> 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.
Yes it's all a bit mismatch at the moment. Coming from a mol file though you
should not get stereo elements - how are getting reading the mol file?
We're in the process of unify this but it's a long process.
J
On 2 Jul 2013, at 10:16, Joos Kiener <[email protected]> wrote:
> 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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