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

[Giuseppe Marco Randazzo]

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:

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Description: Adobe PDF document

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     **********************************************************************   DISCLAIMER   This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business.   ********************************************************************** ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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