From e0bba382f1fc02dc9fa8f51329255df5edefd872 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Sun, 12 Mar 2017 21:27:00 +0100
Subject: [PATCH] further work on data models, based on latest meetings
---
ippisite/db.sqlite3 | Bin 233472 -> 245760 bytes
ippisite/ippidb/admin.py | 13 +-
.../migrations/0002_auto_20170221_1606.py | 41 ++
ippisite/ippidb/models.py | 467 ++++++++----------
4 files changed, 258 insertions(+), 263 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0002_auto_20170221_1606.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index d7af3c51bb79c322ce6fc7f3abdf063b5e007092..b4dfacb9d2067dd66c0af33420cc8ef242c0089c 100644
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diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index b5bd39f2..7ebef2ec 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -1,13 +1,6 @@
from django.contrib import admin
-
from .models import *
+from django.apps import apps
-admin.site.register(Bibliography)
-admin.site.register(Taxonomy)
-admin.site.register(MolecularFunction)
-admin.site.register(Protein)
-admin.site.register(Domain)
-admin.site.register(BindingSite)
-admin.site.register(Complex)
-admin.site.register(Ppi)
-admin.site.register(PpiArchitecture)
+for model in apps.get_app_config('ippidb').models.values():
+ admin.site.register(model)
diff --git a/ippisite/ippidb/migrations/0002_auto_20170221_1606.py b/ippisite/ippidb/migrations/0002_auto_20170221_1606.py
new file mode 100644
index 00000000..eda1599a
--- /dev/null
+++ b/ippisite/ippidb/migrations/0002_auto_20170221_1606.py
@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-02-21 16:06
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Disease',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('disease_name', models.CharField(db_column='Disease', max_length=30)),
+ ('ppi_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi')),
+ ],
+ ),
+ migrations.AlterModelOptions(
+ name='bibliography',
+ options={'verbose_name_plural': 'bibliographies'},
+ ),
+ migrations.AlterModelOptions(
+ name='complex',
+ options={'verbose_name_plural': 'complexes'},
+ ),
+ migrations.AlterModelOptions(
+ name='taxonomy',
+ options={'verbose_name_plural': 'taxonomies'},
+ ),
+ migrations.AlterField(
+ model_name='domain',
+ name='domainfamily',
+ field=models.CharField(max_length=25, verbose_name='Domain family'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index c4d1a4dd..053d9abd 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -67,109 +67,195 @@ class Domain(models.Model):
pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
pfam_description = models.CharField('Pfam Description', max_length=100)
- domainfamily = models.CharField('', max_length=25) #TODO: what is this field? check database contents
-
-class BindingSite(models.Model):
- protein_id = models.ForeignKey('Protein')
- domain_id = models.ForeignKey('Domain')
+ domainfamily = models.CharField('Domain family', max_length=25) #TODO: what is this field? check database contents
-class Complex(models.Model):
+class ProteinDomainComplex(models.Model):
+ complex_id = models.IntegerField('Complex identifier')
protein_id = models.ForeignKey('Protein')
- copy_nb = models.IntegerField('Number of copies')
+ domain_id = models.ForeignKey('Domain')
+ ppc_copy_nb = models.IntegerField('Number of copies of the protein in the complex')
+
class Meta:
verbose_name_plural = "complexes"
+
+#TEST inheritance for complex: BoundComplex and PartnerComplex
+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"
+class ProteinDomainPartnerComplex(ProteinDomainComplex):
+ class Meta:
+ verbose_name_plural = "partner complexes"
-class Ppi(models.Model):
- complex_id_1 = models.ForeignKey(Complex, related_name='cplx_id_1')
- complex_id_2 = models.ForeignKey(Complex, related_name='cplx_id_2')
- binding_site_id_1 = models.ForeignKey(BindingSite, related_name='binding_site_id_1')
- binding_site_id_2 = models.ForeignKey(BindingSite, related_name='binding_site_id_2')
+class Symmetry(models.Model):
+ code = models.CharField('Symmetry code', max_length=2)
+ description = models.CharField('Description', max_length=300)
-class PpiArchitecture(models.Model):
- ppi_id = models.ForeignKey(Ppi)
+ class Meta:
+ verbose_name_plural = "symmetries"
+
+class Ppi(models.Model):
+ ppi_id = models.IntegerField('PPI identifier')
+ complex_id = models.ForeignKey(ProteinDomainComplex)
+ cc_nb = models.IntegerField('Number of copies of the complex in the PPI')
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 Compound(models.Model):
+ canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=250)
+ #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)
+ fsp3 = models.DecimalField('Fsp3', max_digits=3, decimal_places=2)
+ dh_Petitjean = models.DecimalField('Dh Petitjean', max_digits=4, decimal_places=2)
+ diam_graph_non_h_petitjean = models.IntegerField('Diameter for the molecular graph for heavy atoms (Petitjean)')
+ gc_molar_refractivity = models.DecimalField('GC Molar Refractivity', max_digits=5, decimal_places=2)
