| from __future__ import annotations |
|
|
| from pathlib import Path |
|
|
|
|
| def write_receptor_prm( |
| receptor_mol2: str | Path, |
| reference_ligand_sdf: str | Path, |
| out_path: str | Path, |
| radius: float = 6.0, |
| ) -> Path: |
| """Write receptor parameter file required by rbcavity/rbdock.""" |
| receptor_path = Path(receptor_mol2).resolve() |
| reference_path = Path(reference_ligand_sdf).resolve() |
|
|
| payload = ( |
| "RBT_PARAMETER_FILE_V1.00\n" |
| "TITLE rdock_receptor\n" |
| f"RECEPTOR_FILE {receptor_path}\n" |
| "\n" |
| "SECTION MAPPER\n" |
| " SITE_MAPPER RbtLigandSiteMapper\n" |
| f" REF_MOL {reference_path}\n" |
| f" RADIUS {radius:.1f}\n" |
| " SMALL_SPHERE 1.5\n" |
| "END_SECTION\n" |
| "\n" |
| "SECTION CAVITY\n" |
| " SCORING_FUNCTION RbtCavityGridSF\n" |
| "END_SECTION\n" |
| ) |
|
|
| target = Path(out_path) |
| target.parent.mkdir(parents=True, exist_ok=True) |
| target.write_text(payload, encoding="utf-8") |
| return target |
|
|
|
|
| def write_receptor_prm_sphere( |
| receptor_mol2: str | Path, |
| center: tuple[float, float, float], |
| radius: float, |
| out_path: str | Path, |
| ) -> Path: |
| """Write receptor prm using a fixed sphere mapper (stable pocket definition).""" |
| receptor_path = Path(receptor_mol2).resolve() |
| cx, cy, cz = float(center[0]), float(center[1]), float(center[2]) |
| rad = float(radius) |
|
|
| payload = ( |
| "RBT_PARAMETER_FILE_V1.00\n" |
| "TITLE rdock_receptor_fixed_pocket\n" |
| f"RECEPTOR_FILE {receptor_path}\n" |
| "\n" |
| "SECTION MAPPER\n" |
| " SITE_MAPPER RbtSphereSiteMapper\n" |
| f" CENTER ({cx:.4f},{cy:.4f},{cz:.4f})\n" |
| f" RADIUS {rad:.3f}\n" |
| " SMALL_SPHERE 1.5\n" |
| " MIN_VOLUME 100\n" |
| " MAX_CAVITIES 1\n" |
| " VOL_INCR 0.0\n" |
| " GRIDSTEP 0.5\n" |
| "END_SECTION\n" |
| "\n" |
| "SECTION CAVITY\n" |
| " SCORING_FUNCTION RbtCavityGridSF\n" |
| "END_SECTION\n" |
| ) |
|
|
| target = Path(out_path) |
| target.parent.mkdir(parents=True, exist_ok=True) |
| target.write_text(payload, encoding="utf-8") |
| return target |
|
|
