Rchemcpp-package: Rchemcpp provides tools for comparing chemical compounds

Description Details Author(s) References See Also Examples


Compares sets of chemical compounds given as SD/SDF/MOL- or KCF-files and returns pairwise similarities as a matrix (gram matrix). It uses the compiled-in c++ library "chemcpp" to emulate the five chemcpp tools "sd2gram", "sd2gram3Dspectrum", "sd2gramSubtree", "sd2gram3Dpharma" and "sd2gramSpectrum". The tools are made accessible as R functions.


Package: Rchemcpp
Type: Package
Version: 1.1.1
Date: 2013-07-03
License: GPL2.1


Michael Mahr and Guenter Klambauer


(Kashima, 2004) – H. Kashima, K. Tsuda, and A. Inokuchi. Kernels for graphs. In B. Schoelkopf, K. Tsuda, and J.P. Vert, editors, Kernel Methods in Computational Biology, pages 155-170. MIT Press, 2004.

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(Ralaivola, 2005) – L. Ralaivola, S. J. Swamidass, H. Saigo, and P. Baldi. G raph kernels for chemical informatics. Neural Netw., 18(8):1093-1110, Sep 2005.

(Gaertner, 2003) – T. Gaertner, P. Flach, and S. Wrobel. On graph kernels: hardness results and efficient alternatives. In B. Schoelkopf and M. Warmuth, editors, Proceedings of the Sixteenth Annual Conference on Computational Learning Theory and the Seventh Annual Workshop on Kernel Machines, volume 2777 of Lecture Notes in Computer Science, pages 129-143, Heidelberg, 2003.

(Mahe, 2006a) – P. Mahe and J.-P. Vert. Graph kernels based on tree patterns for molecules. Technical Report, HAL:ccsd-00095488, Ecoles des Mines de Paris, September 2006.

(Mahe, 2006b) – P. Mahe, L. Ralaivola, V. Stoven, and J.-P. Vert. The pharmacophore kernel for virtual screening with support vector machines. Technical Report, HAL:ccsd-00020066, Ecole des Mines de Paris, March 2006.

(Leslie, 2002) – C. Leslie, E. Eskin, and W.S. Noble. The spectrum kernel: a string kernel for SVM protein clas- sification. In Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Kevin Lauerdale, and Teri E. Klein, editors, Proceedings of the Pacific Symposium on Biocomputing 2002, pages 564-575. World Scientific, 2002.

(Ramon, 2003) – J. Ramon and T. Gaertner. Expressivity versus efficiency of graph kernels. In T. Washio and L. De Raedt, editors, Proceedings of the First International Workshop on Mining Graphs, Trees and Sequences, pages 65-74, 2003.

See Also

sd2gram sd2gram3Dpharma sd2gramSpectrum sd2gram3Dspectrum sd2gramSubtree


sdfolder <- system.file("extdata",package="Rchemcpp")

sdf <- list.files(sdfolder,full.names=TRUE,pattern="small")
K1 <- sd2gram(sdf)
K2 <- sd2gramSpectrum(sdf)
K3 <- sd2gramSubtree(sdf)

sdf_tiny <- list.files(sdfolder,full.names=TRUE,pattern="tiny")
K3 <- sd2gram3Dspectrum(sdf_tiny)
K4 <- sd2gram3Dpharma(sdf_tiny)

Rchemcpp documentation built on Nov. 1, 2018, 2:34 a.m.