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Table 4 A selection of key CDK modules with major changes

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

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
  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