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) 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_hbond() (pyCADD.Dynamic.common.Analyzer method) calc_rmsd() (pyCADD.Dynamic.common.Analyzer method) calc_rmsf() (pyCADD.Dynamic.common.Analyzer method) calc_scp_score() (in module pyCADD.Dance.core) ChDir (class in pyCADD.utils.common) clean_pdb_data() (pyCADD.Demand.core.QueryClient method) clear_info() (pyCADD.utils.ui.UI 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_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) del_attr() (pyCADD.Dynamic.template.BaseConstructor method)

del_clf() (pyCADD.Dance.common.Evaluator method) del_constructor() (pyCADD.Dynamic.template.MultiConstructorManager method) download_pdb() (in module pyCADD.utils.tool) download_pdb_list() (in module pyCADD.utils.tool)

E

emit() (pyCADD.utils.log.ModifiedFileHandler method) EnsembleInputFile (class in pyCADD.Dock.common) Evaluator (class in pyCADD.Dance.common)

extract_cube() (pyCADD.Density.base.Gauss 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

File (class in pyCADD.utils.common) 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) FixedConfig (class in pyCADD.utils.common)

FixedThread (class in pyCADD.utils.common) from_csv() (pyCADD.Dance.common.Matrix class method) (pyCADD.Dock.common.EnsembleInputFile class method) from_ini() (pyCADD.Dock.common.EnsembleInputFile class method) from_pickle() (pyCADD.Dance.common.Matrix class method) from_splited_data() (pyCADD.Dance.common.Matrix class method) from_yaml() (pyCADD.Dock.common.EnsembleInputFile class method)

G

Gauss (class in pyCADD.Density.base) gauss (pyCADD.Density.base.Gauss property) gbt_default_params (pyCADD.Dance.common.Evaluator property) generate_energy() (in module pyCADD.Density.core) generate_fchk() (in module pyCADD.Density.core) generate_inputfile() (pyCADD.Demand.core.QueryClient method) generate_opt() (in module pyCADD.Density.core) Geo_Average (class in pyCADD.Dance.algorithm.consensus) GeoMean (class in pyCADD.Dance.algorithm.consensus) get_amino_lines() (pyCADD.Dock.common.PDBLineParser method) get_apo() (pyCADD.Demand.core.QueryClient method) get_atom_lines() (pyCADD.Dock.common.PDBLineParser method) get_atom_name() (pyCADD.Dock.common.PDBLine method) get_attr() (pyCADD.Dynamic.template.BaseConstructor method) get_chain() (pyCADD.Dock.common.PDBFile method) get_clf() (pyCADD.Dance.common.Evaluator method) get_clfs_dict() (pyCADD.Dance.common.Evaluator method) get_confirm() (pyCADD.utils.ui.UI method) get_gaussian() (in module pyCADD.Density.core) get_gbt_default_params() (pyCADD.Dance.common.Evaluator method) get_hetatm_lines() (pyCADD.Dock.common.PDBLineParser method) get_input() (pyCADD.utils.ui.UI method) get_ligand_list() (pyCADD.Dock.common.EnsembleInputFile method)

get_line() (pyCADD.Dock.common.PDBLine method) get_lines() (pyCADD.Dock.common.PDBFile method) (pyCADD.Dock.common.PDBLineParser 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_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.EnsembleInputFile method) get_pdbid_list() (pyCADD.Dock.common.EnsembleInputFile method) get_query() (pyCADD.Demand.config.BaseQueryCfg method) (pyCADD.Demand.config.BaseQueryPDB method) get_rf_default_params() (pyCADD.Dance.common.Evaluator method) get_state_dict() (pyCADD.Dynamic.template.BaseConstructor method) (pyCADD.Dynamic.template.HeatInput method) get_str_list() (pyCADD.Dock.common.PDBLineParser 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)

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) is_amber_available() (in module pyCADD.utils.tool) is_amino (pyCADD.Dock.common.PDBLine property) is_atom_line (pyCADD.Dock.common.PDBLine property) is_conect (pyCADD.Dock.common.PDBLine property) is_empty() (pyCADD.Dynamic.template.MultiConstructorManager method)

is_end (pyCADD.Dock.common.PDBLine property) is_gaussian_available() (in module pyCADD.utils.tool) is_hetatm (pyCADD.Dock.common.PDBLine property) is_multiwfn_available() (in module pyCADD.utils.tool) is_pmemd_cuda_available() (in module pyCADD.utils.tool) is_ter (pyCADD.Dock.common.PDBLine property)

J

join() (pyCADD.utils.common.FixedThread method)

L

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) ligand_list (pyCADD.Dock.common.EnsembleInputFile property) line (pyCADD.Dock.common.PDBLine property)

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

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) 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) 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.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.Dynamic pyCADD.Dynamic.cli pyCADD.Dynamic.common pyCADD.Dynamic.core pyCADD.Dynamic.template pyCADD.utils pyCADD.utils.common pyCADD.utils.log pyCADD.utils.tool pyCADD.utils.ui pyCADD.VSW

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) multiprocessing_run() (in module 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.common.FixedConfig method)

P

parse_file() (pyCADD.Dock.common.EnsembleInputFile class method) parse_uniport() (in module pyCADD.Demand.core) pdb_save_dir (pyCADD.Demand.core.QueryClient property) PDBFile (class in pyCADD.Dock.common) pdbid_list (pyCADD.Dock.common.EnsembleInputFile property) PDBLine (class in pyCADD.Dock.common) PDBLineParser (class in pyCADD.Dock.common) 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) 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.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.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.log module pyCADD.utils.tool module pyCADD.utils.ui module pyCADD.VSW 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.EnsembleInputFile method) read_origin_st() (pyCADD.Density.base.Gauss method) repeat_cv() (pyCADD.Dance.common.Evaluator method) 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.Dynamic.core.BaseProcess method) (pyCADD.Dynamic.core.MDProcess method) (pyCADD.utils.common.FixedThread 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_csv() (pyCADD.Dance.common.Dancer method) save_params() (pyCADD.Dance.common.Evaluator method) save_pdb() (pyCADD.Dock.common.PDBLineParser method) save_pickle() (pyCADD.Dance.common.Dancer method) search_params() (pyCADD.Dance.common.Evaluator method) set_attr() (pyCADD.Dynamic.template.BaseConstructor method) set_basis_set() (pyCADD.Density.base.Gauss 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_solvent() (pyCADD.Density.base.Gauss method) set_system() (pyCADD.Density.base.Gauss class method) (pyCADD.Density.ui.UI_Gauss method) shell_run() (in module pyCADD.utils.tool) shwo_cuda_device() (pyCADD.Dynamic.common.Simulator method) SimulationConstructor (class in pyCADD.Dynamic.template) Simulator (class in pyCADD.Dynamic.common) split_train_test_data() (pyCADD.Dance.common.Matrix method) start() (pyCADD.Density.core.Daemon method) std() (in module pyCADD.Dance.algorithm.consensus) stop() (pyCADD.Density.core.Daemon method) 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) TimeoutError 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)

U

UI (class in pyCADD.utils.ui)

UI_Gauss (class in pyCADD.Density.ui) uniprot_save_dir (pyCADD.Demand.core.QueryClient property)

V

version_info (pyCADD.utils.ui.UI property)