Curt & Greg,
Thx for clarification.
> But it's not clear to me why you would need to query in this way.
in my code I use(d) smarts as a smiles with extra features ("regex",
atom numbering). As far as I remember I had some problem with smiles
and therefore decided to switch to smarts. Now I
Rafal,
> this three Mols (m1, m2, m33) below should all represent nitrobenzene,
> right?
> >>> m33=Chem.MolFromSmarts('c1c1[N+](=O)[O-]')
> >>> m1=Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
> >>> m2=Chem.MolFromSmiles('c1c1N(=O)(=O)')
>
I guess m33 represents nitrobenzene in a sense,
Greg,
Thx for answer, but it is still unclear for me. You wrote:
> So, the short answer to your question is: "yes". You will need to rewrite
> your SMARTS queries so that nitro groups are expressed consistently. If you
> want those queries to match what the RDKit's molecule processing code
>
Hi Rafal,
The MolFromSmiles() code is intended to create a "normal" molecule and as
part of doing that some sanitization work is carried out (
http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization). Part of
that includes standardizing nitro groups (as well as a few other functional
hi all,
Is it possible to read smarts with nitro group in form 'N(=O)(=O)'?
Here is the context of my question:
The example below shows that there is some problem with nitro group and
MolFromSmarts:
>>> m1=Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
>>>
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