Index

_

__init__() (pyCADD.Dock.common.EnsembleInputFile method) (pyCADD.Dock.common.PDBFile method) (pyCADD.Dock.common.PDBLine method) (pyCADD.Dock.common.PDBLineParser method) (pyCADD.Dock.schrodinger.api.DockControl method) (pyCADD.Dock.schrodinger.api.DockEnsemble method) (pyCADD.Dock.schrodinger.common.BaseMaestroFile method) (pyCADD.Dock.schrodinger.common.DockResultFile method) (pyCADD.Dock.schrodinger.common.GridFile method) (pyCADD.Dock.schrodinger.common.LigandSearched method) (pyCADD.Dock.schrodinger.common.MaestroFile method) (pyCADD.Dock.schrodinger.common.MetaData method) (pyCADD.Dock.schrodinger.config.DataConfig method) (pyCADD.Dock.schrodinger.config.DefaultDataConfig method) (pyCADD.Dock.schrodinger.config.SPConfig method) (pyCADD.Dock.schrodinger.config.XPConfig method) (pyCADD.Dock.ui.UI_dock method)

A

action (pyCADD.Dock.schrodinger.common.MetaData attribute)

B

BaseMaestroFile (class in pyCADD.Dock.schrodinger.common)

C

chain (pyCADD.Dock.schrodinger.common.LigandSearched property) check_pdb() (in module pyCADD.Dock.utils) check_virtual_environment() (in module pyCADD.Dock.env)

collect_structures() (in module pyCADD.Dock.schrodinger.utils) convert_format() (in module pyCADD.Dock.schrodinger.utils) copy() (pyCADD.Dock.schrodinger.common.MetaData method) create_environment() (in module pyCADD.Dock.env)

D

DataConfig (class in pyCADD.Dock.schrodinger.config) DefaultDataConfig (class in pyCADD.Dock.schrodinger.config) delete() (pyCADD.Dock.schrodinger.common.MetaData method) dock() (in module pyCADD.Dock.schrodinger.core) (pyCADD.Dock.schrodinger.api.DockControl method) (pyCADD.Dock.schrodinger.api.DockEnsemble method)

DockControl (class in pyCADD.Dock.schrodinger.api) DockEnsemble (class in pyCADD.Dock.schrodinger.api) docking_ligand_name (pyCADD.Dock.schrodinger.common.MetaData attribute) DockResultFile (class in pyCADD.Dock.schrodinger.common)

E

EnsembleInputFile (class in pyCADD.Dock.common)

extract_data() (pyCADD.Dock.schrodinger.api.DockEnsemble method) extract_docking_data() (in module pyCADD.Dock.schrodinger.data)

F

find_ligands() (pyCADD.Dock.schrodinger.common.MaestroFile method) from_csv() (pyCADD.Dock.common.EnsembleInputFile class method)

from_ini() (pyCADD.Dock.common.EnsembleInputFile class method) from_yaml() (pyCADD.Dock.common.EnsembleInputFile class method)

G

generate_file_name() (pyCADD.Dock.schrodinger.common.MetaData method) get() (pyCADD.Dock.schrodinger.common.MetaData method) (pyCADD.Dock.schrodinger.config.DefaultDataConfig method) get_amino_lines() (pyCADD.Dock.common.PDBLineParser method) get_atom_lines() (pyCADD.Dock.common.PDBLineParser method) get_atom_name() (pyCADD.Dock.common.PDBLine method) get_centroid() (in module pyCADD.Dock.schrodinger.utils) get_chain() (pyCADD.Dock.common.PDBFile method) get_chain_structure() (pyCADD.Dock.schrodinger.common.MaestroFile method) get_covalent_bond() (pyCADD.Dock.schrodinger.common.MaestroFile method) get_docking_pairs() (in module pyCADD.Dock.schrodinger.ensemble) get_hetatm_lines() (pyCADD.Dock.common.PDBLineParser method) get_input_pdbid() (in module pyCADD.Dock.utils) get_ligand_list() (pyCADD.Dock.common.EnsembleInputFile method) get_ligand_structure() (pyCADD.Dock.schrodinger.common.DockResultFile method) get_line() (pyCADD.Dock.common.PDBLine method)

get_lines() (pyCADD.Dock.common.PDBFile method) (pyCADD.Dock.common.PDBLineParser method) get_molecule_by_res() (pyCADD.Dock.schrodinger.common.MaestroFile method) get_molnum_by_res() (pyCADD.Dock.schrodinger.common.MaestroFile method) get_pairs_list() (pyCADD.Dock.common.EnsembleInputFile method) get_pdbid_list() (pyCADD.Dock.common.EnsembleInputFile method) get_raw_results() (pyCADD.Dock.schrodinger.common.DockResultFile method) get_receptor_structure() (pyCADD.Dock.schrodinger.common.DockResultFile method) get_residue() (pyCADD.Dock.schrodinger.common.MaestroFile method) get_results() (pyCADD.Dock.schrodinger.common.DockResultFile method) get_str_list() (pyCADD.Dock.common.PDBLineParser method) get_structure() (pyCADD.Dock.schrodinger.common.MaestroFile static method) grid_generate() (in module pyCADD.Dock.schrodinger.core) (pyCADD.Dock.schrodinger.api.DockControl method) (pyCADD.Dock.schrodinger.api.DockEnsemble method) GridFile (class in pyCADD.Dock.schrodinger.common)

