY end +link ppg1 head - CIR tail + GLY end + +{ special link from GLY} +link ppg2 head - GLY tail + ALA end +link ppg2 head - GLY tail + CYS end +link ppg2 head - GLY tail + CFE end +link ppg2 head - GLY tail + CYM end +link ppg2 head - GLY tail + CYF end +link ppg2 head - GLY tail + CYC end +link ppg2 head - GLY tail + CSP end +link ppg2 head - GLY tail + ASP end +link ppg2 head - GLY tail + ASH end +link ppg2 head - GLY tail + GLU end +link ppg2 head - GLY tail + GLH end +link ppg2 head - GLY tail + PHE end +link ppg2 head - GLY tail + HIS end +link ppg2 head - GLY tail + NEP end +link ppg2 head - GLY tail + ILE end +link ppg2 head - GLY tail + LYS end +link ppg2 head - GLY tail + ALY end +link ppg2 head - GLY tail + HLY end +link ppg2 head - GLY tail + MLY end +link ppg2 head - GLY tail + MLZ end +link ppg2 head - GLY tail + M3L end +link ppg2 head - GLY tail + LEU end +link ppg2 head - GLY tail + MET end +link ppg2 head - GLY tail + MSE end +link ppg2 head - GLY tail + ASN end +link ppg2 head - GLY tail + PRO end +link ppg2 head - GLY tail + GLN end +link ppg2 head - GLY tail + ARG end +link ppg2 head - GLY tail + SER end +link ppg2 head - GLY tail + SEC end +link ppg2 head - GLY tail + SEP end +link ppg2 head - GLY tail + THR end +link ppg2 head - GLY tail + THP end +link ppg2 head - GLY tail + TOP end +link ppg2 head - GLY tail + VAL end +link ppg2 head - GLY tail + TRP end +link ppg2 head - GLY tail + TYR end +link ppg2 head - GLY tail + TYP end +link ppg2 head - GLY tail + PTR end +link ppg2 head - GLY tail + TYS end +link ppg2 head - GLY tail + HYP end +link ppg2 head - GLY tail + HY3 end +link ppg2 head - GLY tail + DDZ end +link ppg2 head - GLY tail + PNS end +link ppg2 head - GLY tail + QSR end +link ppg2 head - CIR tail + GLY end +link pctn head - GLY tail + CTN end +link pept head - GLY tail + NME end + +{ special link to PRO} +link pepp head - ACE tail + PRO end +link pepp head - ALA tail + PRO end +link pepp head - CYS tail + PRO end +link pepp head - CFE tail + PRO end +link pepp head - CYM tail + PRO end +link pepp head - CYF tail + PRO end +link pepp head - CYC tail + PRO end +link pepp head - CSP tail + PRO end +link pepp head - ASP tail + PRO end +link pepp head - ASH tail + PRO end +link pepp head - GLU tail + PRO end +link pepp head - GLH tail + PRO end +link pepp head - PCA tail + PRO end +link pepp head - PHE tail + PRO end +link pepp head - HIS tail + PRO end +link pepp head - NEP tail + PRO end +link pepp head - ILE tail + PRO end +link pepp head - LYS tail + PRO end +link pepp head - ALY tail + PRO end +link pepp head - HLY tail + PRO end +link pepp head - MLY tail + PRO end +link pepp head - MLZ tail + PRO end +link pepp head - M3L tail + PRO end +link pepp head - LEU tail + PRO end +link pepp head - MET tail + PRO end +link pepp head - MSE tail + PRO end +link pepp head - ASN tail + PRO end +link pepp head - PRO tail + PRO end +link pepp head - GLN tail + PRO end +link pepp head - ARG tail + PRO end +link pepp head - SER tail + PRO end +link pepp head - SEC tail + PRO end +link pepp head - SEP tail + PRO end +link pepp head - THR tail + PRO end +link pepp head - THP tail + PRO end +link pepp head - TOP tail + PRO end +link pepp head - VAL tail + PRO end +link pepp head - TRP tail + PRO end +link pepp head - TYR tail + PRO end +link pepp head - TYP tail + PRO end +link pepp head - PTR tail + PRO end +link pepp head - TYS tail + PRO end +link pepp head - HYP tail + PRO end +link pepp head - HY3 tail + PRO end +link pepp head - QSR tail + PRO end +link pepp head - CIR tail + PRO end + +{ special link to HYP} +link pepp head - ACE tail + HYP end +link pepp head - ALA tail + HYP end +link pepp head - CYS tail + HYP end +link pepp head - CFE tail + HYP end +link pepp head - CYM tail + HYP end +link pepp head - CYF tail + HYP end +link pepp head - CYC tail + HYP end +link pepp head - CSP tail + HYP end +link pepp head - ASP tail + HYP end +link pepp head - ASH tail + HYP end +link pepp head - GLU tail + HYP end +link pepp head - GLH tail + HYP end +link pepp head - PCA tail + HYP end +link pepp head - PHE tail + HYP end +link pepp head - HIS tail + HYP end +link pepp head - NEP tail + HYP end +link pepp head - ILE tail + HYP end +link pepp head - LYS tail + HYP end +link pepp head - ALY tail + HYP end +link pepp head - HLY tail + HYP end +link pepp head - MLY tail + HYP end +link pepp head - MLZ tail + HYP end +link pepp head - M3L tail + HYP end +link pepp head - LEU tail + HYP end +link pepp head - MET tail + HYP end +link pepp head - MSE tail + HYP end +link pepp head - ASN tail + HYP end +link pepp head - PRO tail + HYP end +link pepp head - GLN tail + HYP end +link pepp head - ARG tail + HYP end +link pepp head - SER tail + HYP end +link pepp head - SEC tail + HYP end +link pepp head - SEP tail + HYP end +link pepp head - THR tail + HYP end +link pepp head - THP tail + HYP end +link pepp head - TOP tail + HYP end +link pepp head - VAL tail + HYP end +link pepp head - TRP tail + HYP end +link pepp head - TYR tail + HYP end +link pepp head - TYP tail + HYP end +link pepp head - PTR tail + HYP end +link pepp head - TYS tail + HYP end +link pepp head - HYP tail + HYP end +link pepp head - HY3 tail + HYP end +link pepp head - DDZ tail + HYP end +link pepp head - PNS tail + HYP end +link pepp head - QSR tail + HYP end +link pepp head - CIR tail + HYP end + +{ special link to HYP} +link pepp head - ACE tail + HY3 end +link pepp head - ALA tail + HY3 end +link pepp head - CYS tail + HY3 end +link pepp head - CFE tail + HY3 end +link pepp head - CYM tail + HY3 end +link pepp head - CYF tail + HY3 end +link pepp head - CYC tail + HY3 end +link pepp head - CSP tail + HY3 end +link pepp head - ASP tail + HY3 end +link pepp head - ASH tail + HY3 end +link pepp head - GLU tail + HY3 end +link pepp head - GLH tail + HY3 end +link pepp head - PCA tail + HY3 end +link pepp head - PHE tail + HY3 end +link pepp head - HIS tail + HY3 end +link pepp head - NEP tail + HY3 end +link pepp head - ILE tail + HY3 end +link pepp head - LYS tail + HY3 end +link pepp head - ALY tail + HY3 end +link pepp head - HLY tail + HY3 end +link pepp head - MLY tail + HY3 end +link pepp head - MLZ tail + HY3 end +link pepp head - M3L tail + HY3 end +link pepp head - LEU tail + HY3 end +link pepp head - MET tail + HY3 end +link pepp head - MSE tail + HY3 end +link pepp head - ASN tail + HY3 end +link pepp head - PRO tail + HY3 end +link pepp head - GLN tail + HY3 end +link pepp head - ARG tail + HY3 end +link pepp head - SER tail + HY3 end +link pepp head - SEC tail + HY3 end +link pepp head - SEP tail + HY3 end +link pepp head - THR tail + HY3 end +link pepp head - THP tail + HY3 end +link pepp head - TOP tail + HY3 end +link pepp head - VAL tail + HY3 end +link pepp head - TRP tail + HY3 end +link pepp head - TYR tail + HY3 end +link pepp head - TYP tail + HY3 end +link pepp head - PTR tail + HY3 end +link pepp head - TYS tail + HY3 end +link pepp head - HYP tail + HY3 end +link pepp head - HY3 tail + HY3 end +link pepp head - DDZ tail + HY3 end +link pepp head - PNS tail + HY3 end +link pepp head - QSR tail + HY3 end +link pepp head - CIR tail + HY3 end + +{ peptide linkages for ACE } +link pept head - ACE tail + ALA end +link pept head - ACE tail + CYS end +link pept head - ACE tail + CFE end +link pept head - ACE tail + CYM end +link pept head - ACE tail + CYF end +link pept head - ACE tail + CYC end +link pept head - ACE tail + CSP end +link pept head - ACE tail + ASP end +link pept head - ACE tail + ASH end +link pept head - ACE tail + GLU end +link pept head - ACE tail + GLH end +link pept head - ACE tail + PHE end +link pept head - ACE tail + HIS end +link pept head - ACE tail + NEP end +link pept head - ACE tail + ILE end +link pept head - ACE tail + LYS end +link pept head - ACE tail + ALY end +link pept head - ACE tail + HLY end +link pept head - ACE tail + MLY end +link pept head - ACE tail + MLZ end +link pept head - ACE tail + M3L end +link pept head - ACE tail + LEU end +link pept head - ACE tail + MET end +link pept head - ACE tail + MSE end +link pept head - ACE tail + ASN end +link pept head - ACE tail + PRO end +link pept head - ACE tail + GLN end +link pept head - ACE tail + ARG end +link pept head - ACE tail + SER end +link pept head - ACE tail + SEC end +link pept head - ACE tail + SEP end +link pept head - ACE tail + THR end +link pept head - ACE tail + THP end +link pept head - ACE tail + TOP end +link pept head - ACE tail + VAL end +link pept head - ACE tail + TRP end +link pept head - ACE tail + TYR end +link pept head - ACE tail + TYP end +link pept head - ACE tail + PTR end +link pept head - ACE tail + TYS end +link pept head - ACE tail + HYP end +link pept head - ACE tail + HY3 end +link pept head - ACE tail + DDZ end +link pept head - ACE tail + PNS end +link pept head - ACE tail + QSR end +link pctn head - ACE tail + CTN end +link pept head - ACE tail + NME end +link pept head - ACE tail + CIR end + +{ peptide linkages for ALA } +link pept head - ALA tail + ALA end +link pept head - ALA tail + CYS end +link pept head - ALA tail + CFE end +link pept head - ALA tail + CYM end +link pept head - ALA tail + CYF end +link pept head - ALA tail + CYC end +link pept head - ALA tail + CSP end +link pept head - ALA tail + ASP end +link pept head - ALA tail + ASH end +link pept head - ALA tail + GLU end +link pept head - ALA tail + GLH end +link pept head - ALA tail + PHE end +link pept head - ALA tail + HIS end +link pept head - ALA tail + NEP end +link pept head - ALA tail + ILE end +link pept head - ALA tail + LYS end +link pept head - ALA tail + ALY end +link pept head - ALA tail + HLY end +link pept head - ALA tail + MLY end +link pept head - ALA tail + MLZ end +link pept head - ALA tail + M3L end +link pept head - ALA tail + LEU end +link pept head - ALA tail + MET end +link pept head - ALA tail + MSE end +link pept head - ALA tail + ASN end +link pept head - ALA tail + PRO end +link pept head - ALA tail + GLN end +link pept head - ALA tail + ARG end +link pept head - ALA tail + SER end +link pept head - ALA tail + SEC end +link pept head - ALA tail + SEP end +link pept head - ALA tail + THR end +link pept head - ALA tail + THP end +link pept head - ALA tail + TOP end +link pept head - ALA tail + VAL end +link pept head - ALA tail + TRP end +link pept head - ALA tail + TYR end +link pept head - ALA tail + TYP end +link pept head - ALA tail + PTR end +link pept head - ALA tail + TYS end +link pept head - ALA tail + HYP end +link pept head - ALA tail + HY3 end +link pept head - ALA tail + DDZ end +link pept head - ALA tail + PNS end +link pept head - ALA tail + QSR end +link pctn head - ALA tail + CTN end +link pept head - ALA tail + NME end +link pept head - ALA tail + CIR end + +{ peptide linkages for CYS } +link pept head - CYS tail + ALA end +link pept head - CYS tail + CYS end +link pept head - CYS tail + CFE end +link pept head - CYS tail + CYM end +link pept head - CYS tail + CYF end +link pept head - CYS tail + CYC end +link pept head - CYS tail + CSP end +link pept head - CYS tail + ASP end +link pept head - CYS tail + ASH end +link pept head - CYS tail + GLU end +link pept head - CYS tail + GLH end +link pept head - CYS tail + PHE end +link pept head - CYS tail + HIS end +link pept head - CYS tail + NEP end +link pept head - CYS tail + ILE end +link pept head - CYS tail + LYS end +link pept head - CYS tail + ALY end +link pept head - CYS tail + HLY end +link pept head - CYS tail + MLY end +link pept head - CYS tail + MLZ end +link pept head - CYS tail + M3L end +link pept head - CYS tail + LEU end +link pept head - CYS tail + MET end +link pept head - CYS tail + MSE end +link pept head - CYS tail + ASN end +link pept head - CYS tail + PRO end +link pept head - CYS tail + GLN end +link pept head - CYS tail + ARG end +link pept head - CYS tail + SER end +link pept head - CYS tail + SEC end +link pept head - CYS tail + SEP end +link pept head - CYS tail + THR end +link pept head - CYS tail + THP end +link pept head - CYS tail + TOP end +link pept head - CYS tail + VAL end +link pept head - CYS tail + TRP end +link pept head - CYS tail + TYR end +link pept head - CYS tail + TYP end +link pept head - CYS tail + PTR end +link pept head - CYS tail + TYS end +link pept head - CYS tail + HYP end +link pept head - CYS tail + HY3 end +link pept head - CYS tail + DDZ end +link pept head - CYS tail + PNS end +link pept head - CYS tail + QSR end +link pctn head - CYS tail + CTN end +link pept head - CYS tail + NME end +link pept head - CYS tail + CIR end + +{ peptide linkages for CFE } +link pept head - CFE tail + ALA end +link pept head - CFE tail + CYS end +link pept head - CFE tail + CFE end +link pept head - CFE tail + CYM end +link pept head - CFE tail + CYF end +link pept head - CFE tail + CYC end +link pept head - CFE tail + CSP end +link pept head - CFE tail + ASP end +link pept head - CFE tail + ASH end +link pept head - CFE tail + GLU end +link pept head - CFE tail + GLH end +link pept head - CFE tail + PHE end +link pept head - CFE tail + HIS end +link pept head - CFE tail + NEP end +link pept head - CFE tail + ILE end +link pept head - CFE tail + LYS end +link pept head - CFE tail + ALY end +link pept head - CFE tail + HLY end +link pept head - CFE tail + MLY end +link pept head - CFE tail + MLZ end +link pept head - CFE tail + M3L end +link pept head - CFE tail + LEU end +link pept head - CFE tail + MET end +link pept head - CFE tail + MSE end +link pept head - CFE tail + ASN end +link pept head - CFE tail + PRO end +link pept head - CFE tail + GLN end +link pept head - CFE tail + ARG end +link pept head - CFE tail + SER end +link pept head - CFE tail + SEC end +link pept head - CFE tail + SEP end +link pept head - CFE tail + THR end +link pept head - CFE tail + THP end +link pept head - CFE tail + TOP end +link pept head - CFE tail + VAL end +link pept head - CFE tail + TRP end +link pept head - CFE tail + TYR end +link pept head - CFE tail + TYP end +link pept head - CFE tail + PTR end +link pept head - CFE tail + TYS end +link pept head - CFE tail + HYP end +link pept head - CFE tail + HY3 end +link pept head - CFE tail + DDZ end +link pept head - CFE tail + PNS end +link pept head - CFE tail + QSR end +link pctn head - CFE tail + CTN end +link pept head - CFE tail + NME end +link pept head - CFE tail + CIR end + +{ peptide linkages for CYM } +link pept head - CYM tail + ALA end +link pept head - CYM tail + CYS end +link pept head - CYM tail + CFE end +link pept head - CYM tail + CYM end +link pept head - CYM tail + CYF end +link pept head - CYM tail + CYC end +link pept head - CYM tail + CSP end +link pept head - CYM tail + ASP end +link pept head - CYM tail + ASH end +link pept head - CYM tail + GLU end +link pept head - CYM tail + GLH end +link pept head - CYM tail + PHE end +link pept head - CYM tail + HIS end +link pept head - CYM tail + NEP end +link pept head - CYM tail + ILE end +link pept head - CYM tail + LYS end +link pept head - CYM tail + ALY end +link pept head - CYM tail + HLY end +link pept head - CYM tail + MLY end +link pept head - CYM tail + MLZ end +link pept head - CYM tail + M3L end +link pept head - CYM tail + LEU end +link pept head - CYM tail + MET end +link pept head - CYM tail + MSE end +link pept head - CYM tail + ASN end +link pept head - CYM tail + PRO end +link pept head - CYM tail + GLN end +link pept head - CYM tail + ARG end +link pept head - CYM tail + SER end +link pept head - CYM tail + SEC end +link pept head - CYM tail + SEP end +link pept head - CYM tail + THR end +link pept head - CYM tail + THP end +link pept head - CYM tail + TOP end +link pept head - CYM tail + VAL end +link pept head - CYM tail + TRP end +link pept head - CYM tail + TYR end +link pept head - CYM tail + TYP end +link pept head - CYM tail + PTR end +link pept head - CYM tail + TYS end +link pept head - CYM tail + HYP end +link pept head - CYM tail + HY3 end +link pept head - CYM tail + DDZ end +link pept head - CYM tail + PNS end +link pept head - CYM tail + QSR end +link pctn head - CYM tail + CTN end +link pept head - CYM tail + NME end +link pept head - CYM tail + CIR end + +{ peptide linkages for CYF } +link pept head - CYF tail + ALA end +link pept head - CYF tail + CYS end +link pept head - CYF tail + CYC end +link pept head - CYF tail + CFE end +link pept head - CYF tail + CYM end +link pept head - CYF tail + CYF end +link pept head - CYF tail + CSP end +link pept head - CYF tail + ASP end +link pept head - CYF tail + ASH end +link pept head - CYF tail + GLU end +link pept head - CYF tail + GLH end +link pept head - CYF tail + PHE end +link pept head - CYF tail + HIS end +link pept head - CYF tail + NEP end +link pept head - CYF tail + ILE end +link pept head - CYF tail + LYS end +link pept head - CYF tail + ALY end +link pept head - CYF tail + HLY end +link pept head - CYF tail + MLY end +link pept head - CYF tail + MLZ end +link pept head - CYF tail + M3L end +link pept head - CYF tail + LEU end +link pept head - CYF tail + MET end +link pept head - CYF tail + MSE end +link pept head - CYF tail + ASN end +link pept head - CYF tail + PRO end +link pept head - CYF tail + GLN end +link pept head - CYF tail + ARG end +link pept head - CYF tail + SER end +link pept head - CYF tail + SEC end +link pept head - CYF tail + SEP end +link pept head - CYF tail + THR end +link pept head - CYF tail + THP end +link pept head - CYF tail + TOP end +link pept head - CYF tail + VAL end +link pept head - CYF tail + TRP end +link pept head - CYF tail + TYR end +link pept head - CYF tail + TYP end +link pept head - CYF tail + PTR end +link pept head - 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SEC tail + SER end +link pept head - SEC tail + SEC end +link pept head - SEC tail + SEP end +link pept head - SEC tail + THR end +link pept head - SEC tail + THP end +link pept head - SEC tail + TOP end +link pept head - SEC tail + VAL end +link pept head - SEC tail + TRP end +link pept head - SEC tail + TYR end +link pept head - SEC tail + TYP end +link pept head - SEC tail + PTR end +link pept head - SEC tail + TYS end +link pept head - SEC tail + HYP end +link pept head - SEC tail + HY3 end +link pept head - SEC tail + DDZ end +link pept head - SEC tail + PNS end +link pept head - SEC tail + QSR end +link pctn head - SEC tail + CTN end +link pept head - SEC tail + NME end +link pept head - SEC tail + CIR end + +{ peptide linkages for SEP } +link pept head - SEP tail + ALA end +link pept head - SEP tail + CYS end +link pept head - SEP tail + CFE end +link pept head - SEP tail + CYM end +link pept head - SEP tail + CYF end +link pept head - SEP tail + CYC end +link pept head - SEP tail + CSP end +link pept head - SEP tail + ASP end +link pept head - SEP tail + ASH end +link pept head - SEP tail + GLU end +link pept head - SEP tail + GLH end +link pept head - SEP tail + PHE end +link pept head - SEP tail + HIS end +link pept head - SEP tail + NEP end +link pept head - SEP tail + ILE end +link pept head - SEP tail + LYS end +link pept head - SEP tail + ALY end +link pept head - SEP tail + HLY end +link pept head - SEP tail + MLY end +link pept head - SEP tail + MLZ end +link pept head - SEP tail + M3L end +link pept head - SEP tail + LEU end +link pept head - SEP tail + MET end +link pept head - SEP tail + MSE end +link pept head - SEP tail + ASN end +link pept head - SEP tail + PRO end +link pept head - SEP tail + GLN end +link pept head - SEP tail + ARG end +link pept head - SEP tail + SER end +link pept head - SEP tail + SEC end +link pept head - SEP tail + SEP end +link pept head - SEP tail + THR end +link pept head - SEP tail + THP end +link pept head - SEP tail + TOP end +link pept head - SEP tail + VAL end +link pept head - SEP tail + TRP end +link pept head - SEP tail + TYR end +link pept head - SEP tail + TYP end +link pept head - SEP tail + PTR end +link pept head - SEP tail + TYS end +link pept head - SEP tail + HYP end +link pept head - SEP tail + HY3 end +link pept head - SEP tail + DDZ end +link pept head - SEP tail + PNS end +link pept head - SEP tail + QSR end +link pctn head - SEP tail + CTN end +link pept head - SEP tail + NME end +link pept head - SEP tail + CIR end + +{ peptide linkages for THR } +link pept head - THR tail + ALA end +link pept head - THR tail + CYS end +link pept head - THR tail + CFE end +link pept head - THR tail + CYM end +link pept head - THR tail + CYF end +link pept head - THR tail + CYC end +link pept head - THR tail + CSP end +link pept head - THR tail + ASP end +link pept head - THR tail + ASH end +link pept head - THR tail + GLU end +link pept head - THR tail + GLH end +link pept head - THR tail + PHE end +link pept head - THR tail + HIS end +link pept head - THR tail + NEP end +link pept head - THR tail + ILE end +link pept head - THR tail + LYS end +link pept head - THR tail + ALY end +link pept head - THR tail + HLY end +link pept head - THR tail + MLY end +link pept head - THR tail + MLZ end +link pept head - THR tail + M3L end +link pept head - THR tail + LEU end +link pept head - THR tail + MET end +link pept head - THR tail + MSE end +link pept head - THR tail + ASN end +link pept head - THR tail + PRO end +link pept head - THR tail + GLN end +link pept head - THR tail + ARG end +link pept head - THR tail + SER end +link pept head - THR tail + SEC end +link pept head - THR tail + SEP end +link pept head - THR tail + THR end +link pept head - THR tail + THP end +link pept head - THR tail + TOP end +link pept head - THR tail + VAL end +link pept head - THR tail + TRP end +link pept head - THR tail + TYR end +link pept head - THR tail + TYP end +link pept head - THR tail + PTR end +link pept head - THR tail + TYS end +link pept head - THR tail + HYP end +link pept head - THR tail + HY3 end +link pept head - THR tail + DDZ end +link pept head - THR tail + PNS end +link pept head - THR tail + QSR end +link pctn head - THR tail + CTN end +link pept head - THR tail + NME end +link pept head - THR tail + CIR end + +{ peptide linkages for THP } +link pept head - THP tail + ALA end +link pept head - THP tail + CYS end +link pept head - THP tail + CFE end +link pept head - THP tail + CYM end +link pept head - THP tail + CYF end +link pept head - THP tail + CYC end +link pept head - THP tail + CSP end +link pept head - THP tail + ASP end +link pept head - THP tail + ASH end +link pept head - THP tail + GLU end +link pept head - THP tail + GLH end +link pept head - THP tail + PHE end +link pept head - THP tail + HIS end +link pept head - THP tail + NEP end +link pept head - THP tail + ILE end +link pept head - THP tail + LYS end +link pept head - THP tail + ALY end +link pept head - THP tail + HLY end +link pept head - THP tail + MLY end +link pept head - THP tail + MLZ end +link pept head - THP tail + M3L end +link pept head - THP tail + LEU end +link pept head - THP tail + MET end +link pept head - THP tail + MSE end +link pept head - THP tail + ASN end +link pept head - THP tail + PRO end +link pept head - THP tail + GLN end +link pept head - THP tail + ARG end +link pept head - THP tail + SER end +link pept head - THP tail + SEC end +link pept head - THP tail + SEP end +link pept head - THP tail + THR end +link pept head - THP tail + THP end +link pept head - THP tail + TOP end +link pept head - THP tail + VAL end +link pept head - THP tail + TRP end +link pept head - THP tail + TYR end +link pept head - THP tail + TYP end +link pept head - THP tail + PTR end +link pept head - THP tail + TYS end +link pept head - THP tail + HYP end +link pept head - THP tail + HY3 end +link pept head - THP tail + DDZ end +link pept head - THP tail + PNS end +link pept head - THP tail + QSR end +link pctn head - THP tail + CTN end +link pept head - THP tail + NME end +link pept head - THP tail + CIR end + +{ peptide linkages for TOP } +link pept head - TOP tail + ALA end +link pept head - TOP tail + CYS end +link pept head - TOP tail + CFE end +link pept head - TOP tail + CYM end +link pept head - TOP tail + CYF end +link pept head - TOP tail + CYC end +link pept head - TOP tail + CSP end +link pept head - TOP tail + ASP end +link pept head - TOP tail + ASH end +link pept head - TOP tail + GLU end +link pept head - TOP tail + GLH end +link pept head - TOP tail + PHE end +link pept head - TOP tail + HIS end +link pept head - TOP tail + NEP end +link pept head - TOP tail + ILE end +link pept head - TOP tail + LYS end +link pept head - TOP tail + ALY end +link pept head - TOP tail + HLY end +link pept head - TOP tail + MLY end +link pept head - TOP tail + MLZ end +link pept head - TOP tail + M3L end +link pept head - TOP tail + LEU end +link pept head - TOP tail + MET end +link pept head - TOP tail + MSE end +link pept head - TOP tail + ASN end +link pept head - TOP tail + PRO end +link pept head - TOP tail + GLN end +link pept head - TOP tail + ARG end +link pept head - TOP tail + SER end +link pept head - TOP tail + SEC end +link pept head - TOP tail + SEP end +link pept head - TOP tail + THR end +link pept head - TOP tail + THP end +link pept head - TOP tail + TOP end +link pept head - TOP tail + VAL end +link pept head - TOP tail + TRP end +link pept head - TOP tail + TYR end +link pept head - TOP tail + TYP end +link pept head - TOP tail + PTR end +link pept head - TOP tail + TYS end +link pept head - TOP tail + HYP end +link pept head - TOP tail + HY3 end +link pept head - TOP tail + DDZ end +link pept head - TOP tail + PNS end +link pept head - TOP tail + QSR end +link pctn head - TOP tail + CTN end +link pept head - TOP tail + NME end +link pept head - TOP tail + CIR end + +{ peptide linkages for VAL } +link pept head - VAL tail + ALA end +link pept head - VAL tail + CYS end +link pept head - VAL tail + CFE end +link pept head - VAL tail + CYM end +link pept head - VAL tail + CYF end +link pept head - VAL tail + CYC end +link pept head - VAL tail + CSP end +link pept head - VAL tail + ASP end +link pept head - VAL tail + ASH end +link pept head - VAL tail + GLU end +link pept head - VAL tail + GLH end +link pept head - VAL tail + PHE end +link pept head - VAL tail + HIS end +link pept head - VAL tail + NEP end +link pept head - VAL tail + ILE end +link pept head - VAL tail + LYS end +link pept head - VAL tail + ALY end +link pept head - VAL tail + HLY end +link pept head - VAL tail + MLY end +link pept head - VAL tail + MLZ end +link pept head - VAL tail + M3L end +link pept head - VAL tail + LEU end +link pept head - VAL tail + MET end +link pept head - VAL tail + MSE end +link pept head - VAL tail + ASN end +link pept head - VAL tail + PRO end +link pept head - VAL tail + GLN end +link pept head - VAL tail + ARG end +link pept head - VAL tail + SER end +link pept head - VAL tail + SEC end +link pept head - VAL tail + SEP end +link pept head - VAL tail + THR end +link pept head - VAL tail + THP end +link pept head - VAL tail + TOP end +link pept head - VAL tail + VAL end +link pept head - VAL tail + TRP end +link pept head - VAL tail + TYR end +link pept head - VAL tail + TYP end +link pept head - VAL tail + PTR end +link pept head - VAL tail + TYS end +link pept head - VAL tail + HYP end +link pept head - VAL tail + HY3 end +link pept head - VAL tail + DDZ end +link pept head - VAL tail + PNS end +link pept head - VAL tail + QSR end +link pctn head - VAL tail + CTN end +link pept head - VAL tail + NME end +link pept head - VAL tail + CIR end + +{ peptide linkages for TRP } +link pept head - TRP tail + ALA end +link pept head - TRP tail + CYS end +link pept head - TRP tail + CFE end +link pept head - TRP tail + CYM end +link pept head - TRP tail + CYF end +link pept head - TRP tail + CYC end +link pept head - TRP tail + CSP end +link pept head - TRP tail + ASP end +link pept head - TRP tail + ASH end +link pept head - TRP tail + GLU end +link pept head - TRP tail + GLH end +link pept head - TRP tail + PHE end +link pept head - TRP tail + HIS end +link pept head - TRP tail + NEP end +link pept head - TRP tail + ILE end +link pept head - TRP tail + LYS end +link pept head - TRP tail + ALY end +link pept head - TRP tail + HLY end +link pept head - TRP tail + MLY end +link pept head - TRP tail + MLZ end +link pept head - TRP tail + M3L end +link pept head - TRP tail + LEU end +link pept head - TRP tail + MET end +link pept head - TRP tail + MSE end +link pept head - TRP tail + ASN end +link pept head - TRP tail + PRO end +link pept head - TRP tail + GLN end +link pept head - TRP tail + ARG end +link pept head - TRP tail + SER end +link pept head - TRP tail + SEC end +link pept head - TRP tail + SEP end +link pept head - TRP tail + THR end +link pept head - TRP tail + THP end +link pept head - TRP tail + TOP end +link pept head - TRP tail + VAL end +link pept head - TRP tail + TRP end +link pept head - TRP tail + TYR end +link pept head - TRP tail + TYP end +link pept head - TRP tail + PTR end +link pept head - TRP tail + TYS end +link pept head - TRP tail + HYP end +link pept head - TRP tail + HY3 end +link pept head - TRP tail + DDZ end +link pept head - TRP tail + PNS end +link pept head - TRP tail + QSR end +link pctn head - TRP tail + CTN end +link pept head - TRP tail + NME end +link pept head - TRP tail + CIR end + +{ peptide linkages for TYR } +link pept head - TYR tail + ALA end +link pept head - TYR tail + CYS end +link pept head - TYR tail + CFE end +link pept head - TYR tail + CYM end +link pept head - TYR tail + CYF end +link pept head - TYR tail + CYC end +link pept head - TYR tail + CSP end +link pept head - TYR tail + ASP end +link pept head - TYR tail + ASH end +link pept head - TYR tail + GLU end +link pept head - TYR tail + GLH end +link pept head - TYR tail + PHE end +link pept head - TYR tail + HIS end +link pept head - TYR tail + NEP end +link pept head - TYR tail + ILE end +link pept head - TYR tail + LYS end +link pept head - TYR tail + ALY end +link pept head - TYR tail + HLY end +link pept head - TYR tail + MLY end +link pept head - TYR tail + MLZ end +link pept head - TYR tail + M3L end +link pept head - TYR tail + LEU end +link pept head - TYR tail + MET end +link pept head - TYR tail + MSE end +link pept head - TYR tail + ASN end +link pept head - TYR tail + PRO end +link pept head - TYR tail + GLN end +link pept head - TYR tail + ARG end +link pept head - TYR tail + SER end +link pept head - TYR tail + SEC end +link pept head - TYR tail + SEP end +link pept head - TYR tail + THR end +link pept head - TYR tail + THP end +link pept head - TYR tail + TOP end +link pept head - TYR tail + VAL end +link pept head - TYR tail + TRP end +link pept head - TYR tail + TYR end +link pept head - TYR tail + TYP end +link pept head - TYR tail + PTR end +link pept head - TYR tail + TYS end +link pept head - TYR tail + HYP end +link pept head - TYR tail + HY3 end +link pept head - TYR tail + DDZ end +link pept head - TYR tail + PNS end +link pept head - TYR tail + QSR end +link pctn head - TYR tail + CTN end +link pept head - TYR tail + NME end +link pept head - TYR tail + CIR end + +{ peptide linkages for TYP } +link pept head - TYP tail + ALA end +link pept head - TYP tail + CYS end +link pept head - TYP tail + CFE end +link pept head - TYP tail + CYM end +link pept head - TYP tail + CYF end +link pept head - TYP tail + CYC end +link pept head - TYP tail + CSP end +link pept head - TYP tail + ASP end +link pept head - TYP tail + ASH end +link pept head - TYP tail + GLU end +link pept head - TYP tail + GLH end +link pept head - TYP tail + PHE end +link pept head - TYP tail + HIS end +link pept head - TYP tail + NEP end +link pept head - TYP tail + ILE end +link pept head - TYP tail + LYS end +link pept head - TYP tail + ALY end +link pept head - TYP tail + HLY end +link pept head - TYP tail + MLY end +link pept head - TYP tail + MLZ end +link pept head - TYP tail + M3L end +link pept head - TYP tail + LEU end +link pept head - TYP tail + MET end +link pept head - TYP tail + MSE end +link pept head - TYP tail + ASN end +link pept head - TYP tail + PRO end +link pept head - TYP tail + GLN end +link pept head - TYP tail + ARG end +link pept head - TYP tail + SER end +link pept head - TYP tail + SEC end +link pept head - TYP tail + SEP end +link pept head - TYP tail + THR end +link pept head - TYP tail + THP end +link pept head - TYP tail + TOP end +link pept head - TYP tail + VAL end +link pept head - TYP tail + TRP end +link pept head - TYP tail + TYR end +link pept head - TYP tail + TYP end +link pept head - TYP tail + PTR end +link pept head - TYP tail + TYS end +link pept head - TYP tail + HYP end +link pept head - TYP tail + HY3 end +link pept head - TYP tail + DDZ end +link pept head - TYP tail + PNS end +link pept head - TYP tail + QSR end +link pctn head - TYP tail + CTN end +link pept head - TYP tail + NME end +link pept head - TYP tail + CIR end + +{ peptide linkages for PTR - same as TYP } +link pept head - PTR tail + ALA end +link pept head - PTR tail + CYS end +link pept head - PTR tail + CFE end +link pept head - PTR tail + CYM end +link pept head - PTR tail + CYF end +link pept head - PTR tail + CYC end +link pept head - PTR tail + CSP end +link pept head - PTR tail + ASP end +link pept head - PTR tail + ASH end +link pept head - PTR tail + GLU end +link pept head - PTR tail + GLH end +link pept head - PTR tail + PHE end +link pept head - PTR tail + HIS end +link pept head - PTR tail + NEP end +link pept head - PTR tail + ILE end +link pept head - PTR tail + LYS end +link pept head - PTR tail + ALY end +link pept head - PTR tail + HLY end +link pept head - PTR tail + MLY end +link pept head - PTR tail + MLZ end +link pept head - PTR tail + M3L end +link pept head - PTR tail + LEU end +link pept head - PTR tail + MET end +link pept head - PTR tail + MSE end +link pept head - PTR tail + ASN end +link pept head - PTR tail + PRO end +link pept head - PTR tail + GLN end +link pept head - PTR tail + ARG end +link pept head - PTR tail + SER end +link pept head - PTR tail + SEC end +link pept head - PTR tail + SEP end +link pept head - PTR tail + THR end +link pept head - PTR tail + THP end +link pept head - PTR tail + TOP end +link pept head - PTR tail + VAL end +link pept head - PTR tail + TRP end +link pept head - PTR tail + TYR end +link pept head - PTR tail + TYP end +link pept head - PTR tail + PTR end +link pept head - PTR tail + TYS end +link pept head - PTR tail + HYP end +link pept head - PTR tail + HY3 end +link pept head - PTR tail + DDZ end +link pept head - PTR tail + PNS end +link pept head - PTR tail + QSR end +link pctn head - PTR tail + CTN end +link pept head - PTR tail + NME end +link pept head - PTR tail + CIR end + +{ peptide linkages for TYS } +link pept head - TYS tail + ALA end +link pept head - TYS tail + CYS end +link pept head - TYS tail + CFE end +link pept head - TYS tail + CYM end +link pept head - TYS tail + CYF end +link pept head - TYS tail + CYC end +link pept head - TYS tail + CSP end +link pept head - TYS tail + ASP end +link pept head - TYS tail + ASH end +link pept head - TYS tail + GLU end +link pept head - TYS tail + GLH end +link pept head - TYS tail + PHE end +link pept head - TYS tail + HIS end +link pept head - TYS tail + NEP end +link pept head - TYS tail + ILE end +link pept head - TYS tail + LYS end +link pept head - TYS tail + ALY end +link pept head - TYS tail + HLY end +link pept head - TYS tail + MLY end +link pept head - TYS tail + MLZ end +link pept head - TYS tail + M3L end +link pept head - TYS tail + LEU end +link pept head - TYS tail + MET end +link pept head - TYS tail + MSE end +link pept head - TYS tail + ASN end +link pept head - TYS tail + PRO end +link pept head - TYS tail + GLN end +link pept head - TYS tail + ARG end +link pept head - TYS tail + SER end +link pept head - TYS tail + SEC end +link pept head - TYS tail + SEP end +link pept head - TYS tail + THR end +link pept head - TYS tail + THP end +link pept head - TYS tail + TOP end +link pept head - TYS tail + VAL end +link pept head - TYS tail + TRP end +link pept head - TYS tail + TYR end +link pept head - TYS tail + TYP end +link pept head - TYS tail + PTR end +link pept head - TYS tail + TYS end +link pept head - TYS tail + HYP end +link pept head - TYS tail + HY3 end +link pept head - TYS tail + DDZ end +link pept head - TYS tail + PNS end +link pept head - TYS tail + QSR end +link pctn head - TYS tail + CTN end +link pept head - TYS tail + NME end +link pept head - TYS tail + CIR end + +{ peptide linkages for HYP } +link pept head - HYP tail + ALA end +link pept head - HYP tail + CYS end +link pept head - HYP tail + CFE end +link pept head - HYP tail + CYM end +link pept head - HYP tail + CYF end +link pept head - HYP tail + CYC end +link pept head - HYP tail + CSP end +link pept head - HYP tail + ASP end +link pept head - HYP tail + ASH end +link pept head - HYP tail + GLU end +link pept head - HYP tail + GLH end +link pept head - HYP tail + PHE end +link pept head - HYP tail + HIS end +link pept head - HYP tail + NEP end +link pept head - HYP tail + ILE end +link pept head - HYP tail + LYS end +link pept head - HYP tail + ALY end +link pept head - HYP tail + HLY end +link pept head - HYP tail + MLY end +link pept head - HYP tail + MLZ end +link pept head - HYP tail + M3L end +link pept head - HYP tail + LEU end +link pept head - HYP tail + MET end +link pept head - HYP tail + MSE end +link pept head - HYP tail + ASN end +link pept head - HYP tail + PRO end +link pept head - HYP tail + GLN end +link pept head - HYP tail + ARG end +link pept head - HYP tail + SER end +link pept head - HYP tail + SEC end +link pept head - HYP tail + SEP end +link pept head - HYP tail + THR end +link pept head - HYP tail + THP end +link pept head - HYP tail + TOP end +link pept head - HYP tail + VAL end +link pept head - HYP tail + TRP end +link pept head - HYP tail + TYR end +link pept head - HYP tail + TYP end +link pept head - HYP tail + PTR end +link pept head - HYP tail + TYS end +link pept head - HYP tail + HYP end +link pept head - HYP tail + HY3 end +link pept head - HYP tail + DDZ end +link pept head - HYP tail + QSR end +link pept head - HYP tail + PNS end +link pept head - HYP tail + CIR end + +{ peptide linkages for HY3 } +link pept head - HY3 tail + ALA end +link pept head - HY3 tail + CYS end +link pept head - HY3 tail + CFE end +link pept head - HY3 tail + CYM end +link pept head - HY3 tail + CYF end +link pept head - HY3 tail + CYC end +link pept head - HY3 tail + CSP end +link pept head - HY3 tail + ASP end +link pept head - HY3 tail + ASH end +link pept head - HY3 tail + GLU end +link pept head - HY3 tail + GLH end +link pept head - HY3 tail + PHE end +link pept head - HY3 tail + HIS end +link pept head - HY3 tail + NEP end +link pept head - HY3 tail + ILE end +link pept head - HY3 tail + LYS end +link pept head - HY3 tail + ALY end +link pept head - HY3 tail + HLY end +link pept head - HY3 tail + MLY end +link pept head - HY3 tail + MLZ end +link pept head - HY3 tail + M3L end +link pept head - HY3 tail + LEU end +link pept head - HY3 tail + MET end +link pept head - HY3 tail + MSE end +link pept head - HY3 tail + ASN end +link pept head - HY3 tail + PRO end +link pept head - HY3 tail + GLN end +link pept head - HY3 tail + ARG end +link pept head - HY3 tail + SER end +link pept head - HY3 tail + SEC end +link pept head - HY3 tail + SEP end +link pept head - HY3 tail + THR end +link pept head - HY3 tail + THP end +link pept head - HY3 tail + TOP end +link pept head - HY3 tail + VAL end +link pept head - HY3 tail + TRP end +link pept head - HY3 tail + TYR end +link pept head - HY3 tail + TYP end +link pept head - HY3 tail + PTR end +link pept head - HY3 tail + TYS end +link pept head - HY3 tail + HYP end +link pept head - HY3 tail + HY3 end +link pept head - HY3 tail + DDZ end +link pept head - HY3 tail + QSR end +link pept head - HY3 tail + PNS end +link pept head - HY3 tail + CIR end + +{ peptide linkages for DDZ } +link pept head - DDZ tail + ALA end +link pept head - DDZ tail + CYS end +link pept head - DDZ tail + CFE end +link pept head - DDZ tail + CYM end +link pept head - DDZ tail + CYF end +link pept head - DDZ tail + CYC end +link pept head - DDZ tail + CSP end +link pept head - DDZ tail + ASP end +link pept head - DDZ tail + ASH end +link pept head - DDZ tail + GLU end +link pept head - DDZ tail + GLH end +link pept head - DDZ tail + PHE end +link pept head - DDZ tail + HIS end +link pept head - DDZ tail + NEP end +link pept head - DDZ tail + ILE end +link pept head - DDZ tail + LYS end +link pept head - DDZ tail + ALY end +link pept head - DDZ tail + HLY end +link pept head - DDZ tail + MLY end +link pept head - DDZ tail + MLZ end +link pept head - DDZ tail + M3L end +link pept head - DDZ tail + LEU end +link pept head - DDZ tail + MET end +link pept head - DDZ tail + MSE end +link pept head - DDZ tail + ASN end +link pept head - DDZ tail + PRO end +link pept head - DDZ tail + GLN end +link pept head - DDZ tail + ARG end +link pept head - DDZ tail + SER end +link pept head - DDZ tail + SEC end +link pept head - DDZ tail + SEP end +link pept head - DDZ tail + THR end +link pept head - DDZ tail + THP end +link pept head - DDZ tail + TOP end +link pept head - DDZ tail + VAL end +link pept head - DDZ tail + TRP end +link pept head - DDZ tail + TYR end +link pept head - DDZ tail + TYP end +link pept head - DDZ tail + PTR end +link pept head - DDZ tail + TYS end +link pept head - DDZ tail + HYP end +link pept head - DDZ tail + DDZ end +link pept head - DDZ tail + PNS end +link pept head - DDZ tail + QSR end +link pctn head - DDZ tail + CTN end +link pept head - DDZ tail + NME end +link pept head - DDZ tail + CIR end + +{ peptide linkages for PNS } +link pept head - PNS tail + ALA end +link pept head - PNS tail + CYS end +link pept head - PNS tail + CFE end +link pept head - PNS tail + CYM end +link pept head - PNS tail + CYF end +link pept head - PNS tail + CYC end +link pept head - PNS tail + CSP end +link pept head - PNS tail + ASP end +link pept head - PNS tail + ASH end +link pept head - PNS tail + GLU end +link pept head - PNS tail + GLH end +link pept head - PNS tail + PHE end +link pept head - PNS tail + HIS end +link pept head - PNS tail + NEP end +link pept head - PNS tail + ILE end +link pept head - PNS tail + LYS end +link pept head - PNS tail + ALY end +link pept head - PNS tail + HLY end +link pept head - PNS tail + MLY end +link pept head - PNS tail + MLZ end +link pept head - PNS tail + M3L end +link pept head - PNS tail + LEU end +link pept head - PNS tail + MET end +link pept head - PNS tail + MSE end +link pept head - PNS tail + ASN end +link pept head - PNS tail + PRO end +link pept head - PNS tail + GLN end +link pept head - PNS tail + ARG end +link pept head - PNS tail + SER end +link pept head - PNS tail + SEC end +link pept head - PNS tail + SEP end +link pept head - PNS tail + THR end +link pept head - PNS tail + THP end +link pept head - PNS tail + TOP end +link pept head - PNS tail + VAL end +link pept head - PNS tail + TRP end +link pept head - PNS tail + TYR end +link pept head - PNS tail + TYP end +link pept head - PNS tail + PTR end +link pept head - PNS tail + TYS end +link pept head - PNS tail + HYP end +link pept head - PNS tail + HY3 end +link pept head - PNS tail + DDZ end +link pept head - PNS tail + PNS end +link pept head - PNS tail + QSR end +link pctn head - PNS tail + CTN end +link pept head - PNS tail + NME end +link pept head - PNS tail + CIR end + +{ peptide linkages for QSR } +link pept head - QSR tail + ALA end +link pept head - QSR tail + CYS end +link pept head - QSR tail + CFE end +link pept head - QSR tail + CYM end +link pept head - QSR tail + CYF end +link pept head - QSR tail + CYC end +link pept head - QSR tail + CSP end +link pept head - QSR tail + ASP end +link pept head - QSR tail + ASH end +link pept head - QSR tail + GLU end +link pept head - QSR tail + GLH end +link pept head - QSR tail + PHE end +link pept head - QSR tail + HIS end +link pept head - QSR tail + NEP end +link pept head - QSR tail + ILE end +link pept head - QSR tail + LYS end +link pept head - QSR tail + ALY end +link pept head - QSR tail + HLY end +link pept head - QSR tail + MLY end +link pept head - QSR tail + MLZ end +link pept head - QSR tail + M3L end +link pept head - QSR tail + LEU end +link pept head - QSR tail + MET end +link pept head - QSR tail + MSE end +link pept head - QSR tail + ASN end +link pept head - QSR tail + PRO end +link pept head - QSR tail + GLN end +link pept head - QSR tail + ARG end +link pept head - QSR tail + SER end +link pept head - QSR tail + SEC end +link pept head - QSR tail + SEP end +link pept head - QSR tail + THR end +link pept head - QSR tail + THP end +link pept head - QSR tail + TOP end +link pept head - QSR tail + VAL end +link pept head - QSR tail + TRP end +link pept head - QSR tail + TYR end +link pept head - QSR tail + TYP end +link pept head - QSR tail + PTR end +link pept head - QSR tail + TYS end +link pept head - QSR tail + HYP end +link pept head - QSR tail + HY3 end +link pept head - QSR tail + DDZ end +link pept head - QSR tail + PNS end +link pept head - QSR tail + QSR end +link pctn head - QSR tail + CTN end +link pept head - QSR tail + NME end +link pept head - QSR tail + CIR end + +{ peptide linkages for CIR } +link pept head - CIR tail + ALA end +link pept head - CIR tail + CYS end +link pept head - CIR tail + CFE end +link pept head - CIR tail + CYM end +link pept head - CIR tail + CYF end +link pept head - CIR tail + CYC end +link pept head - CIR tail + CSP end +link pept head - CIR tail + ASP end +link pept head - CIR tail + ASH end +link pept head - CIR tail + GLU end +link pept head - CIR tail + GLH end +link pept head - CIR tail + PHE end +link pept head - CIR tail + HIS end +link pept head - CIR tail + NEP end +link pept head - CIR tail + ILE end +link pept head - CIR tail + LYS end +link pept head - CIR tail + ALY end +link pept head - CIR tail + HLY end +link pept head - CIR tail + MLY end +link pept head - CIR tail + MLZ end +link pept head - CIR tail + M3L end +link pept head - CIR tail + LEU end +link pept head - CIR tail + MET end +link pept head - CIR tail + MSE end +link pept head - CIR tail + ASN end +link pept head - CIR tail + PRO end +link pept head - CIR tail + GLN end +link pept head - CIR tail + ARG end +link pept head - CIR tail + SER end +link pept head - CIR tail + SEC end +link pept head - CIR tail + SEP end +link pept head - CIR tail + THR end +link pept head - CIR tail + THP end +link pept head - CIR tail + TOP end +link pept head - CIR tail + VAL end +link pept head - CIR tail + TRP end +link pept head - CIR tail + TYR end +link pept head - CIR tail + TYP end +link pept head - CIR tail + PTR end +link pept head - CIR tail + TYS end +link pept head - CIR tail + HYP end +link pept head - CIR tail + HY3 end +link pept head - CIR tail + DDZ end +link pept head - CIR tail + PNS end +link pept head - CIR tail + QSR end +link pctn head - CIR tail + CTN end +link pept head - CIR tail + NME end +link pept head - CIR tail + CIR end + +first PROP tail + PRO end +first PROP tail + HYP end +first PROP tail + HY3 end + +first ACET tail + ACE end + +first NTER tail + ALA end +first NTER tail + CYS end +first NTER tail + CFE end +first NTER tail + CYM end +first NTER tail + CYF end +first NTER tail + CYC end +first NTER tail + CSP end +first NTER tail + ASP end +first NTER tail + ASH end +first NTER tail + GLU end +first NTER tail + GLH end +first NTER tail + GLY end +first NTER tail + PHE end +first NTER tail + HIS end +first NTER tail + NEP end +first NTER tail + ILE end +first NTER tail + LYS end +first NTER tail + ALY end +first NTER tail + HLY end +first NTER tail + MLY end +first NTER tail + MLZ end +first NTER tail + M3L end +first NTER tail + LEU end +first NTER tail + MET end +first NTER tail + MSE end +first NTER tail + ASN end +first NTER tail + PRO end +first NTER tail + GLN end +first NTER tail + ARG end +first NTER tail + SER end +first NTER tail + SEC end +first NTER tail + SEP end +first NTER tail + THR end +first NTER tail + THP end +first NTER tail + TOP end +first NTER tail + VAL end +first NTER tail + TRP end +first NTER tail + TYR end +first NTER tail + TYP end +first NTER tail + PTR end +first NTER tail + TYS end +first NTER tail + HYP end +first NTER tail + HY3 end +first NTER tail + DDZ end +first NTER tail + PNS end +first NTER tail + QSR end +first NTER tail + CIR end + +last CTER head - ALA end +last CTER head - CYS end +last CTER head - CFE end +last CTER head - CYM end +last CTER head - CYC end +last CTER head - CYF end +last CTER head - CSP end +last CTER head - ASP end +last CTER head - ASH end +last CTER head - GLU end +last CTER head - GLH end +last CTER head - GLY end +last CTER head - PHE end +last CTER head - HIS end +last CTER head - NEP end +last CTER head - ILE end +last CTER head - LYS end +last CTER head - ALY end +last CTER head - HLY end +last CTER head - MLY end +last CTER head - MLZ end +last CTER head - M3L end +last CTER head - LEU end +last CTER head - MET end +last CTER head - MSE end +last CTER head - ASN end +last CTER head - PCA end +last CTER head - PRO end +last CTER head - GLN end +last CTER head - ARG end +last CTER head - SER end +last CTER head - SEC end +last CTER head - SEP end +last CTER head - THR end +last CTER head - THP end +last CTER head - TOP end +last CTER head - VAL end +last CTER head - TRP end +last CTER head - TYR end +last CTER head - TYP end +last CTER head - PTR end +last CTER head - TYS end +last CTER head - HYP end +last CTER head - HY3 end +last CTER head - DDZ end +last CTER head - PNS end +last CTER head - QSR end +last CTER head - CIR end + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.param new file mode 100644 index 0000000000000000000000000000000000000000..30baf1b43f6af116871e5d700ce72558dab78f7e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.param @@ -0,0 +1,2034 @@ +remarks file toppar/protein-allhdg5-4.param +remark +remark for file protein-allhdg-ucl.top version UCL date 14-MAR-00 +remark for file protein-allhdg-dih-ucl.top version UCL date 07-JUL-01 +remark Geometric energy function parameters for distance geometry and +remark simulated annealing. +remark Original author: Michael Nilges, EMBL Heidelberg +remark Modifications: Mark A. Williams, UCL London +remark Several modifications for HADDOCK: Alexandre Bonvin, Utrecht Uni +remark Last modification 06-02-2021 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +!***********************************************************************! +! Copyright (C) 1995,1996 by Michael Nilges. All rights reserved. ! +! Copying and redistribution of this files is authorized only if etiher ! +! (1) you make absolutely no changes to your copy, including name, or ! +! (2) if you do make changes, you name it something other than ! +! topallhdg.pro and topallhdg.x.xx.pro, and clearly mark the changes. ! +! The information in this software is subject to change without notice ! +! and should not be construed as a commitment by the EMBL, UCL, Yale ! +! University, UCL or by the authors. Neither the EMBL, Yale University, ! +! UCL, nor the authors assume responsibility for the use or reliability ! +! of this software. We do hope, however, to get responses from users, ! +! especially when errors have been found. ! ! +!***********************************************************************! +! Description: ! +! This parameter file was originally derived from the parameter files ! +! PARMALLH6 and PARHCSDX. It was designed specifically for the initial ! +! stages of calculating structures from NMR restraints. ! +!***********************************************************************! +! PARHCSDX includes bond and angle parameters for non-hydrogen atoms ! +! derived from Cambridge Data Base model structures (R. A. Engh and R. ! +! Huber, Acta Cryst. Sect. A., 1991). Hydrogens were added with X-PLOR ! +! scripts for minimization and the PARAmeter LEARn statement. Dihedral, ! +! improper and non-bonded values are from previous PARALLHDG versions, ! +! and assigned to new atom types where appropriate. Due to the ! +! minimization procedure used in the derivation, there are very small ! +! deviations from the parameter values in PARHCSDX. ! +! Heavy atom types are exactly as in PARHCSDX, hydrogen types as in ! +! PARALLHDG. ! +!***********************************************************************! +! History: +! HADDOCK2.3, several additions for special residues and patches +! CNS v1.3, revision 7 (1-10-2012), added improper NE2 CE1 CD2 HE2 for HIS residue +! CNS v1,3, revision 6 (8-18-2011), added parameters for MSE residue +! version CNS 1.3, revision 2: added impropers for Arg planarity +! version UCL (07-Jul-01) : modified backbone & disulphide paprameters +! version UCL (05-Jul-01) : put dihedrals to maximum of 2 kcal/mol +! version UCL (03-Jul-01) : added new backbone dihedral parameters +! version UCL (27-Jun-01) : restored original PROLSQ 1-4 parameters except larger aliphatic H radius +! version UCL (02-Apr-00) : modified 1-4 PROLSQ parameters +! version UCL (02-Apr-00) : modified aliphatic H radii +! version UCL (14-Mar-00) : modified peptide bond and disulphide impropers/dihedrals +! version UCL (12-Mar-00) : added or modified N and C terminus, CH3 & NH3 parameters +! version UCL (10-Mar-00) : added CONTACT non-bond parameters +! version UCL (09-Mar-00) : added or modified planar chi2 or chi3 +! version 5.10 (24-Feb-99) : larger aliphatic hydrogens (test - not now active?) +! version 5.03 (13-Nov-98) : corrected aromatic chi2 +! version 5.02 (19-Aug-98) : corrected cis peptide bond +! version 5.01 (20-Mar-98) : put side-chain dihedrals to 5 kcal/mol +! version 5.00 (16-Feb-98) : allow different nonbonded parameter options +! version 4.04 (28-Jan-98) : added missing dihedral parameters +! version 4.03 (27-Mar-97) : added missing dihedral parameters +! version 4.02 (25-Sep-96) : added missing parameters +! version 4.01 (29-Jul-96) : added missing covalent parameters +! version 4.00 (19-Jul-96) : all atom types from CSDX implemented +! version 3.00 (24-Oct-95) : mapped CSDX parmameters on parallhdg, +! no changes in topallhdg +! +! previous modifications: +! proline residue modified (MN) +! added hbond acceptor and donor definitions for analysis (MN) +! all references to internal coordinates (IC's) removed (MN) +! added stereospecific impropers for all pro-chiral centers (ATB, JK) +! modification of PARMALLH6 parameters to improve geometric consistency (JK) +! all dihedrals defining planarity converted to impropers (MN, PK) +! additional impropers at planar centers (MN) +!***********************************************************************! + +!added by nocky + BOND S C 1000.000 {sd= 0.001} 1.822 + ANGLe CH2E S C 500.00 {sd= 0.031} 100.00 + ANGLe S C CH1E 500.00 {sd= 0.031} 113.00 + ANGLe S C O 500.00 {sd= 0.031} 120.00 + IMPRoper HA CH1E CH2E HA 500.00 {sd= 0.031} 0 180.0000 + DIHEdral O C CH1E HA 5.00 3 0.0000 + DIHEdral CH2E S C CH1E 5.00 3 0.0000 + DIHEdral CH2E S C O 5.00 3 0.0000 + + +!added by hans for trimethyl-lysine (220307) + BOND CH3E NC4 1000.000 {sd= 0.001} 1.4700 + BOND CH2E NC4 1000.000 {sd= 0.001} 1.4700 + ANGLe CH2E NC4 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe CH3E NC4 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe NC4 CH3E HA 500.000 {sd= 0.031} 109.5000 + ANGLe CH2E CH2E NC4 500.000 {sd= 0.031} 109.5000 + ANGLe HA CH2E NC4 500.000 {sd= 0.031} 109.5000 + IMPRoper HA HA CH2E NC4 500.000 {sd= 0.031} 0 35.2640 + IMPRoper CH3E CH3E CH2E CH3E 500.000 {sd= 0.031} 0 35.2640 + DIHEdral NC4 CH2E CH2E CH2E 1.000 3 0.0000 + DIHEdral CH3E NC4 CH2E CH2E 1.000 3 180.0000 + +!added by A. Bonvin for dimethyl-lysine (30-04-2009) + BOND HC NC3 1000.000 {sd= 0.001} 1.040 + BOND CH3E NC3 1000.000 {sd= 0.001} 1.4700 + BOND CH2E NC3 1000.000 {sd= 0.001} 1.4700 + ANGLe CH2E NC3 HC 500.000 {sd= 0.031} 109.5000 + ANGLe CH2E NC3 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe HC NC3 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe CH3E NC3 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe NC3 CH3E HA 500.000 {sd= 0.031} 109.5000 + ANGLe NC3 HC HC 500.000 {sd= 0.031} 109.5000 + ANGLe CH2E CH2E NC3 500.000 {sd= 0.031} 109.5000 + ANGLe HA CH2E NC3 500.000 {sd= 0.031} 109.5000 + IMPRoper HA HA CH2E NC3 500.000 {sd= 0.031} 0 35.2640 + IMPRoper CH3E CH3E CH2E HC 500.000 {sd= 0.031} 0 35.2640 + DIHEdral NC3 CH2E CH2E CH2E 1.000 3 0.0000 + DIHEdral CH3E NC3 CH2E CH2E 1.000 3 180.0000 + +!added by A. Bonvin for monomethyl-lysine (30-04-2009) + BOND HC NC2 1000.000 {sd= 0.001} 1.040 + BOND CH3E NC2 1000.000 {sd= 0.001} 1.4700 + BOND CH2E NC2 1000.000 {sd= 0.001} 1.4700 + ANGLe CH2E NC2 HC 500.000 {sd= 0.031} 109.5000 + ANGLe CH2E NC2 CH3E 500.000 {sd= 0.031} 109.5000 + ANGLe CH3E NC2 HC 500.000 {sd= 0.031} 109.5000 + ANGLe NC2 CH3E HA 500.000 {sd= 0.031} 109.5000 + ANGLe NC2 HC HC 500.000 {sd= 0.031} 109.5000 + ANGLe CH2E CH2E NC2 500.000 {sd= 0.031} 109.5000 + ANGLe HA CH2E NC2 500.000 {sd= 0.031} 109.5000 + IMPRoper HA HA CH2E NC2 500.000 {sd= 0.031} 0 35.2640 + IMPRoper HC CH3E CH2E HC 500.000 {sd= 0.031} 0 35.2640 + DIHEdral NC2 CH2E CH2E CH2E 1.000 3 0.0000 + DIHEdral CH3E NC2 CH2E CH2E 1.000 3 180.0000 + + BOND C CH1E 1000.000 {sd= 0.001} 1.525 + BOND C CH2E 1000.000 {sd= 0.001} 1.516 + BOND C CH3E 1000.000 {sd= 0.001} 1.507 ! added EAB + BOND C CH2G 1000.000 {sd= 0.001} 1.516 + BOND CP CH2P 1000.000 {sd= 0.001} 1.504 ! for PCA - AB + BOND C N 1000.000 {sd= 0.001} 1.341 + BOND CP N 1000.000 {sd= 0.001} 1.341 ! for PCA - AB + BOND C NC2 1000.000 {sd= 0.001} 1.326 + BOND C NH1 1000.000 {sd= 0.001} 1.329 + BOND CP NH1 1000.000 {sd= 0.001} 1.329 ! for PCA - AB + BOND C NH2 1000.000 {sd= 0.001} 1.328 + BOND C O 1000.000 {sd= 0.001} 1.231 + BOND CP O 1000.000 {sd= 0.001} 1.231 ! for PCA - AB + BOND C OC 1000.000 {sd= 0.001} 1.249 + BOND C OH1 1000.000 {sd= 0.001} 1.433 !included Nov-16 for ASH/GLH + BOND C5 CH2E 1000.000 {sd= 0.001} 1.497 + BOND C5 CR1E 1000.000 {sd= 0.001} 1.357 + BOND C5 CR1H 1000.000 {sd= 0.001} 1.354 + BOND C5 NH1 1000.000 {sd= 0.001} 1.378 + BOND C5 NR 1000.000 {sd= 0.001} 1.373 + BOND C5W CH2E 1000.000 {sd= 0.001} 1.498 + BOND C5W CR1E 1000.000 {sd= 0.001} 1.365 + BOND C5W CW 1000.000 {sd= 0.001} 1.433 + BOND CF CH2E 1000.000 {sd= 0.001} 1.502 + BOND CF CR1E 1000.000 {sd= 0.001} 1.385 + BOND CH1E CH1E 1000.000 {sd= 0.001} 1.540 + BOND CH1E CH2E 1000.000 {sd= 0.001} 1.530 + BOND CH1E CH3E 1000.000 {sd= 0.001} 1.521 + BOND CH1E HA 1000.000 {sd= 0.001} 1.080 + BOND CH1E N 1000.000 {sd= 0.001} 1.466 + BOND CH1E NH1 1000.000 {sd= 0.001} 1.458 + BOND CH1E NH3 1000.000 {sd= 0.001} 1.486 + BOND CH1E OH1 1000.000 {sd= 0.001} 1.433 !included 14-apr-99 + BOND CH1E OAS 1000.000 {sd= 0.001} 1.433 !for THR-linked glycans + BOND CH1E OHP 1000.000 {sd= 0.001} 1.433 + BOND CH2E CH2E 1000.000 {sd= 0.001} 1.520 + BOND CH2E CH2P 1000.000 {sd= 0.001} 1.490 + BOND CH2E CH3E 1000.000 {sd= 0.001} 1.513 + BOND CH2E CY 1000.000 {sd= 0.001} 1.512 + BOND CH2E HA 1000.000 {sd= 0.001} 1.080 + BOND CH2E NH1 1000.000 {sd= 0.001} 1.460 + BOND CH2E NH3 1000.000 {sd= 0.001} 1.489 + BOND CH2E OH1 1000.000 {sd= 0.001} 1.417 + BOND CH2E OH1C 1000.000 {sd= 0.001} 1.417 ! for covalent Serine (SEC) + BOND CH2E OHP 1000.000 {sd= 0.001} 1.417 + BOND CH2E S 1000.000 {sd= 0.001} 1.822 + BOND CH2E SH1E 1000.000 {sd= 0.001} 1.808 + BOND CH2E SH1C 1000.000 {sd= 0.001} 1.808 + BOND CH2E SM 1000.000 {sd= 0.001} 1.803 + BOND CH2E SE 1000.000 {sd= 0.001} 1.803 ! for MSE + BOND CH2G HA 1000.000 {sd= 0.001} 1.080 + BOND CH2G NH1 1000.000 {sd= 0.001} 1.451 + BOND CH2G NH3 1000.000 {sd= 0.001} 1.489 + BOND CH2P CH2P 1000.000 {sd= 0.001} 1.504 + BOND CH1E CH1P 1000.000 {sd= 0.001} 1.504 + BOND CH2E CH1P 1000.000 {sd= 0.001} 1.504 + BOND CH2P CH1P 1000.000 {sd= 0.001} 1.504 + BOND CH1P HA 1000.000 {sd= 0.001} 1.080 + BOND CH2P HA 1000.000 {sd= 0.001} 1.080 + BOND CH1P OH1 1000.000 {sd= 0.001} 1.433 + BOND CH2P N 1000.000 {sd= 0.001} 1.473 + BOND CH1P N 1000.000 {sd= 0.001} 1.473 + BOND CH2P NH3 1000.000 {sd= 0.001} 1.474 + BOND CH1P NH3 1000.000 {sd= 0.001} 1.474 + BOND CH3E HA 1000.000 {sd= 0.001} 1.080 + BOND CH3E SM 1000.000 {sd= 0.001} 1.791 + BOND CH3E SE 1000.000 {sd= 0.001} 1.791 ! for MSE + BOND CH3E NH1 1000.000 {sd= 0.001} 1.430 ! for NME + BOND CR1E CR1E 1000.000 {sd= 0.001} 1.382 + BOND CR1E CR1W 1000.000 {sd= 0.001} 1.400 + BOND CR1E CW 1000.000 {sd= 0.001} 1.398 + BOND CR1E CY 1000.000 {sd= 0.001} 1.389 + BOND CR1E CY2 1000.000 {sd= 0.001} 1.379 + BOND CR1E HA 1000.000 {sd= 0.001} 1.080 + BOND CR1E NH1 1000.000 {sd= 0.001} 1.373 + BOND CR1E NR 1000.000 {sd= 0.001} 1.391 + BOND CR1H HA 1000.000 {sd= 0.001} 1.081 + BOND CR1H NH1 1000.000 {sd= 0.001} 1.374 + BOND CR1H NR 1000.000 {sd= 0.001} 1.374 + BOND CR1W CR1W 1000.000 {sd= 0.001} 1.368 + BOND CR1W CY2 1000.000 {sd= 0.001} 1.379 + BOND CR1W CW 1000.000 {sd= 0.001} 1.393 + BOND CR1W HA 1000.000 {sd= 0.001} 1.080 + BOND CRH HA 1000.000 {sd= 0.001} 1.080 + BOND CRH NH1 1000.000 {sd= 0.001} 1.341 + BOND CRH NR 1000.000 {sd= 0.001} 1.319 + BOND CRHH HA 1000.000 {sd= 0.001} 1.080 + BOND CRHH NH1 1000.000 {sd= 0.001} 1.321 + BOND CRHH NR 1000.000 {sd= 0.001} 1.321 + BOND CW CW 1000.000 {sd= 0.001} 1.409 + BOND CW NH1 1000.000 {sd= 0.001} 1.370 + BOND CY2 OH1 1000.000 {sd= 0.001} 1.376 + BOND CY2 OHP 1000.000 {sd= 0.001} 1.376 + BOND CY2 OUF 1000.000 {sd= 0.001} 1.376 + BOND H NH1 1000.000 {sd= 0.001} 0.980 + BOND H NH2 1000.000 {sd= 0.001} 0.980 + BOND H OH1 1000.000 {sd= 0.001} 0.960 + BOND H OH1C 1000.000 {sd= 0.001} 0.960 ! for covalent Serine (SEC) + BOND H SH1E 1000.000 {sd= 0.001} 1.325 ! from CHARMM22 + BOND HC NH3 1000.000 {sd= 0.001} 1.040 + BOND S S 1000.000 {sd= 0.001} 2.030 + BOND CCIS CH1E 1000.000 {sd= 0.001} 1.525 ! CCIS is for cis peptide bond + BOND CCIS CH2E 1000.000 {sd= 0.001} 1.516 + BOND CCIS CH2G 1000.000 {sd= 0.001} 1.516 + BOND CCIS N 1000.000 {sd= 0.001} 1.341 + BOND CCIS NC2 1000.000 {sd= 0.001} 1.326 + BOND CCIS NH1 1000.000 {sd= 0.001} 1.329 + BOND CCIS NH2 1000.000 {sd= 0.001} 1.328 + BOND CCIS O 1000.000 {sd= 0.001} 1.231 + BOND CCIS OC 1000.000 {sd= 0.001} 1.249 + BOND NR PP 1000.0 1.610 + BOND SM PP 1000.0 2.094 + BOND PP OR3 1000.0 1.610 + BOND PP OHP 1000.0 1.610 + BOND PP OP1 1000.0 1.485 + BOND SUF OUF 1000.0 1.475 + BOND OC "CA+2" 1000.0 2.500 +! next ones added for iron-sulphur cluster + BOND SH1E FS 1000.0 2.300 + BOND FS SF 1000.0 2.200 + BOND CD28 O3P 1000.0 1.430 + +! Residue PNS +evaluate ($pd_x = 1.0) + +eval ($pd_v=$pd_x* 15991.7) BOND CD28 OR3 $pd_v 1.430 +eval ($pd_v=$pd_x* 13971.0) BOND CD28 HD28 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD28 HD29 $pd_v 1.090 +eval ($pd_v=$pd_x* 16001.4) BOND CD29 CD28 $pd_v 1.530 +eval ($pd_v=$pd_x* 16001.4) BOND CD29 CD30 $pd_v 1.530 +eval ($pd_v=$pd_x* 16001.4) BOND CD29 CD31 $pd_v 1.530 +eval ($pd_v=$pd_x* 16001.4) BOND CD29 CD32 $pd_v 1.530 +eval ($pd_v=$pd_x* 13971.0) BOND CD30 HD31 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD30 HD32 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD30 HD30 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD31 HD34 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD31 HD35 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD31 HD33 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD32 HD36 $pd_v 1.090 +eval ($pd_v=$pd_x* 15991.7) BOND CD32 OD33 $pd_v 1.430 +eval ($pd_v=$pd_x* 16001.4) BOND CD32 CD34 $pd_v 1.530 +eval ($pd_v=$pd_x* 15009.6) BOND OD33 HD46 $pd_v 1.000 +eval ($pd_v=$pd_x* 24009.7) BOND CD34 OD35 $pd_v 1.230 +eval ($pd_v=$pd_x* 18024.7) BOND CD34 ND36 $pd_v 1.340 +eval ($pd_v=$pd_x* 17877.6) BOND ND36 HD48 $pd_v 1.000 +eval ($pd_v=$pd_x* 17993.7) BOND CD37 ND36 $pd_v 1.470 +eval ($pd_v=$pd_x* 13971.0) BOND CD37 HD37 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD37 HD38 $pd_v 1.090 +eval ($pd_v=$pd_x* 16001.4) BOND CD37 CD38 $pd_v 1.530 +eval ($pd_v=$pd_x* 13971.0) BOND CD38 HD39 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD38 HD4A $pd_v 1.090 +eval ($pd_v=$pd_x* 16001.4) BOND CD39 CD38 $pd_v 1.530 +eval ($pd_v=$pd_x* 24009.7) BOND CD39 OD40 $pd_v 1.230 +eval ($pd_v=$pd_x* 18024.7) BOND CD39 ND41 $pd_v 1.340 +eval ($pd_v=$pd_x* 17877.6) BOND ND41 HD41 $pd_v 1.000 +eval ($pd_v=$pd_x* 17993.7) BOND CD42 ND41 $pd_v 1.470 +eval ($pd_v=$pd_x* 13971.0) BOND CD42 HD42 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD42 HD43 $pd_v 1.090 +eval ($pd_v=$pd_x* 16001.4) BOND CD42 CD43 $pd_v 1.530 +eval ($pd_v=$pd_x* 13971.0) BOND CD43 HD44 $pd_v 1.090 +eval ($pd_v=$pd_x* 13971.0) BOND CD43 HD45 $pd_v 1.090 +eval ($pd_v=$pd_x* 17993.1) BOND CD43 SD44 $pd_v 1.830 +eval ($pd_v=$pd_x* 15000.1) BOND SD44 HD47 $pd_v 1.330 + + +! Residue DRG +evaluate ($pd_x = 1.0) + +eval ($pd_v=$pd_x* 16000.0) BOND CHAC CHAS $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CHAS CHAD $pd_v 1.530 +eval ($pd_v=$pd_x* 18000.0) BOND CHAS NHAQ $pd_v 1.470 +eval ($pd_v=$pd_x* 16000.0) BOND CHAS CHAO $pd_v 1.530 +eval ($pd_v=$pd_x* 12000.0) BOND NHAQ OHAH $pd_v 1.460 +eval ($pd_v=$pd_x* 18000.0) BOND NHAQ CHAR $pd_v 1.470 +eval ($pd_v=$pd_x* 15000.0) BOND OHAH HHAA $pd_v 1.000 +eval ($pd_v=$pd_x* 16000.0) BOND CHAR CHAA $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CHAR CHAB $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CHAR CHAI $pd_v 1.530 +eval ($pd_v=$pd_x* 20000.0) BOND CHAI CHAO $pd_v 1.330 +eval ($pd_v=$pd_x* 16000.0) BOND CHAO CHAJ $pd_v 1.530 +eval ($pd_v=$pd_x* 18000.0) BOND CHAJ SHAL $pd_v 1.830 +eval ($pd_v=$pd_x* 20000.0) BOND SHAL S $pd_v 2.040 +eval ($pd_v=$pd_x* 18000.0) BOND S CHB $pd_v 1.830 +eval ($pd_v=$pd_x* 16000.0) BOND CHB CHA $pd_v 1.530 +eval ($pd_v=$pd_x* 16000.0) BOND CHA CH_Y $pd_v 1.530 +eval ($pd_v=$pd_x* 18000.0) BOND CHA NH_Y $pd_v 1.470 +eval ($pd_v=$pd_x* 20000.0) BOND CH_Y OHXT $pd_v 1.250 +eval ($pd_v=$pd_x* 20000.0) BOND CH_Y OH_Y $pd_v 1.250 +eval ($pd_v=$pd_x* 17900.0) BOND NH_Y HHAC $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NH_Y HHAD $pd_v 1.000 +eval ($pd_v=$pd_x* 17900.0) BOND NH_Y HHAB $pd_v 1.000 + + + ANGLe C CH1E CH1E 500.00 {sd= 0.031} 109.0754 + ANGLe C CH1E CH2E 500.00 {sd= 0.031} 110.1094 + ANGLe C CH1E CH1P 500.00 {sd= 0.031} 110.1094 + ANGLe C CH1E CH3E 500.00 {sd= 0.031} 110.4838 + ANGLe C CH1E HA 500.00 {sd= 0.031} 108.9914 + ANGLe C CH1E N 500.00 {sd= 0.031} 111.9082 + ANGLe C CH1E NH1 500.00 {sd= 0.031} 111.1396 + ANGLe C CH1E NH3 500.00 {sd= 0.031} 111.1703 + ANGLe C CH2E CH1E 500.00 {sd= 0.031} 112.5947 + ANGLe C CH2E CH2E 500.00 {sd= 0.031} 112.5943 + ANGLe C CH2E HA 500.00 {sd= 0.031} 108.5877 + ANGLe C CH3E HA 500.00 {sd= 0.031} 108.5877 + ANGLe C CH2G HA 500.00 {sd= 0.031} 108.8528 + ANGLe C CH2G NH1 500.00 {sd= 0.031} 112.4999 + ANGLe C CH2G NH3 500.00 {sd= 0.031} 112.4990 + ANGLe C N CH1E 500.00 {sd= 0.031} 122.7632 + ANGLe C N CH2E 500.00 {sd= 0.031} 124.1226 + ANGLe C N CH2P 500.00 {sd= 0.031} 125.1134 + ANGLe C N CH1P 500.00 {sd= 0.031} 125.1134 + ANGLe C NC2 HC 500.00 {sd= 0.031} 119.9992 + ANGLe C NH1 CH1E 500.00 {sd= 0.031} 121.6541 + ANGLe CP NH1 CH1E 500.00 {sd= 0.031} 113.0000 + ANGLe C NH1 CH2E 500.00 {sd= 0.031} 124.1226 + ANGLe C NH1 CH3E 500.00 {sd= 0.031} 124.1226 ! for NME + ANGLe C NH1 CH2G 500.00 {sd= 0.031} 120.5859 + ANGLe C NH1 H 500.00 {sd= 0.031} 119.2489 + ANGLe CP NH1 H 500.00 {sd= 0.031} 123.5000 ! for PCA + ANGLe C NH2 H 500.00 {sd= 0.031} 118.1853 + ANGLe C OH1 H 500.00 {sd= 0.031} 109.4969 + ANGLe C5 CH2E CH1E 500.00 {sd= 0.031} 113.7931 + ANGLe C5 CH2E HA 500.00 {sd= 0.031} 108.1195 + ANGLe C5 CR1E HA 500.00 {sd= 0.031} 126.2616 + ANGLe C5 CR1E NH1 500.00 {sd= 0.031} 106.5015 + ANGLe C5 CR1E NR 500.00 {sd= 0.031} 109.4272 + ANGLe C5 CR1H HA 500.00 {sd= 0.031} 126.4031 + ANGLe C5 CR1H NH1 500.00 {sd= 0.031} 107.1610 + ANGLe C5 CR1H NR 500.00 {sd= 0.031} 107.1610 + ANGLe C5 NH1 CRH 500.00 {sd= 0.031} 108.0959 + ANGLe C5 NH1 CRHH 500.00 {sd= 0.031} 109.4352 + ANGLe C5 NR CRHH 500.00 {sd= 0.031} 109.4352 + ANGLe C5 NH1 H 500.00 {sd= 0.031} 126.0497 + ANGLe C5 NR CRH 500.00 {sd= 0.031} 105.7163 + ANGLe C5W CH2E CH1E 500.00 {sd= 0.031} 113.5788 + ANGLe C5W CH2E CH2E 500.00 {sd= 0.031} 113.5788 + ANGLe C5W CH2E HA 500.00 {sd= 0.031} 108.1831 + ANGLe C5W CR1E HA 500.00 {sd= 0.031} 124.5037 + ANGLe C5W CR1E NH1 500.00 {sd= 0.031} 110.0962 + ANGLe C5W CW CR1E 500.00 {sd= 0.031} 133.9320 + ANGLe C5W CW CW 500.00 {sd= 0.031} 107.2333 + ANGLe CF CH2E CH1E 500.00 {sd= 0.031} 113.7937 + ANGLe CF CH2E HA 500.00 {sd= 0.031} 108.1268 + ANGLe CF CR1E CR1E 500.00 {sd= 0.031} 120.7850 + ANGLe CF CR1E HA 500.00 {sd= 0.031} 119.4540 + ANGLe CH1E C N 500.00 {sd= 0.031} 116.9940 + ANGLe CH2E C N 500.00 {sd= 0.031} 116.9940 + ANGLe CH3E C N 500.00 {sd= 0.031} 116.9940 + ANGLe CH1E C NH1 500.00 {sd= 0.031} 116.1998 + ANGLe CH1E C NH2 500.00 {sd= 0.031} 116.1998 + ANGLe CH3E C NH1 500.00 {sd= 0.031} 116.1998 + ANGLe CH1E C O 500.00 {sd= 0.031} 120.8258 + ANGLe CH1E C OC 500.00 {sd= 0.031} 118.0611 + ANGLe CH1E CH1E CH2E 500.00 {sd= 0.031} 110.3824 + ANGLe CH1E CH1E CH3E 500.00 {sd= 0.031} 110.4882 + ANGLe CH1E CH1E HA 500.00 {sd= 0.031} 108.2775 + ANGLe CH1E CH1E NH1 500.00 {sd= 0.031} 111.4875 + ANGLe CH1E CH1E NH3 500.00 {sd= 0.031} 111.4875 + ANGLe CH1E CH1E OH1 500.00 {sd= 0.031} 109.600 ! included 14-APR-99 + ANGLe CH1E CH1E OAS 500.00 {sd= 0.031} 109.600 !for THR-linked glycans + ANGLe CH2E CH1E OH1 500.00 {sd= 0.031} 109.600 + ANGLe NH3 CH1E OH1 500.00 {sd= 0.031} 109.600 + ANGLe CH1E CH1E OHP 500.00 {sd= 0.031} 109.600 + ANGLe CH1E CH2E CH1E 500.00 {sd= 0.031} 116.0385 + ANGLe CH1E CH2E CH2E 500.00 {sd= 0.031} 114.0589 + ANGLe CH1E CH2E CH2P 500.00 {sd= 0.031} 104.3952 + ANGLe CH1E CH2E CH1P 500.00 {sd= 0.031} 104.3952 + ANGLe CH1E CH1P CH2E 500.00 {sd= 0.031} 104.3952 + ANGLe CH1E CH2E CH3E 500.00 {sd= 0.031} 113.7404 + ANGLe CH1E CH2E CY 500.00 {sd= 0.031} 113.8748 + ANGLe CH1E CH2E HA 500.00 {sd= 0.031} 109.2833 + ANGLe CH1E CH2E OH1 500.00 {sd= 0.031} 111.0593 + ANGLe CH1E CH2E OH1C 500.00 {sd= 0.031} 111.0593 ! for covalent Serine (SEC) + ANGLe CH1E CH2E OHP 500.00 {sd= 0.031} 111.0593 + ANGLe CH1E CH2E S 500.00 {sd= 0.031} 114.3551 + ANGLe CH1E CH2E SH1E 500.00 {sd= 0.031} 114.3558 + ANGLe CH1E CH2E SH1C 500.00 {sd= 0.031} 114.3558 + ANGLe C CH2E SM 500.00 {sd= 0.031} 114.3558 + ANGLe CH1E CH2E SM 500.00 {sd= 0.031} 114.3558 + ANGLe CH1E CH2E SE 500.00 {sd= 0.031} 114.3558 ! for MSE + ANGLe CH1E CH3E HA 500.00 {sd= 0.031} 109.4726 + ANGLe CH1E N CH2P 500.00 {sd= 0.031} 112.1234 + ANGLe CH1E N CH1P 500.00 {sd= 0.031} 112.1234 + ANGLe CH1E NH1 H 500.00 {sd= 0.031} 119.2367 + ANGLe CH1E NH3 CH2P 500.00 {sd= 0.031} 110.6738 + ANGLe CH1E NH3 CH1P 500.00 {sd= 0.031} 110.6738 + ANGLe CH1E NH3 HC 500.00 {sd= 0.031} 109.4688 !estimated (from Gly) 14-APR-99 + ANGLe CH1E OH1 H 500.00 {sd= 0.031} 109.5 ! included 14-APR-99 + ANGLe CH1P OH1 H 500.00 {sd= 0.031} 109.5 ! included 14-APR-99 + ANGLe CH1P OHP H 500.00 {sd= 0.031} 109.5 ! included 14-APR-99 + ANGLe CH1 OHP PP 500.00 {sd= 0.031} 120.0000 + ANGLe CH2 OHP PP 500.00 {sd= 0.031} 120.0000 + ANGLe CH1E OHP PP 500.00 {sd= 0.031} 120.0000 + ANGLe CH2E OHP PP 500.00 {sd= 0.031} 120.0000 + ANGLe CH2E C NH1 500.00 {sd= 0.031} 116.1998 + ANGLe CH2E C NH2 500.00 {sd= 0.031} 116.4617 + ANGLe CH2E C O 500.00 {sd= 0.031} 120.9106 + ANGLe CH2P C O 500.00 {sd= 0.031} 120.9106 + ANGLe CH2P CP O 500.00 {sd= 0.031} 124.0000 ! for PCA - AB + ANGLe CH2P CP NH1 500.00 {sd= 0.031} 111.0000 ! for PCA - AB + ANGLe O CP NH1 500.00 {sd= 0.031} 125.0000 ! for PCA - AB + ANGLe CH2E C OH1 500.00 {sd= 0.031} 120.9106 + ANGLe CH3E C O 500.00 {sd= 0.031} 120.9106 ! added EAB + ANGLe CH2E C OC 500.00 {sd= 0.031} 118.4969 + ANGLe CH2E C5 CR1E 500.00 {sd= 0.031} 129.6325 + ANGLe CH2E C5 CR1H 500.00 {sd= 0.031} 131.2043 + ANGLe CH2E C5 NH1 500.00 {sd= 0.031} 123.4237 + ANGLe CH2E C5 NR 500.00 {sd= 0.031} 121.5772 + ANGLe CH2E C5W CR1E 500.00 {sd= 0.031} 126.9191 + ANGLe CH2E C5W CW 500.00 {sd= 0.031} 126.8167 + ANGLe CH2E CF CR1E 500.00 {sd= 0.031} 120.6527 + ANGLe CH2E CH1E CH3E 500.00 {sd= 0.031} 110.6376 + ANGLe CH2E CH1E HA 500.00 {sd= 0.031} 109.2487 + ANGLe CH2E CH1E N 500.00 {sd= 0.031} 103.0552 + ANGLe CH1P CH1E N 500.00 {sd= 0.031} 103.0552 + ANGLe CH2E CH1E NH1 500.00 {sd= 0.031} 110.4763 + ANGLe CH2E CH1E NH3 500.00 {sd= 0.031} 110.4763 ! N term from 108.4924 14-MAR-00 + ANGLe CH2E CH2E CH2E 500.00 {sd= 0.031} 111.3121 + ANGLe CH2E CH2E HA 500.00 {sd= 0.031} 108.7236 + ANGLe CH2E CH2E NH1 500.00 {sd= 0.031} 111.9978 + ANGLe CH2E CH2E NH3 500.00 {sd= 0.031} 111.8939 + ANGLe CH2E CH2E SM 500.00 {sd= 0.031} 112.6822 + ANGLe CH2E CH2E SE 500.00 {sd= 0.031} 112.6822 ! for MSE + ANGLe CH2E CH2P CP 500.00 {sd= 0.031} 103.8000 ! for PCA - AB + ANGLe CH2E CH2P CH2P 500.00 {sd= 0.031} 106.1000 + ANGLe CH1E CH1P CH2P 500.00 {sd= 0.031} 106.1000 + ANGLe CH1P CH2P CH2P 500.00 {sd= 0.031} 106.1000 + ANGLe CH2E CH1P CH2P 500.00 {sd= 0.031} 106.1000 + ANGLe CH2E CH2P CH1P 500.00 {sd= 0.031} 106.1000 + ANGLe CP CH2P HA 500.00 {sd= 0.031} 109.9548 ! for PCA - AB + ANGLe CH1P CH2P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH2P CH1P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH1P CH1E HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH2P CH1E HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH1P CH2E HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH2P CH2E HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH2E CH2P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH1E CH1P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH1E CH2P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH2E CH1P HA 500.00 {sd= 0.031} 109.9548 + ANGLe CH1E CH1P OH1 500.00 {sd= 0.031} 109.9548 + ANGLe CH2E CH1P OH1 500.00 {sd= 0.031} 109.9548 + ANGLe CH1E CH1P OHP 500.00 {sd= 0.031} 109.9548 + ANGLe CH2E CH1P OHP 500.00 {sd= 0.031} 109.9548 + ANGLe CH2E CH3E HA 500.00 {sd= 0.031} 109.4694 + ANGLe CH2E CY CR1E 500.00 {sd= 0.031} 120.9304 + ANGLe CH2E NH1 H 500.00 {sd= 0.031} 118.0987 + ANGLe CH2E NH3 HC 500.00 {sd= 0.031} 109.4693 + ANGLe CH2E OH1 H 500.00 {sd= 0.031} 109.4969 + ANGLe CH2E OH1C H 500.00 {sd= 0.031} 109.4969 ! for covalent Serine (SEC) + ANGLe CH2E S S 500.00 {sd= 0.031} 103.7998 + ANGLe CH2E SH1E H 500.00 {sd= 0.031} 107.9769 + ANGLe CH2E SM CH3E 500.00 {sd= 0.031} 100.8987 + ANGLe CH2E SM CH2E 500.00 {sd= 0.031} 100.8987 + ANGLe CH2E SE CH3E 500.00 {sd= 0.031} 100.8987 ! for MSE + ANGLe CH2E SM PP 500.00 {sd= 0.031} 96.53 + ANGLe CH2G C N 500.00 {sd= 0.031} 117.7918 + ANGLe CH2G C NH1 500.00 {sd= 0.031} 116.3225 + ANGLe CH2G C NH2 500.00 {sd= 0.031} 116.4617 + ANGLe CH2G C O 500.00 {sd= 0.031} 120.6203 + ANGLe CH2G C OC 500.00 {sd= 0.031} 118.4971 + ANGLe CH2G NH1 H 500.00 {sd= 0.031} 119.7297 + ANGLe CH2G NH3 HC 500.00 {sd= 0.031} 109.4688 + ANGLe CH2P CH2P HA 500.00 {sd= 0.031} 110.3818 + ANGLe CH2P CH1P OH1 500.00 {sd= 0.031} 110.3818 + ANGLe CH2P CH1P OHP 500.00 {sd= 0.031} 110.3818 + ANGLe CH2P CH2P N 500.00 {sd= 0.031} 103.2695 + ANGLe CH2P CH2P NH3 500.00 {sd= 0.031} 103.6880 + ANGLe CH2P CH1P N 500.00 {sd= 0.031} 103.2695 + ANGLe CH1P CH2P N 500.00 {sd= 0.031} 103.2695 + ANGLe CH1P CH2P NH3 500.00 {sd= 0.031} 103.6880 + ANGLe CH2P CH1P NH3 500.00 {sd= 0.031} 103.6880 + ANGLe CH2P NH3 HC 500.00 {sd= 0.031} 123.8148 + ANGLe CH1P NH3 HC 500.00 {sd= 0.031} 123.8148 + ANGLe CH3E CH1E CH3E 500.00 {sd= 0.031} 110.7707 + ANGLe CH3E CH1E HA 500.00 {sd= 0.031} 108.1279 + ANGLe CH3E CH1E NH1 500.00 {sd= 0.031} 110.3844 + ANGLe CH3E CH1E NH3 500.00 {sd= 0.031} 110.4751 + ANGLe CH3E CH1E OH1 500.00 {sd= 0.031} 109.300 !included 14-APR-99 + ANGLe CH3E CH1E OAS 500.00 {sd= 0.031} 109.300 !for THR-linked glycans + ANGLe CH3E CH1E OHP 500.00 {sd= 0.031} 109.300 + ANGLe CH3E CH2E HA 500.00 {sd= 0.031} 108.0408 + ANGLe CH3E CH2E OH1 500.00 {sd= 0.031} 108.0961 + ANGLe CH3E CH2E OHP 500.00 {sd= 0.031} 108.0961 + ANGLe CR1E C5 NH1 500.00 {sd= 0.031} 105.6758 + ANGLe CR1E C5 NR 500.00 {sd= 0.031} 109.3402 + ANGLe CR1E C5W CW 500.00 {sd= 0.031} 106.2641 + ANGLe CR1E CF CR1E 500.00 {sd= 0.031} 118.6946 + ANGLe CR1E CR1E CR1E 500.00 {sd= 0.031} 119.9118 + ANGLe CR1E CR1E CR1W 500.00 {sd= 0.031} 121.1513 + ANGLe CR1E CR1E CW 500.00 {sd= 0.031} 118.6734 + ANGLe CR1E CR1E CY 500.00 {sd= 0.031} 121.1348 + ANGLe CR1E CR1E CY2 500.00 {sd= 0.031} 119.6224 + ANGLe CR1E CR1W CY2 500.00 {sd= 0.031} 119.6224 + ANGLe CR1E CR1E HA 500.00 {sd= 0.031} 119.9433 + ANGLe CR1E CR1W CR1W 500.00 {sd= 0.031} 121.4832 + ANGLe CR1E CR1W HA 500.00 {sd= 0.031} 118.7598 + ANGLe CR1E CW CW 500.00 {sd= 0.031} 118.8347 + ANGLe CR1E CY CR1E 500.00 {sd= 0.031} 118.1392 + ANGLe CR1E CY2 CR1E 500.00 {sd= 0.031} 120.3463 + ANGLe CR1E CY2 CR1W 500.00 {sd= 0.031} 120.3463 + ANGLe CR1E CY2 OH1 500.00 {sd= 0.031} 119.8269 + ANGLe CR1E CY2 OHP 500.00 {sd= 0.031} 119.8269 + ANGLe CR1E CY2 OUF 500.00 {sd= 0.031} 119.8269 + ANGLe CR1E NH1 CRH 500.00 {sd= 0.031} 106.8630 + ANGLe CR1E NH1 CW 500.00 {sd= 0.031} 108.9983 + ANGLe CR1E NH1 H 500.00 {sd= 0.031} 125.8235 + ANGLe CR1E NR CRH 500.00 {sd= 0.031} 105.7678 + ANGLe CR1H C5 NH1 500.00 {sd= 0.031} 106.0900 + ANGLe CR1H NH1 CRHH 500.00 {sd= 0.031} 108.9901 + ANGLe CR1H NR CRHH 500.00 {sd= 0.031} 108.9901 + ANGLe CR1H NH1 H 500.00 {sd= 0.031} 125.5054 + ANGLe CR1W CR1E HA 500.00 {sd= 0.031} 119.1706 + ANGLe CR1W CR1W CW 500.00 {sd= 0.031} 117.4515 + ANGLe CR1W CR1W CY2 500.00 {sd= 0.031} 119.6224 + ANGLe CR1W CR1W HA 500.00 {sd= 0.031} 120.2616 + ANGLe CR1W CW CW 500.00 {sd= 0.031} 122.4059 + ANGLe CR1W CW NH1 500.00 {sd= 0.031} 130.1860 + ANGLe CR1W CY2 OH1 500.00 {sd= 0.031} 119.8269 + ANGLe CRH NH1 H 500.00 {sd= 0.031} 126.0322 + ANGLe CRHH NH1 H 500.00 {sd= 0.031} 125.1896 + ANGLe CRHH NR H 500.00 {sd= 0.031} 125.1896 + ANGLe CW CR1E CY2 500.00 {sd= 0.031} 119.6224 + ANGLe CW CR1E HA 500.00 {sd= 0.031} 121.0317 + ANGLe CW CR1W HA 500.00 {sd= 0.031} 121.7822 + ANGLe CW CW NH1 500.00 {sd= 0.031} 107.4081 + ANGLe CW NH1 H 500.00 {sd= 0.031} 125.9221 + ANGLe CY CH2E HA 500.00 {sd= 0.031} 108.0910 + ANGLe CY CR1E HA 500.00 {sd= 0.031} 119.1931 + ANGLe CY2 CR1E HA 500.00 {sd= 0.031} 120.3261 + ANGLe CY2 CR1W HA 500.00 {sd= 0.031} 118.7598 + ANGLe CY2 OH1 H 500.00 {sd= 0.031} 109.4984 + ANGLe CY2 OHP PP 500.00 {sd= 0.031} 120.0000 + ANGLe CY2 OUF SUF 500.00 {sd= 0.031} 120.0000 + ANGLe H NH2 H 500.00 {sd= 0.031} 123.6294 + ANGLe HA CH1E N 500.00 {sd= 0.031} 111.0977 + ANGLe HA CH1E NH1 500.00 {sd= 0.031} 108.0508 + ANGLe HA CH1E NH3 500.00 {sd= 0.031} 108.5074 + ANGLe HA CH1E OH1 500.00 {sd= 0.031} 108.6930 !assume like CH2E + ANGLe HA CH1E OAS 500.00 {sd= 0.031} 108.6930 ! for THR glycosylation + ANGLe HA CH1P OH1 500.00 {sd= 0.031} 108.6930 !assume like CH2E + ANGLe HA CH1E OHP 500.00 {sd= 0.031} 108.6930 !assume like CH2E + ANGLe HA CH2E HA 500.00 {sd= 0.031} 109.4074 + ANGLe HA CH2E NH1 500.00 {sd= 0.031} 108.9030 + ANGLe HA CH2E NH3 500.00 {sd= 0.031} 108.9390 + ANGLe HA CH2E OH1 500.00 {sd= 0.031} 108.6930 + ANGLe HA CH2E OH1C 500.00 {sd= 0.031} 108.6930 ! for covalent Serine (SEC) + ANGLe HA CH2E OHP 500.00 {sd= 0.031} 108.6930 + ANGLe HA CH2E S 500.00 {sd= 0.031} 107.9228 + ANGLe HA CH2E SH1E 500.00 {sd= 0.031} 107.9185 + ANGLe HA CH2E SH1C 500.00 {sd= 0.031} 107.9185 + ANGLe HA CH2E SM 500.00 {sd= 0.031} 108.6768 + ANGLe HA CH2E SE 500.00 {sd= 0.031} 108.6768 ! for MSE + ANGLe HA CH2G HA 500.00 {sd= 0.031} 108.8718 + ANGLe HA CH2G NH1 500.00 {sd= 0.031} 108.8510 + ANGLe HA CH2G NH3 500.00 {sd= 0.031} 108.8586 + ANGLe HA CH2P HA 500.00 {sd= 0.031} 110.4563 + ANGLe HA CH2P N 500.00 {sd= 0.031} 110.8278 + ANGLe HA CH2P NH3 500.00 {sd= 0.031} 110.7246 + ANGLe OH1 CH1P N 500.00 {sd= 0.031} 110.8278 + ANGLe OH1 CH1P NH3 500.00 {sd= 0.031} 110.7246 + ANGLe OHP CH1P N 500.00 {sd= 0.031} 110.8278 + ANGLe OHP CH1P NH3 500.00 {sd= 0.031} 110.7246 + ANGLe HA CH3E HA 500.00 {sd= 0.031} 109.4703 + ANGLe HA CH3E SM 500.00 {sd= 0.031} 109.4700 + ANGLe HA CH3E SE 500.00 {sd= 0.031} 109.4700 ! for MSE + ANGLe HA CH3E NH1 500.00 {sd= 0.031} 120.7000 ! for NME + ANGLe HA CR1E NH1 500.00 {sd= 0.031} 125.8803 + ANGLe HA CR1E NR 500.00 {sd= 0.031} 125.1878 + ANGLe HA CR1H NH1 500.00 {sd= 0.031} 126.4359 + ANGLe HA CR1H NR 500.00 {sd= 0.031} 126.4359 + ANGLe HA CRH NH1 500.00 {sd= 0.031} 124.3534 + ANGLe HA CRH NR 500.00 {sd= 0.031} 124.3404 + ANGLe HA CRHH NH1 500.00 {sd= 0.031} 125.8381 + ANGLe HA CRHH NR 500.00 {sd= 0.031} 125.8381 + ANGLe HC NC2 HC 500.00 {sd= 0.031} 120.0016 + ANGLe HC NH3 HC 500.00 {sd= 0.031} 108.1992 + ANGLe N C O 500.00 {sd= 0.031} 122.1842 ! 14-MAR-00 + ANGLe NC2 C NC2 500.00 {sd= 0.031} 119.7933 + ANGLe NC2 C NH1 500.00 {sd= 0.031} 120.1034 + ANGLe NH1 C O 500.00 {sd= 0.031} 122.9907 + ANGLe NH1 CRH NR 500.00 {sd= 0.031} 111.3061 + ANGLe NH1 CRHH NH1 500.00 {sd= 0.031} 108.3237 + ANGLe NH1 CRHH NR 500.00 {sd= 0.031} 108.3237 + ANGLe NH2 C O 500.00 {sd= 0.031} 122.6277 + ANGLe OC C OC 500.00 {sd= 0.031} 123.3548 + ANGLe OC C OH1 500.00 {sd= 0.031} 123.3548 + ANGLe OH1 CH1E OH1 500.00 {sd= 0.031} 109.600 ! Feb-17 + ANGLe CCIS CH1E CH1E 500.00 {sd= 0.031} 109.0754 + ANGLe CCIS CH1E CH2E 500.00 {sd= 0.031} 110.1094 + ANGLe CCIS CH1E CH3E 500.00 {sd= 0.031} 110.4838 + ANGLe CCIS CH1E HA 500.00 {sd= 0.031} 108.9914 + ANGLe CCIS CH1E N 500.00 {sd= 0.031} 111.9082 + ANGLe CCIS CH1E NH1 500.00 {sd= 0.031} 111.1396 + ANGLe CCIS CH1E NH3 500.00 {sd= 0.031} 111.1703 + ANGLe CCIS CH2E CH1E 500.00 {sd= 0.031} 112.5947 + ANGLe CCIS CH2E CH2E 500.00 {sd= 0.031} 112.5943 + ANGLe CCIS CH2E HA 500.00 {sd= 0.031} 108.5877 + ANGLe CCIS CH2G HA 500.00 {sd= 0.031} 108.8528 + ANGLe CCIS CH2G NH1 500.00 {sd= 0.031} 112.4999 + ANGLe CCIS CH2G NH3 500.00 {sd= 0.031} 112.4990 + ANGLe CCIS N CH1E 500.00 {sd= 0.031} 122.7632 + ANGLe CCIS N CH2P 500.00 {sd= 0.031} 125.1134 + ANGLe CCIS N CH1P 500.00 {sd= 0.031} 125.1134 + ANGLe CCIS NC2 HC 500.00 {sd= 0.031} 119.9992 + ANGLe CCIS NH1 CH1E 500.00 {sd= 0.031} 121.6541 + ANGLe CCIS NH1 CH2E 500.00 {sd= 0.031} 124.1226 + ANGLe CCIS NH1 CH2G 500.00 {sd= 0.031} 120.5859 + ANGLe CCIS NH1 H 500.00 {sd= 0.031} 119.2489 + ANGLe CCIS NH2 H 500.00 {sd= 0.031} 118.1853 + ANGLe CH1E CCIS N 500.00 {sd= 0.031} 116.9940 ! CCIS for cis peptide + ANGLe CH1E CCIS NH1 500.00 {sd= 0.031} 116.1998 + ANGLe CH1E CCIS O 500.00 {sd= 0.031} 120.8258 + ANGLe CH1E CCIS OC 500.00 {sd= 0.031} 118.0611 + ANGLe CH2E CCIS NH2 500.00 {sd= 0.031} 116.4617 + ANGLe CH2E CCIS O 500.00 {sd= 0.031} 120.9106 + ANGLe CH2E CCIS OC 500.00 {sd= 0.031} 118.4969 + ANGLe CH2G CCIS N 500.00 {sd= 0.031} 117.7918 + ANGLe CH2G CCIS NH1 500.00 {sd= 0.031} 116.3225 + ANGLe CH2G CCIS O 500.00 {sd= 0.031} 120.6203 + ANGLe CH2G CCIS OC 500.00 {sd= 0.031} 118.4971 + ANGLe CH3E NH1 H 500.00 {sd= 0.031} 117.1000 ! for NME + ANGLe N CCIS O 500.00 {sd= 0.031} 122.0016 + ANGLe NC2 CCIS NC2 500.00 {sd= 0.031} 119.7933 + ANGLe NC2 CCIS NH1 500.00 {sd= 0.031} 120.1034 + ANGLe NH1 CCIS O 500.00 {sd= 0.031} 122.9907 + ANGLe NH2 CCIS O 500.00 {sd= 0.031} 122.6277 + ANGLe OC CCIS OC 500.00 {sd= 0.031} 123.3548 + ANGLe O C NC2 500.00 {sd= 0.031} 119.2000 ! for CIR - VR + + ANGLE OR3 PP OP1 500.00 109.600 + ANGLE OP1 PP OP1 500.00 120.000 + ANGLE OR3 PP NR 500.00 109.600 + ANGLE OP1 PP NR 500.00 120.000 + ANGLE OR3 PP SM 500.00 109.600 + ANGLE OP1 PP SM 500.00 120.000 + ANGLE OR3 PP OHP 500.00 109.600 + ANGLE OP1 PP OHP 500.00 120.000 + ANGLE PP NR CRHH 500.00 120.000 + ANGLE PP NR CR1H 500.00 120.000 + ANGLE OUF SUF OUF 500.00 109.600 + +! next ones added for iron-sulphur cluster + ANGLE CH2E SH1E FS 500.00 117.900 + ANGLE SH1E FS SH1E 500.00 105.100 + ANGLE SH1E FS SF 500.00 109.500 + ANGLE SF FS SF 500.00 104.700 + ANGLE FS SF FS 500.00 74.600 + + ANGLE PP OR3 CD28 500.00 120.000 + ANGLE OR3 CD28 HD28 500.00 109.500 + ANGLE OR3 CD28 HD29 500.00 109.500 + ANGLE OR3 CD28 CD29 500.00 109.500 + + +! Residue PNS +eval ($pd_v=$pd_x* 760.0) ANGLE P O3P CD28 $pd_v 120.000 +eval ($pd_v=$pd_x* 720.0) ANGLE O3P CD28 HD28 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE O3P CD28 HD29 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE O3P CD28 CD29 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD28 CD28 HD29 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD28 CD28 CD29 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD29 CD28 CD29 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD28 CD29 CD30 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD28 CD29 CD31 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD28 CD29 CD32 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD30 CD29 CD31 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD30 CD29 CD32 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD31 CD29 CD32 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD30 HD31 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD30 HD32 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD30 HD30 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD31 CD30 HD32 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD31 CD30 HD30 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD32 CD30 HD30 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD31 HD34 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD31 HD35 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD31 HD33 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD34 CD31 HD35 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD34 CD31 HD33 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD35 CD31 HD33 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD29 CD32 HD36 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD29 CD32 OD33 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD29 CD32 CD34 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD36 CD32 OD33 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD36 CD32 CD34 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE OD33 CD32 CD34 $pd_v 109.500 +eval ($pd_v=$pd_x* 764.5) ANGLE CD32 OD33 HD46 $pd_v 109.500 +eval ($pd_v=$pd_x* 962.3) ANGLE CD32 CD34 OD35 $pd_v 121.000 +eval ($pd_v=$pd_x* 958.0) ANGLE CD32 CD34 ND36 $pd_v 115.000 +eval ($pd_v=$pd_x* 959.3) ANGLE OD35 CD34 ND36 $pd_v 124.000 +eval ($pd_v=$pd_x* 558.1) ANGLE CD34 ND36 HD48 $pd_v 123.000 +eval ($pd_v=$pd_x* 962.6) ANGLE CD34 ND36 CD37 $pd_v 122.000 +eval ($pd_v=$pd_x* 722.5) ANGLE HD48 ND36 CD37 $pd_v 115.000 +eval ($pd_v=$pd_x* 883.5) ANGLE ND36 CD37 HD37 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE ND36 CD37 HD38 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE ND36 CD37 CD38 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD37 CD37 HD38 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD37 CD37 CD38 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD38 CD37 CD38 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD37 CD38 HD39 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD37 CD38 HD4A $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE CD37 CD38 CD39 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD39 CD38 HD4A $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD39 CD38 CD39 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD4A CD38 CD39 $pd_v 109.500 +eval ($pd_v=$pd_x* 962.3) ANGLE CD38 CD39 OD40 $pd_v 121.000 +eval ($pd_v=$pd_x* 958.0) ANGLE CD38 CD39 ND41 $pd_v 115.000 +eval ($pd_v=$pd_x* 959.3) ANGLE OD40 CD39 ND41 $pd_v 124.000 +eval ($pd_v=$pd_x* 558.1) ANGLE CD39 ND41 HD41 $pd_v 123.000 +eval ($pd_v=$pd_x* 962.6) ANGLE CD39 ND41 CD42 $pd_v 122.000 +eval ($pd_v=$pd_x* 722.5) ANGLE HD41 ND41 CD42 $pd_v 115.000 +eval ($pd_v=$pd_x* 883.5) ANGLE ND41 CD42 HD42 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE ND41 CD42 HD43 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.5) ANGLE ND41 CD42 CD43 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD42 CD42 HD43 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD42 CD42 CD43 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD43 CD42 CD43 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD42 CD43 HD44 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CD42 CD43 HD45 $pd_v 109.500 +eval ($pd_v=$pd_x* 883.0) ANGLE CD42 CD43 SD44 $pd_v 113.000 +eval ($pd_v=$pd_x* 720.0) ANGLE HD44 CD43 HD45 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD44 CD43 SD44 $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE HD45 CD43 SD44 $pd_v 109.500 +eval ($pd_v=$pd_x* 765.9) ANGLE CD43 SD44 HD47 $pd_v 96.000 + +! Residue DRG +eval ($pd_v=$pd_x* 880.0) ANGLE CHAC CHAS CHAD $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAC CHAS NHAQ $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CHAC CHAS CHAO $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAD CHAS NHAQ $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CHAD CHAS CHAO $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE NHAQ CHAS CHAO $pd_v 104.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CHAS NHAQ OHAH $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAS NHAQ CHAR $pd_v 104.000 +eval ($pd_v=$pd_x* 720.0) ANGLE OHAH NHAQ CHAR $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE NHAQ OHAH HHAA $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE NHAQ CHAR CHAA $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE NHAQ CHAR CHAB $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE NHAQ CHAR CHAI $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAA CHAR CHAB $pd_v 111.000 +eval ($pd_v=$pd_x* 760.0) ANGLE CHAA CHAR CHAI $pd_v 109.500 +eval ($pd_v=$pd_x* 760.0) ANGLE CHAB CHAR CHAI $pd_v 109.500 +eval ($pd_v=$pd_x* 800.0) ANGLE CHAR CHAI CHAO $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CHAS CHAO CHAI $pd_v 108.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CHAS CHAO CHAJ $pd_v 120.000 +eval ($pd_v=$pd_x* 800.0) ANGLE CHAI CHAO CHAJ $pd_v 126.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAO CHAJ SHAL $pd_v 111.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CHAJ SHAL S $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE SHAL S CH2E $pd_v 104.000 +eval ($pd_v=$pd_x* 880.0) ANGLE S CHB CHA $pd_v 113.000 +eval ($pd_v=$pd_x* 880.0) ANGLE CHB CHA CH_Y $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CHB CHA NH_Y $pd_v 109.500 +eval ($pd_v=$pd_x* 880.0) ANGLE CH_Y CHA NH_Y $pd_v 109.500 +eval ($pd_v=$pd_x* 960.0) ANGLE CHA CH_Y OHXT $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE CHA CH_Y OH_Y $pd_v 117.000 +eval ($pd_v=$pd_x* 960.0) ANGLE OHXT CH_Y OH_Y $pd_v 126.000 +eval ($pd_v=$pd_x* 720.0) ANGLE CHA NH_Y HHAC $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CHA NH_Y HHAD $pd_v 109.500 +eval ($pd_v=$pd_x* 720.0) ANGLE CHA NH_Y HHAB $pd_v 109.500 +eval ($pd_v=$pd_x* 640.0) ANGLE HHAC NH_Y HHAD $pd_v 109.500 +eval ($pd_v=$pd_x* 640.0) ANGLE HHAC NH_Y HHAB $pd_v 109.500 +eval ($pd_v=$pd_x* 640.0) ANGLE HHAD NH_Y HHAB $pd_v 109.500 + + IMPRoper C CH1E HA HA 500.00 {sd= 0.031} 0 -70.4072 + IMPRoper C CH1E OC OC 500.00 {sd= 0.031} 0 0.0210 + IMPRoper C CH2E HA HA 500.00 {sd= 0.031} 0 -70.4459 + IMPRoper HA HA C HA 500.00 {sd= 0.031} 0 -70.4459 !EAB + IMPRoper C CH1E O NH2 500.00 {sd= 0.031} 0 0.0124 + IMPRoper C CH2E O NH2 500.00 {sd= 0.031} 0 0.0124 + IMPRoper C CH3E O NH2 500.00 {sd= 0.031} 0 0.0124 + IMPRoper C CH2E OC OC 500.00 {sd= 0.031} 0 -0.0137 + IMPRoper C CH2E OC OH1 500.00 {sd= 0.031} 0 -0.0137 + IMPRoper C CH2G OC OC 500.00 {sd= 0.031} 0 0.0223 + IMPRoper C NC2 H NH1 500.00 {sd= 0.031} 0 -0.0121 + IMPRoper C NH1 HA HA 500.00 {sd= 0.031} 0 -70.8745 + IMPRoper C NH1 NC2 NC2 500.00 {sd= 0.031} 0 -0.0088 + IMPRoper C NH3 HA HA 500.00 {sd= 0.031} 0 70.6479 + IMPRoper C5 CH1E HA HA 500.00 {sd= 0.031} 0 -69.9815 + IMPRoper C5 CH2E NH1 CR1E 500.00 {sd= 0.031} 0 -0.0386 + IMPRoper C5 CH2E NH1 CR1H 500.00 {sd= 0.031} 0 -0.0237 + IMPRoper C5 CH2E NR CR1E 500.00 {sd= 0.031} 0 0.0178 + IMPRoper C5 CR1E NH1 CRH 500.00 {sd= 0.031} 0 0.0072 + IMPRoper C5 CR1E NR CRH 500.00 {sd= 0.031} 0 -0.0138 + IMPRoper C5 CR1H NH1 CRHH 500.00 {sd= 0.031} 0 -0.0209 + IMPRoper C5 CR1H NR CRHH 500.00 {sd= 0.031} 0 -0.0209 + IMPRoper C5 NH1 CRH NR 500.00 {sd= 0.031} 0 -0.0652 + IMPRoper C5 NH1 CRHH NH1 500.00 {sd= 0.031} 0 -0.0660 + IMPRoper C5 NH1 CRHH NR 500.00 {sd= 0.031} 0 -0.0660 + IMPRoper C5 NR CRH NH1 500.00 {sd= 0.031} 0 0.0250 + IMPRoper C5W CH1E HA HA 500.00 {sd= 0.031} 0 -70.0142 + IMPRoper C5W CH2E HA HA 500.00 {sd= 0.031} 0 -70.0142 + IMPRoper C5W CW CR1E CR1E 500.00 {sd= 0.031} 0 -179.9506 + IMPRoper C5W CW CR1E CY2 500.00 {sd= 0.031} 0 -179.9506 + IMPRoper C5W CW CW CR1W 500.00 {sd= 0.031} 0 179.9618 + IMPRoper CF CH1E HA HA 500.00 {sd= 0.031} 0 -70.0169 + IMPRoper CF CR1E CR1E CR1E 500.00 {sd= 0.031} 0 0.0069 + IMPRoper CF CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9729 + IMPRoper CH1E C CH2P N 500.00 {sd= 0.031} 0 0.0332 + IMPRoper CH1E C CH1P N 500.00 {sd= 0.031} 0 0.0332 + IMPRoper CH1E C H NH1 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH3E C H NH1 500.00 {sd= 0.031} 0 0.0000 + IMPRoper CH1E C N CH1E 500.00 {sd= 0.031} 0 179.9873 + IMPRoper CH3E C N CH1E 500.00 {sd= 0.031} 0 179.9873 + IMPRoper CH1E C N CH2P 500.00 {sd= 0.031} 0 0.0025 + IMPRoper CH1E C N CH1P 500.00 {sd= 0.031} 0 0.0025 + IMPRoper CH1E N C CH2G 500.00 {sd= 0.031} 0 179.9856 + IMPRoper CH1E NH1 C CH2G 500.00 {sd= 0.031} 0 -179.9916 + IMPRoper CH2E C NH1 CH2G 500.00 {sd= 0.031} 0 -179.9916 !for iso-peptidebond with GLY (AB 2015-10) + IMPRoper CH1E C NH1 CH1E 500.00 {sd= 0.031} 0 -180.0067 + IMPRoper CH1E C NH1 CH2E 500.00 {sd= 0.031} 0 -180.0067 + IMPRoper CH1E C NH1 CH3E 500.00 {sd= 0.031} 0 -180.0067 ! for NME + IMPRoper HA HA CH3E NH1 500.00 {sd= 0.031} 0 35.2640 ! for NME + IMPRoper CH2G C NH1 CH3E 500.00 {sd= 0.031} 0 -180.0067 ! for NME + IMPRoper CH1E C NH1 CH2G 500.00 {sd= 0.031} 0 -180.0018 + IMPRoper CH1E C NH2 H 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH1E C NH1 H 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH3E C NH1 H 500.00 {sd= 0.031} 0 0.0000 + IMPRoper CH1E C NH1 HA 500.00 {sd= 0.031} 0 66.2535 + IMPRoper CH1E NH1 C HA 500.00 {sd= 0.031} 0 66.2535 ! d-amino acid + IMPRoper CH1E CCIS NH1 HA 500.00 {sd= 0.031} 0 66.2535 + IMPRoper CH1E NH1 CCIS HA 500.00 {sd= 0.031} 0 66.2535 ! d-amino acid + IMPRoper CH1E C NH3 HA 500.00 {sd= 0.031} 0 66.3265 + IMPRoper CH1E NH3 C HA 500.00 {sd= 0.031} 0 66.3265 ! d-amino acid + IMPRoper CH1E CH1E HA HA 500.00 {sd= 0.031} 0 -69.6639 + IMPRoper CH1P CH1E HA HA 500.00 {sd= 0.031} 0 -69.6639 + IMPRoper CH2E C N HA 500.00 {sd= 0.031} 0 67.7957 + IMPRoper HA C N CH2E 500.00 {sd= 0.031} 0 67.7957 + IMPRoper CH2E C NH1 H 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH2P CP NH1 H 500.00 {sd= 0.031} 0 0.0000 ! for PCA - AB + IMPRoper CH2E N C HA 500.00 {sd= 0.031} 0 67.7957 ! d-amino acid + IMPRoper CH2E NH1 C O 500.00 {sd= 0.031} 0 0.0000 ! for CIR - VR + IMPRoper CH2E CCIS N HA 500.00 {sd= 0.031} 0 67.7957 ! cis pept + IMPRoper CH2E N CCIS HA 500.00 {sd= 0.031} 0 67.7957 ! cis pept + IMPRoper CH2E C NH1 HA 500.00 {sd= 0.031} 0 66.1640 ! d-amino acid + IMPRoper CH2E NH1 C HA 500.00 {sd= 0.031} 0 66.1640 + IMPRoper CH2E NH1 HA HA 500.00 {sd= 0.031} 0 -70.8745 + IMPRoper CH2E C NH1 HA 500.00 {sd= 0.031} 0 66.1640 + IMPRoper CH2E C NH1 CH1E 500.00 {sd= 0.031} 0 -180.0067 + IMPRoper CH2E C NH1 CH2E 500.00 {sd= 0.031} 0 -180.0067 + IMPRoper CH2E NH1 C CH1E 500.00 {sd= 0.031} 0 -180.0067 ! d-amino acid + IMPRoper CH2E CCIS NH1 HA 500.00 {sd= 0.031} 0 66.1640 + IMPRoper CH2E NH1 CCIS HA 500.00 {sd= 0.031} 0 66.1640 ! d-amino acid + IMPRoper CH2E C NH2 H 500.00 {sd= 0.031} 0 0.0000 + IMPRoper CH2E H C NH2 500.00 {sd= 0.031} 0 0.0032 + IMPRoper CH2E C NH3 HA 500.00 {sd= 0.031} 0 66.3265 + IMPRoper CH2E NH3 C HA 500.00 {sd= 0.031} 0 66.3265 + IMPRoper CH2E C5W CW CW 500.00 {sd= 0.031} 0 179.9679 + IMPRoper CH2E CF CR1E CR1E 500.00 {sd= 0.031} 0 -179.9993 + IMPRoper CH2E CH1E HA HA 500.00 {sd= 0.031} 0 -70.0781 + IMPRoper CH2P CH1E HA HA 500.00 {sd= 0.031} 0 -70.0781 + IMPRoper CH2P CH2E HA OHP 500.00 {sd= 0.031} 0 -65.9907 + IMPRoper CH2P CH2E HA OH1 500.00 {sd= 0.031} 0 -65.9907 + IMPRoper CH2P CH2E HA OHP 500.00 {sd= 0.031} 0 -65.9907 + IMPRoper CH2E CH2E HA HA 500.00 {sd= 0.031} 0 -70.7825 + IMPRoper CH2P CH2E HA HA 500.00 {sd= 0.031} 0 -70.7825 + IMPRoper CP CH2E HA HA 500.00 {sd= 0.031} 0 -70.7825 ! for PCA - AB + IMPRoper CH2E CH1P HA HA 500.00 {sd= 0.031} 0 -70.0781 + IMPRoper CH2E CH2P HA HA 500.00 {sd= 0.031} 0 -70.7825 + IMPRoper CH2E CH3E CH1E HA 500.00 {sd= 0.031} 0 -65.2137 + IMPRoper CH2E CY CR1E CR1E 500.00 {sd= 0.031} 0 -179.9903 + IMPRoper CH2G C N CH2P 500.00 {sd= 0.031} 0 -0.0116 + IMPRoper CH2G C NH1 CH2G 500.00 {sd= 0.031} 0 179.9899 + IMPRoper CH2G C NH1 H 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH2G C NH2 H 500.00 {sd= 0.031} 0 0.0000 !c + IMPRoper CH2P CH1E HA HA 500.00 {sd= 0.031} 0 -71.9385 + IMPRoper CH2P CH1E HC HC 500.00 {sd= 0.031} 0 -70.7727 + IMPRoper CH2P CH2E HA HA 500.00 {sd= 0.031} 0 -71.8986 + IMPRoper CH3E C NH1 H 500.00 {sd= 0.031} 0 65.9907 + IMPRoper CH3E C NH1 HA 500.00 {sd= 0.031} 0 65.9907 + IMPRoper CH3E NH1 C HA 500.00 {sd= 0.031} 0 65.9907 !d-amino acid + IMPRoper CH3E C NH1 CH2G 500.00 {sd= 0.031} 0 -179.9916 + IMPRoper CH3E CCIS NH1 HA 500.00 {sd= 0.031} 0 65.9907 + IMPRoper CH3E NH1 CCIS HA 500.00 {sd= 0.031} 0 65.9907 !d-amino acid + IMPRoper CH3E C NH3 HA 500.00 {sd= 0.031} 0 65.6779 + IMPRoper CH3E NH3 C HA 500.00 {sd= 0.031} 0 65.6779 !d-amino acid + IMPRoper CH3E CCIS NH3 HA 500.00 {sd= 0.031} 0 65.6779 + IMPRoper CH3E NH3 CCIS HA 500.00 {sd= 0.031} 0 65.6779 !d-amino acid + IMPRoper CH3E CH1E HA HA 500.00 {sd= 0.031} 0 -70.1069 + IMPRoper CH3E CH3E CH1E HA 500.00 {sd= 0.031} 0 -65.0462 + IMPRoper CH3E CH3E CH2E HA 500.00 {sd= 0.031} 0 -65.1424 + IMPRoper CH3E OH1 CH1E HA 500.00 {sd= 0.031} 0 66.1521 + IMPRoper CH3E OAS CH1E HA 500.00 {sd= 0.031} 0 66.1521 !for THR glycosylation + IMPRoper CH3E OHP CH1E HA 500.00 {sd= 0.031} 0 66.1521 + IMPRoper CH2P OHP CH1P HA 500.00 {sd= 0.031} 0 66.1521 ! To change sign if stereochemistry is wrong + IMPRoper CH2P OHP CH1E HA 500.00 {sd= 0.031} 0 66.1521 ! To change sign if stereochemistry is wrong + IMPRoper CH3E OH1 CH1E HA 500.00 {sd= 0.031} 0 66.1521 + IMPRoper CH3E OHP CH1E HA 500.00 {sd= 0.031} 0 66.1521 + IMPRoper CH2P OH1 CH1P HA 500.00 {sd= 0.031} 0 66.1521 ! To change sign if stereochemistry is wrong + IMPRoper CH2P OHP CH1P HA 500.00 {sd= 0.031} 0 66.1521 ! To change sign if stereochemistry is wrong + IMPRoper CR1E C5 NH1 CRH 500.00 {sd= 0.031} 0 0.0557 + IMPRoper CR1E C5 NR CRH 500.00 {sd= 0.031} 0 -0.0198 + IMPRoper CR1E C5W CW CR1E 500.00 {sd= 0.031} 0 179.9645 + IMPRoper CR1E CF CR1E CR1E 500.00 {sd= 0.031} 0 -0.0034 + IMPRoper CR1E CF CR1E HA 500.00 {sd= 0.031} 0 -179.9624 + IMPRoper CR1E CR1E CR1E CR1E 500.00 {sd= 0.031} 0 -0.0034 + IMPRoper CR1E CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9935 + IMPRoper CR1E CR1E CR1W CR1W 500.00 {sd= 0.031} 0 -0.0413 + IMPRoper CR1E CY2 CR1W CR1W 500.00 {sd= 0.031} 0 -0.0413 + IMPRoper CR1E CR1E CR1W HA 500.00 {sd= 0.031} 0 -179.9535 + IMPRoper CR1E CR1E CW CW 500.00 {sd= 0.031} 0 -0.0109 + IMPRoper CR1E CR1E CY CR1E 500.00 {sd= 0.031} 0 0.0135 + IMPRoper CR1E CR1E CY2 CR1E 500.00 {sd= 0.031} 0 0.0133 + IMPRoper CR1E CR1E CY2 OH1 500.00 {sd= 0.031} 0 -179.9788 + IMPRoper CR1W CR1W CY2 OH1 500.00 {sd= 0.031} 0 -179.9788 + IMPRoper CR1E CR1E CY2 OHP 500.00 {sd= 0.031} 0 -179.9788 + IMPRoper CR1E CR1E CY2 OUF 500.00 {sd= 0.031} 0 -179.9788 + IMPRoper CR1E CR1W CR1W CW 500.00 {sd= 0.031} 0 0.0360 + IMPRoper CR1E CR1W CR1W HA 500.00 {sd= 0.031} 0 179.9725 + IMPRoper CR1E CW CW CR1W 500.00 {sd= 0.031} 0 0.0072 + IMPRoper CR1E CW CW NH1 500.00 {sd= 0.031} 0 -179.9720 + IMPRoper CR1E CY CR1E HA 500.00 {sd= 0.031} 0 -179.9985 + IMPRoper CR1E CY2 CR1E HA 500.00 {sd= 0.031} 0 179.9891 + IMPRoper CR1E CY2 CR1W HA 500.00 {sd= 0.031} 0 179.9891 + IMPRoper CR1E NH1 C5 HA 500.00 {sd= 0.031} 0 -0.0175 + IMPRoper CR1E NH1 CRH NR 500.00 {sd= 0.031} 0 -0.0206 + IMPRoper CR1E NH1 CW CR1W 500.00 {sd= 0.031} 0 -179.9685 + IMPRoper CR1E NR C5 HA 500.00 {sd= 0.031} 0 -0.0096 + IMPRoper CR1E NR CRH NH1 500.00 {sd= 0.031} 0 0.0490 + IMPRoper CR1H C5 NH1 CRHH 500.00 {sd= 0.031} 0 0.0496 + IMPRoper CR1H C5 NR CRHH 500.00 {sd= 0.031} 0 0.0496 + IMPRoper CR1H NH1 C5 HA 500.00 {sd= 0.031} 0 0.0047 + IMPRoper CR1H NR C5 HA 500.00 {sd= 0.031} 0 0.0047 + IMPRoper CR1H NH1 CRHH NH1 500.00 {sd= 0.031} 0 0.0534 + IMPRoper CR1H NR CRHH NH1 500.00 {sd= 0.031} 0 0.0534 + IMPRoper CR1W CR1E CR1E CW 500.00 {sd= 0.031} 0 0.0275 + IMPRoper CR1W CY2 CR1E CW 500.00 {sd= 0.031} 0 0.0275 + IMPRoper CR1W CR1E CR1E HA 500.00 {sd= 0.031} 0 -179.9902 + IMPRoper CR1W CR1W CR1E HA 500.00 {sd= 0.031} 0 179.9587 + IMPRoper CR1W CR1W CW CW 500.00 {sd= 0.031} 0 -0.0194 + IMPRoper CR1W CR1W CW NH1 500.00 {sd= 0.031} 0 179.9546 + IMPRoper CR1W CY2 CR1E HA 500.00 {sd= 0.031} 0 179.9891 + IMPRoper CR1W CR1W CY2 OH1 500.00 {sd= 0.031} 0 -179.9788 + IMPRoper CRH NH1 NR HA 500.00 {sd= 0.031} 0 0.0429 + IMPRoper CRH NR NH1 HA 500.00 {sd= 0.031} 0 -0.0123 + IMPRoper CRHH NH1 NH1 HA 500.00 {sd= 0.031} 0 0.0414 + IMPRoper CRHH NH1 NR HA 500.00 {sd= 0.031} 0 0.0414 + IMPRoper CW CW CR1E CY2 500.00 {sd= 0.031} 0 0.0275 + IMPRoper CW CW NH1 H 500.00 {sd= 0.031} 0 179.9788 + IMPRoper CW NH1 CR1E HA 500.00 {sd= 0.031} 0 -179.9528 + IMPRoper CY CH1E HA HA 500.00 {sd= 0.031} 0 -70.0662 + IMPRoper CY CR1E CR1E CY2 500.00 {sd= 0.031} 0 -0.0270 + IMPRoper CY CR1E CR1E HA 500.00 {sd= 0.031} 0 -179.9841 + IMPRoper CY2 CR1W CR1W CW 500.00 {sd= 0.031} 0 0.0360 + IMPRoper CY2 CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9517 + IMPRoper CY2 CR1W CR1W HA 500.00 {sd= 0.031} 0 179.9517 + IMPRoper H C CH2E NH1 500.00 {sd= 0.031} 0 0.0051 + IMPRoper H C CH3E NH1 500.00 {sd= 0.031} 0 0.0051 + IMPRoper H C5 CRH NH1 500.00 {sd= 0.031} 0 0.0263 + IMPRoper H CR1H CRHH NH1 500.00 {sd= 0.031} 0 0.0000 ! added for doubly protonated HIS, 1/10/12 Pieter Hendrickx + IMPRoper H CR1E CRH NH1 500.00 {sd= 0.031} 0 0.0000 ! added for doubly protonated HIS, 1/10/12 Pieter Hendrickx + IMPRoper H C5 CRHH NH1 500.00 {sd= 0.031} 0 0.0282 + IMPRoper H H C NH1 500.00 {sd= 0.031} 0 0.0032 + IMPRoper H H C NH2 500.00 {sd= 0.031} 0 0.0032 + IMPRoper HA C NH1 CH1E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA C NH1 CH2E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA C NH1 CH3E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA CCIS NH1 CH1E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA CCIS NH1 CH2E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA CCIS NH1 CH3E 500.00 {sd= 0.031} 0 66.1640 + IMPRoper HA CH1E HA HA 500.00 {sd= 0.031} 0 -66.5692 + IMPRoper HA NH1 HA HA 500.00 {sd= 0.031} 0 -66.5692 ! added for NME CA improper, 6/8/23 Alexandre Bonvin + IMPRoper HA CH2E HA HA 500.00 {sd= 0.031} 0 -66.5934 + IMPRoper HA HA CH1E OH1 500.00 {sd= 0.031} 0 -69.8494 + IMPRoper HA HA CH1E OH1C 500.00 {sd= 0.031} 0 -69.8494 ! for covalent Serine (SEC) + IMPRoper HA HA CH1P OH1 500.00 {sd= 0.031} 0 -69.8494 + IMPRoper HA HA CH1P OHP 500.00 {sd= 0.031} 0 -69.8494 + IMPRoper HA HA CH1E OHP 500.00 {sd= 0.031} 0 -69.8494 + IMPRoper HA HA CH1E S 500.00 {sd= 0.031} 0 -72.0980 + IMPRoper HA HA CH1E SH1E 500.00 {sd= 0.031} 0 -72.0234 + IMPRoper HA HA CH1E SH1C 500.00 {sd= 0.031} 0 -72.0234 + IMPRoper HA HA CH1E SM 500.00 {sd= 0.031} 0 -72.0234 + IMPRoper HA HA CH1E SE 500.00 {sd= 0.031} 0 -72.0234 ! for MSE + IMPRoper HA HA CH2E NH1 500.00 {sd= 0.031} 0 -70.1253 + IMPRoper HA HA CH2E NH3 500.00 {sd= 0.031} 0 -70.4126 + IMPRoper HA HA CH2E SM 500.00 {sd= 0.031} 0 -72.4655 + IMPRoper HA HA CH2E SE 500.00 {sd= 0.031} 0 -72.4655 ! for MSE + IMPRoper HA HA CH2P N 500.00 {sd= 0.031} 0 -72.1561 + IMPRoper HA HA CH1P N 500.00 {sd= 0.031} 0 -72.1561 + IMPRoper CY CR1E CR1E HA 500.00 {sd= 0.031} 0 -179.9841 + IMPRoper O C NC2 HC 500.00 {sd= 0.031} 0 180.0000 ! for CIR - VR + IMPRoper O C NH1 H 500.00 {sd= 0.031} 0 -179.9841 + IMPRoper O CP NH1 H 500.00 {sd= 0.031} 0 0.0000 ! for PCA + IMPRoper OH1 HA CH1P N 500.00 {sd= 0.031} 0 -66.1521 + IMPRoper OHP HA CH2P N 500.00 {sd= 0.031} 0 -66.1521 + IMPRoper OHP HA CH1P N 500.00 {sd= 0.031} 0 -66.1521 + IMPRoper HA HA CH2P NH3 500.00 {sd= 0.031} 0 -71.9018 + IMPRoper OH1 HA CH2P NH3 500.00 {sd= 0.031} 0 -66.1521 + IMPRoper OHP HA CH2P NH3 500.00 {sd= 0.031} 0 -66.1521 + IMPRoper HA HA SM HA 500.00 {sd= 0.031} 0 -65.1411 + IMPRoper HA HA SE HA 500.00 {sd= 0.031} 0 -65.1411 ! for MSE + IMPRoper HC CH1E HC HC 500.00 {sd= 0.031} 0 -66.4313 + IMPRoper HC CH2E HC HC 500.00 {sd= 0.031} 0 -66.4262 + IMPRoper HC CH2G HC HC 500.00 {sd= 0.031} 0 -66.4073 + IMPRoper HC HC C NC2 500.00 {sd= 0.031} 0 -0.0094 + + IMPRoper NH1 C5 CR1E NR 500.00 {sd= 0.031} 0 -0.0249 + IMPRoper NH1 C5 CR1H NH1 500.00 {sd= 0.031} 0 -0.0178 + IMPRoper NH1 C5 CR1H NR 500.00 {sd= 0.031} 0 -0.0178 + IMPRoper NH1 CR1E C5 NR 500.00 {sd= 0.031} 0 0.0078 + IMPRoper NH1 CR1E C5 NR 500.00 {sd= 0.031} 0 0.0078 + IMPRoper NR PP CR1H CRHH 500.00 {sd= 0.031} 0 0.0078 + IMPRoper NR PP OR3 OP1 500.00 {sd= 0.031} 0 -35.0000 + IMPRoper SM PP OR3 OP1 500.00 {sd= 0.031} 0 -35.0000 + IMPRoper OHP PP OR3 OP1 500.00 {sd= 0.031} 0 -35.0000 + + IMPRoper CD28 OR3 HD28 HD29 500.00 {sd= 0.031} 0 35.2640 + + IMPRoper CP CH2P NH1 O 500.00 0 0.0000 ! for PCA + +! peptide group (modified 14-MAR-00) +! omega modified again (MN, 18-MAR-02) + + IMPRoper C CH1E NH1 O 500.00 0 0.0000 ! + IMPRoper C CH2E NH1 O 500.00 0 0.0000 ! + IMPRoper C CH3E NH1 O 500.00 0 0.0000 ! + IMPRoper C CH1E NH2 O 500.00 0 0.0000 ! + IMPRoper C CH1E N O 500.00 0 0.0000 ! aaa-pro + IMPRoper C CH3E N O 500.00 0 0.0000 ! ace-pro + IMPRoper C CH2E N O 500.00 0 0.0000 ! cyclic-ace-pro + IMPRoper C CH2G N O 500.00 0 0.0000 ! gly-pro + IMPRoper C CH2G NH1 O 500.00 0 0.0000 ! gly-aaa + IMPRoper C CH2G NH2 O 500.00 0 0.0000 ! + IMPRoper NH1 C CH1E H 500.00 0 0.0000 ! + IMPRoper NH1 CP CH1E H 500.00 0 0.0000 ! for PCA - AB + IMPRoper NH1 C CH2E H 500.00 0 0.0000 ! + IMPRoper N C CH1E CH2P 500.00 0 0.0000 ! aaa-pro + IMPRoper N C CH1E CH1P 500.00 0 0.0000 ! aaa-pro + IMPRoper NH1 C CH2G H 500.00 0 0.0000 ! aaa-gly + IMPRoper NH1 C CH2E H 500.00 0 0.0000 ! iso-peptide bond + IMPRoper NH1 C CH3E H 500.00 0 0.0000 ! acetylated lysine + + IMPRoper CCIS CH1E NH1 O 500.00 0 0.0000 ! + IMPRoper CCIS CH1E N O 500.00 0 0.0000 ! aaa-pro + IMPRoper CCIS CH2G N O 500.00 0 0.0000 ! gly-pro + IMPRoper CCIS CH2G NH1 O 500.00 0 0.0000 ! gly-aaa + IMPRoper CCIS NH1 HA HA 500.00 0 -78.8745 + IMPRoper CCIS NH1 N CH1E 500.00 0 0.0000 + IMPRoper NH1 CCIS CH1E H 500.00 0 0.0000 ! + IMPRoper N CCIS CH1E CH2P 500.00 0 0.0000 ! aaa-pro + IMPRoper N CCIS CH1E CH1P 500.00 0 0.0000 ! aaa-pro + IMPRoper NH1 CCIS CH2G H 500.00 0 0.0000 ! aaa-gly + + IMPRoper CH1E C NH1 CH1E 500.00 0 180.0000 + IMPRoper CH2E C NH1 CH1E 500.00 0 180.0000 + IMPRoper CH2E C N CH1E 500.00 0 180.0000 ! cyclic-ace-pro + IMPRoper CH3E C NH1 CH1E 500.00 0 180.0000 + IMPRoper CH3E C NH1 CH2E 500.00 0 180.0000 + IMPRoper CH1E C NH1 CH2G 500.00 0 180.0000 + IMPRoper CH1E C N CH2P 500.00 0 180.0000 + IMPRoper CH1E C N CH1P 500.00 0 180.0000 + IMPRoper CH2G C NH1 CH1E 500.00 0 180.0000 + IMPRoper CH2G C NH1 CH2E 500.00 0 180.0000 + IMPRoper CH2G C NH1 CH2G 500.00 0 180.0000 + IMPRoper CH2G C N CH2P 500.00 0 180.0000 + IMPRoper CH2P C NH1 CH1E 500.00 0 180.0000 + IMPRoper CH2P CP NH1 CH1E 500.00 0 0.0000 ! for PCA - AB + IMPRoper CH2P C NH1 CH2G 500.00 0 180.0000 + IMPRoper CH2P C NH1 CH2P 500.00 0 180.0000 + + IMPRoper CH1E CCIS NH1 CH1E 500.00 0 0.0000 + IMPRoper CH1E CCIS NH1 CH2G 500.00 0 0.0000 + IMPRoper CH1E CCIS N CH1E 500.00 0 0.0000 + IMPRoper CH1E CCIS N CH2P 500.00 0 0.0000 + IMPRoper CH1E CCIS N CH1P 500.00 0 0.0000 + IMPRoper CH2G CCIS NH1 CH1E 500.00 0 0.0000 + IMPRoper CH2G CCIS N CH1E 500.00 0 0.0000 + IMPRoper CH2G CCIS NH1 CH2G 500.00 0 0.0000 + IMPRoper CH2G CCIS N CH2P 500.00 0 0.0000 + IMPRoper CH2P CCIS NH1 CH1E 500.00 0 0.0000 + IMPRoper CH2P CCIS NH1 CH2G 500.00 0 0.0000 + IMPRoper CH2P CCIS NH1 CH2P 500.00 0 0.0000 + +! added impropers for Arg planarity to reduce chances of reaching singularity, ATB 8/12/10 + improper CH2E NH1 C NC2 500.0 0 0.0 ! omega torsion angle for ARG and to maintain proper NH1/NH2 stereochemistry + improper C NC2 NC2 NH1 500.0 0 0.0 + improper NH1 C NC2 HC 100.0 2 180.0 ! ARG -c-nh2 dihdedral angle + +! Residue PNS +eval ($pd_v=$pd_x* 160.1) IMPR CD28 O3P HD28 HD29 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD29 CD28 CD30 CD31 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD30 CD29 HD31 HD32 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD31 CD29 HD34 HD35 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD32 CD29 CD34 OD33 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 80.0) IMPR CD34 CD32 OD35 ND36 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 80.0) IMPR ND36 CD34 HD48 CD37 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 160.1) IMPR CD37 ND36 HD37 HD38 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD38 CD37 HD39 HD4A $pd_v 0 35.264 +eval ($pd_v=$pd_x* 80.0) IMPR CD39 CD38 OD40 ND41 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 80.0) IMPR ND41 CD39 HD41 CD42 $pd_v 0 0.000 +eval ($pd_v=$pd_x* 160.1) IMPR CD42 ND41 HD42 HD43 $pd_v 0 35.264 +eval ($pd_v=$pd_x* 160.1) IMPR CD43 CD42 HD44 HD45 $pd_v 0 35.264 + + +! Residue DRG +eval ($pd_v=$pd_x* 800.0) IMPR CHAO CHAS CHAI CHAJ $pd_v 0 0.000 +eval ($pd_v=$pd_x* 800.0) IMPR CH_Y CHA OH_Y OHXT $pd_v 0 0.000 +eval ($pd_v=$pd_x* 400.0) IMPR CHAS CHAC NHAQ CHAD $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR NHAQ CHAS OHAH CHAR $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CHAR NHAQ CHAB CHAA $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR CHA CHB CH_Y NH_Y $pd_v 0 35.264 +eval ($pd_v=$pd_x* 400.0) IMPR NH_Y CHA HHAD HHAC $pd_v 0 35.264 + +! CR3-CR3 sidechain dihedrals + + DIHEdral C CH2E CH2E CH1E 2.00 3 0.0000 + DIHEdral CH1E CH1E CH2E CH3E 2.00 3 0.0000 + DIHEdral CH1E CH2E CH2E CH2E 2.00 3 0.0000 + DIHEdral CH1E CH2E CH2E SM 2.00 3 0.0000 + DIHEdral CH1E CH2E CH2E SE 2.00 3 0.0000 ! for MSE + DIHEdral CH2E CH1E CH1E NH1 2.00 3 0.0000 + DIHEdral CH2E CH2E CH2E CH2E 2.00 3 0.0000 + DIHEdral NH1 CH2E CH2E CH2E 2.00 3 0.0000 + DIHEdral NH3 CH2E CH2E CH2E 2.00 3 0.0000 + DIHEdral CH2E CH2E CH2E NH1 2.00 3 0.0000 + DIHEdral C CH2E SM CH2E 2.00 3 0.0000 + DIHEdral CH1E CH2E SM CH2E 2.00 3 0.0000 + DIHEdral CH2E CH2E SM CH3E 2.00 3 0.0000 + DIHEdral CH2E CH2E SE CH3E 2.00 3 0.0000 ! for MSE + DIHEdral CH3E CH1E CH1E NH1 2.00 3 0.0000 + DIHEdral CH3E CH1E CH1E OH1 2.00 3 0.0000 + DIHEdral CH1E CH1E OAS CCE 2.00 3 0.0000 !for THR-linked glycans + DIHEdral CH2E CH2E CH1E OH1 2.00 3 0.0000 + DIHEdral CH3E CH1E CH2E CH1E 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E C 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E C5 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E C5W 2.00 3 0.0000 + DIHEdral NH1 CH2E CH2E C5W 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E CF 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E CH1E 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E CH2E 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E CY 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E OH1 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E OH1C 2.00 3 0.0000 ! for covalent Serine (SEC) + DIHEdral NH1 CH1E CH1E OH1 2.00 3 0.0000 !added 14-APR-99 + DIHEdral NH1 CH1E CH1E OAS 2.00 3 0.0000 !for THR-linked glycans + DIHEdral NH1 CH1E CH2E OHP 2.00 3 0.0000 + DIHEdral NH1 CH1E CH1E OHP 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E S 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E SH1E 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E SH1C 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E SM 2.00 3 0.0000 + DIHEdral NH1 CH1E CH2E SE 2.00 3 0.0000 ! for MSE + +! chi1 modifications at N-terminus + + DIHEdral NH3 CH1E CH2E C 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E C5 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E C5W 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E CF 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E CH1E 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E CH2E 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E CY 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E OH1 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E OH1C 2.00 3 0.0000 ! for covalent Serine (SEC) + DIHEdral NH3 CH1E CH1E OH1 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E OHP 2.00 3 0.0000 + DIHEdral NH3 CH1E CH1E OHP 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E S 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E SH1E 2.00 3 0.0000 + DIHEdral NH3 CH1E CH2E SH1C 2.00 3 0.0000 + DIHEdral NH3 CH1E CH1E CH3E 2.00 3 0.0000 + DIHEdral NH3 CH1E CH1E CH2E 2.00 3 0.0000 + +! CR3-CR2 (Planar) sidechain dihedrals (modified 09-MAR-00) + + DIHEdral CR1E C5W CH2E CH1E 1.00 2 0.0000 !Trp + DIHEdral CW C5W CH2E CH2E 1.00 2 0.0000 !Qsr + DIHEdral CR1E CF CH2E CH1E 1.00 2 0.0000 !Phe + DIHEdral NH1 C5 CH2E CH1E 0.60 1 0.0000 !His + DIHEdral CR1H C5 CH2E CH1E 0.80 2 0.0000 !His + DIHEdral NR C5 CH2E CH1E 0.60 1 0.0000 !His + DIHEdral CR1E C5 CH2E CH1E 0.80 2 0.0000 !His + DIHEdral CH1E CH2E CY CR1E 1.00 2 0.0000 !Tyr + DIHEDral CR1E CY2 OH1 H 2.00 2 90.000 !Tyr + DIHEDral CR1W CY2 OH1 H 2.00 2 90.000 !Qsr + DIHEDral CR1E CY2 OHP PP 2.00 2 90.000 !Ptr,Typ + DIHEDral CR1E CY2 OUF SUF 2.00 2 90.000 !Tys + DIHEdral CH2E CH2E NH1 C 2.00 1 0.0000 !Arg + DIHEdral O C CH2E CH1E 1.00 6 0.0000 !Asn (+ 3 60.000?) + DIHEdral OC C CH2E CH1E MULT 2 1.00 2 0.0000 0.5 6 0.0000 !Asp + DIHEdral O C CH2E CH2E 2.00 6 0.0000 !Gln (+ 3 60.000?) + DIHEdral OC C CH2E CH2E MULT 2 1.00 2 0.0000 0.5 6 0.0000 !Glu + +! sidechain CH3 and NH3 groups (added 12-MAR-00) + + DIHEdral HC NH3 CH2E CH2E 1.00 3 0.0000 !Lys + DIHEdral H NH1 CH2E CH2E 1.00 3 0.0000 !Lys + DIHEdral HA CH3E CH1E C 1.00 3 0.0000 !Ala + DIHEdral HA CH3E CH2E CH1E 1.00 3 0.0000 !Ile + DIHEdral HA CH3E CH1E CH1E 1.00 3 0.0000 !Ile/Thr/Val + DIHEdral HA CH3E CH1E CH2E 1.00 3 0.0000 !Leu + DIHEdral HA CH3E SM CH2E 1.00 3 0.0000 !Met + DIHEdral HA CH3E SE CH2E 1.00 3 0.0000 !MSE + + ! added by M. Reau 01-06-21 + DIHEdral HA CH3E NH1 H 1.00 3 0.0000 !NME + + ! added by Aart Nederveen July 3 2003 + DIHEdral HA CH3E CH1E CCIS 1.00 3 0.0000 !Ala + +! N and C terminal groups (ace planarity taken care of by peptide bond added 12-MAR-00) + + DIHEdral HC NH3 CH1E CCIS 2.00 3 0.0000 !Non-Gly/Pro N-terminus + DIHEdral HC NH3 CH1E C 2.00 3 0.0000 !Non-Gly/Pro N-terminus + DIHEdral HC NH3 CH2G C 2.00 3 0.0000 !Gly N-terminus + DIHEdral HC NH3 CH2G CCIS 2.00 3 0.0000 !Gly/Pro N-terminus + DIHEdral OC C CH1E NH1 2.00 2 0.0000 !Non-Gly/Pro COO-terminus + DIHEdral O C CH1E NH1 2.00 2 0.0000 + DIHEdral O C CH2G NH1 2.00 2 0.0000 !for iso-peptidebond with GLY (AB 2015-10) + DIHEdral O C CH2G NH2 2.00 2 0.0000 !for iso-peptidebond with GLY (AB 2015-10) + DIHEdral OC C CH1E NH3 2.00 2 0.0000 !Non-Gly/Pro COO-terminus + DIHEdral OC C CH2G NH1 1.00 6 0.0000 !Gly COO-terminus + DIHEdral OC C CH2G NH2 1.00 6 0.0000 !Gly COO-terminus + DIHEdral OC C CH2G NH3 1.00 6 0.0000 !Gly COO-terminus + DIHEdral OC C CH1E N 2.00 2 0.0000 !Pro COO-terminus + DIHEdral NH2 C CH1E NH1 2.00 2 0.0000 !Non-Gly/Pro CONH2-terminus + DIHEdral NH2 C CH2G NH1 1.00 6 0.0000 !Gly CONH2-terminus (+ 3 60.000?) + DIHEdral NH2 C CH2G NH2 1.00 6 0.0000 !Gly CONH2-terminus (+ 3 60.000?) + DIHEdral NH2 C CH1E N 2.00 2 0.0000 !Pro CONH2-terminus + +! backbone psi (not active with usual topology file modified 03-JUL-01) +! DIHEdral NH1 CH1E C NH1 MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !aaa-aaa +! DIHEdral NH1 CH2G C NH1 MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !gly-aaa +! DIHEdral NH3 CH1E C NH1 MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !Nterm-aaa-aaa +! DIHEdral NH3 CH2G C NH1 MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !Nterm-gly-aaa +! DIHEdral N CH1E C NH1 MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !pro-aaa + +! DIHEdral NH1 CH1E C N MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !aaa-pro +! DIHEdral NH1 CH2G C N MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !gly-pro +! DIHEdral NH3 CH1E C N MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !Nterm-aaa-pro +! DIHEdral NH3 CH2G C N MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !Nterm-gly-pro +! DIHEdral N CH1E C N MULT 3 0.175 2 0.0000 0.1 4 0.0000 0.03 6 0.0000 !pro-pro + +! backbone psi related due to O & CB (not active with usual topology file added 07-JUL-01) + DIHEdral CH2E CH1E C O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral CH1P CH1E C O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E C O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E C O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !(ile,thr,val)-aaa + +! backbone psi related due to O & CB (not active with usual topology file added 07-JUL-01) + DIHEdral CH2E CH1E CCIS O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E CCIS O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E CCIS O MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !(ile,thr,val)-aaa + +! backbone psi related due to NH & CB (N.B. 2.0x the strength of above not active with usual topology file added 03-JUL-01 modified 07-JUL-01) + DIHEdral CH2E CH1E C NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH1P CH1E C NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH2E CH2E C NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E C NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E C NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-aaa + DIHEdral CH2E CH1E CCIS NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E CCIS NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E CCIS NH1 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-aaa + DIHEdral CH2E CH1E C NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH2E CH2E C NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E C NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E C NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-aaa + DIHEdral CH2E CH1E CCIS NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CH3E CH1E CCIS NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-aaa + DIHEdral CH1E CH1E CCIS NH2 MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-aaa + + DIHEdral CH2E CH1E C N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-pro + DIHEdral CH3E CH1E C N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-pro + DIHEdral CH1E CH1E C N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-pro + + DIHEdral CH2E CH1E CCIS N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-pro + DIHEdral CH3E CH1E CCIS N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !ala-pro + DIHEdral CH1E CH1E CCIS N MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !(ile,thr,val)-pro + +! backbone phi (not active with usual topology file modified 03-JUL-01) + DIHEdral C NH1 CH1E C MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral C NH1 CH2G C MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-gly +! backbone phi (not active with usual topology file modified 03-JUL-01) + DIHEdral CCIS NH1 CH1E C MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral CCIS NH1 CH2G C MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-gly +! backbone phi (not active with usual topology file modified 03-JUL-01) + DIHEdral C NH1 CH1E CCIS MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral C NH1 CH2G CCIS MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-gly +! backbone phi (not active with usual topology file modified 03-JUL-01) + DIHEdral CCIS NH1 CH1E CCIS MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-aaa + DIHEdral CCIS NH1 CH2G CCIS MULT 6 0.375 1 0.0000 0.3 2 0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6 0.0000 !aaa-gly + +! backbone phi related due to O & CB N.B. 1.33x the strength of phi above (not active with usual topology file added 03-JUL-01) + DIHEdral C NH1 CH1E CH2E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral C NH1 CH1E CH3E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-ala + DIHEdral C NH1 CH1E CH1E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-(ile,thr,val) + DIHEdral CCIS NH1 CH1E CH2E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-aaa + DIHEdral CCIS NH1 CH1E CH3E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-ala + DIHEdral CCIS NH1 CH1E CH1E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.3 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.05 6 0.0000 !aaa-(ile,thr,val) + +! disulphide (modified 07-JUL-01) + + DIHEdral CH2E S S CH2E MULT 6 0.5 1 0.0000 0.4 2 0.0000 0.4 3 0.0000 0.2 4 0.0000 0.1 5 0.0000 0.075 6 0.0000 !aaa-aaa +! DIHEdral CH2E S S CH2E 0.5 2 0.0000 + +! Phosphorylated Histidine (AB 1-05-03) + DIHEdral OR3 PP NR CRHH 2.0 2 0.0 + +! Phosphorylated Cysteine (AB 7-05-03) + DIHEdral OR3 PP SM CH2E 2.0 2 0.0 + +! Phosphorylated Tyrosine (AB 8-05-06) + DIHEdral OR3 PP OHP CY2 2.0 2 0.0 + +! Phosphorylated Serine (AB 25-01-10) + DIHEdral OR3 PP OHP CH2E 2.0 2 0.0 + +! Phosphorylated Threonine (AB 25-01-10) + DIHEdral OR3 PP OHP CH1E 2.0 2 0.0 + +! Suflonated Tyrosine (AB 6-08-08) + DIHEdral OUF SUF OUF CY2 2.0 2 0.0 + +! Acetylated Lyine (AB 20-03-09) + DIHEdral CH2E NH1 C CH3E 500.0 2 180.0 + DIHEdral CH2E NH1 C O 500.0 2 0.0 + DIHEdral H NH1 C O 500.0 2 180.0 + DIHEdral H NH1 C CH3E 500.0 2 0.0 + +! Acetylated GLY (AB 27-02-14) + DIHEdral CH2G NH1 C CH3E 500.0 2 180.0 + DIHEdral CH3E C NH1 CH2G 500.0 2 180.0 + +! Residue PNS +eval ($pd_v=$pd_x* 5.6) DIHE CD28 O3P P OG $pd_v 2 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CD29 CD28 O3P P $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CD32 CD29 CD28 O3P $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE HD30 CD30 CD29 CD28 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE HD33 CD31 CD29 CD28 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CD34 CD32 CD29 CD28 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CD29 CD32 OD33 HD46 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CD29 CD32 CD34 ND36 $pd_v 6 0.000 +eval ($pd_v=$pd_x* 641.1) DIHE CD32 CD34 ND36 CD37 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.6) DIHE CD38 CD37 ND36 CD34 $pd_v 6 180.000 +eval ($pd_v=$pd_x* 19.6) DIHE CD39 CD38 CD37 ND36 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.6) DIHE CD37 CD38 CD39 ND41 $pd_v 6 0.000 +eval ($pd_v=$pd_x* 641.1) DIHE CD38 CD39 ND41 CD42 $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.6) DIHE CD43 CD42 ND41 CD39 $pd_v 6 180.000 +eval ($pd_v=$pd_x* 19.6) DIHE SD44 CD43 CD42 ND41 $pd_v 3 0.000 +eval ($pd_v=$pd_x* 4.9) DIHE CD42 CD43 SD44 HD47 $pd_v 3 0.000 + + +! Residue DRG +eval ($pd_v=$pd_x* 8.1) DIHE CHAC CHAS NHAQ CHAR $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CHAC CHAS CHAO CHAJ $pd_v 6 0.000 +eval ($pd_v=$pd_x* 0.9) DIHE CHAS NHAQ OHAH HHAA $pd_v 3 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CHAI CHAR NHAQ CHAS $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE NHAQ CHAR CHAI CHAO $pd_v 6 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE CHAR CHAI CHAO CHAJ $pd_v 2 180.000 +eval ($pd_v=$pd_x* 0.1) DIHE CHAS CHAO CHAJ SHAL $pd_v 6 0.000 +eval ($pd_v=$pd_x* 4.9) DIHE S SHAL CHAJ CHAO $pd_v 3 0.000 +eval ($pd_v=$pd_x* 160.0) DIHE CH2E S SHAL CHAJ $pd_v 2 0.000 +eval ($pd_v=$pd_x* 4.9) DIHE SHAL S CH2E CH1E $pd_v 3 0.000 +eval ($pd_v=$pd_x* 19.6) DIHE S CHB CHA NH_Y $pd_v 3 0.000 +eval ($pd_v=$pd_x* 0.1) DIHE CHB CHA CH_Y OH_Y $pd_v 6 0.000 +eval ($pd_v=$pd_x* 8.1) DIHE CHB CHA NH_Y HHAB $pd_v 3 0.000 + + +if ( $exist_par_nonbonded = false ) then + evaluate ($par_nonbonded = "OPLSX") +end if + +NONBONDED CD28 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD28 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD29 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD29 0.10000 3.29633 0.10000 3.02906 +NONBONDED CD30 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD31 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD32 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD30 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD31 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD34 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD35 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD33 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD32 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD36 0.10000 2.13816 0.10000 1.87089 +NONBONDED OD33 0.10000 2.58361 0.10000 2.31634 +NONBONDED HD46 0.10000 1.42544 0.10000 1.15817 +NONBONDED CD34 0.10000 3.29633 0.10000 3.02906 +NONBONDED OD35 0.10000 2.58361 0.10000 2.31634 +NONBONDED ND36 0.10000 2.67270 0.10000 2.40543 +NONBONDED HD48 0.10000 1.42544 0.10000 1.15817 +NONBONDED CD37 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD37 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD38 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD38 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD39 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD4A 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD39 0.10000 3.29633 0.10000 3.02906 +NONBONDED OD40 0.10000 2.58361 0.10000 2.31634 +NONBONDED ND41 0.10000 2.67270 0.10000 2.40543 +NONBONDED HD41 0.10000 1.42544 0.10000 1.15817 +NONBONDED CD42 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD42 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD43 0.10000 2.13816 0.10000 1.87089 +NONBONDED CD43 0.10000 3.29633 0.10000 3.02906 +NONBONDED HD44 0.10000 2.13816 0.10000 1.87089 +NONBONDED HD45 0.10000 2.13816 0.10000 1.87089 +NONBONDED SD44 0.10000 3.20724 0.10000 2.93997 +NONBONDED HD47 0.10000 1.42544 0.10000 1.15817 +NONBONDED CHAC 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAS 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAD 0.10000 3.29633 0.10000 3.02906 +NONBONDED NHAQ 0.10000 2.67270 0.10000 2.40543 +NONBONDED OHAH 0.10000 2.58361 0.10000 2.31634 +NONBONDED HHAA 0.10000 1.42544 0.10000 1.15817 +NONBONDED CHAR 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAA 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAB 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAI 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAO 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHAJ 0.10000 3.29633 0.10000 3.02906 +NONBONDED SHAL 0.10000 3.20724 0.10000 2.93997 +NONBONDED SHAM 0.10000 3.20724 0.10000 2.93997 +NONBONDED CHB 0.10000 3.29633 0.10000 3.02906 +NONBONDED CHA 0.10000 3.29633 0.10000 3.02906 +NONBONDED CH_Y 0.10000 3.29633 0.10000 3.02906 +NONBONDED OHXT 0.10000 2.58361 0.10000 2.31634 +NONBONDED OH_Y 0.10000 2.58361 0.10000 2.31634 +NONBONDED NH_Y 0.10000 2.67270 0.10000 2.40543 +NONBONDED HHAC 0.10000 1.42544 0.10000 1.15817 +NONBONDED HHAD 0.10000 1.42544 0.10000 1.15817 +NONBONDED HHAB 0.10000 1.42544 0.10000 1.15817 +NONBonded SE 0.0430 3.5100 0.0430 3.5100 ! added for MSE + + +{* nonbonding parameter section *} +{* ============================ *} + + if ($par_nonbonded = "CONTACT") then { added by 10-MAR-00 } + +! This uses distances consistent with those in a survey of atom-atom contacts +! in high resolution crystal structures (Williams et al. (1994) Protein Science 3, 1224-1235) +! implemented with the PROLSQ form: +! +! fVDW(R) = 16 * ( Rmin - R ) ^ 4 +! +! The Rmin is related to the Lennard-Jones (epsilon,sigma) form by epsilon=0.1(not used) +! and Rmin = sigma * 2 ^ (1/6). +! +{ mandatory values: + NBONds + CUTNB=7.0 WMIN=1.5 + REPEl = 1.0 + REXPonent = 4 + IREXponent = 1 + RCONst = 16.0 + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} + END +} + evaluate ($repel_radius = 1.0) + evaluate ($repel_rcons = 25) + evaluate ($repel_rexpo = 4) + evaluate ($repel_irexp = 1) + +! type sigma +evaluate ($VR_C= 3.15) +evaluate ($VR_N= 2.6) {polar value to reflect H-bonding ability} +evaluate ($VR_O= 2.4) {polar value to reflect H-bonding ability} +evaluate ($VR_S= 3.1) +evaluate ($VR_FE= 2.15) +evaluate ($VR_H= 1.85) {large for aliphatics} +evaluate ($VR_HH= 0.65) {small for H bonds} +evaluate ($VR_P= 3.4) +evaluate ($VR_I= 3.9) + +! compute 1-4 sigmas +evaluate ($VR14_C = $VR_C -0.27) +evaluate ($VR14_N = $VR_N -0.27) +evaluate ($VR14_O = $VR_O -0.27) +evaluate ($VR14_S = $VR_S -0.27) +evaluate ($VR14_FE = $VR_FE -0.27) +evaluate ($VR14_H = $VR_H -0.27) +evaluate ($VR14_HH = $VR_H -0.27) {no 1-4 H bonds are possible} +evaluate ($VR14_P = $VR_P -0.27) +evaluate ($VR14_I = $VR_I -0.27) + +evaluate ($VE=0.1) +evaluate ($VES=0.01) +! + ! eps sigma eps(1:4) sigma(1:4) + ! (kcal/mol) (A) (kcal/mol) (A) + ! -------------------------------------------------- + NONBonded H $VE $VR_HH $VE $VR14_HH + NONBonded HA $VE $VR_H $VE $VR14_H ! aliphatic hydrogen + NONBonded HC $VE $VR_HH $VE $VR14_HH ! h attached to charg. + ! + NONBonded C $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CP $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CCIS $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded C5 $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded C5W $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CF $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CW $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CY $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CY2 $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CH1E $VE $VR_C $VE $VR14_C ! \ + NONBonded CH2E $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH2G $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH2P $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH1P $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH3E $VE $VR_C $VE $VR14_C ! / + NONBonded CR1E $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CR1H $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CR1W $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CRHH $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CRH $VE $VR_C $VE $VR14_C ! ring carbons + + ! + NONBonded N $VE $VR_N $VE $VR14_N + NONBonded NC2 $VE $VR_N $VE $VR14_N + NONBonded NH1 $VE $VR_N $VE $VR14_N + NONBonded NH2 $VE $VR_N $VE $VR14_N + NONBonded NH3 $VE $VR_N $VE $VR14_N + NONBonded NP $VE $VR_N $VE $VR14_N + NONBonded NR $VE $VR_N $VE $VR14_N + ! + NONBonded O $VE $VR_O $VE $VR14_O + NONBonded OC $VE $VR_O $VE $VR14_O + NONBonded OH1 $VE $VR_O $VE $VR14_O + NONBonded OH1C $VES $VR_O $VES $VR14_O + NONBonded OHP $VE $VR_O $VE $VR14_O + NONBonded OUF $VE $VR_O $VE $VR14_O + ! + NONBonded S $VE $VR_S $VE $VR14_S + NONBonded SM $VE $VR_S $VE $VR14_S + NONBonded SH1E $VE $VR_S $VE $VR14_S + NONBonded SH1C $VES $VR_S $VES $VR14_S + NONBonded SUF $VE $VR_S $VE $VR14_S + + + elseif ($par_nonbonded eq "PROLSQ") then +{* nonbonding parameter section *} +{* ============================ *} +!! +! This uses a new form of the REPEL function: +! fVDW(R) = RCON *( Rmin ^ IREX - R ^ IREX ) ^ REXP +! +! PROLSQ uses a function of the form: +! fVDW(R) = (1 / 0.5) ^ 4 * ( Rmin ^ 4 - R ^ 4 ) +! +! The epsilon values are arbitrary since the repel function does not depend +! on epsilon. The sigma values come from converting the Van der Waals +! radii of the PROLSQ program into sigma values using the formula: +! Rmin = sigma * 2 ^ (1/6) +! Note: Prolsq decrements Van der Waals radii for non-bonded contacts +! that involve torsion angles (1:4 contacts) by .30 A, and +! hydrogen bonds (X...Y) by .2 A (X-H...Y) by .9. The former +! decrement is accomplished in CNS by using the +! 1-4 nonbonded terms. The latter decrement is accomplished by +! decreasing the van der Waals radius of hydrogens by 0.8 +! and that of O and N by 0.1 A. +! +{ suggested values: + NBONds + CUTNB=7.0 WMIN=1.5 + REPEl = 1.0 + REXPonent = 4 + IREXponent = 1 + RCONst = 16.0 + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} + END +} + evaluate ($repel_radius = 1.0) + evaluate ($repel_rcons = 25) + evaluate ($repel_rexpo = 4) + evaluate ($repel_irexp = 1) +! type van der Waals radius correction applied for hbond +evaluate ($VR_C= 3.7) +evaluate ($VR_N= 3.0) {-0.1} +evaluate ($VR_O= 2.9) {-0.1} +evaluate ($VR_S= 3.6) +evaluate ($VR_FE= 2.4) +evaluate ($VR_H= 2.0) {from 1.6 02-APRIL-00} +evaluate ($VR_HH= 1.6) {-0.8} +evaluate ($VR_P= 3.8) +evaluate ($VR_I= 4.3) +evaluate ($VR_C_SP2= 3.4) + +{ convert radii into sigmas } +! +! sigma= vdw radius / 2 ^ (1/6) +! +evaluate ($VR_C = $VR_C / 2^(1/6)) +evaluate ($VR_N = $VR_N / 2^(1/6)) +evaluate ($VR_O = $VR_O / 2^(1/6)) +evaluate ($VR_S = $VR_S / 2^(1/6)) +evaluate ($VR_FE = $VR_FE / 2^(1/6)) +evaluate ($VR_H = $VR_H / 2^(1/6)) +evaluate ($VR_HH = $VR_HH / 2^(1/6)) +evaluate ($VR_P = $VR_P / 2^(1/6)) +evaluate ($VR_I = $VR_I / 2^(1/6)) +evaluate ($VR_C_SP2=$VR_C_SP2/ 2^(1/6)) + +{ compute 1-4 sigmas from reduced radii} +evaluate ($VR14_C = $VR_C -(0.3/ 2^(1/6))) +evaluate ($VR14_N = $VR_N -(0.3/ 2^(1/6))) +evaluate ($VR14_O = $VR_O -(0.3/ 2^(1/6))) +evaluate ($VR14_S = $VR_S -(0.3/ 2^(1/6))) +evaluate ($VR14_FE = $VR_FE -(0.3/ 2^(1/6))) +evaluate ($VR14_H = $VR_H -(0.3/ 2^(1/6))) +evaluate ($VR14_HH = $VR_HH -(0.3/ 2^(1/6))) +evaluate ($VR14_P = $VR_P -(0.3/ 2^(1/6))) +evaluate ($VR14_I = $VR_I -(0.3/ 2^(1/6))) +evaluate ($VR14_C_SP2=$VR_C_SP2-(0.3/ 2^(1/6))) + +evaluate ($VE=0.1) +evaluate ($VES=0.1) +! + ! eps sigma eps(1:4) sigma(1:4) + ! (kcal/mol) (A) (kcal/mol) (A) + ! -------------------------------------------------- + NONBonded H $VE $VR_HH $VE $VR14_HH + NONBonded HA $VE $VR_H $VE $VR14_H ! aliphatic hydrogen + NONBonded HC $VE $VR_HH $VE $VR14_HH ! h attached to charg. + ! + NONBonded C $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon + NONBonded CP $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon + NONBonded CCIS $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon + NONBonded C5 $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded C5W $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CF $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CW $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CY $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CY2 $VE $VR_C $VE $VR14_C ! carbonyl carbon + NONBonded CH1E $VE $VR_C $VE $VR14_C ! \ + NONBonded CH2E $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH2G $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH2P $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH1P $VE $VR_C $VE $VR14_C ! extended carbons + NONBonded CH3E $VE $VR_C $VE $VR14_C ! / + NONBonded CR1E $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CR1H $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CR1W $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CRHH $VE $VR_C $VE $VR14_C ! ring carbons + NONBonded CRH $VE $VR_C $VE $VR14_C ! ring carbons + + ! + NONBonded N $VE $VR_N $VE $VR14_N + NONBonded NC2 $VE $VR_N $VE $VR14_N + NONBonded NC3 $VE $VR_N $VE $VR14_N + NONBonded NC4 $VE $VR_N $VE $VR14_N + NONBonded NH1 $VE $VR_N $VE $VR14_N + NONBonded NH2 $VE $VR_N $VE $VR14_N + NONBonded NH3 $VE $VR_N $VE $VR14_N + NONBonded NP $VE $VR_N $VE $VR14_N + NONBonded NR $VE $VR_N $VE $VR14_N + ! + NONBonded O $VE $VR_O $VE $VR14_O + NONBonded OP1 $VE $VR_O $VE $VR14_O + NONBonded OR3 $VE $VR_O $VE $VR14_O + NONBonded OC $VE $VR_O $VE $VR14_O + NONBonded OH1 $VE $VR_O $VE $VR14_O + NONBonded OH1C $VES $VR_O $VES $VR14_O + NONBonded OHP $VE $VR_O $VE $VR14_O + NONBonded OUF $VE $VR_O $VE $VR14_O + ! + NONBonded S $VE $VR_S $VE $VR14_S + NONBonded SM $VE $VR_S $VE $VR14_S + NONBonded SH1E $VE $VR_S $VE $VR14_S + NONBonded SH1C $VES $VR_S $VES $VR14_S + NONBonded SUF $VE $VR_S $VE $VR14_S + + + + elseif ($par_nonbonded eq "PARMALLH6") then +{ suggested values for refinement in vacuo + NBONds + CUTNB=10 WMIN=1.5 + REPEl = 0.0 rdie vswitch + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=9.0 + END + HBOND + AEXP=4 REXP=6 HAEX=4 AAEX=2 ACCEPTORS + CUTHB=4.5 CTOFHB=4.0 CTONHB=3.5 CUTHA=90.0 CTOFHA=70.0 CTONHA=50.0 + end + +or + +{ suggested values: + NBONds + CUTNB=7.0 WMIN=1.5 + REPEl = 0.8 + REXPonent = 2 + IREXponent = 2 + RCONst = 5.0 + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} +END +} +} + evaluate ($repel_radius = 0.8) + evaluate ($repel_rcons = 5.0) + evaluate ($repel_rexpo = 2) + evaluate ($repel_irexp = 2) + NONBonded C 0.0903 3.2072 0.0903 3.2072 + NONBonded CP 0.0903 3.2072 0.0903 3.2072 + NONBonded CCIS 0.0903 3.2072 0.0903 3.2072 + NONBonded CR1E 0.0903 3.2072 0.0903 3.2072 + NONBonded CF 0.0903 3.2072 0.0903 3.2072 + NONBonded CY 0.0903 3.2072 0.0903 3.2072 + NONBonded CY2 0.0903 3.2072 0.0903 3.2072 + NONBonded CR1W 0.0903 3.2072 0.0903 3.2072 + NONBonded CW 0.0903 3.2072 0.0903 3.2072 + NONBonded C5W 0.0903 3.2072 0.0903 3.2072 + NONBonded CN 0.0903 3.2072 0.0903 3.2072 + NONBonded C5 0.0903 3.2072 0.0903 3.2072 + NONBonded CH1E 0.0903 3.2072 0.0903 3.2072 + NONBonded CH2E 0.0903 3.2072 0.0903 3.2072 + NONBonded CH3E 0.0903 3.2072 0.0903 3.2072 + NONBonded CH2G 0.0903 3.2072 0.0903 3.2072 + NONBonded CH2P 0.0903 3.2072 0.0903 3.2072 + NONBonded CH1P 0.0903 3.2072 0.0903 3.2072 + NONBonded CRH 0.0903 3.2072 0.0903 3.2072 + NONBonded CR1H 0.0903 3.2072 0.0903 3.2072 + NONBonded CRHH 0.0903 3.2072 0.0903 3.2072 + NONBonded H 0.0498 1.4254 0.0498 1.4254 + NONBonded HA 0.0045 2.6157 0.0045 2.6157 + NONBonded HC 0.0498 1.4254 0.0498 1.4254 + NONBonded N 0.1592 2.7618 0.1592 2.7618 + NONBonded NR 0.1592 2.7618 0.1592 2.7618 + NONBonded NH1 0.1592 2.7618 0.1592 2.7618 + NONBonded NH2 0.1592 2.7618 0.1592 2.7618 + NONBonded NH3 0.1592 2.7618 0.1592 2.7618 + NONBonded NC2 0.1592 2.7618 0.1592 2.7618 + NONBonded NC3 0.1592 2.7618 0.1592 2.7618 + NONBonded NC4 0.1592 2.7618 0.1592 2.7618 + NONBonded O 0.2342 2.6406 0.2342 2.6406 + NONBonded OC 1.0244 2.6406 1.0244 2.6406 + NONBonded OH1 0.2342 2.6406 0.2342 2.6406 + NONBonded OH1C 0.0023 0.26406 0.0023 0.26406 ! for covalent Serine (SEC) + NONBonded OHP 0.2342 2.6406 0.2342 2.6406 + NONBonded OUF 0.2342 2.6406 0.2342 2.6406 + NONBonded S 0.0239 3.3854 0.0239 3.3854 + NONBonded SM 0.0239 3.3854 0.0239 3.3854 + NONBonded SH1E 0.0239 3.3854 0.0239 3.3854 + NONBonded SH1C 0.00239 0.33854 0.00239 0.33854 + NONBonded SUF 0.0239 3.3854 0.0239 3.3854 + +!! HBOND AEXP=4 REXP=6 HAEX=4 AAEX=2 ACCEPTORS +!! CUTHB=4.5 CTOFHB=4.0 CTONHB=3.5 CUTHA=90.0 CTOFHA=70.0 CTONHA=50.0 +! + AEXP 4 + REXP 6 + HAEX 4 + AAEX 2 +! Emin Rmin +! (Kcal/mol) (A) + hbond N*+* N% -3.00 3.0! VALUES FROM VINOGRADOV AND LINELL FOR + hbond N*+* O* -3.50 2.9! TYPICAL LENGTHS AND DEPTHS. + hbond OH* N% -4.00 2.85 + hbond OH* O* -4.25 2.75 + hbond SH1E N% -3.00 3.0 !! added, ATB + hbond SH1E O* -3.50 2.9 !! added, ATB + + + + elseif ($par_nonbonded eq "OPLSX") then +! these are close to the original OPLS parameters without introducing +! new atom types. The commented out lines are for atom types that +! are unique in OPLS but would require additional atom types in +! allhdg. Michael Nilges. +{ suggested values for refinement in H2O + NBONds + CUTNB=12 WMIN=1.5 + REPEl = 0.0 cdie shift + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=11.0 + END +} + evaluate ($repel_radius = 0.0) + NONBonded C 0.105 3.750 0.013 3.750 {OPLS C}! + NONBonded CP 0.105 3.750 0.013 3.750 {OPLS C}! + NONBonded CYAA 0.105 3.750 0.013 3.750 {OPLS C}! + NONBonded CCIS 0.105 3.750 0.013 3.750 {OPLS C}! + NONBonded CY2 0.105 3.750 0.013 3.750 {OPLS C} + NONBonded CF 0.110 3.750 0.014 3.750 {OPLS CA} + NONBonded CY 0.110 3.750 0.014 3.750 {OPLS CA} + NONBonded CW 0.145 3.750 0.018 3.750 {OPLS CB} + NONBonded CR1E 0.110 3.750 0.014 3.750 {OPLS CD}! + NONBonded CR1H 0.145 3.750 0.018 3.750 {OPLS CGJ} + NONBonded CR1W 0.110 3.750 0.014 3.750 {OPLS CD}! + NONBonded CH1E 0.080 3.800 0.010 3.800 {OPLS CH} + NONBonded CRHH 0.145 3.750 0.018 3.750 {OPLS CP} + NONBonded C5W 0.145 3.750 0.018 3.750 {OPLS CS} + NONBonded CH2G 0.118 3.800 0.015 3.800 {OPLS C2} + NONBonded CH2P 0.118 3.905 0.015 3.905 {OPLS C2J} + NONBonded CH1P 0.118 3.905 0.015 3.905 {OPLS C2J} +! NONBonded CH2P 0.118 3.800 0.015 3.800 {OPLS C2} + NONBonded CH2E 0.118 3.905 0.015 3.905 {OPLS C2J} +! NONBonded CH3E 0.118 3.905 0.015 3.905 {OPLS C3} + NONBonded CH3E 0.160 3.910 0.020 3.910 {OPLS C3J} +! NONBonded CH3E 0.175 3.905 0.022 3.905 {OPLS C3K} +! NONBonded CH3E 0.170 3.800 0.021 3.800 {OPLS C3L} + NONBonded C5 0.145 3.750 0.145 3.750 {OPLS CC} + NONBonded CRH 0.145 3.750 0.145 3.750 {OPLS 43} + + NONBonded H 0.05 0.50 0.004 0.50 + NONBonded HA 0.05 0.50 0.004 0.50 + NONBonded HC 0.05 0.50 0.004 0.50 + +! dummy atom + NONBonded DD 0.01 0.01 0.01 0.01 + + NONBonded N 0.170 3.250 0.021 3.250 + NONBonded NR 0.170 3.250 0.021 3.250 + NONBonded NH1 0.170 3.250 0.021 3.250 + NONBonded NH2 0.170 3.250 0.021 3.250 + NONBonded NH3 0.170 3.250 0.021 3.250 + NONBonded NC2 0.170 3.250 0.021 3.250 + NONBonded NC3 0.170 3.250 0.021 3.250 + NONBonded NC4 0.170 3.250 0.021 3.250 + + NONBonded O 0.210 2.960 0.021 2.960 + NONBonded OC 0.210 2.960 0.021 2.960 + NONBonded OP1 0.210 2.960 0.021 2.960 + NONBonded OR3 0.210 2.960 0.021 2.960 + NONBonded OH1 0.170 3.070 0.021 3.070 + NONBonded OH1C 0.017 0.307 0.0021 0.307 ! for covalent Serine (SEC) + NONBonded OHP 0.170 3.070 0.021 3.070 + NONBonded OUF 0.170 3.070 0.021 3.070 + NONBonded PP 0.2000 3.738 0.085 3.738 + NONBonded S 0.250 3.550 0.031 3.550 + NONBonded SM 0.250 3.550 0.031 3.550 + NONBonded SH1E 0.250 3.550 0.031 3.550 + NONBonded SH1C 0.025 0.355 0.0031 0.355 + NONBonded SUF 0.250 3.550 0.031 3.550 +! next two for iron-sulphur cluster + NONBonded SF 0.250 3.550 0.031 3.550 !same as other S + NONBonded FS 0.010 2.270 0.010 2.270 !taken from FE + + + NBFIX H H 14.013 1.67074 14.013 1.67074 + NBFIX H HA 277.278 4.07473 277.278 4.07473 + NBFIX H HC 14.013 1.67074 14.013 1.67074 + NBFIX HA HA 1846.41 5.76501 1846.41 5.76501 + NBFIX HA HC 277.278 4.07473 277.278 4.07473 + NBFIX HC HC 14.013 1.67074 14.013 1.67074 + + NBFIX SH1E CYAA 0.250 1.8 0.250 1.8 + + elseif ($par_nonbonded eq "PARAM19") then +! these are close to the original OPLS parameters without introducing +! new atom types. The commented out lines are for atom types that +! are unique in OPLS but would require additional atom types in +! allhdg. Michael Nilges. +{ suggested values for refinement in H2O + NBONds + CUTNB=12 WMIN=1.5 + REPEl = 0.0 cdie shift + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=11.0 + END +} + evaluate ($repel_radius = 0.89) + evaluate ($repel_rcons = 25) + evaluate ($repel_rexpo = 4) + evaluate ($repel_irexp = 1) + + NONBonded H 0.0498 1.4254 0.0498 1.4254 + NONBonded HA 0.0498 1.4254 0.0450 2.6157 !- charged group. + NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius + ! + NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CP 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CCIS 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded C5 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded C5W 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CF 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CW 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CY 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CY2 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon + NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \ + NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons + NONBonded CH2G 0.1142 3.9823 0.1000 3.3854 ! extended carbons + NONBonded CH2P 0.1142 3.9823 0.1000 3.3854 ! extended carbons + NONBonded CH1P 0.1142 3.9823 0.1000 3.3854 ! extended carbons + NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! / +!! NONBonded CM 0.0262 4.4367 0.1000 3.3854 + NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons + NONBonded CR1H 0.1200 3.7418 0.1000 3.3854 ! ring carbons + NONBonded CR1W 0.1200 3.7418 0.1000 3.3854 ! ring carbons + NONBonded CRHH 0.1200 3.7418 0.1000 3.3854 ! ring carbons + NONBonded CRH 0.1200 3.7418 0.1000 3.3854 ! ring carbons +!! NONBonded CT 0.0262 4.4367 0.1000 3.3854 + ! + NONBonded N 0.2384 2.8509 0.2384 2.8509 + NONBonded NC2 0.2384 2.8509 0.2384 2.8509 + NONBonded NC3 0.2384 2.8509 0.2384 2.8509 + NONBonded NC4 0.2384 2.8509 0.2384 2.8509 + NONBonded NH1 0.2384 2.8509 0.2384 2.8509 + NONBonded NH2 0.2384 2.8509 0.2384 2.8509 + NONBonded NH3 0.2384 2.8509 0.2384 2.8509 + NONBonded NP 0.2384 2.8509 0.2384 2.8509 + NONBonded NR 0.2384 2.8509 0.2384 2.8509 + ! + NONBonded O 0.1591 2.8509 0.1591 2.8509 + NONBonded OC 0.6469 2.8509 0.6469 2.8509 + NONBonded OH1 0.1591 2.8509 0.1591 2.8509 + NONBonded OHP 0.1591 2.8509 0.1591 2.8509 + NONBonded OUF 0.1591 2.8509 0.1591 2.8509 +!! NONBonded OM 0.1591 2.8509 0.1591 2.8509 + NONBonded OS 0.1591 2.8509 0.1591 2.8509 + ! + NONBonded S 0.0430 3.3676 0.0430 3.3676 + NONBonded SM 0.0430 3.3676 0.0430 3.3676 + NONBonded SH1E 0.0430 3.3676 0.0430 3.3676 + NONBonded SH1C 0.0043 0.33676 0.0043 0.33676 + NONBonded SUF 0.0430 3.3676 0.0430 3.3676 + ! +!! NONBONDED FE 0.0000 1.1582 0.0000 1.1582 + + + + + else {standard PARALLHDG parameters} +{ suggested values: + NBONds + CUTNB=7.0 WMIN=1.5 + REPEl = 0.78 + REXPonent = 2 + IREXponent = 2 + RCONst = 5.0 + TOLErance = 0.5 NBXMOD = 5 + ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} +END +} + evaluate ($repel_radius = 0.78) + evaluate ($repel_rcons = 5.0) + evaluate ($repel_rexpo = 2) + evaluate ($repel_irexp = 2) + NONBonded C 0.0903 3.3409 0.0903 3.3409 + NONBonded CP 0.0903 3.3409 0.0903 3.3409 + NONBonded CCIS 0.0903 3.3409 0.0903 3.3409 + NONBonded CR1E 0.1200 3.3409 0.1200 3.3409 + NONBonded CF 0.1200 3.3409 0.1200 3.3409 + NONBonded CY 0.1200 3.3409 0.1200 3.3409 + NONBonded CY2 0.1200 3.3409 0.1200 3.3409 + NONBonded CR1W 0.1200 3.3409 0.1200 3.3409 + NONBonded CW 0.1450 3.3409 0.1450 3.3409 + NONBonded C5W 0.1450 3.3409 0.1450 3.3409 + NONBonded CN 0.1450 3.3409 0.1450 3.3409 + NONBonded C5 0.1200 3.3409 0.1200 3.3409 + NONBonded CH1E 0.0903 3.3409 0.0903 3.3409 + NONBonded CH2E 0.0903 3.3409 0.0903 3.3409 + NONBonded CH3E 0.0903 3.3409 0.0903 3.3409 + NONBonded CH2G 0.0903 3.3409 0.0903 3.3409 + NONBonded CH2P 0.1450 3.3409 0.1450 3.3409 + NONBonded CH1P 0.1450 3.3409 0.1450 3.3409 + NONBonded CRH 0.1200 3.3409 0.1200 3.3409 + NONBonded CR1H 0.1200 3.3409 0.1200 3.3409 + NONBonded CRHH 0.1200 3.3409 0.1200 3.3409 + NONBonded H 0.0498 2.2272 0.0498 2.2272 + NONBonded HA 0.0045 2.2272 0.0045 2.2272 + NONBonded HC 0.0498 2.2272 0.0498 2.2272 + NONBonded N 0.1592 3.0068 0.1592 3.0068 + NONBonded NR 0.1592 3.0068 0.1592 3.0068 + NONBonded NH1 0.1592 3.0068 0.1592 3.0068 + NONBonded NH2 0.1592 3.0068 0.1592 3.0068 + NONBonded NH3 0.1592 3.0068 0.1592 3.0068 + NONBonded NC2 0.1592 3.0068 0.1592 3.0068 + NONBonded NC3 0.1592 3.0068 0.1592 3.0068 + NONBonded NC4 0.1592 3.0068 0.1592 3.0068 + NONBonded O 0.2342 2.7755 0.2342 2.7755 + NONBonded OC 1.0244 2.7755 1.0244 2.7755 + NONBonded OH1 0.2342 2.7755 0.2342 2.7755 + NONBonded OHP 0.2342 2.7755 0.2342 2.7755 + NONBonded OUF 0.2342 2.7755 0.2342 2.7755 + NONBonded S 0.0239 3.7458 0.0239 3.7458 + NONBonded SM 0.0239 3.7458 0.0239 3.7458 + NONBonded SH1E 0.0239 3.7458 0.0239 3.7458 + NONBonded SH1C 0.00239 0.37458 0.00239 0.37458 + NONBonded SUF 0.0239 3.7458 0.0239 3.7458 + + NBFIx H NR 44.200 1.000 44.200 1.000 + NBFIx H O 44.200 1.000 44.200 1.000 + NBFIx H OC 44.200 1.000 44.200 1.000 + NBFIx H OH1 44.200 1.000 44.200 1.000 + NBFIx HC NR 44.200 1.000 44.200 1.000 + NBFIx HC O 44.200 1.000 44.200 1.000 + NBFIx HC OC 44.200 1.000 44.200 1.000 + NBFIx HC OH1 44.200 1.000 44.200 1.000 + + end if + + +set message=$old_message echo=$old_echo end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.top new file mode 100644 index 0000000000000000000000000000000000000000..264244be78c0848af1c63903e37b42bc7e1b99d8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/protein-allhdg5-4.top @@ -0,0 +1,3532 @@ +remarks file toppar/protein-allhdg5-4.top +remarks +remarks file topallhdg.pro version 5.4 date 07-July-10 +remarks for file parallhdg.pro version 5.4 date 07-July-10 or later +remarks Geometric energy function parameters for distance geometry and +remarks simulated annealing. +remarks Author: Michael Nilges, EMBL Heidelberg; Institut Pasteur, Paris +remarks This file contains modifications from M. Williams, UCL London +remarks and multiple modifications for HADDOCK from A. Bonvin, Utrecht University +remarks Last modification 24-09-2014 + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +!***********************************************************************! +! Copyright (C) 1995,1996 by Michael Nilges. All rights reserved. ! +! Copying and redistribution of this files is authorized only if etiher ! +! (1) you make absolutely no changes to your copy, including name, or ! +! (2) if you do make changes, you name it something other than ! +! topallhdg.pro and topallhdg.x.xx.pro, and clearly mark the changes. ! +! The information in this software is subject to change without notice ! +! and should not be construed as a commitment by the EMBL or by the ! +! authors. Neither the EMBL, Yale University, nor the authors assume ! +! responsibility for the use or reliability of this software. ! +! We do hope, however, to get responses from users, especially when ! +! errors have been found. ! +!***********************************************************************! +! Description: ! +! This parameter file was originally derived from the CHARMM parameter ! +! file PARMALLH6. It was designed specifically for the initial stages ! +! of calculating structures from NMR restraints. ! +!***********************************************************************! +! History: +! HADDOCK2.2, additions for CFE (CYS with iron cluster) +! CNS v1.3, revision 7, 1-10-2012, added IMPRoper NE2 CE1 CD2 HE2 for HIS residue +! CNS V1.3, revision 7, 11-08-2011, changed changes in CYF residue for CB and SG +! CNS v1.3, revision 6, 8-19-2011, added MSE residue +! CNS v1.3, revision 2, 12-Aug-10, modified IMPRopers to maintain Arg planarity, proper stereochemical NH1, NH2 assignments without causing singularities. +! CNS v1.3 (27-Feb-10): changed OT1, OT2 to O, OXT, respectively +! version 5.3 (13-Feb-02) : merged UCL version with EMBL version +! version UCL (07-JUL-01) : added new MULT disulphide/sidechain COO DIHEdral parameters +! version UCL (03-JUL-01) : added new MULT phi/psi DIHEdral related parameters +! version UCL (14-MAR-00) : modified peptide BOND parameters for flexible omega +! version UCL (12-MAR-00) : added C and N terminus and disulphide DIHEdrals +! version UCL (09-MAR-00) : TYR O-H planarity & LYS NH3 stagger +! & HIS DIHEdrals modified +! version 5.2 (18-Jun-99) : new cis peptide patch +! version 4.03 (04-APR-99) : THR CB ATOM TYPE corrected +! version 4.02 (17-DEC-97) : Histidine hBOND acceptor/donor corrected +! version 4.01 (29-Jul-96) : all covalent parameters +! version 4.00 (19-Jul-96) : all ATOM TYPEs from CSDX implemented +! version 3.00 (24-Oct-95) : mapped CSDX parmameters on parallhdg, +! no changes in topallhdg +! previous modifications: +! proline residue modified, puckering enforced (MN) +! added hBOND acceptor and donor definitions for analysis (MN) +! all references to internal coordinates (IC's) removed (MN) +! added stereospecific IMPRopers for all pro-chiral centers (ATB, JK) +! all DIHEdrals defining planarity converted to IMPRopers (MN, PK) +! additional IMPRopers at planar centers (MN) +!***********************************************************************! + +autogenerate + ANGLes=true + DIHEdrals=false +end + +MASS DD 100.000 +MASS H 1.008 +MASS HC 1.008 +MASS HA 1.008 +MASS C 12.011 +MASS CCIS 12.011 +MASS CH1E 12.011 +MASS CH2E 12.011 +MASS CH3E 12.011 +MASS CH2G 12.011 +MASS CH1P 12.011 +MASS CH2P 12.011 +MASS C5W 12.011 +MASS CP 12.011 +MASS CW 12.011 + +MASS CR1E 12.011 +MASS C5 12.011 +MASS CRH 12.011 +MASS CR1H 12.011 +MASS CR1W 12.011 +MASS CRHH 12.011 +MASS CF 12.011 +MASS CY 12.011 +MASS CY2 12.011 +MASS N 14.007 +MASS NR 14.007 +MASS NH1 14.007 +MASS NH2 14.007 +MASS NH3 14.007 +MASS NC2 14.007 +MASS NC3 14.007 +MASS NC4 14.007 +MASS O 15.999 +MASS OP1 15.999 +MASS OR3 15.999 +MASS OC 15.999 +MASS OH1 15.999 +MASS OH1C 15.999 +MASS OHP 15.999 +MASS OUF 15.999 +MASS PP 30.97400 +MASS SH1E 32.060 +MASS SH1C 32.060 +MASS SM 32.060 +MASS S 32.060 +MASS SF 32.060 +MASS SUF 32.060 +MASS FS 55.847 ! iron (for CFE - iron sulfur cluster) +MASS SE 78.960 ! selenium (for MSE) + +MASS DUM 100.0 ! dummy particle + +MASS CHAC 15.0350 ! equivalent to CH3 +MASS CHAS 12.0110 ! equivalent to CH0 +MASS CHAD 15.0350 ! equivalent to CH3 +MASS NHAQ 14.0067 ! equivalent to NL +MASS OHAH 15.9994 ! equivalent to OA +MASS HHAA 1.0080 ! equivalent to HO +MASS CHAR 12.0110 ! equivalent to CH0 +MASS CHAA 15.0350 ! equivalent to CH3 +MASS CHAB 15.0350 ! equivalent to CH3 +MASS CHAI 13.0190 ! equivalent to CR51 +MASS CHAO 12.0110 ! equivalent to CB +MASS CHAJ 14.0270 ! equivalent to CH2 +MASS SHAL 32.0600 ! equivalent to S +MASS SHAM 32.0600 ! equivalent to S +MASS CHB 14.0270 ! equivalent to CH2 +MASS CHA 13.0190 ! equivalent to CH1 +MASS CH_Y 12.0110 ! equivalent to C +MASS OHXT 15.9994 ! equivalent to OM +MASS OH_Y 15.9994 ! equivalent to OM +MASS NH_Y 14.0067 ! equivalent to NL +MASS HHAC 1.0080 ! equivalent to H +MASS HHAD 1.0080 ! equivalent to H +MASS HHAB 1.0080 ! equivalent to H + +MASS CD28 12.0110 ! equivalent to CH2 +MASS HD28 1.0080 ! equivalent to HC +MASS HD29 1.0080 ! equivalent to HC +MASS CD29 12.0110 ! equivalent to CH0 +MASS CD30 12.0110 ! equivalent to CH3 +MASS HD31 1.0080 ! equivalent to HC +MASS HD32 1.0080 ! equivalent to HC +MASS HD30 1.0080 ! equivalent to HC +MASS CD31 12.0110 ! equivalent to CH3 +MASS HD34 1.0080 ! equivalent to HC +MASS HD35 1.0080 ! equivalent to HC +MASS HD33 1.0080 ! equivalent to HC +MASS CD32 12.0110 ! equivalent to CH1 +MASS HD36 1.0080 ! equivalent to HC +MASS OD33 15.9994 ! equivalent to OA +MASS HD46 1.0080 ! equivalent to H +MASS CD34 12.0110 ! equivalent to C +MASS OD35 15.9994 ! equivalent to O +MASS ND36 14.0067 ! equivalent to N +MASS HD48 1.0080 ! equivalent to H +MASS CD37 12.0110 ! equivalent to CH2 +MASS HD37 1.0080 ! equivalent to HC +MASS HD38 1.0080 ! equivalent to HC +MASS CD38 12.0110 ! equivalent to CH2 +MASS HD39 1.0080 ! equivalent to HC +MASS HD4A 1.0080 ! equivalent to HC +MASS CD39 12.0110 ! equivalent to C +MASS OD40 15.9994 ! equivalent to O +MASS ND41 14.0067 ! equivalent to N +MASS HD41 1.0080 ! equivalent to H +MASS CD42 12.0110 ! equivalent to CH2 +MASS HD42 1.0080 ! equivalent to HC +MASS HD43 1.0080 ! equivalent to HC +MASS CD43 12.0110 ! equivalent to CH2 +MASS HD44 1.0080 ! equivalent to HC +MASS HD45 1.0080 ! equivalent to HC +MASS SD44 32.0600 ! equivalent to S +MASS HD47 1.0080 ! equivalent to H + +!---------------------------------------------------------------------- + +residue CYM +GROUP + ATOM CAC TYPE= CHAC CHARge= 0.000 END + ATOM CAS TYPE= CHAS CHARge= 0.000 END + ATOM CAD TYPE= CHAD CHARge= 0.000 END + ATOM NAQ TYPE= NHAQ CHARge= 0.265 END + ATOM OAH TYPE= OHAH CHARge=-0.700 END + ATOM HAA TYPE= HHAA CHARge= 0.435 END + ATOM CAR TYPE= CHAR CHARge= 0.000 END + ATOM CAA TYPE= CHAA CHARge= 0.000 END + ATOM CAB TYPE= CHAB CHARge= 0.000 END + ATOM CAI TYPE= CHAI CHARge= 0.000 END + ATOM CAO TYPE= CHAO CHARge= 0.000 END + ATOM CAJ TYPE= CHAJ CHARge= 0.080 END + ATOM SAL TYPE= SHAL CHARge=-0.080 END + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.080 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=S CHARge=-0.080 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG BOND SG HG + BOND CA C + BOND C O + + BOND CAC CAS + BOND CAS CAD + BOND CAS NAQ + BOND CAS CAO + BOND NAQ OAH + BOND NAQ CAR + BOND OAH HAA + BOND CAR CAA + BOND CAR CAB + BOND CAR CAI + BOND CAI CAO + BOND CAO CAJ + BOND CAJ SAL + BOND SAL SG + + ANGLe CAC CAS CAD + ANGLe CAC CAS NAQ + ANGLe CAC CAS CAO + ANGLe CAD CAS NAQ + ANGLe CAD CAS CAO + ANGLe NAQ CAS CAO + ANGLe CAS NAQ OAH + ANGLe CAS NAQ CAR + ANGLe OAH NAQ CAR + ANGLe NAQ OAH HAA + ANGLe NAQ CAR CAA + ANGLe NAQ CAR CAB + ANGLe NAQ CAR CAI + ANGLe CAA CAR CAB + ANGLe CAA CAR CAI + ANGLe CAB CAR CAI + ANGLe CAR CAI CAO + ANGLe CAS CAO CAI + ANGLe CAS CAO CAJ + ANGLe CAI CAO CAJ + ANGLe CAO CAJ SAL + ANGLe CAJ SAL SG + ANGLe SAL SG CB + + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + IMPRoper CAO CAS CAI CAJ + IMPRoper CAS CAC NAQ CAD + IMPRoper NAQ CAS OAH CAR + IMPRoper CAR NAQ CAB CAA + + DIHEdral SG CB CA N + DIHEdral CAC CAS NAQ CAR + DIHEdral CAC CAS CAO CAJ + DIHEdral CAS NAQ OAH HAA + DIHEdral CAI CAR NAQ CAS + DIHEdral NAQ CAR CAI CAO + DIHEdral CAR CAI CAO CAJ + DIHEdral CAS CAO CAJ SAL + DIHEdral SG SAL CAJ CAO + DIHEdral CB SG SAL CAJ + DIHEdral SAL SG CB CA + + DONO HN N + DONO HG SG + ACCE O C + +END + +!---------------------------------------------------------------------- + +residue ALA + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH3E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM HB3 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 BOND CB HB3 + BOND CA C + BOND C O + + IMPRoper HA N C CB ! chirality CA + IMPRoper HB1 HB2 CA HB3 ! methyl CB + + DIHEdral HB1 CB CA C ! methyl stagger UCL 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ARG + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.070 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.310 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM NE TYPE=NH1 CHARge=-0.700 end + ATOM HE TYPE=H CHARge= 0.440 end + ATOM CZ TYPE=C CHARge= 0.640 end + ATOM NH1 TYPE=NC2 CHARge=-0.800 end + ATOM HH11 TYPE=HC CHARge= 0.460 end + ATOM HH12 TYPE=HC CHARge= 0.460 end + ATOM NH2 TYPE=NC2 CHARge=-0.800 end + ATOM HH21 TYPE=HC CHARge= 0.460 end + ATOM HH22 TYPE=HC CHARge= 0.460 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD NE BOND NE HE + BOND NE CZ + BOND CZ NH1 BOND NH1 HH11 BOND NH1 HH12 + BOND CZ NH2 BOND NH2 HH21 BOND NH2 HH22 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper NE CD CZ HE + +! modified IMPRopers for Arg planarity to reduce chances of reaching singularity, ATB 8/12/10 +! IMPRoper CZ NE NH1 NH2 + IMPRoper CZ NH1 NH2 NE !planar CZ + + IMPRoper NH1 CZ HH11 HH12 + IMPRoper NH2 CZ HH21 HH22 + IMPRoper NE CZ NH1 HH11 + IMPRoper NE CZ NH2 HH21 + +! modified IMPRopers for Arg planarity to reduce chances of reaching singularity, ATB 8/12/10 +!! IMPRoper CZ NH2 HE NE ! planar CZ ! commented out and replaced with IMPRoper that does not involve a hydrogen + IMPRoper CD NE CZ NH1 ! note: this one is defined as a DIHEdral in the protein.top file + +! added IMPRopers for Arg planarity to reduce chances of reaching singularity, ATB 8/12/10 + IMPRoper NE CZ NH1 HH11 !note: one IMPRoper for each hydrogen ! these are defined as DIHEdrals in the protein.top file + IMPRoper NE CZ NH2 HH21 ! + IMPRoper NE CZ NH1 HH12 ! + IMPRoper NE CZ NH2 HH22 ! + + + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG NE !stereo CD + + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral NE CD CG CB + DIHEdral CZ NE CD CG + + DONO HN N + DONO HE NE + DONO HH11 NH1 + DONO HH12 NH1 + DONO HH21 NH2 + DONO HH22 NH2 + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ASN + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C CHARge= 0.500 end + ATOM OD1 TYPE=O CHARge=-0.500 end + ATOM ND2 TYPE=NH2 CHARge=-0.850 end + ATOM HD21 TYPE=H CHARge= 0.425 end + ATOM HD22 TYPE=H CHARge= 0.425 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG OD1 + BOND CG ND2 BOND ND2 HD21 BOND ND2 HD22 + BOND CA C + BOND C O + + IMPRoper HA N C CB ! chirality CA + IMPRoper CG CB OD1 ND2 + IMPRoper ND2 CG HD21 HD22 + IMPRoper CB CG ND2 HD21 + IMPRoper HB1 HB2 CA CG ! stereo CB + + DIHEdral CG CB CA N + DIHEdral OD1 CG CB CA ! mult 2 ! UCL + + DONO HN N + DONO HD21 ND2 + DONO HD22 ND2 + ACCE OD1 CG + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ASP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.100 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C CHARge= 0.700 end + ATOM OD1 TYPE=OC CHARge=-0.800 end + ATOM OD2 TYPE=OC CHARge=-0.800 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG OD1 + BOND CG OD2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CG CB OD1 OD2 + IMPRoper HB1 HB2 CA CG !stereo CB + + DIHEdral CG CB CA N + + DIHEdral OD1 CG CB CA + + DONO HN N + ACCE OD1 CG + ACCE OD2 CG + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ASH + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C CHARge= 0.500 end + ATOM OD1 TYPE=OC CHARge=-0.500 end + ATOM OD2 TYPE=OH1 CHARge=-0.450 end + ATOM HD2 TYPE=H CHARge= 0.450 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG OD1 + BOND CG OD2 BOND OD2 HD2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CG CB OD1 OD2 + IMPRoper HB1 HB2 CA CG !stereo CB + + DIHEdral CG CB CA N + + DIHEdral OD1 CG CB CA + + DONO HN N + DONO HD2 OD2 + ACCE OD1 CG + ACCE OD2 CG + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CSP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.080 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=SM CHARge=-0.440 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG BOND SG P + BOND P O1P + BOND P O2P + BOND P O3P + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + IMPRoper SG P O3P O1P + + DIHEdral SG CB CA N + DIHEdral CB SG P O3P + + DONO HN N + ACCE O C + ACCE O1P P + ACCE O2P P + ACCE O3P P + +end + +!---------------------------------------------------------------------- + +residue CFE + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.020 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=SH1E CHARge=-0.720 end + ATOM FE1 TYPE=FS CHARge= 0.870 end + ATOM SF1 TYPE=SF CHARge=-0.560 end + ATOM FE2 TYPE=FS CHARge= 0.870 end + ATOM SF2 TYPE=SF CHARge=-0.560 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG BOND SG FE1 + BOND FE1 SF1 BOND SF1 FE2 + BOND FE1 SF2 BOND SF2 FE2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + + DIHEdral SG CB CA N + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CYC ! special for covalent docking - vdw of Sulphur reduced + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=SH1C CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + + DIHEdral SG CB CA N + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CYF + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.020 end ! CHARged AB for better Zn coordination + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=SH1E CHARge=-0.720 end ! CHARged AB for better Zn coordination + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + + DIHEdral SG CB CA N + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CYS + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.180 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM SG TYPE=SH1E CHARge=-0.450 end + ATOM HG TYPE=H CHARge= 0.270 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB SG BOND SG HG + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA SG !stereo CB + + DIHEdral SG CB CA N + + DONO HN N + DONO HG SG + ACCE O C +end + +!---------------------------------------------------------------------- + +residue GLN + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=C CHARge= 0.500 end + ATOM OE1 TYPE=O CHARge=-0.500 end + ATOM NE2 TYPE=NH2 CHARge=-0.850 end + ATOM HE21 TYPE=H CHARge= 0.425 end + ATOM HE22 TYPE=H CHARge= 0.425 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD + BOND CD OE1 + BOND CD NE2 BOND NE2 HE21 BOND NE2 HE22 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CD CG OE1 NE2 + IMPRoper NE2 CD HE21 HE22 + IMPRoper CG CD NE2 HE21 + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral OE1 CD CG CB + + DONO HN N + DONO HE21 NE2 + DONO HE22 NE2 + ACCE OE1 CD + ACCE O C +end + +!---------------------------------------------------------------------- + +residue GLU + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge=-0.100 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=C CHARge= 0.700 end + ATOM OE1 TYPE=OC CHARge=-0.800 end + ATOM OE2 TYPE=OC CHARge=-0.800 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD + BOND CD OE1 + BOND CD OE2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CD CG OE1 OE2 + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral OE1 CD CG CB ! mult 2 ! UCL + + DONO HN N + ACCE OE1 CD + ACCE OE2 CD + ACCE O C +end + +!---------------------------------------------------------------------- + +residue GLH + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=C CHARge= 0.500 end + ATOM OE1 TYPE=OC CHARge=-0.500 end + ATOM OE2 TYPE=OH1 CHARge=-0.450 end + ATOM HE2 TYPE=H CHARge= 0.450 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD + BOND CD OE1 + BOND CD OE2 BOND OE2 HE2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CD CG OE1 OE2 + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral OE1 CD CG CB ! mult 2 ! UCL + + DONO HN N + DONO HE2 OE2 + ACCE OE1 CD + ACCE OE2 CD + ACCE O C +end + +!---------------------------------------------------------------------- + +residue GLY + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH2G CHARge= 0.200 end + ATOM HA1 TYPE=HA CHARge= 0.000 end + ATOM HA2 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA1 BOND CA HA2 + BOND CA C + BOND C O + + DONO HN N + ACCE O C + + IMPRoper HA1 HA2 N C !stereo CA +end + +!---------------------------------------------------------------------- + +residue NEP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C5 CHARge= 0.330 end + ATOM ND1 TYPE=NH1 CHARge=-0.540 end + ATOM HD1 TYPE=H CHARge= 0.460 end + ATOM CD2 TYPE=CR1H CHARge= 0.330 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CRHH CHARge= 0.500 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM NE2 TYPE=NR CHARge=-0.440 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG ND1 BOND ND1 HD1 + BOND ND1 CE1 BOND CE1 HE1 + BOND CG CD2 BOND CD2 HD2 + BOND CD2 NE2 BOND NE2 P + BOND CE1 NE2 + BOND P O1P + BOND P O2P + BOND P O3P + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CG CB ND1 CD2 + IMPRoper ND1 CE1 CG HD1 + IMPRoper CD2 NE2 CG HD2 + IMPRoper CE1 ND1 NE2 HE1 + IMPRoper CG ND1 CE1 NE2 + IMPRoper ND1 CE1 NE2 CD2 + IMPRoper CE1 NE2 CD2 CG + IMPRoper NE2 CD2 CG ND1 + IMPRoper CD2 CG ND1 CE1 + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper NE2 P CD2 CE1 + + DIHEdral CG CB CA N + DIHEdral ND1 CG CB CA + DIHEdral CD2 CG CB CA + DIHEdral O3P P NE2 CE1 + + DONO HN N + DONO HD1 ND1 + DONO HE2 NE2 + ACCE O C + ACCE O1P P + ACCE O2P P + ACCE O3P P +end + +!---------------------------------------------------------------------- + +residue HIS ! doubly protonated HIS + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C5 CHARge= 0.330 end + ATOM ND1 TYPE=NH1 CHARge=-0.540 end + ATOM HD1 TYPE=H CHARge= 0.460 end + ATOM CD2 TYPE=CR1H CHARge= 0.330 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CRHH CHARge= 0.500 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM NE2 TYPE=NH1 CHARge=-0.540 end + ATOM HE2 TYPE=H CHARge= 0.460 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG ND1 BOND ND1 HD1 + BOND ND1 CE1 BOND CE1 HE1 + BOND CG CD2 BOND CD2 HD2 + BOND CD2 NE2 BOND NE2 HE2 + BOND CE1 NE2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper CG CB ND1 CD2 + IMPRoper NE2 CE1 CD2 HE2 ! added 1/10/2012 Pieter Hendrickx + IMPRoper ND1 CE1 CG HD1 + IMPRoper CD2 NE2 CG HD2 + IMPRoper CE1 ND1 NE2 HE1 + IMPRoper CG ND1 CE1 NE2 + IMPRoper ND1 CE1 NE2 CD2 + IMPRoper CE1 NE2 CD2 CG + IMPRoper NE2 CD2 CG ND1 + IMPRoper CD2 CG ND1 CE1 + IMPRoper HB1 HB2 CA CG !stereo CB + + DIHEdral CG CB CA N + DIHEdral ND1 CG CB CA + DIHEdral CD2 CG CB CA ! UCL added 09-MAR-00 + + DONO HN N + DONO HD1 ND1 + DONO HE2 NE2 + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ILE + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1E CHARge= 0.000 end + ATOM HB TYPE=HA CHARge= 0.000 end + ATOM CG1 TYPE=CH2E CHARge= 0.000 end + ATOM HG11 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end + ATOM HG12 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23 HD11 HD12 HD13) end + ATOM CG2 TYPE=CH3E CHARge= 0.000 end + ATOM HG21 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end + ATOM HG22 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end + ATOM HG23 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HD11 HD12 HD13) end + ATOM CD1 TYPE=CH3E CHARge= 0.000 end + ATOM HD11 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end + ATOM HD12 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end + ATOM HD13 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23 HG11 HG12) end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB + BOND CB CG1 BOND CG1 HG11 BOND CG1 HG12 + BOND CB CG2 BOND CG2 HG21 BOND CG2 HG22 BOND CG2 HG23 + BOND CG1 CD1 BOND CD1 HD11 BOND CD1 HD12 BOND CD1 HD13 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB CA CG2 CG1 !chirality CB + + IMPRoper HG11 HG12 CB CD1 !stereo CG1 + IMPRoper HG21 HG22 CB HG23 !methyl CG2 + IMPRoper HD11 HD12 CG1 HD13 !methyl CD1 + + DIHEdral CG1 CB CA N + DIHEdral CD1 CG1 CB CA + DIHEdral HD11 CD1 CG1 CB ! UCL methyl stagger 12-MAR-00 + DIHEdral HG21 CG2 CB CA ! UCL methyl stagger 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue LEU + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH1E CHARge= 0.000 end + ATOM HG TYPE=HA CHARge= 0.000 end + ATOM CD1 TYPE=CH3E CHARge= 0.000 end + ATOM HD11 TYPE=HA CHARge= 0.000 excl = (HD21 HD22 HD23 HG) end + ATOM HD12 TYPE=HA CHARge= 0.000 excl = (HD21 HD22 HD23 HG) end + ATOM HD13 TYPE=HA CHARge= 0.000 excl = (HD21 HD22 HD23 HG) end + ATOM CD2 TYPE=CH3E CHARge= 0.000 end + ATOM HD21 TYPE=HA CHARge= 0.000 excl = (HD11 HD12 HD13 HG) end + ATOM HD22 TYPE=HA CHARge= 0.000 excl = (HD11 HD12 HD13 HG) end + ATOM HD23 TYPE=HA CHARge= 0.000 excl = (HD11 HD12 HD13 HG) end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG + BOND CG CD1 BOND CD1 HD11 BOND CD1 HD12 BOND CD1 HD13 + BOND CG CD2 BOND CD2 HD21 BOND CD2 HD22 BOND CD2 HD23 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HG CB CD1 CD2 !stereo CG + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HD11 HD12 CG HD13 !methyl CD1 + IMPRoper HD21 HD22 CG HD23 !methyl CD2 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + DIHEdral HD11 CD1 CG CB ! UCL methyl stagger 12-MAR-00 + DIHEdral HD21 CD2 CG CB ! UCL methyl stagger 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue LYS + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH2E CHARge= 0.310 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM NZ TYPE=NH3 CHARge=-0.300 end + ATOM HZ1 TYPE=HC CHARge= 0.330 end + ATOM HZ2 TYPE=HC CHARge= 0.330 end + ATOM HZ3 TYPE=HC CHARge= 0.330 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE HE2 + BOND CE NZ BOND NZ HZ1 BOND NZ HZ2 BOND NZ HZ3 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG CE !stereo CD + IMPRoper HE1 HE2 CD NZ !stereo CE + IMPRoper HZ1 HZ2 CE HZ3 !methyl NZ + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral CE CD CG CB + DIHEdral NZ CE CD CG + DIHEdral HZ1 NZ CE CD ! UCL stagger NH3 group 12-MAR-00 + + DONO HN N + DONO HZ1 NZ + DONO HZ2 NZ + DONO HZ3 NZ + ACCE O C +end + +!---------------------------------------------------------------------- + +residue HLY ! hydroxyproline + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH1E CHARge= 0.475 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM OZ TYPE=OH1 CHARge=-0.600 end + ATOM HOZ TYPE=H CHARge= 0.435 end + ATOM NZ TYPE=NH3 CHARge=-0.300 end + ATOM HZ1 TYPE=HC CHARge= 0.330 end + ATOM HZ2 TYPE=HC CHARge= 0.330 end + ATOM HZ3 TYPE=HC CHARge= 0.330 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE OZ BOND OZ HOZ + BOND CE NZ BOND NZ HZ1 BOND NZ HZ2 BOND NZ HZ3 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG CE !stereo CD + IMPRoper HE1 OZ CD NZ !stereo CE + IMPRoper HZ1 HZ2 CE HZ3 !methyl NZ + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral CE CD CG CB + DIHEdral NZ CE CD CG + DIHEdral OZ CE CD CG + + DONO HN N + DONO HZ1 NZ + DONO HZ2 NZ + DONO HZ3 NZ + DONO HOZ OZ + ACCE O C +end + +!---------------------------------------------------------------------- + +residue ALY + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH2E CHARge= 0.200 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM NZ TYPE=NH1 CHARge=-0.570 end + ATOM HZ1 TYPE=H CHARge= 0.370 end + ATOM CZ TYPE=C CHARge= 0.500 end + ATOM OZ TYPE=O CHARge=-0.500 end + ATOM CM TYPE=CH3E CHARge= 0.000 end + ATOM HM1 TYPE=HA CHARge= 0.000 end + ATOM HM2 TYPE=HA CHARge= 0.000 end + ATOM HM3 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE HE2 + BOND CE NZ BOND NZ HZ1 BOND NZ CZ BOND CZ OZ BOND CZ CM + BOND CM HM1 BOND CM HM2 BOND CM HM3 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG CE !stereo CD + IMPRoper HE1 HE2 CD NZ !stereo CE + IMPRoper HM1 HM2 CZ HM3 !methyl CM + IMPRoper CZ CM NZ OZ !planar CZ + IMPRoper NZ CZ CM HZ1 !planar NZ + IMPRoper CE NZ CZ CM !side-chain peptide plane + + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral CE CD CG CB + DIHEdral NZ CE CD CG + DIHEdral HZ1 NZ CE CD ! UCL stagger NH3 group 12-MAR-00 +! DIHEdral CE NZ CZ OZ + + DONO HN N + DONO HZ1 NZ + ACCE O C + ACCE OZ CZ +end + +!---------------------------------------------------------------------- + +residue MLZ ! monomethyl lysine, added 30-04-2009 A. Bonvin + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH2E CHARge=-0.157 end + ATOM HE1 TYPE=HA CHARge= 0.250 end + ATOM HE2 TYPE=HA CHARge= 0.250 end + ATOM NZ TYPE=NC2 CHARge=-0.400 end + ATOM HZ1 TYPE=HC CHARge= 0.320 end + ATOM HZ2 TYPE=HC CHARge= 0.320 end + ATOM CM3 TYPE=CH3E CHARge=-0.333 end + ATOM HM31 TYPE=HA CHARge= 0.250 end + ATOM HM32 TYPE=HA CHARge= 0.250 end + ATOM HM33 TYPE=HA CHARge= 0.250 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE HE2 + BOND CE NZ BOND NZ HZ1 BOND NZ HZ2 BOND NZ CM3 + BOND CM3 HM31 BOND CM3 HM32 BOND CM3 HM33 + BOND CA C + BOND C O + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue MLY ! Dimethyl lysine, added 30-04-2009 A. Bonvin + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH2E CHARge=-0.154 end + ATOM HE1 TYPE=HA CHARge= 0.250 end + ATOM HE2 TYPE=HA CHARge= 0.250 end + ATOM NZ TYPE=NC3 CHARge=-0.510 end + ATOM HZ1 TYPE=HC CHARge= 0.330 end + ATOM CM2 TYPE=CH3E CHARge=-0.333 end + ATOM HM21 TYPE=HA CHARge= 0.250 end + ATOM HM22 TYPE=HA CHARge= 0.250 end + ATOM HM23 TYPE=HA CHARge= 0.250 end + ATOM CM3 TYPE=CH3E CHARge=-0.333 end + ATOM HM31 TYPE=HA CHARge= 0.250 end + ATOM HM32 TYPE=HA CHARge= 0.250 end + ATOM HM33 TYPE=HA CHARge= 0.250 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE HE2 + BOND CE NZ BOND NZ HZ1 BOND NZ CM2 BOND NZ CM3 + BOND CM2 HM21 BOND CM2 HM22 BOND CM2 HM23 + BOND CM3 HM31 BOND CM3 HM32 BOND CM3 HM33 + BOND CA C + BOND C O + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue M3L ! trimethyl lysine + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2E CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE TYPE=CH2E CHARge=-0.151 end + ATOM HE1 TYPE=HA CHARge= 0.250 end + ATOM HE2 TYPE=HA CHARge= 0.250 end + ATOM NZ TYPE=NC4 CHARge=-0.600 end + ATOM CM1 TYPE=CH3E CHARge=-0.333 end + ATOM HM11 TYPE=HA CHARge= 0.250 end + ATOM HM12 TYPE=HA CHARge= 0.250 end + ATOM HM13 TYPE=HA CHARge= 0.250 end + ATOM CM2 TYPE=CH3E CHARge=-0.333 end + ATOM HM21 TYPE=HA CHARge= 0.250 end + ATOM HM22 TYPE=HA CHARge= 0.250 end + ATOM HM23 TYPE=HA CHARge= 0.250 end + ATOM CM3 TYPE=CH3E CHARge=-0.333 end + ATOM HM31 TYPE=HA CHARge= 0.250 end + ATOM HM32 TYPE=HA CHARge= 0.250 end + ATOM HM33 TYPE=HA CHARge= 0.250 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD CE BOND CE HE1 BOND CE HE2 + BOND CE NZ BOND NZ CM1 BOND NZ CM2 BOND NZ CM3 + BOND CM1 HM11 BOND CM1 HM12 BOND CM1 HM13 + BOND CM2 HM21 BOND CM2 HM22 BOND CM2 HM23 + BOND CM3 HM31 BOND CM3 HM32 BOND CM3 HM33 + BOND CA C + BOND C O + +! IMPRoper HA N C CB !chirality CA +! IMPRoper HB1 HB2 CA CG !stereo CB +! IMPRoper HG1 HG2 CB CD !stereo CG +! IMPRoper HD1 HD2 CG CE !stereo CD +! IMPRoper HE1 HE2 CD NZ !stereo CE +! IMPRoper CM1 CM2 CE CM3 !methyl NZ +! IMPRoper HM11 HM12 NZ HM13 !methyl CM1 +! IMPRoper HM21 HM22 NZ HM23 !methyl CM1 +! IMPRoper HM31 HM32 NZ HM33 !methyl CM1 + +! DIHEdral CG CB CA N +! DIHEdral CD CG CB CA +! DIHEdral CE CD CG CB +! DIHEdral NZ CE CD CG +! DIHEdral CM1 NZ CE CD ! UCL stagger NH3 group 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue MET + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.235 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM SD TYPE=SM CHARge=-0.470 end + ATOM CE TYPE=CH3E CHARge= 0.235 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM HE3 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG SD + BOND SD CE BOND CE HE1 BOND CE HE2 BOND CE HE3 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB SD !stereo CG + IMPRoper HE1 HE2 SD HE3 !methyl CE + + DIHEdral CG CB CA N + DIHEdral SD CG CB CA + DIHEdral CE SD CG CB + DIHEdral HE1 CE SD CG ! UCL methyl stagger 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue MSE ! SeMET ! added 8-19-2011, ATB + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge=-0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.235 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM SE TYPE=SE CHARge=-0.470 end + ATOM CE TYPE=CH3E CHARge= 0.235 end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM HE3 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG SE + BOND SE CE BOND CE HE1 BOND CE HE2 BOND CE HE3 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB SE !stereo CG + IMPRoper HE1 HE2 SE HE3 !methyl CE + + DIHEdral CG CB CA N + DIHEdral SE CG CB CA + DIHEdral CE SE CG CB + DIHEdral HE1 CE SE CG ! UCL methyl stagger 12-MAR-00 + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue PCA + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2P CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CP CHARge= 0.500 end + ATOM OE TYPE=O CHARge=-0.500 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD + BOND CD OE + BOND CD N + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper OE CD N HN !planar ring carbonyl + IMPRoper CD CG N OE !planar ring carbonyl + IMPRoper CG CD N CA !cyclic peptide bond + IMPRoper N CD CA HN !planar +N + + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + + DONO HN N + ACCE OE CD + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CIR + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM C3 TYPE=CH2E CHARge= 0.000 end + ATOM H31 TYPE=HA CHARge= 0.000 end + ATOM H32 TYPE=HA CHARge= 0.000 end + ATOM C4 TYPE=CH2E CHARge= 0.070 end + ATOM H41 TYPE=HA CHARge= 0.000 end + ATOM H42 TYPE=HA CHARge= 0.000 end + ATOM C5 TYPE=CH2E CHARge= 0.310 end + ATOM H51 TYPE=HA CHARge= 0.000 end + ATOM H52 TYPE=HA CHARge= 0.000 end + ATOM N6 TYPE=NH1 CHARge=-0.700 end + ATOM H6 TYPE=H CHARge= 0.440 end + ATOM C7 TYPE=C CHARge= 0.420 end + ATOM O7 TYPE=O CHARge=-0.660 end + ATOM N8 TYPE=NC2 CHARge=-0.800 end + ATOM H81 TYPE=HC CHARge= 0.460 end + ATOM H82 TYPE=HC CHARge= 0.460 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA C3 BOND C3 H31 BOND C3 H32 + BOND C3 C4 BOND C4 H41 BOND C4 H42 + BOND C4 C5 BOND C5 H51 BOND C5 H52 + BOND C5 N6 + BOND N6 C7 BOND N6 H6 + BOND C7 O7 BOND C7 N8 + BOND N8 H81 BOND N8 H82 + BOND CA C + BOND C O + + IMPRoper HA N C C3 !chirality CA + IMPRoper H31 H32 CA C4 !stereo C3 + IMPRoper H41 H42 C3 C5 !stereo C4 + IMPRoper H51 H52 C4 N6 !stereo C5 + + IMPRoper C5 N6 C7 O7 + IMPRoper H5 N6 C7 O7 + IMPRoper N6 C7 N8 H81 + IMPRoper O7 C7 N8 H82 + + DIHEdral C4 C3 CA N + DIHEdral C5 C4 C3 CA + DIHEdral N6 C5 C4 C3 + DIHEdral C7 N6 C5 C4 + + DONO HN N + DONO H6 N6 + DONO H81 N8 + DONO H82 N8 + ACCE O7 C7 + ACCE O C +end + +!---------------------------------------------------------------------- + +residue PHE + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CF CHARge= 0.000 exclude=(CZ) end + ATOM CD1 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CR1E CHARge= 0.000 exclude=(CE1) end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CR1E CHARge= 0.000 exclude=(CD2) end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM CE2 TYPE=CR1E CHARge= 0.000 exclude=(CD1) end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM CZ TYPE=CR1E CHARge= 0.000 exclude=(CG) end + ATOM HZ TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 BOND CD2 HD2 + BOND CD1 CE1 BOND CE1 HE1 + BOND CD2 CE2 BOND CE2 HE2 + BOND CE1 CZ BOND CZ HZ + BOND CE2 CZ + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! Hs and CB around the ring + IMPRoper HD2 CD2 CE2 CZ + IMPRoper HE2 CE2 CZ CE1 + IMPRoper HZ CZ CE1 CD1 + IMPRoper HE1 CE1 CD1 CG + IMPRoper HD1 CD1 CG CD2 + IMPRoper CB CG CD2 CE2 + +! around the ring + IMPRoper CG CD1 CE1 CZ + IMPRoper CD1 CE1 CZ CE2 + IMPRoper CE1 CZ CE2 CD2 + IMPRoper CZ CE2 CD2 CG + IMPRoper CE2 CD2 CG CD1 + IMPRoper CD2 CG CD1 CE1 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue PRO + group + ATOM N TYPE=N CHARge=-0.570 end + ATOM CA TYPE=CH1E CHARge= 0.285 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2P CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2P CHARge= 0.285 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD N + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG N !stereo CD + + ACCE O C +end + +!---------------------------------------------------------------------- + +residue HYP ! 4R-hydroxyproline + group + ATOM N TYPE=N CHARge=-0.570 end + ATOM CA TYPE=CH1E CHARge= 0.285 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH1P CHARge= 0.485 end + ATOM OG1 TYPE=OH1 CHARge=-0.700 end + ATOM HG1 TYPE=H CHARge= 0.500 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2P CHARge= 0.000 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG OG1 BOND CG HG2 + BOND OG1 HG1 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD N + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper OG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG N !stereo CD + + ACCE O C +end + +!---------------------------------------------------------------------- + +residue HY3 ! 3L-hydroxyproline + group + ATOM N TYPE=N CHARge=-0.570 end + ATOM CA TYPE=CH1E CHARge= 0.285 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1P CHARge= 0.485 end + ATOM OB1 TYPE=OH1 CHARge=-0.700 end + ATOM HB1 TYPE=H CHARge= 0.500 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2P CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=CH2P CHARge= 0.285 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N CA BOND CA HA + BOND CA CB BOND CB OB1 BOND CB HB2 + BOND OB1 HB1 + BOND CB CG BOND CG HG1 BOND CG HG2 + BOND CG CD BOND CD HD1 BOND CD HD2 + BOND CD N + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper OB1 HB2 CA CG !stereo CB + IMPRoper HG1 HG2 CB CD !stereo CG + IMPRoper HD1 HD2 CG N !stereo CD + + ACCE O C +end + +!---------------------------------------------------------------------- + +residue SER + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.265 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM OG TYPE=OH1 CHARge=-0.700 end + ATOM HG TYPE=H CHARge= 0.435 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB OG BOND OG HG + BOND O C + BOND C CA + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA OG !stereo CB + + DIHEdral OG CB CA N + + DONO HN N + DONO HG OG + ACCE OG " " + ACCE O C +end + +!---------------------------------------------------------------------- + +residue SEC !Serine with reduced vdw on the OG1 oxygen for covalent docking + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.200 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM OG TYPE=OH1C CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB OG + BOND O C + BOND C CA + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA OG !stereo CB + + DIHEdral OG CB CA N + + DONO HN N + ACCE O C +end + +!---------------------------------------------------------------------- + +residue SEP !phosphorylated Serine, AB-2008-11 + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.265 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM OG TYPE=OHP CHARge=-0.625 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB OG BOND OG P + BOND P O1P + BOND P O2P + BOND P O3P + BOND O C + BOND C CA + + ANGLe CB OG P + ANGLe OG P O3P + ANGLe O3P P O1P + ANGLe O3P P O2P + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA OG !stereo CB + + DIHEdral OG CB CA N + DIHEdral CB OG P O3P + + DONO HN N + DONO HG OG + ACCE OG " " + ACCE O C + ACCE O1P P + ACCE O2P P + ACCE O3P P +end + +!---------------------------------------------------------------------- + +residue PNS !phosphopanthetine Serine, ANGGAL-2016-02 + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.265 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM OG TYPE=OHP CHARge=-0.118 end + ATOM P TYPE=PP CHARge= 0.722 end + ATOM O1P TYPE=OP1 CHARge=-0.364 end + ATOM O2P TYPE=OP1 CHARge=-0.364 end + ATOM O3P TYPE=OR3 CHARge=-0.117 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + ATOM C28 TYPE=CD28 CHARge= 0.070 END + ATOM H28 TYPE=HD28 CHARge=-0.013 END + ATOM H29 TYPE=HD29 CHARge=-0.013 END + ATOM C29 TYPE=CD29 CHARge= 0.087 END + ATOM C30 TYPE=CD30 CHARge= 0.069 END + ATOM H31 TYPE=HD31 CHARge=-0.013 END + ATOM H32 TYPE=HD32 CHARge=-0.012 END + ATOM H30 TYPE=HD30 CHARge=-0.013 END + ATOM C31 TYPE=CD31 CHARge= 0.069 END + ATOM H34 TYPE=HD34 CHARge=-0.013 END + ATOM H35 TYPE=HD35 CHARge=-0.013 END + ATOM H33 TYPE=HD33 CHARge=-0.013 END + ATOM C32 TYPE=CD32 CHARge= 0.088 END + ATOM H36 TYPE=HD36 CHARge=-0.013 END + ATOM O33 TYPE=OD33 CHARge=-0.124 END + ATOM H46 TYPE=HD46 CHARge= 0.019 END + ATOM C34 TYPE=CD34 CHARge= 0.208 END + ATOM O35 TYPE=OD35 CHARge=-0.430 END + ATOM N36 TYPE=ND36 CHARge= 0.070 END + ATOM H48 TYPE=HD48 CHARge=-0.008 END + ATOM C37 TYPE=CD37 CHARge= 0.070 END + ATOM H37 TYPE=HD37 CHARge=-0.012 END + ATOM H38 TYPE=HD38 CHARge=-0.013 END + ATOM C38 TYPE=CD38 CHARge= 0.070 END + ATOM H39 TYPE=HD39 CHARge=-0.013 END + ATOM H4A TYPE=HD4A CHARge=-0.013 END + ATOM C39 TYPE=CD39 CHARge= 0.208 END + ATOM O40 TYPE=OD40 CHARge=-0.431 END + ATOM N41 TYPE=ND41 CHARge= 0.070 END + ATOM H41 TYPE=HD41 CHARge=-0.008 END + ATOM C42 TYPE=CD42 CHARge= 0.070 END + ATOM H42 TYPE=HD42 CHARge=-0.013 END + ATOM H43 TYPE=HD43 CHARge=-0.013 END + ATOM C43 TYPE=CD43 CHARge= 0.070 END + ATOM H44 TYPE=HD44 CHARge=-0.013 END + ATOM H45 TYPE=HD45 CHARge=-0.013 END + ATOM S44 TYPE=SD44 CHARge= 0.031 END + ATOM H47 TYPE=HD47 CHARge=-0.046 END + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB OG BOND OG P + BOND P O1P + BOND P O2P + BOND P O3P + BOND O C + BOND C CA + BOND C28 O3P + BOND C28 H28 + BOND C28 H29 + BOND C29 C28 + BOND C29 C30 + BOND C29 C31 + BOND C29 C32 + BOND C30 H31 + BOND C30 H32 + BOND C30 H30 + BOND C31 H34 + BOND C31 H35 + BOND C31 H33 + BOND C32 H36 + BOND C32 O33 + BOND C32 C34 + BOND O33 H46 + BOND C34 O35 + BOND C34 N36 + BOND N36 H48 + BOND C37 N36 + BOND C37 H37 + BOND C37 H38 + BOND C37 C38 + BOND C38 H39 + BOND C38 H4A + BOND C39 C38 + BOND C39 O40 + BOND C39 N41 + BOND N41 H41 + BOND C42 N41 + BOND C42 H42 + BOND C42 H43 + BOND C42 C43 + BOND C43 H44 + BOND C43 H45 + BOND C43 S44 + BOND S44 H47 + + + ANGLe CB OG P + ANGLe OG P O3P + ANGLe O3P P O1P + ANGLe O3P P O2P + ANGLe P24 O27 C28 + ANGLe O27 C28 H28 + ANGLe O27 C28 H29 + ANGLe O27 C28 C29 + ANGLe H28 C28 H29 + ANGLe H28 C28 C29 + ANGLe H29 C28 C29 + ANGLe C28 C29 C30 + ANGLe C28 C29 C31 + ANGLe C28 C29 C32 + ANGLe C30 C29 C31 + ANGLe C30 C29 C32 + ANGLe C31 C29 C32 + ANGLe C29 C30 H31 + ANGLe C29 C30 H32 + ANGLe C29 C30 H30 + ANGLe H31 C30 H32 + ANGLe H31 C30 H30 + ANGLe H32 C30 H30 + ANGLe C29 C31 H34 + ANGLe C29 C31 H35 + ANGLe C29 C31 H33 + ANGLe H34 C31 H35 + ANGLe H34 C31 H33 + ANGLe H35 C31 H33 + ANGLe C29 C32 H36 + ANGLe C29 C32 O33 + ANGLe C29 C32 C34 + ANGLe H36 C32 O33 + ANGLe H36 C32 C34 + ANGLe O33 C32 C34 + ANGLe C32 O33 H46 + ANGLe C32 C34 O35 + ANGLe C32 C34 N36 + ANGLe O35 C34 N36 + ANGLe C34 N36 H48 + ANGLe C34 N36 C37 + ANGLe H48 N36 C37 + ANGLe N36 C37 H37 + ANGLe N36 C37 H38 + ANGLe N36 C37 C38 + ANGLe H37 C37 H38 + ANGLe H37 C37 C38 + ANGLe H38 C37 C38 + ANGLe C37 C38 H39 + ANGLe C37 C38 H4A + ANGLe C37 C38 C39 + ANGLe H39 C38 H4A + ANGLe H39 C38 C39 + ANGLe H4A C38 C39 + ANGLe C38 C39 O40 + ANGLe C38 C39 N41 + ANGLe O40 C39 N41 + ANGLe C39 N41 H41 + ANGLe C39 N41 C42 + ANGLe H41 N41 C42 + ANGLe N41 C42 H42 + ANGLe N41 C42 H43 + ANGLe N41 C42 C43 + ANGLe H42 C42 H43 + ANGLe H42 C42 C43 + ANGLe H43 C42 C43 + ANGLe C42 C43 H44 + ANGLe C42 C43 H45 + ANGLe C42 C43 S44 + ANGLe H44 C43 H45 + ANGLe H44 C43 S44 + ANGLe H45 C43 S44 + ANGLe C43 S44 H47 + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA OG !stereo CB + IMPRoper C28 O3P H28 H29 + IMPRoper C29 C28 C30 C31 + IMPRoper C30 C29 H31 H32 + IMPRoper C31 C29 H34 H35 + IMPRoper C32 C29 C34 O33 + IMPRoper C34 C32 O35 N36 + IMPRoper N36 C34 H48 C37 + IMPRoper C37 N36 H37 H38 + IMPRoper C38 C37 H39 H4A + IMPRoper C39 C38 O40 N41 + IMPRoper N41 C39 H41 C42 + IMPRoper C42 N41 H42 H43 + IMPRoper C43 C42 H44 H45 + + DIHEdral OG CB CA N + DIHEdral CB OG P O3P + DIHEdral C28 O27 P24 OG + DIHEdral C29 C28 O27 P24 + DIHEdral C32 C29 C28 O27 + DIHEdral H30 C30 C29 C28 + DIHEdral H33 C31 C29 C28 + DIHEdral C34 C32 C29 C28 + DIHEdral C29 C32 O33 H46 + DIHEdral C29 C32 C34 N36 + DIHEdral C32 C34 N36 C37 + DIHEdral C38 C37 N36 C34 + DIHEdral C39 C38 C37 N36 + DIHEdral C37 C38 C39 N41 + DIHEdral C38 C39 N41 C42 + DIHEdral C43 C42 N41 C39 + DIHEdral S44 C43 C42 N41 + DIHEdral C42 C43 S44 H47 + + DONO HN N + DONO HG OG + ACCE OG " " + ACCE O C + ACCE O1P P + ACCE O2P P +end + + +residue THR + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1E CHARge= 0.265 end + ATOM HB TYPE=HA CHARge= 0.000 end + ATOM OG1 TYPE=OH1 CHARge=-0.700 end + ATOM HG1 TYPE=H CHARge= 0.435 end + ATOM CG2 TYPE=CH3E CHARge=-0.000 end + ATOM HG21 TYPE=HA CHARge= 0.000 end + ATOM HG22 TYPE=HA CHARge= 0.000 end + ATOM HG23 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB + BOND CB OG1 BOND OG1 HG1 + BOND CB CG2 BOND CG2 HG21 BOND CG2 HG22 BOND CG2 HG23 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB CA OG1 CG2 !stereo CB + IMPRoper HG21 HG22 CB HG23 !methyl CG2 + + DIHEdral OG1 CB CA N + DIHEdral HG21 CG2 CB CA ! UCL methyl stagger 12-MAR-00 + + DONO HN N + DONO HG1 OG1 + ACCE OG1 " " + ACCE O C +end + +!---------------------------------------------------------------------- + +residue TOP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1E CHARge= 0.265 end + ATOM HB TYPE=HA CHARge= 0.000 end + ATOM OG1 TYPE=OHP CHARge=-0.625 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM CG2 TYPE=CH3E CHARge=-0.000 end + ATOM HG21 TYPE=HA CHARge= 0.000 end + ATOM HG22 TYPE=HA CHARge= 0.000 end + ATOM HG23 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB + BOND CB OG1 BOND OG1 P + BOND P O1P + BOND P O2P + BOND P O3P + + BOND CB CG2 BOND CG2 HG21 BOND CG2 HG22 BOND CG2 HG23 + BOND CA C + BOND C O + + ANGLe CB OG P + ANGLe OG P O3P + ANGLe O3P P O1P + ANGLe O3P P O2P + + IMPRoper HA N C CB !chirality CA + IMPRoper HB CA OG1 CG2 !stereo CB + IMPRoper HG21 HG22 CB HG23 !methyl CG2 + + DIHEdral OG1 CB CA N + DIHEdral CB OG1 P O3P + DIHEdral HG21 CG2 CB CA ! UCL methyl stagger 12-MAR-00 + + DONO HN N + DONO HG1 OG1 + ACCE OG1 " " + ACCE O C +end + +!---------------------------------------------------------------------- + +residue TRP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=C5W CHARge=-0.055 end + ATOM CD1 TYPE=CR1E CHARge= 0.130 end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CW CHARge=-0.055 exclude=(CH2) end + ATOM NE1 TYPE=NH1 CHARge=-0.570 end + ATOM HE1 TYPE=H CHARge= 0.420 end + ATOM CE2 TYPE=CW CHARge= 0.130 exclude=(CZ3) end + ATOM CE3 TYPE=CR1E CHARge= 0.000 exclude=(CZ2) end + ATOM HE3 TYPE=HA CHARge= 0.000 end + ATOM CZ2 TYPE=CR1W CHARge= 0.000 exclude=(CE3) end + ATOM HZ2 TYPE=HA CHARge= 0.000 end + ATOM CZ3 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HZ3 TYPE=HA CHARge= 0.000 end + ATOM CH2 TYPE=CR1W CHARge= 0.000 exclude=(CD2) end + ATOM HH2 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 + BOND CD1 NE1 BOND NE1 HE1 + BOND NE1 CE2 + BOND CD2 CE2 + BOND CD2 CE3 BOND CE3 HE3 + BOND CE2 CZ2 BOND CZ2 HZ2 + BOND CE3 CZ3 BOND CZ3 HZ3 + BOND CZ2 CH2 BOND CH2 HH2 + BOND CZ3 CH2 + BOND CA C + BOND C O + +! chirality + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! around the 6-ring + IMPRoper CD2 CE2 CZ2 CH2 + IMPRoper CE2 CZ2 CH2 CZ3 + IMPRoper CZ2 CH2 CZ3 CE3 + IMPRoper CH2 CZ3 CE3 CD2 + IMPRoper CZ3 CE3 CD2 CE2 + IMPRoper CE3 CD2 CE2 CZ2 + +! link 5-ring to 6-ring + IMPRoper CD1 NE1 CE2 CZ2 + IMPRoper CD1 CG CD2 CE3 + IMPRoper NE1 CE2 CZ2 CH2 + IMPRoper NE1 CE2 CD2 CE3 + IMPRoper CG CD2 CE3 CZ3 + IMPRoper CG CD2 CE2 CZ2 + +! 6-ring hydrogens + IMPRoper HZ2 CZ2 CH2 CZ3 + IMPRoper HH2 CH2 CZ3 CE3 + IMPRoper HZ3 CZ3 CH2 CZ2 + IMPRoper HE3 CE3 CZ3 CH2 + +! 5-ring hydrogens and CB + IMPRoper HE1 NE1 CE2 CD2 + IMPRoper HD1 CD1 NE1 CE2 + IMPRoper CB CG CD2 CE2 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + + DONO HN N + DONO HE1 NE1 + ACCE O C +end + +residue TYR + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CY CHARge= 0.000 exclude=(CZ) end + ATOM CD1 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CR1E CHARge= 0.000 exclude=(CE1) end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CR1E CHARge= 0.000 exclude=(CD2) end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM CE2 TYPE=CR1E CHARge= 0.000 exclude=(CD1) end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM CZ TYPE=CY2 CHARge= 0.265 exclude=(CG) end + ATOM OH TYPE=OH1 CHARge=-0.700 end + ATOM HH TYPE=H CHARge= 0.435 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 BOND CD2 HD2 + BOND CD1 CE1 BOND CE1 HE1 + BOND CD2 CE2 BOND CE2 HE2 + BOND CE1 CZ + BOND CE2 CZ + BOND CZ OH BOND OH HH + BOND CA C + BOND C O + +! chirality + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! Hs, OH, and CB around the ring + IMPRoper HD2 CD2 CE2 CZ + IMPRoper HE2 CE2 CZ CE1 + IMPRoper OH CZ CE1 CD1 + IMPRoper HE1 CE1 CD1 CG + IMPRoper HD1 CD1 CG CD2 + IMPRoper CB CG CD2 CE2 + +! around the ring + IMPRoper CG CD1 CE1 CZ + IMPRoper CD1 CE1 CZ CE2 + IMPRoper CE1 CZ CE2 CD2 + IMPRoper CZ CE2 CD2 CG + IMPRoper CE2 CD2 CG CD1 + IMPRoper CD2 CG CD1 CE1 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + DIHEdral CE2 CZ OH HH ! UCL Added 12-MAR-00 + + DONO HN N + DONO HH OH + ACCE OH " " + ACCE O C +end + +!---------------------------------------------------------------------- + +residue TYP + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CY CHARge= 0.000 exclude=(CZ) end + ATOM CD1 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CR1E CHARge= 0.000 exclude=(CE1) end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CR1E CHARge= 0.000 exclude=(CD2) end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM CE2 TYPE=CR1E CHARge= 0.000 exclude=(CD1) end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM CZ TYPE=CY2 CHARge= 0.265 exclude=(CG) end + ATOM OH TYPE=OHP CHARge=-0.625 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 BOND CD2 HD2 + BOND CD1 CE1 BOND CE1 HE1 + BOND CD2 CE2 BOND CE2 HE2 + BOND CE1 CZ + BOND CE2 CZ + BOND CZ OH BOND OH P + BOND P O1P + BOND P O2P + BOND P O3P + BOND CA C + BOND C O + + ANGLe CZ OH P + ANGLe OH P O3P + ANGLe O3P P O1P + ANGLe O3P P O2P + +! chirality + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! Hs, OH, and CB around the ring + IMPRoper HD2 CD2 CE2 CZ + IMPRoper HE2 CE2 CZ CE1 + IMPRoper OH CZ CE1 CD1 + IMPRoper HE1 CE1 CD1 CG + IMPRoper HD1 CD1 CG CD2 + IMPRoper CB CG CD2 CE2 + +! around the ring + IMPRoper CG CD1 CE1 CZ + IMPRoper CD1 CE1 CZ CE2 + IMPRoper CE1 CZ CE2 CD2 + IMPRoper CZ CE2 CD2 CG + IMPRoper CE2 CD2 CG CD1 + IMPRoper CD2 CG CD1 CE1 + !IMPRoper OH P O3P O1P ! chirality or flatness IMPRoper -37.36 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + DIHEdral CE2 CZ OH P + DIHEdral CZ OH P O3P + + DONO HN N + DONO HH OH + ACCE OH " " + ACCE O C + ACCE O1P P + ACCE O2P P + ACCE O3P P + +end + +!---------------------------------------------------------------------- + +residue TYS + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CY CHARge= 0.000 exclude=(CZ) end + ATOM CD1 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CR1E CHARge= 0.000 exclude=(CE1) end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CR1E CHARge= 0.000 exclude=(CD2) end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM CE2 TYPE=CR1E CHARge= 0.000 exclude=(CD1) end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM CZ TYPE=CY2 CHARge= 0.265 exclude=(CG) end + ATOM OH TYPE=OUF CHARge=-0.625 end + ATOM S TYPE=SUF CHARge= 0.520 end + ATOM O1S TYPE=OUF CHARge=-0.720 end + ATOM O2S TYPE=OUF CHARge=-0.720 end + ATOM O3S TYPE=OUF CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 BOND CD2 HD2 + BOND CD1 CE1 BOND CE1 HE1 + BOND CD2 CE2 BOND CE2 HE2 + BOND CE1 CZ + BOND CE2 CZ + BOND CZ OH BOND OH S + BOND S O1S + BOND S O2S + BOND S O3S + BOND CA C + BOND C O + + ANGLe CZ OH S + ANGLe OH S O1S + ANGLe OH S O2S + ANGLe OH S O3S + ANGLe O3S S O1S + ANGLe O3S S O2S + ANGLe O2S S O1S + +! chirality + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! Hs, OH, and CB around the ring + IMPRoper HD2 CD2 CE2 CZ + IMPRoper HE2 CE2 CZ CE1 + IMPRoper OH CZ CE1 CD1 + IMPRoper HE1 CE1 CD1 CG + IMPRoper HD1 CD1 CG CD2 + IMPRoper CB CG CD2 CE2 + +! around the ring + IMPRoper CG CD1 CE1 CZ + IMPRoper CD1 CE1 CZ CE2 + IMPRoper CE1 CZ CE2 CD2 + IMPRoper CZ CE2 CD2 CG + IMPRoper CE2 CD2 CG CD1 + IMPRoper CD2 CG CD1 CE1 + IMPRoper OH P O3P O1P ! chirality IMPRoper -37.36 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + DIHEdral CE2 CZ OH S + DIHEdral CZ OH S O3S + + DONO HN N + DONO HH OH + ACCE OH " " + ACCE O C + ACCE O1S S + ACCE O2S S + ACCE O3S S + +end + +!---------------------------------------------------------------------- + +residue PTR + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CY CHARge= 0.000 exclude=(CZ) end + ATOM CD1 TYPE=CR1E CHARge= 0.000 exclude=(CE2) end + ATOM HD1 TYPE=HA CHARge= 0.000 end + ATOM CD2 TYPE=CR1E CHARge= 0.000 exclude=(CE1) end + ATOM HD2 TYPE=HA CHARge= 0.000 end + ATOM CE1 TYPE=CR1E CHARge= 0.000 exclude=(CD2) end + ATOM HE1 TYPE=HA CHARge= 0.000 end + ATOM CE2 TYPE=CR1E CHARge= 0.000 exclude=(CD1) end + ATOM HE2 TYPE=HA CHARge= 0.000 end + ATOM CZ TYPE=CY2 CHARge= 0.265 exclude=(CG) end + ATOM OH TYPE=OHP CHARge=-0.625 end + ATOM P TYPE=PP CHARge= 0.520 end + ATOM O1P TYPE=OP1 CHARge=-0.720 end + ATOM O2P TYPE=OP1 CHARge=-0.720 end + ATOM O3P TYPE=OR3 CHARge=-0.720 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG + BOND CG CD1 BOND CD1 HD1 + BOND CG CD2 BOND CD2 HD2 + BOND CD1 CE1 BOND CE1 HE1 + BOND CD2 CE2 BOND CE2 HE2 + BOND CE1 CZ + BOND CE2 CZ + BOND CZ OH BOND OH P + BOND P O1P + BOND P O2P + BOND P O3P + BOND CA C + BOND C O + + ANGLe CZ OH P + ANGLe OH P O3P + ANGLe O3P P O1P + ANGLe O3P P O2P + +! chirality + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + +! Hs, OH, and CB around the ring + IMPRoper HD2 CD2 CE2 CZ + IMPRoper HE2 CE2 CZ CE1 + IMPRoper OH CZ CE1 CD1 + IMPRoper HE1 CE1 CD1 CG + IMPRoper HD1 CD1 CG CD2 + IMPRoper CB CG CD2 CE2 + +! around the ring + IMPRoper CG CD1 CE1 CZ + IMPRoper CD1 CE1 CZ CE2 + IMPRoper CE1 CZ CE2 CD2 + IMPRoper CZ CE2 CD2 CG + IMPRoper CE2 CD2 CG CD1 + IMPRoper CD2 CG CD1 CE1 + !IMPRoper OH P O3P O1P ! chirality or flatness IMPRoper -37.36 + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + DIHEdral CE2 CZ OH P + DIHEdral CZ OH P O3P + + DONO HN N + DONO HH OH + ACCE OH " " + ACCE O C + ACCE O1P P + ACCE O2P P + ACCE O3P P + +end + +!---------------------------------------------------------------------- + +residue VAL + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1E CHARge= 0.000 end + ATOM HB TYPE=HA CHARge= 0.000 end + ATOM CG1 TYPE=CH3E CHARge= 0.000 end + ATOM HG11 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23) end + ATOM HG12 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23) end + ATOM HG13 TYPE=HA CHARge= 0.000 excl = (HG21 HG22 HG23) end + ATOM CG2 TYPE=CH3E CHARge=-0.000 end + ATOM HG21 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HG13) end + ATOM HG22 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HG13) end + ATOM HG23 TYPE=HA CHARge= 0.000 excl = (HG11 HG12 HG13) end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB + BOND CB CG1 BOND CG1 HG11 BOND CG1 HG12 BOND CG1 HG13 + BOND CB CG2 BOND CG2 HG21 BOND CG2 HG22 BOND CG2 HG23 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB CA CG1 CG2 !stereo CB + IMPRoper HG11 HG12 CB HG13 !methyl G1 + IMPRoper HG21 HG22 CB HG23 !methyl G2 + + DIHEdral CG1 CB CA N + DIHEdral HG11 CG1 CB CA ! UCL methyl stagger 12-MAR-00 + DIHEdral HG21 CG2 CB CA ! UCL methyl stagger 12-MAR-00 + + DONO HN N + ACCE O C +end + + +!---------------------------------------------------------------------- + +residue CHX !! ADDED BY MN + group + ATOM N TYPE=NH1 CHARge=-0.360 end + ATOM HN TYPE=H CHARge= 0.260 end + ATOM CA TYPE=CH1E CHARge= 0.000 end + ATOM HA TYPE=HA CHARge= 0.100 end + ATOM CB TYPE=CH2E CHARge=-0.200 end + ATOM HB1 TYPE=HA CHARge= 0.100 end + ATOM HB2 TYPE=HA CHARge= 0.100 end + ATOM CG TYPE=CH1E CHARge=-0.200 end + ATOM HG TYPE=HA CHARge= 0.100 end + ATOM CD1 TYPE=CH2E CHARge=-0.200 end + ATOM HD11 TYPE=HA CHARge= 0.100 end + ATOM HD12 TYPE=HA CHARge= 0.100 end + ATOM CD2 TYPE=CH2E CHARge=-0.200 end + ATOM HD21 TYPE=HA CHARge= 0.100 end + ATOM HD22 TYPE=HA CHARge= 0.100 end + ATOM CE1 TYPE=CH2E CHARge=-0.200 end + ATOM HE11 TYPE=HA CHARge= 0.100 end + ATOM HE12 TYPE=HA CHARge= 0.100 end + ATOM CE2 TYPE=CH2E CHARge=-0.200 end + ATOM HE21 TYPE=HA CHARge= 0.100 end + ATOM HE22 TYPE=HA CHARge= 0.100 end + ATOM CZ TYPE=CH2E CHARge=-0.200 end + ATOM HZ1 TYPE=HA CHARge= 0.100 end + ATOM HZ2 TYPE=HA CHARge= 0.100 end + ATOM C TYPE=C CHARge= 0.480 end + ATOM O TYPE=O CHARge=-0.480 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB1 BOND CB HB2 + BOND CB CG BOND CG CD1 BOND CG CD2 BOND CG HG + BOND CD1 CE1 BOND CD1 HD11 BOND CD1 HD12 + BOND CD2 CE2 BOND CD2 HD21 BOND CD2 HD22 + BOND CE1 CZ BOND CE1 HE11 BOND CE1 HE12 + BOND CE2 CZ BOND CE2 HE21 BOND CE2 HE22 + BOND CZ HZ1 BOND CZ HZ2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG CB CD1 CD2 !stereo CG + IMPRoper HD11 HD12 CG CE1 !stereo CD1 + IMPRoper HD21 HD22 CG CE2 !stereo CD2 + IMPRoper HE11 HE12 CE1 CZ !stereo CE1 + IMPRoper HE11 HE22 CE2 CZ !stereo CE2 + IMPRoper HZ1 HZ2 CE1 CE2 !stereo CZ + + DIHEdral CG CB CA N + DIHEdral CD1 CG CB CA + + DONO HN N + ACCE O C +end + + +!---------------------------------------------------------------------- + +residue ACE + group + ATOM CA TYPE=CH3E CHARge= 0.000 end + ATOM HA1 TYPE=HA CHARge= 0.000 end + ATOM HA2 TYPE=HA CHARge= 0.000 end + ATOM HA3 TYPE=HA CHARge= 0.000 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND C CA BOND CA HA1 BOND CA HA2 BOND CA HA3 + BOND C O + + IMPRoper HA1 HA2 C HA3 !methyl CA + + ACCE O C +end + +!---------------------------------------------------------------------- + +residue CTN ! C-terminal for all, CONH2 at end "* - CTN" + group + ATOM N TYPE=NH2 CHARge=-0.520 end + ATOM H1 TYPE=H CHARge= 0.260 end + ATOM H2 TYPE=H CHARge= 0.260 end + + BOND N H1 + BOND N H2 + + DONO H1 N + DONO H2 N + +end + +!---------------------------------------------------------------------- + +residue NME ! C-terminal N-Methyl ! Added by M. Reau + group + ATOM HA3 TYPE=HA CHARge= 0.000 end + ATOM CA TYPE=CH3E CHARge= 0.200 end + ATOM HA1 TYPE=HA CHARge= 0.000 end + ATOM HA2 TYPE=HA CHARge= 0.000 end + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + + BOND HA3 CA + BOND CA HA1 + BOND CA HA2 + BOND CA N + BOND N HN + + DONO HN N + + IMPRoper HA1 HA2 N HA3 !methyl CA + +end + + +!---------------------------------------------------------------------- + +residue DUM + group + ATOM DUM TYPE=DD CHARge= 0.000 end + ATOM MAP TYPE=DD CHARge= 0.000 end +end + +!---------------------------------------------------------------------- + +residue DDZ ! THR with CH3 replaced by OH + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH1E CHARge= 0.330 end + ATOM HB TYPE=HA CHARge= 0.000 end + ATOM OG1 TYPE=OH1 CHARge=-0.600 end + ATOM HG1 TYPE=H CHARge= 0.435 end + ATOM OG2 TYPE=OH1 CHARge=-0.600 end + ATOM HG2 TYPE=H CHARge= 0.435 end + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA BOND CA HA + BOND CA CB BOND CB HB + BOND CB OG1 BOND OG1 HG1 + BOND CB OG2 BOND OG2 HG2 + BOND CA C + BOND C O + + IMPRoper HA N C CB !chirality CA + + DIHEdral OG1 CB CA N + + DONO HN N + DONO HG1 OG1 + ACCE OG1 " " + DONO HG2 OG2 + ACCE OG2 " " + ACCE O C +end + +!---------------------------------------------------------------------- + +RESIdue QSR ! Added by Rodrigo Honorato / Alexandre Bonvin 06/01/2021 + + group + ATOM N TYPE=NH1 CHARge=-0.570 end + ATOM HN TYPE=H CHARge= 0.370 end + ATOM CA TYPE=CH1E CHARge= 0.200 end + ATOM HA TYPE=HA CHARge= 0.000 end + ATOM CB TYPE=CH2E CHARge= 0.000 end + ATOM HB1 TYPE=HA CHARge= 0.000 end + ATOM HB2 TYPE=HA CHARge= 0.000 end + ATOM CG TYPE=CH2E CHARge= 0.000 end + ATOM HG1 TYPE=HA CHARge= 0.000 end + ATOM HG2 TYPE=HA CHARge= 0.000 end + ATOM CD TYPE=C CHARge= 0.500 end + ATOM OE1 TYPE=O CHARge=-0.500 end + ATOM NE2 TYPE=NH1 CHARge=-0.570 end + ATOM HE2 TYPE=H CHARge= 0.370 end + ATOM CSA TYPE=CH2E CHARge= 0.200 end + ATOM HSA1 TYPE=HA CHARge= 0.000 end + ATOM HSA2 TYPE=HA CHARge= 0.000 end + ATOM CSB TYPE=CH2E CHARge= 0.000 end + ATOM HSB1 TYPE=HA CHARge= 0.000 end + ATOM HSB2 TYPE=HA CHARge= 0.000 end + ! serotonin + ATOM HSE1 TYPE=H CHARge= 0.420 end + ATOM NSE1 TYPE=NH1 CHARge=-0.570 end + ATOM CSD1 TYPE=CR1E CHARge= 0.130 end + ATOM HSD1 TYPE=HA CHARge= 0.000 end + ATOM CSG TYPE=C5W CHARge=-0.055 end + ATOM CSD2 TYPE=CW CHARge=-0.055 exclude=(CSH2) end + ATOM CSE2 TYPE=CW CHARge= 0.130 exclude=(CSZ3) end + ATOM CSE3 TYPE=CR1E CHARge= 0.000 exclude=(CSZ2) end + ATOM HSE3 TYPE=HA CHARge= 0.000 end + ATOM CSZ3 TYPE=CY2 CHARge= 0.265 exclude=(CSE2) end + ATOM OSZ3 TYPE=OH1 CHARge=-0.700 end + ATOM HSZ3 TYPE=H CHARge= 0.435 end + ATOM CSH2 TYPE=CR1W CHARge= 0.000 exclude=(CSE2) end + ATOM HSH2 TYPE=HA CHARge= 0.000 end + ATOM CSZ2 TYPE=CR1W CHARge= 0.000 exclude=(CSE3) end + ATOM HSZ2 TYPE=HA CHARge= 0.000 end + ! + ATOM C TYPE=C CHARge= 0.500 end + ATOM O TYPE=O CHARge=-0.500 end + + BOND N HN + BOND N CA + BOND CA C BOND CA HA + BOND CA CB + BOND CB CG BOND CB HB1 BOND CB HB2 + BOND CG CD BOND CG HG1 BOND CG HG2 + BOND CD OE1 BOND CD NE2 + BOND NE2 CSA BOND NE2 HE2 + BOND CSA CSB BOND CSA HSA1 BOND CSA HSA2 + BOND CSB CSG BOND CSB HSB1 BOND CSB HSB2 + BOND CSG CSD2 BOND CSG CSD1 + BOND CSD2 CSE2 BOND CSD2 CSE3 + BOND CSE2 NSE1 BOND CSE2 CSZ2 + BOND CSZ2 CSH2 BOND CSZ2 HSZ2 + BOND CSH2 CSZ3 BOND CSH2 HSH2 + BOND CSZ3 CSE3 BOND CSZ3 OSZ3 BOND OSZ3 HSZ3 + BOND CSE3 HSE3 + BOND NSE1 CSD1 BOND NSE1 HSE1 + BOND CSD1 HSD1 + BOND C O + + ANGLe HSE1 NSE1 CSD1 + ANGLe HSE1 NSE1 CSE2 + ANGLe CSD1 NSE1 CSE2 + ANGLe NSE1 CSD1 HSD1 + ANGLe NSE1 CSD1 CSG + ANGLe HSD1 CSD1 CSG + ANGLe CSD1 CSG CSB + ANGLe CSD1 CSG CSD2 + ANGLe CSB CSG CSD2 + ANGLe CSG CSB HSB2 + ANGLe CSG CSB HSB1 + ANGLe CSG CSB CSA + ANGLe HSB2 CSB HSB1 + ANGLe HSB2 CSB CSA + ANGLe HSB1 CSB CSA + ANGLe CSB CSA HSA2 + ANGLe CSB CSA HSA1 + ANGLe CSB CSA NE2 + ANGLe HSA2 CSA HSA1 + ANGLe HSA2 CSA NE2 + ANGLe HSA1 CSA NE2 + ANGLe CSA NE2 HE2 + ANGLe CSG CSD2 CSE3 + ANGLe CSG CSD2 CSE2 + ANGLe CSE3 CSD2 CSE2 + ANGLe CSD2 CSE3 HSE3 + ANGLe CSD2 CSE3 CSZ3 + ANGLe HSE3 CSE3 CSZ3 + ANGLe CSE3 CSZ3 OSZ3 + ANGLe CSE3 CSZ3 CSH2 + ANGLe OSZ3 CSZ3 CSH2 + ANGLe CSZ3 OSZ3 HO1 + ANGLe CSZ3 CSH2 HSH2 + ANGLe CSZ3 CSH2 CSZ2 + ANGLe HSH2 CSH2 CSZ2 + ANGLe CSH2 CSZ2 HSZ2 + ANGLe CSH2 CSZ2 CSE2 + ANGLe HSZ2 CSZ2 CSE2 + ANGLe NSE1 CSE2 CSD2 + ANGLe NSE1 CSE2 CSZ2 + ANGLe CSD2 CSE2 CSZ2 + + ! around the 6-ring + IMPRoper CSD2 CSE2 CSZ2 CSH2 + IMPRoper CSE2 CSZ2 CSH2 CSZ3 + IMPRoper CSZ2 CSH2 CSZ3 CSE3 + IMPRoper CSH2 CSZ3 CSE3 CSD2 + IMPRoper CSZ3 CSE3 CSD2 CSE2 + IMPRoper CSE3 CSD2 CSE2 CSZ2 + + ! link 5-ring to 6-ring + IMPRoper CSD1 NSE1 CSE2 CSZ2 + IMPRoper CSD1 CSG CSD2 CSE3 + IMPRoper NSE1 CSE2 CSZ2 CSH2 + IMPRoper NSE1 CSE2 CSD2 CSE3 + IMPRoper CSG CSD2 CSE3 CSZ3 + IMPRoper CSG CSD2 CSE2 CSZ2 + + ! 6-ring hydrogens + IMPRoper HSZ2 CSZ2 CSH2 CSZ3 + IMPRoper HSH2 CSH2 CSZ3 CSE3 + IMPRoper OSZ3 CSZ3 CSH2 CSZ2 + IMPRoper HSE3 CSE3 CSZ3 CSH2 + + ! 5-ring hydrogens and CB + IMPRoper HSE1 NSE1 CSE2 CSD2 + IMPRoper HSD1 CSD1 NSE1 CSE2 + IMPRoper CSB CSG CSD2 CSE2 + + ! planarity of side-chain CO-N BOND + IMPRoper CD CG OE1 NE2 ! planar -C + IMPRoper NE2 CD CSA HE2 ! planar +N + IMPRoper CG CD NE2 HE2 ! ANGLe across peptide plane + IMPRoper CG CD NE2 CSA ! ANGLe across peptide plane + + ! + IMPRoper HA N C CB !chirality CA + IMPRoper HB1 HB2 CA CG !stereo CB + IMPRoper HG2 HG1 CB CD !stereo CG + IMPRoper HSA1 HSA2 NE2 CSB !stereo CSA + IMPRoper HSB1 HSB2 CSA CSG !stereo CSB + + DIHEdral CSB CSA NE2 HE2 + DIHEdral CSG CSB CSA NE2 + DIHEdral CSD2 CSG CSB CSA + DIHEdral CSH2 CSZ3 OSZ3 HSZ3 + DIHEdral CG CB CA N + DIHEdral CD CG CB CA + DIHEdral OE1 CD CG CB + + DONO HN N + DONO HE2 NE2 + DONO HSE1 NSE1 + DONO HSZ3 OSZ3 + ACCE OSZ3 CSZ3 + ACCE OE1 CD + ACCE O C + + END + +!---------------------------------------------------------------------- + +presidue NTER ! patch as "NTER - *" to any except PRO + group + modify ATOM +N TYPE=NH3 CHARge=-0.300 end + delete ATOM +HN end + add ATOM +HT1 TYPE=HC CHARge= 0.330 end + add ATOM +HT2 TYPE=HC CHARge= 0.330 end + add ATOM +HT3 TYPE=HC CHARge= 0.330 end + modify ATOM +CA CHARge= 0.310 end + + add BOND +HT1 +N + add BOND +HT2 +N + add BOND +HT3 +N + + add ANGLe +HT1 +N +HT2 + add ANGLe +HT2 +N +HT3 + add ANGLe +HT2 +N +CA + add ANGLe +HT1 +N +HT3 + add ANGLe +HT1 +N +CA + add ANGLe +HT3 +N +CA + add IMPRoper +HT1 +HT2 +CA +HT3 !methyl N ??? + + add DIHEdral +C +CA +N +HT1 ! UCL (12-MAR-00) + + ADD DONOr +HT1 +N + ADD DONOr +HT2 +N + ADD DONOr +HT3 +N +end + +!---------------------------------------------------------------------- + +presidue PROP ! N-terminal for PRO: "PROP - PRO" +! the CHARges are guessed from making the residue have CHARge +1 +! and keeping the same CHARge on N as in NTER (Michael Nilges) + modify ATOM +CD CHARge= 0.320 end + modify ATOM +CA CHARge= 0.320 end + modify ATOM +N TYPE=NH3 CHARge=-0.300 end + add ATOM +HT1 TYPE=HC CHARge= 0.330 end + add ATOM +HT2 TYPE=HC CHARge= 0.330 end + + add BOND +HT1 +N + add BOND +HT2 +N + + add ANGLe +HT1 +N +HT2 + add ANGLe +HT2 +N +CA + add ANGLe +HT1 +N +CD + add ANGLe +HT1 +N +CA + add ANGLe +CD +N +HT2 + add IMPRoper +HT1 +HT2 +CA +CD !stereo N + + ADD DONOr +HT1 +N + ADD DONOr +HT2 +N +end + +!---------------------------------------------------------------------- + +presidue CTER ! C-terminal for all amino acids "* - CTER" +! CHARge on -C changed from 0.700 to make group -1, Michael Nilges + group + modify ATOM -CA CHARge= 0.100 end + modify ATOM -C CHARge= 0.700 end + modify ATOM -O TYPE=OC CHARge=-0.800 end + add ATOM -OXT TYPE=OC CHARge=-0.800 end + + add BOND -C -OXT + + add ANGLe -CA -C -OXT + add ANGLe -O -C -OXT + + add IMPRoper -C -CA -OXT -O + + add DIHEdral -N -CA -C -O ! UCL (12-MAR-00) + + ADD ACCEptor -OXT -C +end + +!---------------------------------------------------------------------- + +presidue PCTN ! peptide BOND patch for explitic C-terminal CTN residue + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +H1 + add ANGLe -C +N +H2 + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +H1 +H2 ! planar +N + add IMPRoper -CA -C +N +H1 ! ANGLe across peptide plane + + ADD DONOR -H1 -NT + ADD DONOR -H2 -NT +end + +!---------------------------------------------------------------------- + +presidue CTN ! C-terminal for all, CONH2 at end "* - CTN" +! CHARges not consistent with rest, Michael Nilges + group + modify ATOM -C CHARge= 0.48 end + modify ATOM -O CHARge=-0.48 end + add ATOM -NT TYPE=NH2 CHARge=-0.52 end + add ATOM -H1 TYPE=H CHARge= 0.26 end + add ATOM -H2 TYPE=H CHARge= 0.26 end + + add BOND -C -NT + add BOND -NT -H1 + add BOND -NT -H2 + + add ANGLe -CA -C -NT + add ANGLe -O -C -NT + add ANGLe -CA -C -O + add ANGLe -C -NT -H1 + add ANGLe -C -NT -H2 + add ANGLe -H1 -NT -H2 + + add IMPRoper -C -CA -NT -O + add IMPRoper -C -NT -O -H1 + add IMPRoper -NT -H1 -H2 -C + + add DIHEdral -N -CA -C -NT ! UCL (12-MAR-00) + + ADD DONOR -H1 -NT + ADD DONOR -H2 -NT +end + +!---------------------------------------------------------------------- + + +presidue PEPT ! PEPTide BOND link, for all except the *(-) - (+)PRO link + ! "*(-) - PEPT - (+)*: + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +HN + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +HN ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! phi/psi related topology UCL 05-JUL-01 + + add DIHEdral -C +N +CA +C mult 6 + add DIHEdral -C +N +CA +CB mult 6 + add DIHEdral -CB -CA -C +N mult 6 + add DIHEdral -CB -CA -C -O mult 6 ! corrected from +O 16-Sept-02 +end + +!---------------------------------------------------------------------- + +presidue DPEP ! delete PEPTide BOND link, for all except the *(-) - (+)PRO link + ! "*(-) - PEPT - (+)*:, ATB 07/10/10 + ! This will also work for peptide links involving GLY except that + ! harmless error messages will be produced about not finding certain DIHEdrals. + delete BOND -C +N + + delete ANGLe -CA -C +N + delete ANGLe -O -C +N + delete ANGLe -C +N +CA + delete ANGLe -C +N +HN + + delete IMPRoper -C -CA +N -O ! planar -C + delete IMPRoper +N -C +CA +HN ! planar +N + delete IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! phi/psi related topology UCL 05-JUL-01 + + delete DIHEdral -C +N +CA +C mult 6 + delete DIHEdral -C +N +CA +CB mult 6 + delete DIHEdral -CB -CA -C +N mult 6 + delete DIHEdral -CB -CA -C -O mult 6 ! corrected from +O 16-Sept-02 +end + +!---------------------------------------------------------------------- + +presidue PEPP ! for ...*(-) - (+)PRO link, same as PEPT except + ! replacement H by CD and IMPRoper +N +CA +CD -C + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +CD + +! ADD DIHEdral -C +N +CA +C ! taken out since related to phi MN 18-MAR-02 +! ADD DIHEdral -N -CA -C +N ! taken out since equivalent below MN 18-MAR-02 +! ADD DIHEdral -CA -C +N +CA ! taken out since IMPRoper below MN 18-MAR-02 + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +CD ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! psi related topology N.B. phi is fixed by ring BONDing 05-JUL-01 + + add DIHEdral -CB -CA -C +N mult 6 + add DIHEdral -CB -CA -C -O mult 6 ! corrected from +O 16-Sept-02 +end + +!---------------------------------------------------------------------- + +presidue DPPP ! delete peptide BOND link for ...*(-) - (+)PRO link, same as PEPT except + ! replacement H by CD and IMPRoper +N +CA +CD -C, ATB 07/10/10 + ! This will also work for peptide links involving GLY except that + ! harmless error messages will be produced about not finding certain DIHEdrals. + delete BOND -C +N + + delete ANGLe -CA -C +N + delete ANGLe -O -C +N + delete ANGLe -C +N +CA + delete ANGLe -C +N +CD + +! DELETE DIHEdral -C +N +CA +C ! taken out since related to phi MN 18-MAR-02 +! DELETE DIHEdral -N -CA -C +N ! taken out since equivalent below MN 18-MAR-02 +! DELETE DIHEdral -CA -C +N +CA ! taken out since IMPRoper below MN 18-MAR-02 + + delete IMPRoper -C -CA +N -O ! planar -C + delete IMPRoper +N -C +CA +CD ! planar +N + delete IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! psi related topology N.B. phi is fixed by ring BONDing 05-JUL-01 + + delete DIHEdral -CB -CA -C +N mult 6 + delete DIHEdral -CB -CA -C -O mult 6 ! corrected from +O 16-Sept-02 +end + +!---------------------------------------------------------------------- + +presidue PPGP ! for GLY(-) - (+)PRO link, same as PEPT except + ! replacement H by CD and IMPRoper +N +CA +CD -C + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +CD + +! ADD DIHEdral -C +N +CA +C ! taken out since related to phi MN 18-MAR-02 +! ADD DIHEdral -N -CA -C +N ! taken out since equivalent below MN 18-MAR-02 +! ADD DIHEdral -CA -C +N +CA ! taken out since IMPRoper below MN 18-MAR-02 + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +CD ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +end + +!---------------------------------------------------------------------- + +PRESidue PPGG { for GLY (-) - (+) GLY LINK } + + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +HN + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +HN ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! phi/psi related topology UCL 05-JUL-01 + + add DIHEdral -C +N +CA +C mult 6 +end + +!---------------------------------------------------------------------- + +PRESidue PPG1 { for ...*(-) - (+) GLY LINK } + + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +HN + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +HN ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! phi/psi related topology UCL 05-JUL-01 + + add DIHEdral -C +N +CA +C mult 6 + add DIHEdral -CB -CA -C +N mult 6 + add DIHEdral -CB -CA -C -O mult 6 ! corrected from +O 16-Sept-02 + +end + +!---------------------------------------------------------------------- + +PRESidue PPG2 { for ... GLY(-) - (+) * LINK } + add BOND -C +N + + add ANGLe -CA -C +N + add ANGLe -O -C +N + add ANGLe -C +N +CA + add ANGLe -C +N +HN + + add IMPRoper -C -CA +N -O ! planar -C + add IMPRoper +N -C +CA +HN ! planar +N + add IMPRoper -CA -C +N +CA ! ANGLe across peptide plane + +! phi/psi related topology UCL 05-JUL-01 + + add DIHEdral -C +N +CA +C mult 6 + add DIHEdral -C +N +CA +CB mult 6 +end + +!---------------------------------------------------------------------- + +presidue DISU ! disulfide bridge ...CYS - DISU - CYS... + group + delete ATOM 1HG end + modify ATOM 1CB CHARge= 0.300 end + MODIfy ATOM 1SG TYPE=S CHARge=-0.300 end + group + delete ATOM 2HG end + modify ATOM 2CB CHARge= 0.300 end + MODIfy ATOM 2SG TYPE=S CHARge=-0.300 end + + add BOND 1SG 2SG + + add ANGLe 1CB 1SG 2SG + add ANGLe 1SG 2SG 2CB + + add DIHEdral 1CB 1SG 2SG 2CB mult 6 ! UCL modified 12-MAR-00 & 07-JUL-01 +end + +!