Ensure that stereochemistry of RDKit-generated conformers preserves stereochemistry of double bonds in macrocycles

openforcefield / openff-benchmark

Comparison benchmarks between public force fields and Open Force Field Initiative force fields

MIT License

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Ensure that stereochemistry of RDKit-generated conformers preserves stereochemistry of double bonds in macrocycles #83

Open j-wags opened 3 years ago

j-wags commented 3 years ago

There are user reports of double bonds in macrocycles being generated with different 3D stereochemistry than in the input molecule. We should add a check to catch these cases and discard these conformers.

For reference, see discussion in https://openforcefield.atlassian.net/wiki/spaces/PS/pages/1793785924/2021-05-26+Industry+benchmarks+meeting+notes