MX - Essential Cheminformatics

Web:     http://metamolecular.com/mx
Source:  http://github.com/metamolecular/mx

MX is a lightweight cheminformatics toolkit written in Java that emphasizes
efficiency, modularity, and readability. MX was originally part of
ChemWriter, the 2D chemical structure editor developed by Metamolecular. 

MX currently supports:

- Substructure search and atom mapping based on the VF algorithm
- Exhaustive ring perception based on the Hanser algorithm
- Flexible query atom support
- Depth-First traversal
- Implicit hydrogen detection
- Complete system of atomic masses and isotopes based on the IUPAC Technical Report.
- Model objects (Molecule, Atom, Bond, Superatom) based on MDL CTfile specification
- Molfile reader and writer
- SD File reader and writer
- Flexible generation of path-based binary fingerprints

These features are implemented with an emphasis on readability and flexibility.

MX has been successfully used in both the Ruby and Python scripting
environments through JRuby and Jython.

System requirements:

-  Ant
-  JDK 1.5 or higher