The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Table 4 A selection of key CDK modules with major changes

Module	Description	Major changes	Dependencies
interfaces	Interfaces for the data models		Vecmath 1.5.2
core	Core functionality		Google Guava 17.0
standard	Common functionality
render	Graphical rendering	Redesigned to make it more modular and support Multiple widget toolkits, like AWT and SWT
isomorphism	Isomorphism and substructure searching
atomtype	Various non-core atom type schemes	Unified approach where atom typing is separated from other algorithms
ioformats	Definitions of (chemical) input/output formats
io	Readers and writers for input/output formats	The molfile reader has been rewritten and supports atom types defined in the specification	XPP3 1.1.4c
iordf	Stores data models as in the Resource Description Framework serialization formats	New	Jena 2.7.4
inchi	IUPAC International Chemical Identifier support		JNI-InChI 0.8 [37]
libiocml	Writer for the Chemical Markup Language format		XOM 1.2.5, CMLXOM 3.1 [91]
sdg	Structure diagram generation.	Much improved overlap resolution
smiles	Reading and writing in the SMILES format	SMILES support performance and coverage is greatly improved	Beam 0.9.1 [66]
smarts	Substructure searching with the SMARTS format		Beam 0.9.1 [66]
hash	Molecular hash codes [92]
formula	Chemical formula support	New
fingerprint	Calculate fingerprints	Many new fingerprint types (see text)	Apache Commons Math 3.1.1
qsar and qsarmolecular	Molecular descriptors		XOM 1.2.5, JAMA 1.0.3 [93]
signatures	Calculation of molecular and atomic signatures		Signatures 1.1

An overview of a selection of often used CDK modules with description, dependencies on third-party libraries, and the major changes since version 1.2. Dependencies between modules are depicted in Fig. 7

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