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OpenSMILES Specification

DRAFT: 2007-11-13

Table of Contents

1. Introduction

1.1 Purpose

1.2 Motivation

1.3 Audience

1.4 What is a Molecule? The Valence Model of Chemistry

2. Formal Grammar

2.1 Syntax versus Semantics

2.2 Grammar

3. Reading SMILES

3.1 Atoms

3.1.1 Atomic Symbol

3.1.2 Hydrogens

3.1.3 Charge

3.1.4 Isotopes

3.1.5 "Organic Subset" Elements

3.1.6 The Wildcard '*' Atomic Symbol

3.1.7 Atom Class

3.2 Bonds

3.3 Branches

3.4 Rings

3.5 Aromaticity

3.6 More about Hydrogen

3.7 Disconnected Structures

3.8 Other Uses of Ring Numbers and Dot Bond

3.9 Stereochemistry

3.9.1 Scope of Stereochemistry in SMILES

3.9.2 Tetrahedral Centers

3.9.3 Cis/Trans configuration of Double Bonds

3.9.4 Tetrahedral Allene-like Systems

3.9.5 Partial Stereochemistry

3.9.6 Other Chiral Configurations

3.10 Parsing Termination

3.11 Programming Practices

4. Writing SMILES: Normalizations

4.1 What is Normalization?

4.2 No Normalization

4.3 Standard Form

4.3.1 Atoms

4.3.2 Bonds

4.3.3 Cycles

4.3.4 Starting Atom and Branches

4.3.5 Aromaticity

4.3.6 Chirality

4.4 Canonical SMILES

4.5 SMILES Files

5. Nonstandard Forms of SMILES

6. Proposed Extensions

6.1 External R-Groups

6.2 Polymers and Crystals

6.3 '@' for Cis/Trans around Double Bonds

6.5 Radicals

6.6 Twisted SMILES

7. APPENDIX 1: References and Citations

7.1 Groups

7.2 Documentation

7.3 Toolkits

7.3 Some Key Scientific Papers

7.5 Molecule Editors that can produce SMILES


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