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Fixes on optimization of subunit clusterer for quaternary sym detection of PDB deposited structures #859

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Merged
josemduarte merged 11 commits into from
Jan 25, 2020
Merged

Fixes on optimization of subunit clusterer for quaternary sym detection of PDB deposited structures #859

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6ac8877
Extracting method in test
josemduarte Jan 20, 2020
d415e3c
New test
josemduarte Jan 21, 2020
679f840
Right order of params
josemduarte Jan 21, 2020
4d6a504
Now testing for subunit clustering with entity ids
josemduarte Jan 21, 2020
44cdda1
Removing comments
josemduarte Jan 21, 2020
fc543af
Fixing the cluster by entity id alignment issue. Now tests pass
josemduarte Jan 21, 2020
8b76e96
Some improvements
josemduarte Jan 22, 2020
d851f60
More checks and a warning in case no aligned atoms found. Also a few …
josemduarte Jan 22, 2020
f54b625
Small optimization
josemduarte Jan 22, 2020
ed322e3
Docs, a new StructureTools method and a new performance test (ignored)
josemduarte Jan 22, 2020
f779dc3
Docs
josemduarte Jan 23, 2020
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More checks and a warning in case no aligned atoms found. Also a few … 
…minor fixes
  • Loading branch information
@josemduarte
josemduarte committed Jan 22, 2020
commit d851f6078b50e7fbe5ffde3ff23d7bf16d4a211a
8 changes: 8 additions & 0 deletions .../test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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();
Expand Down
11 changes: 10 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
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Expand Up @@ -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)) {
Expand All @@ -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;
Expand Down Expand Up @@ -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++)
Expand Down
7 changes: 3 additions & 4 deletions ...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
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Expand Up @@ -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();

Expand Down Expand Up @@ -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);
Expand All @@ -145,7 +145,6 @@ private void addEOperation() {

/**
* Adds translational component to rotation matrix
* @param rotTrans
* @param rotation
* @return
*/
Expand Down
20 changes: 9 additions & 11 deletions ...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
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Expand Up @@ -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;
Expand All @@ -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.
Expand All @@ -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;
Expand All @@ -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);
}
Expand Down