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lafitalafita
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Add Demo for CeSymm
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Lines changed: 170 additions & 17 deletions

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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 = "1hiv.A";
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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);
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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/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.StructureException;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.util.AtomCache;
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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
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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 = "4F88";
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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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Atom[] ca = cache.getAtoms(name);
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atoms.add(ca);
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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);
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//Display the results in FatCat format
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System.out.println(MultipleAlignmentWriter.toFatCat(symmetry));
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java‎

Lines changed: 9 additions & 17 deletions
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@@ -26,21 +26,12 @@
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
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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.SymmetryAxes;
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import org.biojava.nbio.structure.symmetry.internal.OrderDetectionFailedException;
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import org.biojava.nbio.structure.symmetry.internal.OrderDetector;
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import org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector;
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import org.biojava.nbio.structure.symmetry.internal.OpenRefiner;
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import org.biojava.nbio.structure.symmetry.internal.Refiner;
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import org.biojava.nbio.structure.symmetry.internal.RefinerFailedException;
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import org.biojava.nbio.structure.symmetry.internal.SingleRefiner;
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import org.biojava.nbio.structure.symmetry.internal.SymmOptimizer;
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import org.biojava.nbio.structure.align.util.AFPChainScorer;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.align.util.RotationAxis;
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import org.biojava.nbio.structure.jama.Matrix;
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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.utils.SymmetryTools;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
@@ -278,7 +269,6 @@ public AFPChain align(Atom[] ca10, Atom[] ca2O, Object param)
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cols = ca2.length;
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if( rows == 0 || cols == 0) {
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logger.warn("Aligning empty structure");
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throw new StructureException("Aligning empty structure");
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}
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try {
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switch (type){
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case CLOSE:
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refiner = new SingleRefiner();
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if (order == 1) return afpChain;
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refiner = new SingleRefiner();
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break;
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default: //case OPEN
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refiner = new OpenRefiner();
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break;
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}
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afpChain = refiner.refine(afpAlignments, ca1, order);
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refined = true;
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} catch (RefinerFailedException e) {
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logger.warn("Could not refine structure!");
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return afpChain;
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this.params = (CESymmParameters) param;
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//If the multiple axes is called, run iterative version
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if (params.isMultipleAxes()){
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if (params.isMultipleAxes() &&
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params.getRefineMethod() != RefineMethod.NOT_REFINED){
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CeSymmIterative iterative = new CeSymmIterative(params);
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MultipleAlignment result = iterative.execute(atomArrays.get(0));
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axes = iterative.getSymmetryAxes();
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executor.shutdown();
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} catch (InterruptedException e) {
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e.printStackTrace();
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logger.warn("Optimization failed!");
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} catch (ExecutionException e) {
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e.printStackTrace();
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logger.warn("Optimization failed!");
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}
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}
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} else {

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