OCDocker.Docking.Future.GEMDOCK module

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

TODO: Unfinished!!! http://gemdock.life.nctu.edu.tw/dock/

Usage:

import OCDocker.Docking.GEMDOCK as ocgemdock

class OCDocker.Docking.Future.GEMDOCK.GEMDOCK(config_path, box_file, receptor, prepared_receptor_path, ligand, prepared_ligand_path, gemdock_log, output_gemdock, name='', overwrite_config=False, spacing=2.9)[source]

Bases: object

GEMDOCK 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) –

  • gemdock_log (str) –

  • output_gemdock (str) –

  • name (str) –

  • overwrite_config (bool) –

  • spacing (float) –

__init__(config_path, box_file, receptor, prepared_receptor_path, ligand, prepared_ligand_path, gemdock_log, output_gemdock, name='', overwrite_config=False, spacing=2.9)[source]

Constructor of the class GEMDOCK.

Parameters:

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

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

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

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

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

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

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

  • outputGEMDOCK (str) – The path for the GEMDOCK output files.

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

  • spacing (float, optional) – The spacing between to expand the box, by default 2.9.

  • config_path (str) –

  • box_file (str) –

  • prepared_receptor_path (str) –

  • prepared_ligand_path (str) –

  • gemdock_log (str) –

  • output_gemdock (str) –

  • overwrite_config (bool) –

Return type:

None