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
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