/*
* 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.symmetry.analysis;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.List;
import java.util.Set;
import org.biojava.nbio.structure.PDBCrystallographicInfo;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.mmcif.AllChemCompProvider;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.rcsb.GetRepresentatives;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
import org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature;
import org.biojava.nbio.structure.symmetry.utils.BlastClustReader;
import org.biojava.nbio.structure.xtal.SpaceGroup;
public class ScanSymmetry implements Runnable {
private AtomCache cache = null;
private static String RESULT_DIR = "/Users/peter/Results/ScanSymmetry/";
public ScanSymmetry() {
initializeCache();
}
public static void main(String[] args) {
new ScanSymmetry().run();
}
@Override
public void run() {
String timeStamp = new SimpleDateFormat("yyyyMMdd_HHmmss")
.format(Calendar.getInstance().getTime());
System.out.println("Reading blastclust files");
//BlastClustReader reader95 = new BlastClustReader(95);
//BlastClustReader reader30 = new BlastClustReader(30);
PrintWriter out = null;
PrintWriter error = null;
try {
out = new PrintWriter(new FileWriter(RESULT_DIR + timeStamp
+ "_symm.csv"));
error = new PrintWriter(new FileWriter(RESULT_DIR + timeStamp
+ "_error.txt"));
} catch (IOException e1) {
e1.printStackTrace();
System.exit(-1);
}
long t1 = System.nanoTime();
int success = 0;
int proteins = 0;
int failure = 0;
String header = "pdbId,bioassembly,local,pseudostoichiometric,stoichiometry,pseudosymmetric,pointgroup,order,"
+ "lowSymmetry,minidentity,maxidentity,subunitrmsd,rmsd,tm,minrmsd,maxrmsd,mintm,maxtm,rmsdintra,tmintra,symdeviation,subunits,nucleiacids,cacount,time,signature95,stoich95,signature30,stoich30,spacegroup";
out.println(header);
//QuatSymmetryParameters parameters = new QuatSymmetryParameters();
Set<String> set = GetRepresentatives.getAll();
// pr testing
set.clear();
set.add("4HHB");
// set skip to true to restart calculation with a specified PDB ID
boolean skip = false;
String restartId = "10MH";
for (String pdbId : set) {
if (skip && pdbId.equals(restartId)) {
skip = false;
}
if (skip) {
continue;
}
System.out.println("------------- " + pdbId + "-------------");
StructureIO.setAtomCache(cache);
List<Structure> structures = null;
try {
structures = StructureIO.getBiologicalAssemblies(pdbId);
} catch (StructureException | IOException e) {
e.printStackTrace();
error.println(pdbId + ": " + e.getMessage());
error.flush();
continue;
}
int i = 0;
for (Structure structure : structures) {
// note: before biojava 5.0 refactoring, the structures without
// bioassemblies would
// use i=0 as the identifier for the default bioassembly (the
// asymmetric unit). Now
// identifier i=1 is used - JD 2016-05-17
i++;
//long ts1 = System.nanoTime();
try {
SpaceGroup spaceGroup = null;
// float resolution = 0.0f;
if (structure != null) {
PDBCrystallographicInfo info = structure
.getCrystallographicInfo();
if (info != null) {
spaceGroup = info.getSpaceGroup();
}
// PDBHeader pdbHeader = structure.getPDBHeader();
// resolution = pdbHeader.getResolution();
}
// QuatSymmetryDetector detector = new
// QuatSymmetryDetector(structure, parameters);
//
// if (detector.hasProteinSubunits()) {
// long ts2 = System.nanoTime();
//
// int time = Math.round((ts2-ts1)/1000000.0f);
//
// // save global symmetry results
// List<QuatSymmetryResults> globalResults =
// detector.getGlobalSymmetry();
// printToCsv(reader95, reader30, out, pdbId,
// i, time, globalResults, spaceGroup);
