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cccapi

R-CMD-check Codecov test coverage Lifecycle: experimental

A ZeroPM R package

The goal of the cccapi package is to provide a minimal and lightweight interface to the CAS Common Chemistry API services. To get access to the API services, you need to register at https://www.cas.org/services/commonchemistry-api.

The dependencies of cccapi are kept at a bare minimum: curl for handling the API requests and jsonlite to parse data from JSON format.

Installation

You can install the development version of cccapi from GitHub with:

# install.packages("remotes")
remotes::install_github("ZeroPM-H2020/cccapi")

Examples

The following examples show the functionality of the three API functions of cccapi: get_detail(), get_export(), and get_search().

This is an example which shows you how to get the record details for a CAS Registry Number. In this case, for atrazine:

library(cccapi)
atz_det <- get_detail("1912-24-9")
str(atz_det)
#> List of 15
#>  $ uri                   : chr "substance/pt/1912249"
#>  $ rn                    : chr "1912-24-9"
#>  $ name                  : chr "Atrazine"
#>  $ image                 : chr "<svg width=\"181.11\" viewBox=\"0 0 6037 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__
#>  $ inchi                 : chr "InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)13-8(14-7)11-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)"
#>  $ inchiKey              : chr "InChIKey=MXWJVTOOROXGIU-UHFFFAOYSA-N"
#>  $ smile                 : chr "N(C(C)C)C=1N=C(NCC)N=C(Cl)N1"
#>  $ canonicalSmile        : chr "ClC=1N=C(N=C(N1)NC(C)C)NCC"
#>  $ molecularFormula      : chr "C<sub>8</sub>H<sub>14</sub>ClN<sub>5</sub>"
#>  $ molecularMass         : chr "215.68"
#>  $ experimentalProperties:'data.frame':  2 obs. of  3 variables:
#>   ..$ name        : chr [1:2] "Melting Point" "Density"
#>   ..$ property    : chr [1:2] "175-177 °C" "1.23 g/cm<sup>3</sup> @ Temp: 22 °C"
#>   ..$ sourceNumber: int [1:2] 1 1
#>  $ propertyCitations     :'data.frame':  1 obs. of  3 variables:
#>   ..$ docUri      : chr ""
#>   ..$ sourceNumber: int 1
#>   ..$ source      : chr "Hazardous Substances Data Bank data were obtained from the National Library of Medicine (US)"
#>  $ synonyms              : chr [1:71] "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em><sup>2</sup>-ethyl-<em>N</em><sup>4</sup>-(1-methylethyl)-" "<em>s</em>-Triazine, 2-chloro-4-(ethylamino)-6-(isopropylamino)-" "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em>-ethyl-<em>N</em>â\200²-(1-methylethyl)-" "6-Chloro-<em>N</em><sup>2</sup>-ethyl-<em>N</em><sup>4</sup>-(1-methylethyl)-1,3,5-triazine-2,4-diamine" ...
#>  $ replacedRns           : chr [1:6] "11121-31-6" "12040-45-8" "12797-72-7" "39400-72-1" ...
#>  $ hasMolfile            : logi TRUE

Here is an example which shows you how to get the MOL file for a CAS Registry Number. In this case, again, for atrazine:

atz_exp <- get_export("1912-24-9")
str(atz_exp)
#>  chr "Atrazine\nC8H14ClN5\n1912-24-9 Copyright (C) 2021 ACS\n 14 14  0  0  0  0  0  0  0  0999 V2000\n    8.0021    0"| __truncated__

And finally, here is an example which shows you how to search for CAS Registry Numbers with a partial name. See ?get_search for details on the available search options!

atz_src <- get_search("atrazin*")
str(atz_src)
#> List of 2
#>  $ count  : int 12
#>  $ results:'data.frame': 12 obs. of  3 variables:
#>   ..$ rn   : chr [1:12] "1007-28-9" "1912-24-9" "2163-68-0" "39324-65-7" ...
#>   ..$ name : chr [1:12] "Deisopropylatrazine" "Atrazine" "Hydroxyatrazine" "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em>-ethyl-<em>N</em>â\200²-(1-methylethyl)-, mixt. with <em>N</em>-"| __truncated__ ...
#>   ..$ image: chr [1:12] "<svg width=\"178.77\" viewBox=\"0 0 5959 4052\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "<svg width=\"181.11\" viewBox=\"0 0 6037 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "<svg width=\"178.77\" viewBox=\"0 0 5959 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "" ...

Acknowledgement

This R package was developed by the EnviData initiative at the Norwegian Geotechnical Institute (NGI) as part of the project ZeroPM: Zero pollution of Persistent, Mobile substances. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101036756.

If you find this package useful and can afford it, please consider making a donation to a humanitarian non-profit organization, such as Sea-Watch. Thank you.