From c10486212a56ed932fcec2a381b6272e71b9b6ce Mon Sep 17 00:00:00 2001
From: fmareuil <fmareuil@pasteur.fr>
Date: Thu, 11 Feb 2021 15:29:20 +0100
Subject: [PATCH] texts and helps
---
ippisite/ippidb/admin.py | 2 +-
.../static/images/Other/PSIequation.png | Bin 0 -> 12938 bytes
.../static/js/targetcentrict_networks.js | 6 +++---
ippisite/ippidb/templates/targetcentric.html | 19 +++++++++---------
.../templates/targetcentric_networks.html | 18 ++++++++---------
5 files changed, 22 insertions(+), 23 deletions(-)
create mode 100644 ippisite/ippidb/static/images/Other/PSIequation.png
diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 5da7a753..e7ed283d 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
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HcmV?d00001
diff --git a/ippisite/ippidb/static/js/targetcentrict_networks.js b/ippisite/ippidb/static/js/targetcentrict_networks.js
index 99368396..a4c72b0b 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 773c14fd..28c4e587 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 1216d116..5e11b506 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>
--
GitLab