besmarts.core namespace

Submodules

• besmarts.core.arrays module
  • argmax()
  • argmin()
  • argsort()
  • array_abs()
  • array_add()
  • array_basis()
  • array_cross()
  • array_difference()
  • array_distance()
  • array_divide()
  • array_inner_product()
  • array_magnitude()
  • array_mean()
  • array_multiply()
  • array_round()
  • array_scale()
  • array_sum()
  • array_translate()
  • array_unit()
  • batched()
  • bitvec
    • bitvec.all()
    • bitvec.any()
    • bitvec.bits()
    • bitvec.clear()
    • bitvec.copy()
    • bitvec.inv()
    • bitvec.is_null()
    • bitvec.maxbits
    • bitvec.off()
    • bitvec.off_first()
    • bitvec.on()
    • bitvec.on_first()
    • bitvec.reduce()
    • bitvec.v
  • bitvec_all()
  • bitvec_and()
  • bitvec_any()
  • bitvec_bits()
  • bitvec_clear()
  • bitvec_copy()
  • bitvec_equal()
  • bitvec_explicit_flip()
  • bitvec_is_inverted()
  • bitvec_is_null()
  • bitvec_not()
  • bitvec_off()
  • bitvec_off_first()
  • bitvec_on()
  • bitvec_on_first()
  • bitvec_or()
  • bitvec_reduce()
  • bitvec_subset()
  • bitvec_subtract()
  • bitvec_sum()
  • bitvec_superset()
  • bitvec_xor()
  • find_unsigned_typecode_min()
  • flatten_list()
  • intvec
    • intvec.v
  • measure_distance()
• besmarts.core.assignments module
  • angle_assignment_float
    • angle_assignment_float.selections
    • angle_assignment_float.topology
  • angle_assignment_float_matrix
    • angle_assignment_float_matrix.selections
    • angle_assignment_float_matrix.topology
  • angle_assignment_str
    • angle_assignment_str.selections
    • angle_assignment_str.topology
  • atom_assignment_float
    • atom_assignment_float.selections
    • atom_assignment_float.topology
  • atom_assignment_str
    • atom_assignment_str.selections
    • atom_assignment_str.topology
  • b2matrix()
  • bmatrix()
  • bond_assignment_float
    • bond_assignment_float.selections
    • bond_assignment_float.topology
  • bond_assignment_float_matrix
    • bond_assignment_float_matrix.selections
    • bond_assignment_float_matrix.topology
  • bond_assignment_str
    • bond_assignment_str.selections
    • bond_assignment_str.topology
  • graph_assignment
    • graph_assignment.copy()
    • graph_assignment.graph
    • graph_assignment.selections
    • graph_assignment.smiles
  • graph_assignment_copy()
  • graph_assignment_float
    • graph_assignment_float.graph
    • graph_assignment_float.selections
  • graph_assignment_float_matrix
    • graph_assignment_float_matrix.graph
    • graph_assignment_float_matrix.selections
  • graph_assignment_geometry_angle_matrix()
  • graph_assignment_geometry_angles()
  • graph_assignment_geometry_bond_matrix()
  • graph_assignment_geometry_bonds()
  • graph_assignment_geometry_outofplane_matrix()
  • graph_assignment_geometry_outofplanes()
  • graph_assignment_geometry_pair_matrix()
  • graph_assignment_geometry_pairs()
  • graph_assignment_geometry_position()
  • graph_assignment_geometry_torsion_matrix()
  • graph_assignment_geometry_torsions()
  • graph_assignment_jacobian2_angle_matrix()
  • graph_assignment_jacobian2_angles()
  • graph_assignment_jacobian2_bond_matrix()
  • graph_assignment_jacobian2_bonds()
  • graph_assignment_jacobian2_outofplane_matrix()
  • graph_assignment_jacobian2_outofplanes()
  • graph_assignment_jacobian2_pair_matrix()
  • graph_assignment_jacobian2_pairs()
  • graph_assignment_jacobian2_torsion_matrix()
  • graph_assignment_jacobian2_torsions()
  • graph_assignment_jacobian_angle_matrix()
  • graph_assignment_jacobian_angles()
  • graph_assignment_jacobian_bond_matrix()
  • graph_assignment_jacobian_bonds()
  • graph_assignment_jacobian_distance_matrix()
  • graph_assignment_jacobian_distances()
  • graph_assignment_jacobian_outofplane_matrix()
  • graph_assignment_jacobian_outofplanes()
  • graph_assignment_jacobian_pair_matrix()
  • graph_assignment_jacobian_pairs()
  • graph_assignment_jacobian_torsion_matrix()
  • graph_assignment_jacobian_torsions()
  • graph_assignment_matrix_angle_indices()
  • graph_assignment_matrix_bond_indices()
  • graph_assignment_matrix_outofplane_indices()
  • graph_assignment_matrix_pair_indices()
  • graph_assignment_matrix_torsion_indices()
  • graph_assignment_to_format_xyz()
  • graph_assignment_to_graph_db_graph()
  • graph_assignment_to_graph_db_row()
  • graph_db
    • graph_db.entries
    • graph_db.graphs
    • graph_db.selections
    • graph_db.smiles
  • graph_db_add_graph()
  • graph_db_add_multi_molecule()
  • graph_db_add_single_molecule_list()
  • graph_db_add_single_molecule_state()
  • graph_db_address
  • graph_db_column
