Hello everyone,
I was working with molecules generated from fragment and I saw a
molecule not right, here is the smiles :
'CC1(C)CC(N)CC(C)(C)[NH2+2]1[O-]'
I tried to 'clean it' with Cleanup, Sanitize, molsvs or standardizer but
I could not change the N with 5 bounds.
So, I also tried to create other molecule to see and you can do the same
with this code in a notebook :
m = Chem.MolFromSmiles('CC1(C)CC(N)CC(C)(C)[NH15+15]1(CCC)')
m=Chem.AddHs(m)
m
It seems that there is no problem for RDKit if you add Hs to N with
charge (if you try m =
Chem.MolFromSmiles('CC1(C)CC(N)CC(C)(C)[NH15]1(CCC)') it won't work.
Also, if you have less charge than H it won't work.
Any idea how to avoid that?
Rdkit version is 2017.09.3
--
*Colin Bournez*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 494 577
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