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lafitalafita
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Port CeSymm for internal symmetry detection code to BioJava
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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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}

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

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package org.biojava.nbio.structure.symmetry.gui;
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import java.awt.event.KeyEvent;
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import java.util.ArrayList;
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import java.util.List;
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import javax.swing.JMenu;
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import javax.swing.JMenuBar;
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import javax.swing.JMenuItem;
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import javax.vecmath.Matrix4d;
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import javax.vecmath.Point3d;
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
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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.align.multiple.util.MultipleAlignmentTools;
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import org.biojava.nbio.structure.align.util.RotationAxis;
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import org.biojava.nbio.structure.symmetry.core.AxisAligner;
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import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
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import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
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import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
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import org.biojava.nbio.structure.symmetry.core.Subunits;
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import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
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import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
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import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup;
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import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
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/**
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* Class that provides visualizations methods for symmetry
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* alignments. Call the display() method for the default
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* visualization of symmetry.
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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 SymmetryDisplay {
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/**
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* Displays a multiple alignment of the symmetry subunits.
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*
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* @param msa the symmetry multiple alignment obtained from CeSymm
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* @throws StructureException
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*/
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public static MultipleAlignmentJmol displaySubunits(MultipleAlignment msa)
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throws StructureException {
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MultipleAlignment subunits = SymmetryTools.toSubunitAlignment(msa);
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return MultipleAlignmentDisplay.display(subunits);
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}
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/**
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* Displays a multiple alignment of the whole structure transformations
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* colored by blocks, corresponding to the subunits.
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*
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* @param msa the symmetry multiple alignment obtained from CeSymm
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* @throws StructureException
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*/
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public static MultipleAlignmentJmol displayFull(MultipleAlignment msa)
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throws StructureException {
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MultipleAlignment full = SymmetryTools.toFullAlignment(msa);
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MultipleAlignmentJmol jmol = MultipleAlignmentDisplay.display(full);
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jmol.setColorByBlocks(true);
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return jmol;
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}
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/**
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* Displays a single structure in a cartoon representation with each
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* symmetric subunit colored differently.
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*
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* @param msa the symmetry multiple alignment obtained from CeSymm
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* @param axes symmetry axes
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* @throws StructureException
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*/
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public static MultipleAlignmentJmol display(MultipleAlignment msa,
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SymmetryAxes axes) throws StructureException {
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List<Atom[]> atoms = msa.getAtomArrays();
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MultipleAlignmentJmol jmol = new MultipleAlignmentJmol(msa, atoms);
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addSymmetryMenu(jmol, axes);
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//Show all the axes and point group symmetry
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if (axes!=null) jmol.evalString(printSymmetryAxes(msa, axes, false));
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jmol.evalString(printPointGroupAxes(msa));
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return jmol;
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}
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/**
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* Displays a single structure in a cartoon representation with each
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* symmetric subunit colored differently.
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*
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* @param msa the symmetry multiple alignment obtained from CeSymm
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* @throws StructureException
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*/
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public static MultipleAlignmentJmol display(MultipleAlignment msa)
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throws StructureException {
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return display(msa, null);
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}
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/**
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* Adds a Symmetry menu to the Jmol display, so that further symmetry
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* analysis can be triggered.
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*
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* @param jmol parent jmol
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* @param axes symmetry axes
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*/
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private static void addSymmetryMenu(MultipleAlignmentJmol jmol,
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SymmetryAxes axes){
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JMenuBar menubar = jmol.getFrame().getJMenuBar();
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JMenu symm = new JMenu("Symmetry");
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symm.setMnemonic(KeyEvent.VK_S);
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SymmetryListener li = new SymmetryListener(jmol, axes);
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JMenuItem subunits = new JMenuItem("Subunit Superposition");
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subunits.addActionListener(li);
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symm.add(subunits);
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JMenuItem multiple = new JMenuItem("Multiple Structure Alignment");
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multiple.addActionListener(li);
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symm.add(multiple);
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JMenuItem pg = new JMenuItem("Point Group Symmetry");
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pg.addActionListener(li);
