NGLVieweR

NGLVieweR/1.0.0/DESCRIPTION

+Package: shinyNGLVieweR
+Title: Shiny application for the NGLVieweR package
+Version: 1.0
+Authors@R: 
+    person(given = "Niels",
+           family = "van der Velden",
+           role = c("aut", "cre"),
+           email = "n.s.j.vandervelden@gmail.com")
+Description: Load, edit and save Protein Database files (PDB) in the webbrowser.
+License: MIT
+Imports: 
+    config,
+    golem,
+    shiny,
+    processx,
+    attempt,
+    DT,
+    glue,
+    htmltools,
+    shinydashboard,
+    shinyWidgets,
+    shinyjs,
+    readr,
+    tools,
+    dplyr,
+    shinydashboardPlus,
+    stringr,
+    tidyr,
+    colourpicker,
+    bsplus,
+    r2d3,
+    NGLVieweR,
+    shinyjqui,
+    uuid,
+    pkgload
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.1
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NGLVieweR/1.0.0/Dockerfile

+# Base image
+FROM continuumio/miniconda3:24.3.0-0
+
+LABEL IMAGE="nglviewer" \
+    IMAGE_VERSION="1.0.0" \
+    AUTHORS="Xin Yang" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+# Set working directory
+WORKDIR /vizapp/
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+# Update conda and create environment
+RUN conda update conda -y && \
+    conda create -y -c bioconda -c defaults -c conda-forge -n r441 r-base=4.4.1 && \
+    echo "r-base ==4.4.1" >> /opt/conda/envs/r441/conda-meta/pinned && \
+    conda update --all -y
+
+# Install required R packages
+RUN conda run -n r441 R -e "install.packages('DT', repos='http://cran.us.r-project.org')" 
+RUN conda run -n r441 R -e "install.packages('shiny', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinyFiles', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('Matrix', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('MASS', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('mgcv', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('ggplot2', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('config', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('golem', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('processx', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('attempt', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('glue', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('htmltools', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinydashboard', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinyWidgets', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinyjs', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('readr', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('tools', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('dplyr', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinydashboardPlus', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('stringr', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('tidyr', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('colourpicker', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('bsplus', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('r2d3', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('NGLVieweR', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('shinyjqui', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('uuid', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('pkgload', repos='http://cran.us.r-project.org')"
+RUN conda run -n r441 R -e "install.packages('testthat', repos='http://cran.us.r-project.org')"
+
+# Copy application files into the container
+COPY tests /vizapp/tests
+COPY rsconnect /vizapp/rsconnect
+COPY R /vizapp/R
+COPY pkgdown /vizapp/pkgdown
+COPY man /vizapp/man
+COPY inst /vizapp/inst
+COPY docs /vizapp/docs
+COPY dev /vizapp/dev
+COPY shinyNGLVieweR.Rproj /vizapp/
+COPY NAMESPACE /vizapp/
+COPY astrocyte_vizapp.R /vizapp/
+COPY DESCRIPTION /vizapp/
+
+COPY entrypoint.sh /vizapp/
+RUN chmod +x /vizapp/entrypoint.sh
+
+ENTRYPOINT ["/vizapp/entrypoint.sh"]
+
+ARG VIZAPP_PORT=8123
+ENV VIZAPP_PORT=$VIZAPP_PORT
+
+# Default command
+CMD ["conda", "run", "-n", "r441", "Rscript", "astrocyte_vizapp.R"]

