Fixes on optimization of subunit clusterer for quaternary sym detection of PDB deposited structures #859
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lafita
approved these changes
Jan 24, 2020
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Even if two chains are from the same entity, they might have different number of residues in the crystal (e.g. disorder). How do you make sure that their alignment is correct when adding them into the cluster? |
lafita
approved these changes
Jan 24, 2020
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| if (!otherChain.getAtomGroups().contains(otherG)) { | ||
| // skip residues that are unobserved in other sequence ("gaps" in the entity alignment) | ||
| continue; |
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Ok I think that answers my question before, makes sense! Thanks Jose
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A follow up to #857
This adds tests and fixes a few problems in the implementation (wasn't updating equivalent residues indices for chains of same entity). Also added docs and a new utility method in StructureTools.
In any case as of this PR I can't reproduce anymore the dramatic difference in runtime mentioned in #857 . One of the new (ignored) tests in this PR is to demonstrate the runtime difference, but it's only ~ 5x