Rchemcpp: Similarity measures for chemical compounds
Version 2.14.0

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.

Browse man pages Browse package API and functions Browse package files

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)
Version2.14.0
URL http://www.bioinf.jku.at/software/Rchemcpp
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rchemcpp")

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...

Functions

Rchemcpp Man page
Rchemcpp-package Man page
Rcpp_Rmolecule-class Man page
Rcpp_Rmoleculeset-class Man page
Rmolecule Man page
Rmoleculeset Man page
SDFsetToRmoleculeset Source code
createRMolecule Man page Source code
getMoleculeNamesFromSDF Man page Source code
getMoleculePropertyFromSDF Man page Source code
length,Rcpp_Rmoleculeset-method Man page
onLoad Source code
plotStruc Source code
readRmoleculeset Man page Source code
sd2gram Man page Source code
sd2gram3Dpharma Man page Source code
sd2gram3Dspectrum Man page Source code
sd2gramSpectrum Man page Source code
sd2gramSubtree Man page Source code
sdf2str Source code
sdf2strWrite Source code

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
Rchemcpp documentation built on May 20, 2017, 9:14 p.m.