Commit 50290b7e authored by Fabien  MAREUIL's avatar Fabien MAREUIL
Browse files

from cavity to pocket

parent cf03f544
Pipeline #50412 failed with stages
in 9 minutes and 50 seconds
......@@ -572,7 +572,7 @@ function loadNGL(url, callback){
var blobcavity = new Blob( [ cavity.mol2 ], {type: 'text/plain' } );
var multiButton = createElement("input", {
type: "button",
value: "load cavity " + cavity.cavity_number + " from " + chain.pdb_chain_id,
value: "load pocket " + cavity.cavity_number + " from " + chain.pdb_chain_id,
onclick: function (e) {
stage.compList.forEach(function(component){
if (component.name.includes("CAVITY")) {
......
......@@ -99,7 +99,7 @@
<a href="{% url 'compound_list' %}">Query compounds</a>
</li>
<li>
<a href="{% url 'cavities' %}">Query cavities</a>
<a href="{% url 'cavities' %}">Query pockets</a>
</li>
<li>
<a href="{% url 'tutorials' %}">Tutorials</a>
......
......@@ -36,7 +36,7 @@
<nav class="breadcrumb breadNav" role="navigation">
<div class="breadNav-label">You are here</div>
<div aria-labelledby="breadNav-label">
{% block breadcrumb %} <a href="{% url 'cavities' %}" class="breadNav-link">Query cavities</a> > Cavity {% endblock %}
{% block breadcrumb %} <a href="{% url 'cavities' %}" class="breadNav-link">Query pockets</a> > Pocket {% endblock %}
</div>
</nav>
<div>
......@@ -60,7 +60,7 @@
</div>
</div>
</form>
{{ cavitiescount }} Cavities in {{ proteincount }} proteins of {{ organismcount }} organisms
{{ cavitiescount }} Pockets in {{ proteincount }} proteins of {{ organismcount }} organisms
</div>
</div>
</div>
......@@ -98,7 +98,7 @@
</div>
</div>
</form>
{{ cavitiescount }} Cavities in {{ proteincount }} proteins of {{ organismcount }} organisms
{{ cavitiescount }} Pockets in {{ proteincount }} proteins of {{ organismcount }} organisms
</div>
</div>
</div>
......@@ -150,16 +150,16 @@
<i class="fas fa-question-circle fa-2x"></i>
<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.
The pocket similarity index value is given when you mouseover a pocket name.
<br><img width="50%" height="50%" src="{% static 'images/Other/PSIequation.png' %}" alt="psi equation" />
</a>
<strong> Cavities </strong>
<strong> Pockets </strong>
</div>
</div>
<div class="row text-justify ml-3 mr-3">
<div class="col-8 text-wrap">
The color gradient for the table is based on maximum and minimum PSI (Pocket Similarity Index) in the matrix.
PSI is given when you mouseover a cavity name.
PSI is given when you mouseover a pocket name.
</div>
<div class="col-4">
<table class="gradiant"><tbody><tr>
......@@ -180,7 +180,7 @@
<table id="cavitiestable" class="table table-hover shadow table-responsive table-sm zui-table table-header-rotated">
<thead class="thead-light">
<tr>
<th class="zui-sticky-col" title="PDB / Chain / Partner / Cavity" scope="col"><div><span>Cavities</span></div></th>
<th class="zui-sticky-col" title="PDB / Chain / Partner / Pocket" scope="col"><div><span>Pockets</span></div></th>
<th class="rotate-45" title="Volume in Aˆ3" scope="col"><div><span>Volume</span></div></th>
<th class="rotate-45" title="Normalized Moment of Inertia PMX/PMZ" scope="col"><div><span>NPR1</span></div></th>
<th class="rotate-45" title="Normalized Moment of Inertia PMY/PMZ" scope="col"><div><span>NPR2</span></div></th>
......@@ -189,23 +189,23 @@
<th class="rotate-45" title="Radius of gyration" scope="col"><div><span>Rgyr</span></div></th>
<th class="rotate-45" title="Spherocity Index" scope="col"><div><span>Spherocity Index</span></div></th>
<th class="rotate-45" title="% of hydrophobic points" scope="col"><div><span>CA</span></div></th>
<th class="rotate-45" title="% of aromatic cavity points" scope="col"><div><span>CZ</span></div></th>
<th class="rotate-45" title="% of aromatic pocket points" scope="col"><div><span>CZ</span></div></th>
<th class="rotate-45" title="% of h‐bond donor points" scope="col"><div><span>N</span></div></th>
<th class="rotate-45" title="% of h‐bond acceptor points" scope="col"><div><span>O</span></div></th>
<th class="rotate-45" title="% of h‐bond acceptor & donor points" scope="col"><div><span>OG</span></div></th>
<th class="rotate-45" title="% of positively ionizable points" scope="col"><div><span>NZ</span></div></th>
<th class="rotate-45" title="% of negatively ionizable points" scope="col"><div><span>OD1</span></div></th>
<th class="rotate-45" title="% of non specific cavity points" scope="col"><div><span>DU</span></div></th>
<th class="rotate-45" title="% cavity points with buridness below 33.3%" scope="col"><div><span>T40</div></th>
<th class="rotate-45" title="% cavity points with buridness between 33.3% and 41.6%" scope="col"><div><span>T40-50</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 41.6% and 50.0%" scope="col"><div><span>T50-60</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 50.0% and 58.3%" scope="col"><div><span>T60-70</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 58.3% and 66.6%" scope="col"><div><span>T70-80</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 66.6% and 75.0%" scope="col"><div><span>T80-90</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 75.0% and 83.3%" scope="col"><div><span>T90-100</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 83.3% and 91.6%" scope="col"><div><span>T100-110</span></div></th>
<th class="rotate-45" title="% cavity points with buridness between 91.6% and 99.9%" scope="col"><div><span>T110-120</span></div></th>
<th class="rotate-45" title="% cavity points with buridness of 100%" scope="col"><div><span>T120</span></div></th>
<th class="rotate-45" title="% of non specific pocket points" scope="col"><div><span>DU</span></div></th>
<th class="rotate-45" title="% pocket points with buridness below 33.3%" scope="col"><div><span>T40</div></th>
<th class="rotate-45" title="% pocket points with buridness between 33.3% and 41.6%" scope="col"><div><span>T40-50</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 41.6% and 50.0%" scope="col"><div><span>T50-60</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 50.0% and 58.3%" scope="col"><div><span>T60-70</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 58.3% and 66.6%" scope="col"><div><span>T70-80</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 66.6% and 75.0%" scope="col"><div><span>T80-90</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 75.0% and 83.3%" scope="col"><div><span>T90-100</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 83.3% and 91.6%" scope="col"><div><span>T100-110</span></div></th>
<th class="rotate-45" title="% pocket points with buridness between 91.6% and 99.9%" scope="col"><div><span>T110-120</span></div></th>
<th class="rotate-45" title="% pocket points with buridness of 100%" scope="col"><div><span>T120</span></div></th>
</tr>
</thead>
<tbody>
......@@ -224,7 +224,7 @@
{{ cavity.chain.pdb_chain_id }} / {{ cavity.chain.protein.short_name }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ cavity.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......@@ -235,7 +235,7 @@
{{ cavity.partner.ligand.pdb_ligand_id }}_{{ cavity.partner.ligand.supplementary_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ cavity.partner.ligand.pdb_ligand_id }}">Query ligand ID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ cavity.partner.ligand.pdb_ligand_id }}">Query ligand ID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?similar_to=ECFP4:{{ cavity.partner.ligand.canonical_smile|urlencode }}">Query SMILES in iPPI-DB compounds</a>
</div>
</span>
......@@ -246,7 +246,7 @@
{{ cavity.partner.chain.pdb_chain_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.partner.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.partner.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ cavity.partner.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......@@ -291,7 +291,7 @@
{{ distance.cavity2.chain.pdb_chain_id }} / {{ distance.cavity2.chain.protein.short_name }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity2.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity2.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ distance.cavity2.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......@@ -302,7 +302,7 @@
{{ distance.cavity2.partner.ligand.pdb_ligand_id }}_{{ distance.cavity2.partner.ligand.supplementary_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ distance.cavity2.partner.ligand.pdb_ligand_id }}">Query ligand ID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ distance.cavity2.partner.ligand.pdb_ligand_id }}">Query ligand ID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?similar_to=ECFP4:{{ distance.cavity2.partner.ligand.canonical_smile|urlencode }}">Query SMILES in iPPI-DB compounds</a>
</div>
</span>
......@@ -313,7 +313,7 @@
{{ distance.cavity2.partner.chain.pdb_chain_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity2.partner.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity2.partner.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ distance.cavity2.partner.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......@@ -356,7 +356,7 @@
{{ distance.cavity1.chain.pdb_chain_id }} / {{ distance.cavity1.chain.protein.short_name }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity1.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity1.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprot_id={{ distance.cavity1.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......@@ -367,7 +367,7 @@
{{ distance.cavity1.partner.ligand.pdb_ligand_id }}_{{ distance.cavity1.partner.ligand.supplementary_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ distance.cavity1.partner.ligand.pdb_ligand_id }}">Query ligand ID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ distance.cavity1.partner.ligand.pdb_ligand_id }}">Query ligand ID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?similar_to=ECFP4:{{ distance.cavity1.partner.ligand.canonical_smile|urlencode }}">Query SMILES in iPPI-DB compounds</a>
</div>
</span>
......@@ -378,7 +378,7 @@
{{ distance.cavity1.partner.chain.pdb_chain_id }}
</button>
<div class="dropdown-content">
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity1.partner.chain.protein.uniprot_id }}">Query UniprotID in cavities</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ distance.cavity1.partner.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
<a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ distance.cavity1.partner.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
</div>
</span>
......
......@@ -13,7 +13,7 @@
<nav class="breadcrumb breadNav" role="navigation">
<div class="breadNav-label">You are here</div>
<div aria-labelledby="breadNav-label">
{% block breadcrumb %} <a href="{% url 'networks' %}" class="breadNav-link">Query cavities</a> > Cavity {% endblock %}
{% block breadcrumb %} <a href="{% url 'networks' %}" class="breadNav-link">Query pockets</a> > Pocket {% endblock %}
</div>
</nav>
<div class="card">
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment