Index

A

a (besmarts.core.mapper.map_vertices_ctx attribute), [1] A (besmarts.core.mapper.union_ctx attribute), [1] (besmarts.core.splits.process_split_ctx attribute), [1] (besmarts.core.topology.transcode_topology attribute), [1] above (besmarts.core.trees.tree_index attribute), [1] accept() (besmarts.core.compute.Listener method), [1] accept_connection() (besmarts.core.compute.Server method), [1] accepter() (besmarts.core.compute.Server method), [1] add_graph_codec() (besmarts.core.codecs.graph_codec_chain method), [1] align_score() (in module besmarts.core.mapper), [1] align_score_ctx (class in besmarts.core.mapper), [1] align_score_parallel() (in module besmarts.core.mapper), [1] all() (besmarts.core.arrays.bitvec method), [1] (besmarts.core.chem.bechem method), [1] angle() (in module besmarts.core.geometry), [1] angle_assignment_float (class in besmarts.core.assignments), [1] angle_assignment_float_matrix (class in besmarts.core.assignments), [1] angle_assignment_str (class in besmarts.core.assignments), [1] angle_topology() (in module besmarts.core.topology), [1] angular_momentum() (in module besmarts.mechanics.vibration) any() (besmarts.core.arrays.bitvec method), [1] (besmarts.core.chem.bechem method), [1] append() (in module besmarts.core.logs), [1] argmax() (in module besmarts.core.arrays), [1] argmin() (in module besmarts.core.arrays), [1] argsort() (in module besmarts.core.arrays), [1] AROMATIC (besmarts.core.primitives.primitive_key attribute), [1] array_abs() (in module besmarts.core.arrays), [1] array_add() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_basis() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_cross() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_difference() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_distance() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_divide() (in module besmarts.core.arrays), [1] array_flatten_assignment() (in module besmarts.mechanics.objectives), [1] array_flatten_matrix_assignment() (in module besmarts.mechanics.objectives), [1] array_geom_energy() (in module besmarts.mechanics.objectives), [1] array_geom_energy_gradient() (in module besmarts.mechanics.objectives), [1] array_geom_force() (in module besmarts.mechanics.objectives), [1] array_geom_gradient() (in module besmarts.mechanics.objectives), [1] array_geom_hessian() (in module besmarts.mechanics.objectives), [1] array_inner_product() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_magnitude() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1]

array_mean() (in module besmarts.core.arrays), [1] array_multiply() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_outer_product() (in module besmarts.core.geometry), [1] array_round() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_scale() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] array_sum() (in module besmarts.core.arrays), [1] array_translate() (in module besmarts.core.arrays), [1] array_unit() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] assert_bonds() (in module besmarts.core.splits), [1] assign() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (besmarts.mechanics.force_pairwise.chemical_model_procedure_antechamber method), [1] (besmarts.mechanics.force_pairwise.chemical_model_procedure_combine_coulomb method), [1] (besmarts.mechanics.force_pairwise.chemical_model_procedure_combine_lj_lorentz_berthelot method), [1] (besmarts.mechanics.molecular_models.chemical_model_procedure method), [1] (besmarts.mechanics.molecular_models.chemical_model_procedure_smarts_assignment method), [1] (besmarts.mechanics.molecular_models.physical_model_procedure method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assign_angles() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assign_atoms() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assign_bonds() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assign_impropers() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] assign_outofplanes() (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assign_torsions() (besmarts.assign.hierarchy_assign_native.smarts_hierarchy_assignment_native method), [1] (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assignment_rdkit method), [1], [2] (besmarts.core.assignments.smarts_hierarchy_assignment method), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] assignments (besmarts.core.assignments.structure_assignment_group attribute), [1] assn (besmarts.core.clusters.clustering_collect_split_candidates_ctx attribute), [1] atom_assignment_float (class in besmarts.core.assignments), [1] atom_assignment_str (class in besmarts.core.assignments), [1] atom_encode_smarts() (besmarts.core.graph_visitors.smiles_visitor method), [1] atom_topology() (in module besmarts.core.topology), [1] AutoProxy() (in module besmarts.core.compute), [1]

B

b (besmarts.core.mapper.map_vertices_ctx attribute), [1] B (besmarts.core.topology.transcode_topology attribute), [1] b2matrix() (in module besmarts.core.assignments), [1] b_matrix() (in module besmarts.core.array_numpy), [1] backmap (besmarts.core.clusters.clustering_collect_split_candidates_ctx attribute), [1] BaseProxy (class in besmarts.core.compute), [1] batched() (in module besmarts.core.arrays), [1] bechem (class in besmarts.core.chem), [1] bechem_add() (in module besmarts.core.chem), [1] bechem_align_score() (in module besmarts.core.chem), [1] bechem_all() (in module besmarts.core.chem), [1] bechem_and() (in module besmarts.core.chem), [1] bechem_and_conditional() (in module besmarts.core.chem), [1] bechem_any() (in module besmarts.core.chem), [1] bechem_bits() (in module besmarts.core.chem), [1] bechem_bits_max() (in module besmarts.core.chem), [1] bechem_check_sane_compare() (in module besmarts.core.chem), [1] bechem_clear() (in module besmarts.core.chem), [1] bechem_copy() (in module besmarts.core.chem), [1] bechem_disable() (in module besmarts.core.chem), [1] bechem_dispatch_op() (in module besmarts.core.chem), [1] bechem_enable() (in module besmarts.core.chem), [1] bechem_fill() (in module besmarts.core.chem), [1] bechem_get() (in module besmarts.core.chem), [1] bechem_iadd() (in module besmarts.core.chem), [1] bechem_iand() (in module besmarts.core.chem), [1] bechem_identity() (in module besmarts.core.chem), [1] bechem_ior() (in module besmarts.core.chem), [1] bechem_is_fragment() (in module besmarts.core.chem), [1] bechem_is_null() (in module besmarts.core.chem), [1] bechem_is_valid() (in module besmarts.core.chem), [1] bechem_isubtract() (in module besmarts.core.chem), [1] bechem_iter() (in module besmarts.core.chem), [1] bechem_ixor() (in module besmarts.core.chem), [1] bechem_neg() (in module besmarts.core.chem), [1] bechem_or() (in module besmarts.core.chem), [1] bechem_recurse_fields() (in module besmarts.core.chem), [1] bechem_reduce() (in module besmarts.core.chem), [1] bechem_reduce_longest() (in module besmarts.core.chem), [1] bechem_subtract() (in module besmarts.core.chem), [1] bechem_subtract_conditional() (in module besmarts.core.chem), [1] bechem_to_fragments() (in module besmarts.core.chem), [1] bechem_xor() (in module besmarts.core.chem), [1] below (besmarts.core.trees.tree_index attribute), [1] bes (besmarts.core.mapper.filter_contains_ctx attribute), [1] besmarts module, [1], [2], [3] besmarts.assign module, [1] besmarts.assign.hierarchy_assign_native module, [1] besmarts.assign.hierarchy_assign_rdkit module, [1], [2] besmarts.cluster module besmarts.cluster.cluster_assignment module, [1] besmarts.cluster.cluster_objective module, [1] besmarts.cluster.cluster_optimization module, [1] besmarts.codecs module, [1] besmarts.codecs.codec_native module, [1] besmarts.codecs.codec_rdkit module, [1], [2] besmarts.core module, [1], [2] besmarts.core.array_numpy module, [1] besmarts.core.arrays module, [1] besmarts.core.assignments module, [1] besmarts.core.chem module, [1] besmarts.core.clusters module, [1] besmarts.core.codecs module, [1] besmarts.core.compute module, [1] besmarts.core.configs module, [1] besmarts.core.db module, [1] besmarts.core.geometry module, [1] besmarts.core.graph_visitors module, [1] besmarts.core.graphs module, [1] besmarts.core.hierarchies module, [1] besmarts.core.hierarchy_merge module, [1] besmarts.core.logs module, [1] besmarts.core.mapper module, [1] besmarts.core.optimization module, [1] besmarts.core.perception module, [1]

besmarts.core.primitives module, [1] besmarts.core.resolve module besmarts.core.returns module, [1] besmarts.core.rulesets module besmarts.core.splits module, [1] besmarts.core.topology module, [1] besmarts.core.tree_iterators module, [1] besmarts.core.tree_visitors module, [1] besmarts.core.trees module, [1] besmarts.mechanics module, [1], [2] besmarts.mechanics.fits module besmarts.mechanics.force_harmonic module, [1] besmarts.mechanics.force_pairwise module, [1] besmarts.mechanics.force_periodic module, [1] besmarts.mechanics.hessians module besmarts.mechanics.masses module, [1] besmarts.mechanics.molecular_models module, [1] besmarts.mechanics.objectives module, [1] besmarts.mechanics.optimizers_scipy module, [1], [2], [3] besmarts.mechanics.smirnoff_models module, [1] besmarts.mechanics.smirnoff_xml module, [1] besmarts.mechanics.vibration module besmarts.perception module besmarts.perception.perception_rdkit module besmarts.sample module besmarts.worker module, [1] bit_search_limit (besmarts.core.configs.smarts_splitter_config attribute), [1] bit_search_min (besmarts.core.configs.smarts_splitter_config attribute), [1] bits() (besmarts.core.arrays.bitvec method), [1] (besmarts.core.chem.bechem method), [1] bits_max() (besmarts.core.chem.bechem method), [1] bitvec (class in besmarts.core.arrays), [1] bitvec_all() (in module besmarts.core.arrays), [1] bitvec_and() (in module besmarts.core.arrays), [1] bitvec_any() (in module besmarts.core.arrays), [1] bitvec_bits() (in module besmarts.core.arrays), [1] bitvec_clear() (in module besmarts.core.arrays), [1] bitvec_copy() (in module besmarts.core.arrays), [1] bitvec_equal() (in module besmarts.core.arrays), [1] bitvec_explicit_flip() (in module besmarts.core.arrays), [1] bitvec_is_inverted() (in module besmarts.core.arrays), [1] bitvec_is_null() (in module besmarts.core.arrays), [1] bitvec_not() (in module besmarts.core.arrays), [1] bitvec_off() (in module besmarts.core.arrays), [1] bitvec_off_first() (in module besmarts.core.arrays), [1] bitvec_on() (in module besmarts.core.arrays), [1] bitvec_on_first() (in module besmarts.core.arrays), [1] bitvec_or() (in module besmarts.core.arrays), [1] bitvec_reduce() (in module besmarts.core.arrays), [1] bitvec_subset() (in module besmarts.core.arrays), [1] bitvec_subtract() (in module besmarts.core.arrays), [1] bitvec_sum() (in module besmarts.core.arrays), [1] bitvec_superset() (in module besmarts.core.arrays), [1] bitvec_xor() (in module besmarts.core.arrays), [1] bmatrix() (in module besmarts.core.array_numpy), [1] (in module besmarts.core.assignments), [1] bmatrix_angles() (in module besmarts.core.array_numpy), [1] bmatrix_bonds() (in module besmarts.core.array_numpy), [1] bmatrix_dense() (in module besmarts.core.array_numpy), [1] bmatrix_ic() (in module besmarts.core.array_numpy), [1] bmatrix_outofplanes() (in module besmarts.core.array_numpy), [1] bmatrix_pairs() (in module besmarts.core.array_numpy), [1] bmatrix_torsions() (in module besmarts.core.array_numpy), [1] bond() (in module besmarts.core.geometry), [1] bond_assignment_float (class in besmarts.core.assignments), [1] bond_assignment_float_matrix (class in besmarts.core.assignments), [1] bond_assignment_str (class in besmarts.core.assignments), [1] bond_encode_smarts() (besmarts.core.graph_visitors.smiles_visitor method), [1] BOND_ORDER (besmarts.core.primitives.primitive_key attribute), [1] BOND_RING (besmarts.core.primitives.primitive_key attribute), [1] bond_topology() (in module besmarts.core.topology), [1] bounds (besmarts.core.optimization.optimization_strategy attribute) branch_depth_limit (besmarts.core.configs.smarts_splitter_config attribute), [1] branch_depth_min (besmarts.core.configs.smarts_splitter_config attribute), [1] branch_limit (besmarts.core.configs.smarts_splitter_config attribute), [1] branch_min (besmarts.core.configs.smarts_splitter_config attribute), [1] build_steps() (besmarts.core.optimization.optimization_strategy method), [1] (besmarts.mechanics.fits.forcefield_optimization_strategy method)

