pychembldb

pychembldb is a Python interface for ChEMBLdb

Requirements

• Python 3.7 or later (not support 2.x)
• MySQL-python >= 1.2.4 or psycopg2 >= 2.5.1
• SQLAlchemy >= 1.3.1

ChEMBLdb and Python version

• pychembldb-0.1.x support chembl_14 and Python2.7
• pychembldb-0.2.x support chembl_15, 16 and Python2.7
• pychembldb-0.3.x support chembl_17,18,19 and Python2.7
• pychembldb-0.4.0 support chembl_25 and Python3.7

Setup

Install

pip install pychembldb

or install from github

git clone https://github.com/kzfm/pychembldb.git
cd pychembldb
sudo python setup.py install
or
pip install -e .

Setting up engine_url

if you change engine_url, you should set CHEMBL_URI environment variable (default:mysql://root@localhost/chembl_25)

ex) PostgreSQL

export CHEMBL_URI="postgresql+psycopg2://localhost/chembl_25"

or

export CHEMBL_URI="postgresql+psycopg2://USER:PASSWORD@localhost/chembl_25"

Basic Usage

from pychembldb import *
for target in chembldb.query(Target).filter_by(pref_name="Tyrosine-protein kinase ABL"):
    for assay in target.assays:
        for activity in assay.activities:
            print(activity.value, activity.compound.molecule.structure.standard_inchi_key)

Examples

filter activities and compound structures by Target(Protein).

from pychembldb import *
for target in chembldb.query(Target).filter_by(pref_name="Tyrosine-protein kinase ABL"):
    for assay in target.assays:
        for activity in assay.activities:
            print(activity.value, activity.compound.molecule.structure.standard_inchi_key)

Search activities and compound structures from Journal-ID(doi).

for journal in chembldb.query(Doc).filter_by(doi="10.1016/S0960-894X(01)80693-4"):
    for assay in journal.assays:
        for activity in assay.activities:
             print(activity.standard_value, activity.compound.molecule.structure.standard_inchi_key)

Get SMILES from Molecule synonyms.

chembldb.query(MoleculeSynonym).filter_by(synonyms="Gleevec").first().molecule.structure.canonical_smiles
# 'CN1CCN(Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)CC1'

Get Target, MoA, and Molecular name

for dm in chembldb.query(DrugMechanism).limit(10):
    print("{0}/{1}: ({2})".format(dm.target.pref_name, dm.mechanism_of_action, dm.molecule.pref_name))

# Carbonic anhydrase VII/Carbonic anhydrase VII inhibitor: (METHAZOLAMIDE)
# Carbonic anhydrase I/Carbonic anhydrase I inhibitor: (METHOCARBAMOL)
# Carbonic anhydrase I/Carbonic anhydrase I inhibitor: (ACETAZOLAMIDE SODIUM)
# Carbonic anhydrase I/Carbonic anhydrase I inhibitor: (DICHLORPHENAMIDE)
# Carbonic anhydrase I/Carbonic anhydrase I inhibitor: (ACETAZOLAMIDE)
# Carbonic anhydrase I/Carbonic anhydrase I inhibitor: (METHAZOLAMIDE)
# Cytochrome b/Cytochrome b inhibitor: (ATOVAQUONE)
# Muscarinic acetylcholine receptor M3/Muscarinic acetylcholine receptor M3 antagonist: (TRIDIHEXETHYL CHLORIDE)
# Muscarinic acetylcholine receptor M3/Muscarinic acetylcholine receptor M3 antagonist: (TOLTERODINE TARTRATE)
# Muscarinic acetylcholine receptor M3/Muscarinic acetylcholine receptor M3 antagonist: (PROPANTHELINE BROMIDE)

Display trade names and their target proteins

for p in chembldb.query(Product).limit(10):
    for m in p.molecules:
        for t in m.targets:
            print("{0} ({1}) - {2}".format(p.trade_name, m.pref_name, t.pref_name))

See also.

• https://docs.sqlalchemy.org/en/13/
• ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_25_schema.png

History

0.4.1 (2020-01-16)

• Fix some relations

0.4.0 (2020-01-15)

• Support ChEMBLdb 25
• Only Support Python 3.7

0.3.6 (2014-09-02)

• Support ChEMBLdb 19

0.3.4 (2014-06-07)

• Update document
• Support ATC Classifications

0.3.3 (2014-06-06)

• Support ChEMBLdb 18

0.3.2 (2014-01-13)

• Fix bug

0.3.1 (2013-12-17)

• Support ChEMBLdb 17

0.2.1 (2013-06-15)

• Support ChEMBLdb 16

0.2.0 (2013-02-03)

• Support ChEMBLdb 15

0.1.1 (2013-01-29)

• Several bug fixes
• Add synonyms relation

0.1 (2013-01-29)

• first release