stanstrup / webchem

Chemical Information from the Web

webchem

webchem is a R package to retrieve chemical information from the web. This package interacts with a suite of web APIs to retrieve chemical information.

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore (prefix_suffix()) They follow the format of source_functionality, e.g.cs_compinfo uses ChemSpider to retrieve compound informations.

Currently implemented in webchem

Source	Function(s)	API Docs	API key
Chemical Identifier Resolver (CIR)	cir_query()	link	none
ChemSpider	get_csid(), cs_compinfo(), cs_extcompinfo() , cs_convert(), cs_prop()	link	required (link)
PubChem	get_cid(), pc_prop(), pc_synonyms()	link	none
Chemical Translation Service (CTS)	cts_convert(), cts_compinfo()	none	none
PAN Pesticide Database	pan_query()	none	none
Alan Wood's Compendium of Pesticide Common Names	aw_query()	none	none
PHYSPROP Database	pp_query()	none	none
ETOX	get_etoxid(), etox_basic(). etox_targets(), etox_tests()	none	none
PPDB	ppdb_parse() (only parsing)	none	none
ChemIDplus	ci_query()	none	none
Wikidata	get_wdid(), wd_ident()	link	none
OPSIN	opsin_query()	link	none
Flavornet	fn_percept	none	none

Moreover, there are some functions to check indentifiers: is.inchikey(), is.cas() and is.smiles().

API keys

Some ChemSpider functions require a security token. Please register at RSC (https://www.rsc.org/rsc-id/register) to retrieve a security token.

Installation

Install from CRAN (stable version)

install.packages("webchem")

Install from Github (development version)

install.packages("devtools")
library("devtools")
install_github("ropensci/webchem")

Quickstart

library("webchem")

Chemical Identifier Resolver (CIR)

CAS numbers and molecular weight for Triclosan. Use first to return only the first hit.

cir_query('Triclosan', 'cas')
#> $Triclosan
#> [1] "3380-34-5"   "112099-35-1" "88032-08-0"
cir_query('Triclosan', 'cas', first = TRUE)
#>   Triclosan 
#> "3380-34-5"
cir_query('Triclosan', 'mw')
#> $Triclosan
#> [1] 289.5451

Query SMILES and InChIKey from CAS (Triclosan). Inputs might by ambiguous and we can specify where to search using resolver=.

cir_query('3380-34-5', 'smiles')
#> $`3380-34-5`
#> [1] "Oc1cc(Cl)ccc1Oc2ccc(Cl)cc2Cl"
cir_query('3380-34-5', 'stdinchikey', resolver = 'cas_number')
#> $`3380-34-5`
#> [1] "InChIKey=XEFQLINVKFYRCS-UHFFFAOYSA-N"

Query the number of rings using the InChiKey (Triclosan)

cir_query('XEFQLINVKFYRCS-UHFFFAOYSA-N', 'ring_count')
#> $`XEFQLINVKFYRCS-UHFFFAOYSA-N`
#> [1] 2

ChemSpider

You'll need a API key:

token = '<YOUR TOKEN HERE'

Retrieve the ChemSpider ID of Triclosan

(id <- get_csid(c('Aspirin', 'Triclosan'), token = token))
#>   Aspirin Triclosan 
#>    "2157"    "5363"

Use this ID to query information from ChemSpider

cs_extcompinfo(id, token = token)
#>   csid                     mf                         smiles
#> 1 2157        C_{9}H_{8}O_{4}          CC(=O)Oc1ccccc1C(=O)O
#> 2 5363 C_{12}H_{7}Cl_{3}O_{2} c1cc(c(cc1Cl)O)Oc2ccc(cc2Cl)Cl
#>                                                                         inchi
#> 1         InChI=1/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
#> 2 InChI=1/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H
#>                    inchikey average_mass       mw monoiso_mass
#> 1 BSYNRYMUTXBXSQ-UHFFFAOYAW     180.1574 180.1574   180.042252
#> 2 XEFQLINVKFYRCS-UHFFFAOYAS     289.5418 289.5418   287.951172
#>   nominal_mass alogp xlogp common_name
#> 1          180     0     0     Aspirin
#> 2          288  5.53     5   Triclosan
#>                                                source_url query
#> 1 https://www.chemspider.com/Chemical-Structure.2157.html     1
#> 2 https://www.chemspider.com/Chemical-Structure.5363.html     2

Note that the URL of the source if also returned (source_url) and can be used for (micro-)attribution.

