Index

A

AAMValidator (class in synkit.Chem.Reaction.aam_validator) add_partial_charges() (synkit.IO.mol_to_graph.MolToGraph static method) automorphism (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute)

available_backends() (synkit.Graph.Matcher.batch_cluster.BatchCluster method) (synkit.Graph.Matcher.graph_cluster.GraphCluster method) (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine static method)

B

BalanceReactionCheck (class in synkit.Chem.Reaction.balance_check) batch_dicts() (synkit.Graph.Matcher.batch_cluster.BatchCluster static method)

BatchCluster (class in synkit.Graph.Matcher.batch_cluster) build() (synkit.Synthesis.CRN.mod_crn.MODCRN method) ButinaCluster (class in synkit.Chem.Cluster.butina)

C

canonical_hash (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_product_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_reactant_graph (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonical_rsmi (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) canonicalise() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI method) canonicaliser (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) CanonRSMI (class in synkit.Chem.Reaction.canon_rsmi) categorize_reactions() (synkit.Chem.Reaction.standardize.Standardize static method)

check_equivariant_graph() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) check_pair() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) cluster() (synkit.Chem.Cluster.butina.ButinaCluster static method) (synkit.Graph.Matcher.batch_cluster.BatchCluster method) collect_data() (in module synkit.IO.data_io), [1] construct() (synkit.Graph.ITS.its_construction.ITSConstruction static method) CORE_EDGE_DEFAULTS (synkit.Graph.ITS.its_construction.ITSConstruction attribute) CORE_NODE_DEFAULTS (synkit.Graph.ITS.its_construction.ITSConstruction attribute)

D

DEFAULT_THRESHOLD (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine attribute) derivation_graph (synkit.Synthesis.CRN.mod_crn.MODCRN property) describe() (synkit.Graph.MTG.mtg.MTG static method) dg (synkit.Synthesis.Reactor.mod_aam.MODAAM property) (synkit.Synthesis.Reactor.mod_reactor.MODReactor 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)

E

edge_attributes (synkit.Vis.graph_visualizer.GraphVisualizer property) embed_pre_filter (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) embed_threshold (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) 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) explicit_h (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) export_report() (synkit.Synthesis.CRN.mod_crn.MODCRN method)

F

filter_smallest_vertex() (synkit.Rule.Compose.rule_compose.RuleCompose static method) filter_valid_molecules() (synkit.Chem.Reaction.standardize.Standardize static method) find_subgraph_mappings() (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine static method) fit() (synkit.Chem.Reaction.standardize.Standardize method) (synkit.Graph.Matcher.batch_cluster.BatchCluster method) (synkit.Graph.Matcher.graph_cluster.GraphCluster method)

FPCalculator (class in synkit.Chem.Fingerprint.fp_calculator) fps (synkit.Chem.Fingerprint.fp_calculator.FPCalculator attribute) from_smiles() (synkit.Synthesis.Reactor.syn_reactor.SynReactor class method)

G

generate_atom_map() (synkit.Rule.Modify.molecule_rule.MoleculeRule static 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) get_aam() (synkit.Graph.MTG.mtg.MTG method) get_aam_pairwise_indices() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI 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_combined_molecular_formula() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) get_compose_its() (synkit.Graph.MTG.mtg.MTG method) get_dg() (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) get_mappings() (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) get_mtg() (synkit.Graph.MTG.mtg.MTG 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_rc() (in module synkit.Graph.ITS.its_decompose)

get_reaction_smiles() (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) get_smarts() (synkit.Synthesis.Reactor.mod_aam.MODAAM method) get_stereochemistry() (synkit.IO.mol_to_graph.MolToGraph static method) 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) graph (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) graph_to_mol() (synkit.IO.graph_to_mol.GraphToMol method) graph_to_rsmi() (in module synkit.IO.chem_converter) graph_to_smi() (in module synkit.IO.chem_converter) GraphCluster (class in synkit.Graph.Matcher.graph_cluster) GraphMatcherEngine (class in synkit.Graph.Matcher.graph_matcher) graphs (synkit.Synthesis.CRN.mod_crn.MODCRN property) GraphToMol (class in synkit.IO.graph_to_mol) GraphVisualizer (class in synkit.Vis.graph_visualizer)

H

has_atom_mapping() (synkit.IO.mol_to_graph.MolToGraph static method) help (synkit.Graph.Matcher.subgraph_matcher.SubgraphSearchEngine property) help() (synkit.Chem.Cluster.butina.ButinaCluster method) (synkit.Chem.Fingerprint.fp_calculator.FPCalculator method) (synkit.Chem.Reaction.canon_rsmi.CanonRSMI method) (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) (synkit.Synthesis.CRN.mod_crn.MODCRN method) (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) (synkit.Synthesis.Reactor.syn_reactor.SynReactor method) (synkit.Vis.graph_visualizer.GraphVisualizer method) (synkit.Vis.rule_vis.RuleVis method)

