Metadata-Version: 1.1
Name: SyGMa
Version: 1.0
Summary: Systematic Generation of potential MetAbolites
Home-page: https://github.com/ridderl/sygma
Author: Lars Ridder
Author-email: lars.ridder@esciencecenter.nl>
License: GPL
Description: SyGMa
        =====
        SyGMa is a python library for the **Sy**\ stematic **G**\ eneration of potential **M**\ et\ **a**\ bolites.
        It is a reimplementation of the metabolic rules outlined in
        `Ridder, L., & Wagener, M. (2008)
        SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites.
        ChemMedChem, 3(5), 821-832
        <http://onlinelibrary.wiley.com/doi/10.1002/cmdc.200700312/full>`_.
        
        .. image:: https://travis-ci.org/3D-e-Chem/sygma.svg?branch=master
            :target: https://travis-ci.org/3D-e-Chem/sygma
        .. image:: https://api.codacy.com/project/badge/Grade/7f18ab1d1a80437f8e28ac1676c70519
            :target: https://www.codacy.com/app/3D-e-Chem/sygma?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=3D-e-Chem/sygma&amp;utm_campaign=Badge_Grade
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        .. image:: https://img.shields.io/badge/docker-ready-blue.svg
            :target: https://hub.docker.com/r/3dechem/sygma
        
        Requirements
        ------------
        SyGMa requires RDKit with INCHI support
        
        Installation
        ------------
        * See http://www.rdkit.org/docs/Install.html for RDKit installation instructions.
        * python setup.py install
        
        Example: generating metabolites of phenol
        -----------------------------------------
        .. code-block:: python
        
            import sygma
            from rdkit import Chem
        
            # Each step in a scenario lists the ruleset and the number of reaction cycles to be applied
            scenario = sygma.Scenario([
                [sygma.ruleset['phase1'], 1],
                [sygma.ruleset['phase2'], 1]])
        
            # An rdkit molecule, optionally with 2D coordinates, is required as parent molecule
            parent = Chem.MolFromSmiles("c1ccccc1O")
        
            metabolic_tree = scenario.run(parent)
            metabolic_tree.calc_scores()
        
            print metabolic_tree.to_smiles()
        
        
        Docker
        ------
        SyGMa can be executed in a Docker (https://www.docker.com/) container as follows:
        
        .. code-block:: bash
        
            docker run 3dechem/sygma c1ccccc1O
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Environment :: Console
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Chemistry
