OCDocker.DB.PDBbind module

Sets of classes and functions that are used to process the PDBbind dataset.

Usage:

import OCDocker.DB.PDBbind as ocpdbbind

OCDocker.DB.PDBbind.prepare(overwrite=False)

Prepares the PDBbind database.

Parameters:

overwrite (bool, optional) – If True, it will overwrite the results. If False, it will not run the preparation if the results already exist, by default False.

Return type:

None

OCDocker.DB.PDBbind.read_index()

Read the index file from pdbbind database and returns a list of dictionaries with the data.

Returns:

A dict of dictionaries where each dictionary represents the data for a single protein. If the file does not exist, it will return None.

Return type:

Dict[str, Dict[str, str | float]] | None

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

Runs PLANTS in the whole database.

Parameters:

overwrite (bool, optional) – If True, it will overwrite the results. If False, it will not run the PLANTS if the results already exist, by default False.

Returns:

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

Return type:

int

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

Runs smina in the whole database.

Parameters:

overwrite (bool, optional) – If True, it will overwrite the results. If False, it will not run the smina if the results already exist, by default False.

Returns:

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

Return type:

int

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

Runs vina in the whole database.

Parameters:

overwrite (bool, optional) – If True, it will overwrite the results. If False, it will not run the vina if the results already exist, by default False.

Returns:

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

Return type:

int