I

internal_ligand_name (pyCADD.Dock.schrodinger.common.MetaData property) is_amino (pyCADD.Dock.common.PDBLine property) is_atom_line (pyCADD.Dock.common.PDBLine property) is_conect (pyCADD.Dock.common.PDBLine property)

is_end (pyCADD.Dock.common.PDBLine property) is_hetatm (pyCADD.Dock.common.PDBLine property) is_ter (pyCADD.Dock.common.PDBLine property) items() (pyCADD.Dock.schrodinger.config.DefaultDataConfig method)

K

keep_single_chain() (in module pyCADD.Dock.schrodinger.core) (pyCADD.Dock.schrodinger.api.DockEnsemble method)

keys() (pyCADD.Dock.schrodinger.config.DefaultDataConfig method)

L

launch() (in module pyCADD.Dock.schrodinger.utils) ligand_list (pyCADD.Dock.common.EnsembleInputFile property) ligand_name (pyCADD.Dock.schrodinger.common.MetaData attribute)

LigandSearched (class in pyCADD.Dock.schrodinger.common) line (pyCADD.Dock.common.PDBLine property) load_library() (pyCADD.Dock.schrodinger.api.DockEnsemble method)

M

MaestroFile (class in pyCADD.Dock.schrodinger.common) main() (in module pyCADD.Dock.env) MetaData (class in pyCADD.Dock.schrodinger.common) MetaData.NoDefault (class in pyCADD.Dock.schrodinger.common) minimize() (in module pyCADD.Dock.schrodinger.core) (pyCADD.Dock.schrodinger.api.DockControl method) (pyCADD.Dock.schrodinger.api.DockEnsemble method) module pyCADD.Dock pyCADD.Dock.cli pyCADD.Dock.common pyCADD.Dock.const pyCADD.Dock.env pyCADD.Dock.schrodinger pyCADD.Dock.schrodinger.api pyCADD.Dock.schrodinger.common pyCADD.Dock.schrodinger.config pyCADD.Dock.schrodinger.core pyCADD.Dock.schrodinger.data pyCADD.Dock.schrodinger.ensemble pyCADD.Dock.schrodinger.utils pyCADD.Dock.ui pyCADD.Dock.utils

molnum (pyCADD.Dock.schrodinger.common.LigandSearched property) multi_dock() (in module pyCADD.Dock.schrodinger.ensemble) multi_extract_data() (in module pyCADD.Dock.schrodinger.ensemble) multi_grid_generate() (in module pyCADD.Dock.schrodinger.ensemble) multi_keep_single_chain() (in module pyCADD.Dock.schrodinger.ensemble) multi_minimize() (in module pyCADD.Dock.schrodinger.ensemble)

P

parse_file() (pyCADD.Dock.common.EnsembleInputFile class method) parse_from_dict() (pyCADD.Dock.schrodinger.common.MetaData class method) parse_from_filename() (pyCADD.Dock.schrodinger.common.MetaData class method) parse_from_metadata() (pyCADD.Dock.schrodinger.common.MetaData class method) PDBFile (class in pyCADD.Dock.common) pdbid (pyCADD.Dock.schrodinger.common.MetaData attribute) pdbid_list (pyCADD.Dock.common.EnsembleInputFile property) PDBLine (class in pyCADD.Dock.common) PDBLineParser (class in pyCADD.Dock.common) pdbres (pyCADD.Dock.schrodinger.common.LigandSearched property) precision (pyCADD.Dock.schrodinger.common.MetaData attribute) pyCADD.Dock module pyCADD.Dock.cli module pyCADD.Dock.common module pyCADD.Dock.const module pyCADD.Dock.env module

pyCADD.Dock.schrodinger module 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 pyCADD.Dock.ui module pyCADD.Dock.utils module

R

read() (pyCADD.Dock.common.EnsembleInputFile method)

resnum (pyCADD.Dock.schrodinger.common.LigandSearched property) run() (pyCADD.Dock.ui.UI_dock method)

S

save_docking_data() (in module pyCADD.Dock.schrodinger.data) save_pdb() (pyCADD.Dock.common.PDBLineParser method) set() (pyCADD.Dock.schrodinger.common.MetaData method) SPConfig (class in pyCADD.Dock.schrodinger.config)

split() (pyCADD.Dock.schrodinger.api.DockControl method) split_complex() (in module pyCADD.Dock.schrodinger.core) split_structure() (in module pyCADD.Dock.schrodinger.ensemble) st_reader (pyCADD.Dock.schrodinger.common.MaestroFile property) structures (pyCADD.Dock.schrodinger.common.MaestroFile property)

U

UI_dock (class in pyCADD.Dock.ui)

V

values() (pyCADD.Dock.schrodinger.config.DefaultDataConfig method)

X

XPConfig (class in pyCADD.Dock.schrodinger.config)