ell to
have an exact structure i.e. Double bonds => 2, triple bonds =>3, aromatic
bonds =>1.5.
But in principal it’s only what you need.
BR,
Guillaume
De : Jan Halborg Jensen
Date : jeudi, 18 janvier 2018 à 10:59
À : GVALMTGG
Cc : Mario Lovrić, RDKit Discuss
Objet : Re: [Rdkit-discu
Dear Jan,
There is not such kind of function in RDKit.
BR,
Guillaume
De : Jan Halborg Jensen
Date : jeudi, 18 janvier 2018 à 11:17
À : GVALMTGG
Cc : Mario Lovrić, RDKit Discuss
Objet : Re: [Rdkit-discuss] edge matrix
Dear Guillaume
I understand that the adjacency matrix, together with the
7 janvier 2018 à 16:31
À : RDKit Discuss
Objet : [Rdkit-discuss] edge matrix
Dear all,
Does any one have an idea how to get an edge matrix (graph theory) out of
Rdkit, I digged deep but didnt find anything.
F.example for:
'CC(C)CC'
it would be:
array([[0, 1, 1, 0],
[1, 0,
ipal it’s only what you need.
BR,
Guillaume
De : Jan Halborg Jensen
Date : jeudi, 18 janvier 2018 à 10:59
À : GVALMTGG
Cc : Mario Lovrić, RDKit Discuss
Objet : Re: [Rdkit-discuss] edge matrix
Is there a function for the reverse process, i.e. getting a molecule object
from an adjacency matr
Dear Chris,
Thanks, thats it :)
On Wed, Jan 17, 2018 at 6:25 PM, Chris Earnshaw
wrote:
> I don't think there's a way to do this using RDKit itself, but it appears
> to be straightforward using Python with numpy and networkx, e.g.
>
> import numpy as np
> import networkx as nx
> a = np.matrix(
I don't think there's a way to do this using RDKit itself, but it appears
to be straightforward using Python with numpy and networkx, e.g.
import numpy as np
import networkx as nx
a = np.matrix([[0, 1, 0, 0, 0],[1, 0, 1, 1, 0],[0, 1, 0, 0, 0],[0, 1, 0, 0,
1],[0, 0, 0, 1, 0]])
b = nx.from_numpy_mat
Correct, I am looking for a rdkit-hidden-option to do it :D
On Wed, Jan 17, 2018 at 5:56 PM, Jason Biggs wrote:
> I am a novice when it comes to graph theory, but it seems like what is
> wanted here is the adjacency matrix of the corresponding line graph (
> http://mathworld.wolfram.com/LineGrap
I am a novice when it comes to graph theory, but it seems like what is
wanted here is the adjacency matrix of the corresponding line graph (
http://mathworld.wolfram.com/LineGraph.html).
I don't know how to do this in python, but if I use mathematica, it goes
like this
adjacencyMatrix = {{0, 1, 0
Dear Marta and Guillaume,
Thank you both.
Your solutions are giving the same output, which is the vertices-adjacency
matrix.
There is something called the edge-adjaceny matrix. Its defined in several
papers by Trinajstic to calculate the M2 Zagreb indices, eg. "The Zagreb
Indices 30 Years After"
T
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 = m.GetNumAtom
our output generation process please ?
BR,
Guillaume
De : Mario Lovrić
Date : mercredi, 17 janvier 2018 à 16:31
À : RDKit Discuss
Objet : [Rdkit-discuss] edge matrix
Dear all,
Does any one have an idea how to get an edge matrix (graph theory) out of
Rdkit, I digged deep but didnt find anything.
F.e
Dear all,
Does any one have an idea how to get an edge matrix (graph theory) out of
Rdkit, I digged deep but didnt find anything.
F.example for:
'CC(C)CC'
it would be:
array([[0, 1, 1, 0],
[1, 0, 1, 0],
[1, 1, 0, 1],
[0, 0, 1, 0]])
Thanks.
--
Mario Lovrić
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