R/utilities.R

In CDK-R/depict: Draw Beautiful Molecular Structures

#' checkJavaClass
#'
#' check if an object is of a specified JavaClass
#'
#' @param jobj Required. A Java Object
#' @param klass Required. A string defining a java class
#' @return Boolean
#' @noRd
checkJavaClass <- function(jobj, klass) {
  if (is.null(attr(jobj, 'jclass'))) stop("this is not a Java Object")

  for (kl in klass) {
    if (attr(jobj, "jclass") == kl) {
      return(TRUE)
    }
  }
  return(FALSE)
}


#' atomcontainer_list_to_jarray
#'
#'
#' @param atomcontainers list (R) of CDK AtomContainers.
#' @return a java ArrayList of AtomContainers
#' 
#' @export
#' @examples 
#' \dontrun{
#' 
#' atmcontnrs <- purrr::map(
#'      c("CCCCCC", "CCC1CCC1NC", "COCCOCCO"),
#'      parse_smiles)
#'      
#' atomcontainer_list_to_jarray(atmcontnrs)
#' 
#' }
#' 
atomcontainer_list_to_jarray <- function(atomcontainers) {
  
  new_array <-  .jnew('java.util.ArrayList')
  for (atmcntnr in as.list(atomcontainers)) {
    new_array$add(atmcntnr)
  }
  
  new_array
}