diff --git a/ippisite/ippidb/management/commands/cache_compound_properties.py b/ippisite/ippidb/management/commands/cache_compound_properties.py
new file mode 100644
index 0000000000000000000000000000000000000000..9fdc5e095f5c52998804c1195ce2e68f9ba3364f
--- /dev/null
+++ b/ippisite/ippidb/management/commands/cache_compound_properties.py
@@ -0,0 +1,13 @@
+from django.core.management import BaseCommand
+
+from ippidb.models import update_compound_cached_properties
+
+class Command(BaseCommand):
+
+ help = "Cache compound properties in the main 'Compound' table"
+
+ def handle(self, *args, **options):
+ self.stdout.write(self.style.SUCCESS('Generating the compound properties cache...'))
+ n = update_compound_cached_properties()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully generated compound properties cache for %s compounds' % n))
\ No newline at end of file
diff --git a/ippisite/ippidb/management/commands/lle_le.py b/ippisite/ippidb/management/commands/lle_le.py
index 7a964dc59658a773991c69d4a6398b72ab996ee0..26a28e2c010ae746a432c1207586015907fd023c 100644
--- a/ippisite/ippidb/management/commands/lle_le.py
+++ b/ippisite/ippidb/management/commands/lle_le.py
@@ -20,10 +20,10 @@ class Command(BaseCommand):
if comp.le is not None:
le = round(comp.le, 7)
lle = round(comp.lle, 7)
- le_lle_data.append({'x': le, 'y': lle, 'id': comp.id, 'family_name': comp.best_pXC50_activity_ppi_family, 'smiles': comp.canonical_smile})
+ le_lle_data.append({'x': le, 'y': lle, 'id': comp.id, 'family_name': comp.best_activity_ppi_family_name, 'smiles': comp.canonical_smile})
else:
self.stdout.write(
- self.style.WARNING('compound %s has no LE (probably because no pXC50 activity results have been registered)' % comp.id))
+ self.style.WARNING('compound %s has no LE' % comp.id))
le_lle_json = json.dumps(le_lle_data, separators=(',',':'))
new = LeLleBiplotData()
new.le_lle_biplot_data = le_lle_json
diff --git a/ippisite/ippidb/management/commands/pca.py b/ippisite/ippidb/management/commands/pca.py
index abdf5a72db02631ff516a09c8522b9a3fb0768bb..47b10fd5bbcdbf876cce5bfbbdfe49d2d28d3792 100644
--- a/ippisite/ippidb/management/commands/pca.py
+++ b/ippisite/ippidb/management/commands/pca.py
@@ -45,7 +45,7 @@ class Command(BaseCommand):
l = []
for comp in Compound.objects.all():
values = model_to_dict(comp, fields=features + ['id','family'])
- values['family'] = comp.best_pXC50_activity_ppi_family
+ values['family'] = comp.best_activity_ppi_family_name
l.append(values)
df = pd.DataFrame(l)
x = df.loc[:, features].values
diff --git a/ippisite/ippidb/migrations/0023_auto_20190524_1456.py b/ippisite/ippidb/migrations/0023_auto_20190524_1456.py
new file mode 100644
index 0000000000000000000000000000000000000000..a06a2393011299b94ba027a5089aeabdf98db371
--- /dev/null
+++ b/ippisite/ippidb/migrations/0023_auto_20190524_1456.py
@@ -0,0 +1,28 @@
+# Generated by Django 2.0.13 on 2019-05-24 14:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0022_auto_20190319_1537'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='bibliography',
+ name='authors_list',
+ field=models.TextField(verbose_name='Authors list'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='journal_name',
+ field=models.TextField(blank=True, null=True, verbose_name='Journal name'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='title',
+ field=models.TextField(verbose_name='Title'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0024_auto_20190602_1546.py b/ippisite/ippidb/migrations/0024_auto_20190602_1546.py
new file mode 100644
index 0000000000000000000000000000000000000000..59598ee442381c945679e18f6cd47fcc03b58e39
--- /dev/null
+++ b/ippisite/ippidb/migrations/0024_auto_20190602_1546.py
@@ -0,0 +1,158 @@
+# Generated by Django 2.2.1 on 2019-06-02 15:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0023_auto_20190524_1456'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='compound',
+ name='best_activity',
+ field=models.DecimalField(blank=True, decimal_places=10, max_digits=12, null=True, verbose_name='Best activity'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='binding_role',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Binding role'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='bindtest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Binding tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='celltest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Cellular tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='cytoxtest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Cytotoxicity tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='hba_hbd',
+ field=models.IntegerField(blank=True, null=True, verbose_name='Sum of Hydrogen bond acceptors and donors'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='inhibition_role',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Inhibition role'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='inhitest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Inhibition tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='insilico_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='In silico tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='le',
+ field=models.FloatField(blank=True, null=True, verbose_name='Ligand efficiency'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Lipinsky ok'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky_a_log_p',
+ field=models.BooleanField(blank=True, null=True, verbose_name='A log P ok for Lipinsky'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky_hba',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Hydrogen bond acceptors ok for Lipinsky'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky_hbd',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Hydrogen bond donors ok for Lipinsky'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky_mw',
+ field=models.BooleanField(blank=True, null=True, verbose_name='MW ok for Lipinsky'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lipinsky_score',
+ field=models.IntegerField(blank=True, null=True, verbose_name='Lipinsky score'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='lle',
+ field=models.FloatField(blank=True, null=True, verbose_name='Lipophilic efficiency'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pdb_ligand_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='PDB ligand available'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pfizer',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Pfizer ok'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pfizer_a_log_p',
+ field=models.BooleanField(blank=True, null=True, verbose_name='A log P ok for Pfizer'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pfizer_tpsa',
+ field=models.BooleanField(blank=True, null=True, verbose_name='TPSA ok for Pfizer'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pktest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Pharmacokinetic tests performed'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='pubs',
+ field=models.IntegerField(blank=True, null=True, verbose_name='Number of publications'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='stabilisation_role',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Stabilisation role'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='tests_av',
+ field=models.IntegerField(blank=True, null=True, verbose_name='Number of tests available'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='veber',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Veber ok'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='veber_hba_hbd',
+ field=models.BooleanField(blank=True, null=True, verbose_name='HBA+HBD ok for Veber'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='veber_rb',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Rotatable bonds ok for Veber'),
+ ),
+ migrations.AddField(
+ model_name='compound',
+ name='veber_tpsa',
+ field=models.BooleanField(blank=True, null=True, verbose_name='TPSA ok for Veber'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0025_compound_stabtest_av.py b/ippisite/ippidb/migrations/0025_compound_stabtest_av.py
new file mode 100644
index 0000000000000000000000000000000000000000..aceea55276782b02fd9a40edfb77ce6cd4f8c368
--- /dev/null
+++ b/ippisite/ippidb/migrations/0025_compound_stabtest_av.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.1 on 2019-06-03 14:42
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0024_auto_20190602_1546'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='compound',
+ name='stabtest_av',
+ field=models.BooleanField(blank=True, null=True, verbose_name='Stabilisation tests performed'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0026_auto_20190604_1937.py b/ippisite/ippidb/migrations/0026_auto_20190604_1937.py
new file mode 100644
index 0000000000000000000000000000000000000000..243293dc757d51c3165c7e49397565f76ed57378
--- /dev/null
+++ b/ippisite/ippidb/migrations/0026_auto_20190604_1937.py
@@ -0,0 +1,17 @@
+# Generated by Django 2.2.1 on 2019-06-04 19:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0025_compound_stabtest_av'),
+ ]
+
+ operations = [
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['molecular_weight'], name='ippidb_comp_molecul_6c82bb_idx'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0027_auto_20190604_1947.py b/ippisite/ippidb/migrations/0027_auto_20190604_1947.py
new file mode 100644
index 0000000000000000000000000000000000000000..42835bc921efbee8ad5cd7c40ae1103845062e32
--- /dev/null
+++ b/ippisite/ippidb/migrations/0027_auto_20190604_1947.py
@@ -0,0 +1,49 @@
+# Generated by Django 2.2.1 on 2019-06-04 19:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0026_auto_20190604_1937'),
+ ]
+
+ operations = [
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['a_log_p'], name='ippidb_comp_a_log_p_d6ed66_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['nb_donor_h'], name='ippidb_comp_nb_dono_0dff51_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['nb_acceptor_h'], name='ippidb_comp_nb_acce_2d9049_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['tpsa'], name='ippidb_comp_tpsa_4a45ab_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['nb_rotatable_bonds'], name='ippidb_comp_nb_rota_c38661_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['nb_aromatic_sssr'], name='ippidb_comp_nb_arom_de89e2_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['nb_chiral_centers'], name='ippidb_comp_nb_chir_d779eb_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['fsp3'], name='ippidb_comp_fsp3_bfbbb7_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['pubs'], name='ippidb_comp_pubs_168d42_idx'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0028_auto_20190604_2058.py b/ippisite/ippidb/migrations/0028_auto_20190604_2058.py
new file mode 100644
index 0000000000000000000000000000000000000000..1b99d0b6e663565293c1fde95b61d9164683c932
--- /dev/null
+++ b/ippisite/ippidb/migrations/0028_auto_20190604_2058.py
@@ -0,0 +1,30 @@
+# Generated by Django 2.2.1 on 2019-06-04 20:58
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0027_auto_20190604_1947'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='compound',
+ name='best_activity_ppi_family_name',
+ field=models.CharField(blank=True, max_length=30, null=True, unique=True, verbose_name='Best activity PPI family name'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['best_activity'], name='ippidb_comp_best_ac_98454a_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['le'], name='ippidb_comp_le_e4dac5_idx'),
+ ),
+ migrations.AddIndex(
+ model_name='compound',
+ index=models.Index(fields=['lle'], name='ippidb_comp_lle_1f7980_idx'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0029_auto_20190605_0606.py b/ippisite/ippidb/migrations/0029_auto_20190605_0606.py
new file mode 100644
index 0000000000000000000000000000000000000000..6623de441610df1176653ce5d81a10d28cab1b46
--- /dev/null
+++ b/ippisite/ippidb/migrations/0029_auto_20190605_0606.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.1 on 2019-06-05 06:06
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0028_auto_20190604_2058'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compound',
+ name='best_activity_ppi_family_name',
+ field=models.CharField(blank=True, max_length=30, null=True, verbose_name='Best activity PPI family name'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index d085312ae5c6ea1b6af6f0c0004c41ae383a2837..a94fc95e3785f9ee80671bae19e9ecb177c826ec 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -12,7 +12,7 @@ from django.contrib.auth import get_user_model
from django.core.exceptions import ValidationError
from django.db import models, transaction
from django.db.models import FloatField, IntegerField, BooleanField
-from django.db.models import Max, Count, F, Q, Case, When
+from django.db.models import Max, Count, F, Q, Case, When, Subquery, OuterRef
from django.db.models.functions import Cast
from django.urls import reverse
from django.utils.translation import ugettext_lazy as _
@@ -450,7 +450,7 @@ class CompoundManager(models.Manager):
of the database query, used for filters and compound card
"""
- def get_queryset(self):
+ def get_queryset_old(self):
# @formatter:off
qs = super().get_queryset()
# with number of publications
@@ -811,8 +811,77 @@ class Compound(AutoFillableModel):
null=True,
)
+ pubs = models.IntegerField(
+ verbose_name='Number of publications', null=True, blank=True
+ )
+ best_activity = models.DecimalField(
+ 'Best activity', max_digits=12, decimal_places=10, null=True, blank=True)
+ best_activity_ppi_family_name = models.CharField('Best activity PPI family name', max_length=30, null=True, blank=True)
+ le = models.FloatField(
+ verbose_name='Ligand efficiency', null=True, blank=True
+ )
+ lle = models.FloatField(
+ verbose_name='Lipophilic efficiency', null=True, blank=True
+ )
+ lipinsky_mw = models.BooleanField('MW ok for Lipinsky', null=True, blank=True)
+ lipinsky_hba = models.BooleanField('Hydrogen bond acceptors ok for Lipinsky', null=True, blank=True)
+ lipinsky_hbd = models.BooleanField('Hydrogen bond donors ok for Lipinsky', null=True, blank=True)
+ lipinsky_a_log_p = models.BooleanField('A log P ok for Lipinsky', null=True, blank=True)
+ lipinsky_score = models.IntegerField(
+ verbose_name='Lipinsky score', null=True, blank=True
+ )
+ lipinsky = models.BooleanField('Lipinsky ok', null=True, blank=True)
+ hba_hbd = models.IntegerField(
+ verbose_name='Sum of Hydrogen bond acceptors and donors', null=True, blank=True
+ )
+ veber_hba_hbd = models.BooleanField('HBA+HBD ok for Veber', null=True, blank=True)
+ veber_tpsa = models.BooleanField('TPSA ok for Veber', null=True, blank=True)
+ veber_rb = models.BooleanField('Rotatable bonds ok for Veber', null=True, blank=True)
+ veber = models.BooleanField('Veber ok', null=True, blank=True)
+ pfizer_a_log_p = models.BooleanField('A log P ok for Pfizer', null=True, blank=True)
+ pfizer_tpsa = models.BooleanField('TPSA ok for Pfizer', null=True, blank=True)
+ pfizer = models.BooleanField('Pfizer ok', null=True, blank=True)
+ pdb_ligand_av = models.BooleanField('PDB ligand available', null=True, blank=True)
+ inhibition_role = models.BooleanField('Inhibition role', null=True, blank=True)
+ binding_role = models.BooleanField('Binding role', null=True, blank=True)
+ stabilisation_role = models.BooleanField('Stabilisation role', null=True, blank=True)
+ celltest_av = models.BooleanField('Cellular tests performed', null=True, blank=True)
+ inhitest_av = models.BooleanField('Inhibition tests performed', null=True, blank=True)
+ stabtest_av = models.BooleanField('Stabilisation tests performed', null=True, blank=True)
+ bindtest_av = models.BooleanField('Binding tests performed', null=True, blank=True)
+ pktest_av = models.BooleanField('Pharmacokinetic tests performed', null=True, blank=True)
+ cytoxtest_av = models.BooleanField('Cytotoxicity tests performed', null=True, blank=True)
+ insilico_av = models.BooleanField('In silico tests performed', null=True, blank=True)
+ tests_av = models.IntegerField(verbose_name='Number of tests available', null=True, blank=True)
+
+
class Meta:
ordering = ['id']
+ indexes = [
+ models.Index(fields=['molecular_weight']),
+ models.Index(fields=['a_log_p']),
+ models.Index(fields=['nb_donor_h']),
+ models.Index(fields=['nb_acceptor_h']),
+ models.Index(fields=['tpsa']),
+ models.Index(fields=['nb_rotatable_bonds']),
+ models.Index(fields=['nb_aromatic_sssr']),
+ models.Index(fields=['nb_chiral_centers']),
+ models.Index(fields=['fsp3']),
+ models.Index(fields=['pubs']),
+ models.Index(fields=['best_activity']),
+ models.Index(fields=['le']),
+ models.Index(fields=['lle']),
+ ]
+ # indexes = [
+ # models.Index(fields=['lipinsky']),
+ # models.Index(fields=['veber']),
+ # models.Index(fields=['pfizer']),
+ # models.Index(fields=['pdb_ligand_av']),
+ # models.Index(fields=['inhibition_role']),
+ # models.Index(fields=['binding_role']),
+ # models.Index(fields=['stabilisation_role']),
+ # models.Index(fields=['binding_role']),
+ # ]
def compute_drugbank_compound_similarity(self):
""" compute Tanimoto similarity to existing DrugBank compounds """
@@ -868,33 +937,11 @@ class Compound(AutoFillableModel):
@property
def best_pXC50_compound_activity_result(self):
- best_pXC50_activity = self.best_pXC50_activity
+ best_pXC50_activity = self.best_activity
if best_pXC50_activity is None:
return None
return self.compoundactivityresult_set.filter(activity=best_pXC50_activity)[0]
- @property
- def best_pXC50_activity_ppi_name(self):
- """
- Name of the PPI corresponding to the best PXC50 activity
- """
- best_activity_car = self.best_pXC50_compound_activity_result
- if best_activity_car is None:
- return None
- ppi_name = best_activity_car.test_activity_description.ppi.name
- return ppi_name
-
- @property
- def best_pXC50_activity_ppi_family(self):
- """
- Family of the PPI corresponding to the best PXC50 activity
- """
- best_activity_car = self.best_pXC50_compound_activity_result
- if best_activity_car is None:
- return None
- ppi_family = best_activity_car.test_activity_description.ppi.family.name
- return ppi_family
-
@property
def bioch_tests_count(self):
"""
@@ -1296,3 +1343,225 @@ class Contribution(models.Model):
def get_absolute_url(self):
return reverse('contribution-detail', kwargs={'contribution_pk': self.pk})
+
+def update_compound_cached_properties():
+ return Compound.objects.update(
+ pubs=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pubs=Count('refcompoundbiblio', distinct=True)
+ ).values('_pubs')[:1]
+ ),
+ best_activity=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _best_activity=Max('compoundactivityresult__activity')
+ ).values('_best_activity')[:1]
+ ),
+ best_activity_ppi_family_name = Subquery(
+ CompoundActivityResult.objects.filter(
+ compound_id=OuterRef('id')
+ ).filter(activity=OuterRef('best_activity')).annotate(
+ _best_activity_ppi_family_name=F('test_activity_description__ppi__family__name')
+ ).values('_best_activity_ppi_family_name')[:1]
+ ),
+ le=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _le=Cast(1.37 * Max('compoundactivityresult__activity') / F('nb_atom_non_h'), FloatField())
+ ).values('_le')[:1]
+ ),
+ lle=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lle=Cast(Max('compoundactivityresult__activity') - F('a_log_p'), FloatField())
+ ).values('_lle')[:1]
+ ),
+ lipinsky_mw=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky_mw=Case(When(molecular_weight__lte=500, then=True), default=False, output_field=BooleanField())
+ ).values('_lipinsky_mw')[:1]
+ ),
+ lipinsky_hba=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky_hba=Case(When(nb_acceptor_h__lte=10, then=True), default=False, output_field=BooleanField())
+ ).values('_lipinsky_hba')[:1]
+ ),
+ lipinsky_hbd=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky_hbd=Case(When(nb_donor_h__lte=5, then=True), default=False, output_field=BooleanField())
+ ).values('_lipinsky_hbd')[:1]
+ ),
+ lipinsky_a_log_p=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky_a_log_p=Case(When(a_log_p__lte=5, then=True), default=False, output_field=BooleanField())
+ ).values('_lipinsky_a_log_p')[:1]
+ ),
+ lipinsky_score=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky_score=Cast(F('lipinsky_mw'), IntegerField()) + Cast(F('lipinsky_hba'), IntegerField()) +
+ Cast(F('lipinsky_hbd'), IntegerField()) + Cast(F('lipinsky_a_log_p'), IntegerField())
+ ).values('_lipinsky_score')[:1]
+ ),
+ lipinsky=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _lipinsky=Case(When(lipinsky_score__gte=3, then=True), default=False, output_field=BooleanField())
+ ).values('_lipinsky')[:1]
+ ),
+ hba_hbd=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _hba_hbd=F('nb_acceptor_h')+F('nb_donor_h'),
+ ).values('_hba_hbd')[:1]
+ ),
+ veber_hba_hbd=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _veber_hba_hbd=Case(When(hba_hbd__lte=12, then=True), default=False, output_field=BooleanField()),
+ ).values('_veber_hba_hbd')[:1]
+ ),
+ veber_tpsa=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _veber_tpsa=Case(When(tpsa__lte=140, then=True), default=False, output_field=BooleanField()),
+ ).values('_veber_tpsa')[:1]
+ ),
+ veber_rb=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _veber_rb=Case(When(nb_rotatable_bonds__lte=10, then=True), default=False, output_field=BooleanField()),
+ ).values('_veber_rb')[:1]
+ ),
+ veber=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _veber=Case(When(Q(Q(nb_rotatable_bonds__lte=10) & (Q(hba_hbd__lte=12) | Q(tpsa__lte=140))), then=True), default=False, output_field=BooleanField()),
+ ).values('_veber')[:1]
+ ),
+ pfizer_a_log_p=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pfizer_a_log_p=Case(When(a_log_p__lte=3, then=True), default=False, output_field=BooleanField()),
+ ).values('_pfizer_a_log_p')[:1]
+ ),
+ pfizer_tpsa=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pfizer_tpsa=Case(When(tpsa__gte=75, then=True), default=False, output_field=BooleanField()),
+ ).values('_pfizer_tpsa')[:1]
+ ),
+ pfizer=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pfizer=Case(When(Q(Q(a_log_p__lte=3) & Q(tpsa__gte=75)), then=True), default=False, output_field=BooleanField()),
+ ).values('_pfizer')[:1]
+ ),
+ pdb_ligand_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pdb_ligand_av=Cast(Max(Case(When(compoundaction__ligand_id__isnull=False, then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_pdb_ligand_av')[:1]
+ ),
+ inhibition_role=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _inhibition_role=Case(When(compoundactivityresult__modulation_type='I', then=True), default=False, output_field=BooleanField()),
+ ).values('_inhibition_role')[:1]
+ ),
+ binding_role=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _binding_role=Case(When(compoundactivityresult__modulation_type='I', then=True), default=False, output_field=BooleanField()),
+ ).values('_binding_role')[:1]
+ ),
+ stabilisation_role=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _stabilisation_role=Case(When(compoundactivityresult__modulation_type='S', then=True), default=False, output_field=BooleanField()),
+ ).values('_stabilisation_role')[:1]
+ ),
+ celltest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _celltest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_type='CELL', then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_celltest_av')[:1]
+ ),
+ inhitest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _inhitest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='I', then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_inhitest_av')[:1]
+ ),
+ stabtest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _stabtest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='S', then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_stabtest_av')[:1]
+ ),
+ bindtest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _bindtest_av=Cast(Max(Case(When(compoundactivityresult__test_activity_description__test_modulation_type='I', then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_bindtest_av')[:1]
+ ),
+ pktest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _pktest_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__pharmacokinetic=True, then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_pktest_av')[:1]
+ ),
+ cytoxtest_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _cytoxtest_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__cytotox=True, then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_cytoxtest_av')[:1]
+ ),
+ insilico_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _insilico_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__in_silico=True, then=1), default=0, output_field=IntegerField())), BooleanField()),
+ ).values('_insilico_av')[:1]
+ ),
+ tests_av=Subquery(
+ Compound.objects.filter(
+ id=OuterRef('id')
+ ).annotate(
+ _tests_av=Count('compoundactivityresult', distinct=True),
+ ).values('_tests_av')[:1]
+ )
+ )
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index 55c649ed312e10b044cb6460ab6ea3342c522dcc..9edd0371abf009e1a60ce88b4567ec1d706e0533 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -126,7 +126,7 @@
<canvas id="pca_biplot" style="width:600px; height:600px;"></canvas>
<script>
- drawCompoundsBiplotChart('pca_biplot', {{ compound.id }}, '{{ compound.best_pXC50_activity_ppi_family|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}, 'physicochemistry');
+ drawCompoundsBiplotChart('pca_biplot', {{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}, 'physicochemistry');
</script>
</div>
</div>
@@ -144,7 +144,7 @@
<div class="card-body">
<canvas id="le_lle_biplot"></canvas>
<script>
- drawCompoundsBiplotChart('le_lle_biplot', {{ compound.id }}, '{{ compound.best_pXC50_activity_ppi_family|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}, 'pharmacology');
+ drawCompoundsBiplotChart('le_lle_biplot', {{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}, 'pharmacology');
</script>
</div>
</div>
diff --git a/ippisite/ippidb/templates/compound_v_item.html b/ippisite/ippidb/templates/compound_v_item.html
index 77d4ee9edc62da4ecae654cc66641cbb8d1208fd..72d60848faa90325c01f6012996f18a8f41769d0 100644
--- a/ippisite/ippidb/templates/compound_v_item.html
+++ b/ippisite/ippidb/templates/compound_v_item.html
@@ -7,7 +7,7 @@
{% endif %}
<div class="card-body" style="overflow:hidden; word-wrap:break-word;">
{%if compound.common_name %}<p title="Common name">{{ compound.common_name }}</p>{% endif %}
- <p title="PPI Family">{{ compound.best_pXC50_activity_ppi_family }}</p>
+ <p title="PPI Family">{{ compound.best_activity_ppi_family_name }}</p>
<p title="Molecular Weight">{{ compound.molecular_weight }} g/mol</p>
</div>
</div>