Index

A

add_attr() (pyCADD.Dynamic.template.BaseConstructor method) add_clf() (pyCADD.Dance.common.Evaluator method) add_constructor() (pyCADD.Dynamic.template.MultiConstructorManager method) add_dataset() (pyCADD.Dance.common.Dancer method) add_decomp() (pyCADD.Dynamic.template.MMGBSAInput method) add_gb() (pyCADD.Dynamic.template.MMGBSAInput method) add_general() (pyCADD.Dynamic.template.MMGBSAInput method) add_heat() (pyCADD.Dynamic.template.HeatInput method) add_heat_process() (pyCADD.Dynamic.common.Processor method) add_minimize_process() (pyCADD.Dynamic.common.Processor method) add_neg_dataset() (pyCADD.Dance.common.Dancer method)

add_nmode() (pyCADD.Dynamic.template.MMGBSAInput method) add_npt_process() (pyCADD.Dynamic.common.Processor method) add_nvt() (pyCADD.Dynamic.template.HeatInput method) add_nvt_process() (pyCADD.Dynamic.common.Processor method) add_pb() (pyCADD.Dynamic.template.MMGBSAInput method) add_pos_dataset() (pyCADD.Dance.common.Dancer method) add_process() (pyCADD.Dynamic.common.Processor method) AnalysisConstructor (class in pyCADD.Dynamic.template) Analyzer (class in pyCADD.Dynamic.common) Average (class in pyCADD.Dance.algorithm.consensus) average() (in module pyCADD.Dance.algorithm.consensus)

B

base_template (pyCADD.Dynamic.template.LeapConstructor property) BaseConfig (class in pyCADD.Dock.config) BaseConstructor (class in pyCADD.Dynamic.template) BaseFile (class in pyCADD.utils.common)

BaseProcess (class in pyCADD.Dynamic.core) BaseQueryCfg (class in pyCADD.Demand.config) BaseQueryPDB (class in pyCADD.Demand.config) basic_info (pyCADD.utils.ui.UI property)

C

calc_admet() (in module pyCADD.Dock.core) (pyCADD.Dock.common.LigandFile method) (pyCADD.Dock.console.Docker method) calc_hbond() (pyCADD.Dynamic.common.Analyzer method) calc_mmgbsa() (in module pyCADD.Dock.core) (pyCADD.Dock.common.DockResultFile method) (pyCADD.Dock.console.Docker method) calc_rmsd() (pyCADD.Dynamic.common.Analyzer method) calc_rmsf() (pyCADD.Dynamic.common.Analyzer method) calc_scp_score() (in module pyCADD.Dance.core) calc_volume() (in module pyCADD.Dock.core) (pyCADD.Dock.console.Docker method) check_file_update_progress() (in module pyCADD.utils.tool) check_pdb() (in module pyCADD.Dock.common) check_virtual_environment() (in module pyCADD.utils.env)

clean_pdb_data() (pyCADD.Demand.core.QueryClient method) clear_info() (pyCADD.utils.ui.UI method) ComplexFile (class in pyCADD.Dock.common) convert_format() (pyCADD.Dock.common.MaestroFile static method) cover_to_pdb() (pyCADD.Dynamic.common.Processor static method) cpu_count (pyCADD.Density.ui.UI_Gauss property) creat_energy_inputfile() (pyCADD.Dynamic.common.Analyzer method) creat_heat_input() (pyCADD.Dynamic.common.Processor method) creat_minimize_input() (pyCADD.Dynamic.common.Processor method) creat_npt_input() (pyCADD.Dynamic.common.Processor method) creat_nvt_input() (pyCADD.Dynamic.common.Processor method) create_environment() (in module pyCADD.utils.env) create_inputfile() (pyCADD.Density.base.Gauss method) create_panel() (pyCADD.utils.ui.UI method) cube_file_generate() (in module pyCADD.Density.core)

D

Daemon (class in pyCADD.Density.core) daemonize() (pyCADD.Density.core.Daemon method) Dancer (class in pyCADD.Dance.common) database_list (pyCADD.VSW.base.VSW property) DataConfig (class in pyCADD.Dock.config) DefaultDataConfig (class in pyCADD.Dock.config) del_attr() (pyCADD.Dynamic.template.BaseConstructor method) del_clf() (pyCADD.Dance.common.Evaluator method) del_constructor() (pyCADD.Dynamic.template.MultiConstructorManager method) del_database() (in module pyCADD.VSW.register)

del_gene() (in module pyCADD.VSW.register) dock() (in module pyCADD.Dock.core) (pyCADD.Dock.console.Docker method) Docker (class in pyCADD.Dock.console) docking_ligand_st (pyCADD.Dock.common.DockResultFile property) docking_receptor_st (pyCADD.Dock.common.DockResultFile property) DockResultFile (class in pyCADD.Dock.common) download_pdb() (in module pyCADD.utils.tool) (pyCADD.Dock.console.Docker method) download_pdb_list() (in module pyCADD.utils.tool)

