Thanks Greg.
I have the problem at CI, too. It was 100% failure rate the last two days. At
home, occasionally. At least, it isn’t only me :-)
Markus
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 6. Mar 2019, at 17:25, Greg Landrum wrote:
>
>
>
On Wed, Mar 6, 2019 at 1:15 PM Markus Sitzmann
wrote:
>
> Does someone maybe has the same problem? And an explanation whats going on
> - the Avalon tools seemed to be unchanged since quite a while.
>
I've seen it a couple of times in the CI builds for the RDKit over the past
couple of days.
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
Hi everybody,
Currently (the last couple of days) the build of one of my Docker images
stopped working:
https://github.com/chembience/chembience/blob/develop/context/build/rdkit-postgres-compile/Dockerfile
That occurred to me sporadically already over the last few years and
usually disappeared
Hi Greg,
in the meantime, I found a solution: I added a "conda update" as final step
when I build my base python/conda container. The RDKit container is build
on top of that and now it finds RDKit 2018.09.2 without telling conda the
version number explicitly. Why this worked beforehand without
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
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