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&utm_medium=referral&utm_content=3D-e-Chem/sygma&utm_campaign=Badge_Grade .. image:: https://api.codacy.com/project/badge/Coverage/7f18ab1d1a80437f8e28ac1676c70519 :target: https://www.codacy.com/app/3D-e-Chem/sygma?utm_source=github.com&utm_medium=referral&utm_content=3D-e-Chem/sygma&utm_campaign=Badge_Coverage .. image:: https://img.shields.io/badge/docker-ready-blue.svg :target: https://hub.docker.com/r/3dechem/sygma .. image:: https://anaconda.org/3d-e-chem/sygma/badges/installer/conda.svg :target: https://conda.anaconda.org/3d-e-chem .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1043307.svg :target: https://doi.org/10.5281/zenodo.1043307

Requirements

SyGMa requires RDKit with INCHI support

Installation

• Install with Anaconda: conda install -c 3d-e-Chem -c rdkit sygma

OR

• Install RDKit following the instructions in http://www.rdkit.org/docs/Install.html

AND

• pip install sygma OR, after downloading sygma, 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