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>
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 }}
378 {% if task.type == "min" %}
380 <li class="list-group-item task-item">
381 <div class="col-md-2"> Etot </div>
382 <div class="col-md-10">{{ task.etot }}</div>
385 <li class="list-group-item task-item">
386 <div class="col-md-2"> UNRES model </div>
387 <div class="col-md-10">
389 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
391 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
392 width="500"></a> </div>
395 <li class="list-group-item task-item">
396 <div class="col-md-2"> UNRES model NGL viewer</div>
397 <div class="col-md-10" id="viewport_unres"
398 style="width:500px;height:500px;">
404 <li class="list-group-item task-item">
405 <div class="col-md-2"> Structure overlap </div>
406 <div class="col-md-10"> <img
407 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
411 <li class="list-group-item task-item">
412 <div class="col-md-2"> Structure overlap NGL viewer</div>
413 <div class="col-md-10" id="viewport_min"
414 style="width:500px;height:500px;">
417 <li class="list-group-item task-item">
418 <div class="col-md-12">
419 <button id="toggleAllatom">Input structure on/off</button>
420 <button id="toggleSidechains2">Side-chains on/off</button>
425 <li class="list-group-item task-item">
426 <div class="col-md-2"> Results </div>
427 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
430 {% if task.type == "md" %}
432 <li class="list-group-item task-item">
433 <div class="col-md-2"> Temperature histogram </div>
434 <div class="col-md-10"> <img
435 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
439 <li class="list-group-item task-item">
440 <div class="col-md-2"> Potential energy </div>
441 <div class="col-md-10"> <img
442 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
446 <li class="list-group-item task-item">
447 <div class="col-md-2"> Movie </div>
448 <div class="col-md-10">
450 <video width="500" height="400"
451 preload="auto" controls="controls">
453 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
454 type="video/ogg; codecs=theora"> </source>
460 {% if task.md_mdpdb %}
461 <li class="list-group-item task-item">
462 <div class="col-md-2"> Trajectory NGL viewer</div>
463 <div class="col-md-10" id="viewport_traj"
464 style="width:500px;height:500px;">
467 <li class="list-group-item task-item">
468 <div class="col-md-6">
469 <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
471 <div class="col-md-6">
472 <button id="toggleRunMDs">run/pause MD</button>
473 <button id="toggleSidechains1">side-chains on/off</button>
479 <li class="list-group-item task-item">
480 <div class="col-md-2"> Radius of gyration based
481 on C<sup>α</sup> coordinates </div>
482 <div class="col-md-10"> <img
483 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
489 {% if task.md_pdbref %}
490 <li class="list-group-item task-item">
491 <div class="col-md-2"> RMSD </div>
492 <div class="col-md-10"> <img
493 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
497 <li class="list-group-item task-item">
498 <div class="col-md-2"> fraction of native
499 side-chain concacts </div>
500 <div class="col-md-10"> <img
501 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
507 {% if task.md_start == "pdbstart" %}
508 <li class="list-group-item task-item">
509 <div class="col-md-2"> fluctuations </div>
510 <div class="col-md-10"> <img
511 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
515 <li class="list-group-item task-item">
516 <div class="col-md-2"> fluctuations putty on
517 starting structure</div>
518 <div class="col-md-10">
520 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
522 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
523 width="500"></a> </div>
526 <li class="list-group-item task-item">
527 <div class="col-md-2"> fluctuations putty on
528 starting structure NGL viewer</div>
529 <div class="col-md-10" id="viewport_putty"
530 style="width:500px;height:500px;">
541 {% if task.type == "remd" or task.type == "dock" %}
543 <li class="list-group-item task-item">
544 <div class="col-md-2"> Energy histogram </div>
545 <div class="col-md-10"> <img
546 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
550 <li class="list-group-item task-item">
551 <div class="col-md-2"> Energy vs. temperature </div>
552 <div class="col-md-10"> <img
553 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
557 <li class="list-group-item task-item">
558 <div class="col-md-2"> Cv vs. temperature </div>
559 <div class="col-md-10"> <img
560 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
564 {% if task.md_pdbref %}
566 <li class="list-group-item task-item">
567 <div class="col-md-2"> Average RMSD vs. temperature </div>
568 <div class="col-md-10"> <img
569 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
573 <li class="list-group-item task-item">
574 <div class="col-md-2"> potential energy vs. RMSD</div>
575 <div class="col-md-10"> <img
576 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
580 <li class="list-group-item task-item">
581 <div class="col-md-2"> RMSD vs. step*replica
582 colored by bath temperature</div>
583 <div class="col-md-10"> <img
584 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
591 <li class="list-group-item task-item">
592 <div class="col-md-2"> exchanges (walk in T) </div>
593 <div class="col-md-10"> <img
594 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