C

cache (besmarts.core.graphs.graph attribute), [1] (besmarts.core.graphs.structure attribute), [1] (besmarts.core.graphs.subgraph attribute), [1] calc_tier_distributed() (in module besmarts.mechanics.fits) callback() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] category (besmarts.core.trees.tree_node attribute), [1] center_of_mass() (in module besmarts.mechanics.vibration) cg (besmarts.core.mapper.map_vertices_ctx attribute), [1] chain_topology() (in module besmarts.core.topology), [1] check_lbls_data_selections_equal() (in module besmarts.core.clusters), [1] chemical_model (class in besmarts.mechanics.molecular_models), [1] chemical_model_angle_harmonic() (in module besmarts.mechanics.force_harmonic), [1] chemical_model_angle_harmonic_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_bond_harmonic() (in module besmarts.mechanics.force_harmonic), [1] chemical_model_bond_harmonic_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_coulomb() (in module besmarts.mechanics.force_pairwise), [1] chemical_model_dihedral_periodic_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_electrostatics_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_iter_smarts_hierarchies() (in module besmarts.mechanics.molecular_models), [1] chemical_model_iter_smarts_hierarchies_nodes() (in module besmarts.mechanics.molecular_models), [1] chemical_model_lennard_jones() (in module besmarts.mechanics.force_pairwise), [1] chemical_model_mass_smarts() (in module besmarts.mechanics.masses), [1] chemical_model_outofplane_periodic() (in module besmarts.mechanics.force_periodic), [1] chemical_model_outofplane_periodic_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_procedure (class in besmarts.mechanics.molecular_models), [1] chemical_model_procedure_antechamber (class in besmarts.mechanics.force_pairwise), [1] chemical_model_procedure_combine_coulomb (class in besmarts.mechanics.force_pairwise), [1] chemical_model_procedure_combine_lj_lorentz_berthelot (class in besmarts.mechanics.force_pairwise), [1] chemical_model_procedure_smarts_assignment (class in besmarts.mechanics.molecular_models), [1] chemical_model_smarts_hierarchy_add_node() (in module besmarts.mechanics.molecular_models), [1] chemical_model_smarts_hierarchy_copy_node() (in module besmarts.mechanics.molecular_models), [1] chemical_model_smarts_hierarchy_remove_node() (in module besmarts.mechanics.molecular_models), [1] chemical_model_to_xml_dict() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_torsion_periodic() (in module besmarts.mechanics.force_periodic), [1] chemical_model_torsion_periodic_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_model_vdw_smirnoff() (in module besmarts.mechanics.smirnoff_models), [1] chemical_objective() (in module besmarts.mechanics.fits) chemical_system (class in besmarts.mechanics.molecular_models), [1] chemical_system_cluster_angles() (in module besmarts.mechanics.fits) chemical_system_cluster_bonds() (in module besmarts.mechanics.fits) chemical_system_cluster_data() (in module besmarts.mechanics.fits) chemical_system_cluster_force_constants() (in module besmarts.mechanics.fits) chemical_system_cluster_geom() (in module besmarts.mechanics.fits) chemical_system_get_angle_means() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_angles() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_bond_length_means() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_bond_lengths() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_ic_measure() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_ic_measure_means() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_node_hierarchy() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_node_model() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_smarts_node() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_value() (in module besmarts.mechanics.molecular_models), [1] chemical_system_get_value_list() (in module besmarts.mechanics.molecular_models), [1] chemical_system_groupby_names() (in module besmarts.mechanics.molecular_models), [1] chemical_system_iter_keys() (in module besmarts.mechanics.molecular_models), [1] chemical_system_iter_smarts_hierarchies() (in module besmarts.mechanics.molecular_models), [1] chemical_system_iter_smarts_hierarchies_nodes() (in module besmarts.mechanics.molecular_models), [1] chemical_system_print() (in module besmarts.mechanics.molecular_models), [1] chemical_system_reset_angles() (in module besmarts.mechanics.molecular_models), [1] chemical_system_reset_bond_lengths() (in module besmarts.mechanics.molecular_models), [1] chemical_system_set_value() (in module besmarts.mechanics.molecular_models), [1] chemical_system_set_value_list() (in module besmarts.mechanics.molecular_models), [1] chemical_system_smarts_complexity() (in module besmarts.mechanics.molecular_models), [1] chemical_system_smarts_hierarchy_add_node() (in module besmarts.mechanics.molecular_models), [1] chemical_system_smarts_hierarchy_get_node_keys() (in module besmarts.mechanics.molecular_models), [1] chemical_system_to_physical_system() (in module besmarts.mechanics.molecular_models), [1] CHIRALITY (besmarts.core.primitives.primitive_key attribute), [1] clear() (besmarts.core.arrays.bitvec method), [1] (besmarts.core.chem.bechem method), [1] clear_iqueue() (besmarts.core.compute.workspace_local method), [1] clear_oqueue() (besmarts.core.compute.workspace_local method), [1] Client() (in module besmarts.core.compute), [1] close() (besmarts.core.compute.workqueue_local method), [1] (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_remote method), [1] close_pools() (in module besmarts.core.compute), [1]

close_workspaces() (in module besmarts.core.compute), [1] cluster_classifications() (in module besmarts.cluster.cluster_optimization), [1] cluster_means() (in module besmarts.cluster.cluster_optimization), [1] clustering_assign() (in module besmarts.core.clusters), [1] clustering_build_assignment_mappings() (in module besmarts.core.clusters), [1] clustering_build_label_mappings() (in module besmarts.core.clusters), [1] clustering_build_ordinal_mappings() (in module besmarts.core.clusters), [1] clustering_collect_split_candidates_ctx (class in besmarts.core.clusters), [1] clustering_collect_split_candidates_serial() (in module besmarts.core.clusters), [1] clustering_collect_split_candidates_single() (in module besmarts.core.clusters), [1] clustering_collect_split_candidates_single_distributed() (in module besmarts.core.clusters), [1] clustering_collect_structures() (in module besmarts.core.clusters), [1] clustering_initial_conditions() (in module besmarts.core.clusters), [1] clustering_node_remove_by_name() (in module besmarts.core.clusters), [1] clustering_objective (class in besmarts.core.clusters), [1] clustering_objective_classification (class in besmarts.cluster.cluster_objective), [1] clustering_objective_mean_separation (class in besmarts.cluster.cluster_objective), [1] clustering_objective_variance_separation (class in besmarts.cluster.cluster_objective), [1] clustering_update_assignments() (in module besmarts.core.clusters), [1] collect() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] columns (besmarts.core.assignments.graph_db_row attribute), [1] compute() (besmarts.cluster.cluster_assignment.smiles_assignment_float method), [1] (besmarts.cluster.cluster_assignment.smiles_assignment_str method), [1] (besmarts.core.assignments.smiles_assignment method), [1] compute_config (class in besmarts.mechanics.fits) compute_config_energy_sapt (class in besmarts.mechanics.fits) compute_config_energy_total (class in besmarts.mechanics.fits) compute_config_gradient (class in besmarts.mechanics.fits) compute_config_hessian (class in besmarts.mechanics.fits) compute_config_penalty (class in besmarts.mechanics.fits) compute_config_position (class in besmarts.mechanics.fits) compute_diff() (besmarts.mechanics.fits.objective_config method) (besmarts.mechanics.fits.objective_config_energy_sapt method) (besmarts.mechanics.fits.objective_config_energy_total method) (besmarts.mechanics.fits.objective_config_gradient method) (besmarts.mechanics.fits.objective_config_hessian method) (besmarts.mechanics.fits.objective_config_penalty method) compute_gradient() (besmarts.mechanics.fits.objective_config method) (besmarts.mechanics.fits.objective_config_energy_sapt method) (besmarts.mechanics.fits.objective_config_energy_total method) (besmarts.mechanics.fits.objective_config_gradient method) (besmarts.mechanics.fits.objective_config_hessian method) (besmarts.mechanics.fits.objective_config_penalty method) compute_hessian() (besmarts.mechanics.fits.objective_config_penalty method) compute_remote() (in module besmarts.core.compute), [1] config (besmarts.core.mapper.union_ctx attribute), [1] connect (besmarts.core.topology.structure_topology attribute), [1] connect() (besmarts.core.compute.workqueue_remote method), [1] (besmarts.core.compute.workspace_remote method), [1] Connection (class in besmarts.core.compute), [1] CONNECTIVITY_RING (besmarts.core.primitives.primitive_key attribute), [1] CONNECTIVITY_TOTAL (besmarts.core.primitives.primitive_key attribute), [1] converteig() (in module besmarts.mechanics.vibration) coords (besmarts.core.assignments.graph_db_selection attribute), [1] copy() (besmarts.cluster.cluster_assignment.smiles_assignment_float method), [1] (besmarts.cluster.cluster_assignment.smiles_assignment_str method), [1] (besmarts.core.arrays.bitvec method), [1] (besmarts.core.assignments.graph_assignment method), [1] (besmarts.core.assignments.smiles_assignment method), [1] (besmarts.core.assignments.smiles_assignment_group method), [1] (besmarts.core.assignments.structure_assignment_group method), [1] (besmarts.core.chem.bechem method), [1] (besmarts.core.configs.mapper_config method), [1] (besmarts.core.configs.smarts_extender_config method), [1] (besmarts.core.configs.smarts_perception_config method), [1] (besmarts.core.configs.smarts_splitter_config method), [1] (besmarts.core.hierarchies.smarts_hierarchy method), [1] (besmarts.core.hierarchies.structure_hierarchy method), [1] (besmarts.core.optimization.optimization_step method), [1] (besmarts.core.trees.tree_index method), [1] (besmarts.core.trees.tree_node method), [1] (besmarts.mechanics.molecular_models.topology_term method), [1] count_carbon_smiles() (besmarts.core.codecs.primitive_codec_element method), [1] count_charge_smiles() (besmarts.core.codecs.primitive_codec_formal_charge method), [1] count_element_smiles() (besmarts.core.codecs.primitive_codec_element method), [1] count_hydrogen_smiles() (besmarts.core.codecs.primitive_codec_hydrogen method), [1] cout_logger() (in module besmarts.core.logs), [1] create() (besmarts.core.compute.workspace_manager method), [1]

D

db_dict (class in besmarts.core.db), [1] db_graph_read() (in module besmarts.core.db), [1] db_graph_write() (in module besmarts.core.db), [1] db_intvec_create() (in module besmarts.core.db), [1] db_intvec_delete() (in module besmarts.core.db), [1] db_intvec_read() (in module besmarts.core.db), [1] db_intvec_read_list() (in module besmarts.core.db), [1] db_intvec_write() (in module besmarts.core.db), [1] db_structure_write() (in module besmarts.core.db), [1] db_structure_write_distributed() (in module besmarts.core.db), [1] decode_int() (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_ring_smallest method), [1] (besmarts.core.primitives.primitive_codec method), [1] decode_smarts() (besmarts.core.codecs.primitive_codec_aromatic method), [1] (besmarts.core.codecs.primitive_codec_bond_order method), [1] (besmarts.core.codecs.primitive_codec_bond_ring method), [1] (besmarts.core.codecs.primitive_codec_chirality method), [1] (besmarts.core.codecs.primitive_codec_connectivity_ring method), [1] (besmarts.core.codecs.primitive_codec_connectivity_total method), [1] (besmarts.core.codecs.primitive_codec_element method), [1] (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_hydrogen method), [1] (besmarts.core.codecs.primitive_codec_ring_smallest method), [1] (besmarts.core.codecs.primitive_codec_unit method), [1] (besmarts.core.codecs.primitive_codec_valence method), [1] (besmarts.core.codecs.primitive_codec_variable method), [1] (besmarts.core.primitives.primitive_codec method), [1] decode_smiles() (besmarts.codecs.codec_rdkit.primitive_codec_aromatic_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_bond_order_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_bond_ring_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_chirality_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_connectivity_ring_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_connectivity_total_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_element_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_formal_charge_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_hydrogen_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_ring_smallest_rdkit method), [1], [2] (besmarts.codecs.codec_rdkit.primitive_codec_valence_rdkit method), [1], [2] (besmarts.core.codecs.primitive_codec_link_dst method), [1] (besmarts.core.codecs.primitive_codec_link_src method), [1] (besmarts.core.codecs.primitive_codec_unit method), [1] (besmarts.core.codecs.primitive_codec_unit_index method), [1] (besmarts.core.codecs.primitive_codec_variable method), [1] (besmarts.core.primitives.primitive_codec method), [1]

decode_supersmarts() (besmarts.core.codecs.primitive_codec_link_dst method), [1] (besmarts.core.codecs.primitive_codec_link_src method), [1] (besmarts.core.primitives.primitive_codec method), [1] decode_supersmiles() (besmarts.core.codecs.primitive_codec_unit_index method), [1] decref() (besmarts.core.compute.Server method), [1] delete_intvec() (besmarts.core.db.db_dict method), [1] depth_max (besmarts.core.configs.smarts_extender_config attribute), [1] depth_min (besmarts.core.configs.smarts_extender_config attribute), [1] difference() (in module besmarts.core.mapper), [1] disable() (besmarts.core.chem.bechem method), [1] dispatch() (in module besmarts.core.compute), [1] dispatch_boolean_op() (in module besmarts.core.mapper), [1] dlc_matrix() (in module besmarts.core.array_numpy), [1] dlcmatrix() (in module besmarts.core.array_numpy), [1] dlcmatrix_project_gradients() (in module besmarts.core.array_numpy), [1] DONE (besmarts.core.compute.workspace_status attribute), [1] dprint() (in module besmarts.core.compute), [1] (in module besmarts.core.logs), [1] (in module besmarts.core.splits), [1]

E

edge() (in module besmarts.core.graphs), [1] edges (besmarts.core.graphs.graph attribute), [1] (besmarts.core.graphs.structure attribute), [1] (besmarts.core.graphs.subgraph attribute), [1] ELEMENT (besmarts.core.primitives.primitive_key attribute), [1] EMPTY (besmarts.core.compute.workspace_status attribute), [1] enable() (besmarts.core.chem.bechem method), [1] encode_int() (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_ring_smallest method), [1] (besmarts.core.primitives.primitive_codec method), [1] encode_smarts() (besmarts.core.codecs.primitive_codec_aromatic method), [1] (besmarts.core.codecs.primitive_codec_bond_order method), [1] (besmarts.core.codecs.primitive_codec_bond_ring method), [1] (besmarts.core.codecs.primitive_codec_chirality method), [1] (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_ring_smallest method), [1] (besmarts.core.codecs.primitive_codec_variable method), [1] (besmarts.core.primitives.primitive_codec method), [1] encode_smiles() (besmarts.core.codecs.primitive_codec_bond_order method), [1] (besmarts.core.codecs.primitive_codec_chirality method), [1] (besmarts.core.codecs.primitive_codec_element method), [1] (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_hydrogen method), [1] (besmarts.core.codecs.primitive_codec_variable method), [1] (besmarts.core.primitives.primitive_codec method), [1]

encode_supersmarts() (besmarts.core.codecs.primitive_codec_link_dst method), [1] (besmarts.core.codecs.primitive_codec_link_src method), [1] (besmarts.core.codecs.primitive_codec_unit method), [1] (besmarts.core.codecs.primitive_codec_unit_index method), [1] (besmarts.core.primitives.primitive_codec method), [1] encoding_visitor (class in besmarts.core.graph_visitors), [1] energy_function_coulomb_mix() (in module besmarts.mechanics.force_pairwise), [1] energy_function_lennard_jones_combined() (in module besmarts.mechanics.force_pairwise), [1] energy_function_periodic_cosine_2term() (in module besmarts.mechanics.force_periodic), [1] energy_function_spring() (in module besmarts.mechanics.force_harmonic), [1] enter_graph() (besmarts.core.graph_visitors.graph_visitor method), [1] (in module besmarts.core.graph_visitors), [1] entries (besmarts.core.assignments.graph_db attribute), [1] equality (besmarts.core.mapper.map_vertices_ctx attribute), [1] extender (besmarts.core.configs.smarts_perception_config attribute), [1]

F

FAIL (besmarts.core.returns.return_status attribute), [1] fail() (in module besmarts.core.returns), [1] ff_obj() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] ff_optimize() (in module besmarts.mechanics.fits) file_logger() (in module besmarts.core.logs), [1] fill() (besmarts.core.chem.bechem method), [1] filter_above (besmarts.core.optimization.optimization_strategy attribute) filter_contains() (in module besmarts.core.mapper), [1] filter_contains_ctx (class in besmarts.core.mapper), [1] filter_contains_parallel() (in module besmarts.core.mapper), [1] find_branches() (in module besmarts.core.graph_visitors), [1] find_successful_candidates_distributed() (in module besmarts.core.clusters), [1] find_unsigned_typecode_min() (in module besmarts.core.arrays), [1] finite_difference_central_2() (in module besmarts.mechanics.fits) finite_difference_forward_1() (in module besmarts.mechanics.fits) fit() (in module besmarts.mechanics.fits) fit_grad_gdb() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] flatten_list() (in module besmarts.core.arrays), [1] force_function_coulomb_mix() (in module besmarts.mechanics.force_pairwise), [1] force_function_lennard_jones_combined() (in module besmarts.mechanics.force_pairwise), [1]

force_function_periodic_cosine_2term() (in module besmarts.mechanics.force_periodic), [1] force_function_spring() (in module besmarts.mechanics.force_harmonic), [1] force_gradient_function_coulomb_mix() (in module besmarts.mechanics.force_pairwise), [1] force_gradient_function_lennard_jones_combined() (in module besmarts.mechanics.force_pairwise), [1] force_gradient_function_periodic_cosine_2term() (in module besmarts.mechanics.force_periodic), [1] force_gradient_function_spring() (in module besmarts.mechanics.force_harmonic), [1] force_gradient_system_coulomb_mix() (in module besmarts.mechanics.force_pairwise), [1] force_gradient_system_lennard_jones_combined() (in module besmarts.mechanics.force_pairwise), [1] force_gradient_system_periodic_cosine_2term() (in module besmarts.mechanics.force_periodic), [1] force_gradient_system_spring() (in module besmarts.mechanics.force_harmonic), [1] force_system_coulomb_mix() (in module besmarts.mechanics.force_pairwise), [1] force_system_lennard_jones_combined() (in module besmarts.mechanics.force_pairwise), [1] force_system_periodic_cosine_2term() (in module besmarts.mechanics.force_periodic), [1] force_system_spring() (in module besmarts.mechanics.force_harmonic), [1] forcefield (class in besmarts.mechanics.molecular_models), [1] forcefield_metadata (class in besmarts.mechanics.molecular_models), [1] forcefield_optimization_strategy (class in besmarts.mechanics.fits) forcefield_optimization_strategy_build_macro_iterations() (in module besmarts.mechanics.fits) forcefield_optimization_strategy_default() (in module besmarts.mechanics.fits) FORMAL_CHARGE (besmarts.core.primitives.primitive_key attribute), [1] format_array() (in module besmarts.cluster.cluster_objective), [1]

G

g_matrix() (in module besmarts.core.array_numpy), [1] gcd (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assign_ctx attribute), [1], [2] gdb_to_physical_systems() (in module besmarts.mechanics.fits) generate_candidates() (in module besmarts.mechanics.fits) get() (besmarts.core.compute.myiqueue method), [1] (besmarts.core.compute.myqueue method), [1] (besmarts.core.compute.shm_local method), [1] get_assns() (in module besmarts.core.clusters), [1] get_edge_frags() (in module besmarts.core.resolve) get_indices() (in module besmarts.codecs.codec_rdkit), [1], [2] get_iqueue() (besmarts.core.compute.workqueue_manager method), [1] (besmarts.core.compute.workspace method), [1] (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_remote method), [1] get_objective() (in module besmarts.core.clusters), [1] get_oqueue() (besmarts.core.compute.workqueue_manager method), [1] (besmarts.core.compute.workspace method), [1] (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_remote method), [1] get_rqueue() (besmarts.core.compute.workqueue_manager method), [1] (besmarts.core.compute.workspace method), [1] get_state() (besmarts.core.compute.workqueue method), [1] (besmarts.core.compute.workqueue_local method), [1] (besmarts.core.compute.workqueue_manager method), [1] (besmarts.core.compute.workqueue_remote method), [1] (besmarts.core.compute.workspace method), [1] (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_manager method), [1] (besmarts.core.compute.workspace_remote method), [1] get_status() (besmarts.core.compute.workqueue method), [1] (besmarts.core.compute.workqueue_remote method), [1] (besmarts.core.compute.workspace method), [1] (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_manager method), [1] (besmarts.core.compute.workspace_remote method), [1] get_tags() (in module besmarts.codecs.codec_rdkit), [1], [2] get_task() (besmarts.mechanics.fits.objective_config method) (besmarts.mechanics.fits.objective_config_energy_sapt method) (besmarts.mechanics.fits.objective_config_energy_total method) (besmarts.mechanics.fits.objective_config_gradient method) (besmarts.mechanics.fits.objective_config_hessian method) (besmarts.mechanics.fits.objective_config_penalty method) (besmarts.mechanics.fits.objective_config_position method) get_term_labels() (besmarts.mechanics.molecular_models.chemical_model_procedure method), [1] (besmarts.mechanics.molecular_models.chemical_model_procedure_smarts_assignment method), [1] (besmarts.mechanics.molecular_models.physical_model_procedure method), [1] get_term_values() (besmarts.mechanics.molecular_models.chemical_model_procedure method), [1] (besmarts.mechanics.molecular_models.chemical_model_procedure_smarts_assignment method), [1] (besmarts.mechanics.molecular_models.physical_model_procedure method), [1] get_threads() (besmarts.core.compute.workqueue_local method), [1] get_workspaces() (besmarts.core.compute.workqueue method), [1] (besmarts.core.compute.workqueue_local method), [1] (besmarts.core.compute.workqueue_remote method), [1] (besmarts.core.compute.workspace_manager method), [1] ginverse() (in module besmarts.core.array_numpy), [1] gradient_cartesian_to_internal_array() (in module besmarts.core.array_numpy), [1] gradient_cartesian_to_internal_matrix() (in module besmarts.core.array_numpy), [1] gram_schmidt() (in module besmarts.mechanics.vibration) graph (besmarts.core.assignments.graph_assignment attribute), [1] (besmarts.core.assignments.graph_assignment_float attribute), [1] (besmarts.core.assignments.graph_assignment_float_matrix attribute), [1] (class in besmarts.core.graphs), [1] graph_all() (in module besmarts.core.graphs), [1] graph_angles() (in module besmarts.core.graphs), [1] graph_any() (in module besmarts.core.graphs), [1] graph_as_structure() (in module besmarts.core.graphs), [1] graph_as_subgraph() (in module besmarts.core.graphs), [1] graph_assignment (class in besmarts.core.assignments), [1] graph_assignment_copy() (in module besmarts.core.assignments), [1] graph_assignment_float (class in besmarts.core.assignments), [1] graph_assignment_float_matrix (class in besmarts.core.assignments), [1] graph_assignment_geometry_angle_matrix() (in module besmarts.core.assignments), [1] graph_assignment_geometry_angles() (in module besmarts.core.assignments), [1] graph_assignment_geometry_bond_matrix() (in module besmarts.core.assignments), [1] graph_assignment_geometry_bonds() (in module besmarts.core.assignments), [1] graph_assignment_geometry_outofplane_matrix() (in module besmarts.core.assignments), [1] graph_assignment_geometry_outofplanes() (in module besmarts.core.assignments), [1] graph_assignment_geometry_pair_matrix() (in module besmarts.core.assignments), [1] graph_assignment_geometry_pairs() (in module besmarts.core.assignments), [1] graph_assignment_geometry_position() (in module besmarts.core.assignments), [1] graph_assignment_geometry_torsion_matrix() (in module besmarts.core.assignments), [1] graph_assignment_geometry_torsions() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_angle_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_angles() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_bond_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_bonds() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_outofplane_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_outofplanes() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_pair_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_pairs() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_torsion_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian2_torsions() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_angle_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_angles() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_bond_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_bonds() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_distance_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_distances() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_outofplane_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_outofplanes() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_pair_matrix() (in module besmarts.core.assignments), [1]

