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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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Right order of params
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@josemduarte
josemduarte committed Jan 21, 2020
commit 679f84081a8afe5f0b162fd9a9ac8c3ebb971de5
44 changes: 22 additions & 22 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,9 @@ public void testMergeIdentical() {

// Merged have to be true, and the merged SubunitCluster is sc1
assertTrue(merged);
assertEquals(sc1.size(), 2);
assertEquals(sc2.size(), 1);
assertEquals(sc1.length(), 10);
assertEquals(2, sc1.size());
assertEquals(1, sc2.size());
assertEquals(10, sc1.length());

// Create an Atom Array of poly-glycine
Atom[] reprAtoms2 = mockAtomArray(10, "GLY", -1, null);
Expand All @@ -83,9 +83,9 @@ public void testMergeIdentical() {

// Merged have to be false, and Clusters result inmodified
assertFalse(merged);
assertEquals(sc1.size(), 2);
assertEquals(sc2.size(), 1);
assertEquals(sc1.length(), 10);
assertEquals(2, sc1.size());
assertEquals(1, sc2.size());
assertEquals(10, sc1.length());

}

Expand Down Expand Up @@ -153,9 +153,9 @@ public void testMergeSequence() throws CompoundNotFoundException {

// Merged have to be true, and the merged SubunitCluster is sc1
assertTrue(merged);
assertEquals(sc1.size(), 2);
assertEquals(sc2.size(), 1);
assertEquals(sc1.length(), 100);
assertEquals(2, sc1.size());
assertEquals(1, sc2.size());
assertEquals(100, sc1.length());

// Create an Atom Array of poly-glycine
Atom[] reprAtoms2 = mockAtomArray(100, "GLY", -1, null);
Expand All @@ -167,9 +167,9 @@ public void testMergeSequence() throws CompoundNotFoundException {

// Merged have to be false, and Clusters result inmodified
assertFalse(merged);
assertEquals(sc1.size(), 2);
assertEquals(sc2.size(), 1);
assertEquals(sc1.length(), 100);
assertEquals(2, sc1.size());
assertEquals(1, sc2.size());
assertEquals(100, sc1.length());

// Create an Atom Array of 9 glycine and 91 alanine
Atom[] reprAtoms3 = mockAtomArray(9, "GLY", 91, "ALA");
Expand All @@ -181,9 +181,9 @@ public void testMergeSequence() throws CompoundNotFoundException {

// Merged have to be true, and the merged SubunitCluster is sc1
assertTrue(merged);
assertEquals(sc1.size(), 3);
assertEquals(sc2.size(), 1);
assertEquals(sc1.length(), 91);
assertEquals(3, sc1.size());
assertEquals(1, sc2.size());
assertEquals(91, sc1.length());

}

Expand Down Expand Up @@ -224,10 +224,10 @@ public void testMergeStructure() throws StructureException, IOException {
// Merged have to be true, and the merged SubunitCluster is sc1
assertTrue(merged13);
assertTrue(merged24);
assertEquals(sc1.size(), 2);
assertEquals(sc2.size(), 2);
assertEquals(sc1.length(), 141);
assertEquals(sc2.length(), 146);
assertEquals(2, sc1.size());
assertEquals(2, sc2.size());
assertEquals(141, sc1.length());
assertEquals(146, sc2.length());
assertEquals(sc1.getAlignedAtomsSubunit(0).length,
sc1.getAlignedAtomsSubunit(1).length);
assertEquals(sc2.getAlignedAtomsSubunit(0).length,
Expand All @@ -237,8 +237,8 @@ public void testMergeStructure() throws StructureException, IOException {
boolean merged = sc1.mergeStructure(sc2, clustererParameters);

assertTrue(merged);
assertEquals(sc1.size(), 4);
assertEquals(sc1.length(), 140, 2);
assertEquals(4, sc1.size());
assertEquals(140, sc1.length(), 2);
assertEquals(sc1.getAlignedAtomsSubunit(0).length,
sc1.getAlignedAtomsSubunit(2).length);

Expand Down Expand Up @@ -270,7 +270,7 @@ public void testDivideInternally() throws StructureException, IOException {

// Divided has to be true, and Subunit length shorter than half
assertTrue(divided);
assertEquals(sc1.size(), 2);
assertEquals(2, sc1.size());
assertTrue(sc1.length() < 178);
assertEquals(sc1.getAlignedAtomsSubunit(0).length,
sc1.getAlignedAtomsSubunit(1).length);
Expand Down