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" %}
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 <li class="list-group-item task-item">
248 <div class="col-md-6"> seed </div>
249 <div class="col-md-6">{{ task.md_seed}}</div>
251 <li class="list-group-item task-item">
252 <div class="col-md-6"> pdbref </div>
253 <div class="col-md-6">{{ task.md_pdbref}}</div>
255 {% if task.md_start == "pdbstart" %}
256 <li class="list-group-item task-item">
257 <div class="col-md-6"> preminim maxfun </div>
258 <div class="col-md-6">{{ task.min_maxfun }}</div>
261 <li class="list-group-item task-item">
262 <div class="col-md-6"> respa </div>
263 <div class="col-md-6">{{ task.md_respa}}</div>
265 <li class="list-group-item task-item">
266 <div class="col-md-6"> nstep </div>
267 <div class="col-md-6">{{ task.md_nstep}}</div>
269 <li class="list-group-item task-item">
270 <div class="col-md-6"> total steps (with restarts) </div>
271 <div class="col-md-6">{{ task.md_total_steps}}</div>
273 <li class="list-group-item task-item">
274 <div class="col-md-6"> ntwe </div>
275 <div class="col-md-6">{{ task.md_ntwe}}</div>
277 <li class="list-group-item task-item">
278 <div class="col-md-6"> nstex </div>
279 <div class="col-md-6">{{ task.remd_nstex}}</div>
281 <li class="list-group-item task-item">
282 <div class="col-md-6"> ntwx </div>
283 <div class="col-md-6">{{ task.md_ntwx}}</div>
285 <li class="list-group-item task-item">
286 <div class="col-md-6"> dt </div>
287 <div class="col-md-6">{{ task.md_dt}}</div>
289 <li class="list-group-item task-item">
290 <div class="col-md-6"> thermostat </div>
291 <div class="col-md-6">{{ task.md_lang}}</div>
294 {% if task.md_lang == "berendsen" %}
296 <li class="list-group-item task-item">
297 <div class="col-md-6"> tau </div>
298 <div class="col-md-6">{{ task.md_tau}}</div>
303 <li class="list-group-item task-item">
304 <div class="col-md-6"> scal_fric </div>
305 <div class="col-md-6">{{ task.md_scal_fric}}</div>
310 <li class="list-group-item task-item">
311 <div class="col-md-6"> RESPA </div>
312 <div class="col-md-6">{{ task.md_respa}}</div>
315 <li class="list-group-item task-item">
316 <div class="col-md-6"> temperatures </div>
317 <div class="col-md-6">{{ task.remd_multi_t}}</div>
319 <li class="list-group-item task-item">
320 <div class="col-md-6"> multiplex </div>
321 <div class="col-md-6">{{ task.remd_multi_m}}</div>
323 <li class="list-group-item task-item">
324 <div class="col-md-6"> temperature for clustering</div>
325 <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
327 {% if task.saxs_data != "" %}
328 <li class="list-group-item task-item">
329 <div class="col-md-6"> wsaxs </div>
330 <div class="col-md-6">{{ task.wsaxs }}</div>
332 <li class="list-group-item task-item">
333 <div class="col-md-6"> scal_rad (saxs) </div>
334 <div class="col-md-6">{{ task.scal_rad }}</div>
336 <li class="list-group-item task-item">
337 <div class="col-md-6"> saxs distribution </div>
338 <div class="col-md-6"><pre> {{ task.saxs_data }}</pre></div>
344 <li class="list-group-item task-item">
345 <div class="col-md-6"> Box X Y Z</div>
346 <div class="col-md-2">{{ task.boxx}}</div>
347 <div class="col-md-2">{{ task.boxy}}</div>
348 <div class="col-md-2">{{ task.boxz}}</div>
355 <li class="list-group-item task-item">
356 <div class="col-md-4"> Directory </div>
357 <div class="col-md-8">
358 <a href="/myfiles/list/{{task.jobdirname}}/">
359 {{ task.jobdirname }}
363 <a class="btn btn-default"
364 href="/{{task.id}}/all.zip">
373 {% if task.type == "min" %}
375 <li class="list-group-item task-item">
376 <div class="col-md-2"> Etot </div>
377 <div class="col-md-10">{{ task.etot }}</div>
380 <li class="list-group-item task-item">
381 <div class="col-md-2"> UNRES model </div>
382 <div class="col-md-10">
384 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
386 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
387 width="500"></a> </div>
390 <li class="list-group-item task-item">
391 <div class="col-md-2"> UNRES model NGL viewer</div>
392 <div class="col-md-10" id="viewport_unres"
393 style="width:500px;height:500px;">
399 <li class="list-group-item task-item">
400 <div class="col-md-2"> Structure overlap </div>
401 <div class="col-md-10"> <img
402 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
406 <li class="list-group-item task-item">
407 <div class="col-md-2"> Structure overlap NGL viewer</div>
408 <div class="col-md-10" id="viewport_min"
409 style="width:500px;height:500px;">
412 <li class="list-group-item task-item">
413 <div class="col-md-12">
414 <button id="toggleAllatom">Input structure on/off</button>
415 <button id="toggleSidechains2">Side-chains on/off</button>
420 <li class="list-group-item task-item">
421 <div class="col-md-2"> Results </div>
422 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
425 {% if task.type == "md" %}
427 <li class="list-group-item task-item">
428 <div class="col-md-2"> Temperature histogram </div>
429 <div class="col-md-10"> <img
430 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
434 <li class="list-group-item task-item">
435 <div class="col-md-2"> Potential energy </div>
436 <div class="col-md-10"> <img
437 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
441 <li class="list-group-item task-item">
442 <div class="col-md-2"> Movie </div>
443 <div class="col-md-10">
445 <video width="500" height="400"
446 preload="auto" controls="controls">
448 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
449 type="video/ogg; codecs=theora"> </source>
455 {% if task.md_mdpdb %}
456 <li class="list-group-item task-item">
457 <div class="col-md-2"> Trajectory NGL viewer</div>
458 <div class="col-md-10" id="viewport_traj"
459 style="width:500px;height:500px;">
462 <li class="list-group-item task-item">
463 <div class="col-md-6">
464 <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
466 <div class="col-md-6">
467 <button id="toggleRunMDs">run/pause MD</button>
468 <button id="toggleSidechains1">side-chains on/off</button>
474 <li class="list-group-item task-item">
475 <div class="col-md-2"> Radius of gyration based
476 on C<sup>α</sup> coordinates </div>
477 <div class="col-md-10"> <img
478 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
484 {% if task.md_pdbref %}
485 <li class="list-group-item task-item">
486 <div class="col-md-2"> C<sup>α</sup> RMSD </div>
487 <div class="col-md-10"> <img
488 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
492 <li class="list-group-item task-item">
493 <div class="col-md-2"> fraction of native
494 side-chain concacts </div>
495 <div class="col-md-10"> <img
496 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
502 {% if task.md_start == "pdbstart" %}
503 <li class="list-group-item task-item">
504 <div class="col-md-2"> fluctuations </div>
505 <div class="col-md-10"> <img
506 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
510 <li class="list-group-item task-item">
511 <div class="col-md-2"> fluctuations putty on
512 starting structure</div>
513 <div class="col-md-10">
515 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
517 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
518 width="500"></a> </div>
521 <li class="list-group-item task-item">
522 <div class="col-md-2"> fluctuations putty on
523 starting structure NGL viewer</div>
524 <div class="col-md-10" id="viewport_putty"
525 style="width:500px;height:500px;">
536 {% if task.type == "remd" %}
538 <li class="list-group-item task-item">
539 <div class="col-md-2"> Energy histogram </div>
540 <div class="col-md-10"> <img
541 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
545 <li class="list-group-item task-item">
546 <div class="col-md-2"> Energy vs. temperature </div>
547 <div class="col-md-10"> <img
548 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
552 <li class="list-group-item task-item">
553 <div class="col-md-2"> Cv vs. temperature </div>
554 <div class="col-md-10"> <img
555 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
559 {% if task.md_pdbref %}
561 <li class="list-group-item task-item">
562 <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
563 <div class="col-md-10"> <img
564 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
568 <li class="list-group-item task-item">
569 <div class="col-md-2"> potential energy vs.
570 C<sup>α</sup> RMSD</div>
571 <div class="col-md-10"> <img
572 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
576 <li class="list-group-item task-item">
577 <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
578 colored by bath temperature</div>
579 <div class="col-md-10"> <img
580 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
587 <li class="list-group-item task-item">
588 <div class="col-md-2"> exchanges (walk in T) </div>
589 <div class="col-md-10"> <img
590 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
594 {% if task.saxs_data != "" %}
595 <li class="list-group-item task-item">
596 <div class="col-md-2"> P(r) of input SAXS data and
597 calculated for 5 models and the input pdb</div>
598 <div class="col-md-10"> <img
599 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
604 <li class="list-group-item task-item">
605 <div class="col-md-4">
606 <button onclick="plusDivs(-1)">❮</button>
608 <div class="col-md-6">
611 <div class="col-md-2">
612 <button onclick="plusDivs(1)">❯</button>
617 <!-- <li class="list-group-item task-item">
618 <div class="col-md-2"> model1 after conversion
620 {{ task.remd_model1|linebreaks }}
622 <div class="col-md-10">
624 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
626 src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
629 <li class="list-group-item task-item">
630 <div class="col-md-2"> model1
631 {% if not task.damino %}
632 after conversion to allatom
634 {{ task.remd_model1|linebreaks }}
636 <div class="col-md-10" id="viewport_M1"
637 style="width:500px;height:500px;">
640 <li class="list-group-item task-item">
641 <div class="col-md-12">
642 {% if task.md_pdbref %}
643 <button id="toggleRefM1">Reference structure on/off</button>
645 <button id="toggleSidechainsM1">Side-chains on/off</button>
646 <a class="btn btn-default"
647 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
653 <!-- <li class="list-group-item task-item">
654 <div class="col-md-2"> model2 after conversion
656 {{ task.remd_model2|linebreaks }}
658 <div class="col-md-10">
660 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
662 src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
665 <li class="list-group-item task-item">
666 <div class="col-md-2"> model2
667 {% if not task.damino %}
668 after conversion to allatom
670 {{ task.remd_model2|linebreaks }}
672 <div class="col-md-10" id="viewport_M2"
673 style="width:500px;height:500px;">
676 <li class="list-group-item task-item">
677 <div class="col-md-12">
678 {% if task.md_pdbref %}
679 <button id="toggleRefM2">Reference structure on/off</button>
681 <button id="toggleSidechainsM2">Side-chains on/off</button>
682 <a class="btn btn-default"
683 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
690 <!-- <li class="list-group-item task-item">
691 <div class="col-md-2"> model3 after conversion
693 {{ task.remd_model3|linebreaks }}
695 <div class="col-md-10">
697 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
699 src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
702 <li class="list-group-item task-item">
703 <div class="col-md-2"> model3
704 {% if not task.damino %}
705 after conversion to allatom
707 {{ task.remd_model3|linebreaks }}
709 <div class="col-md-10" id="viewport_M3"
710 style="width:500px;height:500px;">
713 <li class="list-group-item task-item">
714 <div class="col-md-12">
715 {% if task.md_pdbref %}
716 <button id="toggleRefM3">Reference structure on/off</button>
718 <button id="toggleSidechainsM3">Side-chains on/off</button>
719 <a class="btn btn-default"
720 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
726 <!-- <li class="list-group-item task-item">
727 <div class="col-md-2"> model4 after conversion
729 {{ task.remd_model4|linebreaks }}
731 <div class="col-md-10">
733 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
735 src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
738 <li class="list-group-item task-item">
739 <div class="col-md-2"> model4
740 {% if not task.damino %}
741 after conversion to allatom
743 {{ task.remd_model4|linebreaks }}
745 <div class="col-md-10" id="viewport_M4"
746 style="width:500px;height:500px;">
749 <li class="list-group-item task-item">
750 <div class="col-md-12">
751 {% if task.md_pdbref %}
752 <button id="toggleRefM4">Reference structure on/off</button>
754 <button id="toggleSidechainsM4">Side-chains on/off</button>
755 <a class="btn btn-default"
756 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
762 <!-- <li class="list-group-item task-item">
763 <div class="col-md-2"> model5 after conversion
765 {{ task.remd_model5|linebreaks }}
767 <div class="col-md-10">
769 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
771 src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
774 <li class="list-group-item task-item">
775 <div class="col-md-2"> model5
776 {% if not task.damino %}
777 after conversion to allatom
779 {{ task.remd_model5|linebreaks }}
781 <div class="col-md-10" id="viewport_M5"
782 style="width:500px;height:500px;">
785 <li class="list-group-item task-item">
786 <div class="col-md-12">
787 {% if task.md_pdbref %}
788 <button id="toggleRefM5">Reference structure on/off</button>
790 <button id="toggleSidechainsM5">Side-chains on/off</button>
791 <a class="btn btn-default"
