Matthew, I would try first looking at the Rcdk package. From it sound like what you want to do they already have some very efficient code to that. If you don't want all of CDK then you could try Rdisop from Bioconductor. The package will take a formula and give you it's mass. It won't do a matrix but just 'sapply' the function.
http://cran.r-project.org/web/packages/rcdk/index.html http://www.bioconductor.org/packages/2.6/bioc/vignettes/Rdisop/inst/doc/Rdisop.pdf ## code from above link## library(Rdisop) > molecule <- getMolecule("C2H5OH") > getFormula(molecule) [1] "C2H6O" > getMass(molecule) [1] 46.04186
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