All is clear thanks to your thorough explanations, nothing stands between us
and the Nobel now.
On 9 July 2011 05:28, Greg Landrum <[email protected]> wrote:
> On Fri, Jul 8, 2011 at 8:34 PM, JP <[email protected]> wrote:
> > Can anyone explain why the following seemingingly simple protonation
> won't
> > work?
>
> Yes.
>
> > Why is it illegal? Do you have a workaround?
>
> Also yes. ;-)
>
> > #!/usr/bin/python
> > from rdkit import Chem
> > from rdkit.Chem import AllChem
> > # Tetrazole ionization (Tautomer 1)
> > mol = Chem.MolFromSmiles('CCc1nnn[nH]1')
> > Chem.SanitizeMol(mol)
> > repl = Chem.MolFromSmarts('[n-]')
> > patt = Chem.MolFromSmarts('[$([nH]1nnnc1)]')
> > rms = AllChem.ReplaceSubstructs(mol,patt,repl,replaceAll=True)
> > print "Input: " , Chem.MolToSmiles(mol), " Output: ",
> > Chem.MolToSmiles(rms[0])
> > Chem.SanitizeMol(rms[0])
>
> Your replacement molecule is constructed using MolFromSmarts, not
> MolFromSmiles. This means that the negative charge is a query feature,
> not a property of the atom. So when you try to sanitize your product
> molecule the code doesn't see your charge and it can't kekulize the
> molecule. The fix is:
> repl = Chem.MolFromSmiles('[n-]',False)
>
> -greg
>
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