OpenFreeEnergy / OpenFreeEnergy/openfe
Restraints: potentially switch to protein chain selection when no DSSP filter is used
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
When no dssp filter is used for the Boresch restraints, we currently use all protein atoms (according to the selection string). We might want to instead try and use the protein chain selection first (e.g. removing starts and ends of chains). However, this would only work for proteins.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the Boresch-restraint selection logic and compare the path used when no DSSP filter is provided with the protein chain selection behavior. Clarify how chain starts and ends should be handled and how non-protein systems are excluded; done means the fallback behavior is decided and verified by the relevant tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 32/100