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 -&gt; Uhpc-glc-6p acetyl-ACP -&gt; decenoyl-ACP charged tRNA
019 */
020public interface CovalentBindingFeature extends BindingFeature, ModificationFeature
021{
022
023}