texts and helps

ippisite/ippidb/admin.py

@@ -186,7 +186,7 @@ class DistanceAdmin(admin.ModelAdmin):
 
 @admin.register(MetaInformation)
 class MetaInformationAdmin(admin.ModelAdmin):
-    list_display = ("average", "std", "maximum", "minimum")
+    list_display = ("average", "std", "maximum", "minimum", "normalize_factor")
 
 
 @admin.register(Job)

ippisite/ippidb/static/js/targetcentrict_networks.js

@@ -31,7 +31,7 @@ var node_trace = function(nodes, edges) {
     trace_PL = {
         x: x_PL,
         y: y_PL,
-	name: 'Protein Ligand',
+	name: ' Protein/Ligand complexes',
 	text: text_PL,
         mode: 'markers',
         type: 'scattergl',
@@ -46,7 +46,7 @@ var node_trace = function(nodes, edges) {
     trace_HD = {
         x: x_HD,
         y: y_HD,
-	name: 'Heterodimer',
+	name: 'Heterodimer complexes',
 	text: text_HD,
         mode: 'markers',
         type: 'scattergl',
@@ -86,7 +86,7 @@ $.ajax({
     var data = build_trace(nodes_info_ippidb, edges_ippidb);
     var nodes_coords = data[3];
     var layout = {
-    title:'Complete cavities network',
+    //title:'Complete cavities network',
     height:1200,
     font: {
       family: 'Courier New, monospace',

ippisite/ippidb/templates/targetcentric.html

@@ -40,7 +40,7 @@
         </div>
     </nav>
     <div>
-        <a href="{% url 'networks' %}"><strong>See the complete cavities network</strong></a>
+        <a href="{% url 'networks' %}"><strong>Explore the PPI pocketome</strong></a>
     </div>
     <div class="card">
         <div id="accordion">
@@ -54,7 +54,7 @@
         <div class="card-body">
             <form  id="searchform" autocomplete="off" action="{% url 'cavities' %}" method="get">
             <div class="input-group autocomplete">
-                <input id="id_search" name="search" class="form-control" type="text" placeholder="Search by PDB ID, Protein name, UniProt ID, ligands, organism" aria-label="Search">
+                <input id="id_search" name="search" class="form-control" type="text" placeholder="Search by PDB ID, Protein name, Uniprot ID, ligands, organism" aria-label="Search">
                 <div class="input-group-append">
                     <button data-toggle="modal" data-target="#waitingmodal" type="submit" class="btn btn-outline-secondary"><i class="fas fa-search"></i></button>
                 </div>
@@ -148,19 +148,18 @@
                             <div class="col-12">
                                 <a class="infobulle" href='#'>
                                     <i class="fas fa-question-circle fa-2x"></i>
-                                    <span>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas pulvinar ornare hendrerit. 
-                                        Phasellus urna neque, vehicula in eleifend ut, aliquam quis nunc. Nam dapibus lobortis nulla id faucibus. 
-                                        Morbi rhoncus libero at lectus iaculis sagittis. Phasellus egestas enim odio, porta lobortis neque sodales 
-                                        vitae. Fusce molestie posuere ultricies. Sed interdum ipsum vel metus condimentum, ac vehicula enim molestie. 
-                                        Nunc pharetra tortor ullamcorper lacinia viverra. Pellentesque in tempor mauris. Integer convallis urna a 
-                                        ligula ultricies venenatis. Duis ut congue magna. </span>
-                                </a>
+                                    <span>The color gradient in the table illustrates the pocket similarity index (PSI) of a selected pocket with respect to its most similar neighbors in the PPI pocketome. 
+                                        This pocket similarity index is calculated using a Gaussian kernel of all the pair-wise Euclidean distances between PPI pockets. It is bounded between 0 and 1. 
+                                        The pocket similarity index value is given when you mouseover a cavity name.
+                                        <br><img width="50%" height="50%" src="{% static 'images/Other/PSIequation.png' %}" alt="psi equation" />                     
+                                    </a>
                                 <strong> Cavities </strong>
                             </div>
                     </div>
                         <div class="row text-justify ml-3 mr-3">
                             <div class="col-8 text-wrap">
-                            Gradient colors for table is based on maximum and minimum score in the matrix. Score is given when you mouseover a cavity name.
+                                Gradient colors for table is based on maximum and minimum score in the matrix. 
+                                Score is given when you mouseover a cavity name. 
                             </div>
                             <div class="col-4">
                             <table class="gradiant"><tbody><tr>

ippisite/ippidb/templates/targetcentric_networks.html

@@ -21,7 +21,7 @@
       <div class="input-group">
         <div class="btn-group">
           <button type="button" class="btn btn-info dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
-            Select a threshold (multiplied by standard deviation)
+            Select a vicinity network
           </button>
           <div class="dropdown-menu">
             {% for net in network_list %}
@@ -32,15 +32,13 @@
           <p>
             <a class="infobulle" href='#'>
               <i class="fas fa-question-circle fa-2x m-1 mt-3"></i>
-              <span>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas pulvinar ornare hendrerit. 
-                Phasellus urna neque, vehicula in eleifend ut, aliquam quis nunc. Nam dapibus lobortis nulla id faucibus. 
-                Morbi rhoncus libero at lectus iaculis sagittis. Phasellus egestas enim odio, porta lobortis neque sodales 
-                vitae. Fusce molestie posuere ultricies. Sed interdum ipsum vel metus condimentum, ac vehicula enim molestie. 
-                Nunc pharetra tortor ullamcorper lacinia viverra. Pellentesque in tempor mauris. Integer convallis urna a 
-                ligula ultricies venenatis. Duis ut congue magna. </span>
+              <span>Vicinity network of the PPI pocketome: Displays pockets having a pocket similarity index (PSI) with at least one other pocket above 0.65 
+                    <br><br>Vicinity network of PPI pockets (non-redundant): Same as above but by only considering similar pockets within proteins having a different Uniprot ID. 
+                     The purpose is this network is to highlight unforeseen vicinities within the PPI pocketome.
+              </span>
             </a>
           </p>
-          <input id="id_search" name="search" class="form-control" type="text" placeholder="Cavity" aria-label="Search">
+          <input id="id_search" name="search" class="form-control" type="text" placeholder="Search pocket by PDB ID, Uniprot ID, ligand ID" aria-label="Search">
           <div class="input-group-append">
               <button type="button" class="btn btn-outline-secondary search-button"><i class="fas fa-search"></i></button>
           </div>
@@ -58,7 +56,9 @@
         </div>
       {% endfor %}
     {% else %}
-   
+    <div class="text-center mt-3">
+       <h5>{{ network.label }}</h5>
+    </div>
       <div id='myDiv'><!-- Plotly chart will be drawn inside this DIV -->
         <p class="loader"></p>
       </div>