/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align.xml;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AlignmentTools;
import org.biojava.nbio.structure.jama.Matrix;
import org.biojava.nbio.core.util.PrettyXMLWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
public class AFPChainXMLConverter {
/** Convert an afpChain to a simple XML representation
*
* @param afpChain
* @return XML representation of the AFPCHain
*/
public synchronized static String toXML(AFPChain afpChain, Atom[] ca1, Atom[]ca2) throws IOException{
StringWriter result = new StringWriter();
toXML(afpChain,result,ca1,ca2);
return result.toString();
}
/** Write the XML representation to a StringWriter
*
* @param afpChain
* @param swriter
* @throws IOException
*/
public synchronized static void toXML(AFPChain afpChain, StringWriter swriter,Atom[] ca1, Atom[]ca2) throws IOException{
PrintWriter writer = new PrintWriter(swriter);
PrettyXMLWriter xml = new PrettyXMLWriter(writer);
xml.openTag("AFPChain");
printXMLHeader(xml,afpChain);
// that is the initial alignment...
// we don't serialize that at the present.
//int[] blockResSize = afpChain.getBlockResSize();
//int[][][] blockResList = afpChain.getBlockResList();
// get the alignment blocks
int blockNum = afpChain.getBlockNum();
//int[] optLen = afpChain.getOptLen();
//int[] blockSize = afpChain.getBlockSize();
for(int bk = 0; bk < blockNum; bk ++) {
xml.openTag("block");
printXMLBlockHeader(xml,afpChain, bk);
if ( ca1 == null || ca2 == null) {
try {
printXMLEQRKnownPositions(xml,afpChain,bk);
} catch (StructureException ex ){
throw new IOException(ex.getMessage());
}
}
else
printXMLEQRInferPositions(xml, afpChain,bk,ca1,ca2);
printXMLMatrixShift(xml, afpChain, bk);
xml.closeTag("block");
}
xml.closeTag("AFPChain");
writer.close();
}
private static void printXMLEQRKnownPositions(PrettyXMLWriter xml,
AFPChain afpChain, int blockNr) throws IOException, StructureException{
int[] optLen = afpChain.getOptLen();
String[][][] pdbAln = afpChain.getPdbAln();
if ( pdbAln == null){
throw new StructureException("Can't convert to XML without known the PDB coordinates. Please provide Ca atoms and call toXML(afpChain,ca1, ca2)");
}
for ( int eqrNr = 0 ; eqrNr < optLen[blockNr] ; eqrNr++ ){
String pdbResnum1 = pdbAln[blockNr][0][eqrNr];
String pdbResnum2 = pdbAln[blockNr][1][eqrNr];
//System.out.println(eqrNr + " got resnum: " + pdbResnum1 + " " + pdbResnum2);
String[] spl1 = pdbResnum1.split(":");
String[] spl2 = pdbResnum2.split(":");
String chain1 = spl1[0];
String pdbres1 = spl1[1];
String chain2 = spl2[0];
String pdbres2 = spl2[1];
xml.openTag("eqr");
xml.attribute("eqrNr", String.valueOf(eqrNr));
xml.attribute("pdbres1",pdbres1);
xml.attribute("chain1", chain1);
xml.attribute("pdbres2",pdbres2);
xml.attribute("chain2", chain2);
xml.closeTag("eqr");
}
}
public static void printXMLEQRInferPositions(PrettyXMLWriter xml,
AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2) throws IOException{
int[] optLen = afpChain.getOptLen();
if ( optLen == null)
return;
int[][][] optAln = afpChain.getOptAln();
for ( int pos=0;pos< optLen[bk];pos++){
int pos1 = optAln[bk][0][pos];
int pos2 = optAln[bk][1][pos];
xml.openTag("eqr");
xml.attribute("eqrNr", String.valueOf(pos));
xml.attribute("pdbres1",ca1[pos1].getGroup().getResidueNumber().toString());
xml.attribute("chain1", ca1[pos1].getGroup().getChain().getName());
xml.attribute("pdbres2",ca2[pos2].getGroup().getResidueNumber().toString());
xml.attribute("chain2", ca2[pos2].getGroup().getChain().getName());
xml.closeTag("eqr");
//System.out.println("aligned position: " + pos1 + ":" + pos2 +
//" pdbresnum " + ca1[pos1].getGroup().getResidueNumber().toString() + " " +
