This looks bad:
echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
CC=CC
Notice the cis/trans bonds are lost. In OB 2.2.x, it works correctly:
echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
C/C=C/C
The problem seems to be here in 2.3.x:
echo "C/C=C/C" | babel -i smi -o sdf
OpenBabel05111215342D
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
M END
$$$$
Notice that the bond block has no stereo (cis/trans) markings. Do the same
thing in 2.2.x and the cis/trans bonds are properly marked:
echo "C/C=C/C" | babel -i smi -o sdf
OpenBabel05111215352D
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
1 2 1 1 0 0
2 3 2 3 0 0
3 4 1 6 0 0
M END
$$$$
The bond block is correct here in this output from 2.2.x.
Any ideas when this might have happened and if it was intentional?
Thanks,
Craig
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