Biopax-Explorer code documentation#

biopax-explorer.biopax.dna Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Dna(*args, **kwargs)

Class Dna

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.dna.Dna

biopax-explorer.biopax Package#

biopax-explorer.graph.serializer Module#

Functions#

bp_template()

Generates a BioPAX RDF template.

Classes#

BPSerializer(userns, collec)

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.graph.serializer.BPSerializer

biopax-explorer.graph.view Module#

Functions#

config()

Checks the installed backends and returns a message indicating the available options.

graphString(g)

Generates a string representation of a graph.

Classes#

CytoViewer(graph[, gtype])

A wrapper for the cytoscape.js jupyter widget.

Factory([back])

Factory class for creating graph dataset layers.

GraphDatasetLayerGT()

GraphDatasetLayerGT class for Graph-tool backend.

GraphDatasetLayerNX()

GraphDatasetLayerNX class for NetworkX backend.

GraphModelLayer()

GraphModelLayer class.

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.graph.view.CytoViewer, biopax-explorer.graph.view.Factory, biopax-explorer.graph.view.GraphDatasetLayerGT, biopax-explorer.graph.view.GraphDatasetLayerNX, biopax-explorer.graph.view.GraphModelLayer

biopax-explorer.query.client Module#

Classes#

BIOPAXStoreClient(db, dataset[, ...])

A class for interacting with a BIOPAX RDF store.

BindingFeature(*args, **kwargs)

Class BindingFeature

BioSource(*args, **kwargs)

Class BioSource

BiochemicalPathwayStep(*args, **kwargs)

Class BiochemicalPathwayStep

BiochemicalReaction(*args, **kwargs)

Class BiochemicalReaction

Catalysis(*args, **kwargs)

Class Catalysis

CellVocabulary(*args, **kwargs)

Class CellVocabulary

CellularLocationVocabulary(*args, **kwargs)

Class CellularLocationVocabulary

ChemicalStructure(*args, **kwargs)

Class ChemicalStructure

Complex(*args, **kwargs)

Class Complex

ComplexAssembly(*args, **kwargs)

Class ComplexAssembly

Control(*args, **kwargs)

Class Control

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

Conversion(*args, **kwargs)

Class Conversion

CovalentBindingFeature(*args, **kwargs)

Methods

DataType(code, python_type[, fmt, wrapper])

Xml and Schema data types to native python.

Degradation(*args, **kwargs)

Class Degradation

DeltaG(*args, **kwargs)

Class DeltaG

Dna(*args, **kwargs)

Class Dna

DnaReference(*args, **kwargs)

Class DnaReference

DnaRegion(*args, **kwargs)

Class DnaRegion

DnaRegionReference(*args, **kwargs)

Class DnaRegionReference

Entity(*args, **kwargs)

Class Entity

EntityFeature(*args, **kwargs)

Class EntityFeature

EntityReference(*args, **kwargs)

Class EntityReference

EntityReferenceTypeVocabulary(*args, **kwargs)

Class EntityReferenceTypeVocabulary

Environment([block_start_string, ...])

The core component of Jinja is the Environment.

Evidence(*args, **kwargs)

Class Evidence

EvidenceCodeVocabulary(*args, **kwargs)

Class EvidenceCodeVocabulary

ExperimentalForm(*args, **kwargs)

Class ExperimentalForm

ExperimentalFormVocabulary(*args, **kwargs)

Class ExperimentalFormVocabulary

FileSystemLoader(searchpath[, encoding, ...])

Load templates from a directory in the file system.

FragmentFeature(*args, **kwargs)

Class FragmentFeature

Gene(*args, **kwargs)

Class Gene

GeneticInteraction(*args, **kwargs)

Class GeneticInteraction

Graph([store, identifier, ...])

An RDF Graph

GraphDatasetLayerAbs()

Methods

GraphDatasetLayerAbsBK()

Methods

GraphDatasetLayerAbsBKGT()

Methods

GraphModelLayer()

Methods

Interaction(*args, **kwargs)

Class Interaction

InteractionVocabulary(*args, **kwargs)

Class InteractionVocabulary

KPrime(*args, **kwargs)

Class KPrime

Literal(lexical_or_value[, lang, datatype, ...])

RDF 1.1's Literals Section: http://www.w3.org/TR/rdf-concepts/#section-Graph-Literal

ModelCodeGenerator(package_name, classDict, ...)

Methods

ModelPopulator(classDict, package)

Methods

ModelProcessor(rdfGraphObj, scriptDir[, ...])

Methods

ModelToolBox(classDict)

Methods

ModificationFeature(*args, **kwargs)

Class ModificationFeature

Modulation(*args, **kwargs)

Class Modulation

MolecularInteraction(*args, **kwargs)

Class MolecularInteraction

Namespace(value)

Utility class for quickly generating URIRefs with a common prefix

Path(*args, **kwargs)

PurePath subclass that can make system calls.

Pathway(*args, **kwargs)

Class Pathway

PathwayStep(*args, **kwargs)

Class PathwayStep

PhenotypeVocabulary(*args, **kwargs)

Class PhenotypeVocabulary

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Protein(*args, **kwargs)

Class Protein

ProteinReference(*args, **kwargs)

Class ProteinReference

Provenance(*args, **kwargs)

Class Provenance

PublicationXref(*args, **kwargs)

Class PublicationXref

QNameConverter()

Methods

QNames()

Common qualified names.

RDF()

The RDF Concepts Vocabulary (RDF)

RelationshipTypeVocabulary(*args, **kwargs)

Class RelationshipTypeVocabulary

RelationshipXref(*args, **kwargs)

Class RelationshipXref

Rna(*args, **kwargs)

Class Rna

RnaReference(*args, **kwargs)

Class RnaReference

RnaRegion(*args, **kwargs)

Class RnaRegion

RnaRegionReference(*args, **kwargs)

Class RnaRegionReference

SPARQLWrapper(endpoint[, updateEndpoint, ...])

Wrapper around an online access to a SPARQL Web entry point.

