As Pat pointed out, what's happening here is that you have an explicit H in
your SMARTS.
The RDKit has a function, MergeQueryHs(), to merge this into the query of
the atom it's connected to. Here's the application to your example:
In [2]:
s=Chem.MolFromSmarts('[#8]=[#6]-3-c1c2c(ccc1)2-[#6](-[#
On Tue, Mar 26, 2019 at 8:22 PM Patrick Walters wrote:
> HI Xiaobo,
>
> There's an explicit hydrogen in the SMARTS that shouldn't be there. I
> also wouldn't include the single bonds around the ring closures.
>
To be fair, that explicit hydrogen was in the original SMILES string, so it
is reaso
HI Xiaobo,
There's an explicit hydrogen in the SMARTS that shouldn't be there. I also
wouldn't include the single bonds around the ring closures.
'[#8]=[#6]-3-c1c2c(ccc1)2-[#6](-[#7]-3-*[#1]*)=[#8]')
from rdkit import Chem
from rdkit.Chem import Draw
smi = "O=C(C1=C2C(C=CC=C23)=CC=C1)N([H]
Dear all,
I have a molecule in Smiles
O=C(C1=C2C(C=CC=C23)=CC=C1)N([H])C3=O (Copied from Chemdraw)
then, using online converter to get Smarts
(https://pubchem.ncbi.nlm.nih.gov/edit2/index.html)
[#8]=[#6]-3-c1c2c(ccc1)2-[#6](-[#7]-3-[#1])=[#8]
But I got 'false' with following code
s
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