RDKit支持PostgreSQL配置

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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：

#!/usr/bin/python3

from rdkit import Chem
import psycopg2 as ps

c = ps.connect(dbname='drugbank', user='aspirin', host='127.0.0.1', password='aspirin12369', port="5432")
cursor = c.cursor()
cursor.execute("select version()")
reply = cursor.fetchall()
print(reply)

cursor.execute("drop schema if exists drugbank cascade")
cursor.execute("create schema drugbank")
cursor.execute("""
create table drugbank.drugbank(
       id serial primary key,
       drugbank_id text,
       smiles text,
       hba integer,
       hbd integer,
       mw float,
       logp float
);
""")
cursor.execute("select * from drugbank.drugbank")
print(cursor.fetchall())

supp = Chem.SDMolSupplier("drugbank.sdf")
drugbank = [mol for mol in supp if mol]

query = "insert into drugbank.drugbank (smiles, drugbank_id) values %s" % ((', '.join(["('%s','%s')" % (Chem.MolToSmiles(mol), mol.GetProp('DRUGBANK_ID')) 
                         for mol in drugbank])))
cursor.execute(query)
print(query[:1000])

cursor.execute("select count(*) from drugbank.drugbank")
print(cursor.fetchall(), len(drugbank))

cursor.execute("select * from drugbank.drugbank limit 10")
print(cursor.fetchall())

cursor.execute("select * from drugbank.drugbank where id > 500  and id < 600 limit 10;")
print(cursor.fetchall())

c.commit()