OCDocker.Docking.Vina module

Sets of classes and functions that are used to prepare vina files and run it.

Usage:

import OCDocker.Docking.Vina as ocvina

class OCDocker.Docking.Vina.Vina(config_path, box_file, receptor, prepared_receptor_path, ligand, prepared_ligand_path, vina_log, output_vina, name='', overwrite_config=False)[source]

Bases: object

Vina object with methods for easy run.

Parameters:

  • config_path (str) –

  • box_file (str) –

  • receptor (Receptor) –

  • prepared_receptor_path (str) –

  • ligand (Ligand) –

  • prepared_ligand_path (str) –

  • vina_log (str) –

  • output_vina (str) –

  • name (str) –

  • overwrite_config (bool) –

__init__(config_path, box_file, receptor, prepared_receptor_path, ligand, prepared_ligand_path, vina_log, output_vina, name='', overwrite_config=False)[source]

Constructor of the class Vina.

Parameters:

  • config_path (str) – The path for the config file.

  • box_file (str) – The path for the box file.

  • receptor (ocr.Receptor) – The receptor object.

  • prepared_receptor_path (str) – The path for the prepared receptor.

  • ligand (ocl.Ligand) – The ligand object.

  • prepared_ligand_path (str) – The path for the prepared ligand.

  • vina_log (str) – The path for the vina log file.

  • output_vina (str) – The path for the vina output files.

  • name (str, optional) – The name of the vina object, by default “”.

  • overwrite_config (bool, optional) – If True, overwrite the config file if it already exists, by default False.

Return type:

None

get_docked_poses()[source]

Get the paths for the docked poses.

Returns:

A list with the paths for the docked poses.

Return type:

List[str]

get_input_ligand_path()[source]

Get the input ligand path.

Returns:

The input ligand path.

Return type:

str

get_input_receptor_path()[source]

Get the input receptor path.

Returns:

The input receptor path.

Return type:

str

print_attributes()[source]

Print the class attributes.

Return type:

None

read_log(onlyBest=False)[source]

Read the vina log path, returning a dict with data from complexes.

Parameters:

onlyBest (bool, optional) – If True, only the best pose will be returned. By default False.

Returns:

A dictionary with the data from the vina log file. If any error occurs, it will return the exit code of the command (based on the Error.py code table).

Return type:

Dict[int, Dict[str, float]] | int

read_rescore_logs(outPath, onlyBest=False)[source]

Reads the data from the rescore log files.

Parameters:

  • outPath (str) – Path to the output folder where the rescoring logs are located.

  • onlyBest (bool, optional) – If True, only the best pose will be returned. By default False.

Returns:

A dictionary with the data from the rescore log files.

Return type:

Dict[str, float]

run_prepare_ligand(logFile='', useOpenBabel=False, overwrite=False)[source]

Run ‘prepare_ligand4’ or openbabel to prepare the ligand.

Parameters:

  • logFile (str) – Path to the logFile. If empty, suppress the output.

  • useOpenBabel (bool) – If True, use openbabel instead of prepare_ligand4.

  • overwrite (bool) – If True, overwrite existing output file.

Returns:

The exit code of the command (based on the Error.py code table) or a tuple with the exit code and the stderr of the command. If fails, return the file extension.

Return type:

int | str | Tuple[int, str]

run_prepare_receptor(logFile='', useOpenBabel=False, overwrite=False)[source]

Run ‘prepare_receptor4’ or openbabel to prepare the receptor.

Parameters:

  • logFile (str) – Path to the logFile. If empty, suppress the output.

  • useOpenBabel (bool) – If True, use openbabel instead of prepare_receptor4.

  • overwrite (bool) – If True, overwrite the prepared receptor file.

Returns:

The exit code of the command (based on the Error.py code table) or a tuple with the exit code and the stderr of the command. If fails, return the file extension.

Return type:

int | str | Tuple[int, str]

run_rescore(outPath, ligand, logFile='', skipDefaultScoring=False, splitLigand=False, overwrite=False)[source]

Run vina to rescore the ligand.

Parameters:

  • outPath (str) – Path to the output folder.

  • ligand (str) – Path to the ligand file.

  • logFile (str, optional) – Path to the logFile. If empty, suppress the output. By default “”.

  • skipDefaultScoring (bool, optional) – If True, skip the default scoring function. By default False.

  • splitLigand (bool, optional) – If True, split the ligand before running vina. By default False.

  • overwrite (bool, optional) – If True, overwrite the logFile. By default False.

Return type:

None

run_vina(overwrite=False)[source]

Run vina.

Parameters:

overwrite (bool, optional) – If True, overwrite existing output/log files.

Return type:

int | Tuple[int, str]

split_poses(outPath='', logFile='')[source]

Split the ligand resulted from vina into its poses.

Parameters:

  • outPath (str, optional) – Path to the output folder. By default “”. If empty, the poses will be saved in the same folder as the vina output.

  • logFile (str, optional) – Path to the logFile. If empty, suppress the output. By default “”.

Returns:

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

Return type:

int

OCDocker.Docking.Vina.box_to_vina(box_file, conf_file, receptor)[source]

Convert a box (DUDE like format) to vina input.

Parameters:

  • box_file (str) – The path to the box file.

  • conf_file (str) – The path to the vina configuration file.

  • receptor (str) – The path to the receptor file.

Return type:

int

OCDocker.Docking.Vina.generate_vina_files_database(path, protein, boxPath='')[source]

Generate all vina required files for provided protein.

Parameters:

  • path (str) – The path to the folder where the files will be generated.

  • protein (str) – The path of the protein.

  • boxPath (str) – The path to the box file. If empty, it will set as path + “/boxes”

Return type:

None

OCDocker.Docking.Vina.get_pose_index_from_file_path(filePath)[source]

Get the pose index from the file path.

Parameters:

filePath (str) – The path to the file.

Returns:

The pose index.

Return type:

int

OCDocker.Docking.Vina.get_rescore_log_paths(outPath)[source]

Get the paths for the rescore log files.

Parameters:

outPath (str) – Path to the output folder where the rescoring logs are located.

Returns:

A list with the paths for the rescoring log files.

Return type:

List[str]

OCDocker.Docking.Vina.read_rescore_logs(rescoreLogPaths, onlyBest=False)[source]

Reads the data from the rescore log files.

Parameters:

  • rescoreLogPaths (List[str] | str) – A list with the paths for the rescoring log files.

  • onlyBest (bool, optional) – If True, only the best pose will be returned. By default False.

Returns:

A dictionary with the data from the rescore log files.

Return type:

Dict[str, List[Union[str, float]]]

OCDocker.Docking.Vina.run_prepare_ligand(inputLigandPath, outputLigand, logFile='', overwrite=False)[source]

Prepares the ligand using ‘prepare_ligand’ from MGLTools suite.

Parameters:

  • inputLigandPath (str) – The path to the input ligand.

  • outputLigand (str) – The path to the output ligand.

  • logFile (str) – The path to the log file. If empty, suppress the output.

  • overwrite (bool) –

Return type:

int | str | Tuple[int, str]

OCDocker.Docking.Vina.run_prepare_receptor(inputReceptorPath, outputReceptor, logFile='', overwrite=False)[source]

Convert a box (DUDE like format) to vina input.

Parameters:

  • inputReceptorPath (str) – The path to the input receptor file.

  • outputReceptor (str) – The path to the output receptor file.

  • logFile (str) – The path to the log file. If empty, suppress the output.

  • overwrite (bool) –

Returns:

The exit code of the command (based on the Error.py code table) or a tuple with the exit code and the stderr of the command.

Return type:

int | Tuple[int, str]

OCDocker.Docking.Vina.run_rescore(confFile, ligands, outPath, scoring_function, logFile='', splitLigand=True, overwrite=False)[source]

Run vina to rescore the ligand.

Parameters:

  • confFile (str) – The path to the vina configuration file.

  • ligands (Union[List[str], str]) – The path to a List of ligand files or the ligand file.

  • outPath (str) – The path to the output file.

  • scoring_function (str) – The scoring function to use.

  • logFile (str, optional) – The path to the log file. If empty, suppress the output. By default “”.

  • splitLigand (bool, optional) – If True, split the ligand before running vina. By default True.

  • overwrite (bool, optional) – If True, overwrite the logFile. By default False.

Return type:

None

OCDocker.Docking.Vina.run_vina(confFile, ligand, outPath, logFile='')[source]

Run vina.

Parameters:

  • confFile (str) – The path to the vina configuration file.

  • ligand (str) – The path to the ligand file.

  • outPath (str) – The path to the output file.

  • logFile (str) – The path to the log file. If empty, suppress the output.

Returns:

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

Return type:

int