792 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
804 Regular user cannot use this link.
808 <script src="/static/jquery.min.js"></script>
809 <script src="https://unpkg.com/ngl"></script>
812 $('.majorpointslegend').click(function(){
813 $(this.parentNode).find('.hiders').toggle();
814 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
815 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
817 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
822 {% if task.type == "remd" %}
824 function display_model(numstr){
826 {% if task.md_pdbref %}
827 var stage = new NGL.Stage("viewport_M"+numstr);
828 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
830 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
831 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
833 o.addRepresentation( "line", {name:"refsc",visible: false,
834 sele:"not hydrogen and sidechainAttached"
839 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
841 o.addRepresentation( "licorice",{ name: "unres", color:
842 "residueindex",colorScale:["blue","cyan", "green",
843 "yellow","orange", "red"], sele:".CA"
845 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
846 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
849 o.addRepresentation( "cartoon",{ name: "unres", color:
850 "residueindex",colorScale:["blue","cyan", "green",
851 "yellow","orange", "red"]
853 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
854 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
855 , sele:"not hydrogen and sidechainAttached" })
859 ]).then(function (ol1) {
860 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
865 var toggleAll = document.getElementById( "toggleRefM"+numstr );
866 toggleAll.addEventListener( "click", function(){
868 stage.getRepresentationsByName(
869 "ref" ).list.forEach( function( repre ){
870 repre.setVisibility( !repre.visible );
873 stage.getRepresentationsByName(
874 "refsc" ).list.forEach( function( repre ){
875 repre.setVisibility( !repre.visible );
880 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
881 toggleSidechains.addEventListener( "click", function(){
884 stage.getRepresentationsByName(
885 "refsc" ).list.forEach( function( repre ){
886 repre.setVisibility( !repre.visible );
889 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
890 repre.setVisibility( !repre.visible );
895 var stage = new NGL.Stage("viewport_M"+numstr);
896 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
897 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
899 o.addRepresentation( "licorice",{ name: "unres", color:
900 "residueindex",colorScale:["blue","cyan", "green",
901 "yellow","orange", "red"],sele:".CA"
903 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
904 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
907 o.addRepresentation( "cartoon",{ name: "unres", color:
908 "residueindex",colorScale:["blue","cyan", "green",
909 "yellow","orange", "red"]
911 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
912 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
913 , sele:"not hydrogen and sidechainAttached" });
917 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
918 toggleSidechains.addEventListener( "click", function(){
919 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
920 repre.setVisibility( !repre.visible );
929 window.addEventListener("resize",
931 stage.handleResize();
939 var y = document.getElementsByClassName("model");
942 for (ii = 0; ii < y.length; ii++) {
946 showDivs(slideIndex);
948 function plusDivs(n) {
949 showDivs(slideIndex += n);
952 function showDivs(n) {
954 var x = document.getElementsByClassName("model");
955 if (n > x.length) {slideIndex = 1}
956 if (n < 1) {slideIndex = x.length}
957 for (i = 0; i < x.length; i++) {
958 x[i].style.display = "none";
960 x[slideIndex-1].style.display = "block";
962 if (lista[slideIndex-1] == 0 && slideIndex == 2) {
966 if (lista[slideIndex-1] == 0 && slideIndex == 3) {
970 if (lista[slideIndex-1] == 0 && slideIndex == 4) {
974 if (lista[slideIndex-1] == 0 && slideIndex == 5) {
979 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
984 {% if not task.done %}
988 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
989 url: "/refresh_done1/{{task.id}}/",
991 success: function(data) {
992 document.location.reload();
994 complete: function() {
995 // Schedule the next request when the current one's complete
996 setTimeout(worker, 30000);
1000 $(document).ready(function() {
1001 // run the first time; all subsequent calls will take care of themselves
1002 setTimeout(worker, 30000);
1008 {% if task.type == "min" %}
1010 window.addEventListener("resize",
1012 stage.handleResize();
1015 var stage_unres = new NGL.Stage("viewport_unres");
1016 stage_unres.setParameters( { backgroundColor: "white" } );
1018 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
1020 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
1021 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
1022 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
1023 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
1024 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
1025 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
1026 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
1027 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
1028 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
1029 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
1030 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
1031 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
1032 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
1033 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
1034 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
1035 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
