[Open Babel] [ openbabel-Bugs-1324929 ] SDF to SMI: undefined stereocenters treated as defined

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[Open Babel] [ openbabel-Bugs-1324929 ] SDF to SMI: undefined stereocenters treated as defined

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Bugs item #1324929, was opened at 2005-10-12 07:51
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Category: Command-line Tools
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: SDF to SMI: undefined stereocenters treated as defined

Initial Comment:
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.

Christian Laggner

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