diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
deleted file mode 100644
index 54ce807e6aa9dacb5042158a9d03fbb8b299edf6..0000000000000000000000000000000000000000
Binary files a/ippisite/db.sqlite3 and /dev/null differ
diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
new file mode 100644
index 0000000000000000000000000000000000000000..cb9c5e1693a3710e494a1ba429eeae1858babf29
--- /dev/null
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -0,0 +1 @@
+067f156ca37c93920f1a15dac26337a9956fccbb
\ No newline at end of file
diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 84f0182710f92258d32496198e4c561823df6199..3b32cd020b9245306579d28bf9379a49357f6f86 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -20,13 +20,29 @@ class DomainAdmin(admin.ModelAdmin):
@admin.register(ProteinDomainBoundComplex)
class ProteinDomainBoundComplexAdmin(admin.ModelAdmin):
- list_display = ('protein_id', 'domain_id', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
- list_display_links = ('protein_id', 'domain_id', '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):
- list_display = ('protein_id', 'domain_id', 'ppc_copy_nb')
- list_display_links = ('protein_id', 'domain_id', 'ppc_copy_nb')
+ list_display = ('protein', 'domain', 'ppc_copy_nb')
+ list_display_links = ('protein', 'domain', 'ppc_copy_nb')
+
+@admin.register(Symmetry)
+class Symmetry(admin.ModelAdmin):
+ list_display = ('code', 'description')
+
+@admin.register(MDDRCompoundImport)
+class MDDRCompoundImport(admin.ModelAdmin):
+ list_display = ('mddr_name', 'dvpmt_phase', 'canonical_smile')
+
+@admin.register(Compound)
+class Compound(admin.ModelAdmin):
+ list_display = ('iupac_name', 'common_name', 'canonical_smile')
+
+@admin.register(TestActivityDescription)
+class TextActivityDescription(admin.ModelAdmin):
+ list_display = ('test_name', 'test_type', 'test_modulation_type')
for model in apps.get_app_config('ippidb').models.values():
try:
diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index 955a5f723bce8600bb86e28d87dc9b057c4b7255..7b6f3a5464387d28aa106a1e543b2809b470162e 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -1,7 +1,7 @@
from django.forms import ModelForm
from django import forms
from django.db import models
-from .models import Bibliography, Protein, ProteinDomainComplex, Ppi
+from .models import Bibliography, Protein, ProteinDomainComplex, Ppi, PpiComplex
class IdForm(forms.Form):
id = forms.CharField(label="",max_length=100, widget=forms.TextInput(attrs={'placeholder': 'PubMed ID / DOI / Patent ID'}))
@@ -62,10 +62,14 @@ class ProteinDomainComplexTypeForm(forms.Form):
class ProteinDomainComplexForm(ModelForm):
class Meta:
model = ProteinDomainComplex
- fields = ['protein_id', 'domain_id', 'ppc_copy_nb']
-
+ fields = ['protein', 'domain', 'ppc_copy_nb']
class PpiForm(ModelForm):
class Meta:
model = Ppi
- fields = ['complex_id', 'cc_nb', 'pdb_id', 'symmetry_id']
+ fields = ['pdb_id', 'symmetry']
+
+class PpiComplexForm(ModelForm):
+ class Meta:
+ model = PpiComplex
+ fields = ['complex', 'cc_nb']
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 7de942bfb3338deea3efe79377b0147a6ab3eea3..30a3cab000463365178d210dce125f41096eac6e 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -1,8 +1,25 @@
+import glob
+
+from django.utils import timezone
from django.core.management import BaseCommand, CommandError
import mysql.connector
+from pybel import readfile
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
- Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
+ Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine
+
+class MyConverter(mysql.connector.conversion.MySQLConverter):
+
+ def row_to_python(self, row, fields):
+ row = super(MyConverter, self).row_to_python(row, fields)
+
+ def to_unicode(col):
+ if type(col) == bytearray:
+ return col.decode('utf-8')
+ return col
+
+ return[to_unicode(col) for col in row]
class Command(BaseCommand):
@@ -31,11 +48,39 @@ class Command(BaseCommand):
help='Flush and migrate domains',
)
parser.add_argument(
- '--complexes',
+ '--symmetries',
action='store_true',
- dest='complexes',
+ dest='symmetries',
default=False,
- help='Flush and migrate complexes',
+ help='Flush and create symmetries',
+ )
+ parser.add_argument(
+ '--ppi',
+ action='store_true',
+ dest='ppi',
+ default=False,
+ help='Flush and migrate ppis and complexes',
+ )
+ parser.add_argument(
+ '--mddr',
+ action='store_true',
+ dest='mddr',
+ default=False,
+ help='Flush and import MDDR database',
+ )
+ parser.add_argument(
+ '--compound',
+ action='store_true',
+ dest='compound',
+ default=False,
+ help='Flush and migrate compounds',
+ )
+ parser.add_argument(
+ '--test-activity-description',
+ action='store_true',
+ dest='test-activity-description',
+ default=False,
+ help='Flush and migrate test activity descriptions',
)
parser.add_argument(
'--stoponfail',
@@ -47,7 +92,7 @@ class Command(BaseCommand):
def handle(self, *args, **options):
- conn = mysql.connector.connect(host="localhost",user="root",password="ippidb", database="ippidb")
+ conn = mysql.connector.connect(converter_class=MyConverter, host="localhost", user="root", password="ippidb", database="ippidb")
cursor = conn.cursor()
if options['bibliographies']:
cursor.execute("""SELECT * FROM biblio""")
@@ -110,29 +155,83 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
- if options['complexes']:
+ if options['symmetries']:
+ Symmetry.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed symmetries table'))
+ rows = [
+ ['AS', 'asymmetric'],
+ ['C2', 'C2 symmetry'],
+ ['D2', 'D2 symmetry'],
+ ['C3', 'C3 symmetry'],
+ ['D3', 'D3 symmetry'],
+ ['C4', 'C4 symmetry'],
+ ['D4', 'D4 symmetry'],
+ ['C5', 'C5 symmetry'],
+ ['D5', 'D5 symmetry'],
+ ]
+ for row in rows:
+ try:
+ symmetry = Symmetry()
+ symmetry.code = row[0]
+ symmetry.description = row[1]
+ symmetry.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[0], row[1]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
+ else:
+ self.stdout.write(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 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) union select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound 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)'''
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease 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 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()
- self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables'))
+ Disease.objects.all().delete()
+ Ppi.objects.all().delete()
+ PpiComplex.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex, PPI, and disease tables'))
+ ppi_ids_mapping = {}
for row in rows:
try:
- if row[3]=="null":
+ # create or retrieve Ppi object
+ if row[5]=='part1':
+ 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)
+ ppi.save()
+ ppi_ids_mapping[row[6]]=ppi.id
+ else:
+ ppi = Ppi.objects.get(id=ppi_ids_mapping[row[6]])
+ # create a complex
+ if row[3] is None:
c = ProteinDomainPartnerComplex()
else:
c = ProteinDomainBoundComplex()
protein = Protein.objects.get(uniprot_id=row[0])
- c.protein_id = protein
+ c.protein = protein
domain = Domain.objects.get(pfam_acc=row[1])
- c.domain_id = domain
+ c.domain = domain
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()
+ ppi_complex.ppi = ppi
+ ppi_complex.complex = c
+ ppi_complex.cc_nb = 1
+ ppi_complex.save()
except Exception as e:
if options['stoponfail']:
import traceback
@@ -142,3 +241,129 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+ cursor.execute("""SELECT * FROM testActivityDescription""")
+ rows = cursor.fetchall()
+ TestActivityDescription.objects.all().delete()
+ CellLine.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed test activity descriptions table and cell lines table'))
+ for row in rows:
+ try:
+ tad = TestActivityDescription()
+ cursor.execute("""select IDSource from biblio where IDBiblio={}""".format(row[2]))
+ biblio_row = cursor.fetchone()
+ biblio = Bibliography.objects.get(id_source=biblio_row[0])
+ tad.biblio = biblio
+ tad.ppi = Ppi.objects.get(id=ppi_ids_mapping[row[3]])
+ tad.test_name = row[4]
+ tad.test_type = row[7].upper()
+ tad.test_modulation_type = row[8][0]
+ tad.nb_active_compounds = row[9]
+ if row[16] is not None:
+ tad.cell_line, created = CellLine.objects.get_or_create(name=row[16])
+ tad.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[1], row[2]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ if options['mddr']:
+ MDDRCompoundImport.objects.all().delete()
+ MDDRActivityClass.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed MDDR Compound and Activity class tables'))
+ for sdf_file in glob.glob('/home/hmenager/iPPIDB/mddr20151_2d.sdf/*.sdf'):
+ for item in readfile("sdf", sdf_file):
+ try:
+ m = MDDRCompoundImport()
+ m.mddr_name = item.data['MOLNAME']
+ m.canonical_smile = str(item)
+ m.dvpmt_phase = item.data['PHASE']
+ m.db_import_date = timezone.now()
+ m.save()
+ for activity_class_name in item.data['ACTIV_CLASS'].split(','):
+ activity_class, created = MDDRActivityClass.objects.get_or_create(name=activity_class_name)
+ m.activity_classes.add(activity_class)
+ m.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {}'.format(str(item)))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {}'.format(str(item))))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(item.data['MOLNAME'], str(item))))
+ if options['compound']:
+ cursor.execute("""SELECT * FROM compound""")
+ rows = cursor.fetchall()
+ Compound.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed compound table'))
+ for row in rows:
+ try:
+ compound = Compound()
+ compound.canonical_smile = row[1]
+ compound.is_macrocycle = (row[4]=='Y')
+ compound.aromatic_ratio = row[5]
+ 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] #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']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[1], row[2]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
diff --git a/ippisite/ippidb/migrations/0009_auto_20170517_2020.py b/ippisite/ippidb/migrations/0009_auto_20170517_2020.py
new file mode 100644
index 0000000000000000000000000000000000000000..51fbffd8892fe1bb4048f3d395ac5d898cfd12cf
--- /dev/null
+++ b/ippisite/ippidb/migrations/0009_auto_20170517_2020.py
@@ -0,0 +1,196 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-05-17 20:20
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0008_auto_20170329_1441'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='compound',
+ old_name='mddr_compound_id',
+ new_name='mddr_compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='activity_type_id',
+ new_name='activity_type',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='test_activity_description_id',
+ new_name='test_activity_description',
+ ),
+ migrations.RenameField(
+ model_name='compoundcytotoxicityresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundcytotoxicityresult',
+ old_name='test_cytotoxicity_description_id',
+ new_name='test_cytotoxicity_description',
+ ),
+ migrations.RenameField(
+ model_name='compoundpkresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundpkresult',
+ old_name='test_pk_description_id',
+ new_name='test_pk_description',
+ ),
+ migrations.RenameField(
+ model_name='disease',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='mddrcompoundactivityclass',
+ old_name='mddr_compound_id',
+ new_name='mddr_compound',
+ ),
+ migrations.RenameField(
+ model_name='ppi',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='ppi',
+ old_name='symmetry_id',
+ new_name='symmetry',
+ ),
+ migrations.RenameField(
+ model_name='proteindomaincomplex',
+ old_name='domain_id',
+ new_name='domain',
+ ),
+ migrations.RenameField(
+ model_name='proteindomaincomplex',
+ old_name='protein_id',
+ new_name='protein',
+ ),
+ migrations.RenameField(
+ model_name='refcompoundbiblio',
+ old_name='bibliography_id',
+ new_name='bibliography',
+ ),
+ migrations.RenameField(
+ model_name='refcompoundbiblio',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='testcytotoxdescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RenameField(
+ model_name='testpkdescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='dh_Petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='diam_graph_non_h_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='g_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='ig_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='radius_graph_non_h_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='surface_vdw_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='thickness_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='vol_vdw_petitjean',
