OpenFreeEnergy / OpenFreeEnergy/openfe_analysis
Switch RMSD analysis in `gather_rms_data` to the symmetry corrected RMSD.
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- Dominant language
- Python
- Stars
- 20
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
For the HypTop protocol, this will require handling element changes between the core atoms in the end states.
state_lig = select_state_atoms(u, end_state="A").select_atoms("resname UNK")
# ToDo: Fix elements in the B state
fix_elements
guess_ligand_bonds(state_lig, delete_existing=True)
lig_rmsd = SymmetryCorrectedLigandRMSD(state_lig).run(step=skip)
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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
Locate the gather_rms_data entry point and trace the HypTop path that selects the UNK ligand atoms. Review how element changes between end states affect fix_elements, guess_ligand_bonds, and SymmetryCorrectedLigandRMSD; done means the analysis uses symmetry-corrected RMSD without incorrect element handling.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100