OpenFreeEnergy / OpenFreeEnergy/openfe
Add check / warning for distant waters prior to solvation
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
As discussed with @RiesBen this morning - sometimes you can get silly boxes because you left a water that's really far away from everything in your input structure.
We should have at least a check for any stray waters & ions and warn users that they might get a sub-optimal box.
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 by locating the solvation workflow and the point where input waters and ions are considered before box construction. Determine how distant waters or ions should be identified and where a warning belongs. Done means users are warned when stray waters or ions could produce a sub-optimal box, with checks covering the relevant cases.
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
- Needs clarification
- Newbie friendliness
- 35/100