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This is the development version of fmcsR; for the stable release version, see fmcsR.

Mismatch Tolerant Maximum Common Substructure Searching

Bioconductor version: Development (3.19)

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

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

Citation (from within R, enter citation("fmcsR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

fmcsR HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), ChemmineR, methods
Imports RUnit, methods, ChemmineR, BiocGenerics, parallel
System Requirements
URL https://github.com/girke-lab/fmcsR
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Suggests BiocStyle, knitr, knitcitations, knitrBootstrap, rmarkdown
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Imports Me chemodiv
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Follow Installation instructions to use this package in your R session.

Source Package fmcsR_1.45.0.tar.gz
Windows Binary fmcsR_1.45.0.zip
macOS Binary (x86_64) fmcsR_1.45.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/fmcsR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fmcsR
Bioc Package Browser https://code.bioconductor.org/browse/fmcsR/
Package Short Url https://bioconductor.org/packages/fmcsR/
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