Or to convert to a Mol-Object

mol <- cs_convert(id, from = 'csid', to = 'mol', token = token)
head(mol$ab)
#> NULL

Note that the Molfile is parsed into a R object (via parse_mol()) and that a API-key is needed

cs_convert() handles a lot of input / output formats, even without API-key:

cs_convert('XEFQLINVKFYRCS-UHFFFAOYAS', from = 'inchikey', to = 'csid')
#> [[1]]
#> [1] "5363"
cs_convert('XEFQLINVKFYRCS-UHFFFAOYAS', from = 'inchikey', to = 'inchi')
#> [[1]]
#> [1] "InChI=1/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H"
cs_convert('c1cc(c(cc1Cl)O)Oc2ccc(cc2Cl)Cl', from = 'smiles', to = 'inchi')
#> [[1]]
#> [1] "InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H"

And get EPISuit predictions from ChemSpider

cs_prop('5363')[['5363']]$epi[ , c(1:4)]
#>                                               prop value_pred
#> 1                 Log Octanol-Water Partition Coef     4.6600
#> 2                                    Boiling Point   373.6200
#> 3                                    Melting Point   136.7900
#> 4                        Water Solubility from KOW     4.6210
#> 5                  Water Solubility from Fragments     9.2998
#> 6 Log Octanol-Air Partition Coefficient (25 deg C)    11.4500
#> 7                  Log Soil Adsorption Coefficient     4.2650
#>         unit_pred                     source_pred
#> 1            <NA> Log Kow (KOWWIN v1.67 estimate)
#> 2           deg C                   MPBPWIN v1.42
#> 3           deg C                   MPBPWIN v1.42
#> 4 mg/L (25 deg C)                     WSKOW v1.41
#> 5            mg/L                            <NA>
#> 6            <NA>                    KOAWIN v1.10
#> 7            <NA>                  PCKOCWIN v1.66

PubChem

Retrieve PubChem CID

get_cid(c('Triclosan', 'Aspirin'))
#> $Triclosan
#> [1] 5564
#> 
#> $Aspirin
#> [1] 2244
get_cid('3380-34-5')
#> $`3380-34-5`
#> [1] 5564

Use this CID to retrieve some chemical properties:

pc_prop(c(5564,2244), properties = c('InChIKey', 'MolecularFormula', 'MolecularWeight'))
#>    CID MolecularFormula MolecularWeight                    InChIKey
#> 1 5564       C12H7Cl3O2         289.536 XEFQLINVKFYRCS-UHFFFAOYSA-N
#> 2 2244           C9H8O4         180.159 BSYNRYMUTXBXSQ-UHFFFAOYSA-N

and synonyms

pc_synonyms(5564, from = 'cid')[[1]][1:5]
#> [1] "5564"                                     
#> [2] "triclosan"                                
#> [3] "3380-34-5"                                
#> [4] "5-CHLORO-2-(2,4-DICHLOROPHENOXY)PHENOL"   
#> [5] "2,4,4'-Trichloro-2'-hydroxydiphenyl ether"
pc_synonyms('Triclosan', from = 'name')[[1]][1:5]
#> [1] "5564"                                     
#> [2] "triclosan"                                
#> [3] "3380-34-5"                                
#> [4] "5-CHLORO-2-(2,4-DICHLOROPHENOXY)PHENOL"   
#> [5] "2,4,4'-Trichloro-2'-hydroxydiphenyl ether"

Chemical Translation Service (CTS)

CTS allows to convert from nearly every possible identifier to nearly every possible identifier:

cts_convert(query = '3380-34-5', from = 'CAS', to = 'ChemSpider')
#> $`3380-34-5`
#> [1] "31465"
(inchk <- cts_convert(query = '50-00-0', from = 'CAS', to = 'inchikey'))
#> $`50-00-0`
#> [1] "WSFSSNUMVMOOMR-UHFFFAOYSA-N"

