R/pubchem.R
In ropensci/webchem: Chemical Information from the Web
Defines functions
pc_extract
pc_page
pc_sect
pc_synonyms
pc_prop
get_cid
Documented in
get_cid
pc_prop
pc_sect
pc_synonyms
#' Retrieve Pubchem Compound ID (CID)
#'
#' Retrieve compound IDs (CIDs) from PubChem.
#' @param query character; search term, one or more compounds.
#' @param from character; type of input. See details for more information.
#' @param domain character; query domain, can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}.
#' @param match character; How should multiple hits be handled?, \code{"all"}
#' all matches are returned, \code{"first"} the first matching is returned,
#' \code{"ask"} enters an interactive mode and the user is asked for input,
#' \code{"na"} returns NA if multiple hits are found.
#' @param verbose logical; should a verbose output be printed on the console?
#' @param arg character; optinal arguments like "name_type=word" to match
#' individual words.
#' @param first deprecated. Use `match` instead.
#' @param ... currently unused.
#' @return a tibble.
#' @details Valid values for the \code{from} argument depend on the
#' \code{domain}:
#' \itemize{
#' \item{\code{compound}: \code{"name"}, \code{"smiles"}, \code{"inchi"},
#' \code{"inchikey"}, \code{"formula"}, \code{"sdf"}, \code{"cas"} (an alias for
#' \code{"xref/RN"}), <xref>, <structure search>, <fast search>.}
#' \item{\code{substance}: \code{"name"}, \code{"sid"},
#' \code{<xref>}, \code{"sourceid/<source id>"} or \code{"sourceall"}.}
#' \item{\code{assay}: \code{"aid"}, \code{<assay target>}.}
#' }
#' @details <structure search> is assembled as "{\code{substructure} |
#' \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
#' | \code{inchi} | \code{sdf} | \code{cid}}", e.g.
#' \code{from = "substructure/smiles"}.
#' @details \code{<xref>} is assembled as "\code{xref}/\{\code{RegistryID} |
#' \code{RN} | \code{PubMedID} | \code{MMDBID} | \code{ProteinGI},
#' \code{NucleotideGI} | \code{TaxonomyID} | \code{MIMID} | \code{GeneID} |
#' \code{ProbeID} | \code{PatentID}\}", e.g. \code{from = "xref/RN"} will query
#' by CAS RN.
#' @details <fast search> is either \code{fastformula} or it is assembled as
#' "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
#' \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
#' \code{smarts} | \code{inchi} | \code{sdf} | \code{cid}}", e.g.
#' \code{from = "fastidentity/smiles"}.
#' @details \code{<source id>} is any valid PubChem Data Source ID. When
#' \code{from = "sourceid/<source id>"}, the query is the ID of the substance in
#' the depositor's database.
#' @details If \code{from = "sourceall"} the query is one or more valid Pubchem
#' depositor names. Depositor names are not case sensitive.
#' @details Depositor names and Data Source IDs can be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @details \code{<assay target>} is assembled as "\code{target}/\{\code{gi} |
#' \code{proteinname} | \code{geneid} | \code{genesymbol} | \code{accession}\}",
#' e.g. \code{from = "target/geneid"} will query by GeneID.
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
#' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
#' Information from the Web. Journal of Statistical Software, 93(13).
#' \doi{10.18637/jss.v093.i13}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @import httr
#' @importFrom purrr map map2
#' @importFrom jsonlite fromJSON
#' @importFrom tibble enframe
#' @importFrom utils URLencode
#' @export
#' @examples
#' \dontrun{
#' # might fail if API is not available
#' get_cid("Triclosan")
#' get_cid("Triclosan", arg = "name_type=word")
#' # from SMILES
#' get_cid("CCCC", from = "smiles")
#' # from InChI
#' get_cid("InChI=1S/CH5N/c1-2/h2H2,1H3", from = "inchi")
#' # from InChIKey
#' get_cid("BPGDAMSIGCZZLK-UHFFFAOYSA-N", from = "inchikey")
#' # from formula
#' get_cid("C26H52NO6P", from = "formula")
#' # from CAS RN
#' get_cid("56-40-6", from = "xref/rn")
#' # similarity
#' get_cid(5564, from = "similarity/cid")
#' get_cid("CCO", from = "similarity/smiles")
#' # from SID
#' get_cid("126534046", from = "sid", domain = "substance")
#' # sourceid
#' get_cid("VCC957895", from = "sourceid/23706", domain = "substance")
#' # sourceall
#' get_cid("Optopharma Ltd", from = "sourceall", domain = "substance")
#' # from AID (CIDs of substances tested in the assay)
#' get_cid(170004, from = "aid", domain = "assay")
#' # from GeneID (CIDs of substances tested on the gene)
#' get_cid(25086, from = "target/geneid", domain = "assay")
#'
#' # multiple inputs
#' get_cid(c("Triclosan", "Aspirin"))
#'
#' }
get_cid <-
function(query,
from = "name",
domain = c("compound", "substance", "assay"),
match = c("all", "first", "ask", "na"),
verbose = getOption("verbose"),
arg = NULL,
first = NULL,
...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
#deprecate `first`
if (!is.null(first) && first) {
message("`first = TRUE` is deprecated. Use `match = 'first'` instead")
match <- "first"
} else if (!is.null(first) && !first) {
message("`first = FALSE` is deprecated. Use `match = 'all'` instead")
match <- "all"
}
#input validation
from <- tolower(from)
from <- ifelse(from == "cas", "xref/rn", from)
if (from == "xref/rn"){
query <- as.cas(query, verbose = verbose)
}
domain <- match.arg(domain)
xref <- paste(
"xref",
c("registryid", "rn", "pubmedid", "mmdbid", "proteingi", "nucleotidegi",
"taxonomyid", "mimid", "geneid", "probeid", "patentid"),
sep = "/"
)
structure_search <- expand.grid(
c("substructure", "superstructure", "similarity", "identity"),
c("smiles", "inchi", "sdf", "cid")
)
structure_search <- paste(structure_search$Var1, structure_search$Var2,
sep = "/")
