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<html>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>A minimal Protein Feature View Page</title>
<!-- jquery library -->
<script src="js/vendor/jquery-2.1.3.min.js"></script>
<!-- bootstrap -->
<link href="js/vendor/bootstrap-3.3.5/dist/css/bootstrap.min.css" rel="stylesheet">
<link href="css/bootstrap-slider.css" rel="stylesheet">
<!-- jquery SVG includes -->
<script src="js/vendor/svg/jquery.svg.min.js"></script>
<link rel="stylesheet" type="text/css" href="js/vendor/svg/jquery.svg.css" />
<!-- font awesome icons -->
<link rel="stylesheet" href="css/font-awesome.min.css">
<!-- NGL -->
<script src="js/vendor/ngl.embedded.min.js"></script>
<!-- and finally our own code ... !-->
<link href="css/pfv.css" rel="stylesheet">
<script src="build/proteinfeatureview-1.0.1.min.js"></script>
</head>
<body>
<div class="container-fluid">
<div class="jumbotron">
<h1>Insulin receptor - P06213 (INSR_HUMAN)</h1>
<h3>Protein Feature View - View PDB entries that are mapped to UniProtKB</h3>
</div>
<div id="nglContainer" class="center-block" style="width:300px;height:300px;"></div>
<div class="btn-toolbar " role="toolbar" style="padding-bottom: 3px;">
<div class="col-md-3 input-group pull-left">
<input type="text" class="input-medium form-control" placeholder="UniProt ID" name="up-field" id="up-field">
<div class="input-group-btn">
<button class="btn btn-group" style="height:34px;" type="submit"><i class="fa fa-search"></i></button>
</div>
</div>
<div class="btn-group">
<button class="btn btn-default" href="#" role="button" id="fullScreen"><i class="fa fa-arrows-alt"></i> Full screen</button>
<button class="btn btn-default" style="height:34px" id="zoomOut" role="button"><i class="fa fa-search-minus"></i></button>
<span class="btn btn-default" style="height:34px">
<input id="svgScrollBar" data-slider-id='svgScrollBarSlider' type="text" data-slider-min="0" data-slider-max="100" data-slider-step="1" data-slider-value="0"/>
<!-- <div id="svgScrollBar" style="width:100px; float:left; top:4px; "></div> -->
</span>
<button class="btn btn-default" id="zoomIn" style="height:34px"><i class="fa fa-search-plus"></i></button>
<button class="btn btn-default" id="export"><i class="fa fa-download"></i> Export</button>
</div>
<div class="btn-group">
<div class="dropdown ">
<button class="btn btn-default dropdown-toggle" type="button" id="actionMenu" data-toggle="dropdown">
Action <span class="caret"></span>
</button>
<ul class="dropdown-menu " role="menu" aria-labelledby="actionMenu">
<li role="presentation">
<a href="#" onclick="$('#mySequenceMotifDialog').modal('show'); return false;" role="menuitem" tabindex="-1">
Find Sequence Motif</a>
</li>
</ul>
</div>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-body">
<div class="row-fluid">
<div class="span12">
<div id="pfv-parent"></div>
<div id="dialog" title="Leave Page"> </div>
</div>
</div>
</div>
</div>
<div class="modal fade" tabindex="-1" role="dialog" id="mySequenceMotifDialog" aria-labelledby="mySequenceMotifDialog" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span> </button>
<h4 class="modal-title">Find Sequence Motif
<a href="/pdb/staticHelp.do?p=help/advancedsearch/sequenceMotif.html"><span class="iconSet-main icon-help" title="Help | Motif Search"> </span></a></h4>
</div>
<div class="modal-body">
<form id="findSequenceMotif" class="form-horizontal">
<!-- <label class="input-label" for="enterMotif">Motif:</label> -->
<div class="input-group">
<input class="form-control" id="enterMotif" type="text" placeholder="Enter sequence motif (example: GX[DN]FXKXDE )" />
<span class="input-group-btn">
<button class="btn btn-default" type="button" id="findMotifDialogSubmit" >Find</button>
