Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W _ _parse_block() (in module prodock.io.parser) _parse_mol2_text() (in module prodock.io.parser) _parse_pdb_text() (in module prodock.io.parser) _parse_sdf_text() (in module prodock.io.parser) _parse_xyz_text() (in module prodock.io.parser) _sanitize_text() (in module prodock.io.parser) _supplier_first_mol() (in module prodock.io.parser) _try_blocks() (in module prodock.io.parser) A add_interaction() (PoseDatabase method) affinity (PoseRecord attribute) (ScoreRecord attribute) angle (InteractionRecord attribute) apply_config() (SingleDock method) apply_engine_options() (SingleDock method) artifacts (SingleResult attribute) as_tuple() (GridBox method) autobox_pad (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (ReceptorSpec attribute) (SingleConfig attribute) autobox_ref (DockRow attribute) (DockTask attribute) (ReceptorSpec attribute) (SingleConfig attribute) autobox_ref_key (BatchConfig attribute) available() (in module prodock.dock.registry) available_interactions() (InteractionProfiler method) B background (JournalStyle attribute) BatchConfig (class in prodock.dock.config) BatchDock (class in prodock.dock.batch) best() (PoseCrawler method) best_mols() (PoseCrawler method) Box (class in prodock.dock.config) box (DockRow attribute) (ReceptorSpec attribute) (SingleConfig attribute) build_campaign() (ProDockPipeline method) build_interaction_where_clause() (in module prodock.database.query) build_pose_visualization_table() (in module prodock.postprocess.interaction.visualize) build_pose_where_clause() (in module prodock.database.query) C called (DockResult attribute) (VinaEngine property) campaign (ProDockResult attribute) campaign_json (ProDockResult attribute) CampaignConfig (in module prodock.dock.config) center (Box attribute) (DockRow attribute) (DockTask attribute) (GridBox property) (PreparedReceptorSpec attribute) chain_id (InteractionRecord attribute) clean_solvents_and_cofactors() (PDBEngine method) clear_records() (LigandPrep method) CLIError close() (PoseDatabase method) (PoseQuery method) cocrystal_ligand_path (PDBQuery property) compact_interactions (ProDockResult attribute) compute_with_algo() (in module prodock.preprocess.gridbox.gridbox) configured (LoggerManager property), [1], [2] connection (PoseDatabase property) (PoseQuery property) conversion_backend (ReceptorPrep property) conversion_fallback (ReceptorPrep property) convert() (PoseCrawler method) convert_pose_tree() (in module prodock.postprocess.pose.convert) convert_with_meeko() (in module prodock.structure.conversion) convert_with_mekoo() (in module prodock.structure.conversion) convert_with_obabel() (in module prodock.structure.conversion) count (InteractionProfiler attribute) count_poses() (PoseDatabase method) (PoseQuery method) cpu (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) (SoftwareSpec attribute) crawl() (PoseCrawler method) crawl_mols() (PoseCrawler method) crawl_pose_mols() (in module prodock.postprocess.pose.core) crawl_poses() (in module prodock.postprocess.pose.core) (ProDockPipeline method) crawl_scores() (in module prodock.postprocess.extract.core) create_schema() (PoseDatabase method) create_tasks() (BatchDock method) create_tasks_from_receptors() (BatchDock method) created_at (InteractionRecord attribute) (PoseRecord attribute) D db_path (ProDockResult attribute) default_retries (BatchConfig attribute) delete_interactions() (PoseDatabase method) delete_interactions_for_pose() (PoseDatabase method) delete_poses() (PoseDatabase method) distance (InteractionRecord attribute) docking_results (ProDockResult attribute) DockResult (class in prodock.dock.batch) DockRow (class in prodock.dock.config) DockTask (class in prodock.dock.batch) drop_empty (InteractionProfiler attribute) E elapsed (DockResult attribute) enable_autobox() (SingleDock method) (VinaEngine method) enable_console_logging() (ReceptorPrep