E

emit() (pyCADD.utils.log.ModifiedFileHandler method) Evaluator (class in pyCADD.Dance.common) extra_admet_data() (in module pyCADD.Dock.data) (pyCADD.Dock.console.Docker method) extra_docking_data() (in module pyCADD.Dock.data) (pyCADD.Dock.console.Docker method)

extract_cube() (pyCADD.Density.base.Gauss method) extract_docking_data() (pyCADD.Dock.common.DockResultFile method) extract_frame() (pyCADD.Dynamic.common.Analyzer method) extract_frames() (pyCADD.Dynamic.common.Analyzer method) extract_lowest_energy_st() (pyCADD.Dynamic.common.Analyzer method)

F

fit() (pyCADD.Dance.algorithm.consensus.Average method) (pyCADD.Dance.algorithm.consensus.Geo_Average method) (pyCADD.Dance.algorithm.consensus.Maximum method) (pyCADD.Dance.algorithm.consensus.Minimum method)

forward() (pyCADD.Dance.algorithm.DL.MLP method) from_csv() (pyCADD.Dance.common.Matrix class method) from_pickle() (pyCADD.Dance.common.Matrix class method) from_splited_data() (pyCADD.Dance.common.Matrix class method)

G

Gauss (class in pyCADD.Density.base) gauss (pyCADD.Density.base.Gauss property) gbt_default_params (pyCADD.Dance.common.Evaluator property) gen_input_file() (in module pyCADD.VSW.core) genelist (pyCADD.VSW.base.VSW property) generate_energy() (in module pyCADD.Density.core) generate_fchk() (in module pyCADD.Density.core) generate_input_file() (pyCADD.VSW.base.VSW method) generate_inputfile() (pyCADD.Demand.core.QueryClient method) generate_opt() (in module pyCADD.Density.core) generate_report() (pyCADD.Dock.data.Reporter method) Geo_Average (class in pyCADD.Dance.algorithm.consensus) GeoMean (class in pyCADD.Dance.algorithm.consensus) get_apo() (pyCADD.Demand.core.QueryClient method) get_attr() (pyCADD.Dynamic.template.BaseConstructor method) get_clf() (pyCADD.Dance.common.Evaluator method) get_clfs_dict() (pyCADD.Dance.common.Evaluator method) get_config() (in module pyCADD.utils.tool) get_confirm() (pyCADD.utils.ui.UI method) get_database() (pyCADD.VSW.ui.UI_VSW method) get_first_structure() (pyCADD.Dock.common.MaestroFile static method) get_gaussian() (in module pyCADD.Density.core) get_gbt_default_params() (pyCADD.Dance.common.Evaluator method) get_gene() (pyCADD.VSW.base.VSW method) (pyCADD.VSW.ui.UI_VSW method) get_gridfile_path_list() (pyCADD.Dock.common.MultiInputFile method) get_input() (pyCADD.utils.ui.UI method) get_input_pdbid() (in module pyCADD.Dock.common) get_lib_dir() (in module pyCADD.utils.tool) get_lig() (pyCADD.Dock.common.PDBFile method) get_lig_molnum() (pyCADD.Dock.common.ComplexFile method)

get_lig_name() (pyCADD.Dock.common.PDBFile method) get_ligand_file() (pyCADD.Dock.common.DockResultFile method) get_ligand_list() (pyCADD.Dock.common.MultiInputFile method) get_logfile_name() (in module pyCADD.utils.log) get_lr_default_params() (pyCADD.Dance.common.Evaluator method) get_merged_data() (pyCADD.Dance.common.Dancer method) get_merged_file() (pyCADD.Dock.common.DockResultFile method) get_mo() (in module pyCADD.Density.core) get_mo_info() (pyCADD.Density.base.Gauss method) get_mutation_pdb() (pyCADD.Demand.core.QueryClient method) get_mutations() (pyCADD.Demand.core.QueryClient method) get_nested_value() (in module pyCADD.Demand.core) get_pairs_list() (pyCADD.Dock.common.MultiInputFile method) get_params() (pyCADD.Dance.algorithm.DL.MLP method) get_pdbfile_path_list() (pyCADD.Dock.common.MultiInputFile method) get_pdbid_list() (pyCADD.Dock.common.MultiInputFile method) get_predict_structure() (in module pyCADD.Dock.common) get_query() (pyCADD.Demand.config.BaseQueryCfg method) (pyCADD.Demand.config.BaseQueryPDB method) get_receptor_file() (pyCADD.Dock.common.DockResultFile method) get_receptor_list() (pyCADD.VSW.base.VSW method) get_rf_default_params() (pyCADD.Dance.common.Evaluator method) get_state_dict() (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) get_test_data() (pyCADD.Dance.common.Matrix method) get_train_data() (pyCADD.Dance.common.Matrix method) get_water_resnum() (pyCADD.Dynamic.common.Processor method) get_weights() (pyCADD.Dance.common.Evaluator static method) grid_generate() (in module pyCADD.Dock.core) (pyCADD.Dock.console.Docker method) GridFile (class in pyCADD.Dock.common)