598 {% if task.saxs_data != "" %}
599 <li class="list-group-item task-item">
600 <div class="col-md-2"> P(r) of input SAXS data and
601 calculated for 5 models and the input pdb</div>
602 <div class="col-md-10"> <img
603 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
608 <li class="list-group-item task-item">
609 <div class="col-md-4">
610 <button onclick="plusDivs(-1)">❮</button>
612 <div class="col-md-6">
615 <div class="col-md-2">
616 <button onclick="plusDivs(1)">❯</button>
621 <!-- <li class="list-group-item task-item">
622 <div class="col-md-2"> model1 after conversion
624 {{ task.remd_model1|linebreaks }}
626 <div class="col-md-10">
628 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
630 src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
633 <li class="list-group-item task-item">
634 <div class="col-md-2"> model1
635 {% if not task.damino %}
636 after conversion to allatom
638 {{ task.remd_model1|linebreaks }}
640 <div class="col-md-10" id="viewport_M1"
641 style="width:500px;height:500px;">
644 <li class="list-group-item task-item">
645 <div class="col-md-12">
646 {% if task.md_pdbref %}
647 <button id="toggleRefM1">Reference structure on/off</button>
649 <button id="toggleSidechainsM1">Side-chains on/off</button>
650 <a class="btn btn-default"
651 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
657 <!-- <li class="list-group-item task-item">
658 <div class="col-md-2"> model2 after conversion
660 {{ task.remd_model2|linebreaks }}
662 <div class="col-md-10">
664 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
666 src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
669 <li class="list-group-item task-item">
670 <div class="col-md-2"> model2
671 {% if not task.damino %}
672 after conversion to allatom
674 {{ task.remd_model2|linebreaks }}
676 <div class="col-md-10" id="viewport_M2"
677 style="width:500px;height:500px;">
680 <li class="list-group-item task-item">
681 <div class="col-md-12">
682 {% if task.md_pdbref %}
683 <button id="toggleRefM2">Reference structure on/off</button>
685 <button id="toggleSidechainsM2">Side-chains on/off</button>
686 <a class="btn btn-default"
687 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
694 <!-- <li class="list-group-item task-item">
695 <div class="col-md-2"> model3 after conversion
697 {{ task.remd_model3|linebreaks }}
699 <div class="col-md-10">
701 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
703 src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
706 <li class="list-group-item task-item">
707 <div class="col-md-2"> model3
708 {% if not task.damino %}
709 after conversion to allatom
711 {{ task.remd_model3|linebreaks }}
713 <div class="col-md-10" id="viewport_M3"
714 style="width:500px;height:500px;">
717 <li class="list-group-item task-item">
718 <div class="col-md-12">
719 {% if task.md_pdbref %}
720 <button id="toggleRefM3">Reference structure on/off</button>
722 <button id="toggleSidechainsM3">Side-chains on/off</button>
723 <a class="btn btn-default"
724 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
730 <!-- <li class="list-group-item task-item">
731 <div class="col-md-2"> model4 after conversion
733 {{ task.remd_model4|linebreaks }}
735 <div class="col-md-10">
737 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
739 src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
742 <li class="list-group-item task-item">
743 <div class="col-md-2"> model4
744 {% if not task.damino %}
745 after conversion to allatom
747 {{ task.remd_model4|linebreaks }}
749 <div class="col-md-10" id="viewport_M4"
750 style="width:500px;height:500px;">
753 <li class="list-group-item task-item">
754 <div class="col-md-12">
755 {% if task.md_pdbref %}
756 <button id="toggleRefM4">Reference structure on/off</button>
758 <button id="toggleSidechainsM4">Side-chains on/off</button>
759 <a class="btn btn-default"
760 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
766 <!-- <li class="list-group-item task-item">
767 <div class="col-md-2"> model5 after conversion
769 {{ task.remd_model5|linebreaks }}
771 <div class="col-md-10">
773 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
775 src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
778 <li class="list-group-item task-item">
779 <div class="col-md-2"> model5
780 {% if not task.damino %}
781 after conversion to allatom
783 {{ task.remd_model5|linebreaks }}
785 <div class="col-md-10" id="viewport_M5"
786 style="width:500px;height:500px;">
789 <li class="list-group-item task-item">
790 <div class="col-md-12">
791 {% if task.md_pdbref %}
792 <button id="toggleRefM5">Reference structure on/off</button>
794 <button id="toggleSidechainsM5">Side-chains on/off</button>
795 <a class="btn btn-default"
796 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
807 <script src="/static/jquery.min.js"></script>
808 <script src="https://unpkg.com/ngl"></script>
811 $('.majorpointslegend').click(function(){
812 $(this.parentNode).find('.hiders').toggle();
813 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
814 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
816 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
821 {% if task.type == "remd" or task.type == "dock" %}
823 function display_model(numstr){
825 {% if task.md_pdbref %}
826 var stage = new NGL.Stage("viewport_M"+numstr);
827 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
829 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
830 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
832 o.addRepresentation( "line", {name:"refsc",visible: false,
833 sele:"not hydrogen and sidechainAttached"
838 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
840 o.addRepresentation( "licorice",{ name: "unres", color:
841 "residueindex",colorScale:["blue","cyan", "green",
842 "yellow","orange", "red"], sele:".CA"
844 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
845 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
848 o.addRepresentation( "cartoon",{ name: "unres", color:
849 "residueindex",colorScale:["blue","cyan", "green",
850 "yellow","orange", "red"]
852 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
853 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
854 , sele:"not hydrogen and sidechainAttached" })
858 ]).then(function (ol1) {
859 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
864 var toggleAll = document.getElementById( "toggleRefM"+numstr );
865 toggleAll.addEventListener( "click", function(){
867 stage.getRepresentationsByName(
868 "ref" ).list.forEach( function( repre ){
869 repre.setVisibility( !repre.visible );
872 stage.getRepresentationsByName(
873 "refsc" ).list.forEach( function( repre ){
874 repre.setVisibility( !repre.visible );
879 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
880 toggleSidechains.addEventListener( "click", function(){
883 stage.getRepresentationsByName(
884 "refsc" ).list.forEach( function( repre ){
885 repre.setVisibility( !repre.visible );
888 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
889 repre.setVisibility( !repre.visible );
894 var stage = new NGL.Stage("viewport_M"+numstr);
895 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
896 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
898 o.addRepresentation( "licorice",{ name: "unres", color:
899 "residueindex",colorScale:["blue","cyan", "green",
900 "yellow","orange", "red"],sele:".CA"
902 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
903 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
906 o.addRepresentation( "cartoon",{ name: "unres", color:
907 "residueindex",colorScale:["blue","cyan", "green",
908 "yellow","orange", "red"]
910 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
911 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
912 , sele:"not hydrogen and sidechainAttached" });
916 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
917 toggleSidechains.addEventListener( "click", function(){
918 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
919 repre.setVisibility( !repre.visible );
928 window.addEventListener("resize",
930 stage.handleResize();
938 var y = document.getElementsByClassName("model");
941 for (ii = 0; ii < y.length; ii++) {
945 showDivs(slideIndex);
947 function plusDivs(n) {
948 showDivs(slideIndex += n);
951 function showDivs(n) {
953 var x = document.getElementsByClassName("model");
954 if (n > x.length) {slideIndex = 1}
955 if (n < 1) {slideIndex = x.length}
956 for (i = 0; i < x.length; i++) {
957 x[i].style.display = "none";
959 x[slideIndex-1].style.display = "block";
961 if (lista[slideIndex-1] == 0 && slideIndex == 2) {
965 if (lista[slideIndex-1] == 0 && slideIndex == 3) {
969 if (lista[slideIndex-1] == 0 && slideIndex == 4) {
973 if (lista[slideIndex-1] == 0 && slideIndex == 5) {
978 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
983 {% if not task.done %}
987 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
988 url: "/refresh_done/",
990 success: function(data) {
991 document.location.reload();
993 complete: function() {
994 // Schedule the next request when the current one's complete
995 setTimeout(worker, 30000);
999 $(document).ready(function() {
1000 // run the first time; all subsequent calls will take care of themselves
1001 setTimeout(worker, 30000);
1006 {% if task.type == "min" %}
1008 window.addEventListener("resize",
1010 stage.handleResize();
1013 var stage_unres = new NGL.Stage("viewport_unres");
1014 stage_unres.setParameters( { backgroundColor: "white" } );
1016 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
1018 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
1019 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
1020 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
1021 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
1022 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
1023 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
1024 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
1025 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
1026 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
1027 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
1028 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
1029 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
1030 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
1031 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
1032 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
1033 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
1034 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
1035 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
1036 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
1037 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
1039 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
1041 var shape = new NGL.Shape("shape")
1043 o.addRepresentation("licorice");