method) engine (BatchConfig attribute) (InteractionRecord attribute) (PoseRecord attribute) (ScoreRecord attribute) (SingleConfig attribute) engine_name (DockResult attribute) (DockTask attribute) engine_options (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) (SoftwareSpec attribute) engines() (PoseQuery method) ensure_pdbqt() (in module prodock.structure.conversion) error (DockResult attribute) exe_name (GninaEngine attribute) (QVinaEngine attribute) (QVinaWEngine attribute) (SminaEngine attribute) executable (DockTask attribute) (SingleConfig attribute) (SoftwareSpec attribute) exhaustiveness (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) (SoftwareSpec attribute) expected_output_for() (ReceptorPrep method) expected_output_path (ReceptorPrep property) extract_engine_folders() (Extractor method) (in module prodock.postprocess.extract.core) extract_interactions() (in module prodock.postprocess.interaction.core) (ProDockPipeline method) extract_ligand() (PDBEngine method) extract_log_file() (Extractor method) (in module prodock.postprocess.extract.core) extract_logs_dir() (Extractor method) (in module prodock.postprocess.extract.core) extract_pose_table_interactions() (in module prodock.postprocess.interaction.core) extract_scores() (Extractor method) (in module prodock.postprocess.extract.core) Extractor (class in prodock.postprocess.extract.core) F factory() (in module prodock.dock.registry) failed (LigandPrep property) fetch() (PDBEngine method) filter_chains() (PDBEngine method) filtered_protein_path (PDBQuery property) final_artifact (ReceptorPrep property) fingerprint() (PoseQuery method) flag_map (QVinaEngine attribute) (QVinaWEngine attribute) format() (JSONFormatter method), [1], [2] (SimpleColorFormatter method), [1], [2] from_centroid_fixed() (GridBox method) from_config() (BatchDock class method) (SingleDock class method) from_dataframe() (LigandPrep method) (PoseDatabase class method) from_dict() (BatchConfig class method) (DockRow class method) (LigandSpec class method) (ReceptorSpec class method) (SingleConfig class method) (SoftwareSpec class method) from_file() (BatchConfig class method) (SingleConfig class method) from_ligand_pad() (GridBox method) from_ligand_pad_adv() (GridBox method) from_ligand_pca_aabb() (GridBox method) from_ligand_percentile() (GridBox method) from_ligand_scale() (GridBox method) from_list_of_dicts() (LigandPrep method) from_mapping() (Box class method) from_smiles_list() (LigandPrep method) from_union() (GridBox method) G get_interaction_details() (PoseDatabase method) (PoseQuery method) get_interaction_summary() (PoseDatabase method) (PoseQuery method) get_logger() (in module prodock.io.logging) (in module prodock.io.logging.compat_logging) (in module prodock.io.logging.manager) (LoggerManager method), [1], [2] get_pose() (PoseDatabase method) (PoseQuery method) GninaEngine (class in prodock.dock.gnina) grid_alpha (JournalStyle attribute) grid_color (JournalStyle attribute) GridBox (class in prodock.preprocess.gridbox.gridbox) grow_to_min_cube() (GridBox method) H heatmap_cmap (JournalStyle attribute) help() (PDBQTSanitizer method) histogram_alpha (JournalStyle attribute) I id (DockRow attribute) (LigandSpec attribute) (ReceptorSpec attribute) insert_dataframe() (PoseDatabase method) insert_interactions() (PoseDatabase method) insert_many() (PoseDatabase method) interaction_details (PoseRecord attribute) interaction_details() (PoseQuery method) interaction_df (ProDockResult attribute) interaction_fingerprint() (PoseDatabase method) (PoseQuery method) interaction_id (InteractionRecord attribute) interaction_result (ProDockResult attribute) interaction_summary (PoseRecord attribute) interaction_summary() (PoseQuery method) interaction_type (InteractionRecord attribute) InteractionProfiler (class in prodock.postprocess.interaction.core) InteractionRecord (class in prodock.database.records) interactions (InteractionProfiler