OCDocker.Docking package

Subpackages

• OCDocker.Docking.Future package
  • Submodules
    • OCDocker.Docking.Future.Dock3 module
      • Dock3
    • OCDocker.Docking.Future.Dock6 module
      • Dock6
    • OCDocker.Docking.Future.GEMDOCK module
      • GEMDOCK
    • OCDocker.Docking.Future.Ledock module
      • Ledock
    • OCDocker.Docking.Future.RDock module
      • Dock3
  • Module contents
    • Modules

Submodules

• OCDocker.Docking.PLANTS module
  • PLANTS
    • PLANTS.__init__()
    • PLANTS.get_docked_poses()
    • PLANTS.get_input_ligand_path()
    • PLANTS.get_input_receptor_path()
    • PLANTS.get_rescore_log_paths()
    • PLANTS.print_attributes()
    • PLANTS.read_log()
    • PLANTS.read_rescore_logs()
    • PLANTS.run_plants()
    • PLANTS.run_prepare_ligand()
    • PLANTS.run_prepare_receptor()
    • PLANTS.run_rescore()
    • PLANTS.write_config_file()
    • PLANTS.write_pose_list()
  • box_to_plants()
  • generate_digest()
  • generate_plants_files_database()
  • get_binding_site()
  • get_docked_poses()
  • get_pose_index_from_file_path()
  • read_log()
  • run_plants()
  • run_prepare_ligand()
  • run_prepare_receptor()
  • run_rescore()
  • write_config_file()
  • write_pose_list()
  • write_rescoring_config_file()
  • run_docking()
  • read_rescore_logs()
• OCDocker.Docking.Smina module
  • Smina
    • Smina.__init__()
    • Smina.get_docked_poses()
    • Smina.get_input_ligand_path()
    • Smina.get_input_receptor_path()
    • Smina.print_attributes()
    • Smina.read_log()
    • Smina.read_rescore_logs()
    • Smina.run_prepare_ligand()
    • Smina.run_prepare_ligand_from_cmd()
    • Smina.run_prepare_receptor()
    • Smina.run_prepare_receptor_from_cmd()
    • Smina.run_rescore()
    • Smina.run_smina()
    • Smina.split_poses()
  • gen_smina_conf()
  • get_pose_index_from_file_path()
  • get_rescore_log_paths()
  • read_rescore_logs()
  • run_prepare_ligand()
  • run_prepare_ligand_from_cmd()
  • run_prepare_receptor()
  • run_prepare_receptor_from_cmd()
  • run_rescore()
  • run_smina()
  • run_docking()
• OCDocker.Docking.Vina module
  • Vina
    • Vina.__init__()
    • Vina.get_docked_poses()
    • Vina.get_input_ligand_path()
    • Vina.get_input_receptor_path()
    • Vina.print_attributes()
    • Vina.read_log()
    • Vina.read_rescore_logs()
    • Vina.run_prepare_ligand()
    • Vina.run_prepare_receptor()
    • Vina.run_rescore()
    • Vina.run_vina()
    • Vina.split_poses()
  • box_to_vina()
  • generate_vina_files_database()
  • get_pose_index_from_file_path()
  • get_rescore_log_paths()
  • read_rescore_logs()
  • run_prepare_ligand()
  • run_prepare_receptor()
  • run_rescore()
  • run_vina()
• OCDocker.Docking.Gnina module
  • Gnina
    • Gnina.__init__()
    • Gnina.get_docked_poses()
    • Gnina.get_input_ligand_path()
    • Gnina.get_input_receptor_path()
    • Gnina.print_attributes()
    • Gnina.read_log()
    • Gnina.read_rescore_logs()
    • Gnina.run_prepare_ligand()
    • Gnina.run_prepare_ligand_from_cmd()
    • Gnina.run_prepare_receptor()
    • Gnina.run_prepare_receptor_from_cmd()
    • Gnina.run_rescore()
    • Gnina.run_gnina()
    • Gnina.split_poses()
  • gen_gnina_conf()
  • get_pose_index_from_file_path()
  • get_rescore_log_paths()
  • read_rescore_logs()
  • run_prepare_ligand()
  • run_prepare_ligand_from_cmd()
  • run_prepare_receptor()
  • run_prepare_receptor_from_cmd()
  • run_gnina()
  • run_rescore()
  • run_docking()
• OCDocker.Docking.BaseVinaLike module
  • generate_smina_digest()
  • generate_vina_digest()
  • generate_gnina_digest()
  • get_smina_docked_poses()
  • get_vina_docked_poses()
  • get_gnina_docked_poses()
  • read_smina_log()
  • read_smina_rescoring_log()
  • read_vina_log()
  • read_gnina_log()
  • read_vina_rescoring_log()
  • read_gnina_rescoring_log()

Module contents

Docking engines and helpers.

Usage:

import OCDocker.Docking as ocdocking

Modules

• BaseVinaLike: Shared helpers for Vina-like logs and parsing.

• Gnina: Gnina docking wrapper.

• PLANTS: PLANTS docking wrapper.

• Smina: Smina docking wrapper.

• Vina: Vina docking wrapper.

• Future: Experimental docking engines.