PyBioPAX documentation

• PyBioPAX API
  • model_from_biocyc()
  • model_from_ecocyc()
  • model_from_humancyc()
  • model_from_metacyc()
  • model_from_netpath()
  • model_from_owl_file()
  • model_from_owl_gz()
  • model_from_owl_str()
  • model_from_owl_url()
  • model_from_pc_query()
  • model_from_reactome()
  • model_to_owl_file()
  • model_to_owl_str()
• BioPAX object model
  • BioPaxModel
    • BioPaxModel.objects
    • BioPaxModel.xml_base
    • BioPaxModel.from_xml()
    • BioPaxModel.to_xml()
  • PYBIOPAX_TQDM_CONFIG
  • Base classes
    • BioPaxObject
    • Controller
    • Entity
    • Gene
    • Named
    • Observable
    • Pathway
    • Unresolved
    • XReferrable
  • Interactions
    • BiochemicalReaction
    • Catalysis
    • ComplexAssembly
    • Control
    • Conversion
    • Degradation
    • GeneticInteraction
    • Interaction
    • Modulation
    • MolecularInteraction
    • Process
    • TemplateReaction
    • TemplateReactionRegulation
    • Transport
    • TransportWithBiochemicalReaction
  • Physical entities
    • Complex
    • Dna
    • DnaRegion
    • PhysicalEntity
    • Protein
    • Rna
    • RnaRegion
    • SimplePhysicalEntity
    • SmallMolecule
  • Utility classes
    • BindingFeature
    • BioSource
    • BiochemicalPathwayStep
    • CellVocabulary
    • CellularLocationVocabulary
    • ChemicalConstant
    • ChemicalStructure
    • ControlledVocabulary
    • DeltaG
    • DnaReference
    • DnaRegionReference
    • EntityFeature
    • EntityReference
    • EntityReferenceTypeVocabulary
    • Evidence
    • EvidenceCodeVocabulary
    • ExperimentalForm
    • ExperimentalFormVocabulary
    • FragmentFeature
    • InteractionVocabulary
    • KPrime
    • ModificationFeature
    • NucleicAcidReference
    • NucleicAcidRegionReference
    • PathwayStep
    • PhenotypeVocabulary
    • ProteinReference
    • Provenance
    • PublicationXref
    • RelationshipTypeVocabulary
    • RelationshipXref
    • RnaReference
    • RnaRegionReference
    • Score
    • SequenceEntityReference
    • SequenceInterval
    • SequenceLocation
    • SequenceModificationVocabulary
    • SequenceRegionVocabulary
    • SequenceSite
    • SmallMoleculeReference
    • Stoichiometry
    • TissueVocabulary
    • UnificationXref
    • UtilityClass
    • Xref
• Pathway Commons client
  • graph_query()
• Path finding
  • BiopaxClassConstraintError
  • find_objects()
• XML/OWL processing utilities
  • camel_to_snake()
  • get_attr_tag()
  • get_datatype()
  • get_id_or_about()
  • get_ns()
  • get_resource()
  • get_tag()
  • has_ns()
  • is_datatype()
  • is_url()
  • nselem()
  • nssuffix()
  • snake_to_camel()
  • wrap_xml_elements()
  • xml_to_file()
  • xml_to_str()

• Index

• Module Index