Update Website and Docs

README.md

@@ -9,6 +9,7 @@ Version](https://www.r-pkg.org/badges/version/rcdk?color=green)](https://cran.r-
 Downloads](http://cranlogs.r-pkg.org/badges/grand-total/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
 [![CRAN Downloads
 Monthyl](http://cranlogs.r-pkg.org/badges/last-month/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
+[![R-CMD-check](https://github.com/zachcp/cdkr/workflows/R-CMD-check/badge.svg)](https://github.com/zachcp/cdkr/actions)
 
 # rcdk: a chemistry library
 
@@ -36,25 +37,23 @@ install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")
 Information on building and devloping the CDKR package is available in
 teh Otherwise if you prefer the command line
 
-``` 
-    cd /tmp/
-    git clone git@github.com:CDK-R/rcdklibs.git
-    R CMD INSTALL rcdklibs
-    git clone git@github.com:CDK-R/cdkr.git
-    cd cdkr/rcdkjar
-    ant clean jar
-    cd ../
-    R CMD INSTALL rcdk
-```
+        cd /tmp/
+        git clone git@github.com:CDK-R/rcdklibs.git
+        R CMD INSTALL rcdklibs
+        git clone git@github.com:CDK-R/cdkr.git
+        cd cdkr/rcdkjar
+        ant clean jar
+        cd ../
+        R CMD INSTALL rcdk
 
 Before performing the install, you should have the following
 dependencies installed:
 
-  - rJava
-  - fingerprint
-  - png
-  - RUnit
-  - Java JDK \>= 1.8
+- rJava
+- fingerprint
+- png
+- RUnit
+- Java JDK \>= 1.8
 
 For the png package, I have tested
 [png-0.1-7](http://www.rforge.net/png/files/)
@@ -86,7 +85,7 @@ You can try the following:
     # set the java version
     R CMD javareconf  # or ....
     sudo R CMD javareconf
-    
+
     # re install fromfrom R
     install.packages('rJava', type="source")
 

rcdk/.Rbuildignore

@@ -4,4 +4,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^revdep$
+^revdep$
+README.Rmd

rcdk/.gitignore

@@ -1,2 +1,8 @@
 inst/doc
 docs
+revdep/
+.RData
+.Rhistory
+.Rproj
+*.Rmd
+*.png

rcdk/DESCRIPTION

@@ -1,12 +1,16 @@
 Package: rcdk
-Version: 3.8.1
-Date: 2023-06-25
+Version: 3.9.0
+Date: 2024-03-02
 Title: Interface to the 'CDK' Libraries
-Authors@R: c(person('Rajarshi', 'Guha', role=c('aut',"cph"), email='rajarshi.guha@gmail.com'),
-             person('Zachary', 'Charlop-Powers', role=c('cre'), email='zach.charlop.powers@gmail.com'),
-             person('Emma', 'Schymanski', role=c('ctb'), email='schymane@gmail.com'))
+Authors@R: c(
+  person('Rajarshi', 'Guha', ,'rajarshi.guha@gmail.com', role=c('aut',"cph"),
+    comment = c(ORCID = "0000-0001-7403-8819")),
+  person('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre'), 
+      comment = c(ORCID = "0000-0001-8816-4680")),
+  person('Emma', 'Schymanski', ,'schymane@gmail.com', role=c('ctb'), 
+      comment = c(ORCID = "0000-0001-6868-8145")))
 Depends:
-    rcdklibs (>= 2.8)
+    rcdklibs (>= 2.9)
 Imports:
     fingerprint,
     rJava,
@@ -19,8 +23,10 @@ Suggests:
     RUnit,
     knitr,
     rmarkdown,
-    devtools
+    devtools,
+    depict
 License: LGPL
+URL: https://github.com/CDK-R/cdkr
 LazyLoad: yes
 LazyData: true
 SystemRequirements: Java (>= 8)
@@ -29,6 +35,7 @@ Description: Allows the user to access functionality in the
     'CDK', a Java framework for chemoinformatics. This allows the user to load
     molecules, evaluate fingerprints, calculate molecular descriptors and so on.
     In addition, the 'CDK' API allows the user to view structures in 2D.
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
+Remotes: CDK-R/depict

rcdk/NEWS.md

@@ -1,3 +1,7 @@
+# rcdk 3.9.0
+
+* Update rCDK to work with rcdklibs 2.9
+
 # rcdk 3.8.0
 
