Metadata-Version: 1.1
Name: pychembldb
Version: 0.3.3
Summary: ChEMBLdb interface for Python
Home-page: http://github.com/kzfm/pychembldb
Author: Ohkawa Kazufumi
Author-email: kerolinq@gmail.com
License: MIT
Description: ============
         pychembldb
        ============
        
        `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
        
        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)
        
        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
        -------
        
        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
        
Keywords: chemoinformatics cheminformatics
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
