Hi,
On Fri, Jan 2, 2015 at 3:07 PM, Laetitia Bomble <[email protected]>
wrote:
>
> I would like to generate conformers from the following smiles: [O-]CC[N+].
> My code is te following:
> > ROMol *mol=SmilesToMol([O-]CC[N+);
> > ROMol *mols;
> > mols=addHs(*mol,false,false);
>
> When I write the conformers generated there are no Hs on the nitrogen
> instead of three. If I write explicitly [O-]CC[NH3+], it is fine. Is this
> normal?
>
Yes, this is the expected behavior. It is part of how SMILES works: when
you provide an atom in square brackets in SMILES, you must explicitly
specify the number of Hs that atom has. So when you provide "[N+]" as a
SMILES, you are saying that the N has zero connected Hs.
If you want to be able to use SMILES to provide charges without providing H
counts, you could try reading the molecule from SMILES without
sanitization, calling atom.setNoImplicit(false) on each atom, and then
sanitizing. This is somewhat fragile, but may provide at least the start of
a workaround.
Here's a little demo of that from python:
# the default behavior
In [21]: m = Chem.MolFromSmiles('[O-]C[N+]')
In [22]: for a in m.GetAtoms():
....: print(a.GetSymbol()," ",a.GetTotalNumHs())
....:
O 0
C 2
N 0
# forcing the H calculation:
In [23]: m = Chem.MolFromSmiles('[O-]C[N+]',sanitize=False)
In [24]: for a in m.GetAtoms():
....: a.SetNoImplicit(False)
....:
In [25]: Chem.SanitizeMol(m)
Out[25]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [26]: for a in m.GetAtoms():
....: print(a.GetSymbol()," ",a.GetTotalNumHs())
....:
O 0
C 2
N 3
-greg
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