Index

A

aam (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) AAMValidator (class in synkit.Chem.Reaction.aam_validator) AbstractReactionExtractor (class in synkit.CRN.Construct.abstract) AbstractReactionNetwork (class in synkit.CRN.Construct.abstract) active_flow (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) add() (synkit.Graph.FG.model.FunctionalGroupRegistry method) add_hs_and_clear_radicals() (synkit.Chem.Molecule.standardize.MolStandardizer method) add_hydrogen_nodes_multiple() (synkit.Graph.Hyrogen.hcomplete.HComplete static method) add_hydrogen_nodes_multiple_utils() (synkit.Graph.Hyrogen.hcomplete.HComplete static method) add_partial_charges() (synkit.IO.mol_to_graph.MolToGraph static method) add_place() (synkit.CRN.Petrinet.net.PetriNet method) add_transition() (synkit.CRN.Petrinet.net.PetriNet method) add_unique_subgraph_with_wildcards() (synkit.Graph.Wildcard.wildcard.WildCard static method) add_wildcard_subgraph_for_unmapped() (in module synkit.Graph.utils) adjust_legend_handles() (in module synkit.Vis.chemical_space) advance() (synkit.CRN.Construct.state.DerivationState method) ALL (synkit.Synthesis.Reactor.strategy.Strategy attribute) all_features (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor property) all_in() (synkit.Rule.Apply.rule_matcher.RuleMatcher static method) all_reachable_species (synkit.CRN.Pathway.reachability.ReachabilityLayer attribute) allow_empty_side (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener attribute) allow_self_mixtures (synkit.CRN.Construct.builder.CRNExpand attribute) alpha (synkit.CRN.Visualize.vis.CRNStyle attribute) ammonia_hydroxide_standardize() (synkit.Chem.Reaction.deionize.Deionize static method) anchor_component (synkit.Graph.Matcher.auto_est.AutoEst property) (synkit.Graph.Matcher.automorphism.Automorphism property) anchor_node (synkit.Graph.FG.model.FunctionalGroupPattern attribute) annotate() (synkit.Chem.Molecule.graph_annotator.GraphAnnotator method) app_index (synkit.CRN.Structure.reaction.Reaction attribute) append() (synkit.CRN.Construct.derivation.DerivationLog method) apply_rule_worker() (in module synkit.CRN.Construct.worker) apply_uncharge_smiles_to_reactions() (synkit.Chem.Reaction.deionize.Deionize class method)

approx_embedding_count (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) approx_orbits (synkit.Graph.Matcher.orbit.OrbitAccuracy property) ApproxMCSMatcher (class in synkit.Graph.Matcher.approx_mcs) are_isomorphic() (in module synkit.CRN.Symmetry.isomorphism) are_subhypergraph_isomorphic() (in module synkit.CRN.Symmetry.isomorphism) aromatic() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) AromaticRingSystem (class in synkit.Graph.FG.ring_system) AromaticRingSystemDetector (class in synkit.Graph.FG.ring_system) AromaticSubring (class in synkit.Graph.FG.ring_system) arrow_atom_maps() (in module synkit.Graph.Mech.conversion) arrows (synkit.CRN.Visualize.vis.CRNStyle attribute) arrowsize (synkit.CRN.Visualize.vis.CRNStyle attribute) arrowstyle (synkit.CRN.Visualize.vis.CRNStyle attribute) as_dict() (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig method) (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) as_dicts() (synkit.CRN.Construct.derivation.DerivationLog method) assign_deterministic_maps_and_canonical() (in module synkit.CRN.Construct.smiles) assign_maps_to_unmapped (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) atom_map (synkit.Vis.visual_model.VisualNode attribute) atom_map_reactions() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) atom_map_to_nodes() (in module synkit.Graph.Mech.conversion) AtomFeatureExtractor (class in synkit.Chem.Molecule.atom_features) audit_reaction_smiles() (in module synkit.Graph.FG.audit) auto_reduce_labels_when_dense (synkit.CRN.Visualize.vis.CRNStyle attribute) AutoEst (class in synkit.Graph.Matcher.auto_est) Automorphism (class in synkit.Graph.Matcher.automorphism) automorphism (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) automorphism_count (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) automorphism_result() (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) automorphism_summary() (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) automorphisms_iter() (synkit.CRN.Symmetry.automorphism.CRNAutomorphism method) available_backends() (synkit.Graph.Matcher.batch_cluster.BatchCluster method) (synkit.Graph.Matcher.graph_cluster.GraphCluster method) (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine static method) available_layouts() (in module synkit.CRN.Visualize.layout)

B

background (synkit.CRN.Visualize.palette.ColorPalette attribute) BACKTRACK (synkit.Synthesis.Reactor.strategy.Strategy attribute) backward_its (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) backward_synthesis_search() (synkit.Rule.Apply.retro_reactor.RetroReactor method) badges (synkit.Vis.visual_model.VisualNode attribute) balance_valences() (synkit.Graph.ITS.partial_its.PartialITS static method) BalanceReactionCheck (class in synkit.Chem.Reaction.balance_check) base_url (synkit.CRN.Query.kegg_api.KEGGClient attribute) batch_dicts() (synkit.Graph.Matcher.batch_cluster.BatchCluster static method) BatchCluster (class in synkit.Graph.Matcher.batch_cluster) BatchReactor (class in synkit.Synthesis.Reactor.batch_reactor) bc_cost_acyl_co (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_acyl_co_peroxy (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_aromatic_co (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_order_mismatch_scale (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_other (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_peroxy_oo (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_x_deg1_o (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_x_deg2_o (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) bc_cost_x_deg3_o (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) begin_step() (synkit.CRN.Construct.state.DerivationState method) Benchmark (class in synkit.Synthesis.Reactor.benchmark) best_heuristic_cost (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) best_meta (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) best_pmcd_key (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) best_score (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) BFS() (synkit.Rule.Modify.longest_path.LongestPath method) bip() (synkit.Vis.crn_vis.CRNVisualizer method) bipartite_layout() (in module synkit.CRN.Visualize.layout) bond_change_report (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) bond_minus_type() (in module synkit.Graph.Mech.conversion)

bond_order_sum() (in module synkit.Graph.Mech.electron_accounting) bond_plus_type() (in module synkit.Graph.Mech.conversion) broken_bonds (synkit.Vis.reaction_drawer.ReactionHighlights attribute) build() (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor method) (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder method) (synkit.CRN.Construct.abstract.AbstractReactionExtractor method) (synkit.CRN.Construct.builder.CRNExpand method) (synkit.CRN.Construct.DAG.mod_crn.MODCRN method) (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener method) (synkit.CRN.Construct.DAG.syncrn.SynCRN method) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener method) build_all() (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor method) build_compound_table() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_crn_from_smarts() (in module synkit.CRN.Construct.builder) build_dict() (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor method) build_edge_labels() (in module synkit.CRN.Visualize.labels) build_its_from_rsmi() (in module synkit.Graph.Mech.conversion) build_kegg_json() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_missing_compound_report() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_module_json() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_molecule_pool() (synkit.CRN.Construct.abstract.AbstractReactionExtractor method) build_node_labels() (in module synkit.CRN.Visualize.labels) build_pathway_json() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_petri_net_from_flow() (synkit.CRN.Pathway.realizability.PathwayRealizability method) build_reaction_smiles_dict() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) build_S() (in module synkit.CRN.Props.stoich) build_S_minus_plus() (in module synkit.CRN.Props.stoich) build_signatures() (synkit.Graph.Matcher.wl_sel.WLSel method) build_syncrn_from_smarts() (in module synkit.CRN.Construct.DAG.syncrn) ButinaCluster (class in synkit.Chem.Cluster.butina) by_name() (synkit.Graph.FG.model.FunctionalGroupRegistry method)

C

cache (synkit.Vis.embedding.Embedding property) calculate_charge() (synkit.Chem.Reaction.neutralize.Neutralize static method) calculate_charge_dict() (synkit.Chem.Reaction.neutralize.Neutralize static method) candidate_edge_pool (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) candidate_pairs() (synkit.Graph.Matcher.wl_sel.WLSel method) canon_graph (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) canon_morgan() (in module synkit.Graph.Canon.canon_algs) canonical (synkit.Graph.syn_graph.SynGraph property) canonical() (in module synkit.CRN.Symmetry.canon) canonical_form() (synkit.Graph.Canon.nauty.NautyCanonicalizer method) canonical_from_mol() (in module synkit.CRN.Construct.smiles) canonical_graph (synkit.Graph.Canon.canon_graph.CanonicalGraph property) (synkit.Graph.Canon.canon_graph.CanonicalRule property) (synkit.Graph.canon_graph.CanonicalGraph property) (synkit.Graph.canon_graph.CanonicalRule property) canonical_graph() (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) canonical_hash (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) (synkit.Graph.Canon.canon_graph.CanonicalGraph property) (synkit.Graph.Canon.canon_graph.CanonicalRule property) (synkit.Graph.canon_graph.CanonicalGraph property) (synkit.Graph.canon_graph.CanonicalRule property) canonical_key (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) canonical_key() (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) canonical_order (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) canonical_order() (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) canonical_product_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_reactant_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_result() (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) canonical_rsmi (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_rule (synkit.Graph.Canon.canon_graph.CanonicalRule property) (synkit.Graph.canon_graph.CanonicalRule property) canonical_signature() (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.GraphCanonicaliser method) CanonicalGraph (class in synkit.Graph.Canon.canon_graph) (class in synkit.Graph.canon_graph) canonicalise() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI method) canonicalise_graph() (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.GraphCanonicaliser method) canonicalise_graphs() (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.GraphCanonicaliser method) canonicaliser (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) canonicalize_tautomer() (in module synkit.Chem.Molecule.standardize) (synkit.Chem.Molecule.standardize.MolStandardizer method) CanonicalRule (class in synkit.Graph.Canon.canon_graph) (class in synkit.Graph.canon_graph) CanonRSMI (class in synkit.Chem.Reaction.canon_rsmi) categorize_reactions() (synkit.Chem.Reaction.standardize.Standardize static method) certificate (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) (synkit.CRN.Pathway.realizability.PathwayRealizability property) changed (synkit.Vis.visual_model.VisualNode attribute) changed_atoms (synkit.Vis.reaction_drawer.ReactionHighlights attribute) charge() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) check_arrow_code_coverage() (in module synkit.Graph.Mech.conversion) check_equivariant_graph() (in module synkit.Graph.Hyrogen._misc) (synkit.Chem.Reaction.aam_validator.AAMValidator static method) check_explicit_hydrogen() (in module synkit.Graph.Hyrogen._misc) check_graph_connectivity() (in module synkit.Graph.Feature.graph_descriptors) check_graph_type() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) check_hcount_change() (in module synkit.Graph.Hyrogen._misc) check_pair() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) check_persistence() (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) check_rule() (synkit.Rule.Compose.valence_constrain.ValenceConstrain method) check_typed_conversion_quality() (in module synkit.Graph.Mech.conversion) choose_auto_layout() (in module synkit.CRN.Visualize.layout) circular_bipartite_layout() (in module synkit.CRN.Visualize.layout) classification (synkit.CRN.Props.dynamics.StructuralSingularitySummary property) classify_arrow_shape() (in module synkit.Graph.Mech.conversion) clean_aam() (synkit.Synthesis.Reactor.post_syn.PostSyn method) clean_graph_keep_largest_component() (in module synkit.Graph.utils) clean_radical_rsmi() (in module synkit.Chem.utils)

