SyGMa

SyGMa is a python library for the Systematic Generation of potential Metabolites. 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.

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

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'], 2],
    [sygma.ruleset['phase2'], 1]
    ])

# An rdkit molecule, optionally with 2D coordinates, is required as parent molecule
parent = Chem.MolFromSmiles("c1ccccc1O")
Chem.AllChem.Compute2DCoords(parent)

metabolites_network = scenario.run(parent)
metabolites_network.calc_scores()
metabolites_network.add_coordinates() # Only if a parent molecule was provided with coordinates

print metabolites_network.to_list()