Page Comparison

Fragmenter migration

• Goal: Refactor fragmenter to not be OE-dependent

• The shortest path to do this is to have it rely on the OFFMol class, and make the cheminformatics calls toolkit-agnostic.

• Some of the functionality that we need is already implemented. There are some outstanding ones that need to be implemented.

  • We need a replacement for OE’s AtomBondSet object. It’s probably possible to do this using networkx graphs, but there’s some ambiguity about how stereochemistry will be preserved/interpreted without coordinates

  • We’ll need an RDKit-backed atom/bond.is_in_ring, but this shouldn’t be too hard

    • Maybe SMARTS syntax using rN can do this? Or does that only check for specific values of N?

    • Maybe there’s also some method call involving SSSR that can do this?

    • Maybe NetworkX can do this? find_cycles or something?

      • Are there some cycle sizes that are ignored or treated specially by OETK or fragmenter? What about 3- or 4-membered rings?

  • It’s possible we’ll need a way to force stereochemistry re-perception on command, but it’s unclear how exactly this will be used, since the networkx graphs won’t have coordinates.

• Operational notes:

  • We’ll do this refactor in a large branch/PR of fragmenter and add new functionality in a large branch of OFFTK.

• Priority

  • This is less important than the MVP for bespoke fitting.

• Other issues:

  • Check on whether chemper ring-closing issue is still around/affects bespoke fitting pipeline. One possible wayt o do this is to take Jeff’s error case and see whether all torsion terms are fit using forcebalance, or if some torsions involving ring-closing bonds are ignored

  • https://github.com/openforcefield/openforcefield/pull/601/files#diff-ed408a74921c15f701e188f7c3baa180R54