    • graph_db_column.selections
  • graph_db_entry
    • graph_db_entry.tables
  • graph_db_entry_add_table()
  • graph_db_get()
  • graph_db_get_entries()
  • graph_db_get_graphs()
  • graph_db_graph
    • graph_db_graph.rows
  • graph_db_graph_to_graph_assignment()
  • graph_db_iter_values()
  • graph_db_row
    • graph_db_row.columns
  • graph_db_selection
    • graph_db_selection.coords
  • graph_db_set_gradient()
  • graph_db_set_positions()
  • graph_db_table
    • graph_db_table.graphs
    • graph_db_table.topology
    • graph_db_table.values
  • graph_db_table_get_row_ids()
  • make_structure_assignment_type()
  • outofplane_assignment_float
    • outofplane_assignment_float.selections
    • outofplane_assignment_float.topology
  • outofplane_assignment_float_matrix
    • outofplane_assignment_float_matrix.selections
    • outofplane_assignment_float_matrix.topology
  • outofplane_assignment_str
    • outofplane_assignment_str.selections
    • outofplane_assignment_str.topology
  • pair_assignment_float
    • pair_assignment_float.selections
    • pair_assignment_float.topology
  • pair_assignment_float_matrix
    • pair_assignment_float_matrix.selections
    • pair_assignment_float_matrix.topology
  • parse_xyz()
  • smarts_assignment
    • smarts_assignment.selections
    • smarts_assignment.smarts
  • smarts_assignment_float
    • smarts_assignment_float.selections
    • smarts_assignment_float.smarts
  • smarts_assignment_str
    • smarts_assignment_str.selections
    • smarts_assignment_str.smarts
  • smarts_hierarchy_assignment
    • smarts_hierarchy_assignment.assign()
    • smarts_hierarchy_assignment.assign_angles()
    • smarts_hierarchy_assignment.assign_atoms()
    • smarts_hierarchy_assignment.assign_bonds()
    • smarts_hierarchy_assignment.assign_outofplanes()
    • smarts_hierarchy_assignment.assign_torsions()
  • smiles_assignment
    • smiles_assignment.compute()
    • smiles_assignment.copy()
    • smiles_assignment.selections
    • smiles_assignment.smiles
  • smiles_assignment_copy()
  • smiles_assignment_float
    • smiles_assignment_float.selections
    • smiles_assignment_float.smiles
  • smiles_assignment_geometry_angle_matrix()
  • smiles_assignment_geometry_angles()
  • smiles_assignment_geometry_distance_matrix()
  • smiles_assignment_geometry_distances()
  • smiles_assignment_geometry_outofplane_matrix()
  • smiles_assignment_geometry_outofplanes()
  • smiles_assignment_geometry_torsion_matrix()
  • smiles_assignment_geometry_torsion_matrix_nonlinear()
  • smiles_assignment_geometry_torsions()
  • smiles_assignment_geometry_torsions_nonlinear()
  • smiles_assignment_group
    • smiles_assignment_group.copy()
  • smiles_assignment_group_angles()
  • smiles_assignment_group_atoms()
  • smiles_assignment_group_bonds()
  • smiles_assignment_group_concatenate()
  • smiles_assignment_group_copy()
  • smiles_assignment_group_outofplanes()
  • smiles_assignment_group_pairs()
  • smiles_assignment_group_to_graph_db_entry()
  • smiles_assignment_group_to_structure_assignment_group()
  • smiles_assignment_group_torsions()
  • smiles_assignment_jacobian2_angle_matrix()
  • smiles_assignment_jacobian2_angles()
  • smiles_assignment_jacobian2_distance_matrix()
  • smiles_assignment_jacobian2_distances()
  • smiles_assignment_jacobian2_outofplane_matrix()
  • smiles_assignment_jacobian2_outofplanes()
  • smiles_assignment_jacobian2_torsion_matrix()
  • smiles_assignment_jacobian2_torsions()
  • smiles_assignment_jacobian_angle_matrix()
  • smiles_assignment_jacobian_angles()
  • smiles_assignment_jacobian_distance_matrix()
  • smiles_assignment_jacobian_distances()
  • smiles_assignment_jacobian_outofplane_matrix()
  • smiles_assignment_jacobian_outofplanes()
  • smiles_assignment_jacobian_torsion_matrix()
  • smiles_assignment_jacobian_torsions()
  • smiles_assignment_to_graph_assignment()
  • structure_assignment_float
    • structure_assignment_float.selections
    • structure_assignment_float.topology
  • structure_assignment_group
    • structure_assignment_group.assignments
    • structure_assignment_group.copy()
    • structure_assignment_group.topology
  • structure_assignment_group_copy()
  • structure_assignment_str
    • structure_assignment_str.selections
    • structure_assignment_str.topology
  • topology_assignment_group
  • torsion_assignment_float
    • torsion_assignment_float.selections
    • torsion_assignment_float.topology
  • torsion_assignment_float_matrix
    • torsion_assignment_float_matrix.selections
    • torsion_assignment_float_matrix.topology
  • torsion_assignment_str
