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.

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
chyaml: List of information obtained from a YAML file
TPs: List of transformation products as chent objects
transformations: Data frame of observed transformations
soil_degradation: Dataframe of modelling DT50 values
soil_ff: Dataframe of formation fractions
soil_sorption: Dataframe of 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()`

- -

Usage

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

- -

Method `try_pubchem()`

- -

Usage

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

- -

Method `get_pubchem()`

- -

Usage

chent$get_pubchem(pubchem_cid)

- -

Method `get_rdkit()`

- -

Usage

chent$get_rdkit(template = NULL)

- -

Method `get_chyaml()`

- -

Usage

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

- -

Method `add_p0()`

- -

Usage

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

- -

Method `add_cwsat()`

- -

Usage

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

- -

Method `add_PUF()`

- -

Usage

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

- -

Method `add_TP()`

- -

Usage

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

- -

Method `add_transformation()`

- -

Usage

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

- -

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
-)

- -

Method `add_soil_ff()`

- -

Usage

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

- -

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
-)

- -

Method `pdf()`

- -

Usage

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

- -

Method `png()`

- -

Usage

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

- -

Method `emf()`

- -

Usage

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

- -

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

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
-
#> PubChem:
#> Trying to get chemical information from RDKit using user SMILES
-#> CCCCCCCCO
#> Did not find chyaml file ./1-octanol.yaml
print(oct)
-
#> <chent>
-#> Identifier $identifier 1-octanol 
-#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>              user PubChem_Canonical 
-#>       "CCCCCCCCO"       "CCCCCCCCO" 
-#> Molecular weight $mw: 130.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "1-octanol"        "Octan-1-ol"       "octanol"          "111-87-5"        
-#>  [5] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "caprylic alcohol"
-#>  [9] "n-Octyl alcohol"  "Heptyl carbinol" 
if (!is.null(oct$Picture)) {
-  plot(oct)
-}
-

-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
#> Did not find chyaml file ./caffeine.yaml
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 $mw: 194.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "caffeine"                "58-08-2"                
-#>  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#>  [5] "Thein"                   "Methyltheobromine"      
-#>  [7] "Cafeina"                 "Theine"                 
-#>  [9] "Koffein"                 "Mateina"                
if (!is.null(caffeine$Picture)) {
-  plot(caffeine)
-}
-

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.

Usage

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

+ +

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? +Try to get chemical information from PubChem

+ +

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()`

+ +

Usage

chent$get_rdkit(template = NULL)

+ + +

Method `get_chyaml()`

+ +

Usage

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

+ + +

Method `add_p0()`

+ +

Usage

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

+ + +

Method `add_cwsat()`

+ +

Usage

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

+ + +

Method `add_PUF()`

+ +

Usage

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

+ + +

Method `add_TP()`

+ +

Usage

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

+ + +

Method `add_transformation()`

+ +

Usage

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

+ + +

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
+)

+ + +

Method `add_soil_ff()`

+ +

Usage

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

+ + +

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
+)

+ + +

Method `pdf()`

+ +

Usage

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

+ + +

Method `png()`

+ +

Usage

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

+ + +

Method `emf()`

+ +

Usage

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

+ + +

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

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
+#> Trying to get chemical information from RDKit using user SMILES
+#> CCCCCCCCO
+#> Did not find chyaml file ./1-octanol.yaml
+print(oct)
+#> <chent>
+#> Identifier $identifier 1-octanol 
+#> InChI Key $inchikey 
+#> SMILES string $smiles:
+#>        user 
+#> "CCCCCCCCO" 
+#> Molecular weight $mw: 130.2 
+if (!is.null(oct$Picture)) {
+  plot(oct)
+}
+
+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
+#> Did not find chyaml file ./caffeine.yaml
+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)
+}
+
+

An R6 class for chemical entities with associated data

Format

Public fields

Format

Public fields

Methods

Methods

Public methods

Method new()

Usage

Method try_pubchem()

Usage

Method get_pubchem()

Usage

Method get_rdkit()

Usage

Method get_chyaml()

Usage

Method add_p0()

Usage

Method add_cwsat()

Usage

Method add_PUF()

Usage

Method add_TP()

Usage

Method add_transformation()

Usage

Method add_soil_degradation()

Usage

Method add_soil_ff()

Usage

Method add_soil_sorption()

Usage

Method pdf()

Usage

Method png()

Usage

Method emf()

Usage

Method clone()

Usage

Arguments

Examples

Public methods

Method new()

Usage

Arguments

Method try_pubchem()

Usage

Arguments

Method get_pubchem()

Usage

Arguments

Method get_rdkit()

Usage

Method get_chyaml()

Usage

Method add_p0()

Usage

Method add_cwsat()

Usage

Method add_PUF()

Usage

Method add_TP()

Usage

Method add_transformation()

Usage

Method add_soil_degradation()

Usage

Method add_soil_ff()

Usage

Method add_soil_sorption()

Usage

Method pdf()

Usage

Method png()

Usage

Method emf()

Usage

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()`

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()`