attribute) interactions() (PoseQuery method) is_valid_smiles() (in module prodock.io.rdkit) J job_id (DockResult attribute) (DockTask attribute) JournalStyle (class in prodock.postprocess.interaction.visualize) JSONFormatter (class in prodock.io.logging) (class in prodock.io.logging.compat_logging) (class in prodock.io.logging.formatters) L label_size (JournalStyle attribute) last_simulation_report (ReceptorPrep property) level_name (LoggerManager property), [1], [2] ligand (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) ligand_atom_indices (InteractionRecord attribute) ligand_chain (InteractionProfiler attribute) ligand_dir (ProDockResult attribute) ligand_id (DockResult attribute) (DockTask attribute) (InteractionRecord attribute) (PoseRecord attribute) (ScoreRecord attribute) ligand_parent_atom_indices (InteractionRecord attribute) ligand_residue (InteractionRecord attribute) ligand_resname (InteractionProfiler attribute) ligand_resnumber (InteractionProfiler attribute) ligand_use_segid (InteractionProfiler attribute) LigandPrep (class in prodock.preprocess.ligand.prep) ligands (SoftwareSpec attribute) ligands() (PoseQuery method) LigandSpec (class in prodock.dock.config) LigandTask (in module prodock.dock.config) line_width (JournalStyle attribute) list_engines() (Extractor method) (in module prodock.postprocess.extract.core) (PoseDatabase method) (PoseQuery method) list_ligands() (PoseDatabase method) (PoseQuery method) list_receptors() (PoseDatabase method) (PoseQuery method) load_config() (SingleDock method) (VinaEngine method) load_config_dict() (VinaEngine method) load_ligand() (GridBox method) load_sdf_for_interactions() (in module prodock.structure.conversion) log (DockRow attribute) (LigandSpec attribute) (SingleConfig attribute) log_dir (BatchConfig attribute) (ReceptorSpec attribute) (SoftwareSpec attribute) log_path (DockResult attribute) (DockTask attribute) log_step() (in module prodock.io.logging) (in module prodock.io.logging.compat_logging) (in module prodock.io.logging.decorators) LoggerManager (class in prodock.io.logging) (class in prodock.io.logging.compat_logging) (class in prodock.io.logging.manager) M main() (in module prodock.cli) make_affinity_histogram() (in module prodock.postprocess.interaction.visualize) make_affinity_vs_interaction_count_scatter() (in module prodock.postprocess.interaction.visualize) make_best_pose_bar() (in module prodock.postprocess.interaction.visualize) make_interaction_count_histogram() (in module prodock.postprocess.interaction.visualize) make_interaction_type_bar() (in module prodock.postprocess.interaction.visualize) make_residue_contact_bar() (in module prodock.postprocess.interaction.visualize) make_summary_panel_2x3() (in module prodock.postprocess.interaction.visualize) marker_size (JournalStyle attribute) MatrixDock (in module prodock.dock.batch) mekoo_cmd (ReceptorPrep property) merged_df (ProDockResult attribute) metadata (DockResult attribute) (InteractionRecord attribute) (LigandSpec attribute) (ReceptorSpec attribute) (ScoreRecord attribute) (VinaEngine property) minimized_stage (ReceptorPrep property) module prodock.cli prodock.core prodock.database.pose_db prodock.database.pose_query prodock.database.query prodock.database.records prodock.dock.batch prodock.dock.config prodock.dock.gnina prodock.dock.qvina prodock.dock.qvina_w prodock.dock.registry prodock.dock.single prodock.dock.smina prodock.dock.vina prodock.io.logging prodock.io.logging.compat_logging prodock.io.logging.decorators prodock.io.logging.formatters prodock.io.logging.manager prodock.io.logging.timing prodock.io.parser prodock.io.rdkit prodock.io.utils prodock.postprocess.extract.core prodock.postprocess.extract.reader prodock.postprocess.interaction.core prodock.postprocess.interaction.similarity prodock.postprocess.interaction.visualize prodock.postprocess.pose.convert prodock.postprocess.pose.core