Moreover, we can a lot of information stored in the CTS database using InChIkey

info <- cts_compinfo(inchikey = inchk[[1]])
info[[1]][1:5]
#> $inchikey
#> [1] "WSFSSNUMVMOOMR-UHFFFAOYSA-N"
#> 
#> $inchicode
#> [1] "InChI=1S/CH2O/c1-2/h1H2"
#> 
#> $molweight
#> [1] 30.02602
#> 
#> $exactmass
#> [1] 30.01056
#> 
#> $formula
#> [1] "CH2O"

PAN Pesticide Database

pan_query() returns a list of 75 entries, here I extract only 4 of those:

pan_list <- pan_query('lambda-Cyhalothrin', match = 'best')
pan_list[[1]][c("CAS Number", "Chemical Class", "Water Solubility (Avg, mg/L)", "Adsorption Coefficient (Koc)" )]
#> $`CAS Number`
#> [1] "91465-08-6"
#> 
#> $`Chemical Class`
#> [1] "Pyrethroid"
#> 
#> $`Water Solubility (Avg, mg/L)`
#> [1] 0.005
#> 
#> $`Adsorption Coefficient (Koc)`
#> [1] 157000

Alan Wood's Compendium of Pesticide Common Names

aw_query() returns a list of 9 entries and can query common names and cas numbers:

aw_query('Fluazinam', type = 'commonname')
#> $Fluazinam
#> $Fluazinam$cname
#> [1] "Fluazinam"
#> 
#> $Fluazinam$status
#> [1] "ISO 1750 (published)"
#> 
#> $Fluazinam$pref_iupac_name
#> [1] "3-chloro-N-[3-chloro-2,6-dinitro-4-(trifluoromethyl)phenyl]-5-(trifluoromethyl)pyridin-2-amine"
#> 
#> $Fluazinam$iupac_name
#> [1] "3-chloro-N-(3-chloro-5-trifluoromethyl-2-pyridyl)-α,α,α-trifluoro-2,6-dinitro-p-toluidine"
#> 
#> $Fluazinam$cas
#> [1] "79622-59-6"
#> 
#> $Fluazinam$formula
#> [1] "C13H4Cl2F6N4O4"
#> 
#> $Fluazinam$activity
#> [1] "fungicides"
#> 
#> $Fluazinam$subactivity
#> [1] "pyridine fungicides"
#> 
#> $Fluazinam$inchikey
#> [1] "UZCGKGPEKUCDTF-UHFFFAOYSA-N"
#> 
#> $Fluazinam$inch
#> [1] "InChI=1S/C13H4Cl2F6N4O4/c14-6-1-4(12(16,17)18)3-22-11(6)23-9-7(24(26)27)2-5(13(19,20)21)8(15)10(9)25(28)29/h1-3H,(H,22,23)"
#> 
#> $Fluazinam$source_url
#> [1] "http://www.alanwood.net/pesticides/fluazinam.html"
#> 
#> 
#> attr(,"class")
#> [1] "list"     "aw_query"
aw_query('79622-59-6', type = 'cas')[[1]]$cname
#> [1] "fluazinam"

SRC PHYSPROP Database

SRCs PHYSPROP Database contains chemical structures, names and physical properties for over 41,000 chemicals. You can use pp_query() to query this database using a CAS number:

pp_query('50-00-0')
#> $`50-00-0`
#> $`50-00-0`$cas
#> [1] "50-00-0"
#> 
#> $`50-00-0`$cname
#> [1] "FORMALDEHYDE"
#> 
#> $`50-00-0`$mw
#> [1] 30.026
#> 
#> $`50-00-0`$prop
#>                       variable      value             unit     temp type
#> 1             Water Solubility  4.000e+05             mg/L 20 deg C  EXP
#> 2        Log P (octanol-water)  3.500e-01                  25 deg C  EXP
#> 3               Vapor Pressure  3.886e+03            mm Hg 25 deg C  EXT
#> 4    pKa Dissociation Constant  1.327e+01                  25 deg C  EXP
#> 5         Henry's Law Constant  3.370e-07       atm-m3/mol 25 deg C  EXP
#> 6 Atmospheric OH Rate Constant  9.370e-12 cm3/molecule-sec 25 deg C  EXP
#> 7                Melting Point -9.200e+01            deg C     <NA> <NA>
#> 8                Boiling Point -1.950e+02            deg C     <NA> <NA>
#>                                ref
#> 1        PICKRELL,JA ET AL. (1983)
#> 2           HANSCH,C ET AL. (1995)
#> 3          BOUBLIK,T ET AL. (1984)
#> 4   SERJEANT,EP & DEMPSEY,B (1979)
#> 5 BETTERTON,EA & HOFFMAN,MR (1988)
#> 6     KWOK,ESC & ATKINSON,R (1994)
#> 7                             <NA>
#> 8                             <NA>
#> 
#> $`50-00-0`$source_url
#> [1] "http://esc.syrres.com/fatepointer/webprop.asp?CAS=50000"

