Index _ | A | C | D | E | F | G | H | I | K | L | M | O | P | R | S | T | U | W _ __init__() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersAMS method) (UniqueConformersCrest method) (UniqueConformersRMSD method) (UniqueConformersTFD method) _get_molecule_mask() (UniqueConformersAMS method) _is_prepared() (UniqueConformersCrest method) _rdkit_call_from_thread() (CRESTGenerator static method) (MDExpander static method) (MetadynamicsGenerator static method) (RDKitGenerator static method) _write_geometries() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) A add_conformer() (UniqueConformersAMS method) (UniqueConformersCrest method) (UniqueConformersRMSD method) (UniqueConformersTFD method) add_conformers() (UniqueConformersCrest method) are_geometries_local_minima() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) C clear() (UniqueConformersCrest method) ConformerOptimizer (class in scm.conformers.pestools.optimizer) convert_key_to_camelcase() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) convert_key_to_underscore_case() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) convert_keys_to_camelcase() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) convert_keys_to_underscore_case() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) copy() (UniqueConformersCrest method) create_json_entry() (ConformerOptimizer static method) (CRESTGenerator static method) (GCExpander static method) (MDExpander static method) (MetadynamicsGenerator static method) (RDKitGenerator static method) (UniqueConformersCrest static method) create_tree() (UniqueConformersAMS method) CRESTGenerator (class in scm.conformers.generators.crest_generators.crest_generator) D determine_maxgeoms() (GCExpander method) E estimate_gctime() (GCExpander method) estimate_runtime() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) F filter() (UniqueConformersCrest method) find_clusters() (UniqueConformersCrest method) find_nth_conformer() (UniqueConformersCrest method) fit() (UniqueConformersCrest method) from_rdkitmol() (UniqueConformersCrest class method) fromfile() (UniqueConformersCrest class method) G GCExpander (class in scm.conformers.generators.crest_generators.gc_generator) generate() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) geometry_writer() (ConformerOptimizer method) get_all_energies() (UniqueConformersCrest method) get_all_geometries() (UniqueConformersCrest method) get_all_rmsds() (UniqueConformersCrest method) get_conformers() (UniqueConformersCrest method) get_cost() (UniqueConformersAMS method) get_cost_for_swap() (UniqueConformersAMS method) get_cost_old() (UniqueConformersAMS method) get_dendrogram() (UniqueConformersCrest method) get_diffs_for_candidate() (UniqueConformersAMS method) (UniqueConformersCrest method) (UniqueConformersRMSD method) (UniqueConformersTFD method) get_energies() (UniqueConformersCrest method) get_errors() (UniqueConformersCrest method) get_group_indices() (UniqueConformersAMS method) get_json_settings() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) get_molecule() (UniqueConformersCrest method) get_plot_dendrogram() (UniqueConformersCrest method) get_rdkitmol() (UniqueConformersCrest method) get_rmsd_time() (GCExpander method) get_rmsds_from_frame() (UniqueConformersCrest method) get_torsion_atoms() (UniqueConformersTFD method) get_torsion_values() (UniqueConformersTFD method) H handle_input() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) I indices_to_names() (UniqueConformersCrest method) K keep_ams_running() (ConformerOptimizer method) L last_timings (ConformerOptimizer property) M MDExpander (class in scm.conformers.generators.crest_generators.md_expander) MetadynamicsGenerator (class in scm.conformers.generators.crest_generators.metadynamics_generator) molecule (UniqueConformersCrest property) O optimize() (UniqueConformersCrest method) optimize_and_filter() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) optimize_conformers() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) optimize_geometries() (ConformerOptimizer method) optimize_molecules() (ConformerOptimizer method) P pass_settings() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) prepare_state() (UniqueConformersAMS method) (UniqueConformersCrest method) (UniqueConformersRMSD method) (UniqueConformersTFD method) R RDKitGenerator (class in scm.conformers.generators.simple_generators.rdkit_generator) rdmol (UniqueConformersTFD property) read() (UniqueConformersCrest method) read_default_settings_from_json_file() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) read_settings() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) remove_conformer() (UniqueConformersCrest method) remove_high_energy() (UniqueConformersCrest method) remove_non_minima() (UniqueConformersCrest method) reorder() (UniqueConformersCrest method) rmsds (UniqueConformersCrest property) S score() (UniqueConformersCrest method) set_atom_types() (ConformerOptimizer method) set_blocknames() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) set_cleaning_preference() (ConformerOptimizer method) set_convergence_quality() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_energies() (UniqueConformersCrest method) set_generator() (UniqueConformersCrest method) set_max_energy() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_maxgeoms() (GCExpander method) set_number_initial_conformers() (RDKitGenerator method) set_number_of_identical_mdruns() (MDExpander method) set_number_of_starting_geometries() (MDExpander method) set_optimizer() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_partial_permutator_checks() (UniqueConformersAMS method) set_preoptimizer() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_printing_level() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_rngseed() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) set_shake() (CRESTGenerator method) (MDExpander method) (MetadynamicsGenerator method) set_workdir() (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) subset_indices (UniqueConformersCrest property) T time_to_timestring() (CRESTGenerator static method) (GCExpander static method) (MDExpander static method) (MetadynamicsGenerator static method) (RDKitGenerator static method) to_json() (ConformerOptimizer method) (CRESTGenerator method) (GCExpander method) (MDExpander method) (MetadynamicsGenerator method) (RDKitGenerator method) (UniqueConformersCrest method) U UniqueConformersAMS (class in scm.conformers.conformers.conformers_ams) UniqueConformersCrest (class in scm.conformers.conformers.conformers_crest) UniqueConformersRMSD (class in scm.conformers.conformers.conformers_rmsd) UniqueConformersTFD (class in scm.conformers.conformers.conformers_tfd) W write() (UniqueConformersCrest method) write_geometries() (RDKitGenerator method)