prodock.preprocess.gridbox.gridbox prodock.preprocess.ligand.prep prodock.preprocess.receptor.prep prodock.structure.conversion prodock.structure.pdb_engine prodock.structure.pdb_query prodock.structure.pdbqt_sanitizer mol (PoseRecord attribute) mol2pdb() (in module prodock.io.rdkit) mol2sdf() (in module prodock.io.rdkit) mol2smiles() (in module prodock.io.rdkit) mol_from_smiles_write_all_formats() (in module prodock.io.rdkit) mols (LigandPrep property) N n_jobs (BatchConfig attribute) (InteractionProfiler attribute) n_poses (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) (SoftwareSpec attribute) name (JournalStyle attribute) (SoftwareSpec attribute) O occurrence_index (InteractionRecord attribute) ok (LigandPrep property) out (DockRow attribute) (LigandSpec attribute) (SingleConfig attribute) out_dir (BatchConfig attribute) (ReceptorSpec attribute) (SoftwareSpec attribute) out_path (DockResult attribute) (DockTask attribute) output_paths (LigandPrep property) P palette (JournalStyle attribute) panel_facecolor (JournalStyle attribute) panel_label_size (JournalStyle attribute) parameters (InteractionProfiler attribute) parse_log_text() (in module prodock.postprocess.extract.reader) pdb2mol() (in module prodock.io.rdkit) pdb2smiles() (in module prodock.io.rdkit) pdb_path (PDBQuery property) pdb_to_pdbqt() (in module prodock.structure.conversion) pdb_to_sdf() (in module prodock.structure.conversion) PDBEngine (class in prodock.structure.pdb_engine) pdbqt_to_pdb() (in module prodock.structure.conversion) pdbqt_to_rdkit_mols() (in module prodock.postprocess.pose.convert) pdbqt_to_sdf() (in module prodock.structure.conversion) PDBQTSanitizer (class in prodock.structure.pdbqt_sanitizer) PDBQuery (class in prodock.structure.pdb_query) plot_similarity_heatmap() (in module prodock.postprocess.interaction.visualize) pose() (PoseQuery method) pose_db_id (InteractionRecord attribute) (PoseRecord attribute) (ScoreRecord attribute) pose_df (ProDockResult attribute) pose_id (InteractionRecord attribute) (PoseRecord attribute) (ScoreRecord attribute) pose_key (InteractionRecord property) (PoseRecord property) (ScoreRecord property) pose_metadata (PoseRecord attribute) pose_rank (InteractionRecord attribute) (PoseRecord attribute) (ScoreRecord attribute) PoseCrawler (class in prodock.postprocess.pose.core) PoseDatabase (class in prodock.database.pose_db) PoseQuery (class in prodock.database.pose_query) PoseRecord (class in prodock.database.records) poses() (PoseQuery method) prep() (ReceptorPrep method) prepare_ligands() (ProDockPipeline method) prepare_receptors() (ProDockPipeline method) PreparedReceptorSpec (class in prodock.core) process() (StructuredAdapter method), [1] process_all() (LigandPrep method) process_batch() (PDBQuery class method) prodock() (in module prodock.core) prodock.cli module prodock.core module prodock.database.pose_db module prodock.database.pose_query module prodock.database.query module prodock.database.records module prodock.dock.batch module prodock.dock.config module prodock.dock.gnina module prodock.dock.qvina module prodock.dock.qvina_w module prodock.dock.registry module prodock.dock.single module prodock.dock.smina module prodock.dock.vina module prodock.io.logging module prodock.io.logging.compat_logging module prodock.io.logging.decorators module prodock.io.logging.formatters module prodock.io.logging.manager module prodock.io.logging.timing module prodock.io.parser module prodock.io.rdkit module prodock.io.utils module prodock.postprocess.extract.core module prodock.postprocess.extract.reader module prodock.postprocess.interaction.core module prodock.postprocess.interaction.similarity module prodock.postprocess.interaction.visualize module prodock.postprocess.pose.convert module prodock.postprocess.pose.core module prodock.preprocess.gridbox.gridbox module prodock.preprocess.ligand.prep module prodock.preprocess.receptor.prep module prodock.structure.conversion