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html_templs.py
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html_templs.py
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header_html = '''
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Superimposition Report</title>
<!-- Bootstrap core CSS-->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
<link href="css/sb-admin.css" rel="stylesheet">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" />
<link rel="stylesheet" href="https://drvic10k.github.io/bootstrap-sortable/Contents/bootstrap-sortable.css" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.2.1/jquery.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.19.1/moment.js"></script>
<script src="https://drvic10k.github.io/bootstrap-sortable/Scripts/bootstrap-sortable.js"></script>
<link href="//netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
<script> {ngl} </script>
<style>
div.solid {{border-style: solid; border-color:#bababa;}}
html {{position: relative;min-height: 100%;}}
body {{overflow-x: hidden; font-size: 10pt;line-height: 25px; }}
div.content-wrapper {{min-height: calc(100vh - 56px);padding-top: 1rem;overflow-x: hidden;background: white;}}
#myBtn {{display: none;position: fixed;bottom: 20px;right: 20px;z-index: 99;font-size: 15px;border: none;outline: none;
background-color: #5342f4;color: white;cursor: pointer;padding: 15px;border-radius: 3px;}}
#myBtn:hover {{background-color: #555;}}
div.card-header{{font-weight: bold;}}
.mol-container {{width: 100%;height: 300px;position: relative;}}
.card-body-plot {{text-align: center}}
</style>
</head>
<body id="page-top">
<div class="row">
<div class="col-sm-1"></div>
<div class="col-sm-10">
<button onclick="topFunction()" id="myBtn" title="Go to top">Top</button>
<div class="content-wrapper">
<div class="container-fluid">
<!-- Breadcrumbs-->
<ol class="breadcrumb">
<li class="breadcrumb-item active"><h3>SUPERIMPOSITION by PROTEIN STRUCTURE</h3></li>
</ol>
<!-- Job-->
'''
job_html = '''
<div class="card mb-3">
<div class="card-header">Job</div>
<div class="card-body">
<ul>
<li><b>Commandline arguments:</b> {arguments} </li>
<li><b>Inputfile:</b>
<a class="btn btn-xs btn-default" data-toggle="collapse" data-target="#demo"> <span class="glyphicon glyphicon-eye-open"></span>
</a>
<div id="demo" class="collapse">
<pre>
{pairs_file}
</pre>
</div>
<ul>
<li><b>number of pairs introduced:</b> {n_pairs}</li>
</ul>
</li>
</ul>
</div>
</div>
<ol class="breadcrumb">
<li class="breadcrumb-item active"><h5>RESULT</h5></li>
</ol>
'''
table_header = """
<table class="table table-striped sortable" >
<thead>
<tr>
<th>Intermediate name</th>
<th>Pairs superimposed</th>
<th>RMSD</th>
<th>min distance*</th>
<th>max distance*</th>
<th></th>
</tr>
</thead>
<tfoot>
<tr>
<th>Intermediate name</th>
<th>Pairs superimposed</th>
<th>RMSD</th>
<th>min distance</th>
<th>max distance</th>
<th></th>
</tr>
</tfoot>
<tbody>
"""
table_entry ="""
<tr>
<td> {complex_name} </td>
<td> {pair_1} , {pair_2}</td>
<td>{RMSD}</td>
<td>{min_dist}</td>
<td>{max_dist} </td>
<td><a href = {complex_name}.html target=_black> <span class="glyphicon glyphicon-eye-open"></span></a><td>
</tr>
"""
table_bot= """
</tbody>
</table>
<small>* Distance between previous intermediate complex (base) and the added structure (not the superimposed residues, those are not part of the new complex).</small>
"""
final_html='''
<div class="card mb-2">
<div class="card-header">Final Complex</div>
<div class="card-body">
<div class="row">
<div class="col-sm-2"></div>
<div class="col-sm-8">
<script>
document.addEventListener("DOMContentLoaded", function () {{
var stage = new NGL.Stage("viewport_final");
stage.loadFile("{structure_file}", {{defaultRepresentation: true}});
}});
</script>
<div id="viewport_final" style="width:650px; height:500px;"></div>
</div>
<div class="col-sm-2"></div>
</div>
</div>
</div>
<!-- Area Chart Example-->
<div class="card mb-3">
<div class="card-header">
<i class="fa fa-area-chart"></i>Protein Distance Plot</div>
<div class="card-body-plot">
<img src='{plot_file}' width="90%" height="100%"s>
</div>
</div>
<ol class="breadcrumb">
<li class="breadcrumb-item active"><h5>INTERMEDIATE COMPLEXES:</h5></li>
</ol>
'''
base_html ='''
<br>
<ol class="breadcrumb">
<li class="breadcrumb-item active"><h5>INTERMEDIATE COMPLEX:</h5></li>
</ol>
<div class="bases">
<div class="solid">
<div class="card mb-3">
<div class="card-header">Complex name: {complex_name}</div>
<div class="card-body">
<div class="row">
<div class="col-sm-6" style="padding-left:40px">
Superimposition completed successfully.
<ul>
<li>Pairs being superimposed: {pairs}.</li>
<li>Root mean square deviation (RMSD): {RMSD}</li>
</ul>
Between previous base and added residues:
<ul>
<li>Minimum distance (Amstrong): {min_dist} </li>
<li>Maximum distance (Amstrong): {max_dist} </li>
</ul>
</div>
<div class="col-sm-5">
<script>
document.addEventListener("DOMContentLoaded", function () {{
var stage = new NGL.Stage("viewport_{n}");
var schemeId = NGL.ColormakerRegistry.addScheme(function (params) {{
this.atomColor = function (atom) {{
if ({chain_names_base}.includes(atom.chainname)) {{
return 0xFFE5BC; // red
}}else {{
return 0xFF0202; //
}}
}};
}});
stage.loadFile("{structure_f}").then(function (o) {{
o.addRepresentation("cartoon", {{ color: schemeId }})
o.autoView();}})
}});
</script>
<div id="viewport_{n}" style="width:450px; height:400px;"></div>
</div>
</div>
</div>
</div>
<!-- Area Chart Example-->
<div class="card mb-3">
<div class="card-header">
<i class="fa fa-area-chart"></i> Protein Distance Plot</div>
<div class="card-body-plot">
<img src='{plot_f}' width="100%">
</div>
</div>
</div>'''
footer_html='''
<br>
<br>
<!-- /.container-fluid-->
<footer class="sticky-footer">
<div class="container">
<div class="text-center">
<small>Version 1.0 / Last update: March,2018 / Antía Fernández Pintos, Eva Martín del Pico, Selen Özkan<br></small>
</div>
<div class="text-center">
<small>Universitat Pompeu Fabra, Bioinformatics For Health Sciences, 2018<br></small>
</div>
</div>
</footer>
<script>
// When the user scrolls down 20px from the top of the document, show the button
window.onscroll = function() {scrollFunction()};
function scrollFunction() {
if (document.body.scrollTop > 20 || document.documentElement.scrollTop > 20) {
document.getElementById("myBtn").style.display = "block";
} else {
document.getElementById("myBtn").style.display = "none";
}
}
// When the user clicks on the button, scroll to the top of the document
function topFunction() {
document.body.scrollTop = 0;
document.documentElement.scrollTop = 0;
}
</script>
</div>
<!-- /.content-wrapper-->
</div>
<div class="col-sm-2"></div>
</div>
</body>
</html>'''