Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W | X _ __call__() (biopax-explorer.biopax.utils.validate_utils.ValidationDecorator method) A addStyle() (biopax-explorer.graph.view.CytoViewer method) attr_type_def() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) attribute_type_by_name() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) attributeInfo() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) attributeNames() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) attributeNameString() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) attributesInfo() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) attributeType() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) B BaseDecorator (class in biopax-explorer.biopax.utils.validate_utils) BindingFeature (class in biopax-explorer.biopax.bindingfeature) bindingfeature_DocHelper (class in biopax-explorer.biopax.doc.dh_bindingfeature) bindsTo() (biopax-explorer.pattern.rack.Rack method) BiochemicalPathwayStep (class in biopax-explorer.biopax.biochemicalpathwaystep) biochemicalpathwaystep_DocHelper (class in biopax-explorer.biopax.doc.dh_biochemicalpathwaystep) BiochemicalReaction (class in biopax-explorer.biopax.biochemicalreaction) biochemicalreaction_DocHelper (class in biopax-explorer.biopax.doc.dh_biochemicalreaction) biopax-explorer.biopax module biopax-explorer.biopax.bindingfeature module biopax-explorer.biopax.biochemicalpathwaystep module biopax-explorer.biopax.biochemicalreaction module biopax-explorer.biopax.biosource module biopax-explorer.biopax.catalysis module biopax-explorer.biopax.cellularlocationvocabulary module biopax-explorer.biopax.cellvocabulary module biopax-explorer.biopax.chemicalstructure module biopax-explorer.biopax.complex module biopax-explorer.biopax.complexassembly module biopax-explorer.biopax.control module biopax-explorer.biopax.controlledvocabulary module biopax-explorer.biopax.conversion module biopax-explorer.biopax.covalentbindingfeature module biopax-explorer.biopax.degradation module biopax-explorer.biopax.deltag module biopax-explorer.biopax.dna module, [1] biopax-explorer.biopax.dnareference module biopax-explorer.biopax.dnaregion module biopax-explorer.biopax.dnaregionreference module biopax-explorer.biopax.doc.dh_bindingfeature module biopax-explorer.biopax.doc.dh_biochemicalpathwaystep module biopax-explorer.biopax.doc.dh_biochemicalreaction module biopax-explorer.biopax.doc.dh_biosource module biopax-explorer.biopax.doc.dh_catalysis module biopax-explorer.biopax.doc.dh_cellularlocationvocabulary module biopax-explorer.biopax.doc.dh_cellvocabulary module biopax-explorer.biopax.doc.dh_chemicalstructure module biopax-explorer.biopax.doc.dh_complex module biopax-explorer.biopax.doc.dh_complexassembly module biopax-explorer.biopax.doc.dh_control module biopax-explorer.biopax.doc.dh_controlledvocabulary module biopax-explorer.biopax.doc.dh_conversion module biopax-explorer.biopax.doc.dh_covalentbindingfeature module biopax-explorer.biopax.doc.dh_degradation module biopax-explorer.biopax.doc.dh_deltag module biopax-explorer.biopax.doc.dh_dna module biopax-explorer.biopax.doc.dh_dnareference module biopax-explorer.biopax.doc.dh_dnaregion module biopax-explorer.biopax.doc.dh_dnaregionreference module biopax-explorer.biopax.doc.dh_entity module biopax-explorer.biopax.doc.dh_entityfeature module biopax-explorer.biopax.doc.dh_entityreference module biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary module biopax-explorer.biopax.doc.dh_evidence module biopax-explorer.biopax.doc.dh_evidencecodevocabulary module biopax-explorer.biopax.doc.dh_experimentalform module biopax-explorer.biopax.doc.dh_experimentalformvocabulary module biopax-explorer.biopax.doc.dh_fragmentfeature module biopax-explorer.biopax.doc.dh_gene module biopax-explorer.biopax.doc.dh_geneticinteraction module biopax-explorer.biopax.doc.dh_interaction module biopax-explorer.biopax.doc.dh_interactionvocabulary module biopax-explorer.biopax.doc.dh_kprime module biopax-explorer.biopax.doc.dh_modificationfeature module biopax-explorer.biopax.doc.dh_modulation module biopax-explorer.biopax.doc.dh_molecularinteraction module biopax-explorer.biopax.doc.dh_pathway module biopax-explorer.biopax.doc.dh_pathwaystep module biopax-explorer.biopax.doc.dh_phenotypevocabulary module biopax-explorer.biopax.doc.dh_physicalentity module biopax-explorer.biopax.doc.dh_protein module biopax-explorer.biopax.doc.dh_proteinreference module biopax-explorer.biopax.doc.dh_provenance module biopax-explorer.biopax.doc.dh_publicationxref module biopax-explorer.biopax.doc.dh_relationshiptypevocabulary module biopax-explorer.biopax.doc.dh_relationshipxref module biopax-explorer.biopax.doc.dh_rna module biopax-explorer.biopax.doc.dh_rnareference module biopax-explorer.biopax.doc.dh_rnaregion module biopax-explorer.biopax.doc.dh_rnaregionreference module biopax-explorer.biopax.doc.dh_score module biopax-explorer.biopax.doc.dh_sequenceinterval module biopax-explorer.biopax.doc.dh_sequencelocation module biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary module biopax-explorer.biopax.doc.dh_sequenceregionvocabulary module biopax-explorer.biopax.doc.dh_sequencesite module biopax-explorer.biopax.doc.dh_smallmolecule module biopax-explorer.biopax.doc.dh_smallmoleculereference module biopax-explorer.biopax.doc.dh_stoichiometry module biopax-explorer.biopax.doc.dh_templatereaction module biopax-explorer.biopax.doc.dh_templatereactionregulation module biopax-explorer.biopax.doc.dh_tissuevocabulary module biopax-explorer.biopax.doc.dh_transport module biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction module biopax-explorer.biopax.doc.dh_unificationxref module biopax-explorer.biopax.doc.dh_utilityclass module biopax-explorer.biopax.doc.dh_xref module biopax-explorer.biopax.entity module biopax-explorer.biopax.entityfeature module biopax-explorer.biopax.entityreference module biopax-explorer.biopax.entityreferencetypevocabulary module biopax-explorer.biopax.evidence module biopax-explorer.biopax.evidencecodevocabulary module biopax-explorer.biopax.experimentalform module biopax-explorer.biopax.experimentalformvocabulary module biopax-explorer.biopax.fragmentfeature module biopax-explorer.biopax.gene module biopax-explorer.biopax.geneticinteraction module biopax-explorer.biopax.interaction module biopax-explorer.biopax.interactionvocabulary module biopax-explorer.biopax.kprime module biopax-explorer.biopax.modificationfeature module biopax-explorer.biopax.modulation module biopax-explorer.biopax.molecularinteraction module biopax-explorer.biopax.pathway module biopax-explorer.biopax.pathwaystep module biopax-explorer.biopax.phenotypevocabulary module biopax-explorer.biopax.physicalentity module biopax-explorer.biopax.protein module biopax-explorer.biopax.proteinreference module biopax-explorer.biopax.provenance module biopax-explorer.biopax.publicationxref module biopax-explorer.biopax.relationshiptypevocabulary module biopax-explorer.biopax.relationshipxref module biopax-explorer.biopax.rna module biopax-explorer.biopax.rnareference module biopax-explorer.biopax.rnaregion module biopax-explorer.biopax.rnaregionreference module biopax-explorer.biopax.score module biopax-explorer.biopax.sequenceinterval module biopax-explorer.biopax.sequencelocation module biopax-explorer.biopax.sequencemodificationvocabulary module biopax-explorer.biopax.sequenceregionvocabulary module biopax-explorer.biopax.sequencesite module biopax-explorer.biopax.smallmolecule module biopax-explorer.biopax.smallmoleculereference module biopax-explorer.biopax.stoichiometry module biopax-explorer.biopax.templatereaction module biopax-explorer.biopax.templatereactionregulation module biopax-explorer.biopax.tissuevocabulary module biopax-explorer.biopax.transport module biopax-explorer.biopax.transportwithbiochemicalreaction module biopax-explorer.biopax.unificationxref module biopax-explorer.biopax.utilityclass module biopax-explorer.biopax.utils.class_utils module biopax-explorer.biopax.utils.gen_utils module biopax-explorer.biopax.utils.validate_utils module biopax-explorer.biopax.xref module biopax-explorer.graph.serializer module biopax-explorer.graph.view module biopax-explorer.pattern.pattern module biopax-explorer.pattern.processing module biopax-explorer.pattern.rack module biopax-explorer.pattern.view module biopax-explorer.query.client module BIOPAXStoreClient (class in biopax-explorer.query.client) BioSource (class in biopax-explorer.biopax.biosource) biosource_DocHelper (class in biopax-explorer.biopax.doc.dh_biosource) BlackListFilter (class in biopax-explorer.pattern.processing) blacklistFilter() (in module biopax-explorer.pattern.processing) bp_template() (in module biopax-explorer.graph.serializer) BPSerializer (class in biopax-explorer.graph.serializer) C cast() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) Catalysis (class in biopax-explorer.biopax.catalysis) catalysis_DocHelper (class in biopax-explorer.biopax.doc.dh_catalysis) CellularLocationVocabulary (class in biopax-explorer.biopax.cellularlocationvocabulary) cellularlocationvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_cellularlocationvocabulary) CellVocabulary (class in biopax-explorer.biopax.cellvocabulary) cellvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_cellvocabulary) ChemicalStructure (class in biopax-explorer.biopax.chemicalstructure) chemicalstructure_DocHelper (class in biopax-explorer.biopax.doc.dh_chemicalstructure) class_children() (in module biopax-explorer.biopax.utils.gen_utils) class_for_name() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) classDictConf() (biopax-explorer.biopax.utils.gen_utils.PackageModelPopulator method) classes() (in module biopax-explorer.biopax.utils.gen_utils) classes_children() (in module biopax-explorer.biopax.utils.gen_utils) classesDict() (in module biopax-explorer.biopax.utils.gen_utils) classInfo() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) Complex (class in biopax-explorer.biopax.complex) complex_DocHelper (class in biopax-explorer.biopax.doc.dh_complex) ComplexAssembly (class in biopax-explorer.biopax.complexassembly) complexassembly_DocHelper (class in biopax-explorer.biopax.doc.dh_complexassembly) config() (biopax-explorer.biopax.utils.gen_utils.PackageModelPopulator method) (in module biopax-explorer.graph.view) Control (class in biopax-explorer.biopax.control) control_by_controlled() (in module biopax-explorer.pattern.rack) control_by_controller() (in module biopax-explorer.pattern.rack) control_DocHelper (class in biopax-explorer.biopax.doc.dh_control) ControlledVocabulary (class in biopax-explorer.biopax.controlledvocabulary) controlledvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_controlledvocabulary) controlsExpressionWithConversion() (biopax-explorer.pattern.rack.Rack method) controlsExpressionWithTemplateReac() (biopax-explorer.pattern.rack.Rack method) controlsMetabolicCatalysis() (biopax-explorer.pattern.rack.Rack method) controlsMetabolicCatalysisBothComplex() (biopax-explorer.pattern.rack.Rack method) controlsMetabolicCatalysisBothSimple() (biopax-explorer.pattern.rack.Rack method) controlsMetabolicCatalysisControlledComplex() (biopax-explorer.pattern.rack.Rack method) controlsMetabolicCatalysisControllerComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylation() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationBothComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationBothComplexAndComplexController() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationControllerAndLeftComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationControllerAndRightComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationControllerComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationLeftComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationRightComplex() (biopax-explorer.pattern.rack.Rack method) controlsPhosphorylationRightSimple() (biopax-explorer.pattern.rack.Rack method) controlsStateChange() (biopax-explorer.pattern.rack.Rack method) controlsStateChangeBothComplex() (biopax-explorer.pattern.rack.Rack method) controlsStateChangeComplexController() (biopax-explorer.pattern.rack.Rack method) controlsStateChangeComplexControllerAndBothComplex() (biopax-explorer.pattern.rack.Rack method) controlsStateChangeSimple() (biopax-explorer.pattern.rack.Rack method) Conversion (class in biopax-explorer.biopax.conversion) conversion_DocHelper (class in biopax-explorer.biopax.doc.dh_conversion) conversionClassMapping() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) CovalentBindingFeature (class in biopax-explorer.biopax.covalentbindingfeature) covalentbindingfeature_DocHelper (class in biopax-explorer.biopax.doc.dh_covalentbindingfeature) createInstance() (in module biopax-explorer.biopax.utils.gen_utils) custom_query_list_append() (biopax-explorer.query.client.BIOPAXStoreClient method) CustomEncoder (class in biopax-explorer.biopax.utils.class_utils) CustomEncoderShort (class in biopax-explorer.biopax.utils.class_utils) CValidateArgType (class in biopax-explorer.biopax.utils.validate_utils) CytoViewer (class in biopax-explorer.graph.view) D DataPump (class in biopax-explorer.pattern.pattern) dbstr() (biopax-explorer.query.client.BIOPAXStoreClient method) default() (biopax-explorer.biopax.utils.class_utils.CustomEncoderShort method) define_bp_template() (biopax-explorer.query.client.BIOPAXStoreClient method) define_default_style() (biopax-explorer.graph.view.CytoViewer method) define_model_instance() (in module biopax-explorer.biopax.utils.gen_utils) defineEdgeLabel() (biopax-explorer.graph.view.CytoViewer method) defineEdgeLabelImpl() (biopax-explorer.graph.view.CytoViewer method) defineLocalProcessingCollection() (biopax-explorer.pattern.processing.ProcessingCollection method) defineNodeLabel() (biopax-explorer.graph.view.CytoViewer method) defineNodeLabelImpl() (biopax-explorer.graph.view.CytoViewer method) defineShapes() (biopax-explorer.graph.view.CytoViewer method) defineViewer() (biopax-explorer.graph.view.CytoViewer