1 {% extends "base.html" %}
3 {% load i18n lazysignup_tags %}
6 {% if user|is_lazy_user %}
7 <ul class="list-group">
9 <li class="list-group-item new-task-item task-item">
11 <div class="col-md-2 form-group">
12 <form action="/refresh_done/" method="post">
14 <input type="submit" class="btn" value="Refresh" name="refreshbtn">
18 <div class="col-md-10 form-group">
19 <h5 style="text-align:right;float:right;">
20 {% if not task.done %}
21 {% if task.running > 0 %}
22 {% if task.running == 100 %}
28 waiting in the queue to start
37 <h3> Task <b>{{ task.name }}</b></h3>
38 Created {{ task.created_date }}
39 <ul class="list-group">
41 <li class="list-group-item task-item">
42 <div class="col-md-4"> done ?</div>
43 <div class="col-md-8">
45 <span class="fa fa-check-square-o"></span>
47 {% if task.running > 0 %}
48 <span class="fa fa-spinner
52 <span class="fa fa-square-o"></span>
59 <fieldset class="majorpoints">
60 <legend class="majorpointslegend"
61 style="background-color:#d3d3d3;cursor: pointer;">Show input parameters</legend>
62 <div class="hiders" style="display:none" >
64 <li class="list-group-item task-item">
65 <div class="col-md-6"> type </div>
66 <div class="col-md-6">{{ task.type }}</div>
69 <li class="list-group-item task-item">
70 <div class="col-md-6"> force field </div>
71 <div class="col-md-6">{{ task.unres_ff }}</div>
74 <li class="list-group-item task-item">
75 <div class="col-md-4"> sequence </div>
76 <div class="col-md-8 monospace">{{ task.md_seq}}</div>
79 <li class="list-group-item task-item">
80 <div class="col-md-4"> secondary structure
82 <div class="col-md-8 monospace">{{ task.md_2d}}</div>
86 <li class="list-group-item task-item">
87 <div class="col-md-6"> SSBOND </div>
88 <div class="col-md-6">{{ task.ssbond}}</div>
92 {% if task.type == "min" %}
95 <li class="list-group-item task-item">
96 <div class="col-md-6"> algorithm</div>
97 <div class="col-md-6">{{ task.min_choice }}</div>
99 <li class="list-group-item task-item">
100 <div class="col-md-6"> overlap</div>
101 <div class="col-md-6">{{ task.min_overlap }}</div>
103 <li class="list-group-item task-item">
104 <div class="col-md-6"> searchsc</div>
105 <div class="col-md-6">{{ task.min_searchsc }}</div>
107 <li class="list-group-item task-item">
108 <div class="col-md-6"> maxmin</div>
109 <div class="col-md-6">{{ task.min_maxmin }}</div>
111 <li class="list-group-item task-item">
112 <div class="col-md-6"> maxfun</div>
113 <div class="col-md-6">{{ task.min_maxfun }}</div>
115 <li class="list-group-item task-item">
116 <div class="col-md-6"> pdbout</div>
117 <div class="col-md-6">{{ task.min_pdbout }}</div>
119 <li class="list-group-item task-item">
120 <div class="col-md-6"> input pdb </div>
121 <div class="col-md-6">{{ task.myfile1 }}</div>
123 <li class="list-group-item task-item">
124 <div class="col-md-6"> pdb code</div>
125 <div class="col-md-6">{{ task.pdbcode }}</div>
127 <li class="list-group-item task-item">
128 <div class="col-md-6"> unres_pdb</div>
129 <div class="col-md-6">{{ task.min_unres_pdb }}</div>
133 {% if task.type == "md" %}
134 <li class="list-group-item task-item">
135 <div class="col-md-6"> starting </div>
136 <div class="col-md-6">{{ task.md_start}}</div>
139 <li class="list-group-item task-item">
140 <div class="col-md-6"> input pdb </div>
141 <div class="col-md-6">{{ task.myfile1 }}</div>
143 <li class="list-group-item task-item">
144 <div class="col-md-6"> pdb code</div>
145 <div class="col-md-6">{{ task.pdbcode }}</div>
147 <li class="list-group-item task-item">
148 <div class="col-md-6"> seed </div>
149 <div class="col-md-6">{{ task.md_seed}}</div>
151 <li class="list-group-item task-item">
152 <div class="col-md-6"> pdbref </div>
153 <div class="col-md-6">{{ task.md_pdbref}}</div>
155 <li class="list-group-item task-item">
156 <div class="col-md-6"> respa </div>
157 <div class="col-md-6">{{ task.md_respa}}</div>
159 <li class="list-group-item task-item">
160 <div class="col-md-6"> temperature </div>
161 <div class="col-md-6">{{ task.md_temp}}</div>
163 <li class="list-group-item task-item">
164 <div class="col-md-6"> nstep </div>
165 <div class="col-md-6">{{ task.md_nstep}}</div>
167 <li class="list-group-item task-item">
168 <div class="col-md-6"> ntwe </div>
169 <div class="col-md-6">{{ task.md_ntwe}}</div>
171 <li class="list-group-item task-item">
