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