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; 025import java.io.Serializable; 026 027 028 029/** 030 * A nucleotide group is almost the same as a Hetatm group. 031 * @see HetatomImpl 032 * @see AminoAcidImpl 033 * @author Andreas Prlic 034 * @since 1.4 035 * @version %I% %G% 036 */ 037public class NucleotideImpl extends HetatomImpl implements Group, Serializable, Cloneable { 038 039 private static final long serialVersionUID = -7467726932980288712L; 040 /** this is a "nucleotide", a special occurance of a Hetatom. */ 041 public static final GroupType type = GroupType.NUCLEOTIDE; 042 043 /* 044 * inherits most from Hetero and has just a few extensions. 045 */ 046 public NucleotideImpl() { 047 super(); 048 049 } 050 051 @Override 052 public GroupType getType(){ return type;} 053 054 055 @Override 056 public String toString(){ 057 058 String str = "PDB: "+ pdb_name + " " + residueNumber + " "+ pdb_flag; 059 if (pdb_flag) { 060 str = str + "atoms: "+atoms.size(); 061 } 062 return str ; 063 064 } 065 066 /** 067 * Returns the O3' atom if present, otherwise null 068 * @return O3' atom or null 069 */ 070 public Atom getO3Prime() { 071 072 return getAtom("O3'"); 073 074 } 075 076 /** 077 * Returns the O5' atom if present, otherwise null 078 * @return O5' atom or null 079 */ 080 public Atom getO5Prime() { 081 082 return getAtom("O5'"); 083 084 } 085 086 /** 087 * Returns the P atom if present, otherwise null 088 * @return P atom or null 089 */ 090 public Atom getP() { 091 092 return getAtom("P"); 093 094 } 095 096 // note we need to implement a clone here, despite there's one in super class already, 097 // that's due to issue https://github.com/biojava/biojava/issues/631 - JD 2017-01-21 098 @Override 099 public Object clone() { 100 101 NucleotideImpl n = new NucleotideImpl(); 102 n.setPDBFlag(has3D()); 103 n.setResidueNumber(getResidueNumber()); 104 105 n.setPDBName(getPDBName()); 106 107 // copy the atoms 108 for (Atom atom1 : atoms) { 109 Atom atom = (Atom) atom1.clone(); 110 n.addAtom(atom); 111 atom.setGroup(n); 112 } 113 114 // copying the alt loc groups if present, otherwise they stay null 115 if (getAltLocs()!=null && !getAltLocs().isEmpty()) { 116 for (Group altLocGroup:this.getAltLocs()) { 117 Group nAltLocGroup = (Group)altLocGroup.clone(); 118 n.addAltLoc(nAltLocGroup); 119 } 120 } 121 122 if (chemComp!=null) 123 n.setChemComp(chemComp); 124 125 126 return n; 127 } 128}