Implementation of eRMSD (AA), eRMSD (CG) and RMSD (Kabsch) [all unweighted] #321
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
|
Merging to
|
yihengwuKP
changed the title
<!--pre-commit.ci start--> updates: - [github.com/mwouts/jupytext: v1.15.2 → v1.16.2](mwouts/jupytext@v1.15.2...v1.16.2) <!--pre-commit.ci end-->
pabloferz
requested changes
May 30, 2024
|
not sure why the Docker build test is failing... |
|
Can you rebase into the latest main? |
yihengwuKP
added
stale
|
@pabloferz can we merge this now? |
|
Yes, sorry about the delay. Thank you for adding these! |
|
no problem, glad to help! |
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Outdated suggestions cannot be applied.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.
Hi, I've implemented eRMSD in AA or CG mappings. I've also incorporated Yezhi's implementation of Kabsch RMSD into the code @yzjin . I've implemented tests for all of them.
The eRMSD requires knowing the C2/C4/C6 of the six-membered ring in the base. The implementation of eRMSDCG is for the situation when we only know the other three sites in the base, and we need to first infer the position of C2/C4/C6 before we calculate the eRMSD.
The testing of eRMSD (AA) was done by comparing with the calculation exactly done by barnaba. The testing of eRMSDCG was done by comparing with the eRMSD so it's not exact but very close. The testing for RMSD is done by precalculated examples as in test kabsch as mentioned in #305
Please let me know if there are any suggestions/comments!