OCDocker.DB.baseDB module

Shared database import and workflow adapter utilities.

baseDB.py contains shared helpers used to prepare/populate OCDocker reference databases and coordinate common dataset/database access patterns. It intentionally remains the shared database base/adapter layer in this cleanup; its functionality is not being renamed or relocated.

Usage:

import OCDocker.DB.baseDB as ocbdb

OCDocker.DB.baseDB.prepare(archive, overwrite=False, spacing=0.33, sanitize=True, all_boxes=False)[source]

Prepares the database.

Parameters:

  • archive (str) – The archive to be prepared. The options are [dudez, pdbbind, litpcba].

  • overwrite (bool, optional) – If True overwrites the files, if False does not overwrite the files. The default is False.

  • spacing (float, optional) – The spacing to be used in the grid. The default is 0.33.

  • sanitize (bool, optional) – If True sanitizes the ligands, if False does not sanitize the ligands. The default is True.

  • all_boxes (bool)

Return type:

None

OCDocker.DB.baseDB.run_docking(archive, dockingAlgorithm, digestFormat='json', overwrite=False, all_boxes=False)[source]

Run docking.

Parameters:

  • archive (str) – The archive to be prepared. The options are [dudez, pdbbind, litpcba].

  • dockingAlgorithm (str) – The docking algorithm to be used. The options are [vina, smina, plants].

  • digestFormat (str, optional) – The format of the digest file. The options are [json]. The default is “json”.

  • overwrite (bool, optional) – If True overwrites the files, if False does not overwrite the files. The default is False.

  • all_boxes (bool)

Returns:

The exit code of the command (based on the Error.py code table).

Return type:

int