pyCADD package

Subpackages

• pyCADD.Dance package
  • Subpackages
    • pyCADD.Dance.algorithm package
      • Submodules
      • pyCADD.Dance.algorithm.DL module
      • pyCADD.Dance.algorithm.consensus module
      • pyCADD.Dance.algorithm.default_params module
      • Module contents
  • Submodules
  • pyCADD.Dance.common module
    • Dancer
      • Dancer.add_dataset()
      • Dancer.add_neg_dataset()
      • Dancer.add_pos_dataset()
      • Dancer.get_merged_data()
      • Dancer.prepare_data()
      • Dancer.save()
      • Dancer.save_csv()
      • Dancer.save_pickle()
    • Evaluator
      • Evaluator.add_clf()
      • Evaluator.del_clf()
      • Evaluator.gbt_default_params
      • Evaluator.get_clf()
      • Evaluator.get_clfs_dict()
      • Evaluator.get_gbt_default_params()
      • Evaluator.get_lr_default_params()
      • Evaluator.get_rf_default_params()
      • Evaluator.get_weights()
      • Evaluator.load_params()
      • Evaluator.lr_default_params
      • Evaluator.print_classifier_info()
      • Evaluator.print_cv_results()
      • Evaluator.repeat_cv()
      • Evaluator.rf_default_params
      • Evaluator.save_params()
      • Evaluator.search_params()
      • Evaluator.testset_eval()
    • Matrix
      • Matrix.from_csv()
      • Matrix.from_pickle()
      • Matrix.from_splited_data()
      • Matrix.get_test_data()
      • Matrix.get_train_data()
      • Matrix.split_train_test_data()
  • pyCADD.Dance.core module
    • calc_scp_score()
    • hyperparam_tuning()
  • pyCADD.Dance.metrics module
    • nef_score()
  • Module contents
• pyCADD.Demand package
  • Submodules
  • pyCADD.Demand.cli module
  • pyCADD.Demand.config module
    • BaseQueryCfg
      • BaseQueryCfg.get_query()
    • BaseQueryPDB
      • BaseQueryPDB.get_query()
  • pyCADD.Demand.core module
    • QueryClient
      • QueryClient.clean_pdb_data()
      • QueryClient.generate_inputfile()
      • QueryClient.get_apo()
      • QueryClient.get_mutation_pdb()
      • QueryClient.get_mutations()
      • QueryClient.query()
    • get_nested_value()
    • parse_uniport()
    • query_pdb()
    • query_uniprot()
    • query_uniprot_id_on_pdb()
  • Module contents
• pyCADD.Density package
  • Submodules
  • pyCADD.Density.base module
    • Gauss
      • Gauss.create_inputfile()
      • Gauss.extract_cube()
      • Gauss.gauss
      • Gauss.get_mo_info()
      • Gauss.read_origin_st()
      • Gauss.run()
      • Gauss.set_DFT()
      • Gauss.set_basis_set()
      • Gauss.set_charge()
      • Gauss.set_multiplicity()
      • Gauss.set_solvent()
      • Gauss.set_system()
      • Gauss.system_info
  • pyCADD.Density.core module
    • Daemon
      • Daemon.daemonize()
      • Daemon.restart()
      • Daemon.run()
      • Daemon.start()
      • Daemon.stop()
    • cube_file_generate()
    • generate_energy()
    • generate_fchk()
    • generate_opt()
    • get_gaussian()
    • get_mo()
    • system_default()
  • pyCADD.Density.ui module
    • UI_Gauss
      • UI_Gauss.cpu_count
      • UI_Gauss.mem
      • UI_Gauss.run()
      • UI_Gauss.set_system()
  • Module contents
• pyCADD.Dock package
  • Submodules
  • pyCADD.Dock.cli module
  • pyCADD.Dock.common module
    • ComplexFile
      • ComplexFile.get_lig_molnum()
      • ComplexFile.split()
    • DockResultFile
      • DockResultFile.calc_mmgbsa()
      • DockResultFile.docking_ligand_st
      • DockResultFile.docking_receptor_st
      • DockResultFile.extract_docking_data()
      • DockResultFile.get_ligand_file()