NGLVieweR/1.0.0/NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(aa_clicked_to_ngl)
+export(bs_input_modal)
+export(bs_textInput)
+export(insertUI_component)
+export(insertUI_name)
+export(insertUI_selection)
+export(jsboxCollapse)
+export(loadContacts)
+export(loadLabels)
+export(loadLigand)
+export(loadSelections)
+export(loadStage)
+export(loadStructure)
+export(loadSurface)
+export(loadUI_component)
+export(ngl_to_position)
+export(readFile)
+export(removeUI_component)
+export(run_app)
+export(selection_to_ngl)
+export(sequence_df)
+import(NGLVieweR)
+import(bsplus)
+import(colourpicker)
+import(dplyr)
+import(r2d3)
+import(readr)
+import(shiny)
+import(shinyWidgets)
+import(shinydashboard)
+import(shinydashboardPlus)
+import(shinyjqui)
+import(shinyjs)
+import(stringr)
+import(uuid)
+importFrom(bsplus,bs_attach_modal)
+importFrom(bsplus,bs_modal)
+importFrom(bsplus,shinyInput_label_embed)
+importFrom(bsplus,shiny_iconlink)
+importFrom(config,get)
+importFrom(dplyr,case_when)
+importFrom(dplyr,mutate)
+importFrom(dplyr,rowwise)
+importFrom(golem,activate_js)
+importFrom(golem,add_resource_path)
+importFrom(golem,bundle_resources)
+importFrom(golem,favicon)
+importFrom(golem,with_golem_options)
+importFrom(htmltools,HTML)
+importFrom(htmltools,tagAppendAttributes)
+importFrom(htmltools,tagList)
+importFrom(htmltools,tags)
+importFrom(readr,read_csv)
+importFrom(readr,read_lines)
+importFrom(shiny,NS)
+importFrom(shiny,column)
+importFrom(shiny,htmlTemplate)
+importFrom(shiny,shinyApp)
+importFrom(shiny,tagList)
+importFrom(shiny,textInput)
+importFrom(tidyr,complete)
+importFrom(tidyr,full_seq)
+importFrom(tidyr,replace_na)
+importFrom(tidyr,unnest)
+importFrom(tools,file_ext)

NGLVieweR/1.0.0/R/_disable_autoload.R

+# Disabling shiny autoload
+
+# See ?shiny::loadSupport for more information

NGLVieweR/1.0.0/R/app_config.R

+#' Access files in the current app
+#' 
+#' @param ... Character vector specifying directory and or file to
+#'     point to inside the current package.
+#' 
+#' @noRd
+app_sys <- function(...){
+  system.file(..., package = "shinyNGLVieweR")
+}
+
+
+#' Read App Config
+#' 
+#' @param value Value to retrieve from the config file. 
+#' @param config R_CONFIG_ACTIVE value. 
+#' @param use_parent Logical, scan the parent directory for config file.
+#'     
+#' @importFrom config get
+#' 
+#' @noRd
+get_golem_config <- function(
+  value, 
+  config = Sys.getenv("R_CONFIG_ACTIVE", "default"), 
+  use_parent = TRUE
+){
+  config::get(
+    value = value, 
+    config = config, 
+    # Modify this if your config file is somewhere else:
+    file = app_sys("golem-config.yml"), 
+    use_parent = use_parent
+  )
+}
+

NGLVieweR/1.0.0/R/app_server.R

+#' The application server-side
+#' 
+#' @param input,output,session Internal parameters for {shiny}. 
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @noRd
+app_server <- function(input, output, session) {
+  r <- reactiveValues()
+  
+  observe({
+    r$sequence <- input$`NGLVieweROutput_ui_1-structure_sequence`
+    r$resno <- input$`NGLVieweROutput_ui_1-structure_resno`
+    r$chainname <- input$`NGLVieweROutput_ui_1-structure_chainname`
+    r$sequence_df <- sequence_df(r$sequence, r$resno, r$chainname, selchain = r$sequenceOutput$selectedChain)
+    r$aa_clicked <- input$aa_clicked
+    r$PDB <- input$`NGLVieweROutput_ui_1-structure_PDB`
+  })
+  
+  observe({
+    r$rendering <- input$`NGLVieweROutput_ui_1-structure_rendering`
+  })
+
+  observe({
+    r$sidebarItemExpanded <- input$sidebarItemExpanded #loading of UI_components from .ngl file
+  })
+  
+  #Component handlers
+  observe({
+    r$selection$selectionRemove_id <- input$selectionRemove_id #handler defined in handlers.js
+    r$selection$selectionLink_id <- input$selectionLink_id 
+    r$label$labelRemove_id <- input$labelRemove_id #handler defined in handlers.js
+    r$label$labelLink_id <- input$labelLink_id 
+    r$contact$contactRemove_id <- input$contactRemove_id #handler defined in handlers.js
+    r$contact$contactLink_id <- input$contactLink_id 
+  })
+  
+  observe({
+    r$examples$example_link_id <- input$example_link_id 
+  })
+  
+  callModule(mod_fileInput_server, "fileInput_ui_1", r=r)
+  callModule(mod_fileOutput_server, "fileOutput_ui_1", r=r)
+  callModule(mod_examples_server, "examples_ui_1", r=r)
+  callModule(mod_structure_server, "structure_ui_1", globalSession = session, r=r) #Pass globalSession to access NGLViewer object
+  callModule(mod_surface_server, "surface_ui_1", globalSession = session, r=r)
+  callModule(mod_ligand_server, "ligand_ui_1", globalSession = session, r=r)
+  callModule(mod_selection_server, "selection_ui_1", globalSession = session, r=r)
+  callModule(mod_label_server, "label_ui_1", globalSession = session, r=r)
+  callModule(mod_contact_server, "contact_ui_1", globalSession = session, r=r)
+  callModule(mod_stage_server, "stage_ui_1", globalSession = session, r=r)
+  callModule(mod_snapshot_server, "snapshot_ui_1", globalSession = session)
+  callModule(mod_sidebarcontrols_server, "sidebarcontrols_ui_1", globalSession = session, r=r)
+  callModule(mod_labelcontrols_server, "labelcontrols_ui_1", globalSession = session, r=r)
+  callModule(mod_sequenceOutput_server, "sequenceOutput_ui_1", globalSession = session, r=r)
+  callModule(mod_NGLVieweROutput_server, "NGLVieweROutput_ui_1", r=r)
+
+}