method) defineWrapper() (biopax-explorer.query.client.BIOPAXStoreClient method) definitions() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) Degradation (class in biopax-explorer.biopax.degradation) degradation_DocHelper (class in biopax-explorer.biopax.doc.dh_degradation) delete_from_store_by_uri_id() (biopax-explorer.query.client.BIOPAXStoreClient method) DeltaG (class in biopax-explorer.biopax.deltag) deltag_DocHelper (class in biopax-explorer.biopax.doc.dh_deltag) display() (biopax-explorer.graph.view.CytoViewer method) Dna (class in biopax-explorer.biopax.dna) dna_DocHelper (class in biopax-explorer.biopax.doc.dh_dna) DnaReference (class in biopax-explorer.biopax.dnareference) dnareference_DocHelper (class in biopax-explorer.biopax.doc.dh_dnareference) DnaRegion (class in biopax-explorer.biopax.dnaregion) dnaregion_DocHelper (class in biopax-explorer.biopax.doc.dh_dnaregion) DnaRegionReference (class in biopax-explorer.biopax.dnaregionreference) dnaregionreference_DocHelper (class in biopax-explorer.biopax.doc.dh_dnaregionreference) domain() (in module biopax-explorer.biopax.utils.gen_utils) dot2png() (in module biopax-explorer.pattern.view) dot2svg() (in module biopax-explorer.pattern.view) dottext2png() (in module biopax-explorer.pattern.view) dottext2svg() (in module biopax-explorer.pattern.view) E encode() (biopax-explorer.biopax.utils.class_utils.CustomEncoderShort method) Entity (class in biopax-explorer.biopax.entity) entity_DocHelper (class in biopax-explorer.biopax.doc.dh_entity) EntityFeature (class in biopax-explorer.biopax.entityfeature) entityfeature_DocHelper (class in biopax-explorer.biopax.doc.dh_entityfeature) EntityReference (class in biopax-explorer.biopax.entityreference) entityreference_DocHelper (class in biopax-explorer.biopax.doc.dh_entityreference) EntityReferenceTypeVocabulary (class in biopax-explorer.biopax.entityreferencetypevocabulary) entityreferencetypevocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary) entityToString() (in module biopax-explorer.biopax.utils.gen_utils) Evidence (class in biopax-explorer.biopax.evidence) evidence_DocHelper (class in biopax-explorer.biopax.doc.dh_evidence) EvidenceCodeVocabulary (class in biopax-explorer.biopax.evidencecodevocabulary) evidencecodevocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_evidencecodevocabulary) execute() (biopax-explorer.query.client.BIOPAXStoreClient method) executeQuery() (biopax-explorer.query.client.BIOPAXStoreClient method) ExperimentalForm (class in biopax-explorer.biopax.experimentalform) experimentalform_DocHelper (class in biopax-explorer.biopax.doc.dh_experimentalform) ExperimentalFormVocabulary (class in biopax-explorer.biopax.experimentalformvocabulary) experimentalformvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_experimentalformvocabulary) F Factory (class in biopax-explorer.graph.view) file_to_graph() (biopax-explorer.query.client.BIOPAXStoreClient method) filter() (biopax-explorer.pattern.processing.BlackListFilter method) FragmentFeature (class in biopax-explorer.biopax.fragmentfeature) fragmentfeature_DocHelper (class in biopax-explorer.biopax.doc.dh_fragmentfeature) from_graphtool() (biopax-explorer.graph.view.CytoViewer method) from_json() (biopax-explorer.graph.view.CytoViewer method) from_networkx() (biopax-explorer.graph.view.CytoViewer method) FullValidateArgType (class in biopax-explorer.biopax.utils.validate_utils) funcf() (biopax-explorer.pattern.processing.BlackListFilter method) G Gene (class in biopax-explorer.biopax.gene) gene_DocHelper (class in biopax-explorer.biopax.doc.dh_gene) generate_node_selector() (biopax-explorer.graph.view.CytoViewer method) generate_web_colors() (biopax-explorer.graph.view.CytoViewer method) GeneticInteraction (class in biopax-explorer.biopax.geneticinteraction) geneticinteraction_DocHelper (class in biopax-explorer.biopax.doc.dh_geneticinteraction) get_absoluteRegion() (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) get_author() (biopax-explorer.biopax.publicationxref.PublicationXref method) get_availability() (biopax-explorer.biopax.entity.Entity method) get_bindsTo() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) get_catalysisDirection() (biopax-explorer.biopax.catalysis.Catalysis method) get_cellType() (biopax-explorer.biopax.biosource.BioSource method) get_cellularLocation() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) get_chemicalFormula() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) get_class_from_string() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) get_cofactor() (biopax-explorer.biopax.catalysis.Catalysis method) get_comment() (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.utilityclass.UtilityClass method) get_component() (biopax-explorer.biopax.complex.Complex method) get_componentStoichiometry() (biopax-explorer.biopax.complex.Complex method) get_confidence() (biopax-explorer.biopax.evidence.Evidence method) get_controlled() (biopax-explorer.biopax.control.Control method) get_controller() (biopax-explorer.biopax.control.Control method) get_controlType() (biopax-explorer.biopax.control.Control method) get_conversionDirection() (biopax-explorer.biopax.conversion.Conversion method) get_dataSource() (biopax-explorer.biopax.entity.Entity method) get_db() (biopax-explorer.biopax.xref.Xref method) get_dbVersion() (biopax-explorer.biopax.xref.Xref method) get_deltaG() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) get_deltaGPrime0() (biopax-explorer.biopax.deltag.DeltaG method) get_deltaH() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) get_deltaS() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) get_displayName() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) get_eCNumber() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) get_entityFeature() (biopax-explorer.biopax.entityreference.EntityReference method) get_entityReference() (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) get_entityReferenceType() (biopax-explorer.biopax.entityreference.EntityReference method) get_evidence() (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) get_evidenceCode() (biopax-explorer.biopax.evidence.Evidence method) get_experimentalFeature() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) get_experimentalForm() (biopax-explorer.biopax.evidence.Evidence method) get_experimentalFormDescription() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) get_experimentalFormEntity() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) get_feature() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) get_featureLocation() (biopax-explorer.biopax.entityfeature.EntityFeature method) get_featureLocationType() (biopax-explorer.biopax.entityfeature.EntityFeature method) get_id() (biopax-explorer.biopax.xref.Xref method) get_idVersion() (biopax-explorer.biopax.xref.Xref method) get_interactionScore() (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) get_interactionType() (biopax-explorer.biopax.interaction.Interaction