compound_card.html 23.5 KB
Newer Older
1
{% extends "base.html" %}
2
{% load customtags %}
3

4
5
6
7
8
{% block extra_js %}
<script src="/static/chartjs/Chart.bundle.js"></script>
<script src="/static/js/ippidb-charts.js" type="text/javascript"></script>
{% endblock %}

9
{% block title %}compound {{ compound.id }} detail{% if compound.common_name %} ({{compound.common_name}}){% endif %}{% endblock %}
10
11

{% block content %}
12
13
14
15
16
17
18
19
20
21
22
23
24
<div id="mainnav">
  <nav class="secondary-nav">
    <div class="inner-wrap nav flex-column nav-pills" style="display: inline;" id="tab" role="tablist">
      <a class="second_nav active" id="compound-tab" data-toggle="pill" href="#compound" role="tab"
        aria-controls="compound" aria-expanded="true">Compound</a>
      <a class="second_nav " id="physicochemistry-tab" data-toggle="pill" href="#physicochemistry" role="tab"
        aria-controls="physicochemistry" aria-expanded="true">Physicochemistry</a>
      <a class="second_nav " id="pharmacology-tab" data-toggle="pill" href="#pharmacology" role="tab"
        aria-controls="pharmacology" aria-expanded="true">Pharmacology</a>
      <a class="second_nav " id="drugsimilarity-tab" data-toggle="pill" href="#drugsimilarity" role="tab"
        aria-controls="drugsimilarity" aria-expanded="true">Drug similarity</a>
    </div>
  </nav>
25
</div>
26
27
28
29
30
31
<div class="inner-wrap">
  <nav class="breadcrumb breadNav" role="navigation">
    <div class="breadNav-label">You are here</div>
    <div aria-labelledby="breadNav-label">
      {% block breadcrumb %} <a href="/compounds/" class="breadNav-link">Query compounds</a> > Compound
      {{ compound.id }}{% endblock %}
32
    </div>
33
  </nav>
34
  <div class="container-fluid inner-wrap compound_header_title" id="compound_header_title">
35
    <div class="row {% if compound.is_validated is False %}bg_warning{% endif %}">
36
      {% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile width=250 height=250%}
37
      <div style="display: flex;
38
      align-items: center;">
39
        {% if compound.is_validated is False %}
40
41
        <h1 class="page-title-warning" style="margin: 0;">Compound {{ compound.id }} - This compound has not been
          validated by a curator yet, data might be incomplete or
42
          inaccurate</h1>
43
44
        {% else %}
        <h1 class="page-title" style="margin: 0;">Compound {{ compound.id }}</h1>
45
46
        {% endif %}
      </div>
47
    </div>
48
49
50
51
  </div>
  <div class="top">

  </div>
52
  <div class="row" style="display: inline-block;height:auto; margin-right: 15px; margin-left: 15px;">
53
54
55
56
57
    <div class="tab-content" id="tabContent">
      <div class="tab-pane fade show active" id="compound" role="tabpanel" aria-labelledby="compound-tab">
        <div class="card">
          <div class="card-body">
            {% include "compound_l_item.html" with compound=compound show_detail=True %}
58
          </div>
59
        </div>
60
61
62
63
      </div>
      <div class="tab-pane fade" id="physicochemistry" role="tabpanel" aria-labelledby="physicochemistry-tab">
        <div class="row d-flex justify-content-center">
          <div class="col-sm-12 col-md-9" style="margin: 10px;">
64
            <h5 class="card_title">Physicochemical filters <span class="info_point" onclick="showLegend('show_legend_physico')"><i class="fas fa-info-circle"></i></span>
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
            </h5>
            <div id="show_legend_physico" style="display: none; padding:8px;">
              <div class="row d-flex justify-content-center" style="    box-shadow: 0 3px 11px 0 rgba(0, 0, 0, 0.2);
              padding-top: 9px;">
                <div class="col-4">
                  <div style="border: 1px solid #f2f2f2;">
                    <div style=" background-color: #f2f2f2;text-align: center; font-family:'BrandonGrotesqueBld';">
                      Caption
                    </div>
                    <div style="padding: 5px;">
                      <p>For each descriptor:</p>
                      <p><i class="fas fa-square" style="color:#c3e6cb;"></i> Rule violation</p>
                      <p><i class="fas fa-square" style="color:#f5c6cb;"></i> Rule violation</p>
                      <p><i class="far fa-square" style="color:#b6bfc7;"></i> Not in the rule</p>
                    </div>
                  </div>
                </div>
                <div class="col-8">
                  <table class="table table-striped legend_table">
                    <thead>
                      <tr>
                        <th>Descriptor</th>
                        <th>Lipinski's RO5</th>
                        <th>Veber</th>
                        <th>Pfizer's 3/75</th>
                      </tr>
                    </thead>
                    <tbody>
                      <tr>
                        <td>MW</td>
                        <td>≤ 500 g/mol</td>
                        <td>-</td>
                        <td>-</td>
                      </tr>
                      <tr>
                        <td>AlogP</td>
                        <td>≤ 5</td>
                        <td>-</td>
                        <td>≤ 3</td>
                      </tr>
                      <tr>
                        <td>HBA</td>
                        <td>≤ 10</td>
                        <td>-</td>
                        <td>-</td>
                      </tr>
                      <tr>
                        <td>HBD</td>
                        <td>≤ 5</td>
                        <td>-</td>
                        <td>-</td>
                      </tr>

