An R6 class for chemical entities with associated data

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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.

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chent

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Format

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An R6Class generator object

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Fields

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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
chyaml: List of information obtained from a YAML file
degradation: List of degradation endpoints

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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 3.4.2 (default, Oct  8 2014, 10:47:48) 
+#> [GCC 4.9.1]
#> 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 $mw: 130.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
+#>  [5] "Octyl alcohol"    "N-octanol"        "Capryl alcohol"   "n-Octyl alcohol" 
+#>  [9] "111-87-5"         "caprylic alcohol"
plot(oct)
caffeine <- chent$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] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Cafeina"                
+#>  [7] "Thein"                   "Koffein"                
+#>  [9] "Mateina"                 "Theine"                 
plot(caffeine)

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An R6 class for chemical entities with associated data

Format

Fields

Examples

Contents