Extract Permeability Data from Chembl SQL database

PermeabilityDataFromChembl.py

import psycopg2
import pandas as pd
import pandas.io.sql as sqlio

con = psycopg2.connect(database="chembl_29", user="leelasd", password="", host="127.0.0.1", port="5432")

print("Database opened successfully")
sql="""SELECT m.chembl_id AS compound_chembl_id,   
s.canonical_smiles,   
r.compound_key,   
a.description                   AS assay_description,   act.standard_type,   
d.pubmed_id AS pubmed_id_or_doi,
act.standard_relation,   
act.standard_value,   
act.standard_units,   
act.activity_comment 
FROM compound_structures s,   
molecule_dictionary m,   
compound_records r,   
docs d,   
activities act,   
assays a,   
target_dictionary t 
WHERE s.molregno     = m.molregno 
AND m.molregno       = r.molregno 
AND r.record_id      = act.record_id 
AND r.doc_id         = d.doc_id 
AND act.assay_id     = a.assay_id 
AND a.tid            = t.tid 
AND a.assay_type     = 'A'
AND ((a.description LIKE '%Permeability%') OR (a.description LIKE '%permeability%'))
"""
dat = sqlio.read_sql_query(sql, con)
dat.to_csv('perm.csv',index=False)
print("Operation done successfully")
con.close()