ETOX

ETOX: Information System Ecotoxicology and Environmental Quality Targets is a database run by the Federal Environment Agency of Germany and provides data on synonyms, identifiers, Quality Targest and Effects.

First we need to query a substance ID:

ids <- get_etoxid('Triclosan', match = 'best')
ids
#>   etoxid               match distance     query
#> 1  20179 Triclosan ( 20179 )        0 Triclosan

get_etoxid tries to find the best match for you (check the matched and distance attributes), if multiple hits are found. Other options are match = 'ask' to enter a interactive mode, 'na' to return NA, 'all' to return all hits and 'first' to return the first hit.

get_etoxid('Triclosan', match = 'all')
#> [[1]]
#> [1] "20179" "89236"
#> attr(,"matched")
#> [1] "Triclosan ( 20179 )"       "Methyltriclosan ( 89236 )"
#> attr(,"distance")
#> [1] "all"

With this substance ID we can query further information from ETOX, e.g.:

etox_basic(ids$etoxid)[[1]]
#> $cas
#> [1] "3380-34-5"
#> 
#> $ec
#> character(0)
#> 
#> $gsbl
#> [1] "117338"
#> 
#> $synonyms
#>                                          name  language
#> 4      5-chloro-2-(2,4-dichlorophenoxy)phenol   English
#> 5   Phenol, 5-chloro-2-(2,4-dichlorophenoxy)-   English
#> 8     2,4,4'-Trichlor-2'-hydroxydiphenylether    German
#> 9      2,4,4-Trichlor-2'-hydroxydiphenylether    German
#> 10   2,4,4'-Trichloro-2'-hydroxydiphenylether    German
#> 12     Chlor-2-(2,4-dichlorphenoxy)phenol, 5- universal
#> 13 Trichloro-2'-hydroxydiphenylether, 2,4,4'- universal
#> 14      5-Chlor-2-(2,4-dichlorphenoxy)-phenol universal
#> 15    Chlor-2-(2,4-dichlorphenoxy)-phenol, 5- universal
#> 16       5-Chlor-2-(2,4-dichlorphenoxy)phenol universal
#> 17                                  triclosán   Spanish
#> 18                                triklosaani   Finnish
#> 19                                 triclosano   Italian
#> 20                                  triklosan   Swedish
#> 
#> $source_url
#> [1] "https://webetox.uba.de/webETOX/public/basics/stoff.do?language=en&id=20179"

Which returns CAS, EC and GSBL numbers, as well as a synonym list.

We can also retrieve Quality Targets:

targets <- etox_targets(ids$etoxid)[[1]]
targets$res[ , c('Substance', 'Country_or_Region', 'Designation', 'Value_Target_LR', 'Unit')]
#>    Substance Country_or_Region      Designation Value_Target_LR Unit
#> 1  Triclosan               AUS             PNEC           0.050 µg/l
#> 2  Triclosan               CHE AA-QS_freshwater           0.020 µg/l
#> 3  Triclosan               CHE           MAC-QS           0.020 µg/l
#> 4  Triclosan               DEU           AA-EQS           0.020 µg/l
#> 5  Triclosan               DEU          MAC-EQS           0.200 µg/l
#> 6  Triclosan               DEU       QS_fw, eco           0.020 µg/l
#> 7  Triclosan               DEU   MAC-QS_fw, eco           0.160 µg/l
#> 8  Triclosan               DEU       QS_sw, eco           0.002 µg/l
#> 9  Triclosan               DEU   MAC-QS_sw, eco           0.016 µg/l
#> 10 Triclosan               DEU           AA-EQS           0.020 µg/l
#> 11 Triclosan               DEU           AA-EQS           0.002 µg/l
#> 12 Triclosan               DEU          MAC-EQS           0.200 µg/l
#> 13 Triclosan               DEU          MAC-EQS           0.020 µg/l

