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
Mass Spectrometry Lab: (+44 117) 331 7358.
FAX: (+44 117) 927 7985
WWW URL: http://www.chm.bris.ac.uk/staff/carthur.htm
LinkedIn Profile: https://www.linkedin.com/in/drchrisarthur
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