001package org.biopax.paxtools.model.level3; 002 003/** 004 * Definition: A covalently modified feature on a sequence, relevant to an interaction, 005 * such as a post-translational modification. The difference between this class and BindingFeature is that this is 006 * covalent and BindingFeature is non-covalent. 007 * 008 * Rationale: In Biology, identity of DNA, RNA and Protein entities are defined around a wildtype sequence. Covalent 009 * modifications to this basal sequence are represented using modificaton features. Since small molecules are 010 * identified based on their chemical structure, not sequence, a covalent modification to a small molecule would 011 * result in a different molecule. 012 * 013 * Examples: A phosphorylation feature on a protein that enables the binding of an SH2 domain. 014 * 015 * Usagee: The added groups should be simple and stateless, such as phosphate or methyl groups and are captured 016 * by the modificationType controlled vocabulary. In other cases, such as covalently linked proteins, 017 * use CovalentBindingFeature instead. SmallMolecules can only have covalentBindingFeatures. 018 */ 019public interface ModificationFeature extends EntityFeature 020{ 021 /** 022 * @return Description and classification of the feature. 023 */ 024 SequenceModificationVocabulary getModificationType(); 025 026 /** 027 * @param featureType Description and classification of the feature. 028 */ 029 void setModificationType(SequenceModificationVocabulary featureType); 030 031} 032