method) get_intraMolecular() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) get_ionicStrength() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) get_kEQ() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) get_kPrime() (biopax-explorer.biopax.kprime.KPrime method) get_left() (biopax-explorer.biopax.conversion.Conversion method) get_memberEntityReference() (biopax-explorer.biopax.entityreference.EntityReference method) get_memberFeature() (biopax-explorer.biopax.entityfeature.EntityFeature method) get_memberPhysicalEntity() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) get_modificationType() (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) get_molecularWeight() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) get_name() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) get_nextStep() (biopax-explorer.biopax.pathwaystep.PathwayStep method) get_notFeature() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) get_organism() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) get_parent_hierarchy() (in module biopax-explorer.biopax.utils.gen_utils) get_participant() (biopax-explorer.biopax.interaction.Interaction method) get_participantStoichiometry() (biopax-explorer.biopax.conversion.Conversion method) get_pathwayComponent() (biopax-explorer.biopax.pathway.Pathway method) get_pathwayOrder() (biopax-explorer.biopax.pathway.Pathway method) get_patoData() (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) get_ph() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) get_phenotype() (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) get_physicalEntity() (biopax-explorer.biopax.stoichiometry.Stoichiometry method) get_pMg() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) get_positionStatus() (biopax-explorer.biopax.sequencesite.SequenceSite method) get_product() (biopax-explorer.biopax.templatereaction.TemplateReaction method) get_regionType() (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) get_relationshipType() (biopax-explorer.biopax.relationshipxref.RelationshipXref method) get_right() (biopax-explorer.biopax.conversion.Conversion method) get_scoreSource() (biopax-explorer.biopax.score.Score method) get_sequence() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) get_sequenceIntervalBegin() (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) get_sequenceIntervalEnd() (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) get_sequencePosition() (biopax-explorer.biopax.sequencesite.SequenceSite method) get_source() (biopax-explorer.biopax.publicationxref.PublicationXref method) get_spontaneous() (biopax-explorer.biopax.conversion.Conversion method) get_standardName() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) get_stepConversion() (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) get_stepDirection() (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) get_stepProcess() (biopax-explorer.biopax.pathwaystep.PathwayStep method) get_stoichiometricCoefficient() (biopax-explorer.biopax.stoichiometry.Stoichiometry method) get_structure() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) get_structureData() (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) get_structureFormat() (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) get_subRegion() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) get_temperature() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) get_template() (biopax-explorer.biopax.templatereaction.TemplateReaction method) get_templateDirection() (biopax-explorer.biopax.templatereaction.TemplateReaction method) get_term() (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) get_tissue() (biopax-explorer.biopax.biosource.BioSource method) get_title() (biopax-explorer.biopax.publicationxref.PublicationXref method) get_uri_string() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) get_url() (biopax-explorer.biopax.publicationxref.PublicationXref method) get_validator_config() (in module biopax-explorer.biopax.utils.validate_utils) get_value() (biopax-explorer.biopax.score.Score method) get_xref() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.provenance.Provenance method) get_year() (biopax-explorer.biopax.publicationxref.PublicationXref method) gf2nx() (biopax-explorer.graph.view.CytoViewer method) graphDatasetLayer() (biopax-explorer.graph.view.Factory method) GraphDatasetLayerGT (class in biopax-explorer.graph.view) GraphDatasetLayerNX (class in biopax-explorer.graph.view) GraphModelLayer (class in biopax-explorer.graph.view) graphString() (in module biopax-explorer.graph.view) I ignore_error() (in module biopax-explorer.biopax.utils.validate_utils) inComplexWith() (biopax-explorer.pattern.rack.Rack method) init_caster() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) initStyle() (biopax-explorer.graph.view.CytoViewer method) initViewFromGraph() (biopax-explorer.graph.view.CytoViewer method) inSameActiveComplex() (biopax-explorer.pattern.rack.Rack method) inSameActiveComplexMolecularInteraction() (biopax-explorer.pattern.rack.Rack method) inSameActiveComplexOtherInteraction() (biopax-explorer.pattern.rack.Rack method) inSameComplex() (biopax-explorer.pattern.rack.Rack method) inSameComplexEffectingControl() (biopax-explorer.pattern.rack.Rack method) insert_instance() (biopax-explorer.query.client.BIOPAXStoreClient method) inspect() (biopax-explorer.pattern.rack.Rack method) Interaction (class in biopax-explorer.biopax.interaction) interaction_DocHelper (class in biopax-explorer.biopax.doc.dh_interaction) InteractionVocabulary (class in biopax-explorer.biopax.interactionvocabulary) interactionvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_interactionvocabulary) K KPrime (class in biopax-explorer.biopax.kprime) kprime_DocHelper (class in biopax-explorer.biopax.doc.dh_kprime) L layout() (biopax-explorer.graph.view.CytoViewer method) LocalProcessing (class in biopax-explorer.pattern.pattern) log_error() (in module biopax-explorer.biopax.utils.validate_utils) M modelPopulator() (in module biopax-explorer.biopax.utils.gen_utils) ModificationFeature (class in biopax-explorer.biopax.modificationfeature) modificationfeature_DocHelper (class in biopax-explorer.biopax.doc.dh_modificationfeature) modifierConv() (biopax-explorer.pattern.rack.Rack method) modifierConvComplex() (biopax-explorer.pattern.rack.Rack method) modifierConvNoComplex() (biopax-explorer.pattern.rack.Rack method) Modulation (class in biopax-explorer.biopax.modulation) modulation_DocHelper (class in biopax-explorer.biopax.doc.dh_modulation) module biopax-explorer.biopax biopax-explorer.biopax.bindingfeature biopax-explorer.biopax.biochemicalpathwaystep biopax-explorer.biopax.biochemicalreaction biopax-explorer.biopax.biosource biopax-explorer.biopax.catalysis biopax-explorer.biopax.cellularlocationvocabulary biopax-explorer.biopax.cellvocabulary biopax-explorer.biopax.chemicalstructure biopax-explorer.biopax.complex biopax-explorer.biopax.complexassembly biopax-explorer.biopax.control biopax-explorer.biopax.controlledvocabulary biopax-explorer.biopax.conversion biopax-explorer.biopax.covalentbindingfeature biopax-explorer.biopax.degradation biopax-explorer.biopax.deltag biopax-explorer.biopax.dna, [1] biopax-explorer.biopax.dnareference biopax-explorer.biopax.dnaregion biopax-explorer.biopax.dnaregionreference biopax-explorer.biopax.doc.dh_bindingfeature biopax-explorer.biopax.doc.dh_biochemicalpathwaystep biopax-explorer.biopax.doc.dh_biochemicalreaction biopax-explorer.biopax.doc.dh_biosource biopax-explorer.biopax.doc.dh_catalysis biopax-explorer.biopax.doc.dh_cellularlocationvocabulary biopax-explorer.biopax.doc.dh_cellvocabulary biopax-explorer.biopax.doc.dh_chemicalstructure biopax-explorer.biopax.doc.dh_complex biopax-explorer.biopax.doc.dh_complexassembly biopax-explorer.biopax.doc.dh_control biopax-explorer.biopax.doc.dh_controlledvocabulary biopax-explorer.biopax.doc.dh_conversion biopax-explorer.biopax.doc.dh_covalentbindingfeature biopax-explorer.biopax.doc.dh_degradation biopax-explorer.biopax.doc.dh_deltag biopax-explorer.biopax.doc.dh_dna biopax-explorer.biopax.doc.dh_dnareference biopax-explorer.biopax.doc.dh_dnaregion biopax-explorer.biopax.doc.dh_dnaregionreference biopax-explorer.biopax.doc.dh_entity biopax-explorer.biopax.doc.dh_entityfeature biopax-explorer.biopax.doc.dh_entityreference biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary biopax-explorer.biopax.doc.dh_evidence biopax-explorer.biopax.doc.dh_evidencecodevocabulary biopax-explorer.biopax.doc.dh_experimentalform biopax-explorer.biopax.doc.dh_experimentalformvocabulary biopax-explorer.biopax.doc.dh_fragmentfeature biopax-explorer.biopax.doc.dh_gene biopax-explorer.biopax.doc.dh_geneticinteraction biopax-explorer.biopax.doc.dh_interaction biopax-explorer.biopax.doc.dh_interactionvocabulary biopax-explorer.biopax.doc.dh_kprime biopax-explorer.biopax.doc.dh_modificationfeature biopax-explorer.biopax.doc.dh_modulation biopax-explorer.biopax.doc.dh_molecularinteraction biopax-explorer.biopax.doc.dh_pathway biopax-explorer.biopax.doc.dh_pathwaystep biopax-explorer.biopax.doc.dh_phenotypevocabulary biopax-explorer.biopax.doc.dh_physicalentity biopax-explorer.biopax.doc.dh_protein biopax-explorer.biopax.doc.dh_proteinreference biopax-explorer.biopax.doc.dh_provenance biopax-explorer.biopax.doc.dh_publicationxref biopax-explorer.biopax.doc.dh_relationshiptypevocabulary biopax-explorer.biopax.doc.dh_relationshipxref biopax-explorer.biopax.doc.dh_rna biopax-explorer.biopax.doc.dh_rnareference biopax-explorer.biopax.doc.dh_rnaregion biopax-explorer.biopax.doc.dh_rnaregionreference biopax-explorer.biopax.doc.dh_score biopax-explorer.biopax.doc.dh_sequenceinterval biopax-explorer.biopax.doc.dh_sequencelocation biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary biopax-explorer.biopax.doc.dh_sequenceregionvocabulary biopax-explorer.biopax.doc.dh_sequencesite biopax-explorer.biopax.doc.dh_smallmolecule biopax-explorer.biopax.doc.dh_smallmoleculereference biopax-explorer.biopax.doc.dh_stoichiometry biopax-explorer.biopax.doc.dh_templatereaction biopax-explorer.biopax.doc.dh_templatereactionregulation biopax-explorer.biopax.doc.dh_tissuevocabulary biopax-explorer.biopax.doc.dh_transport biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction biopax-explorer.biopax.doc.dh_unificationxref biopax-explorer.biopax.doc.dh_utilityclass biopax-explorer.biopax.doc.dh_xref biopax-explorer.biopax.entity biopax-explorer.biopax.entityfeature biopax-explorer.biopax.entityreference biopax-explorer.biopax.entityreferencetypevocabulary biopax-explorer.biopax.evidence biopax-explorer.biopax.evidencecodevocabulary biopax-explorer.biopax.experimentalform biopax-explorer.biopax.experimentalformvocabulary biopax-explorer.biopax.fragmentfeature biopax-explorer.biopax.gene biopax-explorer.biopax.geneticinteraction biopax-explorer.biopax.interaction biopax-explorer.biopax.interactionvocabulary biopax-explorer.biopax.kprime biopax-explorer.biopax.modificationfeature biopax-explorer.biopax.modulation biopax-explorer.biopax.molecularinteraction biopax-explorer.biopax.pathway biopax-explorer.biopax.pathwaystep biopax-explorer.biopax.phenotypevocabulary biopax-explorer.biopax.physicalentity biopax-explorer.biopax.protein biopax-explorer.biopax.proteinreference biopax-explorer.biopax.provenance biopax-explorer.biopax.publicationxref biopax-explorer.biopax.relationshiptypevocabulary biopax-explorer.biopax.relationshipxref biopax-explorer.biopax.rna biopax-explorer.biopax.rnareference biopax-explorer.biopax.rnaregion biopax-explorer.biopax.rnaregionreference biopax-explorer.biopax.score biopax-explorer.biopax.sequenceinterval biopax-explorer.biopax.sequencelocation biopax-explorer.biopax.sequencemodificationvocabulary biopax-explorer.biopax.sequenceregionvocabulary biopax-explorer.biopax.sequencesite biopax-explorer.biopax.smallmolecule biopax-explorer.biopax.smallmoleculereference biopax-explorer.biopax.stoichiometry biopax-explorer.biopax.templatereaction biopax-explorer.biopax.templatereactionregulation biopax-explorer.biopax.tissuevocabulary biopax-explorer.biopax.transport biopax-explorer.biopax.transportwithbiochemicalreaction biopax-explorer.biopax.unificationxref biopax-explorer.biopax.utilityclass biopax-explorer.biopax.utils.class_utils biopax-explorer.biopax.utils.gen_utils biopax-explorer.biopax.utils.validate_utils biopax-explorer.biopax.xref biopax-explorer.graph.serializer biopax-explorer.graph.view biopax-explorer.pattern.pattern biopax-explorer.pattern.processing biopax-explorer.pattern.rack biopax-explorer.pattern.view biopax-explorer.query.client MolecularInteraction (class in biopax-explorer.biopax.molecularinteraction) molecularInteraction() (biopax-explorer.pattern.rack.Rack method) molecularinteraction_DocHelper (class in biopax-explorer.biopax.doc.dh_molecularinteraction) molecularInteractionComplex() (biopax-explorer.pattern.rack.Rack method) molecularInteractionNoComplex() (biopax-explorer.pattern.rack.Rack method) N nodeSelector() (biopax-explorer.graph.view.CytoViewer method) notBlackboxComplexInComplex() (biopax-explorer.pattern.rack.Rack method) nxgraph() (biopax-explorer.query.client.BIOPAXStoreClient method) O object_attributes() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) objectAttributeNames() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) P PackageModelPopulator (class in biopax-explorer.biopax.utils.gen_utils) parentTree() (in module biopax-explorer.biopax.utils.gen_utils) Pathway (class in biopax-explorer.biopax.pathway) pathway_DocHelper (class in biopax-explorer.biopax.doc.dh_pathway) PathwayStep (class in biopax-explorer.biopax.pathwaystep) pathwaystep_DocHelper (class in biopax-explorer.biopax.doc.dh_pathwaystep) Pattern (class in biopax-explorer.pattern.pattern) PatternExecutor (class in biopax-explorer.pattern.pattern) PhenotypeVocabulary (class in biopax-explorer.biopax.phenotypevocabulary) phenotypevocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_phenotypevocabulary) PhysicalEntity (class in biopax-explorer.biopax.physicalentity) physicalentity_DocHelper (class in biopax-explorer.biopax.doc.dh_physicalentity) PK (class in biopax-explorer.pattern.pattern) populate_dataset() (biopax-explorer.graph.view.GraphDatasetLayerGT method) (biopax-explorer.graph.view.GraphDatasetLayerNX method) prefix() (in module biopax-explorer.biopax.utils.gen_utils) ProcessingCollection (class in biopax-explorer.pattern.pattern) (class in biopax-explorer.pattern.processing) Protein (class in biopax-explorer.biopax.protein) protein_DocHelper (class in biopax-explorer.biopax.doc.dh_protein) ProteinReference (class in biopax-explorer.biopax.proteinreference) proteinreference_DocHelper (class in biopax-explorer.biopax.doc.dh_proteinreference) Provenance (class in biopax-explorer.biopax.provenance) provenance_DocHelper (class in biopax-explorer.biopax.doc.dh_provenance) PublicationXref (class in biopax-explorer.biopax.publicationxref) publicationxref_DocHelper (class in biopax-explorer.biopax.doc.dh_publicationxref) R Rack (class in biopax-explorer.pattern.rack) raise_error() (in module biopax-explorer.biopax.utils.validate_utils) rdf_xml_string() (biopax-explorer.query.client.BIOPAXStoreClient method) reactsWith() (biopax-explorer.pattern.rack.Rack method) reactsWithComplex() (biopax-explorer.pattern.rack.Rack method) reactsWithNoComplex() (biopax-explorer.pattern.rack.Rack method) RelationshipTypeVocabulary (class in biopax-explorer.biopax.relationshiptypevocabulary) relationshiptypevocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_relationshiptypevocabulary) RelationshipXref (class in biopax-explorer.biopax.relationshipxref) relationshipxref_DocHelper (class in biopax-explorer.biopax.doc.dh_relationshipxref) Rna (class in biopax-explorer.biopax.rna) rna_DocHelper (class in biopax-explorer.biopax.doc.dh_rna) RnaReference (class in biopax-explorer.biopax.rnareference) rnareference_DocHelper (class in biopax-explorer.biopax.doc.dh_rnareference) RnaRegion (class in biopax-explorer.biopax.rnaregion) rnaregion_DocHelper (class in biopax-explorer.biopax.doc.dh_rnaregion) RnaRegionReference (class in biopax-explorer.biopax.rnaregionreference) rnaregionreference_DocHelper (class in biopax-explorer.biopax.doc.dh_rnaregionreference) route_query() (biopax-explorer.query.client.BIOPAXStoreClient method) route_update() (biopax-explorer.query.client.BIOPAXStoreClient method) S save_graph_as_rdf_xml() (biopax-explorer.query.client.BIOPAXStoreClient method) Score (class in biopax-explorer.biopax.score) score_DocHelper (class in biopax-explorer.biopax.doc.dh_score) select_all_query() (biopax-explorer.query.client.BIOPAXStoreClient method) select_list_alternatively() (biopax-explorer.graph.view.CytoViewer method) SequenceInterval (class in biopax-explorer.biopax.sequenceinterval) sequenceinterval_DocHelper (class in biopax-explorer.biopax.doc.dh_sequenceinterval) SequenceLocation (class in biopax-explorer.biopax.sequencelocation) sequencelocation_DocHelper (class in biopax-explorer.biopax.doc.dh_sequencelocation) SequenceModificationVocabulary (class in biopax-explorer.biopax.sequencemodificationvocabulary) sequencemodificationvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary) SequenceRegionVocabulary (class in biopax-explorer.biopax.sequenceregionvocabulary) sequenceregionvocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_sequenceregionvocabulary) SequenceSite (class in biopax-explorer.biopax.sequencesite) sequencesite_DocHelper (class in biopax-explorer.biopax.doc.dh_sequencesite) set() (biopax-explorer.graph.serializer.BPSerializer method) set_absoluteRegion() (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) set_author() (biopax-explorer.biopax.publicationxref.PublicationXref method) set_availability() (biopax-explorer.biopax.entity.Entity method) set_bindsTo() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) set_catalysisDirection() (biopax-explorer.biopax.catalysis.Catalysis method) set_cellType() (biopax-explorer.biopax.biosource.BioSource method) set_cellularLocation() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) set_chemicalFormula() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) set_cofactor() (biopax-explorer.biopax.catalysis.Catalysis method) set_comment() (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.utilityclass.UtilityClass method) set_component() (biopax-explorer.biopax.complex.Complex method) set_componentStoichiometry() (biopax-explorer.biopax.complex.Complex method) set_confidence() (biopax-explorer.biopax.evidence.Evidence method) set_controlled() (biopax-explorer.biopax.control.Control method) set_controller() (biopax-explorer.biopax.control.Control method) set_controlType() (biopax-explorer.biopax.control.Control method) set_conversionDirection() (biopax-explorer.biopax.conversion.Conversion method) set_dataSource() (biopax-explorer.biopax.entity.Entity method) set_db() (biopax-explorer.biopax.xref.Xref method) set_dbVersion() (biopax-explorer.biopax.xref.Xref method) set_deltaG() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) set_deltaGPrime0() (biopax-explorer.biopax.deltag.DeltaG method) set_deltaH() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) set_deltaS() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) set_displayName() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) set_eCNumber() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) set_entityFeature() (biopax-explorer.biopax.entityreference.EntityReference method) set_entityReference() (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) set_entityReferenceType() (biopax-explorer.biopax.entityreference.EntityReference method) set_evidence() (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) set_evidenceCode() (biopax-explorer.biopax.evidence.Evidence method) set_experimentalFeature() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) set_experimentalForm() (biopax-explorer.biopax.evidence.Evidence method) set_experimentalFormDescription() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) set_experimentalFormEntity() (biopax-explorer.biopax.experimentalform.ExperimentalForm method) set_feature() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) set_featureLocation() (biopax-explorer.biopax.entityfeature.EntityFeature method) set_featureLocationType() (biopax-explorer.biopax.entityfeature.EntityFeature method) set_id() (biopax-explorer.biopax.xref.Xref method) set_idVersion() (biopax-explorer.biopax.xref.Xref method) set_interactionScore() (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) set_interactionType() (biopax-explorer.biopax.interaction.Interaction method) set_intraMolecular() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) set_ionicStrength() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) set_kEQ() (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) set_kPrime() (biopax-explorer.biopax.kprime.KPrime method) set_left() (biopax-explorer.biopax.conversion.Conversion method) set_memberEntityReference() (biopax-explorer.biopax.entityreference.EntityReference method) set_memberFeature() (biopax-explorer.biopax.entityfeature.EntityFeature