clean_smiles() (synkit.Chem.Reaction.cleaning.Cleaning static method) clean_wc() (in module synkit.Chem.Reaction.radical_wildcard) Cleaning (class in synkit.Chem.Reaction.cleaning) clear() (synkit.CRN.Construct.derivation.DerivationLog method) clear_cache() (synkit.Vis.embedding.Embedding method) clear_stereochemistry() (in module synkit.Chem.Molecule.standardize) (synkit.Chem.Molecule.standardize.MolStandardizer method) client (synkit.CRN.Query.kegg_extract.KEGGExtractor attribute) cluster() (synkit.Chem.Cluster.butina.ButinaCluster static method) (synkit.Graph.Matcher.batch_cluster.BatchCluster method) collect_data() (in module synkit.IO.data_io) color (synkit.Vis.visual_model.VisualEdge attribute) color_hist (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) color_of() (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) ColorPalette (class in synkit.CRN.Visualize.palette) colors (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) colors() (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) COMPONENT (synkit.Synthesis.Reactor.strategy.Strategy attribute) components (synkit.Graph.Matcher.automorphism.Automorphism property) components() (synkit.Graph.Matcher.auto_est.AutoEst method) ComposeRule (class in synkit.Rule.Compose.compose_rule) compute() (synkit.Chem.Molecule.descriptors.PerMolDescriptors class method) (synkit.Graph.Matcher.orbit.OrbitAccuracy method) compute_all() (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) compute_conservativity() (in module synkit.CRN.Props.thermo) compute_crippen() (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder method) compute_estate() (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder method) compute_gasteiger() (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder method) compute_gasteiger_inplace() (in module synkit.Chem.Molecule.descriptors) compute_layers_multiset() (synkit.CRN.Pathway.reachability.PathwayReachability method) compute_layers_set() (synkit.CRN.Pathway.reachability.PathwayReachability method) compute_layout() (in module synkit.CRN.Visualize.layout) compute_orbits() (synkit.Graph.Canon.nauty.NautyCanonicalizer method) compute_semiflows() (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) compute_siphons_traps() (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) compute_standard_order() (in module synkit.Graph.MTG.utils) compute_thermo_summary() (in module synkit.CRN.Props.thermo) compute_tsne() (synkit.Vis.embedding.Embedding method) configure_warnings_and_logs() (in module synkit.IO.debug) confusion_map (synkit.Graph.Matcher.orbit.OrbitAccuracy property) conservative (synkit.CRN.Props.thermo.ThermoSummary attribute) consistent (synkit.CRN.Props.thermo.ThermoSummary attribute) construct() (synkit.Graph.ITS.its_construction.ITSConstruction static method) (synkit.Graph.ITS.partial_its.PartialITS static method) ConstructionStrategy (class in synkit.CRN.Construct.strategy) context_extraction() (synkit.Graph.Context.radius_expand.RadiusExpand static method) convert_arr2vec() (synkit.Chem.Fingerprint.transformation_fp.TransformationFP static method) convert_arrow_code() (in module synkit.Graph.Mech.conversion) convert_reaction_arrow() (in module synkit.Graph.Mech.conversion) convert_record() (in module synkit.Graph.Mech.conversion) convert_records() (in module synkit.Graph.Mech.conversion) CORE_EDGE_DEFAULTS (synkit.Graph.ITS.its_construction.ITSConstruction attribute) core_mapping_without_wildcard_regions (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) CORE_NODE_DEFAULTS (synkit.Graph.ITS.its_construction.ITSConstruction attribute) count_carbons() (in module synkit.Chem.utils) count_lhs_components() (in module synkit.CRN.Construct.arity) counts (synkit.CRN.Structure.reaction.RXNSide attribute) create_edge_signature() (synkit.Graph.Feature.graph_signature.GraphSignature method) create_graph_signature() (synkit.Graph.Feature.graph_signature.GraphSignature method) create_wl_hash() (synkit.Graph.Feature.graph_signature.GraphSignature method) crippen_logp (synkit.Chem.Molecule.descriptors.PerMolDescriptors attribute) crippen_mr (synkit.Chem.Molecule.descriptors.PerMolDescriptors attribute) CRN (class in synkit.CRN.Construct.DAG.crn) crn() (synkit.Vis.crn_vis.CRNVisualizer method) CRNAutomorphism (class in synkit.CRN.Symmetry.automorphism) CRNCanonicalizer (class in synkit.CRN.Symmetry.canon) CRNExpand (class in synkit.CRN.Construct.builder) CRNGraphInfo (class in synkit.CRN.Visualize.validation) CRNIsomorphism (class in synkit.CRN.Symmetry.isomorphism) CRNStyle (class in synkit.CRN.Visualize.vis) CRNSymmetry (class in synkit.CRN.Symmetry.symmetry) CRNVis (class in synkit.CRN.Visualize.crn_vis) (class in synkit.CRN.Visualize.vis) CRNVisualizer (class in synkit.Vis.crn_vis) curve_radius (synkit.CRN.Visualize.vis.CRNStyle attribute) curved_edges (synkit.CRN.Visualize.vis.CRNStyle attribute)

D

debug_arrow_bond_orders() (in module synkit.Graph.Mech.conversion) debug_record() (in module synkit.Graph.Mech.conversion) decompose() (synkit.Chem.Molecule.formula.Formula method) (synkit.Graph.ITS.its_destruction.ITSDestruction method) dedup_across_rules (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) dedup_delta (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) deduplicate (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener attribute) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener attribute) deduplicate_abstract_reactions() (in module synkit.CRN.Construct.abstract) deduplicate_by_flow (synkit.CRN.Pathway.pathfinder.PathFinderConfig attribute) deduplicate_matches_with_anchor() (in module synkit.Graph.Matcher.dedup_matches) DEFAULT_MAX_DISTANCE (synkit.Chem.Molecule.graph_annotator.GraphAnnotator attribute) default_registry() (in module synkit.Graph.FG.catalog) DEFAULT_THRESHOLD (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine attribute) degree() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) degree_shell_layout() (in module synkit.CRN.Visualize.layout) Deionize (class in synkit.Chem.Reaction.deionize) dense_edge_threshold (synkit.CRN.Visualize.vis.CRNStyle attribute) dense_font_size (synkit.CRN.Visualize.vis.CRNStyle attribute) dense_graph() (synkit.CRN.Visualize.vis.CRNVis method) dense_node_threshold (synkit.CRN.Visualize.vis.CRNStyle attribute) depth (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) (synkit.CRN.Pathway.reachability.ReachabilityLayer attribute) derivation_graph (synkit.CRN.Construct.DAG.mod_crn.MODCRN property) derivation_records (synkit.CRN.Construct.builder.CRNExpand property) DerivationLog (class in synkit.CRN.Construct.derivation) DerivationRecord (class in synkit.CRN.Construct.derivation) derivations (synkit.CRN.Construct.builder.CRNExpand attribute) DerivationState (class in synkit.CRN.Construct.state) describe() (synkit.CRN.Structure.syncrn.SynCRN method) (synkit.Graph.MTG.mtg.MTG static method) (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) (synkit.Graph.Wildcard.radwc.RadWC static method) (synkit.Graph.Wildcard.wildcard.WildCard static method) (synkit.Synthesis.Reactor.batch_reactor.BatchReactor method) (synkit.Synthesis.Reactor.benchmark.Benchmark method) (synkit.Synthesis.Reactor.imba_engine.ImbaEngine static method)

descriptor (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder property) detect() (synkit.Graph.FG.detector.FunctionalGroupDetector method) (synkit.Graph.FG.ring_system.AromaticRingSystemDetector static method) detect_automorphisms() (in module synkit.CRN.Symmetry.automorphism) detect_its_format() (in module synkit.IO.chem_converter) detect_visual_kind() (in module synkit.Vis.visual_model) determinant_checked (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) determinant_expr (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) determinant_is_zero (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) dfs_to_smiles() (in module synkit.IO.chem_converter) dg (synkit.Synthesis.Reactor.mod_aam.MODAAM property) (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) diagnostics (synkit.Rule.Apply.rule_matcher.RuleMatcher property) (synkit.Synthesis.Reactor.imba_engine.ImbaEngine property) (synkit.Synthesis.Reactor.partial_engine.PartialEngine property) (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) dict_balance_check() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) dict_process() (synkit.Chem.Fingerprint.fp_calculator.FPCalculator static method) dicts_balance_check() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck method) digest_size (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) dim_left_kernel (synkit.CRN.Props.stoich.StoichSummary attribute) dim_right_kernel (synkit.CRN.Props.stoich.StoichSummary attribute) draw() (synkit.CRN.Visualize.crn_vis.CRNVis method) (synkit.CRN.Visualize.vis.CRNVis method) draw_crn() (in module synkit.CRN.Visualize.vis) draw_graph() (in module synkit.Vis.visual_drawer) draw_its_from_rsmi() (in module synkit.Vis.its_drawer) draw_its_graph() (in module synkit.Vis.its_drawer) draw_its_only() (in module synkit.Vis.its_drawer) draw_molecule_graph() (in module synkit.Vis.molecule_drawer) draw_mtg_graph() (in module synkit.Vis.mtg_drawer) draw_mtg_steps() (in module synkit.Vis.mtg_drawer) draw_reaction_graph() (in module synkit.Vis.reaction_drawer) draw_reaction_graphs() (in module synkit.Vis.reaction_drawer) drop_non_aam (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) duplicate_atom_maps_in_side() (in module synkit.Graph.Mech.conversion)

E

edge_alpha (synkit.CRN.Visualize.vis.CRNStyle attribute) edge_attr (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) edge_attributes (synkit.Vis.graph_visualizer.GraphVisualizer property) edge_attrs (synkit.Graph.Canon.nauty.NautyCanonicalizer attribute) (synkit.Graph.Matcher.auto_est.AutoEst property) edge_code_u64() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) edge_is_double() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) edge_is_single() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) edge_label (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO property) edge_label_one() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) edge_labels() (synkit.CRN.Visualize.vis.CRNVis method) edge_orders() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) edge_width (synkit.CRN.Visualize.vis.CRNStyle attribute) EdgeMaskCandidate (class in synkit.Chem.Reaction.Mapper.wl_mapper) edges (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) (synkit.Vis.visual_model.VisualGraph attribute) eigen_canonical_signature() (in module synkit.Graph.Canon.canon_algs) elapsed_seconds (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) electron_diagnostics (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) element (synkit.Vis.visual_model.VisualNode attribute) element() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) element_counts (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) (synkit.Graph.FG.ring_system.AromaticSubring attribute) embed_pre_filter (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) embed_threshold (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) Embedding (class in synkit.Vis.embedding) enable_bond_cut (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) enable_dynamic_wl (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) enable_heuristic_scoring (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) enable_rc_refine (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) enable_swap_refine (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) enable_symmetry_pruning (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute)

enabled() (synkit.CRN.Petrinet.net.PetriNet method) engine (synkit.CRN.Symmetry.canon.CRNCanonicalizer property) (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) enumerate_all_unique_mappings() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) enumerate_tautomers() (in module synkit.Chem.utils) equation_to_text() (in module synkit.CRN.Query.kegg_parse) estate (synkit.Chem.Molecule.descriptors.PerMolDescriptors attribute) estimate_automorphism_groups() (in module synkit.Graph.Matcher.auto_est) estimate_available_lone_pairs() (synkit.IO.mol_to_graph.MolToGraph class method) estimate_embeddings_wl() (synkit.Graph.Matcher.partial_matcher.PartialMatcher method) estimate_lone_pairs() (synkit.IO.mol_to_graph.MolToGraph class method) estimate_oxidation_states() (synkit.IO.mol_to_graph.MolToGraph class method) event_id (synkit.CRN.Construct.derivation.DerivationRecord attribute) exact (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) exact_orbits (synkit.Graph.Matcher.orbit.OrbitAccuracy property) example_conservation_law (synkit.CRN.Props.thermo.ThermoSummary attribute) execution_order() (synkit.Graph.FG.model.FunctionalGroupRegistry method) expand_aam() (in module synkit.Synthesis.Reactor.mod_aam) (synkit.Chem.Reaction.canon_rsmi.CanonRSMI method) expand_aam_with_its() (synkit.Graph.ITS.its_expand.ITSExpand static method) expand_stoichiometry() (in module synkit.CRN.Query.kegg_parse) explain() (synkit.CRN.Petrinet.analyzer.PetriAnalyzer method) explicit() (synkit.Chem.Molecule.valence.ValenceResolver static method) explicit_h (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) export_layers_json() (synkit.CRN.Pathway.reachability.PathwayReachability method) export_pnml() (synkit.CRN.Pathway.realizability.PathwayRealizability method) export_report() (synkit.CRN.Construct.DAG.mod_crn.MODCRN method) extend() (synkit.Graph.FG.model.FunctionalGroupRegistry method) extract_atom_maps_from_smiles() (in module synkit.Graph.Mech.conversion) extract_features() (synkit.Graph.Feature.hash_fps.HashFPs method) extract_k() (synkit.Graph.Context.radius_expand.RadiusExpand static method) extract_order_from_edge_data() (in module synkit.Graph.Mech.conversion) extract_order_norm() (in module synkit.Graph.MTG.utils) extract_reactions_and_templates() (synkit.CRN.Construct.abstract.AbstractReactionExtractor method) extract_subgraph() (synkit.Graph.Context.radius_expand.RadiusExpand static method) (synkit.Graph.ITS.normalize_aam.NormalizeAAM static method) extract_syncrn_incidence() (in module synkit.CRN.Petrinet.net) extractor (synkit.CRN.Query.kegg_impute.KEGGImputer attribute)

F

fast_signature() (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) feature (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor property) featurize_smiles() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer class method) figsize (synkit.CRN.Visualize.vis.CRNStyle attribute) filter_best_pairs() (synkit.Graph.Matcher.wl_sel.WLSel method) filter_context() (in module synkit.Rule.Modify.rule_utils) (in module synkit.Rule.Modify.strip_rule) filter_smallest_vertex() (synkit.Rule.Compose.compose_rule.ComposeRule static method) (synkit.Rule.Compose.rule_compose.RuleCompose static method) filter_smiles() (in module synkit.Chem.utils) filter_valid_molecules() (synkit.Chem.Reaction.standardize.Standardize static method) filtered (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector property) finalize_hash() (synkit.Graph.Feature.hash_fps.HashFPs method) find_block() (in module synkit.Rule.Modify.rule_utils) find_common_subgraph() (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher method) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher method) (synkit.Graph.MTG.mcs_matcher.MCSMatcher method) find_common_subgraph_approx() (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher method) find_graph_isomorphism() (in module synkit.Graph.Matcher.graph_morphism) find_longest_fragment() (in module synkit.Chem.utils) find_mtg() (in module synkit.Graph.MTG.mtg_explore) find_nearest_neighbors() (synkit.Graph.Context.radius_expand.RadiusExpand static method) find_p_semiflows() (in module synkit.CRN.Petrinet.semiflows) find_partial_mappings() (synkit.Graph.Matcher.partial_matcher.PartialMatcher static method) find_paths_set() (synkit.CRN.Pathway.pathfinder.PathwayFinder method) find_rc_mapping() (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher method) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher method) (synkit.Graph.MTG.mcs_matcher.MCSMatcher method) find_reaction_highlights() (in module synkit.Vis.reaction_drawer) find_siphons() (in module synkit.CRN.Petrinet.structure) find_subgraph_mappings() (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine static method) find_t_semiflows() (in module synkit.CRN.Petrinet.semiflows) find_traps() (in module synkit.CRN.Petrinet.structure) find_unequal_order_edges() (synkit.Graph.Context.radius_expand.RadiusExpand static method) find_wc_graph_isomorphism() (in module synkit.Graph.Wildcard.fuse_graph) fingerprint() (synkit.Graph.Feature.graph_fps.GraphFP method) fire() (synkit.CRN.Petrinet.net.PetriNet method) fit() (synkit.Chem.Fingerprint.transformation_fp.TransformationFP method) (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper method) (synkit.Chem.Reaction.standardize.Standardize method) (synkit.Graph.Context.hier_context.HierContext method) (synkit.Graph.Hyrogen.hextend.HExtend static method) (synkit.Graph.ITS.its_relabel.ITSRelabel method) (synkit.Graph.ITS.normalize_aam.NormalizeAAM method) (synkit.Graph.Matcher.auto_est.AutoEst method) (synkit.Graph.Matcher.batch_cluster.BatchCluster method) (synkit.Graph.Matcher.graph_cluster.GraphCluster method) (synkit.Graph.Wildcard.wc_matcher.WCMatcher method) (synkit.Rule.Compose.rule_mapping.RuleMapping method) (synkit.Rule.Modify.prune_templates.PruneTemplate method) (synkit.Synthesis.Reactor.batch_reactor.BatchReactor method) (synkit.Synthesis.Reactor.benchmark.Benchmark method) (synkit.Synthesis.Reactor.imba_engine.ImbaEngine method) (synkit.Synthesis.Reactor.partial_engine.PartialEngine method)

fix_aam_rsmi() (synkit.Chem.Reaction.fix_aam.FixAAM static method) fix_aam_smiles() (synkit.Chem.Reaction.fix_aam.FixAAM static method) fix_dict() (synkit.Chem.Reaction.tautomerize.Tautomerize static method) fix_dicts() (synkit.Chem.Reaction.tautomerize.Tautomerize static method) fix_kekulize() (synkit.Graph.ITS.normalize_aam.NormalizeAAM static method) fix_negative_charge() (synkit.Chem.Reaction.neutralize.Neutralize static method) fix_positive_charge() (synkit.Chem.Reaction.neutralize.Neutralize static method) fix_radical_rsmi() (in module synkit.Chem.Molecule.standardize) fix_rsmi_kekulize() (synkit.Graph.ITS.normalize_aam.NormalizeAAM static method) fix_smiles() (synkit.Chem.Reaction.tautomerize.Tautomerize static method) fix_unbalanced_charged() (synkit.Chem.Reaction.neutralize.Neutralize static method) FixAAM (class in synkit.Chem.Reaction.fix_aam) flow (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) font_size (synkit.CRN.Visualize.crn_vis.CRNVis attribute) (synkit.CRN.Visualize.vis.CRNStyle attribute) (synkit.CRN.Visualize.vis.CRNVis attribute) format() (synkit.CRN.Structure.reaction.Reaction method) format_reaction() (synkit.CRN.Structure.syncrn.SynCRN method) format_side() (synkit.CRN.Structure.reaction.Reaction method) formed_bonds (synkit.Vis.reaction_drawer.ReactionHighlights attribute) Formula (class in synkit.Chem.Molecule.formula) forward_its (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) FPCalculator (class in synkit.Chem.Fingerprint.fp_calculator) fps (synkit.Chem.Fingerprint.fp_calculator.FPCalculator attribute) fragments_remover() (in module synkit.Chem.Molecule.standardize) from_crn() (synkit.CRN.Props.stoich.StoichSummary class method) from_digraph() (synkit.CRN.Structure.syncrn.SynCRN class method) from_gml() (synkit.Rule.syn_rule.SynRule class method) from_reaction_strings() (synkit.CRN.Structure.syncrn.SynCRN class method) from_rsmi() (synkit.Graph.Wildcard.wildcard.WildCard static method) from_smart() (synkit.Rule.syn_rule.SynRule class method) from_smiles() (synkit.Chem.Molecule.descriptors.PerMolDescriptors class method) (synkit.Chem.Molecule.standardize.MolStandardizer class method) (synkit.Synthesis.Reactor.syn_reactor.SynReactor class method) from_string() (synkit.Synthesis.Reactor.strategy.Strategy class method) from_syncrn() (synkit.CRN.Petrinet.net.PetriNet class method) frontier_keys (synkit.CRN.Construct.state.DerivationState attribute) FrontierStrategy (class in synkit.CRN.Construct.strategy) FunctionalGroupAudit (class in synkit.Graph.FG.audit) FunctionalGroupDetector (class in synkit.Graph.FG.detector) FunctionalGroupMatch (class in synkit.Graph.FG.model) FunctionalGroupPattern (class in synkit.Graph.FG.model) FunctionalGroupRegistry (class in synkit.Graph.FG.model) fuse_its_graphs() (in module synkit.Graph.Wildcard.its_merge) fuse_wc_graphs() (in module synkit.Graph.Wildcard.fuse_graph) fused_graph (synkit.Graph.Wildcard.its_merge.ITSMerge property) fused_its (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) fused_rsmis (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property)

G

G (synkit.CRN.Symmetry.automorphism.CRNAutomorphism property) (synkit.CRN.Symmetry.canon.CRNCanonicalizer property) (synkit.CRN.Symmetry.isomorphism.CRNIsomorphism property) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer property) (synkit.Graph.ITS.its_destruction.ITSDestruction property) gasteiger (synkit.Chem.Molecule.descriptors.PerMolDescriptors attribute) generate_atom_map() (synkit.Rule.Modify.molecule_rule.MoleculeRule static method) generate_fingerprint() (synkit.Graph.Feature.morgan_fps.MorganFPs method) (synkit.Graph.Feature.path_fps.PathFPs method) generate_molecule_rule() (synkit.Rule.Modify.molecule_rule.MoleculeRule method) generate_molecule_smart() (synkit.Rule.Modify.molecule_rule.MoleculeRule static method) generate_reaction_smiles() (synkit.Synthesis.Reactor.mod_reactor.MODReactor static method) generic_convert_arrow_code() (in module synkit.Graph.Mech.conversion) generic_convert_step() (in module synkit.Graph.Mech.conversion) get() (synkit.CRN.Structure.reaction.RXNSide method) get_aam() (synkit.Graph.MTG.mtg.MTG method) get_aam_pairwise_indices() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI static method) get_avalon_fp() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) get_bond_stereochemistry() (synkit.IO.mol_to_graph.MolToGraph static method) get_bond_type_from_order() (synkit.IO.graph_to_mol.GraphToMol static method) get_child1_to_child2_mapping() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) get_combined_molecular_formula() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) get_compose_its() (synkit.Graph.MTG.mtg.MTG method) get_compound_ids_from_equations() (in module synkit.CRN.Query.kegg_parse) get_compound_ids_from_text() (in module synkit.CRN.Query.kegg_parse) get_compound_molblock() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_compound_name() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_cycle_member_rings() (in module synkit.Graph.Hyrogen._misc) (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) get_descriptors() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) get_dg() (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) get_ecfp() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) get_edges() (synkit.Graph.syn_graph.SynGraph method) get_element_count() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) get_equation_for_reaction() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_its_bond_order() (in module synkit.Graph.Mech.conversion) get_its_steps() (synkit.Graph.MTG.mtg.MTG method) get_maccs_keys() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) get_mappings() (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher method) (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher method) (synkit.Graph.Matcher.partial_matcher.PartialMatcher method) (synkit.Graph.MTG.mcs_matcher.MCSMatcher method) get_max_fragment() (in module synkit.Chem.utils) get_module_equations() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_modules_from_pathway() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_mtg() (synkit.Graph.MTG.mtg.MTG method) get_node() (synkit.Chem.Molecule.graph_annotator.GraphAnnotator method) get_node_attr() (synkit.Chem.Molecule.graph_annotator.GraphAnnotator method) get_node_attribute() (synkit.Graph.ITS.its_construction.ITSConstruction static method) get_node_attributes_with_defaults() (synkit.Graph.ITS.its_construction.ITSConstruction static method) get_nodes() (synkit.Graph.syn_graph.SynGraph method) get_nodes_from_edges() (in module synkit.Rule.Modify.rule_utils) get_optional_text() (synkit.CRN.Query.kegg_api.KEGGClient method) get_palette() (in module synkit.CRN.Visualize.palette) get_pathway_equations() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_priority() (in module synkit.Graph.Hyrogen._misc) get_rc() (in module synkit.Graph.ITS.its_decompose) get_rdk_fp() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) get_reaction_ids_from_module() (synkit.CRN.Query.kegg_extract.KEGGExtractor method) get_reaction_smiles() (synkit.CRN.Construct.DAG.crn.CRN method) (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method)

get_result() (synkit.Rule.Apply.rule_matcher.RuleMatcher method) get_rsmi_steps() (synkit.Graph.MTG.mtg.MTG method) get_rule_comp() (synkit.Rule.Compose.compose_rule.ComposeRule method) get_sanitized_smiles() (in module synkit.Chem.utils) get_smarts() (synkit.Synthesis.Reactor.mod_aam.MODAAM method) get_stereochemistry() (synkit.IO.mol_to_graph.MolToGraph static method) get_text() (synkit.CRN.Query.kegg_api.KEGGClient method) get_unique_graphs_for_clusters() (synkit.Graph.Hyrogen.hextend.HExtend static method) get_unique_node_for_atom_map() (in module synkit.Graph.Mech.conversion) gml_to_its() (in module synkit.IO.chem_converter) gml_to_smart() (in module synkit.IO.chem_converter) GMLToNX (class in synkit.IO.gml_to_nx) goal_atleast (synkit.CRN.Pathway.realizability.PathwayRealizability property) (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) goal_exact (synkit.CRN.Pathway.realizability.PathwayRealizability property) (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) graph (synkit.Chem.Molecule.graph_annotator.GraphAnnotator property) (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener attribute) (synkit.CRN.Visualize.crn_vis.CRNVis attribute) (synkit.CRN.Visualize.vis.CRNVis attribute) (synkit.Graph.FG.model.FunctionalGroupPattern attribute) (synkit.Graph.Matcher.auto_est.AutoEst property) (synkit.IO.mol_to_graph.MolToGraph property) (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) graph() (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) graph_alignment() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) graph_attrs (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) (synkit.CRN.Structure.syncrn.SynCRN attribute) graph_canonical_hash() (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.GraphCanonicaliser method) graph_isomorphism() (in module synkit.Graph.Matcher.graph_morphism) graph_signature() (synkit.Graph.Canon.nauty.NautyCanonicalizer method) graph_to_mol() (synkit.IO.graph_to_mol.GraphToMol method) graph_to_rsmi() (in module synkit.IO.chem_converter) graph_to_sanitized_kekule_mol() (in module synkit.Graph.Mech.electron_accounting) graph_to_smi() (in module synkit.IO.chem_converter) graph_type (synkit.CRN.Symmetry.automorphism.CRNAutomorphism property) (synkit.CRN.Symmetry.canon.CRNCanonicalizer property) (synkit.CRN.Symmetry.isomorphism.CRNIsomorphism property) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer property) (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) GraphAnnotator (class in synkit.Chem.Molecule.graph_annotator) GraphCache (class in synkit.Chem.Reaction.Mapper.wl_mapper) GraphCanonicaliser (class in synkit.Graph.Canon.canon_graph) (class in synkit.Graph.canon_graph) GraphCluster (class in synkit.Graph.Matcher.graph_cluster) GraphCollectionSelector (class in synkit.Graph.Wildcard.graph_wc) GraphDescriptor (class in synkit.Graph.Feature.graph_descriptors) GraphFP (class in synkit.Graph.Feature.graph_fps) GraphMatcherEngine (class in synkit.Graph.Matcher.graph_matcher) graphs (synkit.CRN.Construct.DAG.mod_crn.MODCRN property) GraphSignature (class in synkit.Graph.Feature.graph_signature) GraphToMol (class in synkit.IO.graph_to_mol) GraphVisualizer (class in synkit.Vis.graph_visualizer) greedy_topk_per_u (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) group_nodes (synkit.Graph.FG.model.FunctionalGroupMatch attribute) (synkit.Graph.FG.model.FunctionalGroupPattern attribute) groups (synkit.Graph.Matcher.auto_est.AutoEst property)

H

H (synkit.Graph.ITS.its_destruction.ITSDestruction property) h_to_explicit() (in module synkit.Graph.Hyrogen._misc) h_to_implicit() (in module synkit.Graph.Hyrogen._misc) has_atom_mapping() (synkit.IO.mol_to_graph.MolToGraph static method) has_atom_maps() (in module synkit.CRN.Construct.smiles) has_HH() (in module synkit.Graph.Hyrogen._misc) has_irreversible_futile_cycles() (in module synkit.CRN.Props.thermo) has_nontrivial_automorphism() (synkit.CRN.Symmetry.automorphism.CRNAutomorphism method) (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) has_perfect_matching (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) has_wildcard_node() (in module synkit.Graph.utils) has_XH() (in module synkit.Graph.Hyrogen._misc) hash_fps() (synkit.Graph.Feature.hash_fps.HashFPs method) HashFPs (class in synkit.Graph.Feature.hash_fps) HComplete (class in synkit.Graph.Hyrogen.hcomplete) hcount() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) help (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher property) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher property) (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine property) (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) help() (synkit.Chem.Cluster.butina.ButinaCluster method) (synkit.Chem.Fingerprint.fp_calculator.FPCalculator method) (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer method) (synkit.Chem.Fingerprint.transformation_fp.TransformationFP method) (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor class method) (synkit.Chem.Molecule.graph_annotator.GraphAnnotator class method) (synkit.Chem.Molecule.standardize.MolStandardizer class method) (synkit.Chem.Reaction.canon_rsmi.CanonRSMI method) (synkit.CRN.Construct.DAG.crn.CRN method) (synkit.CRN.Construct.DAG.mod_crn.MODCRN method) (synkit.Graph.Canon.canon_graph.CanonicalGraph method) (synkit.Graph.Canon.canon_graph.CanonicalRule method) (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.CanonicalGraph method) (synkit.Graph.canon_graph.CanonicalRule method) (synkit.Graph.canon_graph.GraphCanonicaliser method) (synkit.Graph.ITS.its_destruction.ITSDestruction method) (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) (synkit.Graph.Matcher.orbit.OrbitAccuracy method) (synkit.Graph.MTG.mcs_matcher.MCSMatcher method) (synkit.Graph.syn_graph.SynGraph method) (synkit.IO.mol_to_graph.MolToGraph class method) (synkit.Rule.Apply.rule_matcher.RuleMatcher method) (synkit.Rule.syn_rule.SynRule method) (synkit.Synthesis.Reactor.batch_reactor.BatchReactor method) (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) (synkit.Synthesis.Reactor.rbl_engine.RBLEngine method) (synkit.Synthesis.Reactor.syn_reactor.SynReactor method) (synkit.Vis.graph_visualizer.GraphVisualizer method) (synkit.Vis.rule_vis.RuleVis method)

hetero_nodes (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) hetero_pattern (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) hetero_sequence (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) (synkit.Graph.FG.ring_system.AromaticSubring attribute) heteroaromatic_systems (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) heuristic_aromatic_c_break_penalty (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) heuristic_candidate_budget (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) heuristic_carbonyl_double_penalty (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) heuristic_max_cut_size (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) heuristics_MCCS() (in module synkit.Graph.Matcher.graph_morphism) HExtend (class in synkit.Graph.Hyrogen.hextend) HierContext (class in synkit.Graph.Context.hier_context) highlight_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) highlight_edge_width (synkit.CRN.Visualize.vis.CRNStyle attribute) highlight_linewidths (synkit.CRN.Visualize.vis.CRNStyle attribute) highlight_node (synkit.CRN.Visualize.palette.ColorPalette attribute) hill_formula() (synkit.Chem.Molecule.formula.Formula method) host (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) host_graph (synkit.Graph.Wildcard.its_merge.ITSMerge property) (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) hosts (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO property) hungarian_max_size (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute)

