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 and configured for use with PythonInR.

chent

Format

An R6Class generator object

Fields

identifier

The identifier that was used to initiate the object, with attribute 'source'

inchikey

InChI Key, with attribute 'source'

smiles

SMILES code, with attribute 'source'

mw

Molecular weight, with attribute 'source'

pubchem

List of information retreived from PubChem

rdkit

List of information obtained with RDKit, if installed and configured for use with PythonInR

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

chyaml

List of information obtained from a YAML file

soil_degradation

Dataframe of modelling DT50 values

soil_ff

Dataframe of formation fractions

soil_sorption

Dataframe of soil sorption data

PUF

Plant uptake factor

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 
#> Initialize Python Version 2.7.13 (default, Sep 26 2018, 18:42:22) 
#> [GCC 6.3.0 20170516]
#> 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 $mw: 130.2 
#> PubChem synonyms (up to 10):
#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
#>  [5] "111-87-5"         "N-octanol"        "Capryl alcohol"   "Octyl alcohol"   
#>  [9] "caprylic alcohol" "n-Octyl alcohol" 
if (!is.null(oct$Picture)) {
  plot(oct)
}
caffeine <- chent$new("caffeine")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 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 $mw: 194.2 
#> PubChem synonyms (up to 10):
#>  [1] "2519"                    "caffeine"               
#>  [3] "58-08-2"                 "Guaranine"              
#>  [5] "1,3,7-Trimethylxanthine" "Thein"                  
#>  [7] "Cafeina"                 "Methyltheobromine"      
#>  [9] "Koffein"                 "Mateina"                
if (!is.null(caffeine$Picture)) {
  plot(caffeine)
}