On Mon, Feb 3, 2014 at 8:12 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > The presence of the hydrogen on the pyridinium nitrogen is critical for
> aromaticity.
>
> Yes, except there are decidedly users who feel that with SMILES, explicit
> hydrogens only need to be used in cases
> The presence of the hydrogen on the pyridinium nitrogen is critical for
> aromaticity.
Yes, except there are decidedly users who feel that with SMILES, explicit
hydrogens only need to be used in cases of stereochemistry.
I remember a thread with Andrew Dalke (now CC'ed) where he argued IIRC,
Hi Geoff,
On 3 Feb 2014, at 05:23, Geoffrey Hutchison wrote:
>> to be molecules with nonsense formal charges on aromatic atoms, which then
>> fail to
>> be Kekulized given the mismatched valence states.
>
> OK, I have an interesting test case from Noel's python testkekulize.py script.
> (Sadly
> to be molecules with nonsense formal charges on aromatic atoms, which then
> fail to
> be Kekulized given the mismatched valence states.
OK, I have an interesting test case from Noel's python testkekulize.py script.
(Sadly, my laptop wasn't set to build the python bindings and so this is
curr
Hi Noel and Geoff,I've been investigating some of the weird SMILES strings distributed by eMolecules,that can't be read into other cheminformatics packages. A significant fraction appearto be molecules with nonsense formal charges on aromatic atoms, which then fail tobe Kekulized given the mismatc