I

id (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.rule.Rule attribute) (synkit.CRN.Structure.species.Species attribute) ImbaEngine (class in synkit.Synthesis.Reactor.imba_engine) implicit() (synkit.Chem.Molecule.valence.ValenceResolver static method) implicit_hydrogen() (in module synkit.Graph.Hyrogen._misc) implicit_temp (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) impute_module() (synkit.CRN.Query.kegg_impute.KEGGImputer method) impute_pathway() (synkit.CRN.Query.kegg_impute.KEGGImputer method) include_initial (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) increment_atom_mapping() (synkit.Chem.Reaction.fix_aam.FixAAM static method) infer_rule_arity() (in module synkit.CRN.Construct.arity) initial_marking (synkit.CRN.Pathway.realizability.PathwayRealizability property) (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) initial_species (synkit.CRN.Pathway.reachability.ReachabilityResult attribute) initialize_hash() (synkit.Graph.Feature.hash_fps.HashFPs method) integer_conservation_laws() (in module synkit.CRN.Props.stoich) invert (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) irreversible_futile_cycles (synkit.CRN.Props.thermo.ThermoSummary attribute) is_acyclic_graph() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) is_acyl_oxygen() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) is_acyl_oxygen_peroxy() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) is_ancestor() (synkit.Graph.FG.model.FunctionalGroupRegistry method) is_borrow_realizable() (synkit.CRN.Pathway.realizability.PathwayRealizability method) is_carbonyl_c() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) is_complex_cyclic_graph() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) is_connected (synkit.Graph.Matcher.automorphism.Automorphism property) is_conservative() (in module synkit.CRN.Props.thermo) is_consistent() (in module synkit.CRN.Props.thermo) is_dag (synkit.CRN.Visualize.validation.CRNGraphInfo attribute) (synkit.CRN.Visualize.vis.CRNVis property) is_full_rank (synkit.CRN.Props.stoich.StoichSummary property) is_fused (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) is_graph_empty() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) is_match (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) is_one() (in module synkit.Graph.Mech.conversion)

is_realizable() (synkit.CRN.Pathway.realizability.PathwayRealizability method) is_realizable_via_konig() (synkit.CRN.Pathway.realizability.PathwayRealizability method) is_scaled_realizable() (synkit.CRN.Pathway.realizability.PathwayRealizability method) is_single_cyclic_graph() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) is_subgraph() (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) is_underdetermined (synkit.CRN.Props.stoich.StoichSummary property) is_zero() (in module synkit.Graph.Mech.conversion) isomorphic() (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) isomorphic_to() (synkit.CRN.Symmetry.isomorphism.CRNIsomorphism method) items() (synkit.CRN.Structure.reaction.RXNSide method) iter_changed_edges() (in module synkit.Vis.visual_model) iter_changed_nodes() (in module synkit.Vis.visual_model) iter_mixtures() (synkit.CRN.Construct.strategy.ConstructionStrategy method) (synkit.CRN.Construct.strategy.FrontierStrategy method) iter_mixtures_arity1() (in module synkit.CRN.Construct.mixtures) iter_mixtures_arity2() (in module synkit.CRN.Construct.mixtures) iter_mixtures_arityk() (in module synkit.CRN.Construct.mixtures) iter_reaction_records() (synkit.CRN.Construct.abstract.AbstractReactionExtractor method) iterations (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) iterative_cluster() (synkit.Graph.Matcher.graph_cluster.GraphCluster method) iterative_deepening() (synkit.Graph.Feature.graph_fps.GraphFP method) (synkit.Graph.Feature.hash_fps.HashFPs method) (synkit.Graph.Feature.morgan_fps.MorganFPs method) (synkit.Graph.Feature.path_fps.PathFPs method) iters_run (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) its (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) its_decompose() (in module synkit.Graph.ITS.its_decompose) its_list (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) its_to_gml() (in module synkit.IO.chem_converter) its_to_rsmi() (in module synkit.IO.chem_converter) ITSBuilder (class in synkit.Graph.ITS.its_builder) ITSConstruction (class in synkit.Graph.ITS.its_construction) ITSDestruction (class in synkit.Graph.ITS.its_destruction) ITSExpand (class in synkit.Graph.ITS.its_expand) ITSGraph() (synkit.Graph.ITS.its_builder.ITSBuilder static method) (synkit.Graph.ITS.its_construction.ITSConstruction static method) ITSMerge (class in synkit.Graph.Wildcard.its_merge) ITSRelabel (class in synkit.Graph.ITS.its_relabel)

J

jacobian_sign_pattern() (in module synkit.CRN.Props.dynamics)

jacobian_sparsity() (in module synkit.CRN.Props.dynamics)

K

k (synkit.Graph.MTG.mtg.MTG property) keep_aam (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) keep_largest_component() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) keep_largest_fragment() (synkit.Chem.Molecule.standardize.MolStandardizer method)

KEGGClient (class in synkit.CRN.Query.kegg_api) KEGGEquation (class in synkit.CRN.Query.kegg_parse) KEGGExtractor (class in synkit.CRN.Query.kegg_extract) KEGGImputer (class in synkit.CRN.Query.kegg_impute) kind (synkit.Vis.visual_model.VisualGraph attribute)

L

label (synkit.CRN.Construct.derivation.DerivationRecord attribute) (synkit.CRN.Petrinet.net.Transition attribute) (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.rule.Rule attribute) (synkit.CRN.Structure.species.Species attribute) (synkit.Vis.visual_model.VisualEdge attribute) (synkit.Vis.visual_model.VisualNode attribute) label_box_alpha (synkit.CRN.Visualize.vis.CRNStyle attribute) label_counts (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) label_fontweight (synkit.CRN.Visualize.vis.CRNStyle attribute) label_mtg_edges() (in module synkit.Graph.MTG.utils) label_text (synkit.CRN.Visualize.palette.ColorPalette attribute) label_to_molecule (synkit.CRN.Construct.abstract.AbstractReactionNetwork attribute) large_bucket_threshold (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) last_reaction (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) last_size (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher property) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher property) (synkit.Graph.MTG.mcs_matcher.MCSMatcher property) layer_spacing (synkit.CRN.Visualize.vis.CRNVis attribute) layers (synkit.CRN.Pathway.reachability.ReachabilityResult attribute) layout (synkit.CRN.Visualize.crn_vis.CRNVis attribute) (synkit.CRN.Visualize.vis.CRNVis attribute) left_nullspace() (in module synkit.CRN.Props.stoich)

left_nullspace_from_matrix() (in module synkit.CRN.Props.thermo) left_right_kernels() (in module synkit.CRN.Props.stoich) legend_text (synkit.CRN.Visualize.palette.ColorPalette attribute) lhs (synkit.CRN.Structure.reaction.Reaction attribute) lib_check() (synkit.Graph.Matcher.batch_cluster.BatchCluster method) linewidths (synkit.CRN.Visualize.vis.CRNStyle attribute) load_compressed() (in module synkit.IO.data_io) load_database() (in module synkit.IO.data_io) load_dg() (in module synkit.IO.data_io) load_dict_from_json() (in module synkit.IO.data_io) load_from_pickle() (in module synkit.IO.data_io) load_from_pickle_generator() (in module synkit.IO.data_io) load_gml_as_text() (in module synkit.IO.data_io) load_hypergraph() (synkit.CRN.Pathway.pathfinder.PathwayFinder method) (synkit.CRN.Pathway.reachability.PathwayReachability method) load_hypergraph_and_flow() (synkit.CRN.Pathway.realizability.PathwayRealizability method) load_list_from_file() (in module synkit.IO.data_io) load_model() (in module synkit.IO.data_io) load_syncrn() (synkit.CRN.Pathway.pathfinder.PathwayFinder method) (synkit.CRN.Pathway.reachability.PathwayReachability method) load_syncrn_and_flow() (synkit.CRN.Pathway.realizability.PathwayRealizability method) longest_radius_extension() (synkit.Graph.Context.radius_expand.RadiusExpand static method) LongestPath (class in synkit.Rule.Modify.longest_path) LongestPathInDisconnectedGraph() (synkit.Rule.Modify.longest_path.LongestPath method)

