new designs for compound query page, WIP

see #43


Former-commit-id: 6863d32646dcfe64d3ad51c428dd28c6358665c4

ippisite/ippidb/models.py

@@ -328,6 +328,19 @@ class Compound(models.Model):
         """
         return RefCompoundBiblio.objects.filter(compound=self)
 
+    @property
+    def pfam_ids(self):
+        """
+        return all PFAM ids for the domain of the proteins of the bound
+        complexes in the PPIs this compound has an action on
+        """
+        pfam_ids = set()
+        for ca in self.compoundaction_set.all():
+            ca.get_complexes()
+            for bound_complex in ca.ppi.get_ppi_bound_complexes():
+                pfam_ids.add(bound_complex.complex.domain.pfam_id)
+        return pfam_ids
+
 class MDDRActivityClass(models.Model):
     name = models.CharField('Activity Class', max_length=100, unique=True)
 

ippisite/ippidb/templates/compound_db_links.html

     {%if compound.pubchem_id or compound.chembl_id or compound.chemspider_id %}
-    <p>in other databases</p>
-    <ul class="list-group">
+    <div class="row">
       {% if compound.pubchem_id %}
-      <li class="list-group-item">PubChem: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank">{{ compound.pubchem_id }}</a></li>
+      <span class="col-sm-4"><a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank"><img src="/static/images/Other/Pubchemlogo.png" style="height: 1.5em;" title="PubChem ID: {{ compound.pubchem_id }}" /></a></span>
       {% endif %}
       {% if compound.chembl_id %}
-      <li class="list-group-item">ChEMBL: <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id}}" target="_blank">{{ compound.chembl_id}}</a></li>
+      <span class="col-sm-4"><a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id }}" target="_blank"><img src="/static/images/Other/Chembl_logo.png" style="height: 1.5em;" title="ChEMBL ID: {{ compound.pubchem_id }}" /></a></span>
       {% endif %}
       {% if compound.chemspider_id %}
-      <li class="list-group-item">ChemSpider: <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank">{{ compound.chemspider_id}}</a></li>
+      <span class="col-sm-4"><a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank"><img src="/static/images/Other/ChemSpider_Logo.png" style="height: 1.5em;" title="ChemSpider ID: {{ compound.chemspider_id }}" /></a></span>
       {% endif %}
-    </ul>
+    </div>
     {% endif %}

ippisite/ippidb/templates/compound_grid_item.html

 <div class="card m-2 border border-info" style="width: 300px">
         <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
         <div class="card-body" style="overflow:hidden; word-wrap:break-word;">
-            {% if compound.common_name %}
-            <p class="card-text">Common name: {{ compound.common_name }}</p>
-            {% endif %}
-            {% if compound.canonical_smile %}
-            <p class="card-text">Canonical SMILES: {{ compound.canonical_smile }}</p>
-            {% endif %}
-            {% if compound.iupac_name %}
-            <p class="card-text">IUPAC name: {{ compound.iupac_name }}</p>
-            {% endif %}
+            <span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span>
+            <p>{% for pfam_id in compound.pfam_ids %}{{ pfam_id }}{% endfor %}</p>
+            <p>Molecular Weight: {{ compound.molecular_weight }} g/mol</p>
         </div>
 </div>
 <!--

ippisite/ippidb/templates/compound_table_item.html

@@ -3,10 +3,8 @@
     <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
   </div>
   <div class="col-sm-9">
+    <span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span>{%if compound.common_name %}<span>Common name: {{ compound.common_name }}</span>{% endif %}
     <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 %}
@@ -14,12 +12,12 @@
       <li class="list-group-item">IUPAC name: {{ compound.iupac_name }}</li>
       {% endif %}
     </ul>
-    <p>in bibliography</p>
+    <p>External links</p>
+    {% include "compound_db_links.html" %}
     <ul class="list-group">
       {% for biblio_ref in compound.biblio_refs %}
       <li class="list-group-item">Mentionned in {% include "biblio_citation.html" with bibliography=biblio_ref.bibliography%} as <i>{{ biblio_ref.compound_name }}</i></li>
       {% endfor %}
     </ul>
-    {% include "compound_db_links.html" %}
   </div>
 </div>