diff --git a/R/buildRecord.R b/R/buildRecord.R
index 1268344..1fcaae7 100644
--- a/R/buildRecord.R
+++ b/R/buildRecord.R
@@ -284,10 +284,10 @@ setMethod("buildRecord", "RmbSpectrum2", function(o, ..., cpd = NULL, mbdata = l
 	# Here is the right place to fix the name of the INTERNAL ID field.
 	if(!is.null(getOption("RMassBank")$annotations$internal_id_fieldname))
 	{
-		id.col <- which(names(mbdata[["COMMENT"]]) == "ID")
-		if(length(id.col) > 0)
+		id_col <- which(names(mbdata[["COMMENT"]]) == "ID")
+		if(length(id_col) > 0)
 		{
-			names(mbdata[["COMMENT"]])[[id.col]] <-
+			names(mbdata[["COMMENT"]])[[id_col]] <-
 			getOption("RMassBank")$annotations$internal_id_fieldname
 		}
 	}
diff --git a/R/createMassBank.R b/R/createMassBank.R
index 63bccf2..6dcf92a 100755
--- a/R/createMassBank.R
+++ b/R/createMassBank.R
@@ -90,14 +90,14 @@ loadInfolist <- function(mb, fileName)
     # dbname_e will be dropped because of the select= in the subset below.
   }
   
-  if("COMMENT.EAWAG_UCHEM_ID" %in% colnames(mbdata_new)) {
-    colnames(mbdata_new)[[which(colnames(mbdata_new)== "COMMENT.EAWAG_UCHEM_ID")]] <-
-      "COMMENT.ID"
+  if("COMMENT_EAWAG_UCHEM_ID" %in% colnames(mbdata_new)) {
+    colnames(mbdata_new)[[which(colnames(mbdata_new) == "COMMENT_EAWAG_UCHEM_ID")]] <-
+      "COMMENT_ID"
   }
   
   # use only the columns present in mbdata_archive, no other columns added in excel
   col_names <- colnames(mb@mbdata_archive)
-  comment_colnames <- colnames(mbdata_new)[grepl(x = colnames(mbdata_new), pattern = "^COMMENT\\.(?!CONFIDENCE)(?!ID)", perl = TRUE)]
+  comment_colnames <- colnames(mbdata_new)[grepl(x = colnames(mbdata_new), pattern = "^COMMENT\\_(?!CONFIDENCE)(?!ID)", perl = TRUE)]
   col_names <- c(col_names, comment_colnames)
 
   ## The read infolists might not have all required / expected columns
@@ -138,8 +138,8 @@ resetInfolists <- function(mb)
 {    
 	mb@mbdata_archive <-
 			structure(list(id = integer(0), dbcas = character(0), 
-							dbname = character(0), dataused = character(0), COMMENT.CONFIDENCE = character(0), 
-							COMMENT.ID = integer(0), `CH$NAME1` = character(0), 
+							dbname = character(0), dataused = character(0), COMMENT_CONFIDENCE = character(0), 
+							COMMENT_ID = integer(0), `CH$NAME1` = character(0), 
 							`CH$NAME2` = character(0), `CH$NAME3` = character(0), `CH$NAME4` = character(0),
 							`CH$NAME5` = character(0), `CH$COMPOUND_CLASS` = character(0), 
 							`CH$FORMULA` = character(0), `CH$EXACT_MASS` = numeric(0),` CH$SMILES` = character(0), 
@@ -149,7 +149,7 @@ resetInfolists <- function(mb)
 							`CH$LINK_CHEMSPIDER` = integer(0), `CH$LINK_COMPTOX` = character(0), 
 							AUTHORS = character(0), COPYRIGHT = character(0)
 							), .Names = c("id", "dbcas", 
-							"dbname", "dataused", "COMMENT.CONFIDENCE", "COMMENT.ID", 
+							"dbname", "dataused", "COMMENT_CONFIDENCE", "COMMENT_ID", 
               "CH$NAME1", "CH$NAME2", "CH$NAME3", "CH$NAME4", "CH$NAME5", "CH$COMPOUND_CLASS", "CH$FORMULA", 
 							"CH$EXACT_MASS", "CH$SMILES", "CH$IUPAC", "CH$LINK_CAS", "CH$LINK_CHEBI", 
 							"CH$LINK_HMDB", "CH$LINK_KEGG", "CH$LINK_LIPIDMAPS", "CH$LINK_PUBCHEM",
@@ -254,7 +254,7 @@ mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.c
 	rmb_log_info("mbWorkflow: Step 2. Export infolist (if required)")
     if(length(mb@mbdata)>0)
     {
-      mbdata <- tibble::as_tibble(flatten(mb@mbdata))
+      mbdata <- flatten(mb@mbdata)
       readr::write_csv(x = mbdata, file = infolist_path, col_names = TRUE, na = "", quote = "needed")
             rmb_log_info(paste("The file", infolist_path, "was generated with new compound information. Please check and edit the table, and add it to your infolist folder."))
       return(mb)
@@ -585,14 +585,19 @@ gatherData <- function(id)
 	
 	if(usebabel){
 		cmdinchikey <- paste0(babeldir, 'obabel -:"',smiles,'" ', '-oinchikey')
-		inchikey_split <- system(cmdinchikey, intern=TRUE, input=smiles, ignore.stderr=TRUE)
-	} else{
-		inchikey <- getCactus(smiles, 'stdinchikey')
+		inchikey_split <- system(cmdinchikey, intern = TRUE, input = smiles, ignore.stderr = TRUE)
+	} else {
+		inchi_key <- getCactus(identifier = smiles, representation = "stdinchikey")
+		
+		if(is.na(inchi_key)) {
+		  inchi_key <- getPcInchiKey(query = smiles, from = "smiles")
+		}
+		
 		if(!is.na(inchikey)){
 			##Split the "InChiKey=" part off the key
-			inchikey_split <- strsplit(inchikey, "=", fixed=TRUE)[[1]][[2]]
-		} else{
-		    inchikey_split <- getPcInchiKey(smiles)
+			inchikey_split <- strsplit(inchi_key, "=", fixed = TRUE)[[1]][[2]]
+		} else {
+		    inchikey_split <- getPcInchiKey(query = smiles, from = "smiles")
 		}
 	}
 	
@@ -1120,7 +1125,7 @@ gatherDataUnknown <- function(id, mode, retrieval){
 #' \code{\link{gatherData}}.
 #' @param row One row of MassBank compound information retrieved from an
 #' infolist.
-#' @return \code{flatten} returns a matrix (not a data frame) to be written to
+#' @return \code{flatten} returns a tibble (not a data frame or matrix) to be written to
 #' CSV.
 #' 
 #' \code{readMbdata} returns a list of type \code{list(id= \var{compoundID},
@@ -1146,7 +1151,7 @@ flatten <- function(mbdata)
   .checkMbSettings()
   
   colNames     <- names(unlist(mbdata[[1]]))
-  commentNames <- colNames[grepl(x = colNames, pattern = "^COMMENT\\.")]
+  commentNames <- colNames[grepl(x = colNames, pattern = "^COMMENT\\_")]
   
   colList <- c(
               "id",
@@ -1154,11 +1159,11 @@ flatten <- function(mbdata)
               "dbname",
               "dataused",
               commentNames,
-              #"COMMENT.CONFIDENCE",
+              #"COMMENT_CONFIDENCE",
               # Note: The field name of the internal id field is replaced with the real name
               # at "compilation" time. Therefore, functions DOWNSTREAM from compileRecord() 
               # must use the full name including the info from options("RMassBank").
-              #"COMMENT.ID",
+              #"COMMENT_ID",
               "CH$NAME1",
               "CH$NAME2",
               "CH$NAME3",
@@ -1177,27 +1182,35 @@ flatten <- function(mbdata)
               "CH$LINK_PUBCHEM",
               "CH$LINK_INCHIKEY",
               "CH$LINK_CHEMSPIDER",
-	          "CH$LINK_COMPTOX"
+	            "CH$LINK_COMPTOX"
 	          )
   # make an empty data frame with the right length
   rows <- length(mbdata)
   cols <- length(colList)
-  mbframe <- matrix(data=NA, nrow=rows, ncol=cols)
-  colnames(mbframe) <- colList
+  
+  mbtbl <- tibble::tibble(!!!colList, .rows = 0, .name_repair = ~ colList)
+  
+  
+  #mbframe <- matrix(data = NA, nrow = rows, ncol = cols)
+  #colnames(mbframe) <- colList
   #browser()
-  for(row in 1:rows)
-  {
+  for(i in 1:rows) {
     # fill in all the data into the dataframe: all columns which 
     # a) exist in the target dataframe and b) exist in the (unlisted) MB record
     # are written into the dataframe.
-    data <- unlist(mbdata[[row]])
+    data <- unlist(mbdata[[i]], use.names = TRUE)
+    names(data) <- gsub("\\.", "_", names(data))
 	# bugfix for the case of only one name
-	if(!("CH$NAME1" %in% names(data)))
-		data[["CH$NAME1"]] <- data[["CH$NAME"]]
-    datacols <- intersect(colList, names(data))
-    mbframe[row,datacols] <- data[datacols]
+	if(!("CH$NAME1" %in% names(data))) {
+		  data[["CH$NAME1"]] <- data[["CH$NAME"]]
+		  }
+  datacols <- intersect(colList, names(data))
+  
+  mbtbl <- mbtbl |> dplyr::bind_rows(data[datacols])
+  
   }
-  return(mbframe)
+  
+  return(mbtbl)
   
 }
 
@@ -1231,8 +1244,8 @@ readMbdata <- function(row)
   # This is not very flexible, as you can see...
     colList <- c(
               commentNames,
-              #"COMMENT.CONFIDENCE",
-              #"COMMENT.ID",
+              #"COMMENT_CONFIDENCE",
+              #"COMMENT_ID",
               "CH$NAME1",
               "CH$NAME2",
               "CH$NAME3",
@@ -1253,10 +1266,10 @@ readMbdata <- function(row)
               "CH$LINK_CHEMSPIDER",
               "CH$LINK_COMPTOX")
   mbdata[["COMMENT"]] = list()
-  #mbdata[["COMMENT"]][["CONFIDENCE"]] <- row[["COMMENT.CONFIDENCE"]]
+  #mbdata[["COMMENT"]][["CONFIDENCE"]] <- row[["COMMENT_CONFIDENCE"]]