---------------------------------------------------------------------- + +presidue DISN ! disulfide bridge ...CYS - DISU - CYS... + ! w/o the actual BOND + group + delete ATOM 1HG end + modify ATOM 1CB CHARge= 0.300 end + MODIfy ATOM 1SG TYPE=S CHARge=-0.300 end + group + delete ATOM 2HG end + modify ATOM 2CB CHARge= 0.300 end + MODIfy ATOM 2SG TYPE=S CHARge=-0.300 end +end + +!---------------------------------------------------------------------- + +presidue CYNH ! deprotonated CYS + + group + delete ATOM 1HG end + modify ATOM 1CB CHARge= 0.000 end + MODIfy ATOM 1SG TYPE=S CHARge=-0.500 end +end + +!---------------------------------------------------------------------- + +presidue LTOD ! change from L to D amino acid + delete IMPRoper HA N C CB + add IMPRoper HA C N CB +end + +!---------------------------------------------------------------------- + +presidue DTOL ! change from L to D amino acid + delete IMPRoper HA C N CB + add IMPRoper HA N C CB +end + +!---------------------------------------------------------------------- + +presidue CISP ! change from trans to cis peptide BOND + modify ATOM C TYPE=CCIS end +end + +!---------------------------------------------------------------------- + +presidue CIPP ! change from trans to cis peptide BOND. not necessary to have separate patch + modify ATOM C TYPE=CCIS end +end + +!-------------------------------------------------------------------------- + +PRESidue HISE ! Patch to change doubly protonated HIS to singly protonated histidine (HE2) + ! has to be patched as REFErence=NIL= + DELETE DONOR ND1 HD1 + MODIFY ATOM CB TYPE=CH2E CHARge= 0.000 END + MODIFY ATOM CG TYPE=C5 CHARge= 0.130 END !# + MODIFY ATOM ND1 TYPE=NR CHARge=-0.490 END !# + MODIFY ATOM CE1 TYPE=CRH CHARge= 0.410 END !# + MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.100 END + MODIFY ATOM NE2 TYPE=NH1 CHARge=-0.570 END !# + MODIFY ATOM HE2 TYPE=H CHARge= 0.420 END !# + DELETE ATOM HD1 END + + ADD ACCEPTOR ND1 " " +END {HISE} + +!-------------------------------------------------------------------------- + +PRES HISD ! Patch to change doubly protonated HIS to singly protonated histidine (HD1) + ! has to be patched as REFErence=NIL= + DELETE DONOR HE2 NE2 + MODIFY ATOM CB TYPE=CH2E CHARge= 0.000 END + MODIFY ATOM CG TYPE=C5 CHARge= 0.130 END !# + MODIFY ATOM ND1 TYPE=NH1 CHARge=-0.570 END !# + MODIFY ATOM HD1 TYPE=H CHARge= 0.420 END !# + MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.100 END !# + MODIFY ATOM NE2 TYPE=NR CHARge=-0.490 END !# + MODIFY ATOM CE1 TYPE=CRH CHARge= 0.410 END !# + DELETE ATOM HE2 END + + ADD ACCEPTOR NE2 " " + +END {HISD} + +!---------------------------------------------------------------------- + +PRESidue DCA2 ! Patch to add a single BOND from an ASP COO- group to a calcium ion + + ADD BOND 1OD1 2CA+2 + +END + +!---------------------------------------------------------------------- + +PRESidue ECA2 ! Patch to add a single BOND from a GLU COO- group to a calcium ion + + ADD BOND 1OE1 2CA+2 + +END + +!---------------------------------------------------------------------- + +PRESidue SEF1 ! Patch for iron-sulphur cluster + + ADD BOND 1FE1 2SG + ADD ANGLe 1SF1 1FE1 2SG + ADD ANGLe 1SF2 1FE1 2SG + ADD ANGLe 1FE1 2SG 2CB + +END + +!---------------------------------------------------------------------- + +PRESidue SEF2 ! Patch for iron-sulphur cluster + + ADD BOND 1FE2 2SG + ADD ANGLe 1SF1 1FE2 2SG + ADD ANGLe 1SF2 1FE2 2SG + ADD ANGLe 1FE2 2SG 2CB + +END + +!---------------------------------------------------------------------- + +PRESidue CLYS ! patch for isoPEPTide BOND link between the Cter and a Lys side-chain + + group + delete ATOM 1OXT end + modify ATOM 1O TYPE=O CHARge=-0.48 end + modify ATOM 1C TYPE=C CHARge= 0.48 end + group + delete ATOM 2HZ2 end + delete ATOM 2HZ3 end + modify ATOM 2NZ TYPE=NH1 CHARge=-0.36 end + modify ATOM 2HZ1 TYPE=H CHARge= 0.26 end + modify ATOM 2CE CHARge=-0.20 end + modify ATOM 2HE1 CHARge= 0.10 end + modify ATOM 2HE2 CHARge= 0.10 end + + add BOND 1C 2NZ + + add ANGLe 1CA 1C 2NZ + add ANGLe 1O 1C 2NZ + add ANGLe 1C 2NZ 2CE + add ANGLe 1C 2NZ 2HZ1 + + add IMPRoper 1C 1CA 2NZ 1O ! planar -C + add IMPRoper 2NZ 1C 2CE 2HZ1 ! planar +N + add IMPRoper 1CA 1C 2NZ 2CE ! ANGLe across peptide plane + +end + +!---------------------------------------------------------------------- + +presidue ACCY ! patch for connecting an acetylated Nter to a CYS SG + group + delete ATOM 1HA3 end + MODIfy ATOM 1CA TYPE=CH2E CHARge=0.235 end + group + delete ATOM 2HG end + modify ATOM 2CB CHARge= 0.235 end + MODIfy ATOM 2SG TYPE=SM CHARge=-0.470 end + + add BOND 1CA 2SG + + add ANGLe 1C 1CA 2SG + add ANGLe 1CA 2SG 2CB + add ANGLe 1HA1 1CA 2SG + add ANGLe 1HA2 1CA 2SG + add ANGLe 1HA2 1CA 1HA1 + + IMPRoper 1HA1 1HA2 1CA 2SG + + add DIHEdral 1C 1CA 2SG 2CB + add DIHEdral 1CA 2SG 2CB 2CA +end + + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/scatter.lib b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/scatter.lib new file mode 100644 index 0000000000000000000000000000000000000000..fc3db9488852b3f6a46163ec4701dba53c3c6ef4 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/scatter.lib @@ -0,0 +1,488 @@ +! file libraries/xray/scatter.lib +! Atomic scattering factors without anomalous contribution +! Library for CNS + +! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger + +!BEWARE: +!(1) element Cf (Californium) has to be referred to as Cff +!(2) element Sm (Samarium) has to be referred to as Smm +!(3) element Np (Neptunium) has to be referred to as Npp +!(3) types of elements with ionic state (i.e., +/-) specifications have +! to be put in double quotes in selection statements. + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + + +SCATter ( chemical H* and not ( + chemical "He" or chemical "HE" or + chemical "Ho" or chemical "HO" or + chemical "Ho+3" or chemical "HO+3" or + chemical "Hf" or chemical "HF" or + chemical "Hf+4" or chemical "HF+4" or + chemical "Hg" or chemical "HG" or + chemical "Hg+1" or chemical "HG+1" or + chemical "Hg+2" or chemical "HG+2" )) + 0.489918 20.6593 0.262003 7.74039 0.196767 49.5519 0.049879 2.20159 0.001305 +SCATter ( chemical "He" or chemical "HE" ) + 0.8734 9.1037 0.6309 3.3568 0.3112 22.9276 0.178 0.9821 0.0064 +SCATter ( chemical "Li" or chemical "LI" ) + 1.1282 3.9546 0.7508 1.0524 0.6175 85.3905 0.4653 168.261 0.0377 +SCATter ( chemical "Li+1" or chemical "LI+1" ) + 0.6968 4.6237 0.7888 1.9557 0.3414 0.6316 0.1563 10.0953 0.0167 +SCATter ( chemical "Be" or chemical "BE" ) + 1.5919 43.6427 1.1278 1.8623 0.5391 103.483 0.7029 0.542 0.0385 +SCATter ( chemical "Be+2" or chemical "BE+2" ) + 6.2603 0.0027 0.8849 0.8313 0.7993 2.2758 0.1647 5.1146 -6.1092 +SCATter ( chemical "B" ) + 2.0545 23.2185 1.3326 1.021 1.0979 60.3498 0.7068 0.1403 -0.1932 +SCATter ( chemical C* and not + ( chem "Ca" or chem "CA" or chem "Ca+2" or chem "CA+2" or + chem "Ce" or chem "CE" or chem "Ce+3" or chem "CE+3" or chem "Ce+4" or chem "CE+4" or + chem "Co" or chem "CO" or chem "Co+2" or chem "CO+2" or chem "Co+3" or chem "CO+3" or + chem "Cr" or chem "CR" or chem "Cr+2" or chem "CR+2" or chem "Cr+3" or chem "CR+3" or + chem "Cu" or chem "CU" or chem "Cu+1" or chem "CU+1" or chem "Cu+2" or chem "CU+2" or + chem "Cd" or chem "CD" or chem "Cd+2" or chem "CD+2" or + chem "Cs" or chem "CS" or chem "Cs+1" or chem "CS+1" or + chem "Cm" or chem "CM" or + chem "Cl" or chem "CL" or chem "Cl-1" or chem "CL-1" or + chem "Cff" or chem "CFF" or chem "Cval" or chem "CVAL" )) + 2.31 20.8439 1.02 10.2075 1.5886 0.5687 0.865 51.6512 0.2156 +SCATter ( chemical "Cval" or chemical "CVAL" ) + 2.26069 22.6907 1.56165 0.656665 1.05075 9.75618 0.839259 55.5949 0.286977 +SCATter ( chemical N* and not + ( chem "Ne" or chem "NE" or + chem "Na" or chem "NA" or chem "Na+1" or chem "NA+1" or + chem "Ni" or chem "NI" or chem "Ni+2" or chem "NI+2" or chem "Ni+3" or chem "NI+3" or + chem "Nb" or chem "NB" or chem "Nb+3" or chem "NB+3" or chem "Nb+5" or chem "NB+5" or + chem "Nd" or chem "ND" or chem "Nd+3" or chem "ND+3" or + chem "Npp" or chem "NPP" or chem "Np+3" or chem "NP+3" or chem "Np+4" or chem "NP+4" or + chem "Np+6" or chem "NP+6" )) + 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.529 +SCATter ( chemical O* and not ( chem "O-1" or chem "Os" or chem "OS" or chem "Os+4" or chem "OS+4" ) ) + 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.867 32.9089 0.2508 +SCATter ( chemical "O-1" ) + 4.1916 12.8573 1.63969 4.17236 1.52673 47.0179 -20.307 -0.01404 21.9412 +SCATter ( chemical "F" ) + 3.5392 10.2825 2.6412 4.2944 1.517 0.2615 1.0243 26.1476 0.2776 +SCATter ( chemical "F-1" ) + 3.6322 5.27756 3.51057 14.7353 1.26064 0.442258 0.940706 47.3437 0.653396 +SCATter ( chemical "Ne" or chemical "NE" ) + 3.9553 8.4042 3.1125 3.4262 1.4546 0.2306 1.1251 21.7184 0.3515 +SCATter ( chemical "Na" or chemical "NA" ) + 4.7626 3.285 3.1736 8.8422 1.2674 0.3136 1.1128 129.424 0.676 +SCATter ( chemical "Na+1" or chemical "NA+1" ) + 3.2565 2.6671 3.9362 6.1153 1.3998 0.2001 1.0032 14.039 0.404 +SCATter ( chemical "Mg" or chemical "MG" ) + 5.4204 2.8275 2.1735 79.2611 1.2269 0.3808 2.3073 7.1937 0.8584 +SCATter ( chemical "Mg+2" or chemical "MG+2" ) + 3.4988 2.1676 3.8378 4.7542 1.3284 0.185 0.8497 10.1411 0.4853 +SCATter ( chemical "Al" or chemical "AL" ) + 6.4202 3.0387 1.9002 0.7426 1.5936 31.5472 1.9646 85.0886 1.1151 +SCATter ( chemical "Al+3" or chemical "AL+3" ) + 4.17448 1.93816 3.3876 4.14553 1.20296 0.228753 0.528137 8.28524 0.706786 +SCATter ( chemical "Si" or chemical "SI" ) + 6.2915 2.4386 3.0353 32.3337 1.9891 0.6785 1.541 81.6937 1.1407 +SCATter ( chemical "Siv" or chemical "SIV" ) + 5.66269 2.6652 3.07164 38.6634 2.62446 0.916946 1.3932 93.5458 1.24707 +SCATter ( chemical "Si+4" or chemical "SI+4" ) + 4.43918 1.64167 3.20345 3.43757 1.19453 0.2149 0.41653 6.65365 0.746297 +SCATter ( chemical P* and not ( + chem "Pd" or chem "Pr" or chem "Pm" or chem "Pt" or + chem "Pb" or chem "Po" or chem "Pa" or chem "Pu" or + chem "PD" or chem "PR" or chem "PM" or chem "PT" or + chem "PB" or chem "PO" or chem "PA" or chem "PU" or + chem "Pr+3" or chem "PR+3" or + chem "Pr+4" or chem "PR+4" or + chem "Pm+3" or chem "PM+3" or + chem "Pt+2" or chem "PT+2" or + chem "Pt+4" or chem "PT+4" or + chem "Pb+2" or chem "PB+2" or + chem "Pb+4" or chem "PB+4" or + chem "Pu+3" or chem "PU+3" or + chem "Pu+4" or chem "PU+4" or + chem "Pu+6" or chem "PU+6" )) + 6.4345 1.9067 4.1791 27.157 1.78 0.526 1.4908 68.1645 1.1149 +SCATter ( chemical S* and not ( + chem "Sc" or chem "SC" or chem "Sc+3" or chem "SC+3" or + chem "Se" or chem "SE" or + chem "Sr" or chem "SR" or chem "Sr+2" or chem "SR+2" or + chem "Sn" or chem "SN" or chem "Sn+2" or chem "SN+2" or chem "Sn+4" or chem "SN+4" or + chem "Sb" or chem "SB" or chem "Sb+3" or chem "SB+3" or chem "Sb+5" or chem "SB+5" or + chem "Smm" or chem "SMM" or chem "Sm+3" or chem "SM+3" or + chem "Si" or chem "SI" or chem "Si+4" or chem "SI+4" )) + 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.172 0.8669 +SCATter ( chemical "Cl" or chemical "CL" ) + 11.4604 0.0104 7.1964 1.1662 6.2556 18.5194 1.6455 47.7784 -9.5574 +SCATter ( chemical "Cl-1" or chemical "CL-1" ) + 18.2915 0.0066 7.2084 1.1717 6.5337 19.5424 2.3386 60.4486 -16.378 +SCATter ( chemical "Ar" or chemical "AR" ) + 7.4845 0.9072 6.7723 14.8407 0.6539 43.8983 1.6442 33.3929 1.4445 +SCATter ( chemical "K" ) + 8.2186 12.7949 7.4398 0.7748 1.0519 213.187 0.8659 41.6841 1.4228 +SCATter ( chemical "K+1" ) + 7.9578 12.6331 7.4917 0.7674 6.359 -0.002 1.1915 31.9128 -4.9978 +SCATter ( chemical "Ca" or chemical "CA" ) + 8.6266 10.4421 7.3873 0.6599 1.5899 85.7484 1.0211 178.437 1.3751 +SCATter ( chemical "Ca+2" or chemical "CA+2" ) + 15.6348 -0.0074 7.9518 0.6089 8.4372 10.3116 0.8537 25.9905 -14.875 +SCATter ( chemical "Sc" or chemical "SC" ) + 9.189 9.0213 7.3679 0.5729 1.6409 136.108 1.468 51.3531 1.3329 +SCATter ( chemical "Sc+3" or chemical "SC+3" ) + 13.4008 0.29854 8.0273 7.9629 1.65943 -0.28604 1.57936 16.0662 -6.6667 +SCATter ( chemical "Ti" or chemical "TI" ) + 9.7595 7.8508 7.3558 0.5 1.6991 35.6338 1.9021 116.105 1.2807 +SCATter ( chemical "Ti+2" or chemical "TI+2" ) + 9.11423 7.5243 7.62174 0.457585 2.2793 19.5361 0.087899 61.6558 0.897155 +SCATter ( chemical "Ti+3" or chemical "TI+3" ) + 17.7344 0.22061 8.73816 7.04716 5.25691 -0.15762 1.92134 15.9768 -14.652 +SCATter ( chemical "Ti+4" or chemical "TI+4" ) + 19.5114 0.178847 8.23473 6.67018 2.01341 -0.29263 1.5208 12.9464 -13.28 +SCATter ( chemical "V" ) + 10.2971 6.8657 7.3511 0.4385 2.0703 26.8938 2.0571 102.478 1.2199 +SCATter ( chemical "V+2" ) + 10.106 6.8818 7.3541 0.4409 2.2884 20.3004 0.0223 115.122 1.2298 +SCATter ( chemical "V+3" ) + 9.43141 6.39535 7.7419 0.383349 2.15343 15.1908 0.016865 63.969 0.656565 +SCATter ( chemical "V+5" ) + 15.6887 0.679003 8.14208 5.40135 2.03081 9.97278 -9.576 0.940464 1.7143 +SCATter ( chemical "Cr" or chemical "CR" ) + 10.6406 6.1038 7.3537 0.392 3.324 20.2626 1.4922 98.7399 1.1832 +SCATter ( chemical "Cr+2" or chemical "CR+2" ) + 9.54034 5.66078 7.7509 0.344261 3.58274 13.3075 0.509107 32.4224 0.616898 +SCATter ( chemical "Cr+3" or chemical "CR+3" ) + 9.6809 5.59463 7.81136 0.334393 2.87603 12.8288 0.113575 32.8761 0.518275 +SCATter ( chemical "Mn" or chemical "MN" ) + 11.2819 5.3409 7.3573 0.3432 3.0193 17.8674 2.2441 83.7543 1.0896 +SCATter ( chemical "Mn+2" or chemical "MN+2" ) + 10.8061 5.2796 7.362 0.3435 3.5268 14.343 0.2184 41.3235 1.0874 +SCATter ( chemical "Mn+3" or chemical "MN+3" ) + 9.84521 4.91797 7.87194 0.294393 3.56531 10.8171 0.323613 24.1281 0.393974 +SCATter ( chemical "Mn+4" or chemical "MN+4" ) + 9.96253 4.8485 7.97057 0.283303 2.76067 10.4852 0.054447 27.573 0.251877 +SCATter ( chemical "Fe" or chemical "FE" ) + 11.7695 4.7611 7.3573 0.3072 3.5222 15.3535 2.3045 76.8805 1.0369 +SCATter ( chemical "Fe+2" or chemical "FE+2" ) + 11.0424 4.6538 7.374 0.3053 4.1346 12.0546 0.4399 31.2809 1.0097 +SCATter ( chemical "Fe+3" or chemical "FE+3" ) + 11.1764 4.6147 7.3863 0.3005 3.3948 11.6729 0.0724 38.5566 0.9707 +SCATter ( chemical "Co" or chemical "CO" ) + 12.2841 4.2791 7.3409 0.2784 4.0034 13.5359 2.3488 71.1692 1.0118 +SCATter ( chemical "Co+2" or chemical "CO+2" ) + 11.2296 4.1231 7.3883 0.2726 4.7393 10.2443 0.7108 25.6466 0.9324 +SCATter ( chemical "Co+3" or chemical "CO+3" ) + 10.338 3.90969 7.88173 0.238668 4.76795 8.35583 0.725591 18.3491 0.286667 +SCATter ( chemical "Ni" or chemical "NI" ) + 12.8376 3.8785 7.292 0.2565 4.4438 12.1763 2.38 66.3421 1.0341 +SCATter ( chemical "Ni+2" or chemical "NI+2" ) + 11.4166 3.6766 7.4005 0.2449 5.3442 8.873 0.9773 22.1626 0.8614 +SCATter ( chemical "Ni+3" or chemical "NI+3" ) + 10.7806 3.5477 7.75868 0.22314 5.22746 7.64468 0.847114 16.9673 0.386044 +SCATter ( chemical "Cu" or chemical "CU" ) + 13.338 3.5828 7.1676 0.247 5.6158 11.3966 1.6735 64.8126 1.191 +SCATter ( chemical "Cu+1" or chemical "CU+1" ) + 11.9475 3.3669 7.3573 0.2274 6.2455 8.6625 1.5578 25.8487 0.89 +SCATter ( chemical "Cu+2" or chemical "CU+2" ) + 11.8168 3.37484 7.11181 0.244078 5.78135 7.9876 1.14523 19.897 1.14431 +SCATter ( chemical "Zn" or chemical "ZN" ) + 14.0743 3.2655 7.0318 0.2333 5.1652 10.3163 2.41 58.7097 1.3041 +SCATter ( chemical "Zn+2" or chemical "ZN+2" ) + 11.9719 2.9946 7.3862 0.2031 6.4668 7.0826 1.394 18.0995 0.7807 +SCATter ( chemical "Ga" or chemical "GA" ) + 15.2354 3.0669 6.7006 0.2412 4.3591 10.7805 2.9623 61.4135 1.7189 +SCATter ( chemical "Ga+3" or chemical "GA+3" ) + 12.692 2.81262 6.69883 0.22789 6.06692 6.36441 1.0066 14.4122 1.53545 +SCATter ( chemical "Ge" or chemical "GE" ) + 16.0816 2.8509 6.3747 0.2516 3.7068 11.4468 3.683 54.7625 2.1313 +SCATter ( chemical "Ge+4" or chemical "GE+4" ) + 12.9172 2.53718 6.70003 0.205855 6.06791 5.47913 0.859041 11.603 1.45572 +SCATter ( chemical "As" or chemical "AS" ) + 16.6723 2.6345 6.0701 0.2647 3.4313 12.9479 4.2779 47.7972 2.531 +SCATter ( chemical "Se" or chemical "SE" ) + 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 2.8409 +SCATter ( chemical "Br" or chemical "BR" ) + 17.1789 2.1723 5.2358 16.5796 5.6377 0.2609 3.9851 41.4328 2.9557 +SCATter ( chemical "Br-1" or chemical "BR-1" ) + 17.1718 2.2059 6.3338 19.3345 5.5754 0.2871 3.7272 58.1535 3.1776 +SCATter ( chemical "Kr" or chemical "KR" ) + 17.3555 1.9384 6.7286 16.5623 5.5493 0.2261 3.5375 39.3972 2.825 +SCATter ( chemical "Rb" or chemical "RB" ) + 17.1784 1.7888 9.6435 17.3151 5.1399 0.2748 1.5292 164.934 3.4873 +SCATter ( chemical "Rb+1" or chemical "RB+1" ) + 17.5816 1.7139 7.6598 14.7957 5.8981 0.1603 2.7817 31.2087 2.0782 +SCATter ( chemical "Sr" or chemical "SR" ) + 17.5663 1.5564 9.8184 14.0988 5.422 0.1664 2.6694 132.376 2.5064 +SCATter ( chemical "Sr+2" or chemical "SR+2" ) + 18.0874 1.4907 8.1373 12.6963 2.5654 24.5651 -34.193 -0.0138 41.4025 +SCATter ( chemical "Y" ) + 17.776 1.4029 10.2946 12.8006 5.72629 0.125599 3.26588 104.354 1.91213 +SCATter ( chemical "Y+3" ) + 17.9268 1.35417 9.1531 11.2145 1.76795 22.6599 -33.108 -0.01319 40.2602 +SCATter ( chemical "Zr" or chemical "ZR" ) + 17.8765 1.27618 10.948 11.916 5.41732 0.117622 3.65721 87.6627 2.06929 +SCATter ( chemical "Zr+4" or chemical "ZR+4" ) + 18.1668 1.2148 10.0562 10.1483 1.01118 21.6054 -2.6479 -0.10276 9.41454 +SCATter ( chemical "Nb" or chemical "NB" ) + 17.6142 1.18865 12.0144 11.766 4.04183 0.204785 3.53346 69.7957 3.75591 +SCATter ( chemical "Nb+3" or chemical "NB+3" ) + 19.8812 0.019175 18.0653 1.13305 11.0177 10.1621 1.94715 28.3389 -12.912 +SCATter ( chemical "Nb+5" or chemical "NB+5" ) + 17.9163 1.12446 13.3417 0.028781 10.799 9.28206 0.337905 25.7228 -6.3934 +SCATter ( chemical "Mo" or chemical "MO" ) + 3.7025 0.2772 17.2356 1.0958 12.8876 11.004 3.7429 61.6584 4.3875 +SCATter ( chemical "Mo+3" or chemical "MO+3" ) + 21.1664 0.014734 18.2017 1.03031 11.7423 9.53659 2.30951 26.6307 -14.421 +SCATter ( chemical "Mo+5" or chemical "MO+5" ) + 21.0149 0.014345 18.0992 1.02238 11.4632 8.78809 0.740625 23.3452 -14.316 +SCATter ( chemical "Mo+6" or chemical "MO+6" ) + 17.8871 1.03649 11.175 8.48061 6.57891 0.058881 0 0 0.344941 +SCATter ( chemical "Tc" or chemical "TC" ) + 19.1301 0.864132 11.0948 8.14487 4.64901 21.5707 2.71263 86.8472 5.40428 +SCATter ( chemical "Ru" or chemical "RU" ) + 19.2674 0.80852 12.9182 8.43467 4.86337 24.7997 1.56756 94.2928 5.37874 +SCATter ( chemical "Ru+3" or chemical "RU+3" ) + 18.5638 0.847329 13.2885 8.37164 9.32602 0.017662 3.00964 22.887 -3.1892 +SCATter ( chemical "Ru+4" or chemical "RU+4" ) + 18.5003 0.844582 13.1787 8.12534 4.71304 0.36495 2.18535 20.8504 1.42357 +SCATter ( chemical "Rh" or chemical "RH" ) + 19.2957 0.751536 14.3501 8.21758 4.73425 25.8749 1.28918 98.6062 5.328 +SCATter ( chemical "Rh+3" or chemical "RH+3" ) + 18.8785 0.764252 14.1259 7.84438 3.32515 21.2487 -6.1989 -0.01036 11.8678 +SCATter ( chemical "Rh+4" or chemical "RH+4" ) + 18.8545 0.760825 13.9806 7.62436 2.53464 19.3317 -5.6526 -0.0102 11.2835 +SCATter ( chemical "Pd" or chemical "PD" ) + 19.3319 0.698655 15.5017 7.98929 5.29537 25.2052 0.605844 76.8986 5.26593 +SCATter ( chemical "Pd+2" or chemical "PD+2" ) + 19.1701 0.696219 15.2096 7.55573 4.32234 22.5057 0 0 5.2916 +SCATter ( chemical "Pd+4" or chemical "PD+4" ) + 19.2493 0.683839 14.79 7.14833 2.89289 17.9144 -7.9492 0.005127 13.0174 +SCATter ( chemical "Ag" or chemical "AG" ) + 19.2808 0.6446 16.6885 7.4726 4.8045 24.6605 1.0463 99.8156 5.179 +SCATter ( chemical "Ag+1" or chemical "AG+1" ) + 19.1812 0.646179 15.9719 7.19123 5.27475 21.7326 0.357534 66.1147 5.21572 +SCATter ( chemical "Ag+2" or chemical "AG+2" ) + 19.1643 0.645643 16.2456 7.18544 4.3709 21.4072 0 0 5.21404 +SCATter ( chemical "Cd" or chemical "CD" ) + 19.2214 0.5946 17.6444 6.9089 4.461 24.7008 1.6029 87.4825 5.0694 +SCATter ( chemical "Cd+2" or chemical "CD+2" ) + 19.1514 0.597922 17.2535 6.80639 4.47128 20.2521 0 0 5.11937 +SCATter ( chemical "In" or chemical "IN" ) + 19.1624 0.5476 18.5596 6.3776 4.2948 25.8499 2.0396 92.8029 4.9391 +SCATter ( chemical "In+3" or chemical "IN+3" ) + 19.1045 0.551522 18.1108 6.3247 3.78897 17.3595 0 0 4.99635 +SCATter ( chemical "Sn" or chemical "SN" ) + 19.1889 5.8303 19.1005 0.5031 4.4585 26.8909 2.4663 83.9571 4.7821 +SCATter ( chemical "Sn+2" or chemical "SN+2" ) + 19.1094 0.5036 19.0548 5.8378 4.5648 23.3752 0.487 62.2061 4.7861 +SCATter ( chemical "Sn+4" or chemical "SN+4" ) + 18.9333 5.764 19.7131 0.4655 3.4182 14.0049 0.0193 -0.7583 3.9182 +SCATter ( chemical "Sb" or chemical "SB" ) + 19.6418 5.3034 19.0455 0.4607 5.0371 27.9074 2.6827 75.2825 4.5909 +SCATter ( chemical "Sb+3" or chemical "SB+3" ) + 18.9755 0.467196 18.933 5.22126 5.10789 19.5902 0.288753 55.5113 4.69626 +SCATter ( chemical "Sb+5" or chemical "SB+5" ) + 19.8685 5.44853 19.0302 0.467973 2.41253 14.1259 0 0 4.69263 +SCATter ( chemical "Te" or chemical "TE" ) + 19.9644 4.81742 19.0138 0.420885 6.14487 28.5284 2.5239 70.8403 4.352 +SCATter ( chemical "I" or chemical "I5U" ) + 20.1472 4.347 18.9949 0.3814 7.5138 27.766 2.2735 66.8776 4.0712 +SCATter ( chemical "I-1" ) + 20.2332 4.3579 18.997 0.3815 7.8069 29.5259 2.8868 84.9304 4.0714 +SCATter ( chemical "Xe" or chemical "XE" ) + 20.2933 3.9282 19.0298 0.344 8.9767 26.4659 1.99 64.2658 3.7118 +SCATter ( chemical "Cs" or chemical "CS" ) + 20.3892 3.569 19.1062 0.3107 10.662 24.3879 1.4953 213.904 3.3352 +SCATter ( chemical "Cs+1" or chemical "CS+1" ) + 20.3524 3.552 19.1278 0.3086 10.2821 23.7128 0.9615 59.4565 3.2791 +SCATter ( chemical "Ba" or chemical "BA" ) + 20.3361 3.216 19.297 0.2756 10.888 20.2073 2.6959 167.202 2.7731 +SCATter ( chemical "Ba+2" or chemical "BA+2" ) + 20.1807 3.21367 19.1136 0.28331 10.9054 20.0558 0.77634 51.746 3.02902 +SCATter ( chemical "La" or chemical "LA" ) + 20.578 2.94817 19.599 0.244475 11.3727 18.7726 3.28719 133.124 2.14678 +SCATter ( chemical "La+3" or chemical "LA+3" ) + 20.2489 2.9207 19.3763 0.250698 11.6323 17.8211 0.336048 54.9453 2.4086 +SCATter ( chemical "Ce" or chemical "CE" ) + 21.1671 2.81219 19.7695 0.226836 11.8513 17.6083 3.33049 127.113 1.86264 +SCATter ( chemical "Ce+3" or chemical "CE+3" ) + 20.8036 2.77691 19.559 0.23154 11.9369 16.5408 0.612376 43.1692 2.09013 +SCATter ( chemical "Ce+4" or chemical "CE+4" ) + 20.3235 2.65941 19.8186 0.21885 12.1233 15.7992 0.144583 62.2355 1.5918 +SCATter ( chemical "Pr" or chemical "PR" ) + 22.044 2.77393 19.6697 0.222087 12.3856 16.7669 2.82428 143.644 2.0583 +SCATter ( chemical "Pr+3" or chemical "PR+3" ) + 21.3727 2.6452 19.7491 0.214299 12.1329 15.323 0.97518 36.4065 1.77132 +SCATter ( chemical "Pr+4" or chemical "PR+4" ) + 20.9413 2.54467 20.0539 0.202481 12.4668 14.8137 0.296689 45.4643 1.24285 +SCATter ( chemical "Nd" or chemical "ND" ) + 22.6845 2.66248 19.6847 0.210628 12.774 15.885 2.85137 137.903 1.98486 +SCATter ( chemical "Nd+3" or chemical "ND+3" ) + 21.961 2.52722 19.9339 0.199237 12.12 14.1783 1.51031 30.8717 1.47588 +SCATter ( chemical "Pm" or chemical "PM" ) + 23.3405 2.5627 19.6095 0.202088 13.1235 15.1009 2.87516 132.721 2.02876 +SCATter ( chemical "Pm+3" or chemical "PM+3" ) + 22.5527 2.4174 20.1108 0.185769 12.0671 13.1275 2.07492 27.4491 1.19499 +SCATter ( chemical "Smm" or chemical "SMM" ) + 24.0042 2.47274 19.4258 0.196451 13.4396 14.3996 2.89604 128.007 2.20963 +SCATter ( chemical "Sm+3" or chemical "SM+3" ) + 23.1504 2.31641 20.2599 0.174081 11.9202 12.1571 2.71488 24.8242 0.954586 +SCATter ( chemical "Eu" or chemical "EU" ) + 24.6274 2.3879 19.0886 0.1942 13.7603 13.7546 2.9227 123.174 2.5745 +SCATter ( chemical "Eu+2" or chemical "EU+2" ) + 24.0063 2.27783 19.9504 0.17353 11.8034 11.6096 3.87243 26.5156 1.36389 +SCATter ( chemical "Eu+3" or chemical "EU+3" ) + 23.7497 2.22258 20.3745 0.16394 11.8509 11.311 3.26503 22.9966 0.759344 +SCATter ( chemical "Gd" or chemical "GD" ) + 25.0709 2.25341 19.0798 0.181951 13.8518 12.9331 3.54545 101.398 2.4196 +SCATter ( chemical "Gd+3" or chemical "GD+3" ) + 24.3466 2.13553 20.4208 0.155525 11.8708 10.5782 3.7149 21.7029 0.645089 +SCATter ( chemical "Tb" or chemical "TB" ) + 25.8976 2.24256 18.2185 0.196143 14.3167 12.6648 2.95354 115.362 3.58324 +SCATter ( chemical "Tb+3" or chemical "TB+3" ) + 24.9559 2.05601 20.3271 0.149525 12.2471 10.0499 3.773 21.2773 0.691967 +SCATter ( chemical "Dy" or chemical "DY" ) + 26.507 2.1802 17.6383 0.202172 14.5596 12.1899 2.96577 111.874 4.29728 +SCATter ( chemical "Dy+3" or chemical "DY+3" ) + 25.5395 1.9804 20.2861 0.143384 11.9812 9.34972 4.50073 19.581 0.68969 +SCATter ( chemical "Ho" or chemical "HO" ) + 26.9049 2.07051 17.294 0.19794 14.5583 11.4407 3.63837 92.6566 4.56796 +SCATter ( chemical "Ho+3" or chemical "HO+3" ) + 26.1296 1.91072 20.0994 0.139358 11.9788 8.80018 4.93676 18.5908 0.852795 +SCATter ( chemical "Er" or chemical "ER" ) + 27.6563 2.07356 16.4285 0.223545 14.9779 11.3604 2.98233 105.703 5.92046 +SCATter ( chemical "Er+3" or chemical "ER+3" ) + 26.722 1.84659 19.7748 0.13729 12.1506 8.36225 5.17379 17.8974 1.17613 +SCATter ( chemical "Tm" or chemical "TM" ) + 28.1819 2.02859 15.8851 0.238849 15.1542 10.9975 2.98706 102.961 6.75621 +SCATter ( chemical "Tm+3" or chemical "TM+3" ) + 27.3083 1.78711 19.332 0.136974 12.3339 7.96778 5.38348 17.2922 1.63929 +SCATter ( chemical "Yb" or chemical "YB" ) + 28.6641 1.9889 15.4345 0.257119 15.3087 10.6647 2.98963 100.417 7.56672 +SCATter ( chemical "Yb+2" or chemical "YB+2" ) + 28.1209 1.78503 17.6817 0.15997 13.3335 8.18304 5.14657 20.39 3.70983 +SCATter ( chemical "Yb+3" or chemical "YB+3" ) + 27.8917 1.73272 18.7614 0.13879 12.6072 7.64412 5.47647 16.8153 2.26001 +SCATter ( chemical "Lu" or chemical "LU" ) + 28.9476 1.90182 15.2208 9.98519 15.1 0.261033 3.71601 84.3298 7.97628 +SCATter ( chemical "Lu+3" or chemical "LU+3" ) + 28.4628 1.68216 18.121 0.142292 12.8429 7.33727 5.59415 16.3535 2.97573 +SCATter ( chemical "Hf" or chemical "HF" ) + 29.144 1.83262 15.1726 9.5999 14.7586 0.275116 4.30013 72.029 8.58154 +SCATter ( chemical "Hf+4" or chemical "HF+4" ) + 28.8131 1.59136 18.4601 0.128903 12.7285 6.76232 5.59927 14.0366 2.39699 +SCATter ( chemical "Ta" or chemical "TA" ) + 29.2024 1.77333 15.2293 9.37046 14.5135 0.295977 4.76492 63.3644 9.24354 +SCATter ( chemical "Ta+5" or chemical "TA+5" ) + 29.1587 1.50711 18.8407 0.116741 12.8268 6.31524 5.38695 12.4244 1.78555 +SCATter ( chemical "W" ) + 29.0818 1.72029 15.43 9.2259 14.4327 0.321703 5.11982 57.056 9.8875 +SCATter ( chemical "W+6" ) + 29.4936 1.42755 19.3763 0.104621 13.0544 5.93667 5.06412 11.1972 1.01074 +SCATter ( chemical "Re" or chemical "RE" ) + 28.7621 1.67191 15.7189 9.09227 14.5564 0.3505 5.44174 52.0861 10.472 +SCATter ( chemical "Os" or chemical "OS" ) + 28.1894 1.62903 16.155 8.97948 14.9305 0.382661 5.67589 48.1647 11.0005 +SCATter ( chemical "Os+4" or chemical "OS+4" ) + 30.419 1.37113 15.2637 6.84706 14.7458 0.165191 5.06795 18.003 6.49804 +SCATter ( chemical "Ir" or chemical "IR" ) + 27.3049 1.59279 16.7296 8.86553 15.6115 0.417916 5.83377 45.0011 11.4722 +SCATter ( chemical "Ir+3" or chemical "IR+3" ) + 30.4156 1.34323 15.862 7.10909 13.6145 0.204633 5.82008 20.3254 8.27903 +SCATter ( chemical "Ir+4" or chemical "IR+4" ) + 30.7058 1.30923 15.5512 6.71983 14.2326 0.167252 5.53672 17.4911 6.96824 +SCATter ( chemical "Pt" or chemical "PT" ) + 27.0059 1.51293 17.7639 8.81174 15.7131 0.424593 5.7837 38.6103 11.6883 +SCATter ( chemical "Pt+2" or chemical "PT+2" ) + 29.8429 1.32927 16.7224 7.38979 13.2153 0.263297 6.35234 22.9426 9.85329 +SCATter ( chemical "Pt+4" or chemical "PT+4" ) + 30.9612 1.24813 15.9829 6.60834 13.7348 0.16864 5.92034 16.9392 7.39534 +SCATter ( chemical "Au" or chemical "AU" ) + 16.8819 0.4611 18.5913 8.6216 25.5582 1.4826 5.86 36.3956 12.0658 +SCATter ( chemical "Au+1" or chemical "AU+1" ) + 28.0109 1.35321 17.8204 7.7395 14.3359 0.356752 6.58077 26.4043 11.2299 +SCATter ( chemical "Au+3" or chemical "AU+3" ) + 30.6886 1.2199 16.9029 6.82872 12.7801 0.212867 6.52354 18.659 9.0968 +SCATter ( chemical "Hg" or chemical "HG" ) + 20.6809 0.545 19.0417 8.4484 21.6575 1.5729 5.9676 38.3246 12.6089 +SCATter ( chemical "Hg+1" or chemical "HG+1" ) + 25.0853 1.39507 18.4973 7.65105 16.8883 0.443378 6.48216 28.2262 12.0205 +SCATter ( chemical "Hg+2" or chemical "HG+2" ) + 29.5641 1.21152 18.06 7.05639 12.8374 0.284738 6.89912 20.7482 10.6268 +SCATter ( chemical "Tl" or chemical "TL" ) + 27.5446 0.65515 19.1584 8.70751 15.538 1.96347 5.52593 45.8149 13.1746 +SCATter ( chemical "Tl+1" or chemical "TL+1" ) + 21.3985 1.4711 20.4723 0.517394 18.7478 7.43463 6.82847 28.8482 12.5258 +SCATter ( chemical "Tl+3" or chemical "TL+3" ) + 30.8695 1.1008 18.3841 6.53852 11.9328 0.219074 7.00574 17.2114 9.8027 +SCATter ( chemical "Pb" or chemical "PB" ) + 31.0617 0.6902 13.0637 2.3576 18.442 8.618 5.9696 47.2579 13.4118 +SCATter ( chemical "Pb+2" or chemical "PB+2" ) + 21.7886 1.3366 19.5682 0.488383 19.1406 6.7727 7.01107 23.8132 12.4734 +SCATter ( chemical "Pb+4" or chemical "PB+4" ) + 32.1244 1.00566 18.8003 6.10926 12.0175 0.147041 6.96886 14.714 8.08428 +SCATter ( chemical "Bi" or chemical "BI" ) + 33.3689 0.704 12.951 2.9238 16.5877 8.7937 6.4692 48.0093 13.5782 +SCATter ( chemical "Bi+3" or chemical "BI+3" ) + 21.8053 1.2356 19.5026 6.24149 19.1053 0.469999 7.10295 20.3185 12.4711 +SCATter ( chemical "Bi+5" or chemical "BI+5" ) + 33.5364 0.91654 25.0946 0.39042 19.2497 5.71414 6.91555 12.8285 -6.7994 +SCATter ( chemical "Po" or chemical "PO" ) + 34.6726 0.700999 15.4733 3.55078 13.1138 9.55642 7.02588 47.0045 13.677 +SCATter ( chemical "At" or chemical "AT" ) + 35.3163 0.68587 19.0211 3.97458 9.49887 11.3824 7.42518 45.4715 13.7108 +SCATter ( chemical "Rn" or chemical "RN" ) + 35.5631 0.6631 21.2816 4.0691 8.0037 14.0422 7.4433 44.2473 13.6905 +SCATter ( chemical "Fr" or chemical "FR" ) + 35.9299 0.646453 23.0547 4.17619 12.1439 23.1052 2.11253 150.645 13.7247 +SCATter ( chemical "Ra" or chemical "RA" ) + 35.763 0.616341 22.9064 3.87135 12.4739 19.9887 3.21097 142.325 13.6211 +SCATter ( chemical "Ra+2" or chemical "RA+2" ) + 35.215 0.604909 21.67 3.5767 7.91342 12.601 7.65078 29.8436 13.5431 +SCATter ( chemical "Ac" or chemical "AC" ) + 35.6597 0.589092 23.1032 3.65155 12.5977 18.599 4.08655 117.02 13.5266 +SCATter ( chemical "Ac+3" or chemical "AC+3" ) + 35.1736 0.579689 22.1112 3.41437 8.19216 12.9187 7.05545 25.9443 13.4637 +SCATter ( chemical "Th" or chemical "TH" ) + 35.5645 0.563359 23.4219 3.46204 12.7473 17.8309 4.80703 99.1722 13.4314 +SCATter ( chemical "Th+4" or chemical "TH+4" ) + 35.1007 0.555054 22.4418 3.24498 9.78554 13.4661 5.29444 23.9533 13.376 +SCATter ( chemical "Pa" or chemical "PA" ) + 35.8847 0.547751 23.2948 3.41519 14.1891 16.9235 4.17287 105.251 13.4287 +SCATter ( chemical "U" ) + 36.0228 0.5293 23.4128 3.3253 14.9491 16.0927 4.188 100.613 13.3966 +SCATter ( chemical "U+3" ) + 35.5747 0.52048 22.5259 3.12293 12.2165 12.7148 5.37073 26.3394 13.3092 +SCATter ( chemical "U+4" ) + 35.3715 0.516598 22.5326 3.05053 12.0291 12.5723 4.7984 23.4582 13.2671 +SCATter ( chemical "U+6" ) + 34.8509 0.507079 22.7584 2.8903 14.0099 13.1767 1.21457 25.2017 13.1665 +SCATter ( chemical "Npp" or chemical "NPP" ) + 36.1874 0.511929 23.5964 3.25396 15.6402 15.3622 4.1855 97.4908 13.3573 +SCATter ( chemical "Np+3" or chemical "NP+3" ) + 35.7074 0.502322 22.613 3.03807 12.9898 12.1449 5.43227 25.4928 13.2544 +SCATter ( chemical "Np+4" or chemical "NP+4" ) + 35.5103 0.498626 22.5787 2.96627 12.7766 11.9484 4.92159 22.7502 13.2116 +SCATter ( chemical "Np+6" or chemical "NP+6" ) + 35.0136 0.48981 22.7286 2.81099 14.3884 12.33 1.75669 22.6581 13.113 +SCATter ( chemical "Pu" or chemical "PU" ) + 36.5254 0.499384 23.8083 3.26371 16.7707 14.9455 3.47947 105.98 13.3812 +SCATter ( chemical "Pu+3" or chemical "PU+3" ) + 35.84 0.484938 22.7169 2.96118 13.5807 11.5331 5.66016 24.3992 13.1991 +SCATter ( chemical "Pu+4" or chemical "PU+4" ) + 35.6493 0.481422 22.646 2.8902 13.3595 11.316 5.18831 21.8301 13.1555 +SCATter ( chemical "Pu+6" or chemical "PU+6" ) + 35.1736 0.473204 22.7181 2.73848 14.7635 11.553 2.28678 20.9303 13.0582 +SCATter ( chemical "Am" or chemical "AM" ) + 36.6706 0.483629 24.0992 3.20647 17.3415 14.3136 3.49331 102.273 13.3592 +SCATter ( chemical "Cm" or chemical "CM" ) + 36.6488 0.465154 24.4096 3.08997 17.399 13.4346 4.21665 88.4834 13.2887 +SCATter ( chemical "Bk" or chemical "BK" ) + 36.7881 0.451018 24.7736 3.04619 17.8919 12.8946 4.23284 86.003 13.2754 +SCATter ( chemical "Cff" or chemical "CFF" ) + 36.9185 0.437533 25.1995 3.00775 18.3317 12.4044 4.24391 83.7881 13.2674 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.param new file mode 100644 index 0000000000000000000000000000000000000000..e311272101b77b0e0075dc3d7b983def08bf6a1f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.param @@ -0,0 +1,8 @@ +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +NONBonded SHA 0.01 0.01 0.01 0.01 + +BOND SHA SHA 0.0 2.0 + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.top new file mode 100644 index 0000000000000000000000000000000000000000..b76ae930d6a6279ea974cf63a491dc4d080b70be --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/shape.top @@ -0,0 +1,16 @@ +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +MASS SHA 100.000 ! dummy atom for shapes + + +RESIdue SHA {dummy atom for shapes} + GROUp + ATOM SHA TYPE=SHA CHARge=0.0 END +END {SHA} + +presidue CON ! + add bond -SHA +SHA +END {con} + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.param b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.param new file mode 100644 index 0000000000000000000000000000000000000000..3cc94ceda3a915360c4a26e2ab8c0f0bc6baa66c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.param @@ -0,0 +1,39 @@ +remarks file toppar/water-allhdg5-4.param +remarks +remarks PARAM19.SOL (solvent parameters) +remarks =========== +remarks available: TIPS3P and DMSO model + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +{* TIP3P model *} +{* =========== *} +BOND HT OT 450.0 0.9572 ! from TIPS3P geometry ( SHAKE w/PARAm) +BOND HT HT 0.0 1.5139 ! from TIPS3P geometry ( SHAKE w/PARAm) +ANGLE HT OT HT 55.0 104.52 ! FROM TIPS3P geometry + + + +{* original TIP3P for ALL interactions since we use OPLS for the protein *} + NONBONDED OT .1521 3.1506 .1521 3.1506 ! ALLOW WAT + !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete + NONBONDED HT .0460 .4000 .0460 .4000 ! ALLOW WAT + !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete +{* *} ! DMSO parameters Alexandre Bonvin Utrecht University +{* DMSO model *} ! GROMOS parameters from Liu et al JACS 117:4363 (1995) +{* ========== *} +BOND CDMS SDMS 300.0 1.950 +BOND SDMS ODMS 350.0 1.530 + +ANGLE CDMS SDMS CDMS 110.0 97.40 +ANGLE CDMS SDMS ODMS 110.0 106.75 + +NONBONDED CDMS 0.2940 3.66 0.2940 3.66 +NONBONDED SDMS 0.2384 3.56 0.2384 3.56 +NONBONDED ODMS 0.0715 2.63 0.0715 2.63 + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.top b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.top new file mode 100644 index 0000000000000000000000000000000000000000..419614fe9f5ed2ad57c1d6506572871f698afcaa --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/solvent-allhdg5-4.top @@ -0,0 +1,170 @@ +remarks file toppar/water-allhdg5-4.top +remarks +remarks TOPH19.SOL +remarks ========== +remarks topology file for solvent molecules +remarks water models available: TIP3P model + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +checkversion 1.3 + +!!the acceptor and donor terms are just for analysis +!!================================================== + +{* default masses *} +MASS HT 1.00800! TIPS3P water hydrogen +MASS OT 15.99940 ! TIPS3P water oxygen +MASS OM 15.99940 ! oxygen in O2 and CO +MASS CM 12.01100 ! carbon in CO +MASS CH2E 14.02700! +MASS CH3E 15.03500! +MASS OH1 15.99940! hydroxy oxygen +MASS H 1.00800! hydrogen which can h-bond to neutral atom +MASS CDMS 15.03500! DMSO methyl group +MASS ODMS 15.99940! DMSO oxygen +MASS SDMS 32.06000! DMSO sulfur + + + +AUTOGENERATE ANGLES=TRUE END + +!------------------------------------------------------------------ + +RESIdue WAT { TIPS3P WATER MODEL } + GROUp + ATOM OH2 TYPE=OT CHARge= -0.834 END + ATOM H1 TYPE=HT CHARge= 0.417 END + ATOM H2 TYPE=HT CHARge= 0.417 END + + BOND OH2 H1 + BOND OH2 H2 + +END {* WAT *} + +!------------------------------------------------------------------ + +RESIdue HOH { alias of WAT, but with O instead of OH2 } + GROUp + ATOM O TYPE=OT CHARge= -0.834 END + ATOM H1 TYPE=HT CHARge= 0.417 END + ATOM H2 TYPE=HT CHARge= 0.417 END + + BOND O H1 + BOND O H2 + +END {* WAT *} + +!------------------------------------------------------------------ + +RESIdue TIP3 { alias of WAT } + GROUp + ATOM OH2 TYPE=OT CHARge= -0.834 END + ATOM H1 TYPE=HT CHARge= 0.417 END + ATOM H2 TYPE=HT CHARge= 0.417 END + + BOND OH2 H1 + BOND OH2 H2 + +END {* WAT *} + +!------------------------------------------------------------------ + +RESIdue TIP { alias of WAT } + GROUp + ATOM OH2 TYPE=OT CHARge= -0.834 END + ATOM H1 TYPE=HT CHARge= 0.417 END + ATOM H2 TYPE=HT CHARge= 0.417 END + + BOND OH2 H1 + BOND OH2 H2 + +END {* WAT *} + +!------------------------------------------------------------------ + +RESIdue DOD { deuterated water } + GROUp + ATOM O TYPE=OT CHARge= -0.834 END + ATOM D1 TYPE=HT CHARge= 0.417 END + ATOM D2 TYPE=HT CHARge= 0.417 END + + BOND O D1 + BOND O D2 + +END {* WAT *} + +!------------------------------------------------------------------ + +RESIdue O2 {* oxygen *} + GROUp + ATOM O1 TYPE=OM CHARGE= 0.021 END + ATOM O2 TYPE=OM CHARGE=-0.021 END + BOND O1 O2 +END {* O2 *} + +!------------------------------------------------------------------- + +RESIdue COM {* carbon monoxide *} + GROUp + ATOM C TYPE=CM CHARGE=0.021 END + ATOM O TYPE=OM CHARGE=-0.021 END + BOND C O +END {* CO *} + +!------------------------------------------------------------------- + +RESIdue ETH {* ethylene *} + GROUp + ATOM C2 TYPE=CH3E CHARge= 0.00 END + GROUp + ATOM C1 TYPE=CH2E CHARge= 0.25 END !# + ATOM O TYPE=OH1 CHARge=-0.65 END !# + ATOM H TYPE=H CHARge= 0.40 END !# + + BOND C2 C1 + BOND C1 O + BOND O H + + DIHEdral C2 C1 O H + + DONOr H O + + ACCEptor O " " + +END {* ETH *} + +!---------------------------------------------------------------------- + +RESIdue COH + GROUp + ATOM C TYPE=CH3E CHARge= 0.25 END + ATOM O TYPE=OH1 CHARge=-0.65 END + ATOM H TYPE=H CHARge=0.40 END + BOND C O BOND O H + DONOr H O + ACCEptor O " " +END {* COH *} + +!---------------------------------------------------------------------- + +RESIdue DMS {* DMSO *} ! Added Jan. 2002 Alexandre Bonvin + GROUp + ATOM SD TYPE=SDMS CHARge= 0.139 END + ATOM CD1 TYPE=CDMS CHARge= 0.16 END + ATOM OD TYPE=ODMS CHARge=-0.459 END + ATOM CD2 TYPE=CDMS CHARge= 0.16 END + + BOND CD1 SD + BOND CD2 SD + BOND SD OD + + ACCEptor OD " " + +END {* ETH *} + +!---------------------------------------------------------------------- + +set message=$old_message echo=$old_echo end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.pdb new file mode 100644 index 0000000000000000000000000000000000000000..7746655f357f86bc780ac00b897cdd8218be7aaa --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.pdb @@ -0,0 +1,45 @@ +REMARK FILENAME="tensor.pdb" +REMARK topology file for dipolar coupling calculations +REMARK DATE:20-Jul-2022 20:50:45 created by user: abonvin +REMARK VERSION:1.3U +ATOM 1 X ANI 990 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 2 Y ANI 990 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 3 Z ANI 990 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 4 OO ANI 990 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 5 X ANI 991 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 6 Y ANI 991 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 7 Z ANI 991 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 8 OO ANI 991 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 9 X ANI 992 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 10 Y ANI 992 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 11 Z ANI 992 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 12 OO ANI 992 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 13 X ANI 993 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 14 Y ANI 993 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 15 Z ANI 993 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 16 OO ANI 993 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 17 X ANI 994 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 18 Y ANI 994 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 19 Z ANI 994 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 20 OO ANI 994 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 21 X ANI 995 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 22 Y ANI 995 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 23 Z ANI 995 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 24 OO ANI 995 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 25 X ANI 996 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 26 Y ANI 996 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 27 Z ANI 996 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 28 OO ANI 996 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 29 X ANI 997 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 30 Y ANI 997 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 31 Z ANI 997 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 32 OO ANI 997 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 33 X ANI 998 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 34 Y ANI 998 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 35 Z ANI 998 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 36 OO ANI 998 0.000 0.000 0.000 1.00 0.00 ANI +ATOM 37 X ANI 999 3.000 0.000 0.000 1.00 0.00 ANI +ATOM 38 Y ANI 999 0.000 3.000 0.000 1.00 0.00 ANI +ATOM 39 Z ANI 999 0.000 0.000 3.000 1.00 0.00 ANI +ATOM 40 OO ANI 999 0.000 0.000 0.000 1.00 0.00 ANI +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.psf b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.psf new file mode 100644 index 0000000000000000000000000000000000000000..e4cf87d5030a4ee9985e9a486f3d3a7d7b56aa34 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor.psf @@ -0,0 +1,207 @@ +data_cns_mtf + +_cns_mtf.title +; FILENAME="tensor.psf" + topology file for dipolar coupling calculations + DATE:20-Jul-2022 20:50:45 created by user: abonvin + VERSION:1.3U +; + +loop_ +_cns_mtf_atom.id +_cns_mtf_atom.segment_id +_cns_mtf_atom.residue_id +_cns_mtf_atom.residue_name +_cns_mtf_atom.atom_name +_cns_mtf_atom.chemical_type +_cns_mtf_atom.charge +_cns_mtf_atom.atom_mass +1 'ANI' '990' 'ANI' 'X' 'XX' 0.00000 100.000 +2 'ANI' '990' 'ANI' 'Y' 'YY' 0.00000 100.000 +3 'ANI' '990' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +4 'ANI' '990' 'ANI' 'OO' 'OO' 0.00000 100.000 +5 'ANI' '991' 'ANI' 'X' 'XX' 0.00000 100.000 +6 'ANI' '991' 'ANI' 'Y' 'YY' 0.00000 100.000 +7 'ANI' '991' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +8 'ANI' '991' 'ANI' 'OO' 'OO' 0.00000 100.000 +9 'ANI' '992' 'ANI' 'X' 'XX' 0.00000 100.000 +10 'ANI' '992' 'ANI' 'Y' 'YY' 0.00000 100.000 +11 'ANI' '992' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +12 'ANI' '992' 'ANI' 'OO' 'OO' 0.00000 100.000 +13 'ANI' '993' 'ANI' 'X' 'XX' 0.00000 100.000 +14 'ANI' '993' 'ANI' 'Y' 'YY' 0.00000 100.000 +15 'ANI' '993' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +16 'ANI' '993' 'ANI' 'OO' 'OO' 0.00000 100.000 +17 'ANI' '994' 'ANI' 'X' 'XX' 0.00000 100.000 +18 'ANI' '994' 'ANI' 'Y' 'YY' 0.00000 100.000 +19 'ANI' '994' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +20 'ANI' '994' 'ANI' 'OO' 'OO' 0.00000 100.000 +21 'ANI' '995' 'ANI' 'X' 'XX' 0.00000 100.000 +22 'ANI' '995' 'ANI' 'Y' 'YY' 0.00000 100.000 +23 'ANI' '995' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +24 'ANI' '995' 'ANI' 'OO' 'OO' 0.00000 100.000 +25 'ANI' '996' 'ANI' 'X' 'XX' 0.00000 100.000 +26 'ANI' '996' 'ANI' 'Y' 'YY' 0.00000 100.000 +27 'ANI' '996' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +28 'ANI' '996' 'ANI' 'OO' 'OO' 0.00000 100.000 +29 'ANI' '997' 'ANI' 'X' 'XX' 0.00000 100.000 +30 'ANI' '997' 'ANI' 'Y' 'YY' 0.00000 100.000 +31 'ANI' '997' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +32 'ANI' '997' 'ANI' 'OO' 'OO' 0.00000 100.000 +33 'ANI' '998' 'ANI' 'X' 'XX' 0.00000 100.000 +34 'ANI' '998' 'ANI' 'Y' 'YY' 0.00000 100.000 +35 'ANI' '998' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +36 'ANI' '998' 'ANI' 'OO' 'OO' 0.00000 100.000 +37 'ANI' '999' 'ANI' 'X' 'XX' 0.00000 100.000 +38 'ANI' '999' 'ANI' 'Y' 'YY' 0.00000 100.000 +39 'ANI' '999' 'ANI' 'Z' 'ZZ' 0.00000 100.000 +40 'ANI' '999' 'ANI' 'OO' 'OO' 0.00000 100.000 +-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000 + +loop_ +_cns_mtf_bond.id[1] +_cns_mtf_bond.id[2] +1 4 +2 4 +3 4 +5 8 +6 8 +7 8 +9 12 +10 12 +11 12 +13 16 +14 16 +15 16 +17 20 +18 20 +19 20 +21 24 +22 24 +23 24 +25 28 +26 28 +27 28 +29 32 +30 32 +31 32 +33 36 +34 36 +35 36 +37 40 +38 40 +39 40 +-1 -1 + +loop_ +_cns_mtf_angle.id[1] +_cns_mtf_angle.id[2] +_cns_mtf_angle.id[3] +1 4 2 +1 4 3 +2 4 3 +5 8 6 +5 8 7 +6 8 7 +9 12 10 +9 12 11 +10 12 11 +13 16 14 +13 16 15 +14 16 15 +17 20 18 +17 20 19 +18 20 19 +21 24 22 +21 24 23 +22 24 23 +25 28 26 +25 28 27 +26 28 27 +29 32 30 +29 32 31 +30 32 31 +33 36 34 +33 36 35 +34 36 35 +37 40 38 +37 40 39 +38 40 39 +-1 -1 -1 + +loop_ +_cns_mtf_dihedral.id[1] +_cns_mtf_dihedral.id[2] +_cns_mtf_dihedral.id[3] +_cns_mtf_dihedral.id[4] +-1 -1 -1 -1 + +loop_ +_cns_mtf_improper.id[1] +_cns_mtf_improper.id[2] +_cns_mtf_improper.id[3] +_cns_mtf_improper.id[4] +-1 -1 -1 -1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.inb +-1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.iblo +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-1 + +loop_ +_cns_mtf_group_linked_list.first_atom_id +0 +4 +8 +12 +16 +20 +24 +28 +32 +36 +-1 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.pdb new file mode 100644 index 0000000000000000000000000000000000000000..8e98b1a06ced62828c47062b1d895c8720af2290 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.pdb @@ -0,0 +1,25 @@ +REMARK FILENAME="/Users/abonvin/haddock2.1/toppar/tensor_dani.pdb" +REMARK topology file for dipolar coupling calculations +REMARK DATE:19-Nov-2007 11:59:42 created by user: abonvin +REMARK VERSION:1.2 +ATOM 1 X DAN 995 3.000 0.000 0.000 1.00 0.00 DAN +ATOM 2 Y DAN 995 0.000 3.000 0.000 1.00 0.00 DAN +ATOM 3 Z DAN 995 0.000 0.000 3.000 1.00 0.00 DAN +ATOM 4 OO DAN 995 0.000 0.000 0.000 1.00 0.00 DAN +ATOM 5 X DAN 996 3.000 0.000 0.000 1.00 0.00 DAN +ATOM 6 Y DAN 996 0.000 3.000 0.000 1.00 0.00 DAN +ATOM 7 Z DAN 996 0.000 0.000 3.000 1.00 0.00 DAN +ATOM 8 OO DAN 996 0.000 0.000 0.000 1.00 0.00 DAN +ATOM 9 X DAN 997 3.000 0.000 0.000 1.00 0.00 DAN +ATOM 10 Y DAN 997 0.000 3.000 0.000 1.00 0.00 DAN +ATOM 11 Z DAN 997 0.000 0.000 3.000 1.00 0.00 DAN +ATOM 12 OO DAN 997 0.000 0.000 0.000 1.00 0.00 DAN +ATOM 13 X DAN 998 3.000 0.000 0.000 1.00 0.00 DAN +ATOM 14 Y DAN 998 0.000 3.000 0.000 1.00 0.00 DAN +ATOM 15 Z DAN 998 0.000 0.000 3.000 1.00 0.00 DAN +ATOM 16 OO DAN 998 0.000 0.000 0.000 1.00 0.00 DAN +ATOM 17 X DAN 999 3.000 0.000 0.000 1.00 0.00 DAN +ATOM 18 Y DAN 999 0.000 3.000 0.000 1.00 0.00 DAN +ATOM 19 Z DAN 999 0.000 0.000 3.000 1.00 0.00 DAN +ATOM 20 OO DAN 999 0.000 0.000 0.000 1.00 0.00 DAN +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.psf b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.psf new file mode 100644 index 0000000000000000000000000000000000000000..10f96d4ad26c1e330882bc55b064c69ec0cf5ad8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_dani.psf @@ -0,0 +1,132 @@ +data_cns_mtf + +_cns_mtf.title +; FILENAME="/Users/abonvin/haddock2.1/toppar/tensor_dani.psf" + topology file for dipolar coupling calculations + DATE:19-Nov-2007 11:59:42 created by user: abonvin + VERSION:1.2 +; + +loop_ +_cns_mtf_atom.id +_cns_mtf_atom.segment_id +_cns_mtf_atom.residue_id +_cns_mtf_atom.residue_name +_cns_mtf_atom.atom_name +_cns_mtf_atom.chemical_type +_cns_mtf_atom.charge +_cns_mtf_atom.atom_mass +1 'DAN' '995' 'DAN' 'X' 'XX' 0.00000 100.000 +2 'DAN' '995' 'DAN' 'Y' 'YY' 0.00000 100.000 +3 'DAN' '995' 'DAN' 'Z' 'ZZ' 0.00000 100.000 +4 'DAN' '995' 'DAN' 'OO' 'OO' 0.00000 100.000 +5 'DAN' '996' 'DAN' 'X' 'XX' 0.00000 100.000 +6 'DAN' '996' 'DAN' 'Y' 'YY' 0.00000 100.000 +7 'DAN' '996' 'DAN' 'Z' 'ZZ' 0.00000 100.000 +8 'DAN' '996' 'DAN' 'OO' 'OO' 0.00000 100.000 +9 'DAN' '997' 'DAN' 'X' 'XX' 0.00000 100.000 +10 'DAN' '997' 'DAN' 'Y' 'YY' 0.00000 100.000 +11 'DAN' '997' 'DAN' 'Z' 'ZZ' 0.00000 100.000 +12 'DAN' '997' 'DAN' 'OO' 'OO' 0.00000 100.000 +13 'DAN' '998' 'DAN' 'X' 'XX' 0.00000 100.000 +14 'DAN' '998' 'DAN' 'Y' 'YY' 0.00000 100.000 +15 'DAN' '998' 'DAN' 'Z' 'ZZ' 0.00000 100.000 +16 'DAN' '998' 'DAN' 'OO' 'OO' 0.00000 100.000 +17 'DAN' '999' 'DAN' 'X' 'XX' 0.00000 100.000 +18 'DAN' '999' 'DAN' 'Y' 'YY' 0.00000 100.000 +19 'DAN' '999' 'DAN' 'Z' 'ZZ' 0.00000 100.000 +20 'DAN' '999' 'DAN' 'OO' 'OO' 0.00000 100.000 +-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000 + +loop_ +_cns_mtf_bond.id[1] +_cns_mtf_bond.id[2] +1 4 +2 4 +3 4 +5 8 +6 8 +7 8 +9 12 +10 12 +11 12 +13 16 +14 16 +15 16 +17 20 +18 20 +19 20 +-1 -1 + +loop_ +_cns_mtf_angle.id[1] +_cns_mtf_angle.id[2] +_cns_mtf_angle.id[3] +1 4 2 +1 4 3 +2 4 3 +5 8 6 +5 8 7 +6 8 7 +9 12 10 +9 12 11 +10 12 11 +13 16 14 +13 16 15 +14 16 15 +17 20 18 +17 20 19 +18 20 19 +-1 -1 -1 + +loop_ +_cns_mtf_dihedral.id[1] +_cns_mtf_dihedral.id[2] +_cns_mtf_dihedral.id[3] +_cns_mtf_dihedral.id[4] +-1 -1 -1 -1 + +loop_ +_cns_mtf_improper.id[1] +_cns_mtf_improper.id[2] +_cns_mtf_improper.id[3] +_cns_mtf_improper.id[4] +-1 -1 -1 -1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.inb +-1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.iblo +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-1 + +loop_ +_cns_mtf_group_linked_list.first_atom_id +0 +4 +8 +12 +16 +-1 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.pdb b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.pdb new file mode 100644 index 0000000000000000000000000000000000000000..1165558071bee406d253bef52200f7416fc797de --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.pdb @@ -0,0 +1,45 @@ +REMARK FILENAME="tensor_para.pdb" +REMARK topology file for dipolar coupling calculations +REMARK DATE:16-Mar-2011 11:48:12 created by user: christophe +REMARK VERSION:1.3 +ATOM 1 X XAN 990 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 2 Y XAN 990 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 3 Z XAN 990 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 4 OO XAN 990 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 5 X XAN 991 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 6 Y XAN 991 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 7 Z XAN 991 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 8 OO XAN 991 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 9 X XAN 992 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 10 Y XAN 992 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 11 Z XAN 992 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 12 OO XAN 992 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 13 X XAN 993 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 14 Y XAN 993 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 15 Z XAN 993 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 16 OO XAN 993 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 17 X XAN 994 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 18 Y XAN 994 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 19 Z XAN 994 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 20 OO XAN 994 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 21 X XAN 995 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 22 Y XAN 995 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 23 Z XAN 995 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 24 OO XAN 995 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 25 X XAN 996 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 26 Y XAN 996 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 27 Z XAN 996 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 28 OO XAN 996 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 29 X XAN 997 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 30 Y XAN 997 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 31 Z XAN 997 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 32 OO XAN 997 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 33 X XAN 998 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 34 Y XAN 998 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 35 Z XAN 998 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 36 OO XAN 998 0.000 0.000 0.000 1.00 0.00 XAN +ATOM 37 X XAN 999 3.000 0.000 0.000 1.00 0.00 XAN +ATOM 38 Y XAN 999 0.000 3.000 0.000 1.00 0.00 XAN +ATOM 39 Z XAN 999 0.000 0.000 3.000 1.00 0.00 XAN +ATOM 40 OO XAN 999 0.000 0.000 0.000 1.00 0.00 XAN +END diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.psf b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.psf new file mode 100644 index 0000000000000000000000000000000000000000..4894d4690197294d5581e6d7816d306edb1c28ca --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/tensor_para.psf @@ -0,0 +1,217 @@ +data_cns_mtf + +_cns_mtf.title +; FILENAME="tensor_para.psf" + topology file for dipolar coupling calculations + DATE:16-Mar-2011 11:48:12 created by user: christophe + VERSION:1.3 +; + +loop_ +_cns_mtf_atom.id +_cns_mtf_atom.segment_id +_cns_mtf_atom.residue_id +_cns_mtf_atom.residue_name +_cns_mtf_atom.atom_name +_cns_mtf_atom.chemical_type +_cns_mtf_atom.charge +_cns_mtf_atom.atom_mass +1 'XAN' '990' 'XAN' 'X' 'XX' 0.00000 100.000 +2 'XAN' '990' 'XAN' 'Y' 'YY' 0.00000 100.000 +3 'XAN' '990' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +4 'XAN' '990' 'XAN' 'OO' 'OO' 0.00000 100.000 +5 'XAN' '991' 'XAN' 'X' 'XX' 0.00000 100.000 +6 'XAN' '991' 'XAN' 'Y' 'YY' 0.00000 100.000 +7 'XAN' '991' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +8 'XAN' '991' 'XAN' 'OO' 'OO' 0.00000 100.000 +9 'XAN' '992' 'XAN' 'X' 'XX' 0.00000 100.000 +10 'XAN' '992' 'XAN' 'Y' 'YY' 0.00000 100.000 +11 'XAN' '992' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +12 'XAN' '992' 'XAN' 'OO' 'OO' 0.00000 100.000 +13 'XAN' '993' 'XAN' 'X' 'XX' 0.00000 100.000 +14 'XAN' '993' 'XAN' 'Y' 'YY' 0.00000 100.000 +15 'XAN' '993' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +16 'XAN' '993' 'XAN' 'OO' 'OO' 0.00000 100.000 +17 'XAN' '994' 'XAN' 'X' 'XX' 0.00000 100.000 +18 'XAN' '994' 'XAN' 'Y' 'YY' 0.00000 100.000 +19 'XAN' '994' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +20 'XAN' '994' 'XAN' 'OO' 'OO' 0.00000 100.000 +21 'XAN' '995' 'XAN' 'X' 'XX' 0.00000 100.000 +22 'XAN' '995' 'XAN' 'Y' 'YY' 0.00000 100.000 +23 'XAN' '995' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +24 'XAN' '995' 'XAN' 'OO' 'OO' 0.00000 100.000 +25 'XAN' '996' 'XAN' 'X' 'XX' 0.00000 100.000 +26 'XAN' '996' 'XAN' 'Y' 'YY' 0.00000 100.000 +27 'XAN' '996' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +28 'XAN' '996' 'XAN' 'OO' 'OO' 0.00000 100.000 +29 'XAN' '997' 'XAN' 'X' 'XX' 0.00000 100.000 +30 'XAN' '997' 'XAN' 'Y' 'YY' 0.00000 100.000 +31 'XAN' '997' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +32 'XAN' '997' 'XAN' 'OO' 'OO' 0.00000 100.000 +33 'XAN' '998' 'XAN' 'X' 'XX' 0.00000 100.000 +34 'XAN' '998' 'XAN' 'Y' 'YY' 0.00000 100.000 +35 'XAN' '998' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +36 'XAN' '998' 'XAN' 'OO' 'OO' 0.00000 100.000 +37 'XAN' '999' 'XAN' 'X' 'XX' 0.00000 100.000 +38 'XAN' '999' 'XAN' 'Y' 'YY' 0.00000 100.000 +39 'XAN' '999' 'XAN' 'Z' 'ZZ' 0.00000 100.000 +40 'XAN' '999' 'XAN' 'OO' 'OO' 0.00000 100.000 +-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000 + +loop_ +_cns_mtf_bond.id[1] +_cns_mtf_bond.id[2] +1 4 +2 4 +3 4 +5 8 +6 8 +7 8 +9 12 +10 12 +11 12 +13 16 +14 16 +15 16 +17 20 +18 20 +19 20 +21 24 +22 24 +23 24 +25 28 +26 28 +27 28 +29 32 +30 32 +31 32 +33 36 +34 36 +35 36 +37 40 +38 40 +39 40 +-1 -1 + +loop_ +_cns_mtf_angle.id[1] +_cns_mtf_angle.id[2] +_cns_mtf_angle.id[3] +1 4 2 +1 4 3 +2 4 3 +5 8 6 +5 8 7 +6 8 7 +9 12 10 +9 12 11 +10 12 11 +13 16 14 +13 16 15 +14 16 15 +17 20 18 +17 20 19 +18 20 19 +21 24 22 +21 24 23 +22 24 23 +25 28 26 +25 28 27 +26 28 27 +29 32 30 +29 32 31 +30 32 31 +33 36 34 +33 36 35 +34 36 35 +37 40 38 +37 40 39 +38 40 39 +-1 -1 -1 + +loop_ +_cns_mtf_dihedral.id[1] +_cns_mtf_dihedral.id[2] +_cns_mtf_dihedral.id[3] +_cns_mtf_dihedral.id[4] +-1 -1 -1 -1 + +loop_ +_cns_mtf_improper.id[1] +_cns_mtf_improper.id[2] +_cns_mtf_improper.id[3] +_cns_mtf_improper.id[4] + 1 2 4 3 + 5 6 8 7 + 9 10 12 11 +13 14 16 15 +17 18 20 19 +21 22 24 23 +25 26 28 27 +29 30 32 31 +33 34 36 35 +37 38 40 39 +-1 -1 -1 -1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.inb +-1 + +loop_ +_cns_mtf_explicit_nonbonded_exclusion.iblo +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-1 + +loop_ +_cns_mtf_group_linked_list.first_atom_id +0 +4 +8 +12 +16 +20 +24 +28 +32 +36 +-1 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis.pro b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis.pro new file mode 100644 index 0000000000000000000000000000000000000000..2a678f9e8bf8144321a0090faa2af57524f961f5 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis.pro @@ -0,0 +1,55 @@ +remark topology file for dipolar coupling calculations + +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +autogenerate + angles=true + dihedrals=false +end + +mass XX 100 +mass YY 100 +mass ZZ 100 +mass OO 100 + +residue ANI + group + atom X type=XX charge=0.0 end + atom Y type=YY charge=0.0 end + atom Z type=ZZ charge=0.0 end + atom OO type=OO charge=0.0 end + + bond X OO + bond Y OO + bond Z OO +end + +residue XAN + group + atom X type=XX charge=0.0 end + atom Y type=YY charge=0.0 end + atom Z type=ZZ charge=0.0 end + atom OO type=OO charge=0.0 end + + bond X OO + bond Y OO + bond Z OO + + improper X Y OO Z +end + +residue DAN + group + atom X type=XX charge=0.0 end + atom Y type=YY charge=0.0 end + atom Z type=ZZ charge=0.0 end + atom OO type=OO charge=0.0 end + + bond X OO + bond Y OO + bond Z OO +end + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis_dani.pro b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis_dani.pro new file mode 100644 index 0000000000000000000000000000000000000000..36331ad69672e954f12359795614729ca8bda546 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/cns/toppar/top_axis_dani.pro @@ -0,0 +1,28 @@ +remark topology file for dipolar coupling calculations +set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) +set message=off echo=off end + +autogenerate + angles=true + dihedrals=false +end + +mass XX 100 +mass YY 100 +mass ZZ 100 +mass OO 100 + +residue DAN + group + atom X type=XX charge=0.0 end + atom Y type=YY charge=0.0 end + atom Z type=ZZ charge=0.0 end + atom OO type=OO charge=0.0 end + + bond X OO + bond Y OO + bond Z OO +end + + +set message=$old_message echo=$old_echo end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/._cns_paths.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._cns_paths.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._cns_paths.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/._defaults.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._defaults.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._defaults.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/._exceptions.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._exceptions.py new file mode 100644 index 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a/.venv_haddock/lib/python3.12/site-packages/haddock/core/._supported_molecules.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._supported_molecules.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._supported_molecules.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/._typing.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._typing.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/core/._typing.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..5fbd962b51feb3911d34d031a864f4d7645ac3fa --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/__init__.py @@ -0,0 +1,3 @@ +""" +Core haddock3 functionalities. +""" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/cns_paths.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/cns_paths.py new file mode 100644 index 0000000000000000000000000000000000000000..4907650677204e2dd08ca5e50eb072cd0da27a22 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/cns_paths.py @@ -0,0 +1,99 @@ +""" +Path to CNS-related files. + +Most paths are defined by dictionaries that gather several related +paths. Here, instead of defining the dictionaries with static paths, we +have functions that create those dict-containing paths dynamically. The +default values are defined by: + +- axis +- tensors +- translation_vectors +- water_box + +But you can re-use the functions to create new dictionaries with updated +paths. This is useful for those cases when the `cns/` folder is moved +to a different folder. +""" +from pathlib import Path + +from haddock import toppar_path +from haddock.core.typing import FilePath + + +# exact file names as present in the cns/ scripts folder +LINK_FILE = "protein-allhdg5-4-noter.link" +SCATTER_LIB = "scatter.lib" +INITIAL_POSITIONS_DIR = "initial_positions" + +PROTEIN_LINK_FILES = { + "NH3+,COO-": "protein-allhdg5-4.link", + "NH,COO-": "protein-allhdg5-4-noNter.link", + "NH3+,CO": "protein-allhdg5-4-noCter.link", + "NH,CO": LINK_FILE, +} +NUCL_LINK_FILES = { + "5'Phosphate": "dna-rna-pho-1.3.link", + "5'OH": "dna-rna-1.3.link", +} + +# default prepared paths +link_file = Path(toppar_path, LINK_FILE) +scatter_lib = Path(toppar_path, SCATTER_LIB) + + +def get_translation_vectors(path: FilePath) -> dict[str, Path]: + """ + Generate paths for translation vectors. + + Parameters + ---------- + path : pathlib.Path + If absolute, paths will be absolute, if relative paths will be + relative. Adds the INITIAL_POSITIONS_DIR path before the file + name. + """ + translation_vectors: dict[str, Path] = {} + for i in range(51): + _s = f'trans_vector_{i}' + _p = Path(path, INITIAL_POSITIONS_DIR, _s) + translation_vectors[_s] = _p + + return translation_vectors + + +def get_tensors(path: FilePath) -> dict[str, Path]: + """Generate paths for tensors.""" + tensors = { + "tensor_psf": Path(path, "tensor.psf"), + "tensor_pdb": Path(path, "tensor.pdb"), + "tensor_para_psf": Path(path, "tensor_para.psf"), + "tensor_para_pdb": Path(path, "tensor_para.pdb"), + "tensor_dani_psf": Path(path, "tensor_dani.psf"), + "tensor_dani_pdb": Path(path, "tensor_dani.pdb"), + } + return tensors + + +def get_axis(path: FilePath) -> dict[str, Path]: + """Generate paths for axis.""" + axis = { + "top_axis": Path(path, "top_axis.pro"), + "par_axis": Path(path, "par_axis.pro"), + "top_axis_dani": Path(path, "top_axis_dani.pro"), + } + return axis + + +def get_water_box(path: FilePath) -> dict[str, Path]: + """Generate paths for water box.""" + water_box = { + "boxtyp20": Path(path, "boxtyp20.pdb"), + } + return water_box + + +axis = get_axis(toppar_path) +tensors = get_tensors(toppar_path) +translation_vectors = get_translation_vectors(toppar_path) +water_box = get_water_box(toppar_path) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/defaults.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/defaults.py new file mode 100644 index 0000000000000000000000000000000000000000..a2b504d4b5e997c0a9bec9e9726dcc577ba681fb --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/defaults.py @@ -0,0 +1,47 @@ +"""All default parameters used by the framework.""" + +import string +from importlib.resources import files +from pathlib import Path + +import yaml + +from haddock import core_path +from haddock.libs.libutil import get_cns_executable, get_prodrg_exec + +cns_exec, cns_exec_linux = get_cns_executable() +prodrg_exec, prodrg_param = get_prodrg_exec() + +CONTACT_FCC_EXEC = Path(files("haddock").joinpath("bin/contact_fcc")) # type: ignore +FAST_RMSDMATRIX_EXEC = Path(files("haddock").joinpath("bin/fast-rmsdmatrix")) # type: ignore + +MODULE_PATH_NAME = "step_" +""" +Module input and generated data will be stored in folder starting by +this prefix""" + +MODULE_IO_FILE = "io.json" +"""Default name for exchange module information file""" + +MAX_NUM_MODULES = 10000 +"""Temptative number of max allowed number of modules to execute""" + +valid_run_dir_chars = string.ascii_letters + string.digits + "._-/\\" + +RUNDIR = "run_dir" +"""Default run directory name.""" + +INTERACTIVE_RE_SUFFIX = "interactive" +"""Suffix added to interactive haddock3-re runs.""" + +MODULE_DEFAULT_YAML = "defaults.yaml" +"""Default name of the yaml default parameters file.""" + +CNS_MODULES = ["rigidbody", "flexref", "emscoring", "mdscoring", "mdref", "emref"] +"""List of CNS modules available in HADDOCK3.""" + + +with open(Path(core_path, "mandatory.yaml"), "r") as fin: + _ycfg = yaml.safe_load(fin) +max_molecules_allowed = _ycfg["molecules"]["maxitems"] +del _ycfg diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/exceptions.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/exceptions.py new file mode 100644 index 0000000000000000000000000000000000000000..de67a3f67ad22853d991aa69dac2406b675dbebc --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/exceptions.py @@ -0,0 +1,79 @@ +"""HADDOCK library custom errors.""" + +from os import linesep + +from haddock.core.typing import FilePath + +class HaddockError(Exception): + """Error in HADDOCK3.""" + + pass + + +class ConfigurationError(HaddockError): + """Error in the configuration file.""" + + pass + + +class ModuleError(HaddockError): + """Error in a HADDOCK3 module.""" + + pass + + +class StepError(HaddockError): + """Error in a HADDOCK3 workflow step.""" + + pass + + +class JobRunningError(HaddockError): + """General job running error.""" + + pass + + +class CNSRunningError(HaddockError): + """CNS run error.""" + + pass + +class KnownCNSError(CNSRunningError): + """Detected CNS output error.""" + + def __init__(self, cns_message: str, hint: str, filepath: FilePath): + self.cns_error = cns_message + self.hint = hint + self.filepath = filepath + + def __str__(self) -> str: + """Generate custom string representation of this exception.""" + full_msg = ( + f"A CNS error occured: `{self.cns_error}`.{linesep}" + f"Here is a hint on how to solve it:{linesep}{self.hint}" + ) + return full_msg + + +class HaddockModuleError(HaddockError): + """General error in a HADDOCK3 module.""" + + pass + + +class ThirdPartyIntallationError(HaddockModuleError): + """General error when a third party module is not properly installed.""" + + pass + +class SetupError(HaddockError): + """Set up error.""" + + pass + + +class HaddockTermination(HaddockError): + """Terminates HADDOCK.""" + + pass diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/mandatory.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/core/mandatory.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f32f96b77e45b352ed960a6cb3fb637c716d0f48 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/mandatory.yaml @@ -0,0 +1,18 @@ +run_dir: + type: dir + title: Run directory + short: Folder to store the HADDOCK3 run + long: The new folder that will be created to save the HADDOCK3 run + explevel: easy +molecules: + type: list + accept: + - ".pdb" + minitems: 1 + maxitems: 20 + title: Input Molecules + short: The input molecules that will be used for docking. + long: + Molecules must be provided in PDB format. These PDB files can be + single molecules or ensembles using the MODEL/ENDMDL statements. + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/optional.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/core/optional.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a07a3d9c1acfcd2131b029a501e6b57105f9e298 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/optional.yaml @@ -0,0 +1,32 @@ +preprocess: + default: false + type: boolean + title: Tries to correct input PDBs + short: If true, evaluates and tries to correct the input PDB before the + workflow. + long: HADDOCK3 checks and processes the input PDB files to ensure they + all comply with HADDOCK3's requirements. These checks concerns, for example, + residue numbering, compatibility of chain IDs, and many others. You can see + all checks performs in the live issue + https://github.com/haddocking/haddock3/issues/143. If set to false, no + checks are performed and HADDOCK3 directly uses the original input PDBs. + explevel: easy +postprocess: + default: true + type: boolean + title: Executes haddock3-analyse on the CAPRI folders at the end of the run + short: If true, executes haddock3-analyse on the CAPRI folders at the end of + the workflow + long: haddock3-analyse is a cli (see https://github.com/haddocking/haddock3/blob/main/src/haddock/clis/cli_analyse.py) + used to plot the results of a HADDOCK3 workflow. If this option, this command + is automatically executed at the end of the workflow (on the caprieval folders). + explevel: easy +gen_archive: + default: false + type: boolean + title: Generates an archive of the run and of the analysis. + short: If true, executes haddock3-analyse in self_contained mode and generates + archives of the run_directory and of the analysis in two separated tgz files. + long: If true, executes haddock3-analyse in self_contained mode and generates + archives of the run_directory and of the analysis in two separated tgz files. + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/supported_molecules.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/supported_molecules.py new file mode 100644 index 0000000000000000000000000000000000000000..4a9f742ce86ab63dd92f96c0368246622ebb830b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/supported_molecules.py @@ -0,0 +1,497 @@ +""" +HADDOCK 3 supported residues. + +The HADDOCK3 supported residues are defined by the different ``.top`` +files in the ``cns/toppar`` source folder. This module will automatically +retrieve any new residue added to the ``.top`` defined in the folder and +add it to the variables here. + +If a new ``.top`` file is added in the folder, that must be added here +inside the :py:func:`read_supported_residues` function, because file retrieve is +not done automatically on purpose. + +``.top`` files considered here: + +* ``carbohydrate.top`` +* ``dna-rna-CG-MARTINI-2-1p.top`` +* ``dna-rna-allatom-hj-opls-1.3.top`` +* ``fragment_probes.top`` +* ``hemes-allhdg.top`` +* ``ion.top`` +* ``protein-CG-Martini-2-2.top`` +* ``protein-CG-Martini.top`` +* ``protein-allhdg5-4.top`` +* ``solvent-allhdg5-4.top`` +* ``shape.top`` +* ``cofactors.top`` + +DNA-related files are all concatenated into a single DNA-supported +residues datastructure. The same occurs for protein residues (natural or +modified). + +You can import from this module the different sets containing the +supported residue names: + +* :py:data:`supported_aminoacids_resnames` +* :py:data:`supported_carbo_resnames` +* :py:data:`supported_fragments_resnames` +* :py:data:`supported_hemes_resnames` +* :py:data:`supported_single_ions_resnames` +* :py:data:`supported_single_ions_elements` +* :py:data:`supported_single_ions_atoms` +* :py:data:`supported_multiatom_ions_resnames` +* :py:data:`supported_nucleic_resnames` +* :py:data:`supported_solvents_resnames` +* :py:data:`supported_shape` +* :py:data:`supported_cofactors_resnames` + +* :py:data:`supported_ATOM` (contains residues and nucleic acids) +* :py:data:`supported_HETATM` (everything not contained in ATOM) +""" +import itertools as it +import re +import string +from copy import copy +from pathlib import Path + +from haddock import toppar_path +from haddock.core.typing import FilePath, Iterable + + +class CNSTopologyResidue: + """CNS topology residue.""" + + def __init__(self, resname: str, charge: float, + atoms: Iterable[str]) -> None: + """ + CNS topology residue. + + This is not an actual topology. It is a namespace storing the + basic parameters defined in CNS residue topologies. + + So far, this is used by the + :py:module:`haddock.gear.preprocessing` step; but this class can + be extended with additional parameters if needed. + + Parameters + ---------- + resname : str + The name of the residue. + + charge : float + The charge of the residue. The charge will be round to two + decimal places. + + atoms : list-like + The list of atom names. Will be converted to a tuple. + """ + self._resname = resname + self._charge = round(charge, 2) + self._atoms = tuple(atoms) + return + + def __repr__(self) -> str: + return str(self) + + def __str__(self) -> str: + return ( + f"{self.__class__.__name__}({self.resname!r}, " + f"{self.charge!r}, {self.atoms!r})" + ) + + @property + def resname(self) -> str: + """Residue name.""" + return self._resname + + @property + def charge(self) -> float: + """Residue total charge.""" + return self._charge + + @property + def atoms(self) -> tuple[str, ...]: + """Tuple of residue atoms.""" + return self._atoms + + @property + def elements(self) -> tuple[str, ...]: + """ + List of elements for all atoms composing the molecule. + + This list is ordered the same as ``atoms``. + + By default ``elements`` is not defined and must be injected manually. + + See Also + -------- + * :py:func:`get_ion_element_from_atoms` + """ + try: + return self._elements + except AttributeError as err: + emsg = "`elements` is not defined." + raise AttributeError(emsg) from err + + @elements.setter + def elements(self, elements: tuple[str, ...]) -> None: + self._elements = elements + + +def get_ion_element_from_atoms(atoms: Iterable[str]) -> tuple[str, ...]: + """ + Generate the element name from the atom name for single atom ions. + + Examples + -------- + >>> get_ion_element_from_atoms(["ZN+2", "CU+2", "NI"]) + ("ZN", "CU", "NI") + + Parameters + ---------- + atom : list + A list of atom names. + """ + ele = (a.rstrip(string.digits + "+-") for a in atoms) + return tuple(ele) + + +def read_residues_from_top_file(topfile: FilePath) -> list[CNSTopologyResidue]: + """ + Read the residues defined in CNS topology file. + + This is a general implementation to read the basic information from + the CNS topology files. This basic information is the information + needed to help the the :py:mod:`haddock.gear.preprocessing` step + in identifying the supported residues and correctly format their PDB + lines. + + Parameters + ---------- + topfile : str or :external:py:class:`pathlib.Path` + Path to the topology file. + + Returns + ------- + list + List of :class:`CNSTopologyResidue` objects. + Each object has information on the residue name, the atoms, + and the total charge of the residue. + + See Also + -------- + * :py:func:`haddock.gear.preprocessing.read_additional_residues` + """ + # just to avoid identention with with + fin = open(topfile, 'r') + lines = fin.readlines() + fin.close() + return _read_residues_from_top_file(lines) + + +def _read_residues_from_top_file( + lines: Iterable[str]) -> list[CNSTopologyResidue]: + # regular expression to parse information from atom lines + atom_regex = ( + r"^ATOM +([A-Z0-9\'\+\-]{1,4}) +.* +(?:charge|CHARGE|CHARge) *= *" + r"([\-|+]?\d+.?\d*).*(?:END|end).*$" + ) + + # helper variables for the for-loop + atoms: list[str] = [] + charges: list[str] = [] + residues: list[CNSTopologyResidue] = [] + in_residue: bool = False + + # all lines are striped before looping + for line in map(str.strip, lines): # it is important to strip spaces + if line.startswith(('RESI', 'residue')): + in_residue = True # defines we start a new residue + + # extracts the resname from the residue line + resname = line.split()[1] + + # ensures there is no bug when changing residues + # before starting a new residue `atoms` and `charges` should be + # empty + if atoms or charges: + emsg = \ + "Starting a new residue without emptying the previous one." + raise ValueError(emsg) + + elif line.startswith('ATOM'): + aname, acharge = re.findall(atom_regex, line)[0] + atoms.append(aname) + charges.append(acharge) + + elif line.startswith(("end", "END")) and in_residue: + + # the total charge of the residue + total_charge = sum(map(float, charges)) + # need to be a copy to avoid unexpected referencing from the list + _atoms = copy(atoms) + + resi = CNSTopologyResidue(resname, total_charge, _atoms) + residues.append(resi) + + # clear help variables + charges.clear() + atoms.clear() + in_residue = False + + return residues + + +# what we will need to inspect if the residues are allowed or not are +# the residue names. So it is nice to have a function that retrieve them +# from the respective named tuples. +def get_resnames( + group: Iterable[CNSTopologyResidue]) -> dict[str, CNSTopologyResidue]: + """ + Make a set of residue names. + + Elements of the group must have a `resname` attribute. + + Parameters + ---------- + group : list of :py:class:`CNSTopologyResidue` + + Returns + ------- + dict + Dict of residue name and residue pairs. + """ + return {i.resname: i for i in group} + + +# this function is necessary because of the `self_contained` option +# where the topology files are not defined in the haddock3 code but in +# the run folder +def read_supported_residues( + source_path: FilePath) -> tuple[dict[str, CNSTopologyResidue], ...]: + """ + Read supported residues from a folder containing ``.top`` files. + + The function expects the ``source_path`` to have the required files. + + Expected files are: + + * ``carbohydrate.top`` + * ``dna-rna-CG-MARTINI-2-1p.top`` + * ``dna-rna-allatom-hj-opls-1.3.top`` + * ``fragment_probes.top`` + * ``hemes-allhdg.top`` + * ``ion.top`` + * ``protein-CG-Martini-2-2.top`` + * ``protein-CG-Martini.top`` + * ``protein-allhdg5-4.top`` + * ``solvent-allhdg5-4.top`` + * ``shape.top`` + * ``cofactors.top`` + + You need to edit this function to account for any additional + ``.top`` file that is added to the ``source_path`` on top of the + above ones. Otherwise, read the residues manually using + :py:func:`read_residues_from_top_file` and :py:func:`get_resnames` + and add them to the relevant set, or have them as a new set. + + Returns + ------- + tuple + A tuple of the residue names supported by HADDOCK3. + """ + # paths to the `.top` files + carbo_top = Path(source_path, "carbohydrate.top") + dna_rna_all_top = Path(source_path, "dna-rna-allatom-hj-opls-1.3.top") + dna_rna_martini_top = Path(source_path, "dna-rna-CG-MARTINI-2-1p.top") + fragment_top = Path(source_path, "fragment_probes.top") + hemes_top = Path(source_path, "hemes-allhdg.top") + ions_top = Path(source_path, "ion.top") + protein_5_4_top = Path(source_path, "protein-allhdg5-4.top") + protein_martini_2_top = Path(source_path, "protein-CG-Martini-2-2.top") + protein_martini_top = Path(source_path, "protein-CG-Martini.top") + solvent_top = Path(source_path, "solvent-allhdg5-4.top") + shape_top = Path(source_path, "shape.top") + cofactors_top = Path(source_path, "cofactors.top") + + # supported Residues (tuple of namedtuples) + supported_carbohydrates = read_residues_from_top_file(carbo_top) + + _1 = read_residues_from_top_file(dna_rna_all_top) + _2 = read_residues_from_top_file(dna_rna_martini_top) + supported_nucleic = set(it.chain(_1, _2)) + + supported_fragments = read_residues_from_top_file(fragment_top) + + supported_hemes = read_residues_from_top_file(hemes_top) + + # all ions are defined here + supported_ions = read_residues_from_top_file(ions_top) + + # separates both kinds of ions + supported_single_ions = \ + tuple(ion for ion in supported_ions if len(ion.atoms) == 1) + supported_multiatom_ions = \ + tuple(ion for ion in supported_ions if len(ion.atoms) > 1) + + _l0 = len(supported_ions) + _l1 = len(supported_single_ions) + _l2 = len(supported_multiatom_ions) + if _l0 != _l1 + _l2: + emsg = ( + "Ions were not parsed correctly. Some atoms were left out " + "when parsing single atom and multiatom ions." + ) + raise ValueError(emsg) + + _1 = read_residues_from_top_file(protein_5_4_top) + _2 = read_residues_from_top_file(protein_martini_2_top) + _3 = read_residues_from_top_file(protein_martini_top) + supported_aminoacids = set(it.chain(_1, _2, _3)) + + supported_solvents = read_residues_from_top_file(solvent_top) + supported_shape = read_residues_from_top_file(shape_top) + supported_cofactors = read_residues_from_top_file(cofactors_top) + + # supported resnames + supported_carbo_resnames = get_resnames(supported_carbohydrates) + supported_nucleic_resnames = get_resnames(supported_nucleic) + supported_fragments_resnames = get_resnames(supported_fragments) + supported_hemes_resnames = get_resnames(supported_hemes) + supported_single_ions_resnames = get_resnames(supported_single_ions) + supported_multiatom_ions_resnames = get_resnames(supported_multiatom_ions) + supported_aminoacids_resnames = get_resnames(supported_aminoacids) + supported_solvents_resnames = get_resnames(supported_solvents) + supported_shape_resnames = get_resnames(supported_shape) + supported_cofactors_resnames = get_resnames(supported_cofactors) + + # other attributes + for ion in supported_single_ions: + ion.elements = get_ion_element_from_atoms(ion.atoms) + + supported_ions_elements = \ + {ion.elements[0]: ion for ion in supported_single_ions} + + supported_ions_atoms = {ion.atoms[0]: ion for ion in supported_ions} + + return ( + supported_carbo_resnames, + supported_nucleic_resnames, + supported_fragments_resnames, + supported_hemes_resnames, + supported_single_ions_resnames, + supported_ions_elements, + supported_ions_atoms, + supported_multiatom_ions_resnames, + supported_aminoacids_resnames, + supported_solvents_resnames, + supported_shape_resnames, + supported_cofactors_resnames, + ) + + +# reads and assigns the supported molecules variables to this module +_supported_carbo_resnames, \ + _supported_nucleic_resnames, \ + _supported_fragments_resnames, \ + _supported_hemes_resnames, \ + _supported_single_ions_resnames, \ + _supported_single_ions_elements, \ + _supported_single_ions_atoms, \ + _supported_multiatom_ions_resnames, \ + _supported_aminoacids_resnames, \ + _supported_solvents_resnames, \ + _supported_shape_resnames, \ + _supported_cofactors_resnames = read_supported_residues(toppar_path) + +# render docstrings +supported_carbo_resnames = set(_supported_carbo_resnames) +"""Supported carbohydrate residues names.""" + +supported_nucleic_resnames = set(_supported_nucleic_resnames) +"""Supported nucleic acid residue names.""" + +supported_fragments_resnames = set(_supported_fragments_resnames) +"""Supported fragments residue names.""" + +supported_hemes_resnames = set(_supported_hemes_resnames) +"""Supported Hemes.""" + +supported_single_ions_resnames_map = _supported_single_ions_resnames +"""Supported single ion resname mapping.""" + +supported_single_ions_elements_map = _supported_single_ions_elements +"""Supported single ions elements mapping.""" + +supported_single_ions_atoms_map = _supported_single_ions_atoms +"""Supported single ion atom names mapping.""" + +supported_single_ions_resnames = set(_supported_single_ions_resnames) +"""Supported single residue names.""" + +supported_single_ions_elements = set(_supported_single_ions_elements) +"""Supported single ions elements.""" + +supported_single_ions_atoms = set(_supported_single_ions_atoms) +"""Supported single ion atom names.""" + +supported_multiatom_ions_resnames = set(_supported_multiatom_ions_resnames) +"""Supported multiatom ions residue names.""" + +supported_aminoacids_resnames = set(_supported_aminoacids_resnames) +"""Supported amino acids residue names.""" + +supported_solvents_resnames = set(_supported_solvents_resnames) +"""Supported solvents.""" + +supported_shape_resnames = set(_supported_shape_resnames) +"""Supported shape.""" + +supported_cofactors_resnames = set(_supported_cofactors_resnames) +"""Supported cofactors.""" + +# +# Residues that must be set as ATOM +supported_ATOM = set(it.chain( + supported_nucleic_resnames, + supported_aminoacids_resnames, + supported_shape_resnames, + )) +""" +Supported ``ATOM`` residues. + +These residues must be defined as ``ATOM`` records +in PDB files for HADDOCK3. +""" + +# non-ion residue names +supported_non_ions = set(it.chain( + supported_ATOM, + supported_carbo_resnames, + supported_fragments_resnames, + supported_hemes_resnames, + supported_solvents_resnames, + supported_shape_resnames, + supported_cofactors_resnames, + )) + +# Residues that must be set as HETATM +supported_HETATM = set(it.chain( + supported_carbo_resnames, + supported_fragments_resnames, + supported_hemes_resnames, + supported_single_ions_resnames, + supported_multiatom_ions_resnames, + supported_solvents_resnames, + supported_cofactors_resnames, + )) +""" +Supported ``HETATM`` residues. + +These residues must be defined as ``HETATM`` records +in PDB files for HADDOCK3. +""" + +supported_residues = supported_ATOM.union(supported_HETATM) +"""All HADDOCK3 supported residues.""" + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/core/typing.py b/.venv_haddock/lib/python3.12/site-packages/haddock/core/typing.py new file mode 100644 index 0000000000000000000000000000000000000000..73a523b0d2eff0c136a7e778134121a39f207a52 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/core/typing.py @@ -0,0 +1,197 @@ +""" +Useful type aliases and type variables for type-hints support. + +Visit [PEP 484 Type Hints](https://peps.python.org/pep-0484/) for more help. + +Variables endswith `T` are TypeVars for generic function signatures. +They are defined to + + - accept constraint types(Any type when no type is given) + - accept any subclass by using keyword `bound` + - be parameter of Generic and subclass of Generic, + espacially for invariant Collections(list,sequence and so on). + - show more than once in generic functions to indicates that + these types are exactly same. + +Don't import other classes, type aliases or type variables defined +in `haddock` into this module. +This may lead to circular import problem. +""" + + +from argparse import ArgumentParser, Namespace +from logging import FileHandler, Handler, StreamHandler +from pathlib import Path +from typing import ( + Any, + Callable, + Container, + Generator, + Generic, + Iterable, + Iterator, + Literal, + Mapping, + MutableMapping, + Optional, + Protocol, + Sequence, + Sized, + SupportsInt, + TextIO, + Type, + TypedDict, + TypeVar, + Union, + runtime_checkable, + ) + +from numpy import float64 +from numpy.typing import NDArray +from pandas import DataFrame +from pandas.core.groupby.generic import DataFrameGroupBy +from plotly.graph_objects import Figure + + +AnyT = TypeVar('AnyT') +"""Arbitrary type for generic function signatures.""" + +PT = TypeVar('PT') +""" +Arbitrary parameter type for generic `Callable` signatures. + +For py3.11+, `ParamSpec` and `Concatenate` may be more explict +while making signatures longer. +""" + +# Literals +ImgFormat = Literal["png", "pdf", "svg", "jpeg", "webp"] +"""Supported image formats by plotly.""" + +ExpertLevel = Literal["all", "easy", "expert", "guru"] +"""The expertise level of the parameters.`hidden` not inclued.""" + +LogLevel = Literal["INFO", "DEBUG", "ERROR", "WARNING", "CRITICAL"] + + +# Protocols +@runtime_checkable +class SupportsAdd(Protocol): + """ + An ABC with one abstract method __add__. + + Can be used in `isinstance` and `issubclass`. + + Assuming that the operands and the result's types + are same for most common situations. + + Examples + -------- + + >>> isinstance(int, SupportsAdd) + True + """ + + __slots__ = () + + def __add__(self: AnyT, other: AnyT, /) -> AnyT: + raise NotImplementedError() + + +SupportsAddT = TypeVar("SupportsAddT", bound=SupportsAdd) +"""TypeVar of SupportsAdd for Generic type check.""" + + +@runtime_checkable +class SupportsRun(Protocol): + """ + An ABC with one abstract method run(). + + Can be used in `isinstance` and `issubclass`. + + Examples + -------- + + >>> from multiprocessing import Process + >>> isinstance(Process, SupportsRun) + True + """ + + __slots__ = () + + def run(self) -> Any: + """Do something.""" + raise NotImplementedError() + + +SupportsRunT = TypeVar("SupportsRunT", bound=SupportsRun) +"""TypeVar of SupportsRun for Generic type check.""" + +# other type alias and type variables +NDFloat = NDArray[float64] + +FilePath = Union[str, Path] + +FilePathT = TypeVar("FilePathT", bound=FilePath) +""" +Generic type variable for file paths. + +If the first annotated variable is str, +the second annotated variable will be str instead of Path,vice versa. +""" + +LineIterSource = Union[Iterable[str], FilePath] +"""An Object who can generate lines in some way.""" + +ParamMap = MutableMapping[str, Any] +""" +A mutable mapping object contains parameters generated from config +files or functions. + +The keys are always `str`. +""" + +ParamMapT = TypeVar('ParamMapT', bound=ParamMap) +""" +Generic type of `MutableMapping[str, Any]` for generic function sigunature. +""" + +ParamDict = dict[str, Any] +""" +A dict contains parameters generated from config files or functions. + +The keys are always `str`. + +Can be called like `dict` and returns a python `dict`. + +Examples +-------- + +>>> ParamDict(a=1) == {'a':1} +True + +>>> ParamDict({'a':1}) == {'a':1} +True + +>>> ParamDict().setdefault('a', 1) +1 +""" + +ParamDictT = TypeVar('ParamDictT', bound=ParamDict) +""" +Generic type of `dict[str, Any]` for generic function sigunature. +""" + +ModuleParams = dict[str, ParamDict] +"""A dict contains modules' parameters.""" + +AtomsDict = dict[str, list[str]] +""" +A dict contains all kinds of residues' atom type infomations +(including non-standard residue and atom type). + +Key is residue name, value is a list of the residue's atom types. +""" + +StreamHandlerT = TypeVar('StreamHandlerT', + bound=Union[StreamHandler, FileHandler]) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._contact_fcc.cpp b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._contact_fcc.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._contact_fcc.cpp differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._fast-rmsdmatrix.c b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._fast-rmsdmatrix.c new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/._fast-rmsdmatrix.c differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/deps/contact_fcc.cpp b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/contact_fcc.cpp new file mode 100644 index 0000000000000000000000000000000000000000..50382d213db1f05511dfee1c6e3becd2ff4ae85b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/contact_fcc.cpp @@ -0,0 +1,124 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace std; + +struct Coor3f { + float x; + float y; + float z; +}; + +struct Residue { + int nr; + vector coor; + vector atom; + int seg; +}; + +vector res; + +bool seg_sorter (Residue res_a, Residue res_b) { + int segA = res_a.seg; + int segB = res_b.seg; + return (segA < segB); +}; + +int main(int argc, char *argv[]) { + char buf[2000]; + + if (argc < 3) { + fprintf(stderr,"ERROR: Too few arguments\n"); + fprintf(stderr, "Usage: contact \n"); + return 1; + } + + char *filename = argv[1]; + float cutoff = atof(argv[2]); + + if (cutoff < 0 || cutoff > 100) { + fprintf(stderr,"ERROR: Cutoff out of range\n"); + fprintf(stderr, "Usage: contact \n"); + return 1; + } + + FILE *fil = fopen(filename, "r"); + if (fil == NULL) { + fprintf(stderr, "ERROR: PDB file %s does not exist\n", filename); + return 1; + } + + int currnr = -99999; + char currseg; + int segid = 0; + + set nonconv; + while (!feof(fil)) { + char code[10]; + char atom[5]; + if (!fgets(buf, 2000, fil)) break; + sscanf(buf, "%s %*d %s", code, atom); + + // Ignore HETATM and hydrogens + if (!strncmp(code,"ATOM", 4) && ( atom[0] != 'H' && !( isdigit(atom[0]) && atom[1] == 'H' ) ) ) { + int nr = atoi(buf + 22); + char seg = buf[72]; + if (seg != currseg) { + currseg = seg; + segid++; + } + if (nr != currnr) { + Residue r; + r.nr = nr+10000; + r.seg = segid; + res.push_back(r); + currnr = r.nr; + } + Residue &rcurr = res[res.size() -1]; + Coor3f ccoor; + ccoor.x = atof(buf+27); + ccoor.y = atof(buf+38); + ccoor.z = atof(buf+46); + rcurr.coor.push_back(ccoor); + string atom2(atom); + rcurr.atom.push_back(atom2); + } + } + + if (!res.size()) {fprintf(stderr, "ERROR: PDB file %s contains no residues\n", filename); return 1;} + + // Sort the residues by segment to avoid random chain ordering problems + sort (res.begin(), res.end(), seg_sorter); + + double cutoffsq = cutoff * cutoff; + + for (int n = 0; n < res.size(); n++) { + vector &c1 = res[n].coor; + int seg1 = res[n].seg; + for (int nn = n + 1; nn < res.size(); nn++) { + int seg2 = res[nn].seg; + if (seg1 == seg2) continue; + vector &c2 = res[nn].coor; + for (int i = 0; i < res[n].coor.size(); i++) { + for (int ii = 0; ii < res[nn].coor.size(); ii++) { + double currdissq = + (c1[i].x - c2[ii].x) * (c1[i].x - c2[ii].x) + + (c1[i].y - c2[ii].y) * (c1[i].y - c2[ii].y) + + (c1[i].z - c2[ii].z) * (c1[i].z - c2[ii].z); + if (currdissq < cutoffsq) { + printf ("%d%d%d%d\n", res[n].nr, res[n].seg, res[nn].nr, res[nn].seg); + } + } + } + } + } + fclose(fil); +} diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/deps/fast-rmsdmatrix.c b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/fast-rmsdmatrix.c new file mode 100644 index 0000000000000000000000000000000000000000..d352bbabc311ea6ad0fadbd5187f0dda91ca1cf0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/deps/fast-rmsdmatrix.c @@ -0,0 +1,883 @@ +#define _GNU_SOURCE +#include +#include +#include +#include +#include +#include +#include +#include +#include + +typedef struct traj{ + int frames; /*!< number of frames in the trajectory */ + double **traj_coords; /*!< 2D array of xyz coordinates */ + int n_at; /*!< number of atoms in the atomistic structure */ + int pairs; /*!< number of possible pairs of structures */ +}traj; + +typedef struct alignments{ + double *rmsd_mat; /*!< condensed pairwise RMSD matrix */ + double **coms; /*!< array of centers of mass */ + int *ref_structs; /*!< array of reference structures */ + int *mod_structs; /*!< array of model structures */ +}alignments; + +void failed(char message[]) { + printf("\n FAILED *** %s ***\n \n", message); + exit(1); +} + +struct arguments; + +void zero_vec_d(double *a, int dim) { + + int i; + for (i = 0; i < dim; i++) { + a[i] = 0; + } +} + +int *i1t(int n1) { + int *p, *a; + int i; + if ((p = (int *) malloc((size_t) n1 * sizeof(int))) == NULL) + failed("i1t: failed"); + for (i = 0, a = p; i < n1; i++) + *a++ = 0; + return p; +} + +double *d1t(int n1) { + double *p, *a; + int i; + if ((p = (double *) malloc((size_t) n1 * sizeof(double))) == NULL) + failed("d1t: failed n1 "); + for (i = 0, a = p; i < n1; i++) + *a++ = 0; + return p; +} + +double **d2t(int n1, int n2) { + double **p, *a; + int i; + if ((p = (double **) malloc((size_t) n1 * sizeof(double *))) == NULL) + failed("d2t: failed n1"); + if ((p[0] = (double *) malloc((size_t) n1 * n2 * sizeof(double))) == NULL) + failed("d2t: failed n2"); + for (i = 0; i < n1 - 1; i++) + p[i + 1] = p[i] + n2; + for (i = 0, a = p[0]; i < n1 * n2; i++) + *a++ = 0; + return p; +} + +void free_d2t(double **p) { + + free(p[0]); + free(p); +} + +void free_d1t(double *p) { + + free(p); +} + +double scal_d(double *a, double *b, int dim) { + + int i; + double temp; + + temp = 0.0; + for (i = 0; i < dim; i++) { + temp += a[i] * b[i]; + } + return (temp); +} + +double norm_d(double *a, int dim) { + + return (sqrt(scal_d(a, a, dim))); +} + +void normalize_d(double *a, int dim) { + int i; + double temp; + + temp = norm_d(a, dim); + for (i = 0; i < dim; i++) { + a[i] = a[i] / temp; + } +} + +void vecprod_d(double *a, double *b, double *c) { + + c[0] = a[1] * b[2] - a[2] * b[1]; + c[1] = a[2] * b[0] - a[0] * b[2]; + c[2] = a[0] * b[1] - a[1] * b[0]; +} + +void myjacobi(double a[][3], int n, double *d, double v[][3], int *nrot) { + + int j, iq, ip, i; + double tresh, theta, tau, t, sm, s, h, g, c; + double b[3], z[3]; + +#define ROTATE(a, i, j, k, l) g=a[i][j];h=a[k][l];a[i][j]=g-s*(h+g*tau);a[k][l]=h+s*(g-h*tau); + + for (ip = 0; ip <= (n - 1); ip++) { + for (iq = 0; iq <= (n - 1); iq++) + v[ip][iq] = 0.0; + v[ip][ip] = 1.0; + } + for (ip = 0; ip <= (n - 1); ip++) { + b[ip] = d[ip] = a[ip][ip]; + z[ip] = 0.0; + } + *nrot = 0; + for (i = 1; i <= 500; i++) { + sm = 0.0; + for (ip = 0; ip <= n - 2; ip++) { + for (iq = ip + 1; iq <= (n - 1); iq++) + sm += fabs(a[ip][iq]); + } + if (sm == 0.0) { + return; + } + if (i < 4) + tresh = 0.2 * sm / (n * n); + else + tresh = 0.0; + for (ip = 0; ip <= n - 2; ip++) { + for (iq = ip + 1; iq <= (n - 1); iq++) { + g = 100.0 * fabs(a[ip][iq]); + if (i > 4 && (fabs((fabs(d[ip]) + g) - fabs(d[ip])) < 1.0e-6) + && (fabs((fabs(d[iq]) + g) - fabs(d[iq])) < 1.0e-6)) + a[ip][iq] = 0.0; + else if (fabs(a[ip][iq]) > tresh) { + h = d[iq] - d[ip]; + if (fabs((fabs(h) + g) - fabs(h)) < 1.0e-6) + t = (a[ip][iq]) / h; + else { + theta = 0.5 * h / (a[ip][iq]); + t = 1.0 / (fabs(theta) + sqrt(1.0 + theta * theta)); + if (theta < 0.0) + t = -t; + } + c = 1.0 / sqrt(1 + t * t); + s = t * c; + tau = s / (1.0 + c); + h = t * a[ip][iq]; + z[ip] -= h; + z[iq] += h; + d[ip] -= h; + d[iq] += h; + a[ip][iq] = 0.0; + for (j = 0; j <= ip - 1; j++) { + ROTATE (a, j, ip, j, iq) + } + for (j = ip + 1; j <= iq - 1; j++) { + ROTATE (a, ip, j, j, iq) + } + for (j = iq + 1; j <= (n - 1); j++) { + ROTATE (a, ip, j, iq, j) + } + for (j = 0; j <= (n - 1); j++) { + ROTATE (v, j, ip, j, iq) + } + ++(*nrot); + } + } + } + for (ip = 0; ip <= (n - 1); ip++) { + b[ip] += z[ip]; + d[ip] = b[ip]; + z[ip] = 0.0; + } + } + printf("Too many iterations in routine JACOBI %lf\n", sm); + /* exit (1); */ +#undef ROTATE +} + +int columns(char* string){ + /** + * routine that returns the number of columns for each row inside the file chosen. + * + * Parameter + * ---------- + * + * `string` : string token in account + */ + + int counter = 0; + + while(string){ + counter++; + string = strtok(NULL, " \t\v\r\n"); + } + return counter; +} + +int n_rows (FILE *f){ + /** + * routine that returns the number of rows in a file. It counts correctly this number even if the last row does not present \n + * + * Parameter + * ---------- + * + * `f` : FILE structure that represents the file opened. + */ + + size_t rows_i = 0, n = 0; + char *buf = NULL; + + fseek(f, 0, SEEK_SET); + + while(getline(&buf, &n, f) != -1) rows_i++; + + free(buf); + + return rows_i; +} + +int get_pair(int nmodels, int idx, int ij_arr[2]){ + if (nmodels < 0 || idx < 0){ + printf("get_pair cannot accept negative numbers"); + printf("Input is %d , %d", nmodels, idx); + exit(EXIT_FAILURE); + } + // solve the second degree equation + int b = 1 - (2 * nmodels); + int i = (-b - sqrt(b * b - 8 * idx)) / 2; + int j = idx + i * (b + i + 2) / 2 + 1; + ij_arr[0] = i; + ij_arr[1] = j; + return 0; +} + +double optimal_alignment(double **x, double **y, int cgnum, double u[][3]) { + /** + * routine that computes the Kabsch alignment and the rmsd between two configurations + * + * + * Parameters + * ---------- + * + * `x`, `y` : CG structures + * + * `cgnum` : length of CG mapping + * + * `u` : rotation matrix + */ + void myjacobi(double a[][3], int n, double *d, double v[][3], int *nrot); + int i, j, k, sign[3], order[3], nrot; + double e, e0; + double r[3][3], rt[3][3], temp; //, **x, **y; + double a[3][3], eval[3], evec[3][3]; + double eigenvalues[3], eigenvectors[3][3], b[3][3]; + int speak = 1; + + e0 = 0.0; + for (i = 0; i < cgnum; i++) { + e0 += 0.5 * norm_d(x[i], 3) * norm_d(x[i], 3); + e0 += 0.5 * norm_d(y[i], 3) * norm_d(y[i], 3); + } + + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + r[i][j] = 0.0; + for (k = 0; k < cgnum; k++) { + r[i][j] += y[k][i] * x[k][j]; + } + rt[j][i] = r[i][j]; + } + } + + if (isnan(e0) == 1) printf("Found a NaN in Kabsch alignment at checkpoint 1\n"); + + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + a[i][j] = 0; + for (k = 0; k < 3; k++) { + a[i][j] += rt[i][k] * r[k][j]; + } + } + } + + myjacobi(a, 3, eval, evec, &nrot); + /* we add small quantities in order to remove potentially dangerous degeneracies */ + if (isnan(eval[0]) == 1) printf("Found a NaN in Kabsch alignment at checkpoint 2\n"); + if (isnan(eval[1]) == 1) printf("Found a NaN in Kabsch alignment at checkpoint 3\n"); + if (isnan(eval[2]) == 1) printf("Found a NaN in Kabsch alignment at checkpoint 4\n"); + + eval[0] += 0.0000000000000001; + eval[1] += 0.00000000000000001; + eval[2] += 0.00000000000000002; + + if ((eval[0] < eval[1]) && (eval[0] < eval[2])) { + order[0] = 1; + order[1] = 2; + order[2] = 0; + } + + if ((eval[1] < eval[0]) && (eval[1] < eval[2])) { + order[0] = 0; + order[1] = 2; + order[2] = 1; + } + + if ((eval[2] < eval[0]) && (eval[2] < eval[1])) { + order[0] = 0; + order[1] = 1; + order[2] = 2; + } + + for (i = 0; i < 3; i++) { + eigenvalues[i] = eval[order[i]]; + for (j = 0; j < 3; j++) { + eigenvectors[i][j] = evec[j][order[i]]; + } + } + + normalize_d(eigenvectors[0], 3); + normalize_d(eigenvectors[1], 3); + vecprod_d(eigenvectors[0], eigenvectors[1], eigenvectors[2]); + normalize_d(eigenvectors[2], 3); + + for (i = 0; i < 2; i++) { + for (j = 0; j < 3; j++) { + b[i][j] = 0; + for (k = 0; k < 3; k++) { + b[i][j] += r[j][k] * eigenvectors[i][k]; + } + } + normalize_d(b[i], 3); + } + + vecprod_d(b[0], b[1], b[2]); + normalize_d(b[2], 3); + + temp = 0.0; + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + temp += b[2][i] * r[i][j] * eigenvectors[2][j]; + } + } + sign[2] = +1; + if (temp < 0) + sign[2] = -1; + sign[0] = sign[1] = 1; + + if (fabs(eigenvalues[2]) < 0.0000001) { + e = e0 - sqrt(eigenvalues[0]) - sqrt(eigenvalues[1]); + } else { + e = e0 - sqrt(eigenvalues[0]) - sqrt(eigenvalues[1]) - sign[2] * sqrt(eigenvalues[2]); + } + + if (isnan(e) == 1) { + printf("Found a NaN in Kabsch alignment at checkpoint 5 | \n"); + printf("e %lf e0 %lf e1 %lf e2 %lf e3 %lf\n", e, e0, eigenvalues[0], eigenvalues[1], eigenvalues[2]); + } +/********************/ + e = 2.0 * e / cgnum; + if (e < 0.0) { + if (fabs(e) < 1.0e-3) { + if (speak == 1) { + //printf("Warning. In Kabsch alignment found slightly negative value of e (%e). Identical structures? Setting it to 0.000001.\n", + // e); + e = 0.000001; + } + } + /* occasionally, when dealing with two practically identical configurations + the value of e may be slightly negative due to the small offsets and roundoff errors. + In this case we set it equal to zero. */ + else { + FILE *fe; + fe = fopen("error.dat", "w"); + fprintf(fe, "Error. In Kabsch alignment found negative value of e: (%lf)\n", e); + printf("Error. In Kabsch alignment found negative value of e: (%lf)\n", e); + fclose(fe); + exit(EXIT_FAILURE); + } + } + e = sqrt(e); + if (isnan(e) == 1) printf("Found a NaN in Kabsch alignment at checkpoint 6\n"); +/********************/ + // filling rotation_matrix + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + u[i][j] = 0.0; + for (k = 0; k < 3; k++) { + u[i][j] += b[k][i] * eigenvectors[k][j]; + } + } + } + return (e); +} + +void cycle_ilrmsd(traj *Trajectory, traj *Ligand_Trajectory, alignments *align, int start_pair[2]) { + /** + * routine that cycles over pairs of frames in a trajectory, aligning on the receptor + * and computing the interface ligand rmsd + * + * Parameters + * ---------- + * + * `Trajectory` : traj object + * + * `align` : alignments object + * + * `start_pair` : pair of structures to begin with + */ + int n; + int i, j; + double **x, **y, **xlig, **ylig, **ylig_rot; + double u[3][3], cm1[3], cm2[3]; + int rot_idx; + // allocating vectors + x = d2t(Trajectory->n_at, 3); + xlig = d2t(Ligand_Trajectory->n_at, 3); + y = d2t(Trajectory->n_at, 3); + ylig = d2t(Ligand_Trajectory->n_at, 3); + ylig_rot = d2t(Ligand_Trajectory->n_at, 3); + int ref = start_pair[0]; + int mod = start_pair[1]; + int old_ref = ref - 1; + + for (n = 0; n < Trajectory->pairs; n++) { + if (ref != old_ref) { + // recalculate com and translate structure + zero_vec_d(cm1, 3); + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + cm1[j] += Trajectory->traj_coords[ref][i * 3 + j] / Trajectory->n_at; + } + } + // filling structure + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + x[i][j] = Trajectory->traj_coords[ref][i * 3 + j] - cm1[j]; + } + } + // now the ligand + for (i = 0; i < Ligand_Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + xlig[i][j] = Ligand_Trajectory->traj_coords[ref][i * 3 + j] - cm1[j]; + } + } + old_ref += 1; + } + + // second structure + zero_vec_d(cm2, 3); + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + cm2[j] += Trajectory->traj_coords[mod][i * 3 + j] / Trajectory->n_at; + } + } + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + y[i][j] = Trajectory->traj_coords[mod][i * 3 + j] - cm2[j]; + } + } + // now ylig + for (i = 0; i < Ligand_Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + ylig[i][j] = Ligand_Trajectory->traj_coords[mod][i * 3 + j] - cm2[j]; + } + } + + // Alignment AND RMSD computation + align->rmsd_mat[n] = optimal_alignment(x, y, Trajectory->n_at, u); + align->ref_structs[n] = ref + 1; + align->mod_structs[n] = mod + 1; + + // now correcting the coordinates of the ligand + for (i = 0; i < Ligand_Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + ylig_rot[i][j] = 0.0; + for (rot_idx = 0; rot_idx < 3; rot_idx++) { + ylig_rot[i][j] += u[rot_idx][j] * ylig[i][rot_idx]; + } + } + } + // calculate rmsd between ligands + double ilrmsd = 0.0; + double delta; + for (i = 0; i < Ligand_Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + delta = ylig_rot[i][j] - xlig[i][j]; + ilrmsd += delta * delta; + } + } + + ilrmsd = sqrt(ilrmsd / Ligand_Trajectory->n_at); + // the value before was the receptor interface rmsd, now let's change it to the ligand interface rmsd + align->rmsd_mat[n] = ilrmsd; + + // update idx + if (mod == Trajectory->frames - 1) { + ref += 1; + mod = ref + 1; + } + else { + mod += 1; + } + + } + free_d2t(x); + free_d2t(y); + free_d2t(xlig); + free_d2t(ylig); + free_d2t(ylig_rot); +} + +void cycle_rmsd(traj *Trajectory, alignments *align, int start_pair[2]) { + /** + * routine that cycles over all pairs of frames in a trajectory, calling `optimal_alignment` + * + * Parameters + * ---------- + * + * `Trajectory` : traj object + * + * `align` : alignments object + * + * `start_pair` : pair of structures to begin with + */ + int n; + int i, j; + double **x, **y; + double u[3][3], cm1[3], cm2[3]; + printf("calculating rotation matrices..\n"); + // allocating vectors + x = d2t(Trajectory->n_at, 3); + y = d2t(Trajectory->n_at, 3); + int ref = start_pair[0]; + int mod = start_pair[1]; + int old_ref = ref - 1; + //for (n = 0; n < Trajectory->frames; n++) { + for (n = 0; n < Trajectory->pairs; n++) { + if (ref != old_ref) { + // recalculate com and translate structure + + zero_vec_d(cm1, 3); + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + cm1[j] += Trajectory->traj_coords[ref][i * 3 + j] / Trajectory->n_at; + } + } + // filling structure + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + x[i][j] = Trajectory->traj_coords[ref][i * 3 + j] - cm1[j]; + } + } + old_ref += 1; + } + // second structure + zero_vec_d(cm2, 3); + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + cm2[j] += Trajectory->traj_coords[mod][i * 3 + j] / Trajectory->n_at; + } + } + for (i = 0; i < Trajectory->n_at; i++) { + for (j = 0; j < 3; j++) { + y[i][j] = Trajectory->traj_coords[mod][i * 3 + j] - cm2[j]; + } + } + // Alignment AND RMSD computation + align->rmsd_mat[n] = optimal_alignment(x, y, Trajectory->n_at, u); + align->ref_structs[n] = ref + 1; + align->mod_structs[n] = mod + 1; + + // update idx + if (mod == Trajectory->frames - 1) { + ref += 1; + mod = ref + 1; + } + else { + mod += 1; + } + + } + free_d2t(x); + free_d2t(y); +} + +void read_TrajectoryFile(char *TrajFileName, traj *Trajectory){ + /** + * routine that reads the input xyz coordinate file + * + * Parameters + * ---------- + * + * `TrajFileName` : trajectory filename + * + * `Trajectory` : traj object + */ + + FILE *ft; // trajectory file; + FILE *fe; // declaring error file; + + int rows_i, cols_i, i, p, frame_idx, j, count; + size_t line_buf_size = 0; + + char *token; + char *token_arr[100]; //*string, *line; + char *string = NULL; + char *line; + + /* Opening and check if it exist and if it is empty */ + ft = fopen(TrajFileName, "r"); + printf("Reading Trajectory FILE %s\n", TrajFileName); + + //check_empty_file(ft, TrajFileName); + + rows_i = n_rows(ft); // Number of rows in trajectory file "ft". + fseek(ft, 0, SEEK_SET); + + line = (char *) malloc (200); // Allocate char line with size (lenght) = 200; + // We are sure that the lenght of each line is less than 200 + + /* Initialize the 2D-array Trajectory->traj_coords[][] */ + for(i = 0; i < Trajectory->frames; i++){ + for(j = 0; j < Trajectory->n_at; j++){ + Trajectory->traj_coords[i][3 * j + 0] = 0.0; + Trajectory->traj_coords[i][3 * j + 1] = 0.0; + Trajectory->traj_coords[i][3 * j + 2] = 0.0; + } + } + + /* Checking for empty rows; + * Checking that there are ONLY rows with one column and three columns + * Checking that the rows with one column correspond to an integer number i.e. the number of atoms; + * Checking that the rows with three columns are float corresponding to x,y,z trajectory coordinate. */ + + frame_idx = 0; // Initialize frame index to 0 + p = 0; // Initialize counter "p" to 0 + + for(i=0; i=3*Trajectory->n_at) // p increases from 0 to 3*atomnum i.e. p=[0;3*230) i.e. p = [0;689] + p = 0; + + getline(&string, &line_buf_size, ft); // Reading entire line; + + strcpy(line, string); // Copying "string" in "line"; we need it in case of three columns. + + //if( i != (Trajectory->n_at + 2)*(frame_idx-1) + 1) // Checking for empty rows except for the 2nd row of each frame representing the title + // check_empty_rows(string); // that could also be an empty string + + token = strtok(string, " \t\v\r\n"); // Splitting the string-line in columns separated by spaces, tabs, or \n or \v or \r + + cols_i = columns(token); // Counting the number of columns in each row of file. + + + if(i!=(Trajectory->n_at + 2)*(frame_idx-1) + 1){ // exclude the 2nd row of each frame + + if(cols_i == 1){ + + if(i != (Trajectory->n_at + 2)*frame_idx) { + printf("Error. The %dth frame contains a different number of rows. Each frame must have %d rows\n", frame_idx+1, Trajectory->n_at + 2); + exit(EXIT_FAILURE); + } + else{ + frame_idx++; + if(frame_idx>Trajectory->frames){ + fe = fopen("error.dat", "w"); + fprintf(fe, "Error. The number of trajectory frames is higher than the declared one in parameter file (%d).\nAborting\n", Trajectory->frames); + fclose(fe); + printf("Error. The number of trajectory frames is higher than the declared one in parameter file (%d).\nAborting\n", Trajectory->frames); + exit(EXIT_FAILURE); + } + //check_int_string(string, i, TrajFileName); // Checking that each row is an INTEGER number. + if(atoi(string) != Trajectory->n_at){ + fe = fopen("error.dat","w"); + fprintf(fe,"Error. The number of atoms at %dth row has length (%d) different from atomnum(%d). Aborting\n",\ + i+1,atoi(string),Trajectory->n_at); + printf("Error. The number of atoms at %dth row has length (%d) different from atomnum(%d). Aborting\n",\ + i+1,atoi(string),Trajectory->n_at); + fclose(fe); + exit(EXIT_FAILURE); + } + } + } + + if(cols_i == 2){ + + if(i != (Trajectory->n_at + 2)*frame_idx + 1){ + fe = fopen("error.dat", "w"); + fprintf(fe,"Error. Each row must not contain 2 columns (except the title in the 2nd row of each frame that can contain N columns).\n\ + ONLY 1 or 4 columns are allowed in Trajectory (%dth row has 2 columns)\n", i+1); + + printf("Error. Each row must not contain 2 columns (except the title in the 2nd row of each frame that can contain N columns)\n\ + ONLY 1 or 4 columns are allowed in Trajectory (%dth row has 2 columns.\n", i+1); + fclose(fe); + exit(EXIT_FAILURE); + } + } + + if(cols_i == 3){ + + if(i != (Trajectory->n_at + 2)*frame_idx + 1){ + fe = fopen("error.dat", "w"); + fprintf(fe,"Error. Each row must not contain 3 columns (except the title in the 2nd row of each frame that can contain N columns). \ + ONLY 1 or 4 columns are allowed in Trajectory (%dth row has 3 columns)\n", i+1); + + printf("Error. Each row must not contain 3 columns (except the title in the 2nd row of each frame that can contain N columns) \ + ONLY 1 or 4 columns are allowed in Trajectory (%dth row has 3 columns.\n", i+1); + fclose(fe); + exit(EXIT_FAILURE); + } + } + + if(cols_i == 4){ + if(i != (Trajectory->n_at + 2)*frame_idx){ + token_arr[0] = strtok(line, " \t\v\r\n"); + + count = 0; + while(token_arr[count]){ + count++; + token_arr[count] = strtok(NULL, " \t\v\r\n"); + } + + for (j=1; j <= count-1 ; j++){ + //check_float_string(token_arr[j], i, TrajFileName); // Checking that each row is an FLOAT number. + Trajectory->traj_coords[frame_idx-1][p] = atof(token_arr[j]); // Assigning each float-string to traj_coords[i][j] 2D-array + p++; + } + + } + + else{ + printf("Error. Each row of the frame (except the 1st row containing the number of atoms and the 2nd row containing the title),\n\ + must contain 4 columns corresponding to at_name, x, y, and z coodinates. Check also if there is one extra row in %dth frame\n", + frame_idx); + exit(EXIT_FAILURE); + } + } + + if(cols_i > 4 ){ + if(i != (Trajectory->n_at + 2)*frame_idx){ + fe = fopen("error.dat","w"); + fprintf(fe, "Error. The maximum number of columns allowed is 4. The %dth row of your file contains %d columns\n", i+1, cols_i); + printf("Error. The maximum number of columns allowed is 4. The %dth row of your file contains %d columns\n", i+1, cols_i); + fclose(fe); + exit(EXIT_FAILURE); + } + } + } + + } // END FOR LOOP + + free(string); + //free(token); + free(line); + fclose(ft);// Close trajectory file. + // 1st check: frame_idx must be = frames + if (frame_idx != Trajectory->frames) { + fe = fopen("error.dat", "w"); + fprintf(fe, "Error. Frames completed: %d, while declared frames in parameter file are %d. Trajectory incomplete.\nAborting\n",frame_idx,\ + Trajectory->frames); + fclose(fe); + printf("Error. Frames completed: %d, while declared frames in parameter file are %d. Trajectory incomplete.\nAborting\n",frame_idx,\ + Trajectory->frames); + exit(EXIT_FAILURE); + } + + // final check: frame_idx corresponds with what we expect but the number of row is not the same => It means that + // the frame completed are frame_idx - 1 + else{ + if(rows_i != (Trajectory->n_at + 2)*Trajectory->frames){ + fe = fopen("error.dat", "w"); + fprintf(fe,"Error. Total number of rows: %d, while expected number of rows are %d. Trajectory incomplete.\nAborting\n",rows_i,\ + (Trajectory->n_at + 2)*Trajectory->frames); + fclose(fe); + printf("Error. Total number of rows: %d, while expected number of rows are %d. Trajectory incomplete.\nAborting\n", rows_i,\ + (Trajectory->n_at + 2)*Trajectory->frames); + exit(EXIT_FAILURE); + } + } +} + + +int main(int argc, char *argv[]) { + /** + * main file of the program + */ + time_t seconds; + time_t seconds_ref = time(NULL); + printf("Starting program at %s\n", ctime(&seconds_ref)); + + printf("input trajectory %s\n", argv[1]); + printf("core index is %s\n", argv[2]); + printf("number of pairs is %s\n", argv[3]); + printf("starting pair is %s-%s\n", argv[4], argv[5]); + traj *Trajectory = malloc (sizeof(traj)); + + int npairs = atoi(argv[3]); + int start_pair[2]; + start_pair[0] = atoi(argv[4]); + start_pair[1] = atoi(argv[5]); + + int rec_frames = atoi(argv[6]); + int rec_atomnum = atoi(argv[7]); + + Trajectory->frames = rec_frames; + Trajectory->n_at = rec_atomnum; + Trajectory->traj_coords = d2t(rec_frames, 3 * rec_atomnum); + Trajectory->pairs = npairs; + + printf("frames = %d\n", Trajectory->frames); + printf("overall pairs = %d\n", Trajectory->pairs); + + // read trajectory + read_TrajectoryFile(argv[1], Trajectory); + alignments *align = malloc (sizeof(alignments)); + align->rmsd_mat = d1t(Trajectory->pairs); + align->ref_structs = i1t(Trajectory->pairs); + align->mod_structs = i1t(Trajectory->pairs); + align->coms = d2t(rec_frames, 3); + + char out_filename[100]; + if (argc == 10){ + // if there are arguments 8 to 10, it is the ligand trajectory, frames and atomnum + traj *Ligand_Trajectory = malloc (sizeof(traj)); + printf("loading ligand data\n"); + + int ligand_atomnum = atoi(argv[9]); + Ligand_Trajectory->frames = rec_frames; + Ligand_Trajectory->n_at = ligand_atomnum; + Ligand_Trajectory->traj_coords = d2t(rec_frames, 3 * ligand_atomnum); + read_TrajectoryFile(argv[8], Ligand_Trajectory); + cycle_ilrmsd(Trajectory, Ligand_Trajectory, align, start_pair); + sprintf(out_filename, "ilrmsd_%s.matrix", argv[2]); + } + else{ + cycle_rmsd(Trajectory, align, start_pair); + sprintf(out_filename, "rmsd_%s.matrix", argv[2]); + } + // write the rmsd matrix + int i; + // check if file exists + if (access(out_filename, F_OK) != -1){ + printf("Warning: file %s already exists.\n", out_filename); + } + // write to file + FILE *frmsd; + frmsd = fopen(out_filename, "w"); + for (i = 0; i < Trajectory->pairs; i++){ + fprintf(frmsd, "%d %d %.3lf\n",align->ref_structs[i],align->mod_structs[i],align->rmsd_mat[i]); + } + + seconds = time(NULL); + printf("\nOverall execution time: %ld seconds\n", seconds-seconds_ref); + free_d2t(align->coms); + free_d1t(align->rmsd_mat); + free(align); + free_d2t(Trajectory->traj_coords); + free(Trajectory); + return 0; +} diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._calc_fcc_matrix.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._calc_fcc_matrix.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._calc_fcc_matrix.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._cluster_fcc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._cluster_fcc.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/._cluster_fcc.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/calc_fcc_matrix.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/calc_fcc_matrix.py new file mode 100644 index 0000000000000000000000000000000000000000..c1e7e2749725e9157677f13f2693e8ae89b9dc49 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/calc_fcc_matrix.py @@ -0,0 +1,96 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 -*- + +""" +Calculates a matrix of fraction of common contacts between two or more structures. + +Authors: + RODRIGUES Joao + TRELLET Mikael + MELQUIOND Adrien +""" + + +# Contact Parsing routines +def parse_contact_file(f_list, ignore_chain): + """Parses a list of contact files.""" + + if ignore_chain: + contacts = [ + [int(l[0:5] + l[6:-1]) for l in open(f)] for f in f_list if f.strip() + ] + else: + contacts = [set([int(l) for l in open(f)]) for f in f_list if f.strip()] + + return contacts + + +# FCC Calculation Routine +def calculate_fcc(listA, listB): + """ + Calculates the fraction of common elements between two lists + taking into account chain IDs + """ + + cc = len(listA.intersection(listB)) + cc_v = len(listB.intersection(listA)) + + return (cc, cc_v) + + +def calculate_fcc_nc(listA, listB): + """ + Calculates the fraction of common elements between two lists + not taking into account chain IDs. Much Slower. + """ + + largest, smallest = sorted([listA, listB], key=len) + ncommon = len([ele for ele in largest if ele in smallest]) + return (ncommon, ncommon) + + +# Matrix Calculation + + +def calculate_pairwise_matrix(contacts, ignore_chain): + """Calculates a matrix of pairwise fraction of common contacts (FCC). + Outputs numeric indexes. + + contacts: list_of_unique_pairs_of_residues [set/list] + + Returns pairwise matrix as an iterator, each entry in the form: + FCC(cplx_1/cplx_2) FCC(cplx_2/cplx_1) + """ + + contact_lengths = [] + for c in contacts: + try: + ic = 1.0 / len(c) + except ZeroDivisionError: + ic = 0 + contact_lengths.append(ic) + + if ignore_chain: + calc_fcc = calculate_fcc_nc + else: + calc_fcc = calculate_fcc + + for i in range(len(contacts)): + + for k in range(i + 1, len(contacts)): + cc, cc_v = calc_fcc(contacts[i], contacts[k]) + fcc, fcc_v = cc * contact_lengths[i], cc * contact_lengths[k] + yield (i + 1, k + 1, fcc, fcc_v) + + +def _output_fcc(output, values, f_buffer): + + buf = [] + for i in values: + buf.append(i) + if len(buf) == f_buffer: + output( + "".join(["%s %s %1.3f %1.3f\n" % (i[0], i[1], i[2], i[3]) for i in buf]) + ) + buf = [] + output("".join(["%s %s %1.3f %1.3f\n" % (i[0], i[1], i[2], i[3]) for i in buf])) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/cluster_fcc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/cluster_fcc.py new file mode 100644 index 0000000000000000000000000000000000000000..a5fc5e36527443709a00ace5b5c0e87e3914a6e5 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/fcc/cluster_fcc.py @@ -0,0 +1,187 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 -*- + +""" +Asymmetric Taylor-Butina Disjoint Clustering Algorithm. + +Authors: + RODRIGUES Joao + TRELLET Mikael + MELQUIOND Adrien +""" + + +class Element(object): + """Defines a 'clusterable' Element""" + + __slots__ = ["name", "cluster", "neighbors"] + + def __init__(self, name): + self.name = name + self.cluster = 0 + self.neighbors = set() + + def add_neighbor(self, neighbor): + """Adds another element to the neighbor list""" + self.neighbors.add(neighbor) + + def assign_cluster(self, clust_id): + """Assigns the Element to Cluster. 0 if unclustered""" + self.cluster = clust_id + + +class Cluster(object): + """Defines a Cluster. A Cluster is created with a name and a center (Element class)""" + + __slots__ = ["name", "center", "members"] + + def __init__(self, name, center): + + self.name = name + self.center = center + + self.members = [] + + self.populate() + + def __len__(self): + return len(self.members) + 1 # +1 Center + + def populate(self): + """ + Populates the Cluster member list through the + neighbor list of its center. + """ + + name = self.name + # Assign center + ctr = self.center + ctr.assign_cluster(name) + + mlist = self.members + # Assign members + ctr_nlist = (n for n in ctr.neighbors if not n.cluster) + for e in ctr_nlist: + mlist.append(e) + e.assign_cluster(name) + + def add_member(self, element): + """ + Adds one single element to the cluster. + """ + l = self.members + l.append(element) + element.assign_cluster(self.name) + + +def read_matrix(path, cutoff, strictness): + """ + Reads in a four column matrix (1 2 0.123 0.456\n) + and creates an dictionary of Elements. + + The strictness factor is a that multiplies by the cutoff + to produce a new cutoff for the second half of the matrix. Used to + allow some variability while keeping very small interfaces from clustering + with anything remotely similar. + """ + + cutoff = float(cutoff) + partner_cutoff = float(cutoff) * float(strictness) + + elements = {} + + f = open(path, "r") + for line in f: + ref, mobi, dRM, dMR = line.split() + ref = int(ref) + mobi = int(mobi) + dRM = float(dRM) + dMR = float(dMR) + + # Create or Retrieve Elements + if ref not in elements: + r = Element(ref) + elements[ref] = r + else: + r = elements[ref] + + if mobi not in elements: + m = Element(mobi) + elements[mobi] = m + else: + m = elements[mobi] + + # Assign neighbors + if dRM >= cutoff and dMR >= partner_cutoff: + r.add_neighbor(m) + if dMR >= cutoff and dRM >= partner_cutoff: + m.add_neighbor(r) + + f.close() + + return elements + + +def remove_true_singletons(element_pool): + """Removes from the pool elements without any neighbor""" + + ep = element_pool + + ts = set([e for e in ep if not ep[e].neighbors]) + + # Remove ts from everybody's neighbor list + ts_e = set(ep[e] for e in ts) + for e in element_pool: + ep[e].neighbors = ep[e].neighbors.difference(ts_e) + + # Remove ts from pool + for e in ts: + del ep[e] + + return (ts, ep) + + +def cluster_elements(element_pool, threshold): + """ + Groups Elements within a given threshold + together in the same cluster. + """ + + clusters = [] + threshold -= 1 # Account for center + ep = element_pool + cn = 1 # Cluster Number + while 1: + # Clusterable elements + ce = [e for e in ep if not ep[e].cluster] + if not ce: # No more elements to cluster + break + + # Select Cluster Center + # Element with largest neighbor list + ctr_nlist, ctr = sorted( + [(len([se for se in ep[e].neighbors if not se.cluster]), e) for e in ce] + )[-1] + + # Cluster until length of remaining elements lists are above threshold + if ctr_nlist < threshold: + break + + # Create Cluster + c = Cluster(cn, ep[ctr]) + cn += 1 + clusters.append(c) + + return (ep, clusters) + + +def 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For example, you wish to defined the +whole logic referring to the preparation steps before the run. +""" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/clean_steps.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/clean_steps.py new file mode 100644 index 0000000000000000000000000000000000000000..b7fddc6307fbef2fea004580b733c12a5f31fbf4 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/clean_steps.py @@ -0,0 +1,254 @@ +""" +Clean workflow steps' output. + +This module concerns removing unnecessary files, compressing, and +archiving files with the same extension to reduce space and stress when +listing files in the modules' step folders. + +The two main functions of this module are: + +* :py:func:`clean_output` +* :py:func:`unpack_compressed_and_archived_files` + +See also the command-line clients ``haddock3-clean`` and +``haddock3-unpack``. +""" +import gzip +import shutil +import tarfile + +from functools import partial +from multiprocessing import Pool +from pathlib import Path + +from haddock import log +from haddock.core.typing import FilePath, FilePathT, Iterable +from haddock.libs.libio import ( + archive_files_ext, + compress_files_ext, + glob_folder, + remove_files_with_ext, + ) + + +UNPACK_FOLDERS: list[FilePath] = [] + + +def clean_output(path: FilePath, ncores: int = 1) -> None: + """ + Clean the output of step folders. + + This functions performs file archiving and file compressing + operations. Files with extension ``seed``, ``inp``, ``out``, and + ``con`` are compressed and archived into ``.tgz`` files. The + original files are deleted. + + Files with ``.pdb`` and ``.psf`` extension are compressed to `.gz` + files. + + Parameters + ---------- + path : str or pathlib.Path + The path to clean. Should point to a folder from a workflow step. + + ncores : int + The number of cores. + """ + log.info(f"Cleaning output for {str(path)!r} using {ncores} cores.") + # add any formats generated to + # `unpack_compressed_and_archived_files` so that the + # uncompressing routines when restarting the run work. + + # Files to delete (all) + file_to_delete_all = ( + "mpi.pkl", + ) + for extension in file_to_delete_all: + for file_ in glob_folder(path, extension): + Path(file_).unlink() + + # Files to delete + # deletes all except the first one + # (keeping one for debugging purposes) + files_to_delete = ( + ".inp", + ".inp.gz", + ".out", + ".out.gz", + ".job", + ".err", + ) + + for extension in files_to_delete: + flist = glob_folder(path, extension) + for file_ in flist[1:]: + Path(file_).unlink() + + # files to archive (all files in single .gz) + files_to_archive = ( + ".seed", + ".seed.gz", + ".con", + ) + + archive_ready = partial(_archive_and_remove_files, path=path) + _ncores = min(ncores, len(files_to_archive)) + with Pool(_ncores) as pool: + imap = pool.imap_unordered(archive_ready, files_to_archive) + for _ in imap: + pass + + # files to compress in .gz + files_to_compress = ( + ".inp", + ".out", + ".pdb", + ".psf", + ".cnserr", + ) + + for ftc in files_to_compress: + found = compress_files_ext(path, ftc, ncores=ncores) + if found: + remove_files_with_ext(path, ftc) + + +def _archive_and_remove_files(fta: str, path: FilePath) -> None: + found = archive_files_ext(path, fta) + if found: + remove_files_with_ext(path, fta) + + +# eventually this function can be moved to `libs.libio` in case of future need. +def unpack_compressed_and_archived_files( + folders: Iterable[FilePathT], + ncores: int = 1, + dec_all: bool = False, + ) -> None: + """ + Unpack compressed and archived files in a folders. + + Works on `.gz` and `.tgz` files. + + Registers folders in :py:data:`UNPACK_FOLDERS` where compressed + and archived files were found. + + Parameters + ---------- + folders : list + List of folders to operate. + + ncores : int + The number of cores. + """ + global UNPACK_FOLDERS + UNPACK_FOLDERS.clear() + + files_to_decompress = [ + ".pdb.gz", + ".psf.gz", + ".seed.gz", + ] + + for folder in folders: + gz_files: list[Path] = [] + for file_to_dec in files_to_decompress: + gz_files.extend(list(glob_folder(folder, file_to_dec))) + + if dec_all: + for dec_all_files in ('.inp.gz', '.out.gz'): + gz_files.extend(list(glob_folder(folder, dec_all_files))) + + tar_files = glob_folder(folder, '.tgz') + + if gz_files or tar_files: + # register the folders that where unpacked + # this is useful for some functionalities of haddock3 + # namely the `--extend-run` option. + UNPACK_FOLDERS.append(folder) + + if gz_files: # avoids creating the Pool if there are no .gz files + with Pool(ncores) as pool: + imap = pool.imap_unordered(_unpack_gz, gz_files) + for _ in imap: + pass + + for tar_file in tar_files: + from haddock.libs.libio import extract_files_flat + extract_files_flat(tar_file, folder) + + tar_file.unlink() + + +def _unpack_gz(gz_file: Path) -> None: + out_file = Path(gz_file.parent, gz_file.stem) + + with gzip.open(gz_file, "rb") as fin, \ + open(out_file, "wb") as fout: + shutil.copyfileobj(fin, fout, 2 * 10**8) + + gz_file.unlink() + + +def update_unpacked_names(prev: Iterable[FilePath], new: Iterable[FilePath], + original: list[FilePath]) -> None: + """ + Update the unpacked path names. + + Sometimes the step folders are renamed to ajust their index number. + Such operation happens after the output data is unpacked. This module, + :py:mod:`haddock.gear.clean_steps`, keeps registry of the folders + unpacked to the correct funtioning of the `extend_run` module. + + Given the : list[FilePath] names and the new names of the step folders, + this function updates them in the storing list. + + Examples + -------- + >>> : list[FilePath] = ['0_topoaa', '4_flexref'] + >>> prev = ['0_topoaa', '4_flexref', '5_seletopclusts'] + >>> new = ['0_topoaa', '1_flexref', '5_seletopclusts'] + >>> update_unpacked_names(prev, new, original) + >>> original + ['0_topoaa', '1_flexref'] + + This function only evaluate the name of the last folder. And + maintains the type in the ``original`` list. + + >>> original = ['0_topoaa', Path('4_flexref'), '5_seletopclusts'] + >>> prev = ['0_topoaa', 'run_dir/4_flexref', '5_seletopclusts'] + >>> new = ['run_dir/0_topoaa', '1_flexref', 'run_dir/2_seletopclusts'] + >>> update_unpacked_names(prev, new, original) + >>> assert original == ['0_topoaa', Path('1_flexref'), '2_seletopclusts'] + + Parameters + ---------- + prev : list of str or pathlib.Path + The list of the original names before they were changed. + + new : list of str or pathlib.Path + The list of the new folder names. + + original : list of pathlib.Path + The list containing the names to record and which names + will be changed. + + Returns + ------- + None + Edits ``original`` in place. + """ + prevs = map(Path, prev) + news = map(Path, new) + original_names = [Path(o).name for o in original] + + # this is used to keep the original types of values in the ``original`` list + + for prev_, new_ in zip(prevs, news): + try: + idx = original_names.index(prev_.name) + except ValueError: # not present + continue + else: + _p = original[idx] + original[idx] = type(_p)(Path(Path(_p).parent, new_.name)) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/config.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/config.py new file mode 100644 index 0000000000000000000000000000000000000000..3a21574b3de8c95810c29b23129aeaee23a730b0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/config.py @@ -0,0 +1,339 @@ +""" +Module to read and write HADDOCK3 configuration files. + +HADDOCK3 user configuration files follow TOML syntax plus additional +features required for HADDOCK3. Therefore, we have implemented our own +TOML-like parser to accommodate the extra features needed for HADDOCK3. +However, HADDOCK3 can also read pure TOML files. + +The most relevant features of HADDOCK3 user configuration files are the +hability to prepare TOML-like files but with repeated header names, for +example: + +.. code:: toml + + [topoaa] + # parameters here... + + [rigidbody] + # parameters here... + + [caprieval] + # parameters here... + + [flexref] + # parameters here... + + [caprieval] + # parameters here... + +From the user perspective, everything else just behaves as in TOML. +Actually, HADDOCK3 uses TOML to finally read the configuration files. +Users can also provide pure TOML compatible files, for example: + +.. code:: toml + + [topoaa] + # parameters here... + + [rigidbody] + # parameters here... + + [caprieval] + # parameters here... + + [flexref] + # parameters here... + + ['caprieval.1'] + # parameters here... + +Because HADDOCK3 uses TOML in the end to read the configuration files, +all TOML rules apply regarding defining ``parameter = value`` pairs. + +Read more about TOML for Python here: https://pypi.org/project/toml/ +""" +import collections.abc +import os +import re +from pathlib import Path + +import toml + +from haddock import EmptyPath +from haddock.core.defaults import RUNDIR +from haddock.core.exceptions import ConfigurationError +from haddock.core.typing import FilePath, ParamDict, ParamMap, ParamMapT, Union +from haddock.libs.libutil import ( + recursive_convert_paths_to_strings, + transform_to_list, +) + + +# the re.ASCII parameter makes sure non-ascii chars are rejected in the \w key + +# Captures the main headers. +# https://regex101.com/r/9urqti/1 +_main_header_re = re.compile(r"^ *\[(\w+)\]", re.ASCII) + +# regex by @sverhoeven +# Matches ['.'] +_main_quoted_header_re = re.compile(r"^ *\[\'(\w+)\.\d+\'\]", re.ASCII) + +# Captures sub-headers +# https://regex101.com/r/6OpJJ8/1 +# thanks https://stackoverflow.com/questions/39158902 +_sub_header_re = re.compile(r"^ *\[(\w+)((?:\.\w+)+)\]", re.ASCII) + +# regex by @sverhoeven +_sub_quoted_header_re = re.compile( + r"^ *\[\'(\w+)\.\d+\'((?:\.\w+)+)\]", + re.ASCII, +) + +# Captures parameter uppercase boolean +_uppercase_bool_re = re.compile(r"(_?\w+((_?\w+?)+)?\s*=\s*)(True|False)", re.ASCII) + +# Some parameters are paths. The configuration reader reads those as +# pathlib.Path so that they are injected properly in the rest of the +# workflow. In general, any parameter ending with `_fname` is a path, +# but there are also other parameters that are paths. Those need to be +# added to this list bellow: +_keys_that_accept_files = [ + "cns_exec", + "executable", + RUNDIR, +] + + +class ConfigFormatError(Exception): + """Exception if there is a format error.""" + + pass + + +# main public API +def load(fpath: FilePath) -> ParamDict: + """ + Load an HADDOCK3 configuration file to a dictionary. + + Accepts HADDOCK3 ``cfg`` files or pure ``toml`` files. + + Parameters + ---------- + fpath : str or :external:py:class:`pathlib.Path` + Path to user configuration file. + + Returns + ------- + dictionary + Representing the user configuration file where first level of + keys are the module names. Step keys will have a numeric + suffix, for example: ``module.1``. + + .. see-also:: + * :py:func:`loads` + """ + try: + return loads(Path(fpath).read_text()) + except Exception as err: + raise ConfigurationError( + "Something is wrong with the config file." + ) from err # noqa: E501 + + +def loads(cfg_str: str) -> ParamDict: + """ + Read a string representing a config file to a dictionary. + + Config strings are converted to toml-compatible format and finally + read by the toml library. + + All headers (dictionary keys) will be suffixed by an integer + starting at ``1``. For example: ``topoaa.1``. If the key is + repeated, ``2`` is appended, and so forth. Even if specific + integers are provided by the user, the suffix integers will be + normalized. + + Parameters + ---------- + cfg_str : str + The string representing the config file. Accepted formats are + the HADDOCK3 config file or pure `toml` syntax. + + Returns + ------- + all_configs : dict + A dictionary holding all the configuration file steps: + + - 'raw_input': Original input file as provided by user. + - 'cleaned_input': Regex cleaned input file. + - 'loaded_cleaned_input': Dict of toml loaded cleaned input. + - 'final_cfg': The config in the form of a dictionary. In which + the order of the keys matters as it defines the order of the + steps in the workflow. + """ + new_lines: list[str] = [] + cfg_lines = cfg_str.split(os.linesep) + counter: dict[str, int] = {} + + # this for-loop normalizes all headers regardless of their input format. + for line in cfg_lines: + if group := _main_header_re.match(line): + name = group[1] + counter.setdefault(name, 0) + counter[name] += 1 + count = counter[name] + new_line = f"['{name}.{count}']" + + elif group := _main_quoted_header_re.match(line): + name = group[1] + counter.setdefault(name, 0) + counter[name] += 1 + count = counter[name] + new_line = f"['{name}.{count}']" + + elif group := _sub_header_re.match(line): + name = group[1] + count = counter[name] # name should be already defined here + new_line = f"['{name}.{count}'{group[2]}]" + + elif group := _sub_quoted_header_re.match(line): + name = group[1] + count = counter[name] # name should be already defined here + new_line = f"['{name}.{count}'{group[2]}]" + + elif group := _uppercase_bool_re.match(line): + param = group[1] # Catches 'param = ' + uppercase_bool = group[4] + new_line = f"{param}{uppercase_bool.lower()}" # Lowercase bool + + else: + new_line = line + + new_lines.append(new_line) + + # Re-build workflow configuration file + cfg = os.linesep.join(new_lines) + + try: + cfg_dict = toml.loads(cfg) # Try to load it with the toml library + except Exception as err: + raise ConfigurationError( + "Some thing is wrong with the config file: " f"{str(err)}" + ) from err + + final_cfg = convert_variables_to_paths(cfg_dict) + + all_configs = { + "raw_input": cfg_str, + "cleaned_input": cfg, + "loaded_cleaned_input": cfg_dict, + "final_cfg": final_cfg, + } + + # Return all configuration steps + return all_configs + + +def convert_variables_to_paths(cfg: ParamMapT) -> ParamMapT: + """ + Convert config variables to paths. + + Applies only to those variables HADDOCK3 needs as paths. + + Parameters + ---------- + cfg : dictionary + A dictionary containing the HADDOCK3 parameters. + + .. see-also:: + :py:func:`match_path_criteria` + """ + for param, value in cfg.items(): + if param == "molecules": + # `transform_to_list` is needed to allow strings OR lists in the + # `molecule` parameter + cfg[param] = [convert_to_path(v) for v in transform_to_list(value)] + + elif match_path_criteria(param): + cfg[param] = convert_to_path(value) + + elif isinstance(value, collections.abc.Mapping): + cfg[param] = convert_variables_to_paths(value) # type: ignore + + return cfg + + +def convert_to_path(value: FilePath) -> Union[Path, EmptyPath]: + """Convert a variable to Path if variable evaluates to true.""" + if value: + return Path(value) + else: + return EmptyPath() + + +def match_path_criteria(param: str) -> bool: + """ + Confirm a parameter should be converted to path. + + This function contains the rules defining which parameter need to be + converted to Path before be sent to HADDOCK3. + """ + return param.endswith("_fname") or param in _keys_that_accept_files + + +def get_module_name(name: str) -> str: + """ + Get the module name according to the config parser. + + Get the name without the integer suffix. + """ + return name.split(".")[0] + + +def save(params: ParamMap, path: FilePath, pure_toml: bool = False) -> None: + """ + Write a dictionary to a HADDOCK3 config file. + + Write the HADDOCK3 parameter dictionary to a `.cfg` file. There is + also the option to write in pure TOML format. Both are compatible with + HADDOCK3. + + Parameters + ---------- + params : dict + The dictionary containing the parameters. + + path : str or pathlib.Path + File name where to save the configuration file. + + pure_toml : bool + Save config in pure toml format. + """ + params = recursive_convert_paths_to_strings(params) + + if pure_toml: + with open(path, "w") as fout: + toml.dump(params, fout) + return + + cfg_str = toml.dumps(params).split(os.linesep) + + new_lines: list[str] = [] + for line in cfg_str: + if group := _main_quoted_header_re.match(line): + name = group[1] + new_line = f"[{name}]" + + elif group := _sub_quoted_header_re.match(line): + name = group[1] + new_line = f"[{name}{group[2]}]" + else: + new_line = line + new_lines.append(new_line) + + cfg_str = os.linesep.join(new_lines) # type: ignore + + with open(path, "w") as fout: + fout.write(cfg_str) # type: ignore diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/expandable_parameters.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/expandable_parameters.py new file mode 100644 index 0000000000000000000000000000000000000000..1676843b1662f8335ca9888946abb39a04b13c5e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/expandable_parameters.py @@ -0,0 +1,934 @@ +""" +Expandable parameter module. + +This module contains all logic for reading and preparing expandable parameters. + +Expandable parameters are parameters that follow a specific name structure. +They can be repeated multiple times (in groups) in the user configuration file +while being defined only once in the `defaults.yaml` files. For example, in the +`refinement.flexref` module there are the parameters: + +- `fle_sta_1_1` +- `fle_end_1_1` + +For these cases, you can also define in the user configuration file the +following: + +- `fle_sta_1_2` +- `fle_end_1_2` + +The above parameters will be accepted and used in the CNS modules. We +say they are the second groupd of the `fle1` group. We explain in detail +below. + +Currently, there are three types of expandable parameters: + +1 - Parameters following the name structure: + +- `name_something_1`, +- `name_something_else_1` + +These two parameters belong to the parameter name `name` and group `1`. +The two parameters have the name `something` and `something_else`. +Therefore, you could define also: + +- `name_something_2` +- `name_something_else_2` + +Numbers are allowed as long as in combination with word characters, for +example: `name_something1_2`, but not `name_something_1_1` because the +latter is of the second type. + +2 - Parameters following the name structure: + +- `name_something_X_Y` +- `name_else_X_Y` + +In these cases, the parameter name is `nameX`, where `X` is an integer. +`Y` is the number of the group, and `something` and `else` are the name +of the parameters. Taking example: + +- `fle_sta_1_1` +- `fle_end_1_1` + +The parameter name is `fle1` and the parameters belonging to the groups +are `sta` and `end`, and the group is either `1`. + +3 - The simplest parameters in the form of: + +- `param_1` + +In these cases, you can define `param_2`, `param_3`, etc, in the user +configuration file despite those are not defined in the `defaults.yaml`. +However, because `_` is too much of a simple rule, we +need to define in this module which parameters are actualy expandable. +If you are developing here look for the `type_simplest_ep` variable. + +4. Parameters that are expandable to the max number of molecules: + +Those are the parameters starting with `mol`. For example: +`mol_fix_origin_1`, which refers to the `fix_origin` parameter for +molecule 1. These parameters are allowed to expand only to the maximum +of input molecules, and at most to the max number of molecules allowed. +""" +import itertools as it +from copy import deepcopy +from functools import partial + +from haddock.core.defaults import max_molecules_allowed +from haddock.core.exceptions import ConfigurationError +from haddock.core.typing import ( + Any, + AnyT, + Callable, + Iterable, + Optional, + ParamMap, + Sequence, + SupportsAddT, +) + + +# error messages used in _read_groups_in_user_config function +# errors messages for single indexed groups +_emsg_no_group_single = ( + "The parameter block '{}_*_{}' is not a valid expandable parameter." +) +_emsg_unexpected_params_single = ( + "These parameters do not belong to the block '{}_*_{}': {!r}." +) + +# errors messages for multiple indexed groups +_emsg_no_group_multiple = ( + "The parameter block '{}_*_{}_*' is not a valid expandable parameter." +) +_emsg_unexpected_params_multiple = ( + "These parameters do not belong to the block '{}_*_{}_*': {!r}." +) + +# common error messages +_emsg_num_differ = ( + "The parameter block {!r} expects " + "{} parameters ({}), but {} are present " + "in the user configuration file: {}. " + "Parameter(s) {} are missing." +) + + +# this dictionary defines which parameters of the form "param_1" are +# expandable, and for which modules. We cannot define a general +# expandable rule for such a simple parameter name because there can be +# many other parameters with the same structure but that are not +# supposed to be expandable. +type_simplest_ep = { + "topoaa": { + "hisd", # hisd_1 should be defined in the `defaults.yaml` + "hise", # hise_1 should be defined in the `defaults.yaml` + }, +} + + +GroupDict = dict[tuple[str, str], Any] + + +# this is an engine function that must be populated with the respective +# functions the specify its behaviour. This engine is used in +# `get_single_index_groups` and `get_multiple_index_groups`, for +# example. The latter are defined later on with `partial`. +def _get_groups( + config: ParamMap, + belongs_to_group: Callable[[Sequence[str]], bool], + make_param_name: Callable[[Sequence[str]], tuple[str, str]], + rejoin_parts: Callable[[Sequence[str]], str], + minimum: int = 2, + reference: bool = True, +) -> GroupDict: + """ + Identify expandable parameter groups - main engine function. + + Parameters + ---------- + config : dict + The configuration file, where keys are the parameter names. + + belongs_to_group : callable + A callable receiving the parameter name after str.split("_") + that returns a boolean identifying if the parameter belongs a + given expadanble group. + + make_param_name : callable + Recreates the parameter preffix from the parameter parts. + + rejoin_parts : callable + Recreates the parameter name from the parts. For example: + `something_else` in `param_something_else_1`. + + minimum : int + Consider only the groups with at least `minimum` parameters. + + reference : bool + Whether reading a default config file or not. If true, only + groups ending with "1" will be considered. This avoids capturing + parameters for molecules, such as "mol_fix_origin_1", + "mol_fix_origin_2", etc. + """ + splitted = (parameter.split("_") for parameter in config) + parts = (_parts for _parts in splitted if belongs_to_group(_parts)) + + # identify groups in config + groups: GroupDict = {} + for p in parts: + group_identity = make_param_name(p) # ("param", "1") + + new = groups.setdefault(group_identity, {}) + + # counts the number of parameters within the block + new.setdefault("counts", 0) + new["counts"] += 1 + + # registers the parameters belonging to the group + new.setdefault("mid", set()) + new["mid"].add(rejoin_parts(p)) + + if reference: + groups = remove_ghost_groups(groups) + + # creates the final dictionary + final_groups = {k: v["mid"] for k, v in groups.items() if v["counts"] >= minimum} + + return final_groups + + +def remove_ghost_groups(groups: GroupDict) -> GroupDict: + """ + Remove ghost groups from dictionary. + + Ghost groups are parameters that are defined in the defaults + in a manner that they look they are already expanded. For example: + + - mol_shape_1 + - mol_shape_2 + - mol_shape_3 + - mol_fix_origin_1 + - mol_fix_origin_2 + - mol_fix_origin_3 + + These integer suffix refer to the input molecules and not to + expandable groups. + + Parameters + ---------- + groups : dict + A dictionary containing the groups. For example as those created + by `get_single_index_groups`. + """ + counter: dict[str, int] = {} + for key in groups: + counter.setdefault(key[0], 0) + counter[key[0]] += 1 + + new_groups = deepcopy(groups) + + for key, value in counter.items(): # type: ignore + if value > 1: + for gk in groups.keys(): + if gk[0] == key: + new_groups.pop(gk) + + return new_groups + + +# this is an engine function that must be populated with the respective +# functions the specify its behaviour. This engine is used in +# `read_single_idx_groups_user_config` and +# `read_multiple_idx_groups_user_config`, for example. The latter are +# defined later on with `partial`. +def _read_groups_in_user_config( + user_config: Iterable[str], + default_groups: GroupDict, + get_user_groups: Callable[..., GroupDict], + extract_params: Callable[..., set[str]], + _emsg_no_group: str = "Parameter block is not a valid expandable group", + _emsg_unexpected_params: str = "Unexpected params for group", +) -> tuple[set[str], dict[str, int]]: + """ + Read groups in user config. + + This is an engine-like function that serves the different expandable + parameter rules. This function should be parametrized with the correct + functions that provide functionality. See `get_` and `read_` functions + defined in this module. + + Parameters + ---------- + user_config : dict + The user configuration dictionary. + + default_groups : dict + The groups present in the default configuration file for the + specific module. This dictionary is that created by, + `get_single_index_groups`, or `get_multiple_index_groups`. + + get_user_groups : callable + A function to extract groups from a parameter dictionary. + See `get_single_index_groups` and `get_multiple_index_groups`. + + extract_params : callable + A function to extract parameters from a parameter dictionary + according to the selected group. See `extract_single_index_params`, + `extract_multiple_index_params`. + + Returns + ------- + new : set[str] + A set with the new parameters in the user configuration file + that are acceptable according to the expandable rules. + param_name_counts : dict[str, int] + Count of expendable parameter parameter names + """ + # minimum=1 is used to capture groups with missing parameters + user_groups = get_user_groups(user_config, minimum=1, reference=False) + default_group_names = set(group[0] for group in default_groups) + + new: set[str] = set() + param_name_counts: dict[str, int] = {} + for (param_name, group_idx), params in user_groups.items(): + if param_name not in default_group_names: + emsg = _emsg_no_group.format(param_name, group_idx) + raise ConfigurationError(emsg) + + default_key = (param_name, "1") + expected_params = default_groups[default_key] + diff = params.difference(expected_params) + if diff: + emsg = _emsg_unexpected_params.format( + param_name, + group_idx, + ", ".join(diff), + ) + raise ConfigurationError(emsg) + + num_found = len(params) + num_expected = len(expected_params) + + # it should only trigger when num_found < num_expected + # when num_found > num_expected the error about in `diff` is + # triggered instead + if num_found != num_expected: + expected_missings = set(expected_params).difference(params) + emsg = _emsg_num_differ.format( + param_name, + num_expected, + ", ".join(expected_params), + num_found, + ", ".join(params), + ", ".join([f"`{p}`" for p in expected_missings]), + ) + raise ConfigurationError(emsg) + + related_params = extract_params(user_config, param_name, group_idx) + # Increment counts for this parameter + if related_params: + param_name_counts.setdefault(param_name, 0) + param_name_counts[param_name] += 1 + new.update(related_params) + return new, param_name_counts + + +def read_simplest_expandable( + config: Iterable[str], expparams: Iterable[str], +) -> set[str]: + """ + Read expandable parameters from config file of the type `param_1`. + + Parameters + ---------- + config : dict, dict.keys, set, or alike + The user configuration file. + expparams : dict, dict.keys, set, or alike + The parameter names that should be considered as expandable. + Usually, this is a module subdictionary of `type_simplest_ep`. + + Returns + ------- + set of str + The parameters in `config` that comply with `expparams`. + """ + new: set[str] = set() + for param in config: + try: + name, idx = param.split("_") + except ValueError: + continue + if idx.isdigit() and name in expparams: + new.add(param) + return new + + +def get_mol_parameters(config: Iterable[str]) -> set[str]: + """Identify expandable `mol` parameters.""" + return set(param for param in config if is_mol_parameter(param)) + + +def is_mol_parameter(param: str) -> bool: + """Identify if a parameter is a `mol` parameter.""" + parts = param.split("_") + return param.startswith("mol_") and parts[-1].isdigit() and len(parts) > 2 + + +def read_mol_parameters( + user_config: ParamMap, + default_groups: Iterable[str], + max_mols: int = max_molecules_allowed, +) -> set[str]: + """ + Read the mol parameters in the user_config following expectations. + + Parameters + ---------- + user_config : dict + The user configuration dictionary. + + default_groups : dict or set. + The mol parameters present in the default configuration file for + the specific module. These are defined by `get_mol_parameters`. + + max_mols : int + HADDOCK3 has a limit in the number of different molecules it + accepts for a calculation. Expandable parameters affecting molecules + should not be allowed to go beyond that number. Defaults to + `core.default.max_molecules_allowed`. + + Returns + ------- + set + The allowed parameters according to the default config and the + max allowed molecules. + """ + # removes the integer suffix from the default mol parameters + default_names = [remove_trail_idx(p) for p in default_groups] + + new: set[str] = set() + for param in get_mol_parameters(user_config): + param_name = remove_trail_idx(param) + param_idx = param.split("_")[-1] + if param_name in default_names and int(param_idx) <= max_mols: + new.add(param) + return new + + +def remove_trail_idx(param: str) -> str: + """ + Remove the trailing integer from a parameter. + + If trail is defined by an underscore "_". + + Examples + -------- + remove_trail_idx('some_parameter_1') + >>> 'some_parameter' + + remove_trail_idx('some_parameter') + >>> 'some_parameter' + + remove_trail_idx('parameter') + >>> 'parameter' + + Parameters + ---------- + param : str + A parameter name. + """ + under_parts = param.rpartition("_") + if under_parts[2].isdigit(): + return under_parts[0] + return param + + +def get_trail_index(param: str) -> Optional[str]: + """ + Get the trail index if underscored. + + Examples + -------- + has_trail_index('some_parameter_1') + >>> '1' + + has_trail_index('some_parameter1') + >>> None + + has_trail_index('some_parameter_1_1') + >>> '1' + + has_trail_index('some_parameter_1-1') + >>> None + + has_trail_index('some_parameter') + >>> None + + Parameters + ---------- + param : str + A parameter name. + + Returns + ------- + str or None + The trail index if exist. ``None`` if not found. + """ + under_parts = param.rpartition("_") + if under_parts[2].isdigit(): + return under_parts[2] + return None + + +def make_param_name_single_index(param_parts: Sequence[AnyT]) -> tuple[AnyT, AnyT]: + """ + Make the key name from param parts. + + For example, ("param", "tag", "1") -> ("param", "1"). + """ + return (param_parts[0], param_parts[-1]) + + +def make_param_name_multiple_index( + param_parts: Sequence[SupportsAddT], +) -> tuple[SupportsAddT, SupportsAddT]: + """ + Make the key name from param parts. + + For example, ("param", "tag", "2", "1") -> ("param2", "1"). + """ + return (param_parts[0] + param_parts[-2], param_parts[-1]) + + +def belongs_to_single_index(param_parts: Sequence[str]) -> bool: + """ + Assert param belong to single index group. + + Parameters + ---------- + param_parts : list of str + The parameter name parts after `str.split("_")`. + + Returns + ------- + boolean + True if the parameter name follows the rules of single index + expandable parameters. + + Rules: + - param names have more than 2 parts + - the last part is a digit + - the part before last is not a digit + """ + return ( + len(param_parts) > 2 + and param_parts[-1].isdigit() + and not param_parts[-2].isdigit() + and not param_parts[0].startswith("mol") + ) + + +def belongs_to_multiple_index(param_parts: Sequence[str]) -> bool: + """ + Assert param belong to multiple index group. + + Parameters + ---------- + param_parts : list of str + The parameter name parts after `str.split("_")`. + + Returns + ------- + boolean + True if the parameter name follows the rules of multiple index + expandable parameters. + + Rules: + - param names have more than 4 parts + - the last part is a digit + - the part before last is a digit + """ + return ( + len(param_parts) >= 4 + and param_parts[-1].isdigit() + and param_parts[-2].isdigit() + and not param_parts[0].startswith("mol") + ) + + +def rejoin_parts_single_index(param_parts: Sequence[str]) -> str: + """Join parameter name parts.""" + return "_".join(param_parts[1:-1]) + + +def rejoin_parts_multiple_index(param_parts: Sequence[str]) -> str: + """Join parameter name parts.""" + return "_".join(param_parts[1:-2]) + + +def extract_single_index_params( + user_config: Iterable[str], param_name: str, group_idx: str +) -> set[str]: + """ + Extract the parameters belonging to a group. + + Descriminates between parameters of other expandable groups. + See: `belongs_to_single_index`. + + Examples + -------- + >>> ES = extract_single_index_params + + >>> ES({"param_some_1", "param_other_1", "param2", "ppp_ooo"}, "param", "1") + {"param_some_1", "param_other_1"} + + >>> ES( + {"param_some_1", "param_other_1", "param_some_2", "param_other_2"}, + "param", "2") + {"param_some_2", "param_other_2"} + + >>> ES( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "param", "1") + {"param_some_1", "param_other_1"} + + >>> ES( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "par", "2") + set() + + >>> ES( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "por", "2") + set() + + Parameters + ---------- + user_config : dict, or dict.keys(), or similar + The user configuration file - parameter keys should be parameter + names. + + param_name : str + The parameter name of the group to select. For example: `c3sym`. + + group_idx : str + The number of the group: "1", "2", "3", etc. Only that group + number will be selected. + + Returns + ------- + set of strings + A set with the selected parameters. + """ + new: set[str] = set() + for param in user_config: + parts = param.split("_") + try: + pname, *_, pidx = parts + except ValueError: + continue + if pname == param_name and pidx == group_idx and belongs_to_single_index(parts): + new.add(param) + return new + + +def extract_multiple_index_params( + user_config: Iterable[str], param_name: str, group_idx: str +) -> set[str]: + """ + Extract the parameters belonging to a group. + + See also: `belongs_to_multiple_index`. + + Examples + -------- + >>> EM = extract_multiple_index_params + + >>> EM({"param_some_1", "param_other_1", "param2", "ppp_ooo"}, "param", "1") + set() + + >>> EM( + {"param_some_1", "param_other_1", "param_some_2", "param_other_2"}, + "param", "2") + set() + + >>> EM( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "param", "1") + {"par_some_2_2", "par_other_2_2"}, + + >>> EM( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "par", "2") + set() + + >>> EM( + {"param_some_1", "param_other_1", "par_some_2_2", "par_other_2_2"}, + "por", "2") + set() + + Parameters + ---------- + user_config : dict, or dict.keys(), or similar + The user configuration file - parameter keys should be parameter + names. + + param_name : str + The parameter name of the group to select. For example: `c3sym`. + + group_idx : str + The number of the group: "1", "2", "3", etc. Only that group + number will be selected. + + Returns + ------- + set of strings + A set with the selected parameters. + """ + new: set[str] = set() + for param in user_config: + parts = param.split("_") + try: + pname, *_, molidx, pidx = parts + except ValueError: + continue + if ( + pname + molidx == param_name + and pidx == group_idx + and belongs_to_multiple_index(parts) + ): + new.add(param) + return new + + +# define public API by functionalizing the engines with the specific +# functions. The docstring below is the docstring of the function. +get_single_index_groups = partial( + _get_groups, + belongs_to_group=belongs_to_single_index, + make_param_name=make_param_name_single_index, + rejoin_parts=rejoin_parts_single_index, +) +""" +Get single indexed blocks from a configuration. + +Block parameters follow the rule __. + +These belong to the same parameter (`param`) of the group `1`: + +- param_something1_1 +- param_something2_1 +- param_something_else_1 +- param_something4_1 + +You could expand these with: + +- param_something1_2 +- param_something2_2 +- param_something_else_2 +- param_something4_2 + +When used to read the modules' default configuration we expect the + to be only "_1". But having allows to identify +blocks from the user configuration. See `reference` parameter. + +When we execute this function, we want to know: + +- param, the parameter name preffix +- how many parameters exist of the block (`something1`, `something2`, ...) +- _1, defines the number of the block + +Returns a dictionary in the form of:: + + { + ("param", "1"): { + "something1", "something2", + "something_else", "something4" + }, + ("otherparam", "1"): {"somename", "othername"}, + } + +Parameters +---------- +config : dictionary + Where keys are the parameter names. The values are not important. + +minimum : int + Consider only the groups with at least `minimum` parameters. + +reference : bool + Whether reading a default config file or not. If true, only + groups ending with "1" will be considered. This avoids capturing + parameters for molecules, such as "mol_fix_origin_1", + "mol_fix_origin_2", etc. + +Returns +------- +dictionary - {tuple: dict} +""" + +get_multiple_index_groups = partial( + _get_groups, + belongs_to_group=belongs_to_multiple_index, + make_param_name=make_param_name_multiple_index, + rejoin_parts=rejoin_parts_multiple_index, +) +""" +Get parameter blocks with multiple indexes. + +These blocks of params apply, for example, to different molecules. +That's why they have two looping indexes: one for the molecule and +other for the group. + +This block of parameters follow the rule: + +___ + +Where the actual param name is `paramN`, where `N` is an integer. + + be can any combination of alphanumeric chars and +underscores. + + is the number of the group, the will be incremented as we +expand. + +These belong to the same parameter (`param1`) of the group `1`: + +- param_something_1_1 +- param_something2_1_1 +- param_something_else_1_1 +- param_something4_1 + +You could expand these with: + +- param_something_1_2 +- param_something2_1_2 +- param_something_else_1_2 +- param_something4_2 + +When used to read the modules' default configuration we expect the + to be only "_1". But having allows to identify +blocks from the user configuration. + +Returns a dictionary in the form of:: + + {("param1", "1"): { + "something1", "something2", "something_else", "something4"} + +Parameters +---------- +config : dict + Where keys are the parameter names. The values are not important. + +minimum : int + Consider only the groups with at least `minimum` parameters. + +reference : bool + Whether reading a default config file or not. If true, only + groups ending with "1" will be considered. This avoids capturing + parameters for molecules, such as "mol_fix_origin_1", + "mol_fix_origin_2", etc. + +Returns +------- +dictionary : {(tuple): dict} +""" + +read_single_idx_groups_user_config = partial( + _read_groups_in_user_config, + get_user_groups=get_single_index_groups, + extract_params=extract_single_index_params, + _emsg_no_group=_emsg_no_group_single, + _emsg_unexpected_params=_emsg_unexpected_params_single, +) +""" +Read single indexed groups in user config. + +Parameters +---------- +user_config : dict + The user configuration dictionary. + +default_groups : dict + The groups present in the default configuration file for the + specific module. This is the dictionary created by, + `get_single_index_groups`. + +Returns +------- +set + A set with the new parameters in the user configuration file + that are acceptable according to the expandable rules. +""" + +read_multiple_idx_groups_user_config = partial( + _read_groups_in_user_config, + get_user_groups=get_multiple_index_groups, + extract_params=extract_multiple_index_params, + _emsg_no_group=_emsg_no_group_multiple, + _emsg_unexpected_params=_emsg_unexpected_params_multiple, +) +""" +Read multiple indexed groups in user config. + +Parameters +---------- +user_config : dict + The user configuration dictionary. + +default_groups : dict + The groups present in the default configuration file for the + specific module. This is the dictionary created by + `get_multiple_index_groups`. + +Returns +------- +set + A set with the new parameters in the user configuration file + that are acceptable according to the expandable rules. +""" + + +def populate_mol_parameters_in_module( + params: ParamMap, num_mols: int, defaults: ParamMap +) -> None: + """ + Populate parameters dictionary with the needed molecule `mol_` parameters. + + The `mol_` prefixed parameters is a subclass of the expandable parameters. + + See :py:mod:`haddock.gear.expandable_parameters`. + + Modules require these parameters to be repeated for the number of input + molecules. + + This function adds `mol_` parameters to the user input parameters, + one per each `molecule` and for those which a values has not been + added yet. + + Parameters + ---------- + modules_params : dict + A dictionary of parameters. + + Returns + ------- + None + Alter the dictionary in place. + """ + # filter to get only the `mol_` parameters that are defaults + # the get_trail_index is needed because defaults only have the '1' + # suffixed parameters. + mol_params = ( + p + for p in list(params.keys()) + if is_mol_parameter(p) and get_trail_index(p) == "1" + ) + + for param, i in it.product(mol_params, range(1, num_mols + 1)): + param_name = remove_trail_idx(param) + params.setdefault(f"{param_name}_{i}", defaults[param]) + + return diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/extend_run.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/extend_run.py new file mode 100644 index 0000000000000000000000000000000000000000..2a9ed9d57ccc9c89ba7176d3c7d493485404ed8a --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/extend_run.py @@ -0,0 +1,283 @@ +"""Gear for ``haddock3-copy`` CLI and `--extend-run`` flag.""" +import shutil +from pathlib import Path + +from haddock import log +from haddock.core.defaults import MODULE_IO_FILE +from haddock.core.exceptions import HaddockTermination +from haddock.core.typing import ( + Any, + ArgumentParser, + FilePath, + FilePathT, + Iterable, + ModuleParams, + Optional, + ) +from haddock.gear.clean_steps import UNPACK_FOLDERS, clean_output +from haddock.gear.zerofill import zero_fill +from haddock.libs.libontology import ModuleIO +from haddock.libs.libtimer import log_time +from haddock.libs.libworkflow import Workflow, WorkflowManager +from haddock.modules import get_module_steps_folders + + +EXTEND_RUN_DEFAULT = None + + +class WorkflowManagerExtend(WorkflowManager): + """Workflow to extend a run.""" + + def __init__(self, + workflow_params: ModuleParams, + start: Optional[int] = 0, + **other_params: Any) -> None: + self.start = start + self.recipe = Workflow(workflow_params, start=start, **other_params) + # terminate is used to synchronize the `clean` option with the + # `exit` module. If the `exit` module is removed in the future, + # you can also remove and clean the `terminate` part here. + self._terminated = 0 + + def run(self) -> None: + """High level workflow composer.""" + for i, step in enumerate(self.recipe.steps, start=0): + try: + step.execute() + except HaddockTermination: + self._terminated = i + break + + def clean(self) -> None: + """Clean the step output.""" + # return compression to the original state + cwd = Path.cwd().name + + # because this WorkflowManagerExtended has no direct access to the + # ncores parameters, it needs to take it from the steps. + ncores: int = max(s.config["ncores"] for s in self.recipe.steps) + + for folder in UNPACK_FOLDERS: + # temporary hack to get the step folder name. + # ensures we can work under the CLI working directory + # or inside the run dir. + folder_ = str(folder).split(cwd)[1][1:] + + log.info( + f'Compressing original folder: {folder_!r} because it ' + 'was originally compressed.' + ) + + with log_time("cleaning output files took"): + clean_output(folder_, ncores) + + # apply compression to the new modules + super().clean(terminated=self._terminated) + + +def add_extend_run(parser: ArgumentParser) -> None: + """Add option to ``--extend-run``.""" + parser.add_argument( + '--extend-run', + help=( + "Start a run from a run directory previously prepared with " + "the `haddock3-copy` CLI. Provide the run directory created " + "with `haddock3-copy` CLI." + ), + default=EXTEND_RUN_DEFAULT, + type=Path, + ) + + +def read_num_molecules_from_folder(folder: FilePath) -> int: + """ + Read the number of molecules from the first step folder. + + 1. Find the lower indexed step folder in `folder`. + 2. Read the `io.json` file. + 3. Count the number of items in the "output" key. + 4. The above is the number of molecules. + + Parameters + ---------- + folder : Path or string + The run directory. + + Returns + ------- + int + The number of molecules found. + """ + parent = Path(folder).resolve() + previous = get_module_steps_folders(folder) + + io = ModuleIO() + previous_io = Path(parent, previous[0], MODULE_IO_FILE) + io.load(previous_io) + + return len(io.output) + + +def copy_renum_step_folders(indir: FilePath, destdir: FilePath, + steps: list[FilePathT]) -> list[Path]: + """ + Copy step folders renumbering them sequentially in the run directory. + + The content of the files is not modified. + See :py:func:`rename_step_contents`. + + py:`gear.zerofill.zero_fill`: must be previously calibrated. + + Example + ------- + >>> steps = ['0_topoaa', '4_flexref'] + >>> zero_fill.set_zerofill_number(len(steps)) + >>> copy_renum_step_folders('run1', 'newrun', steps) + + The initial structure:: + + run1/ + 0_topoaa/ + 1_rigidbody/ + 2_caprieval/ + 3_seletop/ + 4_flexref/ + (etc...) + + Results in:: + + newrun/ + 0_topoaa/ + 1_flexref/ + + Parameters + ---------- + indir : str or Path + The input directory where the original steps reside. + + destdir : str or Path + The output directory where to copy the steps to. + + steps : list of (str or Path) + The list of the folder names in `indir` to copy. + + Returns + ------- + list + The new paths created. + """ + new_steps: list[Path] = [] + step_names = (Path(step).name for step in steps) + for i, step in enumerate(step_names): + ori = Path(indir, step) + _modname = step.split("_")[-1] + dest = Path(destdir, zero_fill.fill(_modname, i)) + shutil.copytree(ori, dest) + log.info(f"Copied {str(ori)} -> {str(dest)}") + new_steps.append(dest) + return new_steps + + +def renum_step_folders(folder: FilePath) -> tuple[list[str], list[str]]: + """ + Renumber the step folders sequentially in the run directory. + + The content of the files is not modified. + + See :py:func:`rename_step_contents`. + + Example + ------- + + The initial structure:: + + folder/ + 0_topoaa/ + 4_flexref/ + + Results in:: + + folder/ + 0_topoaa/ + 1_flexref/ + + Returns + ------- + list + The list of the original step folder names. + + list + The list of the new step folder names. + """ + # these come sorted already + step_folders = get_module_steps_folders(folder) + new_names: list[str] = [] + + # move folders + for i, sf in enumerate(step_folders): + mod_name = sf.split("_")[-1] + new_name = zero_fill.fill(mod_name, i) + new_names.append(new_name) + shutil.move(Path(folder, sf), Path(folder, new_name)) + + return step_folders, new_names + + +def update_contents_of_new_steps(selected_steps: Iterable[str], + olddir: FilePath, newdir: FilePath) -> None: + """ + Find-replace run references in step folders files. + + Find and replaces (updates) all references to step folders and to + the old run directory in all files of selected step folders. + + Example + ------- + >>> update_contents_of_new_steps( + ['0_topoaa', '1_rigidbody'], + 'run1', + 'run2', + ) + + Parameters + ---------- + selected_steps : list of str + The names of the original step folder names that to find in the + new step folders. This function uses + :py:func:`haddock.modules.get_module_steps_folders` to find + the new step folders. ``selected_steps`` must be synchronized + with the new folders; that is, the names in ``selected_steps`` + must be the old names of the new step folders. + + olddir : str or Path + The original run directory to be replaced by `newdir`. + + newdir : str or Path + The new run directory. + + Returns + ------- + None + Save files in place. + + See Also + -------- + :py:func:`haddock.gear.prepare_run.update_step_contents_to_step_names` + """ + olddir = Path(olddir) + newdir = Path(newdir) + new_steps = get_module_steps_folders(newdir) + for ns in new_steps: + new_step = Path(newdir, ns) + for file_ in new_step.iterdir(): + try: + text = file_.read_text() + except UnicodeDecodeError as err: + log.warning(f"Failed to read file {file_}. Error is {err}") + continue + for s1, s2 in zip(selected_steps, new_steps): + text = text.replace(s1, s2) + text = text.replace(olddir.name, newdir.name) + file_.write_text(text) + + log.info("File references updated correctly.") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/greetings.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/greetings.py new file mode 100644 index 0000000000000000000000000000000000000000..b6de6c9ed3e8735abfa1a807dd9e9d8030ee0fd1 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/greetings.py @@ -0,0 +1,116 @@ +"""Greeting messages for the command line clients.""" + +import os +import random +import sys +from datetime import datetime +from functools import partial +from typing import Callable, Sequence + +from haddock import contact_us, version + + +international_good_byes = [ + "Adéu-siau", + "Agur", + "Até logo", + "Au revoir", + "Ciao", + "Dovidenia", + "Good bye", + "Tot ziens", + "La revedere", + "Adiós", + "Do pobachennya", + "Tchau", + "再见", + "Hoşça kal", + "Slán", + "Do widzenia", + "Mandi", + "Αντίο", + "Auf Wiedersehen", +] + +# List of urls to be printed to the screen at the end of a workflow +# Do not hesitate to update / comment one of these +feedback_urls = { + "GitHub issues": "https://github.com/haddocking/haddock3/issues", + "BioExcel feedback": "https://www.bonvinlab.org/feedback", + "BioExcel forum": "https://ask.bioexcel.eu/c/haddock/6", + "Haddock3 user manual": "https://www.bonvinlab.org/haddock3-user-manual/", +} + + +DISCLAIMER = ( + "!! Some of the HADDOCK3 components use CNS (Crystallographic and NMR System)" + f" which is free of use for non-profit applications. !!{os.linesep}" + "!! For commercial use it is your own responsibility" + f" to have a proper license. !!{os.linesep}" + "!! For details refer to the DISCLAIMER file in the HADDOCK3 repository. !!" +) + + +def get_initial_greeting() -> str: + """Create initial greeting message.""" + now = datetime.now().replace(second=0, microsecond=0) + python_version = sys.version + message = ( + f"""{os.linesep}""" + f"""##############################################{os.linesep}""" + f"""# #{os.linesep}""" + f"""# HADDOCK3 #{os.linesep}""" + f"""# #{os.linesep}""" + f"""##############################################{os.linesep}""" + f"""{os.linesep}""" + f"""{DISCLAIMER}{os.linesep}""" + f"""{os.linesep}""" + f"""Starting HADDOCK3 v{version} on {now}{os.linesep}""" + f"""{os.linesep}""" + f"""Python {python_version}{os.linesep}""" + ) + return message + + +def get_greetings( + options: Sequence[str], how_many: int = 3, sep: str = " ", exclamation: str = "!" +) -> str: + """Get greeting messages.""" + n = how_many % len(options) + return sep.join(s + exclamation for s in random.sample(options, k=n)) + + +def get_adieu() -> str: + """Create end-run greeting message.""" + end = datetime.now().strftime("%d/%m/%Y %H:%M:%S") + bye = get_goodbye_greetings() + message = f"Finished at {end}. {bye}" + return message + + +def get_goodbye_help() -> str: + """Create good-bye message with help.""" + end = datetime.now().strftime("%d/%m/%Y %H:%M:%S") + bye = get_goodbye_greetings() + message = f"Finished at {end}. For any help contact us at {contact_us}." + message += f" {bye}." + return message + + +def gen_feedback_messages(print_function: Callable) -> None: + """Print list of feedbacks urls. + + Parameters + ---------- + print_function : Callable + The function used to print message on screen. + This function must accept str as first argument. + """ + print_function( + ("Your feedback matters in Haddock3! Share your experience and help us grow:") + ) + for name, url in feedback_urls.items(): + print_function(f"{name}: {url}") + + +get_goodbye_greetings = partial(get_greetings, international_good_byes) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/haddockmodel.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/haddockmodel.py new file mode 100644 index 0000000000000000000000000000000000000000..8f02c38807384d62579b00732ac08210c7224401 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/haddockmodel.py @@ -0,0 +1,155 @@ +"""Represent an Haddock model.""" + +from haddock.core.typing import FilePath + + +class HaddockModel: + """Represent HADDOCK model.""" + + def __init__(self, pdb_f: FilePath) -> None: + remarks = self._load_remarks(pdb_f) + self.energies = self._load_energies(remarks) + self.interface_energies = self._load_per_interface_energies(remarks) + + @staticmethod + def _load_remarks(pdb_f: FilePath) -> list[str]: + """Load remark lines from PDB file + + Parameters + ---------- + pdb_f : FilePath + Path to a PDB file + + Returns + ------- + remarks : list[str] + List of PDB lines containing remarks. + """ + remarks: list[str] = [] + with open(pdb_f) as fh: + for line in fh.readlines(): + if line.startswith('REMARK'): + remarks.append(line) + return remarks + + @staticmethod + def _load_energies(remarks: list[str]) -> dict[str, float]: + """Load HADDOCK energy terms from PDB remarks. + + Parameters + ---------- + remarks : list[str] + List of PDB lines containing remarks. + + Returns + ------- + energy_dic : dict[str, float] + Dictionary of energy terms with their values + """ + energy_dic: dict[str, float] = {} + for line in remarks: + # TODO: use regex to do this + if 'energies' in line: + energy_values = map( + float, + line.rstrip().split(':')[-1].split(',') + ) + total, bonds, angles, improper, dihe, vdw, elec, air, cdih, coup, rdcs, vean, dani, xpcs, rg = energy_values # noqa: E501 + energy_dic['total'] = total + energy_dic['bonds'] = bonds + energy_dic['angles'] = angles + energy_dic['improper'] = improper + energy_dic['dihe'] = dihe + energy_dic['vdw'] = vdw + energy_dic['elec'] = elec + energy_dic['air'] = air + energy_dic['cdih'] = cdih + energy_dic['coup'] = coup + energy_dic['rdcs'] = rdcs + energy_dic['vean'] = vean + energy_dic['dani'] = dani + energy_dic['xpcs'] = xpcs + energy_dic['rg'] = rg + if 'buried surface area' in line: + bsa = float(line.rstrip().split(':')[-1]) + energy_dic['bsa'] = bsa + if 'Desolvation energy' in line: + desolv = float(line.rstrip().split(':')[-1]) + energy_dic['desolv'] = desolv + if 'Symmetry energy' in line: + sym = float(line.rstrip().split(':')[-1]) + energy_dic['sym'] = sym + + return energy_dic + + @staticmethod + def _load_per_interface_energies( + remarks: list[str], + ) -> dict[str, dict[str, float]]: + """Read a pdb file and parse per interface scores. + + Parameters + ---------- + remarks : list[str] + List of PDB lines containing remarks. + + Returns + ------- + interfaces_scores : dict[str, dict[str, float]] + Dictionary holding per interfaces scores. + """ + header = None + interfaces_scores: dict[str, dict[str, float]] = {} + for _ in remarks: + if _.startswith("REMARK Interface"): + s_ = _.strip().split()[2:] + # Extract header + if not header: + header = s_ + # Extract data + else: + chain1 = s_[header.index("Chain1")] + chain2 = s_[header.index("Chain2")] + haddockscore = float(s_[header.index("HADDOCKscore")]) + evdw = float(s_[header.index("Evdw")]) + eelec = float(s_[header.index("Eelec")]) + edesol = float(s_[header.index("Edesol")]) + bsa = float(s_[header.index("BSA")]) + # Combine chains together + chains_key = f"{chain1}_{chain2}" + # Hold data + interfaces_scores[chains_key] = { + "HADDOCKscore": haddockscore, + "vdw": evdw, + "elec": eelec, + "desolv": edesol, + "bsa": bsa, + } + return interfaces_scores + + def calc_haddock_score(self, **weights: float) -> float: + """Calculate the haddock score based on the weights and energies.""" + return self.calc_score(self.energies, **weights) + + @staticmethod + def calc_score(energies: dict[str, float], **weights: float) -> float: + """Compute sum of weighted energy terms. + + Parameters + ---------- + energies : dict[str, float] + Dict of energy values for each energy term + + Returns + ------- + weighted_score : float + Sum of weighted energy terms + """ + weighted_score: float = 0.0 + for weight_name, weight_value in weights.items(): + component_id = weight_name.split("_")[1] + try: + weighted_score += energies[component_id] * weight_value + except KeyError: + continue + return weighted_score diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/known_cns_errors.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/known_cns_errors.py new file mode 100644 index 0000000000000000000000000000000000000000..6335895f491458bb95086eb3a097e6fef40c51d9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/known_cns_errors.py @@ -0,0 +1,183 @@ +"""Detect known/common CNS errors. + +Inspired from: +https://github.com/haddocking/haddock25/blob/main/tools/check-error-messages.sh +""" + +import gzip +from io import BufferedReader +from pathlib import Path + +from haddock.core.exceptions import KnownCNSError +from haddock.core.typing import FilePath, Optional, Union + +# Dictionary of known errors +# as key: How to catch it in the cns.cnserr +# as value: Message to user +KNOWN_ERRORS = { + "CHAIN LENGTH FOR SYMMETRY RESTRAINTS DOES NOT MATCH": ( + "Mismatch between chain length for symmetry restraints. " + "Check your input molecules and symmetry restraints." + ), + "NCS-restraints error encountered: Improperly defined non-crystallographic symmetry": ( # noqa : E501 + "Improperly defined non-crystallographic symmetry (NCS). " + "Check your symmetry restraints definition." + ), + "error in SYMMETRY potential, check NOE table": ( + "Check your symmetry restraints definition." + ), + "exceeded allocation for NOE-restraints": ( + "Too many distance restraints defined. " + "Try to reduce this number by checking your definition of active " + "and passive residues. " + "Make sure to filter those for solvent accessibility. " + "Or alternatively increase the nres parameter in the noe statements" + " in the relevant CNS scripts." + ), + "SELRPN error encountered: parsing error": ( + "Check your restraint files." + ), + "PARSER error encountered: Encountered too many parsing errors": ( + "Encountered too many parsing errors. " + "Check your input molecules and symmetry restraints." + ), + "XMREAD error encountered: sectioning of map incompatible with resolution": ( # noqa : E501 + "Check your EM map resolution and sectioning." + ), + "ALLHP error encountered: not enough memory available": ( + "Too many distance restraints defined. " + "Try to reduce this number by checking your definition of active and " + "passive residues. " + "Make sure to filter those for solvent accessibility. " + "Try to decrease the size of your system where possible." + ), + "error encountered: missing SCATter definition for SELEcted atoms": ( + "Unsupported atoms/molecules for cryo-EM restraints." + ), + "ROTMAT error encountered: rotation vector has zero length": ( + "Check your input parameters and restraints. " + "Possibly try turning off the sampling of 180 degrees rotation." + ) + } + + +def find_cns_errors(cns_out_fpath: FilePath) -> Optional[KnownCNSError]: + """Detect if a known CNS error is in a cns.cnserr file. + + Parameters + ---------- + cns_out_fpath : FilePath -> Union[str, Path] + Path to the cns.cnserr file to check. + + Returns + ------- + Optional[KnownCNSError] + An exception for known CNS errors, with its hint on how to solve it! + """ + # Check for file extension to open it the appropriate way + if Path(cns_out_fpath).suffix == ".gz": + file_handle = gzip.open(cns_out_fpath, "rb") + else: + file_handle = open(cns_out_fpath, "rb") + # Read the file + try: + _find_cns_errors(file_handle, KNOWN_ERRORS, filepath=cns_out_fpath) + except KnownCNSError as err: + return err + else: + # return the cause + return KnownCNSError( + "An unfortunate CNS error occured at exection time...", + f"Manually check the file `{cns_out_fpath}` to understand why!", + cns_out_fpath, + ) + + +def _find_cns_errors( + file_handle: Union[gzip.GzipFile, BufferedReader], + known_errors: dict[str, str], + chunk_size: int = 4096, + filepath: FilePath = "", + ) -> None: + """Backward reading and detect first known CNS error in file. + + Parameters + ---------- + file_handle: Union[gzip.GzipFile, BufferedReader] + An opened file in read bytes mode. + known_errors : dict[str, str] + Dict of known errors and their hints + chunk_size : int, optional + Check size (in bytes) to read the file backwards, by default 4096 + filepath : FilePath -> Union[str, Path] + Path to the cns.cnserr file currently checked. + + Raises + ------ + KnownCNSError + An exception for known CNS errors, with its hint on how to solve it! + """ + # Find file size + file_handle.seek(0, 2) + size = file_handle.tell() + buffer = b'' + # Set the number of lines to parse + # initiated with high value to read all lines the first time + # updated to the number of lines that were already parsed + # after each chunk iteration, so we do not parse the same lines + parsed_lines = 99999 + for i in range(size - 1, -1, -chunk_size): + # Go to location in file + file_handle.seek(max(i - chunk_size, 0)) + # Read next chunk + chunk = file_handle.read(min(chunk_size, i + 1)) + # Increment buffer + buffer = chunk + buffer + lines = buffer.split(b'\n') + # Read lines + for line in reversed(lines[-len(lines):parsed_lines]): + decoded_line = line.decode('utf-8', errors='replace') + # Loop over known errors + for error_string, hint in known_errors.items(): + # Check if this error is known + if error_string in decoded_line: + # return the cause + raise KnownCNSError( + error_string, + hint, + filepath, + ) + # Update number of parsed lines so we do not check them again + parsed_lines = -len(lines) + + +def find_all_cns_errors( + directory_path: FilePath, + ) -> dict[str, dict[str, Union[int, KnownCNSError]]]: + """Find all errors in a directory. + + Parameters + ---------- + directory_path : FilePath + Path to the directory to be checked. + + Returns + ------- + all_errors : dict[str, dict[str, Union[list[FilePath], KnownCNSError]]] + Dictionary containing all errors found in this directory. + """ + all_errors: dict[str, dict[str, Union[int, KnownCNSError]]] = {} + # Gather list of all `.cnserr` and `.cnserr.gz` files present in directory + all_cns_out_files = list(Path(directory_path).glob("*.cnserr.gz")) + all_cns_out_files += list(Path(directory_path).glob("*.cnserr")) + # Loop over all .cnserr files + for fpath in all_cns_out_files: + # Try to dectect an error + if (detected_error := find_cns_errors(fpath)): + # Hold data if an error is present in that file + error_type = all_errors.setdefault( + detected_error.cns_error, + {"files": [], "error": detected_error} + ) + error_type["files"].append(detected_error.filepath) + return all_errors diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/parameters.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/parameters.py new file mode 100644 index 0000000000000000000000000000000000000000..1ab2a6cd6cb58d0285651ffd88ffe7802a2bf2e9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/parameters.py @@ -0,0 +1,18 @@ +"""Relates to logic or definition of parameters.""" +from pathlib import Path + +from haddock import haddock3_source_path +from haddock.gear.yaml2cfg import read_from_yaml_config + + +MANDATORY_YAML = Path(haddock3_source_path, "core", "mandatory.yaml") +"""The mandatory general arguments of the configuration file.""" + +OPTIONAL_YAML = Path(haddock3_source_path, "core", "optional.yaml") +"""The optional general arguments of the configuration file.""" + +_mandatory_parameters = read_from_yaml_config(MANDATORY_YAML) +config_mandatory_general_parameters = set(_mandatory_parameters) + +config_optional_general_parameters_dict = read_from_yaml_config(OPTIONAL_YAML) +config_optional_general_parameters = set(config_optional_general_parameters_dict) # noqa: E501 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/postprocessing.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/postprocessing.py new file mode 100644 index 0000000000000000000000000000000000000000..349dcbb6b991d53be268bfebb94afb3cb13261da --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/postprocessing.py @@ -0,0 +1,46 @@ +"""Tools for post-processing haddock3 runs.""" + +import os +import shutil +import tarfile + +from haddock import log +from haddock.clis.cli_analyse import ANA_FOLDER +from haddock.core.typing import Optional + + +def archive_run(run_dir: str, delete: bool = True) -> tuple[str, Optional[str]]: + """Create an archive of the haddock3 run directory and analysis. + + Parameters + ---------- + run_dir : str + Path to the run directory + delete : bool, optional + Should the un-archived directory be deleted?, by default False + + Returns + ------- + tuple[str, Optional[str]] + run_archive_fname : str + Path to the run archive + analysis_archive_fname : Optional[str] + Path to the run analysis archive + """ + log.info("Creating an archive of the run") + # Start by archiving the run_directory + run_archive_fname = f"{run_dir}.tgz" + with tarfile.open(run_archive_fname, "w:gz") as tar: + tar.add(run_dir, arcname=os.path.basename(run_dir)) + + # Archive the analysis directory + analysis_archive_fname = None + if os.path.exists(f"{run_dir}/{ANA_FOLDER}"): + analysis_archive_fname = f"{run_dir}_{ANA_FOLDER}.tgz" + with tarfile.open(analysis_archive_fname, "w:gz") as tar: + tar.add(f"{run_dir}/{ANA_FOLDER}", arcname=f"{run_dir}_{ANA_FOLDER}") + + if delete: + shutil.rmtree(run_dir) + + return run_archive_fname, analysis_archive_fname \ No newline at end of file diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/prepare_run.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/prepare_run.py new file mode 100644 index 0000000000000000000000000000000000000000..8f1ee274b0a7214445315e37c919a714cc14198f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/prepare_run.py @@ -0,0 +1,1470 @@ +"""Logic pertraining to preparing the run files and folders.""" + +import difflib +import importlib +import itertools as it +import json +import os +import shutil +import string +import sys +import tarfile +from contextlib import contextmanager, suppress +from copy import copy, deepcopy +from functools import lru_cache, wraps +from pathlib import Path, PosixPath + +from haddock import EmptyPath, contact_us, haddock3_source_path, log +from haddock.core.defaults import RUNDIR, max_molecules_allowed +from haddock.core.exceptions import ConfigurationError, ModuleError +from haddock.core.typing import ( + Any, + Callable, + FilePath, + Generator, + Iterable, + Optional, + ParamDict, + ParamMap, + Union, +) +from haddock.gear.clean_steps import ( + UNPACK_FOLDERS, + unpack_compressed_and_archived_files, + update_unpacked_names, +) +from haddock.gear.config import get_module_name +from haddock.gear.config import load as read_config +from haddock.gear.config import save as save_config +from haddock.gear.expandable_parameters import ( + get_mol_parameters, + get_multiple_index_groups, + get_single_index_groups, + is_mol_parameter, + read_mol_parameters, + read_multiple_idx_groups_user_config, + read_simplest_expandable, + read_single_idx_groups_user_config, + remove_trail_idx, + type_simplest_ep, +) +from haddock.gear.extend_run import ( + read_num_molecules_from_folder, + renum_step_folders, +) +from haddock.gear.greetings import get_goodbye_help +from haddock.gear.parameters import ( + config_mandatory_general_parameters, + config_optional_general_parameters, + config_optional_general_parameters_dict, +) +from haddock.gear.preprocessing import process_pdbs, read_additional_residues +from haddock.gear.restart_run import remove_folders_after_number +from haddock.gear.validations import ( + v_rundir, + validate_defaults_yaml, + ) +from haddock.gear.yaml2cfg import ( + read_from_yaml_config, + find_incompatible_parameters, + ) +from haddock.gear.zerofill import zero_fill +from haddock.libs.libfunc import not_none +from haddock.libs.libio import make_writeable_recursive, extract_files_flat +from haddock.libs.libutil import ( + extract_keys_recursive, + recursive_convert_paths_to_strings, + recursive_dict_update, + remove_dict_keys, + transform_to_list, +) +from haddock.modules import ( + get_module_steps_folders, + modules_category, + modules_names, + non_mandatory_general_parameters_defaults, + incompatible_defaults_params, +) +from haddock.modules.analysis import ( + confirm_resdic_chainid_length, + modules_using_resdic, +) + + +ALL_POSSIBLE_GENERAL_PARAMETERS = set.union( + set(config_mandatory_general_parameters), + set(non_mandatory_general_parameters_defaults), + config_optional_general_parameters, +) + +# Dict mapping string types (in default.yaml) into python3 objects types +TYPES_MAPPER = { + "boolean": (bool,), + "bool": (bool,), + "integer": ( + int, + float, + ), + "int": ( + int, + float, + ), + "long": ( + float, + int, + ), + "float": ( + float, + int, + ), + "double": (float,), + "string": (str,), + "str": (str,), + "list": (list,), + "array": (list,), + "path": ( + str, + Path, + PosixPath, + EmptyPath, + ), + "file": ( + str, + Path, + PosixPath, + EmptyPath, + ), + "dict": ( + dict, + ) +} + + +@contextmanager +def config_key_error() -> Generator[None, None, None]: + """Raise ConfigurationError on KeyError.""" + try: + yield + except KeyError as err: + msg = f"Expected {err.args[0]!r} parameter in configuration file." + raise ConfigurationError(msg) from err + + +def with_config_error(func: Callable[..., Any]) -> Callable[..., Any]: + """Add config error context.""" + + @wraps(func) + def wrapper(*args: Any, **kwargs: Any) -> Callable[..., Any]: + with config_key_error(): + return func(*args, **kwargs) + + return wrapper + + +@lru_cache +def _read_defaults(module_name, default_only=True): + """Read the defaults.yaml given a module name. + + Parameters + ---------- + module_name : str + Name of the HADDOCK3 module + default_only : bool + If True, only the default value of each parameters found in the + default.yaml will be return, else all information are retrieved. + + Return + ------ + mod_default_config : dict + A dict holding default value for each parameters of the module if + default_only == True, + Else a dict of dict, contraining all information present in the + default.yaml file of the module. + """ + module_name_ = get_module_name(module_name) + pdef = gen_defaults_module_param_path(module_name_) + validate_defaults_yaml(pdef) + mod_default_config = read_from_yaml_config(pdef, default_only=default_only) + return mod_default_config + + +def gen_defaults_module_param_path(module_name_: str) -> Path: + """Build path to default parameters of a module. + + Parameters + ---------- + module_name_ : str + Name of the module + + Returns + ------- + Path + Path to the module YAML defaults parameter. + """ + params_defaults_path = Path( + haddock3_source_path, + "modules", + modules_category[module_name_], + module_name_, + "defaults.yaml", + ).resolve() + return params_defaults_path + + +def setup_run( + workflow_path: FilePath, + restart_from: Optional[int] = None, + extend_run: Optional[FilePath] = None, +) -> tuple[ParamDict, ParamDict]: + """ + Set up an HADDOCK3 run. + + This function sets up a HADDOCK3 considering the options `--restart` + and `--extend-run`. The list of actions presented below does + not necessary represents the exact order in which it happens. + + Always performed: + + #. read the user configuration file + #. completes the user configuration file with the default values + for the non-specified parameters + #. validate the config file + * confirm modules' names are correctly spelled + * check if requested modules are installed + * check additional validations + #. validate modules' parameters + #. copy input files to data/ directory + * for ``--restart`` copies only after the restart number + + Performed when ``--restart``: + + #. remove folders after --restart number + #. remove also folders from `data/` dir after the ``--restart`` num + #. renumber step folders according to the number of modules + + Performed when ``--extend-run``: + + #. renumber step folders according to the number of modules + + Performed when start from scratch: + + #. check mandatory arguments are present in the config file + #. check run-dir exists + #. copy molecules to topology key (also in ``--restart``) + #. populate topology parameters (also in ``--restart``) + #. copy molecules to data dir + + Parameters + ---------- + workflow_path : str or pathlib.Path + The path to the configuration file. + + restart_from : int + The step to restart the run from (inclusive). + Defaults to None, which ignores this option. + + extend_run : str or Path + The path created with `haddock3-copy` to start the run from. + Defaults to None, which ignores this option. + + Returns + ------- + tuple of two dicts + A dictionary with the parameters for the haddock3 modules. + A dictionary with the general run parameters. + """ + # read the user config file from path + config_files = read_config(workflow_path) + + # update default non-mandatory parameters with user params + params = recursive_dict_update( + config_optional_general_parameters_dict, config_files["final_cfg"] + ) + + params = recursive_dict_update( + non_mandatory_general_parameters_defaults, + params, + ) + + validate_module_names_are_not_misspelled(params) + + # separate general from modules' parameters + _modules_keys = identify_modules(params) + general_params = remove_dict_keys(params, _modules_keys) + modules_params = remove_dict_keys(params, list(general_params.keys())) + + validate_parameters_are_not_misspelled( + general_params, + reference_parameters=ALL_POSSIBLE_GENERAL_PARAMETERS, + ) + + # Validate there is no incompatible parameters in global parameters + validate_parameters_are_not_incompatible( + general_params, + incompatible_defaults_params, + ) + + # --extend-run configs do not define the run directory + # in the config file. So we take it from the argument. + if not_none(extend_run): + with suppress(TypeError): + extend_run = Path(extend_run) + + general_params[RUNDIR] = extend_run + + check_if_modules_are_installed(modules_params) + check_specific_validations(general_params) + + # define starting conditions + # consider a deeper refactor if additional conditions are implemented + # @joaomcteixeira, 09 May 2022 + from_scratch = restart_from is None and extend_run is None + scratch_rest0 = from_scratch or restart_from == 0 + restarting_from = not_none(restart_from) + starting_from_copy = not_none(extend_run) + + if from_scratch: + check_run_dir_exists(general_params[RUNDIR]) + + if scratch_rest0: + check_mandatory_argments_are_present(general_params) + + if restarting_from: + remove_folders_after_number(general_params[RUNDIR], restart_from) + _data_dir = Path(general_params[RUNDIR], "data") + remove_folders_after_number(_data_dir, restart_from) + + if restarting_from or starting_from_copy: + # get run files in folder + step_folders = get_module_steps_folders(general_params[RUNDIR]) + + log.info( + "Uncompressing previous output files for folders: " + f'{", ".join(step_folders)}' + ) + # unpack the possible compressed and archived files + _step_folders = (Path(general_params[RUNDIR], p) for p in step_folders) + unpack_compressed_and_archived_files( + _step_folders, + general_params["ncores"], + dec_all=True, + ) + + if starting_from_copy: + num_steps = len(step_folders) + _num_modules = len(modules_params) + # has to consider the folders already present, plus the new folders + # in the configuration file + zero_fill.set_zerofill_number(num_steps + _num_modules) + + max_mols = read_num_molecules_from_folder(extend_run) + + else: + copy_molecules_to_topology( + general_params["molecules"], + modules_params["topoaa.1"], + ) + + if len(modules_params["topoaa.1"]["molecules"]) > max_molecules_allowed: + raise ConfigurationError( + f"Too many molecules defined, max is {max_molecules_allowed}." + ) # noqa: E501 + + zero_fill.read(modules_params) + + populate_topology_molecule_params(modules_params["topoaa.1"]) + populate_mol_parameters(modules_params) + + max_mols = len(modules_params["topoaa.1"]["molecules"]) + + if not from_scratch: + _prev, _new = renum_step_folders(general_params[RUNDIR]) + renum_step_folders(Path(general_params[RUNDIR], "data")) + if UNPACK_FOLDERS: # only if there was any folder unpacked + update_unpacked_names(_prev, _new, UNPACK_FOLDERS) + update_step_contents_to_step_names( + _prev, + _new, + general_params[RUNDIR], + ) + + validate_modules_params(modules_params, max_mols) + + # create datadir + data_dir = create_data_dir(general_params[RUNDIR]) + + # Add workflow configuration file in data directory + enhanced_haddock_params = deepcopy(general_params) + enhanced_haddock_params.update(modules_params) + config_files["enhanced_haddock_params"] = enhanced_haddock_params + config_saves = save_configuration_files(config_files, data_dir) # noqa : F841 + + if scratch_rest0: + copy_molecules_to_data_dir( + data_dir, + modules_params["topoaa.1"], + preprocess=general_params["preprocess"], + ) + + if starting_from_copy: + copy_input_files_to_data_dir(data_dir, modules_params, start=num_steps) + + elif restarting_from: + # copies only the input molecules needed + _keys = list(modules_params.keys()) + _partial_params = {k: modules_params[k] for k in _keys[restart_from:]} + copy_input_files_to_data_dir( + data_dir, + _partial_params, + start=restart_from, + ) + + else: + # copies everything + copy_input_files_to_data_dir(data_dir, modules_params) + + # grant write permissions to data/ dir + make_writeable_recursive(data_dir) + + # return the modules' parameters and general parameters separately + return modules_params, general_params + + +def save_configuration_files(configs: dict, datadir: Union[str, Path]) -> dict: + """Write a copy of configuration files (GitHub issue #578). + + Parameters + ---------- + configs : dict + Dictionnary holding the various configuration files + ['raw_input, 'cleaned_input', 'loaded_cleaned_input', + 'final_cfg', 'enhanced_haddock_params'] + datadir : str or :py:class:`libpath.Path` + Directory where to write the configuration. + + Return + ------ + added_files : dict + Dictionary of paths leading to saved configuration files. + """ + # Create directory + confpaths = Path(datadir, "configurations/") + confpaths.mkdir(parents=True, exist_ok=True) + # Initiate files data + infofile = { + "raw_input": ( + "An untouched copy of the raw input file, " "as provided by the user." + ), + "cleaned_input": ( + "Pre-parsed input file where (eventually) " + "some indexing and modifications were " + "applied to ensure further processing." + ), + "enhanced_haddock_params": ( + "Final input file with detailed default parameters." + ), + } + added_files = {} + # Set list of configurations that wish to be saved + list_save_conf = [ + "raw_input", + "cleaned_input", + "enhanced_haddock_params", + ] + + # Loop over configuration files + for confname in list_save_conf: + try: + confdt = configs[confname] + except KeyError: + continue + + toml_fpath = Path(confpaths, f"{confname}.toml") + if isinstance(confdt, dict): + # Save toml version + save_config(confdt, toml_fpath) + # Save json version + json_fpath = Path(confpaths, f"{confname}.json") + jsonconf = recursive_convert_paths_to_strings(confdt) + with open(json_fpath, "w", encoding="utf-8") as f: + json.dump(jsonconf, f, indent=4) + else: + with open(toml_fpath, "w") as f: + f.write(confdt) + + added_files[confname] = toml_fpath + + # Add README to help user + readmepath = Path(confpaths, "README.txt") + with open(readmepath, "w") as f: + f.write( + f"{'#'*80}\n# Information about configuration " + f"files present in the same directory #\n{'#'*80}\n" + ) + for confname in list_save_conf: + if confname not in added_files.keys(): + continue + f.write(f'"{added_files[confname]}": {infofile[confname]}\n') + added_files["readme"] = readmepath + + # Return mapper to added files + return added_files + + +def validate_params(params): + """ + Validate the parameter file. + + #1 : checks for mandatory parameters + #2 : checks for correct modules + """ + check_mandatory_argments_are_present(params) + validate_modules_names(params) + + +def check_mandatory_argments_are_present(params: Iterable[str]) -> None: + """Confirm order key exists in config.""" + for arg in config_mandatory_general_parameters: + if arg not in params: + _msg = ( + f"Parameter {arg!r} is not defined in the configuration file. " + "Please refer to DOCUMENTATION-LINK for more information." + ) + raise ConfigurationError(_msg) + return + + +@with_config_error +def validate_modules_names(params: Iterable[str]) -> None: + """Validate all modules names are spelled correctly.""" + keys = ( + set(params) + - set(config_mandatory_general_parameters) + - set(non_mandatory_general_parameters_defaults) + ) + + for module in keys: + if get_module_name(module) not in modules_category.keys(): + _msg = ( + f"Module {module} not found in HADDOCK3 library. " + "Please refer to the list of available modules at: " + "DOCUMENTATION-LINK" + ) + raise ConfigurationError(_msg) + + +@with_config_error +def validate_modules_params(modules_params: ParamMap, max_mols: int) -> None: + """Validate individual parameters for each module. + + Raises + ------ + ConfigError + If there is any parameter given by the user that is not defined + in the defaults.cfg of the module. + """ + for module_name, args in modules_params.items(): + module_name = get_module_name(module_name) + defaults = _read_defaults(module_name) + if not defaults: + continue + + # Check for parameter incompatibilities + module_incompatibilities = find_incompatible_parameters( + gen_defaults_module_param_path(module_name) + ) + try: + validate_parameters_are_not_incompatible( + args, + module_incompatibilities, + ) + except ValueError as e: + raise ConfigurationError( + f"An issue was discovered in module [{module_name}]: " + f"{e.args[0]}" + ) + + if module_name in modules_using_resdic: + confirm_resdic_chainid_length(args) + + expandable_params = get_expandable_parameters( + args, + defaults, + module_name, + max_mols, + ) + + all_parameters = set.union( + set(extract_keys_recursive(defaults)), + set(non_mandatory_general_parameters_defaults.keys()), + expandable_params, + ) + + diff = set(extract_keys_recursive(args)) - all_parameters + + if diff: + matched = fuzzy_match(diff, all_parameters) + + def pretty_print(match: tuple[str, str]) -> str: + return f" * '{match[0]}' did you mean '{match[1]}'?" + + _msg = ( + "The following parameters do not match any expected " + f"parameters for module {module_name!r}: {os.linesep}" + f"{os.linesep.join(map(pretty_print, matched))}." + ) + raise ConfigurationError(_msg) + + # Now that existence of the parameter was checked, + # it is time to validate the type and value taken by this param + validate_module_params_values(module_name, args) + # Validate ncs parameters + validate_ncs_params(args) + + # Update parameters with defaults ones + _missing_defaults = { + param: default + for param, default in defaults.items() + if param not in args.keys() + } + args.update(_missing_defaults) + + +def validate_module_params_values(module_name: str, args: dict) -> None: + """Validate individual parameters for a module. + + Parameters + ---------- + module_name : + Name of the module to be analyzed + args : dict + Dictionnary of key/value present in user config file for a module + + Raises + ------ + ConfigError + If there is any parameter given by the user that is not following the + types or ranges/choices allowed in the defaults.cfg of the module. + """ + # Load all parameters information from 'defaults.cfg' + default_conf_params = _read_defaults(module_name, default_only=False) + # Loop over user queried parameters keys/values + for key, val in args.items(): + validate_value(default_conf_params, key, val) + + +def validate_value(default_yaml: dict, key: str, value: Any) -> None: + """Validate queried value for a specific parameter of a module. + + Parameters + ---------- + default_yaml : dict + Dictionnary of key/value present in user config file for a module + key : str + Key to be analyzed + value : [bool, int, float, str, list] + The provided value for a parameter + + Raises + ------ + ConfigError + If there is any parameter given by the user that is not following the + types or ranges/choices allowed in the defaults.cfg of the module. + """ + # Special case for molecules... + if key not in default_yaml.keys(): + return + if "group" in default_yaml[key].keys(): + if default_yaml[key]["group"] == "molecules": + return + + # Series of checks + if _msg := validate_param_type(default_yaml[key], value): + raise ConfigurationError(f'Config error for parameter "{key}": {_msg}') + if _msg := validate_param_range(default_yaml[key], value): + raise ConfigurationError(f'Config error for parameter "{key}": {_msg}') + # FIXME: add more checks here ? + + +def validate_param_type(param: dict, val: Any) -> Optional[str]: + """Check if provided parameter type is similar to defined defaults ones. + + Parameters + ---------- + param : dict + Dictionnary of key/value present in user config file for a module + val : [bool, int, float, str, list] + The provided value for a parameter + + Return + ------ + May return a string explaining the issue with the provided value type + """ + if "type" not in param.keys(): + return + # Load type from string to python class + try: + allowed_types = TYPES_MAPPER[param["type"]] + except KeyError as e: + return f'Unrecognized default type "{e}"' + # Check if both of the same type + if (query_type := type(val)) not in allowed_types: + return ( + f'Wrong provided type "{query_type}" with value "{val}". ' + f'It should be of type "{param["type"]}" ' + f'(e.g: {param["default"]})' + ) + + +def validate_param_range(param: dict, val: Any) -> Optional[str]: + """Check if provided value is in range/choices defined for this parameter. + + Parameters + ---------- + param : dict + Dictionnary of key/value present in user config file for a module + val : [bool, int, float, str, list] + The provided value for a parameter + + Return + ------ + May return a string explaining the issue with the provided value range + """ + # Case for choices + if "choices" in param.keys(): + if val not in (choices := param["choices"]): + return f'Value "{val}" is not among the accepted choices: {choices}' # noqa : E501 + # Case for ranges + elif "min" in param.keys() and "max" in param.keys(): + if val < param["min"] or val > param["max"]: + return ( + f'Value "{val}" is not in the allowed boundaries ' + f'ranging from {param["min"]} to {param["max"]}' + ) + # Case for lists + elif "minitems" in param.keys() and "maxitems" in param.keys(): + if (nbitems := len(val)) < param["minitems"] or nbitems > param["maxitems"]: + _desc = "under" if nbitems < param["minitems"] else "exceeding" + return ( + f'Number of items found in "{val}" is {_desc} the ' + "permitted limit. It should range from " + f'{param["minitems"]} to {param["maxitems"]}' + ) + # Case for strings + elif "minchars" in param.keys() and "maxchars" in param.keys(): + if (nbchars := len(val)) < param["minchars"] or nbchars > param["maxchars"]: + _desc = "under" if nbchars < param["minitems"] else "exceeding" + return ( + f'Number of items found in "{val}" is {_desc} the ' + "permitted limit. It should range from " + f'{param["minchars"]} to {param["maxchars"]}' + ) + + +def validate_ncs_params(params: dict) -> None: + """Validate Non-Crystallographic Symmetry parameters. + + This is a particular case where: + - ncs_sta1_X == ncs_sta2_X + - ncs_end1_X == ncs_end2_X + - ncs_seg1_X != ncs_seg2_X + + Parameters + ---------- + params : dict + Dictionary of key/value present in user config file for a module + + Raises + ------ + ConfigurationError + Issue detected when validating NCS parameters. + """ + try: + # Check if ncs_on == False + if not params["ncs_on"]: + return None + # Maybe this module do not have ncs parameters, so we skip it + except KeyError: + return None + # At this stage, ncs_on == True + base_ncs_param_names = ("ncs_sta", "ncs_end", "ncs_seg", ) + # Read and group ncs parameters together + groupped_ncs: dict[int, dict[str, dict[int, Union[int, str]]]] = {} + for paramname, value in params.items(): + # Check if this is a ncs parameter + if paramname[:7] in base_ncs_param_names: + # Point two interesting values here + first_or_second = int(paramname[7]) + x = int(paramname[-1]) + # Point param type ("sta", "end", or "seg") + param_type = paramname.split('_')[1][:-1] + # Point/Create holding dict(s) + ncs_group = groupped_ncs.setdefault(x, {}) + ncs_type = ncs_group.setdefault(param_type, {}) + # Hold value + ncs_type[first_or_second] = value + + # Validate them + error_list: list[str] = [] + # Loop over number of definitions (_X) + for x, paramtype_values in groupped_ncs.items(): + # Loop over parameter types + for paramtype, values in paramtype_values.items(): + two_values = tuple(values.values()) + # First make sure both are defined ! + if len(two_values) != 2: + msg = f"Not two values set of `ncs_{paramtype}Y_{x}" + error_list.append(msg) + continue + if paramtype in ("sta", "end", ): + # Check they are not similar (wrong!) + if not len(set(two_values)) == 1: + msg = ( + f"Values set of `ncs_{paramtype}Y_{x} must be equal: " + f"we parsed `{two_values[0]}` and `{two_values[1]}`" + ) + error_list.append(msg) + else: # paramtype == "seg" + # Check they are similar (wrong!) + if len(set(values.values())) == 1: + msg = ( + f"Chain/Segment IDs for `ncs_{paramtype}Y_{x} must be " + f"different: we parsed `{two_values[0]}` and" + f" `{two_values[1]}`" + ) + error_list.append(msg) + + # Validate value of `numncs` + ncs_suffixes = list(groupped_ncs.keys()) + # Case when number of definition do not match + if params["nncs"] != len(ncs_suffixes): + msg = ( + f'Number of NCS restraints (`nncs = {params["nncs"]}`) ' + " do not match with the number of defined NCS restraints " + f"({len(ncs_suffixes)})" + ) + error_list.append(msg) + else: + # Case when numbers do not match + if max(ncs_suffixes) != params["nncs"]: + msg = ( + f'Number of NCS restraints (`nncs = {params["nncs"]}`) ' + " do not match with the number of defined NCS restraints " + f"({', '.join([str(s) for s in ncs_suffixes])})" + ) + error_list.append(msg) + + # Here we fall into the error case + if len(error_list) > 0: + # Build user message + _msg = ( + "Some errors were discovered in the NCS restraints definition:" + f"{os.linesep}" + f"{os.linesep.join(error_list)}" + ) + # Raise error + raise ConfigurationError(_msg) + return None + + +def check_if_modules_are_installed(params: ParamMap) -> None: + """Validate if third party-libraries are installed.""" + for module_name in params.keys(): + module_import_name = ".".join( + [ + "haddock", + "modules", + modules_category[get_module_name(module_name)], + get_module_name(module_name), + ] + ) + module_lib = importlib.import_module(module_import_name) + try: + module_lib.HaddockModule.confirm_installation() + except Exception as err: + _msg = ( + "A problem occurred while assessing if module " + f"{module_name!r} is installed in your system. Have you " + "installed the packages required to run this module? If " + f"yes, write us at {contact_us!r} describing your system " + "and the problems you are facing. If not, please install " + "the required packages to use the module." + ) + raise ModuleError(_msg) from err + + +# depecrated +# def convert_params_to_path(params): +# """Convert parameters to path.""" +# convert_molecules_to_path(params) +# convert_run_dir_to_path(params) +# return +# +# +# @with_config_error +# def convert_molecules_to_path(params): +# """ +# Convert molecules path strings to Python Paths. +# +# And... convert `molecules` in `params` to a dictionary where keys +# are `key` + `sep` + enumerate(`start`), and values are the new Path +# values. +# """ +# molecules = make_list_if_string(params['molecules']) +# params['molecules'] = [Path(i).resolve() for i in molecules] +# return +# +# +# @with_config_error +# def convert_run_dir_to_path(params): +# """Convert run directory value to Python Path.""" +# params[RUNDIR] = Path(params[RUNDIR]) +# return + + +@with_config_error +def create_data_dir(run_dir: FilePath) -> Path: + """ + Create initial files for HADDOCK3 run. + + Returns + ------- + pathlib.Path + A path referring only to 'data'. + """ + data_dir = Path(run_dir, "data") + data_dir.mkdir(parents=True, exist_ok=True) + return data_dir + + +@with_config_error +def copy_molecules_to_topology( + molecules: Iterable[str], topoaa_params: ParamMap +) -> None: + """Copy molecules to mandatory topology module.""" + topoaa_params["molecules"] = list(map(Path, transform_to_list(molecules))) + + +def copy_molecules_to_data_dir( + data_dir: Path, topoaa_params: ParamMap, preprocess: bool = True +) -> None: + """ + Copy molecules to data directory and to topoaa parameters. + + Parameters + ---------- + data_dir : Path + The data/ directory inside the run directory. Must contain + reference to the run directory. + + topoaa_params : dict + A dictionary containing the topoaa parameters. + + preprocess : bool + Whether to preprocess input molecules. Defaults to ``True``. + See :py:mod:`haddock.gear.preprocessing`. + """ + topoaa_dir = zero_fill.fill("topoaa", 0) + + # define paths + data_topoaa_dir = Path(data_dir, topoaa_dir) + data_topoaa_dir.mkdir(parents=True, exist_ok=True) + rel_data_topoaa_dir = Path(data_dir.name, topoaa_dir) + original_mol_dir = Path(data_dir, "original_molecules") + + new_molecules: list[Path] = [] + for molecule in copy(topoaa_params["molecules"]): + check_if_path_exists(molecule) + + mol_name = Path(molecule).name + + if preprocess: # preprocess PDB files + top_fname = topoaa_params.get("ligand_top_fname", False) + new_residues = read_additional_residues(top_fname) if top_fname else None + + new_pdbs = process_pdbs(molecule, user_supported_residues=new_residues) + + # copy the original molecule + original_mol_dir.mkdir(parents=True, exist_ok=True) + original_mol = Path(original_mol_dir, mol_name) + shutil.copy(molecule, original_mol) + + # write the new processed molecule + new_pdb = os.linesep.join(new_pdbs[0]) + Path(data_topoaa_dir, mol_name).write_text(new_pdb) + + else: + shutil.copy(molecule, Path(data_topoaa_dir, mol_name)) + + new_molecules.append(Path(rel_data_topoaa_dir, mol_name)) + + topoaa_params["molecules"] = copy(new_molecules) + + +def copy_input_files_to_data_dir( + data_dir: Path, modules_params: ParamMap, start: int = 0 +) -> None: + """ + Copy input files to data directory. + + Parameters + ---------- + data_dir : Path + The data/ directory inside the run directory. Must contain + reference to the run directory. + + modules_params : dict + A dictionary with the parameters of the modules. The paths to + data in the dictionary are updated to the new paths copied + to the data/ folder. + + start : int, default to 0 + The starting number of the step folders prefix. + """ + rel_data_dir = data_dir.name + for i, (module, params) in enumerate(modules_params.items(), start=start): + end_path = Path(zero_fill.fill(get_module_name(module), i)) + for parameter, value in params.items(): + if parameter.endswith("_fname"): + if value: + name = Path(value).name + # path is created here to avoid creating empty folders + # for those modules without '_fname' parameters + pf = Path(data_dir, end_path) + pf.mkdir(exist_ok=True) + check_if_path_exists(value) + target_path = Path(pf, name) + shutil.copy(value, target_path) + _p = Path(rel_data_dir, end_path, name) + modules_params[module][parameter] = _p + # account for input .tgz files + if name.endswith("tgz"): + log.info(f"Uncompressing tar {value}") + extract_files_flat(value, pf) + + +def check_run_dir_exists(run_dir: FilePath) -> None: + """Check whether the run directory exists.""" + _p = Path(run_dir) + if _p.exists() and len(list(_p.iterdir())) > 0: + log.info( + f"The {RUNDIR!r} {str(_p)!r} exists and is not empty. " + "We can't work on it unless you provide the `--restart` " + "option. If you want to start a run from scratch, " + "indicate a new folder, or manually delete this one first, " + "or use `--restart 0`." + ) + sys.exit(get_goodbye_help()) + + +def identify_modules(params: Iterable[str]) -> list[str]: + """Identify keys (headings) belonging to HADDOCK3 modules.""" + modules_keys = [k for k in params if get_module_name(k) in modules_category] + return modules_keys + + +def inject_in_modules(modules_params: ParamMap, key: Any, value: Any) -> None: + """Inject a parameter in each module.""" + for params in modules_params.values(): + if key in params: + raise ValueError( + "key {key!r} already in {module!r} parameters. " "Can't inject." + ) + params[key] = value + + +def validate_module_names_are_not_misspelled(params: ParamMap) -> None: + """ + Validate module names are not misspelled in step definitions. + + Parameters + ---------- + params : dict + The user configuration file. + """ + params_to_check = [ + get_module_name(param) + for param, value in params.items() + if isinstance(value, dict) + ] + + validate_parameters_are_not_misspelled( + params_to_check, + reference_parameters=modules_names, + ) + + return + + +def validate_parameters_are_not_incompatible( + params: ParamMap, + incompatible_params: ParamMap, + ) -> None: + """ + Validate parameters are not incompatible. + + Parameters + ---------- + params : ParamMap + A mapping of parameter names to their values. + + Raises + ------ + ValueError + If any parameter in `params` is incompatible with another parameter + as defined by `incompatible_params`. + """ + for limiting_param, incompatibilities in incompatible_params.items(): + # Check if the limiting parameter is present in the parameters + if limiting_param in params: + # Point incompatibilities for the value of the limiting parameter + if params[limiting_param] not in incompatibilities.keys(): + continue + active_incompatibilities = incompatibilities[params[limiting_param]] + # Check each incompatibility for the limiting parameter + for incompatible_param, incompatible_value in active_incompatibilities.items(): + # Check if the incompatible parameter is present and has the incompatible value + if params.get(incompatible_param) == incompatible_value: + raise ValueError( + f"Parameter `{limiting_param}` with value " + f"`{params[limiting_param]}` is incompatible with " + f"`{incompatible_param}={incompatible_value}`." + ) + + +def validate_parameters_are_not_misspelled( + params: Iterable[str], reference_parameters: Iterable[str] +) -> None: + """Validate general parameters are not misspelled.""" + for param_name in params: + if param_name not in reference_parameters: + matched = fuzzy_match([param_name], reference_parameters) + emsg = ( + f"Parameter {param_name!r} is not a valid general parameter," + f" did you mean {matched[0][1]!r}?" + ) + raise ValueError(emsg) + + +@with_config_error +def check_specific_validations(params: ParamMap) -> None: + """Make specific validations.""" + # double check though this is confirmed already in the config reader + v_rundir(params[RUNDIR]) + + +def get_expandable_parameters( + user_config: ParamMap, defaults: ParamMap, module_name: str, max_mols: int +) -> set[str]: + """ + Get configuration expandable blocks. + + Parameters + ---------- + user_config : dict + The user configuration file for a module. + + defaults : dict + The default configuration file defined for the module. + + module_name : str + The name the module being processed. + + max_mols : int + The max number of molecules allowed. + """ + # the topoaa module is an exception because it has subdictionaries + # for the `mol` parameter. Instead of defining a general recursive + # function, I decided to add a simple if/else exception. + # no other module should have subdictionaries has parameters + if get_module_name(module_name) == "topoaa": + ap: set[str] = set() # allowed_parameters + ap.update(_get_expandable(user_config, defaults, module_name, max_mols)) + for i in range(1, max_mols + 1): + key = f"mol{i}" + with suppress(KeyError): + ap.update( + _get_expandable( + user_config[key], + defaults["mol1"], + module_name, + max_mols, + ) + ) + + return ap + + elif module_name in modules_using_resdic: + ep = _get_expandable(user_config, defaults, module_name, max_mols) + for _param in user_config.keys(): + if _param.startswith("resdic_"): + ep.add(_param) + return ep + + else: + return _get_expandable(user_config, defaults, module_name, max_mols) + + +# reading parameter blocks +def _get_expandable( + user_config: ParamMap, defaults: ParamMap, module_name: str, max_mols: int +) -> set[str]: + # Set parsing vars + allowed_params: set[str] = set() + all_counts: dict[str, int] = {} + # Read single indexed groups (terminating by `_X`) + news_t1, counts_t1 = read_single_idx_groups_user_config( + user_config, + get_single_index_groups(defaults), + ) + allowed_params.update(news_t1) + all_counts.update(counts_t1) + # Read multiple indexed groups (terminating by `_X_Y`) + news_t2, counts_t2 = read_multiple_idx_groups_user_config( + user_config, + get_multiple_index_groups(defaults), + ) + allowed_params.update(news_t2) + all_counts.update(counts_t2) + + with suppress(KeyError): + news_t3 = read_simplest_expandable( + user_config, + type_simplest_ep[get_module_name(module_name)], + ) + allowed_params.update(news_t3) + # Read molecule paramters (starting by `mol_`) + _ = read_mol_parameters( + user_config, + get_mol_parameters(defaults), + max_mols=max_mols, + ) + allowed_params.update(_) + + # Add counted parameters to hidden user parameters + for param, count in all_counts.items(): + count_param_name = f"n{param}" + if count_param_name in defaults.keys(): + user_config[count_param_name] = count + # Return new set of allowed parameters + return allowed_params + + +def populate_topology_molecule_params(topoaa: ParamMap) -> None: + """Populate topoaa `molX` subdictionaries.""" + topoaa_dft = _read_defaults("topoaa.1") + + for i in range(1, len(topoaa["molecules"]) + 1): + mol = f"mol{i}" + + topoaa[mol] = recursive_dict_update( + topoaa_dft["mol1"], + topoaa[mol] if mol in topoaa else {}, + ) + return + + +def populate_mol_parameters(modules_params: ParamMap) -> None: + """ + Populate modules subdictionaries with the needed molecule `mol_` parameters. + + The `mol_` prefixed parameters is a subclass of the expandable parameters. + + See `gear.expandable_parameters`. + + Modules require these parameters to be repeated for the number of input + molecules. + + This function adds `mol_` parameters to the user input parameters, + one per each `molecule`. + + Parameters + ---------- + modules_params : dict + A dictionary containing only modules' keys:subdictionaries + parameters. That is, without the general parameters. + + Returns + ------- + None + Alter the dictionary in place. + """ + # the starting number of the `mol_` parameters is 1 by CNS definition. + num_mols = range(1, len(modules_params["topoaa.1"]["molecules"]) + 1) + for module_name, _ in modules_params.items(): + # read the modules default parameters + defaults = _read_defaults(module_name) + + # if there are no `mol_` parameters in the modules default values, + # the `mol_params` generator will be empty and the for-loop below + # won't run. + mol_params = (p for p in list(defaults.keys()) if is_mol_parameter(p)) + + for param, i in it.product(mol_params, num_mols): + param_name = remove_trail_idx(param) + + # the `setdefault` grants that the value is only added if + # the parameter is not present. + modules_params[module_name].setdefault( + f"{param_name}_{i}", + defaults[param], + ) + return + + +def check_if_path_exists(path: FilePath) -> None: + """ + Check if a path exists and raises an error if it does not exist. + + For example given this path "../config/project_01/file.txt" it would find + the following path "../config/project-01". + + Parameters + ---------- + path : AnyStr | PathLike + The path to check. + + Returns + ------- + None + If the path does exist. + + Raises + ------ + ValueError + If the path does not exist. + """ + path = os.path.normpath(path) + if os.path.exists(path): + return None + + reconstituted_path: str = "./" + error = ("", "", "") + elements = Path(path).parts + if elements[0] == ".": + elements = elements[1:] + for part in elements: + next_folder = Path(reconstituted_path, part) + if not next_folder.exists(): + error = ( + reconstituted_path, + fuzzy_match([part], os.listdir(reconstituted_path))[0][1], + part, + ) + break + reconstituted_path = str(next_folder) + + msg = ( + f"The following file could not be found: '{path}'. " + f"In the folder '{error[0]}' the following '{error[1]}' " + f"is the closest match to the supplied '{error[2]}', did " + "you mean to open this?" + ) + raise ValueError(msg) + + +def fuzzy_match( + user_input: Iterable[str], possibilities: Iterable[str] +) -> list[tuple[str, str]]: + """ + Find the closest possibility to the user supplied input. + + Parameters + ---------- + user_input : list(string) + List of strings with the faulty input given by the user. + + possibilities : list(string) + List of strings with all possible options that would be + valid in this context. + + Returns + ------- + list(string, string) + The closest string from the possibilities to each string of the + `user_input`. With as first element of the tuple the user_input + string, and as second element the matched possibility. + """ + results: list[tuple[str, str]] = list() + + for user_word in transform_to_list(user_input): + best: tuple[float, Any] = (-1, "") + for possibility in possibilities: + distance = difflib.SequenceMatcher( + a=user_word, b=possibility + ).ratio() # noqa: E501 + if distance > best[0]: + best = (distance, possibility) + results.append((user_word, best[1])) + + return results + + +def update_step_contents_to_step_names( + prev_names: Iterable[str], new_names: Iterable[str], folder: FilePath +) -> None: + """ + Update step folder names in files after the `--restart` option. + + Runs over the folders defined in `new_names`. + + Parameters + ---------- + prev_names : list + List of step names to find in file contents. + + new_names : list + List of new step names to replace `prev_names`. Both lists need + to be synchronized. That is, the first index of `prev_names` should + correspond to the old names of `new_names`. + + folder : str or Path + Folder where the step folders are. Usually run directory or + data directory. + + Returns + ------- + None + Save files in place. + """ + for new_step in new_names: + new_step_p = Path(folder, new_step) + for file_ in new_step_p.iterdir(): + # goes recursive into the next folder + if file_.is_dir(): + update_step_names_in_subfolders(file_, prev_names, new_names) + + else: + update_step_names_in_file(file_, prev_names, new_names) + + +def update_step_names_in_subfolders( + folder: Path, prev_names: Iterable[str], new_names: Iterable[str] +) -> None: + """ + Update step names in subfolders. + + Some modules may generate subfolders. This function update + its files accordingly to the `--restart` feature. + """ + for file_ in folder.iterdir(): + if file_.is_dir(): + update_step_names_in_subfolders(file_, prev_names, new_names) + else: + update_step_names_in_file(file_, prev_names, new_names) + return + + +def update_step_names_in_file( + file_: Path, prev_names: Iterable[str], new_names: Iterable[str] +) -> None: + """Update step names in file following the `--restart` option.""" + try: + text = file_.read_text() + except UnicodeDecodeError as err: + log.warning(f"Failed to read file {file_}. Error is {err}") + return + for s1, s2 in zip(prev_names, new_names): + text = text.replace(s1, s2) + file_.write_text(text) + return diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/preprocessing.