Use all models sequentially for symmetry analysis

lafita · lafita · commit ff592b85d236 · 2016-05-17T14:21:18.000+02:00
This fixes point 3 of issue biojava#462
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.java
@@ -23,35 +23,35 @@
 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.symmetry.internal.CESymmParameters;
 import org.biojava.nbio.structure.symmetry.internal.CeSymm;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
+import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 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.
+ * 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
  * @since 4.2.0
  *
  */
 public class SymmetryCalc implements AlignmentCalculationRunnable {
 
-	private static final Logger logger =
-			LoggerFactory.getLogger(SymmetryCalc.class);
+	private static final Logger logger = LoggerFactory
+			.getLogger(SymmetryCalc.class);
 
 	boolean interrupted = false;
 
 	private Structure structure;
 	private SymmetryGui parent;
 
-	/** Requests for a structure to analyze.
+	/**
+	 * Requests for a structure to analyze.
 	 */
 	public SymmetryCalc(SymmetryGui p, Structure s) {
 		parent = p;
@@ -65,11 +65,12 @@ public void run() {
 
 		try {
 
-			Atom[] atoms = StructureTools.getRepresentativeAtomArray(structure);
+			Atom[] atoms = SymmetryTools.getRepresentativeAtoms(structure);
+
 			CeSymmResult result = CeSymm.analyze(atoms, params);
 			SymmetryDisplay.display(result);
 
-		} catch (StructureException e){
+		} catch (StructureException e) {
 			logger.warn(e.getMessage());
 		}
 		parent.notifyCalcFinished();
@@ -89,5 +90,6 @@ public void cleanup() {
 	}
 
 	@Override
-	public void setNrCPUs(int useNrCPUs) {}
+	public void setNrCPUs(int useNrCPUs) {
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -977,4 +977,31 @@ public static void updateSymmetryScores(MultipleAlignment symm)
 		symm.putScore(MultipleAlignmentScorer.RMSD, rmsd);
 	}
 
+	/**
+	 * Returns the representative Atom Array of the first model, if the
+	 * structure is NMR, or the Array for each model, if it is a biological
+	 * assembly with multiple models.
+	 * 
+	 * @param structure
+	 * @return representative Atom[]
+	 */
+	public static Atom[] getRepresentativeAtoms(Structure structure) {
+
+		if (structure.isNmr())
+			return StructureTools.getRepresentativeAtomArray(structure);
+
+		else {
+
+			// Get Atoms of all models and rename chains (in case BIO)
+			List<Atom> atomList = new ArrayList<Atom>();
+			for (int m = 0; m < structure.nrModels(); m++) {
+				for (Chain c : structure.getModel(m))
+					atomList.addAll(Arrays.asList(StructureTools
+							.getRepresentativeAtomArray(c)));
+			}
+			return atomList.toArray(new Atom[0]);
+		}
+		
+	}
+
 }
