Open Source cheminformatics library.
The Chemistry Development Kit is a Java library with cheminformatics functionality. It can read many chemistry file formats (MDL molfile and SD file, XYZ, PDB, etc), line notations (SMILES), produce InChI, calculate molecular descriptors, depict chemical structures as 2D SVG, and a lot more.
Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.