Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
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Authors: Rajarshi Guha
Title: Chemical Informatics Functionality in R
Abstract: The flexibility and scope of the R programming environment has made it a popular choice for statistical modeling and scientific prototyping in a number of fields. In the field of chemistry, R provides several tools for a variety of problems related to statistical modeling of chemical information. However, one aspect common to these tools is that they do not have direct access to the information that is available from chemical structures, such as contained in molecular descriptors.

We describe the rcdk package that provides the R user with access to the CDK, a Java framework for cheminformatics. As a result, it is possible to read in a variety of molecular formats, calculate molecular descriptors and evaluate fingerprints. In addition, we describe the rpubchem that will allow access to the data in PubChem, a public repository of molecular structures and associated assay data for approximately 8 million compounds. Currently, the package allows access to structural information as well as some simple molecular properties from PubChem. In addition the package allows access to bio-assay data from the PubChem FTP servers.

Page views:: 14750. Submitted: 2006-09-25. Published: 2007-01-10.
Paper: Chemical Informatics Functionality in R     Download PDF (Downloads: 17196)
Supplements: Data files Download (Downloads: 2081; 493KB)
rcdk_2.6.1.tar.gz: R source package Download (Downloads: 2067; 14MB)
rpubchem_1.4.tar.gz: R source package Download (Downloads: 1951; 6KB) v18i05.R: R example code from the paper Download (Downloads: 1966; 1KB)

DOI: 10.18637/jss.v018.i05

This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.