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# 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"
# }
```
|
