Merge pull request #124 from zachcp/crancompat

Crancompat

Author: rajarshi

rcdk/NAMESPACE

@@ -7,6 +7,7 @@ export(convert.implicit.to.explicit)
 export(copy.image.to.clipboard)
 export(do.aromaticity)
 export(do.isotopes)
+export(do.typing)
 export(eval.atomic.desc)
 export(eval.desc)
 export(generate.2d.coordinates)

rcdk/R/deprecated_functions.R

@@ -0,0 +1,27 @@
+################################################################################
+#' Deprecated functions in the rcdk package.
+#' 
+#' These functions are provided for compatibility with older version of
+#' the phyloseq package.  They may eventually be completely
+#' removed.
+#' 
+#' @usage deprecated_rcdk_function(x, value, ...)
+#' @rdname rcdk-deprecated
+#' @name rcdk-deprecated
+#' @param x For assignment operators, the object that will undergo a replacement
+#'  (object inside parenthesis).
+#' @param value For assignment operators, the value to replace with 
+#'  (the right side of the assignment).
+#' @param ... For functions other than assignment operators, 
+#'  parameters to be passed to the modern version of the function (see table).
+#' @docType package
+#' @export do.typing
+#' @aliases deprecated_rcdk_function do.typing
+#' @details
+#' \tabular{rl}{
+#'   \code{do.typing} \tab now a synonym for \code{\link{set.atom.types}}\cr
+#' }
+#'
+deprecated_rcdk_function <- function(x, value, ...){return(NULL)}
+do.typing <- function(...){.Deprecated("set.atom.types", package="rcdk");return(set.atom.types(...))}
+################################################################################