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@@ -1,60 +1,108 @@ -# chents - -[](https://pkgdown.jrwb.de/chents/) -[](https://jranke.r-universe.dev/chents) -[](https://app.travis-ci.com/jranke/chents) -[](https://app.codecov.io/gh/jranke/chents) -The R package **chents** provides some utilities for working with chemical -entities in R. +<!-- README.md is generated from README.rmd. Please edit that file --> -## Features +# chents -- Some chemical information is retrieved from the PubChem website using the webchem -package -- If Python and RDKit (> 2015.03) are installed and configured for use with - 'reticulate', some basic chemoinformatics functions some additional chemical - information is computed and a 2D graph can be plotted -- Additional information can be read from a local .yaml file +[](https://pkgdown.jrwb.de/chents/) +[](https://jranke.r-universe.dev/chents) +[](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 +``` -## Installation +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 $mw: 194.2 +#> PubChem synonyms (up to 10): +#> [1] "caffeine" "58-08-2" +#> [3] "Guaranine" "1,3,7-Trimethylxanthine" +#> [5] "Methyltheobromine" "Theine" +#> [7] "Thein" "Cafeina" +#> [9] "Koffein" "Mateina" +``` -You can conveniently install chents from the repository kindly made available by the -R-Universe project: +There is a very simple plotting method for the chemical structure. +``` r +plot(caffeine) ``` -install.packages("chents", - repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) + +<!-- --> + +Additional information can be (but is rarely ever) read from a local +.yaml file. This information can be leveraged e.g. by the +[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function +of the ‘pfm’ package. + +If you have a so-called ISO common name of a pesticide active +ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, +which starts with querying the [BCPC +compendium](http://www.bcpcpesticidecompendium.org/) first. + +``` r +lambda <- pai$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) ``` -In order to profit from the chemoinformatics, you need to install RDKit and its -python bindings. On a Debian type Linux distribution, just use +<!-- --> -``` -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. +## Installation -## Configuration of the Python version to use +You can conveniently install chents from the repository kindly made +available by the R-Universe project: -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. + install.packages("chents", + repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) -``` -Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") -``` +In order to profit from the chemoinformatics, you need to install RDKit +and its python bindings. On a Debian type Linux distribution, just use -## Examples + sudo apt install python3-rdkit -Some examples are available from the -[reference on jrwb.de](https://pkgdown.jrwb.de/chents/reference). For example, -in the [example code section of the chent object docs](https://pkgdown.jrwb.de/chents/reference/chent.html#ref-examples) -you can see how to generate an R object for caffeine, show some of the information -retrieved from PubChem and plot it by virtue of 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. + Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") |