skip to navigation
skip to content

Not Logged In

pychembldb 0.2.0

ChEMBLdb interface for Python

Latest Version: 0.3.2

pychembldb is a Python interface for ChEMBLdb

Requirements

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

ChEMBLdb

  • pychembldb-0.1.x support chembl_14
  • pychembldb-0.2.x support chembl_15

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_14)

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

0.2.0 (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
 
File Type Py Version Uploaded on Size
pychembldb-0.2.0.tar.gz (md5) Source 2013-02-03 3KB
  • Downloads (All Versions):
  • 10 downloads in the last day
  • 60 downloads in the last week
  • 464 downloads in the last month