OpenFreeEnergy / OpenFreeEnergy/openfe
How to handle skipping of frames in structural analysis
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- Dominant language
- Python
- Stars
- 332
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
In the hybrid topology protocol, we analyze max 500 frames in the structural analysis, the number of frames to analysis (or how many to skip) is not exposed to the user (https://github.com/OpenFreeEnergy/openfe_analysis/blob/647e8cdf853d04199ad5cfb4836542c916e77a3a/src/openfe_analysis/rmsd.py#L328)
In the SepTop protocol we followed that direction, however since we are exposing the skip argument, maybe we should also allow the user to analyze all frames, even if it's more than 500?
https://github.com/OpenFreeEnergy/openfe/blob/ec7d96a88bfe6835cc884a1ca3bc699af7f8c7f1/src/openfe/protocols/openmm_utils/omm_settings.py#L765-L769
https://github.com/OpenFreeEnergy/openfe/blob/ec7d96a88bfe6835cc884a1ca3bc699af7f8c7f1/src/openfe/protocols/openmm_septop/base_units.py#L1739-L1742
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Research direction
Start by comparing the frame-handling logic in openfe_analysis/rmsd.py around line 328 with the skip setting in openfe/protocols/openmm_utils/omm_settings.py and openfe/protocols/openmm_septop/base_units.py. Clarify how an all-frames option should interact with the existing 500-frame limit and exposed skip argument; done means the intended frame-selection behavior is user-configurable and documented by the relevant tests or configuration checks.
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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