OpenFreeEnergy / OpenFreeEnergy/openfe

`PersesAtomMapper` combined with minimal redundant networks can yield more than one edge/mapping connecting two ligands in a `LigandNetwork`

Open
#882 5 comments 0 reactions 1 assignee View on GitHub

@jthorton is already working on this.

Since Nov 12, 2024.

priority:low question
Dominant language
Python
Stars
331
Forks
56
Avg merge
3d 9h
Merged PRs (30d)
13

Description

The PersesAtomMapper produces one or more atom mappings for any pair of ligands (SmallMoleculeComponents) given to it. This appears to be expected behavior, but when combined with use of the generate_minimal_redundant_network planning approach, it is currently possible that the resulting LigandNetwork features more than one edge/mapping between any two ligands. This can complicate downstream analysis of resulting AlchemicalNetworks and their results.

Is this expected behavior? It's not clear to us if this something we should be concerned about, if it's still scientifically valid, etc.

We observed this in a set of ligands used for project support within ASAP Discovery, and it broke some of our assumptions around the topology of our resulting AlchemicalNetworks.

CC: @hmacdope, @jthorton

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.