Chemical Entities as R Objects

When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package chents provides a way to define an R object corresponding to a chemically defined substances (“chemical entity”) and to collect related information.

When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package ‘chents’ provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. If Python and ‘RDKit’ (> 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.

Usage +

When first defining a chemical entity, some chemical information is retrieved from the PubChem website using the webchem package.

 library(chents)
@@ -78,7 +81,7 @@
 There is a very simple plotting method for the chemical structure.
  plot(caffeine)
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 If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the BCPC compendium first.
  delta <- pai$new("Deltamethrin")
@@ -87,8 +90,9 @@
 #> Get chemical information from RDKit using PubChem SMILES
 #> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C
 plot(delta)
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 Additional information can be read from a local .yaml file. This information can be leveraged e.g. by the PEC_soil function of the ‘pfm’ package. However, this functionality is to be superseded by a dedicated package, defining data for the environmental risk assessment on chemicals, in particular on active ingredients of plant protection products.
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 Installation
 
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