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Diffstat (limited to 'docs/llms.txt')
| -rw-r--r-- | docs/llms.txt | 40 |
1 files changed, 23 insertions, 17 deletions
diff --git a/docs/llms.txt b/docs/llms.txt index 60135e4..28cceea 100644 --- a/docs/llms.txt +++ b/docs/llms.txt @@ -7,8 +7,11 @@ status](https://jranke.r-universe.dev/badges/chents)](https://jranke.r-universe. [](https://pkgdown.jrwb.de/chents/coverage/coverage.html) -The R package **chents** provides some utilities for working with -chemical entities in R. +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 and check the identity of +chemically defined substances (“chemical entities”) and to collect +related information. When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website @@ -17,8 +20,8 @@ using the [webchem](https://docs.ropensci.org/webchem/) package. ``` r library(chents) caffeine <- chent$new("caffeine") -#> Querying PubChem ... -#> Trying to get chemical information from RDKit using PubChem SMILES +#> Querying PubChem for name caffeine ... +#> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C ``` @@ -44,7 +47,7 @@ print(caffeine) #> [3] "Guaranine" "1,3,7-Trimethylxanthine" #> [5] "Methyltheobromine" "Theine" #> [7] "Thein" "Cafeina" -#> [9] "Koffein" "Mateina" +#> [9] "Caffein" "Cafipel" ``` There is a very simple plotting method for the chemical structure. @@ -55,11 +58,6 @@ plot(caffeine)  -Additional information can be (but is rarely ever) read from a local -.yaml file. This information can be leveraged e.g. by the -[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function -of the ‘pfm’ package. - If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the [BCPC @@ -68,22 +66,30 @@ compendium](http://www.bcpcpesticidecompendium.org/) first. ``` r lambda <- pai$new("lambda-cyhalothrin") #> Querying BCPC for lambda-cyhalothrin ... -#> Querying PubChem ... -#> Trying to get chemical information from RDKit using PubChem SMILES +#> Querying PubChem for name lambda-cyhalothrin ... +#> 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 +#> Warning in self$get_rdkit(template = template): RDKit mw is 449.856 while mw is +#> 449.8 plot(lambda) ```  +Additional information can be 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. However, this functionality is to be superseded by +a dedicated package, defining data for the environmental risk assessment +on chemicals, in particular on active ingredients of plant protection +products. + ## Installation You can conveniently install chents from the repository kindly made available by the R-Universe project: -``` R +``` r install.packages("chents", repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) ``` @@ -91,7 +97,7 @@ install.packages("chents", 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 +``` sh sudo apt install python3-rdkit ``` @@ -106,7 +112,7 @@ 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 +``` r Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") ``` |