+ g_petitjean = models.DecimalField('G Petitjean', max_digits=3, decimal_places=2)
+ ig_petitjean = models.DecimalField('Ig Petitjean', max_digits=3, decimal_places=2)
+ log_d = models.DecimalField('LogD (Partition coefficient octanol-1/water, with pKa information)', max_digits=4, decimal_places=2)
+ a_log_p = models.DecimalField('ALogP (Partition coefficient octanol-1/water)', max_digits=4, decimal_places=2)
+ mean_atom_vol_vdw = models.DecimalField('Mean atom volume computed with VdW radii', max_digits=4, decimal_places=2)
+ molecular_weight = models.DecimalField('Molecular weight', max_digits=6, decimal_places=2)
+ nb_acceptor_h = models.IntegerField('Number of hydrogen bond acceptors')
+ nb_aliphatic_amines = models.IntegerField('Number of aliphatics amines')
+ nb_aromatic_bonds = models.IntegerField('Number of aromatic bonds')
+ nb_aromatic_ether = models.IntegerField('Number of aromatic ethers')
+ nb_aromatic_sssr = models.IntegerField('Number of aromatic Smallest Set of System Rings (SSSR)')
+ nb_atom = models.IntegerField('Number of atoms')
+ nb_atom_non_h = models.IntegerField('Number of non hydrogen atoms')
+ nb_benzene_like_rings = models.IntegerField('Number of benzene-like rings')
+ nb_bonds = models.IntegerField('Number of bonds')
+ nb_bonds_non_h = models.IntegerField('Number of bonds not involving a hydrogen')
+ nb_br = models.IntegerField('Number of Bromine atoms')
+ nb_c = models.IntegerField('Number of Carbon atoms')
+ nb_chiral_centers = models.IntegerField('Number of chiral centers')
+ nb_circuits = models.IntegerField('Number of circuits')
+ nb_cl = models.IntegerField('Number of Chlorine atoms')
+ nb_csp2 = models.IntegerField('Number of sp2-hybridized carbon atoms')
+ nb_csp3 = models.IntegerField('Number of sp3-hybridized carbon atoms')
+ nb_donor_h = models.IntegerField('Number of hydrogen bond donors')
+ nb_double_bonds = models.IntegerField('Number of double bonds')
+ nb_f = models.IntegerField('Number of fluorine atoms')
+ nb_i = models.IntegerField('Number of iodine atoms')
+ nb_multiple_bonds = models.IntegerField('Number of multiple bonds')
+ nb_n = models.IntegerField('Number of nitrogen atoms')
+ nb_o = models.IntegerField('Number of oxygen atoms')
+ nb_rings = models.IntegerField('Number of rings')
+ nb_rotatable_bonds = models.IntegerField('Number of rotatable bonds')
+ radius_graph_non_h_petitjean = models.IntegerField('Radius for the molecular graph for heavy atoms (Petitjean)')
+ randic_index = models.DecimalField('Randic index', max_digits=4, decimal_places=2)
+ rdf070m = models.DecimalField('RDF070m, radial distribution function weighted by the atomic masses at 7Ã…', max_digits=5, decimal_places=2)
+ rotatable_bond_fraction = models.DecimalField('Fraction of rotatable bonds', max_digits=3, decimal_places=2)
+ sum_atom_polar = models.DecimalField('Sum of atomic polarizabilities', max_digits=5, decimal_places=2)
+ sum_atom_vol_vdw = models.DecimalField('Sum of atom volumes computed with VdW radii', max_digits=6, decimal_places=2)
+ surface_vdw_petitjean = models.DecimalField('Van der Waals surface area (Petitjean)', max_digits=6, decimal_places=2)
+ thickness_petitjean = models.DecimalField('Thickness (Petitjean)', max_digits=4, decimal_places=2)
+ tpsa = models.DecimalField('Topological Polar Surface Area (TPSA)', max_digits=5, decimal_places=2)
+ ui = models.DecimalField('Unsaturation index', max_digits=4, decimal_places=2)
+ vol_vdw_petitjean = models.DecimalField('Van der Waals volume (Petitjean)', max_digits=7, 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)
+ 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', 'MDDR compound', unique=True, blank=True, null=True)
+
+
+class MDDRCompoundImport(models.Model):
+ mddr_compound_id = models.IntegerField('MDDR compound ID')
+ 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)
+ #TODO index this table on canonical_smile
+ db_import_date = models.DecimalField('MDDR release year/month', max_digits=6, decimal_places=0)
+ 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'),)
-class Actionevidencetest(models.Model):
- idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, db_column='IDCmpdAction') # Field name made lowercase.
- idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, db_column='IDTestActivity') # Field name made lowercase.
- nbcopycompound = models.IntegerField(db_column='NbCopyCompound', blank=True, null=True) # Field name made lowercase.
+class MDDRCompoundActivityClass(models.Model):
+ mddr_compound_id = models.ForeignKey(MDDRCompoundImport)
+ activity_class = models.CharField('Activity Class', max_length=100)
class Meta:
-# managed = False
- db_table = 'actionEvidenceTest'
- unique_together = (('idcmpdaction', 'idtestactivity'),)
+ unique_together = (('mddr_compound_id', 'activity_class'),)
-class Actionevidencexray(models.Model):
- idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, db_column='IDCmpdAction') # Field name made lowercase.
