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Optimization of subunit clusterer for quaternary sym detection of PDB deposited structures #857

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Merged
josemduarte merged 5 commits into from
Jan 12, 2020
Merged

Optimization of subunit clusterer for quaternary sym detection of PDB deposited structures #857

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45f1d70
Logging, cleanups, cosmetics
josemduarte Dec 12, 2019
568a8d4
Extracting duplicate code to a method. Some cleanups
josemduarte Dec 27, 2019
f3515a7
Introduced optimization: now if switch is provided subunit clustering…
josemduarte Jan 5, 2020
47e4cfb
Reverted change that caused TestQsAlignExamples to fail
josemduarte Jan 7, 2020
3b967b0
Using mergeIdentical breaks a test, reverting
josemduarte Jan 7, 2020
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Reverted change that caused TestQsAlignExamples to fail
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@josemduarte
josemduarte committed Jan 7, 2020
commit 47e4cfb039c06a9e92368c9af07b5d1d154d383b
6 changes: 4 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
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Expand Up @@ -518,14 +518,16 @@ private void updateEquivResidues(SubunitCluster other, List<Integer> thisAligned
Collections.sort(otherRemove);
Collections.reverse(otherRemove);

for (Integer column : thisRemove) {
for (int t = 0; t < thisRemove.size(); t++) {
for (List<Integer> eqr : this.subunitEQR) {
int column = thisRemove.get(t);
eqr.remove(column);
}
}

for (Integer column : otherRemove) {
for (int t = 0; t < otherRemove.size(); t++) {
for (List<Integer> eqr : other.subunitEQR) {
int column = otherRemove.get(t);
eqr.remove(column);
}
}
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