    • torsion_assignment_str.selections
    • torsion_assignment_str.topology
  • xyz_to_graph_assignment()
• besmarts.core.chem module
  • bechem
    • bechem.all()
    • bechem.any()
    • bechem.bits()
    • bechem.bits_max()
    • bechem.clear()
    • bechem.copy()
    • bechem.disable()
    • bechem.enable()
    • bechem.fill()
    • bechem.is_null()
    • bechem.is_valid()
    • bechem.primitives
    • bechem.select
    • bechem.to_fragments()
  • bechem_add()
  • bechem_align_score()
  • bechem_all()
  • bechem_and()
  • bechem_and_conditional()
  • bechem_any()
  • bechem_bits()
  • bechem_bits_max()
  • bechem_check_sane_compare()
  • bechem_clear()
  • bechem_copy()
  • bechem_disable()
  • bechem_dispatch_op()
  • bechem_enable()
  • bechem_fill()
  • bechem_get()
  • bechem_iadd()
  • bechem_iand()
  • bechem_identity()
  • bechem_ior()
  • bechem_is_fragment()
  • bechem_is_null()
  • bechem_is_valid()
  • bechem_isubtract()
  • bechem_iter()
  • bechem_ixor()
  • bechem_neg()
  • bechem_or()
  • bechem_recurse_fields()
  • bechem_reduce()
  • bechem_reduce_longest()
  • bechem_subtract()
  • bechem_subtract_conditional()
  • bechem_to_fragments()
  • bechem_xor()
• besmarts.core.clusters module
  • check_lbls_data_selections_equal()
  • clustering_assign()
  • clustering_build_assignment_mappings()
  • clustering_build_label_mappings()
  • clustering_build_ordinal_mappings()
  • clustering_collect_split_candidates_ctx
    • clustering_collect_split_candidates_ctx.assn
    • clustering_collect_split_candidates_ctx.backmap
    • clustering_collect_split_candidates_ctx.ret
  • clustering_collect_split_candidates_serial()
  • clustering_collect_split_candidates_single()
  • clustering_collect_split_candidates_single_distributed()
  • clustering_collect_structures()
  • clustering_initial_conditions()
  • clustering_node_remove_by_name()
  • clustering_objective
    • clustering_objective.is_discrete()
    • clustering_objective.merge()
    • clustering_objective.report()
    • clustering_objective.single()
    • clustering_objective.split()
    • clustering_objective.sum()
  • clustering_update_assignments()
  • find_successful_candidates_distributed()
  • get_assns()
  • get_objective()
  • match_group_assignments()
  • objective_total()
  • perform_operations()
  • smarts_clustering
    • smarts_clustering.group
    • smarts_clustering.group_prefix_str
    • smarts_clustering.hierarchy
    • smarts_clustering.mappings
  • smarts_clustering_find_max_depth()
  • smarts_clustering_optimize()
  • smarts_filter_bond_lengths()
  • smarts_filter_data()
• besmarts.core.codecs module
  • SMILES_ELEMENT()
  • graph_codec
    • graph_codec.smarts_decode()
    • graph_codec.smarts_encode()
    • graph_codec.smiles_decode()
    • graph_codec.smiles_encode()
  • graph_codec_chain
    • graph_codec_chain.add_graph_codec()
    • graph_codec_chain.smarts_decode()
    • graph_codec_chain.smarts_encode()
    • graph_codec_chain.smiles_decode()
    • graph_codec_chain.smiles_encode()
  • intvec_codec
    • intvec_codec.graph_decode()
    • intvec_codec.graph_encode()
    • intvec_codec.structure_decode()
    • intvec_codec.structure_encode()
    • intvec_codec.subgraph_decode()
    • intvec_codec.subgraph_encode()
  • intvec_codec_graph_decode()
  • intvec_codec_graph_decode_auto()
  • intvec_codec_structure_decode()
  • intvec_codec_subgraph_decode()
  • primitive_codec_aromatic
    • primitive_codec_aromatic.decode_smarts()
    • primitive_codec_aromatic.encode_smarts()
    • primitive_codec_aromatic.tokenize_smarts()
  • primitive_codec_bond_order
    • primitive_codec_bond_order.decode_smarts()
    • primitive_codec_bond_order.encode_smarts()
    • primitive_codec_bond_order.encode_smiles()
    • primitive_codec_bond_order.tokenize_smarts()
  • primitive_codec_bond_ring
    • primitive_codec_bond_ring.decode_smarts()
    • primitive_codec_bond_ring.encode_smarts()
    • primitive_codec_bond_ring.tokenize_smarts()
  • primitive_codec_chirality
    • primitive_codec_chirality.decode_smarts()
    • primitive_codec_chirality.encode_smarts()
    • primitive_codec_chirality.encode_smiles()
    • primitive_codec_chirality.tokenize_smarts()
  • primitive_codec_connectivity_ring
    • primitive_codec_connectivity_ring.decode_smarts()
  • primitive_codec_connectivity_total
    • primitive_codec_connectivity_total.decode_smarts()
  • primitive_codec_element
    • primitive_codec_element.count_carbon_smiles()
    • primitive_codec_element.count_element_smiles()
    • primitive_codec_element.decode_smarts()
    • primitive_codec_element.encode_smiles()
  • primitive_codec_formal_charge
