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 * Created on 05.03.2004 021 * @author Andreas Prlic 022 * 023 */ 024package org.biojava.nbio.structure; 025 026/** 027 * AminoAcid inherits most from Hetatom. Adds a few AminoAcid 028 * specific methods. 029 * @author Andreas Prlic 030 * @author Jules Jacobsen 031 * @since 1.4 032 * @version %I% %G% 033 * 034 */ 035public class AminoAcidImpl extends HetatomImpl implements AminoAcid { 036 037 private static final long serialVersionUID = -6018854413829044230L; 038 039 /** this is an Amino acid. type is "amino". */ 040 public static final GroupType type = GroupType.AMINOACID; 041 042 /** IUPAC amino acid residue names 043 */ 044 private Character amino_char ; 045 046 private String recordType; // allows to distinguish between AAs that have been created from SEQRES records and ATOM records 047 048 /** 049 * inherits most from Hetero and has just a few extensions. 050 */ 051 public AminoAcidImpl() { 052 super(); 053 054 amino_char = null; 055 recordType = ATOMRECORD; 056 } 057 058 @Override 059 public GroupType getType(){ return type;} 060 061 /** 062 * {@inheritDoc} 063 */ 064 @Override 065 public Atom getN() {return getAtom("N"); } 066 067 /** 068 * {@inheritDoc} 069 */ 070 @Override 071 public Atom getCA() { 072 // note CA can also be Calcium, but that can't happen in a standard aminoacid, so this should be safe 073 return getAtom("CA"); 074 } 075 076 /** 077 * {@inheritDoc} 078 */ 079 @Override 080 public Atom getC() {return getAtom("C"); } 081 082 /** 083 * {@inheritDoc} 084 */ 085 @Override 086 public Atom getO() {return getAtom("O"); } 087 088 /** 089 * {@inheritDoc} 090 */ 091 @Override 092 public Atom getCB() {return getAtom("CB"); } 093 094 095 /** 096 * {@inheritDoc} 097 */ 098 @Override 099 public Character getAminoType() { 100 return amino_char; 101 } 102 103 /** 104 * {@inheritDoc} 105 */ 106 @Override 107 public void setAminoType(Character aa){ 108 amino_char = aa ; 109 } 110 111 /** 112 * {@inheritDoc} 113 */ 114 @Override 115 public void setRecordType(String recordName) { 116 recordType = recordName; 117 } 118 119 /** 120 * {@inheritDoc} 121 */ 122 @Override 123 public String getRecordType() { 124 return recordType; 125 } 126 127 /** string representation. */ 128 @Override 129 public String toString(){ 130 131 String str = "AminoAcid "+ recordType + ":"+ pdb_name + " " + amino_char + 132 " " + residueNumber + " "+ pdb_flag + " " + recordType ; 133 if (pdb_flag) { 134 str = str + " atoms: "+atoms.size(); 135 } 136 if (!getAltLocs().isEmpty()) 137 str += " has altLocs :" + getAltLocs().size(); 138 139 return str ; 140 141 } 142 /** set three character name of AminoAcid. 143 * 144 * @param s a String specifying the PDBName value 145 * @see #getPDBName() 146 */ 147 @Override 148 public void setPDBName(String s) { 149 150 pdb_name =s ; 151 152 } 153 154 155 /** returns and identical copy of this Group object . 156 * @return and identical copy of this Group object 157 */ 158 @Override 159 public Object clone() { 160 161 AminoAcidImpl n = new AminoAcidImpl(); 162 n.setPDBFlag(has3D()); 163 n.setResidueNumber(getResidueNumber()); 164 165 n.setPDBName(getPDBName()); 166 167 n.setAminoType(getAminoType()); 168 n.setRecordType(recordType); 169 170 //clone atoms and bonds. 171 cloneAtomsAndBonds(n); 172 173 // copying the alt loc groups if present, otherwise they stay null 174 if (getAltLocs()!=null && !getAltLocs().isEmpty()) { 175 for (Group altLocGroup:this.getAltLocs()) { 176 Group nAltLocGroup = (Group)altLocGroup.clone(); 177 n.addAltLoc(nAltLocGroup); 178 } 179 } 180 181 if (chemComp!=null) 182 n.setChemComp(chemComp); 183 184 185 return n; 186 } 187 188 189}