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/preprocessing.py new file mode 100644 index 0000000000000000000000000000000000000000..1df1db513b3bc9b2a8fa3a0d6ab5b203e1dc83a7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/preprocessing.py @@ -0,0 +1,1090 @@ +# TODO: +# 1. single_ions may contain PO4 - verify +# 2. the single_ions_elements map seems not needed +""" +Process input PDB files to ensure compatibility with HADDOCK3. + +This module checks and modifies PDB files for compatibility with +HADDOCK3. There are three types of checks/modifications: + +1. Performed to each PDB line-by-line, in a equal fashion of ``pdb-tools``. + In fact, this step mostly uses the ``pdb-tools`` package. +2. Performed on each PDB as a whole. +3. Performed on all PDBs together. + +Main functions +-------------- + +* :py:func:`process_pdbs` +* :py:func:`read_additional_residues` + +Corrections performed on 1) +--------------------------- + +The following actions are perfomed sequentially over all PDBs: + +#. from ``pdb-tools``: ``pdb_keepcoord`` +#. from ``pdb-tools``: ``pdb_tidy`` with ``strict=True`` +#. from ``pdb-toos``: ``pdb_element`` +#. from ``pdb-tools``: ``pdb_selaltloc`` +#. from ``pdb-tools``: ``pdb_pdb_occ`` with ``occupancy=1.00`` +#. replace ``MSE`` to ``MET`` +#. replace ``HSD`` to ``HIS`` +#. replace ``HSE`` to ``HIS`` +#. replace ``HID`` to ``HIS`` +#. replace ``HIE`` to ``HIS`` +#. add_charges_to_ions, see :py:func:`add_charges_to_ions` +#. convert ``ATOM`` to ``HETATM`` for those atoms that should be ``HETATM``. + Considers the additional residues provided by the user. + See :py:func:`convert_ATOM_to_HETATM`. +#. convert ``HETATM`` to ``ATOM`` for those atoms that should be ``ATOM``, +#. from ``pdb-toos``: ``pdb_fixinsert``, with ``option_list=[]``. +#. remove unsupported ``HETATM``. Considers residues provided by the user. +#. remove unsupported ``ATOM``. Considers residues provided by the user. +#. from ``pdb-tools``: ``pdb_reatom``, start from ``1``. +#. from ``pdb-tools``: ``pdb_tidy`` with ``strict=True`` + +Corrections performed on 2) +--------------------------- + +The following actions are performed sequentially for each PDB: + +* :py:func:`models_should_have_the_same_labels` +* :py:func:`solve_no_chainID_no_segID` +* :py:func:`homogenize_chains` + +Read the documentation of the above functions for details what they do. + +Corrections performed on 3) +--------------------------- + +The following actions are performed to all PDBs together: + +* :py:func:`correct_equal_chain_segids` + +Read the documentation of the above functions for details what they do. + +When it happens +--------------- + +The PDB processing step is performed by default when reading the input +molecules and copying them to the `data/` folder inside the run +directory. When PDBs are processed, a copy of the original input PDBs is +also stored in the `data/` folder. + +To deactivate this initial PDB processing, set ``skip_preprocess = False`` +in the general parameters of the configuration file. + +Additional information +---------------------- + +If you are a developer and want to read more about the history of this +preprocessing module, visit: + +https://github.com/haddocking/haddock3/projects/16 +""" +import io +import itertools as it +import re +import string +from functools import partial, wraps +from os import linesep +from pathlib import Path + +from pdbtools import ( + pdb_chain, + pdb_chainxseg, + pdb_element, + pdb_fixinsert, + pdb_keepcoord, + pdb_occ, + pdb_reatom, + pdb_rplresname, + pdb_segxchain, + pdb_selaltloc, + pdb_shiftres, + pdb_tidy, +) + +from haddock import log +from haddock.core.exceptions import HaddockError +from haddock.core.supported_molecules import ( + supported_ATOM, + supported_HETATM, + supported_non_ions, + supported_single_ions_atoms_map, + supported_single_ions_resnames_map, +) +from haddock.core.typing import ( + Any, + Callable, + Container, + Generator, + Iterable, + LineIterSource, + Optional, + Union, +) +from haddock.libs.libfunc import chainf +from haddock.libs.libio import read_lines +from haddock.libs.libpdb import ( + format_atom_name, + read_chainids, + read_segids, + slc_charge, + slc_element, + slc_name, + slc_resname, +) + + +# defines chain letters for chain and seg IDs +_ascii_letters = list(string.ascii_uppercase + string.ascii_lowercase) +_CHAINS = it.cycle(_ascii_letters) + + +class ModelsDifferError(HaddockError): + """MODELS of the PDB differ in atom labels.""" + + pass + + +def _report(log_msg: str) -> Callable[..., Any]: + """ + Add report functionality to the function (decorator). + + Functions decorated with `_report` log the difference between the + input and the output. Decorated functions gain an additional boolean + parameter `report` to activate or deactivate the report + functionality; defaults to ``False``. + + Note that a generator decorated with ``_report`` no longer behaves + as a generator if ``report=True`` is given. Instead, it returns a + list from the exhausted generator. + + **Important:** Do NOT use ``_report`` with infinite generators, + such as ``itertools.cycle``. + """ + + def decorator(function: Callable[..., Any]) -> Callable[..., Any]: + @wraps(function) + def wrapper( + lines: Iterable[Any], *args: Any, report: bool = False, **kwargs: Any + ) -> Any: + if report: + in_lines = list(lines) + result = list(function(in_lines, *args, **kwargs)) + + # Here we could use sets to increase speed, but for the size + # of the systems, we can actually use lists and get a sorted + # result by default. I tried using difflib from STD but it is + # just too slow. + + # _ is line + additions = [_ for _ in result if _ not in in_lines] + deletions = [_ for _ in in_lines if _ not in result] + + la = len(additions) + ld = len(deletions) + + add_lines = linesep.join(f"+ {_}" for _ in additions) + del_lines = linesep.join(f"- {_}" for _ in deletions) + + log_msg_ = log_msg.format(*args, *kwargs.values()) + extended_log = ( + f"[{log_msg_}] + {la} - {ld} lines", + add_lines, + del_lines, + ) + + log.info(linesep.join(extended_log)) + return result + + # If report=False, maintain the original behaviour + else: + return function(lines, *args, **kwargs) + + return wrapper + + return decorator + + +def _open_or_give(inputdata: Iterable[LineIterSource]) -> list[list[str]]: + """ + Adapt input to the functions. + + Used in py:func:`process_pdbs`. + + Homogenizes input by: + + * removing new line characters at the end of the line + * removing empty lines + + Parameters + ---------- + inputdata : list + A **flat** list where in each index it can contain: + + * file objects + * paths to files + * strings representing paths + * lists or tuples of lines + + The above types can be mixed in the input list. + + Files are read to lines in a list. Line separators are stripped. + + Do not provide nested lists with lists containing paths inside + lists. + + Returns + ------- + list of list of strings + Each sublist has the contents of the input in the same order. + + Raises + ------ + TypeError + In any other circumstances. + """ + + def get_line(lines: Iterable[str]) -> list[str]: + """Ignore empty lines.""" + return [line.rstrip(linesep) for line in lines if line] + + lines: list[list[str]] = [] + for idata in inputdata: + if isinstance(idata, (Path, str)): + lines.append(get_line(Path(idata).read_text().split(linesep))) + + elif isinstance(idata, io.TextIOBase): + lines.append(get_line(idata.readlines())) + + elif isinstance(idata, (list, tuple)): + lines.append(get_line(idata)) + + else: + emsg = f"Unexpected type in `inputdata`: {type(idata)}" + raise TypeError(emsg) + + return lines + + +@read_lines +def read_additional_residues( + lines: Iterable[str], *ignore: Any, **everything: Any +) -> tuple[str, ...]: + """ + Read additional residues listed in a ``*.top`` filename. + + Expects new residues to be defined as:: + + RESIdue XXX + RESI XXX + residue XXX + + where, XXX is the new residue name. Does not read ATOM or charge + information. Reads only the residue name. + + Examples + -------- + Read directly the file: + + >>> read_additional_residues(fpath) + + Read the lines instead: + + >>> lines = Path(fpath).read_text().split(os.linesep) + >>> read_additional_residues.original(lines) + + Parameters + ---------- + fpath : str or pathlib.Path + The path to the file. + + lines : list of lines + You can also use this function in the form of + ``read_additional_residues.original(...)`` and directly give it + a list containing the lines of the file. + + Returns + ------- + tuple + A tuple with the new identified residues names. + """ + # https://regex101.com/r/1H44kO/1 + res_regex = re.compile(r"^(RESIdue|residue|RESI) ([A-Z0-9]{1,3}).*$") + residues: list[str] = [] + for line in map(str.strip, lines): + name = res_regex.findall(line) + if name: + residues.append(name[0][1]) + + return tuple(residues) + + +def process_pdbs( + *inputdata: LineIterSource, + dry: bool = False, + user_supported_residues: Optional[Iterable[str]] = None, +) -> list[list[str]]: + """ + Process PDB file contents for compatibility with HADDOCK3. + + Parameters + ---------- + inputdata : list of (str, path, list of str [lines], file handler) + + A **flat** list where in each index it can contain: + + * file objects + * paths to files + * strings representing paths + * lists or tuples of lines + + The above types can be mixed in the input list. + + Files are read to lines in a list. Line separators are stripped. + + Do not provide nested lists with lists containing paths inside + lists. + + dry : bool + Perform a dry run. That is, does not change anything, and just + report. + + user_supported_residues : list, tuple, or set + The new residues that are allowed. + + Returns + ------- + list of (list of str) + The corrected (processed) PDB content in the same order as + ``inputdata``. + """ + structures = _open_or_give(inputdata) + + # these are the processing or checking functions that should (if needed) + # modify the input PDB and return the corrected lines. + # Follows the same style as for pdb-tools. + # these functions yield line-by-line. + line_by_line_processing_steps = [ + wrep_pdb_keepcoord, # also discards ANISOU + # tidy is important before some other corrections + wrep_pdb_tidy_strict, + wrep_pdb_element, + wrep_pdb_selaltloc, + partial(wrep_pdb_occ, occupancy=1.00), + replace_MSE_to_MET, + replace_HSD_to_HIS, + replace_HSE_to_HIS, + replace_HID_to_HIS, + replace_HIE_to_HIS, + add_charges_to_ions, + partial( + convert_ATOM_to_HETATM, + residues=set.union( + supported_HETATM, + user_supported_residues or set(), + ), + ), + convert_HETATM_to_ATOM, + partial(wrep_pdb_fixinsert, option_list=[]), + ##### + partial( + remove_unsupported_hetatm, user_defined=user_supported_residues + ), # noqa: E501 + partial(remove_unsupported_atom), + #### + # partial(wrep_pdb_shiftres, shifting_factor=0), + partial(wrep_pdb_reatom, starting_value=1), + wrep_pdb_tidy, + ### + wrep_rstrip, + ] + + # these functions take the whole PDB content, evaluate it, and + # modify it if needed. + whole_pdb_processing_steps = [ + models_should_have_the_same_labels, + solve_no_chainID_no_segID, + homogenize_chains, + ] + + # these functions take all structures combined, evulate them + # togehter, and modify them if needed. + processed_combined_steps = [ + correct_equal_chain_segids, + ] + + # START THE ACTUAL PROCESSING + + # individual processing (line-by-line) + result_1 = [ + list(chainf(structure, *line_by_line_processing_steps, report=dry)) + for structure in structures + ] + + # whole structure processing + result_2 = [ + list(chainf(structure, *whole_pdb_processing_steps, report=dry)) + for structure in result_1 + ] + + # combined processing + final_result = chainf(result_2, *processed_combined_steps) + + return final_result + + +# Functions operating line-by-line + +# make pdb-tools reportable +wrep_pdb_chain = _report("pdb_chain")(pdb_chain.run) +wrep_pdb_chainxseg = _report("pbd_segxchain")(pdb_chainxseg.run) +wrep_pdb_element = _report("pdb_element")(pdb_element.run) +wrep_pdb_fixinsert = _report("pdb_fixinsert")(pdb_fixinsert.run) +wrep_pdb_keepcoord = _report("pdb_keepcoord")(pdb_keepcoord.run) +wrep_pdb_occ = _report("pdb_occ")(pdb_occ.run) +wrep_pdb_reatom = _report("pdb_reatom")(pdb_reatom.run) +wrep_pdb_shiftres = _report("pdb_shiftres")(pdb_shiftres.run) +wrep_pdb_rplresname = _report("pdb_rplresname")(pdb_rplresname.run) +wrep_pdb_segxchain = _report("pdb_segxchain")(pdb_segxchain.run) +wrep_pdb_selaltloc = _report("pdb_selaltloc")(pdb_selaltloc.run) +wrep_pdb_tidy = _report("pdb_tidy")(pdb_tidy.run) +wrep_pdb_tidy_strict = _report("pdb_tidy")(partial(pdb_tidy.run, strict=True)) +wrep_rstrip = _report("str.rstrip")( + partial(map, lambda x: x.rstrip(linesep)) +) # noqa: E501 + + +@_report("Replacing HETATM to ATOM for residue {!r}") +def replace_HETATM_to_ATOM( + fhandler: Iterable[str], res: str +) -> Generator[str, None, None]: + """ + Replace record `HETATM` to `ATOM` for `res`. + + Do not alter other lines. + + Parameters + ---------- + fhanlder : file handler or list of lines + List-like of file lines. Consumes over a ``for`` loop. + + res : str + Residue name to match for the substitution. + + Yields + ------ + str + Yield line-by-line. + """ + for line in fhandler: + if line.startswith("HETATM") and line[slc_resname].strip() == res: + yield "ATOM " + line[6:] + else: + yield line + + +@_report("Replace residue ATOM/HETATM {!r} to ATOM {!r}") +def replace_residue( + fhandler: Iterable[str], resin: str, resout: str +) -> Generator[str, None, None]: + """ + Replace residue by another and changes ``HETATM`` to ``ATOM`` if needed. + + Do not alter other lines. + + Parameters + ---------- + fhanlder : file handler or list of lines + List-like of file lines. Consumes over a ``for`` loop. + + resin : str + Residue name to match for the substitution. + + resout : str + Name of the new residue. Renames ``resin`` to ``resout``. + + Yields + ------ + str + Yield line-by-line. + + See Also + -------- + + * :py:func:`replace_HETATM_to_ATOM` + * ``pdb_rplresname`` from ``pdb-tools`` + """ + _ = replace_HETATM_to_ATOM(fhandler, res=resin) + yield from pdb_rplresname.run(_, name_from=resin, name_to=resout) + + +replace_MSE_to_MET = partial(replace_residue, resin="MSE", resout="MET") +""" +Replace ``MSE`` to ``MET``. + +See Also +-------- +* :py:func:`replace_residue` +""" + +replace_HSD_to_HIS = partial(replace_residue, resin="HSD", resout="HIS") +""" +Replace ``HSD`` to ``HIS``. + +See Also +-------- +* :py:func:`replace_residue` +""" + +replace_HSE_to_HIS = partial(replace_residue, resin="HSE", resout="HIS") +""" +Replace ``HSE`` to ``HIS``. + +See Also +-------- +* :py:func:`replace_residue` +""" + +replace_HID_to_HIS = partial(replace_residue, resin="HID", resout="HIS") +""" +Replace ``HID`` to ``HIS``. + +See Also +-------- +* :py:func:`replace_residue` +""" + +replace_HIE_to_HIS = partial(replace_residue, resin="HIE", resout="HIS") +""" +Replace ``HIE`` to ``HIS``. + +See Also +-------- +* :py:func:`replace_residue` +""" + + +@_report("Remove unsupported molecules") +def remove_unsupported_molecules( + lines: Iterable[str], + haddock3_defined: Optional[set[str]] = None, + user_defined: Optional[set[str]] = None, + line_startswith: Union[str, tuple[str, ...]] = ("ATOM", "HETATM"), +) -> Generator[str, None, None]: + """ + Remove HADDOCK3 unsupported molecules. + + This function is abstract and you need to provide the set of + residues supported by HADDOCK3. See parameters. + + Residues not provided in ``haddock3_defined`` and ``user_defined`` + are removed from the PDB lines. + + Other lines are yieled unmodified. + + Parameters + ---------- + lines : list or list-like + Lines of the PDB file. This function will consumes lines over a + ``for`` loop; mind it if you use a generator. + + haddock3_defined : set + Set of residues supported by HADDOCK3. + Defaults to ``None``. + + user_defined : set + An additional set of allowed residues given by the user. + Defaults to ``None``. + + line_startswith : tuple + The lines to consider. Defaults to ``("ATOM", "HETATM")``. + + Yields + ------ + line : str + Line-by-line. + Lines for residues not supported are *not* yielded. + + See Also + -------- + Other functions use this function to create context. + + * :py:func:`remove_unsupported_atom` + * :py:func:`remove_unsupported_hetatm` + """ + user_defined = user_defined or set() + haddock3_defined = haddock3_defined or set() + allowed = set.union(haddock3_defined, user_defined) + + # find a way to report this + not_allowed_found: set[str] = set() + + for line in lines: + if line.startswith(line_startswith): + residue = line[slc_resname].strip() + if residue in allowed: + yield line + else: + not_allowed_found.add(residue) + continue + else: + yield line + + return + + +remove_unsupported_hetatm = partial( + remove_unsupported_molecules, + haddock3_defined=supported_HETATM, + line_startswith="HETATM", +) +""" +Remove unsupported molecules in ``HETATM`` lines. + +Uses :py:func:`remove_unsupported_molecules` by populating its +``haddock3_define`` and ``line_startswith`` parameters. + +See Also +-------- +* :py:func:`remove_unsupported_atom` +""" + +remove_unsupported_atom = partial( + remove_unsupported_molecules, + haddock3_defined=supported_ATOM, + line_startswith="ATOM", +) +""" +Remove unsupported molecules in ``ATOM`` lines. + +Uses :py:func:`remove_unsupported_molecules` by populating its +``haddock3_define`` and ``line_startswith`` parameters. + +See Also +-------- +* :py:func:`remove_unsupported_hetatm` +""" + + +@_report("Add charges to ions.") +def add_charges_to_ions(fhandler: Iterable[str]) -> Generator[str, None, None]: + """ + Add charges to ions according to HADDOCK3 specifications. + + 1. Check if charge is correctly defined in residue name. + If so, yield the line with correct residue name and charge at the + end. + 2. Check if charge is correctly defined in atom name. + 3. Create charge from element. This might need manual edit in case + the atom as an unconventional charge. + + Parameters + ---------- + fhandler : file-hanlder, list, or list-like + Lines of the PDB file. This function will consumes lines over a + ``for`` loop; mind it if you use a generator. + + Yields + ------ + line : str + Line-by-line: modified ion lines and any other line. + """ + # list of functions that correct ion entries + # by order of preference in case a preference is not found. + # see further + ion_correction_cases = [ + _process_ion_case_atom, + _process_ion_case_resname, + _process_ion_case_element_charge, + ] + + for line in fhandler: + if line.startswith(("ATOM", "ANISOU", "HETATM")): + # get values + atom = line[slc_name].strip() # max 4 chars + resname = line[slc_resname].strip() # max 3 chars + element = line[slc_element].strip() # max 2 chars + charge = line[slc_charge].strip() # max 2 chars + + if resname in supported_non_ions: + yield line + continue + + # Which of the above fields has information on the charge? + # If more than one have information on the charge, we give + # the preference to the atom, resname, and then charge + func_to_apply = False + if atom[-1].isdigit(): + func_to_apply = _process_ion_case_atom # type: ignore + elif resname[-1].isdigit(): + func_to_apply = _process_ion_case_resname # type: ignore + elif element and charge and charge[-1].isdigit(): + func_to_apply = _process_ion_case_element_charge # type: ignore + + if func_to_apply: + yield func_to_apply(line) # type: ignore + + # in case none of the fields has information on the charge, + # applies the process functions by giving preference to the + # residue names. + else: + for func in ion_correction_cases: + try: + yield func(line) + except Exception: + # test the next function + continue + else: + break # done + else: + yield line # lines that do not concern to ions + + else: + yield line # lines that are not atoms + + +def _process_ion_case_resname(line: str) -> str: + """ + Process ion information based on resnames. + + case 1: charge is correctly defined in resname, for example, ZN2. + In this case, ignore other fields and write ion information from + scratch even if it's already correct. + """ + resname = line[slc_resname].strip() # max 3 chars + new_atom = supported_single_ions_resnames_map[resname].atoms[0] + new_element = supported_single_ions_resnames_map[resname].elements[0] + charge = new_atom[-2:] if len(new_atom) > 2 else " " + + new_line = ( + line[:12] + + format_atom_name(new_atom, new_element) + + line[16] + + resname.rjust(3, " ") + + line[20:76] + + new_element.rjust(2, " ") + + charge + ) + + return new_line + + +def _process_ion_case_atom(line: str) -> str: + """ + Process ion information based on atom names. + + case 2: charge is correctly defined in atom name ignore other fields + and write them from scratch even if they are already correct. + """ + element = line[slc_element].strip() # max 2 chars + if element == "C": + # element C can have atom name CA which conflicts carbon alpha + # and calcium + raise ValueError("Element is 'C', does not apply to this case.") + + atom = line[slc_name].strip() # max 4 chars + new_resname = supported_single_ions_atoms_map[atom].resname + new_element = supported_single_ions_atoms_map[atom].elements[0] + charge = atom[-2:] if len(atom) > 2 else " " + + new_line = ( + line[:12] + + format_atom_name(atom, new_element) + + line[16] + + new_resname.rjust(3, " ") + + line[20:76] + + new_element.rjust(2, " ") + + charge + ) + + return new_line + + +def _process_ion_case_element_charge(line: str) -> str: + """ + Process ion information based on element and charge. + + case 3: charge is correctly defined in atom name ignore other fields + and write them from scratch even if they are already correct. + """ + element = line[slc_element].strip() # max 2 chars + charge = line[slc_charge].strip() # max 2 chars + atom = element + charge + new_resname = supported_single_ions_atoms_map[atom].resname + + new_line = ( + line[:12] + + format_atom_name(atom, element) + + line[16] + + new_resname.rjust(3, " ") + + line[20:76] + + element.rjust(2, " ") + + charge + ) + + return new_line + + +@_report("Convert record: {!r} to {!r}.") +def convert_record( + fhandler: Iterable[str], record: str, other_record: str, residues: Container[str] +) -> Generator[str, None, None]: + """ + Convert on record to another for specified residues. + + For example, replace ``ATOM`` by ``HETATM`` for specific residues. + + Parameters + ---------- + fhandler : list-like + Contains lines of file. + + record : str + The PDB RECORD to match; for example, ``ATOM`` or ``HETATM``. + + other_record : str + The PDB RECORD to replace with; for example, ``ATOM`` or ``HETATM``. + + residues : list, tuple, or set + List of residues to replace the record. + """ + for line in fhandler: + if line.startswith(record): + resname = line[slc_resname].strip() + if resname in residues: + yield other_record + line[6:] + continue + yield line + + +convert_ATOM_to_HETATM = partial( + convert_record, + record="ATOM", + other_record="HETATM", + residues=supported_HETATM, +) +""" +Convert ``ATOM`` to ``HETATM`` for HADDOCK3 supported ``HETATM``. + +See Also +-------- +* :py:data:`haddock.core.supported_molecules.supported_HETATM` +""" + +convert_HETATM_to_ATOM = partial( + convert_record, + record="HETATM", + other_record="ATOM ", + residues=supported_ATOM, +) +""" +Convert ``HETATM`` to ``ATOM`` for HADDOCK3 supported ``ATOM``. + +See Also +-------- +* :py:data:`haddock.core.supported_molecules.supported_ATOM` +""" + + +# Functions operating in the whole PDB + + +@_report("Solving chain/seg ID issues.") +def solve_no_chainID_no_segID(lines: Iterable[str]) -> Iterable[str]: + """ + Solve inconsistencies with chainID and segID. + + If segID is non-existant, copy chainID over segID, and vice-versa. + If none are present, adds an upper case char starting from A. This + char is not repeated until the alphabet exhausts. + If chainIDs and segIDs differ, copy chainIDs over segIDs. + + Parameters + ---------- + lines : list of str + The lines of a PDB file. + + Returns + ------- + list + With new lines. Or the input ones if no modification was made. + """ + chainids = read_chainids(lines) + segids = read_segids(lines) + + if not chainids and segids: + new_lines = pdb_segxchain.run(lines) + + elif chainids and not segids: + new_lines = pdb_chainxseg.run(lines) + + elif not chainids and not segids: + _chains = pdb_chain.run(lines, next(_CHAINS)) + new_lines = pdb_chainxseg.run(_chains) + + # gives priority to chains + elif chainids != segids: + new_lines = pdb_chainxseg.run(lines) + + else: + # nothing to do + return lines + + return list(new_lines) + + +# TODO: needs to become an option. +# change chain ID and shift the residue of the other chains. +# also needs to be sync with the restraints. +# maybe not an automatic.. maybe used as a CLI +# maybe is a place to have a CHECK instead of a autoprocess +@_report("Homogenizes chains") +def homogenize_chains(lines: list[str]) -> list[str]: + """ + Homogenize chainIDs within the same PDB. + + If there are multiple chain identifiers in the PDB file, make all + them equal to the first one. + + ChainIDs are copied to segIDs afterwards. + + Returns + ------- + list + The modified lines. + """ + chainids = read_chainids(lines) + if len(set(chainids)) > 1: + return list( + chainf( + lines, + partial(pdb_chain.run, chain_id=chainids[0]), + pdb_chainxseg.run, + ) + ) + else: + return lines + + +# Functions operating in all PDBs at once + + +def correct_equal_chain_segids(structures: list[list[str]]) -> list[list[str]]: + """ + Correct for repeated chainID in the input PDB files. + + Repeated chain IDs are replaced by an upper case character (``[A-Z]``) + in order. + + Parameters + ---------- + structures : list of lists of str + The input data. + + Returns + ------- + list of lists of str + The new structures. + """ + _all_chains = (read_chainids(s) for s in structures) + # set of all chain IDs present in the input PDBs + all_chain_ids = set(it.chain.from_iterable(_all_chains)) + + # the remaining available chain characters are the A-Z minus the + # `all_chain_ids` + remaining_chars = it.cycle(sorted(set(_ascii_letters).difference(all_chain_ids))) + + chain_ids: list[Iterable[str]] = [] + new_structures: list[list[str]] = [] + for lines in structures: + new_lines: Optional[list[str]] = None + + # read chain IDs from the structure + chain_id = read_chainids(lines) + + # if chain_id is repeated + if chain_id in chain_ids: + new_lines = list( + chainf( + lines, + # change the chain ID by a new one + partial(pdb_chain.run, chain_id=next(remaining_chars)), + # applies chain ID to seg ID as well + pdb_chainxseg.run, + ) + ) + else: + chain_ids.append(chain_id) + + new_structures.append(new_lines or lines) + + if len(new_structures) != len(structures): + raise AssertionError("Number of lines differ. This is a bug!") + return new_structures + + +# this id bad +@_report("Check models are the same") +def models_should_have_the_same_labels(lines: Iterable[str]) -> Iterable[str]: + """ + Confirm models have the same labels. + + In an ensemble of structures, where the PDB file has multiple MODELS, + all models should have the same labels; hence the same number and + typ of atoms. + + Parameters + ---------- + lines : list of strings. + List containing the lines of the PDB file. Must NOT be a generator. + + Returns + ------- + list + The original ``lines`` in case no errors are found. + + Raises + ------ + ModelsDifferError + In case MODELS differ. Reports on which models differ. + """ + # searchers for the first MODEL line. If found, break the loop + # and continue to the rest of the function. + # + # if not found, return the same input lines. + for line in lines: + if line.startswith("MODEL"): + break + else: + return lines + + # captures all the models + models: dict[Optional[int], set[str]] = {} + new_model: list[str] = [] + new_model_id = None + for line in lines: + if line.startswith("MODEL"): + if new_model_id is not None: + models[new_model_id] = set(new_model) + new_model.clear() + new_model_id = int(line[10:14]) + + elif line.startswith(("ATOM", "HETATM")): + new_model.append(line[12:27]) + else: + models[new_model_id] = set(new_model) + new_model.clear() + + # check if all MODELS are equal, performing all vs all comparison + keys = list(models.keys()) + first_key = keys[0] + for model_num in keys[1:]: + if models[model_num] != models[first_key]: + emsg = f"Labels in MODEL {model_num} differ from MODEL {first_key}." + raise ModelsDifferError(emsg) + + return lines diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/restart_run.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/restart_run.py new file mode 100644 index 0000000000000000000000000000000000000000..a973bc960104ae70efc0a6299f25a84a8faa3452 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/restart_run.py @@ -0,0 +1,67 @@ +"""Features to allow run restart from a given step.""" +from argparse import ArgumentParser, ArgumentTypeError +from functools import partial +from pathlib import Path + +from haddock.libs.libutil import non_negative_int, remove_folder +from haddock.modules import get_module_steps_folders + + +_help_cli = """Restart the run from a given step. Previous folders from +the selected step onward will be deleted.""" + + +_arg_non_neg_int = partial( + non_negative_int, + exception=ArgumentTypeError, + emsg="Minimum value is 0, {!r} given.", + ) + + +def add_restart_arg(parser: ArgumentParser) -> None: + """Add `--restart` option to argument parser.""" + parser.add_argument( + "--restart", + type=_arg_non_neg_int, + default=None, + help=_help_cli, + ) + + +def remove_folders_after_number(run_dir: Path, num: int) -> None: + """ + Remove calculation folder after (included) a given number. + + Example + ------- + If the following step folders exist: + + 00_topoaa + 01_rigidbody + 02_mdref + 03_flexref + + and the number `2` is given, folders `02_` and `03_` will be + deleted. + + Parameters + ---------- + run_dir : pathlib.Path + The run directory. + + num : int + The number of the folder from which to delete calculation step + folders. `num` must be non-negative integer, or equivalent + representation. + """ + num = _arg_non_neg_int(num) + previous = get_module_steps_folders(run_dir.resolve()) + # Filters step folders based on their indices + from_num_folders = [ + folder for folder in previous + if int(folder.split('_')[0]) >= num + ] + # Loop over folders to remove + for torm_folder in from_num_folders: + remove_folder(Path(run_dir, torm_folder)) + return diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/validations.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/validations.py new file mode 100644 index 0000000000000000000000000000000000000000..3279584c00fc3dd94d6d3a2593303ece9514845d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/validations.py @@ -0,0 +1,107 @@ +"""Module to define specific validations in Haddock3.""" +from haddock import config_expert_levels, _hidden_level +from haddock.core.defaults import RUNDIR, valid_run_dir_chars +from haddock.core.exceptions import ConfigurationError +from haddock.core.typing import FilePath, Any, ParamDict +from haddock.libs.libio import read_from_yaml, check_yaml_duplicated_parameters + +_allowed_expert_levels = config_expert_levels + ("all", _hidden_level) +YAML_PARAMETER_BASE_SCHEME = ( + 'title', 'short', 'long', 'group', 'explevel', 'type', 'default', + ) +TYPE_SPECIFIC_SCHEMES = { + "integer": ("min", "max", ), + "float": ("min", "max", "precision", ), + "string": ("minchars", "maxchars", ), + "list": ("minitems", "maxitems", ), + "boolean": (), + "file": (), + "dict": (), + } + + +def v_rundir(rundir: FilePath) -> None: + """Validate string defining the run directory.""" + if set(str(rundir)) - set(valid_run_dir_chars): + emsg = ( + f"The {RUNDIR!r} parameter can only have " + r"[a-zA-Z0-9._-/\] characters." + ) + raise ConfigurationError(emsg) + + +def validate_yaml_params_scheme(yaml_fpath: FilePath) -> None: + """Validate a defaults.yaml file module parameters schemes. + + Parameters + ---------- + yaml_fpath : str + Path to the defaults.yaml file to check. + """ + ycfg = read_from_yaml(yaml_fpath) + # Loop over parameters + for param_name, parameters in ycfg.items(): + try: + validate_parameter_scheme(param_name, parameters) + except AssertionError as error: + raise AssertionError(f"{error} (in {yaml_fpath})") + + +def validate_parameter_scheme( + param_name: str, + parameters: ParamDict, + ) -> None: + """Validate a parameter scheme. + + Parameters + ---------- + param_name : str + Name of this parameter. + parameters : dict[str, Any] + Dictionary of param, value for this parameter. + """ + for base_subparam in YAML_PARAMETER_BASE_SCHEME: + # Check that this parameter contain the basic subparameters + assert base_subparam in parameters.keys(), f"Parameter '{param_name}' is missing base subparam '{base_subparam}'" # noqa : E501 + # Point avlue of this parameter + param_value = parameters[base_subparam] + # Evaluate expertize level + if base_subparam == "explevel": + # Check if expert level is ok + assert parameters[base_subparam] in _allowed_expert_levels, f"Parameter '{param_name}' do not contain appropriate expert level" # noqa : E501 + # Once we know the type, we can make parameter type specific checks + elif base_subparam == "type": + # Check if known type + assert param_value in TYPE_SPECIFIC_SCHEMES.keys(), f"Parameter '{param_name}' contain an unknown parameter type: '{param_value}'" # noqa : E501 + # Skip subsequent checks in case of type: dict + if param_value == "dict": + # Loop over nested parameters + for dict_param_name, dict_param in parameters.items(): + # Make sure they are parameters and not base ones + if dict_param_name not in YAML_PARAMETER_BASE_SCHEME: + # Recursive calls for nested parameters + validate_parameter_scheme(dict_param_name, dict_param) + # Special case of dict, they do not have a default value... + # So we skip the presence of 'default' in this type of params. + # We break the loop before this check + break + + # Check if all specific param for this type of parameter + # are properly specified + for specific_param in TYPE_SPECIFIC_SCHEMES[param_value]: + assert specific_param in parameters.keys(), f"Parameter {param_name} is missing specific subparam '{specific_param}' for type '{base_subparam}'" # noqa : E501 + + +def validate_defaults_yaml(yaml_fpath: FilePath) -> None: + """Validate a defaults.yaml file. + + Parameters + ---------- + yaml_fpath : str + Path to the defaults.yaml file to validate. + """ + try: + check_yaml_duplicated_parameters(yaml_fpath) + validate_yaml_params_scheme(yaml_fpath) + except AssertionError as assert_error: + raise ConfigurationError(assert_error) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/yaml2cfg.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/yaml2cfg.py new file mode 100644 index 0000000000000000000000000000000000000000..be397fa9d4373900fdbe95549597af3fbdbee263 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/yaml2cfg.py @@ -0,0 +1,287 @@ +""" +Parse data from HADDOCK3 to YAML and YAML to HADDOCK3 and related. + +Accross this file you will see references to "yaml" as variables and +function names. In these cases, we always mean the HADDOCK3 YAML +configuration files which have specific keys. +""" + +import os +from collections.abc import Mapping +from pathlib import Path +from typing import Union + +from haddock import _hidden_level, config_expert_levels +from haddock.core.exceptions import ConfigurationError +from haddock.core.typing import ( + ExpertLevel, + FilePath, + Optional, + ParamDict, + ParamMap, +) +from haddock.libs.libio import read_from_yaml + + +def yaml2cfg_text( + ymlcfg: dict, + module: str, + explevel: str, + details: bool = False, + mandatory_param: bool = False, +) -> str: + """ + Convert HADDOCK3 YAML config to HADDOCK3 user config text. + + Adds commentaries with help strings. + + Parameters + ---------- + ymlcfg : dict + The dictionary representing the HADDOCK3 config file. + + module : str + The module to which the config belongs to. + + explevel : str + The expert level to consider. Provides all parameters for that + level and those of inferior hierarchy. If you give "all", all + parameters will be considered. + + details : bool + Whether to add the 'long' description of each parameter. + + mandatory_param : bool + Whether this current parameters are mandatory ones. Special case where + this must be set as they do not contain `default` value, therefore the + downstream functions are not valid anymore. + + Returns + ------- + textual_config : str + Textual representation of a YAML configuration file. + """ + new_config: list[str] = [] + if module is not None: + new_config.append(f"[{module}]") + + new_config.append( + _yaml2cfg_text( + ymlcfg, + module, + explevel, + details=details, + mandatory_param=mandatory_param, + ) + ) + textual_config = os.linesep.join(new_config) + os.linesep + return textual_config + + +def _yaml2cfg_text( + ymlcfg: dict, + module: str, + explevel: str, + details: bool = False, + mandatory_param: bool = False, +) -> str: + """ + Convert HADDOCK3 YAML config to HADDOCK3 user config text. + + Does not consider expert levels. + See :func:`yaml2cfg_text_with_explevels` instead. + + Parameters + ---------- + ymlcfg : dict + The dictionary representing the HADDOCK3 YAML configuration. + This configuration should NOT have the expertise levels. It + expectes the first level of keys to be the parameter name. + + module : str + The module to which the config belongs to. + + explevel : str + The expert level to consider. Provides all parameters for that + level and those of inferior hierarchy. If you give "all", all + parameters will be considered. + + details : bool + Whether to add the 'long' description of each parameter. + + mandatory_param : bool + Whether this current parameters are mandatory ones. Special case where + this must be set as they do not contain `default` value, therefore the + downstream functions are not valid anymore. + + Returns + ------- + str_config : str + String representation of the YAML configuration file. + """ + params: list[str] = [] + exp_levels = { + _el: i for i, _el in enumerate(config_expert_levels + ("all", _hidden_level)) + } + exp_level_idx = exp_levels[explevel] + + # define set of undesired parameter keys + undesired = ["default", "explevel", "type"] + if not details: + # Add long description to undesired if not asked for detailed info + undesired.append("long") + + for param_name, param in ymlcfg.items(): + # Check if param is a dictionary + if isinstance(param, Mapping): + # Without `default` key parameter, assumes this `param` + # is a subdictionaries of parameters + if "default" not in param and not mandatory_param: + params.append("") # give extra space + if module is not None: + curr_module = f"{module}.{param_name}" + else: + curr_module = param_name + params.append(f"[{curr_module}]") + _ = _yaml2cfg_text( + param, # type: ignore + module=curr_module, + explevel=explevel, + details=details, + ) + params.append(_) + + # treats normal parameters + else: + if exp_levels[param["explevel"]] > exp_level_idx: + # ignore this parameter because is of an expert level + # superior to the one request: + continue + + comment: list[str] = [] + for _comment, cvalue in param.items(): + if _comment in undesired: + continue + + if cvalue == "": + continue + + comment.append(f"${_comment} {cvalue}") + + # In the case of mandatory global parameters, there is + # no defined default parameters, so we create a `fake` one + if mandatory_param: + default_value = "Must be defined!" + else: + default_value = param["default"] + + # boolean values have to be lower for compatibility + # with toml cfg + if isinstance(default_value, bool): + default_value = str(default_value).lower() + param_line = "{} = {} # {}" + else: + param_line = "{} = {!r} # {}" + + params.append( + param_line.format( + param_name, + default_value, + " / ".join(comment), + ) + ) + + if param["type"] == "list": + params.append(os.linesep) + + else: + # ignore some other parameters that are defined for sections. + continue + + # Generate one single string containing all parameters representation + str_config = os.linesep.join(params) + return str_config + + +def read_from_yaml_config( + cfg_file: Union[Path, str], default_only: bool = True +) -> dict: + """Read config from yaml by collapsing the expert levels. + + Parameters + ---------- + cfg_file : + Path to a .yaml configuration file + default_only : bool + Set the return value of this function; if True (default value), only + returns default values, else return the fully loaded configuration file + + Return + ------ + ycfg : dict + The full default configuration file as a dict + OR + cfg : dict + A dictionary containing only the default parameters values + """ + ycfg = read_from_yaml(cfg_file) + if default_only: + # there's no need to make a deep copy here, a shallow copy suffices. + cfg = {} + cfg.update(flat_yaml_cfg(ycfg)) + return cfg + return ycfg + + +def flat_yaml_cfg(cfg: ParamMap) -> ParamDict: + """Flat a yaml config.""" + new: ParamDict = {} + for param, values in cfg.items(): + try: + new_value = values["default"] + except KeyError: + new_value = flat_yaml_cfg(values) + except TypeError: + # happens when values is a string for example, + # addresses `explevel` in `mol*` topoaa. + continue + else: + # coordinates with tests. + # users should not edit yaml files. So this error triggers + # only during development + if "explevel" not in values: + emsg = f"`explevel` not defined for: {param!r}" + raise ConfigurationError(emsg) + + new[param] = new_value + + return new + + +def find_incompatible_parameters(yaml_file: Path) -> dict[str, ParamDict]: + """ + Reads a YAML configuration file and identifies nodes containing the 'incompatible' key. + + This function takes the path to a YAML file, reads its contents, and searches for nodes + that include an 'incompatible' key. It returns a dictionary where each key is a node name + and each value is another dictionary representing the 'incompatible' parameters for that node. + + Parameters + ---------- + yaml_file : Path + The path to the YAML file to be read. + + Return + ------ + incompatible_parameters : dict[str, dict[str, str]] + A dictionary with node names as keys and their corresponding + 'incompatible' parameters as values. + """ + config = read_from_yaml(yaml_file=yaml_file) + + # Go over each node and see which contains the `incompatible` key + incompatible_parameters = {} + for node, values in config.items(): + if "incompatible" in values: + incompatible_parameters[node] = values["incompatible"] + return incompatible_parameters diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/gear/zerofill.py b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/zerofill.py new file mode 100644 index 0000000000000000000000000000000000000000..ec0f3bef69a95069d3d43be091ec82423b59814f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/gear/zerofill.py @@ -0,0 +1,135 @@ +""" +Handles zero filling prefix for module folder names. + +To facilitate folder sorting, HADDOCK3 module run folder names have a +integer prefix starting at 0. + +Depending on the number of modules of the run, the integer prefix is a +single digit number or multi-digit number (00, 01, 02, 03...). + +This gear module contains the "zero filling" logic in HADDOCK 3. + +The main class of this module `zerofill` is already instantiated such +that its state can be used and edited throughout the HADDOCK3 library. + +Examples +-------- +>>> from haddock.gear import zerofill +>>> zerofill.read(modules) # a dictionary containing 11 modules +>>> zerofill.zfnum +2 +>>> zerofill.fill("topoaa", 0) +"00_topoaa" +""" +from math import ceil, log10 +from typing import Sized + + +class _ZeroFill: + """ + Register the zero fill number. + + Examples + -------- + >>> _ZeroFill() + >>> zerofill.read(modules) # a dictionary containing five modules + >>> zerofill.zfnum + 1 + + >>> zerofill.fill("topoaa", 0) + "0_topoaa" + + >>> zerofill.fill("rigidbody", 2) + "2_rigidbody" + """ + + def __init__(self, zfnum: int = 1) -> None: + self._zfnum = zfnum + return + + @property + def zfnum(self) -> int: + """ + The zerofill number. + + That is, the number of digits that the numeric prefix has. + """ # noqa: D401 + return self._zfnum + + def set_zerofill_number(self, num_steps: int) -> None: + """ + Register the zerofill number given a certain number of steps. + + Parameters + ---------- + num_steps : int + The number of steps in the run. + """ + self._zfnum = get_zerofill_for_modules(list(range(num_steps))) + + def read(self, modules: Sized) -> None: + """ + Register the zerofill number for current run. + + Zero fill number if available through the attribute: `zfnum`. + + Parameters + ---------- + iterable + Usually a dictionary or a list of the modules names. + Any object implementing `len`. + """ + self._zfnum = get_zerofill_for_modules(modules) + + def fill(self, name: str, num: int) -> str: + """ + Fill a name with the corresponding zero filling. + + Examples + -------- + >>> zerofill.zfum + 1 + + >>> zerofill.fill("topoaa", 0) + "0_topoaa" + + >>> zerofill.fill("rigidody", 1) + "1_rigidbody" + """ + return make_zero_fill(num, self.zfnum) + "_" + name + + +zero_fill = _ZeroFill() + + +def get_number_of_digits(num: int) -> int: + """ + Get the number of digits of a number. + + 10 has two digits. + 100 has three digits. + """ + # also: return len(str(num)) :-) + return max(ceil(log10(num + 1)), 1) + + +def get_zerofill_for_modules(modules: Sized) -> int: + """ + Get a the prefix zerofill for modules. + + If there are 5 modules, zerofill digits is 1. + + If there are 10 modules, zerofill digits is 1 because counting + starts at 0 (for topoaa). + + If there are 100 modules, zerofill digits is 2 because counting + starts at 0 (for topoaa). + + This function is used in combination with `zero_fill`. + """ + return get_number_of_digits(len(modules) - 1) + + +def make_zero_fill(number: int, digits: int) -> str: + """Make a number string zero filled to the left.""" + return str(number).zfill(digits) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/.___pycache__ differ diff 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$p(t),this.depthBuffer=e.depthBuffer,this.stencilBuffer=e.stencilBuffer,e.depthTexture!==null&&(this.depthTexture=e.depthTexture.clone()),this.samples=e.samples,this}dispose(){this.dispatchEvent({type:"dispose"})}},nr=class extends j_{constructor(e=1,t=1,i={}){super(e,t,i),this.isWebGLRenderTarget=!0}},Wp=class extends tr{constructor(e=null,t=1,i=1,r=1){super(null),this.isDataArrayTexture=!0,this.image={data:e,width:t,height:i,depth:r},this.magFilter=en,this.minFilter=en,this.wrapR=Gr,this.generateMipmaps=!1,this.flipY=!1,this.unpackAlignment=1}};var X_=class extends tr{constructor(e=null,t=1,i=1,r=1){super(null),this.isData3DTexture=!0,this.image={data:e,width:t,height:i,depth:r},this.magFilter=en,this.minFilter=en,this.wrapR=Gr,this.generateMipmaps=!1,this.flipY=!1,this.unpackAlignment=1}};var Xn=class{constructor(e=0,t=0,i=0,r=1){this.isQuaternion=!0,this._x=e,this._y=t,this._z=i,this._w=r}static slerpFlat(e,t,i,r,s,o,a){let 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e[t]=this.x,e[t+1]=this.y,e[t+2]=this.z,e}fromBufferAttribute(e,t){return this.x=e.getX(t),this.y=e.getY(t),this.z=e.getZ(t),this}random(){return this.x=Math.random(),this.y=Math.random(),this.z=Math.random(),this}randomDirection(){let e=(Math.random()-.5)*2,t=Math.random()*Math.PI*2,i=Math.sqrt(1-e**2);return this.x=i*Math.cos(t),this.y=i*Math.sin(t),this.z=e,this}*[Symbol.iterator](){yield this.x,yield this.y,yield this.z}},g_=new W,yC=new Xn,sn=class{constructor(e=new W(1/0,1/0,1/0),t=new W(-1/0,-1/0,-1/0)){this.isBox3=!0,this.min=e,this.max=t}set(e,t){return this.min.copy(e),this.max.copy(t),this}setFromArray(e){this.makeEmpty();for(let t=0,i=e.length;tthis.max.x||e.ythis.max.y||e.zthis.max.z)}containsBox(e){return this.min.x<=e.min.x&&e.max.x<=this.max.x&&this.min.y<=e.min.y&&e.max.y<=this.max.y&&this.min.z<=e.min.z&&e.max.z<=this.max.z}getParameter(e,t){return t.set((e.x-this.min.x)/(this.max.x-this.min.x),(e.y-this.min.y)/(this.max.y-this.min.y),(e.z-this.min.z)/(this.max.z-this.min.z))}intersectsBox(e){return!(e.max.xthis.max.x||e.max.ythis.max.y||e.max.zthis.max.z)}intersectsSphere(e){return this.clampPoint(e.center,Ur),Ur.distanceToSquared(e.center)<=e.radius*e.radius}intersectsPlane(e){let t,i;return e.normal.x>0?(t=e.normal.x*this.min.x,i=e.normal.x*this.max.x):(t=e.normal.x*this.max.x,i=e.normal.x*this.min.x),e.normal.y>0?(t+=e.normal.y*this.min.y,i+=e.normal.y*this.max.y):(t+=e.normal.y*this.max.y,i+=e.normal.y*this.min.y),e.normal.z>0?(t+=e.normal.z*this.min.z,i+=e.normal.z*this.max.z):(t+=e.normal.z*this.max.z,i+=e.normal.z*this.min.z),t<=-e.constant&&i>=-e.constant}intersectsTriangle(e){if(this.isEmpty())return!1;this.getCenter(fh),cp.subVectors(this.max,fh),jl.subVectors(e.a,fh),Xl.subVectors(e.b,fh),ql.subVectors(e.c,fh),Fo.subVectors(Xl,jl),Oo.subVectors(ql,Xl),Ca.subVectors(jl,ql);let t=[0,-Fo.z,Fo.y,0,-Oo.z,Oo.y,0,-Ca.z,Ca.y,Fo.z,0,-Fo.x,Oo.z,0,-Oo.x,Ca.z,0,-Ca.x,-Fo.y,Fo.x,0,-Oo.y,Oo.x,0,-Ca.y,Ca.x,0];return!y_(t,jl,Xl,ql,cp)||(t=[1,0,0,0,1,0,0,0,1],!y_(t,jl,Xl,ql,cp))?!1:(up.crossVectors(Fo,Oo),t=[up.x,up.y,up.z],y_(t,jl,Xl,ql,cp))}clampPoint(e,t){return t.copy(e).clamp(this.min,this.max)}distanceToPoint(e){return this.clampPoint(e,Ur).distanceTo(e)}getBoundingSphere(e){return this.isEmpty()?e.makeEmpty():(this.getCenter(e.center),e.radius=this.getSize(Ur).length()*.5),e}intersect(e){return this.min.max(e.min),this.max.min(e.max),this.isEmpty()&&this.makeEmpty(),this}union(e){return this.min.min(e.min),this.max.max(e.max),this}applyMatrix4(e){return 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i=Math.sqrt(t),r=(i-this.radius)*.5;this.center.addScaledVector(ph,r/i),this.radius+=r}return this}union(e){return e.isEmpty()?this:this.isEmpty()?(this.copy(e),this):(this.center.equals(e.center)===!0?this.radius=Math.max(this.radius,e.radius):(__.subVectors(e.center,this.center).setLength(e.radius),this.expandByPoint(ph.copy(e.center).add(__)),this.expandByPoint(ph.copy(e.center).sub(__))),this)}equals(e){return e.center.equals(this.center)&&e.radius===this.radius}clone(){return new this.constructor().copy(this)}},zs=new W,v_=new W,hp=new W,Bo=new W,x_=new W,dp=new W,b_=new W,bh=class{constructor(e=new W,t=new W(0,0,-1)){this.origin=e,this.direction=t}set(e,t){return this.origin.copy(e),this.direction.copy(t),this}copy(e){return this.origin.copy(e.origin),this.direction.copy(e.direction),this}at(e,t){return t.copy(this.origin).addScaledVector(this.direction,e)}lookAt(e){return this.direction.copy(e).sub(this.origin).normalize(),this}recast(e){return 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t=e.distanceToPoint(this.origin);return t===0||e.normal.dot(this.direction)*t<0}intersectBox(e,t){let i,r,s,o,a,l,c=1/this.direction.x,u=1/this.direction.y,d=1/this.direction.z,f=this.origin;return c>=0?(i=(e.min.x-f.x)*c,r=(e.max.x-f.x)*c):(i=(e.max.x-f.x)*c,r=(e.min.x-f.x)*c),u>=0?(s=(e.min.y-f.y)*u,o=(e.max.y-f.y)*u):(s=(e.max.y-f.y)*u,o=(e.min.y-f.y)*u),i>o||s>r||((s>i||isNaN(i))&&(i=s),(o=0?(a=(e.min.z-f.z)*d,l=(e.max.z-f.z)*d):(a=(e.max.z-f.z)*d,l=(e.min.z-f.z)*d),i>l||a>r)||((a>i||i!==i)&&(i=a),(l=0?i:r,t)}intersectsBox(e){return this.intersectBox(e,zs)!==null}intersectTriangle(e,t,i,r,s){x_.subVectors(t,e),dp.subVectors(i,e),b_.crossVectors(x_,dp);let o=this.direction.dot(b_),a;if(o>0){if(r)return null;a=1}else if(o<0)a=-1,o=-o;else return null;Bo.subVectors(this.origin,e);let l=a*this.direction.dot(dp.crossVectors(Bo,dp));if(l<0)return null;let c=a*this.direction.dot(x_.cross(Bo));if(c<0||l+c>o)return null;let u=-a*Bo.dot(b_);return u<0?null:this.at(u/o,s)}applyMatrix4(e){return this.origin.applyMatrix4(e),this.direction.transformDirection(e),this}equals(e){return e.origin.equals(this.origin)&&e.direction.equals(this.direction)}clone(){return new this.constructor().copy(this)}},qe=class n{constructor(e,t,i,r,s,o,a,l,c,u,d,f,m,p,_,y){n.prototype.isMatrix4=!0,this.elements=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1],e!==void 0&&this.set(e,t,i,r,s,o,a,l,c,u,d,f,m,p,_,y)}set(e,t,i,r,s,o,a,l,c,u,d,f,m,p,_,y){let g=this.elements;return g[0]=e,g[4]=t,g[8]=i,g[12]=r,g[1]=s,g[5]=o,g[9]=a,g[13]=l,g[2]=c,g[6]=u,g[10]=d,g[14]=f,g[3]=m,g[7]=p,g[11]=_,g[15]=y,this}identity(){return this.set(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1),this}clone(){return new n().fromArray(this.elements)}copy(e){let t=this.elements,i=e.elements;return t[0]=i[0],t[1]=i[1],t[2]=i[2],t[3]=i[3],t[4]=i[4],t[5]=i[5],t[6]=i[6],t[7]=i[7],t[8]=i[8],t[9]=i[9],t[10]=i[10],t[11]=i[11],t[12]=i[12],t[13]=i[13],t[14]=i[14],t[15]=i[15],this}copyPosition(e){let t=this.elements,i=e.elements;return t[12]=i[12],t[13]=i[13],t[14]=i[14],this}setFromMatrix3(e){let t=e.elements;return this.set(t[0],t[3],t[6],0,t[1],t[4],t[7],0,t[2],t[5],t[8],0,0,0,0,1),this}extractBasis(e,t,i){return e.setFromMatrixColumn(this,0),t.setFromMatrixColumn(this,1),i.setFromMatrixColumn(this,2),this}makeBasis(e,t,i){return this.set(e.x,t.x,i.x,0,e.y,t.y,i.y,0,e.z,t.z,i.z,0,0,0,0,1),this}extractRotation(e){let t=this.elements,i=e.elements,r=1/Yl.setFromMatrixColumn(e,0).length(),s=1/Yl.setFromMatrixColumn(e,1).length(),o=1/Yl.setFromMatrixColumn(e,2).length();return t[0]=i[0]*r,t[1]=i[1]*r,t[2]=i[2]*r,t[3]=0,t[4]=i[4]*s,t[5]=i[5]*s,t[6]=i[6]*s,t[7]=0,t[8]=i[8]*o,t[9]=i[9]*o,t[10]=i[10]*o,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,this}makeRotationFromEuler(e){let t=this.elements,i=e.x,r=e.y,s=e.z,o=Math.cos(i),a=Math.sin(i),l=Math.cos(r),c=Math.sin(r),u=Math.cos(s),d=Math.sin(s);if(e.order==="XYZ"){let f=o*u,m=o*d,p=a*u,_=a*d;t[0]=l*u,t[4]=-l*d,t[8]=c,t[1]=m+p*c,t[5]=f-_*c,t[9]=-a*l,t[2]=_-f*c,t[6]=p+m*c,t[10]=o*l}else if(e.order==="YXZ"){let f=l*u,m=l*d,p=c*u,_=c*d;t[0]=f+_*a,t[4]=p*a-m,t[8]=o*c,t[1]=o*d,t[5]=o*u,t[9]=-a,t[2]=m*a-p,t[6]=_+f*a,t[10]=o*l}else if(e.order==="ZXY"){let f=l*u,m=l*d,p=c*u,_=c*d;t[0]=f-_*a,t[4]=-o*d,t[8]=p+m*a,t[1]=m+p*a,t[5]=o*u,t[9]=_-f*a,t[2]=-o*c,t[6]=a,t[10]=o*l}else if(e.order==="ZYX"){let f=o*u,m=o*d,p=a*u,_=a*d;t[0]=l*u,t[4]=p*c-m,t[8]=f*c+_,t[1]=l*d,t[5]=_*c+f,t[9]=m*c-p,t[2]=-c,t[6]=a*l,t[10]=o*l}else if(e.order==="YZX"){let f=o*l,m=o*c,p=a*l,_=a*c;t[0]=l*u,t[4]=_-f*d,t[8]=p*d+m,t[1]=d,t[5]=o*u,t[9]=-a*u,t[2]=-c*u,t[6]=m*d+p,t[10]=f-_*d}else if(e.order==="XZY"){let f=o*l,m=o*c,p=a*l,_=a*c;t[0]=l*u,t[4]=-d,t[8]=c*u,t[1]=f*d+_,t[5]=o*u,t[9]=m*d-p,t[2]=p*d-m,t[6]=a*u,t[10]=_*d+f}return t[3]=0,t[7]=0,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,this}makeRotationFromQuaternion(e){return this.compose(f4,e,p4)}lookAt(e,t,i){let r=this.elements;return Ji.subVectors(e,t),Ji.lengthSq()===0&&(Ji.z=1),Ji.normalize(),Uo.crossVectors(i,Ji),Uo.lengthSq()===0&&(Math.abs(i.z)===1?Ji.x+=1e-4:Ji.z+=1e-4,Ji.normalize(),Uo.crossVectors(i,Ji)),Uo.normalize(),fp.crossVectors(Ji,Uo),r[0]=Uo.x,r[4]=fp.x,r[8]=Ji.x,r[1]=Uo.y,r[5]=fp.y,r[9]=Ji.y,r[2]=Uo.z,r[6]=fp.z,r[10]=Ji.z,this}multiply(e){return this.multiplyMatrices(this,e)}premultiply(e){return this.multiplyMatrices(e,this)}multiplyMatrices(e,t){let i=e.elements,r=t.elements,s=this.elements,o=i[0],a=i[4],l=i[8],c=i[12],u=i[1],d=i[5],f=i[9],m=i[13],p=i[2],_=i[6],y=i[10],g=i[14],b=i[3],h=i[7],v=i[11],S=i[15],x=r[0],w=r[4],A=r[8],M=r[12],T=r[1],R=r[5],C=r[9],P=r[13],E=r[2],I=r[6],O=r[10],D=r[14],N=r[3],H=r[7],z=r[11],L=r[15];return s[0]=o*x+a*T+l*E+c*N,s[4]=o*w+a*R+l*I+c*H,s[8]=o*A+a*C+l*O+c*z,s[12]=o*M+a*P+l*D+c*L,s[1]=u*x+d*T+f*E+m*N,s[5]=u*w+d*R+f*I+m*H,s[9]=u*A+d*C+f*O+m*z,s[13]=u*M+d*P+f*D+m*L,s[2]=p*x+_*T+y*E+g*N,s[6]=p*w+_*R+y*I+g*H,s[10]=p*A+_*C+y*O+g*z,s[14]=p*M+_*P+y*D+g*L,s[3]=b*x+h*T+v*E+S*N,s[7]=b*w+h*R+v*I+S*H,s[11]=b*A+h*C+v*O+S*z,s[15]=b*M+h*P+v*D+S*L,this}multiplyScalar(e){let t=this.elements;return t[0]*=e,t[4]*=e,t[8]*=e,t[12]*=e,t[1]*=e,t[5]*=e,t[9]*=e,t[13]*=e,t[2]*=e,t[6]*=e,t[10]*=e,t[14]*=e,t[3]*=e,t[7]*=e,t[11]*=e,t[15]*=e,this}determinant(){let e=this.elements,t=e[0],i=e[4],r=e[8],s=e[12],o=e[1],a=e[5],l=e[9],c=e[13],u=e[2],d=e[6],f=e[10],m=e[14],p=e[3],_=e[7],y=e[11],g=e[15];return p*(+s*l*d-r*c*d-s*a*f+i*c*f+r*a*m-i*l*m)+_*(+t*l*m-t*c*f+s*o*f-r*o*m+r*c*u-s*l*u)+y*(+t*c*d-t*a*m-s*o*d+i*o*m+s*a*u-i*c*u)+g*(-r*a*u-t*l*d+t*a*f+r*o*d-i*o*f+i*l*u)}transpose(){let e=this.elements,t;return t=e[1],e[1]=e[4],e[4]=t,t=e[2],e[2]=e[8],e[8]=t,t=e[6],e[6]=e[9],e[9]=t,t=e[3],e[3]=e[12],e[12]=t,t=e[7],e[7]=e[13],e[13]=t,t=e[11],e[11]=e[14],e[14]=t,this}setPosition(e,t,i){let r=this.elements;return e.isVector3?(r[12]=e.x,r[13]=e.y,r[14]=e.z):(r[12]=e,r[13]=t,r[14]=i),this}invert(){let e=this.elements,t=e[0],i=e[1],r=e[2],s=e[3],o=e[4],a=e[5],l=e[6],c=e[7],u=e[8],d=e[9],f=e[10],m=e[11],p=e[12],_=e[13],y=e[14],g=e[15],b=d*y*c-_*f*c+_*l*m-a*y*m-d*l*g+a*f*g,h=p*f*c-u*y*c-p*l*m+o*y*m+u*l*g-o*f*g,v=u*_*c-p*d*c+p*a*m-o*_*m-u*a*g+o*d*g,S=p*d*l-u*_*l-p*a*f+o*_*f+u*a*y-o*d*y,x=t*b+i*h+r*v+s*S;if(x===0)return this.set(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0);let w=1/x;return e[0]=b*w,e[1]=(_*f*s-d*y*s-_*r*m+i*y*m+d*r*g-i*f*g)*w,e[2]=(a*y*s-_*l*s+_*r*c-i*y*c-a*r*g+i*l*g)*w,e[3]=(d*l*s-a*f*s-d*r*c+i*f*c+a*r*m-i*l*m)*w,e[4]=h*w,e[5]=(u*y*s-p*f*s+p*r*m-t*y*m-u*r*g+t*f*g)*w,e[6]=(p*l*s-o*y*s-p*r*c+t*y*c+o*r*g-t*l*g)*w,e[7]=(o*f*s-u*l*s+u*r*c-t*f*c-o*r*m+t*l*m)*w,e[8]=v*w,e[9]=(p*d*s-u*_*s-p*i*m+t*_*m+u*i*g-t*d*g)*w,e[10]=(o*_*s-p*a*s+p*i*c-t*_*c-o*i*g+t*a*g)*w,e[11]=(u*a*s-o*d*s-u*i*c+t*d*c+o*i*m-t*a*m)*w,e[12]=S*w,e[13]=(u*_*r-p*d*r+p*i*f-t*_*f-u*i*y+t*d*y)*w,e[14]=(p*a*r-o*_*r-p*i*l+t*_*l+o*i*y-t*a*y)*w,e[15]=(o*d*r-u*a*r+u*i*l-t*d*l-o*i*f+t*a*f)*w,this}scale(e){let t=this.elements,i=e.x,r=e.y,s=e.z;return t[0]*=i,t[4]*=r,t[8]*=s,t[1]*=i,t[5]*=r,t[9]*=s,t[2]*=i,t[6]*=r,t[10]*=s,t[3]*=i,t[7]*=r,t[11]*=s,this}getMaxScaleOnAxis(){let e=this.elements,t=e[0]*e[0]+e[1]*e[1]+e[2]*e[2],i=e[4]*e[4]+e[5]*e[5]+e[6]*e[6],r=e[8]*e[8]+e[9]*e[9]+e[10]*e[10];return Math.sqrt(Math.max(t,i,r))}makeTranslation(e,t,i){return e.isVector3?this.set(1,0,0,e.x,0,1,0,e.y,0,0,1,e.z,0,0,0,1):this.set(1,0,0,e,0,1,0,t,0,0,1,i,0,0,0,1),this}makeRotationX(e){let t=Math.cos(e),i=Math.sin(e);return this.set(1,0,0,0,0,t,-i,0,0,i,t,0,0,0,0,1),this}makeRotationY(e){let t=Math.cos(e),i=Math.sin(e);return this.set(t,0,i,0,0,1,0,0,-i,0,t,0,0,0,0,1),this}makeRotationZ(e){let t=Math.cos(e),i=Math.sin(e);return this.set(t,-i,0,0,i,t,0,0,0,0,1,0,0,0,0,1),this}makeRotationAxis(e,t){let i=Math.cos(t),r=Math.sin(t),s=1-i,o=e.x,a=e.y,l=e.z,c=s*o,u=s*a;return this.set(c*o+i,c*a-r*l,c*l+r*a,0,c*a+r*l,u*a+i,u*l-r*o,0,c*l-r*a,u*l+r*o,s*l*l+i,0,0,0,0,1),this}makeScale(e,t,i){return this.set(e,0,0,0,0,t,0,0,0,0,i,0,0,0,0,1),this}makeShear(e,t,i,r,s,o){return this.set(1,i,s,0,e,1,o,0,t,r,1,0,0,0,0,1),this}compose(e,t,i){let r=this.elements,s=t._x,o=t._y,a=t._z,l=t._w,c=s+s,u=o+o,d=a+a,f=s*c,m=s*u,p=s*d,_=o*u,y=o*d,g=a*d,b=l*c,h=l*u,v=l*d,S=i.x,x=i.y,w=i.z;return r[0]=(1-(_+g))*S,r[1]=(m+v)*S,r[2]=(p-h)*S,r[3]=0,r[4]=(m-v)*x,r[5]=(1-(f+g))*x,r[6]=(y+b)*x,r[7]=0,r[8]=(p+h)*w,r[9]=(y-b)*w,r[10]=(1-(f+_))*w,r[11]=0,r[12]=e.x,r[13]=e.y,r[14]=e.z,r[15]=1,this}decompose(e,t,i){let r=this.elements,s=Yl.set(r[0],r[1],r[2]).length(),o=Yl.set(r[4],r[5],r[6]).length(),a=Yl.set(r[8],r[9],r[10]).length();this.determinant()<0&&(s=-s),e.x=r[12],e.y=r[13],e.z=r[14],zr.copy(this);let c=1/s,u=1/o,d=1/a;return zr.elements[0]*=c,zr.elements[1]*=c,zr.elements[2]*=c,zr.elements[4]*=u,zr.elements[5]*=u,zr.elements[6]*=u,zr.elements[8]*=d,zr.elements[9]*=d,zr.elements[10]*=d,t.setFromRotationMatrix(zr),i.x=s,i.y=o,i.z=a,this}makePerspective(e,t,i,r,s,o,a=js){let l=this.elements,c=2*s/(t-e),u=2*s/(i-r),d=(t+e)/(t-e),f=(i+r)/(i-r),m,p;if(a===js)m=-(o+s)/(o-s),p=-2*o*s/(o-s);else if(a===Vp)m=-o/(o-s),p=-o*s/(o-s);else throw new Error("THREE.Matrix4.makePerspective(): Invalid coordinate system: "+a);return l[0]=c,l[4]=0,l[8]=d,l[12]=0,l[1]=0,l[5]=u,l[9]=f,l[13]=0,l[2]=0,l[6]=0,l[10]=m,l[14]=p,l[3]=0,l[7]=0,l[11]=-1,l[15]=0,this}makeOrthographic(e,t,i,r,s,o,a=js){let l=this.elements,c=1/(t-e),u=1/(i-r),d=1/(o-s),f=(t+e)*c,m=(i+r)*u,p,_;if(a===js)p=(o+s)*d,_=-2*d;else if(a===Vp)p=s*d,_=-1*d;else throw new Error("THREE.Matrix4.makeOrthographic(): Invalid coordinate system: "+a);return l[0]=2*c,l[4]=0,l[8]=0,l[12]=-f,l[1]=0,l[5]=2*u,l[9]=0,l[13]=-m,l[2]=0,l[6]=0,l[10]=_,l[14]=-p,l[3]=0,l[7]=0,l[11]=0,l[15]=1,this}equals(e){let t=this.elements,i=e.elements;for(let r=0;r<16;r++)if(t[r]!==i[r])return!1;return!0}fromArray(e,t=0){for(let i=0;i<16;i++)this.elements[i]=e[i+t];return this}toArray(e=[],t=0){let i=this.elements;return e[t]=i[0],e[t+1]=i[1],e[t+2]=i[2],e[t+3]=i[3],e[t+4]=i[4],e[t+5]=i[5],e[t+6]=i[6],e[t+7]=i[7],e[t+8]=i[8],e[t+9]=i[9],e[t+10]=i[10],e[t+11]=i[11],e[t+12]=i[12],e[t+13]=i[13],e[t+14]=i[14],e[t+15]=i[15],e}},Yl=new W,zr=new qe,f4=new W(0,0,0),p4=new W(1,1,1),Uo=new W,fp=new W,Ji=new W,_C=new qe,vC=new Xn,Ba=class n{constructor(e=0,t=0,i=0,r=n.DEFAULT_ORDER){this.isEuler=!0,this._x=e,this._y=t,this._z=i,this._order=r}get x(){return this._x}set x(e){this._x=e,this._onChangeCallback()}get y(){return this._y}set y(e){this._y=e,this._onChangeCallback()}get z(){return this._z}set z(e){this._z=e,this._onChangeCallback()}get order(){return this._order}set order(e){this._order=e,this._onChangeCallback()}set(e,t,i,r=this._order){return this._x=e,this._y=t,this._z=i,this._order=r,this._onChangeCallback(),this}clone(){return new this.constructor(this._x,this._y,this._z,this._order)}copy(e){return this._x=e._x,this._y=e._y,this._z=e._z,this._order=e._order,this._onChangeCallback(),this}setFromRotationMatrix(e,t=this._order,i=!0){let r=e.elements,s=r[0],o=r[4],a=r[8],l=r[1],c=r[5],u=r[9],d=r[2],f=r[6],m=r[10];switch(t){case"XYZ":this._y=Math.asin(Ui(a,-1,1)),Math.abs(a)<.9999999?(this._x=Math.atan2(-u,m),this._z=Math.atan2(-o,s)):(this._x=Math.atan2(f,c),this._z=0);break;case"YXZ":this._x=Math.asin(-Ui(u,-1,1)),Math.abs(u)<.9999999?(this._y=Math.atan2(a,m),this._z=Math.atan2(l,c)):(this._y=Math.atan2(-d,s),this._z=0);break;case"ZXY":this._x=Math.asin(Ui(f,-1,1)),Math.abs(f)<.9999999?(this._y=Math.atan2(-d,m),this._z=Math.atan2(-o,c)):(this._y=0,this._z=Math.atan2(l,s));break;case"ZYX":this._y=Math.asin(-Ui(d,-1,1)),Math.abs(d)<.9999999?(this._x=Math.atan2(f,m),this._z=Math.atan2(l,s)):(this._x=0,this._z=Math.atan2(-o,c));break;case"YZX":this._z=Math.asin(Ui(l,-1,1)),Math.abs(l)<.9999999?(this._x=Math.atan2(-u,c),this._y=Math.atan2(-d,s)):(this._x=0,this._y=Math.atan2(a,m));break;case"XZY":this._z=Math.asin(-Ui(o,-1,1)),Math.abs(o)<.9999999?(this._x=Math.atan2(f,c),this._y=Math.atan2(a,s)):(this._x=Math.atan2(-u,m),this._y=0);break;default:console.warn("THREE.Euler: .setFromRotationMatrix() encountered an unknown order: "+t)}return this._order=t,i===!0&&this._onChangeCallback(),this}setFromQuaternion(e,t,i){return _C.makeRotationFromQuaternion(e),this.setFromRotationMatrix(_C,t,i)}setFromVector3(e,t=this._order){return this.set(e.x,e.y,e.z,t)}reorder(e){return vC.setFromEuler(this),this.setFromQuaternion(vC,e)}equals(e){return e._x===this._x&&e._y===this._y&&e._z===this._z&&e._order===this._order}fromArray(e){return this._x=e[0],this._y=e[1],this._z=e[2],e[3]!==void 0&&(this._order=e[3]),this._onChangeCallback(),this}toArray(e=[],t=0){return e[t]=this._x,e[t+1]=this._y,e[t+2]=this._z,e[t+3]=this._order,e}_onChange(e){return this._onChangeCallback=e,this}_onChangeCallback(){}*[Symbol.iterator](){yield this._x,yield this._y,yield this._z,yield this._order}};Ba.DEFAULT_ORDER="XYZ";var jp=class{constructor(){this.mask=1}set(e){this.mask=(1<>>0}enable(e){this.mask|=1<1){for(let t=0;t1){for(let i=0;i0&&(i=i.concat(o))}return i}getWorldPosition(e){return this.updateWorldMatrix(!0,!1),e.setFromMatrixPosition(this.matrixWorld)}getWorldQuaternion(e){return this.updateWorldMatrix(!0,!1),this.matrixWorld.decompose(mh,e,g4),e}getWorldScale(e){return this.updateWorldMatrix(!0,!1),this.matrixWorld.decompose(mh,y4,e),e}getWorldDirection(e){this.updateWorldMatrix(!0,!1);let t=this.matrixWorld.elements;return e.set(t[8],t[9],t[10]).normalize()}raycast(){}traverse(e){e(this);let t=this.children;for(let i=0,r=t.length;i0&&(r.userData=this.userData),r.layers=this.layers.mask,r.matrix=this.matrix.toArray(),r.up=this.up.toArray(),this.matrixAutoUpdate===!1&&(r.matrixAutoUpdate=!1),this.isInstancedMesh&&(r.type="InstancedMesh",r.count=this.count,r.instanceMatrix=this.instanceMatrix.toJSON(),this.instanceColor!==null&&(r.instanceColor=this.instanceColor.toJSON()));function s(a,l){return a[l.uuid]===void 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this.constructor().copy(this,e)}copy(e,t=!0){if(this.name=e.name,this.up.copy(e.up),this.position.copy(e.position),this.rotation.order=e.rotation.order,this.quaternion.copy(e.quaternion),this.scale.copy(e.scale),this.matrix.copy(e.matrix),this.matrixWorld.copy(e.matrixWorld),this.matrixAutoUpdate=e.matrixAutoUpdate,this.matrixWorldNeedsUpdate=e.matrixWorldNeedsUpdate,this.matrixWorldAutoUpdate=e.matrixWorldAutoUpdate,this.layers.mask=e.layers.mask,this.visible=e.visible,this.castShadow=e.castShadow,this.receiveShadow=e.receiveShadow,this.frustumCulled=e.frustumCulled,this.renderOrder=e.renderOrder,this.animations=e.animations.slice(),this.userData=JSON.parse(JSON.stringify(e.userData)),t===!0)for(let i=0;i0?r.multiplyScalar(1/Math.sqrt(s)):r.set(0,0,0)}static getBarycoord(e,t,i,r,s){Vr.subVectors(r,t),Hs.subVectors(i,t),w_.subVectors(e,t);let o=Vr.dot(Vr),a=Vr.dot(Hs),l=Vr.dot(w_),c=Hs.dot(Hs),u=Hs.dot(w_),d=o*c-a*a;if(d===0)return s.set(-2,-1,-1);let 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C_(n,e,t){return t<0&&(t+=1),t>1&&(t-=1),t<1/6?n+(e-n)*6*t:t<1/2?e:t<2/3?n+(e-n)*6*(2/3-t):n}var dt=class{constructor(e,t,i){return this.isColor=!0,this.r=1,this.g=1,this.b=1,this.set(e,t,i)}set(e,t,i){if(t===void 0&&i===void 0){let r=e;r&&r.isColor?this.copy(r):typeof r=="number"?this.setHex(r):typeof r=="string"&&this.setStyle(r)}else this.setRGB(e,t,i);return this}setScalar(e){return this.r=e,this.g=e,this.b=e,this}setHex(e,t=ai){return e=Math.floor(e),this.r=(e>>16&255)/255,this.g=(e>>8&255)/255,this.b=(e&255)/255,Qt.toWorkingColorSpace(this,t),this}setRGB(e,t,i,r=Qt.workingColorSpace){return this.r=e,this.g=t,this.b=i,Qt.toWorkingColorSpace(this,r),this}setHSL(e,t,i,r=Qt.workingColorSpace){if(e=a4(e,1),t=Ui(t,0,1),i=Ui(i,0,1),t===0)this.r=this.g=this.b=i;else{let s=i<=.5?i*(1+t):i+t-i*t,o=2*i-s;this.r=C_(o,s,e+1/3),this.g=C_(o,s,e),this.b=C_(o,s,e-1/3)}return Qt.toWorkingColorSpace(this,r),this}setStyle(e,t=ai){function i(s){s!==void 0&&parseFloat(s)<1&&console.warn("THREE.Color: Alpha component of "+e+" will be ignored.")}let r;if(r=/^(\w+)\(([^\)]*)\)/.exec(e)){let s,o=r[1],a=r[2];switch(o){case"rgb":case"rgba":if(s=/^\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*(?:,\s*(\d*\.?\d+)\s*)?$/.exec(a))return i(s[4]),this.setRGB(Math.min(255,parseInt(s[1],10))/255,Math.min(255,parseInt(s[2],10))/255,Math.min(255,parseInt(s[3],10))/255,t);if(s=/^\s*(\d+)\%\s*,\s*(\d+)\%\s*,\s*(\d+)\%\s*(?:,\s*(\d*\.?\d+)\s*)?$/.exec(a))return i(s[4]),this.setRGB(Math.min(100,parseInt(s[1],10))/100,Math.min(100,parseInt(s[2],10))/100,Math.min(100,parseInt(s[3],10))/100,t);break;case"hsl":case"hsla":if(s=/^\s*(\d*\.?\d+)\s*,\s*(\d*\.?\d+)\%\s*,\s*(\d*\.?\d+)\%\s*(?:,\s*(\d*\.?\d+)\s*)?$/.exec(a))return i(s[4]),this.setHSL(parseFloat(s[1])/360,parseFloat(s[2])/100,parseFloat(s[3])/100,t);break;default:console.warn("THREE.Color: Unknown color model "+e)}}else if(r=/^\#([A-Fa-f\d]+)$/.exec(e)){let s=r[1],o=s.length;if(o===3)return this.setRGB(parseInt(s.charAt(0),16)/15,parseInt(s.charAt(1),16)/15,parseInt(s.charAt(2),16)/15,t);if(o===6)return this.setHex(parseInt(s,16),t);console.warn("THREE.Color: Invalid hex color "+e)}else if(e&&e.length>0)return this.setColorName(e,t);return this}setColorName(e,t=ai){let i=vE[e.toLowerCase()];return i!==void 0?this.setHex(i,t):console.warn("THREE.Color: Unknown color "+e),this}clone(){return new this.constructor(this.r,this.g,this.b)}copy(e){return this.r=e.r,this.g=e.g,this.b=e.b,this}copySRGBToLinear(e){return this.r=lc(e.r),this.g=lc(e.g),this.b=lc(e.b),this}copyLinearToSRGB(e){return this.r=p_(e.r),this.g=p_(e.g),this.b=p_(e.b),this}convertSRGBToLinear(){return this.copySRGBToLinear(this),this}convertLinearToSRGB(){return this.copyLinearToSRGB(this),this}getHex(e=ai){return Qt.fromWorkingColorSpace(_i.copy(this),e),Math.round(Ui(_i.r*255,0,255))*65536+Math.round(Ui(_i.g*255,0,255))*256+Math.round(Ui(_i.b*255,0,255))}getHexString(e=ai){return("000000"+this.getHex(e).toString(16)).slice(-6)}getHSL(e,t=Qt.workingColorSpace){Qt.fromWorkingColorSpace(_i.copy(this),t);let i=_i.r,r=_i.g,s=_i.b,o=Math.max(i,r,s),a=Math.min(i,r,s),l,c,u=(a+o)/2;if(a===o)l=0,c=0;else{let d=o-a;switch(c=u<=.5?d/(o+a):d/(2-o-a),o){case i:l=(r-s)/d+(r0!=e>0&&this.version++,this._alphaTest=e}onBuild(){}onBeforeRender(){}onBeforeCompile(){}customProgramCacheKey(){return this.onBeforeCompile.toString()}setValues(e){if(e!==void 0)for(let t in e){let i=e[t];if(i===void 0){console.warn(`THREE.Material: parameter '${t}' has value of undefined.`);continue}let r=this[t];if(r===void 0){console.warn(`THREE.Material: '${t}' is not a property of THREE.${this.type}.`);continue}r&&r.isColor?r.set(i):r&&r.isVector3&&i&&i.isVector3?r.copy(i):this[t]=i}}toJSON(e){let t=e===void 0||typeof e=="string";t&&(e={textures:{},images:{}});let i={metadata:{version:4.6,type:"Material",generator:"Material.toJSON"}};i.uuid=this.uuid,i.type=this.type,this.name!==""&&(i.name=this.name),this.color&&this.color.isColor&&(i.color=this.color.getHex()),this.roughness!==void 0&&(i.roughness=this.roughness),this.metalness!==void 0&&(i.metalness=this.metalness),this.sheen!==void 0&&(i.sheen=this.sheen),this.sheenColor&&this.sheenColor.isColor&&(i.sheenColor=this.sheenColor.getHex()),this.sheenRoughness!==void 0&&(i.sheenRoughness=this.sheenRoughness),this.emissive&&this.emissive.isColor&&(i.emissive=this.emissive.getHex()),this.emissiveIntensity&&this.emissiveIntensity!==1&&(i.emissiveIntensity=this.emissiveIntensity),this.specular&&this.specular.isColor&&(i.specular=this.specular.getHex()),this.specularIntensity!==void 0&&(i.specularIntensity=this.specularIntensity),this.specularColor&&this.specularColor.isColor&&(i.specularColor=this.specularColor.getHex()),this.shininess!==void 0&&(i.shininess=this.shininess),this.clearcoat!==void 0&&(i.clearcoat=this.clearcoat),this.clearcoatRoughness!==void 0&&(i.clearcoatRoughness=this.clearcoatRoughness),this.clearcoatMap&&this.clearcoatMap.isTexture&&(i.clearcoatMap=this.clearcoatMap.toJSON(e).uuid),this.clearcoatRoughnessMap&&this.clearcoatRoughnessMap.isTexture&&(i.clearcoatRoughnessMap=this.clearcoatRoughnessMap.toJSON(e).uuid),this.clearcoatNormalMap&&this.clearcoatNormalMap.isTexture&&(i.clearcoatNormalMap=this.clearcoatNormalMap.toJSON(e).uuid,i.clearcoatNormalScale=this.clearcoatNormalScale.toArray()),this.iridescence!==void 0&&(i.iridescence=this.iridescence),this.iridescenceIOR!==void 0&&(i.iridescenceIOR=this.iridescenceIOR),this.iridescenceThicknessRange!==void 0&&(i.iridescenceThicknessRange=this.iridescenceThicknessRange),this.iridescenceMap&&this.iridescenceMap.isTexture&&(i.iridescenceMap=this.iridescenceMap.toJSON(e).uuid),this.iridescenceThicknessMap&&this.iridescenceThicknessMap.isTexture&&(i.iridescenceThicknessMap=this.iridescenceThicknessMap.toJSON(e).uuid),this.anisotropy!==void 0&&(i.anisotropy=this.anisotropy),this.anisotropyRotation!==void 0&&(i.anisotropyRotation=this.anisotropyRotation),this.anisotropyMap&&this.anisotropyMap.isTexture&&(i.anisotropyMap=this.anisotropyMap.toJSON(e).uuid),this.map&&this.map.isTexture&&(i.map=this.map.toJSON(e).uuid),this.matcap&&this.matcap.isTexture&&(i.matcap=this.matcap.toJSON(e).uuid),this.alphaMap&&this.alphaMap.isTexture&&(i.alphaMap=this.alphaMap.toJSON(e).uuid),this.lightMap&&this.lightMap.isTexture&&(i.lightMap=this.lightMap.toJSON(e).uuid,i.lightMapIntensity=this.lightMapIntensity),this.aoMap&&this.aoMap.isTexture&&(i.aoMap=this.aoMap.toJSON(e).uuid,i.aoMapIntensity=this.aoMapIntensity),this.bumpMap&&this.bumpMap.isTexture&&(i.bumpMap=this.bumpMap.toJSON(e).uuid,i.bumpScale=this.bumpScale),this.normalMap&&this.normalMap.isTexture&&(i.normalMap=this.normalMap.toJSON(e).uuid,i.normalMapType=this.normalMapType,i.normalScale=this.normalScale.toArray()),this.displacementMap&&this.displacementMap.isTexture&&(i.displacementMap=this.displacementMap.toJSON(e).uuid,i.displacementScale=this.displacementScale,i.displacementBias=this.displacementBias),this.roughnessMap&&this.roughnessMap.isTexture&&(i.roughnessMap=this.roughnessMap.toJSON(e).uuid),this.metalnessMap&&this.metalnessMap.isTexture&&(i.metalnessMap=this.metalnessMap.toJSON(e).uuid),this.emissiveMap&&this.emissiveMap.isTexture&&(i.emissiveMap=this.emissiveMap.toJSON(e).uuid),this.specularMap&&this.specularMap.isTexture&&(i.specularMap=this.specularMap.toJSON(e).uuid),this.specularIntensityMap&&this.specularIntensityMap.isTexture&&(i.specularIntensityMap=this.specularIntensityMap.toJSON(e).uuid),this.specularColorMap&&this.specularColorMap.isTexture&&(i.specularColorMap=this.specularColorMap.toJSON(e).uuid),this.envMap&&this.envMap.isTexture&&(i.envMap=this.envMap.toJSON(e).uuid,this.combine!==void 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0&&this.rotation!==0&&(i.rotation=this.rotation),this.polygonOffset===!0&&(i.polygonOffset=!0),this.polygonOffsetFactor!==0&&(i.polygonOffsetFactor=this.polygonOffsetFactor),this.polygonOffsetUnits!==0&&(i.polygonOffsetUnits=this.polygonOffsetUnits),this.linewidth!==void 0&&this.linewidth!==1&&(i.linewidth=this.linewidth),this.dashSize!==void 0&&(i.dashSize=this.dashSize),this.gapSize!==void 0&&(i.gapSize=this.gapSize),this.scale!==void 0&&(i.scale=this.scale),this.dithering===!0&&(i.dithering=!0),this.alphaTest>0&&(i.alphaTest=this.alphaTest),this.alphaHash===!0&&(i.alphaHash=!0),this.alphaToCoverage===!0&&(i.alphaToCoverage=!0),this.premultipliedAlpha===!0&&(i.premultipliedAlpha=!0),this.forceSinglePass===!0&&(i.forceSinglePass=!0),this.wireframe===!0&&(i.wireframe=!0),this.wireframeLinewidth>1&&(i.wireframeLinewidth=this.wireframeLinewidth),this.wireframeLinecap!=="round"&&(i.wireframeLinecap=this.wireframeLinecap),this.wireframeLinejoin!=="round"&&(i.wireframeLinejoin=this.wireframeLinejoin),this.flatShading===!0&&(i.flatShading=!0),this.visible===!1&&(i.visible=!1),this.toneMapped===!1&&(i.toneMapped=!1),this.fog===!1&&(i.fog=!1),Object.keys(this.userData).length>0&&(i.userData=this.userData);function r(s){let o=[];for(let a in s){let l=s[a];delete l.metadata,o.push(l)}return o}if(t){let s=r(e.textures),o=r(e.images);s.length>0&&(i.textures=s),o.length>0&&(i.images=o)}return i}clone(){return new this.constructor().copy(this)}copy(e){this.name=e.name,this.blending=e.blending,this.side=e.side,this.vertexColors=e.vertexColors,this.opacity=e.opacity,this.transparent=e.transparent,this.blendSrc=e.blendSrc,this.blendDst=e.blendDst,this.blendEquation=e.blendEquation,this.blendSrcAlpha=e.blendSrcAlpha,this.blendDstAlpha=e.blendDstAlpha,this.blendEquationAlpha=e.blendEquationAlpha,this.blendColor.copy(e.blendColor),this.blendAlpha=e.blendAlpha,this.depthFunc=e.depthFunc,this.depthTest=e.depthTest,this.depthWrite=e.depthWrite,this.stencilWriteMask=e.stencilWriteMask,this.stencilFunc=e.stencilFunc,this.stencilRef=e.stencilRef,this.stencilFuncMask=e.stencilFuncMask,this.stencilFail=e.stencilFail,this.stencilZFail=e.stencilZFail,this.stencilZPass=e.stencilZPass,this.stencilWrite=e.stencilWrite;let t=e.clippingPlanes,i=null;if(t!==null){let r=t.length;i=new Array(r);for(let s=0;s!==r;++s)i[s]=t[s].clone()}return this.clippingPlanes=i,this.clipIntersection=e.clipIntersection,this.clipShadows=e.clipShadows,this.shadowSide=e.shadowSide,this.colorWrite=e.colorWrite,this.precision=e.precision,this.polygonOffset=e.polygonOffset,this.polygonOffsetFactor=e.polygonOffsetFactor,this.polygonOffsetUnits=e.polygonOffsetUnits,this.dithering=e.dithering,this.alphaTest=e.alphaTest,this.alphaHash=e.alphaHash,this.alphaToCoverage=e.alphaToCoverage,this.premultipliedAlpha=e.premultipliedAlpha,this.forceSinglePass=e.forceSinglePass,this.visible=e.visible,this.toneMapped=e.toneMapped,this.userData=JSON.parse(JSON.stringify(e.userData)),this}dispose(){this.dispatchEvent({type:"dispose"})}set needsUpdate(e){e===!0&&this.version++}},Xp=class extends Wo{constructor(e){super(),this.isMeshBasicMaterial=!0,this.type="MeshBasicMaterial",this.color=new dt(16777215),this.map=null,this.lightMap=null,this.lightMapIntensity=1,this.aoMap=null,this.aoMapIntensity=1,this.specularMap=null,this.alphaMap=null,this.envMap=null,this.combine=cE,this.reflectivity=1,this.refractionRatio=.98,this.wireframe=!1,this.wireframeLinewidth=1,this.wireframeLinecap="round",this.wireframeLinejoin="round",this.fog=!0,this.setValues(e)}copy(e){return super.copy(e),this.color.copy(e.color),this.map=e.map,this.lightMap=e.lightMap,this.lightMapIntensity=e.lightMapIntensity,this.aoMap=e.aoMap,this.aoMapIntensity=e.aoMapIntensity,this.specularMap=e.specularMap,this.alphaMap=e.alphaMap,this.envMap=e.envMap,this.combine=e.combine,this.reflectivity=e.reflectivity,this.refractionRatio=e.refractionRatio,this.wireframe=e.wireframe,this.wireframeLinewidth=e.wireframeLinewidth,this.wireframeLinecap=e.wireframeLinecap,this.wireframeLinejoin=e.wireframeLinejoin,this.fog=e.fog,this}};var Un=new W,yp=new Et,gn=class{constructor(e,t,i=!1){if(Array.isArray(e))throw new TypeError("THREE.BufferAttribute: array should be a Typed Array.");this.isBufferAttribute=!0,this.name="",this.array=e,this.itemSize=t,this.count=e!==void 0?e.length/t:0,this.normalized=i,this.usage=qs,this.updateRange={offset:0,count:-1},this.gpuType=br,this.version=0}onUploadCallback(){}set needsUpdate(e){e===!0&&this.version++}setUsage(e){return this.usage=e,this}copy(e){return this.name=e.name,this.array=new e.array.constructor(e.array),this.itemSize=e.itemSize,this.count=e.count,this.normalized=e.normalized,this.usage=e.usage,this.gpuType=e.gpuType,this}copyAt(e,t,i){e*=this.itemSize,i*=t.itemSize;for(let r=0,s=this.itemSize;r0&&(e.userData=this.userData),this.parameters!==void 0){let l=this.parameters;for(let c in l)l[c]!==void 0&&(e[c]=l[c]);return e}e.data={attributes:{}};let t=this.index;t!==null&&(e.data.index={type:t.array.constructor.name,array:Array.prototype.slice.call(t.array)});let i=this.attributes;for(let l in i){let c=i[l];e.data.attributes[l]=c.toJSON(e.data)}let r={},s=!1;for(let l in this.morphAttributes){let c=this.morphAttributes[l],u=[];for(let d=0,f=c.length;d0&&(r[l]=u,s=!0)}s&&(e.data.morphAttributes=r,e.data.morphTargetsRelative=this.morphTargetsRelative);let o=this.groups;o.length>0&&(e.data.groups=JSON.parse(JSON.stringify(o)));let a=this.boundingSphere;return a!==null&&(e.data.boundingSphere={center:a.center.toArray(),radius:a.radius}),e}clone(){return new this.constructor().copy(this)}copy(e){this.index=null,this.attributes={},this.morphAttributes={},this.groups=[],this.boundingBox=null,this.boundingSphere=null;let t={};this.name=e.name;let i=e.index;i!==null&&this.setIndex(i.clone(t));let r=e.attributes;for(let c in r){let u=r[c];this.setAttribute(c,u.clone(t))}let s=e.morphAttributes;for(let c in s){let u=[],d=s[c];for(let f=0,m=d.length;f0){let r=t[i[0]];if(r!==void 0){this.morphTargetInfluences=[],this.morphTargetDictionary={};for(let s=0,o=r.length;s(e.far-e.near)**2))&&(MC.copy(s).invert(),Ta.copy(e.ray).applyMatrix4(MC),!(i.boundingBox!==null&&Ta.intersectsBox(i.boundingBox)===!1)&&this._computeIntersections(e,t,Ta)))}_computeIntersections(e,t,i){let r,s=this.geometry,o=this.material,a=s.index,l=s.attributes.position,c=s.attributes.uv,u=s.attributes.uv1,d=s.attributes.normal,f=s.groups,m=s.drawRange;if(a!==null)if(Array.isArray(o))for(let p=0,_=f.length;p<_;p++){let y=f[p],g=o[y.materialIndex],b=Math.max(y.start,m.start),h=Math.min(a.count,Math.min(y.start+y.count,m.start+m.count));for(let v=b,S=h;vt.far?null:{distance:c,point:Ap.clone(),object:n}}function Mp(n,e,t,i,r,s,o,a,l,c){n.getVertexPosition(a,ec),n.getVertexPosition(l,tc),n.getVertexPosition(c,nc);let u=w4(n,e,t,i,ec,tc,nc,Sp);if(u){r&&(xp.fromBufferAttribute(r,a),bp.fromBufferAttribute(r,l),wp.fromBufferAttribute(r,c),u.uv=oc.getInterpolation(Sp,ec,tc,nc,xp,bp,wp,new Et)),s&&(xp.fromBufferAttribute(s,a),bp.fromBufferAttribute(s,l),wp.fromBufferAttribute(s,c),u.uv1=oc.getInterpolation(Sp,ec,tc,nc,xp,bp,wp,new Et),u.uv2=u.uv1),o&&(EC.fromBufferAttribute(o,a),TC.fromBufferAttribute(o,l),PC.fromBufferAttribute(o,c),u.normal=oc.getInterpolation(Sp,ec,tc,nc,EC,TC,PC,new W),u.normal.dot(i.direction)>0&&u.normal.multiplyScalar(-1));let d={a,b:l,c,normal:new W,materialIndex:0};oc.getNormal(ec,tc,nc,d.normal),u.face=d}return u}var Ua=class n extends Vn{constructor(e=1,t=1,i=1,r=1,s=1,o=1){super(),this.type="BoxGeometry",this.parameters={width:e,height:t,depth:i,widthSegments:r,heightSegments:s,depthSegments:o};let a=this;r=Math.floor(r),s=Math.floor(s),o=Math.floor(o);let l=[],c=[],u=[],d=[],f=0,m=0;p("z","y","x",-1,-1,i,t,e,o,s,0),p("z","y","x",1,-1,i,t,-e,o,s,1),p("x","z","y",1,1,e,i,t,r,o,2),p("x","z","y",1,-1,e,i,-t,r,o,3),p("x","y","z",1,-1,e,t,i,r,s,4),p("x","y","z",-1,-1,e,t,-i,r,s,5),this.setIndex(l),this.setAttribute("position",new zn(c,3)),this.setAttribute("normal",new zn(u,3)),this.setAttribute("uv",new zn(d,2));function p(_,y,g,b,h,v,S,x,w,A,M){let T=v/w,R=S/A,C=v/2,P=S/2,E=x/2,I=w+1,O=A+1,D=0,N=0,H=new W;for(let z=0;z0?1:-1,u.push(H.x,H.y,H.z),d.push(F/w),d.push(1-z/A),D+=1}}for(let z=0;z0&&(t.defines=this.defines),t.vertexShader=this.vertexShader,t.fragmentShader=this.fragmentShader,t.lights=this.lights,t.clipping=this.clipping;let i={};for(let r in this.extensions)this.extensions[r]===!0&&(i[r]=!0);return Object.keys(i).length>0&&(t.extensions=i),t}},Zp=class extends xi{constructor(){super(),this.isCamera=!0,this.type="Camera",this.matrixWorldInverse=new qe,this.projectionMatrix=new qe,this.projectionMatrixInverse=new qe,this.coordinateSystem=js}copy(e,t){return super.copy(e,t),this.matrixWorldInverse.copy(e.matrixWorldInverse),this.projectionMatrix.copy(e.projectionMatrix),this.projectionMatrixInverse.copy(e.projectionMatrixInverse),this.coordinateSystem=e.coordinateSystem,this}getWorldDirection(e){return super.getWorldDirection(e).negate()}updateMatrixWorld(e){super.updateMatrixWorld(e),this.matrixWorldInverse.copy(this.matrixWorld).invert()}updateWorldMatrix(e,t){super.updateWorldMatrix(e,t),this.matrixWorldInverse.copy(this.matrixWorld).invert()}clone(){return new this.constructor().copy(this)}},ci=class extends Zp{constructor(e=50,t=1,i=.1,r=2e3){super(),this.isPerspectiveCamera=!0,this.type="PerspectiveCamera",this.fov=e,this.zoom=1,this.near=i,this.far=r,this.focus=10,this.aspect=t,this.view=null,this.filmGauge=35,this.filmOffset=0,this.updateProjectionMatrix()}copy(e,t){return super.copy(e,t),this.fov=e.fov,this.zoom=e.zoom,this.near=e.near,this.far=e.far,this.focus=e.focus,this.aspect=e.aspect,this.view=e.view===null?null:Object.assign({},e.view),this.filmGauge=e.filmGauge,this.filmOffset=e.filmOffset,this}setFocalLength(e){let t=.5*this.getFilmHeight()/e;this.fov=$_*2*Math.atan(t),this.updateProjectionMatrix()}getFocalLength(){let e=Math.tan(Lp*.5*this.fov);return .5*this.getFilmHeight()/e}getEffectiveFOV(){return $_*2*Math.atan(Math.tan(Lp*.5*this.fov)/this.zoom)}getFilmWidth(){return this.filmGauge*Math.min(this.aspect,1)}getFilmHeight(){return this.filmGauge/Math.max(this.aspect,1)}setViewOffset(e,t,i,r,s,o){this.aspect=e/t,this.view===null&&(this.view={enabled:!0,fullWidth:1,fullHeight:1,offsetX:0,offsetY:0,width:1,height:1}),this.view.enabled=!0,this.view.fullWidth=e,this.view.fullHeight=t,this.view.offsetX=i,this.view.offsetY=r,this.view.width=s,this.view.height=o,this.updateProjectionMatrix()}clearViewOffset(){this.view!==null&&(this.view.enabled=!1),this.updateProjectionMatrix()}updateProjectionMatrix(){let e=this.near,t=e*Math.tan(Lp*.5*this.fov)/this.zoom,i=2*t,r=this.aspect*i,s=-.5*r,o=this.view;if(this.view!==null&&this.view.enabled){let l=o.fullWidth,c=o.fullHeight;s+=o.offsetX*r/l,t-=o.offsetY*i/c,r*=o.width/l,i*=o.height/c}let a=this.filmOffset;a!==0&&(s+=e*a/this.getFilmWidth()),this.projectionMatrix.makePerspective(s,s+r,t,t-i,e,this.far,this.coordinateSystem),this.projectionMatrixInverse.copy(this.projectionMatrix).invert()}toJSON(e){let t=super.toJSON(e);return t.object.fov=this.fov,t.object.zoom=this.zoom,t.object.near=this.near,t.object.far=this.far,t.object.focus=this.focus,t.object.aspect=this.aspect,this.view!==null&&(t.object.view=Object.assign({},this.view)),t.object.filmGauge=this.filmGauge,t.object.filmOffset=this.filmOffset,t}},ic=-90,rc=1,q_=class extends xi{constructor(e,t,i){super(),this.type="CubeCamera",this.renderTarget=i,this.coordinateSystem=null,this.activeMipmapLevel=0;let r=new ci(ic,rc,e,t);r.layers=this.layers,this.add(r);let s=new ci(ic,rc,e,t);s.layers=this.layers,this.add(s);let o=new ci(ic,rc,e,t);o.layers=this.layers,this.add(o);let a=new ci(ic,rc,e,t);a.layers=this.layers,this.add(a);let l=new ci(ic,rc,e,t);l.layers=this.layers,this.add(l);let c=new ci(ic,rc,e,t);c.layers=this.layers,this.add(c)}updateCoordinateSystem(){let e=this.coordinateSystem,t=this.children.concat(),[i,r,s,o,a,l]=t;for(let c of t)this.remove(c);if(e===js)i.up.set(0,1,0),i.lookAt(1,0,0),r.up.set(0,1,0),r.lookAt(-1,0,0),s.up.set(0,0,-1),s.lookAt(0,1,0),o.up.set(0,0,1),o.lookAt(0,-1,0),a.up.set(0,1,0),a.lookAt(0,0,1),l.up.set(0,1,0),l.lookAt(0,0,-1);else if(e===Vp)i.up.set(0,-1,0),i.lookAt(-1,0,0),r.up.set(0,-1,0),r.lookAt(1,0,0),s.up.set(0,0,1),s.lookAt(0,1,0),o.up.set(0,0,-1),o.lookAt(0,-1,0),a.up.set(0,-1,0),a.lookAt(0,0,1),l.up.set(0,-1,0),l.lookAt(0,0,-1);else throw new Error("THREE.CubeCamera.updateCoordinateSystem(): Invalid coordinate system: "+e);for(let c of t)this.add(c),c.updateMatrixWorld()}update(e,t){this.parent===null&&this.updateMatrixWorld();let{renderTarget:i,activeMipmapLevel:r}=this;this.coordinateSystem!==e.coordinateSystem&&(this.coordinateSystem=e.coordinateSystem,this.updateCoordinateSystem());let[s,o,a,l,c,u]=this.children,d=e.getRenderTarget(),f=e.getActiveCubeFace(),m=e.getActiveMipmapLevel(),p=e.xr.enabled;e.xr.enabled=!1;let _=i.texture.generateMipmaps;i.texture.generateMipmaps=!1,e.setRenderTarget(i,0,r),e.render(t,s),e.setRenderTarget(i,1,r),e.render(t,o),e.setRenderTarget(i,2,r),e.render(t,a),e.setRenderTarget(i,3,r),e.render(t,l),e.setRenderTarget(i,4,r),e.render(t,c),i.texture.generateMipmaps=_,e.setRenderTarget(i,5,r),e.render(t,u),e.setRenderTarget(d,f,m),e.xr.enabled=p,i.texture.needsPMREMUpdate=!0}},Kp=class extends tr{constructor(e,t,i,r,s,o,a,l,c,u){e=e!==void 0?e:[],t=t!==void 0?t:uc,super(e,t,i,r,s,o,a,l,c,u),this.isCubeTexture=!0,this.flipY=!1}get images(){return this.image}set images(e){this.image=e}},Y_=class extends nr{constructor(e=1,t={}){super(e,e,t),this.isWebGLCubeRenderTarget=!0;let i={width:e,height:e,depth:1},r=[i,i,i,i,i,i];t.encoding!==void 0&&(_h("THREE.WebGLCubeRenderTarget: option.encoding has been replaced by option.colorSpace."),t.colorSpace=t.encoding===Fa?ai:xr),this.texture=new Kp(r,t.mapping,t.wrapS,t.wrapT,t.magFilter,t.minFilter,t.format,t.type,t.anisotropy,t.colorSpace),this.texture.isRenderTargetTexture=!0,this.texture.generateMipmaps=t.generateMipmaps!==void 0?t.generateMipmaps:!1,this.texture.minFilter=t.minFilter!==void 0?t.minFilter:li}fromEquirectangularTexture(e,t){this.texture.type=t.type,this.texture.colorSpace=t.colorSpace,this.texture.generateMipmaps=t.generateMipmaps,this.texture.minFilter=t.minFilter,this.texture.magFilter=t.magFilter;let i={uniforms:{tEquirect:{value:null}},vertexShader:` + + varying vec3 vWorldDirection; + + vec3 transformDirection( in vec3 dir, in mat4 matrix ) { + + return normalize( ( matrix * vec4( dir, 0.0 ) ).xyz ); + + } + + void main() { + + vWorldDirection = transformDirection( position, modelMatrix ); + + #include + #include + + } + `,fragmentShader:` + + uniform sampler2D tEquirect; + + varying vec3 vWorldDirection; + + #include + + void main() { + + vec3 direction = normalize( vWorldDirection ); + + vec2 sampleUV = equirectUv( direction ); + + gl_FragColor = texture2D( tEquirect, sampleUV ); + + } + `},r=new Ua(5,5,5),s=new Ti({name:"CubemapFromEquirect",uniforms:fc(i.uniforms),vertexShader:i.vertexShader,fragmentShader:i.fragmentShader,side:vi,blending:us});s.uniforms.tEquirect.value=t;let o=new er(r,s),a=t.minFilter;return t.minFilter===xh&&(t.minFilter=li),new q_(1,10,this).update(e,o),t.minFilter=a,o.geometry.dispose(),o.material.dispose(),this}clear(e,t,i,r){let s=e.getRenderTarget();for(let o=0;o<6;o++)e.setRenderTarget(this,o),e.clear(t,i,r);e.setRenderTarget(s)}},P_=new W,C4=new W,E4=new Lt,Ws=class{constructor(e=new W(1,0,0),t=0){this.isPlane=!0,this.normal=e,this.constant=t}set(e,t){return this.normal.copy(e),this.constant=t,this}setComponents(e,t,i,r){return this.normal.set(e,t,i),this.constant=r,this}setFromNormalAndCoplanarPoint(e,t){return this.normal.copy(e),this.constant=-t.dot(this.normal),this}setFromCoplanarPoints(e,t,i){let r=P_.subVectors(i,t).cross(C4.subVectors(e,t)).normalize();return this.setFromNormalAndCoplanarPoint(r,e),this}copy(e){return this.normal.copy(e.normal),this.constant=e.constant,this}normalize(){let e=1/this.normal.length();return this.normal.multiplyScalar(e),this.constant*=e,this}negate(){return this.constant*=-1,this.normal.negate(),this}distanceToPoint(e){return this.normal.dot(e)+this.constant}distanceToSphere(e){return this.distanceToPoint(e.center)-e.radius}projectPoint(e,t){return t.copy(e).addScaledVector(this.normal,-this.distanceToPoint(e))}intersectLine(e,t){let i=e.delta(P_),r=this.normal.dot(i);if(r===0)return this.distanceToPoint(e.start)===0?t.copy(e.start):null;let s=-(e.start.dot(this.normal)+this.constant)/r;return s<0||s>1?null:t.copy(e.start).addScaledVector(i,s)}intersectsLine(e){let t=this.distanceToPoint(e.start),i=this.distanceToPoint(e.end);return t<0&&i>0||i<0&&t>0}intersectsBox(e){return e.intersectsPlane(this)}intersectsSphere(e){return e.intersectsPlane(this)}coplanarPoint(e){return e.copy(this.normal).multiplyScalar(-this.constant)}applyMatrix4(e,t){let i=t||E4.getNormalMatrix(e),r=this.coplanarPoint(P_).applyMatrix4(e),s=this.normal.applyMatrix3(i).normalize();return this.constant=-r.dot(s),this}translate(e){return this.constant-=e.dot(this.normal),this}equals(e){return e.normal.equals(this.normal)&&e.constant===this.constant}clone(){return new this.constructor().copy(this)}},Pa=new Oa,Cp=new W,wh=class{constructor(e=new Ws,t=new Ws,i=new Ws,r=new Ws,s=new Ws,o=new Ws){this.planes=[e,t,i,r,s,o]}set(e,t,i,r,s,o){let a=this.planes;return a[0].copy(e),a[1].copy(t),a[2].copy(i),a[3].copy(r),a[4].copy(s),a[5].copy(o),this}copy(e){let t=this.planes;for(let i=0;i<6;i++)t[i].copy(e.planes[i]);return this}setFromProjectionMatrix(e,t=js){let i=this.planes,r=e.elements,s=r[0],o=r[1],a=r[2],l=r[3],c=r[4],u=r[5],d=r[6],f=r[7],m=r[8],p=r[9],_=r[10],y=r[11],g=r[12],b=r[13],h=r[14],v=r[15];if(i[0].setComponents(l-s,f-c,y-m,v-g).normalize(),i[1].setComponents(l+s,f+c,y+m,v+g).normalize(),i[2].setComponents(l+o,f+u,y+p,v+b).normalize(),i[3].setComponents(l-o,f-u,y-p,v-b).normalize(),i[4].setComponents(l-a,f-d,y-_,v-h).normalize(),t===js)i[5].setComponents(l+a,f+d,y+_,v+h).normalize();else if(t===Vp)i[5].setComponents(a,d,_,h).normalize();else throw new Error("THREE.Frustum.setFromProjectionMatrix(): Invalid coordinate system: "+t);return this}intersectsObject(e){if(e.boundingSphere!==void 0)e.boundingSphere===null&&e.computeBoundingSphere(),Pa.copy(e.boundingSphere).applyMatrix4(e.matrixWorld);else{let t=e.geometry;t.boundingSphere===null&&t.computeBoundingSphere(),Pa.copy(t.boundingSphere).applyMatrix4(e.matrixWorld)}return this.intersectsSphere(Pa)}intersectsSprite(e){return Pa.center.set(0,0,0),Pa.radius=.7071067811865476,Pa.applyMatrix4(e.matrixWorld),this.intersectsSphere(Pa)}intersectsSphere(e){let t=this.planes,i=e.center,r=-e.radius;for(let s=0;s<6;s++)if(t[s].distanceToPoint(i)0?e.max.x:e.min.x,Cp.y=r.normal.y>0?e.max.y:e.min.y,Cp.z=r.normal.z>0?e.max.z:e.min.z,r.distanceToPoint(Cp)<0)return!1}return!0}containsPoint(e){let t=this.planes;for(let i=0;i<6;i++)if(t[i].distanceToPoint(e)<0)return!1;return!0}clone(){return new this.constructor().copy(this)}};function bE(){let n=null,e=!1,t=null,i=null;function r(s,o){t(s,o),i=n.requestAnimationFrame(r)}return{start:function(){e!==!0&&t!==null&&(i=n.requestAnimationFrame(r),e=!0)},stop:function(){n.cancelAnimationFrame(i),e=!1},setAnimationLoop:function(s){t=s},setContext:function(s){n=s}}}function T4(n,e){let t=e.isWebGL2,i=new WeakMap;function r(c,u){let d=c.array,f=c.usage,m=n.createBuffer();n.bindBuffer(u,m),n.bufferData(u,d,f),c.onUploadCallback();let p;if(d instanceof Float32Array)p=n.FLOAT;else if(d instanceof Uint16Array)if(c.isFloat16BufferAttribute)if(t)p=n.HALF_FLOAT;else throw new Error("THREE.WebGLAttributes: Usage of Float16BufferAttribute requires WebGL2.");else p=n.UNSIGNED_SHORT;else if(d instanceof Int16Array)p=n.SHORT;else if(d instanceof Uint32Array)p=n.UNSIGNED_INT;else if(d instanceof Int32Array)p=n.INT;else if(d instanceof Int8Array)p=n.BYTE;else if(d instanceof Uint8Array)p=n.UNSIGNED_BYTE;else if(d instanceof Uint8ClampedArray)p=n.UNSIGNED_BYTE;else throw new Error("THREE.WebGLAttributes: Unsupported buffer data format: "+d);return{buffer:m,type:p,bytesPerElement:d.BYTES_PER_ELEMENT,version:c.version}}function s(c,u,d){let f=u.array,m=u.updateRange;n.bindBuffer(d,c),m.count===-1?n.bufferSubData(d,0,f):(t?n.bufferSubData(d,m.offset*f.BYTES_PER_ELEMENT,f,m.offset,m.count):n.bufferSubData(d,m.offset*f.BYTES_PER_ELEMENT,f.subarray(m.offset,m.offset+m.count)),m.count=-1),u.onUploadCallback()}function o(c){return c.isInterleavedBufferAttribute&&(c=c.data),i.get(c)}function a(c){c.isInterleavedBufferAttribute&&(c=c.data);let u=i.get(c);u&&(n.deleteBuffer(u.buffer),i.delete(c))}function l(c,u){if(c.isGLBufferAttribute){let f=i.get(c);(!f||f.version 0 + vec4 plane; + #pragma unroll_loop_start + for ( int i = 0; i < UNION_CLIPPING_PLANES; i ++ ) { + plane = clippingPlanes[ i ]; + if ( dot( vClipPosition, plane.xyz ) > plane.w ) discard; + } + #pragma unroll_loop_end + #if UNION_CLIPPING_PLANES < NUM_CLIPPING_PLANES + bool clipped = true; + #pragma unroll_loop_start + for ( int i = UNION_CLIPPING_PLANES; i < NUM_CLIPPING_PLANES; i ++ ) { + plane = clippingPlanes[ i ]; + clipped = ( dot( vClipPosition, plane.xyz ) > plane.w ) && clipped; + } + #pragma unroll_loop_end + if ( clipped ) discard; + #endif +#endif`,G4=`#if NUM_CLIPPING_PLANES > 0 + varying vec3 vClipPosition; + uniform vec4 clippingPlanes[ NUM_CLIPPING_PLANES ]; +#endif`,$4=`#if NUM_CLIPPING_PLANES > 0 + varying vec3 vClipPosition; +#endif`,W4=`#if NUM_CLIPPING_PLANES > 0 + vClipPosition = - mvPosition.xyz; +#endif`,j4=`#if defined( USE_COLOR_ALPHA ) + diffuseColor *= vColor; +#elif defined( USE_COLOR ) + diffuseColor.rgb *= vColor; +#endif`,X4=`#if defined( USE_COLOR_ALPHA ) + varying vec4 vColor; +#elif defined( USE_COLOR ) + varying vec3 vColor; +#endif`,q4=`#if defined( USE_COLOR_ALPHA ) + varying vec4 vColor; +#elif defined( USE_COLOR ) || defined( USE_INSTANCING_COLOR ) + varying vec3 vColor; +#endif`,Y4=`#if defined( USE_COLOR_ALPHA ) + vColor = vec4( 1.0 ); +#elif defined( USE_COLOR ) || defined( USE_INSTANCING_COLOR ) + vColor = vec3( 1.0 ); +#endif +#ifdef USE_COLOR + vColor *= color; +#endif +#ifdef USE_INSTANCING_COLOR + vColor.xyz *= instanceColor.xyz; +#endif`,Z4=`#define PI 3.141592653589793 +#define PI2 6.283185307179586 +#define PI_HALF 1.5707963267948966 +#define RECIPROCAL_PI 0.3183098861837907 +#define RECIPROCAL_PI2 0.15915494309189535 +#define EPSILON 1e-6 +#ifndef saturate +#define saturate( a ) clamp( a, 0.0, 1.0 ) +#endif +#define whiteComplement( a ) ( 1.0 - saturate( a ) ) +float pow2( const in float x ) { return x*x; } +vec3 pow2( const in vec3 x ) { return x*x; } +float pow3( const in float x ) { return x*x*x; } +float pow4( const in float x ) { float x2 = x*x; return x2*x2; } +float max3( const in vec3 v ) { return max( max( v.x, v.y ), v.z ); } +float average( const in vec3 v ) { return dot( v, vec3( 0.3333333 ) ); } +highp float rand( const in vec2 uv ) { + const highp float a = 12.9898, b = 78.233, c = 43758.5453; + highp float dt = dot( uv.xy, vec2( a,b ) ), sn = mod( dt, PI ); + return fract( sin( sn ) * c ); +} +#ifdef HIGH_PRECISION + float precisionSafeLength( vec3 v ) { return length( v ); } +#else + float precisionSafeLength( vec3 v ) { + float maxComponent = max3( abs( v ) ); + return length( v / maxComponent ) * maxComponent; + } +#endif +struct IncidentLight { + vec3 color; + vec3 direction; + bool visible; +}; +struct ReflectedLight { + vec3 directDiffuse; + vec3 directSpecular; + vec3 indirectDiffuse; + vec3 indirectSpecular; +}; +#ifdef USE_ALPHAHASH + varying vec3 vPosition; +#endif +vec3 transformDirection( in vec3 dir, in mat4 matrix ) { + return normalize( ( matrix * vec4( dir, 0.0 ) ).xyz ); +} +vec3 inverseTransformDirection( in vec3 dir, in mat4 matrix ) { + return normalize( ( vec4( dir, 0.0 ) * matrix ).xyz ); +} +mat3 transposeMat3( const in mat3 m ) { + mat3 tmp; + tmp[ 0 ] = vec3( m[ 0 ].x, m[ 1 ].x, m[ 2 ].x ); + tmp[ 1 ] = vec3( m[ 0 ].y, m[ 1 ].y, m[ 2 ].y ); + tmp[ 2 ] = vec3( m[ 0 ].z, m[ 1 ].z, m[ 2 ].z ); + return tmp; +} +float luminance( const in vec3 rgb ) { + const vec3 weights = vec3( 0.2126729, 0.7151522, 0.0721750 ); + return dot( weights, rgb ); +} +bool isPerspectiveMatrix( mat4 m ) { + return m[ 2 ][ 3 ] == - 1.0; +} +vec2 equirectUv( in vec3 dir ) { + float u = atan( dir.z, dir.x ) * RECIPROCAL_PI2 + 0.5; + float v = asin( clamp( dir.y, - 1.0, 1.0 ) ) * RECIPROCAL_PI + 0.5; + return vec2( u, v ); +} +vec3 BRDF_Lambert( const in vec3 diffuseColor ) { + return RECIPROCAL_PI * diffuseColor; +} +vec3 F_Schlick( const in vec3 f0, const in float f90, const in float dotVH ) { + float fresnel = exp2( ( - 5.55473 * dotVH - 6.98316 ) * dotVH ); + return f0 * ( 1.0 - fresnel ) + ( f90 * fresnel ); +} +float F_Schlick( const in float f0, const in float f90, const in float dotVH ) { + float fresnel = exp2( ( - 5.55473 * dotVH - 6.98316 ) * dotVH ); + return f0 * ( 1.0 - fresnel ) + ( f90 * fresnel ); +} // validated`,K4=`#ifdef ENVMAP_TYPE_CUBE_UV + #define cubeUV_minMipLevel 4.0 + #define cubeUV_minTileSize 16.0 + float getFace( vec3 direction ) { + vec3 absDirection = abs( direction ); + float face = - 1.0; + if ( absDirection.x > absDirection.z ) { + if ( absDirection.x > absDirection.y ) + face = direction.x > 0.0 ? 0.0 : 3.0; + else + face = direction.y > 0.0 ? 1.0 : 4.0; + } else { + if ( absDirection.z > absDirection.y ) + face = direction.z > 0.0 ? 2.0 : 5.0; + else + face = direction.y > 0.0 ? 1.0 : 4.0; + } + return face; + } + vec2 getUV( vec3 direction, float face ) { + vec2 uv; + if ( face == 0.0 ) { + uv = vec2( direction.z, direction.y ) / abs( direction.x ); + } else if ( face == 1.0 ) { + uv = vec2( - direction.x, - direction.z ) / abs( direction.y ); + } else if ( face == 2.0 ) { + uv = vec2( - direction.x, direction.y ) / abs( direction.z ); + } else if ( face == 3.0 ) { + uv = vec2( - direction.z, direction.y ) / abs( direction.x ); + } else if ( face == 4.0 ) { + uv = vec2( - direction.x, direction.z ) / abs( direction.y ); + } else { + uv = vec2( direction.x, direction.y ) / abs( direction.z ); + } + return 0.5 * ( uv + 1.0 ); + } + vec3 bilinearCubeUV( sampler2D envMap, vec3 direction, float mipInt ) { + float face = getFace( direction ); + float filterInt = max( cubeUV_minMipLevel - mipInt, 0.0 ); + mipInt = max( mipInt, cubeUV_minMipLevel ); + float faceSize = exp2( mipInt ); + highp vec2 uv = getUV( direction, face ) * ( faceSize - 2.0 ) + 1.0; + if ( face > 2.0 ) { + uv.y += faceSize; + face -= 3.0; + } + uv.x += face * faceSize; + uv.x += filterInt * 3.0 * cubeUV_minTileSize; + uv.y += 4.0 * ( exp2( CUBEUV_MAX_MIP ) - faceSize ); + uv.x *= CUBEUV_TEXEL_WIDTH; + uv.y *= CUBEUV_TEXEL_HEIGHT; + #ifdef texture2DGradEXT + return texture2DGradEXT( envMap, uv, vec2( 0.0 ), vec2( 0.0 ) ).rgb; + #else + return texture2D( envMap, uv ).rgb; + #endif + } + #define cubeUV_r0 1.0 + #define cubeUV_v0 0.339 + #define cubeUV_m0 - 2.0 + #define cubeUV_r1 0.8 + #define cubeUV_v1 0.276 + #define cubeUV_m1 - 1.0 + #define cubeUV_r4 0.4 + #define cubeUV_v4 0.046 + #define cubeUV_m4 2.0 + #define cubeUV_r5 0.305 + #define cubeUV_v5 0.016 + #define cubeUV_m5 3.0 + #define cubeUV_r6 0.21 + #define cubeUV_v6 0.0038 + #define cubeUV_m6 4.0 + float roughnessToMip( float roughness ) { + float mip = 0.0; + if ( roughness >= cubeUV_r1 ) { + mip = ( cubeUV_r0 - roughness ) * ( cubeUV_m1 - cubeUV_m0 ) / ( cubeUV_r0 - cubeUV_r1 ) + cubeUV_m0; + } else if ( roughness >= cubeUV_r4 ) { + mip = ( cubeUV_r1 - roughness ) * ( cubeUV_m4 - cubeUV_m1 ) / ( cubeUV_r1 - cubeUV_r4 ) + cubeUV_m1; + } else if ( roughness >= cubeUV_r5 ) { + mip = ( cubeUV_r4 - roughness ) * ( cubeUV_m5 - cubeUV_m4 ) / ( cubeUV_r4 - cubeUV_r5 ) + cubeUV_m4; + } else if ( roughness >= cubeUV_r6 ) { + mip = ( cubeUV_r5 - roughness ) * ( cubeUV_m6 - cubeUV_m5 ) / ( cubeUV_r5 - cubeUV_r6 ) + cubeUV_m5; + } else { + mip = - 2.0 * log2( 1.16 * roughness ); } + return mip; + } + vec4 textureCubeUV( sampler2D envMap, vec3 sampleDir, float roughness ) { + float mip = clamp( roughnessToMip( roughness ), cubeUV_m0, CUBEUV_MAX_MIP ); + float mipF = fract( mip ); + float mipInt = floor( mip ); + vec3 color0 = bilinearCubeUV( envMap, sampleDir, mipInt ); + if ( mipF == 0.0 ) { + return vec4( color0, 1.0 ); + } else { + vec3 color1 = bilinearCubeUV( envMap, sampleDir, mipInt + 1.0 ); + return vec4( mix( color0, color1, mipF ), 1.0 ); + } + } +#endif`,J4=`vec3 transformedNormal = objectNormal; +#ifdef USE_INSTANCING + mat3 m = mat3( instanceMatrix ); + transformedNormal /= vec3( dot( m[ 0 ], m[ 0 ] ), dot( m[ 1 ], m[ 1 ] ), dot( m[ 2 ], m[ 2 ] ) ); + transformedNormal = m * transformedNormal; +#endif +transformedNormal = normalMatrix * transformedNormal; +#ifdef FLIP_SIDED + transformedNormal = - transformedNormal; +#endif +#ifdef USE_TANGENT + vec3 transformedTangent = ( modelViewMatrix * vec4( objectTangent, 0.0 ) ).xyz; + #ifdef FLIP_SIDED + transformedTangent = - transformedTangent; + #endif +#endif`,Q4=`#ifdef USE_DISPLACEMENTMAP + uniform sampler2D displacementMap; + uniform float displacementScale; + uniform float displacementBias; +#endif`,e5=`#ifdef USE_DISPLACEMENTMAP + transformed += normalize( objectNormal ) * ( texture2D( displacementMap, vDisplacementMapUv ).x * displacementScale + displacementBias ); +#endif`,t5=`#ifdef USE_EMISSIVEMAP + vec4 emissiveColor = texture2D( emissiveMap, vEmissiveMapUv ); + totalEmissiveRadiance *= emissiveColor.rgb; +#endif`,n5=`#ifdef USE_EMISSIVEMAP + uniform sampler2D emissiveMap; +#endif`,i5="gl_FragColor = linearToOutputTexel( gl_FragColor );",r5=` +const mat3 LINEAR_SRGB_TO_LINEAR_DISPLAY_P3 = mat3( + vec3( 0.8224621, 0.177538, 0.0 ), + vec3( 0.0331941, 0.9668058, 0.0 ), + vec3( 0.0170827, 0.0723974, 0.9105199 ) +); +const mat3 LINEAR_DISPLAY_P3_TO_LINEAR_SRGB = mat3( + vec3( 1.2249401, - 0.2249404, 0.0 ), + vec3( - 0.0420569, 1.0420571, 0.0 ), + vec3( - 0.0196376, - 0.0786361, 1.0982735 ) +); +vec4 LinearSRGBToLinearDisplayP3( in vec4 value ) { + return vec4( value.rgb * LINEAR_SRGB_TO_LINEAR_DISPLAY_P3, value.a ); +} +vec4 LinearDisplayP3ToLinearSRGB( in vec4 value ) { + return vec4( value.rgb * LINEAR_DISPLAY_P3_TO_LINEAR_SRGB, value.a ); +} +vec4 LinearTransferOETF( in vec4 value ) { + return value; +} +vec4 sRGBTransferOETF( in vec4 value ) { + return vec4( mix( pow( value.rgb, vec3( 0.41666 ) ) * 1.055 - vec3( 0.055 ), value.rgb * 12.92, vec3( lessThanEqual( value.rgb, vec3( 0.0031308 ) ) ) ), value.a ); +} +vec4 LinearToLinear( in vec4 value ) { + return value; +} +vec4 LinearTosRGB( in vec4 value ) { + return sRGBTransferOETF( value ); +}`,s5=`#ifdef USE_ENVMAP + #ifdef ENV_WORLDPOS + vec3 cameraToFrag; + if ( isOrthographic ) { + cameraToFrag = normalize( vec3( - viewMatrix[ 0 ][ 2 ], - viewMatrix[ 1 ][ 2 ], - viewMatrix[ 2 ][ 2 ] ) ); + } else { + cameraToFrag = normalize( vWorldPosition - cameraPosition ); + } + vec3 worldNormal = inverseTransformDirection( normal, viewMatrix ); + #ifdef ENVMAP_MODE_REFLECTION + vec3 reflectVec = reflect( cameraToFrag, worldNormal ); + #else + vec3 reflectVec = refract( cameraToFrag, worldNormal, refractionRatio ); + #endif + #else + vec3 reflectVec = vReflect; + #endif + #ifdef ENVMAP_TYPE_CUBE + vec4 envColor = textureCube( envMap, vec3( flipEnvMap * reflectVec.x, reflectVec.yz ) ); + #else + vec4 envColor = vec4( 0.0 ); + #endif + #ifdef ENVMAP_BLENDING_MULTIPLY + outgoingLight = mix( outgoingLight, outgoingLight * envColor.xyz, specularStrength * reflectivity ); + #elif defined( ENVMAP_BLENDING_MIX ) + outgoingLight = mix( outgoingLight, envColor.xyz, specularStrength * reflectivity ); + #elif defined( ENVMAP_BLENDING_ADD ) + outgoingLight += envColor.xyz * specularStrength * reflectivity; + #endif +#endif`,o5=`#ifdef USE_ENVMAP + uniform float envMapIntensity; + uniform float flipEnvMap; + #ifdef ENVMAP_TYPE_CUBE + uniform samplerCube envMap; + #else + uniform sampler2D envMap; + #endif + +#endif`,a5=`#ifdef USE_ENVMAP + uniform float reflectivity; + #if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG ) || defined( LAMBERT ) + #define ENV_WORLDPOS + #endif + #ifdef ENV_WORLDPOS + varying vec3 vWorldPosition; + uniform float refractionRatio; + #else + varying vec3 vReflect; + #endif +#endif`,l5=`#ifdef USE_ENVMAP + #if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG ) || defined( LAMBERT ) + #define ENV_WORLDPOS + #endif + #ifdef ENV_WORLDPOS + + varying vec3 vWorldPosition; + #else + varying vec3 vReflect; + uniform float refractionRatio; + #endif +#endif`,c5=`#ifdef USE_ENVMAP + #ifdef ENV_WORLDPOS + vWorldPosition = worldPosition.xyz; + #else + vec3 cameraToVertex; + if ( isOrthographic ) { + cameraToVertex = normalize( vec3( - viewMatrix[ 0 ][ 2 ], - viewMatrix[ 1 ][ 2 ], - viewMatrix[ 2 ][ 2 ] ) ); + } else { + cameraToVertex = normalize( worldPosition.xyz - cameraPosition ); + } + vec3 worldNormal = inverseTransformDirection( transformedNormal, viewMatrix ); + #ifdef ENVMAP_MODE_REFLECTION + vReflect = reflect( cameraToVertex, worldNormal ); + #else + vReflect = refract( cameraToVertex, worldNormal, refractionRatio ); + #endif + #endif +#endif`,u5=`#ifdef USE_FOG + vFogDepth = - mvPosition.z; +#endif`,h5=`#ifdef USE_FOG + varying float vFogDepth; +#endif`,d5=`#ifdef USE_FOG + #ifdef FOG_EXP2 + float fogFactor = 1.0 - exp( - fogDensity * fogDensity * vFogDepth * vFogDepth ); + #else + float fogFactor = smoothstep( fogNear, fogFar, vFogDepth ); + #endif + gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor ); +#endif`,f5=`#ifdef USE_FOG + uniform vec3 fogColor; + varying float vFogDepth; + #ifdef FOG_EXP2 + uniform float fogDensity; + #else + uniform float fogNear; + uniform float fogFar; + #endif +#endif`,p5=`#ifdef USE_GRADIENTMAP + uniform sampler2D gradientMap; +#endif +vec3 getGradientIrradiance( vec3 normal, vec3 lightDirection ) { + float dotNL = dot( normal, lightDirection ); + vec2 coord = vec2( dotNL * 0.5 + 0.5, 0.0 ); + #ifdef USE_GRADIENTMAP + return vec3( texture2D( gradientMap, coord ).r ); + #else + vec2 fw = fwidth( coord ) * 0.5; + return mix( vec3( 0.7 ), vec3( 1.0 ), smoothstep( 0.7 - fw.x, 0.7 + fw.x, coord.x ) ); + #endif +}`,m5=`#ifdef USE_LIGHTMAP + vec4 lightMapTexel = texture2D( lightMap, vLightMapUv ); + vec3 lightMapIrradiance = lightMapTexel.rgb * lightMapIntensity; + reflectedLight.indirectDiffuse += lightMapIrradiance; +#endif`,g5=`#ifdef USE_LIGHTMAP + uniform sampler2D lightMap; + uniform float lightMapIntensity; +#endif`,y5=`LambertMaterial material; +material.diffuseColor = diffuseColor.rgb; +material.specularStrength = specularStrength;`,_5=`varying vec3 vViewPosition; +struct LambertMaterial { + vec3 diffuseColor; + float specularStrength; +}; +void RE_Direct_Lambert( const in IncidentLight directLight, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in LambertMaterial material, inout ReflectedLight reflectedLight ) { + float dotNL = saturate( dot( geometryNormal, directLight.direction ) ); + vec3 irradiance = dotNL * directLight.color; + reflectedLight.directDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +void RE_IndirectDiffuse_Lambert( const in vec3 irradiance, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in LambertMaterial material, inout ReflectedLight reflectedLight ) { + reflectedLight.indirectDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +#define RE_Direct RE_Direct_Lambert +#define RE_IndirectDiffuse RE_IndirectDiffuse_Lambert`,v5=`uniform bool receiveShadow; +uniform vec3 ambientLightColor; +#if defined( USE_LIGHT_PROBES ) + uniform vec3 lightProbe[ 9 ]; +#endif +vec3 shGetIrradianceAt( in vec3 normal, in vec3 shCoefficients[ 9 ] ) { + float x = normal.x, y = normal.y, z = normal.z; + vec3 result = shCoefficients[ 0 ] * 0.886227; + result += shCoefficients[ 1 ] * 2.0 * 0.511664 * y; + result += shCoefficients[ 2 ] * 2.0 * 0.511664 * z; + result += shCoefficients[ 3 ] * 2.0 * 0.511664 * x; + result += shCoefficients[ 4 ] * 2.0 * 0.429043 * x * y; + result += shCoefficients[ 5 ] * 2.0 * 0.429043 * y * z; + result += shCoefficients[ 6 ] * ( 0.743125 * z * z - 0.247708 ); + result += shCoefficients[ 7 ] * 2.0 * 0.429043 * x * z; + result += shCoefficients[ 8 ] * 0.429043 * ( x * x - y * y ); + return result; +} +vec3 getLightProbeIrradiance( const in vec3 lightProbe[ 9 ], const in vec3 normal ) { + vec3 worldNormal = inverseTransformDirection( normal, viewMatrix ); + vec3 irradiance = shGetIrradianceAt( worldNormal, lightProbe ); + return irradiance; +} +vec3 getAmbientLightIrradiance( const in vec3 ambientLightColor ) { + vec3 irradiance = ambientLightColor; + return irradiance; +} +float getDistanceAttenuation( const in float lightDistance, const in float cutoffDistance, const in float decayExponent ) { + #if defined ( LEGACY_LIGHTS ) + if ( cutoffDistance > 0.0 && decayExponent > 0.0 ) { + return pow( saturate( - lightDistance / cutoffDistance + 1.0 ), decayExponent ); + } + return 1.0; + #else + float distanceFalloff = 1.0 / max( pow( lightDistance, decayExponent ), 0.01 ); + if ( cutoffDistance > 0.0 ) { + distanceFalloff *= pow2( saturate( 1.0 - pow4( lightDistance / cutoffDistance ) ) ); + } + return distanceFalloff; + #endif +} +float getSpotAttenuation( const in float coneCosine, const in float penumbraCosine, const in float angleCosine ) { + return smoothstep( coneCosine, penumbraCosine, angleCosine ); +} +#if NUM_DIR_LIGHTS > 0 + struct DirectionalLight { + vec3 direction; + vec3 color; + }; + uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ]; + void getDirectionalLightInfo( const in DirectionalLight directionalLight, out IncidentLight light ) { + light.color = directionalLight.color; + light.direction = directionalLight.direction; + light.visible = true; + } +#endif +#if NUM_POINT_LIGHTS > 0 + struct PointLight { + vec3 position; + vec3 color; + float distance; + float decay; + }; + uniform PointLight pointLights[ NUM_POINT_LIGHTS ]; + void getPointLightInfo( const in PointLight pointLight, const in vec3 geometryPosition, out IncidentLight light ) { + vec3 lVector = pointLight.position - geometryPosition; + light.direction = normalize( lVector ); + float lightDistance = length( lVector ); + light.color = pointLight.color; + light.color *= getDistanceAttenuation( lightDistance, pointLight.distance, pointLight.decay ); + light.visible = ( light.color != vec3( 0.0 ) ); + } +#endif +#if NUM_SPOT_LIGHTS > 0 + struct SpotLight { + vec3 position; + vec3 direction; + vec3 color; + float distance; + float decay; + float coneCos; + float penumbraCos; + }; + uniform SpotLight spotLights[ NUM_SPOT_LIGHTS ]; + void getSpotLightInfo( const in SpotLight spotLight, const in vec3 geometryPosition, out IncidentLight light ) { + vec3 lVector = spotLight.position - geometryPosition; + light.direction = normalize( lVector ); + float angleCos = dot( light.direction, spotLight.direction ); + float spotAttenuation = getSpotAttenuation( spotLight.coneCos, spotLight.penumbraCos, angleCos ); + if ( spotAttenuation > 0.0 ) { + float lightDistance = length( lVector ); + light.color = spotLight.color * spotAttenuation; + light.color *= getDistanceAttenuation( lightDistance, spotLight.distance, spotLight.decay ); + light.visible = ( light.color != vec3( 0.0 ) ); + } else { + light.color = vec3( 0.0 ); + light.visible = false; + } + } +#endif +#if NUM_RECT_AREA_LIGHTS > 0 + struct RectAreaLight { + vec3 color; + vec3 position; + vec3 halfWidth; + vec3 halfHeight; + }; + uniform sampler2D ltc_1; uniform sampler2D ltc_2; + uniform RectAreaLight rectAreaLights[ NUM_RECT_AREA_LIGHTS ]; +#endif +#if NUM_HEMI_LIGHTS > 0 + struct HemisphereLight { + vec3 direction; + vec3 skyColor; + vec3 groundColor; + }; + uniform HemisphereLight hemisphereLights[ NUM_HEMI_LIGHTS ]; + vec3 getHemisphereLightIrradiance( const in HemisphereLight hemiLight, const in vec3 normal ) { + float dotNL = dot( normal, hemiLight.direction ); + float hemiDiffuseWeight = 0.5 * dotNL + 0.5; + vec3 irradiance = mix( hemiLight.groundColor, hemiLight.skyColor, hemiDiffuseWeight ); + return irradiance; + } +#endif`,x5=`#ifdef USE_ENVMAP + vec3 getIBLIrradiance( const in vec3 normal ) { + #ifdef ENVMAP_TYPE_CUBE_UV + vec3 worldNormal = inverseTransformDirection( normal, viewMatrix ); + vec4 envMapColor = textureCubeUV( envMap, worldNormal, 1.0 ); + return PI * envMapColor.rgb * envMapIntensity; + #else + return vec3( 0.0 ); + #endif + } + vec3 getIBLRadiance( const in vec3 viewDir, const in vec3 normal, const in float roughness ) { + #ifdef ENVMAP_TYPE_CUBE_UV + vec3 reflectVec = reflect( - viewDir, normal ); + reflectVec = normalize( mix( reflectVec, normal, roughness * roughness) ); + reflectVec = inverseTransformDirection( reflectVec, viewMatrix ); + vec4 envMapColor = textureCubeUV( envMap, reflectVec, roughness ); + return envMapColor.rgb * envMapIntensity; + #else + return vec3( 0.0 ); + #endif + } + #ifdef USE_ANISOTROPY + vec3 getIBLAnisotropyRadiance( const in vec3 viewDir, const in vec3 normal, const in float roughness, const in vec3 bitangent, const in float anisotropy ) { + #ifdef ENVMAP_TYPE_CUBE_UV + vec3 bentNormal = cross( bitangent, viewDir ); + bentNormal = normalize( cross( bentNormal, bitangent ) ); + bentNormal = normalize( mix( bentNormal, normal, pow2( pow2( 1.0 - anisotropy * ( 1.0 - roughness ) ) ) ) ); + return getIBLRadiance( viewDir, bentNormal, roughness ); + #else + return vec3( 0.0 ); + #endif + } + #endif +#endif`,b5=`ToonMaterial material; +material.diffuseColor = diffuseColor.rgb;`,w5=`varying vec3 vViewPosition; +struct ToonMaterial { + vec3 diffuseColor; +}; +void RE_Direct_Toon( const in IncidentLight directLight, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in ToonMaterial material, inout ReflectedLight reflectedLight ) { + vec3 irradiance = getGradientIrradiance( geometryNormal, directLight.direction ) * directLight.color; + reflectedLight.directDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +void RE_IndirectDiffuse_Toon( const in vec3 irradiance, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in ToonMaterial material, inout ReflectedLight reflectedLight ) { + reflectedLight.indirectDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +#define RE_Direct RE_Direct_Toon +#define RE_IndirectDiffuse RE_IndirectDiffuse_Toon`,S5=`BlinnPhongMaterial material; +material.diffuseColor = diffuseColor.rgb; +material.specularColor = specular; +material.specularShininess = shininess; +material.specularStrength = specularStrength;`,A5=`varying vec3 vViewPosition; +struct BlinnPhongMaterial { + vec3 diffuseColor; + vec3 specularColor; + float specularShininess; + float specularStrength; +}; +void RE_Direct_BlinnPhong( const in IncidentLight directLight, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) { + float dotNL = saturate( dot( geometryNormal, directLight.direction ) ); + vec3 irradiance = dotNL * directLight.color; + reflectedLight.directDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); + reflectedLight.directSpecular += irradiance * BRDF_BlinnPhong( directLight.direction, geometryViewDir, geometryNormal, material.specularColor, material.specularShininess ) * material.specularStrength; +} +void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) { + reflectedLight.indirectDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +#define RE_Direct RE_Direct_BlinnPhong +#define RE_IndirectDiffuse RE_IndirectDiffuse_BlinnPhong`,M5=`PhysicalMaterial material; +material.diffuseColor = diffuseColor.rgb * ( 1.0 - metalnessFactor ); +vec3 dxy = max( abs( dFdx( nonPerturbedNormal ) ), abs( dFdy( nonPerturbedNormal ) ) ); +float geometryRoughness = max( max( dxy.x, dxy.y ), dxy.z ); +material.roughness = max( roughnessFactor, 0.0525 );material.roughness += geometryRoughness; +material.roughness = min( material.roughness, 1.0 ); +#ifdef IOR + material.ior = ior; + #ifdef USE_SPECULAR + float specularIntensityFactor = specularIntensity; + vec3 specularColorFactor = specularColor; + #ifdef USE_SPECULAR_COLORMAP + specularColorFactor *= texture2D( specularColorMap, vSpecularColorMapUv ).rgb; + #endif + #ifdef USE_SPECULAR_INTENSITYMAP + specularIntensityFactor *= texture2D( specularIntensityMap, vSpecularIntensityMapUv ).a; + #endif + material.specularF90 = mix( specularIntensityFactor, 1.0, metalnessFactor ); + #else + float specularIntensityFactor = 1.0; + vec3 specularColorFactor = vec3( 1.0 ); + material.specularF90 = 1.0; + #endif + material.specularColor = mix( min( pow2( ( material.ior - 1.0 ) / ( material.ior + 1.0 ) ) * specularColorFactor, vec3( 1.0 ) ) * specularIntensityFactor, diffuseColor.rgb, metalnessFactor ); +#else + material.specularColor = mix( vec3( 0.04 ), diffuseColor.rgb, metalnessFactor ); + material.specularF90 = 1.0; +#endif +#ifdef USE_CLEARCOAT + material.clearcoat = clearcoat; + material.clearcoatRoughness = clearcoatRoughness; + material.clearcoatF0 = vec3( 0.04 ); + material.clearcoatF90 = 1.0; + #ifdef USE_CLEARCOATMAP + material.clearcoat *= texture2D( clearcoatMap, vClearcoatMapUv ).x; + #endif + #ifdef USE_CLEARCOAT_ROUGHNESSMAP + material.clearcoatRoughness *= texture2D( clearcoatRoughnessMap, vClearcoatRoughnessMapUv ).y; + #endif + material.clearcoat = saturate( material.clearcoat ); material.clearcoatRoughness = max( material.clearcoatRoughness, 0.0525 ); + material.clearcoatRoughness += geometryRoughness; + material.clearcoatRoughness = min( material.clearcoatRoughness, 1.0 ); +#endif +#ifdef USE_IRIDESCENCE + material.iridescence = iridescence; + material.iridescenceIOR = iridescenceIOR; + #ifdef USE_IRIDESCENCEMAP + material.iridescence *= texture2D( iridescenceMap, vIridescenceMapUv ).r; + #endif + #ifdef USE_IRIDESCENCE_THICKNESSMAP + material.iridescenceThickness = (iridescenceThicknessMaximum - iridescenceThicknessMinimum) * texture2D( iridescenceThicknessMap, vIridescenceThicknessMapUv ).g + iridescenceThicknessMinimum; + #else + material.iridescenceThickness = iridescenceThicknessMaximum; + #endif +#endif +#ifdef USE_SHEEN + material.sheenColor = sheenColor; + #ifdef USE_SHEEN_COLORMAP + material.sheenColor *= texture2D( sheenColorMap, vSheenColorMapUv ).rgb; + #endif + material.sheenRoughness = clamp( sheenRoughness, 0.07, 1.0 ); + #ifdef USE_SHEEN_ROUGHNESSMAP + material.sheenRoughness *= texture2D( sheenRoughnessMap, vSheenRoughnessMapUv ).a; + #endif +#endif +#ifdef USE_ANISOTROPY + #ifdef USE_ANISOTROPYMAP + mat2 anisotropyMat = mat2( anisotropyVector.x, anisotropyVector.y, - anisotropyVector.y, anisotropyVector.x ); + vec3 anisotropyPolar = texture2D( anisotropyMap, vAnisotropyMapUv ).rgb; + vec2 anisotropyV = anisotropyMat * normalize( 2.0 * anisotropyPolar.rg - vec2( 1.0 ) ) * anisotropyPolar.b; + #else + vec2 anisotropyV = anisotropyVector; + #endif + material.anisotropy = length( anisotropyV ); + anisotropyV /= material.anisotropy; + material.anisotropy = saturate( material.anisotropy ); + material.alphaT = mix( pow2( material.roughness ), 1.0, pow2( material.anisotropy ) ); + material.anisotropyT = tbn[ 0 ] * anisotropyV.x - tbn[ 1 ] * anisotropyV.y; + material.anisotropyB = tbn[ 1 ] * anisotropyV.x + tbn[ 0 ] * anisotropyV.y; +#endif`,C5=`struct PhysicalMaterial { + vec3 diffuseColor; + float roughness; + vec3 specularColor; + float specularF90; + #ifdef USE_CLEARCOAT + float clearcoat; + float clearcoatRoughness; + vec3 clearcoatF0; + float clearcoatF90; + #endif + #ifdef USE_IRIDESCENCE + float iridescence; + float iridescenceIOR; + float iridescenceThickness; + vec3 iridescenceFresnel; + vec3 iridescenceF0; + #endif + #ifdef USE_SHEEN + vec3 sheenColor; + float sheenRoughness; + #endif + #ifdef IOR + float ior; + #endif + #ifdef USE_TRANSMISSION + float transmission; + float transmissionAlpha; + float thickness; + float attenuationDistance; + vec3 attenuationColor; + #endif + #ifdef USE_ANISOTROPY + float anisotropy; + float alphaT; + vec3 anisotropyT; + vec3 anisotropyB; + #endif +}; +vec3 clearcoatSpecularDirect = vec3( 0.0 ); +vec3 clearcoatSpecularIndirect = vec3( 0.0 ); +vec3 sheenSpecularDirect = vec3( 0.0 ); +vec3 sheenSpecularIndirect = vec3(0.0 ); +vec3 Schlick_to_F0( const in vec3 f, const in float f90, const in float dotVH ) { + float x = clamp( 1.0 - dotVH, 0.0, 1.0 ); + float x2 = x * x; + float x5 = clamp( x * x2 * x2, 0.0, 0.9999 ); + return ( f - vec3( f90 ) * x5 ) / ( 1.0 - x5 ); +} +float V_GGX_SmithCorrelated( const in float alpha, const in float dotNL, const in float dotNV ) { + float a2 = pow2( alpha ); + float gv = dotNL * sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNV ) ); + float gl = dotNV * sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNL ) ); + return 0.5 / max( gv + gl, EPSILON ); +} +float D_GGX( const in float alpha, const in float dotNH ) { + float a2 = pow2( alpha ); + float denom = pow2( dotNH ) * ( a2 - 1.0 ) + 1.0; + return RECIPROCAL_PI * a2 / pow2( denom ); +} +#ifdef USE_ANISOTROPY + float V_GGX_SmithCorrelated_Anisotropic( const in float alphaT, const in float alphaB, const in float dotTV, const in float dotBV, const in float dotTL, const in float dotBL, const in float dotNV, const in float dotNL ) { + float gv = dotNL * length( vec3( alphaT * dotTV, alphaB * dotBV, dotNV ) ); + float gl = dotNV * length( vec3( alphaT * dotTL, alphaB * dotBL, dotNL ) ); + float v = 0.5 / ( gv + gl ); + return saturate(v); + } + float D_GGX_Anisotropic( const in float alphaT, const in float alphaB, const in float dotNH, const in float dotTH, const in float dotBH ) { + float a2 = alphaT * alphaB; + highp vec3 v = vec3( alphaB * dotTH, alphaT * dotBH, a2 * dotNH ); + highp float v2 = dot( v, v ); + float w2 = a2 / v2; + return RECIPROCAL_PI * a2 * pow2 ( w2 ); + } +#endif +#ifdef USE_CLEARCOAT + vec3 BRDF_GGX_Clearcoat( const in vec3 lightDir, const in vec3 viewDir, const in vec3 normal, const in PhysicalMaterial material) { + vec3 f0 = material.clearcoatF0; + float f90 = material.clearcoatF90; + float roughness = material.clearcoatRoughness; + float alpha = pow2( roughness ); + vec3 halfDir = normalize( lightDir + viewDir ); + float dotNL = saturate( dot( normal, lightDir ) ); + float dotNV = saturate( dot( normal, viewDir ) ); + float dotNH = saturate( dot( normal, halfDir ) ); + float dotVH = saturate( dot( viewDir, halfDir ) ); + vec3 F = F_Schlick( f0, f90, dotVH ); + float V = V_GGX_SmithCorrelated( alpha, dotNL, dotNV ); + float D = D_GGX( alpha, dotNH ); + return F * ( V * D ); + } +#endif +vec3 BRDF_GGX( const in vec3 lightDir, const in vec3 viewDir, const in vec3 normal, const in PhysicalMaterial material ) { + vec3 f0 = material.specularColor; + float f90 = material.specularF90; + float roughness = material.roughness; + float alpha = pow2( roughness ); + vec3 halfDir = normalize( lightDir + viewDir ); + float dotNL = saturate( dot( normal, lightDir ) ); + float dotNV = saturate( dot( normal, viewDir ) ); + float dotNH = saturate( dot( normal, halfDir ) ); + float dotVH = saturate( dot( viewDir, halfDir ) ); + vec3 F = F_Schlick( f0, f90, dotVH ); + #ifdef USE_IRIDESCENCE + F = mix( F, material.iridescenceFresnel, material.iridescence ); + #endif + #ifdef USE_ANISOTROPY + float dotTL = dot( material.anisotropyT, lightDir ); + float dotTV = dot( material.anisotropyT, viewDir ); + float dotTH = dot( material.anisotropyT, halfDir ); + float dotBL = dot( material.anisotropyB, lightDir ); + float dotBV = dot( material.anisotropyB, viewDir ); + float dotBH = dot( material.anisotropyB, halfDir ); + float V = V_GGX_SmithCorrelated_Anisotropic( material.alphaT, alpha, dotTV, dotBV, dotTL, dotBL, dotNV, dotNL ); + float D = D_GGX_Anisotropic( material.alphaT, alpha, dotNH, dotTH, dotBH ); + #else + float V = V_GGX_SmithCorrelated( alpha, dotNL, dotNV ); + float D = D_GGX( alpha, dotNH ); + #endif + return F * ( V * D ); +} +vec2 LTC_Uv( const in vec3 N, const in vec3 V, const in float roughness ) { + const float LUT_SIZE = 64.0; + const float LUT_SCALE = ( LUT_SIZE - 1.0 ) / LUT_SIZE; + const float LUT_BIAS = 0.5 / LUT_SIZE; + float dotNV = saturate( dot( N, V ) ); + vec2 uv = vec2( roughness, sqrt( 1.0 - dotNV ) ); + uv = uv * LUT_SCALE + LUT_BIAS; + return uv; +} +float LTC_ClippedSphereFormFactor( const in vec3 f ) { + float l = length( f ); + return max( ( l * l + f.z ) / ( l + 1.0 ), 0.0 ); +} +vec3 LTC_EdgeVectorFormFactor( const in vec3 v1, const in vec3 v2 ) { + float x = dot( v1, v2 ); + float y = abs( x ); + float a = 0.8543985 + ( 0.4965155 + 0.0145206 * y ) * y; + float b = 3.4175940 + ( 4.1616724 + y ) * y; + float v = a / b; + float theta_sintheta = ( x > 0.0 ) ? v : 0.5 * inversesqrt( max( 1.0 - x * x, 1e-7 ) ) - v; + return cross( v1, v2 ) * theta_sintheta; +} +vec3 LTC_Evaluate( const in vec3 N, const in vec3 V, const in vec3 P, const in mat3 mInv, const in vec3 rectCoords[ 4 ] ) { + vec3 v1 = rectCoords[ 1 ] - rectCoords[ 0 ]; + vec3 v2 = rectCoords[ 3 ] - rectCoords[ 0 ]; + vec3 lightNormal = cross( v1, v2 ); + if( dot( lightNormal, P - rectCoords[ 0 ] ) < 0.0 ) return vec3( 0.0 ); + vec3 T1, T2; + T1 = normalize( V - N * dot( V, N ) ); + T2 = - cross( N, T1 ); + mat3 mat = mInv * transposeMat3( mat3( T1, T2, N ) ); + vec3 coords[ 4 ]; + coords[ 0 ] = mat * ( rectCoords[ 0 ] - P ); + coords[ 1 ] = mat * ( rectCoords[ 1 ] - P ); + coords[ 2 ] = mat * ( rectCoords[ 2 ] - P ); + coords[ 3 ] = mat * ( rectCoords[ 3 ] - P ); + coords[ 0 ] = normalize( coords[ 0 ] ); + coords[ 1 ] = normalize( coords[ 1 ] ); + coords[ 2 ] = normalize( coords[ 2 ] ); + coords[ 3 ] = normalize( coords[ 3 ] ); + vec3 vectorFormFactor = vec3( 0.0 ); + vectorFormFactor += LTC_EdgeVectorFormFactor( coords[ 0 ], coords[ 1 ] ); + vectorFormFactor += LTC_EdgeVectorFormFactor( coords[ 1 ], coords[ 2 ] ); + vectorFormFactor += LTC_EdgeVectorFormFactor( coords[ 2 ], coords[ 3 ] ); + vectorFormFactor += LTC_EdgeVectorFormFactor( coords[ 3 ], coords[ 0 ] ); + float result = LTC_ClippedSphereFormFactor( vectorFormFactor ); + return vec3( result ); +} +#if defined( USE_SHEEN ) +float D_Charlie( float roughness, float dotNH ) { + float alpha = pow2( roughness ); + float invAlpha = 1.0 / alpha; + float cos2h = dotNH * dotNH; + float sin2h = max( 1.0 - cos2h, 0.0078125 ); + return ( 2.0 + invAlpha ) * pow( sin2h, invAlpha * 0.5 ) / ( 2.0 * PI ); +} +float V_Neubelt( float dotNV, float dotNL ) { + return saturate( 1.0 / ( 4.0 * ( dotNL + dotNV - dotNL * dotNV ) ) ); +} +vec3 BRDF_Sheen( const in vec3 lightDir, const in vec3 viewDir, const in vec3 normal, vec3 sheenColor, const in float sheenRoughness ) { + vec3 halfDir = normalize( lightDir + viewDir ); + float dotNL = saturate( dot( normal, lightDir ) ); + float dotNV = saturate( dot( normal, viewDir ) ); + float dotNH = saturate( dot( normal, halfDir ) ); + float D = D_Charlie( sheenRoughness, dotNH ); + float V = V_Neubelt( dotNV, dotNL ); + return sheenColor * ( D * V ); +} +#endif +float IBLSheenBRDF( const in vec3 normal, const in vec3 viewDir, const in float roughness ) { + float dotNV = saturate( dot( normal, viewDir ) ); + float r2 = roughness * roughness; + float a = roughness < 0.25 ? -339.2 * r2 + 161.4 * roughness - 25.9 : -8.48 * r2 + 14.3 * roughness - 9.95; + float b = roughness < 0.25 ? 44.0 * r2 - 23.7 * roughness + 3.26 : 1.97 * r2 - 3.27 * roughness + 0.72; + float DG = exp( a * dotNV + b ) + ( roughness < 0.25 ? 0.0 : 0.1 * ( roughness - 0.25 ) ); + return saturate( DG * RECIPROCAL_PI ); +} +vec2 DFGApprox( const in vec3 normal, const in vec3 viewDir, const in float roughness ) { + float dotNV = saturate( dot( normal, viewDir ) ); + const vec4 c0 = vec4( - 1, - 0.0275, - 0.572, 0.022 ); + const vec4 c1 = vec4( 1, 0.0425, 1.04, - 0.04 ); + vec4 r = roughness * c0 + c1; + float a004 = min( r.x * r.x, exp2( - 9.28 * dotNV ) ) * r.x + r.y; + vec2 fab = vec2( - 1.04, 1.04 ) * a004 + r.zw; + return fab; +} +vec3 EnvironmentBRDF( const in vec3 normal, const in vec3 viewDir, const in vec3 specularColor, const in float specularF90, const in float roughness ) { + vec2 fab = DFGApprox( normal, viewDir, roughness ); + return specularColor * fab.x + specularF90 * fab.y; +} +#ifdef USE_IRIDESCENCE +void computeMultiscatteringIridescence( const in vec3 normal, const in vec3 viewDir, const in vec3 specularColor, const in float specularF90, const in float iridescence, const in vec3 iridescenceF0, const in float roughness, inout vec3 singleScatter, inout vec3 multiScatter ) { +#else +void computeMultiscattering( const in vec3 normal, const in vec3 viewDir, const in vec3 specularColor, const in float specularF90, const in float roughness, inout vec3 singleScatter, inout vec3 multiScatter ) { +#endif + vec2 fab = DFGApprox( normal, viewDir, roughness ); + #ifdef USE_IRIDESCENCE + vec3 Fr = mix( specularColor, iridescenceF0, iridescence ); + #else + vec3 Fr = specularColor; + #endif + vec3 FssEss = Fr * fab.x + specularF90 * fab.y; + float Ess = fab.x + fab.y; + float Ems = 1.0 - Ess; + vec3 Favg = Fr + ( 1.0 - Fr ) * 0.047619; vec3 Fms = FssEss * Favg / ( 1.0 - Ems * Favg ); + singleScatter += FssEss; + multiScatter += Fms * Ems; +} +#if NUM_RECT_AREA_LIGHTS > 0 + void RE_Direct_RectArea_Physical( const in RectAreaLight rectAreaLight, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) { + vec3 normal = geometryNormal; + vec3 viewDir = geometryViewDir; + vec3 position = geometryPosition; + vec3 lightPos = rectAreaLight.position; + vec3 halfWidth = rectAreaLight.halfWidth; + vec3 halfHeight = rectAreaLight.halfHeight; + vec3 lightColor = rectAreaLight.color; + float roughness = material.roughness; + vec3 rectCoords[ 4 ]; + rectCoords[ 0 ] = lightPos + halfWidth - halfHeight; rectCoords[ 1 ] = lightPos - halfWidth - halfHeight; + rectCoords[ 2 ] = lightPos - halfWidth + halfHeight; + rectCoords[ 3 ] = lightPos + halfWidth + halfHeight; + vec2 uv = LTC_Uv( normal, viewDir, roughness ); + vec4 t1 = texture2D( ltc_1, uv ); + vec4 t2 = texture2D( ltc_2, uv ); + mat3 mInv = mat3( + vec3( t1.x, 0, t1.y ), + vec3( 0, 1, 0 ), + vec3( t1.z, 0, t1.w ) + ); + vec3 fresnel = ( material.specularColor * t2.x + ( vec3( 1.0 ) - material.specularColor ) * t2.y ); + reflectedLight.directSpecular += lightColor * fresnel * LTC_Evaluate( normal, viewDir, position, mInv, rectCoords ); + reflectedLight.directDiffuse += lightColor * material.diffuseColor * LTC_Evaluate( normal, viewDir, position, mat3( 1.0 ), rectCoords ); + } +#endif +void RE_Direct_Physical( const in IncidentLight directLight, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) { + float dotNL = saturate( dot( geometryNormal, directLight.direction ) ); + vec3 irradiance = dotNL * directLight.color; + #ifdef USE_CLEARCOAT + float dotNLcc = saturate( dot( geometryClearcoatNormal, directLight.direction ) ); + vec3 ccIrradiance = dotNLcc * directLight.color; + clearcoatSpecularDirect += ccIrradiance * BRDF_GGX_Clearcoat( directLight.direction, geometryViewDir, geometryClearcoatNormal, material ); + #endif + #ifdef USE_SHEEN + sheenSpecularDirect += irradiance * BRDF_Sheen( directLight.direction, geometryViewDir, geometryNormal, material.sheenColor, material.sheenRoughness ); + #endif + reflectedLight.directSpecular += irradiance * BRDF_GGX( directLight.direction, geometryViewDir, geometryNormal, material ); + reflectedLight.directDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +void RE_IndirectDiffuse_Physical( const in vec3 irradiance, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) { + reflectedLight.indirectDiffuse += irradiance * BRDF_Lambert( material.diffuseColor ); +} +void RE_IndirectSpecular_Physical( const in vec3 radiance, const in vec3 irradiance, const in vec3 clearcoatRadiance, const in vec3 geometryPosition, const in vec3 geometryNormal, const in vec3 geometryViewDir, const in vec3 geometryClearcoatNormal, const in PhysicalMaterial material, inout ReflectedLight reflectedLight) { + #ifdef USE_CLEARCOAT + clearcoatSpecularIndirect += clearcoatRadiance * EnvironmentBRDF( geometryClearcoatNormal, geometryViewDir, material.clearcoatF0, material.clearcoatF90, material.clearcoatRoughness ); + #endif + #ifdef USE_SHEEN + sheenSpecularIndirect += irradiance * material.sheenColor * IBLSheenBRDF( geometryNormal, geometryViewDir, material.sheenRoughness ); + #endif + vec3 singleScattering = vec3( 0.0 ); + vec3 multiScattering = vec3( 0.0 ); + vec3 cosineWeightedIrradiance = irradiance * RECIPROCAL_PI; + #ifdef USE_IRIDESCENCE + computeMultiscatteringIridescence( geometryNormal, geometryViewDir, material.specularColor, material.specularF90, material.iridescence, material.iridescenceFresnel, material.roughness, singleScattering, multiScattering ); + #else + computeMultiscattering( geometryNormal, geometryViewDir, material.specularColor, material.specularF90, material.roughness, singleScattering, multiScattering ); + #endif + vec3 totalScattering = singleScattering + multiScattering; + vec3 diffuse = material.diffuseColor * ( 1.0 - max( max( totalScattering.r, totalScattering.g ), totalScattering.b ) ); + reflectedLight.indirectSpecular += radiance * singleScattering; + reflectedLight.indirectSpecular += multiScattering * cosineWeightedIrradiance; + reflectedLight.indirectDiffuse += diffuse * cosineWeightedIrradiance; +} +#define RE_Direct RE_Direct_Physical +#define RE_Direct_RectArea RE_Direct_RectArea_Physical +#define RE_IndirectDiffuse RE_IndirectDiffuse_Physical +#define RE_IndirectSpecular RE_IndirectSpecular_Physical +float computeSpecularOcclusion( const in float dotNV, const in float ambientOcclusion, const in float roughness ) { + return saturate( pow( dotNV + ambientOcclusion, exp2( - 16.0 * roughness - 1.0 ) ) - 1.0 + ambientOcclusion ); +}`,E5=` +vec3 geometryPosition = - vViewPosition; +vec3 geometryNormal = normal; +vec3 geometryViewDir = ( isOrthographic ) ? vec3( 0, 0, 1 ) : normalize( vViewPosition ); +vec3 geometryClearcoatNormal = vec3( 0.0 ); +#ifdef USE_CLEARCOAT + geometryClearcoatNormal = clearcoatNormal; +#endif +#ifdef USE_IRIDESCENCE + float dotNVi = saturate( dot( normal, geometryViewDir ) ); + if ( material.iridescenceThickness == 0.0 ) { + material.iridescence = 0.0; + } else { + material.iridescence = saturate( material.iridescence ); + } + if ( material.iridescence > 0.0 ) { + material.iridescenceFresnel = evalIridescence( 1.0, material.iridescenceIOR, dotNVi, material.iridescenceThickness, material.specularColor ); + material.iridescenceF0 = Schlick_to_F0( material.iridescenceFresnel, 1.0, dotNVi ); + } +#endif +IncidentLight directLight; +#if ( NUM_POINT_LIGHTS > 0 ) && defined( RE_Direct ) + PointLight pointLight; + #if defined( USE_SHADOWMAP ) && NUM_POINT_LIGHT_SHADOWS > 0 + PointLightShadow pointLightShadow; + #endif + #pragma unroll_loop_start + for ( int i = 0; i < NUM_POINT_LIGHTS; i ++ ) { + pointLight = pointLights[ i ]; + getPointLightInfo( pointLight, geometryPosition, directLight ); + #if defined( USE_SHADOWMAP ) && ( UNROLLED_LOOP_INDEX < NUM_POINT_LIGHT_SHADOWS ) + pointLightShadow = pointLightShadows[ i ]; + directLight.color *= ( directLight.visible && receiveShadow ) ? getPointShadow( pointShadowMap[ i ], pointLightShadow.shadowMapSize, pointLightShadow.shadowBias, pointLightShadow.shadowRadius, vPointShadowCoord[ i ], pointLightShadow.shadowCameraNear, pointLightShadow.shadowCameraFar ) : 1.0; + #endif + RE_Direct( directLight, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); + } + #pragma unroll_loop_end +#endif +#if ( NUM_SPOT_LIGHTS > 0 ) && defined( RE_Direct ) + SpotLight spotLight; + vec4 spotColor; + vec3 spotLightCoord; + bool inSpotLightMap; + #if defined( USE_SHADOWMAP ) && NUM_SPOT_LIGHT_SHADOWS > 0 + SpotLightShadow spotLightShadow; + #endif + #pragma unroll_loop_start + for ( int i = 0; i < NUM_SPOT_LIGHTS; i ++ ) { + spotLight = spotLights[ i ]; + getSpotLightInfo( spotLight, geometryPosition, directLight ); + #if ( UNROLLED_LOOP_INDEX < NUM_SPOT_LIGHT_SHADOWS_WITH_MAPS ) + #define SPOT_LIGHT_MAP_INDEX UNROLLED_LOOP_INDEX + #elif ( UNROLLED_LOOP_INDEX < NUM_SPOT_LIGHT_SHADOWS ) + #define SPOT_LIGHT_MAP_INDEX NUM_SPOT_LIGHT_MAPS + #else + #define SPOT_LIGHT_MAP_INDEX ( UNROLLED_LOOP_INDEX - NUM_SPOT_LIGHT_SHADOWS + NUM_SPOT_LIGHT_SHADOWS_WITH_MAPS ) + #endif + #if ( SPOT_LIGHT_MAP_INDEX < NUM_SPOT_LIGHT_MAPS ) + spotLightCoord = vSpotLightCoord[ i ].xyz / vSpotLightCoord[ i ].w; + inSpotLightMap = all( lessThan( abs( spotLightCoord * 2. - 1. ), vec3( 1.0 ) ) ); + spotColor = texture2D( spotLightMap[ SPOT_LIGHT_MAP_INDEX ], spotLightCoord.xy ); + directLight.color = inSpotLightMap ? directLight.color * spotColor.rgb : directLight.color; + #endif + #undef SPOT_LIGHT_MAP_INDEX + #if defined( USE_SHADOWMAP ) && ( UNROLLED_LOOP_INDEX < NUM_SPOT_LIGHT_SHADOWS ) + spotLightShadow = spotLightShadows[ i ]; + directLight.color *= ( directLight.visible && receiveShadow ) ? getShadow( spotShadowMap[ i ], spotLightShadow.shadowMapSize, spotLightShadow.shadowBias, spotLightShadow.shadowRadius, vSpotLightCoord[ i ] ) : 1.0; + #endif + RE_Direct( directLight, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); + } + #pragma unroll_loop_end +#endif +#if ( NUM_DIR_LIGHTS > 0 ) && defined( RE_Direct ) + DirectionalLight directionalLight; + #if defined( USE_SHADOWMAP ) && NUM_DIR_LIGHT_SHADOWS > 0 + DirectionalLightShadow directionalLightShadow; + #endif + #pragma unroll_loop_start + for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) { + directionalLight = directionalLights[ i ]; + getDirectionalLightInfo( directionalLight, directLight ); + #if defined( USE_SHADOWMAP ) && ( UNROLLED_LOOP_INDEX < NUM_DIR_LIGHT_SHADOWS ) + directionalLightShadow = directionalLightShadows[ i ]; + directLight.color *= ( directLight.visible && receiveShadow ) ? getShadow( directionalShadowMap[ i ], directionalLightShadow.shadowMapSize, directionalLightShadow.shadowBias, directionalLightShadow.shadowRadius, vDirectionalShadowCoord[ i ] ) : 1.0; + #endif + RE_Direct( directLight, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); + } + #pragma unroll_loop_end +#endif +#if ( NUM_RECT_AREA_LIGHTS > 0 ) && defined( RE_Direct_RectArea ) + RectAreaLight rectAreaLight; + #pragma unroll_loop_start + for ( int i = 0; i < NUM_RECT_AREA_LIGHTS; i ++ ) { + rectAreaLight = rectAreaLights[ i ]; + RE_Direct_RectArea( rectAreaLight, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); + } + #pragma unroll_loop_end +#endif +#if defined( RE_IndirectDiffuse ) + vec3 iblIrradiance = vec3( 0.0 ); + vec3 irradiance = getAmbientLightIrradiance( ambientLightColor ); + #if defined( USE_LIGHT_PROBES ) + irradiance += getLightProbeIrradiance( lightProbe, geometryNormal ); + #endif + #if ( NUM_HEMI_LIGHTS > 0 ) + #pragma unroll_loop_start + for ( int i = 0; i < NUM_HEMI_LIGHTS; i ++ ) { + irradiance += getHemisphereLightIrradiance( hemisphereLights[ i ], geometryNormal ); + } + #pragma unroll_loop_end + #endif +#endif +#if defined( RE_IndirectSpecular ) + vec3 radiance = vec3( 0.0 ); + vec3 clearcoatRadiance = vec3( 0.0 ); +#endif`,T5=`#if defined( RE_IndirectDiffuse ) + #ifdef USE_LIGHTMAP + vec4 lightMapTexel = texture2D( lightMap, vLightMapUv ); + vec3 lightMapIrradiance = lightMapTexel.rgb * lightMapIntensity; + irradiance += lightMapIrradiance; + #endif + #if defined( USE_ENVMAP ) && defined( STANDARD ) && defined( ENVMAP_TYPE_CUBE_UV ) + iblIrradiance += getIBLIrradiance( geometryNormal ); + #endif +#endif +#if defined( USE_ENVMAP ) && defined( RE_IndirectSpecular ) + #ifdef USE_ANISOTROPY + radiance += getIBLAnisotropyRadiance( geometryViewDir, geometryNormal, material.roughness, material.anisotropyB, material.anisotropy ); + #else + radiance += getIBLRadiance( geometryViewDir, geometryNormal, material.roughness ); + #endif + #ifdef USE_CLEARCOAT + clearcoatRadiance += getIBLRadiance( geometryViewDir, geometryClearcoatNormal, material.clearcoatRoughness ); + #endif +#endif`,P5=`#if defined( RE_IndirectDiffuse ) + RE_IndirectDiffuse( irradiance, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); +#endif +#if defined( RE_IndirectSpecular ) + RE_IndirectSpecular( radiance, iblIrradiance, clearcoatRadiance, geometryPosition, geometryNormal, geometryViewDir, geometryClearcoatNormal, material, reflectedLight ); +#endif`,I5=`#if defined( USE_LOGDEPTHBUF ) && defined( USE_LOGDEPTHBUF_EXT ) + gl_FragDepthEXT = vIsPerspective == 0.0 ? gl_FragCoord.z : log2( vFragDepth ) * logDepthBufFC * 0.5; +#endif`,R5=`#if defined( USE_LOGDEPTHBUF ) && defined( USE_LOGDEPTHBUF_EXT ) + uniform float logDepthBufFC; + varying float vFragDepth; + varying float vIsPerspective; +#endif`,k5=`#ifdef USE_LOGDEPTHBUF + #ifdef USE_LOGDEPTHBUF_EXT + varying float vFragDepth; + varying float vIsPerspective; + #else + uniform float logDepthBufFC; + #endif +#endif`,L5=`#ifdef USE_LOGDEPTHBUF + #ifdef USE_LOGDEPTHBUF_EXT + vFragDepth = 1.0 + gl_Position.w; + vIsPerspective = float( isPerspectiveMatrix( projectionMatrix ) ); + #else + if ( isPerspectiveMatrix( projectionMatrix ) ) { + gl_Position.z = log2( max( EPSILON, gl_Position.w + 1.0 ) ) * logDepthBufFC - 1.0; + gl_Position.z *= gl_Position.w; + } + #endif +#endif`,D5=`#ifdef USE_MAP + vec4 sampledDiffuseColor = texture2D( map, vMapUv ); + #ifdef DECODE_VIDEO_TEXTURE + sampledDiffuseColor = vec4( mix( pow( sampledDiffuseColor.rgb * 0.9478672986 + vec3( 0.0521327014 ), vec3( 2.4 ) ), sampledDiffuseColor.rgb * 0.0773993808, vec3( lessThanEqual( sampledDiffuseColor.rgb, vec3( 0.04045 ) ) ) ), sampledDiffuseColor.w ); + + #endif + diffuseColor *= sampledDiffuseColor; +#endif`,N5=`#ifdef USE_MAP + uniform sampler2D map; +#endif`,F5=`#if defined( USE_MAP ) || defined( USE_ALPHAMAP ) + #if defined( USE_POINTS_UV ) + vec2 uv = vUv; + #else + vec2 uv = ( uvTransform * vec3( gl_PointCoord.x, 1.0 - gl_PointCoord.y, 1 ) ).xy; + #endif +#endif +#ifdef USE_MAP + diffuseColor *= texture2D( map, uv ); +#endif +#ifdef USE_ALPHAMAP + diffuseColor.a *= texture2D( alphaMap, uv ).g; +#endif`,O5=`#if defined( USE_POINTS_UV ) + varying vec2 vUv; +#else + #if defined( USE_MAP ) || defined( USE_ALPHAMAP ) + uniform mat3 uvTransform; + #endif +#endif +#ifdef USE_MAP + uniform sampler2D map; +#endif +#ifdef USE_ALPHAMAP + uniform sampler2D alphaMap; +#endif`,B5=`float metalnessFactor = metalness; +#ifdef USE_METALNESSMAP + vec4 texelMetalness = texture2D( metalnessMap, vMetalnessMapUv ); + metalnessFactor *= texelMetalness.b; +#endif`,U5=`#ifdef USE_METALNESSMAP + uniform sampler2D metalnessMap; +#endif`,z5=`#if defined( USE_MORPHCOLORS ) && defined( MORPHTARGETS_TEXTURE ) + vColor *= morphTargetBaseInfluence; + for ( int i = 0; i < MORPHTARGETS_COUNT; i ++ ) { + #if defined( USE_COLOR_ALPHA ) + if ( morphTargetInfluences[ i ] != 0.0 ) vColor += getMorph( gl_VertexID, i, 2 ) * morphTargetInfluences[ i ]; + #elif defined( USE_COLOR ) + if ( morphTargetInfluences[ i ] != 0.0 ) vColor += getMorph( gl_VertexID, i, 2 ).rgb * morphTargetInfluences[ i ]; + #endif + } +#endif`,V5=`#ifdef USE_MORPHNORMALS + objectNormal *= morphTargetBaseInfluence; + #ifdef MORPHTARGETS_TEXTURE + for ( int i = 0; i < MORPHTARGETS_COUNT; i ++ ) { + if ( morphTargetInfluences[ i ] != 0.0 ) objectNormal += getMorph( gl_VertexID, i, 1 ).xyz * morphTargetInfluences[ i ]; + } + #else + objectNormal += morphNormal0 * morphTargetInfluences[ 0 ]; + objectNormal += morphNormal1 * morphTargetInfluences[ 1 ]; + objectNormal += morphNormal2 * morphTargetInfluences[ 2 ]; + objectNormal += morphNormal3 * morphTargetInfluences[ 3 ]; + #endif +#endif`,H5=`#ifdef USE_MORPHTARGETS + uniform float morphTargetBaseInfluence; + #ifdef MORPHTARGETS_TEXTURE + uniform float morphTargetInfluences[ MORPHTARGETS_COUNT ]; + uniform sampler2DArray morphTargetsTexture; + uniform ivec2 morphTargetsTextureSize; + vec4 getMorph( const in int vertexIndex, const in int morphTargetIndex, const in int offset ) { + int texelIndex = vertexIndex * MORPHTARGETS_TEXTURE_STRIDE + offset; + int y = texelIndex / morphTargetsTextureSize.x; + int x = texelIndex - y * morphTargetsTextureSize.x; + ivec3 morphUV = ivec3( x, y, morphTargetIndex ); + return texelFetch( morphTargetsTexture, morphUV, 0 ); + } + #else + #ifndef USE_MORPHNORMALS + uniform float morphTargetInfluences[ 8 ]; + #else + uniform float morphTargetInfluences[ 4 ]; + #endif + #endif +#endif`,G5=`#ifdef USE_MORPHTARGETS + transformed *= morphTargetBaseInfluence; + #ifdef MORPHTARGETS_TEXTURE + for ( int i = 0; i < MORPHTARGETS_COUNT; i ++ ) { + if ( morphTargetInfluences[ i ] != 0.0 ) transformed += getMorph( gl_VertexID, i, 0 ).xyz * morphTargetInfluences[ i ]; + } + #else + transformed += morphTarget0 * morphTargetInfluences[ 0 ]; + transformed += morphTarget1 * morphTargetInfluences[ 1 ]; + transformed += morphTarget2 * morphTargetInfluences[ 2 ]; + transformed += morphTarget3 * morphTargetInfluences[ 3 ]; + #ifndef USE_MORPHNORMALS + transformed += morphTarget4 * morphTargetInfluences[ 4 ]; + transformed += morphTarget5 * morphTargetInfluences[ 5 ]; + transformed += morphTarget6 * morphTargetInfluences[ 6 ]; + transformed += morphTarget7 * morphTargetInfluences[ 7 ]; + #endif + #endif +#endif`,$5=`float faceDirection = gl_FrontFacing ? 1.0 : - 1.0; +#ifdef FLAT_SHADED + vec3 fdx = dFdx( vViewPosition ); + vec3 fdy = dFdy( vViewPosition ); + vec3 normal = normalize( cross( fdx, fdy ) ); +#else + vec3 normal = normalize( vNormal ); + #ifdef DOUBLE_SIDED + normal *= faceDirection; + #endif +#endif +#if defined( USE_NORMALMAP_TANGENTSPACE ) || defined( USE_CLEARCOAT_NORMALMAP ) || defined( USE_ANISOTROPY ) + #ifdef USE_TANGENT + mat3 tbn = mat3( normalize( vTangent ), normalize( vBitangent ), normal ); + #else + mat3 tbn = getTangentFrame( - vViewPosition, normal, + #if defined( USE_NORMALMAP ) + vNormalMapUv + #elif defined( USE_CLEARCOAT_NORMALMAP ) + vClearcoatNormalMapUv + #else + vUv + #endif + ); + #endif + #if defined( DOUBLE_SIDED ) && ! defined( FLAT_SHADED ) + tbn[0] *= faceDirection; + tbn[1] *= faceDirection; + #endif +#endif +#ifdef USE_CLEARCOAT_NORMALMAP + #ifdef USE_TANGENT + mat3 tbn2 = mat3( normalize( vTangent ), normalize( vBitangent ), normal ); + #else + mat3 tbn2 = getTangentFrame( - vViewPosition, normal, vClearcoatNormalMapUv ); + #endif + #if defined( DOUBLE_SIDED ) && ! defined( FLAT_SHADED ) + tbn2[0] *= faceDirection; + tbn2[1] *= faceDirection; + #endif +#endif +vec3 nonPerturbedNormal = normal;`,W5=`#ifdef USE_NORMALMAP_OBJECTSPACE + normal = texture2D( normalMap, vNormalMapUv ).xyz * 2.0 - 1.0; + #ifdef FLIP_SIDED + normal = - normal; + #endif + #ifdef DOUBLE_SIDED + normal = normal * faceDirection; + #endif + normal = normalize( normalMatrix * normal ); +#elif defined( USE_NORMALMAP_TANGENTSPACE ) + vec3 mapN = texture2D( normalMap, vNormalMapUv ).xyz * 2.0 - 1.0; + mapN.xy *= normalScale; + normal = normalize( tbn * mapN ); +#elif defined( USE_BUMPMAP ) + normal = perturbNormalArb( - vViewPosition, normal, dHdxy_fwd(), faceDirection ); +#endif`,j5=`#ifndef FLAT_SHADED + varying vec3 vNormal; + #ifdef USE_TANGENT + varying vec3 vTangent; + varying vec3 vBitangent; + #endif +#endif`,X5=`#ifndef FLAT_SHADED + varying vec3 vNormal; + #ifdef USE_TANGENT + varying vec3 vTangent; + varying vec3 vBitangent; + #endif +#endif`,q5=`#ifndef FLAT_SHADED + vNormal = normalize( transformedNormal ); + #ifdef USE_TANGENT + vTangent = normalize( transformedTangent ); + vBitangent = normalize( cross( vNormal, vTangent ) * tangent.w ); + #endif +#endif`,Y5=`#ifdef USE_NORMALMAP + uniform sampler2D normalMap; + uniform vec2 normalScale; +#endif +#ifdef USE_NORMALMAP_OBJECTSPACE + uniform mat3 normalMatrix; +#endif +#if ! defined ( USE_TANGENT ) && ( defined ( USE_NORMALMAP_TANGENTSPACE ) || defined ( USE_CLEARCOAT_NORMALMAP ) || defined( USE_ANISOTROPY ) ) + mat3 getTangentFrame( vec3 eye_pos, vec3 surf_norm, vec2 uv ) { + vec3 q0 = dFdx( eye_pos.xyz ); + vec3 q1 = dFdy( eye_pos.xyz ); + vec2 st0 = dFdx( uv.st ); + vec2 st1 = dFdy( uv.st ); + vec3 N = surf_norm; + vec3 q1perp = cross( q1, N ); + vec3 q0perp = cross( N, q0 ); + vec3 T = q1perp * st0.x + q0perp * st1.x; + vec3 B = q1perp * st0.y + q0perp * st1.y; + float det = max( dot( T, T ), dot( B, B ) ); + float scale = ( det == 0.0 ) ? 0.0 : inversesqrt( det ); + return mat3( T * scale, B * scale, N ); + } +#endif`,Z5=`#ifdef USE_CLEARCOAT + vec3 clearcoatNormal = nonPerturbedNormal; +#endif`,K5=`#ifdef USE_CLEARCOAT_NORMALMAP + vec3 clearcoatMapN = texture2D( clearcoatNormalMap, vClearcoatNormalMapUv ).xyz * 2.0 - 1.0; + clearcoatMapN.xy *= clearcoatNormalScale; + clearcoatNormal = normalize( tbn2 * clearcoatMapN ); +#endif`,J5=`#ifdef USE_CLEARCOATMAP + uniform sampler2D clearcoatMap; +#endif +#ifdef USE_CLEARCOAT_NORMALMAP + uniform sampler2D clearcoatNormalMap; + uniform vec2 clearcoatNormalScale; +#endif +#ifdef USE_CLEARCOAT_ROUGHNESSMAP + uniform sampler2D clearcoatRoughnessMap; +#endif`,Q5=`#ifdef USE_IRIDESCENCEMAP + uniform sampler2D iridescenceMap; +#endif +#ifdef USE_IRIDESCENCE_THICKNESSMAP + uniform sampler2D iridescenceThicknessMap; +#endif`,eN=`#ifdef OPAQUE +diffuseColor.a = 1.0; +#endif +#ifdef USE_TRANSMISSION +diffuseColor.a *= material.transmissionAlpha; +#endif +gl_FragColor = vec4( outgoingLight, diffuseColor.a );`,tN=`vec3 packNormalToRGB( const in vec3 normal ) { + return normalize( normal ) * 0.5 + 0.5; +} +vec3 unpackRGBToNormal( const in vec3 rgb ) { + return 2.0 * rgb.xyz - 1.0; +} +const float PackUpscale = 256. / 255.;const float UnpackDownscale = 255. / 256.; +const vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. ); +const vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. ); +const float ShiftRight8 = 1. / 256.; +vec4 packDepthToRGBA( const in float v ) { + vec4 r = vec4( fract( v * PackFactors ), v ); + r.yzw -= r.xyz * ShiftRight8; return r * PackUpscale; +} +float unpackRGBAToDepth( const in vec4 v ) { + return dot( v, UnpackFactors ); +} +vec2 packDepthToRG( in highp float v ) { + return packDepthToRGBA( v ).yx; +} +float unpackRGToDepth( const in highp vec2 v ) { + return unpackRGBAToDepth( vec4( v.xy, 0.0, 0.0 ) ); +} +vec4 pack2HalfToRGBA( vec2 v ) { + vec4 r = vec4( v.x, fract( v.x * 255.0 ), v.y, fract( v.y * 255.0 ) ); + return vec4( r.x - r.y / 255.0, r.y, r.z - r.w / 255.0, r.w ); +} +vec2 unpackRGBATo2Half( vec4 v ) { + return vec2( v.x + ( v.y / 255.0 ), v.z + ( v.w / 255.0 ) ); +} +float viewZToOrthographicDepth( const in float viewZ, const in float near, const in float far ) { + return ( viewZ + near ) / ( near - far ); +} +float orthographicDepthToViewZ( const in float depth, const in float near, const in float far ) { + return depth * ( near - far ) - near; +} +float viewZToPerspectiveDepth( const in float viewZ, const in float near, const in float far ) { + return ( ( near + viewZ ) * far ) / ( ( far - near ) * viewZ ); +} +float perspectiveDepthToViewZ( const in float depth, const in float near, const in float far ) { + return ( near * far ) / ( ( far - near ) * depth - far ); +}`,nN=`#ifdef PREMULTIPLIED_ALPHA + gl_FragColor.rgb *= gl_FragColor.a; +#endif`,iN=`vec4 mvPosition = vec4( transformed, 1.0 ); +#ifdef USE_INSTANCING + mvPosition = instanceMatrix * mvPosition; +#endif +mvPosition = modelViewMatrix * mvPosition; +gl_Position = projectionMatrix * mvPosition;`,rN=`#ifdef DITHERING + gl_FragColor.rgb = dithering( gl_FragColor.rgb ); +#endif`,sN=`#ifdef DITHERING + vec3 dithering( vec3 color ) { + float grid_position = rand( gl_FragCoord.xy ); + vec3 dither_shift_RGB = vec3( 0.25 / 255.0, -0.25 / 255.0, 0.25 / 255.0 ); + dither_shift_RGB = mix( 2.0 * dither_shift_RGB, -2.0 * dither_shift_RGB, grid_position ); + return color + dither_shift_RGB; + } +#endif`,oN=`float roughnessFactor = roughness; +#ifdef USE_ROUGHNESSMAP + vec4 texelRoughness = texture2D( roughnessMap, vRoughnessMapUv ); + roughnessFactor *= texelRoughness.g; +#endif`,aN=`#ifdef USE_ROUGHNESSMAP + uniform sampler2D roughnessMap; +#endif`,lN=`#if NUM_SPOT_LIGHT_COORDS > 0 + varying vec4 vSpotLightCoord[ NUM_SPOT_LIGHT_COORDS ]; +#endif +#if NUM_SPOT_LIGHT_MAPS > 0 + uniform sampler2D spotLightMap[ NUM_SPOT_LIGHT_MAPS ]; +#endif +#ifdef USE_SHADOWMAP + #if NUM_DIR_LIGHT_SHADOWS > 0 + uniform sampler2D directionalShadowMap[ NUM_DIR_LIGHT_SHADOWS ]; + varying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHT_SHADOWS ]; + struct DirectionalLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + }; + uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHT_SHADOWS ]; + #endif + #if NUM_SPOT_LIGHT_SHADOWS > 0 + uniform sampler2D spotShadowMap[ NUM_SPOT_LIGHT_SHADOWS ]; + struct SpotLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + }; + uniform SpotLightShadow spotLightShadows[ NUM_SPOT_LIGHT_SHADOWS ]; + #endif + #if NUM_POINT_LIGHT_SHADOWS > 0 + uniform sampler2D pointShadowMap[ NUM_POINT_LIGHT_SHADOWS ]; + varying vec4 vPointShadowCoord[ NUM_POINT_LIGHT_SHADOWS ]; + struct PointLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + float shadowCameraNear; + float shadowCameraFar; + }; + uniform PointLightShadow pointLightShadows[ NUM_POINT_LIGHT_SHADOWS ]; + #endif + float texture2DCompare( sampler2D depths, vec2 uv, float compare ) { + return step( compare, unpackRGBAToDepth( texture2D( depths, uv ) ) ); + } + vec2 texture2DDistribution( sampler2D shadow, vec2 uv ) { + return unpackRGBATo2Half( texture2D( shadow, uv ) ); + } + float VSMShadow (sampler2D shadow, vec2 uv, float compare ){ + float occlusion = 1.0; + vec2 distribution = texture2DDistribution( shadow, uv ); + float hard_shadow = step( compare , distribution.x ); + if (hard_shadow != 1.0 ) { + float distance = compare - distribution.x ; + float variance = max( 0.00000, distribution.y * distribution.y ); + float softness_probability = variance / (variance + distance * distance ); softness_probability = clamp( ( softness_probability - 0.3 ) / ( 0.95 - 0.3 ), 0.0, 1.0 ); occlusion = clamp( max( hard_shadow, softness_probability ), 0.0, 1.0 ); + } + return occlusion; + } + float getShadow( sampler2D shadowMap, vec2 shadowMapSize, float shadowBias, float shadowRadius, vec4 shadowCoord ) { + float shadow = 1.0; + shadowCoord.xyz /= shadowCoord.w; + shadowCoord.z += shadowBias; + bool inFrustum = shadowCoord.x >= 0.0 && shadowCoord.x <= 1.0 && shadowCoord.y >= 0.0 && shadowCoord.y <= 1.0; + bool frustumTest = inFrustum && shadowCoord.z <= 1.0; + if ( frustumTest ) { + #if defined( SHADOWMAP_TYPE_PCF ) + vec2 texelSize = vec2( 1.0 ) / shadowMapSize; + float dx0 = - texelSize.x * shadowRadius; + float dy0 = - texelSize.y * shadowRadius; + float dx1 = + texelSize.x * shadowRadius; + float dy1 = + texelSize.y * shadowRadius; + float dx2 = dx0 / 2.0; + float dy2 = dy0 / 2.0; + float dx3 = dx1 / 2.0; + float dy3 = dy1 / 2.0; + shadow = ( + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx2, dy2 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy2 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx3, dy2 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx2, 0.0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx3, 0.0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx2, dy3 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy3 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx3, dy3 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) + + texture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z ) + ) * ( 1.0 / 17.0 ); + #elif defined( SHADOWMAP_TYPE_PCF_SOFT ) + vec2 texelSize = vec2( 1.0 ) / shadowMapSize; + float dx = texelSize.x; + float dy = texelSize.y; + vec2 uv = shadowCoord.xy; + vec2 f = fract( uv * shadowMapSize + 0.5 ); + uv -= f * texelSize; + shadow = ( + texture2DCompare( shadowMap, uv, shadowCoord.z ) + + texture2DCompare( shadowMap, uv + vec2( dx, 0.0 ), shadowCoord.z ) + + texture2DCompare( shadowMap, uv + vec2( 0.0, dy ), shadowCoord.z ) + + texture2DCompare( shadowMap, uv + texelSize, shadowCoord.z ) + + mix( texture2DCompare( shadowMap, uv + vec2( -dx, 0.0 ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( 2.0 * dx, 0.0 ), shadowCoord.z ), + f.x ) + + mix( texture2DCompare( shadowMap, uv + vec2( -dx, dy ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( 2.0 * dx, dy ), shadowCoord.z ), + f.x ) + + mix( texture2DCompare( shadowMap, uv + vec2( 0.0, -dy ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( 0.0, 2.0 * dy ), shadowCoord.z ), + f.y ) + + mix( texture2DCompare( shadowMap, uv + vec2( dx, -dy ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( dx, 2.0 * dy ), shadowCoord.z ), + f.y ) + + mix( mix( texture2DCompare( shadowMap, uv + vec2( -dx, -dy ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( 2.0 * dx, -dy ), shadowCoord.z ), + f.x ), + mix( texture2DCompare( shadowMap, uv + vec2( -dx, 2.0 * dy ), shadowCoord.z ), + texture2DCompare( shadowMap, uv + vec2( 2.0 * dx, 2.0 * dy ), shadowCoord.z ), + f.x ), + f.y ) + ) * ( 1.0 / 9.0 ); + #elif defined( SHADOWMAP_TYPE_VSM ) + shadow = VSMShadow( shadowMap, shadowCoord.xy, shadowCoord.z ); + #else + shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ); + #endif + } + return shadow; + } + vec2 cubeToUV( vec3 v, float texelSizeY ) { + vec3 absV = abs( v ); + float scaleToCube = 1.0 / max( absV.x, max( absV.y, absV.z ) ); + absV *= scaleToCube; + v *= scaleToCube * ( 1.0 - 2.0 * texelSizeY ); + vec2 planar = v.xy; + float almostATexel = 1.5 * texelSizeY; + float almostOne = 1.0 - almostATexel; + if ( absV.z >= almostOne ) { + if ( v.z > 0.0 ) + planar.x = 4.0 - v.x; + } else if ( absV.x >= almostOne ) { + float signX = sign( v.x ); + planar.x = v.z * signX + 2.0 * signX; + } else if ( absV.y >= almostOne ) { + float signY = sign( v.y ); + planar.x = v.x + 2.0 * signY + 2.0; + planar.y = v.z * signY - 2.0; + } + return vec2( 0.125, 0.25 ) * planar + vec2( 0.375, 0.75 ); + } + float getPointShadow( sampler2D shadowMap, vec2 shadowMapSize, float shadowBias, float shadowRadius, vec4 shadowCoord, float shadowCameraNear, float shadowCameraFar ) { + vec2 texelSize = vec2( 1.0 ) / ( shadowMapSize * vec2( 4.0, 2.0 ) ); + vec3 lightToPosition = shadowCoord.xyz; + float dp = ( length( lightToPosition ) - shadowCameraNear ) / ( shadowCameraFar - shadowCameraNear ); dp += shadowBias; + vec3 bd3D = normalize( lightToPosition ); + #if defined( SHADOWMAP_TYPE_PCF ) || defined( SHADOWMAP_TYPE_PCF_SOFT ) || defined( SHADOWMAP_TYPE_VSM ) + vec2 offset = vec2( - 1, 1 ) * shadowRadius * texelSize.y; + return ( + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.xyy, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.yyy, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.xyx, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.yyx, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.xxy, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.yxy, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.xxx, texelSize.y ), dp ) + + texture2DCompare( shadowMap, cubeToUV( bd3D + offset.yxx, texelSize.y ), dp ) + ) * ( 1.0 / 9.0 ); + #else + return texture2DCompare( shadowMap, cubeToUV( bd3D, texelSize.y ), dp ); + #endif + } +#endif`,cN=`#if NUM_SPOT_LIGHT_COORDS > 0 + uniform mat4 spotLightMatrix[ NUM_SPOT_LIGHT_COORDS ]; + varying vec4 vSpotLightCoord[ NUM_SPOT_LIGHT_COORDS ]; +#endif +#ifdef USE_SHADOWMAP + #if NUM_DIR_LIGHT_SHADOWS > 0 + uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHT_SHADOWS ]; + varying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHT_SHADOWS ]; + struct DirectionalLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + }; + uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHT_SHADOWS ]; + #endif + #if NUM_SPOT_LIGHT_SHADOWS > 0 + struct SpotLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + }; + uniform SpotLightShadow spotLightShadows[ NUM_SPOT_LIGHT_SHADOWS ]; + #endif + #if NUM_POINT_LIGHT_SHADOWS > 0 + uniform mat4 pointShadowMatrix[ NUM_POINT_LIGHT_SHADOWS ]; + varying vec4 vPointShadowCoord[ NUM_POINT_LIGHT_SHADOWS ]; + struct PointLightShadow { + float shadowBias; + float shadowNormalBias; + float shadowRadius; + vec2 shadowMapSize; + float shadowCameraNear; + float shadowCameraFar; + }; + uniform PointLightShadow pointLightShadows[ NUM_POINT_LIGHT_SHADOWS ]; + #endif +#endif`,uN=`#if ( defined( USE_SHADOWMAP ) && ( NUM_DIR_LIGHT_SHADOWS > 0 || NUM_POINT_LIGHT_SHADOWS > 0 ) ) || ( NUM_SPOT_LIGHT_COORDS > 0 ) + vec3 shadowWorldNormal = inverseTransformDirection( transformedNormal, viewMatrix ); + vec4 shadowWorldPosition; +#endif +#if defined( USE_SHADOWMAP ) + #if NUM_DIR_LIGHT_SHADOWS > 0 + #pragma unroll_loop_start + for ( int i = 0; i < NUM_DIR_LIGHT_SHADOWS; i ++ ) { + shadowWorldPosition = worldPosition + vec4( shadowWorldNormal * directionalLightShadows[ i ].shadowNormalBias, 0 ); + vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * shadowWorldPosition; + } + #pragma unroll_loop_end + #endif + #if NUM_POINT_LIGHT_SHADOWS > 0 + #pragma unroll_loop_start + for ( int i = 0; i < NUM_POINT_LIGHT_SHADOWS; i ++ ) { + shadowWorldPosition = worldPosition + vec4( shadowWorldNormal * pointLightShadows[ i ].shadowNormalBias, 0 ); + vPointShadowCoord[ i ] = pointShadowMatrix[ i ] * shadowWorldPosition; + } + #pragma unroll_loop_end + #endif +#endif +#if NUM_SPOT_LIGHT_COORDS > 0 + #pragma unroll_loop_start + for ( int i = 0; i < NUM_SPOT_LIGHT_COORDS; i ++ ) { + shadowWorldPosition = worldPosition; + #if ( defined( USE_SHADOWMAP ) && UNROLLED_LOOP_INDEX < NUM_SPOT_LIGHT_SHADOWS ) + shadowWorldPosition.xyz += shadowWorldNormal * spotLightShadows[ i ].shadowNormalBias; + #endif + vSpotLightCoord[ i ] = spotLightMatrix[ i ] * shadowWorldPosition; + } + #pragma unroll_loop_end +#endif`,hN=`float getShadowMask() { + float shadow = 1.0; + #ifdef USE_SHADOWMAP + #if NUM_DIR_LIGHT_SHADOWS > 0 + DirectionalLightShadow directionalLight; + #pragma unroll_loop_start + for ( int i = 0; i < NUM_DIR_LIGHT_SHADOWS; i ++ ) { + directionalLight = directionalLightShadows[ i ]; + shadow *= receiveShadow ? getShadow( directionalShadowMap[ i ], directionalLight.shadowMapSize, directionalLight.shadowBias, directionalLight.shadowRadius, vDirectionalShadowCoord[ i ] ) : 1.0; + } + #pragma unroll_loop_end + #endif + #if NUM_SPOT_LIGHT_SHADOWS > 0 + SpotLightShadow spotLight; + #pragma unroll_loop_start + for ( int i = 0; i < NUM_SPOT_LIGHT_SHADOWS; i ++ ) { + spotLight = spotLightShadows[ i ]; + shadow *= receiveShadow ? getShadow( spotShadowMap[ i ], spotLight.shadowMapSize, spotLight.shadowBias, spotLight.shadowRadius, vSpotLightCoord[ i ] ) : 1.0; + } + #pragma unroll_loop_end + #endif + #if NUM_POINT_LIGHT_SHADOWS > 0 + PointLightShadow pointLight; + #pragma unroll_loop_start + for ( int i = 0; i < NUM_POINT_LIGHT_SHADOWS; i ++ ) { + pointLight = pointLightShadows[ i ]; + shadow *= receiveShadow ? getPointShadow( pointShadowMap[ i ], pointLight.shadowMapSize, pointLight.shadowBias, pointLight.shadowRadius, vPointShadowCoord[ i ], pointLight.shadowCameraNear, pointLight.shadowCameraFar ) : 1.0; + } + #pragma unroll_loop_end + #endif + #endif + return shadow; +}`,dN=`#ifdef USE_SKINNING + mat4 boneMatX = getBoneMatrix( skinIndex.x ); + mat4 boneMatY = getBoneMatrix( skinIndex.y ); + mat4 boneMatZ = getBoneMatrix( skinIndex.z ); + mat4 boneMatW = getBoneMatrix( skinIndex.w ); +#endif`,fN=`#ifdef USE_SKINNING + uniform mat4 bindMatrix; + uniform mat4 bindMatrixInverse; + uniform highp sampler2D boneTexture; + uniform int boneTextureSize; + mat4 getBoneMatrix( const in float i ) { + float j = i * 4.0; + float x = mod( j, float( boneTextureSize ) ); + float y = floor( j / float( boneTextureSize ) ); + float dx = 1.0 / float( boneTextureSize ); + float dy = 1.0 / float( boneTextureSize ); + y = dy * ( y + 0.5 ); + vec4 v1 = texture2D( boneTexture, vec2( dx * ( x + 0.5 ), y ) ); + vec4 v2 = texture2D( boneTexture, vec2( dx * ( x + 1.5 ), y ) ); + vec4 v3 = texture2D( boneTexture, vec2( dx * ( x + 2.5 ), y ) ); + vec4 v4 = texture2D( boneTexture, vec2( dx * ( x + 3.5 ), y ) ); + mat4 bone = mat4( v1, v2, v3, v4 ); + return bone; + } +#endif`,pN=`#ifdef USE_SKINNING + vec4 skinVertex = bindMatrix * vec4( transformed, 1.0 ); + vec4 skinned = vec4( 0.0 ); + skinned += boneMatX * skinVertex * skinWeight.x; + skinned += boneMatY * skinVertex * skinWeight.y; + skinned += boneMatZ * skinVertex * skinWeight.z; + skinned += boneMatW * skinVertex * skinWeight.w; + transformed = ( bindMatrixInverse * skinned ).xyz; +#endif`,mN=`#ifdef USE_SKINNING + mat4 skinMatrix = mat4( 0.0 ); + skinMatrix += skinWeight.x * boneMatX; + skinMatrix += skinWeight.y * boneMatY; + skinMatrix += skinWeight.z * boneMatZ; + skinMatrix += skinWeight.w * boneMatW; + skinMatrix = bindMatrixInverse * skinMatrix * bindMatrix; + objectNormal = vec4( skinMatrix * vec4( objectNormal, 0.0 ) ).xyz; + #ifdef USE_TANGENT + objectTangent = vec4( skinMatrix * vec4( objectTangent, 0.0 ) ).xyz; + #endif +#endif`,gN=`float specularStrength; +#ifdef USE_SPECULARMAP + vec4 texelSpecular = texture2D( specularMap, vSpecularMapUv ); + specularStrength = texelSpecular.r; +#else + specularStrength = 1.0; +#endif`,yN=`#ifdef USE_SPECULARMAP + uniform sampler2D specularMap; +#endif`,_N=`#if defined( TONE_MAPPING ) + gl_FragColor.rgb = toneMapping( gl_FragColor.rgb ); +#endif`,vN=`#ifndef saturate +#define saturate( a ) clamp( a, 0.0, 1.0 ) +#endif +uniform float toneMappingExposure; +vec3 LinearToneMapping( vec3 color ) { + return saturate( toneMappingExposure * color ); +} +vec3 ReinhardToneMapping( vec3 color ) { + color *= toneMappingExposure; + return saturate( color / ( vec3( 1.0 ) + color ) ); +} +vec3 OptimizedCineonToneMapping( vec3 color ) { + color *= toneMappingExposure; + color = max( vec3( 0.0 ), color - 0.004 ); + return pow( ( color * ( 6.2 * color + 0.5 ) ) / ( color * ( 6.2 * color + 1.7 ) + 0.06 ), vec3( 2.2 ) ); +} +vec3 RRTAndODTFit( vec3 v ) { + vec3 a = v * ( v + 0.0245786 ) - 0.000090537; + vec3 b = v * ( 0.983729 * v + 0.4329510 ) + 0.238081; + return a / b; +} +vec3 ACESFilmicToneMapping( vec3 color ) { + const mat3 ACESInputMat = mat3( + vec3( 0.59719, 0.07600, 0.02840 ), vec3( 0.35458, 0.90834, 0.13383 ), + vec3( 0.04823, 0.01566, 0.83777 ) + ); + const mat3 ACESOutputMat = mat3( + vec3( 1.60475, -0.10208, -0.00327 ), vec3( -0.53108, 1.10813, -0.07276 ), + vec3( -0.07367, -0.00605, 1.07602 ) + ); + color *= toneMappingExposure / 0.6; + color = ACESInputMat * color; + color = RRTAndODTFit( color ); + color = ACESOutputMat * color; + return saturate( color ); +} +vec3 CustomToneMapping( vec3 color ) { return color; }`,xN=`#ifdef USE_TRANSMISSION + material.transmission = transmission; + material.transmissionAlpha = 1.0; + material.thickness = thickness; + material.attenuationDistance = attenuationDistance; + material.attenuationColor = attenuationColor; + #ifdef USE_TRANSMISSIONMAP + material.transmission *= texture2D( transmissionMap, vTransmissionMapUv ).r; + #endif + #ifdef USE_THICKNESSMAP + material.thickness *= texture2D( thicknessMap, vThicknessMapUv ).g; + #endif + vec3 pos = vWorldPosition; + vec3 v = normalize( cameraPosition - pos ); + vec3 n = inverseTransformDirection( normal, viewMatrix ); + vec4 transmitted = getIBLVolumeRefraction( + n, v, material.roughness, material.diffuseColor, material.specularColor, material.specularF90, + pos, modelMatrix, viewMatrix, projectionMatrix, material.ior, material.thickness, + material.attenuationColor, material.attenuationDistance ); + material.transmissionAlpha = mix( material.transmissionAlpha, transmitted.a, material.transmission ); + totalDiffuse = mix( totalDiffuse, transmitted.rgb, material.transmission ); +#endif`,bN=`#ifdef USE_TRANSMISSION + uniform float transmission; + uniform float thickness; + uniform float attenuationDistance; + uniform vec3 attenuationColor; + #ifdef USE_TRANSMISSIONMAP + uniform sampler2D transmissionMap; + #endif + #ifdef USE_THICKNESSMAP + uniform sampler2D thicknessMap; + #endif + uniform vec2 transmissionSamplerSize; + uniform sampler2D transmissionSamplerMap; + uniform mat4 modelMatrix; + uniform mat4 projectionMatrix; + varying vec3 vWorldPosition; + float w0( float a ) { + return ( 1.0 / 6.0 ) * ( a * ( a * ( - a + 3.0 ) - 3.0 ) + 1.0 ); + } + float w1( float a ) { + return ( 1.0 / 6.0 ) * ( a * a * ( 3.0 * a - 6.0 ) + 4.0 ); + } + float w2( float a ){ + return ( 1.0 / 6.0 ) * ( a * ( a * ( - 3.0 * a + 3.0 ) + 3.0 ) + 1.0 ); + } + float w3( float a ) { + return ( 1.0 / 6.0 ) * ( a * a * a ); + } + float g0( float a ) { + return w0( a ) + w1( a ); + } + float g1( float a ) { + return w2( a ) + w3( a ); + } + float h0( float a ) { + return - 1.0 + w1( a ) / ( w0( a ) + w1( a ) ); + } + float h1( float a ) { + return 1.0 + w3( a ) / ( w2( a ) + w3( a ) ); + } + vec4 bicubic( sampler2D tex, vec2 uv, vec4 texelSize, float lod ) { + uv = uv * texelSize.zw + 0.5; + vec2 iuv = floor( uv ); + vec2 fuv = fract( uv ); + float g0x = g0( fuv.x ); + float g1x = g1( fuv.x ); + float h0x = h0( fuv.x ); + float h1x = h1( fuv.x ); + float h0y = h0( fuv.y ); + float h1y = h1( fuv.y ); + vec2 p0 = ( vec2( iuv.x + h0x, iuv.y + h0y ) - 0.5 ) * texelSize.xy; + vec2 p1 = ( vec2( iuv.x + h1x, iuv.y + h0y ) - 0.5 ) * texelSize.xy; + vec2 p2 = ( vec2( iuv.x + h0x, iuv.y + h1y ) - 0.5 ) * texelSize.xy; + vec2 p3 = ( vec2( iuv.x + h1x, iuv.y + h1y ) - 0.5 ) * texelSize.xy; + return g0( fuv.y ) * ( g0x * textureLod( tex, p0, lod ) + g1x * textureLod( tex, p1, lod ) ) + + g1( fuv.y ) * ( g0x * textureLod( tex, p2, lod ) + g1x * textureLod( tex, p3, lod ) ); + } + vec4 textureBicubic( sampler2D sampler, vec2 uv, float lod ) { + vec2 fLodSize = vec2( textureSize( sampler, int( lod ) ) ); + vec2 cLodSize = vec2( textureSize( sampler, int( lod + 1.0 ) ) ); + vec2 fLodSizeInv = 1.0 / fLodSize; + vec2 cLodSizeInv = 1.0 / cLodSize; + vec4 fSample = bicubic( sampler, uv, vec4( fLodSizeInv, fLodSize ), floor( lod ) ); + vec4 cSample = bicubic( sampler, uv, vec4( cLodSizeInv, cLodSize ), ceil( lod ) ); + return mix( fSample, cSample, fract( lod ) ); + } + vec3 getVolumeTransmissionRay( const in vec3 n, const in vec3 v, const in float thickness, const in float ior, const in mat4 modelMatrix ) { + vec3 refractionVector = refract( - v, normalize( n ), 1.0 / ior ); + vec3 modelScale; + modelScale.x = length( vec3( modelMatrix[ 0 ].xyz ) ); + modelScale.y = length( vec3( modelMatrix[ 1 ].xyz ) ); + modelScale.z = length( vec3( modelMatrix[ 2 ].xyz ) ); + return normalize( refractionVector ) * thickness * modelScale; + } + float applyIorToRoughness( const in float roughness, const in float ior ) { + return roughness * clamp( ior * 2.0 - 2.0, 0.0, 1.0 ); + } + vec4 getTransmissionSample( const in vec2 fragCoord, const in float roughness, const in float ior ) { + float lod = log2( transmissionSamplerSize.x ) * applyIorToRoughness( roughness, ior ); + return textureBicubic( transmissionSamplerMap, fragCoord.xy, lod ); + } + vec3 volumeAttenuation( const in float transmissionDistance, const in vec3 attenuationColor, const in float attenuationDistance ) { + if ( isinf( attenuationDistance ) ) { + return vec3( 1.0 ); + } else { + vec3 attenuationCoefficient = -log( attenuationColor ) / attenuationDistance; + vec3 transmittance = exp( - attenuationCoefficient * transmissionDistance ); return transmittance; + } + } + vec4 getIBLVolumeRefraction( const in vec3 n, const in vec3 v, const in float roughness, const in vec3 diffuseColor, + const in vec3 specularColor, const in float specularF90, const in vec3 position, const in mat4 modelMatrix, + const in mat4 viewMatrix, const in mat4 projMatrix, const in float ior, const in float thickness, + const in vec3 attenuationColor, const in float attenuationDistance ) { + vec3 transmissionRay = getVolumeTransmissionRay( n, v, thickness, ior, modelMatrix ); + vec3 refractedRayExit = position + transmissionRay; + vec4 ndcPos = projMatrix * viewMatrix * vec4( refractedRayExit, 1.0 ); + vec2 refractionCoords = ndcPos.xy / ndcPos.w; + refractionCoords += 1.0; + refractionCoords /= 2.0; + vec4 transmittedLight = getTransmissionSample( refractionCoords, roughness, ior ); + vec3 transmittance = diffuseColor * volumeAttenuation( length( transmissionRay ), attenuationColor, attenuationDistance ); + vec3 attenuatedColor = transmittance * transmittedLight.rgb; + vec3 F = EnvironmentBRDF( n, v, specularColor, specularF90, roughness ); + float transmittanceFactor = ( transmittance.r + transmittance.g + transmittance.b ) / 3.0; + return vec4( ( 1.0 - F ) * attenuatedColor, 1.0 - ( 1.0 - transmittedLight.a ) * transmittanceFactor ); + } +#endif`,wN=`#if defined( USE_UV ) || defined( USE_ANISOTROPY ) + varying vec2 vUv; +#endif +#ifdef USE_MAP + varying vec2 vMapUv; +#endif +#ifdef USE_ALPHAMAP + varying vec2 vAlphaMapUv; +#endif +#ifdef USE_LIGHTMAP + varying vec2 vLightMapUv; +#endif +#ifdef USE_AOMAP + varying vec2 vAoMapUv; +#endif +#ifdef USE_BUMPMAP + varying vec2 vBumpMapUv; +#endif +#ifdef USE_NORMALMAP + varying vec2 vNormalMapUv; +#endif +#ifdef USE_EMISSIVEMAP + varying vec2 vEmissiveMapUv; +#endif +#ifdef USE_METALNESSMAP + varying vec2 vMetalnessMapUv; +#endif +#ifdef USE_ROUGHNESSMAP + varying vec2 vRoughnessMapUv; +#endif +#ifdef USE_ANISOTROPYMAP + varying vec2 vAnisotropyMapUv; +#endif +#ifdef USE_CLEARCOATMAP + varying vec2 vClearcoatMapUv; +#endif +#ifdef USE_CLEARCOAT_NORMALMAP + varying vec2 vClearcoatNormalMapUv; +#endif +#ifdef USE_CLEARCOAT_ROUGHNESSMAP + varying vec2 vClearcoatRoughnessMapUv; +#endif +#ifdef USE_IRIDESCENCEMAP + varying vec2 vIridescenceMapUv; +#endif +#ifdef USE_IRIDESCENCE_THICKNESSMAP + varying vec2 vIridescenceThicknessMapUv; +#endif +#ifdef USE_SHEEN_COLORMAP + varying vec2 vSheenColorMapUv; +#endif +#ifdef USE_SHEEN_ROUGHNESSMAP + varying vec2 vSheenRoughnessMapUv; +#endif +#ifdef USE_SPECULARMAP + varying vec2 vSpecularMapUv; +#endif +#ifdef USE_SPECULAR_COLORMAP + varying vec2 vSpecularColorMapUv; +#endif +#ifdef USE_SPECULAR_INTENSITYMAP + varying vec2 vSpecularIntensityMapUv; +#endif +#ifdef USE_TRANSMISSIONMAP + uniform mat3 transmissionMapTransform; + varying vec2 vTransmissionMapUv; +#endif +#ifdef USE_THICKNESSMAP + uniform mat3 thicknessMapTransform; + varying vec2 vThicknessMapUv; +#endif`,SN=`#if defined( USE_UV ) || defined( USE_ANISOTROPY ) + varying vec2 vUv; +#endif +#ifdef USE_MAP + uniform mat3 mapTransform; + varying vec2 vMapUv; +#endif +#ifdef USE_ALPHAMAP + uniform mat3 alphaMapTransform; + varying vec2 vAlphaMapUv; +#endif +#ifdef USE_LIGHTMAP + uniform mat3 lightMapTransform; + varying vec2 vLightMapUv; +#endif +#ifdef USE_AOMAP + uniform mat3 aoMapTransform; + varying vec2 vAoMapUv; +#endif +#ifdef USE_BUMPMAP + uniform mat3 bumpMapTransform; + varying vec2 vBumpMapUv; +#endif +#ifdef USE_NORMALMAP + uniform mat3 normalMapTransform; + varying vec2 vNormalMapUv; +#endif +#ifdef USE_DISPLACEMENTMAP + uniform mat3 displacementMapTransform; + varying vec2 vDisplacementMapUv; +#endif +#ifdef USE_EMISSIVEMAP + uniform mat3 emissiveMapTransform; + varying vec2 vEmissiveMapUv; +#endif +#ifdef USE_METALNESSMAP + uniform mat3 metalnessMapTransform; + varying vec2 vMetalnessMapUv; +#endif +#ifdef USE_ROUGHNESSMAP + uniform mat3 roughnessMapTransform; + varying vec2 vRoughnessMapUv; +#endif +#ifdef USE_ANISOTROPYMAP + uniform mat3 anisotropyMapTransform; + varying vec2 vAnisotropyMapUv; +#endif +#ifdef USE_CLEARCOATMAP + uniform mat3 clearcoatMapTransform; + varying vec2 vClearcoatMapUv; +#endif +#ifdef USE_CLEARCOAT_NORMALMAP + uniform mat3 clearcoatNormalMapTransform; + varying vec2 vClearcoatNormalMapUv; +#endif +#ifdef USE_CLEARCOAT_ROUGHNESSMAP + uniform mat3 clearcoatRoughnessMapTransform; + varying vec2 vClearcoatRoughnessMapUv; +#endif +#ifdef USE_SHEEN_COLORMAP + uniform mat3 sheenColorMapTransform; + varying vec2 vSheenColorMapUv; +#endif +#ifdef USE_SHEEN_ROUGHNESSMAP + uniform mat3 sheenRoughnessMapTransform; + varying vec2 vSheenRoughnessMapUv; +#endif +#ifdef USE_IRIDESCENCEMAP + uniform mat3 iridescenceMapTransform; + varying vec2 vIridescenceMapUv; +#endif +#ifdef USE_IRIDESCENCE_THICKNESSMAP + uniform mat3 iridescenceThicknessMapTransform; + varying vec2 vIridescenceThicknessMapUv; +#endif +#ifdef USE_SPECULARMAP + uniform mat3 specularMapTransform; + varying vec2 vSpecularMapUv; +#endif +#ifdef USE_SPECULAR_COLORMAP + uniform mat3 specularColorMapTransform; + varying vec2 vSpecularColorMapUv; +#endif +#ifdef USE_SPECULAR_INTENSITYMAP + uniform mat3 specularIntensityMapTransform; + varying vec2 vSpecularIntensityMapUv; +#endif +#ifdef USE_TRANSMISSIONMAP + uniform mat3 transmissionMapTransform; + varying vec2 vTransmissionMapUv; +#endif +#ifdef USE_THICKNESSMAP + uniform mat3 thicknessMapTransform; + varying vec2 vThicknessMapUv; +#endif`,AN=`#if defined( USE_UV ) || defined( USE_ANISOTROPY ) + vUv = vec3( uv, 1 ).xy; +#endif +#ifdef USE_MAP + vMapUv = ( mapTransform * vec3( MAP_UV, 1 ) ).xy; +#endif +#ifdef USE_ALPHAMAP + vAlphaMapUv = ( alphaMapTransform * vec3( ALPHAMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_LIGHTMAP + vLightMapUv = ( lightMapTransform * vec3( LIGHTMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_AOMAP + vAoMapUv = ( aoMapTransform * vec3( AOMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_BUMPMAP + vBumpMapUv = ( bumpMapTransform * vec3( BUMPMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_NORMALMAP + vNormalMapUv = ( normalMapTransform * vec3( NORMALMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_DISPLACEMENTMAP + vDisplacementMapUv = ( displacementMapTransform * vec3( DISPLACEMENTMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_EMISSIVEMAP + vEmissiveMapUv = ( emissiveMapTransform * vec3( EMISSIVEMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_METALNESSMAP + vMetalnessMapUv = ( metalnessMapTransform * vec3( METALNESSMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_ROUGHNESSMAP + vRoughnessMapUv = ( roughnessMapTransform * vec3( ROUGHNESSMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_ANISOTROPYMAP + vAnisotropyMapUv = ( anisotropyMapTransform * vec3( ANISOTROPYMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_CLEARCOATMAP + vClearcoatMapUv = ( clearcoatMapTransform * vec3( CLEARCOATMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_CLEARCOAT_NORMALMAP + vClearcoatNormalMapUv = ( clearcoatNormalMapTransform * vec3( CLEARCOAT_NORMALMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_CLEARCOAT_ROUGHNESSMAP + vClearcoatRoughnessMapUv = ( clearcoatRoughnessMapTransform * vec3( CLEARCOAT_ROUGHNESSMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_IRIDESCENCEMAP + vIridescenceMapUv = ( iridescenceMapTransform * vec3( IRIDESCENCEMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_IRIDESCENCE_THICKNESSMAP + vIridescenceThicknessMapUv = ( iridescenceThicknessMapTransform * vec3( IRIDESCENCE_THICKNESSMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_SHEEN_COLORMAP + vSheenColorMapUv = ( sheenColorMapTransform * vec3( SHEEN_COLORMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_SHEEN_ROUGHNESSMAP + vSheenRoughnessMapUv = ( sheenRoughnessMapTransform * vec3( SHEEN_ROUGHNESSMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_SPECULARMAP + vSpecularMapUv = ( specularMapTransform * vec3( SPECULARMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_SPECULAR_COLORMAP + vSpecularColorMapUv = ( specularColorMapTransform * vec3( SPECULAR_COLORMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_SPECULAR_INTENSITYMAP + vSpecularIntensityMapUv = ( specularIntensityMapTransform * vec3( SPECULAR_INTENSITYMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_TRANSMISSIONMAP + vTransmissionMapUv = ( transmissionMapTransform * vec3( TRANSMISSIONMAP_UV, 1 ) ).xy; +#endif +#ifdef USE_THICKNESSMAP + vThicknessMapUv = ( thicknessMapTransform * vec3( THICKNESSMAP_UV, 1 ) ).xy; +#endif`,MN=`#if defined( USE_ENVMAP ) || defined( DISTANCE ) || defined ( USE_SHADOWMAP ) || defined ( USE_TRANSMISSION ) || NUM_SPOT_LIGHT_COORDS > 0 + vec4 worldPosition = vec4( transformed, 1.0 ); + #ifdef USE_INSTANCING + worldPosition = instanceMatrix * worldPosition; + #endif + worldPosition = modelMatrix * worldPosition; +#endif`,CN=`varying vec2 vUv; +uniform mat3 uvTransform; +void main() { + vUv = ( uvTransform * vec3( uv, 1 ) ).xy; + gl_Position = vec4( position.xy, 1.0, 1.0 ); +}`,EN=`uniform sampler2D t2D; +uniform float backgroundIntensity; +varying vec2 vUv; +void main() { + vec4 texColor = texture2D( t2D, vUv ); + #ifdef DECODE_VIDEO_TEXTURE + texColor = vec4( mix( pow( texColor.rgb * 0.9478672986 + vec3( 0.0521327014 ), vec3( 2.4 ) ), texColor.rgb * 0.0773993808, vec3( lessThanEqual( texColor.rgb, vec3( 0.04045 ) ) ) ), texColor.w ); + #endif + texColor.rgb *= backgroundIntensity; + gl_FragColor = texColor; + #include + #include +}`,TN=`varying vec3 vWorldDirection; +#include +void main() { + vWorldDirection = transformDirection( position, modelMatrix ); + #include + #include + gl_Position.z = gl_Position.w; +}`,PN=`#ifdef ENVMAP_TYPE_CUBE + uniform samplerCube envMap; +#elif defined( ENVMAP_TYPE_CUBE_UV ) + uniform sampler2D envMap; +#endif +uniform float flipEnvMap; +uniform float backgroundBlurriness; +uniform float backgroundIntensity; +varying vec3 vWorldDirection; +#include +void main() { + #ifdef ENVMAP_TYPE_CUBE + vec4 texColor = textureCube( envMap, vec3( flipEnvMap * vWorldDirection.x, vWorldDirection.yz ) ); + #elif defined( ENVMAP_TYPE_CUBE_UV ) + vec4 texColor = textureCubeUV( envMap, vWorldDirection, backgroundBlurriness ); + #else + vec4 texColor = vec4( 0.0, 0.0, 0.0, 1.0 ); + #endif + texColor.rgb *= backgroundIntensity; + gl_FragColor = texColor; + #include + #include +}`,IN=`varying vec3 vWorldDirection; +#include +void main() { + vWorldDirection = transformDirection( position, modelMatrix ); + #include + #include + gl_Position.z = gl_Position.w; +}`,RN=`uniform samplerCube tCube; +uniform float tFlip; +uniform float opacity; +varying vec3 vWorldDirection; +void main() { + vec4 texColor = textureCube( tCube, vec3( tFlip * vWorldDirection.x, vWorldDirection.yz ) ); + gl_FragColor = texColor; + gl_FragColor.a *= opacity; + #include + #include +}`,kN=`#include +#include +#include +#include +#include +#include +#include +varying vec2 vHighPrecisionZW; +void main() { + #include + #include + #ifdef USE_DISPLACEMENTMAP + #include + #include + #include + #endif + #include + #include + #include + #include + #include + #include + #include + vHighPrecisionZW = gl_Position.zw; +}`,LN=`#if DEPTH_PACKING == 3200 + uniform float opacity; +#endif +#include +#include +#include +#include +#include +#include +#include +#include +#include +varying vec2 vHighPrecisionZW; +void main() { + #include + vec4 diffuseColor = vec4( 1.0 ); + #if DEPTH_PACKING == 3200 + diffuseColor.a = opacity; + #endif + #include + #include + #include + #include + #include + float fragCoordZ = 0.5 * vHighPrecisionZW[0] / vHighPrecisionZW[1] + 0.5; + #if DEPTH_PACKING == 3200 + gl_FragColor = vec4( vec3( 1.0 - fragCoordZ ), opacity ); + #elif DEPTH_PACKING == 3201 + gl_FragColor = packDepthToRGBA( fragCoordZ ); + #endif +}`,DN=`#define DISTANCE +varying vec3 vWorldPosition; +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #ifdef USE_DISPLACEMENTMAP + #include + #include + #include + #endif + #include + #include + #include + #include + #include + #include + #include + vWorldPosition = worldPosition.xyz; +}`,NN=`#define DISTANCE +uniform vec3 referencePosition; +uniform float nearDistance; +uniform float farDistance; +varying vec3 vWorldPosition; +#include +#include +#include +#include +#include +#include +#include +#include +void main () { + #include + vec4 diffuseColor = vec4( 1.0 ); + #include + #include + #include + #include + float dist = length( vWorldPosition - referencePosition ); + dist = ( dist - nearDistance ) / ( farDistance - nearDistance ); + dist = saturate( dist ); + gl_FragColor = packDepthToRGBA( dist ); +}`,FN=`varying vec3 vWorldDirection; +#include +void main() { + vWorldDirection = transformDirection( position, modelMatrix ); + #include + #include +}`,ON=`uniform sampler2D tEquirect; +varying vec3 vWorldDirection; +#include +void main() { + vec3 direction = normalize( vWorldDirection ); + vec2 sampleUV = equirectUv( direction ); + gl_FragColor = texture2D( tEquirect, sampleUV ); + #include + #include +}`,BN=`uniform float scale; +attribute float lineDistance; +varying float vLineDistance; +#include +#include +#include +#include +#include +#include +#include +void main() { + vLineDistance = scale * lineDistance; + #include + #include + #include + #include + #include + #include + #include + #include + #include +}`,UN=`uniform vec3 diffuse; +uniform float opacity; +uniform float dashSize; +uniform float totalSize; +varying float vLineDistance; +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + if ( mod( vLineDistance, totalSize ) > dashSize ) { + discard; + } + vec3 outgoingLight = vec3( 0.0 ); + vec4 diffuseColor = vec4( diffuse, opacity ); + #include + #include + #include + outgoingLight = diffuseColor.rgb; + #include + #include + #include + #include + #include +}`,zN=`#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #if defined ( USE_ENVMAP ) || defined ( USE_SKINNING ) + #include + #include + #include + #include + #include + #endif + #include + #include + #include + #include + #include + #include + #include + #include + #include +}`,VN=`uniform vec3 diffuse; +uniform float opacity; +#ifndef FLAT_SHADED + varying vec3 vNormal; +#endif +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + #include + #include + #include + #include + #include + #include + #include + ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); + #ifdef USE_LIGHTMAP + vec4 lightMapTexel = texture2D( lightMap, vLightMapUv ); + reflectedLight.indirectDiffuse += lightMapTexel.rgb * lightMapIntensity * RECIPROCAL_PI; + #else + reflectedLight.indirectDiffuse += vec3( 1.0 ); + #endif + #include + reflectedLight.indirectDiffuse *= diffuseColor.rgb; + vec3 outgoingLight = reflectedLight.indirectDiffuse; + #include + #include + #include + #include + #include + #include + #include +}`,HN=`#define LAMBERT +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vViewPosition = - mvPosition.xyz; + #include + #include + #include + #include +}`,GN=`#define LAMBERT +uniform vec3 diffuse; +uniform vec3 emissive; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); + vec3 totalEmissiveRadiance = emissive; + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + totalEmissiveRadiance; + #include + #include + #include + #include + #include + #include + #include +}`,$N=`#define MATCAP +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vViewPosition = - mvPosition.xyz; +}`,WN=`#define MATCAP +uniform vec3 diffuse; +uniform float opacity; +uniform sampler2D matcap; +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + #include + #include + #include + #include + #include + #include + #include + #include + vec3 viewDir = normalize( vViewPosition ); + vec3 x = normalize( vec3( viewDir.z, 0.0, - viewDir.x ) ); + vec3 y = cross( viewDir, x ); + vec2 uv = vec2( dot( x, normal ), dot( y, normal ) ) * 0.495 + 0.5; + #ifdef USE_MATCAP + vec4 matcapColor = texture2D( matcap, uv ); + #else + vec4 matcapColor = vec4( vec3( mix( 0.2, 0.8, uv.y ) ), 1.0 ); + #endif + vec3 outgoingLight = diffuseColor.rgb * matcapColor.rgb; + #include + #include + #include + #include + #include + #include +}`,jN=`#define NORMAL +#if defined( FLAT_SHADED ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP_TANGENTSPACE ) + varying vec3 vViewPosition; +#endif +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include +#if defined( FLAT_SHADED ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP_TANGENTSPACE ) + vViewPosition = - mvPosition.xyz; +#endif +}`,XN=`#define NORMAL +uniform float opacity; +#if defined( FLAT_SHADED ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP_TANGENTSPACE ) + varying vec3 vViewPosition; +#endif +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + gl_FragColor = vec4( packNormalToRGB( normal ), opacity ); + #ifdef OPAQUE + gl_FragColor.a = 1.0; + #endif +}`,qN=`#define PHONG +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vViewPosition = - mvPosition.xyz; + #include + #include + #include + #include +}`,YN=`#define PHONG +uniform vec3 diffuse; +uniform vec3 emissive; +uniform vec3 specular; +uniform float shininess; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); + vec3 totalEmissiveRadiance = emissive; + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveRadiance; + #include + #include + #include + #include + #include + #include + #include +}`,ZN=`#define STANDARD +varying vec3 vViewPosition; +#ifdef USE_TRANSMISSION + varying vec3 vWorldPosition; +#endif +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vViewPosition = - mvPosition.xyz; + #include + #include + #include +#ifdef USE_TRANSMISSION + vWorldPosition = worldPosition.xyz; +#endif +}`,KN=`#define STANDARD +#ifdef PHYSICAL + #define IOR + #define USE_SPECULAR +#endif +uniform vec3 diffuse; +uniform vec3 emissive; +uniform float roughness; +uniform float metalness; +uniform float opacity; +#ifdef IOR + uniform float ior; +#endif +#ifdef USE_SPECULAR + uniform float specularIntensity; + uniform vec3 specularColor; + #ifdef USE_SPECULAR_COLORMAP + uniform sampler2D specularColorMap; + #endif + #ifdef USE_SPECULAR_INTENSITYMAP + uniform sampler2D specularIntensityMap; + #endif +#endif +#ifdef USE_CLEARCOAT + uniform float clearcoat; + uniform float clearcoatRoughness; +#endif +#ifdef USE_IRIDESCENCE + uniform float iridescence; + uniform float iridescenceIOR; + uniform float iridescenceThicknessMinimum; + uniform float iridescenceThicknessMaximum; +#endif +#ifdef USE_SHEEN + uniform vec3 sheenColor; + uniform float sheenRoughness; + #ifdef USE_SHEEN_COLORMAP + uniform sampler2D sheenColorMap; + #endif + #ifdef USE_SHEEN_ROUGHNESSMAP + uniform sampler2D sheenRoughnessMap; + #endif +#endif +#ifdef USE_ANISOTROPY + uniform vec2 anisotropyVector; + #ifdef USE_ANISOTROPYMAP + uniform sampler2D anisotropyMap; + #endif +#endif +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); + vec3 totalEmissiveRadiance = emissive; + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vec3 totalDiffuse = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse; + vec3 totalSpecular = reflectedLight.directSpecular + reflectedLight.indirectSpecular; + #include + vec3 outgoingLight = totalDiffuse + totalSpecular + totalEmissiveRadiance; + #ifdef USE_SHEEN + float sheenEnergyComp = 1.0 - 0.157 * max3( material.sheenColor ); + outgoingLight = outgoingLight * sheenEnergyComp + sheenSpecularDirect + sheenSpecularIndirect; + #endif + #ifdef USE_CLEARCOAT + float dotNVcc = saturate( dot( geometryClearcoatNormal, geometryViewDir ) ); + vec3 Fcc = F_Schlick( material.clearcoatF0, material.clearcoatF90, dotNVcc ); + outgoingLight = outgoingLight * ( 1.0 - material.clearcoat * Fcc ) + ( clearcoatSpecularDirect + clearcoatSpecularIndirect ) * material.clearcoat; + #endif + #include + #include + #include + #include + #include + #include +}`,JN=`#define TOON +varying vec3 vViewPosition; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vViewPosition = - mvPosition.xyz; + #include + #include + #include +}`,QN=`#define TOON +uniform vec3 diffuse; +uniform vec3 emissive; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec4 diffuseColor = vec4( diffuse, opacity ); + ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); + vec3 totalEmissiveRadiance = emissive; + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + totalEmissiveRadiance; + #include + #include + #include + #include + #include + #include +}`,eF=`uniform float size; +uniform float scale; +#include +#include +#include +#include +#include +#include +#ifdef USE_POINTS_UV + varying vec2 vUv; + uniform mat3 uvTransform; +#endif +void main() { + #ifdef USE_POINTS_UV + vUv = ( uvTransform * vec3( uv, 1 ) ).xy; + #endif + #include + #include + #include + #include + #include + gl_PointSize = size; + #ifdef USE_SIZEATTENUATION + bool isPerspective = isPerspectiveMatrix( projectionMatrix ); + if ( isPerspective ) gl_PointSize *= ( scale / - mvPosition.z ); + #endif + #include + #include + #include + #include +}`,tF=`uniform vec3 diffuse; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec3 outgoingLight = vec3( 0.0 ); + vec4 diffuseColor = vec4( diffuse, opacity ); + #include + #include + #include + #include + #include + outgoingLight = diffuseColor.rgb; + #include + #include + #include + #include + #include +}`,nF=`#include +#include +#include +#include +#include +#include +void main() { + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include + #include +}`,iF=`uniform vec3 color; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + gl_FragColor = vec4( color, opacity * ( 1.0 - getShadowMask() ) ); + #include + #include + #include +}`,rF=`uniform float rotation; +uniform vec2 center; +#include +#include +#include +#include +#include +void main() { + #include + vec4 mvPosition = modelViewMatrix * vec4( 0.0, 0.0, 0.0, 1.0 ); + vec2 scale; + scale.x = length( vec3( modelMatrix[ 0 ].x, modelMatrix[ 0 ].y, modelMatrix[ 0 ].z ) ); + scale.y = length( vec3( modelMatrix[ 1 ].x, modelMatrix[ 1 ].y, modelMatrix[ 1 ].z ) ); + #ifndef USE_SIZEATTENUATION + bool isPerspective = isPerspectiveMatrix( projectionMatrix ); + if ( isPerspective ) scale *= - mvPosition.z; + #endif + vec2 alignedPosition = ( position.xy - ( center - vec2( 0.5 ) ) ) * scale; + vec2 rotatedPosition; + rotatedPosition.x = cos( rotation ) * alignedPosition.x - sin( rotation ) * alignedPosition.y; + rotatedPosition.y = sin( rotation ) * alignedPosition.x + cos( rotation ) * alignedPosition.y; + mvPosition.xy += rotatedPosition; + gl_Position = projectionMatrix * mvPosition; + #include + #include + #include +}`,sF=`uniform vec3 diffuse; +uniform float opacity; +#include +#include +#include +#include +#include +#include +#include +#include +#include +void main() { + #include + vec3 outgoingLight = vec3( 0.0 ); + vec4 diffuseColor = vec4( diffuse, opacity ); + #include + #include + #include + #include + #include + outgoingLight = diffuseColor.rgb; + #include + #include + #include + #include +}`,It={alphahash_fragment:P4,alphahash_pars_fragment:I4,alphamap_fragment:R4,alphamap_pars_fragment:k4,alphatest_fragment:L4,alphatest_pars_fragment:D4,aomap_fragment:N4,aomap_pars_fragment:F4,begin_vertex:O4,beginnormal_vertex:B4,bsdfs:U4,iridescence_fragment:z4,bumpmap_pars_fragment:V4,clipping_planes_fragment:H4,clipping_planes_pars_fragment:G4,clipping_planes_pars_vertex:$4,clipping_planes_vertex:W4,color_fragment:j4,color_pars_fragment:X4,color_pars_vertex:q4,color_vertex:Y4,common:Z4,cube_uv_reflection_fragment:K4,defaultnormal_vertex:J4,displacementmap_pars_vertex:Q4,displacementmap_vertex:e5,emissivemap_fragment:t5,emissivemap_pars_fragment:n5,colorspace_fragment:i5,colorspace_pars_fragment:r5,envmap_fragment:s5,envmap_common_pars_fragment:o5,envmap_pars_fragment:a5,envmap_pars_vertex:l5,envmap_physical_pars_fragment:x5,envmap_vertex:c5,fog_vertex:u5,fog_pars_vertex:h5,fog_fragment:d5,fog_pars_fragment:f5,gradientmap_pars_fragment:p5,lightmap_fragment:m5,lightmap_pars_fragment:g5,lights_lambert_fragment:y5,lights_lambert_pars_fragment:_5,lights_pars_begin:v5,lights_toon_fragment:b5,lights_toon_pars_fragment:w5,lights_phong_fragment:S5,lights_phong_pars_fragment:A5,lights_physical_fragment:M5,lights_physical_pars_fragment:C5,lights_fragment_begin:E5,lights_fragment_maps:T5,lights_fragment_end:P5,logdepthbuf_fragment:I5,logdepthbuf_pars_fragment:R5,logdepthbuf_pars_vertex:k5,logdepthbuf_vertex:L5,map_fragment:D5,map_pars_fragment:N5,map_particle_fragment:F5,map_particle_pars_fragment:O5,metalnessmap_fragment:B5,metalnessmap_pars_fragment:U5,morphcolor_vertex:z5,morphnormal_vertex:V5,morphtarget_pars_vertex:H5,morphtarget_vertex:G5,normal_fragment_begin:$5,normal_fragment_maps:W5,normal_pars_fragment:j5,normal_pars_vertex:X5,normal_vertex:q5,normalmap_pars_fragment:Y5,clearcoat_normal_fragment_begin:Z5,clearcoat_normal_fragment_maps:K5,clearcoat_pars_fragment:J5,iridescence_pars_fragment:Q5,opaque_fragment:eN,packing:tN,premultiplied_alpha_fragment:nN,project_vertex:iN,dithering_fragment:rN,dithering_pars_fragment:sN,roughnessmap_fragment:oN,roughnessmap_pars_fragment:aN,shadowmap_pars_fragment:lN,shadowmap_pars_vertex:cN,shadowmap_vertex:uN,shadowmask_pars_fragment:hN,skinbase_vertex:dN,skinning_pars_vertex:fN,skinning_vertex:pN,skinnormal_vertex:mN,specularmap_fragment:gN,specularmap_pars_fragment:yN,tonemapping_fragment:_N,tonemapping_pars_fragment:vN,transmission_fragment:xN,transmission_pars_fragment:bN,uv_pars_fragment:wN,uv_pars_vertex:SN,uv_vertex:AN,worldpos_vertex:MN,background_vert:CN,background_frag:EN,backgroundCube_vert:TN,backgroundCube_frag:PN,cube_vert:IN,cube_frag:RN,depth_vert:kN,depth_frag:LN,distanceRGBA_vert:DN,distanceRGBA_frag:NN,equirect_vert:FN,equirect_frag:ON,linedashed_vert:BN,linedashed_frag:UN,meshbasic_vert:zN,meshbasic_frag:VN,meshlambert_vert:HN,meshlambert_frag:GN,meshmatcap_vert:$N,meshmatcap_frag:WN,meshnormal_vert:jN,meshnormal_frag:XN,meshphong_vert:qN,meshphong_frag:YN,meshphysical_vert:ZN,meshphysical_frag:KN,meshtoon_vert:JN,meshtoon_frag:QN,points_vert:eF,points_frag:tF,shadow_vert:nF,shadow_frag:iF,sprite_vert:rF,sprite_frag:sF},it={common:{diffuse:{value:new 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e=(this.right-this.left)/(2*this.zoom),t=(this.top-this.bottom)/(2*this.zoom),i=(this.right+this.left)/2,r=(this.top+this.bottom)/2,s=i-e,o=i+e,a=r+t,l=r-t;if(this.view!==null&&this.view.enabled){let c=(this.right-this.left)/this.view.fullWidth/this.zoom,u=(this.top-this.bottom)/this.view.fullHeight/this.zoom;s+=c*this.view.offsetX,o=s+c*this.view.width,a-=u*this.view.offsetY,l=a-u*this.view.height}this.projectionMatrix.makeOrthographic(s,o,a,l,this.near,this.far,this.coordinateSystem),this.projectionMatrixInverse.copy(this.projectionMatrix).invert()}toJSON(e){let t=super.toJSON(e);return t.object.zoom=this.zoom,t.object.left=this.left,t.object.right=this.right,t.object.top=this.top,t.object.bottom=this.bottom,t.object.near=this.near,t.object.far=this.far,this.view!==null&&(t.object.view=Object.assign({},this.view)),t}},ac=4,IC=[.125,.215,.35,.446,.526,.582],La=20,I_=new jo,RC=new dt,R_=null,k_=0,L_=0,Ra=(1+Math.sqrt(5))/2,sc=1/Ra,kC=[new W(1,1,1),new W(-1,1,1),new W(1,1,-1),new 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this._fromTexture(e,t)}compileCubemapShader(){this._cubemapMaterial===null&&(this._cubemapMaterial=NC(),this._compileMaterial(this._cubemapMaterial))}compileEquirectangularShader(){this._equirectMaterial===null&&(this._equirectMaterial=DC(),this._compileMaterial(this._equirectMaterial))}dispose(){this._dispose(),this._cubemapMaterial!==null&&this._cubemapMaterial.dispose(),this._equirectMaterial!==null&&this._equirectMaterial.dispose()}_setSize(e){this._lodMax=Math.floor(Math.log2(e)),this._cubeSize=Math.pow(2,this._lodMax)}_dispose(){this._blurMaterial!==null&&this._blurMaterial.dispose(),this._pingPongRenderTarget!==null&&this._pingPongRenderTarget.dispose();for(let e=0;e2?h:0,h,h),u.setRenderTarget(r),_&&u.render(p,a),u.render(e,a)}p.geometry.dispose(),p.material.dispose(),u.toneMapping=f,u.autoClear=d,e.background=y}_textureToCubeUV(e,t){let i=this._renderer,r=e.mapping===uc||e.mapping===hc;r?(this._cubemapMaterial===null&&(this._cubemapMaterial=NC()),this._cubemapMaterial.uniforms.flipEnvMap.value=e.isRenderTargetTexture===!1?-1:1):this._equirectMaterial===null&&(this._equirectMaterial=DC());let s=r?this._cubemapMaterial:this._equirectMaterial,o=new er(this._lodPlanes[0],s),a=s.uniforms;a.envMap.value=e;let l=this._cubeSize;Tp(t,0,0,3*l,2*l),i.setRenderTarget(t),i.render(o,I_)}_applyPMREM(e){let t=this._renderer,i=t.autoClear;t.autoClear=!1;for(let r=1;rLa&&console.warn(`sigmaRadians, ${s}, is too large and will clip, as it requested ${y} samples when the maximum is set to ${La}`);let g=[],b=0;for(let w=0;wh-ac?r-h+ac:0),x=4*(this._cubeSize-v);Tp(t,S,x,3*v,2*v),l.setRenderTarget(t),l.render(d,I_)}};function dF(n){let e=[],t=[],i=[],r=n,s=n-ac+1+IC.length;for(let o=0;on-ac?l=IC[o-n+ac-1]:o===0&&(l=0),i.push(l);let c=1/(a-2),u=-c,d=1+c,f=[u,u,d,u,d,d,u,u,d,d,u,d],m=6,p=6,_=3,y=2,g=1,b=new Float32Array(_*p*m),h=new Float32Array(y*p*m),v=new Float32Array(g*p*m);for(let x=0;x2?0:-1,M=[w,A,0,w+2/3,A,0,w+2/3,A+1,0,w,A,0,w+2/3,A+1,0,w,A+1,0];b.set(M,_*p*x),h.set(f,y*p*x);let T=[x,x,x,x,x,x];v.set(T,g*p*x)}let S=new Vn;S.setAttribute("position",new gn(b,_)),S.setAttribute("uv",new gn(h,y)),S.setAttribute("faceIndex",new gn(v,g)),e.push(S),r>ac&&r--}return{lodPlanes:e,sizeLods:t,sigmas:i}}function LC(n,e,t){let i=new nr(n,e,t);return i.texture.mapping=cm,i.texture.name="PMREM.cubeUv",i.scissorTest=!0,i}function Tp(n,e,t,i,r){n.viewport.set(e,t,i,r),n.scissor.set(e,t,i,r)}function fF(n,e,t){let i=new Float32Array(La),r=new W(0,1,0);return new Ti({name:"SphericalGaussianBlur",defines:{n:La,CUBEUV_TEXEL_WIDTH:1/e,CUBEUV_TEXEL_HEIGHT:1/t,CUBEUV_MAX_MIP:`${n}.0`},uniforms:{envMap:{value:null},samples:{value:1},weights:{value:i},latitudinal:{value:!1},dTheta:{value:0},mipInt:{value:0},poleAxis:{value:r}},vertexShader:Ev(),fragmentShader:` + + precision mediump float; + precision mediump int; + + varying vec3 vOutputDirection; + + uniform sampler2D envMap; + uniform int samples; + uniform float weights[ n ]; + uniform bool latitudinal; + uniform float dTheta; + uniform float mipInt; + uniform vec3 poleAxis; + + #define ENVMAP_TYPE_CUBE_UV + #include + + vec3 getSample( float theta, vec3 axis ) { + + float cosTheta = cos( theta ); + // Rodrigues' axis-angle rotation + vec3 sampleDirection = vOutputDirection * cosTheta + + cross( axis, vOutputDirection ) * sin( theta ) + + axis * dot( axis, vOutputDirection ) * ( 1.0 - cosTheta ); + + return bilinearCubeUV( envMap, sampleDirection, mipInt ); + + } + + void main() { + + vec3 axis = latitudinal ? poleAxis : cross( poleAxis, vOutputDirection ); + + if ( all( equal( axis, vec3( 0.0 ) ) ) ) { + + axis = vec3( vOutputDirection.z, 0.0, - vOutputDirection.x ); + + } + + axis = normalize( axis ); + + gl_FragColor = vec4( 0.0, 0.0, 0.0, 1.0 ); + gl_FragColor.rgb += weights[ 0 ] * getSample( 0.0, axis ); + + for ( int i = 1; i < n; i++ ) { + + if ( i >= samples ) { + + break; + + } + + float theta = dTheta * float( i ); + gl_FragColor.rgb += weights[ i ] * getSample( -1.0 * theta, axis ); + gl_FragColor.rgb += weights[ i ] * getSample( theta, axis ); + + } + + } + `,blending:us,depthTest:!1,depthWrite:!1})}function DC(){return new Ti({name:"EquirectangularToCubeUV",uniforms:{envMap:{value:null}},vertexShader:Ev(),fragmentShader:` + + precision mediump float; + precision mediump int; + + varying vec3 vOutputDirection; + + uniform sampler2D envMap; + + #include + + void main() { + + vec3 outputDirection = normalize( vOutputDirection ); + vec2 uv = equirectUv( outputDirection ); + + gl_FragColor = vec4( texture2D ( envMap, uv ).rgb, 1.0 ); + + } + `,blending:us,depthTest:!1,depthWrite:!1})}function NC(){return new Ti({name:"CubemapToCubeUV",uniforms:{envMap:{value:null},flipEnvMap:{value:-1}},vertexShader:Ev(),fragmentShader:` + + precision mediump float; + precision mediump int; + + uniform float flipEnvMap; + + varying vec3 vOutputDirection; + + uniform samplerCube envMap; + + void main() { + + gl_FragColor = textureCube( envMap, vec3( flipEnvMap * vOutputDirection.x, vOutputDirection.yz ) ); + + } + `,blending:us,depthTest:!1,depthWrite:!1})}function Ev(){return` + + precision mediump float; + precision mediump int; + + attribute float faceIndex; + + varying vec3 vOutputDirection; + + // RH coordinate system; PMREM face-indexing convention + vec3 getDirection( vec2 uv, float face ) { + + uv = 2.0 * uv - 1.0; + + vec3 direction = vec3( uv, 1.0 ); + + if ( face == 0.0 ) { + + direction = direction.zyx; // ( 1, v, u ) pos x + + } else if ( face == 1.0 ) { + + direction = direction.xzy; + direction.xz *= -1.0; // ( -u, 1, -v ) pos y + + } else if ( face == 2.0 ) { + + direction.x *= -1.0; // ( -u, v, 1 ) pos z + + } else if ( face == 3.0 ) { + + direction = direction.zyx; + direction.xz *= -1.0; // ( -1, v, -u ) neg x + + } else if ( face == 4.0 ) { + + direction = direction.xzy; + direction.xy *= -1.0; // ( -u, -1, v ) neg y + + } else if ( face == 5.0 ) { + + direction.z *= -1.0; // ( u, v, -1 ) neg z + + } + + return direction; + + } + + void main() { + + vOutputDirection = getDirection( uv, faceIndex ); + gl_Position = vec4( position, 1.0 ); + + } + `}function pF(n){let e=new WeakMap,t=null;function i(a){if(a&&a.isTexture){let l=a.mapping,c=l===U_||l===z_,u=l===uc||l===hc;if(c||u)if(a.isRenderTargetTexture&&a.needsPMREMUpdate===!0){a.needsPMREMUpdate=!1;let d=e.get(a);return t===null&&(t=new Jp(n)),d=c?t.fromEquirectangular(a,d):t.fromCubemap(a,d),e.set(a,d),d.texture}else{if(e.has(a))return e.get(a).texture;{let d=a.image;if(c&&d&&d.height>0||u&&d&&r(d)){t===null&&(t=new Jp(n));let f=c?t.fromEquirectangular(a):t.fromCubemap(a);return e.set(a,f),a.addEventListener("dispose",s),f.texture}else return null}}}return a}function r(a){let l=0,c=6;for(let u=0;ue.maxTextureSize&&(T=Math.ceil(M/e.maxTextureSize),M=e.maxTextureSize);let R=new Float32Array(M*T*4*p),C=new 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pO(n,e){let t=fO(e);return`vec4 ${n}( vec4 value ) { return ${t[0]}( ${t[1]}( value ) ); }`}function mO(n,e){let t;switch(e){case DD:t="Linear";break;case ND:t="Reinhard";break;case FD:t="OptimizedCineon";break;case OD:t="ACESFilmic";break;case BD:t="Custom";break;default:console.warn("THREE.WebGLProgram: Unsupported toneMapping:",e),t="Linear"}return"vec3 "+n+"( vec3 color ) { return "+t+"ToneMapping( color ); }"}function gO(n){return[n.extensionDerivatives||n.envMapCubeUVHeight||n.bumpMap||n.normalMapTangentSpace||n.clearcoatNormalMap||n.flatShading||n.shaderID==="physical"?"#extension GL_OES_standard_derivatives : enable":"",(n.extensionFragDepth||n.logarithmicDepthBuffer)&&n.rendererExtensionFragDepth?"#extension GL_EXT_frag_depth : enable":"",n.extensionDrawBuffers&&n.rendererExtensionDrawBuffers?"#extension GL_EXT_draw_buffers : require":"",(n.extensionShaderTextureLOD||n.envMap||n.transmission)&&n.rendererExtensionShaderTextureLod?"#extension GL_EXT_shader_texture_lod : enable":""].filter(yh).join(` +`)}function yO(n){let e=[];for(let t in n){let i=n[t];i!==!1&&e.push("#define "+t+" "+i)}return e.join(` +`)}function _O(n,e){let t={},i=n.getProgramParameter(e,n.ACTIVE_ATTRIBUTES);for(let r=0;r/gm;function Q_(n){return n.replace(vO,bO)}var xO=new Map([["encodings_fragment","colorspace_fragment"],["encodings_pars_fragment","colorspace_pars_fragment"],["output_fragment","opaque_fragment"]]);function bO(n,e){let t=It[e];if(t===void 0){let i=xO.get(e);if(i!==void 0)t=It[i],console.warn('THREE.WebGLRenderer: Shader chunk "%s" has been deprecated. Use "%s" instead.',e,i);else throw new Error("Can not resolve #include <"+e+">")}return Q_(t)}var wO=/#pragma unroll_loop_start\s+for\s*\(\s*int\s+i\s*=\s*(\d+)\s*;\s*i\s*<\s*(\d+)\s*;\s*i\s*\+\+\s*\)\s*{([\s\S]+?)}\s+#pragma unroll_loop_end/g;function jC(n){return n.replace(wO,SO)}function SO(n,e,t,i){let r="";for(let s=parseInt(e);s0&&(y+=` +`),g=[m,"#define SHADER_TYPE "+t.shaderType,"#define SHADER_NAME "+t.shaderName,p].filter(yh).join(` +`),g.length>0&&(g+=` +`)):(y=[XC(t),"#define SHADER_TYPE "+t.shaderType,"#define SHADER_NAME "+t.shaderName,p,t.instancing?"#define USE_INSTANCING":"",t.instancingColor?"#define USE_INSTANCING_COLOR":"",t.useFog&&t.fog?"#define USE_FOG":"",t.useFog&&t.fogExp2?"#define FOG_EXP2":"",t.map?"#define USE_MAP":"",t.envMap?"#define USE_ENVMAP":"",t.envMap?"#define "+u:"",t.lightMap?"#define USE_LIGHTMAP":"",t.aoMap?"#define USE_AOMAP":"",t.bumpMap?"#define USE_BUMPMAP":"",t.normalMap?"#define USE_NORMALMAP":"",t.normalMapObjectSpace?"#define 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p(y,g){g.matcap&&(y.matcap.value=g.matcap)}function _(y,g){let b=e.get(g).light;y.referencePosition.value.setFromMatrixPosition(b.matrixWorld),y.nearDistance.value=b.shadow.camera.near,y.farDistance.value=b.shadow.camera.far}return{refreshFogUniforms:i,refreshMaterialUniforms:r}}function YO(n,e,t,i){let r={},s={},o=[],a=t.isWebGL2?n.getParameter(n.MAX_UNIFORM_BUFFER_BINDINGS):0;function l(b,h){let v=h.program;i.uniformBlockBinding(b,v)}function c(b,h){let v=r[b.id];v===void 0&&(p(b),v=u(b),r[b.id]=v,b.addEventListener("dispose",y));let S=h.program;i.updateUBOMapping(b,S);let x=e.render.frame;s[b.id]!==x&&(f(b),s[b.id]=x)}function u(b){let h=d();b.__bindingPointIndex=h;let v=n.createBuffer(),S=b.__size,x=b.usage;return n.bindBuffer(n.UNIFORM_BUFFER,v),n.bufferData(n.UNIFORM_BUFFER,S,x),n.bindBuffer(n.UNIFORM_BUFFER,null),n.bindBufferBase(n.UNIFORM_BUFFER,h,v),v}function d(){for(let b=0;b0){x=v%S;let C=S-x;x!==0&&C-T.boundary<0&&(v+=S-x,M.__offset=v)}v+=T.storage}return 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Ah=class{constructor(e={}){let{canvas:t=l4(),context:i=null,depth:r=!0,stencil:s=!0,alpha:o=!1,antialias:a=!1,premultipliedAlpha:l=!0,preserveDrawingBuffer:c=!1,powerPreference:u="default",failIfMajorPerformanceCaveat:d=!1}=e;this.isWebGLRenderer=!0;let f;i!==null?f=i.getContextAttributes().alpha:f=o;let m=new Uint32Array(4),p=new Int32Array(4),_=null,y=null,g=[],b=[];this.domElement=t,this.debug={checkShaderErrors:!0,onShaderError:null},this.autoClear=!0,this.autoClearColor=!0,this.autoClearDepth=!0,this.autoClearStencil=!0,this.sortObjects=!0,this.clippingPlanes=[],this.localClippingEnabled=!1,this._outputColorSpace=ai,this._useLegacyLights=!1,this.toneMapping=Ho,this.toneMappingExposure=1;let h=this,v=!1,S=0,x=0,w=null,A=-1,M=null,T=new ti,R=new ti,C=null,P=new dt(0),E=0,I=t.width,O=t.height,D=1,N=null,H=null,z=new ti(0,0,I,O),L=new ti(0,0,I,O),F=!1,te=new wh,Q=!1,Z=!1,J=null,re=new qe,X=new Et,se=new 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vt=0,Ce=nt.length;vt0&&ue(ge,rt,he,be),Me&&Re.viewport(T.copy(Me)),ge.length>0&&me(ge,he,be),rt.length>0&&me(rt,he,be),ct.length>0&&me(ct,he,be),Re.buffers.depth.setTest(!0),Re.buffers.depth.setMask(!0),Re.buffers.color.setMask(!0),Re.setPolygonOffset(!1)}function ue(j,he,be,Me){if((be.isScene===!0?be.overrideMaterial:null)!==null)return;let rt=Se.isWebGL2;J===null&&(J=new nr(1,1,{generateMipmaps:!0,type:xe.has("EXT_color_buffer_half_float")?Go:wr,minFilter:xh,samples:rt?4:0})),h.getDrawingBufferSize(X),rt?J.setSize(X.x,X.y):J.setSize(W_(X.x),W_(X.y));let ct=h.getRenderTarget();h.setRenderTarget(J),h.getClearColor(P),E=h.getClearAlpha(),E<1&&h.setClearColor(16777215,.5),h.clear();let Ke=h.toneMapping;h.toneMapping=Ho,me(j,be,Me),_e.updateMultisampleRenderTarget(J),_e.updateRenderTargetMipmap(J);let nt=!1;for(let 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0&&(ot.numClippingPlanes!==Be.numPlanes||ot.numIntersection!==Be.numIntersection)||ot.vertexAlphas!==vt||ot.vertexTangents!==Ce||ot.morphTargets!==Ve||ot.morphNormals!==ft||ot.morphColors!==St||ot.toneMapping!==pt||Se.isWebGL2===!0&&ot.morphTargetsCount!==xt)&&(_t=!0):(_t=!0,ot.__version=Me.version);let fn=ot.currentProgram;_t===!0&&(fn=ze(Me,he,ge));let Kn=!1,Ir=!1,Cs=!1,Ln=fn.getUniforms(),Wi=ot.uniforms;if(Re.useProgram(fn.program)&&(Kn=!0,Ir=!0,Cs=!0),Me.id!==A&&(A=Me.id,Ir=!0),Kn||M!==j){Ln.setValue(ee,"projectionMatrix",j.projectionMatrix),Ln.setValue(ee,"viewMatrix",j.matrixWorldInverse);let $n=Ln.map.cameraPosition;$n!==void 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hl=0,ca=$n.length;hl0&&_e.useMultisampledRTT(j)===!1?ge=$e.get(j).__webglMultisampledFramebuffer:Array.isArray(Ce)?ge=Ce[be]:ge=Ce,T.copy(j.viewport),R.copy(j.scissor),C=j.scissorTest}else T.copy(z).multiplyScalar(D).floor(),R.copy(L).multiplyScalar(D).floor(),C=F;if(Re.bindFramebuffer(ee.FRAMEBUFFER,ge)&&Se.drawBuffers&&Me&&Re.drawBuffers(j,ge),Re.viewport(T),Re.scissor(R),Re.setScissorTest(C),rt){let nt=$e.get(j.texture);ee.framebufferTexture2D(ee.FRAMEBUFFER,ee.COLOR_ATTACHMENT0,ee.TEXTURE_CUBE_MAP_POSITIVE_X+he,nt.__webglTexture,be)}else if(ct){let nt=$e.get(j.texture),vt=he||0;ee.framebufferTextureLayer(ee.FRAMEBUFFER,ee.COLOR_ATTACHMENT0,nt.__webglTexture,be||0,vt)}A=-1},this.readRenderTargetPixels=function(j,he,be,Me,ge,rt,ct){if(!(j&&j.isWebGLRenderTarget)){console.error("THREE.WebGLRenderer.readRenderTargetPixels: renderTarget is not THREE.WebGLRenderTarget.");return}let Ke=$e.get(j).__webglFramebuffer;if(j.isWebGLCubeRenderTarget&&ct!==void 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+}`),zt.add("shader/Quad.frag",`varying vec2 vUv; +uniform sampler2D tForeground; +uniform float scale; +void main() { +vec4 foreground = texture2D( tForeground, vUv ); +gl_FragColor = foreground * scale; +}`);var $x=class{constructor(){this.signals={updated:new Td.Signal},this.maxDuration=-1/0,this.minDuration=1/0,this.avgDuration=14,this.lastDuration=1/0,this.prevFpsTime=0,this.lastFps=1/0,this.lastFrames=1,this.frames=0,this.count=0,this.begin()}update(){this.startTime=this.end(),this.currentTime=this.startTime,this.signals.updated.dispatch()}begin(){this.startTime=window.performance.now(),this.lastFrames=this.frames}end(){let e=window.performance.now();return 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+}`),zt.add("shader/chunk/matrix_scale.glsl",`float matrixScale( in mat4 m ){ +vec4 r = m[ 0 ]; +return sqrt( r[ 0 ] * r[ 0 ] + r[ 1 ] * r[ 1 ] + r[ 2 ] * r[ 2 ] ); +}`),zt.add("shader/chunk/nearclip_vertex.glsl",`#ifdef NEAR_CLIP +if( vViewPosition.z < clipNear - 5.0 ) +gl_Position.z = 2.0 * gl_Position.w; +#endif`),zt.add("shader/chunk/nearclip_fragment.glsl",`#ifdef NEAR_CLIP +if( vViewPosition.z < clipNear ) +discard; +#endif`),zt.add("shader/chunk/opaque_back_fragment.glsl",`#ifdef OPAQUE_BACK +#ifdef FLIP_SIDED +if( gl_FrontFacing == true ){ +gl_FragColor.a = 1.0; +} +#else +if( gl_FrontFacing == false ){ +gl_FragColor.a = 1.0; +} +#endif +#endif`),zt.add("shader/chunk/radiusclip_vertex.glsl",`#ifdef RADIUS_CLIP +if( distance( vViewPosition, vClipCenter ) > clipRadius + 5.0 ) +gl_Position.z = 2.0 * gl_Position.w; +#endif`),zt.add("shader/chunk/radiusclip_fragment.glsl",`#ifdef RADIUS_CLIP +if( distance( vViewPosition, vClipCenter ) > clipRadius ) +discard; +#endif`),zt.add("shader/chunk/unpack_color.glsl",`vec3 unpackColor(float f) { +vec3 color; +color.r = floor(f / 256.0 / 256.0); +color.g = floor((f - color.r * 256.0 * 256.0) / 256.0); +color.b = floor(f - color.r * 256.0 * 256.0 - color.g * 256.0); +return color / 255.0; +}`);var NB=/^(?!\/\/)\s*#include\s+(\S+)/gim,Dv={};function Xh(n,e={}){let t=n+"|";for(let i in e)t+=i+":"+e[i];if(!Dv[t]){let i=function(s){if(s===void 0)return"";let o=[];for(let a in s){let l=s[a];l&&o.push(`#define ${a} ${l}`)}return o.join(` +`)+` +`}(e),r=zt.get(`shader/${n}`);if(!r)throw new Error(`empty shader, '${n}'`);r=r.replace(NB,function(s,o){let a=`shader/chunk/${o}.glsl`,l=zt.get(a)||It[o];if(!l)throw new Error(`empty chunk, '${o}'`);return l}),Dv[t]=i+r}return Dv[t]}if(typeof WebGLRenderingContext<"u"){let n=WebGLRenderingContext.prototype,e=n.getShaderParameter;n.getShaderParameter=function(){return!Le||e.apply(this,arguments)};let t=n.getShaderInfoLog;n.getShaderInfoLog=function(){return 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vec4 u_color; +uniform sampler2D u_texture; + +void main() { + gl_FragColor = texture2D(u_texture, vec2(0.5, 0.5)) * u_color; +}`,t.FRAGMENT_SHADER);if(!i||!r)return!1;let s=function(p,_,y,g){let b=p.createProgram();return b?(_.forEach(h=>p.attachShader(b,h)),y&&y.forEach((h,v)=>{p.bindAttribLocation(b,g?g[v]:v,h)}),p.linkProgram(b),p.getProgramParameter(b,p.LINK_STATUS)?b:(console.log(`error linking program: ${p.getProgramInfoLog(b)}`),p.deleteProgram(b),null)):void console.log("error creating WebGL program")}(t,[i,r]);if(!s)return console.log("error creating WebGL program"),!1;t.useProgram(s);let o=t.getAttribLocation(s,"a_position"),a=t.getUniformLocation(s,"u_color");if(!a)return console.log("error getting 'u_color' uniform location"),!1;let l=t.createBuffer();t.bindBuffer(t.ARRAY_BUFFER,l),t.bufferData(t.ARRAY_BUFFER,BB,t.STATIC_DRAW),t.enableVertexAttribArray(o),t.vertexAttribPointer(o,2,t.FLOAT,!1,0,0);let c=t.createTexture(),u=new 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t=this.container.getBoundingClientRect();this.width=t.width||1,this.height=t.height||1,this.container.style.overflow="hidden"}this.wrapper=document.createElement("div"),this.wrapper.style.position="relative",this.container.appendChild(this.wrapper),this._initParams(),this._initStats(),this._initCamera(),this._initScene(),this._initRenderer()!==!1?(this._initHelper(),this.setBackground(),this.setFog(),this.animate=this.animate.bind(this)):we.error("Viewer: could not initialize renderer")}_initParams(){this.parameters={fogColor:new dt(0),fogNear:50,fogFar:100,backgroundColor:new dt(0),cameraType:"perspective",cameraFov:40,cameraEyeSep:.3,cameraZ:-80,clipNear:0,clipFar:100,clipDist:10,clipMode:"scene",clipScale:"relative",lightColor:new dt(14540253),lightIntensity:1.2,ambientColor:new dt(14540253),ambientIntensity:.3,sampleLevel:0,outputColorSpace:"srgb-linear"}}_initCamera(){let e=new W(0,0,0),{width:t,height:i}=this;this.perspectiveCamera=new 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Your browser/graphics card does not seem to support WebGL.

