Hi Dmitri,
The results that come back from the MCS in that examples really describe
queries, not necessarily stable molecules or things that can be accurately
translated into SMILES.
I'll describe below what's going on to cause the error, but the more
important question is: what are you trying to do?
In this case there are two problems. One has to do with the aromatic bonds
in the SMILES coming from C atoms that are written as capital letters.
Here's a simplified version of your example:
In [11]: Chem.MolFromSmiles('O=C1:[NH]:C:N:N2:C:*:C:C:1:2')
[06:43:37] Explicit valence for atom # 1 C, 5, is greater than permitted
If I rewrite the SMILES to have the atoms with aromatic bonds written with
lower case letters everything is fine:
In [12]: Chem.MolFromSmiles('O=c1:[nH]:c:n:n2:c:*:c:c:1:2')
Out[12]:
This shouldn't make a difference in SMILES, so I'm inclined to think that
it's a bug.
The second problem was the missing hydrogen specification on the aromatic
nitrogen that has an H (I fixed this in the SMILES above). Since the RDKit
does not attempt to guess at chemistry, the general rule is that aromatic
heteroatoms should have Hs specified if they have any. There have been a
number of mailing list threads on this topic.
Best,
-greg
On Mon, Jun 27, 2016 at 8:26 PM, DmitriR wrote:
> 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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