1 {% extends "base.html" %}
3 {% load i18n lazysignup_tags %}
6 {% if task.owner|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_done1/{{task.id}}/" 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
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>
46 {% if task.type == "md" or task.type == "remd" %}
47 <form action="restart/"
49 style="text-align;float:right;">
52 class="btn btn-default"
59 {% if task.running > 0 %}
60 <span class="fa fa-spinner
64 <span class="fa fa-square-o"></span>
71 <fieldset class="majorpoints">
72 <legend class="majorpointslegend"
73 style="background-color:#d3d3d3;cursor: pointer;">Show input parameters</legend>
74 <div class="hiders" style="display:none" >
76 <li class="list-group-item task-item">
77 <div class="col-md-6"> type </div>
78 <div class="col-md-6">{{ task.type }}</div>
81 <li class="list-group-item task-item">
82 <div class="col-md-6"> force field </div>
83 <div class="col-md-6">{{ task.unres_ff }}</div>
86 <li class="list-group-item task-item">
87 <div class="col-md-4"> sequence </div>
88 <div class="col-md-8 monospace">{{ task.md_seq}}</div>
91 <li class="list-group-item task-item">
92 <div class="col-md-4"> secondary structure
94 <div class="col-md-8 monospace">{{ task.md_2d}}</div>
98 <li class="list-group-item task-item">
99 <div class="col-md-6"> SSBOND </div>
100 <div class="col-md-6">{{ task.ssbond}}</div>
104 {% if task.type == "min" %}
107 <li class="list-group-item task-item">
108 <div class="col-md-6"> algorithm</div>
109 <div class="col-md-6">{{ task.min_choice }}</div>
111 <li class="list-group-item task-item">
112 <div class="col-md-6"> overlap</div>
113 <div class="col-md-6">{{ task.min_overlap }}</div>
115 <li class="list-group-item task-item">
116 <div class="col-md-6"> searchsc</div>
117 <div class="col-md-6">{{ task.min_searchsc }}</div>
119 <li class="list-group-item task-item">
120 <div class="col-md-6"> maxmin</div>
121 <div class="col-md-6">{{ task.min_maxmin }}</div>
123 <li class="list-group-item task-item">
124 <div class="col-md-6"> maxfun</div>
125 <div class="col-md-6">{{ task.min_maxfun }}</div>
127 <li class="list-group-item task-item">
128 <div class="col-md-6"> pdbout</div>
129 <div class="col-md-6">{{ task.min_pdbout }}</div>
131 <li class="list-group-item task-item">
132 <div class="col-md-6"> input pdb </div>
133 <div class="col-md-6">{{ task.myfile1 }}</div>
135 <li class="list-group-item task-item">
136 <div class="col-md-6"> pdb code</div>
137 <div class="col-md-6">{{ task.pdbcode }}</div>
139 <li class="list-group-item task-item">
140 <div class="col-md-6"> unres_pdb</div>
141 <div class="col-md-6">{{ task.min_unres_pdb }}</div>
145 {% if task.type == "md" %}
146 <li class="list-group-item task-item">
147 <div class="col-md-6"> starting </div>
148 <div class="col-md-6">{{ task.md_start}}</div>
151 <li class="list-group-item task-item">
152 <div class="col-md-6"> input pdb </div>
153 <div class="col-md-6">{{ task.myfile1 }}</div>
155 <li class="list-group-item task-item">
156 <div class="col-md-6"> pdb code</div>
157 <div class="col-md-6">{{ task.pdbcode }}</div>
159 <li class="list-group-item task-item">
160 <div class="col-md-6"> seed </div>
161 <div class="col-md-6">{{ task.md_seed}}</div>
163 <li class="list-group-item task-item">
164 <div class="col-md-6"> pdbref </div>
165 <div class="col-md-6">{{ task.md_pdbref}}</div>
167 <li class="list-group-item task-item">
168 <div class="col-md-6"> respa </div>
169 <div class="col-md-6">{{ task.md_respa}}</div>
171 <li class="list-group-item task-item">
172 <div class="col-md-6"> temperature </div>
173 <div class="col-md-6">{{ task.md_temp}}</div>
175 <li class="list-group-item task-item">
176 <div class="col-md-6"> nstep </div>
177 <div class="col-md-6">{{ task.md_nstep}}</div>
179 <li class="list-group-item task-item">
180 <div class="col-md-6"> total steps (with restarts) </div>
