[WIP] Biopolymer rdkit smarts (continuing from #1301) #1306
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* first pass at doing structure matching with rdkit instead of networkx * current best attempt at fuzzy rdkit query Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com>
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Alright! For a 500ish residue protein,this drops graph matching time from 49 sec to 2 sec. Now I'll refactor this out to RDKitToolkitWrapper and work on making something similar for OpenEye. |
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…s and bonds. get dipeptide+disulfide assignment going again. Remove unneeded code.
…opolymer_rdkit_smarts # Conflicts: # openff/toolkit/topology/molecule.py # openff/toolkit/utils/rdkit_wrapper.py
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This will break PDB loading for OE-only builds, but this important improvement is languishing too long in a PR, and if I don't merge this now it'll have to wait until next week. So I'm going to merge this and I'll do OE support in a different PR. |
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Continues work from #1301 to do PDB loading and polymer info assignment using rdkit (and hopefully openeye) instead of networkx.