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 }}
367 {% if task.type == "min" %}
369 <li class="list-group-item task-item">
370 <div class="col-md-2"> Etot </div>
371 <div class="col-md-10">{{ task.etot }}</div>
374 <li class="list-group-item task-item">
375 <div class="col-md-2"> UNRES model </div>
376 <div class="col-md-10">
378 href="/myfiles/download-file/{{task.jobdirname}}/unres.pse">
380 src="/myfiles/download-file/{{task.jobdirname}}/unres.png"
381 width="500"></a> </div>
384 <li class="list-group-item task-item">
385 <div class="col-md-2"> UNRES model NGL viewer</div>
386 <div class="col-md-10" id="viewport_unres"
387 style="width:500px;height:500px;">
393 <li class="list-group-item task-item">
394 <div class="col-md-2"> Structure overlap </div>
395 <div class="col-md-10"> <img
396 src="/myfiles/download-file/{{task.jobdirname}}/unres_overlap.png"
400 <li class="list-group-item task-item">
401 <div class="col-md-2"> Structure overlap NGL viewer</div>
402 <div class="col-md-10" id="viewport_min"
403 style="width:500px;height:500px;">
406 <li class="list-group-item task-item">
407 <div class="col-md-12">
408 <button id="toggleAllatom">Input structure on/off</button>
409 <button id="toggleSidechains2">Side-chains on/off</button>
414 <li class="list-group-item task-item">
415 <div class="col-md-2"> Results </div>
416 <div class="col-md-10">{{ task.results_text|linebreaks }}</div>
419 {% if task.type == "md" %}
421 <li class="list-group-item task-item">
422 <div class="col-md-2"> Temperature histogram </div>
423 <div class="col-md-10"> <img
424 src="/myfiles/download-file/{{task.jobdirname}}/temp_hist.png"
428 <li class="list-group-item task-item">
429 <div class="col-md-2"> Potential energy </div>
430 <div class="col-md-10"> <img
431 src="/myfiles/download-file/{{task.jobdirname}}/md_ene.png"
435 <li class="list-group-item task-item">
436 <div class="col-md-2"> Movie </div>
437 <div class="col-md-10">
439 <video width="500" height="400"
440 preload="auto" controls="controls">
442 src="/myfiles/download-file/{{task.jobdirname}}/md.ogv"
443 type="video/ogg; codecs=theora"> </source>
449 {% if task.md_mdpdb %}
450 <li class="list-group-item task-item">
451 <div class="col-md-2"> Trajectory NGL viewer</div>
452 <div class="col-md-10" id="viewport_traj"
453 style="width:500px;height:500px;">
456 <li class="list-group-item task-item">
457 <div class="col-md-6">
458 <input id="clipRange" type="range" value=0 min=0 max= {% widthratio task.md_total_steps task.md_ntwx 1 %} step=1 ></input><span id="clipRange_val">0</span> frame
460 <div class="col-md-6">
461 <button id="toggleRunMDs">run/pause MD</button>
462 <button id="toggleSidechains1">side-chains on/off</button>
468 <li class="list-group-item task-item">
469 <div class="col-md-2"> Radius of gyration based
470 on C<sup>α</sup> coordinates </div>
471 <div class="col-md-10"> <img
472 src="/myfiles/download-file/{{task.jobdirname}}/md_gyr.png"
478 {% if task.md_pdbref %}
479 <li class="list-group-item task-item">
480 <div class="col-md-2"> RMSD </div>
481 <div class="col-md-10"> <img
482 src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
486 <li class="list-group-item task-item">
487 <div class="col-md-2"> fraction of native
488 side-chain concacts </div>
489 <div class="col-md-10"> <img
490 src="/myfiles/download-file/{{task.jobdirname}}/md_fracn.png"
496 {% if task.md_start == "pdbstart" %}
497 <li class="list-group-item task-item">
498 <div class="col-md-2"> fluctuations </div>
499 <div class="col-md-10"> <img
500 src="/myfiles/download-file/{{task.jobdirname}}/fluct_plot.png"
504 <li class="list-group-item task-item">
505 <div class="col-md-2"> fluctuations putty on
506 starting structure</div>
507 <div class="col-md-10">
509 href="/myfiles/download-file/{{task.jobdirname}}/fluct.pse">
511 src="/myfiles/download-file/{{task.jobdirname}}/fluct.png"
512 width="500"></a> </div>
515 <li class="list-group-item task-item">
516 <div class="col-md-2"> fluctuations putty on
517 starting structure NGL viewer</div>
518 <div class="col-md-10" id="viewport_putty"
519 style="width:500px;height:500px;">
530 {% if task.type == "remd" %}
532 <li class="list-group-item task-item">
533 <div class="col-md-2"> Energy histogram </div>
534 <div class="col-md-10"> <img
535 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_hist.png"
539 <li class="list-group-item task-item">
540 <div class="col-md-2"> Energy vs. temperature </div>
541 <div class="col-md-10"> <img
