Set the default minimum SSE per subunit to 2

lafita · lafita · commit a34c8e1db7af · 2015-11-30T17:49:43.000+01:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -51,7 +51,7 @@ public static void main(String[] args)
 		 */
 
 		//Set the name of the protein structure to analyze
-		String name = "4i4q";
+		String name = "1u6d";
 
 		//Download the atoms
 		AtomCache cache = new AtomCache();
@@ -66,7 +66,7 @@ public static void main(String[] args)
 		params.setSymmType(SymmetryType.AUTO);
 		params.setOptimization(true);
 		params.setSymmLevels(0);
-		params.setSSEThreshold(1);
+		params.setSSEThreshold(2);
 
 		//Run the alignment
 		MultipleAlignment symmetry = ceSymm.analyze(atoms, params);
diff --git a/biojava-structure/src/main/java/demo/DemoCeSymm.java b/biojava-structure/src/main/java/demo/DemoCeSymm.java
@@ -69,6 +69,7 @@ public static void main(String[] args)
 		params.setSymmType(SymmetryType.AUTO);
 		params.setOptimization(true);
 		params.setSymmLevels(0);
+		params.setSSEThreshold(2);
 
 		//Run the alignment
 		MultipleAlignment symmetry = ceSymm.analyze(atoms, params);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
@@ -111,7 +111,7 @@ public void reset() {
 		rndSeed = new Random().nextInt(10000);
 		symmLevels = 0;
 		scoreThreshold = DEFAULT_SYMMETRY_THRESHOLD;
-		sseThreshold = 1;
+		sseThreshold = 2;
 		minCoreLength = 15;
 		distanceCutoff = 7.0;
 		gaps = true;