1044 o.structure.eachAtom(function(atom){
1045 if (atom.atomname == "CA" && atom.chainname == chain) {
1046 px=CAx+(atom.x-CAx)/2;
1047 py=CAy+(atom.y-CAy)/2;
1048 pz=CAz+(atom.z-CAz)/2;
1049 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
1051 if (atom.atomname == "CA") {
1052 chain= atom.chainname
1057 if (atom.atomname == "CB") {
1061 norm=Math.sqrt(mx*mx+my*my+mz*mz);
1063 var longaxis=resdb[res][4]
1064 var shortaxis=resdb[res][3]
1065 mx = mx /norm*longaxis;
1066 my = my /norm*longaxis;
1067 mz = mz /norm*longaxis;
1069 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
1070 [ resdb[res][0], resdb[res][1], resdb[res][2]],
1071 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
1074 var shapeComp = stage_unres.addComponentFromObject(shape)
1075 shapeComp.addRepresentation("buffer")
1081 var stage = new NGL.Stage("viewport_min");
1082 stage.setParameters( { backgroundColor: "white" } );
1084 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
1085 o.addRepresentation( "backbone",{ color:
1086 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1088 o.addRepresentation( "licorice",{ color:
1089 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
1094 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
1095 o.addRepresentation( "backbone",{ name: "allatom", color:
1096 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
1098 o.addRepresentation( "line",{ name: "allatomsc", color:
1099 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1100 ,sele:"not hydrogen and sidechainAttached"
1104 ]).then(function (ol) {
1105 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
1111 var toggleAll = document.getElementById( "toggleAllatom" );
1112 toggleAll.addEventListener( "click", function(){
1114 stage.getRepresentationsByName(
1115 "allatom" ).list.forEach( function( repre ){
1116 repre.setVisibility( !repre.visible );
1119 stage.getRepresentationsByName(
1120 "allatomsc" ).list.forEach( function( repre ){
1121 repre.setVisibility( !repre.visible );
1125 var toggleSidechains = document.getElementById("toggleSidechains2" );
1126 toggleSidechains.addEventListener( "click", function(){
1129 stage.getRepresentationsByName(
1130 "allatomsc" ).list.forEach( function( repre ){
1131 repre.setVisibility( !repre.visible );
1135 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1136 repre.setVisibility( !repre.visible );
1143 {% if task.type == "md" and task.md_start == "pdbstart" %}
1145 window.addEventListener("resize",
1147 stage.handleResize();
1150 var stage = new NGL.Stage("viewport_putty");
1151 stage.setParameters( { backgroundColor: "white" } );
1153 var tooltip = document.createElement("div")
1154 Object.assign(tooltip.style, {
1158 pointerEvents: "none",
1159 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1162 fontFamily: "sans-serif"
1164 document.body.appendChild(tooltip)
1166 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1168 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1171 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1172 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1176 // remove default hoverPick mouse action
1177 stage.mouseControls.remove("hoverPick")
1179 stage.signals.hovered.add(function (pickingProxy) {
1180 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1181 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1182 var mp = pickingProxy.mouse.position
1183 var bf= atom.bfactor.toFixed(2)
1184 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1185 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1186 tooltip.style.left = mp.x + 3 + "px"
1187 tooltip.style.display = "block"
1189 tooltip.style.display = "none"
1195 {% if task.type == "md" and task.md_mdpdb %}
1197 window.addEventListener("resize",
1199 stage.handleResize();
1202 var stage = new NGL.Stage("viewport_traj");
1203 stage.setParameters( { backgroundColor: "white" } );
1204 stage.setParameters( { cameraType: "orthographic" } );
1207 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1208 asTrajectory: true } ) .then( function( o ){
1209 o.setName ("unres_md");
1210 o.addRepresentation( "backbone",{ color:
1211 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1213 o.addRepresentation( "licorice",{ color:
1214 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1216 o.setPosition([0, 0, 100]);
1221 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1222 toggleSidechains.addEventListener( "click", function(){
1223 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1224 repre.setVisibility( !repre.visible );
1229 function numberWithCommas(x) {
1230 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1232 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1233 var isRunning = false;
1234 toggleRunMDs.addEventListener( "click", function(){
1235 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1236 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1241 trajComp.signals.frameChanged.add(function(){
1242 var fnum=trajComp.trajectory.currentFrame+1;
1243 clipRange.value = fnum;
1244 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1253 var clipRange = document.getElementById( "clipRange" );
1254 var clipRange_val = document.getElementById( "clipRange_val" );
1255 clipRange.oninput = function( e ){
1256 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1257 trajComp.setFrame(e.target.value-1)
1258 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));