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 Jan. 22, 2016 021 * 022 */ 023package org.biojava.nbio.structure.io; 024 025import java.util.List; 026 027import org.biojava.nbio.structure.Atom; 028import org.biojava.nbio.structure.Chain; 029import org.biojava.nbio.structure.Group; 030import org.biojava.nbio.structure.Structure; 031import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory; 032import org.biojava.nbio.structure.io.mmcif.model.ChemComp; 033import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom; 034import org.slf4j.Logger; 035import org.slf4j.LoggerFactory; 036 037/** 038 * A class to add appropriate charge information to a structure. 039 * @author Anthony Bradley 040 * 041 */ 042public class ChargeAdder { 043 044 private static final Logger logger = LoggerFactory.getLogger(ChargeAdder.class); 045 046 /** 047 * Function to add the charges to a given structure. 048 */ 049 public static void addCharges(Structure structure) { 050 // Loop through the models 051 for(int i=0; i<structure.nrModels(); i++){ 052 for(Chain c: structure.getChains(i)){ 053 for(Group g: c.getAtomGroups()){ 054 ChemComp thisChemComp = ChemCompGroupFactory.getChemComp(g.getPDBName()); 055 List<ChemCompAtom> chemAtoms = thisChemComp.getAtoms(); 056 for(ChemCompAtom chemCompAtom : chemAtoms) { 057 Atom atom = g.getAtom(chemCompAtom.getAtom_id()); 058 String stringCharge = chemCompAtom.getCharge(); 059 short shortCharge = 0; 060 if (stringCharge!=null){ 061 if(!stringCharge.equals("?")){ 062 try{ 063 shortCharge = Short.parseShort(stringCharge); 064 } 065 catch(NumberFormatException e){ 066 logger.warn("Number format exception. Parsing '"+stringCharge+"' to short"); 067 } 068 } 069 else{ 070 logger.warn("? charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId()); 071 } 072 } 073 else{ 074 logger.warn("Null charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId()); 075 } 076 if(atom!=null){ 077 atom.setCharge(shortCharge); 078 } 079 // Now do the same for alt locs 080 for (Group altLoc : g.getAltLocs()) { 081 Atom altAtom = altLoc.getAtom(chemCompAtom.getAtom_id()); 082 if(altAtom!=null){ 083 altAtom.setCharge(shortCharge); 084 } 085 } 086 } 087 } 088 089 } 090 } 091 } 092}