Dear RDKitters,
I would appreciate any comments on the following:
I am looking at the 'SureChEMBL iPython Notebook Tutorial'
http://nbviewer.jupyter.org/github/rdkit/UGM_2014/blob/master/Notebooks/Vardenafil.ipynb
following along with rdkit '2016.03.1' on OSX
In Cell 142, there is this SMILES:
MCS SMILES: O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2
This is a representation of a generalized structure, not any particular
molecule.
It was generated with Chem.MolToSmiles(mcsM,isomericSmiles=True)
But when I try
Chem.MolFromSmiles('O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2')
I get "RDKit ERROR: [14:11:32] Explicit valence for atom # 1 C, 5, is greater
than permitted"
So there is no "round-trip" possible here.
Which behavior is "correct", given the aromaticity and structure as specified?
Should this be rendering/creating molecule, or failing?
Thanks!
(MarvinSketch does display the SMILES without complaints.;
image is attached)
Dmitri
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