Page Comparison

What Topology functionality is needed in the short run?

• Some way to load a protein topology to begin with

• Pathways where we’ll need to export a molecule with residues

  • The molecule was parameterized using OFFTK

  • The molecule was loaded from .gro or .prmtop

• Will OpenFF parameterization ever affect residue/atom definitions?

  • Let’s assume “No”

• Will we need to know residues, segments, chains, etc?

  • Let’s assume “yes” and that the final biopolymer object will be able to support efficient lookups based on arbitrary metadata

• Can we have a topology where some components have residues/chains and others don't?

  • Yes, it should be allowed to an OpenFF System to exist with a mix of atomtyped / residue-organized components, and residue-agnostic components. The exporters will, at the last minute, assign residue names to things that need them.

Would we want to use a MDTraj Topology directly, or wrap one in such a way that it looks like an OpenFF Topology with extra API points?

• What is required?

  • Build one up atom-by-atom and bond-by-bond (natively supporting atom types!)

  • Read PDBs

  • Maybe read some other formats (eg prmtop) good too

What kind of workflow should we try to make that REQUIRES correct atom typing?

• ???

• Could try to mimic the output of AMBER protein param (but we don’t have an AMBER exporter yet)

What’s the difference between using eg. an MDTraj topology, and just carrying around a bunch of dictionaries with an OFF Topology that have residue mappings and stuff?

• So, what if we effectively had OFFBioTop = (OFFTop, MDTrajTop)?

• We should carry around a MDTraj topology becuase it has an API and a dictionary doesn’t