Dear Rui,
Thank you for your reply.
I do have actually access to the chemical symbols: I have started to
refactor and enhance the Rpdb package, see Rpdb::elements:
https://github.com/discoleo/Rpdb
However, the regex that you have constructed is quite heavy, as it needs
to iterate through all chemical symbols (in decreasing nchar). Elements
like C, and especially O, P or S, appear late in the regex expression -
but are quite common in chemistry.
The alternative regex is (in this respect) simpler. It actually works
(once you know about the workaround).
Q: My question focused if there is anything like is.numeric, but to
parse each element of a vector.
Sincerely,
Leonard
On 10/18/2023 6:53 PM, Rui Barradas wrote:
Às 15:59 de 18/10/2023, Leonard Mada via R-help escreveu:
Dear List members,
What is the best way to test for numeric digits?
suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
# [1] NA NA NA 2 NA NA 3
The above requires the use of the suppressWarnings function. Are there
any better ways?
I was working to extract chemical elements from a formula, something
like this:
split.symbol.character = function(x, rm.digits = TRUE) {
# Perl is partly broken in R 4.3, but this works:
regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
# stringi::stri_split(x, regex = regex);
s = strsplit(x, regex, perl = TRUE);
if(rm.digits) {
s = lapply(s, function(s) {
isNotD = is.na(suppressWarnings(as.numeric(s)));
s = s[isNotD];
});
}
return(s);
}
split.symbol.character(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"))
Sincerely,
Leonard
Note:
# works:
regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
# broken in R 4.3.1
# only slightly "erroneous" with stringi::stri_split
regex = "(?<=[A-Z])(?![a-z]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
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Hello,
If you want to extract chemical elements symbols, the following might work.
It uses the periodic table in GitHub package chemr and a package stringr
function.
devtools::install_github("paleolimbot/chemr")
split_chem_elements <- function(x) {
data(pt, package = "chemr", envir = environment())
el <- pt$symbol[order(nchar(pt$symbol), decreasing = TRUE)]
pat <- paste(el, collapse = "|")
stringr::str_extract_all(x, pat)
}
mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
split_chem_elements(mol)
#> [[1]]
#> [1] "C" "Cl" "F"
#>
#> [[2]]
#> [1] "Li" "Al" "H"
#>
#> [[3]]
#> [1] "C" "Cl" "C" "O" "Al" "P" "O" "Si" "O" "Cl"
It is also possible to rewrite the function without calls to non base
packages but that will take some more work.
Hope this helps,
Rui Barradas
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