2021-07-12 Core Developers meeting notes

Updates

AD

• Finishing up a molecule parsing/catching PR

  • disconnected SMILES

  • wild card atoms in SMILES

• Finished coverage tool (version 1.0)

  • Now parses molecules the same way with both toolkits

  • looked through 45,000 ChEBI records

    • ran is_isomorphic_with rdkit vs openeye on each record

  • One cool molecular causing a bunch of failures:

• Found a bug with toolkits handling sulfoxides differently

MT

• Virtual sites

  • A simple case (sigma hole on chloromethane) working in GROMACS

• Amber stuff

  • Slow going.

PB

• Theory benchmarking

  • Constrained optimizations at a high level of theory are not aligning with existing torsion scans

  • Looked at chemistries noted by TF, did not find notable differences. Did not report back yet.