1 {% extends "base.html" %}
4 {% load i18n lazysignup_tags %}
7 {% if user|is_lazy_user %}
8 <ul class="list-group">
10 <li class="list-group-item new-task-item task-item">
12 <div class="col-md-2 form-group">
13 <form action="/refresh_done/" method="post">
15 <input type="submit" class="btn" value="Refresh" name="refreshbtn">
19 <div class="col-md-10 form-group">
20 <h5 style="text-align:right;float:right;">
21 {% if not task.done %}
22 {% if task.running > 0 %}
23 {% if task.running == 100 %}
29 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
64 {% if task.running == 100 %}
68 <span class="fa fa-square-o"></span>
75 <fieldset class="majorpoints">
76 <legend class="majorpointslegend"
77 style="background-color:#d3d3d3;cursor: pointer;">Show input parameters</legend>
78 <div class="hiders" style="display:none" >
80 <li class="list-group-item task-item">
81 <div class="col-md-6"> type </div>
82 <div class="col-md-6">{{ task.type }}</div>
85 <li class="list-group-item task-item">
86 <div class="col-md-6"> pbsjob </div>
87 <div class="col-md-6">{{ task.pbsjob }}</div>
91 <li class="list-group-item task-item">
92 <div class="col-md-6"> force field </div>
93 <div class="col-md-6">{{ task.unres_ff }}</div>
96 <li class="list-group-item task-item">
97 <div class="col-md-4"> sequence </div>
98 <div class="col-md-8 monospace">{{ task.md_seq}}</div>
101 <li class="list-group-item task-item">
102 <div class="col-md-4"> secondary structure
104 <div class="col-md-8 monospace">{{ task.md_2d}}</div>
108 <li class="list-group-item task-item">
109 <div class="col-md-6"> SSBOND </div>
110 <div class="col-md-6">{{ task.ssbond}}</div>
114 {% if task.type == "min" %}
117 <li class="list-group-item task-item">
118 <div class="col-md-6"> algorithm</div>
119 <div class="col-md-6">{{ task.min_choice }}</div>
121 <li class="list-group-item task-item">
122 <div class="col-md-6"> overlap</div>
123 <div class="col-md-6">{{ task.min_overlap }}</div>
125 <li class="list-group-item task-item">
126 <div class="col-md-6"> searchsc</div>
127 <div class="col-md-6">{{ task.min_searchsc }}</div>
129 <li class="list-group-item task-item">
130 <div class="col-md-6"> maxmin</div>
131 <div class="col-md-6">{{ task.min_maxmin }}</div>
133 <li class="list-group-item task-item">
134 <div class="col-md-6"> maxfun</div>
135 <div class="col-md-6">{{ task.min_maxfun }}</div>
137 <li class="list-group-item task-item">
138 <div class="col-md-6"> pdbout</div>
139 <div class="col-md-6">{{ task.min_pdbout }}</div>
141 <li class="list-group-item task-item">
142 <div class="col-md-6"> input pdb </div>
143 <div class="col-md-6">{{ task.myfile1 }}</div>
145 <li class="list-group-item task-item">
146 <div class="col-md-6"> pdb code</div>
147 <div class="col-md-6">{{ task.pdbcode }}</div>
149 <li class="list-group-item task-item">
150 <div class="col-md-6"> unres_pdb</div>
151 <div class="col-md-6">{{ task.min_unres_pdb }}</div>
155 {% if task.type == "md" %}
156 <li class="list-group-item task-item">
157 <div class="col-md-6"> starting </div>
158 <div class="col-md-6">{{ task.md_start}}</div>
161 <li class="list-group-item task-item">
162 <div class="col-md-6"> input pdb </div>
163 <div class="col-md-6">{{ task.myfile1 }}</div>
165 <li class="list-group-item task-item">
166 <div class="col-md-6"> pdb code</div>
167 <div class="col-md-6">{{ task.pdbcode }}</div>
169 <li class="list-group-item task-item">
170 <div class="col-md-6"> seed </div>
171 <div class="col-md-6">{{ task.md_seed}}</div>
173 <li class="list-group-item task-item">
174 <div class="col-md-6"> pdbref </div>
175 <div class="col-md-6">{{ task.md_pdbref}}</div>
177 <li class="list-group-item task-item">
178 <div class="col-md-6"> respa </div>
179 <div class="col-md-6">{{ task.md_respa}}</div>
181 <li class="list-group-item task-item">
182 <div class="col-md-6"> temperature </div>
183 <div class="col-md-6">{{ task.md_temp}}</div>
185 <li class="list-group-item task-item">
186 <div class="col-md-6"> nstep </div>
187 <div class="col-md-6">{{ task.md_nstep}}</div>
189 <li class="list-group-item task-item">
190 <div class="col-md-6"> total steps (with restarts) </div>
191 <div class="col-md-6">{{ task.md_total_steps}}</div>
193 <li class="list-group-item task-item">
194 <div class="col-md-6"> ntwe </div>
195 <div class="col-md-6">{{ task.md_ntwe}}</div>
197 <li class="list-group-item task-item">
198 <div class="col-md-6"> ntwx </div>
199 <div class="col-md-6">{{ task.md_ntwx}}</div>
201 <li class="list-group-item task-item">
202 <div class="col-md-6"> dt </div>
203 <div class="col-md-6">{{ task.md_dt}}</div>
205 <li class="list-group-item task-item">
206 <div class="col-md-6"> thermostat </div>
207 <div class="col-md-6">{{ task.md_lang}}</div>
210 {% if task.md_lang == "berendsen" %}
212 <li class="list-group-item task-item">
213 <div class="col-md-6"> tau </div>
214 <div class="col-md-6">{{ task.md_tau}}</div>
219 <li class="list-group-item task-item">
220 <div class="col-md-6"> scal_fric </div>
221 <div class="col-md-6">{{ task.md_scal_fric}}</div>
226 <li class="list-group-item task-item">
227 <div class="col-md-6"> mdpdb </div>
228 <div class="col-md-6">{{ task.md_mdpdb}}</div>
230 <li class="list-group-item task-item">
231 <div class="col-md-6"> RESPA </div>
232 <div class="col-md-6">{{ task.md_respa}}</div>
238 {% if task.type == "remd" or task.type == "dock" %}
240 <li class="list-group-item task-item">
241 <div class="col-md-6"> nrep </div>
242 <div class="col-md-6">{{ task.remd_nrep}}</div>
244 <li class="list-group-item task-item">
245 <div class="col-md-6"> starting </div>
246 <div class="col-md-6">{{ task.md_start}}</div>
249 <li class="list-group-item task-item">
250 <div class="col-md-6"> input pdb </div>
251 <div class="col-md-6">{{ task.myfile1 }}</div>
253 <li class="list-group-item task-item">
254 <div class="col-md-6"> pdb code</div>
255 <div class="col-md-6">{{ task.pdbcode }}</div>
257 {% if task.type == "dock" %}
258 <li class="list-group-item task-item">
259 <div class="col-md-6"> input pdb2 </div>
260 <div class="col-md-6">{{ task.myfile2 }}</div>
262 <li class="list-group-item task-item">
263 <div class="col-md-6"> pdb code2</div>
264 <div class="col-md-6">{{ task.pdbcode2 }}</div>
266 <li class="list-group-item task-item">
267 <div class="col-md-6"> dock_peptide</div>
268 <div class="col-md-6">{{ task.dock_peptide }}</div>
272 <li class="list-group-item task-item">
273 <div class="col-md-6"> seed </div>
274 <div class="col-md-6">{{ task.md_seed}}</div>
276 <li class="list-group-item task-item">
277 <div class="col-md-6"> pdbref </div>
278 <div class="col-md-6">{{ task.md_pdbref}}</div>
280 {% if task.md_start == "pdbstart" %}
281 <li class="list-group-item task-item">
282 <div class="col-md-6"> preminim maxfun </div>
283 <div class="col-md-6">{{ task.min_maxfun }}</div>
286 <li class="list-group-item task-item">
287 <div class="col-md-6"> respa </div>
288 <div class="col-md-6">{{ task.md_respa}}</div>
290 <li class="list-group-item task-item">
291 <div class="col-md-6"> nstep </div>
292 <div class="col-md-6">{{ task.md_nstep}}</div>
294 <li class="list-group-item task-item">
295 <div class="col-md-6"> total steps (with restarts) </div>
296 <div class="col-md-6">{{ task.md_total_steps}}</div>
298 <li class="list-group-item task-item">
299 <div class="col-md-6"> ntwe </div>
300 <div class="col-md-6">{{ task.md_ntwe}}</div>
302 <li class="list-group-item task-item">
303 <div class="col-md-6"> nstex </div>
304 <div class="col-md-6">{{ task.remd_nstex}}</div>
306 <li class="list-group-item task-item">
307 <div class="col-md-6"> ntwx </div>
308 <div class="col-md-6">{{ task.md_ntwx}}</div>
310 <li class="list-group-item task-item">
311 <div class="col-md-6"> dt </div>
312 <div class="col-md-6">{{ task.md_dt}}</div>
314 <li class="list-group-item task-item">
315 <div class="col-md-6"> thermostat </div>
316 <div class="col-md-6">{{ task.md_lang}}</div>
319 {% if task.md_lang == "berendsen" %}
321 <li class="list-group-item task-item">
322 <div class="col-md-6"> tau </div>
323 <div class="col-md-6">{{ task.md_tau}}</div>
328 <li class="list-group-item task-item">
329 <div class="col-md-6"> scal_fric </div>
330 <div class="col-md-6">{{ task.md_scal_fric}}</div>
335 <li class="list-group-item task-item">
336 <div class="col-md-6"> RESPA </div>
337 <div class="col-md-6">{{ task.md_respa}}</div>
340 <li class="list-group-item task-item">
341 <div class="col-md-6"> temperatures </div>
342 <div class="col-md-6">{{ task.remd_multi_t}}</div>
344 <li class="list-group-item task-item">
345 <div class="col-md-6"> multiplex </div>
346 <div class="col-md-6">{{ task.remd_multi_m}}</div>
348 <li class="list-group-item task-item">
349 <div class="col-md-6"> temperature for clustering</div>
350 <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
352 <li class="list-group-item task-item">
353 <div class="col-md-6"> number of clusters</div>
354 <div class="col-md-6">{{ task.remd_cluster_n}}</div>
356 {% if task.saxs_data != "" %}
357 <li class="list-group-item task-item">
358 <div class="col-md-6"> wsaxs </div>
359 <div class="col-md-6">{{ task.wsaxs }}</div>
361 <li class="list-group-item task-item">
362 <div class="col-md-6"> scal_rad (saxs) </div>
363 <div class="col-md-6">{{ task.scal_rad }}</div>
365 <li class="list-group-item task-item">
