More checks and a warning in case no aligned atoms found. Also a few minor fixes

josemduarte · josemduarte · commit d851f6078b50 · 2020-01-21T16:40:53.000-08:00
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
@@ -32,6 +32,7 @@
 import org.biojava.nbio.structure.cluster.SubunitClusterer;
 import org.biojava.nbio.structure.cluster.SubunitClustererMethod;
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
+import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
@@ -369,6 +370,13 @@ public void testPseudoIdentity95() throws IOException, StructureException {
 
 	@Test
 	public void testSymDetectionWithSubunitClusterByEntityId() throws IOException, StructureException {
+		AtomCache cache = new AtomCache();
+		cache.setUseMmtf(false);
+		cache.setUseMmCif(true);
+		FileParsingParameters params = new FileParsingParameters();
+		params.setAlignSeqRes(true);
+		cache.setFileParsingParams(params);
+		StructureIO.setAtomCache(cache);
 		Structure pdb = StructureIO.getStructure("BIO:1SMT:1");
 
 		SubunitClustererParameters cp = new SubunitClustererParameters();
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
@@ -293,6 +293,11 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
 
 			int seqresIndex = entityInfo.getAlignedResIndex(g, thisChain);
 
+			if (seqresIndex == -1) {
+				// this might mean that FileParsingParameters.setAlignSeqRes() wasn't set to true during parsing
+				continue;
+			}
+
 			Group otherG = otherChain.getSeqResGroups().get(seqresIndex - 1);
 
 			if (!otherChain.getAtomGroups().contains(otherG)) {
@@ -310,6 +315,10 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
 			}
 		}
 
+		if (thisAligned.size() == 0 && otherAligned.size() == 0) {
+			logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity seqres alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
+		}
+
 		updateEquivResidues(other, thisAligned, otherAligned);
 
 		return true;
@@ -743,7 +752,7 @@ public SubunitClustererMethod getClustererMethod() {
 	 */
 	public List<Atom[]> getAlignedAtomsSubunits() {
 
-		List<Atom[]> alignedAtoms = Collections.emptyList();
+		List<Atom[]> alignedAtoms = new ArrayList<>();
 
 		// Loop through all subunits and add the aligned positions
 		for (int s = 0; s < subunits.size(); s++)
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
@@ -39,8 +39,8 @@
  * @author Peter
  */
 public class C2RotationSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits = null;
-	private QuatSymmetryParameters parameters = null;
+	private QuatSymmetrySubunits subunits;
+	private QuatSymmetryParameters parameters;
 	private Vector3d centroid = new Vector3d();
 	private Matrix4d centroidInverse = new Matrix4d();
 
@@ -132,7 +132,7 @@ private void solve() {
 	}
 
 	private void addEOperation() {
-		List<Integer> permutation = Arrays.asList(new Integer[]{0,1});
+		List<Integer> permutation = Arrays.asList(0,1);
 		Matrix4d transformation = new Matrix4d();
 		transformation.setIdentity();
 		combineWithTranslation(transformation);
@@ -145,7 +145,6 @@ private void addEOperation() {
 
 	/**
 	 * Adds translational component to rotation matrix
-	 * @param rotTrans
 	 * @param rotation
 	 * @return
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -21,6 +21,7 @@
 package org.biojava.nbio.structure.symmetry.core;
 
 import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.cluster.SubunitCluster;
 import org.biojava.nbio.structure.geometry.CalcPoint;
@@ -34,7 +35,7 @@
 import java.util.stream.Collectors;
 
 /**
- * A bean to represent information about the set of {@link Subunit} being
+ * A bean to represent information about the set of {@link org.biojava.nbio.structure.cluster.Subunit}s being
  * considered for symmetry detection. This class is a helper for the
  * {@link QuatSymmetryDetector} algorithm, since it calculates and caches the
  * {@link MomentsOfInertia} and the centroids of each Subunit.
@@ -45,13 +46,13 @@
  */
 public class QuatSymmetrySubunits {
 
-	private List<Point3d[]> caCoords = new ArrayList<Point3d[]>();
-	private List<Point3d> originalCenters = new ArrayList<Point3d>();
-	private List<Point3d> centers = new ArrayList<Point3d>();
-	private List<Vector3d> unitVectors = new ArrayList<Vector3d>();
+	private List<Point3d[]> caCoords = new ArrayList<>();
+	private List<Point3d> originalCenters = new ArrayList<>();
+	private List<Point3d> centers = new ArrayList<>();
+	private List<Vector3d> unitVectors = new ArrayList<>();
 
-	private List<Integer> folds = new ArrayList<Integer>();
-	private List<Integer> clusterIds = new ArrayList<Integer>();
+	private List<Integer> folds = new ArrayList<>();
+	private List<Integer> clusterIds = new ArrayList<>();
 	private List<SubunitCluster> clusters;
 
 	private Point3d centroid;
@@ -75,10 +76,7 @@ public QuatSymmetrySubunits(List<SubunitCluster> clusters) {
 				clusterIds.add(c);
 				Atom[] atoms = clusters.get(c).getAlignedAtomsSubunit(s);
 
-				// Convert atoms to points
-				Point3d[] points = new Point3d[atoms.length];
-				for (int i = 0; i < atoms.length; i++)
-					points[i] = atoms[i].getCoordsAsPoint3d();
+				Point3d[] points = Calc.atomsToPoints(atoms);
 
 				caCoords.add(points);
 			}