    • primitive_codec_formal_charge.count_charge_smiles()
    • primitive_codec_formal_charge.decode_int()
    • primitive_codec_formal_charge.decode_smarts()
    • primitive_codec_formal_charge.encode_int()
    • primitive_codec_formal_charge.encode_smarts()
    • primitive_codec_formal_charge.encode_smiles()
    • primitive_codec_formal_charge.tokenize_smarts()
  • primitive_codec_hydrogen
    • primitive_codec_hydrogen.count_hydrogen_smiles()
    • primitive_codec_hydrogen.decode_smarts()
    • primitive_codec_hydrogen.encode_smiles()
  • primitive_codec_link_dst
    • primitive_codec_link_dst.decode_smiles()
    • primitive_codec_link_dst.decode_supersmarts()
    • primitive_codec_link_dst.encode_supersmarts()
    • primitive_codec_link_dst.tokenize_smarts()
  • primitive_codec_link_src
    • primitive_codec_link_src.decode_smiles()
    • primitive_codec_link_src.decode_supersmarts()
    • primitive_codec_link_src.encode_supersmarts()
    • primitive_codec_link_src.tokenize_smarts()
  • primitive_codec_ring_smallest
    • primitive_codec_ring_smallest.decode_int()
    • primitive_codec_ring_smallest.decode_smarts()
    • primitive_codec_ring_smallest.encode_int()
    • primitive_codec_ring_smallest.encode_smarts()
    • primitive_codec_ring_smallest.tokenize_smarts()
  • primitive_codec_unit
    • primitive_codec_unit.decode_smarts()
    • primitive_codec_unit.decode_smiles()
    • primitive_codec_unit.encode_supersmarts()
    • primitive_codec_unit.tokenize_smarts()
  • primitive_codec_unit_index
    • primitive_codec_unit_index.decode_smiles()
    • primitive_codec_unit_index.decode_supersmiles()
    • primitive_codec_unit_index.encode_supersmarts()
    • primitive_codec_unit_index.tokenize_smarts()
  • primitive_codec_valence
    • primitive_codec_valence.decode_smarts()
  • primitive_codec_variable
    • primitive_codec_variable.decode_smarts()
    • primitive_codec_variable.decode_smiles()
    • primitive_codec_variable.encode_smarts()
    • primitive_codec_variable.encode_smiles()
    • primitive_codec_variable.tokenize_smarts()
  • primitive_codecs_get()
  • smarts_decode_distributed()
  • smiles_decode_distributed()
  • smiles_decode_list_distributed()
• besmarts.core.compute module
  • AutoProxy()
  • BaseProxy
  • Client()
  • Connection
  • Listener
    • Listener.accept()
  • MakeProxyType()
  • Process()
  • Server
    • Server.accept_connection()
    • Server.accepter()
    • Server.decref()
    • Server.handle_request()
    • Server.incref()
    • Server.recv_request()
    • Server.run_request()
    • Server.send_request()
    • Server.serve_client()
    • Server.serve_forever()
  • SocketClient()
  • close_pools()
  • close_workspaces()
  • compute_remote()
  • dispatch()
  • dprint()
  • manager_connect()
  • manager_remote_get_iqueue()
  • manager_remote_get_iqueue_thread()
  • manager_remote_get_oqueue()
  • manager_remote_get_oqueue_thread()
  • manager_remote_get_state()
  • manager_remote_get_state_thread()
  • manager_remote_get_status()
  • manager_remote_get_status_thread()
  • manager_remote_queue_put()
  • manager_remote_queue_put_thread()
  • manager_remote_queue_qsize()
  • manager_remote_queue_qsize_thread()
  • myiqueue
    • myiqueue.get()
  • myqueue
    • myqueue.get()
    • myqueue.put()
  • queue_get_nowait()
  • queue_get_nowait_thread()
  • register_pool()
  • register_workspace()
  • remote_connect()
  • remote_init_thread()
  • shm_init()
  • shm_local
    • shm_local.get()
    • shm_local.remote_init()
  • signal_kill_processes()
  • thread_name_set()
  • unregister_pool()
  • unregister_workspace()
  • workqueue
    • workqueue.get_state()
    • workqueue.get_status()
    • workqueue.get_workspaces()
  • workqueue_get_workspace()
  • workqueue_is_active()
  • workqueue_list_workspaces()
  • workqueue_local
    • workqueue_local.close()
    • workqueue_local.get_state()
    • workqueue_local.get_threads()
    • workqueue_local.get_workspaces()
    • workqueue_local.put_workspaces()
    • workqueue_local.remove_workspace()
  • workqueue_manager
    • workqueue_manager.get_iqueue()
    • workqueue_manager.get_oqueue()
    • workqueue_manager.get_rqueue()
    • workqueue_manager.get_state()
  • workqueue_new_workspace()
  • workqueue_push_workspace()
  • workqueue_remote
    • workqueue_remote.connect()
    • workqueue_remote.get_state()
    • workqueue_remote.get_status()
    • workqueue_remote.get_workspaces()
    • workqueue_remote.put_workspaces()
  • workqueue_remote_get_workspaces()
  • workqueue_remote_get_workspaces_thread()
  • workqueue_remote_is_active()
