diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py index 5da7a7530e846c7b2a2cd244b6a4b71a7bb01dab..e7ed283d59d928dc88c6982bac8c2a7d3cfce40a 100644 --- a/ippisite/ippidb/admin.py +++ b/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) diff --git a/ippisite/ippidb/static/images/Other/PSIequation.png b/ippisite/ippidb/static/images/Other/PSIequation.png new file mode 100644 index 0000000000000000000000000000000000000000..856548fc8d239a51e2ba3930108097e563956551 Binary files /dev/null and b/ippisite/ippidb/static/images/Other/PSIequation.png differ diff --git a/ippisite/ippidb/static/js/targetcentrict_networks.js b/ippisite/ippidb/static/js/targetcentrict_networks.js index 993683961542f6cdde3d04eaaf48f44d126ce445..a4c72b0bfafe16948c82f1f6cca77263f3b19257 100644 --- a/ippisite/ippidb/static/js/targetcentrict_networks.js +++ b/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', diff --git a/ippisite/ippidb/templates/targetcentric.html b/ippisite/ippidb/templates/targetcentric.html index 773c14fdf141d010a4d210cc5068aa712ffb087d..28c4e587398b85de75b4f7262e61c44df8fa891c 100644 --- a/ippisite/ippidb/templates/targetcentric.html +++ b/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> diff --git a/ippisite/ippidb/templates/targetcentric_networks.html b/ippisite/ippidb/templates/targetcentric_networks.html index 1216d11668e85770786ffa9701bc7851ca35de71..5e11b50615c00f2945771525d5dc30f7ceb815c9 100644 --- a/ippisite/ippidb/templates/targetcentric_networks.html +++ b/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>