graph_assignment_jacobian_pairs() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_torsion_matrix() (in module besmarts.core.assignments), [1] graph_assignment_jacobian_torsions() (in module besmarts.core.assignments), [1] graph_assignment_matrix_angle_indices() (in module besmarts.core.assignments), [1] graph_assignment_matrix_bond_indices() (in module besmarts.core.assignments), [1] graph_assignment_matrix_outofplane_indices() (in module besmarts.core.assignments), [1] graph_assignment_matrix_pair_indices() (in module besmarts.core.assignments), [1] graph_assignment_matrix_torsion_indices() (in module besmarts.core.assignments), [1] graph_assignment_to_format_xyz() (in module besmarts.core.assignments), [1] graph_assignment_to_graph_db_graph() (in module besmarts.core.assignments), [1] graph_assignment_to_graph_db_row() (in module besmarts.core.assignments), [1] graph_atoms() (in module besmarts.core.graphs), [1] graph_bits() (in module besmarts.core.graphs), [1] graph_bits_max() (in module besmarts.core.graphs), [1] graph_bonds() (in module besmarts.core.graphs), [1] graph_clear() (in module besmarts.core.graphs), [1] graph_codec (class in besmarts.core.codecs), [1] graph_codec_chain (class in besmarts.core.codecs), [1] graph_codec_native (class in besmarts.codecs.codec_native), [1] graph_codec_native_encode() (in module besmarts.codecs.codec_native), [1] graph_codec_native_load() (in module besmarts.codecs.codec_native), [1] graph_codec_native_read() (in module besmarts.codecs.codec_native), [1] graph_codec_native_save() (in module besmarts.codecs.codec_native), [1] graph_codec_native_write() (in module besmarts.codecs.codec_native), [1] graph_codec_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] graph_complexity() (in module besmarts.core.graphs), [1] graph_connection() (in module besmarts.core.graphs), [1] graph_connections() (in module besmarts.core.graphs), [1] graph_copy() (in module besmarts.core.graphs), [1] graph_db (class in besmarts.core.assignments), [1] graph_db_add_graph() (in module besmarts.core.assignments), [1] graph_db_add_multi_molecule() (in module besmarts.core.assignments), [1] graph_db_add_single_molecule_list() (in module besmarts.core.assignments), [1] graph_db_add_single_molecule_state() (in module besmarts.core.assignments), [1] graph_db_address (class in besmarts.core.assignments), [1] graph_db_column (class in besmarts.core.assignments), [1] graph_db_entry (class in besmarts.core.assignments), [1] graph_db_entry_add_table() (in module besmarts.core.assignments), [1] graph_db_get() (in module besmarts.core.assignments), [1] graph_db_get_entries() (in module besmarts.core.assignments), [1] graph_db_get_graphs() (in module besmarts.core.assignments), [1] graph_db_graph (class in besmarts.core.assignments), [1] graph_db_graph_to_graph_assignment() (in module besmarts.core.assignments), [1] graph_db_iter_values() (in module besmarts.core.assignments), [1] graph_db_row (class in besmarts.core.assignments), [1] graph_db_selection (class in besmarts.core.assignments), [1] graph_db_set_gradient() (in module besmarts.core.assignments), [1] graph_db_set_positions() (in module besmarts.core.assignments), [1] graph_db_table (class in besmarts.core.assignments), [1] graph_db_table_get_row_ids() (in module besmarts.core.assignments), [1] graph_decode() (besmarts.core.codecs.intvec_codec method), [1] graph_detect_rings() (in module besmarts.core.graphs), [1] graph_disable_primitives_atom() (in module besmarts.core.graphs), [1] graph_disable_primitives_bond() (in module besmarts.core.graphs), [1] graph_edges_copy() (in module besmarts.core.graphs), [1] graph_encode() (besmarts.core.codecs.intvec_codec method), [1] graph_fill() (in module besmarts.core.graphs), [1] graph_hash() (in module besmarts.core.graphs), [1] graph_invert() (in module besmarts.core.graphs), [1] graph_invert_all() (in module besmarts.core.graphs), [1] graph_invert_any() (in module besmarts.core.graphs), [1] graph_is_null() (in module besmarts.core.graphs), [1] graph_is_valid() (in module besmarts.core.graphs), [1] graph_load() (in module besmarts.codecs.codec_native), [1] graph_minimum_spanning_tree() (in module besmarts.core.graphs), [1] graph_nodes_copy() (in module besmarts.core.graphs), [1] graph_outofplanes() (in module besmarts.core.graphs), [1] graph_pairs() (in module besmarts.core.graphs), [1] graph_relabel_nodes() (in module besmarts.core.graphs), [1] graph_remove_hydrogen() (in module besmarts.core.graphs), [1] graph_remove_nodes() (in module besmarts.core.graphs), [1] graph_same() (in module besmarts.core.graphs), [1] graph_save() (in module besmarts.codecs.codec_native), [1] graph_set_primitives_atom() (in module besmarts.core.graphs), [1] graph_set_primitives_bond() (in module besmarts.core.graphs), [1] graph_shortest_path() (in module besmarts.core.graphs), [1] graph_shortest_path_length() (in module besmarts.core.graphs), [1] graph_shortest_paths() (in module besmarts.core.graphs), [1] graph_symbols() (in module besmarts.core.graphs), [1] graph_to_intvec() (in module besmarts.core.graphs), [1] graph_to_structure() (in module besmarts.core.graphs), [1] graph_to_structure_angles() (in module besmarts.core.graphs), [1] graph_to_structure_atoms() (in module besmarts.core.graphs), [1] graph_to_structure_bonds() (in module besmarts.core.graphs), [1] graph_to_structure_outofplanes() (in module besmarts.core.graphs), [1] graph_to_structure_pairs() (in module besmarts.core.graphs), [1] graph_to_structure_topology() (in module besmarts.core.graphs), [1] graph_to_structure_torsions() (in module besmarts.core.graphs), [1] graph_to_structures() (in module besmarts.core.graphs), [1] graph_to_subgraph() (in module besmarts.core.graphs), [1] graph_to_subgraphs() (in module besmarts.core.graphs), [1] graph_topology() (in module besmarts.core.graphs), [1] graph_torsions() (in module besmarts.core.graphs), [1] graph_visitor (class in besmarts.core.graph_visitors), [1] graphs (besmarts.core.assignments.graph_db attribute), [1] (besmarts.core.assignments.graph_db_table attribute), [1] group (besmarts.core.clusters.smarts_clustering attribute), [1] group_by_isomorphism() (in module besmarts.core.mapper), [1] group_prefix_str (besmarts.core.clusters.smarts_clustering attribute), [1] gs() (in module besmarts.mechanics.vibration) gs2() (in module besmarts.mechanics.vibration)

H

H (besmarts.core.mapper.map_vertices_ctx attribute), [1] handle_request() (besmarts.core.compute.Server method), [1] hash_fragment() (in module besmarts.core.resolve) hashes (besmarts.core.graphs.structure attribute), [1] hessian_frequencies() (in module besmarts.mechanics.hessians) hessian_modes() (in module besmarts.mechanics.vibration)

hessian_project_onto_ics() (in module besmarts.mechanics.hessians) hessian_transform() (in module besmarts.mechanics.hessians) hessian_transform_mass_weighted() (in module besmarts.mechanics.vibration) hier (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assign_ctx attribute), [1], [2] hierarchy (besmarts.core.clusters.smarts_clustering attribute), [1] HYDROGEN (besmarts.core.primitives.primitive_key attribute), [1]

I

icd (besmarts.core.mapper.union_ctx attribute), [1] INACTIVE (besmarts.core.compute.workspace_status attribute), [1] include_hydrogen (besmarts.core.configs.smarts_extender_config attribute), [1] incref() (besmarts.core.compute.Server method), [1] index (besmarts.core.hierarchies.smarts_hierarchy attribute), [1] (besmarts.core.hierarchies.structure_hierarchy attribute), [1] (besmarts.core.trees.tree_node attribute), [1] index_of() (in module besmarts.core.topology), [1] index_visitor (class in besmarts.core.graph_visitors), [1] inertia_tensor() (in module besmarts.mechanics.vibration) init_dihedral_common() (in module besmarts.mechanics.force_periodic), [1] insert_candidates() (in module besmarts.mechanics.fits) intersection() (in module besmarts.core.mapper), [1] intersection_conditional() (in module besmarts.core.mapper), [1] intersection_list() (in module besmarts.core.mapper), [1] intersection_list_dispatch() (in module besmarts.core.mapper), [1] intersection_list_parallel() (in module besmarts.core.mapper), [1] intvec (class in besmarts.core.arrays), [1] intvec_codec (class in besmarts.core.codecs), [1] intvec_codec_graph_decode() (in module besmarts.core.codecs), [1] intvec_codec_graph_decode_auto() (in module besmarts.core.codecs), [1]

intvec_codec_structure_decode() (in module besmarts.core.codecs), [1] intvec_codec_subgraph_decode() (in module besmarts.core.codecs), [1] inv() (besmarts.core.arrays.bitvec method), [1] INVALID (besmarts.core.compute.workspace_status attribute), [1] iqueue_get() (besmarts.core.compute.workspace_remote method), [1] iqueue_put() (besmarts.core.compute.workspace_remote method), [1] is_dihedral() (in module besmarts.core.geometry), [1] is_discrete() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] (besmarts.cluster.cluster_objective.clustering_objective_mean_separation method), [1] (besmarts.cluster.cluster_objective.clustering_objective_variance_separation method), [1] (besmarts.core.clusters.clustering_objective method), [1] is_done() (besmarts.cluster.cluster_optimization.optimization_iteration_default method), [1] (besmarts.core.optimization.optimization_iteration method), [1] (besmarts.core.optimization.optimization_strategy method), [1] is_isomorphic() (in module besmarts.core.mapper), [1] is_null() (besmarts.core.arrays.bitvec method), [1] (besmarts.core.chem.bechem method), [1] is_outofplane() (in module besmarts.core.geometry), [1] is_torsion() (in module besmarts.core.geometry), [1] is_valid() (besmarts.core.chem.bechem method), [1] isomorphic() (in module besmarts.core.mapper), [1]

J

jacobian2_angle() (in module besmarts.core.geometry), [1] jacobian2_angle_term_reduce() (in module besmarts.core.geometry), [1] jacobian2_angle_terms() (in module besmarts.core.geometry), [1] jacobian2_distance() (in module besmarts.core.geometry), [1] jacobian2_distance_terms() (in module besmarts.core.geometry), [1] jacobian2_outofplane() (in module besmarts.core.geometry), [1] jacobian2_reshape_to_matrix() (in module besmarts.core.geometry), [1] jacobian2_torsion() (in module besmarts.core.geometry), [1]

jacobian2_torsion_term_reduce() (in module besmarts.core.geometry), [1] jacobian2_torsion_terms() (in module besmarts.core.geometry), [1] jacobian_angle() (in module besmarts.core.geometry), [1] jacobian_distance() (in module besmarts.core.geometry), [1] jacobian_outofplane() (in module besmarts.core.geometry), [1] jacobian_outofplane_v2() (in module besmarts.core.geometry), [1] jacobian_torsion() (in module besmarts.core.geometry), [1] jacobian_torsion_v2() (in module besmarts.core.geometry), [1]

K

keep_below (besmarts.core.optimization.optimization_strategy attribute)

key_filter() (besmarts.mechanics.fits.objective_tier method)

L

labels (besmarts.mechanics.molecular_models.physical_model attribute), [1] LINK_DST (besmarts.core.primitives.primitive_key attribute), [1] LINK_SRC (besmarts.core.primitives.primitive_key attribute), [1] list_atom_primitives() (in module besmarts.codecs.codec_rdkit), [1], [2]

list_bond_primitives() (in module besmarts.codecs.codec_rdkit), [1], [2] list_implemented_atom_primitives() (besmarts.codecs.codec_rdkit.graph_codec_rdkit static method), [1], [2] list_implemented_bond_primitives() (besmarts.codecs.codec_rdkit.graph_codec_rdkit static method), [1], [2] Listener (class in besmarts.core.compute), [1] longest_path() (in module besmarts.core.graph_visitors), [1]

