diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index db5d773a7c69fd5c0d0e7127f3eb1efe378bb8eb..7ec7dd61212668b2fff2d44382e67427c4c30d13 100644
Binary files a/ippisite/db.sqlite3 and b/ippisite/db.sqlite3 differ
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index f5419e9bc6c182f2262b7447d36e855de388c538..de644fccde949c7dd2019a953793a6a7b502fb61 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -228,7 +228,50 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
compound.log_d = row[13] #LogD
compound.a_log_p = row[14] #ALogP
compound.mean_atom_vol_vdw = row[15] #MeanAtomVolVdW
- compound.molecular_weight = row[16]
+ compound.molecular_weight = row[16] #MolecularWeight
+ compound.nb_acceptor_h = row[17] #NbAcceptorH
+ compound.nb_aliphatic_amines = row[18] #NbAliphaticsAmines
+ compound.nb_aromatic_bonds = row[19] #NbAromaticBonds
+ compound.nb_aromatic_ether = row[20] #NbAromaticsEther
+ compound.nb_aromatic_sssr = row[21] #NbAromaticsSSSR
+ compound.nb_atom = row[22] #NbAtom
+ compound.nb_atom_non_h = row[23] #NbAtomNonH
+ compound.nb_benzene_like_rings = row[24] #NbBenzLikeRings
+ compound.nb_bonds = row[25] #NbBonds
+ compound.nb_bonds_non_h = row[26] #NbBondsNonH
+ compound.nb_br = row[27] #NbBr
+ compound.nb_c = row[28] #NbC
+ compound.nb_chiral_centers = row[29] #NbChiralCenters
+ compound.nb_circuits = row[30] #NbCircuits
+ compound.nb_cl = row[31] #NbCl
+ compound.nb_csp2 = row[32] #NbCsp2
+ compound.nb_csp3 = row[33] #NbCsp3
+ compound.nb_donor_h = row[34] #NbDonorH
+ compound.nb_double_bonds = row[35] #NbDoubleBonds
+ compound.nb_f = row[36] #NbF
+ compound.nb_i = row[37] #NbI
+ compound.nb_multiple_bonds = row[38] #NbMultBonds
+ compound.nb_n = row[39] #NbN
+ compound.nb_o = row[40] #NbO
+ compound.nb_rings = row[41] #NbRings
+ compound.nb_rotatable_bonds = row[42] #NbRotatableBonds
+ compound.randic_index = row[44] #RandicIndex
+ compound.rdf070m = row[45] #RDF070m
+ compound.rotatable_bond_fraction = row[46] #RotatableBondFraction
+ compound.sum_atom_polar = row[47] #SumAtomPolar
+ compound.sum_atom_vol_vdw = row[48] #SumAtomVolVdW
+ compound.tpsa = row[51] #TPSA
+ compound.ui = row[52] #Ui
+ compound.wiener_index = row[54] #WienerIndex
+ if row[55]!='N':
+ compound.common_name = row[55] #CmpdNameSh
+ compound.pubchem_id = row[56] #IdPubchem
+ if row[57]!='N':
+ compound.chemspider_id = row[57] #IdPubchem
+ compound.chembl_id = row[58]
+ compound.iupac_name = row[59]
+ #compound.mddr_compound = row[60]
+ #FIXME lookup MDDR to get the right ID
compound.save()
except Exception as e:
if options['stoponfail']:
diff --git a/ippisite/ippidb/migrations/0015_auto_20170519_1442.py b/ippisite/ippidb/migrations/0015_auto_20170519_1442.py
new file mode 100644
index 0000000000000000000000000000000000000000..1fca3005fce46c0e16f303ccfd014beb9c630e59
--- /dev/null
+++ b/ippisite/ippidb/migrations/0015_auto_20170519_1442.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-19 14:42
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0014_auto_20170519_1243'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compound',
+ name='pubchem_id',
+ field=models.CharField(blank=True, max_length=10, null=True, verbose_name='Pubchem ID'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0016_auto_20170519_1453.py b/ippisite/ippidb/migrations/0016_auto_20170519_1453.py
new file mode 100644
index 0000000000000000000000000000000000000000..f33ad147e4718a43b7b49bbe90ed61510e000e8e
--- /dev/null
+++ b/ippisite/ippidb/migrations/0016_auto_20170519_1453.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-19 14:53
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0015_auto_20170519_1442'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compound',
+ name='iupac_name',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name='IUPAC name'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0017_auto_20170519_1500.py b/ippisite/ippidb/migrations/0017_auto_20170519_1500.py
new file mode 100644
index 0000000000000000000000000000000000000000..f62efeeaadac44fe2c45aed5f9a3e3a704165015
--- /dev/null
+++ b/ippisite/ippidb/migrations/0017_auto_20170519_1500.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-19 15:00
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0016_auto_20170519_1453'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compound',
+ name='chembl_id',
+ field=models.CharField(blank=True, max_length=30, null=True, verbose_name='Chembl ID'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0018_auto_20170522_1501.py b/ippisite/ippidb/migrations/0018_auto_20170522_1501.py
new file mode 100644
index 0000000000000000000000000000000000000000..2986ba98f06fc35caa42f508d3876dc97978a3d9
--- /dev/null
+++ b/ippisite/ippidb/migrations/0018_auto_20170522_1501.py
@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 15:01
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0017_auto_20170519_1500'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='MDDRActivityClass',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('activity_class', models.CharField(max_length=100, unique=True, verbose_name='Activity Class')),
+ ],
+ options={
+ 'verbose_name_plural': 'MDDR activity classes',
+ },
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundactivityclass',
+ unique_together=set([]),
+ ),
+ migrations.RemoveField(
+ model_name='mddrcompoundactivityclass',
+ name='mddr_compound',
+ ),
+ migrations.DeleteModel(
+ name='MDDRCompoundActivityClass',
+ ),
+ migrations.AddField(
+ model_name='mddrcompoundimport',
+ name='activity_classes',
+ field=models.ManyToManyField(to='ippidb.MDDRActivityClass'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 5678657f079b2806ecc3062e716539eb0b563a72..48fb10e3e572e09bb0d6d417c1f654449194c7e8 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -236,13 +236,22 @@ class Compound(models.Model):
ui = models.DecimalField('Unsaturation index', max_digits=4, decimal_places=2)
wiener_index = models.IntegerField('Wiener index')
common_name = models.CharField('Common name', unique=True, max_length=20, blank=True, null=True)
- pubchem_id = models.CharField('Pubchem ID', unique=True, max_length=10, blank=True, null=True)
+ pubchem_id = models.CharField('Pubchem ID', max_length=10, blank=True, null=True)
chemspider_id = models.CharField('Chemspider ID', unique=True, max_length=10, blank=True, null=True)
- chembl_id = models.CharField('Chembl ID', unique=True, max_length=30, blank=True, null=True)
- iupac_name = models.CharField('IUPAC name', unique=True, max_length=255, blank=True, null=True)
+ chembl_id = models.CharField('Chembl ID', max_length=30, blank=True, null=True)
+ iupac_name = models.CharField('IUPAC name', max_length=255, blank=True, null=True)
mddr_compound = models.ForeignKey('MDDRCompoundImport', blank=True, null=True)
+class MDDRActivityClass(models.Model):
+ activity_class = models.CharField('Activity Class', max_length=100, unique=True)
+
+ class Meta:
+ verbose_name_plural = "MDDR activity classes"
+
+ def __str__(self):
+ return self.activity_class
+
class MDDRCompoundImport(models.Model):
mddr_compound_id = models.IntegerField('MDDR compound ID')
mddr_name = models.CharField('MDDR name', max_length=40)
@@ -250,6 +259,7 @@ class MDDRCompoundImport(models.Model):
canonical_smile = models.CharField('Canonical Smile', max_length=500, unique=True, blank=True, null=True)
#TODO index this table on canonical_smile
db_import_date = models.DecimalField('MDDR release year/month', max_digits=6, decimal_places=0)
+ activity_classes = models.ManyToManyField(MDDRActivityClass)
class Meta:
# over multiple releases of the MDDR database, the same compound can evolve in its development phase
@@ -257,16 +267,6 @@ class MDDRCompoundImport(models.Model):
unique_together = (('mddr_compound_id', 'mddr_name', 'dvpmt_phase'),)
verbose_name_plural = "MDDR compound imports"
-
-class MDDRCompoundActivityClass(models.Model):
- mddr_compound = models.ForeignKey(MDDRCompoundImport)
- activity_class = models.CharField('Activity Class', max_length=100)
-
- class Meta:
- unique_together = (('mddr_compound', 'activity_class'),)
- verbose_name_plural = "MDDR compound activity classes"
-
-
class MDDRSimilarity(models.Model):
canonical_smile_ippidb = models.CharField('Canonical Smile for IPPIDB compound', max_length=500, unique=True, blank=True, null=True)
canonical_smile_mddr = models.CharField('Canonical Smile for MDDR Compound', max_length=500, unique=True, blank=True, null=True)