1036 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
1037 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
1038 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
1039 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
1041 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
1043 var shape = new NGL.Shape("shape")
1045 o.addRepresentation("licorice");
1046 o.structure.eachAtom(function(atom){
1047 if (atom.atomname == "CA" && atom.chainname == chain) {
1048 px=CAx+(atom.x-CAx)/2;
1049 py=CAy+(atom.y-CAy)/2;
1050 pz=CAz+(atom.z-CAz)/2;
1051 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
1053 if (atom.atomname == "CA") {
1054 chain= atom.chainname
1059 if (atom.atomname == "CB") {
1063 norm=Math.sqrt(mx*mx+my*my+mz*mz);
1065 var longaxis=resdb[res][4]
1066 var shortaxis=resdb[res][3]
1067 mx = mx /norm*longaxis;
1068 my = my /norm*longaxis;
1069 mz = mz /norm*longaxis;
1071 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
1072 [ resdb[res][0], resdb[res][1], resdb[res][2]],
1073 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
1076 var shapeComp = stage_unres.addComponentFromObject(shape)
1077 shapeComp.addRepresentation("buffer")
1083 var stage = new NGL.Stage("viewport_min");
1084 stage.setParameters( { backgroundColor: "white" } );
1086 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
1087 o.addRepresentation( "backbone",{ color:
1088 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1090 o.addRepresentation( "licorice",{ color:
1091 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
1096 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
1097 o.addRepresentation( "backbone",{ name: "allatom", color:
1098 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
1100 o.addRepresentation( "line",{ name: "allatomsc", color:
1101 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1102 ,sele:"not hydrogen and sidechainAttached"
1106 ]).then(function (ol) {
1107 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
1113 var toggleAll = document.getElementById( "toggleAllatom" );
1114 toggleAll.addEventListener( "click", function(){
1116 stage.getRepresentationsByName(
1117 "allatom" ).list.forEach( function( repre ){
1118 repre.setVisibility( !repre.visible );
1121 stage.getRepresentationsByName(
1122 "allatomsc" ).list.forEach( function( repre ){
1123 repre.setVisibility( !repre.visible );
1127 var toggleSidechains = document.getElementById("toggleSidechains2" );
1128 toggleSidechains.addEventListener( "click", function(){
1131 stage.getRepresentationsByName(
1132 "allatomsc" ).list.forEach( function( repre ){
1133 repre.setVisibility( !repre.visible );
1137 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1138 repre.setVisibility( !repre.visible );
1145 {% if task.type == "md" and task.md_start == "pdbstart" %}
1147 window.addEventListener("resize",
1149 stage.handleResize();
1152 var stage = new NGL.Stage("viewport_putty");
1153 stage.setParameters( { backgroundColor: "white" } );
1155 var tooltip = document.createElement("div")
1156 Object.assign(tooltip.style, {
1160 pointerEvents: "none",
1161 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1164 fontFamily: "sans-serif"
1166 document.body.appendChild(tooltip)
1168 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1170 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1173 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1174 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1178 // remove default hoverPick mouse action
1179 stage.mouseControls.remove("hoverPick")
1181 stage.signals.hovered.add(function (pickingProxy) {
1182 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1183 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1184 var mp = pickingProxy.mouse.position
1185 var bf= atom.bfactor.toFixed(2)
1186 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1187 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1188 tooltip.style.left = mp.x + 3 + "px"
1189 tooltip.style.display = "block"
1191 tooltip.style.display = "none"
1197 {% if task.type == "md" and task.md_mdpdb %}
1199 window.addEventListener("resize",
1201 stage.handleResize();
1204 var stage = new NGL.Stage("viewport_traj");
1205 stage.setParameters( { backgroundColor: "white" } );
1206 stage.setParameters( { cameraType: "orthographic" } );
1209 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1210 asTrajectory: true } ) .then( function( o ){
1211 o.setName ("unres_md");
1212 o.addRepresentation( "backbone",{ color:
1213 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1215 o.addRepresentation( "licorice",{ color:
1216 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1218 o.setPosition([0, 0, 100]);
1223 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1224 toggleSidechains.addEventListener( "click", function(){
1225 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1226 repre.setVisibility( !repre.visible );
1231 function numberWithCommas(x) {
1232 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1234 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1235 var isRunning = false;
1236 toggleRunMDs.addEventListener( "click", function(){
1237 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1238 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1243 trajComp.signals.frameChanged.add(function(){
1244 var fnum=trajComp.trajectory.currentFrame+1;
1245 clipRange.value = fnum;
1246 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1255 var clipRange = document.getElementById( "clipRange" );
1256 var clipRange_val = document.getElementById( "clipRange_val" );
1257 clipRange.oninput = function( e ){
1258 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1259 trajComp.setFrame(e.target.value-1)
1260 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));