Index A | B | C | D | E | F | G | L | M | P | R | S | U A aggregate_results_per_id() (in module mockdock.analysis) ALLOWED_RECEPTOR_EXTENSIONS (mockdock.docking.AutoDockGPUOracle attribute) assign_bond_orders_from_template() (in module mockdock.utils) AutoDockGPUOracle (class in mockdock.docking) AutoDockVinaOracle (class in mockdock.docking) B BenchmarkLoader (class in mockdock.loader) budget_remaining (mockdock.oracle.MDOracle property) C calculate_rmsd() (mockdock.analysis.DockingAnalyzer method) check_2d_match() (in module mockdock.utils) compute_metrics() (mockdock.evaluator.MDEvaluator method) config (mockdock.oracle.MDOracle property) D DEFAULT_ADGPU_EXECUTABLE (mockdock.docking.AutoDockGPUOracle attribute) detect_gpus() (in module mockdock.utils) dock_batch() (mockdock.docking.AutoDockGPUOracle method) (mockdock.docking.AutoDockVinaOracle method) (mockdock.docking.DockingOracle method) DockingAnalyzer (class in mockdock.analysis) DockingOracle (class in mockdock.docking) E effective_cpu_count() (in module mockdock.utils) evaluate() (mockdock.filters.MDFilters method) export_top_poses() (mockdock.oracle.MDOracle method) extract_protein_and_ligand() (in module mockdock.receptor) F fetch_ligand_expo_sdf() (in module mockdock.utils) fetch_poses() (mockdock.oracle.MDOracle method) filter_poses_by_rmsd() (mockdock.analysis.DockingAnalyzer method) fragment_smiles (mockdock.oracle.MDOracle property) fragment_smiles_with_dummies (mockdock.oracle.MDOracle property) G generation_round (mockdock.oracle.MDOracle property) get_full_data_and_threshold() (mockdock.loader.BenchmarkLoader method) get_initial_compounds() (mockdock.loader.BenchmarkLoader method) (mockdock.oracle.MDOracle method) get_receptor_and_ligand_pdb() (mockdock.receptor.ReceptorPreparer method) get_robust_match() (in module mockdock.utils) get_validation_compounds() (mockdock.loader.BenchmarkLoader method) (mockdock.oracle.MDOracle method) GridPrepError L libinvent_scaffold_with_dummies (mockdock.oracle.MDOracle property) ligand_resname (mockdock.oracle.MDOracle property) LigandNotFoundError LigandPreparer (class in mockdock.ligand_prep) list_benchmarks() (mockdock.loader.BenchmarkLoader class method) (mockdock.oracle.MDOracle class method) M main() (in module mockdock.evaluator) MDEvaluator (class in mockdock.evaluator) MDFilters (class in mockdock.filters) MDOracle (class in mockdock.oracle) mockdock.analysis module mockdock.docking module mockdock.evaluator module mockdock.filters module mockdock.ligand_prep module mockdock.loader module mockdock.oracle module mockdock.receptor module mockdock.utils module module mockdock.analysis mockdock.docking mockdock.evaluator mockdock.filters mockdock.ligand_prep mockdock.loader mockdock.oracle mockdock.receptor mockdock.utils P passes() (mockdock.filters.MDFilters method) pdb_id (mockdock.oracle.MDOracle property) PDBDownloadError plot_activity_distribution() (in module mockdock.utils) plot_docking_results() (in module mockdock.utils) prepare_batch() (mockdock.ligand_prep.LigandPreparer method) prepare_receptor_and_grid() (mockdock.receptor.ReceptorPreparer method) R ReceptorPreparer (class in mockdock.receptor) resolve_backend() (in module mockdock.utils) rmsd_threshold (mockdock.oracle.MDOracle property) run_autogrid() (mockdock.receptor.ReceptorPreparer method) run_dir (mockdock.oracle.MDOracle property) run_mk_prepare_receptor() (mockdock.receptor.ReceptorPreparer method) run_reduce2() (mockdock.receptor.ReceptorPreparer method) S save_best_poses_sdf() (mockdock.analysis.DockingAnalyzer method) save_metrics() (mockdock.oracle.MDOracle method) score() (mockdock.oracle.MDOracle method) set_backend_config() (mockdock.oracle.MDOracle method) standardize_smiles() (in module mockdock.utils) status (mockdock.oracle.MDOracle property) U unroll_multiconf_rdkit_mols() (in module mockdock.analysis)