M

make_canonical_graph() (synkit.Graph.Canon.canon_graph.GraphCanonicaliser method) (synkit.Graph.canon_graph.GraphCanonicaliser method) make_dedup_key() (in module synkit.CRN.Construct.keys) mapped_rsmi (synkit.Chem.Reaction.Mapper.wl_mapper.Solution attribute) (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) mapper_cls (synkit.CRN.Query.kegg_extract.KEGGExtractor attribute) mapping (synkit.Chem.Reaction.Mapper.wl_mapper.MappingResult attribute) (synkit.Graph.FG.model.FunctionalGroupMatch attribute) mapping_count (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) mapping_direction (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher property) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher property) mapping_pairs (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) mapping_success_rate() (in module synkit.Chem.utils) MappingResult (class in synkit.Chem.Reaction.Mapper.wl_mapper) mappings (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher property) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher property) (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) margins (synkit.CRN.Visualize.vis.CRNStyle attribute) marking_to_tuple() (synkit.CRN.Petrinet.net.PetriNet method) masked() (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) MaskView (class in synkit.Chem.Reaction.Mapper.wl_mapper) matches (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) matches() (synkit.Graph.FG.detector.FunctionalGroupDetector method) max_bond_cut_size (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) max_candidates (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) max_components (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) max_depth (synkit.CRN.Pathway.pathfinder.PathFinderConfig attribute) (synkit.CRN.Pathway.realizability.RealizabilityConfig attribute) max_iter (synkit.Graph.Matcher.auto_est.AutoEst property) max_label_chars (synkit.CRN.Visualize.vis.CRNVis attribute) max_layers (synkit.CRN.Pathway.reachability.ReachabilityConfig attribute) max_mixtures_per_rule_step (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) max_paths (synkit.CRN.Pathway.pathfinder.PathFinderConfig attribute) max_solutions (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) max_states (synkit.CRN.Pathway.realizability.RealizabilityConfig attribute) max_tasks_per_step (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) maximum_connected_common_subgraph() (in module synkit.Graph.Matcher.graph_morphism) MCSMatcher (class in synkit.Graph.Matcher.mcs_matcher) (class in synkit.Graph.MTG.mcs_matcher) merge() (synkit.Graph.Wildcard.its_merge.ITSMerge method) merge_reaction() (in module synkit.Chem.utils) meta (synkit.Chem.Reaction.Mapper.wl_mapper.EdgeMaskCandidate attribute) (synkit.Chem.Reaction.Mapper.wl_mapper.MappingResult attribute) metadata (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) (synkit.CRN.Petrinet.net.Transition attribute) (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.rule.Rule attribute) (synkit.CRN.Structure.species.Species attribute) (synkit.CRN.Structure.syncrn.SynCRN attribute) (synkit.Vis.visual_model.VisualGraph attribute) metrics (synkit.Graph.Matcher.orbit.OrbitAccuracy property) mod_vis() (synkit.Vis.rule_vis.RuleVis method) MODAAM (class in synkit.Synthesis.Reactor.mod_aam) MODCRN (class in synkit.CRN.Construct.DAG.mod_crn) MODReactor (class in synkit.Synthesis.Reactor.mod_reactor) module synkit.Chem.Cluster.butina synkit.Chem.Fingerprint.fp_calculator synkit.Chem.Fingerprint.smiles_featurizer synkit.Chem.Fingerprint.transformation_fp synkit.Chem.Molecule.atom_features synkit.Chem.Molecule.descriptors synkit.Chem.Molecule.formula synkit.Chem.Molecule.graph_annotator synkit.Chem.Molecule.standardize synkit.Chem.Molecule.valence synkit.Chem.Reaction.aam_validator synkit.Chem.Reaction.balance_check synkit.Chem.Reaction.canon_rsmi synkit.Chem.Reaction.cleaning synkit.Chem.Reaction.deionize synkit.Chem.Reaction.fix_aam synkit.Chem.Reaction.Mapper.wl_mapper synkit.Chem.Reaction.neutralize synkit.Chem.Reaction.radical_wildcard synkit.Chem.Reaction.standardize synkit.Chem.Reaction.tautomerize synkit.Chem.utils synkit.CRN.Construct.abstract synkit.CRN.Construct.arity synkit.CRN.Construct.builder synkit.CRN.Construct.DAG.crn synkit.CRN.Construct.DAG.mod_crn synkit.CRN.Construct.DAG.syncrn synkit.CRN.Construct.derivation synkit.CRN.Construct.flattener synkit.CRN.Construct.keys synkit.CRN.Construct.mixtures synkit.CRN.Construct.smiles synkit.CRN.Construct.state synkit.CRN.Construct.strategy synkit.CRN.Construct.worker synkit.CRN.Pathway.pathfinder synkit.CRN.Pathway.reachability synkit.CRN.Pathway.realizability synkit.CRN.Petrinet.analyzer synkit.CRN.Petrinet.net synkit.CRN.Petrinet.persistence synkit.CRN.Petrinet.semiflows synkit.CRN.Petrinet.structure synkit.CRN.Props.dynamics synkit.CRN.Props.helper synkit.CRN.Props.stoich synkit.CRN.Props.thermo synkit.CRN.Query.kegg_api synkit.CRN.Query.kegg_extract synkit.CRN.Query.kegg_impute synkit.CRN.Query.kegg_parse synkit.CRN.Structure.reaction synkit.CRN.Structure.rule synkit.CRN.Structure.species synkit.CRN.Structure.syncrn synkit.CRN.Symmetry.automorphism synkit.CRN.Symmetry.canon synkit.CRN.Symmetry.isomorphism synkit.CRN.Symmetry.symmetry synkit.CRN.Symmetry.wl_canon synkit.CRN.Visualize.crn_vis synkit.CRN.Visualize.labels synkit.CRN.Visualize.layout synkit.CRN.Visualize.palette synkit.CRN.Visualize.validation synkit.CRN.Visualize.vis synkit.Graph.Canon.canon_algs synkit.Graph.Canon.canon_graph synkit.Graph.Canon.nauty synkit.Graph.canon_graph synkit.Graph.Context.hier_context synkit.Graph.Context.radius_expand synkit.Graph.Feature.graph_descriptors synkit.Graph.Feature.graph_fps synkit.Graph.Feature.graph_signature synkit.Graph.Feature.hash_fps synkit.Graph.Feature.morgan_fps synkit.Graph.Feature.path_fps synkit.Graph.Feature.wl_hash synkit.Graph.FG.api synkit.Graph.FG.audit synkit.Graph.FG.catalog synkit.Graph.FG.detector synkit.Graph.FG.model synkit.Graph.FG.ring_system synkit.Graph.Hyrogen._misc synkit.Graph.Hyrogen.hcomplete synkit.Graph.Hyrogen.hextend synkit.Graph.ITS.its_builder synkit.Graph.ITS.its_construction synkit.Graph.ITS.its_decompose synkit.Graph.ITS.its_destruction synkit.Graph.ITS.its_expand synkit.Graph.ITS.its_relabel synkit.Graph.ITS.normalize_aam synkit.Graph.ITS.partial_its synkit.Graph.Matcher.approx_mcs synkit.Graph.Matcher.auto_est synkit.Graph.Matcher.automorphism synkit.Graph.Matcher.batch_cluster synkit.Graph.Matcher.dedup_matches synkit.Graph.Matcher.graph_cluster synkit.Graph.Matcher.graph_matcher synkit.Graph.Matcher.graph_morphism synkit.Graph.Matcher.mcs_matcher synkit.Graph.Matcher.multi_turbo_iso synkit.Graph.Matcher.orbit synkit.Graph.Matcher.partial_matcher synkit.Graph.Matcher.sing synkit.Graph.Matcher.subgraph_matcher synkit.Graph.Matcher.turbo_iso synkit.Graph.Matcher.wl_sel synkit.Graph.Mech.conversion synkit.Graph.Mech.electron_accounting synkit.Graph.MTG.mcs_matcher synkit.Graph.MTG.mtg synkit.Graph.MTG.mtg_explore synkit.Graph.MTG.utils synkit.Graph.syn_graph synkit.Graph.utils synkit.Graph.Wildcard.fuse_graph synkit.Graph.Wildcard.graph_wc synkit.Graph.Wildcard.its_merge synkit.Graph.Wildcard.radwc synkit.Graph.Wildcard.wc_matcher synkit.Graph.Wildcard.wildcard synkit.IO.chem_converter synkit.IO.data_io synkit.IO.debug synkit.IO.gml_to_nx synkit.IO.graph_to_mol synkit.IO.mol_to_graph synkit.IO.nx_to_gml synkit.Rule.Apply.reactor_rule synkit.Rule.Apply.retro_reactor synkit.Rule.Apply.rule_matcher synkit.Rule.Apply.rule_rbl synkit.Rule.Compose.compose_rule synkit.Rule.Compose.rule_compose synkit.Rule.Compose.rule_mapping synkit.Rule.Compose.seq_comp synkit.Rule.Compose.valence_constrain synkit.Rule.Modify.longest_path synkit.Rule.Modify.molecule_rule synkit.Rule.Modify.prune_templates synkit.Rule.Modify.rule_utils synkit.Rule.Modify.strip_rule synkit.Rule.syn_rule synkit.Synthesis.Metrics._base synkit.Synthesis.Metrics._plot synkit.Synthesis.Metrics._ranking synkit.Synthesis.MSR.multi_steps synkit.Synthesis.MSR.path_finder synkit.Synthesis.Reactor.batch_reactor synkit.Synthesis.Reactor.benchmark synkit.Synthesis.Reactor.imba_engine synkit.Synthesis.Reactor.mod_aam synkit.Synthesis.Reactor.mod_reactor synkit.Synthesis.Reactor.partial_engine synkit.Synthesis.Reactor.post_syn synkit.Synthesis.Reactor.rbl_engine synkit.Synthesis.Reactor.rule_filter synkit.Synthesis.Reactor.single_predictor synkit.Synthesis.Reactor.strategy synkit.Synthesis.Reactor.syn_reactor synkit.Synthesis.reactor_utils synkit.Vis.chemical_space synkit.Vis.crn_vis synkit.Vis.embedding synkit.Vis.graph_visualizer synkit.Vis.its_drawer synkit.Vis.molecule_drawer synkit.Vis.mtg_drawer synkit.Vis.reaction_drawer synkit.Vis.rule_vis synkit.Vis.rxn_vis synkit.Vis.visual_drawer synkit.Vis.visual_model

mol (synkit.Chem.Molecule.standardize.MolStandardizer property) mol_from_smiles_safe() (in module synkit.CRN.Construct.smiles) mol_to_ap() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) mol_to_graph() (synkit.IO.mol_to_graph.MolToGraph class method) mol_to_pharm2d() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) mol_to_torsion() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) mol_weight() (synkit.Chem.Molecule.formula.Formula method) molblock_to_smiles() (in module synkit.CRN.Query.kegg_parse) molecule_pool (synkit.CRN.Construct.abstract.AbstractReactionNetwork attribute) MoleculeRule (class in synkit.Rule.Modify.molecule_rule) molecules (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) MolStandardizer (class in synkit.Chem.Molecule.standardize) MolToGraph (class in synkit.IO.mol_to_graph) MorganFPs (class in synkit.Graph.Feature.morgan_fps) MTG (class in synkit.Graph.MTG.mtg) multi_solutions (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) multi_step() (synkit.Synthesis.MSR.multi_steps.MultiSteps method) multipartite_step_layout() (in module synkit.CRN.Visualize.layout) MultiSteps (class in synkit.Synthesis.MSR.multi_steps) MultiTurboISO (class in synkit.Graph.Matcher.multi_turbo_iso)

N

n_automorphisms (synkit.Graph.Matcher.automorphism.Automorphism property) n_groups (synkit.Graph.Matcher.auto_est.AutoEst property) n_orbits (synkit.Graph.Matcher.auto_est.AutoEst property) n_reactions (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) (synkit.CRN.Props.stoich.StoichSummary attribute) (synkit.CRN.Structure.syncrn.SynCRN property) n_rules (synkit.CRN.Structure.syncrn.SynCRN property) n_species (synkit.CRN.Pathway.realizability.RealizabilitySummary attribute) (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) (synkit.CRN.Props.stoich.StoichSummary attribute) (synkit.CRN.Structure.syncrn.SynCRN property) name (synkit.Graph.FG.model.FunctionalGroupMatch attribute) (synkit.Graph.FG.model.FunctionalGroupPattern attribute) named_heteroaromatic_systems (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) NautyCanonicalizer (class in synkit.Graph.Canon.nauty) neigh_codes() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) neighbors() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) neighbors_set() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) (synkit.Chem.Reaction.Mapper.wl_mapper.MaskView method) Neutralize (class in synkit.Chem.Reaction.neutralize) new_rules (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) newly_enabled_reactions (synkit.CRN.Pathway.reachability.ReachabilityLayer attribute) newly_reachable_species (synkit.CRN.Pathway.reachability.ReachabilityLayer attribute) node_alpha (synkit.CRN.Visualize.vis.CRNStyle attribute) node_attributes (synkit.Vis.graph_visualizer.GraphVisualizer property) node_attrs (synkit.Graph.Canon.nauty.NautyCanonicalizer attribute) (synkit.Graph.Matcher.auto_est.AutoEst property) node_color_overrides (synkit.CRN.Visualize.vis.CRNVis attribute) node_colors (synkit.Graph.Matcher.auto_est.AutoEst property) node_data() (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache method) node_id (synkit.Vis.visual_model.VisualNode attribute)

node_index_text (synkit.CRN.Visualize.palette.ColorPalette attribute) node_label (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO property) node_label_keys (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) node_labels() (synkit.CRN.Visualize.vis.CRNVis method) node_mapping (synkit.Graph.MTG.mtg.MTG property) node_set (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache attribute) node_sort_key() (in module synkit.CRN.Visualize.validation) node_spacing (synkit.CRN.Visualize.vis.CRNVis attribute) nodes (synkit.Chem.Reaction.Mapper.wl_mapper.GraphCache attribute) (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) (synkit.Graph.FG.ring_system.AromaticSubring attribute) (synkit.Vis.visual_model.VisualGraph attribute) normalize() (synkit.Chem.Molecule.descriptors.PerMolDescriptorsBuilder method) (synkit.Chem.Molecule.standardize.MolStandardizer method) normalize_aromatic_bonds (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) normalize_dfs_for_compare() (in module synkit.IO.chem_converter) normalize_edge_orders() (in module synkit.Graph.Hyrogen._misc) normalize_h_pair_graph() (in module synkit.Graph.Hyrogen._misc) normalize_hcount_and_typesGH() (in module synkit.Graph.MTG.utils) normalize_module_id() (in module synkit.CRN.Query.kegg_parse) normalize_molecule() (in module synkit.Chem.Molecule.standardize) normalize_order() (in module synkit.Graph.MTG.utils) NormalizeAAM (class in synkit.Graph.ITS.normalize_aam) num_atoms (synkit.Chem.Molecule.descriptors.PerMolDescriptors property) num_edges (synkit.CRN.Construct.DAG.mod_crn.MODCRN property) num_hosts (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO property) num_mappings (synkit.Graph.Matcher.approx_mcs.ApproxMCSMatcher property) (synkit.Graph.Matcher.mcs_matcher.MCSMatcher property) (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) num_pattern_components (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) num_vertices (synkit.CRN.Construct.DAG.mod_crn.MODCRN property) nx_vis() (synkit.Vis.rule_vis.RuleVis method) NXToGML (class in synkit.IO.nx_to_gml)

O

orbit_components() (synkit.Graph.Matcher.auto_est.AutoEst method) orbit_index (synkit.Graph.Matcher.auto_est.AutoEst property) OrbitAccuracy (class in synkit.Graph.Matcher.orbit) orbits (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) (synkit.Graph.Matcher.auto_est.AutoEst property) (synkit.Graph.Matcher.automorphism.Automorphism property) orbits() (synkit.CRN.Symmetry.automorphism.CRNAutomorphism method) (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) order_changed_bonds (synkit.Vis.reaction_drawer.ReactionHighlights attribute)

orient_equation_to_module() (in module synkit.CRN.Query.kegg_parse) orientation (synkit.CRN.Visualize.vis.CRNVis attribute) original_graph (synkit.Graph.Canon.canon_graph.CanonicalGraph property) (synkit.Graph.Canon.canon_graph.CanonicalRule property) (synkit.Graph.canon_graph.CanonicalGraph property) (synkit.Graph.canon_graph.CanonicalRule property) original_rule (synkit.Graph.Canon.canon_graph.CanonicalRule property) (synkit.Graph.canon_graph.CanonicalRule property) other_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) other_style (synkit.CRN.Visualize.vis.CRNStyle attribute) oxidation_states_by_atom_map() (synkit.IO.mol_to_graph.MolToGraph class method)

