RDKit支持PostgreSQL配置

安装RDKit的PostgreSQL支持

conda install -c rdkit rdkit-postgresql

安装psycopg2，是Python语言的PostgreSQL数据库接口

pip install psycopg2

为drugbank数据库创建扩展：

psql -c 'create extension rdkit' drugbank

代码示例

1. #!/usr/bin/python3
3. from rdkit import Chem
4. import psycopg2 as ps
6. c = ps.connect(dbname='drugbank', user='aspirin', host='127.0.0.1', password='aspirin12369', port="5432")
7. cursor = c.cursor()
8. cursor.execute("select version()")
9. reply = cursor.fetchall()
10. print(reply)
12. cursor.execute("drop schema if exists drugbank cascade")
13. cursor.execute("create schema drugbank")
14. cursor.execute("""
15. create table drugbank.drugbank(
16. id serial primary key,
17. drugbank_id text,
18. smiles text,
19. hba integer,
20. hbd integer,
21. mw float,
22. logp float
23. );
24. """)
25. cursor.execute("select * from drugbank.drugbank")
26. print(cursor.fetchall())
28. supp = Chem.SDMolSupplier("drugbank.sdf")
29. drugbank = [mol for mol in supp if mol]
31. query = "insert into drugbank.drugbank (smiles, drugbank_id) values %s" % ((', '.join(["('%s','%s')" % (Chem.MolToSmiles(mol), mol.GetProp('DRUGBANK_ID'))
32. for mol in drugbank])))
33. cursor.execute(query)
34. print(query[:1000])
36. cursor.execute("select count(*) from drugbank.drugbank")
37. print(cursor.fetchall(), len(drugbank))
39. cursor.execute("select * from drugbank.drugbank limit 10")
40. print(cursor.fetchall())
42. cursor.execute("select * from drugbank.drugbank where id > 500 and id < 600 limit 10;")
43. print(cursor.fetchall())
45. c.commit()