   # Again, our ID field. 
-  #mbdata[["COMMENT"]][["ID"]] <- row[["COMMENT.ID"]]
-  mbdata[["COMMENT"]][gsub(x = commentNames, pattern = "^COMMENT\\.", replacement = "")] <- row[commentNames]
+  #mbdata[["COMMENT"]][["ID"]] <- row[["COMMENT_D"]]
+  mbdata[["COMMENT"]][gsub(x = commentNames, pattern = "^COMMENT\\_", replacement = "")] <- row[commentNames]
   
   names = c(row[["CH$NAME1"]], row[["CH$NAME2"]], row[["CH$NAME3"]], row[["CH$NAME4"]], row[["CH$NAME5"]])
   names = names[which(!is.na(names))]
@@ -1283,8 +1296,8 @@ readMbdata <- function(row)
   mbdata[["CH$LINK"]] <- link
 
     ## SP$SAMPLE
-  if(all(nchar(row[["SP.SAMPLE"]]) > 0, row[["SP.SAMPLE"]] != "NA", !is.na(row[["SP.SAMPLE"]]), na.rm = TRUE))
-    mbdata[['SP$SAMPLE']] <- row[["SP.SAMPLE"]]
+  if(all(nchar(row[["SP_SAMPLE"]]) > 0, row[["SP_SAMPLE"]] != "NA", !is.na(row[["SP_SAMPLE"]]), na.rm = TRUE))
+    mbdata[['SP$SAMPLE']] <- row[["SP_SAMPLE"]]
   
   if(!is.na(row[["AUTHORS"]]))
     mbdata[["AUTHORS"]] = row[["AUTHORS"]]
diff --git a/R/webAccess.R b/R/webAccess.R
index b199fc3..2517c1c 100755
--- a/R/webAccess.R
+++ b/R/webAccess.R
@@ -1,570 +1,570 @@
-#' @import XML rjson httr
-NULL
-## library(XML)
-## library(httr)
-## library(jsonlite)
-
-
-retrieveDataWithRetry <- function(url, timeout, maximumNumberOfRetries = 5, retryDelayInSeconds = 3){
-
-  data <- NULL
-  queryIsSuccessful <- FALSE
-  numberOfRetries <- 0
-  while(!queryIsSuccessful & numberOfRetries < maximumNumberOfRetries){
-    data <- tryCatch(
-      expr = {
-        res <- GET(utils::URLencode(url))
-        data <- httr::content(res, type="text", encoding="UTF-8")
-        
-        queryIsSuccessful <- TRUE
-        data
-      },
-      warning=function(w){
-        numberOfRetries <<- numberOfRetries + 1
-        if(RMassBank.env$verbose.output)
-          cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of warning '", w, "'\n", sep = ""))
-        if(numberOfRetries < maximumNumberOfRetries)
-          Sys.sleep(time = retryDelayInSeconds)
-      },
-      error=function(e){
-        numberOfRetries <<- numberOfRetries + 1
-        if(RMassBank.env$verbose.output)
-          cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of error '", e, "'\n", sep = ""))
-        if(numberOfRetries < maximumNumberOfRetries)
-          Sys.sleep(time = retryDelayInSeconds)
-      }
-    )
-  }
-  
-  return(data)
-}
-
-#' Retrieve information from Cactus
-#' 
-#' Retrieves information from the Cactus Chemical Identifier Resolver
-#' (PubChem).
-#' 
-#' It is not necessary to specify in which format the \code{identifier} is.
-#' Somehow, cactus does this automatically.
-#' 
-#' @usage getCactus(identifier, representation)
-#' @param identifier Any identifier interpreted by the resolver, e.g. an InChI
-#' key or a SMILES code.
-#' @param representation The desired representation, as required from the
-#' resolver. e.g. \code{stdinchikey}, \code{chemspider_id}, \code{formula}...
-#' Refer to the webpage for details.
-#' @return The result of the query, in plain text. Can be NA, or one or
-#' multiple lines (character array) of results.
-#' @note Note that the InChI key is retrieved with a prefix (\code{InChIkey=}),
-#' which must be removed for most database searches in other databases (e.g.
-#' CTS).
-#' @author Michael Stravs
-#' @seealso \code{\link{getCtsRecord}}, \code{\link{getPcId}}
-#' @references cactus Chemical Identifier Resolver:
-#' \url{http://cactus.nci.nih.gov/chemical/structure}
-#' @examples
-#' 
-#' # Benzene:
-#' getCactus("C1=CC=CC=C1", "cas")
-#' getCactus("C1=CC=CC=C1", "stdinchikey")
-#' getCactus("C1=CC=CC=C1", "chemspider_id")
-#' 
-#' @export 
-#' 
-#' 
-getCactus <- function(identifier,representation){
-  identifier <- gsub('#', '%23', identifier)
-  ret <- tryCatch(httr::GET(paste("https://cactus.nci.nih.gov/chemical/structure/",
-                            utils::URLencode(identifier), "/", representation, sep = "")),
-                  error = function(e) NA)
-  if (all(is.na(ret)))
-    return(NA)
-  if (ret["status_code"] == 404)
-    return(NA)
-  ret <- httr::content(ret)
-  return(unlist(strsplit(ret, "\n")))
-  
-}
-
-#' Search Pubchem CID
-#' 
-#' Retrieves PubChem CIDs 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 getPcId(query, from = "inchikey")
-#' @param query ID to be converted
-#' @param from Type of input ID
-#' @return The PubChem CID (in string type).
-#' @author Michael Stravs, Erik Mueller
-#' @seealso \code{\link{getCtsRecord}}, \code{\link{getCactus}}
-#' @references PubChem search: \url{http://pubchem.ncbi.nlm.nih.gov/} 
-#' 
-#' Pubchem REST:
-#' \url{https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html}
-#' @examples
-#' getPcId("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
-#' 
-#' @export
-getPcId <- function(query, from = "inchikey")
-{
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "description", "json", sep="/")
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-	    res <- GET(utils::URLencode(url))
-	    data <- httr::content(res, type="text", encoding="UTF-8")
-    },
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	# This happens if the InChI key is not found:
-	r <- fromJSON(data)
-	
-	if(!is.null(r$Fault))
-	return(NA)
-	
-	titleEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Title))))
-	
-	titleEntry <- titleEntry[which.min(sapply(titleEntry, function(x)r$InformationList$Information[[x]]$CID))]
-
-	PcID <- r$InformationList$Information[[titleEntry]]$CID
-	
-	if(is.null(PcID)){
-		return(NA)
-	} else{
-		return(PcID)
-	}
-}
-
-
-#' Retrieve information from CTS
-#' 
-#' Retrieves a complete CTS record from the InChI key.
-#' 
-#' @usage getCtsRecord(key)
-#' 
-#' @param key The InChI key. 
-#' @return Returns a list with all information from CTS: \code{inchikey, 
-#' 	inchicode, formula, exactmass} contain single values. \code{synonyms} contains
-#' an unordered list of scored synonyms (\code{type, name, score}, where \code{type}
-#' indicates either a normal name or a specific IUPAC name, see below).
-#'  \code{externalIds} contains an unordered list of identifiers of the compound in 
-#' various databases (\code{name, value}, where \code{name} is the database name and
-#' \code{value} the identifier in that database.)
-#' 
-#' @note Currently, the CTS results are still incomplete; the name scores are all 0,
-#' formula and exact mass return zero.
-#' @references Chemical Translation Service:
-#' \url{https://cts.fiehnlab.ucdavis.edu}
-#' 
-#' @examples
-#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
-#' # show all synonym "types"
-#' types <- unique(unlist(lapply(data$synonyms, function(i) i$type)))
-#' \dontrun{print(types)}
-#' 
-#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
-#' @export
-getCtsRecord <- function(key)
-{
-	baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/compound/"
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	##tryCatch a CTS timeout
-	##
-	tryCatch({
-			url <- paste0(baseURL,key)
-			res <- GET(utils::URLencode(url))
-			data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-			currEnvir$errorvar <- 1
-		}
-	)
-  
-	if(errorvar){
-		warning("CTS seems to be currently unavailable or incapable of interpreting your request")
-		return(NULL)
-	}
-
-	r <- fromJSON(data)
-	if(length(r) == 1)
-		if(r == "You entered an invalid InChIKey")
-			return(list())
-	return(r)
-}
-
-#' Convert a single ID to another using CTS.
-#' 
-#' @usage getCtsKey(query, from = "Chemical Name", to = "InChIKey")
-#' @param query ID to be converted
-#' @param from Type of input ID
-#' @param to Desired output ID 
-#' @return An unordered array with the resulting converted key(s). 
-#' 
-#' @examples 
-#' k <- getCtsKey("benzene", "Chemical Name", "InChIKey")
-#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
-#' @export
-getCtsKey <- function(query, from = "Chemical Name", to = "InChIKey")
-{
-	baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/convert"
-	url <- paste(baseURL, from, to, query, sep='/')
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	##tryCatch a CTS timeout
-	##
-	tryCatch({
-			res <- GET(utils::URLencode(url))
-			data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-			currEnvir$errorvar <- 1
-		}
-	)
-  
-	if(errorvar){
-		warning("CTS seems to be currently unavailable or incapable of interpreting your request")
-		return(NULL)
-	}
-
-	if(res$status_code != 200){
-	  warning(paste("CTS has return code", res$status_code))
-	  return(NULL)
-	}
-	
-	r <- fromJSON(data)
-	if(length(r) == 0)
-		return(NULL)
-	else
-	{
-		# read out the results in simplest form:
-		results <- unlist(lapply(r, function(row) row$result))
-		return(results)
-	}
-}
-
-#' Select a subset of external IDs from a CTS record.
-#' 
-#' @usage CTS.externalIdSubset(data, database)
-#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}. 
-#' @param database The database for which keys should be returned. 
-#' @return Returns an array of all external identifiers stored in the record for the
-#' given database.
-#' 
-#' @examples 
-#' 
-#' \dontrun{
-#' # Return all CAS registry numbers stored for benzene.
-#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
-#' cas <- CTS.externalIdSubset(data, "CAS")
-#' } 
-#' 
-#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
-#' @export
-CTS.externalIdSubset <- function(data, database)
-{
-	select <- which(unlist(lapply(data$externalIds, function(id)
-							{
-								id[["name"]] == database
-							})))
-	keyEntries <- data$externalIds[select]
-	keys <- unlist(lapply(keyEntries, function(e) e[["value"]]))
-}
-
-#' Find all available databases for a CTS record
-#' 
-#' @usage CTS.externalIdTypes(data)
-#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.  
-#' @return Returns an array of all database names for which there are external 
-#' identifiers stored in the record.
-#' 
-#' @examples 
-#' 
-#' \dontrun{
-#' # Return all databases for which the benzene entry has
-#' # links in the CTS record.
-#' 
-#' data <- getCTS("UHOVQNZJYSORNB-UHFFFAOYSA-N")
-#' databases <- CTS.externalIdTypes(data)
-#' } 
-#' 
-#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
-#' @export
-CTS.externalIdTypes <- function(data)
-{
-	unique(unlist(lapply(data$externalIds, function(id)
-							{
-								id[["name"]]
-							})))
-}
-
-.pubChemOnline <- function(){
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, "inchikey", "QEIXBXXKTUNWDK-UHFFFAOYSA-N", "description", "json", sep="/")
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	tryCatch({
-	    res <- GET(utils::URLencode(url))
-	    ret <- httr::content(res, type="text", encoding="UTF-8")
-	  },
-	  error=function(e){
-		currEnvir$errorvar <- 1
-	})
-  
-  if(errorvar){
-	warning("Pubchem is currently offline")
-	return(FALSE)
-  } else{
-	return(TRUE)
-  }
-}
-
-
-
-getPcCHEBI <- function(query, from = "inchikey")
-{
-	# Get the JSON-Data from Pubchem
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "synonyms", "json", sep="/")
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-		  res <- GET(utils::URLencode(url))
-		  data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	r <- fromJSON(data)
-	
-	# This happens if the InChI key is not found:
-	if(!is.null(r$Fault))
-	return(NA)
-	
-	# Find the entries which contain Chebi-links
-	synonymEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Synonym))))
-	synonymList <- r$InformationList$Information[[synonymEntry]]$Synonym
-	matchChebi <- which(grepl("CHEBI:", synonymList, fixed=TRUE))
-	
-	# It doesn't matter if the db is down or if chebi isn't found, so return NA also
-	if(length(matchChebi) == 0){
-		return (NA) 
-	} else {
-		return (sapply(matchChebi, function(x) synonymList[[x]]))
-	}
-}
-
-#' Retrieve the Chemspider ID for a given compound
-#' 
-#' Given an InChIKey, this function queries the chemspider web API to retrieve
-#' the Chemspider ID of he compound with that InChIkey. 
