pai: An R6 class for pesticidal active ingredients and associated...

In jranke/chents: Chemical Entities as R Objects

An R6 class for pesticidal active ingredients and associated data

Description

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 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

# 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)
}

}

jranke/chents documentation built on Dec. 6, 2024, 10:55 p.m.