From 8cf43282ed99fad29ff00e1b8e8c5f17a955e248 Mon Sep 17 00:00:00 2001 From: zachcp Date: Sun, 3 Mar 2024 09:49:20 -0500 Subject: [PATCH] Update Website and Docs (#150) --- README.md | 31 ++-- rcdk/.Rbuildignore | 3 +- rcdk/.gitignore | 6 + rcdk/DESCRIPTION | 23 ++- rcdk/NEWS.md | 4 + rcdk/R/atoms.R | 2 +- rcdk/README.Rmd | 36 ++++ rcdk/man/Atoms.Rd | 2 +- rcdk/man/figures/logo.png | Bin 0 -> 46011 bytes rcdk/man/rcdk-deprecated.Rd | 1 + rcdk/{ => pkgdown}/_pkgdown.yml | 14 +- .../favicon/apple-touch-icon-120x120.png | Bin 0 -> 4213 bytes .../favicon/apple-touch-icon-152x152.png | Bin 0 -> 5555 bytes .../favicon/apple-touch-icon-180x180.png | Bin 0 -> 6794 bytes .../favicon/apple-touch-icon-60x60.png | Bin 0 -> 2053 bytes .../favicon/apple-touch-icon-76x76.png | Bin 0 -> 2575 bytes rcdk/pkgdown/favicon/apple-touch-icon.png | Bin 0 -> 6794 bytes rcdk/pkgdown/favicon/favicon-16x16.png | Bin 0 -> 692 bytes rcdk/pkgdown/favicon/favicon-32x32.png | Bin 0 -> 1123 bytes rcdk/pkgdown/favicon/favicon.ico | Bin 0 -> 15086 bytes rcdk/vignettes/Features_29.Rmd | 174 ++++++++++++++++++ rcdk/vignettes/{using-rcdk.Rmd => rcdk.Rmd} | 14 ++ 22 files changed, 281 insertions(+), 29 deletions(-) create mode 100644 rcdk/README.Rmd create mode 100644 rcdk/man/figures/logo.png rename rcdk/{ => pkgdown}/_pkgdown.yml (91%) create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon-120x120.png create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon-152x152.png create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon-180x180.png create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon-60x60.png create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon-76x76.png create mode 100644 rcdk/pkgdown/favicon/apple-touch-icon.png create mode 100644 rcdk/pkgdown/favicon/favicon-16x16.png create mode 100644 rcdk/pkgdown/favicon/favicon-32x32.png create mode 100644 rcdk/pkgdown/favicon/favicon.ico create mode 100644 rcdk/vignettes/Features_29.Rmd rename rcdk/vignettes/{using-rcdk.Rmd => rcdk.Rmd} (98%) mode change 100755 => 100644 diff --git a/README.md b/README.md index b76746b120..c322bd0878 100755 --- a/README.md +++ b/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") diff --git a/rcdk/.Rbuildignore b/rcdk/.Rbuildignore index 3b22b06422..9620f7bb6f 100755 --- a/rcdk/.Rbuildignore +++ b/rcdk/.Rbuildignore @@ -4,4 +4,5 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ -^revdep$ \ No newline at end of file +^revdep$ +README.Rmd diff --git a/rcdk/.gitignore b/rcdk/.gitignore index 31d5365dcf..3a8d2860f7 100755 --- a/rcdk/.gitignore +++ b/rcdk/.gitignore @@ -1,2 +1,8 @@ inst/doc docs +revdep/ +.RData +.Rhistory +.Rproj +*.Rmd +*.png \ No newline at end of file diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index 1ce30d2983..85815618ea 100755 --- a/rcdk/DESCRIPTION +++ b/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 diff --git a/rcdk/NEWS.md b/rcdk/NEWS.md index 46f71cc9f2..93b8833b64 100755 --- a/rcdk/NEWS.md +++ b/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 diff --git a/rcdk/R/atoms.R b/rcdk/R/atoms.R index 8536aa0520..fffdcacbd4 100755 --- a/rcdk/R/atoms.R +++ b/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 diff --git a/rcdk/README.Rmd b/rcdk/README.Rmd new file mode 100644 index 0000000000..c1a28e7d79 --- /dev/null +++ b/rcdk/README.Rmd @@ -0,0 +1,36 @@ +--- +output: github_document +--- + + + +```{r, echo = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/" +) +``` + +# rcdk + + +[![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) + + +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") +``` +::: + + + diff --git a/rcdk/man/Atoms.Rd b/rcdk/man/Atoms.Rd index e926fcbaf9..39b754a2e2 100755 --- a/rcdk/man/Atoms.Rd +++ b/rcdk/man/Atoms.