SMARTSviewer

DESCRIPTION

@@ -34,6 +34,6 @@ Imports:
     dplyr,
     purrr
 Suggests:
-    testthat,
+    testthat (>= 2.1.0),
     rcdk
 RoxygenNote: 7.1.0

NAMESPACE

@@ -73,6 +73,7 @@ export(pp_query)
 export(ppdb)
 export(ppdb_parse)
 export(ppdb_query)
+export(smarts_viewer)
 export(smiles)
 export(srs_query)
 export(wd_ident)

NEWS

@@ -1,28 +1,11 @@
 webchem 0.6.0
 ======================
 
-NEW FEATURES
-
-MINOR IMPROVEMENTS
-
-BUG FIXES
-
-* get_csid() now returns all csids when queried from formula
-* get_csid() returned an error when query was NA [PR #226, fixed by stitam]
-* get_chebiid() and chebi_comp_entity() fixed for invalid queries [PR #225, fixed by stitam]
-* get_cid() returned the PubChem ID of sodium when the query was NA [PR #223, fixed by stitam]
-* aw_query() returned a list for successful queries, NA for unsuccessful queries [PR #222, fixed by stitam]
-
-DEPRECATED FUNCTIONS
-
-DEFUNCT FUNCTIONS
-
-webchem 0.5.0
-======================
 
 NEW FEATURES
 
 * Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest [contributed by @andschar].
+* Submit a query to the ZBH Center for Bioinformatics' SMARTS viewer webservice at (https://smartsview.zbh.uni-hamburg.de) with smarts_viewer(). Retrieves images for plotting in R or downloads image in specified format [contributed by @gjgetzinger].
 * Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() [PR #154, contributed by @Aariq]
 * Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() [PR #179]
 * "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated.  Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return. [contributed by @Aariq]

R/smarts_viewer.R

@@ -0,0 +1,100 @@
+#' Query SMARTS Viewer
+#'
+#' Submit a query to the SMARTS viewer webservice at
+#' \url{http://smartsview.zbh.uni-hamburg.de}, ZBH Center for Bioinformatics,
+#' University of Hamburg
+#'
+#' @param smarts A SMARTS string to visualize
+#' @param output The type of response generated (image or download). See
+#'   description for details.
+#' @param image_format Image file format (pdf, png, or svg)
+#' @param visualization_modus 1 or 2 (1 = Complete Visualization, 2 = Element
+#'   Symbols)
+#' @param legend_option both, none, static, dynamic
+#' @param filename Filename to use if output is to be downloaded
+#'
+#' @return Either a raster object (output = image) suitable for adding to an
+#'   R plot using \code{rasterImage} or the image is downloaded in the specified
+#'   format to the indicated filename.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' img <- smarts_viewer(
+#'    "[CX3](=[OX1])[OX2][CX3](=[OX1])",
+#'    "image", "png", 1, "both"
+#'    )
+#' plot(0:1,0:1, 'n')
+#' rasterImage(img[[1]],0,0,1,1)
+#'
+#' smarts <- c("[CX3](=[OX1])[OX2][CX3](=[OX1])",
+#' "[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]",
+#' "[#6][$([NX2]=O),$(N=C=O),$(OC#N),$(SC#N)]"
+#' )
+#' img <- smarts_viewer(smarts, "image", "png", 1, "both")
+#' par(mfcol = c(1,length(smarts)))
+#' sapply(img, function(i){
+#'  plot(0:1,0:1, 'n')
+#'  rasterImage(i,0,0,1,1)
+#' })
+#'
+#' smarts_viewer(
+#'     smarts, output = "download",
+#'     image_format = "pdf",
+#'     visualization_modus = 1,
+#'     legend_option = "both", filename = "test.pdf")
+#' }
+#'
+smarts_viewer <-
+  function(smarts,
+           output = c('image', 'download'),
+           image_format = c('pdf', 'png', 'svg'),
+           visualization_modus = c(1, 2),
+           legend_option = c('both', 'none', 'static', 'dynamic'),
+           filename = NULL) {
+    entity_url <- "https://smartsview.zbh.uni-hamburg.de/auto"
+    if(output == 'download' & is.null(filename)){
+      stop("Must provide a filename for output type 'download'.")
+    }
+    if (length(smarts) > 1 &
+        output == 'download') {
+      message(
+        paste(
+          "Warning:",
+          "Multiple SMARTS strings entered with output option = download.",
+          "One file per SMARTS string will be downloaded automatically.",
+          sep = '\n'
+        )
+      )
+      resp <- NA
+      while (!resp %in% c("Y", "N", "y", "n")) {
+        resp <- readline(prompt = "Do you wish to continue? (Y/N)")
+      }
+      stopifnot(tolower(resp) == 'y')
+    }
+
+    lapply(seq(along = smarts), function(x) {
+      entity_query <-
+        paste(entity_url,
+              image_format,
+              visualization_modus,
+              legend_option,
+              utils::URLencode(smarts[x], T),
+              sep = '/')
+      response <- httr::GET(entity_query)
+       if (response$status_code == 200) {
+          if (output == 'image') {
+            httr::content(response, as = 'parsed', type = 'Image/png')
+          } else {
+            utils::download.file(url = response$url,
+                                 destfile = gsub(
+                                   pattern = paste0('.', image_format),
+                                   paste0('_', x, '.', image_format),
+                                   filename
+                                 ))
+          }
+        } else {
+          stop(httr::http_status(response)$message)
+        }
+    })
+  }

README.Rmd

@@ -347,7 +347,14 @@ smiles(wi)
 # smiles(etox_basic(5564))
 ```
 
+#### SMARTS Viewer 
+Render a depiction of a SMARTS string (\url{https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html}) by submitting a query to the SMARTS viewer web service at \url{http://smartsview.zbh.uni-hamburg.de}, ZBH Center for Bioinformatics, University of Hamburg. 
 
+```{r smartsviewer}
+smarts_viewer("[CX3](=[OX1])[OX2][CX3](=[OX1])","image", "png", 1, "both")
+plot(0:1,0:1, 'n')
+rasterImage(img[[1]],0,0,1,1)
+```
 
 #### Misc functions
 

tests/testthat/test-smartsview.R

@@ -0,0 +1,13 @@
+context("smartsview")
+
+a <- smarts_viewer("[CX3](=[OX1])[OX2][CX3](=[OX1])", "image", "png", 1, "both" )
+b <- smarts_viewer("[CX3](=[OX1])[OX2][CX3](=[OX1])", "download", "png", 1, "both", "smartsview_test.png" )
+
+test_that("nist returns correct results", {
+  skip_on_cran()
+
+  expect_is(a[[1]], 'array')
+  expect_equal(b[[1]], 0)
+  expect_true(file.exists('smartsview_test.png'))
+  expect_error(smarts_viewer("[CX3](=[OX1])[OX2][CX3](=[OX1])", "download", "png", 1, "both"))
+})

tests/testthat/test-test_smartsview.R

@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})