- codepdb = models.CharField(db_column='CodePDB', max_length=4) # Field name made lowercase.
- nbcopycompound = models.IntegerField(db_column='NbCopyCompound') # Field name made lowercase.
- idbindingsite = models.ForeignKey('Bindingsite', models.DO_NOTHING, db_column='IDBindingSite') # Field name made lowercase.
- idbiblio = models.ForeignKey('Biblio', models.DO_NOTHING, db_column='IDBiblio', blank=True, null=True) # Field name made lowercase.
+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)
+ tanimoto = models.DecimalField('Tanimoto', max_digits=6, decimal_places=5)
class Meta:
-# managed = False
- db_table = 'actionEvidenceXRay'
- unique_together = (('idcmpdaction', 'codepdb'),)
+ unique_together = (('canonical_smile_ippidb', 'canonical_smile_mddr'),)
+
+"""
+class TestActivityDescription(models.Model):
+ complex_id = models.ForeignKey(Complex)
+ biblio_id = models.ForeignKey(Biblio)
+ idppi = models.ForeignKey(Ppi, models.DO_NOTHING, ='IDPPI', blank=True, null=True)
+ testnameactivity = models.CharField(='TestNameActivity', max_length=40)
+ isprimary = models.CharField(='IsPrimary', max_length=1)
+ protboundconstruct = models.CharField(='ProtBoundConstruct', max_length=11)
+ testtype = models.CharField(='TestType', max_length=5)
+ testmodulationtype = models.CharField(='TestModulationType', max_length=13)
+ nbactivescmpdstot = models.IntegerField(='NbActivesCmpdsTot')
+ conccmpds = models.DecimalField(='ConcCmpds', max_digits=7, decimal_places=3, blank=True, null=True)
+ protocol = models.TextField(='Protocol', blank=True, null=True)
+ concproteinbound = models.DecimalField(='ConcProteinBound', max_digits=7, decimal_places=3, blank=True, null=True)
+ concprotein2 = models.DecimalField(='ConcProtein2', max_digits=7, decimal_places=3, blank=True, null=True)
+ controlepos = models.CharField(='ControlePos', max_length=50, blank=True, null=True)
+ controleneg = models.CharField(='ControleNeg', max_length=50, blank=True, null=True)
+ cellline = models.CharField(='CellLine', max_length=50, blank=True, null=True)
+ pepseq = models.CharField(='PepSeq', max_length=100, blank=True, null=True)
+ marker = models.CharField(='Marker', max_length=35, blank=True, null=True)
-class Biblio(models.Model):
- idbiblio = models.AutoField(db_column='IDBiblio', primary_key=True) # Field name made lowercase.
- source = models.CharField(db_column='Source', max_length=7) # Field name made lowercase.
- idsource = models.CharField(db_column='IDSource', max_length=25) # Field name made lowercase.
- title = models.CharField(db_column='Title', max_length=300) # Field name made lowercase.
- listauthor = models.CharField(db_column='ListAuthor', max_length=500) # Field name made lowercase.
- yearbiblio = models.IntegerField(db_column='YearBiblio') # Field name made lowercase.
- cytotox = models.CharField(db_column='Cytotox', max_length=1) # Field name made lowercase.
- insilico = models.CharField(db_column='InSilico', max_length=1) # Field name made lowercase.
- invitro = models.CharField(db_column='InVitro', max_length=1) # Field name made lowercase.
- invivo = models.CharField(db_column='InVivo', max_length=1) # Field name made lowercase.
- incellulo = models.CharField(db_column='InCellulo', max_length=1) # Field name made lowercase.
- pharmacokinetic = models.CharField(db_column='Pharmacokinetic', max_length=1) # Field name made lowercase.
- xray = models.CharField(db_column='XRay', max_length=1) # Field name made lowercase.
- journalname = models.CharField(db_column='JournalName', max_length=50, blank=True, null=True) # Field name made lowercase.
- class Meta:
-# managed = False
- db_table = 'biblio'
- unique_together = (('source', 'idsource'),)
-class Bindingsite(models.Model):
- idbindingsite = models.IntegerField(db_column='IDBindingSite') # Field name made lowercase.
- idprotein = models.ForeignKey('Protein', models.DO_NOTHING, db_column='IDProtein') # Field name made lowercase.
- iddomain = models.ForeignKey('Domain', models.DO_NOTHING, db_column='IDDomain') # Field name made lowercase.
+
+class Actionevidencetest(models.Model):
+ idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
+ idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
+ nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)
class Meta:
# managed = False
- db_table = 'bindingSite'
- unique_together = (('idbindingsite', 'idprotein', 'iddomain'),)
+ db_table = 'actionEvidenceTest'
+ unique_together = (('idcmpdaction', 'idtestactivity'),)
-class Bindingsiteevidence(models.Model):
- idppi = models.ForeignKey('Ppi', models.DO_NOTHING, db_column='IDPPI') # Field name made lowercase.
- idbindingsite = models.ForeignKey(Bindingsite, models.DO_NOTHING, db_column='IDBindingSite') # Field name made lowercase.
- codepdb = models.CharField(db_column='CodePDB', max_length=4) # Field name made lowercase.
