OpenFreeEnergy / OpenFreeEnergy/Lomap
Ligands not part of a thermodynamic cycle on perturbation mapping
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- Dominant language
- Python
- Stars
- 45
- Forks
- 16
- Avg merge
- 55m
- Merged PRs (30d)
- 1
Description
While working with Lomap I noticed that some of the ligands in the perturbation mapping weren't part of a thermodynamic cycle, with only one edge connecting them to the rest of the network. I tried using the radial parameter but still observed the same.
Is there a way to force this behavior so that all ligands are part of a thermodynamic cycle?
I also noticed a slight misalignment between some of my ligands (3D coordinates). Could that play a role in the scoring from Lomap since they're obtained from gufe?
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with Lomap's perturbation-mapping behavior around the radial parameter and the gufe-provided 3D coordinates mentioned in the issue. Determine whether the requested change is enforcing thermodynamic cycles, addressing ligand alignment in scoring, or both, then define completion criteria before implementation.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100