<div class="col-md-6"> pdbref </div>
<div class="col-md-6">{{ task.md_pdbref}}</div>
</li>
+ {% if task.md_start == "pdbstart" %}
+ <li class="list-group-item task-item">
+ <div class="col-md-6"> preminim maxfun </div>
+ <div class="col-md-6">{{ task.min_maxfun }}</div>
+ </li>
+ {% endif %}
<li class="list-group-item task-item">
<div class="col-md-6"> respa </div>
<div class="col-md-6">{{ task.md_respa}}</div>
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 %}
{% if task.saxs_data != "" %}
<li class="list-group-item task-item">
<div class="col-md-2"> P(r) of input SAXS data and
- calculated for 5 models </div>
+ calculated for 5 models and the input pdb</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
width="500"> </div>
</li>
<div class="model">
- <li class="list-group-item task-item">
+<!-- <li class="list-group-item task-item">
<div class="col-md-2"> model1 after conversion
to allatom
{{ task.remd_model1|linebreaks }}
<img
src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
</a></div>
+ </li> -->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> model1 after conversion
+ to allatom {{ task.remd_model1|linebreaks }}
+ NGL viewer</div>
+ <div class="col-md-10" id="viewport_M1"
+ style="width:500px;height:500px;">
+ </div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ {% if task.md_pdbref %}
+ <button id="toggleRefM1">Reference structure on/off</button>
+ {% endif %}
+ <button id="toggleSidechainsM1">Side-chains on/off</button>
+ <a class="btn btn-default"
+ href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
+ </div>
+ </li>
+
</div>
<div class="model">
- <li class="list-group-item task-item">
+<!-- <li class="list-group-item task-item">
<div class="col-md-2"> model2 after conversion
to allatom
{{ task.remd_model2|linebreaks }}
<img
src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
</a></div>
+ </li> -->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> model2 after conversion
+ to allatom {{ task.remd_model2|linebreaks }}
+ NGL viewer</div>
+ <div class="col-md-10" id="viewport_M2"
+ style="width:500px;height:500px;">
+ </div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ {% if task.md_pdbref %}
+ <button id="toggleRefM2">Reference structure on/off</button>
+ {% endif %}
+ <button id="toggleSidechainsM2">Side-chains on/off</button>
+ <a class="btn btn-default"
+ href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
+ </div>
+ </li>
+
+
</div>
<div class="model">
- <li class="list-group-item task-item">
+<!-- <li class="list-group-item task-item">
<div class="col-md-2"> model3 after conversion
to allatom
{{ task.remd_model3|linebreaks }}
<img
src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
</a></div>
+ </li>-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> model3 after conversion
+ to allatom {{ task.remd_model3|linebreaks }}
+ NGL viewer</div>
+ <div class="col-md-10" id="viewport_M3"
+ style="width:500px;height:500px;">
+ </div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ {% if task.md_pdbref %}
+ <button id="toggleRefM3">Reference structure on/off</button>
+ {% endif %}
+ <button id="toggleSidechainsM3">Side-chains on/off</button>
+ <a class="btn btn-default"
+ href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
+ </div>
+ </li>
+
</div>
<div class="model">
- <li class="list-group-item task-item">
+<!-- <li class="list-group-item task-item">
<div class="col-md-2"> model4 after conversion
to allatom
{{ task.remd_model4|linebreaks }}
<img
src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
</a></div>
+ </li>-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> model4 after conversion
+ to allatom {{ task.remd_model4|linebreaks }}
+ NGL viewer</div>
+ <div class="col-md-10" id="viewport_M4"
+ style="width:500px;height:500px;">
+ </div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ {% if task.md_pdbref %}
+ <button id="toggleRefM4">Reference structure on/off</button>
+ {% endif %}
+ <button id="toggleSidechainsM4">Side-chains on/off</button>
+ <a class="btn btn-default"
+ href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
+ </div>
+ </li>
+
</div>
<div class="model">
- <li class="list-group-item task-item">
+<!-- <li class="list-group-item task-item">
<div class="col-md-2"> model5 after conversion
to allatom
{{ task.remd_model5|linebreaks }}
<img
src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
</a></div>