H

HEAT_TEMPLATE (pyCADD.Dynamic.template.HeatInput attribute)

HeatInput (class in pyCADD.Dynamic.template) hyperparam_tuning() (in module pyCADD.Dance.core)

I

info_index (pyCADD.utils.ui.UI property) initialize() (pyCADD.Dance.algorithm.DL.MLP method) is_amber_available() (in module pyCADD.utils.tool)

is_empty() (pyCADD.Dynamic.template.MultiConstructorManager method) is_gaussian_available() (in module pyCADD.utils.tool) is_multiwfn_available() (in module pyCADD.utils.tool) is_pmemd_cuda_available() (in module pyCADD.utils.tool)

K

keep_chain() (pyCADD.Dock.common.PDBFile method) (pyCADD.Dock.console.Docker method)

L

launch() (in module pyCADD.Dock.common) leap_prepare() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Processor method) leap_prepare_for_apo() (in module pyCADD.Dynamic.core) LeapConstructor (class in pyCADD.Dynamic.template) LeapInput (class in pyCADD.Dynamic.template) lig_info (pyCADD.Dock.console.Docker property) lig_name (pyCADD.Dock.console.Docker property) ligand_list (pyCADD.Dock.common.MultiInputFile property)

LigandFile (class in pyCADD.Dock.common) load_frcmod_file() (pyCADD.Dynamic.common.Processor method) load_mdout() (pyCADD.Dynamic.common.Analyzer method) load_params() (pyCADD.Dance.common.Evaluator method) load_processed_molfile() (pyCADD.Dynamic.common.Processor method) load_processed_profile() (pyCADD.Dynamic.common.Processor method) load_topfile() (pyCADD.Dynamic.common.Analyzer method) load_traj() (pyCADD.Dynamic.common.Analyzer method) lr_default_params (pyCADD.Dance.common.Evaluator property)

M

MaestroFile (class in pyCADD.Dock.common) main() (in module pyCADD.utils.env) makedirs_from_list() (in module pyCADD.utils.tool) Matrix (class in pyCADD.Dance.common) Maximum (class in pyCADD.Dance.algorithm.consensus) maximum() (in module pyCADD.Dance.algorithm.consensus) MDProcess (class in pyCADD.Dynamic.core) Mean (class in pyCADD.Dance.algorithm.consensus) mem (pyCADD.Density.ui.UI_Gauss property) merged_file (pyCADD.Dock.common.DockResultFile property) minimize() (in module pyCADD.Dock.core) (pyCADD.Dock.common.MaestroFile method) (pyCADD.Dock.console.Docker method) MinimizeInput (class in pyCADD.Dynamic.template) MinimizeProcess (class in pyCADD.Dynamic.core) Minimum (class in pyCADD.Dance.algorithm.consensus) minimum() (in module pyCADD.Dance.algorithm.consensus) MLP (class in pyCADD.Dance.algorithm.DL) MMGBSAInput (class in pyCADD.Dynamic.template) ModifiedFileHandler (class in pyCADD.utils.log) module pyCADD pyCADD.Dance pyCADD.Dance.algorithm pyCADD.Dance.algorithm.consensus pyCADD.Dance.algorithm.default_params pyCADD.Dance.algorithm.DL pyCADD.Dance.common pyCADD.Dance.core pyCADD.Dance.metrics pyCADD.Demand pyCADD.Demand.cli pyCADD.Demand.config pyCADD.Demand.core pyCADD.Density pyCADD.Density.base pyCADD.Density.core pyCADD.Density.ui pyCADD.Dock pyCADD.Dock.cli pyCADD.Dock.common pyCADD.Dock.config pyCADD.Dock.console pyCADD.Dock.core pyCADD.Dock.data pyCADD.Dock.ensemble pyCADD.Dock.ui pyCADD.Dynamic pyCADD.Dynamic.cli pyCADD.Dynamic.common pyCADD.Dynamic.core pyCADD.Dynamic.template pyCADD.utils pyCADD.utils.common pyCADD.utils.env pyCADD.utils.log pyCADD.utils.tool pyCADD.utils.ui pyCADD.VSW pyCADD.VSW.base pyCADD.VSW.core pyCADD.VSW.register pyCADD.VSW.ui

