Requirements

• Python 3.7 or later (not support 2.x)

• MySQL-python >= 1.2.4 or psycopg2 >= 2.5.1

• SQLAlchemy >= 1.3.1

Setup

pip install pychembldb

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

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 Taeget, 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)

See also.

• https://docs.sqlalchemy.org/en/13/

• ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_25_schema.png

History