org.biopax.paxtools.model.level3
Interface CovalentBindingFeature

All Superinterfaces:

BindingFeature, BioPAXElement, java.lang.Cloneable, EntityFeature, Level3Element, ModificationFeature, Observable, java.io.Serializable, UtilityClass

All Known Implementing Classes:

CovalentBindingFeatureImpl

public interface CovalentBindingFeature
extends BindingFeature, ModificationFeature

Definition: An entity feature that represent the covalently bound state of a physical entity.

Rationale: Most frequent covalent modifications to proteins and DNA, such as phosphorylation and metylation are covered by the ModificationFeature class. In these cases, the added groups are simple and stateless therefore they can be captured by a controlled vocabulary. In other cases, such as ThiS-Thilacyl-disulfide, the covalently linked molecules are best represented as a molecular complex. CovalentBindingFeature should be used to model such covalently linked complexes.

Usage: Using this construct, it is possible to represent small molecules as a covalent complex of two other small molecules. The demarcation of small molecules is a general problem and is delegated to small molecule databases.The best practice is not to model using covalent complexes unless at least one of the participants is a protein, DNA or RNA.

Examples: disulfide bond UhpC + glc-6P -> Uhpc-glc-6p acetyl-ACP -> decenoyl-ACP charged tRNA

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

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

getBindsTo, getIntraMolecular, setBindsTo, setIntraMolecular

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

getModificationType, setModificationType

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

addMemberFeature, atEquivalentLocation, getEntityFeatureOf, getFeatureLocation, getFeatureLocationType, getFeatureOf, getMemberFeature, getMemberFeatureOf, getNotFeatureOf, removeMemberFeature, setFeatureLocation, setFeatureLocationType

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

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence