biojava · sbliven · Sep 4, 2024 · Aug 30, 2024 · Aug 30, 2024 · Aug 30, 2024
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
@@ -76,7 +76,7 @@ public class MenuCreator {
 	 * Menus included:
 	 * <ul><li>File: open, save, export, import, exit.
 	 * <li>Align: new pairwise alignment, new multiple alignment.
-	 * <li>View: aligment panel, aligned pairs, text format,
+	 * <li>View: alignment panel, aligned pairs, text format,
 	 * FatCat format, distance matrices, dot plot.
 	 * <li>Help
 	 * </ul>

diff --git a/...-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java b/...-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
@@ -92,6 +92,15 @@ else if (pos < ca.length) {
 		return lst;
 	}
 
+	/**
+	 * @deprecated Replace with {@see showMultipleAlignmentPanel}
+	 */
+	@Deprecated
+	public static void showMultipleAligmentPanel(MultipleAlignment multAln,
+			AbstractAlignmentJmol jmol) throws StructureException {
+		showMultipleAlignmentPanel(multAln, jmol);
+	}
+
 	/**
 	 * Creates a new Frame with the MultipleAlignment Sequence Panel.
 	 * The panel can communicate with the Jmol 3D visualization by
@@ -102,7 +111,7 @@ else if (pos < ca.length) {
 
 	 * @throws StructureException
 	 */
-	public static void showMultipleAligmentPanel(MultipleAlignment multAln,
+	public static void showMultipleAlignmentPanel(MultipleAlignment multAln,
 			AbstractAlignmentJmol jmol) throws StructureException {
 
 		MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);

diff --git a/...-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java b/...-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
@@ -47,7 +47,7 @@
  * and from a Jmol view an XML format is saved.
  *
  * @author Aleix Lafita
- * @version 2.0 - adapted for MultipleAligments
+ * @version 2.0 - adapted for MultipleAlignments
  *
  */
 public class MySaveFileListener implements ActionListener {

diff --git a/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -385,7 +385,7 @@ public void actionPerformed(ActionEvent ae) {
 						.showAlignmentImage(multAln, result);
 
 			} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
-				MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
+				MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(multAln,
 						this);
 
 			} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {

diff --git a/...org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/...org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -684,7 +684,8 @@ private String drawSymmetryAxes() {
 		return s.toString();
 	}
 
-	private Vector3d getAligmentVector(Point3d point, Vector3d axis) {
+
+	private Vector3d getAlignmentVector(Point3d point, Vector3d axis) {
 		// for system with a single Cn axis
 		if (rotationGroup.getPointGroup().startsWith("C") || rotationGroup.getPointGroup().startsWith("D")) {
 			// if axis is orthogonal to principal axis, use principal axis as reference axis
@@ -760,14 +761,14 @@ private String getSymmetryAxis(int i, int j, String pointGroup, int n, Vector3d
 		if (drawPolygon) {
 			double polygonRadius = getMeanExtension() * 0.06;
 			if (n == 2) {
-				referenceAxis = getAligmentVector(p1, axis);
+				referenceAxis = getAlignmentVector(p1, axis);
 				s.append(getC2PolygonJmol(i, p1, referenceAxis, axis, color, polygonRadius, name));
-				referenceAxis = getAligmentVector(p2, axis);
+				referenceAxis = getAlignmentVector(p2, axis);
 				s.append(getC2PolygonJmol(j, p2,  referenceAxis, axis, color, polygonRadius, name));
 			} else if (n > 2) {
-				referenceAxis = getAligmentVector(p1, axis);
+				referenceAxis = getAlignmentVector(p1, axis);
 				s.append(getPolygonJmol(i, p1, referenceAxis, axis, n, color, polygonRadius, name));
-				referenceAxis = getAligmentVector(p2, axis);
+				referenceAxis = getAlignmentVector(p2, axis);
 				s.append(getPolygonJmol(j, p2, referenceAxis, axis, n, color, polygonRadius, name));
 			}
 		}

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -124,8 +124,8 @@ public interface Block extends ScoresCache {
 
 	/**
 	 * Calculates and returns the first position of the specified structure in
-	 * the alignment that is not null. This will return the aligment index, not
-	 * the reisude aligned in that position.
+	 * the alignment that is not null. This will return the alignment index, not
+	 * the residue aligned in that position.
 	 *
 	 * @param str
 	 *            structure index
@@ -148,8 +148,8 @@ public interface Block extends ScoresCache {
 
