1 {% extends "base.html" %}
4 {% load i18n lazysignup_tags %}
7 {% if task.owner|is_lazy_user %}
9 <ul class="list-group">
11 <li class="list-group-item new-task-item task-item">
13 <div class="col-md-2 form-group">
14 <form action="/refresh_done1/{{task.id}}/" method="post">
16 <input type="submit" class="btn" value="Refresh" name="refreshbtn">
20 <div class="col-md-10 form-group">
21 <h5 style="text-align:right;float:right;">
22 {% if not task.done %}
23 {% if task.running > 0 %}
24 {% if task.running == 100 %}
30 waiting in the queue to start
38 <h3> Task <b>{{ task.name }}</b></h3>
39 Created {{ task.created_date }}
40 <ul class="list-group">
42 <li class="list-group-item task-item">
43 <div class="col-md-4"> done ?</div>
44 <div class="col-md-8">
46 <span class="fa fa-check-square-o"></span>
47 {% if task.type == "md" or task.type == "remd" or task.type == "dock" %}
48 <form action="restart/"
50 style="text-align;float:right;">
53 class="btn btn-default"
60 {% if task.running > 0 %}
61 <span class="fa fa-spinner
65 <span class="fa fa-square-o"></span>
72 <fieldset class="majorpoints">
73 <legend class="majorpointslegend"
74 style="background-color:#d3d3d3;cursor: pointer;">Show input parameters</legend>
75 <div class="hiders" style="display:none" >
77 <li class="list-group-item task-item">
78 <div class="col-md-6"> type </div>
79 <div class="col-md-6">{{ task.type }}</div>
82 <li class="list-group-item task-item">
83 <div class="col-md-6"> force field </div>
84 <div class="col-md-6">{{ task.unres_ff }}</div>
87 <li class="list-group-item task-item">
88 <div class="col-md-4"> sequence </div>
89 <div class="col-md-8 monospace">{{ task.md_seq}}</div>
92 <li class="list-group-item task-item">
93 <div class="col-md-4"> secondary structure
95 <div class="col-md-8 monospace">{{ task.md_2d}}</div>
99 <li class="list-group-item task-item">
100 <div class="col-md-6"> SSBOND </div>
101 <div class="col-md-6">{{ task.ssbond}}</div>
105 {% if task.type == "min" %}
108 <li class="list-group-item task-item">
109 <div class="col-md-6"> algorithm</div>
110 <div class="col-md-6">{{ task.min_choice }}</div>
112 <li class="list-group-item task-item">
113 <div class="col-md-6"> overlap</div>
114 <div class="col-md-6">{{ task.min_overlap }}</div>
116 <li class="list-group-item task-item">
117 <div class="col-md-6"> searchsc</div>
118 <div class="col-md-6">{{ task.min_searchsc }}</div>
120 <li class="list-group-item task-item">
121 <div class="col-md-6"> maxmin</div>
122 <div class="col-md-6">{{ task.min_maxmin }}</div>
124 <li class="list-group-item task-item">
125 <div class="col-md-6"> maxfun</div>
126 <div class="col-md-6">{{ task.min_maxfun }}</div>
128 <li class="list-group-item task-item">
129 <div class="col-md-6"> pdbout</div>
130 <div class="col-md-6">{{ task.min_pdbout }}</div>
132 <li class="list-group-item task-item">
133 <div class="col-md-6"> input pdb </div>
134 <div class="col-md-6">{{ task.myfile1 }}</div>
136 <li class="list-group-item task-item">
137 <div class="col-md-6"> pdb code</div>
138 <div class="col-md-6">{{ task.pdbcode }}</div>
140 <li class="list-group-item task-item">
141 <div class="col-md-6"> unres_pdb</div>
142 <div class="col-md-6">{{ task.min_unres_pdb }}</div>
146 {% if task.type == "md" %}
147 <li class="list-group-item task-item">
148 <div class="col-md-6"> starting </div>
149 <div class="col-md-6">{{ task.md_start}}</div>
152 <li class="list-group-item task-item">
153 <div class="col-md-6"> input pdb </div>
154 <div class="col-md-6">{{ task.myfile1 }}</div>
156 <li class="list-group-item task-item">
157 <div class="col-md-6"> pdb code</div>
158 <div class="col-md-6">{{ task.pdbcode }}</div>
160 <li class="list-group-item task-item">
161 <div class="col-md-6"> seed </div>
162 <div class="col-md-6">{{ task.md_seed}}</div>
