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This is the core of venn. It can be used : - To rebuild Venn :) - To build mashups similar to Venn which use EBI / NCBI web services - To learn how to use Neodatis in a real application that is performant. - As a sandbox for datamining against the PDB. It is capable of reasonably fast protein-protein lookups and comparisons, since it stores native PDB java objects and deserializes them directly from a byte stream. - There is an adoption of the older biojava Needleman-Wunsch implementation for amino acids which uses 2D arrays. ---- A note on ODB errors ---- file locks and empty file error To prevent a file lock, make sure every access has a "close" after it. To prevent a file empty error, never create a file .... just reference a new file name and odb will automatically make it for you.