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, 0, 0}, {1, 0, 1, 1, 0}, {0, 1, 0, 0,
0}, {0, 1, 0, 0, 1}, {0, 0, 0, 1, 0}};
graph = AdjacencyGraph[adjacencyMatrix];
lineGraph = LineGraph[graph];
AdjacencyMatrix[lineGraph] // MatrixForm
[image: Inline image 1]
Jason Biggs
On Wed, Jan 17, 2018 at 10:21 AM, Marta Stępniewska-Dziubińska via
Rdkit-discuss <rdkit-discuss@lists.sourceforge.net> wrote:
> 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.GetNumAtoms()
> E = np.zeros((n, n))
> for b in m.GetBonds():
> i = b.GetBeginAtomIdx()
> j = b.GetEndAtomIdx()
> E[[i,j], [j,i]] = 1
>
>
> Hope this helps,
> Marta SD
>
>
>
> 2018-01-17 16:31 GMT+01:00 Mario Lovrić <mario.lovri...@gmail.com>:
>
>> 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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>>
>
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