P

p_semiflows (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) pair_indices (synkit.Graph.Matcher.wl_sel.WLSel property) pair_scores (synkit.Graph.Matcher.wl_sel.WLSel property) palette (synkit.CRN.Visualize.vis.CRNVis attribute) palette_names() (in module synkit.CRN.Visualize.palette) palette_overrides (synkit.CRN.Visualize.vis.CRNVis attribute) paralle_context_extraction() (synkit.Graph.Context.radius_expand.RadiusExpand class method) parallel_fix_unbalanced_charge() (synkit.Chem.Reaction.neutralize.Neutralize class method) parallel_process() (synkit.Chem.Fingerprint.fp_calculator.FPCalculator method) parents (synkit.Graph.FG.model.FunctionalGroupPattern attribute) parse_arrow_step() (in module synkit.Graph.Mech.conversion) parse_atom_list() (in module synkit.Graph.Mech.conversion) parse_context() (in module synkit.Rule.Modify.rule_utils) parse_equation() (in module synkit.CRN.Query.kegg_parse) parse_failures (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) parse_input() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) parse_kegg_field_blocks() (in module synkit.CRN.Query.kegg_parse) parse_module_reaction_directions() (in module synkit.CRN.Query.kegg_parse) parse_reaction() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) (synkit.Chem.Reaction.neutralize.Neutralize static method) parse_side() (in module synkit.CRN.Query.kegg_parse) PARTIAL (synkit.Synthesis.Reactor.strategy.Strategy attribute) partial (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) PartialEngine (class in synkit.Synthesis.Reactor.partial_engine) PartialITS (class in synkit.Graph.ITS.partial_its) PartialMatcher (class in synkit.Graph.Matcher.partial_matcher) PathFinder (class in synkit.Synthesis.MSR.path_finder) PathFinderConfig (class in synkit.CRN.Pathway.pathfinder) PathFPs (class in synkit.Graph.Feature.path_fps) PathwayCandidate (class in synkit.CRN.Pathway.pathfinder) PathwayFinder (class in synkit.CRN.Pathway.pathfinder) PathwayReachability (class in synkit.CRN.Pathway.reachability) PathwayRealizability (class in synkit.CRN.Pathway.realizability) pattern (synkit.Graph.FG.model.FunctionalGroupMatch attribute) pattern_graph (synkit.Graph.Wildcard.its_merge.ITSMerge property) (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) pattern_singular (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) pattern_to_host (synkit.Graph.Wildcard.its_merge.ITSMerge property) patterns (synkit.Graph.FG.model.FunctionalGroupRegistry attribute) (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) PAULING_EN (synkit.IO.mol_to_graph.MolToGraph attribute) PerMolDescriptors (class in synkit.Chem.Molecule.descriptors) PerMolDescriptorsBuilder (class in synkit.Chem.Molecule.descriptors) persistence_details (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) persistence_ok (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) (synkit.CRN.Petrinet.persistence.PersistenceCheckResult attribute) PersistenceCheckResult (class in synkit.CRN.Petrinet.persistence) petri (synkit.CRN.Pathway.realizability.PathwayRealizability property) (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) PetriAnalyzer (class in synkit.CRN.Petrinet.analyzer)

PetriNet (class in synkit.CRN.Petrinet.net) PetriSummary (class in synkit.CRN.Petrinet.analyzer) pgraph_signature() (in module synkit.Graph.Canon.canon_algs) place_name() (synkit.CRN.Petrinet.net.PetriNet method) place_order (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) (synkit.CRN.Petrinet.net.PetriNet property) plot_as_mol() (synkit.Vis.graph_visualizer.GraphVisualizer method) plot_bip() (in module synkit.Vis.crn_vis) plot_crn() (in module synkit.Vis.crn_vis) plot_f2_scores_line() (in module synkit.Synthesis.Metrics._plot) plot_its() (synkit.Vis.graph_visualizer.GraphVisualizer method) plot_recognition_coverage_curve() (in module synkit.Synthesis.Metrics._plot) plot_stoich() (in module synkit.Vis.crn_vis) pmcd_bond_weight (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) pmcd_hcount_weight (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) pmcd_unmapped_weight (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) pool_keys (synkit.CRN.Construct.state.DerivationState attribute) positions() (synkit.CRN.Visualize.vis.CRNVis method) post (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) (synkit.CRN.Petrinet.net.Transition attribute) post() (synkit.Vis.rule_vis.RuleVis method) PostSyn (class in synkit.Synthesis.Reactor.post_syn) pre (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) (synkit.CRN.Petrinet.net.Transition attribute) pre_filter (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) prediction_count (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) prepare_template() (synkit.Synthesis.Reactor.rbl_engine.RBLEngine method) print_graph_attributes() (in module synkit.Graph.utils) print_summary() (synkit.CRN.Construct.DAG.mod_crn.MODCRN method) prior_score (synkit.Chem.Reaction.Mapper.wl_mapper.EdgeMaskCandidate attribute) priority (synkit.Graph.FG.model.FunctionalGroupPattern attribute) process() (synkit.Synthesis.Reactor.post_syn.PostSyn method) (synkit.Synthesis.Reactor.rbl_engine.RBLEngine method) process_data() (synkit.Graph.Feature.wl_hash.WLHash method) process_entries_in_parallel() (synkit.Graph.Feature.graph_descriptors.GraphDescriptor static method) process_graph_data_parallel() (synkit.Graph.Hyrogen.hcomplete.HComplete method) process_list() (synkit.Chem.Molecule.formula.Formula method) process_list_dict() (synkit.Chem.Molecule.formula.Formula method) process_multiple_hydrogens() (synkit.Graph.Hyrogen.hcomplete.HComplete static method) process_single_graph_data() (synkit.Graph.Hyrogen.hcomplete.HComplete static method) process_smiles_list() (in module synkit.Chem.utils) product_count (synkit.Synthesis.Reactor.mod_aam.MODAAM property) product_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) product_edge_attrs (synkit.CRN.Structure.reaction.Reaction attribute) product_sets (synkit.CRN.Construct.DAG.crn.CRN property) (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) product_smiles (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) product_style (synkit.CRN.Visualize.vis.CRNStyle attribute) products (synkit.CRN.Construct.derivation.DerivationRecord attribute) (synkit.CRN.Query.kegg_parse.KEGGEquation attribute) progressive_fallback (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) PruneTemplate (class in synkit.Rule.Modify.prune_templates) public (synkit.Graph.FG.model.FunctionalGroupPattern attribute)

R

radial_step_layout() (in module synkit.CRN.Visualize.layout) RadicalWildcardAdder (class in synkit.Chem.Reaction.radical_wildcard) RadiusExpand (class in synkit.Graph.Context.radius_expand) RadWC (class in synkit.Graph.Wildcard.radwc) random_atom_mapping() (synkit.IO.mol_to_graph.MolToGraph static method) random_pair_ions() (synkit.Chem.Reaction.deionize.Deionize static method) rank (synkit.CRN.Props.stoich.StoichSummary attribute) raw (synkit.Graph.syn_graph.SynGraph property) (synkit.Vis.visual_model.VisualEdge attribute) (synkit.Vis.visual_model.VisualNode attribute) raw_matches() (synkit.Graph.FG.detector.FunctionalGroupDetector method) raw_product_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) raw_reactant_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) raw_rsmi (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) rbl() (synkit.Rule.Apply.rule_rbl.RuleRBL method) RBLEngine (class in synkit.Synthesis.Reactor.rbl_engine) rc_distance_weight (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) rc_expand_hops (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) rc_only_bond_changes (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) rc_only_hcount_changes (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) ReachabilityConfig (class in synkit.CRN.Pathway.reachability) ReachabilityLayer (class in synkit.CRN.Pathway.reachability) ReachabilityResult (class in synkit.CRN.Pathway.reachability) reached_species (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) react() (synkit.Synthesis.Reactor.rbl_engine.RBLEngine method) reactant_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) reactant_edge_attrs (synkit.CRN.Structure.reaction.Reaction attribute) reactant_style (synkit.CRN.Visualize.vis.CRNStyle attribute) reactants (synkit.CRN.Construct.derivation.DerivationRecord attribute) (synkit.CRN.Query.kegg_parse.KEGGEquation attribute) Reaction (class in synkit.CRN.Structure.reaction) reaction_first_depth (synkit.CRN.Pathway.reachability.ReachabilityResult attribute) reaction_id_to_token (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) reaction_ids (synkit.CRN.Structure.syncrn.SynCRN property) reaction_labels (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) reaction_order (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) reaction_oxidation_state_delta_from_rsmi() (synkit.IO.mol_to_graph.MolToGraph class method) reaction_smiles (synkit.Synthesis.Reactor.mod_aam.MODAAM property) (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) reaction_smiles_from_equation() (in module synkit.CRN.Query.kegg_parse) reaction_source_node_ids (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) reaction_token_to_id (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) ReactionDeltaFlattener (class in synkit.CRN.Construct.DAG.syncrn) (class in synkit.CRN.Construct.flattener) ReactionHighlights (class in synkit.Vis.reaction_drawer) reactions (synkit.CRN.Construct.abstract.AbstractReactionNetwork attribute) (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener property) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener property) (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) (synkit.CRN.Structure.syncrn.SynCRN attribute) (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) ReactorRule (class in synkit.Rule.Apply.reactor_rule) RealizabilityConfig (class in synkit.CRN.Pathway.realizability) RealizabilitySummary (class in synkit.CRN.Pathway.realizability) realizable (synkit.CRN.Pathway.pathfinder.PathwayCandidate attribute) recognizer (synkit.Graph.FG.model.FunctionalGroupPattern attribute) recompute_charge() (in module synkit.Graph.Mech.electron_accounting) records (synkit.CRN.Construct.derivation.DerivationLog attribute) refresh_electron_fields() (in module synkit.Graph.Mech.electron_accounting) reindex() (synkit.Graph.Matcher.sing.SING method) reindex_side_graph_by_atom_map() (synkit.Graph.ITS.its_expand.ITSExpand static method) remap_graph() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI static method) remove_atom_mapping() (synkit.Chem.Reaction.standardize.Standardize static method) remove_atom_mappings() (in module synkit.Chem.utils) remove_common_reagents() (in module synkit.Chem.utils) remove_duplicates() (in module synkit.Chem.utils) (synkit.Chem.Reaction.cleaning.Cleaning static method) remove_edges_by_attribute() (synkit.Rule.Modify.prune_templates.PruneTemplate static method) remove_edges_from_left_right() (synkit.Rule.Modify.molecule_rule.MoleculeRule static method) remove_explicit_H_from_rsmi() (in module synkit.Chem.utils) remove_explicit_hs() (synkit.Chem.Molecule.standardize.MolStandardizer method) remove_explicit_hydrogens() (in module synkit.Chem.Molecule.standardize) remove_isotopes() (in module synkit.Chem.Molecule.standardize) (synkit.Chem.Molecule.standardize.MolStandardizer method) remove_non_arrow_atom_maps() (in module synkit.Graph.Mech.conversion) remove_normal_edges() (synkit.Graph.Context.radius_expand.RadiusExpand static method)

remove_radicals_and_add_hydrogens() (in module synkit.Chem.Molecule.standardize) remove_salts() (synkit.Chem.Molecule.standardize.MolStandardizer method) remove_wildcard_nodes() (in module synkit.Graph.utils) remove_wildcards() (synkit.Graph.ITS.its_destruction.ITSDestruction method) removed_pairs (synkit.Chem.Reaction.Mapper.wl_mapper.EdgeMaskCandidate attribute) render() (synkit.Vis.rxn_vis.RXNVis method) repeats (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) replace_wildcard_with_H() (synkit.Synthesis.Reactor.rbl_engine.RBLEngine method) report() (synkit.Graph.Matcher.orbit.OrbitAccuracy method) requires (synkit.Graph.FG.model.FunctionalGroupPattern attribute) reset() (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper method) (synkit.CRN.Construct.builder.CRNExpand method) (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) reset_indices_and_atom_map() (synkit.Graph.ITS.normalize_aam.NormalizeAAM method) reset_tsne_params() (synkit.Vis.embedding.Embedding method) result (synkit.Chem.Reaction.Mapper.wl_mapper.Solution attribute) (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) RetroReactor (class in synkit.Rule.Apply.retro_reactor) reverse_reaction() (in module synkit.Chem.utils) reversible (synkit.CRN.Query.kegg_parse.KEGGEquation attribute) rhs (synkit.CRN.Structure.reaction.Reaction attribute) right_nullspace() (in module synkit.CRN.Props.stoich) ring_canonical_graph() (in module synkit.Graph.Canon.canon_algs) ring_sizes (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) rsmarts_to_rsmi() (in module synkit.IO.chem_converter) rsmi_balance_check() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) rsmi_to_graph() (in module synkit.IO.chem_converter) rsmi_to_its() (in module synkit.IO.chem_converter) rsmi_to_rsmarts() (in module synkit.IO.chem_converter) rsmi_with_wildcards() (synkit.Graph.Wildcard.wildcard.WildCard static method) Rule (class in synkit.CRN.Structure.rule) rule (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) rule_cluster() (synkit.Rule.Compose.compose_rule.ComposeRule static method) (synkit.Rule.Compose.rule_compose.RuleCompose static method) rule_cmap (synkit.CRN.Visualize.vis.CRNVis attribute) rule_color_attr (synkit.CRN.Visualize.vis.CRNVis attribute) rule_color_mode (synkit.CRN.Visualize.vis.CRNVis attribute) rule_count (synkit.CRN.Construct.DAG.crn.CRN property) rule_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) rule_fill (synkit.CRN.Visualize.palette.ColorPalette attribute) rule_id (synkit.CRN.Structure.reaction.Reaction attribute) rule_ids (synkit.CRN.Structure.syncrn.SynCRN property) rule_index (synkit.CRN.Construct.derivation.DerivationRecord attribute) (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.rule.Rule attribute) rule_label (synkit.CRN.Visualize.crn_vis.CRNVis attribute) (synkit.CRN.Visualize.vis.CRNVis attribute) rule_node_shape (synkit.CRN.Visualize.vis.CRNStyle attribute) rule_node_size (synkit.CRN.Visualize.vis.CRNStyle attribute) rule_nodes (synkit.CRN.Visualize.validation.CRNGraphInfo attribute) (synkit.CRN.Visualize.vis.CRNVis property) rule_repr (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.rule.Rule attribute) rule_subgraph_morphism() (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) RuleCompose (class in synkit.Rule.Compose.rule_compose) RuleFilter (class in synkit.Synthesis.Reactor.rule_filter) RuleMapping (class in synkit.Rule.Compose.rule_mapping) RuleMatcher (class in synkit.Rule.Apply.rule_matcher) RuleRBL (class in synkit.Rule.Apply.rule_rbl) rules (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.mod_crn.MODCRN property) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.CRN.Structure.syncrn.SynCRN attribute) (synkit.Synthesis.Reactor.rule_filter.RuleFilter property) RuleVis (class in synkit.Vis.rule_vis) run() (synkit.CRN.Construct.DAG.crn.CRN method) (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) run_pathfinder_from_syncrn() (in module synkit.CRN.Pathway.pathfinder) run_reachability_from_syncrn() (in module synkit.CRN.Pathway.reachability) run_realizability_from_syncrn() (in module synkit.CRN.Pathway.realizability) rxn_nodes (synkit.CRN.Construct.builder.CRNExpand property) (synkit.CRN.Construct.DAG.syncrn.SynCRN property) RXNSide (class in synkit.CRN.Structure.reaction) RXNVis (class in synkit.Vis.rxn_vis)