542 src="/myfiles/download-file/{{task.jobdirname}}/remd_Tene.png"
546 <li class="list-group-item task-item">
547 <div class="col-md-2"> Cv vs. temperature </div>
548 <div class="col-md-10"> <img
549 src="/myfiles/download-file/{{task.jobdirname}}/remd_cv.png"
553 {% if task.md_pdbref %}
555 <li class="list-group-item task-item">
556 <div class="col-md-2"> Average RMSD vs. temperature </div>
557 <div class="col-md-10"> <img
558 src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
562 <li class="list-group-item task-item">
563 <div class="col-md-2"> potential energy vs. RMSD</div>
564 <div class="col-md-10"> <img
565 src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
569 <li class="list-group-item task-item">
570 <div class="col-md-2"> RMSD vs. step*replica
571 colored by bath temperature</div>
572 <div class="col-md-10"> <img
573 src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
580 <li class="list-group-item task-item">
581 <div class="col-md-2"> exchanges (walk in T) </div>
582 <div class="col-md-10"> <img
583 src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png"
587 {% if task.saxs_data != "" %}
588 <li class="list-group-item task-item">
589 <div class="col-md-2"> P(r) of input SAXS data and
590 calculated for 5 models and the input pdb</div>
591 <div class="col-md-10"> <img
592 src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
597 <li class="list-group-item task-item">
598 <div class="col-md-4">
599 <button onclick="plusDivs(-1)">❮</button>
601 <div class="col-md-6">
604 <div class="col-md-2">
605 <button onclick="plusDivs(1)">❯</button>
610 <!-- <li class="list-group-item task-item">
611 <div class="col-md-2"> model1 after conversion
613 {{ task.remd_model1|linebreaks }}
615 <div class="col-md-10">
617 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
619 src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
622 <li class="list-group-item task-item">
623 <div class="col-md-2"> model1
624 {% if not task.damino %}
625 after conversion to allatom
627 {{ task.remd_model1|linebreaks }}
629 <div class="col-md-10" id="viewport_M1"
630 style="width:500px;height:500px;">
633 <li class="list-group-item task-item">
634 <div class="col-md-12">
635 {% if task.md_pdbref %}
636 <button id="toggleRefM1">Reference structure on/off</button>
638 <button id="toggleSidechainsM1">Side-chains on/off</button>
639 <a class="btn btn-default"
640 href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>
646 <!-- <li class="list-group-item task-item">
647 <div class="col-md-2"> model2 after conversion
649 {{ task.remd_model2|linebreaks }}
651 <div class="col-md-10">
653 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
655 src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
658 <li class="list-group-item task-item">
659 <div class="col-md-2"> model2
660 {% if not task.damino %}
661 after conversion to allatom
663 {{ task.remd_model2|linebreaks }}
665 <div class="col-md-10" id="viewport_M2"
666 style="width:500px;height:500px;">
669 <li class="list-group-item task-item">
670 <div class="col-md-12">
671 {% if task.md_pdbref %}
672 <button id="toggleRefM2">Reference structure on/off</button>
674 <button id="toggleSidechainsM2">Side-chains on/off</button>
675 <a class="btn btn-default"
676 href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>
683 <!-- <li class="list-group-item task-item">
684 <div class="col-md-2"> model3 after conversion
686 {{ task.remd_model3|linebreaks }}
688 <div class="col-md-10">
690 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
692 src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
695 <li class="list-group-item task-item">
696 <div class="col-md-2"> model3
697 {% if not task.damino %}
698 after conversion to allatom
700 {{ task.remd_model3|linebreaks }}
702 <div class="col-md-10" id="viewport_M3"
703 style="width:500px;height:500px;">
706 <li class="list-group-item task-item">
707 <div class="col-md-12">
708 {% if task.md_pdbref %}
709 <button id="toggleRefM3">Reference structure on/off</button>
711 <button id="toggleSidechainsM3">Side-chains on/off</button>
712 <a class="btn btn-default"
713 href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>
719 <!-- <li class="list-group-item task-item">
720 <div class="col-md-2"> model4 after conversion
722 {{ task.remd_model4|linebreaks }}
724 <div class="col-md-10">
726 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
728 src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
731 <li class="list-group-item task-item">