Find out how to get it here.

',!1}this.renderer.setPixelRatio(e),this.renderer.setSize(t,i),this.renderer.autoClear=!1,this.renderer.sortObjects=!0,this.renderer.outputColorSpace=this.parameters.outputColorSpace,this.renderer.useLegacyLights=!0;let r=this.renderer.getContext();this.renderer.capabilities.isWebGL2?(FE(!0),NE(this.renderer.extensions.get("EXT_color_buffer_float")),this.supportsHalfFloat=!0):(FE(this.renderer.extensions.get("EXT_frag_depth")),this.renderer.extensions.get("OES_element_index_uint"),NE(this.renderer.extensions.get("OES_texture_float")&&this.renderer.extensions.get("WEBGL_color_buffer_float")||this.renderer.extensions.get("OES_texture_float")&&gm(r.FLOAT)),this.renderer.extensions.get("OES_texture_float"),this.supportsHalfFloat=this.renderer.extensions.get("OES_texture_half_float")&&gm(36193)),this.wrapper.appendChild(this.renderer.domElement);let s=t*e,o=i*e;Le&&console.log(JSON.stringify({Browser:FP,OES_texture_float:!!this.renderer.extensions.get("OES_texture_float"),OES_texture_half_float:!!this.renderer.extensions.get("OES_texture_half_float"),WEBGL_color_buffer_float:!!this.renderer.extensions.get("WEBGL_color_buffer_float"),"testTextureSupport Float":gm(r.FLOAT),"testTextureSupport HalfFloat":gm(36193),"this.supportsHalfFloat":this.supportsHalfFloat,SupportsReadPixelsFloat:gs},null,2)),this.pickingTarget=new nr(s,o,{minFilter:en,magFilter:en,stencilBuffer:!1,format:Ei,type:gs?br:wr}),this.pickingTarget.texture.generateMipmaps=!1,this.pickingTarget.texture.colorSpace=this.parameters.outputColorSpace,this.renderer.setRenderTarget(this.pickingTarget),this.renderer.clear(),this.renderer.setRenderTarget(null),this.sampleTarget=new nr(s,o,{minFilter:li,magFilter:li,format:Ei,type:this.supportsHalfFloat?Go:gs?br:wr}),this.sampleTarget.texture.colorSpace=this.parameters.outputColorSpace,this.holdTarget=new nr(s,o,{minFilter:en,magFilter:en,format:Ei,type:this.supportsHalfFloat?Go:gs?br:wr}),this.holdTarget.texture.colorSpace=this.parameters.outputColorSpace,this.compositeUniforms={tForeground:new Rh(this.sampleTarget.texture),scale:new Rh(1)},this.compositeMaterial=new Ti({uniforms:this.compositeUniforms,vertexShader:Xh("Quad.vert"),fragmentShader:Xh("Quad.frag"),premultipliedAlpha:!0,transparent:!0,blending:Dp,depthTest:!1,depthWrite:!1}),this.compositeCamera=new jo(-1,1,1,-1,0,1),this.compositeScene=new Mh,this.compositeScene.name="compositeScene",this.compositeScene.add(new er(new Sh(2,2),this.compositeMaterial))}_initHelper(){let e=new Uint16Array([0,1,1,2,2,3,3,0,4,5,5,6,6,7,7,4,0,4,1,5,2,6,3,7]),t=new Float32Array(24),i=new Vn;i.setIndex(new gn(e,1)),i.setAttribute("position",new gn(t,3));let r=new Ti({uniforms:{uColor:{value:new dt("skyblue")}},vertexShader:Xh("BasicLine.vert"),fragmentShader:Xh("BasicLine.frag")});this.boundingBoxMesh=new mc(i,r),this.helperGroup.add(this.boundingBoxMesh)}updateHelper(){let e=this.boundingBoxMesh.geometry.attributes.position,t=e.array,{min:i,max:r}=this.boundingBox;t[0]=r.x,t[1]=r.y,t[2]=r.z,t[3]=i.x,t[4]=r.y,t[5]=r.z,t[6]=i.x,t[7]=i.y,t[8]=r.z,t[9]=r.x,t[10]=i.y,t[11]=r.z,t[12]=r.x,t[13]=r.y,t[14]=i.z,t[15]=i.x,t[16]=r.y,t[17]=i.z,t[18]=i.x,t[19]=i.y,t[20]=i.z,t[21]=r.x,t[22]=i.y,t[23]=i.z,e.needsUpdate=!0,this.boundingBox.isEmpty()||this.boundingBoxMesh.geometry.computeBoundingSphere()}get cameraDistance(){return Math.abs(this.camera.position.z)}set cameraDistance(e){this.camera.position.z=-e}add(e,t){t?t.forEach(i=>this.addBuffer(e,i)):this.addBuffer(e),e.group.name="meshGroup",e.wireframeGroup.name="wireframeGroup",e.parameters.background?(this.backgroundGroup.add(e.group),this.backgroundGroup.add(e.wireframeGroup)):(this.modelGroup.add(e.group),this.modelGroup.add(e.wireframeGroup)),e.pickable&&this.pickingGroup.add(e.pickingGroup),Le&&this.updateHelper()}addBuffer(e,t){function i(o){o instanceof $t?o.children.forEach(i):(o.userData.buffer=e,o.userData.instance=t,o.onBeforeRender=VB)}let r=e.getMesh();t&&r.applyMatrix4(t.matrix),i(r),e.group.add(r);let s=e.getWireframeMesh();if(t&&(s.matrix.copy(r.matrix),s.position.copy(r.position),s.quaternion.copy(r.quaternion),s.scale.copy(r.scale)),i(s),e.wireframeGroup.add(s),e.pickable){let o=e.getPickingMesh();t&&(o.matrix.copy(r.matrix),o.position.copy(r.position),o.quaternion.copy(r.quaternion),o.scale.copy(r.scale)),i(o),e.pickingGroup.add(o)}t?this._updateBoundingBox(e.geometry,e.matrix,t.matrix):this._updateBoundingBox(e.geometry,e.matrix)}remove(e){this.translationGroup.children.forEach(function(t){t.remove(e.group),t.remove(e.wireframeGroup)}),e.pickable&&this.pickingGroup.remove(e.pickingGroup),this.updateBoundingBox(),Le&&this.updateHelper()}_updateBoundingBox(e,t,i){let r=this.boundingBox;function s(a,l,c){a.boundingBox==null&&a.computeBoundingBox();let u=a.boundingBox.clone();l&&u.applyMatrix4(l),c&&u.applyMatrix4(c),u.min.equals(u.max)&&u.expandByScalar(5),r.union(u)}function o(a){if(a.geometry!==void 0){let l,c;a.userData.buffer&&(l=a.userData.buffer.matrix),a.userData.instance&&(c=a.userData.instance.matrix),s(a.geometry,l,c)}}e?s(e,t,i):(r.makeEmpty(),this.modelGroup.traverse(o),this.backgroundGroup.traverse(o)),r.getSize(this.boundingBoxSize),this.boundingBoxLength=this.boundingBoxSize.length()}updateBoundingBox(){this._updateBoundingBox(),Le&&this.updateHelper()}getPickingPixels(){let{width:e,height:t}=this,i=e*t*4,r=gs?new Float32Array(i):new Uint8Array(i);return this.render(!0),this.renderer.readRenderTargetPixels(this.pickingTarget,0,0,e,t,r),r}getImage(e){return new Promise(t=>{if(e){let{width:i,height:r}=this,s=i*r*4,o=this.getPickingPixels();if(gs){let u=new Uint8Array(s);for(let d=0;d500&&!this.isStill&&this.sampleLevel<3&&this.sampleLevel!==-1){let e=this.sampleLevel;this.sampleLevel=3,this.renderPending=!0,this.render(),this.isStill=!0,this.sampleLevel=e,Le&&we.log("rendered still frame")}this.frameRequest=window.requestAnimationFrame(this.animate)}pick(e,t){if(this.parameters.cameraType==="stereo")return{pid:0,instance:void 0,picker:void 0};e*=window.devicePixelRatio,t*=window.devicePixelRatio,e=Math.max(e-2,0),t=Math.max(t-2,0);let i,r,s=0,o=gs?UB:zB;this.render(!0),this.renderer.readRenderTargetPixels(this.pickingTarget,e,t,5,5,o);for(let a=0;a22&&(this.stats.begin(),this.isStill=!1),this.renderPending=!0,window.requestAnimationFrame(()=>{this.render(),this.stats.update()}))}updateZoom(){let e=En(this.perspectiveCamera.fov),t=2*Math.tan(e/2)*this.cameraDistance;this.orthographicCamera.zoom=this.height/t}absoluteToRelative(e){return 50*(1-e/this.bRadius)}relativeToAbsolute(e){return this.bRadius*(1-e/50)}__updateClipping(){let e=this.parameters;this.bRadius=Math.max(10,.5*this.boundingBoxLength),isFinite(this.bRadius)||(this.bRadius=50),this.camera.getWorldPosition(this.distVector),this.cDist=this.distVector.length(),this.cDist||(this.cameraDistance=Math.abs(e.cameraZ),this.cDist=Math.abs(e.cameraZ));let t=this.scene.fog;if(t.color.set(e.fogColor),e.clipMode==="camera")this.camera.near=e.clipNear,this.camera.far=e.clipFar,t.near=e.fogNear,t.far=e.fogFar;else if(e.clipScale==="absolute")this.camera.near=this.cDist-e.clipNear,this.camera.far=this.cDist+e.clipFar,t.near=this.cDist-e.fogNear,t.far=this.cDist+e.fogFar;else{let i=(50-e.clipNear)/50,r=-(50-e.clipFar)/50;this.camera.near=this.cDist-this.bRadius*i,this.camera.far=this.cDist+this.bRadius*r;let s=(50-e.fogNear)/50,o=-(50-e.fogFar)/50;t.near=this.cDist-this.bRadius*s,t.far=this.cDist+this.bRadius*o}e.clipMode!=="camera"&&(this.camera.type==="PerspectiveCamera"?(this.camera.near=Math.max(.1,e.clipDist,this.camera.near),this.camera.far=Math.max(1,this.camera.far),t.near=Math.max(.1,t.near),t.far=Math.max(1,t.far)):this.camera.type==="OrthographicCamera"&&e.clipDist>0&&(this.camera.near=Math.max(e.clipDist,this.camera.near)))}__updateCamera(){let e=this.camera;e.updateMatrix(),e.updateMatrixWorld(!0),e.updateProjectionMatrix(),function(t,i,r,s,o){let a=new Et;r.getSize(a);let l=a.height,c=r.getPixelRatio(),u=i.type==="OrthographicCamera";VE.set(a.width,a.height),rg.copy(i.projectionMatrix).invert(),sg.copy(i.projectionMatrix).transpose(),t.traverse(function(d){let f=d.material;if(!f)return;let m=f.uniforms;if(m){if(f.clipNear){let p=(50-f.clipNear)/50,_=s-o*p;m.clipNear.value=_}m.canvasHeight&&(m.canvasHeight.value=l),m.resolution&&m.resolution.value.copy(VE),m.pixelRatio&&(m.pixelRatio.value=c),m.projectionMatrixInverse&&m.projectionMatrixInverse.value.copy(rg),m.projectionMatrixTranspose&&m.projectionMatrixTranspose.value.copy(sg),m.ortho&&(m.ortho.value=u)}})}(this.scene,e,this.renderer,this.cDist,this.bRadius),function(t,i){t.traverseVisible(function(r){if(!(r instanceof Ch&&r.userData.buffer.parameters.sortParticles))return;let s=r.geometry.attributes,o=s.position.count;if(o===0)return;let a,l,c,u,d,f,m,p;UE.multiplyMatrices(i.matrixWorldInverse,r.matrixWorld),zE.multiplyMatrices(i.projectionMatrix,UE),r.userData.sortData?(a=r.userData.sortData,c=a.__zArray,l=a.__sortArray,u=a.__cmpFn):(c=new Float32Array(o),l=new Uint32Array(o),u=function(_,y){let g=c[_],b=c[y];return g>b?1:gC?1:R=A&&y(_[S],v)>0;)_[S+1]=_[S],--S;_[S+1]=v}if(w===-1)break;M=h[w--],A=h[w--]}else{for(S=A+1,x=M,T(A+M>>1,S),y(_[A],_[M])>0&&T(A,M),y(_[S],_[M])>0&&T(S,M),y(_[A],_[S])>0&&T(A,S),v=_[S];;){do S++;while(y(_[S],v)<0);do x--;while(y(_[x],v)>0);if(x=x-A?(h[++w]=S,h[++w]=M,M=x-1):(h[++w]=A,h[++w]=x-1,A=S)}})(l,u);for(let _ in s){let y=s[_],g=y.array,b=y.itemSize;a[_]||(a[_]=new Float32Array(b*o)),p=a[_],a[_]=g;for(let h=0;h0&&this.parameters.cameraType!=="stereo"?this.__renderSuperSample(t,i):this.__renderModelGroup(t,i)}render(e=!1,t){if(this.rendering)we.warn("'tried to call 'render' from within 'render'");else{this.rendering=!0;try{this.__updateClipping(),this.__updateCamera(),this.__updateLights(),this.updateInfo(!0),this.parameters.cameraType==="stereo"?this.__renderStereo(e,t):this.__render(e,this.camera,t),this.lastRenderedPicking=e}finally{this.rendering=!1,this.renderPending=!1}this.signals.rendered.dispatch()}}clear(){we.log("scene cleared"),this.scene.remove(this.rotationGroup),this._initScene(),this.renderer.clear()}dispose(){this.renderer.dispose(),window.cancelAnimationFrame(this.frameRequest)}};function $E(n){let e=n.touches[0].pageX-n.touches[1].pageX,t=n.touches[0].pageY-n.touches[1].pageY;return Math.sqrt(e*e+t*t)}var qx=class{constructor(e,t={}){this.domElement=e,this.signals={moved:new Pt.Signal,scrolled:new Pt.Signal,dragged:new Pt.Signal,dropped:new Pt.Signal,clicked:new Pt.Signal,hovered:new Pt.Signal,doubleClicked:new Pt.Signal},this.position=new Et,this.prevPosition=new Et,this.down=new Et,this.canvasPosition=new Et,this.prevClickCP=new Et,this.moving=!1,this.hovering=!0,this.scrolled=!1,this.lastMoved=1/0,this.which=0,this.buttons=0,this.pressed=!1,this.altKey=!1,this.ctrlKey=!1,this.metaKey=!1,this.shiftKey=!1,this.domElement.style.touchAction="none",this.hoverTimeout=U(t.hoverTimeout,50),this.handleScroll=U(t.handleScroll,!0),this.doubleClickSpeed=U(t.doubleClickSpeed,500),this._listen=this._listen.bind(this),this._onMousewheel=this._onMousewheel.bind(this),this._onMousemove=this._onMousemove.bind(this),this._onMousedown=this._onMousedown.bind(this),this._onMouseup=this._onMouseup.bind(this),this._onContextmenu=this._onContextmenu.bind(this),this._onTouchstart=this._onTouchstart.bind(this),this._onTouchend=this._onTouchend.bind(this),this._onTouchmove=this._onTouchmove.bind(this),this._listen();let i={passive:!1};document.addEventListener("mousewheel",this._onMousewheel,i),document.addEventListener("wheel",this._onMousewheel,i),document.addEventListener("MozMousePixelScroll",this._onMousewheel,i),document.addEventListener("mousemove",this._onMousemove,i),document.addEventListener("mousedown",this._onMousedown,i),document.addEventListener("mouseup",this._onMouseup,i),document.addEventListener("contextmenu",this._onContextmenu,i),document.addEventListener("touchstart",this._onTouchstart,i),document.addEventListener("touchend",this._onTouchend,i),document.addEventListener("touchmove",this._onTouchmove,i)}get key(){let e=0;return this.altKey&&(e+=1),this.ctrlKey&&(e+=2),this.metaKey&&(e+=4),this.shiftKey&&(e+=8),e}setParameters(e={}){this.hoverTimeout=U(e.hoverTimeout,this.hoverTimeout)}_listen(){let e=window.performance.now(),t=this.canvasPosition;this.doubleClickPending&&e-this.lastClicked>this.doubleClickSpeed&&(this.doubleClickPending=!1),e-this.lastMoved>this.hoverTimeout&&(this.moving=!1),(this.scrolled||!this.moving&&!this.hovering)&&(this.scrolled=!1,this.hoverTimeout!==-1&&this.overElement&&(this.hovering=!0,this.signals.hovered.dispatch(t.x,t.y))),this.frameRequest=window.requestAnimationFrame(this._listen)}_onMousewheel(e){if(e.target!==this.domElement||!this.handleScroll)return;e.preventDefault(),this._setKeys(e);let t=0;"deltaY"in e&&"deltaMode"in e&&e.deltaY!==void 0&&e.deltaMode!==void 0?t=e.deltaMode===WheelEvent.DOM_DELTA_PIXEL?.025*-e.deltaY:e.deltaMode===WheelEvent.DOM_DELTA_LINE?-e.deltaY*(2.5/3):2.5*-e.deltaY:"deltaY"in e&&!("detail"in e)?t=.025*-e.deltaY:e.wheelDelta!==void 0?t=.025*-e.wheelDelta:e.wheelDeltaY!==void 0?t=.025*-e.wheelDeltaY:e.detail!==void 0&&(t=-e.detail/3),this.signals.scrolled.dispatch(t),setTimeout(()=>{this.scrolled=!0},this.hoverTimeout)}_onMousemove(e){e.target===this.domElement?(e.preventDefault(),this.overElement=!0):this.overElement=!1,this._setKeys(e),this.moving=!0,this.hovering=!1,this.lastMoved=window.performance.now(),this.prevPosition.copy(this.position),this.position.set(e.clientX,e.clientY),this._setCanvasPosition(e);let t=this.prevPosition.x-this.position.x,i=this.prevPosition.y-this.position.y;this.signals.moved.dispatch(t,i),this.pressed&&this.signals.dragged.dispatch(t,i)}_onMousedown(e){e.target===this.domElement&&(e.preventDefault(),this._setKeys(e),this.moving=!1,this.hovering=!1,this.down.set(e.clientX,e.clientY),this.position.set(e.clientX,e.clientY),this.which=e.which,this.buttons=function(t){if(typeof t=="object"){if("buttons"in t)return t.buttons;if("which"in t){let i=t.which;if(i===2)return 4;if(i===3)return 2;if(i>0)return 1<=0)return 1<2&&this.handleScroll&&this.position.distanceTo(this.prevPosition)<2)this.which=0,this.buttons=0,this.signals.scrolled.dispatch(i/2);else{this.which=3,this.buttons=2;let r=this.prevPosition.x-this.position.x,s=this.prevPosition.y-this.position.y;this.signals.moved.dispatch(r,s),this.pressed&&this.signals.dragged.dispatch(r,s)}}}}_distance(){return this.position.distanceTo(this.down)}_setCanvasPosition(e){let t=this.domElement.getBoundingClientRect(),i,r;"clientX"in e&&"clientY"in e?(i=e.clientX-t.left,r=e.clientY-t.top):(i=e.offsetX,r=e.offsetY),this.canvasPosition.set(i,t.height-r)}_setKeys(e){this.altKey=e.altKey,this.ctrlKey=e.ctrlKey,this.metaKey=e.metaKey,this.shiftKey=e.shiftKey}dispose(){document.removeEventListener("mousewheel",this._onMousewheel),document.removeEventListener("wheel",this._onMousewheel),document.removeEventListener("MozMousePixelScroll",this._onMousewheel),document.removeEventListener("mousemove",this._onMousemove),document.removeEventListener("mousedown",this._onMousedown),document.removeEventListener("mouseup",this._onMouseup),document.removeEventListener("contextmenu",this._onContextmenu),document.removeEventListener("touchstart",this._onTouchstart),document.removeEventListener("touchend",this._onTouchend),document.removeEventListener("touchmove",this._onTouchmove),window.cancelAnimationFrame(this.frameRequest)}},Vv=new qe,Hv=new qe,WE=new qe,ir=new qe,jE=new qe,Sr=new W,Oh=new Xn,XE=new Xn,Xo=new qe,Ga=new W,_m=new W,Yx=class{constructor(e,t={}){this.stage=e,this.rotateSpeed=U(t.rotateSpeed,2),this.zoomSpeed=U(t.zoomSpeed,1.2),this.panSpeed=U(t.panSpeed,1),this.viewer=e.viewer,this.mouse=e.mouseObserver,this.controls=e.viewerControls}get component(){return this.stage.transformComponent}get atom(){return this.stage.transformAtom}_setPanVector(e,t,i=0){let r=this.controls.getCanvasScaleFactor(i);Ga.set(e,t,0),Ga.multiplyScalar(this.panSpeed*r)}_getRotateXY(e,t){return[this.rotateSpeed*-e*.01,this.rotateSpeed*t*.01]}_getCameraRotation(e){return e.extractRotation(this.viewer.camera.matrixWorld),e.multiply(Hv.makeRotationY(Math.PI)),e}_transformPanVector(){this.component&&(Xo.extractRotation(this.component.transform),Xo.premultiply(this.viewer.rotationGroup.matrix),Xo.invert(),Xo.multiply(this._getCameraRotation(ir)),Ga.applyMatrix4(Xo))}zoom(e){this.controls.zoom(this.zoomSpeed*e*.02)}pan(e,t){this._setPanVector(e,t),Xo.copy(this.viewer.rotationGroup.matrix).invert(),Xo.multiply(this._getCameraRotation(ir)),Ga.applyMatrix4(Xo),this.controls.translate(Ga)}panComponent(e,t){this.component&&(this._setPanVector(e,t),this._transformPanVector(),this.component.position.add(Ga),this.component.updateMatrix())}panAtom(e,t){this.atom&&this.component&&(this.atom.positionToVector3(_m),_m.add(this.viewer.translationGroup.position),_m.applyMatrix4(this.viewer.rotationGroup.matrix),this._setPanVector(e,t,_m.z),this._transformPanVector(),this.atom.positionAdd(Ga),this.component.updateRepresentations({position:!0}))}rotate(e,t){let[i,r]=this._getRotateXY(e,t);this._getCameraRotation(ir),Sr.set(1,0,0),Sr.applyMatrix4(ir),Oh.setFromAxisAngle(Sr,r),Sr.set(0,1,0),Sr.applyMatrix4(ir),XE.setFromAxisAngle(Sr,i),Oh.multiply(XE),ir.makeRotationFromQuaternion(Oh),this.controls.applyMatrix(ir)}zRotate(e,t){let i=this.rotateSpeed*((-e+t)/-2)*.01;WE.makeRotationZ(i),this.controls.applyMatrix(WE)}rotateComponent(e,t){if(!this.component)return;let[i,r]=this._getRotateXY(e,t);this._getCameraRotation(jE),ir.extractRotation(this.component.transform),ir.premultiply(this.viewer.rotationGroup.matrix),ir.invert(),ir.premultiply(jE),Sr.set(1,0,0),Sr.applyMatrix4(ir),Vv.makeRotationAxis(Sr,r),Sr.set(0,1,0),Sr.applyMatrix4(ir),Hv.makeRotationAxis(Sr,i),Vv.multiply(Hv),Oh.setFromRotationMatrix(Vv),this.component.quaternion.premultiply(Oh),this.component.quaternion.normalize(),this.component.updateMatrix()}},_c=new W,Zx=class{constructor(e,t){this.stage=t,this.pid=e.pid,this.picker=e.picker,this.instance=e.instance,this.stage=t,this.controls=t.viewerControls,this.mouse=t.mouseObserver}get type(){return this.picker.type}get altKey(){return this.mouse.altKey}get ctrlKey(){return this.mouse.ctrlKey}get metaKey(){return this.mouse.metaKey}get shiftKey(){return this.mouse.shiftKey}get canvasPosition(){return this.mouse.canvasPosition}get component(){return this.stage.getComponentsByObject(this.picker.data).list[0]}get object(){return this.picker.getObject(this.pid)}get position(){return this.picker.getPosition(this.pid,this.instance,this.component)}get closestBondAtom(){if(this.type!=="bond"||!this.bond)return;let e=this.bond,t=this.controls,i=this.canvasPosition,r=e.atom1.positionToVector3(),s=e.atom2.positionToVector3();r.applyMatrix4(this.component.matrix),s.applyMatrix4(this.component.matrix);let o=t.getPositionOnCanvas(r),a=t.getPositionOnCanvas(s);return c=o,u=a,(l=i).distanceTo(c)=r.length))return new Zx(i,this.stage);console.error("pid >= picker.array.length")}}},qE=new Xn,YE=new W,ZE=new W,Gv=new W,HB=new W,KE=new qe,JE=new W,QE=new qe,Jx=class{constructor(e){this.stage=e,this.signals={changed:new Td.Signal},this.viewer=e.viewer}get position(){return this.viewer.translationGroup.position}get rotation(){return this.viewer.rotationGroup.quaternion}changed(){this.viewer.requestRender(),this.signals.changed.dispatch()}getPositionOnCanvas(e,t){let i=C0(t,Et),r=this.viewer;return Gv.copy(e).add(r.translationGroup.position).applyMatrix4(r.rotationGroup.matrix).project(r.camera),i.set((Gv.x+1)*r.width/2,(Gv.y+1)*r.height/2)}getCanvasScaleFactor(e=0){let t=this.viewer.camera;if(t instanceof jo)return 1/t.zoom;{e=Math.abs(e),e+=this.getCameraDistance();let i=En(t.fov);return 2*e*Math.tan(i/2)/this.viewer.height}}getOrientation(e){let t=jh(e);t.copy(this.viewer.rotationGroup.matrix);let i=this.getCameraDistance();return t.scale(HB.set(i,i,i)),t.setPosition(this.viewer.translationGroup.position),t}orient(e){jh(e).decompose(YE,qE,ZE);let t=this.viewer;t.rotationGroup.setRotationFromQuaternion(qE),t.translationGroup.position.copy(YE),t.cameraDistance=ZE.z,t.updateZoom(),this.changed()}translate(e){this.viewer.translationGroup.position.add(Za(e)),this.changed()}center(e){this.viewer.translationGroup.position.copy(Za(e)).negate(),this.changed()}zoom(e){this.distance(this.getCameraDistance()*(1-e))}getCameraDistance(){return 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dt(e).getHex();t?(t.colorScheme="uniform",t.colorValue=r):this.setParameters({colorScheme:"uniform",colorValue:r})}return this}prepare(e){}create(){}update(e){this.build()}build(e){if(!this.lazy||this.visible&&this.opacity){if(!this.toBePrepared)return this.tasks.increment(),void this.make();this.queue.length()>0?(this.tasks.change(1-this.queue.length()),this.queue.kill()):this.tasks.increment(),this.queue.push(e||!1)}else this.lazyProps.build=!0}make(e,t){Le&&we.time("Representation.make "+this.type);let i=()=>{e?(this.update(e),this.viewer.requestRender(),this.tasks.decrement(),t&&t()):(this.clear(),this.create(),this.manualAttach||this.disposed||(Le&&we.time("Representation.attach "+this.type),this.attach(()=>{Le&&we.timeEnd("Representation.attach "+this.type),this.tasks.decrement(),t&&t()}))),Le&&we.timeEnd("Representation.make 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r=this.pool[i];if(r.pending===0){e=r;break}r.pendingr&&(r=c),u>s&&(s=u),d>o&&(o=d)}return[Mt([e,t,i]),Mt([r,s,o])]}function T0(n,e){for(let t=0,i=e.length;t0){let a=1/Math.sqrt(o);n[e]=i*a,n[e+1]=r*a,n[e+2]=s*a}}}function Mt(n){return new Float32Array(n||3)}function $i(n,e,t){let i=e[0],r=e[1],s=e[2],o=t[0],a=t[1],l=t[2];n[0]=r*l-s*a,n[1]=s*o-i*l,n[2]=i*a-r*o}function Vi(n,e){return n[0]*e[0]+n[1]*e[1]+n[2]*e[2]}function xn(n,e,t){n[0]=e[0]-t[0],n[1]=e[1]-t[1],n[2]=e[2]-t[2]}function Zr(n,e,t){n[0]=e[0]+t[0],n[1]=e[1]+t[1],n[2]=e[2]+t[2]}function Ri(n,e,t=0){n[0]=e[t],n[1]=e[t+1],n[2]=e[t+2]}function Tt(n,e,t=0){e[t]=n[0],e[t+1]=n[1],e[t+2]=n[2]}function HP(n){return n[0]*n[0]+n[1]*n[1]+n[2]*n[2]}function Qo(n){return Math.sqrt(n[0]*n[0]+n[1]*n[1]+n[2]*n[2])}function Pc(n,e,t){Jt(n,e,1/t)}function Jt(n,e,t){n[0]=e[0]*t,n[1]=e[1]*t,n[2]=e[2]*t}function Cn(n,e){let t=HP(e);t==0?(n[0]=e[0],n[1]=e[1],n[2]=e[2]):Jt(n,e,1/Math.sqrt(t))}function 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Float32Array(a),v.picking=n.picking),l&&(v.primitiveId=new Float32Array(l)),v}md.prototype.constructor=md,gd.__deps=[Mt],Pc.__deps=[Jt],Cn.__deps=[Jt,HP];var na=new W,Ss=class{static get Picker(){return Mr.get(this.type)}static get Buffer(){return cr.get(this.type)}static getShapeKey(e){return this.type+e[0].toUpperCase()+e.substr(1)}static expandBoundingBox(e,t){}static valueToShape(e,t,i){let r=e._primitiveData[this.getShapeKey(t)];switch(this.fields[t]){case"v3":case"c":(function(s,o){s.toArray!==void 0?s=s.toArray():s.x!==void 0?s=[s.x,s.y,s.z]:s.r!==void 0&&(s=[s.r,s.g,s.b]),o.push.apply(o,s)})(i,r);break;default:r.push(i)}}static objectToShape(e,t){Object.keys(this.fields).forEach(i=>{this.valueToShape(e,i,t[i])}),this.valueToShape(e,"name",t.name),this.expandBoundingBox(e.boundingBox,t)}static valueFromShape(e,t,i){let r=e._primitiveData[this.getShapeKey(i)];switch(this.fields[i]){case"v3":return new W().fromArray(r,3*t);case"c":return new dt().fromArray(r,3*t);default:return r[t]}}static objectFromShape(e,t){let i=this.valueFromShape(e,t,"name");i===void 0&&(i=`${this.type}: ${t} (${e.name})`);let r={shape:e,name:i};return Object.keys(this.fields).forEach(s=>{r[s]=this.valueFromShape(e,t,s)}),r}static arrayFromShape(e,t){let i=e._primitiveData[this.getShapeKey(t)];return this.fields[t]==="s"?i:new Float32Array(i)}static dataFromShape(e){let t={};return this.Picker&&(t.picking=new this.Picker(e)),Object.keys(this.fields).forEach(i=>{t[i]=this.arrayFromShape(e,i)}),t}static bufferFromShape(e,t){return new this.Buffer(this.dataFromShape(e),t)}};Ss.type="",Ss.fields={};var ia=class extends Ss{static positionFromShape(e,t){return this.valueFromShape(e,t,"position")}static expandBoundingBox(e,t){e.expandByPoint(na.fromArray(t.position))}};ia.type="sphere",ia.fields={position:"v3",color:"c",radius:"f"};var ro=class extends Ss{static positionFromShape(e,t){return this.valueFromShape(e,t,"position")}static 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null");e.set(this.wireframeIndex),e.needsUpdate=this.wireframeIndexCount>0,e.updateRange.count=this.wireframeIndexCount}this.wireframeGeometry.setDrawRange(0,this.wireframeIndexCount)}}getRenderOrder(){let e=0;return this.isText?e=1:this.transparent&&(e=this.isSurface?3:2),e}_getMesh(e){this.material||this.makeMaterial();let t=this.geometry,i=this[e],r;return r=this.isLine?new mc(t,i):this.isPoint?new Ch(t,i):new er(t,i),r.frustumCulled=!1,r.renderOrder=this.getRenderOrder(),r}getMesh(){return this._getMesh("material")}getWireframeMesh(){let e;return this.material||this.makeMaterial(),this.wireframeGeometry||this.makeWireframeGeometry(),e=new mc(this.wireframeGeometry,this.wireframeMaterial),e.frustumCulled=!1,e.renderOrder=this.getRenderOrder(),e}getPickingMesh(){return this._getMesh("pickingMaterial")}getShader(e,t){return Xh(e,this.getDefines(t))}getVertexShader(e){return this.getShader(this.vertexShader,e)}getFragmentShader(e){return this.getShader(this.fragmentShader,e)}getDefines(e){let t={};return this.parameters.clipNear&&(t.NEAR_CLIP=1),this.parameters.clipRadius&&(t.RADIUS_CLIP=1),e==="picking"?t.PICKING=1:((e==="background"||this.parameters.background)&&(t.NOLIGHT=1),this.parameters.flatShaded&&(t.FLAT_SHADED=1),this.parameters.opaqueBack&&(t.OPAQUE_BACK=1),this.parameters.diffuseInterior&&(t.DIFFUSE_INTERIOR=1),this.parameters.useInteriorColor&&(t.USE_INTERIOR_COLOR=1)),t}getParameters(){return this.parameters}addUniforms(e){this.uniforms=Lh.merge([this.uniforms,e]),this.pickingUniforms=Lh.merge([this.pickingUniforms,e])}addAttributes(e){for(let t in e){let i,r=e[t],s=this.attributeSize*cT[r.type];r.value?(s!==r.value.length&&we.error("attribute value has wrong length",t),i=r.value):i=kP("float32",s),this.geometry.setAttribute(t,new gn(i,cT[r.type]).setUsage(this.dynamic?Ha:qs))}}updateRenderOrder(){let e=this.getRenderOrder();function t(i){i.renderOrder=e}this.group.children.forEach(t),this.pickingGroup&&this.pickingGroup.children.forEach(t)}updateShader(){let e=this.material,t=this.wireframeMaterial,i=this.pickingMaterial;e.vertexShader=this.getVertexShader(),e.fragmentShader=this.getFragmentShader(),e.needsUpdate=!0,t.vertexShader=this.getShader("Line.vert"),t.fragmentShader=this.getShader("Line.frag"),t.needsUpdate=!0,i.vertexShader=this.getVertexShader("picking"),i.fragmentShader=this.getFragmentShader("picking"),i.needsUpdate=!0}setParameters(e){let t=e,i=this.parameterTypes,r=this.parameters,s={},o={},a=!1,l=!1;for(let c in t){let u=t[c];u!==void 0&&(r[c]=u,i[c]!==void 0&&(i[c].property&&(i[c].property!==!0?s[i[c].property]=u:s[c]=u),i[c].uniform&&(i[c].uniform!==!0?o[i[c].uniform]=u:o[c]=u),i[c].updateShader&&(a=!0),i[c].updateVisibility&&(l=!0),this.dynamic&&c==="wireframe"&&u===!0&&this.updateWireframeIndex(),c==="forceTransparent"&&(s.transparent=this.transparent),c==="matrix"&&(this.matrix=u)))}this.setProperties(s),this.setUniforms(o),a&&this.updateShader(),l&&this.setVisibility(this.visible)}setAttributes(e){let t=this.geometry,i=t.attributes;for(let r in e){if(r==="picking")continue;let s=e[r],o=s.length;if(r==="index"){let a=t.getIndex();if(!a){we.error("Index is null");continue}t.setDrawRange(0,1/0),o>a.array.length?t.setIndex(new gn(s,1).setUsage(this.dynamic?Ha:qs)):(a.set(s),a.needsUpdate=o>0,a.updateRange.count=o,t.setDrawRange(0,o)),this.indexVersion++,this.parameters.wireframe&&this.updateWireframeIndex()}else{let a=i[r];o>a.array.length?t.setAttribute(r,new gn(s,a.itemSize).setUsage(this.dynamic?Ha:qs)):(i[r].set(s),i[r].needsUpdate=o>0,i[r].updateRange.count=o)}}}setUniforms(e){if(!e)return;let t=this.material.uniforms,i=this.wireframeMaterial.uniforms,r=this.pickingMaterial.uniforms;for(let s in e)s==="opacity"&&this.setProperties({transparent:this.transparent}),t[s]!==void 0&&(t[s].value.isVector3?t[s].value.copy(e[s]):t[s].value.set?t[s].value.set(e[s]):t[s].value=e[s]),i[s]!==void 0&&(i[s].value.isVector3?i[s].value.copy(e[s]):i[s].value.set?i[s].value.set(e[s]):i[s].value=e[s]),r[s]!==void 0&&(r[s].value.isVector3?r[s].value.copy(e[s]):r[s].value.set?r[s].value.set(e[s]):r[s].value=e[s])}setProperties(e){if(!e)return;let t=this.material,i=this.wireframeMaterial,r=this.pickingMaterial;for(let s in e){let o=s,a=e[o];o==="transparent"?this.updateRenderOrder():o==="side"&&(a=lT(a)),t[o]=a,i[o]=a,r[o]=a}t.needsUpdate=!0,i.needsUpdate=!0,r.needsUpdate=!0}setVisibility(e){this.visible=e,this.parameters.wireframe?(this.group.visible=!1,this.wireframeGroup.visible=e,this.pickable&&(this.pickingGroup.visible=!1)):(this.group.visible=e,this.wireframeGroup.visible=!1,this.pickable&&(this.pickingGroup.visible=e))}dispose(){this.material&&this.material.dispose(),this.wireframeMaterial&&this.wireframeMaterial.dispose(),this.pickingMaterial&&this.pickingMaterial.dispose(),this.geometry.dispose(),this.wireframeGeometry&&this.wireframeGeometry.dispose()}toJSON(){var e={};for(var t in this)t!=="group"&&t!=="wireframeGroup"&&t!="pickingGroup"&&t!=="picking"&&(e[t]=this[t]);return e}},Jr=class extends Pr{constructor(e,t={}){super(e,t),this.vertexShader="Mesh.vert",this.fragmentShader="Mesh.frag",this.addAttributes({normal:{type:"v3",value:e.normal}}),e.normal===void 0&&this.geometry.computeVertexNormals()}},mg=class extends Jr{constructor(){super(...arguments),this.isSurface=!0}};function wm(n){n.visible=!0}function uT(n){n.visible=!1}var gg=class{constructor(e){this.group=new $t,this.wireframeGroup=new $t,this.pickingGroup=new $t,this.frontMeshes=[],this.backMeshes=[],this.size=e.size,this.side=e.parameters.side,this.visible=e.visible,this.geometry=e.geometry,this.picking=e.picking,this.group=new $t,this.wireframeGroup=new $t,this.pickingGroup=new $t,this.matrix=e.matrix;let t=e,i=new e.constructor({position:new Float32Array(0)});t.makeMaterial(),i.makeMaterial(),i.picking=e.picking,i.geometry=e.geometry,i.wireframeGeometry=e.wireframeGeometry,i.setParameters(e.getParameters()),i.updateShader(),t.setParameters({side:"front"}),i.setParameters({side:"back",opacity:i.parameters.opacity}),this.buffer=e,this.frontBuffer=t,this.backBuffer=i}set matrix(e){Pr.prototype.setMatrix.call(this,e)}get matrix(){return this.group.matrix.clone()}get pickable(){return!!this.picking&&!this.parameters.disablePicking}get parameters(){return this.buffer.parameters}getParameters(){let e=Object.assign({},this.buffer.parameters);return e.side=this.side,e}getMesh(e){let t,i;return e?(i=this.backBuffer.getPickingMesh(),t=this.frontBuffer.getPickingMesh()):(i=this.backBuffer.getMesh(),t=this.frontBuffer.getMesh()),this.frontMeshes.push(t),this.backMeshes.push(i),this.setParameters({side:this.side}),new $t().add(i,t)}getWireframeMesh(){return this.buffer.getWireframeMesh()}getPickingMesh(){return this.getMesh(!0)}setAttributes(e){this.buffer.setAttributes(e)}setParameters(e){(e=Object.assign({},e)).side==="front"?(this.frontMeshes.forEach(wm),this.backMeshes.forEach(uT)):e.side==="back"?(this.frontMeshes.forEach(uT),this.backMeshes.forEach(wm)):e.side==="double"&&(this.frontMeshes.forEach(wm),this.backMeshes.forEach(wm)),e.side!==void 0&&(this.side=e.side),delete e.side,e.matrix!==void 0&&(this.matrix=e.matrix),delete e.matrix,this.frontBuffer.setParameters(e),e.wireframe!==void 0&&(this.wireframe=e.wireframe,this.setVisibility(this.visible)),delete e.wireframe,this.backBuffer.setParameters(e)}setVisibility(e){this.visible=e,this.parameters.wireframe?(this.group.visible=!1,this.wireframeGroup.visible=e,this.pickable&&(this.pickingGroup.visible=!1)):(this.group.visible=e,this.wireframeGroup.visible=!1,this.pickable&&(this.pickingGroup.visible=e))}dispose(){this.frontBuffer.dispose(),this.backBuffer.dispose()}toJSON(){var e={};for(var t in this)["side","size","visible","matrix","parameters"].includes(t)&&(e[t]=this[t]);return e}};zt.add("shader/Line.vert",`uniform float clipNear; +uniform vec3 clipCenter; +varying vec3 vViewPosition; +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +#include color_pars_vertex +void main(){ +#include color_vertex +#include begin_vertex +#include project_vertex +vViewPosition = -mvPosition.xyz; +#if defined( RADIUS_CLIP ) +vClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz; +#endif +#include nearclip_vertex +}`),zt.add("shader/Line.frag",`uniform float opacity; +uniform float clipNear; +uniform float clipRadius; +varying vec3 vViewPosition; +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +#include common +#include color_pars_fragment +#include fog_pars_fragment +void main(){ +#include nearclip_fragment +#include radiusclip_fragment +gl_FragColor = vec4( vColor, opacity ); +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +}`);var yg=class extends Pr{constructor(){super(...arguments),this.isLine=!0,this.vertexShader="Line.vert",this.fragmentShader="Line.frag"}},vd=class extends el{constructor(e,t,i){super(e,t,i),this.type="surface",this.parameters=Object.assign({isolevelType:{type:"select",options:{value:"value",sigma:"sigma"}},isolevel:{type:"number",precision:2,max:1e3,min:-1e3},negateIsolevel:{type:"boolean"},isolevelScroll:{type:"boolean"},smooth:{type:"integer",precision:1,max:10,min:0},background:{type:"boolean",rebuild:!0},opaqueBack:{type:"boolean",buffer:!0},boxSize:{type:"integer",precision:1,max:100,min:0},colorVolume:{type:"hidden"},contour:{type:"boolean",rebuild:!0},useWorker:{type:"boolean",rebuild:!0},wrap:{type:"boolean",rebuild:!0}},this.parameters),e instanceof Hi?(this.surface=void 0,this.volume=e):(this.surface=e,this.volume=void 0),this.boxCenter=new W,this.__boxCenter=new W,this.box=new sn,this.__box=new sn,this._position=new W,this.inverseMatrix=new qe,this.setBox=function(){this._position.copy(t.translationGroup.position).negate(),this._position.applyMatrix4(this.inverseMatrix),this._position.equals(this.boxCenter)||this.setParameters({boxCenter:this._position})},this.toBePrepared=!0,this.viewer.signals.ticked.add(this.setBox,this),this.init(i)}init(e){let t=e||{};t.colorScheme=U(t.colorScheme,"uniform"),t.colorValue=U(t.colorValue,14540253),this.isolevelType=U(t.isolevelType,"sigma"),this.isolevel=U(t.isolevel,2),this.negateIsolevel=U(t.negateIsolevel,!1),this.isolevelScroll=U(t.isolevelScroll,!1),this.smooth=U(t.smooth,0),this.background=U(t.background,!1),this.opaqueBack=U(t.opaqueBack,!0),this.boxSize=U(t.boxSize,0),this.colorVolume=U(t.colorVolume,void 0),this.contour=U(t.contour,!1),this.useWorker=U(t.useWorker,!0),this.wrap=U(t.wrap,!1),super.init(t),this.inverseMatrix.copy(this.matrix).invert(),this.build()}attach(e){this.bufferList.forEach(t=>{this.viewer.add(t)}),this.setVisibility(this.visible),e()}prepare(e){if(this.volume){let t;if(t=this.isolevelType==="sigma"?this.volume.getValueForSigma(this.isolevel):this.isolevel,this.negateIsolevel&&(t*=-1),!this.surface||this.__isolevel!==t||this.__smooth!==this.smooth||this.__contour!==this.contour||this.__wrap!==this.wrap||this.__boxSize!==this.boxSize||this.boxSize>0&&!this.__boxCenter.equals(this.boxCenter)){this.__isolevel=t,this.__smooth=this.smooth,this.__contour=this.contour,this.__wrap=this.wrap,this.__boxSize=this.boxSize,this.__boxCenter.copy(this.boxCenter),this.__box.copy(this.box);let i=r=>{this.surface=r,e()};this.useWorker?this.volume.getSurfaceWorker(t,this.smooth,this.boxCenter,this.boxSize,this.contour,this.wrap,i):i(this.volume.getSurface(t,this.smooth,this.boxCenter,this.boxSize,this.contour,this.wrap))}else e()}else e()}create(){let e={position:this.surface.getPosition(),color:this.surface.getColor(this.getColorParams()),index:this.surface.getIndex()},t;if(this.contour)t=new yg(e,this.getBufferParams({wireframe:!1}));else{Object.assign(e,{normal:this.surface.getNormal(),picking:this.surface.getPicking()});let i=new mg(e,this.getBufferParams({background:this.background,opaqueBack:this.opaqueBack,dullInterior:!1}));t=new gg(i)}this.bufferList.push(t)}update(e){if(this.bufferList.length===0)return;let t={};(e=e||{}).position&&(t.position=this.surface.getPosition()),e.color&&(t.color=this.surface.getColor(this.getColorParams())),e.index&&(t.index=this.surface.getIndex()),e.normal&&(t.normal=this.surface.getNormal()),this.bufferList.forEach(function(i){i.setAttributes(t)})}setParameters(e,t,i){return e&&e.isolevelType!==void 0&&this.volume&&(this.isolevelType==="value"&&e.isolevelType==="sigma"?this.isolevel=this.volume.getSigmaForValue(this.isolevel):this.isolevelType==="sigma"&&e.isolevelType==="value"&&(this.isolevel=this.volume.getValueForSigma(this.isolevel)),this.isolevelType=e.isolevelType),e&&e.boxCenter&&(this.boxCenter.copy(e.boxCenter),delete e.boxCenter),e&&e.wireframe&&(e.contour||e.contour===void 0&&this.contour)&&(e.wireframe=!1),super.setParameters(e,t,i),e.matrix&&this.inverseMatrix.copy(e.matrix).invert(),this.volume&&this.volume.getBox(this.boxCenter,this.boxSize,this.box),e&&e.colorVolume!==void 0&&t&&(t.color=!0),this.surface&&(e.isolevel!==void 0||e.negateIsolevel!==void 0||e.smooth!==void 0||e.wrap!==void 0||e.boxSize!==void 0||this.boxSize>0&&!this.__box.equals(this.box))&&this.build({position:!0,color:!0,index:!0,normal:!this.contour}),this}getColorParams(){let e=super.getColorParams();return e.volume=this.colorVolume,e}dispose(){this.viewer.signals.ticked.remove(this.setBox,this),super.dispose()}},Nt=class{static zoomScroll(e,t){e.trackballControls.zoom(t)}static clipNearScroll(e,t){let i=e.getParameters();e.setParameters({clipNear:i.clipNear+t/10})}static focusScroll(e,t){let i=e.getFocus(),r=Math.sign(t)*function(s,o,a){if(s>o)return s;let l=s/o;return((2*a-o)*l+(2*o-3*a))*l*l+a}((100-i)/10,5,.2);e.setFocus(i+r)}static zoomFocusScroll(e,t){e.trackballControls.zoom(t);let i=e.viewer.camera.position.z;e.setFocus(100-Math.abs(i/8))}static isolevelScroll(e,t){let i=Math.sign(t)/10;e.eachRepresentation((r,s)=>{if(r.repr instanceof vd){let o=r.getParameters();o.isolevelScroll&&r.setParameters({isolevel:o.isolevel+i})}})}static panDrag(e,t,i){e.trackballControls.pan(t,i)}static rotateDrag(e,t,i){e.trackballControls.rotate(t,i)}static zRotateDrag(e,t,i){e.trackballControls.zRotate(t,i)}static zoomDrag(e,t,i){e.trackballControls.zoom((t+i)/-2)}static zoomFocusDrag(e,t,i){e.trackballControls.zoom((t+i)/-2);let r=e.viewer.camera.position.z;e.setFocus(100-Math.abs(r/8))}static panComponentDrag(e,t,i){e.trackballControls.panComponent(t,i)}static panAtomDrag(e,t,i){e.trackballControls.panAtom(t,i)}static rotateComponentDrag(e,t,i){e.trackballControls.rotateComponent(t,i)}static movePick(e,t){t&&e.animationControls.move(t.position.clone())}static tooltipPick(e,t){let i=e.tooltip;if(e.getParameters().tooltip&&t){let r=t.mouse.position;i.innerText=t.getLabel(),i.style.bottom=window.innerHeight-r.y+3+"px",i.style.left=r.x+3+"px",i.style.display="block"}else i.style.display="none"}static measurePick(e,t){if(t&&(t.atom||t.bond)){let i=t.atom||t.closestBondAtom;t.component.measurePick(i)}else e.measureClear()}},oI={default:[["scroll",Nt.zoomScroll],["scroll-shift",Nt.focusScroll],["scroll-ctrl",Nt.isolevelScroll],["scroll-shift-ctrl",Nt.zoomFocusScroll],["drag-left",Nt.rotateDrag],["drag-right",Nt.panDrag],["drag-ctrl-left",Nt.panDrag],["drag-ctrl-right",Nt.zRotateDrag],["drag-shift-left",Nt.zoomDrag],["drag-middle",Nt.zoomFocusDrag],["drag-ctrl-shift-right",Nt.panComponentDrag],["drag-ctrl-shift-left",Nt.rotateComponentDrag],["clickPick-right",Nt.measurePick],["clickPick-ctrl-left",Nt.measurePick],["clickPick-middle",Nt.movePick],["clickPick-left",Nt.movePick],["hoverPick",Nt.tooltipPick]],pymol:[["drag-left",Nt.rotateDrag],["drag-middle",Nt.panDrag],["drag-right",Nt.zoomDrag],["scroll",Nt.focusScroll],["drag-shift-right",Nt.focusScroll],["clickPick-ctrl+shift-middle",Nt.movePick],["hoverPick",Nt.tooltipPick]],coot:[["scroll",Nt.isolevelScroll],["drag-left",Nt.rotateDrag],["drag-middle",Nt.panDrag],["drag-ctrl-left",Nt.panDrag],["drag-right",Nt.zoomFocusDrag],["drag-ctrl-right",Nt.focusScroll],["clickPick-middle",Nt.movePick],["hoverPick",Nt.tooltipPick]],astexviewer:[["drag-left",Nt.rotateDrag],["drag-ctrl-left",Nt.panDrag],["drag-shift-left",Nt.zoomDrag],["scroll",Nt.focusScroll],["clickPick-middle",Nt.movePick],["hoverPick",Nt.tooltipPick]]};function hT(n){let e=n.split(/[-+]/),t="";e.includes("scroll")&&(t="scroll"),e.includes("drag")&&(t="drag"),e.includes("click")&&(t="click"),e.includes("doubleClick")&&(t="doubleClick"),e.includes("hover")&&(t="hover"),e.includes("clickPick")&&(t="clickPick"),e.includes("hoverPick")&&(t="hoverPick");let i=0;e.includes("alt")&&(i+=1),e.includes("ctrl")&&(i+=2),e.includes("meta")&&(i+=4),e.includes("shift")&&(i+=8);let r=0;return e.includes("left")&&(r+=1),e.includes("right")&&(r+=2),e.includes("middle")&&(r+=4),[t,i,r]}var Sb=class{constructor(e,t={}){this.stage=e,this.actionList=[],this.mouse=e.mouseObserver,this.disabled=t.disabled||!1,this.preset(t.preset||"default")}run(e,...t){if(this.disabled)return;let i=this.mouse.key||0,r=this.mouse.buttons||0;this.actionList.forEach(s=>{s.type===e&&s.key===i&&s.button===r&&s.callback(this.stage,...t)})}add(e,t){let[i,r,s]=hT(e);this.actionList.push({type:i,key:r,button:s,callback:t})}remove(e,t){let i=e.includes("*"),[r,s,o]=hT(e),a=this.actionList.filter(function(l){return!((l.type===r||i&&r==="")&&(l.key===s||i&&s===0)&&(l.button===o||i&&o===0)&&(l.callback===t||t===void 0))});this.actionList=a}preset(e){this.clear(),(oI[e]||[]).forEach(t=>this.add(t[0],t[1]))}clear(){this.actionList.length=0}},Xa=class{static autoView(e){e.autoView(1e3)}static toggleAnimations(e){e.animationControls.toggle()}static toggleRock(e){e.toggleRock()}static toggleSpin(e){e.toggleSpin()}static toggleAntialiasing(e){let t=e.getParameters();e.setParameters({sampleLevel:t.sampleLevel===-1?0:-1})}},CU={default:[["i",Xa.toggleSpin],["k",Xa.toggleRock],["p",Xa.toggleAnimations],["a",Xa.toggleAntialiasing],["r",Xa.autoView]]},Ab=class{constructor(e,t={}){this.stage=e,this.actionList=[],this.disabled=t.disabled||!1,this.preset(t.preset||"default")}run(e){this.disabled||this.actionList.forEach(t=>{t.key===e&&t.callback(this.stage)})}add(e,t){this.actionList.push({key:e,callback:t})}remove(e,t){let i=this.actionList.filter(function(r){return!(r.key===e&&(r.callback===t||t===void 0))});this.actionList=i}preset(e){this.clear(),(CU[e]||[]).forEach(t=>this.add(t[0],t[1]))}clear(){this.actionList.length=0}},Mb=class{constructor(e){this.stage=e,this.stage=e,this.mouse=e.mouseObserver,this.controls=e.mouseControls,this.mouse.signals.clicked.add(this._onClick,this),this.mouse.signals.hovered.add(this._onHover,this)}_onClick(e,t){let i=this.stage.pickingControls.pick(e,t);this.stage.signals.clicked.dispatch(i),this.controls.run("clickPick",i)}_onHover(e,t){let i=this.stage.pickingControls.pick(e,t);i&&this.mouse.down.equals(this.mouse.position)&&(this.stage.transformComponent=i.component,this.stage.transformAtom=i.atom),this.stage.signals.hovered.dispatch(i),this.controls.run("hoverPick",i)}dispose(){this.mouse.signals.clicked.remove(this._onClick,this),this.mouse.signals.hovered.remove(this._onHover,this)}},Cb=class{constructor(e){this.stage=e,this.stage=e,this.mouse=e.mouseObserver,this.controls=e.mouseControls,this.mouse.signals.moved.add(this._onMove,this),this.mouse.signals.scrolled.add(this._onScroll,this),this.mouse.signals.dragged.add(this._onDrag,this),this.mouse.signals.clicked.add(this._onClick,this),this.mouse.signals.hovered.add(this._onHover,this),this.mouse.signals.doubleClicked.add(this._onDblclick,this)}_onMove(){this.stage.tooltip.style.display="none"}_onScroll(e){this.controls.run("scroll",e)}_onDrag(e,t){this.controls.run("drag",e,t)}_onClick(e,t){this.controls.run("click",e,t)}_onDblclick(e,t){this.controls.run("doubleClick",e,t)}_onHover(e,t){this.controls.run("hover",e,t)}dispose(){this.mouse.signals.moved.remove(this._onMove,this),this.mouse.signals.scrolled.remove(this._onScroll,this),this.mouse.signals.dragged.remove(this._onDrag,this),this.mouse.signals.clicked.remove(this._onClick,this),this.mouse.signals.hovered.remove(this._onHover,this)}},Eb=class{constructor(e){this.stage=e,this.viewer=e.viewer,this.animationControls=e.animationControls,this.viewer.signals.ticked.add(this._onTick,this)}_onTick(e){this.animationControls.run(e)}dispose(){this.viewer.signals.ticked.remove(this._onTick,this)}},dT=!!OP&&{passive:!0},Tb=class{constructor(e){this.stage=e,this.stage=e,this.controls=e.keyControls,this.domElement=e.viewer.renderer.domElement,this.domElement.setAttribute("tabIndex","-1"),this.domElement.style.outline="none",this._focusDomElement=this._focusDomElement.bind(this),this._onKeydown=this._onKeydown.bind(this),this._onKeyup=this._onKeyup.bind(this),this._onKeypress=this._onKeypress.bind(this),this.domElement.addEventListener("mousedown",this._focusDomElement),this.domElement.addEventListener("touchstart",this._focusDomElement,dT),this.domElement.addEventListener("keydown",this._onKeydown),this.domElement.addEventListener("keyup",this._onKeyup),this.domElement.addEventListener("keypress",this._onKeypress)}_onKeydown(){}_onKeyup(){}_onKeypress(e){let t;t="key"in KeyboardEvent.prototype?e.key:String.fromCharCode(e.which||e.keyCode),this.controls.run(t)}_focusDomElement(){this.domElement.focus()}dispose(){this.domElement.removeEventListener("mousedown",this._focusDomElement),this.domElement.removeEventListener("touchstart",this._focusDomElement,dT),this.domElement.removeEventListener("keydown",this._onKeypress),this.domElement.removeEventListener("keyup",this._onKeypress),this.domElement.removeEventListener("keypress",this._onKeypress)}},Pb=class{constructor(e,t,i,r={}){this.component=e,this.position=t,this.offsetX=U(r.offsetX,0),this.offsetY=U(r.offsetY,0),this.visible=U(r.visible,!0),this.stage=e.stage,this.viewer=e.stage.viewer,this._viewerPosition=new W,this._updateViewerPosition(),this._canvasPosition=new Et,this._cameraPosition=new W,this.element=document.createElement("div"),Object.assign(this.element.style,{display:"block",position:"absolute",pointerEvents:"none",whiteSpace:"nowrap",left:"-10000px"}),this.viewer.wrapper.appendChild(this.element),this.setContent(i),this.updateVisibility(),this.viewer.signals.rendered.add(this._update,this),this.component.signals.matrixChanged.add(this._updateViewerPosition,this)}setContent(e){let t=this.element.style.display;if(t==="none"&&(this.element.style.left="-10000px",this.element.style.display="block"),e instanceof HTMLElement)this.element.appendChild(e);else{let i=document.createElement("div");i.innerText=e,Object.assign(i.style,{backgroundColor:"rgba( 0, 0, 0, 0.6 )",color:"lightgrey",padding:"8px",fontFamily:"sans-serif"}),this.element.appendChild(i)}this._clientRect=this.element.getBoundingClientRect(),t==="none"&&(this.element.style.display=t)}setVisibility(e){this.visible=e,this.updateVisibility()}getVisibility(){return this.visible&&this.component.parameters.visible}updateVisibility(){this.element.style.display=this.getVisibility()?"block":"none"}_updateViewerPosition(){this._viewerPosition.copy(this.position).applyMatrix4(this.component.matrix)}_update(){if(!this.getVisibility())return;let e=this.element.style,t=this._canvasPosition,i=this._viewerPosition,r=this._clientRect;if(this._cameraPosition.copy(i).add(this.viewer.translationGroup.position).applyMatrix4(this.viewer.rotationGroup.matrix).sub(this.viewer.camera.position),this._cameraPosition.z<0)return void(e.display="none");e.display="block";let s=this._cameraPosition.length(),o=this.viewer.scene.fog;e.opacity=(1-Pd(o.near,o.far,s)).toString(),e.zIndex=Math.round(100*(o.far-s)).toString(),this.stage.viewerControls.getPositionOnCanvas(i,t),e.bottom=this.offsetX+t.y+r.height/2+"px",e.left=this.offsetY+t.x-r.width/2+"px"}dispose(){this.viewer.wrapper.removeChild(this.element),this.viewer.signals.ticked.remove(this._update,this),this.component.signals.matrixChanged.remove(this._updateViewerPosition,this)}},qo=new qe,Sm=new W,fT=new Xn,Ib=class{constructor(e){this.component=e,this.signals={changed:new Td.Signal},this.stage=e.stage,this.viewer=e.stage.viewer}get position(){return this.component.position}get rotation(){return 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i=e.sstruc;t=i==="h"||i==="g"||i==="i"||i==="e"||i==="b"?.25:QP.includes(e.atomname)?.4:.1;break;case"data":t=U(this.data[e.index],1);break;case"explicit":t=e.radius,t===null&&(t=this.size);break;default:t=this.size}return Math.min(t*this.scale,this.max)}};Qr.types=aI;var EU=new W(-1,-1,-1),TU=new qe,_g=class{constructor(e){let t=e.rows,i=t/3,r=new Ht(t,3),s=new Ht(3,3),o=new Ht(1,3),a=new Ht(3,3),l=new Ht(3,3),c=_b(e);vb(e,c),Kr(r,e),Ym(s,r,r),iI(s,o,a,l);let u=new W(c[0],c[1],c[2]),d=new W(a.data[0],a.data[3],a.data[6]),f=new W(a.data[1],a.data[4],a.data[7]),m=new W(a.data[2],a.data[5],a.data[8]),p=d.clone().multiplyScalar(Math.sqrt(o.data[0]/i)),_=f.clone().multiplyScalar(Math.sqrt(o.data[1]/i)),y=m.clone().multiplyScalar(Math.sqrt(o.data[2]/i));this.begA=u.clone().sub(p),this.endA=u.clone().add(p),this.begB=u.clone().sub(_),this.endB=u.clone().add(_),this.begC=u.clone().sub(y),this.endC=u.clone().add(y),this.center=u,this.vecA=p,this.vecB=_,this.vecC=y,this.normVecA=d,this.normVecB=f,this.normVecC=m}getBasisMatrix(e=new qe){let t=e;return t.makeBasis(this.normVecB,this.normVecA,this.normVecC),t.determinant()<0&&t.scale(EU),t}getRotationQuaternion(e=new Xn){let t=e;return t.setFromRotationMatrix(this.getBasisMatrix(TU)),t.invert()}getProjectedScaleForAtoms(e){let t=-1/0,i=-1/0,r=-1/0,s=-1/0,o=-1/0,a=-1/0,l=new W,c=new W,u=this.center,d=this.normVecA,f=this.normVecB,m=this.normVecC;return e.eachAtom(function(p){Ka(l.copy(p),d,u);let _=c.subVectors(l,u).normalize().dot(d),y=l.distanceTo(u);_>0?y>t&&(t=y):y>i&&(i=y),Ka(l.copy(p),f,u);let g=c.subVectors(l,u).normalize().dot(f),b=l.distanceTo(u);g>0?b>r&&(r=b):b>s&&(s=b),Ka(l.copy(p),m,u);let h=c.subVectors(l,u).normalize().dot(m),v=l.distanceTo(u);h>0?v>o&&(o=v):v>a&&(a=v)}),{d1a:t,d2a:r,d3a:o,d1b:-i,d2b:-s,d3b:-a}}},qr=class{constructor(e,t,i,r){this.volume=e,this.setFilter(t,i,r)}get header(){return this.volume.header}get matrix(){return this.volume.matrix}get normalMatrix(){return this.volume.normalMatrix}get inverseMatrix(){return this.volume.inverseMatrix}get center(){return this.volume.center}get boundingBox(){return this.volume.boundingBox}get min(){return this.volume.min}get max(){return this.volume.max}get mean(){return this.volume.mean}get rms(){return this.volume.rms}_getFilterHash(e,t,i){return JSON.stringify([e,t,i])}setFilter(e,t,i){isNaN(e)&&this.header&&(e=this.header.DMEAN+2*this.header.ARMS),e=e===void 0||isNaN(e)?-1/0:e,t=U(t,1/0),i=U(i,!1);let r=this.volume.data,s=this.volume.position,o=this.volume.atomindex,a=this._getFilterHash(e,t,i);if(a!==this._filterHash){if(e===-1/0&&t===1/0)this.data=r,this.position=s,this.atomindex=o;else{let l=r.length;this._dataBuffer||(this._dataBuffer=new ArrayBuffer(4*l),this._positionBuffer=new ArrayBuffer(3*l*4),o&&(this._atomindexBuffer=new ArrayBuffer(4*l)));let c=new Float32Array(this._dataBuffer),u=new Float32Array(this._positionBuffer),d;o&&(d=new Uint32Array(this._atomindexBuffer));let f=0;for(let m=0;m=e&&_<=t||i&&(_t)){let y=3*f;c[f]=_,u[y+0]=s[p+0],u[y+1]=s[p+1],u[y+2]=s[p+2],o&&d&&(d[f]=o[m]),f+=1}}this.data=new Float32Array(this._dataBuffer,0,f),this.position=new Float32Array(this._positionBuffer,0,3*f),o&&(this.atomindex=new Int32Array(this._atomindexBuffer,0,f))}this._filterHash=a}}};qr.prototype.getValueForSigma=Hi.prototype.getValueForSigma,qr.prototype.getSigmaForValue=Hi.prototype.getSigmaForValue,qr.prototype.getDataAtomindex=Hi.prototype.getDataAtomindex,qr.prototype.getDataPosition=Hi.prototype.getDataPosition,qr.prototype.getDataColor=Hi.prototype.getDataColor,qr.prototype.getDataPicking=Hi.prototype.getDataPicking,qr.prototype.getDataSize=Hi.prototype.getDataSize;var Rb=class{constructor(e,t){let i=WP({nodeArray1:e.atomIndex1,nodeArray2:e.atomIndex2,edgeCount:e.count,nodeCount:t});this.countArray=i.countArray,this.offsetArray=i.offsetArray,this.indexArray=i.indexArray}},Bc=class extends sa{get _defaultFields(){return[["atomIndex1",1,"int32"],["atomIndex2",1,"int32"],["bondOrder",1,"int8"]]}addBond(e,t,i){this.growIfFull();let r=this.count,s=e.index,o=t.index;s0&&(a[N]=v.angleTo(S));let z=Math.cos(_.angleTo(y));u[N]=180/Math.PI*Math.acos(z);let L=_.length(),F=y.length();l[N]=Math.sqrt(F*L)/Math.max(2,2*(1-z)),c[N]=Math.abs(m.dot(v)),g.copy(_).multiplyScalar(l[N]/L),b.copy(y).multiplyScalar(l[N]/F),g.subVectors(T,g),b.subVectors(R,b),g.toArray(s,H+3),b.toArray(s,H+6),x.subVectors(M,w),x.toArray(d,H),S.copy(v),w.copy(g)}g.fromArray(s,3),b.fromArray(s,6),v.subVectors(g,b).normalize(),M.index=e.getAtomIndexByType(0,A),w.copy(M),h.copy(M),Ka(h,v,g),h.toArray(s,0),x.subVectors(w,g),x.toArray(d,0),g.fromArray(s,3*i-6),b.fromArray(s,3*i-9),v.subVectors(g,b).normalize(),M.index=e.getAtomIndexByType(i-1,A),w.copy(M),h.copy(M),Ka(h,v,g),h.toArray(s,3*i-3);for(let N=i-3;Nt||u.bending[F]>e)&&(z=!0)),z){if(F-p<4){p=F,z=!1;continue}D.index=I.traceAtomIndex,R=u.axis.subarray(3*p+3,3*F),C=u.center.subarray(3*p,3*F+3),M=sb(R).normalize(),T=sb(C),P.fromArray(C),Ka(P,M,T),E.fromArray(C,C.length-3),Ka(E,M,T),M.subVectors(E,P),M.toArray(y,_),T.toArray(g,_),P.toArray(b,_),E.toArray(h,_),f.atomColorToArray(D,v,_),S.push(D.index),x.push(m.atomRadius(D)),w.push(c+p),A.push(c+F+1-p),_+=3,p=F,z=!1}let L=new Float32Array(S);return{axis:new Float32Array(y),center:new Float32Array(g),begin:new Float32Array(b),end:new Float32Array(h),color:new Float32Array(v),picking:new oo(L,a),size:new Float32Array(x),residueOffset:w,residueCount:A}}},Fb=class{constructor(e){this.scoreFunction=e,this.content=[],this.scoreFunction=e}push(e){this.content.push(e),this.bubbleUp(this.content.length-1)}pop(){let e=this.content[0],t=this.content.pop();return t&&this.content.length>0&&(this.content[0]=t,this.sinkDown(0)),e}peek(){return this.content[0]}remove(e){let t=this.content.length;for(let i=0;i0;){let i=Math.floor((e+1)/2)-1,r=this.content[i];if(!(this.scoreFunction(t)this.maxDepth&&(this.maxDepth=e);let s=r-i;if(s===0)return-1;let o=4*this.currentNode,a=this.nodes;if(this.currentNode+=1,s===1)return a[o]=i,a[o+1]=-1,a[o+2]=-1,a[o+3]=t,o;let l=this.indices,c=this.points,u=i+Math.floor(s/2),d=e%3,f,m,p,_,y,g=i,b=r-1;for(;b>g;){for(p=g+b>>1,_=c[3*l[p]+d],m=l[p],l[p]=l[b],l[b]=m,y=g,f=g;f-u[1]),s=this.nodes,o=this.points,a=this.indices,l=u=>{let d,f,m=this.getNodeDepth(u)%3,p=3*a[s[u]],_=[o[p+0],o[p+1],o[p+2]],y=this.metric(e,_);function g(x,w){r.push([x,w]),r.size()>t&&r.pop()}let b=s[u+1],h=s[u+2];if(h===-1&&b===-1)return void((r.size()o[3*a[s[e]]+r])throw new Error("left child is > parent!");i+=this.verify(l,t+1)}if(c!==-1){if(o[3*a[s[c]]+r]0}isBackbone(){let e=this.residueType.backboneIndexList;return e.length>0&&e.includes(this.index-this.residueAtomOffset)}isPolymer(){if(this.structure.entityList.length>0)return this.entity.isPolymer();{let e=this.residueType.moleculeType;return e===3||e===4||e===5}}isSidechain(){return this.isPolymer()&&!this.isBackbone()}isCg(){let e=this.residueType.backboneType;return e===4||e===5||e===6}isTrace(){return this.index===this.residueType.traceAtomIndex+this.residueAtomOffset}isHetero(){return this.residueType.hetero===1}isProtein(){return this.residueType.moleculeType===3}isNucleic(){let e=this.residueType.moleculeType;return e===4||e===5}isRna(){return this.residueType.moleculeType===4}isDna(){return this.residueType.moleculeType===5}isWater(){return this.residueType.moleculeType===1}isIon(){return this.residueType.moleculeType===2}isSaccharide(){return this.residueType.moleculeType===6}isHelix(){return XP.includes(this.sstruc)}isSheet(){return qP.includes(this.sstruc)}isTurn(){return YP.includes(this.sstruc)&&this.isProtein()}isBonded(){return this.bondHash.countArray[this.index]!==0}isRing(){return this.residueType.getRings().atomRings[this.index-this.residueAtomOffset]!==void 0}isAromatic(){return this.aromatic===1}isPolarHydrogen(){let e=!1;return this.number!==1||(e=!this.hasBondToElement(6)),e}isMetal(){return this.atomType.isMetal()}isNonmetal(){return this.atomType.isNonmetal()}isMetalloid(){return this.atomType.isMetalloid()}isHalogen(){return this.atomType.isHalogen()}isDiatomicNonmetal(){return this.atomType.isDiatomicNonmetal()}isPolyatomicNonmetal(){return this.atomType.isPolyatomicNonmetal()}isAlkaliMetal(){return this.atomType.isAlkaliMetal()}isAlkalineEarthMetal(){return this.atomType.isAlkalineEarthMetal()}isNobleGas(){return this.atomType.isNobleGas()}isTransitionMetal(){return this.atomType.isTransitionMetal()}isPostTransitionMetal(){return this.atomType.isPostTransitionMetal()}isLanthanide(){return this.atomType.isLanthanide()}isActinide(){return this.atomType.isActinide()}getDefaultValence(){return this.atomType.getDefaultValence()}getValenceList(){return this.atomType.getValenceList()}getOuterShellElectronCount(){return this.atomType.getOuterShellElectronCount()}distanceTo(e){let t=this.atomStore,i=e.atomStore,r=this.index,s=e.index,o=t.x[r]-i.x[s],a=t.y[r]-i.y[s],l=t.z[r]-i.z[s],c=o*o+a*a+l*l;return Math.sqrt(c)}connectedTo(e){let t=this.atomStore,i=e.atomStore,r=this.index,s=e.index;if(t.altloc&&i.altloc){let m=t.altloc[r],p=i.altloc[s];if(m!==0&&p!==0&&m!==32&&p!==32&&m!==p)return!1}let o=t.x[r]-i.x[s],a=t.y[r]-i.y[s],l=t.z[r]-i.z[s],c=o*o+a*a+l*l;if(c<48&&this.isCg())return!0;if(isNaN(c))return!1;let u=this.covalent+e.covalent,d=u+.3,f=u-.5;return cf*f}positionFromArray(e,t=0){return this.x=e[t+0],this.y=e[t+1],this.z=e[t+2],this}positionToArray(e=[],t=0){let i=this.index,r=this.atomStore;return e[t+0]=r.x[i],e[t+1]=r.y[i],e[t+2]=r.z[i],e}positionToVector3(e){return e===void 0&&(e=new W),e.x=this.x,e.y=this.y,e.z=this.z,e}positionFromVector3(e){return this.x=e.x,this.y=e.y,this.z=e.z,this}positionAdd(e){return 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this.matrixList.forEach(function(o){i.copy(s).applyMatrix4(o),t.expandByPoint(i.min),t.expandByPoint(i.max)}),t}getSelection(){return cI(this.chainList)}getView(e){let t=this.getSelection();return t?e.getView(t):e}getInstanceList(){let e=[];for(let t=0,i=this.matrixList.length;t0&&this.addResidueType(this.ri-1),u.growIfFull(),u.resno[this.ri]=s,a!==void 0&&(u.sstruc[this.ri]=a.charCodeAt(0)),l!==void 0&&(u.inscode[this.ri]=l.charCodeAt(0)),u.atomOffset[this.ri]=this.ai,u.atomCount[this.ri]=0,u.count+=1,u.chainIndex[this.ri]=this.ci,d.residueCount[this.ci]+=1),c.count+=1,c.residueIndex[this.ai]=this.ri,u.atomCount[this.ri]+=1,this.currentModelindex=e,this.currentChainid=i,this.currentResname=r,this.currentResno=s,this.currentInscode=l,this.currentHetero=o}finalize(){this.previousResname=this.currentResname,this.previousHetero=this.currentHetero,this.ri>-1&&this.addResidueType(this.ri)}};function uI(n,e){if(!e)return;Le&&we.time("assignSecondaryStructure");let t=[];n.eachModel(function(c){c.eachChain(function(u){t.push(u.chainname)})});let i=t.slice().sort(),r=[];i.forEach(function(c){r.push(t.indexOf(c))});let s=e.helices.filter(function(c){return ja(i,c[0])>=0});s.sort(function(c,u){let d=c[0],f=u[0],m=c[1],p=u[1];if(d===f)return m===p?0:m=0});a.sort(function(c,u){let d=c[0],f=u[0];if(d===f)return 0;let m=ja(i,d),p=ja(i,f);return r[m]=i.residueCount)continue;c.index=l+m,u.index=l+m+p,d.index=c.traceAtomIndex,f.index=u.traceAtomIndex;let _=d.distanceTo(f);if(Math.abs(_-s[p-2])>o)return!1}return!0},e=function(i,r){return n(i,r,[5.45,5.18,6.37],2.1)},t=function(i,r){return n(i,r,[6.1,10.4,13],1.42)};return function(i){Le&&we.time("calculateSecondaryStructure"),i.eachPolymer(function(r){if(r.residueCount<4)return;if(r.isCg())(function(a){let l=a.residueStore,c=a.residueIndexStart,u=new vg(a).position,d=new W,f=new W;for(let m=0,p=a.residueCount;m1&&u.bending[m]<20&&(l.sstruc[c+m]=104,l.sstruc[c+m+1]=104)}})(r);else{if(!r.isProtein())return;(function(a){let l=a.residueStore,c=a.residueIndexStart;for(let u=0,d=a.residueCount;u=e;)t=Math.floor(t/e),r+=qv[t%e],i+=1;return i>=5&&we.warn("chainname overflow"),r}function R0(n,e=!1){Le&&we.time("calculateChainnames");let t=!0;if(n.eachChain(function(i){i.chainname&&(t=!1)}),t){let i=n.modelStore,r=n.chainStore,s=n.residueStore,o=function(_,y,g,b){let h=r.count;for(let v=0;v{u.add(f),d.forEach(m=>{u.add(m)})})),n.eachResidue(function(d){if(!e&&c){let p=d.atomCount,_=d.atomOffset;if(p>500)return void we.warn("more than 500 atoms, skip residue for auto-bonding",d.qualifiedName());if(t==="auto"&&d.hetero){for(let S=d.atomOffset;S{u.forEach(y=>{p.push(_.clone().multiply(y))})}),l.addPart(p)}else l.addPart(c);let d=new W,f=new As("SUPERCELL"),m=Array.prototype.concat.call(a(d.set(1,0,0)),a(d.set(0,1,0)),a(d.set(0,0,1)),a(d.set(-1,0,0)),a(d.set(0,-1,0)),a(d.set(0,0,-1)),a(d.set(1,1,0)),a(d.set(1,0,1)),a(d.set(0,1,1)),a(d.set(-1,-1,0)),a(d.set(-1,0,-1)),a(d.set(0,-1,-1)),a(d.set(1,-1,-1)),a(d.set(1,1,-1)),a(d.set(1,-1,1)),a(d.set(-1,1,1)),a(d.set(-1,-1,1)),a(d.set(-1,1,-1)),a(d.set(0,1,-1)),a(d.set(0,-1,1)),a(d.set(1,0,-1)),a(d.set(-1,0,1)),a(d.set(1,-1,0)),a(d.set(-1,1,0)),a(),a(d.set(1,1,1)),a(d.set(-1,-1,-1)));if(n.biomolDict.NCS){let p=[];m.forEach(function(_){u.forEach(function(y){p.push(_.clone().multiply(y))})}),f.addPart(p)}else f.addPart(m);n.biomolDict.UNITCELL=l,n.biomolDict.SUPERCELL=f,Le&&we.timeEnd("buildUnitcellAssembly")}var mT=["H","C","O","N","S","P"],DU=["NA","CL","FE"];function Ew(n){let e=n.toUpperCase(),t=0,i=0;for(let s=0;s0)break;++t}else i=s+1;(t>0||i=3&&mT.indexOf(e[0])!==-1?e[0]:""}function sl(n){let e=n.bondHash,t=e.countArray,i=e.offsetArray,r=e.indexArray,s=n.getBondProxy();n.eachResidue(function(o){let a=o.residueType;if(a.bonds!==void 0)return;var l=o.atomOffset,c=[],u=[],d=[],f={};let m=l+o.atomCount;o.eachAtom(function(p){let _=p.index,y=i[_];for(let g=0,b=t[_];g=m)continue;let v=s.atomIndex2;if(v=m)continue;if(h>v){let x=v;v=h,h=x}let S=h+"|"+v;f[S]===void 0&&(f[S]=!0,c.push(h-l),u.push(v-l),d.push(s.bondOrder))}}),a.bonds={atomIndices1:c,atomIndices2:u,bondOrders:d}})}var NU=[3,11,19,37,55,87],FU=[4,12,20,38,56,88],OU=[6,15,16,34],BU=[1,7,8,9,17,35,53],UU=[2,10,18,36,54,86],zU=[13,30,31,48,49,50,80,81,82,83,84,85,112],VU=[5,14,32,33,51,52,85],HU=[9,17,35,53,85],Vb=class{constructor(e,t,i){this.structure=e,this.atomname=t,i=i||Ew(t),this.element=i,this.number=ZP[i]||0,this.vdw=YB[this.number]||2,this.covalent=ZB[this.number]||1.6}getDefaultValence(){let e=eT[this.number];return e?e[0]:-1}getValenceList(){return eT[this.number]||[]}getOuterShellElectronCount(){return KB[this.number]||2}isMetal(){return this.isAlkaliMetal()||this.isAlkalineEarthMetal()||this.isLanthanide()||this.isActinide()||this.isTransitionMetal()||this.isPostTransitionMetal()}isNonmetal(){return this.isDiatomicNonmetal()||this.isPolyatomicNonmetal()||this.isNobleGas()}isMetalloid(){return VU.includes(this.number)}isHalogen(){return HU.includes(this.number)}isDiatomicNonmetal(){return BU.includes(this.number)}isPolyatomicNonmetal(){return OU.includes(this.number)}isAlkaliMetal(){return NU.includes(this.number)}isAlkalineEarthMetal(){return FU.includes(this.number)}isNobleGas(){return UU.includes(this.number)}isTransitionMetal(){let e=this.number;return e>=21&&e<=29||e>=39&&e<=47||e>=72&&e<=79||e>=104&&e<=108}isPostTransitionMetal(){return zU.includes(this.number)}isLanthanide(){return this.number>=57&&this.number<=71}isActinide(){return this.number>=89&&this.number<=103}},Hb=class{constructor(e){this.structure=e,this.dict={},this.list=[],this.structure=e}add(e,t){let i=function(s,o){return s+"|"+o}(e=e.toUpperCase(),t=t?t.toUpperCase():Ew(e)),r=this.dict[i];if(r===void 0){let s=new Vb(this.structure,e,t);r=this.list.length,this.dict[i]=r,this.list.push(s)}return r}get(e){return this.list[e]}},Gb=class{constructor(e,t,i,r,s,o){this.structure=e,this.bondReferenceAtomIndices=[],this.resname=t,this.atomTypeIdList=i,this.hetero=r?1:0,this.chemCompType=s,this.bonds=o,this.atomCount=i.length,this.moleculeType=this.getMoleculeType(),this.backboneType=this.getBackboneType(0),this.backboneEndType=this.getBackboneType(-1),this.backboneStartType=this.getBackboneType(1),this.backboneIndexList=this.getBackboneIndexList();let a=Yh[this.backboneType],l=Yh[this.backboneStartType],c=Yh[this.backboneEndType],u=this.getAtomIndexByName(a.trace);this.traceAtomIndex=U(u,-1);let d=this.getAtomIndexByName(a.direction1);this.direction1AtomIndex=U(d,-1);let f=this.getAtomIndexByName(a.direction2);this.direction2AtomIndex=U(f,-1);let m=this.getAtomIndexByName(l.backboneStart);this.backboneStartAtomIndex=U(m,-1);let p=this.getAtomIndexByName(c.backboneEnd),_;this.backboneEndAtomIndex=U(p,-1),_=QB.includes(t)?this.getAtomIndexByName("N1"):this.getAtomIndexByName("N3"),this.rungEndAtomIndex=U(_,-1)}getBackboneIndexList(){let e=[],t;switch(this.moleculeType){case 3:t=nU;break;case 4:case 5:t=QP;break;default:return e}let i=this.structure.atomMap,r=this.atomTypeIdList;for(let s=0,o=this.atomCount;s500)Le&&we.warn("more than 500 atoms, skip residue for auto-bonding",t.qualifiedName());else if(o>50){let f=new Bb(t,!0),m=t.isCg()?1.2:2.3;for(let p=a;p=0||jU(e,t);this.rings={atomRings:e.atomRings,rings:e.rings}}isAromatic(e){return this.aromaticAtoms=this.getAromatic(e),this.aromaticAtoms[e.index-e.residueAtomOffset]===1}calculateAromatic(e){let t=this.aromaticAtoms=new Uint8Array(this.atomCount),i=this.getRings().rings,r=i.map(o=>function(a){if(a.some(d=>!GU.includes(d.number)))return!1;let l=0,c=new Ht(3,a.length),u=c.data;return a.forEach(d=>{u[l+0]=d.x,u[l+1]=d.y,u[l+2]=d.z,l+=3}),new _g(c).vecC.length()<$U}(o.map(a=>this.structure.getAtomProxy(a+e.atomOffset)))),s=this.aromaticRings=[];i.forEach((o,a)=>{r[a]&&(s.push(o),o.forEach(l=>t[l]=1))})}assignBondReferenceAtomIndices(){let e=this.getBondGraph(),t=this.getRings(),i=t.atomRings,r=t.rings,s=this.bonds,o=s.atomIndices1,a=s.atomIndices2,l=s.bondOrders,c=this.bondReferenceAtomIndices,u=s.atomIndices1.length;c.length=0;for(let d=0;d1)for(let g=0;g1)for(let g=0;g=0;g--)p[_++]=o[g];let y=n.rings.length;for(let g=0;g0?s[f]!==l&&s[l]!==f&&WU(n,l,f):(i[f]=1,r[a++]=f,s[f]=l)}}}var id=4,$b=class{constructor(e){this.structure=e,this.dict={},this.list=[]}add(e,t,i,r="",s){let o=function(l,c,u,d=""){return l+"|"+c.join(",")+"|"+(u?1:0)+"|"+d}(e=e.toUpperCase(),t,i,r),a=this.dict[o];if(a===void 0){let l=new Gb(this.structure,e,t,i,r,s);a=this.list.length,this.dict[o]=a,this.list.push(l)}return a}get(e){return this.list[e]}},Wb=class n{constructor(e,t=0){this.structure=e,this.index=t,this.bondStore=e.bondStore,this._v12=new W,this._v13=new W,this._ap1=this.structure.getAtomProxy(),this._ap2=this.structure.getAtomProxy(),this._ap3=this.structure.getAtomProxy()}get atom1(){return this.structure.getAtomProxy(this.atomIndex1)}get atom2(){return this.structure.getAtomProxy(this.atomIndex2)}get atomIndex1(){return this.bondStore.atomIndex1[this.index]}set atomIndex1(e){this.bondStore.atomIndex1[this.index]=e}get atomIndex2(){return this.bondStore.atomIndex2[this.index]}set atomIndex2(e){this.bondStore.atomIndex2[this.index]=e}get bondOrder(){return this.bondStore.bondOrder[this.index]}set bondOrder(e){this.bondStore.bondOrder[this.index]=e}getOtherAtomIndex(e){return e===this.atomIndex1?this.atomIndex2:this.atomIndex1}getOtherAtom(e){return this.structure.getAtomProxy(this.getOtherAtomIndex(e.index))}getReferenceAtomIndex(){let e=this._ap1,t=this._ap2;if(e.index=this.atomIndex1,t.index=this.atomIndex2,e.residueIndex!==t.residueIndex)return;let i=e.index-e.residueAtomOffset,r=t.index-t.residueAtomOffset,s=e.residueType.getBondReferenceAtomIndex(i,r);if(s!==void 0)return s+e.residueAtomOffset;console.warn("No reference atom found",e.index,t.index)}calculateShiftDir(e=new W){let t=this._ap1,i=this._ap2,r=this._ap3,s=this._v12,o=this._v13;t.index=this.atomIndex1,i.index=this.atomIndex2;let a=this.getReferenceAtomIndex();s.subVectors(t,i).normalize(),a!==void 0?(r.index=a,o.subVectors(t,r)):o.copy(t),o.normalize();let l=s.dot(o);return 1-Math.abs(l)<1e-5&&(o.set(1,0,0),l=s.dot(o),1-Math.abs(l)<1e-5&&(o.set(0,1,0),l=s.dot(o))),e.copy(o.sub(s.multiplyScalar(l))).normalize()}qualifiedName(){return this.atomIndex1+"="+this.atomIndex2}clone(){return new n(this.structure,this.index)}toObject(){return{atomIndex1:this.atomIndex1,atomIndex2:this.atomIndex2,bondOrder:this.bondOrder}}},jb=class n{constructor(e,t=0){this.structure=e,this.index=t,this.chainStore=e.chainStore,this.residueStore=e.residueStore,this.atomStore=e.atomStore,this.residueMap=e.residueMap,this.atomMap=e.atomMap}get entity(){return this.structure.entityList[this.entityIndex]}get entityIndex(){return this.chainStore.entityIndex[this.chainIndex]}get chain(){return this.structure.getChainProxy(this.chainIndex)}get chainIndex(){return this.residueStore.chainIndex[this.index]}set chainIndex(e){this.residueStore.chainIndex[this.index]=e}get atomOffset(){return this.residueStore.atomOffset[this.index]}set atomOffset(e){this.residueStore.atomOffset[this.index]=e}get atomCount(){return this.residueStore.atomCount[this.index]}set atomCount(e){this.residueStore.atomCount[this.index]=e}get atomEnd(){return this.atomOffset+this.atomCount-1}get modelIndex(){return this.chainStore.modelIndex[this.chainIndex]}get chainname(){return this.chainStore.getChainname(this.chainIndex)}get chainid(){return this.chainStore.getChainid(this.chainIndex)}get resno(){return this.residueStore.resno[this.index]}set resno(e){this.residueStore.resno[this.index]=e}get sstruc(){return this.residueStore.getSstruc(this.index)}set sstruc(e){this.residueStore.setSstruc(this.index,e)}get inscode(){return this.residueStore.getInscode(this.index)}set inscode(e){this.residueStore.setInscode(this.index,e)}get residueType(){return this.residueMap.get(this.residueStore.residueTypeId[this.index])}get resname(){return this.residueType.resname}get hetero(){return this.residueType.hetero}get moleculeType(){return this.residueType.moleculeType}get backboneType(){return this.residueType.backboneType}get backboneStartType(){return this.residueType.backboneStartType}get backboneEndType(){return this.residueType.backboneEndType}get traceAtomIndex(){return this.residueType.traceAtomIndex+this.atomOffset}get direction1AtomIndex(){return this.residueType.direction1AtomIndex+this.atomOffset}get direction2AtomIndex(){return this.residueType.direction2AtomIndex+this.atomOffset}get backboneStartAtomIndex(){return this.residueType.backboneStartAtomIndex+this.atomOffset}get backboneEndAtomIndex(){return this.residueType.backboneEndAtomIndex+this.atomOffset}get rungEndAtomIndex(){return this.residueType.rungEndAtomIndex+this.atomOffset}get x(){let e=0;for(let t=this.atomOffset;t<=this.atomEnd;++t)e+=this.atomStore.x[t];return e/this.atomCount}get y(){let e=0;for(let t=this.atomOffset;t<=this.atomEnd;++t)e+=this.atomStore.y[t];return e/this.atomCount}get z(){let e=0;for(let t=this.atomOffset;t<=this.atomEnd;++t)e+=this.atomStore.z[t];return e/this.atomCount}eachAtom(e,t){let i=this.atomCount,r=this.atomOffset,s=this.structure._ap,o=r+i;if(t&&t.atomOnlyTest){let a=t.atomOnlyTest;for(let l=r;l0)return this.entity.isPolymer();{let e=this.residueType.moleculeType;return e===3||e===4||e===5}}isHetero(){return this.residueType.hetero===1}isWater(){return this.residueType.moleculeType===1}isIon(){return this.residueType.moleculeType===2}isSaccharide(){return this.residueType.moleculeType===6}isStandardAminoacid(){return this.residueType.isStandardAminoacid()}isStandardBase(){return this.residueType.isStandardBase()}isHelix(){return XP.includes(this.sstruc)}isSheet(){return qP.includes(this.sstruc)}isTurn(){return YP.includes(this.sstruc)&&this.isProtein()}getAtomType(e){return this.atomMap.get(this.atomStore.atomTypeId[e])}getResname1(){return hg[this.resname.toUpperCase()]||"X"}getBackboneType(e){switch(e){case-1:return this.residueType.backboneStartType;case 1:return this.residueType.backboneEndType;default:return this.residueType.backboneType}}getAtomIndexByName(e){let t=this.residueType.getAtomIndexByName(e);return t!==void 0&&(t+=this.atomOffset),t}hasAtomWithName(e){return this.residueType.hasAtomWithName(e)}getAtomnameList(){console.warn("getAtomnameList - might be expensive");let e=this.atomCount,t=this.atomOffset,i=new Array(e);for(let r=0;r=t){let r=U(e,this.structure.getResidueProxy());if(r.index=i,r.connectedTo(this))return r}else if(i===t-1){let r=this.chainStore.residueCount[this.chainIndex],s=U(e,this.structure.getResidueProxy());if(s.index=t+r-1,s.connectedTo(this))return s}}getBonds(){return this.residueType.getBonds(this)}getRings(){return this.residueType.getRings()}getAromaticRings(){return this.residueType.getAromaticRings(this)}qualifiedName(e=!1){let t="";return this.resname&&!e&&(t+="["+this.resname+"]"),this.resno!==void 0&&(t+=this.resno),this.inscode&&(t+="^"+this.inscode),this.chain&&(t+=":"+this.chainname),t+="/"+this.modelIndex,t}clone(){return new n(this.structure,this.index)}toObject(){return{index:this.index,chainIndex:this.chainIndex,atomOffset:this.atomOffset,atomCount:this.atomCount,resno:this.resno,resname:this.resname,sstruc:this.sstruc}}},rd=class{constructor(e,t,i){this.structure=e,this.residueIndexStart=t,this.residueIndexEnd=i,this.chainStore=e.chainStore,this.residueStore=e.residueStore,this.atomStore=e.atomStore,this.residueCount=i-t+1;let r=this.structure.getResidueProxy(this.residueIndexStart),s=this.structure.getResidueProxy(this.residueIndexEnd);this.isPrevConnected=r.getPreviousConnectedResidue()!==void 0;let o=s.getNextConnectedResidue();this.isNextConnected=o!==void 0,this.isNextNextConnected=o!==void 0&&o.getNextConnectedResidue()!==void 0,this.isCyclic=s.connectedTo(r),this.__residueProxy=this.structure.getResidueProxy()}get chainIndex(){return this.residueStore.chainIndex[this.residueIndexStart]}get modelIndex(){return this.chainStore.modelIndex[this.chainIndex]}get chainname(){return this.chainStore.getChainname(this.chainIndex)}isProtein(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isProtein()}isCg(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isCg()}isNucleic(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isNucleic()}getMoleculeType(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.moleculeType}getBackboneType(e){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.getBackboneType(e)}getAtomIndexByType(e,t){this.isCyclic?e===-1?e=this.residueCount-1:e===this.residueCount&&(e=0):(e!==-1||this.isPrevConnected||(e+=1),e!==this.residueCount||this.isNextNextConnected||(e-=1));let i=this.__residueProxy,r;switch(i.index=this.residueIndexStart+e,t){case"trace":r=i.traceAtomIndex;break;case"direction1":r=i.direction1AtomIndex;break;case"direction2":r=i.direction2AtomIndex;break;default:r=i.getAtomIndexByName(t)}return r}eachAtom(e,t){this.eachResidue(function(i){i.eachAtom(e,t)})}eachAtomN(e,t,i){let r=this.residueCount,s=new Array(e);for(let a=0;a1&&e(new rd(o,i,u.index)),i=r)):(y!==rl&&u.index-i>1&&e(new rd(o,i,u.index)),i=r)}r-i>1&&this.structure.getResidueProxy(i).backboneEndType&&e(new rd(o,i,r))}qualifiedName(){return":"+this.chainname+"/"+this.modelIndex}clone(){return new n(this.structure,this.index)}toObject(){return{index:this.index,residueOffset:this.residueOffset,residueCount:this.residueCount,chainname:this.chainname}}},qb=class n{constructor(e,t=0){this.structure=e,this.index=t,this.modelStore=e.modelStore,this.chainStore=e.chainStore,this.residueStore=e.residueStore}get chainOffset(){return this.modelStore.chainOffset[this.index]}set chainOffset(e){this.modelStore.chainOffset[this.index]=e}get chainCount(){return this.modelStore.chainCount[this.index]}set chainCount(e){this.modelStore.chainCount[this.index]=e}get residueOffset(){return this.chainStore.residueOffset[this.chainOffset]}get atomOffset(){return this.residueStore.atomOffset[this.residueOffset]}get chainEnd(){return this.chainOffset+this.chainCount-1}get residueEnd(){return this.chainStore.residueOffset[this.chainEnd]+this.chainStore.residueCount[this.chainEnd]-1}get atomEnd(){return this.residueStore.atomOffset[this.residueEnd]+this.residueStore.atomCount[this.residueEnd]-1}get residueCount(){return this.chainCount===0?0:this.residueEnd-this.residueOffset+1}get atomCount(){return this.residueCount===0?0:this.atomEnd-this.atomOffset+1}eachAtom(e,t){this.eachChain(function(i){i.eachAtom(e,t)},t)}eachResidue(e,t){this.eachChain(function(i){i.eachResidue(e,t)},t)}eachPolymer(e,t){if(t&&t.chainOnlyTest){let i=t.chainOnlyTest;this.eachChain(function(r){i(r)&&r.eachPolymer(e,t)})}else this.eachChain(function(i){i.eachPolymer(e,t)})}eachChain(e,t){let i=this.chainCount,r=this.chainOffset,s=this.structure._cp,o=r+i;if(t&&t.test){let a=t.chainOnlyTest;if(a)for(let l=r;l{let g=3*y;l.index=_,u&&l.positionToArray(u,g),d&&o.atomColorToArray(l,d,g),f&&(f.array[y]=_),m&&(m[y]=s.atomRadius(l)),p&&(p[y]=_)}),a}getBondData(e){let t=Object.assign({},e);t.colorParams&&(t.colorParams.structure=this.getStructure());let i=t.what,r=U(t.bondSet,this.bondSet),s=U(t.multipleBond,"off"),o=s!=="off",a=s==="offset",l=U(t.bondScale,.4),c=U(t.bondSpacing,1),u,d,f={},m=this.getBondProxy();t.bondStore&&(m.bondStore=t.bondStore);let p=this.getAtomProxy(),_=this.getAtomProxy(),y;if(o){let N=m.bondStore.bondOrder;y=0,r.forEach(function(H){y+=N[H]})}else y=r.getSize();i&&!i.position||(f.position1=new Float32Array(3*y),f.position2=new Float32Array(3*y)),i&&!i.color||!t.colorParams||(f.color=new Float32Array(3*y),f.color2=new Float32Array(3*y),d=Dt.getScheme(t.colorParams)),i&&!i.picking||(f.picking=new fg(new Float32Array(y),this.getStructure(),t.bondStore)),(!i||i.radius||o&&i.position)&&(u=new Qr(t.radiusParams)),i&&!i.radius||(f.radius=new Float32Array(y),t.radius2&&(f.radius2=new Float32Array(y)));let{position1:g,position2:b,color:h,color2:v,picking:S,radius:x,radius2:w}=f,A,M,T,R,C,P,E=0,I=new W,O=new W,D=new W;return r.forEach(N=>{if(M=3*E,m.index=N,p.index=m.atomIndex1,_.index=m.atomIndex2,R=m.bondOrder,g)if(o&&R>1){let H=u.atomRadius(p);P=H*l/(.5*R),m.calculateShiftDir(D),a?(C=2*c*H,D.multiplyScalar(C),D.negate(),O.subVectors(_,p).multiplyScalar(Math.max(.1,C/1.88)),p.positionToArray(g,M),_.positionToArray(b,M),R>=2&&(I.addVectors(p,D).add(O).toArray(g,M+3),I.addVectors(_,D).sub(O).toArray(b,M+3),R>=3&&(I.subVectors(p,D).add(O).toArray(g,M+6),I.subVectors(_,D).sub(O).toArray(b,M+6)))):(C=(c-l)*H,D.multiplyScalar(C),R===2?(I.addVectors(p,D).toArray(g,M),I.subVectors(p,D).toArray(g,M+3),I.addVectors(_,D).toArray(b,M),I.subVectors(_,D).toArray(b,M+3)):R===3?(p.positionToArray(g,M),I.addVectors(p,D).toArray(g,M+3),I.subVectors(p,D).toArray(g,M+6),_.positionToArray(b,M),I.addVectors(_,D).toArray(b,M+3),I.subVectors(_,D).toArray(b,M+6)):(p.positionToArray(g,M),_.positionToArray(b,M)))}else p.positionToArray(g,M),_.positionToArray(b,M);if(h&&v&&(d.bondColorToArray(m,1,h,M),d.bondColorToArray(m,0,v,M),o&&R>1))for(A=1;A1))for(A=1;A1))for(P=x[E]*l/(a?1:.5*R),A=a?1:0;A1))for(P=w[E]*l/(a?1:.5*R),A=a?1:0;A{let u=c.x,d=c.y,f=c.z;uo&&(o=u),d>a&&(a=d),f>l&&(l=f)},e),t.min.set(i,r,s),t.max.set(o,a,l),Le&&we.timeEnd("getBoundingBox"),t}getPrincipalAxes(e){Le&&we.time("getPrincipalAxes");let t=0,i=new Ht(3,this.atomCount),r=i.data;return this.eachAtom(s=>{r[t+0]=s.x,r[t+1]=s.y,r[t+2]=s.z,t+=3},e),Le&&we.timeEnd("getPrincipalAxes"),new _g(i)}atomCenter(e){return e?this.getBoundingBox(e).getCenter(new W):this.center.clone()}hasCoords(){if(this._hasCoords===void 0){let e=this.atomStore;this._hasCoords=jm(e.x)!==0||Wm(e.x)!==0||jm(e.y)!==0||Wm(e.y)!==0||jm(e.z)!==0||Wm(e.z)!==0||e.count/this.modelStore.count==1}return this._hasCoords}getSequence(e){let t=[],i=this.getResidueProxy();return this.eachAtom(function(r){i.index=r.residueIndex,r.index===i.traceAtomIndex&&t.push(i.getResname1())},e),t}getAtomIndices(e){if(e&&e.string){let t=[];return this.eachAtom(function(i){t.push(i.index)},e),new Uint32Array(t)}{let t={what:{index:!0}};return this.getAtomData(t).index}}getChainnameCount(e){let t=new Set;return this.eachChain(function(i){i.residueCount&&t.add(i.chainname)},e),t.size}updatePosition(e,t=!0){let i=0;this.eachAtom(function(r){r.positionFromArray(e,i),i+=3},void 0),this._hasCoords=void 0,t&&this.refreshPosition()}refreshPosition(){this.getBoundingBox(void 0,this.boundingBox),this.boundingBox.getCenter(this.center),this.spatialHash=new il(this.atomStore,this.boundingBox),this.signals.refreshed.dispatch(this)}dispose(){this.frames&&(this.frames.length=0),this.boxes&&(this.boxes.length=0),this.bondStore.dispose(),this.backboneBondStore.dispose(),this.rungBondStore.dispose(),this.atomStore.dispose(),this.residueStore.dispose(),this.chainStore.dispose(),this.modelStore.dispose(),delete this.bondSet,delete this.atomSet}},gT=new sn,Yv=[jc,ro,Xc,so,ra,$c,ia,Wc,Yc,qc,tl,nl],XU={aspectRatio:1.5,sphereDetail:2,radialSegments:50,disableImpostor:!1,openEnded:!1,dashedCylinder:!1,labelParams:{},pointSize:2,sizeAttenuation:!1,useTexture:!0,linewidth:2},Yb=class{constructor(e="shape",t={}){this.boundingBox=new sn,this.bufferList=[],this.meshCount=0,this._primitiveData={},this.name=e,this.parameters=or(t,XU),Yv.forEach(i=>{Object.keys(i.fields).forEach(r=>{this._primitiveData[i.getShapeKey(r)]=[]}),this._primitiveData[i.getShapeKey("name")]=[]})}addBuffer(e){this.bufferList.push(e);let t=e.geometry;return t.boundingBox||t.computeBoundingBox(),this.boundingBox.union(t.boundingBox),this}addMesh(e,t,i,r,s){let o;e=Iv(e),t=Iv(t),Array.isArray(i)&&(i=bs(i,e.length)),r&&(r=Iv(r)),o=r===void 0||r.length==0?{position:e,color:t,index:i}:{position:e,color:t,index:i,normal:r};let a=new pb(this,Object.assign({serial:this.meshCount,name:s},o)),l=new Jr(Object.assign({picking:a},o));return this.bufferList.push(l),gT.setFromArray(e),this.boundingBox.union(gT),this.meshCount+=1,this}addSphere(e,t,i,r){return ia.objectToShape(this,{position:e,color:t,radius:i,name:r}),this}addEllipsoid(e,t,i,r,s,o){return ra.objectToShape(this,{position:e,color:t,radius:i,majorAxis:r,minorAxis:s,name:o}),this}addTorus(e,t,i,r,s,o){return qc.objectToShape(this,{position:e,color:t,radius:i,majorAxis:r,minorAxis:s,name:o}),this}addCylinder(e,t,i,r,s){return so.objectToShape(this,{position1:e,position2:t,color:i,radius:r,name:s}),this}addCone(e,t,i,r,s){return Xc.objectToShape(this,{position1:e,position2:t,color:i,radius:r,name:s}),this}addArrow(e,t,i,r,s){return jc.objectToShape(this,{position1:e,position2:t,color:i,radius:r,name:s}),this}addBox(e,t,i,r,s,o){return ro.objectToShape(this,{position:e,color:t,size:i,heightAxis:r,depthAxis:s,name:o}),this}addOctahedron(e,t,i,r,s,o){return $c.objectToShape(this,{position:e,color:t,size:i,heightAxis:r,depthAxis:s,name:o}),this}addTetrahedron(e,t,i,r,s,o){return Wc.objectToShape(this,{position:e,color:t,size:i,heightAxis:r,depthAxis:s,name:o}),this}addText(e,t,i,r){return Yc.objectToShape(this,{position:e,color:t,size:i,text:r}),this}addPoint(e,t,i){return tl.objectToShape(this,{position:e,color:t,name:i}),this}addWideline(e,t,i,r,s){return this.parameters.linewidth=r,nl.objectToShape(this,{position1:e,position2:t,color:i,name:s}),this}addLabel(e,t,i,r){return console.warn("Shape.addLabel is deprecated, use .addText instead"),this.addText(e,t,i,r)}getBufferList(){let e=[];return Yv.forEach(t=>{this._primitiveData[t.getShapeKey("color")].length&&e.push(t.bufferFromShape(this,this.parameters))}),this.bufferList.concat(e)}dispose(){this.bufferList.forEach(function(e){e.dispose()}),this.bufferList.length=0,Yv.forEach(e=>{Object.keys(e.fields).forEach(t=>{this._primitiveData[e.getShapeKey(t)].length=0}),this._primitiveData[e.getShapeKey("name")].length=0})}get center(){return this._center||(this._center=this.boundingBox.getCenter(new W)),this._center}get type(){return"Shape"}},Sg=class extends el{constructor(e,t,i){Array.isArray(e)||(e=[e]),super(e,t,i),this.type="buffer",this.parameters=Object.assign({},this.parameters,{colorScheme:null,colorScale:null,colorValue:null,colorDomain:null,colorMode:null}),this.buffer=e,this.init(i)}init(e){super.init(e),this.build()}create(){this.bufferList.push.apply(this.bufferList,this.buffer)}attach(e){this.bufferList.forEach(t=>{this.viewer.add(t),t.setParameters(this.getBufferParams())}),this.setVisibility(this.visible),e()}},Am=new qe,yT=new Lt,Ms=class extends Jr{constructor(e,t={},i){super(function(l,c){let u=c.attributes.position.array,d=c.index?c.index.array:void 0,f=l.position.length/3,m=u.length/3,p=f*m,_=new Float32Array(3*p),y=new Float32Array(3*p),g=new Float32Array(3*p),b;return d&&(b=bs(f*d.length,p)),{position:_,color:g,index:b,normal:y,primitiveId:l.primitiveId||jx(f,m),picking:l.picking}}(e,i),t),this.updateNormals=!1;let r=i.attributes.position.array,s=i.attributes.normal.array,o=i.index?i.index.array:void 0;this.geoPosition=r,this.geoNormal=s,this.geoIndex=o,this.positionCount=e.position.length/3,this.geoPositionCount=r.length/3,this.transformedGeoPosition=new Float32Array(3*this.geoPositionCount),this.transformedGeoNormal=new Float32Array(3*this.geoPositionCount);let a=this.geometry.attributes;if(this.meshPosition=a.position.array,this.meshColor=a.color.array,this.meshNormal=a.normal.array,this.setAttributes(e),o){let l=this.geometry.getIndex();if(!l)return void we.error("Index is null");this.meshIndex=l.array,this.makeIndex()}}setAttributes(e={},t=!1){let i=this.geometry.attributes,r,s,o,a,l,c,u,d,f,m=this.updateNormals;e.position&&(r=e.position,o=this.geoPosition,u=this.meshPosition,l=this.transformedGeoPosition,i.position.needsUpdate=!0,(m||t)&&(a=this.geoNormal,f=this.meshNormal,c=this.transformedGeoNormal,i.normal.needsUpdate=!0)),e.color&&(s=e.color,d=this.meshColor,i.color.needsUpdate=!0);let p=this.positionCount,_=this.geoPositionCount;for(let y=0;y 0.0 ){ +cameraPos = rayDirection * posT + rayOrigin; +interior = true; +flag2 = true; +} +#else +if( calcDepth( cameraPos ) <= 0.0 ){ +cameraPos = rayDirection * posT + rayOrigin; +interior = true; +} +#endif +cameraNormal = normalize( cameraPos - cameraSpherePos ); +cameraNormal *= float(!interior) * 2.0 - 1.0; +return !interior; +} +void main(void){ +bool flag = Impostor( cameraPos, cameraNormal ); +#ifdef NEAR_CLIP +if( calcClip( cameraPos ) > 0.0 ) +discard; +#endif +gl_FragDepthEXT = calcDepth( cameraPos ); +if( !flag ){ +#ifdef NEAR_CLIP +if( flag2 ){ +gl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( clipNear - 0.5 ) ) ) + ( 0.0000001 / vRadius ) ); +}else if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius ); +} +#else +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius ); +} +#endif +} +if (gl_FragDepthEXT < 0.0) +discard; +if (gl_FragDepthEXT > 1.0) +discard; +#ifdef PICKING +if( opacity < 0.3 ) +discard; +gl_FragColor = vec4( vPickingColor, objectId ); +#else +vec3 vNormal = cameraNormal; +vec3 vViewPosition = -cameraPos; +vec4 diffuseColor = vec4( diffuse, opacity ); +ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); +vec3 totalEmissiveLight = emissive; +#include color_fragment +#include roughnessmap_fragment +#include metalnessmap_fragment +#include normal_fragment_begin +#include lights_physical_fragment +#include lights_fragment_begin +#include lights_fragment_end +vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight; +if( interior ){ +#ifdef USE_INTERIOR_COLOR +outgoingLight.xyz = interiorColor; +#else +#ifdef DIFFUSE_INTERIOR +outgoingLight.xyz = vColor; +#endif +#endif +outgoingLight.xyz *= 1.0 - interiorDarkening; +} +gl_FragColor = vec4( outgoingLight, diffuseColor.a ); +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +#endif +}`);var bd=class extends Pr{constructor(e,t,i={}){super(t,i),this.index=bs(this.indexSize,this.attributeSize),this.makeIndex(),this.initIndex(this.index),this.addAttributes({mapping:{type:e,value:null}}),this.setAttributes({primitiveId:au(this.size)})}get attributeSize(){return this.size*this.mappingSize}get indexSize(){return this.size*this.mappingIndicesSize}addAttributes(e){let t={};for(let i in e){let r=e[i];t[i]={type:r.type,value:null}}super.addAttributes(t)}getAttributeIndex(e){return 3*e*this.mappingSize}setAttributes(e){e&&!e.position&&e.position1&&e.position2&&(e.position=_s(e.position1,e.position2));let t=this.size,i=this.mappingSize,r=this.geometry.attributes,s,o,a,l,c,u,d;for(let f in e)if(f!=="index"&&f!=="picking"){o=e[f],s=r[f],a=s.itemSize,l=s.array;for(let m=0;m0&&this.parameters.alphaTest<=1&&(t.USE_ALPHATEST=1),t}setUniforms(e){e&&e.edgeBleach!==void 0&&(this.makeTexture(),e.map=this.tex),super.setUniforms(e)}dispose(){super.dispose(),this.tex&&this.tex.dispose()}};cr.add("point",Sd);var Ag=class extends el{constructor(e,t,i){super(e,t,i),this.type="dot",this.parameters=Object.assign({thresholdType:{type:"select",rebuild:!0,options:{value:"value",sigma:"sigma"}},thresholdMin:{type:"number",precision:3,max:1/0,min:-1/0,rebuild:!0},thresholdMax:{type:"number",precision:3,max:1/0,min:-1/0,rebuild:!0},thresholdOut:{type:"boolean",rebuild:!0},dotType:{type:"select",rebuild:!0,options:{"":"",sphere:"sphere",point:"point"}},radiusType:{type:"select",options:{"":"",value:"value","abs-value":"abs-value","value-min":"value-min",deviation:"deviation",size:"size"}},radius:{type:"number",precision:3,max:10,min:.001,property:"size"},scale:{type:"number",precision:3,max:10,min:.001},sphereDetail:!0,disableImpostor:!0,pointSize:{type:"number",precision:1,max:100,min:0,buffer:!0},sizeAttenuation:{type:"boolean",buffer:!0},sortParticles:{type:"boolean",rebuild:!0},useTexture:{type:"boolean",buffer:!0},alphaTest:{type:"range",step:.001,max:1,min:0,buffer:!0},forceTransparent:{type:"boolean",buffer:!0},edgeBleach:{type:"range",step:.001,max:1,min:0,buffer:!0}},this.parameters,{colorScheme:{type:"select",update:"color",options:{"":"",value:"value",uniform:"uniform",random:"random"}}}),e instanceof Hi?(this.surface=void 0,this.volume=new qr(e)):(this.surface=e,this.volume=void 0),this.init(i)}init(e){var t=e||{};t.colorScheme=U(t.colorScheme,"uniform"),t.colorValue=U(t.colorValue,14540253),this.thresholdType=U(t.thresholdType,"sigma"),this.thresholdMin=U(t.thresholdMin,2),this.thresholdMax=U(t.thresholdMax,1/0),this.thresholdOut=U(t.thresholdOut,!1),this.dotType=U(t.dotType,"point"),this.radius=U(t.radius,.1),this.scale=U(t.scale,1),this.pointSize=U(t.pointSize,1),this.sizeAttenuation=U(t.sizeAttenuation,!0),this.sortParticles=U(t.sortParticles,!1),this.useTexture=U(t.useTexture,!1),this.alphaTest=U(t.alphaTest,.5),this.forceTransparent=U(t.forceTransparent,!1),this.edgeBleach=U(t.edgeBleach,0),super.init(t),this.build()}attach(e){this.bufferList.forEach(t=>{this.viewer.add(t)}),this.setVisibility(this.visible),e()}create(){var e={};if(this.volume){var t,i,r=this.volume;this.thresholdType==="sigma"?(t=r.getValueForSigma(this.thresholdMin),i=r.getValueForSigma(this.thresholdMax)):(t=this.thresholdMin,i=this.thresholdMax),r.setFilter(t,i,this.thresholdOut),Object.assign(e,{position:r.getDataPosition(),color:r.getDataColor(this.getColorParams())}),this.dotType==="sphere"&&Object.assign(e,{radius:r.getDataSize(this.radius,this.scale),picking:r.getDataPicking()})}else{var s=this.surface;Object.assign(e,{position:s.getPosition(),color:s.getColor(this.getColorParams())}),this.dotType==="sphere"&&Object.assign(e,{radius:s.getSize(this.radius,this.scale),picking:s.getPicking()})}this.dotType==="sphere"?this.dotBuffer=new la(e,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!1})):this.dotBuffer=new Sd(e,this.getBufferParams({pointSize:this.pointSize,sizeAttenuation:this.sizeAttenuation,sortParticles:this.sortParticles,useTexture:this.useTexture,alphaTest:this.alphaTest,forceTransparent:this.forceTransparent,edgeBleach:this.edgeBleach})),this.bufferList.push(this.dotBuffer)}update(e={}){if(this.bufferList.length===0)return;let t={};e.color&&(this.volume?Object.assign(t,{color:this.volume.getDataColor(this.getColorParams())}):Object.assign(t,{color:this.surface.getColor(this.getColorParams())})),this.dotType==="sphere"&&(e.radius||e.scale)&&(this.volume?Object.assign(t,{radius:this.volume.getDataSize(this.radius,this.scale)}):Object.assign(t,{radius:this.surface.getSize(this.radius,this.scale)})),this.dotBuffer.setAttributes(t)}setParameters(e,t={},i){return e&&e.thresholdType!==void 0&&this.volume instanceof Hi&&(this.thresholdType==="value"&&e.thresholdType==="sigma"?(this.thresholdMin=this.volume.getSigmaForValue(this.thresholdMin),this.thresholdMax=this.volume.getSigmaForValue(this.thresholdMax)):this.thresholdType==="sigma"&&e.thresholdType==="value"&&(this.thresholdMin=this.volume.getValueForSigma(this.thresholdMin),this.thresholdMax=this.volume.getValueForSigma(this.thresholdMax)),this.thresholdType=e.thresholdType),e&&e.radiusType!==void 0&&(e.radiusType==="radius"?this.radius=.1:this.radius=parseFloat(e.radiusType),t.radius=!0,this.dotType!=="sphere"||ys&&!this.disableImpostor||(i=!0)),e&&e.radius!==void 0&&(t.radius=!0,this.dotType!=="sphere"||ys&&!this.disableImpostor||(i=!0)),e&&e.scale!==void 0&&(t.scale=!0,this.dotType!=="sphere"||ys&&!this.disableImpostor||(i=!0)),super.setParameters(e,t,i),this}};zt.add("shader/Image.vert",`uniform float clipRadius; +uniform vec3 clipCenter; +varying vec2 vUv; +#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING ) +varying vec3 vViewPosition; +#endif +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +void main() { +#include begin_vertex +#include project_vertex +vUv = uv; +#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING ) +vViewPosition = -mvPosition.xyz; +#endif +#if defined( RADIUS_CLIP ) +vClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz; +#endif +}`),zt.add("shader/Image.frag",`uniform sampler2D map; +uniform float opacity; +uniform vec2 mapSize; +uniform float clipNear; +uniform float clipRadius; +varying vec2 vUv; +#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING ) +varying vec3 vViewPosition; +#endif +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +#if defined( PICKING ) +uniform sampler2D pickingMap; +uniform float objectId; +#else +#include fog_pars_fragment +#endif +#if defined( CUBIC_INTERPOLATION ) +#if defined( CATMULROM_FILTER ) || defined( MITCHELL_FILTER ) +#if defined( CATMULROM_FILTER ) +const float B = 0.0; +const float C = 0.5; +#elif defined( MITCHELL_FILTER ) +const float B = 0.333; +const float C = 0.333; +#endif +float applyFilter( float x ){ +float f = x; +if( f < 0.0 ){ +f = -f; +} +if( f < 1.0 ){ +return ( ( 12.0 - 9.0 * B - 6.0 * C ) * ( f * f * f ) + +( -18.0 + 12.0 * B + 6.0 *C ) * ( f * f ) + +( 6.0 - 2.0 * B ) ) / 6.0; +}else if( f >= 1.0 && f < 2.0 ){ +return ( ( -B - 6.0 * C ) * ( f * f * f ) ++ ( 6.0 * B + 30.0 * C ) * ( f *f ) + +( - ( 12.0 * B ) - 48.0 * C ) * f + +8.0 * B + 24.0 * C ) / 6.0; +}else{ +return 0.0; +} +} +#elif defined( BSPLINE_FILTER ) +float applyFilter( float x ){ +float f = x; +if( f < 0.0 ){ +f = -f; +} +if( f >= 0.0 && f <= 1.0 ){ +return ( 2.0 / 3.0 ) + ( 0.5 ) * ( f * f * f ) - ( f * f ); +}else if( f > 1.0 && f <= 2.0 ){ +return 1.0 / 6.0 * pow( ( 2.0 - f ), 3.0 ); +} +return 1.0; +} +#else +float applyFilter( float x ){ +return 1.0; +} +#endif +vec4 biCubic( sampler2D tex, vec2 texCoord ){ +vec2 texelSize = 1.0 / mapSize; +texCoord -= texelSize / 2.0; +vec4 nSum = vec4( 0.0 ); +float nDenom = 0.0; +vec2 cell = fract( texCoord * mapSize ); +for( float m = -1.0; m <= 2.0; ++m ){ +for( float n = -1.0; n <= 2.0; ++n ){ +vec4 vecData = texture2D( +tex, texCoord + texelSize * vec2( m, n ) +); +float c = applyFilter( m - cell.x ) * applyFilter( -n + cell.y ); +nSum += vecData * c; +nDenom += c; +} +} +return nSum / nDenom; +} +#endif +void main(){ +#include nearclip_fragment +#include radiusclip_fragment +#if defined( CUBIC_INTERPOLATION ) +gl_FragColor = biCubic( map, vUv ); +#else +gl_FragColor = texture2D( map, vUv ); +#endif +#if defined( PICKING ) +if( gl_FragColor.a < 0.3 ) +discard; +gl_FragColor = vec4( texture2D( pickingMap, vUv ).xyz, objectId ); +#else +if( gl_FragColor.a < 0.01 ) +discard; +gl_FragColor.a *= opacity; +#include fog_fragment +#endif +}`);var QU=new Uint16Array([0,1,2,1,3,2]),ez=new Float32Array([0,1,0,0,1,1,1,0]),tz=Object.assign({filter:"nearest",forceTransparent:!0},ki),nz=Object.assign({filter:{updateShader:!0,uniform:!0}},cl),Jb=class extends Pr{constructor(e,t){super({position:e.position,index:QU,picking:e.picking},t),this.parameterTypes=nz,this.alwaysTransparent=!0,this.hasWireframe=!1,this.vertexShader="Image.vert",this.fragmentShader="Image.frag";let{imageData:i,width:r,height:s}=e,o=new pc(i,r,s);o.flipY=!0,this.tex=o;let a=i.length,l=new Uint8Array(a);for(let u=0;u>16&255,l[u+1]=d>>8&255,l[u+2]=255&d}let c=new pc(l,r,s);c.flipY=!0,c.minFilter=en,c.magFilter=en,this.pickingTex=c,this.addUniforms({map:{value:o},pickingMap:{value:c},mapSize:{value:new Et(r,s)}}),this.geometry.setAttribute("uv",new gn(ez,2))}get defaultParameters(){return tz}getDefines(e){let t=super.getDefines(e),i=this.parameters.filter;return i.startsWith("cubic")&&(t.CUBIC_INTERPOLATION=1,i.endsWith("bspline")?t.BSPLINE_FILTER=1:i.endsWith("catmulrom")?t.CATMULROM_FILTER=1:i.endsWith("mitchell")&&(t.MITCHELL_FILTER=1)),t}updateTexture(){let e=this.tex,t=this.parameters.filter;t.startsWith("cubic")?(e.minFilter=en,e.magFilter=en):t==="linear"?(e.minFilter=li,e.magFilter=li):(e.minFilter=en,e.magFilter=en),e.needsUpdate=!0,this.pickingTex.needsUpdate=!0}makeMaterial(){super.makeMaterial(),this.updateTexture();let e=this.material;e.uniforms.map.value=this.tex,e.blending=hs,e.needsUpdate=!0;let t=this.wireframeMaterial;t.uniforms.map.value=this.tex,t.blending=hs,t.needsUpdate=!0;let i=this.pickingMaterial;i.uniforms.map.value=this.tex,i.uniforms.pickingMap.value=this.pickingTex,i.blending=hs,i.needsUpdate=!0}setUniforms(e){e&&e.filter!==void 0&&(this.updateTexture(),e.map=this.tex),super.setUniforms(e)}},Qb=class{constructor(e,t){let i=t||{};this.dimension=U(i.dimension,"x"),this.positionType=U(i.positionType,"percent"),this.position=U(i.position,30),this.thresholdType=U(i.thresholdType,"sigma"),this.thresholdMin=U(i.thresholdMin,-1/0),this.thresholdMax=U(i.thresholdMax,1/0),this.normalize=U(i.normalize,!1),this.volume=e}getPositionFromCoordinate(e){let t=this.dimension,i=this.volume,r=i.matrix,s=new W().setFromMatrixPosition(r)[t],o=new W().setFromMatrixScale(r)[t],a;return a=t==="x"?i.nx:t==="y"?i.ny:i.nz,Math.round(((e-s)/(a/100)+1)/o)}getData(e){e=e||{};let t=this.volume,i=t.data,r=t.matrix,s;function o(z){return Math.round(z/100*(s-1))}function a(z,L,F,te){return 3*(F*t.ny*t.nx+L*t.nx+z)+te}s=this.positionType==="coordinate"?this.getPositionFromCoordinate(this.position):this.position;let l=new Float32Array(12),c=new W,u,d,f,m,p,_=0,y=0,g=0,b=t.nx,h=t.ny,v=t.nz;function S(z,L,F,te){c.set(z,L,F).applyMatrix4(r).toArray(l,te)}this.dimension==="x"?(f=o(t.nx),m=t.ny-1,p=t.nz-1,u=t.nz,d=t.ny,_=f,b=_+1,S(f,0,0,0),S(f,m,0,3),S(f,0,p,6),S(f,m,p,9)):this.dimension==="y"?(f=t.nx-1,m=o(t.ny),p=t.nz-1,u=t.nz,d=t.nx,y=m,h=y+1,S(0,m,0,0),S(f,m,0,3),S(0,m,p,6),S(f,m,p,9)):this.dimension==="z"&&(f=t.nx-1,m=t.ny-1,p=o(t.nz),u=t.nx,d=t.ny,g=p,v=g+1,S(0,0,p,0),S(0,m,p,3),S(f,0,p,6),S(f,m,p,9));let x=0,w=0,A=new Uint8Array(u*d*4),M=new Float32Array(u*d),T,R;this.thresholdType==="sigma"?(T=t.getValueForSigma(this.thresholdMin),R=t.getValueForSigma(this.thresholdMax)):(T=this.thresholdMin,R=this.thresholdMax);let C=Object.assign({},e.colorParams,{volume:t});this.normalize&&(C.domain=[0,1]);let P=Dt.getScheme(C),E=new Float32Array(3),I=P.getScale(),O,D=0,N=0;if(this.normalize){D=1/0,O=-1/0;for(let z=y;zO&&(O=te)}N=O-D}for(let z=y;zT&&Q{this.viewer.add(t)}),this.setVisibility(this.visible),e()}create(){let e=new Qb(this.volume,{positionType:this.positionType,position:this.position,dimension:this.dimension,thresholdType:this.thresholdType,thresholdMin:this.thresholdMin,thresholdMax:this.thresholdMax,normalize:this.normalize}),t=new Jb(e.getData({colorParams:this.getColorParams()}),this.getBufferParams({filter:this.filter}));this.bufferList.push(t)}};function Zv(n){we.error(`makeRepresentation: representation type ${n} unknown`)}var Tw={name:"some element",status:""},Mg=class{constructor(e,t={}){this.stage=e,this.signals={statusChanged:new Pt.Signal,nameChanged:new Pt.Signal,disposed:new Pt.Signal},this.parameters=or(t,this.defaultParameters),this.uuid=vw()}get defaultParameters(){return Tw}get name(){return this.parameters.name}setStatus(e){return this.parameters.status=e,this.signals.statusChanged.dispatch(e),this}setName(e){return this.parameters.name=e,this.signals.nameChanged.dispatch(e),this}dispose(){this.signals.disposed.dispatch()}},iz=Object.assign({visible:!0},Tw),t2=class extends Mg{constructor(e,t,i={},r){super(e,Object.assign({name:t.type},i)),this.parent=r,this.signals=Object.assign({visibilityChanged:new Pt.Signal,parametersChanged:new Pt.Signal},this.signals),this.setRepresentation(t)}get defaultParameters(){return iz}get visible(){return this.parameters.visible}get type(){return"representation"}getType(){return this.repr.type}setRepresentation(e){this._disposeRepresentation(),this.repr=e,this.stage.tasks.listen(this.repr.tasks),this.updateVisibility()}_disposeRepresentation(){this.repr&&(this.stage.tasks.unlisten(this.repr.tasks),this.repr.dispose())}dispose(){this.parent&&this.parent.hasRepresentation(this)?this.parent.removeRepresentation(this):(this._disposeRepresentation(),this.signals.disposed.dispatch())}setVisibility(e){return this.parameters.visible=e,this.updateVisibility(),this.signals.visibilityChanged.dispatch(this.parameters.visible),this}getVisibility(){return this.parent?this.parent.parameters.visible&&this.parameters.visible:this.parameters.visible}toggleVisibility(){return this.setVisibility(!this.parameters.visible)}updateVisibility(){this.repr.setVisibility(this.getVisibility())}update(e){return this.repr.update(e),this}build(e){return this.repr.build(e),this}setSelection(e){let t=this.repr;return t.setSelection&&t.setSelection(e),this}setParameters(e){return this.repr.setParameters(e),this.signals.parametersChanged.dispatch(this.repr.getParameters()),this}getParameters(){return this.repr.getParameters()}setColor(e){return this.repr.setColor(e),this}},vc=new qe,rz=new W,dI={name:"",status:"",visible:!0},Jc=class{constructor(e,t,i={}){this.stage=e,this.object=t,this.signals={representationAdded:new Pt.Signal,representationRemoved:new Pt.Signal,visibilityChanged:new Pt.Signal,matrixChanged:new Pt.Signal,statusChanged:new Pt.Signal,nameChanged:new Pt.Signal,disposed:new Pt.Signal},this.reprList=[],this.annotationList=[],this.matrix=new qe,this.position=new W,this.quaternion=new Xn,this.scale=new W(1,1,1),this.transform=new qe,this.parameters=or(i,this.defaultParameters),this.uuid=vw(),this.viewer=e.viewer,this.controls=new Ib(this)}get defaultParameters(){return dI}get name(){return this.parameters.name}get status(){return this.parameters.status}get visible(){return this.parameters.visible}setPosition(e){return Array.isArray(e)?this.position.fromArray(e):this.position.copy(e),this.updateMatrix(),this}setRotation(e){if(Array.isArray(e))if(e.length===3){let t=new Ba().fromArray(e);this.quaternion.setFromEuler(t)}else this.quaternion.fromArray(e);else e instanceof Ba?this.quaternion.setFromEuler(e):this.quaternion.copy(e);return this.updateMatrix(),this}setScale(e){return this.scale.set(e,e,e),this.updateMatrix(),this}setTransform(e){return this.transform.copy(e),this.updateMatrix(),this}updateMatrix(){let e=this.getCenterUntransformed(rz);this.matrix.makeTranslation(-e.x,-e.y,-e.z),vc.makeRotationFromQuaternion(this.quaternion),this.matrix.premultiply(vc),vc.makeScale(this.scale.x,this.scale.y,this.scale.z),this.matrix.premultiply(vc);let t=this.position;vc.makeTranslation(t.x+e.x,t.y+e.y,t.z+e.z),this.matrix.premultiply(vc),this.matrix.premultiply(this.transform),this.updateRepresentationMatrices(),this.stage.viewer.updateBoundingBox(),this.signals.matrixChanged.dispatch(this.matrix)}updateRepresentationMatrices(){this.reprList.forEach(e=>{e.setParameters({matrix:this.matrix})})}addAnnotation(e,t,i){let r=new Pb(this,e,t,i);return this.annotationList.push(r),r}eachAnnotation(e){this.annotationList.slice().forEach(e)}removeAnnotation(e){let t=this.annotationList.indexOf(e);t!==-1&&(this.annotationList.splice(t,1),e.dispose())}removeAllAnnotations(){this.eachAnnotation(e=>e.dispose()),this.annotationList.length=0}_addRepresentation(e,t,i,r=!1){let s=i||{},o=this.stage.getParameters();s.matrix=this.matrix.clone(),s.quality=s.quality||o.quality,s.disableImpostor=U(s.disableImpostor,!o.impostor),s.useWorker=U(s.useWorker,o.workerDefault),s.visible=U(s.visible,!0);let a=Object.assign({},s,{visible:this.parameters.visible&&s.visible}),l=function(u,d,f,m){var p;if(Le&&we.time("makeRepresentation "+u),d instanceof Er){if(!(p=on.get(u)))return void Zv(u)}else if(d instanceof Zc)if(u==="surface")p=vd;else{if(u!=="dot")return void Zv(u);p=Ag}else if(d instanceof Hi)if(u==="surface")p=vd;else if(u==="dot")p=Ag;else{if(u!=="slice")return void Zv(u);p=e2}else if(d instanceof Yb)p=Sg,d=d.getBufferList();else{if(u!=="buffer")return void we.error("makeRepresentation: object "+d+" unknown");p=Sg}let _=new p(d,f,m);return Le&&we.timeEnd("makeRepresentation "+u),_}(e,t,this.viewer,a),c=new t2(this.stage,l,s,this);return r||(this.reprList.push(c),this.signals.representationAdded.dispatch(c)),c}addBufferRepresentation(e,t){return this._addRepresentation.call(this,"buffer",e,t)}hasRepresentation(e){return this.reprList.indexOf(e)!==-1}eachRepresentation(e){this.reprList.slice().forEach(e)}removeRepresentation(e){let t=this.reprList.indexOf(e);t!==-1&&(this.reprList.splice(t,1),e.dispose(),this.signals.representationRemoved.dispatch(e))}updateRepresentations(e){this.reprList.forEach(t=>t.update(e)),this.stage.viewer.requestRender()}removeAllRepresentations(){this.eachRepresentation(e=>e.dispose())}dispose(){this.removeAllAnnotations(),this.removeAllRepresentations(),this.reprList.length=0,this.signals.disposed.dispatch()}setVisibility(e){return this.parameters.visible=e,this.eachRepresentation(t=>t.updateVisibility()),this.eachAnnotation(t=>t.updateVisibility()),this.signals.visibilityChanged.dispatch(e),this}setStatus(e){return this.parameters.status=e,this.signals.statusChanged.dispatch(e),this}setName(e){return this.parameters.name=e,this.signals.nameChanged.dispatch(e),this}getBox(...e){return this.getBoxUntransformed(...e).clone().applyMatrix4(this.matrix)}getCenter(...e){return this.getCenterUntransformed(...e).clone().applyMatrix4(this.matrix)}getZoom(...e){return this.stage.getZoomForBox(this.getBox(...e))}getBoxUntransformed(...e){return new sn}getCenterUntransformed(...e){return this.getBoxUntransformed().getCenter(new W)}autoView(e){this.stage.animationControls.zoomMove(this.getCenter(),this.getZoom(),U(e,0))}},Cg=class{constructor(e=[]){this.list=e;let t=e.length;for(let i=0;i0?this.list[0]:void 0}forEach(e){return this.list.forEach(e),this}dispose(){return this.forEach(e=>e.dispose())}},Eg=class extends Cg{setParameters(e){return this.forEach(t=>t.setParameters(e))}setVisibility(e){return this.forEach(t=>t.setVisibility(e))}setSelection(e){return this.forEach(t=>t.setSelection(e))}setColor(e){return this.forEach(t=>t.setColor(e))}update(e){return this.forEach(t=>t.update(e))}build(e){return this.forEach(t=>t.build(e))}dispose(e){return this.forEach(t=>t.dispose())}},sz=Object.assign({defaultStep:1,defaultTimeout:50,defaultInterpolateType:"",defaultInterpolateStep:5,defaultMode:"loop",defaultDirection:"forward",initialFrame:0},Tw),n2=class extends Mg{constructor(e,t,i={}){super(e,Object.assign({name:t.name},i)),this.trajectory=t,this.signals=Object.assign(this.signals,{frameChanged:new Pt.Signal,playerChanged:new Pt.Signal,countChanged:new Pt.Signal,parametersChanged:new Pt.Signal}),t.signals.frameChanged.add(r=>{this.signals.frameChanged.dispatch(r)}),t.signals.playerChanged.add(r=>{this.signals.playerChanged.dispatch(r)}),t.signals.countChanged.add(r=>{this.signals.countChanged.dispatch(r)}),i.initialFrame!==void 0&&this.setFrame(i.initialFrame)}get defaultParameters(){return sz}get type(){return"trajectory"}setFrame(e){this.trajectory.setFrame(e)}setParameters(e={}){this.trajectory.setParameters(e),this.signals.parametersChanged.dispatch(e)}dispose(){this.trajectory.dispose(),super.dispose()}},Tg=class{constructor(e,t){this.name=e,this.path=t,this.coordinates=[],this.boxes=[],this.times=[],this.timeOffset=0,this.deltaTime=1}get type(){return"Frames"}},Pg=class{constructor(e,t){let i,r;if(this.A=new Ht(3,3),this.W=new Ht(1,3),this.U=new Ht(3,3),this.V=new Ht(3,3),this.VH=new Ht(3,3),this.R=new Ht(3,3),this.tmp=new Ht(3,3),this.c=new Ht(3,3),e instanceof Er)i=e.atomCount;else{if(!(e instanceof Float32Array))return;i=e.length/3}if(t instanceof Er)r=t.atomCount;else{if(!(t instanceof Float32Array))return;r=t.length/3}let s=Math.min(i,r),o=new Ht(3,s),a=new Ht(3,s);this.coords1t=new Ht(s,3),this.coords2t=new Ht(s,3),this.transformationMatrix=new qe,this.c.data.set([1,0,0,0,1,0,0,0,-1]),this.prepCoords(e,o,s,!1),this.prepCoords(t,a,s,!1),this._superpose(o,a)}_superpose(e,t){this.mean1=_b(e),this.mean2=_b(t),vb(e,this.mean1),vb(t,this.mean2),Kr(this.coords1t,e),Kr(this.coords2t,t),Ym(this.A,this.coords2t,this.coords1t),iI(this.A,this.W,this.U,this.V),function(f,m){let p=f.data,_=m.data,y=p[4],g=p[8],b=p[5],h=p[7],v=p[0],S=v*y,x=v*b,w=p[3],A=p[1],M=w*A,T=p[2],R=w*T,C=p[6],P=C*A,E=C*T,I=1/(S*g-x*h-M*g+R*h+P*b-E*y);_[0]=(y*g-b*h)*I,_[1]=-(A*g-T*h)*I,_[2]=-(-A*b+T*y)*I,_[3]=-(w*g-b*C)*I,_[4]=(v*g-E)*I,_[5]=-(x-R)*I,_[6]=-(-w*h+y*C)*I,_[7]=-(v*h-P)*I,_[8]=(S-M)*I}(this.V,this.VH),$v(this.R,this.U,this.VH),function(f){let m=f.data;return m[0]*m[4]*m[8]-m[0]*m[5]*m[7]-m[3]*m[1]*m[8]+m[3]*m[2]*m[7]+m[6]*m[1]*m[5]-m[6]*m[2]*m[4]}(this.R)<0&&(Le&&we.log("R not a right handed system"),$v(this.tmp,this.c,this.VH),$v(this.R,this.U,this.tmp));let i=new Ht(4,4),r=new Ht(4,4),s=new Ht(4,4),o=new Ht(4,4),a=new Ht(4,4),l=new Ht(4,4),c=this.R.data,u=this.mean1,d=this.mean2;o.data.set([1,0,0,-u[0],0,1,0,-u[1],0,0,1,-u[2],0,0,0,1]),a.data.set([c[0],c[1],c[2],0,c[3],c[4],c[5],0,c[6],c[7],c[8],0,0,0,0,1]),l.data.set([1,0,0,d[0],0,1,0,d[1],0,0,1,d[2],0,0,0,1]),Kr(r,o),Ym(i,a,r),Kr(s,i),Ym(r,l,s),Kr(i,r),this.transformationMatrix.elements=i.data}prepCoords(e,t,i,r){let s=0,o=t.data,a=3,l=3*i;if(r&&(l=4*i,a=4),e instanceof Er)e.eachAtom(function(c){s{r!==this&&this.pause()},this);let i=U(e.frameCount,1);this.traj=e,this.parameters=or(t,oz),this.parameters.end=Math.min(U(t.end,i-1),i-1),this.parameters.step=U(t.step,Math.ceil((i+1)/100)),this._currentFrame=this.parameters.start,this._direction=this.parameters.direction==="bounce"?"forward":this.parameters.direction,e.signals.countChanged.add(r=>{this.parameters.end=Math.min(U(this.parameters.end,r-1),r-1)},this),this._animate=this._animate.bind(this)}get isRunning(){return this._run}setParameters(e={}){RP(this.parameters,e),e.direction!==void 0&&this.parameters.direction!=="bounce"&&(this._direction=this.parameters.direction)}_animate(){if(!this._run)return;this._currentTime=window.performance.now();let e=this._currentTime-this._previousTime,t=this.parameters.interpolateType?this.parameters.interpolateStep:1,i=this.parameters.timeout/t,r=this.traj;if(r&&r.frameCount&&!r.inProgress&&e>=i)if(this.parameters.interpolateType)if(this._currentStep>this.parameters.interpolateStep&&(this._currentStep=1),this._currentStep===1&&(this._currentFrame=this._nextInterpolated()),r.hasFrame(this._currentFrame)){this._currentStep+=1;let s=this._currentStep/(this.parameters.interpolateStep+1),[o,a,l,c]=this._currentFrame;r.setFrameInterpolated(o,a,l,c,s,this.parameters.interpolateType),this._previousTime=this._currentTime}else r.loadFrame(this._currentFrame);else{let s=this._next();r.hasFrame(s)?(r.setFrame(s),this._previousTime=this._currentTime):r.loadFrame(s)}window.requestAnimationFrame(this._animate)}_next(){let e=this.parameters,t;return t=this._direction==="forward"?this.traj.currentFrame+e.step:this.traj.currentFrame-e.step,(t>e.end||t=e.end?i=e.start:e.direction==="backward"&&t<=e.start&&(i=e.end),this.traj.setFrame(i),this._run=!0,this._animate(),this.signals.startedRunning.dispatch()}}pause(){this._run=!1,this.signals.haltedRunning.dispatch()}stop(){this.pause(),this.traj.setFrame(this.parameters.start)}},Qc=class{constructor(e,t,i={}){this.signals={countChanged:new Pt.Signal,frameChanged:new Pt.Signal,playerChanged:new Pt.Signal},this.frameCache={},this.loadQueue={},this.boxCache={},this.pathCache={},this.frameCacheSize=0,this._frameCount=0,this._currentFrame=-1,this._disposed=!1,this.deltaTime=U(i.deltaTime,0),this.timeOffset=U(i.timeOffset,0),this.centerPbc=U(i.centerPbc,!1),this.removePbc=U(i.removePbc,!1),this.removePeriodicity=U(i.removePeriodicity,!1),this.superpose=U(i.superpose,!1),this.name=e.replace(/^.*[\\/]/,""),this.trajPath=e,this.selection=new tn(U(i.sele,"backbone and not hydrogen")),this.selection.signals.stringChanged.add(()=>{this.selectionIndices=this.structure.getAtomIndices(this.selection),this._resetCache(),this._saveInitialCoords(),this.setFrame(this._currentFrame)})}get frameCount(){return this._frameCount}get currentFrame(){return this._currentFrame}_init(e){this.setStructure(e),this._loadFrameCount(),this.setPlayer(new i2(this))}_loadFrameCount(){}setStructure(e){this.structure=e,this.atomCount=e.atomCount,this.backboneIndices=this._getIndices(new tn("backbone and not hydrogen")),this._makeAtomIndices(),this._saveStructureCoords(),this.selectionIndices=this._getIndices(this.selection),this._resetCache(),this._saveInitialCoords(),this.setFrame(this._currentFrame)}_saveInitialCoords(){this.structure.hasCoords()?(this.initialCoords=new Float32Array(this.structureCoords),this._makeSuperposeCoords()):this.frameCache[0]?(this.initialCoords=new Float32Array(this.frameCache[0]),this._makeSuperposeCoords()):this.loadFrame(0,()=>this._saveInitialCoords())}_saveStructureCoords(){this.structureCoords=this.structure.getAtomData({what:{position:!0}}).position}setSelection(e){return this.selection.setString(e),this}_getIndices(e){let t=0,i=e.test,r=[];return i&&this.structure.eachAtom(s=>{i(s)&&r.push(t),t+=1}),r}_makeSuperposeCoords(){let e=3*this.selectionIndices.length;this.coords1=new Float32Array(e),this.coords2=new Float32Array(e);let t=this.initialCoords,i=this.coords2;for(let r=0;r!!this.frameCache[t]):!!this.frameCache[e]}setFrame(e,t){return e===void 0||(this.inProgress=!0,e===-1||this.frameCache[e]?(this._updateStructure(e),t&&t()):this.loadFrame(e,()=>{this._updateStructure(e),t&&t()})),this}_interpolate(e,t,i,r,s,o){let a=this.frameCache,l;l=o==="spline"?function(c,u,d,f,m){let p=c.length,_=new Float32Array(p);for(let y=0;y{this._interpolate(e,t,i,r,s,o),a&&a()}):(this._interpolate(e,t,i,r,s,o),a&&a()),this}loadFrame(e,t){Array.isArray(e)?e.forEach(i=>{this.loadQueue[i]||this.frameCache[i]||(this.loadQueue[i]=!0,this._loadFrame(i,()=>{delete this.loadQueue[i]}))}):this.loadQueue[e]||this.frameCache[e]||(this.loadQueue[e]=!0,this._loadFrame(e,()=>{delete this.loadQueue[e],t&&t()}))}_loadFrame(e,t){we.error("Trajectory._loadFrame not implemented",e,t)}_updateStructure(e){this._disposed?console.error("updateStructure: traj disposed"):(e===-1?this.structureCoords&&this.structure.updatePosition(this.structureCoords):this.structure.updatePosition(this.frameCache[e]),this.structure.trajectory={name:this.trajPath,frame:e},this._currentFrame=e,this.inProgress=!1,this.signals.frameChanged.dispatch(e))}_doSuperpose(e){let t=3*this.selectionIndices.length,i=this.coords1,r=this.coords2;for(let s=0;s0&&this.centerPbc){let s=[t[0],t[4],t[8]],o=function(a,l,c){return[Fv(l,c[0],3,0,a),Fv(l,c[1],3,1,a),Fv(l,c[2],3,2,a)]}(this.backboneIndices,i,s);(function(a,l,c){if(c[0]===0||c[8]===0||c[4]===0)return;let u=a.length,d=c[0],f=c[1],m=c[2],p=-l[0]+d+d/2,_=-l[1]+f+f/2,y=-l[2]+m+m/2;for(let g=0;g.5&&(o[u+d]-=a[3*d+d]*Math.round(f))}})(i,t,s)}this.removePbc&&function(s,o){if(o[0]===0||o[8]===0||o[4]===0)return;let a=s.length;for(let l=3;l.9*o[3*c+c])if(u>0)for(let d=0;d<3;++d)s[l+d]-=o[3*c+d];else for(let d=0;d<3;++d)s[l+d]+=o[3*c+d]}}(i,t)}this.selectionIndices.length>0&&this.coords1&&this.superpose&&this._doSuperpose(i),this.frameCache[e]=i,this.boxCache[e]=t,this.frameCacheSize+=1}_setFrameCount(e){e!==this._frameCount&&(this._frameCount=e,this.signals.countChanged.dispatch(e))}dispose(){this._resetCache(),this._disposed=!0,this.player&&this.player.stop()}setPlayer(e){this.player=e,this.signals.playerChanged.dispatch(e)}getFrameTime(e){return this.timeOffset+e*this.deltaTime}},r2=class extends Qc{constructor(e,t,i){let r=i||{};r.timeOffset=U(r.timeOffset,e.timeOffset),r.deltaTime=U(r.deltaTime,e.deltaTime),super("",t,r),this.name=e.name,this.path=e.path,this.frames=e.coordinates,this.boxes=e.boxes,this._init(t)}get type(){return"frames"}_makeAtomIndices(){this.structure.type==="StructureView"?this.atomIndices=this.structure.getAtomIndices():this.atomIndices=void 0}_loadFrame(e,t){let i,r=this.frames[e];if(this.atomIndices){let a=this.atomIndices,l=a.length;i=new Float32Array(3*l);for(let c=0;c{let o=i.response;if(!o)return void we.error(`empty arrayBuffer for '${r}'`);let a=new Int32Array(o,0,1)[0],l=new Float32Array(o,8,9),c=new Float32Array(o,44);this._process(e,l,c,a),typeof t=="function"&&t()},!1),i.send(s)}_loadFrameCount(){let e=new XMLHttpRequest,t=kv.getCountUrl(this.trajPath);e.open("GET",t,!0),e.addEventListener("load",()=>{this._setFrameCount(parseInt(e.response))},!1),e.send()}},a2=class extends Qc{constructor(e,t,i){super("",t,i),this.requestCallback=e,this._init(t)}get type(){return"callback"}_makeAtomIndices(){let e=[];if(this.structure.type==="StructureView"){let t=this.structure.getAtomIndices(),i=t.length,r=t[0],s=t[0];for(let o=1;o{this._process(i,r,s,o),typeof t=="function"&&t()},e,this.atomIndices)}_loadFrameCount(){this.requestCallback(e=>this._setFrameCount(e))}};Er.prototype.getView=function(n){return new Ig(this,n)};var Ig=class extends Er{constructor(e,t){super(),this.structure=e,this.selection=t,this.center=new W,this.boundingBox=new sn,this._bp=this.getBondProxy(),this._ap=this.getAtomProxy(),this._rp=this.getResidueProxy(),this._cp=this.getChainProxy(),this.selection&&this.selection.signals.stringChanged.add(this.refresh,this),this.structure.signals.refreshed.add(this.refresh,this),this.refresh()}init(){}get type(){return"StructureView"}get name(){return this.structure.name}get path(){return this.structure.path}get title(){return this.structure.title}get id(){return this.structure.id}get data(){return this.structure.data}get atomSetDict(){return this.structure.atomSetDict}get biomolDict(){return this.structure.biomolDict}get entityList(){return this.structure.entityList}get unitcell(){return this.structure.unitcell}get frames(){return this.structure.frames}get boxes(){return this.structure.boxes}get validation(){return this.structure.validation}get bondStore(){return this.structure.bondStore}get backboneBondStore(){return this.structure.backboneBondStore}get rungBondStore(){return this.structure.rungBondStore}get atomStore(){return this.structure.atomStore}get residueStore(){return this.structure.residueStore}get chainStore(){return this.structure.chainStore}get modelStore(){return this.structure.modelStore}get atomMap(){return this.structure.atomMap}get residueMap(){return this.structure.residueMap}get bondHash(){return this.structure.bondHash}get spatialHash(){return this.structure.spatialHash}get _hasCoords(){return this.structure._hasCoords}set _hasCoords(e){this.structure._hasCoords=e}refresh(){Le&&we.time("StructureView.refresh"),this.atomSetCache={};let e=this.structure;if(this.selection.isAllSelection()&&e!==this&&e.atomSet&&e.bondSet){this.atomSet=e.atomSet.clone(),this.bondSet=e.bondSet.clone();for(let t in this.atomSetDict){let i=this.atomSetDict[t];this.atomSetCache["__"+t]=i.clone()}this.atomCount=e.atomCount,this.bondCount=e.bondCount,this.boundingBox.copy(e.boundingBox),this.center.copy(e.center)}else if(this.selection.isNoneSelection()&&e!==this&&e.atomSet&&e.bondSet){this.atomSet=new ii(e.atomCount),this.bondSet=new ii(e.bondCount);for(let t in this.atomSetDict)this.atomSetCache["__"+t]=new ii(e.atomCount);this.atomCount=0,this.bondCount=0,this.boundingBox.makeEmpty(),this.center.set(0,0,0)}else{this.atomSet=this.getAtomSet(this.selection,!0),e.atomSet&&(this.atomSet=this.atomSet.intersection(e.atomSet)),this.bondSet=this.getBondSet();for(let t in this.atomSetDict){let i=this.atomSetDict[t];this.atomSetCache["__"+t]=i.makeIntersection(this.atomSet)}this.atomCount=this.atomSet.getSize(),this.bondCount=this.bondSet.getSize(),this.boundingBox=this.getBoundingBox(),this.center=this.boundingBox.getCenter(new W)}Le&&we.timeEnd("StructureView.refresh"),this.signals.refreshed.dispatch()}setSelection(e){this.selection=e,this.refresh()}getSelection(e){let t=[];e&&e.string&&t.push(e.string);let i=this.structure.getSelection();i&&i.string&&t.push(i.string),this.selection&&this.selection.string&&t.push(this.selection.string);let r="";return t.length>0&&(r=`( ${t.join(" ) AND ( ")} )`),new tn(r)}getStructure(){return this.structure.getStructure()}eachBond(e,t){this.structure.eachBond(e,this.getSelection(t))}eachAtom(e,t){let i=this.getAtomProxy(),r=this.getAtomSet(t),s=this.atomStore.count;if(r.getSize()=this.V[i][r]?(t="S",this.score=this.S[i][r]):this.V[i][r]>=this.H[i][r]?(t="V",this.score=this.V[i][r]):(t="H",this.score=this.H[i][r]),Le&&we.log("Alignment: SCORE",this.score),Le&&we.log("Alignment: S, V, H",this.S[i][r],this.V[i][r],this.H[i][r]);i>0&&r>0;)t==="S"?this.S[i][r]===this.S[i-1][r-1]+e(i-1,r-1)?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2=this.seq2[r-1]+this.ali2,--i,--r,t="S"):this.S[i][r]===this.V[i][r]?t="V":this.S[i][r]===this.H[i][r]?t="H":(--i,--r):t==="V"?this.V[i][r]===this.V[i-1][r]+this.gapExtensionPenalty?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i,t="V"):this.V[i][r]===this.S[i-1][r]+this.gap(0)?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i,t="S"):--i:t==="H"?this.H[i][r]===this.H[i][r-1]+this.gapExtensionPenalty?(this.ali1="-"+this.ali1,this.ali2=this.seq2[r-1]+this.ali2,--r,t="H"):this.H[i][r]===this.S[i][r-1]+this.gap(0)?(this.ali1="-"+this.ali1,this.ali2=this.seq2[r-1]+this.ali2,--r,t="S"):--r:we.error("Alignment: no matrix");for(;i>0;)this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i;for(;r>0;)this.ali1="-"+this.ali1,this.ali2=this.seq2[r-1]+this.ali2,--r;Le&&we.timeEnd("Alignment.trace"),Le&&we.log([this.ali1,this.ali2])}};function cz(n,e,t=!1,i="",r=""){let s,o,a,l,c;if(t){let d=n,f=e;i&&r&&(d=n.getView(new tn(i)),f=e.getView(new tn(r)));let m=d.getSequence(),p=f.getSequence(),_=new l2(m.join(""),p.join("")),y,g;_.calc(),_.trace(),s=0,o=0,a=_.ali1.length;let b=[],h=[];for(let A=0;Ar[s])}}}(),this.spacefillRepresentation=this.addRepresentation("spacefill",{sele:"none",opacity:Fh.opacity,color:Fh.color,disablePicking:!0,radiusType:"data"},!0),this.distanceRepresentation=this.addRepresentation("distance",Fh,!0),this.angleRepresentation=this.addRepresentation("angle",Fh,!0),this.dihedralRepresentation=this.addRepresentation("dihedral",Fh,!0),this.measureRepresentations=new Eg([this.spacefillRepresentation,this.distanceRepresentation,this.angleRepresentation,this.dihedralRepresentation]),this.setDefaultAssembly(this.parameters.defaultAssembly),this.structure.signals.refreshed.add(()=>{this.updateRepresentations({position:!0})})}get defaultParameters(){return uz}get type(){return"structure"}initSelection(e){this.selection=new tn(e),this.structureView=new Ig(this.structure,this.selection),this.selection.signals.stringChanged.add(()=>{this.structureView.setSelection(this.selection),this.rebuildRepresentations(),this.rebuildTrajectories()})}setSelection(e){return this.parameters.sele=e,this.selection.setString(e),this}setDefaultAssembly(e){if(this.structure.biomolDict[e]===void 0&&(e=""),this.parameters.defaultAssembly!==e){let t={defaultAssembly:e};this.reprList.forEach(i=>i.setParameters(t)),this.measureRepresentations.setParameters(t),this.parameters.defaultAssembly=e,this.signals.defaultAssemblyChanged.dispatch(e)}return this}rebuildRepresentations(){this.reprList.forEach(e=>{e.build()}),this.measureRepresentations.build()}rebuildTrajectories(){this.trajList.forEach(e=>{e.trajectory.setStructure(this.structureView)})}updateRepresentations(e){super.updateRepresentations(e),this.measureRepresentations.update(e)}updateRepresentationMatrices(){super.updateRepresentationMatrices(),this.measureRepresentations.setParameters({matrix:this.matrix})}addRepresentation(e,t={},i=!1){t.defaultAssembly=this.parameters.defaultAssembly;let r=this._addRepresentation(e,this.structureView,t,i);return i||r.signals.parametersChanged.add(()=>this.measureUpdate()),r}addTrajectory(e="",t={}){let i=function(s,o,a){let l;return l=s&&s instanceof Tg?new r2(s,o,a):!s&&o.frames?new s2(s,o,a):s&&typeof s=="function"?new a2(s,o,a):new o2(s,o,a),l}(e,this.structureView,t),r=new n2(this.stage,i,t);return this.trajList.push(r),this.signals.trajectoryAdded.dispatch(r),r}removeTrajectory(e){let t=this.trajList.indexOf(e);t!==-1&&this.trajList.splice(t,1),e.dispose(),this.signals.trajectoryRemoved.dispatch(e)}dispose(){this.trajList.slice().forEach(e=>e.dispose()),this.trajList.length=0,this.structure.dispose(),this.measureRepresentations.dispose(),super.dispose()}autoView(e,t){typeof e=="number"&&(t=e,e=""),this.stage.animationControls.zoomMove(this.getCenter(e),this.getZoom(e),U(t,0))}getBoxUntransformed(e){let t;return t=e?this.structureView.getBoundingBox(new tn(e)):this.structureView.boundingBox,t}getCenterUntransformed(e){return e&&typeof e=="string"?this.structure.atomCenter(new tn(e)):this.structure.center}superpose(e,t,i,r){return cz(this.structureView,e.structureView,t,i,r),this.updateRepresentations({position:!0}),this}getMaxRepresentationRadius(e){let t=0,i=this.structure.getAtomProxy(e);return this.eachRepresentation(r=>{if(r.getVisibility()){let s=r.repr;t=Math.max(s.getAtomRadius(i),t)}}),t}measurePick(e){let t=this.pickBuffer.count;if(this.lastPick===e.index&&t>=1){if(t>1){let i=this.pickBuffer.data,r=this.pickBuffer.data.sort();this.pickDict.has(r)?this.pickDict.del(r):this.pickDict.add(r,i),t===2?this.distanceRepresentation.setParameters({atomPair:this.pickDict.values.filter(s=>s.length===2)}):t===3?this.angleRepresentation.setParameters({atomTriple:this.pickDict.values.filter(s=>s.length===3)}):t===4&&this.dihedralRepresentation.setParameters({atomQuad:this.pickDict.values.filter(s=>s.length===4)})}this.pickBuffer.clear(),this.lastPick=void 0}else this.pickBuffer.has(e.index)||this.pickBuffer.push(e.index),this.lastPick=e.index;this.measureUpdate()}measureClear(){this.pickBuffer.clear(),this.lastPick=void 0,this.spacefillRepresentation.setSelection("none")}measureBuild(){let e=this.measureData();this.distanceRepresentation.setParameters({atomPair:e.distance}),this.angleRepresentation.setParameters({atomTriple:e.angle}),this.dihedralRepresentation.setParameters({atomQuad:e.dihedral})}measureUpdate(){let e=this.pickBuffer.data,t={};e.forEach(i=>{let r=Math.max(.1,this.getMaxRepresentationRadius(i));t[i]=r*(2.3-Pd(.1,2,r))}),this.spacefillRepresentation.setSelection(e.length?"@"+e.join(","):"none"),e.length&&this.spacefillRepresentation.setParameters({radiusData:t})}measureData(){let e=this.pickDict.values;return{distance:e.filter(t=>t.length===2),angle:e.filter(t=>t.length===3),dihedral:e.filter(t=>t.length===4)}}removeAllMeasurements(e){let t=this.pickDict,i=t.values,r=function(s){i.filter(o=>o.length===s).forEach(o=>t.del(o.slice().sort()))};(!e||1&e)&&r(2),(!e||2&e)&&r(3),(!e||4&e)&&r(4),this.measureBuild()}removeMeasurement(e){this.pickDict.del(e.slice().sort()),this.measureBuild()}addMeasurement(e){if(e.length<2||e.length>4)return;let t=e.slice().sort();this.pickDict.has(t)||this.pickDict.add(t,e),this.measureBuild()}};Gc.add("structure",Ad),Gc.add("structureview",Ad);var Rg=class extends Jc{constructor(e,t,i={}){super(e,t,Object.assign({name:t.name},i)),this.surface=t}get type(){return"surface"}addRepresentation(e,t={}){return this._addRepresentation(e,this.surface,t)}getBoxUntransformed(){return this.surface.boundingBox}getCenterUntransformed(){return this.surface.center}dispose(){this.surface.dispose(),super.dispose()}};Gc.add("surface",Rg);var kg=class extends Jc{constructor(e,t,i={}){super(e,t,Object.assign({name:t.name},i)),this.volume=t}get type(){return"volume"}addRepresentation(e,t={}){return this._addRepresentation(e,this.volume,t)}getBoxUntransformed(){return this.volume.boundingBox}getCenterUntransformed(){return this.volume.center}dispose(){this.volume.dispose(),super.dispose()}};Gc.add("volume",kg);var Lg=class extends Cg{addRepresentation(e,t){return this.forEach(i=>i.addRepresentation(e,t))}autoView(e){return this.forEach(t=>t.autoView(e))}};function xT(n,e){return n instanceof RegExp?e.name.match(n)!==null:e.name===n}var hz=new W,dz={impostor:!0,quality:"medium",workerDefault:!0,sampleLevel:0,backgroundColor:"black",rotateSpeed:2,zoomSpeed:1.2,panSpeed:1,clipNear:0,clipFar:100,clipDist:10,clipMode:"scene",clipScale:"relative",fogNear:50,fogFar:100,cameraFov:40,cameraEyeSep:.3,cameraType:"perspective",lightColor:14540253,lightIntensity:1.2,ambientColor:14540253,ambientIntensity:.3,hoverTimeout:0,tooltip:!0,mousePreset:"default"},Dg=class{constructor(e,t={}){this.signals={parametersChanged:new Pt.Signal,fullscreenChanged:new Pt.Signal,componentAdded:new Pt.Signal,componentRemoved:new Pt.Signal,clicked:new Pt.Signal,hovered:new Pt.Signal},this.tasks=new ig,this.compList=[],this.defaultFileParams={},this.logList=[],this.viewer=new Xx(e),this.viewer.renderer&&(this.tooltip=document.createElement("div"),Object.assign(this.tooltip.style,{display:"none",position:"fixed",zIndex:"1000000",pointerEvents:"none",backgroundColor:"rgba( 0, 0, 0, 0.6 )",color:"lightgrey",padding:"8px",fontFamily:"sans-serif"}),this.viewer.container.appendChild(this.tooltip),this.mouseObserver=new qx(this.viewer.renderer.domElement),this.viewerControls=new Jx(this),this.trackballControls=new Yx(this),this.pickingControls=new Kx(this),this.animationControls=new ib(this),this.mouseControls=new Sb(this),this.keyControls=new Ab(this),this.pickingBehavior=new Mb(this),this.mouseBehavior=new Cb(this),this.animationBehavior=new Eb(this),this.keyBehavior=new Tb(this),this.spinAnimation=this.animationControls.spin([0,1,0],.005),this.spinAnimation.pause(!0),this.rockAnimation=this.animationControls.rock([0,1,0],.005),this.rockAnimation.pause(!0),this.parameters=or(t,dz),this.setParameters(this.parameters),this.viewer.animate())}setParameters(e={}){RP(this.parameters,e);let t=e,i=this.parameters,r=this.viewer,s=this.trackballControls;return t.quality!==void 0&&this.setQuality(i.quality),t.impostor!==void 0&&this.setImpostor(i.impostor),t.rotateSpeed!==void 0&&(s.rotateSpeed=i.rotateSpeed),t.zoomSpeed!==void 0&&(s.zoomSpeed=i.zoomSpeed),t.panSpeed!==void 0&&(s.panSpeed=i.panSpeed),t.mousePreset!==void 0&&this.mouseControls.preset(i.mousePreset),this.mouseObserver.setParameters({hoverTimeout:i.hoverTimeout}),r.setClip(i.clipNear,i.clipFar,i.clipDist,i.clipMode,i.clipScale),r.setFog(void 0,i.fogNear,i.fogFar),r.setCamera(i.cameraType,i.cameraFov,i.cameraEyeSep),r.setSampling(i.sampleLevel),r.setBackground(i.backgroundColor),r.setLight(i.lightColor,i.lightIntensity,i.ambientColor,i.ambientIntensity),this.signals.parametersChanged.dispatch(this.getParameters()),this}log(e){console.log("STAGE LOG",e),this.logList.push(e)}getParameters(){return Object.assign({},this.parameters)}defaultFileRepresentation(e){if(e instanceof Ad){let t,i,r;e.setSelection("/0");let s=e.structure;if(s.biomolDict.BU1){let d=s.biomolDict.BU1;t=d.getAtomCount(s),i=d.getResidueCount(s),r=d.getInstanceCount(),e.setDefaultAssembly("BU1")}else t=s.getModelProxy(0).atomCount,i=s.getModelProxy(0).residueCount,r=1;let o=t;BP&&(o*=4);let a=s.atomStore.count/s.residueStore.count<2;a&&(o*=10);let l="chainname",c="RdYlBu",u=!1;if(s.getChainnameCount(new tn("polymer and /0"))===1&&(l="residueindex",c="Spectral",u=!0),Le&&console.log(o,t,r,a),i/r<4)e.addRepresentation("ball+stick",{colorScheme:"element",radiusScale:2,aspectRatio:1.5,bondScale:.3,bondSpacing:.75,quality:"auto"});else if(r>5&&o>15e3||o>7e5){let d=Math.min(2,Math.max(.1,6e3/(o/r)));a&&(d=Math.min(d,.5)),e.addRepresentation("surface",{colorScheme:l,colorScale:c,colorReverse:u,sele:"polymer",surfaceType:"av",probeRadius:1.4,scaleFactor:d,useWorker:!1})}else o>25e4?e.addRepresentation("backbone",{colorScheme:l,colorScale:c,colorReverse:u,lineOnly:!0}):o>1e5?e.addRepresentation("backbone",{colorScheme:l,colorScale:c,colorReverse:u,quality:"low",disableImpostor:!0,radiusScale:2}):o>8e4?e.addRepresentation("backbone",{colorScheme:l,colorScale:c,colorReverse:u,radiusScale:2}):(e.addRepresentation("cartoon",{colorScheme:l,colorScale:c,colorReverse:u,radiusScale:.7,aspectRatio:5,quality:"auto"}),o<5e4&&e.addRepresentation("base",{colorScheme:l,colorScale:c,colorReverse:u,quality:"auto"}),e.addRepresentation("ball+stick",{sele:"ligand",colorScheme:"element",radiusScale:2,aspectRatio:1.5,bondScale:.3,bondSpacing:.75,quality:"auto"}));e.structure.frames.length&&e.addTrajectory()}else(e instanceof Rg||e instanceof kg)&&e.addRepresentation("surface");this.tasks.onZeroOnce(this.autoView,this)}loadFile(e,t={}){let i=Object.assign({},this.defaultFileParams,t),r=Gi(e).name;this.tasks.increment(),this.log(`loading file '${r}'`);let s=U(i.ext,Gi(e).ext),o;return o=At.isTrajectory(s)?Promise.reject(new Error(`loadFile: ext '${s}' is a trajectory and must be loaded into a structure component`)):OE(e,i),o.then(a=>{this.log(`loaded '${r}'`);let l=this.addComponentFromObject(a,i);return i.defaultRepresentation&&this.defaultFileRepresentation(l),this.tasks.decrement(),l},a=>{this.tasks.decrement();let l=`error loading file: '${a}'`;throw this.log(l),l})}loadScript(e){let t=Gi(e).name;return this.log(`loading script '${t}'`),OE(e).then(i=>{this.tasks.increment(),this.log(`running script '${t}'`),i.run(this).then(()=>{this.tasks.decrement(),this.log(`finished script '${t}'`)}),this.log(`called script '${t}'`)},i=>{this.tasks.decrement();let r=`errored script '${t}' "${i}"`;throw this.log(r),r})}addComponent(e){e?(this.compList.push(e),this.signals.componentAdded.dispatch(e)):we.warn("Stage.addComponent: no component given")}addComponentFromObject(e,t={}){let i=Gc.get(e.type);if(i){let r=new i(this,e,t);return this.addComponent(r),r}we.warn("no component for object type",e.type)}removeComponent(e){let t=this.compList.indexOf(e);t!==-1&&(this.compList.splice(t,1),e.dispose(),this.signals.componentRemoved.dispatch(e))}removeAllComponents(){this.compList.slice().forEach(e=>this.removeComponent(e))}handleResize(){this.viewer.handleResize()}setSize(e,t){let i=this.viewer.container;i!==document.body&&(e!==void 0&&(i.style.width=e),t!==void 0&&(i.style.height=t),this.handleResize())}toggleFullscreen(e){if(!(document.fullscreenEnabled||document.mozFullScreenEnabled||document.webkitFullscreenEnabled||document.msFullscreenEnabled))return void we.log("fullscreen mode (currently) not possible");let t=this;function i(){return document.fullscreenElement||document.mozFullScreenElement||document.webkitFullscreenElement||document.msFullscreenElement}function r(){if(!i()&&t.lastFullscreenElement){let s=t.lastFullscreenElement;s.style.width=s.dataset.normalWidth||"",s.style.height=s.dataset.normalHeight||"",document.removeEventListener("fullscreenchange",r),document.removeEventListener("mozfullscreenchange",r),document.removeEventListener("webkitfullscreenchange",r),document.removeEventListener("MSFullscreenChange",r),t.handleResize(),t.signals.fullscreenChanged.dispatch(!1)}}e=e||this.viewer.container,this.lastFullscreenElement=e,i()?document.exitFullscreen?document.exitFullscreen():document.msExitFullscreen?document.msExitFullscreen():document.mozCancelFullScreen?document.mozCancelFullScreen():document.webkitExitFullscreen&&document.webkitExitFullscreen():(e.dataset.normalWidth=e.style.width||"",e.dataset.normalHeight=e.style.height||"",e.style.width=window.screen.width+"px",e.style.height=window.screen.height+"px",e.requestFullscreen?e.requestFullscreen():e.msRequestFullscreen?e.msRequestFullscreen():e.mozRequestFullScreen?e.mozRequestFullScreen():e.webkitRequestFullscreen&&e.webkitRequestFullscreen(),document.addEventListener("fullscreenchange",r),document.addEventListener("mozfullscreenchange",r),document.addEventListener("webkitfullscreenchange",r),document.addEventListener("MSFullscreenChange",r),this.handleResize(),this.signals.fullscreenChanged.dispatch(!0),setTimeout(function(){t.handleResize()},100))}setSpin(e){e?(this.spinAnimation.resume(!0),this.rockAnimation.pause(!0)):this.spinAnimation.pause(!0)}setRock(e){e?(this.rockAnimation.resume(!0),this.spinAnimation.pause(!0)):this.rockAnimation.pause(!0)}toggleSpin(){this.setSpin(this.spinAnimation.paused)}toggleRock(){this.setRock(this.rockAnimation.paused)}getFocus(){let e=this.parameters;if(e.clipMode!=="scene")return 0;let t=e.clipNear;return e.clipScale==="absolute"&&(t=this.viewer.absoluteToRelative(t)),2*t}setFocus(e){if(this.parameters.clipMode!=="scene")return;let t,i,r,s;this.parameters.clipScale==="relative"?(t=Fx(e/2,0,49.9),i=100-t,r=50,s=function(o){return Fx(o,0,100)}(2*i-50)):(t=this.viewer.relativeToAbsolute(e/2),i=t,r=0,s=2*i),this.setParameters({clipNear:t,clipFar:i,fogNear:r,fogFar:s})}getZoomForBox(e){let t=e.getSize(hz),i=Math.max(t.x,t.y,t.z),r=Math.min(t.x,t.y,t.z),s=i+Math.sqrt(r),o=En(this.viewer.perspectiveCamera.fov),a=this.viewer.width,l=this.viewer.height,c=l{this.tasks.onZeroOnce(()=>{this.tasks.increment(),this.viewer.makeImage(e).then(r=>{this.tasks.decrement(),t(r)}).catch(r=>{this.tasks.decrement(),i(r)})})})}setImpostor(e){this.parameters.impostor=e;let t=["spacefill","ball+stick","licorice","hyperball","backbone","rocket","helixorient","contact","distance","dot"];this.eachRepresentation(function(i){if(!t.includes(i.getType()))return;let r=i.getParameters();r.disableImpostor=!e,i.build(r)})}setQuality(e){this.parameters.quality=e;let t=["tube","cartoon","ribbon","trace","rope"],i=["spacefill","ball+stick","licorice","hyperball","backbone","rocket","helixorient","contact","distance","dot"];this.eachRepresentation(function(r){let s=r.getParameters();if(!t.includes(r.getType())){if(!i.includes(r.getType()))return;if(!s.disableImpostor)return void(r.repr.quality=e)}s.quality=e,r.build(s)})}eachComponent(e,t){this.compList.slice().forEach(i=>{t!==void 0&&t!==i.type||e(i)})}eachRepresentation(e,t){this.eachComponent(i=>{i.reprList.slice().forEach(r=>{t!==void 0&&t!==r.getType()||e(r,i)})})}getComponentsByName(e){let t=[];return this.eachComponent(i=>{(e===void 0||xT(e,i))&&t.push(i)}),new Lg(t)}getComponentsByObject(e){let t=[];return this.eachComponent(i=>{i.object===e&&t.push(i)}),new Lg(t)}getRepresentationsByName(e){let t=[];return this.eachRepresentation((i,r)=>{(e===void 0||xT(e,i))&&t.push(i)}),new Eg(t)}measureClear(){this.eachComponent(e=>e.measureClear(),"structure")}measureUpdate(){this.eachComponent(e=>e.measureUpdate(),"structure")}dispose(){this.tasks.dispose(),this.viewer.dispose(),this.mouseObserver.dispose()}},c2=class extends Jc{constructor(e,t,i={}){super(e,t,Object.assign({name:t.name},i)),this.shape=t}get type(){return"shape"}addRepresentation(e,t={}){return this._addRepresentation(e,this.shape,t)}getBoxUntransformed(){return this.shape.boundingBox}getCenterUntransformed(){return this.shape.center}dispose(){this.shape.dispose(),super.dispose()}};function qt(n,e,t,i){var r,s=arguments.length,o=s<3?e:i===null?i=Object.getOwnPropertyDescriptor(e,t):i;if(typeof Reflect=="object"&&typeof Reflect.decorate=="function")o=Reflect.decorate(n,e,t,i);else for(var a=n.length-1;a>=0;a--)(r=n[a])&&(o=(s<3?r(o):s>3?r(e,t,o):r(e,t))||o);return s>3&&o&&Object.defineProperty(e,t,o),o}function fI(n,e,t,i){return new(t||(t=Promise))(function(r,s){function o(c){try{l(i.next(c))}catch(u){s(u)}}function a(c){try{l(i.throw(c))}catch(u){s(u)}}function l(c){c.done?r(c.value):function(u){return u instanceof t?u:new t(function(d){d(u)})}(c.value).then(o,a)}l((i=i.apply(n,e||[])).next())})}Gc.add("shape",c2),typeof SuppressedError=="function"&&SuppressedError;var Ng=class extends Yt{constructor(e){super(e),e.scale||(this.parameters.scale="rainbow",this.parameters.reverse=U(e.reverse,!0)),this.scalePerModel={},e.structure.eachModel(t=>{this.parameters.domain=[t.atomOffset,t.atomEnd],this.scalePerModel[t.index]=this.getScale()})}atomColor(e){return this.scalePerModel[e.modelIndex](e.index)}};qt([Xt],Ng.prototype,"atomColor",null),Dt.add("atomindex",Ng);var Fg=class extends Yt{constructor(e){if(super(e),e.scale||(this.parameters.scale="OrRd"),!e.domain){let t,i=1/0,r=-1/0;e.sele&&(t=new tn(e.sele)),e.structure.eachAtom(function(s){let o=s.bfactor;i=Math.min(i,o),r=Math.max(r,o)},t),this.parameters.domain=[i,r]}this.bfactorScale=this.getScale()}atomColor(e){return this.bfactorScale(e.bfactor)}};qt([Xt],Fg.prototype,"atomColor",null),Dt.add("bfactor",Fg);var Og=class extends Yt{constructor(e){super(e),this.chainidDictPerModel={},this.scalePerModel={},e.scale||(this.parameters.scale="Spectral"),e.structure.eachModel(t=>{let i=0,r={};t.eachChain(function(s){r[s.chainid]===void 0&&(r[s.chainid]=i,i+=1)}),this.parameters.domain=[0,i-1],this.chainidDictPerModel[t.index]=r,this.scalePerModel[t.index]=this.getScale()})}atomColor(e){let t=this.chainidDictPerModel[e.modelIndex];return this.scalePerModel[e.modelIndex](t[e.chainid])}};qt([Xt],Og.prototype,"atomColor",null),Dt.add("chainid",Og);var Bg=class extends Yt{constructor(e){super(e),this.scalePerModel={},e.scale||(this.parameters.scale="Spectral"),e.structure.eachModel(t=>{this.parameters.domain=[t.chainOffset,t.chainEnd],this.scalePerModel[t.index]=this.getScale()})}atomColor(e){return this.scalePerModel[e.modelIndex](e.chainIndex)}};qt([Xt],Bg.prototype,"atomColor",null),Dt.add("chainindex",Bg);var Ug=class extends Yt{constructor(e){super(e),this.chainnameDictPerModel={},this.scalePerModel={},e.scale||(this.parameters.scale="Spectral"),e.structure.eachModel(t=>{let i=0,r={};t.eachChain(function(s){r[s.chainname]===void 0&&(r[s.chainname]=i,i+=1)}),this.parameters.domain=[0,i-1],this.chainnameDictPerModel[t.index]=r,this.scalePerModel[t.index]=this.getScale()})}atomColor(e){let t=this.chainnameDictPerModel[e.modelIndex];return this.scalePerModel[e.modelIndex](t[e.chainname])}};qt([Xt],Ug.prototype,"atomColor",null),Dt.add("chainname",Ug);var zg=class extends Yt{constructor(e){super(e),this.rsrzDict={},this.rsccDict={},e.scale||(this.parameters.scale="RdYlBu"),this.rsrzScale=this.getScale({domain:[2,0]}),this.rsccScale=this.getScale({domain:[.678,1]});let t=e.structure.validation;t&&(this.rsrzDict=t.rsrzDict,this.rsccDict=t.rsccDict)}atomColor(e){let t=e.resno+"";e.inscode&&(t+="^"+e.inscode),e.chainname&&(t+=":"+e.chainname),t+="/"+e.modelIndex;let i=this.rsrzDict[t];if(i!==void 0)return this.rsrzScale(i);let r=this.rsccDict[t];return r!==void 0?this.rsccScale(r):9474192}};qt([Xt],zg.prototype,"atomColor",null),Dt.add("densityfit",zg);var Kv={ARG:{CD:.1,CZ:.5,NE:-.1},ASN:{CG:.55,OD1:-.55},ASP:{CB:-.16,CG:.36,OD1:-.6,OD2:-.6},CYS:{CB:.19,SG:-.19},GLN:{CD:.55,OE1:-.55},GLU:{CD:.36,CG:-.16,OE1:-.6,OE2:-.6},HIS:{CB:.1,CD2:.2,CE1:.45,CG:.15,ND1:.05,NE2:.05},LYS:{CE:.25,NZ:.75},MET:{CE:.06,CG:.06,SD:-.12},PTR:{C:.55,CA:.1,CZ:.25,N:-.35,O:-.55,O1P:-.85,O2P:-.85,O3P:-.85,OG1:-1.1,P:1.4},SEP:{C:.55,CA:.1,CB:.25,N:-.35,O:-.55,O1P:-.85,O2P:-.85,O3P:-.85,OG1:-1.1,P:1.4},SER:{CB:.25,OG:-.25},THR:{CB:.25,OG1:-.25},TPO:{C:.55,CA:.1,CB:.25,N:-.35,O:-.55,OG1:-1.1,O1P:-.85,O2P:-.85,O3P:-.85,P:1.4},TRP:{CD1:.06,CD2:.1,CE2:-.04,CE3:-.03,CG:-.03,NE1:-.06},TYR:{CZ:.25,OH:-.25},backbone:{C:.55,O:-.55,N:-.35,CA:.1}},Vg=class extends Yt{constructor(e){super(e),this.delta=new W,this.hCharges=[],e.scale||(this.parameters.scale="rwb"),e.domain||(this.parameters.domain=[-50,50]),this.scale=this.getScale(),this.charges=new Float32Array(e.structure.atomCount);let t=[];e.structure.eachAtom(r=>{var s;if(this.charges[r.index]=((s=r).partialCharge!==null?s.partialCharge:s.isProtein()&&(Kv[s.resname]&&Kv[s.resname][s.atomname]||Kv.backbone[s.atomname])||0)*r.occupancy,r.atomname==="N"){if(r.bondCount>=3||r.bondToElementCount(1))return;let o=function(a,l=new W){let c=!1,u=!1,d=!1;return l.set(2*a.x,2*a.y,2*a.z),a.eachBondedAtom(function(f){if(!c)return f.atomname==="H"?(l.set(f.x,f.y,f.z),void(c=!0)):void(u||f.atomname!=="CA"?d||f.atomname!=="C"||(d=!0,l.sub(f)):(l.sub(f),u=!0))}),c?l:u&&d?(l.normalize(),l.multiplyScalar(1.04),l.add(a),l):void 0}(r);o!==void 0&&(t.push(o),this.hCharges.push(.25*r.occupancy))}});let i=e.structure.getBoundingBox();i.expandByScalar(1.04),this.hStore=function(r){let s=r.length,o=new Float32Array(s),a=new Float32Array(s),l=new Float32Array(s);for(let c=0;c{let a=t[s];a!==0&&(r+=a/o)}),this.hHash.eachWithin(e.x,e.y,e.z,12,(s,o)=>{let a=i[s];a!==0&&(r+=a/o)}),this.scale(332*r)}};qt([Xt],Vg.prototype,"positionColor",null),Dt.add("electrostatic",Vg);var bT={H:16777215,HE:14286847,LI:13402367,BE:12779264,B:16758197,C:9474192,N:3166456,O:16715021,F:9494608,NE:11789301,NA:11230450,MG:9109248,AL:12560038,SI:1578e4,P:16744448,S:16777008,CL:2093087,AR:8442339,K:9388244,CA:4062976,SC:15132390,TI:12567239,V:10921643,CR:9083335,MN:10255047,FE:14706227,CO:15765664,NI:5296208,CU:13140019,ZN:8224944,GA:12750735,GE:6721423,AS:12419299,SE:16752896,BR:10889513,KR:6076625,RB:7351984,SR:65280,Y:9764863,ZR:9756896,NB:7586505,MO:5551541,TC:3907230,RU:2396047,RH:687500,PD:27013,AG:12632256,CD:16767375,IN:10909043,SN:6717568,SB:10380213,TE:13924864,I:9699476,XE:9699476,CS:5707663,BA:51456,LA:7394559,CE:16777159,PR:14286791,ND:13107143,PM:10747847,SM:9437127,EU:6422471,GD:4587463,TB:3211207,DY:2097095,HO:65436,ER:58997,TM:54354,YB:48952,LU:43812,HF:5096191,TA:5089023,W:2200790,RE:2522539,OS:2516630,IR:1528967,PT:13684960,AU:16765219,HG:12105936,TL:10900557,PB:5724513,BI:10375093,PO:11230208,AT:7688005,RN:4358806,FR:4325478,RA:32e3,AC:7384058,TH:47871,PA:41471,U:36863,NP:33023,PU:27647,AM:5528818,CM:7888099,BK:9064419,CF:10565332,ES:11739092,FM:11739066,MD:11734438,NO:12389767,LR:13041766,RF:13369433,DB:13697103,SG:14221381,BH:14680120,HS:15073326,MT:15400998,DS:16777215,RG:16777215,CN:16777215,UUT:16777215,FL:16777215,UUP:16777215,LV:16777215,UUH:16777215,D:16777152,T:16777120},Hg=class extends Yt{constructor(e){e.value=U(e.value,bT.C),super(e)}atomColor(e){let t=e.element;return t==="C"?this.parameters.value:bT[t]||16777215}};qt([Xt],Hg.prototype,"atomColor",null),Dt.add("element",Hg);var Gg=class extends Yt{constructor(e){super(e),e.scale||(this.parameters.scale="Spectral"),e.domain||(this.parameters.domain=[0,e.structure.entityList.length-1]),this.entityindexScale=this.getScale()}atomColor(e){return this.entityindexScale(e.entityIndex)}};qt([Xt],Gg.prototype,"atomColor",null),Dt.add("entityindex",Gg);var $g=class extends Yt{atomColor(e){let t=e.entity;switch(t?t.entityType:void 0){case 1:return 8374655;case 2:return 16629894;case 3:return 12496596;case 4:return 3697840;default:return 16777113}}};qt([Xt],$g.prototype,"atomColor",null),Dt.add("entitytype",$g);var Wg=class extends Yt{constructor(e){super(e),this.geoAtomDict={},this.geoDict={};let t=e.structure.validation;t&&(this.geoAtomDict=t.geoAtomDict,this.geoDict=t.geoDict)}atomColor(e){let t,i=e.resno+"";e.inscode&&(i+="^"+e.inscode),e.chainname&&(i+=":"+e.chainname),i+="/"+e.modelIndex;let r=this.geoAtomDict[i];r!==void 0?(s=r[e.atomname]||0,t=16843009*((s=(858993459&(s-=s>>1&1431655765))+(s>>2&858993459))+(s>>4)&252645135)>>24):t=this.geoDict[i]||0;var s;return t===0?2188972:t===1?16703627:t===2?16018755:t>=3?10813478:9474192}};qt([Xt],Wg.prototype,"atomColor",null),Dt.add("geoquality",Wg);var jg=class extends Yt{constructor(e){super(e),this.resHF={},e.scale||(this.parameters.scale="RdYlGn");for(let t in tT)this.resHF[t]=tT[t][0];if(this.defaultResidueHydrophobicity=JB[0],!e.domain){let t=1/0,i=-1/0;for(let r in this.resHF){let s=this.resHF[r];t=Math.min(t,s),i=Math.max(i,s)}this.parameters.domain=[t,0,i]}this.hfScale=this.getScale()}atomColor(e){return this.hfScale(this.resHF[e.resname]||this.defaultResidueHydrophobicity)}};qt([Xt],jg.prototype,"atomColor",null),Dt.add("hydrophobicity",jg);var Xg=class extends Yt{constructor(e){super(e),e.scale||(this.parameters.scale="rainbow"),e.domain||(this.parameters.domain=[0,e.structure.modelStore.count]),this.modelindexScale=this.getScale()}atomColor(e){return this.modelindexScale(e.modelIndex)}};qt([Xt],Xg.prototype,"atomColor",null),Dt.add("modelindex",Xg);var qg=class extends Yt{atomColor(e){switch(e.residueType.moleculeType){case 1:return 3697840;case 2:return 15729279;case 3:return 12496596;case 4:return 16629894;case 5:return 12540695;case 6:return 8374655;default:return 16777113}}};qt([Xt],qg.prototype,"atomColor",null),Dt.add("moleculetype",qg);var Yg=class extends Yt{constructor(e){super(e),e.scale||(this.parameters.scale="PuBu"),e.domain||(this.parameters.domain=[0,1]),this.occupancyScale=this.getScale()}atomColor(e){return this.occupancyScale(e.occupancy)}};qt([Xt],Yg.prototype,"atomColor",null),Dt.add("occupancy",Yg);var Zg=class extends Yt{constructor(e){super(e),e.scale||(this.parameters.scale="rwb"),e.domain||(this.parameters.domain=[-1,1]),this.partialchargeScale=this.getScale()}atomColor(e){return this.partialchargeScale(e.partialCharge||0)}};function Jv(){return 16777215*Math.random()}qt([Xt],Zg.prototype,"atomColor",null),Dt.add("partialcharge",Zg);var Ic=class extends Yt{atomColor(){return Jv()}volumeColor(){return Jv()}positionColor(){return Jv()}};qt([Xt],Ic.prototype,"atomColor",null),qt([Xt],Ic.prototype,"volumeColor",null),qt([Xt],Ic.prototype,"positionColor",null),Dt.add("random",Ic);var Kg=class extends Yt{constructor(e){super(e),this.rciDict={},e.scale||(this.parameters.scale="RdYlBu"),this.rciScale=this.getScale({domain:[.6,0]});let t=e.structure.validation;t&&(this.rciDict=t.rciDict)}atomColor(e){let t=`[${e.resname}]${e.resno}`;e.chainname&&(t+=":"+e.chainname);let i=this.rciDict[t];return i!==void 0?this.rciScale(i):9474192}};qt([Xt],Kg.prototype,"atomColor",null),Dt.add("randomcoilindex",Kg);var Jg=class extends Yt{constructor(e){super(e),this.scalePerChain={},e.scale||(this.parameters.scale="rainbow",this.parameters.reverse=U(e.reverse,!0)),e.structure.eachChain(t=>{this.parameters.domain=[t.residueOffset,t.residueEnd],this.scalePerChain[t.index]=this.getScale()})}atomColor(e){return this.scalePerChain[e.chainIndex](e.residueIndex)}};qt([Xt],Jg.prototype,"atomColor",null),Dt.add("residueindex",Jg);var fz={ALA:9240460,ARG:124,ASN:16743536,ASP:10485826,CYS:16777072,GLN:16731212,GLU:6684672,GLY:16777215,HIS:7368959,ILE:19456,LEU:4546117,LYS:4671416,MET:12099650,PHE:5459026,PRO:5395026,SER:16740418,THR:12078080,TRP:5195264,TYR:9203788,VAL:16747775,ASX:16711935,GLX:16711935,ASH:16711935,GLH:16711935,A:14423100,G:3329330,I:10145074,X:8190976,C:16766720,T:4286945,U:4251856,D:35723,DA:14423100,DG:3329330,DI:10145074,DX:8190976,DC:16766720,DT:4286945,DU:4251856,DD:35723},Qg=class extends Yt{atomColor(e){return fz[e.resname]||16711935}};qt([Xt],Qg.prototype,"atomColor",null),Dt.add("resname",Qg);var pz=16711808,mz=10485888,gz=6291584,yz=16762880,_z=6324479,vz=16777215,xz=11403518,bz=16580962,wz=10921722,e0=class extends Yt{constructor(e){super(e),this.residueProxy=e.structure.getResidueProxy()}atomColor(e){let t=e.sstruc,i=this.residueProxy;return t==="h"?pz:t==="g"?mz:t==="i"?gz:t==="e"||t==="b"?yz:t==="t"?_z:(i.index=e.residueIndex,i.isDna()?xz:i.isRna()?bz:i.isSaccharide()?wz:i.isProtein()||t==="s"||t==="l"?vz:8421504)}};qt([Xt],e0.prototype,"atomColor",null),Dt.add("sstruc",e0);var sd=class extends Yt{constructor(e){var t,i;super(e),e.scale||(this.parameters.scale="rwb"),this.atomData=(t=this.parameters.data)===null||t===void 0?void 0:t.atomData,this.bondData=(i=this.parameters.data)===null||i===void 0?void 0:i.bondData,this.scale=this.getScale(this.parameters)}atomColor(e){var t;let i=(t=this.atomData)===null||t===void 0?void 0:t[e.index];return i!==void 0?this.scale(i):this.parameters.value}bondColor(e,t){var i;let r=(i=this.bondData)===null||i===void 0?void 0:i[e.index];return r!==void 0?this.scale(r):this.atomProxy?(this.atomProxy.index=t?e.atomIndex1:e.atomIndex2,this.atomColor(this.atomProxy)):this.parameters.value}};qt([Xt],sd.prototype,"atomColor",null),qt([Xt],sd.prototype,"bondColor",null),Dt.add("structuredata",sd);var qa=class extends Yt{atomColor(){return this.parameters.value}bondColor(){return this.parameters.value}valueColor(){return this.parameters.value}volumeColor(){return this.parameters.value}};qt([Xt],qa.prototype,"atomColor",null),qt([Xt],qa.prototype,"bondColor",null),qt([Xt],qa.prototype,"valueColor",null),qt([Xt],qa.prototype,"volumeColor",null),Dt.add("uniform",qa);var t0=class extends Yt{constructor(e){super(e),this.valueScale=this.getScale()}volumeColor(e){return this.valueScale(this.parameters.volume.data[e])}};qt([Xt],t0.prototype,"volumeColor",null),Dt.add("value",t0);var n0=class extends Yt{constructor(e){super(e),this.vec=new W,this.valueScale=this.getScale()}positionColor(e){let t=this.parameters.volume;if(!t||!t.inverseMatrix)return this.parameters.value;let i=this.vec,r=t.data,s=t.nx,o=t.ny,a=s*o;i.copy(e),i.applyMatrix4(t.inverseMatrix);let l=Math.floor(i.x),c=Math.floor(i.y),u=Math.floor(i.z),d=(u*o+c)*s+l,f=d+1,m=d+s,p=d+a,_=m+1,y=p+1,g=m+a,b=g+1,h=r[d],v=r[f],S=r[m],x=r[p],w=r[_],A=r[y],M=r[g],T=r[b],R=i.x-l,C=i.y-c,P=i.z-u,E=Cr(h,v,R),I=Cr(x,A,R),O=Cr(S,w,R),D=Cr(M,T,R),N=Cr(E,O,C),H=Cr(I,D,C),z=Cr(N,H,P);return this.valueScale(z)}};qt([Xt],n0.prototype,"positionColor",null),Dt.add("volume",n0);var Zn=class extends el{constructor(e,t,i){let r=i||{};if(super(e,t,r),this.type="structure",this.parameters=Object.assign({radiusType:{type:"select",options:Qr.types},radiusData:{type:"hidden"},radiusSize:{type:"number",precision:3,max:10,min:.001},radiusScale:{type:"number",precision:3,max:10,min:.001},assembly:null,defaultAssembly:{type:"hidden"}},this.parameters),this.selection=new tn(r.sele),this.dataList=[],this.structure=e,this.structureView=this.structure.getView(this.selection),e.biomolDict){let s={default:"default","":e.unitcell?"AU":"FULL"};Object.keys(e.biomolDict).forEach(function(o){s[o]=o}),this.parameters.assembly={type:"select",options:s,rebuild:!0}}else this.parameters.assembly=null}get defaultScale(){return{vdw:1,covalent:1,bfactor:.01,sstruc:1}}init(e){let t=e||{};t.colorScheme=U(t.colorScheme,"element"),this.setRadius(t.radius,t),this.radiusType=U(t.radiusType,"vdw"),this.radiusData=U(t.radiusData,{}),this.radiusSize=U(t.radiusSize,1),this.radiusScale=U(t.radiusScale,1),this.assembly=U(t.assembly,"default"),this.defaultAssembly=U(t.defaultAssembly,""),t.quality==="auto"&&(t.quality=this.getQuality()),super.init(t),this.selection.signals.stringChanged.add(()=>{this.build()}),this.build()}setRadius(e,t){let i=Object.keys(aI);return typeof e=="string"&&i.includes(e.toLowerCase())?t.radiusType=e:e!==void 0&&(t.radiusType="size",t.radiusSize=e),this}getAssembly(){let e=this.assembly==="default"?this.defaultAssembly:this.assembly;return this.structure.biomolDict[e]}getQuality(){let e,t=this.structureView,i=this.getAssembly();return e=i?i.getAtomCount(t):t.atomCount,BP&&(e*=4),t.atomStore.count/t.residueStore.count<2&&(e*=10),e<15e3?"high":e<8e4?"medium":"low"}create(){if(this.structureView.atomCount===0)return;if(!this.structureView.hasCoords())return void(this.needsBuild=!0);this.needsBuild=!1;let e=this.getAssembly();if(e)e.partList.forEach((t,i)=>{let r=t.getView(this.structureView);if(r.atomCount===0)return;let s=this.createData(r,i);s&&(s.sview=r,s.instanceList=t.getInstanceList(),this.dataList.push(s))});else{let t=this.createData(this.structureView,0);t&&(t.sview=this.structureView,this.dataList.push(t))}}update(e){!this.lazy||this.visible?this.needsBuild?this.build():this.dataList.forEach(t=>{t.bufferList.length>0&&this.updateData(e,t)},this):Object.assign(this.lazyProps.what,e)}updateData(e,t){this.build()}getColorParams(){return Object.assign(Object.assign({},super.getColorParams()),{structure:this.structure})}getRadiusParams(e){return{type:this.radiusType,scale:this.radiusScale,size:this.radiusSize,data:this.radiusData}}getAtomParams(e,t){return Object.assign({what:e,colorParams:this.getColorParams(),radiusParams:this.getRadiusParams()},t)}getBondParams(e,t){return Object.assign({what:e,colorParams:this.getColorParams(),radiusParams:this.getRadiusParams()},t)}getAtomRadius(e){return this.structureView.atomSet.isSet(e.index)?new Qr(this.getRadiusParams()).atomRadius(e):0}setSelection(e,t){return this.selection.setString(e,t),this}setParameters(e,t={},i=!1){let r=e||{};return this.setRadius(r.radius,r),r.radiusType===void 0&&r.radiusData===void 0&&r.radiusSize===void 0&&r.radiusScale===void 0||(t.radius=!0,ys&&!this.disableImpostor||(i=!0)),r.defaultAssembly!==void 0&&r.defaultAssembly!==this.defaultAssembly&&(this.assembly==="default"&&r.assembly===void 0||r.assembly==="default")&&(i=!0),super.setParameters(r,t,i),this}getParameters(){return Object.assign(super.getParameters(),{sele:this.selection?this.selection.string:void 0,defaultAssembly:this.defaultAssembly})}attach(e){let t=this.viewer,i=this.bufferList;this.dataList.forEach(function(r){r.bufferList.forEach(function(s){i.push(s),t.add(s,r.instanceList)})}),this.setVisibility(this.visible),e()}clear(){this.dataList.length=0,super.clear()}dispose(){this.structureView.dispose(),super.dispose()}},Md=class extends Zn{constructor(e,t,i){super(e,t,i),this.n=0,this.parameters=Object.assign({labelVisible:{type:"boolean"},labelSize:{type:"number",precision:3,max:10,min:.001},labelColor:{type:"color"},labelFontFamily:{type:"select",options:{"sans-serif":"sans-serif",monospace:"monospace",serif:"serif"},buffer:"fontFamily"},labelFontStyle:{type:"select",options:{normal:"normal",italic:"italic"},buffer:"fontStyle"},labelFontWeight:{type:"select",options:{normal:"normal",bold:"bold"},buffer:"fontWeight"},labelsdf:{type:"boolean",buffer:"sdf"},labelXOffset:{type:"number",precision:1,max:20,min:-20,buffer:"xOffset"},labelYOffset:{type:"number",precision:1,max:20,min:-20,buffer:"yOffset"},labelZOffset:{type:"number",precision:1,max:20,min:-20,buffer:"zOffset"},labelAttachment:{type:"select",options:{"bottom-left":"bottom-left","bottom-center":"bottom-center","bottom-right":"bottom-right","middle-left":"middle-left","middle-center":"middle-center","middle-right":"middle-right","top-left":"top-left","top-center":"top-center","top-right":"top-right"},rebuild:!0},labelBorder:{type:"boolean",buffer:"showBorder"},labelBorderColor:{type:"color",buffer:"borderColor"},labelBorderWidth:{type:"number",precision:2,max:.3,min:0,buffer:"borderWidth"},labelBackground:{type:"boolean",rebuild:!0},labelBackgroundColor:{type:"color",buffer:"backgroundColor"},labelBackgroundMargin:{type:"number",precision:2,max:2,min:0,rebuild:!0},labelBackgroundOpacity:{type:"range",step:.01,max:1,min:0,buffer:"backgroundOpacity"},labelFixedSize:{type:"boolean",buffer:"fixedSize"},lineOpacity:{type:"range",min:0,max:1,step:.01},linewidth:{type:"integer",max:50,min:1,buffer:!0}},this.parameters,{flatShaded:null})}init(e){let t=e||{};this.labelVisible=U(t.labelVisible,!0),this.labelSize=U(t.labelSize,2),this.labelColor=U(t.labelColor,16777215),this.labelFontFamily=U(t.labelFontFamily,"sans-serif"),this.labelFontStyle=U(t.labelFontstyle,"normal"),this.labelFontWeight=U(t.labelFontWeight,"bold"),this.labelsdf=U(t.labelsdf,FP==="Chrome"),this.labelXOffset=U(t.labelXOffset,0),this.labelYOffset=U(t.labelYOffset,0),this.labelZOffset=U(t.labelZOffset,.5),this.labelAttachment=U(t.labelAttachment,"bottom-left"),this.labelBorder=U(t.labelBorder,!1),this.labelBorderColor=U(t.labelBorderColor,"lightgrey"),this.labelBorderWidth=U(t.labelBorderWidth,.15),this.labelBackground=U(t.labelBackground,!1),this.labelBackgroundColor=U(t.labelBackgroundColor,"lightgrey"),this.labelBackgroundMargin=U(t.labelBackgroundMargin,.5),this.labelBackgroundOpacity=U(t.labelBackgroundOpacity,1),this.labelFixedSize=U(t.labelFixedSize,!1),this.lineOpacity=U(t.lineOpacity,1),this.linewidth=U(t.linewidth,2),super.init(t)}update(e){e.position?this.build():super.update(e)}updateData(e,t){let i={};if(e&&!e.labelSize||Object.assign(i,{size:ar(this.n,this.labelSize)}),!e||e.labelColor){let r=new dt(this.labelColor);Object.assign(i,{color:Kt(this.n,r.r,r.g,r.b)})}this.textBuffer.setAttributes(i)}setParameters(e,t={},i=!1){return e&&e.labelSize&&(t.labelSize=!0),e&&(e.labelColor||e.labelColor===0)&&(t.labelColor=!0,i=!0),super.setParameters(e,t,i),e&&e.opacity!==void 0&&this.textBuffer.setParameters({opacity:1}),e&&e.labelVisible!==void 0&&this.setVisibility(this.visible),this}setVisibility(e,t){return super.setVisibility(e,!0),this.textBuffer&&this.textBuffer.setVisibility(this.labelVisible&&this.visible),t||this.viewer.requestRender(),this}getLabelBufferParams(e={}){return super.getBufferParams(Object.assign({fontFamily:this.labelFontFamily,fontStyle:this.labelFontStyle,fontWeight:this.labelFontWeight,sdf:this.labelsdf,xOffset:this.labelXOffset,yOffset:this.labelYOffset,zOffset:this.labelZOffset,attachment:this.labelAttachment,showBorder:this.labelBorder,borderColor:this.labelBorderColor,borderWidth:this.labelBorderWidth,showBackground:this.labelBackground,backgroundColor:this.labelBackgroundColor,backgroundMargin:this.labelBackgroundMargin,backgroundOpacity:this.labelBackgroundOpacity,fixedSize:this.labelFixedSize,disablePicking:!0,visible:this.labelVisible},e,{opacity:1}))}getAtomRadius(){return 0}};function Pw(n,e){let t=n.getAtomProxy(),i=new tn,r=e.length;if(r===0)return new Float32Array(0);let s=e[0].length,o=n.getAtomSet(),a=new Float32Array(r*s*3),l=0;return e.forEach(function(c){let u=!1;for(let d=0;d 1.0 ){ +gl_FragColor = vec4( backgroundColor, backgroundOpacity ); +}else{ +float sdf = texture2D( fontTexture, texCoord ).a; +if( showBorder ) sdf += borderWidth; +float a = smoothstep(padding - gamma, padding + gamma, sdf); +if( a < 0.2 ) discard; +a *= opacity; +vec3 outgoingLight = vColor; +if( showBorder && sdf < ( padding + borderWidth ) ){ +outgoingLight = borderColor; +} +gl_FragColor = vec4( outgoingLight, a ); +} +#if defined( PICKING ) +if( opacity < 0.3 ) +discard; +gl_FragColor = vec4( vPickingColor, objectId ); +#else +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +#endif +}`);var Qv={},Sz={font:"sans-serif",size:36,style:"normal",variant:"normal",weight:"normal",outline:3,width:1024,height:1024},u2=class{constructor(e={}){this.gamma=1,this.mapped={},this.scratchW=0,this.scratchH=0,this.currentX=0,this.currentY=0,this.cutoff=.25,this.parameters=or(e,Sz);let t=this.parameters;this.radius=t.size/8,this.padding=t.size/3;let i=this.lineHeight=t.size+2*t.outline+Math.round(t.size/4),r=this.maxWidth=t.width/4,s=this.canvas=document.createElement("canvas");s.width=r,s.height=i;let o=this.context=this.canvas.getContext("2d",{willReadFrequently:!0});o.font=`${t.style} ${t.variant} ${t.weight} ${t.size}px ${t.font}`,o.fillStyle="black",o.textAlign="left",o.textBaseline="bottom",o.lineJoin="round",this.gridOuter=new Float64Array(i*r),this.gridInner=new Float64Array(i*r),this.f=new Float64Array(Math.max(i,r)),this.d=new Float64Array(Math.max(i,r)),this.z=new Float64Array(Math.max(i,r)+1),this.v=new Int16Array(Math.max(i,r)),this.data=new Uint8Array(t.width*t.height*4),this.canvas2=document.createElement("canvas"),this.canvas2.width=t.width,this.canvas2.height=t.height,this.context2=this.canvas2.getContext("2d"),this.placeholder=this.map("\uFFFD");for(let a=32;a<=126;++a)this.map(String.fromCharCode(a));this.map("\xB0"),this.map("\u212B"),this.texture=new em(this.canvas2),this.texture.flipY=!1,this.texture.needsUpdate=!0}map(e){let t=this.parameters;return this.mapped[e]===void 0&&(this.draw(e),this.currentX+this.scratchW>t.width&&(this.currentX=0,this.currentY+=this.scratchH),this.currentY+this.scratchH>t.height&&console.warn("canvas to small"),this.mapped[e]={x:this.currentX,y:this.currentY,w:this.scratchW,h:this.scratchH},this.context2.drawImage(this.canvas,0,0,this.scratchW,this.scratchH,this.currentX,this.currentY,this.scratchW,this.scratchH),this.currentX+=this.scratchW),this.mapped[e]}get(e){return this.mapped[e]||this.placeholder}draw(e){let t=this.parameters,i=this.lineHeight,r=t.outline,s=this.context,o=this.maxWidth,a=r,l=i-t.outline,c=s.measureText(e),u=Math.min(o,Math.ceil(c.width+2*a+1)),d=u*i;s.clearRect(0,0,u,i),s.fillText(e,a,l);let f=s.getImageData(0,0,u,i),m=f.data;for(let p=0;p= 0.0 ) { +trimSegment( start, end ); +} else if ( end.z < 0.0 && start.z >= 0.0 ) { +trimSegment( end, start ); +} +} +vec4 clipStart = projectionMatrix * start; +vec4 clipEnd = projectionMatrix * end; +vec2 ndcStart = clipStart.xy / clipStart.w; +vec2 ndcEnd = clipEnd.xy / clipEnd.w; +vec2 dir = ndcEnd - ndcStart; +dir.x *= aspect; +dir = normalize( dir ); +vec2 offset = vec2( dir.y, - dir.x ); +dir.x /= aspect; +offset.x /= aspect; +if ( mapping.x < 0.0 ) offset *= - 1.0; +offset *= linewidth; +offset /= resolution.y; +vec4 clip = ( mapping.y < 0.5 ) ? clipStart : clipEnd; +offset *= clip.w; +clip.xy += offset; +gl_Position = clip; +#ifndef PICKING +vViewPosition = ( projectionMatrixInverse * clip ).xyz; +#endif +#if defined( RADIUS_CLIP ) +vClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz; +#endif +#include nearclip_vertex +}`),zt.add("shader/WideLine.frag",`uniform vec3 diffuse; +uniform float opacity; +uniform float clipNear; +uniform float clipRadius; +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +#ifdef PICKING +uniform float objectId; +varying vec3 vPickingColor; +#else +#include common +#include fog_pars_fragment +varying vec3 vViewPosition; +varying vec3 vColor; +varying vec3 vColor2; +varying float flag; +#endif +void main() { +#include nearclip_fragment +#include radiusclip_fragment +#if defined( PICKING ) +if( opacity < 0.3 ) +discard; +gl_FragColor = vec4( vPickingColor, objectId ); +#else +vec3 outgoingLight = vec3( 0.0 ); +vec4 diffuseColor = vec4( diffuse, 1.0 ); +if ( flag < 0.0 ) { +diffuseColor.rgb *= vColor; +} else { +diffuseColor.rgb *= vColor2; +} +#include alphatest_fragment +outgoingLight = diffuseColor.rgb; +gl_FragColor = vec4( outgoingLight, diffuseColor.a * opacity ); +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +#endif +}`);var Cz=Object.assign({linewidth:2},ki),Ez=Object.assign({linewidth:{uniform:!0}},cl),es=class extends wd{constructor(e,t={}){super(e,t),this.parameterTypes=Ez,this.vertexShader="WideLine.vert",this.fragmentShader="WideLine.frag",!e.color2&&e.color&&(e.color2=e.color),this.addUniforms({linewidth:{value:this.parameters.linewidth},resolution:{value:new Et},projectionMatrixInverse:{value:new qe}}),this.addAttributes({position1:{type:"v3",value:null},position2:{type:"v3",value:null},color2:{type:"c",value:null}}),this.setAttributes(e),this.makeMapping()}get defaultParameters(){return Cz}setParameters(e){super.setParameters(e)}};cr.add("wideline",es);var h2=class extends Md{constructor(e,t,i){super(e,t,i),this.type="angle",this.parameters=Object.assign({atomTriple:{type:"hidden",rebuild:!0},vectorVisible:{type:"boolean",default:!0},arcVisible:{type:"boolean",default:!0},sectorVisible:{type:"boolean",default:!0}},this.parameters),this.init(i)}init(e){let t=e||{};t.side=U(t.side,"double"),t.opacity=U(t.opacity,.5),this.atomTriple=U(t.atomTriple,[]),this.arcVisible=U(t.arcVisible,!0),this.sectorVisible=U(t.sectorVisible,!0),this.vectorVisible=U(t.vectorVisible,!0),super.init(t)}createData(e){if(!e.atomCount||!this.atomTriple.length)return;let t=function(a,l){return function(c){let u=[],d=c.length/9;for(let p=0;p radius2) { +discard; +} +#ifdef CAP +surface_point = front_point; +_normal = axis; +#else +surface_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction; +dNV = dot(-axis, ray_direction); +near = dot(axis, end) / dNV; +new_point2 = ray_direction * near + ray_origin; +if (dot(new_point2 - end, new_point2-base) < radius2) { +discard; +} +interior = true; +#endif +} +if( end_cap_test > 0.0 ) +{ +float dNV; +float near; +vec3 end_point; +if ( ortho == 1.0 ) { +end_point = ray_target; +} else { +dNV = dot(axis, ray_direction); +if (dNV < 0.0) { +discard; +} +near = dot(axis, end) / dNV; +end_point = ray_direction * near + ray_origin; +} +if( dot(end_point - end, end_point-base) > radius2 ) { +discard; +} +#ifdef CAP +surface_point = end_point; +_normal = axis; +#else +surface_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction; +dNV = dot(-axis, ray_direction); +near = dot(-axis, (base)) / dNV; +new_point2 = ray_direction * near + ray_origin; +if (dot(new_point2 - base, new_point2-base) < radius2) { +discard; +} +interior = true; +#endif +} +gl_FragDepthEXT = calcDepth( surface_point ); +#ifdef NEAR_CLIP +if( calcClip( surface_point ) > 0.0 ){ +dist = (-a1 - sqrt(d)) / a2; +surface_point = ray_target + dist * ray_direction; +if( calcClip( surface_point ) > 0.0 ) { +discard; +} +interior = true; +gl_FragDepthEXT = calcDepth( surface_point ); +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( clipNear - 0.5 ) ) ) + ( 0.0000001 / vRadius ) ); +} +}else if( gl_FragDepthEXT <= 0.0 ){ +dist = (-a1 - sqrt(d)) / a2; +surface_point = ray_target + dist * ray_direction; +interior = true; +gl_FragDepthEXT = calcDepth( surface_point ); +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius ); +} +} +#else +if( gl_FragDepthEXT <= 0.0 ){ +dist = (-a1 - sqrt(d)) / a2; +surface_point = ray_target + dist * ray_direction; +interior = true; +gl_FragDepthEXT = calcDepth( surface_point ); +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius ); +} +} +#endif +if (gl_FragDepthEXT < 0.0) { +discard; +} +if (gl_FragDepthEXT > 1.0) { +discard; +} +#ifdef PICKING +if( opacity < 0.3 ) +discard; +gl_FragColor = vec4( vPickingColor, objectId ); +#else +vec3 vViewPosition = -surface_point; +vec3 vNormal = _normal; +vec3 vColor; +if( distSq3( surface_point, end ) < distSq3( surface_point, base ) ){ +if( b < 0.0 ){ +vColor = vColor1; +}else{ +vColor = vColor2; +} +}else{ +if( b > 0.0 ){ +vColor = vColor1; +}else{ +vColor = vColor2; +} +} +vec4 diffuseColor = vec4( diffuse, opacity ); +ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); +vec3 totalEmissiveLight = emissive; +#include color_fragment +#include roughnessmap_fragment +#include metalnessmap_fragment +vec3 normal = normalize( vNormal ); +vec3 nonPerturbedNormal = normal; +#include lights_physical_fragment +#include lights_fragment_begin +#include lights_fragment_end +vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight; +if( interior ){ +#ifdef USE_INTERIOR_COLOR +outgoingLight.xyz = interiorColor; +#else +#ifdef DIFFUSE_INTERIOR +outgoingLight.xyz = vColor; +#endif +#endif +outgoingLight.xyz *= 1.0 - interiorDarkening; +} +gl_FragColor = vec4( outgoingLight, diffuseColor.a ); +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +#endif +}`);var Pz=new Float32Array([-1,1,-1,-1,-1,-1,1,1,-1,1,1,1,1,-1,-1,1,-1,1]),Iz=new Uint16Array([0,1,2,1,4,2,2,4,3,4,5,3]),r0=class extends bd{constructor(e,t={}){super("v3",e,t)}get mapping(){return Pz}get mappingIndices(){return Iz}get mappingIndicesSize(){return 12}get mappingSize(){return 6}get mappingItemSize(){return 3}},pI=Object.assign({openEnded:!1},ki),Rz=Object.assign({openEnded:{updateShader:!0}},cl),d2=class extends r0{constructor(e,t={}){super(e,t),this.parameterTypes=Rz,this.isImpostor=!0,this.vertexShader="CylinderImpostor.vert",this.fragmentShader="CylinderImpostor.frag",this.addUniforms({modelViewMatrixInverse:{value:new qe},ortho:{value:0}}),this.addAttributes({position1:{type:"v3",value:null},position2:{type:"v3",value:null},color2:{type:"c",value:null},radius:{type:"f",value:null}}),this.setAttributes(e),this.makeMapping()}get defaultParameters(){return pI}getDefines(e){let t=r0.prototype.getDefines.call(this,e);return this.parameters.openEnded||(t.CAP=1),t}};Object.assign({disableImpostor:!1},Iw,pI);var ao=class{constructor(n,e={}){return!n.color2&&n.color&&(n.color2=n.color),!ys||e&&e.disableImpostor?new i0(n,e):new d2(n,e)}};cr.add("cylinder",ao);var f2=class extends Zn{constructor(e,t,i){super(e,t,i),this.type="axes",this.parameters=Object.assign({radiusSize:{type:"number",precision:3,max:10,min:.001},sphereDetail:!0,radialSegments:!0,disableImpostor:!0,showAxes:{type:"boolean",rebuild:!0},showBox:{type:"boolean",rebuild:!0}},this.parameters,{assembly:null}),this.init(i)}init(e){let t=e||{};t.radiusSize=U(t.radiusSize,.5),t.colorValue=U(t.colorValue,"lightgreen"),t.useInteriorColor=U(t.useInteriorColor,!0),this.showAxes=U(t.showAxes,!0),this.showBox=U(t.showBox,!1),super.init(t)}getPrincipalAxes(){let e,t=this.getAssembly();return t&&(e=t.partList[0].getSelection()),this.structureView.getPrincipalAxes(e)}getAxesData(e){let t=this.getPrincipalAxes(),i=new dt(this.colorValue),r=0,s=0;this.showAxes&&(r+=6,s+=3),this.showBox&&(r+=8,s+=12);let o=new Float32Array(3*r),a=Kt(r,i.r,i.g,i.b),l=ar(r,this.radiusSize),c=new Float32Array(3*s),u=new Float32Array(3*s),d=Kt(s,i.r,i.g,i.b),f=ar(s,this.radiusSize),m=0;if(this.showAxes){let _=function(y,g){y.toArray(o,2*m),g.toArray(o,2*m+3),y.toArray(c,m),g.toArray(u,m),m+=3};_(t.begA,t.endA),_(t.begB,t.endB),_(t.begC,t.endC)}if(this.showBox){let _=new W,{d1a:y,d2a:g,d3a:b,d1b:h,d2b:v,d3b:S}=t.getProjectedScaleForAtoms(e),x=2*m,w=function(T,R,C){_.copy(t.center).addScaledVector(t.normVecA,T).addScaledVector(t.normVecB,R).addScaledVector(t.normVecC,C),_.toArray(o,x),x+=3};w(y,g,b),w(y,g,S),w(y,v,S),w(y,v,b),w(h,v,S),w(h,v,b),w(h,g,b),w(h,g,S);let A=m,M=function(T,R){_.fromArray(o,2*m+3*T).toArray(c,A),_.fromArray(o,2*m+3*R).toArray(u,A),A+=3};M(0,1),M(0,3),M(0,6),M(1,2),M(1,7),M(2,3),M(2,4),M(3,5),M(4,5),M(4,7),M(5,6),M(6,7)}let p=new cb(t);return{vertex:{position:o,color:a,radius:l,picking:p},edge:{position1:c,position2:u,color:d,color2:d,radius:f,picking:p}}}create(){let e=this.getAxesData(this.structureView);this.sphereBuffer=new la(e.vertex,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0})),this.cylinderBuffer=new ao(e.edge,this.getBufferParams({openEnded:!0,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0})),this.dataList.push({sview:this.structureView,bufferList:[this.sphereBuffer,this.cylinderBuffer]})}createData(e){}updateData(e,t){let i=this.getAxesData(t.sview),r={},s={};e&&!e.position||(Object.assign(r,{position:i.vertex.position}),Object.assign(s,{position1:i.edge.position1,position2:i.edge.position2})),e&&!e.color||(Object.assign(r,{color:i.vertex.color}),Object.assign(s,{color:i.edge.color,color2:i.edge.color})),e&&!e.radius||(Object.assign(r,{radius:i.vertex.radius}),Object.assign(s,{radius:i.edge.radius})),this.sphereBuffer.setAttributes(r),this.cylinderBuffer.setAttributes(s)}};on.add("axes",f2);var eu=class extends Zn{constructor(e,t,i){super(e,t,i),this.type="ball+stick",this.parameters=Object.assign({sphereDetail:!0,radialSegments:!0,openEnded:!0,disableImpostor:!0,aspectRatio:{type:"number",precision:1,max:10,min:1},lineOnly:{type:"boolean",rebuild:!0},cylinderOnly:{type:"boolean",rebuild:!0},multipleBond:{type:"select",rebuild:!0,options:{off:"off",symmetric:"symmetric",offset:"offset"}},bondScale:{type:"number",precision:2,max:1,min:.01},bondSpacing:{type:"number",precision:2,max:2,min:.5},linewidth:{type:"integer",max:50,min:1,buffer:!0}},this.parameters),this.init(i)}init(e){var t=e||{};t.radiusType=U(t.radiusType,"size"),t.radiusSize=U(t.radiusSize,.15),t.useInteriorColor=U(t.useInteriorColor,!0),this.aspectRatio=U(t.aspectRatio,2),this.lineOnly=U(t.lineOnly,!1),this.cylinderOnly=U(t.cylinderOnly,!1),this.multipleBond=U(t.multipleBond,"off"),this.bondSpacing=U(t.bondSpacing,1),this.bondScale=U(t.bondScale,.4),this.linewidth=U(t.linewidth,2),super.init(t)}getAtomRadius(e){return this.aspectRatio*super.getAtomRadius(e)}getAtomParams(e,t){var i=super.getAtomParams(e,t);return i.radiusParams.scale*=this.aspectRatio,i}getAtomData(e,t,i){return e.getAtomData(this.getAtomParams(t,i))}getBondParams(e,t){return t=Object.assign({multipleBond:this.multipleBond,bondSpacing:this.bondSpacing,bondScale:this.bondScale},t),super.getBondParams(e,t)}getBondData(e,t,i){return e.getBondData(this.getBondParams(t,i))}createData(e){let t=[];if(this.lineOnly)this.lineBuffer=new es(this.getBondData(e,{position:!0,color:!0,picking:!0}),this.getBufferParams({linewidth:this.linewidth})),t.push(this.lineBuffer);else{let i=new ao(this.getBondData(e),this.getBufferParams({openEnded:this.openEnded,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0}));if(t.push(i),!this.cylinderOnly){let r=new la(this.getAtomData(e),this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0}));t.push(r)}}return{bufferList:t}}updateData(e,t){this.multipleBond!=="off"&&e&&e.radius&&(e.position=!0);let i=this.getBondData(t.sview,e);if(this.lineOnly){let a={};e&&!e.position||Object.assign(a,{position1:i.position1,position2:i.position2}),e&&!e.color||Object.assign(a,{color:i.color,color2:i.color2}),t.bufferList[0].setAttributes(a)}else{var r={};if(e&&!e.position||Object.assign(r,{position1:i.position1,position2:i.position2}),e&&!e.color||Object.assign(r,{color:i.color,color2:i.color2}),e&&!e.radius||Object.assign(r,{radius:i.radius}),t.bufferList[0].setAttributes(r),!this.cylinderOnly){var s=this.getAtomData(t.sview,e),o={};e&&!e.position||Object.assign(o,{position:s.position}),e&&!e.color||Object.assign(o,{color:s.color}),e&&!e.radius||Object.assign(o,{radius:s.radius}),t.bufferList[1].setAttributes(o)}}}setParameters(e={}){let t=!1,i={};return(e.aspectRatio||e.bondSpacing||e.bondScale)&&(Object.assign(i,{radius:!0}),ys&&!this.disableImpostor||(t=!0)),super.setParameters(e,i,t),this}};on.add("ball+stick",eu);var p2=class extends eu{constructor(e,t,i){super(e,t,i),this.type="backbone",this.parameters=Object.assign({},this.parameters,{multipleBond:null,bondSpacing:null}),this.init(i)}init(e){var t=e||{};t.aspectRatio=U(t.aspectRatio,1),t.radiusSize=U(t.radiusSize,.25),super.init(t)}getAtomRadius(e){return e.isTrace()?super.getAtomRadius(e):0}getAtomData(e,t,i){return e.getBackboneAtomData(this.getAtomParams(t,i))}getBondData(e,t,i){return e.getBackboneBondData(this.getBondParams(t,i))}};on.add("backbone",p2);var m2=class extends eu{constructor(e,t,i){super(e,t,i),this.type="base",this.parameters=Object.assign({},this.parameters,{multipleBond:null,bondSpacing:null})}init(e){let t=e||{};t.aspectRatio=U(t.aspectRatio,1),t.radiusSize=U(t.radiusSize,.3),super.init(t)}getAtomData(e,t,i){return e.getRungAtomData(this.getAtomParams(t,i))}getBondData(e,t,i){let r=this.getBondParams(t,i);return Object.assign(r.colorParams,{rung:!0}),e.getRungBondData(r)}};on.add("base",m2);var g2=class{constructor(e,t){this.m=e,this.tension=t,this.dt=1/this.m,this.delta=1e-4,this.vec1=new W,this.vec2=new W,this.vDir=new W,this.vTan=new W,this.vNorm=new W,this.vBin=new W,this.m2=Math.ceil(this.m/2)}interpolateToArr(e,t,i,r,s,o,a){o[a+0]=no(e.x,t.x,i.x,r.x,s,this.tension),o[a+1]=no(e.y,t.y,i.y,r.y,s,this.tension),o[a+2]=no(e.z,t.z,i.z,r.z,s,this.tension)}interpolateToVec(e,t,i,r,s,o){o.x=no(e.x,t.x,i.x,r.x,s,this.tension),o.y=no(e.y,t.y,i.y,r.y,s,this.tension),o.z=no(e.z,t.z,i.z,r.z,s,this.tension)}interpolatePosition(e,t,i,r,s,o){for(var a=0;a1&&(u=1),this.interpolateToVec(e,t,i,r,c,this.vec1),this.interpolateToVec(e,t,i,r,u,this.vec2),this.vec2.sub(this.vec1).normalize(),this.vec2.toArray(s,d)}}vectorSubdivide(e,t,i,r,s){let o,a=t.next(),l=t.next(),c=t.next(),u=t.size,d=u-1,f=r||0;for(let m=0;m0&&m{if(r.residueCount<4)return;i.push(r);let s=this.getSpline(r),o=this.getAspectRatio(r),a=s.getSubdividedPosition(),l=s.getSubdividedOrientation(),c=s.getSubdividedColor(this.getColorParams()),u=s.getSubdividedPicking(),d=s.getSubdividedSize(this.getRadiusParams());t.push(new y2(Object.assign({},a,l,c,u,d),this.getBufferParams({radialSegments:this.radialSegments,aspectRatio:o,capped:this.capped})))},e.getSelection()),{bufferList:t,polymerList:i}}updateData(e,t){Le&&we.time(this.type+" repr update"),e=e||{};for(var i=0,r=t.polymerList.length;i0;xn(P,M,E);let ee=Vi(P,R)<0;if(Jt(P,R,Vi(R,T)),xn(I,T,P),Jt(P,R,Vi(R,C)),xn(O,C,P),Qo(I)===0||Qo(O)===0)continue;Cn(I,I),Cn(O,O);let le=f[L]=GB(I,O);p[L]=(zP*le).toFixed(1)+"\xB0",$i(H,I,R),Cn(H,H),Vi(H,O)<0&&P0(H,H),Yr(P,E,I,H,le/2),Tt(P,m,3*L);let xe=Math.ceil(le/c),Se=xe+(l.extendLine?4:2),Re=l.extendLine?36:0,ke=new Float32Array(3*Se),$e=new Float32Array(3*Se),_e=new Float32Array(9*xe),Ie=new Float32Array(Re);_[L]=ke,y[L]=$e,g[L]=_e,b[L]=Ie,l.extendLine&&(oe?(xn(P,x,A),Cn(P,P),Jt(D,P,1/Vi(I,P)),Zr(D,D,A)):(Jt(D,T,1/Vi(I,T)),Zr(D,D,w)),ee?(xn(P,M,w),Cn(P,P),Jt(N,P,1/Vi(O,P)),Zr(N,N,w)):(Jt(N,C,1/Vi(O,C)),Zr(N,N,A))),Zr(z,E,I);let We=0;l.extendLine?(Tt(x,ke,We),Tt(D,$e,We),We+=3,Tt(D,ke,We),Tt(z,$e,We),We+=3,Tt(D,Ie,0),Tt(z,Ie,3),Tt(oe?A:w,Ie,6),Tt(oe?A:w,Ie,9),Tt(z,Ie,12),Tt(E,Ie,15)):(Tt(E,ke,We),Tt(z,$e,We),We+=3);let Fe=function($,de){let Te=9*de;Tt(E,_e,Te),Tt(z,_e,Te+3),Tt(z,ke,We),Yr(z,E,I,H,$),Tt(z,_e,Te+6),Tt(z,$e,We),We+=3},Y=0;for(let $=c;${let o=nx(i,s);Object.assign(s,o)}),t.side=U(t.side,"double"),t.opacity=U(t.opacity,.5),t.radiusType=U(t.radiusType,"size"),t.radiusSize=U(t.radiusSize,.15),super.init(t)}getHistogramBinBorderBufferParameters(){return this.getBufferParams({linewidth:this.histogramBinBorderWidth,visible:this.histogramBinBorderVisible,opacity:this.histogramBinBorderOpacity})}getBondArrowsBufferParameters(){return this.getBufferParams({linewidth:this.bondArrowWidth,visible:this.bondArrowVisible,opacity:this.bondArrowOpacity})}getOpaqueMiddleDiscBufferParameters(){return this.getBufferParams({visible:this.opaqueMiddleDiscVisible,opacity:this.opaqueMiddleDiscOpacity})}getHistogramBufferParameters(){return this.getBufferParams({visible:!0,opacity:this.histogramOpacity,side:"double"})}createData(e){if(!e.atomCount||!this.histogramsData.length)return;this.histogramsData.forEach(a=>a.atomPositions=Pw(e,[a.atomQuad]));let t=this.scaleBinToSectorArea?function(a){return Math.sqrt(a)}:function(a){return a};function i(a){let l=a.map(d=>d.length),c=new Float32Array(ww(l)),u=0;for(let d=0;dc.startPoints)),position2:i(a.map(c=>c.endPoints)),color:i(a.map(c=>c.startColors)),color2:i(a.map(c=>c.endColors))},l)}function s(a,l){return new Jr({position:i(a.map(c=>c.triangles)),color:i(a.map(c=>c.triangleColors))},l)}this.histogramsData.forEach(a=>a.histogram360Scaled=a.histogram360.map(t));let o=[];for(let a=0;a=3&&(l=Lz(c)),l!==void 0&&o.push(l)}return this.frontHistogramBinBordersBuffer=r(o.map(a=>a.frontHistogramBinBorders),this.getHistogramBinBorderBufferParameters()),this.backHistogramBinBordersBuffer=r(o.map(a=>a.backHistogramBinBorders),this.getHistogramBinBorderBufferParameters()),this.adjacentBondArrowsBuffer=r(o.map(a=>a.adjacentBondArrows),this.getBondArrowsBufferParameters()),this.distantBondArrowsBuffer=r(o.map(a=>a.distantBondArrows),this.getBondArrowsBufferParameters()),this.opaqueMiddleDiscBuffer=s(o.map(a=>a.opaqueMiddleDisc),this.getOpaqueMiddleDiscBufferParameters()),this.frontHistogramBuffer=s(o.map(a=>a.frontHistogram),this.getHistogramBufferParameters()),this.backHistogramBuffer=s(o.map(a=>a.backHistogram),this.getHistogramBufferParameters()),{bufferList:[].concat(this.frontHistogramBinBordersBuffer,this.backHistogramBinBordersBuffer,this.adjacentBondArrowsBuffer,this.distantBondArrowsBuffer,this.opaqueMiddleDiscBuffer,this.frontHistogramBuffer,this.backHistogramBuffer)}}setParameters(e){return super.setParameters(e,{},!1),e&&e.histogramBinBorderVisible!==void 0&&this.setVisibility(this.visible),this}setVisibility(e,t){return super.setVisibility(e,!0),this.frontHistogramBinBordersBuffer&&this.frontHistogramBinBordersBuffer.setVisibility(this.histogramBinBorderVisible),this.backHistogramBinBordersBuffer&&this.backHistogramBinBordersBuffer.setVisibility(this.histogramBinBorderVisible),t||this.viewer.requestRender(),this}};function Lz(n){let e=n.atomPositions,t=n.histogram360Scaled,i=t.length<=180?360:2*t.length,r={triangles:new Float32Array(3*i*3),triangleColors:Wr(n.opaqueMiddleDiscColor,3*i)},s={triangles:new Float32Array(3*t.length*3),triangleColors:Wr(n.frontHistogramColor,3*t.length)},o={triangles:new Float32Array(3*t.length*3),triangleColors:Wr(n.backHistogramColor,3*t.length)},a={startPoints:new Float32Array(3*t.length),endPoints:new Float32Array(3*t.length),startColors:Wr(n.histogramBinBorderColor,t.length),endColors:Wr(n.histogramBinBorderColor,t.length)},l={startPoints:new Float32Array(3*t.length),endPoints:new Float32Array(3*t.length),startColors:Wr(n.histogramBinBorderColor,t.length),endColors:Wr(n.histogramBinBorderColor,t.length)},c={startPoints:new Float32Array(6),endPoints:new Float32Array(6),startColors:Wr(n.adjacentBondArrowColor,t.length),endColors:Wr(n.adjacentBondArrowColor,t.length)},u={startPoints:new Float32Array(6),endPoints:new Float32Array(6),startColors:Wr(n.distantBondArrowColor,t.length),endColors:Wr(n.distantBondArrowColor,t.length)},d=Mt(),f=Mt(),m=Mt(),p=Mt(),_=Mt(),y=Mt(),g=Mt(),b=Mt(),h=Mt(),v=Mt(),S=Mt(),x=Mt(),w=Mt(),A=Mt(),M=Mt(),T=Mt(),R=[d,f,m,p];for(let H=0;H{let y=p[0],g=p[1];if(typeof y=="number"&&Number.isInteger(y)&&typeof g=="number"&&Number.isInteger(g)){if(!f.get(y)||!f.get(g))return void(d+=1);c.index=y,u.index=g}else{o.setString(y),a.setString(g);var b=e.getAtomIndices(o),h=e.getAtomIndices(a);if(!b.length||!h.length)return void(d+=1);c.index=b[0],u.index=h[0]}l.addBond(c,u,1),_-=d;var v=c.distanceTo(u);switch(this.labelUnit){case"angstrom":r[_]=v.toFixed(2)+" \u212B";break;case"nm":r[_]=(v/10).toFixed(2)+" nm";break;default:r[_]=v.toFixed(2)}var S=3*_;s[S+0]=(c.x+u.x)/2,s[S+1]=(c.y+u.y)/2,s[S+2]=(c.z+u.z)/2}),d>0&&(i-=d,s=s.subarray(0,3*i));var m=new ii(l.count,!0);return{text:r,position:s,bondSet:m,bondStore:l}}getBondData(e,t,i){let r=e.getBondData(this.getBondParams(t,i));return r.picking&&(r.picking=new db(r.picking.array,r.picking.structure,i.bondStore)),r}createData(e){if(!e.atomCount||!this.atomPair.length)return;let t=this.atomPair.length,i=new dt(this.labelColor),r=this.getDistanceData(e,this.atomPair);this.textBuffer=new oa({position:r.position,size:ar(t,this.labelSize),color:Kt(t,i.r,i.g,i.b),text:r.text},this.getLabelBufferParams());let s={bondSet:r.bondSet,bondStore:r.bondStore},o=this.getBondData(e,{position:!0,color:!0,picking:!0,radius:this.useCylinder},s);return this.useCylinder?this.distanceBuffer=new ao(o,this.getBufferParams({openEnded:this.openEnded,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0})):this.distanceBuffer=new es($P(o),this.getBufferParams({linewidth:this.linewidth,visible:this.lineVisible,opacity:this.lineOpacity})),{bondSet:r.bondSet,bondStore:r.bondStore,position:r.position,bufferList:[this.textBuffer,this.distanceBuffer]}}updateData(e,t){super.updateData(e,t);let i={bondSet:t.bondSet,bondStore:t.bondStore},r=this.getBondData(t.sview,e,i),s={};e&&!e.color||Object.assign(s,{color:r.color,color2:r.color2}),e&&!e.radius||Object.assign(s,{radius:r.radius}),this.distanceBuffer.setAttributes(s)}setParameters(e){return super.setParameters(e,{},!1),this.useCylinder||(e&&e.lineOpacity&&this.distanceBuffer.setParameters({opacity:e.lineOpacity}),e&&e.opacity!==void 0&&this.distanceBuffer.setParameters({opacity:this.lineOpacity}),e&&e.linewidth&&this.distanceBuffer.setParameters({linewidth:e.linewidth})),this}};function ix(n){return 2*(n.position.length/3)*3}on.add("distance",b2);var Dz=Object.assign({scale:1,color:"grey"},ki),s0=class extends Pr{constructor(e,t={}){super({position:new Float32Array(ix(e)),color:new Float32Array(ix(e))},t),this.isLine=!0,this.vertexShader="Line.vert",this.fragmentShader="Line.frag";let i=new dt(this.parameters.color),r=this.geometry.attributes;Kt(ix(e)/3,i.r,i.g,i.b,r.color.array),this.setAttributes(e)}get defaultParameters(){return Dz}setAttributes(e={}){let t=this.geometry.attributes,i,r,s;e.position&&e.vector&&(i=e.position,r=e.vector,s=t.position.array,t.position.needsUpdate=!0);let o=this.size/2,a=this.parameters.scale;if(i&&r)for(let l=0;l{if(r.residueCount<4)return;i.push(r);let s=new Kc(r),o=s.getPosition(),a=s.getColor(this.getColorParams()),l=s.getSize(this.getRadiusParams()),c=s.getPicking();t.push(new la({position:o.center,color:a.color,radius:l.size,picking:c.picking},this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0})),new s0({position:o.center,vector:o.axis},this.getBufferParams({color:"skyblue",scale:1})),new s0({position:o.center,vector:o.resdir},this.getBufferParams({color:"lightgreen",scale:1})))},e.getSelection()),{bufferList:t,polymerList:i}}updateData(e,t){Le&&we.time(this.type+" repr update"),e=e||{};for(let i=0,r=t.polymerList.length;i radius2) { +spaceposition.y = mapping.y * 1.5 * radius1; +spaceposition.x = mapping.x * 1.5 * radius1; +} else { +spaceposition.y = mapping.y * 1.5 * radius2; +spaceposition.x = mapping.x * 1.5 * radius2; +} +spaceposition.w = 1.0; +vec4 e3 = vec4( 1.0 ); +vec3 e1, e1_temp, e2, e2_temp; +e3.xyz = normalize(position_atom1-position_atom2); +if (e3.z == 0.0) { e3.z = 0.0000000000001;} +if ( (position_atom1.x - position_atom2.x) == 0.0) { position_atom1.x += 0.001;} +if ( (position_atom1.y - position_atom2.y) == 0.0) { position_atom1.y += 0.001;} +if ( (position_atom1.z - position_atom2.z) == 0.0) { position_atom1.z += 0.001;} +vec4 focus = vec4( 1.0 ); +focus.x = ( position_atom1.x*position_atom1.x - position_atom2.x*position_atom2.x + +( radius2*radius2 - radius1*radius1 )*e3.x*e3.x/shrink )/(2.0*(position_atom1.x - position_atom2.x)); +focus.y = ( position_atom1.y*position_atom1.y - position_atom2.y*position_atom2.y + +( radius2*radius2 - radius1*radius1 )*e3.y*e3.y/shrink )/(2.0*(position_atom1.y - position_atom2.y)); +focus.z = ( position_atom1.z*position_atom1.z - position_atom2.z*position_atom2.z + +( radius2*radius2 - radius1*radius1 )*e3.z*e3.z/shrink )/(2.0*(position_atom1.z - position_atom2.z)); +e1.x = 1.0; +e1.y = 1.0; +e1.z = ( (e3.x*focus.x + e3.y*focus.y + e3.z*focus.z) - e1.x*e3.x - e1.y*e3.y)/e3.z; +e1_temp = e1 - focus.xyz; +e1 = normalize(e1_temp); +e2_temp = e1.yzx * e3.zxy - e1.zxy * e3.yzx; +e2 = normalize(e2_temp); +mat3 R= mat3( e1.xyz, e2.xyz, e3.xyz ); +vertex_position.xyz = R * spaceposition.xyz; +vertex_position.w = 1.0; +vertex_position.x += (position_atom1.x+position_atom2.x) / 2.0; +vertex_position.y += (position_atom1.y+position_atom2.y) / 2.0; +vertex_position.z += (position_atom1.z+position_atom2.z) / 2.0; +gl_Position = modelViewProjectionMatrix * vertex_position; +vec4 i_near, i_far; +vec4 near = gl_Position; +near.z = 0.0 ; +near = modelViewProjectionMatrixInverse * near; +i_near = near; +vec4 far = gl_Position; +far.z = far.w ; +i_far = modelViewProjectionMatrixInverse * far; +prime1 = vec4( position_atom1 - (position_atom1 - focus.xyz)*shrink, 1.0 ); +prime2 = vec4( position_atom2 - (position_atom2 - focus.xyz)*shrink, 1.0 ); +float Rsquare = (radius1*radius1/shrink) - ( +(position_atom1.x - focus.x)*(position_atom1.x - focus.x) + +(position_atom1.y - focus.y)*(position_atom1.y - focus.y) + +(position_atom1.z - focus.z)*(position_atom1.z - focus.z) +); +focus.w = Rsquare; +matrix_near = mat4( i_near, i_far, focus, e3 ); +gl_Position.z = 1.0; +}`),zt.add("shader/HyperballStickImpostor.frag",`#define STANDARD +#define IMPOSTOR +uniform vec3 diffuse; +uniform vec3 emissive; +uniform vec3 interiorColor; +uniform float interiorDarkening; +uniform float roughness; +uniform float metalness; +uniform float opacity; +uniform float clipNear; +uniform float shrink; +uniform mat4 modelViewMatrix; +uniform mat4 modelViewProjectionMatrix; +uniform mat4 modelViewMatrixInverseTranspose; +uniform mat4 projectionMatrix; +varying mat4 matrix_near; +varying vec4 prime1; +varying vec4 prime2; +varying float vRadius; +varying float vRadius2; +#ifdef PICKING +uniform float objectId; +varying vec3 vPickingColor; +#else +varying vec3 vColor1; +varying vec3 vColor2; +#include common +#include fog_pars_fragment +#include bsdfs +#include lights_pars_begin +#include lights_physical_pars_fragment +#endif +bool interior = false; +float calcClip( vec4 cameraPos ){ +return dot( cameraPos, vec4( 0.0, 0.0, 1.0, clipNear - 0.5 ) ); +} +float calcClip( vec3 cameraPos ){ +return calcClip( vec4( cameraPos, 1.0 ) ); +} +float calcDepth( in vec3 cameraPos ){ +vec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw; +return 0.5 + 0.5 * clipZW.x / clipZW.y; +} +struct Ray { +vec3 origin ; +vec3 direction ; +}; +bool cutoff_plane (vec3 M, vec3 cutoff, vec3 x3){ +float a = x3.x; +float b = x3.y; +float c = x3.z; +float d = -x3.x*cutoff.x-x3.y*cutoff.y-x3.z*cutoff.z; +float l = a*M.x+b*M.y+c*M.z+d; +if (l<0.0) {return true;} +else{return false;} +} +vec3 isect_surf(Ray r, mat4 matrix_coef){ +vec4 direction = vec4(r.direction, 0.0); +vec4 origin = vec4(r.origin, 1.0); +float a = dot(direction,(matrix_coef*direction)); +float b = dot(origin,(matrix_coef*direction)); +float c = dot(origin,(matrix_coef*origin)); +float delta =b*b-a*c; +gl_FragColor.a = 1.0; +if (delta<0.0){ +discard; +} +float t1 =(-b-sqrt(delta))/a; +return r.origin+t1*r.direction; +} +vec3 isect_surf2(Ray r, mat4 matrix_coef){ +vec4 direction = vec4(r.direction, 0.0); +vec4 origin = vec4(r.origin, 1.0); +float a = dot(direction,(matrix_coef*direction)); +float b = dot(origin,(matrix_coef*direction)); +float c = dot(origin,(matrix_coef*origin)); +float delta =b*b-a*c; +gl_FragColor.a = 1.0; +if (delta<0.0){ +discard; +} +float t2 =(-b+sqrt(delta))/a; +return r.origin+t2*r.direction; +} +Ray primary_ray(vec4 near1, vec4 far1){ +vec3 near=near1.xyz/near1.w; +vec3 far=far1.xyz/far1.w; +return Ray(near,far-near); +} +float update_z_buffer(vec3 M, mat4 ModelViewP){ +float depth1; +vec4 Ms=(ModelViewP*vec4(M,1.0)); +return depth1=(1.0+Ms.z/Ms.w)/2.0; +} +void main(){ +float radius = max( vRadius, vRadius2 ); +vec4 i_near, i_far, focus; +vec3 e3, e1, e1_temp, e2; +i_near = vec4(matrix_near[0][0],matrix_near[0][1],matrix_near[0][2],matrix_near[0][3]); +i_far = vec4(matrix_near[1][0],matrix_near[1][1],matrix_near[1][2],matrix_near[1][3]); +focus = vec4(matrix_near[2][0],matrix_near[2][1],matrix_near[2][2],matrix_near[2][3]); +e3 = vec3(matrix_near[3][0],matrix_near[3][1],matrix_near[3][2]); +e1.x = 1.0; +e1.y = 1.0; +e1.z = ( (e3.x*focus.x + e3.y*focus.y + e3.z*focus.z) - e1.x*e3.x - e1.y*e3.y)/e3.z; +e1_temp = e1 - focus.xyz; +e1 = normalize(e1_temp); +e2 = normalize(cross(e1,e3)); +vec4 equation = focus; +float shrinkfactor = shrink; +float t1 = -1.0/(1.0-shrinkfactor); +float t2 = 1.0/(shrinkfactor); +vec4 colonne1, colonne2, colonne3, colonne4; +mat4 mat; +vec3 equation1 = vec3(t2,t2,t1); +float A1 = - e1.x*equation.x - e1.y*equation.y - e1.z*equation.z; +float A2 = - e2.x*equation.x - e2.y*equation.y - e2.z*equation.z; +float A3 = - e3.x*equation.x - e3.y*equation.y - e3.z*equation.z; +float A11 = equation1.x*e1.x*e1.x + equation1.y*e2.x*e2.x + equation1.z*e3.x*e3.x; +float A21 = equation1.x*e1.x*e1.y + equation1.y*e2.x*e2.y + equation1.z*e3.x*e3.y; +float A31 = equation1.x*e1.x*e1.z + equation1.y*e2.x*e2.z + equation1.z*e3.x*e3.z; +float A41 = equation1.x*e1.x*A1 + equation1.y*e2.x*A2 + equation1.z*e3.x*A3; +float A22 = equation1.x*e1.y*e1.y + equation1.y*e2.y*e2.y + equation1.z*e3.y*e3.y; +float A32 = equation1.x*e1.y*e1.z + equation1.y*e2.y*e2.z + equation1.z*e3.y*e3.z; +float A42 = equation1.x*e1.y*A1 + equation1.y*e2.y*A2 + equation1.z*e3.y*A3; +float A33 = equation1.x*e1.z*e1.z + equation1.y*e2.z*e2.z + equation1.z*e3.z*e3.z; +float A43 = equation1.x*e1.z*A1 + equation1.y*e2.z*A2 + equation1.z*e3.z*A3; +float A44 = equation1.x*A1*A1 + equation1.y*A2*A2 + equation1.z*A3*A3 - equation.w; +colonne1 = vec4(A11,A21,A31,A41); +colonne2 = vec4(A21,A22,A32,A42); +colonne3 = vec4(A31,A32,A33,A43); +colonne4 = vec4(A41,A42,A43,A44); +mat = mat4(colonne1,colonne2,colonne3,colonne4); +Ray ray = primary_ray(i_near,i_far) ; +vec3 M; +M = isect_surf(ray, mat); +if (cutoff_plane(M, prime1.xyz, -e3) || cutoff_plane(M, prime2.xyz, e3)){ discard; } +vec4 M1 = vec4(M,1.0); +vec4 M2 = mat*M1; +vec3 _normal = ( modelViewMatrixInverseTranspose * M2 ).xyz; +gl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ; +#ifdef NEAR_CLIP +if( calcClip( modelViewMatrix * vec4( M, 1.0 ) ) > 0.0 ){ +M = isect_surf2(ray, mat); +if( calcClip( modelViewMatrix * vec4( M, 1.0 ) ) > 0.0 ) +discard; +interior = true; +gl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ; +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( clipNear - 0.5 ) ) ) + ( 0.0000001 / radius ) ); +} +}else if( gl_FragDepthEXT <= 0.0 ){ +M = isect_surf2(ray, mat); +interior = true; +gl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix); +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / radius ); +} +} +#else +if( gl_FragDepthEXT <= 0.0 ){ +M = isect_surf2(ray, mat); +interior = true; +gl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ; +if( gl_FragDepthEXT >= 0.0 ){ +gl_FragDepthEXT = 0.0 + ( 0.0000001 / radius ); +} +} +#endif +if (cutoff_plane(M, prime1.xyz, -e3) || cutoff_plane(M, prime2.xyz, e3)){ discard; } +if (gl_FragDepthEXT < 0.0) +discard; +if (gl_FragDepthEXT > 1.0) +discard; +float distance_ratio = ((M.x-prime2.x)*e3.x + (M.y-prime2.y)*e3.y +(M.z-prime2.z)*e3.z) / +distance(prime2.xyz,prime1.xyz); +#ifdef PICKING +if( opacity < 0.3 ) +discard; +gl_FragColor = vec4( vPickingColor, objectId ); +#else +vec3 vViewPosition = -( modelViewMatrix * vec4( M, 1.0 ) ).xyz; +vec3 vNormal = _normal; +vec3 vColor; +if( distance_ratio>0.5 ){ +vColor = vColor1; +}else{ +vColor = vColor2; +} +vec4 diffuseColor = vec4( diffuse, opacity ); +ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) ); +vec3 totalEmissiveLight = emissive; +#include color_fragment +#include roughnessmap_fragment +#include metalnessmap_fragment +vec3 normal = normalize( vNormal ); +vec3 nonPerturbedNormal = normal; +#include lights_physical_fragment +#include lights_fragment_begin +#include lights_fragment_end +vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight; +if( interior ){ +#ifdef USE_INTERIOR_COLOR +outgoingLight.xyz = interiorColor; +#else +#ifdef DIFFUSE_INTERIOR +outgoingLight.xyz = vColor; +#endif +#endif +outgoingLight.xyz *= 1.0 - interiorDarkening; +} +gl_FragColor = vec4( outgoingLight, diffuseColor.a ); +#include premultiplied_alpha_fragment +#include tonemapping_fragment +#include colorspace_fragment +#include fog_fragment +#endif +}`);var Nz=new Float32Array([-1,-1,-1,1,-1,-1,1,-1,1,-1,-1,1,-1,1,-1,1,1,-1,1,1,1,-1,1,1]),Fz=new Uint16Array([0,1,2,0,2,3,1,5,6,1,6,2,4,6,5,4,7,6,0,7,4,0,3,7,0,5,1,0,4,5,3,2,6,3,6,7]),S2=class extends bd{constructor(e,t={}){super("v3",e,t)}get mapping(){return Nz}get mappingIndices(){return Fz}get mappingIndicesSize(){return 36}get mappingSize(){return 8}get mappingItemSize(){return 3}},mI=Object.assign({shrink:.14},ki),Oz=Object.assign({shrink:{uniform:!0}},cl),A2=class extends S2{constructor(e,t={}){super(e,t),this.parameterTypes=Oz,this.isImpostor=!0,this.vertexShader="HyperballStickImpostor.vert",this.fragmentShader="HyperballStickImpostor.frag",this.addUniforms({modelViewProjectionMatrix:{value:new qe},modelViewProjectionMatrixInverse:{value:new qe},modelViewMatrixInverseTranspose:{value:new qe},shrink:{value:this.parameters.shrink}}),this.addAttributes({position1:{type:"v3",value:null},position2:{type:"v3",value:null},color2:{type:"c",value:null},radius:{type:"f",value:null},radius2:{type:"f",value:null}}),this.setAttributes(e),this.makeMapping()}get defaultParameters(){return mI}};Object.assign({disableImpostor:!1},Iw,mI);var Bz=class{constructor(n,e={}){return!ys||e&&e.disableImpostor?(n.radius=function(t,i){let r=t.length,s=new Float32Array(r);for(let o=0;ol.push(r.atomLabel(m))))}else if(this.labelGrouping==="residue"){t&&!t.position||(c=[]),t&&!t.color||(d=[]),t&&!t.radius||(u=[]),t&&!t.text||(l=[]),i.colorParams&&(i.colorParams.structure=e.getStructure());let f=Dt.getScheme(i.colorParams),m=new Qr(i.radiusParams),p=e.getAtomProxy(),_=0;e.eachResidue(y=>{let g=3*_;y.isProtein()||y.isNucleic()?