diff --git a/app.R b/app.R
deleted file mode 100644
index 93d9167..0000000
--- a/app.R
+++ /dev/null
@@ -1,324 +0,0 @@
-#
-# This is a Shiny web application. You can run the application by clicking
-# the 'Run App' button above.
-#
-# Find out more about building applications with Shiny here:
-#
-#    http://shiny.rstudio.com/
-#
-
-library(shiny)
-library(shinyjs)
-library(shinydashboard)
-#library("wesanderson") # ayyyy lmao hipster af
-library(dplyr)
-library(DT)
-library(ggplot2)
-library(grid) # for the info box
-library(plotly)
-library(shinycssloaders)
-library(NGLVieweR)
-library(httr)
-library(readr)
-library(RCurl)
-# make shiny non-stupid
-options(shiny.launch.browser = FALSE) # i am a big girl and can tie my own laces
-options(shiny.port = 8000) # don't change the port every time
-options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
-options(DT.options = list(scrollX = TRUE))
-
-
-# An "application token" is required here. I generated this one like this:
-# curl -H "Content-Type: application/json" -d '{"name":"r-data"}' -u <username>:<password> https://git.tunstall.in/api/v1/users/sethp/tokens
-
-# Gitea access token
-access_token = read_lines("~/secret-token")
-
-gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/list_unique_missense_genes.csv"
-missense_gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/missense_genes_params.csv"
-alphafold_url = "https://alphafold.ebi.ac.uk/files/"
-
-genes=read_csv(paste0(gene_url,"?token=",access_token))
-unique_missense_genes = read_delim(paste0(missense_gene_url,"?token=",access_token))
-#genes = c("Gene 1", "Gene 2", "Gene 3", "Gene 4", "Gene 5")
-
-# Define UI for application that draws a histogram
-ui=dashboardPage(skin="purple",
-                 dashboardHeader(title="Tuberculosis Host"),
-                 dashboardSidebar(
-                   radioButtons("gene",
-                                label="Gene",
-                                choices = genes$Gene,
-                                selected="alr" # "alr" is a value
-                   ),
-                   actionButton("clear_ngl",
-                                "Reset Structures"),
-                   actionButton("all_mutations",
-                                "All Mutations")
-                 ),
-                 dashboardBody(
-                   useShinyjs(),
-                   fluidRow(
-                     box(
-                       title="Crystallised Structure",
-                       width=5,
-                       column(
-                         NGLVieweROutput("structure"),
-                         width=12
-                       ) 
-                     ),
-                     box(
-                       title="AlphaFold Structure",
-                       width=5,
-                       column(
-                         NGLVieweROutput("af_structure"),
-                         width=12
-                       )
-                     ),
-                     box(
-                       title="Mutation Information",
-                       width=2,
-                       column(
-                         htmlOutput("information"),
-                         width=12
-                       )
-                     )
-                   ),
-                   fluidRow(
-                     column(
-                       DT::dataTableOutput('table'),
-                       width=12
-                     )
-                   ),
-                   verbatimTextOutput("debug")
-                 )
-)
-
-# Define server logic required to draw a histogram
-server <- function(input, output) {
-  
-  output$distPlot <- renderPlot({
-    # generate bins based on input$bins from ui.R
-    x    <- faithful[, 2]
-    bins <- seq(min(x), max(x), length.out = input$bins + 1)
-    
-    # draw the histogram with the specified number of bins
-    hist(x, breaks = bins, col = 'darkgray', border = 'white',
-         xlab = 'Waiting time to next eruption (in mins)',
-         main = 'Histogram of waiting times')
-  })
-  ### NGLViewer ####
-  # Structure Viewer WebGL/NGLViewR window
-  output$structure <- renderNGLVieweR({
-    selected_gene=input$gene
-    ngl_gene=as.character(genes[genes$Gene==selected_gene,"PDB"])
-    NGLVieweR(ngl_gene) %>%
-      addRepresentation("cartoon",
-                        param = list(name = "cartoon",
-                                     color="tan",
-                                     #colorScheme = "bfactor",
-                                     opacity = 1
-                        )
-      ) %>%
-      stageParameters(backgroundColor = "white") %>%
-      setQuality("high") %>%
-      setFocus(0) %>%
-      setSpin(FALSE)
-  })
-  output$af_structure <- renderNGLVieweR({
-    selected_af_gene=input$gene
-    ngl_af_gene=as.character(genes[genes$Gene==selected_af_gene,"AF_PDB"])
-    
-    #af_pdb=cat(content(GET(paste0(alphafold_url,"AF-",ngl_af_gene,"-F1-model_v4.pdb")), as="text"), "\n")
