The package can be installed directly from GitHub:
if( !require(devtools) ) install.packages("devtools")
devtools::install_github("ArtemSokolov/morgancpp")Once installed, the package can be loaded through the standard library() interface:
library( morgancpp )The package works with Morgan fingerprints specified as hexadecimal strings of length 512. An example set of 100,000 fingerprints is included with the package. It can be loaded as follows:
fn <- system.file( "examples/example1.txt.gz", package="morgancpp" )
fps <- scan( fn, what=character() )
# [1] "020000000000000000000100...
# [2] "020004000000000000808101...
# [3] "200000000000000000000000...The tanimoto similarity can be computed directly on hexadecimal strings:
tanimoto( fps[1], fps[1] ) # 1
tanimoto( fps[1], fps[2] ) # 0.1627907
tanimoto( fps[1], "FFF" )
# Error in tanimoto(fps[1], "FFF") : Input hex string must be of length 512However, doing this for a large number of fingerprints will be slow. Instead, we can initialize the c++ data structure to store fingerprints in an effcient manner and query that structure for similarity:
m <- MorganFPS$new( fps )
# C++ object <0x559fa18f2c40> of class 'MorganFPS' <0x559fa484d570>
object.size(fps)
57467704 bytes
m$size()
[1] 25600000Similarity between fingerprints in the structure can be computed by indexing:
m$tanimoto( 1, 1 ) # 1
m$tanimoto( 1, 2 ) # 0.1627907The entire similarity profile against all other fingerprints in the collection can be obtained for compounds already in the collection (specified as index i) or new external compounds (specified as hexadecimal strings):
res1 <- m$tanimoto_all( 1 ) # Compound 1 against all 100,000 fingerprints
res2 <- m$tanimoto_ext( fps[1] ) # External compound against all 100,000 fingerprintsObtaining additional information about functionality of the package can be done through the standard R interface:
# All available functions
library( help = morgancpp )
# Help for individual functions / data structures
?morgancpp::tanimoto
?morgancpp::MorganFPS
# C++ docstrings providing full signatures of each method
morgancpp::MorganFPS
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