  • workqueue_remote_put_workspaces()
  • workqueue_remote_put_workspaces_thread()
  • workqueue_remove_workspace()
  • workspace
    • workspace.get_iqueue()
    • workspace.get_oqueue()
    • workspace.get_rqueue()
    • workspace.get_state()
    • workspace.get_status()
  • workspace_flush()
  • workspace_is_active()
  • workspace_local
    • workspace_local.clear_iqueue()
    • workspace_local.clear_oqueue()
    • workspace_local.close()
    • workspace_local.get_iqueue()
    • workspace_local.get_oqueue()
    • workspace_local.get_state()
    • workspace_local.get_status()
    • workspace_local.manager_start()
    • workspace_local.pool_close()
    • workspace_local.pool_start()
    • workspace_local.reset()
    • workspace_local.set_status()
    • workspace_local.start()
  • workspace_local_remote_gather_thread()
  • workspace_local_remote_loadbalance_thread()
  • workspace_local_run()
  • workspace_local_run_thread()
  • workspace_local_submit()
  • workspace_manager
    • workspace_manager.create()
    • workspace_manager.get_state()
    • workspace_manager.get_status()
    • workspace_manager.get_workspaces()
  • workspace_pool
    • workspace_pool.Process()
  • workspace_remote
    • workspace_remote.close()
    • workspace_remote.connect()
    • workspace_remote.get_iqueue()
    • workspace_remote.get_oqueue()
    • workspace_remote.get_state()
    • workspace_remote.get_status()
    • workspace_remote.iqueue_get()
    • workspace_remote.iqueue_put()
    • workspace_remote.oqueue_put()
    • workspace_remote.start()
  • workspace_remote_compute()
  • workspace_remote_local_gather_thread()
  • workspace_remote_local_pusher_thread()
  • workspace_remote_shm_init()
  • workspace_remote_shm_init_thread()
  • workspace_run()
  • workspace_run_init()
  • workspace_status
    • workspace_status.DONE
    • workspace_status.EMPTY
    • workspace_status.INACTIVE
    • workspace_status.INVALID
    • workspace_status.RUNNING
    • workspace_status.SUBMITTING
    • workspace_status.WAITING
  • workspace_submit_and_flush()
• besmarts.core.configs module
  • mapper_config
    • mapper_config.copy()
  • smarts_extender_config
    • smarts_extender_config.copy()
    • smarts_extender_config.depth_max
    • smarts_extender_config.depth_min
    • smarts_extender_config.include_hydrogen
  • smarts_perception_config
    • smarts_perception_config.copy()
    • smarts_perception_config.extender
    • smarts_perception_config.splitter
  • smarts_perception_config_copy()
  • smarts_splitter_config
    • smarts_splitter_config.bit_search_limit
    • smarts_splitter_config.bit_search_min
    • smarts_splitter_config.branch_depth_limit
    • smarts_splitter_config.branch_depth_min
    • smarts_splitter_config.branch_limit
    • smarts_splitter_config.branch_min
    • smarts_splitter_config.copy()
    • smarts_splitter_config.max_splits
    • smarts_splitter_config.primitives
    • smarts_splitter_config.return_matches
    • smarts_splitter_config.split_general
    • smarts_splitter_config.split_specific
    • smarts_splitter_config.unique
    • smarts_splitter_config.unique_complements
    • smarts_splitter_config.unique_complements_prefer_min
  • smiles_perception_config
• besmarts.core.db module
  • db_dict
    • db_dict.delete_intvec()
    • db_dict.read_graph()
    • db_dict.read_graph_list()
    • db_dict.read_intvec()
    • db_dict.read_intvec_list()
    • db_dict.read_structure()
    • db_dict.read_structure_list()
    • db_dict.remove()
    • db_dict.write_graph()
    • db_dict.write_intvec()
    • db_dict.write_structure()
    • db_dict.write_subgraph()
  • db_graph_read()
  • db_graph_write()
  • db_intvec_create()
  • db_intvec_delete()
  • db_intvec_read()
  • db_intvec_read_list()
  • db_intvec_write()
  • db_structure_write()
  • db_structure_write_distributed()
• besmarts.core.geometry module
  • angle()
  • array_add()
  • array_basis()
  • array_cross()
  • array_difference()
  • array_distance()
  • array_inner_product()
  • array_magnitude()
  • array_multiply()
  • array_outer_product()
  • array_round()
  • array_scale()
  • array_unit()
  • bond()
  • is_dihedral()
  • is_outofplane()
  • is_torsion()
  • jacobian2_angle()
  • jacobian2_angle_term_reduce()
  • jacobian2_angle_terms()
  • jacobian2_distance()
  • jacobian2_distance_terms()
  • jacobian2_outofplane()
  • jacobian2_reshape_to_matrix()
  • jacobian2_torsion()
  • jacobian2_torsion_term_reduce()
  • jacobian2_torsion_terms()
  • jacobian_angle()
  • jacobian_distance()
  • jacobian_outofplane()
  • jacobian_outofplane_v2()
  • jacobian_torsion()
  • jacobian_torsion_v2()
  • measure_angle()