181 <div class="col-md-6">{{ task.md_total_steps}}</div>
183 <li class="list-group-item task-item">
184 <div class="col-md-6"> ntwe </div>
185 <div class="col-md-6">{{ task.md_ntwe}}</div>
187 <li class="list-group-item task-item">
188 <div class="col-md-6"> ntwx </div>
189 <div class="col-md-6">{{ task.md_ntwx}}</div>
191 <li class="list-group-item task-item">
192 <div class="col-md-6"> dt </div>
193 <div class="col-md-6">{{ task.md_dt}}</div>
195 <li class="list-group-item task-item">
196 <div class="col-md-6"> thermostat </div>
197 <div class="col-md-6">{{ task.md_lang}}</div>
200 {% if task.md_lang == "berendsen" %}
202 <li class="list-group-item task-item">
203 <div class="col-md-6"> tau </div>
204 <div class="col-md-6">{{ task.md_tau}}</div>
209 <li class="list-group-item task-item">
210 <div class="col-md-6"> scal_fric </div>
211 <div class="col-md-6">{{ task.md_scal_fric}}</div>
216 <li class="list-group-item task-item">
217 <div class="col-md-6"> mdpdb </div>
218 <div class="col-md-6">{{ task.md_mdpdb}}</div>
220 <li class="list-group-item task-item">
221 <div class="col-md-6"> RESPA </div>
222 <div class="col-md-6">{{ task.md_respa}}</div>
228 {% if task.type == "remd" or task.type == "dock" %}
230 <li class="list-group-item task-item">
231 <div class="col-md-6"> nrep </div>
232 <div class="col-md-6">{{ task.remd_nrep}}</div>
234 <li class="list-group-item task-item">
235 <div class="col-md-6"> starting </div>
236 <div class="col-md-6">{{ task.md_start}}</div>
239 <li class="list-group-item task-item">
240 <div class="col-md-6"> input pdb </div>
241 <div class="col-md-6">{{ task.myfile1 }}</div>
243 <li class="list-group-item task-item">
244 <div class="col-md-6"> pdb code</div>
245 <div class="col-md-6">{{ task.pdbcode }}</div>
247 {% if task.type == "dock" %}
248 <li class="list-group-item task-item">
249 <div class="col-md-6"> input pdb2 </div>
250 <div class="col-md-6">{{ task.myfile2 }}</div>
252 <li class="list-group-item task-item">
253 <div class="col-md-6"> pdb code2</div>
254 <div class="col-md-6">{{ task.pdbcode2 }}</div>
258 <li class="list-group-item task-item">
259 <div class="col-md-6"> seed </div>
260 <div class="col-md-6">{{ task.md_seed}}</div>
262 <li class="list-group-item task-item">
263 <div class="col-md-6"> pdbref </div>
264 <div class="col-md-6">{{ task.md_pdbref}}</div>
266 {% if task.md_start == "pdbstart" %}
267 <li class="list-group-item task-item">
268 <div class="col-md-6"> preminim maxfun </div>
269 <div class="col-md-6">{{ task.min_maxfun }}</div>
272 <li class="list-group-item task-item">
273 <div class="col-md-6"> respa </div>
274 <div class="col-md-6">{{ task.md_respa}}</div>
276 <li class="list-group-item task-item">
277 <div class="col-md-6"> nstep </div>
278 <div class="col-md-6">{{ task.md_nstep}}</div>
280 <li class="list-group-item task-item">
281 <div class="col-md-6"> total steps (with restarts) </div>
282 <div class="col-md-6">{{ task.md_total_steps}}</div>
284 <li class="list-group-item task-item">
285 <div class="col-md-6"> ntwe </div>
286 <div class="col-md-6">{{ task.md_ntwe}}</div>
288 <li class="list-group-item task-item">
289 <div class="col-md-6"> nstex </div>
290 <div class="col-md-6">{{ task.remd_nstex}}</div>
292 <li class="list-group-item task-item">
293 <div class="col-md-6"> ntwx </div>
294 <div class="col-md-6">{{ task.md_ntwx}}</div>
296 <li class="list-group-item task-item">
297 <div class="col-md-6"> dt </div>
298 <div class="col-md-6">{{ task.md_dt}}</div>
300 <li class="list-group-item task-item">
301 <div class="col-md-6"> thermostat </div>
302 <div class="col-md-6">{{ task.md_lang}}</div>
305 {% if task.md_lang == "berendsen" %}
307 <li class="list-group-item task-item">
308 <div class="col-md-6"> tau </div>
309 <div class="col-md-6">{{ task.md_tau}}</div>
314 <li class="list-group-item task-item">
315 <div class="col-md-6"> scal_fric </div>
316 <div class="col-md-6">{{ task.md_scal_fric}}</div>
321 <li class="list-group-item task-item">
322 <div class="col-md-6"> RESPA </div>
323 <div class="col-md-6">{{ task.md_respa}}</div>
326 <li class="list-group-item task-item">
327 <div class="col-md-6"> temperatures </div>
328 <div class="col-md-6">{{ task.remd_multi_t}}</div>
330 <li class="list-group-item task-item">
331 <div class="col-md-6"> multiplex </div>
332 <div class="col-md-6">{{ task.remd_multi_m}}</div>
334 <li class="list-group-item task-item">
335 <div class="col-md-6"> temperature for clustering</div>
336 <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
338 {% if task.saxs_data != "" %}
339 <li class="list-group-item task-item">
340 <div class="col-md-6"> wsaxs </div>
341 <div class="col-md-6">{{ task.wsaxs }}</div>
343 <li class="list-group-item task-item">
344 <div class="col-md-6"> scal_rad (saxs) </div>
345 <div class="col-md-6">{{ task.scal_rad }}</div>
347 <li class="list-group-item task-item">
348 <div class="col-md-6"> saxs distribution </div>
349 <div class="col-md-6"><pre> {{ task.saxs_data }}</pre></div>
355 <li class="list-group-item task-item">
356 <div class="col-md-6"> Box X Y Z</div>
357 <div class="col-md-2">{{ task.boxx}}</div>
358 <div class="col-md-2">{{ task.boxy}}</div>
359 <div class="col-md-2">{{ task.boxz}}</div>
366 <li class="list-group-item task-item">
367 <div class="col-md-4"> Directory </div>
368 <div class="col-md-8">
369 <a href="/myfiles/list/{{task.jobdirname}}/">
370 {{ task.jobdirname }}
374 <a class="btn btn-default"
375 href="/{{task.id}}/all.zip">
384 {% if task.type == "min" %}
386 <li class="list-group-item task-item">
387 <div class="col-md-2"> Etot </div>
388 <div class="col-md-10">{{ task.etot }}</div>
391 <li class="list-group-item task-item">
392 <div class="col-md-2"> UNRES model </div>
393 <div class="col-md-10">
395 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
397 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
398 width="500"></a> </div>
401 <li class="list-group-item task-item">
402 <div class="col-md-2"> UNRES model NGL viewer</div>
403 <div class="col-md-10" id="viewport_unres"
404 style="width:500px;height:500px;">
410 <li class="list-group-item task-item">
411 <div class="col-md-2"> Structure overlap </div>
412 <div class="col-md-10"> <img
413 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
417 <li class="list-group-item task-item">
418 <div class="col-md-2"> Structure overlap NGL viewer</div>
419 <div class="col-md-10" id="viewport_min"
420 style="width:500px;height:500px;">
423 <li class="list-group-item task-item">
424 <div class="col-md-12">
425 <button id="toggleAllatom">Input structure on/off</button>
426 <button id="toggleSidechains2">Side-chains on/off</button>
431 <li class="list-group-item task-item">
432 <div class="col-md-2"> Results </div>
433 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
436 {% if task.type == "md" %}
438 <li class="list-group-item task-item">
439 <div class="col-md-2"> Temperature histogram </div>
440 <div class="col-md-10"> <img
441 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
445 <li class="list-group-item task-item">
446 <div class="col-md-2"> Potential energy </div>
447 <div class="col-md-10"> <img
448 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
452 <li class="list-group-item task-item">
453 <div class="col-md-2"> Movie </div>
454 <div class="col-md-10">
456 <video width="500" height="400"
457 preload="auto" controls="controls">
459 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
460 type="video/ogg; codecs=theora"> </source>
466 {% if task.md_mdpdb %}
467 <li class="list-group-item task-item">
468 <div class="col-md-2"> Trajectory NGL viewer</div>
469 <div class="col-md-10" id="viewport_traj"
470 style="width:500px;height:500px;">
473 <li class="list-group-item task-item">
474 <div class="col-md-6">
475 <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
477 <div class="col-md-6">
478 <button id="toggleRunMDs">run/pause MD</button>
479 <button id="toggleSidechains1">side-chains on/off</button>
485 <li class="list-group-item task-item">
486 <div class="col-md-2"> Radius of gyration based
487 on C<sup>α</sup> coordinates </div>
488 <div class="col-md-10"> <img
489 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
495 {% if task.md_pdbref %}
496 <li class="list-group-item task-item">
497 <div class="col-md-2"> C<sup>α</sup> RMSD </div>
498 <div class="col-md-10"> <img
499 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
503 <li class="list-group-item task-item">
504 <div class="col-md-2"> fraction of native
505 side-chain concacts </div>
506 <div class="col-md-10"> <img
507 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
513 {% if task.md_start == "pdbstart" %}
514 <li class="list-group-item task-item">
515 <div class="col-md-2"> fluctuations </div>
516 <div class="col-md-10"> <img
517 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
521 <li class="list-group-item task-item">
522 <div class="col-md-2"> fluctuations putty on
523 starting structure</div>
524 <div class="col-md-10">
526 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
528 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
529 width="500"></a> </div>
532 <li class="list-group-item task-item">
533 <div class="col-md-2"> fluctuations putty on
534 starting structure NGL viewer</div>
535 <div class="col-md-10" id="viewport_putty"
536 style="width:500px;height:500px;">
547 {% if task.type == "remd" or task.type == "dock" %}
549 <li class="list-group-item task-item">
550 <div class="col-md-2"> Energy histogram </div>
551 <div class="col-md-10"> <img
552 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
556 <li class="list-group-item task-item">
557 <div class="col-md-2"> Energy vs. temperature </div>
558 <div class="col-md-10"> <img
559 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
563 <li class="list-group-item task-item">
564 <div class="col-md-2"> Cv vs. temperature </div>
565 <div class="col-md-10"> <img
566 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
570 {% if task.md_pdbref %}
572 <li class="list-group-item task-item">
573 <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
574 <div class="col-md-10"> <img
575 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
579 <li class="list-group-item task-item">
580 <div class="col-md-2"> potential energy vs.
581 C<sup>α</sup> RMSD</div>
582 <div class="col-md-10"> <img
583 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
587 <li class="list-group-item task-item">
588 <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
589 colored by bath temperature</div>
590 <div class="col-md-10"> <img
591 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
598 <li class="list-group-item task-item">
599 <div class="col-md-2"> exchanges (walk in T) </div>
600 <div class="col-md-10"> <img
601 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
605 {% if task.saxs_data != "" %}
606 <li class="list-group-item task-item">
607 <div class="col-md-2"> P(r) of input SAXS data and
608 calculated for 5 models and the input pdb</div>
609 <div class="col-md-10"> <img
610 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
615 <li class="list-group-item task-item">
616 <div class="col-md-4">
617 <button onclick="plusDivs(-1)">❮</button>
619 <div class="col-md-6">
622 <div class="col-md-2">
623 <button onclick="plusDivs(1)">❯</button>
628 <!-- <li class="list-group-item task-item">
629 <div class="col-md-2"> model1 after conversion
631 {{ task.remd_model1|linebreaks }}
633 <div class="col-md-10">
635 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
637 src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
640 <li class="list-group-item task-item">
641 <div class="col-md-2"> model1
