OCDocker.DB.LITPCBA module

Sets of classes and functions that are used to process the LIT-PCBA external validation subset (see scripts/litpcba_validation_subset.py and docs/litpcba_validation_subset.md for how the raw archive was built).

Usage:

import OCDocker.DB.LITPCBA as oclitpcba

OCDocker.DB.LITPCBA.prepare(overwrite=False, spacing=0.33, sanitize=True)

Prepares the LIT-PCBA database.

Parameters:

• overwrite (bool, optional) – If True, all files will be generated, otherwise will try to optimize file generation, skipping files with output already generated, by default False.

• spacing (float, optional) – The spacing between the grid points, by default 0.33.

• sanitize (bool, optional) – If True, sanitizes the ligands, by default True.

Raises:

None –

Return type:

None

OCDocker.DB.LITPCBA.run_gnina(overwrite=False)

Runs gnina in the whole database.

Parameters:

overwrite (bool, optional) – If True, all files will be generated, otherwise will try to optimize file generation, skipping files with output already generated, by default False.

Returns:

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

Return type:

int

Raises:

None –

OCDocker.DB.LITPCBA.run_plants(overwrite=False)

Runs PLANTS in the whole database.

Parameters:

overwrite (bool, optional) – If True, all files will be generated, otherwise will try to optimize file generation, skipping files with output already generated, by default False.

Returns:

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

Return type:

int

Raises:

None –

OCDocker.DB.LITPCBA.run_smina(overwrite=False)

Runs smina in the whole database.

Parameters:

overwrite (bool, optional) – If True, all files will be generated, otherwise will try to optimize file generation, skipping files with output already generated, by default False.

Returns:

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

Return type:

int

Raises:

None –

OCDocker.DB.LITPCBA.run_vina(overwrite=False)

Runs vina in the whole database.

Parameters:

overwrite (bool, optional) – If True, all files will be generated, otherwise will try to optimize file generation, skipping files with output already generated, by default False.

Returns:

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

Return type:

int

Raises:

None –