Merge branch 'master' of https://gitlab.pasteur.fr/odoppelt/iPPIDB

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']:

ippisite/ippidb/migrations/0015_auto_20170519_1442.py

+# -*- 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'),
+        ),
+    ]

ippisite/ippidb/migrations/0016_auto_20170519_1453.py

+# -*- 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'),
+        ),
+    ]

ippisite/ippidb/migrations/0017_auto_20170519_1500.py

+# -*- 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'),
+        ),
+    ]

ippisite/ippidb/migrations/0018_auto_20170522_1501.py

+# -*- 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'),
+        ),
+    ]

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)