2025-02-20 Besmarts knowledge transfer notes

Initial task list (knowing that these will change radically in the future, and that JM won’t complete this list before we meet next Weds)

• First, read the docs and run the examples

• Start implementing OpenFF interface. Assume that we’re not implementing anything distributed (set one process/no multithreading). This will likely be hard in ways we don’t yet understand.  Likely needed things implemented in interface

  • Read a FF file and get its smarts out

  • Convert between BeSMARTS mol objects and OpenFF mols

  • (possibly) Pull in an already-created OpenMM system ocject (TG will need to help with this)

• Try making example notebooks for some use cases

  • Re-implement example 8 (“find all splits”) using this wrapper

  • Take a molecule and do a split based on minimizations, where it tries to split bonds/angles/or torsions, and uses OpenMM to minimize (possibly