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

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Merged
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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josemduarte committed Jan 23, 2020
commit f779dc3d32958ca5a717a40129f73c20acca47b7
11 changes: 8 additions & 3 deletions .../test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
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Expand Up @@ -398,7 +398,6 @@ public void testSymDetectionWithClusteringByEntityId() throws IOException, Struc
/**
* A performance test that demonstrates how the SubunitClustererParameters.setUseEntityIdForSeqIdentityDetermination()
* has a dramatic effect in runtime versus doing alignments.
* This takes minutes with the parameter on, but hours without the parameter.
*/
@Ignore("This is a performance test to be run manually")
@Test
Expand All @@ -413,14 +412,20 @@ public void testSymDetectionPerformanceLargeCapsid() throws IOException, Structu
StructureIO.setAtomCache(cache);

// making sure we remove all atoms but representative before we expand, otherwise memory requirements are huge
// 6Q1F is another good example
Structure au = StructureIO.getStructure("6NHJ");
StructureTools.reduceToRepresentativeAtoms(au);
BiologicalAssemblyBuilder builder = new BiologicalAssemblyBuilder();
List<BiologicalAssemblyTransformation> transforms = au.getPDBHeader().getBioAssemblies().get(1).getTransforms();
Structure pdb =builder.rebuildQuaternaryStructure(au, transforms, true, false);
Structure pdb = builder.rebuildQuaternaryStructure(au, transforms, true, false);

SubunitClustererParameters cp = new SubunitClustererParameters();
cp.setUseEntityIdForSeqIdentityDetermination(true); // this is the parameter that makes this fast

// This is the parameter that makes this fast, set it to false to see the difference.
// As of git commit ed322e387cd46344a7864a, the difference in runtime is not that huge:
// 2 minutes with true, 10 minutes with false. I observed a much larger difference before, but can't reproduce anymore - JD 2020-01-23
cp.setUseEntityIdForSeqIdentityDetermination(true);

cp.setClustererMethod(SubunitClustererMethod.SEQUENCE);
QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
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