 	/**
 	 * Calculates and returns the last position of the specified structure in
-	 * the alignment that is not null. This will return the aligment index, not
-	 * the reisude aligned in that position.
+	 * the alignment that is not null. This will return the alignment index, not
+	 * the residue aligned in that position.
 	 *
 	 * @param str
 	 *            structure index

diff --git a/...cture/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/...cture/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -210,7 +210,7 @@ private void initialize() throws StructureException {
 			}
 		}
 
-		// Set the superposition and score for the seed aligment
+		// Set the superposition and score for the seed alignment
 		checkGaps();
 		msa.clear();
 		imposer.superimpose(msa);

diff --git a/.../src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/.../src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -57,6 +57,7 @@
 import org.biojava.nbio.structure.align.multiple.BlockSet;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
 import org.biojava.nbio.structure.jama.Matrix;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
@@ -721,7 +722,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {
 
 	/**
 	 * Calculate a List of alignment indicies that correspond to the core of a
-	 * Block, which means that all structures have a residue in that positon.
+	 * Block, which means that all structures have a residue in that position.
 	 *
 	 * @param block
 	 *            alignment Block
@@ -964,4 +965,46 @@ public static Phylogeny getStructuralTree(MultipleAlignment msta) {
 		return tree;
 	}
 
+	/**
+	 * Convert an MSA into a matrix of equivalent residues.
+	 *
+	 * This concatenates all blocks, meaning that the indices might not be
+	 * sequential.
+	 *
+	 * Indices should be consistent with `msa.getAtomArrays()`.
+	 * @param msa Multiple alignment
+	 * @param coreOnly Include only core (ungapped) columns. Otherwise gaps are
+	 *        represented with null.
+	 * @return
+	 */
+	public static List<List<Integer>> getEquivalentResidues(MultipleAlignment msa, boolean coreOnly) {
+		List<List<Integer>> eqr = new ArrayList<>();
+		for (int str = 0; str < msa.size(); str++) {
+			eqr.add(new ArrayList<>());
+		}
+
+		for(Block block: msa.getBlocks()) {
+			List<List<Integer>> aln = block.getAlignRes();
+			for (int col = 0; col < block.length(); col++) {
+				// skip non-core columns
+				if(coreOnly) {
+					boolean core = true;
+					for (int str = 0; str < block.size(); str++) {
+						if (aln.get(str).get(col) == null) {
+							core = false;
+							break;
+						}
+					}
+					if(!core) {
+						continue;
+					}
+				}
+				// add column to eqr
+				for (int str = 0; str < block.size(); str++) {
+					eqr.get(str).add(aln.get(str).get(col));
+				}
+			}
+		}
+		return eqr;
+	}
 }
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
@@ -158,6 +158,22 @@ public SubunitCluster(SubunitCluster other, List<Integer> subunitsToRetain) {
 		setAlpha(other.getAlpha());
 	}
 
+	/**
+	 * Create the cluster manually by specifying subunits and the equivalent residues
+	 * @param subunits List of aligned subunits
+	 * @param subunitEQR Double list giving the aligned residue indices in each subunit
+	 */
+	public SubunitCluster(List<Subunit> subunits, List<List<Integer>> subunitEQR) {
+		if(subunits.size() != subunitEQR.size()) {
+			throw new IllegalArgumentException("Mismatched subunit length");
+		}
+		this.subunits = subunits;
+		this.subunitEQR = subunitEQR;
+		this.representative = 0;
+		this.method = SubunitClustererMethod.MANUAL;
+		this.pseudoStoichiometric = false;
+	}
+
 	/**
 	 * Subunits contained in the SubunitCluster.
 	 *
@@ -496,6 +512,12 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
 				other.subunits.get(other.representative)
 						.getRepresentativeAtoms());
 
+		if (afp.getOptLength() < 1) {
+			// alignment failed (eg if chains were too short)
+			throw new StructureException(
+					String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm()));
+		}
+
 		// Convert AFPChain to MultipleAlignment for convenience
 		MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
 				afp,

diff --git a/...va-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClustererMethod.java b/...va-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClustererMethod.java
@@ -59,6 +59,10 @@ public enum SubunitClustererMethod {
 	 * sequence and structure clustering differ, the cluster contains
 	 * pseudosymmetry (by definition).
 	 */
-	SEQUENCE_STRUCTURE
-}
+	SEQUENCE_STRUCTURE,
 
+	/**
+	 * Some other method was used when clustering.
+	 */
+	MANUAL,
+}
diff --git a/...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -76,6 +76,10 @@ public QuatSymmetrySubunits(List<SubunitCluster> clusters) {
 				clusterIds.add(c);
 				Atom[] atoms = clusters.get(c).getAlignedAtomsSubunit(s);
 
