Re: [Rdkit-discuss] edge matrix

[Guillaume G. <Gui...@fi...>]

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 <Gui...@fi...<mailto:Gui...@fi...>> 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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