Document Updates (#18)

* move from magrittr to base r * fix imports and add url * update docs and Description * style pkgdown * add orcid * rename * update depict for rxn check * add rxn smiles test * style pass * update allowable classes * add a get_svg_string function * add icon * update to use SVG strings directly * use cat to get cleaner vignette * fix imports and update example code * remove rcdk * update jovs * update docs and description * more CRAN compat * update docs --------- Co-authored-by: Zachary Charlop-Powers <zcpowers@Zacharys-MacBook-Air.local>
CDK-R · Mar 5, 2024 · 9402251 · 9402251
1 parent 5c2b5e0
commit 9402251
Show file tree

Hide file tree

Showing 26 changed files with 105 additions and 60 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,15 +3,13 @@ Type: Package
 Title: Draw Beautiful Molecular Structures
 Version: 0.4.0
 Authors@R: c(
-  person('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre'), 
+  person('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre', 'aut'), 
       comment = c(ORCID = "0000-0001-8816-4680")))
-Description: Generate images of molecules using the Depiction API of  the 'Chemistry Development Kit'. 
-    CDK's Depict Api
+Description: Generate images of molecules using the Depiction API of  the 'Chemistry Development Kit'.
 License: LGPL
 LazyData: TRUE
 Depends:
     rJava (>= 1.0-11),
-    rcdk (>= 3.7),
     rcdklibs (>= 2.8)
 Imports:
     png

diff --git a/NAMESPACE b/NAMESPACE
@@ -17,4 +17,6 @@ export(read_mol)
 export(save_image)
 export(set_size)
 export(set_zoom)
+import(rJava)
+import(rcdklibs)
 importFrom(png,readPNG)
diff --git a/R/IO.R b/R/IO.R
@@ -6,6 +6,7 @@
 #' @param generatecoords Optional. Default \code{TRUE}. Whether
 #'  to generate coordinates from the smiles
 #' @param kekulise Optional. Boolean. Default \code{TRUE}
+#' @return an IAtomContainer
 #' @export
 #'
 parse_smiles <- function(smi, generatecoords = TRUE, kekulise = TRUE) {
@@ -31,7 +32,7 @@ parse_smiles <- function(smi, generatecoords = TRUE, kekulise = TRUE) {
 
 #' read_mol
 #'
-#' Read a Molfile and return an AtomContainer
+#' Read a Molfile and return an `AtomContainer`
 #'
 #' @param molfile Required. A filepath to a MOLfile.
 #' @return an AtomContainer

diff --git a/R/depict.R b/R/depict.R
@@ -2,6 +2,8 @@
 #'
 #' create the CDK depiction object that can be manipulated
 #'
+#' @return DepictionGenerator
+#' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 depiction <- function() {
   .jnew("org/openscience/cdk/depict/DepictionGenerator")
@@ -13,6 +15,7 @@ depiction <- function() {
 #'
 #' @param dg a CDK DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
+#' @return DepictionGenerator
 #' @export
 color_atoms <- function(dg) {
   if (!checkJavaClass(dg, "org/openscience/cdk/depict/DepictionGenerator")) {
@@ -24,6 +27,7 @@ color_atoms <- function(dg) {
 #' outerglow
 #'
 #' @param dg a CDK Depiction Generator
+#' @return DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 outerglow <- function(dg) {
@@ -38,6 +42,7 @@ outerglow <- function(dg) {
 #' @param dg a CDK Depiction Generator
 #' @param width width (int)
 #' @param height height  (int)
+#' @return DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 set_size <- function(dg, width, height) {
@@ -51,6 +56,7 @@ set_size <- function(dg, width, height) {
 #' add_title
 #'
 #' @param dg a CDK  Depiction Generator
+#' @return DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 add_title <- function(dg) {
@@ -64,6 +70,7 @@ add_title <- function(dg) {
 #' add terminal carbons
 #'
 #' @param dg a Depiction Generator
+#' @return DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 add_terminal_carbons <- function(dg) {
@@ -83,9 +90,8 @@ add_terminal_carbons <- function(dg) {
 #'
 #' @param dg Required. A DepictionGenerator
 #' @param mol Required. An AtomContainer
-#' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
-#' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/AtomContainer.html}
-#'
+#' @return A Depiction
+#' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/Depiction.html}
 #' @export
 depict <- function(dg, mol) {
   if (!checkJavaClass(dg, "org/openscience/cdk/depict/DepictionGenerator")) {
@@ -117,7 +123,7 @@ depict <- function(dg, mol) {
 #' Highlight atoms
 #'
 #' @param dg Required. A Depiction Generator
-#' @param highlights Required. A list of CDK IChemOjbects, usually atoms or bonds
+#' @param atoms Required. A list of CDK IChemOjbects, usually atoms or bonds
 #' @param color Required. A java.awt.Color
 #' @export
 highlight_atoms <- function(dg, atoms, color) {
@@ -129,20 +135,20 @@ highlight_atoms <- function(dg, atoms, color) {
 