method) set_memberPhysicalEntity() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) set_modificationType() (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) set_molecularWeight() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) set_name() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) set_nextStep() (biopax-explorer.biopax.pathwaystep.PathwayStep method) set_notFeature() (biopax-explorer.biopax.physicalentity.PhysicalEntity method) set_organism() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) set_participant() (biopax-explorer.biopax.interaction.Interaction method) set_participantStoichiometry() (biopax-explorer.biopax.conversion.Conversion method) set_pathwayComponent() (biopax-explorer.biopax.pathway.Pathway method) set_pathwayOrder() (biopax-explorer.biopax.pathway.Pathway method) set_patoData() (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) set_ph() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) set_phenotype() (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) set_physicalEntity() (biopax-explorer.biopax.stoichiometry.Stoichiometry method) set_pMg() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) set_positionStatus() (biopax-explorer.biopax.sequencesite.SequenceSite method) set_product() (biopax-explorer.biopax.templatereaction.TemplateReaction method) set_regionType() (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) set_relationshipType() (biopax-explorer.biopax.relationshipxref.RelationshipXref method) set_right() (biopax-explorer.biopax.conversion.Conversion method) set_scoreSource() (biopax-explorer.biopax.score.Score method) set_sequence() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) set_sequenceIntervalBegin() (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) set_sequenceIntervalEnd() (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) set_sequencePosition() (biopax-explorer.biopax.sequencesite.SequenceSite method) set_source() (biopax-explorer.biopax.publicationxref.PublicationXref method) set_spontaneous() (biopax-explorer.biopax.conversion.Conversion method) set_standardName() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.provenance.Provenance method) set_stepConversion() (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) set_stepDirection() (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) set_stepProcess() (biopax-explorer.biopax.pathwaystep.PathwayStep method) set_stoichiometricCoefficient() (biopax-explorer.biopax.stoichiometry.Stoichiometry method) set_structure() (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) set_structureData() (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) set_structureFormat() (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) set_subRegion() (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) set_temperature() (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.kprime.KPrime method) set_template() (biopax-explorer.biopax.templatereaction.TemplateReaction method) set_templateDirection() (biopax-explorer.biopax.templatereaction.TemplateReaction method) set_term() (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) set_tissue() (biopax-explorer.biopax.biosource.BioSource method) set_title() (biopax-explorer.biopax.publicationxref.PublicationXref method) set_uri_string() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) set_url() (biopax-explorer.biopax.publicationxref.PublicationXref method) set_value() (biopax-explorer.biopax.score.Score method) set_xref() (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.provenance.Provenance method) set_year() (biopax-explorer.biopax.publicationxref.PublicationXref method) shortPrefix() (in module biopax-explorer.biopax.utils.gen_utils) SmallMolecule (class in biopax-explorer.biopax.smallmolecule) smallmolecule_DocHelper (class in biopax-explorer.biopax.doc.dh_smallmolecule) SmallMoleculeReference (class in biopax-explorer.biopax.smallmoleculereference) smallmoleculereference_DocHelper (class in biopax-explorer.biopax.doc.dh_smallmoleculereference) split_mod() (biopax-explorer.biopax.utils.validate_utils.CValidateArgType method) stateChange() (biopax-explorer.pattern.rack.Rack method) stateChangeComplex() (biopax-explorer.pattern.rack.Rack method) stateChangeNoComplex() (biopax-explorer.pattern.rack.Rack method) stateChangeSimple() (biopax-explorer.pattern.rack.Rack method) Step (class in biopax-explorer.pattern.pattern) Stoichiometry (class in biopax-explorer.biopax.stoichiometry) stoichiometry_DocHelper (class in biopax-explorer.biopax.doc.dh_stoichiometry) store_custom_query_to_graph() (biopax-explorer.query.client.BIOPAXStoreClient method) store_to_graph() (biopax-explorer.query.client.BIOPAXStoreClient method) string_to_graph() (biopax-explorer.query.client.BIOPAXStoreClient method) style() (biopax-explorer.graph.view.CytoViewer method) subobjrep() (biopax-explorer.biopax.utils.class_utils.CustomEncoder method) (biopax-explorer.biopax.utils.class_utils.CustomEncoderShort method) T TemplateReaction (class in biopax-explorer.biopax.templatereaction) templatereaction_DocHelper (class in biopax-explorer.biopax.doc.dh_templatereaction) TemplateReactionRegulation (class in biopax-explorer.biopax.templatereactionregulation) templatereactionregulation_DocHelper (class in biopax-explorer.biopax.doc.dh_templatereactionregulation) TissueVocabulary (class in biopax-explorer.biopax.tissuevocabulary) tissuevocabulary_DocHelper (class in biopax-explorer.biopax.doc.dh_tissuevocabulary) to_json() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) tojson() (in module biopax-explorer.biopax.utils.class_utils) tooltip() (biopax-explorer.graph.view.CytoViewer method) tostring() (in module biopax-explorer.biopax.utils.class_utils) Transport (class in biopax-explorer.biopax.transport) transport_DocHelper (class in biopax-explorer.biopax.doc.dh_transport) TransportWithBiochemicalReaction (class in biopax-explorer.biopax.transportwithbiochemicalreaction) transportwithbiochemicalreaction_DocHelper (class in biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction) type_attributes() (biopax-explorer.biopax.bindingfeature.BindingFeature method) (biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep method) (biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction method) (biopax-explorer.biopax.biosource.BioSource method) (biopax-explorer.biopax.catalysis.Catalysis method) (biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary method) (biopax-explorer.biopax.cellvocabulary.CellVocabulary method) (biopax-explorer.biopax.chemicalstructure.ChemicalStructure method) (biopax-explorer.biopax.complex.Complex method) (biopax-explorer.biopax.complexassembly.ComplexAssembly method) (biopax-explorer.biopax.control.Control method) (biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary method) (biopax-explorer.biopax.conversion.Conversion method) (biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature method) (biopax-explorer.biopax.degradation.Degradation