Move Subunits back to the symmetry.core package

lafita · lafita · commit 4d034f4fc8d3 · 2016-06-22T14:52:40.000+02:00
It is not needed for clustering and very specific to quaternary symmetry
detection
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/analysis/CalcBioAssemblySymmetry.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/analysis/CalcBioAssemblySymmetry.java
@@ -27,7 +27,6 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.util.ResourceManager;
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.axis.AxisAligner;
 import org.biojava.nbio.structure.symmetry.core.*;
 import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -23,8 +23,8 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.jcolorbrewer.ColorBrewer;
 
 import javax.vecmath.*;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -23,10 +23,10 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.core.Rotation;
 import org.biojava.nbio.structure.symmetry.core.RotationGroup;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.Polyhedron;
 import org.jcolorbrewer.ColorBrewer;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -36,6 +36,7 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.java
@@ -33,14 +33,14 @@
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.AllChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.rcsb.GetRepresentatives;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature;
 import org.biojava.nbio.structure.symmetry.utils.BlastClustReader;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java
@@ -25,8 +25,8 @@
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 
 import java.util.List;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.symmetry.axis;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.core.Helix;
 import org.biojava.nbio.structure.symmetry.core.HelixLayers;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.symmetry.axis;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
 import org.biojava.nbio.structure.symmetry.core.Rotation;
 import org.biojava.nbio.structure.symmetry.core.RotationGroup;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
@@ -21,7 +21,6 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.AxisAngle4d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Point3d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Matrix4d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.AxisAngle4d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -21,7 +21,6 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Matrix4d;
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
@@ -25,8 +25,6 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.cluster.ChainClusterer;
 import org.biojava.nbio.structure.cluster.ClusterProteinChains;
-import org.biojava.nbio.structure.cluster.SubunitGraph;
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.utils.CombinationGenerator;
 import org.jgrapht.UndirectedGraph;
 import org.jgrapht.alg.ConnectivityInspector;
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
@@ -22,7 +22,6 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 
 /**
  * Holds the results of quaternary symmetry perception.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -21,7 +21,6 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.DistanceBox;
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SphereSampler;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.cluster;
+package org.biojava.nbio.structure.symmetry.core;
 
 import javax.vecmath.Point3d;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.biojava.nbio.structure.cluster;
+package org.biojava.nbio.structure.symmetry.core;
 
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -21,7 +21,6 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 import org.biojava.nbio.structure.symmetry.utils.PermutationGenerator;
 
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
@@ -55,11 +55,11 @@
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
 import org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer;
-import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.jama.Matrix;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
 import org.jgrapht.UndirectedGraph;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/core/TestQuatSymmetryDetection.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/core/TestQuatSymmetryDetection.java
@@ -71,6 +71,7 @@ public void test4hhb() throws Exception {
 		params.setParseBioAssembly(true);
 		params.setAlignSeqRes(true);
 		AtomCache cache = new AtomCache();
+		cache.setUseMmCif(true);
 		cache.setFileParsingParams(params);
 		StructureIO.setAtomCache(cache);
 		Structure pdb = StructureIO.getStructure("4hhb");