732 <div class="col-md-2"> model4
733 {% if not task.damino %}
734 after conversion to allatom
736 {{ task.remd_model4|linebreaks }}
738 <div class="col-md-10" id="viewport_M4"
739 style="width:500px;height:500px;">
742 <li class="list-group-item task-item">
743 <div class="col-md-12">
744 {% if task.md_pdbref %}
745 <button id="toggleRefM4">Reference structure on/off</button>
747 <button id="toggleSidechainsM4">Side-chains on/off</button>
748 <a class="btn btn-default"
749 href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>
755 <!-- <li class="list-group-item task-item">
756 <div class="col-md-2"> model5 after conversion
758 {{ task.remd_model5|linebreaks }}
760 <div class="col-md-10">
762 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
764 src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
767 <li class="list-group-item task-item">
768 <div class="col-md-2"> model5
769 {% if not task.damino %}
770 after conversion to allatom
772 {{ task.remd_model5|linebreaks }}
774 <div class="col-md-10" id="viewport_M5"
775 style="width:500px;height:500px;">
778 <li class="list-group-item task-item">
779 <div class="col-md-12">
780 {% if task.md_pdbref %}
781 <button id="toggleRefM5">Reference structure on/off</button>
783 <button id="toggleSidechainsM5">Side-chains on/off</button>
784 <a class="btn btn-default"
785 href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>
797 Regular user cannot use this link.
801 <script src="/static/jquery.min.js"></script>
802 <script src="https://unpkg.com/ngl"></script>
805 $('.majorpointslegend').click(function(){
806 $(this.parentNode).find('.hiders').toggle();
807 if($(this.parentNode).find('.majorpointslegend').text()=='Show input parameters'){
808 $(this.parentNode).find('.majorpointslegend').text('Hide input parameters');
810 $(this.parentNode).find('.majorpointslegend').text('Show input parameters');
815 {% if task.type == "remd" %}
817 function display_model(numstr){
819 {% if task.md_pdbref %}
820 var stage = new NGL.Stage("viewport_M"+numstr);
821 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
823 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/plik1.pdb" ,{defaultRepresentation: false}) .then( function( o ){
824 o.addRepresentation( "cartoon",{ name:"ref", color:"grey"
826 o.addRepresentation( "line", {name:"refsc",visible: false,
827 sele:"not hydrogen and sidechainAttached"
832 "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
834 o.addRepresentation( "licorice",{ name: "unres", color:
835 "residueindex",colorScale:["blue","cyan", "green",
836 "yellow","orange", "red"], sele:".CA"
838 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
839 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
842 o.addRepresentation( "cartoon",{ name: "unres", color:
843 "residueindex",colorScale:["blue","cyan", "green",
844 "yellow","orange", "red"]
846 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
847 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
848 , sele:"not hydrogen and sidechainAttached" })
852 ]).then(function (ol1) {
853 ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
858 var toggleAll = document.getElementById( "toggleRefM"+numstr );
859 toggleAll.addEventListener( "click", function(){
861 stage.getRepresentationsByName(
862 "ref" ).list.forEach( function( repre ){
863 repre.setVisibility( !repre.visible );
866 stage.getRepresentationsByName(
867 "refsc" ).list.forEach( function( repre ){
868 repre.setVisibility( !repre.visible );
873 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
874 toggleSidechains.addEventListener( "click", function(){
877 stage.getRepresentationsByName(
878 "refsc" ).list.forEach( function( repre ){
879 repre.setVisibility( !repre.visible );
882 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
883 repre.setVisibility( !repre.visible );
888 var stage = new NGL.Stage("viewport_M"+numstr);
889 stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
890 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
892 o.addRepresentation( "licorice",{ name: "unres", color:
893 "residueindex",colorScale:["blue","cyan", "green",
894 "yellow","orange", "red"],sele:".CA"
896 o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
897 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
900 o.addRepresentation( "cartoon",{ name: "unres", color:
901 "residueindex",colorScale:["blue","cyan", "green",
902 "yellow","orange", "red"]
904 o.addRepresentation( "line",{ name: "unressc", visible: false, color:
905 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
906 , sele:"not hydrogen and sidechainAttached" });
910 var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
911 toggleSidechains.addEventListener( "click", function(){
912 stage.getRepresentationsByName("unressc").list.forEach( function( repre ){
913 repre.setVisibility( !repre.visible );
922 window.addEventListener("resize",
924 stage.handleResize();
932 var y = document.getElementsByClassName("model");
935 for (ii = 0; ii < y.length; ii++) {
939 showDivs(slideIndex);
941 function plusDivs(n) {
942 showDivs(slideIndex += n);
945 function showDivs(n) {
947 var x = document.getElementsByClassName("model");
948 if (n > x.length) {slideIndex = 1}
949 if (n < 1) {slideIndex = x.length}
950 for (i = 0; i < x.length; i++) {
951 x[i].style.display = "none";
953 x[slideIndex-1].style.display = "block";
955 if (lista[slideIndex-1] == 0 && slideIndex == 2) {
959 if (lista[slideIndex-1] == 0 && slideIndex == 3) {
963 if (lista[slideIndex-1] == 0 && slideIndex == 4) {
967 if (lista[slideIndex-1] == 0 && slideIndex == 5) {
972 if (lista[slideIndex-1] == 0) {lista[slideIndex-1]=1}
977 {% if not task.done %}
981 data:{csrfmiddlewaretoken: '{{ csrf_token }}'},
982 url: "/refresh_done1/{{task.id}}/",
984 success: function(data) {
985 document.location.reload();
987 complete: function() {
988 // Schedule the next request when the current one's complete
989 setTimeout(worker, 30000);
993 $(document).ready(function() {
994 // run the first time; all subsequent calls will take care of themselves
995 setTimeout(worker, 30000);
1001 {% if task.type == "min" %}
1003 window.addEventListener("resize",
1005 stage.handleResize();
1008 var stage_unres = new NGL.Stage("viewport_unres");
1009 stage_unres.setParameters( { backgroundColor: "white" } );
1011 [color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
1013 var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
1014 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
1015 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
1016 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
1017 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
1018 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
1019 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
1020 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
1021 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
1022 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
1023 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
1024 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
1025 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
1026 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
1027 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
1028 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
1029 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
1030 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
1031 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
1032 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
1034 stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
1036 var shape = new NGL.Shape("shape")
1038 o.addRepresentation("licorice");
1039 o.structure.eachAtom(function(atom){
1040 if (atom.atomname == "CA" && atom.chainname == chain) {
1041 px=CAx+(atom.x-CAx)/2;
1042 py=CAy+(atom.y-CAy)/2;
1043 pz=CAz+(atom.z-CAz)/2;
1044 shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
1046 if (atom.atomname == "CA") {
1047 chain= atom.chainname
1052 if (atom.atomname == "CB") {
1056 norm=Math.sqrt(mx*mx+my*my+mz*mz);
1058 var longaxis=resdb[res][4]
1059 var shortaxis=resdb[res][3]
1060 mx = mx /norm*longaxis;
1061 my = my /norm*longaxis;
1062 mz = mz /norm*longaxis;
1064 shape.addEllipsoid([ atom.x, atom.y, atom.z ],
1065 [ resdb[res][0], resdb[res][1], resdb[res][2]],
1066 shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
1069 var shapeComp = stage_unres.addComponentFromObject(shape)
1070 shapeComp.addRepresentation("buffer")
1076 var stage = new NGL.Stage("viewport_min");
1077 stage.setParameters( { backgroundColor: "white" } );
1079 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb" ,{defaultRepresentation: false}) .then( function( o ){
1080 o.addRepresentation( "backbone",{ color:
1081 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1083 o.addRepresentation( "licorice",{ color:
1084 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange","red"]
1089 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik.pdb",{defaultRepresentation: false}) .then( function( o ){
1090 o.addRepresentation( "backbone",{ name: "allatom", color:
1091 "residueindex",colorScale:["blue","cyan", "green","yellow","orange", "red"]
1093 o.addRepresentation( "line",{ name: "allatomsc", color:
1094 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1095 ,sele:"not hydrogen and sidechainAttached"
1099 ]).then(function (ol) {
1100 ol[ 0 ].superpose(ol[ 1 ], false, ".CA")
1106 var toggleAll = document.getElementById( "toggleAllatom" );
1107 toggleAll.addEventListener( "click", function(){
1109 stage.getRepresentationsByName(
1110 "allatom" ).list.forEach( function( repre ){
1111 repre.setVisibility( !repre.visible );
1114 stage.getRepresentationsByName(
1115 "allatomsc" ).list.forEach( function( repre ){
1116 repre.setVisibility( !repre.visible );
1120 var toggleSidechains = document.getElementById("toggleSidechains2" );
1121 toggleSidechains.addEventListener( "click", function(){
1124 stage.getRepresentationsByName(
1125 "allatomsc" ).list.forEach( function( repre ){
1126 repre.setVisibility( !repre.visible );
1130 stage.getRepresentationsByName("licorice").list.forEach( function( repre ){
1131 repre.setVisibility( !repre.visible );
1138 {% if task.type == "md" and task.md_start == "pdbstart" %}
1140 window.addEventListener("resize",
1142 stage.handleResize();
1145 var stage = new NGL.Stage("viewport_putty");
1146 stage.setParameters( { backgroundColor: "white" } );
1148 var tooltip = document.createElement("div")
1149 Object.assign(tooltip.style, {
1153 pointerEvents: "none",
1154 backgroundColor: "rgba( 0, 0, 0, 0.6 )",
1157 fontFamily: "sans-serif"
1159 document.body.appendChild(tooltip)
1161 stage.loadFile("/myfiles/download-file/{{task.jobdirname}}/plik_bf.pdb", {defaultRepresentation: false}).then
1163 o.addRepresentation("tube",{ color: "bfactor" , scale: 0.25,
1166 colorScale:["blue","cyan", "green", "yellow","orange", "red"] });
1167 o.addRepresentation("licorice",{sele:"sidechainAttached and CYS and not hydrogen"});
1171 // remove default hoverPick mouse action
1172 stage.mouseControls.remove("hoverPick")
1174 stage.signals.hovered.add(function (pickingProxy) {
1175 if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) {
1176 var atom = pickingProxy.atom || pickingProxy.closestBondAtom
1177 var mp = pickingProxy.mouse.position
1178 var bf= atom.bfactor.toFixed(2)
1179 tooltip.innerText = atom.qualifiedName()+" Fluctuation="+ bf
1180 tooltip.style.bottom = window.innerHeight - mp.y + 3 + "px"
1181 tooltip.style.left = mp.x + 3 + "px"
1182 tooltip.style.display = "block"
1184 tooltip.style.display = "none"
1190 {% if task.type == "md" and task.md_mdpdb %}
1192 window.addEventListener("resize",
1194 stage.handleResize();
1197 var stage = new NGL.Stage("viewport_traj");
1198 stage.setParameters( { backgroundColor: "white" } );
1199 stage.setParameters( { cameraType: "orthographic" } );
1202 stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/file_MD000.pdb", {
1203 asTrajectory: true } ) .then( function( o ){
1204 o.setName ("unres_md");
1205 o.addRepresentation( "backbone",{ color:
1206 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1208 o.addRepresentation( "licorice",{ color:
1209 "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
1215 var toggleSidechains = document.getElementById( "toggleSidechains1" );
1216 toggleSidechains.addEventListener( "click", function(){
1217 stage.getRepresentationsByName( "licorice" ).list.forEach( function( repre ){
1218 repre.setVisibility( !repre.visible );
1223 function numberWithCommas(x) {
1224 return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
1226 var toggleRunMDs = document.getElementById( "toggleRunMDs" );
1227 var isRunning = false;
1228 toggleRunMDs.addEventListener( "click", function(){
1229 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1230 var player = new NGL.TrajectoryPlayer(trajComp.trajectory, {timeout: 10, mode: "once"});
1235 trajComp.signals.frameChanged.add(function(){
1236 var fnum=trajComp.trajectory.currentFrame;
1237 clipRange.value = fnum;
1238 clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
1247 var clipRange = document.getElementById( "clipRange" );
1248 var clipRange_val = document.getElementById( "clipRange_val" );
1249 clipRange.oninput = function( e ){
1250 var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
1251 trajComp.setFrame(e.target.value)
1252 clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));