Ligands not part of a thermodynamic cycle on perturbation mapping

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data

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.

Written by the indexing model from the issue text.

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?

Dominant language
Python
Stars
45
Forks
15
Avg merge
18h 11m
Merged PRs (30d)
4

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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