IDP go interactions and secondary structure #628
Closed
Conversation
This file contains 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
- enforce that the cgsecstruct is "C" to make sure we don't overapply a folded domain in the links later - adapt the secondary structure header to get the header from the cg not atomistic graph
- in FFs where we have -go but not -water-bias, cross disordered-folded go bonds won't be removed because this is buried in the water_bias processor. - so call it anyway with an empty list of water biases, which will remove them
- reverting dssp sequence_from_residues behaviour so doesn't default to something with cg - move the ss_cg conversion into martinize2 using a global variable
csbrasnett
had a problem deploying
to
testpypi
GitHub Actions
Failure
|
This PR also needs to be moved to the marrink-lab repo |
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Outdated suggestions cannot be applied.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.
This PR fixes two problems with Go models/water biasing as we currently have it, particularly for multi domain proteins.
If you assign secondary structure using
-dssp, and have-id-regions, then there's a chance that you'll get folded links written into disordered domains. This is fixed by overwriting the cgsecstruct to be coiled everywhere in disordered domains.Currently if you have disordered and folded regions, the go interactions between them are removed based on the fact that you have water biasing in the disordered region. This requires the
-water-biasflag to be given. However, if you were to have some disordered domain annotation that didn't require water biasing, then these bonds remain. So, we call the ComputeWaterBias processor in this case, and the bonds are removed through the functionality there.