To troubleshoot your sanitization problems, I think it would be helpful if
you could share your SMARTS reaction string and the rdkit version you are
using.
I just simulated the Hantzsch thiazole synthesis shown on Wikipedia, and
everythink worked normally for me. Admittedly, my reaction definition is
overly tailored toward these two reactants, but I think it shows that rdkit
can *Sanitize()* thiazoles correctly.
# Hantzsch thiazole synthesis
thiourea = Chem.MolFromSmiles('CN(C)C(=S)N')
haloketone = Chem.MolFromSmiles('c1ccccc1C(=O)C(C)Cl')
rxn_smarts =
'[NH2:1][C:2](=[S:3])[NH0:4].[C:5](=[O:6])[C:7][Cl:8]>>[N:4][c:2]1[s:3][c:5][c:7][n:1]1'
rxn = AllChem.ReactionFromSmarts(rxn_smarts)
product = rxn.RunReactants((thiourea, haloketone))[0][0]
Chem.SanitizeMol(product)
Chem.MolToSmiles(product)
Out[33]: 'Cc1nc(N(C)C)sc1-c1ccccc1'
On Tue, Jan 17, 2017 at 9:29 AM, Curt Fischer <curt.r.fisc...@gmail.com>
wrote:
> I can't answer your root question, but if you want to go to SMILES and
> then back, I think you want *Chem.MolFromSmiles()*, not
> *Chem.MolToSmiles()*.
>
> Curt
>
> On Tue, Jan 17, 2017 at 8:52 AM, Chris Arthur <chris.art...@bristol.ac.uk>
> wrote:
>
>> Dear all
>>
>>
>> I have a molecule containing a thiazole ring which has been generated by
>> a reaction in Rdkit.
>>
>> Sanitising the molecule gives kekulization error...
>>
>> Chem.SanitizeMol(forwardProduct_)
>> Traceback (most recent call last):
>>
>> File "<ipython-input-29-649525efe840>", line 1, in <module>
>> Chem.SanitizeMol(forwardProduct_)
>>
>> ValueError: Sanitization error: Can't kekulize mol
>>
>> I can generate a smiles string from it (I had thought of doing a smiles
>> to molecule conversion)
>>
>> #Rdkit generated smiles that started us down this rabbit-hole
>> temp = Chem.MolToSmiles('CC(=O)c1sc(C2CCOCC2)nc1C')
>>
>> But this fails....
>>
>> ArgumentError: Python argument types in
>> rdkit.Chem.rdmolfiles.MolToSmiles(str)
>> did not match C++ signature:
>> MolToSmiles(class RDKit::ROMol mol, bool isomericSmiles=False, bool
>> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
>> allBondsExplicit=False, bool allHsExplicit=False)
>>
>>
>> So I thought I would try with simpler thiazoles....
>>
>> #ChemDraws smiles representation
>> temp = Chem.MolToSmiles('C1=CN=CS1')
>>
>> #From wikipedias smile for thiazole
>> temp = Chem.MolToSmiles('n1ccsc1')
>>
>> These however also fail.
>>
>> Can anyone suggest how I can proceed in order to sanitize such molecules
>>
>> Thanks
>>
>> Chris
>>
>>
>>
>> --
>> Dr Christopher J. Arthur
>> School of Chemistry
>> University of Bristol
>> BRISTOL, BS8 1TS, UK
>> E-mail: chris.art...@bristol.ac.uk
>>
>> Office: (+44 117) 331 7192 <+44%20117%20331%207192>
>> Mass Spectrometry Lab: (+44 117) 331 7358 <+44%20117%20331%207358>.
>> FAX: (+44 117) 927 7985 <+44%20117%20927%207985>
>>
>> WWW URL: http://www.chm.bris.ac.uk/staff/carthur.htm
>> LinkedIn Profile: https://www.linkedin.com/in/drchrisarthur
>>
>>
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>>
>
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