It looks like the problem here is a covalent bond to the counter ion.
Pat
On Thu, Apr 24, 2014 at 6:04 AM, Christos Kannas <[email protected]>wrote:
> Hi all,
>
> I'm having a dozen of compounds, where some of them have a charged atom
> (see the attached SMILES file).
>
> When I parse the file I get sanitization errors on the compounds with the
> charged atoms.
> But when I view them with MarvinView 6.2.0 all goes fine.
>
> I'm using an RDKit build from github, version "2014.03.1pre".
>
> In order to see what sanitization error occurs in each case I did the
> following:
>
> 1. To parse all compounds without sanitization
>
> suppl = Chem.SmilesMolSupplier('data/SurfactantTestCompounds.smi',
> titleLine=True, sanitize=False)
> molsList = [x for x in suppl if x is not None]
> print len(molsList)
>
> 2. Sanitize the compounds and catch specific errors
>
> for m in molsList:
> error = Chem.SanitizeMol(m, catchErrors=True)
> if error:
> print m.GetProp("_Name"), Chem.MolToSmiles(m), error
>
> 2.1 the output is as follows
>
> NaLAS CCCCCCCC(CCCC)c1ccc(S(=O)(=O)O[Na+])cc1 SANITIZE_PROPERTIES
> NaOLAS CCCCCCCC(CCCC)C1=CC=CC=C1S(=O)(=O)O[Na+] SANITIZE_PROPERTIES
> SLES3EO CCCCCCCCCCCCOCCOCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
> SLES2EO CCCCCCCCCCCCOCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
> SLES1EO CCCCCCCCCCCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
> SDS CCCCCCCCCCCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
> DTAC CCCCCCCCCCCC[N+](C)(C)(C)[Cl-] SANITIZE_PROPERTIES
> Sdoc CCCCCCCCCCCC(=O)O[Na+] SANITIZE_PROPERTIES
>
> 3. Visualize compounds
>
> Draw.MolsToGridImage(molsList, molsPerRow=5, legends=[x.GetProp('_Name')
> for x in molsList], kekulize=True)
>
> For visualized output check
> http://nbviewer.ipython.org/gist/anonymous/11248962/Sanitization_Errors.ipynb
>
> Is this an expected behaviour?
> Is there something I can do as a fix?
>
> Regards,
>
> Christos
>
> Christos Kannas
>
> Researcher
> Ph.D Student
>
> Mob (UK): +44 (0) 7447700937
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>
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>
>
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