Score(*args, **kwargs)

Class Score

SequenceInterval(*args, **kwargs)

Class SequenceInterval

SequenceLocation(*args, **kwargs)

Class SequenceLocation

SequenceModificationVocabulary(*args, **kwargs)

Class SequenceModificationVocabulary

SequenceRegionVocabulary(*args, **kwargs)

Class SequenceRegionVocabulary

SequenceSite(*args, **kwargs)

Class SequenceSite

SmallMolecule(*args, **kwargs)

Class SmallMolecule

SmallMoleculeReference(*args, **kwargs)

Class SmallMoleculeReference

Stoichiometry(*args, **kwargs)

Class Stoichiometry

StoreClient(classDict)

Methods

TAttributeModel(name, base, tp, xtp)

Methods

TClassModel(name, parent, domain, prefix, ...)

Methods

TemplateReaction(*args, **kwargs)

Class TemplateReaction

TemplateReactionRegulation(*args, **kwargs)

Class TemplateReactionRegulation

TissueVocabulary(*args, **kwargs)

Class TissueVocabulary

Transport(*args, **kwargs)

Class Transport

TransportWithBiochemicalReaction(*args, **kwargs)

Methods

URIRef(value[, base])

RDF 1.1's IRI Section https://www.w3.org/TR/rdf11-concepts/#section-IRIs

UnificationXref(*args, **kwargs)

Class UnificationXref

UtilityClass(*args, **kwargs)

Class UtilityClass

Xref(*args, **kwargs)

Class Xref

islice

islice(iterable, stop) --> islice object islice(iterable, start, stop[, step]) --> islice object

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.query.client.BIOPAXStoreClient

biopax-explorer.pattern.rack Module#

Functions#

control_by_controlled(ent)

control_by_controller(ent)

tostring(cls)

Classes#

BindingFeature(*args, **kwargs)

Class BindingFeature

BioSource(*args, **kwargs)

Class BioSource

BiochemicalPathwayStep(*args, **kwargs)

Class BiochemicalPathwayStep

BiochemicalReaction(*args, **kwargs)

Class BiochemicalReaction

Catalysis(*args, **kwargs)

Class Catalysis

CellVocabulary(*args, **kwargs)

Class CellVocabulary

CellularLocationVocabulary(*args, **kwargs)

Class CellularLocationVocabulary

ChemicalStructure(*args, **kwargs)

Class ChemicalStructure

Complex(*args, **kwargs)

Class Complex

ComplexAssembly(*args, **kwargs)

Class ComplexAssembly

Control(*args, **kwargs)

Class Control

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

Conversion(*args, **kwargs)

Class Conversion

CovalentBindingFeature(*args, **kwargs)

Methods

Degradation(*args, **kwargs)

Class Degradation

DeltaG(*args, **kwargs)

Class DeltaG

Dna(*args, **kwargs)

Class Dna

DnaReference(*args, **kwargs)

Class DnaReference

DnaRegion(*args, **kwargs)

Class DnaRegion

DnaRegionReference(*args, **kwargs)

Class DnaRegionReference

Entity(*args, **kwargs)

Class Entity

EntityFeature(*args, **kwargs)

Class EntityFeature

EntityNode(label, clsIL)

Methods

EntityReference(*args, **kwargs)

Class EntityReference

EntityReferenceTypeVocabulary(*args, **kwargs)

Class EntityReferenceTypeVocabulary

Evidence(*args, **kwargs)

Class Evidence

EvidenceCodeVocabulary(*args, **kwargs)

Class EvidenceCodeVocabulary

ExperimentalForm(*args, **kwargs)

Class ExperimentalForm

ExperimentalFormVocabulary(*args, **kwargs)

Class ExperimentalFormVocabulary

FragmentFeature(*args, **kwargs)

Class FragmentFeature

Gene(*args, **kwargs)

Class Gene

GeneticInteraction(*args, **kwargs)

Class GeneticInteraction

Interaction(*args, **kwargs)

Class Interaction

InteractionVocabulary(*args, **kwargs)

Class InteractionVocabulary

KPrime(*args, **kwargs)

Class KPrime

LocalProcessing()

LocalProcessing class represents local processing operations.

ModificationFeature(*args, **kwargs)

Class ModificationFeature

Modulation(*args, **kwargs)

Class Modulation

MolecularInteraction(*args, **kwargs)

Class MolecularInteraction

Path(*args, **kwargs)

PurePath subclass that can make system calls.

Pathway(*args, **kwargs)

Class Pathway

PathwayStep(*args, **kwargs)

Class PathwayStep

Pattern()

Pattern class represents a container for processing steps.

PhenotypeVocabulary(*args, **kwargs)

Class PhenotypeVocabulary

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

ProcessingCollection()

A class representing a processing collection.

Protein(*args, **kwargs)

Class Protein

ProteinReference(*args, **kwargs)

Class ProteinReference

Provenance(*args, **kwargs)

Class Provenance

PublicationXref(*args, **kwargs)

Class PublicationXref

Rack()

A reference list of Patterns related to BIOPAX use cases.

RelationshipTypeVocabulary(*args, **kwargs)

Class RelationshipTypeVocabulary

RelationshipXref(*args, **kwargs)

Class RelationshipXref

Rna(*args, **kwargs)

Class Rna

RnaReference(*args, **kwargs)

Class RnaReference

RnaRegion(*args, **kwargs)

Class RnaRegion

RnaRegionReference(*args, **kwargs)

Class RnaRegionReference

Score(*args, **kwargs)

Class Score

SequenceInterval(*args, **kwargs)

Class SequenceInterval

SequenceLocation(*args, **kwargs)

Class SequenceLocation

SequenceModificationVocabulary(*args, **kwargs)

Class SequenceModificationVocabulary

SequenceRegionVocabulary(*args, **kwargs)

Class SequenceRegionVocabulary

SequenceSite(*args, **kwargs)

Class SequenceSite

SmallMolecule(*args, **kwargs)

Class SmallMolecule

SmallMoleculeReference(*args, **kwargs)

Class SmallMoleculeReference

Step(core[, add_children, op])

Step class represents a step in the processing sequence of a Pattern.

Stoichiometry(*args, **kwargs)

Class Stoichiometry

TemplateReaction(*args, **kwargs)

Class TemplateReaction

TemplateReactionRegulation(*args, **kwargs)

Class TemplateReactionRegulation

TissueVocabulary(*args, **kwargs)

Class TissueVocabulary

Transport(*args, **kwargs)

Class Transport

TransportWithBiochemicalReaction(*args, **kwargs)

Methods

UnificationXref(*args, **kwargs)

Class UnificationXref

UtilityClass(*args, **kwargs)

Class UtilityClass

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.pattern.rack.Rack

biopax-explorer.pattern.processing Module#

Functions#

blacklistFilter(param)

Filter the collection using a blacklist.

tostring(cls)

usedToProduceProcessing(param)

Eliminate the matches where the small molecule at the left and at the right is the same.

