| """gdock integration sampling module.""" |
|
|
| import time |
| 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.libs import libpdb |
| from haddock.libs.libontology import PDBFile |
| from haddock.modules import BaseHaddockModule |
| from haddock.modules.sampling.gdock.gdock import ( |
| GdockWrapper, |
| gdock_is_available, |
| parse_restraints, |
| ) |
|
|
|
|
| RECIPE_PATH = Path(__file__).resolve().parent |
| DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) |
|
|
|
|
| class HaddockModule(BaseHaddockModule): |
| """HADDOCK3 gdock module.""" |
|
|
| name = RECIPE_PATH.name |
|
|
| def __init__( |
| self, |
| order: int, |
| path: Path, |
| *ignore: Any, |
| initial_params: FilePath = DEFAULT_CONFIG, |
| **everything: Any, |
| ) -> None: |
| super().__init__(order, path, initial_params) |
|
|
| @classmethod |
| def confirm_installation(cls) -> None: |
| """Confirm if the module is ready to use.""" |
| if not gdock_is_available(): |
| raise Exception( |
| "You are trying to use the `gdock` module but it is not" |
| " available, please check the installation instructions" |
| ) |
|
|
| def _split_combination( |
| self, combination: tuple[PDBFile, ...] |
| ) -> tuple[PDBFile, str, PDBFile, str]: |
| """Return (receptor, rec_chain, ligand, lig_chain) from a combination. |
| |
| The molecule order follows the `molecules` list in the run config, so |
| index 0 is always the receptor and index 1 is always the ligand. |
| Chain IDs are read directly from the files. |
| """ |
| if len(combination) != 2: |
| self.finish_with_error( |
| f"gdock requires exactly 2 input molecules per combination, " |
| f"got {len(combination)}: {[c.file_name for c in combination]}" |
| ) |
|
|
| receptor, ligand = combination[0], combination[1] |
|
|
| _, rec_chains = libpdb.identify_chainseg( |
| Path(receptor.path, receptor.file_name) |
| ) |
| _, lig_chains = libpdb.identify_chainseg(Path(ligand.path, ligand.file_name)) |
|
|
| if not rec_chains or not lig_chains: |
| self.finish_with_error( |
| f"Could not detect chain IDs in receptor '{receptor.file_name}' " |
| f"or ligand '{ligand.file_name}'" |
| ) |
|
|
| return receptor, rec_chains[0], ligand, lig_chains[0] |
|
|
| def _run(self) -> None: |
| """Execute module.""" |
| |
| |
| models_to_dock = self.previous_io.retrieve_models( |
| crossdock=self.params["crossdock"] |
| ) |
|
|
| log.info(f"ncores={self.params['ncores']} sampling={self.params['sampling']}") |
|
|
| expected: list[PDBFile] = [] |
| for idx, combination in enumerate(models_to_dock, start=1): |
| receptor, rec_chain, ligand, lig_chain = self._split_combination( |
| combination |
| ) |
|
|
| |
| restraints = None |
| ambig_fname = self.params["ambig_fname"] |
| if ambig_fname: |
| restraints = parse_restraints(ambig_fname, rec_chain, lig_chain) |
|
|
| gdock_wrapper = GdockWrapper( |
| receptor_pdb_file=Path(receptor.path, receptor.file_name), |
| ligand_pdb_file=Path(ligand.path, ligand.file_name), |
| restraints=restraints, |
| max_generations=self.params["max_generations"], |
| number_of_individuals=self.params["number_of_individuals"], |
| ncores=self.params["ncores"], |
| seed=self.params["seed"], |
| sampling=self.params["sampling"], |
| ) |
| t0 = time.monotonic() |
| gdock_wrapper.run() |
| elapsed = time.monotonic() - t0 |
| log.info( |
| f"gdock run {idx}: {receptor.file_name} + {ligand.file_name}" |
| f" generations={gdock_wrapper.result['generationsRun']}" |
| f" models={len(gdock_wrapper.result['models'])}" |
| f" elapsed={elapsed:.1f}s" |
| ) |
| models = gdock_wrapper.save_models(".", prefix=f"gdock_{idx}") |
|
|
| for m in models: |
| expected.append( |
| PDBFile( |
| m["file_name"], |
| topology=[receptor.topology, ligand.topology], |
| path=self.path, |
| score=m["fitness"], |
| unw_energies={ |
| "vdw": m["vdw"], |
| "elec": m["elec"], |
| "desolv": m["desolv"], |
| "air": m["air"], |
| }, |
| ) |
| ) |
|
|
| self.output_models = expected |
| self.export_io_models() |
|
|
