Hi all,
is there any way to preserve stereochemistry? I tried a lot of stuff but
regardless if I read a molfile or chiral smiles, as soon as it is in CDK I
can't output that information anymore. Lets assume a simple format
conversion from molfile to smiles:
TestMol
ChemDraw07021308052D
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0717 0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0717 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0717 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 6 1 0
6 1 1 0
3 7 1 6
5 8 1 1
M END
With OpenBabel canonical smiles I get:
C[C@@H]1CNC[C@H](C1)C
How can I get the same output from CDK?
After reading the molfile the AtomContainer object has 2 Stereo Elements
but all bonds have IBond.Stereo.None and hence
the BondTools.makeUpDownBonds does absolutely nothing because looking at
the source code it only does something if there already are up or down
bonds.
Suggestions?
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