module prodock.structure.pdb_engine module prodock.structure.pdb_query module prodock.structure.pdbqt_sanitizer module ProDockPipeline (class in prodock.core) ProDockResult (class in prodock.core) progress (BatchConfig attribute) (InteractionProfiler attribute) project_dir (ProDockResult attribute) protein_atom_indices (InteractionRecord attribute) protein_parent_atom_indices (InteractionRecord attribute) Q query_interactions() (PoseDatabase method) (PoseQuery method) query_poses() (PoseDatabase method) (PoseQuery method) query_scores() (PoseDatabase method) (PoseQuery method) QVinaEngine (class in prodock.dock.qvina) QVinaWEngine (class in prodock.dock.qvina_w) R read() (PDBQTSanitizer method) receptor (DockRow attribute) (DockTask attribute) (ReceptorSpec attribute) (SingleConfig attribute) receptor_guess_bonds (InteractionProfiler attribute) receptor_id (DockResult attribute) (DockTask attribute) (InteractionRecord attribute) (PoseRecord attribute) (PreparedReceptorSpec attribute) (ScoreRecord attribute) receptor_pdb_by_id (ProDockResult attribute) receptor_pdbqt (PreparedReceptorSpec attribute) receptor_selection (InteractionProfiler attribute) receptor_use_segid (InteractionProfiler attribute) receptor_vdwradii (InteractionProfiler attribute) ReceptorPrep (class in prodock.preprocess.receptor.prep) receptors (BatchConfig attribute) (ProDockResult attribute) receptors() (PoseQuery method) ReceptorSpec (class in prodock.dock.config) records (LigandPrep property) records() (PoseCrawler method) reference_ligand_path (PDBQuery property) register() (in module prodock.dock.registry) register_many() (in module prodock.dock.registry) residue_id (InteractionRecord attribute) residue_name (InteractionRecord attribute) residue_number (InteractionRecord attribute) resolve_order_by() (in module prodock.database.query) resolved_box() (DockRow method) retries (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) rows (BatchConfig attribute) run() (BatchDock method) (InteractionProfiler method) (ProDockPipeline method) (SingleDock method) (VinaEngine method) run_all() (PDBEngine method) (PDBQuery method) run_from_config() (BatchDock class method) (SingleDock class method) run_pose_table() (InteractionProfiler method) run_prodock() (in module prodock.core) run_receptors() (BatchDock method) run_tasks() (BatchDock method) run_with_config() (SingleDock method) S sanitize() (PDBQTSanitizer method) sanitize_file() (PDBQTSanitizer class method) sanitize_inplace() (PDBQTSanitizer method) save_affinity_histogram() (in module prodock.postprocess.interaction.visualize) save_affinity_vs_interaction_count_scatter() (in module prodock.postprocess.interaction.visualize) save_best_pose_bar() (in module prodock.postprocess.interaction.visualize) save_campaign() (ProDockPipeline method) save_database() (ProDockPipeline method) save_filtered_protein() (PDBEngine method) save_interaction_count_histogram() (in module prodock.postprocess.interaction.visualize) save_interaction_type_bar() (in module prodock.postprocess.interaction.visualize) save_manifest() (LigandPrep method) save_pose_sdf() (in module prodock.postprocess.pose.convert) save_report() (ReceptorPrep method) save_residue_contact_bar() (in module prodock.postprocess.interaction.visualize) save_similarity_heatmap() (in module prodock.postprocess.interaction.visualize) save_summary_panel_2x3() (in module prodock.postprocess.interaction.visualize) scatter_alpha (JournalStyle attribute) score_data (PoseRecord attribute) (ScoreRecord attribute) score_metadata (PoseRecord attribute) ScoreRecord (class in prodock.database.records) scores() (PoseQuery method) sdf2mol() (in module prodock.io.rdkit) sdf2mols() (in module prodock.io.rdkit) sdf_sanitize (InteractionProfiler attribute) sdf_strings (LigandPrep property) sdf_to_pdb() (in module prodock.structure.conversion) sdf_to_pdbqt() (in module prodock.structure.conversion) sdftosmiles() (in