-#'
-#' @usage getCSID(query)
-#'
-#' @param query The InChIKey of the compound 
-#' @return Returns the chemspide
-#' 
-#' @examples 
-#' 
-#' \dontrun{
-#' # Return all CAS registry numbers stored for benzene.
-#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
-#' cas <- CTS.externalIdSubset(data, "CAS")
-#' } 
-#' 
-#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
-#' @author Erik Mueller, UFZ <erik.mueller@@ufz.de>
-#' @export
-getCSID <- function(query)
-{
-	baseURL <- "http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key="
-	url <- paste0(baseURL, query)
-	
-	data <- retrieveDataWithRetry(url = utils::URLencode(url), timeout=8)
-	if(is.null(data)) {
-		warning("Chemspider is currently offline")
-		return(NA)
-	}
-	
-	xml <- xmlParseDoc(data,asText=TRUE)
-	# the returned XML document contains only the root node called "string" which contains the correct CSID
-	idNodes <- getNodeSet(xml, "/")
-	id <- xmlValue(idNodes[[1]])
-	return(id)
-} 
-
-##This function returns a sensible name for the compound
-getPcSynonym <- function (query, from = "inchikey")
-{
-	# Get the JSON-Data from Pubchem
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "description", "json", sep="/")
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-		  res <- GET(utils::URLencode(url))
-		  data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	r <- fromJSON(data)
-	
-	# This happens if the InChI key is not found:
-	if(!is.null(r$Fault))
-	return(NA)
-	
-	# Find the synonym
-	
-	titleEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Title))))
-	
-	titleEntry <- titleEntry[which.min(sapply(titleEntry, function(x)r$InformationList$Information[[x]]$CID))]
-	
-	title <- r$InformationList$Information[[titleEntry]]$Title
-	
-	if(is.null(title)){
-		return(NA)
-	} else{
-		return(title)
-	}
-} 
-
-
-##A function to retrieve a IUPAC Name from Pubchem
-getPcIUPAC <- function (query, from = "inchikey")
-{
-	# Get the JSON-Data from Pubchem
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "record", "json", sep="/")
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-		  res <- GET(utils::URLencode(url))
-		  data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	r <- fromJSON(data)
-	
-	# This happens if the InChI key is not found:
-	if(!is.null(r$Fault))
-	return(NA)
-	
-	# Find the IUPAC-Names
-	if(!is.null(r$PC_Compounds[[1]]$props)){
-		IUPACIndex <- which(unlist(lapply(r$PC_Compounds[[1]]$props, function(i) (i$urn$label == "IUPAC Name"))))
-		if(length(IUPACIndex) > 0){
-			# Retrieve all IUPAC-Names
-			IUPACEntries <- lapply(IUPACIndex, function(x) r$PC_Compounds[[1]]$props[[x]])
-			if(!is.null(IUPACEntries)){
-				# Is there a preferred IUPAC-Name? If yes, retrieve that
-				PrefIUPAC <- which(unlist(lapply(IUPACEntries, function(x) x$urn$name == "Preferred")))
-			}	else{return(NA)}
-		}	else{return(NA)}
-	}	else{return(NA)}
-	
-
-	if(length(PrefIUPAC) == 1){
-		return(IUPACEntries[[PrefIUPAC]]$value$sval)
-	} else{
-		# Else it doesn't matter which
-		return(IUPACEntries[[1]]$value$sval)
-	}
-} 
-
-getPcInchiKey <- function(query, from = "smiles"){
-	# Get the JSON-Data from Pubchem
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "record", "json", sep="/")
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-		  res <- GET(utils::URLencode(url))
-		  data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	r <- fromJSON(data)
-	
-	# This happens if the InChI key is not found:
-	if(!is.null(r$Fault))
-	return(NA)
-	
-	# Find the entries which contain Chebi-links
-	if(!is.null(r$PC_Compounds[[1]]$props)){
-		INKEYindex <- which(sapply(r$PC_Compounds[[1]]$props, function(x) x$urn$label) == "InChIKey")
-		if(length(INKEYindex) > 0){
-			return(r$PC_Compounds[[1]]$props[[INKEYindex]]$value$sval)
-		}	else{return(NA)}
-	}	else{return(NA)}
-
-	
-}
-
-getPcSDF <- function(query, from = "smiles"){
-	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
-	url <- paste(baseURL, from, query, "sdf", sep="/")
-	
-	errorvar <- 0
-	currEnvir <- environment()
-	
-	tryCatch({
-		  res <- GET(utils::URLencode(url))
-		  data <- httr::content(res, type="text", encoding="UTF-8")
-		},
-		error=function(e){
-		currEnvir$errorvar <- 1
-	})
-	
-	if(errorvar){
-		return(NA)
-	}
-	
-	molEnd <- regexpr(data,pattern="M  END",fixed=TRUE)+5
-	data <- c(strsplit(substring(data,1,molEnd),"\n")[[1]],"$$$$")
-	return(data)
-}
-
+#' @import XML rjson httr
+NULL
+## library(XML)
+## library(httr)
+## library(jsonlite)
+
+
+retrieveDataWithRetry <- function(url, timeout, maximumNumberOfRetries = 5, retryDelayInSeconds = 3){
+
+  data <- NULL
+  queryIsSuccessful <- FALSE
+  numberOfRetries <- 0
+  while(!queryIsSuccessful & numberOfRetries < maximumNumberOfRetries){
+    data <- tryCatch(
+      expr = {
+        res <- GET(utils::URLencode(url))
+        data <- httr::content(res, type="text", encoding="UTF-8")
+        
+        queryIsSuccessful <- TRUE
+        data
+      },
+      warning=function(w){
+        numberOfRetries <<- numberOfRetries + 1
+        if(RMassBank.env$verbose.output)
+          cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of warning '", w, "'\n", sep = ""))
+        if(numberOfRetries < maximumNumberOfRetries)
+          Sys.sleep(time = retryDelayInSeconds)
+      },
+      error=function(e){
+        numberOfRetries <<- numberOfRetries + 1
+        if(RMassBank.env$verbose.output)
+          cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of error '", e, "'\n", sep = ""))
+        if(numberOfRetries < maximumNumberOfRetries)
+          Sys.sleep(time = retryDelayInSeconds)
+      }
+    )
+  }
+  
+  return(data)
+}
+
+#' Retrieve information from Cactus
+#' 
+#' Retrieves information from the Cactus Chemical Identifier Resolver
+#' (PubChem).
+#' 
+#' It is not necessary to specify in which format the \code{identifier} is.
+#' Somehow, cactus does this automatically.
+#' 
+#' @usage getCactus(identifier, representation)
+#' @param identifier Any identifier interpreted by the resolver, e.g. an InChI
+#' key or a SMILES code.
+#' @param representation The desired representation, as required from the
+#' resolver. e.g. \code{stdinchikey}, \code{chemspider_id}, \code{formula}...
+#' Refer to the webpage for details.
+#' @return The result of the query, in plain text. Can be NA, or one or
+#' multiple lines (character array) of results.
+#' @note Note that the InChI key is retrieved with a prefix (\code{InChIkey=}),
+#' which must be removed for most database searches in other databases (e.g.
+#' CTS).
+#' @author Michael Stravs
+#' @seealso \code{\link{getCtsRecord}}, \code{\link{getPcId}}
+#' @references cactus Chemical Identifier Resolver:
+#' \url{http://cactus.nci.nih.gov/chemical/structure}
+#' @examples
+#' 
+#' # Benzene:
+#' getCactus("C1=CC=CC=C1", "cas")
+#' getCactus("C1=CC=CC=C1", "stdinchikey")
+#' getCactus("C1=CC=CC=C1", "chemspider_id")
+#' 
+#' @export 
+#' 
+#' 
+getCactus <- function(identifier, representation){
+  identifier <- gsub('#', '%23', identifier)
+  ret <- tryCatch(httr::GET(paste("https://cactus.nci.nih.gov/chemical/structure/",
+                            utils::URLencode(identifier), "/", representation, sep = "")),
+                  error = function(e) NA)
+  if (all(is.na(ret)))
+    return(NA)
+  if (ret["status_code"] == 404)
+    return(NA)
+  ret <- httr::content(ret)
+  return(unlist(strsplit(ret, "\n")))
+  
+}
+
+#' Search Pubchem CID
+#' 
+#' Retrieves PubChem CIDs 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 getPcId(query, from = "inchikey")
+#' @param query ID to be converted
+#' @param from Type of input ID
+#' @return The PubChem CID (in string type).
+#' @author Michael Stravs, Erik Mueller
+#' @seealso \code{\link{getCtsRecord}}, \code{\link{getCactus}}
+#' @references PubChem search: \url{http://pubchem.ncbi.nlm.nih.gov/} 
+#' 
+#' Pubchem REST:
+#' \url{https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html}
+#' @examples
+#' getPcId("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
+#' 
+#' @export
+getPcId <- function(query, from = "inchikey")
+{
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "description", "json", sep="/")
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+	    res <- GET(utils::URLencode(url))
+	    data <- httr::content(res, type="text", encoding="UTF-8")
+    },
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	# This happens if the InChI key is not found:
+	r <- fromJSON(data)
+	
+	if(!is.null(r$Fault))
+	return(NA)
+	
+	titleEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Title))))
+	
+	titleEntry <- titleEntry[which.min(sapply(titleEntry, function(x)r$InformationList$Information[[x]]$CID))]
+
+	PcID <- r$InformationList$Information[[titleEntry]]$CID
+	
+	if(is.null(PcID)){
+		return(NA)
+	} else{
+		return(PcID)
+	}
+}
+
+
+#' Retrieve information from CTS
+#' 
+#' Retrieves a complete CTS record from the InChI key.
+#' 
+#' @usage getCtsRecord(key)
+#' 
+#' @param key The InChI key. 
+#' @return Returns a list with all information from CTS: \code{inchikey, 
+#' 	inchicode, formula, exactmass} contain single values. \code{synonyms} contains
+#' an unordered list of scored synonyms (\code{type, name, score}, where \code{type}
+#' indicates either a normal name or a specific IUPAC name, see below).
+#'  \code{externalIds} contains an unordered list of identifiers of the compound in 
+#' various databases (\code{name, value}, where \code{name} is the database name and
+#' \code{value} the identifier in that database.)
+#' 
+#' @note Currently, the CTS results are still incomplete; the name scores are all 0,
+#' formula and exact mass return zero.
+#' @references Chemical Translation Service:
+#' \url{https://cts.fiehnlab.ucdavis.edu}
+#' 
+#' @examples
+#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
+#' # show all synonym "types"
+#' types <- unique(unlist(lapply(data$synonyms, function(i) i$type)))
+#' \dontrun{print(types)}
+#' 
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @export
+getCtsRecord <- function(key)
+{
+	baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/compound/"
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	##tryCatch a CTS timeout
+	##
+	tryCatch({
+			url <- paste0(baseURL,key)
+			res <- GET(utils::URLencode(url))
+			data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+			currEnvir$errorvar <- 1
+		}
+	)
+  
+	if(errorvar){
+		warning("CTS seems to be currently unavailable or incapable of interpreting your request")
+		return(NULL)
+	}
+
+	r <- fromJSON(data)
+	if(length(r) == 1)
+		if(r == "You entered an invalid InChIKey")
+			return(list())
+	return(r)
+}
+
+#' Convert a single ID to another using CTS.
+#' 
+#' @usage getCtsKey(query, from = "Chemical Name", to = "InChIKey")
+#' @param query ID to be converted
+#' @param from Type of input ID
+#' @param to Desired output ID 
+#' @return An unordered array with the resulting converted key(s). 
+#' 
+#' @examples 
+#' k <- getCtsKey("benzene", "Chemical Name", "InChIKey")
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @export
+getCtsKey <- function(query, from = "Chemical Name", to = "InChIKey")
+{
+	baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/convert"
+	url <- paste(baseURL, from, to, query, sep='/')
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	##tryCatch a CTS timeout
+	##
+	tryCatch({
+			res <- GET(utils::URLencode(url))
+			data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+			currEnvir$errorvar <- 1
+		}
+	)
+  
+	if(errorvar){
+		warning("CTS seems to be currently unavailable or incapable of interpreting your request")
+		return(NULL)
+	}
+
+	if(res$status_code != 200){
+	  warning(paste("CTS has return code", res$status_code))
+	  return(NULL)
+	}
+	
+	r <- fromJSON(data)
+	if(length(r) == 0)
+		return(NULL)
+	else
+	{
+		# read out the results in simplest form:
+		results <- unlist(lapply(r, function(row) row$result))
+		return(results)
+	}
+}
+
+#' Select a subset of external IDs from a CTS record.
+#' 
+#' @usage CTS.externalIdSubset(data, database)
+#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}. 
+#' @param database The database for which keys should be returned. 
+#' @return Returns an array of all external identifiers stored in the record for the
+#' given database.
+#' 
+#' @examples 
+#' 
+#' \dontrun{
+#' # Return all CAS registry numbers stored for benzene.
+#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
+#' cas <- CTS.externalIdSubset(data, "CAS")
+#' } 
+#' 
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @export
+CTS.externalIdSubset <- function(data, database)
+{
+	select <- which(unlist(lapply(data$externalIds, function(id)
+							{
+								id[["name"]] == database
+							})))
+	keyEntries <- data$externalIds[select]
+	keys <- unlist(lapply(keyEntries, function(e) e[["value"]]))
+}
+
+#' Find all available databases for a CTS record
+#' 
+#' @usage CTS.externalIdTypes(data)
+#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.  
+#' @return Returns an array of all database names for which there are external 
+#' identifiers stored in the record.
+#' 
+#' @examples 
+#' 
+#' \dontrun{
+#' # Return all databases for which the benzene entry has
+#' # links in the CTS record.
+#' 
+#' data <- getCTS("UHOVQNZJYSORNB-UHFFFAOYSA-N")
+#' databases <- CTS.externalIdTypes(data)
+#' } 
+#' 
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @export
+CTS.externalIdTypes <- function(data)
+{
+	unique(unlist(lapply(data$externalIds, function(id)
+							{
+								id[["name"]]
+							})))
+}
+
+.pubChemOnline <- function(){
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, "inchikey", "QEIXBXXKTUNWDK-UHFFFAOYSA-N", "description", "json", sep="/")
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	tryCatch({
+	    res <- GET(utils::URLencode(url))
+	    ret <- httr::content(res, type="text", encoding="UTF-8")
+	  },
+	  error=function(e){
+		currEnvir$errorvar <- 1
+	})
+  
+  if(errorvar){
+	warning("Pubchem is currently offline")
+	return(FALSE)
+  } else{
+	return(TRUE)
+  }
+}
+
+
+
+getPcCHEBI <- function(query, from = "inchikey")
+{
+	# Get the JSON-Data from Pubchem
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "synonyms", "json", sep="/")
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+		  res <- GET(utils::URLencode(url))
+		  data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	r <- fromJSON(data)
+	
+	# This happens if the InChI key is not found:
+	if(!is.null(r$Fault))
+	return(NA)
+	
+	# Find the entries which contain Chebi-links
+	synonymEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Synonym))))
+	synonymList <- r$InformationList$Information[[synonymEntry]]$Synonym
+	matchChebi <- which(grepl("CHEBI:", synonymList, fixed=TRUE))
+	
+	# It doesn't matter if the db is down or if chebi isn't found, so return NA also
+	if(length(matchChebi) == 0){
+		return (NA) 
+	} else {
+		return (sapply(matchChebi, function(x) synonymList[[x]]))
+	}
+}
+
+#' Retrieve the Chemspider ID for a given compound
+#' 
+#' Given an InChIKey, this function queries the chemspider web API to retrieve
+#' the Chemspider ID of he compound with that InChIkey. 