NGLVieweR/1.0.0/R/app_ui.R

+#' The application User-Interface
+#' 
+#' @param request Internal parameter for `{shiny}`. 
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @import shinydashboard
+#' @import shinydashboardPlus
+#' @import colourpicker
+#' @import bsplus
+#' @import shinyWidgets
+#' @import shinyjs
+#' @import r2d3
+#' @import NGLVieweR
+#' @import shinyjqui
+#' @import uuid
+#' @import readr
+#' @noRd
+app_ui <- function(request) {
+  tagList(
+    # Leave this function for adding external resources
+    golem_add_external_resources(),
+    # List the first level UI elements here
+    dashboardPage(
+      title = "AphaFold Output",
+      skin = "purple",
+      dashboardHeader(
+        title = HTML("BioHPC protein viewer"),titleWidth = "100%"
+      ),
+      dashboardSidebar(
+        minified = FALSE,
+        sidebarMenu(
+            mod_fileInput_ui("fileInput_ui_1"),
+            mod_structure_ui("structure_ui_1"),
+            mod_surface_ui("surface_ui_1"),
+            mod_ligand_ui("ligand_ui_1"),
+            mod_selection_ui("selection_ui_1"),
+            mod_label_ui("label_ui_1"),
+            mod_contact_ui("contact_ui_1"),
+            mod_stage_ui("stage_ui_1"),
+            mod_snapshot_ui("snapshot_ui_1"),
+            mod_sidebarcontrols_ui("sidebarcontrols_ui_1")
+        )
+      ),
+      dashboardBody(
+        fillPage(
+          mod_labelcontrols_ui("labelcontrols_ui_1"),
+          mod_sequenceOutput_ui("sequenceOutput_ui_1"),
+          mod_NGLVieweROutput_ui("NGLVieweROutput_ui_1")
+        )
+      )
+    )
+  )
+}
+
+#' Add external Resources to the Application
+#' 
+#' This function is internally used to add external 
+#' resources inside the Shiny application. 
+#' 
+#' @import shiny
+#' @importFrom golem add_resource_path activate_js favicon bundle_resources
+#' @noRd
+golem_add_external_resources <- function() {
+  add_resource_path(
+    "www", app_sys("app/www")
+    
+  )
+  
+  tags$head(
+    favicon(
+      ext='ico'
+    ),
+    bundle_resources(
+      path = app_sys("app/www"),
+      app_title = "shinyNGLVieweR"
+    ),
+    useShinyjs(),
+    extendShinyjs(text = jsboxCollapse, functions = c("collapse")), #Collapse box when clicking on title
+    # Input modals
+    bsplus::use_bs_tooltip(),
+    bsplus::use_bs_popover(),
+    bs_input_modal("select_modal", "Selection Language", htmlTemplate(app_sys("app/www/selectionModal.html")), "medium"),
+    bs_input_modal("contact_modal", "Contact Selection", htmlTemplate(app_sys("app/www/contactModal.html")), "medium")
+  )
+}
+
+

