From 5c7fd64c4cfa89e4b8e593676694d495642abda5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 11 Apr 2018 16:52:02 +0200
Subject: [PATCH] add model and template code for compound pharmacology tab
still missing:
- sort pXC50 with ki > kd > ic50 > ec50 rule
- add PPI families in the model (and migrate them)
Former-commit-id: 222c0792c744baa037d5c109337d865669e4fa1a
---
ippisite/ippidb/models.py | 25 ++++++++++
ippisite/ippidb/templates/compound_card.html | 49 ++++++++++++++++++++
2 files changed, 74 insertions(+)
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 9031e296..6b3b1ac3 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -451,6 +451,21 @@ class Compound(models.Model):
ppi_name = best_activity_car.test_activity_description.ppi.name
return ppi_name
+ @property
+ def bioch_tests_count(self):
+ """
+ return the number of associated biochemical tests
+ """
+ return self.compoundactivityresult_set.all().filter(test_activity_description__test_type='BIOCH').count()
+
+ @property
+ def cell_tests_count(self):
+ """
+ return the number of associated cell tests
+ """
+ return self.compoundactivityresult_set.all().filter(test_activity_description__test_type='CELL').count()
+
+
class LeLleBiplotData(models.Model):
le_lle_biplot_data = models.CharField('LE-LLE biplot JSON data', max_length=150000, blank=True, null=True)
@@ -561,6 +576,13 @@ class TestActivityDescription(models.Model):
else:
return self.ppi.get_ppi_bound_complexes()
+ @property
+ def protein_domain_partner_complex(self):
+ for ppic in self.ppi.ppicomplex_set.all():
+ if hasattr(ppic.complex,'proteindomainpartnercomplex'):
+ return ppic.complex.proteindomainpartnercomplex
+ return None
+
class CompoundActivityResult(models.Model):
MODULATION_TYPES = (
@@ -592,6 +614,9 @@ class CompoundActivityResult(models.Model):
def __str__(self):
return 'Compound activity result for {} test {} on {}'.format(self.activity_type, self.test_activity_description.id, self.compound.id)
+ def is_best(self):
+ return self.compound.best_pXC50_compound_activity_result.id == self.id
+
class TestCytotoxDescription(models.Model):
biblio = models.ForeignKey(Bibliography, models.CASCADE)
test_name = models.CharField('Cytotoxicity test name', max_length=100)
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index be68a796..889b110f 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -166,6 +166,55 @@
</script>
</div>
</div>
+ <div class="card col-sm-12 col-md-12">
+ <h5 class="card-header">Summary</h5>
+ <div class="card-body row">
+ <div class="col-md-4">
+ <h6>Bibliographic ressources</h6>
+ <p>{{ compound.biblio_refs.count }}</p>
+ </div>
+ <div class="col-md-4">
+ <h6>Biochemical tests</h6>
+ <p>{{ compound.bioch_tests_count }}</p>
+ </div>
+ <div class="col-md-4">
+ <h6>Cellular tests</h6>
+ <p>{{ compound.cell_tests_count }}</p>
+ </div>
+ </div>
+ </div>
+ <div class="card col-sm-12 col-md-12">
+ <h5 class="card-header">Pharmacological data</h5>
+ <div class="card-body">
+ <table class="table table-sm col-sm-12 col-md-6">
+ <thead>
+ <tr>
+ <th class="col-sm-1" scope="col">Bibliography</th>
+ <th class="col-sm-1" scope="col">Target</th>
+ <th class="col-sm-1" scope="col">Competition</th>
+ <th class="col-sm-2" scope="col">Assay type</th>
+ <th class="col-sm-5" scope="col">Assay name</th>
+ <th class="col-sm-1" scope="col">Activity type</th>
+ <th class="col-sm-1" scope="col">Activity</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for car in compound.compoundactivityresult_set.all %}
+ <tr {% if car.is_best %}class="border border-primary"{% endif %}>
+ <td>{% include "biblio_simplelink.html" with bibliography=car.test_activity_description.biblio %}</td>
+ <td>{{ car.test_activity_description.protein_domain_bound_complex.name }} {{ car.test_activity_description.protein_domain_bound_complex.protein.uniprot_id }}</td>
+ <td>{{ car.test_activity_description.protein_domain_partner_complex.name }} {{ car.test_activity_description.protein_domain_partner_complex.protein.uniprot_id }}</td>
+ <td>{{ car.test_activity_description.get_test_type_display }}</td>
+ <td>{{ car.test_activity_description.test_name }}</td>
+ <td>{{ car.get_activity_type_display }}</td>
+ <td>{{ car.activity|floatformat:2 }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
+
</div>
<div class="tab-pane fade" id="v-pills-drugsimilarity" role="tabpanel" aria-labelledby="v-pills-drugsimilarity-tab">
</div>
--
GitLab