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1. Introduction
2. Molecules In A Computer

2.1 Representing Molecules
2.2 Analyzing Molecules

2.2.1 Cycles
2.2.2 Bond type, bond order, and aromaticity
2.2.3 Symmetry
2.2.4 Canonical Labeling
2.2.5 Chirality

2.3 Representing Reactions
2.4 Depictions

3. SMILES - A Simplified Chemical Language

3.1 Canonicalization
3.2 SMILES Specification Rules

3.2.1 Atoms
3.2.2 Bonds
3.2.3 Branches
3.2.4 Cyclic Structures
3.2.5 Disconnected Structures

3.3 Isomeric SMILES

3.3.1 Isotopic Specification
3.3.2 Configuration Around Double Bonds
3.3.3 Configuration Around Tetrahedral Centers
3.3.4 General Chiral Specification

3.4 SMILES Conventions

3.4.1 Hydrogens
3.4.2 Aromaticity
3.4.3 Aromatic Nitrogen Compounds
3.4.4 Bonding Conventions
3.4.5 Tautomers

3.5 Extensions for Reactions

3.5.1 Reaction Atom Maps
3.5.2 Hydrogens
3.6 Acknowledgments

4. SMARTS

4.1 Atomic Primitives
4.2 Bond Primitives
4.3 Logical Operators
4.4 Recursive SMARTS
4.5 Component-level grouping of SMARTS
4.6 Reaction Queries
4.7 SMARTS Versus SMILES
4.8 Efficiency Considerations
4.9 Examples

5. SMIRKS - A Reaction Transform Language

5.1 Description
5.2 Representation
5.3 Transform Grammar
5.4 Examples

6. Fingerprints- Screening and Similarity

6.1 A Brief History of Screening Large Databases

6.1.1 Structural Keys
6.1.2 Fingerprints
6.1.3 Variable-sized Fingerprints
6.1.4 In-memory Screening

6.2 Fingerprints and Reactions

6.2.1 Structural Reaction Fingerprints
6.2.2 Reaction Difference Fingerprints

6.3 Similarity Measures
6.3.1 Tversky index
6.3.2 User-Defined and Named Similarity Indexes

7. THOR - Chemical Database System

7.1 Hash Table
7.2 Servers and Clients
7.3 Identifiers
7.4 The THOR Data Tree
7.5 Datatypes

7.5.1 Creating Datatypes
7.5.2 Standardization

7.6 Database Anatomy
7.7 Database Files
7.8 Reactions in THOR

8. Merlin - Exploratory Data Analysis Program

8.1 In-Memory Searching
8.2 Servers and Clients
8.3 Pools
8.4 Columns and Cells
8.5 Column-creation Functions
8.6 Hitlists