Indigo is a c++ based organic chemistry and cheminformatics software environment. features include:

* molecule and reaction rendering including svg support
* automatic layout for smiles-represented molecules and reactions
* canonical (isomeric) smiles computation
* exact matching, substructure matching, smarts matching
* matching of tautomers and resonance structures
* molecule fingerprinting, molecule similarity computation
* fast enumeration of sssr rings, subtrees, and edge sugraphs
* molecular weight, molecular formula computation
* r-group deconvolution and scaffold detection
* computation of the exact maximum common substructure for an
arbitrary amount of input structures
* combinatorial chemistry
* plugin support in the api
file formats indigo support include mdl mol, sdf, rdf, cml, smiles and smarts.

this package contains the java packages.