NGLVieweR/1.0.0/R/fct_aa_clicked_to_ngl.R

+#' Clicked residues to NGL query
+#'
+#' @description
+#' Match clicked residues to chain and transform to NGL query
+#'
+#' @param selected_aa selected aa in list format
+#' @param chainnames all chainnames of the sequence
+#' @param selchain selected chainname
+#' 
+#' @examples
+#' \dontrun{
+#' NGLVieweR_proxy("structure") %>% updateSelection("aa_clicked", 
+#' sele = aa_clicked_to_ngl(aa_clicked(), structure_chainname(), selectedChain()))
+#' }
+#' @export
+aa_clicked_to_ngl <- function(selected_aa, chainnames, selchain = NULL) {
+  
+  aa_sel <- paste(selected_aa, collapse = " OR ")
+  
+  if (!is.null(selchain) && nchar(selchain) != 0 && any(chainnames %in% selchain)) {
+    output <- sprintf(":%s and (%s)", selchain, aa_sel)
+  } else {
+    output <- aa_sel
+  }
+  return(output)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_insertUI_component.R

+#' Insert components to UI
+#'
+#' @description
+#' Function to add UI components on submission 
+#'
+#' @param type type of components. E.g. label, selection, contact.
+#' @param name name of the components. Use \code{insertUI_name()} to generate a unique name. 
+#' @param uu_id uniqueID used to name the UI components. 
+#' 
+#' @examples 
+#' \dontrun{
+#' insertUI_component('selection', insertUI_name('ligand'), 
+#'                    counter = 3, uu_id = "575ceb43-9ff5-40fb-85a4-9a8e9e06ceff")
+#' }
+#' @export
+insertUI_component <- function(type, name, uu_id){
+  insertUI(
+    selector = sprintf('#%sPlaceholder', type),
+    ui = tags$div(
+      style = 'display:flex;',
+      id = sprintf('%s-%s', type, uu_id),
+      class = sprintf("%sholder", type),
+      style = 'font-size: 100%; padding: 0;',
+      actionLink(
+        sprintf('%sLink-%s', type, uu_id),
+        label = name,
+        class = sprintf("%sLink btn-link", type),
+      ),
+      actionLink(
+        sprintf('%sRemove-%s', type, uu_id),
+        label = NULL,
+        icon = icon('trash'),
+        class = sprintf("%sRemove", type),
+        style = 'color: red;'
+      )
+    )
+  )
+}
+
+#' component UI name
+#'
+#' @description
+#' Function to add a unique name  
+#'
+#' @param name name of the selection. Defaults to selection-\code{counter} if input is \code{NULL} or \code{""} 
+#' @param counter value to create unique \code{name} if none is provided
+#' @param type type of selection. E.g. label, selection, contact.
+#' 
+#' @examples 
+#' \dontrun{
+#' insertUI_name('selection', '', 3)
+#' "selection-3"
+#' }
+#' @export
+insertUI_name <- function(type, name = NULL, counter = 0) {
+  
+  if (is.null(name)) {
+    name <- type
+  } else if (nchar(name) < 1) {
+    name <- type
+  } else {
+    name <- name
+  }
+  
+  if (name == type && counter != 0) {
+    name <- sprintf("%s-%s", name, counter)
+  }
+  return(name)
+}
+
+#' components UI selection
+#'
+#' @description
+#' Function to transform ngl.js selection for UI component  
+#'
+#' @param selection ngl.js query to be transformed. Uses \code{selection_to_ngl()}
+#' @param sequence protein sequence in string format.
+#' 
+#' @examples 
+#' \dontrun{
+#' insertUI_selection("1-3 OR <GHK>", "NGLSDFGHK")
+#' }
+#' @export
+insertUI_selection <- function(sequence, selection) {
+  
+  if (nchar(isolate(selection)) > 0) {
+    selection <- selection_to_ngl(sequence, selection)
+  } else {
+    selection <- 'none'
+  }
+  return(selection)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_loadContacts.R

