Do not divide internal repeats into chains to calculate QS

lafita · lafita · commit 9a24074019ef · 2016-06-13T15:31:26.000+02:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -210,6 +210,7 @@ public static String printSymmetryAxes(CeSymmResult symm)
 			throws StructureException {
 		return printSymmetryAxes(symm,true);
 	}
+	
 	/**
 	 * Generates a String that displays the symmetry axes of a structure.
 	 *
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
@@ -593,7 +593,7 @@ public static MultipleAlignment toRepeatsAlignment(CeSymmResult result)
 
 		MultipleAlignment msa = result.getMultipleAlignment();
 		MultipleAlignmentEnsemble newEnsemble = msa.getEnsemble().clone();
-		
+
 		// Modify atom arrays to include the repeat atoms only
 		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
 		Structure divided = SymmetryTools.getQuaternaryStructure(result);
@@ -734,10 +734,10 @@ public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result)
 			throws StructureException {
 
 		// Obtain the clusters of aligned Atoms and repeat variables
-		MultipleAlignment repeats = SymmetryTools.toRepeatsAlignment(result);
-		List<Atom[]> alignedCA = repeats.getAtomArrays();
-		List<Integer> corePos = MultipleAlignmentTools.getCorePositions(repeats
-				.getBlock(0));
+		List<Atom[]> alignedCA = result.getMultipleAlignment().getAtomArrays();
+		MultipleAlignment msa = result.getMultipleAlignment();
+		List<Integer> corePos = MultipleAlignmentTools.getCorePositions(result
+				.getMultipleAlignment().getBlock(0));
 
 		List<Point3d[]> caCoords = new ArrayList<Point3d[]>();
 		List<Integer> folds = new ArrayList<Integer>();
@@ -752,7 +752,7 @@ public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result)
 		for (int str = 0; str < alignedCA.size(); str++) {
 			Atom[] array = alignedCA.get(str);
 			List<Point3d> points = new ArrayList<Point3d>();
-			List<Integer> alignedRes = repeats.getBlock(0).getAlignRes()
+			List<Integer> alignedRes = msa.getBlock(0).getAlignRes()
 					.get(str);
 			for (int pos = 0; pos < alignedRes.size(); pos++) {
 				Integer residue = alignedRes.get(pos);
@@ -1000,7 +1000,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) {
 			}
 			return atomList.toArray(new Atom[0]);
 		}
-		
+
 	}
 
 }

Original file line number	Diff line number	Diff line change
`@@ -210,6 +210,7 @@ public static String printSymmetryAxes(CeSymmResult symm)`
`210`	`210`	`throws StructureException {`
`211`	`211`	`return printSymmetryAxes(symm,true);`
`212`	`212`	`}`
	`213`	`+`
`213`	`214`	`/**`
`214`	`215`	`* Generates a String that displays the symmetry axes of a structure.`
`215`	`216`	`*`