Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

For what it's worth, the RDKit allows you to get the adjacency matrix for a molecule with the function Chem.GetAdjacencyMatrix (from python) or MolOps::getAdjacencyMatrix (from c++). -greg On Wednesday, 3 February 2016, Maciek Wójcikowski wrote: > So my initial guess was

Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

Hello, I'd guess they mean a graph = 2D representation of molecule. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-02-03 14:24 GMT+01:00 Guillaume GODIN : > Dear All, > > > > Can you explain me a little how to reproduce this

Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

-discuss] reproduce this method to obtain graph using RDkit So my initial guess was wrong. They also include a github repo, where you can exactly see how the graph is formed: https://github.com/HIPS/neural-fingerprint/blob/master/neuralfingerprint/mol_graph.py#L75 Pozdrawiam, | Best regards

Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

The graph it’s a simple adjacency matrix (square matrix) which is able to represent the connectivity of the  molecule.The element of this matrix are the atoms which can be connected. If you have a simple smile like c1c1 this means that your molecule is a ring of six atoms (6*c), and the small

Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

So my initial guess was wrong. They also include a github repo, where you can exactly see how the graph is formed: https://github.com/HIPS/neural-fingerprint/blob/master/neuralfingerprint/mol_graph.py#L75 Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-02-03