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.
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
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
Examples
# On Travis, we get a certificate validation error,
# likely because the system (xenial) is so old,
# therefore don't run this example on Travis
if (Sys.getenv("TRAVIS") == "") {
atr <- pai$new("atrazine")
print(atr)
if (!is.null(atr$Picture)) {
plot(atr)
}
}
#> BCPC:
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
#> <pai> with ISO common name $iso atrazine
#> <chent>
#> Identifier $identifier atrazine
#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N
#> SMILES string $smiles:
#> PubChem_Canonical
#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
#> Molecular weight $mw: 215.7
#> PubChem synonyms (up to 10):
#> [1] "atrazine" "1912-24-9" "Gesaprim" "Atranex" "Oleogesaprim"
#> [6] "Atazinax" "Atrasine" "Chromozin" "Gesoprim" "Hungazin"