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='canonical_smile',
+ field=models.CharField(max_length=500, unique=True, verbose_name='Canonical Smile'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('complex', 'compound', 'pdb_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundactivityresult',
+ unique_together=set([('compound', 'test_activity_description', 'activity_type')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundcytotoxicityresult',
+ unique_together=set([('compound', 'test_cytotoxicity_description')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundpkresult',
+ unique_together=set([('compound', 'test_pk_description')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundactivityclass',
+ unique_together=set([('mddr_compound', 'activity_class')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound', 'bibliography')]),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0010_auto_20170518_1142.py b/ippisite/ippidb/migrations/0010_auto_20170518_1142.py
new file mode 100644
index 0000000000000000000000000000000000000000..520ae2dce8e60f030c0fe11f1d218dbad969ca5f
--- /dev/null
+++ b/ippisite/ippidb/migrations/0010_auto_20170518_1142.py
@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 11:42
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0009_auto_20170517_2020'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='PpiComplex',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('cc_nb', models.IntegerField(default=1, verbose_name='Number of copies of the complex in the PPI')),
+ ('complex', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainComplex')),
+ ],
+ options={
+ 'verbose_name_plural': 'Ppi complexes',
+ },
+ ),
+ migrations.RemoveField(
+ model_name='ppi',
+ name='cc_nb',
+ ),
+ migrations.RemoveField(
+ model_name='ppi',
+ name='complex',
+ ),
+ migrations.RemoveField(
+ model_name='ppi',
+ name='ppi_id',
+ ),
+ migrations.RemoveField(
+ model_name='testactivitydescription',
+ name='complex',
+ ),
+ migrations.AlterField(
+ model_name='compoundactivityresult',
+ name='activity_type',
+ field=models.CharField(choices=[('pIC50', 'pIC50 (half maximal inhibitory concentration, -log10)'), ('pEC50', 'pEC50 (half maximal effective concentration, -log10)'), ('pKd', 'pKd (dissociation constant, -log10)'), ('pKi', 'pKi (inhibition constant, -log10)')], max_length=5, verbose_name='Activity type'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('compound', 'activation_mode', 'pdb_id')]),
+ ),
+ migrations.RemoveField(
+ model_name='cmpdaction',
+ name='complex',
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('ppi', 'compound', 'activation_mode', 'pdb_id')]),
+ ),
+ migrations.DeleteModel(
+ name='ActivityType',
+ ),
+ migrations.AddField(
+ model_name='ppicomplex',
+ name='ppi',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0011_auto_20170518_1404.py b/ippisite/ippidb/migrations/0011_auto_20170518_1404.py
new file mode 100644
index 0000000000000000000000000000000000000000..9abe3d730559d93e1f8dfbcf9b6caa7543b582dd
--- /dev/null
+++ b/ippisite/ippidb/migrations/0011_auto_20170518_1404.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 14:04
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0010_auto_20170518_1142'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='ppi',
+ name='pdb_id',
+ field=models.CharField(max_length=4, null=True, verbose_name='PDB ID'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0012_auto_20170518_1913.py b/ippisite/ippidb/migrations/0012_auto_20170518_1913.py
new file mode 100644
index 0000000000000000000000000000000000000000..118254a486dd69356b14d2072192c33a593b080b
--- /dev/null
+++ b/ippisite/ippidb/migrations/0012_auto_20170518_1913.py
@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 19:13
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0011_auto_20170518_1404'),
+ ]
+
+ operations = [
+ migrations.RenameModel(
+ old_name='CmpdAction',
+ new_name='CompoundAction',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0013_auto_20170518_1943.py b/ippisite/ippidb/migrations/0013_auto_20170518_1943.py
new file mode 100644
index 0000000000000000000000000000000000000000..bc133acbe966237dbe441307e21939d0b1f84aa0
--- /dev/null
