From ecf0680a0bb9e3718e93e914c55402492ed47fa4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 18 May 2017 13:54:27 +0200
Subject: [PATCH] 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/db.sqlite3 | Bin 569344 -> 569344 bytes
ippisite/ippidb/forms.py | 10 ++-
.../migrations/0010_auto_20170518_1142.py | 68 ++++++++++++++++++
ippisite/ippidb/models.py | 36 +++++++---
4 files changed, 102 insertions(+), 12 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0010_auto_20170518_1142.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index d0f0db2af8cd80bce56b7148c24a74b09675dec6..585c05bac9b5bb713a7f404b36981aaa02f2ba17 100644
GIT binary patch
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diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index d7364dac..d7ef84c1 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -1,7 +1,7 @@
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']
diff --git a/ippisite/ippidb/migrations/0010_auto_20170518_1142.py b/ippisite/ippidb/migrations/0010_auto_20170518_1142.py
new file mode 100644
index 00000000..520ae2dc
--- /dev/null
+++ b/ippisite/ippidb/migrations/0010_auto_20170518_1142.py
@@ -0,0 +1,68 @@
+# -*- 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'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 226227f7..50288a93 100644
--- a/ippisite/ippidb/models.py
+++ b/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)
--
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