org.biopax.paxtools.model.level3

Interface Complex

All Superinterfaces:

BioPAXElement, Cloneable, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, Serializable, XReferrable

All Known Implementing Classes:

ComplexImpl

public interface Complex
extends PhysicalEntity

Definition: 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.

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
void	addComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	addComponentStoichiometry(Stoichiometry stoichiometry) The stoichiometry of components in a complex.
Set<PhysicalEntity>	getComponent() Defines the PhysicalEntity subunits of this complex.
Set<Stoichiometry>	getComponentStoichiometry() The stoichiometry of components in a complex.
Set<EntityReference>	getMemberReferences() Gets the EntityReferences of the member simple physical entities.
Set<SimplePhysicalEntity>	getSimpleMembers() Gets the member physical entities which are not complex.
void	removeComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	removeComponentStoichiometry(Stoichiometry stoichiometry) The stoichiometry of components in a complex.

Methods inherited from interface org.biopax.paxtools.model.level3.PhysicalEntity

addFeature, addMemberPhysicalEntity, addNotFeature, getCellularLocation, getComponentOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getModelInterface, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation

Methods inherited from interface org.biopax.paxtools.model.level3.Controller

getControllerOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getUri, isEquivalent

Method Detail

getComponent

Set<PhysicalEntity> getComponent()

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Returns:

components of this complex

addComponent

void addComponent(PhysicalEntity component)

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Parameters:

component - to be added as a new member

removeComponent

void removeComponent(PhysicalEntity component)

Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.

Parameters:

component - to be removed from members.

getComponentStoichiometry

Set<Stoichiometry> getComponentStoichiometry()

The stoichiometry of components in a complex.

Returns:

the stoichiometry of components in a complex.

addComponentStoichiometry

void addComponentStoichiometry(Stoichiometry stoichiometry)

The stoichiometry of components in a complex.

Parameters:

stoichiometry - add a stoichiometry for the member.

removeComponentStoichiometry

void removeComponentStoichiometry(Stoichiometry stoichiometry)

The stoichiometry of components in a complex.

Parameters:

stoichiometry - remove a stoichiometry for the member.

getSimpleMembers

Set<SimplePhysicalEntity> getSimpleMembers()

Gets the member physical entities which are not complex. When the complex is nested, members of inner complexes are added to the returned set recursively.

Returns:

non-complex member physical entities

getMemberReferences

Set<EntityReference> getMemberReferences()

Gets the EntityReferences of the member simple physical entities. When the complex is nested, contents of the member complexes are retrieved recursively.

Returns:

non-complex members' entity references