 #' save_image
 #'
-#' Highlight atoms
+#' save image to disk
 #'
 #' @param molgrid Required. A MolGridDepiction. Usually obtained from
 #' the \code{depict} function.
 #' @param outfile Required. Filepath to the output
 #' @export
-save_image <- function(molgrid, filepath) {
+save_image <- function(molgrid, outfile) {
   if (!checkJavaClass(molgrid, c(
     "org/openscience/cdk/depict/MolGridDepiction",
     "org/openscience/cdk/depict/ReactionDepiction"
   ))) {
     stop("highlight_atoms requires a Depiction Generator")
   }
-  molgrid$writeTo(filepath)
+  molgrid$writeTo(outfile)
 }
 
 #' get_image
@@ -151,7 +157,6 @@ save_image <- function(molgrid, filepath) {
 #'
 #' @param molgrid Required. A MolGridDepiction. Usually obtained from
 #' the \code{depict} function.
-#' @param outfile Required. Filepath to the output
 #' @importFrom png readPNG
 #' @export
 #'
@@ -208,6 +213,7 @@ get_svg_string <- function(molgrid) {
 #'
 #' @param dg a Depiction Generator
 #' @param zoom Optional. Default \code{1}
+#' @return DepictionGenerator
 #' @export
 #'
 set_zoom <- function(dg, zoom = 1) {

diff --git a/R/smarts.R b/R/smarts.R
@@ -3,8 +3,8 @@
 #' return a named list of SMARTS
 #' patterns for amino_acids
 #'
-#' @seealso \url{http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html}
-#' @seealso \url{http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html}
+#' @seealso \url{https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html}
+#' @seealso \url{https://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html}
 #' @export
 #'
 #'

diff --git a/R/utilities.R b/R/utilities.R
@@ -5,6 +5,7 @@
 #' @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")
 
@@ -17,8 +18,6 @@ checkJavaClass <- function(jobj, klass) {
 }
 
 
-
-
 #' atomcontainer_list_to_jarray
 #'
 #'
@@ -27,10 +26,10 @@ checkJavaClass <- function(jobj, klass) {
 #' 
 #' @export
 #' @examples 
-#' \dontrun {
+#' \dontrun{
 #' 
 #' atmcontnrs <- purrr::map(
-#'      c("CCCCCC", "CCC1CCC1NC", "COCCOCCO")
+#'      c("CCCCCC", "CCC1CCC1NC", "COCCOCCO"),
 #'      parse_smiles)
 #'      
 #' atomcontainer_list_to_jarray(atmcontnrs)

diff --git a/man/add_terminal_carbons.Rd b/man/add_terminal_carbons.Rd
diff --git a/man/add_title.Rd b/man/add_title.Rd
diff --git a/man/amino_acids.Rd b/man/amino_acids.Rd
diff --git a/man/atomcontainer_list_to_jarray.Rd b/man/atomcontainer_list_to_jarray.Rd
diff --git a/man/checkJavaClass.Rd b/man/checkJavaClass.Rd
diff --git a/man/color_atoms.Rd b/man/color_atoms.Rd
diff --git a/man/depict-package.Rd b/man/depict-package.Rd
diff --git a/man/depict.Rd b/man/depict.Rd
diff --git a/man/depiction.Rd b/man/depiction.Rd
diff --git a/man/get_image.Rd b/man/get_image.Rd
diff --git a/man/highlight_atoms.Rd b/man/highlight_atoms.Rd
diff --git a/man/outerglow.Rd b/man/outerglow.Rd
diff --git a/man/parse_smiles.Rd b/man/parse_smiles.Rd
diff --git a/man/read_mol.Rd b/man/read_mol.Rd
diff --git a/man/save_image.Rd b/man/save_image.Rd
diff --git a/man/set_size.Rd b/man/set_size.Rd