fast_search <- expand.grid(
c("fastidentity", "fastsimilarity_2d", "fastsimilarity_3d",
"fastsubstructure", "fastsuperstructure"),
c("smiles", "smarts", "inchi", "sdf", "cid")
)
fast_search <- c(with(fast_search, paste(Var1, Var2, sep = "/")),
"fastformula")
targets <- paste("target", c("gi", "proteinname", "geneid", "genesymbol",
"accession"), sep = "/")
if (domain == "compound") {
from_choices <- c("cid", "name", "smiles", "inchi", "sdf", "inchikey",
"formula", structure_search, xref, fast_search)
from <- match.arg(from, choices = from_choices)
}
if (domain == "substance") {
if (!grepl("^sourceid/", from)) {
from <- match.arg(from, choices = c("sid", "name", xref, "sourceall"))
}
}
if (domain == "assay") {
from <- match.arg(from, choices = c("aid", targets))
}
match <- match.arg(match)
foo <- function(query, from, domain, match, verbose, arg, ...) {
if (is.na(query)) {
if (verbose) webchem_message("na")
return(tibble::tibble("query" = NA, "cid" = NA))
}
if (verbose) webchem_message("query", query, appendLF = FALSE)
if (from %in% structure_search) {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain,
from,
URLencode(as.character(query), reserved = TRUE),
"json",
sep = "/")
} else {
if (from == "smiles") {
qurl <- paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/",
domain, "/",
from, "/",
"cids/JSON?smiles=",
URLencode(as.character(query), reserved = TRUE))
} else {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain,
from,
URLencode(as.character(query), reserved = TRUE),
"cids",
"json",
sep = "/")
}
}
if (!is.null(arg)) qurl <- paste0(qurl, "?", arg)
webchem_sleep(type = 'API')
if (from == "inchi") {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain, from, "cids", "json", sep = "/")
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
body = paste0("inchi=", query),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
} else {
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = c(202, 404),
quiet = TRUE), silent = TRUE)
}
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(tibble::tibble("query" = query, "cid" = NA))
}
if (res$status_code != 200) {
if (res$status_code == 202) {
cont <- httr::content(res, type = "text", encoding = "UTF-8")
listkey <- jsonlite::fromJSON(cont)$Waiting$ListKey
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug/", domain,
"listkey", listkey, "cids", "json", sep = "/")
while (res$status_code == 202) {
webchem_sleep(time = 5)
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(tibble::tibble("query" = query, "cid" = NA))
}
}
if (res$status_code != 200) {
if (verbose) message(httr::message_for_status(res))
return(tibble::tibble("query" = query, "cid" = NA))
}
}
else{
if (verbose) message(httr::message_for_status(res))
return(tibble::tibble("query" = query, "cid" = NA))
}
}
if (verbose) message(httr::message_for_status(res))
cont <- httr::content(res, type = "text", encoding = "UTF-8")
if (domain == "compound") {
cont <- jsonlite::fromJSON(cont)$IdentifierList$CID
}
if (domain == "substance") {
cont <- jsonlite::fromJSON(cont)$InformationList$Information$CID
}
if (domain == "assay") {
cont <- jsonlite::fromJSON(cont)$InformationList$Information$CID
}
out <- unique(unlist(cont))
out <- matcher(x = out, query = query, match = match, from = from,
verbose = verbose)
out <- as.character(out)
return(tibble::tibble("query" = query, "cid" = out))
}
out <- map(query,
~foo(query = .x, from = from, domain = domain, match = match,
verbose = verbose, arg = arg))
out <- dplyr::bind_rows(out)
return(out)
}
#' Retrieve compound properties from a pubchem CID
#'
#' Retrieve compound information from pubchem CID, see
#' \url{https://pubchem.ncbi.nlm.nih.gov/}
#' @import httr jsonlite
#'
#' @param cid numeric; a vector of Pubchem IDs (CIDs). The input vector will be
#' coerced to a vector of positive integers. The function will return a row of
#' NAs for elements that cannot be coerced to positive integers.
#' @param properties character; a vector of properties to retrieve, e.g.
#' c("MolecularFormula", "MolecularWeight"). If NULL (default) all available
#' properties are retrieved. See
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest}
#' for a list of all available properties.
#' @param verbose logical; should a verbose output be printed to the console?
#' @param ... currently not used.
#'
#' @return a tibble; each row is a queried CID, each column is a requested
#' property.
#' @seealso \code{\link{get_cid}}, \code{\link{pc_sect}}
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
#' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
#' Information from the Web. Journal of Statistical Software, 93(13).
#' \doi{10.18637/jss.v093.i13}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @export
#' @examples
#' \dontrun{
#' # might fail if API is not available
#' pc_prop(5564)
#'
#' ###
#' # multiple CIDS
#' comp <- c("Triclosan", "Aspirin")
#' cids <- get_cid(comp)
#' pc_prop(cids$cid, properties = c("MolecularFormula", "MolecularWeight",
#' "CanonicalSMILES"))
#' }
pc_prop <- function(cid, properties = NULL, verbose = getOption("verbose"), ...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
cid_o <- cid
if (verbose) message("Coercing queries to positive integers. ", appendLF = FALSE)
cid <- suppressWarnings(as.integer(cid))
if (verbose) {
index <- which(is.na(cid) & !is.na(cid_o))
if (length(index) > 0) {
for (i in index) {
message(paste0(cid_o[index], " coerced to NA. "), appendLF = FALSE)
}
}
}
if (any(cid <= 0, na.rm = TRUE)) {
index <- which(cid <= 0)
cid[index] <- NA
if (verbose) {
for (i in index) {
message(paste0(cid_o[index], " coerced to NA. "), appendLF = FALSE)
}
}
}
if (verbose) message("Done.")