+#' Load contacts from a .ngl file
+#' 
+#' @description    
+#' Load contacts from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param contacts data.frame of contacts loaded from .ngl file.
+#' @param contactTypes list of all different contactTypes that should be matched.
+#' 
+#' @import NGLVieweR
+#' @import stringr
+#' @export
+loadContacts <- function(NGLVieweR, contacts, contactTypes = list(
+                             "hydrogenBond",
+                             "weakHydrogenBond", "waterHydrogenBond",
+                             "backboneHydrogenBond", "hydrophobic",
+                             "halogenBond", "ionicInteraction",
+                             "metalCoordination", "cationPi",
+                             "piStacking"
+                           )) {
+  viewer <- NGLVieweR
+  if (!is.null(contacts)) {
+    for (n in 1:nrow(contacts)) {
+
+      # get selected contactTypes
+      cont_inp <- unlist(str_split(contacts[n, "contactTypes"], ","))
+      cont_df <- contactTypes %in% cont_inp
+      if (is.na(cont_inp)) {
+        cont_df[] <- TRUE
+      }
+      viewer <- addRepresentation(viewer, "contact",
+        param =
+          list(
+            name = paste(contacts[n, "id"]),
+            sele = paste(contacts[n, "selection"]),
+            filterSele = list(
+              contacts[n, "selectionA"],
+              contacts[n, "selectionB"]
+            ),
+            labelVisible = contacts[n, "labelVisible"],
+            labelUnit = contacts[n, "labelUnit"],
+            hydrogenBond = cont_df[1],
+            weakHydrogenBond = cont_df[2],
+            waterHydrogenBond = cont_df[3],
+            backboneHydrogenBond = cont_df[4],
+            hydrophobic = cont_df[5],
+            halogenBond = cont_df[6],
+            ionicInteraction = cont_df[7],
+            metalCoordination = cont_df[8],
+            cationPi = cont_df[9],
+            piStacking = cont_df[10]
+          )
+      )
+    }
+  }
+  return(viewer)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_loadLabels.R

+#' Load labels from a .ngl file
+#' 
+#' @description    
+#' Load labels from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param labels data.frame of labels loaded from .ngl file.
+#' 
+#' @import NGLVieweR
+#' @export
+loadLabels <- function(NGLVieweR, labels) {
+  viewer <- NGLVieweR
+  if (!is.null(labels)) {
+    for (n in 1:nrow(labels)) {
+      viewer <- addRepresentation(viewer, "label",
+                                     param =
+                                       list(
+                                         name = labels[n, "id"],
+                                         sele = paste(labels[n, "selection"]),
+                                         labelType = "format",
+                                         labelFormat = labels[n, "labelFormat"],
+                                         labelGrouping = labels[n, "labelGrouping"],
+                                         color = labels[n, "textColor"],
+                                         showBackground = labels[n, "labelBackground"],
+                                         backgroundColor = labels[n, "labelbackgroundColor"],
+                                         backgroundOpacity = labels[n, "labelbackgroundOpacity"],
+                                         radiusType = 1,
+                                         xOffset = labels[n, "xOffset"],
+                                         yOffset = labels[n, "yOffset"],
+                                         zOffset = labels[n, "zOffset"],
+                                         radiusSize = labels[n, "labelSize"],
+                                         fixedSize = labels[n, "fixedSize"],
+                                         fontFamily = "sans-serif"
+                                       )
+      )
+    }
+  }
+  return(viewer)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_loadLigand.R

+#' Load structure from a .ngl file
+#'
+#' @description
+#' Load structure from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param ligand data.frame of ligand loaded from .ngl file.
+#'
+#' @import NGLVieweR
+#' @export
+loadLigand <- function(NGLVieweR, ligand) {
+  viewer <- NGLVieweR
+  if (!is.null(ligand)) {
+    if (ligand$ligand != "hide") {
+      viewer <- addRepresentation(viewer,
+        ligand$ligand,
+        param = list(
+          name = "ligand",
+          sele = "( not polymer or not ( protein or nucleic ) ) and not ( water or ACE or NH2 or ion)",
+          colorScheme = ligand$colorScheme,
+          colorValue = ligand$colorValue
+        )
+      )
+    }
+    if (!is.na(ligand$waterIon)) {
+      if (grepl("Water", ligand$waterIon)) {
+        viewer <- addRepresentation(viewer,
+          "ball+stick",
+          param = list(
+            name = "water",
+            sele = "water"
+          )
+        )
+      }
+      if (grepl("Ion", ligand$waterIon)) {
+        viewer <- addRepresentation(viewer,
+          "ball+stick",
+          param = list(
+            name = "ion",
+            sele = "ion"
+          )
+        )
+      }
+    }
+  } else {
+    viewer <- NGLVieweR
+  }
+  return(viewer)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_loadSelections.R

