Rchemcpp: Similarity measures for chemical compounds

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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.

Author
Michael Mahr, Guenter Klambauer
Date of publication
None
Maintainer
Guenter Klambauer <klambauer@bioinf.jku.at>
License
GPL (>= 2.1)
Version
2.12.0
URLs

View on Bioconductor

Man pages

createRMolecule
createRMolecule
getMoleculeNamesFromSDF
getMoleculeNamesFromSDF - a helper function
getMoleculePropertyFromSDF
getMoleculePropertyFromSDF - a helper function
Rchemcpp-package
Rchemcpp provides tools for comparing chemical compounds
Rcpp_Rmolecule-class
Class '"Rcpp_Rmolecule"'
Rcpp_Rmoleculeset-class
Class '"Rcpp_Rmoleculeset"'
readRmoleculeset
Generating an Rmoleculeset from an SDF file
sd2gram
sd2gram - Similarity of molecules by the marginalized kernel...
sd2gram3Dpharma
sd2gram3Dpharma - Similarity of molecules by the exact...
sd2gram3Dspectrum
sd2gram3Dspectrum - Similarity of molecules by fast...
sd2gramSpectrum
sd2gramSpectrum - Similarity of molecules by walk-based graph...
sd2gramSubtree
sd2gramSubtree - Similarity of molecules by several graph...

Files in this package

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