Index

_

__init__() (docktopus.docking.Docking method) (docktopus.gdock_engine.GDockHEMEDockingEngine method) (docktopus.gnina_engine.GninaDockingEngine method) (docktopus.preprocessor.DataPreprocessor method) (docktopus.rfaa_engine.RFAADockingEngine method) (docktopus.validator.RFAAValidator method) (docktopus.vina_engine.VinaDockingEngine method)

_validator (docktopus.rfaa_engine.RFAADockingEngine attribute)

A

adjacency_with_orders() (docktopus.validator.RFAAValidator method)

Analyser (class in docktopus.analyser) autobox_ligand (docktopus.gnina_engine.GninaDockingEngine attribute)

B

bootstrap_mae_error() (docktopus.analyser.Analyser method)

bootstrap_ratio_error() (docktopus.analyser.Analyser method) box_center (docktopus.gdock_engine.GDockHEMEDockingEngine attribute)

C

calculate_molecular_weights() (docktopus.analyser.Analyser method) calculate_num_rotatable_bonds() (docktopus.analyser.Analyser method) convert_format() (docktopus.preprocessor.DataPreprocessor method)

convert_pdb_to_sdf() (docktopus.validator.RFAAValidator method) count_bond_diffs() (docktopus.validator.RFAAValidator method) cpu (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

D

DataPreprocessor (class in docktopus.preprocessor) dock() (docktopus.docking.Docking method) (docktopus.gdock_engine.GDockHEMEDockingEngine method) (docktopus.gnina_engine.GninaDockingEngine method) (docktopus.rfaa_engine.RFAADockingEngine method) (docktopus.vina_engine.VinaDockingEngine method) dock_many() (docktopus.docking.Docking method) dock_single() (docktopus.docking.Docking method) Docking (class in docktopus.docking) docktopus.analyser module docktopus.docking module

docktopus.gdock_engine module docktopus.gnina_engine module docktopus.preprocessor module docktopus.rfaa_engine module docktopus.validator module docktopus.vina_engine module

E

engine (docktopus.docking.Docking attribute) exhaustiveness (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

extract_ligand() (docktopus.validator.RFAAValidator method)

F

fasta_file (docktopus.rfaa_engine.RFAADockingEngine attribute)

fix_bond_orders() (docktopus.validator.RFAAValidator method)

G

gd2_scratch_dir (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) gdock_dir (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) gdock_script (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) GDockHEMEDockingEngine (class in docktopus.gdock_engine) generate_config_files() (docktopus.rfaa_engine.RFAADockingEngine method)

generate_conformers() (docktopus.preprocessor.DataPreprocessor method) get_Fedistance() (docktopus.analyser.Analyser method) get_sample_Fedist() (docktopus.analyser.Analyser method) get_similarity_scores() (docktopus.analyser.Analyser method) gnina_path (docktopus.gnina_engine.GninaDockingEngine attribute) GninaDockingEngine (class in docktopus.gnina_engine)

H

hem_file (docktopus.rfaa_engine.RFAADockingEngine attribute)

L

ligand_format (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute) logger (docktopus.docking.Docking attribute) (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.rfaa_engine.RFAADockingEngine attribute) (docktopus.validator.RFAAValidator attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

M

model_runner_class (docktopus.rfaa_engine.RFAADockingEngine attribute) module docktopus.analyser docktopus.docking docktopus.gdock_engine docktopus.gnina_engine docktopus.preprocessor docktopus.rfaa_engine docktopus.validator docktopus.vina_engine

N

num_modes (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

P

precheck() (docktopus.gdock_engine.GDockHEMEDockingEngine method) (docktopus.gnina_engine.GninaDockingEngine method) (docktopus.rfaa_engine.RFAADockingEngine method) (docktopus.vina_engine.VinaDockingEngine method) prepare_ligand() (docktopus.preprocessor.DataPreprocessor method) prepare_ligand_vina() (docktopus.preprocessor.DataPreprocessor method)

prepare_ligands() (docktopus.docking.Docking method) prepare_protein() (docktopus.preprocessor.DataPreprocessor method) prepare_protein_vina() (docktopus.preprocessor.DataPreprocessor method) prepare_receptor() (docktopus.docking.Docking method) preprocessor (docktopus.docking.Docking attribute) protonate() (docktopus.preprocessor.DataPreprocessor method)

R

receptor_format (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

results_dir (docktopus.rfaa_engine.RFAADockingEngine attribute) RFAADockingEngine (class in docktopus.rfaa_engine) RFAAValidator (class in docktopus.validator)

S

seed (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)

set_target() (docktopus.rfaa_engine.RFAADockingEngine method) standardize_smiles() (docktopus.validator.RFAAValidator method)

T

target_dir (docktopus.rfaa_engine.RFAADockingEngine attribute)

template_pdb (docktopus.rfaa_engine.RFAADockingEngine attribute) tmp_dir (docktopus.rfaa_engine.RFAADockingEngine attribute)

V

validate_ligand() (docktopus.validator.RFAAValidator method) validation_enabled (docktopus.rfaa_engine.RFAADockingEngine attribute)

vina (docktopus.vina_engine.VinaDockingEngine attribute) VinaDockingEngine (class in docktopus.vina_engine)

W

work_dir (docktopus.docking.Docking attribute) (docktopus.gdock_engine.GDockHEMEDockingEngine attribute) (docktopus.gnina_engine.GninaDockingEngine attribute) (docktopus.preprocessor.DataPreprocessor attribute) (docktopus.rfaa_engine.RFAADockingEngine attribute) (docktopus.vina_engine.VinaDockingEngine attribute)