642 {% if not task.damino %}
643 after conversion to allatom
645 {{ task.remd_model1|linebreaks }}
647 <div class="col-md-10" id="viewport_M1"
648 style="width:500px;height:500px;">
651 <li class="list-group-item task-item">
652 <div class="col-md-12">
653 {% if task.md_pdbref %}
654 <button id="toggleRefM1">Reference structure on/off</button>
656 <button id="toggleSidechainsM1">Side-chains on/off</button>
657 <a class="btn btn-default"
658 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
664 <!-- <li class="list-group-item task-item">
665 <div class="col-md-2"> model2 after conversion
667 {{ task.remd_model2|linebreaks }}
669 <div class="col-md-10">
671 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
673 src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
676 <li class="list-group-item task-item">
677 <div class="col-md-2"> model2
678 {% if not task.damino %}
679 after conversion to allatom
681 {{ task.remd_model2|linebreaks }}
683 <div class="col-md-10" id="viewport_M2"
684 style="width:500px;height:500px;">
687 <li class="list-group-item task-item">
688 <div class="col-md-12">
689 {% if task.md_pdbref %}
690 <button id="toggleRefM2">Reference structure on/off</button>
692 <button id="toggleSidechainsM2">Side-chains on/off</button>
693 <a class="btn btn-default"
694 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
701 <!-- <li class="list-group-item task-item">
702 <div class="col-md-2"> model3 after conversion
704 {{ task.remd_model3|linebreaks }}
706 <div class="col-md-10">
708 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
710 src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
713 <li class="list-group-item task-item">
714 <div class="col-md-2"> model3
715 {% if not task.damino %}
716 after conversion to allatom
718 {{ task.remd_model3|linebreaks }}
720 <div class="col-md-10" id="viewport_M3"
721 style="width:500px;height:500px;">
724 <li class="list-group-item task-item">
725 <div class="col-md-12">
726 {% if task.md_pdbref %}
727 <button id="toggleRefM3">Reference structure on/off</button>
729 <button id="toggleSidechainsM3">Side-chains on/off</button>
730 <a class="btn btn-default"
731 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
737 <!-- <li class="list-group-item task-item">
738 <div class="col-md-2"> model4 after conversion
740 {{ task.remd_model4|linebreaks }}
742 <div class="col-md-10">
744 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
746 src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
749 <li class="list-group-item task-item">
750 <div class="col-md-2"> model4
751 {% if not task.damino %}
752 after conversion to allatom
754 {{ task.remd_model4|linebreaks }}
756 <div class="col-md-10" id="viewport_M4"
757 style="width:500px;height:500px;">
760 <li class="list-group-item task-item">
761 <div class="col-md-12">
762 {% if task.md_pdbref %}
763 <button id="toggleRefM4">Reference structure on/off</button>
765 <button id="toggleSidechainsM4">Side-chains on/off</button>
766 <a class="btn btn-default"
767 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
773 <!-- <li class="list-group-item task-item">
774 <div class="col-md-2"> model5 after conversion
776 {{ task.remd_model5|linebreaks }}
778 <div class="col-md-10">
780 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
782 src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
785 <li class="list-group-item task-item">
786 <div class="col-md-2"> model5
787 {% if not task.damino %}
788 after conversion to allatom
790 {{ task.remd_model5|linebreaks }}
792 <div class="col-md-10" id="viewport_M5"
793 style="width:500px;height:500px;">
796 <li class="list-group-item task-item">
797 <div class="col-md-12">
798 {% if task.md_pdbref %}
799 <button id="toggleRefM5">Reference structure on/off</button>
801 <button id="toggleSidechainsM5">Side-chains on/off</button>
802 <a class="btn btn-default"
