continue working on compound query interface (#43), WIP

- three visualization modes now
- most of the requested primary information is there


Former-commit-id: 9d5310f273011035e53643d4baf153d4769b6ca8

ippisite/ippidb/models.py

@@ -341,6 +341,16 @@ class Compound(models.Model):
                 pfam_ids.add(bound_complex.complex.domain.pfam_id)
         return pfam_ids
 
+    @property
+    def compound_action_pdb_ids(self):
+        """
+        return all PDB codes of the corresponding compound actions
+        """
+        pdb_ids = set()
+        for ca in self.compoundaction_set.all():
+            pdb_ids.add(ca.pdb_id)
+        return pdb_ids
+
 class MDDRActivityClass(models.Model):
     name = models.CharField('Activity Class', max_length=100, unique=True)
 

ippisite/ippidb/templates/compound_list.html

@@ -67,27 +67,50 @@
             {% endif %}
         </span>
         <span class="btn-group float-right">
-            <a class="btn btn-default btn-outline-primary {% if not display_list %}active{% endif %}" href="#" {% if display_list %}onclick="modifyUrl('display_list', null)"{% endif %}>
+            <a class="btn btn-default btn-outline-primary {% if display == 'v' %}active{% endif %}" href="#" {% if display != 'v' %}onclick="modifyUrl('display', 'v')"{% endif %}>
                 <i class="fa fa-th" title="Vignettes"></i>
             </a>
-            <a class="btn btn-default btn-outline-primary {% if display_list %}active{% endif %}" href="#" {% if not display_list %}onclick="modifyUrl('display_list', true)"{% endif %}>
+            <a class="btn btn-default btn-outline-primary {% if display == 'l' %}active{% endif %}" href="#" {% if display != 'l' %}onclick="modifyUrl('display', 'l')"{% endif %}>
                 <i class="fa fa-bars" title="List"></i>
             </a>
+            <a class="btn btn-default btn-outline-primary {% if display == 't' %}active{% endif %}" href="#" {% if display != 't' %}onclick="modifyUrl('display', 't')"{% endif %}>
+                <i class="fa fa-table" title="Table"></i>
+            </a>
         </span>
         </div>
     </form>
 {% if compounds %}
-    {% if display_list %}
+    <div class="row">
+    {% if display == 'v' %}
+        {% for compound in compounds %}
+            {% include "compound_v_item.html" with compound=compound %}
+        {% endfor %}
+    {% elif display == 'l'%}
         {% for compound in compounds %}
-            {% include "compound_table_item.html" with compound=compound %}
+            {% include "compound_l_item.html" with compound=compound %}
         {% endfor %}
     {% else %}
-    <div class="row">
+        <table class="table">
+            <thead>
+                <tr>
+                    <th scope="col">#</th>
+                    <th scope="col">Common name</th>
+                    <th scope="col">Molecular weight</th>
+                    <th scope="col">AlogP</th>
+                    <th scope="col">PDB ligand</th>
+                    <th scope="col">MDDR phase</th>
+                    <th scope="col">Available tests</th>
+                    <th scope="col">Available publications</th>
+                </tr>
+          </thead>
+          <tbody>
         {% for compound in compounds %}
-            {% include "compound_grid_item.html" with compound=compound %}
+            {% include "compound_t_item.html" with compound=compound %}
         {% endfor %}
-    </div>
+          </tbody>
+          </table>
     {% endif %}
+    </div>
 {% else %}
     <p>Nothing found there!</p>
 {% endif %}					

ippisite/ippidb/templates/compound_t_item.html

+<tr>
+    <th scope="col"><span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span></th>
+    <th scope="col">{{ compound.common_name|default_if_none:"-" }}</th>
+    <th scope="col">{{ compound.molecular_weight}}  g/mol</th>
+    <th scope="col">{{ compound.a_log_p }}</th>
+    <th scope="col">{% for pdb_id in compound.compound_action_pdb_ids %}{{ pdb_id }}{% endfor %}</th>
+    <th scope="col"> ? </th>
+    <th scope="col"> ? </th>
+    <th scope="col">{{ compound.biblio_refs|length }}</th>
+</tr>

ippisite/ippidb/templates/compound_grid_item.html → ippisite/ippidb/templates/compound_v_item.html

@@ -6,23 +6,3 @@
             <p>Molecular Weight: {{ compound.molecular_weight }} g/mol</p>
         </div>
 </div>
-<!--
-<div class="col-md-4 border border-info bg-light">
-  <div class="row border-info d-flex justify-content-center align-content-center">
-    <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
-  </div>
-  <div class="row">
-    <ul class="list-group">
-      {% if compound.common_name %}
-      <li class="list-group-item">Common name: {{ compound.common_name }}</li>
-      {% endif %}
-      {% if compound.canonical_smile %}
-      <li class="list-group-item">Canonical SMILES: {{ compound.canonical_smile }}</li>
-      {% endif %}
-      {% if compound.iupac_name %}
-      <li class="list-group-item">IUPAC name: {{ compound.iupac_name }}</li>
-      {% endif %}
-    </ul>
-  </div>
-</div>
--->

ippisite/ippidb/views.py

@@ -211,7 +211,9 @@ def compound_list(request):
     except EmptyPage:
         # If page is out of range (e.g. 9999), deliver last page of results.
         compounds = paginator.page(paginator.num_pages)
-    display_list = request.GET.get('display_list')
+    display = request.GET.get('display')
+    if display not in ['l', 't']:
+        display = 'v'
     return render(request, 'compound_list.html', {'compounds': compounds,
                                                   'count': count,
                                                   'selected_ppis': selected_ppis,
@@ -226,7 +228,7 @@ def compound_list(request):
                                                   'selected_boundcomplexes': selected_boundcomplexes,
                                                   'boundcomplexes': boundcomplexes,
                                                   'boundcomplexes_all': boundcomplexes_all,
-                                                  'display_list': display_list
+                                                  'display': display
                                                 })
 
 def compound_card(request, compound_id):