pinder.methods package

Subpackages

• pinder.methods.preprocess package
  • Module contents
    • prepare_inference_inputs()
• pinder.methods.run package
  • Subpackages
    • pinder.methods.run.af2mm package
      • Module contents
    • pinder.methods.run.frodock package
      • Submodules
      • pinder.methods.run.frodock.predict module
        • frodock()
        • predict_frodock()
      • Module contents
    • pinder.methods.run.hdock package
      • Submodules
      • pinder.methods.run.hdock.predict module
        • hdock()
        • predict_hdock()
      • Module contents
    • pinder.methods.run.patchdock package
      • Submodules
      • pinder.methods.run.patchdock.predict module
        • patchdock()
        • predict_patchdock()
      • Module contents
  • Module contents
• pinder.methods.train package
  • Module contents

Submodules

pinder.methods.main module

pinder.methods.main.json_reader(file: IO[Any]) → dict[str, Any]

pinder.methods.main.yaml_reader(file: IO[Any]) → dict[str, Any]

pinder.methods.main.preprocess(method: str, data_dir: Path, subset: str | None = None, ids: list[str] | None = None, config: dict[str, Any] = {}, pairs: SUPPORTED_PAIRS = SUPPORTED_PAIRS.ALL) → None

pinder.methods.main.train(method: str, data_dir: Path, subset: str | None = None, ids: list[str] | None = None, config: dict[str, Any] = {}) → None

pinder.methods.main.predict(method: str, results_dir: Path | None = None, data_dir: Path | None = None, subset: str | None = None, ids: list[str] | None = None, config: Path | None = None, pairs: SUPPORTED_PAIRS = SUPPORTED_PAIRS.ALL) → None

Run inference/prediction with the specified method on a subset of index set or on a list of PINDER IDs.

Parameters:

• method (str) – The method to use for prediction.

• results_dir (Path) – Path to the directory where the results will be saved.

• data_dir (Path) – Path to the directory where the preprocessed data is stored if available.

• subset (str) – Optional subset of index to run prediction on (pinder-xl/s/af2).

• ids (list) – A list of PINDER IDs to run prediction on. Takes priority over subset if provided.

• pairs (all/holo/apo/predicted) – The type of monomer pairs to run prediction on.

• config (Path) – An optional configuration file containing key-value parameters to pass to method. Supported formats are json and yaml.

pinder.methods.main.main() → None

Module contents

Namespace package root for pinder-methods.

class pinder.methods.SUPPORTED_PAIRS(value)

Bases: Enum

An enumeration.

ALL = 'all'

HOLO = 'holo'

APO = 'apo'

PREDICTED = 'predicted'

class pinder.methods.SUPPORTED_ACTIONS(value)

Bases: Enum

An enumeration.

PREPROCESS = 'preprocess'

TRAIN = 'train'

PREDICT = 'predict'