Parsing a Simple Chemical Formula

Well let me just say thanks and WOW!  Four great ideas, each worthy of 
study and I'll learn several things from each.  Interestingly, these 
solutions seem more general and more compact than the solutions I 
found on the 'net using python and perl.  More evidence for the power 
of R!  A big thanks to each of you!  Bryan

On Dec 26, 2010, at 7:26 PM, Gabor Grothendieck wrote:

On Sun, Dec 26, 2010 at 6:29 PM, Bryan Hanson <hanson at depauw.edu> wrote:

Hello R Folks...

I've been looking around the 'net and I see many complex solutions in
various languages to this question, but I have a pretty simple need 
(and I'm
not much good at regex).  I want to use a chemical formula as a 
function
argument.  The formula would be in "Hill order" which is to list C, 
then H,
then all other elements in alphabetical order.  My example will have 
only a
limited number of elements, few enough that one can search directly 
for each
element.  So some examples would be C5H12, or C5H12O or C5H11BrO 
(note that
for oxygen and bromine, O or Br, there is no following number 
meaning a 1 is
implied).

Let's say

form <- "C5H11BrO"

I'd like to get the count of each element, so in this case I need to 
extract
C and 5, H and 11, Br and 1, O and 1 (I want to calculate the molecular
weight by mulitplying).  Sounds pretty simple, but my experiments 
with grep
and strsplit don't immediately clue me into an obvious solution.  As 
I said,
I don't need a general solution to the problem of calculating molecular
weight from an arbitrary formula, that seems quite challenging, just 
a way
to convert "form" into a list or data frame which I can then do the 
math on.

Here's hoping this is a simple issue for more experienced R users!  
TIA,

This can be done by strapply in gsubfn.  It matches the regular
expression to the target string passing the back references (the
parenthesized portions of the regular expression) through a specified
function as successive arguments.

Thus the first arg is form, your input string.  The second arg is the
regular expression which matches an upper case letter optionally
followed by lower case letters and all that is optionally followed by
digits.  The third arg is a function shown in a formula
representation. strapply passes the back references (i.e. the portions
within parentheses) to the function as the two arguments.  Finally
simplify is another function in formula notation which turns the
result into a matrix and then a data frame.  Finally we make the
second column of the data frame numeric.

library(gsubfn)

DF <- strapply(form,
  "([A-Z][a-z]*)(\\d*)",
  ~ c(..1, if (nchar(..2)) ..2 else 1),
  simplify = ~ as.data.frame(t(matrix(..1, 2)), stringsAsFactors = 
FALSE))
DF[[2]] <- as.numeric(DF[[2]])

DF looks like this:

DF

 V1 V2
1  C  5
2  H 11
3 Br  1
4  O  1



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