Rchemcpp: Similarity measures for chemical compounds

The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rchemcpp")
AuthorMichael Mahr, Guenter Klambauer
Bioconductor views Bioinformatics CellBasedAssays Clustering DataImport Infrastructure MicrotitrePlateAssay Proteomics Software Visualization
Date of publicationNone
MaintainerGuenter Klambauer <klambauer@bioinf.jku.at>
LicenseGPL (>= 2.1)
Version2.12.0
http://www.bioinf.jku.at/software/Rchemcpp

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/getMoleculeNamesFromSDF.R R/methods.R R/roxygen.R R/sd2gram.R R/sd2gram3Dpharma.R R/sd2gram3Dspectrum.R R/sd2gramSpectrum.R R/sd2gramSubtree.R R/utility.R R/zzz.R
build
build/vignette.rds
cleanup
inst
inst/CITATION
inst/chemcpp
inst/chemcpp/data
inst/chemcpp/data/elements.csv
inst/chemcpp/data/gramAtoms.ad5.dotproduct.csv
inst/chemcpp/data/gramAtoms.ad5.gaussian.csv
inst/chemcpp/data/gramAtoms.ad5.polynomial.csv
inst/chemcpp/data/gramAtoms.binary.csv
inst/chemcpp/data/gramAtoms.cren.dotproduct.csv
inst/chemcpp/data/gramAtoms.cren.gaussian.csv
inst/chemcpp/data/gramAtoms.cren.polynomial.csv
inst/chemcpp/data/gramAtoms.expert.csv
inst/chemcpp/data/gramAtoms.kashima.csv
inst/chemcpp/data/gramBonds.csv
inst/chemcpp/data/gramKeggAtoms.binary.csv
inst/chemcpp/data/gramKeggAtoms.kashima.csv
inst/chemcpp/data/keggatoms.csv
inst/chemcpp/data/toto.csv
inst/doc
inst/doc/Rchemcpp.R
inst/doc/Rchemcpp.Rnw
inst/doc/Rchemcpp.pdf
inst/extdata
inst/extdata/Mohr.sdf
inst/extdata/mutag.sdf
inst/extdata/mutag_small.sdf
inst/extdata/mutag_tiny.sdf
inst/scripts
inst/scripts/testing.R
man
man/Rchemcpp-package.Rd man/Rcpp_Rmolecule-class.Rd man/Rcpp_Rmoleculeset-class.Rd man/createRMolecule.Rd man/getMoleculeNamesFromSDF.Rd man/getMoleculePropertyFromSDF.Rd man/readRmoleculeset.Rd man/sd2gram.Rd man/sd2gram3Dpharma.Rd man/sd2gram3Dspectrum.Rd man/sd2gramSpectrum.Rd man/sd2gramSubtree.Rd
src
src/Makevars
src/Makevars.win
src/Relements.cpp
src/Relements.h
src/Rmolecule.cpp
src/Rmolecule.h
src/Rmoleculeset.cpp
src/Rmoleculeset.h
src/chemcpp
src/chemcpp/src
src/chemcpp/src/Makefile
src/chemcpp/src/atom.cpp
src/chemcpp/src/atom.h
src/chemcpp/src/bond.cpp
src/chemcpp/src/bond.h
src/chemcpp/src/cerror.cpp
src/chemcpp/src/cerror.h
src/chemcpp/src/chemcpp.cpp
src/chemcpp/src/constant.cpp
src/chemcpp/src/constant.h
src/chemcpp/src/datacontainer.cpp
src/chemcpp/src/datacontainer.h
src/chemcpp/src/descriptor.cpp
src/chemcpp/src/descriptor.h
src/chemcpp/src/elements.cpp
src/chemcpp/src/elements.h
src/chemcpp/src/jlpioutils.cpp
src/chemcpp/src/jlpioutils.h
src/chemcpp/src/kcfmolecule.cpp
src/chemcpp/src/kcfmolecule.h
src/chemcpp/src/molecule.cpp
src/chemcpp/src/molecule.h
src/chemcpp/src/moleculeset.cpp
src/chemcpp/src/moleculeset.h
src/chemcpp/src/moleculeutils.cpp
src/chemcpp/src/moleculeutils.h
src/chemcpp/src/node.cpp
src/chemcpp/src/node.h
src/chemcpp/src/ring.cpp
src/chemcpp/src/ring.h
src/chemcpp/src/stringutils.cpp
src/chemcpp/src/stringutils.h
src/spectrum3Dhelper.cpp
src/spectrum3Dhelper.h
src/spectrumhelper.cpp
src/spectrumhelper.h
src/subtreehelper.cpp
src/subtreehelper.h
vignettes
vignettes/Figures
vignettes/Figures/productgraph.png
vignettes/Rchemcpp.Rnw
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/literature.bib
vignettes/natbib.bst
vignettes/natbib.sty

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