if (mean(is.na(cid)) == 1) {
if (verbose) webchem_message("na")
return(NA)
}
napos <- which(is.na(cid))
cid <- cid[!is.na(cid)]
prolog <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
input <- "/compound/cid"
if (is.null(properties))
properties <- c("MolecularFormula", "MolecularWeight", "CanonicalSMILES",
"IsomericSMILES", "InChI", "InChIKey", "IUPACName",
"XLogP", "ExactMass", "MonoisotopicMass", "TPSA",
"Complexity", "Charge", "HBondDonorCount",
"HBondAcceptorCount", "RotatableBondCount", "HeavyAtomCount",
"IsotopeAtomCount", "AtomStereoCount",
"DefinedAtomStereoCount", "UndefinedAtomStereoCount",
"BondStereoCount", "DefinedBondStereoCount",
"UndefinedBondStereoCount", "CovalentUnitCount", "Volume3D",
"XStericQuadrupole3D", "YStericQuadrupole3D",
"ZStericQuadrupole3D", "FeatureCount3D",
"FeatureAcceptorCount3D", "FeatureDonorCount3D",
"FeatureAnionCount3D", "FeatureCationCount3D",
"FeatureRingCount3D", "FeatureHydrophobeCount3D",
"ConformerModelRMSD3D", "EffectiveRotorCount3D",
"ConformerCount3D", "Fingerprint2D")
properties <- paste(properties, collapse = ",")
output <- paste0("/property/", properties, "/JSON")
qurl <- paste0(prolog, input, output)
if (verbose) webchem_message("query_all", appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
httr::user_agent(webchem_url()),
body = list("cid" = paste(cid, collapse = ",")),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200) {
cont <- jsonlite::fromJSON(rawToChar(res$content))
if (names(cont) == "Fault") {
if (verbose) {
message(cont$Fault$Message, ". ", cont$Fault$Details, ". Returning NA.")
}
return(NA)
}
out <- cont$PropertyTable[[1]]
# insert NA rows
narow <- rep(NA, ncol(out))
for (i in seq_along(napos)) {
#capture NAs at beginning
firstnna <- min(which(!is.na(cid_o)))
if (napos[i] < firstnna) {
out <- rbind(narow, out)
} else {
# capture NAs at end
if (napos[i] > nrow(out)) {
# print(napos[i])
out <- rbind(out, narow)
} else {
out <- rbind(out[1:(napos[i] - 1), ], narow, out[napos[i]:nrow(out), ])
}
}}
rownames(out) <- NULL
out$CID <- cid_o
out <- tibble::as_tibble(out)
class(out) <- c("pc_prop", class(out))
return(out)
}
else {
return(NA)
}
}
#' Search synonyms in pubchem
#'
#' Search synonyms using PUG-REST,
#' see \url{https://pubchem.ncbi.nlm.nih.gov/}.
#' @import httr jsonlite
#' @importFrom utils menu
#'
#' @param query character; search term.
#' @param from character; type of input, can be one of "name" (default), "cid",
#' "sid", "aid", "smiles", "inchi", "inchikey"
#' @param match character; How should multiple hits be handled? \code{"all"}
#' returns all matches, \code{"first"} returns only the first result,
#' \code{"ask"} enters an interactive mode and the user is asked for input,
#' \code{"na"} returns \code{NA} if multiple hits are found.
#' @param choices deprecated. Use the \code{match} argument instead.
#' @param verbose logical; should a verbose output be printed on the console?
#' @param arg character; optional arguments like "name_type=word" to match
#' individual words.
#' @param ... currently unused
#' @return a named list.
#'
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @export
#' @examples
#' \dontrun{
#' pc_synonyms("Aspirin")
#' pc_synonyms(c("Aspirin", "Triclosan"))
#' pc_synonyms(5564, from = "cid")
#' pc_synonyms(c("Aspirin", "Triclosan"), match = "ask")
#' }
pc_synonyms <- function(query,
from = c("name", "cid", "sid", "aid", "smiles", "inchi", "inchikey"),
match = c("all", "first", "ask", "na"),
verbose = getOption("verbose"),
arg = NULL, choices = NULL, ...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
# from can be cid | name | smiles | inchi | sdf | inchikey | formula
# query <- c("Aspirin")
# from = "name"
from <- match.arg(from)
match <- match.arg(match)
names(query) <- query
if (!missing("choices"))
stop("'choices' is deprecated. Use 'match' instead.")
foo <- function(query, from, verbose, ...) {
if (is.na(query)) {
if (verbose) webchem_message("na")
return(NA)
}
prolog <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
input <- paste0("/compound/", from)
output <- "/synonyms/JSON"
if (!is.null(arg))
arg <- paste0("?", arg)
qurl <- paste0(prolog, input, output, arg)
if (verbose) webchem_message("query", query, appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
httr::user_agent(webchem_url()),
body = paste0(from, "=", query),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200){
cont <- httr::content(res)
if (names(cont) == "Fault") {
message(cont$Fault$Details, ". Returning NA.")
return(NA)
}
out <- unlist(cont)[-1] #first result is always an ID number
names(out) <- NULL
out <- matcher(out, query = query, match = match, from = from,
verbose = verbose)
}
else {
return(NA)
}
}
out <- lapply(query, foo, from = from, verbose = verbose)
if (!is.null(choices)) #if only one choice is returned, convert list to vector
out <- unlist(out)
return(out)
}
#' Retrieve data from PubChem content pages
#'
#' When you search for an entity at \url{https://pubchem.ncbi.nlm.nih.gov/},
#' e.g. a compound or a substance, and select the record you are interested in,
#' you will be forwarded to a PubChem content page. When you look at a PubChem
#' content page, you can see that chemical information is organised into
#' sections, subsections, etc. The chemical data live at the lowest levels of
#' these sections. Use this function to retrieve the lowest level information
#' from PubChem content pages.
#' @param id numeric or character; a vector of PubChem identifiers to search
#' for.
#' @param section character; the section of the content page to be imported.
#' @param domain character; the query domain. Can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}, \code{"gene"}, \code{"protein"} or
#' \code{"patent"}.
#' @param verbose logical; should a verbose output be printed on the console?
#' @return Returns a tibble of query results. In the returned tibble,
#' \code{SourceName} is the name of the depositor, and \code{SourceID} is the
#' ID of the search term within the depositor's database. You can browse
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/} for more information about
#' the depositors.
#' @details \code{section} is not case sensitive but it is sensitive to typing
#' errors and it requires the full name of the section as it is printed on the
#' content page. The PubChem Table of Contents Tree can also be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the individual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @seealso \code{\link{get_cid}}, \code{\link{pc_prop}}
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' pc_sect(176, "Dissociation Constants")
#' pc_sect(c(176, 311), "density")
#' pc_sect(2231, "depositor-supplied synonyms", "substance")
#' pc_sect(780286, "modify date", "assay")
#' pc_sect(9023, "Ensembl ID", "gene")
#' pc_sect("1ZHY_A", "Sequence", "protein")
#' }
#' @export
pc_sect <- function(id,
section,
domain = c("compound", "substance", "assay", "gene",
"protein", "patent"),
verbose = getOption("verbose")) {
domain <- match.arg(domain)
section <- tolower(gsub(" +", "+", section))
if (section %in% c("standard non-polar",
"Semi-standard non-polar",
"Standard polar")) {
stop("use nist_ri() to obtain more information on this.")