Classes#

BindingFeature(*args, **kwargs)

Class BindingFeature

BioSource(*args, **kwargs)

Class BioSource

BiochemicalPathwayStep(*args, **kwargs)

Class BiochemicalPathwayStep

BiochemicalReaction(*args, **kwargs)

Class BiochemicalReaction

BlackListFilter(blacklist)

A class representing a Black List Filter.

Catalysis(*args, **kwargs)

Class Catalysis

CellVocabulary(*args, **kwargs)

Class CellVocabulary

CellularLocationVocabulary(*args, **kwargs)

Class CellularLocationVocabulary

ChemicalStructure(*args, **kwargs)

Class ChemicalStructure

Complex(*args, **kwargs)

Class Complex

ComplexAssembly(*args, **kwargs)

Class ComplexAssembly

Control(*args, **kwargs)

Class Control

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

Conversion(*args, **kwargs)

Class Conversion

CovalentBindingFeature(*args, **kwargs)

Methods

Degradation(*args, **kwargs)

Class Degradation

DeltaG(*args, **kwargs)

Class DeltaG

Dna(*args, **kwargs)

Class Dna

DnaReference(*args, **kwargs)

Class DnaReference

DnaRegion(*args, **kwargs)

Class DnaRegion

DnaRegionReference(*args, **kwargs)

Class DnaRegionReference

Entity(*args, **kwargs)

Class Entity

EntityFeature(*args, **kwargs)

Class EntityFeature

EntityReference(*args, **kwargs)

Class EntityReference

EntityReferenceTypeVocabulary(*args, **kwargs)

Class EntityReferenceTypeVocabulary

Evidence(*args, **kwargs)

Class Evidence

EvidenceCodeVocabulary(*args, **kwargs)

Class EvidenceCodeVocabulary

ExperimentalForm(*args, **kwargs)

Class ExperimentalForm

ExperimentalFormVocabulary(*args, **kwargs)

Class ExperimentalFormVocabulary

FragmentFeature(*args, **kwargs)

Class FragmentFeature

Gene(*args, **kwargs)

Class Gene

GeneticInteraction(*args, **kwargs)

Class GeneticInteraction

Interaction(*args, **kwargs)

Class Interaction

InteractionVocabulary(*args, **kwargs)

Class InteractionVocabulary

KPrime(*args, **kwargs)

Class KPrime

ModificationFeature(*args, **kwargs)

Class ModificationFeature

Modulation(*args, **kwargs)

Class Modulation

MolecularInteraction(*args, **kwargs)

Class MolecularInteraction

PK(pk[, cls, meta_label])

Methods

Path(*args, **kwargs)

PurePath subclass that can make system calls.

Pathway(*args, **kwargs)

Class Pathway

PathwayStep(*args, **kwargs)

Class PathwayStep

PhenotypeVocabulary(*args, **kwargs)

Class PhenotypeVocabulary

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

ProcessingCollection()

A class representing a processing collection.

Protein(*args, **kwargs)

Class Protein

ProteinReference(*args, **kwargs)

Class ProteinReference

Provenance(*args, **kwargs)

Class Provenance

PublicationXref(*args, **kwargs)

Class PublicationXref

RelationshipTypeVocabulary(*args, **kwargs)

Class RelationshipTypeVocabulary

RelationshipXref(*args, **kwargs)

Class RelationshipXref

Rna(*args, **kwargs)

Class Rna

RnaReference(*args, **kwargs)

Class RnaReference

RnaRegion(*args, **kwargs)

Class RnaRegion

RnaRegionReference(*args, **kwargs)

Class RnaRegionReference

Score(*args, **kwargs)

Class Score

SequenceInterval(*args, **kwargs)

Class SequenceInterval

SequenceLocation(*args, **kwargs)

Class SequenceLocation

SequenceModificationVocabulary(*args, **kwargs)

Class SequenceModificationVocabulary

SequenceRegionVocabulary(*args, **kwargs)

Class SequenceRegionVocabulary

SequenceSite(*args, **kwargs)

Class SequenceSite

SmallMolecule(*args, **kwargs)

Class SmallMolecule

SmallMoleculeReference(*args, **kwargs)

Class SmallMoleculeReference

Stoichiometry(*args, **kwargs)

Class Stoichiometry

TemplateReaction(*args, **kwargs)

Class TemplateReaction

TemplateReactionRegulation(*args, **kwargs)

Class TemplateReactionRegulation

TissueVocabulary(*args, **kwargs)

Class TissueVocabulary

Transport(*args, **kwargs)

Class Transport

TransportWithBiochemicalReaction(*args, **kwargs)

Methods

UnificationXref(*args, **kwargs)

Class UnificationXref

UtilityClass(*args, **kwargs)

Class UtilityClass

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.pattern.processing.BlackListFilter, biopax-explorer.pattern.processing.ProcessingCollection

biopax-explorer.pattern.view Module#

Functions#

dot2png(dotfile, gimagepath)

Converts DOT file to PNG image.

dot2svg(dotfile, gimagepath)

Converts DOT file to SVG image.

dottext2png(dot_string, gimagepath)

Converts DOT string to PNG image.

dottext2svg(dot_string, gimagepath)

Converts DOT string to SVG image.

writePatternGraphView(p1, gimagepath[, format])

Generates a graph view of a given Pattern and writes it to an image file.

biopax-explorer.pattern.pattern Module#

Classes#

DataPump([level])

This class fills the entities with void attributes.

LocalProcessing()

This class manages 'in-memory processing' to post-process a SPARQL query.

PK(pk[, cls])

Utility class to mock model entities with a lower memory footprint.

Pattern()

This class holds a list of Step objects containing Patterns or LocalProcessings.

PatternExecutor([db, dataset, blacklist, ...])

This class manages the execution of a 'Pattern' instance.

ProcessingCollection()

This class manages a list of referenced 'in-memory processing'.

Step(core[, add_children, op])

This class holds two kinds of data: - a list of EntityNodes used to generate a SPARQL query, or - a LocalProcessing that enables local in-memory filter operations on entities.