+++ b/ippisite/ippidb/migrations/0013_auto_20170518_1943.py
@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 19:43
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0012_auto_20170518_1913'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='disease',
+ name='disease_name',
+ ),
+ migrations.RemoveField(
+ model_name='disease',
+ name='ppi',
+ ),
+ migrations.AddField(
+ model_name='disease',
+ name='name',
+ field=models.CharField(default=None, max_length=30, unique=True, verbose_name='Disease'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='ppi',
+ name='diseases',
+ field=models.ManyToManyField(to='ippidb.Disease'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0014_auto_20170519_1243.py b/ippisite/ippidb/migrations/0014_auto_20170519_1243.py
new file mode 100644
index 0000000000000000000000000000000000000000..3aef4f320ee659e960a6df1b4ea503dbabb02eb3
--- /dev/null
+++ b/ippisite/ippidb/migrations/0014_auto_20170519_1243.py
@@ -0,0 +1,24 @@
+# -*- 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'),
+ ),
+ ]
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/migrations/0019_auto_20170522_1931.py b/ippisite/ippidb/migrations/0019_auto_20170522_1931.py
new file mode 100644
index 0000000000000000000000000000000000000000..4b1fb04481fafdec61d4558534bdf62b5fa66ae4
--- /dev/null
+++ b/ippisite/ippidb/migrations/0019_auto_20170522_1931.py
@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:31
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0018_auto_20170522_1501'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='db_import_date',
+ field=models.DateTimeField(verbose_name='MDDR release year/month'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundimport',
+ unique_together=set([('mddr_name', 'dvpmt_phase', 'canonical_smile')]),
+ ),
+ migrations.RemoveField(
+ model_name='mddrcompoundimport',
+ name='mddr_compound_id',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0020_auto_20170522_1945.py b/ippisite/ippidb/migrations/0020_auto_20170522_1945.py
new file mode 100644
index 0000000000000000000000000000000000000000..1aee4b1079c721331c6ba6b99acf0ad0e3faae37
--- /dev/null
+++ b/ippisite/ippidb/migrations/0020_auto_20170522_1945.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:45
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0019_auto_20170522_1931'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='mddractivityclass',
+ old_name='activity_class',
+ new_name='name',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0021_auto_20170522_1949.py b/ippisite/ippidb/migrations/0021_auto_20170522_1949.py
new file mode 100644
index 0000000000000000000000000000000000000000..fcb415f24dc5e13d83edaf296c11b704dc711bfc
--- /dev/null
+++ b/ippisite/ippidb/migrations/0021_auto_20170522_1949.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-22 19:49
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0020_auto_20170522_1945'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='canonical_smile',
+ field=models.CharField(blank=True, max_length=500, null=True, verbose_name='Canonical Smile'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0022_auto_20170523_1311.py b/ippisite/ippidb/migrations/0022_auto_20170523_1311.py
new file mode 100644
index 0000000000000000000000000000000000000000..24690d2087d0133ef86a6d373b7c6ddf25e7dd1d
--- /dev/null
+++ b/ippisite/ippidb/migrations/0022_auto_20170523_1311.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-23 13:11
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0021_auto_20170522_1949'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='dvpmt_phase',
+ field=models.CharField(choices=[('Biological Testing', ''), ('Preclinical', ''), ('Phase III', ''), ('Phase II', ''), ('Phase I/II', ''), ('Phase I', ''), ('Launched', ''), ('Pre-Registered', ''), ('Not Applicable', ''), ('Discontinued', ''), ('Clinical', ''), ('Withdrawn', ''), ('Registered', ''), ('Not Determined', ''), ('Phase II/III', ''), ('IND Filed', '')], max_length=20, verbose_name='Development phase'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0023_auto_20170523_1858.py b/ippisite/ippidb/migrations/0023_auto_20170523_1858.py
new file mode 100644