}
res <- pc_page(id, section, domain, verbose)
out <- pc_extract(res, section)
return(out)
}
#' Import PubChem content pages
#'
#' @importFrom jsonlite fromJSON
#' @importFrom data.tree as.Node Do
#' @param id numeric or character; a vector of identifiers to search for.
#' @param section character; the section of the content page to be imported.
#' @param domain character; the query domain. Can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}, \code{"gene"}, \code{"protein"} or
#' \code{"patent"}.
#' @return A named list of content pages where each element is either a
#' data.tree or NA.
#' @details \code{section} can be any section of a PubChem content page, e.g.
#' \code{section = "solubility"} will import the section on solubility, or
#' \code{section = "experimental properties"} will import all experimental
#' properties. The \code{section} argument is not case sensitive but it
#' is sensitive to typing errors and it requires the full name of the section as
#' it is printed on the content page. The PubChem Table of Contents Tree can
#' also be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' pc_page(c(176, 311), "Dissociation Constants")
#' pc_page(49854366, "external id", domain = "substance")
#' }
#' @noRd
pc_page <- function(id,
section,
domain = c("compound", "substance", "assay", "gene",
"protein", "patent"),
verbose = getOption("verbose")) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
domain <- match.arg(domain)
section <- tolower(gsub(" +", "+", section))
foo <- function(id, section, domain) {
if (is.na(id)) {
if (verbose) webchem_message("na")
return(NA)
}
qurl <- paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/",
domain, "/", id, "/JSON?heading=", section)
if (verbose) webchem_message("query", id, appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200) {
cont <- httr::content(res, type = "text", encoding = "UTF-8")
# Intercepting any NA cont before it gets to fromJSON.
if(is.na(cont)) {
return(NA)
}
cont <- jsonlite::fromJSON(cont, simplifyDataFrame = FALSE)
tree <- data.tree::as.Node(cont, nameName = "TOCHeading")
tree$Do(function(node) node$name <- tolower(node$name))
return(tree)
}
else {
return(NA)
}
}
cont <- lapply(id, function(x) foo(x, section, domain))
names(cont) <- id
attr(cont, "domain") <- domain
attr(cont, "id") <- switch(domain, compound = "CID", substance = "SID",
assay = "AID", gene = "GeneID", protein = "pdbID",
patent = "PatentID")
return(cont)
}
#' Extract data from PubChem content pages
#'
#' This function takes a list of PubChem content pages, and extracts the
#' required information from them.
#' @importFrom data.tree FindNode
#' @importFrom dplyr bind_rows
#' @importFrom tibble as_tibble
#' @param pages list; a list of PubChem content pages.
#' @param section character; the lowest level section of the data to be
#' accessed.
#' @return A tibble of chemical information with references.
#' @details When you look at a PubChem content page, you can see that chemical
#' information is organised into sections, subsections, etc. The chemical data
#' live at the lowest levels of these sections. Use this function to extract the
#' lowest level information from PubChem content pages, e.g. IUPAC Name, Boiling
#' Point, Lower Explosive Limit (LEL).
#' @details The \code{section} argument is not case sensitive, but it is
#' sensitive to typing errors, and requires the full name of the section as it
#' is printed on the content page. The PubChem Table of Contents Tree can also
#' be found at \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' comps <- pc_page(c(176, 311), "Dissociation Constants")
#' pc_extract(comps, "Dissociation Constants")
#' subs <- pc_page(49854366, "external id", domain = "substance")
#' pc_extract(subs, "external id")
#' }
#' @noRd
pc_extract <- function(page, section) {
section <- tolower(section)
ids <- names(page)
foo <- function(i, section) {
tree <- page[[i]]
if (length(tree) == 1 && is.na(tree)) return(tibble(ID = ids[i]))
node <- FindNode(tree, "information")
if (is.null(node)) return(tibble(ID = ids[i],
Name = tree$record$RecordTitle))
info <- lapply(node, function(y) {
lownode <- data.tree::FindNode(data.tree::as.Node(y), "stringwithmarkup")
if (is.null(lownode)) {
info <- tibble(Result = paste(y$value, collapse = " "),
ReferenceNumber = y$ReferenceNumber)
return(info)
}
else{
string <- sapply(lownode, function(z) z$String)
info <- tibble(Result = string,
ReferenceNumber = y$ReferenceNumber)
}
})
info <- dplyr::bind_rows(info)
info <- tibble(ID = ids[i],
Name = tree$record$RecordTitle,
info)
node <- FindNode(tree, "reference")
if (is.null(node)) return(tibble(info, SourceName = NA, SourceID = NA))
ref <- lapply(node, function(y) {
ref <- tibble(ReferenceNumber = y$ReferenceNumber,
SourceName = y$SourceName,
SourceID = y$SourceID)
return(ref)
})
ref <- dplyr::bind_rows(ref)
info$SourceName <- sapply(info$ReferenceNumber, function(x) {
ref$SourceName[ref$ReferenceNumber == x]
})
info$SourceID <- sapply(info$ReferenceNumber, function(x) {
ref$SourceID[ref$ReferenceNumber == x]
})
return(info)
}
info <- lapply(seq_along(page), function(x) foo(x, section))
info <- dplyr::bind_rows(info)
info <- info[, -which(names(info) == "ReferenceNumber")]
names(info)[1] <- attr(page, "id")
return(info)
}
ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions pc_extract pc_page pc_sect pc_synonyms pc_prop get_cid
Documented in get_cid pc_prop pc_sect pc_synonyms
#' Retrieve Pubchem Compound ID (CID)
#'
#' Retrieve compound IDs (CIDs) from PubChem.
#' @param query character; search term, one or more compounds.
#' @param from character; type of input. See details for more information.
#' @param domain character; query domain, can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}.
#' @param match character; How should multiple hits be handled?, \code{"all"}
#' all matches are returned, \code{"first"} the first matching is returned,
#' \code{"ask"} enters an interactive mode and the user is asked for input,
#' \code{"na"} returns NA if multiple hits are found.
