CDK Workshop 2009 Intro Course Material

Contents

Bibliography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2.1 Binaries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.2 Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.2.1 Git. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.2.2 Compiling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52.3 Debian GNU/Linux & Ubuntu. . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Writing CDK Applications6

3.1 A (Very) Basic Java Application. . . . . . . . . . . . . . . . . . . . . . . . . 63.2 BeanShell. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63.3 Groovy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73.3.1 Closures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83.4 Other Languages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93.4.1 Bioclipse. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103.4.2 Cinfony. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103.4.3 R. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

4 Documentation11

4.1 JavaDoc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.2 Other Sources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Bibliography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5 Atoms, Bonds and Molecules12

5.1 Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125.1.1 IElement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125.1.2 IIsotope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.1.3 IAtomType. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.2 Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.3 Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145.3.1 Iterating of atoms and bonds. . . . . . . . . . . . . . . . . . . . . . . 15

6 Graph Properties17

6.1 Partitioning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176.2 Spanning Tree. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

7 Missing Information19

7.1 Reconnecting Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197.2 Missing Hydrogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207.2.1 Implicit Hydrogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

8 Input/Output22

8.1 File Format Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228.2 Example: Downloading Domoic Acid from PubChem. . . . . . . . . . . . . . 23Bibliography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

9 Keyword List24

2

Chapter 1

Preface

This book is written to help people start developing cheminformatics software using theChemistry Development Kit, an open source cheminformatics toolkit written in Java [1,2].This book is written for version 1.2.1 and all code snippets in this book are compiled againstthis version when the book is build.Each snippet is actually a small Groovy script, BeanShell script, or Java Application, andall code is compiled and run. Some sections show the output of the code snippets. Each codesnippet has an orange bar which points to name of the script or application from which thesnippet was derived.

Bibliography

[1] C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, and E. Willighagen. Thechemistry development kit (cdk): an open-source java library for chemo- and bioinformat-ics.

J Chem Inf Comput Sci

, 43(2):493–500, 2003.[2] Christoph Steinbeck, Christian Hoppe, Stefan Kuhn, Matteo Floris, Rajarshi Guha, andEgon L. Willighagen. Recent developments of the chemistry development kit (cdk) - anopen-source java library for chemo- and bioinformatics.

Current Pharmaceutical Design

,pages 2111–2120, June 2006.3