164 <li class="list-group-item task-item">
165 <div class="col-md-6"> pdbref </div>
166 <div class="col-md-6">{{ task.md_pdbref}}</div>
168 <li class="list-group-item task-item">
169 <div class="col-md-6"> respa </div>
170 <div class="col-md-6">{{ task.md_respa}}</div>
172 <li class="list-group-item task-item">
173 <div class="col-md-6"> temperature </div>
174 <div class="col-md-6">{{ task.md_temp}}</div>
176 <li class="list-group-item task-item">
177 <div class="col-md-6"> nstep </div>
178 <div class="col-md-6">{{ task.md_nstep}}</div>
180 <li class="list-group-item task-item">
181 <div class="col-md-6"> total steps (with restarts) </div>
182 <div class="col-md-6">{{ task.md_total_steps}}</div>
184 <li class="list-group-item task-item">
185 <div class="col-md-6"> ntwe </div>
186 <div class="col-md-6">{{ task.md_ntwe}}</div>
188 <li class="list-group-item task-item">
189 <div class="col-md-6"> ntwx </div>
190 <div class="col-md-6">{{ task.md_ntwx}}</div>
192 <li class="list-group-item task-item">
193 <div class="col-md-6"> dt </div>
194 <div class="col-md-6">{{ task.md_dt}}</div>
196 <li class="list-group-item task-item">
197 <div class="col-md-6"> thermostat </div>
198 <div class="col-md-6">{{ task.md_lang}}</div>
201 {% if task.md_lang == "berendsen" %}
203 <li class="list-group-item task-item">
204 <div class="col-md-6"> tau </div>
205 <div class="col-md-6">{{ task.md_tau}}</div>
210 <li class="list-group-item task-item">
211 <div class="col-md-6"> scal_fric </div>
212 <div class="col-md-6">{{ task.md_scal_fric}}</div>
217 <li class="list-group-item task-item">
218 <div class="col-md-6"> mdpdb </div>
219 <div class="col-md-6">{{ task.md_mdpdb}}</div>
221 <li class="list-group-item task-item">
222 <div class="col-md-6"> RESPA </div>
223 <div class="col-md-6">{{ task.md_respa}}</div>
229 {% if task.type == "remd" or task.type == "dock" %}
231 <li class="list-group-item task-item">
232 <div class="col-md-6"> nrep </div>
233 <div class="col-md-6">{{ task.remd_nrep}}</div>
235 <li class="list-group-item task-item">
236 <div class="col-md-6"> starting </div>
237 <div class="col-md-6">{{ task.md_start}}</div>
240 <li class="list-group-item task-item">
241 <div class="col-md-6"> input pdb </div>
242 <div class="col-md-6">{{ task.myfile1 }}</div>
244 <li class="list-group-item task-item">
245 <div class="col-md-6"> pdb code</div>
246 <div class="col-md-6">{{ task.pdbcode }}</div>
248 {% if task.type == "dock" %}
249 <li class="list-group-item task-item">
250 <div class="col-md-6"> input pdb2 </div>
251 <div class="col-md-6">{{ task.myfile2 }}</div>
253 <li class="list-group-item task-item">
254 <div class="col-md-6"> pdb code2</div>
255 <div class="col-md-6">{{ task.pdbcode2 }}</div>
257 <li class="list-group-item task-item">
258 <div class="col-md-6"> dock_peptide</div>
259 <div class="col-md-6">{{ task.dock_peptide }}</div>
263 <li class="list-group-item task-item">
264 <div class="col-md-6"> seed </div>
265 <div class="col-md-6">{{ task.md_seed}}</div>
267 <li class="list-group-item task-item">
268 <div class="col-md-6"> pdbref </div>
269 <div class="col-md-6">{{ task.md_pdbref}}</div>
271 {% if task.md_start == "pdbstart" %}
272 <li class="list-group-item task-item">
273 <div class="col-md-6"> preminim maxfun </div>
274 <div class="col-md-6">{{ task.min_maxfun }}</div>
277 <li class="list-group-item task-item">
278 <div class="col-md-6"> respa </div>
279 <div class="col-md-6">{{ task.md_respa}}</div>
281 <li class="list-group-item task-item">
282 <div class="col-md-6"> nstep </div>
283 <div class="col-md-6">{{ task.md_nstep}}</div>
285 <li class="list-group-item task-item">
286 <div class="col-md-6"> total steps (with restarts) </div>
287 <div class="col-md-6">{{ task.md_total_steps}}</div>
