Does anybody remember disabling chirality features for SMARTS matching
somewhere around version 2.3.2? I have a vague memory that using '@' for a
tetrahedral center was just broken and gave wrong answers prior to Tim's
work, so it was disabled and SMARTS were matched as though they had no
chiral markings. I tested earlier versions (pre-2.3.2), and they use the
'@' markings correctly. I also tested the latest dev branch and it works
correctly. But the official 2.3.2 release seems to ignore the '@' flag.
wrong: OpenBabel 2.3.2:
$ echo "C[C@H](Br)Cl" | babel -s"C[C@H](Br)Cl" -i smi -o can
C[C@H](Br)Cl
1 molecule converted
$ echo "C[C@H](Br)Cl" | babel -s"C[C@@H](Br)Cl" -i smi -o can
C[C@H](Br)Cl
1 molecule converted
correct: OpenBabel 2.3.x-dev (HEAD)
$ echo "C[C@H](Br)Cl" | obabel -s"C[C@H](Br)Cl" -i smi -o can
C[C@H](Br)Cl
1 molecule converted
[radon:emi] ~ $ echo "C[C@H](Br)Cl" | obabel -s"C[C@@H](Br)Cl" -i smi -o can
0 molecules converted
I'm in the middle of deploying a new version of some of our internal
software, and ran into this while testing. Normally I like to use the
production version, but in this case I'll probably want to use the fixed
version. I tried to dig through the source to find something, but there
are so many changes in the stereo code I couldn't pinpoint anything.
Thanks,
Craig
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