OpenFreeEnergy / OpenFreeEnergy/openfe_analysis
Easy access to non-hybrid topologies for endstates
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- Dominant language
- Python
- Stars
- 20
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
Is there an easy way to get access to a clean representation (non-hybrid) of the ligand trajectory at lambda[0] and lambda[-1]? Maybe I'm overcomplicating the indexing procedure, but actually it seems quite tedious.
In an ideal world I would envision something like an extra flag for the reader, e.g.:
u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, state_id=0, hybrid=False)
This would make subsequent analyses a lot easier!
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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 tracing the FEReader entry point and the state_id and hybrid options shown in the issue's MDAnalysis example. Determine how ligand trajectories at lambda[0] and lambda[-1] are currently indexed, then define completion as providing straightforward non-hybrid endpoint representations for subsequent analysis.
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
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100