An R6 class for chemical entities with associated data

The class is initialised with an identifier. Chemical information is retrieved from the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed.

Format

An R6Class generator object

Public fields

identifier: (character(1))
The identifier that was used to initiate the object, with attribute 'source'
inchikey: (character(1))
InChI Key, with attribute 'source'
smiles: (character())
SMILES code(s), with attribute 'source'
mw: (numeric(1))
Molecular weight, with attribute 'source'
pubchem: (list())
List of information retrieved from PubChem
rdkit: List of information obtained with RDKit
mol: <rdkit.Chem.rdchem.Mol> object
svg: SVG code
Picture: Graph as a picture object obtained using grImport
Pict_font_size: Font size as extracted from the intermediate PostScript file
pdf_height: Height of the MediaBox in the pdf after cropping
p0: Vapour pressure in Pa
cwsat: Water solubility in mg/L
PUF: Plant uptake factor
chyaml: List of information obtained from a YAML file
TPs: List of transformation products as chent objects Add a transformation product to the internal list
transformations: Data frame of observed transformations Add a line in the internal dataframe holding observed transformations
soil_degradation: Dataframe of modelling DT50 values Add a line in the internal dataframe holding modelling DT50 values
soil_ff: Dataframe of formation fractions
soil_sorption: Dataframe of soil sorption data Add soil sorption data

Methods

Public methods

chent$new()
chent$try_pubchem()
chent$get_pubchem()
chent$get_rdkit()
chent$get_chyaml()
chent$add_p0()
chent$add_cwsat()
chent$add_PUF()
chent$add_TP()
chent$add_transformation()
chent$add_soil_degradation()
chent$add_soil_ff()
chent$add_soil_sorption()
chent$pdf()
chent$png()
chent$emf()
chent$clone()

Method `new()`

Creates a new instance of this R6 class.

Try to get chemical information from PubChem

Usage

chent$new(
  identifier,
  smiles = NULL,
  inchikey = NULL,
  pubchem = TRUE,
  pubchem_from = c("name", "smiles", "inchikey"),
  rdkit = TRUE,
  template = NULL,
  chyaml = FALSE
)

Arguments

identifier: Identifier to be stored in the object
smiles: Optional user provided SMILES code
inchikey: Optional user provided InChI Key
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 directory?

Method `try_pubchem()`

Usage

chent$try_pubchem(query, from = "name")

Arguments

query: Query string to be passed to get_cid
from: Passed to get_cid Get chemical information from PubChem for a known PubChem CID

Method `get_pubchem()`

Usage

chent$get_pubchem(pubchem_cid)

Arguments

pubchem_cid: CID

Method `get_rdkit()`

Get chemical information from RDKit if available Obtain information from a YAML file

Usage

chent$get_rdkit(template = NULL)

Arguments

template: An optional SMILES code to be used as template for RDKit

Method `get_chyaml()`

Usage

chent$get_chyaml(
  repo = c("wd", "local", "web"),
  chyaml = paste0(URLencode(self$identifier), ".yaml")
)

Arguments

repo: Should the file be looked for in the current working directory, a local git repository under ~/git/chyaml, or from the web (not implemented).
chyaml: The filename to be looked for Add a vapour pressure

Method `add_p0()`

Usage

chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")

Arguments

p0: The vapour pressure in Pa Add a water solubility
T: Temperature
source: An acronym specifying the source of the information
page: The page from which the information was taken
remark: A remark

Method `add_cwsat()`

Usage

chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")

Arguments

cwsat: The water solubility in mg/L Add a plant uptake factor
T: Temperature
pH: pH value
source: An acronym specifying the source of the information
page: The page from which the information was taken
remark: A remark

Method `add_PUF()`

Usage

chent$add_PUF(
  PUF = 0,
  source = "focus_generic_gw_2014",
  page = 41,
  remark = "Conservative default value"
)

Arguments

PUF: The plant uptake factor, a number between 0 and 1
source: An acronym specifying the source of the information
page: The page from which the information was taken
remark: A remark

Method `add_TP()`

Usage

chent$add_TP(x, smiles = NULL, pubchem = FALSE)

Arguments

x: A chent object, or an identifier to generate a chent object
smiles: Optional user provided SMILES code
pubchem: Should chemical information be obtained from PubChem?

Method `add_transformation()`

Usage

chent$add_transformation(
  study_type,
  TP_identifier,
  max_occurrence,
  remark = "",
  source = NA,
  pages = NA
)

Arguments

study_type: A characterisation of the study type
TP_identifier: An identifier of one of the transformation products in self$TPs
max_occurrence: The maximum observed occurrence of the transformation product, expressed as a fraction of the amount that would result from stochiometric transformation
remark: A remark
source: An acronym specifying the source of the information
pages: The pages from which the information was taken

Method `add_soil_degradation()`

Usage

chent$add_soil_degradation(
  soils,
  DT50_mod,
  DT50_mod_ref,
  type = NA,
  country = NA,
  pH_orig = NA,
  pH_medium = NA,
  pH_H2O = NA,
  perc_OC = NA,
  temperature = NA,
  moisture = NA,
  category = "lab",
  formulation = NA,
  model = NA,
  chi2 = NA,
  remark = "",
  source,
  page = NA
)

