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

ippisite/ippidb/admin.py

@@ -20,8 +20,8 @@ class DomainAdmin(admin.ModelAdmin):
 
 @admin.register(ProteinDomainBoundComplex)
 class ProteinDomainBoundComplexAdmin(admin.ModelAdmin):
-    list_display = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
-    list_display_links = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
+    list_display = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p')
+    list_display_links = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p')
 
 @admin.register(ProteinDomainPartnerComplex)
 class ProteinDomainPartnerComplexAdmin(admin.ModelAdmin):

ippisite/ippidb/management/commands/import_v1_data.py

@@ -175,6 +175,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                         ppi = Ppi()
                         disease, created = Disease.objects.get_or_create(name=row[7])
                         ppi.pdb_id = row[4]
+                        ppi.pockets_nb = 1
                         ppi.symmetry = Symmetry.objects.get(code='AS')
                         ppi.save()
                         ppi.diseases.add(disease)
@@ -194,7 +195,6 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     c.ppc_copy_nb = row[2]
                     if isinstance(c, ProteinDomainBoundComplex):
                         c.ppp_copy_nb_per_p = 1
-                        c.pockets_nb = 1
                     c.save()
                     # create the PpiComplex object
                     ppi_complex = PpiComplex()
@@ -223,7 +223,12 @@ select distinct protein.NumUniprot, domain.PfamNumAccession  , complexe.NbCopy,
                     compound.is_macrocycle = (row[4]=='Y')
                     compound.aromatic_ratio = row[5]
                     compound.balaban_index = row[6]
-                    compound.balaban_index = row[6]
+                    compound.fsp3 = row[7] #Csp3Ratio
+                    compound.gc_molar_refractivity=row[10] #GCMolarRefractivity
+                    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.save()
                 except Exception as e:
                     if options['stoponfail']:

ippisite/ippidb/migrations/0014_auto_20170519_1243.py

+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-19 12:43
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0013_auto_20170518_1943'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='proteindomainboundcomplex',
+            name='pockets_nb',
+        ),
+        migrations.AddField(
+            model_name='ppi',
+            name='pockets_nb',
+            field=models.IntegerField(default=1, verbose_name='Total number of pockets in the complex'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -131,7 +131,6 @@ class ProteinDomainComplex(models.Model):
 
 class ProteinDomainBoundComplex(ProteinDomainComplex):
     ppp_copy_nb_per_p = models.IntegerField('Number of copies of the protein in the pocket')
-    pockets_nb = models.IntegerField('Total number of pockets in the complex')
     class Meta:
         verbose_name_plural = "bound complexes"
     
@@ -158,6 +157,7 @@ class Disease(models.Model):
 
 class Ppi(models.Model):
     pdb_id = models.CharField('PDB ID', max_length=4, null=True)
+    pockets_nb = models.IntegerField('Total number of pockets in the complex', default=1)
     symmetry = models.ForeignKey(Symmetry)
     diseases = models.ManyToManyField(Disease)