+class Actionevidencexray(models.Model):
+ idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
+ codepdb = models.CharField(='CodePDB', max_length=4)
+ nbcopycompound = models.IntegerField(='NbCopyCompound')
+ idbindingsite = models.ForeignKey('Bindingsite', models.DO_NOTHING, ='IDBindingSite')
+ idbiblio = models.ForeignKey('Biblio', models.DO_NOTHING, ='IDBiblio', blank=True, null=True)
class Meta:
# managed = False
- db_table = 'bindingSiteEvidence'
- unique_together = (('idppi', 'idbindingsite'),)
+ db_table = 'actionEvidenceXRay'
+ unique_together = (('idcmpdaction', 'codepdb'),)
class Cmpdaction(models.Model):
- idcmpdaction = models.AutoField(db_column='IDCmpdAction', primary_key=True) # Field name made lowercase.
- idcomplexebound = models.ForeignKey('Complexe', models.DO_NOTHING, db_column='IDComplexeBound') # Field name made lowercase.
- idcompound = models.ForeignKey('Compound', models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- activationmode = models.CharField(db_column='ActivationMode', max_length=11) # Field name made lowercase.
- modulationtype = models.CharField(db_column='ModulationType', max_length=10) # Field name made lowercase.
+ idcmpdaction = models.AutoField(='IDCmpdAction', primary_key=True)
+ idcomplexebound = models.ForeignKey('Complexe', models.DO_NOTHING, ='IDComplexeBound')
+ idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
+ activationmode = models.CharField(='ActivationMode', max_length=11)
+ modulationtype = models.CharField(='ModulationType', max_length=10)
class Meta:
# managed = False
@@ -177,11 +263,11 @@ class Cmpdaction(models.Model):
class Cmpdactiveresult(models.Model):
- idcompound = models.ForeignKey('Compound', models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, db_column='IDTestActivity') # Field name made lowercase.
- activitytype = models.CharField(db_column='ActivityType', max_length=5) # Field name made lowercase.
- activity = models.DecimalField(db_column='Activity', max_digits=4, decimal_places=2) # Field name made lowercase.
- pourcentinhib = models.IntegerField(db_column='PourcentInhib', blank=True, null=True) # Field name made lowercase.
+ idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
+ idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
+ activitytype = models.CharField(='ActivityType', max_length=5)
+ activity = models.DecimalField(='Activity', max_digits=4, decimal_places=2)
+ pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)
class Meta:
# managed = False
@@ -190,9 +276,9 @@ class Cmpdactiveresult(models.Model):
class Cmpdcytotoxresult(models.Model):
- idcompound = models.ForeignKey('Compound', models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- idtestcytotox = models.ForeignKey('Testcytotoxdescription', models.DO_NOTHING, db_column='IDTestCytotox') # Field name made lowercase.
- toxicity = models.CharField(db_column='Toxicity', max_length=1) # Field name made lowercase.
+ idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
+ idtestcytotox = models.ForeignKey('Testcytotoxdescription', models.DO_NOTHING, ='IDTestCytotox')
+ toxicity = models.CharField(='Toxicity', max_length=1)
class Meta:
# managed = False
@@ -201,9 +287,9 @@ class Cmpdcytotoxresult(models.Model):
class Cmpdinactiveresult(models.Model):
- idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, db_column='IDTestActivity') # Field name made lowercase.
- idcompound = models.ForeignKey('Compound', models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- pourcentinhib = models.IntegerField(db_column='PourcentInhib', blank=True, null=True) # Field name made lowercase.
+ idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
+ idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
+ pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)
class Meta:
# managed = False
@@ -212,16 +298,16 @@ class Cmpdinactiveresult(models.Model):
class Cmpdpkresult(models.Model):
- idcompound = models.ForeignKey('Compound', models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- idtestpk = models.ForeignKey('Testpkdescription', models.DO_NOTHING, db_column='IDTestPK') # Field name made lowercase.
- tolerated = models.CharField(db_column='Tolerated', max_length=1) # Field name made lowercase.
- auc = models.IntegerField(db_column='AUC', blank=True, null=True) # Field name made lowercase.
- clearance = models.DecimalField(db_column='Clearance', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- cmax = models.DecimalField(db_column='Cmax', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- oralbioavailability = models.IntegerField(db_column='OralBioavailability', blank=True, null=True) # Field name made lowercase.
- tdemi = models.IntegerField(db_column='Tdemi', blank=True, null=True) # Field name made lowercase.
- tmax = models.IntegerField(db_column='Tmax', blank=True, null=True) # Field name made lowercase.
- voldistribution = models.DecimalField(db_column='VolDistribution', max_digits=5, decimal_places=2, blank=True, null=True) # Field name made lowercase.
+ idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
+ idtestpk = models.ForeignKey('Testpkdescription', models.DO_NOTHING, ='IDTestPK')
+ tolerated = models.CharField(='Tolerated', max_length=1)
+ auc = models.IntegerField(='AUC', blank=True, null=True)
+ clearance = models.DecimalField(='Clearance', max_digits=7, decimal_places=3, blank=True, null=True)
+ cmax = models.DecimalField(='Cmax', max_digits=7, decimal_places=3, blank=True, null=True)
+ oralbioavailability = models.IntegerField(='OralBioavailability', blank=True, null=True)
+ tdemi = models.IntegerField(='Tdemi', blank=True, null=True)
+ tmax = models.IntegerField(='Tmax', blank=True, null=True)
+ voldistribution = models.DecimalField(='VolDistribution', max_digits=5, decimal_places=2, blank=True, null=True)
class Meta:
# managed = False
@@ -229,87 +315,6 @@ class Cmpdpkresult(models.Model):
unique_together = (('idcompound', 'idtestpk'),)
-class Complexe(models.Model):
- idcomplexe = models.AutoField(db_column='IDComplexe', primary_key=True) # Field name made lowercase.
- idprotein = models.ForeignKey('Protein', models.DO_NOTHING, db_column='IDProtein') # Field name made lowercase.
- nbcopy = models.IntegerField(db_column='NbCopy') # Field name made lowercase.
-
- class Meta:
-# managed = False
- db_table = 'complexe'
-
-
-class Compound(models.Model):
- idcompound = models.AutoField(db_column='IDCompound', primary_key=True) # Field name made lowercase.
- canonicalsmile = models.CharField(db_column='CanonicalSmile', unique=True, max_length=250) # Field name made lowercase.
- physchemfilter = models.CharField(db_column='PhysChemFilter', max_length=2) # Field name made lowercase.
- htsfilter = models.CharField(db_column='HTSFilter', max_length=1) # Field name made lowercase.
- ismacrocycle = models.CharField(db_column='IsMacrocycle', max_length=1) # Field name made lowercase.
- aromaticratio = models.DecimalField(db_column='AromaticRatio', max_digits=3, decimal_places=2) # Field name made lowercase.
- balabanindex = models.DecimalField(db_column='BalabanIndex', max_digits=3, decimal_places=2) # Field name made lowercase.
- csp3ratio = models.DecimalField(db_column='Csp3Ratio', max_digits=3, decimal_places=2) # Field name made lowercase.
- dhpetitjean = models.DecimalField(db_column='DhPetitjean', max_digits=4, decimal_places=2) # Field name made lowercase.
- diamgraphnonhpetitjean = models.IntegerField(db_column='DiamGraphNonHPetitjean') # Field name made lowercase.
- gcmolarrefractivity = models.DecimalField(db_column='GCMolarRefractivity', max_digits=5, decimal_places=2) # Field name made lowercase.
- gpetitjean = models.DecimalField(db_column='GPetitjean', max_digits=3, decimal_places=2) # Field name made lowercase.
- igpetitjean = models.DecimalField(db_column='IgPetitjean', max_digits=3, decimal_places=2) # Field name made lowercase.
- logd = models.DecimalField(db_column='LogD', max_digits=4, decimal_places=2) # Field name made lowercase.
- alogp = models.DecimalField(db_column='ALogP', max_digits=4, decimal_places=2) # Field name made lowercase.
- meanatomvolvdw = models.DecimalField(db_column='MeanAtomVolVdW', max_digits=4, decimal_places=2) # Field name made lowercase.
- molecularweight = models.DecimalField(db_column='MolecularWeight', max_digits=6, decimal_places=2) # Field name made lowercase.
- nbacceptorh = models.IntegerField(db_column='NbAcceptorH') # Field name made lowercase.
- nbaliphaticsamines = models.IntegerField(db_column='NbAliphaticsAmines') # Field name made lowercase.
- nbaromaticbonds = models.IntegerField(db_column='NbAromaticBonds') # Field name made lowercase.
- nbaromaticsether = models.IntegerField(db_column='NbAromaticsEther') # Field name made lowercase.
- nbaromaticssssr = models.IntegerField(db_column='NbAromaticsSSSR') # Field name made lowercase.
- nbatom = models.IntegerField(db_column='NbAtom') # Field name made lowercase.
- nbatomnonh = models.IntegerField(db_column='NbAtomNonH') # Field name made lowercase.
- nbbenzlikerings = models.IntegerField(db_column='NbBenzLikeRings') # Field name made lowercase.
- nbbonds = models.IntegerField(db_column='NbBonds') # Field name made lowercase.
- nbbondsnonh = models.IntegerField(db_column='NbBondsNonH') # Field name made lowercase.
- nbbr = models.IntegerField(db_column='NbBr') # Field name made lowercase.
- nbc = models.IntegerField(db_column='NbC') # Field name made lowercase.
- nbchiralcenters = models.IntegerField(db_column='NbChiralCenters') # Field name made lowercase.
- nbcircuits = models.IntegerField(db_column='NbCircuits') # Field name made lowercase.
- nbcl = models.IntegerField(db_column='NbCl') # Field name made lowercase.
- nbcsp2 = models.IntegerField(db_column='NbCsp2') # Field name made lowercase.
- nbcsp3 = models.IntegerField(db_column='NbCsp3') # Field name made lowercase.
- nbdonorh = models.IntegerField(db_column='NbDonorH') # Field name made lowercase.
- nbdoublebonds = models.IntegerField(db_column='NbDoubleBonds') # Field name made lowercase.
- nbf = models.IntegerField(db_column='NbF') # Field name made lowercase.
