OpenFreeEnergy / OpenFreeEnergy/feflow
Support for different protein conformations in the protocol
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 20
- Forks
- 4
- PR merge metrics
- No merged PRs in 30d
Description
Support for different protein conformations in the protocol would be desirable for some of our users. for the Non Equilibrium Cycling or Switching this can be done just by allowing different protein conformations in the protocol. We are now forcing the protein component to be the same here.
As long as we have a protocol that allows for different protein conformations we should be good to go in terms of the code.
There are some concerns about bookkeeping that we might need to consider, for example what if there are big clashes or the conformational changes are "too big".
Contributor guide
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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 reading feflow/protocols/nonequilibrium_cycling.py around line 63, where the protein component is forced to be the same. Trace how protein conformations are represented and tracked through the Non Equilibrium Cycling or Switching protocol. Done means different conformations can be supplied without breaking bookkeeping, while the issue's concerns about clashes and overly large changes are resolved or explicitly scoped.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100