Package org.biopax.paxtools.model.level3

Interface CovalentBindingFeature

All Superinterfaces:
BindingFeature, BioPAXElement, Cloneable, EntityFeature, Level3Element, ModificationFeature, Observable, 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