From a2da0027042f826347e4b972438c8451857872c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 25 Jul 2018 16:03:00 +0200
Subject: [PATCH] add squashed migration for pristine DBs ;)
Former-commit-id: d062fb81c1f37bcb3e205375dd440b5c3a0fd59e
---
.../0001_squashed_0035_auto_20180725_1347.py | 840 ++++++++++++++++++
1 file changed, 840 insertions(+)
create mode 100644 ippisite/ippidb/migrations/0001_squashed_0035_auto_20180725_1347.py
diff --git a/ippisite/ippidb/migrations/0001_squashed_0035_auto_20180725_1347.py b/ippisite/ippidb/migrations/0001_squashed_0035_auto_20180725_1347.py
new file mode 100644
index 00000000..d799bccb
--- /dev/null
+++ b/ippisite/ippidb/migrations/0001_squashed_0035_auto_20180725_1347.py
@@ -0,0 +1,840 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-07-25 14:00
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ replaces = [('ippidb', '0001_initial'), ('ippidb', '0002_auto_20170221_1606'), ('ippidb', '0003_auto_20170313_1948'), ('ippidb', '0004_auto_20170314_1449'), ('ippidb', '0005_auto_20170327_1301'), ('ippidb', '0006_auto_20170327_1439'), ('ippidb', '0007_auto_20170328_2045'), ('ippidb', '0008_auto_20170329_1441'), ('ippidb', '0009_auto_20170517_2020'), ('ippidb', '0010_auto_20170518_1142'), ('ippidb', '0011_auto_20170518_1404'), ('ippidb', '0012_auto_20170518_1913'), ('ippidb', '0013_auto_20170518_1943'), ('ippidb', '0014_auto_20170519_1243'), ('ippidb', '0015_auto_20170519_1442'), ('ippidb', '0016_auto_20170519_1453'), ('ippidb', '0017_auto_20170519_1500'), ('ippidb', '0018_auto_20170522_1501'), ('ippidb', '0019_auto_20170522_1931'), ('ippidb', '0020_auto_20170522_1945'), ('ippidb', '0021_auto_20170522_1949'), ('ippidb', '0022_auto_20170523_1311'), ('ippidb', '0023_auto_20170523_1858'), ('ippidb', '0024_auto_20170523_2000'), ('ippidb', '0025_auto_20171110_1046'), ('ippidb', '0026_auto_20171110_1426'), ('ippidb', '0027_auto_20180307_1327'), ('ippidb', '0028_auto_20180307_1405'), ('ippidb', '0029_auto_20180308_1935'), ('ippidb', '0030_testpkdescription_concentration'), ('ippidb', '0031_compoundactivityresult_inhibition_percentage'), ('ippidb', '0032_lellebiplotdata'), ('ippidb', '0033_auto_20180502_1500'), ('ippidb', '0034_auto_20180503_2110'), ('ippidb', '0035_auto_20180725_1347')]
+
+ initial = True
+
+ dependencies = [
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Bibliography',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('source', models.CharField(choices=[('PM', 'PubMed article'), ('PT', 'Patent')], max_length=2, verbose_name='Bibliographic type')),
+ ('id_source', models.CharField(max_length=25, verbose_name='Bibliographic ID')),
+ ('title', models.CharField(max_length=300, verbose_name='Title')),
+ ('journal_name', models.CharField(max_length=50, null=True, verbose_name='Journal name')),
+ ('authors_list', models.CharField(max_length=500, verbose_name='Authors list')),
+ ('biblio_year', models.PositiveSmallIntegerField(verbose_name='Year')),
+ ('cytotox', models.BooleanField(default=False, verbose_name='Cytotoxicity data')),
+ ('in_silico', models.BooleanField(default=False, verbose_name='in silico study performed')),
+ ('in_vitro', models.BooleanField(default=False, verbose_name='in vitro study performed')),
+ ('in_vivo', models.BooleanField(default=False, verbose_name='in vivo study performed')),
+ ('in_cellulo', models.BooleanField(default=False, verbose_name='in cellulo study performed')),
+ ('pharmacokinetic', models.BooleanField(default=False, verbose_name='pharmacokinetic study performed')),
+ ('xray', models.BooleanField(default=False, verbose_name='contains xray data')),
+ ],
+ options={
+ 'verbose_name_plural': 'bibliographies',
+ },
+ ),
+ migrations.CreateModel(
+ name='Complex',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('copy_nb', models.IntegerField(verbose_name='Number of copies')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='Domain',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('pfam_acc', models.CharField(max_length=10, unique=True, verbose_name='Pfam Accession')),
+ ('pfam_id', models.CharField(max_length=20, verbose_name='Pfam Family Identifier')),
+ ('pfam_description', models.CharField(max_length=100, verbose_name='Pfam Description')),
+ ('domain_family', models.CharField(max_length=25, verbose_name='Domain family')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='MolecularFunction',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('go_id', models.CharField(max_length=10, unique=True, verbose_name='Gene Ontology ID')),
+ ('description', models.CharField(max_length=500, verbose_name='description')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='Ppi',
+ 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')),
+ ('pdb_id', models.CharField(default=1, max_length=4, verbose_name='PDB ID')),
+ ('ppi_id', models.IntegerField(default=1, verbose_name='PPI identifier')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='Protein',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('uniprot_id', models.CharField(max_length=10, unique=True, verbose_name='Uniprot ID')),
+ ('recommended_name_long', models.CharField(max_length=75, verbose_name='Uniprot Recommended Name (long)')),
+ ('short_name', models.CharField(max_length=50, verbose_name='Short name')),
+ ('gene_name', models.CharField(max_length=30, unique=True, verbose_name='Gene name')),
+ ('entry_name', models.CharField(max_length=30, verbose_name='Entry name')),
+ ('molecular_functions', models.ManyToManyField(to='ippidb.MolecularFunction')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='Taxonomy',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('taxonomy_id', models.DecimalField(decimal_places=0, max_digits=9, unique=True, verbose_name='NCBI TaxID')),
+ ('name', models.CharField(max_length=200, verbose_name='Organism name')),
+ ],
+ options={
+ 'verbose_name_plural': 'taxonomies',
+ },
+ ),
+ migrations.AddField(
+ model_name='protein',
+ name='organism',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Taxonomy'),
+ ),
+ migrations.AddField(
+ model_name='complex',
+ name='protein_id',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Protein'),
+ ),
+ migrations.CreateModel(
+ name='Disease',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(default=None, max_length=30, unique=True, verbose_name='Disease')),
+ ],
+ ),
+ migrations.AlterModelOptions(
+ name='complex',
+ options={'verbose_name_plural': 'complexes'},
+ ),
+ migrations.CreateModel(
+ name='Compound',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('canonical_smile', models.CharField(max_length=250, unique=True, verbose_name='Canonical Smile')),
+ ('is_macrocycle', models.BooleanField(verbose_name='Contains one or more macrocycles')),
+ ('aromatic_ratio', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='Aromatic ratio')),
+ ('balaban_index', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='Balaban index')),
+ ('fsp3', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='Fsp3')),
+ ('dh_Petitjean', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='Dh Petitjean')),
+ ('diam_graph_non_h_petitjean', models.IntegerField(verbose_name='Diameter for the molecular graph for heavy atoms (Petitjean)')),
+ ('gc_molar_refractivity', models.DecimalField(decimal_places=2, max_digits=5, verbose_name='GC Molar Refractivity')),
+ ('g_petitjean', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='G Petitjean')),
+ ('ig_petitjean', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='Ig Petitjean')),
+ ('log_d', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='LogD (Partition coefficient octanol-1/water, with pKa information)')),
+ ('a_log_p', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='ALogP (Partition coefficient octanol-1/water)')),
+ ('mean_atom_vol_vdw', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='Mean atom volume computed with VdW radii')),
+ ('molecular_weight', models.DecimalField(decimal_places=2, max_digits=6, verbose_name='Molecular weight')),
+ ('nb_acceptor_h', models.IntegerField(verbose_name='Number of hydrogen bond acceptors')),
+ ('nb_aliphatic_amines', models.IntegerField(verbose_name='Number of aliphatics amines')),
+ ('nb_aromatic_bonds', models.IntegerField(verbose_name='Number of aromatic bonds')),
+ ('nb_aromatic_ether', models.IntegerField(verbose_name='Number of aromatic ethers')),
+ ('nb_aromatic_sssr', models.IntegerField(verbose_name='Number of aromatic Smallest Set of System Rings (SSSR)')),
+ ('nb_atom', models.IntegerField(verbose_name='Number of atoms')),
+ ('nb_atom_non_h', models.IntegerField(verbose_name='Number of non hydrogen atoms')),
+ ('nb_benzene_like_rings', models.IntegerField(verbose_name='Number of benzene-like rings')),
+ ('nb_bonds', models.IntegerField(verbose_name='Number of bonds')),
+ ('nb_bonds_non_h', models.IntegerField(verbose_name='Number of bonds not involving a hydrogen')),
+ ('nb_br', models.IntegerField(verbose_name='Number of Bromine atoms')),
+ ('nb_c', models.IntegerField(verbose_name='Number of Carbon atoms')),
+ ('nb_chiral_centers', models.IntegerField(verbose_name='Number of chiral centers')),
+ ('nb_circuits', models.IntegerField(verbose_name='Number of circuits')),
+ ('nb_cl', models.IntegerField(verbose_name='Number of Chlorine atoms')),
+ ('nb_csp2', models.IntegerField(verbose_name='Number of sp2-hybridized carbon atoms')),
+ ('nb_csp3', models.IntegerField(verbose_name='Number of sp3-hybridized carbon atoms')),
+ ('nb_donor_h', models.IntegerField(verbose_name='Number of hydrogen bond donors')),
+ ('nb_double_bonds', models.IntegerField(verbose_name='Number of double bonds')),
+ ('nb_f', models.IntegerField(verbose_name='Number of fluorine atoms')),
+ ('nb_i', models.IntegerField(verbose_name='Number of iodine atoms')),
+ ('nb_multiple_bonds', models.IntegerField(verbose_name='Number of multiple bonds')),
+ ('nb_n', models.IntegerField(verbose_name='Number of nitrogen atoms')),
+ ('nb_o', models.IntegerField(verbose_name='Number of oxygen atoms')),
+ ('nb_rings', models.IntegerField(verbose_name='Number of rings')),
+ ('nb_rotatable_bonds', models.IntegerField(verbose_name='Number of rotatable bonds')),
+ ('radius_graph_non_h_petitjean', models.IntegerField(verbose_name='Radius for the molecular graph for heavy atoms (Petitjean)')),
+ ('randic_index', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='Randic index')),
+ ('rdf070m', models.DecimalField(decimal_places=2, max_digits=5, verbose_name='RDF070m, radial distribution function weighted by the atomic masses at 7Ã…')),
+ ('rotatable_bond_fraction', models.DecimalField(decimal_places=2, max_digits=3, verbose_name='Fraction of rotatable bonds')),
+ ('sum_atom_polar', models.DecimalField(decimal_places=2, max_digits=5, verbose_name='Sum of atomic polarizabilities')),
+ ('sum_atom_vol_vdw', models.DecimalField(decimal_places=2, max_digits=6, verbose_name='Sum of atom volumes computed with VdW radii')),
+ ('surface_vdw_petitjean', models.DecimalField(decimal_places=2, max_digits=6, verbose_name='Van der Waals surface area (Petitjean)')),
+ ('thickness_petitjean', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='Thickness (Petitjean)')),
+ ('tpsa', models.DecimalField(decimal_places=2, max_digits=5, verbose_name='Topological Polar Surface Area (TPSA)')),
+ ('ui', models.DecimalField(decimal_places=2, max_digits=4, verbose_name='Unsaturation index')),
+ ('vol_vdw_petitjean', models.DecimalField(decimal_places=2, max_digits=7, verbose_name='Van der Waals volume (Petitjean)')),
+ ('wiener_index', models.IntegerField(verbose_name='Wiener index')),
+ ('common_name', models.CharField(blank=True, max_length=20, null=True, unique=True, verbose_name='Common name')),
+ ('pubchem_id', models.CharField(blank=True, max_length=10, null=True, unique=True, verbose_name='Pubchem ID')),
+ ('chemspider_id', models.CharField(blank=True, max_length=10, null=True, unique=True, verbose_name='Chemspider ID')),
+ ('chembl_id', models.CharField(blank=True, max_length=30, null=True, unique=True, verbose_name='Chembl ID')),
+ ('iupac_name', models.CharField(blank=True, max_length=255, null=True, unique=True, verbose_name='IUPAC name')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='MDDRCompoundActivityClass',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('activity_class', models.CharField(max_length=100, verbose_name='Activity Class')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='MDDRCompoundImport',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('mddr_compound_id', models.IntegerField(verbose_name='MDDR compound ID')),
+ ('mddr_name', models.CharField(max_length=40, verbose_name='MDDR name')),
+ ('dvpmt_phase', models.CharField(max_length=20, verbose_name='Development phase')),
+ ('canonical_smile', models.CharField(blank=True, max_length=500, null=True, unique=True, verbose_name='Canonical Smile')),
+ ('db_import_date', models.DecimalField(decimal_places=0, max_digits=6, verbose_name='MDDR release year/month')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='MDDRSimilarity',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('canonical_smile_ippidb', models.CharField(blank=True, max_length=500, null=True, unique=True, verbose_name='Canonical Smile for IPPIDB compound')),
+ ('canonical_smile_mddr', models.CharField(blank=True, max_length=500, null=True, unique=True, verbose_name='Canonical Smile for MDDR Compound')),
+ ('tanimoto', models.DecimalField(decimal_places=5, max_digits=6, verbose_name='Tanimoto')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='ProteinDomainComplex',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('ppc_copy_nb', models.IntegerField(verbose_name='Number of copies of the protein in the complex')),
+ ],
+ options={
+ 'verbose_name_plural': 'complexes',
+ },
+ ),
+ migrations.CreateModel(
+ name='Symmetry',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('code', models.CharField(max_length=2, verbose_name='Symmetry code')),
+ ('description', models.CharField(max_length=300, verbose_name='Description')),
+ ],
+ options={
+ 'verbose_name_plural': 'symmetries',
+ },
+ ),
+ migrations.RemoveField(
+ model_name='complex',
+ name='protein_id',
+ ),
+ migrations.CreateModel(
+ name='ProteinDomainBoundComplex',
+ fields=[
+ ('proteindomaincomplex_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='ippidb.ProteinDomainComplex')),
+ ('ppp_copy_nb_per_p', models.IntegerField(verbose_name='Number of copies of the protein in the pocket')),
+ ('pockets_nb', models.IntegerField(verbose_name='Total number of pockets in the complex')),
+ ],
+ options={
+ 'verbose_name_plural': 'bound complexes',
+ },
+ bases=('ippidb.proteindomaincomplex',),
+ ),
+ migrations.CreateModel(
+ name='ProteinDomainPartnerComplex',
+ fields=[
+ ('proteindomaincomplex_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='ippidb.ProteinDomainComplex')),
+ ],
+ options={
+ 'verbose_name_plural': 'partner complexes',
+ },
+ bases=('ippidb.proteindomaincomplex',),
+ ),
+ migrations.DeleteModel(
+ name='Complex',
+ ),
+ migrations.AddField(
+ model_name='proteindomaincomplex',
+ name='domain',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Domain'),
+ ),
+ migrations.AddField(
+ model_name='proteindomaincomplex',
+ name='protein',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Protein'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrsimilarity',
+ unique_together=set([('canonical_smile_ippidb', 'canonical_smile_mddr')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundimport',
+ unique_together=set([('mddr_compound_id', 'mddr_name', 'dvpmt_phase')]),
+ ),
+ migrations.AddField(
+ model_name='mddrcompoundactivityclass',
+ name='mddr_compound_id',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.MDDRCompoundImport'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='mddr_compound_id',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.MDDRCompoundImport'),
+ ),
+ migrations.AddField(
+ model_name='ppi',
+ name='complex_id',
+ field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainComplex'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='ppi',
+ name='symmetry_id',
+ field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Symmetry'),
+ preserve_default=False,
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundactivityclass',
+ unique_together=set([('mddr_compound_id', 'activity_class')]),
+ ),
+ migrations.CreateModel(
+ name='CellLine',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(max_length=50, unique=True, verbose_name='Name')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='TestActivityDescription',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('test_name', models.CharField(max_length=100, verbose_name='Test name')),
+ ('test_type', models.CharField(choices=[('BIOCH', 'Biochemical assay'), ('CELL', 'Cellular assay')], max_length=5, verbose_name='Test type')),
+ ('test_modulation_type', models.CharField(choices=[('B', 'Binding'), ('I', 'Inhibition'), ('S', 'Stabilization')], max_length=1, verbose_name='Test modulation type')),
+ ('nb_active_compounds', models.IntegerField(verbose_name='Total number of active compounds')),
+ ('biblio_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('cell_line', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.CellLine')),
+ ('complex_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex')),
+ ('ppi_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi')),
+ ],
+ ),
+ migrations.AlterModelOptions(
+ name='mddrcompoundactivityclass',
+ options={'verbose_name_plural': 'MDDR compound activity classes'},
+ ),
+ migrations.AlterModelOptions(
+ name='mddrcompoundimport',
+ options={'verbose_name_plural': 'MDDR compound imports'},
+ ),
+ migrations.AlterModelOptions(
+ name='mddrsimilarity',
+ options={'verbose_name_plural': 'MDDR similarities'},
+ ),
+ migrations.CreateModel(
+ name='ActivityType',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(max_length=50, unique=True, verbose_name='Name')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='CmpdAction',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('activation_mode', models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric')], max_length=1, verbose_name='Activation mode')),
+ ('complex_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ('nb_copy_compounds', models.IntegerField(default=1, verbose_name='Number of copies for the compound')),
+ ('pdb_id', models.CharField(default='NA', max_length=4, verbose_name='PDB ID')),
+ ('ppi_id', models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='CompoundActivityResult',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('activity', models.DecimalField(decimal_places=10, max_digits=12, verbose_name='Activity')),
+ ('activity_type_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ActivityType')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ('test_activity_description_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestActivityDescription')),
+ ('modulation_type', models.CharField(choices=[('B', 'Binding'), ('I', 'Inhibition'), ('S', 'Stabilization')], default='B', max_length=1, verbose_name='Modulation type')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='CompoundCytotoxicityResult',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('toxicity', models.BooleanField(default=False, verbose_name='Toxicity')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='CompoundPKResult',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('tolerated', models.NullBooleanField(verbose_name='Tolerated')),
+ ('auc', models.IntegerField(blank=True, null=True, verbose_name='Area under curve (ng.mL-1.hr)')),
+ ('clearance', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Clearance (mL/hr)')),
+ ('cmax', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Maximal concentration (ng/mL)')),
+ ('oral_bioavailability', models.IntegerField(blank=True, null=True, verbose_name='Oral Bioavailability (%F)')),
+ ('t_demi', models.IntegerField(blank=True, null=True, verbose_name='t½')),
+ ('t_max', models.IntegerField(blank=True, null=True, verbose_name='tmax')),
+ ('voldistribution', models.DecimalField(blank=True, decimal_places=2, max_digits=5, null=True, verbose_name='Volume distribution (Vd)')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='TestCytotoxDescription',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('test_name', models.CharField(max_length=100, verbose_name='Cytotoxicity test name')),
+ ('compound_concentration', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Compound concentration in μM')),
+ ('biblio', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('cell_line', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.CellLine')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='TestPKDescription',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('test_name', models.CharField(max_length=100, verbose_name='Pharmacokinetic test name')),
+ ('dose', models.DecimalField(blank=True, decimal_places=4, max_digits=9, null=True, verbose_name='Dose in mg/kg')),
+ ('dose_interval', models.IntegerField(blank=True, null=True, verbose_name='Dose interval, in hours')),
+ ('administration_mode', models.CharField(blank=True, choices=[('IV', ''), ('PO', ''), ('IP', ''), ('SL', 'SL')], max_length=2, null=True, verbose_name='Administration mode')),
+ ('biblio', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('organism', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Taxonomy')),
+ ('concentration', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Concentration in mg/l')),
+ ],
+ ),
+ migrations.AddField(
+ model_name='compoundpkresult',
+ name='test_pk_description_id',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestPKDescription'),
+ ),
+ migrations.AddField(
+ model_name='compoundcytotoxicityresult',
+ name='test_cytotoxicity_description_id',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestCytotoxDescription'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundpkresult',
+ unique_together=set([('compound_id', 'test_pk_description_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundcytotoxicityresult',
+ unique_together=set([('compound_id', 'test_cytotoxicity_description_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundactivityresult',
+ unique_together=set([('compound_id', 'test_activity_description_id', 'activity_type_id')]),
+ ),
+ migrations.CreateModel(
+ name='RefCompoundBiblio',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('compound_name', models.CharField(max_length=50, verbose_name='Compound name in the publication')),
+ ('bibliography_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ],
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('complex_id', 'compound_id', 'pdb_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound_id', 'bibliography_id')]),
+ ),
+ 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='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='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.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.RemoveField(
+ model_name='cmpdaction',
+ name='complex',
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('ppi', 'compound', 'activation_mode', '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.RenameField(
+ model_name='compoundpkresult',
+ old_name='cmax',
+ new_name='c_max',
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundpkresult',
+ unique_together=set([('compound', 'test_pk_description')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundactivityclass',
+ unique_together=set([]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound', 'bibliography')]),
+ ),
+ 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.DeleteModel(
+ name='ActivityType',
+ ),
+ migrations.AddField(
+ model_name='ppicomplex',
+ name='ppi',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi'),
+ ),
+ migrations.AlterField(
+ model_name='ppi',
+ name='pdb_id',
+ field=models.CharField(max_length=4, null=True, verbose_name='PDB ID'),
+ ),
+ migrations.RenameModel(
+ old_name='CmpdAction',
+ new_name='CompoundAction',
+ ),
+ migrations.AddField(
+ model_name='ppi',
+ name='diseases',
+ field=models.ManyToManyField(to='ippidb.Disease'),
+ ),
+ 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'),
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='pubchem_id',
+ field=models.CharField(blank=True, max_length=10, null=True, verbose_name='Pubchem ID'),
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='iupac_name',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name='IUPAC name'),
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='chembl_id',
+ field=models.CharField(blank=True, max_length=30, null=True, verbose_name='Chembl ID'),
+ ),
+ migrations.CreateModel(
+ name='MDDRActivityClass',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(max_length=100, unique=True, verbose_name='Activity Class')),
+ ],
+ options={
+ 'verbose_name_plural': 'MDDR activity classes',
+ },
+ ),
+ 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'),
+ ),
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='db_import_date',
+ field=models.DateTimeField(verbose_name='MDDR release year/month'),
+ ),
+ migrations.RemoveField(
+ model_name='mddrcompoundimport',
+ name='mddr_compound_id',
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundimport',
+ unique_together=set([('mddr_name', 'dvpmt_phase', 'canonical_smile')]),
+ ),
+ migrations.AlterField(
+ model_name='mddrcompoundimport',
+ name='canonical_smile',
+ field=models.CharField(blank=True, max_length=500, null=True, verbose_name='Canonical Smile'),
+ ),
+ 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'),
+ ),
+ 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'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_cellulo',
+ field=models.BooleanField(default=False, verbose_name='in cellulo study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_silico',
+ field=models.BooleanField(default=False, verbose_name='in silico study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_vitro',
+ field=models.BooleanField(default=False, verbose_name='in vitro study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_vivo',
+ field=models.BooleanField(default=False, verbose_name='in vivo study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='pharmacokinetic',
+ field=models.BooleanField(default=False, verbose_name='pharmacokinetic study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='source',
+ field=models.CharField(choices=[('PM', 'PubMed ID'), ('PT', 'Patent'), ('DO', 'DOI ID')], default='PM', max_length=2, verbose_name='Bibliographic type'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='xray',
+ field=models.BooleanField(default=False, verbose_name='X-Ray data'),
+ ),
+ migrations.AlterField(
+ model_name='compoundaction',
+ name='activation_mode',
+ field=models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric'), ('U', 'Unspecified')], max_length=1, verbose_name='Activation mode'),
+ ),
+ migrations.AlterField(
+ model_name='compoundaction',
+ name='pdb_id',
+ field=models.CharField(blank=True, max_length=4, null=True, verbose_name='PDB ID'),
+ ),
+ migrations.AddField(
+ model_name='testactivitydescription',
+ name='is_primary',
+ field=models.BooleanField(default=False, verbose_name='Is primary'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='testactivitydescription',
+ name='protein_bound_construct',
+ field=models.CharField(blank=True, choices=[('F', 'Full length'), ('U', 'Unspecified')], max_length=5, null=True, verbose_name='Protein bound construct'),
+ ),
+ migrations.AddField(
+ model_name='testactivitydescription',
+ name='protein_domain_bound_complex',
+ field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundactivityresult',
+ name='inhibition_percentage',
+ field=models.DecimalField(decimal_places=0, max_digits=3, null=True, verbose_name='Inhibition percentage'),
+ ),
+ migrations.CreateModel(
+ name='LeLleBiplotData',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('le_lle_biplot_data', models.CharField(blank=True, max_length=150000, null=True, verbose_name='LE-LLE biplot JSON data')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='PpiFamily',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(max_length=30, unique=True, verbose_name='Name')),
+ ],
+ options={
+ 'verbose_name_plural': 'PPI Families',
+ },
+ ),
+ migrations.AddField(
+ model_name='ppi',
+ name='family',
+ field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.PpiFamily'),
+ ),
+ migrations.CreateModel(
+ name='PcaBiplotData',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('pca_biplot_data', models.CharField(blank=True, max_length=150000, null=True, verbose_name='PCA biplot JSON data')),
+ ],
+ ),
+ ]
--
GitLab