fmcsR: Mismatch Tolerant Maximum Common Substructure Searching
Version 1.18.0

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

Browse man pages Browse package API and functions Browse package files

AuthorYan Wang, Tyler Backman, Kevin Horan, Thomas Girke
Bioconductor views BiomedicalInformatics CellBasedAssays Cheminformatics Clustering DataImport Infrastructure MicrotitrePlateAssay Pharmacogenetics Pharmacogenomics Proteomics Visualization
Date of publicationNone
MaintainerThomas Girke <thomas.girke@ucr.edu>
LicenseArtistic-2.0
Version1.18.0
URL https://github.com/girke-lab/fmcsR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("fmcsR")

Man pages

fmcs: Flexible MCS (FMCS) Finder
fmcsBatch: FMCS Search Function
fmcsR-package: A FMCS solver package.
fmcstest: SD file stored in 'SDFset' object
mcs2sdfset: Return MCS object as SDFset
MCS-class: Class '"MCS"'
plotMCS: Plot MCS

Functions

MCS-class Man page
[[,MCS-method Man page
coerce,list,MCS-method Man page
fmcs Man page Source code
fmcsBatch Man page Source code
fmcsR Man page
fmcsR-package Man page
fmcstest Man page
mcs1 Man page
mcs1,MCS-method Man page
mcs2 Man page
mcs2,MCS-method Man page
mcs2sdfset Man page Source code
plotMCS Man page Source code
show,MCS-method Man page
stats Man page
stats,MCS-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/fmcs.R
R/fmcsBatch.R
README
README.md
autogen.sh
build
build/vignette.rds
config.h
config.h.in
configure
configure.ac
data
data/fmcstest.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/fmcsR.R
inst/doc/fmcsR.Rmd
inst/doc/fmcsR.html
inst/unitTests
inst/unitTests/test_main.R
man
man/MCS-class.Rd
man/fmcs.Rd
man/fmcsBatch.Rd
man/fmcsR-package.Rd
man/fmcstest.Rd
man/mcs2sdfset.Rd
man/plotMCS.Rd
src
src/MCS.cpp
src/MCS.h
src/MCSCompound.cpp
src/MCSCompound.h
src/MCSList.h
src/MCSMap.cpp
src/MCSMap.h
src/MCSRingDetector.cpp
src/MCSRingDetector.h
src/Makevars
src/Makevars.in
src/fmcs_R_wrap.cpp
src/util.cpp
src/util.h
vignettes
vignettes/Makefile_bootstrap
vignettes/bibtex.bib
vignettes/fmcsR.Rmd
vignettes/fmcsR.Rmd_bootstrap
vignettes/header.html
vignettes/html.template_bootstrap
vignettes/references.bib
fmcsR documentation built on May 20, 2017, 9:48 p.m.