Yes, exactly
On Thu, Apr 24, 2014 at 7:19 AM, Christos Kannas <[email protected]>wrote:
> 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
>
> Mob (UK): +44 (0) 7447700937
> Mob (Cyprus): +357 99530608
>
> [image: View Christos Kannas's profile on
> LinkedIn]<http://cy.linkedin.com/in/christoskannas>
>
>
> 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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>>
>
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