Dear Jan,
Adjacency matrix is a molecule object encoder.
To do reverse process:
You will need atoms list.
And, you will need to have bond encoding in the Adjacency matrix as well 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-discuss] edge matrix
Is there a function for the reverse process, i.e. getting a molecule object
from an adjacency matrix?
Best regards, Jan
On 17 Jan 2018, at 17:19, Guillaume GODIN
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote:
Dear Mario,
There is a adjacency matrix available:
from rdkit import Chem
mol = Chem.MolFromSmiles('CC(C)CC')
adj = Chem.GetAdjacencyMatrix(mol)
print adj
[[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]]
But this is not what you want…
Can you explain your 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.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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