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 14:35 GMT+01:00 Giuseppe Marco Randazzo <gmranda...@gmail.com>:
> 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 c1ccccc1 this means that your molecule is
> a ring of six atoms (6*c), and the small letter “c” means that your atom is
> of aromatic type. thus you can write
> your adjacency matrix in this manner:
>
>
>
> Adjacency matrix:
>
>
> c1 c2 c3 c4 c5 c6
> c1 0 1 0 0 0 1
> c2 1 0 1 0 0 0
> c3 0 1 0 1 0 0
> c4 0 0 1 0 1 0
> c5 0 0 0 1 0 1
> c6 1 0 0 0 1 0
>
> 1 means that there is a bond between two atoms.
>
> That’s it.
>
> Marco
>
>
> On 03 Feb 2016, at 14:24, Guillaume GODIN <guillaume.go...@firmenich.com>
> wrote:
>
> Dear All,
>
> Can you explain me a little how to reproduce this paper experimental
> process:http://www.broadinstitute.org/~jbloom/smrc/neural-fingerprints.pdf
> page 5 using RDKit.
>
> Look like they tweak RDKit:
>
> From page 5: “Experimental setup:
> 1 Our pipeline takes as input the SMILES [30] string encoding of each
> molecule, which is then converted into a graph using RDKit [20].
> 2 We also used RDKit to produce the extended circular fingerprints used in
> the baseline.
> 3 Hydrogen atoms were treated implicitly.
>
> In our convolutional networks, the initial atom and bond features were
> chosen to be similar to those used by ECFP: Initial atom features
> concatenated a one-hot encoding of the atom’s element, its degree, the
> number of attached hydrogen atoms, and the implicit valence, and an
> aromaticity indicator.
> The bond features were a concatenation of whether the bond type was
> single, double, triple, or aromatic, whether the bond was conjugated, and
> whether the bond was part of a ring.”
>
> My question: I don’t see how to obtain the graph from the smile.
>
> Best regards,
>
> *Dr. Guillaume GODIN*
> Project Manager
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645
> MOBILE +41 (0)79 536 1039
> *Firmenich SA*
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
>
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