S

salts_remover() (in module synkit.Chem.Molecule.standardize) sanitize_and_canonicalize_smiles() (in module synkit.Chem.Molecule.standardize) sanitize_safe() (in module synkit.CRN.Construct.smiles) save() (synkit.CRN.Visualize.vis.CRNVis method) save_compressed() (in module synkit.IO.data_io) save_database() (in module synkit.IO.data_io) save_dg() (in module synkit.IO.data_io) save_dict_to_json() (in module synkit.IO.data_io) save_gml_from_text() (synkit.Rule.Compose.rule_compose.RuleCompose static method) save_json() (synkit.CRN.Construct.abstract.AbstractReactionNetwork method) (synkit.CRN.Query.kegg_extract.KEGGExtractor static method) save_list_to_file() (in module synkit.IO.data_io) save_model() (in module synkit.IO.data_io) save_molecule() (synkit.Vis.graph_visualizer.GraphVisualizer method) save_pdf() (synkit.Vis.rxn_vis.RXNVis method) save_png() (synkit.Vis.rxn_vis.RXNVis method) save_text_as_gml() (in module synkit.IO.data_io) save_to_pickle() (in module synkit.IO.data_io) scale_edge_width_by_stoich (synkit.CRN.Visualize.vis.CRNStyle attribute) scatter_plot() (in module synkit.Vis.chemical_space) score (synkit.Chem.Reaction.Mapper.wl_mapper.MappingResult attribute) score_pairs() (synkit.Graph.Matcher.wl_sel.WLSel method) search() (synkit.Graph.Matcher.sing.SING method) (synkit.Graph.Matcher.turbo_iso.TurboISO method) search_many() (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO method) search_one() (synkit.Graph.Matcher.multi_turbo_iso.MultiTurboISO method) search_paths() (synkit.Synthesis.MSR.path_finder.PathFinder method) seed (synkit.CRN.Visualize.vis.CRNVis attribute) select_by_node_attr() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_by_node_attr_in() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_by_node_pred() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_by_pred() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_wc() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_with_wc() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) select_without_wc() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) semiflow_supports (synkit.CRN.Petrinet.persistence.PersistenceCheckResult attribute) semiflow_supports() (in module synkit.CRN.Petrinet.semiflows) SeqComp (class in synkit.Rule.Compose.seq_comp) sequence_map() (synkit.Rule.Compose.seq_comp.SeqComp static method) set_initial() (synkit.CRN.Construct.state.DerivationState method) set_initial_marking() (synkit.CRN.Pathway.realizability.PathwayRealizability method) set_tsne_params() (synkit.Vis.embedding.Embedding method) setup_logging() (in module synkit.IO.debug) show_label_boxes (synkit.CRN.Visualize.vis.CRNStyle attribute) show_node_outline (synkit.CRN.Visualize.vis.CRNStyle attribute) show_rule_labels (synkit.CRN.Visualize.vis.CRNVis attribute) show_species_labels (synkit.CRN.Visualize.vis.CRNVis attribute) side (synkit.Chem.Reaction.Mapper.wl_mapper.EdgeMaskCandidate attribute) signature (synkit.CRN.Structure.rule.Rule property) (synkit.Graph.syn_graph.SynGraph property) SING (class in synkit.Graph.Matcher.sing) SinglePredictor (class in synkit.Synthesis.Reactor.single_predictor) siphon_persistence_condition() (in module synkit.CRN.Petrinet.persistence) siphon_persistence_details() (in module synkit.CRN.Petrinet.persistence) siphons (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) (synkit.CRN.Petrinet.persistence.PersistenceCheckResult attribute) skip_no_change (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.ReactionDeltaFlattener attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.CRN.Construct.flattener.ReactionDeltaFlattener attribute) smart_to_gml() (in module synkit.IO.chem_converter) smarts (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) smarts_list (synkit.Synthesis.Reactor.imba_engine.ImbaEngine property) (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) smiles (synkit.CRN.Structure.species.Species attribute) smiles_check() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) smiles_check_tautomer() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) smiles_list (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) smiles_to_dfs() (in module synkit.IO.chem_converter) smiles_to_graph() (in module synkit.IO.chem_converter) smiles_to_graph_and_functional_groups() (in module synkit.Graph.FG.api) smiles_to_mol() (synkit.Chem.Fingerprint.smiles_featurizer.SmilesFeaturizer static method) SmilesFeaturizer (class in synkit.Chem.Fingerprint.smiles_featurizer) Solution (class in synkit.Chem.Reaction.Mapper.wl_mapper) solution_score_slack (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) solutions (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapper property) source (synkit.Vis.visual_model.VisualEdge attribute) source_attrs (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.species.Species attribute) source_kind (synkit.CRN.Structure.reaction.Reaction attribute) source_node_id (synkit.CRN.Structure.reaction.Reaction attribute) (synkit.CRN.Structure.species.Species attribute) source_reaction_id (synkit.CRN.Petrinet.net.Transition attribute) Species (class in synkit.CRN.Structure.species) species (synkit.CRN.Structure.syncrn.SynCRN attribute) species() (synkit.Vis.crn_vis.CRNVisualizer method) species_cmap (synkit.CRN.Visualize.vis.CRNVis attribute) species_color_attr (synkit.CRN.Visualize.vis.CRNVis attribute) species_color_mode (synkit.CRN.Visualize.vis.CRNVis attribute) species_edge (synkit.CRN.Visualize.palette.ColorPalette attribute) species_fill (synkit.CRN.Visualize.palette.ColorPalette attribute) species_first_depth (synkit.CRN.Pathway.reachability.ReachabilityResult attribute) species_id_to_token (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) species_ids (synkit.CRN.Structure.syncrn.SynCRN property) species_influence_graph() (in module synkit.CRN.Props.dynamics) species_label (synkit.CRN.Visualize.crn_vis.CRNVis attribute) (synkit.CRN.Visualize.vis.CRNVis attribute) species_labels (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) species_node_shape (synkit.CRN.Visualize.vis.CRNStyle attribute) species_node_size (synkit.CRN.Visualize.vis.CRNStyle attribute) species_nodes (synkit.CRN.Construct.builder.CRNExpand property) (synkit.CRN.Construct.DAG.syncrn.SynCRN property) (synkit.CRN.Visualize.validation.CRNGraphInfo attribute) (synkit.CRN.Visualize.vis.CRNVis property) species_order (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) species_source_node_ids (synkit.CRN.Petrinet.net.SynCRNIncidence attribute) species_token_to_id (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) species_transition_neighborhoods() (in module synkit.CRN.Petrinet.structure) split() (synkit.Rule.Compose.valence_constrain.ValenceConstrain method) split_arrow_code() (in module synkit.Graph.Mech.conversion) stabilized (synkit.CRN.Symmetry.wl_canon.WLCanonicalResult attribute) Standardize (class in synkit.Chem.Reaction.standardize) standardize_enol() (synkit.Chem.Reaction.tautomerize.Tautomerize static method) standardize_hemiketal() (synkit.Chem.Reaction.tautomerize.Tautomerize static method) standardize_hydrogen() (in module synkit.Graph.Hyrogen._misc) standardize_order() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) standardize_rsmi() (synkit.Chem.Reaction.standardize.Standardize static method) standardize_smiles() (synkit.Chem.Molecule.standardize.MolStandardizer class method) standardize_smiles_rdkit() (in module synkit.CRN.Construct.smiles) start_atom_map (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) state (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.Vis.visual_model.VisualEdge attribute) stats() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) step (synkit.CRN.Construct.derivation.DerivationRecord attribute) (synkit.CRN.Construct.state.DerivationState attribute) (synkit.CRN.Structure.reaction.Reaction attribute) step_layout() (in module synkit.CRN.Visualize.layout) stoich() (synkit.Vis.crn_vis.CRNVisualizer method) stoich_width_factor (synkit.CRN.Visualize.vis.CRNStyle attribute) stoichiometric_matrix() (in module synkit.CRN.Petrinet.semiflows) (in module synkit.CRN.Props.stoich) stoichiometric_rank() (in module synkit.CRN.Props.stoich) StoichSummary (class in synkit.CRN.Props.stoich) stop_after_first (synkit.CRN.Pathway.pathfinder.PathFinderConfig attribute) stop_when_no_new_species (synkit.CRN.Pathway.reachability.ReachabilityConfig attribute) Strategy (class in synkit.Synthesis.Reactor.strategy) strategy (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) strategy_engine (synkit.CRN.Construct.builder.CRNExpand attribute) strict (synkit.CRN.Visualize.vis.CRNVis attribute) strip_context() (in module synkit.Rule.Modify.rule_utils) (in module synkit.Rule.Modify.strip_rule) strip_maps_and_canonical_from_mol() (in module synkit.CRN.Construct.smiles) strongly_connected_species() (synkit.CRN.Visualize.vis.CRNVis method) structural_rank (synkit.CRN.Props.dynamics.StructuralSingularitySummary attribute) structural_singularity_summary() (in module synkit.CRN.Props.dynamics) StructuralSingularitySummary (class in synkit.CRN.Props.dynamics) style (synkit.CRN.Visualize.vis.CRNVis attribute) subgraph() (synkit.CRN.Visualize.vis.CRNVis method) subgraph_isomorphic_to() (synkit.CRN.Symmetry.isomorphism.CRNIsomorphism method) subgraph_isomorphism() (in module synkit.Graph.Matcher.graph_morphism) (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) SubgraphMatch (class in synkit.Graph.Matcher.subgraph_matcher) SubgraphSearchEngine (class in synkit.Graph.Matcher.subgraph_matcher) subrings (synkit.Graph.FG.ring_system.AromaticRingSystem attribute) substrate (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) substrate_smiles (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) subtract_parent_from_child() (synkit.Rule.Compose.rule_mapping.RuleMapping static method) summarize_last_error() (synkit.Chem.Molecule.standardize.MolStandardizer method) summarize_visual_graph() (in module synkit.Vis.visual_model) summary (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) summary() (in module synkit.CRN.Props.stoich) (synkit.CRN.Pathway.realizability.PathwayRealizability method) (synkit.CRN.Symmetry.automorphism.CRNAutomorphism method) (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method) SUPPORTED_PROFILES (synkit.Chem.Molecule.atom_features.AtomFeatureExtractor attribute) (synkit.IO.mol_to_graph.MolToGraph attribute) suppresses (synkit.Graph.FG.model.FunctionalGroupPattern attribute) swap_refine_class_depth (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) swap_refine_max_group_size (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) swap_refine_max_iter (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) symbolic_jacobian() (in module synkit.CRN.Props.dynamics) symbolic_reactivity_matrix() (in module synkit.CRN.Props.dynamics) symmetry_depth (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) sync_atom_map_with_index() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI static method) SynCRN (class in synkit.CRN.Construct.DAG.syncrn) (class in synkit.CRN.Structure.syncrn) syncrn_to_pr_inputs() (in module synkit.CRN.Pathway.realizability) syncrn_to_reachability_inputs() (in module synkit.CRN.Pathway.reachability) SynCRNIncidence (class in synkit.CRN.Petrinet.net) SynGraph (class in synkit.Graph.syn_graph) synkit.Chem.Cluster.butina module synkit.Chem.Fingerprint.fp_calculator module synkit.Chem.Fingerprint.smiles_featurizer module synkit.Chem.Fingerprint.transformation_fp module synkit.Chem.Molecule.atom_features module synkit.Chem.Molecule.descriptors module synkit.Chem.Molecule.formula module synkit.Chem.Molecule.graph_annotator module synkit.Chem.Molecule.standardize module synkit.Chem.Molecule.valence module synkit.Chem.Reaction.aam_validator module synkit.Chem.Reaction.balance_check module synkit.Chem.Reaction.canon_rsmi module synkit.Chem.Reaction.cleaning module synkit.Chem.Reaction.deionize module synkit.Chem.Reaction.fix_aam module synkit.Chem.Reaction.Mapper.wl_mapper module synkit.Chem.Reaction.neutralize module synkit.Chem.Reaction.radical_wildcard module synkit.Chem.Reaction.standardize module synkit.Chem.Reaction.tautomerize module synkit.Chem.utils module synkit.CRN.Construct.abstract module synkit.CRN.Construct.arity module synkit.CRN.Construct.builder module synkit.CRN.Construct.DAG.crn module synkit.CRN.Construct.DAG.mod_crn module synkit.CRN.Construct.DAG.syncrn module synkit.CRN.Construct.derivation module synkit.CRN.Construct.flattener module synkit.CRN.Construct.keys module synkit.CRN.Construct.mixtures module synkit.CRN.Construct.smiles module synkit.CRN.Construct.state module synkit.CRN.Construct.strategy module synkit.CRN.Construct.worker module synkit.CRN.Pathway.pathfinder module synkit.CRN.Pathway.reachability module synkit.CRN.Pathway.realizability module synkit.CRN.Petrinet.analyzer module synkit.CRN.Petrinet.net module synkit.CRN.Petrinet.persistence module synkit.CRN.Petrinet.semiflows module synkit.CRN.Petrinet.structure module