+#' Load selections from a .ngl file
+#' 
+#' @description    
+#' Load selections from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param selections data.frame of selections loaded from .ngl file.
+#' 
+#' @import NGLVieweR
+#' @export
+loadSelections <- function(NGLVieweR, selections) {
+  viewer <- NGLVieweR
+  if (!is.null(selections)) {
+    for (n in 1:nrow(selections)) {
+      viewer <- addRepresentation(viewer, selections[n, "structureType"],
+        param =
+          list(
+            name = selections[n, "id"],
+            colorValue = selections[n, "colorValue"],
+            colorScheme = selections[n, "colorScheme"],
+            opacity = as.numeric(selections[n, "opacity"]),
+            sele = selections[n, "selection"]
+          )
+      )
+    }
+  }
+  return(viewer)
+}
+

NGLVieweR/1.0.0/R/fct_loadStage.R

+#' Load stage from a .ngl file
+#'
+#' @description
+#' Load stage from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param stage data.frame of selections loaded from .ngl file.
+#'
+#' @import NGLVieweR
+#' @export
+loadStage <- function(NGLVieweR, stage) {
+  viewer <- NGLVieweR
+  if (!is.null(stage)) {
+    viewer <- stageParameters(
+      viewer,
+        cameraType = stage$cameraType,
+        backgroundColor = stage$backgroundColor,
+        lightIntensity = stage$lightIntensity,
+        clipNear = stage$clipNear,
+        clipFar = stage$clipFar
+      )
+  } else{
+    viewer <- stageParameters(
+      viewer,
+      cameraType = "orthographic",
+      backgroundColor = "black",
+      lightIntensity = 1,
+      clipNear = 0,
+      clipFar = 100
+    )
+  }
+  return(viewer)
+}

NGLVieweR/1.0.0/R/fct_loadStructure.R

+#' Load structure from a .ngl file
+#'
+#' @description
+#' Load structure from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param structure data.frame of structure loaded from .ngl file.
+#' @param format File 
+#'
+#' @import NGLVieweR
+#' @export
+loadStructure <- function(NGLVieweR, structure, fileName=NULL, format = NULL) {
+  viewer <- NGLVieweR
+  if (is.null(structure)) {
+    if (fileName=="biohpc") {
+      representation <- "ball+stick"
+    } else if(format == "pdb" || format == "ngl" || is.null(format)){
+      representation <- "cartoon"
+    } else {
+      representation <- "ball+stick"
+    }
+    viewer <- addRepresentation(viewer, representation, param = list(
+      name = "structure",
+      colorScheme = "residueindex"
+    ))
+  } else if (!is.null(structure) && !structure$type == "hide") {
+    viewer <- addRepresentation(viewer,
+      structure$type,
+      param =
+        list(
+          name = "structure",
+          colorScheme = structure$colorScheme,
+          colorValue = structure$colorValue,
+          sele = structure$selection,
+          visible = structure$visible
+        )
+    )
+  } else if (structure$type == "hide") {
+    viewer <- addRepresentation(viewer, "cartoon", param = list(
+      name = "structure",
+      colorScheme = structure$colorScheme,
+      colorValue = structure$colorValue,
+      sele = structure$selection,
+      visible = structure$visible
+    ))
+  } else {
+    viewer <- NGLVieweR
+  }
+  return(viewer)
+}

NGLVieweR/1.0.0/R/fct_loadSurface.R

+#' Load surface from a .ngl file
+#'
+#' @description
+#' Load surface from a .ngl file
+#'
+#' @param NGLVieweR NGLVIeweR object.
+#' @param surface data.frame of surface loaded from .ngl file.
+#'
+#' @import NGLVieweR
+#' @export
+loadSurface <- function(NGLVieweR, surface) {
+  viewer <- NGLVieweR
+  if (!is.null(surface)) {
+    viewer <- addRepresentation(viewer,
+      "surface",
+      param =
+        list(
+          name = "surface",
+          colorScheme = surface$colorScheme,
+          colorValue = surface$colorValue,
+          sele = surface$selection,
+          opacity = surface$opacity,
+          visible = surface$visible
+        )
+    )
+  } else {
+    if (is.null(surface)) {
+      viewer <- addRepresentation(viewer, "surface", param = list(
+        visible = FALSE
+      ))
+    }
+  }
+  return(viewer)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_loadUI_component.R