289 <li class="list-group-item task-item">
290 <div class="col-md-6"> ntwe </div>
291 <div class="col-md-6">{{ task.md_ntwe}}</div>
293 <li class="list-group-item task-item">
294 <div class="col-md-6"> nstex </div>
295 <div class="col-md-6">{{ task.remd_nstex}}</div>
297 <li class="list-group-item task-item">
298 <div class="col-md-6"> ntwx </div>
299 <div class="col-md-6">{{ task.md_ntwx}}</div>
301 <li class="list-group-item task-item">
302 <div class="col-md-6"> dt </div>
303 <div class="col-md-6">{{ task.md_dt}}</div>
305 <li class="list-group-item task-item">
306 <div class="col-md-6"> thermostat </div>
307 <div class="col-md-6">{{ task.md_lang}}</div>
310 {% if task.md_lang == "berendsen" %}
312 <li class="list-group-item task-item">
313 <div class="col-md-6"> tau </div>
314 <div class="col-md-6">{{ task.md_tau}}</div>
319 <li class="list-group-item task-item">
320 <div class="col-md-6"> scal_fric </div>
321 <div class="col-md-6">{{ task.md_scal_fric}}</div>
326 <li class="list-group-item task-item">
327 <div class="col-md-6"> RESPA </div>
328 <div class="col-md-6">{{ task.md_respa}}</div>
331 <li class="list-group-item task-item">
332 <div class="col-md-6"> temperatures </div>
333 <div class="col-md-6">{{ task.remd_multi_t}}</div>
335 <li class="list-group-item task-item">
336 <div class="col-md-6"> multiplex </div>
337 <div class="col-md-6">{{ task.remd_multi_m}}</div>
339 <li class="list-group-item task-item">
340 <div class="col-md-6"> temperature for clustering</div>
341 <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
343 <li class="list-group-item task-item">
344 <div class="col-md-6"> number of clusters</div>
345 <div class="col-md-6">{{ task.remd_cluster_n}}</div>
348 {% if task.saxs_data != "" %}
349 <li class="list-group-item task-item">
350 <div class="col-md-6"> wsaxs </div>
351 <div class="col-md-6">{{ task.wsaxs }}</div>
353 <li class="list-group-item task-item">
354 <div class="col-md-6"> scal_rad (saxs) </div>
355 <div class="col-md-6">{{ task.scal_rad }}</div>
357 <li class="list-group-item task-item">
358 <div class="col-md-6"> saxs distribution </div>
359 <div class="col-md-6"><pre> {{ task.saxs_data }}</pre></div>
365 <li class="list-group-item task-item">
366 <div class="col-md-6"> Box X Y Z</div>
367 <div class="col-md-2">{{ task.boxx}}</div>
368 <div class="col-md-2">{{ task.boxy}}</div>
369 <div class="col-md-2">{{ task.boxz}}</div>
376 <li class="list-group-item task-item">
377 <div class="col-md-4"> Directory </div>
378 <div class="col-md-8">
379 <a href="/myfiles/list/{{task.jobdirname}}/">
380 {{ task.jobdirname }}
384 <a class="btn btn-default"
385 href="/{{task.id}}/all.zip">
394 {% if task.type == "min" %}
396 <li class="list-group-item task-item">
397 <div class="col-md-2"> Etot </div>
398 <div class="col-md-10">{{ task.etot }}</div>
401 <li class="list-group-item task-item">
402 <div class="col-md-2"> UNRES model </div>
403 <div class="col-md-10">
405 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
407 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
408 width="500"></a> </div>
411 <li class="list-group-item task-item">
412 <div class="col-md-2"> UNRES model NGL viewer</div>
413 <div class="col-md-10" id="viewport_unres"
414 style="width:500px;height:500px;">
420 <li class="list-group-item task-item">
421 <div class="col-md-2"> Structure overlap </div>
422 <div class="col-md-10"> <img
423 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
427 <li class="list-group-item task-item">
428 <div class="col-md-2"> Structure overlap NGL viewer</div>
429 <div class="col-md-10" id="viewport_min"
430 style="width:500px;height:500px;">
433 <li class="list-group-item task-item">
434 <div class="col-md-12">
435 <button id="toggleAllatom">Input structure on/off</button>
