From 88027b7a70510b48bd7525ffcd536f0808d263e7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 3 Jul 2026 11:51:32 +0200 Subject: Improve description with README text Also, read the description into the Readme to have them in sync and update docs with roxygen 8. --- DESCRIPTION | 14 +- README.md | 15 +- README.rmd | 8 +- docs/404.html | 2 +- docs/authors.html | 6 +- docs/authors.md | 4 +- docs/index.html | 16 +- docs/index.md | 15 +- docs/llms.txt | 15 +- docs/news/index.html | 2 +- docs/reference/chent.html | 418 +++++------ docs/reference/chent.md | 38 +- docs/reference/draw_svg.chent.html | 4 +- .../reference/figures/README-unnamed-chunk-5-1.png | Bin 16259 -> 6180 bytes .../reference/figures/README-unnamed-chunk-6-1.png | Bin 0 -> 16259 bytes docs/reference/index.html | 2 +- docs/reference/pai.html | 87 +-- docs/reference/pai.md | 41 +- docs/reference/plot.chent.html | 2 +- docs/reference/ppp.html | 49 +- docs/reference/ppp.md | 6 +- docs/reference/print.chent.html | 4 +- docs/reference/print.pai.html | 4 +- docs/reference/print.ppp.html | 4 +- docs/search.json | 2 +- log/build.log | 2 +- log/check.log | 15 +- man/chent.Rd | 764 ++++++++++----------- man/figures/README-unnamed-chunk-5-1.png | Bin 16259 -> 6180 bytes man/figures/README-unnamed-chunk-6-1.png | Bin 0 -> 16259 bytes man/pai.Rd | 145 ++-- man/ppp.Rd | 101 ++- 32 files changed, 837 insertions(+), 948 deletions(-) create mode 100644 docs/reference/figures/README-unnamed-chunk-6-1.png create mode 100644 man/figures/README-unnamed-chunk-6-1.png diff --git a/DESCRIPTION b/DESCRIPTION index 9b6be00..1a09aea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,16 @@ Package: chents Type: Package Title: Chemical Entities as R Objects -Version: 0.4.1 -Date: 2026-03-05 +Version: 0.4.2 +Date: 2026-07-03 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de")) -Description: Utilities for dealing with chemical entities and associated - data as R objects. If Python and 'RDKit' (> 2015.03) are installed and +Description: + When working with data on chemical substances, we often need a reliable + link between the data and the chemical identity of the substances. The R + package 'chents' provides a way to define an R object corresponding to a + chemically defined substances, i.e. a chemical entity and to collect + related information. If Python and 'RDKit' (> 2015.03) are installed and configured for use with 'reticulate', some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available. @@ -28,5 +32,5 @@ LazyData: yes Encoding: UTF-8 URL: https://pkgdown.jrwb.de/chents/, https://github.com/jranke/chents Roxygen: list(markdown = TRUE, r6 = TRUE) -RoxygenNote: 7.3.3 Config/testthat/edition: 3 +Config/roxygen2/version: 8.0.0 diff --git a/README.md b/README.md index 3df1492..0b1f83b 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,14 @@ coverage](https://img.shields.io/badge/coverage-jrwb.de-blue.svg)](https://pkgdo When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R -package **chents** provides a way to define an R object corresponding to -a chemically defined substances (“chemical entity”) and to collect -related information. +package ‘chents’ provides a way to define an R object corresponding to a +chemically defined substances, i.e. a chemical entity and to collect +related information. If Python and ‘RDKit’ (\> 2015.03) are installed +and configured for use with ‘reticulate’, some basic chemoinformatics +functions like the calculation of molecular weight and plotting of +chemical structures in R graphics are available. + +## Usage When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website @@ -59,7 +64,7 @@ There is a very simple plotting method for the chemical structure. plot(caffeine) ``` -![](man/figures/README-unnamed-chunk-4-1.png) +![](man/figures/README-unnamed-chunk-5-1.png) If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, @@ -75,7 +80,7 @@ delta <- pai$new("Deltamethrin") plot(delta) ``` -![](man/figures/README-unnamed-chunk-5-1.png) +![](man/figures/README-unnamed-chunk-6-1.png) Additional information can be read from a local .yaml file. This information can be leveraged e.g. by the diff --git a/README.rmd b/README.rmd index 89462ac..cc15d07 100644 --- a/README.rmd +++ b/README.rmd @@ -14,11 +14,11 @@ knitr::opts_chunk$set( [![R-Universe status](https://jranke.r-universe.dev/badges/chents)](https://jranke.r-universe.dev/chents) [![Code coverage](https://img.shields.io/badge/coverage-jrwb.de-blue.svg)](https://pkgdown.jrwb.de/chents/coverage/coverage.html) -When working with data on chemical substances, we often need a reliable link between -the data and the chemical identity of the substances. The R package **chents** -provides a way to define an R object corresponding to a chemically defined substances -("chemical entity") and to collect related information. +```{r, results = "asis", echo = FALSE} +read.dcf("DESCRIPTION")[, "Description"] |> cat() +``` +## Usage When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website using diff --git a/docs/404.html b/docs/404.html index 22c2979..e909978 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,7 +20,7 @@ chents - 0.4.1 + 0.4.2