fmcsR: Mismatch Tolerant Maximum Common Substructure Searching

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.

Author
Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke
Date of publication
None
Maintainer
Thomas Girke <thomas.girke@ucr.edu>
License
Artistic-2.0
Version
1.16.0
URLs

View on Bioconductor

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

Files in this package

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