multiple model modifications

- separate Ppi into Ppi and PpiComplex classes (fixes #36)
- replace ActivityType table with an enumerated type
- remove complex from foreign keys when not required

ippisite/ippidb/forms.py

 from django.forms import ModelForm
 from django import forms
 from django.db import models
-from .models import Bibliography, Protein, ProteinDomainComplex, Ppi
+from .models import Bibliography, Protein, ProteinDomainComplex, Ppi, PpiComplex
 
 class IdForm(forms.Form):
 	id = forms.CharField(label="",max_length=100, widget=forms.TextInput(attrs={'placeholder': 'PubMed ID / DOI / Patent ID'}))
@@ -24,8 +24,12 @@ class ProteinDomainComplexForm(ModelForm):
 		model = ProteinDomainComplex
 		fields = ['protein', 'domain', 'ppc_copy_nb']
 
-
 class PpiForm(ModelForm):
 	class Meta:
 		model = Ppi
-		fields = ['complex', 'cc_nb', 'pdb_id', 'symmetry']
+		fields = ['pdb_id', 'symmetry']
+
+class PpiComplexForm(ModelForm):
+	class Meta:
+		model = PpiComplex
+		fields = ['complex', 'cc_nb']

ippisite/ippidb/migrations/0010_auto_20170518_1142.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 11:42
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0009_auto_20170517_2020'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PpiComplex',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('cc_nb', models.IntegerField(default=1, verbose_name='Number of copies of the complex in the PPI')),
+                ('complex', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainComplex')),
+            ],
+            options={
+                'verbose_name_plural': 'Ppi complexes',
+            },
+        ),
+        migrations.RemoveField(
+            model_name='ppi',
+            name='cc_nb',
+        ),
+        migrations.RemoveField(
+            model_name='ppi',
+            name='complex',
+        ),
+        migrations.RemoveField(
+            model_name='ppi',
+            name='ppi_id',
+        ),
+        migrations.RemoveField(
+            model_name='testactivitydescription',
+            name='complex',
+        ),
+        migrations.AlterField(
+            model_name='compoundactivityresult',
+            name='activity_type',
+            field=models.CharField(choices=[('pIC50', 'pIC50 (half maximal inhibitory concentration, -log10)'), ('pEC50', 'pEC50 (half maximal effective concentration, -log10)'), ('pKd', 'pKd (dissociation constant, -log10)'), ('pKi', 'pKi (inhibition constant, -log10)')], max_length=5, verbose_name='Activity type'),
+        ),
+        migrations.AlterUniqueTogether(
+            name='cmpdaction',
+            unique_together=set([('compound', 'activation_mode', 'pdb_id')]),
+        ),
+        migrations.RemoveField(
+            model_name='cmpdaction',
+            name='complex',
+        ),
+        migrations.AlterUniqueTogether(
+            name='cmpdaction',
+            unique_together=set([('ppi', 'compound', 'activation_mode', 'pdb_id')]),
+        ),
+        migrations.DeleteModel(
+            name='ActivityType',
+        ),
+        migrations.AddField(
+            model_name='ppicomplex',
+            name='ppi',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -150,12 +150,17 @@ class Symmetry(models.Model):
         return '{} ({})'.format(self.code, self.description)
 
 class Ppi(models.Model):
-    ppi_id = models.IntegerField('PPI identifier')
-    complex = models.ForeignKey(ProteinDomainComplex)
-    cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)
     pdb_id = models.CharField('PDB ID', max_length=4)
     symmetry = models.ForeignKey(Symmetry)
 
+class PpiComplex(models.Model):
+    ppi = models.ForeignKey(Ppi)
+    complex = models.ForeignKey(ProteinDomainComplex)
+    cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)
+
+    class Meta:
+        verbose_name_plural = "Ppi complexes"
+
 class Disease(models.Model):
     ppi = models.ForeignKey(Ppi)
     disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
@@ -261,7 +266,6 @@ class TestActivityDescription(models.Model):
         ('I', 'Inhibition'),
         ('S', 'Stabilization')
     )
-    complex = models.ForeignKey(ProteinDomainBoundComplex)
     biblio = models.ForeignKey(Bibliography)
     ppi = models.ForeignKey(Ppi, blank=True, null=True)  
     test_name = models.CharField('Test name', max_length=100)  
@@ -270,8 +274,12 @@ class TestActivityDescription(models.Model):
     nb_active_compounds = models.IntegerField('Total number of active compounds')  
     cell_line = models.ForeignKey(CellLine)
 
-class ActivityType(models.Model):
-    name = models.CharField('Name', max_length=50, unique=True)
+    def get_complexes(self):
+        return None
+        # if test_modulation_type is Binding, return all bound complexes for the Ppi
+        # if test_modulation_type is Inhibition, return all Ppi complexes
+        # if test_modulation_type is Stabilization, return all bound complexes for the Ppi
+        # this should be added to the Ppi class as well
 
 class CompoundActivityResult(models.Model):
     MODULATION_TYPES = (
@@ -279,9 +287,15 @@ class CompoundActivityResult(models.Model):
         ('I', 'Inhibition'),
         ('S', 'Stabilization')
     )
+    ACTIVITY_TYPES = (
+        ('pIC50','pIC50 (half maximal inhibitory concentration, -log10)'),
+        ('pEC50','pEC50 (half maximal effective concentration, -log10)'),
+        ('pKd','pKd (dissociation constant, -log10)'),
+        ('pKi','pKi (inhibition constant, -log10)'),
+    )
     compound = models.ForeignKey(Compound)  
     test_activity_description = models.ForeignKey(TestActivityDescription)  
-    activity_type = models.ForeignKey(ActivityType)  
+    activity_type = models.CharField('Activity type', max_length=5, choices=ACTIVITY_TYPES)
     activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)  
     modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)  
 
@@ -334,7 +348,6 @@ class CmpdAction(models.Model):
         ('O', 'Orthosteric'),
         ('A', 'Allosteric')
     )
-    complex = models.ForeignKey(ProteinDomainBoundComplex)
     compound = models.ForeignKey(Compound)  
     activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)  
     ppi = models.ForeignKey(Ppi)
@@ -342,7 +355,12 @@ class CmpdAction(models.Model):
     nb_copy_compounds = models.IntegerField('Number of copies for the compound')  
 
     class Meta:
-        unique_together = (('complex', 'compound', 'pdb_id'),)
+        unique_together = (('ppi', 'compound', 'activation_mode', 'pdb_id'),)
+
+    def get_complexes(self):
+        return None
+        # return all bound complexes for the Ppi
+        # this should be added to the Ppi class as well
 
 class RefCompoundBiblio(models.Model):
     compound = models.ForeignKey(Compound)