M

macro_accept_max_per_cluster (besmarts.core.optimization.optimization_strategy attribute) macro_accept_max_total (besmarts.core.optimization.optimization_strategy attribute) macro_iteration() (besmarts.core.optimization.optimization_strategy method), [1] (besmarts.mechanics.fits.forcefield_optimization_strategy method) make_branches() (in module besmarts.core.splits), [1] make_rdmol() (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] make_structure_assignment_type() (in module besmarts.core.assignments), [1] MakeProxyType() (in module besmarts.core.compute), [1] manager_connect() (in module besmarts.core.compute), [1] manager_remote_get_iqueue() (in module besmarts.core.compute), [1] manager_remote_get_iqueue_thread() (in module besmarts.core.compute), [1] manager_remote_get_oqueue() (in module besmarts.core.compute), [1] manager_remote_get_oqueue_thread() (in module besmarts.core.compute), [1] manager_remote_get_state() (in module besmarts.core.compute), [1] manager_remote_get_state_thread() (in module besmarts.core.compute), [1] manager_remote_get_status() (in module besmarts.core.compute), [1] manager_remote_get_status_thread() (in module besmarts.core.compute), [1] manager_remote_queue_put() (in module besmarts.core.compute), [1] manager_remote_queue_put_thread() (in module besmarts.core.compute), [1] manager_remote_queue_qsize() (in module besmarts.core.compute), [1] manager_remote_queue_qsize_thread() (in module besmarts.core.compute), [1] manager_start() (besmarts.core.compute.workspace_local method), [1] map_to() (in module besmarts.core.mapper), [1] map_to_descend() (in module besmarts.core.mapper), [1] map_vertices() (in module besmarts.core.mapper), [1] map_vertices_ctx (class in besmarts.core.mapper), [1] map_vertices_parallel() (in module besmarts.core.mapper), [1] mapped_type (class in besmarts.core.mapper), [1] mapper() (in module besmarts.core.mapper), [1] mapper_compose() (in module besmarts.core.mapper), [1] mapper_compose_graphs() (in module besmarts.core.mapper), [1] mapper_config (class in besmarts.core.configs), [1] mapper_force_equality() (in module besmarts.core.mapper), [1] mapper_force_subset() (in module besmarts.core.mapper), [1] mapper_invert() (in module besmarts.core.mapper), [1] mapper_match() (in module besmarts.core.mapper), [1] mappings (besmarts.core.clusters.smarts_clustering attribute), [1] match_group_assignments() (in module besmarts.core.clusters), [1] matched_idx (besmarts.core.splits.split_return_type attribute), [1] max_splits (besmarts.core.configs.smarts_splitter_config attribute), [1] maxbits (besmarts.core.arrays.bitvec attribute), [1] measure_angle() (in module besmarts.core.geometry), [1] measure_dihedral() (in module besmarts.core.geometry), [1] measure_distance() (in module besmarts.core.arrays), [1] (in module besmarts.core.geometry), [1] MERGE (besmarts.core.optimization.optimization_strategy attribute), [1] merge() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] (besmarts.cluster.cluster_objective.clustering_objective_mean_separation method), [1] (besmarts.cluster.cluster_objective.clustering_objective_variance_separation method), [1] (besmarts.core.clusters.clustering_objective method), [1] metadata (besmarts.mechanics.molecular_models.forcefield attribute), [1] micro_accept_max_per_cluster (besmarts.core.optimization.optimization_strategy attribute) micro_accept_max_total (besmarts.core.optimization.optimization_strategy attribute) mode_COM_to_xyz() (in module besmarts.mechanics.vibration) mode_to_xyz() (in module besmarts.mechanics.vibration) models (besmarts.mechanics.molecular_models.forcefield attribute), [1] MODIFY (besmarts.core.optimization.optimization_strategy attribute), [1] module besmarts, [1], [2], [3] besmarts.assign, [1] besmarts.assign.hierarchy_assign_native, [1] besmarts.assign.hierarchy_assign_rdkit, [1], [2] besmarts.cluster besmarts.cluster.cluster_assignment, [1] besmarts.cluster.cluster_objective, [1] besmarts.cluster.cluster_optimization, [1] besmarts.codecs, [1] besmarts.codecs.codec_native, [1] besmarts.codecs.codec_rdkit, [1], [2] besmarts.core, [1], [2] besmarts.core.array_numpy, [1] besmarts.core.arrays, [1] besmarts.core.assignments, [1] besmarts.core.chem, [1] besmarts.core.clusters, [1] besmarts.core.codecs, [1] besmarts.core.compute, [1] besmarts.core.configs, [1] besmarts.core.db, [1] besmarts.core.geometry, [1] besmarts.core.graph_visitors, [1] besmarts.core.graphs, [1] besmarts.core.hierarchies, [1] besmarts.core.hierarchy_merge, [1] besmarts.core.logs, [1] besmarts.core.mapper, [1] besmarts.core.optimization, [1] besmarts.core.perception, [1] besmarts.core.primitives, [1] besmarts.core.resolve besmarts.core.returns, [1] besmarts.core.rulesets besmarts.core.splits, [1] besmarts.core.topology, [1] besmarts.core.tree_iterators, [1] besmarts.core.tree_visitors, [1] besmarts.core.trees, [1] besmarts.mechanics, [1], [2] besmarts.mechanics.fits besmarts.mechanics.force_harmonic, [1] besmarts.mechanics.force_pairwise, [1] besmarts.mechanics.force_periodic, [1] besmarts.mechanics.hessians besmarts.mechanics.masses, [1] besmarts.mechanics.molecular_models, [1] besmarts.mechanics.objectives, [1] besmarts.mechanics.optimizers_scipy, [1], [2], [3] besmarts.mechanics.smirnoff_models, [1] besmarts.mechanics.smirnoff_xml, [1] besmarts.mechanics.vibration besmarts.perception besmarts.perception.perception_rdkit besmarts.sample besmarts.worker, [1]

myiqueue (class in besmarts.core.compute), [1] myqueue (class in besmarts.core.compute), [1]

N

n_body_topology() (in module besmarts.core.topology), [1] name (besmarts.core.trees.tree_node attribute), [1] neg() (in module besmarts.core.mapper), [1] next() (besmarts.cluster.cluster_optimization.optimization_iteration_default method), [1] (besmarts.core.optimization.optimization_iteration method), [1] node_add() (besmarts.core.trees.tree_index method), [1] node_add_below() (besmarts.core.trees.tree_index method), [1]

node_remove() (besmarts.core.trees.tree_index method), [1] node_remove_by_name() (besmarts.core.trees.tree_index method), [1] nodes (besmarts.core.graphs.graph attribute), [1] (besmarts.core.graphs.structure attribute), [1] (besmarts.core.graphs.subgraph attribute), [1] (besmarts.core.trees.tree_index attribute), [1] NONE (besmarts.core.returns.return_status attribute), [1] null_topology() (in module besmarts.core.topology), [1]

O

o (besmarts.core.mapper.map_vertices_ctx attribute), [1] objective_config (class in besmarts.mechanics.fits) objective_config_energy_sapt (class in besmarts.mechanics.fits) objective_config_energy_total (class in besmarts.mechanics.fits) objective_config_gradient (class in besmarts.mechanics.fits) objective_config_hessian (class in besmarts.mechanics.fits) objective_config_penalty (class in besmarts.mechanics.fits) objective_config_position (class in besmarts.mechanics.fits) objective_gradient_gdb() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] objective_hess() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] objective_hessp() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] objective_run_distributed() (in module besmarts.mechanics.fits) objective_tier (class in besmarts.mechanics.fits) objective_tier_get_keys() (in module besmarts.mechanics.fits) objective_tier_run() (in module besmarts.mechanics.fits) objective_total() (in module besmarts.core.clusters), [1] off() (besmarts.core.arrays.bitvec method), [1] off_first() (besmarts.core.arrays.bitvec method), [1] on() (besmarts.core.arrays.bitvec method), [1] on_ascend() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.tree_visitors.tree_visitor method), [1] on_descend() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.tree_visitors.tree_visitor method), [1] on_edge() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smarts_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_edge_enter() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_edge_exit() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_first() (besmarts.core.arrays.bitvec method), [1] on_graph() (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) on_node() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smarts_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1]

on_node_edges() (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_node_enter() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smarts_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.tree_visitors.tree_visitor method), [1] on_node_exit() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.graph_visitors.smarts_visitor method), [1] (besmarts.core.graph_visitors.smiles_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_nodes() (besmarts.core.rulesets.visitor_ruleset method) on_start() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_stop() (besmarts.core.graph_visitors.encoding_visitor method), [1] (besmarts.core.graph_visitors.graph_visitor method), [1] (besmarts.core.graph_visitors.index_visitor method), [1] (besmarts.core.rulesets.visitor_ruleset method) (besmarts.core.tree_visitors.tree_visitor method), [1] on_tree() (besmarts.core.tree_visitors.tree_visitor method), [1] optimization_iteration (class in besmarts.core.optimization), [1] optimization_iteration_default (class in besmarts.cluster.cluster_optimization), [1] optimization_iteration_is_done() (in module besmarts.core.optimization), [1] optimization_iteration_next() (in module besmarts.core.optimization), [1] optimization_iteration_repeat_step() (in module besmarts.core.optimization), [1] optimization_step (class in besmarts.core.optimization), [1] optimization_step_copy() (in module besmarts.core.optimization), [1] optimization_strategy (class in besmarts.core.optimization), [1] optimization_strategy_build_macro_iterations() (in module besmarts.core.optimization), [1] optimization_strategy_default (class in besmarts.cluster.cluster_optimization), [1] optimization_strategy_is_done() (in module besmarts.core.optimization), [1] optimization_strategy_iteration_next() (in module besmarts.core.optimization), [1] optimization_strategy_repeat_step() (in module besmarts.core.optimization), [1] optimization_strategy_restart() (in module besmarts.core.optimization), [1] optimize_forcefield_gdb_scipy() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] optimize_positions_scipy() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] oqueue_put() (besmarts.core.compute.workspace_remote method), [1] ordered_align_score() (in module besmarts.core.mapper), [1] ordered_contains() (in module besmarts.core.mapper), [1] outofplane() (in module besmarts.core.geometry), [1] outofplane_assignment_float (class in besmarts.core.assignments), [1] outofplane_assignment_float_matrix (class in besmarts.core.assignments), [1] outofplane_assignment_str (class in besmarts.core.assignments), [1] outofplane_topology() (in module besmarts.core.topology), [1] overlap() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] overlap_scores() (in module besmarts.core.mapper), [1]

P

pair() (in module besmarts.core.geometry), [1] pair_assignment_float (class in besmarts.core.assignments), [1] pair_assignment_float_matrix (class in besmarts.core.assignments), [1] pair_topology() (in module besmarts.core.topology), [1] pairwise_overlap() (in module besmarts.core.mapper), [1] parent_id_add() (in module besmarts.mechanics.smirnoff_models), [1] parse_atom() (in module besmarts.codecs.codec_rdkit), [1], [2] parse_bond() (in module besmarts.codecs.codec_rdkit), [1], [2] parse_chem() (in module besmarts.codecs.codec_rdkit), [1], [2] parse_xyz() (in module besmarts.core.assignments), [1] perception (besmarts.mechanics.molecular_models.forcefield attribute), [1] perception_model (class in besmarts.core.perception), [1] perception_model_rdkit() (in module besmarts.perception.perception_rdkit) perform_operations() (in module besmarts.core.clusters), [1] (in module besmarts.mechanics.fits) permutations (besmarts.core.topology.structure_topology attribute), [1] physical_model (class in besmarts.mechanics.molecular_models), [1] physical_model_energy() (in module besmarts.mechanics.objectives), [1] physical_model_internal_energy() (in module besmarts.mechanics.objectives), [1] physical_model_procedure (class in besmarts.mechanics.molecular_models), [1] physical_model_values_copy() (in module besmarts.mechanics.molecular_models), [1] physical_system (class in besmarts.mechanics.molecular_models), [1] physical_system_bmatrix() (in module besmarts.mechanics.objectives), [1] physical_system_energy() (in module besmarts.mechanics.objectives), [1] physical_system_force() (in module besmarts.mechanics.objectives), [1] physical_system_force_gradient() (in module besmarts.mechanics.objectives), [1] physical_system_force_gradient_internal() (in module besmarts.mechanics.objectives), [1] physical_system_force_internal() (in module besmarts.mechanics.objectives), [1] physical_system_force_system() (in module besmarts.mechanics.objectives), [1] physical_system_gradient() (in module besmarts.mechanics.objectives), [1] physical_system_gradient_gradient_internal() (in module besmarts.mechanics.objectives), [1] physical_system_gradient_internal() (in module besmarts.mechanics.objectives), [1] physical_system_gradient_system() (in module besmarts.mechanics.objectives), [1] physical_system_hessian() (in module besmarts.mechanics.objectives), [1] physical_system_hessian_analytic() (in module besmarts.mechanics.objectives), [1] physical_system_internals() (in module besmarts.mechanics.objectives), [1] physical_system_iter_keys() (in module besmarts.mechanics.molecular_models), [1] physical_system_set_value() (in module besmarts.mechanics.molecular_models), [1] pool (besmarts.core.splits.process_split_ctx attribute), [1] pool_close() (besmarts.core.compute.workspace_local method), [1] pool_start() (besmarts.core.compute.workspace_local method), [1] positions (besmarts.mechanics.molecular_models.physical_model attribute), [1] prepare_systems() (besmarts.mechanics.fits.compute_config method) primary (besmarts.core.topology.structure_topology attribute), [1] primitive_codec (class in besmarts.core.primitives), [1] primitive_codec_aromatic (class in besmarts.core.codecs), [1] primitive_codec_aromatic_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_bond_order (class in besmarts.core.codecs), [1] primitive_codec_bond_order_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_bond_ring (class in besmarts.core.codecs), [1] primitive_codec_bond_ring_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_chirality (class in besmarts.core.codecs), [1] primitive_codec_chirality_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_connectivity_ring (class in besmarts.core.codecs), [1] primitive_codec_connectivity_ring_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2]