436 <button id="toggleSidechains2">Side-chains on/off</button>
441 <li class="list-group-item task-item">
442 <div class="col-md-2"> Results </div>
443 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
446 {% if task.type == "md" %}
448 <li class="list-group-item task-item">
449 <div class="col-md-2"> Temperature histogram </div>
450 <div class="col-md-10"> <img
451 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
455 <li class="list-group-item task-item">
456 <div class="col-md-2"> Potential energy </div>
457 <div class="col-md-10"> <img
458 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
462 <li class="list-group-item task-item">
463 <div class="col-md-2"> Movie </div>
464 <div class="col-md-10">
466 <video width="500" height="400"
467 preload="auto" controls="controls">
469 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
470 type="video/ogg; codecs=theora"> </source>
476 {% if task.md_mdpdb %}
477 <li class="list-group-item task-item">
478 <div class="col-md-2"> Trajectory NGL viewer</div>
479 <div class="col-md-10" id="viewport_traj"
480 style="width:500px;height:500px;">
483 <li class="list-group-item task-item">
484 <div class="col-md-6">
485 <input id="clipRange" type="range" value=1 min=1 max= {% widthratio task.md_total_steps task.md_ntwx 1 %} step=1 ></input><span id="clipRange_val">1</span> frame
487 <div class="col-md-6">
488 <button id="toggleRunMDs">run/pause MD</button>
489 <button id="toggleSidechains1">side-chains on/off</button>
495 <li class="list-group-item task-item">
496 <div class="col-md-2"> Radius of gyration based
497 on C<sup>α</sup> coordinates </div>
498 <div class="col-md-10"> <img
499 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
505 {% if task.md_pdbref %}
506 <li class="list-group-item task-item">
507 <div class="col-md-2"> C<sup>α</sup> RMSD </div>
508 <div class="col-md-10"> <img
509 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
513 <li class="list-group-item task-item">
514 <div class="col-md-2"> fraction of native
515 side-chain concacts </div>
516 <div class="col-md-10"> <img
517 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
523 {% if task.md_start == "pdbstart" %}
524 <li class="list-group-item task-item">
525 <div class="col-md-2"> fluctuations </div>
526 <div class="col-md-10"> <img
527 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
531 <li class="list-group-item task-item">
532 <div class="col-md-2"> fluctuations putty on
533 starting structure</div>
534 <div class="col-md-10">
536 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
538 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
539 width="500"></a> </div>
542 <li class="list-group-item task-item">
543 <div class="col-md-2"> fluctuations putty on
544 starting structure NGL viewer</div>
545 <div class="col-md-10" id="viewport_putty"
546 style="width:500px;height:500px;">
557 {% if task.type == "remd" or task.type == "dock" %}
559 <li class="list-group-item task-item">
560 <div class="col-md-2"> Energy histogram </div>
561 <div class="col-md-10"> <img
562 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
566 <li class="list-group-item task-item">
567 <div class="col-md-2"> Energy vs. temperature </div>
568 <div class="col-md-10"> <img
569 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
573 <li class="list-group-item task-item">
574 <div class="col-md-2"> Cv vs. temperature </div>
575 <div class="col-md-10"> <img
576 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
580 {% if task.md_pdbref %}
582 <li class="list-group-item task-item">
583 <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
584 <div class="col-md-10"> <img
585 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
589 <li class="list-group-item task-item">
590 <div class="col-md-2"> potential energy vs.
591 C<sup>α</sup> RMSD</div>
592 <div class="col-md-10"> <img
593 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
597 <li class="list-group-item task-item">
598 <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
599 colored by bath temperature</div>
600 <div class="col-md-10"> <img
601 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
608 <li class="list-group-item task-item">
609 <div class="col-md-2"> exchanges (walk in T) </div>
610 <div class="col-md-10"> <img
611 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
615 {% if task.saxs_data != "" %}
616 <li class="list-group-item task-item">
617 <div class="col-md-2"> P(r) of input SAXS data and
618 calculated for 5 models and the input pdb</div>
619 <div class="col-md-10"> <img
620 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
625 <li class="list-group-item task-item">
626 <div class="col-md-4">
627 <button onclick="plusDivs(-1)">❮</button>
629 <div class="col-md-6">
632 <div class="col-md-2">
633 <button onclick="plusDivs(1)">❯</button>
637 {% for iii in range %}
639 {% with istr=forloop.counter|stringformat:"s" %}
640 {% with MODELi="MODEL"|add:istr|add:".pdb" %}
641 {% with viewporti="viewport_M"|add:istr %}
642 {% with toggleRefi="toggleRefM"|add:istr %}
643 {% with toggleSidechainsi="toggleSidechainsM"|add:istr %}
646 <li class="list-group-item task-item">
647 <div class="col-md-2"> model {{ iii }}
648 {% if not task.damino %}
649 after conversion to allatom
651 {{ remd_models|index:iii|linebreaks }}
653 <div class="col-md-10" id={{viewporti}}
654 style="width:500px;height:500px;">
657 <li class="list-group-item task-item">
658 <div class="col-md-12">
659 {% if task.md_pdbref %}
660 <button id={{toggleRefi}}>Reference structure on/off</button>
662 <button id={{toggleSidechainsi}}>Side-chains on/off</button>
663 <a class="btn btn-default"
