diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
index bdaa3c932d4fa59e49c154e7e115fc2ca8b41d7e..fd53f17841cc869b6ca829b14b0481d2a188a538 100644
--- a/ippisite/db.sqlite3.REMOVED.git-id
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -1 +1 @@
-b5ded9e1a05b9a0751e6d1addad0faf88524c8ca
\ No newline at end of file
+a45fec449759455268a158a1fc5ca4b76146fb4c
\ No newline at end of file
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index e525b46f460e13f0a66b0eef7a9fd99d9b27e9a5..eaa1b6523bac54833dab33eedfebc66667aad849 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/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')
diff --git a/ippisite/ippidb/migrations/0033_auto_20180502_1500.py b/ippisite/ippidb/migrations/0033_auto_20180502_1500.py
new file mode 100644
index 0000000000000000000000000000000000000000..428dab5fd7e9119d1b164accdf34f34f1699330d
--- /dev/null
+++ b/ippisite/ippidb/migrations/0033_auto_20180502_1500.py
@@ -0,0 +1,28 @@
+# -*- 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'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 6b3b1ac31b91837ae77edfd56acd230349b07281..2ec0acd07776509b9d7feea7f504fd3d91973671 100644
--- a/ippisite/ippidb/models.py
+++ b/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')