diff options
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 54 |
1 files changed, 32 insertions, 22 deletions
@@ -10,8 +10,11 @@ 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 @@ -20,8 +23,8 @@ using the [webchem](https://docs.ropensci.org/webchem/) package. ``` r library(chents) caffeine <- chent$new("caffeine") -#> Querying PubChem ... -#> Trying to get chemical information from RDKit using PubChem SMILES +#> Querying PubChem for name caffeine ... +#> Get chemical information from RDKit using PubChem SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C ``` @@ -47,7 +50,7 @@ print(caffeine) #> [3] "Guaranine" "1,3,7-Trimethylxanthine" #> [5] "Methyltheobromine" "Theine" #> [7] "Thein" "Cafeina" -#> [9] "Koffein" "Mateina" +#> [9] "Caffein" "Cafipel" ``` There is a very simple plotting method for the chemical structure. @@ -58,41 +61,46 @@ plot(caffeine) <!-- --> -Additional information can be (but is rarely ever) read from a local -.yaml file. This information can be leveraged e.g. by the -[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function -of the ‘pfm’ package. - If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the [BCPC compendium](http://www.bcpcpesticidecompendium.org/) first. ``` r -lambda <- pai$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) +delta <- pai$new("deltamethrin") +#> Querying BCPC for deltamethrin ... +#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ... +#> 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(Br)Br)C +plot(delta) ``` <!-- --> +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: - install.packages("chents", - repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) +``` 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 - sudo apt install python3-rdkit +``` sh +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 @@ -105,4 +113,6 @@ 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") +``` r +Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") +``` |