synkit.CRN.Props.dynamics module synkit.CRN.Props.helper module synkit.CRN.Props.stoich module synkit.CRN.Props.thermo module synkit.CRN.Query.kegg_api module synkit.CRN.Query.kegg_extract module synkit.CRN.Query.kegg_impute module synkit.CRN.Query.kegg_parse module synkit.CRN.Structure.reaction module synkit.CRN.Structure.rule module synkit.CRN.Structure.species module synkit.CRN.Structure.syncrn module synkit.CRN.Symmetry.automorphism module synkit.CRN.Symmetry.canon module synkit.CRN.Symmetry.isomorphism module synkit.CRN.Symmetry.symmetry module synkit.CRN.Symmetry.wl_canon module synkit.CRN.Visualize.crn_vis module synkit.CRN.Visualize.labels module synkit.CRN.Visualize.layout module synkit.CRN.Visualize.palette module synkit.CRN.Visualize.validation module synkit.CRN.Visualize.vis module synkit.Graph.Canon.canon_algs module synkit.Graph.Canon.canon_graph module synkit.Graph.Canon.nauty module synkit.Graph.canon_graph module synkit.Graph.Context.hier_context module synkit.Graph.Context.radius_expand module synkit.Graph.Feature.graph_descriptors module synkit.Graph.Feature.graph_fps module synkit.Graph.Feature.graph_signature module synkit.Graph.Feature.hash_fps module synkit.Graph.Feature.morgan_fps module synkit.Graph.Feature.path_fps module synkit.Graph.Feature.wl_hash module synkit.Graph.FG.api module synkit.Graph.FG.audit module synkit.Graph.FG.catalog module synkit.Graph.FG.detector module synkit.Graph.FG.model module synkit.Graph.FG.ring_system module synkit.Graph.Hyrogen._misc module synkit.Graph.Hyrogen.hcomplete module synkit.Graph.Hyrogen.hextend module synkit.Graph.ITS.its_builder module synkit.Graph.ITS.its_construction module synkit.Graph.ITS.its_decompose module synkit.Graph.ITS.its_destruction module synkit.Graph.ITS.its_expand module synkit.Graph.ITS.its_relabel module synkit.Graph.ITS.normalize_aam module synkit.Graph.ITS.partial_its module synkit.Graph.Matcher.approx_mcs module synkit.Graph.Matcher.auto_est module synkit.Graph.Matcher.automorphism module synkit.Graph.Matcher.batch_cluster module synkit.Graph.Matcher.dedup_matches module synkit.Graph.Matcher.graph_cluster module synkit.Graph.Matcher.graph_matcher module synkit.Graph.Matcher.graph_morphism module synkit.Graph.Matcher.mcs_matcher module synkit.Graph.Matcher.multi_turbo_iso module synkit.Graph.Matcher.orbit module synkit.Graph.Matcher.partial_matcher module synkit.Graph.Matcher.sing module synkit.Graph.Matcher.subgraph_matcher module synkit.Graph.Matcher.turbo_iso module synkit.Graph.Matcher.wl_sel module synkit.Graph.Mech.conversion module synkit.Graph.Mech.electron_accounting module synkit.Graph.MTG.mcs_matcher module synkit.Graph.MTG.mtg module synkit.Graph.MTG.mtg_explore module synkit.Graph.MTG.utils module synkit.Graph.syn_graph module synkit.Graph.utils module synkit.Graph.Wildcard.fuse_graph module synkit.Graph.Wildcard.graph_wc module synkit.Graph.Wildcard.its_merge module synkit.Graph.Wildcard.radwc module synkit.Graph.Wildcard.wc_matcher module synkit.Graph.Wildcard.wildcard module synkit.IO.chem_converter module synkit.IO.data_io module synkit.IO.debug module synkit.IO.gml_to_nx module synkit.IO.graph_to_mol module synkit.IO.mol_to_graph module synkit.IO.nx_to_gml module synkit.Rule.Apply.reactor_rule module synkit.Rule.Apply.retro_reactor module synkit.Rule.Apply.rule_matcher module synkit.Rule.Apply.rule_rbl module synkit.Rule.Compose.compose_rule module synkit.Rule.Compose.rule_compose module synkit.Rule.Compose.rule_mapping module synkit.Rule.Compose.seq_comp module synkit.Rule.Compose.valence_constrain module synkit.Rule.Modify.longest_path module synkit.Rule.Modify.molecule_rule module synkit.Rule.Modify.prune_templates module synkit.Rule.Modify.rule_utils module synkit.Rule.Modify.strip_rule module synkit.Rule.syn_rule module synkit.Synthesis.Metrics._base module synkit.Synthesis.Metrics._plot module synkit.Synthesis.Metrics._ranking module synkit.Synthesis.MSR.multi_steps module synkit.Synthesis.MSR.path_finder module synkit.Synthesis.Reactor.batch_reactor module synkit.Synthesis.Reactor.benchmark module synkit.Synthesis.Reactor.imba_engine module synkit.Synthesis.Reactor.mod_aam module synkit.Synthesis.Reactor.mod_reactor module synkit.Synthesis.Reactor.partial_engine module synkit.Synthesis.Reactor.post_syn module synkit.Synthesis.Reactor.rbl_engine module synkit.Synthesis.Reactor.rule_filter module synkit.Synthesis.Reactor.single_predictor module synkit.Synthesis.Reactor.strategy module synkit.Synthesis.Reactor.syn_reactor module synkit.Synthesis.reactor_utils module synkit.Vis.chemical_space module synkit.Vis.crn_vis module synkit.Vis.embedding module synkit.Vis.graph_visualizer module synkit.Vis.its_drawer module synkit.Vis.molecule_drawer module synkit.Vis.mtg_drawer module synkit.Vis.reaction_drawer module synkit.Vis.rule_vis module synkit.Vis.rxn_vis module synkit.Vis.visual_drawer module synkit.Vis.visual_model module SynReactor (class in synkit.Synthesis.Reactor.syn_reactor) SynRule (class in synkit.Rule.syn_rule)

T

t_semiflows (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) target (synkit.Vis.visual_model.VisualEdge attribute) Tautomerize (class in synkit.Chem.Reaction.tautomerize) temp_results (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) template (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) template_format (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) template_its (synkit.Synthesis.Reactor.rbl_engine.RBLEngine property) templates (synkit.CRN.Construct.abstract.AbstractReactionNetwork attribute) ThermoSummary (class in synkit.CRN.Props.thermo) threshold (synkit.Graph.Matcher.partial_matcher.PartialMatcher property) tid (synkit.CRN.Petrinet.net.Transition attribute) time_limit_s (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) timeout (synkit.CRN.Query.kegg_api.KEGGClient attribute) title (synkit.Vis.visual_model.VisualGraph attribute) title_text (synkit.CRN.Visualize.palette.ColorPalette attribute) to_dataframe() (synkit.Graph.MTG.mtg.MTG method) to_dict() (synkit.Chem.Molecule.descriptors.PerMolDescriptors method) (synkit.CRN.Construct.abstract.AbstractReactionNetwork method) (synkit.CRN.Props.dynamics.StructuralSingularitySummary method) (synkit.CRN.Props.stoich.StoichSummary method) (synkit.CRN.Structure.reaction.Reaction method) (synkit.CRN.Structure.reaction.RXNSide method) (synkit.CRN.Structure.rule.Rule method) (synkit.CRN.Structure.species.Species method) (synkit.CRN.Structure.syncrn.SynCRN method) to_digraph() (synkit.CRN.Structure.syncrn.SynCRN method) to_equations() (synkit.CRN.Structure.syncrn.SynCRN method)

to_json_payload() (synkit.CRN.Construct.abstract.AbstractReactionNetwork method) to_list() (synkit.Graph.Wildcard.graph_wc.GraphCollectionSelector method) (synkit.Synthesis.Reactor.imba_engine.ImbaEngine method) to_petrinet() (synkit.CRN.Structure.syncrn.SynCRN method) to_pre_post() (synkit.CRN.Petrinet.net.PetriNet method) to_smi() (synkit.Graph.Wildcard.wildcard.WildCard static method) to_smiles() (synkit.Chem.Molecule.standardize.MolStandardizer method) to_stoichiometric_matrices() (synkit.CRN.Structure.syncrn.SynCRN method) to_visual_graph() (in module synkit.Vis.visual_model) total() (synkit.Chem.Molecule.valence.ValenceResolver static method) transform() (synkit.Chem.Reaction.radical_wildcard.RadicalWildcardAdder method) (synkit.Graph.Wildcard.radwc.RadWC static method) (synkit.IO.gml_to_nx.GMLToNX method) (synkit.IO.mol_to_graph.MolToGraph method) (synkit.IO.nx_to_gml.NXToGML static method) transform_store() (synkit.IO.mol_to_graph.MolToGraph method) TransformationFP (class in synkit.Chem.Fingerprint.transformation_fp) Transition (class in synkit.CRN.Petrinet.net) transition_name() (synkit.CRN.Petrinet.net.PetriNet method) transition_order (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) (synkit.CRN.Petrinet.net.PetriNet property) traps (synkit.CRN.Petrinet.analyzer.PetriAnalyzer property) (synkit.CRN.Petrinet.analyzer.PetriSummary attribute) tuple_to_marking() (synkit.CRN.Petrinet.net.PetriNet method) TurboISO (class in synkit.Graph.Matcher.turbo_iso) typed_convert_arrow_code() (in module synkit.Graph.Mech.conversion) typed_convert_step() (in module synkit.Graph.Mech.conversion) typesGH_info() (synkit.Graph.ITS.its_construction.ITSConstruction static method)

U

uncharge() (synkit.Chem.Molecule.standardize.MolStandardizer method) uncharge_anion() (synkit.Chem.Reaction.deionize.Deionize static method) uncharge_cation() (synkit.Chem.Reaction.deionize.Deionize static method) uncharge_molecule() (in module synkit.Chem.Molecule.standardize) uncharge_smiles() (synkit.Chem.Reaction.deionize.Deionize static method) uncovered_atom_signatures (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) uncovered_edge_signatures (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) uncovered_siphons (synkit.CRN.Petrinet.persistence.PersistenceCheckResult attribute)

unmapped_value (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) unnamed_heteroaromatic_count (synkit.Graph.FG.audit.FunctionalGroupAudit property) unnamed_heteroaromatic_systems (synkit.Graph.FG.audit.FunctionalGroupAudit attribute) update_atom_map() (synkit.Graph.ITS.its_builder.ITSBuilder static method) use_frontier (synkit.CRN.Construct.builder.CRNExpand attribute) (synkit.CRN.Construct.DAG.syncrn.SynCRN attribute) use_index_as_atom_map (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute) use_its_final (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig attribute)

V

valence() (synkit.Rule.Compose.valence_constrain.ValenceConstrain method) ValenceConstrain (class in synkit.Rule.Compose.valence_constrain) ValenceResolver (class in synkit.Chem.Molecule.valence) VALID_FP_TYPES (synkit.Chem.Fingerprint.fp_calculator.FPCalculator attribute) validate_arrow_maps() (in module synkit.Graph.Mech.conversion) validate_candidates() (synkit.CRN.Pathway.pathfinder.PathwayFinder method) validate_crn_graph() (in module synkit.CRN.Visualize.validation) validate_parameters() (synkit.Graph.Feature.hash_fps.HashFPs method) validate_smiles() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) validated() (synkit.Chem.Reaction.Mapper.wl_mapper.WLMapperConfig method)

validator (synkit.Graph.FG.model.FunctionalGroupPattern attribute) vertices (synkit.CRN.Pathway.pathfinder.PathwayFinder attribute) vis() (synkit.Vis.rule_vis.RuleVis method) VisualEdge (class in synkit.Vis.visual_model) VisualGraph (class in synkit.Vis.visual_model) visualize() (synkit.Chem.Cluster.butina.ButinaCluster static method) visualize_its() (synkit.Vis.graph_visualizer.GraphVisualizer method) visualize_its_grid() (synkit.Vis.graph_visualizer.GraphVisualizer method) visualize_molecule() (synkit.Vis.graph_visualizer.GraphVisualizer method) VisualNode (class in synkit.Vis.visual_model)

W

WCMatcher (class in synkit.Graph.Wildcard.wc_matcher) weisfeiler_lehman_graph_hash() (synkit.Graph.Feature.wl_hash.WLHash method) weisfeiler_lehman_subgraph_hashes() (synkit.Graph.Feature.wl_hash.WLHash method) width (synkit.Vis.visual_model.VisualEdge attribute) WildCard (class in synkit.Graph.Wildcard.wildcard) wildcard_subgraph_mapping (synkit.Graph.Wildcard.wc_matcher.WCMatcher property) WildcardPatternMatcher (in module synkit.Graph.Wildcard.wc_matcher) with_overrides() (synkit.CRN.Visualize.palette.ColorPalette method) wl_canonical() (in module synkit.CRN.Symmetry.wl_canon) wl_orbits() (synkit.CRN.Symmetry.automorphism.CRNAutomorphism method) (synkit.CRN.Symmetry.canon.CRNCanonicalizer method) (synkit.CRN.Symmetry.symmetry.CRNSymmetry method) (synkit.CRN.Symmetry.wl_canon.WLCanonicalizer method)

WLCanonicalizer (class in synkit.CRN.Symmetry.wl_canon) WLCanonicalResult (class in synkit.CRN.Symmetry.wl_canon) WLHash (class in synkit.Graph.Feature.wl_hash) WLMapper (class in synkit.Chem.Reaction.Mapper.wl_mapper) WLMapperConfig (class in synkit.Chem.Reaction.Mapper.wl_mapper) WLSel (class in synkit.Graph.Matcher.wl_sel) wrap_label_at (synkit.CRN.Visualize.vis.CRNVis attribute)