Interface to the 'CDK' Libraries

Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.


v3.4.7 - minor update to comply with CRAN policy. Minimum Java 8 required; fix an issue where unittests were writing to system files.

v3.3.5 - update to work with CDK 1.5.13 with the new Depiction module

v2.9 - Updated to the new package structure where the CDK libs are removed. As a result, this package now depends on the rcdklibs package

v2.8.1 - Fixed typos in the docs

v2.8 - Updated code to provide accessors for atoms and bonds of a molecule. Also provide methods to access atom and bond properties. Currently, setters for these objects are not provided

v2.7 - Removed support for JChemPaint due to it being in flux at this point. Also removed support for viewing tables of 3D structures. Restructured the descriptor functions to utilize descriptor names and i general make descriptor calculations more R-like

Reference manual

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3.6.0 by Zachary Charlop-Powers, 3 months ago

Browse source code at

Authors: Rajarshi Guha [aut, cph] , Zachary Charlop-Powers [cre] , Emma Schymanski [ctb]

Documentation:   PDF Manual  

Task views: Chemometrics and Computational Physics

LGPL license

Imports fingerprint, rJava, methods, png, iterators, itertools

Depends on rcdklibs

Suggests xtable, RUnit, knitr, rmarkdown, devtools

System requirements: Java JDK 8 or higher

Imported by MetaDBparse, RxnSim, chemmodlab.

Suggested by webchem.

See at CRAN