cdkbook

Groovy Cheminformatics with the Chemistry Development Kit

Edition 2.0-5

Egon L. Willighagen PhD
Long time CDK developer

© E.L. Willighagen 2011-2019

License: CC-BY-SA 4.0 International

Warning

This book is being opensourced. This involves transforming the LaTeX source into Markdown, and updating all scripts to ensure all the automation works well. I have made good steps forward, but it will take some time for things to iron out.

Contents

  1. Introduction
  2. Cheminformatics
  3. Atoms, Bonds and Molecules
    3.1. Atoms
    3.1.1. IElement
    3.1.2. IIsotope
    3.1.3. IAtomType
    3.1.4. Coordinates
    3.2. Bonds
    3.2.1. Electron counts
    3.2.2. Bond stereochemistry
    3.3. Molecules
  4. Stereochemistry
    4.1. Stereochemistry in a flat world
    4.2. Tetrahedral chirality
  5. Salts and other disconnected structures
    5.1. Salts
    5.2. Crystals
  6. Paired and unpaired electrons
    6.1. Lone Pairs
    6.2. Unpaired electrons
  7. From IChemObject to IChemFile
    7.1. IAtomContainerSet
    7.2. IReactionSet and IRingSet
    7.3. IChemModel
    7.4. IChemSequence
    7.5. IChemFile
  8. Input/Output
    8.1. File Format Detection
    8.1.1. Custom format matchers
    8.2. Reading from Readers and InputStreams
    8.3. Customizing the Output
    8.3.1. Setting Properties
    8.4. Example: creating unit tests for atom type perception
  9. Chemistry Toolkit Rosetta
    9.1. Heavy atom counts from an SD file
    9.2. Depict a compound as an image
  10. Migration
    10.1. CDK 1.4 to 2.0
    10.1.1. Removed classes
    10.1.2. Renamed classes and methods
    10.1.3. Changed behavior
    10.1.4. Constructors that now require a builder
    10.1.5. Static methods that are no longer
    10.1.6. IsotopeFactory
    10.1.7. IFingerPrinter
    10.1.8. SMILESGenerator
    Index
    Appendix A
    A.1 CDK Atom Types
    A.2 Sybyl Atom Types