Chemistry Development Kit 1.4.0

The CDK design originated from a meeting on September 27-29 2000, Christoph Steinbeck, Egon Willighagen and Dan Gezelter met at Notre Dame University, South Bend, USA, to discuss the architecture of the package. The first actual implementation very much relied on the on the earlier work by the lab of Christoph Steinbeck and his older compchem libraries, which urgently needed a rewrite. On the flight back to Europe, a first draft of the data classes were written.

In the following years, the CDK library evolved into a fully blown open source and open development chemoinformatics package with code reaching from QSAR descriptor calculations to 2D and 3D model building. Programs like the 2D structure editor jchempaint, nmrshiftdb, a database of organic molecules and their NMR spectra, and Bioclipse are based on or use the CDK. You can learn about these and others on the page Software using CDK. 

Major Features:

1. Chemoinformatics
   • 2D Diagrams
   • • Jchempaint 2D diagram editor
     • • Edits molecules and reactions
     • Structure Diagram Layout
     • • Small library of templates
   • 3D Rendering
   • • Integration with Jmol
   • Input/Output
   • • Chemical Markup Language
     • SMILES parsing/generation
     • MDL molfile support (limited)
     • Inchi (via JNI bridge)
     • Many other readers
     • • XYZ, shelx, HIN, ghemicalmm, Mol2
     • Interface to openbabel (via command line)
     • Rule based IUPAC name parser
   • Virtual Screening
   • • Molecular, atomic and bond descriptors
     • Logp, TPSA, Rule-of-Five, many more
     • Gasteiger-Marsili charges (sigma *and* pi)
     • Interface to R and Weka for modeling
     • Path-based Fingerprinter
   • Modelling
   • • 3D model builder
     • Atom typing
     • • MM2, MMFF94, CDK-internal
     • MMFF94 force field
     • Kabsch alignment
   • Chemical Graphs
   • • Isomorphism detection
     • Maximal common substructure search
     • Substructure searching (SMARTS like)
     • Ring searches (SSSR, all rings)
   • Properties
   • • NMR prediction
   • Structure Generation
   • • Deterministic generator
     • Stochastic generators
     • • Genetic algorithm based
       • Simulated annealing based
2. Bioinformatics
   • Biojava interface
   • Protein Structures
   • • PDB reading
     • Active site detection
     • Sequence to connectivity table