primitive_codec_connectivity_total (class in besmarts.core.codecs), [1] primitive_codec_connectivity_total_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_element (class in besmarts.core.codecs), [1] primitive_codec_element_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_formal_charge (class in besmarts.core.codecs), [1] primitive_codec_formal_charge_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_hydrogen (class in besmarts.core.codecs), [1] primitive_codec_hydrogen_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_link_dst (class in besmarts.core.codecs), [1] primitive_codec_link_src (class in besmarts.core.codecs), [1] primitive_codec_ring_smallest (class in besmarts.core.codecs), [1] primitive_codec_ring_smallest_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_unit (class in besmarts.core.codecs), [1] primitive_codec_unit_index (class in besmarts.core.codecs), [1] primitive_codec_valence (class in besmarts.core.codecs), [1] primitive_codec_valence_rdkit (class in besmarts.codecs.codec_rdkit), [1], [2] primitive_codec_variable (class in besmarts.core.codecs), [1] primitive_codecs_get() (in module besmarts.codecs.codec_native), [1] (in module besmarts.codecs.codec_rdkit), [1], [2] (in module besmarts.core.codecs), [1] primitive_codecs_get_atom() (in module besmarts.codecs.codec_native), [1] primitive_codecs_get_bond() (in module besmarts.codecs.codec_native), [1] primitive_key (class in besmarts.core.primitives), [1] primitive_load() (in module besmarts.codecs.codec_native), [1] primitives (besmarts.core.chem.bechem attribute), [1] (besmarts.core.configs.smarts_splitter_config attribute), [1] print_chemical_system() (in module besmarts.mechanics.fits) print_parameterization() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] print_xyz() (in module besmarts.mechanics.fits) printmat() (in module besmarts.mechanics.vibration) printortho() (in module besmarts.mechanics.vibration) Process() (besmarts.core.compute.workspace_pool method), [1] (in module besmarts.core.compute), [1] process() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] process_accepted_candidates() (in module besmarts.mechanics.fits) process_split() (in module besmarts.core.splits), [1] process_split_ctx (class in besmarts.core.splits), [1] process_split_difference() (in module besmarts.core.splits), [1] process_split_difference_distributed() (in module besmarts.core.splits), [1] process_split_distributed() (in module besmarts.core.splits), [1] process_split_general_distributed() (in module besmarts.core.splits), [1] process_split_intersect() (in module besmarts.core.splits), [1] process_split_intersect_distributed() (in module besmarts.core.splits), [1] process_split_matches() (in module besmarts.core.splits), [1] process_split_matches_distributed() (in module besmarts.core.splits), [1] process_split_specific_distributed() (in module besmarts.core.splits), [1] process_tiers() (in module besmarts.mechanics.fits) project_gradient() (in module besmarts.core.array_numpy), [1] (in module besmarts.mechanics.hessians) project_hessian() (in module besmarts.core.array_numpy), [1] project_ics() (in module besmarts.mechanics.hessians) project_onto_ics_from_data() (in module besmarts.mechanics.hessians) project_torsions() (in module besmarts.mechanics.fits) put() (besmarts.core.compute.myqueue method), [1] put_workspaces() (besmarts.core.compute.workqueue_local method), [1] (besmarts.core.compute.workqueue_remote method), [1]

Q

queue_get_nowait() (in module besmarts.core.compute), [1]

queue_get_nowait_thread() (in module besmarts.core.compute), [1]

R

rdkit_mol_decode() (in module besmarts.codecs.codec_rdkit), [1], [2] rdkit_sdf_to_smiles_assignment() (in module besmarts.codecs.codec_rdkit), [1], [2] rdkit_smarts_decode() (in module besmarts.codecs.codec_rdkit), [1], [2] rdkit_smiles_decode() (in module besmarts.codecs.codec_rdkit), [1], [2] rdkit_xyz_to_smiles_assignment() (in module besmarts.codecs.codec_rdkit), [1], [2] rdmol_decode() (besmarts.codecs.codec_rdkit.graph_codec_rdkit method), [1], [2] read_graph() (besmarts.core.db.db_dict method), [1] read_graph_list() (besmarts.core.db.db_dict method), [1] read_intvec() (besmarts.core.db.db_dict method), [1] read_intvec_list() (besmarts.core.db.db_dict method), [1] read_structure() (besmarts.core.db.db_dict method), [1] read_structure_list() (besmarts.core.db.db_dict method), [1] recv_request() (besmarts.core.compute.Server method), [1] reduce() (besmarts.core.arrays.bitvec method), [1] ref (besmarts.core.mapper.align_score_ctx attribute), [1] reference (besmarts.core.mapper.union_ctx attribute), [1] register_pool() (in module besmarts.core.compute), [1] register_workspace() (in module besmarts.core.compute), [1] remote_connect() (in module besmarts.core.compute), [1] remote_init() (besmarts.core.compute.shm_local method), [1] remote_init_thread() (in module besmarts.core.compute), [1] remove() (besmarts.core.db.db_dict method), [1] remove_tr() (in module besmarts.mechanics.hessians) remove_workspace() (besmarts.core.compute.workqueue_local method), [1] repeat_step() (besmarts.cluster.cluster_optimization.optimization_iteration_default method), [1] (besmarts.core.optimization.optimization_iteration method), [1] (besmarts.core.optimization.optimization_strategy method), [1] report() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] (besmarts.cluster.cluster_objective.clustering_objective_mean_separation method), [1] (besmarts.cluster.cluster_objective.clustering_objective_variance_separation method), [1] (besmarts.core.clusters.clustering_objective method), [1]

reset() (besmarts.core.compute.workspace_local method), [1] (in module besmarts.mechanics.fits) reset_project_dihedrals() (in module besmarts.mechanics.fits) reset_project_torsions() (in module besmarts.mechanics.fits) reset_unique() (in module besmarts.mechanics.fits) reset_unique_dihedral() (in module besmarts.mechanics.fits) resolve_process_fragment() (in module besmarts.core.resolve) resolve_smiles() (in module besmarts.core.resolve) resolve_smiles_distributed() (in module besmarts.core.resolve) resolve_smiles_iter() (in module besmarts.core.resolve) resolve_smiles_recurse_distributed() (in module besmarts.core.resolve) resolve_smiles_recurse_iter() (in module besmarts.core.resolve) restart() (besmarts.core.optimization.optimization_strategy method), [1] ret (besmarts.core.clusters.clustering_collect_split_candidates_ctx attribute), [1] return_g() (in module besmarts.core.hierarchy_merge), [1] return_matches (besmarts.core.configs.smarts_splitter_config attribute), [1] return_status (class in besmarts.core.returns), [1] return_value (class in besmarts.core.returns), [1] RING_SMALLEST (besmarts.core.primitives.primitive_key attribute), [1] ring_topology() (in module besmarts.core.topology), [1] rows (besmarts.core.assignments.graph_db_graph attribute), [1] run() (besmarts.mechanics.fits.compute_config method) (besmarts.mechanics.fits.compute_config_energy_sapt method) (besmarts.mechanics.fits.compute_config_energy_total method) (besmarts.mechanics.fits.compute_config_gradient method) (besmarts.mechanics.fits.compute_config_hessian method) (besmarts.mechanics.fits.compute_config_penalty method) (besmarts.mechanics.fits.compute_config_position method) run_objective() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] run_request() (besmarts.core.compute.Server method), [1] RUNNING (besmarts.core.compute.workspace_status attribute), [1]

