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diff --git a/docs/reference/pai.md b/docs/reference/pai.md new file mode 100644 index 0000000..2291653 --- /dev/null +++ b/docs/reference/pai.md @@ -0,0 +1,187 @@ +# An R6 class for pesticidal active ingredients and associated data + +This class is derived from +[chent](https://pkgdown.jrwb.de/chents/reference/chent.md). It makes it +easy to create a +[chent](https://pkgdown.jrwb.de/chents/reference/chent.md) from the ISO +common name of a pesticide active ingredient, and additionally stores +the ISO name as well as the complete result of querying the BCPC +compendium using +[bcpc_query](https://docs.ropensci.org/webchem/reference/bcpc_query.html). + +## Format + +An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator +object + +## Super class + +[`chents::chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) -\> +`pai` + +## Public fields + +- `iso`: + + ISO common name of the active ingredient according to ISO 1750 + +- `bcpc`: + + Information retrieved from the BCPC compendium available online at + \<pesticidecompendium.bcpc.org\> + +## Methods + +### Public methods + +- [`pai$new()`](#method-pai-new) + +- [`pai$clone()`](#method-pai-clone) + +Inherited methods + +- [`chents::chent$add_PUF()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_PUF) +- [`chents::chent$add_TP()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_TP) +- [`chents::chent$add_cwsat()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_cwsat) +- [`chents::chent$add_p0()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_p0) +- [`chents::chent$add_soil_degradation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_degradation) +- [`chents::chent$add_soil_ff()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_ff) +- [`chents::chent$add_soil_sorption()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_sorption) +- [`chents::chent$add_transformation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_transformation) +- [`chents::chent$emf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-emf) +- [`chents::chent$get_chyaml()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_chyaml) +- [`chents::chent$get_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_pubchem) +- [`chents::chent$get_rdkit()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_rdkit) +- [`chents::chent$pdf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-pdf) +- [`chents::chent$png()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-png) +- [`chents::chent$try_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-try_pubchem) + +------------------------------------------------------------------------ + +### Method `new()` + +Create a new pai object + +#### Usage + + pai$new( + iso, + identifier = iso, + smiles = NULL, + inchikey = NULL, + bcpc = TRUE, + pubchem = TRUE, + pubchem_from = "auto", + rdkit = TRUE, + template = NULL, + chyaml = FALSE + ) + +#### Arguments + +- `iso`: + + The ISO common name to be used in the query of the BCPC compendium + +- `identifier`: + + Alternative identifier used for querying pubchem + +- `smiles`: + + Optional user provided SMILES code + +- `inchikey`: + + Optional user provided InChI Key + +- `bcpc`: + + Should the BCPC compendium be queried? + +- `pubchem`: + + Should an attempt be made to retrieve chemical information from + PubChem via the webchem package? + +- `pubchem_from`: + + Possibility to select the argument that is used to query pubchem + +- `rdkit`: + + Should an attempt be made to retrieve chemical information from a + local rdkit installation via python and the reticulate package? + +- `template`: + + An optional SMILES code to be used as template for RDKit + +- `chyaml`: + + Should we look for a identifier.yaml file in the working + +------------------------------------------------------------------------ + +### Method `clone()` + +The objects of this class are cloneable with this method. + +#### Usage + + pai$clone(deep = FALSE) + +#### Arguments + +- `deep`: + + Whether to make a deep clone. + +## Examples + +``` r +# Don't run examples per default, as PubChem may be unavailable +# \dontrun{ +atr <- pai$new("atrazine") +#> Querying BCPC for atrazine ... +#> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ... +#> Get chemical information from RDKit using PubChem SMILES +#> CCNC1=NC(=NC(=N1)Cl)NC(C)C +print(atr) +#> <pai> with ISO common name $iso atrazine +#> <chent> +#> Identifier $identifier atrazine +#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N +#> SMILES string $smiles: +#> PubChem +#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" +#> Molecular weight $mw: 215.7 +#> PubChem synonyms (up to 10): +#> [1] "atrazine" "1912-24-9" "Gesaprim" "Aatrex" "Atranex" +#> [6] "Atrazin" "Oleogesaprim" "Atazinax" "Atrasine" "Chromozin" +if (!is.null(atr$Picture)) { + plot(atr) +} + +# We can also define pais that are not found on the BCPC site +decanol <- pai$new("1-Decanol") +#> Querying BCPC for 1-Decanol ... +#> Common name 1-Decanol is not known at the BCPC compendium, trying PubChem +#> Querying PubChem for name 1-Decanol ... +#> Get chemical information from RDKit using PubChem SMILES +#> CCCCCCCCCCO +print(decanol) +#> <pai> without ISO common name +#> <chent> +#> Identifier $identifier 1-Decanol +#> InChI Key $inchikey MWKFXSUHUHTGQN-UHFFFAOYSA-N +#> SMILES string $smiles: +#> PubChem +#> "CCCCCCCCCCO" +#> Molecular weight $mw: 158.3 +#> PubChem synonyms (up to 10): +#> [1] "1-DECANOL" "Decan-1-ol" "Decyl alcohol" "112-30-1" +#> [5] "n-Decyl alcohol" "n-Decanol" "Capric alcohol" "Nonylcarbinol" +#> [9] "Antak" "Royaltac" +# } +``` |