OCDocker.Docking.Gnina module

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

Usage:

import OCDocker.Docking.Gnina as ocgnina

class OCDocker.Docking.Gnina.Gnina(config_path, box_file, receptor, prepared_receptor_path, ligand, prepared_ligand_path, gnina_log, output_gnina, name='', overwrite_config=False)[source]

Bases: object

Gnina 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) –

  • gnina_log (str) –

  • output_gnina (str) –

  • name (str) –

  • overwrite_config (bool) –

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

Constructor of the class Gnina.

Parameters:

  • config_path (str) – Path to the configuration file.

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

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

  • prepared_receptor_path (str) – Path to the prepared receptor.

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

  • prepared_ligand_path (str) – Path to the prepared ligand.

  • gnina_log (str) – Path to the gnina log file.

  • output_gnina (str) – Path to the output gnina file.

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

  • overwrite_config (bool, optional) – If the config file should be overwritten, 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 gnina 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 gnina log file.

Return type:

Dict[int, Dict[str, float]]

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(overwrite=False)[source]

Run Open Babel conversion for ligand.

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]

Parameters:

overwrite (bool) –

run_prepare_ligand_from_cmd(logFile='')[source]

Run Open Babel conversion for ligand. [DEPRECATED]

Parameters:

logFile (str) – The path for the log file.

Return type:

int | str | Tuple[int, str]

run_prepare_receptor(overwrite=False)[source]

Run Open Babel conversion for receptor.

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]

Parameters:

overwrite (bool) –

run_prepare_receptor_from_cmd(logFile='', overwrite=False)[source]

Run Open Babel conversion for receptor. [DEPRECATED]

Parameters:

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

  • 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]

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

Run gnina to rescore the ligand.

Parameters:

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

  • ligand (str) – Path to the ligand to be rescored.

  • 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 rescoring. By default False.

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

Return type:

None

run_gnina(logFile='', overwrite=False)[source]

Run gnina.

Parameters:

  • logFile (str) – The path for the extra execution log.

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

Returns:

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

Return type:

int | Tuple[int, str]

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

Split the ligand resulted from gnina 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 gnina 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.Gnina.gen_gnina_conf(box_file, conf_file, receptor)[source]

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

Parameters:

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

  • conf_file (str) – The path for the conf file.

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

Returns:

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

Return type:

int

OCDocker.Docking.Gnina.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.Gnina.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.Gnina.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, float]

OCDocker.Docking.Gnina.run_prepare_ligand(input_ligand_path, prepared_ligand, overwrite=False)[source]

Run Open Babel convert ligand to pdbqt.

Parameters:

  • input_ligand_path (str) – The path for the input ligand.

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

  • 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 output of the command.

Return type:

int | Tuple[int, str]

OCDocker.Docking.Gnina.run_prepare_ligand_from_cmd(input_ligand_path, prepared_ligand, log_file='')[source]

Converts the ligand to .pdbqt using Open Babel. [DEPRECATED]

Parameters:

  • input_ligand_path (str) – The path for the input ligand.

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

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

Returns:

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

Return type:

int | Tuple[int, str]

OCDocker.Docking.Gnina.run_prepare_receptor(input_receptor_path, prepared_receptor, overwrite=False)[source]

Run Open Babel convert receptor to pdbqt.

Parameters:

  • input_receptor_path (str) – The path for the input receptor.

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

  • 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 output of the command.

Return type:

int | Tuple[int, str]

OCDocker.Docking.Gnina.run_prepare_receptor_from_cmd(input_receptor_path, output_receptor, log_file='')[source]

Converts the receptor to .pdbqt using Open Babel. [DEPRECATED]

Parameters:

  • input_receptor_path (str) – The path for the input receptor.

  • output_receptor (str) – The path for the output receptor.

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

Returns:

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

Return type:

int | Tuple[int, str]

OCDocker.Docking.Gnina.run_gnina(config, prepared_ligand, output_gnina, gnina_log, log_path)[source]

Run gnina.

Parameters:

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

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

  • output_gnina (str) – The path for the output gnina file.

  • gnina_log (str) – The path for the gnina log file.

  • log_path (str) – The path for the execution log file.

Returns:

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

Return type:

int | Tuple[int, str]

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

Run gnina to rescore the ligand.

Parameters:

  • confFile (str) – The path to the gnina 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 gnina. By default True.

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

  • cnn_model (str, optional) – Built-in CNN model to evaluate (via –cnn). By default “”.

  • disable_cnn (bool, optional) – If True, force empirical-only scoring with –cnn_scoring none. By default False.

Return type:

None

OCDocker.Docking.Gnina.run_docking(config, prepared_ligand, output_gnina, gnina_log, log_path)

Run gnina.

Parameters:

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

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

  • output_gnina (str) – The path for the output gnina file.

  • gnina_log (str) – The path for the gnina log file.

  • log_path (str) – The path for the execution log file.

Returns:

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

Return type:

int | Tuple[int, str]