Metadata-Version: 2.1
Name: pychembldb
Version: 0.4.1
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 3.7 or later (not support 2.x)
        * MySQL-python >= 1.2.4 or psycopg2 >= 2.5.1
        * SQLAlchemy >= 1.3.1
        
        ChEMBLdb and Python version
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        * pychembldb-0.1.x support chembl_14 and Python2.7
        * pychembldb-0.2.x support chembl_15, 16 and Python2.7
        * pychembldb-0.3.x support chembl_17,18,19 and Python2.7
        * pychembldb-0.4.0 support chembl_25 and Python3.7
        
        Setup
        -----
        
        Install
        ~~~~~~~
        
        ::
        
            pip install pychembldb
        
        or install from github
        
        ::
        
            git clone https://github.com/kzfm/pychembldb.git
            cd pychembldb
            sudo python setup.py install
            or 
            pip install -e .
        
        Setting up engine_url
        ~~~~~~~~~~~~~~~~~~~~~
        
        if you change engine_url, you should set CHEMBL_URI environment variable (default:mysql://root@localhost/chembl_25)
        
        ex) PostgreSQL
        
        ::
        
            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
        -------
        
        0.4.1 (2020-01-16)
        ~~~~~~~~~~~~~~~~~~
        * Fix some relation
        
        0.4.0 (2020-01-15)
        ~~~~~~~~~~~~~~~~~~
        * Support ChEMBLdb 25
        * Only Support Python 3.7
        
        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
        
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
Description-Content-Type: text/x-rst