-    af_pdb=content(GET(paste0(alphafold_url,"AF-",ngl_af_gene,"-F1-model_v4.pdb")), as="text")
-    #print(af_pdb)
-    #ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
-    NGLVieweR(af_pdb, format="pdb") %>%
-      addRepresentation("cartoon",
-                        param = list(name = "cartoon",
-                                     #color="tan"
-                                     colorScheme = "bfactor",
-                                     opacity = 1
-                        )
-      ) %>%
-      stageParameters(backgroundColor = "white") %>%
-      setQuality("high") %>%
-      setFocus(0) %>%
-      setSpin(FALSE)
-  })
-  
-  # output$table <- DT::renderDataTable({
-  #   selected_gene=input$gene
-  #   gene=as.character(genes[genes$Gene==selected_gene,"Gene"])
-  #   #unique_missense_genes[unique_missense_genes$gene_name==gene,]
-  #   unique_missense_genes
-  # },
-  # selection = "single",
-  # search = list(search="alr"))
-  output$table <- DT::renderDataTable(
-    unique_missense_genes,
-    selection = "single",
-    options=list(
-      search = list(search=as.character(genes[genes$Gene==input$gene,"Gene"]))
-    )
-  )
-  
-  observeEvent(input$table_rows_selected,{
-    #req(length(input$table_row_selected) > 0)
-    mutation = as.character(unique_missense_genes[input$table_rows_selected,"hgvd_p"])
-    chain = as.character(unique_missense_genes[input$table_rows_selected,"chain"])
-    # what the absolute FUCK is this mess? I JUST WANT THE MATCH ASDLASJASDASHFKLJASDFK
-    # coming down from the trees was a mistake, and abandoning Perl doubly so.
-    clicked_position = regmatches(mutation, regexpr("[0-9]+", mutation, perl=TRUE))
-    
-    # Now update the 3D structure to highlight the clicked thing and then zoom in.
-    
-    NGLVieweR_proxy("structure") %>%
-      #addSelection('ball+stick'
-      addSelection('spacefill'
-                   , param = list(
-                     name = "Pos"
-                     , sele = trimws(paste0(clicked_position,':', chain))
-                     , color = "red"
-                     #, colorValue="00ff00"
-                     #, colorScheme="element"
-                   )
-      )
-    NGLVieweR_proxy("af_structure") %>%
-      #addSelection('ball+stick'
-      addSelection('spacefill'
-                   , param = list(
-                     name = "Pos"
-                     , sele = clicked_position
-                     , color = "red"
-                     #, colorValue="00ff00"
-                     #, colorScheme="element"
-                   )
-      )
-    
-    NGLVieweR_proxy("af_structure") %>% updateZoomMove(
-      center = clicked_position,
-      zoom = clicked_position,
-      duration = 1000, # animation time in ms
-      z_offSet = -1
-    )
-    NGLVieweR_proxy("structure") %>% updateZoomMove(
-      center = trimws(paste0(clicked_position,':', chain)),
-      zoom = trimws(paste0(clicked_position,':', chain)),
-      duration = 1000, # animation time in ms
-      z_offSet = -1
-    )
-    output$information <- renderUI({
-      selected_gene=input$gene
-      HTML(paste0("<strong>Mutation: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mutationinformation"]),"<br/>",
-                  "<strong>PDB ID: </strong>", as.character(genes[genes$Gene==selected_gene,"PDB"]),"<br/>",
-                  "<strong>AlphaFold ID: </strong>", as.character(genes[genes$Gene==selected_gene,"AF_PDB"]), "<br/>",
-                  "<strong>Ligand Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ligand_distance"]), "<br/>",
-                  "<strong>mCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_lig"]), "<br/>",
-                  "<strong>mmCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mmcsm_lig"]), "<br/>",
-                  "<strong>mCSM DUET: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_duet"]), "<br/>",
-                  "<strong>FoldX: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_foldx"]), "<br/>",
-                  "<strong>DeepDDG: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_deepddg"]), "<br/>",
-                  "<strong>Dynamut2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_dynamut2"]), "<br/>",
-                  "<strong>mCSM PPI2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_ppi2_affinity"]), "<br/>",
-                  "<strong>Interface Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"interface_dist"]), "<br/>",
-                  "<strong>mCSM NA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_na_affinity"]), "<br/>",
-                  "<strong>Consurf: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"consurf_score"]), "<br/>",
-                  #"<strong>SNAP2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_score"]), "<br/>",
-                  "<strong>SNAP2 Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_outcome"]), "<br/>",
-                  #"<strong>PROVEAN: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_score"]), "<br/>",