172 <div class="col-md-6"> ntwx </div>
173 <div class="col-md-6">{{ task.md_ntwx}}</div>
175 <li class="list-group-item task-item">
176 <div class="col-md-6"> dt </div>
177 <div class="col-md-6">{{ task.md_dt}}</div>
179 <li class="list-group-item task-item">
180 <div class="col-md-6"> thermostat </div>
181 <div class="col-md-6">{{ task.md_lang}}</div>
184 {% if task.md_lang == "berendsen" %}
186 <li class="list-group-item task-item">
187 <div class="col-md-6"> tau </div>
188 <div class="col-md-6">{{ task.md_tau}}</div>
193 <li class="list-group-item task-item">
194 <div class="col-md-6"> scal_fric </div>
195 <div class="col-md-6">{{ task.md_scal_fric}}</div>
200 <li class="list-group-item task-item">
201 <div class="col-md-6"> mdpdb </div>
202 <div class="col-md-6">{{ task.md_mdpdb}}</div>
204 <li class="list-group-item task-item">
205 <div class="col-md-6"> RESPA </div>
206 <div class="col-md-6">{{ task.md_respa}}</div>
212 {% if task.type == "remd" %}
214 <li class="list-group-item task-item">
215 <div class="col-md-6"> nrep </div>
216 <div class="col-md-6">{{ task.remd_nrep}}</div>
218 <li class="list-group-item task-item">
219 <div class="col-md-6"> starting </div>
220 <div class="col-md-6">{{ task.md_start}}</div>
223 <li class="list-group-item task-item">
224 <div class="col-md-6"> input pdb </div>
225 <div class="col-md-6">{{ task.myfile1 }}</div>
227 <li class="list-group-item task-item">
228 <div class="col-md-6"> pdb code</div>
229 <div class="col-md-6">{{ task.pdbcode }}</div>
231 <li class="list-group-item task-item">
232 <div class="col-md-6"> seed </div>
233 <div class="col-md-6">{{ task.md_seed}}</div>
235 <li class="list-group-item task-item">
236 <div class="col-md-6"> pdbref </div>
237 <div class="col-md-6">{{ task.md_pdbref}}</div>
239 {% if task.md_start == "pdbstart" %}
240 <li class="list-group-item task-item">
241 <div class="col-md-6"> preminim maxfun </div>
242 <div class="col-md-6">{{ task.min_maxfun }}</div>
245 <li class="list-group-item task-item">
246 <div class="col-md-6"> respa </div>
247 <div class="col-md-6">{{ task.md_respa}}</div>
249 <li class="list-group-item task-item">
250 <div class="col-md-6"> nstep </div>
251 <div class="col-md-6">{{ task.md_nstep}}</div>
253 <li class="list-group-item task-item">
254 <div class="col-md-6"> ntwe </div>
255 <div class="col-md-6">{{ task.md_ntwe}}</div>
257 <li class="list-group-item task-item">
258 <div class="col-md-6"> nstex </div>
259 <div class="col-md-6">{{ task.remd_nstex}}</div>
261 <li class="list-group-item task-item">
262 <div class="col-md-6"> ntwx </div>
263 <div class="col-md-6">{{ task.md_ntwx}}</div>
265 <li class="list-group-item task-item">
266 <div class="col-md-6"> dt </div>
267 <div class="col-md-6">{{ task.md_dt}}</div>
269 <li class="list-group-item task-item">
270 <div class="col-md-6"> thermostat </div>
271 <div class="col-md-6">{{ task.md_lang}}</div>
274 {% if task.md_lang == "berendsen" %}
276 <li class="list-group-item task-item">
277 <div class="col-md-6"> tau </div>
278 <div class="col-md-6">{{ task.md_tau}}</div>
283 <li class="list-group-item task-item">
284 <div class="col-md-6"> scal_fric </div>
285 <div class="col-md-6">{{ task.md_scal_fric}}</div>
290 <li class="list-group-item task-item">
291 <div class="col-md-6"> RESPA </div>
292 <div class="col-md-6">{{ task.md_respa}}</div>
295 <li class="list-group-item task-item">
296 <div class="col-md-6"> temperatures </div>
297 <div class="col-md-6">{{ task.remd_multi_t}}</div>
299 <li class="list-group-item task-item">
300 <div class="col-md-6"> multiplex </div>
301 <div class="col-md-6">{{ task.remd_multi_m}}</div>
303 <li class="list-group-item task-item">
304 <div class="col-md-6"> temperature for clustering</div>
305 <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
307 {% if task.saxs_data != "" %}
308 <li class="list-group-item task-item">
309 <div class="col-md-6"> wsaxs </div>
310 <div class="col-md-6">{{ task.wsaxs }}</div>
312 <li class="list-group-item task-item">
313 <div class="col-md-6"> scal_rad (saxs) </div>
314 <div class="col-md-6">{{ task.scal_rad }}</div>
316 <li class="list-group-item task-item">
317 <div class="col-md-6"> saxs distribution </div>
318 <div class="col-md-6"><pre> {{ task.saxs_data }}</pre></div>
324 <li class="list-group-item task-item">
325 <div class="col-md-6"> Box X Y Z</div>