803 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
815 Regular user cannot use this link.
819 <script src="/static/jquery.min.js"></script>
820 <script src="https://unpkg.com/ngl"></script>
823 $('.majorpointslegend').click(function(){
824 $(this.parentNode).find('.hiders').toggle();
825 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
826 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
828 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
833 {% if task.type == "remd" or task.type == "dock" %}
835 function display_model(numstr){
837 {% if task.md_pdbref %}
838 var stage = new NGL.Stage("viewport_M"+numstr);
839 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
841 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
842 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
844 o.addRepresentation( "line", {name:"refsc",visible: false,
845 sele:"not hydrogen and sidechainAttached"
850 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
852 o.addRepresentation( "licorice",{ name: "unres", color:
853 "residueindex",colorScale:["blue","cyan", "green",
854 "yellow","orange", "red"], sele:".CA"
856 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
857 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
860 o.addRepresentation( "cartoon",{ name: "unres", color:
861 "residueindex",colorScale:["blue","cyan", "green",
862 "yellow","orange", "red"]
864 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
865 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
866 , sele:"not hydrogen and sidechainAttached" })
870 ]).then(function (ol1) {
871 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
876 var toggleAll = document.getElementById( "toggleRefM"+numstr );
877 toggleAll.addEventListener( "click", function(){
879 stage.getRepresentationsByName(
880 "ref" ).list.forEach( function( repre ){
881 repre.setVisibility( !repre.visible );
884 stage.getRepresentationsByName(
885 "refsc" ).list.forEach( function( repre ){
886 repre.setVisibility( !repre.visible );
891 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
892 toggleSidechains.addEventListener( "click", function(){
895 stage.getRepresentationsByName(
896 "refsc" ).list.forEach( function( repre ){
897 repre.setVisibility( !repre.visible );
900 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
901 repre.setVisibility( !repre.visible );
906 var stage = new NGL.Stage("viewport_M"+numstr);
907 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
908 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
910 o.addRepresentation( "licorice",{ name: "unres", color:
911 "residueindex",colorScale:["blue","cyan", "green",
912 "yellow","orange", "red"],sele:".CA"
914 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
915 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
918 o.addRepresentation( "cartoon",{ name: "unres", color:
919 "residueindex",colorScale:["blue","cyan", "green",
920 "yellow","orange", "red"]
922 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
923 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
924 , sele:"not hydrogen and sidechainAttached" });
928 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
929 toggleSidechains.addEventListener( "click", function(){
930 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
931 repre.setVisibility( !repre.visible );
940 window.addEventListener("resize",
942 stage.handleResize();
950 var y = document.getElementsByClassName("model");
953 for (ii = 0; ii < y.length; ii++) {
957 showDivs(slideIndex);
959 function plusDivs(n) {
960 showDivs(slideIndex += n);
963 function showDivs(n) {
965 var x = document.getElementsByClassName("model");
966 if (n > x.length) {slideIndex = 1}
967 if (n < 1) {slideIndex = x.length}
968 for (i = 0; i < x.length; i++) {
969 x[i].style.display = "none";
971 x[slideIndex-1].style.display = "block";
973 if (lista[slideIndex-1] == 0 && slideIndex == 2) {
977 if (lista[slideIndex-1] == 0 && slideIndex == 3) {
981 if (lista[slideIndex-1] == 0 && slideIndex == 4) {
985 if (lista[slideIndex-1] == 0 && slideIndex == 5) {
990 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
995 {% if not task.done %}
999 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
1000 url: "/refresh_done1/{{task.id}}/",
1002 success: function(data) {
1003 document.location.reload();
1005 complete: function() {
1006 // Schedule the next request when the current one's complete
1007 setTimeout(worker, 30000);
1011 $(document).ready(function() {
1012 // run the first time; all subsequent calls will take care of themselves
1013 setTimeout(worker, 30000);
1019 {% if task.type == "min" %}
1021 window.addEventListener("resize",
1023 stage.handleResize();
1026 var stage_unres = new NGL.Stage("viewport_unres");
1027 stage_unres.setParameters( { backgroundColor: "white" } );
1029 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
1031 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
1032 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
1033 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
1034 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
1035 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
1036 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
1037 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
1038 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
1039 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
1040 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
1041 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
1042 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
1043 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
1044 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
1045 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
1046 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