I

implicit_temp (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) invert (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) is_subgraph() (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) isomorphic() (synkit.Graph.Matcher.graph_matcher.GraphMatcherEngine method) iterative_cluster() (synkit.Graph.Matcher.graph_cluster.GraphCluster method) 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) ITSConstruction (class in synkit.Graph.ITS.its_construction) ITSExpand (class in synkit.Graph.ITS.its_expand) ITSGraph() (synkit.Graph.ITS.its_construction.ITSConstruction static method)

K

k (synkit.Graph.MTG.mtg.MTG property)

L

lib_check() (synkit.Graph.Matcher.batch_cluster.BatchCluster method) load_compressed() (in module synkit.IO.data_io), [1] load_database() (in module synkit.IO.data_io), [1] load_dg() (in module synkit.IO.data_io), [1] load_dict_from_json() (in module synkit.IO.data_io), [1]

load_from_pickle() (in module synkit.IO.data_io), [1] load_from_pickle_generator() (in module synkit.IO.data_io), [1] load_gml_as_text() (in module synkit.IO.data_io), [1] load_list_from_file() (in module synkit.IO.data_io), [1] load_model() (in module synkit.IO.data_io), [1]

M

mapping_count (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) mapping_pairs (synkit.Chem.Reaction.canon_rsmi.CanonRSMI property) mappings (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) mod_vis() (synkit.Vis.rule_vis.RuleVis method) MODAAM (class in synkit.Synthesis.Reactor.mod_aam) MODCRN (class in synkit.Synthesis.CRN.mod_crn) MODReactor (class in synkit.Synthesis.Reactor.mod_reactor) module synkit.Chem.Cluster.butina synkit.Chem.Fingerprint.fp_calculator synkit.Chem.Reaction.aam_validator synkit.Chem.Reaction.balance_check synkit.Chem.Reaction.canon_rsmi synkit.Chem.Reaction.standardize synkit.Graph.ITS.its_construction synkit.Graph.ITS.its_decompose synkit.Graph.ITS.its_expand synkit.Graph.Matcher.batch_cluster synkit.Graph.Matcher.graph_cluster synkit.Graph.Matcher.graph_matcher synkit.Graph.Matcher.sing synkit.Graph.Matcher.subgraph_matcher synkit.Graph.Matcher.turbo_iso synkit.Graph.MTG.mtg synkit.IO.chem_converter synkit.IO.data_io, [1] 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.Compose.rule_compose synkit.Rule.Modify.molecule_rule synkit.Synthesis.CRN.mod_crn synkit.Synthesis.Reactor.mod_aam synkit.Synthesis.Reactor.mod_reactor synkit.Synthesis.Reactor.syn_reactor synkit.Vis.graph_visualizer synkit.Vis.rule_vis synkit.Vis.rxn_vis

mol_to_graph() (synkit.IO.mol_to_graph.MolToGraph class method) MoleculeRule (class in synkit.Rule.Modify.molecule_rule) MolToGraph (class in synkit.IO.mol_to_graph) MTG (class in synkit.Graph.MTG.mtg)

N

node_attributes (synkit.Vis.graph_visualizer.GraphVisualizer property) node_mapping (synkit.Graph.MTG.mtg.MTG property) num_edges (synkit.Synthesis.CRN.mod_crn.MODCRN property)

num_vertices (synkit.Synthesis.CRN.mod_crn.MODCRN property) nx_vis() (synkit.Vis.rule_vis.RuleVis method) NXToGML (class in synkit.IO.nx_to_gml)

P

parallel_process() (synkit.Chem.Fingerprint.fp_calculator.FPCalculator method) parse_input() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) parse_reaction() (synkit.Chem.Reaction.balance_check.BalanceReactionCheck static method) partial (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) plot_as_mol() (synkit.Vis.graph_visualizer.GraphVisualizer method) plot_its() (synkit.Vis.graph_visualizer.GraphVisualizer method)

post() (synkit.Vis.rule_vis.RuleVis method) prediction_count (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) print_summary() (synkit.Synthesis.CRN.mod_crn.MODCRN method) product_count (synkit.Synthesis.Reactor.mod_aam.MODAAM property) product_sets (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) product_smiles (synkit.Synthesis.Reactor.mod_reactor.MODReactor property)

R

random_atom_mapping() (synkit.IO.mol_to_graph.MolToGraph static 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) reaction_smiles (synkit.Synthesis.Reactor.mod_aam.MODAAM property) (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) ReactorRule (class in synkit.Rule.Apply.reactor_rule) remap_graph() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI static method) remove_atom_mapping() (synkit.Chem.Reaction.standardize.Standardize static method) remove_edges_from_left_right() (synkit.Rule.Modify.molecule_rule.MoleculeRule static method) render() (synkit.Vis.rxn_vis.RXNVis method) 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) rule (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) rule_cluster() (synkit.Rule.Compose.rule_compose.RuleCompose static method) rule_subgraph_morphism() (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) RuleCompose (class in synkit.Rule.Compose.rule_compose) rules (synkit.Synthesis.CRN.mod_crn.MODCRN property) RuleVis (class in synkit.Vis.rule_vis) run() (synkit.Synthesis.Reactor.mod_aam.MODAAM method) (synkit.Synthesis.Reactor.mod_reactor.MODReactor method) RXNVis (class in synkit.Vis.rxn_vis)

S

save_compressed() (in module synkit.IO.data_io), [1] save_database() (in module synkit.IO.data_io), [1] save_dg() (in module synkit.IO.data_io), [1] save_dict_to_json() (in module synkit.IO.data_io), [1] save_gml_from_text() (synkit.Rule.Compose.rule_compose.RuleCompose static method) save_list_to_file() (in module synkit.IO.data_io), [1] save_model() (in module synkit.IO.data_io), [1] 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), [1] save_to_pickle() (in module synkit.IO.data_io), [1] search() (synkit.Graph.Matcher.sing.SING method) (synkit.Graph.Matcher.turbo_iso.TurboISO method) SING (class in synkit.Graph.Matcher.sing) smart_to_gml() (in module synkit.IO.chem_converter) smarts (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) smarts_list (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) 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_graph() (in module synkit.IO.chem_converter) Standardize (class in synkit.Chem.Reaction.standardize) standardize_rsmi() (synkit.Chem.Reaction.standardize.Standardize static method) strategy (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) subgraph_isomorphism() (synkit.Graph.Matcher.subgraph_matcher.SubgraphMatch static method) SubgraphMatch (class in synkit.Graph.Matcher.subgraph_matcher) SubgraphSearchEngine (class in synkit.Graph.Matcher.subgraph_matcher) substrate (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) substrate_smiles (synkit.Synthesis.Reactor.syn_reactor.SynReactor property) sync_atom_map_with_index() (synkit.Chem.Reaction.canon_rsmi.CanonRSMI static method) synkit.Chem.Cluster.butina module synkit.Chem.Fingerprint.fp_calculator module synkit.Chem.Reaction.aam_validator module synkit.Chem.Reaction.balance_check module synkit.Chem.Reaction.canon_rsmi module synkit.Chem.Reaction.standardize module synkit.Graph.ITS.its_construction module synkit.Graph.ITS.its_decompose module synkit.Graph.ITS.its_expand module

synkit.Graph.Matcher.batch_cluster module synkit.Graph.Matcher.graph_cluster module synkit.Graph.Matcher.graph_matcher module synkit.Graph.Matcher.sing module synkit.Graph.Matcher.subgraph_matcher module synkit.Graph.Matcher.turbo_iso module synkit.Graph.MTG.mtg module synkit.IO.chem_converter module synkit.IO.data_io module, [1] 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.Compose.rule_compose module synkit.Rule.Modify.molecule_rule module synkit.Synthesis.CRN.mod_crn module synkit.Synthesis.Reactor.mod_aam module synkit.Synthesis.Reactor.mod_reactor module synkit.Synthesis.Reactor.syn_reactor module synkit.Vis.graph_visualizer module synkit.Vis.rule_vis module synkit.Vis.rxn_vis module SynReactor (class in synkit.Synthesis.Reactor.syn_reactor)

T

temp_results (synkit.Synthesis.Reactor.mod_reactor.MODReactor property) template (synkit.Synthesis.Reactor.syn_reactor.SynReactor attribute) to_dataframe() (synkit.Graph.MTG.mtg.MTG method) transform() (synkit.IO.gml_to_nx.GMLToNX method) (synkit.IO.mol_to_graph.MolToGraph method) (synkit.IO.nx_to_gml.NXToGML static method)

TurboISO (class in synkit.Graph.Matcher.turbo_iso) typesGH_info() (synkit.Graph.ITS.its_construction.ITSConstruction static method)

V

VALID_FP_TYPES (synkit.Chem.Fingerprint.fp_calculator.FPCalculator attribute) validate_smiles() (synkit.Chem.Reaction.aam_validator.AAMValidator static method) vis() (synkit.Vis.rule_vis.RuleVis method)

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)