326 <div class="col-md-2">{{ task.boxx}}</div>
327 <div class="col-md-2">{{ task.boxy}}</div>
328 <div class="col-md-2">{{ task.boxz}}</div>
335 <li class="list-group-item task-item">
336 <div class="col-md-4"> Directory </div>
337 <div class="col-md-8">
338 <a href="/myfiles/list/{{task.jobdirname}}/">
339 {{ task.jobdirname }}
347 {% if task.type == "min" %}
349 <li class="list-group-item task-item">
350 <div class="col-md-2"> Etot </div>
351 <div class="col-md-10">{{ task.etot }}</div>
354 <li class="list-group-item task-item">
355 <div class="col-md-2"> UNRES model </div>
356 <div class="col-md-10">
358 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
360 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
361 width="500"></a> </div>
364 <li class="list-group-item task-item">
365 <div class="col-md-2"> UNRES model NGL viewer</div>
366 <div class="col-md-10" id="viewport_unres"
367 style="width:500px;height:500px;">
373 <li class="list-group-item task-item">
374 <div class="col-md-2"> Structure overlap </div>
375 <div class="col-md-10"> <img
376 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
380 <li class="list-group-item task-item">
381 <div class="col-md-2"> Structure overlap NGL viewer</div>
382 <div class="col-md-10" id="viewport_min"
383 style="width:500px;height:500px;">
386 <li class="list-group-item task-item">
387 <div class="col-md-12">
388 <button id="toggleAllatom">Input structure on/off</button>
389 <button id="toggleSidechains2">Side-chains on/off</button>
394 <li class="list-group-item task-item">
395 <div class="col-md-2"> Results </div>
396 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
399 {% if task.type == "md" %}
401 <li class="list-group-item task-item">
402 <div class="col-md-2"> Temperature histogram </div>
403 <div class="col-md-10"> <img
404 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
408 <li class="list-group-item task-item">
409 <div class="col-md-2"> Potential energy </div>
410 <div class="col-md-10"> <img
411 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
415 <li class="list-group-item task-item">
416 <div class="col-md-2"> Movie </div>
417 <div class="col-md-10">
419 <video width="500" height="400" preload controls>
421 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
422 type="video/ogg; codecs=theora"> </source>
428 {% if task.md_mdpdb %}
429 <li class="list-group-item task-item">
430 <div class="col-md-2"> Trajectory NGL viewer</div>
431 <div class="col-md-10" id="viewport_traj"
432 style="width:500px;height:500px;">
435 <li class="list-group-item task-item">
436 <div class="col-md-6">
437 <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
439 <div class="col-md-6">
440 <button id="toggleRunMDs">run/pause MD</button>
441 <button id="toggleSidechains1">side-chains on/off</button>
447 <li class="list-group-item task-item">
448 <div class="col-md-2"> Radius of gyration based
449 on C<sup>α</sup> coordinates </div>
450 <div class="col-md-10"> <img
451 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
457 {% if task.md_pdbref %}
458 <li class="list-group-item task-item">
459 <div class="col-md-2"> RMSD </div>
460 <div class="col-md-10"> <img
461 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
465 <li class="list-group-item task-item">
466 <div class="col-md-2"> fraction of native
467 side-chain concacts </div>
468 <div class="col-md-10"> <img
469 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
475 {% if task.md_start == "pdbstart" %}
476 <li class="list-group-item task-item">
477 <div class="col-md-2"> fluctuations </div>
478 <div class="col-md-10"> <img
479 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
483 <li class="list-group-item task-item">
484 <div class="col-md-2"> fluctuations putty on
485 starting structure</div>
486 <div class="col-md-10">
488 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
490 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
491 width="500"></a> </div>
494 <li class="list-group-item task-item">
495 <div class="col-md-2"> fluctuations putty on
496 starting structure NGL viewer</div>
497 <div class="col-md-10" id="viewport_putty"
498 style="width:500px;height:500px;">
509 {% if task.type == "remd" %}
511 <li class="list-group-item task-item">
512 <div class="col-md-2"> Energy histogram </div>
513 <div class="col-md-10"> <img
514 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
518 <li class="list-group-item task-item">
519 <div class="col-md-2"> Energy vs. temperature </div>
520 <div class="col-md-10"> <img
521 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
525 <li class="list-group-item task-item">
526 <div class="col-md-2"> Cv vs. temperature </div>
527 <div class="col-md-10"> <img
528 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
532 {% if task.md_pdbref %}
534 <li class="list-group-item task-item">
535 <div class="col-md-2"> Average RMSD vs. temperature </div>
536 <div class="col-md-10"> <img
537 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
541 <li class="list-group-item task-item">
542 <div class="col-md-2"> potential energy vs. RMSD</div>
543 <div class="col-md-10"> <img
544 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
548 <li class="list-group-item task-item">
549 <div class="col-md-2"> RMSD vs. step*replica
550 colored by bath temperature</div>
551 <div class="col-md-10"> <img
552 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
559 <li class="list-group-item task-item">
560 <div class="col-md-2"> exchanges (walk in T) </div>
561 <div class="col-md-10"> <img
562 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
566 {% if task.saxs_data != "" %}
567 <li class="list-group-item task-item">
568 <div class="col-md-2"> P(r) of input SAXS data and
569 calculated for 5 models and the input pdb</div>
570 <div class="col-md-10"> <img
571 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
576 <li class="list-group-item task-item">
577 <div class="col-md-4">
578 <button onclick="plusDivs(-1)">❮</button>
580 <div class="col-md-6">
583 <div class="col-md-2">
584 <button onclick="plusDivs(1)">❯</button>
589 <!-- <li class="list-group-item task-item">
590 <div class="col-md-2"> model1 after conversion
592 {{ task.remd_model1|linebreaks }}
594 <div class="col-md-10">
596 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
598 src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
601 <li class="list-group-item task-item">
602 <div class="col-md-2"> model1
603 {% if not task.damino %}
604 after conversion to allatom
606 {{ task.remd_model1|linebreaks }}
608 <div class="col-md-10" id="viewport_M1"
609 style="width:500px;height:500px;">
612 <li class="list-group-item task-item">
613 <div class="col-md-12">
614 {% if task.md_pdbref %}
615 <button id="toggleRefM1">Reference structure on/off</button>
617 <button id="toggleSidechainsM1">Side-chains on/off</button>
618 <a class="btn btn-default"
619 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
625 <!-- <li class="list-group-item task-item">
626 <div class="col-md-2"> model2 after conversion
628 {{ task.remd_model2|linebreaks }}
630 <div class="col-md-10">
632 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
634 src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
637 <li class="list-group-item task-item">
638 <div class="col-md-2"> model2
639 {% if not task.damino %}
640 after conversion to allatom
642 {{ task.remd_model2|linebreaks }}
644 <div class="col-md-10" id="viewport_M2"
645 style="width:500px;height:500px;">
648 <li class="list-group-item task-item">
649 <div class="col-md-12">
650 {% if task.md_pdbref %}
651 <button id="toggleRefM2">Reference structure on/off</button>
653 <button id="toggleSidechainsM2">Side-chains on/off</button>
654 <a class="btn btn-default"
655 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
662 <!-- <li class="list-group-item task-item">
663 <div class="col-md-2"> model3 after conversion
665 {{ task.remd_model3|linebreaks }}
667 <div class="col-md-10">
669 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
671 src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
674 <li class="list-group-item task-item">
675 <div class="col-md-2"> model3
676 {% if not task.damino %}
677 after conversion to allatom
679 {{ task.remd_model3|linebreaks }}
681 <div class="col-md-10" id="viewport_M3"
682 style="width:500px;height:500px;">
685 <li class="list-group-item task-item">
686 <div class="col-md-12">
687 {% if task.md_pdbref %}
688 <button id="toggleRefM3">Reference structure on/off</button>
690 <button id="toggleSidechainsM3">Side-chains on/off</button>
691 <a class="btn btn-default"
692 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
698 <!-- <li class="list-group-item task-item">
699 <div class="col-md-2"> model4 after conversion
701 {{ task.remd_model4|linebreaks }}
703 <div class="col-md-10">
705 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
707 src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
710 <li class="list-group-item task-item">
711 <div class="col-md-2"> model4
712 {% if not task.damino %}
713 after conversion to allatom
715 {{ task.remd_model4|linebreaks }}
717 <div class="col-md-10" id="viewport_M4"
718 style="width:500px;height:500px;">
721 <li class="list-group-item task-item">
722 <div class="col-md-12">
723 {% if task.md_pdbref %}
724 <button id="toggleRefM4">Reference structure on/off</button>
726 <button id="toggleSidechainsM4">Side-chains on/off</button>
727 <a class="btn btn-default"
728 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
734 <!-- <li class="list-group-item task-item">
735 <div class="col-md-2"> model5 after conversion
737 {{ task.remd_model5|linebreaks }}
739 <div class="col-md-10">
741 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
743 src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
746 <li class="list-group-item task-item">
747 <div class="col-md-2"> model5
748 {% if not task.damino %}
749 after conversion to allatom
751 {{ task.remd_model5|linebreaks }}
753 <div class="col-md-10" id="viewport_M5"
754 style="width:500px;height:500px;">
757 <li class="list-group-item task-item">
758 <div class="col-md-12">
759 {% if task.md_pdbref %}
760 <button id="toggleRefM5">Reference structure on/off</button>
762 <button id="toggleSidechainsM5">Side-chains on/off</button>
763 <a class="btn btn-default"
764 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
775 <script src="/static/jquery.min.js"></script>
776 <script src="https://unpkg.com/ngl"></script>
779 $('.majorpointslegend').click(function(){
780 $(this.parentNode).find('.hiders').toggle();
781 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
782 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
784 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
789 {% if task.type == "remd" %}
791 function display_model(numstr){
793 {% if task.md_pdbref %}
794 var stage = new NGL.Stage("viewport_M"+numstr);
795 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
797 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
798 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
800 o.addRepresentation( "line", {name:"refsc",visible: false,
801 sele:"not hydrogen and sidechainAttached"
806 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
808 o.addRepresentation( "licorice",{ name: "unres", color:
809 "residueindex",colorScale:["blue","cyan", "green",
810 "yellow","orange", "red"], sele:".CA"
812 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
813 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
816 o.addRepresentation( "cartoon",{ name: "unres", color:
817 "residueindex",colorScale:["blue","cyan", "green",
818 "yellow","orange", "red"]
820 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
821 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
822 , sele:"not hydrogen and sidechainAttached" })
826 ]).then(function (ol1) {
827 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
832 var toggleAll = document.getElementById( "toggleRefM"+numstr );
833 toggleAll.addEventListener( "click", function(){
835 stage.getRepresentationsByName(
836 "ref" ).list.forEach( function( repre ){
837 repre.setVisibility( !repre.visible );
840 stage.getRepresentationsByName(
841 "refsc" ).list.forEach( function( repre ){
842 repre.setVisibility( !repre.visible );
847 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
848 toggleSidechains.addEventListener( "click", function(){
851 stage.getRepresentationsByName(
852 "refsc" ).list.forEach( function( repre ){
853 repre.setVisibility( !repre.visible );
856 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
857 repre.setVisibility( !repre.visible );
862 var stage = new NGL.Stage("viewport_M"+numstr);
863 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
864 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
866 o.addRepresentation( "licorice",{ name: "unres", color:
867 "residueindex",colorScale:["blue","cyan", "green",
868 "yellow","orange", "red"],sele:".CA"
870 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
871 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
874 o.addRepresentation( "cartoon",{ name: "unres", color:
875 "residueindex",colorScale:["blue","cyan", "green",
876 "yellow","orange", "red"]
878 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
879 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
880 , sele:"not hydrogen and sidechainAttached" });
884 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
885 toggleSidechains.addEventListener( "click", function(){
886 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
887 repre.setVisibility( !repre.visible );
896 window.addEventListener("resize",
898 stage.handleResize();
906 var y = document.getElementsByClassName("model");
909 for (ii = 0; ii < y.length; ii++) {
913 showDivs(slideIndex);
915 function plusDivs(n) {
916 showDivs(slideIndex += n);
919 function showDivs(n) {
921 var x = document.getElementsByClassName("model");
922 if (n > x.length) {slideIndex = 1}
923 if (n < 1) {slideIndex = x.length}
924 for (i = 0; i < x.length; i++) {
925 x[i].style.display = "none";
927 x[slideIndex-1].style.display = "block";
929 if (lista[slideIndex-1] == 0 && slideIndex == 2) {
933 if (lista[slideIndex-1] == 0 && slideIndex == 3) {
937 if (lista[slideIndex-1] == 0 && slideIndex == 4) {
941 if (lista[slideIndex-1] == 0 && slideIndex == 5) {
946 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
951 {% if not task.done %}
955 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
956 url: "/refresh_done/",
958 success: function(data) {
959 document.location.reload();
961 complete: function() {
962 // Schedule the next request when the current one's complete
963 setTimeout(worker, 30000);
967 $(document).ready(function() {
968 // run the first time; all subsequent calls will take care of themselves
969 setTimeout(worker, 30000);
975 {% if task.type == "min" %}
977 window.addEventListener("resize",
979 stage.handleResize();
982 var stage_unres = new NGL.Stage("viewport_unres");
983 stage_unres.setParameters( { backgroundColor: "white" } );
985 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
987 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
988 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
989 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
990 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
991 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
992 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
993 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
994 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
995 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
996 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
997 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
998 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
999 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
1000 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
1001 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
1002 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
1003 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
1004 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
1005 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
1006 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
1008 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
1010 var shape = new NGL.Shape("shape")
1012 o.addRepresentation("licorice");
1013 o.structure.eachAtom(function(atom){
1014 if (atom.atomname == "CA" && atom.chainname == chain) {
1015 px=CAx+(atom.x-CAx)/2;
1016 py=CAy+(atom.y-CAy)/2;
1017 pz=CAz+(atom.z-CAz)/2;
1018 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
1020 if (atom.atomname == "CA") {
1021 chain= atom.chainname
1026 if (atom.atomname == "CB") {
1030 norm=Math.sqrt(mx*mx+my*my+mz*mz);
1032 var longaxis=resdb[res][4]
1033 var shortaxis=resdb[res][3]
1034 mx = mx /norm*longaxis;
1035 my = my /norm*longaxis;
1036 mz = mz /norm*longaxis;
1038 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
1039 [ resdb[res][0], resdb[res][1], resdb[res][2]],
1040 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
1043 var shapeComp = stage_unres.addComponentFromObject(shape)
1044 shapeComp.addRepresentation("buffer")
1050 var stage = new NGL.Stage("viewport_min");
1051 stage.setParameters( { backgroundColor: "white" } );
1053 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
1054 o.addRepresentation( "backbone",{ color:
1055 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1057 o.addRepresentation( "licorice",{ color:
1058 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
1063 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
1064 o.addRepresentation( "backbone",{ name: "allatom", color:
1065 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
1067 o.addRepresentation( "line",{ name: "allatomsc", color:
1068 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1069 ,sele:"not hydrogen and sidechainAttached"
1073 ]).then(function (ol) {
1074 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
1080 var toggleAll = document.getElementById( "toggleAllatom" );
1081 toggleAll.addEventListener( "click", function(){
1083 stage.getRepresentationsByName(
1084 "allatom" ).list.forEach( function( repre ){
1085 repre.setVisibility( !repre.visible );
1088 stage.getRepresentationsByName(
1089 "allatomsc" ).list.forEach( function( repre ){
1090 repre.setVisibility( !repre.visible );
1094 var toggleSidechains = document.getElementById("toggleSidechains2" );
1095 toggleSidechains.addEventListener( "click", function(){
1098 stage.getRepresentationsByName(
1099 "allatomsc" ).list.forEach( function( repre ){
1100 repre.setVisibility( !repre.visible );
1104 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1105 repre.setVisibility( !repre.visible );
1112 {% if task.type == "md" and task.md_start == "pdbstart" %}
1114 window.addEventListener("resize",
1116 stage.handleResize();
1119 var stage = new NGL.Stage("viewport_putty");
1120 stage.setParameters( { backgroundColor: "white" } );
1122 var tooltip = document.createElement("div")
1123 Object.assign(tooltip.style, {
1127 pointerEvents: "none",
1128 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1131 fontFamily: "sans-serif"
1133 document.body.appendChild(tooltip)
1135 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1137 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1140 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1141 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1145 // remove default hoverPick mouse action
1146 stage.mouseControls.remove("hoverPick")
1148 stage.signals.hovered.add(function (pickingProxy) {
1149 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1150 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1151 var mp = pickingProxy.mouse.position
1152 var bf= atom.bfactor.toFixed(2)
1153 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1154 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1155 tooltip.style.left = mp.x + 3 + "px"
1156 tooltip.style.display = "block"
1158 tooltip.style.display = "none"
1164 {% if task.type == "md" and task.md_mdpdb %}
1166 window.addEventListener("resize",
1168 stage.handleResize();
1171 var stage = new NGL.Stage("viewport_traj");
1172 stage.setParameters( { backgroundColor: "white" } );
1173 stage.setParameters( { cameraType: "orthographic" } );
1176 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1177 asTrajectory: true } ) .then( function( o ){
1178 o.setName ("unres_md");
1179 o.addRepresentation( "backbone",{ color:
1180 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1182 o.addRepresentation( "licorice",{ color:
1183 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1189 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1190 toggleSidechains.addEventListener( "click", function(){
1191 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1192 repre.setVisibility( !repre.visible );
1197 function numberWithCommas(x) {
1198 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1200 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1201 var isRunning = false;
1202 toggleRunMDs.addEventListener( "click", function(){
1203 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1204 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1209 trajComp.signals.frameChanged.add(function(){
1210 var fnum=trajComp.trajectory.currentFrame;
1211 clipRange.value = fnum;
1212 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1221 var clipRange = document.getElementById( "clipRange" );
1222 var clipRange_val = document.getElementById( "clipRange_val" );
1223 clipRange.oninput = function( e ){
1224 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1225 trajComp.setFrame(e.target.value)
1226 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));