Hi,
On Sun, Mar 2, 2014 at 3:57 AM, S.L. Chan wrote:
> Good evening,
>
> I have some molecules with neutral amidine heads. I would like to
> make them positively charged. So I do:
>
> mol = Chem.MolFromMolFile('input.mol', removeHs=False)
> q = Chem.MolFromSmarts('[NH]=C[NH2]')
> for mat in mol.GetSubstructMatches(q):
> mol.GetAtomWithIdx(mat[0]).SetFormalCharge(1)
> mol.GetAtomWithIdx(mat[0]).SetNumExplicitHs(2)
>
> m1 = Chem.AddHs(mol, addCoords=True)
>
> However, RDKit complains that the valence for the N in concern is 4,
> which is greater than permitted.
>
You need to sanitize the molecule after you change the charge. This will
automatically adjust the H count for you:
In [5]: mol = Chem.MolFromSmiles('CC(=N)N')
In [6]: q = Chem.MolFromSmarts('[NH]=C[NH2]')
In [7]: for mat in mol.GetSubstructMatches(q):
mol.GetAtomWithIdx(mat[0]).SetFormalCharge(1)
...:
In [8]: Chem.SanitizeMol(mol)
Out[8]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [11]: mh=Chem.AddHs(mol)
In [12]: print Chem.MolToSmiles(mol)
CC(N)=[NH2+]
In [13]: print Chem.MolToSmiles(mh)
[H]N([H])C(=[N+]([H])[H])C([H])([H])[H]
Best,
-greg
>
> I also tried it without the "SetNumExplicitHs" line. While it did not
> crash, it refused to add any H to the charged N.
>
> Attached is an example input file. But I got the same result with
> other input files too.
>
> Have I missed some steps?
>
> Thank you.
>
> Ling
>
>
>
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