biojava · andreasprlic · Aug 4, 2015 · Aug 3, 2015 · Aug 3, 2015 · Aug 4, 2015
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -0,0 +1,82 @@
+package demo;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
+import org.biojava.nbio.structure.symmetry.internal.CeSymm;
+
+/**
+ * Quick demo of how to call CE-Symm programmatically.
+ * Some examples of different symmetry types are proposed.
+ *
+ * @author Spencer Bliven
+ * @author Aleix Lafita
+ *
+ */
+public class DemoCeSymm {
+
+	public static void main(String[] args) 
+			throws IOException, StructureException {
+
+		/* 
+		 * Some examples:
+		 * 
+		 * CLOSED
+		 * 2-fold: 1hiv.A, 
+		 * 3-fold: 4i4q, 4dou
+		 * 5-fold: 2jaj.A
+		 * 6-fold: 1u6d
+		 * 7-fold: 1jof.A
+		 * 8-fold: 1vzw, d1i4na_
+		 * 
+		 * OPEN
+		 * ankyrin: 1n0r.A, 3ehq.A
+		 * leucine repeats: 2bnh.A, 3o6n
+		 * helical: 1d0b.A
+		 * 
+		 * MULTIPLE AXES
+		 * dihedral: 4hhb, 1vym, 1hiv
+		 * hierarchical: 4gcr, 1ppr.O, 1hiv
+		 * monoclonal Ab: 4NZU
+		 * 
+		 * - For more examples see the symmetry benchmark
+		 */
+
+		//Set the name of the protein structure to analyze
+		String name = "1u6d";
+		List<Atom[]> atoms = new ArrayList<Atom[]>();
+
+		//Download the atoms
+		AtomCache cache = new AtomCache();
+		Structure s = cache.getStructure(name);
+		Atom[] array = StructureTools.getRepresentativeAtomArray(s);
+		atoms.add(array);
+
+		CeSymm ceSymm = new CeSymm();
+
+		//Choose some parameters
+		CESymmParameters params = (CESymmParameters) ceSymm.getParameters();
+		params.setRefineMethod(RefineMethod.SINGLE);
+		params.setSymmetryType(SymmetryType.AUTO);
+		params.setOptimization(true);
+		params.setMultipleAxes(true);
+
+		//Run the alignment
+		MultipleAlignment symmetry = ceSymm.align(atoms, params);
+
+		//Display the results in jmol
+		SymmetryDisplay.display(symmetry, ceSymm.getSymmetryAxes());
+	}
+
+}
diff --git a/...ava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.java b/...ava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.java
@@ -0,0 +1,96 @@
+package org.biojava.nbio.structure.symmetry.gui;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable;
+import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
+import org.biojava.nbio.structure.symmetry.internal.CeSymm;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/** 
+ * Calculates a symmetry analysis and displays the results.
+ * Linked to the SymmetryGUI.
+ * Does not generalize, uses CeSymm class directly to allow
+ * for the symmetry axis recovery.
+ *  
+ * @author Aleix Lafita
+ * 
+ */
+public class SymmetryCalc implements AlignmentCalculationRunnable {
+
+	private static final Logger logger = 
+			LoggerFactory.getLogger(SymmetryCalc.class);
+
+	boolean interrupted = false;
+
+	private String name;
+	private Structure structure;
+	private SymmetryGui parent;
+
+	/** Requests for a structure to analyze.
+	 */
+	public SymmetryCalc(SymmetryGui p, Structure s, String n) {
+		parent = p;
+		structure = s;
+		name = n;
+	}
+
+	@Override
+	public void run() {
+
+		//The structure has been downloaded, now calculate the alignment ...
+		CeSymm algorithm = parent.getSymmetryAlgorithm();
+		CESymmParameters params = (CESymmParameters) algorithm.getParameters();
+
+		try {
+
+			List<Atom[]> atoms = new ArrayList<Atom[]>();
+			atoms.add(StructureTools.getRepresentativeAtomArray(structure));
+
+			MultipleAlignment msa = algorithm.align(atoms);
+
+			List<String> names = new ArrayList<String>();
+			for (int su=0; su<msa.size(); su++){
+				names.add(name);
+			}
+			msa.getEnsemble().setStructureNames(names);
+
+			MultipleAlignmentJmol jmol = 
+					SymmetryDisplay.display(msa, algorithm.getSymmetryAxes());
+			String title = jmol.getTitle();
+
+			if (params != null) 
+				title += " | OrderDetector=" + params.getOrderDetectorMethod()+
+				" Refiner: "+params.getRefineMethod();
+			jmol.setTitle(title);
+
+		} catch (StructureException e){
+			logger.warn(e.getMessage());
+		}
+		parent.notifyCalcFinished();
+	}
+
+	@Override
+	public void interrupt() {
+		interrupted = true;
+	}
+
+	@Override
+	public void cleanup() {
+
+		parent.notifyCalcFinished();
+		parent = null;
+		structure = null;
+	}
+
+	@Override
+	public void setNrCPUs(int useNrCPUs) {}
+}