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DemoSymmetry.java
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119 lines (87 loc) · 4.15 KB
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/*
* 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 demo;
import java.util.List;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.cluster.SubunitCluster;
import org.biojava.nbio.structure.cluster.SubunitClustererMethod;
import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
/**
* A demo on how to use the quaternary symmetry detection algorithms.
*
* @author Jose Duarte
*
*/
public class DemoSymmetry {
public static void main(String[] args) throws Exception {
System.out.println("Getting all bioassemblies");
List<Structure> bioAssemblies = StructureIO.getBiologicalAssemblies("4hhb");
for (Structure bioAssembly : bioAssemblies) {
findQuatSym(bioAssembly);
}
}
private static void findQuatSym(Structure bioAssembly) throws StructureException {
QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
System.out.println("GLOBAL SYMMETRY, NO CLUSTERING");
SubunitClustererParameters clusterParams = new SubunitClustererParameters();
clusterParams.setSequenceIdentityThreshold(0.95);
clusterParams.setRMSDThreshold(0.0);
clusterParams.setClustererMethod(SubunitClustererMethod.SEQUENCE);
QuatSymmetryResults globalResults = QuatSymmetryDetector.calcGlobalSymmetry(bioAssembly, symmParams, clusterParams);
System.out.println(globalResults.getSymmetry() + (globalResults.isPseudoStoichiometric()?"(pseudo)":""));
System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
int i = 1;
for (SubunitCluster suc : globalResults.getSubunitClusters()) {
//System.out.println(suc.getClustererMethod());
MultipleAlignment ma = suc.getMultipleAlignment();
System.out.printf("Cluster %d (clustered by %s), RMSD = %4.2f\n", i, suc.getClustererMethod(), ma.getScore("RMSD"));
i++;
}
System.out.println("\nGLOBAL SYMMETRY, WITH CLUSTERING (PSEUDO-SYMMETRY)");
clusterParams = new SubunitClustererParameters();
// we can either set sequence identity to 40% or rmsd to 2, both would have the same effect of clustering the alpha/beta subunits together
clusterParams.setSequenceIdentityThreshold(0.4);
clusterParams.setClustererMethod(SubunitClustererMethod.STRUCTURE);
clusterParams.setRMSDThreshold(3.0);
globalResults = QuatSymmetryDetector.calcGlobalSymmetry(bioAssembly, symmParams, clusterParams);
System.out.println(globalResults.getSymmetry() + (globalResults.isPseudoStoichiometric()?"(pseudo)":""));
System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
i = 1;
for (SubunitCluster suc : globalResults.getSubunitClusters()) {
//System.out.println(suc.getClustererMethod());
MultipleAlignment ma = suc.getMultipleAlignment();
System.out.printf("Cluster %d (clustered by %s), RMSD = %4.2f\n", i, suc.getClustererMethod(), ma.getScore("RMSD"));
i++;
}
System.out.println("\n\nLOCAL SYMMETRIES");
List<QuatSymmetryResults> localResults = QuatSymmetryDetector.calcLocalSymmetries(bioAssembly, symmParams, clusterParams);
System.out.println("Number of local symmetries: "+localResults.size());
for (QuatSymmetryResults results : localResults) {
System.out.println(results.getSymmetry()+" "+results.getStoichiometry());
}
}
}