The Rchemcpp package is part of the CRAN project. The functionality of Chemcpp (http://chemcpp.sourceforge.net/html/index.html) is provided in R, that is the computation of similarities between molecules by kernel functions.
The following kernels are implemented: the marginalized graph kernel between labeled graphs, extensions of the marginalized kernel, Tanimoto kernels, graph kernels based on tree patterns, kernels based on pharmacophores for 3D structure of molecules.
Input are molecules provided in the SDF format (MOL format) and output is a numeric kernel matrix. This kernel matrix easily be used in R for clustering and prediction tasks, like the prediction of toxicity or biological activity of a given molecule.
- Changes to previous version:
Improved documentation and data handling.
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