- nbi = models.IntegerField(db_column='NbI') # Field name made lowercase.
- nbmultbonds = models.IntegerField(db_column='NbMultBonds') # Field name made lowercase.
- nbn = models.IntegerField(db_column='NbN') # Field name made lowercase.
- nbo = models.IntegerField(db_column='NbO') # Field name made lowercase.
- nbrings = models.IntegerField(db_column='NbRings') # Field name made lowercase.
- nbrotatablebonds = models.IntegerField(db_column='NbRotatableBonds') # Field name made lowercase.
- radiusgraphnonhpetitjean = models.IntegerField(db_column='RadiusGraphNonHPetitjean') # Field name made lowercase.
- randicindex = models.DecimalField(db_column='RandicIndex', max_digits=4, decimal_places=2) # Field name made lowercase.
- rdf070m = models.DecimalField(db_column='RDF070m', max_digits=5, decimal_places=2) # Field name made lowercase.
- rotatablebondfraction = models.DecimalField(db_column='RotatableBondFraction', max_digits=3, decimal_places=2) # Field name made lowercase.
- sumatompolar = models.DecimalField(db_column='SumAtomPolar', max_digits=5, decimal_places=2) # Field name made lowercase.
- sumatomvolvdw = models.DecimalField(db_column='SumAtomVolVdW', max_digits=6, decimal_places=2) # Field name made lowercase.
- surfacevdwpetitjean = models.DecimalField(db_column='SurfaceVDWPetitjean', max_digits=6, decimal_places=2) # Field name made lowercase.
- thicknesspetitjean = models.DecimalField(db_column='ThicknessPetitjean', max_digits=4, decimal_places=2) # Field name made lowercase.
- tpsa = models.DecimalField(db_column='TPSA', max_digits=5, decimal_places=2) # Field name made lowercase.
- ui = models.DecimalField(db_column='Ui', max_digits=4, decimal_places=2) # Field name made lowercase.
- volvdwpetitjean = models.DecimalField(db_column='VolVDWPetitjean', max_digits=7, decimal_places=2) # Field name made lowercase.
- wienerindex = models.IntegerField(db_column='WienerIndex') # Field name made lowercase.
- cmpdnamesh = models.CharField(db_column='CmpdNameSh', max_length=20, blank=True, null=True) # Field name made lowercase.
- idpubchem = models.CharField(db_column='IdPubchem', max_length=10, blank=True, null=True) # Field name made lowercase.
- idchemspider = models.CharField(db_column='IdChemspider', max_length=10, blank=True, null=True) # Field name made lowercase.
- idchembl = models.CharField(db_column='IDChembl', max_length=30, blank=True, null=True) # Field name made lowercase.
- cmpdiupacname = models.CharField(db_column='CmpdIUPACName', max_length=255, blank=True, null=True) # Field name made lowercase.
- idmddrcompound = models.ForeignKey('Mddrcompound', models.DO_NOTHING, db_column='IDMDDRCompound', blank=True, null=True) # Field name made lowercase.
-
- class Meta:
-# managed = False
- db_table = 'compound'
-
-
-class Disease(models.Model):
- idppi = models.ForeignKey('Ppi', models.DO_NOTHING, db_column='IDPPI') # Field name made lowercase.
- disease = models.CharField(db_column='Disease', max_length=30) # Field name made lowercase.
class Meta:
# managed = False
@@ -328,45 +333,21 @@ class DjangoMigrations(models.Model):
class Domain(models.Model):
- iddomain = models.AutoField(db_column='IDDomain', primary_key=True) # Field name made lowercase.
- pfamid = models.CharField(db_column='PfamID', max_length=20) # Field name made lowercase.
- pfamnumaccession = models.CharField(db_column='PfamNumAccession', unique=True, max_length=10) # Field name made lowercase.
- domaindescription = models.CharField(db_column='DomainDescription', max_length=100) # Field name made lowercase.
- domainfamily = models.CharField(db_column='DomainFamily', max_length=25) # Field name made lowercase.
+ iddomain = models.AutoField(='IDDomain', primary_key=True)
+ pfamid = models.CharField(='PfamID', max_length=20)
+ pfamnumaccession = models.CharField(='PfamNumAccession', unique=True, max_length=10)
+ domaindescription = models.CharField(='DomainDescription', max_length=100)
+ domainfamily = models.CharField(='DomainFamily', max_length=25)
class Meta:
# managed = False
db_table = 'domain'
-
-class Mddrcmpdactclass(models.Model):
- idmddrcompound = models.ForeignKey('Mddrcompound', models.DO_NOTHING, db_column='IDMDDRCompound') # Field name made lowercase.
- activityclass = models.CharField(db_column='ActivityClass', max_length=60) # Field name made lowercase.
-
- class Meta:
-# managed = False
- db_table = 'mDDRCmpdActClass'
- unique_together = (('idmddrcompound', 'activityclass'),)
-
-
-class Mddrcompound(models.Model):
- idmddrcompound = models.IntegerField(db_column='IDMDDRCompound') # Field name made lowercase.
- mddrcmpdname = models.CharField(db_column='MDDRCmpdName', max_length=40) # Field name made lowercase.
- phasedvpmt = models.CharField(db_column='PhaseDvpmt', max_length=20) # Field name made lowercase.
- canonicalsmile = models.CharField(db_column='CanonicalSmile', max_length=500, blank=True, null=True) # Field name made lowercase.
- versionmddr = models.CharField(db_column='VersionMDDR', max_length=7) # Field name made lowercase.
-
- class Meta:
-# managed = False
- db_table = 'mDDRCompound'
- unique_together = (('idmddrcompound', 'mddrcmpdname', 'phasedvpmt'),)
-
-
class Mddrsimilarity(models.Model):
- idcompound = models.ForeignKey(Compound, models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- idmddrcompound = models.ForeignKey(Mddrcompound, models.DO_NOTHING, db_column='IDMDDRCompound') # Field name made lowercase.
- versionmddr = models.CharField(db_column='VersionMDDR', max_length=7) # Field name made lowercase.
- tanimoto = models.DecimalField(db_column='Tanimoto', max_digits=6, decimal_places=5) # Field name made lowercase.
+ idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')
+ idmddrcompound = models.ForeignKey(Mddrcompound, models.DO_NOTHING, ='IDMDDRCompound')
+ versionmddr = models.CharField(='VersionMDDR', max_length=7)
+ tanimoto = models.DecimalField(='Tanimoto', max_digits=6, decimal_places=5)
class Meta:
# managed = False
@@ -375,12 +356,12 @@ class Mddrsimilarity(models.Model):
class Ppi(models.Model):
- idppi = models.AutoField(db_column='IDPPI', primary_key=True) # Field name made lowercase.
- idcomplexe1 = models.ForeignKey(Complexe, models.DO_NOTHING, db_column='IDComplexe1', related_name='cplx_id_1') # Field name made lowercase.
- idcomplexe2 = models.ForeignKey(Complexe, models.DO_NOTHING, db_column='IDComplexe2', related_name='cplx_id_2') # Field name made lowercase.
- idbindingsite1 = models.ForeignKey(Bindingsite, models.DO_NOTHING, db_column='IDBindingSite1', related_name='bs_id_1') # Field name made lowercase.
- idbindingsite2 = models.ForeignKey(Bindingsite, models.DO_NOTHING, db_column='IDBindingSite2', related_name='bs_id_2') # Field name made lowercase.
- family = models.CharField(db_column='Family', max_length=25) # Field name made lowercase.
+ idppi = models.AutoField(='IDPPI', primary_key=True)
+ idcomplexe1 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe1', related_name='cplx_id_1')
+ idcomplexe2 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe2', related_name='cplx_id_2')
+ idbindingsite1 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite1', related_name='bs_id_1')
+ idbindingsite2 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite2', related_name='bs_id_2')
+ family = models.CharField(='Family', max_length=25)
class Meta:
# managed = False
@@ -389,13 +370,13 @@ class Ppi(models.Model):
class Protein(models.Model):
- idprotein = models.AutoField(db_column='IDProtein', primary_key=True) # Field name made lowercase.
- numuniprot = models.CharField(db_column='NumUniprot', unique=True, max_length=10) # Field name made lowercase.
- protnamelg = models.CharField(db_column='ProtNameLg', max_length=75) # Field name made lowercase.
- protnamesh = models.CharField(db_column='ProtNameSh', max_length=50) # Field name made lowercase.
- protalias = models.CharField(db_column='ProtAlias', unique=True, max_length=30) # Field name made lowercase.
- protnamesp = models.CharField(db_column='ProtNameSp', max_length=30) # Field name made lowercase.
- organism = models.CharField(db_column='Organism', max_length=80) # Field name made lowercase.
+ idprotein = models.AutoField(='IDProtein', primary_key=True)
+ numuniprot = models.CharField(='NumUniprot', unique=True, max_length=10)
+ protnamelg = models.CharField(='ProtNameLg', max_length=75)
+ protnamesh = models.CharField(='ProtNameSh', max_length=50)
+ protalias = models.CharField(='ProtAlias', unique=True, max_length=30)
+ protnamesp = models.CharField(='ProtNameSp', max_length=30)
+ organism = models.CharField(='Organism', max_length=80)
class Meta:
# managed = False
@@ -403,9 +384,9 @@ class Protein(models.Model):
class Refcmpdbiblio(models.Model):
- idcompound = models.ForeignKey(Compound, models.DO_NOTHING, db_column='IDCompound') # Field name made lowercase.
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, db_column='IDBiblio') # Field name made lowercase.
- cmpdnameinbiblio = models.CharField(db_column='CmpdNameInBiblio', max_length=20, blank=True, null=True) # Field name made lowercase.
+ idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')
+ idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
+ cmpdnameinbiblio = models.CharField(='CmpdNameInBiblio', max_length=20, blank=True, null=True)
class Meta:
# managed = False
@@ -414,8 +395,8 @@ class Refcmpdbiblio(models.Model):
class Refproteinfonction(models.Model):
- idprotein = models.ForeignKey(Protein, models.DO_NOTHING, db_column='IDProtein') # Field name made lowercase.
