The document summarizes a presentation given at the 6th RDKit User Group Meeting in Cambridge, UK in September 2018. It discusses DeepSMILES, a modification of the SMILES notation for chemical structures that is designed for use in machine learning applications. DeepSMILES was presented by Noel O'Boyle and Andrew Dalke. The document provides examples of DeepSMILES notation for ring closures, branches, and installation instructions.

1. 6th RDKit UGM Cambridge UK Sep 2018
DeepSMILES
Noel O’Boyle
Andrew Dalke
Gómez-Bombarelli et al. Automatic Chemical Design Using
a Data-Driven Continuous Representation of Molecules.
ACS Central Science 2018, 4, 268–276.
c1ccccc1
c1ccccc1

2. 6th RDKit UGM Cambridge UK Sep 2018
DeepSMILES
Noel O’Boyle
Andrew Dalke
Gómez-Bombarelli et al. Automatic Chemical Design Using
a Data-Driven Continuous Representation of Molecules.
ACS Central Science 2018, 4, 268–276.
c1ccccc1
c1ccccc1 c1ccccc2c1ccc(cc1c1ccccc1(C)C
Invalid syntax

3. 6th RDKit UGM Cambridge UK Sep 2018
c1ccccc1
c1ccccc1 c1ccccc2c1ccc(cc1c1ccccc1(C)C
Invalid syntax
DeepSMILES
SMILES input
DeepSMILES

4. 6th RDKit UGM Cambridge UK Sep 2018
c1ccccc1
c1ccccc1 c1ccccc1(C)C
DeepSMILES
SMILES input
DeepSMILES

5. 6th RDKit UGM Cambridge UK Sep 2018
RING CLOSURE Notation
SMILES ….c2ccccc2 ….c3ccccc3…c1ccccc1

6. 6th RDKit UGM Cambridge UK Sep 2018
RING CLOSURE Notation
DeepSMILES
SMILES
…cccccc6
….c2ccccc2 ….c3ccccc3…c1ccccc1

7. 6th RDKit UGM Cambridge UK Sep 2018
Branch NOTATION
DeepSMILES
SMILES
c1cccC=O)Cl))cc1
c1ccc(C(=O)Cl)cc1
=O
C
c
c
c
c1
Cl
C
c
c
c
c1
c1
c
c
c
c
c1
SH Eisman. A Polish-type notation for chemical structures. J. Chem. Doc. 1964, 4, 186.
H Hiz. A linearization of chemical graphs. J. Chem. Doc. 1964, 4, 173.

8. 6th RDKit UGM Cambridge UK Sep 2018
DeepSMILES
Noel O’Boyle
Andrew Dalke
O'Boyle, Noel; Dalke, Andrew (2018): DeepSMILES: An Adaptation of
SMILES for Use in Machine-Learning of Chemical Structures. ChemRxiv.
Preprint.
https://doi.org/10.26434/chemrxiv.7097960.v1
pip install deepsmiles
https://github.com/nextmovesoftware/deepsmiles