When exporting molecules from a qcarchive instance we use the from_qcschema method with allow_undefined_stereo=False this is then causing the export to fail if we hit any unspecified stereochemistry cases in which some users are. As we preprocess all molecules into the pipeline these issues should not arise but from reports, this seems to be related to nitrogen stereochemistry which has a history of toolkit issues collected here https://github.com/openforcefield/openff-toolkit/issues/146.
I propose that we allow undefined stereochemistry at this point as any major issues should have been prefiltered but it would good to get your opinion @j-wags.
dotsdl
commented
3 years ago
When exporting molecules from a qcarchive instance we use the from_qcschema method with
allow_undefined_stereo=Falsethis is then causing the export to fail if we hit any unspecified stereochemistry cases in which some users are. As we preprocess all molecules into the pipeline these issues should not arise but from reports, this seems to be related to nitrogen stereochemistry which has a history of toolkit issues collected here https://github.com/openforcefield/openff-toolkit/issues/146.I propose that we allow undefined stereochemistry at this point as any major issues should have been prefiltered but it would good to get your opinion @j-wags.