  • measure_dihedral()
  • measure_distance()
  • outofplane()
  • pair()
  • torsion()
• besmarts.core.graph_visitors module
  • encoding_visitor
    • encoding_visitor.on_ascend()
    • encoding_visitor.on_descend()
    • encoding_visitor.on_edge()
    • encoding_visitor.on_edge_enter()
    • encoding_visitor.on_edge_exit()
    • encoding_visitor.on_node()
    • encoding_visitor.on_node_enter()
    • encoding_visitor.on_node_exit()
    • encoding_visitor.on_start()
    • encoding_visitor.on_stop()
  • enter_graph()
  • find_branches()
  • graph_visitor
    • graph_visitor.enter_graph()
    • graph_visitor.on_ascend()
    • graph_visitor.on_descend()
    • graph_visitor.on_edge()
    • graph_visitor.on_edge_enter()
    • graph_visitor.on_edge_exit()
    • graph_visitor.on_graph()
    • graph_visitor.on_node()
    • graph_visitor.on_node_edges()
    • graph_visitor.on_node_enter()
    • graph_visitor.on_node_exit()
    • graph_visitor.on_start()
    • graph_visitor.on_stop()
  • index_visitor
    • index_visitor.on_ascend()
    • index_visitor.on_descend()
    • index_visitor.on_edge()
    • index_visitor.on_edge_enter()
    • index_visitor.on_edge_exit()
    • index_visitor.on_node()
    • index_visitor.on_node_enter()
    • index_visitor.on_node_exit()
    • index_visitor.on_start()
    • index_visitor.on_stop()
  • longest_path()
  • smarts_visitor
    • smarts_visitor.on_edge()
    • smarts_visitor.on_node()
    • smarts_visitor.on_node_enter()
    • smarts_visitor.on_node_exit()
  • smiles_visitor
    • smiles_visitor.atom_encode_smarts()
    • smiles_visitor.bond_encode_smarts()
    • smiles_visitor.on_edge()
    • smiles_visitor.on_edge_enter()
    • smiles_visitor.on_edge_exit()
    • smiles_visitor.on_node()
    • smiles_visitor.on_node_enter()
    • smiles_visitor.on_node_exit()
  • structure_iter_bits()
  • visit_descend()
  • visit_graph()
• besmarts.core.graphs module
  • edge()
  • graph
    • graph.cache
    • graph.edges
    • graph.nodes
  • graph_all()
  • graph_angles()
  • graph_any()
  • graph_as_structure()
  • graph_as_subgraph()
  • graph_atoms()
  • graph_bits()
  • graph_bits_max()
  • graph_bonds()
  • graph_clear()
  • graph_complexity()
  • graph_connection()
  • graph_connections()
  • graph_copy()
  • graph_detect_rings()
  • graph_disable_primitives_atom()
  • graph_disable_primitives_bond()
  • graph_edges_copy()
  • graph_fill()
  • graph_hash()
  • graph_invert()
  • graph_invert_all()
  • graph_invert_any()
  • graph_is_null()
  • graph_is_valid()
  • graph_minimum_spanning_tree()
  • graph_nodes_copy()
  • graph_outofplanes()
  • graph_pairs()
  • graph_relabel_nodes()
  • graph_remove_hydrogen()
  • graph_remove_nodes()
  • graph_same()
  • graph_set_primitives_atom()
  • graph_set_primitives_bond()
  • graph_shortest_path()
  • graph_shortest_path_length()
  • graph_shortest_paths()
  • graph_symbols()
  • graph_to_intvec()
  • graph_to_structure()
  • graph_to_structure_angles()
  • graph_to_structure_atoms()
  • graph_to_structure_bonds()
  • graph_to_structure_outofplanes()
  • graph_to_structure_pairs()
  • graph_to_structure_topology()
  • graph_to_structure_torsions()
  • graph_to_structures()
  • graph_to_subgraph()
  • graph_to_subgraphs()
  • graph_topology()
  • graph_torsions()
  • structure
    • structure.cache
    • structure.edges
    • structure.hashes
    • structure.nodes
    • structure.select
    • structure.topology
  • structure_angle()
  • structure_atom()
  • structure_bits()
  • structure_bond()
  • structure_branch()
  • structure_build()
  • structure_clear()
  • structure_connections()
  • structure_copy()
  • structure_edges()
  • structure_extend()
  • structure_fill()
  • structure_frontier_nodes()
  • structure_hash()
  • structure_invert()
  • structure_invert_any()
  • structure_max_depth()
  • structure_node_depth()
  • structure_node_depths()
  • structure_nodes()
  • structure_outofplane()
  • structure_print()
  • structure_prune_null_nodes()
  • structure_relabel_nodes()
  • structure_remove_empty_leaves()
  • structure_remove_full_leaves()
  • structure_remove_hydrogen()
  • structure_remove_nodes()
  • structure_remove_unselected()
  • structure_to_graph()
  • structure_to_intvec()
  • structure_to_subgraph()
  • structure_topology_edges()
  • structure_topology_nodes()
  • structure_torsion()
  • structure_unreachable_nodes()
  • structure_up_to_depth()
  • structure_vertices_at_depth()
  • subgraph
    • subgraph.cache
    • subgraph.edges
    • subgraph.nodes
    • subgraph.select
  • subgraph_any()
  • subgraph_as_graph()
  • subgraph_as_structure()
