CB – Words like “Topology” and “residue” have different meanings to different people. We should make sure we harmonize terminology moving forward.
CB – The connection point chemistry might be best handled by SMIRKS
CB – The amide bond parameters will be influenced by aromaticity. That may throw a wrench into capping since that may mess up linker electronic structure.
LW – Our fragmentation would keep aromatic rings together. I think that should handle this case.
CB – How do you fragment molecules into chemistries that are self-contained?
LW – This code doesn’t focus on that yet.
CB – Bill Swope would be good to involve in polymer stuff
LW – Parsnip currently is based on ecosystem-specific parameterized systems – Gromacs in this case, and handling the process of breaking and joining the whole molecule
CBy – I wonder how much of this process is Gromacs-specific? If we made this more ecosystem-agnostic, would the overall workflow would change much? There are several ways to generate coordinates, but I don’t see a way around needing to recognize residues. I think residue perception may be harder, so it may be good to focus on answers to the latter.
LW – One of my big constraints was having an object model that could help us break the polymer down into small pieces suitable for partial charge calculation and combination.
TG – When parsnip splices things together, where are the 3d coordinates coming from?
LW – RDKit’s alignment, followed by a short minimization.
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