+#' Load UI components
+#'
+#' @description
+#' Function to load UI components 
+#'
+#' @param data data.frame of saved components
+#' @param type type of component. E.g. label, selection, contact
+#' 
+#' @import stringr
+#' @export
+loadUI_component <- function(data, type) {
+    removeUI(selector = sprintf(".%sholder", type), multiple = TRUE)
+    if (!is.null(data)) {
+      for (n in 1:nrow(data)) {
+        uu_id <- stringr::str_replace(data[n, "id"], sprintf("%s-", type), "")
+        insertUI(
+          selector = sprintf("#%sPlaceholder", type),
+          ui = tags$div(
+            style = "display:flex;",
+            id = data[n, "id"],
+            class = sprintf("%sholder", type),
+            actionLink(
+              sprintf("%sLink-%s", type, uu_id),
+              label = data[n, "name"],
+              class = sprintf("%sLink btn-link", type),
+            ),
+            actionLink(
+              sprintf("%sRemove-%s", type, uu_id),
+              label = NULL,
+              icon = icon("trash"),
+              class = sprintf("%sRemove", type),
+              style = "color: red;"
+            )
+          )
+        )
+      }
+  }
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_ngl_to_position.R

+#' AA positions from NGL query
+#'
+#' @description
+#' Find all AA positions in protein sequence from a NGL query. Returns a list of all matched positions. 
+#'
+#' @param sequence Protein sequence in string format
+#' @param input sequence to find the positions for
+#' 
+#' @examples 
+#' ngl_to_position("ALAAGSDFG", "1-5 OR <DFG>")
+#' @import stringr
+#' @importFrom dplyr rowwise mutate
+#' @importFrom tidyr full_seq unnest
+#' @export
+ngl_to_position <- function(sequence, input){
+  
+  #Get string matches
+  strings <- stringr::str_extract_all(input, "(?<=\\<)(.*?)(?=\\>)", simplify = TRUE)[1,]
+  
+  #Get sequence matches
+  seq_match <- stringr::str_extract_all(input, '\\d+-\\d+', simplify = TRUE) [1,]
+  if(length(seq_match) != 0){
+    seq_match <- stringr::str_replace_all(seq_match, "-", ":")
+    seq_match <- unlist(lapply(seq_match, function(x) {eval(parse(text = x))}))
+    seq_match <- unique(seq_match)
+    input <- stringr::str_replace_all(input, '\\d+-\\d+', "")
+  } else {
+    seq_match <- NULL
+  }
+  #get numeric matches
+  numeric_match <- as.numeric(stringr::str_extract_all(input, '[0-9]+', simplify = TRUE)[1,])
+  
+  numeric <- unique(c(seq_match, numeric_match))
+  
+  #Return NULL if no numeric or string matches
+  if(length(strings) == 0 && length(numeric) == 0){
+    return(NULL)
+  } else if(length(numeric) != 0 && length(strings) == 0) {
+    return(numeric)
+  } else {
+    #Find positions
+    matchPositions <- stringr::str_locate_all(sequence, strings)
+    matchPositions <- do.call(rbind, matchPositions)
+    if(nrow(matchPositions) == 0){
+      return(NULL)
+    }
+    matchPositions <- data.frame(matchPositions) %>% dplyr::rowwise() %>% dplyr::mutate(sequence = list(tidyr::full_seq(c(.data$start, .data$end), 1)))
+    matchPositions <- tidyr::unnest(matchPositions, sequence)
+    
+    positions <- sort(unique(matchPositions$sequence))
+    
+    if(length(numeric != 0)){
+      positions <- sort(unique(c(positions, numeric)))
+    }
+    
+    return(positions)
+  }
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_readFile.R

