A fix for biojava#708

josemduarte · josemduarte · commit 276e5cc3b3e5 · 2017-10-09T16:21:46.000-07:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
@@ -87,12 +87,13 @@ public void testDihedral() throws IOException, StructureException {
 		// D3 symmetry non pseudosymmetric
 		assertEquals("D3", symmetry.getSymmetry());
 		assertEquals("A6B6", symmetry.getStoichiometry());
+		assertFalse(symmetry.isPseudoStoichiometric());
+
 
 	}
 
 	/**
 	 * Hemoglobin has both symmetry and pseudosymmetry: 4HHB
-	 * TODO pseudosymmetry in hemoglobin fails
 	 * 
 	 * @throws StructureException
 	 * @throws IOException
@@ -121,6 +122,7 @@ public void testPseudosymmetry() throws IOException, StructureException {
 		// D2 pseudo-symmetry
 		assertEquals("D2", symmetry.getSymmetry());
 		assertEquals("A4", symmetry.getStoichiometry());
+		assertTrue(symmetry.isPseudoStoichiometric());
 	}
 
 	/**
diff --git a/biojava-structure-gui/src/main/java/demo/DemoQuatSymmetryJmol.java b/biojava-structure-gui/src/main/java/demo/DemoQuatSymmetryJmol.java
@@ -94,7 +94,7 @@ private static void showResults(Structure s, String name,
 		String title = name + ": " + results.getStoichiometry()
 				+ ", " + results.getSymmetry();
 
-		if (results.isPseudosymmetric())
+		if (results.isPseudoStoichiometric())
 			title += ", pseudosymmetric";
 
 		if (results.isLocal())
diff --git a/biojava-structure/src/main/java/demo/DemoSymmetry.java b/biojava-structure/src/main/java/demo/DemoSymmetry.java
@@ -45,7 +45,7 @@ private static void findQuatSym(Structure bioAssembly) throws StructureException
 		
 		
 		
-		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudosymmetric()?"(pseudo)":""));
+		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudoStoichiometric()?"(pseudo)":""));
 		
 		System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
 		int i = 1;
@@ -68,7 +68,7 @@ private static void findQuatSym(Structure bioAssembly) throws StructureException
 		
 		
 		
-		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudosymmetric()?"(pseudo)":""));
+		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudoStoichiometric()?"(pseudo)":""));
 		
 		System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
 		i = 1;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterUtils.java
@@ -56,7 +56,7 @@ public static String getStoichiometryString(List<SubunitCluster> clusters) {
 
 	/**
 	 * A pseudostoichiometric {@link SubunitCluster} was obtained using the
-	 * {@link SubunitClustererMethod#STRUCTURE} similarity.
+	 * {@link SubunitClustererMethod#STRUCTURE} or {@link SubunitClustererMethod#SEQUENCE} similarity.
 	 * 
 	 * @param clusters
 	 * @return true if any of the clusters is pseudostoichiometric, false
@@ -65,7 +65,8 @@ public static String getStoichiometryString(List<SubunitCluster> clusters) {
 	public static boolean isPseudoStoichiometric(List<SubunitCluster> clusters) {
 
 		for (SubunitCluster c : clusters) {
-			if (c.getClustererMethod() == SubunitClustererMethod.STRUCTURE)
+			if (c.getClustererMethod() == SubunitClustererMethod.STRUCTURE ||
+				c.getClustererMethod() == SubunitClustererMethod.SEQUENCE)
 				return true;
 		}
 		return false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -282,10 +282,6 @@ private static QuatSymmetryResults calcQuatSymmetry(
 
 		String symmetry = results.getSymmetry();
 
-		// asymmetric structures cannot be pseudosymmetric
-		if (symmetry.equals("C1"))
-			results.setPseudosymmetric(false);
-
 		// Check structures with Cn symmetry (n = 1, ...) for helical symmetry
 		if (symmetry.startsWith("C")) {
 			HelixSolver hc = new HelixSolver(subunits,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
@@ -56,7 +56,6 @@ public class QuatSymmetryResults {
 	private SymmetryPerceptionMethod method;
 	private RotationGroup rotationGroup;
 	private HelixLayers helixLayers;
-	private boolean pseudosymmetric = false;
 
 	// TODO we should unify rotational and roto-translational results
 
@@ -210,26 +209,6 @@ void setLocal(boolean local) {
 		this.local = local;
 	}
 
-	/**
-	 * A symmetry result is pseudosymmetric when using pseudostoichiometry
-	 * extended the symmetry over the
-	 * 
-	 * @return true is pseudosymmetric, false otherwise
-	 */
-	public boolean isPseudosymmetric() {
-		return pseudosymmetric;
-	}
-
-	/**
-	 * A symmetry result is pseudosymmetric when using pseudostoichiometry
-	 * extended the symmetry over the
-	 * 
-	 * @param pseudosymmetric true if pseudosymmetric, false otherwise
-	 */
-	public void setPseudosymmetric(boolean pseudosymmetric) {
-		this.pseudosymmetric = pseudosymmetric;
-	}
-	
 	public Structure getStructure() {
 		return structure;
 	}

Original file line number	Diff line number	Diff line change
`@@ -87,12 +87,13 @@ public void testDihedral() throws IOException, StructureException {`
`87`	`87`	`// D3 symmetry non pseudosymmetric`
`88`	`88`	`assertEquals("D3", symmetry.getSymmetry());`
`89`	`89`	`assertEquals("A6B6", symmetry.getStoichiometry());`
	`90`	`+ assertFalse(symmetry.isPseudoStoichiometric());`
	`91`	`+`
`90`	`92`
`91`	`93`	`}`
`92`	`94`
`93`	`95`	`/**`
`94`	`96`	`* Hemoglobin has both symmetry and pseudosymmetry: 4HHB`
`95`		`- * TODO pseudosymmetry in hemoglobin fails`
`96`	`97`	`*`
`97`	`98`	`* @throws StructureException`
`98`	`99`	`* @throws IOException`
`@@ -121,6 +122,7 @@ public void testPseudosymmetry() throws IOException, StructureException {`
`121`	`122`	`// D2 pseudo-symmetry`
`122`	`123`	`assertEquals("D2", symmetry.getSymmetry());`
`123`	`124`	`assertEquals("A4", symmetry.getStoichiometry());`
	`125`	`+ assertTrue(symmetry.isPseudoStoichiometric());`
`124`	`126`	`}`
`125`	`127`
`126`	`128`	`/**`