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andreasprlicandreasprlic
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Merge pull request #311 from lafita/cesymm
Import Internal Symmetry Code to BioJava #246
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‎biojava-structure-gui/src/main/java/demo/DemoCeSymm.java‎

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package demo;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay;
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import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
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import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod;
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import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
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import org.biojava.nbio.structure.symmetry.internal.CeSymm;
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/**
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* Quick demo of how to call CE-Symm programmatically.
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* Some examples of different symmetry types are proposed.
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*
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* @author Spencer Bliven
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* @author Aleix Lafita
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*
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*/
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public class DemoCeSymm {
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public static void main(String[] args)
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throws IOException, StructureException {
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/*
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* Some examples:
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*
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* CLOSED
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* 2-fold: 1hiv.A,
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* 3-fold: 4i4q, 4dou
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* 5-fold: 2jaj.A
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* 6-fold: 1u6d
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* 7-fold: 1jof.A
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* 8-fold: 1vzw, d1i4na_
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*
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* OPEN
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* ankyrin: 1n0r.A, 3ehq.A
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* leucine repeats: 2bnh.A, 3o6n
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* helical: 1d0b.A
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*
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* MULTIPLE AXES
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* dihedral: 4hhb, 1vym, 1hiv
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* hierarchical: 4gcr, 1ppr.O, 1hiv
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* monoclonal Ab: 4NZU
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*
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* - For more examples see the symmetry benchmark
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*/
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//Set the name of the protein structure to analyze
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String name = "1u6d";
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List<Atom[]> atoms = new ArrayList<Atom[]>();
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//Download the atoms
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AtomCache cache = new AtomCache();
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Structure s = cache.getStructure(name);
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Atom[] array = StructureTools.getRepresentativeAtomArray(s);
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atoms.add(array);
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CeSymm ceSymm = new CeSymm();
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//Choose some parameters
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CESymmParameters params = (CESymmParameters) ceSymm.getParameters();
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params.setRefineMethod(RefineMethod.SINGLE);
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params.setSymmetryType(SymmetryType.AUTO);
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params.setOptimization(true);
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params.setMultipleAxes(true);
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//Run the alignment
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MultipleAlignment symmetry = ceSymm.align(atoms, params);
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//Display the results in jmol
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SymmetryDisplay.display(symmetry, ceSymm.getSymmetryAxes());
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}
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}

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.java‎

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package org.biojava.nbio.structure.symmetry.gui;
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable;
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import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
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import org.biojava.nbio.structure.symmetry.internal.CeSymm;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* Calculates a symmetry analysis and displays the results.
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* Linked to the SymmetryGUI.
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* Does not generalize, uses CeSymm class directly to allow
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* for the symmetry axis recovery.
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*
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* @author Aleix Lafita
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*
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*/
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public class SymmetryCalc implements AlignmentCalculationRunnable {
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private static final Logger logger =
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LoggerFactory.getLogger(SymmetryCalc.class);
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boolean interrupted = false;
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private String name;
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private Structure structure;
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private SymmetryGui parent;
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/** Requests for a structure to analyze.
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*/
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public SymmetryCalc(SymmetryGui p, Structure s, String n) {
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parent = p;
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structure = s;
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name = n;
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}
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@Override
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public void run() {
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//The structure has been downloaded, now calculate the alignment ...
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CeSymm algorithm = parent.getSymmetryAlgorithm();
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CESymmParameters params = (CESymmParameters) algorithm.getParameters();
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try {
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List<Atom[]> atoms = new ArrayList<Atom[]>();
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atoms.add(StructureTools.getRepresentativeAtomArray(structure));
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MultipleAlignment msa = algorithm.align(atoms);
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List<String> names = new ArrayList<String>();
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for (int su=0; su<msa.size(); su++){
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names.add(name);
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}
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msa.getEnsemble().setStructureNames(names);
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MultipleAlignmentJmol jmol =
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SymmetryDisplay.display(msa, algorithm.getSymmetryAxes());
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String title = jmol.getTitle();
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if (params != null)
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title += " | OrderDetector=" + params.getOrderDetectorMethod()+
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" Refiner: "+params.getRefineMethod();
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jmol.setTitle(title);
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} catch (StructureException e){
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logger.warn(e.getMessage());
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}
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parent.notifyCalcFinished();
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}
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@Override
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public void interrupt() {
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interrupted = true;
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}
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@Override
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public void cleanup() {
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parent.notifyCalcFinished();
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parent = null;
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structure = null;
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}
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@Override
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public void setNrCPUs(int useNrCPUs) {}
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}

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