Arguments

soils: Names of the soils
DT50_mod: The modelling DT50 in the sense of regulatory pesticide fate modelling
DT50_mod_ref: The normalised modelling DT50 in the sense of regulatory pesticide fate modelling
type: The soil type
country: The country (mainly for field studies)
pH_orig: The pH stated in the study
pH_medium: The medium in which this pH was measured
pH_H2O: The pH extrapolated to pure water
perc_OC: The percentage of organic carbon in the soil
temperature: The temperature during the study in degrees Celsius
moisture: The moisture during the study
category: Is it a laboratory ('lab') or field study ('field')
formulation: Name of the formulation applied, if it was not the technical active ingredient
model: The degradation model used for deriving DT50_mod
chi2: The relative error as defined in FOCUS kinetics
remark: A remark
source: An acronym specifying the source of the information
page: The page from which the information was taken

Method `add_soil_ff()`

Usage

chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)

Arguments

target: The identifier(s) of the transformation product
soils: The soil name(s) in which the transformation was observed
ff: The formation fraction(s)
remark: A remark
source: An acronym specifying the source of the information
page: The page from which the information was taken

Method `add_soil_sorption()`

Usage

chent$add_soil_sorption(
  soils,
  Kf,
  Kfoc,
  N,
  type = NA,
  pH_orig = NA,
  pH_medium = NA,
  pH_H2O = NA,
  perc_OC = NA,
  perc_clay = NA,
  CEC = NA,
  remark = "",
  source,
  page = NA
)

Arguments

soils: Names of the soils
Kf: The sorption constant in L/kg, either linear (then N is 1) or according to Freundlich
Kfoc: The constant from above, normalised to soil organic carbon
N: The Freundlich exponent
type: The soil type
pH_orig: The pH stated in the study
pH_medium: The medium in which this pH was measured
pH_H2O: The pH extrapolated to pure water
perc_OC: The percentage of organic carbon in the soil
perc_clay: The percentage of clay in the soil
CEC: The cation exchange capacity
remark: A remark
source: An acronym specifying the source of the information
page: The page from which the information was taken

Method `pdf()`

Write a PDF image of the structure Write a PNG image of the structure

Usage

chent$pdf(
  file = paste0(self$identifier, ".pdf"),
  dir = "structures/pdf",
  template = NULL
)

Arguments

file: The file to write to
dir: The directory to write the file to
template: An optional SMILES code to be used as template for RDKit

Method `png()`

Usage

chent$png(
  file = paste0(self$identifier, ".png"),
  dir = "structures/png",
  antialias = "gray"
)

Arguments

file: The file to write to
dir: The directory to write the file to
antialias: Passed to png

Method `emf()`

Write an EMF image of the structure using emf

Usage

chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")

Arguments

file: The file to write to
dir: The directory to write the file to

Method `clone()`

The objects of this class are cloneable with this method.

Usage

chent$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

caffeine <- chent$new("caffeine")
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
print(caffeine)
#> <chent>
#> Identifier $identifier caffeine 
#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
#> SMILES string $smiles:
#>              PubChem_Canonical 
#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
#> Molecular weight $mw: 194.2 
#> PubChem synonyms (up to 10):
#>  [1] "caffeine"                "58-08-2"                
#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
#>  [5] "Methyltheobromine"       "Theine"                 
#>  [7] "Thein"                   "Cafeina"                
#>  [9] "Koffein"                 "Mateina"                
if (!is.null(caffeine$Picture)) {
  plot(caffeine)
}

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
#> Trying to get chemical information from RDKit using user SMILES
#> CCCCCCCCO
print(oct)
#> <chent>
#> Identifier $identifier 1-octanol 
#> InChI Key $inchikey NA 
#> SMILES string $smiles:
#>        user 
#> "CCCCCCCCO" 
#> Molecular weight $mw: 130.2

An R6 class for chemical entities with associated data

Format

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Method try_pubchem()

Usage

Arguments

Method get_pubchem()

Usage

Arguments

Method get_rdkit()

Usage

Arguments

Method get_chyaml()

Usage

Arguments

Method add_p0()

Usage

Arguments

Method add_cwsat()

Usage

Arguments

Method add_PUF()

Usage

Arguments

Method add_TP()

Usage

Arguments

Method add_transformation()

Usage

Arguments

Method add_soil_degradation()

Usage

Arguments

Method add_soil_ff()

Usage

Arguments

Method add_soil_sorption()

Usage

Arguments

Method pdf()

Usage

Arguments

Method png()

Usage

Arguments

Method emf()

Usage

Arguments

Method clone()

Usage

Arguments

Examples

Method `new()`

Method `try_pubchem()`

Method `get_pubchem()`

Method `get_rdkit()`

Method `get_chyaml()`

Method `add_p0()`

Method `add_cwsat()`

Method `add_PUF()`

Method `add_TP()`

Method `add_transformation()`

Method `add_soil_degradation()`

Method `add_soil_ff()`

Method `add_soil_sorption()`

Method `pdf()`

Method `png()`

Method `emf()`

Method `clone()`