(p.index=y.traceAtomIndex,t&&!t.position||p.positionToArray(c,g)):(p.index=y.atomOffset,t&&!t.position||y.positionToArray(c,g)),t&&!t.color||f.atomColorToArray(p,d,g),t&&!t.radius||(u[_]=m.atomRadius(p)),t&&!t.text||l.push(r.atomLabel(p)),++_}),t&&!t.position||(s=new Float32Array(c)),t&&!t.color||(a=new Float32Array(d)),t&&!t.radius||(o=new Float32Array(u))}return{position:s,size:o,color:a,text:l}}createData(e){return{bufferList:[new oa(this.getTextData(e,{position:!0,color:!0,radius:!0,text:!0}),this.getBufferParams({fontFamily:this.fontFamily,fontStyle:this.fontStyle,fontWeight:this.fontWeight,xOffset:this.xOffset,yOffset:this.yOffset,zOffset:this.zOffset,attachment:this.attachment,showBorder:this.showBorder,borderColor:this.borderColor,borderWidth:this.borderWidth,showBackground:this.showBackground,backgroundColor:this.backgroundColor,backgroundMargin:this.backgroundMargin,backgroundOpacity:this.backgroundOpacity,fixedSize:this.fixedSize}))]}}updateData(e,t){t.bufferList[0].setAttributes(this.getTextData(t.sview,e))}getAtomRadius(){return 0}};function Uz(n){let e=n.getAtomSet(),t=n.getBondSet(),i=n.getBondProxy();return t.forEach(function(r){i.index=r,e.clear(i.atomIndex1),e.clear(i.atomIndex2)}),e}on.add("label",C2);var E2=class extends Zn{constructor(e,t,i){super(e,t,i),this.type="line",this.parameters=Object.assign({multipleBond:{type:"select",rebuild:!0,options:{off:"off",symmetric:"symmetric",offset:"offset"}},bondSpacing:{type:"number",precision:2,max:2,min:.5},linewidth:{type:"integer",max:50,min:1,buffer:!0},lines:{type:"boolean",rebuild:!0},crosses:{type:"select",rebuild:!0,options:{off:"off",lone:"lone",all:"all"}},crossSize:{type:"number",precision:2,max:2,min:.1}},this.parameters,{flatShaded:null,side:null,wireframe:null,roughness:null,metalness:null}),this.init(i)}init(e){var t=e||{};this.multipleBond=U(t.multipleBond,"off"),this.bondSpacing=U(t.bondSpacing,1),this.linewidth=U(t.linewidth,2),this.lines=U(t.lines,!0),this.crosses=U(t.crosses,"lone"),this.crossSize=U(t.crossSize,.4),super.init(t)}getAtomRadius(e){return .1}getBondParams(e,t){return t=Object.assign({multipleBond:this.multipleBond,bondSpacing:this.bondSpacing,radiusParams:{type:"size",size:.1,scale:1}},t),super.getBondParams(e,t)}_crossData(e,t){if(e&&!e.position&&!e.color)return;let i={};this.crosses==="lone"&&Object.assign(i,{atomSet:Uz(t)});let r=t.getAtomData(this.getAtomParams(e,i)),s={},o=r.position,a=r.color,l=r.picking,c=(o||a).length,u=3*c,d=new Float32Array(0),f=new Float32Array(0),m=new Float32Array(0),p=new Float32Array(0),_=0,y=new Float32Array(0);e&&!e.position||(d=s.position1=new Float32Array(u),f=s.position2=new Float32Array(u),_=this.crossSize/2),e&&!e.color||(m=s.color=new Float32Array(u),p=s.color2=new Float32Array(u)),e&&!e.picking||(y=new Float32Array(3*r.picking.array.length));for(let g=0;gte?J[re]=-1:(F=Math.sqrt(te-L),J[re]=Math.floor(F)),++re;p[X]=Z,m[X]=J}}function C(D){var N,H,z,L,F,te,Q,Z,J,re,X,se,ne,oe,ee,le,xe,Se,Re=3*D,ke=D;N=Math.floor(.5+o*(n[Re]+f[0])),H=Math.floor(.5+o*(n[Re+1]+f[1])),z=Math.floor(.5+o*(n[Re+2]+f[2]));var $e,_e=e[ke],Ie=m[_e],We=0,Fe=c*u,Y=p[_e];for(re=0;re=l||oe>=c||ee>=u)){var $=ne*Fe+oe*u+ee;if(y)if(g[$]&w){if(g[$]&w){var de=h[$];de!==Re&&Q*Q+Z*Z+J*J<(L=N+Q-Math.floor(.5+o*(n[de]+f[0])))*L+(F=H+Z-Math.floor(.5+o*(n[de+1]+f[1])))*F+(te=z+J-Math.floor(.5+o*(n[de+2]+f[2])))*te&&(h[$]=D)}}else g[$]|=w,h[$]=D;else g[$]|=w}}}We++}}function P(D){var N,H;for(console.time("EDTSurface fillvoxels"),N=0,H=g.length;N=l||X>=c||se>=u)){var Fe=re*We+X*u+se;if(g[Fe]&A){if(y){var Y=h[Fe];Q*Q+Z*Z+J*J<(L=Math.floor(.5+o*(n[Y]+f[0])))*L+(F=Math.floor(.5+o*(n[Y+1]+f[1])))*F+(te=Math.floor(.5+o*(n[Y+2]+f[2])))*te&&(h[Fe]=D)}}else g[Fe]|=A,y&&(h[Fe]=D)}}}_e++}}function I(){var D,N,H,z;console.time("EDTSurface fastdistancemap");var L,F=gI(l,c,u,Uint16Array,3),te=c*u,Q=_*_,Z=0;for(D=0;D0);var ne,oe=a*a,ee=new Uint16Array(3);for(D=0;D=oe)||(g[L]|=M,y&&g[L]&A&&(F.toArray(D,N,H,ee),ne=ee[0]*te+ee[1]*u+ee[2],h[L]=h[ne])));console.timeEnd("EDTSurface fastdistancemap")}function O(D,N,H,z){var L,F,te,Q,Z,J,re,X,se,ne,oe,ee,le=new Uint16Array(3),xe=0;if(H===0)return xe;var Se=-1,Re=-1,ke=-1,$e=c*u;for(re=0,se=H;re-1&&Re-1&&ke-1&&(g[oe=Se*$e+u*Re+ke]&w&&!(g[oe]&A)?(N.fromArray(Se,Re,ke,le),ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J,b[oe]=ne,g[oe]|=A,g[oe]|=M,z[xe]=Se,z[xe+1]=Re,z[xe+2]=ke,xe+=3):g[oe]&w&&g[oe]&A&&(ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J)-1&&Re-1&&ke-1&&(g[oe=Se*$e+u*Re+ke]&w&&!(g[oe]&A)?(N.fromArray(Se,Re,ke,le),ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J,b[oe]=ne,g[oe]|=A,g[oe]|=M,z[xe]=Se,z[xe+1]=Re,z[xe+2]=ke,xe+=3):g[oe]&w&&g[oe]&A&&(ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J)-1&&Re-1&&ke-1&&(g[oe=Se*$e+u*Re+ke]&w&&!(g[oe]&A)?(N.fromArray(Se,Re,ke,le),ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J,b[oe]=ne,g[oe]|=A,g[oe]|=M,z[xe]=Se,z[xe+1]=Re,z[xe+2]=ke,xe+=3):g[oe]&w&&g[oe]&A&&(ne=(Q=Se-le[0])*Q+(Z=Re-le[1])*Z+(J=ke-le[2])*J)-1&&oe-1&&le-1&&eeE&&(E=N)}return{neighbourListLength:27*E+1,withinRadii:function(H,z,L,F,te){for(var Q=0,Z=p(H,l),J=p(z,c),re=p(L,u),X=Math.max(0,Z-1),se=Math.max(0,J-1),ne=Math.max(0,re-1),oe=Math.min(b,Z+2),ee=Math.min(h,J+2),le=Math.min(v,re+2),xe=X;xef&&(f=u[ne]);(function(){let ne=_d(l,c,f,p,0);p=ne.scaleFactor,g=ne.dim,b=ne.matrix,D=Math.max(5,2+Math.floor(m*p)),h=ar(g[0]*g[1]*g[2],-1001),v=new Int32Array(h.length),S=new Float32Array(g[0]),x=new Float32Array(g[1]),w=new Float32Array(g[2]),H(S,l[0],1/p),H(x,l[1],1/p),H(w,l[2],1/p)})(),function(){var ne=0,oe=2*Math.PI/y;M=new Float32Array(y),A=new Float32Array(y);for(var ee=0;ee=0;){if(ne!==X&&ne!==se&&L(ne,Z,J,re))return C=ne,ne;ne=R[++oe]}return C=-1,-1}function L(Z,J,re,X){var se=3*Z,ne=d[Z],oe=n[se]-J,ee=n[se+1]-re,le=n[se+2]-X;return oe*oe+ee*ee+le*le0&&ee=0;)X{t(this._makeSurface(u.data.sd,i))},u=>{console.warn("MolecularSurface.getSurfaceWorker error - trying without worker",u),this.worker.terminate(),this.worker=void 0;let d=this.getSurface(i);t(d)})}else{let r=this.getSurface(i);t(r)}}dispose(){this.worker&&this.worker.terminate()}},P2=class extends Zn{constructor(e,t,i){super(e,t,i),this.type="surface",this.parameters=Object.assign({surfaceType:{type:"select",rebuild:!0,options:{vws:"vws",sas:"sas",ms:"ms",ses:"ses",av:"av"}},probeRadius:{type:"number",precision:1,max:20,min:0,rebuild:!0},smooth:{type:"integer",precision:1,max:10,min:0,rebuild:!0},scaleFactor:{type:"number",precision:1,max:5,min:0,rebuild:!0},cutoff:{type:"number",precision:2,max:50,min:0,rebuild:!0},contour:{type:"boolean",rebuild:!0},background:{type:"boolean",rebuild:!0},opaqueBack:{type:"boolean",buffer:!0},filterSele:{type:"text",rebuild:!0},colorVolume:{type:"hidden"},useWorker:{type:"boolean",rebuild:!0}},this.parameters,{radius:null,scale:null}),this.__infoList=[],this.structure.signals.refreshed.add(()=>{this.__forceNewMolsurf=!0}),this.toBePrepared=!0,this.init(i)}init(e){let t=e||{};t.colorScheme=U(t.colorScheme,"uniform"),t.colorValue=U(t.colorValue,14540253),t.disablePicking=U(t.disablePicking,!0),this.surfaceType=U(t.surfaceType,"ms"),this.probeRadius=U(t.probeRadius,1.4),this.smooth=U(t.smooth,2),this.scaleFactor=U(t.scaleFactor,2),this.cutoff=U(t.cutoff,0),this.contour=U(t.contour,!1),this.background=U(t.background,!1),this.opaqueBack=U(t.opaqueBack,!0),this.filterSele=U(t.filterSele,""),this.colorVolume=U(t.colorVolume,void 0),this.useWorker=U(t.useWorker,!0),super.init(e)}prepareData(e,t,i){let r=this.__infoList[t];if(r||(r={},this.__infoList[t]=r),r.molsurf&&r.sele===e.selection.string)i(t);else{if(this.filterSele){let a=e.structure.getView(new tn(this.filterSele)),l=a.boundingBox.getSize(new W),c=Math.max(l.x,l.y,l.z),u=e.getAtomSetWithinPoint(a.center,c/2+6);if((e=e.getView(new tn(e.getAtomSetWithinSelection(u,3).toSeleString()))).atomCount===0)return void i(t)}r.sele=e.selection.string,r.molsurf=new T2(e);let s=this.getSurfaceParams(),o=a=>{r.surface=a,i(t)};this.useWorker?r.molsurf.getSurfaceWorker(s,o):o(r.molsurf.getSurface(s))}}prepare(e){if((this.__forceNewMolsurf||this.__sele!==this.selection.string||this.__surfaceParams!==JSON.stringify(this.getSurfaceParams()))&&(this.__infoList.forEach(s=>{s&&s.molsurf&&s.molsurf.dispose()}),this.__infoList.length=0),this.structureView.atomCount===0)return void e();let t=()=>{this.__sele=this.selection.string,this.__surfaceParams=JSON.stringify(this.getSurfaceParams()),this.__forceNewMolsurf=!1,e()},i=this.assembly==="default"?this.defaultAssembly:this.assembly,r=this.structure.biomolDict[i];r?r.partList.forEach((s,o)=>{let a=s.getView(this.structureView);this.prepareData(a,o,l=>{l===r.partList.length-1&&t()})}):this.prepareData(this.structureView,0,t)}createData(e,t){let i=this.__infoList[t],r=i.surface;if(!r)return;let s={position:r.getPosition(),color:r.getColor(this.getColorParams()),index:r.getFilteredIndex(this.filterSele,e)},o=[];if(r.contour){let a=new yg(s,this.getBufferParams({wireframe:!1}));o.push(a)}else{Object.assign(s,{normal:r.getNormal(),picking:r.getPicking(e.getStructure())});let a=new mg(s,this.getBufferParams({background:this.background,opaqueBack:this.opaqueBack,dullInterior:!1}));if(this.getBufferParams().side=="double"){let l=new gg(a);o.push(l)}else o.push(a)}return{bufferList:o,info:i}}updateData(e,t){let i={};if(e.position||e.radius)return this.__forceNewMolsurf=!0,void this.build();e.color&&(i.color=t.info.surface.getColor(this.getColorParams())),e.index&&(i.index=t.info.surface.getFilteredIndex(this.filterSele,t.sview)),t.bufferList[0].setAttributes(i)}setParameters(e,t={},i){return e&&e.filterSele&&(t.index=!0),e&&e.colorVolume!==void 0&&(t.color=!0),e&&e.wireframe&&(e.contour||e.contour===void 0&&this.contour)&&(e.wireframe=!1),super.setParameters(e,t,i),this}getSurfaceParams(e={}){return Object.assign({type:this.surfaceType,probeRadius:this.probeRadius,scaleFactor:this.scaleFactor,smooth:this.smooth&&!this.contour,cutoff:this.cutoff,contour:this.contour,useWorker:this.useWorker,radiusParams:this.getRadiusParams()},e)}getColorParams(){let e=super.getColorParams();return e.volume=this.colorVolume,e}getAtomRadius(){return 0}clear(){super.clear()}dispose(){this.__infoList.forEach(e=>{e&&e.molsurf&&e.molsurf.dispose()}),this.__infoList.length=0,super.dispose()}};on.add("surface",P2);var I2=class extends Zn{constructor(e,t,i){super(e,t,i),this.type="point",this.parameters=Object.assign({pointSize:{type:"number",precision:1,max:100,min:0,buffer:!0},sizeAttenuation:{type:"boolean",buffer:!0},sortParticles:{type:"boolean",rebuild:!0},useTexture:{type:"boolean",buffer:!0},alphaTest:{type:"range",step:.001,max:1,min:0,buffer:!0},forceTransparent:{type:"boolean",buffer:!0},edgeBleach:{type:"range",step:.001,max:1,min:0,buffer:!0}},this.parameters,{flatShaded:null,wireframe:null,linewidth:null,side:null,roughness:null,metalness:null}),this.init(i)}init(e){var t=e||{};this.pointSize=U(t.pointSize,1),this.sizeAttenuation=U(t.sizeAttenuation,!0),this.sortParticles=U(t.sortParticles,!1),this.useTexture=U(t.useTexture,!1),this.alphaTest=U(t.alphaTest,.5),this.forceTransparent=U(t.forceTransparent,!1),this.edgeBleach=U(t.edgeBleach,0),super.init(t)}createData(e){var t=e.getAtomData(this.getAtomParams({position:!0,color:!0,picking:!0}));return{bufferList:[new Sd(t,this.getBufferParams({pointSize:this.pointSize,sizeAttenuation:this.sizeAttenuation,sortParticles:this.sortParticles,useTexture:this.useTexture,alphaTest:this.alphaTest,forceTransparent:this.forceTransparent,edgeBleach:this.edgeBleach}))]}}updateData(e,t){var i=t.sview.getAtomData(this.getAtomParams(e)),r={};e&&!e.position||Object.assign(r,{position:i.position}),e&&!e.color||Object.assign(r,{color:i.color}),t.bufferList[0].setAttributes(r)}getAtomRadius(){return .1}};on.add("point",I2),zt.add("shader/Ribbon.vert",`#define STANDARD +uniform float clipNear; +uniform vec3 clipCenter; +#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING ) +varying vec3 vViewPosition; +#endif +#if defined( RADIUS_CLIP ) +varying vec3 vClipCenter; +#endif +attribute vec3 dir; +attribute float size; +#ifdef PICKING +#include unpack_color +attribute float primitiveId; +varying vec3 vPickingColor; +#else +#include color_pars_vertex +#ifndef FLAT_SHADED +varying vec3 vNormal; +#endif +#endif +#include common +void main(void){ +#ifdef PICKING +vPickingColor = unpackColor( primitiveId ); +#else +#include color_vertex +#include beginnormal_vertex +#include defaultnormal_vertex +#ifndef FLAT_SHADED +vNormal = normalize( transformedNormal ); +#endif +#endif +#include begin_vertex +transformed += normalize( dir ) * size; +#include project_vertex +#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING ) +vViewPosition = -mvPosition.xyz; +#endif +#if defined( RADIUS_CLIP ) +vClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz; +#endif +#include nearclip_vertex +}`);var zz=new Uint16Array([0,1,2,1,3,2]);function Uh(n){return 3*(4*(n.position.length/3-1))}var R2=class extends Jr{constructor(e,t={}){super({position:new Float32Array(Uh(e)),color:new Float32Array(Uh(e)),index:bs(Uh(e),Uh(e)/3),normal:new Float32Array(Uh(e)),picking:e.picking},t),this.vertexShader="Ribbon.vert";let i=e.position.length/3-1,r=4*i,s=3*r;this.addAttributes({dir:{type:"v3",value:new Float32Array(s)}}),this.addAttributes({size:{type:"f",value:new Float32Array(r)}}),e.primitiveId=au(i),this.setAttributes(e),this.makeIndex()}setAttributes(e={}){let t=this.size/4,i=this.geometry.attributes,r,s,o,a,l,c,u,d,f,m,p,_,y,g,b,h,v,S,x;e.position&&(r=e.position,u=i.position.array,i.position.needsUpdate=!0),e.normal&&(s=e.normal,d=i.normal.array,i.normal.needsUpdate=!0),e.size&&(o=e.size,f=i.size.array,i.size.needsUpdate=!0),e.dir&&(a=e.dir,m=i.dir.array,i.dir.needsUpdate=!0),e.color&&(l=e.color,p=i.color.array,i.color.needsUpdate=!0),e.primitiveId&&(c=e.primitiveId,_=i.primitiveId.array,i.primitiveId.needsUpdate=!0);let w=o?o[0]:null;for(y=0;y{if(!(r.residueCount<4)){i.push(r);var s=new aa(r,this.getSplineParams()),o=s.getSubdividedPosition(),a=s.getSubdividedOrientation(),l=s.getSubdividedColor(this.getColorParams()),c=s.getSubdividedPicking(),u=s.getSubdividedSize(this.getRadiusParams());t.push(new R2({position:o.position,normal:a.binormal,dir:a.normal,color:l.color,size:u.size,picking:c.picking},this.getBufferParams()))}},e.getSelection()),{bufferList:t,polymerList:i}}updateData(e,t){e=e||{};var i=0,r=t.polymerList.length;for(i=0;i{if(l.residueCount<4||l.isNucleic())return;let c=new vg(l),u=c.getAxis(this.localAngle,this.centerDist,this.ssBorder,this.getColorParams(),this.getRadiusParams());t+=u.size.length,i.push(u),r.push(c)},e.getSelection());let s={begin:new Float32Array(3*t),end:new Float32Array(3*t),size:new Float32Array(t),color:new Float32Array(3*t),picking:{}},o=new Float32Array(t),a=0;return i.forEach(function(l){s.begin.set(l.begin,3*a),s.end.set(l.end,3*a),s.size.set(l.size,a),s.color.set(l.color,3*a),o.set(l.picking.array,a),a+=l.size.length}),t&&(s.picking=new oo(o,e.getStructure())),{bufferList:[new ao({position1:s.begin,position2:s.end,color:s.color,color2:s.color,radius:s.size,picking:s.picking},this.getBufferParams({openEnded:this.openEnded,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0}))],axisList:i,helixbundleList:r,axisData:s}}updateData(e,t){if((e=e||{}).position)this.build();else{var i={};if(e.color||e.radius){var r=0;t.helixbundleList.forEach(s=>{var 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t,i,r,s,o=this.geometry.attributes;if(e.position&&(t=e.position,r=o.position.array,o.position.needsUpdate=!0),e.color&&(i=e.color,s=o.color.array,o.color.needsUpdate=!0),!t&&!i)return void we.warn("TraceBuffer.prototype.setAttributes no data");let a,l,c=this.size-1;for(let u=0;u{if(!(r.residueCount<4)){i.push(r);var s=new aa(r,this.getSplineParams()),o=s.getSubdividedPosition(),a=s.getSubdividedColor(this.getColorParams());t.push(new F2(Object.assign({},o,a),this.getBufferParams()))}},e.getSelection()),{bufferList:t,polymerList:i}}updateData(e,t){e=e||{};var i=0,r=t.polymerList.length;for(i=0;i{e.boundingBox||e.computeBoundingBox(),this.boundingBox.union(e.boundingBox)})}},Gz=Object.assign({aspectRatio:1.5,radialSegments:50,openEnded:!1,disableImpostor:!1},ki),H2=class{constructor(e,t={}){this.group=new $t,this.wireframeGroup=new $t,this.pickingGroup=new $t,this.visible=!0,this.parameters=or(t,this.defaultParameters),this.splitPosition=new 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text-sm",r),children:[(0,Ut.jsx)("thead",{className:Mn("",s)}),(0,Ut.jsx)("tbody",{className:Mn("",o),children:e.map(_=>(0,Ut.jsxs)("tr",{className:Mn("transition-colors",a),children:[(0,Ut.jsx)(KI,{header:_,sortState:f,setSortState:m,orientation:n,className:Mn("h-12 border-r px-4 text-left align-middle font-medium text-muted-foreground",l)},_.key),p.map((y,g)=>(0,Ut.jsx)("td",{className:Mn("p-4 align-middle",{"border-r":g + * Released under the MIT license + * Author: Miller Medeiros + * Version: 1.0.0 - Build: 268 (2012/11/29 05:48 PM) + *) + +react/cjs/react-jsx-runtime.production.min.js: + (** + * @license React + * react-jsx-runtime.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + *) + +three/build/three.module.js: + (** + * @license + * Copyright 2010-2023 Three.js Authors + * SPDX-License-Identifier: MIT + *) + +ngl/dist/ngl.esm.js: + (** + * Kdtree + * @class + * @author Alexander Rose , 2016 + * @author Roman Bolzern , 2013 + * @author I4DS http://www.fhnw.ch/i4ds, 2013 + * @license MIT License + * @description + * k-d Tree for typed arrays of 3d points (e.g. for Float32Array), in-place + * provides fast nearest neighbour search + * + * Based on https://github.com/ubilabs/kd-tree-javascript by Ubilabs + * + * Further information (including mathematical properties) + * http://en.wikipedia.org/wiki/Binary_tree + * http://en.wikipedia.org/wiki/K-d_tree + * + * @example + * points: [x, y, z, x, y, z, x, y, z, ...] + * metric: function(a, b){ + * return Math.pow(a[0]-b[0], 2) + Math.pow(a[1]-b[1], 2) + Math.pow(a[2]-b[2], 2); + * } + * + * @param {Float32Array} points - points + * @param {Function} metric - metric + *) +*/ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libalign.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libalign.py new file mode 100644 index 0000000000000000000000000000000000000000..365dd93fb6c896eefa65f171d1ebdcc475fa5616 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libalign.py @@ -0,0 +1,1387 @@ +""" +Library of functions to perform sequence and structural alignments. + +Main functions +-------------- + +* :py:func:`calc_rmsd` +* :py:func:`centroid` +* :py:func:`kabsch` +* :py:func:`load_coords` +* :py:func:`pdb2fastadic` +* :py:func:`get_atoms` +* :py:func:`get_align` +* :py:func:`align_struct` +* :py:func:`align_seq` +* :py:func:`make_range` +* :py:func:`dump_as_izone` +""" + +import os +import shlex +import subprocess +from functools import partial +from pathlib import Path + +import numpy as np +from Bio import Align +from Bio.Align import substitution_matrices +from Bio.Seq import Seq + +from haddock import log +from haddock.core.typing import AtomsDict, FilePath, Literal, NDFloat, Optional +from haddock.libs.libio import pdb_path_exists +from haddock.libs.libontology import PDBFile, PDBPath +from haddock.libs.libpdb import ( + slc_chainid, + slc_element, + slc_name, + slc_resname, + slc_resseq, + slc_x, + slc_y, + slc_z, + split_by_chain, + ) + + +RES_TO_BE_IGNORED = ["SHA", "WAT"] + +PROT_RES = [ + "ALA", + "ARG", + "ASN", + "ASP", + "CYS", + "GLN", + "GLU", + "GLY", + "HIS", + "ILE", + "LEU", + "LYS", + "MET", + "PHE", + "PRO", + "SER", + "THR", + "TRP", + "TYR", + "VAL", +] + +DNA_RES = ["DA", "DC", "DT", "DG"] +# Backbone +PROT_ATOMS = ["C", "N", "CA", "O"] +# Side chains +PROT_SIDE_CHAINS_DICT = { + "ALA": ["C", "N", "CA", "O", "CB"], + "ARG": ["C", "N", "CA", "O", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"], + "ASN": ["C", "N", "CA", "O", "CB", "CG", "OD1", "ND2"], + "ASP": ["C", "N", "CA", "O", "CB", "CG", "OD1", "OD2"], + "CYS": ["C", "N", "CA", "O", "CB", "SG"], + "GLN": ["C", "N", "CA", "O", "CB", "CG", "CD", "OE1", "NE2"], + "GLU": ["C", "N", "CA", "O", "CB", "CG", "CD", "OE1", "OE2"], + "GLY": ["C", "N", "CA", "O"], + "HIS": ["C", "N", "CA", "O", "CB", "CG", "ND1", "CD2", "CE1", "NE2"], + "ILE": ["C", "N", "CA", "O", "CB", "CG1", "CG2", "CD1"], + "LEU": ["C", "N", "CA", "O", "CB", "CG", "CD1", "CD2"], + "LYS": ["C", "N", "CA", "O", "CB", "CG", "CD", "CE", "NZ"], + "MET": ["C", "N", "CA", "O", "CB", "CG", "SD", "CE"], + "PHE": ["C", "N", "CA", "O", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ"], + "PRO": ["C", "N", "CA", "O", "CB", "CG", "CD"], + "SER": ["C", "N", "CA", "O", "CB", "OG"], + "THR": ["C", "N", "CA", "O", "CB", "OG1", "CG2"], + "TRP": [ + "C", + "N", + "CA", + "O", + "CB", + "CG", + "CD1", + "CD2", + "NE1", + "CE2", + "CE3", + "CZ2", + "CZ3", + "CH2", + ], + "TYR": [ + "C", + "N", + "CA", + "O", + "CB", + "CG", + "CD1", + "CD2", + "CE1", + "CE2", + "CZ", + "OH", + ], + "VAL": ["C", "N", "CA", "O", "CB", "CG1", "CG2"], +} + +# Bases +DNA_ATOMS = [ + "C5", + "N9", + "N2", + "C8", + "O2", + "N4", + "N7", + "C7", + "N1", + "N6", + "C2", + "O4", + "C6", + "N3", + "C4", + "O6", +] + +DNA_FULL_DICT = { + "DA": [ + "P", + "O1P", + "O2P", + "O5'", + "C5'", + "C4'", + "O4'", + "C1'", + "N9", + "C4", + "N3", + "C2", + "N1", + "C6", + "N6", + "C5", + "N7", + "C8", + "C2'", + "C3'", + "O3'", + "N2", + "O2", + "N4", + "C7", + "O4", + "O6", + ], + "DG": [ + "P", + "O1P", + "O2P", + "O5'", + "C5'", + "C4'", + "O4'", + "C1'", + "N9", + "C4", + "N3", + "C2", + "N2", + "N1", + "C6", + "O6", + "C5", + "N7", + "C8", + "C2'", + "C3'", + "O3'", + "O2", + "N4", + "C7", + "N6", + "O4", + ], + "DC": [ + "P", + "O1P", + "O2P", + "O5'", + "C5'", + "C4'", + "O4'", + "C1'", + "N1", + "C6", + "C2", + "O2", + "N3", + "C4", + "N4", + "C5", + "C2'", + "C3'", + "O3'", + "N9", + "N2", + "C8", + "N7", + "C7", + "N6", + "O4", + "O6", + ], + "DT": [ + "P", + "O1P", + "O2P", + "O5'", + "C5'", + "C4'", + "O4'", + "C1'", + "N1", + "C6", + "C2", + "O2", + "N3", + "C4", + "O4", + "C5", + "C7", + "C2'", + "C3'", + "O3'", + "N9", + "N2", + "C8", + "N4", + "N7", + "N6", + "O6", + ], +} + +RNA_RES = ["A", "G", "C", "U"] +RNA_ATOMS = ["P", "O5'", "C5'", "C4'", "C3'", "O3'"] + +RNA_FULL_DICT = { + "A": [ + "P", + "OP1", + "OP2", + "O5'", + "C5'", + "C4'", + "O4'", + "C3'", + "O3'", + "C2'", + "O2'", + "C1'", + "N9", + "C8", + "N7", + "C5", + "C6", + "N6", + "N1", + "C2", + "N3", + "C4", + ], + "G": [ + "P", + "OP1", + "OP2", + "O5'", + "C5'", + "C4'", + "O4'", + "C3'", + "O3'", + "C2'", + "O2'", + "C1'", + "N9", + "C8", + "N7", + "C5", + "C6", + "O6", + "N1", + "C2", + "N2", + "N3", + "C4", + ], + "C": [ + "P", + "OP1", + "OP2", + "O5'", + "C5'", + "C4'", + "O4'", + "C3'", + "O3'", + "C2'", + "O2'", + "C1'", + "N9", + "C5", + "C6", + "O6", + "N1", + "C2", + "N2", + "N3", + "C4", + "N4", + ], + "U": [ + "P", + "OP1", + "OP2", + "O5'", + "C5'", + "C4'", + "O4'", + "C3'", + "O3'", + "C2'", + "O2'", + "C1'", + "N1", + "C2", + "O2", + "N3", + "C4", + "O4", + "C5", + "C6", + ], +} + + +class ALIGNError(Exception): + """Raised when something goes wrong with the ALIGNMENT library.""" + + def __init__(self, msg: object = "") -> None: + self.msg = msg + super().__init__(self.msg) + + +def calc_rmsd(V: NDFloat, W: NDFloat) -> float: + """ + Calculate the RMSD from two vectors. + + Parameters + ---------- + V : np.array dtype=float, shape=(n_atoms,3) + W : np.array dtype=float, shape=(n_atoms,3) + + Returns + ------- + rmsd : float + """ + diff = np.array(V) - np.array(W) + N = len(V) + rmsd = np.sqrt((diff * diff).sum() / N) + return rmsd + + +def kabsch(P: NDFloat, Q: NDFloat) -> NDFloat: + """ + Find the rotation matrix using Kabsch algorithm. + + Parameters + ---------- + P : np.array dtype=float, shape=(n_atoms,3) + Q : np.array dtype=float, shape=(n_atoms,3) + + Returns + ------- + U : np.array dtype=float, shape=(3,3) + """ + # Covariance matrix + P = np.array(P) + Q = np.array(Q) + C = np.dot(np.transpose(P), Q) + # use SVD + V, S, W = np.linalg.svd(C) + d = (np.linalg.det(V) * np.linalg.det(W)) < 0.0 + if d: + S[-1] = -S[-1] + V[:, -1] = -V[:, -1] + # Create Rotation matrix U + U = np.dot(V, W) + return U + + +def centroid(X: NDFloat) -> NDFloat: + """ + Get the centroid. + + Parameters + ---------- + X : np.array dtype=float, shape=(n_atoms,3) + + Returns + ------- + C : np.array dtype=float, shape=(3,) + """ + X = np.array(X) + C = X.mean(axis=0) + return C + + +def load_coords( + pdb_f, + atoms, + filter_resdic=None, + numbering_dic=None, + model2ref_chain_dict=None, + add_resname=None, + keep_hetatm: bool = False, +): + """Load coordinates from PDB. + + Parameters + ---------- + pdb_f : PDBFile + + atoms : dict + dictionary of atoms + + filter_resdic : dict + dictionary of residues to be loaded (one list per chain) + + numbering_dic : dict + dict of numbering dictionaries (one dictionary per chain) + + add_resname : bool + use the residue name in the identifier + + keep_hetatm : bool + Should HETATM lines be considered ? + + Returns + ------- + coord_dic : dict + dictionary of coordinates (one per chain) + + chain_ranges: dict + dictionary of chain ranges + """ + coord_dic: CoordsDict = {} + chain_dic: ResDict = {} + idx: int = 0 + # Set types of coordinates lines to extract + if keep_hetatm: + coordinates_line_to_extract = ("ATOM", "HETATM", ) + else: + coordinates_line_to_extract = ("ATOM", ) + # Check filetype + if isinstance(pdb_f, PDBFile): + pdb_f = pdb_f.rel_path + # Read file + with open(pdb_f, "r") as fh: + for line in fh.readlines(): + # Skip non ATOM records lines + if not line.startswith(coordinates_line_to_extract): + continue + # Extract PDB line data + atom_name = line[slc_name].strip() + resname = line[slc_resname].strip() + # Skip entries to be ignored + if resname in RES_TO_BE_IGNORED: + continue + else: + if atom_name not in atoms[resname]: + continue + # Continue parsing of the PDB line + chain = line[slc_chainid] + resnum = int(line[slc_resseq]) + x = float(line[slc_x]) + y = float(line[slc_y]) + z = float(line[slc_z]) + coords = np.asarray([x, y, z]) + # Remap chain name + if model2ref_chain_dict: + # Skip chain matching if not present in reference structure + if chain not in model2ref_chain_dict.keys(): + continue + chain = model2ref_chain_dict[chain] + + if numbering_dic: + try: + resnum = numbering_dic[chain][resnum] + except KeyError: + # this residue is not matched, and so it should + # not be considered + # self.log( + # f"WARNING: {chain}.{resnum}.{atom_name}" + # " was not matched!" + # ) + continue + + # Create identifier tuple + if add_resname is True: + identifier = (chain, resnum, atom_name, resname) + else: + identifier = (chain, resnum, atom_name) + # Create empty chain entries + if chain not in chain_dic.keys(): + if filter_resdic: + if chain in filter_resdic.keys(): + chain_dic[chain] = [] + else: + chain_dic[chain] = [] + + # Check if must eventually filter this entry + if filter_resdic: + # Only retrieve coordinates from the filter_resdic + if chain in filter_resdic.keys(): + if resnum in filter_resdic[chain]: + coord_dic[identifier] = coords + chain_dic[chain].append(idx) + idx += 1 + else: + # retrieve everything + coord_dic[identifier] = coords + chain_dic[chain].append(idx) + idx += 1 + + # Obtain chain ranges + chain_ranges: ChainsRange = {} + for chain, indice in chain_dic.items(): + # Check if NONE residues indices were extracted (empty list) + if not indice: + continue + else: + min_idx = min(indice) + max_idx = max(indice) + chain_ranges[chain] = (min_idx, max_idx) + + # Check that chain_ranges is not empty + # NOTE: this may happen when filter_resdic is defined on a different set + # of chains or residues + if chain_ranges == {}: + # Build error message + _err_msg = ( + f"Chain matching error on {pdb_f}! " + f"Filtering scheme used: {filter_resdic}." + "\nPlease check the input file and queried filterings." + ) + # Raise the error + raise ALIGNError(_err_msg) + return coord_dic, chain_ranges + + +def get_atoms(pdb: PDBPath, full: bool = False) -> AtomsDict: + """Identify what is the molecule type of each PDB. + + Parameters + ---------- + pdb : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file to have its atoms identified + full : bool + Weather or not to take `full` atoms into consideration. + If False, only main-chain atoms retrieved. + If True, all heavy atoms retrieved. + + Returns + ------- + atom_dic : dict + dictionary of atoms + """ + atom_dic: AtomsDict = {} + atom_dic.update((r, PROT_ATOMS) for r in PROT_RES) + atom_dic.update((r, DNA_ATOMS) for r in DNA_RES) + atom_dic.update((r, RNA_ATOMS) for r in RNA_RES) + if full: + atom_dic.update(PROT_SIDE_CHAINS_DICT) + atom_dic.update(DNA_FULL_DICT) + atom_dic.update(RNA_FULL_DICT) + + if isinstance(pdb, PDBFile): + pdb = pdb.rel_path + + exists, msg = pdb_path_exists(pdb) + if not exists: + raise Exception(msg) + + with open(pdb) as fh: + for line in fh.readlines(): + if line.startswith(("ATOM", "HETATM")): + resname = line[slc_resname].strip() + atom_name = line[slc_name].strip() + element = line[slc_element].strip() + if all( + [ + resname not in PROT_RES, + resname not in DNA_RES, + resname not in RNA_RES, + resname not in RES_TO_BE_IGNORED, + ] + ): + # its neither DNA/RNA nor protein, use the heavy atoms + # WARNING: Atoms that belong to unknown residues must + # be bound to a residue name; + # For example: residue NEP, also contains + # CB and CG atoms, if we do not bind it to the + # residue name, the next functions will include + # CG and CG atoms in the calculations for all + # other residue names + if element != "H": + if resname not in atom_dic: + atom_dic[resname] = [] + if atom_name not in atom_dic[resname]: + atom_dic[resname].append(atom_name) + return atom_dic + + +ResCode = Literal[ + "C", + "D", + "S", + "Q", + "K", + "I", + "P", + "T", + "F", + "N", + "G", + "H", + "L", + "R", + "W", + "A", + "V", + "E", + "Y", + "M", + "A", + "G", + "C", + "T", + "X", +] +""" +The single letter code of a residue. + +Unrecognized residues' code is `X`. +""" + + +def pdb2fastadic(pdb_f: PDBPath, keep_hetatm: bool = False) -> dict[str, dict[int, str]]: + """ + Write the sequence as a fasta. + + Parameters + ---------- + pdb_f : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + Path to a PDB file. + keep_hetatm : bool + Should HETATM coordinates be kept ? + + Returns + ------- + seq_dic : dict + dict of fasta sequences (one per chain) + """ + res_codes = dict( + [ + ("CYS", "C"), + ("ASP", "D"), + ("SER", "S"), + ("GLN", "Q"), + ("LYS", "K"), + ("ILE", "I"), + ("PRO", "P"), + ("THR", "T"), + ("PHE", "F"), + ("ASN", "N"), + ("GLY", "G"), + ("HIS", "H"), + ("LEU", "L"), + ("ARG", "R"), + ("TRP", "W"), + ("ALA", "A"), + ("VAL", "V"), + ("GLU", "E"), + ("TYR", "Y"), + ("MET", "M"), + ("DA", "A"), + ("DG", "G"), + ("DC", "C"), + ( + "DT", + "T", + ), # 9/8/2023: adding non-standard amino-acids (src/haddock/cns/toppar/protein-allhdg5-4.top) # noqa: E501 + ("ALY", "K"), + ("ASH", "D"), + ("CFE", "C"), + ("CSP", "C"), + ("CYC", "C"), + ("CYF", "C"), + ("CYM", "C"), + ("DDZ", "A"), + ("GLH", "E"), + ("HLY", "P"), + ("HY3", "P"), + ("HYP", "P"), + ("M3L", "K"), + ("MLY", "K"), + ("MLZ", "K"), + ("MSE", "M"), + ("NEP", "H"), + ("PNS", "S"), + ("PTR", "Y"), + ("SEP", "S"), + ("TOP", "T"), + ("TYP", "Y"), + ("TYS", "Y"), + ] + ) + + seq_dic: dict[str, dict[int, str]] = {} + + if isinstance(pdb_f, PDBFile): + pdb_f = pdb_f.rel_path + + coord_req = ("ATOM", "HETATM", ) if keep_hetatm else ("ATOM", ) + with open(pdb_f) as fh: + for line in fh.readlines(): + if line.startswith(coord_req): + res_num = int(line[slc_resseq]) + res_name = line[slc_resname].strip() + chain = line[slc_chainid] + if res_name in RES_TO_BE_IGNORED: + continue + try: + one_letter = res_codes[res_name] + except KeyError: + one_letter = "X" + if chain not in seq_dic: + seq_dic[chain] = {} + seq_dic[chain][res_num] = one_letter + return seq_dic + + +def get_align( + method: str, lovoalign_exec: FilePath, keep_hetatm: bool = False, +) -> partial[dict[str, dict[int, int]]]: + """ + Get the alignment function. + + Parameters + ---------- + method : str + Available options: ``sequence`` and ``structure``. + + lovoalign_exec : str + Path to the lovoalign executable. + + keep_hetatm : bool + Should HETATM be considered in the analysis ? + + Returns + ------- + align_func : functools.partial + desired alignment function + """ + if method == "structure": + align_func = partial(align_strct, lovoalign_exec=lovoalign_exec) + elif method == "sequence": + align_func = partial(align_seq, keep_hetatm=keep_hetatm) + else: + available_alns = ("sequence", "structure") + raise ValueError( + f"Alignment method {method!r} not recognized. " + f"Available options are {', '.join(available_alns)}" + ) + return align_func + + +def align_strct( + reference: PDBFile, + model: PDBFile, + output_path: FilePath, + lovoalign_exec: Optional[FilePath] = None, +) -> dict[str, dict[int, int]]: + """ + Structuraly align and get numbering relationship. + + Parameters + ---------- + reference : :py:class:`haddock.libs.libontology.PDBFile` + + model : :py:class:`haddock.libs.libontology.PDBFile` + + output_path : Path + + lovoalign_exec : Path + lovoalign executable + + Returns + ------- + numbering_dic : dict + dict of numbering dictionaries (one dictionary per chain) + """ + if lovoalign_exec is None: + log.error( + "Structural alignment needs LovoAlign " "get it at github.com/m3g/lovoalign" + ) + raise ALIGNError("Path to LovoAlign executable required.") + + if not lovoalign_exec: + raise ALIGNError("lovoalign_exec parameter not defined ") + + if not os.access(lovoalign_exec, os.X_OK): + raise ALIGNError(f"{lovoalign_exec!r} for LovoAlign is not executable") + + numbering_dic: dict[str, dict[int, int]] = {} + protein_a_dic = { + e.stem.split("_")[-1]: e for e in split_by_chain(reference.rel_path) + } + protein_b_dic = {e.stem.split("_")[-1]: e for e in split_by_chain(model.rel_path)} + + # check if chain ids match + if protein_a_dic.keys() != protein_b_dic.keys(): + # TODO: Make this a clearer raise + return numbering_dic + + for chain in protein_a_dic.keys(): + pa_seqdic = pdb2fastadic(protein_a_dic[chain]) + pb_seqdic = pdb2fastadic(protein_b_dic[chain]) + # logging.debug(f"Structurally aligning chain {chain}") + numbering_dic[chain] = {} + cmd = ( + f"{lovoalign_exec} -p1 {protein_a_dic[chain]} " + f"-p2 {protein_b_dic[chain]} " + f"-c1 {chain} -c2 {chain}" + ) + + # logging.debug(f"Command is: {cmd}") + p = subprocess.run(shlex.split(cmd), capture_output=True, text=True) + lovoalign_out = p.stdout.split(os.linesep) + + # we don"t need the splitted proteins anymore + protein_a_dic[chain].unlink() + protein_b_dic[chain].unlink() + + # find out where the alignment starts and ends + alignment_pass = True + for i, line in enumerate(lovoalign_out): + if "SEQUENCE ALIGNMENT" in line: + # there are 2 extra white lines after this header + alignment_start_index = i + 2 + elif "FINAL" in line: + # there are 2 extra white lines after this header + alignment_end_index = i - 2 + elif "ERROR" in line: + failed_pdb = line.split()[-1] + _msg = f"LovoAlign could not read {failed_pdb} " "is it a ligand?" + log.warning(_msg) + alignment_pass = False + + for elem in [k for k in pa_seqdic[chain]]: + numbering_dic[chain][elem] = elem + + if not alignment_pass: + # This alignment failed, move on to the next + log.warning( + f"Skipping alignment of chain {chain}, " "used sequential matching" + ) + continue + + aln_l = lovoalign_out[alignment_start_index:alignment_end_index] + + # dump this alignment to a file + aln_fname = Path(output_path, f"lovoalign_{chain}.aln") + with open(aln_fname, "w") as fh: + fh.write(os.linesep.join(aln_l)) + + # remove the line between the alignment segments + alignment = [aln_l[i : i + 3][:2] for i in range(0, len(aln_l), 3)] + # 100% (5 identical nucleotides / min(length(A),length(B))). + len_seq_a = len(pa_seqdic[chain]) + len_seq_b = len(pb_seqdic[chain]) + identity = ( + (len_seq_a - sum([e[0].count("-") for e in alignment])) + / min(len_seq_a, len_seq_b) + * 100 + ) + + if identity <= 40.0: + log.warning( + f'"Structural" identity of chain {chain} is {identity:.2f}%' + ", please check the results carefully" + ) + else: + log.info(f'"Structural" identity of chain {chain} is {identity:.2f}%') + + # logging.debug("Reading alignment and matching numbering") + for element in alignment: + line_a, line_b = element + + resnum_a, seq_a, _ = line_a.split() + resnum_b, seq_b, _ = line_b.split() + + resnum_a = int(resnum_a) - 1 # type: ignore + resnum_b = int(resnum_b) - 1 # type: ignore + + for resname_a, resname_b in zip(seq_a, seq_b): + if resname_a != "-": + resnum_a += 1 # type: ignore + + if resname_b != "-": + resnum_b += 1 # type: ignore + + if resname_a != "-" and resname_b != "-": + numbering_dic[chain][resnum_b] = resnum_a # type: ignore + + izone_fname = Path(output_path, "lovoalign.izone") + dump_as_izone(izone_fname, numbering_dic) + + return numbering_dic + + +def write_alignment(top_aln, output_path, ref_ch): + """ + Write the alignment to a file. + + Parameters + ---------- + top_aln : Bio.Align.PairwiseAlignments + alignment object + + ref_ch : str + reference chain + """ + aln_fname = Path(output_path, f"blosum62_{ref_ch}.aln") + with open(aln_fname, "w") as fh: + fh.write(str(top_aln)) + return aln_fname + + +def sequence_alignment(seq_ref, seq_model): + """ + Perform a sequence alignment. + + Parameters + ---------- + seq_ref : str + reference sequence + + seq_model : str + model sequence + + Returns + ------- + identity : float + sequence identity + + top_aln : Bio.Align.PairwiseAlignments + alignment object + + aln_ref_seg : tuple + aligned reference segment + + aln_mod_seg : tuple + aligned model segment + """ + aligner = Align.PairwiseAligner() + aligner.substitution_matrix = substitution_matrices.load("BLOSUM62") + alns = aligner.align(seq_ref, seq_model) + top_aln = alns[0] + + aln_denom = min(len(seq_ref), len(seq_model)) + identity = (str(top_aln).count("|") / float(aln_denom)) * 100 + + aln_ref_seg, aln_mod_seg = top_aln.aligned + # check alignment length + len_ref = len(aln_ref_seg) + len_mod = len(aln_mod_seg) + if len_ref != len_mod: + raise ALIGNError(f"Alignment length mismatch ({len_ref} != {len_mod})") + + return identity, top_aln, aln_ref_seg, aln_mod_seg + + +class SeqAlign: + """SeqAlign class.""" + + def __init__(self): + """Initialize the class.""" + self.align_dic = {} # the alignment dictionary, important for CAPRI + self.model2ref_chain_dict = {} # model to reference chain dictionary + self.ref2model_chain_dict = {} # reference to model chain dictionary + self.seqdic_ref = None # reference sequence dictionary + self.seqdic_model = None # model sequence dictionary + self.seqs_ref = {} # reference sequences + self.seqs_model = {} # model sequences + self.identities = [] # list of identity values + self.aln_model_segs = [] # list of aligned model segments + self.aln_ref_segs = [] # list of aligned reference segments + self.top_alns = [] # list of alignment objects + + def postprocess_alignment(self, ref_ch, mod_ch, align_id): + """ + Postprocess the alignment. + + Parameters + ---------- + ref_ch : str + reference chain + mod_ch : str + model chain + align_id : int + alignment id (index of the alignment) + """ + self.align_dic[ref_ch] = {} + if not np.any(self.top_alns[align_id].aligned): + # No alignment! + log.warning( + f"No alignment for chain {ref_ch} is it protein/dna-rna? " + "Matching sequentially" + ) + if all("X" in s for s in self.seqs_ref[ref_ch]) and all( + "X" in s for s in self.seqs_model[mod_ch] + ): + # this sequence contains only ligands, do it manually + if len(self.seqs_ref[ref_ch]) != len(self.seqs_model[mod_ch]): + # we cannot handle this + # FIXME: This should raise a proper exception instead + raise f"Cannot align chain {mod_ch}" # noqa: B016 + for ref_res, model_res in zip( + self.seqdic_ref[ref_ch], self.seqdic_model[mod_ch] + ): + self.align_dic[ref_ch].update({model_res: ref_res}) + else: + identity = self.identities[align_id] + if identity <= 40.0: + # Identity is very low + log.warning( + f"Sequence identity of chain {ref_ch} is " + f"{identity:.2f}%, please check the results carefully" + ) + else: + log.debug( + f"Sequence identity between chain {ref_ch} " + f" of reference and {mod_ch} of model is " + f"{identity:.2f}%" + ) + for ref_segment, model_segment in zip( + self.aln_ref_segs[align_id], self.aln_model_segs[align_id] + ): + start_ref_segment, end_ref_segment = ref_segment + start_model_segment, end_model_segment = model_segment + reslist_ref = list(self.seqdic_ref[ref_ch].keys())[ + start_ref_segment:end_ref_segment + ] + reslist_model = list(self.seqdic_model[mod_ch].keys())[ + start_model_segment:end_model_segment + ] + for _ref_res, _model_res in zip(reslist_ref, reslist_model): + self.align_dic[ref_ch].update({_model_res: _ref_res}) + + +def align_seq(reference, model, output_path, keep_hetatm: bool = False): + """ + Sequence align and get the numbering relationship. + + Parameters + ---------- + reference : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + + model : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + + output_path : Path + + keep_hetatm : bool + Should HETATM be considered when performing the alignment ? + + Returns + ------- + align_dic : dict + dictionary of sequence alignments (one per chain) + """ + SeqAln = SeqAlign() + SeqAln.seqdic_ref = pdb2fastadic(reference, keep_hetatm=keep_hetatm) + SeqAln.seqdic_model = pdb2fastadic(model, keep_hetatm=keep_hetatm) + + # assign sequences + for ref_ch in SeqAln.seqdic_ref.keys(): + ref_seq = Seq("".join(SeqAln.seqdic_ref[ref_ch].values())) + SeqAln.seqs_ref[ref_ch] = ref_seq + for mod_ch in SeqAln.seqdic_model.keys(): + mod_seq = Seq("".join(SeqAln.seqdic_model[mod_ch].values())) + SeqAln.seqs_model[mod_ch] = mod_seq + + # check if chain ids match + if SeqAln.seqdic_ref.keys() != SeqAln.seqdic_model.keys(): + # they do not match, we need to do chain matching + n_partners = min(len(SeqAln.seqdic_ref.keys()), len(SeqAln.seqdic_model.keys())) + + # unique combinations of chains + combs = [] + for ref_key in SeqAln.seqdic_ref.keys(): + for mod_key in SeqAln.seqdic_model.keys(): + combs.append((ref_key, mod_key)) + identities = [] + aln_model_segs = [] + aln_ref_segs = [] + top_alns = [] + # loop over combinations + for ref_ch, mod_ch in combs: + # align + identity, top_aln, aln_ref_seg, aln_mod_seg = sequence_alignment( + SeqAln.seqs_ref[ref_ch], SeqAln.seqs_model[mod_ch] + ) + # append values to lists + identities.append(identity) + aln_model_segs.append(aln_mod_seg) + aln_ref_segs.append(aln_ref_seg) + top_alns.append(top_aln) + # chain matching + matches = 0 # counter for matched chains + while matches < n_partners: + # get the best alignment + max_identity = max(identities) + max_idx = identities.index(max_identity) + # assigning chains + ref_ch, mod_ch = combs[max_idx] + SeqAln.model2ref_chain_dict[mod_ch] = ref_ch + SeqAln.ref2model_chain_dict[ref_ch] = mod_ch + SeqAln.aln_ref_segs.append(aln_ref_segs[max_idx]) + SeqAln.aln_model_segs.append(aln_model_segs[max_idx]) + SeqAln.identities.append(identities[max_idx]) + SeqAln.top_alns.append(top_alns[max_idx]) + + # writing the alignment + write_alignment(top_alns[max_idx], output_path, ref_ch) + + # postprocess alignment + SeqAln.postprocess_alignment(ref_ch, mod_ch, matches) + # update identities to avoid double matches + identities = [ + identities[n] if combs[n][0] != ref_ch and combs[n][1] != mod_ch else -1 + for n in range(len(combs)) + ] + matches += 1 + log.info(f"model2ref chain matching is {SeqAln.model2ref_chain_dict}") + else: + # chains do match. no need to do chain matching. Chains are the same. + # of course if the structures do not correspond the output will be a + # mess + matches = 0 + for ref_ch in SeqAln.seqdic_ref.keys(): + SeqAln.model2ref_chain_dict[ref_ch] = ref_ch + SeqAln.ref2model_chain_dict[ref_ch] = ref_ch + # extract sequences + seq_ref = SeqAln.seqs_ref[ref_ch] + seq_model = SeqAln.seqs_model[ref_ch] + # sequence alignment + identity, top_aln, aln_ref_seg, aln_mod_seg = sequence_alignment( + seq_ref, seq_model + ) + # update quantities + SeqAln.identities.append(identity) + SeqAln.aln_model_segs.append(aln_mod_seg) + SeqAln.aln_ref_segs.append(aln_ref_seg) + SeqAln.top_alns.append(top_aln) + # write alignment + write_alignment(top_aln, output_path, ref_ch) + # postprocess alignment + SeqAln.postprocess_alignment(ref_ch, ref_ch, matches) + matches += 1 + # dump the .izone file + izone_fname = Path(output_path, "blosum62.izone") + dump_as_izone(izone_fname, SeqAln.align_dic, SeqAln.ref2model_chain_dict) + + return SeqAln.align_dic, SeqAln.model2ref_chain_dict + + +def make_range( + chain_range_dic: dict[str, list[int]], +) -> dict[str, tuple[int, int]]: + """ + Expand a chain dictionary into ranges. + + Parameters + ---------- + chain_range_dic : dict + dictionary of chain indexes (one list per chain) + + Returns + ------- + chain_ranges : dict + dictionary of chain ranges (one tuple per chain) + """ + chain_ranges: dict[str, tuple[int, int]] = {} + for chain in chain_range_dic: + min_idx = min(chain_range_dic[chain]) + max_idx = max(chain_range_dic[chain]) + chain_ranges[chain] = (min_idx, max_idx) + return chain_ranges + + +def dump_as_izone(fname, numbering_dic, model2ref_chain_dict=None): + """ + Dump the numbering dictionary as .izone. + + Parameters + ---------- + fname : str + output filename + + numbering_dic : dict + dict of numbering dictionaries (one dictionary per chain) + """ + # FIXME: Collapse the izones so its faster to load in profit + with open(fname, "w") as fh: + for chain in numbering_dic: + for bound_res in numbering_dic[chain]: + unbound_res = numbering_dic[chain][bound_res] + unb_chain = chain + if model2ref_chain_dict: + unb_chain = model2ref_chain_dict[chain] + # + izone_str = ( + "ZONE " + f"{chain}{bound_res}:{unb_chain}{unbound_res}" + f"{os.linesep}" + ) + fh.write(izone_str) + + +def rearrange_xyz_files(output_name: FilePath, path: FilePath, ncores: int) -> None: + """Combine different xyz outputs in a single file. + + Parameters + ---------- + output_name : FilePath + output name + + path : FilePath + path to the output files + + ncores : int + number of cores + """ + output_fname = Path(path, output_name) + # take the name without the xyz extension + output_fname_str = output_fname.stem + log.info(f"rearranging xyz files into {output_fname}") + # Combine files + with open(output_fname, "w") as out_file: + for core in range(ncores): + tmp_file = Path(path, output_fname_str + "_" + str(core) + ".xyz") + with open(tmp_file) as infile: + out_file.write(infile.read()) + log.debug(f"File number {core} written") + tmp_file.unlink() + log.info("Completed reconstruction of xyz files.") + log.info(f"{output_fname} created.") + + +def check_common_atoms(models, filter_resdic, allatoms, atom_similarity): + """ + Check if the models share the same atoms. + + Parameters + ---------- + models : list + list of models + + filter_resdic : dict + dictionary of residues to be loaded (one list per chain) + + allatoms : bool + use all the heavy atoms + + atom_similarity : float + minimum atom similarity required between models + + Returns + ------- + n_atoms : int + number of common atoms + + common_keys : list + list of common atom keys + """ + # checking the common keys + common_keys: list[str] = [] + coord_keys_lengths = [] + for mod in models: + atoms: AtomsDict = get_atoms(mod, allatoms) + + ref_coord_dic, _ = load_coords(mod, atoms, filter_resdic) + coord_keys_lengths.append(len(ref_coord_dic.keys())) + if common_keys != []: + common_keys = set(ref_coord_dic.keys()).intersection(common_keys) + else: + common_keys = ref_coord_dic.keys() + + # checking the common atoms + n_atoms = len(common_keys) # common atoms + max_n_atoms = max(coord_keys_lengths) + perc = (n_atoms / max_n_atoms) * 100 + if perc == 100.0: + log.info("All the models share the same atoms.") + elif perc > atom_similarity and perc < 100.0: + # if it's between 0.9 and 1, it's likely that the models share the same atoms + # but still the user may want to see a warning + log.warning( + "Not all the atoms are common to all the models." + f" Common atoms ({n_atoms}) != max_n_atoms {max_n_atoms}. Similarity ({perc:.2f}%) higher than allowed ({atom_similarity:.2f}%)." + ) + else: + # common keys are less than 90% of the previous keys + # something is likely wrong + _err_msg = ( + "Input atoms are not the same for all the models." + f" Common atoms ({n_atoms}) != max_n_atoms {max_n_atoms}. Similarity ({perc:.2f}%) lower than allowed ({atom_similarity:.2f}%)." + " Please check the input ensemble." + ) + raise ALIGNError(_err_msg) + return n_atoms, list(common_keys) + + +# TODO: Add type signature +def check_chains(obs_chains, inp_r_chain, inp_l_chains): + """Check observed chains against the expected ones. + + Logic: if at least one of inp_l_chains is among the observed chains and is + not selected as the receptor chain, then ligand_chains is equal to this + interesection. Otherwise, ligand_chains becomes equal to all the other + chains (once receptor chain is removed). + + Parameters + ---------- + obs_chains : list + List of observed chains. + + inp_r_chain : str + Receptor chain. + + inp_l_chains : list + List of ligand chains. + """ + # Find receptor chain + r_chain = inp_r_chain if inp_r_chain in obs_chains else obs_chains[0] + # Remove it so cannot be selected as ligand chain + obs_chains.remove(r_chain) + # Define ligand chain(s) + l_chains = [el for el in inp_l_chains if el in obs_chains] + # If empty, select all remaining chains + if not l_chains: + l_chains = [el for el in obs_chains] + return r_chain, l_chains diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcli.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcli.py new file mode 100644 index 0000000000000000000000000000000000000000..d3bbe6d80f98b22e3e7f68af8f8ce9c9a44adb3e --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcli.py @@ -0,0 +1,105 @@ +"""Add functionalities for CLIs.""" +from argparse import Action, ArgumentParser, ArgumentTypeError +from functools import partial +from pathlib import Path + +from haddock import version +from haddock.libs.libio import file_exists, folder_exists + + +arg_file_exist = partial( + file_exists, + exception=ArgumentTypeError, + emsg="File {!r} does not exist or is not a file.", +) + +arg_folder_exist = partial( + folder_exists, + exception=ArgumentTypeError, + emsg="Folder {!r} does not exist.", +) + + +def add_version_arg(ap: ArgumentParser) -> None: + """Add version `-v` argument to client.""" + ap.add_argument( + "-v", + "--version", + help="show version", + action="version", + version=f"{ap.prog} - {version}", + ) + + +def add_rundir_arg(ap: ArgumentParser) -> None: + """Add run directory option.""" + ap.add_argument( + "run_dir", + help="The run directory.", + type=arg_folder_exist, + ) + + +def add_ncores_arg(ap: ArgumentParser) -> None: + """Add number of cores option.""" + ap.add_argument( + "-n", + "--ncores", + dest="ncores", + help=( + "The number of threads to use. Uses 1 if not specified. " + "Uses all available threads if `-n` is given. Else, uses the " + "number indicated, for example: `-n 4` will use 4 threads." + ), + type=int, + default=1, + const=None, + nargs="?", + ) + + +def add_output_dir_arg(ap: ArgumentParser) -> None: + """Add output dir argument.""" + ap.add_argument( + "-odir", + "--output-directory", + dest="output_directory", + help="The directory where to save the output.", + type=Path, + default=Path.cwd(), + ) + + +class _ParamsToDict(Action): + """ + Convert command-line parameters in an argument to a dictionary. + + Example + ------- + + Where ``-x`` is an optional argument of the command-line client + interface. + + >>> par1 1 par2 'my name' par3 [1,2,3] par4 True + >>> {'par1': 1, 'par2': 'my name', 'par3': [1, 2, 3]} + + """ + + def __call__(self, parser, namespace, ivalues, option_string=None): + """Execute.""" + params = ivalues[::2] + values = ivalues[1::2] + + if len(params) != len(values): + raise parser.error( + "The parameters and value pairs " "do not match for argument `-p`" + ) + + param_dict = {} + for k, v in zip(params, values): + try: + param_dict[k] = v + except (ValueError, TypeError, SyntaxError): + raise parser.error(f"Parameter {k} with invalid value {v}") + + setattr(namespace, self.dest, param_dict) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libclust.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libclust.py new file mode 100644 index 0000000000000000000000000000000000000000..3650e97fe7251961c6c3091ee18b0670f34ee3a7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libclust.py @@ -0,0 +1,316 @@ +""" +Library of functions related to the clustering modules. + +Main functions +-------------- + +* :py:func:`write_unclustered_list` +* :py:func:`plot_cluster_matrix` +""" + +import os +from pathlib import Path + +from haddock import log +from haddock.core.typing import FilePath, Union, ParamDictT, Optional +from haddock.libs.libontology import PDBFile +from haddock.libs.libplots import heatmap_plotly + +import numpy as np +from scipy.spatial.distance import squareform + + +MAX_NB_ENTRY_HTML_MATRIX = 3100 + + +def write_structure_list(input_models: list[PDBFile], + clustered_models: list[PDBFile], + out_fname: FilePath) -> None: + """ + Get the list of unclustered structures. + + Parameters + ---------- + input_models : list + list of input models + clustered_models : list + list of clustered models + """ + output_fname = Path(out_fname) + output_str = f'rank\tmodel_name\tscore\tcluster_id{os.linesep}' + structure_list: list[PDBFile] = [] + # checking which input models have not been clustered + for model in input_models: + if model not in clustered_models: + model.clt_id = "-" + structure_list.append(model) + # extending and sorting + structure_list.extend(clustered_models) + structure_list.sort(key=lambda model: model.score) + # adding models to output string + for mdl_rank, mdl in enumerate(structure_list, start=1): + output_str += ( + f'{mdl_rank}\t{mdl.file_name}\t{mdl.score:.2f}\t{mdl.clt_id}' + f'{os.linesep}' + ) + output_str += os.linesep + log.info(f'Saving structure list to {out_fname}') + with open(output_fname, 'w') as out_fh: + out_fh.write(output_str) + + +def plot_cluster_matrix( + matrix_path: Union[Path, FilePath, str], + final_order_idx: list[int], + labels: list[str], + dttype: str = '', + diag_fill: Union[int, float] = 1, + color_scale: str = "Blues", + reverse: bool = False, + output_fname: Union[str, Path, FilePath] = 'clust_matrix', + matrix_cluster_dt: Optional[list[list[list[int]]]] = None, + cluster_limits: Optional[list[dict[str, float]]] = None, + ) -> Optional[str]: + """Plot a plotly heatmap of a matrix file. + + Parameters + ---------- + matrix_path : Union[Path, FilePath, str] + Path to a half-matrix + final_order_idx : list[int] + Index orders + labels : list[str] + Ordered labels + dttype : str + Name of the data type, by default `` + color_scale : str, optional + Color scale for the plot, by default "Blues" + reversed : bool, optional + Should the color scale be reversed ?, by default False + output_fname : Union[str, Path, FilePath], optional + Name of the output file to generate, by default 'clust_matrix.html' + matrix_cluster_dt: Optional[list[list[list[int]]]] + A matrix of cluster ids, used for extra hover annotation in plotly. + cluster_limits: Optional[list[dict[str, float]]] + A list of dict enabling to draw lines separating cluster ids. + + Return + ------ + output_fname_ext : str + Path to the generated file containing the figure. + """ + # Check that we will be able to generate a functional interactive plot + if len(final_order_idx) > MAX_NB_ENTRY_HTML_MATRIX: + return None + + upper_diag, lower_diag = [], [] + # Read matrix + with open(matrix_path, "r") as f: + # Loop over lines + for _ in f: + # Split line + s_ = _.strip().split() + # Point first value + uv = float(s_[2]) + # Point second value (if exists) + lv = float(s_[3]) if len(s_) == 4 else uv + # Hold them + upper_diag.append(uv) + lower_diag.append(lv) + + # Genereate full matrix from N*(N-1)/2 vector + upper_matrix = squareform(upper_diag) + lower_matrix = squareform(lower_diag) + # Update diagonal with data + np.fill_diagonal(upper_matrix, diag_fill) + + # Full matrix (lower triangle + upper triangle) + full_matrix = np.tril(lower_matrix, k=-1) + np.triu(upper_matrix) + + # Extract submatrix of selected models and re-order them + submat = full_matrix[np.ix_(final_order_idx, final_order_idx)] + + # Check if must reverse the colorscale + if reverse: + if color_scale[-2:] == '_r': + color_scale = color_scale[:-2] + else: + color_scale += '_r' + + # Define hovering tempalte string + if matrix_cluster_dt: + hovertemplate = ( + f' {dttype}: %{{z}}
' + f' Model1: %{{x}} ClusterID: %{{customdata[0]}}
' + f' Model2: %{{y}} ClusterID: %{{customdata[1]}} ' + '' + ) + else: + hovertemplate = ( + f' {dttype}: %{{z}}
' + f' Model1: %{{x}}
' + f' Model2: %{{y}} ' + '' + ) + + # Generate file name + output_fname_ext = f"{output_fname}.html" + # Draw heatmap + heatmap_plotly( + submat, + labels={'color': dttype}, + xlabels=labels, + ylabels=labels, + color_scale=color_scale, + title=f"{dttype} clustering matrix", + output_fname=output_fname_ext, + hovertemplate=hovertemplate, + customdata=matrix_cluster_dt, + delineation_traces=cluster_limits, + ) + # Return generated filepath + return output_fname_ext + + +def get_cluster_matrix_plot_clt_dt( + cluster_ids: list[int], + ) -> tuple[list[list[list[int]]], list[dict[str, float]]]: + """Generate cluster matrix data for plotly. + + Parameters + ---------- + cluster_ids : list[int] + List containing ordered cluster ids. + + Returns + ------- + matrix_cluster_dt: list[list[list[int]]] + A matrix of cluster ids, used for plotly. + + cluster_limits: list[dict[str, float]]] + Boundaries to draw lines between clusters with plotly. + """ + # Set custom data + matrix_cluster_dt = [ + [[clix, cliy] for clix in cluster_ids] + for cliy in cluster_ids + ] + # Build delineation lines + del_ind = -0.5 + del_posi = [] + current_clid = cluster_ids[0] + for clid in cluster_ids: + if clid != current_clid: + del_posi.append(del_ind) + current_clid = clid + del_ind += 1 + cluster_limits = [ + { + "x0": delpos, + "x1": delpos, + "y0": -0.5, + "y1": len(cluster_ids) - 0.5, + } + for delpos in del_posi + ] + [ + { + "y0": delpos, + "y1": delpos, + "x0": -0.5, + "x1": len(cluster_ids) - 0.5, + } + for delpos in del_posi + ] + return matrix_cluster_dt, cluster_limits + + +def rank_clusters(clt_dic, threshold): + """ + Rank the clusters by their average score. + + Parameters + ---------- + clt_dic : :obj:`dict` + Dictionary with the clusters. + + threshold : int + Number of models to consider for the average score. + + Returns + ------- + score_dic : :obj:`dict` + Dictionary with the cluster ID as key and the average score as value. + + sorted_score_dic : :obj:`list` + List of tuples with the cluster ID and the average score, sorted by + the average score. + """ + score_dic = {} + for clt_id in clt_dic: + score_l = [p.score for p in clt_dic[clt_id]] + score_l.sort() + denom = float(min(threshold, len(score_l))) + top4_score = sum(score_l[:threshold]) / denom + score_dic[clt_id] = top4_score + + sorted_score_dic = sorted(score_dic.items(), key=lambda k: k[1]) + return score_dic, sorted_score_dic + + +def add_cluster_info(sorted_score_dic, clt_dic): + """ + Add cluster information to the models. + + Parameters + ---------- + sorted_score_dic : :obj:`list` + List of tuples with the cluster ID and the average score, sorted by + the average score. + + clt_dic : :obj:`dict` + Dictionary with the clusters. + + Returns + ------- + output_models : :obj:`list` + List of models with the cluster information. + """ + # Add this info to the models + output_models = [] + for cluster_rank, _e in enumerate(sorted_score_dic, start=1): + cluster_id, _ = _e + # sort the models by score + clt_dic[cluster_id].sort() + # rank the models + for model_ranking, pdb in enumerate(clt_dic[cluster_id], + start=1): + pdb.clt_id = int(cluster_id) + pdb.clt_rank = cluster_rank + pdb.clt_model_rank = model_ranking + output_models.append(pdb) + return output_models + + +def clustrmsd_tolerance_params( + parameters: ParamDictT, + ) -> tuple[str, Union[int, float]]: + """Provide parameters of interest for clust rmsd. + + Parameters + ---------- + parameters : ParamDictT + The clustrmsd module parameters + + Returns + ------- + tuple[str, Union[int, float]] + Name of the tolerance parameter and its value. + """ + # adjust the parameters + if parameters["criterion"] == "maxclust": + tolerance_param_name = "n_clusters" + tolerance = parameters[tolerance_param_name] + else: # Expected to be parameters["criterion"] == "distance" + tolerance_param_name = "clust_cutoff" + tolerance = parameters[tolerance_param_name] + return tolerance_param_name, tolerance diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcns.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcns.py new file mode 100644 index 0000000000000000000000000000000000000000..f39bc8b78ec8e5bcb03190a7000dd93560c6ad4f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libcns.py @@ -0,0 +1,441 @@ +"""CNS scripts util functions.""" + +import itertools +import math +from functools import partial +from os import linesep +from pathlib import Path + +from haddock import EmptyPath, log +from haddock.core import cns_paths +from haddock.core.typing import Any, FilePath, FilePathT, Optional, Union +from haddock.libs import libpdb +from haddock.libs.libfunc import false, true +from haddock.libs.libmath import RandomNumberGenerator +from haddock.libs.libontology import PDBFile +from haddock.libs.libpdb import check_combination_chains +from haddock.libs.libutil import transform_to_list + + +RND = RandomNumberGenerator() + + +def generate_default_header( + path: Optional[FilePath] = None, +) -> tuple[str, str, str, str, str, str]: + """Generate CNS default header.""" + # TODO: Remove the `type: ignore` comments + if path is not None: + axis = load_axis(**cns_paths.get_axis(path)) # type: ignore + link = load_link(Path(path, cns_paths.LINK_FILE)) + scatter = load_scatter(Path(path, cns_paths.SCATTER_LIB)) + tensor = load_tensor(**cns_paths.get_tensors(path)) # type: ignore + trans_vec = load_trans_vectors( + **cns_paths.get_translation_vectors(path) # type: ignore + ) # noqa: E501 + water_box = load_boxtyp20(cns_paths.get_water_box(path)["boxtyp20"]) + + else: + axis = load_axis(**cns_paths.axis) # type: ignore + link = load_link(cns_paths.link_file) + scatter = load_scatter(cns_paths.scatter_lib) + tensor = load_tensor(**cns_paths.tensors) # type: ignore + trans_vec = load_trans_vectors(**cns_paths.translation_vectors) # type: ignore + water_box = load_boxtyp20(cns_paths.water_box["boxtyp20"]) + + return ( + link, + trans_vec, + tensor, + scatter, + axis, + water_box, + ) + + +def find_desired_linkfiles( + charged_nter: bool = False, + charged_cter: bool = False, + phosphate_5: bool = False, + path: Optional[FilePath] = None, + ) -> dict[str, Path]: + """Find appropriate link files to use depending on terminis states. + + Parameters + ---------- + charged_nter : bool, optional + Must the Nter be charged ?, by default False + charged_cter : bool, optional + Must the Cter be charged ?, by default False + phosphate_5 : bool, optional + Must 5' be a phosphate ?, by default False + path : Optional[FilePath], optional + Path to where CNS topology/parameters are, by default None + + Returns + ------- + linkfiles : dict[str, Path] + Dict of CNS parameters/arguments/variable as keys + and Path to link files to be used during topology + generation. + """ + # Set output variable + linkfiles = {} + # Logic to find appropriate link for proteins + if charged_nter and charged_cter: + prot_link_key = "NH3+,COO-" + elif not charged_nter and charged_cter: + prot_link_key = "NH,COO-" + elif charged_nter and not charged_cter: + prot_link_key= "NH3+,CO" + elif not charged_nter and not charged_cter: + prot_link_key = "NH,CO" + # Point to corresponding file + linkfiles["prot_link_infile"] = cns_paths.PROTEIN_LINK_FILES[prot_link_key] + + # Logic to find linkfile for dna + nucl_link_key = "5'Phosphate" if phosphate_5 else "5'OH" + # Point to corresponding file + linkfiles["nucl_link_infile"] = cns_paths.NUCL_LINK_FILES[nucl_link_key] + # Converts to real paths + if path is not None: + linkfiles = {key: Path(path, p) for key, p in linkfiles.items()} + return linkfiles + + +def _is_nan(x: Any) -> bool: + """Inspect if is nan.""" + try: + return math.isnan(x) + except (ValueError, TypeError): + return False + + +def filter_empty_vars(v: Any) -> bool: + """ + Filter empty variables. + + See: https://github.com/haddocking/haddock3/issues/162 + + Returns + ------- + bool + Returns `True` if the variable is not empty, and `False` if + the variable is empty. That is, `False` reflects those variables + that should not be written in CNS. + + Raises + ------ + TypeError + If the type of `value` is not supported by CNS. + """ + cases = ( + (lambda x: _is_nan(x), false), + (lambda x: isinstance(x, str) and bool(x), true), + (lambda x: isinstance(x, str) and not bool(x), false), + (lambda x: isinstance(x, bool), true), # it should return True + (lambda x: isinstance(x, (EmptyPath, Path)), true), + (lambda x: type(x) in (int, float), true), + (lambda x: x is None, false), + ) + + for detect, give in cases: + if detect(v): + return give(v) + else: + emsg = f"Value {v!r} has a unknown type for CNS: {type(v)}." + log.error(emsg) + raise TypeError(emsg) + + +def load_workflow_params( + param_header: str = f"{linesep}! Parameters{linesep}", + **params: Any, +) -> str: + """ + Write the values at the header section. + + "Empty variables" are ignored. These are defined accoring to + :func:`filter_empty_vars`. + + Parameters + ---------- + params : dict + Dictionary containing the key:value pairs for the parameters to + be written to CNS. Values cannot be of dictionary type. + + Returns + ------- + param_header: str + The string with the CNS parameters defined. + """ + non_empty_parameters = ( + (k, v) for k, v in params.items() + if filter_empty_vars(v) + ) + + # types besides the ones in the if-statements should not enter this loop + for param, v in non_empty_parameters: + param_header += write_eval_line(param, v) + + assert isinstance(param_header, str) + return param_header + + +def write_eval_line(param: Any, value: Any, eval_line: str = "eval (${}={})") -> str: + """Write the CNS eval line depending on the type of `value`.""" + eval_line += linesep + + if isinstance(value, bool): + value = str(value).lower() + return eval_line.format(param, value) + + elif isinstance(value, str): + value = '"' + value + '"' + return eval_line.format(param, value) + + elif isinstance(value, Path): + value = '"' + str(value) + '"' + return eval_line.format(param, value) + + elif isinstance(value, EmptyPath): + return eval_line.format(param, '""') + + elif isinstance(value, (int, float)): + return eval_line.format(param, value) + + else: + emsg = f"Unexpected type when writing CNS header: {type(value)}" + log.error(emsg) + raise TypeError(emsg) + + +def load_link(mol_link: Path) -> str: + """Add the link header.""" + return load_workflow_params( + param_header=f"{linesep}! Link file{linesep}", + prot_link_infile=mol_link, + ) + + +load_axis = partial( + load_workflow_params, param_header=f"{linesep}! Axis{linesep}" +) # noqa: E501 +load_tensor = partial( + load_workflow_params, param_header=f"{linesep}! Tensors{linesep}" +) # noqa: E501 +prepare_output = partial( + load_workflow_params, param_header=f"{linesep}! Output structure{linesep}" +) # noqa: E501 +load_trans_vectors = partial( + load_workflow_params, param_header=f"{linesep}! Translation vectors{linesep}" +) # noqa: E501 + +load_ambig = partial(write_eval_line, "ambig_fname") +load_unambig = partial(write_eval_line, "unambig_fname") +load_hbond = partial(write_eval_line, "hbond_fname") +load_dihe = partial(write_eval_line, "dihe_f") +load_tensor_tbl = partial(write_eval_line, "tensor_tbl") + + +def load_scatter(scatter_lib: Path) -> str: + """Add scatter library.""" + return load_workflow_params( + param_header=f"{linesep}! Scatter lib{linesep}", scatter_lib=scatter_lib + ) + + +def load_boxtyp20(waterbox_param: Path) -> str: + """Add boxtyp20 eval line.""" + return load_workflow_params( + param_header=f"{linesep}! Water box{linesep}", boxtyp20=waterbox_param + ) + + +# This is used by docking +def prepare_multiple_input(pdb_input_list: list[str], psf_input_list: list[str]) -> str: + """Prepare multiple input files.""" + input_str = f"{linesep}! Input structure{linesep}" + for psf in psf_input_list: + input_str += f"structure{linesep}" + input_str += f" @@{psf}{linesep}" + input_str += f"end{linesep}" + + ncount = 1 + for pdb in pdb_input_list: + input_str += f"coor @@{pdb}{linesep}" + input_str += write_eval_line(f"input_pdb_filename_{ncount}", pdb) + ncount += 1 + + # check how many chains there are across all the PDBs + chain_l: list[list[str]] = [] + for pdb in pdb_input_list: + for element in libpdb.identify_chainseg(pdb): + chain_l.append(element) + ncomponents = len(set(itertools.chain(*chain_l))) + input_str += write_eval_line("ncomponents", ncomponents) + + return input_str + + +# This is used by Topology and Scoring +def prepare_single_input( + pdb_input: FilePath, psf_input: Union[None, FilePath, list[FilePathT]] = None +) -> str: + """Input of the CNS file. + + This section will be written for any recipe even if some CNS variables + are not used, it should not be an issue. + """ + input_str = f"{linesep}! Input structure{linesep}" + + if psf_input: + # if isinstance(psf_input, str): + input_str += f"structure{linesep}" + input_str += f" @@{psf_input}{linesep}" + input_str += f"end{linesep}" + input_str += f"coor @@{pdb_input}{linesep}" + if isinstance(psf_input, list): + input_str += f"structure{linesep}" + for psf in psf_input: + input_str += f" @@{psf}{linesep}" + input_str += f"end{linesep}" + + # $file variable is still used by some CNS recipes, need refactoring! + input_str += write_eval_line("file", pdb_input) + segids, chains = libpdb.identify_chainseg(pdb_input) + chainsegs = sorted(list(set(segids) | set(chains))) + + ncomponents = len(chainsegs) + input_str += write_eval_line("ncomponents", ncomponents) + + for i, segid in enumerate(chainsegs, start=1): + input_str += write_eval_line(f"prot_segid_{i}", segid) + + seed = RND.randint(100, 99999) + input_str += write_eval_line("seed", seed) + + return input_str + + +def prepare_cns_input( + model_number: int, + input_element: Union[PDBFile, list[PDBFile]], + step_path: FilePath, + recipe_str: str, + defaults: Any, + identifier: str, + ambig_fname: FilePath = "", + native_segid: bool = False, + default_params_path: Optional[Path] = None, + debug: Optional[bool] = False, + seed: Optional[int] = None, +) -> Union[Path, str]: + """ + Generate the .inp file needed by the CNS engine. + + Parameters + ---------- + model_number : int + The number of the model. Will be used as file name suffix. + + input_element : `libs.libontology.Persisten`, list of those + """ + # TODO: Refactor this function into smaller functions or classes + # read the default parameters + default_params = load_workflow_params(**defaults) + default_params += write_eval_line("ambig_fname", ambig_fname) + + # write the PDBs + pdb_list = [pdb.rel_path for pdb in transform_to_list(input_element)] + + # write the PSFs + psf_list: list[Path] = [] + if isinstance(input_element, (list, tuple)): + for pdb in input_element: + if isinstance(pdb.topology, (list, tuple)): + for psf in pdb.topology: + psf_fname = psf.rel_path + psf_list.append(psf_fname) + else: + if pdb.topology is None: + raise ValueError(f"Topology not found for pdb {pdb.rel_path}.") + psf_fname = pdb.topology.rel_path + psf_list.append(psf_fname) + + elif isinstance(input_element.topology, (list, tuple)): + pdb = input_element # for clarity + if pdb.topology is None: + raise ValueError(f"Topology not found for pdb {pdb.rel_path}.") + for psf in pdb.topology: + psf_fname = psf.rel_path + psf_list.append(psf_fname) + else: + pdb = input_element # for clarity + if pdb.topology is None: + raise ValueError(f"Topology not found for pdb {pdb.rel_path}.") + psf_fname = pdb.topology.rel_path + psf_list.append(psf_fname) + + input_str = prepare_multiple_input( + pdb_input_list=[str(p) for p in pdb_list], + psf_input_list=[str(p) for p in psf_list], + ) + + output_pdb_filename = f"{identifier}_{model_number}.pdb" + + output = f"{linesep}! Output structure{linesep}" + output += write_eval_line("output_pdb_filename", output_pdb_filename) + + # prepare chain/seg IDs + segid_str = "" + if native_segid: + if isinstance(input_element, (list, tuple)): + chainid_list = check_combination_chains(input_element) + + for i, _chainseg in enumerate(chainid_list, start=1): + segid_str += write_eval_line(f"prot_segid_{i}", _chainseg) + + else: + chainid_list: list[str] = [] + segids, chains = libpdb.identify_chainseg( + input_element.rel_path, sort=False + ) + + chainsegs = sorted(list(set(segids) | set(chains))) + + for i, _chainseg in enumerate(chainsegs, start=1): + segid_str += write_eval_line(f"prot_segid_{i}", _chainseg) + + output += write_eval_line("count", model_number) + + if seed is None: + seed = RND.randint(100, 99999) + + seed_str = write_eval_line("seed", seed) + + inp = default_params + input_str + seed_str + output + segid_str + recipe_str + + if not debug: + return inp + else: + inp_file = Path(f"{identifier}_{model_number}.inp") + inp_file.write_text(inp) + return inp_file + + +def prepare_expected_pdb( + model_obj: Union[PDBFile, tuple[PDBFile, ...]], + model_nb: int, + path: FilePath, + identifier: str, +) -> PDBFile: + """Prepare a PDBobject.""" + expected_pdb_fname = Path(path, f"{identifier}_{model_nb}.pdb") + pdb = PDBFile(expected_pdb_fname, path=path) + if isinstance(model_obj, tuple): + pdb.topology = [p.topology for p in model_obj] + else: + pdb.topology = model_obj.topology + pdb.seed = model_obj.seed + return pdb diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfcc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfcc.py new file mode 100644 index 0000000000000000000000000000000000000000..bdce73dcf2224a52df6c5fee3d8e3783efb6b79f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfcc.py @@ -0,0 +1,250 @@ +"""FCC related functions + +NOTE: This functions were ported directly from `https://github.com/haddocking/fcc`! +""" + + +class Element: + """Defines a 'clusterable' Element""" + + __slots__ = ["name", "cluster", "neighbors"] + + def __init__(self, name): + self.name = name + self.cluster = 0 + self.neighbors = set() + + def add_neighbor(self, neighbor): + """Adds another element to the neighbor list""" + self.neighbors.add(neighbor) + + def assign_cluster(self, clust_id): + """Assigns the Element to Cluster. 0 if unclustered""" + self.cluster = clust_id + + +class Cluster: + """Defines a Cluster. A Cluster is created with a name and a center (Element class)""" + + __slots__ = ["name", "center", "members"] + + def __init__(self, name, center): + self.name = name + self.center = center + + self.members = [] + + self.populate() + + def __len__(self): + return len(self.members) + 1 # +1 Center + + def populate(self): + """ + Populates the Cluster member list through the + neighbor list of its center. + """ + + name = self.name + # Assign center + ctr = self.center + ctr.assign_cluster(name) + + mlist = self.members + # Assign members + ctr_nlist = (n for n in ctr.neighbors if not n.cluster) + for e in ctr_nlist: + mlist.append(e) + e.assign_cluster(name) + + def add_member(self, element): + """ + Adds one single element to the cluster. + """ + line = self.members + line.append(element) + element.assign_cluster(self.name) + + +def cluster_elements(e_pool, threshold): + """ + Groups Elements within a given threshold + together in the same cluster. + """ + + cluster_list = [] + threshold -= 1 # Account for center + ep = e_pool + cn = 1 # Cluster Number + while 1: + # Clusterable elements + ce = [e for e in ep if not ep[e].cluster] + if not ce: # No more elements to cluster + break + + # Select Cluster Center + # Element with largest neighbor list + ctr_nlist, ctr = sorted( + [(len([se for se in ep[e].neighbors if not se.cluster]), e) for e in ce] + )[-1] + + # Cluster until length of remaining elements lists are above threshold + if ctr_nlist < threshold: + break + + # Create Cluster + c = Cluster(cn, ep[ctr]) + cn += 1 + cluster_list.append(c) + + return ep, cluster_list + + +def output_clusters(handle, cluster): + """Outputs the cluster name, center, and members.""" + + write = handle.write + + for c in cluster: + write("Cluster %s -> %s " % (c.name, c.center.name)) + for m in sorted(c.members, key=lambda k: k.name): + write("%s " % m.name) + write("\n") + + +def load_matrix(matrix_path) -> list[tuple[int, int, float, float]]: + """Read in a four column matrix (1 2 0.123 0.456\n) + + Parameters + ---------- + matrix_path : str or Path + Path to the matrix file + + Returns + ------- + matrix : list[tuple[int, int, float, float]] + Content of the matrix + """ + matrix: list[tuple[int, int, float, float]] = [] + with open(matrix_path, "r") as fin: + for line in fin: + ref, mobi, d_rm, d_mr = line.split() + ref = int(ref) + mobi = int(mobi) + d_rm = float(d_rm) + d_mr = float(d_mr) + matrix.append((ref, mobi, d_rm, d_mr)) + return matrix + + +def create_elements(matrix, cutoff_param, strictness): + """Creates an dictionary of Elements. + + The strictness factor is a that multiplies by the cutoff + to produce a new cutoff for the second half of the matrix. Used to + allow some variability while keeping very small interfaces from clustering + with anything remotely similar. + """ + + cutoff_param = float(cutoff_param) + partner_cutoff = float(cutoff_param) * float(strictness) + + elements = {} + + # Loop over matrix rows + for row in matrix: + ref, mobi, d_rm, d_mr = row + + # Create or Retrieve Elements + if ref not in elements: + r = Element(ref) + elements[ref] = r + else: + r = elements[ref] + + if mobi not in elements: + m = Element(mobi) + elements[mobi] = m + else: + m = elements[mobi] + + # Assign neighbors + if d_rm >= cutoff_param and d_mr >= partner_cutoff: + r.add_neighbor(m) + if d_mr >= cutoff_param and d_rm >= partner_cutoff: + m.add_neighbor(r) + + return elements + + +def parse_contact_file(f_list, ignore_chain): + """Parses a list of contact files.""" + + if ignore_chain: + contacts = [ + [int(line[0:5] + line[6:-1]) for line in open(con_f)] + for con_f in f_list + if con_f.strip() + ] + else: + contacts = [ + set([int(line) for line in open(con_f)]) + for con_f in f_list + if con_f.strip() + ] + + return contacts + + +def calculate_fcc(list_a, list_b): + """ + Calculates the fraction of common elements between two lists + taking into account chain IDs + """ + + cc = len(list_a.intersection(list_b)) + cc_v = len(list_b.intersection(list_a)) + + return cc, cc_v + + +def calculate_fcc_nc(list_a, list_b): + """ + Calculates the fraction of common elements between two lists + not taking into account chain IDs. Much Slower. + """ + + largest, smallest = sorted([list_a, list_b], key=len) + ncommon = len([ele for ele in largest if ele in smallest]) + return ncommon, ncommon + + +def calculate_pairwise_matrix(contacts, ignore_chain): + """Calculates a matrix of pairwise fraction of common contacts (FCC). + Outputs numeric indexes. + + contacts: list_of_unique_pairs_of_residues [set/list] + + Returns pairwise matrix as an iterator, each entry in the form: + FCC(cplx_1/cplx_2) FCC(cplx_2/cplx_1) + """ + + contact_lengths = [] + for con in contacts: + try: + ic = 1.0 / len(con) + except ZeroDivisionError: + ic = 0 + contact_lengths.append(ic) + + if ignore_chain: + calc_fcc = calculate_fcc_nc + else: + calc_fcc = calculate_fcc + + for i in range(len(contacts)): + + for k in range(i + 1, len(contacts)): + cc, cc_v = calc_fcc(contacts[i], contacts[k]) + fcc, fcc_v = cc * contact_lengths[i], cc * contact_lengths[k] + yield i + 1, k + 1, fcc, fcc_v diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfunc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfunc.py new file mode 100644 index 0000000000000000000000000000000000000000..ab52826d33e5ad500a02caab9658b5a806f74432 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libfunc.py @@ -0,0 +1,100 @@ +""" +Tools for Functional-Programming in Python. + +From: https://github.com/joaomcteixeira/libfuncpy +""" +import time + +from functools import wraps +from operator import is_not +from typing import Any, Callable, Literal + + +def chainf(init: Any, *funcs: Callable[..., Any], **common: Any) -> Any: + """ + Apply a sequence of functions to an initial value. + + Example + ------- + >>> chainf(2, *[str, int, float]) + 2.0 + + Parameters + ---------- + init : anything + The initial value. + + **common : keyword arguments + Common key word arguments to all functions. + + Returns + ------- + anything + The result of the chain of functions; this is, the return value + of the last function. + """ + for func in funcs: + init = func(init, **common) + return init + + +def chainfs(*funcs: Callable[..., Any], **common: Any) -> Callable[..., Any]: + """ + Store functions be executed on a value. + + Example + ------- + >>> do = chainfs(str, int, float) + >>> do(2) + 2.0 + + See Also + -------- + :py:func:`chainf` + """ + def execute(value: Any) -> Any: + return chainf(value, *funcs, **common) + + return execute + + +def give_same(value: Any) -> Any: + """Return what is given.""" + return value + + +def true(*ignore: Any, **everything: Any) -> Literal[True]: + """Give True regardless of the input.""" + return True + + +def false(*ignore: Any, **everything: Any) -> Literal[False]: + """Give False regardless of the input.""" + return False + + +def none(*ignore: Any, **everything: Any) -> Literal[None]: + """Give None regardless of the input.""" + return None + + +def nan(*ignore: Any, **everything: Any) -> float: + """Give nan regardless of the input.""" + return float('nan') + + +def not_none(value: Any) -> bool: + """Give True if value is not None, or False otherwise.""" + return is_not(value, None) + + +def exec_time(func): + @wraps(func) + def timeit_wrapper(*args, **kwargs): + start_time = time.perf_counter() + result = func(*args, **kwargs) + end_time = time.perf_counter() + total_time = end_time - start_time + print(f'Function {func.__name__}{args} {kwargs} Took {total_time:.4f} seconds') + return result + return timeit_wrapper diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libgrid.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libgrid.py new file mode 100644 index 0000000000000000000000000000000000000000..d0c302659cd9c89dde3c32092db3dc79d0b9424c --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libgrid.py @@ -0,0 +1,798 @@ +import glob +import math +import os +import random +import re +import shutil +import subprocess +import tempfile +import uuid +import warnings +import zipfile +from abc import ABC, abstractmethod +from concurrent.futures import ThreadPoolExecutor +from datetime import datetime +from enum import Enum +from pathlib import Path +from typing import Optional, Tuple, Union + +from haddock import log +from haddock.core.defaults import cns_exec_linux as CNS_EXEC +from haddock.libs.libsubprocess import CNSJob +from haddock.libs.libutil import parse_ncores + +# NOTE: When creating the payload.zip, this warning appears because we are replicating `toppar_path` +# subdirectory structure. It can be ignored safely, but keep an eye on it to make sure +# not many operations are being duplicated +warnings.filterwarnings("ignore", message="Duplicate name:*", category=UserWarning) +# =====================================================================# +# EXPLANATION # +# =====================================================================# +# `JOB_TYPE` is an environment variable that can be set to specify the +# type of job associated with a given VO. This is usually important for +# accounting purposes, as different job types may have different resources +# associated with it. +# There is an explanation about this in the user manual. +# =====================================================================# +JOB_TYPE = os.getenv("HADDOCK3_GRID_JOB_TYPE", "WeNMR-DEV") +MAX_RETRIES = 10 + +# Important patterns to adjust the paths in the `.inp` file +OUTPUT_PATTERN = r'\$output_\w+\s*=\s*"([^"]+)"|\$output_\w+\s*=\s*([^\s;]+)' +VAR_PATTERN = r"\(\$\s*[^=]*=(?!.?\$)(.*)\)" # https://regex101.com/r/dYqlZP/1 +AT_PATTERN = r"@@(?!\$)(.*)" + + +def ping_dirac() -> bool: + """Ping the Dirac server to check if it's reachable.""" + if not validate_dirac(): + return False + + result = subprocess.run(["dirac-proxy-info"], capture_output=True) + if result.returncode != 0: + log.error(f"Dirac proxy info failed: {result.stderr.decode().strip()}") + return False + + return True + + +def validate_dirac() -> bool: + """Check if the DIRAC client is valid and configured.""" + expected_cmds = [ + "dirac-proxy-info", + "dirac-wms-job-submit", + "dirac-wms-job-status", + "dirac-wms-job-get-output", + ] + + for cmd in expected_cmds: + # Expect the commands to be in the PATH + which_cmd = shutil.which(cmd) + if not which_cmd: + log.error(f"Command '{cmd}' not found in PATH.") + return False + + return True + + +class JobStatus(Enum): + WAITING = "Waiting" + RUNNING = "Running" + UNKNOWN = "Unknown" + DONE = "Done" + MATCHED = "Matched" + COMPLETING = "Completing" + FAILED = "Failed" + STAGED = "Staged" + + @classmethod + def from_string(cls, value): + """Convert string to JobStatus enum.""" + value = value.strip().lower() + for status in cls: + if status.value.lower() == value: + return status + return cls.UNKNOWN + + +class Tag(Enum): + PROBING = "Probing" + DEFAULT = "Default" + + +class GridInterface(ABC): + + def __init__( + self, + input: Union[Path, str, list[str]], + toppar_path: Path, + module_path: Path, + ) -> None: + # Common attributes for all grid jobs can be defined here + # Unique name for the job + self.name = str(uuid.uuid4()) + # Create a temporary directory for the job + self.loc = Path(tempfile.mkdtemp(prefix="haddock_grid_")) + # working directory where the GridJob was created, this is important + # so we know where to put the files coming from the grid + self.wd = Path.cwd() + # `id` is given by DIRAC + self.id = None + # Site where the job is running + self.site = None + # Script that will be executed in the grid + self.job_script = self.loc / "job.sh" + # JDL file that describes the job to DIRAC + self.jdl = self.loc / "job.jdl" + # Internal status of the job + self.status = JobStatus.STAGED + # `expected_outputs` is what will be produced by this `.inp` file + self.expected_outputs = [] + # Output and error files generated by the job.sh execution + self.stdout_f = None + self.stderr_f = None + # List of files to be included in the payload + self.payload_fnames = [] + # Counter for retries + self.retries = 0 + # Tracker for timings + self.timings: dict[JobStatus, datetime] = {} + # Tag for the job + self.tag = Tag.DEFAULT + # `input_str` is the content of the `.inp` file + self.input_str = "" + # `input_str_list` is a list of separate recipes` + self.input_str_list = [] # Initialize the list to store separate recipes + # `module_path` is the path to the CNS module files + self.module_path = module_path + # `toppar_path` is the path to the TOPPAR files` + self.toppar_path = toppar_path + # Indicator if this job has been packaged + self.packaged = False + + # `parse_input` is an abstract compatibility method that will handle + # different types of input. It can be either a string, a path or + # a list of paths/strings + self.parse_input(input) + + def package(self) -> None: + + # We need to process the input file first to adjust paths and identify outputs + self.process_input_f() + + # CREATE JOB FILE + self.create_job_script() + + # CREATE THE JDL + self.create_jdl() + + # CREATE PAYLOAD + self.prepare_payload( + cns_script_path=Path(self.module_path), + toppar_path=Path(self.toppar_path), + ) + + self.packaged = True + + @abstractmethod + def parse_input(self, input: Union[Path, str, list[str]]) -> None: + """placeholder""" + pass + + @abstractmethod + def create_job_script(self) -> None: + """Create the job script that will be executed in the grid.""" + pass + + @abstractmethod + def process_input_f(self) -> None: + """Process the input file to adjust paths and identify outputs.""" + pass + + def create_jdl(self) -> None: + """Create the JDL file that describes the job to DIRAC.""" + output_sandbox = ["job.out", "job.err"] + output_sandbox.extend(self.expected_outputs) + output_sandbox_str = ", ".join(f'"{fname}"' for fname in output_sandbox) + jdl_lines = [ + f'JobName = "{self.name}";', + 'Executable = "job.sh";', + 'Arguments = "";', + 'StdOutput = "job.out";', + 'StdError = "job.err";', + f'JobType = "{JOB_TYPE}";', + 'InputSandbox = {"job.sh", "payload.zip"};', + "OutputSandbox = {" + f"{output_sandbox_str}" + "};", + ] + + jdl_string = "[\n " + "\n ".join(jdl_lines) + "\n]\n" + # log.debug(f"JDL for job {self.name}:\n{jdl_string}") + + with open(self.jdl, "w") as f: + f.write(jdl_string) + + def update_status(self) -> None: + """Update the status of the job by querying DIRAC.""" + try: + result = subprocess.run( + ["dirac-wms-job-status", str(self.id)], + shell=False, + capture_output=True, + text=True, + ) + except subprocess.CalledProcessError as e: + log.error( + f"Updating the status failed: {e}\nStdout: {e.stdout}\nStderr: {e.stderr}" + ) + raise + + output_dict = self.parse_output(result.stdout) + + self.id = output_dict["JobID"] + self.status = JobStatus.from_string(output_dict["Status"]) + self.site = output_dict.get("Site", "Unknown") + + log.debug(self) + + if self.status == JobStatus.RUNNING and JobStatus.RUNNING not in self.timings: + # job is running and we have not tracket it yet, save the time + self.timings[JobStatus.RUNNING] = datetime.now() + elif self.status == JobStatus.DONE and JobStatus.DONE not in self.timings: + # job is done and we have not tracked it yet, save the time + self.timings[JobStatus.DONE] = datetime.now() + + def prepare_payload(self, cns_script_path: Path, toppar_path: Path) -> None: + """Prepare the payload.zip file containing all necessary files.""" + + # Find the CNS scripts that should be inside the payload + for f in cns_script_path.glob("*"): + self.payload_fnames.append(Path(f)) + + # Find the TOPPAR files that should be inside the payload + for f in toppar_path.rglob("*"): + if f.is_file(): # Only add files, not directories + self.payload_fnames.append(f) + + # Create the payload.zip + with zipfile.ZipFile(f"{self.loc}/payload.zip", "w") as z: + # It must contain the CNS executable and the input file, + # z.write(self.input_f, arcname=f"{self.input_f.name}") + z.write(CNS_EXEC, arcname="cns") + for f in set(self.payload_fnames): + # NOTE: Preserve the relative path structure from `toppar_path`! + # This is important because some CNS scripts have relative paths + # hardcoded in it + if f.is_relative_to(toppar_path): + relative_path = f.relative_to(toppar_path) + z.write(f, arcname=str(relative_path)) + else: + z.write(f, arcname=Path(f).name) + + def submit(self) -> None: + """Interface to submit the job to DIRAC.""" + + # If this is a re-submission the timings will already be set, + # make sure it is clean + self.clean_timings() + + if not self.packaged: + self.package() + + self.timings[JobStatus.WAITING] = datetime.now() + + try: + # The SUBMIT_CMD returns the job ID in stdout + result = subprocess.run( + ["dirac-wms-job-submit", f"{self.loc}/job.jdl"], + shell=False, + capture_output=True, + text=True, + cwd=self.loc, + check=True, + ) + except subprocess.CalledProcessError as e: + log.error( + f"Job submission failed: {e}\nStdout: {e.stdout}\nStderr: {e.stderr}" + ) + # TODO: Add some sort of retry/fallback mechanism here? + raise + + # Add the ID to the object + self.id = int(result.stdout.split()[-1]) + + # Update the status + self.update_status() + + def retrieve_output(self) -> None: + """Retrieve the output files from DIRAC. + + The `dirac-wms-job-get-output` command downloads the output sandbox, this means that + anything that was specified in the `OutputSandbox` section of the JDL file will be + put in the current working directory following the pattern: `working_dir/job_id/` + """ + try: + subprocess.run( + ["dirac-wms-job-get-output", str(self.id)], + shell=False, + capture_output=True, + text=True, + cwd=self.loc, + ) + except subprocess.CalledProcessError as e: + log.error( + f"Retrieving output failed: {e}\nStdout: {e.stdout}\nStderr: {e.stderr}" + ) + raise + + # NOTE: This is the output of the `job.sh` + self.stdout_f = Path(f"{self.loc}/{self.id}/job.out") + self.stderr_f = Path(f"{self.loc}/{self.id}/job.err") + + # If the job failed for some reason, save the output + if self.stderr_f.exists(): + dst = Path(self.wd / f"{self.id}_dirac.err") + shutil.copy(self.stderr_f, dst) + log.debug(f"ID stderr: {self.stderr_f.read_text()}") + + ls = glob.glob(f"{self.loc}/{self.id}/*") + log.debug(f"Files in the output sandbox: {ls}") + log.debug(f"Expected outputs: {self.expected_outputs}") + + # Copy the output to the expected location + for output_f in self.expected_outputs: + src = Path(f"{self.loc}/{self.id}/{output_f}") + dst = Path(self.wd / f"{output_f}") + shutil.copy(src, dst) + + def clean_timings(self) -> None: + """Clean the timings dictionary.""" + self.timings = {} + + def clean(self) -> None: + """Clean up the temporary directory where the job lives.""" + shutil.rmtree(self.loc) + + @staticmethod + def parse_output(output_str: str) -> dict[str, str]: + """Parse the output string from DIRAC commands into a dictionary.""" + items = output_str.replace(";", "") + status_dict = {} + for item in items.split(" "): + if "=" in item: + key, value = item.split("=", 1) + status_dict[key.strip()] = value.strip() + return status_dict + + @staticmethod + def _process_line(line: str) -> Tuple[str, Optional[str]]: + """Process a line to identify and adjust paths.""" + + match_var = re.findall(VAR_PATTERN, line) + match_at = re.findall(AT_PATTERN, line) + + # NOTE: In CNS it cannot match both patterns at the same time + if match_at: + item = match_at[0].strip('"').strip("'") + elif match_var: + item = match_var[0].strip('"').strip("'") + else: + # no match + return line, None + + if Path(item).exists(): + # This is a path + return line.replace(item, Path(item).name), item + else: + # This is not a path + return line, None + + @staticmethod + def _find_output(line) -> Optional[str]: + """Parse the line and identify if this contains an output file declaration.""" + match = re.search(OUTPUT_PATTERN, line) + if match: + return match.group(1) if match.group(1) else match.group(2) + return None + + def __repr__(self) -> str: + return f"ID: {self.id} Name: {self.name} Output: {self.expected_outputs} Status: {self.status.value} Site: {self.site}" + + +class GridJob(GridInterface): + """GridJob is a class tha represents a job to be run on the GRID via DIRAC.""" + + def __init__( + self, + input: Union[Path, str], + toppar_path: Path, + module_path: Path, + ) -> None: + super().__init__( + input=input, + toppar_path=toppar_path, + module_path=module_path, + ) # initialize the base class + + def parse_input(self, input: Union[Path, str, list[str]]) -> None: + """placeholder""" + # NOTE: `input` can be a string or a path, handle the polymorfism here + if isinstance(input, Path): + self.input_str = input.read_text() + + elif isinstance(input, str): + self.input_str = input + + elif isinstance(input, list): + raise ValueError("GridJob input cannot be a list, use CompositeGridJob") + + def create_job_script(self) -> None: + """Create the job script that will be executed in the grid.""" + # NOTE: We use `\n` instead of `os.linesep` because this will + # be executed in a Linux environment inside the grid + inp_name = f"{self.name}.inp" + cns_out_name = f"{self.name}.out" + self.expected_outputs.append(cns_out_name) + + instructions = "#!/bin/bash\n" + instructions += "export MODULE=./\n" + instructions += "export TOPPAR=./\n" + instructions += "unzip payload.zip\n" + instructions += f"./cns < {inp_name} > {cns_out_name}\n" + # Remove `cns.log` if there is no error + instructions += f"[ $? -eq 0 ] && rm {cns_out_name} || exit 1\n" + + with open(self.job_script, "w") as f: + f.write(instructions) + + def process_input_f(self) -> None: + """Process the input file to adjust paths and identify outputs.""" + + # Write the modified lines back + inp_name = Path(f"{self.loc}/{self.name}.inp") + self.payload_fnames.append(inp_name) + with open(inp_name, "w") as f: + for line in self.input_str.splitlines(keepends=True): + + # Parse this line and try to identify output files + output = self._find_output(line) + if output: + self.expected_outputs.append(output) + + # Process the line to adjust paths, if any + new_line, found_fname = self._process_line(line) + + f.write(new_line) + + # Collect the files that need to be in the payload + if found_fname: + src_path = Path(found_fname) + dst_path = self.loc / Path(found_fname).name + shutil.copy(src_path, dst_path) + self.payload_fnames.append(dst_path) + + +class CompositeGridJob(GridInterface): + + def __init__( + self, + input: list[str], + toppar_path: Path, + module_path: Path, + ) -> None: + super().__init__( + input=input, + toppar_path=toppar_path, + module_path=module_path, + ) # initialize the base class + + def create_job_script(self) -> None: + """Create the job script that will be executed in the grid.""" + # NOTE: We use `\n` instead of `os.linesep` because this will + # be executed in a Linux environment inside the grid + instructions = "#!/bin/bash\n" + instructions += "export MODULE=./\n" + instructions += "export TOPPAR=./\n" + instructions += "unzip payload.zip\n" + for idx, _ in enumerate(self.input_str_list): + inp_name = f"{idx}_{self.name}.inp" + cns_out_name = f"{idx}_{self.name}.out" + self.expected_outputs.append(cns_out_name) + instructions += f"./cns < {inp_name} > {cns_out_name}\n" + instructions += f"[ $? -eq 0 ] && rm {cns_out_name} || exit 1\n" + + with open(self.job_script, "w") as f: + f.write(instructions) + + def parse_input(self, input: Union[Path, str, list[str]]) -> None: + """Read a concatenated list of `.inp` files and split them into separate recipes.""" + if not isinstance(input, list): + raise ValueError("CompositeGridJob input must be a list of strings") + + # Join all the `.inp` contents into a single string + inp = "".join(input) + _input = "" + + lines_iter = iter(inp.split("\n")) + for line in lines_iter: + if line.startswith("stop"): + _input += "! end of the recipe\nstop\n" + self.input_str_list.append(_input.rstrip("\n")) + _input = "" # Reset for next recipe + else: + # If next line is not "stop", we still need to add it back + _input += line + "\n" + + # If there's remaining content without a termination signal, add it as the last recipe + if _input.strip(): + _input += "! end of the recipe\nstop\n" + self.input_str_list.append(_input.rstrip("\n")) + + # Keep the original behavior for backward compatibility + self.input_str = "\n".join(self.input_str_list) + + def process_input_f(self) -> None: + """Process each recipe section separately.""" + for recipe_idx, recipe_str in enumerate(self.input_str_list): + inp_name = Path(f"{self.loc}/{recipe_idx}_{self.name}.inp") + self.payload_fnames.append(inp_name) + with open(inp_name, "w") as f: + for line in recipe_str.splitlines(keepends=True): + # Parse this line and try to identify output files + output = self._find_output(line) + if output: + self.expected_outputs.append(output) + + # Process the line to adjust paths, if any + new_line, found_fname = self._process_line(line) + + # Collect the files that need to be in the payload + if found_fname: + src_path = Path(found_fname) + dst_path = self.loc / Path(found_fname).name + shutil.copy(src_path, dst_path) + self.payload_fnames.append(dst_path) + + f.write(new_line) + + +class GRIDScheduler: + """Scheduler to manage and run jobs on the GRID via DIRAC.""" + + def __init__( + self, tasks: list[CNSJob], params: dict, probing: float = 0.05 + ) -> None: + + self.probing: bool = True + self.ncores = parse_ncores(params["ncores"]) + self.batch_size = 1 + + self.workload: list[GridJob] = [ + GridJob( + input=t.input_file, + toppar_path=t.envvars["TOPPAR"], + module_path=t.envvars["MODULE"], + ) + for t in tasks + ] + + # ===============================================================# + # + # ! IMPORTANT ! + # + # The `subset_size` is the number of jobs to be used for probing the grid + # In theory we could send any number of jobs, but in practice we need to + # consider that the submission itself takes time. So we can come to the + # scenario in which we spend more time submitting jobs than measuring, + # this means that we would not be able to properly evaluate the grid + # capacity. + # Here we set the `subset_size` to be the minimum between `ncores` + # and the 5% of the total number of jobs. By setting it to the number + # of cores, we can be sure that we will be able to measure the metrics. + # We also need to ensure there is at least one job to probe the grid. + # + # HACK: This is not ideal, but it is a compromise between accuracy and speed. + subset_size = min(self.ncores, max(1, math.ceil(len(self.workload) * probing))) + # ===============================================================# + + # Randomly select that many jobs + if len(self.workload) >= subset_size: + for i in random.sample(range(len(self.workload)), subset_size): + self.workload[i].tag = Tag.PROBING + else: + log.warning("> Not enough jobs to probe the grid, skipping probing step <") + self.probing = False + + def run(self) -> None: + """Execute the tasks.""" + log.info("#" * 42) + log.info("=== Running tasks with GRID Scheduler ===") + + self.probe_grid_efficiency() + + self.create_batches() + + self.submit_jobs() + + self.wait_for_completion() + + log.info("#" * 42) + + def create_batches(self) -> None: + """Create batches of jobs to be submitted together.""" + log.info("++ Concatenating jobs to increase efficiency...") + + jobs = [j for j in self.workload if j.tag == Tag.DEFAULT] + + toppar_path = jobs[0].toppar_path + module_path = jobs[0].module_path + + composite_jobs = [] + for i, batch in enumerate(range(0, len(jobs), self.batch_size), start=1): + input = [j.input_str for j in jobs[batch : batch + self.batch_size]] + log.debug(f" Payload {i}, n={len(input)} job(s)") + job = CompositeGridJob( + input=input, + toppar_path=toppar_path, + module_path=module_path, + ) + composite_jobs.append(job) + + log.info( + f"++ Created {len(composite_jobs)} payload(s) with up to {self.batch_size} job(s) each" + ) + self.workload = composite_jobs + + def wait_for_completion(self) -> None: + """Wait for jobs with status WAITING or RUNNING to complete.""" + log.info("++ Waiting...") + complete = False + while not complete: + jobs_to_check = [ + job + for job in self.workload + if job.status + not in {JobStatus.STAGED, JobStatus.DONE, JobStatus.FAILED} + ] + if jobs_to_check: + log.debug(f"+ Checking status of {len(jobs_to_check)} payload(s)...") + with ThreadPoolExecutor(max_workers=self.ncores) as executor: + executor.map(self.process_job, jobs_to_check) + else: + complete = True + + def submit_jobs(self, tag: Tag = Tag.DEFAULT) -> None: + """Submit jobs to the GRID in parallel.""" + queue = [ + job + for job in self.workload + if job.tag == tag and job.status == JobStatus.STAGED + ] + + log.info(f"++ Submitting {len(queue)} '{tag.value}' payloads to the grid...") + with ThreadPoolExecutor(max_workers=self.ncores) as executor: + executor.map(lambda job: job.package(), queue) + + with ThreadPoolExecutor(max_workers=self.ncores) as executor: + executor.map(lambda job: job.submit(), queue) + + def probe_grid_efficiency(self) -> None: + """Submit a small number of jobs to probe the efficiency of the GRID.""" + if not self.probing: + return + + log.info("++ Probing grid efficiency...") + + # Submit + self.submit_jobs(tag=Tag.PROBING) + + # Wait + self.wait_for_completion() + + # Calculate actual durations from timestamps + waiting_durations = [] + running_durations = [] + + for job in self.workload: + wait_start = job.timings.get(JobStatus.WAITING) + run_start = job.timings.get(JobStatus.RUNNING) + done_time = job.timings.get(JobStatus.DONE) + + if wait_start is None or run_start is None or done_time is None: + continue # Skip jobs without complete timing info + + else: + log.debug(f"Job {job.expected_outputs}") + log.debug(f" timings: {job.timings}") + + # Calculate waiting duration (WAITING to RUNNING) + waiting_duration = (run_start - wait_start).total_seconds() + waiting_durations.append(waiting_duration) + + # Calculate running duration (RUNNING to DONE) + running_duration = (done_time - run_start).total_seconds() + running_durations.append(running_duration) + + if not running_durations or not waiting_durations: + log.warning( + "> Average running time is zero, cannot calculate optimal batch size <" + ) + return + + # Calculate average durations + avg_waiting = sum(waiting_durations) / len(waiting_durations) + avg_running = sum(running_durations) / len(running_durations) + + target_efficiency = 0.9 + batch_size = self.calculate_optimal_batch_size( + N=self.batch_size, + W=avg_waiting, + R=avg_running, + T=target_efficiency, + ) + + # Make sure batch size is not larger than the number of default jobs + # TODO: Add a warning if this happens? + batch_size = min( + batch_size, len([j for j in self.workload if j.tag == Tag.DEFAULT]) + ) + + self.batch_size = batch_size + + @staticmethod + def calculate_optimal_batch_size(N: int, W: float, R: float, T: float) -> int: + """Calculate the optimal batch size to achieve target efficiency.""" + # The efficiency of a given batch can be described as: + # + # E = N * R / W + N * R + # + # Where E is efficiency, N is the number of jobs running at the same time + # R is the average running time, W is the average waiting time + # + # The current efficiency is then: + E = (N * R) / (W + N * R) + + log.info(f"+ Current efficiency with {N} job(s) per payload: {E:.1%}") + + # So to achieve a target efficiency T + # We solve for N, which is the batch size: + # E = N * R / W + N * R + # T * (W + N * R) = N * R + # T * W + T * N * R = N * R + # T * W = N * R - T * N * R + # T * W = N * R * (1 - T) + # N = T * W / R * (1 - T) + batch_size = (T * W) / (R * (1 - T)) + + batch_size = max(1, round(batch_size)) # Ensure at least 1 job + return batch_size + + @staticmethod + def process_job(job: GridJob) -> None: + """Process a single job: update status, retrieve output if done, handle retries if failed. + + NOTE: This function is parallelized, that is why things like cleaning, download, retry + are here. If you are adding new functionality, consider if it should be here or in the + sequential part of the code. + """ + + job.update_status() + + if job.status == JobStatus.FAILED: + # Jobs on the grid can fail for many reasons outside our control + # So if the job is failed, resubmit it up to MAX_RETRIES times + if job.retries < MAX_RETRIES: + expected_output_str = ",".join(job.expected_outputs) + job.retries += 1 + log.warning( + f"> Job {job.name} ({expected_output_str}) failed on {job.site}, re-submitting - {job.retries}/{MAX_RETRIES} <" + ) + log.debug(f"job {job.name} at {job.loc}") + job.submit() + + # TODO: Add some sort of fallback mechanism here if it reaches the MAX_RETRIES + + if job.status == JobStatus.DONE: + log.debug(f"Job {job.name} is done, retrieving output...") + job.retrieve_output() + log.debug(f"job {job.name} at {job.loc}") + job.clean() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libhpc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libhpc.py new file mode 100644 index 0000000000000000000000000000000000000000..651eb870d2ecda8e3563c4afde39a8ff86ab86d8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libhpc.py @@ -0,0 +1,392 @@ +"""Module in charge of running tasks in HPC.""" + +import os +import re +import shlex +import subprocess +import time +from pathlib import Path + +from haddock import log, modules_defaults_path +from haddock.core.typing import Any, Container, FilePath, Optional +from haddock.gear.yaml2cfg import read_from_yaml_config +from haddock.libs.libsubprocess import CNSJob + + +STATE_REGEX = r"JobState=(\w*)" + +JOB_STATUS_DIC = { + "PENDING": "submitted", + "RUNNING": "running", + "SUSPENDED": "hold", + "COMPLETING": "running", + "COMPLETED": "finished", + "FAILED": "failed", + "TIMEOUT": "timed-out", +} + +TERMINATED_STATUS = ( + "finished", + "failed", + "timed-out", +) + +# if you change these defaults, change also the values in the +# modules/defaults.cfg file +_tmpcfg = read_from_yaml_config(modules_defaults_path) +HPCScheduler_CONCAT_DEFAULT: int = _tmpcfg["concat"] # original value 1 +HPCWorker_QUEUE_LIMIT_DEFAULT: int = _tmpcfg[ + "queue_limit" +] # original value 100 # noqa: E501 +HPCWorker_QUEUE_DEFAULT: str = _tmpcfg["queue"] # original value "" +del _tmpcfg + + +class HPCWorker: + """Defines the HPC Job.""" + + def __init__( + self, + tasks: list[CNSJob], + num: int, + job_id: Optional[int] = None, + workfload_manager: str = "slurm", + queue: Optional[str] = None, + ) -> None: + """ + Define the HPC job. + + Parameters + ---------- + tasks : list of libs.libcns.CNSJob objects + + num : int + The number of the worker. + """ + self.tasks = tasks + log.debug(f"HPCWorker ready with {len(self.tasks)}") + self.job_num = num + self.job_id = job_id + self.job_status = "unknown" + + self.moddir = Path(tasks[0].envvars["MODDIR"]) + self.toppar = tasks[0].envvars["TOPPAR"] + self.cns_folder = tasks[0].envvars["MODULE"] + module_name = Path(tasks[0].envvars["MODDIR"]).resolve().stem.split("_")[-1] + self.job_fname = Path(self.moddir, f"{module_name}_{num}.job") + self.workload_manager = workfload_manager + self.queue = queue + + def prepare_job_file(self, queue_type: str = "slurm") -> None: + """Prepare the job file for all the jobs in the task list.""" + job_file_contents = create_job_header_funcs[queue_type]( + job_name="haddock3", + queue=self.queue, + ncores=1, + work_dir=self.moddir, + stdout_path=self.job_fname.with_suffix(".out"), + stderr_path=self.job_fname.with_suffix(".err"), + ) + + job_file_contents += create_CNS_export_envvars( + MODDIR=self.moddir, + MODULE=self.cns_folder, + TOPPAR=self.toppar, + ) + + job_file_contents += f"cd {self.moddir}{os.linesep}" + for job in self.tasks: + cmd = ( + f"{job.cns_exec} < {job.input_file} > {job.output_file}" f"{os.linesep}" + ) + job_file_contents += cmd + + self.job_fname.write_text(job_file_contents) + + def run(self) -> None: + """Execute the tasks.""" + self.prepare_job_file(queue_type=self.workload_manager) + cmd = f"sbatch {self.job_fname}" + p = subprocess.run(shlex.split(cmd), capture_output=True) + self.job_id = int(p.stdout.decode("utf-8").split()[-1]) + self.job_status = "submitted" + + def update_status(self) -> str: + """Retrieve the status of this worker.""" + cmd = f"scontrol show jobid -dd {self.job_id}" + p = subprocess.run(shlex.split(cmd), capture_output=True) + out = p.stdout.decode("utf-8") + # err = p.stderr.decode('utf-8') + if out: + status = extract_slurm_status(out) + self.job_status = JOB_STATUS_DIC[status] + else: + self.job_status = "finished" + + return self.job_status + + def cancel(self, bypass_statuses: Container[str] = ("finished", "failed")) -> None: + """Cancel the execution.""" + if self.update_status() not in bypass_statuses: + log.info(f"Canceling {self.job_fname.name} - {self.job_id}") + cmd = f"scancel {self.job_id}" + _ = subprocess.run(shlex.split(cmd), capture_output=True) + + +class HPCScheduler: + """Schedules tasks to run in HPC.""" + + def __init__( + self, + task_list: list[CNSJob], + target_queue: str = HPCWorker_QUEUE_DEFAULT, + queue_limit: int = HPCWorker_QUEUE_LIMIT_DEFAULT, + concat: int = HPCScheduler_CONCAT_DEFAULT, + ) -> None: + self.num_tasks = len(task_list) + self.queue_limit = queue_limit + self.concat = concat + + # split tasks according to concat level + if concat > 1: + log.info( + f"Concatenating, each .job will produce {concat} " "(or less) models" + ) + job_list = [task_list[i : i + concat] for i in range(0, len(task_list), concat)] + + self.worker_list = [HPCWorker(t, j) for j, t in enumerate(job_list, start=1)] + + # set the queue + # (this is outside the comprehension for clarity) + if target_queue: + for worker in self.worker_list: + worker.queue = target_queue + + log.debug(f"{self.num_tasks} HPC tasks ready.") + + def run(self) -> None: + """Run tasks in the Queue.""" + # split by maximum number of submission so we do it in batches + batch = [ + self.worker_list[i : i + self.queue_limit] + for i in range(0, len(self.worker_list), self.queue_limit) + ] + total_batches = len(batch) + try: + for batch_num, worker_list in enumerate(batch, start=1): + log.info(f"> Running batch {batch_num}/{total_batches}") + start = time.time() + for worker in worker_list: + worker.run() + + # check if those finished + completed: bool = False + elapsed: float = 0.0 + while not completed: + # Initiate count of terminated jobs + terminated_count: int = 0 + # Loop over workers + for worker in worker_list: + worker.update_status() + # Log status if not finished + if worker.job_status != "finished": + log.info( + f">> {worker.job_fname.name}" f" {worker.job_status}" + ) + # Increment number of terminated works + if worker.job_status in TERMINATED_STATUS: + terminated_count += 1 + + # Check if all terminated + if terminated_count == len(worker_list): + # Set while loop condition + completed = True + end = time.time() + elapsed = end - start + else: + # use pre-defined waits + if len(worker_list) < 10: + sleep_timer = 10 + elif len(worker_list) < 50: + sleep_timer = 30 + else: + sleep_timer = 60 + log.info(f">> Waiting... ({sleep_timer:.2f}s)") + time.sleep(sleep_timer) + + per = (float(batch_num) / float(total_batches)) * 100 + log.info( + f">> Batch {batch_num}/{total_batches} took " + f"{elapsed:.2f}s to finish, {per:.2f}% complete" + ) + + except KeyboardInterrupt as err: + self.terminate() + raise err + + def terminate(self) -> None: + """Terminate all jobs in the queue in a controlled way.""" + log.info("Terminate signal received, removing jobs from the queue...") + for worker in self.worker_list: + worker.cancel() + + log.info("The jobs in the queue were terminated in a controlled way") + + +def create_slurm_header( + job_name: FilePath = "haddock3_slurm_job", + work_dir: FilePath = ".", + stdout_path: FilePath = "haddock3_job.out", + stderr_path: FilePath = "haddock3_job.err", + queue: Optional[str] = None, + ncores: int = 48, +) -> str: + """ + Create HADDOCK3 Slurm Batch job file. + + Parameters + ---------- + job_name : str + The name of the job. + + work_dir : pathlib.Path + The working dir of the example. That is, the directory where + `input`, `jobs`, and `logs` reside. Injected in `create_job_header`. + + time : int + Time in minutes before job reach TIMEOUT status. + + **job_params + According to `job_setup`. + + Return + ------ + str + Slurm-based job file for HADDOCK3. + """ + header = f"#!/usr/bin/env bash{os.linesep}" + header += f"#SBATCH -J {job_name}{os.linesep}" + if queue: + header += f"#SBATCH -p {queue}{os.linesep}" + header += f"#SBATCH --nodes=1{os.linesep}" + header += f"#SBATCH --tasks-per-node={str(ncores)}{os.linesep}" + header += f"#SBATCH --output={stdout_path}{os.linesep}" + header += f"#SBATCH --error={stderr_path}{os.linesep}" + # commenting the workdir option (not supported by all versions of slurm) + # header += f"#SBATCH --workdir={work_dir}{os.linesep}" + return header + + +def create_torque_header( + job_name: FilePath = "haddock3_slurm_job", + work_dir: FilePath = ".", + stdout_path: FilePath = "haddock3_job.out", + stderr_path: FilePath = "haddock3_job.err", + queue: Optional[str] = None, + ncores: int = 48, +) -> str: + """ + Create HADDOCK3 Alcazar job file. + + Parameters + ---------- + job_name : str + The name of the job. + + work_dir : pathlib.Path + The working dir of the example. That is, the directory where + `input`, `jobs`, and `logs` reside. Injected in `create_job_header`. + + **job_params + According to `job_setup`. + + Return + ------ + str + Torque-based job file for HADDOCK3 benchmarking. + """ + header = f"#!/usr/bin/env tcsh{os.linesep}" + header += f"#PBS -N {job_name}{os.linesep}" + if queue: + header += f"#PBS -q {queue}{os.linesep}" + header += f"#PBS -l nodes=1:ppn={str(ncores)}{os.linesep}" + header += f"#PBS -S /bin/tcsh{os.linesep}" + header += f"#PBS -o {stdout_path}{os.linesep}" + header += f"#PBS -e {stderr_path}{os.linesep}" + header += f"#PBS -wd {work_dir}{os.linesep}" + return header + + +def to_torque_time(time: int) -> str: + """Convert time in minutes to the form hh:mm:ss. + + Parameters + ---------- + time : int + Time in minutes. + + Return + ------ + hh_mm_ss : str + Time in the form for HH:MM:SS + """ + hours = time // 60 + remain_mins = time - (hours * 60) + # Convert to hh:mm:ss string + hh_mm_ss_l = [hours, remain_mins, 0] + # Make sure hours contain at least 2 characters + hh_mm_ss = "{0:02d}:{1:02d}:{2:02d}".format(*hh_mm_ss_l) + return hh_mm_ss + + +def extract_slurm_status(slurm_out: str) -> str: + """Extract job status from slurm scontrol stdout. + + Parameters + ---------- + slurm_out : str + StdOut of `scontrol show jobid -dd {job_id}` command. + Return + ------ + status : str + Status of the slurm job. + May also return `error`, when job do not exists. + """ + try: + # https://regex101.com/r/M2vbAc/1 + status = re.findall(STATE_REGEX, slurm_out)[0] + except IndexError: + status = "FAILED" + return status + + +def create_CNS_export_envvars(**envvars: Any) -> str: + """Create a string exporting envvars needed for CNS. + + Parameters + ---------- + envvars : dict + A dictionary containing envvariables where keys are var names + and values are the values. + + Returns + ------- + str + In the form of: + export VAR1=VALUE1 + export VAR2=VALUE2 + export VAR3=VALUE3 + + """ + exports = os.linesep.join( + f"export {key.upper()}={value}" for key, value in envvars.items() + ) + + return exports + os.linesep + os.linesep + + +# the different job submission queues +create_job_header_funcs = { + "torque": create_torque_header, + "slurm": create_slurm_header, +} diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libinteractive.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libinteractive.py new file mode 100644 index 0000000000000000000000000000000000000000..fbba30f14c8e1b2ee05e542770786d10114897fe --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libinteractive.py @@ -0,0 +1,202 @@ +"""Set of functions related to haddock3 interactive rescoring `haddock3-re`.""" + +from haddock import log +from haddock.clis.cli_traceback import get_steps_without_pdbs +from haddock.core.typing import Union +import pandas as pd +import numpy as np +from pathlib import Path +from haddock.libs.libplots import read_capri_table +from haddock.modules import get_module_steps_folders + + +def handle_ss_file( + df_ss: pd.DataFrame, + ) -> tuple[pd.DataFrame, dict]: + """ + Manage a caprieval capri_ss file focusing on 4 first elements + per cluster. + + Parameters + ---------- + df_ss : pd.DataFrame + The caprieval ss data. + + Returns + ------- + df_ss : pd.DataFrame + The input dataframe + clt_ranks_dict : dict + Dictionary with the cluster ranks + """ + # now we want to calculate mean and std dev of the scores on df_ss + # first sort the dataframe by score + df_ss.sort_values(by=["score", "caprieval_rank"], inplace=True) + # groupby cluster_id + df_ss_grouped = df_ss.groupby("cluster_id") + # calculate the mean and standard deviation of the first 4 elements + # of each group + new_values = [] + # loop over df_ss_grouped with enumerate + for clt_id in df_ss_grouped: + ave_score = np.mean(clt_id[1]["score"].iloc[:4]) + std_score = np.std(clt_id[1]["score"].iloc[:4]) + new_values.append([ave_score, std_score, clt_id[0]]) + # get the index that sorts the array by the first column + new_values_arr = np.array(new_values) + clt_ranks = np.argsort(new_values_arr[:, 0]) + # the ranked clusters are the third column of the new_values array + clt_sorted = new_values_arr[clt_ranks, 2] + clt_ranks_dict = {clt_sorted[i]: i + 1 for i in range(len(clt_sorted))} + # adjust clustering values if there are clusters + if list(np.unique(df_ss["cluster_id"])) != ["-"]: + df_ss['model-cluster_ranking'] = df_ss.groupby('cluster_id')['score'].rank(ascending=True).astype(int) # noqa : E501 + # assign to the values of cluster_ranking the corresponding clt_ranks + df_ss["cluster_ranking"] = df_ss["cluster_id"].apply(lambda x: clt_ranks_dict[x]) # noqa : E501 + # assign to the column caprieval_rank the index of the dataframe + df_ss.index = range(1, len(df_ss) + 1) + df_ss["caprieval_rank"] = df_ss.index + return df_ss, clt_ranks_dict + + +def rewrite_capri_tables( + caprieval_folder: str, + clt_dic: dict, + outdir: str, + ) -> None: + """Rewrite the capri tables with new values. + + Parameters + ---------- + caprieval_folder : str + Path to the capriveal folder to be changed + clt_dic : dict + Data for each cluster + outdir : str + Output directory + """ + capri_ss = Path(caprieval_folder, "capri_ss.tsv") + capri_clt = Path(caprieval_folder, "capri_clt.tsv") + if not capri_ss.exists() or not capri_clt.exists(): + # raise warning and exit + log.warning("Capri evaluation files not found. Skipping...") + return + # ss file + df_ss = read_capri_table(capri_ss) + for cl in clt_dic: + models = [ + f"../{model.path.split('/')[-1]}/{model.file_name}" + for model in clt_dic[cl] + ] + # all the models should now have the cluster_id field + df_ss.loc[df_ss['model'].isin(models), 'cluster_id'] = cl + + # delete all the models that are not in the clusters + df_ss = df_ss[df_ss['cluster_id'] != "-"] + # assign cluster_ranking to cluster_id (aka random assignment) + df_ss['cluster_ranking'] = df_ss['cluster_id'] + # handle ss file + df_ss, clt_ranks_dict = handle_ss_file(df_ss) + + # save capri_ss file + capri_ss_file = Path(outdir, "capri_ss.tsv") + log.info(f"Saving capri_ss file to {capri_ss_file}") + df_ss.to_csv(capri_ss_file, sep="\t", index=False) + + # retrieve df_clt object + df_clt = handle_clt_file(df_ss, clt_ranks_dict) + # save capri_clt file + capri_clt_file = Path(outdir, "capri_clt.tsv") + log.info(f"Saving capri_clt file to {capri_clt_file}") + df_clt.to_csv(capri_clt_file, sep="\t", index=False, float_format='%.3f') + return + + +def look_for_capri(run_dir: str, module_id: int) -> Union[Path, None]: + """Look for capri evaluation files previous to clustfcc_dir. + + Parameters + ---------- + run_dir : str + Path to the haddock3 run directory + module_id : int + Id of the module. + + Returns + ------- + capri_eval : Path + Path to the capri evaluation file + """ + prev_modules_id = range(1, module_id) + prev_modules = get_module_steps_folders(run_dir, prev_modules_id) + # remove possible interactive modules + prev_modules = [ + mod for mod in prev_modules + if not mod.endswith("interactive") + ] + # analysis modules + ana_modules = get_steps_without_pdbs(run_dir, prev_modules) + # loop over the reversed list of previous modules + capri_folder = None + for prev_module in reversed(prev_modules): + log.info(f"prev_module {prev_module}") + if prev_module.endswith("caprieval"): + # caprieval module found before any module that generates models + capri_folder = Path(run_dir, prev_module) + break + elif prev_module not in ana_modules: + break + else: + continue + log.info(f"capri_folder {capri_folder}") + return capri_folder + + +def handle_clt_file(df_ss, clt_ranks_dict): + """Handle capri.clt file. + + Parameters + ---------- + df_ss : pd.DataFrame + The caprieval ss data. + clt_ranks_dict : dict + New cluster ranking dictionary. + + Reclustering modifies the cluster data, so capri_clt.tsv must be updated. + """ + capri_keys = ["score", "irmsd", "fnat", "lrmsd", "dockq"] + model_keys = ["air", "bsa", "desolv", "elec", "total", "vdw"] + df_ss_grouped = df_ss.groupby("cluster_id") + # loop over df_ss_grouped + cl_data = [] + for clt_id in df_ss_grouped: + cl_rank = clt_ranks_dict[clt_id[0]] # the rank of the cluster is the key + data = [cl_rank, clt_id[0], clt_id[1].shape[0], "-", ] + # updating capri quantities + for column in capri_keys: + ave_score = np.mean(clt_id[1][column].iloc[:4]) + std_score = np.std(clt_id[1][column].iloc[:4]) + data.extend([ave_score, std_score]) + # updating model quantities + for column in model_keys: + ave_score = np.mean(clt_id[1][column].iloc[:4]) + std_score = np.std(clt_id[1][column].iloc[:4]) + data.extend([ave_score, std_score]) + cl_data.append(data) + + # create the dataframe + capri_clt_columns = ["cluster_rank", "cluster_id", "n", "under_eval"] + for column in capri_keys: + capri_clt_columns.append(f"{column}") + capri_clt_columns.append(f"{column}_std") + for column in model_keys: + capri_clt_columns.append(f"{column}") + capri_clt_columns.append(f"{column}_std") + # capri_clt_columns.append("caprieval_rank") + df_clt = pd.DataFrame(cl_data, columns=capri_clt_columns) + df_clt.sort_values(by="score", inplace=True) + df_clt.index = range(1, len(df_clt) + 1) + df_clt["caprieval_rank"] = df_clt.index + # + df_clt.sort_values(by="caprieval_rank", inplace=True) + return df_clt diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libio.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libio.py new file mode 100644 index 0000000000000000000000000000000000000000..8f0b17c7788596943feb9722f2f48778db897e31 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libio.py @@ -0,0 +1,638 @@ +"""Lib I/O.""" +import contextlib +import glob +import gzip +import os +import stat +import tarfile +import re +from functools import partial +from multiprocessing import Pool +from pathlib import Path + +import yaml + +from haddock import log +from haddock.core.typing import ( + Any, + Callable, + FilePath, + Generator, + Iterable, + Mapping, + Optional, + Union, + ) +from haddock.libs.libontology import PDBFile +from haddock.libs.libutil import sort_numbered_paths + + +def clean_suffix(ext: str) -> str: + """ + Remove the preffix dot of an extension if exists. + + Parameters + ---------- + ext : str + The extension string. + + Examples + -------- + >>> clean_suffix('.pdb') + 'pdb' + + >>> clean_suffix('pdb') + 'pdb' + """ + return ext.lstrip(r".") + + +def dot_suffix(ext: str) -> str: + """ + Add the dot preffix to an extension if missing. + + Parameters + ---------- + ext : str + The extension string. + + Examples + -------- + >>> clean_suffix('.pdb') + '.pdb' + + >>> clean_suffix('pdb') + '.pdb' + """ + return "." + clean_suffix(ext) + + +def read_lines(func: Callable[..., Any]) -> Callable[..., Any]: + """ + Open the file and read lines for the decorated function. + + Send to the decorated function the lines of the file in the form + of list. + """ + + def wrapper(fpath: FilePath, *args: Any, **kwargs: Any) -> Any: + lines = Path(fpath).read_text().split(os.linesep) + return func(lines, *args, **kwargs) + + # manual wrapping for displaying documentation properly + wrapper.original = func # type: ignore + wrapper.__doc__ = func.__doc__ + wrapper.__name__ = func.__name__ + return wrapper + + +def read_from_yaml(yaml_file: FilePath) -> dict[Any, Any]: + """ + Read a YAML file to a dictionary. + + Used internally to read HADDOCK3's default configuration files. + + Parameters + ---------- + yaml_file : str or Path + Path to the YAML file. + + Returns + ------- + dict + Always returns a dictionary. + Returns empty dictionary if yaml_file is empty. + """ + # Check that this yaml file do not contain duplicated parameters + check_yaml_duplicated_parameters(yaml_file) + + # Load yaml file using the yaml lib + with open(yaml_file, "r") as fin: + ycfg = yaml.safe_load(fin) + + # ycfg is None if yaml_file is empty + # returns an empty dictionary to comply with HADDOCK workflow + if ycfg is None: + return {} + + assert isinstance(ycfg, dict), type(ycfg) + return ycfg + + +def check_yaml_duplicated_parameters(yaml_fpath: str) -> None: + """Make sure the provided yaml file do not contain duplicated parameters. + + Parameters + ---------- + yaml_fpath : str + Path to a yaml file + """ + # Build regular expression + # Note: Understand behavior here -> https://regex101.com/r/AaFHp4/1 + yaml_param_regex = re.compile("^(([A-Za-z0-9]_?)+):") + # Read content as string + with open(yaml_fpath, 'r') as filin: + yaml_content = filin.readlines() + parsed_param_names: dict[str, int] = {} + # Loop over lines + for i, line in enumerate(yaml_content, start=1): + # Check if new parameter + if (match := yaml_param_regex.search(line)): + # Point parameter name + param_name = match.group(1) + # Make sure this parameter has not yet been used + assert param_name not in parsed_param_names.keys(), f"Parameter '{param_name}' in {yaml_fpath} has duplicates: l.{parsed_param_names[param_name]} and l.{i}" # noqa : E501 + # Hold line were this parameter is, in case of duplication, to help + parsed_param_names[param_name] = i + + +def open_files_to_lines(*files: FilePath) -> list[list[str]]: + """ + Open files to lines. + + New-lines are stripped. + + Returns + ------- + list of lists of strings + The lines of the files. + Input order is maintained. + """ + f_paths = map(Path, files) + return [f.read_text().split(os.linesep) for f in f_paths] + + +def save_lines_to_files( + files: Iterable[FilePath], + lines: Iterable[Iterable[str]] + ) -> None: + """ + Save a list of list of lines to files. + + The first list of strings in `lines` will be saved in the first file + of `files`, and so on. + + Lines are saved using `pathlib.Path.write_text` function. + + Parameters + ---------- + files : list + The list of file names to save. + + lines : list of lists of str + A list containing lists of lines that are the file contents. + Must be synched with `files`. + """ + for file_, content in zip(files, lines): + Path(file_).write_text(os.linesep.join(content) + os.linesep) + + return + + +def add_suffix_to_files( + files: Iterable[FilePath], + suffix: str + ) -> Generator[Path, None, None]: + """ + Add a suffix to file paths. + + Yields + ------ + pathlib.Path objects + Exhausts when files exhaust. + """ + for file_ in files: + p = Path(file_) + folder = p.parent + psuffix = p.suffix + name = p.stem + suffix + psuffix + path = Path(folder, name) + yield path + + +def write_dic_to_file( + data_dict: Mapping[Any, Any], + output_fname: FilePath, + info_header: str = "", + sep: str = "\t", + ) -> None: + """ + Create a table from a dictionary. + + Parameters + ---------- + data_dict : dict + Dictionary to write. + output_fname : str or Path + Name of the output file. + info_header : str + Header to write before the data. + """ + header = "\t".join(data_dict.keys()) + + if info_header: + header = info_header + os.linesep + header + + with open(output_fname, "w") as out_fh: + out_fh.write(header + os.linesep) + row_l: list[str] = [] + for element in data_dict: + value = data_dict[element] + if isinstance(value, Path): + row_l.append(str(value)) + elif isinstance(value, PDBFile): + row_l.append(str(value.rel_path)) + elif isinstance(value, int): + row_l.append(f"{value}") + elif isinstance(value, str): + row_l.append(f"{value}") + elif value is None: + row_l.append("-") + else: + row_l.append(f"{value:.3f}") + out_fh.write(sep.join(row_l) + os.linesep) + + +def write_nested_dic_to_file( + data_dict: Mapping[Any, Any], + output_fname: FilePath, + info_header: str = "", + sep: str = "\t", + ) -> None: + """ + Create a table from a nested dictionary. + + Parameters + ---------- + data_dict : dict + Dictionary to write. + output_fname : str or Path + Name of the output file. + + Notes + ----- + This function is used to write nested dictionaries. + {int: {key: value}}, the int key will be discarded. + """ + first_key = list(data_dict.keys())[0] + header = "\t".join(data_dict[first_key].keys()) + + if info_header: + header = info_header + os.linesep + header + + with open(output_fname, "w") as out_fh: + out_fh.write(header + os.linesep) + for row in data_dict: + row_l: list[str] = [] + for element in data_dict[row]: + value = data_dict[row][element] + if isinstance(value, Path): + row_l.append(str(value)) + elif isinstance(value, PDBFile): + row_l.append(str(value.rel_path)) + elif isinstance(value, int): + row_l.append(f"{value}") + elif isinstance(value, str): + row_l.append(f"{value}") + elif value is None: + row_l.append("-") + else: + row_l.append(f"{value:.3f}") + out_fh.write(sep.join(row_l) + os.linesep) + + +# thanks to @brianjimenez +@contextlib.contextmanager +def working_directory(path: FilePath) -> Generator[None, None, None]: + """Change working directory and returns to previous on exit.""" + prev_cwd = Path.cwd() + os.chdir(path) + try: + yield + finally: + os.chdir(prev_cwd) + + +def compress_files_ext( + path: FilePath, + ext: str, + ncores: int = 1, + **kwargs: Any + ) -> bool: + """ + Compress all files with same extension in folder to `.gz`. + + Do not archive the files in TAR, only compress files individually. + + Parameters + ---------- + path : str or :external:py:class:`pathlib.Path` + The folder containing the files. + + ext : str + The extension of the files. + + **kwargs : anything + Arguments passed to :py:func:`gzip_files`. + + Returns + ------- + bool + ``True`` if files with ``ext`` were found and the compressed + `.gz` files created. + + ``False`` if no files with ``ext`` were found and, hence, the + `.gz` files were not created. + """ + files = glob_folder(path, ext) + gzip_ready = partial(gzip_files, **kwargs) + if files: + with Pool(ncores) as pool: + imap = pool.imap_unordered(gzip_ready, files) + for _ in imap: + pass + return True + return False + + +def gzip_files( + file_: FilePath, + block_size: Optional[int] = None, + compresslevel: int = 9, + remove_original: bool = False, + ) -> None: + """ + Gzip a file. + + Parameters + ---------- + file_ : str or :external:py:class:`pathlib.Path` + The path to the file to compress. + + block_size : int + The block size to treat per cycle. Defaults to 200MB (2*10**8 + (2*10**8). + + compresslevel : int + The compress level. Defaults to 9. + """ + if block_size is None: + block_size = 2 * 10**8 + + gfile = str(file_) + ".gz" + with open(file_, "rb") as fin, gzip.open( + gfile, mode="wb", compresslevel=compresslevel + ) as gout: + content = fin.read(block_size) # read the first + while content: + gout.write(content) + content = fin.read(block_size) + + if remove_original: + Path(file_).unlink() + + +def archive_files_ext(path: FilePath, ext: str, compresslevel: int = 9) -> bool: + """ + Archive all files with same extension in folder. + + Parameters + ---------- + path : str or :external:py:class:`pathlib.Path` + The folder containing the files. + + ext : str + The extension of the files. + + compresslevel : int + The compression level. + + Returns + ------- + bool + ``True`` if files with ``ext`` were found and the Zip files created. + ``False`` if no files with ``ext`` were found and, hence, the + Zip files was not created. + """ + files = glob_folder(path, clean_suffix(ext)) + + ext = clean_suffix(ext) + + if files: + with tarfile.open( + Path(path, f"{ext}.tgz"), + mode="w:gz", + compresslevel=compresslevel, + ) as tarout: + for file_ in files: + tarout.add(file_, arcname=file_.name) + + return True + return False + + +def glob_folder(folder: FilePath, ext: str) -> list[Path]: + """ + List files with extention `ext` in `folder`. + + Does NOT perform recursive search. + + Parameters + ---------- + folder : str + The path to the folder to investigate. + + ext : str + The file extention. Can be with or without the dot [.] + preffix. + + Returns + ------- + list of Path objects + SORTED list of matching results. + """ + ext = f"*{dot_suffix(ext)}" + files = glob.glob(str(Path(folder, ext))) + return sort_numbered_paths(*(Path(file) for file in files)) + + +def remove_files_with_ext(folder: FilePath, ext: str) -> None: + """ + Remove files with ``ext`` in folder. + + Parameters + ---------- + folder : str + The path to the folder. + + ext : str + The extention of files to delete. Can be with or without the dot ``.`` + preffix. + """ + files = sort_numbered_paths(*glob_folder(folder, ext)) + # if there are no files, the for loop won't run. + for file_ in files: + log.debug(f"removing: {file_}") + file_.unlink() + + +def folder_exists( + path: FilePath, + exception: type[Exception] = ValueError, + emsg: str = "The folder {!r} does not exist or is not a folder.", + ) -> Path: + """ + Assert if a folder exist. + + Parameters + ---------- + path : str or pathlib.Path + The path to the folder. + + exception : Exception + The Exception to raise in case `path` is not file or does not + exist. + + emsg : str + The error message to give to `exception`. May accept formatting + to pass `path`. + + Returns + ------- + pathlib.Path + The Path representation of the input ``path`` if condition is + true. + + Raises + ------ + Exception + Any exception that pathlib.Path can raise. + """ + p = Path(path) + + valid = [p.exists, p.is_dir] + + if all(f() for f in valid): + return p + + # don't change to f-strings, .format has a purpose + raise exception(emsg.format(str(path))) + + +def file_exists( + path: FilePath, + exception: type[Exception] = ValueError, + emsg: str = "`path` is not a file or does not exist", + ) -> Path: + """ + Assert if file exist. + + Parameters + ---------- + path : str or pathlib.Path + The file path. + + exception : Exception + The Exception to raise in case `path` is not file or does not + exist. + + emsg : str + The error message to give to `exception`. May accept formatting + to pass `path`. + + Returns + ------- + pathlib.Path + The Path representation of the input ``path`` if condition is + true. + + Raises + ------ + Exception + Any exception that pathlib.Path can raise. + """ + p = Path(path) + + valid = [p.exists, p.is_file] + + if all(f() for f in valid): + return p + + # don't change to f-strings, .format has a purpose + raise exception(emsg.format(str(path))) + + +def pdb_path_exists(pdb_path: Path) -> tuple[bool, Optional[str]]: + """ + Check if a pdb path exists. + + If not, checks for the existence of a gzipped pdb file and informs the user + that the file is gzipped + + Parameters + ---------- + pdb_path : pathlib.Path + path to the pdb + + Returns + ------- + exists : bool + True if file exists + msg : str or None + the error message + """ + exists, msg = True, None + if not pdb_path.exists(): + msg = f"PDB file {pdb_path} not found." + gz_pdb_path = pdb_path.with_suffix(pdb_path.suffix + ".gz") + if gz_pdb_path.exists(): + msg += f" A compressed file ({gz_pdb_path}) exists though." + msg += "Use haddock3-unpack to unpack the run." + exists = False + return exists, msg + + +def get_perm(fname: FilePath) -> int: + """Get permissions of file.""" + # https://stackoverflow.com/questions/6874970 + return stat.S_IMODE(os.lstat(fname)[stat.ST_MODE]) + + +def make_writeable_recursive(path: FilePath) -> None: + """ + Add writing to a folder, its subfolders and files. + + Parameters + ---------- + path : str or Path + The path to add writing permissions. + """ + # https://stackoverflow.com/questions/6874970 + for root, dirs, files in os.walk(path, topdown=False): + for dir_ in (os.path.join(root, d) for d in dirs): + os.chmod(dir_, get_perm(dir_) | stat.S_IWUSR) + + for file_ in (os.path.join(root, f) for f in files): + os.chmod(file_, get_perm(file_) | stat.S_IWUSR) + + +def extract_files_flat(tar_path: Union[str, FilePath], + dest_path: Union[str, FilePath]) -> None: + """ + Extract files from a tarball to a destination folder. + + Parameters + ---------- + tar_path : str or Path + The path to the tarball file. + + dest_path : str or Path + The path to the destination folder. + """ + with tarfile.open(tar_path, "r:gz") as tar: + for member in tar.getmembers(): + # Extract only files (skip directories) + if member.isfile(): + # Modify the member name to remove the directory structure + member.name = os.path.basename(member.name) + tar.extract(member, dest_path) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libligand.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libligand.py new file mode 100644 index 0000000000000000000000000000000000000000..426fb14cfd924e6c718fdd0142b161feb594ea22 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libligand.py @@ -0,0 +1,172 @@ +"""Ligand topology utilities.""" + +import re +import subprocess +import tempfile +from pathlib import Path + +from haddock.core.supported_molecules import supported_residues +from haddock.core.defaults import prodrg_exec, prodrg_param +from haddock import log +import shutil + +from haddock.core.typing import FilePath + + +def identify_unknown_hetatms(pdb_file: FilePath) -> list[str]: + """Return residue names in a PDB that are not in the supported residues. + + Parameters + ---------- + pdb_file : FilePath + Path to the PDB file to inspect. + + Returns + ------- + list[str] + Unique residue names not found in the supported residues set, + in order of first appearance. + """ + seen: list[str] = [] + with open(pdb_file) as fh: + for line in fh: + if not line.startswith(("ATOM ", "HETATM")): + continue + resname = line[17:20].strip() + if resname and resname not in supported_residues and resname not in seen: + seen.append(resname) + return seen + + +def run_prodrg( + pdb_file: FilePath, + output_dir: FilePath, +) -> tuple[Path, Path]: + """Run prodrg on a ligand PDB and write CNS topology and parameter files. + + prodrg writes its output to fixed filenames in the current working + directory, so the process is executed inside a managed temporary directory + that is cleaned up automatically. The resulting files are written to + ``output_dir`` named after the input PDB stem. + + Parameters + ---------- + pdb_file : FilePath + Path to the ligand PDB file. + output_dir : FilePath + Directory where the named ``.top`` and ``.param`` files are written. + + Returns + ------- + tuple[Path, Path] + Paths to the written ``_prodrg.top`` and ``_prodg.param`` files. + + Raises + ------ + RuntimeError + If prodrg exits with a non-zero return code or the expected output + files are not created. + """ + if prodrg_exec is None or prodrg_param is None: + raise RuntimeError( + "prodrg is not available on this platform. " + "Provide the binary path via the PRODRG_EXEC environment variable." + ) + + pdb_file = Path(pdb_file).resolve() + output_dir = Path(output_dir).resolve() + + # PRODRG will write its output in its `pwd`, so run it in a temporary one + with tempfile.TemporaryDirectory() as tmpdir: + # NOTE: PRODRG has a max of 79 chars as input, make sure to pass relative paths + # so we need to copy everything to this temporary dir + dst = Path(tmpdir, prodrg_param.name) + shutil.copy(prodrg_param, dst) + + dst = Path(tmpdir, pdb_file.name) + shutil.copy(pdb_file, dst) + + result = subprocess.run( + # NOTE: We need this `PDBELEM` flag here + [str(prodrg_exec), str(pdb_file.name), str(prodrg_param.name), "PDBELEM"], + cwd=tmpdir, + capture_output=True, + text=True, + ) + + if result.returncode != 0: + raise RuntimeError( + f"prodrg failed with return code {result.returncode}:\n{result.stderr}" + ) + + tmp_top = Path(tmpdir) / "DRGCNS.TOP" + tmp_par = Path(tmpdir) / "DRGCNS.PAR" + + # TODO: Check if the atom names have been changed! + # tmp_pdb = Path(tmpdir) / ".pdb" + + if not tmp_top.exists() or not tmp_par.exists(): + ls = list(Path(tmpdir).iterdir()) + prodrg_err = Path(tmpdir) / "DRGDRG.ERR" + prodrg_log = Path(tmpdir) / "DRGDRG.LOG" + log.error(f"DRGDRG.log: {prodrg_log.read_text()}") + log.error(f"DRGDRG.err: {prodrg_err.read_text()}") + log.debug(f"ls: {ls}") + raise RuntimeError( + f"prodrg finished but expected output files are missing in {tmpdir} " + ) + + top_path = output_dir / f"{pdb_file.stem}_prodrg.top" + par_path = output_dir / f"{pdb_file.stem}_prodrg.param" + + top_content = _sanitize_atom_names(tmp_top.read_text()) + par_content = _sanitize_atom_names(_remove_nbonds(tmp_par.read_text())) + + top_path.write_text(top_content) + par_path.write_text(par_content) + + return top_path, par_path + + +def _sanitize_atom_names(content: str) -> str: + """Remove colons from atom type names in prodrg CNS output. + + prodrg may generate atom type names containing colons (e.g. ``HT:A``) + and this is not compatible with CNS so they must be removed. + + Parameters + ---------- + content : str + Contents of a prodrg-generated CNS file. + + Returns + ------- + str + Content with colons stripped from non-comment lines. + """ + lines = [] + for line in content.splitlines(keepends=True): + if line.lstrip().startswith("!"): + lines.append(line) + else: + lines.append(line.replace(":", "")) + return "".join(lines) + + +def _remove_nbonds(par_content: str) -> str: + """Remove the NBONds...END block from a prodrg CNS parameter string. + + PRODRG definition of NBONds might interfere with HADDOCK's internal parameters, + so we must remove the NBONds lines from the param generated by HADDOCK + + Parameters + ---------- + par_content : str + Contents of the ``DRGCNS.PAR`` file. + + Returns + ------- + str + Parameter content with the NBONds block removed. + """ + return re.sub(r"(?s)NBONds.*?END", "", par_content) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/liblog.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/liblog.py new file mode 100644 index 0000000000000000000000000000000000000000..0fe401ff85883e1d83ee9c0a22db7d3cc1d50319 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/liblog.py @@ -0,0 +1,83 @@ +"""Manage logging and logging helper functions.""" +import io +import logging +import sys +from argparse import ArgumentParser +from functools import partial +from logging import FileHandler, Logger, StreamHandler +from typing import TextIO, Union + +from haddock.core.typing import FilePath, StreamHandlerT + + +log_file_name = 'log' + + +info_formatter = '[%(asctime)s %(module)s %(levelname)s] %(message)s' +debug_formatter = ( + "[%(asctime)s] " + "%(filename)s:%(name)s:%(funcName)s:%(lineno)d: " + "%(message)s" + ) + +log_formatters = { + 'DEBUG': debug_formatter, + 'INFO': info_formatter, + 'WARNING': info_formatter, + 'ERROR': info_formatter, + 'CRITICAL': info_formatter, + } + +log_levels = { + 'DEBUG': logging.DEBUG, + 'INFO': logging.INFO, + 'WARNING': logging.WARNING, + 'ERROR': logging.ERROR, + 'CRITICAL': logging.CRITICAL, + } + + +def add_loglevel_arg(parser: ArgumentParser) -> None: + """Add log level argument to CLI.""" + parser.add_argument( + "--log-level", + default='INFO', + choices=list(log_levels.keys()), + ) + return + + +def add_handler( + log_obj: Logger, + handler: type[StreamHandlerT], + stream: Union[FilePath, TextIO], + log_level: str = 'INFO', + formatter: str = info_formatter, + ) -> StreamHandlerT: + """Add a logging Handler to the log object.""" + ch = handler(stream) + ch.setLevel(log_levels[log_level.upper()]) + ch.setFormatter(logging.Formatter(formatter)) + log_obj.addHandler(ch) + return ch + + +def add_log_for_CLI(log: Logger, log_level: str, logfile: FilePath) -> None: + """Configure log for command-line clients.""" + llu = log_level.upper() + + params = { + 'log_level': llu, + 'formatter': log_formatters[llu], + } + + log.handlers.clear() + add_sysout_handler(log, **params) + add_logfile_handler(log, stream=logfile, **params) + return + + +add_sysout_handler = partial(add_handler, handler=StreamHandler, stream=sys.stdout) # noqa: E501 +add_syserr_handler = partial(add_handler, handler=StreamHandler, stream=sys.stderr, log_level='ERROR') # noqa: E501 +add_logfile_handler = partial(add_handler, handler=FileHandler, stream=log_file_name) # noqa: E501 +add_stringio_handler = partial(add_handler, handler=StreamHandler, stream=io.StringIO()) # noqa: E501 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmath.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmath.py new file mode 100644 index 0000000000000000000000000000000000000000..26a1d92118c3a1d8bc2ff28ccd5f850fb13a9f71 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmath.py @@ -0,0 +1,27 @@ +"""Mathematical functions.""" +import random + + +class RandomNumberGenerator: + """ + Generate random numbers. + + Python uses the Mersenne Twister as the core generator. + It produces 53-bit precision floats and has a period of 2**19937-1 + """ + + def __init__(self, seed: int = 494) -> None: + """494 = sum([ord(i) for i in 'HADDOCK']).""" + self.seed = seed + self.random = random.Random() + self.random.seed(self.seed) + + def __call__(self, + lower_limit: float = 0., + upper_limit: float = 1.) -> float: + """Generate a random number between range.""" + return self.random.uniform(lower_limit, upper_limit) + + def randint(self, lower_limit: int = 0, upper_limit: int = 9) -> int: + """Generate a random integer.""" + return int(self() * (upper_limit + 1)) + lower_limit diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmpi.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmpi.py new file mode 100644 index 0000000000000000000000000000000000000000..6de88d4ba4409a0f1285819db29608ed43e2b669 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libmpi.py @@ -0,0 +1,58 @@ +"""Module in charge of MPI execution of tasks.""" +import pickle +import shlex +import subprocess +import sys +from pathlib import Path +from typing import Any, Optional +from shutil import which + +from haddock import log +from haddock.core.exceptions import HaddockTermination + + +class MPIScheduler: + """Schedules tasks to be executed via MPI.""" + + def __init__(self, tasks: list[Any], ncores: Optional[int] = None) -> None: + self.tasks = tasks + self.cwd = Path.cwd() + self.ncores = ncores + + def run(self) -> None: + """Send it to the haddock3-mpitask runner.""" + pkl_tasks = self._pickle_tasks() + log.info( + f"Executing tasks with the haddock3-mpitask runner using " + f"{self.ncores} processors..." + ) + if which("mpirun") is not None: + cmd = f"mpirun -np {self.ncores} haddock3-mpitask {pkl_tasks}" + elif which("srun") is not None: + cmd = f"srun haddock3-mpitask {pkl_tasks}" + else: + log.error("mpirun or srun are not available on the system") + log.error("Terminating run!") + raise HaddockTermination + + log.debug(f"MPI cmd is {cmd}") + + p = subprocess.run( + shlex.split(cmd), stdout=subprocess.PIPE, stderr=subprocess.PIPE + ) + + # out = p.stdout.decode("utf-8") + err = p.stderr.decode("utf-8") + + if err: + log.error(err) + log.error("Terminating run!") + raise HaddockTermination + + def _pickle_tasks(self) -> Path: + """Pickle the tasks.""" + fpath = Path(self.cwd, "mpi.pkl") + log.debug(f"Pickling the tasks at {fpath}") + with open(fpath, "wb") as output_handler: + pickle.dump(self.tasks, output_handler) + return fpath diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libnotebooks.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libnotebooks.py new file mode 100644 index 0000000000000000000000000000000000000000..e61dc39151d618a58f4cdea82dc48710aaf9d64d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libnotebooks.py @@ -0,0 +1,293 @@ +""" +Helper functions for HADDOCK3 notebooks +""" + +import gzip +import os +from io import StringIO + +from Bio.PDB import PDBIO, PDBParser, Superimposer + +# NOTE: `py3Dmol` is an optional dependency, it might not be installed +# this is why we have the conditional import here +try: + import py3Dmol +except ImportError: + py3Dmol = None + + +def load_pdb_file(file_path): + """.""" + if not os.path.exists(file_path): + print(f"Error: File not found at {file_path}") + return None + + if file_path.endswith(".gz"): + with gzip.open(file_path, "rt") as f: + return f.read() + else: + with open(file_path, "r") as f: + return f.read() + + +def pdb_string_to_structure(pdb_string, structure_id): + """.""" + parser = PDBParser(QUIET=True) + pdb_io = StringIO(pdb_string) + structure = parser.get_structure(structure_id, pdb_io) + return structure + + +def structure_to_pdb_string(structure): + """.""" + pdb_io = PDBIO() + pdb_io.set_structure(structure) + output = StringIO() + pdb_io.save(output) + return output.getvalue() + + +# Full alignement - user-given chains used +# FIXME: This function has too many arguments, needs to be refactored +def align_full( + pdb_path1, + pdb_path2, + chains=["A", "B"], + width=800, + height=600, + model1_colors={"A": "red", "B": "orange", "C": "pink"}, + model2_colors={"A": "blue", "B": "green", "C": "lime"}, + atom_types=["P", "C1", "CA"], + show_labels=False, + show_per_chain_rmsd=True, +): + """.""" + """ + Align two protein structures using all specified chains and visualize with py3Dmol. + + Parameters: + ----------- + pdb_path1 : str + Path to the first (reference) PDB file + pdb_path2 : str + Path to the second PDB file to align to the first + chains : list, default ['A', 'B'] + List of chain IDs to include in alignment + width : int, default 800 + Viewer width in pixels + height : int, default 600 + Viewer height in pixels + model1_colors : dict, default {'A': 'red', 'B': 'orange'} + Colors for chains in model 1 + model2_colors : dict, default {'A': 'blue', 'B': 'green'} + Colors for chains in model 2 + atom_types : list, default ['CA', 'P', 'C1'] + Atom types to use for alignment (['CA'] or ['CA', 'CB', 'N', 'C']) + show_labels : bool, default False + Whether to show descriptive labels + show_per_chain_rmsd : bool, default True + Whether to calculate and display per-chain RMSD values + + Returns: + -------- + py3Dmol.view object + + Example: + -------- + align_full_molecule('model1.pdb.gz', 'model2.pdb.gz') + """ + + def get_atoms_from_chains(structure, chain_ids, atom_types): + atoms = [] + chain_info = {} + + for model in structure: + for chain_id in chain_ids: + if chain_id in model: + chain = model[chain_id] + chain_atoms = [] + for residue in chain: + for atom_type in atom_types: + if atom_type in residue: + atoms.append(residue[atom_type]) + chain_atoms.append(residue[atom_type]) + chain_info[chain_id] = len(chain_atoms) + + return atoms, chain_info + + # Create viewer + view = py3Dmol.view(width=width, height=height) + + # Load PDB files + model_1_data = load_pdb_file(pdb_path1) + model_2_data = load_pdb_file(pdb_path2) + + if not (model_1_data and model_2_data): + print("Failed to load one or both PDB files") + return view, None, {} + + overall_rmsd = None + per_chain_rmsd = {} + + try: + # Parse structures + struct1 = pdb_string_to_structure(model_1_data, "model1") + struct2 = pdb_string_to_structure(model_2_data, "model2") + + # Get atoms from all specified chains + atoms_1, chain_info_1 = get_atoms_from_chains(struct1, chains, atom_types) + atoms_2, chain_info_2 = get_atoms_from_chains(struct2, chains, atom_types) + + print(f"Atoms for alignment - Model 1: {chain_info_1}, Total: {len(atoms_1)}") + print(f"Atoms for alignment - Model 2: {chain_info_2}, Total: {len(atoms_2)}") + print( + "Model 1: " + + "; ".join( + [ + f"chain {chain} in {color}" + for chain, color in model1_colors.items() + if chain in chains + ] + ) + ) + print( + "Model 2: " + + "; ".join( + [ + f"chain {chain} in {color}" + for chain, color in model2_colors.items() + if chain in chains + ] + ) + ) + + if len(atoms_1) > 0 and len(atoms_2) > 0: + # Align using all atoms from specified chains + min_atoms = min(len(atoms_1), len(atoms_2)) + ref_atoms = atoms_1[:min_atoms] + alt_atoms = atoms_2[:min_atoms] + + print(f"Using {min_atoms} atom pairs for alignment") + + # Perform superimposition + sup = Superimposer() + sup.set_atoms(ref_atoms, alt_atoms) + overall_rmsd = sup.rms + + print(f"Whole molecule alignment RMSD: {overall_rmsd:.3f} Å") + + # Apply transformation to all atoms in structure 2 + sup.apply(struct2.get_atoms()) + + # Calculate per-chain RMSD if requested + if show_per_chain_rmsd: + for chain_id in chains: + try: + chain_atoms_1, _ = get_atoms_from_chains( + struct1, [chain_id], atom_types + ) + chain_atoms_2, _ = get_atoms_from_chains( + struct2, [chain_id], atom_types + ) + if len(chain_atoms_1) > 0 and len(chain_atoms_2) > 0: + min_chain = min(len(chain_atoms_1), len(chain_atoms_2)) + sup_chain = Superimposer() + sup_chain.set_atoms( + chain_atoms_1[:min_chain], chain_atoms_2[:min_chain] + ) + per_chain_rmsd[chain_id] = sup_chain.rms + print(f"Chain {chain_id} RMSD: {sup_chain.rms:.3f} Å") + except Exception as e: + print(f"Could not calculate RMSD for chain {chain_id}: {e}") + + # Convert back to PDB strings + aligned_pdb_1 = structure_to_pdb_string(struct1) + aligned_pdb_2 = structure_to_pdb_string(struct2) + + # Add models to viewer + view.addModel(aligned_pdb_1, "pdb") + view.addModel(aligned_pdb_2, "pdb") + + else: + print( + "Could not find sufficient atoms for alignment, adding original models" + ) + view.addModel(model_1_data, "pdb") + view.addModel(model_2_data, "pdb") + + except Exception as e: + print(f"Alignment failed: {e}") + view.addModel(model_1_data, "pdb") + view.addModel(model_2_data, "pdb") + + # Apply styling + view.setStyle({"model": 0}, {"cartoon": {}}) + view.setStyle({"model": 1}, {"cartoon": {}}) + + for chain, color in model1_colors.items(): + if chain in chains: + view.addStyle( + {"model": 0, "chain": chain}, + {"cartoon": {"color": color, "opacity": 0.9}}, + ) + + for chain, color in model2_colors.items(): + if chain in chains: + view.addStyle( + {"model": 1, "chain": chain}, + {"cartoon": {"color": color, "opacity": 0.6}}, + ) + + # Add labels if requested + if show_labels: + view.addLabel( + "Model 1 (Reference)", + { + "position": {"x": -20, "y": 20, "z": 0}, + "backgroundColor": "darkred", + "fontColor": "white", + }, + ) + view.addLabel( + "Model 2 (Aligned)", + { + "position": {"x": 20, "y": 20, "z": 0}, + "backgroundColor": "darkgreen", + "fontColor": "white", + }, + ) + view.addLabel( + "Full Molecule Alignment", + { + "position": {"x": 0, "y": -20, "z": 0}, + "backgroundColor": "navy", + "fontColor": "white", + }, + ) + if overall_rmsd: + view.addLabel( + f"Overall RMSD: {overall_rmsd:.3f} Å", + { + "position": {"x": 0, "y": -30, "z": 0}, + "backgroundColor": "purple", + "fontColor": "white", + }, + ) + + # Add per-chain RMSD labels + y_offset = -40 + for chain_id, rmsd_val in per_chain_rmsd.items(): + view.addLabel( + f"Chain {chain_id}: {rmsd_val:.3f} Å", + { + "position": {"x": 0, "y": y_offset, "z": 0}, + "backgroundColor": "gray", + "fontColor": "white", + "fontSize": 10, + }, + ) + y_offset -= 8 + + view.zoomTo() + + return view diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libontology.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libontology.py new file mode 100644 index 0000000000000000000000000000000000000000..4646c9cc9607aa2b7a0e9c40491bb136f75071fb --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libontology.py @@ -0,0 +1,250 @@ +"""Describe the Haddock3 ontology used for communicating between modules.""" + +import datetime +import itertools +from enum import Enum +from os import linesep +from pathlib import Path + + +import jsonpickle + +from haddock.core.defaults import MODULE_IO_FILE +from haddock.core.typing import FilePath, Literal, Optional, TypeVar, Union +from typing import List, Any + + +NaN = float("nan") + + +class Format(Enum): + """Input and Output possible formats.""" + + PDB = "pdb" + PDB_ENSEMBLE = "pdb" + CNS_INPUT = "inp" + CNS_OUTPUT = "out" + TOPOLOGY = "psf" + MATRIX = "matrix" + + def __str__(self) -> str: + return str(self.value) + + +class Persistent: + """Any persistent file generated by this framework.""" + + def __init__( + self, + file_name: FilePath, + file_type: Format, + path: FilePath = ".", + md5: Optional[str] = None, + restr_fname: Optional[FilePath] = None, + ) -> None: + self.created = datetime.datetime.now().isoformat(" ", "seconds") + self.file_name = Path(file_name).name + self.file_type = file_type + self.path = str(Path(path).resolve()) + self.full_name = str(Path(path, self.file_name)) + self.rel_path = Path("..", Path(self.path).name, file_name) + self.md5 = md5 + self.restr_fname = restr_fname + + def __repr__(self) -> str: + rep = ( + f"[{self.file_type}|{self.created}] " f"{Path(self.path) / self.file_name}" + ) + return rep + + def is_present(self) -> bool: + """Check if the persisent file exists on disk.""" + return self.rel_path.resolve().exists() + + +class PDBFile(Persistent): + """Represent a PDB file.""" + + def __init__( + self, + file_name: Union[Path, str], + topology: Optional[Any] = None, + path: Union[Path, str] = ".", + score: float = NaN, + md5: Optional[str] = None, + restr_fname: Optional[Union[Path, str]] = None, + unw_energies: Optional[dict[str, float]] = None, + ) -> None: + super().__init__(file_name, Format.PDB, path, md5, restr_fname) + + self.topology = topology + self.score = score + self.ori_name: Optional[str] = None + self.clt_id: Union[str, int, None] = None + self.clt_rank: Optional[int] = None + self.clt_model_rank: Optional[int] = None + self.len = score + self.unw_energies = unw_energies + self.seed = None + + def __lt__(self, other: "PDBFile") -> bool: + return self.score < other.score + + def __gt__(self, other: "PDBFile") -> bool: + return self.score > other.score + + def __eq__(self, other: "PDBFile") -> bool: # type: ignore + return self.score == other.score + + def __hash__(self) -> int: + return id(self) + + +class RMSDFile(Persistent): + """Represents a RMSD matrix file.""" + + def __init__(self, file_name: FilePath, npairs: int, path: FilePath = ".") -> None: + super().__init__(file_name, Format.MATRIX, path) + self.npairs = npairs + + def __hash__(self) -> int: + return id(self) + + +class TopologyFile(Persistent): + """Represent a CNS-generated topology file.""" + + def __init__(self, file_name: FilePath, path: FilePath = ".") -> None: + super().__init__(file_name, Format.TOPOLOGY, path) + + +class ModuleIO: + """Intercommunicating modules and exchange input/output information.""" + + def __init__(self) -> None: + self.input: List[Any] = [] + self.output: List[Any] = [] + + def add(self, persistent, mode="i"): + """Add a given filename as input or output.""" + if mode == "i": + if isinstance(persistent, list): + self.input.extend(persistent) + else: + self.input.append(persistent) + else: + if isinstance(persistent, list): + self.output.extend(persistent) + else: + self.output.append(persistent) + + def save(self, path: FilePath = ".", filename: FilePath = MODULE_IO_FILE) -> Path: + """Save Input/Output needed files by this module to disk.""" + fpath = Path(path, filename) + with open(fpath, "w") as output_handler: + to_save = {"input": self.input, "output": self.output} + jsonpickle.set_encoder_options("json", sort_keys=True, indent=4) + output_handler.write(jsonpickle.encode(to_save)) # type: ignore + return fpath + + def load(self, filename: FilePath) -> None: + """Load the content of a given IO filename.""" + with open(filename) as json_file: + content = jsonpickle.decode(json_file.read()) + self.input = content["input"] # type: ignore + self.output = content["output"] # type: ignore + + def retrieve_models( + self, crossdock: bool = False, individualize: bool = False + ) -> list[Union[PDBFile, list[PDBFile]]]: + """Retrieve the PDBobjects to be used in the module.""" + # Get the models generated in previous step + model_list: list[PDBFile] = [] + input_dic: dict[int, list[PDBFile]] = {} + + for i, element in enumerate(self.output): + if isinstance(element, dict): + position_list: list[PDBFile] = input_dic.setdefault(i, []) + for key in element: + position_list.append(element[key]) # type: ignore + + elif element.file_type == Format.PDB: # type: ignore + model_list.append(element) # type: ignore + + if input_dic and not crossdock and not individualize: + # check if all ensembles contain the same number of models + sub_lists = iter(input_dic.values()) + _len = len(next(sub_lists)) + if not all(len(sub) == _len for sub in sub_lists): + _msg = ( + "Different number of models in molecules," + " cannot prepare pairwise complexes." + ) + raise Exception(_msg) + + # prepare pairwise combinations + model_list = [values for values in zip(*input_dic.values())] # type: ignore + elif input_dic and crossdock and not individualize: + model_list = [values for values in itertools.product(*input_dic.values())] # type: ignore + elif input_dic and individualize: + model_list = list(itertools.chain(*input_dic.values())) + + return model_list # type: ignore + + def check_faulty(self) -> float: + """Check how many of the output exists.""" + total = 0.0 + present = 0.0 + for element in self.output: + if isinstance(element, dict): + total += len(element) + present += sum(j.is_present() for j in element.values()) + else: + total += 1 + if element.is_present(): + present += 1 + + if total == 0: + _msg = "No expected output was passed to ModuleIO" + raise Exception(_msg) + + faulty_per = (1 - (present / total)) * 100 + + # added this method here to avoid modifying all calls in the + # modules' run method. We can think about restructure this part + # in the future. + self.remove_missing() + + return faulty_per + + def remove_missing(self) -> None: + """Remove missing structure from `output`.""" + # can't modify a list/dictionary within a loop + idxs: list[int] = [] + for idx, element in enumerate(self.output): + if isinstance(element, dict): + to_pop = [] + for key2 in element: + if not element[key2].is_present(): + to_pop.append(key2) + for pop_me in to_pop: + element.pop(pop_me) + else: + if not element.is_present(): + idxs.append(idx) + + self.output = [value for i, value in enumerate(self.output) if i not in idxs] + + def __repr__(self) -> str: + return f"Input: {self.input}{linesep}Output: {self.output}" + + +PDBPath = Union[PDBFile, Path] + +PDBPathT = TypeVar("PDBPathT", bound=Union[PDBFile, Path]) +""" +Generic type variable for PDBFile or Path. + +If the first annotated variable is PDBFile, +the second annotated variable will be PDBFile instead of Path,vice versa. +""" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libparallel.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libparallel.py new file mode 100644 index 0000000000000000000000000000000000000000..0490453ab291e98a63a7ef3dc74bd13d75ab4c06 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libparallel.py @@ -0,0 +1,208 @@ +"""Module in charge of parallelizing the execution of tasks.""" + +import math +from multiprocessing import Process, Queue + +from haddock import log +from haddock.core.typing import ( + AnyT, + FilePath, + Generator, + Optional, + Sequence, + SupportsRunT, + Union, +) +from haddock.libs.libutil import parse_ncores + + +def split_tasks(lst: Sequence[AnyT], n: int) -> Generator[Sequence[AnyT], None, None]: + """Split tasks into N-sized chunks.""" + n = math.ceil(len(lst) / n) + for j in range(0, len(lst), n): + chunk = lst[j : n + j] + yield chunk + + +def get_index_list(nmodels, ncores): + """ + Optimal distribution of models among cores + + Parameters + ---------- + nmodels : int + Number of models to be distributed. + + ncores : int + Number of cores to be used. + + Returns + ------- + index_list : list + List of model indexes to be used for the parallel scanning. + """ + if nmodels < 1: + raise ValueError(f"nmodels ({nmodels})) must be greater than 0") + if ncores < 1: + raise ValueError(f"ncores ({ncores}) must be greater than 0") + spc = nmodels // ncores + # now the remainder + rem = nmodels % ncores + # now the list of indexes to be used for the SCAN calculation + index_list = [0] + for core in range(ncores): + if core < rem: + index_list.append(index_list[-1] + spc + 1) + else: + index_list.append(index_list[-1] + spc) + return index_list + + +class GenericTask: + """Generic task to be executed.""" + + def __init__(self, function, *args, **kwargs): + if not callable(function): + raise TypeError("The 'function' argument must be callable") + self.function = function + self.args = args + self.kwargs = kwargs + + def run(self): + return self.function(*self.args, **self.kwargs) + + +class Worker(Process): + """Work on tasks.""" + + def __init__(self, tasks: Sequence[SupportsRunT], results: Queue) -> None: + super(Worker, self).__init__() + self.tasks = tasks + self.result_queue = results + log.debug(f"Worker ready with {len(self.tasks)} tasks") + + def run(self) -> None: + """Execute tasks.""" + results = [] + for task in self.tasks: + r = None + try: + r = task.run() + except Exception as e: + log.warning(f"Exception in task execution: {e}") + + results.append(r) + + # Put results into the queue + self.result_queue.put(results) + + # Signal completion by putting a unique identifier into the queue + self.result_queue.put(f"{self.name}_done") + + # log.debug(f"{self.name} executed") + + +class Scheduler: + """Schedules tasks to run in multiprocessing.""" + + def __init__( + self, + tasks: list[SupportsRunT], + ncores: Optional[int] = None, + max_cpus: bool = False, + ) -> None: + """ + Schedule tasks to a defined number of processes. + + Parameters + ---------- + tasks : list + The list of tasks to execute. Tasks must have method `run()`. + + ncores : None or int + The number of cores to use. If `None` is given uses the + maximum number of CPUs allowed by + `libs.libututil.parse_ncores` function. + """ + self.max_cpus = max_cpus + self.num_tasks = len(tasks) + self.num_processes = ncores # first parses num_cores + self.queue: Queue = Queue() + self.results: list = [] + + # Sort the tasks by input_file name and its length, so we know that 2 comes before 10 + ### Q? Whys is this necessary? + # Only CNSJobs can be sorted like this + if all(hasattr(t, "input_file") for t in tasks): + task_name_dic: dict[int, tuple[FilePath, int]] = {} + for i, t in enumerate(tasks): + task_name_dic[i] = (t.input_file, len(str(t.input_file))) # type: ignore + + sorted_task_list: list[SupportsRunT] = [] + for e in sorted(task_name_dic.items(), key=lambda x: (x[0], x[1])): + idx = e[0] + sorted_task_list.append(tasks[idx]) + else: + sorted_task_list = tasks + + job_list = split_tasks(sorted_task_list, self.num_processes) + self.worker_list = [Worker(jobs, self.queue) for jobs in job_list] + + log.info(f"Using {self.num_processes} cores") + log.debug(f"{self.num_tasks} tasks ready.") + + @property + def num_processes(self) -> int: + """Number of processors to use.""" # noqa: D401 + return self._ncores + + @num_processes.setter + def num_processes(self, n: Union[str, int, None]) -> None: + self._ncores = parse_ncores( + n, + njobs=self.num_tasks, + max_cpus=self.max_cpus, + ) + log.debug(f"Scheduler configured for {self._ncores} cpu cores.") + + def run(self) -> None: + """Run tasks in parallel.""" + + try: + for w in self.worker_list: + w.start() + + # Collect results until all workers have signaled completion + all_results = [] + num_workers = len(self.worker_list) + completed_workers = 0 + + while completed_workers < num_workers: + result = self.queue.get() + if isinstance(result, str) and result.endswith("_done"): + completed_workers += 1 + else: + all_results.append(result) + + for w in self.worker_list: + w.join() + + self.results = [item for sublist in all_results for item in sublist] + + log.info(f"{self.num_tasks} tasks finished") + + except KeyboardInterrupt as err: + # Q: why have a keyboard interrupt here? + # A: To have a controlled break if the user Ctrl+c during CNS run + self.terminate() + # this raises sends the error to libs.libworkflow.Step + # if Scheduler is used independently the error will propagate to + # whichever has to catch it + raise err + + def terminate(self) -> None: + """Terminate tasks in a controlled way.""" + for worker in self.worker_list: + worker.terminate() + + log.info("The workers terminated in a controlled way") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libpdb.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libpdb.py new file mode 100644 index 0000000000000000000000000000000000000000..ba926c48753c9410df864fe2fced301871264a33 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libpdb.py @@ -0,0 +1,508 @@ +"""Parse molecular structures in PDB format.""" + +import os +from copy import deepcopy +from functools import partial +from pathlib import Path + +from pdbtools.pdb_segxchain import run as place_seg_on_chain +from pdbtools.pdb_splitchain import run as split_chain +from pdbtools.pdb_splitmodel import run as split_model +from pdbtools.pdb_tidy import run as tidy_pdbfile + +from haddock.core.exceptions import SetupError +from haddock.core.supported_molecules import supported_residues +from haddock.core.typing import ( + Callable, + FilePath, + FilePathT, + Iterable, + Optional, + TypeVar, + Union, +) +from haddock.libs.libio import PDBFile, working_directory +from haddock.libs.libutil import get_result_or_same_in_list, sort_numbered_paths + +slc_record = slice(0, 6) +slc_serial = slice(6, 11) +slc_name = slice(12, 16) +slc_altloc = slice(16, 17) +slc_resname = slice(17, 20) +slc_chainid = slice(21, 22) +slc_resseq = slice(22, 26) +slc_icode = slice(26, 27) +slc_x = slice(30, 38) +slc_y = slice(38, 46) +slc_z = slice(46, 54) +slc_occ = slice(54, 60) +slc_temp = slice(60, 66) +slc_segid = slice(72, 76) +slc_element = slice(76, 78) +slc_charge = slice(78, 80) + + +def format_atom_name(atom: str, element: str) -> str: + """ + Format PDB atom name. + + Further Reading: + + * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html + + Parameters + ---------- + atom : str + The atom name. + + element : str + The atom element code. + + Returns + ------- + str + Formatted atom name. + """ + # string formats for atom name + _3 = " {:<3s}" + _4 = "{:<4s}" + # len of element, atom formatting string + # anything outside this is an error + _atom_format_dict = { + # len of element: {len of atom name} + 1: {1: _3, 2: _3, 3: _3, 4: _4}, + 2: {1: _4, 2: _4, 3: _4, 4: _4}, + } + + atm = atom.strip() + len_atm = len(atm) + len_ele = len(element.strip()) + + try: + return _atom_format_dict[len_ele][len_atm].format(atm) + except KeyError as err: + _ = f"Could not format this atom:type -> {atom}:{element}" + # raising KeyError assures that no context in IDPConfGen + # will handle it. @joaomcteixeira never handles pure Python + # exceptions, those are treated as bugs. + raise KeyError(_) from err + + +def get_supported_residues(haddock_topology: FilePath) -> list[str]: + """Read the topology file and identify which data is supported.""" + supported: list[str] = [] + with open(haddock_topology) as input_handler: + for line in input_handler: + if "resi" in line[:4].casefold(): + res = line.split()[1] + supported.append(res) + return supported + + +_to_remove = ["REMAR", "CTERB", "CTERA", "NTERA", "NTERB", "CONECT"] + +_to_rename = { + "HSD": "HIS", + "HSE": "HIS", + "HID": "HIS", + "HIE": "HIS", + "WAT ": "TIP3", + " 0.00969": " 0.00 ", +} + +# Get list of supported residues to keep when pre-processing +_to_keep = list(supported_residues) + + +def split_ensemble(pdb_file_path: Path, dest: Optional[FilePath] = None) -> list[Path]: + """ + Split a multimodel PDB file into different structures. + + Parameters + ---------- + dest : str or pathlib.Path + Destination folder. + """ + if dest is None: + dest = Path.cwd() + assert pdb_file_path.is_file(), pdb_file_path + with open(pdb_file_path) as input_handler: + with working_directory(dest): + # tidy pdb before splitting + tidied = tidy_pdbfile(input_handler) + split_model(tidied, outname=str(pdb_file_path.stem)) + + return sort_numbered_paths(*get_new_models(pdb_file_path)) + + +def split_by_chain(pdb_file_path: FilePath) -> list[Path]: + """Split a PDB file into multiple structures for each chain.""" + abs_path = Path(pdb_file_path).resolve().parent.absolute() + with open(pdb_file_path) as input_handler: + with working_directory(abs_path): + split_chain(input_handler) + + return get_new_models(pdb_file_path) + + +def tidy(pdb_file_path: FilePath, new_pdb_file_path: FilePath) -> None: + """Tidy PDB structure.""" + abs_path = Path(pdb_file_path).resolve().parent.absolute() + with open(pdb_file_path) as input_handler: + with working_directory(abs_path): + with open(new_pdb_file_path, "w") as output_handler: + for line in tidy_pdbfile(input_handler): + output_handler.write(line) + + +def swap_segid_chain(pdb_file_path: FilePath, new_pdb_file_path: FilePath) -> None: + """Add to the Chain ID column the found Segid.""" + abs_path = Path(pdb_file_path).resolve().parent.absolute() + with open(pdb_file_path) as input_handler: + with working_directory(abs_path): + with open(new_pdb_file_path, "w") as output_handler: + for line in place_seg_on_chain(input_handler): + output_handler.write(line) + + +def sanitize( + pdb_file_path: FilePathT, + overwrite: bool = True, + custom_topology: Optional[FilePath] = None, +) -> Union[FilePathT, Path]: + """Sanitize a PDB file.""" + to_keep = deepcopy(_to_keep) + if custom_topology: + custom_res_to_keep = get_supported_residues(custom_topology) + to_keep.extend(custom_res_to_keep) + + good_lines: list[str] = [] + with open(pdb_file_path) as input_handler: + for line in input_handler: + line = line.rstrip(os.linesep) + # Ignoring lines containing any tag from __to_remove + if not any([tag in line for tag in _to_remove]): + for tag, new_tag in _to_rename.items(): + line = line.replace(tag, new_tag) + # check if this residue is known + res = line[17:20].strip() + if res and res in to_keep: + good_lines.append(line) + # Terminate file with an END statement + if len(good_lines) > 0 and good_lines[-1] != "END": + good_lines.append("END") + + # Check if anything has been kept from this file + if len(good_lines) == 0: + raise SetupError(f"No coordinates kept after sanitzing {pdb_file_path.name}.") + + if overwrite: + with open(pdb_file_path, "w") as output_handler: + for line in good_lines: + output_handler.write(line + os.linesep) + return pdb_file_path + + basename = Path(pdb_file_path) + new_pdb_file = Path(f"{basename.stem}_cleaned{basename.suffix}") + new_pdb_file.write_text(os.linesep.join(good_lines) + os.linesep) + return new_pdb_file + + +def identify_chainseg( + pdb_file_path: FilePath, sort: bool = True +) -> tuple[list[str], list[str]]: + """Return segID OR chainID.""" + segids: list[str] = [] + chains: list[str] = [] + with open(pdb_file_path) as input_handler: + for line in input_handler: + if line.startswith(("ATOM ", "HETATM")): + try: + segid = line[72:76].strip()[:1] + except IndexError: + segid = "" + try: + chainid = line[21].strip() + except IndexError: + chainid = "" + + if segid: + segids.append(segid) + if chainid: + chains.append(chainid) + + if not segid and not chainid: + raise ValueError( + f"Could not identify chainID or segID in pdb {pdb_file_path}, line {line}" + ) + + if sort: + segids = sorted(list(set(segids))) + chains = sorted(list(set(chains))) + else: + segids = list(set(segids)) + chains = list(set(chains)) + return segids, chains + + +def get_new_models(pdb_file_path: FilePath) -> list[Path]: + """ + Get new PDB models if they exist. + + If no new models are found, return the original path within a list. + """ + new_models = get_result_or_same_in_list( + get_pdb_file_suffix_variations, + pdb_file_path, + ) + return new_models + + +def get_pdb_file_suffix_variations(file_name: FilePath, sep: str = "_") -> list[Path]: + """ + List suffix variations of a PDB file in the current path. + + If `file.pdb` is given, and files `file_1.pdb`, `file_2.pdb`, exist + in the folder, those will be listed. + + Parameters + ---------- + file_name : str or Path + The name of the file with extension. + + sep : str + The separation between the file base name and the suffix. + Defaults to "_". + + Returns + ------- + list + List of Paths with the identified PBD files. + If no files are found return an empty list. + """ + basename = Path(file_name) + return list(Path(".").glob(f"{basename.stem}{sep}*{basename.suffix}")) + + +def read_RECORD_section( + lines: Iterable[str], + section_slice: slice, + func: Callable[[Iterable[str]], Iterable[str]] = set, +) -> Iterable[str]: + """ + Create a set of observations from a section of the ATOM line. + + Returns + ------- + set + A set of the observations. + """ + # read the chain ID + chainids = func( + the_line + for line in lines + if line.startswith(("ATOM", "HETATM")) + and (the_line := line[section_slice].strip()) # noqa: E501 + ) + return chainids + + +read_chainids = partial(read_RECORD_section, section_slice=slc_chainid, func=list) +read_segids = partial(read_RECORD_section, section_slice=slc_segid, func=list) + + +def add_TER_on_chain_breaks( + input_pdb: FilePath, + output_pdb: FilePath, +) -> None: + """Detect chain breaks and add TER statements between them. + + Parameters + ---------- + input_pdb : FilePath + Input PDB filepath with potential chain breaks. + output_pdb : FilePath + Output PDB filepath with added TER statements between chain breaks. + """ + Residue = dict[str, Union[list[str], list[float], str]] + residueT = TypeVar("residueT", bound=Residue) + + def euclidean_dist(atm1: list[float], atm2: list[float]) -> float: + """Compute Euclidean distances between two points. + + Parameters + ---------- + atm1 : list[float] + Atom 1 coordinates. + atm2 : list[float] + Atom 2 coordinates. + + Returns + ------- + float + Distance between the two atoms. + """ + return sum([(c1 - c2) ** 2 for c1, c2 in zip(atm1, atm2)]) ** 0.5 + + def detected_chain_break(residue1: residueT, residue2: residueT) -> bool: + """Detect chain break between two consecutive residues. + + Currently limitted to DNA and protein chains. + + Parameters + ---------- + residue1 : residueT + Previous residue (N-1) + residue2 : residueT + Current residue (N) + + Returns + ------- + bool + True if chain break detected, else False + """ + # Expected backbone distances set + backbone_dists = { + "protein": 3.5, # very loose ! + "DNA": 4.5, + } + # Detect type of residues + # DNA case + try: + # Extract coordinates + atm1 = residue1["O3'"] + atm2 = residue2["O5'"] + except KeyError: + # Protein case + try: + # Extract coordinates + atm1 = residue1["C"] # C of -1 residue + atm2 = residue2["N"] # N of 0 residue + # Error in detection of any of the atoms + except KeyError: + # Must be a chain break + # FIXME : This assumes that it is NOT a DNA nor a protein. + # In the future, if future there is, it may cause an issue if + # lipids, glycans, other type of entities are added, + # as this will trigger a TER statement between them. + return True + else: + entity_type = "protein" + else: + entity_type = "DNA" + # Point distance + upper_dist = backbone_dists[entity_type] + # Check if distance is within acceptable peptide bond limit + return euclidean_dist(atm1, atm2) > upper_dist + + def write_residue(fhandler, residue_lines: list[str]) -> None: + """Writes residues line to file. + + Parameters + ---------- + fhandler : _type_ + File object on which to write the residue lines. + residue_lines : list[str] + Residue to write. + """ + for _ in residue_lines: + fhandler.write(_) + + def write_previous_residue( + fhandler, + previous: residueT, + current: residueT, + ) -> None: + """Write residue lines to file, possibly ending by TER. + + Parameters + ---------- + fhandler : _type_ + File object on which to write the residue lines. + previous : residueT + Previous residue (N-1) + current : residueT + Current residue (N) + """ + # Write previous residue + write_residue(fhandler, previous["lines"]) + # Check if bond observed between -2 and -1 + chain_break = detected_chain_break( + previous, + current, + ) + # If chain break detected or new chain in file + if chain_break or previous["chain"] != current["chain"]: + fhandler.write(f"TER{os.linesep}") + + # Initiate parsing variables + BB_atomnames: tuple[str, str, str, str] = ( + "C", + "N", # for peptide bonds + "O3'", + "O5'", # for DNA/RNA + ) + current_resid: tuple[str, str] = ("-", "-") + previous_residue: residueT = {"lines": []} + current_residue: residueT = {"lines": []} + # Read input file + with open(input_pdb, "r") as fin, open(output_pdb, "w") as fout: + for _ in fin: + if _.startswith( + ( + "ATOM", + "HETATM", + ) + ): + # Extract specific data from coordinates record + chainid = _[slc_chainid].strip() + resid = _[slc_resseq].strip() + atname = _[slc_name].strip() + + # Case when new residue + if current_resid != (chainid, resid): + # Make sure it is not first residue + if len(previous_residue["lines"]) > 0: + # Write previous residue + write_previous_residue(fout, previous_residue, current_residue) + # Reset previous residue to current residue + previous_residue = current_residue + # Initialize new current residue + current_resid = ( + chainid, + resid, + ) + current_residue = {"lines": [], "chain": chainid} + + # Hold residue line + current_residue["lines"].append(_) + + # If atom name is in the backbone atoms + if atname in BB_atomnames: + # Hold backbone atom coordinates in current residue + current_residue[atname] = [ + float(_[slc_x]), + float(_[slc_y]), + float(_[slc_z]), + ] + # Last previous residue + write_previous_residue(fout, previous_residue, current_residue) + # Last residue + write_residue(fout, current_residue["lines"]) + # Write final TER statement + fout.write(f"TER{os.linesep}") + # Write END statement + fout.write(f"END{os.linesep}") + + +def check_combination_chains(combination: list[PDBFile]) -> list[str]: + """Check if chain IDs are unique for each pdb in combination.""" + chainid_list: list[str] = [] + for pdb in combination: + segids, chains = identify_chainseg(pdb.rel_path, sort=False) + chainsegs = sorted(list(set(segids) | set(chains))) + # check if any of chainsegs is already in chainid_list + if any(chainseg in chainid_list for chainseg in chainsegs): + raise ValueError(f"Chain/seg IDs are not unique for pdbs {combination}.") + chainid_list.extend(chainsegs) + return chainid_list diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libplots.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libplots.py new file mode 100644 index 0000000000000000000000000000000000000000..43dfea1b27d47da2ca1c99c278543d3681ac9595 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libplots.py @@ -0,0 +1,1641 @@ +"""Plotting functionalities.""" + +import json +import shutil + +import numpy as np +import pandas as pd +import plotly.colors as px_colors +import plotly.express as px +import plotly.graph_objects as go +from plotly.io._utils import plotly_cdn_url +from plotly.offline.offline import get_plotlyjs +from plotly.subplots import make_subplots + +from pathlib import Path + +from haddock import log +from haddock.core.typing import ( + Any, + DataFrameGroupBy, + Figure, + FilePath, + ImgFormat, + NDFloat, + Optional, + Union, + ) +from haddock.libs.assets import haddock_ui_path + + +SCATTER_PAIRS = [ + ("irmsd", "score"), + ("irmsd", "desolv"), + ("irmsd", "vdw"), + ("irmsd", "elec"), + ("irmsd", "air"), + ("dockq", "score"), + ("dockq", "desolv"), + ("dockq", "vdw"), + ("dockq", "elec"), + ("dockq", "air"), + ("lrmsd", "score"), + ("lrmsd", "desolv"), + ("lrmsd", "vdw"), + ("lrmsd", "elec"), + ("lrmsd", "air"), + ("ilrmsd", "score"), + ("ilrmsd", "desolv"), + ("ilrmsd", "vdw"), + ("ilrmsd", "elec"), + ("ilrmsd", "air"), + ("fnat", "score"), + ("fnat", "desolv"), + ("fnat", "vdw"), + ("fnat", "elec"), + ("fnat", "air"), + ] + + +# if SCATTER_PAIRS changes, SCATTER_MATRIX_SIZE should change too! +SCATTER_MATRIX_SIZE = (5, 5) # (number of rows, number of columns) + +TITLE_NAMES = { + "score": "HADDOCK score", + "irmsd": "i-RMSD", + "lrmsd": "l-RMSD", + "ilrmsd": "il-RMSD", + "dockq": "DOCKQ", + "desolv": "Edesolv", + "vdw": "Evdw", + "elec": "Eelec", + "air": "Eair", + "fnat": "FCC", + "bsa": "BSA", + } + +AXIS_NAMES = { + "score": "HADDOCK score [a.u.]", + "vdw": "Van der Waals Energy", + "elec": "Electrostatic Energy", + "air": "Restraints Energy", + "desolv": "Desolvation Energy", + "irmsd": "interface RMSD [A]", + "lrmsd": "ligand RMSD [A]", + "ilrmsd": "interface-ligand RMSD [A]", + "fnat": "Fraction of Common Contacts", + "dockq": "DOCKQ", + "bsa": "Buried Surface Area [A^2]", + } + +ClRank = dict[int, int] +""" +A dict representing clusters' rank. + +key (int): cluster's id + +value(int): cluster's rank +""" + +HEATMAP_DEFAULT_PATH = Path('contacts.html') +SUPPORTED_OUTPUT_FORMATS = ('png', 'jpeg', 'webp', 'svg', 'pdf', 'eps', ) + +def create_html( + json_content: str, + plot_id: int = 1, + plotly_js_import: Optional[str] = None, + figure_height: int = 800, + figure_width: int = 1000, + ) -> str: + """Create html content given a plotly json. + + Parameters + ---------- + json_content : str + plotly json content + + plot_id : int + plot id to be used in the html content + + figure_height : int + figure height (in pixels) + + figure_width : int + figure width (in pixels) + + Returns + ------- + html_content : str + html content + """ + # Check if plotly javascript must be flushed in this file + if not plotly_js_import: + plotly_js_import = f'' + + # Write HTML content + html_content = f""" +
+ + {plotly_js_import} +
+
+ + +
+ """ # noqa : E501 + return html_content + + +def read_capri_table( + capri_filename: FilePath, + comment: str = "#", + ) -> pd.DataFrame: + """Read capri table with pandas. + + Parameters + ---------- + capri_filename : str or Path + capri single structure filename + comment : str + the string used to denote a commented line in capri tables + + Returns + ------- + capri_df : pandas DataFrame + dataframe of capri values + """ + capri_df = pd.read_csv(capri_filename, sep="\t", comment=comment) + return capri_df + + +def in_capri(column: str, df_columns: pd.Index) -> bool: + """ + Check if the selected column is in the set of available columns. + + Parameters + ---------- + column : str + column name + df_columns : pandas.DataFrame.columns + columns of a pandas.DataFrame + + Returns + ------- + resp : bool + if True, the column is present + """ + resp = True + if column not in df_columns: + log.warning(f"quantity {column} not present in capri table") + resp = False + return resp + + +def update_layout_plotly( + fig: Figure, + x_label: str, + y_label: str, + title: Optional[str] = None, + ) -> Figure: + """ + Update layout of plotly plot. + + Parameters + ---------- + fig : plotly Figure + figure + x_label : str + x axis name + y_label : str + y axis name + title : str or None + plot title + """ + px_dict = { + "title": title, + "xaxis": dict( + title=dict(text=x_label, font=dict(size=40)), + tickfont_size=14, + ), + "yaxis": dict( + title=dict(text=y_label, font=dict(size=40)), + tickfont_size=14, + ), + "legend": dict(x=1.01, y=1.0, font_family="Helvetica", font_size=16), + "hoverlabel": dict(font_size=16, font_family="Helvetica"), + } + fig.update_layout(px_dict) + return fig + + +def box_plot_plotly( + gb_full: pd.DataFrame, + y_ax: str, + cl_rank: dict[int, int], + format: Optional[ImgFormat], + scale: Optional[float], + offline: bool = False, + ) -> Figure: + """ + Create a scatter plot in plotly. + + Parameters + ---------- + gb_full : pandas DataFrame + data to box plot + y_ax : str + variable to plot + cl_rank : dict + {cluster_id : cluster_rank} dictionary + format : str + Produce images in the selected format. + scale : int + scale of image + + Returns + ------- + fig_list : list + a list of figures + """ + colors = px_colors.qualitative.Dark24 + color_map = {} + for cl_id in sorted(cl_rank.keys()): + color_idx = (cl_rank[cl_id] - 1) % len(colors) # color index + + # Note: the rank format (float/int) in "cl_rank" is different from + # gb_full["cluster_ranking"] + rns = gb_full[gb_full["cluster_id"] == cl_id]["cluster_ranking"] + rn = rns.unique()[0] + color_map[f"{rn}"] = colors[color_idx] + + # Choose a different color for "Other" like in scatter plots + color_map["Other"] = "#DDDBDA" + + # to use color_discrete_map, cluster_ranking column should be str not int + gb_full_string = gb_full.astype({"cluster_ranking": "string"}) + + # Rename for a better name in legend + gb_full_string.rename( + columns={"cluster_ranking": "Cluster Rank"}, + inplace=True, + ) + + # "Cluster Rank" is equivalent to "capri_rank"! + fig = px.box( + gb_full_string, + x="capri_rank", + y=f"{y_ax}", + color="Cluster Rank", + color_discrete_map=color_map, + boxmode="overlay", + points="outliers", + width=1000, + height=800, + hover_data=["caprieval_rank"], + ) + # layout + update_layout_plotly(fig, "Cluster Rank", AXIS_NAMES[y_ax]) + # save figure + px_fpath = Path(f"{y_ax}_clt.html") + json_content = fig.to_json() + html_content = create_html( + json_content, + plotly_js_import=offline_js_manager(px_fpath, offline), + ) + # write html_content to px_fname + px_fpath.write_text(html_content) + # create format boxplot if necessary + if format: + fig.write_image(f"{y_ax}_clt.{format}", scale=scale) + return fig + + +def box_plot_data(capri_df: pd.DataFrame, cl_rank: ClRank) -> pd.DataFrame: + """ + Retrieve box plot data. + + Parameters + ---------- + capri_df : pandas DataFrame + capri table dataframe + cl_rank : dict + {cluster_id : cluster_rank} dictionary + + Returns + ------- + gb_full : pandas DataFrame + DataFrame of all the clusters to be plotted + """ + gb_cluster = capri_df.groupby("cluster_id") + gb_other = pd.DataFrame([]) + gb_good = pd.DataFrame([]) + for cl_id, cl_df in gb_cluster: + if cl_id not in cl_rank.keys(): + gb_other = pd.concat([gb_other, cl_df]) + else: + cl_df["capri_rank"] = cl_rank[cl_id] # type: ignore + gb_good = pd.concat([gb_good, cl_df]) + + gb_other["cluster_id"] = "Other" + gb_other["capri_rank"] = len(cl_rank.keys()) + 1 + gb_other["cluster_ranking"] = "Other" + gb_full = pd.concat([gb_good, gb_other]) + + # Sort based on "capri_rank" + gb_full.sort_values(by=["capri_rank"], inplace=True) + return gb_full + + +def box_plot_handler( + capri_filename: FilePath, + cl_rank: ClRank, + format: Optional[ImgFormat], + scale: Optional[float], + offline: bool = False, + ) -> list[Figure]: + """Create box plots. + + The idea is that for each of the top X-ranked clusters we create a box plot + showing how the basic statistics are distributed within each model. + + Parameters + ---------- + capri_filename : str or Path + capri single structure filename + cl_rank : dict + {cluster_id : cluster_rank} dictionary + format : str + Produce images in the selected format. + scale : int + scale for images. + """ + # generating the correct dataframe + capri_df = read_capri_table(capri_filename, comment="#") + gb_full = box_plot_data(capri_df, cl_rank) + + # iterate over the variables + fig_list: list[Figure] = [] + for y_ax in AXIS_NAMES.keys(): + if not in_capri(y_ax, capri_df.columns): + continue + fig = box_plot_plotly( + gb_full, y_ax, cl_rank, format, scale, offline=offline, + ) + fig_list.append(fig) + return fig_list + + +def scatter_plot_plotly( + gb_cluster: DataFrameGroupBy, + gb_other: pd.DataFrame, + cl_rank: ClRank, + x_ax: str, + y_ax: str, + colors: list[str], + format: Optional[ImgFormat], + scale: Optional[float], + offline: bool = False, + ) -> Figure: + """Create a scatter plot in plotly. + + Parameters + ---------- + gb_cluster : pandas DataFrameGroupBy + capri DataFrame grouped by cluster_id + gb_other : pandas DataFrame + DataFrame of clusters not in the top cluster ranking + cl_rank : dict + {cluster_id : cluster_rank} dictionary + x_ax : str + name of the x column + y_ax : str + name of the y column + colors : list + list of colors to be used + format : str + Produce images in the selected format. + scale : int + scale for images. + + Returns + ------- + fig : + an instance of plotly.graph_objects.Figure + """ + + def _build_hover_text(df): + """Build a nice text for hover text.""" + text_list = [] + for _, row in df.iterrows(): + model_text = f"Model: {row['model'].split('/')[-1]}" + score_text = f"Score: {row['score']}" + caprieval_rank_text = f"Caprieval rank: {row['caprieval_rank']}" + text_list.append( + f"{model_text}
{score_text}" + f"
{caprieval_rank_text}" + ) + return text_list + + fig = go.Figure(layout={"width": 1000, "height": 800}) + traces: list[go.Scatter] = [] + n_colors = len(colors) + cl_rank_swap = {v: k for k, v in cl_rank.items()} + + for cl_rn in sorted(cl_rank_swap.keys()): + cl_id = cl_rank_swap[cl_rn] + cl_df = gb_cluster.get_group(cl_id) + if cl_id in cl_rank.keys(): + if cl_id == "-": + cl_name = "Unclustered" + else: + cl_name = f"Cluster {cl_rank[cl_id]}" # use rank + color_idx = (cl_rank[cl_id] - 1) % n_colors # color index + + traces.append( + go.Scatter( + x=cl_df[x_ax], + y=cl_df[y_ax], + name=cl_name, + mode="markers", + text=_build_hover_text(cl_df), + legendgroup=cl_name, + marker_color=colors[color_idx], + hoverlabel=dict( + bgcolor=colors[color_idx], + font_size=16, + font_family="Helvetica", + ), + ) + ) + clt_text = f"{cl_name}
" + + # mean and std deviations for the top 4 members + x_mean = np.mean(cl_df[x_ax].iloc[:4]) + y_mean = np.mean(cl_df[y_ax].iloc[:4]) + x_std = np.std(cl_df[x_ax].iloc[:4]) + y_std = np.std(cl_df[y_ax].iloc[:4]) + + if "score" not in [x_ax, y_ax]: + clt_text += f"Score: {np.mean(cl_df['score'].iloc[:4]):.3f}
" + clt_text += f"{x_ax}: {x_mean:.3f}
{y_ax}: {y_mean:.3f}" + + clt_text_list = [clt_text] + traces.append( + go.Scatter( + x=[x_mean], + y=[y_mean], + # error bars + error_x=dict( + type="data", array=[x_std], visible=True + ), + error_y=dict( + type="data", array=[y_std], visible=True + ), + # color and text + marker_color=colors[color_idx], + text=clt_text_list, + legendgroup=cl_name, + showlegend=False, + mode="markers", + marker=dict(size=10, symbol="square-dot"), + hovertemplate=f"{clt_text}", + hoverlabel=dict( + bgcolor=colors[color_idx], + font_size=16, + font_family="Helvetica", + ), + ) + ) + # append trace other + if not gb_other.empty: + traces.append( + go.Scatter( + x=gb_other[x_ax], + y=gb_other[y_ax], + name="Other", + mode="markers", + text=_build_hover_text(gb_other), + legendgroup="Other", + marker=dict( + color="white", + line=dict(width=2, color="DarkSlateGrey"), + ), + hoverlabel=dict( + bgcolor="white", + font_size=16, + font_family="Helvetica", + ), + ) + ) + for trace in traces: + fig.add_trace(trace) + px_fpath = Path(f"{x_ax}_{y_ax}.html") + update_layout_plotly( + fig, + TITLE_NAMES[x_ax], + TITLE_NAMES[y_ax], + title=f"{TITLE_NAMES[x_ax]} vs {TITLE_NAMES[y_ax]}", + ) + json_content = fig.to_json() + html_content = create_html( + json_content, + plotly_js_import=offline_js_manager(px_fpath, offline), + ) + # write html_content to px_fname + Path(px_fpath).write_text(html_content) + + # create format boxplot if necessary + if format: + fig.write_image(f"{x_ax}_{y_ax}.{format}", scale=scale) + return fig + + +def scatter_plot_data( + capri_df: pd.DataFrame, + cl_rank: ClRank, + ) -> tuple[DataFrameGroupBy, pd.DataFrame]: + """Retrieve scatter plot data. + + Parameters + ---------- + capri_df : pandas DataFrame + capri table dataframe + cl_rank : dict + {cluster_id : cluster_rank} dictionary + + Returns + ------- + gb_cluster : pandas DataFrameGroupBy + capri DataFrame grouped by cluster_id + gb_other : pandas DataFrame + DataFrame of clusters not in the top cluster ranking + """ + gb_cluster = capri_df.groupby("cluster_id") + gb_other = pd.DataFrame([]) + for cl_id, cl_df in gb_cluster: + if cl_id not in cl_rank.keys(): + gb_other = pd.concat([gb_other, cl_df]) + return gb_cluster, gb_other + + +def scatter_plot_handler( + capri_filename: FilePath, + cl_rank: ClRank, + format: Optional[ImgFormat], + scale: Optional[float], + offline: bool = False, + ) -> list[Figure]: + """Create scatter plots. + + The idea is that for each pair of variables of interest (SCATTER_PAIRS, + declared as global) we create a scatter plot. + If available, each scatter plot containts cluster information. + + Parameters + ---------- + capri_filename : str or Path + capri single structure filename + cl_rank : dict + {cluster_id : cluster_rank} dictionary + format : str + Produce images in the selected format. + scale : int + scale for images. + + Returns + ------- + fig_list : list + a list of figures + """ + capri_df = read_capri_table(capri_filename, comment="#") + gb_cluster, gb_other = scatter_plot_data(capri_df, cl_rank) + + # defining colors + colors = px_colors.qualitative.Dark24 + fig_list = [] + for x_ax, y_ax in SCATTER_PAIRS: + if not in_capri(x_ax, capri_df.columns): + continue + if not in_capri(y_ax, capri_df.columns): + continue + fig = scatter_plot_plotly( + gb_cluster, + gb_other, + cl_rank, + x_ax, + y_ax, + colors, + format, + scale, + offline=offline, + ) + fig_list.append(fig) + return fig_list + + +def _report_grid_size(plot_list: list[Figure]) -> tuple[int, int, int, int]: + """ + Calculate the size of the grid in the report. + + By size, it means the number of rows/columns, and the width/height + of an individual plot. In the report, some of the axes are shared. The + settings for sharing axes depends on the type (scatters or boxes). The + number of columns is set to the number of columns in SCATTER_MATRIX_SIZE. If + the number of clusters is more than 5, it increases the width which causes + horizontal scrolling in the report. + + Parameters + ---------- + plot_list : list + list of plots generated by analyse command + + Returns + ------- + number_of_rows : int + number of rows in the grid + number_of_cols : int + number of columns in the grid + width : int + the width of an individual plot + height: int + the height of an individual plot + """ + # Calculate grid size for subplots + number_of_plots = len(plot_list) + number_of_clusters = len({trace.legendgroup for trace in plot_list[0].data}) + # same number of cols for both boxes and scatters + number_of_cols = SCATTER_MATRIX_SIZE[1] + number_of_rows = int(np.ceil(number_of_plots / number_of_cols)) + # enable horizontal scroll + width = 600 if number_of_clusters > 5 else 350 + height = 600 if number_of_clusters > 5 else 350 + return number_of_rows, number_of_cols, width, height + + +def report_plots_handler(plots, shared_xaxes=False, shared_yaxes=False): + """ + Create a figure that holds subplots. + + The idea is that for each type (scatters or boxes), the individual plots are + considered subplots. In the report, some of the axes are shared. The + settings for sharing axes depends on the type (scatters or boxes). + + Parameters + ---------- + plots : list + list of plots generated by `analyse` command + shared_xaxes: boolean or str (default False) + a parameter of plotly.subplots.make_subplots + shared_yaxes: boolean or str (default False) + a parameter of plotly.subplots.make_subplots + + Returns + ------- + fig : + an instance of plotly.graph_objects.Figure + """ + number_of_rows, number_of_cols, width, height = _report_grid_size(plots) + fig = make_subplots( + rows=number_of_rows, + cols=number_of_cols, + shared_xaxes=shared_xaxes, + shared_yaxes=shared_yaxes, + vertical_spacing=(0.4 / number_of_rows), + horizontal_spacing=(0.3 / number_of_cols), + ) + for i, sub_fig in enumerate(plots): + col_index = int((i % number_of_cols) + 1) + row_index = int(np.floor(i / number_of_cols) + 1) + # hide legend of plots except one + if i != 0: + sub_fig.for_each_trace(lambda trace: trace.update(showlegend=False)) + fig.add_traces(sub_fig.data, rows=row_index, cols=col_index) + fig.update_yaxes( + title_text=sub_fig.layout.yaxis.title.text, + row=row_index, + col=col_index, + title_standoff=5, + automargin=True, + ) + # x title only on the last row + if shared_xaxes == "all": + row_index = number_of_rows + fig.update_xaxes( + title_text=sub_fig.layout.xaxis.title.text, + row=row_index, + col=col_index, + title_standoff=5, + automargin=True, + ) + legend_title_text = sub_fig.layout.legend.title.text + fig.update_layout( + legend_title_text=legend_title_text, + height=height * number_of_rows, + width=width * number_of_cols, + ) + return fig + + +def find_best_struct( + df: pd.DataFrame, + max_best_structs: int = 4, + ) -> pd.DataFrame: + """Find best structures for each cluster. + + Parameters + ---------- + df: pd.DataFrame + The loaded capri_ss.tsv dataframe + max_best_structs: int + The maximum number of best structures to return. + + Returns + ------- + best_df: pd.DataFrame + DataFrame of best structures with + `cluster_id` and `best` columns + and empty strings for missing values. + """ + df = df[["cluster_id", "model-cluster_ranking", "model"]] + df = df[df["model-cluster_ranking"] <= max_best_structs] + + best_df = df.pivot( + index="cluster_id", + columns="model-cluster_ranking", + values="model", + ) + + best_df = best_df.fillna('').reset_index() + best_df.columns = [ + f"best{col}" if col != "cluster_id" else col + for col in best_df.columns + ] + # Remove empty columns + best_df = best_df.loc[:, (best_df != '').any(axis=0)] + return best_df + + +def clean_capri_table(df: pd.DataFrame) -> pd.DataFrame: + """ + Create a tidy capri table for the report. + + It also combines mean and std values in one column. + Also it drops the columns that are not needed in the report. + + Makes inplace changes to the dataframe. + + Parameters + ---------- + df : pandas DataFrame + dataframe of capri values + + Returns + ------- + pandas DataFrame + DataFrame of capri table with new column names + """ + for col_name in AXIS_NAMES.keys(): + if not in_capri(col_name, df.columns): + continue + mean_value = df[col_name] + std_value = df[f"{col_name}_std"] + df[col_name] = [ + {'mean': mean_value, 'std': std_value} + for mean_value, std_value in zip(mean_value, std_value) + ] + + # Drop columns ending with '_std' + df = df.drop(df.filter(regex='_std$').columns, axis=1) + return df + + +def create_other_cluster( + clusters_df: pd.DataFrame, + structs_df: pd.DataFrame, + max_clusters: int, + ) -> tuple[pd.DataFrame, pd.DataFrame]: + """ + Combine all clusters with rank >= max_clusters into an "Other" cluster. + + Parameters + ---------- + clusters_df : pandas DataFrame + DataFrame of clusters + structs_df : pandas DataFrame + DataFrame of structures + max_clusters : int + From which cluster rank to consider as "Other" + + Returns + ------- + tuple with clusters_df and structs_df + """ + if len(clusters_df) <= max_clusters: + return clusters_df, structs_df + # other clusters + other_structs_df = structs_df[structs_df['cluster_ranking'] >= max_clusters].copy() + # drop other clusters from structs_df + structs_df = structs_df[structs_df['cluster_ranking'] < max_clusters].copy() + other_structs_df.loc[:,'cluster_id'] = 'Other' + other_structs_df.loc[:,'cluster_ranking'] = max_clusters + inner_rank = other_structs_df['caprieval_rank'].rank(method='first').astype(int) # noqa : E501 + other_structs_df['model-cluster_ranking'] = inner_rank + structs_df = pd.concat([structs_df, other_structs_df]) + + clusters_df = clusters_df[clusters_df['cluster_rank'] < max_clusters] + other_cluster = { + 'cluster_id': 'Other', + 'cluster_rank': max_clusters, + 'n': len(other_structs_df), + 'caprieval_rank': max_clusters, + } + for col in AXIS_NAMES.keys(): + if any([ + col not in other_structs_df.columns, + col not in clusters_df.columns, + ]): + continue + other_cluster[col] = other_structs_df[col].mean() + other_cluster[col + '_std'] = other_structs_df[col].std() + other_cluster_df = pd.DataFrame([other_cluster]) + clusters_df = pd.concat([clusters_df, other_cluster_df], ignore_index=True).round(2) + return clusters_df, structs_df + + +def clt_table_handler( + clt_file: FilePath, + ss_file: FilePath, + is_cleaned: bool = False, + topX_clusters: int = 10, + clustered_topX: int = 4, + unclustered_topX: int = 10, + top_ranked_mapping: Optional[dict[Path, Path]] = None, + ) -> pd.DataFrame: + """ + Create a dataframe including data for tables. + + The idea is to create tidy tables that report statistics available in + capri_clt.tsv and capri_ss.tsv files. + + Parameters + ---------- + clt_file : str or Path + path to capri_clt.tsv file + ss_file: str or Path + path to capri_ss.tsv file + is_cleaned: bool + is the run going to be cleaned? + + Returns + ------- + df_merged : pandas DataFrame + a data frame including data for tables + """ + # table of statistics + clusters_df = read_capri_table(clt_file) + structs_df = read_capri_table(ss_file) + + # Round all numbers to 2 decimal places + clusters_df = clusters_df.round(2) + structs_df = structs_df.round(2) + + # if the run will be cleaned, the structures are going to be gzipped + if not top_ranked_mapping: + if is_cleaned: + # substitute the values in the df by adding .gz at the end + structs_df['model'] = structs_df['model'].replace( + to_replace=r"(\.pdb)$", value=r".pdb.gz", regex=True, + ) + else: + # ss_file is in NN_caprieval/ while report is in + # analysis/NN_caprieval_analysis/ + # need to correct model paths by prepending ../ + def correct_relative_paths( + path: str, + top_ranked_mapping: Optional[dict[Path, Path]], + ) -> str: + """Prepend model paths in capri_ss files get their relative paths. + + Parameters + ---------- + path : str + Original path to a model file. + top_ranked_mapping : Optional[dict[Path, Path]] + Optional filepath mapping of top ranked models. + + Returns + ------- + new_path : str + New path to the file + """ + try: + # If top ranked is provided, use that information + new_path = top_ranked_mapping[path] + except (KeyError, TypeError, ): + # Otherwise just prepend by `../` + new_path = f"../{path}" + return new_path + + structs_df['model'] = structs_df['model'].apply( + lambda x: correct_relative_paths(x, top_ranked_mapping) + ) + + is_unclustered = clusters_df["cluster_rank"].unique().tolist() == ["-"] + # If unclustered, we only want to show the top 10 structures in a table. + if is_unclustered: + structs_df = structs_df[:unclustered_topX] + cols2keep = ['caprieval_rank', 'model'] + list(AXIS_NAMES.keys()) + structs_df = structs_df[cols2keep] + # model has ../../01_rigidbody/rigidbody_62.pdb.gz + # add id column with 62 as value + structs_df['id'] = structs_df['model'].str.extract(r'(\d+).pdb') + return structs_df + + clusters_df, structs_df = create_other_cluster( + clusters_df, + structs_df, + max_clusters=topX_clusters + 1, + ) + + clusters_df = clean_capri_table(clusters_df) + structs_df = find_best_struct(structs_df, max_best_structs=clustered_topX) + df_merged = pd.merge(clusters_df, structs_df, on="cluster_id") + return df_merged + + +def _css_styles_for_report(offline: bool) -> str: + """ + Generate custom CSS styles for an analysis report. + + Parameters + ---------- + offline : bool + If True, the HTML will be generated for offline use. + + Returns + ------- + The CSS styles as a string. + """ + custom_css = """ + .title { + font-family: Arial, sans-serif; + font-size: 32px; + font-weight: bold; + } + body { + margin-left: 1em; + } + table { + border-collapse: collapse; + } + th { + background-color: #f2f2f2; + padding: 8px; + border: 1px solid #ddd; + text-align: left; + } + th[scope="row"] { + position: sticky; + min-width: 16rem; + left: 0; + z-index: 1 + } + td { + border: 1px solid #ddd; + padding: 8px; + text-align: left; + } + tr:nth-child(even) { + background-color: #f2f2f2 + } + .js-plotly-plot .plotly .modebar svg { + display: inline; + } + """ + css_link = "https://cdn.jsdelivr.net/npm/@i-vresse/haddock3-ui@~0.3.0/dist/index.css" + if offline: + # copy the css file to the report directory + src = haddock_ui_path / 'index.css' + shutil.copyfile(str(src), "../data/ui/index.css") + css_link = "../../data/ui/index.css" + table_css = f' ' + return f"{table_css}" + + +def _generate_html_report( + step: str, + figures: list[Union[Figure, pd.DataFrame]], + report_path: FilePath, + offline: bool = False, + ) -> str: + """ + Generate an HTML report for a specific step of analysis, including figures. + + Parameters + ---------- + step : str + The step number. + figures : list + A list of figures to include in the HTML body. + Each figure can be either a string representing a table or a + plotly.graph_objects.Figure object. + offline : bool + If True, the HTML will be generated for offline use. + + Returns + ------- + html_report : str + The generated HTML report as a string. + """ + html_report = "" + html_report += _generate_html_head(step, offline) + html_report += _generate_html_body(figures, report_path, offline=offline) + html_report += "" + return html_report + + +def _generate_html_head(step, offline): + """ + Generate the HTML head section for an analysis report. + + Parameters + ---------- + step : str + The step number. + offline : bool + If True, the HTML will be generated for offline use. + + Returns + ------- + head : str + The HTML head section as a string. + """ + head = "" + head += f"Analysis report of step {step}" + head += f"

Analysis report of step {step}

" + head += _css_styles_for_report(offline) + head += "" + return head + + +def _generate_unclustered_table_html( + table_id: str, + df: pd.DataFrame, + bundle_url: str, + ) -> str: + data = df.to_json(orient='records') + headers = [ + {'key': "caprieval_rank", 'label': "Structure Rank", 'sorted': "asc"}, + {'key': "model", 'label': "Structure", + 'sortable': False, 'type': "structure" + }, + ] + [ + {'key': k, 'label': v, 'type': 'stats'} + for k, v in AXIS_NAMES.items() + if k in df.columns + ] + [ + {'key': "id", 'label': "Structure ID"}, + ] + return f""" +
+ + """ # noqa : E501 + + +def _generate_clustered_table_html( + table_id: str, + df: pd.DataFrame, + bundle_url: str, + ) -> str: + data = df.to_json(orient='records') + nr_best_columns = df.filter(like="best").shape[1] + headers = [ + {'key': "cluster_rank", 'label': "Cluster Rank", 'sorted': "asc"}, + {'key': "cluster_id", 'label': "Cluster ID"}, + {'key': "n", 'label': "Cluster size"}, + ] + [ + {'key': k, 'label': v, 'type': 'stats'} + for k, v in AXIS_NAMES.items() + if k in df.columns + ] + [ + {'key': f"best{i}", 'label': f"Nr {i} best structure", + 'sortable': False, 'type': "structure" + } + for i in range(1, nr_best_columns + 1) + ] + + caption = '' + if df['cluster_id'].isin(['Other']).any(): + caption = ( + 'The "Other" cluster is not a real cluster it contains' + 'all structures that are not in the top 10 clusters.' + ) + + return f""" +
+
{caption}
+ + """ # noqa : E501 + + +def _generate_html_body( + figures: list[Union[Figure, pd.DataFrame]], + report_path: FilePath, + offline: bool = False, + ) -> str: + """ + Generate an HTML body section containing figures for an analysis report. + + Parameters + ---------- + figures : list + A list of figures to include in the HTML body. + Each figure can be either a string representing a table or a + plotly.graph_objects.Figure object. + offline : bool + If True, the HTML will be generated for offline use. + + Returns + ------- + body : str + The generated HTML body as a string. + """ + body = "" + table_index: int = 1 + fig_index: int = 1 + for figure in figures: + if isinstance(figure, pd.DataFrame): # tables + table_index += 1 + table_id = f"table{table_index}" + + is_unclustered = 'cluster_rank' not in figure + bundle_url = "https://cdn.jsdelivr.net/npm/@i-vresse/haddock3-ui@~0.3.0/dist/report.bundle.js" + if offline: + # copy the bundle to the run_dir folder + src = haddock_ui_path / 'report.bundle.js' + shutil.copyfile(str(src), "../data/ui/report.bundle.js") + bundle_url = "../../data/ui/report.bundle.js" + if is_unclustered: + inner_html = _generate_unclustered_table_html(table_id, figure, bundle_url) + else: + inner_html = _generate_clustered_table_html(table_id, figure, bundle_url) + else: # plots + inner_json = figure.to_json() + inner_html = create_html( + inner_json, + fig_index, + plotly_js_import=offline_js_manager(report_path, offline), + figure_height=figure.layout.height, + figure_width=figure.layout.width, + ) + fig_index += 1 # type: ignore + body += "
