Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V _ __call__() (chemrecon.Scorer method) __init__() (chemrecon.ExplorationProtocol method) (chemrecon.Scorer method) A AAM (class in chemrecon) AAMConvert (class in chemrecon) AAMInvolvesMolStructure (class in chemrecon) AAMRepr (class in chemrecon) AAMReprInvolvesMolStructureRepr (class in chemrecon) add_edge() (chemrecon.EntryGraph method) add_entries() (chemrecon.PopulateQueryHandler method) add_entry() (chemrecon.PopulateQueryHandler method) add_entry_with_relations() (chemrecon.PopulateQueryHandler method) add_procedural_entry() (chemrecon.QueryHandler method) add_relation() (chemrecon.PopulateQueryHandler method) add_relation_by_entries() (chemrecon.PopulateQueryHandler method) add_relation_by_recon_ids() (chemrecon.PopulateQueryHandler method) add_relations_by_entries() (chemrecon.PopulateQueryHandler method) add_relations_by_recon_ids() (chemrecon.PopulateQueryHandler method) add_relations_to_entry_with_reconid() (chemrecon.PopulateQueryHandler method) add_vertex() (chemrecon.EntryGraph method) add_vertex_from() (chemrecon.EntryGraph method) alt_names (chemrecon.IdentifierType attribute) B BACKWARDS (chemrecon.Direction attribute) bigg (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) biocyc (chemrecon.schema.IdTypeCompoundEnum attribute) BOTH (chemrecon.Direction attribute) brenda (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) C chebi (chemrecon.schema.IdTypeCompoundEnum attribute) chemrecon.query module chemrecon.query.default_protocols module cname (chemrecon.schema.IdTypeCompoundEnum attribute) Compound (class in chemrecon) CompoundHasConjugateAcid (class in chemrecon) CompoundHasConjugateBase (class in chemrecon) CompoundHasInstance (class in chemrecon) CompoundHasIsotopologue (class in chemrecon) CompoundHasMolStructure (class in chemrecon) CompoundHasNewID (class in chemrecon) CompoundHasOldID (class in chemrecon) CompoundHasPart (class in chemrecon) CompoundHasStereoIsomer (class in chemrecon) CompoundHasStructureRepresentation (class in chemrecon) CompoundHasTautomer (class in chemrecon) CompoundIsA (class in chemrecon) CompoundIsPartOf (class in chemrecon) CompoundParticipatesInReaction (class in chemrecon) CompoundReference (class in chemrecon) CompoundSelectStructure (class in chemrecon) connect() (in module chemrecon.connection) connect_local_docker (class in chemrecon) connect_local_docker_dev (class in chemrecon) connect_public (class in chemrecon) connection_string() (chemrecon.database.params.Params method) D Direction (class in chemrecon) draw() (chemrecon.EntryGraph method) E ec (chemrecon.schema.IdTypeEnzymeEnum attribute) ecmdb (chemrecon.schema.IdTypeCompoundEnum attribute) Edge (class in chemrecon) edge_index (chemrecon.Edge attribute) edges() (chemrecon.EntryGraph method) ename (chemrecon.schema.IdTypeEnzymeEnum attribute) entry (chemrecon.Vertex attribute) Entry (class in chemrecon) entry_filters (chemrecon.ExplorationProtocol attribute) entry_types (chemrecon.ExplorationProtocol attribute) EntryGraph (class in chemrecon) enum_type (chemrecon.IdentifierType attribute) envipath (chemrecon.schema.IdTypeCompoundEnum attribute) Enzyme (class in chemrecon) EnzymeCatalyzesReaction (class in chemrecon) EnzymeHasInstance (class in chemrecon) EnzymeIsA (class in chemrecon) ExplorationProtocol (class in chemrecon) explore() (in module chemrecon) explore_vertex() (chemrecon.QueryHandler method) F feat (chemrecon.MolStructureStandardization attribute) find_aam_entry() (in module chemrecon.query) find_aam_representation_entry() (in module chemrecon.query) find_compound_entry() (in module chemrecon.query) find_entry() (in module chemrecon.query) find_enzyme_entry() (in module chemrecon.query) find_reaction_entry() (in module chemrecon.query) find_structure_entry() (in module chemrecon.query) find_structure_representation_entry() (in module chemrecon.query) FORWARDS (chemrecon.Direction attribute) G generate() (chemrecon.AAMConvert class method) (chemrecon.MolStructureConvert class method) (chemrecon.MolStructureStandardization class method) generation (chemrecon.Vertex attribute) get_all_relations() (in module chemrecon.query) get_columns_with_values() (chemrecon.Entry method) (chemrecon.Relation method) get_entries_by_indices() (chemrecon.QueryHandler method) get_entries_by_recon_ids() (chemrecon.QueryHandler method) get_entry_by_index() (chemrecon.QueryHandler method) get_entry_by_recon_id() (chemrecon.QueryHandler method) get_index_columns_with_values() (chemrecon.Entry method) (chemrecon.Relation method) get_number_of_entries() (chemrecon.QueryHandler method) get_out_edges_of_vertex() (chemrecon.EntryGraph method) get_query_handler() (in module chemrecon.connection) get_relations_by_recon_ids() (chemrecon.QueryHandler method) get_relations_from_entry() (in module chemrecon.query) get_relations_with_entries_by_recon_ids() (chemrecon.QueryHandler method) get_relations_with_entries_by_recon_ids_of_t1() (chemrecon.QueryHandler method) get_relations_with_entries_by_recon_ids_of_t2() (chemrecon.QueryHandler method) get_relations_with_entries_by_recon_ids_symmetric() (chemrecon.QueryHandler method) get_vertex_by_entry() (chemrecon.EntryGraph method) get_vertex_by_vertex_index() (chemrecon.EntryGraph method) get_vertex_index_by_recon_id() (chemrecon.EntryGraph method) gml (chemrecon.schema.IdTypeStructureRepresentationEnum attribute) gml_rule (chemrecon.schema.IdTypeAAMEnum attribute) H hmdb (chemrecon.schema.IdTypeCompoundEnum attribute) I id_org_prefix (chemrecon.IdentifierType attribute) id_type (chemrecon.AAMRepr attribute) (chemrecon.Compound attribute) (chemrecon.Enzyme attribute) (chemrecon.MolStructureRepr attribute) (chemrecon.Reaction attribute) IdentifierType (class in chemrecon) implicit (chemrecon.MolStructureRepr attribute) inchi (chemrecon.schema.IdTypeStructureRepresentationEnum attribute) inchikey (chemrecon.schema.IdTypeCompoundEnum attribute) index (chemrecon.AAMReprInvolvesMolStructureRepr attribute) (chemrecon.MolStructureReprParticipatesInAAMRepr attribute) is_reversible (chemrecon.Reaction attribute) is_transport (chemrecon.Reaction attribute) iterate_relation_with_entries() (chemrecon.QueryHandler method) iterate_table() (chemrecon.QueryHandler method) K kegg (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) L lipidmaps (chemrecon.schema.IdTypeCompoundEnum attribute) M mcsa (chemrecon.schema.IdTypeReactionEnum attribute) metacyc (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) metamdb (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) mnx (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) module chemrecon.query chemrecon.query.default_protocols molfile (chemrecon.schema.IdTypeStructureRepresentationEnum attribute) molformula (chemrecon.MolStructure attribute) MolStructure (class in chemrecon) MolStructureConvert (class in chemrecon) MolStructureParticipatesInAAM (class in chemrecon) MolStructureRepr (class in chemrecon) MolStructureReprParticipatesInAAMRepr (class in chemrecon) MolStructureStandardization (class in chemrecon) N n (chemrecon.CompoundParticipatesInReaction attribute) (chemrecon.ReactionInvolvesCompound attribute) name (chemrecon.Compound attribute) (chemrecon.Enzyme attribute) (chemrecon.IdentifierType attribute) P Params (class in chemrecon.database.params) pdbe (chemrecon.schema.IdTypeCompoundEnum attribute) PopulateQueryHandler (class in chemrecon) properties (chemrecon.Compound attribute) (chemrecon.Enzyme attribute) (chemrecon.Reaction attribute) protocol_compound_structure (in module chemrecon.query.default_protocols) pubchem_cid (chemrecon.schema.IdTypeCompoundEnum attribute) Q quality (chemrecon.Compound attribute) (chemrecon.Enzyme attribute) (chemrecon.Reaction attribute) QueryHandler (class in chemrecon) R Reaction (class in chemrecon) reaction_smiles (chemrecon.AAM attribute) ReactionHasAAM (class in chemrecon) ReactionHasAAMRepr (class in chemrecon) ReactionHasEnzyme (class in chemrecon) ReactionHasInstance (class in chemrecon) ReactionHasNewID (class in chemrecon) ReactionHasOldID (class in chemrecon) ReactionInvolvesCompound (class in chemrecon) ReactionIsA (class in chemrecon) ReactionReference (class in chemrecon) ReactionSelectAAM (class in chemrecon) reactionsmiles (chemrecon.schema.IdTypeAAMEnum attribute) reactome (chemrecon.schema.IdTypeCompoundEnum attribute) recogniser (chemrecon.IdentifierType attribute) recon_id (chemrecon.Entry attribute) (chemrecon.Vertex attribute) recon_id_1 (chemrecon.CompoundSelectStructure attribute) (chemrecon.Edge attribute) (chemrecon.ReactionSelectAAM attribute) (chemrecon.Relation attribute) recon_id_2 (chemrecon.CompoundSelectStructure attribute) (chemrecon.Edge attribute) (chemrecon.ReactionSelectAAM attribute) (chemrecon.Relation attribute) relation (chemrecon.Edge attribute) Relation (class in chemrecon) relation_filters (chemrecon.ExplorationProtocol attribute) relation_types (chemrecon.ExplorationProtocol attribute) rhea (chemrecon.schema.IdTypeReactionEnum attribute) rname (chemrecon.schema.IdTypeReactionEnum attribute) rxn (chemrecon.schema.IdTypeAAMEnum attribute) S sabiork (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) score (chemrecon.CompoundSelectStructure attribute) (chemrecon.ReactionSelectAAM attribute) Scorer (class in chemrecon) seed (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) shortname (chemrecon.IdentifierType attribute) show() (chemrecon.EntryGraph method) side (chemrecon.AAMInvolvesMolStructure attribute) (chemrecon.MolStructureParticipatesInAAM attribute) slm (chemrecon.schema.IdTypeCompoundEnum attribute) smiles (chemrecon.MolStructure attribute) (chemrecon.schema.IdTypeStructureRepresentationEnum attribute) source_id (chemrecon.AAMRepr attribute) (chemrecon.Compound attribute) (chemrecon.Enzyme attribute) (chemrecon.MolStructureRepr attribute) (chemrecon.Reaction attribute) src (chemrecon.CompoundHasConjugateAcid attribute) (chemrecon.CompoundHasConjugateBase attribute) (chemrecon.CompoundHasInstance attribute) (chemrecon.CompoundHasIsotopologue attribute) (chemrecon.CompoundHasMolStructure attribute) (chemrecon.CompoundHasNewID attribute) (chemrecon.CompoundHasOldID attribute) (chemrecon.CompoundHasPart attribute) (chemrecon.CompoundHasStereoIsomer attribute) (chemrecon.CompoundHasStructureRepresentation attribute) (chemrecon.CompoundHasTautomer attribute) (chemrecon.CompoundIsA attribute) (chemrecon.CompoundIsPartOf attribute) (chemrecon.CompoundReference attribute) (chemrecon.EnzymeCatalyzesReaction attribute) (chemrecon.EnzymeHasInstance attribute) (chemrecon.EnzymeIsA attribute) (chemrecon.ReactionHasAAM attribute) (chemrecon.ReactionHasAAMRepr attribute) (chemrecon.ReactionHasEnzyme attribute) (chemrecon.ReactionHasInstance attribute) (chemrecon.ReactionHasNewID attribute) (chemrecon.ReactionHasOldID attribute) (chemrecon.ReactionIsA attribute) (chemrecon.ReactionReference attribute) std_feats (chemrecon.MolStructure attribute) std_identifier() (chemrecon.IdentifierType method) stdfunc (chemrecon.IdentifierType attribute) stoich (chemrecon.AAMReprInvolvesMolStructureRepr attribute) (chemrecon.MolStructureReprParticipatesInAAMRepr attribute) structure_atom_index_in_aam (chemrecon.AAMInvolvesMolStructure attribute) (chemrecon.MolStructureParticipatesInAAM attribute) SYMMETRIC (chemrecon.Direction attribute) T trim() (chemrecon.IdentifierType method) U unknown (chemrecon.schema.IdTypeAAMEnum attribute) (chemrecon.schema.IdTypeCompoundEnum attribute) (chemrecon.schema.IdTypeEnzymeEnum attribute) (chemrecon.schema.IdTypeReactionEnum attribute) (chemrecon.schema.IdTypeStructureRepresentationEnum attribute) V Vertex (class in chemrecon) vertex_index (chemrecon.Vertex attribute) vertices() (chemrecon.EntryGraph method)