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.pattern.pattern.DataPump, biopax-explorer.pattern.pattern.LocalProcessing, biopax-explorer.pattern.pattern.PK, biopax-explorer.pattern.pattern.Pattern, biopax-explorer.pattern.pattern.PatternExecutor, biopax-explorer.pattern.pattern.ProcessingCollection, biopax-explorer.pattern.pattern.Step

biopax-explorer.biopax.bindingfeature Module#

Classes#

BindingFeature(*args, **kwargs)

Class BindingFeature

CValidateArgType(error_function[, logger, ...])

Methods

EntityFeature(*args, **kwargs)

Class EntityFeature

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.bindingfeature.BindingFeature

biopax-explorer.biopax.biochemicalpathwaystep Module#

Classes#

BiochemicalPathwayStep(*args, **kwargs)

Class BiochemicalPathwayStep

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PathwayStep(*args, **kwargs)

Class PathwayStep

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.biochemicalpathwaystep.BiochemicalPathwayStep

biopax-explorer.biopax.biochemicalreaction Module#

Classes#

BiochemicalReaction(*args, **kwargs)

Class BiochemicalReaction

CValidateArgType(error_function[, logger, ...])

Methods

Conversion(*args, **kwargs)

Class Conversion

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction

biopax-explorer.biopax.biosource Module#

Classes#

BioSource(*args, **kwargs)

Class BioSource

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.biosource.BioSource

biopax-explorer.biopax.catalysis Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Catalysis(*args, **kwargs)

Class Catalysis

Control(*args, **kwargs)

Class Control

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.catalysis.Catalysis

biopax-explorer.biopax.cellularlocationvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

CellularLocationVocabulary(*args, **kwargs)

Class CellularLocationVocabulary

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.cellularlocationvocabulary.CellularLocationVocabulary

biopax-explorer.biopax.cellvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

CellVocabulary(*args, **kwargs)

Class CellVocabulary

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.cellvocabulary.CellVocabulary

biopax-explorer.biopax.chemicalstructure Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ChemicalStructure(*args, **kwargs)

Class ChemicalStructure

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.chemicalstructure.ChemicalStructure

biopax-explorer.biopax.complex Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Complex(*args, **kwargs)

Class Complex

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.complex.Complex

biopax-explorer.biopax.complexassembly Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ComplexAssembly(*args, **kwargs)

Class ComplexAssembly

Conversion(*args, **kwargs)

Class Conversion

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.complexassembly.ComplexAssembly

biopax-explorer.biopax.control Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Control(*args, **kwargs)

Class Control

FullValidateArgType(error_function[, logger])

Methods

Interaction(*args, **kwargs)

Class Interaction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.control.Control

biopax-explorer.biopax.controlledvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.controlledvocabulary.ControlledVocabulary

biopax-explorer.biopax.conversion Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Conversion(*args, **kwargs)

Class Conversion

FullValidateArgType(error_function[, logger])

Methods

Interaction(*args, **kwargs)

Class Interaction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.conversion.Conversion

biopax-explorer.biopax.covalentbindingfeature Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

CovalentBindingFeature(*args, **kwargs)

Methods

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.covalentbindingfeature.CovalentBindingFeature

biopax-explorer.biopax.degradation Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Conversion(*args, **kwargs)

Class Conversion

Degradation(*args, **kwargs)

Class Degradation

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.degradation.Degradation

biopax-explorer.biopax.deltag Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

DeltaG(*args, **kwargs)

Class DeltaG

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.deltag.DeltaG

biopax-explorer.biopax.dna Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Dna(*args, **kwargs)

Class Dna

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.dna.Dna

biopax-explorer.biopax.dnareference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

DnaReference(*args, **kwargs)

Class DnaReference

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.dnareference.DnaReference

biopax-explorer.biopax.dnaregion Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

DnaRegion(*args, **kwargs)

Class DnaRegion

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.dnaregion.DnaRegion

biopax-explorer.biopax.dnaregionreference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

DnaRegionReference(*args, **kwargs)

Class DnaRegionReference

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.dnaregionreference.DnaRegionReference

biopax-explorer.biopax.entity Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Entity(*args, **kwargs)

Class Entity

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.entity.Entity

biopax-explorer.biopax.entityfeature Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityFeature(*args, **kwargs)

Class EntityFeature

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.entityfeature.EntityFeature

biopax-explorer.biopax.entityreference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.entityreference.EntityReference

biopax-explorer.biopax.entityreferencetypevocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

EntityReferenceTypeVocabulary(*args, **kwargs)

Class EntityReferenceTypeVocabulary

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.entityreferencetypevocabulary.EntityReferenceTypeVocabulary

biopax-explorer.biopax.evidence Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Evidence(*args, **kwargs)

Class Evidence

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.evidence.Evidence

biopax-explorer.biopax.evidencecodevocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

EvidenceCodeVocabulary(*args, **kwargs)

Class EvidenceCodeVocabulary

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.evidencecodevocabulary.EvidenceCodeVocabulary

biopax-explorer.biopax.experimentalform Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ExperimentalForm(*args, **kwargs)

Class ExperimentalForm

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.experimentalform.ExperimentalForm

biopax-explorer.biopax.experimentalformvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

ExperimentalFormVocabulary(*args, **kwargs)

Class ExperimentalFormVocabulary

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.experimentalformvocabulary.ExperimentalFormVocabulary

biopax-explorer.biopax.fragmentfeature Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityFeature(*args, **kwargs)

Class EntityFeature

FragmentFeature(*args, **kwargs)

Class FragmentFeature

FullValidateArgType(error_function[, logger])

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.fragmentfeature.FragmentFeature

biopax-explorer.biopax.gene Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Entity(*args, **kwargs)

Class Entity

FullValidateArgType(error_function[, logger])

Methods

Gene(*args, **kwargs)

Class Gene

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.gene.Gene

biopax-explorer.biopax.geneticinteraction Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

GeneticInteraction(*args, **kwargs)

Class GeneticInteraction

Interaction(*args, **kwargs)

Class Interaction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.geneticinteraction.GeneticInteraction

biopax-explorer.biopax.interaction Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Entity(*args, **kwargs)

Class Entity

FullValidateArgType(error_function[, logger])

Methods

Interaction(*args, **kwargs)

Class Interaction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.interaction.Interaction

biopax-explorer.biopax.interactionvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

InteractionVocabulary(*args, **kwargs)

Class InteractionVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.interactionvocabulary.InteractionVocabulary

biopax-explorer.biopax.kprime Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

KPrime(*args, **kwargs)