      • DockResultFile.get_merged_file()
      • DockResultFile.get_receptor_file()
      • DockResultFile.merged_file
      • DockResultFile.property
    • GridFile
    • LigandFile
      • LigandFile.calc_admet()
    • MaestroFile
      • MaestroFile.convert_format()
      • MaestroFile.get_first_structure()
      • MaestroFile.minimize()
      • MaestroFile.st_reader
      • MaestroFile.structures
    • MultiInputFile
      • MultiInputFile.get_gridfile_path_list()
      • MultiInputFile.get_ligand_list()
      • MultiInputFile.get_pairs_list()
      • MultiInputFile.get_pdbfile_path_list()
      • MultiInputFile.get_pdbid_list()
      • MultiInputFile.ligand_list
      • MultiInputFile.parse_file()
      • MultiInputFile.pdbid_list
      • MultiInputFile.read()
      • MultiInputFile.read_from_config()
    • PDBFile
      • PDBFile.get_lig()
      • PDBFile.get_lig_name()
      • PDBFile.keep_chain()
    • ReceptorFile
    • check_pdb()
    • get_input_pdbid()
    • get_predict_structure()
    • launch()
  • pyCADD.Dock.config module
    • BaseConfig
    • DataConfig
    • DefaultDataConfig
  • pyCADD.Dock.console module
    • Docker
      • Docker.calc_admet()
      • Docker.calc_mmgbsa()
      • Docker.calc_volume()
      • Docker.dock()
      • Docker.download_pdb()
      • Docker.extra_admet_data()
      • Docker.extra_docking_data()
      • Docker.grid_generate()
      • Docker.keep_chain()
      • Docker.lig_info
      • Docker.lig_name
      • Docker.minimize()
      • Docker.pdb_file
      • Docker.pdb_file_path
      • Docker.pdbid
      • Docker.save_admet_data()
      • Docker.save_docking_data()
      • Docker.set_calc_rmsd()
      • Docker.set_precision()
      • Docker.split_complex()
  • pyCADD.Dock.core module
    • calc_admet()
    • calc_mmgbsa()
    • calc_volume()
    • dock()
    • grid_generate()
    • minimize()
  • pyCADD.Dock.data module
    • Reporter
      • Reporter.generate_report()
    • extra_admet_data()
    • extra_docking_data()
    • save_admet_data()
    • save_docking_data()
    • save_ensemble_docking_data()
    • save_redocking_data()
  • pyCADD.Dock.ensemble module
    • split_ligand()
  • pyCADD.Dock.ui module
    • UI_dock
      • UI_dock.run()
  • Module contents
• pyCADD.Dynamic package
  • Submodules
  • pyCADD.Dynamic.analysis module
  • pyCADD.Dynamic.cli module
  • pyCADD.Dynamic.common module
    • Analyzer
      • Analyzer.calc_hbond()
      • Analyzer.calc_rmsd()
      • Analyzer.calc_rmsf()
      • Analyzer.creat_energy_inputfile()
      • Analyzer.extract_frame()
      • Analyzer.extract_frames()
      • Analyzer.extract_lowest_energy_st()
      • Analyzer.load_mdout()
      • Analyzer.load_topfile()
      • Analyzer.load_traj()
      • Analyzer.run_energy_calc()
      • Analyzer.trace_angle()
      • Analyzer.trace_distance()
    • Processor
      • Processor.add_heat_process()
      • Processor.add_minimize_process()
      • Processor.add_npt_process()
      • Processor.add_nvt_process()
      • Processor.add_process()
      • Processor.cover_to_pdb()
      • Processor.creat_heat_input()
      • Processor.creat_minimize_input()
      • Processor.creat_npt_input()
      • Processor.creat_nvt_input()
      • Processor.get_water_resnum()
      • Processor.leap_prepare()
      • Processor.load_frcmod_file()
      • Processor.load_processed_molfile()
      • Processor.load_processed_profile()
      • Processor.molecule_prepare()
      • Processor.protein_prepare()
      • Processor.set_comsolvate_file()
    • Simulator
      • Simulator.run_simulation()
      • Simulator.set_cuda_device()
      • Simulator.shwo_cuda_device()
  • pyCADD.Dynamic.core module
    • BaseProcess
      • BaseProcess.run()
    • MDProcess
      • MDProcess.run()
    • MinimizeProcess
    • NPTProcess
    • NVTProcess
    • leap_prepare()
    • leap_prepare_for_apo()
    • molecule_prepare_bcc()
    • molecule_prepare_resp2()
    • protein_prepare()
  • pyCADD.Dynamic.template module
    • AnalysisConstructor
      • AnalysisConstructor.to_string()
    • BaseConstructor
      • BaseConstructor.add_attr()
      • BaseConstructor.del_attr()
      • BaseConstructor.get_attr()
      • BaseConstructor.get_state_dict()
      • BaseConstructor.save()
      • BaseConstructor.set_attr()
      • BaseConstructor.to_dict()
      • BaseConstructor.to_str()
      • BaseConstructor.to_string()
    • HeatInput
      • HeatInput.HEAT_TEMPLATE
      • HeatInput.add_heat()
      • HeatInput.add_nvt()
      • HeatInput.get_state_dict()
      • HeatInput.save()
      • HeatInput.to_string()
    • LeapConstructor
      • LeapConstructor.base_template
      • LeapConstructor.to_string()
    • LeapInput
    • MMGBSAInput
      • MMGBSAInput.add_decomp()
      • MMGBSAInput.add_gb()
      • MMGBSAInput.add_general()
      • MMGBSAInput.add_nmode()
      • MMGBSAInput.add_pb()
      • MMGBSAInput.save()
      • MMGBSAInput.to_string()
    • MinimizeInput
    • MultiConstructorManager
      • MultiConstructorManager.add_constructor()
      • MultiConstructorManager.del_constructor()
      • MultiConstructorManager.is_empty()
      • MultiConstructorManager.save()
      • MultiConstructorManager.to_string()
    • NPTInput
    • NVTInput
    • RestrainedMinimizeInput
    • SimulationConstructor
      • SimulationConstructor.to_string()
  • Module contents
• pyCADD.VSW package
  • Submodules
  • pyCADD.VSW.base module
    • VSW
      • VSW.database_list
      • VSW.genelist
      • VSW.generate_input_file()
      • VSW.get_gene()
      • VSW.get_receptor_list()
      • VSW.read_databse()
      • VSW.read_gene()
      • VSW.required_dir
      • VSW.run()
      • VSW.select_database()
      • VSW.vsw_dir
  • pyCADD.VSW.core module
    • gen_input_file()
    • read_database_config()
    • read_gene_config()
  • pyCADD.VSW.register module
    • del_database()
    • del_gene()
    • reg_database()
    • reg_gene()
  • pyCADD.VSW.ui module
    • UI_VSW
      • UI_VSW.get_database()
      • UI_VSW.get_gene()
      • UI_VSW.run()
  • Module contents
• pyCADD.utils package
  • Submodules
  • pyCADD.utils.common module
    • BaseFile
  • pyCADD.utils.env module
    • check_virtual_environment()
    • create_environment()
    • main()
  • pyCADD.utils.log module
    • ModifiedFileHandler
      • ModifiedFileHandler.emit()
    • get_logfile_name()
  • pyCADD.utils.tool module
    • Myconfig
      • Myconfig.optionxform()
    • check_file_update_progress()
    • download_pdb()
    • download_pdb_list()
    • get_config()
    • get_lib_dir()
    • is_amber_available()
    • is_gaussian_available()
    • is_multiwfn_available()
    • is_pmemd_cuda_available()
    • makedirs_from_list()
    • timeit()
  • pyCADD.utils.ui module
    • UI
      • UI.basic_info
      • UI.clear_info()
      • UI.create_panel()
      • UI.get_confirm()
      • UI.get_input()
      • UI.info_index
      • UI.system_info
      • UI.title
      • UI.version_info
  • Module contents

Module contents