and results of ecotox tests:

tests <- etox_tests(ids$etoxid)[[1]]
tests$res[ , c('Organism', 'Effect', 'Duration', 'Time_Unit','Endpoint', 'Value', 'Unit')]
#>                           Organism                  Effect Duration
#> 1              Anabaena flos-aquae                    k.A.        4
#> 2          Brachionus calyciflorus                    k.A.        2
#> 3          Brachionus calyciflorus                    k.A.        2
#> 4          Brachionus calyciflorus                    k.A.        2
#> 5                Brachydanio rerio Embryo-Larval-Toxizität       10
#> 6               Ceriodaphnia dubia               Letalität        7
#> 7               Ceriodaphnia dubia              Mortalität        2
#> 8               Ceriodaphnia dubia              Mortalität        7
#> 9               Ceriodaphnia dubia                    k.A.        7
#> 10              Ceriodaphnia dubia            Reproduktion        7
#> 11              Ceriodaphnia dubia            Reproduktion        7
#> 12                   Daphnia magna              Mortalität       21
#> 13                   Daphnia magna            Reproduktion       21
#> 14         Desmodesmus subspicatus          Zellvermehrung        4
#> 15          Dunaliella tertiolecta          Zellvermehrung        4
#> 16          Dunaliella tertiolecta          Zellvermehrung        4
#> 17             Oncorhynchus mykiss Embryo-Larval-Toxizität        4
#> 18             Pimephales promelas              Mortalität        4
#> 19 Pseudokirchneriella subcapitata        Wachstumshemmung        3
#> 20         Scenedesmus subspicatus                Biomasse        3
#> 21         Scenedesmus subspicatus                    k.A.        4
#> 22         Scenedesmus subspicatus                    k.A.        4
#> 23         Scenedesmus subspicatus                    k.A.        4
#> 24         Scenedesmus subspicatus            Reproduktion        3
#> 25                 Hyalella azteca              Mortalität       10
#>    Time_Unit Endpoint   Value Unit
#> 1          d     NOEC   0.810     
#> 2          d     NOEC  50.000 µg/l
#> 3          d     NOEC  50.000 µg/l
#> 4          d     NOEC  50.000 µg/l
#> 5          d     NOEC 200.000 µg/l
#> 6          d     NOEC 339.000 µg/l
#> 7          d     EC50 120.000 µg/l
#> 8          d     NOEC  50.000 µg/l
#> 9          d     NOEC   4.000 µg/l
#> 10         d     NOEC   6.000 µg/l
#> 11         d     NOEC 182.000 µg/l
#> 12         d     NOEC 132.000 µg/l
#> 13         d     NOEC  40.000 µg/l
#> 14         d    ErC50   1.610 µg/l
#> 15         d     NOEC   1.600 µg/l
#> 16         d    EbC50   3.550 µg/l
#> 17         d     NOEC  34.100 µg/l
#> 18         d     LC50 260.000 µg/l
#> 19         d     NOEC   0.200 µg/l
#> 20         d     NOEC   0.500 µg/l
#> 21         d     NOEC   0.690 µg/l
#> 22         d     NOEC   0.742 µg/l
#> 23         d     NOEC   2.380 µg/l
#> 24         d     NOEC   0.500 µg/l
#> 25         d     NOEC   5.000 µg/l

PPDB

The PPDB holds a lot of chemical and ecotoxicological information. Earlier versions of webchem allowed also to search and download the database. However, this is explicitly against the terms and conditions of use. On request we also removed all links to the database.

Therefore, webchem can only provide a function to parse html-code into a R object: parse_ppdb(). However, no examples can be given as saving and downloading the html source is explicitly against the terms and conditions of use.

