Dock Module Documentation

Contents

• pyCADD.Dock package
  • Subpackages
    • pyCADD.Dock.schrodinger package
      • Submodules
      • pyCADD.Dock.schrodinger.api module
      • pyCADD.Dock.schrodinger.common module
      • pyCADD.Dock.schrodinger.config module
      • pyCADD.Dock.schrodinger.core module
      • pyCADD.Dock.schrodinger.data module
      • pyCADD.Dock.schrodinger.ensemble module
      • pyCADD.Dock.schrodinger.utils module
      • Module contents
  • Submodules
  • pyCADD.Dock.cli module
  • pyCADD.Dock.common module
    • PDBLine
      • PDBLine.__init__()
      • PDBLine.is_atom_line
      • PDBLine.is_amino
      • PDBLine.is_hetatm
      • PDBLine.is_conect
      • PDBLine.is_ter
      • PDBLine.is_end
      • PDBLine.line
      • PDBLine.get_line()
      • PDBLine.get_atom_name()
    • PDBLineParser
      • PDBLineParser.__init__()
      • PDBLineParser.get_lines()
      • PDBLineParser.get_atom_lines()
      • PDBLineParser.get_amino_lines()
      • PDBLineParser.get_hetatm_lines()
      • PDBLineParser.get_str_list()
      • PDBLineParser.save_pdb()
    • PDBFile
      • PDBFile.__init__()
      • PDBFile.get_lines()
      • PDBFile.get_chain()
    • EnsembleInputFile
      • EnsembleInputFile.__init__()
      • EnsembleInputFile.pdbid_list
      • EnsembleInputFile.ligand_list
      • EnsembleInputFile.from_csv()
      • EnsembleInputFile.from_ini()
      • EnsembleInputFile.from_yaml()
      • EnsembleInputFile.parse_file()
      • EnsembleInputFile.read()
      • EnsembleInputFile.get_pairs_list()
      • EnsembleInputFile.get_pdbid_list()
      • EnsembleInputFile.get_ligand_list()
  • pyCADD.Dock.const module
  • pyCADD.Dock.env module
    • check_virtual_environment()
    • create_environment()
    • main()
  • pyCADD.Dock.ui module
    • UI_dock
      • UI_dock.__init__()
      • UI_dock.run()
  • pyCADD.Dock.utils module
    • check_pdb()
    • get_input_pdbid()
  • Module contents
• pyCADD.Dock.schrodinger package
  • Submodules
  • pyCADD.Dock.schrodinger.api module
    • DockControl
      • DockControl.__init__()
      • DockControl.split()
      • DockControl.minimize()
      • DockControl.grid_generate()
      • DockControl.dock()
    • DockEnsemble
      • DockEnsemble.__init__()
      • DockEnsemble.load_library()
      • DockEnsemble.keep_single_chain()
      • DockEnsemble.minimize()
      • DockEnsemble.grid_generate()
      • DockEnsemble.dock()
      • DockEnsemble.extract_data()
  • pyCADD.Dock.schrodinger.common module
    • MetaData
      • MetaData.pdbid
      • MetaData.ligand_name
      • MetaData.action
      • MetaData.docking_ligand_name
      • MetaData.precision
      • MetaData.internal_ligand_name
      • MetaData.parse_from_filename()
      • MetaData.parse_from_dict()
      • MetaData.parse_from_metadata()
      • MetaData.generate_file_name()
      • MetaData.copy()
      • MetaData.set()
      • MetaData.NoDefault
      • MetaData.get()
      • MetaData.delete()
      • MetaData.__init__()
    • BaseMaestroFile
      • BaseMaestroFile.__init__()
    • GridFile
      • GridFile.__init__()
    • LigandSearched
      • LigandSearched.__init__()
      • LigandSearched.pdbres
      • LigandSearched.chain
      • LigandSearched.resnum
      • LigandSearched.molnum
    • MaestroFile
      • MaestroFile.__init__()
      • MaestroFile.st_reader
      • MaestroFile.structures
      • MaestroFile.get_structure()
      • MaestroFile.get_chain_structure()
      • MaestroFile.get_residue()
      • MaestroFile.get_molecule_by_res()
      • MaestroFile.get_covalent_bond()
      • MaestroFile.get_molnum_by_res()
      • MaestroFile.find_ligands()
    • DockResultFile
      • DockResultFile.__init__()
      • DockResultFile.get_receptor_structure()
      • DockResultFile.get_ligand_structure()
      • DockResultFile.get_raw_results()
      • DockResultFile.get_results()
  • pyCADD.Dock.schrodinger.config module
    • DefaultDataConfig
      • DefaultDataConfig.__init__()
      • DefaultDataConfig.items()
      • DefaultDataConfig.keys()
      • DefaultDataConfig.values()
      • DefaultDataConfig.get()
    • SPConfig
      • SPConfig.__init__()
    • XPConfig
      • XPConfig.__init__()
    • DataConfig
      • DataConfig.__init__()
  • pyCADD.Dock.schrodinger.core module
    • split_complex()
    • minimize()
    • grid_generate()
    • dock()
    • keep_single_chain()
  • pyCADD.Dock.schrodinger.data module
    • extract_docking_data()
    • save_docking_data()
  • pyCADD.Dock.schrodinger.ensemble module
    • split_structure()
    • multi_keep_single_chain()
    • multi_minimize()
    • multi_grid_generate()
    • get_docking_pairs()
    • multi_dock()
    • multi_extract_data()
  • pyCADD.Dock.schrodinger.utils module
    • launch()
    • collect_structures()
    • convert_format()
    • get_centroid()
  • Module contents
• Dock User Guide
  • Download PDB file(s)
  • Docking of Many-to-many (Ensemble Docking)
  • Generate Input Files for Ensemble Docking

Indices and tables

• Index

• Module Index

• Search Page