OpenFreeEnergy / OpenFreeEnergy/openfe
Protein RFE: Define a suitable prootein-protein atom mapping object
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
One of the current "hurdles" to doing protein RFEs is that we haven't decided on the right AtomMapping object for protein-protein transformations.
Could we just use LigandAtomMapping for now and do the giant int:int dictionary optimization later?
TODO:
- Rename LigandAtomMapping?
- Add necessary convenience / docs to get protein-protein atom mappings out of Kartograf?
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 reviewing the existing LigandAtomMapping object and how Kartograf currently exposes atom mappings. Resolve whether the object should be renamed and what convenience methods or documentation are needed for protein-protein transformations; done means those requirements are agreed and supported.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100