ChemIDplus

out <- ci_query(query = 'Triclosan', type = 'name', match = 'best')
out[['Triclosan']]$physprop
#>              Physical Property    Value            Units Temp (deg C)
#> 1                Melting Point       NA            deg C           NA
#> 2        log P (octanol-water) 4.76e+00           (none)           NA
#> 3             Water Solubility 1.00e+01             mg/L           20
#> 4               Vapor Pressure 6.45e-07            mm Hg           25
#> 5         Henry's Law Constant 4.99e-09      atm-m3/mole           25
#> 6 Atmospheric OH Rate Constant 1.61e-11 cm3/molecule-sec           25
#>   Source
#> 1    EXP
#> 2    EXP
#> 3    EXP
#> 4    EST
#> 5    EST
#> 6    EST

Wikidata

ids <- get_wdid(query = 'Triclosan')
ids
#>        id     match distance     query
#> 1 Q408646 triclosan        0 Triclosan

# quera identifiers from wikidata
wd_ident(ids$id)[1:5]
#>                                   smiles       cas  cid    einecs csid
#> 1 C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl 3380-34-5 5564 222-182-2 5363

OPSIN

opsin_query(c('Cyclopropane', 'Octane'))
#>                                                    inchi
#> Cyclopropane                InChI=1/C3H6/c1-2-3-1/h1-3H2
#> Octane       InChI=1/C8H18/c1-3-5-7-8-6-4-2/h3-8H2,1-2H3
#>                                                  stdinchi
#> Cyclopropane                InChI=1S/C3H6/c1-2-3-1/h1-3H2
#> Octane       InChI=1S/C8H18/c1-3-5-7-8-6-4-2/h3-8H2,1-2H3
#>                              stdinchikey   smiles message        query
#> Cyclopropane LVZWSLJZHVFIQJ-UHFFFAOYSA-N    C1CC1         Cyclopropane
#> Octane       TVMXDCGIABBOFY-UHFFFAOYSA-N CCCCCCCC               Octane

flavornet

fn_percept(c("75-07-0", "123-32-0"))
#>                                    75-07-0 
#>                           "pungent, ether" 
#>                                   123-32-0 
#> "cocoa, roasted nut, roast beef, medicine"

Extractor functions

The sources provide a lot of informations that can be retrieved using the functions described above. Often only specific inforamtion is needed. Therefore, we added extractor functions for common identifiers.

wi <- wd_ident("Q408646")
wi
#>                                   smiles       cas  cid    einecs csid
#> 1 C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl 3380-34-5 5564 222-182-2 5363
#>                                                                    inchi
#> 1 1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H
#>                      inchikey drugbank    zvg  chebi    chembl       unii
#> 1 XEFQLINVKFYRCS-UHFFFAOYSA-N    08604 490400 164200 CHEMBL849 4NM5039Y5X
#>                              source_url   query
#> 1 https://www.wikidata.org/wiki/Q408646 Q408646
cas(wi)
#> [1] "3380-34-5"
inchikey(wi)
#> [1] "XEFQLINVKFYRCS-UHFFFAOYSA-N"
smiles(wi)
#> [1] "C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl"

smiles(etox_basic(5564))
#> Error in smiles.etox_basic(etox_basic(5564)): InChIkey is not returned by this datasource!

Misc functions

Check if a string is a valid CAS registry number

is.cas('64-17-5')
#> [1] TRUE
is.cas('64-17-6')
#> [1] FALSE

Check if a string is a valid InChIKey

Using a pure R implementation:

is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N')
#> [1] TRUE
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKXA-N')
#> [1] FALSE

Using the ChemSpider API

is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N', type = 'chemspider')
#> [1] TRUE
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKXA-N', type = 'chemspider')
#> [1] FALSE

Check if a string is a valid SMILES

is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1Cl')
#> [1] TRUE
# 'J' is not found in the periodic table
is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1ClJ')
#> [1] FALSE

Acknowledgements

Without the fantastic web services webchem wouldn't be here. Therefore, kudos to the web service providers and developers!

Related Projects

If you're more familiar with Python you should check out Matt Swains repositories: ChemSpiPy, PubChemPy and CirPy provide similar functionality as webchem.

Contributors

• Eduard Szöcs
• Daniel Münch
• Johannes Ranke

Want to contribute?

Checkout our contribution guide here.

Meta

• Please report any issues, bugs or feature requests.
• License: MIT
• Get citation information for webchem in R doing citation(package = 'webchem')