#' @param verbose logical; should a verbose output be printed on the console?
#' @param arg character; optinal arguments like "name_type=word" to match
#' individual words.
#' @param first deprecated. Use `match` instead.
#' @param ... currently unused.
#' @return a tibble.
#' @details Valid values for the \code{from} argument depend on the
#' \code{domain}:
#' \itemize{
#' \item{\code{compound}: \code{"name"}, \code{"smiles"}, \code{"inchi"},
#' \code{"inchikey"}, \code{"formula"}, \code{"sdf"}, \code{"cas"} (an alias for
#' \code{"xref/RN"}), <xref>, <structure search>, <fast search>.}
#' \item{\code{substance}: \code{"name"}, \code{"sid"},
#' \code{<xref>}, \code{"sourceid/<source id>"} or \code{"sourceall"}.}
#' \item{\code{assay}: \code{"aid"}, \code{<assay target>}.}
#' }
#' @details <structure search> is assembled as "{\code{substructure} |
#' \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
#' | \code{inchi} | \code{sdf} | \code{cid}}", e.g.
#' \code{from = "substructure/smiles"}.
#' @details \code{<xref>} is assembled as "\code{xref}/\{\code{RegistryID} |
#' \code{RN} | \code{PubMedID} | \code{MMDBID} | \code{ProteinGI},
#' \code{NucleotideGI} | \code{TaxonomyID} | \code{MIMID} | \code{GeneID} |
#' \code{ProbeID} | \code{PatentID}\}", e.g. \code{from = "xref/RN"} will query
#' by CAS RN.
#' @details <fast search> is either \code{fastformula} or it is assembled as
#' "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
#' \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
#' \code{smarts} | \code{inchi} | \code{sdf} | \code{cid}}", e.g.
#' \code{from = "fastidentity/smiles"}.
#' @details \code{<source id>} is any valid PubChem Data Source ID. When
#' \code{from = "sourceid/<source id>"}, the query is the ID of the substance in
#' the depositor's database.
#' @details If \code{from = "sourceall"} the query is one or more valid Pubchem
#' depositor names. Depositor names are not case sensitive.
#' @details Depositor names and Data Source IDs can be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @details \code{<assay target>} is assembled as "\code{target}/\{\code{gi} |
#' \code{proteinname} | \code{geneid} | \code{genesymbol} | \code{accession}\}",
#' e.g. \code{from = "target/geneid"} will query by GeneID.
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
#' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
#' Information from the Web. Journal of Statistical Software, 93(13).
#' \doi{10.18637/jss.v093.i13}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @import httr
#' @importFrom purrr map map2
#' @importFrom jsonlite fromJSON
#' @importFrom tibble enframe
#' @importFrom utils URLencode
#' @export
#' @examples
#' \dontrun{
#' # might fail if API is not available
#' get_cid("Triclosan")
#' get_cid("Triclosan", arg = "name_type=word")
#' # from SMILES
#' get_cid("CCCC", from = "smiles")
#' # from InChI
#' get_cid("InChI=1S/CH5N/c1-2/h2H2,1H3", from = "inchi")
#' # from InChIKey
#' get_cid("BPGDAMSIGCZZLK-UHFFFAOYSA-N", from = "inchikey")
#' # from formula
#' get_cid("C26H52NO6P", from = "formula")
#' # from CAS RN
#' get_cid("56-40-6", from = "xref/rn")
#' # similarity
#' get_cid(5564, from = "similarity/cid")
#' get_cid("CCO", from = "similarity/smiles")
#' # from SID
#' get_cid("126534046", from = "sid", domain = "substance")
#' # sourceid
#' get_cid("VCC957895", from = "sourceid/23706", domain = "substance")
#' # sourceall
#' get_cid("Optopharma Ltd", from = "sourceall", domain = "substance")
#' # from AID (CIDs of substances tested in the assay)
#' get_cid(170004, from = "aid", domain = "assay")
#' # from GeneID (CIDs of substances tested on the gene)
#' get_cid(25086, from = "target/geneid", domain = "assay")
#'
#' # multiple inputs
#' get_cid(c("Triclosan", "Aspirin"))
#'
#' }
get_cid <-
function(query,
from = "name",
domain = c("compound", "substance", "assay"),
match = c("all", "first", "ask", "na"),
verbose = getOption("verbose"),
arg = NULL,
first = NULL,
...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
#deprecate `first`
if (!is.null(first) && first) {
message("`first = TRUE` is deprecated. Use `match = 'first'` instead")
match <- "first"
} else if (!is.null(first) && !first) {
message("`first = FALSE` is deprecated. Use `match = 'all'` instead")
match <- "all"
}
#input validation
from <- tolower(from)
from <- ifelse(from == "cas", "xref/rn", from)
if (from == "xref/rn"){
query <- as.cas(query, verbose = verbose)
}
domain <- match.arg(domain)
xref <- paste(
"xref",
c("registryid", "rn", "pubmedid", "mmdbid", "proteingi", "nucleotidegi",
"taxonomyid", "mimid", "geneid", "probeid", "patentid"),
sep = "/"
)
structure_search <- expand.grid(
c("substructure", "superstructure", "similarity", "identity"),
c("smiles", "inchi", "sdf", "cid")
)
structure_search <- paste(structure_search$Var1, structure_search$Var2,
sep = "/")
fast_search <- expand.grid(
c("fastidentity", "fastsimilarity_2d", "fastsimilarity_3d",
"fastsubstructure", "fastsuperstructure"),
c("smiles", "smarts", "inchi", "sdf", "cid")
)
fast_search <- c(with(fast_search, paste(Var1, Var2, sep = "/")),
"fastformula")
targets <- paste("target", c("gi", "proteinname", "geneid", "genesymbol",
"accession"), sep = "/")
if (domain == "compound") {
from_choices <- c("cid", "name", "smiles", "inchi", "sdf", "inchikey",
"formula", structure_search, xref, fast_search)
from <- match.arg(from, choices = from_choices)
}
if (domain == "substance") {
if (!grepl("^sourceid/", from)) {
from <- match.arg(from, choices = c("sid", "name", xref, "sourceall"))
}
}
if (domain == "assay") {
from <- match.arg(from, choices = c("aid", targets))
}
match <- match.arg(match)
foo <- function(query, from, domain, match, verbose, arg, ...) {
if (is.na(query)) {
if (verbose) webchem_message("na")
return(tibble::tibble("query" = NA, "cid" = NA))
}
if (verbose) webchem_message("query", query, appendLF = FALSE)
if (from %in% structure_search) {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain,
from,
URLencode(as.character(query), reserved = TRUE),
"json",
sep = "/")
} else {
