On Wed, Jun 15, 2016 at 3:22 PM, cgram <colingram...@gmail.com> wrote:
> Hi,
>
> I have this MDL file (I removed the header):
>
> *12 11* 0 0 0 0 0 0 0 0999 V2000
>
With 12 atoms and 11 bonds, this structure can't be right if it has a ring
in it. It would have to have 12 bonds.
Craig
> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 O 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
> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 5 1 0 0 0 0
> 1 2 1 0 0 0 0
> 2 3 1 0 0 0 0
> 3 9 1 0 0 0 0
> 3 8 1 0 0 0 0
> 3 4 1 0 0 0 0
> 4 11 1 0 0 0 0
> 4 10 1 0 0 0 0
> 4 5 1 0 0 0 0
> 5 12 1 0 0 0 0
> 5 6 1 0 0 0 0
> 6 7 1 0 0 0 0
> M END
>
> It should correspond to this molecule: O1OCCC1O (in SMILES format). I
> verified the MDL file manually. However, when I convert the file to a
> SMILES
> string with openbabel, I get this: O1OCCC1O.[H], which is almost correct,
> but for some reason it decides to add on a random hydrogen. I am treating
> the hydrogens explicitly in the MDL file, because I have to keep track of
> their exact indices, so I cannot remove them from the file. The script I am
> using is
>
> import pybel
>
> mol = pybel.readfile('mdl', 'mol.mdl').next()
> print mol.write(format='smi')
>
> What am I missing?
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Erroneous-molecule-from-MDL-file-tp4659331.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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--
---------------------------------
Craig A. James
Chief Technology Officer
eMolecules, Inc.
---------------------------------
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