pcapi

A ZeroPM R package

The goal of the pcapi package is to provide a minimal and lightweight interface to the PubChem API services.

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

Currently, the following formats can be used to retrieve PubChem CIDs: InChI, InChIKey, names (including synonyms), SDF, and SMILES.

But what about webchem?

First of all, webchem is a fantastic package - please use it! webchem offers support for many different API services, not only PubChem’s API service. However, there are issues related to the way webchem sets up the queries against PubChem API services, which can result in errors. This has been observed, for example, when SMILES or InChI strings contain backslashes, or an MOL/SDF is used as input. With pcapi, these problems are (hopefully) solved. Additionally, pcapi will continuously implement some of the lesser known functionalities, such as the retrival of transformation products.

Installation

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

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

Functions

PubChem’s API services are vast and flexible. Not all functionality will be available immediately, and some functionalities may not be worth it to implement. That being said, the goal of pcapi is to provide a satisfying user-experience, covering the most relevant functionalities of the API. The following table gives an overview of the available functions, as well as their expected inputs and outputs.

Function	Expected input	Output
`post_to_cid()`	InChI, InChIKey, MOL, name, SDF, SMILES, synonym	integer vector of PubChem CID(s)
`post_to_property()`	PubChem CID	data frame of properties
`post_to_transformation()`	PubChem CID	data frame of transformation products
`post_to_use()`	PubChem CID	data frame of use categories
`post_to_standardize()`	InChI, SDF, SMILES	data frame of standardized compounds

Examples

The following examples show the functionality of two API functions of pcapi: post_to_cid() and post_to_property().

This is an example which shows you how to get the PubChem CID for the herbicide atrazine:

library(pcapi)

atrazine_cid <- post_to_cid("atrazine", format = "name")
atrazine_cid
#> [1] 2256

Using this PubChem CID, we can now get all available descriptors and physico-chemical properties for atrazine:

atrazine_properties <- post_to_property(atrazine_cid, property = "all")
str(atrazine_properties)
#> 'data.frame':    1 obs. of  42 variables:
#>  $ CID                     : int 2256
#>  $ MolecularFormula        : chr "C8H14ClN5"
#>  $ MolecularWeight         : num 216
#>  $ CanonicalSMILES         : chr "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
#>  $ IsomericSMILES          : chr "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
#>  $ 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 "MXWJVTOOROXGIU-UHFFFAOYSA-N"
#>  $ IUPACName               : chr "6-chloro-4-N-ethyl-2-N-propan-2-yl-1,3,5-triazine-2,4-diamine"
#>  $ XLogP                   : num 2.6
#>  $ ExactMass               : num 215
#>  $ MonoisotopicMass        : num 215
#>  $ TPSA                    : num 62.7
#>  $ Complexity              : int 166
#>  $ Charge                  : int 0
#>  $ HBondDonorCount         : int 2
#>  $ HBondAcceptorCount      : int 5
#>  $ RotatableBondCount      : int 4
#>  $ HeavyAtomCount          : int 14
#>  $ IsotopeAtomCount        : int 0
#>  $ AtomStereoCount         : int 0
#>  $ DefinedAtomStereoCount  : int 0
#>  $ UndefinedAtomStereoCount: int 0
#>  $ BondStereoCount         : int 0
#>  $ DefinedBondStereoCount  : int 0
#>  $ UndefinedBondStereoCount: int 0
#>  $ CovalentUnitCount       : int 1
#>  $ Volume3D                : num 158
#>  $ XStericQuadrupole3D     : num 5.3
#>  $ YStericQuadrupole3D     : num 4.27
#>  $ ZStericQuadrupole3D     : num 0.75
#>  $ FeatureCount3D          : int 6
#>  $ FeatureAcceptorCount3D  : int 0
#>  $ FeatureDonorCount3D     : int 2
#>  $ FeatureAnionCount3D     : int 0
#>  $ FeatureCationCount3D    : int 2
#>  $ FeatureRingCount3D      : int 1
#>  $ FeatureHydrophobeCount3D: int 1
#>  $ ConformerModelRMSD3D    : num 0.6
#>  $ EffectiveRotorCount3D   : int 4
#>  $ ConformerCount3D        : int 10
#>  $ Fingerprint2D           : chr "AAADccBzgAAEAAAAAAAAAAAAAAAAAAAAAAAsAAAAAAAAAAABgAAAHAIQAAAACCjBAAQDEAbIEAAgAAAAJAAAAAkAAIABAIAIAACACAAACAAAAAA"| __truncated__
#>  $ Title                   : chr "Atrazine"

To get an overview of all transformation products, the PubChem CID can be used as well:

atrazine_transformations <- post_to_transformation(atrazine_cid)
str(atrazine_transformations)
#> 'data.frame':    31 obs. of  13 variables:
#>  $ cids             :List of 31
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 135398733
#>   ..$ : int  2256 135408770
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 18831
#>   ..$ : int  2256 18831
#>   ..$ : int  2256 18831
#>   ..$ : int  2256 18831
#>   ..$ : int  2256 135398733
#>   ..$ : int  2256 135510207
#>   ..$ : int  2256 15818023
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 22563
#>   ..$ : int  2256 135398733
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 135510207
#>   ..$ : int  2256 135398733
#>   ..$ : int  2256 13878
#>   ..$ : int  2256 22563
#>  $ predecessor      : chr  "atrazine" "atrazine" "atrazine" "Atrazine" ...
#>  $ predecessorcid   : int  2256 2256 2256 2256 2256 2256 2256 2256 2256 2256 ...
#>  $ transformation   : chr  "Environmental" "Environmental" "Environmental" "Mammalian metabolism" ...
#>  $ successor        : chr  "6-deisopropyl atrazine" "deethylatrazine" "2-hydroxyatrazine" "Ammeline" ...
#>  $ successorcid     : int  13878 22563 135398733 135408770 13878 13878 13878 13878 18831 18831 ...
#>  $ evidencedoi      : chr  "10.1021/acs.est.1c00466" "10.1021/acs.est.1c00466" "10.1021/acs.est.1c00466" "10.5281/zenodo.3827487" ...
#>  $ evidenceref      : chr  "Menger, F. et al (2021); Identification of pesticide transformation products in surface water using suspect scr"| __truncated__ "Menger, F. et al (2021); Identification of pesticide transformation products in surface water using suspect scr"| __truncated__ "Menger, F. et al (2021); Identification of pesticide transformation products in surface water using suspect scr"| __truncated__ "Kearney, P.C., and D. D. Kaufman (eds.) Herbicides: Chemistry, Degredation and Mode of Action. Volumes 1 and 2."| __truncated__ ...
#>  $ sourcecomment    : chr  "10.5281/zenodo.4687924" "10.5281/zenodo.4687924" "10.5281/zenodo.4687924" "HSDB" ...
#>  $ sourcecommentfull:List of 31
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "HSDB is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. See https://pu"| __truncated__
#>   ..$ : chr "Eawag: Swiss Federal Institute for Aquatic Science and Technology (https://www.eawag.ch/en/)"
#>   ..$ : chr "Eawag: Swiss Federal Institute for Aquatic Science and Technology (https://www.eawag.ch/en/)"
#>   ..$ : chr "Eawag: Swiss Federal Institute for Aquatic Science and Technology (https://www.eawag.ch/en/)"
#>   ..$ : chr "Eawag: Swiss Federal Institute for Aquatic Science and Technology (https://www.eawag.ch/en/)"
#>   ..$ : chr "Pesticides Properties DataBase; Lewis, K.A., Tzilivakis, J., Warner, D.J. and Green, A., 2016. An international"| __truncated__
#>   ..$ : chr "Pesticides Properties DataBase; Lewis, K.A., Tzilivakis, J., Warner, D.J. and Green, A., 2016. An international"| __truncated__
#>   ..$ : chr "Pesticides Properties DataBase; Lewis, K.A., Tzilivakis, J., Warner, D.J. and Green, A., 2016. An international"| __truncated__
#>  $ datasetdoi       : chr  "10.5281/zenodo.4687924" "10.5281/zenodo.4687924" "10.5281/zenodo.4687924" "10.5281/zenodo.3827487" ...
#>  $ datasetref       :List of 31
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr  "S78 " " SLUPESTTPS " " Pesticides and TPs from SLU, Sweden"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S68 " " HSDBTPS " " Transformation Products Extracted from HSDB Content in PubChem, validated by LCSB-ECI"
#>   ..$ : chr  "S66 " " EAWAGTPS " " Parent-Transformation Product Pairs from Eawag " " Parent-Transformation Product Pairs from Schollee et al 2017, Eawag."
#>   ..$ : chr  "S66 " " EAWAGTPS " " Parent-Transformation Product Pairs from Eawag " " Parent-Transformation Product Pairs from Schollee et al 2017, Eawag."
#>   ..$ : chr  "S66 " " EAWAGTPS " " Parent-Transformation Product Pairs from Eawag " " Parent-Transformation Product Pairs from Schollee et al 2017, Eawag."
#>   ..$ : chr  "S66 " " EAWAGTPS " " Parent-Transformation Product Pairs from Eawag " " Parent-Transformation Product Pairs from Schollee et al 2017, Eawag."
#>   ..$ : chr  "S60 " " SWISSPEST19 " " Swiss Pesticides and Metabolites from Kiefer et al 2019 " " Swiss Pesticides and Metabolites from Kiefer et al 2019."
#>   ..$ : chr  "S60 " " SWISSPEST19 " " Swiss Pesticides and Metabolites from Kiefer et al 2019 " " Swiss Pesticides and Metabolites from Kiefer et al 2019."
#>   ..$ : chr  "S60 " " SWISSPEST19 " " Swiss Pesticides and Metabolites from Kiefer et al 2019 " " Swiss Pesticides and Metabolites from Kiefer et al 2019."
#>  $ biosystem        : chr  "soil" "soil" "soil" NA ...

The use categories can also be retrieved using the PubChem CID:

atrazine_uses <- post_to_use(atrazine_cid)
str(atrazine_uses)
#> 'data.frame':    11 obs. of  5 variables:
#>  $ category    : chr  "Laboratory supplies" "Landscape/yard -> herbicide" "Landscape/yard -> lawn fertilizer" "biocide" ...
#>  $ cid         : int  2256 2256 2256 2256 2256 2256 2256 2256 2256 2256 ...
#>  $ catogorydesc: chr  "Products specifically used in a laboratory setting, e.g. laboratory diagnostics or consumables, solvents and re"| __truncated__ "Products used to control or kill unwanted plants" "Fertilizers for lawns, including in combination with pest/weed controllers" NA ...
#>  $ source      : chr  "Product Use Category (PUC)" "Product Use Category (PUC)" "Product Use Category (PUC)" "OECD Functional Use" ...
#>  $ cmpdname    : chr  "Atrazine" "Atrazine" "Atrazine" "Atrazine" ...

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.