366 <div class="col-md-6"> saxs distribution </div>
367 <div class="col-md-6"><pre> {{ task.saxs_data }}</pre></div>
373 <li class="list-group-item task-item">
374 <div class="col-md-6"> Box X Y Z</div>
375 <div class="col-md-2">{{ task.boxx}}</div>
376 <div class="col-md-2">{{ task.boxy}}</div>
377 <div class="col-md-2">{{ task.boxz}}</div>
384 <li class="list-group-item task-item">
385 <div class="col-md-4"> Directory </div>
386 <div class="col-md-8">
387 <a href="/myfiles/list/{{task.jobdirname}}/">
388 {{ task.jobdirname }}
392 <a class="btn btn-default"
393 href="/{{task.id}}/all.zip">
402 {% if task.type == "min" %}
404 <li class="list-group-item task-item">
405 <div class="col-md-2"> Etot </div>
406 <div class="col-md-10">{{ task.etot }}</div>
409 <li class="list-group-item task-item">
410 <div class="col-md-2"> UNRES model </div>
411 <div class="col-md-10">
413 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
415 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
416 width="500"></a> </div>
419 <li class="list-group-item task-item">
420 <div class="col-md-2"> UNRES model NGL viewer</div>
421 <div class="col-md-10" id="viewport_unres"
422 style="width:500px;height:500px;">
428 <li class="list-group-item task-item">
429 <div class="col-md-2"> Structure overlap </div>
430 <div class="col-md-10"> <img
431 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
435 <li class="list-group-item task-item">
436 <div class="col-md-2"> Structure overlap NGL viewer</div>
437 <div class="col-md-10" id="viewport_min"
438 style="width:500px;height:500px;">
441 <li class="list-group-item task-item">
442 <div class="col-md-12">
443 <button id="toggleAllatom">Input structure on/off</button>
444 <button id="toggleSidechains2">Side-chains on/off</button>
449 <li class="list-group-item task-item">
450 <div class="col-md-2"> Results </div>
451 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
454 {% if task.type == "md" %}
456 <li class="list-group-item task-item">
457 <div class="col-md-2"> Temperature histogram </div>
458 <div class="col-md-10"> <img
459 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
463 <li class="list-group-item task-item">
464 <div class="col-md-2"> Potential energy </div>
465 <div class="col-md-10"> <img
466 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
470 <li class="list-group-item task-item">
471 <div class="col-md-2"> Movie </div>
472 <div class="col-md-10">
474 <video width="500" height="400"
475 preload="auto" controls="controls">
477 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
478 type="video/ogg; codecs=theora"> </source>
484 {% if task.md_mdpdb %}
485 <li class="list-group-item task-item">
486 <div class="col-md-2"> Trajectory NGL viewer</div>
487 <div class="col-md-10" id="viewport_traj"
488 style="width:500px;height:500px;">
491 <li class="list-group-item task-item">
492 <div class="col-md-6">
493 <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
495 <div class="col-md-6">
496 <button id="toggleRunMDs">run/pause MD</button>
497 <button id="toggleSidechains1">side-chains on/off</button>
503 <li class="list-group-item task-item">
504 <div class="col-md-2"> Radius of gyration based
505 on C<sup>α</sup> coordinates </div>
506 <div class="col-md-10"> <img
507 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
513 {% if task.md_pdbref %}
514 <li class="list-group-item task-item">
515 <div class="col-md-2"> C<sup>α</sup> RMSD </div>
516 <div class="col-md-10"> <img
517 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
521 <li class="list-group-item task-item">
522 <div class="col-md-2"> fraction of native
523 side-chain concacts </div>
524 <div class="col-md-10"> <img
525 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
531 {% if task.md_start == "pdbstart" %}
532 <li class="list-group-item task-item">
533 <div class="col-md-2"> fluctuations </div>
534 <div class="col-md-10"> <img
535 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
539 <li class="list-group-item task-item">
540 <div class="col-md-2"> fluctuations putty on
541 starting structure</div>
542 <div class="col-md-10">
544 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
546 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
547 width="500"></a> </div>
550 <li class="list-group-item task-item">
551 <div class="col-md-2"> fluctuations putty on
552 starting structure NGL viewer</div>
553 <div class="col-md-10" id="viewport_putty"
554 style="width:500px;height:500px;">
565 {% if task.type == "remd" or task.type == "dock" %}
567 <li class="list-group-item task-item">
568 <div class="col-md-2"> Energy histogram </div>
