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sat_mutagen.php
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sat_mutagen.php
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<!DOCTYPE html>
<html lang="en">
<head>
<?php
readfile("./html/header.html");
include 'src/php/utils.php';
?>
</head>
<body>
<?php
$currentPage = 'sat_mutagen';
include './html/navbar.php';
?>
<div class="jumbotron">
<div class="container text-center">
<h2><i>In silico</i> saturation mutagenesis</h2>
scan of all possible amino acid substitutions in a human protein sequence
</div>
</div>
<div class="container">
<form class="needs-validation" novalidate action="submit_job.php"
method="post" enctype="multipart/form-data">
<!-- row for query -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-group">
<label for="sm_query">
<h5>Uniprot sequence ID</h5>
</label>
<input type="text" class="form-control" name="sm_query" id="sm_query"
placeholder="P01112" value="">
<small id="jobIDHelp" class="form-text text-muted">type the
<a href="query_Uniprot.php" target='_blank'>Uniprot accession number</a>
of a human sequence <?php faq_link('whyhuman',
'only human sequences are accepted (click for more info...)')?>
or leave blank to run test case. <br>
optional: add a specific position for single-site scanning, e.g.
<code>P01112 100</code>
<?php faq_link('formats', 'click for more info on accepted formats...') ?>
</small>
<div class="invalid-feedback">
Invalid query
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- row with checkbox for opening collapsable row below -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-group">
<button type="button" class="btn btn-outline-info btn-sm"
data-toggle="collapse" data-target="#collapse1"
aria-expanded="false" aria-controls="collapse1">
advanced settings
</button>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- collapsable row with radio buttons for typing/uploading PDB -->
<div class="panel-collapse collapse" id="collapse1">
<!-- "Rhapsody+EVmutation" classifier checkbox -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-group">
<div class="custom-control custom-checkbox">
<input type="checkbox" class="custom-control-input"
name="EVmutation_checkbox" id="EVmutation_checkbox" autocomplete="off">
<label class="custom-control-label" for="EVmutation_checkbox">
include EVmutation feature
<?php faq_link('EVmutation',
'check to use “full+EVmutation” classifier for ' .
'predictions (click for more info...)') ?>
</label>
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- "use custom PDB structure" checkbox -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-group">
<div class="custom-control custom-checkbox">
<input type="checkbox" class="custom-control-input"
name="customPDB_checkbox" id="customPDB_checkbox" autocomplete="off"
onchange="document.getElementById('radios').disabled = !this.checked;">
<label class="custom-control-label" for="customPDB_checkbox">
use custom PDB structure
<?php faq_link('noPDB', 'check and provide a PDB ID or PDB file '.
'to run predictions on a specific protein structure or '.
'conformation (click for more info...)') ?>
</label>
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- radio buttons controled by "custom PDB" checkbox -->
<fieldset class="ml-4" id="radios" disabled>
<!-- "type PDB code" radio button -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-check pb-2">
<input class="form-check-input" type="radio" name="customPDB_radios"
id="customPDBID_radio" value="PDBID" checked>
<div class="input-group input-group-sm">
<input class="form-control" type="text" name="customPDBID" value=""
id="customPDBID" maxlength="4" placeholder="type a PDB code..."
onfocus="document.getElementById('customPDBID_radio').checked=true">
<!-- <small id="PDBIDHelp" class="form-text text-muted">PDB ID</small> -->
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- "upload PDB file" radio button -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-check">
<input class="form-check-input" type="radio" name="customPDB_radios"
id="customPDBfile_radio" value="PDBfile">
<div class="form-group">
<!-- "classic" upload button -->
<input type="file" accept=".pdb,.pdb.gz" name="customPDBFile"
id="customPDBFile" autocomplete="off"
onfocus="document.getElementById('customPDBfile_radio').checked=true">
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- environment yes/no -->
<div class="form-row pb-4">
<div class="col-md"></div>
<div class="col-md-6">
<div class="custom-control custom-checkbox">
<input type="checkbox" class="custom-control-input"
name="environment_checkbox" id="environment_checkbox" autocomplete="off">
<label class="custom-control-label" for="environment_checkbox">
<small>include "environmental effects"</small>
<?php faq_link('environment', 'check to include the effect of the '.
'presence of other chains in the PDB structure (click for '.
'more info...)') ?>
</label>
</div>
</div>
<div class="col-md"></div>
</div>
</fieldset>
</div> <!-- end of collapsable -->
<!-- email row -->
<div class="form-row">
<div class="col-md"></div>
<div class="col-md-6">
<div class="form-group">
<label for="email">
<h5>email</h5>
</label>
<input type="email" class="form-control" name="email" id="email"
aria-describedby="emailHelp" value="" placeholder="(optional)">
<small id="emailHelp" class="form-text text-muted">
you'll be notified when results are ready
</small>
<div class="invalid-feedback">
Invalid email address
</div>
</div>
</div>
<div class="col-md"></div>
</div>
<!-- submit button row -->
<div class="form-row py-2">
<div class="col-md text-center">
<div class="form-group">
<button class="btn btn-primary" type="submit">submit job</button>
</div>
</div>
</div>
</form>
</div>
<?php readfile("./html/footer.html"); ?>
<?php readfile("./html/js_src.html"); ?>
<script>
// show collapsable if requested
if (<?php if (isset($_GET['showCollapsable'])) echo 'true';?>) {
setTimeout(function() {
$('#collapse1').collapse('show');
setTimeout(function() {
$('#customPDB_checkbox').prop('checked', true);
$('#radios').prop('disabled', false);
}, 300);
}, 300);
}
// Example starter JavaScript for disabling form submissions if there are invalid fields
(function() {
'use strict';
window.addEventListener('load', function() {
// Fetch all the forms we want to apply custom Bootstrap validation styles to
var forms = document.getElementsByClassName('needs-validation');
// Loop over them and prevent submission
var validation = Array.prototype.filter.call(forms, function(form) {
form.addEventListener('submit', function(event) {
if (form.checkValidity() === false) {
event.preventDefault();
event.stopPropagation();
}
form.classList.add('was-validated');
}, false);
});
}, false);
})();
</script>
</body>
</html>