+				if( atoms.length == 0) {
+					throw new IllegalArgumentException("No aligned atoms in subunit");
+				}
+
 				Point3d[] points = Calc.atomsToPoints(atoms);
 
 				caCoords.add(points);
@@ -213,7 +217,7 @@ private void run() {
 		calcOriginalCenters();
 		calcCentroid();
 		calcCenters();
-		calcMomentsOfIntertia();
+		calcMomentsOfInertia();
 	}
 
 	private void calcOriginalCenters() {
@@ -272,7 +276,7 @@ public Point3d getUpperBound() {
 		return upper;
 	}
 
-	private void calcMomentsOfIntertia() {
+	private void calcMomentsOfInertia() {
 		for (Point3d[] trace : caCoords) {
 			for (Point3d p : trace) {
 				momentsOfInertia.addPoint(p, 1.0f);

diff --git a/...a-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/...a-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -101,7 +101,7 @@ public class SymmOptimizer {
 	private List<Double> mcScoreHistory;
 
 	/**
-	 * Constructor with a seed MultipleAligment storing a refined symmetry
+	 * Constructor with a seed MultipleAlignment storing a refined symmetry
 	 * alignment of the repeats. To perform the optimization use the call or
 	 * optimize methods after instantiation.
 	 *

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
@@ -53,15 +53,18 @@
 import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
 import org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer;
 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.Subunit;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
 import org.biojava.nbio.structure.cluster.SubunitClustererMethod;
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 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.Stoichiometry;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
 import org.jgrapht.Graph;
@@ -706,21 +709,18 @@ public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result)
 			throws StructureException {
 
 		// Obtain the subunits of the repeats
-		List<Atom[]> atoms = toRepeatsAlignment(result).getAtomArrays();
+		MultipleAlignment msa = toRepeatsAlignment(result);
+		List<Atom[]> atoms = msa.getAtomArrays();
 		List<Subunit> subunits = atoms.stream()
 				.map(a -> new Subunit(a, null, null, null))
 				.collect(Collectors.toList());
-
-		// The clustering thresholds are set to 0 so that all always merged
-		SubunitClustererParameters cp = new SubunitClustererParameters();
-		cp.setClustererMethod(SubunitClustererMethod.STRUCTURE);
-		cp.setRMSDThreshold(10.0);
-		cp.setStructureCoverageThreshold(0.0);
+		List<List<Integer>> eqr = MultipleAlignmentTools.getEquivalentResidues(msa, true);
+		SubunitCluster cluster = new SubunitCluster(subunits, eqr);
+		Stoichiometry composition = new Stoichiometry(Arrays.asList(cluster));
 
 		QuatSymmetryParameters sp = new QuatSymmetryParameters();
-
 		QuatSymmetryResults gSymmetry = QuatSymmetryDetector
-				.calcGlobalSymmetry(subunits, sp, cp);
+				.calcGlobalSymmetry(composition, sp);
 
 		return gSymmetry;
 	}

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java
@@ -22,6 +22,7 @@
 
 import static org.junit.Assert.*;
 import static org.junit.Assume.assumeNotNull;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -60,7 +61,7 @@ public void testEasyCases() throws IOException, StructureException {
 			CeSymmResult result = CeSymm.analyze(atoms);
 
 			assertTrue(result.isSignificant());
-			assertEquals(result.getNumRepeats(), orders[i]);
+			assertEquals(orders[i], result.getNumRepeats());
 		}
 	}
 
@@ -75,4 +76,26 @@ public void testAlphafold() throws IOException, StructureException {
 		CeSymmResult result = CeSymm.analyze(atoms);
 		assertNotNull(result);
 	}
+
+	@Test
+	public void testShort() throws IOException, StructureException {
+		// ERIC2_c35200, a near-perfect 15 residue beta-solenoid
+		// At 15 residues this should reliably trigger rcsb/symmetry#118
+		URL url = this.getClass().getResource("/AF-V9WDR2-F1-model_v4.cif");
+		assumeNotNull(url);
+		String file = url.getPath();
+		Structure s = StructureIO.getStructure(file);
+		assertNull(s.getPdbId());
+		Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
+		CESymmParameters params = new CESymmParameters();
+		params.setMinCoreLength(10); // Ensure it gets refined (should be 15 long)
+		CeSymmResult result = CeSymm.analyze(atoms, params);
+		assertNotNull(result);
+		assertTrue(result.isSignificant());
+		assertEquals(9, result.getNumRepeats());
+		assertEquals("H",result.getSymmGroup());
+		assertNotNull(result.getAxes());
+		assertNotEquals("Error", result.getReason());
+
+	}
 }