if (from == "smiles") {
qurl <- paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/",
domain, "/",
from, "/",
"cids/JSON?smiles=",
URLencode(as.character(query), reserved = TRUE))
} else {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain,
from,
URLencode(as.character(query), reserved = TRUE),
"cids",
"json",
sep = "/")
}
}
if (!is.null(arg)) qurl <- paste0(qurl, "?", arg)
webchem_sleep(type = 'API')
if (from == "inchi") {
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug",
domain, from, "cids", "json", sep = "/")
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
body = paste0("inchi=", query),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
} else {
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = c(202, 404),
quiet = TRUE), silent = TRUE)
}
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(tibble::tibble("query" = query, "cid" = NA))
}
if (res$status_code != 200) {
if (res$status_code == 202) {
cont <- httr::content(res, type = "text", encoding = "UTF-8")
listkey <- jsonlite::fromJSON(cont)$Waiting$ListKey
qurl <- paste("https://pubchem.ncbi.nlm.nih.gov/rest/pug/", domain,
"listkey", listkey, "cids", "json", sep = "/")
while (res$status_code == 202) {
webchem_sleep(time = 5)
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(tibble::tibble("query" = query, "cid" = NA))
}
}
if (res$status_code != 200) {
if (verbose) message(httr::message_for_status(res))
return(tibble::tibble("query" = query, "cid" = NA))
}
}
else{
if (verbose) message(httr::message_for_status(res))
return(tibble::tibble("query" = query, "cid" = NA))
}
}
if (verbose) message(httr::message_for_status(res))
cont <- httr::content(res, type = "text", encoding = "UTF-8")
if (domain == "compound") {
cont <- jsonlite::fromJSON(cont)$IdentifierList$CID
}
if (domain == "substance") {
cont <- jsonlite::fromJSON(cont)$InformationList$Information$CID
}
if (domain == "assay") {
cont <- jsonlite::fromJSON(cont)$InformationList$Information$CID
}
out <- unique(unlist(cont))
out <- matcher(x = out, query = query, match = match, from = from,
verbose = verbose)
out <- as.character(out)
return(tibble::tibble("query" = query, "cid" = out))
}
out <- map(query,
~foo(query = .x, from = from, domain = domain, match = match,
verbose = verbose, arg = arg))
out <- dplyr::bind_rows(out)
return(out)
}
#' Retrieve compound properties from a pubchem CID
#'
#' Retrieve compound information from pubchem CID, see
#' \url{https://pubchem.ncbi.nlm.nih.gov/}
#' @import httr jsonlite
#'
#' @param cid numeric; a vector of Pubchem IDs (CIDs). The input vector will be
#' coerced to a vector of positive integers. The function will return a row of
#' NAs for elements that cannot be coerced to positive integers.
#' @param properties character; a vector of properties to retrieve, e.g.
#' c("MolecularFormula", "MolecularWeight"). If NULL (default) all available
#' properties are retrieved. See
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest}
#' for a list of all available properties.
#' @param verbose logical; should a verbose output be printed to the console?
#' @param ... currently not used.
#'
#' @return a tibble; each row is a queried CID, each column is a requested
#' property.
#' @seealso \code{\link{get_cid}}, \code{\link{pc_sect}}
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
#' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
#' Information from the Web. Journal of Statistical Software, 93(13).
#' \doi{10.18637/jss.v093.i13}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @export
#' @examples
#' \dontrun{
#' # might fail if API is not available
#' pc_prop(5564)
#'
#' ###
#' # multiple CIDS
#' comp <- c("Triclosan", "Aspirin")
#' cids <- get_cid(comp)
#' pc_prop(cids$cid, properties = c("MolecularFormula", "MolecularWeight",
#' "CanonicalSMILES"))
#' }
pc_prop <- function(cid, properties = NULL, verbose = getOption("verbose"), ...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
cid_o <- cid
if (verbose) message("Coercing queries to positive integers. ", appendLF = FALSE)
cid <- suppressWarnings(as.integer(cid))
if (verbose) {
index <- which(is.na(cid) & !is.na(cid_o))
if (length(index) > 0) {
for (i in index) {
message(paste0(cid_o[index], " coerced to NA. "), appendLF = FALSE)
}
}
}
if (any(cid <= 0, na.rm = TRUE)) {
index <- which(cid <= 0)
cid[index] <- NA
if (verbose) {
for (i in index) {
message(paste0(cid_o[index], " coerced to NA. "), appendLF = FALSE)
}
}
}
if (verbose) message("Done.")
if (mean(is.na(cid)) == 1) {
if (verbose) webchem_message("na")
return(NA)
}
napos <- which(is.na(cid))
cid <- cid[!is.na(cid)]
prolog <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
input <- "/compound/cid"
if (is.null(properties))
properties <- c("MolecularFormula", "MolecularWeight", "CanonicalSMILES",
"IsomericSMILES", "InChI", "InChIKey", "IUPACName",
"XLogP", "ExactMass", "MonoisotopicMass", "TPSA",
"Complexity", "Charge", "HBondDonorCount",
"HBondAcceptorCount", "RotatableBondCount", "HeavyAtomCount",
"IsotopeAtomCount", "AtomStereoCount",
"DefinedAtomStereoCount", "UndefinedAtomStereoCount",
"BondStereoCount", "DefinedBondStereoCount",
"UndefinedBondStereoCount", "CovalentUnitCount", "Volume3D",
"XStericQuadrupole3D", "YStericQuadrupole3D",
"ZStericQuadrupole3D", "FeatureCount3D",
"FeatureAcceptorCount3D", "FeatureDonorCount3D",
"FeatureAnionCount3D", "FeatureCationCount3D",
"FeatureRingCount3D", "FeatureHydrophobeCount3D",
"ConformerModelRMSD3D", "EffectiveRotorCount3D",
"ConformerCount3D", "Fingerprint2D")
properties <- paste(properties, collapse = ",")
output <- paste0("/property/", properties, "/JSON")
qurl <- paste0(prolog, input, output)
if (verbose) webchem_message("query_all", appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
httr::user_agent(webchem_url()),
body = list("cid" = paste(cid, collapse = ",")),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200) {
cont <- jsonlite::fromJSON(rawToChar(res$content))
if (names(cont) == "Fault") {
if (verbose) {
message(cont$Fault$Message, ". ", cont$Fault$Details, ". Returning NA.")
}
return(NA)
}
out <- cont$PropertyTable[[1]]
# insert NA rows
narow <- rep(NA, ncol(out))
for (i in seq_along(napos)) {
#capture NAs at beginning
firstnna <- min(which(!is.na(cid_o)))
if (napos[i] < firstnna) {
out <- rbind(narow, out)
} else {
# capture NAs at end
if (napos[i] > nrow(out)) {
# print(napos[i])
out <- rbind(out, narow)
} else {
out <- rbind(out[1:(napos[i] - 1), ], narow, out[napos[i]:nrow(out), ])
}
}}
rownames(out) <- NULL
out$CID <- cid_o
out <- tibble::as_tibble(out)
class(out) <- c("pc_prop", class(out))
return(out)
}
else {
return(NA)
}
}
#' Search synonyms in pubchem
#'
#' Search synonyms using PUG-REST,
#' see \url{https://pubchem.ncbi.nlm.nih.gov/}.
#' @import httr jsonlite
#' @importFrom utils menu
#'
#' @param query character; search term.
#' @param from character; type of input, can be one of "name" (default), "cid",
#' "sid", "aid", "smiles", "inchi", "inchikey"
#' @param match character; How should multiple hits be handled? \code{"all"}
#' returns all matches, \code{"first"} returns only the first result,
#' \code{"ask"} enters an interactive mode and the user is asked for input,
#' \code{"na"} returns \code{NA} if multiple hits are found.
#' @param choices deprecated. Use the \code{match} argument instead.
#' @param verbose logical; should a verbose output be printed on the console?
#' @param arg character; optional arguments like "name_type=word" to match
#' individual words.
#' @param ... currently unused
#' @return a named list.
#'
#' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
#' Information System for
#' Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37:
#' 623–633.
#'
#' Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016
#' PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1):
#' D1202–D1213.
#'
#' Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015).
#' PUG-SOAP and PUG-REST: web services for programmatic access to chemical
#' information in PubChem. Nucleic acids research, gkv396.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the indicidual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @export
#' @examples
#' \dontrun{
#' pc_synonyms("Aspirin")
#' pc_synonyms(c("Aspirin", "Triclosan"))
#' pc_synonyms(5564, from = "cid")
#' pc_synonyms(c("Aspirin", "Triclosan"), match = "ask")
#' }
pc_synonyms <- function(query,
from = c("name", "cid", "sid", "aid", "smiles", "inchi", "inchikey"),
match = c("all", "first", "ask", "na"),
verbose = getOption("verbose"),
arg = NULL, choices = NULL, ...) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
# from can be cid | name | smiles | inchi | sdf | inchikey | formula
# query <- c("Aspirin")
# from = "name"
from <- match.arg(from)
match <- match.arg(match)
names(query) <- query
if (!missing("choices"))
stop("'choices' is deprecated. Use 'match' instead.")
foo <- function(query, from, verbose, ...) {
if (is.na(query)) {
if (verbose) webchem_message("na")
return(NA)
}
prolog <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
input <- paste0("/compound/", from)
output <- "/synonyms/JSON"
if (!is.null(arg))
arg <- paste0("?", arg)
qurl <- paste0(prolog, input, output, arg)
if (verbose) webchem_message("query", query, appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
httr::user_agent(webchem_url()),
body = paste0(from, "=", query),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200){
cont <- httr::content(res)
if (names(cont) == "Fault") {
message(cont$Fault$Details, ". Returning NA.")
return(NA)
}
out <- unlist(cont)[-1] #first result is always an ID number
names(out) <- NULL
out <- matcher(out, query = query, match = match, from = from,
verbose = verbose)
}
else {
return(NA)
}
}
out <- lapply(query, foo, from = from, verbose = verbose)
if (!is.null(choices)) #if only one choice is returned, convert list to vector
out <- unlist(out)
return(out)
}
#' Retrieve data from PubChem content pages
#'
#' When you search for an entity at \url{https://pubchem.ncbi.nlm.nih.gov/},
#' e.g. a compound or a substance, and select the record you are interested in,
#' you will be forwarded to a PubChem content page. When you look at a PubChem
#' content page, you can see that chemical information is organised into
#' sections, subsections, etc. The chemical data live at the lowest levels of
#' these sections. Use this function to retrieve the lowest level information
#' from PubChem content pages.
#' @param id numeric or character; a vector of PubChem identifiers to search
#' for.
#' @param section character; the section of the content page to be imported.
#' @param domain character; the query domain. Can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}, \code{"gene"}, \code{"protein"} or
#' \code{"patent"}.
#' @param verbose logical; should a verbose output be printed on the console?
#' @return Returns a tibble of query results. In the returned tibble,
#' \code{SourceName} is the name of the depositor, and \code{SourceID} is the
#' ID of the search term within the depositor's database. You can browse
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/} for more information about
#' the depositors.
#' @details \code{section} is not case sensitive but it is sensitive to typing
#' errors and it requires the full name of the section as it is printed on the
#' content page. The PubChem Table of Contents Tree can also be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @note Please respect the Terms and Conditions of the National Library of
#' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
#' usage policies of National Center for Biotechnology Information,
#' \url{https://www.ncbi.nlm.nih.gov/home/about/policies/},
#' \url{https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access}, and the data
#' usage policies of the individual data sources
#' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @seealso \code{\link{get_cid}}, \code{\link{pc_prop}}
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' pc_sect(176, "Dissociation Constants")
#' pc_sect(c(176, 311), "density")
#' pc_sect(2231, "depositor-supplied synonyms", "substance")
#' pc_sect(780286, "modify date", "assay")
#' pc_sect(9023, "Ensembl ID", "gene")
#' pc_sect("1ZHY_A", "Sequence", "protein")
#' }
#' @export
pc_sect <- function(id,
section,
domain = c("compound", "substance", "assay", "gene",
"protein", "patent"),
verbose = getOption("verbose")) {
domain <- match.arg(domain)
section <- tolower(gsub(" +", "+", section))
if (section %in% c("standard non-polar",
"Semi-standard non-polar",
"Standard polar")) {
stop("use nist_ri() to obtain more information on this.")
}
res <- pc_page(id, section, domain, verbose)
out <- pc_extract(res, section)
return(out)
}
#' Import PubChem content pages
#'
#' @importFrom jsonlite fromJSON
#' @importFrom data.tree as.Node Do
#' @param id numeric or character; a vector of identifiers to search for.
#' @param section character; the section of the content page to be imported.
#' @param domain character; the query domain. Can be one of \code{"compound"},
#' \code{"substance"}, \code{"assay"}, \code{"gene"}, \code{"protein"} or
#' \code{"patent"}.
#' @return A named list of content pages where each element is either a
#' data.tree or NA.
#' @details \code{section} can be any section of a PubChem content page, e.g.
#' \code{section = "solubility"} will import the section on solubility, or
#' \code{section = "experimental properties"} will import all experimental
#' properties. The \code{section} argument is not case sensitive but it
#' is sensitive to typing errors and it requires the full name of the section as
#' it is printed on the content page. The PubChem Table of Contents Tree can
#' also be found at
#' \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' pc_page(c(176, 311), "Dissociation Constants")
#' pc_page(49854366, "external id", domain = "substance")
#' }
#' @noRd
pc_page <- function(id,
section,
domain = c("compound", "substance", "assay", "gene",
"protein", "patent"),
verbose = getOption("verbose")) {
if (!ping_service("pc")) stop(webchem_message("service_down"))
domain <- match.arg(domain)
section <- tolower(gsub(" +", "+", section))
foo <- function(id, section, domain) {
if (is.na(id)) {
if (verbose) webchem_message("na")
return(NA)
}
qurl <- paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/",
domain, "/", id, "/JSON?heading=", section)
if (verbose) webchem_message("query", id, appendLF = FALSE)
webchem_sleep(type = 'API')
res <- try(httr::RETRY("POST",
qurl,
user_agent(webchem_url()),
terminate_on = 404,
quiet = TRUE), silent = TRUE)
if (inherits(res, "try-error")) {
if (verbose) webchem_message("service_down")
return(NA)
}
if (verbose) message(httr::message_for_status(res))
if (res$status_code == 200) {
cont <- httr::content(res, type = "text", encoding = "UTF-8")
# Intercepting any NA cont before it gets to fromJSON.
if(is.na(cont)) {
return(NA)
}
cont <- jsonlite::fromJSON(cont, simplifyDataFrame = FALSE)
tree <- data.tree::as.Node(cont, nameName = "TOCHeading")
tree$Do(function(node) node$name <- tolower(node$name))
return(tree)
}
else {
return(NA)
}
}
cont <- lapply(id, function(x) foo(x, section, domain))
names(cont) <- id
attr(cont, "domain") <- domain
attr(cont, "id") <- switch(domain, compound = "CID", substance = "SID",
assay = "AID", gene = "GeneID", protein = "pdbID",
patent = "PatentID")
return(cont)
}
#' Extract data from PubChem content pages
#'
#' This function takes a list of PubChem content pages, and extracts the
#' required information from them.
#' @importFrom data.tree FindNode
#' @importFrom dplyr bind_rows
#' @importFrom tibble as_tibble
#' @param pages list; a list of PubChem content pages.
#' @param section character; the lowest level section of the data to be
#' accessed.
#' @return A tibble of chemical information with references.
#' @details When you look at a PubChem content page, you can see that chemical
#' information is organised into sections, subsections, etc. The chemical data
#' live at the lowest levels of these sections. Use this function to extract the
#' lowest level information from PubChem content pages, e.g. IUPAC Name, Boiling
#' Point, Lower Explosive Limit (LEL).
#' @details The \code{section} argument is not case sensitive, but it is
#' sensitive to typing errors, and requires the full name of the section as it
#' is printed on the content page. The PubChem Table of Contents Tree can also
#' be found at \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
#' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
#' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
#' (2019). \doi{10.1186/s13321-019-0375-2}.
#' @examples
#' # might fail if API is not available
#' \dontrun{
#' comps <- pc_page(c(176, 311), "Dissociation Constants")
#' pc_extract(comps, "Dissociation Constants")
#' subs <- pc_page(49854366, "external id", domain = "substance")
#' pc_extract(subs, "external id")
#' }
#' @noRd
pc_extract <- function(page, section) {
section <- tolower(section)
ids <- names(page)
foo <- function(i, section) {
tree <- page[[i]]
if (length(tree) == 1 && is.na(tree)) return(tibble(ID = ids[i]))
node <- FindNode(tree, "information")
if (is.null(node)) return(tibble(ID = ids[i],
Name = tree$record$RecordTitle))
info <- lapply(node, function(y) {
lownode <- data.tree::FindNode(data.tree::as.Node(y), "stringwithmarkup")
if (is.null(lownode)) {
info <- tibble(Result = paste(y$value, collapse = " "),
ReferenceNumber = y$ReferenceNumber)
return(info)
}
else{
string <- sapply(lownode, function(z) z$String)
info <- tibble(Result = string,
ReferenceNumber = y$ReferenceNumber)
}
})
info <- dplyr::bind_rows(info)
info <- tibble(ID = ids[i],
Name = tree$record$RecordTitle,
info)
node <- FindNode(tree, "reference")
if (is.null(node)) return(tibble(info, SourceName = NA, SourceID = NA))
ref <- lapply(node, function(y) {
ref <- tibble(ReferenceNumber = y$ReferenceNumber,
SourceName = y$SourceName,
SourceID = y$SourceID)
return(ref)
})
ref <- dplyr::bind_rows(ref)
info$SourceName <- sapply(info$ReferenceNumber, function(x) {
ref$SourceName[ref$ReferenceNumber == x]
})
info$SourceID <- sapply(info$ReferenceNumber, function(x) {
ref$SourceID[ref$ReferenceNumber == x]
})
return(info)
}
info <- lapply(seq_along(page), function(x) foo(x, section))
info <- dplyr::bind_rows(info)
info <- info[, -which(names(info) == "ReferenceNumber")]
names(info)[1] <- attr(page, "id")
return(info)
}
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