" # add a break between tables and plots + body += inner_html + body += "" + return body + + +def report_generator( + boxes: list[Figure], + scatters: list[Figure], + tables: list, + step: str, + directory: FilePath = ".", + offline: bool = False + ) -> None: + """ + Create a figure include plots and tables. + + The idea is to create a report.html file that includes all the plots and + tables generated by the command `analyse`. + + Parameters + ---------- + boxes : list + list of box plots generated by box_plot_handler + scatters: list + list of scatter plots generated by scatter_plot_handler + table: list + a list including tables generated by clt_table_handler + directory : Path + path to the output folder + offline: bool + If True, the HTML will be generated for offline use. + """ + figures = [tables] + # Combine scatters + figures.append( + report_plots_handler( + scatters, + shared_xaxes="rows", + shared_yaxes="columns", + ) + ) + # Combine boxes" + figures.append(report_plots_handler(boxes)) + + if offline: + Path('../data/ui').mkdir(parents=True, exist_ok=True) + # Write everything to a html file + report_path = Path(directory, "report.html") + html_report = _generate_html_report(step, figures, report_path, offline) + with open(report_path, "w", encoding="utf-8") as report: + report.write(html_report) + + +def heatmap_plotly( + matrix: NDFloat, + labels: Optional[dict] = None, + xlabels: Optional[list] = None, + ylabels: Optional[list] = None, + color_scale: str = 'Greys_r', + title: Optional[str] = None, + output_fname: Path = HEATMAP_DEFAULT_PATH, + offline: bool = False, + hovertemplate: Optional[str] = None, + customdata: Optional[list[list[Any]]] = None, + delineation_traces: Optional[list[dict[str, float]]] = None, + ) -> Path: + """Generate a `plotly heatmap` based on matrix content. + + Parameters + ---------- + matrix : NDFloat + The 2D matrix containing data to be shown. + labels : dict + Labels of the horizontal (x), vertical (y) and colorscale (color) axis. + xlabels : list + List of columns names. + ylabels : list + List of row names. + color_scale : str + Color scale to use. + title : str + Title of the figure. + output_fname : Path + Path to the output filename to generate. + hovertemplate: Optional[str] + Custrom string used to format data for hover annotation in plotly. + customdata: Optional[list[list[list[int]]]] + A matrix of cluster ids, used for extra hover annotation in plotly. + delineation_traces: Optional[list[dict[str, float]]] + A list of dict enabling to draw lines separating cluster ids. + + Return + ------ + output_fname : Path + Path to the generated filename + """ + # Generate heatmap trace + fig = px.imshow( + matrix, + labels=labels, + x=xlabels, + y=ylabels, + color_continuous_scale=color_scale, + title=title, + ) + # Place X axis on top + fig.update_xaxes(side="top") + fig.update_traces( + hovertemplate=hovertemplate, + customdata=customdata, + ) + # Add delineation traces + if delineation_traces: + # Loop over lines + for trace in delineation_traces: + # Draw them + fig.add_shape( + type="line", + line={"dash": "5px"}, + x0=trace["x0"], + x1=trace["x1"], + y0=trace["y0"], + y1=trace["y1"], + ) + + # Compute pixels + nb_entries = matrix.shape[0] + scaled_log = int(np.log(nb_entries)) * 200 + lower_bound = max(scaled_log, 1000) + uppder_bound = min(lower_bound, 2000) + # Set hight and width + height = uppder_bound + # Increment width for legend space + width = height + 70 + + # Save figure as html file + export_plotly_figure( + fig, + output_fname, + offline=offline, + figure_height=height, + figure_width=width, + ) + + return output_fname + + +def export_plotly_figure( + fig: Figure, + output_fname: Union[str, Path], + figure_height: int = 1000, + figure_width: int = 1000, + offline: bool = False, + ) -> None: + """Write a plotly figure. + + Parameters + ---------- + fig : Figure + The plotly Figure object + output_fname : Union[str, Path] + Where to write it + figure_height : int, optional + Height of the figure (in pixels), by default 1000 + figure_width : int, optional + Width of the figure (in pixels), by default 1000 + offline : bool, optional + If True add the plotly js library to the file, by default False + """ + # Detect output file extension + _suffix = Path(output_fname).suffix + suffix = _suffix[1:] + # Check corresponding function + if suffix == "html": + fig_to_html( + fig, + output_fname, + figure_height=figure_height, + figure_width=figure_width, + offline=offline, + ) + elif suffix in SUPPORTED_OUTPUT_FORMATS: + fig.write_image(output_fname) + + +def make_alascan_plot( + df: pd.DataFrame, + clt_id: int, + scan_res: str = "ALA", + offline: bool = False, + ) -> str: + """ + Make a plotly interactive plot. + + Score components are here **weighted** by their respective + contribution to the total score. + + Parameters + ---------- + df : pandas.DataFrame + DataFrame containing the results of the alanine scan. + clt_id : int + Cluster ID. + scan_res : str, optional + Residue name used for the scan, by default "ALA" + + Returns + ------- + html_output_filename : str + Name of the plot generated + """ + plot_name = f"scan_clt_{clt_id}" + log.info(f"Generating {scan_res} scanning plot {plot_name}") + + # create figure + width, height = 2000, 1000 + fig = go.Figure(layout={"width": width, "height": height}) + # add traces + # Delta HADDOCK score + fig.add_trace( + go.Bar( + x=df["full_resname"], + y=df["delta_score"], + error_y={"type": "data", "array": df["delta_score_std"]}, + name="delta_score", + ) + ) + # Delta VdW + fig.add_trace( + go.Bar( + x=df["full_resname"], + y=df["delta_vdw"], + error_y={"type": "data", "array": df["delta_vdw_std"]}, + name="delta_vdw", + ) + ) + # delta_elec is given its weight in the emscoring module + fig.add_trace( + go.Bar( + x=df["full_resname"], + y=0.2 * df["delta_elec"], + error_y={"type": "data", "array": df["delta_elec_std"]}, + name="delta_elec", + ) + ) + # Delta desolvation score + fig.add_trace( + go.Bar( + x=df["full_resname"], + y=df["delta_desolv"], + error_y={"type": "data", "array": df["delta_desolv_std"]}, + name="delta_desolv", + ) + ) + # prettifying layout + fig.update_layout( + title=f"{scan_res} scanning cluster {clt_id}", + xaxis={ + "title": {"text": "Residue Name", "font": {"size": 16}}, + "tickfont_size": 14, + "tick0": df["full_resname"], + # in case we want to show less residues + # "dtick": 10, + }, + yaxis={ + "title": { + "text": "Average Delta (WT - mutant)", + "font": {"size": 16} + }, + "tickfont_size": 14, + }, + legend={ + "x": 1.01, "y": 1.0, + "font_family": "Helvetica", + "font_size": 16 + }, + barmode="group", + bargap=0.05, + bargroupgap=0.05, + hovermode="x unified", + hoverlabel={"font_size": 16, "font_family": "Helvetica"}, + ) + for n in range(df.shape[0] - 1): + fig.add_vline(x=0.5 + n, line_color="gray", opacity=0.2) + + # save html + html_output_filename = f"{plot_name}.html" + export_plotly_figure( + fig, + html_output_filename, + figure_height=height, + figure_width=width, + offline=offline, + ) + return html_output_filename + + +def fig_to_html( + fig: Figure, + fpath: Union[str, Path], + plot_id: int = 1, + figure_height: int = 800, + figure_width: int = 1000, + offline: bool = False, + ) -> None: + """Workaround plotly html file generation. + + Parameters + ---------- + fig : Figure + A Figure object created by Plotly + fpath : Union[str, Path] + Where to write the content + json_content : str + plotly json content + plot_id : int + plot id to be used in the html content + figure_height : int + figure height (in pixels) + figure_width : int + figure width (in pixels) + offline : bool + If set to False, use the cdn url to obtain the javascript content + for the rendering. + """ + # Convert to json + json_content = fig.to_json() + # Create custom html file + html_content = create_html( + json_content, + plot_id=plot_id, + plotly_js_import=offline_js_manager(fpath, offline), + figure_height=figure_height, + figure_width=figure_width, + ) + # Write it + Path(fpath).write_text(html_content) + + +def offline_js_manager(fpath: FilePath, offline: bool) -> str: + """Build string to access plotly javascript content. + + Parameters + ---------- + fpath : FilePath + Path to the figure about to be written. + offline : bool + if True use the offline approach. + + Returns + ------- + plotly_js_import : str + HTML solution for the importation of the plotly javascript content. + """ + # Case when offline is true + if offline: + # Obtain directory where the figure should be written + fig_dir = Path(fpath).parent + # Set plotly js filepath + plotly_js_fpath = Path(fig_dir, "plotly_bundle.js") + # Check that this file do not already exists + if not plotly_js_fpath.exists(): + # Write the plotly java script content + plotly_js_fpath.write_text(get_plotlyjs()) + # Build HTML string + plotly_js_import = f'' + else: + # Use CDN url to obtain the script + plotly_js_import = f'' + return plotly_js_import + + +def make_traceback_plot(tr_subset, plot_filename, offline=False): + """ + Create a traceback barplot with the 40 best ranked models. + + Parameters + ---------- + tr_subset : pandas.DataFrame + DataFrame containing the top traceback results + plot_filename : Path + Path to the output filename to generate + """ + rank_columns = tr_subset.columns[tr_subset.columns.str.endswith("rank")] + # for each row, plot a bar with the values of the rank columns + fig = px.bar(tr_subset, x="Model", y=rank_columns) + # vertical legend on the right with legend name 'Modules' + fig.update_layout(legend_orientation="v", legend_title="Modules") + # legend should have bigger font size + fig.update_layout( + legend=dict( + title_font_size=24, + font_size=24, + ), + ) + # y axis title 'Sum of Ranks' + fig.update_layout(yaxis_title="Sum of Ranks", xaxis_title="Models") + # bigger axis labels + fig.update_layout( + yaxis=dict(title_font_size=30, tickfont_size=16), + xaxis=dict(title_font_size=30, tickfont_size=16), + ) + # bigger title + fig.update_layout( + title_text=f"Top ranked {tr_subset.shape[0]} Models", + title_font_size=30 + ) + fig_to_html( + fig, + plot_filename, + figure_height=1200, + figure_width=2000, + offline=offline, + ) + return plot_filename diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libprodigy.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libprodigy.py new file mode 100644 index 0000000000000000000000000000000000000000..95d8e2756f46980c0fe5b719630fa9894c6d8817 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libprodigy.py @@ -0,0 +1,176 @@ +"""Set of functionalities to run prodigy.""" + +import logging +from abc import ABC, abstractmethod + +import numpy as np + +from haddock import log +from haddock.core.exceptions import ModuleError +from haddock.core.typing import FilePath, Optional, ParamDict +from haddock.libs.libontology import PDBFile + + +# Define conversion constants +R_GAS_CONST = 8.31446261815324 # (J x mol−1 x K−1) +CALS_TO_JOULES = 4.184 +KELVIN_TO_CELCIUS = 273.15 + + +class CheckInstall: + """Verify that installation of prodigy is ok.""" + + def __init__(self): + """Verify that installation of prodigy is ok. + + Raises + ------ + ModuleError + Raised when prodigy libraries could not be loaded. + """ + try: + self.import_prodigy_libs() + except ModuleNotFoundError: + raise ModuleError( + "Issue detected with the installation of Prodigy. " + "Consider installing it with: " + "pip install prodigy-prot prodigy-lig" + ) + + @staticmethod + def import_prodigy_libs() -> None: + """Import prodigy prot and lig libraries.""" + import prodigy_prot # noqa : F401 + import prodigy_lig # noqa : F401 + return None + + +class ProdigyWorker(ABC): + """Prodigy Worker class.""" + + def __init__(self, model: FilePath, params: ParamDict) -> None: + # Use by both prodigy -prot and -lig + self.model = model + self.topKd = params["to_pkd"] + self.temperature = params["temperature"] + self.dist_cutoff = params["distance_cutoff"] + # Output values + self.score: Optional[float] = None + self.error: Optional[Exception] = None + + def _run(self) -> None: + """Evaluate complex and compute score.""" + # Patching the logging to not print everything on screen + logging.getLogger("Prodigy").setLevel(logging.CRITICAL) + # Running the predictions + self.score = self.pkd_converter(self.evaluate_complex()) + + def run(self) -> None: + """Execute the _run method.""" + try: + self._run() + except ModuleError as error: + self.error = error + + def pkd_converter(self, deltaG: float) -> float: + """Decide if deltaG must be converted to pKd. + + Parameters + ---------- + deltaG : float + Input DeltaG value + + Returns + ------- + score : float + The converted DeltaG to pKd if self.topKd is true, + else the input DeltaG. + """ + if self.topKd: + score = self.deltaG_to_pKd( + deltaG, + kelvins=self.temperature + KELVIN_TO_CELCIUS, + ) + else: + score = deltaG + return round(score, 3) + + @staticmethod + def deltaG_to_pKd(deltaG: float, kelvins: float = 298.3) -> float: + """Convert a deltaG (in Kcal/mol) to pKd. + + Parameters + ---------- + deltaG : float + DeltaG value (in Kcal/mol) + kelvins : float, optional + Temperature at which to perform the conversion. + By default 298.3 (25 degrees Celcius) + + Returns + ------- + pKd : float + The corresponding pKd value at given temperature. + """ + # Convert Kcals to joules + deltaG_joules = deltaG * CALS_TO_JOULES * 1000 + # Use formula + Kd = np.exp(-deltaG_joules / (R_GAS_CONST * kelvins)) + # Convert to pKd + _pKd = np.log10(Kd) + # Reduce number of decimals + pKd = round(_pKd, 2) + return -pKd + + @abstractmethod + def evaluate_complex(self) -> float: + """Logic to evaluate a complex using prodigy.""" + pass + + +class ModelScore: + """Simple class for holding score for a model.""" + + def __init__(self, model_index: int) -> None: + """Initiate models scores.""" + self.index = model_index + self.score = None + self.error = None + + +class ProdigyBaseJob(ABC): + """Managing the computation of prodigy scores within haddock3.""" + + def __init__( + self, + model: PDBFile, + params: ParamDict, + index: int = 1, + ) -> None: + """Initiate a worker.""" + self.score = ModelScore(index) + worker = self.get_worker() + self.worker = worker(model.rel_path, params) + + def _run(self) -> ModelScore: + """Run the worker and retrieve output values.""" + try: + self.worker.run() + except Exception as e: + log.error(e) + self.worker.error = str(e) + self.score.error = str(e) + else: + self.score.score = self.worker.score + self.score.error = self.worker.error + return self.score + + def run(self) -> ModelScore: + """Execute the _run method.""" + return self._run() + + @staticmethod + @abstractmethod + def get_worker() -> object: + """Return the appropriate worker.""" + pass diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/librestraints.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/librestraints.py new file mode 100644 index 0000000000000000000000000000000000000000..20cc6ef0f0b774266ea111bb84dd29e004849536 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/librestraints.py @@ -0,0 +1,856 @@ +from pathlib import Path +import logging +import itertools +import re +import random +import sys +import os +from typing import Generator + +from Bio.PDB import PDBParser, NeighborSearch +from freesasa import Classifier, structureFromBioPDB, calc + +# Scaling factors for relative ASA +# Calculated using extended ALA-X-ALA peptides +# Taken from NACCESS +REL_ASA = { + 'total': + { + 'ALA': 107.95, + 'CYS': 134.28, + 'ASP': 140.39, + 'GLU': 172.25, + 'PHE': 199.48, + 'GLY': 80.10, + 'HIS': 182.88, + 'ILE': 175.12, + 'LYS': 200.81, + 'LEU': 178.63, + 'MET': 194.15, + 'ASN': 143.94, + 'PRO': 136.13, + 'GLN': 178.50, + 'ARG': 238.76, + 'SER': 116.50, + 'THR': 139.27, + 'VAL': 151.44, + 'TRP': 249.36, + 'TYR': 212.76, + 'ASH': 140.39, + 'DDZ': 107.95, + 'GLH': 172.25, + 'CYM': 134.28, + 'CSP': 134.28, + 'CYF': 134.28, + 'CYC': 134.28, + 'CFE': 134.28, + 'NEP': 182.88, + 'ALY': 200.81, + 'MLZ': 200.81, + 'MLY': 200.81, + 'M3L': 200.81, + 'HYP': 136.13, + 'SEP': 116.50, + 'TOP': 139.27, + 'TYP': 212.76, + 'PTR': 212.76, + 'TYS': 212.76, + 'PNS': 116.50, + }, + 'bb': + { + 'ALA': 38.54, + 'CYS': 37.53, + 'ASP': 37.70, + 'GLU': 37.51, + 'PHE': 35.37, + 'GLY': 47.77, + 'HIS': 35.80, + 'ILE': 37.16, + 'LYS': 37.51, + 'LEU': 37.51, + 'MET': 37.51, + 'ASN': 37.70, + 'PRO': 16.23, + 'GLN': 37.51, + 'ARG': 37.51, + 'SER': 38.40, + 'THR': 37.57, + 'VAL': 37.16, + 'TRP': 38.10, + 'TYR': 35.38, + 'ASH': 37.70, + 'DDZ': 38.54, + 'GLH': 37.51, + 'CYM': 37.53, + 'CYC': 37.53, + 'CSP': 37.53, + 'CYF': 37.53, + 'CFE': 37.53, + 'NEP': 35.80, + 'ALY': 37.51, + 'MLZ': 37.51, + 'MLY': 37.51, + 'M3L': 37.51, + 'HYP': 16.23, + 'SEP': 38.40, + 'TOP': 37.57, + 'TYP': 35.38, + 'PTR': 35.38, + 'TYS': 35.38, + 'PNS': 38.40, + }, + 'sc': + { + 'ALA': 69.41, + 'CYS': 96.75, + 'ASP': 102.69, + 'GLU': 134.74, + 'PHE': 164.11, + 'GLY': 32.33, + 'HIS': 147.08, + 'ILE': 137.96, + 'LYS': 163.30, + 'LEU': 141.12, + 'MET': 156.64, + 'ASN': 106.24, + 'PRO': 119.90, + 'GLN': 140.99, + 'ARG': 201.25, + 'SER': 78.11, + 'THR': 101.70, + 'VAL': 114.28, + 'TRP': 211.26, + 'TYR': 177.38, + 'ASH': 102.69, + 'DDZ': 69.41, + 'GLH': 134.74, + 'CYM': 96.75, + 'CYC': 96.75, + 'CSP': 96.75, + 'CYF': 96.75, + 'CFE': 96.75, + 'NEP': 147.08, + 'ALY': 163.30, + 'MLZ': 163.30, + 'MLY': 163.30, + 'M3L': 163.30, + 'HYP': 119.90, + 'SEP': 78.11, + 'TOP': 101.70, + 'TYP': 177.38, + 'PTR': 177.38, + 'TYS': 177.38, + 'PNS': 78.11, + } + } +DEFAULT_PROBE_RADIUS = 1.4 + +def get_surface_resids(structure, cutoff=15): + """ + Calls freesasa using its Python API and returns + per-residue accessibilities. + """ + asa_data, rsa_data, rel_main_chain, rel_side_chain = {}, {}, {}, {} + _rsa = REL_ASA['total'] + _rsa_bb = REL_ASA['bb'] + _rsa_sc = REL_ASA['sc'] + + #classifier = Classifier(config_path) + classifier = Classifier() + + struct = structureFromBioPDB(structure, classifier, ) + result = calc(struct) + + # iterate over all atoms to get SASA and residue name + for idx in range(struct.nAtoms()): + atname = struct.atomName(idx).strip() + resname = struct.residueName(idx) + resid = int(struct.residueNumber(idx)) + chain = struct.chainLabel(idx) + at_uid = (chain, resname, resid, atname) + res_uid = (chain, resname, resid) + + asa = result.atomArea(idx) + asa_data[at_uid] = asa + # add asa to residue + rsa_data[res_uid] = rsa_data.get(res_uid, 0) + asa + + if atname in ('C', 'N', 'O'): + rel_main_chain[res_uid] = rel_main_chain.get(res_uid, 0) + asa + else: + rel_side_chain[res_uid] = rel_side_chain.get(res_uid, 0) + asa + + # convert total asa ro relative asa + rsa_data.update((res_uid, asa / _rsa[res_uid[1]]) for res_uid, asa in rsa_data.items()) + rel_main_chain.update((res_uid, asa / _rsa_bb[res_uid[1]] * 100) for res_uid, asa in rel_main_chain.items()) + rel_side_chain.update((res_uid, asa / _rsa_sc[res_uid[1]] * 100) for res_uid, asa in rel_side_chain.items()) + + # We format to fit the pipeline + resid_access = {} + for res_uid, access in rel_main_chain.items(): + resid_access[res_uid[2]] = {'side_chain_rel': rel_side_chain.get(res_uid), 'main_chain_rel': access} + surface_resids = [r for r, v in resid_access.items() if v['side_chain_rel'] >= cutoff or + v['main_chain_rel'] >= cutoff] + return surface_resids + + +def parse_actpass_file(actpass_file): + """Parse actpass file + + Parameters + ---------- + actpass_file: str or Path + path to actpass_file + + Returns + ------- + active: list + list of active residues + passive: list + list of passive residues + """ + + if Path(actpass_file).exists() is False: + raise Exception(f"actpass file {actpass_file} does not exist.") + + lines = open(actpass_file, "r").readlines() + nlines = len(lines) + if nlines != 2: + raise Exception(f"actpass file {actpass_file} does not have two lines (counted {nlines})") + active, passive = [[int(x) for x in line.split()] for line in lines] + return active, passive + + +def active_passive_to_ambig(active1, passive1, active2, passive2, segid1='A', segid2='B'): + """Convert active and passive residues to Ambiguous Interaction Restraints + + Parameters + ---------- + active1 : list + List of active residue numbers of the first segid + + passive1 : list + List of passive residue numbers of the first segid + + passive2 : list + List of passive residue numbers of the second segid + + active2 : list + List of active residue numbers of the second segid + + active2 : list + List of passive residue numbers of the second segid + + segid1 : string + Segid to use for the first model + + segid2 : string + Segid to use for the second model + + """ + + all1 = active1 + passive1 + all2 = active2 + passive2 + + for resi1 in active1: + print('assign (resi {:d} and segid {:s})'.format(resi1, segid1)) + print('(') + c = 0 + for resi2 in all2: + print(' (resi {:d} and segid {:s})'.format(resi2, segid2)) + c += 1 + if c != len(all2): + print(' or') + + print(') 2.0 2.0 0.0\n') + + for resi2 in active2: + print('assign (resi {:d} and segid {:s})'.format(resi2, segid2)) + print('(') + c = 0 + for resi1 in all1: + print(' (resi {:d} and segid {:s})'.format(resi1, segid1)) + c += 1 + if c != len(all1): + print(' or') + + print(') 2.0 2.0 0.0\n') + + +# Functions/Methods + +def calc_euclidean(i, j): + return ((j[0]-i[0])**2 + (j[1]-i[1])**2 + (j[2]-i[2])**2)**0.5 + + +def read_structure(pdbf, exclude=None): + """ + Reads a PDB file and returns a list of parsed atoms + """ + _atoms = {'CA', 'P'} # Alpha-Carbon (Prot), Backbone Phosphorous (DNA) + _altloc = {' ', 'A'} + + if not exclude: + exclude = set() + else: + exclude = set(exclude) + + res_list = [] + with open(pdbf, 'r') as pdb_handle: + for line in pdb_handle: + field = line[0:4] + if field != 'ATOM': + continue + + aname = line[12:16].strip() + chain = line[21] if line[21].strip() else line[72:76].strip() # chain ID or segID + if chain not in exclude and aname in _atoms and line[16] in _altloc: + resi = int(line[22:26]) + coords = (float(line[30:38]), float(line[38:46]), float(line[46:54])) + res_list.append((chain, resi, aname, coords)) + + if not res_list: + logging.critical('[!] PDB File seems empty or no CA/P atoms found: {0}'.format(pdbf)) + sys.exit(1) + + return res_list + + +def get_bodies(atom_lst, prot_threshold=4.0, dna_threshold=7.5): + """ + Determines gaps in an atom list following simple distance based criteria. + Returns continuous fragments. + """ + + bodies = [] + + threshold = {'CA': prot_threshold, 'P': dna_threshold} + + body_start = 0 + i = None + for i, atom in enumerate(atom_lst[1:], start=1): + p_atom = atom_lst[i-1] + + chain, resi, aname, xyz = atom + p_chain, p_resi, p_aname, p_xyz = p_atom + + if (chain == p_chain) and (aname == p_aname): # Internal Gap + d_xyz = calc_euclidean(xyz, p_xyz) + if d_xyz >= threshold[aname]: + logging.debug('[+++] (Internal) Body: {0}:{1}'.format(body_start, i-1)) + bodies.append((body_start, i-1)) + body_start = i # Set new beginning + + elif (chain != p_chain) or (aname != p_aname): # Different molecules/types + logging.debug('[+++] Body: {0}:{1}'.format(body_start, i-1)) + bodies.append((body_start, i-1)) + body_start = i # Set new beginning + + if not bodies: # Single continuous molecule + bodies.append((0, len(atom_lst))) + else: + logging.debug('[+++] Body: {0}:{1}'.format(body_start, i)) + bodies.append((body_start, i)) # Last body + + logging.info('[++] Found {0} bodies'.format(len(bodies))) + + return bodies + + +def build_restraints(bodies): + """ + Generates distance restraints to maintain the relative + orientation of the different bodies during the simulations. + + Generates two unique restraints per pair of bodies. + + Each restraint is created using two random atoms on each body + and using their exact euclidean distance as target distance. + """ + + def pick_residues(body, max_trials=10): + # Pick two random residues in each body + # Make sure they are far apart from each other + n_trials = 0 + while 1: + try: + res_i, res_ii = random.sample(body, 2) + except ValueError: + # Likely, sample size is 1 + logging.warning('[!] One-sized body found. This may lead to problems..') + return body[0], body[0] + + logging.debug('[+++] Trial {0}: {1} & {2}'.format(n_trials, res_i, res_ii)) + if abs(res_i - res_ii) > 3: + logging.info('[++] Picked residues {0} & {1}'.format(res_i, res_ii)) + return res_i, res_ii + n_trials += 1 + if n_trials == max_trials: + msg = '[!] Could not pick two unique distant residues in body after {0} tries' + logging.info(msg.format(max_trials)) + return res_i, res_ii + + restraints = [] + + n_bodies = range(len(bodies)) + combinations = itertools.combinations(n_bodies, 2) + + for pair_bodies in combinations: + body_i, body_j = pair_bodies + logging.debug('[+++] Restraining body {0} to body {1}'.format(body_i, body_j)) + + st_body_i, en_body_i = bodies[body_i] + st_body_j, en_body_j = bodies[body_j] + res_i, res_ii = pick_residues(range(st_body_i, en_body_i+1)) + res_j, res_jj = pick_residues(range(st_body_j, en_body_j+1)) + + logging.info('[++] Created restraint: {0}:{1} <--> {2}:{3}'.format(body_i, res_i, body_j, res_j)) + restraints.append((res_i, res_j)) + logging.info('[++] Created restraint: {0}:{1} <--> {2}:{3}'.format(body_i, res_ii, body_j, res_jj)) + restraints.append((res_ii, res_jj)) + + return restraints + + +def generate_tbl(atom_lst, restraints): + """ + Makes a list of TBL-formatted restraints. + + Parameters + ---------- + atom_lst : list + List of atoms in the form (chain, resi, aname, coords) + + restraints : list + List of restraints in the form (res_i, res_j) + """ + + for r in restraints: + i, j = r + atom_i, atom_j = atom_lst[i], atom_lst[j] + dist_ij = calc_euclidean(atom_i[3], atom_j[3]) + + tbl = "assign (segid {0[0]} and resi {0[1]} and name {0[2]}) ".format(atom_i) + tbl += "(segid {0[0]} and resi {0[1]} and name {0[2]}) ".format(atom_j) + tbl += "{0:3.3f} 0.0 0.0".format(dist_ij) + print(tbl) + + +def check_parenthesis(file): + open_parenthesis = re.compile('[(]') + close_parenthesis = re.compile('[)]') + quotation_marks = re.compile('[\"]') + opened = 0 + closed = 0 + quote = 0 + for _match in open_parenthesis.finditer(file): + opened += 1 + for _match in close_parenthesis.finditer(file): + closed += 1 + for _match in quotation_marks.finditer(file): + quote += 1 + if opened != closed: + raise Exception("Problem with TBL file parentheses ({:d} opening for {:d} " + "closing parentheses)".format(opened, closed)) + if quote % 2 != 0: + raise Exception("Problem with TBL file, odd number of quotation marks " + "({:d} quotation marks)".format(quote)) + + +def validate_tbldata(restraints, pcs=False): + # List of selection keywords + selectors = ('name', 'resn', 'atom', 'resi', 'attr', 'segi', 'chem', 'id', + 'byres', 'not') + connectors = ('and', 'or', 'not', 'byres') + output = "" + parentmatch = re.compile('[()]') + # Global mode is activated outside any assign statement + mode = "global" + # Remove any carriage return/new line caracters + lines = restraints.replace('\r', '').split("\n") + # Line number + lnr = 0 + # Temporary line storage for future output + tmp_output = None + tmp = None + level = None + s = None + selections = None + postselections = None + numbers = None + types = None + lastassign = None + for line in lines: + lnr += 1 + # Take everything which is before putative "!" (comment) caracter + if line.find("!") > -1: + line = line[:line.find("!")] + # Remove whitespaces and merge with previous line if in OR statement + # for AIR restraints + if mode != "format": + line = line.strip() + else: + line = tmp + line.strip() + mode = "postassign" + # End of line + if not len(line): + continue + # Check if all "" are closed + if line.count('"') % 2 > 0: + raise Exception('Unclosed " at line {:d} for line: {}'.format(lnr, line)) + if mode in ("global", "postglobal"): + # Start of an assign statement + if line.lower().startswith("assi"): + if mode == "postglobal": + output += "\n!\n" + output += tmp_output + mode = "assign" + selections = [] + # assign is the only character of the line,check following lines + if line.find("(") == -1: + continue + # Reset temporary buffer + tmp_output = None + # Check for "OR" restraint + elif mode == "postglobal" and line.lower().startswith("or"): + mode = "postassign" + selections = [] + line = line[len("or"):] + # Case where "OR" statement is the only one on the line + # (rest of selection at the next line) + if line == "": + continue + # We are not treating an assign params (postglobal) or at the + # end (global) and no "OR" restraint is present -> ERROR + else: + raise Exception("Invalid TBL file: Unknown statement (line {:d}): {}".format(lnr, line)) + # We check if the selection is made over two lines + # (thanks to "segid" keyword) + if mode == "postassign": + if line.count("segid") == 1: + mode = "format" + tmp = line + continue + + matched = True + while matched: + matched = False + # We are looking for parenthesis as start of the selections + if mode in ("assign", "postassign"): + # Ambiguous restraint for two different pairs of atoms + # (ex: THR 1 B <-> ALA 2 A OR GLY 2 B <-> ASP 10 A ) + pos = line.find("(") + if pos != -1: + matched = True + line = line[pos + 1:] + # We look for an "OR" selection + if mode == "postassign": + mode = "postsel" + else: + mode = "sel" + lastassign = lnr + s = "" + level = 1 + # Get the structural selections + if mode in ("sel", "postsel"): + # Detect opening and closing parenthesis + for match in parentmatch.finditer(line): + if match.group() == "(": + level += 1 + else: + level -= 1 + # End of the parenthesis content + if level == 0: + if mode == "postsel": + mode = "postassign" + else: + mode = "assign" + matched = True + # print l[:match.start()] + # Get back the parentheses content and check + # for selection keywords + idx_connectors = [] + sel = line[:match.start()] + # We can directly check for the 1st keyword presence + if len(sel) > 0: + syntax_ok = False + for s in selectors: + if sel.strip().startswith(s): + syntax_ok = True + if not syntax_ok and not \ + sel.strip().startswith('byres') and not \ + sel.strip().startswith('not'): + raise Exception("1) Missing or wrong keyword in-term {} (stopped at line {:d})". + format(sel, lnr)) + # Get indexes of connectors (AND, OR, etc.) + for c in connectors: + idx_connectors.append([m.start()+len(c) for m in + re.finditer(c, sel)]) + # Flatten the list + tmp_list = [item for sublist in idx_connectors for + item in sublist] + idx_connectors = tmp_list + # Check that each connector is followed by a keyword + for i in idx_connectors: + new_sel = sel[i:].strip().strip("(").strip() + if len(new_sel) > 0: + syntax_ok = False + for s in selectors: + if new_sel.startswith(s): + syntax_ok = True + break + if not syntax_ok: + raise Exception("Missing or wrong keyword in-term {} (stopped at line {:d})". + format(sel, lnr)) + s += sel + selections.append(s) + s = None + # Get the rest of the line + line = line[match.end():] + # Go to the process of the selection + break + # No parenthesis, we get the whole line + if level > 0: + if line != "": + s += line + "\n\t" + else: + # To avoid multiple blank lines + if repr(s) == "''": + # print repr(l), repr(s), selections + s += "\n\t" + # TBD + if mode in ("sel", "postsel"): + continue + # Selection parsed for "OR" line + if mode == "postassign": + if len(selections) != postselections: + raise Exception("Invalid TBL file: wrong number of selections: in-term {:d}, cross-term {:d} " + "(stopped at line {:d})".format(postselections, len(selections), lnr)) + tmp_output += " or" + for s in selections: + tmp_output += "\t({})\n".format(s) + # We let the possibility for other "OR" + mode = "postglobal" + if len(line) == 0: + continue + # Define the distance restraints type to adapt the parsing + if mode == "assign": + mode = "numbers" + if pcs: + if len(selections) == 5: + types = (" {:.3f}", " {:.3f}") + else: + raise Exception("Invalid TBL file: wrong number of selections (must be 5 in PCS mode)") + else: + if len(selections) == 2: + types = (" {:.3f}", " {:.3f}", " {:.3f}") + elif len(selections) == 4: + types = (" {:.3f}", " {:.3f}", " {:.3f}", " {:d}") + elif len(selections) == 5: + raise Exception("Invalid TBL file: wrong number of selections (can be 5 only in PCS mode)") + elif len(selections) == 6: + types = (" {:.3f}", " {:.3f}") + else: + check_parenthesis(restraints) + raise Exception("Invalid TBL file: wrong number of selections (must be 2, 4 or 6)") + postselections = len(selections) + numbers = [] + # Distance restraints parsing + if mode == "numbers": + ll = line.split() + for num in ll: + if len(numbers) == len(types): + break + numbers.append(float(num)) + if len(numbers) == len(types): + tmp_output = "assign " + for s in selections: + tmp_output += "\t({})\n".format(s) + tmp_output = tmp_output[:-len("\n")] + for n, t in zip(numbers, types): + tmp_output += t.format(n) + tmp_output += "\n" + mode = "postglobal" + # "OR" lines have been parsed, we store the selections + if mode == "postglobal": + output += "!\n" + output += tmp_output + mode = "global" + # If mode is not back to global, something has not been processed properly + if mode != "global": + raise Exception("Invalid TBL file: Malformed ASSIGN statement (line {:d}), use --quick to check for " + "putative syntax issues".format(lastassign)) + if not len(output.strip()): + raise Exception("Invalid or empty TBL file") + + # Remove extra lines before each assign statement + output = output.replace("\n\n", "\n") + # Remove extra line at the beginning of the file + if output.startswith("\n"): + output = output.replace("\n", "", 1) + return output + +def passive_from_active_raw(structure, active, chain_id=None, surface=None, radius=6.5): + """Get the passive residues. + + Parameters + ---------- + + structure : str + path to the PDB file + + active : list + List of active residues + + chain_id : str + Chain ID + + surface : list + List of surface residues. + + radius : float + Radius from active residues + """ + + # Parse the PDB file + if Path(structure).exists(): + p = PDBParser(QUIET=True) + s = p.get_structure('pdb', structure) + else: + raise FileNotFoundError('File not found: {0}'.format(structure)) + + try: + if chain_id: + atom_list = [a for a in s[0][chain_id].get_atoms()] + else: + atom_list = [a for a in s[0].get_atoms()] + except KeyError as e: + raise KeyError('Chain {0} does not exist in the PDB file {1}, please enter a proper chain id'. + format(chain_id, structure)) from e + + act_atoms = [a.get_coord() for a in atom_list if a.parent.id[1] in active] + + try: + if not surface: + surface = get_surface_resids(s) + except Exception as e: + raise Exception("There was an error while calculating surface residues: {}".format(e)) from e + + ns = NeighborSearch(atom_list) + neighbors = [] + for a in act_atoms: + neighbors.append(ns.search(a, radius, "R")) # HADDOCK used 6.5A as default + + passive_list = set() + for n in neighbors: + for r in n: + passive_list.add(r.id[1]) + tmp = passive_list & set(surface) + passive_list = tmp - set(active) + return sorted(passive_list) + + +def get_restraint_subset( + tblfile: str, + rd_removed_ratio: float, + seed: int = 917, + ) -> Generator[list[str], None, None]: + """Generator of restraints subsets. + + Parameters + ---------- + tblfile : str + Path to a AIR.tbl file containing restraints. + rd_removed_ratio : float + Ratio of the number of restraints to remove. + seed : int, optional + Pseudo-random seed, by default 917 + + Yields + ------ + subset_restraints: list[str] + A subset of the input restraints. + + Raises + ------ + ValueError + When random removal ratio is too high and no restraints a kept. + ValueError + When random removal ratio is too low and all restraints a kept. + """ + # Extract all restraints + input_restraints = extract_restraint_entries(tblfile) + # Compute number of restraints to be placed in each file + _nb_rest_per_file = (1 - rd_removed_ratio) * len(input_restraints) + nb_rest_per_file = int(round(_nb_rest_per_file, 0)) + # Indicies + rest_indices = list(range(len(input_restraints))) + # Validate that it should result in something OK + if nb_rest_per_file == len(input_restraints): + raise ValueError(f"Error: Subset of restraints equal to number of restraints") + elif nb_rest_per_file == 0: + raise ValueError(f"Error: Subset of restraints equal to 0") + + try: + # Forever loop + while True: + # Reset seed + random.seed(seed) + # Obtain a subset of restraints indices + subset_restraints_ids = random.sample( + rest_indices, + nb_rest_per_file, + ) + # Get subset of restraints + subset_restraints = [ + f"! restraint id {i + 1}{os.linesep}{input_restraints[i]}" + for i in subset_restraints_ids + ] + # Return / Yield them + yield subset_restraints + # Increase seed + seed += 1 + finally: + pass + + +def extract_restraint_entries(tbl_filepath: str) -> list[str]: + """Read and extract restraints in a AIR.tbl file. + + Parameters + ---------- + tbl_filepath : str + Path to a AIR.tbl file containing restraints. + + Returns + ------- + restraints: list[str] + Loaded restraints as a list. + """ + restraints: list[str] = [] + assi: str = "" + # Open the file + with open(tbl_filepath, "r") as fin: + # Loop over lines + for _ in fin: + # Chekf if the line is starting with `assi` == new restraint def + if _.strip().lower().startswith("assi"): + # See if previous assign statement is not empty + if assi != "": + # Hold this one + restraints.append(assi) + # Reset the assign statement with current line + assi = _ + # Skip lines with comments + elif _.strip().startswith("!"): + continue + else: + # Add line to current assign statement + if assi != "": + assi += _ + # Hold last assign statement + if assi != "": + restraints.append(assi) + # Return loaded restraints as a list of string + return restraints diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libstructure.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libstructure.py new file mode 100644 index 0000000000000000000000000000000000000000..9f816443671bc82cc50854d0f145281b8b283f90 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libstructure.py @@ -0,0 +1,44 @@ +"""Molecular data structures.""" +from functools import partial +from pathlib import Path +from typing import Any, Iterable, Optional + + +class Molecule: + """ + Input molecule, usually a PDB file. + + Parameters + ---------- + file_name : :external:py:class:`pathlib.Path` + The path to the molecule file. + + segid : int, optional + The ID of the segment. Defaults to ``None``. + + no_parent : boolean + Whether to add the parent path ``..`` to the + :py:attr:`haddock.libs.libstructure.Molecule.with_parent`. + When set to true, the ``with_parent`` attribute returns the same + as ``file_name``. + """ + + def __init__(self, + file_name: Path, + segid: Optional[int] = None, + no_parent: bool = False) -> None: + # the rest of the code is too dependent on the Path API + assert isinstance(file_name, Path), \ + f"`file_name` must be pathlib.Path: {type(file_name)} given" + + self.file_name = file_name + self.segid = segid + if no_parent: + self.with_parent = file_name + else: + self.with_parent = Path('..', file_name) + + +def make_molecules(paths: Iterable[Path], **kwargs: Any) -> list[Molecule]: + """Get input molecules from the data stream.""" + return list(map(partial(Molecule, **kwargs), paths)) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libsubprocess.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libsubprocess.py new file mode 100644 index 0000000000000000000000000000000000000000..d66fc0022eedd88e9dfb5af63de4b2f71642acb0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libsubprocess.py @@ -0,0 +1,275 @@ +"""Run subprocess jobs.""" + +import os +import shlex +import subprocess +from contextlib import suppress +from pathlib import Path + +from haddock.core.defaults import cns_exec as global_cns_exec +from haddock.core.exceptions import ( + CNSRunningError, + JobRunningError, + KnownCNSError, + ) +from haddock.core.typing import Any, FilePath, Optional, ParamDict +from haddock.gear.known_cns_errors import KNOWN_ERRORS as KNOWN_CNS_ERRORS +from haddock.libs.libio import gzip_files + + +class BaseJob: + """Base class for a subprocess job.""" + + def __init__( + self, input_: Path, output: Path, executable: Path, *args: Any + ) -> None: + self.input = input_ + self.output = output + self.executable = executable + self.args = args + self.cmd: str + + def run(self) -> bytes: + """Execute job in subprocess.""" + self.make_cmd() + + with open(self.output, "w") as outf: + p = subprocess.Popen( + shlex.split(self.cmd), + stdout=outf, + close_fds=True, + ) + out, error = p.communicate() + + p.kill() + + if error: + raise JobRunningError(error) + + return out + + def make_cmd(self) -> None: + """Execute subprocess job.""" + raise NotImplementedError() + + +class Job(BaseJob): + """ + Instantiate a standard job. + + Runs with the following scheme: + + $ cmd ARGS INPUT + """ + + def make_cmd(self) -> None: + """Execute subprocess job.""" + self.cmd = " ".join( + [ + os.fspath(self.executable), + "".join(map(str, self.args)), # empty string if no args + os.fspath(self.input), + ] + ) + return + + +class JobInputFirst(BaseJob): + """ + Instantiate a subprocess job with inverted args and input. + + Runs with the following scheme, INPUT comes first: + + $ cmd INPUT ARGS + """ + + def make_cmd(self) -> None: + """Execute job in subprocess.""" + self.cmd = " ".join( + [ + os.fspath(self.executable), + os.fspath(self.input), + "".join(map(str, self.args)), # empty string if no args + ] + ) + return + + +class CNSJob: + """A CNS job script.""" + + def __init__( + self, + input_file: FilePath, + output_file: Optional[FilePath] = None, + error_file: Optional[FilePath] = None, + envvars: Optional[ParamDict] = None, + cns_exec: Optional[FilePath] = None, + ) -> None: + """ + CNS subprocess. + + To execute the job, call the `.run()` method. + + Parameters + ---------- + input_file : str or pathlib.Path + The path to the .inp CNS file. + + output_file : str or pathlib.Path + The path to the .out CNS file, where the standard output + will be saved. + + envvars : dict + A dictionary containing the environment variables needed for + the CNSJob. These will be passed to subprocess.Popen.env + argument. + """ + self.input_file = input_file + self.output_file = output_file + self.error_file = error_file + self.envvars = envvars + self.cns_exec = cns_exec + + def __repr__(self) -> str: + _input_file = self.input_file + if isinstance(self.input_file, str): + _input_file = "IO Stream" + return ( + f"CNSJob({_input_file}, {self.output_file}, " + f"envvars={self.envvars}, cns_exec={self.cns_exec})" + ) + + def __str__(self) -> str: + return repr(self) + + @property + def envvars(self) -> ParamDict: + """CNS environment vars.""" + return self._envvars + + @envvars.setter + def envvars(self, envvars: Optional[ParamDict]) -> None: + """CNS environment vars.""" + self._envvars = envvars or {} + if not isinstance(self._envvars, dict): + raise ValueError("`envvars` must be a dictionary.") + + for k, v in self._envvars.items(): + if isinstance(v, Path): + self._envvars[k] = str(v) + + @property + def cns_exec(self) -> FilePath: + """CNS executable path.""" + return self._cns_exec + + @cns_exec.setter + def cns_exec(self, cns_exec_path: Optional[FilePath]) -> None: + if not cns_exec_path: + cns_exec_path = global_cns_exec # global cns_exec + + if not os.access(cns_exec_path, mode=os.X_OK): + raise ValueError( + f"{str(cns_exec_path)!r} binary file not found, " + "or is not executable." + ) + + self._cns_exec = cns_exec_path + + def run( + self, + compress_inp: bool = False, + compress_out: bool = True, + compress_seed: bool = False, + compress_err: bool = True, + ) -> bytes: + """ + Run this CNS job script. + + Parameters + ---------- + compress_inp : bool + Compress the *.inp file to '.gz' after the run. Defaults to + ``False``. + + compress_out : bool + Compress the *.out file to '.gz' after the run. Defaults to + ``True``. + + compress_seed : bool + Compress the *.seed file to '.gz' after the run. Defaults to + ``False``. + """ + + if isinstance(self.input_file, str): + p = subprocess.Popen( + self.cns_exec, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + close_fds=True, + env=self.envvars, + ) + out, error = p.communicate(input=self.input_file.encode()) + p.kill() + + elif isinstance(self.input_file, Path) and self.output_file is not None: + with open(self.input_file) as inp: + p = subprocess.Popen( + self.cns_exec, + stdin=inp, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + close_fds=True, + env=self.envvars, + ) + out, error = p.communicate() + p.kill() + # Write out file + with open(self.output_file, "wb+") as outf: + outf.write(out) + + if compress_inp: + gzip_files(self.input_file, remove_original=True) + + if compress_out: + gzip_files(self.output_file, remove_original=True) + + if compress_seed: + with suppress(FileNotFoundError): + gzip_files( + Path(Path(self.output_file).stem).with_suffix(".seed"), + remove_original=True, + ) + + # If undetected error or detect an error in the STDOUT + if error or self.contains_cns_stdout_error(out): + # Write .err file + with open(self.error_file, "wb+") as errf: + errf.write(out) + # Compress it + if compress_err: + gzip_files(self.error_file, remove_original=True) + if error: + raise CNSRunningError(error) + + # Return STDOUT + return out + + @staticmethod + def contains_cns_stdout_error(out: bytes) -> bool: + # Decode end of STDOUT + # Search in last 24000 characters (300 lines * 80 characters) + sout = out[-24000:].split(bytes(os.linesep, "utf-8")) + # Reverse loop on lines (read backward) + for bytes_line in reversed(sout): + line = bytes_line.decode("utf-8") + # This checks for an unknown CNS error + # triggered when CNS is about to crash due to internal error + if "^^^^^" in line: + return True + # Check if a known error is found + elif any([error in line for error in KNOWN_CNS_ERRORS.keys()]): + return True + return False diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libtimer.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libtimer.py new file mode 100644 index 0000000000000000000000000000000000000000..30b8ccb069e2542697ac46fb9389baa6abe9fca5 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libtimer.py @@ -0,0 +1,75 @@ +"""Tools related to timing functions.""" +from contextlib import contextmanager +from time import time +from typing import Generator + +from haddock import log + + +@contextmanager +def log_time(pre_msg: str) -> Generator[None, None, None]: + """ + Log the time taken to execute the code under the context. + + Examples + -------- + >>> with log_time("function took"): + do_something() + do_more() + + logged: "function tooked 10 minutes" + + Parameters + ---------- + pre_msg : str + String to log with appended time. + + See Also + -------- + :py:func:`convert_seconds_to_min_sec` + """ + start = time() + yield + end = time() + elapsed = convert_seconds_to_min_sec(end - start) + log.info(f"{pre_msg} {elapsed}") + + +def convert_seconds_to_min_sec(seconds: float) -> str: + """ + Convert seconds to min&sec. + + Examples + -------- + >>> convert_seconds_to_min_sec(60) + 1 minute + + >>> convert_seconds_to_min_sec(120) + 2 minutes and 0 seconds + + >>> convert_seconds_to_min_sec(179) + 2 minutes and 59 seconds + + Parameters + ---------- + seconds : int + The elapsed time in seconds. Seconds are round to integers. + + Returns + ------- + str + """ + seconds = int(round(seconds, 0)) + hours = seconds // 3600 + minutes = (seconds) // 60 % 60 + seconds = (seconds) % 60 + + if hours: + return f"{hours}h{minutes}m{seconds}s" + + if minutes: + s = "" if minutes == 1 else "s" + return f"{minutes} minute{s} and {seconds} seconds" + + s = "" if seconds == 1 else "s" + return f"{seconds} seconds" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libutil.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libutil.py new file mode 100644 index 0000000000000000000000000000000000000000..410cf89b0227b6abb43e68e54c7a26ec7ffff438 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libutil.py @@ -0,0 +1,526 @@ +"""General utilities.""" + +import collections.abc +import contextlib +import os +import platform +import re +import shutil +import subprocess +import sys +from copy import deepcopy +from functools import partial +from importlib.resources import files +from pathlib import Path + +import haddock +from haddock import EmptyPath, log +from haddock.core.exceptions import SetupError +from haddock.core.typing import ( + PT, + Any, + AnyT, + Callable, + Container, + FilePath, + FilePathT, + Generator, + Iterable, + Optional, + ParamDict, + ParamMap, + ParamMapT, + Union, +) +from haddock.gear.greetings import get_goodbye_help + +check_subprocess = partial( + subprocess.run, + shell=True, + check=True, + stdout=subprocess.DEVNULL, +) + + +def get_result_or_same_in_list( + function: Callable[[PT], AnyT], value: PT +) -> Union[AnyT, list[PT]]: + """ + Return the result if True or the value within a list. + + Applies `function` to `value` and returns its result if it evaluates + to True. Otherwise, return the value within a list. + + `function` should receive a single argument, the `value`. + """ + result = function(value) + return result if result else [value] + + +def make_list_if_string(item: Union[str, list[str]]) -> list[str]: + """Put `item` into a list.""" + if isinstance(item, str): + return [item] + return item + + +def transform_to_list( + item: Union[Iterable[AnyT], AnyT], +) -> Union[list[AnyT], tuple[AnyT, ...]]: + """ + Put `item` into a list if not a list already. + + If it is set, transforms the set into a list. + + If it is a dict, returns a list of the keys. + + If it is tuple, returns the tuple. + + If a list, returns the same. + + Everything else returns `item` inside a one element list. + """ + if isinstance(item, (set, dict)): + return list(item) + + if isinstance(item, (list, tuple)): + return item + + return [item] + + +def copy_files_to_dir(paths: Iterable[FilePath], directory: FilePath) -> None: + """ + Copy files to directory. + + Parameters + ---------- + paths : iterable of paths + Source files. + + directory : path + Where to copy files to. + """ + for path in paths: + shutil.copy(path, directory) + + +def remove_folder(folder: FilePath) -> None: + """ + Remove a folder if it exists. + + Parameters + ---------- + folder : str or Path + Path to folder to remove. + """ + if Path(folder).exists(): + log.warning(f"{folder} exists and it will be REMOVED!") + shutil.rmtree(folder) + + +def remove_dict_keys(d: ParamMap, keys: Container[str]) -> ParamDict: + """ + Remove `keys` from dictionary (`d`). + + Return + ------ + dict + A copy of `d` dictionary without the `keys`. + """ + return {k: deepcopy(v) for k, v in d.items() if k not in keys} + + +def cpu_count() -> int: + """Count number of available CPU for the process. + + User suggestion, by https://github.com/EricDeveaud + + Note: pid 0 == current process + + FIXME: from python3.13, better to use os.process_cpu_count() + + Returns + ------- + process_ncores : int + Number of cores allocated to the process pid. + """ + + def _cpu_count() -> int: + """Detect number of cores available. + + Returns + ------- + ncores : int + Maximum number of cores that can be used. + """ + try: + # Try to obtain the number of cpu allocated to the process + _process_ncores = os.sched_getaffinity(0) + if isinstance(_process_ncores, set): + ncores = len(_process_ncores) + else: + ncores = int(_process_ncores) + except AttributeError: + # If unsucessful, return the number cores detected in the machine + # Note: this can happen on MacOS, where the os.sched_getaffinity + # may not be defined/exist. + ncores = int(os.cpu_count()) + return ncores + + try: + process_ncores = int(os.process_cpu_count()) + except AttributeError: + process_ncores = _cpu_count() + return process_ncores + + +def parse_ncores( + n: Optional[Union[int, str]] = None, + njobs: Optional[int] = None, + max_cpus: Optional[bool] = None, +) -> int: + """ + Check the number of cores according to HADDOCK3 architecture. + + Parameters + ---------- + n : int or str + The desired number of cores. If `None` is given, returns the + maximum number of cores allowed, see `max_cpus`. + + njobs : int + The number of jobs to execute. Optional. The number of cores + will be compared to `njobs`. + + max_cpus : int + The maximum number of CPUs allowed. If not specified, defaults + to the available CPUs minus one. + + Raises + ------ + SetupError + If `n` is not positive or not convertable to `int`. + + Returns + ------- + int + A correct number of cores according to specifications. + """ + if max_cpus is None or max_cpus is False: + max_cpus = max(cpu_count() - 1, 1) # type: ignore + if max_cpus is True: + max_cpus = cpu_count() # type: ignore + elif not isinstance(max_cpus, int): + raise TypeError(f"`max_cpus` not of valid type: {type(max_cpus)}") + + if n is None: + return max_cpus + + try: + n = int(n) + except (TypeError, ValueError) as err: + _msg = f"`n` must be `int` or `int`-convertable `str`: {n!r} given." + raise SetupError(_msg) from err + + if n < 1: + _msg = f"`n` is not positive, this is not possible: {n!r}" + raise SetupError(_msg) + + if njobs is not None: + ncores = min(n, njobs, max_cpus) + log.info( + f"Selected {ncores} cores to process {njobs} jobs, with {max_cpus} " + "maximum available cores." + ) + return ncores + + log.debug(f"`njobs` not specified, evaluating initial value {n}...") + ncores = min(n, max_cpus) + log.debug(f"Selected {ncores} for a maximum of {max_cpus} CPUs") + return ncores + + +def non_negative_int( + n: Any, + exception: type[Exception] = ValueError, + emsg: str = "`n` do not satisfies", +) -> int: + """ + Transform `n` in int and returns if `compare` evaluates to True. + + Parameters + ---------- + n : int-convertable + Something that can be converted to int. + + exception : Exception + The Exception to raise in case `n` is not a positive integer. + + emsg : str + The error message to give to `exception`. May accept formatting + to pass `n`. + + Raises + ------ + ValueError, TypeError + If `n` cannot be converted to `int` + """ + try: + n1 = int(n) + if n1 >= 0: + return n1 + except Exception as e: + raise e + else: + # don't change to f-strings, .format has a purpose + raise exception(emsg.format(n)) + + +def recursive_dict_update(d: ParamMapT, u: ParamMap) -> ParamMapT: + """ + Update dictionary `d` according to `u` recursively. + + https://stackoverflow.com/questions/3232943 + + Returns + ------- + dict + A new dict object with updated key: values. The original dictionaries + are not modified. + """ + + def _recurse(d_: ParamMapT, u_: ParamMap) -> ParamMapT: + for k, v in u_.items(): + if isinstance(v, collections.abc.Mapping): + d_[k] = _recurse(d_.get(k, {}), v) + else: + d_[k] = deepcopy(v) # in case these are also lists + + return d_ + + new = deepcopy(d) + _recurse(new, u) + + return new + + +def get_number_from_path_stem(path: FilePath) -> int: + """ + Extract tail number from path. + + Examples + -------- + + >>> get_number_from_path_stem('src/file_1.pdb') + >>> 1 + + >>> get_number_from_path_stem('src/file_3.pdb') + >>> 3 + + >>> get_number_from_path_stem('file_1231.pdb') + >>> 1231 + + >>> get_number_from_path_stem('src/file11') + >>> 11 + + >>> get_number_from_path_stem('src/file_1234_1.pdb') + >>> 1 + + Parameters + ---------- + path : str or Path obj + The path to evaluate. + + Returns + ------- + int + The tail integer of the path. + """ + stem = Path(path).stem + number = re.findall(r"\d+", stem)[-1] + return int(number) + + +def sort_numbered_paths(*paths: FilePathT) -> list[FilePathT]: + """ + Sort input paths to tail number. + + If possible, sort criteria is provided by + :py:func:`get_number_from_path_stem`. + If paths do not have a numbered tag, sort paths alphabetically. + + Parameters + ---------- + *inputs : str or pathlib.Path + Paths to files. + + Returns + ------- + list + The sorted pathlist. The original types are not modified. If + strings are given, strings are returns, if Paths are given + paths are returned. + """ + try: + return sorted(paths, key=get_number_from_path_stem) + except TypeError as err: + log.exception(err) + emsg = ( + "Mind the packing *argument, input should be strings or Paths, not a list." + ) + raise TypeError(emsg) + except IndexError: + return sorted(paths, key=lambda x: Path(x).stem) + + +@contextlib.contextmanager +def log_error_and_exit() -> Generator[None, None, None]: + """Exit with exception.""" + try: + yield + except Exception as err: + log.exception(err) + log.error(err) + log.error( + "An error has occurred, see log file. And contact the developers if needed." + ) + log.info(get_goodbye_help()) + sys.exit(1) + + +def extract_keys_recursive(config: ParamMap) -> Generator[str, None, None]: + """Extract keys recursively for the needed modules.""" + for param_name, value in config.items(): + if isinstance(value, collections.abc.Mapping): + yield from extract_keys_recursive(value) + else: + yield param_name + + +def recursive_convert_paths_to_strings(params: ParamMapT) -> ParamMapT: + """ + Convert paths to strings recursively over a dictionary. + + Parameters + ---------- + params : dictionary + + Returns + ------- + dictionary + A copy of the original dictionary with paths converted to strings. + """ + params = deepcopy(params) + for param, value in params.items(): + if isinstance(value, (Path, EmptyPath)): + params[param] = str(value) + elif isinstance(value, collections.abc.Mapping): + params[param] = recursive_convert_paths_to_strings(value) + elif isinstance(value, (tuple, list)): + for i, v in enumerate(value): + if isinstance(v, (Path, EmptyPath)): + value[i] = str(v) + params[param] = value + + return params + + +def get_arch(): + """Helper function to figure out the architetchure""" + system = platform.system().lower() + machine = platform.machine().lower() + + return f"{machine}-{system}" + + +def get_cns_executable() -> tuple[Path, Path]: + """ + Locate CNS executable and its Linux variant for grid execution. + + Returns: + Tuple of (cns_exec, cns_exec_linux) paths + + Raises: + SystemExit: If CNS executable cannot be found + """ + cns_exec_dir = Path(files(haddock).joinpath("cns/bin")) # type: ignore + arch = get_arch() + cns_exec = Path(cns_exec_dir, f"{arch}.bin") + if not cns_exec.exists(): + log.error("CNS executable not found at %s", cns_exec) + + # Fall back to environment variable + cns_exec_env = os.environ.get("CNS_EXEC") + if cns_exec_env is None: + log.error( + "Please define the CNS binary location by setting the CNS_EXEC " + "environment variable" + ) + sys.exit(1) + + cns_exec = Path(cns_exec_env) + if not cns_exec.exists(): + log.error("CNS executable not found at %s", cns_exec) + sys.exit(1) + + # Determine Linux-specific executable for grid usage + cns_exec_linux = Path(cns_exec_dir, "x86_64-linux.bin") + + if not cns_exec_linux.exists(): + log.warning( + "Current architecture is %s, but grid execution requires " + "an x86_64-linux binary", + arch, + ) + log.warning("Linux CNS binary not found at %s", cns_exec_linux) + log.warning("GRID mode will not be available") + + return cns_exec, cns_exec_linux + + +def get_prodrg_exec() -> tuple[Optional[Path], Optional[Path]]: + """ + Locate the prodrg binary and its parameter file. + + Returns ``(None, None)`` with a warning if the binary cannot be found, + allowing the application to start normally. The error will surface later + if ``run_prodrg`` is actually called. + + Returns: + Tuple of (prodrg_exec, prodrg_param) paths, or (None, None) if not found + """ + prodrg_dir = Path(files(haddock).joinpath("prodrg")) # type: ignore + arch = get_arch() + prodrg_exec = prodrg_dir / f"prodrg_{arch}" + + if not prodrg_exec.exists(): + prodrg_exec_env = os.environ.get("PRODRG_EXEC") + if prodrg_exec_env is not None: + prodrg_exec = Path(prodrg_exec_env) + else: + log.warning( + "prodrg binary not found for arch %s and PRODRG_EXEC is not set. " + "Automated ligand topology generation will not be available.", + arch, + ) + return None, None + + if not prodrg_exec.exists(): + log.warning( + "prodrg executable not found at %s. " + "Automated ligand topology generation will not be available.", + prodrg_exec, + ) + return None, None + + prodrg_param = prodrg_dir / "prodrg.param" + if not prodrg_param.exists(): + log.warning( + "prodrg.param not found at %s. " + "Automated ligand topology generation will not be available.", + prodrg_param, + ) + return None, None + + return prodrg_exec, prodrg_param diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libworkflow.py b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libworkflow.py new file mode 100644 index 0000000000000000000000000000000000000000..38254fb845729fc9a65e3702b0d68cdb0fb6d6b4 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/libs/libworkflow.py @@ -0,0 +1,202 @@ +"""HADDOCK3 workflow logic.""" + +import importlib +import sys +from pathlib import Path +from time import time + +from haddock import log +from haddock.clis.cli_analyse import main as cli_analyse +from haddock.clis.cli_traceback import main as cli_traceback +from haddock.core.exceptions import HaddockError, HaddockTermination, StepError +from haddock.core.typing import Any, ModuleParams, Optional +from haddock.gear.clean_steps import clean_output +from haddock.gear.config import get_module_name +from haddock.gear.zerofill import zero_fill +from haddock.libs.libtimer import convert_seconds_to_min_sec, log_time +from haddock.libs.libutil import recursive_dict_update +from haddock.modules import ( + modules_category, + non_mandatory_general_parameters_defaults, +) + + +class WorkflowManager: + """Read and execute workflows.""" + + def __init__( + self, + workflow_params: ModuleParams, + start: Optional[int] = 0, + **other_params: Any, + ) -> None: + self.start = 0 if start is None else start + self.recipe = Workflow(workflow_params, start=0, **other_params) + # terminate is used to synchronize the `clean` option with the + # `exit` module. If the `exit` module is removed in the future, + # you can also remove and clean the `terminate` part here. + self._terminated = None + + def run(self) -> None: + """High level workflow composer.""" + for i, step in enumerate(self.recipe.steps[self.start :], start=self.start): + try: + step.execute() + except HaddockTermination: + self._terminated = i # type: ignore + break + + # Forward any params generated at runtime by some module, for example + # auto-generated ligand topology/parameter files to every subsequent + # step that exposes the same key in its config, + # Do this ONLY when the user has not already set a value for that key. + output_params = getattr(step.module, "_output_params", {}) + if output_params: + for future_step in self.recipe.steps[i + 1 :]: + for key, value in output_params.items(): + if future_step.config.get(key) in (None, ""): + future_step.config[key] = value + + def clean(self, terminated: Optional[int] = None) -> None: + """ + Clean steps. + + Parameters + ---------- + terminated : int, None + At which index of the workflow to stop the cleaning. If ``None``, + uses the internal class configuration. + """ + terminated = self._terminated if terminated is None else terminated + for step in self.recipe.steps[:terminated]: + step.clean() + + def postprocess(self, self_contained: bool = False) -> None: + """Postprocess the workflow.""" + # is the workflow going to be cleaned? + is_cleaned = self.recipe.steps[0].config["clean"] + # Is the workflow supposed to run offline + offline = self.recipe.steps[0].config["offline"] + # running mode + mode = self.recipe.steps[0].config["mode"] + # ncores + ncores = self.recipe.steps[0].config["ncores"] + + capri_steps: list[int] = [] + for step in self.recipe.steps: + if step.module_name == "caprieval": + capri_steps.append(step.order) # type: ignore + # call cli_analyse (no need for capri_dicts, it's all precalculated) + cli_analyse( + "./", + capri_steps, + top_clusters=10, + format=None, + scale=None, + inter=False, + is_cleaned=is_cleaned, + offline=offline, + mode=mode, + ncores=ncores, + self_contained=self_contained, + ) + # call cli_traceback. If it fails, it's not a big deal + try: + cli_traceback("./", offline=offline) + except Exception as e: + log.warning(f"Error running traceback: {e}") + + +class Workflow: + """Represent a set of stages to be executed by HADDOCK.""" + + def __init__( + self, + modules_parameters: ModuleParams, + start: Optional[int] = 0, + **other_params: Any, + ) -> None: + if start is None: + start = 0 + + # filter out those parameters not belonging to the modules + general_modules = { + k: v + for k, v in other_params.items() + if k in non_mandatory_general_parameters_defaults + } + + # Create the list of steps contained in this workflow + self.steps: list[Step] = [] + _items = enumerate(modules_parameters.items(), start=start) + for num_stage, (stage_name, params) in _items: + stage_name = get_module_name(stage_name) + log.info(f"Reading instructions step {num_stage}_{stage_name}") + + # updates the module's specific parameter with global parameters + # that are applicable to the modules. But keep priority to the local + # level + params_up = recursive_dict_update(general_modules, params) + + try: + _ = Step( + stage_name, + order=num_stage, + **params_up, + ) + self.steps.append(_) + + except StepError as re: + log.error(f"Error found while parsing course {stage_name}") + raise HaddockError from re + + +class Step: + """Represents a Step of the Workflow.""" + + def __init__( + self, + module_name: str, + order: Optional[int] = None, + **config_params: Any, + ) -> None: + self.config = config_params + self.module_name = module_name + self.order = order + self.working_path = Path(zero_fill.fill(self.module_name, self.order)) # type: ignore + self.module = None + + def execute(self) -> None: + """Execute simulation step.""" + self.working_path.resolve().mkdir(parents=False, exist_ok=False) + + # Import the module given by the mode or default + module_name = ".".join( + ["haddock", "modules", modules_category[self.module_name], self.module_name] + ) + module_lib = importlib.import_module(module_name) + self.module = module_lib.HaddockModule(order=self.order, path=self.working_path) + + # Run module + start = time() + try: + self.module.update_params(**self.config) # type: ignore + self.module.save_config(Path(self.working_path, "params.cfg")) # type: ignore + self.module.run() # type: ignore + except KeyboardInterrupt: + log.info("You have halted subprocess execution by hitting Ctrl+c") + log.info("Exiting...") + sys.exit(1) + + end = time() + elapsed = convert_seconds_to_min_sec(end - start) + self.module.log(f"took {elapsed}") # type: ignore + + def clean(self) -> None: + """Clean step output.""" + if self.module is None and self.config["clean"]: + with log_time("cleaning output files took"): + clean_output(self.working_path, self.config["ncores"]) + + elif self.module is not None and self.module.params["clean"]: + self.module.clean_output() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/.___init__.py 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index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/._topology differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..692112783467e9f09f00564d04fa621e4b6ac10a --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/__init__.py @@ -0,0 +1,537 @@ +"""HADDOCK3 modules.""" + +import re + +from abc import ABC, abstractmethod +from contextlib import contextmanager, suppress +from copy import deepcopy +from functools import partial +from os import linesep +from pathlib import Path + +from haddock import EmptyPath, log, modules_defaults_path +from haddock.core.defaults import MODULE_IO_FILE, INTERACTIVE_RE_SUFFIX +from haddock.core.exceptions import ConfigurationError +from haddock.core.typing import ( + Any, + Container, + FilePath, + Generator, + Literal, + Optional, + ParamDict, + Union, +) +from haddock.gear import config +from haddock.gear.clean_steps import clean_output +from haddock.gear.known_cns_errors import find_all_cns_errors +from haddock.gear.parameters import config_mandatory_general_parameters +from haddock.gear.yaml2cfg import read_from_yaml_config, find_incompatible_parameters +from haddock.libs.libhpc import HPCScheduler +from haddock.libs.libgrid import GRIDScheduler, ping_dirac +from haddock.libs.libio import folder_exists, working_directory +from haddock.libs.libmpi import MPIScheduler +from haddock.libs.libontology import ModuleIO, PDBFile +from haddock.libs.libparallel import Scheduler +from haddock.libs.libtimer import log_time +from haddock.libs.libutil import recursive_dict_update + + +modules_folder = Path(__file__).resolve().parent + +_folder_match_regex = "[a-zA-Z]*/" +modules_category = { + module.name: category.name + for category in modules_folder.glob(_folder_match_regex) + for module in category.glob(_folder_match_regex) +} +"""Indexes each module in its specific category. Keys are Paths to the module, +values are their categories. Categories are the modules parent folders.""" + +modules_names = set(modules_category.keys()) + +category_hierarchy = [ + "topology", + "sampling", + "refinement", + "scoring", + "analysis", + "extras", +] + +# this dictionary defines non-mandatory general parameters that can be defined +# as global parameters thus affect all modules, or, instead, can be defined per +# module where the module definition overwrites global definition. Not all +# modules will use these parameters. It is the responsibility of the module to +# extract the parameters it needs. +# the config file is in modules/defaults.cfg +non_mandatory_general_parameters_defaults = read_from_yaml_config(modules_defaults_path) # noqa : E501 + +incompatible_defaults_params = find_incompatible_parameters(modules_defaults_path) + +config_readers = { + ".yaml": read_from_yaml_config, + ".cfg": config.load, +} + +_step_folder_regex = tuple( + r"[0-9]+_" + mod_name for mod_name in modules_category.keys() +) +step_folder_regex = "(" + "|".join(_step_folder_regex) + ")" +""" +String for regular expression to match module folders in a run directory. + +It will match folders with a numeric prefix followed by underscore ("_") +followed by the name of a module. + +Example: https://regex101.com/r/roHls9/1 +""" + +step_folder_regex_re = re.compile(step_folder_regex) +""" +Compiled regular expression from :py:const:`step_folder_regex`. + +It will match folders with a numeric prefix followed by underscore ("_") +followed by the name of a module. + +Example: https://regex101.com/r/roHls9/1 +""" + + +@contextmanager +def _not_valid_config() -> Generator[None, None, None]: + try: + yield + except KeyError as err: + emsg = ( + "The configuration file extension is not supported. " + f"Supported types are {', '.join(config_readers.keys())}." + ) + raise ConfigurationError(emsg) from err + + +class BaseHaddockModule(ABC): + """HADDOCK3 module's base class.""" + + name: str + + def __init__(self, order: int, path: Path, params_fname: FilePath) -> None: + """ + HADDOCK3 modules base class. + + Parameters + ---------- + params : dict or path to HADDOCK3 configuration file + A dictionary or a path to a HADDOCK3 configuration file + containing the initial module parameters. Usually this is + defined by the default params. + """ + self.order = order + self.path = path + self.previous_io = self._load_previous_io() + + # instantiate module's parameters + self._origignal_config_file = params_fname + with _not_valid_config(): + extension = Path(params_fname).suffix + self._original_params = config_readers[extension](params_fname) + + self._params: ParamDict = {} + self.update_params(update_from_cfg_file=params_fname) + + # Some modules might need to overwrite parameters defined by the user + # This can be done via `_output_params` - whatever the module adds to this + # variable, will be propagated down to other modules. + # For example: `topoaa` needs to pass `ligand_param_fname` to `rigidbody` module + # so somewhere in the `topoaa` module we need to set: `self._output_params[VALUE] = VAR` + # IMPORANT: This will be propagated to ALL modules and can have unexpected effects + self._output_params: dict = {} + + @property + def params(self) -> ParamDict: + """Configuration parameters.""" # noqa: D401 + return self._params + + def reset_params(self) -> None: + """Reset parameters to the ones used to instantiate the class.""" + self._params.clear() + self.update_params(**self._original_params) + + def update_params( + self, + update_from_cfg_file: Optional[FilePath] = None, + **params: Any, + ) -> None: + """ + Update the modules parameters. + + Add/update to the current modules parameters the ones given in + the function call. If you want to enterily replace the modules + parameters to their default values use the `reset_params()` + method. + + Update takes places recursively, that is, nested dictionaries + will be updated accordingly. + + To update the current config with the parameters defined in an + HADDOCK3 configuration file use the `update_from_cfg_file` + parameter. + + To update from a JSON file, first load the JSON into a + dictionary and unpack the dictionary to the function call. + + Examples + -------- + >>> m.update_params(param1=value1, param2=value2) + + >>> m.update_params(**param_dict) + + >>> m.update_params(update_from_cfg_file=path_to_file) + + # if you wish to start from scratch + >>> m.reset_params() + >>> m.update_params(...) + """ + if update_from_cfg_file and params: + _msg = "You can not provide both `update_from_cfg_file` and key arguments." + raise TypeError(_msg) + + if update_from_cfg_file: + with _not_valid_config(): + extension = Path(update_from_cfg_file).suffix + params = config_readers[extension](update_from_cfg_file) + + # the updating order is relevant + _n = recursive_dict_update( + non_mandatory_general_parameters_defaults, self._params + ) + self._params = recursive_dict_update(_n, params) + self._fill_emptypaths() + self._confirm_fnames_exist() + + def save_config(self, path: FilePath) -> None: + """Save current parameters to a HADDOCK3 config file.""" + # creates this dictionary for the config to have the module name + # key in brackets, for example: + # + # [topoaa] + # ... + ignore = config_mandatory_general_parameters.union( + non_mandatory_general_parameters_defaults + ) # noqa: 501 + params = deepcopy(self.params) + + with suppress(KeyError): + for key in list(ignore): + params.pop(key) + + config.save({self.name: params}, path) + + def add_parent_to_paths(self) -> None: + """Add parent path to paths.""" + # convert paths to relative by appending parent + for key, value in self.params.items(): + if value and key.endswith("_fname"): + if not Path(value).is_absolute(): + self.params[key] = Path("..", value) + return + + @abstractmethod + def _run(self) -> None: ... + + def run(self, **params: Any) -> None: + """Execute the module.""" + log.info(f"Running [{self.name}] module") + + self.update_params(**params) + self.add_parent_to_paths() + + with working_directory(self.path): + self._run() + + log.info(f"Module [{self.name}] finished.") + + def clean_output(self) -> None: + """ + Clean module output folder. + + See Also + -------- + :py:func:`haddock.gear.clean_steps.clean_output` + """ + with log_time("cleaning output files took"): + clean_output(self.path, self.params["ncores"]) + + @classmethod + @abstractmethod + def confirm_installation(cls) -> None: + """ + Confirm the third-party software needed for the module is installed. + + HADDOCK3's own modules should just return. + """ + return + + def export_io_models(self, faulty_tolerance: float = 0.0) -> None: + """ + Export input/output to the ModuleIO interface. + + Modules that do not perform any operation on PDB files should have + input = output. + + This function implements a common interface for all modules. + + Parameters + ---------- + faulty_tolerance : int, default 0 + The percentage of missing output allowed. If 20 is given, + raises an error if 20% of the expected output is missing (not + saved to disk). + """ + self.output_models: Union[list[PDBFile], dict[int, PDBFile]] + assert self.output_models, "`self.output_models` cannot be empty." + io = ModuleIO() + # add the input models + io.add(self.previous_io.output, "i") + # add the output models + io.add(self.output_models, "o") + # Removes un-generated outputs and compute percentage of ungenerated + faulty = io.check_faulty() + # Save outputs + io.save() + # Check if number of generated outputs is under the tolerance threshold + if faulty > faulty_tolerance: + _msg = ( + f"{faulty:.2f}% of output was not generated for this module " + f"and tolerance was set to {faulty_tolerance:.2f}%." + ) + # Try to detect CNS errors + if detected_errors := find_all_cns_errors(self.path): + _msg += linesep + for error in detected_errors.values(): + _msg += f"{str(error['error'])}{linesep}" + # Show final error message + self.finish_with_error(_msg) + + def finish_with_error(self, reason: object = "Module has failed.") -> None: + """Finish with error message.""" + if isinstance(reason, Exception): + raise RuntimeError("Module has failed.") from reason + + else: + raise RuntimeError(reason) + + def _load_previous_io( + self, + filename: FilePath = MODULE_IO_FILE, + ) -> ModuleIO: + if self.order == 0: + self._num_of_input_molecules = 0 + return ModuleIO() + + io = ModuleIO() + previous_io = Path(self.previous_path(), filename) + + if previous_io.is_file(): + io.load(previous_io) + + self._num_of_input_molecules = len(io.output) + + return io + + def previous_path(self) -> Path: + """Give the path from the previous calculation.""" + previous = get_module_steps_folders(self.path.resolve().parent) + + try: + # return Path(previous[self.order - 1]) + return self.last_step_folder(previous, self.order - 1) + except IndexError: + return self.path + + @staticmethod + def last_step_folder(folders, index): + """Retrieve last step folder.""" + with_ind = [folder for folder in folders if int(folder.split("_")[0]) == index] + nb_with_ind = len(with_ind) + # No matching index + if nb_with_ind == 0: + raise IndexError + # Only one matching index + elif nb_with_ind == 1: + return with_ind[0] + # Case of multiple matching index + else: + for folder in with_ind: + if folder.split("_")[-1] != INTERACTIVE_RE_SUFFIX: + return folder + return with_ind[0] + + def log(self, msg: str, level: str = "info") -> None: + """ + Log a message with a common header. + + Currently the header is the [MODULE NAME] in square brackets. + + Parameters + ---------- + msg : str + The log message. + + level : str + The level log: 'debug', 'info', ... + Defaults to 'info'. + """ + getattr(log, level)(f"[{self.name}] {msg}") + + def _confirm_fnames_exist(self) -> None: + for param, value in self._params.items(): + if param.endswith("_fname") and value: + if not Path(value).exists(): + raise FileNotFoundError(f"File not found: {str(value)!r}") + + def _fill_emptypaths(self) -> None: + """Fill empty paths.""" + for param, value in list(self._params.items()): + if param.endswith("_fname") and not value: + self._params[param] = EmptyPath() + + +EngineMode = Literal["batch", "local", "mpi"] + + +def get_engine( + mode: str, + params: dict[Any, Any], +) -> partial[Union[HPCScheduler, Scheduler, MPIScheduler, GRIDScheduler]]: + """ + Create an engine to run the jobs. + + Parameters + ---------- + mode : str + The type of engine to create + + params : dict + A dictionary containing parameters for the engine. + `get_engine` will retrieve from `params` only those parameters + needed and ignore the others. + """ + # a bit of a factory pattern here + # this might end up in another module but for now its fine here + if mode == "batch": + return partial( # type: ignore + HPCScheduler, + target_queue=params["queue"], + queue_limit=params["queue_limit"], + concat=params["concat"], + ) + + elif mode == "local": + return partial( # type: ignore + Scheduler, + ncores=params["ncores"], + max_cpus=params["max_cpus"], + ) + elif mode == "mpi": + return partial(MPIScheduler, ncores=params["ncores"]) # type: ignore + + elif mode == "grid": + # `grid` mode should only be used IF the grid is reachable, + # if not it should fallback to `local` + grid_available = ping_dirac() + + if grid_available: + return partial(GRIDScheduler, params=params) # type: ignore + else: + log.warning("GRID is not available, activating fallback using `mode=local`") + return partial( # type: ignore + Scheduler, + ncores=params["ncores"], + max_cpus=params["max_cpus"], + ) + + else: + available_engines = ("batch", "local", "mpi", "grid") + raise ValueError( + f"Scheduler `mode` {mode!r} not recognized. " + f"Available options are {', '.join(available_engines)}" + ) + + +def get_module_steps_folders( + folder: FilePath, + modules: Optional[Container[int]] = None, +) -> list[str]: + """ + Return a sorted list of the step folders in a running directory. + + Example + ------- + Consider the folder structure: + + run_dir/ + 0_topoaa/ + 1_rigidbody/ + 2_caprieval/ + 3_bad_module_name/ + data/ + + >>> get_module_steps_folders("run_dir") + >>> ["0_topoaa", "1_rigidbody", "2_caprieval"] + + Parameters + ---------- + folder : str or Path + Path to the run directory, or to the folder containing the step + folders. + + Returns + ------- + list of str + List containing strings with the names of the step folders. + """ + folders = (p.name for p in Path(folder).iterdir() if p.is_dir()) + steps = sorted( + (f for f in folders if step_folder_regex_re.search(f)), + key=lambda x: int(x.split("_")[0]), + ) + if modules: + steps = [ + st + for st in steps + if all( + [ + int(st.split("_")[0]) in modules, + st.split("_")[1] in modules_names, + ] + ) + ] + return steps + + +def is_step_folder(path: FilePath) -> bool: + """ + Assess whether a folder is a possible step folder. + + The folder is considered a step folder if has a zero or positive + integer index followed by a name of a module. + + Parameters + ---------- + path : str or pathlib.Path + The path to the folder. + + Returns + ------- + bool + Whether the folder is a step folder or not. + """ + path = Path(path) + folder_exists(path) + main_folder_name = path.name + parts = main_folder_name.split("_") + if len(parts) == 2 and parts[0].isdigit() and parts[1] in modules_category: + return True + else: + return False diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/._README.md b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/._README.md new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/._README.md differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/.__template_mod b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/.__template_mod new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/.__template_mod differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/README.md b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/README.md new file mode 100644 index 0000000000000000000000000000000000000000..ed5ec452d1f6b189dfad37da83bd226aefba3d80 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/README.md @@ -0,0 +1,30 @@ +Welcome! + +To develop your own HADDOCK3 module follow the patterns used in other modules. + +1. If your module belongs to a new category, create a folder for that category + under the `modules` folder. +1. Else, create a folder for your module inside its relevant category. + The name of that folder is the name of the module, i.e., the name used to call + the module in the haddock3 configuration files and used throughout the code base. +1. Copy the `__init__.py` file here to the new module's folder and edit it accordingly + to the instructions there. +1. Do the same for the `defaults.yaml` file. +1. You can then add any extra files needed inside your module's folder in order to + develop your module fully. +1. If your module requires any extra libraries, describe how to install those libraries + in the `docs/INSTALL.md` file. Unless approved by the Haddock Team, do not add + those dependencies to the `requirements.*` files. +1. HADDOCK3 has already many features related to IO, subprocess run, sending jobs, + etc. Please, look around the `libs` folder for pertinent functions, but, above all, + feel welcomed to reach out to us with any doubts. +1. Please write also tests for your module. Our testing machinery already + tests for the common patterns, for example, inspecting the `defaults.yaml` file. + But you should write any additional tests to ensure that your module works properly. + See other examples in the `tests/` folder. +1. Finally, add an example of how to use your module in the `examples/` folder. + The example should have a short sampling scheme. Name the config file ending with + `-test.cfg`. + +Thanks, and we are happy to help you! :-) +@ The Haddock Team diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..8fe31b4f76dc1868dbc8fd3619681f75e3361f07 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/__init__.py @@ -0,0 +1,142 @@ +""" +Template module +=============== + +Use this template to implement your own HADDOCK3 module. + +In this docstring, please write the documentation explaining what the module +does technically, scientifically, and its purpose. + +Anything you want to write to describe the module, also do it here. +You should use restructureText syntax: + + https://docutils.sourceforge.io/docs/user/rst/quickstart.html +""" +# Import here what you need +from pathlib import Path +from haddock.core.typing import FilePath, Any +from haddock.core.defaults import MODULE_DEFAULT_YAML + +# In case you need to import a Python library that is a run-time dependency, +# you should import it inside the `_run` method to avoid import errors for those +# users not using the new module, thus not having its dependencies installed. + +# If your module does not use CNS, import the following +from haddock.modules import BaseHaddockModule + +# If your module uses CNS import +from haddock.modules.base_cns_module import BaseCNSModule + + +# this is mandatory, don't erase nor edit these lines +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +# this is the main class of the module. It should be named exactly as this. +class HaddockModule(BaseHaddockModule): + # inherit from BaseCNSModule in case the module uses CNS + """ + Here you can write any extra documentation you wish about the class. + + Use numpydoc syntax: + + https://numpydoc.readthedocs.io/en/latest/format.html + """ + + # this is mandatory + name = RECIPE_PATH.name + + # this __init__ structure is mandatory, but you can extend it to the + # module's needs as long as you keep the main structure. Surely, + # *ignore and **everything can be edited to fit your needs. + def __init__( + self, + order: int, + path: Path, + *ignore: Any, + init_params: FilePath = DEFAULT_CONFIG, + **everything: Any, + ) -> None: + + # if your module uses CNS you might need to define where the main CNS + # script is localted. See examples in `topoaa`, `emref`. + # else leave it out. + # cns_script = Path(RECIPE_PATH, "cns", "main.cns") + + # use one of the following: + # if the module does not use CNS: + super().__init__(order, path, init_params) + + # if the module uses CNS: + super().__init__(order, path, initial_params, cns_script=cns_script) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if the module is ready to use.""" + # here, you should write any code needed to confirm that all the + # dependencies required by your module are installed. + # this class method will be executed when HADDOCK3 starts. + + # if you module does not import any run-time dependency, just leave + # this method blank + return + + # here is where the module magic will happen + def _run(self) -> None: + # Import here any Python run-time dependencies that your module needs. + + # you can refer to other modules as examples to see how they perform. + # Likely, the new module will need to load the output from the previous + # module. For example: + models_to_use = self.previous_io.retrieve_models() + + # once the module loads, you can access its parameters in + # `self.params`. See more in the BaseHaddockModule class. + # `self.params` is a dictionary that contains both the general + # parameters such as the number of processors + # `self.params['ncores']` parameters as well as those + # defined in your `defaults.yml` + + # Add here all the magic that your module does. You can split this part + # into many functions, classes, or add any extra files or subfolders to + # the module's folder as you may need. You can even import other modules + # if needed. + + # If you module creates models, the line below is almost mandatory. + # see other modules, such as topoaa or mdref, emref to see how they + # handle `output_models`. + # the PDB references in `list_of_created_models` below must be instances + # of the `libs.libontology.PDBFile` class. + + output_model_list = your_function(models_to_use, self.params) + # output_model_list = [(pdb, psf, score), ...] + + list_of_created_models = [] + for element in output_model_list: + pdb, psf, score = element + # IMPORTANT: pass `file_name=Path.name` + + # alternatively to the strategy below, you can use the + # `libs.libcns.prepare_expected_pdb` function if it better fits + # your case. See `emref` and `mdref` for examples. + pdb_object = PDBFile( + Path(pdb).name, + topology=TopologyFile(Path(psf).name, path="."), + path=".") + + pdb_object.score = score + list_of_created_models.append(pdb_object) + + # final section + self.output_models = list_of_created_models + self.export_io_models() + # in case your module considers possible tolerance for generated models, + # you can use: + # self.export_io_models(faulty_tolerance=self.params["tolerance"]) + + +# Finally, the haddock module's class inherit from BaseHaddockModule. It is +# important that you go through the BaseHaddockModule interface to understand +# it's functionalities. If you find any spots of missing documentation, let us +# know. Thanks! @ The Haddock Team diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cf7713327796250684798caa81873420399c3420 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/_template_cat/_template_mod/defaults.yaml @@ -0,0 +1,106 @@ +# this is an example of the default parameters +# add here the parameters of your module. You can follow examples +# in other default config files. Each parameter type has it's own specific extra +# fields. Below an example of parameters of different types: +# explevel can only be easy, expert, guru + +# You may wish to read our functionalities in "extended parameters": +# https://github.com/haddocking/haddock3/blob/main/src/haddock/gear/expandable_parameters.py#L1-L73 + +# INTEGER parameter +random_seed: + default: 42 + type: integer + min: 0 + max: 999 + title: + short: + long: + group: "" + explevel: easy + +# FLOAT parameter +indpb: + default: 0.2 + type: float + min: 0 + max: 1 + precision: 2 + title: + short: + long: + group: "" + explevel: expert + +# LIST parameter +region: + default: [] + type: list + minitems: 0 + maxitems: 1000 + title: + short: + long: + group: "" + explevel: guru + +# STRING parameter with CHOICES +initial_mutation: + default: keep + type: string + minchars: 0 + maxchars: 7 + choices: + - alanine + - random + - keep + title: + short: + long: + group: "" + explevel: guru + +# STRING parameter without CHOICES +target_chain: + default: "A" + type: string + minchars: 1 + maxchars: 1 + title: + short: + long: + group: "" + explevel: hidden + +# a DICTIONARY parameter +# these parameter are tricky to maintain, use them only if strickly needed. +dict_like_par: + explevel: easy + title: Example of a dictionary mdule + short: Some short explanation on dick_like_par + long: Some long explanationon dick_like_par + group: "the group it belongs" + type: dict + # here are the parameters belonging to the `dict_like_par` key + somepar: + default: 0.2 + type: float + min: 0 + max: 1 + precision: 2 + title: + short: + long: + group: "" + explevel: expert + + otherpar: + default: [] + type: list + minitems: 0 + maxitems: 1000 + title: + short: + long: + group: "" + explevel: guru diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/.___init__.py new file mode 100644 index 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b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/__init__.py @@ -0,0 +1,61 @@ +"""HADDOCK3 modules related to model analysis.""" + +from typing import Iterable + + +modules_using_resdic = ("caprieval", "rmsdmatrix", "alascan", "sasascore") + + +def confirm_resdic_chainid_length(params: Iterable[str]) -> None: + """ + Confirm resdic params have chain IDs of length one. + + Parameters + ---------- + params : dict, or list of keys + The parameters. + + Raises + ------ + ValueError + If a `resdic_*` parameter has chain IDs with more than one letter. + For example, `resdic_AB`. + """ + resdic_params = (p for p in params if p.startswith("resdic_")) + for param in resdic_params: + chainid = param.split("_")[-1] + if len(chainid) > 1: + raise ValueError( + f"We found the parameter {param!r} which has " + "more than one character in the chain " + "identifier. Chain IDs should have only one character." + ) + + +def get_analysis_exec_mode(mode: str) -> str: + """ + Get the execution mode for analysis modules. + + Parameters + ---------- + exec_mode : str + The execution mode to use. + + Returns + ------- + str + The execution mode to use for the analysis modules. + If it's "batch", it will be changed to "local". + """ + # =====================================================================# + # EXPLANATION # + # =====================================================================# + # This function is called in the analysis-based modules to OVERWRITE + # the mode selected by the user. + # This must be done because the analysis modules do not support being + # executed over the HPC system or the GRID + # + # The function below returns "local" if the user selected either + # `batch` or `grid` as execution mode. Thus effectively forcing the + # execution to be local. + return "local" if mode in ("batch", "grid") else mode diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._scan.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._scan.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/._scan.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..7c73aabb5fb3aa07db2be3a6dd0c50de1dbbdae3 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/__init__.py @@ -0,0 +1,205 @@ +""" +HADDOCK3 module for alanine scan. + +This module is responsible for the alanine (or any other residue) scan analysis +of the model(s) generated in the previous step of the workflow. +For each model, this module will mutate the interface residues and calculate +the differences in the haddock score and its individual components between the +wild type and the mutant, thus providing a measure of the impact of such mutation. +Such difference (delta_score) is always calculated as: + + delta_score = score_wildtype - score_mutant + +Therefore, a _positive_ delta_score indicates that the mutation is destabilizing +while a _negative_ delta_score indicates that the mutation is stabilizing. + +If cluster information is available, the module will also calculate the +average haddock score difference for each cluster of models. For each amino acid, +a Z score is calculated as: + + Z = (delta_score - mean) / std + +where mean and std are the mean and standard deviation of the delta_score over +all the amino acids. + +The module will also generate plots of the alanine scan data, showing the +distribution of the delta_score (and every component) for each amino acid at the +interface. + +You can use the parameters below to customize the behavior of the module: + + * `chains`: list of chains to be considered for the alanine scan. In some + cases you may want to limit the analysis to a single chain. + * `output_mutants`: if True, the module will output the models with the + mutations applied (only possible if there is only one model) + * `output_bfactor`: if True, the module will output the non-mutated models + with the rescaled delta_score in the B-factor column + * `plot`: if True, the module will generate plots of the alanine scan data + * `scan_residue`: the residue to scan (default is 'ALA') + * `resdic`: list of residues to be used for the scanning. An example is: + + >>> resdic_A = [1,2,3,4] + >>> resdic_B = [2,3,4] +""" + +from pathlib import Path + +from haddock import log +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.libs.libparallel import GenericTask +from haddock.modules import BaseHaddockModule, get_engine +from haddock.modules.analysis import get_analysis_exec_mode +from haddock.modules.analysis.alascan.scan import ( + AddDeltaBFactor, + ClusterOutputer, + group_scan_by_cluster, + InterfaceScanner, + write_scan_out, +) + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module for alanine scan.""" + + name = RECIPE_PATH.name + + def __init__(self, order, path, *ignore, init_params=DEFAULT_CONFIG, + **everything): + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls): + """Confirm if module is installed.""" + return + + def validate_ouput_mutant_parameter(self, nmodels: int) -> None: + """Validate the output mutant parameter. + + This parameter can be set to True if only one input model is provided, + otherewise we risk to generate too many PDB files. + + Parameters + ---------- + nmodels: int + Number of input models. + """ + if self.params["output_mutants"]: + # output mutants is only possible if there is only one model + if nmodels > 1: + log.warning( + "'output_mutants' parameter is set to True, " + "but more than one model was found. " + "Setting 'output_mutant' parameter to False." + ) + self.params["output_mutants"] = False + + def _run(self): + """Execute module.""" + # Get the models generated in previous step + try: + models = self.previous_io.retrieve_models(individualize=True) + except Exception as e: + self.finish_with_error(e) + + # Compute number of input model + nmodels = len(models) + + # Validate `output_mutant` parameter + self.validate_ouput_mutant_parameter(nmodels) + + # Step1: "get mutations" i.e. get target interface residues per input model + # 1 scan_obj per input model, merged into scan_objects to give to Engine + scan_objects = [ + InterfaceScanner( + mutation_res=self.params["scan_residue"], + model=model, + params=self.params, + library_mode=False, + ) + for model in models + ] + + log.info(f"Scanning {nmodels} models for possible mutations") + exec_mode = get_analysis_exec_mode(self.params["mode"]) + Engine = get_engine(exec_mode, self.params) + engine = Engine(scan_objects) + engine.run() + + # Step2: perform mutations + # Collect all point mutations to be performed + mutation_objects = [] + for mutations_to_perform in engine.results: + if mutations_to_perform: + mutation_objects.extend(mutations_to_perform) + + total_mutations = len(mutation_objects) + log.info(f"Found {total_mutations} mutations") + + if mutation_objects: + # let engine take care of parallelization + engine = Engine(mutation_objects) + engine.run() + + # Organize engine output by model + results_by_model = {} + for result in engine.results: + if result and result.success: + if result.model_id not in results_by_model: + results_by_model[result.model_id] = [] + results_by_model[result.model_id].append(result) + + # Save to .tsv + scan_writter_jobs = [ + GenericTask(write_scan_out, results, model_id) + for model_id, results in results_by_model.items() + ] + engine = Engine(scan_writter_jobs) + engine.run() + + # Generate output models with bfactors if requested + if self.params["output_bfactor"]: + update_with_bfactor_jobs = [] + for model in models: + model_id = model.file_name.removesuffix(".pdb") + try: + model_results = results_by_model[model_id] + except KeyError: + # Case when no data computed for this model + model_results = [] + update_with_bfactor_jobs.append( + AddDeltaBFactor(model, self.path, model_results) + ) + engine = Engine(update_with_bfactor_jobs) + engine.run() + models_to_export = engine.results + self.output_models = models_to_export + else: + # Send models to the next step, no operation is done on them + self.output_models = models + + # Cluster-based analysis + clt_scan, clt_pops = group_scan_by_cluster(models, results_by_model) + alascan_cluster_jobs = [ + ClusterOutputer( + clt_data, + clt_id, + clt_pops[clt_id], + scan_residue=self.params["scan_residue"], + generate_plot=self.params["plot"], + offline=self.params["offline"], + ) + for clt_id, clt_data in clt_scan.items() + ] + engine = Engine(alascan_cluster_jobs) + engine.run() + + else: + log.info("No interface residues found - skipping mutation analysis") + # Send models to the next step, no operation is done on them + self.output_models = models + + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..649a7ffc5eb6938b1511b579ec0294fa3b17c80a --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/defaults.yaml @@ -0,0 +1,87 @@ +resdic_: + default: [] + type: list + minitems: 0 + maxitems: 100 + title: List of residues to be mutated + short: List of residues to be mutated. By default all the interface residues are + mutated. + long: List of residues to be mutated. By default all the interface residues are + mutated. resdic_* is an expandable parameter. You can provide resdic_A, + resdic_B, resdic_C, etc, where the last capital letter is the chain + identifier. + group: analysis + explevel: expert +int_cutoff: + default: 5.0 + type: float + min: 1.0 + max: 20. + precision: 3 + title: Distance cutoff (Å) used to define interface contacts. + short: Distance cutoff (Å) used to define interface contacts between two interacting molecules. + long: Distance cutoff (Å) used to define interface contacts between two interacting molecules. + group: analysis + explevel: easy +output_bfactor: + default: false + type: boolean + title: Dump the input models with the rescaled delta_score written in the b-factor column. + short: Dump the input models with the rescaled delta_score written in the b-factor column. + long: Dump the input models with the rescaled delta_score written in the b-factor column. Those files do not contain the mutations, but rather will display the normalized (between 0 and 100) delta HADDOCK score (100 * (delta_score - min_score) / (max_score - min_score)) in the b-factor column. The higher the b-factor, the more favourable (or less unfavourable) the mutation. You can color the PDB files according to this attribute (in pymol, type "spectrum b") + group: analysis + explevel: easy +scan_residue: + default: "ALA" + type: string + minchars: 3 + maxchars: 3 + choices: [ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ALY, ASH, CFE, CSP, CYC, CYF, CYM, DDZ, GLH, HLY, HY3, HYP, M3L, MLY, MLZ, MSE, NEP, PNS, PTR, SEP, TOP, TYP, TYS, CIR] + title: Residue to be used for the scanning + short: Residue to be used for the scanning. The default is alanine. + long: Residue to be used for the scanning. The default is alanine. Use bigger residues at your own risk. + group: analysis + explevel: easy +plot: + default: false + type: boolean + title: Plot scanning data. + short: Plot scanning data. + long: Plot scanning data. + group: analysis + explevel: easy +chains: + default: [] + type: list + minitems: 0 + maxitems: 10 + title: ChainIDs to be considered for the scanning. + short: ChainIDs to be considered for the scanning. + long: ChainIDs to be considered for the scanning. If empty, all the chains will be considered. If not empty, only residues part of the specified chains will be mutated. Do not use this parameter if you are using the resdic_* parameter. + group: analysis + explevel: easy +output_mutants: + default: false + type: boolean + title: Dump the mutated, energy-minimized PDB files. + short: Dump the mutated, energy-minimized PDB files. + long: Dump the mutated, energy-minimized PDB files. As the number of mutants can be very large, this option is allowed only when a single model is provided in input. + group: analysis + explevel: easy +ligand_param_fname: + default: '' + type: file + title: Custom ligand parameter file + short: Ligand parameter file in CNS format + long: Ligand parameter file in CNS format, for any ligand/residues/molecules not supported by default by HADDOCK. + group: 'force field' + explevel: easy +ligand_top_fname: + default: '' + type: file + title: Custom ligand topology file + short: Ligand topology file in CNS format + long: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK + group: 'force field' + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/scan.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/scan.py new file mode 100644 index 0000000000000000000000000000000000000000..dc7ae060f88bbac148371082df1a382eaaac2ae9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/alascan/scan.py @@ -0,0 +1,954 @@ +"""alascan module.""" +import os +import io +import shutil +from pathlib import Path +from contextlib import redirect_stdout +from dataclasses import dataclass +from typing import List, Tuple, Dict + +import numpy as np +import pandas as pd + + +from haddock import log +from haddock.core.typing import Any, Optional, Union +from haddock.libs.libalign import get_atoms, load_coords +from haddock.libs.libontology import PDBFile +from haddock.libs.libplots import make_alascan_plot +from haddock.modules.analysis.caprieval.capri import CAPRI +from haddock.clis import cli_score + +ATOMS_TO_BE_MUTATED = ['C', 'N', 'CA', 'O', 'CB'] + +RES_CODES = dict([ + ("CYS", "C"), + ("ASP", "D"), + ("SER", "S"), + ("GLN", "Q"), + ("LYS", "K"), + ("ILE", "I"), + ("PRO", "P"), + ("THR", "T"), + ("PHE", "F"), + ("ASN", "N"), + ("GLY", "G"), + ("HIS", "H"), + ("LEU", "L"), + ("ARG", "R"), + ("TRP", "W"), + ("ALA", "A"), + ("VAL", "V"), + ("GLU", "E"), + ("TYR", "Y"), + ("MET", "M"), + ("ALY", "K"), + ("ASH", "D"), + ("CFE", "C"), + ("CSP", "C"), + ("CYC", "C"), + ("CYF", "C"), + ("CYM", "C"), + ("DDZ", "A"), + ("GLH", "E"), + ("HLY", "P"), + ("HY3", "P"), + ("HYP", "P"), + ("M3L", "K"), + ("MLY", "K"), + ("MLZ", "K"), + ("MSE", "M"), + ("NEP", "H"), + ("PNS", "S"), + ("PTR", "Y"), + ("SEP", "S"), + ("TOP", "T"), + ("TYP", "Y"), + ("TYS", "Y"), + ("CIR", "R"), + ]) + + +@dataclass +class MutationResult: + """Result from a single mutation.""" + model_id: str + chain: str + resid: int + ori_resname: str + target_resname: str + # components of "mutant_scores": score, vdw, elec, desolv, bsa + mutant_scores: Tuple[float, float, float, float, float] + delta_scores: Tuple[float, float, float, float, float] + success: bool + error_msg: Optional[str] = None + + +def mutate(pdb_f, target_chain, target_resid, mut_resname): + """ + Mutate a residue in a PDB file into a different residue. + + Parameters + ---------- + pdb_f : str + Path to the pdb file. + + target_chain : str + Chain of the residue to be mutated. + + target_resid : int + Residue number of the residue to be mutated. + + mut_resname : str + Residue name of the residue to be mutated. + + Returns + ------- + mut_pdb_fname : str + Path to the mutated pdb file. + """ + mut_pdb_l = [] + resname = "" + with open(pdb_f, "r") as fh: + for line in fh.readlines(): + if line.startswith("ATOM"): + chain = line[21] + resid = int(line[22:26]) + atom_name = line[12:16].strip() + if target_chain == chain and target_resid == resid: + if not resname: + resname = line[17:20].strip() + if atom_name in ATOMS_TO_BE_MUTATED: + # mutate + line = line[:17] + mut_resname + line[20:] + mut_pdb_l.append(line) + else: + mut_pdb_l.append(line) + try: + mut_id = f"{RES_CODES[resname]}{target_resid}{RES_CODES[mut_resname]}" + except KeyError: + raise KeyError(f"Could not mutate {resname} into {mut_resname}.") + mut_pdb_fname = Path( + pdb_f.name.replace(".pdb", f"-{target_chain}_{mut_id}.pdb")) + with open(mut_pdb_fname, "w") as fh: + fh.write("".join(mut_pdb_l)) + return mut_pdb_fname + + +def get_score_string( + pdb_f: str, + run_dir: str, + outputpdb: bool = False, + ligand_param_fname: Union[Path, str] = "", + ligand_top_fname: Union[Path, str] = "", + ) -> List[str]: + """Get score output from cli_score.main. + + Parameters + ---------- + pdb_f : str + Path to the pdb file. + run_dir : str + Path to the run directory. + outputpdb : bool, optional + If True, the output, energy-minimized pdb file will be written. + Default is False. + ligand_param_fname : Union[Path, str] + Path to additional parameter file used by CNS. + ligand_top_fname : Union[Path, str] + Path to additional topology file used by CNS. + + Returns + ------- + out : list[str] + List of strings with the score output. + """ + stdout = io.StringIO() + with redirect_stdout(stdout): + cli_score.main( + pdb_f, + run_dir, + full=True, + outputpdb=outputpdb, + ligand_param_fname=ligand_param_fname, + ligand_top_fname=ligand_top_fname, + ) + out = stdout.getvalue().split(os.linesep) + return out + + +def calc_score( + pdb_f: str, + run_dir: str, + outputpdb: bool = False, + ligand_param_fname: Union[Path, str] = "", + ligand_top_fname: Union[Path, str] = "", + ) -> Tuple[float, float, float, float, float]: + """Calculate the score of a model. + + Parameters + ---------- + pdb_f : str + Path to the pdb file. + run_dir : str + Path to the run directory. + outputpdb : bool, optional + If True, the output, energy-minimized pdb file will be written. + Default is False. + ligand_param_fname : Union[Path, str] + Path to additional parameter file used by CNS + ligand_top_fname : Union[Path, str] + Path to additional topology file used by CNS + + Returns + ------- + Tuple[float, float, float, float, float] + All the scores + score : float + Haddock score. + vdw : float + Van der Waals energy. + elec : float + Electrostatic energy. + desolv : float + Desolvation energy. + bsa : float + Buried surface area. + + Raises + ------ + FileNotFoundError + Error when the file could not be located. + """ + scores_strings = get_score_string( + pdb_f, run_dir, + outputpdb=outputpdb, + ligand_param_fname=ligand_param_fname, + ligand_top_fname=ligand_top_fname, + ) + # Loop over lines to search for the score and components + for ln in scores_strings: + if ln.startswith("> HADDOCK-score (emscoring)"): + score = float(ln.split()[-1]) + if ln.startswith("> vdw"): + vdw = float(ln.split("vdw=")[1].split(",")[0]) + elec = float(ln.split("elec=")[1].split(",")[0]) + desolv = float(ln.split("desolv=")[1].split(",")[0]) + bsa = float(ln.split("bsa=")[1].split(",")[0]) + if ln.startswith("> writing") and outputpdb: + outpdb = ln.split()[-1] + # check if the output pdb file exists + if not os.path.exists(outpdb): + raise FileNotFoundError(f"Could not find output pdb file {outpdb}") + return score, vdw, elec, desolv, bsa + + +def add_zscores(df_scan_clt, column='delta_score'): + """Add z-scores to the dataframe. + + Parameters + ---------- + df_scan : pandas.DataFrame + Dataframe with the scan results for the model. + + colunm : str + Column to calculate the z-score. + + Returns + ------- + df_scan : pandas.DataFrame + Dataframe with the z-scores added. + """ + mean_delta = np.mean(df_scan_clt[column]) + std_delta = np.std(df_scan_clt[column]) + if std_delta > 0.0: + df_scan_clt['z_score'] = (df_scan_clt[column] - mean_delta) / std_delta + else: + df_scan_clt['z_score'] = 0.0 + return df_scan_clt + + +class ClusterOutputer(): + """Manage the generation of alascan outputs for cluster-based analysis.""" + def __init__( + self, + cluster_scan_data: Dict[str, Dict[str, Union[float, int]]], + clt_id: str, + clt_population: int, + scan_residue: str = "ALA", + generate_plot: bool = False, + offline: bool = False, + ): + """Initialization function + + Parameters + ---------- + cluster_scan_data : Dict[str, Dict[str, Union[float, int]]] + Dictionary containing alascan data per residue identifier. + clt_id : str + Cluster identifier + clt_population : int + Number of entries in this cluster. + scan_residue : str, optional + Residue scanned, by default "ALA" + generate_plot : bool, optional + Defines if a plot must be generated, by default False + offline : bool, optional + Defines if the plot should be functional offline, by default False + """ + self.cluster_scan_data = cluster_scan_data + self.clt_id = clt_id + self.clt_population = clt_population + self.scanned_residue = scan_residue + self.generate_plot = generate_plot + self.offline = offline + + def run(self) -> str: + """Wrtie cluster alascan output to scan_clt_X.tsv file, + including average and stdard deviation data per residue + and optionally save cluster alascan plots (if generate_plot == True) + + Return + ------ + scan_clt_filename : str + Name of the tsv file written + """ + # Gather all data in a list + clt_data = [] + # Loop over residues + for ident, clt_res_dt in self.cluster_scan_data.items(): + # Split identifier to retrieve residue data + chain = ident.split("-")[0] + resid = int(ident.split("-")[1]) + resname = ident.split("-")[2] + # Compute averages and stddev and hold data. + clt_data.append([ + chain, + resid, + resname, + ident, + np.mean(clt_res_dt['delta_score']), + np.std(clt_res_dt['delta_score']), + np.mean(clt_res_dt['delta_vdw']), + np.std(clt_res_dt['delta_vdw']), + np.mean(clt_res_dt['delta_elec']), + np.std(clt_res_dt['delta_elec']), + np.mean(clt_res_dt['delta_desolv']), + np.std(clt_res_dt['delta_desolv']), + np.mean(clt_res_dt['delta_bsa']), + np.std(clt_res_dt['delta_bsa']), + clt_res_dt['frac_pr'] / self.clt_population, + ]) + df_cols = [ + 'chain', 'resid', 'resname', 'full_resname', + 'delta_score', 'delta_score_std', 'delta_vdw', 'delta_vdw_std', + 'delta_elec', 'delta_elec_std', 'delta_desolv', 'delta_desolv_std', + 'delta_bsa', 'delta_bsa_std', 'frac_pres', + ] + df_scan_clt = pd.DataFrame(clt_data, columns=df_cols) + # adding clt-based Z score + df_scan_clt = add_zscores(df_scan_clt, 'delta_score') + # Sort rows + df_scan_clt.sort_values(by=['chain', 'resid'], inplace=True) + # Generate output CSV data + csv_data = io.StringIO() + df_scan_clt.to_csv( + csv_data, + index=False, + float_format='%.2f', + sep="\t") + csv_data.seek(0) + # Define output csv filepath + scan_clt_filename = f"scan_clt_{self.clt_id}.tsv" + # Write the file + with open(scan_clt_filename, "w") as fout: + # add comment to the file + fout.write(f"{'#' * 80}{os.linesep}") + fout.write(f"# `alascan` cluster results for cluster {self.clt_id}{os.linesep}") # noqa E501 + fout.write(f"# reported values are the average for the cluster{os.linesep}") # noqa E501 + fout.write(f"#{os.linesep}") + fout.write(f"# z_score is calculated with respect to the mean values of all residues{os.linesep}") # noqa E501 + fout.write(f"{'#' * 80}{os.linesep}") + # Write csv data content + fout.write(csv_data.read()) + + # Generate plot + self.gen_alascan_plot(df_scan_clt) + + return scan_clt_filename + + def gen_alascan_plot(self, df_scan_clt: pd.DataFrame) -> None: + """Generate the alascan plot based on provided data. + + Parameters + ---------- + df_scan_clt : pd.DataFrame + The data frame containing the data to be plotted. + """ + # Check if the plot must be generated + if not self.generate_plot: + return + + # Try to plot the data + try: + make_alascan_plot( + df_scan_clt, + self.clt_id, + self.scanned_residue, + offline=self.offline, + ) + except Exception as e: + log.warning( + "Could not create interactive plot. The following error" + f" occurred {e}" + ) + + +class AddDeltaBFactor(): + """Add delta score in bfactor column of a PDB.""" + def __init__( + self, + model: PDBFile, + path: Path, + model_results: List[MutationResult], + ): + """Initialisation function + + Parameters + ---------- + model : PDBFile + PDBfile model to be modified + path : Path + Where to write the new file + """ + self.model = model + self.path = path + self.input_results = model_results + + def run(self) -> PDBFile: + """Perform the addition of delta scores as bfactor in pdb file.""" + self.reorder_results() + # Define new pdb filename + model_fname = self.model.file_name.removesuffix(".pdb") + output_fname = f"{model_fname}_alascan.pdb" + # Add delta_score as a bfactor to the model + self.write_delta_score_to_pdb(output_fname) + # Update attributes of the model + self.model.ori_name = self.model.file_name + self.model.file_name = output_fname + self.model.full_name = output_fname + self.model.rel_path = Path("..", Path(self.path).name, output_fname) + self.model.path = str(Path(".").resolve()) + return self.model + + def write_delta_score_to_pdb(self, output_path: Path) -> Path: + """Add delta scores as b-factors in PDB file. + + Parameters + ---------- + output_path : Path + Path to the pdb file. + + Returns + ------- + output_path : Path + Path to the pdb file with the b-factors added. + """ + # Input pdb file path + input_pdbfile = Path(self.model.path, self.model.file_name) + # Start writting file containing bfactor + with open(input_pdbfile, "r") as fin, open(output_path, "w") as fout: + for line in fin: + if line.startswith("ATOM"): + chain = line[21] + resid = int(line[22:26]) + chain_res_key = f"{chain}-{resid}" + try: + delta_score = self.model_results[chain_res_key] + norm_delta = self.normalize_score(delta_score) + except KeyError: + norm_delta = 0.0 + # Generate the bfactor string + delta_str = f"{norm_delta:.2f}".rjust(6, " ") + # Modify the PDB line + line = line[:60] + delta_str + line[66:] + fout.write(line) + return output_path + + def reorder_results(self) -> None: + """Perform initial data manuputation to simply downstream access. + + Organise mutation results into dictionary, with chain-resid keys + and values delta score (e.g.: {"A-115": 5}), + and determine min and max score within the model to normalize data. + """ + self.model_results: Dict[str, float] = {} + all_delta_scores: List[float] = [] + # Loop over mutation results + for mut_result in self.input_results: + # Create key + chain_res_key = f"{mut_result.chain}-{mut_result.resid}" + # Point delta score value + delta_score = mut_result.delta_scores[0] + # Hold data + self.model_results[chain_res_key] = delta_score + all_delta_scores.append(delta_score) + # Obtain min and max delta score to be able to normalize later + if len(all_delta_scores) >= 1: + self.min_score = min(all_delta_scores) + self.max_score = max(all_delta_scores) + else: + self.min_score = -1 + self.max_score = 1 + + def normalize_score(self, score: float) -> float: + """Normalise the input score based on observed scores for this model + + In case normalisation cannot be performed, returns 50.0 + + Parameters + ---------- + score : float + Input score to be normalized + + Returns + ------- + norm100 : float + Normalized score between 0 and 100 + """ + try: + norm = (score - self.min_score) / (self.max_score - self.min_score) + except ZeroDivisionError: + norm = 0.5 + norm100 = 100 * norm + return norm100 + + +def write_scan_out(results: List[MutationResult], model_id: str) -> None: + """ + Save mutation results per model to tsv file. + + Parameters + ---------- + results : List[MutationResult] + List of mutation results from scanning (comes from MutationResult) + model_id : str + Identifier for the model used in filename. + + Returns + ------- + None + Function saves results to file `scan_{model_id}.tsv`. + + Notes + ----- + If results list is empty, no file is created. + """ + if not results: + print(f"No scan results for model {model_id}") + return + + # Convert scan output to dataframe + scan_data = [] + native_score = None + for result in results: + if result.success: + m_score, m_vdw, m_elec, m_des, m_bsa = result.mutant_scores + d_score, d_vdw, d_elec, d_des, d_bsa = result.delta_scores + + scan_data.append([ + result.chain, result.resid, result.ori_resname, + result.target_resname, m_score, m_vdw, m_elec, m_des, m_bsa, + d_score, d_vdw, d_elec, d_des, d_bsa + ]) + + # Get native score from first result (mutant + delta = native) + if native_score is None: + native_score = result.mutant_scores[0] + result.delta_scores[0] + + if scan_data: + df_columns = ['chain', 'res', 'ori_resname', 'end_resname', + 'score', 'vdw', 'elec', 'desolv', 'bsa', + 'delta_score', 'delta_vdw', 'delta_elec', + 'delta_desolv', 'delta_bsa'] + + df_scan = pd.DataFrame(scan_data, columns=df_columns) + # Compute z-scores + df_scan = add_zscores(df_scan, 'delta_score') + + # Sort by chain id, then by residue id + df_scan.sort_values(by=['chain', 'res'], inplace=True) + + # Get csv data as string + csv_io = io.StringIO() + df_scan.to_csv(csv_io, index=False, float_format="%.2f", sep="\t") + csv_io.seek(0) + # Save to tsv + output_file = f"scan_{model_id}.tsv" + with open(output_file, "w") as fout: + # Write comments at start of the file + fout.write(f"{'#' * 80}{os.linesep}") + fout.write(f"# `alascan` results for {model_id}{os.linesep}") + fout.write(f"#{os.linesep}") + fout.write(f"# native score = {native_score}{os.linesep}") + fout.write(f"#{os.linesep}") + fout.write(f"# z_score is calculated with respect to the other residues{os.linesep}") + fout.write(f"{'#' * 80}{os.linesep}") + # Write csv content + fout.write(csv_io.read()) + + +def group_scan_by_cluster( + models: List[PDBFile], + results_by_model: Dict[str, MutationResult] + ) -> Tuple[ + Dict[str, Dict[str, Dict[str, Union[float, int]]]], + Dict[str, int] + ]: + """Group models alascan data per cluster. + + Parameters + ---------- + models : List[PDBFile] + List of input models + + Returns + ------- + clt_scan : Dict[str, Dict[str, Dict[str, Union[float, int]]]] + Dictionary containing alascan data for each cluster, grouped by + residue identifyer. + clt_pops: Dict[str, int] + Dictionary containing number of entries for each cluster. + """ + # Define holders + clt_scan: Dict[str, Dict[str, Dict[str, Union[float, int]]]] = {} + clt_pops: Dict[str, int] = {} + # Loop over models + for model in models: + # Point cluster id + cl_id = model.clt_id + # unclustered models have cl_id = None + if cl_id is None: + cl_id = "unclustered" + # Initiate key if this cluster id is encountered for the first time + if cl_id not in clt_scan: + clt_scan[cl_id] = {} + clt_pops[cl_id] = 0 + # Increase the population of that cluster + clt_pops[cl_id] += 1 + # Point scan results for this model + model_id = model.file_name.removesuffix(".pdb") + try: + model_scan_dt = results_by_model[model_id] + except KeyError: + pass + # Loop over the mutation results + for mut_result in model_scan_dt: + # Extract data related to residue information + chain = mut_result.chain + res = mut_result.resid + ori_resname = mut_result.ori_resname + # Define unique string identifying this residue + ident = f"{chain}-{res}-{ori_resname}" + # Create variable with appropriate key + if ident not in clt_scan[cl_id].keys(): + clt_scan[cl_id][ident] = { + "delta_score": [], + "delta_vdw": [], + "delta_elec": [], + "delta_desolv": [], + "delta_bsa": [], + "frac_pr": 0, + } + # Add data + delta_scores = mut_result.delta_scores + clt_scan[cl_id][ident]["delta_score"].append(delta_scores[0]) + clt_scan[cl_id][ident]["delta_vdw"].append(delta_scores[1]) + clt_scan[cl_id][ident]["delta_elec"].append(delta_scores[2]) + clt_scan[cl_id][ident]["delta_desolv"].append(delta_scores[3]) + clt_scan[cl_id][ident]["delta_bsa"].append(delta_scores[4]) + clt_scan[cl_id][ident]["frac_pr"] += 1 + return clt_scan, clt_pops + + +class InterfaceScanner: + """Scan interface of a model to get tartget residues and create + corresponding mutation jobs. + """ + + def __init__( + self, + model: Union[str, Path, Any], + mutation_res: str = "ALA", + params: Optional[Dict[str, Any]] = None, + library_mode: bool = True + ) -> None: + """ + Initialize InterfaceScanner for a single model. + + Parameters + ---------- + model : str, Path, or model object + HADDOCK model object (if library_mode = False) or + Path to PDB file (if library mode = True) + mutation_res : str + Target residue for mutation (default: "ALA") + params : dict, optional + Additional parameters for interface detection + (list on top of alascan/__inint__.py) + library_mode : bool + If True, execute mutations sequentially inside InterfaceScanner.run() + If False, just prepare jobs - execution will be taken care of in init.py + of alascan module by haddock Engine + """ + self.model = model + self.mutation_res = mutation_res + self.library_mode = library_mode + self.params = params or {} + self.point_mutations_jobs = [] + self.ligand_param_fname = self.params.get("ligand_param_fname", "") + self.ligand_top_fname = self.params.get("ligand_top_fname", "") + self.filter_resdic = { + key[-1]: value for key, value + in self.params.items() + if key.startswith("resdic") + } + if isinstance(model, PDBFile): + self.model_path = model.rel_path + self.model_id = model.file_name.removesuffix(".pdb") + else: + # for library mode + self.model_path = Path(model) + self.model_id = self.model_path.stem + + def run(self): + """ + Get interface residues and create mutation jobs. + If library_mode=True, also execute the mutations sequentially. + + Returns + ------- + Optional[List[ModelPointMutation]] + List of mutation jobs if library_mode=False, None if library_mode=True + """ + try: + # Calculate native scores + sc_dir = f"haddock3-score-{self.model_id}-{os.getpid()}" + try: + native_scores = calc_score( + self.model_path, + run_dir=sc_dir, + outputpdb=False, + ligand_param_fname=self.ligand_param_fname, + ligand_top_fname=self.ligand_top_fname, + ) + finally: + if os.path.exists(sc_dir): + shutil.rmtree(sc_dir) + + # Load coordinates + atoms = get_atoms(self.model_path) + coords, _chain_ranges = load_coords( + self.model_path, + atoms, + add_resname=True, + ) + + # Determine target residues: get interface, then apply user filers, if given + # Get all interface residues + cutoff = self.params.get("int_cutoff", 5.0) + interface = CAPRI.identify_interface(self.model_path, cutoff=cutoff) + + # get user_chains for the check down the line + user_chains = self.params.get("chains", []) + + # if user defined target residues, check they are in the interface + if self.filter_resdic != {'_': []}: + filtered_interface = {} + for chain in self.filter_resdic: + if chain in interface: + # Search for the intersection of user queried residues and interface residues + user_res_valid = list(set(self.filter_resdic[chain]).intersection(set(interface[chain]))) + # If at least one residue must be analyzed, add it to residues to be scanned + if user_res_valid: + filtered_interface[chain] = user_res_valid + interface = filtered_interface + + # if (user defined target chains) & (no user target residues) - do use user chains + elif user_chains: + interface = { + chain: res + for chain, res in interface.items() + if chain in user_chains + } + + # get all atoms of the model to verifiy residue type down the line + resname_dict = {} + for chain, resid, _atom, resname in coords.keys(): + key = f"{chain}-{resid}" + if key not in resname_dict: + resname_dict[key] = resname + + # Create mutation + output_mutants = self.params.get("output_mutants", False) + for chain in interface: + for res in interface[chain]: + ori_resname = resname_dict[f"{chain}-{res}"] + end_resname = self.mutation_res + # Skip if scan_residue is the same as original + # (e.g. skip ALA->ALA) + if ori_resname != end_resname: + job = ModelPointMutation( + model_path=self.model_path, + model_id=self.model_id, + chain=chain, + resid=res, + ori_resname=ori_resname, + target_resname=end_resname, + native_scores=native_scores, + output_mutants=output_mutants, + ligand_param_fname=self.ligand_param_fname, + ligand_top_fname=self.ligand_top_fname, + ) + self.point_mutations_jobs.append(job) + + # Execute jobs if in library mode + if self.library_mode: + log.info( + f"Executing {len(self.point_mutations_jobs)} " + f"mutations for {self.model_id}" + ) + results = [] + total = len(self.point_mutations_jobs) + + for i, job in enumerate(self.point_mutations_jobs, 1): + log.info( + f"Processing mutation {i}/{total}: " + f"{job.chain}:{job.resid} {job.ori_resname}" + f"->{job.target_resname}" + ) + result = job.run() + results.append(result) + if result.success: + log.info(f"Delta score: {result.delta_scores[0]:.2f}") + else: + log.warning(f"Failed: {result.error_msg}") + + write_scan_out(results, self.model_id) + else: + # return point_mutations_jobs back to alascan/__init__.py + return self.point_mutations_jobs + + except Exception as e: + log.error(f"Failed to scan model {self.model_id}: {e}") + raise + + +class ModelPointMutation: + """Executes a single point mutation.""" + def __init__( + self, + model_path: Path, + model_id: str, + chain: str, + resid: int, + ori_resname: str, + target_resname: str, + native_scores: Tuple[float, float, float, float, float], + output_mutants: bool = False, + ligand_param_fname: Union[Path, str] = "", + ligand_top_fname: Union[Path, str] = "", + ) -> None: + """ + Initialize a single point mutation job. + + Parameters + ---------- + model_path : Path + Path to the PDB file + model_id : str + Identifier for the model + chain : str + Chain identifier + resid : int + Residue number + ori_resname : str + Original residue name + target_resname : str + Target residue name for mutation + native_scores : tuple + Native model scores (score, vdw, elec, desolv, bsa) + output_mutants : bool + Whether to keep mutant PDB files + ligand_param_fname : Union[Path, str] + Path to additional parameter file used by CNS + ligand_top_fname : Union[Path, str] + Path to additional topology file used by CNS + """ + self.model_path = Path(model_path) + self.model_id = model_id + self.chain = chain + self.resid = resid + self.ori_resname = ori_resname + self.target_resname = target_resname + self.native_scores = native_scores + self.output_mutants = output_mutants + self.ligand_param_fname = ligand_param_fname + self.ligand_top_fname = ligand_top_fname + + def run(self): + """Execute the point mutation.""" + mutation_id = f"{self.model_id}_{self.chain}{self.resid}{self.target_resname}" + + try: + # Setup working directory + sc_dir = f"haddock3-score-{mutation_id}" + os.makedirs(sc_dir, exist_ok=True) + + # Perform point mutation on pdb file + mut_pdb = mutate(self.model_path, self.chain, self.resid, self.target_resname) + + # Calculate mutant scores + mutant_scores = calc_score( + mut_pdb, + run_dir=sc_dir, + outputpdb=self.output_mutants, + ligand_param_fname=self.ligand_param_fname, + ligand_top_fname=self.ligand_top_fname, + ) + + # Calculate deltas (native - mutant) + n_score, n_vdw, n_elec, n_des, n_bsa = self.native_scores + m_score, m_vdw, m_elec, m_des, m_bsa = mutant_scores + delta_scores = (n_score - m_score, n_vdw - m_vdw, n_elec - m_elec, + n_des - m_des, n_bsa - m_bsa) + + # Handle output files + em_mut_pdb = Path(f"{mut_pdb.stem}_hs.pdb") + if not self.output_mutants: + # if output_mutants = False, then remove both files + if os.path.exists(mut_pdb): + os.remove(mut_pdb) + if em_mut_pdb.exists(): + os.remove(em_mut_pdb) + else: + # othervise keep energy-minimized pdb + if os.path.exists(em_mut_pdb): + shutil.move(em_mut_pdb, mut_pdb) + # clean up scoring dir + if os.path.exists(sc_dir): + shutil.rmtree(sc_dir) + + return MutationResult( + model_id=self.model_id, chain=self.chain, resid=self.resid, + ori_resname=self.ori_resname, target_resname=self.target_resname, + mutant_scores=mutant_scores, delta_scores=delta_scores, success=True + ) + + except Exception as e: + return MutationResult( + model_id=self.model_id, chain=self.chain, resid=self.resid, + ori_resname=self.ori_resname, target_resname=self.target_resname, + mutant_scores=(0, 0, 0, 0, 0), delta_scores=(0, 0, 0, 0, 0), + success=False, error_msg=str(e) + ) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/.___pycache__ new file 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b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..69e4bcd297543c338b4ca0b482305bd45fb43c25 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/__init__.py @@ -0,0 +1,262 @@ +"""Calculate CAPRI metrics for the input models. + +By default the following metrics are calculated: + +- FNAT (fraction of native contacts), namely the fraction of + intermolecular contacts in the docked complex that are also + present in the reference complex. +- IRMSD (interface root mean square deviation), namely the RMSD + of the interface of the docked complex with respect + to the reference complex. +- LRMSD (ligand root mean square deviation), namely the RMSD of the + ligand of the docked complex with respect to the + reference complex upon superposition of the receptor. +- DOCKQ, a measure of the quality of the docked model obtained + by combining FNAT, IRMSD and LRMSD (see + Basu and Wallner 2016, 11 (8), e0161879). +- ILRMSD (interface ligand root mean square deviation), the RMSD of the + ligand of the docked complex with respect to the reference complex + upon superposition of the interface of the receptor. +- GLOBAL_RMSD, the full RMSD between the reference and the model. + +The following files are generated: + +- **capri_ss.tsv**: a table with the CAPRI metrics for each model. +- **capri_clt.tsv**: a table with the CAPRI metrics for each cluster of models (if clustering information is available). +""" + + +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import FilePath, Union +from haddock.libs.libontology import PDBFile +from haddock.libs.libparallel import Scheduler +from haddock.modules import BaseHaddockModule +from haddock.modules.analysis.caprieval.capri import ( + CAPRI, + capri_cluster_analysis, + dump_weights, + extract_data_from_capri_class, + extract_models_best_references, + ) +from pdbtools.pdb_wc import run as pdb_wc +from pdbtools.pdb_splitmodel import run as pdb_splitmodel + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module to calculate the CAPRI metrics.""" + + name = RECIPE_PATH.name + + def __init__( + self, + order: int, + path: Path, + init_params: FilePath = DEFAULT_CONFIG, + ) -> None: + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if contact executable is compiled.""" + return + + @staticmethod + def is_nested(models: list[Union[PDBFile, list[PDBFile]]]) -> bool: + for model in models: + if isinstance(model, list): + return True + return False + + def handle_input_reference(self, reference: Path) -> list[Path]: + """Validate the reference file by returning only one model. + + Parameters + ---------- + reference : Path + Path to the input reference structure, possibly containing + an ensemble. + + Returns + ------- + reference or first_model_path : Path + Path to the reference structure to be used downstream. + """ + # Extremly complicated stuff to manage the gathering of the sys.stdout, + # as the pdb_tools.pdb_wc is basically writing on it. + import sys + from io import TextIOWrapper, BytesIO + # Memorize previous sys.stdout + original_stdout = sys.stdout + # setup the new stdout environment + sys.stdout = TextIOWrapper(BytesIO(), sys.stdout.encoding) + + # Count number of models + with open(reference, "r") as fh: + pdb_wc(fh, "m") + # Get output + sys.stdout.seek(0) # Jump to the start + wc_return = sys.stdout.read() # Read output + # Restore original stdout + sys.stdout.close() + sys.stdout = original_stdout + # Parse output + # using here `\n` (and not os.linesep) as it is the output for pdb_wc + for line in wc_return.split("\n"): + if "No. models" in line: + sline = line.strip().split() + nb_models = int(sline[-1]) + break + # Return reference as only one structure present + if nb_models == 1: + return [reference] + + self.log( + f"Multiple structures ({nb_models}) found in reference file. " + "Using all conformations as reference." + ) + # Split models + with open(reference, "r") as ref_in: + pdb_splitmodel(ref_in, "reference_model") + # Gather individual references and sort them + references = sorted( + list(Path(".").glob("reference_model_*.pdb")), + key=lambda k: int(k.stem.split("_")[-1]), + ) + assert len(references) == nb_models, ( + "Issue while splitting references conformation: " + f"{nb_models} detected, {len(references)} generated" + ) + return references + + def get_reference(self, models: list[PDBFile]) -> list[Path]: + """Manage to obtain the reference structure to be used downstream. + + Parameters + ---------- + models : list[PDBFile] + List of input model to be evaluated, among which the best + can serve as reference structure if none provided. + + Returns + ------- + references : list[Path] + List of paths to the reference(s) structure to be used downstream. + """ + if self.params["reference_fname"]: + _reference = Path(self.params["reference_fname"]) + references = self.handle_input_reference(_reference) + else: + self.log( + "No reference structure provided. " + "Using the structure with the lowest score from previous step" + ) + # Sort by score to find the "best" + models.sort() + best_model = models[0] + assert isinstance(best_model, PDBFile), "Best model is not a PDBFile" + best_model_fname = best_model.rel_path + references = [best_model_fname] + return references + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + if type(self.previous_io) == iter: + _e = "This module cannot come after one that produced an iterable." + self.finish_with_error(_e) + + models = self.previous_io.retrieve_models(individualize=True) + if self.is_nested(models): + raise ValueError( + "CAPRI module cannot be executed after " + "modules that produce a nested list of models." + ) + + # dump previously used weights + dump_weights(self.order) + + # Get reference file + references = self.get_reference(models) + + # Each model is a job; this is not the most efficient way + # but by assigning each model to an individual job + # we can handle scenarios in which the models are hetergoneous + # for example during CAPRI scoring + jobs: list[CAPRI] = [] + # Loop over models + for i, model_to_be_evaluated in enumerate(models, start=1): + # `models_to_be_evaluated` cannot be a list, + # `CAPRI` class is expecting a single model + if isinstance(model_to_be_evaluated, list): + raise ValueError( + "CAPRI module cannot handle a list " + "of `model_to_be_evaluated`" + ) + # Loop over references + for ref_id, reference in enumerate(references, start=1): + jobs.append( + CAPRI( + identificator=i, + model=model_to_be_evaluated, + path=Path("."), + reference=reference, + params=self.params, + ref_id=ref_id, + ) + ) + + engine = Scheduler( + tasks=jobs, + ncores=self.params["ncores"], + max_cpus=self.params["max_cpus"], + ) + engine.run() + + jobs = engine.results + jobs = sorted(jobs, key=lambda capri: capri.identificator) + + # Extract best references per input model + best_ref_jobs = extract_models_best_references(jobs) + + # Write standard capri_ss file + extract_data_from_capri_class( + capri_objects=best_ref_jobs, + output_fname=Path(".", "capri_ss.tsv"), + sort_key=self.params["sortby"], + sort_ascending=self.params["sort_ascending"], + add_reference_id=len(references) > 1, + ) + + # Perform cluster analysis + capri_cluster_analysis( + capri_list=best_ref_jobs, + model_list=models, # type: ignore # ignore this here only if we are checking the return type of `retrieve_models` is not nested!! + output_fname="capri_clt.tsv", + clt_threshold=self.params["clt_threshold"], + # output_count=len(capri_jobs), + sort_key=self.params["sortby"], + sort_ascending=self.params["sort_ascending"], + path=Path("."), + ) + + # In case multiple references are provided, generate an additional file + # containing the information to traceback metrics related to each ref + if len(references) > 1: + extract_data_from_capri_class( + capri_objects=jobs, + output_fname=Path(".", "capri_ss_multiref.tsv"), + sort_key=self.params["sortby"], + sort_ascending=self.params["sort_ascending"], + add_reference_id=True, + ) + + # Send models to the next step, + # no operation is done on them + self.output_models = models # type: ignore # ignore this here only if we are checking the return type of `retrieve_models` is not nested!! + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/capri.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/capri.py new file mode 100644 index 0000000000000000000000000000000000000000..863e6cf643463eeeac9de54f4a2778bc816e05c1 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/capri.py @@ -0,0 +1,1150 @@ +"""CAPRI module.""" + +import copy +import json +import os +import shutil +import tempfile +from itertools import combinations +from math import isnan +from pathlib import Path + + +os.environ["OPENBLAS_NUM_THREADS"] = "1" + +import numpy as np +from pdbtools import pdb_segxchain +from scipy.spatial.distance import cdist + +from haddock import log +from haddock.core.defaults import CNS_MODULES +from haddock.core.typing import ( + Any, + AtomsDict, + FilePath, + Iterable, + NDFloat, + Optional, + ParamDict, + ParamMap, + Union, + ) +from haddock.gear.config import load as read_config +from haddock.libs.libalign import ( + ALIGNError, + calc_rmsd, + centroid, + check_chains, + get_align, + get_atoms, + kabsch, + load_coords, + make_range, + ) +from haddock.libs.libio import write_dic_to_file, write_nested_dic_to_file +from haddock.libs.libontology import PDBFile, PDBPath +from haddock.modules import get_module_steps_folders + + +WEIGHTS = ["w_elec", "w_vdw", "w_desolv", "w_bsa", "w_air"] + + +def get_previous_cns_step(sel_steps: list, st_order: int) -> Union[str, None]: + """ + Get the previous CNS step. + + Parameters + ---------- + run_path : Path + Path to the run folder. + + Returns + ------- + cns_step : str + Name of the CNS step. + """ + # get the previous CNS step + cns_step = None + # just to be careful, remove steps with more than one underscore + sel_steps = [step for step in sel_steps if step.count("_") == 1] + mod = min(st_order - 1, len(sel_steps) - 1) + # loop + while mod > -1: + st_name = sel_steps[mod].split("_")[1] + if st_name in CNS_MODULES: + cns_step = sel_steps[mod] + break + mod -= 1 + + return cns_step + + +def save_scoring_weights(cns_step: str) -> Path: + """Save the scoring weights in a json file. + + Parameters + ---------- + cns_step : str + Name of the CNS step. + + Returns + ------- + scoring_params_fname : Path + Path to the json file. + """ + cns_params = read_config(Path("..", cns_step, "params.cfg")) + key = list(cns_params["final_cfg"].keys())[0] + scoring_pars = {kv: cns_params["final_cfg"][key][kv] for kv in WEIGHTS} + + scoring_params_fname = Path("weights_params.json") + # write json file + with open(scoring_params_fname, "w", encoding="utf-8") as jsonf: + json.dump( + scoring_pars, + jsonf, + indent=4, + ) + return scoring_params_fname + + +def load_contacts( + pdb_f: Union[Path, PDBFile], + cutoff: float = 5.0, + numbering_dic: Optional[dict[str, dict[int, int]]] = None, + model2ref_chain_dict: Optional[dict[str, str]] = None, + keep_hetatm: bool = False, +) -> set[tuple]: + """Load residue-based contacts. + + Parameters + ---------- + pdb_f : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file of the model to have its atoms identified + cutoff : float, optional + Cutoff distance for the interface identification. + keep_hetatm : bool + Should HETATM coordinates be considered ? (default False) + + Returns + ------- + set(con_list) : set + set of unique contacts + """ + if isinstance(pdb_f, PDBFile): + pdb_f = pdb_f.rel_path + # get also side chains atoms + atoms = get_atoms(pdb_f, full=True) + ref_coord_dic, _ = load_coords( + pdb_f, + atoms, + numbering_dic=numbering_dic, + model2ref_chain_dict=model2ref_chain_dict, + keep_hetatm=keep_hetatm, + ) + # create coordinate arrays + coord_arrays: dict[str, NDFloat] = {} + coord_ids: dict[str, list[int]] = {} + for atom in ref_coord_dic.keys(): + chain = atom[0] + if chain not in coord_arrays.keys(): # initialize lists + coord_arrays[chain], coord_ids[chain] = [], [] # type: ignore + coord_arrays[chain].append(ref_coord_dic[atom]) # type: ignore + coord_ids[chain].append(atom[1]) # only the resid is appended + for chain in coord_arrays.keys(): + coord_arrays[chain] = np.array(coord_arrays[chain]) + + # combinations of chains + unique_chain_combs = list(combinations(sorted(coord_arrays.keys()), 2)) + + # calculating contacts + con_list: list[tuple] = [] + for pair in unique_chain_combs: + # cycling over each coordinate of the first chain + for s in range(coord_arrays[pair[0]].shape[0]): + s_xyz = coord_arrays[pair[0]][s].reshape(1, 3) + s_cid = coord_ids[pair[0]][s] + dist = cdist(s_xyz, coord_arrays[pair[1]]) + npw = np.where(dist < cutoff) + del dist + for k in range(npw[0].shape[0]): + con = (pair[0], s_cid, pair[1], coord_ids[pair[1]][npw[1][k]]) + con_list.append(con) + return set(con_list) + + +class CAPRI: + """CAPRI class.""" + + def __init__( + self, + identificator: int, + model: PDBPath, + path: Path, + reference: PDBPath, + params: ParamMap, + ref_id: int = 1, + ) -> None: + """ + Initialize the class. + + Parameters + ---------- + identificator : int + The identificator of the object. + model : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + The model to be evaluated. + path : Path + Reference that defines where output should be saved. + reference : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + The reference structure. + params : dict + The parameters for the CAPRI evaluation. + """ + self.reference = reference + if not isinstance(model, PDBFile): + self.model = PDBFile(model) + self.md5 = "" + self.score = float("nan") + else: + self.model = model + self.md5 = model.md5 + self.score = model.score + self.path = path + self.params = params + self.irmsd = float("nan") + self.lrmsd = float("nan") + self.ilrmsd = float("nan") + self.fnat = float("nan") + self.dockq = float("nan") + self.rmsd = float("nan") + self.allatoms = params["allatoms"] + self.atoms = self._load_atoms(model, reference, full=self.allatoms) + self.r_chain = params["receptor_chain"] + self.l_chains = params["ligand_chains"] + self.keep_hetatm = params["keep_hetatm"] + self.model2ref_numbering = None + self.model2ref_chain_dict = None + self.output_ss_fname = Path(f"capri_ss_{identificator}.tsv") + self.output_clt_fname = Path(f"capri_clt_{identificator}.tsv") + self.output = self.output_ss_fname + self.identificator = identificator + self.core_model_idx = identificator + self.ref_id = ref_id + + def calc_irmsd(self, cutoff: float = 5.0) -> None: + """Calculate the I-RMSD. + + Parameters + ---------- + cutoff : float + The cutoff distance for the intermolecular contacts. + """ + # Identify reference interface + ref_interface_resdic = self.identify_interface( + self.reference, + cutoff, + keep_hetatm=self.keep_hetatm, + ) + + if len(ref_interface_resdic) == 0: + log.warning("No reference interface found") + else: + # Load interface coordinates + ref_coord_dic, _ = load_coords( + self.reference, + self.atoms, + ref_interface_resdic, + keep_hetatm=self.keep_hetatm, + ) + try: + mod_coord_dic, _ = load_coords( + self.model, + self.atoms, + ref_interface_resdic, + numbering_dic=self.model2ref_numbering, + model2ref_chain_dict=self.model2ref_chain_dict, + keep_hetatm=self.keep_hetatm, + ) + except ALIGNError as alignerror: + log.warning(alignerror) + return + + # Here _coord_dic keys are matched + # and formatted as (chain, resnum, atom) + # we will use atoms that are present in both + P = [] + Q = [] + + for k in ref_coord_dic.keys() & mod_coord_dic.keys(): + ref_xyz = ref_coord_dic[k] + mod_xyz = mod_coord_dic[k] + + Q.append(ref_xyz) + P.append(mod_xyz) + + Q = np.asarray(Q) + P = np.asarray(P) + # write_coords("model.pdb", P) + # write_coords("ref.pdb", Q) + + Q = Q - centroid(Q) + P = P - centroid(P) + U = kabsch(P, Q) + P = np.dot(P, U) + + self.irmsd = calc_rmsd(P, Q) + # write_coords("model_aln.pdb", P) + # write_coords("ref_aln.pdb", Q) + + def calc_lrmsd(self) -> None: + """Calculate the L-RMSD.""" + ref_coord_dic, _ = load_coords( + self.reference, + self.atoms, + keep_hetatm=self.keep_hetatm, + ) + try: + mod_coord_dic, _ = load_coords( + self.model, + self.atoms, + numbering_dic=self.model2ref_numbering, + model2ref_chain_dict=self.model2ref_chain_dict, + keep_hetatm=self.keep_hetatm, + ) + except ALIGNError as alignerror: + log.warning(alignerror) + return + + Q = [] + P = [] + # Note: this MUST be sorted since we will use the indexes to + # separate between receptor and ligand coordinates + intersection = sorted(ref_coord_dic.keys() & mod_coord_dic.keys()) + + chain_ranges: dict[Any, Any] = {} + for i, segment in enumerate(intersection): + chain, _, _ = segment + if chain not in chain_ranges: + chain_ranges[chain] = [] + chain_ranges[chain].append(i) + + chain_ranges = make_range(chain_ranges) + obs_chains = list(chain_ranges.keys()) # observed chains + if len(obs_chains) < 2: + log.warning("Not enough chains for calculating lrmsd") + else: + r_chain, l_chains = check_chains(obs_chains, self.r_chain, self.l_chains) + r_start, r_end = chain_ranges[r_chain] + l_starts = [chain_ranges[_l][0] for _l in l_chains] + l_ends = [chain_ranges[_l][1] for _l in l_chains] + + for k in intersection: + ref_xyz = ref_coord_dic[k] + mod_xyz = mod_coord_dic[k] + + Q.append(ref_xyz) + P.append(mod_xyz) + + Q = np.asarray(Q) + P = np.asarray(P) + + # write_coords("ref_first.pdb", Q) + # write_coords("model_first.pdb", P) + + # get receptor and ligand coordinates + Q_r_first = Q[r_start : r_end + 1] + P_r_first = P[r_start : r_end + 1] + # write_coords("ref_r_first.pdb", Q_r_first) + # write_coords("model_r_first.pdb", P_r_first) + # Q_l_first = Q[l_start: l_end + 1] + # P_l_first = P[l_start: l_end + 1] + # write_coords("ref_l_first.pdb", Q_l_first) + # write_coords("model_l_first.pdb", P_l_first) + + # move to the origin of the receptor + + Q = Q - centroid(Q_r_first) + P = P - centroid(P_r_first) + + # get receptor coordinates + Q_r = Q[r_start : r_end + 1] + P_r = P[r_start : r_end + 1] + # Center receptors and get rotation matrix + # Q_r = Q_r - centroid(Q_r) + # P_r = P_r - centroid(P_r) + # write_coords("ref_r_centr.pdb", Q_r) + # write_coords("model_r_centr.pdb", P_r) + + U_r = kabsch(P_r, Q_r) + + # Apply rotation to complex + # - complex are now aligned by the receptor + P = np.dot(P, U_r) + + # write_coords("ref.pdb", Q) + # write_coords("model.pdb", P) + + # Identify ligand coordinates concatenating all the ligand chains + Q_l = np.empty((0, 3)) + P_l = np.empty((0, 3)) + for l_start, l_end in zip(l_starts, l_ends): + Q_l = np.concatenate((Q_l, Q[l_start : l_end + 1])) + P_l = np.concatenate((P_l, P[l_start : l_end + 1])) + # Q_l = Q[l_start: l_end + 1] + # P_l = P[l_start: l_end + 1] + + # write_coords("ref_l.pdb", Q_l) + # write_coords("model_l.pdb", P_l) + + # Calculate the RMSD of the ligands + self.lrmsd = calc_rmsd(P_l, Q_l) + + def calc_ilrmsd(self, cutoff: float = 10.0) -> None: + """Calculate the Interface Ligand RMSD. + + Parameters + ---------- + cutoff : float + The cutoff distance for the intermolecular contacts. + """ + # Identify interface + ref_interface_resdic = self.identify_interface( + self.reference, + cutoff, + keep_hetatm=self.keep_hetatm, + ) + # Load interface coordinates + + ref_int_coord_dic, _ = load_coords( + self.reference, + self.atoms, + ref_interface_resdic, + keep_hetatm=self.keep_hetatm, + ) + try: + mod_int_coord_dic, _ = load_coords( + self.model, + self.atoms, + ref_interface_resdic, + numbering_dic=self.model2ref_numbering, + model2ref_chain_dict=self.model2ref_chain_dict, + keep_hetatm=self.keep_hetatm, + ) + except ALIGNError as alignerror: + log.warning(alignerror) + return + + # write_coord_dic("ref.pdb", ref_int_coord_dic) + # write_coord_dic("model.pdb", mod_int_coord_dic) + + # find atoms present in both interfaces + Q_int = [] + P_int = [] + common_keys = ref_int_coord_dic.keys() & mod_int_coord_dic.keys() + for k in sorted(common_keys): + ref_xyz = ref_int_coord_dic[k] + mod_xyz = mod_int_coord_dic[k] + + Q_int.append(ref_xyz) + P_int.append(mod_xyz) + + Q_int = np.asarray(Q_int) + P_int = np.asarray(P_int) + + # write_coords("ref.pdb", Q_int) + # write_coords("model.pdb", P_int) + + chain_ranges: dict[Any, Any] = {} + for i, segment in enumerate(sorted(common_keys)): + chain, _, _ = segment + if chain not in chain_ranges: + chain_ranges[chain] = [] + chain_ranges[chain].append(i) + + chain_ranges = make_range(chain_ranges) + obs_chains = list(chain_ranges.keys()) # observed chains + if len(obs_chains) < 2: + log.warning("Not enough chains for calculating ilrmsd") + else: + r_chain, l_chains = check_chains(obs_chains, self.r_chain, self.l_chains) + r_start, r_end = chain_ranges[r_chain] + l_starts = [chain_ranges[l_chain][0] for l_chain in l_chains] + l_ends = [chain_ranges[l_chain][1] for l_chain in l_chains] + + # write_coords("ref.pdb", Q) + # write_coords("model.pdb", P) + + # put system at origin of the receptor interface + Q_r_int = Q_int[r_start : r_end + 1] + P_r_int = P_int[r_start : r_end + 1] + + Q_int = Q_int - centroid(Q_r_int) + P_int = P_int - centroid(P_r_int) + # put interfaces at the origin + + # find the rotation that minimizes the receptor interface rmsd + Q_r_int = Q_int[r_start : r_end + 1] + P_r_int = P_int[r_start : r_end + 1] + + U_int = kabsch(P_r_int, Q_r_int) + P_int = np.dot(P_int, U_int) + # just for checks. + # the interface rmsd for the rec interface should be almost zero + # Q_r_int = Q_int[r_start: r_end + 1] + # P_r_int = P_int[r_start: r_end + 1] + # r_rmsd = calc_rmsd(Q_r_int, P_int[r_start: r_end + 1]) + # print(r_rmsd) + # Identify ligand coordinates concatenating all the ligand chains + Q_l_int = np.empty((0, 3)) + P_l_int = np.empty((0, 3)) + for l_start, l_end in zip(l_starts, l_ends): + Q_l_int = np.concatenate((Q_l_int, Q_int[l_start : l_end + 1])) + P_l_int = np.concatenate((P_l_int, P_int[l_start : l_end + 1])) + # prior to multibody: + # Q_l_int = Q_int[l_start: l_end + 1] + # P_l_int = P_int[l_start: l_end + 1] + # write_coords("ref_l_int_fin.pdb", Q_l_int) + # write_coords("mod_l_int_fin.pdb", P_l_int) + + # # this will be the interface-ligand-rmsd + self.ilrmsd = calc_rmsd(P_l_int, Q_l_int) + + def calc_fnat(self, cutoff: float = 5.0) -> None: + """Calculate the frequency of native contacts. + + Parameters + ---------- + cutoff : float + The cutoff distance for the intermolecular contacts. + """ + ref_contacts = load_contacts( + self.reference, + cutoff, + keep_hetatm=self.keep_hetatm, + ) + if len(ref_contacts) != 0: + try: + model_contacts = load_contacts( + self.model, + cutoff, + numbering_dic=self.model2ref_numbering, # type: ignore + model2ref_chain_dict=self.model2ref_chain_dict, # type: ignore + keep_hetatm=self.keep_hetatm, + ) + except ALIGNError as alignerror: + log.warning(alignerror) + else: + intersection = ref_contacts & model_contacts + self.fnat = len(intersection) / float(len(ref_contacts)) + else: + log.warning("No reference contacts found") + + def calc_global_rmsd(self) -> None: + """Calculate the full structure RMSD.""" + # Load reference atomic coordinates + ref_coord_dic, _ = load_coords( + self.reference, + self.atoms, + keep_hetatm=self.keep_hetatm, + ) + # Load model atomic coordinates + try: + model_coord_dic, _ = load_coords( + self.model, + self.atoms, + numbering_dic=self.model2ref_numbering, + model2ref_chain_dict=self.model2ref_chain_dict, + keep_hetatm=self.keep_hetatm, + ) + except ALIGNError as alignerror: + log.warning(alignerror) + return + # Obtain list of coordinates + Q = [] + P = [] + for k in ref_coord_dic.keys() & model_coord_dic.keys(): + ref_xyz = ref_coord_dic[k] + mod_xyz = model_coord_dic[k] + Q.append(ref_xyz) + P.append(mod_xyz) + # Cast indo array + Q = np.asarray(Q) + P = np.asarray(P) + # Center to 0 + Q = Q - centroid(Q) + P = P - centroid(P) + # Obtain rotation matrix + U = kabsch(P, Q) + # Rotate model (the actual superimposition) + P = np.dot(P, U) + # Compute full RMSD + self.rmsd = calc_rmsd(P, Q) + + def calc_dockq(self) -> None: + """Calculate the DockQ metric.""" + self.dockq = 0.0 + if self.fnat: + self.dockq += float(self.fnat) / 3 + if self.irmsd: + irmsd_denom = 1 + (self.irmsd / 1.5) * (self.irmsd / 1.5) + self.dockq += (1 / irmsd_denom) / 3 + if self.lrmsd: + lrmsd_denom = 1 + (self.lrmsd / 8.5) * (self.lrmsd / 8.5) + self.dockq += (1 / lrmsd_denom) / 3 + + def has_cluster_info(self) -> bool: + """ + Check wether this object contains cluster information. + + Returns + ------- + bool + True if this object contains cluster information. + """ + has_cluster_info = False + if self.model.clt_id: + has_cluster_info = True + return has_cluster_info + + def run(self) -> Union[None, "CAPRI"]: + """Get the CAPRI metrics.""" + try: + align_func = get_align( + method=self.params["alignment_method"], + lovoalign_exec=self.params["lovoalign_exec"], + keep_hetatm=self.keep_hetatm, + ) + self.model2ref_numbering, self.model2ref_chain_dict = align_func( + self.reference, self.model, self.path + ) + except ALIGNError: + log.warning( + f"Alignment failed between {self.reference} " + f"and {self.model}, skipping..." + ) + return + # print(f"model2ref_numbering {self.model2ref_numbering}") + # print(f"model2ref_chain_dict {self.model2ref_chain_dict}") + if self.params["fnat"]: + fnat_cutoff = self.params["fnat_cutoff"] + self.calc_fnat(cutoff=fnat_cutoff) + + if self.params["irmsd"]: + irmsd_cutoff = self.params["irmsd_cutoff"] + self.calc_irmsd(cutoff=irmsd_cutoff) + + if self.params["lrmsd"]: + self.calc_lrmsd() + + if self.params["ilrmsd"]: + ilrmsd_cutoff = self.params["irmsd_cutoff"] + self.calc_ilrmsd(cutoff=ilrmsd_cutoff) + + if self.params["dockq"]: + self.calc_dockq() + + if self.params["global_rmsd"]: + self.calc_global_rmsd() + + # The scheduler will use the return of the `run` method as the output of the tasks + return copy.deepcopy(self) + + def __eq__(self, other): + if self.params["dockq"] and \ + not (isnan(self.dockq) or isnan(other.dockq)): + return self.dockq == other.dockq + elif self.params["fnat"] and \ + not (isnan(self.fnat) or isnan(other.fnat)): + return self.fnat == other.fnat + elif self.params["ilrmsd"] and \ + not (isnan(self.ilrmsd) or isnan(other.ilrmsd)): + return self.ilrmsd == other.ilrmsd + elif self.params["lrmsd"] and \ + not (isnan(self.lrmsd) or isnan(other.lrmsd)): + return self.lrmsd == other.lrmsd + elif self.params["irmsd"] and \ + not (isnan(self.irmsd) or isnan(other.irmsd)): + return self.irmsd == other.irmsd + elif self.params["global_rmsd"] and \ + not (isnan(self.rmsd) or isnan(other.rmsd)): + return self.rmsd == other.rmsd + return True + + def __lt__(self, other): + if self.params["dockq"] and \ + not (isnan(self.dockq) or isnan(other.dockq)): + return self.dockq > other.dockq + elif self.params["fnat"] and \ + not (isnan(self.fnat) or isnan(other.fnat)): + return self.fnat > other.fnat + elif self.params["ilrmsd"] and \ + not (isnan(self.ilrmsd) or isnan(other.ilrmsd)): + return self.ilrmsd < other.ilrmsd + elif self.params["lrmsd"] and \ + not (isnan(self.lrmsd) or isnan(other.lrmsd)): + return self.lrmsd < other.lrmsd + elif self.params["irmsd"] and \ + not (isnan(self.irmsd) or isnan(other.irmsd)): + return self.irmsd < other.irmsd + elif self.params["global_rmsd"] and \ + not (isnan(self.rmsd) or isnan(other.rmsd)): + return self.rmsd < other.rmsd + return False + + @staticmethod + def _load_atoms( + model: PDBPath, + reference: PDBPath, + full: bool = False, + ) -> AtomsDict: + """ + Load atoms from a model and reference. + + Parameters + ---------- + model : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file of the model to have its atoms identified + reference : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file of the model to have its atoms identified + full : bool + If False, only backbone atoms will be retrieved, otherwise all atoms + + Returns + ------- + atom_dic : dict + Dictionary containing atoms observed in model and reference + """ + model_atoms = get_atoms(model, full=full) + reference_atoms = get_atoms(reference, full=full) + atoms_dict: AtomsDict = {} + atoms_dict.update(model_atoms) + atoms_dict.update(reference_atoms) + return atoms_dict + + @staticmethod + def identify_interface( + pdb_f: PDBPath, + cutoff: float = 5.0, + keep_hetatm: bool = False, + ) -> dict[str, list[int]]: + """Identify the interface. + + Parameters + ---------- + pdb_f : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file of the model to have its atoms identified + cutoff : float, optional + Cutoff distance for the interface identification. + keep_hetatm : bool + Should HETATM coordinates be considered ? (default False) + + Returns + ------- + interface_resdic : dict[str, list[int]] + Dictionary holding list of interface residues ids for each chains. + """ + if isinstance(pdb_f, PDBFile): + pdb_f = pdb_f.rel_path + + interface_resdic: dict[str, list[int]] = {} + contacts = load_contacts(pdb_f, cutoff, keep_hetatm=keep_hetatm) + + for contact in contacts: + first_chain, first_resid, sec_chain, sec_resid = contact + + if first_chain not in interface_resdic: + interface_resdic[first_chain] = [] + if sec_chain not in interface_resdic: + interface_resdic[sec_chain] = [] + + if first_resid not in interface_resdic[first_chain]: + interface_resdic[first_chain].append(first_resid) + if sec_resid not in interface_resdic[sec_chain]: + interface_resdic[sec_chain].append(sec_resid) + + return interface_resdic + + @staticmethod + def add_chain_from_segid(pdb_path: PDBPath) -> Path: + """ + Replace the chainID with the segID. + + Parameters + ---------- + pdb_path : PosixPath or :py:class:`haddock.libs.libontology.PDBFile` + PDB file to be replaced + """ + if isinstance(pdb_path, PDBFile): + pdb_path = pdb_path.rel_path + temp_f = tempfile.NamedTemporaryFile(delete=False, mode="w+t") + with open(pdb_path) as fh: + for line in list(pdb_segxchain.run(fh)): + temp_f.writelines(line) + temp_f.close() + # REPLACE! + new_pdb_path = shutil.move(temp_f.name, pdb_path) + return new_pdb_path + + +def rank_according_to_score( + data: dict[int, ParamDict], sort_key: str, sort_ascending: bool +) -> dict[int, ParamDict]: + """ + Ranks a dictionary of data based on a specified sort key and sort order, + and assigns a rank to each entry based on its 'score' attribute. + + Args: + data (dict[int, ParamDict]): Dictionary where each key is an index and each + value is a ParamDict containing data attributes. + sort_key (str): Key by which to sort the data within the ParamDict. + Must correspond to a valid attribute in ParamDict. + sort_ascending (bool): If True, sorts the data in ascending order based on + the sort_key; if False, sorts in descending order. + + Returns: + dict[int, ParamDict]: A new dictionary where entries are sorted according + to the sort_key and optionally sorted order. Each entry + also includes a 'caprieval_rank' attribute indicating + its rank based on the 'score'. + """ + score_rankkey_values = [(k, v["score"]) for k, v in data.items()] + score_rankkey_values.sort(key=lambda x: x[1]) + + for i, k in enumerate(score_rankkey_values): + data_idx, _ = k + data[data_idx]["caprieval_rank"] = i + 1 + + # Sort according to the sort key + rankkey_values = [(k, v[sort_key]) for k, v in data.items()] + rankkey_values.sort( + key=lambda x: x[1], + reverse=True if not sort_ascending else False, + ) + + _data = {} + for i, (data_idx, _) in enumerate(rankkey_values): + _data[i + 1] = data[data_idx] + data = _data + + return _data + + +def extract_models_best_references(capri_objects: list[CAPRI]) -> list[CAPRI]: + """Extract best reference for each input model. + + Same input models are combined and best reference is later found by + sorting the CAPRI objects. Only the best performing CAPRI object is + kept and returned. + This step was implemented to handle comparisons against multiple refs. + + Parameters + ---------- + capri_objects : list[CAPRI] + List of CAPRI object. + + Returns + ------- + selected_capri_objects : list[CAPRI] + List of selected best CAPIR object for each model. + """ + # Group results by models + by_model_data: dict[int, dict[Path, CAPRI]] = {} + for capri in capri_objects: + model_data = by_model_data.setdefault(capri.identificator, []) + model_data.append(capri) + # Finds best performances for each model + selected_capri_objects: list[CAPRI] = [] + # Loop over model referneces performances + for references_perfs in by_model_data.values(): + # Sort them using built in __eq__ and __lt__ CAPRI methods + sorted_perfs = sorted(references_perfs) + # Select first on (best) + best_perf = sorted_perfs[0] + # Hold that guy + selected_capri_objects.append(best_perf) + return selected_capri_objects + + +def extract_data_from_capri_class( + capri_objects: list[CAPRI], + sort_key: str, + sort_ascending: bool, + output_fname: Path, + add_reference_id: bool = False, +) -> Union[dict[int, ParamDict], None]: + """Extracts data attributes from a list of CAPRI objects into a structured + dictionary, optionally sorts the data based on a specified key, and writes + the sorted data to a file. + + Parameters + ---------- + capri_objects : list[CAPRI] + List of CAPRI objects containing data attributes to be extracted. + sort_key : str + Key by which to sort the extracted data. Must correspond to a valid + attribute in the CAPRI object (e.g., 'score', 'irmsd'). + sort_ascending : bool + If True, sorts the data in ascending order based on the sort_key; + if False, sorts in descending order. + output_fname : Path + Path to the output file where the sorted data will be written. + add_reference_id : bool, optional + Should the reference id be added to the capri table?, by default False + + Returns + ------- + ranked_data : Union[dict[int, ParamDict], None] + The sorted and structured data dictionary if successful, + None if no data was processed. + """ + # Retrieve data for each model + data: dict[int, ParamDict] = {} + for i, c in enumerate(capri_objects, start=1): + data[i] = { + "model": c.model, + "md5": c.md5, + "caprieval_rank": None, + "score": c.score, + "irmsd": c.irmsd, + "fnat": c.fnat, + "lrmsd": c.lrmsd, + "ilrmsd": c.ilrmsd, + "dockq": c.dockq, + "rmsd": c.rmsd, + "cluster_id": c.model.clt_id if c.model.clt_id else None, + "cluster_ranking": c.model.clt_rank if c.model.clt_rank else None, + "model-cluster_ranking": ( + c.model.clt_model_rank if c.model.clt_model_rank else None + ), + } + if c.model.unw_energies is not None: + data[i].update(c.model.unw_energies) + if add_reference_id: + data[i]["ref_id"] = c.ref_id + # Sort models + ranked_data = rank_according_to_score( + data, sort_key=sort_key, sort_ascending=sort_ascending + ) + if not ranked_data: + # This means no files have been collected + return + else: + write_nested_dic_to_file(data_dict=ranked_data, output_fname=output_fname) + return ranked_data + + +def calc_stats(data: list) -> tuple[float, float]: + """ + Calculate the mean and stdev. + + Parameters + ---------- + data : list + List of values. + + Returns + ------- + mean : float + Mean of the values. + stdev : float + Standard deviation of the values. + """ + mean = np.mean(data) + stdev = np.std(data) + return mean, stdev + + +# Define dict types +CltData = dict[tuple[Optional[int], Union[int, str, None]], list[tuple[CAPRI, PDBFile]]] + + +def capri_cluster_analysis( + capri_list: Iterable[CAPRI], + model_list: Iterable[PDBFile], + output_fname: FilePath, + clt_threshold: int, + sort_key: str, + sort_ascending: bool, + path: FilePath, +) -> None: + """Consider the cluster results for the CAPRI evaluation.""" + capri_keys = ["irmsd", "fnat", "lrmsd", "dockq", "ilrmsd", "rmsd"] + model_keys = ["air", "bsa", "desolv", "elec", "total", "vdw"] + log.info(f"Rearranging cluster information into {output_fname}") + # get the cluster data + clt_data: CltData = dict(((m.clt_rank, m.clt_id), []) for m in model_list) + + # add models to each cluster + for capri, model in zip(capri_list, model_list): + clt_data[(model.clt_rank, model.clt_id)].append((capri, model)) + + output_dic: dict[int, ParamDict] = {} + + for i, element in enumerate(clt_data): + data: ParamDict = {} + number_of_models_in_cluster = len(clt_data[element]) + # rank, cluster id, number of models in cluster + data["cluster_rank"] = element[0] + data["cluster_id"] = element[1] + data["n"] = number_of_models_in_cluster + if number_of_models_in_cluster < clt_threshold: + # under-evaluated, the mean was divided by a value + # larger than the total number of models in the cluster + data["under_eval"] = "yes" + else: + data["under_eval"] = "-" + # score + try: + score_array = [e[1].score for e in clt_data[element][:clt_threshold]] + data["score"], data["score_std"] = calc_stats(score_array) + except KeyError: + data["score"] = float("nan") + data["score_std"] = float("nan") + + # capri keys + for key in capri_keys: + std_key = f"{key}_std" + try: + key_array = [vars(e[0])[key] for e in clt_data[element][:clt_threshold]] + data[key], data[std_key] = calc_stats(key_array) + except KeyError: + data[key] = float("nan") + data[std_key] = float("nan") + + # model keys + for key in model_keys: + std_key = f"{key}_std" + if clt_data[element][0][1].unw_energies: + try: + key_array = [ + vars(e[1])["unw_energies"][key] + for e in clt_data[element][:clt_threshold] + ] + data[key], data[std_key] = calc_stats(key_array) + except KeyError: + data[key] = float("nan") + data[std_key] = float("nan") + + output_dic[i] = data + + # Rank according to the score + score_rankkey_values = [(key, v["score"]) for key, v in output_dic.items()] + score_rankkey_values.sort(key=lambda x: x[1]) + for i, k in enumerate(score_rankkey_values): + idx, _ = k + output_dic[idx]["caprieval_rank"] = i + 1 + + # Rank according to the sorting key + rankkey_values = [(key, v[sort_key]) for key, v in output_dic.items()] + rankkey_values.sort( + key=lambda x: x[1], + reverse=True if not sort_ascending else False, + ) + + _output_dic = {} + for i, k in enumerate(rankkey_values): + idx, _ = k + _output_dic[i + 1] = output_dic[idx] + output_dic = _output_dic + + output_fname = Path(path, output_fname) + + info_header = "#" * 40 + os.linesep + info_header += "# `caprieval` cluster-based analysis" + os.linesep + info_header += "#" + os.linesep + info_header += f"# > sortby_key={sort_key}" + os.linesep + info_header += f"# > sort_ascending={sort_ascending}" + os.linesep + info_header += f"# > clt_threshold={clt_threshold}" + os.linesep + info_header += "#" + os.linesep + info_header += ( + "# NOTE: if under_eval=yes, it means that there were less models in" + " a cluster than" + os.linesep + ) + info_header += ( + "# clt_threshold, thus these values were under " "evaluated." + os.linesep + ) + info_header += ( + "# You might need to tweak the value of clt_threshold or change" + " some parameters" + os.linesep + ) + info_header += "# in `clustfcc` depending on your " "analysis." + os.linesep + info_header += "#" + os.linesep + info_header += "#" * 40 + + if not data: + # This means there were only "dummy" values + return + else: + write_nested_dic_to_file( + output_dic, + output_fname, + info_header=info_header, + ) + + +class CAPRIError(Exception): + """Raised when something goes wrong with the CAPRI class.""" + + def __init__(self, msg: str = "") -> None: + self.msg = msg + super().__init__(self.msg) + + +def dump_weights(order: int) -> None: + sel_steps = get_module_steps_folders(Path("..")) + cns_step = get_previous_cns_step(sel_steps=sel_steps, st_order=order) + if cns_step: + log.info(f"Found previous CNS step: {cns_step}") + scoring_params_fname = save_scoring_weights(cns_step) + log.info(f"Saved scoring weights to: {scoring_params_fname}") + else: + log.info("No previous CNS step found. Cannot save scoring weights.") + + +# # debug only +# def write_coord_dic(output_name, coord_dic): +# """Add a dummy atom to a PDB file according to a list of coordinates.""" +# with open(output_name, "w") as fh: +# for i, k in enumerate(coord_dic): +# atom_num = f"{i+1}".rjust(4, " ") +# chain, resnum, atom = k +# resnum = int(resnum) +# resnum = f"{resnum}".rjust(3, " ") +# atom_name = f"{atom}".rjust(3, " ") +# x, y, z = coord_dic[k] +# dum_x = f"{x:.3f}".rjust(7, " ") +# dum_y = f"{y:.3f}".rjust(7, " ") +# dum_z = f"{z:.3f}".rjust(7, " ") +# dummy_line = ( +# f"ATOM {atom_num} {atom_name} DUM {chain} {resnum} " +# f" {dum_x} {dum_y} {dum_z} 1.00 1.00 " +# " H " + os.linesep +# ) +# fh.write(dummy_line) + + +# # debug only +# def write_coords(output_name, coor_list): +# """Add a dummy atom to a PDB file according to a list of coordinates.""" +# with open(output_name, "w") as fh: +# for i, dummy_coord in enumerate(coor_list): +# atom_num = f"{i}".rjust(4, " ") +# resnum = f"{i}".rjust(3, " ") +# dum_x = f"{dummy_coord[0]:.3f}".rjust(7, " ") +# dum_y = f"{dummy_coord[1]:.3f}".rjust(7, " ") +# dum_z = f"{dummy_coord[2]:.3f}".rjust(7, " ") +# dummy_line = ( +# f"ATOM {atom_num} H DUM X {resnum} " +# f" {dum_x} {dum_y} {dum_z} 1.00 1.00 " +# " H " + os.linesep +# ) +# fh.write(dummy_line) + + +# # debug only +# def write_pymol_viz(resdic): +# """Write PyMol vizualitation.""" +# for k in resdic: +# reslist = "+".join(map(str, resdic[k])) +# cmd = f"sele {k}, chain {k} and resid {reslist}" +# print(cmd) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..62821a00e2d48631ff6abf652cc4dfa8bd9f71b3 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/defaults.yaml @@ -0,0 +1,209 @@ +reference_fname: + default: '' + type: file + title: Reference structure + short: Structure to be used when calculating the CAPRI metrics. + long: Reference tructure to be used when calculating the CAPRI metrics. + If none is defined then the lowest scoring model is selected by default. + group: analysis + explevel: easy + +irmsd: + default: true + type: boolean + title: Calculate I-RMSD + short: Performs Interface RMSD calculations. + long: Calculates the Interface Root Mean Square Deviation. + This calculate the RMSD of interface backbone atoms after fitting on the interface backbone atoms. + The interface is idenfied based on intermolecular contacts shorter than the defined irmsd_cutoff. + group: analysis + explevel: easy + +fnat: + default: true + type: boolean + title: Calculate FNAT + short: Performs FNAT calculations. + long: Calculates the Fraction of Native Contacts. This evaluates how many contacts observed + in the reference are present in the model. The distance cutoff used to define intermolecular contacts is + defined by the fnat_cutoff parameter. + group: analysis + explevel: easy + +lrmsd: + default: true + type: boolean + title: Calculate L-RMSD + short: Performs Ligand RMSD calculations. + long: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing + the receptors (defined by the receptor_chain parameter) and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). + Superposition and RMSD calculations are done on backbone heavy atoms. + group: analysis + explevel: easy + +ilrmsd: + default: true + type: boolean + title: Calculate I-L-RMSD + short: Performs Interface Ligand RMSD calculations. + long: Calculates the Interface Ligand Root Mean Square Deviation. This calculation is done by superimposing the model and the target + on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms + of the ligand (defined by the ligand_chains parameter). + group: analysis + explevel: easy + +dockq: + default: true + type: boolean + title: Calculate DockQ + short: Evaluate DockQ. + long: Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, + a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879` + group: analysis + explevel: easy + +global_rmsd: + default: true + type: boolean + title: Calculate global RMSD + short: Calculate full structure RMSD. + long: Compute full structure RMSD between reference structure and the model + after superimposition. Note that a sequence alignment is performed to + obtain the mapping between the reference and the model. If the one of + the structure contain a 'small-molecule', we assume that the compared + structure atoms are in the same order. With default parameters `allatoms = false`, only + backbone RMSD will be computed. + group: analysis + explevel: easy + +irmsd_cutoff: + default: 10.0 + type: float + min: 3.0 + max: 20.0 + precision: 3 + title: Distance cutoff (Å) used to define interface residues. + short: Distance cutoff (Å) used to define interface residues based on intermolecular contacts. + long: Distance cutoff (Å) used to define interface residues based on intermolecular contacts. + group: analysis + explevel: easy + +fnat_cutoff: + default: 5.0 + type: float + min: 3.0 + max: 20. + precision: 3 + title: Distance cutoff (Å) used to define interface contacts. + short: Distance cutoff (Å) used to define interface contacts between two interacting molecules. + long: Distance cutoff (Å) used to define interface contacts between two interacting molecules. + group: analysis + explevel: easy + +receptor_chain: + default: A + type: string + minchars: 1 + maxchars: 1 + title: Receptor ChainID + short: Receptor ChainID to be considered for the RMSD calculations. + long: Receptor ChainID to be considered for the RMSD calculations. This determines which chain will be + treated as the receptor for the L-RMSD and for I-L-RMSD. + group: analysis + explevel: easy + +ligand_chains: + default: [] + type: list + minitems: 0 + maxitems: 100 + title: Ligand ChainIDs + short: Ligand ChainIDs to be considered for the RMSD calculations. + long: Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be + treated as the ligand for the L-RMSD and for I-L-RMSD. + group: analysis + explevel: easy + +sortby: + default: score + type: string + minchars: 0 + maxchars: 20 + choices: + - score + - irmsd + - lrmsd + - ilrmsd + - fnat + - dockq + title: Sort the structures/clusters in the output file by this value + short: Which value should be used to sort the output. + long: Which value should be used to sort the output, the output table will be sorted accordingly. + group: analysis + explevel: easy + +sort_ascending: + default: true + type: boolean + title: Sort in ascending order + short: Sort in ascending order. + long: Sort in ascending order. + group: analysis + explevel: easy + +alignment_method: + default: sequence + type: string + minchars: 0 + maxchars: 100 + choices: + - structure + - sequence + title: Alignment method used to match the numbering. + short: Which alignment method should be used to match the numbering. + long: Alignment method used to match the numbering. Sequence alignment is haddock3-friendly but might not produce best results + for structures that are too different, for that use + group: analysis + explevel: easy + +lovoalign_exec: + default: '' + type: string + minchars: 0 + maxchars: 200 + title: Location (path) of the LovoAlign executable + short: Location (path) of the LovoAlign executable. + long: Location (path) of the LovoAlign executable. + group: analysis + explevel: easy + +clt_threshold: + default: 4 + type: integer + min: 1 + max: 1000 + title: Threshold (n) used for the average evaluation in the cluster-based output + short: Threshold (n) used for the average evaluation in the cluster-based output. + long: Threshold (n) used for the average evaluation in the cluster-based output. + group: analysis + explevel: easy + +allatoms: + default: false + type: boolean + title: Atoms to be considered during the analysis. + short: Atoms to be considered during the analysis. + long: Atoms to be considered during the analysis. If false (default), only + backbone atoms will be considered, otherwise all the heavy-atoms. + group: analysis + explevel: easy + +keep_hetatm: + default: false + type: boolean + title: HETATM to be considered during the analysis. + short: HETATM to be considered during the analysis. + long: HETATM to be considered during the analysis. If false (default), only + ATOM coordinates lines will be used, otherwise the HETATM from reference will also be used. + group: analysis + explevel: easy \ No newline at end of file diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._clustfcc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._clustfcc.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._clustfcc.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..fca46cb8644b3bd7b63344a6f38df69020e49f96 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/__init__.py @@ -0,0 +1,220 @@ +"""Fraction of Common Contacts (FCC) clustering module. + +The module takes the models generated in the previous step and calculates the +contacts between them. Then, the module calculates the FCC matrix and clusters +the models based on their contact similarities. + +For more details please check +*Rodrigues, J. P. et al. +Proteins: Struct. Funct. Bioinform. +80, 1810–1817 (2012)* +""" + +import os +from pathlib import Path + +from haddock import log +from haddock.core.defaults import CONTACT_FCC_EXEC, MODULE_DEFAULT_YAML +from haddock.core.exceptions import ModuleError +from haddock.core.typing import Union +from haddock.libs.libclust import ( + add_cluster_info, + get_cluster_matrix_plot_clt_dt, + plot_cluster_matrix, + rank_clusters, + write_structure_list, + ) +from haddock.libs.libfcc import ( + calculate_pairwise_matrix, + Cluster, + Element, + parse_contact_file, + create_elements, + ) +from haddock.libs.libsubprocess import JobInputFirst +from haddock.modules import BaseHaddockModule, get_engine +from haddock.modules.analysis import get_analysis_exec_mode +from haddock.modules.analysis.clustfcc.clustfcc import ( + get_cluster_centers, + iterate_clustering, + write_clusters, + write_clustfcc_file, + ) + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module for clustering with FCC.""" + + name = RECIPE_PATH.name + + def __init__( + self, + order: int, + path: Path, + initial_params: Union[Path, str] = DEFAULT_CONFIG, + ) -> None: + super().__init__(order, path, initial_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if FCC is installed and available.""" + # The FCC binary can be either in the default binary path or in the + if not CONTACT_FCC_EXEC.exists(): + raise ModuleError( + f"CONTACT FCC execultable not found at: {CONTACT_FCC_EXEC}" + ) + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + models_to_clust = self.previous_io.retrieve_models(individualize=True) + + # Calculate the contacts for each model + log.info("Calculating contacts") + contact_jobs: list[JobInputFirst] = [] + for model in models_to_clust: + pdb_f = Path(model.rel_path) # type: ignore + contact_f = Path(model.file_name.replace(".pdb", ".con")) # type: ignore # noqa : E501 + job = JobInputFirst( + pdb_f, + contact_f, + CONTACT_FCC_EXEC, + self.params["contact_distance_cutoff"], + ) + contact_jobs.append(job) + + exec_mode = get_analysis_exec_mode(self.params["mode"]) + + Engine = get_engine(exec_mode, self.params) + engine = Engine(contact_jobs) + engine.run() + + contact_file_l: list[str] = [] + not_found: list[str] = [] + for job in contact_jobs: + if not job.output.exists(): + # NOTE: If there is no output, most likely the models are not in + # contact there is no way of knowing how many models are not in + # contact, it can be only one, or could be all of them. + not_found.append(job.input.name) + log.warning(f"Contact was not calculated for {job.input.name}") + else: + contact_file_l.append(str(job.output)) + + # Check if any contact file could not be retrieved + if not_found: + # No contacts were calculated, we cannot cluster + self.finish_with_error( + f"Several files were not generated: {not_found}" + ) + + log.info("Calculating the FCC matrix") + parsed_contacts = parse_contact_file( + contact_file_l, + False, + ) + + # Imporant: matrix is a generator object, be careful with it + matrix_gen = calculate_pairwise_matrix( + parsed_contacts, + False, + ) + + # write the matrix to a file, so we can read it afterwards and don't + # need to reinvent the wheel handling this + fcc_matrix_f = Path("fcc.matrix") + matrix = list(matrix_gen) + with open(fcc_matrix_f, "w") as fh: + for data in matrix: + data_str = f"{data[0]} {data[1]} {data[2]:.2f} {data[3]:.3f}" + fh.write(f"{data_str}{os.linesep}") + + # Cluster + log.info("Clustering...") + pool = create_elements( + matrix, + self.params["clust_cutoff"], + self.params["strictness"], + ) + + if not pool: + self.params["min_population"] = 1 + clusters = [Cluster(1, Element(1))] + else: + # iterate clustering until at least one cluster is found + clusters, min_population = iterate_clustering( + pool, + self.params["min_population"], + ) + self.params["min_population"] = min_population + + # Prepare output and read the elements + if clusters: + # Write the clusters + write_clusters(clusters) + + # Get the cluster centers + clt_dic, clt_centers = get_cluster_centers( + clusters, + models_to_clust, + ) + + # ranking clusters + _scores, sorted_score_dic = rank_clusters( + clt_dic, self.params["min_population"], + ) + + # Add this info to the models + self.output_models = add_cluster_info(sorted_score_dic, clt_dic) + + # Write unclustered structures + write_structure_list( + models_to_clust, + self.output_models, + out_fname="clustfcc.tsv", + ) + + write_clustfcc_file( + clusters, clt_centers, clt_dic, self.params, sorted_score_dic + ) + else: + log.warning("No clusters were found") + self.output_models = models_to_clust # type: ignore + + # Draw the matrix + if self.params["plot_matrix"]: + # Obtain final models indices + final_order_idx, labels, cluster_ids = [], [], [] + for pdb in self.output_models: + final_order_idx.append(models_to_clust.index(pdb)) + labels.append(pdb.file_name.replace(".pdb", "")) + cluster_ids.append(pdb.clt_id) + # Get custom cluster data + matrix_cluster_dt, cluster_limits = get_cluster_matrix_plot_clt_dt( + cluster_ids + ) + + # Define output filename + html_matrix_basepath = "fcc_matrix" + # Plot matrix + html_matrixpath = plot_cluster_matrix( + fcc_matrix_f, + final_order_idx, + labels, + dttype="FCC", + diag_fill=1, + output_fname=html_matrix_basepath, + matrix_cluster_dt=matrix_cluster_dt, + cluster_limits=cluster_limits, + ) + if html_matrixpath: + log.info(f"Plotting matrix in {html_matrixpath}") + else: + log.warning("Cluster matrix was not generated") + + # Export models for next module + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/clustfcc.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/clustfcc.py new file mode 100644 index 0000000000000000000000000000000000000000..a50e28bed8af3e0f2f4f2527245d3ef3250145b7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/clustfcc.py @@ -0,0 +1,209 @@ +"""FCC clustering.""" + +import os +from pathlib import Path + +import numpy as np + +from haddock import log +from haddock.libs.libfcc import ( + Cluster, + cluster_elements, + Element, + output_clusters, + ) + + +def iterate_clustering( + pool: dict[int, Element], + min_population_param: int, + ) -> tuple[list[Cluster], int]: + """ + Iterate over the clustering process until a cluster is found. + + Parameters + ---------- + pool : fcc.Pool + The pool object containing the fcc matrix. + + min_population_param : int + The min_population parameter to start the clustering process. + + Returns + ------- + clusters : list[Cluster] + A list of clusters. + + min_population : int + The min_population used to obtain the clusters. + """ + # Loop from min_population to population == 1 + for min_population in range(min_population_param, 0, -1): + log.info(f"Clustering with min_population={min_population}") + _, clusters = cluster_elements( + pool, + threshold=min_population, + ) + # No clusters found + if not clusters: + log.info("[WARNING] No cluster was found, decreasing min_population!") + # Clusters were generated + else: + break + return clusters, min_population + + +def write_clusters(clusters, out_filename="cluster.out"): + """ + Write the clusters to the cluster.out file. + + Parameters + ---------- + clusters : list + A list of clusters. + + out_filename : str, optional + The name of the output file. The default is "cluster.out". + + Returns + ------- + None + """ + # write the classic output file for compatibility reasons + log.info(f"Saving output to {out_filename}") + cluster_out = Path(out_filename) + with open(cluster_out, "w") as fh: + output_clusters(fh, clusters) + fh.close() + + +def get_cluster_centers(clusters, models_to_cluster): + """ + Get the cluster centers and the cluster dictionary. + + Parameters + ---------- + clusters : list + A list of clusters. + + models_to_cluster : list + A list of models to cluster. + + Returns + ------- + clt_dic : dict + A dictionary containing the clusters. + + clt_centers : dict + A dictionary containing the cluster centers. + """ + clt_dic = {} + clt_centers = {} + # iterate over the clusters + for clt in clusters: + cluster_id = clt.name + cluster_center_id = clt.center.name - 1 + cluster_center_pdb = models_to_cluster[cluster_center_id] + + clt_dic[cluster_id] = [] + clt_centers[cluster_id] = cluster_center_pdb + clt_dic[cluster_id].append(cluster_center_pdb) + # iterate over the models in the cluster + for model in clt.members: + model_id = model.name + model_pdb = models_to_cluster[model_id - 1] + clt_dic[cluster_id].append(model_pdb) + return clt_dic, clt_centers + + +def write_clustfcc_file( + clusters, + clt_centers, + clt_dic, + params, + sorted_score_dic, + output_fname="clustfcc.txt", +): # noqa: E501 + """ + Write the clustfcc.txt file. + + Parameters + ---------- + clusters : list + A list of clusters. + + clt_centers : dict + A dictionary containing the cluster centers. + + clt_dic : dict + A dictionary containing the clusters. + + params : dict + A dictionary containing the clustering parameters. + + sorted_score_dic : list + A list of sorted scores. + + Returns + ------- + None + """ + # Prepare clustfcc.txt + output_str = f"### clustfcc output ###{os.linesep}" + output_str += os.linesep + output_str += f"Clustering parameters {os.linesep}" + output_str += ( + "> contact_distance_cutoff=" + f"{params['contact_distance_cutoff']}A" + f"{os.linesep}" + ) + output_str += f"> clust_cutoff={params['clust_cutoff']}" f"{os.linesep}" + output_str += f"> min_population={params['min_population']}{os.linesep}" + output_str += f"> strictness={params['strictness']}{os.linesep}" + output_str += os.linesep + output_str += ( + "Note: Models marked with * represent the center of the cluster" f"{os.linesep}" + ) + output_str += f"-----------------------------------------------{os.linesep}" + output_str += os.linesep + output_str += f"Total # of clusters: {len(clusters)}{os.linesep}" + + for cluster_rank, _e in enumerate(sorted_score_dic, start=1): + cluster_id, _ = _e + center_pdb = clt_centers[cluster_id] + model_score_l = [(e.score, e) for e in clt_dic[cluster_id]] + model_score_l.sort() + # subset_score_l = [e[0] for e in model_score_l][:min_population] + subset_score_l = [e[0] for e in model_score_l] + subset_score_l = subset_score_l[: params["min_population"]] + top_mean_score = np.mean(subset_score_l) + top_std = np.std(subset_score_l) + output_str += ( + f"{os.linesep}" + "-----------------------------------------------" + f"{os.linesep}" + f"Cluster {cluster_rank} (#{cluster_id}, " + f"n={len(model_score_l)}, " + f"top{params['min_population']}_avg_score = {top_mean_score:.2f} " + f"+-{top_std:.2f})" + f"{os.linesep}" + ) + output_str += os.linesep + output_str += f"clt_rank\tmodel_name\tscore{os.linesep}" + for model_ranking, element in enumerate(model_score_l, start=1): + score, pdb = element + if pdb.file_name == center_pdb.file_name: + output_str += ( + f"{model_ranking}\t{pdb.file_name}\t{score:.2f}\t*" f"{os.linesep}" + ) + else: + output_str += ( + f"{model_ranking}\t{pdb.file_name}\t{score:.2f}" f"{os.linesep}" + ) + output_str += "-----------------------------------------------" f"{os.linesep}" + + log.info("Saving detailed output to clustfcc.txt") + with open(output_fname, "w") as out_fh: + out_fh.write(output_str) + + return diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f5c48a8283caf9b066ca699de482afb87350e771 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustfcc/defaults.yaml @@ -0,0 +1,59 @@ +executable: + default: src/contact_fcc + type: file + title: Relative path to contact_fcc executable. + short: Relative path to contact_fcc executable. + long: As contact_fcc is an external tool, its path must be provided. Basically, this parameter should not be changed, as the tool is downloaded at the same time as haddock3. Nevertheless, one could try to have the contact_fcc tool written in another programming language or whatever. + group: executable + explevel: expert +contact_distance_cutoff: + default: 5.00 + type: float + min: 2.00 + max: 999.99 + precision: 2 + title: Cutoff distance (A) for contact detection. + short: Cutoff distance (A) for contact detection. By default 5.0 Angstroms. + long: Cutoff distance between two atoms for contact detection. By default 5.0 Angstroms. + group: analysis + explevel: easy +clust_cutoff: + default: 0.60 + type: float + min: 0.00 + max: 1.00 + precision: 2 + title: Minimum fraction of common contacts to be considered in a cluster. + short: Minimum fraction of common contacts to be considered in a cluster. By default 0.6. + long: Minimum fraction of common contacts (fcc) to cluster complexes together. Complexes not sharing fraction of common contacts above the `fraction_cutoff` parameter cannot belong to the same cluster. + group: analysis + explevel: easy +min_population: + default: 4 + type: integer + min: 1 + max: 9999 + title: Clustering population threshold. + short: Threshold employed to exclude clusters with less than this number of members. By default 4. + long: Minimum set of grouped complexes to define a cluster. If a potential cluster is composed of less than this number of members, it will be considered as `singleton` and discarded from final clusters. If set to 1, all complexes will be part of a cluster. By default 4. + group: analysis + explevel: easy +strictness: + default: 0.75 + type: float + min: 0.00 + max: 1.00 + precision: 2 + title: Strictness factor. + short: Strictness factor. It's multiplied by the fraction_cutoff to obtain a new cutoff for the second half of the matrix. By default 0.75. + long: Strictness factor. It's multiplied by the fraction_cutoff to obtain a new cutoff for the second half of the matrix. Used to allow for some variability. By default 0.75. + group: analysis + explevel: easy +plot_matrix: + default: false + type: boolean + title: Plot matrix of members + short: Plot matrix of members. By default is false. + long: Plot matrix of members. By default is false. + group: analysis + explevel: easy \ No newline at end of file diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._clustrmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._clustrmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._clustrmsd.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..8ff94fe3720be21b3bbc4552f3e9208ed21d25fe --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/__init__.py @@ -0,0 +1,191 @@ +""" +RMSD clustering module. + +This module takes in input the RMSD matrix calculated in the previous step and +performs a hierarchical clustering procedure on it, leveraging `scipy routines`_ +for this purpose. + +Essentially, the procedure amounts at lumping the input models in a +progressively coarser hierarchy of clusters, called the dendrogram. + +Four parameters can be defined in this context: + +* `linkage`: governs the way clusters are merged together in the creation of + the dendrogram +* `criterion`: defines the prescription to cut the dendrogram and obtain the + desired clusters +* `n_clusters`: number of desired clusters (if `criterion` is `maxclust`). +* `clust_cutoff`: value of distance that separates distinct clusters (if `criterion` is + ``distance``) +* `min_population` : analogously to the `clustfcc` module, it is the minimum number + of models that should be present in a cluster to consider it. If criterion is + `maxclust`, the value is ignored. + +This module passes the path to the RMSD matrix is to the next step of the +workflow through the `rmsd_matrix.json` file, thus allowing to execute several +`clustrmsd` modules (possibly with different parameters) on the same RMSD +matrix. + +.. _scipy routines: https://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html +""" # noqa: E501 +from pathlib import Path + +from haddock import log +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import Union +from haddock.libs.libclust import ( + add_cluster_info, + clustrmsd_tolerance_params, + get_cluster_matrix_plot_clt_dt, + plot_cluster_matrix, + rank_clusters, + write_structure_list, + ) +from haddock.libs.libontology import ModuleIO +from haddock.modules import BaseHaddockModule +from haddock.modules.analysis.clustrmsd.clustrmsd import ( + get_clusters, + get_dendrogram, + get_matrix_path, + iterate_min_population, + order_clusters, + read_matrix, + write_clusters, + write_clustrmsd_file, + ) + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module for clustering with RMSD.""" + + name = RECIPE_PATH.name + + def __init__( + self, + order: int, + path: Path, + initial_params: Union[Path, str] = DEFAULT_CONFIG, + ) -> None: + super().__init__(order, path, initial_params) + + self.matrix_json = self._load_previous_io("rmsd_matrix.json") + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if contact executable is compiled.""" + return + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + models = self.previous_io.retrieve_models() + + # Cluster + rmsd_matrix = read_matrix(self.matrix_json.input[0]) + # loading parameters + min_population = self.params["min_population"] + + # getting clusters_list + dendrogram = get_dendrogram(rmsd_matrix, self.params["linkage"]) + + # adjust the parameters + tolerance_param_name, tolerance = clustrmsd_tolerance_params( + self.params, + ) + + log.info( + f"Clustering with {tolerance_param_name} = {tolerance}, " + f"and criterion {self.params['criterion']}" + ) + + cluster_arr = get_clusters( + dendrogram, + tolerance, + self.params["criterion"], + ) + + # when crit == distance, apply clustering min_population + if self.params['criterion'] == "distance": + cluster_arr, min_population = iterate_min_population( + cluster_arr, + self.params['min_population'], + ) + self.params['min_population'] = min_population + + clusters, cluster_arr = order_clusters(cluster_arr) + log.info(f"clusters = {clusters}") + + out_filename = Path('cluster.out') + clt_dic, cluster_centers = write_clusters( + clusters, + cluster_arr, + models, + rmsd_matrix, + out_filename, + centers=True, + ) + + # ranking clusters + score_dic, sorted_score_dic = rank_clusters( + clt_dic, + self.params['min_population'], + ) + + self.output_models = add_cluster_info(sorted_score_dic, clt_dic) + + # Write unclustered structures + write_structure_list( + models, + self.output_models, + out_fname="clustrmsd.tsv", + ) # type: ignore + + write_clustrmsd_file( + clusters, + clt_dic, + cluster_centers, + score_dic, + sorted_score_dic, + self.params, + ) + + # Draw the matrix + if self.params['plot_matrix']: + # Obtain final models indices + final_order_idx, labels, cluster_ids = [], [], [] + for pdb in self.output_models: + final_order_idx.append(models.index(pdb)) + labels.append(pdb.file_name.replace('.pdb', '')) + cluster_ids.append(pdb.clt_id) + # Get custom cluster data + matrix_cluster_dt, cluster_limits = get_cluster_matrix_plot_clt_dt( + cluster_ids + ) + + # Define output filename + html_matrix_basepath = 'rmsd_matrix' + # Plot matrix + html_matrixpath = plot_cluster_matrix( + get_matrix_path(self.matrix_json.input[0]), + final_order_idx, + labels, + dttype='RMSD(Å)', + reverse=True, + diag_fill=0, + output_fname=html_matrix_basepath, + matrix_cluster_dt=matrix_cluster_dt, + cluster_limits=cluster_limits, + ) + if html_matrixpath: + log.info(f"Plotting matrix in {html_matrixpath}") + else: + log.warning("Cluster matrix was not generated") + + self.export_io_models() + # sending matrix to next step of the workflow + matrix_io = ModuleIO() + matrix_io.add(self.matrix_json.input[0]) + matrix_io.save(filename="rmsd_matrix.json") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/clustrmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/clustrmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..5bd2647937cb94d3d7bca6bcd3732de146c54cd8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/clustrmsd.py @@ -0,0 +1,400 @@ +"""RMSD clustering.""" +import os +from pathlib import Path + +import numpy as np +from scipy.cluster.hierarchy import fcluster, linkage + +from haddock import log +from haddock.libs.libontology import RMSDFile + + +def get_matrix_path(rmsd_matrix: RMSDFile) -> Path: + """From an RMSDFile object returns the rmsd matrix path. + + Parameters + ---------- + rmsd_matrix : :obj:`RMSDFile` + RMSDFile object with the path to the RMSD matrix. + + Returns + ------- + matrix_fpath : Path + Path to the RMSD matrix + + Raises + ------ + TypeError + If input rmsd_matrix is not of type RMSDFile + """ + if not isinstance(rmsd_matrix, RMSDFile): + err = f"{type(rmsd_matrix)} is not a RMSDFile object." + raise TypeError(err) + matrix_fpath = Path(rmsd_matrix.path, rmsd_matrix.file_name) + return matrix_fpath + + +def write_clusters(clusters, cluster_arr, models, rmsd_matrix, out_filename="cluster.out", centers=False): # noqa: E501 + """ + Write the clusters to a file. + + Parameters + ---------- + clusters : list + List of clusters to write. + cluster_arr : np.array + Array with the cluster assignment for each model. + models : list + List of models. + rmsd_matrix : np.array + RMSD matrix. + out_filename : str, optional + Output filename. The default is "cluster.out". + centers : bool, optional + Whether to calculate the cluster centers. The default is False. + + Returns + ------- + clt_dic : :obj:`dict` + Dictionary with the clusters. + + cluster_centers : :obj:`dict` + Dictionary with the cluster ID as key and the cluster center as value. + """ + n_obs = len(cluster_arr) + cluster_centers = {} + # preparing output + clt_dic = {} + log.info(f'Saving output to {out_filename}') + cluster_out = Path(out_filename) + with open(cluster_out, 'w') as fh: + for cl_id in clusters: + if cl_id != -1: + npw = np.where(cluster_arr == cl_id)[0] + clt_dic[cl_id] = [models[n] for n in npw] + fh.write(f"Cluster {cl_id} -> ") + + # find the cluster center + if centers: + clt_center = get_cluster_center(npw, n_obs, rmsd_matrix) + cluster_centers[cl_id] = models[clt_center].file_name + + # write the cluster + for el in npw[:-1]: + fh.write(f"{el + 1} ") + fh.write(f"{npw[-1] + 1}") + fh.write(os.linesep) + + return clt_dic, cluster_centers + + +def read_matrix(rmsd_matrix: RMSDFile) -> np.ndarray: + """ + Read the RMSD matrix. + + Parameters + ---------- + rmsd_matrix : :obj:`RMSDFile` + RMSDFile object with the path to the RMSD matrix. + + Returns + ------- + matrix : :obj:`numpy.ndarray` + Numpy array with the RMSD matrix. + """ + filename = get_matrix_path(rmsd_matrix) + # count lines + nlines = sum(1 for line in open(filename)) + log.info(f"input rmsd matrix has {nlines} entries") + # must be a 1D condensed distance matrix + d = int(np.ceil(np.sqrt(nlines * 2))) + if (d * (d - 1) / 2) != nlines: + err = f"{nlines} is not a valid binomial coefficient" + raise ValueError(err) + if nlines != rmsd_matrix.npairs: + err = f"number of pairs {nlines} != expected ({rmsd_matrix.npairs})" + raise ValueError(err) + # creating and filling matrix obj + matrix = np.zeros((nlines)) + c = 0 + with open(filename, "r") as mf: + for line in mf: + data = line.split() + if len(data) != 3: + raise ValueError(f"line {line} malformed") + else: + matrix[[c]] = float(data[2]) + c += 1 + return np.array(matrix) + + +def get_dendrogram(rmsd_matrix, linkage_type): + """Get and save the dendrogram. + + Parameters + ---------- + rmsd_matrix : :obj:`numpy.ndarray` + Numpy array with the RMSD matrix. + + linkage_type : str + Linkage type for the clustering. + + Returns + ------- + Z : :obj:`numpy.ndarray` + Numpy array with the dendrogram. + """ + Z = linkage(rmsd_matrix, linkage_type) + np.savetxt("dendrogram.txt", Z, fmt='%.5f') + return Z + + +def get_clusters(dendrogram, tolerance, criterion): + """Obtain the clusters.""" + log.info("Clustering dendrogram...") + cluster_arr = fcluster(dendrogram, t=tolerance, criterion=criterion) + return cluster_arr + + +def apply_min_population( + cluster_arr: np.ndarray, + min_population: int, + ) -> np.ndarray: + """ + Apply min_population to cluster list. + + Parameters + ---------- + cluster_arr : np.ndarray + Array of clusters. + min_population : int + min_population value on cluster population. + + Returns + ------- + cluster_arr : np.ndarray + Array of clusters (unclustered structures are labelled with -1) + """ + new_cluster_arr = cluster_arr.copy() + log.info(f"Applying min_population {min_population} to cluster list") + cluster_pops = np.unique(cluster_arr, return_counts=True) + uncl_idx = np.where(cluster_pops[1] < min_population)[0] + invalid_clusters = cluster_pops[0][uncl_idx] + log.info(f"Invalid clusters: {invalid_clusters}") + # replacing invalid clusters with -1 + uncl_models = 0 + for cl_idx, cl_id in enumerate(new_cluster_arr): + if cl_id in invalid_clusters: + new_cluster_arr[cl_idx] = -1 + uncl_models += 1 + log.info(f"min_population applied, {uncl_models} models left unclustered") + return new_cluster_arr + + +def iterate_min_population( + cluster_arr: np.ndarray, + min_population: int, + ) -> np.ndarray: + """ + Find one valid valuster satisfying the min_population parameter. + + Logic: Iterate over the min_population values until we find + at least one valid cluster. + + Parameters + ---------- + cluster_arr : np.ndarray + Array of clusters. + min_population : int + min_population value on cluster population. + + Returns + ------- + new_cluster_arr : np.ndarray + Array of clusters (unclustered structures are labelled with -1) + """ + new_cluster_arr: np.ndarray = np.ndarray([]) + for curr_thr in range(min_population, 0, -1): + log.info(f"Clustering with min_population={curr_thr}") + new_cluster_arr = apply_min_population(cluster_arr, curr_thr) + ncl = len(np.unique(new_cluster_arr)) + if -1 in new_cluster_arr: # contains -1 (unclustered) + ncl -= 1 + # if no clusters found, try with a lower min_population + if ncl == 0: + log.warning(f'No clusters found with min_population={curr_thr}') + else: + break + return new_cluster_arr, curr_thr + + +def cond_index(i: int, j: int, n: int) -> float: + """ + Get the condensed index from two matrix indexes. + + Parameters + ---------- + i : int + Index of the first element. + j : int + Index of the second element. + n : int + Number of observations. + """ + return n * (n - 1) / 2 - (n - i) * (n - i - 1) / 2 + j - i - 1 + + +def get_cluster_center( + npw: np.ndarray, + n_obs: int, + rmsd_matrix: np.ndarray, + ) -> int: + """ + Get the cluster centers. + + Parameters + ---------- + npw: np.ndarray + Indexes of the cluster over cluster_list array + n_obs : int + Number of overall observations (models). + rmsd_matrix : np.ndarray + RMSD matrix. + + Returns + ------- + cluster_center : int + Index of cluster center + """ + intra_cl_distances = {el: 0.0 for el in npw} + + # iterating over the elements of the cluster + for m_idx in range(len(npw)): + npws = npw[m_idx + 1:] + pairs = [int(cond_index(npw[m_idx], npw_el, n_obs)) for npw_el in npws] + for pair_idx in range(len(pairs)): + intra_cl_distances[npw[m_idx]] += rmsd_matrix[pairs[pair_idx]] + intra_cl_distances[npws[pair_idx]] += rmsd_matrix[pairs[pair_idx]] + cluster_center = min(intra_cl_distances, key=intra_cl_distances.get) # type: ignore # noqa : E501 + return cluster_center + + +def write_clustrmsd_file(clusters, clt_dic, cluster_centers, score_dic, sorted_score_dic, params, output_fname='clustrmsd.txt'): # noqa E501 + """ + Write the clustrmsd.txt file. + + Parameters + ---------- + clusters : np.ndarray + Array of clusters. + + clt_dic : dict + Dictionary with the clusters. + + cluster_centers : dict + Dictionary with the cluster centers. + + score_dic : dict + Dictionary with the scores. + + sorted_score_dic : dict + Dictionary with the sorted scores. + + params : dict + Dictionary with the clustering parameters. + + output_fname : str + Output filename. + """ + # Prepare clustrmsd.txt + output_str = f'### clustrmsd output ###{os.linesep}' + output_str += os.linesep + output_str += f'Clustering parameters {os.linesep}' + output_str += f"> linkage_type={params['linkage']}{os.linesep}" + output_str += f"> criterion={params['criterion']}{os.linesep}" + if params['criterion'] == "distance": + output_str += f"> clust_cutoff={params['clust_cutoff']:.2f}{os.linesep}" + else: + output_str += f"> n_clusters={params['n_clusters']}{os.linesep}" + output_str += f"> min_population={params['min_population']}{os.linesep}" + output_str += os.linesep + + output_str += ( + f"-----------------------------------------------{os.linesep}") + output_str += os.linesep + output_str += f'Total # of clusters: {len(clusters)}{os.linesep}' + for cluster_rank, _e in enumerate(sorted_score_dic, start=1): + cluster_id, _ = _e + + model_score_l = [(e.score, e) for e in clt_dic[cluster_id]] + model_score_l.sort() + top_score = score_dic[cluster_id] + + output_str += ( + f"{os.linesep}" + "-----------------------------------------------" + f"{os.linesep}" + f"Cluster {cluster_rank} (#{cluster_id}, " + f"n={len(model_score_l)}, " + f"top{params['min_population']}_avg_score = {top_score:.2f})" + f"{os.linesep}") + output_str += os.linesep + output_str += f'clt_rank\tmodel_name\tscore{os.linesep}' + for model_ranking, element in enumerate(model_score_l, start=1): + score, pdb = element + output_str += ( + f"{model_ranking}\t{pdb.file_name}\t{score:.2f}" + ) + if cluster_centers: + # is the model the cluster center? + if pdb.file_name == cluster_centers[cluster_id]: + output_str += "\t*" + output_str += (f"{os.linesep}") + output_str += ( + "-----------------------------------------------" + f"{os.linesep}") + log.info('Saving detailed output to clustrmsd.txt') + with open(output_fname, 'w') as out_fh: + out_fh.write(output_str) + + +def order_clusters(cluster_arr): + """ + Order the clusters by population. + + The most populated cluster will be assigned the ID 1, the second most + populated the ID 2, and so on. + + Parameters + ---------- + cluster_arr : np.ndarray + Array of clusters. + + Returns + ------- + clusters : list + List of clusters. + + cluster_arr : np.ndarray + Array of clusters. + """ + unique_clusters, cluster_counts = np.unique(cluster_arr, return_counts=True) + + sorted_indices = np.argsort(-cluster_counts) # must use negative to sort ascending + sorted_clusters = unique_clusters[sorted_indices] + + # delete -1 from sorted_clusters if present + sorted_clusters = sorted_clusters[sorted_clusters != -1] + clusters = [] + # for every element of sorted_clusters I want to assign a new ID + # to the elements of cluster_arr that match the order of sorted_clusters + index_dict = {} + for c in sorted_clusters: + # index of cluster_arr where the cluster is equal to c + idx = np.where(cluster_arr == c) + index_dict[c] = idx + # now the assignment + for i, c in enumerate(sorted_clusters): + clusters.append(i + 1) + cluster_arr[index_dict[c]] = i + 1 + return clusters, cluster_arr diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c354211cc8ab112cb7dfb9afc682e85ec8cc573b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/clustrmsd/defaults.yaml @@ -0,0 +1,70 @@ +criterion: + default: "distance" + type: "string" + minchars: 0 + maxchars: 100 + title: Criterion for fcluster + short: Criterion to be used to cut the dendrogram + long: if criterion is maxclust, the dendrogram is cut when a certain number of clusters is formed. If criterion is distance, the dendrogram will be cut based on the value of the cophenetic distance + group: analysis + explevel: expert + choices: + - distance + - maxclust +linkage: + default: "average" + type: "string" + minchars: 0 + maxchars: 100 + title: Linkage type + short: How to lump together clusters in hierarchical clustering + long: check out the full description at https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html + group: analysis + explevel: expert + choices: + - average + - centroid + - complete + - median + - single + - ward + - weighted +min_population: + default: 4 + type: integer + min: 1 + max: 9999 + title: Clustering population threshold + short: Threshold employed to exclude clusters with less than this number of members. By default 4. + long: Threshold employed to exclude clusters with less than this number of members. By default 4. When criterion is maxclust, this value is ignored. + group: analysis + explevel: easy +clust_cutoff: + default: 7.5 + type: float + min: 0.1 + max: 100 + precision: 3 + title: Clustering cutoff distance + short: Value of cutoff cophenetic distance. + long: Value of cutoff cophenetic distance. When criterion is maxclust, this value is ignored. + group: analysis + explevel: easy +plot_matrix: + default: false + type: boolean + title: Plot matrix of members + short: Plot matrix of members. By default is false. + long: Plot matrix of members. By default is false. + explevel: easy + group: analysis +n_clusters: + default: 4 + type: integer + min: 1 + max: 9999 + title: Number of clusters + short: Number of clusters to be formed + long: Number of clusters to be formed. 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Get the models generated in previous step + if type(self.previous_io) == iter: + _e = "This module cannot come after one that produced an iterable." + self.finish_with_error(_e) + try: + models = self.previous_io.retrieve_models(individualize=True) + except AttributeError as e: + self.finish_with_error(e) + + # Obtain clusters + clusters_sets = get_clusters_sets(models) + + # Initiate holder of all jobs to be run by the `Scheduler` + contact_jobs: list[SupportsRunT] = [] + # Loop over clusters + for (clust_id, clust_rank), clt_models in clusters_sets.items(): + # In case of unclustered models + if clust_id is None: + # Obtain subset of top models + top_models = topX_models(clt_models, topX=self.params["topX"]) + + # Create single model analysis params + single_models_params = deepcopy(self.params) + single_models_params["single_model_analysis"] = True + + # Loop over models to analyse + for model in top_models: + # Set names + modelfname = Path(model.file_name).stem + jobname = f"Unclustered_{modelfname}" + # Create a contact map object + contmap_job = ContactsMap( + Path(model.rel_path), + Path(jobname), + single_models_params, + ) + contact_jobs.append(contmap_job) + + # For clustered models + else: + # Handles case where clustered models were not scored before + rank_id = "Unranked" if clust_rank is None else clust_rank + # Building basename for the job + name = f"cluster{rank_id}" + # Create a contact map object + contmap_job = ClusteredContactMap( + [Path(model.rel_path) for model in clt_models], + Path(name), + self.params, + ) + contact_jobs.append(contmap_job) + + # Find execution engine + exec_mode = get_analysis_exec_mode(self.params["mode"]) + Engine = get_engine(exec_mode, self.params) + engine = Engine(contact_jobs) + engine.run() + + # Generate report + make_contactmap_report(contact_jobs, "ContactMapReport.html") + + # Send models to the next step, no operation is done on them + self.output_models = models + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/contmap.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/contmap.py new file mode 100644 index 0000000000000000000000000000000000000000..bf76a924f534b04a311ae3dff13bd73b7ef50055 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/contmap.py @@ -0,0 +1,2377 @@ +"""Module computing contact maps of complexes, alone or grouped by cluster. + +Chord diagram functions were adapted from: +https://plotly.com/python/v3/filled-chord-diagram/ +""" + + +import os +import glob +from pathlib import Path + +import numpy as np +import plotly.graph_objs as go +from scipy.spatial.distance import pdist, squareform + +from haddock import log +from haddock.libs.libontology import PDBFile +from haddock.libs.libpdb import ( + slc_name, + slc_resname, + slc_chainid, + slc_resseq, + slc_x, + slc_y, + slc_z, + ) +from haddock.core.typing import ( + Any, + NDFloat, + NDArray, + Optional, + Union, + SupportsRun, + ) +from haddock.libs.libplots import heatmap_plotly, fig_to_html + + +############################### +# Global variable definitions # +############################### +RESIDUE_POLARITY = { + "CYS": "polar", + "HIS": "polar", + "ASN": "polar", + "GLN": "polar", + "SER": "polar", + "THR": "polar", + "TYR": "polar", + "TRP": "polar", + "ALA": "apolar", + "PHE": "apolar", + "GLY": "apolar", + "ILE": "apolar", + "VAL": "apolar", + "MET": "apolar", + "PRO": "apolar", + "LEU": "apolar", + "GLU": "negative", + "ASP": "negative", + "LYS": "positive", + "ARG": "positive", + } +DNA_RNA_POLARITY = { + "A": "negative", + "DA": "negative", + "T": "negative", + "DT": "negative", + "U": "negative", + "DU": "negative", + "C": "negative", + "DC": "negative", + "G": "negative", + "DG": "negative", + } +RESIDUE_POLARITY.update(DNA_RNA_POLARITY) + +PI = np.pi + +# Define interaction types colors +CONNECT_COLORS = { + "polar-polar": (153, 255, 153), + "polar-apolar": (255, 204, 204), + "polar-negative": (255, 204, 153), + "polar-positive": (153, 204, 255), + "apolar-apolar": (255, 255, 0), + "apolar-negative": (255, 229, 204), + "apolar-positive": (204, 229, 255), + "negative-negative": (255, 127, 0), + "negative-positive": (0, 204, 0), + "positive-positive": (255, 127, 0), + } +# Also add reversed keys order +REVERSED_CONNECT_COLORS_KEYS = { + '-'.join(k.split('-')[::-1]): v + for k, v in CONNECT_COLORS.items() + } +CONNECT_COLORS.update(REVERSED_CONNECT_COLORS_KEYS) + +# Colors for each amino-acids +RESIDUES_COLORS = { + "CYS": "rgba(229, 255, 204, 0.80)", + "MET": "rgba(229, 255, 204, 0.80)", + "ASN": "rgba(128, 255, 0, 0.80)", + "GLN": "rgba(128, 255, 0, 0.80)", + "SER": "rgba(153, 255, 51, 0.80)", + "THR": "rgba(153, 255, 51, 0.80)", + "TYR": "rgba(204, 155, 53, 0.80)", + "TRP": "rgba(204, 155, 53, 0.80)", + "HIS": "rgba(204, 155, 53, 0.80)", + "PHE": "rgba(255, 255, 51, 0.80)", + "ALA": "rgba(255, 255, 0, 0.80)", + "ILE": "rgba(255, 255, 0, 0.80)", + "VAL": "rgba(255, 255, 0, 0.80)", + "PRO": "rgba(255, 255, 0 0.80)", + "LEU": "rgba(255, 255, 0, 0.80)", + "GLY": "rgba(255, 255, 255, 0.80)", + "GLU": "rgba(255, 0, 0, 0.80)", + "ASP": "rgba(255, 0, 0, 0.80)", + "LYS": "rgba(0, 0, 255, 0.80)", + "ARG": "rgba(0, 0, 255, 0.80)", + } + +# Colors for DNA / RNA +# Note: Based on WebLogo color scheme +DNARNA_COLORS = { + "A": "rgba(51, 204, 51, 0.80)", + "T": "rgba(204, 0, 0, 0.80)", + "U": "rgba(204, 0, 0, 0.80)", + "C": "rgba(51, 102, 255, 0.80)", + "G": "rgba(255, 163, 26, 0.80)", + } +FULL_DNARNA_COLORS = {f"D{k}": rgba for k, rgba in DNARNA_COLORS.items()} + +# Combine all of them +AA_DNA_RNA_COLORS = {} +AA_DNA_RNA_COLORS.update(RESIDUES_COLORS) +AA_DNA_RNA_COLORS.update(DNARNA_COLORS) +AA_DNA_RNA_COLORS.update(FULL_DNARNA_COLORS) + +# Chain colors +CHAIN_COLORS = [ + 'rgba(51, 255, 51, 0.85)', + 'rgba(51, 153, 255, 0.85)', + 'rgba(255, 153, 51, 0.85)', + 'rgba(255, 255, 51, 0.85)', + 'rgba(255, 0, 0, 0.85)', + 'rgba(255, 0, 127, 0.85)', + 'rgba(0, 255, 0, 0.85)', + 'rgba(0, 0, 255, 0.85)', + 'rgba(0, 153, 0, 0.85)', + ] +CHAIN_COLORS = CHAIN_COLORS[::-1] + + +################## +# Define classes # +################## +class ContactsMap(SupportsRun): + """ContactMap analysis for single structure.""" + + def __init__( + self, + model: Path, + output: Path, + params: dict, + ) -> None: + self.model = model + self.output = output + self.params = params + self.files: dict[str, Union[str, Path]] = {} + + def run(self): + """Process analysis of contacts of a PDB structure.""" + # Load pdb + pdb_dt = extract_pdb_dt(self.model) + # Extract all cordinates + all_coords, resid_keys, resid_dt = get_ordered_coords(pdb_dt) + # Compute distance matrix + full_dist_matrix = compute_distance_matrix(all_coords) + + res_res_contacts = [] + all_heavy_interchain_contacts = [] + # First loop over residues + for ri, reskey_1 in enumerate(resid_keys): + # Second loop over residues (half matrix only) + for _rj, reskey_2 in enumerate(resid_keys[ri + 1:], start=ri + 1): + # Extract data + contact_dt = gen_contact_dt( + full_dist_matrix, + resid_dt, + reskey_1, + reskey_2, + ) + res_res_contacts.append(contact_dt) + + # Extract interchain heavy atoms data + if reskey_2.split('-')[0] == reskey_1.split('-')[0]: + continue + heavy_atoms_contacts = extract_heavyatom_contacts( + full_dist_matrix, + resid_dt, + reskey_1, + reskey_2, + contact_distance=self.params['shortest_dist_threshold'], + ) + all_heavy_interchain_contacts += heavy_atoms_contacts + + # generate outputs for single models + if self.params['single_model_analysis']: + self.generate_output( + res_res_contacts, all_heavy_interchain_contacts, + ) + + return res_res_contacts, all_heavy_interchain_contacts + + def generate_output( + self, + res_res_contacts: list[dict], + all_heavy_interchain_contacts: list[dict], + ) -> None: + """Generate several outputs based on contacts. + + Parameters + ---------- + res_res_contacts : list[dict] + List of residue-residue contacts + all_heavy_interchain_contacts : list[dict] + List of heavy atoms interchain contacts + """ + # write contacts tsv files + header = ['res1', 'res2'] + header += [ + v for v in sorted(res_res_contacts[0]) + if v not in header + ] + fpath = write_res_contacts( + res_res_contacts, + header, + f'{self.output}_contacts.tsv', + interchain_data={ + 'path': f'{self.output}_interchain_contacts.tsv', + 'data_key': 'ca-ca-dist', + 'contact_threshold': self.params['ca_ca_dist_threshold'], + } + ) + log.info(f'Generated contacts file: {fpath}') + self.files['res-res-contacts'] = fpath + + # Genreate corresponding heatmap + if self.params['generate_heatmap']: + heatmap = tsv_to_heatmap( + fpath, + data_key='ca-ca-dist', + contact_threshold=self.params['ca_ca_dist_threshold'], + colorscale=self.params['color_ramp'], + output_fname=f'{self.output}_heatmap.html', + offline=self.params["offline"], + ) + log.info(f'Generated single model heatmap file: {heatmap}') + self.files['res-res-contactmap'] = heatmap + + # Generate corresponding chord chart + if self.params['generate_chordchart']: + # find theshold type + if self.params['chordchart_datatype'] == 'ca-ca-dist': + threshold = self.params['ca_ca_dist_threshold'] + else: + threshold = self.params['shortest_dist_threshold'] + chordp = tsv_to_chordchart( + fpath, + data_key=self.params['chordchart_datatype'], + contact_threshold=threshold, + output_fname=f'{self.output}_chordchart.html', + filter_intermolecular_contacts=True, + title=Path(self.output).stem.replace('_', ' '), + offline=self.params["offline"], + ) + log.info(f'Generated single model chordchart file: {chordp}') + self.files['res-res-chordchart'] = chordp + + # Write interchain heavy atoms contacts tsv file + header2 = ['atom1', 'atom2', 'dist'] + fpath2 = write_res_contacts( + all_heavy_interchain_contacts, + header2, + f'{self.output}_heavyatoms_interchain_contacts.tsv', + ) + log.info(f'Generated contacts file: {fpath2}') + self.files['atom-atom-interchain-contacts'] = fpath2 + + +class ClusteredContactMap(SupportsRun): + """ContactMap analysis for set of clustered structures.""" + + def __init__( + self, + models: list[Path], + output: Path, + params: dict, + ) -> None: + self.models = models + self.output = output + self.params = params + self.files: dict[str, Union[str, Path]] = {} + self.terminated = False + + @staticmethod + def aggregate_contacts( + contacts_holder: dict, + contact_keys: list[str], + contacts: list[dict], + key1: str, + key2: str, + ) -> None: + """Aggregate single models data belonging to a cluster. + + Parameters + ---------- + contacts_holder : dict + Dictionnary holding list of contact data + contact_keys : list[str] + Order of the keys to access the dictionnary + contacts : list[dict] + Singel model contact data. + key1 : str + Name of the key to access first entry in data. + key2 : str + Name of the key to access second entry in data. + """ + # Parse outputs to aggregate contacts in `clusters_contacts` + for cont in contacts: + # Check key + combined_key = f'{cont[key2]}/{cont[key1]}' # resversed + if combined_key not in contacts_holder.keys(): + combined_key = f'{cont[key1]}/{cont[key2]}' # normal + if combined_key not in contacts_holder.keys(): + # Add key order + contact_keys.append(combined_key) + # Initiate key + contacts_holder[combined_key] = { + k: [] + for k in cont.keys() + if k not in [key1, key2] + } + # Add data + for dtk in contacts_holder[combined_key].keys(): + contacts_holder[combined_key][dtk].append(cont[dtk]) + + def run(self): + """Process analysis of contacts of a set of PDB structures.""" + # initiate holding variables + clusters_contacts = {} # Residue-residue contacts + resres_keys_list = [] # Ordered residue-residue contacts keys + clusters_heavyatm_contacts = {} # Interchain atom-atom contacts + atat_keys_list = [] # Ordered interchain atom-atom contacts keys + + # loop over models/structures + for pdb_path in self.models: + # initiate object + contact_map_obj = ContactsMap( + pdb_path, + f'{self.output}_{pdb_path.stem}', + self.params, + ) + # Run it + pdb_contacts, interchain_heavy_contacts = contact_map_obj.run() + + # Parse outputs to aggregate contacts in `clusters_contacts` + self.aggregate_contacts( + clusters_contacts, resres_keys_list, + pdb_contacts, + "res1", "res2", + ) + + # Parse outputs for heavy atoms contacts + self.aggregate_contacts( + clusters_heavyatm_contacts, atat_keys_list, + interchain_heavy_contacts, + "atom1", "atom2", + ) + + # Initiate heavy atoms contact cluster aggrated data + heavy_atm_clust_list = [] + for atatk in atat_keys_list: + at1, at2 = atatk.split('/') + # point corresponding list of distances + h_dists = clusters_heavyatm_contacts[atatk]['dist'] + # Summerize it + heavy_atm_clust_list.append({ + "atom1": at1, + "atom2": at2, + "nb_dists": len(h_dists), + "avg_dist": round(np.mean(h_dists), 2), + "std_dist": round(np.std(h_dists), 2), + }) + # write contacts + header = ['atom1', 'atom2'] + header += [ + v for v in sorted(heavy_atm_clust_list[0]) + if v not in header + ] + hfpath = write_res_contacts( + heavy_atm_clust_list, + header, + f'{self.output}_heavyatoms_interchain_contacts.tsv', + ) + log.info(f'Generated heavy atoms interchain contacts file: {hfpath}') + + # Initiate cluster aggregated data holder + combined_clusters_list = [] + # Loop over ordered keys + for combined_key in resres_keys_list: + # point data + dt = clusters_contacts[combined_key] + + # Compute averages Ca-Ca distances + avg_ca_ca_dist = np.mean(dt['ca-ca-dist']) + # Compute nb. times cluster members holds a value under threshold + ca_ca_under_thresh = [ + v for v in dt['ca-ca-dist'] + if v <= self.params['ca_ca_dist_threshold'] + ] + nb_under = len(ca_ca_under_thresh) + # Compute probability + ca_ca_cont_probability = nb_under / len(dt['ca-ca-dist']) + + # Compute averages for shortest distances + avg_shortest = np.mean(dt['shortest-dist']) + # Generate list of shortest distances observed between two residues + short_under_threshold = [ + v for v in dt['shortest-dist'] + if v <= self.params['shortest_dist_threshold'] + ] + short_nb_und = len(short_under_threshold) + # Compute nb. time the cluster members holds a value under threshold + short_cont_proba = short_nb_und / len(dt['shortest-dist']) + + # Find most representative contact type + cont_ts = list(set(dt['contact-type'])) + # Decreasing sorting of cluster contact types and pick highest one + cont_t = sorted( + cont_ts, + key=lambda k: cont_ts.count(k), + reverse=True, + )[0] + + # Split key to recover resiudes names + res1, res2 = combined_key.split('/') + + # Hold summary data for cluster + combined_clusters_list.append({ + 'res1': res1, + 'res2': res2, + 'ca-ca-dist': round(avg_ca_ca_dist, 1), + 'ca-ca-cont-probability': round(ca_ca_cont_probability, 2), + 'shortest-dist': round(avg_shortest, 1), + 'shortest-cont-probability': round(short_cont_proba, 2), + 'contact-type': cont_t, + }) + + # write contacts + header = ['res1', 'res2'] + header += [ + v for v in sorted(combined_clusters_list[0]) + if v not in header + ] + fpath = write_res_contacts( + combined_clusters_list, + header, + f'{self.output}_contacts.tsv', + interchain_data={ + 'path': f'{self.output}_interchain_contacts.tsv', + 'data_key': 'ca-ca-dist', + 'contact_threshold': self.params['ca_ca_dist_threshold'], + } + ) + log.info(f'Generated contacts file: {fpath}') + self.files['res-res-contacts'] = fpath + self.files['atom-atom-interchain-contacts'] = f'{self.output}_interchain_contacts.tsv' # noqa : E501 + + # Generate corresponding heatmap + if self.params['generate_heatmap']: + heatmap_path = tsv_to_heatmap( + fpath, + data_key=self.params['cluster_heatmap_datatype'], + contact_threshold=1, + colorscale=self.params['color_ramp'], + output_fname=f'{self.output}_heatmap.html', + offline=self.params["offline"], + ) + log.info(f'Generated cluster contacts heatmap: {heatmap_path}') + self.files['res-res-contactmap'] = heatmap_path + + # Generate corresponding chord chart + if self.params['generate_chordchart']: + # find theshold type + if self.params['chordchart_datatype'] == 'ca-ca-dist': + threshold = self.params['ca_ca_dist_threshold'] + else: + threshold = self.params['shortest_dist_threshold'] + chordp = tsv_to_chordchart( + fpath, + data_key=self.params['chordchart_datatype'], + contact_threshold=threshold, + output_fname=f'{self.output}_chordchart.html', + filter_intermolecular_contacts=True, + title=Path(self.output).stem.replace('_', ' '), + offline=self.params["offline"], + ) + log.info(f'Generated cluster contacts chordchart file: {chordp}') + self.files['res-res-chordchart'] = chordp + + self.terminated = True + + +def make_contactmap_report( + contactmap_jobs: list[Union[ContactsMap, ClusteredContactMap]], + outputpath: Union[str, Path], + ) -> Union[str, Path]: + """Generate a HTML navigation page holding all generated files. + + Parameters + ---------- + contact_jobs : list[Union[ClusteredContactMap, ContactsMap]] + All the terminated jobs + outputpath : Union[str, Path] + Output filepath where to write the report. + + Returns + ------- + outputpath: Union[str, Path] + Path to the generated report. + """ + ordered_files = [] + # Loop over terminated jobs + for job in contactmap_jobs: + basepath = f"{job.output}_" + # Gather all files generated by this job + job_files = glob.glob(f"{basepath}*") + + # Sort them by file extension + ext_names: dict[str, Union[str, Path]] = {} + for fpath in job_files: + _fname, ext = os.path.splitext(fpath) + if ext not in ext_names.keys(): + ext_names[ext] = [] + ext_names[ext].append(fpath) + # Sort each keys filepaths + for ext in ext_names.keys(): + ext_names[ext] = sorted( + ext_names[ext], + key=lambda k: k.replace(basepath, ""), + ) + # Get final list order + sorted_jobfiles = [ + fpath + for ext in sorted(ext_names) + for fpath in ext_names[ext] + ] + + # Initiate html links holding list + job_list: list[str] = [] + # Loop over generated files + for fpath in sorted_jobfiles: + # Generate html link + shortname = fpath.replace(basepath, "") + html_string = f'{shortname}' + job_list.append(html_string) + # Combine all links in one string + job_list_combined = ', '.join(job_list) + # Create final string + job_access = f"{job.output}: {job_list_combined}" + # Hold that guy + ordered_files.append(job_access) + + # Combine all jobs outputs as a list + all_access = '\n