+#'
+#' @usage getCSID(query)
+#'
+#' @param query The InChIKey of the compound 
+#' @return Returns the chemspide
+#' 
+#' @examples 
+#' 
+#' \dontrun{
+#' # Return all CAS registry numbers stored for benzene.
+#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
+#' cas <- CTS.externalIdSubset(data, "CAS")
+#' } 
+#' 
+#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
+#' @author Erik Mueller, UFZ <erik.mueller@@ufz.de>
+#' @export
+getCSID <- function(query)
+{
+	baseURL <- "http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key="
+	url <- paste0(baseURL, query)
+	
+	data <- retrieveDataWithRetry(url = utils::URLencode(url), timeout=8)
+	if(is.null(data)) {
+		warning("Chemspider is currently offline")
+		return(NA)
+	}
+	
+	xml <- xmlParseDoc(data,asText=TRUE)
+	# the returned XML document contains only the root node called "string" which contains the correct CSID
+	idNodes <- getNodeSet(xml, "/")
+	id <- xmlValue(idNodes[[1]])
+	return(id)
+} 
+
+##This function returns a sensible name for the compound
+getPcSynonym <- function (query, from = "inchikey")
+{
+	# Get the JSON-Data from Pubchem
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "description", "json", sep="/")
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+		  res <- GET(utils::URLencode(url))
+		  data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	r <- fromJSON(data)
+	
+	# This happens if the InChI key is not found:
+	if(!is.null(r$Fault))
+	return(NA)
+	
+	# Find the synonym
+	
+	titleEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Title))))
+	
+	titleEntry <- titleEntry[which.min(sapply(titleEntry, function(x)r$InformationList$Information[[x]]$CID))]
+	
+	title <- r$InformationList$Information[[titleEntry]]$Title
+	
+	if(is.null(title)){
+		return(NA)
+	} else{
+		return(title)
+	}
+} 
+
+
+##A function to retrieve a IUPAC Name from Pubchem
+getPcIUPAC <- function (query, from = "inchikey")
+{
+	# Get the JSON-Data from Pubchem
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "record", "json", sep="/")
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+		  res <- GET(utils::URLencode(url))
+		  data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	r <- fromJSON(data)
+	
+	# This happens if the InChI key is not found:
+	if(!is.null(r$Fault))
+	return(NA)
+	
+	# Find the IUPAC-Names
+	if(!is.null(r$PC_Compounds[[1]]$props)){
+		IUPACIndex <- which(unlist(lapply(r$PC_Compounds[[1]]$props, function(i) (i$urn$label == "IUPAC Name"))))
+		if(length(IUPACIndex) > 0){
+			# Retrieve all IUPAC-Names
+			IUPACEntries <- lapply(IUPACIndex, function(x) r$PC_Compounds[[1]]$props[[x]])
+			if(!is.null(IUPACEntries)){
+				# Is there a preferred IUPAC-Name? If yes, retrieve that
+				PrefIUPAC <- which(unlist(lapply(IUPACEntries, function(x) x$urn$name == "Preferred")))
+			}	else{return(NA)}
+		}	else{return(NA)}
+	}	else{return(NA)}
+	
+
+	if(length(PrefIUPAC) == 1){
+		return(IUPACEntries[[PrefIUPAC]]$value$sval)
+	} else{
+		# Else it doesn't matter which
+		return(IUPACEntries[[1]]$value$sval)
+	}
+} 
+
+getPcInchiKey <- function(query, from = "smiles"){
+	# Get the JSON-Data from Pubchem
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "json", sep="/")
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+		  res <- httr::GET(utils::URLencode(url))
+		  data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	r <- rjson::fromJSON(data)
+	
+	# This happens if the InChI key is not found:
+	if(!is.null(r$Fault))
+	return(NA)
+	
+	# Find the entries which contain Chebi-links
+	if(!is.null(r$PC_Compounds[[1]]$props)){
+		INKEYindex <- which(sapply(r$PC_Compounds[[1]]$props, function(x) x$urn$label) == "InChIKey")
+		if(length(INKEYindex) > 0){
+			return(r$PC_Compounds[[1]]$props[[INKEYindex]]$value$sval)
+		}	else{return(NA)}
+	}	else{return(NA)}
+
+	
+}
+
+getPcSDF <- function(query, from = "smiles"){
+	baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
+	url <- paste(baseURL, from, query, "sdf", sep="/")
+	
+	errorvar <- 0
+	currEnvir <- environment()
+	
+	tryCatch({
+		  res <- GET(utils::URLencode(url))
+		  data <- httr::content(res, type="text", encoding="UTF-8")
+		},
+		error=function(e){
+		currEnvir$errorvar <- 1
+	})
+	
+	if(errorvar){
+		return(NA)
+	}
+	
+	molEnd <- regexpr(data,pattern="M  END",fixed=TRUE)+5
+	data <- c(strsplit(substring(data,1,molEnd),"\n")[[1]],"$$$$")
+	return(data)
+}
+
diff --git a/man/flatten.Rd b/man/flatten.Rd
index 0069371..2d60a06 100755
--- a/man/flatten.Rd
+++ b/man/flatten.Rd
@@ -17,7 +17,7 @@ readMbdata(row)
 infolist.}
 }
 \value{
-\code{flatten} returns a matrix (not a data frame) to be written to
+\code{flatten} returns a tibble (not a data frame or matrix) to be written to
 CSV.
 
 \code{readMbdata} returns a list of type \code{list(id= \var{compoundID},