1047 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
1048 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
1049 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
1050 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
1052 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
1054 var shape = new NGL.Shape("shape")
1056 o.addRepresentation("licorice");
1057 o.structure.eachAtom(function(atom){
1058 if (atom.atomname == "CA" && atom.chainname == chain) {
1059 px=CAx+(atom.x-CAx)/2;
1060 py=CAy+(atom.y-CAy)/2;
1061 pz=CAz+(atom.z-CAz)/2;
1062 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
1064 if (atom.atomname == "CA") {
1065 chain= atom.chainname
1070 if (atom.atomname == "CB") {
1074 norm=Math.sqrt(mx*mx+my*my+mz*mz);
1076 var longaxis=resdb[res][4]
1077 var shortaxis=resdb[res][3]
1078 mx = mx /norm*longaxis;
1079 my = my /norm*longaxis;
1080 mz = mz /norm*longaxis;
1082 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
1083 [ resdb[res][0], resdb[res][1], resdb[res][2]],
1084 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
1087 var shapeComp = stage_unres.addComponentFromObject(shape)
1088 shapeComp.addRepresentation("buffer")
1094 var stage = new NGL.Stage("viewport_min");
1095 stage.setParameters( { backgroundColor: "white" } );
1097 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
1098 o.addRepresentation( "backbone",{ color:
1099 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1101 o.addRepresentation( "licorice",{ color:
1102 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
1107 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
1108 o.addRepresentation( "backbone",{ name: "allatom", color:
1109 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
1111 o.addRepresentation( "line",{ name: "allatomsc", color:
1112 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1113 ,sele:"not hydrogen and sidechainAttached"
1117 ]).then(function (ol) {
1118 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
1124 var toggleAll = document.getElementById( "toggleAllatom" );
1125 toggleAll.addEventListener( "click", function(){
1127 stage.getRepresentationsByName(
1128 "allatom" ).list.forEach( function( repre ){
1129 repre.setVisibility( !repre.visible );
1132 stage.getRepresentationsByName(
1133 "allatomsc" ).list.forEach( function( repre ){
1134 repre.setVisibility( !repre.visible );
1138 var toggleSidechains = document.getElementById("toggleSidechains2" );
1139 toggleSidechains.addEventListener( "click", function(){
1142 stage.getRepresentationsByName(
1143 "allatomsc" ).list.forEach( function( repre ){
1144 repre.setVisibility( !repre.visible );
1148 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1149 repre.setVisibility( !repre.visible );
1156 {% if task.type == "md" and task.md_start == "pdbstart" %}
1158 window.addEventListener("resize",
1160 stage.handleResize();
1163 var stage = new NGL.Stage("viewport_putty");
1164 stage.setParameters( { backgroundColor: "white" } );
1166 var tooltip = document.createElement("div")
1167 Object.assign(tooltip.style, {
1171 pointerEvents: "none",
1172 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1175 fontFamily: "sans-serif"
1177 document.body.appendChild(tooltip)
1179 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1181 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1184 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1185 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1189 // remove default hoverPick mouse action
1190 stage.mouseControls.remove("hoverPick")
1192 stage.signals.hovered.add(function (pickingProxy) {
1193 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1194 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1195 var mp = pickingProxy.mouse.position
1196 var bf= atom.bfactor.toFixed(2)
1197 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1198 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1199 tooltip.style.left = mp.x + 3 + "px"
1200 tooltip.style.display = "block"
1202 tooltip.style.display = "none"
1208 {% if task.type == "md" and task.md_mdpdb %}
1210 window.addEventListener("resize",
1212 stage.handleResize();
1215 var stage = new NGL.Stage("viewport_traj");
1216 stage.setParameters( { backgroundColor: "white" } );
1217 stage.setParameters( { cameraType: "orthographic" } );
1220 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1221 asTrajectory: true } ) .then( function( o ){
1222 o.setName ("unres_md");
1223 o.addRepresentation( "backbone",{ color:
1224 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1226 o.addRepresentation( "licorice",{ color:
1227 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1229 o.setPosition([0, 0, 100]);
1234 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1235 toggleSidechains.addEventListener( "click", function(){
1236 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1237 repre.setVisibility( !repre.visible );
1242 function numberWithCommas(x) {
1243 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1245 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1246 var isRunning = false;
1247 toggleRunMDs.addEventListener( "click", function(){
1248 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1249 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1254 trajComp.signals.frameChanged.add(function(){
1255 var fnum=trajComp.trajectory.currentFrame+1;
1256 clipRange.value = fnum;
1257 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1266 var clipRange = document.getElementById( "clipRange" );
1267 var clipRange_val = document.getElementById( "clipRange_val" );
1268 clipRange.oninput = function( e ){
1269 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1270 trajComp.setFrame(e.target.value-1)
1271 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));