Skip to main content

Systematic Generation of potential MetAbolites

Project description

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.

https://travis-ci.org/3D-e-Chem/sygma.svg?branch=master https://api.codacy.com/project/badge/Grade/7f18ab1d1a80437f8e28ac1676c70519 https://api.codacy.com/project/badge/Coverage/7f18ab1d1a80437f8e28ac1676c70519 https://img.shields.io/badge/docker-ready-blue.svg

Requirements

SyGMa requires RDKit with INCHI support

Installation

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

OR

AND

  • pip install sygma OR, after downloading sygma, 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'], 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:

docker run 3dechem/sygma c1ccccc1O

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for SyGMa, version 1.0.1
Filename, size File type Python version Upload date Hashes
Filename, size SyGMa-1.0.1.tar.gz (13.7 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page