S

S0 (besmarts.core.splits.process_split_ctx attribute), [1] sample_angles() (in module besmarts.sample) sample_bonds() (in module besmarts.sample) sample_ic() (in module besmarts.sample) sample_outofplanes() (in module besmarts.sample) sample_torsions() (in module besmarts.sample) sample_valence() (in module besmarts.sample) save_xyz() (in module besmarts.mechanics.vibration) sdf_decode() (besmarts.codecs.codec_rdkit.graph_codec_rdkit method), [1], [2] select (besmarts.core.chem.bechem attribute), [1] (besmarts.core.graphs.structure attribute), [1] (besmarts.core.graphs.subgraph attribute), [1] select_best_accepted() (in module besmarts.mechanics.fits) selections (besmarts.cluster.cluster_assignment.smiles_assignment_float attribute), [1] (besmarts.cluster.cluster_assignment.smiles_assignment_str attribute), [1] (besmarts.core.assignments.angle_assignment_float attribute), [1] (besmarts.core.assignments.angle_assignment_float_matrix attribute), [1] (besmarts.core.assignments.angle_assignment_str attribute), [1] (besmarts.core.assignments.atom_assignment_float attribute), [1] (besmarts.core.assignments.atom_assignment_str attribute), [1] (besmarts.core.assignments.bond_assignment_float attribute), [1] (besmarts.core.assignments.bond_assignment_float_matrix attribute), [1] (besmarts.core.assignments.bond_assignment_str attribute), [1] (besmarts.core.assignments.graph_assignment attribute), [1] (besmarts.core.assignments.graph_assignment_float attribute), [1] (besmarts.core.assignments.graph_assignment_float_matrix attribute), [1] (besmarts.core.assignments.graph_db attribute), [1] (besmarts.core.assignments.graph_db_column attribute), [1] (besmarts.core.assignments.outofplane_assignment_float attribute), [1] (besmarts.core.assignments.outofplane_assignment_float_matrix attribute), [1] (besmarts.core.assignments.outofplane_assignment_str attribute), [1] (besmarts.core.assignments.pair_assignment_float attribute), [1] (besmarts.core.assignments.pair_assignment_float_matrix attribute), [1] (besmarts.core.assignments.smarts_assignment attribute), [1] (besmarts.core.assignments.smarts_assignment_float attribute), [1] (besmarts.core.assignments.smarts_assignment_str attribute), [1] (besmarts.core.assignments.smiles_assignment attribute), [1] (besmarts.core.assignments.smiles_assignment_float attribute), [1] (besmarts.core.assignments.structure_assignment_float attribute), [1] (besmarts.core.assignments.structure_assignment_str attribute), [1] (besmarts.core.assignments.torsion_assignment_float attribute), [1] (besmarts.core.assignments.torsion_assignment_float_matrix attribute), [1] (besmarts.core.assignments.torsion_assignment_str attribute), [1] send_request() (besmarts.core.compute.Server method), [1] serve_client() (besmarts.core.compute.Server method), [1] serve_forever() (besmarts.core.compute.Server method), [1] Server (class in besmarts.core.compute), [1] set_status() (besmarts.core.compute.workspace_local method), [1] shards (besmarts.core.splits.split_return_type attribute), [1] shm_init() (in module besmarts.core.compute), [1] shm_local (class in besmarts.core.compute), [1] signal_kill_processes() (in module besmarts.core.compute), [1] single() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] (besmarts.cluster.cluster_objective.clustering_objective_mean_separation method), [1] (besmarts.cluster.cluster_objective.clustering_objective_variance_separation method), [1] (besmarts.core.clusters.clustering_objective method), [1] singlepoint_forcefield_gdb_scipy() (in module besmarts.mechanics.optimizers_scipy), [1], [2], [3] smarts (besmarts.core.assignments.smarts_assignment attribute), [1] (besmarts.core.assignments.smarts_assignment_float attribute), [1] (besmarts.core.assignments.smarts_assignment_str attribute), [1] (besmarts.core.hierarchies.smarts_hierarchy attribute), [1] (besmarts.core.hierarchies.structure_hierarchy attribute), [1] smarts_assignment (class in besmarts.core.assignments), [1] smarts_assignment_float (class in besmarts.core.assignments), [1] smarts_assignment_str (class in besmarts.core.assignments), [1] smarts_clustering (class in besmarts.core.clusters), [1] smarts_clustering_find_max_depth() (in module besmarts.core.clusters), [1] smarts_clustering_optimize() (in module besmarts.core.clusters), [1] smarts_decode() (besmarts.codecs.codec_rdkit.graph_codec_rdkit method), [1], [2] (besmarts.core.codecs.graph_codec method), [1] (besmarts.core.codecs.graph_codec_chain method), [1] smarts_decode_distributed() (in module besmarts.core.codecs), [1] smarts_encode() (besmarts.codecs.codec_native.graph_codec_native method), [1] (besmarts.core.codecs.graph_codec method), [1] (besmarts.core.codecs.graph_codec_chain method), [1] smarts_extender_config (class in besmarts.core.configs), [1] smarts_filter_bond_lengths() (in module besmarts.core.clusters), [1] smarts_filter_data() (in module besmarts.core.clusters), [1] smarts_hierarchy (class in besmarts.core.hierarchies), [1] smarts_hierarchy_assign() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_angles() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_atoms() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_bonds() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_ctx (class in besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_outofplanes() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_smiles() (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assign_structures() (in module besmarts.assign.hierarchy_assign_native), [1] smarts_hierarchy_assign_torsions() (in module besmarts.assign.hierarchy_assign_native), [1] (in module besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_assignment (class in besmarts.core.assignments), [1] smarts_hierarchy_assignment_native (class in besmarts.assign.hierarchy_assign_native), [1] smarts_hierarchy_assignment_rdkit (class in besmarts.assign.hierarchy_assign_rdkit), [1], [2] smarts_hierarchy_copy() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_print() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_rename() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy_angles() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy_atoms() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy_bonds() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy_outofplanes() (in module besmarts.core.hierarchies), [1] smarts_hierarchy_to_structure_hierarchy_torsions() (in module besmarts.core.hierarchies), [1] smarts_perception_config (class in besmarts.core.configs), [1] smarts_perception_config_copy() (in module besmarts.core.configs), [1] smarts_splitter_config (class in besmarts.core.configs), [1] smarts_visitor (class in besmarts.core.graph_visitors), [1] smiles (besmarts.cluster.cluster_assignment.smiles_assignment_float attribute), [1] (besmarts.cluster.cluster_assignment.smiles_assignment_str attribute), [1] (besmarts.core.assignments.graph_assignment attribute), [1] (besmarts.core.assignments.graph_db attribute), [1] (besmarts.core.assignments.smiles_assignment attribute), [1] (besmarts.core.assignments.smiles_assignment_float attribute), [1] smiles_assignment (class in besmarts.core.assignments), [1] smiles_assignment_copy() (in module besmarts.core.assignments), [1] smiles_assignment_energy_function_spring() (in module besmarts.mechanics.force_harmonic), [1] smiles_assignment_energy_function_spring_matrix() (in module besmarts.mechanics.force_harmonic), [1] smiles_assignment_float (class in besmarts.cluster.cluster_assignment), [1] (class in besmarts.core.assignments), [1] smiles_assignment_float_compute() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_float_copy() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_force_constants() (in module besmarts.mechanics.fits) smiles_assignment_function() (in module besmarts.mechanics.molecular_models), [1] smiles_assignment_geometry_angle_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_angles() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_distance_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_distances() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_outofplane_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_outofplanes() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_torsion_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_torsion_matrix_nonlinear() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_torsions() (in module besmarts.core.assignments), [1] smiles_assignment_geometry_torsions_nonlinear() (in module besmarts.core.assignments), [1] smiles_assignment_group (class in besmarts.core.assignments), [1] smiles_assignment_group_angles() (in module besmarts.core.assignments), [1] smiles_assignment_group_atoms() (in module besmarts.core.assignments), [1] smiles_assignment_group_bonds() (in module besmarts.core.assignments), [1] smiles_assignment_group_concatenate() (in module besmarts.core.assignments), [1] smiles_assignment_group_copy() (in module besmarts.core.assignments), [1] smiles_assignment_group_outofplanes() (in module besmarts.core.assignments), [1] smiles_assignment_group_pairs() (in module besmarts.core.assignments), [1] smiles_assignment_group_to_graph_db_entry() (in module besmarts.core.assignments), [1] smiles_assignment_group_to_structure_assignment_group() (in module besmarts.core.assignments), [1] smiles_assignment_group_torsions() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_angle_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_angles() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_distance_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_distances() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_outofplane_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_outofplanes() (in module besmarts.core.assignments), [1]

smiles_assignment_jacobian2_torsion_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian2_torsions() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_angle_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_angles() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_distance_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_distances() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_outofplane_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_outofplanes() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_torsion_matrix() (in module besmarts.core.assignments), [1] smiles_assignment_jacobian_torsions() (in module besmarts.core.assignments), [1] smiles_assignment_matrix_function() (in module besmarts.mechanics.molecular_models), [1] smiles_assignment_str (class in besmarts.cluster.cluster_assignment), [1] smiles_assignment_str_compute() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_str_copy() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_str_diff() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_str_modified() (in module besmarts.cluster.cluster_assignment), [1] smiles_assignment_to_graph_assignment() (in module besmarts.core.assignments), [1] smiles_decode() (besmarts.codecs.codec_rdkit.graph_codec_rdkit method), [1], [2] (besmarts.core.codecs.graph_codec method), [1] (besmarts.core.codecs.graph_codec_chain method), [1] smiles_decode_distributed() (in module besmarts.core.codecs), [1] smiles_decode_list_distributed() (in module besmarts.core.codecs), [1] SMILES_ELEMENT() (in module besmarts.core.codecs), [1] smiles_encode() (besmarts.codecs.codec_native.graph_codec_native method), [1] (besmarts.core.codecs.graph_codec method), [1] (besmarts.core.codecs.graph_codec_chain method), [1] smiles_perception_config (class in besmarts.core.configs), [1] smiles_visitor (class in besmarts.core.graph_visitors), [1] smirnoff_dihedral_load() (in module besmarts.mechanics.smirnoff_models), [1] smirnoff_load() (in module besmarts.mechanics.smirnoff_models), [1] smirnoff_write_version_0p3() (in module besmarts.mechanics.smirnoff_models), [1] smirnoff_xml_read() (in module besmarts.mechanics.smirnoff_xml), [1] smirnoff_xml_write() (in module besmarts.mechanics.smirnoff_xml), [1] SocketClient() (in module besmarts.core.compute), [1] SPLIT (besmarts.core.optimization.optimization_strategy attribute), [1] split() (besmarts.cluster.cluster_objective.clustering_objective_classification method), [1] (besmarts.cluster.cluster_objective.clustering_objective_mean_separation method), [1] (besmarts.cluster.cluster_objective.clustering_objective_variance_separation method), [1] (besmarts.core.clusters.clustering_objective method), [1] split_all_partitions() (in module besmarts.core.splits), [1] split_branches() (in module besmarts.core.splits), [1] split_general (besmarts.core.configs.smarts_splitter_config attribute), [1] split_partition() (in module besmarts.core.splits), [1] split_return_type (class in besmarts.core.splits), [1] split_shm_load() (in module besmarts.core.splits), [1] split_single_bits() (in module besmarts.core.splits), [1] split_specific (besmarts.core.configs.smarts_splitter_config attribute), [1] split_structures() (in module besmarts.core.splits), [1] split_structures_distributed() (in module besmarts.core.splits), [1] split_subgraphs() (in module besmarts.core.splits), [1] split_subgraphs_distributed() (in module besmarts.core.splits), [1] splits (besmarts.core.splits.split_return_type attribute), [1] splitter (besmarts.core.configs.smarts_perception_config attribute), [1] (besmarts.core.splits.process_split_ctx attribute), [1] start() (besmarts.core.compute.workspace_local method), [1] (besmarts.core.compute.workspace_remote method), [1] steps (besmarts.core.optimization.optimization_strategy attribute) strict (besmarts.core.mapper.map_vertices_ctx attribute), [1] structure (class in besmarts.core.graphs), [1] structure_angle() (in module besmarts.core.graphs), [1] structure_assignment_float (class in besmarts.core.assignments), [1] structure_assignment_group (class in besmarts.core.assignments), [1] structure_assignment_group_copy() (in module besmarts.core.assignments), [1] structure_assignment_str (class in besmarts.core.assignments), [1] structure_atom() (in module besmarts.core.graphs), [1] structure_bits() (in module besmarts.core.graphs), [1] structure_bond() (in module besmarts.core.graphs), [1] structure_branch() (in module besmarts.core.graphs), [1] structure_build() (in module besmarts.core.graphs), [1] structure_clear() (in module besmarts.core.graphs), [1] structure_connections() (in module besmarts.core.graphs), [1] structure_copy() (in module besmarts.core.graphs), [1] structure_decode() (besmarts.core.codecs.intvec_codec method), [1] structure_edges() (in module besmarts.core.graphs), [1] structure_encode() (besmarts.core.codecs.intvec_codec method), [1] structure_extend() (in module besmarts.core.graphs), [1] structure_fill() (in module besmarts.core.graphs), [1] structure_frontier_nodes() (in module besmarts.core.graphs), [1] structure_hash() (in module besmarts.core.graphs), [1] structure_hierarchy (class in besmarts.core.hierarchies), [1] structure_hierarchy_add_hierarchy() (in module besmarts.core.hierarchy_merge), [1] structure_hierarchy_assign() (in module besmarts.assign.hierarchy_assign_native), [1] structure_hierarchy_copy() (in module besmarts.core.hierarchies), [1] structure_hierarchy_fit() (in module besmarts.core.hierarchy_merge), [1] structure_hierarchy_merge() (in module besmarts.core.hierarchy_merge), [1] structure_hierarchy_prune_unused() (in module besmarts.core.hierarchy_merge), [1] structure_hierarchy_to_smarts_hierarchy() (in module besmarts.core.hierarchies), [1] structure_invert() (in module besmarts.core.graphs), [1] structure_invert_any() (in module besmarts.core.graphs), [1] structure_iter_bits() (in module besmarts.core.graph_visitors), [1] structure_max_depth() (in module besmarts.core.graphs), [1] structure_node_depth() (in module besmarts.core.graphs), [1] structure_node_depths() (in module besmarts.core.graphs), [1] structure_nodes() (in module besmarts.core.graphs), [1] structure_outofplane() (in module besmarts.core.graphs), [1] structure_print() (in module besmarts.core.graphs), [1] structure_prune_null_nodes() (in module besmarts.core.graphs), [1] structure_relabel_nodes() (in module besmarts.core.graphs), [1] structure_remove_empty_leaves() (in module besmarts.core.graphs), [1] structure_remove_full_leaves() (in module besmarts.core.graphs), [1] structure_remove_hydrogen() (in module besmarts.core.graphs), [1] structure_remove_nodes() (in module besmarts.core.graphs), [1] structure_remove_unselected() (in module besmarts.core.graphs), [1] structure_to_graph() (in module besmarts.core.graphs), [1] structure_to_intvec() (in module besmarts.core.graphs), [1] structure_to_subgraph() (in module besmarts.core.graphs), [1] structure_topology (class in besmarts.core.topology), [1] structure_topology_edges() (in module besmarts.core.graphs), [1] structure_topology_nodes() (in module besmarts.core.graphs), [1] structure_torsion() (in module besmarts.core.graphs), [1] structure_unreachable_nodes() (in module besmarts.core.graphs), [1] structure_up_to_depth() (in module besmarts.core.graphs), [1] structure_vertices_at_depth() (in module besmarts.core.graphs), [1] subgraph (class in besmarts.core.graphs), [1] subgraph_any() (in module besmarts.core.graphs), [1] subgraph_as_graph() (in module besmarts.core.graphs), [1] subgraph_as_structure() (in module besmarts.core.graphs), [1] subgraph_bits() (in module besmarts.core.graphs), [1] subgraph_connection() (in module besmarts.core.graphs), [1] subgraph_connections() (in module besmarts.core.graphs), [1] subgraph_copy() (in module besmarts.core.graphs), [1] subgraph_decode() (besmarts.core.codecs.intvec_codec method), [1] subgraph_edges() (in module besmarts.core.graphs), [1] subgraph_encode() (besmarts.core.codecs.intvec_codec method), [1] subgraph_fill() (in module besmarts.core.graphs), [1] subgraph_hash() (in module besmarts.core.graphs), [1] subgraph_invert() (in module besmarts.core.graphs), [1] subgraph_invert_null() (in module besmarts.core.graphs), [1] subgraph_nodes() (in module besmarts.core.graphs), [1] subgraph_print() (in module besmarts.core.graphs), [1] subgraph_relabel_nodes() (in module besmarts.core.graphs), [1] subgraph_remove_unselected() (in module besmarts.core.graphs), [1] subgraph_to_graph() (in module besmarts.core.graphs), [1] subgraph_to_intvec() (in module besmarts.core.graphs), [1] subgraph_to_structure() (in module besmarts.core.graphs), [1] subgraph_to_structure_angle() (in module besmarts.core.graphs), [1] subgraph_to_structure_bond() (in module besmarts.core.graphs), [1] subgraph_to_structure_outofplane() (in module besmarts.core.graphs), [1] subgraph_to_structure_torsion() (in module besmarts.core.graphs), [1] subgraph_validate_structure() (in module besmarts.core.graphs), [1] subgraphs (besmarts.core.hierarchies.structure_hierarchy attribute), [1] (besmarts.core.splits.split_return_type attribute), [1] SUBMITTING (besmarts.core.compute.workspace_status attribute), [1] subtract() (in module besmarts.core.mapper), [1] subtract_conditional() (in module besmarts.core.mapper), [1] subtract_conditional_left() (in module besmarts.core.mapper), [1] subtract_conditional_right() (in module besmarts.core.mapper), [1] subtract_projection() (in module besmarts.mechanics.hessians) SUCCESS (besmarts.core.returns.return_status attribute), [1] success() (in module besmarts.core.returns), [1] sum() (besmarts.core.clusters.clustering_objective method), [1] sum_obj() (in module besmarts.cluster.cluster_objective), [1] system_term (class in besmarts.mechanics.molecular_models), [1]