+#' Function to read structural files or NGL session
+#' 
+#' @description    
+#' Function to read .PDB, .PQR, or .NGL files
+#'
+#' @param file The file input. Either a PDB/PQR code or structural file.
+#' 
+#' @importFrom tools file_ext
+#' @importFrom readr read_lines read_csv
+#' @export
+readFile <- function(file) {
+  
+  File <- list(
+    PDB = NULL,
+    structure = NULL,
+    surface = NULL,
+    ligand = NULL,
+    stage = NULL,
+    selections = NULL,
+    labels = NULL,
+    contacts = NULL,
+    fileExt = NULL
+  )
+  
+  #If code is entered
+  fileExt <- tools::file_ext(file)
+  if(nchar(file) < 8 && tools::file_ext(file) == ""){
+    File$PDB <- file
+    return(File)
+  }
+  
+  # #If file is not NGL format
+  # if (fileExt != "ngl" && fileExt != "NGL") {
+  #   File$PDB <- file
+  #   File$fileExt <- fileExt
+  #   return(File)
+  # }
+  
+    # If file is not NGL format
+  if (fileExt != "ngl" && fileExt != "NGL") {
+    # Handle .pdb and .pqr files
+    if (fileExt == "pdb" || fileExt == "PDB" || fileExt == "pqr" || fileExt == "PQR") {
+      File$PDB <- readr::read_lines(file)
+      File$fileExt <- tolower(fileExt)  # Normalize extension to lowercase
+      return(File)
+    } else {
+      stop("Unsupported file format")
+    }
+  }
+  
+  NGL <- readr::read_lines(file)
+  File$fileExt <- "pdb"
+  File$PDB <- NGL
+  # Get file start
+  structure_start <- grep(pattern = "#STRUCTURE", x = NGL)
+  surface_start <- grep(pattern = "#SURFACE", x = NGL)
+  ligand_start <- grep(pattern = "#LIGAND", x = NGL)
+  sel_start <- grep(pattern = "#SELECTIONS", x = NGL)
+  labels_start <- grep(pattern = "#LABELS", x = NGL)
+  contacts_start <- grep(pattern = "#CONTACTS", x = NGL)
+  stage_start <- grep(pattern = "#STAGE", x = NGL)
+  PDB_start <- grep(pattern = "#PDB", x = NGL)
+  
+  
+  # load data frames
+  if(surface_start - structure_start > 1){
+    File$structure <- data.frame(readr::read_csv(file, skip = structure_start, n_max = surface_start - (structure_start + 2)))
+  }
+  if(ligand_start - surface_start > 1){
+    File$surface <- data.frame(readr::read_csv(file, skip = surface_start, n_max = ligand_start - (surface_start + 2)))
+  }
+  if(stage_start - ligand_start > 1){
+    File$ligand <- data.frame(readr::read_csv(file, skip = ligand_start, n_max = stage_start - (ligand_start + 2)))
+  }
+  if(sel_start - stage_start > 1){
+    File$stage <- data.frame(readr::read_csv(file, skip = stage_start, n_max = sel_start - (stage_start + 2)))
+  }
+  if ((labels_start - (sel_start +1)) > 1) {
+    File$selections <- data.frame(readr::read_csv(file, skip = sel_start, n_max = labels_start - (sel_start + 2)))
+  }
+  if ((contacts_start - (labels_start + 1)) > 1) {
+    File$labels <- data.frame(readr::read_csv(file, skip = labels_start, n_max = contacts_start - (labels_start + 2)))
+  }
+  if ((PDB_start - (contacts_start + 1)) > 1) {
+    File$contacts <- data.frame(readr::read_csv(file, skip = contacts_start, n_max = PDB_start - (contacts_start + 2)))
+  }
+  return(File)
+}
\ No newline at end of file

NGLVieweR/1.0.0/R/fct_removeUI_component.R

+#' Remove component from UI
+#'
+#' @description
+#' Function to add a UI once a component has been submitted 
+#'
+#' @param NGLVieweR viewer component 
+#' @param data data.frame of saved components
+#' @param type type of component. E.g. label, selection, contact
+#' @param id ID of selected remove link
+#' 
+#' @examples 
+#' removeUI_component('selection', input$selectionRemove_id)
+#' @import stringr
+#' @export
+removeUI_component <- function(NGLVieweR, data, type, id) {
+  id <- stringr::str_replace(id, sprintf("%sRemove-", type), "")
+  type_id <- sprintf("%s-%s", type, id)
+  # removeUI
+  removeUI(selector = sprintf("#%s", type_id))
+  # remove structure component
+  NGLVieweR %>% removeSelection(type_id)
+  # remove seletion from data.frame
+  data <- subset(data, id != type_id)
+  return(data)
+}
+