664 href="/myfiles/download-file/{{task.jobdirname}}/{{MODELi}}">Download</a>
682 Regular user cannot use this link.
686 <script src="/static/jquery.min.js"></script>
687 <script src="https://unpkg.com/ngl"></script>
690 $('.majorpointslegend').click(function(){
691 $(this.parentNode).find('.hiders').toggle();
692 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
693 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
695 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
700 {% if task.type == "remd" or task.type == "dock" %}
702 function display_model(num){
704 numstr=num.toString();
705 {% if task.md_pdbref %}
706 var stage = new NGL.Stage("viewport_M"+numstr);
707 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
709 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
710 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
712 o.addRepresentation( "line", {name:"refsc",visible: false,
713 sele:"not hydrogen and sidechainAttached"
718 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
720 o.addRepresentation( "licorice",{ name: "unres", color:
721 "residueindex",colorScale:["blue","cyan", "green",
722 "yellow","orange", "red"], sele:".CA"
724 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
725 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
728 o.addRepresentation( "cartoon",{ name: "unres", color:
729 "residueindex",colorScale:["blue","cyan", "green",
730 "yellow","orange", "red"]
732 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
733 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
734 , sele:"not hydrogen and sidechainAttached" })
738 ]).then(function (ol1) {
739 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
744 var toggleAll = document.getElementById( "toggleRefM"+numstr );
745 toggleAll.addEventListener( "click", function(){
747 stage.getRepresentationsByName(
748 "ref" ).list.forEach( function( repre ){
749 repre.setVisibility( !repre.visible );
752 stage.getRepresentationsByName(
753 "refsc" ).list.forEach( function( repre ){
754 repre.setVisibility( !repre.visible );
759 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
760 toggleSidechains.addEventListener( "click", function(){
763 stage.getRepresentationsByName(
764 "refsc" ).list.forEach( function( repre ){
765 repre.setVisibility( !repre.visible );
768 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
769 repre.setVisibility( !repre.visible );
774 var stage = new NGL.Stage("viewport_M"+numstr);
775 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
776 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
778 o.addRepresentation( "licorice",{ name: "unres", color:
779 "residueindex",colorScale:["blue","cyan", "green",
780 "yellow","orange", "red"],sele:".CA"
782 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
783 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
786 o.addRepresentation( "cartoon",{ name: "unres", color:
787 "residueindex",colorScale:["blue","cyan", "green",
788 "yellow","orange", "red"]
790 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
791 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
792 , sele:"not hydrogen and sidechainAttached" });
796 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
797 toggleSidechains.addEventListener( "click", function(){
798 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
799 repre.setVisibility( !repre.visible );
808 window.addEventListener("resize",
810 stage.handleResize();
818 var y = document.getElementsByClassName("model");
821 for (ii = 0; ii < y.length; ii++) {
825 showDivs(slideIndex);
827 function plusDivs(n) {
828 showDivs(slideIndex += n);
831 function showDivs(n) {
833 var x = document.getElementsByClassName("model");
834 if (n > x.length) {slideIndex = 1}
835 if (n < 1) {slideIndex = x.length}
836 for (i = 0; i < x.length; i++) {
837 x[i].style.display = "none";
839 x[slideIndex-1].style.display = "block";
841 if (lista[slideIndex-1] == 0) {
842 display_model(slideIndex)
846 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
851 {% if not task.done %}
855 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
856 url: "/refresh_done1/{{task.id}}/",
858 success: function(data) {
859 document.location.reload();
861 complete: function() {
862 // Schedule the next request when the current one's complete
863 setTimeout(worker, 30000);
867 $(document).ready(function() {
868 // run the first time; all subsequent calls will take care of themselves
869 setTimeout(worker, 30000);
875 {% if task.type == "min" %}
877 window.addEventListener("resize",
879 stage.handleResize();
882 var stage_unres = new NGL.Stage("viewport_unres");
883 stage_unres.setParameters( { backgroundColor: "white" } );
885 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
887 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
888 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
889 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
890 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
891 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
892 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
893 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
894 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
895 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
896 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
897 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
898 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
899 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
900 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
901 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
902 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
903 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
