From 0a597cbbe53f15e5860203cc594519d6f0c8f6f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 20 Nov 2018 20:44:40 +0100
Subject: [PATCH] add Drugbank compound similarity computation
Former-commit-id: 528aac3f93450a16ae1fb8cc56dda0cf0080afb2
---
ippisite/db.sqlite3.REMOVED.git-id | 2 +-
.../management/commands/import_drugbank.py | 24 ++++++++++++++++--
.../0016_drugbankcompoundtanimoto.py | 25 +++++++++++++++++++
ippisite/ippidb/models.py | 6 +++++
4 files changed, 54 insertions(+), 3 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0016_drugbankcompoundtanimoto.py
diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
index 075f65e3..c765cbc7 100644
--- a/ippisite/db.sqlite3.REMOVED.git-id
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -1 +1 @@
-371b75bfeea17504694f84b9c6a2fe579e2249a1
\ No newline at end of file
+2de38b2f569a1cecc7dd4e6dd360602d2f81e8a5
\ No newline at end of file
diff --git a/ippisite/ippidb/management/commands/import_drugbank.py b/ippisite/ippidb/management/commands/import_drugbank.py
index 8404e46b..2c1c2782 100644
--- a/ippisite/ippidb/management/commands/import_drugbank.py
+++ b/ippisite/ippidb/management/commands/import_drugbank.py
@@ -1,8 +1,12 @@
-from ippidb.models import DrugBankCompound
+import operator
+
import pandas as pd
from django.core.management import BaseCommand, CommandError
+from ippidb.models import DrugBankCompound, DrugbankCompoundTanimoto, Compound
+from ippidb.utils import FingerPrinter
+
class Command(BaseCommand):
@@ -16,6 +20,7 @@ class Command(BaseCommand):
)
def handle(self, *args, **options):
+ '''
df = pd.read_csv(options['path'],sep='\t')
DrugBankCompound.objects.all().delete()
self.stdout.write(
@@ -37,4 +42,19 @@ class Command(BaseCommand):
else:
self.stdout.write(
self.style.SUCCESS('Successfully inserted {}'.format(row.loc['DRUGBANK_ID'])))
-
+ '''
+ DrugbankCompoundTanimoto.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed DrugBank Compound Tanimoto table'))
+ smiles_dict = {c.id:c.canonical_smiles for c in DrugBankCompound.objects.all()}
+ for c in Compound.objects.all():
+ fingerprinter = FingerPrinter("ECFP4")
+ #1. compute tanimoto for SMILES query vs all compounds
+ tanimoto_dict = fingerprinter.tanimoto_smiles(c.canonical_smile, smiles_dict)
+ tanimoto_dict = dict(sorted(tanimoto_dict.items(), key=operator.itemgetter(1), reverse=True)[:15])
+ dbcts = []
+ for id_, tanimoto in tanimoto_dict.items():
+ dbcts.append(DrugbankCompoundTanimoto(compound=c, drugbank_compound=DrugBankCompound.objects.get(id=id_), tanimoto=tanimoto))
+ DrugbankCompoundTanimoto.objects.bulk_create(dbcts)
+ self.stdout.write(
+ self.style.SUCCESS('Successfully inserted {} DrugBank Compound Tanimoto lines for Compound {}'.format(len(dbcts), c.id)))
diff --git a/ippisite/ippidb/migrations/0016_drugbankcompoundtanimoto.py b/ippisite/ippidb/migrations/0016_drugbankcompoundtanimoto.py
new file mode 100644
index 00000000..d86f908b
--- /dev/null
+++ b/ippisite/ippidb/migrations/0016_drugbankcompoundtanimoto.py
@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-11-19 22:20
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0015_drugbankcompound'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='DrugbankCompoundTanimoto',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('tanimoto', models.DecimalField(decimal_places=4, max_digits=5, verbose_name='Tanimoto value')),
+ ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ('drugbank_compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.DrugBankCompound')),
+ ],
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 7508ba7d..b716cc7c 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -736,3 +736,9 @@ class DrugBankCompound(models.Model):
common_name = models.TextField('Common name')
canonical_smiles = models.TextField(
'Canonical SMILES')
+
+class DrugbankCompoundTanimoto(models.Model):
+ compound = models.ForeignKey(Compound, models.CASCADE)
+ drugbank_compound = models.ForeignKey(DrugBankCompound, models.CASCADE)
+ tanimoto = models.DecimalField(
+ 'Tanimoto value', max_digits=5, decimal_places=4)
\ No newline at end of file
--
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