Hello,
I'd guess they mean a graph = 2D representation of molecule.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2016-02-03 14:24 GMT+01:00 Guillaume GODIN <[email protected]>:
> 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
>
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