Skip to content
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.

Sign up for GitHub

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

Jump to bottom

Re-implement nuclinfo using AnalysisBase style subclasses #3720

Open
2 of 5 tasks
ALescoulie opened this issue Jun 17, 2022 · 4 comments · Fixed by #3735
Open
2 of 5 tasks

Re-implement nuclinfo using AnalysisBase style subclasses #3720

ALescoulie opened this issue Jun 17, 2022 · 4 comments · Fixed by #3735
Assignees
@ALescoulie
Labels
Component-Analysis refactoring

Comments

@ALescoulie
Copy link
Contributor

ALescoulie commented Jun 17, 2022 •
edited
Loading

Is your feature request related to a problem?

To complete the overhaul of nucinfo we need to rebuild the rest of the functions in the analysis base style in the nucleicacids module.

Describe the solution you'd like

Using the NucPairDist as a super class rebuild

dists = MinorPairDist([ag1, ag2],[ag3,ag4], U)
dists.run()

TODO

  • rebuild minor_pair
  • rebuild major_pair
  • rebuild phase_cp
  • rebuild phase_as
  • rebuild tors

Additional context

In the last update in PR #3611 the I began the process of overhauling nuclinfo, and I would like to finish that process.
@ALescoulie
Copy link
Contributor Author

I'm starting on this and hopefully can get a PR out soon.

@ALescoulie ALescoulie mentioned this issue Jun 26, 2022
Merged
4 tasks
@ALescoulie
Copy link
Contributor Author

I just pushed PR #3735 which add major and minor pair, I'm also working on the torsion angle class, which is a little more involved.

@orbeckst
Copy link
Member

See #3744 for a discussion on how to represent the typical output data in the Results dict.

orbeckst added a commit that referenced this issue Oct 10, 2023
@ALescoulie @orbeckst @IAlibay
Nuclinfo Major Pair and Minor Pair overhaul (#3735)
18372f1 
* add major pair and minor pair classes with optimized distance calculations to nucleicacids module
* partially completes #3720
* refactor to use new select_strand_atoms static method
* use typealias for union[residue, reiduegroup]
* deprecate  List[Residue] as input for WatsonCrickDist (remove in 3.0.0): use ResidueGroup
* refactor results dict and clarify result structure in docs:
  - use results.distances
  - deprecate results.pair_distances for WatsonCrickDist (remove in 3.0.0)
* add tests (match the old nuclinfo ones)
* refactor previous tests to use pytest approx
* update CHANGELOG

---------

Co-authored-by: Alia <alia.lescouile@gmail.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
@orbeckst
Copy link
Member

Re-open because PR #3735 did not update all classes.

@orbeckst orbeckst reopened this Oct 10, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ALescoulie ALescoulie

Labels
Component-Analysis refactoring
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Nuclinfo Major Pair and Minor Pair overhaul ALescoulie/mdanalysis
2 participants
@orbeckst @ALescoulie