Add multimodel input to KVFinder-web portal (#32)

    * add multimodel selection

    ---------

    Co-authored-by: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>

kvfinder-web-portal/R/app_server.R

@@ -67,13 +67,10 @@ app_server <- function(input, output, session) {
   observeEvent(input$input_pdb, {
     # run process_upload of mod_server_upload module to create boxes and buttons of run mode
     process_upload(input = input, output = output, session = session)
-    get_nonstand_check_upload <<- report_nonstand(pdb_input =input$input_pdb$datapath)
+    get_nonstand_check_upload <<- report_nonstand(pdb_input =input$input_pdb$datapath, show_modal=TRUE)
   })
 
   observeEvent(input$show_preview_upload, {
-    print(input$input_pdb$datapath)
-    print(pdb_name_click_load)
-    print(get_nonstand)
     showModal(modalDialog(
       #title = tags$a('Structure preview', style = "text-align: right;" ),
       #NGLVieweROutput("structure_prev", width = "100%", height = "75vh"),
@@ -82,11 +79,13 @@ app_server <- function(input, output, session) {
         renderNGLVieweR({
           # get input protein PDB with output cavities
           pdb <- input$input_pdb$datapath
+          print(paste("/",as.numeric(input$model_number),sep=""))
           # create initial scene
           NGLVieweR(pdb) %>%
             # start protein with visible cartoon representation 
-            addRepresentation("cartoon") %>%
-            addRepresentation("ball+stick", param = list(sele = paste(get_nonstand_check_upload, collapse = " or "))) %>%
+            addRepresentation("cartoon", param=list(sele = paste("/",as.numeric(input$model_number)-1,sep=""))) %>%
+            addRepresentation("ball+stick", param = list(sele = paste(paste(get_nonstand_check_upload, collapse = " or "),"/",as.numeric(input$model_number)-1,sep=""))) %>%
+
             # start cavity with points
             stageParameters(backgroundColor = "black") %>%
             setQuality("high") %>%
@@ -111,8 +110,7 @@ app_server <- function(input, output, session) {
     pdb_name_click_load <<- input$pdb_id
     # check if the PDB code is valid by using get_nonstand
     showModal(modalDialog("Loading and checking PDB...", footer = NULL, fade = FALSE))
-    get_nonstand_check <<- report_nonstand(pdb_input = input$pdb_id)
-    print(get_nonstand_check)
+    get_nonstand_check <<- report_nonstand(pdb_input = input$pdb_id, show_modal=TRUE)
     removeModal()
     if (length(which(is.na(get_nonstand_check))) != 0) {
       shinyWidgets::sendSweetAlert(session = session, title = "Oops!", text = "Please insert a valid PDB ID.", type = "error")
@@ -137,8 +135,8 @@ app_server <- function(input, output, session) {
           # create initial scene
           NGLVieweR(pdb) %>%
             # start protein with visible cartoon representation 
-            addRepresentation("cartoon") %>%
-            addRepresentation("ball+stick", param = list(sele = paste(get_nonstand_check, collapse = " or "))) %>%
+            addRepresentation("cartoon", param=list(sele = paste("/",as.numeric(input$model_number)-1,sep=""))) %>%
+            addRepresentation("ball+stick", param = list(sele = paste(paste(get_nonstand_check, collapse = " or "),"/",as.numeric(input$model_number)-1,sep=""))) %>%
             # start cavity with points
             stageParameters(backgroundColor = "black") %>%
             setQuality("high") %>%

kvfinder-web-portal/R/mod_server_checkResults.R

@@ -72,8 +72,10 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
       retrieve_content <- content(retrieve_get)
       # get retrivied input PDB
       retrieve_input_pdb <- retrieve_content$input$pdb
+      print(content_get_output$output$report)
       # table with results
       result_toml <- parseTOML(input = content_get_output$output$report, fromFile = FALSE, escape = TRUE)$RESULTS
+      #print(result_toml$AREA)
       #print(names(result_toml))
       #print(result_toml$MAX_DEPTH)
       # check if the at least one cavity was found

kvfinder-web-portal/R/mod_server_pdbProcess.R

@@ -26,10 +26,11 @@ pdb_process <- function(input, output, get_nonstand, mode, session) {
   }
   # create a processed PDB for each run mode: default, customized, ligand or box mode
   if (input$run_mode == "mode_def") {
-    pdb_processed <- deal_sele_nonstand(pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
+
+    pdb_processed <- deal_sele_nonstand(input=input,pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
     pdb_processed <- list(pdb_processed = pdb_processed)
   } else if (input$run_mode == "mode_cust") {
-    pdb_processed <- deal_sele_nonstand(pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
+    pdb_processed <- deal_sele_nonstand(input=input,pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
     pdb_processed <- list(pdb_processed = pdb_processed)
   } else if (input$run_mode == "box_mode") {
     # in the case of running the box mode, we have to check if the target residues are correctly in the PDB input
@@ -38,7 +39,7 @@ pdb_process <- function(input, output, get_nonstand, mode, session) {
       shinyWidgets::sendSweetAlert(session = session, title = "Oops!", text = "Please insert a valid list of residues for box mode run.", type = "error")
       pdb_processed <- "wrong_target_res"
     } else {
-      pdb_processed <- deal_sele_nonstand(pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
+      pdb_processed <- deal_sele_nonstand(input=input,pdb_input = pdb_input, nonstand_list = get_nonstand, include_list = include_list, session = session)
       pdb_processed <- list(pdb_processed = pdb_processed)
     }
   } else { # enter in the ligand mode
@@ -47,7 +48,7 @@ pdb_process <- function(input, output, get_nonstand, mode, session) {
     # update nonstandard residues list to exclude the ligand
     get_nonstand_noLig <- setdiff(get_nonstand, input$lig_name) # get all non-standand but the ligand
     # by default remove all non standards residues and the ligand
-    pdb_processed <- deal_sele_nonstand(pdb_input = pdb_input, nonstand_list = c(get_nonstand, input$lig_name), include_list = include_list, session = session)
+    pdb_processed <- deal_sele_nonstand(input=input,pdb_input = pdb_input, nonstand_list = c(get_nonstand, input$lig_name), include_list = include_list, session = session)
     pdb_processed <- list(pdb_processed = pdb_processed, pdb_lig_processed = pdb_ligand_processed)
   }
   return(pdb_processed)