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symm.add(pg);
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JMenuItem ax = new JMenuItem("Show Symmetry Axes");
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ax.addActionListener(li);
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symm.add(ax);
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JMenuItem news = new JMenuItem("New Symmetry Analysis");
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news.addActionListener(li);
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symm.add(news);
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menubar.add(symm, 3);
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jmol.getFrame().pack();
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}
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/**
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* Generates a String that displays the symmetry axes of a structure.
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*
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* @param msa
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* @param axes
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* @param elementary only print elementary axes if true
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* @return
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*/
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public static String printSymmetryAxes(MultipleAlignment msa,
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SymmetryAxes axes, boolean elementary) {
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int id = 0;
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String script = "";
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Atom[] atoms = msa.getAtomArrays().get(0);
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List<Matrix4d> symmAxes = null;
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if (elementary){
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symmAxes = axes.getElementaryAxes();
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} else {
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symmAxes = axes.getSymmetryAxes();
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}
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for (Matrix4d axis : symmAxes) {
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RotationAxis rot = new RotationAxis(axis);
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script += rot.getJmolScript(atoms, id);
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id++;
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}
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return script;
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}
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/**
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* Given a symmetry alignment, it draws the point group symmetry axes
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* and the polyhedron box around the structure.
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* It uses the quaternary symmetry detection code, but tries to factor
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* out the alignment and detection steps.
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*
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* @param symm
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* @return
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*/
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public static String printPointGroupAxes(MultipleAlignment symm){
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//Obtain the clusters of aligned Atoms and subunit variables
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MultipleAlignment subunits = SymmetryTools.toSubunitAlignment(symm);
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List<Atom[]> alignedCA = subunits.getAtomArrays();
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List<Integer> corePos = MultipleAlignmentTools.getCorePositions(
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subunits.getBlock(0));
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List<Point3d[]> caCoords = new ArrayList<Point3d[]>();
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List<Integer> folds = new ArrayList<Integer>();
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List<Boolean> pseudo = new ArrayList<Boolean>();
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List<String> chainIds = new ArrayList<String>();
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List<Integer> models = new ArrayList<Integer>();
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List<Double> seqIDmin = new ArrayList<Double>();
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List<Double> seqIDmax = new ArrayList<Double>();
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List<Integer> clusterIDs = new ArrayList<Integer>();
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int fold = 1;
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Character chain = 'A';
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for (int str=0; str<alignedCA.size(); str++){
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Atom[] array = alignedCA.get(str);
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List<Point3d> points = new ArrayList<Point3d>();
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List<Integer> alignedRes =
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subunits.getBlock(0).getAlignRes().get(str);
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for (int pos=0; pos<alignedRes.size(); pos++){
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Integer residue = alignedRes.get(pos);
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if (residue == null) continue;
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else if (!corePos.contains(pos)) continue;
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Atom a = array[residue];
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points.add(new Point3d(a.getCoords()));
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}
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caCoords.add(points.toArray(new Point3d[points.size()]));
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if (alignedCA.size() % fold == 0){
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folds.add(fold); //the folds are the common denominators
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}
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fold++;
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pseudo.add(false);
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chainIds.add(chain+"");
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chain++;
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models.add(0);
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seqIDmax.add(1.0);
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seqIDmin.add(1.0);
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clusterIDs.add(0);
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}
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//Create directly the subunits, because we know the aligned CA
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Subunits globalSubunits = new Subunits(caCoords, clusterIDs,
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pseudo, seqIDmin, seqIDmax,
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folds, chainIds, models);
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//Quaternary Symmetry Detection
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QuatSymmetryParameters param = new QuatSymmetryParameters();
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param.setRmsdThreshold(symm.size() * 1.5);
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QuatSymmetryResults gSymmetry =
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QuatSymmetryDetector.calcQuatSymmetry(globalSubunits, param);
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AxisAligner axes = AxisAligner.getInstance(gSymmetry);
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//Draw the axes as in the quaternary symmetry
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JmolSymmetryScriptGenerator scriptGenerator =
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JmolSymmetryScriptGeneratorPointGroup.getInstance(axes, "g");
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String script = "save selection; set defaultStructureDSSP true; "
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+ "set measurementUnits ANGSTROMS; select all; "
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+ "spacefill off; wireframe off;"
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+ "set antialiasDisplay true; autobond=false; ";
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script += scriptGenerator.getOrientationWithZoom(0);
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script += "restore selection; ";
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script += scriptGenerator.drawPolyhedron();
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script += scriptGenerator.drawAxes();
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script += "draw axes* on; draw poly* on; ";
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return script;
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}
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}

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