index 0000000000000000000000000000000000000000..904209de44969541baed91edb7396d3cb0cbe27e
--- /dev/null
+++ b/ippisite/ippidb/migrations/0023_auto_20170523_1858.py
@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-23 18:58
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0022_auto_20170523_1311'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='testpkdescription',
+ name='administration_mode',
+ field=models.CharField(blank=True, choices=[('IV', ''), ('PO', ''), ('IP', ''), ('SL', 'SL')], max_length=2, null=True, verbose_name='Administration mode'),
+ ),
+ migrations.DeleteModel(
+ name='AdministrationMode',
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0024_auto_20170523_2000.py b/ippisite/ippidb/migrations/0024_auto_20170523_2000.py
new file mode 100644
index 0000000000000000000000000000000000000000..d107a840d0bc9cda5e69578a73dcba995c0968a0
--- /dev/null
+++ b/ippisite/ippidb/migrations/0024_auto_20170523_2000.py
@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-23 20:00
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0023_auto_20170523_1858'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='testactivitydescription',
+ name='cell_line',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.CellLine'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index dbd49d260c49d0af56530de3bf49e79b077dcfc4..2b188a844e95c994bdab6b68ff3c26a33c801887 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -40,6 +40,8 @@ class Bibliography(models.Model):
class Meta:
verbose_name_plural = "bibliographies"
+ def __str__(self):
+ return '{}, {}'.format(self.source, self.id_source)
class Taxonomy(models.Model):
@@ -119,16 +121,18 @@ class Domain(models.Model):
return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
class ProteinDomainComplex(models.Model):
- protein_id = models.ForeignKey('Protein')
- domain_id = models.ForeignKey('Domain')
+ protein = models.ForeignKey('Protein')
+ domain = models.ForeignKey('Domain')
ppc_copy_nb = models.IntegerField('Number of copies of the protein in the complex')
class Meta:
verbose_name_plural = "complexes"
+ def __str__(self):
+ return '{}-{}'.format(self.protein_id, self.domain_id)
+
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"
@@ -143,21 +147,53 @@ class Symmetry(models.Model):
class Meta:
verbose_name_plural = "symmetries"
+ def __str__(self):
+ return '{} ({})'.format(self.code, self.description)
+
+
+class Disease(models.Model):
+ name = models.CharField('Disease', max_length=30, unique=True) # is there any database/nomenclature for diseases?
+
+ def __str__(self):
+ return self.name
+
class Ppi(models.Model):
- ppi_id = models.IntegerField('PPI identifier')
- complex_id = models.ForeignKey(ProteinDomainComplex)
+ 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)
+
+ def __str__(self):
+ return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')
+
+ def get_ppi_complexes(self):
+ """
+ return all ppi complexes belonging to this ppi
+ """
+ return PpiComplex.objects.filter(ppi=self)
+
+ def get_ppi_bound_complexes(self):
+ """
+ return bound ppi complexes belonging to this ppi
+ """
+ #this is the less efficient query ever seen, FIXME
+ return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
+
+
+class PpiComplex(models.Model):
+ ppi = models.ForeignKey(Ppi)
+ complex = models.ForeignKey(ProteinDomainComplex)
cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)
- pdb_id = models.CharField('PDB ID', max_length=4)
- symmetry_id = models.ForeignKey(Symmetry)
-class Disease(models.Model):
- ppi_id = models.ForeignKey(Ppi)
- disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
+ class Meta:
+ verbose_name_plural = "Ppi complexes"
+
+ def __str__(self):
+ return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
class Compound(models.Model):
canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=500)
- #TODO index this table on canonical_smile
is_macrocycle = models.BooleanField('Contains one or more macrocycles')
aromatic_ratio = models.DecimalField('Aromatic ratio', max_digits=3, decimal_places=2)
balaban_index = models.DecimalField('Balaban index', max_digits=3, decimal_places=2)
@@ -202,37 +238,56 @@ 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)