 * Change DESCRIPTION in accordance with CRAN rules about JDKs

rcdk/R/atoms.R

@@ -53,7 +53,7 @@
 #'  length \code{2}.
 #'  
 #' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
-#' @docType package
+#' @aliases rcdk-package
 NULL
 
 ## An example of getting all the coordinates for a molecule

rcdk/README.Rmd

@@ -0,0 +1,36 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/"
+)
+```
+
+# rcdk <img src="man/figures/logo.png" align="right" alt="" width="120" />
+
+<!-- badges: start -->
+[![CRAN Status](https://www.r-pkg.org/badges/version/rcdk)](https://cran.r-project.org/package=rcdk){.rcdk-release}
+[![R-CMD-check](https://github.com/CDK-R/rcdk/workflows/R-CMD-check/badge.svg)](https://github.com/CDK-R/cdkr/actions){.rcdk-devel}
+[![Codecov test coverage](https://codecov.io/gh/r-lib/rcdk/branch/main/graph/badge.svg)](https://app.codecov.io/gh/CDK-R/cdkr?branch=main)
+<!-- badges: end -->
+
+Allows the user to access functionality in the `CDK`, a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
+
+
+## Installation
+
+::: .rcdk-release
+```{r, eval = FALSE}
+# Install released version from CRAN
+install.packages("rcdk")
+```
+:::
+
+
+

rcdk/_pkgdown.yml → rcdk/pkgdown/_pkgdown.yml

@@ -1,14 +1,24 @@
 url: https://cdk-r.github.io/cdkr/
 
+home:
+  title: Interact with the Chemistry Development Kit
+
+
 template:
   bootstrap: 5
+  bslib:
+    primary: "#0054AD"
+    border-radius: 0.5rem
+    btn-border-radius: 0.25rem
+
+development:
+  mode: auto
 
 
 reference:
 - title: rCDK Functions
 
 
-
 - subtitle: rCDK Data and Docs
   desc: >
     Available Datasets or Documentation
@@ -115,4 +125,4 @@ reference:
   contents:
   - cdk.version
   - cdkFormula-class
-  - rcdk-deprecated
+  - rcdk-deprecated