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/atoms.R -\docType{package} \name{Atoms} \alias{Atoms} +\alias{rcdk-package} \title{Operations on Atoms} \description{ \code{\link{get.symbol}} returns the chemical symbol for an atom diff --git a/rcdk/man/figures/logo.png b/rcdk/man/figures/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..40018498ccc1dba57763d91884a9dcffb0d82648 GIT binary patch literal 46011 zcmeFYcQ}{*`#=6dHrXS4RkHUU*(;R2_uhLGk+MmMWJR(pe&?n8 zevj|xa~!|peH_23WaWj z{Kdh7J1-sXO~Xfbh@O$3j&&fDmyf4|vztAWU$B=wlYNl00}2&1>3-GyY$p@W(a@!U 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z&sbw||7|jum$;9Wor~Mr+M2cJo36RJlev;L8ul`NL&rO|Ad_*OeI7dG2cVr#Q@o~& zuah+$a}YepVNS$;ev@SLA8Rk{fF{Y$9BuZao3$zP7jqhZu&&@8KnuU*Oj9~t=tL%S zA8}x2G0CrQM~@G@!$X>ea+&jAWXY2hG{@2Ch+L2PuCSDcd@ekkOvH4hKrXQMx!b5&r);Hr9XTLm*Uq){! zc^v{{+_?6ekaLI1zbkML89a!alSa|rBP + %\VignetteIndexEntry{Features 2.9} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + + +# CDK 2.9 Release Notes Vignettes + +[CDK 2.9 Release Notes](https://github.com/cdk/cdk/releases/tag/cdk-2.9) + +[rJava](https://rforge.net/rJava/docs/reference/index.html) + + +## RXN Arrows + +https://github.com/cdk/cdk/pull/927 + +```{r setup, message=FALSE} + +library(rcdklibs) +library(depict) + + +# Java Imports +sp <- J('org.openscience.cdk.smiles.SmilesParser') +silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder") +smiles_parser <- new(sp, silentchemobject$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$parseReactionSetSmiles(multi_smiles) +svg <- depiction() |> depict(rxn_set) +to_svg(svg) +``` + + +## Features 2.8 + +### Maygen + + + +```{r} + +maygen_cls <- J('org.openscience.cdk.structgen.maygen.Maygen') +#smioutout_cls <- J('org.openscience.cdk.structgen.maygen.SmiOutputConsumer') +silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder") +smigen_cls <- J('org.openscience.cdk.smiles.SmilesGenerator') +smigen <- .jnew('org.openscience.cdk.smiles.SmilesGenerator') +#IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance(); +#SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default); + + +maygen <- new(maygen_cls, silentchemobject$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 + +``` + diff --git a/rcdk/vignettes/using-rcdk.Rmd b/rcdk/vignettes/rcdk.Rmd old mode 100755 new mode 100644 similarity index 98% rename from rcdk/vignettes/using-rcdk.Rmd rename to rcdk/vignettes/rcdk.Rmd index 29b34f8a91..36696c4355 --- a/rcdk/vignettes/using-rcdk.Rmd +++ b/rcdk/vignettes/rcdk.Rmd @@ -1,3 +1,17 @@ +--- +title: "Using the CDK from R" +author: "Rajarshi Guha" +date: "`r Sys.Date()`" +description: > + Learn how to get started with the basics of pkgdown. +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Using the CDK from R} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + + --- title: "Using the CDK from R" author: "Rajarshi Guha"