From: hanson at depauw.edu
To: ggrothendieck at gmail.com
Date: Sun, 26 Dec 2010 20:01:45 -0500
CC: r-help at stat.math.ethz.ch
Subject: Re: [R] 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
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
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:
V1 V2
1 C 5
2 H 11
3 Br 1
4 O 1
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