+ </li>-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> model5 after conversion
+ to allatom {{ task.remd_model5|linebreaks }}
+ NGL viewer</div>
+ <div class="col-md-10" id="viewport_M5"
+ style="width:500px;height:500px;">
+ </div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-md-12">
+ {% if task.md_pdbref %}
+ <button id="toggleRefM5">Reference structure on/off</button>
+ {% endif %}
+ <button id="toggleSidechainsM5">Side-chains on/off</button>
+ <a class="btn btn-default"
+ href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
+ </div>
+ </li>
+
</div>
{% endif %}
</ul>
<script src="/static/jquery.min.js"></script>
+<script src="https://unpkg.com/ngl"></script>
<script>
$('.majorpointslegend').click(function(){
});
</script>
+{% if task.type == "remd" %}
<script>
+function display_model(numstr){
+
+{% if task.md_pdbref %}
+ var stage = new NGL.Stage("viewport_M"+numstr);
+ stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
+ Promise.all([
+ stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
+ o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
+ })
+ o.addRepresentation( "line", {name:"refsc",visible: false,
+ sele:"not hydrogen and sidechainAttached"
+ })
+ return o
+ }),
+ stage.loadFile(
+ "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
+ {% if task.damino %}
+ o.addRepresentation( "licorice",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"], sele:".CA"
+ })
+ o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"*" })
+ {% else %}
+ o.addRepresentation( "cartoon",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"]
+ })
+ o.addRepresentation( "line",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"not hydrogen and sidechainAttached" })
+ {% endif %}
+ return o
+ })
+ ]).then(function (ol1) {
+ ol1[ 0 ].superpose(ol1[ 1 ], false, ".CA")
+ ol1[ 0 ].autoView()
+ })
+ var ref=true;
+ var side=false;
+ var toggleAll = document.getElementById( "toggleRefM"+numstr );
+ toggleAll.addEventListener( "click", function(){
+ ref=! ref;
+ stage.getRepresentationsByName(
+ "ref" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ if (side) {
+ stage.getRepresentationsByName(
+ "refsc" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ }
+
+ } );
+ var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
+ toggleSidechains.addEventListener( "click", function(){
+ side=!side;
+ if (ref) {
+ stage.getRepresentationsByName(
+ "refsc" ).list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+ }
+ stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+
+ } );
+{% else %}
+ var stage = new NGL.Stage("viewport_M"+numstr);
+ stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
+ stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
+ {% if task.damino %}
+ o.addRepresentation( "licorice",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"],sele:".CA"
+ });
+ o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"*" });
+ {% else %}
+ o.addRepresentation( "cartoon",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"]
+ });
+ o.addRepresentation( "line",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"not hydrogen and sidechainAttached" });
+ {% endif %}
+ o.autoView();
+ })
+ var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
+ toggleSidechains.addEventListener( "click", function(){
+ stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
+ repre.setVisibility( !repre.visible );
+ } );
+
+ } );
+
+{% endif %}
+}
+
+
+window.addEventListener("resize",
+function (event) {
+ stage.handleResize();
+},false);
+
+
+display_model("1")
+
+
var slideIndex = 1;
+var y = document.getElementsByClassName("model");
+var lista=[];
+var ii;
+for (ii = 0; ii < y.length; ii++) {
+ lista.push(0)
+}
+lista[0]=1;
showDivs(slideIndex);
function plusDivs(n) {
x[i].style.display = "none";
}
x[slideIndex-1].style.display = "block";
+
+ if (lista[slideIndex-1] == 0 && slideIndex == 2) {
+ display_model("2")
+ }
+
+ if (lista[slideIndex-1] == 0 && slideIndex == 3) {
+ display_model("3")
+ }
+
+ if (lista[slideIndex-1] == 0 && slideIndex == 4) {
+ display_model("4")
+ }
+
+ if (lista[slideIndex-1] == 0 && slideIndex == 5) {
+ display_model("5")
+ }
+
+
+ if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
}
</script>
+{% endif %}
{% if not task.done %}
<script>
</script>
{% endif %}
-
+
+{% 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 %}
projects / django_unres.git / blobdiff