method) (biopax-explorer.biopax.deltag.DeltaG method) (biopax-explorer.biopax.dna.Dna method) (biopax-explorer.biopax.dnareference.DnaReference method) (biopax-explorer.biopax.dnaregion.DnaRegion method) (biopax-explorer.biopax.dnaregionreference.DnaRegionReference method) (biopax-explorer.biopax.entity.Entity method) (biopax-explorer.biopax.entityfeature.EntityFeature method) (biopax-explorer.biopax.entityreference.EntityReference method) (biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary method) (biopax-explorer.biopax.evidence.Evidence method) (biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary method) (biopax-explorer.biopax.experimentalform.ExperimentalForm method) (biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary method) (biopax-explorer.biopax.fragmentfeature.FragmentFeature method) (biopax-explorer.biopax.gene.Gene method) (biopax-explorer.biopax.geneticinteraction.GeneticInteraction method) (biopax-explorer.biopax.interaction.Interaction method) (biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary method) (biopax-explorer.biopax.kprime.KPrime method) (biopax-explorer.biopax.modificationfeature.ModificationFeature method) (biopax-explorer.biopax.modulation.Modulation method) (biopax-explorer.biopax.molecularinteraction.MolecularInteraction method) (biopax-explorer.biopax.pathway.Pathway method) (biopax-explorer.biopax.pathwaystep.PathwayStep method) (biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary method) (biopax-explorer.biopax.physicalentity.PhysicalEntity method) (biopax-explorer.biopax.protein.Protein method) (biopax-explorer.biopax.proteinreference.ProteinReference method) (biopax-explorer.biopax.provenance.Provenance method) (biopax-explorer.biopax.publicationxref.PublicationXref method) (biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary method) (biopax-explorer.biopax.relationshipxref.RelationshipXref method) (biopax-explorer.biopax.rna.Rna method) (biopax-explorer.biopax.rnareference.RnaReference method) (biopax-explorer.biopax.rnaregion.RnaRegion method) (biopax-explorer.biopax.rnaregionreference.RnaRegionReference method) (biopax-explorer.biopax.score.Score method) (biopax-explorer.biopax.sequenceinterval.SequenceInterval method) (biopax-explorer.biopax.sequencelocation.SequenceLocation method) (biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary method) (biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary method) (biopax-explorer.biopax.sequencesite.SequenceSite method) (biopax-explorer.biopax.smallmolecule.SmallMolecule method) (biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference method) (biopax-explorer.biopax.stoichiometry.Stoichiometry method) (biopax-explorer.biopax.templatereaction.TemplateReaction method) (biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation method) (biopax-explorer.biopax.tissuevocabulary.TissueVocabulary method) (biopax-explorer.biopax.transport.Transport method) (biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction method) (biopax-explorer.biopax.unificationxref.UnificationXref method) (biopax-explorer.biopax.utilityclass.UtilityClass method) (biopax-explorer.biopax.xref.Xref method) typeAttributeNames() (biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper method) (biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper method) (biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper method) (biopax-explorer.biopax.doc.dh_complex.complex_DocHelper method) (biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper method) (biopax-explorer.biopax.doc.dh_control.control_DocHelper method) (biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper method) (biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper method) (biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper method) (biopax-explorer.biopax.doc.dh_dna.dna_DocHelper method) (biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entity.entity_DocHelper method) (biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper method) (biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper method) (biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper method) (biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_gene.gene_DocHelper method) (biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper method) (biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper method) (biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper method) (biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper method) (biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper method) (biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper method) (biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper method) (biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper method) (biopax-explorer.biopax.doc.dh_protein.protein_DocHelper method) (biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper method) (biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper method) (biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper method) (biopax-explorer.biopax.doc.dh_rna.rna_DocHelper method) (biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper method) (biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper method) (biopax-explorer.biopax.doc.dh_score.score_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper method) (biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper method) (biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper method) (biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper method) (biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper method) (biopax-explorer.biopax.doc.dh_transport.transport_DocHelper method) (biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper method) (biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper method) (biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper method) (biopax-explorer.biopax.doc.dh_xref.xref_DocHelper method) U UnificationXref (class in biopax-explorer.biopax.unificationxref) unificationxref_DocHelper (class in biopax-explorer.biopax.doc.dh_unificationxref) update_or_insert_instance() (biopax-explorer.query.client.BIOPAXStoreClient method) update_validator_config() (in module biopax-explorer.biopax.utils.validate_utils) usedToProduce() (biopax-explorer.pattern.rack.Rack method) usedToProduceBothComplex() (biopax-explorer.pattern.rack.Rack method) usedToProduceLeftComplex() (biopax-explorer.pattern.rack.Rack method) usedToProduceNoComplex() (biopax-explorer.pattern.rack.Rack method) usedToProduceProcessing() (in module biopax-explorer.pattern.processing) usedToProduceRightComplex() (biopax-explorer.pattern.rack.Rack method) UtilityClass (class in biopax-explorer.biopax.utilityclass) utilityclass_DocHelper (class in biopax-explorer.biopax.doc.dh_utilityclass) V ValidationDecorator (class in biopax-explorer.biopax.utils.validate_utils) W writePatternGraphView() (in module biopax-explorer.pattern.view) X Xref (class in biopax-explorer.biopax.xref) xref_DocHelper (class in biopax-explorer.biopax.doc.dh_xref)