Rebuild docs

1 files changed, 133 insertions, 0 deletions

diff --git a/docs/llms.txt b/docs/llms.txt
new file mode 100644
index 0000000..60135e4
--- /dev/null
+++ b/docs/llms.txt
@@ -0,0 +1,133 @@
+# chents
+
+[![Online
+documentation](https://img.shields.io/badge/docs-jrwb.de-blue.svg)](https://pkgdown.jrwb.de/chents/)
+[![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)
+
+The R package **chents** provides some utilities for working with
+chemical entities in R.
+
+When first defining a chemical entity, some chemical information is
+retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website
+using the [webchem](https://docs.ropensci.org/webchem/) package.
+
+``` r
+library(chents)
+caffeine <- chent$new("caffeine")
+#> Querying PubChem ...
+#> Trying to get chemical information from RDKit using PubChem SMILES
+#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+```
+
+If Python and [RDKit](https://rdkit.org) (\> 2015.03) are installed and
+configured for use with the
+[reticulate](https://rstudio.github.io/reticulate/) package, some
+additional chemical information including a 2D graph are computed.
+
+The print method gives an overview of the information that was
+collected.
+
+``` r
+print(caffeine)
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>                        PubChem 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"
+```
+
+There is a very simple plotting method for the chemical structure.
+
+``` r
+plot(caffeine)
+```
+
+![](reference/figures/README-unnamed-chunk-4-1.png)
+
+Additional information can be (but is rarely ever) read from a local
+.yaml file. This information can be leveraged e.g. by the
+[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function
+of the ‘pfm’ package.
+
+If you have a so-called ISO common name of a pesticide active
+ingredient, you can use the ‘pai’ class derived from the ‘chent’ class,
+which starts with querying the [BCPC
+compendium](http://www.bcpcpesticidecompendium.org/) first.
+
+``` r
+lambda <- pai$new("lambda-cyhalothrin")
+#> Querying BCPC for lambda-cyhalothrin ...
+#> Querying PubChem ...
+#> Trying to get chemical information from RDKit using PubChem SMILES
+#> CC1([C@@H]([C@@H]1C(=O)O[C@@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)/C=C(/C(F)(F)F)\Cl)C
+#> RDKit mw is 449.856
+#> mw is 449.8
+plot(lambda)
+```
+
+![](reference/figures/README-unnamed-chunk-5-1.png)
+
+## Installation
+
+You can conveniently install chents from the repository kindly made
+available by the R-Universe project:
+
+``` R
+install.packages("chents",
+  repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org"))
+```
+
+In order to profit from the chemoinformatics, you need to install RDKit
+and its python bindings. On a Debian type Linux distribution, just use
+
+``` R
+sudo apt install python3-rdkit
+```
+
+If you use this package on Windows or MacOS, I would be happy to include
+installation instructions here if you share them with me, e.g. via a
+Pull Request.
+
+## Configuration of the Python version to use
+
+On Debian type Linux distributions, you can use the following line in
+your global or project specific `.Rprofile` file to tell the
+`reticulate` package to use the system Python version that will find the
+RDKit installed in the system location.
+
+``` R
+Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3")
+```
+
+# Package index
+
+## R6 Class definitions and methods
+
+- [`chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) : An R6
+  class for chemical entities with associated data
+- [`pai`](https://pkgdown.jrwb.de/chents/reference/pai.md) : An R6 class
+  for pesticidal active ingredients and associated data
+- [`ppp`](https://pkgdown.jrwb.de/chents/reference/ppp.md) : R6 class
+  for a plant protection product with at least one active ingredient
+- [`draw_svg.chent()`](https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.md)
+  : Draw SVG graph from a chent object using RDKit
+- [`plot(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/plot.chent.md)
+  : Plot method for chent objects
+- [`print(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.chent.md)
+  : Printing method for chent objects
+- [`print(`*`<pai>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.pai.md)
+  : Printing method for pai objects (pesticidal active ingredients)
+- [`print(`*`<ppp>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.ppp.md)
+  : Printing method for ppp objects (plant protection products)
+