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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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Small optimization
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@josemduarte
josemduarte committed Jan 22, 2020
commit f54b62595cb799481a7e2aef3212388c74929335
10 changes: 5 additions & 5 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
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Original file line number Diff line number Diff line change
Expand Up @@ -298,15 +298,15 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
continue;
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@lafita lafita Jan 24, 2020

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Ok I think that answers my question before, makes sense! Thanks Jose

}

// note the seqresindex is 1-based
Group otherG = otherChain.getSeqResGroups().get(seqresIndex - 1);

if (!otherChain.getAtomGroups().contains(otherG)) {
// skip residues that are unobserved in other sequence ("gaps" in the entity alignment)
int otherIndex = otherChain.getAtomGroups().indexOf(otherG);
if (otherIndex == -1) {
// skip residues that are unobserved in other sequence ("gaps" in the entity SEQRES alignment)
continue;
}

int otherIndex = otherChain.getAtomGroups().indexOf(otherG);

// Only consider residues that are part of the SubunitCluster
if (this.subunitEQR.get(this.representative).contains(thisIndex)
&& other.subunitEQR.get(other.representative).contains(otherIndex)) {
Expand All @@ -316,7 +316,7 @@ 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);
logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
}

updateEquivResidues(other, thisAligned, otherAligned);
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