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# chents
[](https://pkgdown.jrwb.de/chents/)
[](https://jranke.r-universe.dev/chents)
[](https://pkgdown.jrwb.de/chents/coverage/coverage.html)
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 and check the identity of
chemically defined substances (“chemical entities”) and to collect
related information.
When first defining a chemical entity, some chemical information is
retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website
using the [webchem](https://docs.ropensci.org/webchem/) package.
``` r
library(chents)
caffeine <- chent$new("Caffeine")
#> Querying PubChem for name Caffeine ...
#> Get chemical information from RDKit using PubChem SMILES
#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
```
If Python and [RDKit](https://rdkit.org) (\> 2015.03) are installed and
configured for use with the
[reticulate](https://rstudio.github.io/reticulate/) package, some
additional chemical information including a 2D graph are computed.
The print method gives an overview of the information that was
collected.
``` r
print(caffeine)
#> <chent>
#> Identifier $identifier Caffeine
#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#> SMILES string $smiles:
#> PubChem
#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#> Molecular weight $mw: 194.2
#> PubChem synonyms (up to 10):
#> [1] "caffeine" "58-08-2"
#> [3] "Guaranine" "1,3,7-Trimethylxanthine"
#> [5] "Methyltheobromine" "Theine"
#> [7] "Thein" "Cafeina"
#> [9] "Caffein" "Cafipel"
```
There is a very simple plotting method for the chemical structure.
``` r
plot(caffeine)
```
If you have a so-called ISO common name of a pesticide active
ingredient, you can use the ‘pai’ class derived from the ‘chent’ class,
which starts with querying the [BCPC
compendium](http://www.bcpcpesticidecompendium.org/) first.
``` r
delta <- pai$new("Deltamethrin")
#> Querying BCPC for Deltamethrin ...
#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ...
#> 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)
```
Additional information can be read from a local .yaml file. This
information can be leveraged e.g. by the
[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) 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 However, this functionality is to be superseded by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.
## Installation
You can conveniently install chents from the repository kindly made
available by the R-Universe project:
``` r
install.packages("chents",
repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org"))
```
In order to profit from the chemoinformatics, you need to install RDKit
and its python bindings. On a Debian type Linux distribution, just use
``` sh
sudo apt install python3-rdkit
```
If you use this package on Windows or MacOS, I would be happy to include
installation instructions here if you share them with me, e.g. via a
Pull Request.
## Configuration of the Python version to use
On Debian type Linux distributions, you can use the following line in
your global or project specific `.Rprofile` file to tell the
`reticulate` package to use the system Python version that will find the
RDKit installed in the system location.
``` r
Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3")
```
## Using R6 classes
Note that the `chent` objects defined by this package are
[R6](https://r6.r-lib.org/articles/Introduction.html) classes.
Therefore, if you think you make a copy by assigning them to a new name,
the objects will still be connected, because only the reference is
copied. For example, you can create a molecule without retrieving data
from PubChem
``` r
but <- chent$new("Butane", smiles = "CCCC", pubchem = FALSE)
#> Get chemical information from RDKit using user SMILES
#> CCCC
print(but)
#> <chent>
#> Identifier $identifier Butane
#> InChI Key $inchikey NA
#> SMILES string $smiles:
#> user
#> "CCCC"
#> Molecular weight $mw: 58.1
```
If you then assign a new name and add PubChem information to the object
with the new name, the information will also be added to the original
`chent` object:
``` r
but_pubchem <- but
but_pubchem$try_pubchem()
#> Querying PubChem for name Butane ...
print(but)
#> <chent>
#> Identifier $identifier Butane
#> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N
#> SMILES string $smiles:
#> user PubChem
#> "CCCC" "CCCC"
#> Molecular weight $mw: 58.1
#> PubChem synonyms (up to 10):
#> [1] "BUTANE" "n-Butane" "106-97-8"
#> [4] "Diethyl" "Methylethylmethane" "Butanen"
#> [7] "Butani" "Butyl hydride" "HC 600"
#> [10] "A 21 (lowing agent)"
```
You can create a derived, independent object using the `clone()` method
that will not be affected by operations on the original object:
``` r
but_new <- chent$new("Butane", smiles = "CCCC", pubchem = FALSE)
#> Get chemical information from RDKit using user SMILES
#> CCCC
but_clone <- but_new$clone()
but_new$try_pubchem()
#> Querying PubChem for name Butane ...
but_clone
#> <chent>
#> Identifier $identifier Butane
#> InChI Key $inchikey NA
#> SMILES string $smiles:
#> user
#> "CCCC"
#> Molecular weight $mw: 58.1
```
# Package index
## R6 Class definitions and methods
- [`chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) : An R6
class for chemical entities with associated data
- [`pai`](https://pkgdown.jrwb.de/chents/reference/pai.md) : An R6 class
for pesticidal active ingredients and associated data
- [`ppp`](https://pkgdown.jrwb.de/chents/reference/ppp.md) : R6 class
for a plant protection product with at least one active ingredient
- [`draw_svg.chent()`](https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.md)
: Draw SVG graph from a chent object using RDKit
- [`plot(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/plot.chent.md)
: Plot method for chent objects
- [`print(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.chent.md)
: Printing method for chent objects
- [`print(`*`<pai>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.pai.md)
: Printing method for pai objects (pesticidal active ingredients)
- [`print(`*`<ppp>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.ppp.md)
: Printing method for ppp objects (plant protection products)
|