  • '.join(ordered_files) + # Generate small html file + htmldt = f""" +
    +
      +
    • + {all_access} +
      • +
    +
    +""" + + # Write it + with open(outputpath, 'w') as reportout: + reportout.write(htmldt) + log.info(f'Generated report file: {outputpath}') + # Return generate outputfilepath + return outputpath + + +def get_clusters_sets( + models: list[PDBFile], + ) -> dict[tuple[Optional[int], Optional[int]], list[PDBFile]]: + """Split models by clusters ids. + + Parameters + ---------- + models : list + List of pdb models/complexes. + + Return + ------ + clust_sets : dict[tuple[Optional[int], Optional[int]], list[PDBFile]] + Dictionary of (cluster ids, cluster rank) keys containing their + respective models as list of PDBFiles. + """ + clust_sets: dict[tuple[Optional[int], Optional[int]], list[PDBFile]] = {} + # Loop over models + for model in models: + # Set key + cluster_key = (model.clt_id, model.clt_rank) + # Create/Gather the corresponding list + cluster_list = clust_sets.setdefault(cluster_key, []) + # Add model + cluster_list.append(model) + return clust_sets + + +def topX_models(models: list[PDBFile], topX: int = 10) -> list[Any]: + """Sort and return subset of top X best models. + + Parameters + ---------- + models : list + List of pdb models/complexes. + topX : int + Number of models to return after sorting. + + Return + ------ + subset_bests : list + List of top `X` best models. + """ + try: + sorted_models = sorted(models, key=lambda m: m.score) + except AttributeError: + sorted_models = models + finally: + subset_bests = sorted_models[:topX] + return subset_bests + + +#################### +# Define functions # +#################### +def extract_pdb_dt(path: Path) -> dict: + """Read and extract ATOM/HETATM records from a pdb file. + + Parameters + ---------- + path : Path + Path to a pdb file. + + Return + ------ + pdb_chains : dict + A dictionary of the pdb file accesible using chains as keys. + """ + pdb_chains: dict = {'chain_order': []} + # Read file + with open(path, 'r') as f: + # Loop over lines + for _ in f: + # Skip non ATOM / HETATM lines + if not any([ + _.startswith('ATOM'), + _.startswith('HETATM'), + ]): + continue + + # Extract residue name + resname = _[slc_resname] + # Extract chain id + chainid = _[slc_chainid] + # Extract resid + resid = _[slc_resseq].strip() + + # Check if chain already parsed + if chainid not in pdb_chains.keys(): + # Add to ordered chains + pdb_chains['chain_order'].append(chainid) + # Initiate new chain holder + pdb_chains[chainid] = {'order': []} + + # Check if new resid id + if resid not in pdb_chains[chainid].keys(): + # Add to oredered resids + pdb_chains[chainid]['order'].append(resid) + # Initiate new residue holder + pdb_chains[chainid][resid] = { + 'index': len(pdb_chains[chainid]['order']) - 1, + 'resname': resname, + 'chainid': chainid, + 'resid': resid, + 'position': len(pdb_chains[chainid]['order']), + 'atoms_order': [], + 'atoms': {}, + } + # extract atome name + atname = _[slc_name].strip() + # check if not an hydrogen + if atname[0] == 'H': + continue + + # extact atome coordinates + coords = extract_pdb_coords(_) + pdb_chains[chainid][resid]['atoms_order'].append(atname) + pdb_chains[chainid][resid]['atoms'][atname] = coords + + return pdb_chains + + +def extract_pdb_coords(line: str) -> list[float]: + """Extract coordinated from a PDB line. + + Parameters + ---------- + line : str + A strandard ATOM/HETATM pdb record. + + Return + ------ + coords : list[float] + List of the X, Y and Z coordinate of this atom. + """ + x = float(line[slc_x].strip()) + y = float(line[slc_y].strip()) + z = float(line[slc_z].strip()) + coords = [x, y, z] + return coords + + +def get_ordered_coords( + pdb_chains: dict, + ) -> tuple[list[list[float]], list[str], dict]: + """Generate list of all atom coordinates. + + Parameters + ---------- + pdb_chains : dict + A dictionary of the pdb file accesible using chains as keys, + as provided by the `extract_pdb_dt()` function. + + Return + ------ + all_coords : list[list[float]] + All atomic coordinates in a single list. + resid_keys : list[str] + Ordered list of residues keys. + resid_dt : dict + Dictionary of coordinates indices for each residue. + """ + # Define holders + all_coords = [] + resid_keys = [] + resid_dt = {} + i = 0 + # Loop over chains + for chainid in pdb_chains['chain_order']: + # Loop over residues of this chain + for resid in pdb_chains[chainid]['order']: + # create a resdiue key + resname = pdb_chains[chainid][resid]['resname'] + reskey = f'{chainid}-{resid}-{resname}' + resdt = { + 'atoms_indices': [], + 'resname': resname, + 'atoms_order': pdb_chains[chainid][resid]['atoms_order'], + } + # Loop over atoms of this residue + for atname in pdb_chains[chainid][resid]['atoms_order']: + # list of internal indices + resdt['atoms_indices'].append(i) + # index of a CA + if atname == 'CA': + resdt['CA'] = i + # Point atome submatrix coordinates index + all_coords.append(pdb_chains[chainid][resid]['atoms'][atname]) + # increment atom index + i += 1 + resid_dt[reskey] = resdt + resid_keys.append(reskey) + return (all_coords, resid_keys, resid_dt) + + +def compute_distance_matrix(all_atm_coords: list[list[float]]) -> NDFloat: + """Compute all vs all distance matrix. + + Paramaters + ---------- + all_atm_coords : list[list[float]] + List of atomic coordinates. + + Return + ------ + dist_matrix : NDFloat + N*N distance matrix between all coordinates. + """ + dist_matrix = squareform(pdist(all_atm_coords)) + return dist_matrix + + +def extract_submatrix( + matrix: NDFloat, + indices: list[int], + indices2: Optional[list[int]] = None, + ) -> NDFloat: + """Extract submatrix based on desired indices. + + Paramaters + ---------- + matrix : NDFloat + A N*N matrix. + indices : list[int] + List of `row` indices to extract from this matrix + indices2 : list[int] + List of `columns` indices to extract from this matrix. + if unspecified, indices2 == indices and symetric matrix + is extracted. + + Return + ------ + submat : NDFloat + The extracted submatrix. + """ + # Set second set of indices (columns) to first if not defined + if not indices2: + indices2 = indices + # extract submatrix + submat = matrix[np.ix_(indices, indices2)] + return submat + + +def gen_contact_dt( + matrix: NDFloat, + resdt: dict, + res1_key: str, + res2_key: str, + ) -> dict: + """Generate contacts data. + + Parameters + ---------- + matrix : NDFloat + The distance matrix. + resdt : dict + Residues data with atom indices as returned by `get_ordered_coords()`. + res1_key : str + First residue of interest. + res2_key : str + Second residue of interest + + Return + ------ + cont_dt : dict + Dictionary holding contact data + """ + # point residues data + res1_dt = resdt[res1_key] + res2_dt = resdt[res2_key] + # point ca-ca dist + try: + ca_ca_dist = matrix[res1_dt['CA'], res2_dt['CA']] + except KeyError: + ca_ca_dist = 9999 + # obtain submatrix + res1_res2_atm_submat = extract_submatrix( + matrix, + res1_dt['atoms_indices'], + res2_dt['atoms_indices'], + ) + # obtain clostest contact + clostest_contact = min_dist(res1_res2_atm_submat) + # contact type + cont_type = get_cont_type(res1_dt['resname'], res2_dt['resname']) + # set return variable + cont_dt = { + 'res1': res1_key, + 'res2': res2_key, + 'ca-ca-dist': round(ca_ca_dist, 1), + 'shortest-dist': round(clostest_contact, 1), + 'contact-type': cont_type, + } + return cont_dt + + +def extract_heavyatom_contacts( + matrix: NDFloat, + resdt: dict, + res1_key: str, + res2_key: str, + contact_distance: float = 4.5, + ) -> list[dict[str, Union[float, str]]]: + """Generate contacts data. + + Parameters + ---------- + matrix : NDFloat + The distance matrix. + resdt : dict + Residues data with atom indices as returned by `get_ordered_coords()`. + res1_key : str + First residue of interest. + res2_key : str + Second residue of interest. + contact_distance : float + Distance defining a contact. + + Return + ------ + all_contacts : list[dict[str, Union[float, str]]] + List holding contact data + """ + all_contacts: list[dict[str, Union[float, str]]] = [] + # point data for first residue + res1_indices = resdt[res1_key]['atoms_indices'] + res1_atnames = resdt[res1_key]['atoms_order'] + # point data for second residue + res2_indices = resdt[res2_key]['atoms_indices'] + res2_atnames = resdt[res2_key]['atoms_order'] + # Loop over res1 atoms / indices + for r1_atname, r1_atindex in zip(res1_atnames, res1_indices): + # Loop over res2 atoms / indices + for r2_atname, r2_atindex in zip(res2_atnames, res2_indices): + # Point corresponding distance in matrix + r1_r2_dist = matrix[r1_atindex, r2_atindex] + # Check if distance <= threshold + if r1_r2_dist <= contact_distance: + # Hold data + contactdt = { + 'atom1': f'{res1_key}-{r1_atname}', + 'atom2': f'{res2_key}-{r2_atname}', + 'dist': r1_r2_dist, + } + all_contacts.append(contactdt) + return all_contacts + + +def get_cont_type(resn1: str, resn2: str) -> str: + """Generate polarity key between two residues. + + Parameters + ---------- + resn1 : str + 3 letters code of fist residue. + resn2 : str + 3 letters code of second residue. + + Return + ------ + pol_key : str + Combined residues polarities + """ + pol_keys: list[str] = [] + for resn in [resn1, resn2]: + if resn.strip() in RESIDUE_POLARITY.keys(): + pol_keys.append(RESIDUE_POLARITY[resn.strip()]) + else: + pol_keys.append('unknow') + pol_key = '-'.join(pol_keys) + return pol_key + + +def min_dist(matrix: NDFloat) -> float: + """Find minimum value in a matrix.""" + return np.min(matrix) + + +def write_res_contacts( + res_res_contacts: list[dict], + header: list[str], + path: Union[Path, str], + sep: str = '\t', + interchain_data: Union[bool, dict] = None, + ) -> Path: + """Write a tsv file based on residues-residues contacts data. + + Parameters + ---------- + res_res_contacts : list[dict] + List of dict holding data for each residue-residue contacts. + header : list[str] + Ordered list of keys to access in the dicts. + path : Path + Path to the output file to generate. + sep : str + Character used to separate data within a line. + + Return + ------ + path : Path + Path to the generated file. + """ + # define README data type content + dttype_info = { + 'res1': 'Chain-Resname-ResID key identifying first residue', + 'res2': 'Chain-Resname-ResID key identifying second residue', + 'ca-ca-dist': 'Observed distances between the two carbon alpha (Ca) atoms', + 'ca-ca-cont-probability': 'Fraction of times a contact is observed under the ca-ca-dist threshold over all analysed models of the same cluster', # noqa : E501 + 'shortest-dist': 'Observed shortest distance between the two residues', + 'shortest-cont-probability': 'Fraction of times a contact is observed under the shortest-dist threshold over all analysed models of the same cluster', # noqa : E501 + 'contact-type': 'ResidueType - ResidueType contact name', + 'atom1': 'Chain-Resname-ResID-Atome key identifying first atom', + 'atom2': 'Chain-Resname-ResID-Atome key identifying second atom', + 'dist': 'Observed distance between two atoms', + 'nb_dists': 'Total number of observed distances', + 'avg_dist': 'Cluster average distance', + 'std_dist': 'Cluster distance standard deviation', + } + + # Check for inter chain contacts + gen_interchain_tsv: bool = False + if interchain_data and type(interchain_data) == dict: + expected_keys = ('path', 'contact_threshold', 'data_key', ) + if all([k in interchain_data.keys() for k in expected_keys]): + gen_interchain_tsv = True + interchain_tsvdt: list[list[str]] = [header] + else: + raise KeyError + + # initiate file content + tsvdt: list[list[str]] = [header] + for res_res_cont in res_res_contacts: + tsvdt.append([str(res_res_cont[h]) for h in header]) + if gen_interchain_tsv: + chain1 = res_res_cont['res1'].split('-')[0] + chain2 = res_res_cont['res2'].split('-')[0] + if chain1 != chain2: + dist = res_res_cont[interchain_data['data_key']] + if dist < interchain_data['contact_threshold']: + interchain_tsvdt.append(tsvdt[-1]) + tsv_str = '\n'.join([sep.join(_) for _ in tsvdt]) + + # generate commented lines to be placed on top of file + readme = [ + '#' * 80, + '# This file contains extracted contacts half-matrix information', + '#' * 80, + '', + ] + for head in header[::-1]: + readme.insert(2, f'# {head}: {dttype_info[head]}') + + # Write file + with open(path, 'w') as tsvout: + tsvout.write('\n'.join(readme)) + tsvout.write(tsv_str) + + # Write inter chain file + if gen_interchain_tsv: + # Modify readme + readme[1] = readme[1].replace( + 'contacts half-matrix', + 'interchain contacts', + ) + # Write file + with open(interchain_data['path'], 'w') as f: + f.write('\n'.join(readme)) + # Write data string + f.write('\n'.join([sep.join(_) for _ in interchain_tsvdt])) + + return path + + +def tsv_to_heatmap( + tsv_path: Path, + sep: str = '\t', + data_key: str = 'ca-ca-dist', + contact_threshold: float = 7.5, + colorscale: str = 'Greys', + output_fname: Union[Path, str] = 'contacts.html', + offline: bool = False, + ) -> Union[Path, str]: + """Read a tsv file and generate a heatmap from it. + + Paramters + --------- + tsv_path : Path + Path a the .tsv file containing contact data. + sep : str + Separator character used to split data in each line. + data_key : str + Data key used to draw the plot. + contact_threshold : float + Upper boundary of maximum value to be plotted. + any value above it will be set to this value. + output_fname : Path + Path to the generated graph. + + Return + ------ + output_filepath : Union[Path, str] + Path to the generated file. + """ + half_matrix: list[float] = [] + labels: list[str] = [] + header: Union[bool, list[str]] = None + with open(tsv_path, 'r') as f: + for line in f: + # skip commented lines + if line.startswith('#'): + continue + # split line + s_ = line.strip().split(sep) + # gather header + if not header: + header = s_ + continue + # point labels + label1 = s_[header.index('res1')] + label2 = s_[header.index('res2')] + # Add them to set of labels + if label1 not in labels: + labels.append(label1) + if label2 not in labels: + labels.append(label2) + + # point data + value = float(s_[header.index(data_key)]) + # bound data to contact_threshold + bounded_value = min(value, contact_threshold) + # add it to matrix + half_matrix.append(bounded_value) + + # Genereate full matrix + matrix = squareform(half_matrix) + + # set data label + color_scale = datakey_to_colorscale(data_key, color_scale=colorscale) + if 'probability' in data_key: + data_label = 'probability' + np.fill_diagonal(matrix, 1) + else: + data_label = 'distance' + + # Compute chains length + chains_length: dict[str, int] = {} + ordered_chains: list[str] = [] + for label in labels: + chainid = label.split('-')[0] + if chainid not in chains_length.keys(): + chains_length[chainid] = 0 + ordered_chains.append(chainid) + chains_length[chainid] += 1 + # Compute chains delineations positions + del_posi = [0] + for chainid in ordered_chains: + del_posi.append(del_posi[-1] + chains_length[chainid]) + # Compute chains delineations lines + chains_limits: list[dict[str, float]] = [] + for delpos in del_posi: + # Vertical lines + chains_limits.append({ + "x0": delpos - 0.5, + "x1": delpos - 0.5, + "y0": -0.5, + "y1": len(labels) - 0.5, + }) + # Horizontal lines + chains_limits.append({ + "y0": delpos - 0.5, + "y1": delpos - 0.5, + "x0": -0.5, + "x1": len(labels) - 0.5, + }) + # Generate hover template + hovertemplate = ( + ' %{y} ↭ %{x}
    ' + f' Contact {data_label}: %{{z}}' + '' + ) + + # Generate heatmap + output_filepath = heatmap_plotly( + matrix, + labels={'color': data_label}, + xlabels=labels, + ylabels=labels, + color_scale=color_scale, + output_fname=output_fname, + offline=offline, + delineation_traces=chains_limits, + hovertemplate=hovertemplate, + ) + + return output_filepath + + +def datakey_to_colorscale(data_key: str, color_scale: str = 'Greys') -> str: + """Convert color scale into reverse if data implies to do it. + + data_key : str + A dictionary key pointing to data type. + color_scale : str + Name of a base plotpy color_scale. + + Return + ------ + color_scale : str + Possibly the reverse name of the color_scale. + """ + return f'{color_scale}_r' if 'probability' not in data_key else color_scale + + +###################################### +# Start of the chord chart functions # +###################################### +def moduloAB(val: float, lb: float, ub: float) -> float: + """Map a real number onto the unit circle. + + The unit circle is identified with the interval [lb, ub), ub-lb=2*PI. + + Parameters + ---------- + val : float + The value to be mapped into the unit circle. + lb : float + The lower boundary. + ub : float + The upper boundary + + Return + ------ + moduloab : float + The modulo of val between lb and ub + """ + if lb >= ub: + raise ValueError('Incorrect interval ends') + y = (val - lb) % (ub - lb) + moduloab = y + ub if y < 0 else y + lb + return moduloab + + +def within_2PI(val: float) -> bool: + """Check if float value is within unit circle value range. + + Parameters + ---------- + val : float + The value to be tested. + """ + return 0 <= val < 2 * PI + + +def check_square_matrix(data_matrix: NDArray) -> int: + """Check if the matrix is a square one. + + Parameters + ---------- + data_matrix : NDArray (2DArray) + The matrix to be checked. + + Return + ------ + nb_rows : int + Number of rows in this matrix. + """ + matrixshape = data_matrix.shape + nb_rows = matrixshape[0] + if len(matrixshape) > 2: + raise ValueError('Data array must have only two dimensions') + if nb_rows != matrixshape[1]: + raise ValueError('Data array must have (n,n) shape') + return nb_rows + + +def get_ideogram_ends( + ideogram_len: NDFloat, + gap: float, + ) -> list[tuple[float, float]]: + """Generate ideogram ends. + + Paramaters + ---------- + ideogram_len : NDArray + Length of each ideograms. + gap : float + Gap to add in between each ideogram. + + Return + ------ + ideo_ends : list[tuple[float]] + List of start and end position for each ideograms. + """ + ideo_ends: list[tuple[float, float]] = [] + start = 0.0 + for k in range(len(ideogram_len)): + end = float(start + ideogram_len[k]) + ideo_ends.append((start, end)) + # Increment new start by gap for next origin + start = end + gap + return ideo_ends + + +def make_ideogram_arc( + radius: float, + _phi: tuple[float, float], + nb_points: float = 50, + ) -> NDFloat: + """Generate ideogran arc. + + Parameters + ---------- + radius : float + The circle radius. + phi : tuple[float, float] + Tuple of ends angle coordinates of an arc. + nb_points : float + Parameter that controls the number of points to be evaluated on an arc + + Return + ------ + arc_positions : NDArray + Array of 2D coorinates defining an arc. + """ + if not within_2PI(_phi[0]) or not within_2PI(_phi[1]): + phi = [moduloAB(t, 0, 2 * PI) for t in _phi] + else: + phi = [t for t in _phi] + length = (phi[1] - phi[0]) % (2 * PI) + nr = 5 if length <= (PI / 4) else int((nb_points * length) / PI) + if phi[0] < phi[1]: + theta = np.linspace(phi[0], phi[1], nr) + else: + theta = np.linspace( + moduloAB(phi[0], -PI, PI), + moduloAB(phi[1], -PI, PI), + nr, + ) + arc_positions = radius * np.exp(1j * theta) + return arc_positions + + +def make_ribbon_ends( + matrix: NDArray, + row_sum: list[int], + ideo_ends: list[tuple[float, float]], + L: int, + ) -> list[list[tuple[float, float]]]: + """Generate all connecting ribbons coordinates. + + Parameters + ---------- + matrix : NDArray + The data matrix. + row_sum : list[int] + Number of connexions in each row. + ideo_ends : list[tuple[float, float]] + List of start and end position for each ideograms. + + Returns + ------- + ribbon_boundary : list[list[tuple[float, float]]] + Matrix of per residue ribbons start and end positions. + """ + ribbon_boundary: list[list[tuple[float, float]]] = [] + for k, ideo_end in enumerate(ideo_ends): + # Point stating coordinates of this residue ideo + start = float(ideo_end[0]) + # No ribbon to be formed + if row_sum[k] == 0: + # Add empty set of ribbons + ribbon_boundary.append([(0., 0.) for i in range(len(ideo_ends))]) + continue + # Initiate row ribbons + row_ribbon_ends: list[tuple[float, float]] = [] + # Compute increment + increment = (ideo_end[1] - start) / row_sum[k] + # Loop over positions + for j in range(1, L + 1): + # Skip if no ribbon to add for this k, j pair + if matrix[k][j - 1] == 0: + row_ribbon_ends.append((0., 0.)) + continue + # Define end + end = float(start + increment) + # Hold data + row_ribbon_ends.append((start, end)) + # Set next start to current end + start = end + # Add full row + ribbon_boundary.append(row_ribbon_ends) + return ribbon_boundary + + +def control_pts( + angle: list[float], + radius: float, + ) -> list[tuple[float, float]]: + """Generate control points to draw a SVGpath. + + Parameters + ---------- + angle : list[float] + A list containing angular coordinates of the control points b0, b1, b2. + radius : float + The distance from b1 to the origin O(0,0) + + Returns + ------- + control_points : list[tuple[float, float]] + The set of control points. + + Raises + ------ + ValueError + Raised if the number of angular coordinates is not equal to 3. + """ + # Check number of angular coordinates + if len(angle) != 3: + raise ValueError('angle must have len = 3') + b_cplx = np.array([np.exp(1j * angle[k]) for k in range(3)]) + # Give it its size + b_cplx[1] = radius * b_cplx[1] + # Generate control points as a list for two values + control_points = list(zip(b_cplx.real, b_cplx.imag)) + return control_points + + +def ctrl_rib_chords( + side1: tuple[float, float], + side2: tuple[float, float], + radius: float, + ) -> list[list[tuple[float, float]]]: + """Generate poligons points aiming at drawing ribbons. + + Parameters + ---------- + side1 : tuple[float, float] + List of angular variables of the ribbon arc ends defining + the ribbon starting (ending) arc + side2 : tuple[float, float] + List of angular variables of the ribbon arc ends defining + the ribbon starting (ending) arc + radius : float, optional + Circle radius size + + Returns + ------- + list[list[tuple[float, float]]] + _description_ + """ + if len(side1) != 2 or len(side2) != 2: + raise ValueError('the arc ends must be elements in a list of len 2') + poligons = [ + control_pts( + [side1[j], (side1[j] + side2[j]) / 2, side2[j]], + radius, + ) + for j in range(2) + ] + return poligons + + +def make_q_bezier(control_points: list[tuple[float, float]]) -> str: + """Define the Plotly SVG path for a quadratic Bezier curve. + + defined by the list of its control points. + + Parameters + ---------- + control_points : list[tuple[float, float]] + List of control points + + Return + ------ + svgpath : str + An SVG path + """ + if len(control_points) != 3: + raise ValueError('control poligon must have 3 points') + _a, _b, _c = control_points + svgpath = 'M ' + str(_a[0]) + ',' + str(_a[1]) + ' Q ' +\ + str(_b[0]) + ', ' + str(_b[1]) + ' ' +\ + str(_c[0]) + ', ' + str(_c[1]) + return svgpath + + +def make_ribbon_arc(theta0: float, theta1: float) -> str: + """Generate a SVGpath to draw a ribbon arc. + + Parameters + ---------- + theta0 : float + Starting angle value + theta1 : float + Ending angle value + + Returns + ------- + string_arc : str + A string representing the SVGpath of the ribbon arc. + + Raises + ------ + ValueError + If provided theta0 and theta1 angles are incorrect for a ribbon. + ValueError + If the angle coordinates for an arc side of a ribbon are not + in the appropriate range [0, 2*pi] + """ + if within_2PI(theta0) and within_2PI(theta1): + if theta0 < theta1: + theta0 = moduloAB(theta0, -PI, PI) + theta1 = moduloAB(theta1, -PI, PI) + if theta0 * theta1 > 0: + raise ValueError('incorrect angle coordinates for ribbon') + + nr = int(40 * (theta0 - theta1) / PI) + if nr <= 2: + nr = 3 + theta = np.linspace(theta0, theta1, nr) + pts = np.exp(1j * theta) # points on arc in polar complex form + + string_arc: str = '' + for k in range(len(theta)): + string_arc += f'L {str(pts.real[k])}, {str(pts.imag[k])} ' + return string_arc + else: + raise ValueError('the angle coordinates for an arc side of a ribbon ' + 'must be in [0, 2*pi]') + + +def make_layout( + title: str, + plot_size: float, + layout_shapes: list[dict], + ) -> go.Layout: + """Generate the chart layout. + + Parameters + ---------- + title : str + Title to be given to the chart. + plot_size : float + Size of the chart. + layout_shapes : list[dict] + Shapes to be drawn. + + Returns + ------- + layout : go.Layout + The plotly layout. + """ + # Set axis parameters to hide axis line, grid, ticklabels and title + axis = { + 'showline': False, + 'zeroline': False, + 'showgrid': False, + 'showticklabels': False, + 'title': '', + } + # Getenate the layout + layout = go.Layout( + title=title, + xaxis=axis, + yaxis=axis, + showlegend=True, # Important to show legend + # legend={'font': {'size': 10}}, # Lower font size + width=plot_size + 150, # +150 to accomodate legend / keep circle round + height=plot_size, + margin={"t": 25, "b": 25, "l": 25, "r": 25}, + hovermode='closest', + shapes=layout_shapes, + ) + return layout + + +def make_ideo_shape( + path: str, + line_color: str, + fill_color: str, + ) -> dict: + """Generate data to draw a ideogram shape. + + Parameters + ---------- + path : str + A SVGPath to be drawn. + line_color : str + Color of the shape boundary. + fill_color : str + Shape filling color fr the ribbon shape. + + Returns + ------- + dict + Data enabling to draw a ideogram shape in layout. + """ + return { + "line": {"color": line_color, "width": 0.45}, + "path": path, + "type": 'path', + "fillcolor": fill_color, + "layer": 'below', + } + + +def make_ribbon( + side1: tuple[float, float], + side2: tuple[float, float], + line_color: str, + fill_color: str, + radius: float = 0.2, + ) -> dict: + """Generate data to draw a ribbon. + + Parameters + ---------- + side1 : list[float] + List of angular variables of first ribbon arc ends defining + the ribbon starting (ending) arc. + side2 : list[float] + List of angular variables of the other ribbon arc ends defining + the ribbon starting (ending) arc. + line_color : str + Color of the shape boundary. + fill_color : str + Shape filling color fr the ribbon shape. + radius : float, optional + Circle radius size, by default 0.2. + + Returns + ------- + dict + Data enabling to draw a ribbon in layout. + """ + poligon = ctrl_rib_chords(side1, side2, radius) + _b, _c = poligon + # Generate the SVGpath + path = make_q_bezier(_b) + path += make_ribbon_arc(side2[0], side2[1]) + path += make_q_bezier(_c[::-1]) + path += make_ribbon_arc(side1[1], side1[0]) + + return { + 'line': {'color': line_color, 'width': 0.5}, + 'path': path, + 'type': 'path', + 'fillcolor': fill_color, + 'layer': 'below', + } + + +def invPerm(perm: list[int]) -> list[int]: + """Generate the inverse of a permutation. + + Parameters + ---------- + perm : _type_ + A permutation. + + Returns + ------- + inv : list[int] + Inverse of a permutation. + """ + # Fill with zeros + inv = [0] * len(perm) + for i, s in enumerate(perm): + inv[s] = i + return inv + + +def get_chains_ideograms_ends( + chains: dict[str, list[str]], + gap: float = 2 * PI * 0.005, + ) -> tuple[list[tuple[float, float]], NDFloat]: + """Build ideogram ends to represent protein chains. + + Parameters + ---------- + chains : dict[str, list[str]] + Dictionary mapping chains with their respective set of residues labels. + gap : float, optional + Gap between two ideograms, by default 2*PI*0.005 + + Returns + ------- + chain_ideo_ends : list[tuple[float, float]] + Ideogram ends to represent protein chains. + chain_ideogram_length : NDFloat + + """ + chain_row_sum = [len(chains[chain]) + for chain in sorted(chains, reverse=True)] + chain_ideogram_length = 2 * PI * np.asarray(chain_row_sum) + chain_ideogram_length /= sum(chain_row_sum) + chain_ideogram_length -= gap * np.ones(len(chain_row_sum)) + chain_ideo_ends = get_ideogram_ends(chain_ideogram_length, gap) + return chain_ideo_ends, chain_ideogram_length + + +def get_all_ideograms_ends( + chains: dict, + gap: float = 2 * PI * 0.005, + ) -> tuple[list[tuple[float, float]], list[tuple[float, float]]]: + """Generate both chain and residues ideograms ends. + + Parameters + ---------- + chains : dict + Dictionary mapping to list of residues labels. + gap : float, optional + Gap distance used to separate two ideograms, by default 2*PI*0.005 + + Returns + ------- + tuple[ideo_ends, chain_ideo_ends] + A tuple containing residues ideo ends and chains ideo ends. + + ideo_ends : list[tuple[float, float]] + List of residues ideograms start and ending positions. + chain_ideo_ends : list[tuple[float, float]] + List of chain ideograms start and ending positions. + """ + chain_ideo_ends, chain_ideogram_length = get_chains_ideograms_ends( + chains, + gap=gap, + ) + + ideo_ends: list[tuple[float, float]] = [] + left = 0 + for ind, chain in enumerate(sorted(chains, reverse=True)): + chain_labels = chains[chain] + for _label in chain_labels: + right = left + (chain_ideogram_length[ind] / len(chain_labels)) + ideo_ends.append((left, right)) + left = right + left = right + gap + return ideo_ends, chain_ideo_ends + + +def split_labels_by_chains(labels: list[str]) -> dict[str, list[str]]: + """Map each label to its chain. + + Parameters + ---------- + labels : list[str] + List of residues keys. e.g.: A-SER-123 (chain A, serine 123) + + Returns + ------- + chains : dict[str, list[str]] + Dictionary mapping chains with their respective set of residues labels. + """ + chains: dict[str, list] = {} + for lab in labels: + chain, resname, resid = lab.split('-') + if chain not in chains.keys(): + chains[chain] = [] + chains[chain].append(lab) + return chains + + +def contacts_to_connect_matrix( + matrix: NDFloat, + labels: list[str], + ) -> list[list[int]]: + """. + + Parameters + ---------- + matrix : NDFloat + A square contact matrix. + labels : list[str] + List of labels corresponding row & columns entries. + + Returns + ------- + connect_matrix : list[list[Union[str, int]]] + The connectivity matrix without self contacts. + """ + connect_matrix: list[list[int]] = [] + for ri, label_i in enumerate(labels): + # Point label chain name + chain1 = label_i.split('-')[0] + new_contact_mat_row: list[int] = [] + # Loop over columns + for ci, label_j in enumerate(labels): + # Point label chain name + chain2 = label_j.split('-')[0] + if chain1 != chain2 and matrix[ri, ci] == 1: + interaction = 1 + else: + interaction = 0 + new_contact_mat_row.append(interaction) + # Hold row + connect_matrix.append(new_contact_mat_row) + return connect_matrix + + +def to_nice_label(label: str) -> str: + """Convert a label into a user friendly label. + + Parameters + ---------- + label : str + Label name as found in csv + + Returns + ------- + nicelabel : str + User friendly description of the label. + """ + slabel = label.split('-') + nicelabel = f"Chain {slabel[0]}, residue {slabel[2]} {slabel[1]}" + return nicelabel + + +def to_color_weight( + distance: float, + max_dist: float, + min_dist: float = 2., + min_weight: float = 0.2, + max_weight: float = 0.90, + ) -> float: + """Compute color weight based on distance. + + Parameters + ---------- + distance : float + The distance to weight. + max_dist : float + The max distance observed in the dataset. + min_dist : float, optional + The minumu, distance observed in the dataset, by default 2. + min_weight : float, optional + Color wight for the maximum distance, by default 0.2 + max_weight : float, optional + Color wight for the minimum distance, by default 0.90 + + Returns + ------- + weight : float + The color weight. in range [min_weight, max_weight] + """ + # Scale dist into minimum + dist = max(distance, min_dist) + # Compute probability + probability_dist = (dist - min_dist) / (max_dist - min_dist) + # Obtain corresponding weight + weight = ((min_weight - max_weight) * probability_dist) + max_weight + # Return rounded value of weight + return round(weight, 2) + + +def to_rgba_color_string( + connect_color: tuple[int, int, int], + alpha: float, + ) -> str: + """Generate a rgba string from list of colors and alpha. + + Parameters + ---------- + connect_color : list[int] + A 3-values list of integers defining the red, green and blue colors. + alpha : float + color_weight + + Returns + ------- + rgba_color : str + The html like rgba colors. e.g.: 'rgba(123, 123, 123, 0.5)' + """ + colors_str = ",".join([str(v) for v in connect_color]) + rgba_color = f'rgba({colors_str},{alpha})' + return rgba_color + + +def to_full_matrix( + half_matrix: list[Union[int, float, str]], + diag_val: Union[int, float, str], + ) -> NDArray: + """Generate a full matrix from a half matrix. + + Parameters + ---------- + half_matrix : list[Any] + Values of the N*(N-1)/2 half matrix. + diag_val : Any + Value to be placed in diagonal of the full matrix. + + Returns + ------- + matrix : NDArry + The reconstituted full matrix. + """ + # Genereate full matrix from N*(N-1)/2 vector + matrix = squareform(half_matrix) + # Update diagonal with data + np.fill_diagonal(matrix, diag_val) + return matrix + + +def make_chordchart( + _contact_matrix: list[list[int]], + _dist_matrix: list[list[float]], + _interttype_matrix: list[list[str]], + _labels: list[str], + gap: float = 2 * PI * 0.005, + output_fpath: Union[str, Path] = 'chordchart.html', + title: str = 'Chord diagram', + offline: bool = False, + ) -> Union[str, Path]: + """Generate a plotly chordchart graph. + + Parameters + ---------- + _contact_matrix : list[list[int]] + The contact matrix + _dist_matrix : list[list[float]] + The distance matrix + _interttype_matrix : list[list[str]] + The interaction type matrix + _labels : list[str] + Labels of each matrix rows (and columns as supposed to be symetric) + gap : float, optional + Gap between two ideograms, by default 2*PI*0.005 + output_fpath : Union[str, Path], optional + Path to the output file, by default 'chordchart.html' + title : str, optional + Title to give to the diagram, by default 'Chord diagram' + + Returns + ------- + output_fpath : Union[str, Path] + Path to the genereated output file. + """ + # Unpack matrices + contact_matrix = contacts_to_connect_matrix(_contact_matrix, _labels) + + # Reverse data order so later graph displayed clockwise + matrix = np.array([ri[::-1] for ri in contact_matrix[::-1]]) + dist_matrix = [ri[::-1] for ri in _dist_matrix[::-1]] + interttype_matrix = [ri[::-1] for ri in _interttype_matrix[::-1]] + labels = _labels[::-1] + + # Check matrix shape + L = check_square_matrix(matrix) + + # Map labels into respective chains + chains = split_labels_by_chains(labels) + # Set matrix of indices + idx_sort = [list(range(L)) for i in range(L)] + + # Compute residues and chain ideograms positions + ideo_ends, chain_ideo_ends = get_all_ideograms_ends(chains, gap=gap) + + # Compute number of connexion per residues + row_sum = [np.sum(matrix[k, :]) for k in range(L)] + + # Compute connexion ribbons positions + ribbon_ends = make_ribbon_ends(matrix, row_sum, ideo_ends, L) + + # Initiate shape holder + layout_shapes: list[dict] = [] + # Initiate ribbon info holder + ribbon_info: list[go.Scatter] = [] + # Loop over entries + for k, label1 in enumerate(labels): + sigma = idx_sort[k] + sigma_inv = invPerm(sigma) + # Half matrix loop to avoid duplicates + for j in range(k, L): + # No data to draw + if matrix[k][j] == 0 and matrix[j][k] == 0: + continue + + # Obtain ribbon color for this interaction type + try: + connect_color = CONNECT_COLORS[interttype_matrix[k][j]] + except KeyError: + connect_color = (123, 123, 123) + color_weight = to_color_weight(dist_matrix[k][j], 9.5) + rgba_color = to_rgba_color_string(connect_color, color_weight) + + # Point ribbons data + side1 = ribbon_ends[k][sigma_inv[j]] + eta = idx_sort[j] + eta_inv = invPerm(eta) + side2 = ribbon_ends[j][eta_inv[k]] + zi = 0.9 * np.exp(1j * (side1[0] + side1[1]) / 2) + zf = 0.9 * np.exp(1j * (side2[0] + side2[1]) / 2) + + # reverse interaction type for second label + s_intertype = interttype_matrix[k][j].split('-') + rev_s_intertype = s_intertype[::-1] + rev_interttype = '-'.join(rev_s_intertype) + # Obtain nice labels + nicelabel1 = to_nice_label(label1) + nicelabel2 = to_nice_label(labels[j]) + # texti and textf are the strings that will be displayed when + # hovering the mouse over the two ribbon ends + texti = f'{nicelabel1} {rev_interttype} with {nicelabel2}' + textf = f'{nicelabel2} {interttype_matrix[j][k]} with {nicelabel1}' # noqa : E501 + # Generate interactive labels + for zv, text in zip([zi, zf], [texti, textf]): + # Generate ribbon info + ribbon_info.append( + go.Scatter( + x=[zv.real], + y=[zv.imag], + mode='markers', + marker={"size": 0.5, "color": rgba_color}, + text=text, + hoverinfo='text', + showlegend=False, + ) + ) + # Note: must reverse these arc ends to avoid twisted ribbon + side2_rev = (side2[1], side2[0]) + # Append the ribbon shape + layout_shapes.append( + make_ribbon( + side1, + side2_rev, + 'rgba(175,175,175)', + rgba_color, + ) + ) + + ideograms: list[go.Scatter] = [] + # Draw ideograms for residues + for k, label in enumerate(labels): + z = make_ideogram_arc(1.1, ideo_ends[k]) + zi = make_ideogram_arc(1.0, ideo_ends[k]) + + # Point residue name + resname = label.split('-')[2] + + # Point corresponding color + try: + rescolor = AA_DNA_RNA_COLORS[resname.strip()] + except KeyError: + rescolor = 'rgba(123, 123, 123, 0.7)' + + # Build textual info + text_info = f'{to_nice_label(label)}
    ' + if row_sum[k] == 0: + text_info += 'No interaction' + else: + text_info += f'Total of {row_sum[k]:d} interaction' + if row_sum[k] >= 2: + text_info += 's' + # Add info + ideograms.append( + go.Scatter( + x=z.real, + y=z.imag, + mode='lines', + line={ + "color": rescolor, + "shape": 'spline', + "width": 0.25, + }, + text=text_info, + hoverinfo='text', + showlegend=False, + ) + ) + + # Build corresponding SVG path + m = len(z) + svgpath = 'M ' + for s in range(m): + svgpath += f'{str(z.real[s])}, {str(z.imag[s])} L ' + + Zi = np.array(zi.tolist()[::-1]) + for s in range(m): + svgpath += f'{str(Zi.real[s])}, {str(Zi.imag[s])} L ' + svgpath += f'{str(z.real[0])}, {str(z.imag[0])}' + # Hold it + layout_shapes.append( + make_ideo_shape( + svgpath, + 'rgba(150,150,150)', + rescolor, + ) + ) + + # Draw ideograms for chains + for k, chainid in enumerate(sorted(chains, reverse=True)): + z = make_ideogram_arc(1.2, chain_ideo_ends[k]) + zi = make_ideogram_arc(1.11, chain_ideo_ends[k]) + m = len(z) + ideograms.append( + go.Scatter( + x=z.real, + y=z.imag, + mode='lines', + line={ + "color": CHAIN_COLORS[k], + "shape": 'spline', + "width": 0.25, + }, + text=f'Chain {chainid}', + hoverinfo='text', + showlegend=False, + ) + ) + + # Build corresponding SVG path + svgpath = 'M ' + for s in range(m): + svgpath += f'{str(z.real[s])}, {str(z.imag[s])} L ' + Zi = np.array(zi.tolist()[::-1]) + for s in range(m): + svgpath += f'{str(Zi.real[s])}, {str(Zi.imag[s])} L ' + svgpath += f'{str(z.real[0])}, {str(z.imag[0])}' + + layout_shapes.append( + make_ideo_shape( + svgpath, + 'rgba(150,150,150)', + CHAIN_COLORS[k], + ) + ) + + # Compute figure size + fig_size = 100 * np.log(L * L) + # Create plotly layout + layout = make_layout(title, fig_size, layout_shapes) + # combine all data info + data = ideograms + ribbon_info + # Generate the figure + fig = go.Figure(data=data, layout=layout) + # Fine tune figure + fig.update_layout( + plot_bgcolor='white', + ) + # Add legend(s) + add_chordchart_legends(fig) + # Write it as html file + fig_to_html( + fig, + output_fpath, + figure_height=fig_size, + figure_width=fig_size, + offline=offline, + ) + return output_fpath + + +def add_chordchart_legends(fig: go.Figure) -> None: + """Add custom legend to chordchart. + + Parameters + ---------- + fig : go.Figure + A plotly figure. + """ + # Add connection types legends + for key_key, color in REVERSED_CONNECT_COLORS_KEYS.items(): + # Create dummy traces + fig.add_trace( + go.Scatter( + x=[None], + y=[None], + legendgroup="connect_color", + legendgrouptitle_text="Interaction types", + showlegend=True, + name=key_key.replace('-', '↭'), + mode="lines", + marker={ + "color": to_rgba_color_string(color, 0.75), + "size": 10, + "symbol": "line-ew-open", + }, + ) + ) + # Add unknown interaction type + fig.add_trace( + go.Scatter( + x=[None], + y=[None], + legendgroup="connect_color", + legendgrouptitle_text="Interaction types", + showlegend=True, + name="Unknown", + mode="lines", + marker={ + "color": to_rgba_color_string((111, 111, 111), 0.75), + "size": 10, + "symbol": "line-ew-open", + }, + ) + ) + + # Add aa types legend + for aa, rgba_color in RESIDUES_COLORS.items(): + # Create dummy traces + fig.add_trace( + go.Scatter( + x=[None], + y=[None], + legendgroup="aa_color", + legendgrouptitle_text="Residues/Bases", + showlegend=True, + name=aa, + mode="lines", + marker={ + "color": rgba_color, + "size": 10, + "symbol": "line-ew-open", + }, + ) + ) + # Add nucleobases legend + for na, rgba_color in DNARNA_COLORS.items(): + # Create dummy traces + fig.add_trace( + go.Scatter( + x=[None], + y=[None], + legendgroup="aa_color", + legendgrouptitle_text="Residues/Bases", + showlegend=True, + name=na, + mode="lines", + marker={ + "color": rgba_color, + "size": 10, + "symbol": "line-ew-open", + }, + ) + ) + # Add unknown type + fig.add_trace( + go.Scatter( + x=[None], + y=[None], + legendgroup="aa_color", + legendgrouptitle_text="Residues/Bases", + showlegend=True, + name="Unknown", + mode="lines", + marker={ + "color": to_rgba_color_string((111, 111, 111), 0.75), + "size": 10, + "symbol": "line-ew-open", + }, + ) + ) + + +def tsv_to_chordchart( + tsv_path: Path, + sep: str = '\t', + data_key: str = 'ca-ca-dist', + contact_threshold: float = 7.5, + filter_intermolecular_contacts: bool = True, + output_fname: Union[Path, str] = 'contacts_chordchart.html', + title: str = 'Chord diagram', + offline: bool = False, + ) -> Union[Path, str]: + """Read a tsv file and generate a chord diagram from it. + + Paramters + --------- + tsv_path : Path + Path a the .tsv file containing contact data. + sep : str + Separator character used to split data in each line. + data_key : str + Data key used to draw the plot. + contact_threshold : float + Upper boundary of maximum value to be plotted. + any value above it will be set to this value. + output_fname : Union[Path, str] + Path where to generate the graph. + title : str + Title to give to the Chord diagram + + Return + ------ + chord_chart_fpath : Union[Path, str] + Path to the generated graph + """ + # Initiate holders + half_contact_matrix: list[int] = [] + half_value_matrix: list[float] = [] + half_intertype_matrix: list[str] = [] + labels: list[str] = [] + header: Union[bool, list[str]] = None + # Read tsv file + with open(tsv_path, 'r') as f: + for line in f: + # skip commented lines + if line.startswith('#'): + continue + # split line + s_ = line.strip().split(sep) + # gather header + if not header: + header = s_ + continue + # point labels + label1 = s_[header.index('res1')] + label2 = s_[header.index('res2')] + # Add them to set of labels + if label1 not in labels: + labels.append(label1) + if label2 not in labels: + labels.append(label2) + + # point data + value = float(s_[header.index(data_key)]) + # check if in contact + contact = 1 if value <= contact_threshold else 0 + # Point interaction type + inter_type = s_[header.index('contact-type')] + # add it to matrix + half_contact_matrix.append(contact) + half_value_matrix.append(value) + half_intertype_matrix.append(inter_type) + + # Genereate full matrices + contact_matrix = to_full_matrix(half_contact_matrix, 1) + dist_matrix = to_full_matrix(half_value_matrix, 0.) + intertype_matrix = to_full_matrix(half_intertype_matrix, 'self-self') + + # Check if must get only the intermolecular contacts submatrix + if filter_intermolecular_contacts: + # Filter positions where: intermolecular contacts + dist <= threshold + intmol_cont_labels: list[str] = [] + for ri, label1 in enumerate(labels): + label1_chain = label1.split('-')[0] + for ci, label2 in enumerate(labels): + label2_chain = label2.split('-')[0] + # Skip same chains + if label1_chain == label2_chain: + continue + # Check contacts + if contact_matrix[ri, ci] == 1: + intmol_cont_labels += [label1, label2] + + # Obtain sorted subset + nodoubles_intmol_cont_labels = list(set(intmol_cont_labels)) + sorted_intmol_cont_labels = sorted( + nodoubles_intmol_cont_labels, + key=lambda k: labels.index(k), + ) + + # Get indices to be extracted + sorted_indices = [labels.index(k) for k in sorted_intmol_cont_labels] + + # Get submatrix + contact_submatrix = extract_submatrix(contact_matrix, sorted_indices) + dist_submatrix = extract_submatrix(dist_matrix, sorted_indices) + intert_submatrix = extract_submatrix(intertype_matrix, sorted_indices) + sublabels = sorted_intmol_cont_labels + + else: + contact_submatrix = contact_matrix + dist_submatrix = dist_matrix + intert_submatrix = intertype_matrix + sublabels = labels + + # Generate chord chart + chord_chart_fpath = make_chordchart( + contact_submatrix, + dist_submatrix, + intert_submatrix, + sublabels, + output_fpath=output_fname, + title=title, + offline=offline, + ) + + return chord_chart_fpath diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a022c9a21d3c5ff9e0a8a2ab0e534e44b4d754cc --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/contactmap/defaults.yaml @@ -0,0 +1,120 @@ +ca_ca_dist_threshold: + default: 9.0 + min: 4.0 + max: 1000.0 + type: float + precision: 1 + title: Ca-Ca distance defining a contact. + short: Distance between Ca atoms of two residues defining a contact. + long: Distance between Ca atoms of two residues defining a contact. + group: analysis + explevel: easy + +shortest_dist_threshold: + default: 4.5 + type: float + min: 2.0 + max: 1000.0 + precision: 1 + title: Distance defining a contact between two residues. + short: Shortest distance between any atom of two residues defining a contact. + long: Shortest distance between any atom of two residues defining a contact. + group: analysis + explevel: easy + +color_ramp: + default: 'Greys' + type: string + minchars: 3 + maxchars: 10 + choices: + - Greys + - Purples + - BuPu + - Blues + - BuGn + - Greens + - deep + - tempo + - algae + - dense + - amp + title: Color ramp used to color heatmap. + short: Color ramp used to color heatmap. + long: Color ramp used to color heatmap. Please refer to `plotly builtin-colorscales` for more information + group: analysis + explevel: easy + +single_model_analysis: + default: false + type: boolean + title: Analyse contacts at single model level. + short: Analyse contacts at single model level. + long: In addition to cluster analysis, also perform single model analyses. + group: analysis + explevel: easy + +generate_heatmap: + default: true + type: boolean + title: Generate contact heatmap. + short: Generate plotly heatmap matrix representation of the contacts. + long: Uses generated contact matrices files to generate heatmap. + group: analysis + explevel: easy + +generate_chordchart: + default: true + type: boolean + title: Generate chordchart. + short: Generate plotly chordchart representation of the contacts. + long: Uses generated contact matrices files to generate chord chart. + group: analysis + explevel: easy + +topX: + default: 10 + type: integer + min: 1 + max: 100 + title: Number of unclustered models to analyse. + short: Number of unclustered models to analyse. + long: Top `X` unclustered models to analyse. Models are sorted based on + their score (if accessible) and only a subset defined + by this variable are analysed. If no score available, a random set of + `topX` models are analysed. + group: analysis + explevel: expert + +cluster_heatmap_datatype: + default: 'shortest-cont-probability' + type: string + minchars: 5 + maxchars: 30 + choices: + - ca-ca-dist + - ca-ca-cont-probability + - shortest-dist + - shortest-cont-probability + title: Type of data to be used in the heatmap. + short: Type of data to be used in the heatmap. + long: ca-ca-dist & shortest-dist are averages distances observed in cluster. + ca-ca-cont-probability & shortest-cont-probability are probability of + the distances to be observed under their respective thresholds. + group: analysis + explevel: easy + +chordchart_datatype: + default: 'shortest-dist' + type: string + minchars: 5 + maxchars: 30 + choices: + - ca-ca-dist + - shortest-dist + title: Type of data to be used in the chordchart. + short: Type of data to be used in the chordchart. + long: ca-ca-dist and shortest-dist are averages distances observed in + cluster. + group: analysis + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..6dadcbfb9a336cae1c98b1f303ccf6f71dc54200 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/__init__.py @@ -0,0 +1,104 @@ +"""Filter models based on their score. + +This module filters the input models based on their score using a threshold +value. Models having higher score than the threshold value are filtered out. + +The number of models to be selected is unknown, and is the set of models that +have a score below the defined threshold. +For this module to be functional, a score must be first computed. This can be +performed by running a CNS module or a scoring module. If scores are not +accessible, the workflow will terminate with an error message. + +If the threshold value is too stringent, resulting in no models passed to the +next module, the workflow will stop with an error message. +""" + +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import Any, FilePath +from haddock.libs.libontology import Format, PDBFile +from haddock.modules import BaseHaddockModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module to select top cluster/model.""" + + name = RECIPE_PATH.name + + def __init__(self, + order: int, + path: Path, + *ignore: Any, + init_params: FilePath = DEFAULT_CONFIG, + **everything: Any) -> None: + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if module is installed.""" + return + + def _run(self) -> None: + """Execute module.""" + # Make sure we have access to complexes + if type(self.previous_io) == iter: + self.finish_with_error( + "[filter] This module cannot come after one" + " that produced an iterable." + ) + # Get the models generated in previous step + models: list[PDBFile] = [ + p + for p in self.previous_io.output + if p.file_type == Format.PDB + ] + + # Get the filter by parameter + filter_by = "score" + threshold = self.params["threshold"] + + # Make sure we can access this attribute on models + models_with_attributes: list[PDBFile] = [ + m for m in models + if getattr(m, filter_by, None) != None + ] + + # Check how many of them are available + ratio_models_with_attr = len(models_with_attributes) / len(models) + self.log( + f"{100 * (1 - ratio_models_with_attr):6.2f} % " + "of the input models have accessible scores." + ) + if len(models_with_attributes) == 0: + self.finish_with_error( + "Input models do not have scores. " + "Please consider running a scoring module before!" + ) + + # Process to the actual filtering step + filtered_models: list[PDBFile] = [ + m for m in models_with_attributes + if getattr(m, filter_by) <= threshold + ] + + # Final evaluation of the outcome of the filtering + percent_filtered = (1 - (len(filtered_models) / len(models))) * 100 + if len(filtered_models) == 0: + self.finish_with_error( + f"With the currently set 'threshold' value of {threshold}, " + "ALL models were filtered out." + ) + else: + self.log( + f"With currently set 'threshold' value of {threshold}, " + f"{percent_filtered:6.2f}% of the models were filtered out." + ) + + # select the models based on the parameter + self.output_models = filtered_models + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..abdf4ef5116b0afc9a0ca67dfaf08d56cc954780 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/filter/defaults.yaml @@ -0,0 +1,12 @@ +threshold: + default: 0.00 + type: float + min: -99999.99 + max: 99999.99 + precision: 2 + title: Threshold value to filter models. + short: Threshold value to filter models based on their score. + long: Threshold value to filter models based on their score. + Models having higher score than the threshold value will be filtered out. + group: analysis + explevel: easy \ No newline at end of file diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._ilrmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._ilrmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/._ilrmsd.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ce1e64595645abd636667eed3d6eb783d5501349 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/__init__.py @@ -0,0 +1,371 @@ +""" +ilRMSD matrix module. + +This module calculates of the interface-ligand RMSD (ilRMSD) matrix between all +the models generated in the previous step. + +As all the pairwise ilRMSD calculations are independent, the module distributes +them over all the available cores in an optimal way. + +Once created, the ilRMSD matrix is saved in text form in the current +`ilrmsdmatrix` folder. The path to this file is then shared with the following +step of the workflow by means of the json file `rmsd_matrix.json`. + +IMPORTANT: the module assumes coherent numbering for all the receptor and ligand +chains, as no alignment is performed. The user must ensure that the numbering +is coherent. +""" + +import os +from pathlib import Path + +import numpy as np + +from haddock import RMSD_path, log +from haddock.core.defaults import FAST_RMSDMATRIX_EXEC, MODULE_DEFAULT_YAML +from haddock.libs.libalign import ( + check_chains, + check_common_atoms, + get_atoms, + load_coords, + rearrange_xyz_files, + ) +from haddock.libs.libontology import ModuleIO, RMSDFile +from haddock.libs.libparallel import get_index_list +from haddock.libs.libutil import parse_ncores +from haddock.modules import BaseHaddockModule, get_engine +from haddock.modules.analysis import get_analysis_exec_mode +from haddock.modules.analysis.ilrmsdmatrix.ilrmsd import Contact, ContactJob +from haddock.modules.analysis.rmsdmatrix import RMSDJob, rmsd_dispatcher +from haddock.modules.analysis.rmsdmatrix.rmsd import XYZWriter, XYZWriterJob + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) +EXEC_PATH = FAST_RMSDMATRIX_EXEC + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module for clustering with RMSD.""" + + name = RECIPE_PATH.name + + def __init__(self, order, path, *ignore, init_params=DEFAULT_CONFIG, **everything): + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if fast-rmsdmatrix is installed and available.""" + if not os.access(EXEC_PATH, mode=os.F_OK): + raise Exception( + f"Required {str(EXEC_PATH)} file does not exist.{os.linesep}" + "Old HADDOCK3 installation? Please follow the new installation instructions at https://github.com/haddocking/haddock3/blob/main/docs/INSTALL.md" # noqa : E501 + ) + + if not os.access(EXEC_PATH, mode=os.X_OK): + raise Exception(f"Required {str(EXEC_PATH)} file is not executable") + + return + + @staticmethod + def _rearrange_output(output_name, path, ncores): + """Combine different ilrmsd outputs in a single file.""" + output_fname = Path(path, output_name) + log.info(f"rearranging output files into {output_fname}") + # Combine files + with open(output_fname, "w") as out_file: + for core in range(ncores): + tmp_file = Path(path, "ilrmsd_" + str(core) + ".matrix") + with open(tmp_file) as infile: + out_file.write(infile.read()) + log.debug(f"File number {core} written") + tmp_file.unlink() + log.info("Completed reconstruction of rmsd files.") + log.info(f"{output_fname} created.") + + @staticmethod + def _rearrange_contact_output(output_name, path, ncores): + """Combine different contact outputs in a single file. + + Parameters + ---------- + output_name : str + Name of the output file. + path : str + Path to the output file. + ncores : int + Number of cores used in the calculation. + + Returns + ------- + res_resdic_npu : dict + Dictionary of the unique residues in the interfaces. + """ + output_fname = Path(path, output_name) + log.info(f"rearranging contact files into {output_fname}") + # Combine residues + res_resdic = {} + for core in range(ncores): + tmp_file = Path(path, "interface_contacts_" + str(core) + ".con") + for ln in tmp_file.read_text().split(os.linesep)[:-1]: + ch = ln.split()[0] + resids = [int(el) for el in ln.split()[1:]] + if ch not in res_resdic: + res_resdic[ch] = [resids] + else: + res_resdic[ch].append(resids) + tmp_file.unlink() + + # Unique residues + npu_resdic = {} + for ch in res_resdic.keys(): + resids = np.concatenate(res_resdic[ch]) + resids_npu = np.unique(resids) + npu_resdic[ch] = resids_npu + log.info(f"Overall interface residues: {npu_resdic}") + + # Write to file + with open(output_fname, "w") as out_file: + for chain in npu_resdic.keys(): + out_file.write(f"{chain} ") + out_file.write(" ".join([str(el) for el in npu_resdic[chain]])) + out_file.write(os.linesep) + + log.info("Completed reconstruction of contact files.") + log.info(f"{output_fname} created.") + return npu_resdic + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + if type(self.previous_io) == iter: + _e = "This module cannot come after one that produced an iterable." + self.finish_with_error(_e) + + # Get the models generated in previous step + models = self.previous_io.retrieve_models(individualize=True) + + # Parallelisation : optimal dispatching of models + nmodels = len(models) + ncores = parse_ncores(n=self.params["ncores"], njobs=nmodels) + + if nmodels > self.params["max_models"]: + # too many input models : ilRMSD matrix would be too big => Abort! + raise Exception( + f"Too many models ({nmodels} > {self.params['max_models']}) " + "for ilRMSD matrix calculation" + ) + + # find the existing chains + model_atoms = get_atoms(models[0]) + mod_coord_dic, _ = load_coords( + models[0], + model_atoms, + ) + obs_chains = np.unique([el[0] for el in mod_coord_dic.keys()]) + obs_chains = list(obs_chains) + log.info(f"Observed chains: {obs_chains}") + # assigning the chains to the receptor and ligand + r_chain, l_chains = check_chains( + obs_chains, self.params["receptor_chain"], self.params["ligand_chains"] + ) + log.info(f"Receptor chain: {r_chain}") + log.info(f"Ligand chains: {l_chains}") + self.params["receptor_chain"] = r_chain + self.params["ligand_chains"] = l_chains + + # Find the common residues making contacts for the receptor and ligand. + index_list = get_index_list(nmodels, ncores) + # contact jobs + contact_jobs = [] + for core in range(ncores): + output_name = "interface_contacts_" + str(core) + ".con" + contact_obj = Contact( + model_list=models[index_list[core] : index_list[core + 1]], + output_name=output_name, + core=core, + path=Path("."), + contact_distance_cutoff=self.params["contact_distance_cutoff"], + params=self.params, + ) + # running now the ContactJob + job_f = Path(output_name) + # init RMSDJob + job = ContactJob( + job_f, + self.params, + contact_obj, + ) + contact_jobs.append(job) + + exec_mode = get_analysis_exec_mode(self.params["mode"]) + Engine = get_engine(exec_mode, self.params) + contact_engine = Engine(contact_jobs) + contact_engine.run() + + # check if all the jobs have been completed + contact_file_l = [] + not_found = [] + for job in contact_jobs: + if not job.output.exists(): + not_found.append(job.output.name) + wrn = f"Contacts were not calculated for {job.output.name}" + log.warning(wrn) + else: + contact_file_l.append(str(job.output)) + + if not_found: + # Not all contacts were calculated, cannot proceed + self.finish_with_error( + "Several contact files were not generated:" f" {not_found}" + ) + + # Post-processing : single file + output_name = "receptor_contacts.con" + res_resdic = self._rearrange_contact_output( + output_name, path=contact_obj.path, ncores=ncores + ) + + # if the receptor chain in res_resdic is empty, then the receptor has made no contacts and + # the ilrmsd matrix cannot be calculated. This probably means that single chains structures + # reached this step or that something went (very) wrong in the docking process. + if res_resdic[r_chain].size == 0: + _msg = f"No contacts found for receptor chain {r_chain}. Impossible to calculate ilRMSD matrix." + _msg += " Please check your input and make sure that there are at least two chains in contact." + self.finish_with_error(_msg) + + rec_traj_filename = Path("traj_rec.xyz") + lig_traj_filename = Path("traj_lig.xyz") + + res_resdic_rec = {k: res_resdic[k] for k in res_resdic if k[0] == r_chain} + # ligand_chains is a list of chains + res_resdic_lig = {k: res_resdic[k] for k in l_chains} + + log.info( + f"Check common atoms for receptor (chain {list(res_resdic_rec.keys())})" + ) + n_atoms_rec, common_keys_rec = check_common_atoms( + models, + res_resdic_rec, + self.params["allatoms"], + self.params["atom_similarity"], + ) + + log.info( + f"Check common atoms for ligand (chains {list(res_resdic_lig.keys())})" + ) + n_atoms_lig, common_keys_lig = check_common_atoms( + models, + res_resdic_lig, + self.params["allatoms"], + self.params["atom_similarity"], + ) + + xyzwriter_jobs: list[XYZWriterJob] = [] + for core in range(ncores): + output_name_rec = Path("traj_rec_" + str(core) + ".xyz") + # init XYZWriter + xyzwriter_obj_rec = XYZWriter( + model_list=models[index_list[core] : index_list[core + 1]], + output_name=output_name_rec, + core=core, + n_atoms=n_atoms_rec, + common_keys=common_keys_rec, + filter_resdic=res_resdic_rec, + allatoms=self.params["allatoms"], + ) + # job_rec + job_rec = XYZWriterJob( + xyzwriter_obj_rec, + ) + + xyzwriter_jobs.append(job_rec) + + output_name_lig = Path("traj_lig_" + str(core) + ".xyz") + # init XYZWriter + xyzwriter_obj_lig = XYZWriter( + model_list=models[index_list[core] : index_list[core + 1]], + output_name=output_name_lig, + core=core, + n_atoms=n_atoms_lig, + common_keys=common_keys_lig, + filter_resdic=res_resdic_lig, + allatoms=self.params["allatoms"], + ) + # job_lig + job_lig = XYZWriterJob( + xyzwriter_obj_lig, + ) + xyzwriter_jobs.append(job_lig) + + # run jobs + engine = Engine(xyzwriter_jobs) + engine.run() + + rearrange_xyz_files(rec_traj_filename, path=Path("."), ncores=ncores) + rearrange_xyz_files(lig_traj_filename, path=Path("."), ncores=ncores) + + # Parallelisation : optimal dispatching of models + tot_npairs = nmodels * (nmodels - 1) // 2 + ncores = parse_ncores(n=self.params["ncores"], njobs=tot_npairs) + log.info(f"total number of pairs {tot_npairs}") + npairs, ref_structs, mod_structs = rmsd_dispatcher(nmodels, tot_npairs, ncores) + + # Calculate the rmsd for each set of models + ilrmsd_jobs: list[RMSDJob] = [] + self.log(f"running RmsdFast Jobs with {ncores} cores") + for core in range(ncores): + output_name = f"ilrmsd_{core:d}.out" + job_f = Path(output_name) + # init RMSDJob + job = RMSDJob( + rec_traj_filename, + job_f, + EXEC_PATH, + core, + npairs[core], + ref_structs[core], + mod_structs[core], + len(models), + n_atoms_rec, + lig_traj_filename, + n_atoms_lig, + ) + ilrmsd_jobs.append(job) + + ilrmsd_engine = Engine(ilrmsd_jobs) + ilrmsd_engine.run() + + ilrmsd_file_l = [] + not_found = [] + for j in ilrmsd_jobs: + if not j.output.exists(): + # NOTE: If there is no output, most likely the RMSD calculation + # timed out + not_found.append(j.output.name) + wrn = f"ilRMSD results were not calculated for {j.output.name}" + log.warning(wrn) + else: + ilrmsd_file_l.append(str(j.output)) + + if not_found: + # Not all distances were calculated, cannot create the full matrix + self.finish_with_error("Several files were not generated:" f" {not_found}") + + # Post-processing : single file + output_name = "ilrmsd.matrix" + self._rearrange_output(output_name, path=Path("."), ncores=ncores) + # Delete the trajectory files + if rec_traj_filename.exists(): + os.unlink(rec_traj_filename) + if lig_traj_filename.exists(): + os.unlink(lig_traj_filename) + + # Sending models to the next step of the workflow + self.output_models = models + self.export_io_models() + # Sending matrix path to the next step of the workflow + matrix_io = ModuleIO() + ilrmsd_matrix_file = RMSDFile(output_name, npairs=tot_npairs) + matrix_io.add(ilrmsd_matrix_file) + matrix_io.save(filename="rmsd_matrix.json") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ac5113d2f4e25a27f1c30692b1f8598d01457e65 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/defaults.yaml @@ -0,0 +1,71 @@ +receptor_chain: + default: A + type: string + minchars: 1 + maxchars: 1 + title: Receptor ChainID + short: Receptor ChainID to be considered for the RMSD calculations. + long: Receptor ChainID to be considered for the RMSD calculations. This determines which chain will be + treated as the receptor for the L-RMSD and for I-L-RMSD. + group: analysis + explevel: easy + +ligand_chains: + default: [] + type: list + minitems: 0 + maxitems: 100 + title: Ligand ChainIDs + short: Ligand ChainIDs to be considered for the IL-RMSD calculations. + long: Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be + treated as the ligand for the IL-RMSD. By default, all chains are considered with the exception of the receptor chain. + group: analysis + explevel: easy + +max_models: + default: 10000 + type: integer + min: 1 + max: 20000 + title: Maximum number of models + short: Maximum number of models to be considered when calculating the matrix. + long: Maximum number of models to be considered when calculating the matrix. If the number of models in the input file is larger than + this number, the execution will be aborted. + group: analysis + explevel: guru + +atom_similarity: + default: 90.0 + type: float + min: 10.0 + max: 100.0 + precision: 3 + title: Required atom similarity + short: Required similarity (in %) between the number of atoms in the input models. + long: Required similarity (in %) between the number of atoms in the input models. If the similarity is higher than this value, the RMSD calculation is performed on the common atoms. Otherwise, the calculation is stopped. The lower the value the looser the checks. + group: analysis + explevel: easy + +allatoms: + default: false + type: boolean + title: Atoms to be considered during the analysis. + short: Atoms to be considered during the analysis. + long: Atoms to be considered during the analysis. If false (default), only + backbone atoms will be considered, otherwise all the heavy-atoms. + group: analysis + explevel: easy + +contact_distance_cutoff: + default: 5.0 + type: float + min: 0.1 + max: 30.0 + precision: 3 + title: Distance cutoff defining a contact. + short: Cutoff distance (in Angstrom) defining a contact. + long: Distance (in Angstrom) cutoff defining a contact. Any atoms within this + cutoff range will be used to define the interface. Standard values are + usually 3.9 A or 5.0 A. + group: analysis + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..62002a6e084111d6c04d1f274f5ff2c4165a9d98 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.py @@ -0,0 +1,110 @@ +"""ilRMSD calculations.""" +import os +from pathlib import Path + +import numpy as np + +from haddock import log +from haddock.core.typing import NDFloat, Any +from haddock.libs.libalign import ( + get_atoms, + ) +from haddock.libs.libontology import PDBFile +from haddock.modules.analysis.caprieval.capri import load_contacts + + +class ContactJob: + """A Job dedicated to the fast retrieval of receptor contacts.""" + + def __init__( + self, + output, + params, + contact_obj): + + log.info(f"core {contact_obj.core}, initialising Contact...") + self.params = params + self.output = output + self.contact_obj = contact_obj + log.info(f"core {contact_obj.core}, Contact initialised") + + def run(self): + """Run this ContactJob.""" + log.info(f"core {self.contact_obj.core}, running Contact...") + self.contact_obj.run() + self.contact_obj.output() + return + + +class Contact: + """Contact class.""" + + def __init__( + self, + model_list: list[PDBFile], + output_name: str, + core: int, + path: Path, + contact_distance_cutoff: float = 5.0, + **params: dict[str, Any], + ): + """Initialise Contact class.""" + self.model_list = model_list + self.output_name = output_name + self.core = core + self.path = path + self.contact_distance_cutoff = contact_distance_cutoff + self.atoms = {} + self.receptor_chain = params["params"]["receptor_chain"] + self.ligand_chains = params["params"]["ligand_chains"] + self.unique_rec_res: NDFloat = [] + self.unique_lig_res: NDFloat = [] + for m in model_list: + self.atoms.update(get_atoms(m)) + + def run(self): + """Run contact calculations.""" + nmodels = len(self.model_list) + # create empty set of receptor interface residues + receptor_interface_residues = [] + ligand_interface_residues = [] + for n in range(nmodels): + contacts = load_contacts( + self.model_list[n], + cutoff=self.contact_distance_cutoff, + ) + rec_resids = [ + con[1] if con[0] == self.receptor_chain + else con[3] for con in contacts + ] + lig_resids = [ + con[1] if con[0] in self.ligand_chains + else con[3] for con in contacts + ] + if rec_resids != []: + receptor_interface_residues.append(np.unique(rec_resids)) + if lig_resids != []: + ligand_interface_residues.append(np.unique(lig_resids)) + # concatenate all the receptor residues + if receptor_interface_residues != []: + rec_np_arr = np.concatenate(receptor_interface_residues) + self.unique_rec_res = np.unique(rec_np_arr) + # now the ligand residues + if ligand_interface_residues != []: + lig_np_arr = np.concatenate(ligand_interface_residues) + self.unique_lig_res = np.unique(lig_np_arr) + + def output(self): + """Write down unique contacts to file.""" + output_fname = Path(self.path, self.output_name) + with open(output_fname, "w") as out_fh: + # first the receptor + out_fh.write(f"{self.receptor_chain} ") + out_fh.write(" ".join([str(res) for res in self.unique_rec_res])) + out_fh.write(f"{os.linesep}") + # now the ligand + for chain in self.ligand_chains: + out_fh.write(f"{chain} ") + res_str = " ".join([str(res) for res in self.unique_lig_res]) + out_fh.write(res_str) + out_fh.write(f"{os.linesep}") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._rmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._rmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/._rmsd.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..07e4047ac2b3992816dd1c85b46d6a5052dd1dee --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/__init__.py @@ -0,0 +1,228 @@ +""" +RMSD matrix module. + +This module calculates of the RMSD matrix between all the models +generated in the previous step. + +As all the pairwise RMSD calculations are independent, the module distributes +them over all the available cores in an optimal way. + +Once created, the RMSD matrix is saved in text form in the current `rmsdmatrix` +folder. The path to this file is then shared with the following step of the +workflow by means of the json file `rmsd_matrix.json`. + +The module accepts two parameters in input, namely: + +* `max_models` (default = 10000) +* `resdic_` : an expandable parameter to specify which residues must be + considered for the alignment and the RMSD calculation. If there are + two proteins denoted by chain IDs A and B, then the user can operate + such selection in the following way inside the configuration file + +>>> resdic_A = [1,2,3,4] +>>> resdic_B = [2,3,4] + +thus telling the module to consider residues from 1 to 4 of chain A and from 2 +to 4 of chain B for the alignment and RMSD calculation. +""" + +import contextlib +import os +from pathlib import Path + +from haddock import RMSD_path, log +from haddock.core.defaults import FAST_RMSDMATRIX_EXEC, MODULE_DEFAULT_YAML +from haddock.core.typing import Any, AtomsDict, FilePath +from haddock.libs.libalign import check_common_atoms, rearrange_xyz_files +from haddock.libs.libontology import ModuleIO, RMSDFile +from haddock.libs.libparallel import get_index_list +from haddock.libs.libutil import parse_ncores +from haddock.modules import BaseHaddockModule, get_engine +from haddock.modules.analysis import ( + confirm_resdic_chainid_length, + get_analysis_exec_mode, + ) +from haddock.modules.analysis.rmsdmatrix.rmsd import ( + RMSDJob, + XYZWriter, + XYZWriterJob, + rmsd_dispatcher, + ) + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) +EXEC_PATH = FAST_RMSDMATRIX_EXEC + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module for clustering with RMSD.""" + + name = RECIPE_PATH.name + + def __init__( + self, order: int, path: Path, initial_params: FilePath = DEFAULT_CONFIG + ) -> None: + super().__init__(order, path, initial_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if fast-rmsdmatrix is installed and available.""" + + if not os.access(EXEC_PATH, mode=os.F_OK): + raise Exception( + f"Required {str(EXEC_PATH)} file does not exist.{os.linesep}" + "Old HADDOCK3 installation? Please follow the new installation instructions at https://github.com/haddocking/haddock3/blob/main/docs/INSTALL.md" + ) + + if not os.access(EXEC_PATH, mode=os.X_OK): + raise Exception(f"Required {str(EXEC_PATH)} file is not executable") + + return + + def _rearrange_output( + self, output_name: FilePath, path: FilePath, ncores: int + ) -> None: + """Combine different rmsd outputs in a single file.""" + output_fname = Path(path, output_name) + self.log(f"rearranging output files into {output_fname}") + # Combine files + with open(output_fname, "w") as out_file: + for core in range(ncores): + tmp_file = Path(path, "rmsd_" + str(core) + ".matrix") + with open(tmp_file) as infile: + out_file.write(infile.read()) + log.debug(f"File number {core} written") + tmp_file.unlink() + log.info("Completed reconstruction of rmsd files.") + log.info(f"{output_fname} created.") + + def update_params(self, *args: Any, **kwargs: Any) -> None: + """Update parameters.""" + super().update_params(*args, **kwargs) + with contextlib.suppress(KeyError): + self.params.pop("resdic_") + + confirm_resdic_chainid_length(self._params) + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + if type(self.previous_io) == iter: + _e = "This module cannot come after one that produced an iterable." + self.finish_with_error(_e) + + # Get the models generated in previous step + models = self.previous_io.retrieve_models(individualize=True) + + nmodels = len(models) + if nmodels > self.params["max_models"]: + # too many input models : RMSD matrix would be too big => Abort! + raise Exception("Too many models for RMSD matrix calculation") + + # index_list for the jobs with linear scaling + ncores = parse_ncores(n=self.params["ncores"], njobs=len(models)) + index_list = get_index_list(nmodels, ncores) + + traj_filename = Path("traj.xyz") + + filter_resdic = { + key[-1]: value + for key, value in self.params.items() + if key.startswith("resdic") + } + + # check common atoms + n_atoms, common_keys = check_common_atoms( + models, + filter_resdic, + self.params["allatoms"], + self.params["atom_similarity"], + ) + + xyzwriter_jobs: list[XYZWriterJob] = [] + for core in range(ncores): + output_name = Path("traj_" + str(core) + ".xyz") + # init RMSDJobFast + xyzwriter_obj = XYZWriter( + model_list=models[index_list[core] : index_list[core + 1]], + output_name=output_name, + core=core, + n_atoms=n_atoms, + common_keys=common_keys, + filter_resdic=filter_resdic, + allatoms=self.params["allatoms"], + ) + # job_f = output_name + job = XYZWriterJob( + xyzwriter_obj, + ) + xyzwriter_jobs.append(job) + + # run jobs + exec_mode = get_analysis_exec_mode(self.params["mode"]) + Engine = get_engine(exec_mode, self.params) + engine = Engine(xyzwriter_jobs) + engine.run() + + rearrange_xyz_files(traj_filename, path=Path("."), ncores=ncores) + + # Parallelisation : optimal dispatching of models + tot_npairs = nmodels * (nmodels - 1) // 2 + log.info(f"total number of pairs {tot_npairs}") + ncores = parse_ncores(n=self.params["ncores"], njobs=tot_npairs) + npairs, ref_structs, mod_structs = rmsd_dispatcher(nmodels, tot_npairs, ncores) + + # Calculate the rmsd for each set of models + rmsd_jobs: list[RMSDJob] = [] + self.log(f"running RmsdFast Jobs with {ncores} cores") + for core in range(ncores): + output_name = Path("rmsd_" + str(core) + ".out") + # init RMSDJobFast + job = RMSDJob( + traj_filename, + output_name, + EXEC_PATH, + core, + npairs[core], + ref_structs[core], + mod_structs[core], + len(models), + n_atoms, + ) + rmsd_jobs.append(job) + + engine = Engine(rmsd_jobs) + engine.run() + + rmsd_file_l: list[str] = [] + not_found: list[str] = [] + for job in rmsd_jobs: + if not job.output.exists(): + # NOTE: If there is no output, most likely the RMSD calculation + # timed out + not_found.append(job.output.name) + wrn = f"Rmsd results were not calculated for {job.output.name}" + log.warning(wrn) + else: + rmsd_file_l.append(str(job.output)) + + if not_found: + # Not all distances were calculated, cannot create the full matrix + self.finish_with_error("Several files were not generated:" f" {not_found}") + + # Post-processing : single file + final_output_name = "rmsd.matrix" + self._rearrange_output(final_output_name, path=Path("."), ncores=ncores) + # Delete the trajectory file + if traj_filename.exists(): + os.unlink(traj_filename) + + # Sending models to the next step of the workflow + self.output_models = models + self.export_io_models() + # Sending matrix path to the next step of the workflow + matrix_io = ModuleIO() + rmsd_matrix_file = RMSDFile(final_output_name, npairs=tot_npairs) + matrix_io.add(rmsd_matrix_file) + matrix_io.save(filename="rmsd_matrix.json") diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2d4d43231060b9e0c2dc3b9bdea4fa323f476776 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/defaults.yaml @@ -0,0 +1,45 @@ +max_models: + default: 10000 + type: integer + min: 1 + max: 20000 + title: Maximum number of models to calculate RMSD matrix + short: If the number of models exceeds max_models the execution is blocked + long: If the number of models exceeds the few thousands, the calculation of + the RMSD matrix is computationally demanding, especially in terms of CPU + and disk space. + group: analysis + explevel: easy +resdic_: + default: [] + type: list + minitems: 0 + maxitems: 100 + title: List of residues + short: The residue numbers that should be used in the alignment and in the + RMSD calculation. + long: resdic_* is an expandable parameter. You can provide resdic_A, + resdic_B, resdic_C, etc, where the last capital letter is the chain + identifier. + group: analysis + explevel: easy +atom_similarity: + default: 90.0 + type: float + min: 10.0 + max: 100.0 + precision: 3 + title: Required atom similarity + short: Required similarity (in %) between the number of atoms in the input models. + long: Required similarity (in %) between the number of atoms in the input models. If the similarity is higher than this value, the RMSD calculation is performed on the common atoms. Otherwise, the calculation is stopped. The lower the value the looser the checks. + group: analysis + explevel: easy +allatoms: + default: false + type: boolean + title: Atoms to be considered during the analysis. + short: Atoms to be considered during the analysis. + long: Atoms to be considered during the analysis. If false (default), only + backbone atoms will be considered, otherwise all the heavy-atoms. + group: analysis + explevel: easy \ No newline at end of file diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/rmsd.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/rmsd.py new file mode 100644 index 0000000000000000000000000000000000000000..45adf7d772c188e2545923c97d02d3a8bef9dece --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/rmsdmatrix/rmsd.py @@ -0,0 +1,124 @@ +"""RMSD calculations.""" +import os +import numpy as np +from pathlib import Path + +from haddock import log +from haddock.core.typing import AtomsDict +from haddock.libs.libalign import get_atoms, load_coords +from haddock.libs.libsubprocess import BaseJob + + +class RMSDJob(BaseJob): + """ + Instantiate a subprocess job with inverted args and input. + + Runs with the following scheme, INPUT comes first: + + $ cmd INPUT ARGS + """ + + def make_cmd(self) -> None: + """Execute job in subprocess.""" + self.cmd = " ".join([ + os.fspath(self.executable), + os.fspath(self.input), + ' '.join(map(str, self.args)), # empty string if no args + ]) + return + + +def get_pair(nmodels: int, idx: int) -> tuple[int, int]: + """Get the pair of structures given the 1D matrix index.""" + if (nmodels < 0 or idx < 0): + err = "get_pair cannot accept negative numbers" + err += f"Input is {nmodels} , {idx}" + raise ValueError(err) + # solve the second degree equation + b = 1 - (2 * nmodels) + i = (-b - np.sqrt(b ** 2 - 8 * idx)) // 2 + j = idx + i * (b + i + 2) // 2 + 1 + return (int(i), int(j)) + + +def rmsd_dispatcher(nmodels: int, tot_npairs: int, + ncores: int) -> tuple[list[int], list[int], list[int]]: + """Optimal dispatching of rmsd jobs.""" + base_pairs = tot_npairs // ncores + modulo = tot_npairs % ncores + npairs: list[int] = [] + for core in range(ncores): + if core < modulo: + npairs.append(base_pairs + 1) + else: + npairs.append(base_pairs) + # each core must know how many pairs and where to start + index = 0 + start_structures = [0] + end_structures = [1] + for el in npairs[:-1]: + index += el + pair = get_pair(nmodels, index) + start_structures.append(pair[0]) + end_structures.append(pair[1]) + return npairs, start_structures, end_structures + + +class XYZWriterJob: + """A Job dedicated to the parallel writing of xyz files.""" + + def __init__( + self, + xyzwriter_obj): + """Initialise XYZWriterJob.""" + self.xyzwriter_obj = xyzwriter_obj + self.output = xyzwriter_obj.output_name + + def run(self): + """Run this XYZWriterJob.""" + log.info(f"core {self.xyzwriter_obj.core}, running XYZWriter...") + self.xyzwriter_obj.run() + return + + +class XYZWriter: + """XYZWriter class.""" + + def __init__( + self, + model_list, + output_name, + core, + n_atoms, + common_keys, + filter_resdic, + allatoms=False, + ): + """Initialise Contact class.""" + self.model_list = model_list + self.output_name = output_name + self.core = core + self.n_atoms = n_atoms + self.common_keys = common_keys + self.filter_resdic = filter_resdic + self.allatoms = allatoms + + def run(self) -> None: + """write xyz coordinates.""" + with open(self.output_name, "w") as traj_xyz: + for mod in self.model_list: + atoms: AtomsDict = get_atoms(mod, self.allatoms) + + ref_coord_dic, _ = load_coords( + mod, atoms, self.filter_resdic + ) + # now we filter the dictionary with the common keys + common_coord_dic = {k: v for k, v in ref_coord_dic.items() if k in self.common_keys} + # write header + traj_xyz.write(f"{self.n_atoms}{os.linesep}{os.linesep}") + # write the coordinates + for k in self.common_keys: + v = common_coord_dic[k] + at_string = ''.join([str(el) for el in k]) + traj_xyz.write(f"{at_string} {v[0]} {v[1]} {v[2]}{os.linesep}") + return diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..43393e95b382973f95e0f15e14f4072aee72fbda --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/__init__.py @@ -0,0 +1,65 @@ +"""Select a number of models. + +This module selects a number of models from the input models. By default, the +selection is based on the HADDOCK score of the models. + +The number of models to be selected is defined by the parameter `select`. +In the standard HADDOCK protocol, this number is 200, which can be increased +if more models should be refined. +""" +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import Any, FilePath +from haddock.libs.libontology import Format, PDBFile +from haddock.modules import BaseHaddockModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """HADDOCK3 module to select top cluster/model.""" + + name = RECIPE_PATH.name + + def __init__(self, + order: int, + path: Path, + *ignore: Any, + init_params: FilePath = DEFAULT_CONFIG, + **everything: Any) -> None: + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if module is installed.""" + return + + def _run(self) -> None: + """Execute module.""" + # Get the models generated in previous step + if type(self.previous_io) == iter: + self.finish_with_error('[seletop] This module cannot come after one' + ' that produced an iterable') + + models_to_select: list[PDBFile] = [ + p + for p in self.previous_io.output + if p.file_type == Format.PDB + ] + + # sort the models based on their score + models_to_select.sort(key=lambda x: x.score) + + if len(models_to_select) < self.params['select']: + self.log(( + 'Number of models to be selected is larger' + ' than generated models, selecting ALL'), + level='warning', + ) + + # select the models based on the parameter + self.output_models = models_to_select[:self.params['select']] + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a96700476b64c9408362d77bf1fc446e13a0a3c0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletop/defaults.yaml @@ -0,0 +1,10 @@ +select: + default: 200 + type: integer + min: 1 + max: 50000 + title: Number of best-ranked models to select + short: Number of best-ranked models to select for further steps of the workflow + long: Number of best-ranked models to select for further steps of the workflow. 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The +selection is based on the score of the models within the clusters. + +In the standard HADDOCK analysis, the top 4 models of the top 10 clusters +are shown. In case seletopclusts is run after a sampling module, we can +keep a few models from all the clusters to have more diversity at the +refinement stage(s). +""" + +from pathlib import Path + +from haddock import log +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import Any, FilePath +from haddock.modules import BaseHaddockModule +from haddock.modules.analysis.seletopclusts.seletopclusts import ( + select_top_clusts_models, + write_selected_models, + ) + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """Haddock Module for 'seletopclusts'.""" + + name = RECIPE_PATH.name + + def __init__(self, + order: int, + path: Path, + *ignore: Any, + init_params: FilePath = DEFAULT_CONFIG, + **everything: Any) -> None: + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if module is installed.""" + return + + def _run(self) -> None: + """Execute the module's protocol.""" + # Check parameters validity + if self.params["top_models"] <= 0: + _msg = "top_models must be either > 0 or nan." + self.finish_with_error(_msg) + + if not isinstance(self.params["top_clusters"], int): + _msg = "top_clusters must be an integer." + self.finish_with_error(_msg) + + # Retrieve list of previous models + models_to_select = self.previous_io.retrieve_models() + + # Check if cluster info is accessible + if any([mdl.clt_rank is None for mdl in models_to_select]): + _msg = ( + "Impossible to obtain cluster information. Please consider " + "running a clustering method prior to this module." + ) + self.finish_with_error(_msg) + + # Make model selection + selected_models, _notes = select_top_clusts_models( + self.params["sortby"], + models_to_select, + self.params["top_clusters"], + self.params["top_models"], + ) + # Log notes + for note in _notes: + log.info(note) + + # dump the models to disk and change their attributes + renamed_models = write_selected_models( + "seletopclusts.txt", + selected_models, + self.path, + ) + + # Make these new models the output of this module + self.output_models = renamed_models + # Export outputs + self.export_io_models() diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6f6ece8b70ddb824c76aacf92edbe54cdfcea6c9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/defaults.yaml @@ -0,0 +1,33 @@ +top_clusters: + type: integer + default: 1000 + min : 1 + max : 99999 + title: Number of clusters to consider + short: Number of clusters to consider (ranked by score) + long: Number of clusters to consider (ranked by score) + group: analysis + explevel: easy +top_models: + default: 10 + type: integer + min: 1 + max: 99999 + title: Number of best-ranked models to select per cluster + short: Number of best-ranked models to select per cluster. By default, 10 models are selected. + long: Number of best-ranked models to select per cluster. By default, 10 models are selected. If one expects to find many clusters (e.g., in the case of vague restraints), this number can be reduced to speed up the protocol. Instead, if few clusters are expected (very specific and localized restraints) this number can be increased. + group: analysis + explevel: easy +sortby: + default: score + type: string + minchars: 2 + maxchars: 15 + choice: + - score + - size + title: Method used to define `best cluster`. + short: Best cluster can be defined based either on cluster models scores, or on cluster size. By default, 'score' is selected. + long: if the selection is done by 'score' the average score of the top (4) models of each cluster is used to define the cluster rank. When clustering by 'size', a bigger cluster size corresponds to a higher rank. By default, 'score' is selected. + group: analysis + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/seletopclusts.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/seletopclusts.py new file mode 100644 index 0000000000000000000000000000000000000000..ffde8259e1c65c9ea91860450588704c8921e1f0 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/analysis/seletopclusts/seletopclusts.py @@ -0,0 +1,236 @@ +"""Set of functions related to the selection of top clusters.""" + +import os +import math +from pathlib import Path +from haddock.core.typing import Union +from haddock.libs.libontology import PDBFile + + +def select_top_clusts_models( + sortby: str, + models_to_select: list[PDBFile], + top_clusters: int, + top_models: Union[int, float], + ) -> tuple[list[PDBFile], list[str]]: + """Select best clusters based on structures scores. + + Parameters + ---------- + sortby : str + How to order clusters: by `score` or by `size`. + models_to_select : list[PDBFile] + List of input models on which selection must be performed. + top_clusters : int + Number of best clusters to take into account. + top_models : int + Number of best models in each cluster to take into account. + + Returns + ------- + models_to_export : list[PDBFile] + List of PDBfiles to export. + notes : list[str] + List of notes to be printed. + """ + notes: list[str] = [] + by_clusters = map_clusters_models(models_to_select) + + # Get cluster order + if sortby == "size": + cluster_rankings = size_clust_order(by_clusters) + else: + cluster_rankings = rank_clust_order(by_clusters) + + # Check if number of clusters >= set of rank + if top_clusters >= len(cluster_rankings): + # select all clusters + cluster_rankins_str = ",".join(map(str, cluster_rankings)) + notes.append(f"Selecting all clusters: {cluster_rankins_str}") + else: + # select top_clusters clusters + cluster_rankings = cluster_rankings[:top_clusters] + cluster_rankins_str = ",".join(map(str, cluster_rankings)) + notes.append( + f"Selecting top {top_clusters} clusters: " + f"{cluster_rankins_str}" + ) + + # Initiate set of selected models to export + models_to_export: list[PDBFile] = [] + # Loop over cluster ranks + for clt_rank in cluster_rankings: + # Sort models by model rank + clt_mdls, note = sort_models(by_clusters[clt_rank]) + if note: + notes.append(note) + + # Set new ranks to models + for mdl_rank, pdb in enumerate(clt_mdls, start=1): + pdb.clt_rank = clt_rank + pdb.clt_model_rank = mdl_rank + # In case number of models is not set (nan.) + if math.isnan(top_models): + for pdb in clt_mdls: + models_to_export.append(pdb) + # In case number of models is a integer + else: + # Loop over first `top_models` models + for pdb in clt_mdls[:top_models]: + models_to_export.append(pdb) + return models_to_export, notes + + +def sort_models( + models: list[PDBFile] + ) -> tuple[list[PDBFile], Union[None, str]]: + """Sort models based on their rank in cluster. + + Parameters + ---------- + models : list[PDBFile] + List of input models on which ordering must be performed. + + Returns + ------- + sorted_mdls : list[PDBFile] + List of sorted models. + """ + note: Union[None, str] = None + try: + sorted_mdls = sorted( + models, + key=lambda k: k.clt_model_rank, + ) + except TypeError: + note = 'model rank unavailable, falling back to input order' + sorted_mdls = models + return sorted_mdls, note + + +def rank_clust_order( + by_clusters: dict[int, list[PDBFile]], + ) -> list[int]: + """Select best clusters based on structures scores. + + Parameters + ---------- + models_to_select : list[PDBFile] + List of input models on which selection must be performed. + top_clusters : int + Number of best clusters to take into account. + top_models : int + Number of best models in each cluster to take into account. + + Returns + ------- + models_to_export : list[PDBFile] + List of PDBfiles to export. + notes : list[str] + List of notes to be printed. + """ + # Generate set of all cluster rank available + cluster_rankings = sorted(by_clusters) + return cluster_rankings + + +def size_clust_order( + by_clusters: dict[int, list[PDBFile]], + ) -> list[int]: + """Select best clusters based on structures scores. + + Parameters + ---------- + models_to_select : list[PDBFile] + List of input models on which selection must be performed. + top_clusters : int + Number of best clusters to take into account. + top_models : int + Number of best models in each cluster to take into account. + + Returns + ------- + models_to_export : list[PDBFile] + List of PDBfiles to export. + notes : list[str] + List of notes to be printed. + """ + # Generate set of all cluster rank available + cluster_rankings = sorted( + by_clusters, + key=lambda k: len(by_clusters[k]), + reverse=True, + ) + return cluster_rankings + + +def map_clusters_models(models: list[PDBFile]) -> dict[int, list[PDBFile]]: + """Group models by clusters. + + Parameters + ---------- + models : list[PDBFile] + List of PDBfiles models to be grouped. + + Returns + ------- + by_clusters : dict[int, list[PDBFile]] + _description_ + """ + # Preset dictionary keys + by_clusters: dict[int, list[PDBFile]] = { + clrank: [] + for clrank in list(set([pdb.clt_rank for pdb in models])) + } + # Loop over models + for pdb in models: + # Add model to cluster + by_clusters[pdb.clt_rank].append(pdb) + return by_clusters + + +def write_selected_models( + output_path: Union[str, Path], + models: list[PDBFile], + module_path: Union[str, Path], + ) -> list[PDBFile]: + """Dump selected models and new names in a file. + + Parameters + ---------- + output_path : Union[str, Path] + Name of tne file to create. + models : list[PDBFile] + List of PDBfiles of selected models. + module_path : Union[str, Path] + Path of the module. + + Returns + ------- + models : list[PDBFile] + Updated list of selected models. + """ + # dump the models to disk and change their attributes + with open(output_path, 'w') as fh: + fh.write("rel_path\tori_name\tcluster_name\tmd5" + os.linesep) + for model in models: + name = ( + f"cluster_{model.clt_rank}_model" + f"_{model.clt_model_rank}.pdb" + ) + # writing name + fh.write( + f"{model.rel_path}\t" + f"{model.ori_name}\t" + f"{name}\t" + f"{model.md5}" + os.linesep + ) + # changing attributes + name_path = Path(name) + name_path.write_text(model.rel_path.read_text()) + model.ori_name = model.file_name + model.file_name = name + model.full_name = name + model.rel_path = Path('..', Path(module_path).name, name) + model.path = str(Path(".").resolve()) + return models diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/base_cns_module.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/base_cns_module.py new file mode 100644 index 0000000000000000000000000000000000000000..01af52d2fd39920bad72e483ccef3614a72d51d2 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/base_cns_module.py @@ -0,0 +1,170 @@ +"""Functionalities related to CNS modules.""" +import os +import shutil +import tarfile +from pathlib import Path + +from haddock import log +from haddock import toppar_path as global_toppar +from haddock.core.defaults import cns_exec as global_cns_exec +from haddock.core.typing import Any, FilePath, Optional, Union +from haddock.gear.expandable_parameters import populate_mol_parameters_in_module +from haddock.libs.libio import working_directory +from haddock.modules import BaseHaddockModule + + +class BaseCNSModule(BaseHaddockModule): + """ + Operation module for CNS. + + Contains additional functionalities excusive for CNS modules. + """ + + def __init__(self, order: int, path: Path, initial_params: FilePath, + cns_script: FilePath) -> None: + """ + Instantitate CNSModule. + + Parameters + ---------- + cns_script : str or pathlib.Path + Path to the main module's cns script. + """ + super().__init__(order, path, initial_params) + + self.cns_folder_path = Path(Path(cns_script).resolve().parent) + self.cns_protocol_path = Path(cns_script) + self.toppar_path = global_toppar + self.recipe_str = self.cns_protocol_path.read_text() + + def run(self, **params: Any) -> None: + """Execute the module.""" + log.info(f'Running [{self.name}] module') + + self.update_params(**params) + + # the `mol_*` parameters exist only for CNS jobs. + if self._num_of_input_molecules: + populate_mol_parameters_in_module( + self._params, + self._num_of_input_molecules, + self._original_params, + ) + + self.add_parent_to_paths() + self.envvars = self.default_envvars() + + if self.params['self_contained']: + self.make_self_contained() + + with working_directory(self.path): + self._run() + + log.info(f'Module [{self.name}] finished.') + + def default_envvars(self) -> dict[str, str]: + """Return default env vars updated to `envvars` (if given).""" + default_envvars = { + "MODULE": str(self.cns_folder_path), + "MODDIR": ".", + "TOPPAR": str(self.toppar_path), + } + + return default_envvars + + def save_envvars(self, filename: FilePath = "envvars") -> None: + """Save envvars needed for CNS to a file in the module's folder.""" + # there are so few variables, best to handle them by hand + lines = ( + "#!/bin/bash", + "# for debugging purposes source this file from within the ", + "# module folder for example, from within '00_topoaa'", + "export MODULE=cns", + "export MODDIR=.", + "export TOPPAR=../toppar", + ) + + fstr = os.linesep.join(lines) + Path(self.path, filename).write_text(fstr) + return + + def make_self_contained(self) -> None: + """Create folders to make run self-contained.""" + _ = Path(self.path, "cns") + shutil.copytree(self.cns_folder_path, _) + self.cns_folder_path = Path(".", "cns") + + self.cns_protocol_path = Path( + self.cns_folder_path, + self.cns_protocol_path.name, + ) + + if not Path(self.toppar_path.name).exists(): + shutil.copytree(self.toppar_path, self.toppar_path.name) + self.toppar_path = Path("..", self.toppar_path.name) + + self.envvars = self.default_envvars() + self.save_envvars() + + _cns_exec = self.params["cns_exec"] or global_cns_exec + new_cns = Path(".", Path(_cns_exec).name) + if not new_cns.exists(): + self.params["cns_exec"] = shutil.copyfile(_cns_exec, new_cns) + shutil.copystat(_cns_exec, new_cns) + self.params["cns_exec"] = Path("..", Path(_cns_exec).name) + + def get_ambig_fnames( + self, prev_ambig_fnames: list[Union[None, FilePath]] + ) -> Union[list[FilePath], None]: + """Get the correct ambiguous restraint names. + + Parameters + ---------- + prev_ambig_fnames : list + list of ambig_fname files encoded in previous models + + Returns + ------- + ambig_fnames : list or None + list of ambig_fname files to be used by the CNS module + """ + ambig_fname: Optional[Path] = self.params["ambig_fname"] + ambig_fnames: Union[list[FilePath], None] = None + if ambig_fname: + if ambig_fname.name.endswith("tgz"): + self.log(f"Searching for tbl files in {ambig_fname}") + basepath = ambig_fname.parent + # Open archive to retrieve members + with tarfile.open(ambig_fname, mode="r:gz") as targz: + # Get filenames + tbl_files = targz.getmembers() + # At that stage, they should be already extracted + # and we simply need to generate the full paths + ambig_fnames = [] + for tbl in tbl_files: + fname = tbl.name + # Filter non-".tbl" and hidden files + if fname.startswith("."): + continue + # Build path + tbl_fpath = Path(basepath, fname) + # Make sure it exists + if tbl_fpath.exists() and tbl_fpath.suffix == ".tbl": + ambig_fnames.append(tbl_fpath) + # abort execution if no files are found + if len(ambig_fnames) == 0: + raise Exception(f"No tbl files found in {ambig_fname} !") + self.log(f"Found {len(ambig_fnames)} tbl files") + # Sort them to make sure we get the same order every time + ambig_fnames.sort() + else: + if self.params["previous_ambig"]: + # check if there is restraint information in all models + if None in prev_ambig_fnames: + raise Exception( + "'previous_ambig' option selected but no available " + "restraint information in models" + ) + self.log("Using previously defined restraints") + ambig_fnames = prev_ambig_fnames.copy() + return ambig_fnames diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9571db2b07f619610476669767d277e707b27b16 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/defaults.yaml @@ -0,0 +1,154 @@ +cns_exec: + default: "" + type: file + title: "Path to the CNS executable" + short: If not provided, HADDOCK3 will use the cns path configured + during the installation. + long: CNS is a required component to run HADDOCK. Ideally it should have been + configured during installation. If not you can specify with the cns_exec parameter + its path. + group: "execution" + explevel: easy +ncores: + default: 4 + type: integer + min: 1 + max: 500 + title: Number of CPU cores + short: Number of CPU cores to use for the CNS calculations. + It is truncated to max available CPUs minus 1. + long: Number of CPU cores to use for the CNS calculations. + This will define the number of concurrent jobs being executed. + Note that is truncated to the total number of available CPUs minus 1. + group: "execution" + explevel: easy +max_cpus: + default: true + type: boolean + title: The max number of CPUs allowed. + short: By default the max number of CPUs allowed is the max available on the system. + long: + If you want to spare a minimum amount of resources for daily tasks, set max_cpus + to false; in that case the maximum number of CPUs allowed will be the total available + in the machine minus 1. This calculation is done automatically. + group: "execution" + explevel: expert +mode: + default: local + type: string + minchars: 0 + maxchars: 20 + choices: + - local + - batch + title: Mode of execution + short: Mode of execution of the jobs, either local or using a batch system. + long: Mode of execution of the jobs, either local or using a batch system. + Currently slurm and torque are supported. For the batch mode the queue command must be + specified in the queue parameter. + group: "execution" + explevel: easy +batch_type: + default: "slurm" + type: string + minchars: 0 + maxchars: 100 + choices: + - slurm + - torque + title: Batch system + short: Type of batch system running on your server + long: Type of batch system running on your server. Only slurm and torque are supported at this time + group: "execution" + explevel: "easy" +queue: + default: "" + type: string + minchars: 0 + maxchars: 100 + title: Queue name + short: Name of the batch queue to which jobs will be submitted + long: Name of the batch queue to which jobs will be submitted. If not defined the batch system default will be used. + group: "execution" + explevel: easy +queue_limit: + default: 100 + type: integer + min: 1 + max: 9999 + title: Number of jobs to submit to the batch system + short: Number of jobs to submit to the batch system + long: This parameter controls the number of jobs that will be submitted to the batch system. In combination with the concat parameter this allow to limit the load on the queueing system and also make sure jobs remain in the queue for some time (if concat > 1) to avoid high system loads on the batch system. + group: "execution" + explevel: easy +concat: + default: 1 + type: integer + min: 1 + max: 9999 + precision: 0 + title: Number of models to produce per job. + short: Multiple models can be calculated within one job + long: + This defines the number of models that will be generated within on job script. + This allows to concatenate the generation of models into one script. + In that way jobs might run longer in the batch system and reduce the load on the scheduler. + group: "execution" + explevel: easy +self_contained: + default: false + type: boolean + title: Create a self-contained run + short: This option will copy the CNS scripts and executable to the run folder. + long: + This option will copy the CNS scripts and executable to the run folder to ensure that all scripts are available within the run dir. + This can be useful for for example remote execution of a job or for debugging purpose to allow to edit the scripts without touching the + main installation. + group: "execution" + explevel: guru +clean: + default: true + type: boolean + title: Clean the module output files. + short: Clean the module if run succeeds by compressing or removing output files. + long: + When running haddock through the command-line, the 'clean' parameter will + instruct the workflow to clean the output files of the module if the whole + run succeeds. In this process, PDB and PSF files are compressed to gzip, + with the extension `.gz`. While files with extension `.seed`, `.inp`, and + `.out` files are archived, and the original files deleted. The time to + perform a cleaning operation depends on the number of files in the folders + and the size of the files. However, it should not represent a limit step in + the workflow. For example, a rigidbody sampling 10,000 structures takes + about 4 minutes in our servers. This operation uses as many cores as allowed + by the user in the 'ncores' parameter. SSD disks will perform faster by + definition. See also the 'haddock3-clean' and 'haddock3-unpack' command-line + clients. + group: "clean" + explevel: easy +offline: + default: false + type: boolean + title: Isolate haddock3 from internet. + short: Completely isolate the haddock3 run & results from internet. + long: For interactive plots, we are using the plotly library. It can be + embedded as a link to the plotly.js library and fetched from the web, + or directly copied on the html files AT THE COST OF ~3Mb per file. + Setting this parameter to `true` will add the javascript library in + generated files, therefore completely isolating haddock3 from any web call. + group: "execution" + explevel: easy +debug: + default: false + type: boolean + title: Write intermediate and stdout files. + short: Write intermediate and stdout files. + long: When set to true, this option will increase the amount of I/O + operations by writing intermediate input, output and error files on disk. + Turning it to false can be useful for example when running on a network + file system where I/O operations are slow. + group: "execution" + explevel: easy + incompatible: + false: + mode: batch diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/._exit b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/._exit new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/._exit differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..10d3d334736334f4676159de3e9a2fd2e4bb69ff --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/__init__.py @@ -0,0 +1,6 @@ +""" +HADDOCK3 extra modules. + +The extra modules are modules that do not belong to any of the standard +simulation categories but that help further configuring the workflow. +""" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/.___pycache__ differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/._defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/._defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/._defaults.yaml differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..1cb6993c8ebc6e274adf7e7bb6b0c06a03b70c2b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/__init__.py @@ -0,0 +1,68 @@ +""" +Exit module +=========== + +Stop the workflow when this module is reached. This allows users to execute +only a certain initial part of the workflow without having to comment/uncomment +the unwanted lines. + +Examples +-------- + +Consider the following config file example:: + + [topoaa] + (...) + + [rigidbody] + (...) + + [exit] # <- workflow will stop here + + [flexref] + (...) + +The workflow will stop at ``[exit]`` and ``[flexref]`` will not be performed. + +You can also use this option combined with ``--restart`` and ``--extend-run``. +See examples in ``examples/docking-protein-protein/*-exit-test.cfg`` files. +""" +import shutil +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.exceptions import HaddockTermination +from haddock.core.typing import Any, FilePath +from haddock.modules import BaseHaddockModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseHaddockModule): + """Stop the workflow when this module is reached.""" + + name = RECIPE_PATH.name + + def __init__( + self, + order: int, + path: Path, + *ignore: Any, + init_params: FilePath = DEFAULT_CONFIG, + **everything: Any, + ) -> None: + super().__init__(order, path, init_params) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if contact executable is compiled.""" + return + + def _run(self) -> None: + # removes the `exit` step folder + self.log(self.params["message"]) + shutil.rmtree(Path.cwd()) + error = HaddockTermination() + raise error diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..58d787ab9969904edfa30b0f5e73d1f8870d6636 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/extras/exit/defaults.yaml @@ -0,0 +1,10 @@ +message: + default: Stopping the workflow. + type: string + minchars: 0 + maxchars: 1000 + title: Exiting message. + short: The message to print when exiting. + long: The message to print when exiting. + group: execution + explevel: easy diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/.___pycache__ 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+"""HADDOCK3 actions referring to refinement.""" diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/.___pycache__ differ diff --git 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b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..acdefc58989568ed6983629f6605671e71634745 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/__init__.py @@ -0,0 +1,142 @@ +"""Energy minimization refinement with CNS. + +The ``[emref]`` module refine the input complexes by energy minimization using +conjugate gradient method implemented in CNS. + +Coordinates of the energy minimized structures are saved, and each +complex is then evaluated using the HADDOCK scoring function. +""" + +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import FilePath +from haddock.gear.haddockmodel import HaddockModel +from haddock.libs.libcns import prepare_cns_input, prepare_expected_pdb +from haddock.libs.libontology import PDBFile +from haddock.libs.libsubprocess import CNSJob +from haddock.modules import get_engine +from haddock.modules.base_cns_module import BaseCNSModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseCNSModule): + """HADDOCK3 module energy minimization refinement.""" + + name = RECIPE_PATH.name + + def __init__( + self, order: int, path: Path, initial_params: FilePath = DEFAULT_CONFIG + ) -> None: + """.""" + cns_script = Path(RECIPE_PATH, "cns", "emref.cns") + super().__init__(order, path, initial_params, cns_script=cns_script) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm module is installed.""" + return + + def _run(self) -> None: + """Execute module.""" + # Pool of jobs to be executed by the CNS engine + jobs: list[CNSJob] = [] + + # Get the models generated in previous step + try: + models_to_refine = self.previous_io.retrieve_models() + except Exception as e: + self.finish_with_error(e) + + self.output_models = [] + sampling_factor = self.params["sampling_factor"] + if sampling_factor > 1: + self.log(f"sampling_factor={sampling_factor}") + if sampling_factor == 0: + self.log("[Warning] sampling_factor cannot be 0, setting it to 1") + sampling_factor = 1 + if sampling_factor > 100: + self.log("[Warning] sampling_factor is larger than 100") + + max_nmodels = self.params["max_nmodels"] + nmodels = len(models_to_refine) * sampling_factor + if nmodels > max_nmodels: + self.finish_with_error( + f"Too many models ({nmodels}) to refine, max_nmodels =" + f" {max_nmodels}. Please reduce the number of models or" + " decrease the sampling_factor." + ) + + # checking the ambig_fname: + try: + prev_ambig_fnames = [mod.restr_fname for mod in models_to_refine] + except Exception as e: # noqa:F841 + # cannot extract restr_fname info from tuples + prev_ambig_fnames = [None for model in models_to_refine] + + ambig_fnames = self.get_ambig_fnames(prev_ambig_fnames) + + model_idx = 0 + idx = 1 + for model in models_to_refine: + # assign ambig_fname + if ambig_fnames: + ambig_fname = ambig_fnames[model_idx] + else: + ambig_fname = self.params["ambig_fname"] + model_idx += 1 + + for _ in range(self.params["sampling_factor"]): + emref_input = prepare_cns_input( + idx, + model, + self.path, + self.recipe_str, + self.params, + "emref", + ambig_fname=ambig_fname, + native_segid=True, + debug=self.params["debug"], + seed=model.seed if isinstance(model, PDBFile) else None, + ) + out_file = f"emref_{idx}.out" + err_fname = f"emref_{idx}.cnserr" + + # create the expected PDBobject + expected_pdb = prepare_expected_pdb(model, idx, ".", "emref") + expected_pdb.restr_fname = ambig_fname + try: + expected_pdb.ori_name = model.file_name + except AttributeError: + expected_pdb.ori_name = None + self.output_models.append(expected_pdb) + + job = CNSJob(emref_input, out_file, err_fname, envvars=self.envvars) + + jobs.append(job) + + idx += 1 + + # Run CNS Jobs + self.log(f"Running CNS Jobs n={len(jobs)}") + Engine = get_engine(self.params["mode"], self.params) + engine = Engine(jobs) + engine.run() + self.log("CNS jobs have finished") + + # Get the weights needed for the CNS module + _weight_keys = ("w_vdw", "w_elec", "w_desolv", "w_air", "w_bsa") + weights = {e: self.params[e] for e in _weight_keys} + + for pdb in self.output_models: + if pdb.is_present(): + haddock_model = HaddockModel(pdb.file_name) + pdb.unw_energies = haddock_model.energies + + haddock_score = haddock_model.calc_haddock_score(**weights) + pdb.score = haddock_score + + 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-0,0 +1,24 @@ +! calc_free-ene.cns +! Calculate the total energy of the separated components +! +! Script uses the store1 and store2 atom object, and COMP, REF and RMSD object +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +@MODULE:scale_intra_only.cns + +evaluate ($eintfree = 0.0) +@MODULE:flex_segment_back.cns +fix sele=(((attr store5 = 0) or resn ANI or resn DAN or resn XAN or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP*)) end + +minimize powell nstep=100 drop=10.0 nprint=25 end +fix sele=(not all) end +energy end +evaluate ($eintfree = $bond + $angl + $impr + $dihe + $vdw + $elec) + +display FREE MOLECULES INTERNAL ENERGY = $eintfree diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/check_coordinates.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/check_coordinates.cns new file mode 100644 index 0000000000000000000000000000000000000000..d23c8e64804060c61ff6aeea38925dc8e61dc8d6 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/check_coordinates.cns @@ -0,0 +1,100 @@ +! check_coordinates.cns +! Check max/min coordinates for compatibility with PDB format +! +! *********************************************************************** +! * Copyright 2025 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +evaluate ($failure = false) + +!check for coordinates >9999.999 (max writable in PDB format) + +show max (x) (all) +evaluate ($maxcoor = $result) +show max (y) (all) +if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) +end if +show max (z) (all) +if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) +end if +if ($maxcoor gt 9999.999) then + evaluate ($failure = true) +end if + +!check for coordinates <-999.999 (min writable in PDB format) + +show min (x) (all) +evaluate ($mincoor = $result) +show min (y) (all) +if ($result lt $mincoor) then + evaluate ($maxcoor = $result) +end if +show min (z) (all) +if ($result lt $mincoor) then + evaluate ($mincoor = $result) +end if +if ($mincoor lt -999.999) then + evaluate ($failure = true) +end if + +!if problem detected try correcting it by centering the system around 4500,4500,4500 +!but only if no EM restraints are used + +if ($failure eq true) then + if ($data.flags.em eq false) then + + evaluate ($xc = 0.0) + evaluate ($yc = 0.0) + evaluate ($zc = 0.0) + show ave (x) (all) + evaluate ($xc = 4500 - $result) + show ave (y) (all) + evaluate ($yc = 4500 - $result) + show ave (z) (all) + evaluate ($zc = 4500 -$result) + + do (x = x + $xc) (all) + do (y = y + $yc) (all) + do (z = z + $zc) (all) + + evaluate ($failure = false) + evaluate ($maxcoor = -999) + evaluate ($mincoor = 9999) + !check again for coordinates >9999.999 (max writable in PDB format) + show max (x) (all) + evaluate ($maxcoor = $result) + show max (y) (all) + if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) + end if + show max (z) (all) + if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) + end if + if ($maxcoor gt 9999.999) then + evaluate ($failure = true) + end if + + !check for coordinates <-999.999 (min writable in PDB format) + show min (x) (all) + evaluate ($mincoor = $result) + show min (y) (all) + if ($result lt $mincoor) then + evaluate ($maxcoor = $result) + end if + show min (z) (all) + if ($result lt $mincoor) then + evaluate ($mincoor = $result) + end if + if ($mincoor lt -999.999) then + evaluate ($failure = true) + end if + end if +end if + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/contactairs.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/contactairs.cns new file mode 100644 index 0000000000000000000000000000000000000000..aa8028ab7d3b40e56df692afec9eda66b1a45c68 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/contactairs.cns @@ -0,0 +1,27 @@ +! contactairs.cns +! Define ambiguous distance restraints between residues at interfaces +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +eval($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + for $id in id (tag and segid $prot_segid_$nchain1 + and (not (segid $prot_segid_$nchain1 or resn ANI or resn DAN or resn XAN + or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM) around 5.0)) loop defnoe1 + show (resid) (id $id) + evaluate ($inres = $result) + noe + assign (resid $inres and segid $prot_segid_$nchain1) + (byres (not (segid $prot_segid_$nchain1 or resn ANI or resn DAN or resn XAN + or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM) + and (segid $prot_segid_$nchain1) around 5.0)) 2.0 2.0 0.0 + end + end loop defnoe1 +end loop nloop1 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/def_solv_param.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/def_solv_param.cns new file mode 100644 index 0000000000000000000000000000000000000000..5a9e07a042e08d15d5b98d859fa199151e7b4a43 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/def_solv_param.cns @@ -0,0 +1,105 @@ +! def_solv_param.cns +! Define atomic solvation parameters +! Original valus taken from Fernandez-Recio et al. JMB 335:843 (2004) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +evaluate ($arofac = 6.26) +evaluate ($alifac = 1.27) +evaluate ($polfac = 2.30) + + +do (store1 = 0.0000) (all) +do (store1 = 0.0151 * $alifac) (name C*) +do (store1 = 0.0176 * $arofac) ((name CG* or name CD* or name CE* or name CH* or name CZ*) and (resn PHE or resn TYR or resn HIS or resn TRP)) +do (store1 = -0.0170 * $polfac) (name N*) +do (store1 = -0.0548 * $polfac) (name NT* or (name NZ* and resn LYS)) +do (store1 = -0.0273 * $polfac) (name NH* and resn ARG) +do (store1 = -0.0136 * $polfac) (name O*) +do (store1 = -0.0185 * $polfac) (name OG* or name OH) +do (store1 = -0.0299 * $polfac) ((name OD* and resn ASP) or (name OE* and resn GLU)) +do (store1 = 0.0112 * $polfac) (name S*) +do (store1 = 0.0022 * $polfac) ((name S* and attr charge = -0.3) or (name SD and resn MET)) +do (store1 = 0.0000) (name SHA) + +! +! CG parameters matched from the original terms +! +! Edesolv_aa +! ASP_cg = _________________________ +! ASA_cg +! +! ASA_cg and Edesol_aa calculated on a GGXGG peptide +! accuracy=0.0025, rh2o=1.4, delete H, sele=(resn X) +! +! e.g. BB bead alanine +! +! BB = CA + C + N + O +! ASA_cg = 176.4940 +! Edesolv_aa = -1.8889 +! +! ASP_cg = -0.0107 +! +! Charleen Don (2012), JR (2014), Jorge Roel (2017) +! +! + +do (store1 = 0.0000) (name BB or name SC*) +! Backbone beads +do (store1 = -0.0107) (name BB and resn ALA) +do (store1 = -0.0089) (name BB and resn GLY) +do (store1 = -0.0153) (name BB and resn ILE) +do (store1 = -0.0158) (name BB and resn VAL) +do (store1 = -0.0046) (name BB and resn PRO) +do (store1 = -0.0137) (name BB and resn ASN) +do (store1 = -0.0147) (name BB and resn GLN) +do (store1 = -0.0165) (name BB and resn THR) +do (store1 = -0.0154) (name BB and resn SER) +do (store1 = -0.0130) (name BB and resn MET) +do (store1 = -0.0167) (name BB and resn CYS) +do (store1 = -0.0126) (name BB and resn PHE) +do (store1 = -0.0134) (name BB and resn TYR) +do (store1 = -0.0134) (name BB and resn TRP) +do (store1 = -0.0169) (name BB and resn ASP) +do (store1 = -0.0150) (name BB and resn GLU) +do (store1 = -0.0155) (name BB and resn HIS) +do (store1 = -0.0163) (name BB and resn LYS) +do (store1 = -0.0162) (name BB and resn ARG) + +! Side-chain beads +!do (store1 = 0.0000) (name SC* and resn ALA) +!do (store1 = 0.0000) (name SC* and resn GLY) +do (store1 = 0.0255) (name SC* and resn ILE) +do (store1 = 0.0222) (name SC* and resn VAL) +do (store1 = 0.0230) (name SC* and resn PRO) +do (store1 = -0.0192) (name SC* and resn ASN) +do (store1 = -0.0135) (name SC* and resn GLN) +do (store1 = -0.0009) (name SC* and resn THR) +do (store1 = -0.0056) (name SC* and resn SER) +do (store1 = 0.0202) (name SC* and resn MET) +do (store1 = 0.0201) (name SC* and resn CYS) +do (store1 = 0.1005) (name SC* and resn PHE) +do (store1 = 0.0669) (name SC* and resn TYR) +do (store1 = 0.0872) (name SC* and resn TRP) +do (store1 = -0.0360) (name SC* and resn ASP) +do (store1 = -0.0301) (name SC* and resn GLU) +do (store1 = 0.0501) (name SC* and resn HIS) +do (store1 = -0.0210) (name SC* and resn LYS) +do (store1 = -0.0229) (name SC* and resn ARG) + +! Fake beads +do (store1 = 0.0) (name SCD* and resn ASN) +do (store1 = 0.0) (name SCD* and resn GLN) +do (store1 = 0.0) (name SCD* and resn SER) +do (store1 = 0.0) (name SCD* and resn THR) +do (store1 = 0.0) (name SCD* and resn ARG) +do (store1 = 0.0) (name SCD* and resn LYS) +do (store1 = 0.0) (name SCD* and resn GLU) +do (store1 = 0.0) (name SCD* and resn ASP) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/dna-rna_restraints.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/dna-rna_restraints.cns new file mode 100644 index 0000000000000000000000000000000000000000..feb27b3999cec077b4e20abd921dac061b7ded1f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/dna-rna_restraints.cns @@ -0,0 +1,424 @@ +! dna-rna_restraints.def +! Define backbone dihedral angles, hbonds and planarity restraints +! for nucleic acids +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: dna-rna_restraints.def +} +{+ description: Creates restraints to maintain conformation of DNA/RNA +} +{+ Additions and changes were made to allow for flexibility during docking +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin and Marc van Dijk for HADDOCK use +} + +{============================================== base planarity =============================================} + +{* Restrain base planarity. This selection must only include nucleotide residues *} +evaluate ($dna_bases_planar=true) + +{=================================== sugar-pucker dihedral angle restraints ================================} + +{* Pick the dihedral angles of the sugar pucker from the input structure + and restrain them within the given error range *} +evaluate ($dna_pick_pucdih=true) + +{* dihedral C1'-C2'-C3'-C4' error range *} +evaluate ($error_nu2=0.0) +{* dihedral C5'-C4'-C3'-C2' error range *} +evaluate ($error_nu3=0.0) +{* dihedral C1'-O4'-C4'-C5' error range *} +evaluate ($error_nu4=0.0) + +{================================ phosphate backbone dihedral angle restraints =============================} + +{* Pick the dihedral angles of the phosphate backbone from the input structure and + restrain them within the given error range *} +evaluate ($dna_pick_bacdih=true) + +{* Error range for phosphate backbone dihedrals *} +{* alpha dihedral O3'-P-O5'-C5' error range *} +evaluate ($error_alpha=10.0) +{* beta dihedral P-O5'-C5'-C4' error range *} +evaluate ($error_beta=40.0) +{* gamma dihedral O5'-C5'-C4'-C3' error range *} +evaluate ($error_gamma=20.0) +{* delta dihedral C5'-C4'-C3'-O3' error range *} +evaluate ($error_delta=50.0) +{* epsilon dihedral C4'-C3'-O3'-P error range *} +evaluate ($error_eps=10.0) +{* zeta dihedral C3'-O3'-P-O5' error range *} +evaluate ($error_zeta=50.0) + + +{=========================================== Watson-Crick base pairs =======================================} + +{* automatically pick Watson-Crick restraint values from structure *} +evaluate ($dna_pick_wc=true) + +{* error range used for dna_pick_wc defined Watson-Crick restraints *} +evaluate ($wc_low=0.05) +evaluate ($wc_up=0.05) + + +{=========================================== Coarse-Grained ===========================================================} +{* Is the DNA/RNA molecule CG? *} +evaluate ($dna_cg=false) + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + + +{- find max and min residue numbers -} +evaluate ($min_resid = 99999) +evaluate ($max_resid = -99999) +show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) +if ( $result > 0 ) then + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($min_resid = max($min_resid,$resid)) + evaluate ($max_resid = max($max_resid,$resid)) + end loop resid +end if + +{- the planarity restraints single bases -} +if ($dna_bases_planar=true) then + for $id in id ( tag and (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) ) loop plan + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) (id $id) + evaluate ($resid=decode($result)) + evaluate ($plweight = 20) + + restraints plane + group + selection=( segid $segid and resid $resid and + (resn T or resn C or resn G or resn A or resn U or + resn DT or resn DC or resn DG or resn DA) and + not (name c#' or name h#' or name h#'' or name o#p or + name h7# or name o#' or name p or name h#t or name o#t)) + weight=$plweight + end + end + end loop plan +end if + +{- Dihedral restraints for the sugar pucker -} + +if ($dna_pick_pucdih=true) then + show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) + if ( $result > 0 ) then + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + pick dihedral + ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name c2' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c4' ) + geometry + evaluatate ($dihedral_nu2=$result) + pick dihedral + ( segid $segid and resid $resid and name c5' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c2' ) + geometry + evaluatate ($dihedral_nu3=$result) + pick dihedral + ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name o4' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c5' ) + geometry + evaluatate ($dihedral_nu4=$result) + restraints dihedral + assign ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name c2' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c4' ) + 20.0 $dihedral_nu2 $error_nu2 2 + assign ( segid $segid and resid $resid and name c5' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c2' ) + 20.0 $dihedral_nu3 $error_nu3 2 + assign ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name o4' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c5' ) + 20.0 $dihedral_nu4 $error_nu4 2 + scale=20.0 + end + end loop resid + flags include cdih end + end if +end if + +{- Dihedral restraints for the phosphate backbone -} + +if ($dna_pick_bacdih=true) then + show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) + if ( $result > 0 ) then + evaluate ($resid=$min_resid) + evaluate ($nres=$max_resid - $min_resid + 1) + evaluate ($error_alpha=$error_alpha) + evaluate ($error_beta=$error_beta) + evaluate ($error_gamma=$error_gamma) + evaluate ($error_zeta=$error_zeta) + evaluate ($error_epsilon=$error_eps) + evaluate ($error_delta=$error_delta) + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + if ($resid > $min_resid) then + evaluate ($rprec = $resid - 1) + ! check if previous residue exists + show sum(1) ( resid $rprec and tag ) + if ( $result > 0 ) then + pick dihedral + ( segid $segid and resid $rprec and name O3' ) + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + geometry + evaluatate ($dihedral_alpha=$result) + pick dihedral + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + geometry + evaluatate ($dihedral_beta=$result) + restraint dihedral + ! alpha + assign ( segid $segid and resid $rprec and name O3' ) + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + 1.0 $dihedral_alpha $error_alpha 2 + ! beta + assign ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + 1.0 $dihedral_beta $error_beta 2 + scale 200.0 + end + end if + end if + + pick dihedral + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + geometry + evaluatate ($dihedral_gamma=$result) + pick dihedral + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + geometry + evaluatate ($dihedral_delta=$result) + + restraints dihedral + ! gamma + assign ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + 1.0 $dihedral_gamma $error_gamma 2 + ! delta + assign ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + 1.0 $dihedral_delta $error_delta 2 + scale=200.0 + end + + if ($resid < $max_resid) then + evaluate ($rfoll = $resid + 1) + ! check if next residue exists + show sum(1) ( resid $rfoll and segid $segid and tag ) + if ( $result > 0 ) then + pick dihedral + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + geometry + evaluatate ($dihedral_epsilon=$result) + pick dihedral + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + ( segid $segid and resid $rfoll and name O5' ) + geometry + evaluatate ($dihedral_zeta=$result) + restraint dihedral + ! epsilon + assign ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + 1.0 $dihedral_epsilon $error_epsilon 2 + ! zeta + assign ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + ( segid $segid and resid $rfoll and name O5' ) + 1.0 $dihedral_zeta $error_zeta 2 + scale 200.0 + end + end if + end if + end loop resid + flags include cdih end + end if +end if + +{- Watson-Crick base pairing -} + +if ($dna_pick_wc = true) then + evaluate ($hbcut = 3.5) + ! We only to check for ADE and CYT + show sum(1) ( (resn DA or resn A or resn DC or resn C) and tag ) + if ( $result > 0 ) then + noe + class hres + averaging hres cent + potential hres square + sqconstant hres 1. + sqexponent hres 2 + scale hres 70. + end + for $id in id ( (resn DA or resn A or resn DC or resn C) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($presid=$resid-1) + evaluate ($fresid=$resid+1) + evaluate ($ares_name = none) + show ( resn ) (id $id) + evaluate ($ares=$result) + + if ( $ares = DA ) then + eval ($ares_name = ADE) + elseif ( $ares = A ) then + eval ($ares_name = ADE) + end if + + if ( $ares = DC ) then + eval ($ares_name = CYT) + elseif ( $ares = C ) then + eval ($ares_name = CYT) + end if + + if ($ares_name = ADE) then + show sum(1) ( ((resn DT or resn T or resn U) and not (resid $presid or resid $fresid) and name N3) + and (resid $resid and name N1) around $hbcut) + if ($result = 1) then + show (resid) ( ((resn DT or resn T or resn U) and not (resid $presid or resid $fresid) and name N3) + and (resid $resid and name N1) around $hbcut) + evaluate ($rpair = $result) + pick bond + (resid $resid and name N6) + (resid $rpair and name O4) + geometry + evaluate ($n6o4=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name N3) + geometry + evaluate ($n1n3=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name O4) + geometry + evaluate ($n1o4=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name O2) + geometry + evaluate ($n1o2=$result) + noe + assign (resid $resid and name N6) + (resid $rpair and name O4) + $n6o4 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name N3) + $n1n3 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name O4) + $n1o4 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name O2) + $n1o2 $wc_low $wc_up + end + end if + end if + + !find possible pairing for DC/C with DG/G + if ($ares_name = CYT) then + show sum(1) ( ((resn DG or resn G) and not (resid $presid or resid $fresid) and name N1) + and (resid $resid and name N3) around $hbcut) + if ($result = 1) then + show (resid) ( ((resn DG or resn G) and not (resid $presid or resid $fresid) and name N1) + and (resid $resid and name N3) around $hbcut) + evaluate ($rpair = $result) + pick bond + (resid $resid and name N3) + (resid $rpair and name N1) + geometry + evaluate ($n3n1=$result) + pick bond + (resid $resid and name N4) + (resid $rpair and name O6) + geometry + evaluate ($n4o6=$result) + pick bond + (resid $resid and name O2) + (resid $rpair and name N2) + geometry + evaluate ($o2n2=$result) + pick bond + (resid $resid and name N3) + (resid $rpair and name O6) + geometry + evaluate ($n3o6=$result) + pick bond + (resid $resid and name N3) + (resid $rpair and name N2) + geometry + evaluate ($n3n2=$result) + noe + assign (resid $resid and name N3) + (resid $rpair and name N1) $n3n1 $wc_low $wc_up + assign (resid $resid and name N4) + (resid $rpair and name O6) $n4o6 $wc_low $wc_up + assign (resid $resid and name O2) + (resid $rpair and name N2) $o2n2 $wc_low $wc_up + assign (resid $resid and name N3) + (resid $rpair and name O6) $n3o6 $wc_low $wc_up + assign (resid $resid and name N3) + (resid $rpair and name N2) $n3n2 $wc_low $wc_up + end + end if + end if + end loop resid + end if +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/emref.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/emref.cns new file mode 100644 index 0000000000000000000000000000000000000000..703ce5ee43019cc1bb8e29268ce8aa6f37c067d6 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/emref.cns @@ -0,0 +1,494 @@ +! emref.cns +! Performs an energy minimization +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +if ( $log_level = "verbose" ) then + set message=all echo=on end +elseif ( $log_level = "normal" ) then + set message=normal echo=off end +else + set message=off echo=off end +end if + +!==================================================================! +! Initialisation of variables +!==================================================================! + +evaluate ($ini_count =1) + +evaluate ($data.ncomponents=$ncomponents) + + +! non-bonded parameter set to use +evaluate ($toppar.par_nonbonded = "OPLSX" ) + + +!Dihedrals, DNA and distance restraints +evaluate ($data.dihedrals_scale=$dihedrals_scale) +evaluate ($data.flags.cdih =$dihedrals_on) +evaluate ($data.dnarest =$dnarest_on) +evaluate ($data.ssdihed =$ssdihed) +evaluate ($data.error_dih =$error_dih) + + +! planarity restraints +evaluate ($data.flags.plan = false) + +! distance restraints +evaluate ($data.flags.noe = true) +evaluate ($data.randremoval=$randremoval) +evaluate ($data.npart=$npart) + +evaluate ($data.ambig_scale=$ambig_scale) +evaluate ($data.unambig_scale=$unambig_scale) +evaluate ($data.hbond_scale=$hbond_scale) + +evaluate ($data.contactairs=$contactairs) +if ($data.contactairs eq true) then + evaluate ($data.randremoval = false) +end if +evaluate ($data.kcont=$kcont) + +! NCS restraints +evaluate ($data.kncs = $kncs) +evaluate ($Data.flags.ncs = $ncs_on) +evaluate ($data.nncs = $nncs) + +! Symmetry restraints +evaluate ($data.ksym = $ksym) +evaluate ($Data.flags.sym = $sym_on) +evaluate ($data.nc2sym = $nc2sym) +evaluate ($data.nc3sym = $nc3sym) +evaluate ($data.ns3sym = $ns3sym) +evaluate ($data.nc4sym = $nc4sym) +evaluate ($data.nc5sym = $nc5sym) +evaluate ($data.nc6sym = $nc6sym) + +!Dihedral angle energy term: +evaluate ($data.flags.dihed = true) + +!Electrostatics: +evaluate ($data.flags.elec =$elecflag) +evaluate ($data.epsilon =$epsilon) +evaluate ($data.dielec =$dielec) + +!Interaction matrix: +evaluate ($nmol1=1) +while ($nmol1 <=$data.ncomponents) loop mol1 + evaluate ($nmol2=$nmol1 + 1) + evaluate ($scale.int_$nmol1_$nmol1 =$int_$nmol1_$nmol1) + while ($nmol2 <=$data.ncomponents) loop mol2 + evaluate ($scale.int_$nmol1_$nmol2 =$int_$nmol1_$nmol2) + evaluate ($scale.int_$nmol2_$nmol1 =$int_$nmol1_$nmol2) + evaluate ($nmol2=$nmol2 + 1) + end loop mol2 + evaluate ($nmol1 = $nmol1 + 1) +end loop mol1 + + +! Unsupported restraints +evaluate ($data.flags.em = false) +evaluate ($data.flags.rg = false) +evaluate ($data.flags.zres = false) +evaluate ($data.flags.sani = false) +evaluate ($data.flags.xrdc = false) +evaluate ($data.flags.xpcs = false) +evaluate ($data.flags.dani = false) +evaluate ($data.flags.vean = false) + +! Other parameters +evaluate ($refine.keepwater = false) + +!==================================================================! + +{* Read paramters and set various force field related variables *} + +@MODULE:read_param.cns + +parameter + bond (resn WAT ) (resn WAT ) 1000 TOKEN + angle (resn WAT ) (resn WAT ) (resn WAT ) 500 TOKEN + bond (resn HOH ) (resn HOH ) 1000 TOKEN + angle (resn HOH ) (resn HOH ) (resn HOH ) 500 TOKEN + bond (resn TIP*) (resn TIP*) 1000 TOKEN + angle (resn TIP*) (resn TIP*) (resn TIP*) 500 TOKEN +end + +igroup + interaction (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1 end + interaction (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) + (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) weight * 1 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0 end +end + +flag include bond angle impr vdw end + +if ($data.flags.dihed eq true) then + flag include dihed end +end if + +if ($data.flags.elec eq true) then + flag include elec end + if ($data.dielec eq "rdie") then + parameter nbonds eps=$data.epsilon rdie shift switch end end + ! shift statement needed first to activate switch (CNS bug?) + else + parameter nbonds eps=$data.epsilon cdie end end + end if + parameter nbonds ? end end +else + evaluate ($elec=0.0) + flag exclude elec end +end if + + +{* Read the distance restraints ================================ *} +set seed $seed end +set message=normal echo=on end +inline @MODULE:read_data.cns + +! random removal of restaints +if ($data.randremoval eq true) then + noe cv $npart ? end +end if + +if ( $log_level = "verbose" ) then + set message=all echo=on end +elseif ( $log_level = "normal" ) then + set message=normal echo=off end +else + set message=off echo=off end +end if + + +evaluate ($numnoe = 0) + +!Make sure that at least as many distance restraints are successfully +!read as the number of partitions for cross-validation +evaluate ($numnoe = 999) +noe ? end + +if ($NUMNOE lt $data.npart) then + noe part=1 end + evaluate ($data.npart = 1) + evaluate ($data.randremoval = FALSE) +end if + +noe + averaging * sum + potential * soft + scale * 1.0 + scale ambi $ambig_scale + scale dist $unambig_scale + scale hbon $hbond_scale + sqconstant * 1.0 + sqexponent * 2 + soexponent * 1 + rswitch * 0.5 + sqoffset * 0.0 + asymptote * 0.1 + msoexponent * 1 + masymptote * -0.1 + mrswitch * 0.5 +end + +{* set the energy flags ======================================================== *} + +inline @MODULE:setflags.cns + + +{* Check for other restraints ================================================== *} + +@MODULE:symmultimer.cns + +if ($data.contactairs eq true ) then + @MODULE:contactairs.cns +end if + +if ($data.dnarest eq true ) then + @MODULE:dna-rna_restraints.cns +end if + +if ($data.ssdihed eq "all" ) then + inline @MODULE:/protein-ss-restraints-all.cns +end if +if ($data.ssdihed eq "alpha" ) then + inline @MODULE:protein-ss-restraints-alpha.cns +end if +if ($data.ssdihed eq "alphabeta" ) then + inline @MODULE:protein-ss-restraints-alpha-beta.cns +end if + + +restraints dihedral + scale=$data.dihedrals_scale +end + +if ($data.flags.cdih eq true) then + flag incl cdih end +end if + + +{* Check for the presence of ions and add distance restraints / covalent bond == *} + +@MODULE:restrain-ions.cns + +{* Energy minimisation ========================================================= *} + +fix sele = (not all) end + +! fix the shape +fix sele = (resn SHA) end + +! fix rigid molecules +evaluate($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate($nchain1 = $nchain1 + 1) + evaluate($fcounter=0) + if ($nseg$nchain1 = 0) then + display NO FLEXIBLE SIDE-CHAINS SEGMENTS for molecule $nchain1 + display FIXING IT + fix sele = (segid $prot_segid_$nchain1 and not name H*) end + end if +end loop nloop1 + +! first round of minimization with weak harmonic restraints on non interface heavy atoms +do (refx=x) (all) +do (refy=y) (all) +do (refz=z) (all) +restraints harmonic + exponent = 2 +end +do (harm = 0) (all) +do (harm = 5) (not name h* and not resn ANI and not resn DAN and not resn XAN and not (resn WAT or resn HOH or resn TIP3)) + +!define flexible segments: +@MODULE:flex_segment_back.cns + +eval ($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + eval ($nchain1=$nchain1+1) + do (harm = 0) (attribute store5 = $nchain1) +end loop nloop1 + +if ($nemsteps > 0) then + minimize powell nstep=$nemsteps drop=10 end +end if + +! second round of minimization with weak harmonic restraints on non interface backbone atoms +do (harm = 0) (all) +do (harm = 1) (name CA or name BB or name C or name N or name P or name C# or name C##) + +eval ($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + eval ($nchain1=$nchain1+1) + do (harm = 0) (attribute store5 = $nchain1) +end loop nloop1 + +if ($nemsteps > 0) then + minimize powell nstep=$nemsteps drop=10 end +end if + +! final minimization without harmonic restraints + +flag excl harm end +mini powell nstep 200 drop=10 end + +{* ======================= calculate free molecules internal energy ============ *} + +igroup + interaction (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) + (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) weight * 1 end +end + +do (refx=x) (all) +do (refy=y) (all) +do (refz=z) (all) + +fix sele=(resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DMS) end + +flag excl noe dani sani vean xrdc xpcs coll cdih zhar end +flag include bond angle dihe impr vdw end + +evaluate ($elec = 0.0) +evaluate ($eintfree = 0.0) +if ($data.flags.elec eq true) then + flag include elec end +end if + +if ($data.dielec eq "rdie") then + parameter nbonds eps=$data.epsilon rdie shift switch end end + ! shift statement needed first to activate switch (CNS bug?) +else + parameter nbonds eps=$data.epsilon cdie end end +end if +parameter nbonds ? end end +inline @MODULE:calc_free-ene.cns + +fix sele=(not all) end + +do (x = refx) (all) +do (y = refy) (all) +do (z = refz) (all) + + +{* ===================== calculate complex internal energy *} + +evaluate ($kinter = 1.0) +flag include bond angle dihe impr vdw end +energy end + +@MODULE:scale_intra_only.cns + +evaluate ($elec = 0.0) +evaluate ($eintcplx = 0.0) +if ($data.flags.elec eq true) then + flag include elec end +end if + +energy end + +evaluate ($eintcplx = $bond + $angl + $impr + $dihe + $vdw + $elec) +evaluate ($ebond = $bond) +evaluate ($eangl= $angl) +evaluate ($eimpr= $impr) +evaluate ($edihe= $dihe) + +evaluate ($result=0) +print thres=0.05 bonds +evaluate ($rms_bonds=$result) +evaluate ($result=0) +print thres=5. angles +evaluate ($rms_angles=$result) +evaluate ($result=0) +print thres=5. impropers +evaluate ($rms_impropers=$result) +evaluate ($result=0) +print thres=30. dihedrals +evaluate ($rms_dihedrals=$result) + + +{* ===================== calculate final energies and write structure *} +evaluate ($cdih=0.0) +flag incl noe cdih end +if ($data.ncomponents > 1) then + evaluate ($kinter = 1.0) + @MODULE:scale_inter_final.cns +else + @MODULE:scale_intra_only.cns +end if + +noe + scale dist $data.unambig_scale + scale ambi $data.ambig_scale + scale hbon $data.hbond_scale + scale symm 0.0 + scale cont 0.0 +end +energy end +evaluate ($eair= $noe) + +evaluate ($esym = 0.0) +evaluate ($ncs = 0.0) +evaluate ($zhar = 0.0) +evaluate ($rms_test_noe = 0.0) +evaluate ($violations_test_noe = 0) +if ($data.flags.sym eq true) then + ! calculatee first the symmetry energy + noe reset nres= 1200000 end + @MODULE:symmultimer.cns + noe + scale symm $data.ksym + end + energy end + evaluate ($esym = $noe) + if ($data.randremoval eq true) then + evaluate ($violations_test_noe=0) + evaluate ($rms_test_noe=0.0) + display Print out of cross-validated violations and rms not + display possible in combination with symmetry restraints + display CV values set therefore to 0 + end if + noe reset end + set seed=$seed end + !read back all the distance restraints: + @@MODULE:read_noes.cns + !random removal of restaints + if ($data.randremoval eq true) then + noe cv $npart ? end + end if + noe + scale dist $data.unambig_scale + scale ambi $data.ambig_scale + scale hbon $data.hbond_scale + end + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) + if ($data.randremoval eq true) then + evaluate ($rms_test_noe=$test_rms) + evaluate ($violations_test_noe=$test_violations) + end if +else + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) + if ($data.randremoval eq true) then + evaluate ($rms_test_noe=$test_rms) + evaluate ($violations_test_noe=$test_violations) + end if +end if + +if ($data.dnarest eq true ) then + @MODULE:dna-rna_restraints.cns +end if + +energy end +evaluate ($etot = $ener - $noe) +evaluate ($noe = $eair) +evaluate ($etot = $etot + $noe) + +inline @MODULE:print_coorheader.cns + + +{* determine whether the final models should be reoriented along their principal *} +{* axes before writing to file ================================================= *} +eval($reorient = true) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop orientmol + evaluate ($ncount = $ncount + 1) + eval($watersegname_$ncount="WA" + encode($ncount)) + if ($mol_fix_origin_$ncount eq true) then + eval($reorient = false) + end if +end loop orientmol + +if ($reorient = true) then + coor sele= (not name H* and not resn ANI and not resn XAN and not resn DAN) orient end +end if + +inline @MODULE:check_coordinates.cns + +if ($failure eq true) then + evaluate ($failfile = $output_pdb_filename - ".pdb" + ".fail") + set display=$failfile end + display "MAX/MIN possible coordinates exceeded - stopping" + close $failfile end + stop +else + write coordinates format=pdbo output=$output_pdb_filename end +end if + +set message=normal echo=on end + +display OUTPUT: $output_pdb_filename + +stop diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flex_segment_back.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flex_segment_back.cns new file mode 100644 index 0000000000000000000000000000000000000000..7baf1c9ad9a7e857e14e08c816806b9ff285f010 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flex_segment_back.cns @@ -0,0 +1,58 @@ +! flex_segment_back.cns +! Define the semi-flexible segments (both side-chains and backbone) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +do (store5 = 0) (all) +do (store6 = 0) (all) + +!first flexible segments for docking +evaluate($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate($nchain1 = $nchain1 + 1) + evaluate($nf=0) + + if ($nseg$nchain1 = 0) then + display NO FLEXIBLE SEGMENTS for molecule $nchain1 + else + if ($nseg$nchain1 < 0) then + display AUTOMATIC DEFINITION OF FLEXIBLE SEGMENTS BASED ON INTERMOLECULAR PROXIMITY FOR MOLECULE $nchain1 + inline @MODULE:flexauto-neighbors.cns + else + display FLEXIBLE SIDE-CHAINS SEGMENTS for molecule $nchain1 + while ($nf < $nseg$nchain1) loop Xflex + evaluate($nf=$nf + 1) + do (store5 = $nchain1) ( resid $seg_sta_$nchain1_$nf : $seg_end_$nchain1_$nf + and segid $prot_segid_$nchain1) + display FLEXIBLE SEGMENT NR $nf FROM $seg_sta_$nchain1_$nf TO $seg_end_$nchain1_$nf + end loop Xflex + end if + end if +end loop nloop1 + +!then fully flexible segments for all stages +display NO FLEXIBLE SEGMENTS for all molecule at this stage +if ($nfle = 0) then + display NO FULLY FLEXIBLE SEGMENTS +else + evaluate($nf=0) + while ($nf < $nfle) loop Xfflex + evaluate($nf=$nf + 1) + do (store5 = 1) ( resid $fle_sta_$nf : $fle_end_$nf and segid $fle_seg_$nf ) + display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nf TO $fle_end_$nf FOR CHAIN $fle_seg_$nf + end loop Xfflex +end if + +do (store5 = 21) (resn WAT or resn HOH or resn TIP*) + +do (store1 = 0) (all) +do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) +show sum (store1) ((resn WAT or resn HOH or resn TIP*)) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flexauto-neighbors.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flexauto-neighbors.cns new file mode 100644 index 0000000000000000000000000000000000000000..f3fe74b83b0aa2a99d80a117239d87e052648b11 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/flexauto-neighbors.cns @@ -0,0 +1,42 @@ +! flexauto-neighbors.cns +! Automatic definition of flexible segments for docking for contacting residues +! including neighboring residues of residues making contacts +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($flcut = 5.0) + +do (store5 = $nchain1) (byres (segid $prot_segid_$nchain1 + and (not (segid $prot_segid_$nchain1 or resn SHA)) around $flcut)) + +do (store6 = 0) (segid $prot_segid_$nchain1) +for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres1 + show (resid) (id $id) + evaluate ($inres = decode($result)) + evaluate ($preres = $inres) + evaluate ($nexres = $inres) + evaluate ($preres = $preres - 1) + do (store6 = $nchain1) (resid $preres and segid $prot_segid_$nchain1) + do (store6 = $nchain1) (resid $nexres and segid $prot_segid_$nchain1) +end loop flexres1 + +do (store5 = store6) (segid $prot_segid_$nchain1) + +display THE FOLLOWING RESIDUES HAVE BEEN DEFINED AS FLEXIBLE for molecule $nchain1 +for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres2 + show (resid) (id $id) + evaluate ($inres = $result) + show (resn) (id $id) + evaluate ($nares = $result) + show (segid) (id $id) + evaluate ($seres = $result) + display AUTOMATICALLY SELECTED SEGMENT: $nares,$inres,$seres +end loop flexres2 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/print_coorheader.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/print_coorheader.cns new file mode 100644 index 0000000000000000000000000000000000000000..1a06f68f63b409e44be920b6dada5a05ff1e762f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/print_coorheader.cns @@ -0,0 +1,308 @@ +! print_coorheader.cns +! Generate the coordinate header (REMARKS) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +if ($Data.flags.dihed eq false) then evaluate ($dihe = 0) end if +if ($Data.flags.sani eq false) then evaluate ($sani = 0) end if +if ($Data.flags.xrdc eq false) then evaluate ($xrdc = 0) end if +if ($Data.flags.xpcs eq false) then evaluate ($xpcs = 0) end if +if ($Data.flags.dani eq false) then evaluate ($dani = 0) end if +if ($Data.flags.vean eq false) then evaluate ($vean = 0) end if +if ($Data.flags.cdih eq false) then evaluate ($cdih = 0) end if +if ($Data.flags.noe eq false) then evaluate ($noe = 0) end if +if ($Data.flags.rg eq false) then evaluate ($coll = 0) end if +if ($Data.flags.zres eq false) then evaluate ($zhar = 0) end if +if ($Data.flags.em eq false) then evaluate ($lcc = 0) end if + +evaluate($enerall=$etot) +evaluate($bondall=$ebond) +evaluate($anglall=$eangl) +evaluate($imprall=$eimpr) +evaluate($diheall=$edihe) +evaluate($vdwall=$vdw) +evaluate($elecall=$elec) +evaluate($noeall=$noe) +evaluate($rgall=$coll) +evaluate($zresall=$zhar) +evaluate($cdihall=$cdih) +evaluate($coupall=0) +evaluate($saniall=$sani+$xrdc) +evaluate($veanall=$vean) +evaluate($xpcsall=$xpcs) +evaluate($daniall=$dani) + +if ($Data.flags.sym eq true) then + evaluate ($result=0) + evaluate ($violations=0) + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) +end if + +if ($Data.randremoval eq false) then + evaluate ($violations_test_noe= 0) + evaluate ($rms_test_noe = 0) + evaluate ($npart = 0) +end if + +evaluate ($result=0) +evaluate ($violations=0) +print threshold=5. cdih +evaluate ($rms_cdih=$result) +evaluate ($violations_cdih=$violations) +evaluate ($result=0) +evaluate ($violations=0) +evaluate ($rms_coup = 0) +evaluate ($violations_coup = 0) + +evaluate( $rms_sani = 0) +evaluate( $violations_sani = 0) +if ($Data.flags.sani eq TRUE) then + sani print threshold = 0.20 class rd* end + evaluate( $rms_sani = $result) + evaluate( $violations_sani = $violations) +end if + +evaluate( $rms_xrdc = 0) +evaluate( $violations_xrdc = 0) +if ($Data.flags.xrdc eq TRUE) then + xrdc print threshold = 0.2 class xr* end + evaluate( $rms_xrdc = $result) + evaluate( $violations_xrdc = $violations) +end if + +evaluate( $violations_sani = $violations_sani + $violations_xrdc) +evaluate( $rms_sani = $rms_sani + $rms_xrdc) + +evaluate( $rms_xpcs = 0) +evaluate( $violations_xpcs = 0) +if ($Data.flags.xpcs eq TRUE) then + xpcs print threshold = 0.2 class pc* end + evaluate( $rms_xpcs = $result) + evaluate( $violations_xpcs = $violations) +end if + +evaluate( $rms_vean = 0) +evaluate( $violations_vean = 0) +if ($Data.flags.vean eq TRUE) then + vean print threshold = 5.00 class ve* end + evaluate( $rms_vean = $result) + evaluate( $violations_vean = $violations) +end if + +evaluate( $rms_dani = 0) +evaluate( $violations_dani = 0) +if ($Data.flags.dani eq TRUE) then + dani print threshold = 0.20 class da* end + evaluate( $rms_dani = $result) + evaluate( $violations_dani = $violations) +end if + +{====>} {* define ASA-based solvation parameters *} +inline @MODULE:def_solv_param.cns + +{====>} {* buried surface area and desolvation*} +evaluate ($nchain1 = 0) +evaluate ($saafree = 0) +evaluate ($esolfree = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate ($nchain1 = $nchain1 + 1) + {====>} {* buried surface area and desolvation*} + do (rmsd = 0) (all) + surface mode=access accu=0.075 rh2o=1.4 sele=(segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) end + show sum (rmsd) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + evaluate ($saafree = $saafree + $result) + do (store2 = rmsd * store1) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + show sum (store2) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + evaluate ($esolfree = $esolfree + $result) +end loop nloop1 + +do (rmsd = 0) (all) +do (store2 = 0) (all) +surface mode=access accu=0.075 rh2o=1.4 sele=(not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) end +show sum (rmsd) (not ((resn WAT or resn HOH or resn TIP*) or resn DMS or resn SHA)) +evaluate ($satot = $result) +do (store2 = rmsd * store1) (not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) +show sum (store2) (not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) +evaluate ($esolcplx = $result) +evaluate ($saburied = $saafree - $satot) +if ($saburied < 0) then + evaluate ($saburied = -999999) +end if + +evaluate ($edesolv = $esolcplx - $esolfree) + +evaluate ($dhbinding = $edesolv + $eintcplx - $eintfree + $elecall + $vdwall) + +evaluate ($nshape = 0) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop shape + evaluate ($ncount = $ncount + 1) + if ($mol_shape_$ncount eq true) then + evaluate ($nshape = $nshape + 1) + end if +end loop shape + +evaluate ($nonshape = $Data.ncomponents - $nshape) + +if ($nonshape = 1) then + evaluate ($saburied = 0) + evaluate ($edesolv = 0) + evaluate ($dhbinding = 0) + evaluate ($eintfree = $eintcplx) +end if + +if ($Data.flags.sym eq true) then + evaluate ($enerall = $enerall + $esym) +end if +if ($Data.flags.ncs eq true) then + evaluate ($enerall = $enerall + $ncs) +end if + +evaluate ($procwat = false) +if ($refine.keepwater eq true) then + evaluate ($procwat = true) +end if + +if ($procwat eq true) then + ident (store3) (not all) + flag exclude * include vdw elec end + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + igroup + interaction (segid $prot_segid_$nchain1) ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) weight * 1.0 end + interaction (not segid $prot_segid_$nchain1) (resn WAT or resn HOH or resn TIP* or resn DMS) weight * 0.0 end + interaction (segid $prot_segid_$nchain1) (not ((resn WAT or resn HOH or resn TIP* or resn DMS) and store3)) weight * 0.0 end + end + energy end + evaluate ($ener_water_$nchain1 = $ener) + evaluate ($enerall = $enerall + $ener) + evaluate ($vdw_water_$nchain1 = $vdw) + evaluate ($elec_water_$nchain1 = $elec) + + end loop nloop1 + if ($data.ncomponents > 1) then + eval($nchain1 = $data.ncomponents) + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + evaluate ($ener_water_$nchain1 = 0.0) + evaluate ($vdw_water_$nchain1 = 0.0) + evaluate ($elec_water_$nchain1 = 0.0) + end loop nloop1 + end if + + eval($nchain1 = 0) + + igroup + while ($nchain1 < $data.ncomponents) loop nloop2 + eval($nchain1 = $nchain1 + 1) + interaction (segid $prot_segid_$nchain1) (all) weight * 0.0 end + end loop nloop2 + interaction ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) + ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) weight * 1.0 end + interaction (store3) (store3) weight * 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + interaction (resn SHA) (resn SHA) weight * 0.0 end + end + energy end + evaluate ($ener_water_water = $ener) + evaluate ($enerall = $enerall + $ener) + evaluate ($vdw_water_water = $vdw) + evaluate ($elec_water_water = $elec) +else + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents ) loop nloop1 + eval($nchain1 = $nchain1 + 1) + evaluate ($ener_water_$nchain1 = 0.0) + evaluate ($vdw_water_$nchain1 = 0.0) + evaluate ($elec_water_$nchain1 = 0.0) + end loop nloop1 + evaluate ($ener_water_water = 0.0) + evaluate ($vdw_water_water = 0.0) + evaluate ($elec_water_water = 0.0) +end if + +! calculate the HADDOCK score +evaluate ($hscore = $w_vdw * $vdwall) +evaluate ($hscore = $hscore + $w_elec * $elecall) +evaluate ($hscore = $hscore + $w_air * $noeall) +evaluate ($hscore = $hscore + $w_rg * $rgall) +evaluate ($hscore = $hscore + $w_cdih * $cdihall) +evaluate ($hscore = $hscore + $w_sani * $saniall) +evaluate ($hscore = $hscore + $w_xpcs * $xpcsall) +evaluate ($hscore = $hscore + $w_dani * $daniall) +evaluate ($hscore = $hscore + $w_vean * $veanall) +evaluate ($hscore = $hscore + $w_sym * $esym) +evaluate ($hscore = $hscore + $w_bsa * $saburied) +evaluate ($hscore = $hscore + $w_desolv * $edesolv) +evaluate ($hscore = $hscore + $w_lcc * $lcc) + +set message=on echo=on end +set remarks=reset end +set remarks=accumulate end +remarks =============================================================== +remarks HADDOCK stats for $output_pdb_filename +remarks =============================================================== +remarks HADDOCK score: $hscore +remarks =============================================================== + +!list input molecules +evaluate ($nmol=1) +while ($nmol <=$data.ncomponents) loop mol + if ( $exist_input_pdb_filename_$nmol = true) then + remarks initial structure $nmol - $input_pdb_filename_$nmol + end if + evaluate ($nmol = $nmol + 1) +end loop mol + +remarks =============================================================== +remarks total,bonds,angles,improper,dihe,vdw,elec,air,cdih,coup,rdcs,vean,dani,xpcs,rg +remarks energies: $enerall, $bondall, $anglall, $imprall, $diheall, $vdwall, $elecall, $noeall, $cdihall, $coupall, $saniall, $veanall, $daniall, $xpcsall, $rgall +remarks =============================================================== +remarks bonds,angles,impropers,dihe,air,cdih,coup,rdcs,vean,dani,xpcs +remarks rms-dev.: $rms_bonds,$rms_angles,$rms_impropers,$rms_dihedrals,$rms_noe,$rms_cdih,$rms_coup, $rms_sani, $rms_vean, $rms_dani, $rms_xpcs +remarks =============================================================== +remarks air,cdih,coup,rdcs,vean,dani,xpcs +remarks >0.3,>5,>1,>0,>5,>0.2,>0.2 +remarks violations.: $violations_noe, $violations_cdih, $violations_coup, $violations_sani, $violations_vean, $violations_dani, $violations_xpcs +remarks =============================================================== +remarks CVpartition#,violations,rms +remarks AIRs cross-validation: $npart, $violations_test_noe, $rms_test_noe +remarks =============================================================== +remarks NCS energy: $ncs +remarks =============================================================== +remarks Symmetry energy: $esym +remarks =============================================================== +remarks Membrane restraining energy: $zresall +remarks =============================================================== +remarks Local cross-correlation: $lcc[f7.4] +remarks =============================================================== +remarks Desolvation energy: $edesolv +remarks Internal energy free molecules: $eintfree +remarks Internal energy complex: $eintcplx +remarks Binding energy: $dhbinding +remarks =============================================================== +remarks buried surface area: $saburied +remarks =============================================================== +set remark accumulate end +evaluate($ncount = 0) +while ($ncount < $data.ncomponents) loop waterremark + evaluate ($ncount = $ncount +1) + remarks water - chain_$ncount: $ener_water_$ncount $vdw_water_$ncount $elec_water_$ncount +end loop waterremark +remarks =============================================================== +remarks water - water: $ener_water_water $vdw_water_water $elec_water_water +remarks =============================================================== diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-all.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-all.cns new file mode 100644 index 0000000000000000000000000000000000000000..ce6537b77378451041f63bb9fb07cb9fce35b4d7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-all.cns @@ -0,0 +1,88 @@ +! protein-ss-restraints-all.def +! Define automatically secondary stucture dihedral angle restraints for all residues +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ authors: Axel T. Brunger, and Paul D. Adams, +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone -} +restraint dihedral + nass = 50000 +end +do (store1 = 1) (all) +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id ( segid $prot_segid_$group and tag and not resn TIP3 ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + evaluate ($rprec = $resid - 1) + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluatate ($dihedral_phi=$result) + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + scale 200.0 + end + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluatate ($dihedral_psi=$result) + restraint dihedral + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha-beta.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha-beta.cns new file mode 100644 index 0000000000000000000000000000000000000000..0d6d8e4aa9b00b11bd201f8f9917a4628821978b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha-beta.cns @@ -0,0 +1,128 @@ +! protein-ss-restraints-alpha-beta.cns +! Define automatically secondary structure dihedral angle restraints +! for helical and beta-sheet segments +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone in alpha-beta regions -} + +do (store1 = 1) (all) +restraint dihedral + nass = 50000 +end +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id ( segid $prot_segid_$group and tag and not resn TIP* ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($alphaphi = 0) + evaluate ($alphapsi = 0) + evaluate ($alpha_check = 0) + evaluate ($betaphi = 0) + evaluate ($betapsi = 0) + evaluate ($beta_check = 0) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluate ($dihedral_phi=$result) + evaluate ($alphaphi=max($dihedral_phi,-77)) + evaluate ($alphaphi=max($dihedral_phi,-37)) + if ($alphaphi eq -37) then + evaluate ($alpha_check = 1) + else + evaluate ($alpha_check = 0) + end if + evaluate ($betaphi=max($dihedral_phi,-145)) + evaluate ($betaphi=max($dihedral_phi,-105)) + if ($betaphi eq -105) then + evaluate ($beta_check = 1) + else + evaluate ($beta_check = 0) + end if + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluate ($dihedral_psi=$result) + evaluate ($alphapsi=max($dihedral_psi,-67)) + evaluate ($alphapsi=max($dihedral_psi,-27)) + if ($alphapsi eq -27) then + evaluate ($alpha_check = $alpha_check + 1) + end if + evaluate ($betapsi=max($dihedral_psi,105)) + evaluate ($betapsi=max($dihedral_psi,145)) + if ($betapsi eq 145) then + evaluate ($beta_check = $beta_check + 1) + end if + end if + evaluate ($defrest = 0) + if ($alpha_check eq 2) then + evaluate ($defrest = 1) + end if + if ($beta_check eq 2) then + evaluate ($defrest = 1) + end if + if ($defrest = 1) then + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha.cns new file mode 100644 index 0000000000000000000000000000000000000000..38416657fc086d88a8288b50371b1f3e697103a8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/protein-ss-restraints-alpha.cns @@ -0,0 +1,109 @@ +! protein-ss-restraints-alpha.cns +! Define automatically secondary structure dihedral angle restraints +! for helical segments +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone in alpha-helical regions -} +restraint dihedral + nass = 50000 +end +do (store1 = 1) (all) +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id (segid $prot_segid_$group and tag and not resn TIP3 ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($alphaphi = 0) + evaluate ($alphapsi = 0) + evaluate ($alpha_check = 0) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluate ($dihedral_phi=$result) + evaluate ($alphaphi=max($dihedral_phi,-77)) + evaluate ($alphaphi=max($dihedral_phi,-37)) + if ($alphaphi eq -37) then + evaluate ($alpha_check = 1) + else + evaluate ($alpha_check = 0) + end if + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluate ($dihedral_psi=$result) + evaluate ($alphapsi=max($dihedral_psi,-67)) + evaluate ($alphapsi=max($dihedral_psi,-27)) + if ($alphapsi eq -27) then + evaluate ($alpha_check = $alpha_check + 1) + end if + end if + evaluate ($defrest = 0) + if ($alpha_check eq 2) then + evaluate ($defrest = 1) + end if + if ($defrest = 1) then + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_data.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_data.cns new file mode 100644 index 0000000000000000000000000000000000000000..0499183803224fbed8de2940b8499c9eb8f29d50 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_data.cns @@ -0,0 +1,81 @@ +! read_data.cns +! Read the various restraints data +! (distances and dihedral angles only in this version) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +! Ambiguous and unambiguous distance restraints, hbonds +noe + reset + nrestraints = 12000000 ! allocate space for NOEs + ceiling 1000 +end + +evaluate ($filenam0 = $ambig_fname + "_" + encode($count)) +fileexist $filenam0 end +if ($result eq false) then + evaluate ($filenam0 = $ambig_fname) +end if + +if ($filenam0 # "") then + fileexist $filenam0 end + if ($result eq true) then + noe class ambi @@$filenam0 end + end if +end if + +if ($Data.randremoval eq true) then + noe part $Data.npart end +end if + +if ($unambig_fname # "") then + fileexist $unambig_fname end + if ($result eq true) then + noe class dist @@$unambig_fname end + end if +end if + +if ($hbond_fname # "") then + fileexist $hbond_fname end + if ($result eq true) then + noe class hbon @@$hbond_fname end + end if +end if + +noe + averaging * sum + potential * soft + scale * 1.0 + sqconstant * 1.0 + sqexponent * 2 + soexponent * 1 + rswitch * 1.0 + sqoffset * 0.0 + asymptote * 2.0 + msoexponent * 1 + masymptote * -0.1 + mrswitch * 1.0 +end + + +!dihedral restraints: +restraints dihedral + reset + nassign 50000 +end +if ($dihe_fname # "") then + fileexist $dihe_fname end + if ($result eq true) then + restraints dihedral + @@$dihe_fname + end + end if +end if + +restraints dihedral ? end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_noes.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_noes.cns new file mode 100644 index 0000000000000000000000000000000000000000..be5c0b8c55dbbd984e82a3fceb10553d0ee60281 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_noes.cns @@ -0,0 +1,65 @@ +! read_noes.cns +! Read the various restraints data +! In this version only distance-based restraints +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +! Ambiguous and unambiguous distance restraints, hbonds +noe + reset + nrestraints = 12000000 ! allocate space for NOEs + ceiling 1000 +end + +evaluate ($filenam0 = $ambig_fname + "_" + encode($count)) +fileexist $filenam0 end +if ($result eq false) then + evaluate ($filenam0 = $ambig_fname) +end if + +if ($filenam0 # "") then + fileexist $filenam0 end + if ($result eq true) then + noe class ambi @@$filenam0 end + end if +end if + +if ($Data.randremoval eq true) then + noe part $Data.npart end +end if + +if ($unambig_fname # "") then + fileexist $unambig_fname end + if ($result eq true) then + noe class dist @@$unambig_fname end + end if +end if + +if ($hbond_fname # "") then + fileexist $hbond_fname end + if ($result eq true) then + noe class hbon @@$hbond_fname end + end if +end if + +noe + averaging * sum + potential * soft + scale * 1.0 + sqconstant * 1.0 + sqexponent * 2 + soexponent * 1 + rswitch * 1.0 + sqoffset * 0.0 + asymptote * 2.0 + msoexponent * 1 + masymptote * -0.1 + mrswitch * 1.0 +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_param.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_param.cns new file mode 100644 index 0000000000000000000000000000000000000000..6f549a453e49c118de295658c1294a8a429b9365 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/read_param.cns @@ -0,0 +1,64 @@ +! read_param.cns +! Reads parameter files. +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +!! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** + +{* protein parameter file *} +eval ($prot_parameter_infile="TOPPAR:protein-allhdg5-4.param") + +{* nucleic acid parameter file *} +eval ($nucl_parameter_infile="TOPPAR:dna-rna-allatom-hj-opls-1.3.param") + +{* carbohydrate parameter file *} +eval ($carbo_parameter_infile="TOPPAR:carbohydrate.param") + +{* solvent parameter file *} +eval ($solv_parameter_infile="TOPPAR:solvent-allhdg5-4.param") + +{* fragment probes parameter file *} +eval ($ligands_parameter_infile="TOPPAR:fragment_probes.param") + +{* ion parameter file *} +eval ($ion_parameter_infile="TOPPAR:ion.param") + +{* heme parameter file *} +eval ($heme_parameter_infile="TOPPAR:hemes-allhdg.param") + +{* shape parameter file *} +eval ($shape_parameter_infile="TOPPAR:shape.param") + +{* cofactors parameter file *} +eval ($cofactors_parameter_infile="TOPPAR:cofactors.param") + +parameter + @@$prot_parameter_infile + @@$ion_parameter_infile + @@$nucl_parameter_infile + @@$carbo_parameter_infile + @@$solv_parameter_infile + @@$ligands_parameter_infile + @@$heme_parameter_infile + @@$shape_parameter_infile + @@$cofactors_parameter_infile + if ($ligand_param_fname # "") then + fileexist $ligand_param_fname end + if ($result eq true) then + @@$ligand_param_fname + end if + end if +end + +parameter + nbonds + nbxmod=5 atom cdie shift + cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25 + wmin=0.5 tolerance 0.5 + end +end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/restrain-ions.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/restrain-ions.cns new file mode 100644 index 0000000000000000000000000000000000000000..52a5b3d2024ac21f44456d9ed204d455d8380ac2 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/restrain-ions.cns @@ -0,0 +1,109 @@ +! restrain-ions.cns +! distance restraints between an ion and any coordinating atom within 5A +! to maintain the coordination topologu +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +noe class dist end + +! first deal with monoatomic ions +evaluate ($pcount = 0) +for $id1 in id ( name "LI+1" or name "F-1" or name "NA+1" or name "MG+2" or name "AL+3" + or name "CL-1" or name "K+1" or name "CA+2" or name "V+2" or name "V+3" + or name "CR+2" or name "CR+3" or name "MN+2" or name "MN+3" or name "FE+2" + or name "FE+3" or name "NI+2" or name "CO+2" or name "CO+3" or name "CU+1" + or name "CU+2" or name "ZN+2" or name "BR-1" or name "SR+2" or name "MO+3" + or name "AG+1" or name "CD+2" or name "I-1" or name "CS+2" or name "HO+3" + or name "YB+2" or name "YB+3" or name "OS+4" or name "IR+3" or name "PT+2" + or name "AU+1" or name "AU+2" or name "HG+1" or name "HG+2" or name "PB+2" + or name "U+3" or name "U+4" or name "ZN+1" or name "ZN" ) loop sions + + show (segid) (id $id1) + evaluate ($segid1=$result) + show (resid) (id $id1) + evaluate ($resid1=$result) + show (resname) (id $id1) + evaluate ($resname1=$result) + show (name) (id $id1) + evaluate ($name1=$result) + + evaluate ($mindis = 4.0) + for $id2 in id ( (name O* or name S* or name N*) and (id $id1) around $mindis and + (resn ACE or resn ALA or resn ALY or resn ARG or resn ASN or resn ASH or resn ASP or + resn CSP or resn CTN or resn CYC or resn CYF or resn CYM or resn CYS or resn DDZ or + resn GLN or resn GLH or resn GLU or resn GLY or resn HIS or resn HY3 or resn HYP or + resn ILE or resn LEU or resn LYS or resn M3L or resn MLY or resn MLZ or resn MET or + resn MSE or resn NEP or resn NME or resn PHE or resn PNS or resn PRO or resn PTR or + resn QSR or resn SEP or resn SER or resn SEC or resn THR or resn TOP or resn TRP or + resn TYP or resn TYR or resn TYS or resn VAL or resn A or resn C or resn G or + resn T or resn DA or resn DC or resn DG or resn DT or resn DJ )) loop search + + pick bond (id $id1) (id $id2) geometry + evaluate ($upper = $result) + show (segid) (id $id2) + evaluate ($segid2=$result) + show (resid) (id $id2) + evaluate ($resid2=$result) + show (name) (id $id2) + evaluate ($name2=$result) + + if ($segid1 eq $segid2) then + noe + assign (resid $resid1 and segid $segid1 and name $name1) + (resid $resid2 and segid $segid2 and name $name2) $upper 0.1 0.1 + end + end if + + end loop search + +end loop sions + +! then deal with multiatomic mions +evaluate ($pcount = 0) +for $id1 in id ( (resn SO4 or resn PO4 or resn WO4) and name O* ) loop mions + + show (segid) (id $id1) + evaluate ($segid1=$result) + show (resid) (id $id1) + evaluate ($resid1=$result) + show (resname) (id $id1) + evaluate ($resname1=$result) + show (name) (id $id1) + evaluate ($name1=$result) + + evaluate ($mindis = 4.0) + for $id2 in id ( (name O* or name S* or name N*) and (id $id1) around $mindis and + (resn ACE or resn ALA or resn ALY or resn ARG or resn ASN or resn ASH or resn ASP or + resn CSP or resn CTN or resn CYC or resn CYF or resn CYM or resn CYS or resn DDZ or + resn GLN or resn GLH or resn GLU or resn GLY or resn HIS or resn HY3 or resn HYP or + resn ILE or resn LEU or resn LYS or resn M3L or resn MLY or resn MLZ or resn MET or + resn MSE or resn NEP or resn NME or resn PHE or resn PNS or resn PRO or resn PTR or + resn QSR or resn SEP or resn SER or resn SEC or resn THR or resn TOP or resn TRP or + resn TYP or resn TYR or resn TYS or resn VAL or resn A or resn C or resn G or + resn T or resn DA or resn DC or resn DG or resn DT or resn DJ )) loop search + + pick bond (id $id1) (id $id2) geometry + evaluate ($upper = $result) + show (segid) (id $id2) + evaluate ($segid2=$result) + show (resid) (id $id2) + evaluate ($resid2=$result) + show (name) (id $id2) + evaluate ($name2=$result) + + if ($segid1 eq $segid2) then + noe + assign (resid $resid1 and segid $segid1 and name $name1) + (resid $resid2 and segid $segid2 and name $name2) $upper 0.1 0.1 + end + end if + + end loop search + +end loop mions diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter.cns new file mode 100644 index 0000000000000000000000000000000000000000..7088087a65b71bcdb213cce29d86ab6c043225e8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter.cns @@ -0,0 +1,45 @@ +! scale_inter.cns +! Scaling of intermolecular interactions +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * $scale.int_$nchain1_$nchain1 end + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + ((resn WAT or resn HOH or resn TIP* or resn DMS)) weight * 1.0 vdw $kinter elec $kinter end + + eval($nchain2 = $nchain1 ) + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + eval($scalfac = $kinter * $scale.int_$nchain1_$nchain2) + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain2 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1.0 vdw $scalfac elec $scalfac end + end loop nloop2 + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + + interaction ((resn WAT or resn HOH or resn TIP* or resn DMS)) ((resn WAT or resn HOH or resn TIP* or resn DMS)) weight * 1.0 end + +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter_final.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter_final.cns new file mode 100644 index 0000000000000000000000000000000000000000..efae5ce10a1fdafe1ef2f1d47a0ff9ebe57a1c8f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_inter_final.cns @@ -0,0 +1,39 @@ +! scale_inter_final.cns +! Scaling of intermolecular interactions +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + eval($nchain2 = $nchain1 ) + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + eval($scalfac = $kinter * $scale.int_$nchain1_$nchain2) + interaction (segid $prot_segid_$nchain1 and not + (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA or resn DPP or resn PCW or resn PEE)) + (segid $prot_segid_$nchain2 and not + (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA or resn DPP or resn PCW or resn PEE)) weight * 1.0 vdw $scalfac elec $scalfac end + end loop nloop2 + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_intra_only.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_intra_only.cns new file mode 100644 index 0000000000000000000000000000000000000000..15b0adfbb562862214f161c494c14a17dbf6beb7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/scale_intra_only.cns @@ -0,0 +1,36 @@ +! scale_intra_only.cns +! Scaling of intramolecular energies (no intermolecular energies) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1.0 end + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + +end + + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/setflags.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/setflags.cns new file mode 100644 index 0000000000000000000000000000000000000000..fd3e181f3cc822ca390f8d3f0ec6368c7305498b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/setflags.cns @@ -0,0 +1,21 @@ +! setflags.cns +! Defines energy flags +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +if ($Data.flags.noe = TRUE) then + flags include noe end +end if +if ($Data.flags.cdih = TRUE) then + flags include cdih end +end if +if ($Data.flags.ncs = TRUE) then + flags include ncs end +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/symmultimer.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/symmultimer.cns new file mode 100644 index 0000000000000000000000000000000000000000..3b4f731e948bf1d58eab0f71f457da6e52afc3e9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/cns/symmultimer.cns @@ -0,0 +1,677 @@ +! symmultimer.cns +! Define symmetry restraints +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +if ($Data.flags.sym eq true) then + + noe class symm end + + ! Define C2 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.nc2sym) loop c2symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c2sym_sta1_$ncount) + evaluate ($i1end = $c2sym_end1_$ncount) + evaluate ($chain1 = $c2sym_seg1_$ncount) + evaluate ($i2start = $c2sym_sta2_$ncount) + evaluate ($i2end = $c2sym_end2_$ncount) + evaluate ($chain2 = $c2sym_seg2_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + if ($diff1 ne $diff2) then + display CHAIN LENGTH FOR SYMMETRY RESTRAINTS DOES NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc2sym + + evaluate ($resid1 = $i1start) + evaluate ($resid2 = $i2end - $icount) + evaluate ($resid3 = $i2start) + evaluate ($resid4 = $i1end - $icount) + + noe + assign (resid $resid1 and (name CA or name P or name BB) and segid $chain1) + (resid $resid2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resid3 and (name CA or name P or name BB) and segid $chain2) + (resid $resid4 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + end + + evaluate ($icount = $icount + 1) + evaluate ($i1start = $i1start + 1) + evaluate ($i2start = $i2start + 1) + + end loop genc2sym + + end loop c2symloop + + + ! Define C3 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.nc3sym) loop c3symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c3sym_sta1_$ncount) + evaluate ($i1end = $c3sym_end1_$ncount) + evaluate ($chain1 = $c3sym_seg1_$ncount) + evaluate ($i2start = $c3sym_sta2_$ncount) + evaluate ($i2end = $c3sym_end2_$ncount) + evaluate ($chain2 = $c3sym_seg2_$ncount) + evaluate ($i3start = $c3sym_sta3_$ncount) + evaluate ($i3end = $c3sym_end3_$ncount) + evaluate ($chain3 = $c3sym_seg3_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc3sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + + noe + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + 2) + evaluate ($i1start = $i1start + 2) + evaluate ($i2start = $i2start + 2) + evaluate ($i3start = $i3start + 2) + + end loop genc3sym + + end loop c3symloop + + ! Define S3 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.ns3sym) loop s3symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $s3sym_sta1_$ncount) + evaluate ($i1end = $s3sym_end1_$ncount) + evaluate ($chain1 = $s3sym_seg1_$ncount) + evaluate ($i2start = $s3sym_sta2_$ncount) + evaluate ($i2end = $s3sym_end2_$ncount) + evaluate ($chain2 = $s3sym_seg2_$ncount) + evaluate ($i3start = $s3sym_sta3_$ncount) + evaluate ($i3end = $s3sym_end3_$ncount) + evaluate ($chain3 = $s3sym_seg3_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + eval ($istep = 4) + eval ($istop = $i1end - $istep) + while ($i1start < $istop) loop gens3sym + + evaluate ($resst11 = $i1start) + evaluate ($resst21 = $i1start+1) + evaluate ($resst12 = $i2start) + evaluate ($resst22 = $i2start+1) + evaluate ($resst13 = $i3start) + evaluate ($resst23 = $i3start+1) + + + noe + + assign (resid $resst11 and (name CA or name P or name BB) and segid $chain1) + (resid $resst12 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst12 and (name CA or name P or name BB) and segid $chain2) + (resid $resst13 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst21 and (name CA or name P or name BB) and segid $chain1) + (resid $resst22 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst22 and (name CA or name P or name BB) and segid $chain2) + (resid $resst23 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + + end loop gens3sym + + end loop s3symloop + + ! Define C4 symmetry restraints for symmetrical multimers + ! + eval ($istep = 10) + eval ($ncount = 0) + while ($ncount < $data.nc4sym) loop c4symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c4sym_sta1_$ncount) + evaluate ($i1end = $c4sym_end1_$ncount) + evaluate ($chain1 = $c4sym_seg1_$ncount) + evaluate ($i2start = $c4sym_sta2_$ncount) + evaluate ($i2end = $c4sym_end2_$ncount) + evaluate ($chain2 = $c4sym_seg2_$ncount) + evaluate ($i3start = $c4sym_sta3_$ncount) + evaluate ($i3end = $c4sym_end3_$ncount) + evaluate ($chain3 = $c4sym_seg3_$ncount) + evaluate ($i4start = $c4sym_sta4_$ncount) + evaluate ($i4end = $c4sym_end4_$ncount) + evaluate ($chain4 = $c4sym_seg4_$ncount) + + !first check that the chain lengths are equal for the four defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc4sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + + noe + + ! N to N sequential restraints to prevent anti-parallel arrangements + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + ! N to C sequential restraints to assure planarity + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + assign (resid $resen1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resen2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resen2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resen3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resen3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resen4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resen4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resen1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + + end loop genc4sym + + end loop c4symloop + + + ! Define C5 symmetry restraints for symmetrical multimers + ! + eval ($istep = 4) + eval ($ncount = 0) + while ($ncount < $data.nc5sym) loop c5symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c5sym_sta1_$ncount) + evaluate ($i1end = $c5sym_end1_$ncount) + evaluate ($chain1 = $c5sym_seg1_$ncount) + evaluate ($i2start = $c5sym_sta2_$ncount) + evaluate ($i2end = $c5sym_end2_$ncount) + evaluate ($chain2 = $c5sym_seg2_$ncount) + evaluate ($i3start = $c5sym_sta3_$ncount) + evaluate ($i3end = $c5sym_end3_$ncount) + evaluate ($chain3 = $c5sym_seg3_$ncount) + evaluate ($i4start = $c5sym_sta4_$ncount) + evaluate ($i4end = $c5sym_end4_$ncount) + evaluate ($chain4 = $c5sym_seg4_$ncount) + evaluate ($i5start = $c5sym_sta5_$ncount) + evaluate ($i5end = $c5sym_end5_$ncount) + evaluate ($chain5 = $c5sym_seg5_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + evaluate ($diff5 = $i5end - $i5start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff4 ne $diff5) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc5sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resst5 = $i5start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + evaluate ($resen5 = $i5end - $icount) + + noe + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + evaluate ($i5start = $i5start + $istep) + + end loop genc5sym + + end loop c5symloop + + ! Define C6 symmetry restraints for symmetrical multimers + ! + eval ($istep = 10) + eval ($ncount = 0) + while ($ncount < $data.nc6sym) loop c6symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c6sym_sta1_$ncount) + evaluate ($i1end = $c6sym_end1_$ncount) + evaluate ($chain1 = $c6sym_seg1_$ncount) + evaluate ($i2start = $c6sym_sta2_$ncount) + evaluate ($i2end = $c6sym_end2_$ncount) + evaluate ($chain2 = $c6sym_seg2_$ncount) + evaluate ($i3start = $c6sym_sta3_$ncount) + evaluate ($i3end = $c6sym_end3_$ncount) + evaluate ($chain3 = $c6sym_seg3_$ncount) + evaluate ($i4start = $c6sym_sta4_$ncount) + evaluate ($i4end = $c6sym_end4_$ncount) + evaluate ($chain4 = $c6sym_seg4_$ncount) + evaluate ($i5start = $c6sym_sta5_$ncount) + evaluate ($i5end = $c6sym_end5_$ncount) + evaluate ($chain5 = $c6sym_seg5_$ncount) + evaluate ($i6start = $c6sym_sta6_$ncount) + evaluate ($i6end = $c6sym_end6_$ncount) + evaluate ($chain6 = $c6sym_seg6_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + evaluate ($diff5 = $i5end - $i5start) + evaluate ($diff6 = $i6end - $i6start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff4 ne $diff5) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff5 ne $diff6) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc6sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resst5 = $i5start) + evaluate ($resst6 = $i6start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + evaluate ($resen5 = $i5end - $icount) + evaluate ($resen6 = $i6end - $icount) + + noe + + ! Around the C6 ring + ! N to N sequential restraints to prevent anti-parallel arrangements + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + ! N to C sequential restraints to assure planarity + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + ! Triples + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + evaluate ($i5start = $i5start + $istep) + evaluate ($i6start = $i6start + $istep) + + end loop genc6sym + + end loop c6symloop + + + noe + potential symm symmetry + scale symm $Data.ksym + sqconstant symm 1.0 + sqexponent symm 2 + soexponent symm 1 + rswitch symm 0.5 + sqoffset symm 0.0 + asymptote symm 1.0 + end + +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1d7fc880e06e040a41c2519abe74ddd11a97a2fa --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/emref/defaults.yaml @@ -0,0 +1,4652 @@ +# +# Group molecule +# +mol_fix_origin_1: + default: false + type: boolean + title: Fix molecule + short: Fixes the molecule in its original position. + long: Fixes the molecule in its original position. + group: 'molecule' + explevel: expert +mol_shape_1: + default: false + type: boolean + title: Is the molecule a shape? + short: Defines a molecule as a shape. + long: Defines a molecule as a shape, which is a collection of beads. + group: 'molecule' + explevel: easy +# +# Group distance restraints +# +ambig_fname: + default: '' + type: file + title: Ambiguous distance restraints filename + short: Filename of the ambiguous distance restraints file + long: Filename of the ambiguous distance restraints file. By default 50% of those restraints will be randomly discared. + This can be changed/turned off and is controlled by the randremoval and npart parameters. + Note that this file can contain both ambiguous and unambiguous restraints. + group: 'distance restraints' + explevel: easy +previous_ambig: + default: false + type: boolean + title: Boolean condition on the previous ambiguous distance restraints file + short: Boolean condition on the previous ambiguous distance restraints file. + If true, use the the restraint information coming from the previous CNS module. If false, don't use previous information. + long: Boolean condition on the ambiguous distance restraints file. + If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. + If false, don't use previous information. + group: 'distance restraints' + explevel: expert +unambig_fname: + default: '' + type: file + title: Unambiguous restraints filename + short: Filename of the unambiguous distance restraints file + long: Filename of the unambiguous distance restraints file. All restraints in that file will be used. + Note that this file can contain both ambiguous and unambiguous restraints. + group: 'distance restraints' + explevel: easy +hbond_fname: + default: '' + type: file + title: H-bond restraints filename + short: Filename of the hydrogen bond distance restraints file + long: Filename of the hydrogen bond distance restraints file. Note that this file can contain any type of distance restraints. + group: 'distance restraints' + explevel: easy +ambig_scale: + default: 50 + type: integer + min: 0 + max: 1000 + title: Force constant for ambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname. + long: Force constant applied to the distance restraints defined in ambig_fname. + group: 'distance restraints' + explevel: expert +unambig_scale: + default: 50 + type: integer + min: 0 + max: 1000 + title: Force constant for unambiguous distance restraints + short: Force constant applied to the distance restraints defined in unambig_fname. + long: Force constant applied to the distance restraints defined in unambig_fname. + group: 'distance restraints' + explevel: expert +hbond_scale: + default: 50 + type: integer + min: 0 + max: 1000 + title: Force constant for hbonds distance restraints + short: Force constant applied to the distance restraints defined in hbond_fname. + long: Force constant applied to the distance restraints defined in hbond_fname. + group: 'distance restraints' + explevel: expert +randremoval: + default: true + type: boolean + title: Random removal of ambiguous restraints + short: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. + long: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. + The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. + The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart. + group: 'distance restraints' + explevel: expert +npart: + default: 2 + type: integer + min: 1 + max: 20 + title: Number partitions for ambiguous restraints + short: Number of sets into which to randomly partition the ambiguous restraints. + long: Number of sets into which to randomly partition the ambiguous restraints. + The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. + The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart. + group: 'distance restraints' + explevel: expert +contactairs: + default: false + type: boolean + title: Contact restraints + short: Contact restraints between molecules + long: Contact restraints between molecules. These are defined as ambiguous distance restraint + between each residue of a molecule and all residues of the other molecules with 5A from that residue. + This can be used to restraint the contacts between the interfaces. Note that this can generate a large number of ambiguous restraints + and slow down the computations + group: 'distance restraints' + explevel: expert +kcont: + default: 1.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Contact restraints force constant + short: Force constant applied to the contact restraints. + long: Force constant applied to the contact restraints. + group: 'distance restraints' + explevel: expert +# +# Group dihedral restraints +# +dihe_fname: + default: '' + type: file + title: Dihedral angle restraints filename + short: Filename of the Dihedral angle restraints file + long: Filename of the Dihedral angle restraints file. + group: 'dihedral restraints' + explevel: easy +dihedrals_on: + default: false + type: boolean + title: Use dihedral angle restraints + short: Turns on dihedral angle restraints. + long: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file. + group: 'dihedral restraints' + explevel: easy +dihedrals_scale: + default: 200 + type: integer + min: 0 + max: 9999 + title: Force constant for dihedral angle restraints + short: Force constant applied to the dihedral angle restraints read from dihe_fname. + long: Force constant applied to the dihedral angle restraints read from dihe_fname. + group: 'dihedral restraints' + explevel: easy +ssdihed: + default: none + type: string + minchars: 0 + maxchars: 100 + choices: + - none + - all + - alpha + - alphabeta + title: Define automatically backbone dihedral angle restraints + short: If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions. + long: This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. + The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from + the measured angle in the input structure, and the error bound defined by the error_dih parameter. + Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or + only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations. + group: 'dihedral restraints' + explevel: easy +error_dih: + default: 10 + type: integer + min: 0 + max: 180 + title: Force constant for backbone dihedral angle restraints + short: Force constant for backbone dihedral angle restraints (ssdihed option) + long: Force constant for backbone dihedral angle restraints (ssdihed option) + group: 'dihedral restraints' + explevel: easy +# +# Group other restraints +# +dnarest_on: + default: false + type: boolean + title: Restrain the DNA conformation + short: Automatically creates restraints to maintain the conformation of DNA/RNA + long: "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. + The following restraints will be automatically defined: + - single base planarity + - sugar pucker + - phosphate backbone diherdral angle restraints + - Watson-Crick base pairing" + group: 'other restraints' + explevel: easy +# +# Group symmetry +# +sym_on: + default: false + type: boolean + title: Symmetry restraints + short: Enables symmetry restraints + long: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 supported) + and the segments to which those apply must be defined. In addition a custom symmetry restraint file can be supplied (symrest_fname). + group: 'symmetry' + explevel: expert +ksym: + default: 10.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Force constant for symmetry restraints + short: Force constant for symmetry restraints + long: Force constant for symmetry restraints + group: 'symmetry' + explevel: expert +symtbl_fname: + default: '' + type: file + title: Custom symmetry restraints filename + short: Filename of the custom symmetry restraints file + long: Filename of the custom symmetry restraints file. + group: 'symmetry' + explevel: expert +nc2sym: + default: 0 + type: integer + min: 0 + max: 40 + title: Number of C2 symmetry restraints + short: Defines the number of C2 symmetry restraints. + long: Defines the number of C2 symmetry restraints. + For each, a pair of segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c2sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C2 symmetry segment + long: Residue number of first residue in the first C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C2 symmetry segment + long: Residue number of last residue in the first C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C2 segment + short: Segment ID of first C2 segment + long: Segment ID of first C2 segment + group: 'symmetry' + explevel: expert +c2sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C2 symmetry segment + long: Residue number of first residue in the second C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C2 symmetry segment + long: Residue number of last residue in the second C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C2 segment + short: Segment ID of second C2 segment + long: Segment ID of second C2 segment + group: 'symmetry' + explevel: expert +nc3sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C3 symmetry restraints + short: Defines the number of C3 symmetry restraints. + long: Defines the number of C3 symmetry restraints. + For each, three segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c3sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C3 symmetry segment + long: Residue number of first residue in the first C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C3 symmetry segment + long: Residue number of last residue in the first C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C3 segment + short: Segment ID of first C3 segment + long: Segment ID of first C3 segment + group: 'symmetry' + explevel: expert +c3sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C3 symmetry segment + long: Residue number of first residue in the second C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C3 symmetry segment + long: Residue number of last residue in the second C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C3 segment + short: Segment ID of second C3 segment + long: Segment ID of second C3 segment + group: 'symmetry' + explevel: expert +c3sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C3 symmetry segment + long: Residue number of first residue in the third C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C3 symmetry segment + long: Residue number of last residue in the third C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C3 segment + short: Segment ID of third C3 segment + long: Segment ID of third C3 segment + group: 'symmetry' + explevel: expert +nc4sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C4 symmetry restraints + short: Defines the number of C4 symmetry restraints. + long: Defines the number of C4 symmetry restraints. + For each, four segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c4sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C4 symmetry segment + long: Residue number of first residue in the first C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C4 symmetry segment + long: Residue number of last residue in the first C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C4 segment + short: Segment ID of first C4 segment + long: Segment ID of first C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C4 symmetry segment + long: Residue number of first residue in the second C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C4 symmetry segment + long: Residue number of last residue in the second C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C4 segment + short: Segment ID of second C4 segment + long: Segment ID of second C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C4 symmetry segment + long: Residue number of first residue in the third C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C4 symmetry segment + long: Residue number of last residue in the third C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C4 segment + short: Segment ID of third C4 segment + long: Segment ID of third C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C4 symmetry segment + long: Residue number of first residue in the fourth C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C4 symmetry segment + long: Residue number of last residue in the fourth C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C4 segment + short: Segment ID of fourth C4 segment + long: Segment ID of fourth C4 segment + group: 'symmetry' + explevel: expert +nc5sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C5 symmetry restraints + short: Defines the number of C5 symmetry restraints. + long: Defines the number of C5 symmetry restraints. + For each, five segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c5sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C5 symmetry segment + long: Residue number of first residue in the first C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C5 symmetry segment + long: Residue number of last residue in the first C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C5 segment + short: Segment ID of first C5 segment + long: Segment ID of first C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C5 symmetry segment + long: Residue number of first residue in the second C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C5 symmetry segment + long: Residue number of last residue in the second C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C5 segment + short: Segment ID of second C5 segment + long: Segment ID of second C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C5 symmetry segment + long: Residue number of first residue in the third C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C5 symmetry segment + long: Residue number of last residue in the third C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C5 segment + short: Segment ID of third C5 segment + long: Segment ID of third C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C5 symmetry segment + long: Residue number of first residue in the fourth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C5 symmetry segment + long: Residue number of last residue in the fourth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C5 segment + short: Segment ID of fourth C5 segment + long: Segment ID of fourth C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fifth C5 symmetry segment + long: Residue number of first residue in the fifth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fifth C5 symmetry segment + long: Residue number of last residue in the fifth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg5_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fifth C5 segment + short: Segment ID of fifth C5 segment + long: Segment ID of fifth C5 segment + group: 'symmetry' + explevel: expert +nc6sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C6 symmetry restraints + short: Defines the number of C6 symmetry restraints. + long: Defines the number of C6 symmetry restraints. + For each, six segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c6sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C6 symmetry segment + long: Residue number of first residue in the first C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C6 symmetry segment + long: Residue number of last residue in the first C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C6 segment + short: Segment ID of first C6 segment + long: Segment ID of first C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C6 symmetry segment + long: Residue number of first residue in the second C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C6 symmetry segment + long: Residue number of last residue in the second C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C6 segment + short: Segment ID of second C6 segment + long: Segment ID of second C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C6 symmetry segment + long: Residue number of first residue in the third C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C6 symmetry segment + long: Residue number of last residue in the third C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C6 segment + short: Segment ID of third C6 segment + long: Segment ID of third C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C6 symmetry segment + long: Residue number of first residue in the fourth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C6 symmetry segment + long: Residue number of last residue in the fourth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C6 segment + short: Segment ID of fourth C6 segment + long: Segment ID of fourth C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fifth C6 symmetry segment + long: Residue number of first residue in the fifth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fifth C6 symmetry segment + long: Residue number of last residue in the fifth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg5_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fifth C6 segment + short: Segment ID of fifth C6 segment + long: Segment ID of fifth C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the sixth C6 symmetry segment + long: Residue number of first residue in the sixth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the sixth C6 symmetry segment + long: Residue number of last residue in the sixth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg6_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of sixth C6 segment + short: Segment ID of sixth C6 segment + long: Segment ID of sixth C6 segment + group: 'symmetry' + explevel: expert +ns3sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of S3 symmetry restraints + short: Defines the number of S3 symmetry restraints. + long: Defines the number of S3 symmetry restraints. + For each, three segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +s3sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first S3 symmetry segment + long: Residue number of first residue in the first S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first S3 symmetry segment + long: Residue number of last residue in the first S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first S3 segment + short: Segment ID of first S3 segment + long: Segment ID of first S3 segment + group: 'symmetry' + explevel: expert +s3sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second S3 symmetry segment + long: Residue number of first residue in the second S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second S3 symmetry segment + long: Residue number of last residue in the second S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second S3 segment + short: Segment ID of second S3 segment + long: Segment ID of second S3 segment + group: 'symmetry' + explevel: expert +s3sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third S3 symmetry segment + long: Residue number of first residue in the third S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third S3 symmetry segment + long: Residue number of last residue in the third S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third S3 segment + short: Segment ID of third S3 segment + long: Segment ID of third S3 segment + group: 'symmetry' + explevel: expert +ncs_on: + default: false + type: boolean + title: Non-crystallographic symmetry restraints + short: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. + long: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. + This does not apply any symmetry between the two molecules but rather defines restraints such as the RMSD between those is 0. + group: 'symmetry' + explevel: expert +kncs: + default: 1.