kvfinder-web-portal/R/utils_pdbProcess_.R

@@ -4,13 +4,19 @@
 #' Get non standard protein/nucleic residues from PDB
 #'
 #' @param pdb_input Pdb path
+#' @param show_modal
 #'
 #' @import bio3d
 #'
 #' @examples
 #' @export
 
-report_nonstand <- function(pdb_input) {
+report_nonstand <- function(pdb_input, show_modal) {
+  if(missing(show_modal)){ #in some calls there's no need to inform the if want to use the show modal presented below for multi models
+    show_modal = FALSE
+  } else{
+    show_modal = show_modal
+  }
   pdb <- tryCatch(
     {
       read.pdb(pdb_input, multi = T)
@@ -21,8 +27,16 @@ report_nonstand <- function(pdb_input) {
   )
   if (class(pdb)[1] == "pdb") {
     # check multimodels
-    if (class(pdb)[1] == "pdb" & dim(pdb$xyz)[1] > 1) {
-      shinyWidgets::sendSweetAlert(title = "Oops!", text = "A multimodel structure was detected as input: Using only the first structure from the multimodel...", type = "warning")
+    if (class(pdb)[1] == "pdb" & dim(pdb$xyz)[1] > 1 & show_modal == TRUE) {
+      #shinyWidgets::sendSweetAlert(title = "Oops!", text = "A multimodel structure was detected as input: Using only the first structure from the multimodel...", type = "warning")
+      showModal(modalDialog(
+        tags$h3('The input contains multiple models.'),
+        tags$h5('Please select a single model below:'),
+        selectInput('model_number', 'Model number',seq(1,dim(pdb$xyz)[1])),
+        footer=tagList(
+          modalButton('Select')
+        )
+      ))  
     }
     # get protein
     indx_p <- atom.select(pdb, string = "protein", inverse = TRUE)
@@ -45,6 +59,7 @@ report_nonstand <- function(pdb_input) {
 #' @description
 #' Process PDB file according to the selected non-standard residues
 #'
+#' @param input
 #' @param pdb_input Pdb path
 #' @param nonstand_list List of non-standard residues
 #' @param include_list List of non-standard residues that must be maintained in the PDB
@@ -57,11 +72,14 @@ report_nonstand <- function(pdb_input) {
 #' @export
 #'
 
-deal_sele_nonstand <- function(pdb_input, nonstand_list, include_list, session = session) {
+deal_sele_nonstand <- function(input,pdb_input, nonstand_list, include_list, session = session) {
   tryCatch(
     { # test if the pdb_input is an appropriated PDB ID and if the read,pdb function can download successfully this pdb
-      pdb <- read.pdb(pdb_input)
+      pdb <- read.pdb(pdb_input, multi=T)
+      print(dim(pdb$xyz)[1])
+      print(include_list)
       if (is.null(include_list)) {
+
         # get nonstandard selected
         indx_s <- atom.select(pdb, resid = nonstand_list, inverse = TRUE)
         # subset pdb
@@ -70,7 +88,11 @@ deal_sele_nonstand <- function(pdb_input, nonstand_list, include_list, session =
         rand <- sample(x = 1:100000, size = 1)
         outfile <- file.path(tempdir(), paste(rand, ".pdb", sep = ""))
         # write tmp
-        write.pdb(pdb = clean_pdb, file = outfile)
+        if(dim(pdb$xyz)[1] > 1){ #case of multimodel, use the model selected by the user
+          write.pdb(pdb = clean_pdb, file = outfile, xyz=clean_pdb$xyz[as.numeric(input$model_number),])
+        } else{
+          write.pdb(pdb = clean_pdb, file = outfile)
+        } 
         return(outfile)
       } else {
         indx_s <- atom.select(pdb, resid = nonstand_list, inverse = TRUE)
@@ -81,7 +103,13 @@ deal_sele_nonstand <- function(pdb_input, nonstand_list, include_list, session =
         rand <- sample(x = 1:100000, size = 1)
         outfile <- file.path(tempdir(), paste(rand, ".pdb", sep = ""))
         # write tmp
-        write.pdb(pdb = clean_pdb, file = outfile)
+        if(dim(pdb$xyz)[1] > 1){#case of multimodel, use the model selected by the user
+          print(input$model_number)
+          print('multimodel')
+          write.pdb(pdb = clean_pdb, file = outfile, xyz=clean_pdb$xyz[as.numeric(input$model_number),])
+        } else{
+          write.pdb(pdb = clean_pdb, file = outfile)
+        } 
         return(outfile)
       }
     },