Atom 20 appears to be an NH. Shouldn’t it be a pyridine N?
On Wed, Mar 6, 2019 at 5:04 AM Colin Bournez
wrote:
> Hi Greg,
>
> Indeed it seems one bond is not tagged as aromatic.
>
> Here are the aromatics bond (begin atom, end atom) :
>
> 0 1
> 1 19
> 19 16
> 11 14
> 14 12
> 12 7
> 7 20
> 11 0
Sorry, I mistakenly replied to just Colin before, rather than the whole
list.
I think the answer is that the outer ring is aromatic, but the two inner
rings, the 5-ring and the 6-ring, aren’t. This would mean that the bond
between 11 and 16 isn’t aromatic.
It is certainly true that the bond
Yes I know it's a tautomer, but I don't figure out how to handle it
without returning to the other form.
If I transform the SINGLE bond to AROMATIC, it can't be sanitized still
returns 0 NAR
Colin
On 06/03/19 11:11, Michal Krompiec wrote:
It’s because the molecule with atom indices is a
It’s because the molecule with atom indices is a tautomer of the other one
(H at the other N), hence different Kekule structure and different
behaviour of the aromaticity perception code.
Best,
Michal
On Wed, 6 Mar 2019 at 10:04, Colin Bournez
wrote:
> Hi Greg,
>
> Indeed it seems one bond is
Hi Greg,
Indeed it seems one bond is not tagged as aromatic.
Here are the aromatics bond (begin atom, end atom) :
0 1
1 19
19 16
11 14
14 12
12 7
7 20
11 0
20 16
We see that between the atom 11 and 16 it is not aromatic.
It is a single type:
16 11 SINGLE
The problem remains after sanitizing
Hi Colin,
The aromatic ring counting code identifies rings where every *bond* is
aromatic, so I guess one or more bonds in the rings of the first molecule
are not aromatic.
Could it be that you haven't sanitized the molecule before calculating
descriptors?
-greg
On Tue, Mar 5, 2019 at 6:00 PM
6 matches
Mail list logo
