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 atom list, holds all
the necessary information once bond orders are included, to define the molecule
object, but do you know if there is an RDKit function that does this: something
like mol = Chem.MolFromAdjacencyMatrix(adj)?
Best regard, Jan
On 18 Jan 2018, at 11:07, Guillaume GODIN
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote:
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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