pychembldb 0.2.0

Requirements

• Python 2.7 or later (not support 3.x)

• MySQL-python >= 1.2.4

• SQLAlchemy >= 0.8.0b2

Setup

pip install pychembldb

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

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.published_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.published_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.published_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'

Count the number of MedChem Friendly Compounds.

chembldb.query(CompoundProperty).filter_by(med_chem_friendly='Y').count()

See also.

• http://docs.sqlalchemy.org/en/rel_0_8/orm/tutorial.html

• ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_14_erd.png

History