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Category: Command-line Tools
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: SDF to SMI: undefined stereocenters treated as defined
I have an sdf file with 3D structures, some of which have carbon
atoms with undefined stereochemistry ("3" for atom stereo parity
in the atom block). However, upon conversion to smiles strings
these atoms are treated as if they had a defined stereo chemistry,
resulting in the corresponding atoms [C@H] or [C@@H]. This is
especially troublesome, since there are other stereocenters
present in the molecules which *are* defined (so no simple
removal of "@"s possible).
Got the same results with versions 1.100.2 and 2.0.0b5.