Class KPrime

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.kprime.KPrime

biopax-explorer.biopax.modificationfeature Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityFeature(*args, **kwargs)

Class EntityFeature

FullValidateArgType(error_function[, logger])

Methods

ModificationFeature(*args, **kwargs)

Class ModificationFeature

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.modificationfeature.ModificationFeature

biopax-explorer.biopax.modulation Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Control(*args, **kwargs)

Class Control

FullValidateArgType(error_function[, logger])

Methods

Modulation(*args, **kwargs)

Class Modulation

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.modulation.Modulation

biopax-explorer.biopax.molecularinteraction Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

Interaction(*args, **kwargs)

Class Interaction

MolecularInteraction(*args, **kwargs)

Class MolecularInteraction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.molecularinteraction.MolecularInteraction

biopax-explorer.biopax.pathway Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Entity(*args, **kwargs)

Class Entity

FullValidateArgType(error_function[, logger])

Methods

Pathway(*args, **kwargs)

Class Pathway

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.pathway.Pathway

biopax-explorer.biopax.pathwaystep Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PathwayStep(*args, **kwargs)

Class PathwayStep

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.pathwaystep.PathwayStep

biopax-explorer.biopax.phenotypevocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

PhenotypeVocabulary(*args, **kwargs)

Class PhenotypeVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary

biopax-explorer.biopax.physicalentity Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Entity(*args, **kwargs)

Class Entity

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.physicalentity.PhysicalEntity

biopax-explorer.biopax.protein Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Protein(*args, **kwargs)

Class Protein

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.protein.Protein

biopax-explorer.biopax.proteinreference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

ProteinReference(*args, **kwargs)

Class ProteinReference

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.proteinreference.ProteinReference

biopax-explorer.biopax.provenance Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

Provenance(*args, **kwargs)

Class Provenance

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.provenance.Provenance

biopax-explorer.biopax.publicationxref Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PublicationXref(*args, **kwargs)

Class PublicationXref

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.publicationxref.PublicationXref

biopax-explorer.biopax.relationshiptypevocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

RelationshipTypeVocabulary(*args, **kwargs)

Class RelationshipTypeVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.relationshiptypevocabulary.RelationshipTypeVocabulary

biopax-explorer.biopax.relationshipxref Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

RelationshipXref(*args, **kwargs)

Class RelationshipXref

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.relationshipxref.RelationshipXref

biopax-explorer.biopax.rna Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Rna(*args, **kwargs)

Class Rna

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.rna.Rna

biopax-explorer.biopax.rnareference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

RnaReference(*args, **kwargs)

Class RnaReference

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.rnareference.RnaReference

biopax-explorer.biopax.rnaregion Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

RnaRegion(*args, **kwargs)

Class RnaRegion

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.rnaregion.RnaRegion

biopax-explorer.biopax.rnaregionreference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

RnaRegionReference(*args, **kwargs)

Class RnaRegionReference

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.rnaregionreference.RnaRegionReference

biopax-explorer.biopax.score Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

Score(*args, **kwargs)

Class Score

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.score.Score

biopax-explorer.biopax.sequenceinterval Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

SequenceInterval(*args, **kwargs)

Class SequenceInterval

SequenceLocation(*args, **kwargs)

Class SequenceLocation

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.sequenceinterval.SequenceInterval

biopax-explorer.biopax.sequencelocation Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

SequenceLocation(*args, **kwargs)

Class SequenceLocation

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.sequencelocation.SequenceLocation

biopax-explorer.biopax.sequencemodificationvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

SequenceModificationVocabulary(*args, **kwargs)

Class SequenceModificationVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.sequencemodificationvocabulary.SequenceModificationVocabulary

biopax-explorer.biopax.sequenceregionvocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

SequenceRegionVocabulary(*args, **kwargs)

Class SequenceRegionVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.sequenceregionvocabulary.SequenceRegionVocabulary

biopax-explorer.biopax.sequencesite Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

SequenceLocation(*args, **kwargs)

Class SequenceLocation

SequenceSite(*args, **kwargs)

Class SequenceSite

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.sequencesite.SequenceSite

biopax-explorer.biopax.smallmolecule Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

SmallMolecule(*args, **kwargs)

Class SmallMolecule

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.smallmolecule.SmallMolecule

biopax-explorer.biopax.smallmoleculereference Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

EntityReference(*args, **kwargs)

Class EntityReference

FullValidateArgType(error_function[, logger])

Methods

SmallMoleculeReference(*args, **kwargs)

Class SmallMoleculeReference

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.smallmoleculereference.SmallMoleculeReference

biopax-explorer.biopax.stoichiometry Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

Stoichiometry(*args, **kwargs)

Class Stoichiometry

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.stoichiometry.Stoichiometry

biopax-explorer.biopax.templatereaction Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

Interaction(*args, **kwargs)

Class Interaction

TemplateReaction(*args, **kwargs)

Class TemplateReaction

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.templatereaction.TemplateReaction

biopax-explorer.biopax.templatereactionregulation Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Control(*args, **kwargs)

Class Control

FullValidateArgType(error_function[, logger])

Methods

TemplateReactionRegulation(*args, **kwargs)

Class TemplateReactionRegulation

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.templatereactionregulation.TemplateReactionRegulation

biopax-explorer.biopax.tissuevocabulary Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

FullValidateArgType(error_function[, logger])

Methods

TissueVocabulary(*args, **kwargs)

Class TissueVocabulary

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.tissuevocabulary.TissueVocabulary

biopax-explorer.biopax.transport Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

Conversion(*args, **kwargs)

Class Conversion

FullValidateArgType(error_function[, logger])

Methods

Transport(*args, **kwargs)

Class Transport

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.transport.Transport

biopax-explorer.biopax.transportwithbiochemicalreaction Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

TransportWithBiochemicalReaction(*args, **kwargs)

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.transportwithbiochemicalreaction.TransportWithBiochemicalReaction

biopax-explorer.biopax.unificationxref Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

UnificationXref(*args, **kwargs)

Class UnificationXref

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.unificationxref.UnificationXref

biopax-explorer.biopax.utilityclass Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.utilityclass.UtilityClass

biopax-explorer.biopax.xref Module#

Classes#

CValidateArgType(error_function[, logger, ...])

Methods

FullValidateArgType(error_function[, logger])

Methods

UtilityClass(*args, **kwargs)

Class UtilityClass

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.xref.Xref

biopax-explorer.biopax.utils.class_utils Module#

Functions#

tojson(o)

tostring(cls)

Classes#

CustomEncoder(*args, **kwargs)

CustomEncoder : a Custom Class for instance serialization

CustomEncoderShort(*args, **kwargs)

A Class to limit recursion in serialization

Decimal([value, context])

Construct a new Decimal object.

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.utils.class_utils.CustomEncoder, biopax-explorer.biopax.utils.class_utils.CustomEncoderShort

biopax-explorer.biopax.utils.gen_utils Module#

Functions#

class_children(cln)

classes()

classesDict()

classes_children()

createInstance(cln)

define_model_instance(clsn)

domain()

entityToString(entity, help)

get_parent_hierarchy(cls)

modelPopulator()

parentTree()

prefix()

shortPrefix()

Classes#

BindingFeature(*args, **kwargs)

Class BindingFeature

BioSource(*args, **kwargs)

Class BioSource

BiochemicalPathwayStep(*args, **kwargs)

Class BiochemicalPathwayStep

BiochemicalReaction(*args, **kwargs)

Class BiochemicalReaction

Catalysis(*args, **kwargs)

Class Catalysis

CellVocabulary(*args, **kwargs)

Class CellVocabulary

CellularLocationVocabulary(*args, **kwargs)

Class CellularLocationVocabulary

ChemicalStructure(*args, **kwargs)

Class ChemicalStructure

Complex(*args, **kwargs)

Class Complex

ComplexAssembly(*args, **kwargs)

Class ComplexAssembly

Control(*args, **kwargs)

Class Control

ControlledVocabulary(*args, **kwargs)

Class ControlledVocabulary

Conversion(*args, **kwargs)

Class Conversion

CovalentBindingFeature(*args, **kwargs)

Methods

Degradation(*args, **kwargs)

Class Degradation

DeltaG(*args, **kwargs)

Class DeltaG

Dna(*args, **kwargs)

Class Dna

DnaReference(*args, **kwargs)

Class DnaReference

DnaRegion(*args, **kwargs)

Class DnaRegion

DnaRegionReference(*args, **kwargs)

Class DnaRegionReference

Entity(*args, **kwargs)

Class Entity

EntityFeature(*args, **kwargs)

Class EntityFeature

EntityReference(*args, **kwargs)

Class EntityReference

EntityReferenceTypeVocabulary(*args, **kwargs)

Class EntityReferenceTypeVocabulary

Evidence(*args, **kwargs)

Class Evidence

EvidenceCodeVocabulary(*args, **kwargs)

Class EvidenceCodeVocabulary

ExperimentalForm(*args, **kwargs)

Class ExperimentalForm

ExperimentalFormVocabulary(*args, **kwargs)

Class ExperimentalFormVocabulary

FragmentFeature(*args, **kwargs)

Class FragmentFeature

Gene(*args, **kwargs)

Class Gene

GeneticInteraction(*args, **kwargs)

Class GeneticInteraction

Interaction(*args, **kwargs)

Class Interaction

InteractionVocabulary(*args, **kwargs)

Class InteractionVocabulary

KPrime(*args, **kwargs)

Class KPrime

ModelPopulator(classDict, package)

Methods

ModificationFeature(*args, **kwargs)

Class ModificationFeature

Modulation(*args, **kwargs)

Class Modulation

MolecularInteraction(*args, **kwargs)

Class MolecularInteraction

PackageModelPopulator()

Methods

Pathway(*args, **kwargs)

Class Pathway

PathwayStep(*args, **kwargs)

Class PathwayStep

PhenotypeVocabulary(*args, **kwargs)

Class PhenotypeVocabulary

PhysicalEntity(*args, **kwargs)

Class PhysicalEntity

Protein(*args, **kwargs)

Class Protein

ProteinReference(*args, **kwargs)

Class ProteinReference

Provenance(*args, **kwargs)

Class Provenance

PublicationXref(*args, **kwargs)

Class PublicationXref

RelationshipTypeVocabulary(*args, **kwargs)

Class RelationshipTypeVocabulary

RelationshipXref(*args, **kwargs)

Class RelationshipXref

Rna(*args, **kwargs)

Class Rna

RnaReference(*args, **kwargs)

Class RnaReference

RnaRegion(*args, **kwargs)

Class RnaRegion

RnaRegionReference(*args, **kwargs)

Class RnaRegionReference

Score(*args, **kwargs)

Class Score

SequenceInterval(*args, **kwargs)

Class SequenceInterval

SequenceLocation(*args, **kwargs)

Class SequenceLocation

SequenceModificationVocabulary(*args, **kwargs)

Class SequenceModificationVocabulary

SequenceRegionVocabulary(*args, **kwargs)

Class SequenceRegionVocabulary

SequenceSite(*args, **kwargs)

Class SequenceSite

SmallMolecule(*args, **kwargs)

Class SmallMolecule

SmallMoleculeReference(*args, **kwargs)

Class SmallMoleculeReference

Stoichiometry(*args, **kwargs)

Class Stoichiometry

TemplateReaction(*args, **kwargs)

Class TemplateReaction

TemplateReactionRegulation(*args, **kwargs)

Class TemplateReactionRegulation

TissueVocabulary(*args, **kwargs)

Class TissueVocabulary

Transport(*args, **kwargs)

Class Transport

TransportWithBiochemicalReaction(*args, **kwargs)

Methods

UnificationXref(*args, **kwargs)

Class UnificationXref

UtilityClass(*args, **kwargs)

Class UtilityClass

Xref(*args, **kwargs)

Class Xref

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.utils.gen_utils.PackageModelPopulator

biopax-explorer.biopax.utils.validate_utils Module#

Functions#

get_validator_config()

ignore_error(msg, func_name, logger)

log_error(msg, func_name, logger)

raise_error(msg, func_name, logger)

update_validator_config(new_config)

wraps(wrapped[, assigned, updated])

Decorator factory to apply update_wrapper() to a wrapper function

Classes#

BaseDecorator(validation_function, ...[, logger])

Bool(value[, strict_level])

|result_matrix_desc|

CValidateArgType(error_function[, logger, ...])

Methods

DateTime(value[, strict_level])

|result_matrix_desc|

FullValidateArgType(error_function[, logger])

Methods

Integer(value[, strict_level])

|result_matrix_desc|

RealNumber(value[, strict_level])

|result_matrix_desc|

String(value[, strict_level])

|result_matrix_desc|

TypeConversionError

Exception raised when failed to convert data.

