Indeed - as shown in RDKit 2012.01 by:
#!/usr/bin/env python
from rdkit import Chem
mol = Chem.MolFromSmiles("C[NH]C")
for atom in mol.GetAtoms():
neighbours = [x.GetSymbol() for x in atom.GetNeighbors()]
# where is my H dude?
print "%s has neighbours %s" % (atom.GetSymbol(), ', '.join(neighbours))
Output:
C has neighbours N
N has neighbours C, C # Here, here!
C has neighbours N
Filed an incident report (and assigned it to you :-) ): ID: 3504238
-
Jean-Paul Ebejer
Early Stage Researcher
On 14 March 2012 08:10, Greg Landrum <[email protected]> wrote:
> Why is it that for a molecule with H explicitly defined (mol =
> > Chem.MolFromSmiles("C[NH]C") ) when I do a GetNeighbours on the atom
> index
> > of the N I do not get the Hs but only the two carbon atoms?
>
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