Skip to main content
Join the official Python Developers Survey 2018 and win valuable prizes: Start the survey!

ChEMBLdb interface for Python

Project description

pychembldb is a Python interface for ChEMBLdb

Requirements

  • Python 2.7 or later (not support 3.x)
  • MySQL-python >= 1.2.4 or psycopg2 >= 2.5.1
  • SQLAlchemy >= 0.8.0b2

ChEMBLdb

  • pychembldb-0.1.x support chembl_14
  • pychembldb-0.2.x support chembl_15 and chembl_16
  • pychembldb-0.3.x support chembl_17,18,19

Setup

Install

pip install pychembldb

or install from github

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

Setting up engine_url

if you change engine_url, you should set CHEMBL_URI environment variable (default:mysql://root@localhost/chembl_18)

ex) PostgreSQL

export CHEMBL_URI="postgresql+psycopg2://localhost/chembl_18"

or

export CHEMBL_URI="postgresql+psycopg2://USER:PASSWORD@localhost/chembl_18"

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.

History

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
pychembldb-0.3.6.tar.gz (4.3 kB) Copy SHA256 hash SHA256 Source None Sep 2, 2014

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page