ValidationDecorator(validation_function, ...)

Methods

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.utils.validate_utils.BaseDecorator, biopax-explorer.biopax.utils.validate_utils.CValidateArgType, biopax-explorer.biopax.utils.validate_utils.FullValidateArgType, biopax-explorer.biopax.utils.validate_utils.ValidationDecorator

biopax-explorer.biopax.doc.dh_bindingfeature Module#

Classes#

bindingfeature_DocHelper()

Class bindingfeature_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_bindingfeature.bindingfeature_DocHelper

biopax-explorer.biopax.doc.dh_biochemicalpathwaystep Module#

Classes#

biochemicalpathwaystep_DocHelper()

Class biochemicalpathwaystep_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_biochemicalpathwaystep.biochemicalpathwaystep_DocHelper

biopax-explorer.biopax.doc.dh_biochemicalreaction Module#

Classes#

biochemicalreaction_DocHelper()

Class biochemicalreaction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_biochemicalreaction.biochemicalreaction_DocHelper

biopax-explorer.biopax.doc.dh_biosource Module#

Classes#

biosource_DocHelper()

Class biosource_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_biosource.biosource_DocHelper

biopax-explorer.biopax.doc.dh_catalysis Module#

Classes#

catalysis_DocHelper()

Class catalysis_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_catalysis.catalysis_DocHelper

biopax-explorer.biopax.doc.dh_cellularlocationvocabulary Module#

Classes#

cellularlocationvocabulary_DocHelper()

Class cellularlocationvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_cellularlocationvocabulary.cellularlocationvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_cellvocabulary Module#

Classes#

cellvocabulary_DocHelper()

Class cellvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_cellvocabulary.cellvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_chemicalstructure Module#

Classes#

chemicalstructure_DocHelper()

Class chemicalstructure_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_chemicalstructure.chemicalstructure_DocHelper

biopax-explorer.biopax.doc.dh_complex Module#

Classes#

complex_DocHelper()

Class complex_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_complex.complex_DocHelper

biopax-explorer.biopax.doc.dh_complexassembly Module#

Classes#

complexassembly_DocHelper()

Class complexassembly_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_complexassembly.complexassembly_DocHelper

biopax-explorer.biopax.doc.dh_control Module#

Classes#

control_DocHelper()

Class control_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_control.control_DocHelper

biopax-explorer.biopax.doc.dh_controlledvocabulary Module#

Classes#

controlledvocabulary_DocHelper()

Class controlledvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_controlledvocabulary.controlledvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_conversion Module#

Classes#

conversion_DocHelper()

Class conversion_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_conversion.conversion_DocHelper

biopax-explorer.biopax.doc.dh_covalentbindingfeature Module#

Classes#

covalentbindingfeature_DocHelper()

Class covalentbindingfeature_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_covalentbindingfeature.covalentbindingfeature_DocHelper

biopax-explorer.biopax.doc.dh_degradation Module#

Classes#

degradation_DocHelper()

Class degradation_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_degradation.degradation_DocHelper

biopax-explorer.biopax.doc.dh_deltag Module#

Classes#

deltag_DocHelper()

Class deltag_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_deltag.deltag_DocHelper

biopax-explorer.biopax.doc.dh_dna Module#

Classes#

dna_DocHelper()

Class dna_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_dna.dna_DocHelper

biopax-explorer.biopax.doc.dh_dnareference Module#

Classes#

dnareference_DocHelper()

Class dnareference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_dnareference.dnareference_DocHelper

biopax-explorer.biopax.doc.dh_dnaregion Module#

Classes#

dnaregion_DocHelper()

Class dnaregion_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_dnaregion.dnaregion_DocHelper

biopax-explorer.biopax.doc.dh_dnaregionreference Module#

Classes#

dnaregionreference_DocHelper()

Class dnaregionreference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_dnaregionreference.dnaregionreference_DocHelper

biopax-explorer.biopax.doc.dh_entity Module#

Classes#

entity_DocHelper()

Class entity_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_entity.entity_DocHelper

biopax-explorer.biopax.doc.dh_entityfeature Module#

Classes#

entityfeature_DocHelper()

Class entityfeature_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_entityfeature.entityfeature_DocHelper

biopax-explorer.biopax.doc.dh_entityreference Module#

Classes#

entityreference_DocHelper()

Class entityreference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_entityreference.entityreference_DocHelper

biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary Module#

Classes#

entityreferencetypevocabulary_DocHelper()

Class entityreferencetypevocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_entityreferencetypevocabulary.entityreferencetypevocabulary_DocHelper

biopax-explorer.biopax.doc.dh_evidence Module#

Classes#

evidence_DocHelper()

Class evidence_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_evidence.evidence_DocHelper

biopax-explorer.biopax.doc.dh_evidencecodevocabulary Module#

Classes#

evidencecodevocabulary_DocHelper()

Class evidencecodevocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_evidencecodevocabulary.evidencecodevocabulary_DocHelper

biopax-explorer.biopax.doc.dh_experimentalform Module#

Classes#

experimentalform_DocHelper()

Class experimentalform_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_experimentalform.experimentalform_DocHelper

biopax-explorer.biopax.doc.dh_experimentalformvocabulary Module#

Classes#

experimentalformvocabulary_DocHelper()

Class experimentalformvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_experimentalformvocabulary.experimentalformvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_fragmentfeature Module#

Classes#

fragmentfeature_DocHelper()

Class fragmentfeature_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_fragmentfeature.fragmentfeature_DocHelper

biopax-explorer.biopax.doc.dh_gene Module#

Classes#

gene_DocHelper()

Class gene_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_gene.gene_DocHelper

biopax-explorer.biopax.doc.dh_geneticinteraction Module#

Classes#

geneticinteraction_DocHelper()

Class geneticinteraction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_geneticinteraction.geneticinteraction_DocHelper

biopax-explorer.biopax.doc.dh_interaction Module#

Classes#

interaction_DocHelper()

Class interaction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_interaction.interaction_DocHelper

biopax-explorer.biopax.doc.dh_interactionvocabulary Module#

Classes#

interactionvocabulary_DocHelper()

Class interactionvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_interactionvocabulary.interactionvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_kprime Module#

Classes#

kprime_DocHelper()

Class kprime_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_kprime.kprime_DocHelper

biopax-explorer.biopax.doc.dh_modificationfeature Module#

Classes#

modificationfeature_DocHelper()

Class modificationfeature_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_modificationfeature.modificationfeature_DocHelper

biopax-explorer.biopax.doc.dh_modulation Module#

Classes#

modulation_DocHelper()

Class modulation_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_modulation.modulation_DocHelper

biopax-explorer.biopax.doc.dh_molecularinteraction Module#

Classes#

molecularinteraction_DocHelper()

Class molecularinteraction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_molecularinteraction.molecularinteraction_DocHelper

biopax-explorer.biopax.doc.dh_pathway Module#

Classes#

pathway_DocHelper()

Class pathway_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_pathway.pathway_DocHelper

biopax-explorer.biopax.doc.dh_pathwaystep Module#

Classes#

pathwaystep_DocHelper()

Class pathwaystep_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_pathwaystep.pathwaystep_DocHelper

biopax-explorer.biopax.doc.dh_phenotypevocabulary Module#

Classes#

phenotypevocabulary_DocHelper()

Class phenotypevocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_phenotypevocabulary.phenotypevocabulary_DocHelper

biopax-explorer.biopax.doc.dh_physicalentity Module#

Classes#

physicalentity_DocHelper()

Class physicalentity_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_physicalentity.physicalentity_DocHelper

biopax-explorer.biopax.doc.dh_protein Module#

Classes#

protein_DocHelper()

Class protein_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_protein.protein_DocHelper

biopax-explorer.biopax.doc.dh_proteinreference Module#

Classes#

proteinreference_DocHelper()

Class proteinreference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_proteinreference.proteinreference_DocHelper

biopax-explorer.biopax.doc.dh_provenance Module#

Classes#

provenance_DocHelper()

Class provenance_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_provenance.provenance_DocHelper

biopax-explorer.biopax.doc.dh_publicationxref Module#

Classes#

publicationxref_DocHelper()

Class publicationxref_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_publicationxref.publicationxref_DocHelper

biopax-explorer.biopax.doc.dh_relationshiptypevocabulary Module#

Classes#

relationshiptypevocabulary_DocHelper()

Class relationshiptypevocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_relationshiptypevocabulary.relationshiptypevocabulary_DocHelper

biopax-explorer.biopax.doc.dh_relationshipxref Module#

Classes#

relationshipxref_DocHelper()

Class relationshipxref_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_relationshipxref.relationshipxref_DocHelper

biopax-explorer.biopax.doc.dh_rna Module#

Classes#

rna_DocHelper()

Class rna_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_rna.rna_DocHelper

biopax-explorer.biopax.doc.dh_rnareference Module#

Classes#

rnareference_DocHelper()

Class rnareference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_rnareference.rnareference_DocHelper

biopax-explorer.biopax.doc.dh_rnaregion Module#

Classes#

rnaregion_DocHelper()

Class rnaregion_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_rnaregion.rnaregion_DocHelper

biopax-explorer.biopax.doc.dh_rnaregionreference Module#

Classes#

rnaregionreference_DocHelper()

Class rnaregionreference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_rnaregionreference.rnaregionreference_DocHelper

biopax-explorer.biopax.doc.dh_score Module#

Classes#

score_DocHelper()

Class score_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_score.score_DocHelper

biopax-explorer.biopax.doc.dh_sequenceinterval Module#

Classes#

sequenceinterval_DocHelper()

Class sequenceinterval_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_sequenceinterval.sequenceinterval_DocHelper

biopax-explorer.biopax.doc.dh_sequencelocation Module#

Classes#

sequencelocation_DocHelper()

Class sequencelocation_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_sequencelocation.sequencelocation_DocHelper

biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary Module#

Classes#

sequencemodificationvocabulary_DocHelper()

Class sequencemodificationvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_sequencemodificationvocabulary.sequencemodificationvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_sequenceregionvocabulary Module#

Classes#

sequenceregionvocabulary_DocHelper()

Class sequenceregionvocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_sequenceregionvocabulary.sequenceregionvocabulary_DocHelper

biopax-explorer.biopax.doc.dh_sequencesite Module#

Classes#

sequencesite_DocHelper()

Class sequencesite_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_sequencesite.sequencesite_DocHelper

biopax-explorer.biopax.doc.dh_smallmolecule Module#

Classes#

smallmolecule_DocHelper()

Class smallmolecule_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_smallmolecule.smallmolecule_DocHelper

biopax-explorer.biopax.doc.dh_smallmoleculereference Module#

Classes#

smallmoleculereference_DocHelper()

Class smallmoleculereference_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_smallmoleculereference.smallmoleculereference_DocHelper

biopax-explorer.biopax.doc.dh_stoichiometry Module#

Classes#

stoichiometry_DocHelper()

Class stoichiometry_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_stoichiometry.stoichiometry_DocHelper

biopax-explorer.biopax.doc.dh_templatereaction Module#

Classes#

templatereaction_DocHelper()

Class templatereaction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_templatereaction.templatereaction_DocHelper

biopax-explorer.biopax.doc.dh_templatereactionregulation Module#

Classes#

templatereactionregulation_DocHelper()

Class templatereactionregulation_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_templatereactionregulation.templatereactionregulation_DocHelper

biopax-explorer.biopax.doc.dh_tissuevocabulary Module#

Classes#

tissuevocabulary_DocHelper()

Class tissuevocabulary_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_tissuevocabulary.tissuevocabulary_DocHelper

biopax-explorer.biopax.doc.dh_transport Module#

Classes#

transport_DocHelper()

Class transport_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_transport.transport_DocHelper

biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction Module#

Classes#

transportwithbiochemicalreaction_DocHelper()

Class transportwithbiochemicalreaction_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_transportwithbiochemicalreaction.transportwithbiochemicalreaction_DocHelper

biopax-explorer.biopax.doc.dh_unificationxref Module#

Classes#

unificationxref_DocHelper()

Class unificationxref_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_unificationxref.unificationxref_DocHelper

biopax-explorer.biopax.doc.dh_utilityclass Module#

Classes#

utilityclass_DocHelper()

Class utilityclass_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_utilityclass.utilityclass_DocHelper

biopax-explorer.biopax.doc.dh_xref Module#

Classes#

xref_DocHelper()

Class xref_DocHelper

Class Inheritance Diagram#

Inheritance diagram of biopax-explorer.biopax.doc.dh_xref.xref_DocHelper

Indices and tables#