molecule_prepare() (pyCADD.Dynamic.common.Processor method) molecule_prepare_bcc() (in module pyCADD.Dynamic.core) molecule_prepare_resp2() (in module pyCADD.Dynamic.core) MultiConstructorManager (class in pyCADD.Dynamic.template) MultiInputFile (class in pyCADD.Dock.common) Myconfig (class in pyCADD.utils.tool)

N

nef_score() (in module pyCADD.Dance.metrics) NPTInput (class in pyCADD.Dynamic.template)

NPTProcess (class in pyCADD.Dynamic.core) NVTInput (class in pyCADD.Dynamic.template) NVTProcess (class in pyCADD.Dynamic.core)

O

optionxform() (pyCADD.utils.tool.Myconfig method)

P

parse_file() (pyCADD.Dock.common.MultiInputFile method) parse_uniport() (in module pyCADD.Demand.core) pdb_file (pyCADD.Dock.console.Docker property) pdb_file_path (pyCADD.Dock.console.Docker property) PDBFile (class in pyCADD.Dock.common) pdbid (pyCADD.Dock.console.Docker property) pdbid_list (pyCADD.Dock.common.MultiInputFile property) predict() (pyCADD.Dance.algorithm.DL.MLP method) predict_proba() (pyCADD.Dance.algorithm.DL.MLP method) prepare_data() (pyCADD.Dance.common.Dancer method) print_classifier_info() (pyCADD.Dance.common.Evaluator method) print_cv_results() (pyCADD.Dance.common.Evaluator method) Processor (class in pyCADD.Dynamic.common) property (pyCADD.Dock.common.DockResultFile property) protein_prepare() (in module pyCADD.Dynamic.core) (pyCADD.Dynamic.common.Processor method) pyCADD module pyCADD.Dance module pyCADD.Dance.algorithm module pyCADD.Dance.algorithm.consensus module pyCADD.Dance.algorithm.default_params module pyCADD.Dance.algorithm.DL module pyCADD.Dance.common module pyCADD.Dance.core module pyCADD.Dance.metrics module pyCADD.Demand module pyCADD.Demand.cli module pyCADD.Demand.config module pyCADD.Demand.core module pyCADD.Density module pyCADD.Density.base module pyCADD.Density.core module pyCADD.Density.ui module

pyCADD.Dock module pyCADD.Dock.cli module pyCADD.Dock.common module pyCADD.Dock.config module pyCADD.Dock.console module pyCADD.Dock.core module pyCADD.Dock.data module pyCADD.Dock.ensemble module pyCADD.Dock.ui module pyCADD.Dynamic module pyCADD.Dynamic.cli module pyCADD.Dynamic.common module pyCADD.Dynamic.core module pyCADD.Dynamic.template module pyCADD.utils module pyCADD.utils.common module pyCADD.utils.env module pyCADD.utils.log module pyCADD.utils.tool module pyCADD.utils.ui module pyCADD.VSW module pyCADD.VSW.base module pyCADD.VSW.core module pyCADD.VSW.register module pyCADD.VSW.ui module

Q

query() (pyCADD.Demand.core.QueryClient method) query_pdb() (in module pyCADD.Demand.core)

query_uniprot() (in module pyCADD.Demand.core) query_uniprot_id_on_pdb() (in module pyCADD.Demand.core) QueryClient (class in pyCADD.Demand.core)