T

tables (besmarts.core.assignments.graph_db_entry attribute), [1] take_left() (in module besmarts.core.hierarchy_merge), [1] take_right() (in module besmarts.core.hierarchy_merge), [1] thread_name_set() (in module besmarts.core.compute), [1] timestamp() (in module besmarts.core.logs), [1] to_check (besmarts.core.mapper.align_score_ctx attribute), [1] (besmarts.core.mapper.filter_contains_ctx attribute), [1] to_fragments() (besmarts.core.chem.bechem method), [1] tokenize_smarts() (besmarts.core.codecs.primitive_codec_aromatic method), [1] (besmarts.core.codecs.primitive_codec_bond_order method), [1] (besmarts.core.codecs.primitive_codec_bond_ring method), [1] (besmarts.core.codecs.primitive_codec_chirality method), [1] (besmarts.core.codecs.primitive_codec_formal_charge method), [1] (besmarts.core.codecs.primitive_codec_link_dst method), [1] (besmarts.core.codecs.primitive_codec_link_src method), [1] (besmarts.core.codecs.primitive_codec_ring_smallest method), [1] (besmarts.core.codecs.primitive_codec_unit method), [1] (besmarts.core.codecs.primitive_codec_unit_index method), [1] (besmarts.core.codecs.primitive_codec_variable method), [1] (besmarts.core.primitives.primitive_codec method), [1] topo (besmarts.assign.hierarchy_assign_rdkit.smarts_hierarchy_assign_ctx attribute), [1], [2] topology (besmarts.core.assignments.angle_assignment_float attribute), [1] (besmarts.core.assignments.angle_assignment_float_matrix attribute), [1] (besmarts.core.assignments.angle_assignment_str attribute), [1] (besmarts.core.assignments.atom_assignment_float attribute), [1] (besmarts.core.assignments.atom_assignment_str attribute), [1] (besmarts.core.assignments.bond_assignment_float attribute), [1] (besmarts.core.assignments.bond_assignment_float_matrix attribute), [1] (besmarts.core.assignments.bond_assignment_str attribute), [1] (besmarts.core.assignments.graph_db_table attribute), [1] (besmarts.core.assignments.outofplane_assignment_float attribute), [1] (besmarts.core.assignments.outofplane_assignment_float_matrix attribute), [1] (besmarts.core.assignments.outofplane_assignment_str attribute), [1] (besmarts.core.assignments.pair_assignment_float attribute), [1] (besmarts.core.assignments.pair_assignment_float_matrix attribute), [1] (besmarts.core.assignments.structure_assignment_float attribute), [1] (besmarts.core.assignments.structure_assignment_group attribute), [1] (besmarts.core.assignments.structure_assignment_str attribute), [1] (besmarts.core.assignments.torsion_assignment_float attribute), [1] (besmarts.core.assignments.torsion_assignment_float_matrix attribute), [1] (besmarts.core.assignments.torsion_assignment_str attribute), [1] (besmarts.core.graphs.structure attribute), [1] (besmarts.core.hierarchies.structure_hierarchy attribute), [1] (besmarts.core.mapper.union_ctx attribute), [1] (besmarts.core.splits.split_return_type attribute), [1] (besmarts.mechanics.molecular_models.physical_model attribute), [1]

topology_assignment_group (class in besmarts.core.assignments), [1] topology_term (class in besmarts.mechanics.molecular_models), [1] topology_term_copy() (in module besmarts.mechanics.molecular_models), [1] torsion() (in module besmarts.core.geometry), [1] torsion_assignment_float (class in besmarts.core.assignments), [1] torsion_assignment_float_matrix (class in besmarts.core.assignments), [1] torsion_assignment_str (class in besmarts.core.assignments), [1] torsion_topology() (in module besmarts.core.topology), [1] trans_rot_modes() (in module besmarts.mechanics.vibration) transcode (besmarts.core.topology.transcode_topology attribute), [1] transcode_topology (class in besmarts.core.topology), [1] transform() (in module besmarts.core.array_numpy), [1] (in module besmarts.mechanics.hessians) transform_dlcs() (in module besmarts.core.array_numpy), [1] transform_v2() (in module besmarts.core.array_numpy), [1] (in module besmarts.mechanics.hessians) transform_v3() (in module besmarts.core.array_numpy), [1] (in module besmarts.mechanics.hessians) tree_index (class in besmarts.core.trees), [1] tree_index_copy() (in module besmarts.core.trees), [1] tree_index_node_add() (in module besmarts.core.trees), [1] tree_index_node_depth() (in module besmarts.core.trees), [1] tree_index_node_remove() (in module besmarts.core.trees), [1] tree_index_node_remove_by_name() (in module besmarts.core.trees), [1] tree_index_roots() (in module besmarts.core.trees), [1] tree_iter_breadth_first() (in module besmarts.core.tree_iterators), [1] tree_iter_breadth_first_single() (in module besmarts.core.tree_iterators), [1] tree_iter_depth_first() (in module besmarts.core.tree_iterators), [1] tree_iter_depth_first_single() (in module besmarts.core.tree_iterators), [1] tree_iter_dive() (in module besmarts.core.tree_iterators), [1] tree_iter_dive_reverse() (in module besmarts.core.tree_iterators), [1] tree_iter_dive_single() (in module besmarts.core.tree_iterators), [1] tree_iter_dive_single_reverse() (in module besmarts.core.tree_iterators), [1] tree_iter_to_root() (in module besmarts.core.tree_iterators), [1] tree_iter_to_root_single() (in module besmarts.core.tree_iterators), [1] tree_iterator (besmarts.core.optimization.optimization_strategy attribute) tree_node (class in besmarts.core.trees), [1] tree_node_copy() (in module besmarts.core.trees), [1] tree_visitor (class in besmarts.core.tree_visitors), [1] type (besmarts.core.trees.tree_node attribute), [1]

U

union() (in module besmarts.core.mapper), [1] union_ctx (class in besmarts.core.mapper), [1] union_list() (in module besmarts.core.mapper), [1] union_list_dispatch() (in module besmarts.core.mapper), [1] union_list_dispatch_distributed() (in module besmarts.core.mapper), [1] union_list_distributed() (in module besmarts.core.mapper), [1] union_list_parallel() (in module besmarts.core.mapper), [1]

unique (besmarts.core.configs.smarts_splitter_config attribute), [1] unique_complements (besmarts.core.configs.smarts_splitter_config attribute), [1] unique_complements_prefer_min (besmarts.core.configs.smarts_splitter_config attribute), [1] UNIT (besmarts.core.primitives.primitive_key attribute), [1] UNIT_INDEX (besmarts.core.primitives.primitive_key attribute), [1] unmatch_idx (besmarts.core.splits.split_return_type attribute), [1] unregister_pool() (in module besmarts.core.compute), [1] unregister_workspace() (in module besmarts.core.compute), [1]

V

v (besmarts.core.arrays.bitvec attribute), [1] (besmarts.core.arrays.intvec attribute), [1] VALENCE (besmarts.core.primitives.primitive_key attribute), [1] values (besmarts.core.assignments.graph_db_table attribute), [1] (besmarts.mechanics.molecular_models.physical_model attribute), [1]

VARIABLE (besmarts.core.primitives.primitive_key attribute), [1] visit_descend() (in module besmarts.core.graph_visitors), [1] visit_graph() (in module besmarts.core.graph_visitors), [1] visitor_ruleset (class in besmarts.core.rulesets)

W

WAITING (besmarts.core.compute.workspace_status attribute), [1] workqueue (class in besmarts.core.compute), [1] workqueue_get_workspace() (in module besmarts.core.compute), [1] workqueue_is_active() (in module besmarts.core.compute), [1] workqueue_list_workspaces() (in module besmarts.core.compute), [1] workqueue_local (class in besmarts.core.compute), [1] workqueue_manager (class in besmarts.core.compute), [1] workqueue_new_workspace() (in module besmarts.core.compute), [1] workqueue_push_workspace() (in module besmarts.core.compute), [1] workqueue_remote (class in besmarts.core.compute), [1] workqueue_remote_get_workspaces() (in module besmarts.core.compute), [1] workqueue_remote_get_workspaces_thread() (in module besmarts.core.compute), [1] workqueue_remote_is_active() (in module besmarts.core.compute), [1] workqueue_remote_put_workspaces() (in module besmarts.core.compute), [1] workqueue_remote_put_workspaces_thread() (in module besmarts.core.compute), [1] workqueue_remove_workspace() (in module besmarts.core.compute), [1] workspace (class in besmarts.core.compute), [1] workspace_flush() (in module besmarts.core.compute), [1] workspace_is_active() (in module besmarts.core.compute), [1] workspace_local (class in besmarts.core.compute), [1]

workspace_local_remote_gather_thread() (in module besmarts.core.compute), [1] workspace_local_remote_loadbalance_thread() (in module besmarts.core.compute), [1] workspace_local_run() (in module besmarts.core.compute), [1] workspace_local_run_thread() (in module besmarts.core.compute), [1] workspace_local_submit() (in module besmarts.core.compute), [1] workspace_manager (class in besmarts.core.compute), [1] workspace_pool (class in besmarts.core.compute), [1] workspace_remote (class in besmarts.core.compute), [1] workspace_remote_compute() (in module besmarts.core.compute), [1] workspace_remote_local_gather_thread() (in module besmarts.core.compute), [1] workspace_remote_local_pusher_thread() (in module besmarts.core.compute), [1] workspace_remote_shm_init() (in module besmarts.core.compute), [1] workspace_remote_shm_init_thread() (in module besmarts.core.compute), [1] workspace_run() (in module besmarts.core.compute), [1] workspace_run_init() (in module besmarts.core.compute), [1] workspace_status (class in besmarts.core.compute), [1] workspace_submit_and_flush() (in module besmarts.core.compute), [1] write_graph() (besmarts.core.db.db_dict method), [1] write_intvec() (besmarts.core.db.db_dict method), [1] write_structure() (besmarts.core.db.db_dict method), [1] write_subgraph() (besmarts.core.db.db_dict method), [1]

X

xor() (in module besmarts.core.mapper), [1]

xyz_decode() (besmarts.codecs.codec_rdkit.graph_codec_rdkit method), [1], [2] xyz_to_graph_assignment() (in module besmarts.core.assignments), [1]

Y

yield_if() (in module besmarts.core.tree_iterators), [1]

yield_if_single() (in module besmarts.core.tree_iterators), [1] yield_single() (in module besmarts.core.tree_iterators), [1]