-
Notifications
You must be signed in to change notification settings - Fork 38
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
sasascore module #862
Merged
Merged
sasascore module #862
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
mgiulini
added
enhancement
Enhancing an existing feature of adding a new one
community
contributions from people outside the haddock team
m|accscoring
related to accessibility (a posteriori) scoring
labels
Apr 16, 2024
amjjbonvin
reviewed
Apr 25, 2024
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I would suggest to rename this module to sasascore
…nto accscoring
…nto accscoring
VGPReys
reviewed
Oct 4, 2024
VGPReys
previously approved these changes
Oct 4, 2024
Co-authored-by: Victor Reys <[email protected]>
VGPReys
previously approved these changes
Oct 8, 2024
sverhoeven
added a commit
to i-VRESSE/workflow-builder
that referenced
this pull request
Oct 9, 2024
rvhonorato
requested changes
Oct 9, 2024
rvhonorato
approved these changes
Oct 16, 2024
VGPReys
approved these changes
Oct 16, 2024
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
🚀
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Labels
community
contributions from people outside the haddock team
enhancement
Enhancing an existing feature of adding a new one
m|accscoring
related to accessibility (a posteriori) scoring
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.
You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and that you comply with the following criteria:
tox
tests pass. Runtox
command inside the repository folder-test.cfg
examples execute without errors. Insideexamples/
runpython run_tests.py -b
Closes #861 by creating a
sasascore
module, which allows to score PDB files against existing accessibility information.As an example, if some glycosylation sites on chain A (say residues 40 and 50) are known to be preserved upon complex formation, a penalty can be added if they are buried in the resulting model. At the same time, if some residues are known to be buried in the complex, we can impose a penalty if they are accessible.
An example application of the module:
This will create a sasascore.tsv file, analogous to the other scoring tsv files.
Here the score is the number of times the input information has not be satisfied (the lower the better). A file named violations.tsv is also produced, with a detailed picture of the violations: