Hi Patrick,
Thanks.
So the correct would be, sodium should not have an explicit bond with the
oxygen.
>From O=S(c1ccc(C(CCCCCCC)CCCC)cc1)(O-[Na+])=O I should
have O=S(c1ccc(C(CCCCCCC)CCCC)cc1)([O-])=O.[Na+]
Similar to the rest of my compounds.
And regarding nitrogen it already has 4 bonds with carbons so chloride
should be disconnected.
CCCCCCCCCCCC[N+]([Cl-])(C)(C)C -> CCCCCCCCCCCC[N+](C)(C)C.[Cl-]
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
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On 24 April 2014 11:37, Patrick Walters <[email protected]> wrote:
> 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
>> Mob (Cyprus): +357 99530608
>>
>> [image: View Christos Kannas's profile on
>> LinkedIn]<http://cy.linkedin.com/in/christoskannas>
>>
>>
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