Are you sure the hydrogens are not implicit by default? On Wed, Mar 14, 2012 at 10:11, JP <[email protected]> wrote: > 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? > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