module prodock.io.rdkit) seed (BatchConfig attribute) (DockRow attribute) (DockTask attribute) (LigandSpec attribute) (SingleConfig attribute) (SoftwareSpec attribute) select_best_pose_mols() (in module prodock.postprocess.pose.core) select_best_poses() (in module prodock.postprocess.pose.core) set_backend() (LigandPrep method) set_box() (SingleDock method) (VinaEngine method) set_conformer_jobs() (LigandPrep method) set_conformer_seed() (LigandPrep method) set_converter_backend() (LigandPrep method) set_cpu() (SingleDock method) (VinaEngine method) set_embed_method() (LigandPrep method) set_executable() (SingleDock method) set_exhaustiveness() (SingleDock method) (VinaEngine method) set_keep_intermediate() (LigandPrep method) set_ligand() (SingleDock method) (VinaEngine method) set_log() (SingleDock method) (VinaEngine method) set_num_modes() (SingleDock method) (VinaEngine method) set_opt_max_iters() (LigandPrep method) set_opt_method() (LigandPrep method) set_options() (LigandPrep method) set_out() (SingleDock method) (VinaEngine method) set_output_dir() (LigandPrep method) set_output_format() (LigandPrep method) set_receptor() (SingleDock method) (VinaEngine method) set_seed() (SingleDock method) (VinaEngine method) settings_snapshot() (InteractionProfiler method) setup() (LoggerManager method), [1], [2] setup_logging() (in module prodock.io.logging) (in module prodock.io.logging.compat_logging) (in module prodock.io.logging.manager) shutdown_pymol() (in module prodock.io.utils) SimpleColorFormatter (class in prodock.io.logging) (class in prodock.io.logging.compat_logging) (class in prodock.io.logging.formatters) SingleConfig (class in prodock.dock.config) SingleDock (class in prodock.dock.single) SingleResult (class in prodock.dock.single) size (Box attribute) (DockRow attribute) (DockTask attribute) (GridBox property) (PreparedReceptorSpec attribute) smiles2mol() (in module prodock.io.rdkit) smiles2pdb() (in module prodock.io.rdkit) smiles2sdf() (in module prodock.io.rdkit) SminaEngine (class in prodock.dock.smina) snap() (GridBox method) softwares (ReceptorSpec attribute) SoftwareSpec (class in prodock.dock.config) spine_color (JournalStyle attribute) StructuredAdapter (class in prodock.io.logging) (class in prodock.io.logging.compat_logging) success (DockResult attribute) summarize() (PoseDatabase method) (PoseQuery method) summary (LigandPrep property) summary() (PoseQuery method) summary_df (ProDockResult attribute) supports_autobox (GninaEngine attribute) (QVinaEngine attribute) (QVinaWEngine attribute) (SminaEngine attribute) suppress_mdanalysis_info_logs (InteractionProfiler attribute) suppress_mdanalysis_warnings (InteractionProfiler attribute) T tanimoto_similarity_matrix() (in module prodock.postprocess.interaction.similarity) text_color (JournalStyle attribute) tick_size (JournalStyle attribute) timeout (BatchConfig attribute) (DockTask attribute) Timer (class in prodock.io.logging) (class in prodock.io.logging.compat_logging) (class in prodock.io.logging.timing) title_size (JournalStyle attribute) tmp_root (BatchConfig attribute) to_dict() (BatchConfig method) (Box method) (DockRow method) (LigandSpec method) (ReceptorPrep method) (ReceptorSpec method) (SingleConfig method) (SoftwareSpec method) to_vina_lines() (GridBox method) toggle_meeko() (ReceptorPrep method) traceback (DockResult attribute) U upsert_interaction_payload() (PoseDatabase method) upsert_pose() (PoseDatabase method) use_meeko (ReceptorPrep property) used_obabel (ReceptorPrep property) V vacuum() (PoseDatabase method) validate() (PDBEngine method) (PDBQTSanitizer method) (PDBQuery method) validate_receptor (ReceptorSpec attribute) (SingleConfig attribute) vicinity_cutoff (InteractionProfiler attribute) vina_dict (GridBox property) VinaEngine (class in prodock.dock.vina) W worker_process_job_using_singledock() (in module prodock.dock.batch) write() (PDBQTSanitizer method)