</span>
</div>
</form>
</div>
</div>
</div>
</div>
</div>
<script>
'use strict';
requirejs.config({
baseUrl: 'js',
paths: {
colors: 'pfv/colors',
viewer: 'pfv/viewer',
draw: 'pfv/draw',
params: 'pfv/params',
icons: 'pfv/icons',
popups: 'pfv/popups',
jquery: 'vendor/jquery-2.1.3.min',
jquerysvg: 'vendor/svg/jquery.svg.min',
'bootstrap/tooltip': 'vendor/bootstrap-3.3.5/js/tooltip',
'bootstrap/modal': 'vendor/bootstrap-3.3.5/js/modal',
'bootstrap/button': 'vendor/bootstrap-3.3.5/js/button',
'bootstrap/dropdown': 'vendor/bootstrap-3.3.5/js/dropdown',
bootstrapslider: 'vendor/bootstrap-slider.min'
},
shim: {
'jquerysvg': {
exports: "$",
deps: ['jquery']
},
'bootstrap/affix': {
deps: ['jquery'],
exports: '$.fn.affix'
},
'bootstrap/alert': {
deps: ['jquery'],
exports: '$.fn.alert'
},
'bootstrap/button': {
deps: ['jquery'],
exports: '$.fn.button'
},
'bootstrap/carousel': {
deps: ['jquery'],
exports: '$.fn.carousel'
},
'bootstrap/collapse': {
deps: ['jquery'],
exports: '$.fn.collapse'
},
'bootstrap/dropdown': {
deps: ['jquery'],
exports: '$.fn.dropdown'
},
'bootstrap/modal': {
deps: ['jquery'],
exports: '$.fn.modal'
},
'bootstrap/popover': {
deps: ['jquery'],
exports: '$.fn.popover'
},
'bootstrap/scrollspy': {
deps: ['jquery'],
exports: '$.fn.scrollspy'
},
'bootstrap/tab': {
deps: ['jquery'],
exports: '$.fn.tab'
},
'bootstrap/tooltip': {
deps: ['jquery'],
exports: '$.fn.tooltip'
},
'bootstrap/transition': {
deps: ['jquery'],
exports: '$.fn.transition'
},
'bootstrapslider': {
deps: ['bootstrap/tooltip']
}
}
});
<!-- NGL code part I -->
NGL.useWorker = false;
var stage = new NGL.Stage("nglContainer", {
'theme': 'light',
'overwritePreferences': 'true'
});
var viewer;
require(['viewer', 'jquerysvg', 'bootstrap/tooltip', 'bootstrap/modal', 'bootstrap/dropdown', 'bootstrapslider'], function(PFV) {
viewer = PFV;
var featureView = new Object();
$(document).ready(function() {
var uniprotID = "P06213";
$(function() {
// if has not been initialized, initialize...
try {
featureView = new viewer.PFV();
console.log("init of Protein Feature View " + featureView.getVersion());
featureView.setParentDiv('#pfv-parent');
featureView.setDialogDiv('#dialog');
featureView.setScrollBarDiv('#svgScrollBar');
featureView.setRcsbServer("http://www.rcsb.org");
featureView.setShowSeqres(true);
featureView.loadUniprot(uniprotID);
$('#up-field').val(uniprotID);
$('#up-field').change(function() {
var val = $('#up-field').val();
console.log("loading new uniprot " + val);
featureView.loadUniprot(val);
});
$("#zoomOut").click(function() {
var val = featureView.getScrollBarValue();
val -= 25;
featureView.setScrollValue(val);
});
$("#zoomIn").click(function() {
var val = featureView.getScrollBarValue();
val += 25;
featureView.setScrollValue(val);
});
$('#fullScreen').click(function() {
featureView.requestFullscreen();
return false;
});
$('#export').click(
function() {
var svg = featureView.getSVGWrapper();
var xml = svg.toSVG();
open("data:image/svg+xml," + encodeURIComponent(xml));
});
} catch (err) {
console.error(err);
}
});
});
$('#findMotifDialogSubmit').click(function() {
console.log('dialog submit clicked');
// $('mySequenceMotifDialog').modal({'show':false});
$("#findSequenceMotif").submit()
});
var previousMotif = "";
var myRegExp = new RegExp("$");
$("#findSequenceMotif").submit(function(event) {
var motif = $('#enterMotif').val();
// to upper case
motif = motif.toUpperCase();
//replaceAll("X", "[A-Z]"
motif = motif.replace(/X/g, '[A-Z]');
console.log('looking for motif ' + motif);
var seq = featureView.getSequence();
if (previousMotif != motif) {
previousMotif = motif;
myRegExp = new RegExp(motif, "g");
}
var match = myRegExp.exec(seq);
var pos = -1;
//if ( match[0].length > 0)
try {
if (match != null)