- mddr_compound_id = models.ForeignKey('MDDRCompoundImport', 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):
+ name = models.CharField('Activity Class', max_length=100, unique=True)
+
+ class Meta:
+ verbose_name_plural = "MDDR activity classes"
+
+ def __str__(self):
+ return self.name
class MDDRCompoundImport(models.Model):
- mddr_compound_id = models.IntegerField('MDDR compound ID')
+
+ MDDR_DEVELOPMENT_PHASES = (
+ ('Biological Testing',''),
+ ('Preclinical',''),
+ ('Phase III',''),
+ ('Phase II',''),
+ ('Phase I/II',''),
+ ('Phase I',''),
+ ('Launched',''),
+ ('Pre-Registered',''),
+ ('Not Applicable',''),
+ ('Discontinued',''),
+ ('Clinical',''),
+ ('Withdrawn',''),
+ ('Registered',''),
+ ('Not Determined',''),
+ ('Phase II/III',''),
+ ('IND Filed',''),
+ )
+
mddr_name = models.CharField('MDDR name', max_length=40)
- dvpmt_phase = models.CharField('Development phase', max_length=20)
- canonical_smile = models.CharField('Canonical Smile', max_length=500, unique=True, blank=True, null=True)
+ dvpmt_phase = models.CharField('Development phase', max_length=20, choices=MDDR_DEVELOPMENT_PHASES)
+ canonical_smile = models.CharField('Canonical Smile', max_length=500, 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)
+ db_import_date = models.DateTimeField('MDDR release year/month')
+ activity_classes = models.ManyToManyField(MDDRActivityClass)
class Meta:
# over multiple releases of the MDDR database, the same compound can evolve in its development phase
# the same compound can have different names and development phases in the same MDDR release
- unique_together = (('mddr_compound_id', 'mddr_name', 'dvpmt_phase'),)
+ unique_together = (('mddr_name', 'dvpmt_phase', 'canonical_smile'),)
verbose_name_plural = "MDDR compound imports"
-
-class MDDRCompoundActivityClass(models.Model):
- mddr_compound_id = models.ForeignKey(MDDRCompoundImport)
- activity_class = models.CharField('Activity Class', max_length=100)
-
- class Meta:
- unique_together = (('mddr_compound_id', '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)
@@ -245,6 +300,9 @@ class MDDRSimilarity(models.Model):
class CellLine(models.Model):
name = models.CharField('Name', max_length=50, unique=True)
+ def __str__(self):
+ return self.name
+
class TestActivityDescription(models.Model):
TEST_TYPES = (
('BIOCH', 'Biochemical assay'),
@@ -255,17 +313,23 @@ class TestActivityDescription(models.Model):
('I', 'Inhibition'),
('S', 'Stabilization')
)
- complex_id = models.ForeignKey(ProteinDomainBoundComplex)
- biblio_id = models.ForeignKey(Bibliography)
- ppi_id = models.ForeignKey(Ppi, blank=True, null=True)
+ biblio = models.ForeignKey(Bibliography)
+ ppi = models.ForeignKey(Ppi, blank=True, null=True)
test_name = models.CharField('Test name', max_length=100)
test_type = models.CharField('Test type', max_length=5, choices=TEST_TYPES)
test_modulation_type = models.CharField('Test modulation type', max_length=1, choices=TEST_MODULATION_TYPES)
nb_active_compounds = models.IntegerField('Total number of active compounds')
- cell_line = models.ForeignKey(CellLine)
-
-class ActivityType(models.Model):
- name = models.CharField('Name', max_length=50, unique=True)
+ cell_line = models.ForeignKey(CellLine, blank=True, null=True)
+
+ def get_complexes(self):
+ """
+ get the complexes tested for this PPI
+ depends on the modulation type
+ """
+ if self.test_modulation_type=='I':
+ return self.ppi.get_ppi_complexes()
+ else:
+ return self.ppi.get_ppi_bound_complexes()
class CompoundActivityResult(models.Model):
MODULATION_TYPES = (
@@ -273,43 +337,52 @@ class CompoundActivityResult(models.Model):
('I', 'Inhibition'),
('S', 'Stabilization')
)
- compound_id = models.ForeignKey(Compound)
- test_activity_description_id = models.ForeignKey(TestActivityDescription)
- activity_type_id = models.ForeignKey(ActivityType)
+ ACTIVITY_TYPES = (
+ ('pIC50','pIC50 (half maximal inhibitory concentration, -log10)'),
+ ('pEC50','pEC50 (half maximal effective concentration, -log10)'),
+ ('pKd','pKd (dissociation constant, -log10)'),
+ ('pKi','pKi (inhibition constant, -log10)'),
+ )
+ compound = models.ForeignKey(Compound)
+ test_activity_description = models.ForeignKey(TestActivityDescription)
