R/utils.R

In nanxstats/tidychem: Tidy Chemical Data

#' Generate path to the example data.
#'
#' @param file Filename of the example dataset in the tidychem package,
#' under the `inst/extdata/` directory.
#'
#' @export tidychem_example

tidychem_example <- function(file) {
  system.file("extdata", file, package = "tidychem", mustWork = TRUE)
}

#' Get RDKit version.
#'
#' @export rdkit_version
#'
#' @examplesIf is_installed_rdkit()
#' rdkit_version()
rdkit_version <- function() {
  rdkit$rdBase$rdkitVersion
}

# count the number of molecules in the SDF text block
count_mol_sdf <- function(x) str_count(x, pattern = "M  END")

# parse molecule from a SMILES string
mol_from_smiles <- function(x) rdkit$Chem$MolFromSmiles(as.character(x))

# stylize cli output
#' @importFrom crayon green
cat_sys <- function(...) cat(crayon::green(paste0(...), sep = ""))

# setdiff without worrying about x, y order
set_diff <- function(x, y) setdiff(union(x, y), intersect(x, y))

# String operations
str_count <- function(x, pattern) {
  loc <- gregexpr(pattern = pattern, text = x, fixed = TRUE)
  sapply(loc, function(x) length(attr(x, "match.length")))
}