<div class="col-md-8">
{% if task.done %}
<span class="fa fa-check-square-o"></span>
+ {% if task.type == "md" or task.type == "remd" %}
+ <form action="restart/"
+ method="get"
+ style="text-align;float:right;">
+ {% csrf_token %}
+ <input type="submit"
+ class="btn btn-default"
+ value="Restart"
+ name="restartbtn">
+ </button>
+ </form>
+ {% endif %}
{% else %}
{% if task.running > 0 %}
<span class="fa fa-spinner
<div class="col-md-6">{{ task.md_nstep}}</div>
</li>
<li class="list-group-item task-item">
+ <div class="col-md-6"> total steps (with restarts) </div>
+ <div class="col-md-6">{{ task.md_total_steps}}</div>
+ </li>
+ <li class="list-group-item task-item">
<div class="col-md-6"> ntwe </div>
<div class="col-md-6">{{ task.md_ntwe}}</div>
</li>
{% endif %}
- {% if task.type == "remd" %}
+ {% if task.type == "remd" or task.type == "dock" %}
<li class="list-group-item task-item">
<div class="col-md-6"> nrep </div>
<div class="col-md-6"> pdb code</div>
<div class="col-md-6">{{ task.pdbcode }}</div>
</li>
+ {% if task.type == "dock" %}
+ <li class="list-group-item task-item">
+ <div class="col-md-6"> input pdb2 </div>
+ <div class="col-md-6">{{ task.myfile2 }}</div>
+ </li>
+ <li class="list-group-item task-item">
+ <div class="col-md-6"> pdb code2</div>
+ <div class="col-md-6">{{ task.pdbcode2 }}</div>
+ </li>
+
+ {% endif %}
<li class="list-group-item task-item">
<div class="col-md-6"> seed </div>
<div class="col-md-6">{{ task.md_seed}}</div>
<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>
<div class="col-md-6">{{ task.md_nstep}}</div>
</li>
<li class="list-group-item task-item">
+ <div class="col-md-6"> total steps (with restarts) </div>
+ <div class="col-md-6">{{ task.md_total_steps}}</div>
+ </li>
+ <li class="list-group-item task-item">
<div class="col-md-6"> ntwe </div>
<div class="col-md-6">{{ task.md_ntwe}}</div>
</li>
<div class="col-md-2"> Etot </div>
<div class="col-md-10">{{ task.etot }}</div>
</li>
-
+<!--
<li class="list-group-item task-item">
<div class="col-md-2"> UNRES model </div>
<div class="col-md-10">
src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
width="500"></a> </div>
</li>
+-->
+ <li class="list-group-item task-item">
+ <div class="col-md-2"> UNRES model NGL viewer</div>
+ <div class="col-md-10" id="viewport_unres"
+ style="width:500px;height:500px;">
+ </div>
+ </li>
+
<!--
<li class="list-group-item task-item">
<div class="col-md-2"> Movie </div>
<div class="col-md-10">
- <video width="500" height="400" preload controls>
+ <video width="500" height="400"
+ preload="auto" controls="controls">
<source
src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
type="video/ogg; codecs=theora"> </source>
</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
+<input id="clipRange" type="range" value=0 min=0 max= {% widthratio task.md_total_steps 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>
{% endif %}
- {% if task.type == "remd" %}
+ {% if task.type == "remd" or task.type == "dock" %}
<li class="list-group-item task-item">
<div class="col-md-2"> Energy histogram </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
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ 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
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ 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
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ 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
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ 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
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ 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" %}
+{% if task.type == "remd" or task.type == "dock" %}
<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[ 1 ].superpose(ol1[ 0 ], 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 %}
setTimeout(worker, 30000);
});
</script>
-{% endif %}
-
-<script src="https://unpkg.com/ngl"></script>
+{% endif %}
+
{% if task.type == "min" %}
<script>
window.addEventListener("resize",
stage.handleResize();
},false);
+var stage_unres = new NGL.Stage("viewport_unres");
+stage_unres.setParameters( { backgroundColor: "white" } );
+/**
+[color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
+*/
+var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
+ 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
+ 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
+ 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
+ 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
+ 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
+ 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
+ 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
+ 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
+ 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
+ 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
+ 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
+ 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
+ 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
+ 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
+ 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
+ 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
+ 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
+ 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
+ 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
+ };
+stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
+ (function ( o ){
+ var shape = new NGL.Shape("shape")
+ var chain = ""
+ o.addRepresentation("licorice");
+ o.structure.eachAtom(function(atom){
+ if (atom.atomname == "CA" && atom.chainname == chain) {
+ px=CAx+(atom.x-CAx)/2;
+ py=CAy+(atom.y-CAy)/2;
+ pz=CAz+(atom.z-CAz)/2;
+ shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
+ }
+ if (atom.atomname == "CA") {
+ chain= atom.chainname
+ CAx= atom.x;
+ CAy= atom.y
+ CAz= atom.z
+ }
+ if (atom.atomname == "CB") {
+ mx = (atom.x-CAx);
+ my = (atom.y-CAy);
+ mz = (atom.z-CAz);
+ norm=Math.sqrt(mx*mx+my*my+mz*mz);
+ res=atom.resname;
+ var longaxis=resdb[res][4]
+ var shortaxis=resdb[res][3]
+ mx = mx /norm*longaxis;
+ my = my /norm*longaxis;
+ mz = mz /norm*longaxis;
+ resn=res+atom.resno
+ shape.addEllipsoid([ atom.x, atom.y, atom.z ],
+ [ resdb[res][0], resdb[res][1], resdb[res][2]],
+ shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
+ }
+ });
+ var shapeComp = stage_unres.addComponentFromObject(shape)
+ shapeComp.addRepresentation("buffer")
+ o.autoView();
+});
+
+
+
var stage = new NGL.Stage("viewport_min");
stage.setParameters( { backgroundColor: "white" } );
Promise.all([
projects / django_unres.git / blobdiff