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_matrix(a)
lg = nx.line_graph(b)
ea = nx.adjacency_matrix(lg)
ea
matrix([[ 0., 1., 1., 0.],
[ 1., 0., 1., 0.],
[ 1., 1., 0., 1.],
[ 0., 0., 1., 0.]])
Hope this helps - but I'm way out of my depth here!
Best regards,
Chris
On 17 January 2018 at 16:57, Mario Lovrić <mario.lovri...@gmail.com> wrote:
> Correct, I am looking for a rdkit-hidden-option to do it :D
>
> On Wed, Jan 17, 2018 at 5:56 PM, Jason Biggs <jasondbi...@gmail.com>
> 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/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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>>>
>>
>
>
> --
> Mario Lovrić
>
> ------------------------------------------------------------
> ------------------
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