569 <div class="col-md-10"> <img
570 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
574 <li class="list-group-item task-item">
575 <div class="col-md-2"> Energy vs. temperature </div>
576 <div class="col-md-10"> <img
577 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
581 <li class="list-group-item task-item">
582 <div class="col-md-2"> Cv vs. temperature </div>
583 <div class="col-md-10"> <img
584 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
588 {% if task.md_pdbref %}
590 <li class="list-group-item task-item">
591 <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
592 <div class="col-md-10"> <img
593 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
597 <li class="list-group-item task-item">
598 <div class="col-md-2"> potential energy vs.
599 C<sup>α</sup> RMSD</div>
600 <div class="col-md-10"> <img
601 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
605 <li class="list-group-item task-item">
606 <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
607 colored by bath temperature</div>
608 <div class="col-md-10"> <img
609 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
616 <li class="list-group-item task-item">
617 <div class="col-md-2"> exchanges (walk in T) </div>
618 <div class="col-md-10"> <img
619 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
623 {% if task.saxs_data != "" %}
624 <li class="list-group-item task-item">
625 <div class="col-md-2"> P(r) of input SAXS data and
626 calculated for 5 models and the input pdb</div>
627 <div class="col-md-10"> <img
628 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
633 <li class="list-group-item task-item">
634 <div class="col-md-4">
635 <button onclick="plusDivs(-1)">❮</button>
637 <div class="col-md-6">
640 <div class="col-md-2">
641 <button onclick="plusDivs(1)">❯</button>
645 {% for iii in range %}
647 {% with istr=forloop.counter|stringformat:"s" %}
648 {% with MODELi="MODEL"|add:istr|add:".pdb" %}
649 {% with viewporti="viewport_M"|add:istr %}
650 {% with toggleRefi="toggleRefM"|add:istr %}
651 {% with toggleSidechainsi="toggleSidechainsM"|add:istr %}
654 <li class="list-group-item task-item">
655 <div class="col-md-2"> model {{ iii }}
656 {% if not task.damino %}
657 after conversion to allatom
659 {{ remd_models|index:iii|linebreaks }}
661 <div class="col-md-10" id={{viewporti}}
662 style="width:500px;height:500px;">
665 <li class="list-group-item task-item">
666 <div class="col-md-12">
667 {% if task.md_pdbref %}
668 <button id={{toggleRefi}}>Reference structure on/off</button>
670 <button id={{toggleSidechainsi}}>Side-chains on/off</button>
671 <a class="btn btn-default"
672 href="/myfiles/download-file/{{task.jobdirname}}/{{MODELi}}">Download</a>
689 <script src="/static/jquery.min.js"></script>
690 <script src="https://unpkg.com/ngl"></script>
693 $('.majorpointslegend').click(function(){
694 $(this.parentNode).find('.hiders').toggle();
695 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
696 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
698 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
703 {% if task.type == "remd" or task.type == "dock" %}
705 function display_model(num){
707 numstr=num.toString();
708 {% if task.md_pdbref %}
709 var stage = new NGL.Stage("viewport_M"+numstr);
710 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
712 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
713 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
715 o.addRepresentation( "line", {name:"refsc",visible: false,
716 sele:"not hydrogen and sidechainAttached"
721 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
723 o.addRepresentation( "licorice",{ name: "unres", color:
724 "residueindex",colorScale:["blue","cyan", "green",
725 "yellow","orange", "red"], sele:".CA"
727 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
728 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
731 o.addRepresentation( "cartoon",{ name: "unres", color:
732 "residueindex",colorScale:["blue","cyan", "green",
733 "yellow","orange", "red"]
735 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
736 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
737 , sele:"not hydrogen and sidechainAttached" })
741 ]).then(function (ol1) {
742 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
747 var toggleAll = document.getElementById( "toggleRefM"+numstr );
748 toggleAll.addEventListener( "click", function(){
750 stage.getRepresentationsByName(
751 "ref" ).list.forEach( function( repre ){
752 repre.setVisibility( !repre.visible );
755 stage.getRepresentationsByName(
756 "refsc" ).list.forEach( function( repre ){
757 repre.setVisibility( !repre.visible );
762 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
763 toggleSidechains.addEventListener( "click", function(){
766 stage.getRepresentationsByName(
767 "refsc" ).list.forEach( function( repre ){
768 repre.setVisibility( !repre.visible );
771 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
772 repre.setVisibility( !repre.visible );
777 var stage = new NGL.Stage("viewport_M"+numstr);
778 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
779 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
781 o.addRepresentation( "licorice",{ name: "unres", color:
782 "residueindex",colorScale:["blue","cyan", "green",
783 "yellow","orange", "red"],sele:".CA"
785 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
786 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
789 o.addRepresentation( "cartoon",{ name: "unres", color:
790 "residueindex",colorScale:["blue","cyan", "green",
791 "yellow","orange", "red"]
793 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
794 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
795 , sele:"not hydrogen and sidechainAttached" });
799 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
800 toggleSidechains.addEventListener( "click", function(){
801 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
802 repre.setVisibility( !repre.visible );
811 window.addEventListener("resize",
813 stage.handleResize();
821 var y = document.getElementsByClassName("model");
824 for (ii = 0; ii < y.length; ii++) {
828 showDivs(slideIndex);
830 function plusDivs(n) {
831 showDivs(slideIndex += n);
834 function showDivs(n) {
836 var x = document.getElementsByClassName("model");
837 if (n > x.length) {slideIndex = 1}
838 if (n < 1) {slideIndex = x.length}
839 for (i = 0; i < x.length; i++) {
840 x[i].style.display = "none";
842 x[slideIndex-1].style.display = "block";
844 if (lista[slideIndex-1] == 0) {
845 display_model(slideIndex)
848 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
853 {% if not task.done %}
857 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
858 url: "/refresh_done/",
860 success: function(data) {
861 document.location.reload();
863 complete: function() {
864 // Schedule the next request when the current one's complete
865 setTimeout(worker, 30000);
869 $(document).ready(function() {
870 // run the first time; all subsequent calls will take care of themselves
871 setTimeout(worker, 30000);
876 {% if task.type == "min" %}
878 window.addEventListener("resize",
880 stage.handleResize();
883 var stage_unres = new NGL.Stage("viewport_unres");
884 stage_unres.setParameters( { backgroundColor: "white" } );
886 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
888 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
889 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
890 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
891 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
892 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
893 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
894 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
895 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
896 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
897 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
898 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
899 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
900 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
901 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
902 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
903 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
904 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
905 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
906 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
907 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
909 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
911 var shape = new NGL.Shape("shape")
913 o.addRepresentation("licorice");
914 o.structure.eachAtom(function(atom){
915 if (atom.atomname == "CA" && atom.chainname == chain) {
916 px=CAx+(atom.x-CAx)/2;
917 py=CAy+(atom.y-CAy)/2;
918 pz=CAz+(atom.z-CAz)/2;
919 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
921 if (atom.atomname == "CA") {
922 chain= atom.chainname
927 if (atom.atomname == "CB") {
931 norm=Math.sqrt(mx*mx+my*my+mz*mz);
933 var longaxis=resdb[res][4]
934 var shortaxis=resdb[res][3]
935 mx = mx /norm*longaxis;
936 my = my /norm*longaxis;
937 mz = mz /norm*longaxis;
939 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
940 [ resdb[res][0], resdb[res][1], resdb[res][2]],
941 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
