001package org.biopax.paxtools.model.level3; 002 003/** 004 * <b>Definition:</b> An entity feature that represent the covalently bound state of a physical entity. 005 * 006 * Rationale: Most frequent covalent modifications to proteins and DNA, such as phosphorylation and 007 * metylation are covered by the ModificationFeature class. In these cases, the added groups are 008 * simple and stateless therefore they can be captured by a controlled vocabulary. In other cases, 009 * such as ThiS-Thilacyl-disulfide, the covalently linked molecules are best represented as a 010 * molecular complex. CovalentBindingFeature should be used to model such covalently linked 011 * complexes. 012 * 013 * Usage: Using this construct, it is possible to represent small molecules as a covalent complex of 014 * two other small molecules. The demarcation of small molecules is a general problem and is 015 * delegated to small molecule databases.The best practice is not to model using covalent complexes 016 * unless at least one of the participants is a protein, DNA or RNA. 017 * 018 * Examples: disulfide bond UhpC + glc-6P -> Uhpc-glc-6p acetyl-ACP -> decenoyl-ACP charged tRNA 019 */ 020public interface CovalentBindingFeature extends BindingFeature, ModificationFeature 021{ 022 023}