Add smiles retrival and fix some typos

NAMESPACE

@@ -72,6 +72,7 @@ export(getCtsKey)
 export(getCtsRecord)
 export(getDTXCID)
 export(getDTXSID)
+export(getDTXSMILES)
 export(getField)
 export(getMolecule)
 export(getPcId)

R/createMassBank.R

@@ -536,13 +536,14 @@ gatherPubChem <- function(key){
 #' substance ID, the CAS-RN, the DTX preferred name, and the DTXCID (chemical ID).
 #' 
 #' @usage gatherCCTE(key, api_key)
-#' @param key An Inchi-Key
+#' @param key An Inchi-Key or other chemical identifier (e.g. Chemical name, DTXSID, CASRN, InChIKey, DTXCID)
 #' @param api_key An US EPA CCTE API key (personal or application)
-#' @return Returns a list with 4 slots:
+#' @return Returns a list with 5 slots:
 #' \code{dtxsid} The US EPA chemical dashboard substance id
 #' \code{dtxcid} The US EPA chemical dashboard chemical id
 #' \code{preferredName} The US EPA chemical dashboard preferred name
 #' \code{casrn} The latest CAS registration number
+#' \code{smiles} The SMILES annotation of the structure
 #' @author Tobias Schulze
 #' @seealso \code{\link{mbWorkflow}}
 #' @references CCTE REST:
@@ -562,6 +563,7 @@ gatherCCTE <- function(key, api_key = NA) {
  CTTE_data$dtxcid <- NA
  CTTE_data$preferredname <- NA
  CTTE_data$casrn <- NA
+ CTTE_data$smiles <- NA
  return(CCTE_data)
  }
 
@@ -598,6 +600,13 @@ gatherCCTE <- function(key, api_key = NA) {
  CCTE_data$casrn <<- NA
  })
 
+ ##Retrieve latest CAS RN
+ tryCatch(
+ CCTE_data$smiles <- getDTXSMILES(key, api_key),
+ error=function(e){
+ CCTE_data$smiles <<- NA
+ })
+
  return(CCTE_data)
 }
 

R/webAccess.R

@@ -157,7 +157,7 @@ getPcId <- function(query, from = "inchikey")
 #' CCTE REST:
 #' \url{https://api-ccte.epa.gov/docs}
 #' @examples
-#' getPcId("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
+#' getDTXSID("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
 #' 
 #' @export
 getDTXSID <- function(key, api_key)
@@ -226,7 +226,6 @@ getDTXCID <- function(key, api_key)
 
  },
  error=function(e){
- currEnvir$errorvar <- 1
  })
 
  if(errorvar){
@@ -345,6 +344,56 @@ getCASRN <- function(key, api_key)
  }
 }
 
+#' Search CCTE SMILES
+#' 
+#' Retrieves CCTE SMILES from US EPA for a search term.
+#' 
+#' Only the first result is returned currently. \bold{The function should be
+#' regarded as experimental and has not thoroughly been tested.}
+#' 
+#' @usage getDTXSMILES(key, api_key)
+#' @param key ID to be converted
+#' @param api_key API key for CCTE
+#' @return The SMILES (in string type)
+#' @author Tobias Schulze
+#' @references CCTE search: \url{https://api-ccte.epa.gov/docs} 
+#' 
+#' CCTE REST:
+#' \url{https://api-ccte.epa.gov/docs}
+#' @examples
+#' getDTXSMILES("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
+#' 
+#' @export
+getDTXSMILES <- function(key, api_key)
+
+{
+ errorvar <- 0
+ currEnvir <- environment()
+
+ tryCatch({
+ base_url <- paste0("https://api-ccte.epa.gov/chemical/search/equal/", key)
+ url <- httr2::request(base_url)
+ url <- url |> httr2::req_headers("x-api-key" = api_key, "accept" = "application/json")
+ resp <- httr2::req_perform(url)
+ data <- resp |> httr2::resp_body_json()
+
+ },
+ error=function(e){
+ currEnvir$errorvar <- 1
+ })
+
+ if(errorvar){
+ return(NA)
+ }
+
+ smiles <- data[[1]]$smiles
+
+ if(is.null(smiles)){
+ return(NA)
+ } else{
+ return(smiles)
+ }
+}
 
 #' Retrieve information from CTS
 #'