Hi Michael,
This is by design: the RDKit picks which bonds are wedged when a CTAB
is generated. The wedging information provided in the input CTAB is
only used to determine chirality.
-greg
On Sun, Aug 19, 2012 at 2:37 AM, Michael Palmer <mpalmer@...> wrote:
>
>>>> from rdkit import Chem
>>>> block = open('truncated.mol').read()
>>>> print block
> 16134395
> Marvin 08171214412D
>
> 9 8 0 0 0 0 999 V2000
> 6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 7.1667 4.9795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
> 7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 2 3 1 0 0 0 0
> 2 4 1 6 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 5 7 1 0 0 0 0
> 3 8 1 0 0 0 0
> 3 9 2 0 0 0 0
> M END
>
> # input contains stereo bond between atoms 2 and 4
>
>>>> m=Chem.MolFromMolBlock(block)
>>>> from rdkit.Chem import AllChem
>>>> block2 = AllChem.MolToMolBlock(m)
>>>> print block2
> 16134395
> RDKit 2D
>
> 9 8 0 0 0 0 0 0 0 0999 V2000
> 6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 7.1667 4.9795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 6
> 2 4 1 0
> 4 5 1 0
> 5 6 2 0
> 5 7 1 0
> 3 8 1 0
> 3 9 2 0
> M END
>
> # stereo bond has migrated to atoms 2 and 3 in the output
>
>
> --
> Michael Palmer
> University of Waterloo
> Waterloo, Canada
> science.uwaterloo.ca/~mpalmer
>
>
>
>
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