From 1fa55bb54d6c571b5268147d7c4069f5b7bfffee Mon Sep 17 00:00:00 2001 From: Zach Charlop-Powers Date: Sat, 10 Jul 2021 17:08:33 -0400 Subject: [PATCH 1/2] add a deprecation function for do.typing --- rcdk/NAMESPACE | 1 + rcdk/R/deprecated_functions.R | 27 +++++++++++++++++++++++++++ rcdk/man/rcdk-deprecated.Rd | 31 +++++++++++++++++++++++++++++++ 3 files changed, 59 insertions(+) create mode 100644 rcdk/R/deprecated_functions.R create mode 100644 rcdk/man/rcdk-deprecated.Rd diff --git a/rcdk/NAMESPACE b/rcdk/NAMESPACE index b4a4faa15..4c976c258 100755 --- a/rcdk/NAMESPACE +++ b/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) diff --git a/rcdk/R/deprecated_functions.R b/rcdk/R/deprecated_functions.R new file mode 100644 index 000000000..4632ef0a9 --- /dev/null +++ b/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(...))} +################################################################################ \ No newline at end of file diff --git a/rcdk/man/rcdk-deprecated.Rd b/rcdk/man/rcdk-deprecated.Rd new file mode 100644 index 000000000..24a19b761 --- /dev/null +++ b/rcdk/man/rcdk-deprecated.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated_functions.R +\docType{package} +\name{rcdk-deprecated} +\alias{rcdk-deprecated} +\alias{deprecated_rcdk_function} +\alias{do.typing} +\title{Deprecated functions in the rcdk package.} +\usage{ +deprecated_rcdk_function(x, value, ...) +} +\arguments{ +\item{x}{For assignment operators, the object that will undergo a replacement +(object inside parenthesis).} + +\item{value}{For assignment operators, the value to replace with +(the right side of the assignment).} + +\item{...}{For functions other than assignment operators, +parameters to be passed to the modern version of the function (see table).} +} +\description{ +These functions are provided for compatibility with older version of +the phyloseq package. They may eventually be completely +removed. +} +\details{ +\tabular{rl}{ + \code{do.typing} \tab now a synonym for \code{\link{set.atom.types}}\cr +} +} From bbc70f777b49237649c8e9b84602df486f43ca39 Mon Sep 17 00:00:00 2001 From: Zach Charlop-Powers Date: Sat, 10 Jul 2021 17:09:17 -0400 Subject: [PATCH 2/2] update docs. --- rcdk/man/do.aromaticity.Rd | 2 +- rcdk/man/do.isotopes.Rd | 2 +- rcdk/man/get.desc.categories.Rd | 2 +- rcdk/man/get.volume.Rd | 2 +- rcdk/man/view.table.Rd | 18 ++++++++++++++++++ 5 files changed, 22 insertions(+), 4 deletions(-) create mode 100644 rcdk/man/view.table.Rd diff --git a/rcdk/man/do.aromaticity.Rd b/rcdk/man/do.aromaticity.Rd index 3572a48a3..b582a6494 100755 --- a/rcdk/man/do.aromaticity.Rd +++ b/rcdk/man/do.aromaticity.Rd @@ -4,7 +4,7 @@ \alias{do.aromaticity} \title{do.aromaticity} \usage{ -\method{do}{aromaticity}(mol) +do.aromaticity(mol) } \arguments{ \item{mol}{The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`} diff --git a/rcdk/man/do.isotopes.Rd b/rcdk/man/do.isotopes.Rd index 26c7136c0..e933de984 100755 --- a/rcdk/man/do.isotopes.Rd +++ b/rcdk/man/do.isotopes.Rd @@ -4,7 +4,7 @@ \alias{do.isotopes} \title{do.isotopes} \usage{ -\method{do}{isotopes}(mol) +do.isotopes(mol) } \arguments{ \item{mol}{The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`} diff --git a/rcdk/man/get.desc.categories.Rd b/rcdk/man/get.desc.categories.Rd index cee00af00..df2face09 100755 --- a/rcdk/man/get.desc.categories.Rd +++ b/rcdk/man/get.desc.categories.Rd @@ -7,7 +7,7 @@ get.desc.categories() } \value{ -A character vector listing available descriptor categories. This can be +A character vector listing available descriptor categories. This can be used in \link{get.desc.names} } \description{ diff --git a/rcdk/man/get.volume.Rd b/rcdk/man/get.volume.Rd index ef5295690..4e0c8a80f 100755 --- a/rcdk/man/get.volume.Rd +++ b/rcdk/man/get.volume.Rd @@ -13,7 +13,7 @@ get.volume(molecule) A double value representing the volume } \description{ -This method does not require 3D coordinates. As a result its an +This method does not require 3D coordinates. As a result its an approximation } \author{ diff --git a/rcdk/man/view.table.Rd b/rcdk/man/view.table.Rd new file mode 100644 index 000000000..f6e527d91 --- /dev/null +++ b/rcdk/man/view.table.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visual.R +\name{view.table} +\alias{view.table} +\title{view.table} +\usage{ +view.table(molecules, dat, depictor = NULL) +} +\arguments{ +\item{molecules}{A list of molecule objects (`jobjRef` representing an `IAtomContainer`)} + +\item{dat}{The \code{data.frame} associated with the molecules, one per row} + +\item{depictor}{Default \code{NULL}} +} +\description{ +Create a tabular view of a set of molecules (in 2D) and associated data columns +}