001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure; 022 023/** 024 * 025 * The type of entity (polymer, non-polymer, water, macrolide) 026 * as defined in the mmCIF dictionary: <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity.type.html"></a> 027 * <p> 028 * Entities are of four types: polymer, non-polymer, macrolide and water. 029 * <p> 030 * Note that the water category includes only water; ordered 031 * solvent such as sulfate ion or acetone would be described as 032 * individual non-polymer entities. 033 * It is not clear what macrolides are, but they appear to be supported since mmCIF 4.0. 034 * 035 * 036 * @author Anthony Bradley 037 * @author Jose Duarte 038 * 039 */ 040public enum EntityType { 041 042 /** 043 * Polymeric entities: poly-peptides and nucleotide chains 044 */ 045 POLYMER("polymer"), 046 047 /** 048 * The 'branched' type use mainly to represent carbohydrates. 049 * The type was introduced in these versions of the mmcif dictionary: 050 * 5.101 2012-08-22 051 * 5.291 2017-09-10 052 * 5.304 2018-08-01 053 * The type will only be used for PDB-deposited files from July 2020, as part of 054 * the carbohydrate remediation project. 055 * @since 5.4.0 056 */ 057 BRANCHED("branched"), 058 059 /** 060 * Non-polymeric entities: ligands, metal ions, buffer molecules, etc 061 */ 062 NONPOLYMER("non-polymer"), 063 064 /** 065 * Water 066 */ 067 WATER("water"), 068 069 /** 070 * Macrolide. Supported in mmCIF 4.0 dictionary. Not clear what it refers to. 071 */ 072 MACROLIDE("macrolide"); 073 074 private String entityType; 075 076 /** 077 * @param entType the type of the Entity 078 */ 079 private EntityType(String entType) { 080 081 this.setEntityType(entType); 082 083 } 084 085 /** 086 * Returns the type of the Entity as a String 087 * 088 * @return String representation of the entity type. 089 */ 090 public String getEntityType() { 091 return entityType; 092 } 093 094 095 private void setEntityType(String entityType) { 096 this.entityType = entityType; 097 } 098 099 /** 100 * Creates a new EntityType from a String value. 101 * Returns null if entityType is null or not one of the supported 102 * standard types. 103 * 104 * @param entityType String value , should be one of "polymer","non-polymer","water","macrolide" 105 * @return an EntityType object 106 */ 107 public static EntityType entityTypeFromString(String entityType) 108 { 109 110 if ( entityType == null) 111 return null; 112 113 for(EntityType et : EntityType.values()) 114 { 115 if(entityType.equals(et.entityType)) 116 { 117 return et; 118 } 119 } 120 return null; 121 } 122 123}