org.biopax.paxtools.model.level2
Interface complex

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, entity, InteractionParticipant, Level2Element, physicalEntity, java.io.Serializable, XReferrable

public interface complex
extends physicalEntity

A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction. Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need.

Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

void	addCOMPONENTS(physicalEntityParticipant COMPONENTS)
java.util.Set<physicalEntityParticipant>	getCOMPONENTS()
bioSource	getORGANISM()
void	removeCOMPONENTS(physicalEntityParticipant COMPONENTS)
void	setCOMPONENTS(java.util.Set<physicalEntityParticipant> COMPONENTS)
void	setORGANISM(bioSource ORGANISM)

Methods inherited from interface org.biopax.paxtools.model.level2.physicalEntity

addPHYSICAL_ENTITYof, getAllInteractions, getAllInteractions, isPHYSICAL_ENTITYof, removePHYSICAL_ENTITYof

Methods inherited from interface org.biopax.paxtools.model.level2.entity

addAVAILABILITY, addDATA_SOURCE, addSYNONYMS, getAVAILABILITY, getDATA_SOURCE, getNAME, getSHORT_NAME, getSYNONYMS, removeAVAILABILITY, removeDATA_SOURCE, removeSYNONYMS, setAVAILABILITY, setDATA_SOURCE, setNAME, setSHORT_NAME, setSYNONYMS

Methods inherited from interface org.biopax.paxtools.model.level2.XReferrable

addXREF, findCommonPublications, findCommonRelationships, findCommonUnifications, getXREF, removeXREF, setXREF

Methods inherited from interface org.biopax.paxtools.model.level2.InteractionParticipant

isPARTICIPANTSof

Methods inherited from interface org.biopax.paxtools.model.level2.Level2Element

addCOMMENT, getCOMMENT, removeCOMMENT, setCOMMENT

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getCOMPONENTS

java.util.Set<physicalEntityParticipant> getCOMPONENTS()

setCOMPONENTS

void setCOMPONENTS(java.util.Set<physicalEntityParticipant> COMPONENTS)

addCOMPONENTS

void addCOMPONENTS(physicalEntityParticipant COMPONENTS)

removeCOMPONENTS

void removeCOMPONENTS(physicalEntityParticipant COMPONENTS)

getORGANISM

bioSource getORGANISM()

setORGANISM

void setORGANISM(bioSource ORGANISM)