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 023import org.biojava.nbio.structure.io.mmcif.chem.PolymerType; 024import org.biojava.nbio.structure.io.mmcif.chem.ResidueType; 025 026import java.util.*; 027 028 029/** 030 * This contains basic categories for Group types. It reflects the categorization 031 * used in old PDB file (e.g. for storing whether a residue is composed of 032 * ATOM or HETATM records. It is less specific than the mmCIF/PDBx-defined 033 * ResidueType enum, which may be more suitable for future applications. 034 * 035 * @author Andreas Prlic 036 * @author Spencer Bliven 037 * @since 1.7 038 * @see ResidueType 039 * 040 */ 041public enum GroupType { 042 043 044 /** 045 * The type for amino acids (L-peptides) 046 */ 047 AMINOACID("amino",GroupType.matchPolymerTypes(PolymerType.PROTEIN_ONLY)), 048 049 /** 050 * The type for nucleotide groups (dna and rna) 051 */ 052 NUCLEOTIDE("nucleotide",GroupType.matchPolymerTypes(PolymerType.POLYNUCLEOTIDE_ONLY)), 053 054 /** 055 * The type for hetero groups (everything else) 056 */ 057 HETATM("hetatm",GroupType.getHetatmTypes()); 058 059 private final String name; 060 private final Set<ResidueType> types; 061 private GroupType(String name,Set<ResidueType> types) { 062 this.name = name; 063 this.types = types; 064 } 065 066 /** 067 * The 3-letter codes used in the PDB to identify water molecules 068 * @see Group#isWater() 069 */ 070 public static final List<String> WATERNAMES = Arrays.asList("HOH", "DOD", "WAT"); 071 072 /** 073 * @return The name of this GroupType. One of "amino", "nucleotide", or "hetatm" 074 */ 075 @Override 076 public String toString() { 077 return name; 078 } 079 080 /** 081 * Get a set of ResidueTypes loosely equivalent to this GroupType. 082 * 083 * <p>Because mmCIF and PDB handle modified residues differently, some 084 * Groups may have a well-defined ResidueType yet still be HETATMs. 085 * @return A Set of ResidueTypes commonly classified as this GroupType 086 */ 087 public Set<ResidueType> getResidueTypes() { 088 return types; 089 } 090 091 /** 092 * Get ResidueTypes whose polymerType is contained in a certain set. 093 * This is used for defining the AMINOACID and NUCLEOTIDE sets. 094 * @param allowedTypes 095 * @return 096 */ 097 private static Set<ResidueType> matchPolymerTypes(Set<PolymerType> allowedTypes) { 098 Set<ResidueType> matched = new HashSet<ResidueType>(); 099 for(ResidueType restype : ResidueType.values()) { 100 if(allowedTypes.contains(restype.polymerType)) { 101 matched.add(restype); 102 } 103 } 104 return Collections.unmodifiableSet(matched); 105 } 106 107 /** 108 * Bundles everything not in AMINOACID or NUCLEOTIDE into the HETATM entry 109 * @return 110 */ 111 private static Set<ResidueType> getHetatmTypes() { 112 Set<ResidueType> unmatched = new HashSet<ResidueType>(); 113 for(ResidueType restype : ResidueType.values()) { 114 if(!AMINOACID.getResidueTypes().contains(restype) && 115 !NUCLEOTIDE.getResidueTypes().contains(restype) ) { 116 unmatched.add(restype); 117 } 118 } 119 return Collections.unmodifiableSet(unmatched); 120 } 121}