An R6 class for pesticidal active ingredients and associated data

This class is derived from chent. It makes it easy to create a chent 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.

Format

An R6::R6Class generator object

Super class

chents::chent -> 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()

• pai$clone()

Inherited methods

• chents::chent$add_PUF()
• chents::chent$add_TP()
• chents::chent$add_cwsat()
• chents::chent$add_p0()
• chents::chent$add_soil_degradation()
• chents::chent$add_soil_ff()
• chents::chent$add_soil_sorption()
• chents::chent$add_transformation()
• chents::chent$emf()
• chents::chent$get_chyaml()
• chents::chent$get_pubchem()
• chents::chent$get_rdkit()
• chents::chent$pdf()
• chents::chent$png()
• chents::chent$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

# 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"       
# }