Fixes on optimization of subunit clusterer for quaternary sym detection of PDB deposited structures - #859
Merged
josemduarte merged 11 commits intoJan 25, 2020
Conversation
Copy link
Copy Markdown
Contributor
Sorry, something went wrong.
lafita
approved these changes
Jan 24, 2020
Copy link
Copy Markdown
Member
|
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? |
Sorry, something went wrong.
lafita
approved these changes
Jan 24, 2020
Comment thread
biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
|
|
||
| if (!otherChain.getAtomGroups().contains(otherG)) { | ||
| // skip residues that are unobserved in other sequence ("gaps" in the entity alignment) | ||
| continue; |
Copy link
Copy Markdown
Member
There was a problem hiding this comment.
Ok I think that answers my question before, makes sense! Thanks Jose
Sorry, something went wrong.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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