904 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
905 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
906 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
908 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
910 var shape = new NGL.Shape("shape")
912 o.addRepresentation("licorice");
913 o.structure.eachAtom(function(atom){
914 if (atom.atomname == "CA" && atom.chainname == chain) {
915 px=CAx+(atom.x-CAx)/2;
916 py=CAy+(atom.y-CAy)/2;
917 pz=CAz+(atom.z-CAz)/2;
918 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
920 if (atom.atomname == "CA") {
921 chain= atom.chainname
926 if (atom.atomname == "CB") {
930 norm=Math.sqrt(mx*mx+my*my+mz*mz);
932 var longaxis=resdb[res][4]
933 var shortaxis=resdb[res][3]
934 mx = mx /norm*longaxis;
935 my = my /norm*longaxis;
936 mz = mz /norm*longaxis;
938 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
939 [ resdb[res][0], resdb[res][1], resdb[res][2]],
940 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
943 var shapeComp = stage_unres.addComponentFromObject(shape)
944 shapeComp.addRepresentation("buffer")
950 var stage = new NGL.Stage("viewport_min");
951 stage.setParameters( { backgroundColor: "white" } );
953 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
954 o.addRepresentation( "backbone",{ color:
955 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
957 o.addRepresentation( "licorice",{ color:
958 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
963 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
964 o.addRepresentation( "backbone",{ name: "allatom", color:
965 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
967 o.addRepresentation( "line",{ name: "allatomsc", color:
968 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
969 ,sele:"not hydrogen and sidechainAttached"
973 ]).then(function (ol) {
974 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
980 var toggleAll = document.getElementById( "toggleAllatom" );
981 toggleAll.addEventListener( "click", function(){
983 stage.getRepresentationsByName(
984 "allatom" ).list.forEach( function( repre ){
985 repre.setVisibility( !repre.visible );
988 stage.getRepresentationsByName(
989 "allatomsc" ).list.forEach( function( repre ){
990 repre.setVisibility( !repre.visible );
994 var toggleSidechains = document.getElementById("toggleSidechains2" );
995 toggleSidechains.addEventListener( "click", function(){
998 stage.getRepresentationsByName(
999 "allatomsc" ).list.forEach( function( repre ){
1000 repre.setVisibility( !repre.visible );
1004 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1005 repre.setVisibility( !repre.visible );
1012 {% if task.type == "md" and task.md_start == "pdbstart" %}
1014 window.addEventListener("resize",
1016 stage.handleResize();
1019 var stage = new NGL.Stage("viewport_putty");
1020 stage.setParameters( { backgroundColor: "white" } );
1022 var tooltip = document.createElement("div")
1023 Object.assign(tooltip.style, {
1027 pointerEvents: "none",
1028 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1031 fontFamily: "sans-serif"
1033 document.body.appendChild(tooltip)
1035 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1037 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1040 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1041 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1045 // remove default hoverPick mouse action
1046 stage.mouseControls.remove("hoverPick")
1048 stage.signals.hovered.add(function (pickingProxy) {
1049 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1050 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1051 var mp = pickingProxy.mouse.position
1052 var bf= atom.bfactor.toFixed(2)
1053 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1054 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1055 tooltip.style.left = mp.x + 3 + "px"
1056 tooltip.style.display = "block"
1058 tooltip.style.display = "none"
1064 {% if task.type == "md" and task.md_mdpdb %}
1066 window.addEventListener("resize",
1068 stage.handleResize();
1071 var stage = new NGL.Stage("viewport_traj");
1072 stage.setParameters( { backgroundColor: "white" } );
1073 stage.setParameters( { cameraType: "orthographic" } );
1076 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1077 asTrajectory: true } ) .then( function( o ){
1078 o.setName ("unres_md");
1079 o.addRepresentation( "backbone",{ color:
1080 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1082 o.addRepresentation( "licorice",{ color:
1083 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1085 o.setPosition([0, 0, 100]);
1090 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1091 toggleSidechains.addEventListener( "click", function(){
1092 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1093 repre.setVisibility( !repre.visible );
1098 function numberWithCommas(x) {
1099 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1101 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1102 var isRunning = false;
1103 toggleRunMDs.addEventListener( "click", function(){
1104 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1105 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1110 trajComp.signals.frameChanged.add(function(){
1111 var fnum=trajComp.trajectory.currentFrame+1;
1112 clipRange.value = fnum;
1113 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1122 var clipRange = document.getElementById( "clipRange" );
1123 var clipRange_val = document.getElementById( "clipRange_val" );
1124 clipRange.oninput = function( e ){
1125 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1126 trajComp.setFrame(e.target.value-1)
1127 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));