Docking Backends

class mockdock.docking.DockingOracle(receptor_file, n_poses=10, n_cpus=None, n_gpus=None, save_dir=None, **kwargs)

Bases: ABC

Abstract base class for docking oracles.

Parameters:

• receptor_file (str | Path)

• n_poses (int)

• n_cpus (int | None)

• n_gpus (int | None)

• save_dir (str | Path | None)

abstractmethod dock_batch(docking_tasks, chunk_idx)

Dock a batch of prepared ligands. docking_tasks: list of {‘smiles’: str, ‘pdbqt_paths’: [Path]} Returns list of results per task: [[conformer_res, …], [conformer_res, …]]

Parameters:

• docking_tasks (list[dict])

• chunk_idx (int)

Return type:

list[list[dict]]

class mockdock.docking.AutoDockGPUOracle(receptor_file, adgpu_executable=None, n_poses=10, n_cpus=None, n_gpus=1, save_dir=None, **kwargs)

Bases: DockingOracle

Parameters:

• receptor_file (str | Path)

• adgpu_executable (str | None)

• n_poses (int)

• n_cpus (int | None)

• n_gpus (int)

• save_dir (str | Path | None)

DEFAULT_ADGPU_EXECUTABLE = 'adgpu'

ALLOWED_RECEPTOR_EXTENSIONS = {'.fld', '.map', '.pdbqt', '.xyz'}

dock_batch(docking_tasks, chunk_idx)

Implementation of ADGPU docking for a batch of PDBQT files.

Parameters:

• docking_tasks (list[dict])

• chunk_idx (int)

Return type:

list[dict]

class mockdock.docking.AutoDockVinaOracle(receptor_file, n_poses=10, n_cpus=None, exhaustiveness=32, save_dir=None, **kwargs)

Bases: DockingOracle

Parameters:

• receptor_file (str | Path)

• n_poses (int)

• n_cpus (int | None)

• exhaustiveness (int)

• save_dir (str | Path | None)

dock_batch(docking_tasks, chunk_idx)

Implementation of Vina docking for a batch of PDBQT files.

Parameters:

• docking_tasks (list[dict])

• chunk_idx (int)

Return type:

list[list[dict]]