pos = match.index;
console.log("found at at position " + pos);
if (pos < 0) {
alert('Motif not found!');
event.preventDefault();
} else {
//console.log(pos + " " + match[0] + " lastIndex:" + myRegExp.lastIndex);
var seqLength = match[0].length;
featureView.highlight(pos, pos + seqLength - 1);
if (myRegExp.lastIndex == 0)
$('#mySequenceMotifDialog').modal('hide');
}
} catch (e) {
console.log(e);
}
event.preventDefault();
});
<!-- NGL code part II-->
featureView.addListener('viewerReady', function() {
console.log("viewer ready")
var data = featureView.getData();
console.log(data.uniprotID + " " + data.desc);
$("#dispUniprotID").html(data.uniprotID);
$("#dispUniprotName").html(data.desc + "");
var tracks = data.tracks;
if (typeof tracks !== 'undefined' && data.tracks.length > 0) {
var firstTrack = data.tracks[0];
showPdb3d(firstTrack.pdbID, firstTrack.chainID);
featureView.set3dViewFlag(firstTrack.pdbID, firstTrack.chainID);
}
});
featureView.addListener('dataReloaded', function(event) {
console.log("Data got reloaded .. " + event.data.uniprotID);
var tracks = event.data.tracks;
if (typeof tracks !== 'undefined' && tracks.length > 0) {
var firstTrack = tracks[0];
showPdb3d(firstTrack.pdbID, firstTrack.chainID);
featureView.set3dViewFlag(firstTrack.pdbID, firstTrack.chainID);
}
});
featureView.addListener("showPositionIn3d", function(event, data, moredate) {
//console.log("event:" + event);
console.log("data:" + JSON.stringify(event));
var pdbId = event.pdbId;
var chainId = event.chainId;
showPdb3d(pdbId, chainId, event.pdbStart, event.pdbEnd);
featureView.set3dViewFlag(pdbId, chainId);
});
}); <!-- end of require -->
var currentPdbId = "";
function highlight3d(comp, chainId, pdbStart, pdbEnd) {
comp.addRepresentation("licorice", {
sele: 'not polymer and not water',
color: "green"
});
if (chainId !== undefined && pdbStart !== undefined && pdbEnd !== undefined) {
var color = 'red';
var style = 'licorice';
if (pdbEnd - pdbStart < 10) {
color = 'yellow';
style = 'spacefill';
}
if (pdbEnd - pdbStart < 10) {
comp.addRepresentation(style, {
sele: pdbStart + "-" + pdbEnd + ":" + chainId,
color: "element"
});
}
comp.addRepresentation("cartoon", {
sele: pdbStart + "-" + pdbEnd + ":" + chainId,
color: color
});
comp.addRepresentation("cartoon", {
sele: "not " + pdbStart + "-" + pdbEnd + ":" + chainId,
color: "grey"
});
} else if (chainId !== undefined && pdbStart !== undefined) {
comp.addRepresentation("spacefill", {
sele: pdbStart + ":" + chainId,
color: "element"
});
comp.addRepresentation("cartoon", {
color: "grey"
});
} else if (chainId !== undefined) {
comp.addRepresentation("cartoon", {
sele: ":" + chainId,
color: "sstruc"
});
comp.addRepresentation("cartoon", {
sele: "not :" + chainId,
color: "grey"
});
} else {
comp.addRepresentation("cartoon", {
colorScheme: "sstruc"
});
}
}
function showPdb3d(pdbId, chainId, pdbStart, pdbEnd) {
if (currentPdbId === pdbId) {
stage.eachComponents(function(comp) {
highlight3d(comp, chainId, pdbStart, pdbEnd);
});
return;
}
try {
stage.removeAllComponents();
} catch (e) {
console.error(e);
}
//console.log("Showing in NGL " + pdbId + " " + chainId + " " + pdbStart + " " + pdbEnd);
stage.loadFile("rcsb://" + pdbId + ".mmtf").then(function(comp) {
highlight3d(comp, chainId, pdbStart, pdbEnd);
stage.centerView();
});
}
// stage.loadFile("rcsb://1crn.mmtf").then(function(comp){
// comp.addRepresentation("cartoon");
// licorice = comp.addRepresentation("licorice", {sele: "30:A"});
//
// stage.centerView();
//
//
// })
function changeHighlight(sele) {
licorice.setParameters({
sele: sele
});
}
stage.signals.onPicking.add(function(info) {
console.log(info);
// info.atom.resno; // .chainname
// info.bond.atom1.resno;
});
</script>
</body>
</html>