R

read() (pyCADD.Dock.common.MultiInputFile method) read_database_config() (in module pyCADD.VSW.core) read_databse() (pyCADD.VSW.base.VSW method) read_from_config() (pyCADD.Dock.common.MultiInputFile static method) read_gene() (pyCADD.VSW.base.VSW method) read_gene_config() (in module pyCADD.VSW.core) read_origin_st() (pyCADD.Density.base.Gauss method) ReceptorFile (class in pyCADD.Dock.common) reg_database() (in module pyCADD.VSW.register) reg_gene() (in module pyCADD.VSW.register) repeat_cv() (pyCADD.Dance.common.Evaluator method) Reporter (class in pyCADD.Dock.data) required_dir (pyCADD.VSW.base.VSW property)

restart() (pyCADD.Density.core.Daemon method) RestrainedMinimizeInput (class in pyCADD.Dynamic.template) rf_default_params (pyCADD.Dance.common.Evaluator property) run() (pyCADD.Density.base.Gauss method) (pyCADD.Density.core.Daemon method) (pyCADD.Density.ui.UI_Gauss method) (pyCADD.Dock.ui.UI_dock method) (pyCADD.Dynamic.core.BaseProcess method) (pyCADD.Dynamic.core.MDProcess method) (pyCADD.VSW.base.VSW method) (pyCADD.VSW.ui.UI_VSW method) run_energy_calc() (pyCADD.Dynamic.common.Analyzer method) run_simulation() (pyCADD.Dynamic.common.Simulator method)

S

save() (pyCADD.Dance.common.Dancer method) (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) (pyCADD.Dynamic.template.MMGBSAInput method) (pyCADD.Dynamic.template.MultiConstructorManager method) save_admet_data() (in module pyCADD.Dock.data) (pyCADD.Dock.console.Docker method) save_csv() (pyCADD.Dance.common.Dancer method) save_docking_data() (in module pyCADD.Dock.data) (pyCADD.Dock.console.Docker method) save_ensemble_docking_data() (in module pyCADD.Dock.data) save_params() (pyCADD.Dance.common.Evaluator method) save_pickle() (pyCADD.Dance.common.Dancer method) save_redocking_data() (in module pyCADD.Dock.data) search_params() (pyCADD.Dance.common.Evaluator method) select_database() (pyCADD.VSW.base.VSW method) set_attr() (pyCADD.Dynamic.template.BaseConstructor method) set_basis_set() (pyCADD.Density.base.Gauss method) set_calc_rmsd() (pyCADD.Dock.console.Docker method) set_charge() (pyCADD.Density.base.Gauss method) set_comsolvate_file() (pyCADD.Dynamic.common.Processor method)

set_cuda_device() (pyCADD.Dynamic.common.Simulator method) set_DFT() (pyCADD.Density.base.Gauss method) set_multiplicity() (pyCADD.Density.base.Gauss method) set_precision() (pyCADD.Dock.console.Docker method) set_solvent() (pyCADD.Density.base.Gauss method) set_system() (pyCADD.Density.base.Gauss class method) (pyCADD.Density.ui.UI_Gauss method) shwo_cuda_device() (pyCADD.Dynamic.common.Simulator method) SimulationConstructor (class in pyCADD.Dynamic.template) Simulator (class in pyCADD.Dynamic.common) split() (pyCADD.Dock.common.ComplexFile method) split_complex() (pyCADD.Dock.console.Docker method) split_ligand() (in module pyCADD.Dock.ensemble) split_train_test_data() (pyCADD.Dance.common.Matrix method) st_reader (pyCADD.Dock.common.MaestroFile property) start() (pyCADD.Density.core.Daemon method) std() (in module pyCADD.Dance.algorithm.consensus) stop() (pyCADD.Density.core.Daemon method) structures (pyCADD.Dock.common.MaestroFile property) system_default() (in module pyCADD.Density.core) system_info (pyCADD.Density.base.Gauss property) (pyCADD.utils.ui.UI property)

T

testset_eval() (pyCADD.Dance.common.Evaluator method) timeit() (in module pyCADD.utils.tool) title (pyCADD.utils.ui.UI property) to_dict() (pyCADD.Dynamic.template.BaseConstructor method) to_str() (pyCADD.Dynamic.template.BaseConstructor method) to_string() (pyCADD.Dynamic.template.AnalysisConstructor method) (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) (pyCADD.Dynamic.template.LeapConstructor method) (pyCADD.Dynamic.template.MMGBSAInput method) (pyCADD.Dynamic.template.MultiConstructorManager method) (pyCADD.Dynamic.template.SimulationConstructor method)

trace_angle() (pyCADD.Dynamic.common.Analyzer method) trace_distance() (pyCADD.Dynamic.common.Analyzer method) training (pyCADD.Dance.algorithm.DL.MLP attribute)

U

UI (class in pyCADD.utils.ui) UI_dock (class in pyCADD.Dock.ui)

UI_Gauss (class in pyCADD.Density.ui) UI_VSW (class in pyCADD.VSW.ui)

V

version_info (pyCADD.utils.ui.UI property)

VSW (class in pyCADD.VSW.base) vsw_dir (pyCADD.VSW.base.VSW property)