pinder.methods.run.patchdock package#
Submodules#
pinder.methods.run.patchdock.predict module#
- pinder.methods.run.patchdock.predict.patchdock(results_dir: Path, n_solutions: int, complex_id: str, complex_kind: str, complex_receptor: Path, complex_ligand: Path) None[source][source]#
Run PatchDock on a single receptor-ligand complex and generate n_solutions docking solutions. Assume that all paths provided are local and all the files exist. Assume that patchdock binary is available in PATH. Save results to the specified results_dir. Directory will be created if needed.
- Parameters:
- results_dirPath
Path to the docking dataset. resulting path will be: {results_dir}/patchdock/{id}/{kind}_decoys/model_{i}.pdb
- n_solutionsint
Number of solutions i = {1..n_solutions} to generate.
- idstr
PINDER ID of the complex.
- kindstr
holo, apo or predicted.
- receptorPath
All structures are expected to be pre-transformed and ready for docking.
- ligandPath
All structures are expected to be pre-transformed and ready for docking.
- pinder.methods.run.patchdock.predict.predict_patchdock(complex_config: dict[str, str | Path], params: dict[str, Any]) None[source][source]#
Run PatchDock on a single receptor-ligand complex and generate n_solutions docking solutions. Assume that all the specified paths are local and the files exist. Save results to the specified results_dir. Directory is created if needed.
- Parameters:
- complex_configdict[str, str | Path]
Dictionary containing configuration for the complex.
- idstr
PINDER ID of the complex.
- kindstr
holo, apo or predicted.
- receptorPath
All structures are expected to be pre-transformed and ready for docking.
- ligandPath
All structures are expected to be pre-transformed and ready for docking.
- paramsdict[str, Any]
Dictionary containing additional parameters.
- results_dirPath
Path to the docking dataset. Resulting path will be: {results_dir}/patchdock/{id}/{kind}_decoys/model_{i}.pdb.
- n_solutionsint
Number of solutions i = {1..n_solutions} to generate.
- forcebool
Force re-running the docking even if the results already exist.