                      <tr>
                        <td>(HBA + HBD)</td>
                        <td>-</td>
                        <td>≤ 12</td>
                        <td>-</td>
                      </tr>

                      <tr>
                        <td>TPSA</td>
                        <td>-</td>
                        <td>≤ 140 Å<sup>2</sup></td>
                        <td>≥ 75 Å<sup>2</sup></td>
                      </tr>
                      <tr>
                        <td>RB</td>
                        <td>-</td>
                        <td>≤ 10</td>
                        <td>-</td>
                      </tr>
                    </tbody>
                  </table>
                </div>
              </div>
            </div>
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
            <div>
              <table class="table table-sm col-sm-12 col-md-6 card_border" style="text-align: center;">
                <thead>
                  <tr>
                    <th scope="col" class="card_title col_width"></th>
                    <th scope="col" class="card_title col_width">Descriptor</th>
                    <th scope="col" class="card_title col_width">Lipinski's RO5</th>
                    <th scope="col" class="card_title col_width">Veber</th>
                    <th scope="col" class="card_title col_width">Pfizer's 3/75</th>
                  </tr>
                </thead>
                <tbody>
                  <tr>
                    <th scope="row">Compliance</th>
                    <td></td>
                    <td class="{% status_class compound.lipinsky %}" title="at least 3 criteria ok"></td>
                    <td class="{% status_class compound.veber %}" title="RB and HBA+HBD or TPSA ok"></td>
                    <td class="{% status_class compound.pfizer %}" title="AlogP and TPSA ok"></td>
                  </tr>
                  <tr>
                    <th scope="row">MW</th>
                    <td>{% if compound.molecular_weight is not None %}
                      {{ compound.molecular_weight }} g/mol
                      {% else %}
                      not available
                      {% endif %}</td>
                    <td class="text-center {% status_class compound.lipinsky_mw %}"
                      title="Molecular weight <= 500g/mol">
170

171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
                    </td>
                    <td class="table-light"></td>
                    <td class="table-light"></td>
                  </tr>
                  <tr>
                    <th scope="row">HBA</th>
                    <td>
                      {{ compound.nb_acceptor_h | default_if_none:"not available" }}</td>
                    <td class="text-center {% status_class compound.lipinsky_hba %}" title="HBA <= 10"></td>
                    <td class="table-light"></td>
                    <td class="table-light"></td>
                  </tr>
                  <tr>
                    <th scope="row">HBD</th>
                    <td>
                      {{ compound.nb_donor_h | default_if_none:"not available" }}</td>
                    <td class="text-center {% status_class compound.lipinsky_hbd %}" title="HBD <= 5"></td>
                    <td class="table-light"></td>
                    <td class="table-light"></td>
                  </tr>
                  <tr>
                    <th scope="row">HBA + HBD</th>
                    <td>{{ compound.hba_hbd | default_if_none:"not available" }}</td>
                    <td class="table-light"></td>
                    <td class="text-center {% status_class compound.veber_hba_hbd %}" title="HBD + HBA <= 12">
196
                    </td>
197
198
199
200
201
202
                    <td class="table-light"></td>
                  </tr>
                  <tr>
                    <th scope="row">AlogP</th>
                    <td>{{ compound.a_log_p  | default_if_none:"not available" }}</td>
                    <td class="text-center {% status_class compound.lipinsky_a_log_p %}" title="AlogP <= 5">
203
                    </td>
204
205
206
207
208
209
210
211
212
                    <td class="table-light"></td>
                    <td class="text-center {% status_class compound.pfizer_a_log_p %}" title="AlogP <= 3">
                    </td>
                  </tr>
                  <tr>
                    <th scope="row">TPSA</th>
                    <td>{{ compound.tpsa | default_if_none:"not available" }}</td>
                    <td class="table-light"></td>
                    <td class="text-center {% status_class compound.veber_tpsa %}" title="TPSA <= 140">
213
214
215
216
                    </td>
                    <td class="text-center default_if_none:" not available" }}</td>
                  </tr>
                  <tr>
217
218
219
220
                    <th scope="row">RB</th>
                    <td>{{ compound.nb_rotatable_bonds | default_if_none:"not available"}}</td>
                    <td class="table-light"></td>
                    <td class="text-center {% status_class compound.veber_rb %}" title="RB <= 10">
221
                    </td>
222
223
224
225
                    <td class="table-light"></td>
                  </tr>
                </tbody>
              </table>
226
            </div>
227
            <div class="col" style="margin: 10px;">
228
              <h5 class="card_title">Radar chart<span class="info_point" onclick="showLegend('show_legend_radar')"> <i class="fas fa-info-circle"></i></span>
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
              </h5>
              <div id="show_legend_radar" style="display: none; padding:8px;">
                <div class="row d-flex justify-content-center" style="    box-shadow: 0 3px 11px 0 rgba(0, 0, 0, 0.2);
                padding-top: 9px;">
                  <div class="col-8">
                    <div style="border: 1px solid #f2f2f2;">
                      <div style=" background-color: #f2f2f2;text-align: center; font-family:'BrandonGrotesqueBld';">
                        Caption
                      </div>
                      <div style="padding: 5px;">
                        <p><i class="fas fa-draw-polygon" style="color:#ff6384;"></i> Descriptor's value for the
                          compound</p>
                        <p><i class="fas fa-draw-polygon" style="color:#36a2eb;"></i> Descriptor's threshold</p>
                        <p>Those thresholds correspond either to the limits of both the Lipinski's RO5 and Veber's rule,
                          or to the rule of thumb of Ritchie for the number of aromatic rings - Ar, and the mean values
                          usually observed among drugs for Fsp3 and the number of chiral centers - R/S.</p>
                      </div>
                    </div>
                  </div>
                  <div class="col-4">
                    <table class="table table-striped legend_table">
                      <thead>
                        <tr>
                          <th>Short name</th>
                          <th>Threshold</th>
                        </tr>
                      </thead>
                      <tbody>
                        <tr>
                          <td>MW</td>
                          <td>≤ 500 g/mol</td>
                        </tr>
                        <tr>
                          <td>AlogP</td>
                          <td>≤ 5</td>
                        </tr>
                        <tr>
                          <td>HBD</td>
                          <td>≤ 5</td>
                        </tr>
                        <tr>
                          <td>HBA</td>
                          <td>≤ 10</td>
                        </tr>
                        <tr>
                          <td>TPSA</td>
                          <td>≤ 140 Å<sup>2</sup></td>
                        </tr>
                        <tr>
                          <td>RB</td>
                          <td>≤ 10</td>
                        </tr>
                        <tr>
                          <td>ArRing</td>
                          <td>≤ 4</td>
                        </tr>
                        <tr>
                          <td>Fsp3</td>
                          <td>≥ 0.4</td>
                        </tr>
                        <tr>
                          <td>R/S</td>
                          <td>≥ 1</td>
                        </tr>
                      </tbody>
                    </table>
                  </div>
                </div>
              </div>
298
299
              <div class="card_border">
                {% if compound.molecular_weight is not None %}
300
                <canvas id="radar" data-radarh="500px" data-radarw="500px"></canvas>
301
                <script>
302
303
304
                  $('a.second_nav').on('shown.bs.tab', function (e) {
                    drawCompoundDescriptorRadarChart('radar', {{ compound.molecular_weight }}, {{ compound.a_log_p }}, {{ compound.nb_donor_h }}, {{ compound.nb_acceptor_h }}, {{ compound.tpsa }}, {{ compound.nb_rotatable_bonds }}, {{ compound.nb_benzene_like_rings }}, {{ compound.fsp3 }}, {{ compound.nb_chiral_centers }});          
                  });
305
306
307
308
309
                </script>
                {% else %}
                <p class="text-secondary">Compound properties unavailable</p>
                {% endif %}
              </div>
310
            </div>
311
          </div>
312
313
314
315
316
        </div>
        <div class="row d-flex justify-content-center">
          <div class="col-sm-12 col-md-9" style="margin: 10px;">
            <h5 class="card_title">PCA : iPPI-DB chemical space</h5>
            <div class="card_border">
317

318
319
320
321
              <canvas id="pca_biplot"></canvas>
              <script>
                drawCompoundsBiplotChart('pca_biplot', prepareCompoundFamilyBiplotData({{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}), 'physicochemistry');
              </script>
322
            </div>
323
324
325
326
327
          </div>
          <div class="col-sm-12 col-md-7" style="margin: 10px;">
            <h5 class="card_title">PCA : Correlation circle</h5>
            <div class="card_border">
              <img src="data:image/png;base64,{{ pca_biplot_cc }}" style="width: 100%; height:auto" \>
328
            </div>
329
          </div>
330
        </div>
331
332
333
334
      </div>
      <div class="tab-pane fade" id="pharmacology" role="tabpanel" aria-labelledby="pharmacology-tab">
        <div class="row d-flex justify-content-center">
          <div class="col-sm-12 col-md-9" style="margin: 10px;">
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
            <h5 class="card_title">Efficiencies: iPPI-DB biplot LE versus LLE <span class="info_point"
              onclick="showLegend('show_legend_LLE')"> <i class="fas fa-info-circle fa-sm"></i></span></h5>

            <div id="show_legend_LLE" style="display: none; padding:8px; margin-left: auto;
            margin-right: auto;">
            <div class="row d-flex justify-content-center" style="box-shadow: 0 3px 11px 0 rgba(0, 0, 0, 0.2);
            padding-top: 9px;">
              <div class="col-12" style="margin-bottom: 10px;">
                <div style="border: 1px solid #f2f2f2;">
                  <div style=" background-color: #f2f2f2;text-align: center; font-family:'BrandonGrotesqueBld';">
                    Caption
                  </div>
                  <div style="padding: 5px;">
                    <ul>
                      <li>LE: Ligand Efficiency</li>
                      <img src="/static/images/Other/formLE_petit.png">
                      <li>LLE: Lipophilic Efficiency</li>
                      <img src="/static/images/Other/formLLE_petit.png">
                    </ul>
                    <p>
                      For the calculation of the efficiencies, we select a reference activity such that Ki and Kd
                      are favored over IC50 and EC50 and biochemical assays over cellular assays.
                    </p>
                  </div>
                </div>
              </div>
            </div>
          </div>
            
364
365
366
367
368
            <div class="card_border">
              <canvas id="le_lle_biplot"></canvas>
              <script>
                drawCompoundsBiplotChart('le_lle_biplot', prepareCompoundFamilyBiplotData({{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}), 'pharmacology');
              </script>
369
            </div>
370
          </div>
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
        </div>
        <div class="row d-flex justify-content-center">
          <div class="col-sm-12 col-md-9" style="margin: 10px;">
            <h5 class="card_title">Summary</h5>
            <div class="card_border row" style="text-align: center;">
              <div class="col-md-4">
                <h6 class="card_title">Bibliographic ressources</h6>
                <p>{{ compound.biblio_refs.count }}</p>
              </div>
              <div class="col-md-4">
                <h6 class="card_title">Biochemical tests</h6>
                <p>{{ compound.bioch_tests_count }}</p>
              </div>
              <div class="col-md-4">
                <h6 class="card_title">Cellular tests</h6>
                <p>{{ compound.cell_tests_count }}</p>
387
388
              </div>
            </div>
389
          </div>
390
        </div>
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
        <div class="row d-flex justify-content-center">
          <div class="col-sm-12 col-md-12" style="margin: 10px;">
            <h5 class="card_title">Pharmacological data</h5>
            <div class="card_border">
              <table class="table table-sm col-sm-12 col-md-12">
                <thead style="text-align: center;">
                  <tr>
                    <th class="card_title" scope="col">Bibliography</th>
                    <th class="card_title" scope="col" title="Compound name in publication">Name</th>
                    <th class="card_title" scope="col">Target</th>
                    <th class="card_title" scope="col">Competition</th>
                    <th class="card_title" scope="col">Assay type</th>
                    <th class="card_title" scope="col">Assay name</th>
                    <th class="card_title" scope="col">Cell line</th>
                    <th class="card_title" scope="col">Activity type</th>
                    <th class="card_title" scope="col">Activity</th>
                  </tr>
                </thead>
                <tbody style="text-align: center;">
                  {% for car in compound.compoundactivityresult_set.all %}
                  <tr {% if car.is_best %}class="table-primary" {% endif %}>
                    <td>{% include "biblio_simplelink.html" with bibliography=car.test_activity_description.biblio %}
                    </td>
                    {% for rcb in car.test_activity_description.biblio.refcompoundbiblio_set.all  %}
                    {% if rcb.compound == compound  %}
                    <td>{{ rcb.compound_name }}</td>
                    {% endif %}
                    {% endfor %}
                    <td>{{ car.test_activity_description.protein_domain_bound_complex.name }} <br /><a
                        href="http://www.uniprot.org/uniprot/{{ car.test_activity_description.protein_domain_bound_complex.protein.uniprot_id }}"
                        target="_blank">{{ car.test_activity_description.protein_domain_bound_complex.protein.uniprot_id }}</a>
                    </td>
                    <td>{{ car.test_activity_description.protein_domain_partner_complex.name }} <br /><a
                        href="http://www.uniprot.org/uniprot/{{ car.test_activity_description.protein_domain_partner_complex.protein.uniprot_id }}"
                        target="_blank">{{ car.test_activity_description.protein_domain_partner_complex.protein.uniprot_id }}</a>
                    </td>
                    <td>{{ car.test_activity_description.get_test_type_display }}</td>
                    <td>{{ car.test_activity_description.test_name }}</td>
                    <td>{{ car.test_activity_description.cell_line.name }}</td>
                    <td>{{ car.get_activity_type_display }}</td>
                    <td>{{ car.activity|floatformat:2 }}</td>
                  </tr>
433
                  {% endfor %}
434
                </tbody>
435
              </table>
436
            </div>
437
          </div>
438
439
        </div>

440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
      </div>
      <div class="tab-pane fade" id="drugsimilarity" role="tabpanel" aria-labelledby="drugsimilarity-tab">
        <table class="table table-striped" style="border:1px solid #E3E3E3;">
          <thead>
            <tr>
              <th title="Tanimoto index" class="table_title">Ta</th>
              <th class="table_title">Structure</th>
              <th class="table_title">Name</th>
              <th class="table_title">Drugbank ID</th>
            </tr>
          </thead>
          <tbody>
            {% for dbct in compound.sorted_similar_drugbank_compounds %}
            <tr>
              <td>{{ dbct.tanimoto }}</td>
              <td>
                {% include "compound_smiles_draw.html" with id=dbct.drugbank_compound.id smile=dbct.drugbank_compound.canonical_smiles %}
              </td>
              <td>{{ dbct.drugbank_compound.common_name }}</td>
              <td><a target="_blank"
                  href="https://www.drugbank.ca/drugs/{{ dbct.drugbank_compound.id }}">{{ dbct.drugbank_compound.id }}</a>
              </td>
            </tr>
            {% endfor %}
          </tbody>
        </table>
      </div>
467
    </div>
468

469
  </div>
470
</div>
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
<script id='JSON_LD' type="application/ld+json">

  {
"url": "{{ compound.get_absolute_url }}",
"inChI": "{{ compound.inchi }}",
"iupacName": "{{ compound.iupac_name }}",
"molecularWeight": {{ compound.molecular_weight }},
"identifier": "{{ compound.id }}",
"inChIKey": "{{ compound.inchi }}",
"@type": "MolecularEntity",
"image": "https://www.ebi.ac.uk/chembl/api/data/image/CHEMBL3623057.svg",
"smiles": [
  "{{ compound.canonical_smile }}"
],
"@context": "http://schema.org"
}

</script>
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
<script>
  var showTab = function (hash) {
    window.location.hash = hash;
    window.scrollTo(0, 0);
  };
  $('a.second_nav').on('shown.bs.tab', function (e) {
    showTab(e.target.hash);
    drawSmiles();
  });
  $(document).ready(function () {
    var tabHash = document.location.hash;
    if ($(tabHash).length == 0) {
      tabHash = $('.second_nav.active').attr('href');
      showTab(tabHash);
    }
    $('[href="' + tabHash + '"]').tab('show');
  });
506
507
508
509
510
511
512
513
514
  function showLegend(legend) {
    var x = document.getElementById(legend);
    console.log(x)
    if (x.style.display === "none") {
      x.style.display = "block";
    } else {
      x.style.display = "none";
    }
  }
515
516
</script>
{% endblock %}