Hi Mario,
What exactly do you mean by 'edge matrix'? Are you sure you provided a
correct example? If you want to get an adjacency matrix of a molecular
graph you can iterate over bonds to get it:
from rdkit.Chem import MolFromSmiles
import numpy as np
m = MolFromSmiles('CC(C)CC')
n =
You should install jupyter (and all other packages you need) in the same
environment as rdkit. Also, you need to activate the environment in order
to use it. Try running the following commands (assuming that you've already
created my-rdkit-env):
$ source activate my-rdkit-env
$ conda install
Dear Guillaume,
I'm not sure what your code should do and what behavior you expect. I see
that you do not change the value of t when you see a single bond. So maybe
you just do not update this value and print and old one? Also, you iterate
over bonds of atom's last neighbor (so for H you loop
Thanks Greg!
BondCompare.CompareAny is exactly what I needed
Best,
Marta
2016-07-06 7:47 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:
> Marta,
>
> On Tue, Jul 5, 2016 at 11:14 AM, Marta Stępniewska-Dziubińska
> <mart...@ibb.waw.pl> wrote:
>>
>>
&g
Hi Greg,
To be honest, I expected it to fail :)
I want to find structures with a defined topology, but allow for
different bond types. My first idea was to use SMARTS with ~ bonds,
and it works fine with GetSubstructMatch.
I don't really need MCS, I just used it to check different patterns.
But
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