  • subgraph_bits()
  • subgraph_connection()
  • subgraph_connections()
  • subgraph_copy()
  • subgraph_edges()
  • subgraph_fill()
  • subgraph_hash()
  • subgraph_invert()
  • subgraph_invert_null()
  • subgraph_nodes()
  • subgraph_print()
  • subgraph_relabel_nodes()
  • subgraph_remove_unselected()
  • subgraph_to_graph()
  • subgraph_to_intvec()
  • subgraph_to_structure()
  • subgraph_to_structure_angle()
  • subgraph_to_structure_bond()
  • subgraph_to_structure_outofplane()
  • subgraph_to_structure_torsion()
  • subgraph_validate_structure()
• besmarts.core.hierarchies module
  • smarts_hierarchy
    • smarts_hierarchy.copy()
    • smarts_hierarchy.index
    • smarts_hierarchy.smarts
  • smarts_hierarchy_copy()
  • smarts_hierarchy_print()
  • smarts_hierarchy_rename()
  • smarts_hierarchy_to_structure_hierarchy()
  • smarts_hierarchy_to_structure_hierarchy_angles()
  • smarts_hierarchy_to_structure_hierarchy_atoms()
  • smarts_hierarchy_to_structure_hierarchy_bonds()
  • smarts_hierarchy_to_structure_hierarchy_outofplanes()
  • smarts_hierarchy_to_structure_hierarchy_torsions()
  • structure_hierarchy
    • structure_hierarchy.copy()
    • structure_hierarchy.index
    • structure_hierarchy.smarts
    • structure_hierarchy.subgraphs
    • structure_hierarchy.topology
  • structure_hierarchy_copy()
  • structure_hierarchy_to_smarts_hierarchy()
• besmarts.core.hierarchy_merge module
  • return_g()
  • structure_hierarchy_add_hierarchy()
  • structure_hierarchy_fit()
  • structure_hierarchy_merge()
  • structure_hierarchy_prune_unused()
  • take_left()
  • take_right()
• besmarts.core.logs module
  • append()
  • cout_logger()
  • dprint()
  • file_logger()
  • timestamp()
• besmarts.core.mapper module
  • align_score()
  • align_score_ctx
    • align_score_ctx.ref
    • align_score_ctx.to_check
  • align_score_parallel()
  • difference()
  • dispatch_boolean_op()
  • filter_contains()
  • filter_contains_ctx
    • filter_contains_ctx.bes
    • filter_contains_ctx.to_check
  • filter_contains_parallel()
  • group_by_isomorphism()
  • intersection()
  • intersection_conditional()
  • intersection_list()
  • intersection_list_dispatch()
  • intersection_list_parallel()
  • is_isomorphic()
  • isomorphic()
  • map_to()
  • map_to_descend()
  • map_vertices()
  • map_vertices_ctx
    • map_vertices_ctx.H
    • map_vertices_ctx.a
    • map_vertices_ctx.b
    • map_vertices_ctx.cg
    • map_vertices_ctx.equality
    • map_vertices_ctx.o
    • map_vertices_ctx.strict
  • map_vertices_parallel()
  • mapped_type
  • mapper()
  • mapper_compose()
  • mapper_compose_graphs()
  • mapper_force_equality()
  • mapper_force_subset()
  • mapper_invert()
  • mapper_match()
  • neg()
  • ordered_align_score()
  • ordered_contains()
  • overlap_scores()
  • pairwise_overlap()
  • subtract()
  • subtract_conditional()
  • subtract_conditional_left()
  • subtract_conditional_right()
  • union()
  • union_ctx
    • union_ctx.A
    • union_ctx.config
    • union_ctx.icd
    • union_ctx.reference
    • union_ctx.topology
  • union_list()
  • union_list_dispatch()
  • union_list_dispatch_distributed()
  • union_list_distributed()
  • union_list_parallel()
  • xor()
• besmarts.core.optimization module
  • optimization_iteration
    • optimization_iteration.is_done()
    • optimization_iteration.next()
    • optimization_iteration.repeat_step()
  • optimization_iteration_is_done()
  • optimization_iteration_next()
  • optimization_iteration_repeat_step()
  • optimization_step
    • optimization_step.copy()
  • optimization_step_copy()
  • optimization_strategy
    • optimization_strategy.MERGE
    • optimization_strategy.MODIFY
    • optimization_strategy.SPLIT
    • optimization_strategy.bounds
    • optimization_strategy.build_steps()
    • optimization_strategy.filter_above
    • optimization_strategy.is_done()
    • optimization_strategy.keep_below
    • optimization_strategy.macro_accept_max_per_cluster
    • optimization_strategy.macro_accept_max_total
    • optimization_strategy.macro_iteration()
    • optimization_strategy.micro_accept_max_per_cluster
    • optimization_strategy.micro_accept_max_total
    • optimization_strategy.repeat_step()
    • optimization_strategy.restart()
    • optimization_strategy.steps
    • optimization_strategy.tree_iterator
  • optimization_strategy_build_macro_iterations()
  • optimization_strategy_is_done()
  • optimization_strategy_iteration_next()
  • optimization_strategy_repeat_step()
  • optimization_strategy_restart()
• besmarts.core.perception module
  • perception_model
• besmarts.core.primitives module