rcdk/vignettes/Features_29.Rmd

@@ -0,0 +1,174 @@
+---
+title: "Features 2.9"
+author: "Zachary Charlop-Powers"
+date: "`r Sys.Date()`"
+output: 
+  rmarkdown::html_vignette:
+    toc: true	
+vignette: >
+  %\VignetteIndexEntry{Features 2.9}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+# CDK 2.9 Release Notes Vignettes
+
+[CDK 2.9 Release Notes](https://github.com/cdk/cdk/releases/tag/cdk-2.9)
+
+[rJava](https://rforge.net/rJava/docs/reference/index.html)
+
+
+## RXN Arrows
+
+https://github.com/cdk/cdk/pull/927
+
+```{r setup, message=FALSE}
+
+library(rcdklibs)
+library(depict)
+
+
+# Java Imports
+sp <- J('org.openscience.cdk.smiles.SmilesParser')
+silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")
+smiles_parser <- new(sp, silentchemobject$getInstance())
+ReactionManipulator <- J('org.openscience.cdk.tools.manipulator.ReactionManipulator')
+IReaction <- J('org.openscience.cdk.interfaces.IReaction')
+dg <- .jnew('org.openscience.cdk.depict.DepictionGenerator')
+
+to_svg <- function(grd) {
+  svg_str <- grd$toSvgStr()
+  svg_list <- strsplit(svg_str, "\n")[[1]]
+  paste(svg_list[3:length(svg_list)], collapse="\n")
+}
+
+
+abbreviations <- .jnew('org.openscience.cdk.depict.Abbreviations')
+abbreviations$add("[Al+3].[Cl-].[Cl-].[Cl-] AlCl3")
+abbreviations$add("ClCCl DCM")
+abbreviations$setContractToSingleLabel(TRUE)
+
+```
+
+
+```{r results='asis'}
+
+rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")
+
+# note `as.list`
+for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
+ abbreviations$apply(mol) 
+}
+
+rxn$setDirection(IReaction$Direction$NO_GO)
+svg  <- depiction() |> depict(rxn)
+to_svg(svg)
+
+```
+
+
+
+```{r results='asis'}
+rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")
+
+for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
+ abbreviations$apply(mol) 
+}
+
+rxn$setDirection(IReaction$Direction$RETRO_SYNTHETIC)
+svg  <- depiction() |> depict(rxn)
+to_svg(svg)
+
+```
+
+
+```{r results='asis'}
+rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")
+
+for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
+ abbreviations$apply(mol) 
+}
+
+rxn$setDirection(IReaction$Direction$BIDIRECTIONAL)
+svg  <- depiction() |> depict(rxn)
+to_svg(svg)
+
+```
+
+```{r results='asis'}
+rxn <- smiles_parser$parseReactionSmiles("c1c(Cl)cccc1[N-][N+]#N>>c1c(Cl)cccc1N=[N+]=[N-]")
+
+
+for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
+ abbreviations$apply(mol) 
+}
+
+rxn$setDirection(IReaction$Direction$RESONANCE)
+svg  <- depiction() |> depict(rxn)
+to_svg(svg)
+```
+
+
+
+## Multi-Step Smiles
+
+```java
+SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
+IReactionSet rset = sp.parseReactionSetSmiles("[Pb]>>[Ag]>>[Au] lead-to-silver-to-gold");
+```
+
+```{r results='asis'}
+
+multi_smiles <- "ClC1=NC=2N(C(=C1)N(CC3=CC=CC=C3)CC4=CC=CC=C4)N=CC2C(OCC)=O>C1(=CC(=CC(=N1)C)N)N2C[C@H](CCC2)O.O1CCOCC1.CC1(C2=C(C(=CC=C2)P(C3=CC=CC=C3)C4=CC=CC=C4)OC5=C(C=CC=C15)P(C6=CC=CC=C6)C7=CC=CC=C7)C.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.[Pd].[Pd].[Cs]OC(=O)O[Cs]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(OCC)=O)N6C[C@H](CCC6)O>CO.C1CCOC1.O.O[Li]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(O)=O)N6C[C@H](CCC6)O>CN(C)C(=[N+](C)C)ON1C2=C(C=CC=N2)N=N1.F[P-](F)(F)(F)(F)F.[NH4+].[Cl-].CN(C)C=O.CCN(C(C)C)C(C)C>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(N)=O)N6C[C@H](CCC6)O>>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N)N=CC3C(N)=O)N4C[C@H](CCC4)O |f:4.5.6.7.8,16.17,18.19|  US20190241576A1"
+
+rxn_set <- smiles_parser$parseReactionSetSmiles(multi_smiles)
+svg  <- depiction() |> depict(rxn_set)
+to_svg(svg)
+```
+
+
+## Features 2.8
+
+### Maygen
+
+<WIP>
+
+```{r}
+
+maygen_cls    <- J('org.openscience.cdk.structgen.maygen.Maygen')
+#smioutout_cls <- J('org.openscience.cdk.structgen.maygen.SmiOutputConsumer')
+silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")
+smigen_cls    <- J('org.openscience.cdk.smiles.SmilesGenerator')
+smigen <- .jnew('org.openscience.cdk.smiles.SmilesGenerator')
+#IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+#SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default);
+
+
+maygen <- new(maygen_cls, silentchemobject$getInstance())
+maygen$setFormula("C3Cl2H4")
+
+
+# smigen$create()
+# consumer
+# maygen$setConsumer(mol)
+# maygen$run()
+
+
+# StringWriter sw = new StringWriter();
+# maygen.setConsumer(new SmiOutputConsumer(sw));
+
+# StringWriter sw = new StringWriter();
+# SdfOutputConsumer consumer = new SdfOutputConsumer(sw);
+# consumer.setCoordinates(true);
+
+# maygen.setConsumer(mol -> {
+#              try {
+#                  System.out.println(smigen.create(mol));
+#              } catch (CDKException ignore) { }
+#          });
+# 
+# int count = maygen.getCount(); // number of structures generated
+
+```
+