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Force constant for non-crystallographic restraints + short: Force constant for non-crystallographic restraints + long: Force constant for non-crystallographic restraints + group: 'symmetry' + explevel: expert +nncs: + default: 0 + type: integer + min: 0 + max: 100 + title: Number of non-crystallographic symmetry restraints + short: Number of non-crystallographic symmetry restraints (NCS). + long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined. + Note that those must contain exactly the same residues/atom combinations. + group: 'symmetry' + explevel: hidden +ncs_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first NCS segment + long: Residue number of first residue in the first NCS segment + group: 'symmetry' + explevel: expert +ncs_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first NCS segment + long: Residue number of last residue in the first NCS segment + group: 'symmetry' + explevel: expert +ncs_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 100 + title: Segment ID of first NCS segment + short: Segment ID of first NCS segment + long: Segment ID of first NCS segment + group: 'symmetry' + explevel: expert +ncs_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second NCS segment + long: Residue number of first residue in the second NCS segment + group: 'symmetry' + explevel: expert +ncs_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second NCS segment + long: Residue number of last residue in the second NCS segment + group: 'symmetry' + explevel: expert +ncs_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 100 + title: Segment ID of second NCS segment + short: Segment ID of second NCS segment + long: Segment ID of second NCS segment + group: 'symmetry' + explevel: expert +# +# Group scoring +# +w_air: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the distance restraint energy + short: Weight of the distance restraints energy in the scoring function + long: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. + group: 'scoring' + explevel: expert +w_bsa: + default: 0.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the buried surface area term + short: Weight of the buried surface area term in the scoring function + long: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. + group: 'scoring' + explevel: expert +w_cdih: + default: 0.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the dihedral angle restraint energy + short: Weight of the dihedral angle restraints energy in the scoring function + long: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + group: 'scoring' + explevel: expert +w_dani: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the relaxation anisotropy (DANI) restraint energy + short: Weight of the relaxation anisotropy (DANI) restraint energy + long: Weight of the relaxation anisotropy (DANI) restraint energy + group: 'scoring' + explevel: hidden +w_deint: + default: 0.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the interaction energy term + short: Weight of the interaction energy term + long: Weight of the interaction energy term calculated as the difference in total energy of the complex and of the separate components + group: 'scoring' + explevel: hidden +w_desolv: + default: 1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the desolvation energy term + short: Weight of the desolvation energy term in the scoring function + long: Weight of the desolvation energy term in the scoring function. + Note that the desolvation energy is only used for scoring. + group: 'scoring' + explevel: expert +w_elec: + default: 0.2 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the intermolecular electrostatic energy + short: Weight of the intermolecular electrostatic energy in the scoring function + long: Weight of the intermolecular electrostatic energy in the scoring function. + Note that this does not affect the electostatic energy during the EM minimization. + group: 'scoring' + explevel: expert +w_lcc: + default: -10000.0 + type: float + min: -10000.0 + max: 0 + precision: 3 + title: Weight of the EM local correlation coefficient + short: Weight of the EM local correlation coefficient + long: Weight of the EM local correlation coefficient + group: 'scoring' + explevel: hidden +w_rg: + default: 1.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the radius of gyration restraint energy + short: Weight of the radius of gyration restraint energy + long: Weight of the radius of gyration restraint energy + group: 'scoring' + explevel: hidden +w_sani: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (SANI) restraint energy + short: Weight of the residual dipolar coupling (SANI) restraint energy + long: Weight of the residual dipolar coupling (SANI) restraint energy + group: 'scoring' + explevel: hidden +w_sym: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the symmetry restraint energy + short: Weight of the symmetry restraints energy in the scoring function + long: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + group: 'scoring' + explevel: expert +w_vdw: + default: 1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the intermolecular van der Waals energy + short: Weight of the intermolecular van der Waals energy in the scoring function + long: Weight of the intermolecular van der Waals energy in the scoring function. + Note that this does not affect the van der Waals energy during the EM minimization. + group: 'scoring' + explevel: expert +w_vean: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (VEAN) restraint energy + short: Weight of the residual dipolar coupling (VEAN) restraint energy + long: Weight of the residual dipolar coupling (VEAN) restraint energy + group: 'scoring' + explevel: hidden +w_xpcs: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the pseudo contact shifts (XPCS) restraint energy + short: Weight of the pseudo contact shifts (XPCS) restraint energy + long: Weight of the pseudo contact shifts (XPCS) restraint energy + group: 'scoring' + explevel: hidden +w_xrdc: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (XRDC) restraint energy + short: Weight of the residual dipolar coupling (XRDC) restraint energy + long: Weight of the residual dipolar coupling (XRDC) restraint energy + group: 'scoring' + explevel: hidden +w_zres: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the Z-restraining potential energy + short: Weight of the Z-restraining potential energy + long: Weight of the Z-restraining potential energy + group: 'scoring' + explevel: hidden +# +# Group force field +# +ligand_param_fname: + default: '' + type: file + title: Custom ligand parameter file + short: Ligand parameter file in CNS format + long: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK + group: 'force field' + explevel: easy +ligand_top_fname: + default: '' + type: file + title: Custom ligand topology file + short: Ligand topology file in CNS format + long: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK + group: 'force field' + explevel: easy +elecflag: + default: true + type: boolean + title: Include electrostatics energy + short: Include electrostatics energy during the calculations. + long: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. + group: 'force field' + explevel: easy +dielec: + default: cdie + type: string + minchars: 0 + maxchars: 4 + choices: + - cdie + - rdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + short: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. + long: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. + A distance dependent dielectric constant will effectively scale down the electrostatic energy + by having a 1/r**2 dependency instead of 1/r + group: 'force field' + explevel: expert +epsilon: + default: 1.0 + type: float + min: 1 + max: 78 + precision: 1 + title: Dielectric constant + short: Dielectric constant for the electrostatic Coulomb energy term. + long: Dielectric constant for the electrostatic Coulomb energy term. + group: 'force field' + explevel: expert +dihedflag: + default: true + type: boolean + title: Use torsion angle dihedral energy term + short: Turns on the torsion angle dihedral energy terms of the force field. + long: Turns on the torsion angle dihedral energy terms of the force field. + group: 'force field' + explevel: expert +# +# Group sampling +# +sampling_factor: + default: 1 + type: integer + min: 1 + max: 500 + title: Sampling factor for each starting model + short: This parameter control how many times a model will be refined. + long: This parameter control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation. + group: 'sampling' + explevel: expert +max_nmodels: + default: 50000 + type: integer + min: 1 + max: 100000 + title: Maximum number of models to refine + short: This parameter controls the maximum number of models to refine. + long: This parameter controls the maximum number of models to refine. + group: 'sampling' + explevel: expert +nemsteps: + default: 200 + type: integer + min: 0 + max: 10000 + title: Number of EM steps + short: Number of energy minimisation steps to perform. + long: Number of energy minimisation steps to perform. Note that the effective number might be smaller if the minimisation converges earlier. + group: 'sampling' + explevel: expert +iniseed: + default: 917 + type: integer + min: 0 + max: 9999999999999999 + title: Random seed + short: Random seed used in CNS to initialize the random seed function + long: Random seed used in CNS to initialize the random seed function + group: 'sampling' + explevel: guru +keepwater: + default: false + type: boolean + title: Write water molecules to output file + short: Write water molecules if present to the output file. + long: Write water molecules if present to the output file. + group: 'sampling' + explevel: guru +tolerance: + default: 5 + type: integer + min: 0 + max: 99 + precision: 3 + title: Failure tolerance percentage + short: Percentage of allowed failures for a module to successfully complete + long: Percentage of allowed failures for a module to successfully complete + group: 'module' + explevel: expert +log_level: + default: quiet + type: string + minchars: 0 + maxchars: 100 + choices: + - verbose + - normal + - quiet + title: Log level verbosity for CNS + short: Set the log level verbosity for CNS + long: CNS, the computational engine used by HADDOCK can generate a lot of output + messages. This parameter controls the verbosity of CNS (verbose, normal or quiet). + group: module + explevel: guru +# +# Group flexibility +# +# +# Semi-flexible segments +# +nseg1: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg2: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg3: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg4: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg5: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg6: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg7: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_7_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_7_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg8: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_8_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_8_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg9: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_9_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_9_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg10: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_10_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_10_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg11: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_11_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_11_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg12: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_12_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_12_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg13: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_13_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_13_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg14: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_14_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_14_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg15: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_15_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_15_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg16: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_16_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_16_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg17: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_17_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_17_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg18: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_18_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_18_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg19: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_19_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_19_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg20: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_20_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_20_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +# +# Fully flexible segments +# +nfle: + default: 0 + type: integer + min: 0 + max: 1000 + title: Number of fully flexible segments + short: This defines the number of fully flexible segments. + long: This parameter defines the number of fully flexible segments for all molecules. + If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, + followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables. + group: 'flexibility' + explevel: hidden +fle_sta_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the fully flexible segment. + long: Residue number defining the start of this (1st) fully flexible segment. + group: 'flexibility' + explevel: expert +fle_end_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: End residue number + short: Residue number defining the end of the fully flexible segment. + long: Residue number defining the end of this (1st) fully flexible segment. + group: 'flexibility' + explevel: expert +fle_seg_1: + default: none + type: string + minchars: 1 + maxchars: 4 + title: Segment ID (segid) + short: Segment ID of the molecule for which this flexible segment is defined. + long: Segment ID of the molecule for which this (1st) flexible segment is defined. + group: 'flexibility' + explevel: expert +# +# Group interaction matrix +# +int_1_1: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_2: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_2: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_19_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_19_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_20_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and 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a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..bdbea226eb0275756c2c83b6ac20872ae876586f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/__init__.py @@ -0,0 +1,159 @@ +"""Flexible refinement with CNS. + +The ``[flexref]`` module (also known as ``it1`` stage in HADDOCK2.X series), +is a semi-flexible simulated annealing (SA) protocol based on molecular +dynamics in torsion angle space. + + +This semi-flexible SA consists of several stages: + +* High temperature rigid body molecular dynamics +* Rigid body SA +* Semi-flexible SA with flexible side-chains at the interface +* Semi-flexible SA with fully flexible interface (both backbone and side-chains) + +By default, only the interface regions is treated as flexible. It is automatically +defined based on the intermolecular contacts made. It is also possible to manually +define the semi-flexible regions, and also define fully flexible regions that are +allowed to move throughout the entire protocol from the high temperature rigid +body molecular dynamics on. + +The temperature and number of steps for the various stages can be tuned. +""" + +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import FilePath +from haddock.gear.haddockmodel import HaddockModel +from haddock.libs.libcns import prepare_cns_input, prepare_expected_pdb +from haddock.libs.libontology import PDBFile +from haddock.libs.libsubprocess import CNSJob +from haddock.modules import get_engine +from haddock.modules.base_cns_module import BaseCNSModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseCNSModule): + """HADDOCK3 module for flexible refinement.""" + + name = RECIPE_PATH.name + + def __init__( + self, order: int, path: Path, initial_params: FilePath = DEFAULT_CONFIG + ) -> None: + cns_script = Path(RECIPE_PATH, "cns", "flexref.cns") + super().__init__(order, path, initial_params, cns_script=cns_script) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm module is installed.""" + return + + def _run(self) -> None: + """Execute module.""" + # Pool of jobs to be executed by the CNS engine + jobs: list[CNSJob] = [] + + # Get the models generated in previous step + try: + models_to_refine = self.previous_io.retrieve_models() + except Exception as e: + self.finish_with_error(e) + + self.output_models: list[PDBFile] = [] + idx = 1 + sampling_factor = self.params["sampling_factor"] + if sampling_factor > 1: + self.log(f"sampling_factor={sampling_factor}") + if sampling_factor == 0: + self.log("[Warning] sampling_factor cannot be 0, setting it to 1") + sampling_factor = 1 + if sampling_factor > 100: + self.log("[Warning] sampling_factor is larger than 100") + + max_nmodels = self.params["max_nmodels"] + nmodels = len(models_to_refine) * sampling_factor + if nmodels > max_nmodels: + self.finish_with_error( + f"Too many models ({nmodels}) to refine, max_nmodels =" + f" {max_nmodels}. Please reduce the number of models or" + " decrease the sampling_factor." + ) + + # checking the ambig_fname: + try: + prev_ambig_fnames = [mod.restr_fname for mod in models_to_refine] + except Exception as e: # noqa:F841 + # cannot extract restr_fname info from tuples + prev_ambig_fnames = [None for model in models_to_refine] + + ambig_fnames = self.get_ambig_fnames(prev_ambig_fnames) + + model_idx = 0 + idx = 1 + for model in models_to_refine: + # assign ambig_fname + if ambig_fnames: + ambig_fname = ambig_fnames[model_idx] + else: + ambig_fname = self.params["ambig_fname"] + model_idx += 1 + + for _ in range(self.params["sampling_factor"]): + # prepare cns input + flexref_input = prepare_cns_input( + idx, + model, + self.path, + self.recipe_str, + self.params, + "flexref", + ambig_fname=ambig_fname, + native_segid=True, + debug=self.params["debug"], + seed=model.seed if isinstance(model, PDBFile) else None, + ) + + out_file = f"flexref_{idx}.out" + err_fname = f"flexref_{idx}.cnserr" + + # create the expected PDBobject + expected_pdb = prepare_expected_pdb(model, idx, ".", "flexref") + expected_pdb.restr_fname = ambig_fname + try: + expected_pdb.ori_name = model.file_name + except AttributeError: + expected_pdb.ori_name = None + self.output_models.append(expected_pdb) + + job = CNSJob(flexref_input, out_file, err_fname, envvars=self.envvars) + + jobs.append(job) + + idx += 1 + + # Run CNS Jobs + self.log(f"Running CNS Jobs n={len(jobs)}") + Engine = get_engine(self.params["mode"], self.params) + engine = Engine(jobs) + engine.run() + self.log("CNS jobs have finished") + + # Get the weights from the defaults + _weight_keys = ("w_vdw", "w_elec", "w_desolv", "w_air", "w_bsa") + weights = {e: self.params[e] for e in _weight_keys} + + for pdb in self.output_models: + if pdb.is_present(): + haddock_model = HaddockModel(pdb.file_name) + pdb.unw_energies = haddock_model.energies + + haddock_score = haddock_model.calc_haddock_score(**weights) + 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b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/calc_free-ene.cns @@ -0,0 +1,24 @@ +! calc_free-ene.cns +! Calculate the total energy of the separated components +! +! Script uses the store1 and store2 atom object, and COMP, REF and RMSD object +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +@MODULE:scale_intra_only.cns + +evaluate ($eintfree = 0.0) +@MODULE:flex_segment_back.cns +fix sele=(((attr store5 = 0) or resn ANI or resn DAN or resn XAN or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP*)) end + +minimize powell nstep=100 drop=10.0 nprint=25 end +fix sele=(not all) end +energy end +evaluate ($eintfree = $bond + $angl + $impr + $dihe + $vdw + $elec) + +display FREE MOLECULES INTERNAL ENERGY = $eintfree diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check-homomers.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check-homomers.cns new file mode 100644 index 0000000000000000000000000000000000000000..7faf7a4c90f49812724e0a5e217f380cba1b712f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check-homomers.cns @@ -0,0 +1,56 @@ +! check-homomers.cns +! check for homomeric complexes +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($homosymmetry = false) + +evaluate($n_moving_mol = 0) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop checkmol + evaluate ($ncount = $ncount + 1) + if ($mol_shape_$ncount eq false) then + evaluate($n_moving_mol = $n_moving_mol + 1) + end if +end loop checkmol + +if ($data.flags.sym eq true) then + if ($data.nc2sym > 0) then + if ($n_moving_mol = 2) then + evaluate ($homosymmetry = true) + end if + end if + if ($data.nc2sym = 6) then + if ($n_moving_mol = 4) then + evaluate ($homosymmetry = true) + end if + end if + if ($data.nc3sym > 0) then + if ($n_moving_mol = 3) then + evaluate ($homosymmetry = true) + end if + end if + if ($data.nc4sym > 0) then + if ($n_moving_mol = 4) then + evaluate ($homosymmetry = true) + end if + end if + if ($data.nc5sym > 0) then + if ($n_moving_mol = 5) then + evaluate ($homosymmetry = true) + end if + end if + if ($data.nc6sym > 0) then + if ($n_moving_mol = 6) then + evaluate ($homosymmetry = true) + end if + end if +end if + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check_coordinates.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check_coordinates.cns new file mode 100644 index 0000000000000000000000000000000000000000..d23c8e64804060c61ff6aeea38925dc8e61dc8d6 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/check_coordinates.cns @@ -0,0 +1,100 @@ +! check_coordinates.cns +! Check max/min coordinates for compatibility with PDB format +! +! *********************************************************************** +! * Copyright 2025 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +evaluate ($failure = false) + +!check for coordinates >9999.999 (max writable in PDB format) + +show max (x) (all) +evaluate ($maxcoor = $result) +show max (y) (all) +if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) +end if +show max (z) (all) +if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) +end if +if ($maxcoor gt 9999.999) then + evaluate ($failure = true) +end if + +!check for coordinates <-999.999 (min writable in PDB format) + +show min (x) (all) +evaluate ($mincoor = $result) +show min (y) (all) +if ($result lt $mincoor) then + evaluate ($maxcoor = $result) +end if +show min (z) (all) +if ($result lt $mincoor) then + evaluate ($mincoor = $result) +end if +if ($mincoor lt -999.999) then + evaluate ($failure = true) +end if + +!if problem detected try correcting it by centering the system around 4500,4500,4500 +!but only if no EM restraints are used + +if ($failure eq true) then + if ($data.flags.em eq false) then + + evaluate ($xc = 0.0) + evaluate ($yc = 0.0) + evaluate ($zc = 0.0) + show ave (x) (all) + evaluate ($xc = 4500 - $result) + show ave (y) (all) + evaluate ($yc = 4500 - $result) + show ave (z) (all) + evaluate ($zc = 4500 -$result) + + do (x = x + $xc) (all) + do (y = y + $yc) (all) + do (z = z + $zc) (all) + + evaluate ($failure = false) + evaluate ($maxcoor = -999) + evaluate ($mincoor = 9999) + !check again for coordinates >9999.999 (max writable in PDB format) + show max (x) (all) + evaluate ($maxcoor = $result) + show max (y) (all) + if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) + end if + show max (z) (all) + if ($result gt $maxcoor) then + evaluate ($maxcoor = $result) + end if + if ($maxcoor gt 9999.999) then + evaluate ($failure = true) + end if + + !check for coordinates <-999.999 (min writable in PDB format) + show min (x) (all) + evaluate ($mincoor = $result) + show min (y) (all) + if ($result lt $mincoor) then + evaluate ($maxcoor = $result) + end if + show min (z) (all) + if ($result lt $mincoor) then + evaluate ($mincoor = $result) + end if + if ($mincoor lt -999.999) then + evaluate ($failure = true) + end if + end if +end if + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/cm-restraints.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/cm-restraints.cns new file mode 100644 index 0000000000000000000000000000000000000000..51a4b9e4a4ed699653e4e65c1ddaa729202f3628 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/cm-restraints.cns @@ -0,0 +1,131 @@ +! cm-restraints.cns +! Define center-of-mass restraints between molecules +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +!define center of mass restraints between all molecules +!using distance restraints between CA, BB or N1 atoms with center averaging + +evaluate ($ncount = 0) + +! store original coordinates +do (refx = x) (all) +do (refy = y) (all) +do (refz = z) (all) + +while ($ncount < $data.ncomponents) loop nloop1 + evaluate ($ncount = $ncount +1) + evaluate ($dim_$ncount = 0.0) + + !orient molecule + coor orient sele=(segid $prot_segid_$ncount) end + + ! find dimensions + show max (x) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($xdim = $result) + show max (y) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($ydim = $result) + show max (z) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($zdim = $result) + show min (x) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($xdim = $xdim - $result) + show min (y) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($ydim = $ydim - $result) + show min (z) (segid $prot_segid_$ncount and (name CA or name BB or name N1)) + evaluate ($zdim = $zdim - $result) + + evaluate ($corr = max($xdim,$ydim)) + evaluate ($corr = max($corr,$zdim)) + + if ($data.cmtight eq false) then + ! use average of all three dimensions + evaluate ($dim_$ncount = ($xdim + $ydim + $zdim)/6.0) + else + ! use only the average of the smallest two dimensions + evaluate ($dim_$ncount = ($xdim + $ydim + $zdim - $corr)/4.0) + end if + + ! check for anything not protein + do (store6 = 0) (all) + do (store6 = 1) (segid $prot_segid_$ncount and (name CA or name BB)) + show sum (store6) (all) + if ($result eq 0) then + ! we are dealing with a ligand, nucleic acid or glycan -> set dimension to 0 + evaluate ($dim_$ncount = 0.0) + end if + +end loop nloop1 + +! restore original coordinates +do (x = refx) (all) +do (y = refy) (all) +do (z = refz) (all) + +eval($nchain = 0) +do (store9 = 0) (all) +do (store9 = 1) (name CA or name BB or name N1) +while ($nchain < $data.ncomponents) loop nloop0 + eval($nchain = $nchain + 1) + show sum (store9) (segid $prot_segid_$nchain) + if ($result < 3) then + evaluate ($selat$nchain = 0 ) + else + evaluate ($selat$nchain = 1 ) + end if +end loop nloop0 + +eval($nchain1 = 0) +noe + class contact + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + eval($nchain2 = $nchain1 ) + if ($mol_shape_$nchain1 eq false) then + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + if ($mol_shape_$nchain2 eq false) then + if ($data.cmtight eq false) then + eval($cm_dist = $dim_$nchain1 + $dim_$nchain2) + else + eval($cm_dist = ($dim_$nchain1 + $dim_$nchain2)/2 ) + end if + if ($selat$nchain1 = 1) then + if ($selat$nchain2 = 1) then + assign (segid $prot_segid_$nchain1 and ( name CA or name BB or name N1 )) + (segid $prot_segid_$nchain2 and ( name CA or name BB or name N1 )) $cm_dist $cm_dist 1.0 + else + assign (segid $prot_segid_$nchain1 and ( name CA or name BB or name N1 )) + (segid $prot_segid_$nchain2) $cm_dist $cm_dist 1.0 + end if + else + if ($selat$nchain2 = 1) then + assign (segid $prot_segid_$nchain1) + (segid $prot_segid_$nchain2 and ( name CA or name BB or name N1 )) $cm_dist $cm_dist 1.0 + else + assign (segid $prot_segid_$nchain1) + (segid $prot_segid_$nchain2) $cm_dist $cm_dist 1.0 + end if + end if + end if + end loop nloop2 + end if + end loop nloop1 + + averaging contact center + scale contact $data.kcm + sqconstant contact 1.0 + sqexponent contact 2 + soexponent contact 1 + rswitch contact 1.0 + sqoffset contact 0.0 + asymptote contact 2.0 + msoexponent contact 1 + masymptote contact -0.1 + mrswitch contact 1.0 +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/contactairs.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/contactairs.cns new file mode 100644 index 0000000000000000000000000000000000000000..aa8028ab7d3b40e56df692afec9eda66b1a45c68 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/contactairs.cns @@ -0,0 +1,27 @@ +! contactairs.cns +! Define ambiguous distance restraints between residues at interfaces +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +eval($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + for $id in id (tag and segid $prot_segid_$nchain1 + and (not (segid $prot_segid_$nchain1 or resn ANI or resn DAN or resn XAN + or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM) around 5.0)) loop defnoe1 + show (resid) (id $id) + evaluate ($inres = $result) + noe + assign (resid $inres and segid $prot_segid_$nchain1) + (byres (not (segid $prot_segid_$nchain1 or resn ANI or resn DAN or resn XAN + or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM) + and (segid $prot_segid_$nchain1) around 5.0)) 2.0 2.0 0.0 + end + end loop defnoe1 +end loop nloop1 diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/covalions.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/covalions.cns new file mode 100644 index 0000000000000000000000000000000000000000..85d6417f7c77bc719af19199aa24d2b197c4cd71 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/covalions.cns @@ -0,0 +1,83 @@ +! covalions.cns +! Add a covalent bond between an ion and its closest coordinating atom +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +evaluate ($pcount = 0) +for $id1 in id ( name "LI+1" or name "F-1" or name "NA+1" or name "MG+2" or name "AL+3" + or name "CL-1" or name "K+1" or name "CA+2" or name "V+2" or name "V+3" + or name "CR+2" or name "CR+3" or name "MN+2" or name "MN+3" or name "FE+2" + or name "FE+3" or name "NI+2" or name "CO+2" or name "CO+3" or name "CU+1" + or name "CU+2" or name "ZN+2" or name "BR-1" or name "SR+2" or name "MO+3" + or name "AG+1" or name "CD+2" or name "I-1" or name "CS+2" or name "HO+3" + or name "YB+2" or name "YB+3" or name "OS+4" or name "IR+3" or name "PT+2" + or name "AU+1" or name "AU+2" or name "HG+1" or name "HG+2" or name "PB+2" + or name "U+3" or name "U+4" or name "ZN+1" or name "ZN" ) loop ions + + show (segid) (id $id1) + evaluate ($segid1=$result) + show (resid) (id $id1) + evaluate ($resid1=$result) + show (resname) (id $id1) + evaluate ($resname1=$result) + show (name) (id $id1) + evaluate ($name1=$result) + show (chem) (id $id1) + evaluate ($chem1=$result) + + evaluate ($mindis = 7.5) + evaluate ($minid = 0) + for $id2 in id ( (name O* or name S* or name N*) and (id $id1) around $mindis and + (resn ACE or resn ALA or resn ALY or resn ARG or resn ASN or resn ASH or resn ASP or + resn CSP or resn CTN or resn CYC or resn CYF or resn CYM or resn CYS or resn DDZ or + resn GLN or resn GLH or resn GLU or resn GLY or resn HIS or resn HY3 or resn HYP or + resn ILE or resn LEU or resn LYS or resn M3L or resn MLY or resn MLZ or resn MET or + resn MSE or resn NEP or resn NME or resn PHE or resn PNS or resn PRO or resn PTR or + resn QSR or resn SEP or resn SER or resn SEC or resn THR or resn TOP or resn TRP or + resn TYP or resn TYR or resn TYS or resn VAL or resn A or resn C or resn G or + resn T or resn DA or resn DC or resn DG or resn DT or resn DJ )) loop search + + pick bond (id $id1) (id $id2) geometry + + if ( $result < $mindis) then + evaluate ($mindis = $result) + evaluate ($minid = $id2) + end if + + end loop search + + if ($minid> 0) then + show (segid) (id $minid) + evaluate ($segid2=$result) + show (resid) (id $minid) + evaluate ($resid2=$result) + show (resname) (id $minid) + evaluate ($resname2=$result) + show (name) (id $minid) + evaluate ($name2=$result) + show (chem) (id $minid) + evaluate ($chem2=$result) + + evaluate ($pat1 = "1"+$name1) + evaluate ($pat2 = "2"+$name2) + evaluate ($pcount = $pcount + 1) + evaluate ($pname = "cb" + encode($pcount)) + topology + presidue $pname ! Patch to add a covalent bond between two atoms + add bond $pat1 $pat2 + end + end + patch $pname refe=1=(resid $resid1 and segid $segid1) refe=2=(resid $resid2 and segid $segid2) end + display COVALION: ADDED ONE COVALENT BOND BETWEEN $name1 $resid1 AND $name2 $resname2 $resid2 + end if + + param bond $chem1 $chem2 0.0 $mindis end + +end loop ions + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/def_solv_param.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/def_solv_param.cns new file mode 100644 index 0000000000000000000000000000000000000000..5a9e07a042e08d15d5b98d859fa199151e7b4a43 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/def_solv_param.cns @@ -0,0 +1,105 @@ +! def_solv_param.cns +! Define atomic solvation parameters +! Original valus taken from Fernandez-Recio et al. JMB 335:843 (2004) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +evaluate ($arofac = 6.26) +evaluate ($alifac = 1.27) +evaluate ($polfac = 2.30) + + +do (store1 = 0.0000) (all) +do (store1 = 0.0151 * $alifac) (name C*) +do (store1 = 0.0176 * $arofac) ((name CG* or name CD* or name CE* or name CH* or name CZ*) and (resn PHE or resn TYR or resn HIS or resn TRP)) +do (store1 = -0.0170 * $polfac) (name N*) +do (store1 = -0.0548 * $polfac) (name NT* or (name NZ* and resn LYS)) +do (store1 = -0.0273 * $polfac) (name NH* and resn ARG) +do (store1 = -0.0136 * $polfac) (name O*) +do (store1 = -0.0185 * $polfac) (name OG* or name OH) +do (store1 = -0.0299 * $polfac) ((name OD* and resn ASP) or (name OE* and resn GLU)) +do (store1 = 0.0112 * $polfac) (name S*) +do (store1 = 0.0022 * $polfac) ((name S* and attr charge = -0.3) or (name SD and resn MET)) +do (store1 = 0.0000) (name SHA) + +! +! CG parameters matched from the original terms +! +! Edesolv_aa +! ASP_cg = _________________________ +! ASA_cg +! +! ASA_cg and Edesol_aa calculated on a GGXGG peptide +! accuracy=0.0025, rh2o=1.4, delete H, sele=(resn X) +! +! e.g. BB bead alanine +! +! BB = CA + C + N + O +! ASA_cg = 176.4940 +! Edesolv_aa = -1.8889 +! +! ASP_cg = -0.0107 +! +! Charleen Don (2012), JR (2014), Jorge Roel (2017) +! +! + +do (store1 = 0.0000) (name BB or name SC*) +! Backbone beads +do (store1 = -0.0107) (name BB and resn ALA) +do (store1 = -0.0089) (name BB and resn GLY) +do (store1 = -0.0153) (name BB and resn ILE) +do (store1 = -0.0158) (name BB and resn VAL) +do (store1 = -0.0046) (name BB and resn PRO) +do (store1 = -0.0137) (name BB and resn ASN) +do (store1 = -0.0147) (name BB and resn GLN) +do (store1 = -0.0165) (name BB and resn THR) +do (store1 = -0.0154) (name BB and resn SER) +do (store1 = -0.0130) (name BB and resn MET) +do (store1 = -0.0167) (name BB and resn CYS) +do (store1 = -0.0126) (name BB and resn PHE) +do (store1 = -0.0134) (name BB and resn TYR) +do (store1 = -0.0134) (name BB and resn TRP) +do (store1 = -0.0169) (name BB and resn ASP) +do (store1 = -0.0150) (name BB and resn GLU) +do (store1 = -0.0155) (name BB and resn HIS) +do (store1 = -0.0163) (name BB and resn LYS) +do (store1 = -0.0162) (name BB and resn ARG) + +! Side-chain beads +!do (store1 = 0.0000) (name SC* and resn ALA) +!do (store1 = 0.0000) (name SC* and resn GLY) +do (store1 = 0.0255) (name SC* and resn ILE) +do (store1 = 0.0222) (name SC* and resn VAL) +do (store1 = 0.0230) (name SC* and resn PRO) +do (store1 = -0.0192) (name SC* and resn ASN) +do (store1 = -0.0135) (name SC* and resn GLN) +do (store1 = -0.0009) (name SC* and resn THR) +do (store1 = -0.0056) (name SC* and resn SER) +do (store1 = 0.0202) (name SC* and resn MET) +do (store1 = 0.0201) (name SC* and resn CYS) +do (store1 = 0.1005) (name SC* and resn PHE) +do (store1 = 0.0669) (name SC* and resn TYR) +do (store1 = 0.0872) (name SC* and resn TRP) +do (store1 = -0.0360) (name SC* and resn ASP) +do (store1 = -0.0301) (name SC* and resn GLU) +do (store1 = 0.0501) (name SC* and resn HIS) +do (store1 = -0.0210) (name SC* and resn LYS) +do (store1 = -0.0229) (name SC* and resn ARG) + +! Fake beads +do (store1 = 0.0) (name SCD* and resn ASN) +do (store1 = 0.0) (name SCD* and resn GLN) +do (store1 = 0.0) (name SCD* and resn SER) +do (store1 = 0.0) (name SCD* and resn THR) +do (store1 = 0.0) (name SCD* and resn ARG) +do (store1 = 0.0) (name SCD* and resn LYS) +do (store1 = 0.0) (name SCD* and resn GLU) +do (store1 = 0.0) (name SCD* and resn ASP) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/dna-rna_restraints.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/dna-rna_restraints.cns new file mode 100644 index 0000000000000000000000000000000000000000..feb27b3999cec077b4e20abd921dac061b7ded1f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/dna-rna_restraints.cns @@ -0,0 +1,424 @@ +! dna-rna_restraints.def +! Define backbone dihedral angles, hbonds and planarity restraints +! for nucleic acids +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: dna-rna_restraints.def +} +{+ description: Creates restraints to maintain conformation of DNA/RNA +} +{+ Additions and changes were made to allow for flexibility during docking +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin and Marc van Dijk for HADDOCK use +} + +{============================================== base planarity =============================================} + +{* Restrain base planarity. This selection must only include nucleotide residues *} +evaluate ($dna_bases_planar=true) + +{=================================== sugar-pucker dihedral angle restraints ================================} + +{* Pick the dihedral angles of the sugar pucker from the input structure + and restrain them within the given error range *} +evaluate ($dna_pick_pucdih=true) + +{* dihedral C1'-C2'-C3'-C4' error range *} +evaluate ($error_nu2=0.0) +{* dihedral C5'-C4'-C3'-C2' error range *} +evaluate ($error_nu3=0.0) +{* dihedral C1'-O4'-C4'-C5' error range *} +evaluate ($error_nu4=0.0) + +{================================ phosphate backbone dihedral angle restraints =============================} + +{* Pick the dihedral angles of the phosphate backbone from the input structure and + restrain them within the given error range *} +evaluate ($dna_pick_bacdih=true) + +{* Error range for phosphate backbone dihedrals *} +{* alpha dihedral O3'-P-O5'-C5' error range *} +evaluate ($error_alpha=10.0) +{* beta dihedral P-O5'-C5'-C4' error range *} +evaluate ($error_beta=40.0) +{* gamma dihedral O5'-C5'-C4'-C3' error range *} +evaluate ($error_gamma=20.0) +{* delta dihedral C5'-C4'-C3'-O3' error range *} +evaluate ($error_delta=50.0) +{* epsilon dihedral C4'-C3'-O3'-P error range *} +evaluate ($error_eps=10.0) +{* zeta dihedral C3'-O3'-P-O5' error range *} +evaluate ($error_zeta=50.0) + + +{=========================================== Watson-Crick base pairs =======================================} + +{* automatically pick Watson-Crick restraint values from structure *} +evaluate ($dna_pick_wc=true) + +{* error range used for dna_pick_wc defined Watson-Crick restraints *} +evaluate ($wc_low=0.05) +evaluate ($wc_up=0.05) + + +{=========================================== Coarse-Grained ===========================================================} +{* Is the DNA/RNA molecule CG? *} +evaluate ($dna_cg=false) + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + + +{- find max and min residue numbers -} +evaluate ($min_resid = 99999) +evaluate ($max_resid = -99999) +show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) +if ( $result > 0 ) then + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($min_resid = max($min_resid,$resid)) + evaluate ($max_resid = max($max_resid,$resid)) + end loop resid +end if + +{- the planarity restraints single bases -} +if ($dna_bases_planar=true) then + for $id in id ( tag and (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) ) loop plan + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) (id $id) + evaluate ($resid=decode($result)) + evaluate ($plweight = 20) + + restraints plane + group + selection=( segid $segid and resid $resid and + (resn T or resn C or resn G or resn A or resn U or + resn DT or resn DC or resn DG or resn DA) and + not (name c#' or name h#' or name h#'' or name o#p or + name h7# or name o#' or name p or name h#t or name o#t)) + weight=$plweight + end + end + end loop plan +end if + +{- Dihedral restraints for the sugar pucker -} + +if ($dna_pick_pucdih=true) then + show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) + if ( $result > 0 ) then + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + pick dihedral + ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name c2' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c4' ) + geometry + evaluatate ($dihedral_nu2=$result) + pick dihedral + ( segid $segid and resid $resid and name c5' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c2' ) + geometry + evaluatate ($dihedral_nu3=$result) + pick dihedral + ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name o4' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c5' ) + geometry + evaluatate ($dihedral_nu4=$result) + restraints dihedral + assign ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name c2' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c4' ) + 20.0 $dihedral_nu2 $error_nu2 2 + assign ( segid $segid and resid $resid and name c5' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c3' ) + ( segid $segid and resid $resid and name c2' ) + 20.0 $dihedral_nu3 $error_nu3 2 + assign ( segid $segid and resid $resid and name c1' ) + ( segid $segid and resid $resid and name o4' ) + ( segid $segid and resid $resid and name c4' ) + ( segid $segid and resid $resid and name c5' ) + 20.0 $dihedral_nu4 $error_nu4 2 + scale=20.0 + end + end loop resid + flags include cdih end + end if +end if + +{- Dihedral restraints for the phosphate backbone -} + +if ($dna_pick_bacdih=true) then + show sum(1) ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) + if ( $result > 0 ) then + evaluate ($resid=$min_resid) + evaluate ($nres=$max_resid - $min_resid + 1) + evaluate ($error_alpha=$error_alpha) + evaluate ($error_beta=$error_beta) + evaluate ($error_gamma=$error_gamma) + evaluate ($error_zeta=$error_zeta) + evaluate ($error_epsilon=$error_eps) + evaluate ($error_delta=$error_delta) + for $id in id ( (resn DA or resn A or resn DG or resn G or resn DT or resn T or resn DC or resn C or resn U) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + if ($resid > $min_resid) then + evaluate ($rprec = $resid - 1) + ! check if previous residue exists + show sum(1) ( resid $rprec and tag ) + if ( $result > 0 ) then + pick dihedral + ( segid $segid and resid $rprec and name O3' ) + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + geometry + evaluatate ($dihedral_alpha=$result) + pick dihedral + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + geometry + evaluatate ($dihedral_beta=$result) + restraint dihedral + ! alpha + assign ( segid $segid and resid $rprec and name O3' ) + ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + 1.0 $dihedral_alpha $error_alpha 2 + ! beta + assign ( segid $segid and resid $resid and name P ) + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + 1.0 $dihedral_beta $error_beta 2 + scale 200.0 + end + end if + end if + + pick dihedral + ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + geometry + evaluatate ($dihedral_gamma=$result) + pick dihedral + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + geometry + evaluatate ($dihedral_delta=$result) + + restraints dihedral + ! gamma + assign ( segid $segid and resid $resid and name O5' ) + ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + 1.0 $dihedral_gamma $error_gamma 2 + ! delta + assign ( segid $segid and resid $resid and name C5' ) + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + 1.0 $dihedral_delta $error_delta 2 + scale=200.0 + end + + if ($resid < $max_resid) then + evaluate ($rfoll = $resid + 1) + ! check if next residue exists + show sum(1) ( resid $rfoll and segid $segid and tag ) + if ( $result > 0 ) then + pick dihedral + ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + geometry + evaluatate ($dihedral_epsilon=$result) + pick dihedral + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + ( segid $segid and resid $rfoll and name O5' ) + geometry + evaluatate ($dihedral_zeta=$result) + restraint dihedral + ! epsilon + assign ( segid $segid and resid $resid and name C4' ) + ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + 1.0 $dihedral_epsilon $error_epsilon 2 + ! zeta + assign ( segid $segid and resid $resid and name C3' ) + ( segid $segid and resid $resid and name O3' ) + ( segid $segid and resid $rfoll and name P ) + ( segid $segid and resid $rfoll and name O5' ) + 1.0 $dihedral_zeta $error_zeta 2 + scale 200.0 + end + end if + end if + end loop resid + flags include cdih end + end if +end if + +{- Watson-Crick base pairing -} + +if ($dna_pick_wc = true) then + evaluate ($hbcut = 3.5) + ! We only to check for ADE and CYT + show sum(1) ( (resn DA or resn A or resn DC or resn C) and tag ) + if ( $result > 0 ) then + noe + class hres + averaging hres cent + potential hres square + sqconstant hres 1. + sqexponent hres 2 + scale hres 70. + end + for $id in id ( (resn DA or resn A or resn DC or resn C) and tag ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($presid=$resid-1) + evaluate ($fresid=$resid+1) + evaluate ($ares_name = none) + show ( resn ) (id $id) + evaluate ($ares=$result) + + if ( $ares = DA ) then + eval ($ares_name = ADE) + elseif ( $ares = A ) then + eval ($ares_name = ADE) + end if + + if ( $ares = DC ) then + eval ($ares_name = CYT) + elseif ( $ares = C ) then + eval ($ares_name = CYT) + end if + + if ($ares_name = ADE) then + show sum(1) ( ((resn DT or resn T or resn U) and not (resid $presid or resid $fresid) and name N3) + and (resid $resid and name N1) around $hbcut) + if ($result = 1) then + show (resid) ( ((resn DT or resn T or resn U) and not (resid $presid or resid $fresid) and name N3) + and (resid $resid and name N1) around $hbcut) + evaluate ($rpair = $result) + pick bond + (resid $resid and name N6) + (resid $rpair and name O4) + geometry + evaluate ($n6o4=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name N3) + geometry + evaluate ($n1n3=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name O4) + geometry + evaluate ($n1o4=$result) + pick bond + (resid $resid and name N1) + (resid $rpair and name O2) + geometry + evaluate ($n1o2=$result) + noe + assign (resid $resid and name N6) + (resid $rpair and name O4) + $n6o4 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name N3) + $n1n3 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name O4) + $n1o4 $wc_low $wc_up + assign (resid $resid and name N1) + (resid $rpair and name O2) + $n1o2 $wc_low $wc_up + end + end if + end if + + !find possible pairing for DC/C with DG/G + if ($ares_name = CYT) then + show sum(1) ( ((resn DG or resn G) and not (resid $presid or resid $fresid) and name N1) + and (resid $resid and name N3) around $hbcut) + if ($result = 1) then + show (resid) ( ((resn DG or resn G) and not (resid $presid or resid $fresid) and name N1) + and (resid $resid and name N3) around $hbcut) + evaluate ($rpair = $result) + pick bond + (resid $resid and name N3) + (resid $rpair and name N1) + geometry + evaluate ($n3n1=$result) + pick bond + (resid $resid and name N4) + (resid $rpair and name O6) + geometry + evaluate ($n4o6=$result) + pick bond + (resid $resid and name O2) + (resid $rpair and name N2) + geometry + evaluate ($o2n2=$result) + pick bond + (resid $resid and name N3) + (resid $rpair and name O6) + geometry + evaluate ($n3o6=$result) + pick bond + (resid $resid and name N3) + (resid $rpair and name N2) + geometry + evaluate ($n3n2=$result) + noe + assign (resid $resid and name N3) + (resid $rpair and name N1) $n3n1 $wc_low $wc_up + assign (resid $resid and name N4) + (resid $rpair and name O6) $n4o6 $wc_low $wc_up + assign (resid $resid and name O2) + (resid $rpair and name N2) $o2n2 $wc_low $wc_up + assign (resid $resid and name N3) + (resid $rpair and name O6) $n3o6 $wc_low $wc_up + assign (resid $resid and name N3) + (resid $rpair and name N2) $n3n2 $wc_low $wc_up + end + end if + end if + end loop resid + end if +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment.cns new file mode 100644 index 0000000000000000000000000000000000000000..6902f602e00b8280aa423711db2c34ef8dd5df0a --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment.cns @@ -0,0 +1,32 @@ +! flex_segment.cns +! Define fully flexible segments for docking +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +do (store5 = 0) (all) + +display NO FLEXIBLE SEGMENTS for all molecule at this stage +if ($nfle = 0) then + display NO FULLY FLEXIBLE SEGMENTS +else + evaluate($nf=0) + while ($nf < $nfle) loop Xfflex + evaluate($nf=$nf + 1) + do (store5 = 1) ( resid $fle_sta_$nf : $fle_end_$nf and segid $fle_seg_$nf ) + display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nf TO $fle_end_$nf FOR CHAIN $fle_seg_$nf + end loop Xfflex +end if + +do (store5 = 21) (resn WAT or resn HOH or resn TIP*) + +do (store1 = 0) (all) +do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) +show sum (store1) ((resn WAT or resn HOH or resn TIP*)) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_back.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_back.cns new file mode 100644 index 0000000000000000000000000000000000000000..7baf1c9ad9a7e857e14e08c816806b9ff285f010 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_back.cns @@ -0,0 +1,58 @@ +! flex_segment_back.cns +! Define the semi-flexible segments (both side-chains and backbone) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +do (store5 = 0) (all) +do (store6 = 0) (all) + +!first flexible segments for docking +evaluate($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate($nchain1 = $nchain1 + 1) + evaluate($nf=0) + + if ($nseg$nchain1 = 0) then + display NO FLEXIBLE SEGMENTS for molecule $nchain1 + else + if ($nseg$nchain1 < 0) then + display AUTOMATIC DEFINITION OF FLEXIBLE SEGMENTS BASED ON INTERMOLECULAR PROXIMITY FOR MOLECULE $nchain1 + inline @MODULE:flexauto-neighbors.cns + else + display FLEXIBLE SIDE-CHAINS SEGMENTS for molecule $nchain1 + while ($nf < $nseg$nchain1) loop Xflex + evaluate($nf=$nf + 1) + do (store5 = $nchain1) ( resid $seg_sta_$nchain1_$nf : $seg_end_$nchain1_$nf + and segid $prot_segid_$nchain1) + display FLEXIBLE SEGMENT NR $nf FROM $seg_sta_$nchain1_$nf TO $seg_end_$nchain1_$nf + end loop Xflex + end if + end if +end loop nloop1 + +!then fully flexible segments for all stages +display NO FLEXIBLE SEGMENTS for all molecule at this stage +if ($nfle = 0) then + display NO FULLY FLEXIBLE SEGMENTS +else + evaluate($nf=0) + while ($nf < $nfle) loop Xfflex + evaluate($nf=$nf + 1) + do (store5 = 1) ( resid $fle_sta_$nf : $fle_end_$nf and segid $fle_seg_$nf ) + display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nf TO $fle_end_$nf FOR CHAIN $fle_seg_$nf + end loop Xfflex +end if + +do (store5 = 21) (resn WAT or resn HOH or resn TIP*) + +do (store1 = 0) (all) +do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) +show sum (store1) ((resn WAT or resn HOH or resn TIP*)) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_side.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_side.cns new file mode 100644 index 0000000000000000000000000000000000000000..ac5276c3225b214778fdd02b4db81408857eaea9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flex_segment_side.cns @@ -0,0 +1,61 @@ +! flex_segment_side.cns +! Define semi-flexible segments (side-chains only) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +do (store5 = 0) (all) +do (store6 = 0) (all) + +!first flexible segments for docking +evaluate($nchain1 = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate($nchain1 = $nchain1 + 1) + evaluate($nf=0) + if ($nseg$nchain1 = 0) then + display NO FLEXIBLE SIDE-CHAINS SEGMENTS for molecule $nchain1 + else + if ($nseg$nchain1 < 0) then + display AUTOMATIC DEFINITION OF FLEXIBLE SEGMENTS BASED ON INTERMOLECULAR PROXIMITY FOR MOLECULE $nchain1 + inline @MODULE:flexauto-neighbors.cns + do (store5 = 0) (name CA or name BB or name C or name N or name O) + else + display FLEXIBLE SIDE-CHAINS SEGMENTS for molecule $nchain1 + while ($nf < $nseg$nchain1) loop Xflex + evaluate($nf=$nf + 1) + do (store5 = $nchain1) ( resid $seg_sta_$nchain1_$nf : $seg_end_$nchain1_$nf + and segid $prot_segid_$nchain1 + and not(name CA or name BB or name C or name N or name O) ) + display FLEXIBLE SIDE-CHAINS SEGMENT NR $nf FROM $seg_sta_$nchain1_$nf TO $seg_end_$nchain1_$nf + end loop Xflex + end if + end if +end loop nloop1 + +!then fully flexible segments for all stages + +!then fully flexible segments for all stages +display NO FLEXIBLE SEGMENTS for all molecule at this stage +if ($nfle = 0) then + display NO FULLY FLEXIBLE SEGMENTS +else + evaluate($nf=0) + while ($nf < $nfle) loop Xfflex + evaluate($nf=$nf + 1) + do (store5 = 1) ( resid $fle_sta_$nf : $fle_end_$nf and segid $fle_seg_$nf ) + display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nf TO $fle_end_$nf FOR CHAIN $fle_seg_$nf + end loop Xfflex +end if + +do (store5 = 21) (resn WAT or resn HOH or resn TIP*) + +do (store1 = 0) (all) +do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) +show sum (store1) ((resn WAT or resn HOH or resn TIP*)) + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexauto-neighbors.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexauto-neighbors.cns new file mode 100644 index 0000000000000000000000000000000000000000..f3fe74b83b0aa2a99d80a117239d87e052648b11 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexauto-neighbors.cns @@ -0,0 +1,42 @@ +! flexauto-neighbors.cns +! Automatic definition of flexible segments for docking for contacting residues +! including neighboring residues of residues making contacts +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($flcut = 5.0) + +do (store5 = $nchain1) (byres (segid $prot_segid_$nchain1 + and (not (segid $prot_segid_$nchain1 or resn SHA)) around $flcut)) + +do (store6 = 0) (segid $prot_segid_$nchain1) +for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres1 + show (resid) (id $id) + evaluate ($inres = decode($result)) + evaluate ($preres = $inres) + evaluate ($nexres = $inres) + evaluate ($preres = $preres - 1) + do (store6 = $nchain1) (resid $preres and segid $prot_segid_$nchain1) + do (store6 = $nchain1) (resid $nexres and segid $prot_segid_$nchain1) +end loop flexres1 + +do (store5 = store6) (segid $prot_segid_$nchain1) + +display THE FOLLOWING RESIDUES HAVE BEEN DEFINED AS FLEXIBLE for molecule $nchain1 +for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres2 + show (resid) (id $id) + evaluate ($inres = $result) + show (resn) (id $id) + evaluate ($nares = $result) + show (segid) (id $id) + evaluate ($seres = $result) + display AUTOMATICALLY SELECTED SEGMENT: $nares,$inres,$seres +end loop flexres2 + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexref.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexref.cns new file mode 100644 index 0000000000000000000000000000000000000000..54d07b35feae7a8addc154b6621cb904564139df --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/flexref.cns @@ -0,0 +1,621 @@ +! flexref.cns +! The HADDOCK semi-flexible refinement in torsion angle space +! This version supports only distance and symmetry/ncs restraints +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** + +if ( $log_level = "verbose" ) then + set message=all echo=on end +elseif ( $log_level = "normal" ) then + set message=normal echo=off end +else + set message=off echo=off end +end if + +!==================================================================! +! Initialisation of variables +!==================================================================! + +evaluate ($saprotocol.randorien=$randorien) +evaluate ($saprotocol.tadhigh_t=$temp_high) +evaluate ($saprotocol.t1_init=$temp_cool1_init) +evaluate ($saprotocol.t2_init=$temp_cool2_init) +evaluate ($saprotocol.t3_init=$temp_cool3_init) +evaluate ($saprotocol.t1_final=$temp_cool1_final) +evaluate ($saprotocol.t2_final=$temp_cool2_final) +evaluate ($saprotocol.t3_final=$temp_cool3_final) +evaluate ($saprotocol.inter_init_rigid=$sinter_rigid_init) +evaluate ($saprotocol.inter_fin_rigid=$sinter_rigid_final) +evaluate ($saprotocol.inter_init_cool2=$sinter_cool2_init) +evaluate ($saprotocol.inter_fin_cool2=$sinter_cool2_final) +evaluate ($saprotocol.inter_init_cool3=$sinter_cool3_init) +evaluate ($saprotocol.inter_fin_cool3=$sinter_cool3_final) +evaluate ($saprotocol.tempstep=50) +evaluate ($saprotocol.timestep=$timestep) +evaluate ($saprotocol.tadfactor=$tadfactor) +evaluate ($saprotocol.initiosteps=$mdsteps_rigid) +evaluate ($saprotocol.cool1_steps=$mdsteps_cool1) +evaluate ($saprotocol.cool2_steps=$mdsteps_cool2) +evaluate ($saprotocol.cool3_steps=$mdsteps_cool3) +evaluate ($saprotocol.fbeta=100) +evaluate ($saprotocol.mass=100) + +evaluate ($data.ncomponents=$ncomponents) + + +! non-bonded parameter set to use +evaluate ($toppar.par_nonbonded = "OPLSX") + +! dihedrals, DNA and distance restraints +evaluate ($Data.dnarest =$dnarest_on) +evaluate ($Data.flags.cdih =$dihedrals_on) +evaluate ($Data.cdih.on =$dihedrals_on) +evaluate ($Data.ssdihed =$ssdihed) +evaluate ($Data.error_dih =$error_dih) +evaluate ($data.dihedrals.on=$dihedrals_on) +evaluate ($data.dihedrals_hot=$dihedrals_hot) +evaluate ($data.dihedrals_cool1=$dihedrals_cool1) +evaluate ($data.dihedrals_cool2=$dihedrals_cool2) +evaluate ($data.dihedrals_cool3=$dihedrals_cool3) + +! planarity restraints +evaluate ($Data.flags.plan = false) + +! distance restraints +evaluate ($Data.flags.noe = true) +evaluate ($data.unambig_hot=$unambig_hot) +evaluate ($data.unambig_cool1=$unambig_cool1) +evaluate ($data.unambig_cool2=$unambig_cool2) +evaluate ($data.unambig_cool3=$unambig_cool3) +evaluate ($data.randremoval=$randremoval) +evaluate ($data.npart=$npart) + +evaluate ($data.ambig_hot=$ambig_hot) +evaluate ($data.ambig_cool1=$ambig_cool1) +evaluate ($data.ambig_cool2=$ambig_cool2) +evaluate ($data.ambig_cool3=$ambig_cool3) + +evaluate ($data.hbond_hot=$hbond_hot) +evaluate ($data.hbond_cool1=$hbond_cool1) +evaluate ($data.hbond_cool2=$hbond_cool2) +evaluate ($data.hbond_cool3=$hbond_cool3) + +evaluate ($data.mrswi_hot=$mrswi_hot) +evaluate ($data.mrswi_cool1=$mrswi_cool1) +evaluate ($data.mrswi_cool2=$mrswi_cool2) +evaluate ($data.mrswi_cool3=$mrswi_cool3) + +evaluate ($data.rswi_hot=$rswi_hot) +evaluate ($data.rswi_cool1=$rswi_cool1) +evaluate ($data.rswi_cool2=$rswi_cool2) +evaluate ($data.rswi_cool3=$rswi_cool3) + +evaluate ($data.masy_hot=$masy_hot) +evaluate ($data.masy_cool1=$masy_cool1) +evaluate ($data.masy_cool2=$masy_cool2) +evaluate ($data.masy_cool3=$masy_cool3) + +evaluate ($data.asy_hot=$asy_hot) +evaluate ($data.asy_cool1=$asy_cool1) +evaluate ($data.asy_cool2=$asy_cool2) +evaluate ($data.asy_cool3=$asy_cool3) + +evaluate ($data.cmrest=$cmrest) +evaluate ($data.cmtight=$cmtight) +evaluate ($data.kcm=$kcm) +evaluate ($data.kcont=$kcont) +evaluate ($data.contactairs=$contactairs) +if ($data.contactairs eq true) then + evaluate ($data.randremoval = false) +end if + +! NCS restraints +evaluate ($data.kncs = $kncs) +evaluate ($Data.flags.ncs = $ncs_on) +evaluate ($data.nncs = $nncs) + +! Symmetry restraints +evaluate ($data.ksym = $ksym) +evaluate ($Data.flags.sym = $sym_on) +evaluate ($data.nc2sym = $nc2sym) +evaluate ($data.nc3sym = $nc3sym) +evaluate ($data.ns3sym = $ns3sym) +evaluate ($data.nc4sym = $nc4sym) +evaluate ($data.nc5sym = $nc5sym) +evaluate ($data.nc6sym = $nc6sym) + +!Electrostatics: +evaluate ($Data.flags.dihed =$dihedflag) +evaluate ($Data.flags.elec =$elecflag) +evaluate ($Data.epsilon =$epsilon) +evaluate ($Data.dielec =$dielec) + +!Interaction matrix: +evaluate ($nmol1=1) +while ($nmol1 <=$data.ncomponents) loop mol1 + evaluate ($nmol2=$nmol1 + 1) + evaluate ($scale.int_$nmol1_$nmol1 =$int_$nmol1_$nmol1) + while ($nmol2 <=$data.ncomponents) loop mol2 + evaluate ($scale.int_$nmol1_$nmol2 =$int_$nmol1_$nmol2) + evaluate ($scale.int_$nmol2_$nmol1 =$int_$nmol1_$nmol2) + evaluate ($nmol2=$nmol2 + 1) + end loop mol2 + evaluate ($nmol1 = $nmol1 + 1) +end loop mol1 + + +! Unsupported restraints +evaluate ($Data.flags.em = false) +evaluate ($Data.flags.rg = false) +evaluate ($Data.flags.zres = false) +evaluate ($Data.flags.sani = false) +evaluate ($Data.flags.xrdc = false) +evaluate ($Data.flags.xpcs = false) +evaluate ($Data.flags.dani = false) +evaluate ($Data.flags.vean = false) + +! Other parameters +evaluate ($refine.keepwater = false) + +!==================================================================! + +evaluate ($whichMD="torsion") + +{* Read paramters and set various force field related variables *} + +@MODULE:read_param.cns + +parameter + bond (resn WAT ) (resn WAT ) 1000 TOKEN + angle (resn WAT ) (resn WAT ) (resn WAT ) 500 TOKEN + bond (resn HOH ) (resn HOH ) 1000 TOKEN + angle (resn HOH ) (resn HOH ) (resn HOH ) 500 TOKEN + bond (resn TIP*) (resn TIP*) 1000 TOKEN + angle (resn TIP*) (resn TIP*) (resn TIP*) 500 TOKEN +end + +{* Check for the presence of ions and add distance restraints / covalent bond == *} + +@MODULE:restrain-ions.cns +@MODULE:covalions.cns + + +{* Define various interaction and energetics settings *} + +igroup + interaction (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1 end + interaction (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) + (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) weight * 1 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0 end +end + +flag include bond angle impr vdw end + +if ($Data.flags.dihed eq true) then + flag include dihed end +end if + +if ($Data.flags.elec eq true) then + flag include elec end + if ($Data.dielec eq "rdie") then + parameter nbonds eps=$Data.epsilon rdie shift switch end end + ! shift statement needed first to activate switch (CNS bug?) + else + parameter nbonds eps=$Data.epsilon cdie end end + end if + parameter nbonds ? end end +else + evaluate ($elec=0.0) + flag exclude elec end +end if + +do (fbeta=$Saprotocol.fbeta) (all) +do (mass=$Saprotocol.mass) (all) + +!catch possible bound water and set high T steps to 0 +coor select ((resn WAT or resn HOH or resn TIP*)) end +if ($select gt 0) then + evaluate ($SaProtocol.initiosteps = 0) + evaluate ($SaProtocol.cool1_steps = 0) + evaluate ($refine.keepwater = true) +end if + +! random placement of molecules +if ($SaProtocol.randorien eq true) then + @MODULE:separate.cns + @MODULE:random_rotations.cns +end if + +{* Read the distance restraints ================================ *} +set seed $seed end +set message=normal echo=on end +inline @MODULE:read_data.cns + +! random removal of restaints +if ($Data.randremoval eq true) then + noe cv $npart ? end +end if + +if ( $log_level = "verbose" ) then + set message=all echo=on end +elseif ( $log_level = "normal" ) then + set message=normal echo=off end +else + set message=off echo=off end +end if + +evaluate ($numnoe = 0) + +!Make sure that at least as many distance restraints are successfully +!read as the number of partitions for cross-validation +evaluate ($numnoe = 999) +noe ? end +if ($NUMNOE = 0) then + if ($Data.ncomponents > 1) then + if ($Data.contactairs eq FALSE) then + if ($Data.cmrest eq FALSE) then + evaluate ($errfile = "MODDIR:WARNING") + fileexist $errfile end + if ($result eq false) then + set display=$errfile end + display TOTAL NUMBER OF DISTANCE RESTRAINTS FOR FLEXIBLE REFINEMENT IS ZERO! + display CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS + close $errfile end + end if + end if + end if + end if + evaluate ($Data.npart = 1) + evaluate ($Data.randremoval = FALSE) +end if + +if ($NUMNOE lt $Data.npart) then + noe part=1 end + evaluate ($Data.npart = 1) + evaluate ($Data.randremoval = FALSE) +end if + + +{* set the energy flags ======================================================== *} + +inline @MODULE:setflags.cns + +{* Check for other restraints ================================================== *} + +@MODULE:symmultimer.cns + +if ($Data.cmrest eq true ) then + @MODULE:cm-restraints.cns +end if + +if ($Data.contactairs eq true ) then + @MODULE:contactairs.cns +end if + +if ($Data.dnarest eq true ) then + @MODULE:dna-rna_restraints.cns +end if + +if ($Data.ssdihed eq "all" ) then + inline @MODULE:protein-ss-restraints-all.cns +end if +if ($Data.ssdihed eq "alpha" ) then + inline @MODULE:protein-ss-restraints-alpha.cns +end if +if ($Data.ssdihed eq "alphabeta" ) then + inline @MODULE:protein-ss-restraints-alpha-beta.cns +end if + + +{* Check first for failed structures =========================================== *} +evaluate ($failure = false) +evaluate ($filefail=$output_pdb_filename - ".pdb" + ".fail") +fileexist $filefail end +evaluate ($failure = $result) + + +{* Define initial weights for distance restraints ============================== *} +evaluate ($unambig_scale = $Data.unambig_hot) +evaluate ($ambig_scale = $Data.ambig_hot) +evaluate ($hbond_scale = $Data.hbond_hot) + +noe + scale dist $unambig_scale + scale ambi $ambig_scale + scale hbon $hbond_scale +end + +{* Stage 0 ================================== initial EM for flexible parts only *} + +! get initial energy +energy end + +! fix the residues describing the shape +fix sele=(resn SHA) end + +! define flexible interface +@MODULE:flex_segment_back.cns +fix sele=((attr store5 = 0 or name OO or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP*)) end + +! energy minimization +if ($nemsteps > 0) then + minimize powell nstep=$nemsteps drop=10.0 nprint=25 end +end if + +fix sele=(not all) end + +! get initial energy +energy end + +! fix the residues describing the shape +fix sele=(resn SHA) end + +! the following is added to avoid the generation of the torsion angle topology if not needed +! in cases where the number of steps is set to 0 (avoid issues with isolated atoms) +eval ($torsiondone = false) + +! start SA in torsion angle unless a failure was detected +if ($failure eq false) then + + {* Stage 1 ======================================= rigid body high temperature search*} + + if ($nfle > 0) then + ! reduce timestep in case of fully flexible segments + evaluate ($SaProtocol.tadfactor = min(4,$SaProtocol.tadfactor)) + end if + if ($SaProtocol.initiosteps > 0) then + inline @MODULE:flex_segment.cns + @MODULE:torsiontop.cns + eval ($torsiondone = true) + @MODULE:sa_ltad_hightemp.cns + end if + + {* Stage 2 ======================================= rigid body first slow cooling *} + + if ($SaProtocol.cool1_steps > 0) then + if ($torsiondone ne true) then + inline @MODULE:flex_segment.cns + @MODULE:torsiontop.cns + eval ($torsiondone = true) + end if + if ($nfle > 0) then + ! reduce timestep in case of fully flexible segments + evaluate ($SaProtocol.tadfactor = min(4,$SaProtocol.tadfactor)) + end if + @MODULE:sa_ltad_cool1.cns + end if + + {* Stage 3 ======================================= second slow cooling *} + {* flexible side-chains and reduced time step *} + + if ($SaProtocol.cool2_steps > 0) then + if ($torsiondone eq true) then + dyna tors topo reset end end + end if + inline @MODULE:flex_segment_side.cns + @MODULE:torsiontop.cns + eval ($torsiondone = true) + evaluate ($SaProtocol.tadfactor = 1) + @MODULE:sa_ltad_cool2.cns + end if + + {* Stage 4 ============================================ third slow cooling *} + {* flexible side-chains and backbone at interface and reduced time step *} + + if ($SaProtocol.cool3_steps > 0) then + if ($torsiondone eq true) then + dyna tors topo reset end end + end if + inline @MODULE:flex_segment_back.cns + @MODULE:torsiontop.cns + eval ($torsiondone = true) + evaluate ($SaProtocol.tadfactor = 1) + @MODULE:sa_ltad_cool3.cns + end if + +end if + +{* Stage 5 =========================== final minimization *} + +! define flexible segments and fix the remaining of the structure +@MODULE:flex_segment_back.cns +fix sele=((attr store5 = 0 or name OO or resn SHA) and not name H* and not (resn WAT or resn HOH or resn TIP* or resn XAN)) end + +! energy minimization +if ($nemsteps > 0) then + minimize powell nstep=$nemsteps drop=10.0 nprint=25 end +end if + +! final energy +fix sele=(not all) end + +{* ======================= calculate free molecules internal energy *} + +igroup + interaction (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) + (not (resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DUM)) weight * 1 end +end + +do (refx=x) (all) +do (refy=y) (all) +do (refz=z) (all) + +fix sele=(resn ANI or resn DAN or resn XAN or resn SHA or resn WAT or resn HOH or resn TIP* or resn DMS) end + +flag excl noe dani sani vean xrdc xpcs coll cdih zhar end +flag include bond angle dihe impr vdw end + +evaluate ($elec = 0.0) +evaluate ($eintfree = 0.0) +if ($Data.flags.elec eq true) then + flag include elec end +end if + +if ($Data.dielec eq "rdie") then + parameter nbonds eps=$Data.epsilon rdie shift switch end end + ! shift statement needed first to activate switch (CNS bug?) +else + parameter nbonds eps=$Data.epsilon cdie end end +end if +parameter nbonds ? end end +inline @MODULE:calc_free-ene.cns + +fix sele=(not all) end + +do (x = refx) (all) +do (y = refy) (all) +do (z = refz) (all) + + +{* ===================== calculate complex internal energy *} + +evaluate ($kinter = 1.0) +flag include bond angle dihe impr vdw end +energy end + +@MODULE:scale_intra_only.cns + +evaluate ($elec = 0.0) +evaluate ($eintcplx = 0.0) +if ($Data.flags.elec eq true) then + flag include elec end +end if + +energy end + +evaluate ($eintcplx = $bond + $angl + $impr + $dihe + $vdw + $elec) +evaluate ($ebond = $bond) +evaluate ($eangl= $angl) +evaluate ($eimpr= $impr) +evaluate ($edihe= $dihe) + +evaluate ($result=0) +print thres=0.05 bonds +evaluate ($rms_bonds=$result) +evaluate ($result=0) +print thres=5. angles +evaluate ($rms_angles=$result) +evaluate ($result=0) +print thres=5. impropers +evaluate ($rms_impropers=$result) +evaluate ($result=0) +print thres=30. dihedrals +evaluate ($rms_dihedrals=$result) + + +{* ===================== calculate final energies and write structure *} +evaluate ($cdih=0.0) +flag incl noe cdih end +if ($Data.ncomponents > 1) then + evaluate ($kinter = 1.0) + @MODULE:scale_inter_final.cns +else + @MODULE:scale_intra_only.cns +end if + +noe + scale dist $Data.unambig_cool3 + scale ambi $Data.ambig_cool3 + scale hbon $Data.hbond_cool3 + scale symm 0.0 + scale cont 0.0 +end +energy end +evaluate ($eair= $noe) + +evaluate ($esym = 0.0) +evaluate ($ncs = 0.0) +evaluate ($zhar = 0.0) +evaluate ($rms_test_noe = 0.0) +evaluate ($violations_test_noe = 0) +if ($Data.flags.sym eq true) then + ! calculatee first the symmetry energy + noe reset nres= 1200000 end + @MODULE:symmultimer.cns + noe + scale symm $Data.ksym + end + energy end + evaluate ($esym = $noe) + noe reset end + set seed=$seed end + !read back all the distance restraints: + @@MODULE:read_noes.cns + ! random removal of restaints + if ($Data.randremoval eq true) then + noe cv $npart ? end + end if + noe + scale dist $Data.unambig_cool3 + scale ambi $Data.ambig_cool3 + scale hbon $Data.hbond_cool3 + end + evaluate ($result = 0) + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) + if ($Data.randremoval eq true) then + evaluate ($rms_test_noe=$test_rms) + evaluate ($violations_test_noe=$test_violations) + end if +else + evaluate ($result = 0) + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) + if ($Data.randremoval eq true) then + evaluate ($rms_test_noe=$test_rms) + evaluate ($violations_test_noe=$test_violations) + end if +end if + +if ($Data.dnarest eq true ) then + @MODULE:dna-rna_restraints.cns +end if + +energy end +evaluate ($etot = $ener - $noe) +evaluate ($noe = $eair) +evaluate ($etot = $etot + $noe) + +inline @MODULE:print_coorheader.cns + + +{* determine whether the final models should be reoriented along their principal *} +{* axes before writing to file ================================================= *} +eval($reorient = true) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop orientmol + evaluate ($ncount = $ncount + 1) + eval($watersegname_$ncount="WA" + encode($ncount)) + if ($mol_fix_origin_$ncount eq true) then + eval($reorient = false) + end if +end loop orientmol + +if ($reorient = true) then + coor sele= (not name H* and not resn ANI and not resn XAN and not resn DAN) orient end +end if + +inline @MODULE:check_coordinates.cns + +if ($failure eq true) then + evaluate ($failfile = $output_pdb_filename - ".pdb" + ".fail") + set display=$failfile end + display "MAX/MIN possible coordinates exceeded - stopping" + close $failfile end + stop +else + write coordinates format=pdbo output=$output_pdb_filename end +end if + +display OUTPUT: $output_pdb_filename + +stop diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/numtrees.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/numtrees.cns new file mode 100644 index 0000000000000000000000000000000000000000..4157f2121a9852ebb623fac1dd426e2fff02384d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/numtrees.cns @@ -0,0 +1,83 @@ +! numtrees.cns +! Define the number of trees for torsion angle MD +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($numtrees = 1) +evaluate ($ncount = 0) +evaluate ($break=$data.ncomponents) + +while ($ncount < $data.ncomponents) loop nsloop + + evaluate ($ncount = $ncount + 1) + + for $id1 in id ( name C and bondedto(name CA) and segid $prot_segid_$ncount) loop break + show (resid) (id $id1) + evaluate ($resid1=$result) + evaluate ($resid2=encode(decode($resid1)+1)) + show sum(1) (id $id1 and known) + if ( $result ne 0 ) then + identity (store1) ( name N and bondedto(name CA) and segid $prot_segid_$ncount and resid $resid2 ) + show element (store1) (attribute store1 > 0) + if ( $result ne 0) then + evaluate ($id2=$result) + show sum(1) (id $id2 and known) + if ( $result ne 0 ) then + pick bond + (name c and segid $prot_segid_$ncount and resid $resid1) + (name n and segid $prot_segid_$ncount and resid $resid2) + geometry + if ( $result > 2.5 ) then + evaluate ($break=$break+1) + end if + else + evaluate ($break=$break+1) + end if + end if + end if + end loop break + + for $id1 in id ( name BB ) loop bbbreak + show (resid) (id $id1) + evaluate ($resid1=$result) + evaluate ($resid2=encode(decode($resid1)+1)) + show sum(1) (id $id1 and known) + if ( $result ne 0 ) then + identity (store1) ( name BB and segid $prot_segid_$ncount and resid $resid2 ) + show element (store1) (attribute store1 > 0) + if ( $result ne 0) then + evaluate ($id2=$result) + show sum(1) (id $id2 and known) + if ( $result ne 0 ) then + pick bond + (name BB and segid $prot_segid_$ncount and resid $resid1) + (name BB and segid $prot_segid_$ncount and resid $resid2) + geometry + if ( $result > 8.0 ) then + evaluate ($break=$break+1) + end if + else + evaluate ($break=$break+1) + end if + end if + end if + end loop bbbreak + +end loop nsloop + +! check for water molecules + +do (store1 = 0) (all) +do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) +show sum (store1) ((resn WAT or resn HOH or resn TIP*)) +evaluate ($numtrees = $numtrees + $break + $result) + +evaluate ($numtrees = $numtrees + 300) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/print_coorheader.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/print_coorheader.cns new file mode 100644 index 0000000000000000000000000000000000000000..1a06f68f63b409e44be920b6dada5a05ff1e762f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/print_coorheader.cns @@ -0,0 +1,308 @@ +! print_coorheader.cns +! Generate the coordinate header (REMARKS) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +if ($Data.flags.dihed eq false) then evaluate ($dihe = 0) end if +if ($Data.flags.sani eq false) then evaluate ($sani = 0) end if +if ($Data.flags.xrdc eq false) then evaluate ($xrdc = 0) end if +if ($Data.flags.xpcs eq false) then evaluate ($xpcs = 0) end if +if ($Data.flags.dani eq false) then evaluate ($dani = 0) end if +if ($Data.flags.vean eq false) then evaluate ($vean = 0) end if +if ($Data.flags.cdih eq false) then evaluate ($cdih = 0) end if +if ($Data.flags.noe eq false) then evaluate ($noe = 0) end if +if ($Data.flags.rg eq false) then evaluate ($coll = 0) end if +if ($Data.flags.zres eq false) then evaluate ($zhar = 0) end if +if ($Data.flags.em eq false) then evaluate ($lcc = 0) end if + +evaluate($enerall=$etot) +evaluate($bondall=$ebond) +evaluate($anglall=$eangl) +evaluate($imprall=$eimpr) +evaluate($diheall=$edihe) +evaluate($vdwall=$vdw) +evaluate($elecall=$elec) +evaluate($noeall=$noe) +evaluate($rgall=$coll) +evaluate($zresall=$zhar) +evaluate($cdihall=$cdih) +evaluate($coupall=0) +evaluate($saniall=$sani+$xrdc) +evaluate($veanall=$vean) +evaluate($xpcsall=$xpcs) +evaluate($daniall=$dani) + +if ($Data.flags.sym eq true) then + evaluate ($result=0) + evaluate ($violations=0) + print threshold=0.3 noe + evaluate ($rms_noe=$result) + evaluate ($violations_noe=$violations) +end if + +if ($Data.randremoval eq false) then + evaluate ($violations_test_noe= 0) + evaluate ($rms_test_noe = 0) + evaluate ($npart = 0) +end if + +evaluate ($result=0) +evaluate ($violations=0) +print threshold=5. cdih +evaluate ($rms_cdih=$result) +evaluate ($violations_cdih=$violations) +evaluate ($result=0) +evaluate ($violations=0) +evaluate ($rms_coup = 0) +evaluate ($violations_coup = 0) + +evaluate( $rms_sani = 0) +evaluate( $violations_sani = 0) +if ($Data.flags.sani eq TRUE) then + sani print threshold = 0.20 class rd* end + evaluate( $rms_sani = $result) + evaluate( $violations_sani = $violations) +end if + +evaluate( $rms_xrdc = 0) +evaluate( $violations_xrdc = 0) +if ($Data.flags.xrdc eq TRUE) then + xrdc print threshold = 0.2 class xr* end + evaluate( $rms_xrdc = $result) + evaluate( $violations_xrdc = $violations) +end if + +evaluate( $violations_sani = $violations_sani + $violations_xrdc) +evaluate( $rms_sani = $rms_sani + $rms_xrdc) + +evaluate( $rms_xpcs = 0) +evaluate( $violations_xpcs = 0) +if ($Data.flags.xpcs eq TRUE) then + xpcs print threshold = 0.2 class pc* end + evaluate( $rms_xpcs = $result) + evaluate( $violations_xpcs = $violations) +end if + +evaluate( $rms_vean = 0) +evaluate( $violations_vean = 0) +if ($Data.flags.vean eq TRUE) then + vean print threshold = 5.00 class ve* end + evaluate( $rms_vean = $result) + evaluate( $violations_vean = $violations) +end if + +evaluate( $rms_dani = 0) +evaluate( $violations_dani = 0) +if ($Data.flags.dani eq TRUE) then + dani print threshold = 0.20 class da* end + evaluate( $rms_dani = $result) + evaluate( $violations_dani = $violations) +end if + +{====>} {* define ASA-based solvation parameters *} +inline @MODULE:def_solv_param.cns + +{====>} {* buried surface area and desolvation*} +evaluate ($nchain1 = 0) +evaluate ($saafree = 0) +evaluate ($esolfree = 0) +while ($nchain1 < $data.ncomponents) loop nloop1 + evaluate ($nchain1 = $nchain1 + 1) + {====>} {* buried surface area and desolvation*} + do (rmsd = 0) (all) + surface mode=access accu=0.075 rh2o=1.4 sele=(segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) end + show sum (rmsd) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + evaluate ($saafree = $saafree + $result) + do (store2 = rmsd * store1) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + show sum (store2) (segid $prot_segid_$nchain1 and not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) + evaluate ($esolfree = $esolfree + $result) +end loop nloop1 + +do (rmsd = 0) (all) +do (store2 = 0) (all) +surface mode=access accu=0.075 rh2o=1.4 sele=(not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) end +show sum (rmsd) (not ((resn WAT or resn HOH or resn TIP*) or resn DMS or resn SHA)) +evaluate ($satot = $result) +do (store2 = rmsd * store1) (not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) +show sum (store2) (not (resn WAT or resn HOH or resn TIP* or resn DMS or resn SHA)) +evaluate ($esolcplx = $result) +evaluate ($saburied = $saafree - $satot) +if ($saburied < 0) then + evaluate ($saburied = -999999) +end if + +evaluate ($edesolv = $esolcplx - $esolfree) + +evaluate ($dhbinding = $edesolv + $eintcplx - $eintfree + $elecall + $vdwall) + +evaluate ($nshape = 0) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop shape + evaluate ($ncount = $ncount + 1) + if ($mol_shape_$ncount eq true) then + evaluate ($nshape = $nshape + 1) + end if +end loop shape + +evaluate ($nonshape = $Data.ncomponents - $nshape) + +if ($nonshape = 1) then + evaluate ($saburied = 0) + evaluate ($edesolv = 0) + evaluate ($dhbinding = 0) + evaluate ($eintfree = $eintcplx) +end if + +if ($Data.flags.sym eq true) then + evaluate ($enerall = $enerall + $esym) +end if +if ($Data.flags.ncs eq true) then + evaluate ($enerall = $enerall + $ncs) +end if + +evaluate ($procwat = false) +if ($refine.keepwater eq true) then + evaluate ($procwat = true) +end if + +if ($procwat eq true) then + ident (store3) (not all) + flag exclude * include vdw elec end + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + igroup + interaction (segid $prot_segid_$nchain1) ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) weight * 1.0 end + interaction (not segid $prot_segid_$nchain1) (resn WAT or resn HOH or resn TIP* or resn DMS) weight * 0.0 end + interaction (segid $prot_segid_$nchain1) (not ((resn WAT or resn HOH or resn TIP* or resn DMS) and store3)) weight * 0.0 end + end + energy end + evaluate ($ener_water_$nchain1 = $ener) + evaluate ($enerall = $enerall + $ener) + evaluate ($vdw_water_$nchain1 = $vdw) + evaluate ($elec_water_$nchain1 = $elec) + + end loop nloop1 + if ($data.ncomponents > 1) then + eval($nchain1 = $data.ncomponents) + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + evaluate ($ener_water_$nchain1 = 0.0) + evaluate ($vdw_water_$nchain1 = 0.0) + evaluate ($elec_water_$nchain1 = 0.0) + end loop nloop1 + end if + + eval($nchain1 = 0) + + igroup + while ($nchain1 < $data.ncomponents) loop nloop2 + eval($nchain1 = $nchain1 + 1) + interaction (segid $prot_segid_$nchain1) (all) weight * 0.0 end + end loop nloop2 + interaction ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) + ((resn WAT or resn HOH or resn TIP* or resn DMS) and not store3) weight * 1.0 end + interaction (store3) (store3) weight * 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + interaction (resn SHA) (resn SHA) weight * 0.0 end + end + energy end + evaluate ($ener_water_water = $ener) + evaluate ($enerall = $enerall + $ener) + evaluate ($vdw_water_water = $vdw) + evaluate ($elec_water_water = $elec) +else + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents ) loop nloop1 + eval($nchain1 = $nchain1 + 1) + evaluate ($ener_water_$nchain1 = 0.0) + evaluate ($vdw_water_$nchain1 = 0.0) + evaluate ($elec_water_$nchain1 = 0.0) + end loop nloop1 + evaluate ($ener_water_water = 0.0) + evaluate ($vdw_water_water = 0.0) + evaluate ($elec_water_water = 0.0) +end if + +! calculate the HADDOCK score +evaluate ($hscore = $w_vdw * $vdwall) +evaluate ($hscore = $hscore + $w_elec * $elecall) +evaluate ($hscore = $hscore + $w_air * $noeall) +evaluate ($hscore = $hscore + $w_rg * $rgall) +evaluate ($hscore = $hscore + $w_cdih * $cdihall) +evaluate ($hscore = $hscore + $w_sani * $saniall) +evaluate ($hscore = $hscore + $w_xpcs * $xpcsall) +evaluate ($hscore = $hscore + $w_dani * $daniall) +evaluate ($hscore = $hscore + $w_vean * $veanall) +evaluate ($hscore = $hscore + $w_sym * $esym) +evaluate ($hscore = $hscore + $w_bsa * $saburied) +evaluate ($hscore = $hscore + $w_desolv * $edesolv) +evaluate ($hscore = $hscore + $w_lcc * $lcc) + +set message=on echo=on end +set remarks=reset end +set remarks=accumulate end +remarks =============================================================== +remarks HADDOCK stats for $output_pdb_filename +remarks =============================================================== +remarks HADDOCK score: $hscore +remarks =============================================================== + +!list input molecules +evaluate ($nmol=1) +while ($nmol <=$data.ncomponents) loop mol + if ( $exist_input_pdb_filename_$nmol = true) then + remarks initial structure $nmol - $input_pdb_filename_$nmol + end if + evaluate ($nmol = $nmol + 1) +end loop mol + +remarks =============================================================== +remarks total,bonds,angles,improper,dihe,vdw,elec,air,cdih,coup,rdcs,vean,dani,xpcs,rg +remarks energies: $enerall, $bondall, $anglall, $imprall, $diheall, $vdwall, $elecall, $noeall, $cdihall, $coupall, $saniall, $veanall, $daniall, $xpcsall, $rgall +remarks =============================================================== +remarks bonds,angles,impropers,dihe,air,cdih,coup,rdcs,vean,dani,xpcs +remarks rms-dev.: $rms_bonds,$rms_angles,$rms_impropers,$rms_dihedrals,$rms_noe,$rms_cdih,$rms_coup, $rms_sani, $rms_vean, $rms_dani, $rms_xpcs +remarks =============================================================== +remarks air,cdih,coup,rdcs,vean,dani,xpcs +remarks >0.3,>5,>1,>0,>5,>0.2,>0.2 +remarks violations.: $violations_noe, $violations_cdih, $violations_coup, $violations_sani, $violations_vean, $violations_dani, $violations_xpcs +remarks =============================================================== +remarks CVpartition#,violations,rms +remarks AIRs cross-validation: $npart, $violations_test_noe, $rms_test_noe +remarks =============================================================== +remarks NCS energy: $ncs +remarks =============================================================== +remarks Symmetry energy: $esym +remarks =============================================================== +remarks Membrane restraining energy: $zresall +remarks =============================================================== +remarks Local cross-correlation: $lcc[f7.4] +remarks =============================================================== +remarks Desolvation energy: $edesolv +remarks Internal energy free molecules: $eintfree +remarks Internal energy complex: $eintcplx +remarks Binding energy: $dhbinding +remarks =============================================================== +remarks buried surface area: $saburied +remarks =============================================================== +set remark accumulate end +evaluate($ncount = 0) +while ($ncount < $data.ncomponents) loop waterremark + evaluate ($ncount = $ncount +1) + remarks water - chain_$ncount: $ener_water_$ncount $vdw_water_$ncount $elec_water_$ncount +end loop waterremark +remarks =============================================================== +remarks water - water: $ener_water_water $vdw_water_water $elec_water_water +remarks =============================================================== diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-all.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-all.cns new file mode 100644 index 0000000000000000000000000000000000000000..ce6537b77378451041f63bb9fb07cb9fce35b4d7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-all.cns @@ -0,0 +1,88 @@ +! protein-ss-restraints-all.def +! Define automatically secondary stucture dihedral angle restraints for all residues +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ authors: Axel T. Brunger, and Paul D. Adams, +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone -} +restraint dihedral + nass = 50000 +end +do (store1 = 1) (all) +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id ( segid $prot_segid_$group and tag and not resn TIP3 ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + evaluate ($rprec = $resid - 1) + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluatate ($dihedral_phi=$result) + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + scale 200.0 + end + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluatate ($dihedral_psi=$result) + restraint dihedral + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha-beta.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha-beta.cns new file mode 100644 index 0000000000000000000000000000000000000000..0d6d8e4aa9b00b11bd201f8f9917a4628821978b --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha-beta.cns @@ -0,0 +1,128 @@ +! protein-ss-restraints-alpha-beta.cns +! Define automatically secondary structure dihedral angle restraints +! for helical and beta-sheet segments +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone in alpha-beta regions -} + +do (store1 = 1) (all) +restraint dihedral + nass = 50000 +end +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id ( segid $prot_segid_$group and tag and not resn TIP* ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($alphaphi = 0) + evaluate ($alphapsi = 0) + evaluate ($alpha_check = 0) + evaluate ($betaphi = 0) + evaluate ($betapsi = 0) + evaluate ($beta_check = 0) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluate ($dihedral_phi=$result) + evaluate ($alphaphi=max($dihedral_phi,-77)) + evaluate ($alphaphi=max($dihedral_phi,-37)) + if ($alphaphi eq -37) then + evaluate ($alpha_check = 1) + else + evaluate ($alpha_check = 0) + end if + evaluate ($betaphi=max($dihedral_phi,-145)) + evaluate ($betaphi=max($dihedral_phi,-105)) + if ($betaphi eq -105) then + evaluate ($beta_check = 1) + else + evaluate ($beta_check = 0) + end if + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluate ($dihedral_psi=$result) + evaluate ($alphapsi=max($dihedral_psi,-67)) + evaluate ($alphapsi=max($dihedral_psi,-27)) + if ($alphapsi eq -27) then + evaluate ($alpha_check = $alpha_check + 1) + end if + evaluate ($betapsi=max($dihedral_psi,105)) + evaluate ($betapsi=max($dihedral_psi,145)) + if ($betapsi eq 145) then + evaluate ($beta_check = $beta_check + 1) + end if + end if + evaluate ($defrest = 0) + if ($alpha_check eq 2) then + evaluate ($defrest = 1) + end if + if ($beta_check eq 2) then + evaluate ($defrest = 1) + end if + if ($defrest = 1) then + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha.cns new file mode 100644 index 0000000000000000000000000000000000000000..38416657fc086d88a8288b50371b1f3e697103a8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/protein-ss-restraints-alpha.cns @@ -0,0 +1,109 @@ +! protein-ss-restraints-alpha.cns +! Define automatically secondary structure dihedral angle restraints +! for helical segments +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +{+ file: protein-ss-restraints.def +} +{+ description: Creates dihedral angle restraints to maintain conformation of the protein backbone +} +{+ comment:This file is to be read by refinement files that modify atom coordinates +} +{+ authors: Axel T. Brunger, and Paul D. Adams +} +{+ modified by Alexandre Bonvin for HADDOCK use +} + +{=========================================================================================================} +{ things below this line do not normally need to be changed } +{=========================================================================================================} + +{- Dihedral restraints for the protein backbone in alpha-helical regions -} +restraint dihedral + nass = 50000 +end +do (store1 = 1) (all) +evaluate ($group=1) +evaluate ($done=false) +while ( $done = false ) loop bdihe + if ( $exist_prot_segid_$group = true ) then + show sum(1) ( segid $prot_segid_$group ) + if ( $result > 0 ) then + evaluate ($error_phi=$Data.error_dih) + evaluate ($error_psi=$Data.error_dih) + for $id in id (segid $prot_segid_$group and tag and not resn TIP3 ) loop resid + show (segid) (id $id) + evaluate ($segid=$result) + show (resid) ( id $id ) + evaluate ($resid=decode($result)) + evaluate ($alphaphi = 0) + evaluate ($alphapsi = 0) + evaluate ($alpha_check = 0) + evaluate ($rprec = $resid - 1) + show sum (store1) (resid $rprec and name C) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + geometry + evaluate ($dihedral_phi=$result) + evaluate ($alphaphi=max($dihedral_phi,-77)) + evaluate ($alphaphi=max($dihedral_phi,-37)) + if ($alphaphi eq -37) then + evaluate ($alpha_check = 1) + else + evaluate ($alpha_check = 0) + end if + end if + evaluate ($rnext = $resid + 1) + show sum (store1) (resid $rnext and name N) + if ($result ne 0) then + pick dihedral + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + geometry + evaluate ($dihedral_psi=$result) + evaluate ($alphapsi=max($dihedral_psi,-67)) + evaluate ($alphapsi=max($dihedral_psi,-27)) + if ($alphapsi eq -27) then + evaluate ($alpha_check = $alpha_check + 1) + end if + end if + evaluate ($defrest = 0) + if ($alpha_check eq 2) then + evaluate ($defrest = 1) + end if + if ($defrest = 1) then + restraint dihedral + ! phi + assign ( segid $segid and resid $rprec and name C ) + ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + 1.0 $dihedral_phi $error_phi 2 + ! psi + assign ( segid $segid and resid $resid and name N ) + ( segid $segid and resid $resid and name CA ) + ( segid $segid and resid $resid and name C ) + ( segid $segid and resid $rnext and name N ) + 1.0 $dihedral_psi $error_psi 2 + scale 200.0 + end + end if + end loop resid + end if + else + evaluate ($done=true) + end if + evaluate ($group=$group+1) +end loop bdihe + +flags include cdih end + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/random_rotations.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/random_rotations.cns new file mode 100644 index 0000000000000000000000000000000000000000..a50e9f5624abb6405affc6a2d38b29187ea5c9bc --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/random_rotations.cns @@ -0,0 +1,180 @@ +! random_rotations.cns +! Perform a random rotation +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +! check if homomer + +inline @MODULE:check-homomers.cns + +do (store4 = 0) (all) +evaluate ($ncount = 0) +while ($ncount < $data.ncomponents) loop fixed + evaluate ($ncount = $ncount + 1) + eval($watersegname_$ncount="WA" + encode($ncount)) + if ($mol_fix_origin_$ncount eq true) then + do (store4 = 1) (segid $prot_segid_$ncount) + end if +end loop fixed + +if ($homosymmetry eq false) then + ! Random translation within a 10A cube + evaluate ($ncount = 0) + while ($ncount < $data.ncomponents) loop randtrans + evaluate ($ncount = $ncount +1) + if ($mol_fix_origin_$ncount eq false) then + evaluate ($xd = 10.0 * (0.5 - ran())) + evaluate ($yd = 10.0 * (0.5 - ran())) + evaluate ($zd = 10.0 * (0.5 - ran())) + coor trans sele=(segid $prot_segid_$ncount or segid $watersegname_$ncount) vector=($xd,$yd,$zd) end + end if + end loop randtrans +end if + +! Random rotation of molecules +evaluate ($ncount = 0) +evaluate ($nrotset = 0) +while ($ncount < $data.ncomponents) loop randrot + evaluate ($ncount = $ncount +1) + if ($mol_fix_origin_$ncount eq false) then + show ave (x) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($xc = $result) + show ave (y) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($yc = $result) + show ave (z) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($zc = $result) + + ! Random rotation for each molecule except for symmtrical homomers for which + ! the same rotation is applied to all molecules to keep the symmetry + if ($nrotset = 0) then + !1. Generate random e1 e2 e3 and e4 in [-1, 1] so that e1^2 + e2^2 < 1 and e3^2+e4^2 < 1 + evaluate ($RRM_e1 = ran () * 2 - 1) + evaluate ($RRM_e2 = ran () * 2 - 1) + evaluate ($RRM_s1 = ($RRM_e1)*($RRM_e1) + ($RRM_e2)*($RRM_e2)) + + while ( $RRM_s1 >= 1) loop s1loop + evaluate ($RRM_e1 = ran () * 2 - 1) + evaluate ($RRM_e2 = ran () * 2 - 1) + evaluate ($RRM_s1 = ($RRM_e1)*($RRM_e1) + ($RRM_e2)*($RRM_e2)) + end loop s1loop + + evaluate ($RRM_e3 = ran () * 2 - 1) + evaluate ($RRM_e4 = ran () * 2 - 1) + evaluate ($RRM_s2 = ($RRM_e3)*($RRM_e3) + ($RRM_e4)*($RRM_e4)) + while ( $RRM_s2 >= 1) loop s2loop + evaluate ($RRM_e3 = ran () * 2 - 1) + evaluate ($RRM_e4 = ran () * 2 - 1) + evaluate ($RRM_s2 = ($RRM_e3)*($RRM_e3) + ($RRM_e4)*($RRM_e4)) + end loop s2loop + + !2. the quaternion q0 q1 q2 q3 + evaluate($RRM_q0 = $RRM_e1) + evaluate($RRM_q1 = $RRM_e2) + evaluate($RRM_q2 = $RRM_e3 * sqrt((1 - $RRM_s1)/$RRM_s2) ) + evaluate($RRM_q3 = $RRM_e4 * sqrt((1 - $RRM_s1)/$RRM_s2) ) + + !3. The rotation matrix from the quaternion + evaluate ($x1 = $RRM_q0 * $RRM_q0 + $RRM_q1 * $RRM_q1 - $RRM_q2 * $RRM_q2 - $RRM_q3 * $RRM_q3) + evaluate ($x2 = 2 * ($RRM_q1 * $RRM_q2 - $RRM_q0 * $RRM_q3) ) + evaluate ($x3 = 2 * ($RRM_q1 * $RRM_q3 + $RRM_q0 * $RRM_q2) ) + evaluate ($y1 = 2 * ($RRM_q1 * $RRM_q2 + $RRM_q0 * $RRM_q3) ) + evaluate ($y2 = $RRM_q0 * $RRM_q0 - $RRM_q1 * $RRM_q1 + $RRM_q2 * $RRM_q2 - $RRM_q3 * $RRM_q3) + evaluate ($y3 = 2 * ($RRM_q2 * $RRM_q3 - $RRM_q0 * $RRM_q1) ) + evaluate ($z1 = 2 * ($RRM_q1 * $RRM_q3 - $RRM_q0 * $RRM_q2) ) + evaluate ($z2 = 2 * ($RRM_q2 * $RRM_q3 + $RRM_q0 * $RRM_q1) ) + evaluate ($z3 = $RRM_q0 * $RRM_q0 - $RRM_q1 * $RRM_q1 - $RRM_q2 * $RRM_q2 + $RRM_q3 * $RRM_q3) + + if ($homosymmetry eq true) then + evaluate ($nrotset = 1) + end if + end if + + !4. The rotation + coor + center=($xc $yc $zc) + rotate matrix=($x1 $x2 $x3) ($y1 $y2 $y3) ($z1 $z2 $z3) + sele=(segid $prot_segid_$ncount or segid $watersegname_$ncount) + end + end if +end loop randrot + + +! If there are fixed molecules, randomly rotate as one unit all non-fixed ones +! around the geometric center of the fixed ones + +show sum (store4) (all) + +if ($result > 0) then + + show ave (x) (attribute store4 = 1) + evaluate ($xc = $result) + show ave (y) (attribute store4 = 1) + evaluate ($yc = $result) + show ave (z) (attribute store4 = 1) + evaluate ($zc = $result) + + ! Random rotation for each molecule except for symmtrical homomers for which + ! the same rotation is applied to all molecules to keep the symmetry + if ($nrotset = 0) then + !1. Generate random e1 e2 e3 and e4 in [-1, 1] so that e1^2 + e2^2 < 1 and e3^2+e4^2 < 1 + evaluate ($RRM_e1 = ran () * 2 - 1) + evaluate ($RRM_e2 = ran () * 2 - 1) + evaluate ($RRM_s1 = ($RRM_e1)*($RRM_e1) + ($RRM_e2)*($RRM_e2)) + + while ( $RRM_s1 >= 1) loop s1loop + evaluate ($RRM_e1 = ran () * 2 - 1) + evaluate ($RRM_e2 = ran () * 2 - 1) + evaluate ($RRM_s1 = ($RRM_e1)*($RRM_e1) + ($RRM_e2)*($RRM_e2)) + end loop s1loop + + evaluate ($RRM_e3 = ran () * 2 - 1) + evaluate ($RRM_e4 = ran () * 2 - 1) + evaluate ($RRM_s2 = ($RRM_e3)*($RRM_e3) + ($RRM_e4)*($RRM_e4)) + while ( $RRM_s2 >= 1) loop s2loop + evaluate ($RRM_e3 = ran () * 2 - 1) + evaluate ($RRM_e4 = ran () * 2 - 1) + evaluate ($RRM_s2 = ($RRM_e3)*($RRM_e3) + ($RRM_e4)*($RRM_e4)) + end loop s2loop + + !2. the quaternion q0 q1 q2 q3 + evaluate($RRM_q0 = $RRM_e1) + evaluate($RRM_q1 = $RRM_e2) + evaluate($RRM_q2 = $RRM_e3 * sqrt((1 - $RRM_s1)/$RRM_s2) ) + evaluate($RRM_q3 = $RRM_e4 * sqrt((1 - $RRM_s1)/$RRM_s2) ) + + !3. The rotation matrix from the quaternion + evaluate ($x1 = $RRM_q0 * $RRM_q0 + $RRM_q1 * $RRM_q1 - $RRM_q2 * $RRM_q2 - $RRM_q3 * $RRM_q3) + evaluate ($x2 = 2 * ($RRM_q1 * $RRM_q2 - $RRM_q0 * $RRM_q3) ) + evaluate ($x3 = 2 * ($RRM_q1 * $RRM_q3 + $RRM_q0 * $RRM_q2) ) + evaluate ($y1 = 2 * ($RRM_q1 * $RRM_q2 + $RRM_q0 * $RRM_q3) ) + evaluate ($y2 = $RRM_q0 * $RRM_q0 - $RRM_q1 * $RRM_q1 + $RRM_q2 * $RRM_q2 - $RRM_q3 * $RRM_q3) + evaluate ($y3 = 2 * ($RRM_q2 * $RRM_q3 - $RRM_q0 * $RRM_q1) ) + evaluate ($z1 = 2 * ($RRM_q1 * $RRM_q3 - $RRM_q0 * $RRM_q2) ) + evaluate ($z2 = 2 * ($RRM_q2 * $RRM_q3 + $RRM_q0 * $RRM_q1) ) + evaluate ($z3 = $RRM_q0 * $RRM_q0 - $RRM_q1 * $RRM_q1 - $RRM_q2 * $RRM_q2 + $RRM_q3 * $RRM_q3) + + if ($homosymmetry eq true) then + evaluate ($nrotset = 1) + end if + end if + + !4. The rotation + coor + center=($xc $yc $zc) + rotate matrix=($x1 $x2 $x3) ($y1 $y2 $y3) ($z1 $z2 $z3) + sele=(attribute store4 = 0) + end +end if + +do (x = refx) (resn ANI or resn DAN or resn XAN or resn SHA) +do (y = refy) (resn ANI or resn DAN or resn XAN or resn SHA) +do (z = refz) (resn ANI or resn DAN or resn XAN or resn SHA) + +!evaluate ($outname = "MODULE:" + "begin/" + $Filenames.fileroot + "_init_" + encode($count) + ".pdb") +!write coor format=pdbo output=$outname end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_data.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_data.cns new file mode 100644 index 0000000000000000000000000000000000000000..0499183803224fbed8de2940b8499c9eb8f29d50 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_data.cns @@ -0,0 +1,81 @@ +! read_data.cns +! Read the various restraints data +! (distances and dihedral angles only in this version) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +! Ambiguous and unambiguous distance restraints, hbonds +noe + reset + nrestraints = 12000000 ! allocate space for NOEs + ceiling 1000 +end + +evaluate ($filenam0 = $ambig_fname + "_" + encode($count)) +fileexist $filenam0 end +if ($result eq false) then + evaluate ($filenam0 = $ambig_fname) +end if + +if ($filenam0 # "") then + fileexist $filenam0 end + if ($result eq true) then + noe class ambi @@$filenam0 end + end if +end if + +if ($Data.randremoval eq true) then + noe part $Data.npart end +end if + +if ($unambig_fname # "") then + fileexist $unambig_fname end + if ($result eq true) then + noe class dist @@$unambig_fname end + end if +end if + +if ($hbond_fname # "") then + fileexist $hbond_fname end + if ($result eq true) then + noe class hbon @@$hbond_fname end + end if +end if + +noe + averaging * sum + potential * soft + scale * 1.0 + sqconstant * 1.0 + sqexponent * 2 + soexponent * 1 + rswitch * 1.0 + sqoffset * 0.0 + asymptote * 2.0 + msoexponent * 1 + masymptote * -0.1 + mrswitch * 1.0 +end + + +!dihedral restraints: +restraints dihedral + reset + nassign 50000 +end +if ($dihe_fname # "") then + fileexist $dihe_fname end + if ($result eq true) then + restraints dihedral + @@$dihe_fname + end + end if +end if + +restraints dihedral ? end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_noes.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_noes.cns new file mode 100644 index 0000000000000000000000000000000000000000..be5c0b8c55dbbd984e82a3fceb10553d0ee60281 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_noes.cns @@ -0,0 +1,65 @@ +! read_noes.cns +! Read the various restraints data +! In this version only distance-based restraints +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +! Ambiguous and unambiguous distance restraints, hbonds +noe + reset + nrestraints = 12000000 ! allocate space for NOEs + ceiling 1000 +end + +evaluate ($filenam0 = $ambig_fname + "_" + encode($count)) +fileexist $filenam0 end +if ($result eq false) then + evaluate ($filenam0 = $ambig_fname) +end if + +if ($filenam0 # "") then + fileexist $filenam0 end + if ($result eq true) then + noe class ambi @@$filenam0 end + end if +end if + +if ($Data.randremoval eq true) then + noe part $Data.npart end +end if + +if ($unambig_fname # "") then + fileexist $unambig_fname end + if ($result eq true) then + noe class dist @@$unambig_fname end + end if +end if + +if ($hbond_fname # "") then + fileexist $hbond_fname end + if ($result eq true) then + noe class hbon @@$hbond_fname end + end if +end if + +noe + averaging * sum + potential * soft + scale * 1.0 + sqconstant * 1.0 + sqexponent * 2 + soexponent * 1 + rswitch * 1.0 + sqoffset * 0.0 + asymptote * 2.0 + msoexponent * 1 + masymptote * -0.1 + mrswitch * 1.0 +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_param.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_param.cns new file mode 100644 index 0000000000000000000000000000000000000000..6f549a453e49c118de295658c1294a8a429b9365 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/read_param.cns @@ -0,0 +1,64 @@ +! read_param.cns +! Reads parameter files. +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +!! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** + +{* protein parameter file *} +eval ($prot_parameter_infile="TOPPAR:protein-allhdg5-4.param") + +{* nucleic acid parameter file *} +eval ($nucl_parameter_infile="TOPPAR:dna-rna-allatom-hj-opls-1.3.param") + +{* carbohydrate parameter file *} +eval ($carbo_parameter_infile="TOPPAR:carbohydrate.param") + +{* solvent parameter file *} +eval ($solv_parameter_infile="TOPPAR:solvent-allhdg5-4.param") + +{* fragment probes parameter file *} +eval ($ligands_parameter_infile="TOPPAR:fragment_probes.param") + +{* ion parameter file *} +eval ($ion_parameter_infile="TOPPAR:ion.param") + +{* heme parameter file *} +eval ($heme_parameter_infile="TOPPAR:hemes-allhdg.param") + +{* shape parameter file *} +eval ($shape_parameter_infile="TOPPAR:shape.param") + +{* cofactors parameter file *} +eval ($cofactors_parameter_infile="TOPPAR:cofactors.param") + +parameter + @@$prot_parameter_infile + @@$ion_parameter_infile + @@$nucl_parameter_infile + @@$carbo_parameter_infile + @@$solv_parameter_infile + @@$ligands_parameter_infile + @@$heme_parameter_infile + @@$shape_parameter_infile + @@$cofactors_parameter_infile + if ($ligand_param_fname # "") then + fileexist $ligand_param_fname end + if ($result eq true) then + @@$ligand_param_fname + end if + end if +end + +parameter + nbonds + nbxmod=5 atom cdie shift + cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25 + wmin=0.5 tolerance 0.5 + end +end + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/restrain-ions.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/restrain-ions.cns new file mode 100644 index 0000000000000000000000000000000000000000..52a5b3d2024ac21f44456d9ed204d455d8380ac2 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/restrain-ions.cns @@ -0,0 +1,109 @@ +! restrain-ions.cns +! distance restraints between an ion and any coordinating atom within 5A +! to maintain the coordination topologu +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +noe class dist end + +! first deal with monoatomic ions +evaluate ($pcount = 0) +for $id1 in id ( name "LI+1" or name "F-1" or name "NA+1" or name "MG+2" or name "AL+3" + or name "CL-1" or name "K+1" or name "CA+2" or name "V+2" or name "V+3" + or name "CR+2" or name "CR+3" or name "MN+2" or name "MN+3" or name "FE+2" + or name "FE+3" or name "NI+2" or name "CO+2" or name "CO+3" or name "CU+1" + or name "CU+2" or name "ZN+2" or name "BR-1" or name "SR+2" or name "MO+3" + or name "AG+1" or name "CD+2" or name "I-1" or name "CS+2" or name "HO+3" + or name "YB+2" or name "YB+3" or name "OS+4" or name "IR+3" or name "PT+2" + or name "AU+1" or name "AU+2" or name "HG+1" or name "HG+2" or name "PB+2" + or name "U+3" or name "U+4" or name "ZN+1" or name "ZN" ) loop sions + + show (segid) (id $id1) + evaluate ($segid1=$result) + show (resid) (id $id1) + evaluate ($resid1=$result) + show (resname) (id $id1) + evaluate ($resname1=$result) + show (name) (id $id1) + evaluate ($name1=$result) + + evaluate ($mindis = 4.0) + for $id2 in id ( (name O* or name S* or name N*) and (id $id1) around $mindis and + (resn ACE or resn ALA or resn ALY or resn ARG or resn ASN or resn ASH or resn ASP or + resn CSP or resn CTN or resn CYC or resn CYF or resn CYM or resn CYS or resn DDZ or + resn GLN or resn GLH or resn GLU or resn GLY or resn HIS or resn HY3 or resn HYP or + resn ILE or resn LEU or resn LYS or resn M3L or resn MLY or resn MLZ or resn MET or + resn MSE or resn NEP or resn NME or resn PHE or resn PNS or resn PRO or resn PTR or + resn QSR or resn SEP or resn SER or resn SEC or resn THR or resn TOP or resn TRP or + resn TYP or resn TYR or resn TYS or resn VAL or resn A or resn C or resn G or + resn T or resn DA or resn DC or resn DG or resn DT or resn DJ )) loop search + + pick bond (id $id1) (id $id2) geometry + evaluate ($upper = $result) + show (segid) (id $id2) + evaluate ($segid2=$result) + show (resid) (id $id2) + evaluate ($resid2=$result) + show (name) (id $id2) + evaluate ($name2=$result) + + if ($segid1 eq $segid2) then + noe + assign (resid $resid1 and segid $segid1 and name $name1) + (resid $resid2 and segid $segid2 and name $name2) $upper 0.1 0.1 + end + end if + + end loop search + +end loop sions + +! then deal with multiatomic mions +evaluate ($pcount = 0) +for $id1 in id ( (resn SO4 or resn PO4 or resn WO4) and name O* ) loop mions + + show (segid) (id $id1) + evaluate ($segid1=$result) + show (resid) (id $id1) + evaluate ($resid1=$result) + show (resname) (id $id1) + evaluate ($resname1=$result) + show (name) (id $id1) + evaluate ($name1=$result) + + evaluate ($mindis = 4.0) + for $id2 in id ( (name O* or name S* or name N*) and (id $id1) around $mindis and + (resn ACE or resn ALA or resn ALY or resn ARG or resn ASN or resn ASH or resn ASP or + resn CSP or resn CTN or resn CYC or resn CYF or resn CYM or resn CYS or resn DDZ or + resn GLN or resn GLH or resn GLU or resn GLY or resn HIS or resn HY3 or resn HYP or + resn ILE or resn LEU or resn LYS or resn M3L or resn MLY or resn MLZ or resn MET or + resn MSE or resn NEP or resn NME or resn PHE or resn PNS or resn PRO or resn PTR or + resn QSR or resn SEP or resn SER or resn SEC or resn THR or resn TOP or resn TRP or + resn TYP or resn TYR or resn TYS or resn VAL or resn A or resn C or resn G or + resn T or resn DA or resn DC or resn DG or resn DT or resn DJ )) loop search + + pick bond (id $id1) (id $id2) geometry + evaluate ($upper = $result) + show (segid) (id $id2) + evaluate ($segid2=$result) + show (resid) (id $id2) + evaluate ($resid2=$result) + show (name) (id $id2) + evaluate ($name2=$result) + + if ($segid1 eq $segid2) then + noe + assign (resid $resid1 and segid $segid1 and name $name1) + (resid $resid2 and segid $segid2 and name $name2) $upper 0.1 0.1 + end + end if + + end loop search + +end loop mions diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool1.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool1.cns new file mode 100644 index 0000000000000000000000000000000000000000..50f5c12224d2bb294a7de5b33b6a586ca1e7dd75 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool1.cns @@ -0,0 +1,130 @@ +! sa_ltad_cool1.cns +! Perform the first simulated annealing stage of it1 +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($ncycle = 10) + +evaluate ($interstep = ($SaProtocol.inter_fin_rigid - $SaProtocol.inter_init_rigid)/($ncycle-1)) +evaluate ($kinter = $SaProtocol.inter_init_rigid) + +evaluate ($asy_add = ($Data.asy_cool1-$Data.asy_hot)/$ncycle) +evaluate ($masy_add = ($Data.masy_cool1-$Data.masy_hot)/$ncycle) + +evaluate ($asy=$Data.asy_hot) +evaluate ($masy=$Data.masy_hot) +noe + rswitch ambi $Data.Rswi_hot + rswitch dist $Data.Rswi_hot + rswitch hbon $Data.Rswi_hot + + mrswitch ambi $Data.mRswi_hot + mrswitch dist $Data.mRswi_hot + mrswitch hbon $Data.mRswi_hot + + asym ambi $Data.asy_hot + asym dist $Data.asy_hot + asym hbon $Data.asy_hot + + masym ambi $Data.masy_hot + masym dist $Data.masy_hot + masym hbon $Data.masy_hot +end + +restraints dihedral scale=$Data.dihedrals_cool1 end + + +evaluate ($tempstep = ($SaProtocol.t1_init - $SaProtocol.t1_final)/$ncycle) +evaluate ($calcsteps = int($SaProtocol.cool1_steps/$ncycle)) +evaluate ($printsteps = int($calcsteps / 4)) +evaluate ($timestep = $SaProtocol.timestep*$SaProtocol.tadfactor) + +if ($Data.unambig_hot = 0) then + evaluate ($Data.unambig_hot = 0.000001) +end if +if ($Data.unambig_cool1 = 0) then + evaluate ($Data.unambig_cool1 = 0.000001) +end if +if ($Data.ambig_hot = 0)then + evaluate ($Data.ambig_hot = 0.000001) +end if +if ($Data.ambig_cool1 = 0) then + evaluate ($Data.ambig_cool1 = 0.000001) +end if +if ($Data.hbond_hot = 0) then + evaluate ($Data.hbond_hot = 0.000001) +end if +if ($Data.hbond_cool1 = 0) then + evaluate ($Data.hbond_cool1 = 0.000001) +end if + +evaluate ($k_unamb= $Data.unambig_hot) +evaluate ($unambig_fac = ($Data.unambig_cool1/$Data.unambig_hot)^(1/$ncycle)) +evaluate ($k_amb= $Data.ambig_hot) +evaluate ($ambig_fac = ($Data.ambig_cool1/$Data.ambig_hot)^(1/$ncycle)) +evaluate ($k_hbond= $Data.hbond_hot) +evaluate ($hbond_fac = ($Data.hbond_cool1/$Data.hbond_hot)^(1/$ncycle)) + + +evaluate ($bath = $SaProtocol.t1_init) +do (vx=maxwell($bath)) ( all ) +do (vy=maxwell($bath)) ( all ) +do (vz=maxwell($bath)) ( all ) + + + +evaluate ($reassign = TRUE) +evaluate ($i_cool = 0) +while ($i_cool < $ncycle) loop cool + + evaluate ($i_cool=$i_cool+1) + + evaluate ($bath = $bath - $tempstep) + evaluate ($k_unamb = $k_unamb*$unambig_fac) + evaluate ($k_amb = $k_amb*$ambig_fac) + evaluate ($k_hbond = $k_hbond*$hbond_fac) + evaluate ($asy=$asy+$asy_add) + evaluate ($masy=$masy+$masy_add) + + noe + scale dist $k_unamb + scale ambi $k_amb + scale hbon $k_hbond + asym ambi $asy + asym dist $asy + asym hbon $asy + masym ambi $masy + masym dist $masy + masym hbon $masy + end + + !scale intermolecular interactions + inline @MODULE:scale_inter.cns + evaluate ($kinter = $kinter + $interstep) + + dyna tors + reassign $reassign + timestep=$timestep + nstep=$calcsteps + nprint=$printsteps + ntrfrq=0 + tcoupling = true temperature = $bath + end + + energy end + if ($ener > 99999999) then + display ENERGY PROBLEM, THE SYSTEM IS BLOWING UP: ==> STOPPING + stop + end if + evaluate ($reassign = FALSE) + +end loop cool + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool2.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool2.cns new file mode 100644 index 0000000000000000000000000000000000000000..eac233612324c1350e4513e2996a029f27b34dab --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool2.cns @@ -0,0 +1,130 @@ +! sa_ltad_cool2.cns +! Perform the second simulation annealing stage of it1 +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($ncycle = 10) + +evaluate ($asy_add = ($Data.asy_cool2-$Data.asy_cool1)/$ncycle) +evaluate ($masy_add = ($Data.masy_cool2-$Data.masy_cool1)/$ncycle) + +evaluate ($asy=$Data.asy_cool1) +evaluate ($masy=$Data.masy_cool1) + +noe + rswitch ambi $Data.Rswi_cool1 + rswitch dist $Data.Rswi_cool1 + rswitch hbon $Data.Rswi_cool1 + + mrswitch ambi $Data.mRswi_cool1 + mrswitch dist $Data.mRswi_cool1 + mrswitch hbon $Data.mRswi_cool1 + + asym ambi $Data.asy_cool1 + asym dist $Data.asy_cool1 + asym hbon $Data.asy_cool1 + + masym ambi $Data.masy_cool1 + masym dist $Data.masy_cool1 + masym hbon $Data.masy_cool1 +end + +restraints dihedral scale=$Data.dihedrals_cool2 end + + +evaluate ($interstep = ($SaProtocol.inter_fin_cool2 - $SaProtocol.inter_init_cool2)/($ncycle-1)) +evaluate ($kinter = $SaProtocol.inter_init_cool2) + +evaluate ($tempstep = ($SaProtocol.t2_init - $SaProtocol.t2_final)/$ncycle) +evaluate ($calcsteps = int($SaProtocol.cool2_steps/$ncycle)) +evaluate ($printsteps = int($calcsteps / 4)) +evaluate ($timestep = $SaProtocol.timestep*$SaProtocol.tadfactor) + +if ($Data.unambig_cool1 = 0) then + evaluate ($Data.unambig_cool1 = 0.000001) +end if +if ($Data.unambig_cool2 = 0) then + evaluate ($Data.unambig_cool2 = 0.000001) +end if +if ($Data.ambig_cool1 = 0) then + evaluate ($Data.ambig_cool1 = 0.000001) +end if +if ($Data.ambig_cool2 = 0) then + evaluate ($Data.ambig_cool2 = 0.000001) +end if +if ($Data.hbond_cool1 = 0) then + evaluate ($Data.hbond_cool1 = 0.000001) +end if +if ($Data.hbond_cool2 = 0) then + evaluate ($Data.hbond_cool2 = 0.000001) +end if + +evaluate ($k_unamb= $Data.unambig_cool1) +evaluate ($unambig_fac = ($Data.unambig_cool2/$Data.unambig_cool1)^(1/$ncycle)) +evaluate ($k_amb= $Data.ambig_cool1) +evaluate ($ambig_fac = ($Data.ambig_cool2/$Data.ambig_cool1)^(1/$ncycle)) +evaluate ($k_hbond= $Data.hbond_cool1) +evaluate ($hbond_fac = ($Data.hbond_cool2/$Data.hbond_cool1)^(1/$ncycle)) + + +evaluate ($bath = $SaProtocol.t2_init) +do (vx=maxwell($bath)) ( all ) +do (vy=maxwell($bath)) ( all ) +do (vz=maxwell($bath)) ( all ) + +evaluate ($reassign = TRUE) +evaluate ($i_cool = 0) +while ($i_cool < $ncycle) loop cool + + evaluate ($i_cool=$i_cool+1) + + evaluate ($bath = $bath - $tempstep) + evaluate ($k_unamb = $k_unamb*$unambig_fac) + evaluate ($k_amb = $k_amb*$ambig_fac) + evaluate ($k_hbond = $k_hbond*$hbond_fac) + evaluate ($asy=$asy+$asy_add) + evaluate ($masy=$masy+$masy_add) + + + noe + scale dist $k_unamb + scale ambi $k_amb + scale hbon $k_hbond + asym ambi $asy + asym dist $asy + asym hbon $asy + masym ambi $masy + masym dist $masy + masym hbon $masy + end + + !scale intermolecular interactions: + inline @MODULE:scale_inter.cns + evaluate ($kinter = $kinter + $interstep) + + dyna tors + reassign $reassign + timestep=$timestep + nstep=$calcsteps + nprint=$printsteps + ntrfrq=0 + tcoupling = true temperature = $bath + end + evaluate ($reassign = FALSE) + + energy end + if ($ener > 99999999) then + display ENERGY PROBLEM, THE SYSTEM IS BLOWING UP: ==> STOPPING + stop + end if + +end loop cool + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool3.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool3.cns new file mode 100644 index 0000000000000000000000000000000000000000..892a824572ffe8c839b07d655cd8b47f21882f43 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_cool3.cns @@ -0,0 +1,128 @@ +! sa_ltad_cool3.cns +! Perfrom the third simulated annealing stage of it1 +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($ncycle = 20) + +evaluate ($asy_add = ($Data.asy_cool3-$Data.asy_cool2)/$ncycle) +evaluate ($masy_add = ($Data.masy_cool3-$Data.masy_cool2)/$ncycle) + +evaluate ($asy=$Data.asy_cool2) +evaluate ($masy=$Data.masy_cool2) + +noe + rswitch ambi $Data.Rswi_cool2 + rswitch dist $Data.Rswi_cool2 + rswitch hbon $Data.Rswi_cool2 + + mrswitch ambi $Data.mRswi_cool2 + mrswitch dist $Data.mRswi_cool2 + mrswitch hbon $Data.mRswi_cool2 + + asym ambi $Data.asy_cool2 + asym dist $Data.asy_cool2 + asym hbon $Data.asy_cool2 + + masym ambi $Data.masy_cool2 + masym dist $Data.masy_cool2 + masym hbon $Data.masy_cool2 +end + +restraints dihedral scale=$Data.dihedrals_cool3 end + + +evaluate ($interstep = ($SaProtocol.inter_fin_cool3 - $SaProtocol.inter_init_cool3)/($ncycle-1)) +evaluate ($kinter = $SaProtocol.inter_init_cool3) + +evaluate ($tempstep = ($SaProtocol.t3_init - $SaProtocol.t3_final)/$ncycle) +evaluate ($calcsteps = int($SaProtocol.cool3_steps/$ncycle)) +evaluate ($printsteps = int($calcsteps / 4)) +evaluate ($timestep = $SaProtocol.timestep*$SaProtocol.tadfactor) + +if ($Data.unambig_cool2 = 0) then + evaluate ($Data.unambig_cool2 = 0.000001) +end if +if ($Data.unambig_cool3 = 0) then + evaluate ($Data.unambig_cool3 = 0.000001) +end if +if ($Data.ambig_cool2 = 0) then + evaluate ($Data.ambig_cool2 = 0.000001) +end if +if ($Data.ambig_cool3 = 0) then + evaluate ($Data.ambig_cool3 = 0.000001) +end if +if ($Data.hbond_cool2 = 0) then + evaluate ($Data.hbond_cool2 = 0.000001) +end if +if ($Data.hbond_cool3 = 0) then + evaluate ($Data.hbond_cool3 = 0.000001) +end if + +evaluate ($k_unamb= $Data.unambig_cool2) +evaluate ($unambig_fac = ($Data.unambig_cool3/$Data.unambig_cool2)^(1/$ncycle)) +evaluate ($k_amb= $Data.ambig_cool2) +evaluate ($ambig_fac = ($Data.ambig_cool3/$Data.ambig_cool2)^(1/$ncycle)) +evaluate ($k_hbond= $Data.hbond_cool2) +evaluate ($hbond_fac = ($Data.hbond_cool3/$Data.hbond_cool2)^(1/$ncycle)) + +evaluate ($bath = $SaProtocol.t3_init) +do (vx=maxwell($bath)) ( all ) +do (vy=maxwell($bath)) ( all ) +do (vz=maxwell($bath)) ( all ) + +evaluate ($reassign = TRUE) +evaluate ($i_cool = 0) +while ($i_cool < $ncycle) loop cool + + evaluate ($i_cool=$i_cool+1) + + evaluate ($bath = $bath - $tempstep) + evaluate ($k_unamb = $k_unamb*$unambig_fac) + evaluate ($k_amb = $k_amb*$ambig_fac) + evaluate ($k_hbond = $k_hbond*$hbond_fac) + evaluate ($asy=$asy+$asy_add) + evaluate ($masy=$masy+$masy_add) + + noe + scale dist $k_unamb + scale ambi $k_amb + scale hbon $k_hbond + asym ambi $asy + asym dist $asy + asym hbon $asy + masym ambi $masy + masym dist $masy + masym hbon $masy + end + + !scale intermolecular interactions: + inline @MODULE:scale_inter.cns + evaluate ($kinter = $kinter + $interstep) + + dyna tors + reassign $reassign + timestep=$timestep + nstep=$calcsteps + nprint=$printsteps + ntrfrq=0 + tcoupling = true temperature = $bath + end + evaluate ($reassign = FALSE) + + energy end + if ($ener > 99999999) then + display ENERGY PROBLEM, THE SYSTEM IS BLOWING UP: ==> STOPPING + stop + end if + +end loop cool + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_hightemp.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_hightemp.cns new file mode 100644 index 0000000000000000000000000000000000000000..8b346d4ab71650e35d1a527508d745457fcd8b19 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/sa_ltad_hightemp.cns @@ -0,0 +1,65 @@ +! sa_ltad_hightemp.cns +! Perform the high-temperature rigid-body MD of it1 +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($calcsteps= $SaProtocol.initiosteps) +evaluate ($printsteps= max(int($calcsteps/10),1)) + +noe + rswitch ambi $Data.Rswi_hot + rswitch dist $Data.Rswi_hot + rswitch hbon $Data.Rswi_hot + + mrswitch ambi $Data.mRswi_hot + mrswitch dist $Data.mRswi_hot + mrswitch hbon $Data.mRswi_hot + + asym ambi $Data.asy_hot + asym dist $Data.asy_hot + asym hbon $Data.asy_hot + + masym ambi $Data.masy_hot + masym dist $Data.masy_hot + masym hbon $Data.masy_hot +end + +evaluate ($bath = $SaPRotocol.tadhigh_t) +evaluate ($timestep = $SaProtocol.timestep*$SaProtocol.tadfactor) + +do (vx = maxwell($bath)) (all) +do (vy = maxwell($bath)) (all) +do (vz = maxwell($bath)) (all) + + +restraints dihedral scale $Data.dihedrals_hot end + +evaluate ($reassign = TRUE) + +noe + scale dist $Data.unambig_hot + scale ambi $Data.ambig_hot + scale hbon $Data.hbond_hot +end + +evaluate ($kinter = $SaProtocol.inter_init_rigid) +inline @MODULE:scale_inter.cns + +dyna tors + reassign $reassign + timestep=$timestep + nstep=$calcsteps + nprint=$printsteps + ntrfrq=0 + tcoupling = true temperature = $bath +end + +evaluate ($reassign = FALSE) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter.cns new file mode 100644 index 0000000000000000000000000000000000000000..7088087a65b71bcdb213cce29d86ab6c043225e8 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter.cns @@ -0,0 +1,45 @@ +! scale_inter.cns +! Scaling of intermolecular interactions +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * $scale.int_$nchain1_$nchain1 end + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + ((resn WAT or resn HOH or resn TIP* or resn DMS)) weight * 1.0 vdw $kinter elec $kinter end + + eval($nchain2 = $nchain1 ) + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + eval($scalfac = $kinter * $scale.int_$nchain1_$nchain2) + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain2 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1.0 vdw $scalfac elec $scalfac end + end loop nloop2 + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + + interaction ((resn WAT or resn HOH or resn TIP* or resn DMS)) ((resn WAT or resn HOH or resn TIP* or resn DMS)) weight * 1.0 end + +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_final.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_final.cns new file mode 100644 index 0000000000000000000000000000000000000000..efae5ce10a1fdafe1ef2f1d47a0ff9ebe57a1c8f --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_final.cns @@ -0,0 +1,39 @@ +! scale_inter_final.cns +! Scaling of intermolecular interactions +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + eval($nchain2 = $nchain1 ) + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + eval($scalfac = $kinter * $scale.int_$nchain1_$nchain2) + interaction (segid $prot_segid_$nchain1 and not + (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA or resn DPP or resn PCW or resn PEE)) + (segid $prot_segid_$nchain2 and not + (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA or resn DPP or resn PCW or resn PEE)) weight * 1.0 vdw $scalfac elec $scalfac end + end loop nloop2 + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_only.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_only.cns new file mode 100644 index 0000000000000000000000000000000000000000..7abf15e4f42ad05aaeaf8c654c01ad1ea178d2c5 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_inter_only.cns @@ -0,0 +1,41 @@ +! scale_inter_only.cns +! Scaling of intermolecular interaction (not internal energies) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + eval($nchain2 = $nchain1 ) + while ($nchain2 < $data.ncomponents) loop nloop2 + eval($nchain2 = $nchain2 + 1) + eval($scalfac = $kinter * $mol_int_$nchain1_$nchain2) + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain2 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1.0 vdw $scalfac elec $scalfac end + end loop nloop2 + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + ((resn WAT or resn HOH or resn TIP* or resn DMS)) weight * 1.0 vdw $kinter elec $kinter end + + end loop nloop1 + + interaction ((resn WAT or resn HOH or resn TIP*)) ((resn WAT or resn HOH or resn TIP*)) weight * 1.0 end + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_intra_only.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_intra_only.cns new file mode 100644 index 0000000000000000000000000000000000000000..15b0adfbb562862214f161c494c14a17dbf6beb7 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/scale_intra_only.cns @@ -0,0 +1,36 @@ +! scale_intra_only.cns +! Scaling of intramolecular energies (no intermolecular energies) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! +igroup interaction (not all) (not all) end + +igroup + + eval($nchain1 = 0) + + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + + interaction (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) + (segid $prot_segid_$nchain1 and not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1.0 end + + end loop nloop1 + + interaction (resn ANI) (resn ANI) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DAN) (resn DAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn XAN) (resn XAN) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn DUM) (resn DUM) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (resn SHA) weight * 1.0 vdw 0.0 elec 0.0 end + interaction (resn SHA) (not resn SHA) weight * 0.0 end + +end + + + diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/separate.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/separate.cns new file mode 100644 index 0000000000000000000000000000000000000000..b25ebaee28aca28e90322a5466a5700a2f100538 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/separate.cns @@ -0,0 +1,236 @@ +! separate.cns +! Distribute molecules in 3D space +! Orient each molecule according to its principal axes +! and restore them all at the end (after the while loop) +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +! first flag all fixed molecules +do (store4 = 0) (all) +evaluate ($ncount = 0) +evaluate ($nfixed = 0) +while ($ncount < $data.ncomponents) loop orientmol + evaluate ($ncount = $ncount + 1) + if ($mol_fix_origin_$ncount eq true) then + evaluate ($nfixed = $nfixed + 1) + do (store4 = 1) (segid $prot_segid_$ncount) + end if +end loop orientmol + +if ($nfixed < $data.ncomponents) then + + evaluate ($xc = 0.0) + evaluate ($yc = 0.0) + evaluate ($zc = 0.0) + ! then define the geometrical center of the fixed molecules if present + show sum (store4) (all) + if ($result > 0) then + show ave (x) (attribute store4 = 1) + evaluate ($xc = $result) + show ave (y) (attribute store4 = 1) + evaluate ($yc = $result) + show ave (z) (attribute store4 = 1) + evaluatee ($zc = $result) + end if + + do (xcomp = x) (all) + do (ycomp = y) (all) + do (zcomp = z) (all) + + ! then orient each moving molecule separately at the origin + ! and translate it to the geometric center of the fixed molecules + evaluate ($ncount = 0) + while ($ncount < $data.ncomponents) loop orientmol + evaluate ($ncount = $ncount +1) + eval($watersegname_$ncount="WA" + encode($ncount)) + if ($mol_fix_origin_$ncount eq false) then + coor orient sele=(segid $prot_segid_$ncount or segid $watersegname_$ncount) end + coor sele=(segid $prot_segid_$ncount or segid $watersegname_$ncount) translate vector = ($xc $yc $zc) end + do (xcomp = x) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + do (ycomp = y) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + do (zcomp = z) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + end if + end loop orientmol + + do (x = xcomp) (not (resn ANI or resn XAN or resn DAN)) + do (y = ycomp) (not (resn ANI or resn XAN or resn DAN)) + do (z = zcomp) (not (resn ANI or resn XAN or resn DAN)) + + ! Find the largest axis of all molecules + evaluate ($minispacing = 25.0) + evaluate ($mxdim = 0) + evaluate ($ncount = 0) + + while ($ncount < $data.ncomponents) loop findmax + evaluate ($ncount = $ncount +1) + + show max (x) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($xdim = $result) + show min (x) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($xdim = $xdim - $result) + + show max (y) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($ydim = $result) + show min (y) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($ydim = $ydim - $result) + + show max (z) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($zdim = $result) + show min (z) (segid $prot_segid_$ncount or segid $watersegname_$ncount) + evaluate ($zdim = $zdim - $result) + + ! Check which dimension (x,y,z) is the largest = mxdim + evaluate ($mxdim = max($mxdim, $xdim, $ydim, $zdim)) + + end loop findmax + + evaluate ($spacing = $minispacing + $mxdim ) + display SPACING SET TO $spacing ANGSTROM + + ! This has to be manually coded because of the variable name + ! Should be fine since we support only a few types of symmetry + ! Maybe change the variable name later if these are expanded + ! to have the number at the end? + + inline @MODULE:check-homomers.cns + + if ($homosymmetry eq true) then + ! In case of homosymmetry, place molecules in a plane + do (store4 = 0) (all) + evaluate ($ncount = 0) + while ($ncount < $data.ncomponents) loop orientmol + evaluate ($ncount = $ncount + 1) + if ($mol_fix_origin_$ncount eq false) then + do (store4 = 1) (segid $prot_segid_$ncount) + end if + end loop orientmol + + {* translate and generate symmetric positions by rotation around z *} + coor trans sele=(attr store4=1) vector=($spacing,0,0) end + + ! if one molecule is fixed (e.g. plane), move all others along z-axis + !if ($data.ncomponents > $n_moving_mol) then + ! coor trans sele=(attr store4=1) vector=(0,0,$spacing) end + !end if + + evaluate ($ncount = 2) + evaluate ($increment = 360/$n_moving_mol) + while ($ncount le $data.ncomponents) loop orientsym + + if ($mol_fix_origin_$ncount eq false) then + {* rotate around z axis *} + evaluate ($xr = $increment) + evaluate ($x1 = cos($xr)) + evaluate ($x2 = -sin($xr)) + evaluate ($x3 = 0 ) + evaluate ($y1 = sin($xr)) + evaluate ($y2 = cos($xr)) + evaluate ($y3 = 0 ) + evaluate ($z1 = 0 ) + evaluate ($z2 = 0 ) + evaluate ($z3 = 1 ) + coor + center=($xc $yc $zc) + rotate matrix=($x1 $x2 $x3) ($y1 $y2 $y3) ($z1 $z2 $z3) + sele=(segid $prot_segid_$ncount or segid $watersegname_$ncount) + end + evaluate ($increment = $xr + 360/$n_moving_mol) + + end if + evaluate ($ncount = $ncount + 1) + + end loop orientsym + + else + ! Do we need fix any molecule? + evaluate($n_moving_mol = 0) + evaluate ($ncount = 0) + while ($ncount < $data.ncomponents) loop centermol + evaluate ($ncount = $ncount + 1) + if ($mol_fix_origin_$ncount eq false) then + evaluate($n_moving_mol = $n_moving_mol + 1) + end if + end loop centermol + + ! Translate molecules to positions calculated using an algorithm + ! based on minimization of electrostatic potential of N equally charged particles. + ! See Thomson problem: http://en.wikipedia.org/wiki/Thomson_problem + evaluate ($filename = "TOPPAR:initial_positions/trans_vector_" + encode($n_moving_mol) ) + inline @@$filename + + ! Logic: + ! Assign a random number larger than 0 to every molecule + ! Assign 0.0 to fixed molecules + ! For every i up to the number of molecules + ! pick the mol with the largest number and displace it + ! then zero its number. + ! This will place molecules in space sort of randomly + ! Stop when the sum of all numbers is zero + + ! Generate as many random numbers as the # of mols + evaluate ($ncount = 0) + while ($ncount < $data.ncomponents) loop genrandom + evaluate ($ncount = $ncount + 1) + if ($mol_fix_origin_$ncount eq true) then + evaluate ($random_$ncount = 0.0) + else + evaluate ($random_$ncount = random()) + end if + end loop genrandom + + ! Randomly pick a molecule and place it + ! on the pre-defined position - iterate + evaluate ($sum_random = 999) + evaluate ($molcounter = 1) + + while ($sum_random > 0) loop placemol + evaluate ($maximum = 0) + evaluate ($maxid = 0) + evaluate ($ncount = 0) + + ! Select molecule with largest random number + while ($ncount < $data.ncomponents) loop selectmol + evaluate ($ncount = $ncount + 1) + if ($random_$ncount > $maximum) then + evaluate ($maximum = $random_$ncount) + evaluate ($maxid = $ncount) + end if + end loop selectmol + + if ($mol_fix_origin_$maxid eq false) then + coor trans + sele=(segid $prot_segid_$maxid or segid $watersegname_$maxid) + vector=($x_$molcounter, $y_$molcounter, $z_$molcounter) + end + + ! Reset random_ncount to 0 to avoid re-selecting + evaluate ($random_$maxid = 0) + + ! Increment molcounter to update new + evaluate ($molcounter = $molcounter + 1) + + ! Update sum_random + evaluate ($ncount = 0) + evaluate ($sum_random = 0) + + while ($ncount < $data.ncomponents) loop resetsumrandom + evaluate ($ncount = $ncount + 1) + evaluate( $sum_random = $sum_random + $random_$ncount) + end loop resetsumrandom + + end if + end loop placemol + end if + + do (x = refx) (resn ANI or resn DAN or resn XAN) + do (y = refy) (resn ANI or resn DAN or resn XAN) + do (z = refz) (resn ANI or resn DAN or resn XAN) + +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/setflags.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/setflags.cns new file mode 100644 index 0000000000000000000000000000000000000000..754df3959432795dadf9f62a136995689f23ef0d --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/setflags.cns @@ -0,0 +1,24 @@ +! setflags.cns +! Defines energy flags +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +if ($Data.cdih.on eq true) then + evaluate ($Data.flags.cdih = true) +end if +if ($Data.flags.noe = TRUE) then + flags include noe end +end if +if ($Data.flags.cdih = TRUE) then + flags include cdih end +end if +if ($Data.flags.ncs = TRUE) then + flags include ncs end +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/symmultimer.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/symmultimer.cns new file mode 100644 index 0000000000000000000000000000000000000000..3b4f731e948bf1d58eab0f71f457da6e52afc3e9 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/symmultimer.cns @@ -0,0 +1,677 @@ +! symmultimer.cns +! Define symmetry restraints +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +if ($Data.flags.sym eq true) then + + noe class symm end + + ! Define C2 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.nc2sym) loop c2symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c2sym_sta1_$ncount) + evaluate ($i1end = $c2sym_end1_$ncount) + evaluate ($chain1 = $c2sym_seg1_$ncount) + evaluate ($i2start = $c2sym_sta2_$ncount) + evaluate ($i2end = $c2sym_end2_$ncount) + evaluate ($chain2 = $c2sym_seg2_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + if ($diff1 ne $diff2) then + display CHAIN LENGTH FOR SYMMETRY RESTRAINTS DOES NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc2sym + + evaluate ($resid1 = $i1start) + evaluate ($resid2 = $i2end - $icount) + evaluate ($resid3 = $i2start) + evaluate ($resid4 = $i1end - $icount) + + noe + assign (resid $resid1 and (name CA or name P or name BB) and segid $chain1) + (resid $resid2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resid3 and (name CA or name P or name BB) and segid $chain2) + (resid $resid4 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + end + + evaluate ($icount = $icount + 1) + evaluate ($i1start = $i1start + 1) + evaluate ($i2start = $i2start + 1) + + end loop genc2sym + + end loop c2symloop + + + ! Define C3 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.nc3sym) loop c3symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c3sym_sta1_$ncount) + evaluate ($i1end = $c3sym_end1_$ncount) + evaluate ($chain1 = $c3sym_seg1_$ncount) + evaluate ($i2start = $c3sym_sta2_$ncount) + evaluate ($i2end = $c3sym_end2_$ncount) + evaluate ($chain2 = $c3sym_seg2_$ncount) + evaluate ($i3start = $c3sym_sta3_$ncount) + evaluate ($i3end = $c3sym_end3_$ncount) + evaluate ($chain3 = $c3sym_seg3_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc3sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + + noe + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + 2) + evaluate ($i1start = $i1start + 2) + evaluate ($i2start = $i2start + 2) + evaluate ($i3start = $i3start + 2) + + end loop genc3sym + + end loop c3symloop + + ! Define S3 symmetry restraints for symmetrical multimers + ! + eval ($ncount = 0) + while ($ncount < $data.ns3sym) loop s3symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $s3sym_sta1_$ncount) + evaluate ($i1end = $s3sym_end1_$ncount) + evaluate ($chain1 = $s3sym_seg1_$ncount) + evaluate ($i2start = $s3sym_sta2_$ncount) + evaluate ($i2end = $s3sym_end2_$ncount) + evaluate ($chain2 = $s3sym_seg2_$ncount) + evaluate ($i3start = $s3sym_sta3_$ncount) + evaluate ($i3end = $s3sym_end3_$ncount) + evaluate ($chain3 = $s3sym_seg3_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + eval ($istep = 4) + eval ($istop = $i1end - $istep) + while ($i1start < $istop) loop gens3sym + + evaluate ($resst11 = $i1start) + evaluate ($resst21 = $i1start+1) + evaluate ($resst12 = $i2start) + evaluate ($resst22 = $i2start+1) + evaluate ($resst13 = $i3start) + evaluate ($resst23 = $i3start+1) + + + noe + + assign (resid $resst11 and (name CA or name P or name BB) and segid $chain1) + (resid $resst12 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst12 and (name CA or name P or name BB) and segid $chain2) + (resid $resst13 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst21 and (name CA or name P or name BB) and segid $chain1) + (resid $resst22 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst22 and (name CA or name P or name BB) and segid $chain2) + (resid $resst23 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + + end loop gens3sym + + end loop s3symloop + + ! Define C4 symmetry restraints for symmetrical multimers + ! + eval ($istep = 10) + eval ($ncount = 0) + while ($ncount < $data.nc4sym) loop c4symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c4sym_sta1_$ncount) + evaluate ($i1end = $c4sym_end1_$ncount) + evaluate ($chain1 = $c4sym_seg1_$ncount) + evaluate ($i2start = $c4sym_sta2_$ncount) + evaluate ($i2end = $c4sym_end2_$ncount) + evaluate ($chain2 = $c4sym_seg2_$ncount) + evaluate ($i3start = $c4sym_sta3_$ncount) + evaluate ($i3end = $c4sym_end3_$ncount) + evaluate ($chain3 = $c4sym_seg3_$ncount) + evaluate ($i4start = $c4sym_sta4_$ncount) + evaluate ($i4end = $c4sym_end4_$ncount) + evaluate ($chain4 = $c4sym_seg4_$ncount) + + !first check that the chain lengths are equal for the four defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc4sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + + noe + + ! N to N sequential restraints to prevent anti-parallel arrangements + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + ! N to C sequential restraints to assure planarity + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + assign (resid $resen1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resen2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resen2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resen3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resen3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resen4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resen4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resen1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + + end loop genc4sym + + end loop c4symloop + + + ! Define C5 symmetry restraints for symmetrical multimers + ! + eval ($istep = 4) + eval ($ncount = 0) + while ($ncount < $data.nc5sym) loop c5symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c5sym_sta1_$ncount) + evaluate ($i1end = $c5sym_end1_$ncount) + evaluate ($chain1 = $c5sym_seg1_$ncount) + evaluate ($i2start = $c5sym_sta2_$ncount) + evaluate ($i2end = $c5sym_end2_$ncount) + evaluate ($chain2 = $c5sym_seg2_$ncount) + evaluate ($i3start = $c5sym_sta3_$ncount) + evaluate ($i3end = $c5sym_end3_$ncount) + evaluate ($chain3 = $c5sym_seg3_$ncount) + evaluate ($i4start = $c5sym_sta4_$ncount) + evaluate ($i4end = $c5sym_end4_$ncount) + evaluate ($chain4 = $c5sym_seg4_$ncount) + evaluate ($i5start = $c5sym_sta5_$ncount) + evaluate ($i5end = $c5sym_end5_$ncount) + evaluate ($chain5 = $c5sym_seg5_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + evaluate ($diff5 = $i5end - $i5start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff4 ne $diff5) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc5sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resst5 = $i5start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + evaluate ($resen5 = $i5end - $icount) + + noe + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + evaluate ($i5start = $i5start + $istep) + + end loop genc5sym + + end loop c5symloop + + ! Define C6 symmetry restraints for symmetrical multimers + ! + eval ($istep = 10) + eval ($ncount = 0) + while ($ncount < $data.nc6sym) loop c6symloop + + eval ($ncount = $ncount + 1) + evaluate ($i1start = $c6sym_sta1_$ncount) + evaluate ($i1end = $c6sym_end1_$ncount) + evaluate ($chain1 = $c6sym_seg1_$ncount) + evaluate ($i2start = $c6sym_sta2_$ncount) + evaluate ($i2end = $c6sym_end2_$ncount) + evaluate ($chain2 = $c6sym_seg2_$ncount) + evaluate ($i3start = $c6sym_sta3_$ncount) + evaluate ($i3end = $c6sym_end3_$ncount) + evaluate ($chain3 = $c6sym_seg3_$ncount) + evaluate ($i4start = $c6sym_sta4_$ncount) + evaluate ($i4end = $c6sym_end4_$ncount) + evaluate ($chain4 = $c6sym_seg4_$ncount) + evaluate ($i5start = $c6sym_sta5_$ncount) + evaluate ($i5end = $c6sym_end5_$ncount) + evaluate ($chain5 = $c6sym_seg5_$ncount) + evaluate ($i6start = $c6sym_sta6_$ncount) + evaluate ($i6end = $c6sym_end6_$ncount) + evaluate ($chain6 = $c6sym_seg6_$ncount) + + !first check that the chain lengths are equal for the two defined molecules + evaluate ($diff1 = $i1end - $i1start) + evaluate ($diff2 = $i2end - $i2start) + evaluate ($diff3 = $i3end - $i3start) + evaluate ($diff4 = $i4end - $i4start) + evaluate ($diff5 = $i5end - $i5start) + evaluate ($diff6 = $i6end - $i6start) + if ($diff1 ne $diff2) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff1 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff2 ne $diff3) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff3 ne $diff4) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff4 ne $diff5) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + if ($diff5 ne $diff6) then + display CHAIN LENGHT FOR SYMMETRY RESTRAINTS DO NOT MATCH + display PLEASE CHECK CAREFULLY YOUR INPUT + display ... stopping ... + stop + end if + + eval ($icount = 0) + while ($i1start < $i1end) loop genc6sym + + evaluate ($resst1 = $i1start) + evaluate ($resst2 = $i2start) + evaluate ($resst3 = $i3start) + evaluate ($resst4 = $i4start) + evaluate ($resst5 = $i5start) + evaluate ($resst6 = $i6start) + evaluate ($resen1 = $i1end - $icount) + evaluate ($resen2 = $i2end - $icount) + evaluate ($resen3 = $i3end - $icount) + evaluate ($resen4 = $i4end - $icount) + evaluate ($resen5 = $i5end - $icount) + evaluate ($resen6 = $i6end - $icount) + + noe + + ! Around the C6 ring + ! N to N sequential restraints to prevent anti-parallel arrangements + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resst3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resst4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resst5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resst6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resst1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resst2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + ! N to C sequential restraints to assure planarity + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + ! Triples + + assign (resid $resst1 and (name CA or name P or name BB) and segid $chain1) + (resid $resen3 and (name CA or name P or name BB) and segid $chain3) 0 0 0 + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + + assign (resid $resst3 and (name CA or name P or name BB) and segid $chain3) + (resid $resen5 and (name CA or name P or name BB) and segid $chain5) 0 0 0 + assign (resid $resst5 and (name CA or name P or name BB) and segid $chain5) + (resid $resen1 and (name CA or name P or name BB) and segid $chain1) 0 0 0 + + assign (resid $resst2 and (name CA or name P or name BB) and segid $chain2) + (resid $resen4 and (name CA or name P or name BB) and segid $chain4) 0 0 0 + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + + assign (resid $resst4 and (name CA or name P or name BB) and segid $chain4) + (resid $resen6 and (name CA or name P or name BB) and segid $chain6) 0 0 0 + assign (resid $resst6 and (name CA or name P or name BB) and segid $chain6) + (resid $resen2 and (name CA or name P or name BB) and segid $chain2) 0 0 0 + + end + + evaluate ($icount = $icount + $istep) + evaluate ($i1start = $i1start + $istep) + evaluate ($i2start = $i2start + $istep) + evaluate ($i3start = $i3start + $istep) + evaluate ($i4start = $i4start + $istep) + evaluate ($i5start = $i5start + $istep) + evaluate ($i6start = $i6start + $istep) + + end loop genc6sym + + end loop c6symloop + + + noe + potential symm symmetry + scale symm $Data.ksym + sqconstant symm 1.0 + sqexponent symm 2 + soexponent symm 1 + rswitch symm 0.5 + sqoffset symm 0.0 + asymptote symm 1.0 + end + +end if diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/torsiontop.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/torsiontop.cns new file mode 100644 index 0000000000000000000000000000000000000000..020935d984922bfa9297a80ed3df38b7732548c5 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/cns/torsiontop.cns @@ -0,0 +1,108 @@ +! torsiontop.cns +! Create the topology for torsion angle MD first stage +! +! *********************************************************************** +! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * +! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * +! * All rights reserved. * +! * This code is part of the HADDOCK software and governed by its * +! * license. Please see the LICENSE file that should have been included * +! * as part of this package. * +! *********************************************************************** +! + +evaluate ($numtrees=$data.ncomponents) +inline @MODULE:numtrees.cns + +DISPLAY NUMTREES set to $numtrees + +dyna tors + topology + maxtree $numtrees + kdihmax = 23. + + evaluate ($N_atom_id = 0) + evaluate ($atom_id = 0) + + for $atom_id in id ( name CA ) loop main + if ( $N_atom_id > 0 ) then + fix group ( ( byresidue ( id $N_atom_id ) and (name C or name O) ) + or ( byresidue ( id $atom_id ) and (name N or name HN ) ) + ) + end if + evaluate ($N_atom_id = $atom_id) + end loop main + + if ( $atom_id > 0 ) then + fix group ( byresidue ( id $atom_id ) and (name C or name OT1 or name OT2 or name OXT) ) + end if + + for $atom_id in id ( name BB and not (resn PHE or resn TYR or resn TRP or resn HIS or resn ARG or resn LYS)) loop main + if ( $atom_id > 0 ) then + fix group ( byresidue ( id $atom_id )) + end if + end loop main + + for $atom_id in id ( (name CA or name BB) and + (resn PHE or resn TRP or resn HIS or resn ASP or resn ASN or resn NEP)) + loop main + fix group ( byresidue ( id $atom_id ) and (name CG or name %D* or name %Z* or name %E* or name %H* or name SC# )) + end loop main + + for $atom_id in id ( (name CA or name BB) and (resn TYR)) loop main + fix group + ( byresidue ( id $atom_id ) + and (name CG or name %D* or name %Z* or name %E* or name OH or name SC# )) + end loop main + + for $atom_id in id ( (name CA or name BB) and (resn gln or resn glu)) loop main + fix group ( byresidue ( id $atom_id ) and (name %D* or name %E*)) + end loop main + + for $atom_id in id ( (name CA or name BB) and (resn ARG)) loop main + fix group ( byresidue ( id $atom_id ) and ( name %E* or name %Z* or name %H* or name SC# )) + + end loop main + fix group ( resn PRO and not (name C or name O) ) + + !next loop is for all sugars defined in glycans-uu.top + for $atom_id in id + ( name c1 and + (resn GCP or resn GCF or resn GTP or resn GTF or resn MNP + or resn MNF or resn ALP or resn ALF or resn ARP or resn ARF or resn GLP + or resn GLF or resn IDP or resn IDF or resn TLP or resn TLF or resn PCP + or resn PCF or resn FTP or resn FTF or resn SBP or resn SBF or resn TTP + or resn TTF or resn NAA or resn RBP or resn RBF or resn ANF or resn XLF + or resn LXF or resn RLF or resn LLF) + ) loop main + fix group ( byresidue ( id $atom_id ) + and (name %1 or name %2 or name %3 or name %4 or name %5 or name O5)) + end loop main + + for $id in id (name C1') loop freeribose + free bond (id $id) (byresid (id $id) and name C2') + end loop freeribose + + fix group ( resn HEC and (name C1* or name C2* or name C3* or name C4* or name N* or name CH*)) + + fix group ( resn CYM and not (name CA or name BB or name C or name O or name OXT or + name N or name HN or name HA or name CB or name HB1 or name HB2 or + name SG or name SAL or name CAJ)) + + fix group ( byresidue (resn WAT)) + fix group ( byresidue (resn HOH)) + fix group ( byresidue (resn TIP*)) + fix group ( byresidue (resn ANI)) + fix group ( byresidue (resn DAN)) + fix group ( byresidue (resn XAN)) + fix group (resn SHA) + + eval($nchain1 = 0) + while ($nchain1 < $data.ncomponents) loop nloop1 + eval($nchain1 = $nchain1 + 1) + fix group (segid $prot_segid_$nchain1 + and not (attribute store5 > 0) + and not ((resn WAT or resn HOH or resn TIP*))) + end loop nloop1 + end +end diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/defaults.yaml b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1f716e5cd6efee5c54c7e69b2f9873752f80f6d2 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/flexref/defaults.yaml @@ -0,0 +1,5195 @@ +# +# Group molecule +# +mol_fix_origin_1: + default: false + type: boolean + title: Fix molecule + short: Fixes the molecule in its original position. + long: Fixes the molecule in its original position. + group: 'molecule' + explevel: expert +mol_shape_1: + default: false + type: boolean + title: Is the molecule a shape? + short: Defines a molecule as a shape. + long: Defines a molecule as a shape, which is a collection of beads. + group: 'molecule' + explevel: easy +# +# Group distance restraints +# +ambig_fname: + default: '' + type: file + title: Ambiguous distance restraints filename + short: Filename of the ambiguous distance restraints file + long: Filename of the ambiguous distance restraints file. By default 50% of those restraints will be randomly discared. + This can be changed/turned off and is controlled by the randremoval and npart parameters. + Note that this file can contain both ambiguous and unambiguous restraints. + group: 'distance restraints' + explevel: easy +previous_ambig: + default: false + type: boolean + title: Boolean condition on the previous ambiguous distance restraints file + short: Boolean condition on the previous ambiguous distance restraints file. + If true, use the the restraint information coming from the previous CNS module. If false, don't use previous information. + long: Boolean condition on the ambiguous distance restraints file. + If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. + If false, don't use previous information. + group: 'distance restraints' + explevel: expert +unambig_fname: + default: '' + type: file + title: Unambiguous restraints filename + short: Filename of the unambiguous distance restraints file + long: Filename of the unambiguous distance restraints file. All restraints in that file will be used. + Note that this file can contain both ambiguous and unambiguous restraints. + group: 'distance restraints' + explevel: easy +hbond_fname: + default: '' + type: file + title: H-bond restraints filename + short: Filename of the hydrogen bond distance restraints file + long: Filename of the hydrogen bond distance restraints file. Note that this file can contain any type of distance restraints. + group: 'distance restraints' + explevel: easy +ambig_hot: + default: 10 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for ambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA. + long: Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +ambig_cool1: + default: 10 + type: integer + min: 0 + max: 1000 + title: First cooling SA force constant for ambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the SA. + long: Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +ambig_cool2: + default: 50 + type: integer + min: 0 + max: 1000 + title: Second cooling SA force constant for ambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the SA. + long: Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter). + group: 'distance restraints' + explevel: expert +ambig_cool3: + default: 50 + type: integer + min: 0 + max: 1000 + title: Third cooling SA force constant for ambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the SA. + long: Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter). + group: 'distance restraints' + explevel: expert +unambig_hot: + default: 10 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for unambiguous distance restraints + short: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA. + long: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +unambig_cool1: + default: 10 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for unambiguous distance restraints + short: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA. + long: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +unambig_cool2: + default: 50 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for unambiguous distance restraints + short: Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA. + long: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +unambig_cool3: + default: 50 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for unambiguous distance restraints + short: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA. + long: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +hbond_hot: + default: 10 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for hbond distance restraints + short: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA. + long: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +hbond_cool1: + default: 10 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for hydrogen bond restraints + short: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA. + long: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +hbond_cool2: + default: 50 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for hydrogen bond restraints + short: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA. + long: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +hbond_cool3: + default: 50 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for hydrogen bond restraints + short: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA. + long: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter). + group: 'distance restraints' + explevel: expert +randremoval: + default: true + type: boolean + title: Random removal of ambiguous restraints + short: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. + long: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. + The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. + The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart. + group: 'distance restraints' + explevel: expert +npart: + default: 2 + type: integer + min: 1 + max: 20 + title: Number partitions for ambiguous restraints + short: Number of sets into which to randomly partition the ambiguous restraints. + long: Number of sets into which to randomly partition the ambiguous restraints. + The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. + The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart. + group: 'distance restraints' + explevel: expert +contactairs: + default: false + type: boolean + title: Contact restraints + short: Contact restraints between molecules + long: Contact restraints between molecules. These are defined as ambiguous distance restraint + between each residue of a molecule and all residues of the other molecules with 5A from that residue. + This can be used to restraint the contacts between the interfaces. Note that this can generate a large number of ambiguous restraints + and slow down the computations + group: 'distance restraints' + explevel: expert +kcont: + default: 1.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Contact restraints force constant + short: Force constant applied to the contact restraints. + long: Force constant applied to the contact restraints. + group: 'distance restraints' + explevel: expert +cmrest: + default: false + type: boolean + title: Center of mass restraints + short: Automatically defines distance restraints between the geometric center of the various molecules. + long: When turned on, this option will automatically define center of mass restraints between the various molecules. + This allows HADDOCK to operate in ab-initio mode in the absence of any other restraints. But those restraints can also + be combined with other restraints to ensure more compact solutions. The distance restraints are defined between the + geometrical centers of the various molecules (calculated on CA atoms for proteins (BB in case of Martini coarse-grained + molecules) and N1 atoms for nucleic acids. For small ligands, all atoms will be used to define the geometric center. + The upper limit distance is automatically calculated based on the dimension of the molecules (see cmtight description). + group: 'distance restraints' + explevel: expert +cmtight: + default: true + type: boolean + title: Center of mass restraint tightness + short: Defines the upper distance limit based on the sum of the average dimension of the two molecule, + if cmtight=false all three dimensions are used, if set to true the shortest two only are used, + resulting in tighter distance restraints. + long: This parameter controls how the upper limit distance is defined for the center of mass restraints between molecules. + Each molecule is oriented along its principle components and the x,y and z dimensions are calculated. + If cmtight=true, the molecule distance (size) is set to the average of its smallest two half dimensions. + If cmtight=false, the molecule distance (size) is set to the average of its three half dimensions.. + In case of DNA or small ligands the molecule distance (size) is set to 0. + The effective upper distance limit for the center or mass distance restraint is the sum of the two molecule distances. + group: 'distance restraints' + explevel: expert +kcm: + default: 1.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Center of mass restraints force constant + short: Force constant applied to the center of mass restraints + long: Force constant applied to the center of mass restraints + group: 'distance restraints' + explevel: expert +# +# Group dihedral restraints +# +dihe_fname: + default: '' + type: file + title: Dihedral angle restraints filename + short: Filename of the Dihedral angle restraints file + long: Filename of the Dihedral angle restraints file. + group: 'dihedral restraints' + explevel: easy +dihedrals_on: + default: false + type: boolean + title: Use dihedral angle restraints + short: Turns on dihedral angle restraints. + long: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file. + group: 'dihedral restraints' + explevel: easy +dihedrals_hot: + default: 5 + type: integer + min: 0 + max: 1000 + title: Hot phase SA force constant for dihedral angle restraints + short: Hot phase SA force constant for dihedral angle restraints read from dihe_fname. + long: Force constant applied to the dihedral angle restraints read from dihe_fname during the initial hot phase of the simulatd annealing protocol. + group: 'dihedral restraints' + explevel: expert +dihedrals_cool1: + default: 5 + type: integer + min: 0 + max: 1000 + title: First cooling SA force constant for dihedral angle restraints + short: First cooling SA force constant for dihedral angle restraints read from dihe_fname. + long: Force constant applied to the dihedral angle restraints read from dihe_fname during the first cooling phase of the simulatd annealing protocol. + group: 'dihedral restraints' + explevel: expert +dihedrals_cool2: + default: 50 + type: integer + min: 0 + max: 1000 + title: Second cooling SA force constant for dihedral angle restraints + short: Second cooling SA force constant for dihedral angle restraints read from dihe_fname. + long: Force constant applied to the dihedral angle restraints read from dihe_fname during the second cooling phase of the simulatd annealing protocol. + group: 'dihedral restraints' + explevel: expert +dihedrals_cool3: + default: 200 + type: integer + min: 0 + max: 1000 + title: Third cooling SA force constant for dihedral angle restraints + short: Third cooling SA force constant for dihedral angle restraints read from dihe_fname. + long: Force constant applied to the dihedral angle restraints read from dihe_fname during the third cooling phase of the simulatd annealing protocol. + group: 'dihedral restraints' + explevel: expert +ssdihed: + default: none + type: string + minchars: 0 + maxchars: 100 + choices: + - none + - all + - alpha + - alphabeta + title: Define automatically backbone dihedral angle restraints + short: If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions. + long: This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. + The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from + the measured angle in the input structure, and the error bound defined by the error_dih parameter. + Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or + only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations. + group: 'dihedral restraints' + explevel: easy +error_dih: + default: 10 + type: integer + min: 0 + max: 180 + title: Force constant for backbone dihedral angle restraints + short: Force constant for backbone dihedral angle restraints (ssdihed option) + long: Force constant for backbone dihedral angle restraints (ssdihed option) + group: 'dihedral restraints' + explevel: easy +# +# Group other restraints +# +dnarest_on: + default: false + type: boolean + title: Restrain the DNA conformation + short: Automatically creates restraints to maintain the conformation of DNA/RNA + long: "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. + The following restraints will be automatically defined: + - single base planarity + - sugar pucker + - phosphate backbone diherdral angle restraints + - Watson-Crick base pairing" + group: 'other restraints' + explevel: easy + + +mrswi_hot: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +mrswi_cool1: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +mrswi_cool2: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +mrswi_cool3: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +rswi_hot: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +rswi_cool1: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +rswi_cool2: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +rswi_cool3: + default: 0.5 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +masy_hot: + default: -1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +masy_cool1: + default: -1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +masy_cool2: + default: -0.1 + type: float + min: -9999 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +masy_cool3: + default: -0.1 + type: float + min: -9999 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +asy_hot: + default: 1.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +asy_cool1: + default: 1.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +asy_cool2: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +asy_cool3: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: No title yet + short: No short description yet + long: No long description yet + group: 'hidden' + explevel: hidden +# +# Group symmetry +# +sym_on: + default: false + type: boolean + title: Symmetry restraints + short: Enables symmetry restraints + long: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 supported) + and the segments to which those apply must be defined. In addition a custom symmetry restraint file can be supplied (symrest_fname). + group: 'symmetry' + explevel: expert +ksym: + default: 10.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Force constant for symmetry restraints + short: Force constant for symmetry restraints + long: Force constant for symmetry restraints + group: 'symmetry' + explevel: expert +symtbl_fname: + default: '' + type: file + title: Custom symmetry restraints filename + short: Filename of the custom symmetry restraints file + long: Filename of the custom symmetry restraints file. + group: 'symmetry' + explevel: expert +nc2sym: + default: 0 + type: integer + min: 0 + max: 40 + title: Number of C2 symmetry restraints + short: Defines the number of C2 symmetry restraints. + long: Defines the number of C2 symmetry restraints. + For each, a pair of segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c2sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C2 symmetry segment + long: Residue number of first residue in the first C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C2 symmetry segment + long: Residue number of last residue in the first C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C2 segment + short: Segment ID of first C2 segment + long: Segment ID of first C2 segment + group: 'symmetry' + explevel: expert +c2sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C2 symmetry segment + long: Residue number of first residue in the second C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C2 symmetry segment + long: Residue number of last residue in the second C2 symmetry segment + group: 'symmetry' + explevel: expert +c2sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C2 segment + short: Segment ID of second C2 segment + long: Segment ID of second C2 segment + group: 'symmetry' + explevel: expert +nc3sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C3 symmetry restraints + short: Defines the number of C3 symmetry restraints. + long: Defines the number of C3 symmetry restraints. + For each, three segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c3sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C3 symmetry segment + long: Residue number of first residue in the first C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C3 symmetry segment + long: Residue number of last residue in the first C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C3 segment + short: Segment ID of first C3 segment + long: Segment ID of first C3 segment + group: 'symmetry' + explevel: expert +c3sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C3 symmetry segment + long: Residue number of first residue in the second C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C3 symmetry segment + long: Residue number of last residue in the second C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C3 segment + short: Segment ID of second C3 segment + long: Segment ID of second C3 segment + group: 'symmetry' + explevel: expert +c3sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C3 symmetry segment + long: Residue number of first residue in the third C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C3 symmetry segment + long: Residue number of last residue in the third C3 symmetry segment + group: 'symmetry' + explevel: expert +c3sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C3 segment + short: Segment ID of third C3 segment + long: Segment ID of third C3 segment + group: 'symmetry' + explevel: expert +nc4sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C4 symmetry restraints + short: Defines the number of C4 symmetry restraints. + long: Defines the number of C4 symmetry restraints. + For each, four segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c4sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C4 symmetry segment + long: Residue number of first residue in the first C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C4 symmetry segment + long: Residue number of last residue in the first C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C4 segment + short: Segment ID of first C4 segment + long: Segment ID of first C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C4 symmetry segment + long: Residue number of first residue in the second C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C4 symmetry segment + long: Residue number of last residue in the second C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C4 segment + short: Segment ID of second C4 segment + long: Segment ID of second C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C4 symmetry segment + long: Residue number of first residue in the third C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C4 symmetry segment + long: Residue number of last residue in the third C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C4 segment + short: Segment ID of third C4 segment + long: Segment ID of third C4 segment + group: 'symmetry' + explevel: expert +c4sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C4 symmetry segment + long: Residue number of first residue in the fourth C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C4 symmetry segment + long: Residue number of last residue in the fourth C4 symmetry segment + group: 'symmetry' + explevel: expert +c4sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C4 segment + short: Segment ID of fourth C4 segment + long: Segment ID of fourth C4 segment + group: 'symmetry' + explevel: expert +nc5sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C5 symmetry restraints + short: Defines the number of C5 symmetry restraints. + long: Defines the number of C5 symmetry restraints. + For each, five segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c5sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C5 symmetry segment + long: Residue number of first residue in the first C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C5 symmetry segment + long: Residue number of last residue in the first C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C5 segment + short: Segment ID of first C5 segment + long: Segment ID of first C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C5 symmetry segment + long: Residue number of first residue in the second C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C5 symmetry segment + long: Residue number of last residue in the second C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C5 segment + short: Segment ID of second C5 segment + long: Segment ID of second C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C5 symmetry segment + long: Residue number of first residue in the third C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C5 symmetry segment + long: Residue number of last residue in the third C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C5 segment + short: Segment ID of third C5 segment + long: Segment ID of third C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C5 symmetry segment + long: Residue number of first residue in the fourth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C5 symmetry segment + long: Residue number of last residue in the fourth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C5 segment + short: Segment ID of fourth C5 segment + long: Segment ID of fourth C5 segment + group: 'symmetry' + explevel: expert +c5sym_sta5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fifth C5 symmetry segment + long: Residue number of first residue in the fifth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_end5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fifth C5 symmetry segment + long: Residue number of last residue in the fifth C5 symmetry segment + group: 'symmetry' + explevel: expert +c5sym_seg5_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fifth C5 segment + short: Segment ID of fifth C5 segment + long: Segment ID of fifth C5 segment + group: 'symmetry' + explevel: expert +nc6sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of C6 symmetry restraints + short: Defines the number of C6 symmetry restraints. + long: Defines the number of C6 symmetry restraints. + For each, six segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +c6sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first C6 symmetry segment + long: Residue number of first residue in the first C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first C6 symmetry segment + long: Residue number of last residue in the first C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first C6 segment + short: Segment ID of first C6 segment + long: Segment ID of first C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second C6 symmetry segment + long: Residue number of first residue in the second C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second C6 symmetry segment + long: Residue number of last residue in the second C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second C6 segment + short: Segment ID of second C6 segment + long: Segment ID of second C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third C6 symmetry segment + long: Residue number of first residue in the third C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third C6 symmetry segment + long: Residue number of last residue in the third C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third C6 segment + short: Segment ID of third C6 segment + long: Segment ID of third C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fourth C6 symmetry segment + long: Residue number of first residue in the fourth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fourth C6 symmetry segment + long: Residue number of last residue in the fourth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg4_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fourth C6 segment + short: Segment ID of fourth C6 segment + long: Segment ID of fourth C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the fifth C6 symmetry segment + long: Residue number of first residue in the fifth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the fifth C6 symmetry segment + long: Residue number of last residue in the fifth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg5_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of fifth C6 segment + short: Segment ID of fifth C6 segment + long: Segment ID of fifth C6 segment + group: 'symmetry' + explevel: expert +c6sym_sta6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the sixth C6 symmetry segment + long: Residue number of first residue in the sixth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_end6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the sixth C6 symmetry segment + long: Residue number of last residue in the sixth C6 symmetry segment + group: 'symmetry' + explevel: expert +c6sym_seg6_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of sixth C6 segment + short: Segment ID of sixth C6 segment + long: Segment ID of sixth C6 segment + group: 'symmetry' + explevel: expert +ns3sym: + default: 0 + type: integer + min: 0 + max: 10 + title: Number of S3 symmetry restraints + short: Defines the number of S3 symmetry restraints. + long: Defines the number of S3 symmetry restraints. + For each, three segments on which the symmetry restraint is applied will have to be defined. + Those must all have the same length. + group: 'symmetry' + explevel: hidden +s3sym_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first S3 symmetry segment + long: Residue number of first residue in the first S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first S3 symmetry segment + long: Residue number of last residue in the first S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of first S3 segment + short: Segment ID of first S3 segment + long: Segment ID of first S3 segment + group: 'symmetry' + explevel: expert +s3sym_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second S3 symmetry segment + long: Residue number of first residue in the second S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second S3 symmetry segment + long: Residue number of last residue in the second S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of second S3 segment + short: Segment ID of second S3 segment + long: Segment ID of second S3 segment + group: 'symmetry' + explevel: expert +s3sym_sta3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the third S3 symmetry segment + long: Residue number of first residue in the third S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_end3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the third S3 symmetry segment + long: Residue number of last residue in the third S3 symmetry segment + group: 'symmetry' + explevel: expert +s3sym_seg3_1: + default: '' + type: string + minchars: 0 + maxchars: 4 + title: Segment ID of third S3 segment + short: Segment ID of third S3 segment + long: Segment ID of third S3 segment + group: 'symmetry' + explevel: expert +ncs_on: + default: false + type: boolean + title: Non-crystallographic symmetry restraints + short: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. + long: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. + This does not apply any symmetry between the two molecules but rather defines restraints such as the RMSD between those is 0. + group: 'symmetry' + explevel: expert +kncs: + default: 1.0 + type: float + min: 0 + max: 1000 + precision: 1 + title: Force constant for non-crystallographic restraints + short: Force constant for non-crystallographic restraints + long: Force constant for non-crystallographic restraints + group: 'symmetry' + explevel: expert +nncs: + default: 0 + type: integer + min: 0 + max: 100 + title: Number of non-crystallographic symmetry restraints + short: Number of non-crystallographic symmetry restraints (NCS). + long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined. + Note that those must contain exactly the same residues/atom combinations. + group: 'symmetry' + explevel: hidden +ncs_sta1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the first NCS segment + long: Residue number of first residue in the first NCS segment + group: 'symmetry' + explevel: expert +ncs_end1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the first NCS segment + long: Residue number of last residue in the first NCS segment + group: 'symmetry' + explevel: expert +ncs_seg1_1: + default: '' + type: string + minchars: 0 + maxchars: 100 + title: Segment ID of first NCS segment + short: Segment ID of first NCS segment + long: Segment ID of first NCS segment + group: 'symmetry' + explevel: expert +ncs_sta2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of first residue + short: Residue number of first residue in the second NCS segment + long: Residue number of first residue in the second NCS segment + group: 'symmetry' + explevel: expert +ncs_end2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Residue number of last residue + short: Residue number of last residue in the second NCS segment + long: Residue number of last residue in the second NCS segment + group: 'symmetry' + explevel: expert +ncs_seg2_1: + default: '' + type: string + minchars: 0 + maxchars: 100 + title: Segment ID of second NCS segment + short: Segment ID of second NCS segment + long: Segment ID of second NCS segment + group: 'symmetry' + explevel: expert +# +# Group scoring +# +w_air: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the distance restraint energy + short: Weight of the distance restraints energy in the scoring function + long: Weight of the distance restraints energy in the scoring function. + Note that this is different from the force constants used during the calculations. + group: 'scoring' + explevel: expert +w_bsa: + default: -0.01 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the buried surface area term + short: Weight of the buried surface area term in the scoring function + long: Weight of the buried surface area (BSA) term in the scoring function. + Note that the BSA is only used for scoring. + group: 'scoring' + explevel: expert +w_cdih: + default: 0.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the dihedral angle restraint energy + short: Weight of the dihedral angle restraints energy in the scoring function + long: Weight of the dihedral angle restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + group: 'scoring' + explevel: expert +w_dani: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the relaxation anisotropy (DANI) restraint energy + short: Weight of the relaxation anisotropy (DANI) restraint energy + long: Weight of the relaxation anisotropy (DANI) restraint energy + group: 'scoring' + explevel: hidden +w_deint: + default: 0.0 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the interaction energy term + short: Weight of the interaction energy term + long: Weight of the interaction energy term calculated as the difference in total energy of the complex and of the separate components + group: 'scoring' + explevel: hidden +w_desolv: + default: 1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the desolvation energy term + short: Weight of the desolvation energy term in the scoring function + long: Weight of the desolvation energy term in the scoring function. + Note that the desolvation energy is only used for scoring. + group: 'scoring' + explevel: expert +w_elec: + default: 1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the intermolecular electrostatic energy + short: Weight of the intermolecular electrostatic energy in the scoring function + long: Weight of the intermolecular electrostatic energy in the scoring function. + Note that this does not affect the electostatic energy during the MD refinement. + group: 'scoring' + explevel: expert +w_lcc: + default: -10000.0 + type: float + min: -10000.0 + max: 0 + precision: 3 + title: Weight of the EM local correlation coefficient + short: Weight of the EM local correlation coefficient + long: Weight of the EM local correlation coefficient + group: 'scoring' + explevel: hidden +w_rg: + default: 1.000 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the radius of gyration restraint energy + short: Weight of the radius of gyration restraint energy + long: Weight of the radius of gyration restraint energy + group: 'scoring' + explevel: hidden +w_sani: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (SANI) restraint energy + short: Weight of the residual dipolar coupling (SANI) restraint energy + long: Weight of the residual dipolar coupling (SANI) restraint energy + group: 'scoring' + explevel: hidden +w_sym: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the symmetry restraint energy + short: Weight of the symmetry restraints energy in the scoring function + long: Weight of the symmetry restraints energy in the scoring function. + Note that this is different from the force constant used during the calculations. + group: 'scoring' + explevel: expert +w_vdw: + default: 1.0 + type: float + min: -9999 + max: 9999 + precision: 3 + title: Weight of the intermolecular van der Waals energy + short: Weight of the intermolecular van der Waals energy in the scoring function + long: Weight of the intermolecular van der Waals energy in the scoring function. + Note that this does not affect the van der Waals energy during the MD refinement. + group: 'scoring' + explevel: expert +w_vean: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (VEAN) restraint energy + short: Weight of the residual dipolar coupling (VEAN) restraint energy + long: Weight of the residual dipolar coupling (VEAN) restraint energy + group: 'scoring' + explevel: hidden +w_xpcs: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the pseudo contact shifts (XPCS) restraint energy + short: Weight of the pseudo contact shifts (XPCS) restraint energy + long: Weight of the pseudo contact shifts (XPCS) restraint energy + group: 'scoring' + explevel: hidden +w_xrdc: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the residual dipolar coupling (XRDC) restraint energy + short: Weight of the residual dipolar coupling (XRDC) restraint energy + long: Weight of the residual dipolar coupling (XRDC) restraint energy + group: 'scoring' + explevel: hidden +w_zres: + default: 0.1 + type: float + min: 0 + max: 9999 + precision: 3 + title: Weight of the Z-restraining potential energy + short: Weight of the Z-restraining potential energy + long: Weight of the Z-restraining potential energy + group: 'scoring' + explevel: hidden +# +# Group force field +# +ligand_param_fname: + default: '' + type: file + title: Custom ligand parameter file + short: Ligand parameter file in CNS format + long: Ligand parameter file in CNS format containing all force field parameters + (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK + group: 'force field' + explevel: easy +ligand_top_fname: + default: '' + type: file + title: Custom ligand topology file + short: Ligand topology file in CNS format + long: Ligand topology file in CNS format containing the ligand topologies + (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK + group: 'force field' + explevel: easy +elecflag: + default: true + type: boolean + title: Include electrostatics energy + short: Include electrostatics energy during the calculations. + long: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered. + group: 'force field' + explevel: easy +dielec: + default: rdie + type: string + minchars: 0 + maxchars: 4 + choices: + - cdie + - rdie + title: Constant (cdie) or distance-dependent dielectric (rdie) constant. + short: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. + long: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. + A distance dependent dielectric constant will effectively scale down the electrostatic energy + by having a 1/r**2 dependency instead of 1/r + group: 'force field' + explevel: expert +epsilon: + default: 1.0 + type: float + min: 1 + max: 78 + precision: 1 + title: Dielectric constant + short: Dielectric constant for the electrostatic Coulomb energy term. + long: Dielectric constant for the electrostatic Coulomb energy term. + group: 'force field' + explevel: expert +dihedflag: + default: true + type: boolean + title: Use torsion angle dihedral energy term + short: Turns on the torsion angle dihedral energy terms of the force field. + long: Turns on the torsion angle dihedral energy terms of the force field. + group: 'force field' + explevel: expert +# +# Group sampling +# +sampling_factor: + default: 1 + type: integer + min: 1 + max: 500 + title: Sampling factor for each starting model + short: This paramater controls how many times a model will be refined. + long: This paramater controls how many times a model will be refined. + group: 'sampling' + explevel: expert +max_nmodels: + default: 10000 + type: integer + min: 1 + max: 50000 + title: Maximum number of models to refine + short: This paramater controls the maximum number of models to refine. + long: This paramater controls the maximum number of models to refine. + group: 'sampling' + explevel: expert +nemsteps: + default: 200 + type: integer + min: 0 + max: 10000 + title: Number of EM steps + short: Number of energy minimisation steps to perform. + long: Number of energy minimisation steps to perform in the various EM stages of this refinement protocol. + Note that the effective number might be smaller if the minimisation converges earlier. + group: 'sampling' + explevel: expert +mdsteps_rigid: + default: 500 + type: integer + min: 0 + max: 10000 + title: Hot phase SA MD steps + short: Number of MD steps for the hot phase of the SA. + long: Number of MD steps for the hot phase rigid body dynamics of the simulated annealing protocol. + group: 'sampling' + explevel: expert +mdsteps_cool1: + default: 500 + type: integer + min: 0 + max: 10000 + title: First cooling phase SA MD steps + short: Number of MD steps for the first cooling phase of the SA. + long: Number of MD steps for the first cooling phase of rigid body dynamics of the simulated annealing protocol. + group: 'sampling' + explevel: expert +mdsteps_cool2: + default: 1000 + type: integer + min: 0 + max: 10000 + title: Second cooling phase SA MD steps + short: Number of MD steps for the second cooling phase of the SA. + long: Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters). + group: 'sampling' + explevel: expert +mdsteps_cool3: + default: 1000 + type: integer + min: 0 + max: 10000 + title: Third cooling phase SA MD steps + short: Number of MD steps for the third cooling phase of the SA. + long: Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters). + group: 'sampling' + explevel: expert +randorien: + default: false + type: boolean + title: Randomize starting orientations + short: Randomize starting orientations + long: Randomize starting orientations by separating the molecules in space and randomly rotating those + group: 'sampling' + explevel: guru +timestep: + default: 0.002 + type: float + min: 0.0005 + max: 0.004 + precision: 4 + title: MD integrating time step + short: Integration time step for the torsion angle molecular dynamics. + long: Integration time step for the torsion angle molecular dynamics. + group: 'sampling' + explevel: guru +tadfactor: + default: 8 + type: integer + min: 1 + max: 10 + title: Scaling factor for the integration time step. + short: Initial scaling factor for the integration time step of the hot phase SA. + long: Scaling factor applied at the start of the simulated annealing protocol to the timestep using during torsion angle molecular dynamics. This factor is automatically reduced during the SA protocol. + group: 'sampling' + explevel: guru +temp_high: + default: 2000 + type: integer + min: 1 + max: 5000 + title: Initial rigid-body MD temperature + short: Temperature for the initial rigid-body MD phase in Kelvin. + long: Temperature in Kelvin for the initial rigid-body molecular dynamic phase of the simulated annealing protocol. + group: 'sampling' + explevel: guru +temp_cool1_init: + default: 2000 + type: integer + min: 1 + max: 5000 + title: Start temperature for the 1st cooling phase + short: Starting temperature for the first rigid-body MD cooling phase in Kelvin. + long: Starting temperature in Kelvin for the first rigid-body molecular dynamic cooling phase of the simulated annealing protocol. + group: 'sampling' + explevel: guru +temp_cool1_final: + default: 500 + type: integer + min: 1 + max: 1000 + title: End temperature for the 1st cooling phase + short: End temperature for the first rigid-body MD cooling phase in Kelvin. + long: End temperature in Kelvin for the first rigid-body molecular dynamic cooling phase of the simulated annealing protocol. + group: 'sampling' + explevel: guru +temp_cool2_init: + default: 1000 + type: integer + min: 1 + max: 2000 + title: Start temperature for the 2nd cooling phase + short: Starting temperature for the second MD cooling phase in Kelvin. + long: Starting temperature in Kelvin for the second torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains at the interface are treated as flexible. + group: 'sampling' + explevel: guru +temp_cool2_final: + default: 50 + type: integer + min: 1 + max: 1000 + title: End temperature for the 2nd cooling phase + short: End temperature for the second MD cooling phase in Kelvin. + long: End temperature in Kelvin for the second torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains at the interface are treated as flexible. + group: 'sampling' + explevel: guru +temp_cool3_init: + default: 1000 + type: integer + min: 1 + max: 1000 + title: Start temperature for the 3rd cooling phase + short: Starting temperature for the third MD cooling phase in Kelvin. + long: Starting temperature in Kelvin for the third and final torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains and backbone at the interface are treated as flexible. + group: 'sampling' + explevel: guru +temp_cool3_final: + default: 50 + type: integer + min: 1 + max: 1000 + title: End temperature for the 3rd cooling phase + short: End temperature for the third MD cooling phase in Kelvin. + long: End temperature in Kelvin for the third and final torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains and backbone at the interface are treated as flexible. + group: 'sampling' + explevel: guru +sinter_rigid_init: + default: 0.001 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: Initial rigid-body MD intermolecular interactions scaling factor. + short: Initial scaling factor for intermolecular interactions in the first two SA stages + long: Initial scaling factor applied to intermolecular interactions during the first rigid-body molecular dynamics stage and at the start of the first cooling stage of the of the simulated annealing protocol. + group: 'sampling' + explevel: guru +sinter_rigid_final: + default: 0.001 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: End rigid-body MD intermolecular interactions scaling factor. + short: End scaling factor for intermolecular interactions in the first cooling stage. + long: End scaling factor applied to intermolecular interactions during the first cooling stage of the simulated annealing protocol. + group: 'sampling' + explevel: easy +sinter_cool2_init: + default: 0.001 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: Initial intermolecular interactions scaling factor for the 2nd cooling phase. + short: Initial scaling factor for intermolecular interactions in the second MD cooling SA stage. + long: Initial scaling factor applied to intermolecular interactions during the second torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which side-chains at the interface are treated as flexible. + group: 'sampling' + explevel: guru +sinter_cool2_final: + default: 1.0 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: End intermolecular interactions scaling factor for the 2nd cooling phase. + short: End scaling factor for intermolecular interactions in the second MD cooling SA stage. + long: End scaling factor applied to intermolecular interactions during the second torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which side-chains at the interface are treated as flexible. + group: 'sampling' + explevel: guru +sinter_cool3_init: + default: 0.05 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: Initial intermolecular interactions scaling factor for the 3rd cooling phase. + short: Initial scaling factor for intermolecular interactions in the third MD cooling SA stage. + long: Initial scaling factor applied to intermolecular interactions during the third and final torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which both side-chains and backbone at the interface are treated as flexible. + group: 'sampling' + explevel: guru +sinter_cool3_final: + default: 1.0 + type: float + min: 0.00001 + max: 1 + precision: 5 + title: End intermolecular interactions scaling factor for the 3rd cooling phase. + short: End scaling factor for intermolecular interactions in the third MD cooling SA stage. + long: End scaling factor applied to intermolecular interactions during the third and final torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which both side-chains and backbone at the interface are treated as flexible. + group: 'sampling' + explevel: guru +iniseed: + default: 917 + type: integer + min: 0 + max: 9999999999999999 + title: Random seed + short: Random seed used in CNS to initialize the random seed function + long: Random seed used in CNS to initialize the random seed function + group: 'sampling' + explevel: guru +keepwater: + default: false + type: boolean + title: Write water molecules to output file + short: Write water molecules if present to the output file. + long: Write water molecules if present to the output file. + group: 'sampling' + explevel: guru +tolerance: + default: 5 + type: integer + min: 0 + max: 99 + precision: 3 + title: Failure tolerance percentage + short: Percentage of allowed failures for a module to successfully complete + long: Percentage of allowed failures for a module to successfully complete + group: 'module' + explevel: expert +log_level: + default: quiet + type: string + minchars: 0 + maxchars: 100 + choices: + - verbose + - normal + - quiet + title: Log level verbosity for CNS + short: Set the log level verbosity for CNS + long: CNS, the computational engine used by HADDOCK can generate a lot of output + messages. This parameter controls the verbosity of CNS (verbose, normal or quiet). + group: module + explevel: guru +# +# Group flexibility +# +# +# Semi-flexible segments +# +nseg1: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_1_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg2: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_2_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg3: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_3_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg4: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_4_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg5: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_5_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg6: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_6_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg7: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_7_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_7_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg8: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_8_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_8_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg9: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_9_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_9_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg10: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_10_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_10_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg11: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_11_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_11_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg12: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_12_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_12_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg13: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_13_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_13_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg14: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_14_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_14_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg15: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_15_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_15_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg16: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_16_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_16_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg17: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_17_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_17_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg18: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_18_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_18_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg19: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_19_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_19_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +nseg20: + default: -1 + type: integer + min: -1 + max: 1000 + title: Number of semi-flexible segments + short: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition). + long: This parameter defines the number of semi-flexible segments for the specified molecule. + If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). + In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions + will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig. + group: 'flexibility' + explevel: expert +seg_sta_20_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the semi-flexible segment. + long: Residue number defining the start of the semi-flexible segment. + group: 'flexibility' + explevel: expert +seg_end_20_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Ending residue number + short: Residue number defining the end of the semi-flexible segment. + long: Residue number defining the end of the semi-flexible segment. + group: 'flexibility' + explevel: expert +# +# Fully flexible segments +# +nfle: + default: 0 + type: integer + min: 0 + max: 1000 + title: Number of fully flexible segments + short: This defines the number of fully flexible segments. + long: This parameter defines the number of fully flexible segments for all molecules. + If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, + followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables. + group: 'flexibility' + explevel: hidden +fle_sta_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: Starting residue number + short: Residue number defining the start of the fully flexible segment. + long: Residue number defining the start of this (1st) fully flexible segment. + group: 'flexibility' + explevel: expert +fle_end_1: + default: .nan + type: integer + min: -9999 + max: 9999 + title: End residue number + short: Residue number defining the end of the fully flexible segment. + long: Residue number defining the end of this (1st) fully flexible segment. + group: 'flexibility' + explevel: expert +fle_seg_1: + default: none + type: string + minchars: 1 + maxchars: 4 + title: Segment ID (segid) + short: Segment ID of the molecule for which this flexible segment is defined. + long: Segment ID of the molecule for which this (1st) flexible segment is defined. + group: 'flexibility' + explevel: expert +# +# Group interaction matrix +# +int_1_1: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_2: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_1_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_2: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_2_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_3: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_3_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_4: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_4_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_5: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_5_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_6: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_6_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_7: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_8: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_7_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_8_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_9: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_9_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_10: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_10_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_11: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_11_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_12: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_12_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_13: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_13_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_14: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_14_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_15: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_15_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_16: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_16_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_17: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_17_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_18: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_18_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_19_19: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_19_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden +int_20_20: + default: 1.0 + type: float + min: 0 + max: 1 + precision: 3 + title: Scaling factor for intermolecular energies + short: Scaling factor for intermolecular energies + long: Scaling factor for intermolecular energies between the two molecules. + This can be used for example in ensemble docking to have two molecules binding to the same site without seeing eachother. + group: 'interaction matrix' + explevel: hidden diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/.___init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/.___init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/.___init__.py differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/.___pycache__ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/.___pycache__ new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and 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a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/__init__.py b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..3d651f585d911d18d0afee7d22b30d2ea4458711 --- /dev/null +++ b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/__init__.py @@ -0,0 +1,156 @@ +"""Explicit solvent MD refinement with CNS. + +The ``[mdref]`` module (also known as ``itw`` in HADDOCK2.X series), is a small +molecular dynamics simulation, in cartesian space, using explicit solvent. + +A layer of solvent (8A for water, 12.5A for DMSO) is generated around +surface residues. + +The `mdref` protocol is composed of 4 sequential steps: +- Short energy minimization +- 3 stages of molecular dynamics to reach 300K (at 100, 200 and 300K) +- Molecular dynamics at 300K. +- 3 stages of molecular dynamics, to reach 100K (at 300, 200 and 100K) + +Using this protocol, with default parameters, no spectacular changes are +expected, however, the scoring of the various structures might be improved. + + +Number of MD steps can be modified using the ``waterheatsteps``, ``watersteps`` +and ``watercoolsteps``. +""" + +from pathlib import Path + +from haddock.core.defaults import MODULE_DEFAULT_YAML +from haddock.core.typing import FilePath +from haddock.gear.haddockmodel import HaddockModel +from haddock.libs.libcns import prepare_cns_input, prepare_expected_pdb +from haddock.libs.libontology import PDBFile +from haddock.libs.libsubprocess import CNSJob +from haddock.modules import get_engine +from haddock.modules.base_cns_module import BaseCNSModule + + +RECIPE_PATH = Path(__file__).resolve().parent +DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) + + +class HaddockModule(BaseCNSModule): + """HADDOCK3 module for water refinement.""" + + name = RECIPE_PATH.name + + def __init__( + self, order: int, path: Path, initial_params: FilePath = DEFAULT_CONFIG + ) -> None: + cns_script = Path(RECIPE_PATH, "cns", "mdref.cns") + super().__init__(order, path, initial_params, cns_script=cns_script) + + @classmethod + def confirm_installation(cls) -> None: + """Confirm if module is installed.""" + return + + def _run(self) -> None: + """Execute module.""" + # Pool of jobs to be executed by the CNS engine + jobs: list[CNSJob] = [] + + # Get the models generated in previous step + try: + models_to_refine = self.previous_io.retrieve_models() + except Exception as e: + self.finish_with_error(e) + + self.output_models: list[PDBFile] = [] + + sampling_factor = self.params["sampling_factor"] + if sampling_factor > 1: + self.log(f"sampling_factor={sampling_factor}") + if sampling_factor == 0: + self.log("[Warning] sampling_factor cannot be 0, setting it to 1") + sampling_factor = 1 + if sampling_factor > 100: + self.log("[Warning] sampling_factor is larger than 100") + + max_nmodels = self.params["max_nmodels"] + nmodels = len(models_to_refine) * sampling_factor + if nmodels > max_nmodels: + self.finish_with_error( + f"Too many models ({nmodels}) to refine, max_nmodels =" + f" {max_nmodels}. Please reduce the number of models or" + " decrease the sampling_factor." + ) + + # checking the ambig_fname: + try: + prev_ambig_fnames = [mod.restr_fname for mod in models_to_refine] + except Exception as e: # noqa:F841 + # cannot extract restr_fname info from tuples + prev_ambig_fnames = [None for mod in models_to_refine] + + ambig_fnames = self.get_ambig_fnames(prev_ambig_fnames) + + model_idx = 0 + idx = 1 + for model in models_to_refine: + # assign ambig_fname + if ambig_fnames: + ambig_fname = ambig_fnames[model_idx] + else: + ambig_fname = self.params["ambig_fname"] + model_idx += 1 + + for _ in range(self.params["sampling_factor"]): + mdref_input = prepare_cns_input( + idx, + model, + self.path, + self.recipe_str, + self.params, + "mdref", + ambig_fname=ambig_fname, + native_segid=True, + debug=self.params["debug"], + seed=model.seed if isinstance(model, PDBFile) else None, + ) + out_file = f"mdref_{idx}.out" + err_fname = f"mdref_{idx}.cnserr" + + # create the expected PDBobject + expected_pdb = prepare_expected_pdb(model, idx, ".", "mdref") + expected_pdb.restr_fname = ambig_fname + try: + expected_pdb.ori_name = model.file_name + except AttributeError: + expected_pdb.ori_name = None + self.output_models.append(expected_pdb) + + job = CNSJob(mdref_input, out_file, err_fname, envvars=self.envvars) + + jobs.append(job) + + idx += 1 + + # Run CNS Jobs + self.log(f"Running CNS Jobs n={len(jobs)}") + Engine = get_engine(self.params["mode"], self.params) + engine = Engine(jobs) + engine.run() + self.log("CNS jobs have finished") + + # Get the weights from the defaults + _weight_keys = ("w_vdw", "w_elec", "w_desolv", "w_air", "w_bsa") + weights = {e: self.params[e] for e in _weight_keys} + + for pdb in self.output_models: + if pdb.is_present(): + haddock_model = HaddockModel(pdb.file_name) + pdb.unw_energies = haddock_model.energies + + haddock_score = haddock_model.calc_haddock_score(**weights) + pdb.score = haddock_score + + # Save module information + self.export_io_models(faulty_tolerance=self.params["tolerance"]) diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._calc_free-ene.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._calc_free-ene.cns new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._calc_free-ene.cns differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._check_coordinates.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._check_coordinates.cns new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._check_coordinates.cns differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._cm-restraints.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._cm-restraints.cns new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._cm-restraints.cns differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._contactairs.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._contactairs.cns new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._contactairs.cns differ diff --git a/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._def_solv_param.cns b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._def_solv_param.cns new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/.venv_haddock/lib/python3.12/site-packages/haddock/modules/refinement/mdref/cns/._def_solv_param.cns differ