[R] Parsing a Simple Chemical Formula

Gabor Grothendieck ggrothendieck at gmail.com
Mon Dec 27 01:26:33 CET 2010

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.


DF <- strapply(form,
   ~ 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

Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

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