//
// // save local symmetry results
// for (List<QuatSymmetryResults> localResults:
// detector.getLocalSymmetries()) {
// printToCsv(reader95, reader30, out, pdbId,
// i, time, localResults, spaceGroup);
// }
// proteins++;
// }
success++;
out.flush();
} catch (Exception e) {
failure++;
e.printStackTrace();
error.println(pdbId + "[" + i + "]: " + e.getMessage());
error.flush();
}
}
}
long t2 = System.nanoTime();
System.out.println("PDBs succeeded: " + success);
System.out.println("PDBs failed : " + failure);
System.out.println("Proteins : " + proteins);
System.out.println("Total structure: " + set.size());
System.out.println("Cpu time: " + (t2 - t1) / 1000000 + " ms.");
out.close();
error.close();
}
private void printToCsv(BlastClustReader reader95,
BlastClustReader reader30, PrintWriter out, String pdbId,
int bioAssemblyId, int time, List<QuatSymmetryResults> resultsList,
SpaceGroup spaceGroup) {
for (QuatSymmetryResults results : resultsList) {
ProteinComplexSignature s95 = new ProteinComplexSignature(pdbId,
new QuatSymmetrySubunits(results.getSubunitClusters())
.getChainIds(), reader95);
String signature95 = s95.getComplexSignature();
String stoich95 = s95.getComplexStoichiometry();
ProteinComplexSignature s30 = new ProteinComplexSignature(pdbId,
new QuatSymmetrySubunits(results.getSubunitClusters())
.getChainIds(), reader30);
String signature30 = s30.getComplexSignature();
String stoich30 = s30.getComplexStoichiometry();
int order = 1;
if (!results.getSymmetry().equals("H")) {
order = results.getRotationGroup().getOrder();
}
out.println("PDB"
+ pdbId
+ ","
+ bioAssemblyId
+ ","
+ results.isLocal()
+ ","
+ results.isPseudoStoichiometric()
+ ","
+ results.getStoichiometry()
+ ","
+ results.getSymmetry()
+ ","
+ order
+ ","
+ isLowSymmetry(results)
+ ","
+ Math.round(100)// results.getSubunits().getMinSequenceIdentity()
// * 100.0)
+ ","
+ Math.round(100) // results.getSubunits().getMaxSequenceIdentity()
// * 100.0)
+ ","
+ (float) results.getScores().getRmsdCenters()
+ ","
+ (float) results.getScores().getRmsd()
+ ","
+ (float) results.getScores().getTm()
+ ","
+ (float) results.getScores().getMinRmsd()
+ ","
+ (float) results.getScores().getMaxRmsd()
+ ","
+ (float) results.getScores().getMinTm()
+ ","
+ (float) results.getScores().getMaxTm()
+ ","
+ (float) results.getScores().getRmsdIntra()
+ ","
+ (float) results.getScores().getTmIntra()
+ ","
+ (float) results.getScores().getSymDeviation()
+ ","
+ results.getSubunitClusters().size()
+ ",NA"
+ ","
+ new QuatSymmetrySubunits(results.getSubunitClusters())
.getCalphaCount() + "," + time + "," + signature95
+ "," + stoich95 + "," + signature30 + "," + stoich30 + ","
+ spaceGroup);
}
}
private boolean isLowSymmetry(QuatSymmetryResults results) {
return getMinFold(new QuatSymmetrySubunits(results.getSubunitClusters())) > 1
&& results.getRotationGroup() != null
&& results.getRotationGroup().getPointGroup().equals("C1");
}
private int getMinFold(QuatSymmetrySubunits subunits) {
if (subunits.getFolds().size() > 1) {
return subunits.getFolds().get(1);
}
return subunits.getFolds().get(0);
}
private void initializeCache() {
cache = new AtomCache();
FileParsingParameters params = cache.getFileParsingParams();
cache.setUseMmCif(true);
params.setParseCAOnly(true);
// MmCifBiolAssemblyProvider mmcifProvider = new
// MmCifBiolAssemblyProvider();
// BioUnitDataProviderFactory.setBioUnitDataProvider(mmcifProvider.getClass().getCanonicalName());
ChemCompGroupFactory.setChemCompProvider(new AllChemCompProvider());
// ChemCompGroupFactory.setChemCompProvider(new
// DownloadChemCompProvider());
}
}
