R help - Jan 2012 - Need to Write a Code that can find the molecular weight of various compounds

Hi!

Just started working at a lab and have only minimal experience with R.

I was wondering if there was a way to write a code that would intake a data
set of chemical compounds (ex: H2O, CH3)
and be able to give an output column of the molecular weight?

I tried some really basic coding to try to work with a being a matrix of
data with the assigned variables.

if (A<-'H') A<-a[50,3]
else (B<-'O') B<-a[86,3]

ifelse (A=='H',A<-a[50,3],ifelse(B=='O',B<-a[86,3],0]

I was thinking to have the program read the formula and compute the output
of molecular mass by reading information off of a separate data sheet with
the individual weights of the molecules, and then output that into another
column.

Any suggestions? Thanks!

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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