MX - Essential Cheminformatics

This site is no longer maintained. For the most up-to-date documentation and news on MX, visit http://metamolecular.com/mx .

Summary

MX is a suite of lightweight, general-purpose cheminformatics tools for building chemistry applications.

Fully-implemented features include:

• Substructure Search/Mapping
• Depth-first Traversal
• Molfile Reader/Writer
• Structure Data File (SD File) Reader/Writer
• Implicit Hydrogen Detection
• Complete System of Atomic Masses and Isotopes Linked to the Primary Literature
• Exhaustive Ring Perception

Partially-implemented features include:

• SMILES Parser

Features currently in-progress include:

• Binary Fingerprint Generation

Example

import com.metamolecular.mx.calc.MassCalculator;
import com.metamolecular.mx.io.daylight.SMILESReader;
import com.metamolecular.mx.map.DefaultMapper;
import com.metamolecular.mx.model.Molecule;

public class Example
{
  public static void main(String[] args)
  {
    Molecule benzene = SMILESReader.read("C1=CC=CC=C1");
    Molecule naphthalene = SMILESReader.read("C1=CC=C2C=CC=CC2=C1");
    DefaultMapper mapper = new DefaultMapper(benzene);
    
    System.out.println(mapper.hasMap(naphthalene)); // true
    System.out.println(mapper.countMaps(naphthalene)); // 24
    
    MassCalculator calc = new MassCalculator();
    
    System.out.println(calc.findAveragedMass(naphthalene)); // 128.17052
  }
}

Background

MX was originally part of ChemWriter, the 2D chemical structure editor developed by Metamolecular, LLC. It was subsequently used to create ChemPhoto, the 2D chemical structure imaging application. The MX library was factored out of these applications, and is now offered to the cheminformatics community under the flexible MIT License.

Using MX With Scripting Languages

MX can be used directly in both Python and Ruby through the Jython and JRuby implementations. Because it's written in Java, MX can automatically be used in a variety of other scripting languages as well.

MX in Jython:

Jython 2.5b0 (trunk:5540, Oct 31 2008, 13:55:41) 
[Java HotSpot(TM) Client VM (Sun Microsystems Inc.)] on java1.5.0_16
>>> import sys
>>> sys.path.append("mx-0.106.0.jar")
>>> from com.metamolecular.mx.io import Molecules
>>> benzene = Molecules.createBenzene()
>>> benzene.countAtoms()
6

MX in JRuby:

irb(main):001:0> require 'mx-0.106.0.jar'
=> true
irb(main):002:0> import com.metamolecular.mx.io.Molecules
=> Java::ComMetamolecularMxIo::Molecules
irb(main):003:0> benzene = Molecules.createBenzene
=> #<Java::ComMetamolecularMxModel::DefaultMolecule:0x9770a3 @java_object=com.metamolecular.mx.model.DefaultMolecule@1536eec>
irb(main):004:0> benzene.countAtoms
=> 6

Resources

• Introducing MX: Lightweight and Free Cheminformatics Tools for Java Background and motivation for MX.

• Getting Started with MX Everything you need to know to start using MX quickly.

• Open Source Cheminformatics in Python with MX MX can be used, unmodified, in Python through Jython.

• JavaScript for Cheminformatics: Cross-Compiling Java to JavaScript with GWT MX can be cross-compiled to JavaScript for plugin-free client-side cheminformatics applications.

• Flexible Depth-First Search With MX MX makes it easy to use this important graph traversal strategy.

• Calculating Molecular Mass With MX: Using a Complete Hydrogen to Uranium System of Atomic Masses Linked to the Primary Literature Discussion of how MX calculates molecular mass.

• Killer GitHub Feature: Visualizing Branch/Merge Activity in MX MX uses GitHub as its public source code management system. This article illustrates one of the many useful features of this service.

• Open Benchmarks for Cheminformatics Performance comparison of MX with other cheminformatics toolkits (coming soon).

• Reading SMILES with MX Example using JRuby.

• Exhaustive Ring Perception With MX Find all rings of a molecule.