- protfonctionsp = models.CharField(db_column='ProtFonctionSP', max_length=200) # Field name made lowercase.
+ idprotein = models.ForeignKey(Protein, models.DO_NOTHING, ='IDProtein')
+ protfonctionsp = models.CharField(='ProtFonctionSP', max_length=200)
class Meta:
# managed = False
@@ -423,26 +404,6 @@ class Refproteinfonction(models.Model):
unique_together = (('protfonctionsp', 'idprotein'),)
-class Testactivitydescription(models.Model):
- idtestactivity = models.AutoField(db_column='IDTestActivity', primary_key=True) # Field name made lowercase.
- idcomplexebound = models.ForeignKey(Complexe, models.DO_NOTHING, db_column='IDComplexeBound') # Field name made lowercase.
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, db_column='IDBiblio') # Field name made lowercase.
- idppi = models.ForeignKey(Ppi, models.DO_NOTHING, db_column='IDPPI', blank=True, null=True) # Field name made lowercase.
- testnameactivity = models.CharField(db_column='TestNameActivity', max_length=40) # Field name made lowercase.
- isprimary = models.CharField(db_column='IsPrimary', max_length=1) # Field name made lowercase.
- protboundconstruct = models.CharField(db_column='ProtBoundConstruct', max_length=11) # Field name made lowercase.
- testtype = models.CharField(db_column='TestType', max_length=5) # Field name made lowercase.
- testmodulationtype = models.CharField(db_column='TestModulationType', max_length=13) # Field name made lowercase.
- nbactivescmpdstot = models.IntegerField(db_column='NbActivesCmpdsTot') # Field name made lowercase.
- conccmpds = models.DecimalField(db_column='ConcCmpds', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- protocol = models.TextField(db_column='Protocol', blank=True, null=True) # Field name made lowercase.
- concproteinbound = models.DecimalField(db_column='ConcProteinBound', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- concprotein2 = models.DecimalField(db_column='ConcProtein2', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- controlepos = models.CharField(db_column='ControlePos', max_length=50, blank=True, null=True) # Field name made lowercase.
- controleneg = models.CharField(db_column='ControleNeg', max_length=50, blank=True, null=True) # Field name made lowercase.
- cellline = models.CharField(db_column='CellLine', max_length=50, blank=True, null=True) # Field name made lowercase.
- pepseq = models.CharField(db_column='PepSeq', max_length=100, blank=True, null=True) # Field name made lowercase.
- marker = models.CharField(db_column='Marker', max_length=35, blank=True, null=True) # Field name made lowercase.
class Meta:
# managed = False
@@ -450,11 +411,11 @@ class Testactivitydescription(models.Model):
class Testcytotoxdescription(models.Model):
- idtestcytotox = models.AutoField(db_column='IDTestCytotox', primary_key=True) # Field name made lowercase.
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, db_column='IDBiblio') # Field name made lowercase.
- testnamecytotox = models.CharField(db_column='TestNameCytotox', max_length=40) # Field name made lowercase.
- cellline = models.CharField(db_column='CellLine', max_length=50) # Field name made lowercase.
- conccmpd = models.DecimalField(db_column='ConcCmpd', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
+ idtestcytotox = models.AutoField(='IDTestCytotox', primary_key=True)
+ idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
+ testnamecytotox = models.CharField(='TestNameCytotox', max_length=40)
+ cellline = models.CharField(='CellLine', max_length=50)
+ conccmpd = models.DecimalField(='ConcCmpd', max_digits=7, decimal_places=3, blank=True, null=True)
class Meta:
# managed = False
@@ -462,14 +423,14 @@ class Testcytotoxdescription(models.Model):
class Testpkdescription(models.Model):
- idtestpk = models.AutoField(db_column='IDTestPK', primary_key=True) # Field name made lowercase.
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, db_column='IDBiblio') # Field name made lowercase.
- testnamepk = models.CharField(db_column='TestNamePK', max_length=40) # Field name made lowercase.
- animal = models.CharField(db_column='Animal', max_length=100) # Field name made lowercase.
- administrationmode = models.CharField(db_column='AdministrationMode', max_length=2, blank=True, null=True) # Field name made lowercase.
- concentration = models.DecimalField(db_column='Concentration', max_digits=7, decimal_places=3, blank=True, null=True) # Field name made lowercase.
- dose = models.DecimalField(db_column='Dose', max_digits=7, decimal_places=2, blank=True, null=True) # Field name made lowercase.
- doseinterval = models.IntegerField(db_column='DoseInterval', blank=True, null=True) # Field name made lowercase.
+ idtestpk = models.AutoField(='IDTestPK', primary_key=True)
+ idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
+ testnamepk = models.CharField(='TestNamePK', max_length=40)
+ animal = models.CharField(='Animal', max_length=100)
+ administrationmode = models.CharField(='AdministrationMode', max_length=2, blank=True, null=True)
+ concentration = models.DecimalField(='Concentration', max_digits=7, decimal_places=3, blank=True, null=True)
+ dose = models.DecimalField(='Dose', max_digits=7, decimal_places=2, blank=True, null=True)
+ doseinterval = models.IntegerField(='DoseInterval', blank=True, null=True)
class Meta:
# managed = False
--
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