+ activity_type = models.CharField('Activity type', max_length=5, choices=ACTIVITY_TYPES)
activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)
modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
class Meta:
- unique_together = (('compound_id', 'test_activity_description_id', 'activity_type_id'),)
+ unique_together = (('compound', 'test_activity_description', 'activity_type'),)
class TestCytotoxDescription(models.Model):
- biblio_id = models.ForeignKey(Bibliography)
+ biblio = models.ForeignKey(Bibliography)
test_name = models.CharField('Cytotoxicity test name', max_length=100)
cell_line = models.ForeignKey(CellLine)
compound_concentration = models.DecimalField('Compound concentration in μM', max_digits=7, decimal_places=3, blank=True, null=True)
class CompoundCytotoxicityResult(models.Model):
- compound_id = models.ForeignKey(Compound)
- test_cytotoxicity_description_id = models.ForeignKey(TestCytotoxDescription)
+ compound = models.ForeignKey(Compound)
+ test_cytotoxicity_description = models.ForeignKey(TestCytotoxDescription)
toxicity = models.BooleanField('Toxicity', default=False)
class Meta:
- unique_together = (('compound_id', 'test_cytotoxicity_description_id'),)
-
-class AdministrationMode(models.Model):
- name = models.CharField('Administration mode', max_length=20, blank=True, null=True)
+ unique_together = (('compound', 'test_cytotoxicity_description'),)
class TestPKDescription(models.Model):
- biblio_id = models.ForeignKey(Bibliography)
+ ADMINISTRATION_MODES = (
+ ('IV', ''),
+ ('PO', ''),
+ ('IP', ''),
+ ('SL', 'SL')
+ )
+ biblio = models.ForeignKey(Bibliography)
test_name = models.CharField('Pharmacokinetic test name', max_length=100)
organism = models.ForeignKey(Taxonomy)
- administration_mode = models.ForeignKey(AdministrationMode, blank=True, null=True)
+ administration_mode = models.CharField('Administration mode', max_length=2, choices=ADMINISTRATION_MODES,blank=True, null=True)
dose = models.DecimalField('Dose in mg/kg', max_digits=7, decimal_places=4, blank=True, null=True)
dose_interval = models.IntegerField('Dose interval, in hours', blank=True, null=True)
class CompoundPKResult(models.Model):
- compound_id = models.ForeignKey(Compound)
- test_pk_description_id = models.ForeignKey(TestPKDescription)
+ compound = models.ForeignKey(Compound)
+ test_pk_description = models.ForeignKey(TestPKDescription)
tolerated = models.NullBooleanField('Tolerated', null=True)
auc = models.IntegerField('Area under curve (ng.mL-1.hr)', blank=True, null=True)
clearance = models.DecimalField('Clearance (mL/hr)', max_digits=7, decimal_places=3, blank=True, null=True)
@@ -320,28 +393,34 @@ class CompoundPKResult(models.Model):
voldistribution = models.DecimalField('Volume distribution (Vd)', max_digits=5, decimal_places=2, blank=True, null=True)
class Meta:
- unique_together = (('compound_id', 'test_pk_description_id'),)
+ unique_together = (('compound', 'test_pk_description'),)
-class CmpdAction(models.Model):
+class CompoundAction(models.Model):
ACTIVATION_MODES = (
('O', 'Orthosteric'),
('A', 'Allosteric')
)
- complex_id = models.ForeignKey(ProteinDomainBoundComplex)
- compound_id = models.ForeignKey(Compound)
+ compound = models.ForeignKey(Compound)
activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)
- ppi_id = models.ForeignKey(Ppi)
+ ppi = models.ForeignKey(Ppi)
pdb_id = models.CharField('PDB ID', max_length=4)
nb_copy_compounds = models.IntegerField('Number of copies for the compound')
class Meta:
- unique_together = (('complex_id', 'compound_id', 'pdb_id'),)
+ unique_together = (('ppi', 'compound', 'activation_mode', 'pdb_id'),)
+
+ def get_complexes(self):
+ """
+ get the complexes involved in the compound action
+ which are always the bound complexes
+ """
+ return ppi.get_ppi_bound_complexes()
class RefCompoundBiblio(models.Model):
- compound_id = models.ForeignKey(Compound)
- bibliography_id = models.ForeignKey(Bibliography)
+ compound = models.ForeignKey(Compound)
+ bibliography = models.ForeignKey(Bibliography)
compound_name = models.CharField('Compound name in the publication', max_length=50)
class Meta:
- unique_together = (('compound_id', 'bibliography_id'),)
+ unique_together = (('compound', 'bibliography'),)