Hey
I am currently working on developing a Virtual Reality simulation platform for
nanosystems.
So far we are able to compute electron transmission through 2D structures
consisting of Carbon, but want to extend the capabilities using Extended Huckel.
As, there is no manual for usage of
On Wed, Feb 12, 2020 at 4:37 PM Grzegorz Skoraczyński <
g.skoraczyn...@mimuw.edu.pl> wrote:
> Hi Greg,
>
> Thanks for your reply. Could you explain more which pattern you use for
> GetSubstructMatch?
>
Doh! Sorry I didn't include that:
In [7]: pattern = Chem.MolFromSmarts('[O-]-[#1+]')
How
Hi Greg,
Thanks for your reply. Could you explain more which pattern you use for
GetSubstructMatch? How can we guess which product' atoms are mapped to a
reaction template?
Best
GS.
śr., 12 lut 2020 o 15:50 Greg Landrum napisał(a):
> Hi Grzegorz,
>
> Nice one! This is a bug in the way
Hi Grzegorz,
Nice one! This is a bug in the way Reaction SMARTS (or Reaction SMILES for
that matter) is parsed.
At the moment there's not any way to directly work around the problem. You
can add a single bond in the reaction and then manually convert that to a
dative bond in the products.
Hello,
Imagine that we want to simulate an ESI protonation of the molecule. We
want to add a positively charged proton to a lone pair of the oxygen atom
of the molecule. I tried to create a reaction SMARTS with extended molecule
SMARTS definition, but unfortunately, it results in ValueError
Dear Puck,
Sure; I'll get back to you later today.
Cheers,
p.
On 12/02/2020 10:03, Puck van Gerwen wrote:
Dear all,
I am trying to read in SMILES to generate mol objects which I then
break into fragments using rwmol.RemoveBond(). Thereafter I want to
sanitize the fragments by saturating
Dear all,
I am trying to read in SMILES to generate mol objects which I then break
into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the
fragments by saturating with hydrogen. However, I am finding that rdkit
often doesn't sanitize the fragments consistently, leaving
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