Mike Marchywka's post mentioned a CRAN package, "rpubchem",
missed by my search for "chemical formula". A further search for
"chemical" and "chemistry" still missed it. "compound" found it.
Adding "compounds" and combining them with "union" produced a list of
564 links in 219 packages; 7 of the help pages were for "rpubchem".
The package with the most matches is "seacarb" (seawater carbonate
chemistry with R: 21 matches), followed by "CHNOSZ", previously
mentioned (19 matches). " rpubchem" is the 22nd package on this list (5
matches, with a max score of 32, less than the max score of 2 other
packages with 5 matches).
Spencer
On 12/26/2010 7:36 PM, Bryan Hanson wrote:
Hi David & others...
I did find the function you recommended, plus, it's even easier (but a
little hidden in the doc): >element(form, "mass"). But, this uses the
atomic masses from the periodic table, which are weighted averages of
the isotopes of each element. What I'm doing actually involves mass
spectrometry, so I need the isotope masses, which are integers (think
12C, 13C, 14C, but the periodic table says 12.011 reflecting the
relative abundances). I used Gabor's solution and got my little
function humming. Plus, I have several things to read through from
the various recommendations.
Thanks again, Bryan
On Dec 26, 2010, at 10:21 PM, David Winsemius wrote:
On Dec 26, 2010, at 8:28 PM, Bryan Hanson wrote:
Thanks Spencer, I'll definitely have a look at this package and it's
vignettes. I believe I have looked at it before, but didn't catch
it on this particular search. Bryan
Using the thermo list that the makeup function accesses to get its
valid atomic symbols one can arrive at the the answer you posited
would be too difficult in you first posting, the atomic weight from
the formulae:
> str(thermo$element)
'data.frame': 130 obs. of 6 variables:
$ element: chr "Z" "O" "H" "He" ...
$ state : chr "aq" "gas" "gas" "gas" ...
$ source : chr "CWM89" "CWM89" "CWM89" "CWM89" ...
$ mass : num 0 16 1.01 4 20.18 ...
$ s : num -15.6 49 31.2 30.2 35 ...
$ n : int 1 2 2 1 1 1 1 1 2 2 ...
patts <- paste("^", rownames(makeup(form)), "$", sep="")
makuform<- makeup(form)
makuform$amass <- sapply(patts, function(x) {return( thermo$element[
grep(x, thermo$element[[1]])[1], "mass"])} )
sum(makuform$amass *makuform$count)
# [1] 167.0457
On Dec 26, 2010, at 8:16 PM, Spencer Graves wrote:
p.s. help(pac=CHNOSZ) reveals that this package has 3 vignettes.
I have not looked at these vignettes, but most vignettes provide
excellent introductions (though rarely with complete coverage) of
important capabilities of the package. (The 'sos' package includes
a vignette, which exposes more capabilities than the example below.)
######################
Have you considered the 'CHNOSZ' package?
makeup("C5H11BrO" )
count
C 5
H 11
Br 1
O 1
I found this using the 'sos' package as follows:
library(sos)
cf <- ???'chemical formula'
found 21 matches; retrieving 2 pages
cf
The print method for "cf" opened the results in a web browser,
which showed that the "CHNOSZ" package had 14 of these 11 matches,
and the other 7 were in 7 different packages. Moreover, the
"CHNOSZ" package is devoted to "Chemical Thermodynamics and
Activity Diagrams" and provides many more capabilities that might
interest you.
Hope this helps.
Spencer
On 12/26/2010 5:01 PM, Bryan Hanson wrote:
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 <han...@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
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
