pinder.methods.run.hdock package

Submodules

pinder.methods.run.hdock.predict module

pinder.methods.run.hdock.predict.hdock(results_dir: Path, n_solutions: int, complex_id: str, complex_kind: str, complex_receptor: Path, complex_ligand: Path) → None

Run HDockLite 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 hdock 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}/hdock/{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.hdock.predict.predict_hdock(complex_config: dict[str, str | Path], params: dict[str, Any]) → None

Run HDockLite 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}/hdock/{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.

Module contents