  • primitive_codec
    • primitive_codec.decode_int()
    • primitive_codec.decode_smarts()
    • primitive_codec.decode_smiles()
    • primitive_codec.decode_supersmarts()
    • primitive_codec.encode_int()
    • primitive_codec.encode_smarts()
    • primitive_codec.encode_smiles()
    • primitive_codec.encode_supersmarts()
    • primitive_codec.tokenize_smarts()
  • primitive_key
    • primitive_key.AROMATIC
    • primitive_key.BOND_ORDER
    • primitive_key.BOND_RING
    • primitive_key.CHIRALITY
    • primitive_key.CONNECTIVITY_RING
    • primitive_key.CONNECTIVITY_TOTAL
    • primitive_key.ELEMENT
    • primitive_key.FORMAL_CHARGE
    • primitive_key.HYDROGEN
    • primitive_key.LINK_DST
    • primitive_key.LINK_SRC
    • primitive_key.RING_SMALLEST
    • primitive_key.UNIT
    • primitive_key.UNIT_INDEX
    • primitive_key.VALENCE
    • primitive_key.VARIABLE
• besmarts.core.resolve module
  • get_edge_frags()
  • hash_fragment()
  • resolve_process_fragment()
  • resolve_smiles()
  • resolve_smiles_distributed()
  • resolve_smiles_iter()
  • resolve_smiles_recurse_distributed()
  • resolve_smiles_recurse_iter()
• besmarts.core.returns module
  • fail()
  • return_status
    • return_status.FAIL
    • return_status.NONE
    • return_status.SUCCESS
  • return_value
  • success()
• besmarts.core.rulesets module
  • visitor_ruleset
    • visitor_ruleset.on_edge()
    • visitor_ruleset.on_edge_enter()
    • visitor_ruleset.on_edge_exit()
    • visitor_ruleset.on_graph()
    • visitor_ruleset.on_node()
    • visitor_ruleset.on_node_edges()
    • visitor_ruleset.on_node_exit()
    • visitor_ruleset.on_nodes()
    • visitor_ruleset.on_start()
    • visitor_ruleset.on_stop()
• besmarts.core.splits module
  • assert_bonds()
  • dprint()
  • make_branches()
  • process_split()
  • process_split_ctx
    • process_split_ctx.A
    • process_split_ctx.S0
    • process_split_ctx.pool
    • process_split_ctx.splitter
  • process_split_difference()
  • process_split_difference_distributed()
  • process_split_distributed()
  • process_split_general_distributed()
  • process_split_intersect()
  • process_split_intersect_distributed()
  • process_split_matches()
  • process_split_matches_distributed()
  • process_split_specific_distributed()
  • split_all_partitions()
  • split_branches()
  • split_partition()
  • split_return_type
    • split_return_type.matched_idx
    • split_return_type.shards
    • split_return_type.splits
    • split_return_type.subgraphs
    • split_return_type.topology
    • split_return_type.unmatch_idx
  • split_shm_load()
  • split_single_bits()
  • split_structures()
  • split_structures_distributed()
  • split_subgraphs()
  • split_subgraphs_distributed()
• besmarts.core.topology module
  • angle_topology()
  • atom_topology()
  • bond_topology()
  • chain_topology()
  • index_of()
  • n_body_topology()
  • null_topology()
  • outofplane_topology()
  • pair_topology()
  • ring_topology()
  • structure_topology
    • structure_topology.connect
    • structure_topology.permutations
    • structure_topology.primary
  • torsion_topology()
  • transcode_topology
    • transcode_topology.A
    • transcode_topology.B
    • transcode_topology.transcode
• besmarts.core.tree_iterators module
  • tree_iter_breadth_first()
  • tree_iter_breadth_first_single()
  • tree_iter_depth_first()
  • tree_iter_depth_first_single()
  • tree_iter_dive()
  • tree_iter_dive_reverse()
  • tree_iter_dive_single()
  • tree_iter_dive_single_reverse()
  • tree_iter_to_root()
  • tree_iter_to_root_single()
  • yield_if()
  • yield_if_single()
  • yield_single()
• besmarts.core.tree_visitors module
  • tree_visitor
    • tree_visitor.on_ascend()
    • tree_visitor.on_descend()
    • tree_visitor.on_edge()
    • tree_visitor.on_edge_enter()
    • tree_visitor.on_edge_exit()
    • tree_visitor.on_node()
    • tree_visitor.on_node_edges()
    • tree_visitor.on_node_enter()
    • tree_visitor.on_node_exit()
    • tree_visitor.on_start()
    • tree_visitor.on_stop()
    • tree_visitor.on_tree()
• besmarts.core.trees module
  • tree_index
    • tree_index.above
    • tree_index.below
    • tree_index.copy()
    • tree_index.node_add()
    • tree_index.node_add_below()
    • tree_index.node_remove()
    • tree_index.node_remove_by_name()
    • tree_index.nodes
  • tree_index_copy()
  • tree_index_node_add()
  • tree_index_node_depth()
  • tree_index_node_remove()
  • tree_index_node_remove_by_name()
  • tree_index_roots()
  • tree_node
    • tree_node.category
    • tree_node.copy()
    • tree_node.index
    • tree_node.name
    • tree_node.type
  • tree_node_copy()