width="500"></a> </div>
</li>
-
+<!--
<li class="list-group-item task-item">
<div class="col-md-2"> Structure overlap </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
width="500"> </div>
</li>
-
-
+-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> Structure overlap NGL viewer</div>
+ <div class="col-md-10" id="viewport_min"
+ style="width:500px;height:500px;">
+ </div>
+ </li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ <button id="toggleAllatom">Input structure on/off</button>
+ <button id="toggleSidechains2">Side-chains on/off</button>
+ </div>
+ </li>
{% endif %}
<li class="list-group-item task-item">
</div>
</li>
+
+{% if task.md_mdpdb %}
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> Trajectory NGL viewer</div>
+ <div class="col-md-10" id="viewport_traj"
+ style="width:500px;height:500px;">
+ </div>
+ </li>
+ <li class="list-group-item task-item">
+ <div class="col-md-6">
+<input id="clipRange" type="range" value=0 min=0 max= {% widthratio task.md_nstep task.md_ntwx 1 %} step=1 ></input><span id="clipRange_val">0</span> frame
+</div>
+<div class="col-md-6">
+<button id="toggleRunMDs">run/pause MD</button>
+<button id="toggleSidechains1">side-chains on/off</button>
+</div>
+ </li>
+
+{% endif %}
<li class="list-group-item task-item">
<div class="col-md-2"> Radius of gyration based
src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
width="500"> </div>
</li>
-
+<!--
<li class="list-group-item task-item">
<div class="col-md-2"> fluctuations putty on
starting structure</div>
src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
width="500"></a> </div>
</li>
+-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> fluctuations putty on
+ starting structure NGL viewer</div>
+ <div class="col-md-10" id="viewport_putty"
+ style="width:500px;height:500px;">
+ </div>
+ </li>
+
{% endif %}
});
</script>
+{% if task.type == "remd" %}
<script>
var slideIndex = 1;
showDivs(slideIndex);
x[slideIndex-1].style.display = "block";
}
</script>
+{% endif %}
{% if not task.done %}
<script>
</script>
{% endif %}
-
+<script src="https://unpkg.com/ngl"></script>
+{% if task.type == "min" %}
+<script>
+window.addEventListener("resize",
+ function (event) {
+ stage.handleResize();
+ },false);
+
+var stage = new NGL.Stage("viewport_min");
+stage.setParameters( { backgroundColor: "white" } );
+Promise.all([
+ stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
+ o.addRepresentation( "backbone",{ color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ })
+ o.addRepresentation( "licorice",{ color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
+ })
+ return o
+ }),
+
+ stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
+ o.addRepresentation( "backbone",{ name: "allatom", color:
+ "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
+ })
+ o.addRepresentation( "line",{ name: "allatomsc", color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ ,sele:"not hydrogen and sidechainAttached"
+ })
+ return o
+ })
+]).then(function (ol) {
+ ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
+ ol[ 0 ].autoView()
+})
+
+var allatom=true;
+var side=true;
+var toggleAll = document.getElementById( "toggleAllatom" );
+toggleAll.addEventListener( "click", function(){
+ allatom=! allatom;
+ stage.getRepresentationsByName(
+ "allatom" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ if (side) {
+ stage.getRepresentationsByName(
+ "allatomsc" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ }
+} );
+var toggleSidechains = document.getElementById("toggleSidechains2" );
+toggleSidechains.addEventListener( "click", function(){
+ side=!side;
+ if (allatom) {
+ stage.getRepresentationsByName(
+ "allatomsc" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+
+ }
+ stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+
+} );
+</script>
+{% endif %}
+
+{% if task.type == "md" and task.md_start == "pdbstart" %}
+<script>
+window.addEventListener("resize",
+ function (event) {
+ stage.handleResize();
+ },false);
+
+var stage = new NGL.Stage("viewport_putty");
+stage.setParameters( { backgroundColor: "white" } );
+
+var tooltip = document.createElement("div")
+Object.assign(tooltip.style, {
+ display: "none",
+ position: "fixed",
+ zIndex: 10,
+ pointerEvents: "none",
+ backgroundColor: "rgba( 0, 0, 0, 0.6 )",
+ color: "lightgrey",
+ padding: "8px",
+ fontFamily: "sans-serif"
+})
+document.body.appendChild(tooltip)
+
+stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
+ (function ( o ){
+ o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
+ sele: "backbone",
+ radius:"bfactor",
+ colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
+ o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
+ o.autoView();
+})
+
+// remove default hoverPick mouse action
+stage.mouseControls.remove("hoverPick")
+
+stage.signals.hovered.add(function (pickingProxy) {
+ if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
+ var atom = pickingProxy.atom || pickingProxy.closestBondAtom
+ var mp = pickingProxy.mouse.position
+ var bf= atom.bfactor.toFixed(2)
+ tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
+ tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
+ tooltip.style.left = mp.x + 3 + "px"
+ tooltip.style.display = "block"
+ } else {
+ tooltip.style.display = "none"
+ }
+})
+</script>
+{% endif %}
+
+{% if task.type == "md" and task.md_mdpdb %}
+<script>
+window.addEventListener("resize",
+ function (event) {
+ stage.handleResize();
+ },false);
+
+ var stage = new NGL.Stage("viewport_traj");
+ stage.setParameters( { backgroundColor: "white" } );
+ stage.setParameters( { cameraType: "orthographic" } );
+ var traj;
+ var player;
+ stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
+ asTrajectory: true } ) .then( function( o ){
+ o.setName ("unres_md");
+ o.addRepresentation( "backbone",{ color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ });
+ o.addRepresentation( "licorice",{ color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ });
+ o.autoView();
+ o.addTrajectory();
+ });
+
+ var toggleSidechains = document.getElementById( "toggleSidechains1" );
+ toggleSidechains.addEventListener( "click", function(){
+ stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ } );
+
+
+ function numberWithCommas(x) {
+ return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
+ }
+ var toggleRunMDs = document.getElementById( "toggleRunMDs" );
+ var isRunning = false;
+ toggleRunMDs.addEventListener( "click", function(){
+ var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
+ var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
+ if( !isRunning ){
+ player.play();
+ isRunning = true;
+
+ trajComp.signals.frameChanged.add(function(){
+ var fnum=trajComp.trajectory.currentFrame;
+ clipRange.value = fnum;
+ clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
+ });
+
+ }else{
+ player.play();
+ player.pause();
+ isRunning = false;
+ }
+ } );
+ var clipRange = document.getElementById( "clipRange" );
+ var clipRange_val = document.getElementById( "clipRange_val" );
+ clipRange.oninput = function( e ){
+ var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
+ trajComp.setFrame(e.target.value)
+ clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));
+ };
+
+</script>
+{% endif %}
+
+
{% endblock %}