-                  "<strong>PROVEAN Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_outcome"]), "<br/>",
-                  "<strong>RSA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rsa"]), "<br/>",
-                  "<strong>Residue Depth: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rd_values"]), "<br/>",
-                  "<strong>Total Samples: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"total_sample_count"]), "<br/>",
-                  "<strong>Distinct Lineages: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"distinct_lineage_count"]), "<br/>"
-                  
-      )
-      )
-      
-    })
-    
-    # output$debug <- renderPrint({
-    #   print(c(mutation, clicked_position))
-    # })
-  })
-  observeEvent(
-    {
-      input$clear_ngl
-    }, {
-      NGLVieweR_proxy("structure") %>%
-        removeSelection("Pos") %>%
-        removeSelection("all_mutations_surface") %>%
-        updateVisibility("cartoon", TRUE) %>%
-        removeSelection("all_mutations")
-      NGLVieweR_proxy("af_structure") %>%
-        removeSelection("Pos") %>%
-        removeSelection("all_mutations_surface") %>%
-        updateVisibility("cartoon", TRUE) %>%
-        removeSelection("all_mutations")
-    })
-  # add a surface representation and highlight all mutations on it
-  observeEvent(
-    {
-      input$all_mutations
-    }, {
-      gene = input$gene
-      mutations = paste0(":",
-                         as.matrix(unique_missense_genes[unique_missense_genes$gene_name == gene,c("chain")])[1],
-                         " and (",
-                         paste0(
-                           apply(
-                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
-                             1,
-                             function(x){
-                               paste0(trimws(x[1])
-                               )}
-                           ),
-                           collapse=", "
-                         ), ")"
-      )
-      #print(mutations)
-      
-      
-      NGLVieweR_proxy("structure") %>%
-        updateVisibility("cartoon", FALSE) %>%
-        addSelection(type="cartoon",
-                     param = list(name = "all_mutations_surface",
-                                  sele = "all",
-                                  color="tan",
-                                  opacity = 0.2
-                     )
-        ) %>%
-        addSelection(type="ball+stick", #spacefill
-                     param = list(name = "all_mutations",
-                                  color="orange",
-                                  sele = mutations
-                                  #colorScheme = "bfactor",
-                                  #opacity = 1
-                     )
-        )
-      NGLVieweR_proxy("af_structure") %>%
-        updateVisibility("cartoon", FALSE) %>%
-        addSelection(type="cartoon",
-                     param = list(name = "all_mutations_surface",
-                                  sele = "all",
-                                  #color="tan",
-                                  colorScheme = "bfactor",
-                                  opacity = 0.2
-                     )
-        ) %>%
-        addSelection(type="ball+stick", #spacefill
-                     param = list(name = "all_mutations",
-                                  color="orange",
-                                  sele = mutations
-                                  #colorScheme = "bfactor",
-                                  #opacity = 1
-                     )
-        )
-    })
-}
-
-# Run the application 
-shinyApp(ui = ui, server = server)
-
-
diff --git a/server.R b/server.R
index 3acb764..dacb105 100644
--- a/server.R
+++ b/server.R
@@ -197,20 +197,19 @@ shinyServer(function(input, output){
                            collapse=", "
                          ), ")"
       )
-      mutations_af = paste0(":",
-                         as.matrix(unique_missense_genes[unique_missense_genes$gene_name == gene,c("chain")])[1],
-                         " and (",
-                         paste0(
-                           apply(
-                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_af","chain")],
-                             1,
-                             function(x){
-                               paste0(trimws(x[1])
-                               )}
-                           ),
-                           collapse=", "
-                         ), ")"
+      mutations_af = paste0(":A and (",
+                            paste0(
+                              apply(
+                                unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_af","chain")],
+                                1,
+                                function(x){
+                                  paste0(trimws(x[1])
+                                  )}
+                              ),
+                              collapse=", "
+                            ), ")"
       )
+
       #print(mutations)