Contents

1. Introduction

2. Generating a Molecular Structure

2.1. How Klotho Describes Molecules

2.2. Coding Your First Molecule

2.2.1. Preliminary Considerations

2.2.2. Specifying the Architecture of the Molecule

2.2.3. Choosing a Path through the Molecule

2.2.4. Describing the Groups and Atoms in the Molecule

2.2.5. Specifying the Bond Types

2.2.6. Some Config Rules for Ethanol

2.2.7. Checking the Rule by Studying the Output

2.2.8. Summary of Config Rule Writing

2.3. Specifying the Atom Numbering

2.4. Specifying the Orientation around an Atom or Group (Local Chirality)

2.5. Nesting Moieties within Other Moieties

2.6. Specifying Geometric Isomerism

2.7. Building Rings and Ring Systems

2.8. Building Big Molecules from Little Ones

2.8.1. Naming Molecules and Substituents in Klotho

2.8.2. Building from a Model Molecule or Substituent: Model/Diff

2.8.3. Building with Larger Substituent Groups: Substituent/ Linkage

2.8.4. An Old Locution: Sides/Center

2.9. How to Read the Low-Level Language

2.9.1 A Simple Example

2.9.2 Geometric Isomerism

2.9.3 Chirality

2.10. Debugging Config Rules

3. How to Search for a Molecule, Substructure, or Class of Molecules

4. Reference Section

4.1. Using Klotho

4.1.1. Checking a Config Rule via Direct Login

4.1.2. Using the Web Interface

4.2. Miscellaneous Examples

4.2.1. Different Architectures

4.2.2. Different Locutions

4.2.3. Different bond types

4.2.4. Specifying Stereospecificity using cis/trans locution

4.2.5. Specifying Stereospecificity around Chiral Atoms

4.2.6. Known Bugs and Desiderata

4.3. List of Terminals

4.4. List of Substituents

4.5. List of Molecules