add PPI family field to PPIs.

Former-commit-id: a5b2d51710ea8e062168e7e40676d0c86cf7ec4a

ippisite/db.sqlite3.REMOVED.git-id

-b5ded9e1a05b9a0751e6d1addad0faf88524c8ca
\ No newline at end of file
+a45fec449759455268a158a1fc5ca4b76146fb4c
\ No newline at end of file

ippisite/ippidb/management/commands/import_v1_data.py

@@ -8,7 +8,7 @@ from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
     Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
     Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, \
     CompoundAction, TestCytotoxDescription, TestPKDescription, CompoundActivityResult, \
-    CompoundCytotoxicityResult, CompoundPKResult
+    CompoundCytotoxicityResult, CompoundPKResult, PpiFamily
 
 
 class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -221,19 +221,20 @@ class Command(BaseCommand):
                         self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
         if options['ppi']:
             sql_request_string = '''
-select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease, complexe.IDComplexe  from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease, complexe.IDComplexe, ppi.Family  from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
 union
-select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease, complexe.IDComplexe  from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI)'''
+select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease, complexe.IDComplexe, ppi.Family  from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI)'''
             cursor.execute(sql_request_string)
             rows = cursor.fetchall()
             ProteinDomainBoundComplex.objects.all().delete()
             ProteinDomainPartnerComplex.objects.all().delete()
             Disease.objects.all().delete()
             Ppi.objects.all().delete()
+            PpiFamily.objects.all().delete()
             PpiComplex.objects.all().delete()
             CompoundAction.objects.all().delete()
             self.stdout.write(
-                self.style.SUCCESS('Successfully flushed protein domain complex, PPI, compound actions, and disease tables'))
+                self.style.SUCCESS('Successfully flushed protein domain complex, PPI, PPI families, compound actions, and disease tables'))
             ppi_ids_mapping = {}
             protein_domain_bound_complexes_mapping = {}
             for row in rows:
@@ -243,6 +244,8 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                         ppi = Ppi()
                         disease, created = Disease.objects.get_or_create(
                             name=row[7])
+                        ppi_family, created = PpiFamily.objects.get_or_create(
+                            name=row[9])
                         ppi.pdb_id = row[4]
                         ppi.pockets_nb = 1
                         ppi.symmetry = Symmetry.objects.get(code='AS')

ippisite/ippidb/migrations/0033_auto_20180502_1500.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-05-02 15:00
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0032_lellebiplotdata'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PpiFamily',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=30, unique=True, verbose_name='Name')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='ppi',
+            name='family',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.PpiFamily'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -201,6 +201,11 @@ class Disease(models.Model):
     def __str__(self):
         return self.name
 
+class PpiFamily(models.Model):
+    name = models.CharField('Name', max_length=30, unique=True)
+
+    def __str__(self):
+        return self.name
 
 class Ppi(models.Model):
     pdb_id = models.CharField('PDB ID', max_length=4, null=True)
@@ -208,6 +213,7 @@ class Ppi(models.Model):
         'Total number of pockets in the complex', default=1)
     symmetry = models.ForeignKey(Symmetry, models.CASCADE)
     diseases = models.ManyToManyField(Disease)
+    family = models.ForeignKey(PpiFamily, models.CASCADE, null=True)
 
     def __str__(self):
         return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')