//ca1[pos1].getParent().getPDBName()+":" +
//ca2[pos2].getGroup().getResidueNumber().toString() + " " + ca2[pos2].getParent().getPDBName());
}
}
private static void printXMLBlockHeader(PrettyXMLWriter xml,
AFPChain afpChain,int blockNr) throws IOException{
int bk = blockNr;
int[] blockSize = afpChain.getBlockSize();
//if ( blockSize[bk] == 0) {
// return;
//}
int[] blockGap = afpChain.getBlockGap();
double[]blockScore = afpChain.getBlockScore();
double[] blockRmsd = afpChain.getBlockRmsd();
xml.attribute("blockNr", String.valueOf(bk));
xml.attribute("blockSize", String.valueOf(blockSize[bk]));
xml.attribute("blockScore", String.format("%5.2f",blockScore[bk]).trim());
xml.attribute("blockRmsd", String.format("%5.2f",blockRmsd[bk]).trim());
xml.attribute("blockGap", String.valueOf(blockGap[bk]));
}
private static void printXMLMatrixShift(PrettyXMLWriter xml,
AFPChain afpChain, int blockNr) throws IOException {
Matrix[] ms = afpChain.getBlockRotationMatrix();
if ( ms == null || ms.length == 0)
return;
Matrix matrix = ms[blockNr];
if ( matrix == null)
return;
xml.openTag("matrix");
for (int x=0;x<3;x++){
for (int y=0;y<3;y++){
String key = "mat"+(x+1)+(y+1);
xml.attribute(key,String.format("%.6f",matrix.get(x,y)));
}
}
xml.closeTag("matrix");
Atom[] shifts = afpChain.getBlockShiftVector();
Atom shift = shifts[blockNr];
xml.openTag("shift");
xml.attribute("x", String.format("%.3f",shift.getX()));
xml.attribute("y", String.format("%.3f",shift.getY()));
xml.attribute("z", String.format("%.3f",shift.getZ()));
xml.closeTag("shift");
}
public static String toXML(AFPChain afpChain) throws IOException{
return toXML(afpChain, null, null);
}
public static void printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain) throws IOException{
xml.attribute("name1", afpChain.getName1());
xml.attribute("name2", afpChain.getName2());
xml.attribute("method", afpChain.getAlgorithmName());
xml.attribute("version" , afpChain.getVersion());
xml.attribute("alnLength", afpChain.getAlnLength() + "");
xml.attribute("blockNum", afpChain.getBlockNum() + "");
xml.attribute("gapLen", afpChain.getGapLen() + "");
xml.attribute("optLength", afpChain.getOptLength() + "");
xml.attribute("totalLenIni", afpChain.getTotalLenIni() + "");
xml.attribute("alignScore", String.format("%5.2f", afpChain.getAlignScore() ).trim());
xml.attribute("chainRmsd", String.format("%5.2f", afpChain.getChainRmsd() ).trim());
xml.attribute("identity",String.format("%5.4f", afpChain.getIdentity() ).trim());
xml.attribute("normAlignScore", String.format("%5.2f",afpChain.getNormAlignScore()).trim());
xml.attribute("probability", String.format("%.2e", afpChain.getProbability() ).trim());
xml.attribute("similarity", String.format("%5.4f", afpChain.getSimilarity() ).trim());
xml.attribute("similarity1", afpChain.getCoverage1() + "");
xml.attribute("similarity2", afpChain.getCoverage2() + "");
xml.attribute("totalRmsdIni", String.format("%5.2f",afpChain.getTotalRmsdIni() ).trim());
xml.attribute("totalRmsdOpt", String.format("%5.2f",afpChain.getTotalRmsdOpt() ).trim());
xml.attribute("ca1Length", afpChain.getCa1Length()+"");
xml.attribute("ca2Length", afpChain.getCa2Length()+"");
xml.attribute("afpNum",afpChain.getAfpSet().size()+"");
xml.attribute("alignScoreUpdate",String.format("%5.2f",afpChain.getAlignScoreUpdate()).trim());
xml.attribute("time", String.format("%d",afpChain.getCalculationTime()));
if ( afpChain.getTMScore() != -1){
xml.attribute("tmScore", String.format("%.2f",afpChain.getTMScore()));
}
// test if alignment is CP:
if ( ! AlignmentTools.isSequentialAlignment(afpChain,false)) {
xml.attribute("cp","true");
}
}
}