944 var shapeComp = stage_unres.addComponentFromObject(shape)
945 shapeComp.addRepresentation("buffer")
951 var stage = new NGL.Stage("viewport_min");
952 stage.setParameters( { backgroundColor: "white" } );
954 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
955 o.addRepresentation( "backbone",{ color:
956 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
958 o.addRepresentation( "licorice",{ color:
959 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
964 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
965 o.addRepresentation( "backbone",{ name: "allatom", color:
966 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
968 o.addRepresentation( "line",{ name: "allatomsc", color:
969 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
970 ,sele:"not hydrogen and sidechainAttached"
974 ]).then(function (ol) {
975 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
981 var toggleAll = document.getElementById( "toggleAllatom" );
982 toggleAll.addEventListener( "click", function(){
984 stage.getRepresentationsByName(
985 "allatom" ).list.forEach( function( repre ){
986 repre.setVisibility( !repre.visible );
989 stage.getRepresentationsByName(
990 "allatomsc" ).list.forEach( function( repre ){
991 repre.setVisibility( !repre.visible );
995 var toggleSidechains = document.getElementById("toggleSidechains2" );
996 toggleSidechains.addEventListener( "click", function(){
999 stage.getRepresentationsByName(
1000 "allatomsc" ).list.forEach( function( repre ){
1001 repre.setVisibility( !repre.visible );
1005 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1006 repre.setVisibility( !repre.visible );
1013 {% if task.type == "md" and task.md_start == "pdbstart" %}
1015 window.addEventListener("resize",
1017 stage.handleResize();
1020 var stage = new NGL.Stage("viewport_putty");
1021 stage.setParameters( { backgroundColor: "white" } );
1023 var tooltip = document.createElement("div")
1024 Object.assign(tooltip.style, {
1028 pointerEvents: "none",
1029 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1032 fontFamily: "sans-serif"
1034 document.body.appendChild(tooltip)
1036 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1038 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1041 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1042 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1046 // remove default hoverPick mouse action
1047 stage.mouseControls.remove("hoverPick")
1049 stage.signals.hovered.add(function (pickingProxy) {
1050 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1051 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1052 var mp = pickingProxy.mouse.position
1053 var bf= atom.bfactor.toFixed(2)
1054 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1055 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1056 tooltip.style.left = mp.x + 3 + "px"
1057 tooltip.style.display = "block"
1059 tooltip.style.display = "none"
1065 {% if task.type == "md" and task.md_mdpdb %}
1067 window.addEventListener("resize",
1069 stage.handleResize();
1072 var stage = new NGL.Stage("viewport_traj");
1073 stage.setParameters( { backgroundColor: "white" } );
1074 stage.setParameters( { cameraType: "orthographic" } );
1077 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1078 asTrajectory: true } ) .then( function( o ){
1079 o.setName ("unres_md");
1080 o.addRepresentation( "backbone",{ color:
1081 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1083 o.addRepresentation( "licorice",{ color:
1084 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1086 o.setPosition([0, 0, 100]);
1091 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1092 toggleSidechains.addEventListener( "click", function(){
1093 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1094 repre.setVisibility( !repre.visible );
1099 function numberWithCommas(x) {
1100 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1102 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1103 var isRunning = false;
1104 toggleRunMDs.addEventListener( "click", function(){
1105 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1106 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1111 trajComp.signals.frameChanged.add(function(){
1112 var fnum=trajComp.trajectory.currentFrame+1;
1113 clipRange.value = fnum;
1114 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1123 var clipRange = document.getElementById( "clipRange" );
1124 var clipRange_val = document.getElementById( "clipRange_val" );
1125 clipRange.oninput = function( e ){
1126 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1127 trajComp.setFrame(e.target.value-1)
1128 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));