Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | W A add_surrounding_edges() (lomap.graphgen.GraphGen method) all_atom_match_list() (lomap.mcs.MCS method) atomic_number_rule() (lomap.mcs.MCS method) atomic_number_score() (in module lomap.gufe_bindings.scorers) B build_graph() (lomap.dbmol.DBMolecules method) build_matrices() (lomap.dbmol.DBMolecules method) C check_constraints() (lomap.graphgen.GraphGen method) check_cycle_covering() (lomap.graphgen.GraphGen static method) check_distance_to_active() (lomap.graphgen.GraphGen method) check_max_distance() (lomap.graphgen.GraphGen static method) compute_mtx() (lomap.dbmol.DBMolecules method) connect_graph_components_brute_force() (lomap.graphgen.GraphGen method) connect_graph_components_brute_force_2() (lomap.graphgen.GraphGen method) connect_subgraphs() (lomap.graphgen.GraphGen method) copy_with_replacements() (lomap.LomapAtomMapper method) count_distance_to_active_failures() (lomap.graphgen.GraphGen static method) D DBMolecules (class in lomap.dbmol) default_lomap_score() (in module lomap) defaults() (lomap.LomapAtomMapper class method) draw() (lomap.graphgen.GraphGen method) E ecr_score() (in module lomap.gufe_bindings.scorers) F from_dict() (lomap.LomapAtomMapper class method) from_json() (lomap.LomapAtomMapper class method) from_keyed_chain() (lomap.LomapAtomMapper class method) from_keyed_dict() (lomap.LomapAtomMapper class method) from_msgpack() (lomap.LomapAtomMapper class method) from_shallow_dict() (lomap.LomapAtomMapper class method) G generate_depictions() (lomap.graphgen.GraphGen method) generate_initial_subgraph_list() (lomap.graphgen.GraphGen static method) generate_lomap_network() (in module lomap) generate_subgraph_scores_lists() (lomap.graphgen.GraphGen static method) generate_working_subgraphs_list() (lomap.graphgen.GraphGen static method) getID() (lomap.dbmol.Molecule method) getMapping() (lomap.mcs.MCS static method) getMolecule() (lomap.dbmol.Molecule method) getName() (lomap.dbmol.Molecule method) GraphGen (class in lomap.graphgen) H heavy_atom_match_list() (lomap.mcs.MCS method) heavy_atom_mcs_map() (lomap.mcs.MCS method) heterocycles_rule() (lomap.mcs.MCS method) heterocycles_score() (in module lomap.gufe_bindings.scorers) hybridization_rule() (lomap.mcs.MCS method) hybridization_score() (in module lomap.gufe_bindings.scorers) I isActive() (lomap.dbmol.Molecule method) K key (lomap.LomapAtomMapper property) L logger (lomap.LomapAtomMapper property) LomapAtomMapper (class in lomap) M mat_size() (lomap.dbmol.SMatrix method) MCS (class in lomap.mcs) mcsr() (lomap.mcs.MCS method) mcsr_score() (in module lomap.gufe_bindings.scorers) merge_all_subgraphs() (lomap.graphgen.GraphGen static method) minimize_edges() (lomap.graphgen.GraphGen method) mncar() (lomap.mcs.MCS method) mncar_score() (in module lomap.gufe_bindings.scorers) Molecule (class in lomap.dbmol) N next() (lomap.dbmol.DBMolecules method) nums() (lomap.dbmol.DBMolecules method) P pick_lead() (lomap.graphgen.GraphGen static method) R read_molecule_files() (lomap.dbmol.DBMolecules method) remains_connected() (lomap.graphgen.GraphGen static method) remove_edges_below_hard_limit() (lomap.graphgen.GraphGen static method) S serialization_migration() (lomap.LomapAtomMapper class method) setActive() (lomap.dbmol.Molecule method) SMatrix (class in lomap.dbmol) suggest_mappings() (lomap.LomapAtomMapper method) sulfonamides_rule() (lomap.mcs.MCS method) sulfonamides_score() (in module lomap.gufe_bindings.scorers) T to_dict() (lomap.LomapAtomMapper method) to_json() (lomap.LomapAtomMapper method) to_keyed_chain() (lomap.LomapAtomMapper method) to_keyed_dict() (lomap.LomapAtomMapper method) to_msgpack() (lomap.LomapAtomMapper method) to_numpy_2D_array() (lomap.dbmol.SMatrix method) to_shallow_dict() (lomap.LomapAtomMapper method) transmuting_methyl_into_ring_rule() (lomap.mcs.MCS method) transmuting_methyl_into_ring_score() (in module lomap.gufe_bindings.scorers) transmuting_ring_sizes_rule() (lomap.mcs.MCS method) transmuting_ring_sizes_score() (in module lomap.gufe_bindings.scorers) W write_dic() (lomap.dbmol.DBMolecules method) write_graph() (lomap.graphgen.GraphGen method)