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...databases that are too large to fit into memory. Objects should be loaded only when necessary and should be removed from memory when they are no longer needed. Most of these efforts are focused on providing persistence using relational database data. The efforts are, for the most part, proceeding independently. Each will attempt to address the above requirements independently, with much duplication of effort. The Zope Object Database (ZODB) has satisfied the abo...
...database of molecules and fragments. Biomolecules (proteins, DNA, and RNA) are handled by subclasses of the generic Molecule class. Another important subset of MMTK implements schemas for calculating interaction energies (called somewhat incorrectly "force fields" in the simulation community). I/O-related code is the third pillar of MMTK. It reads and writes a few popular file formats plus its own trajectory format that is based on the netCDF format. Contrary to other trajectory file f...
...database be closed properly, else the on-disk data and directory files can be left in mutually inconsistent states. dumbdbm.py's _Database.__del__() method attempted to close the database properly, but a shutdown race in _Database._commit() could prevent this from working, so that a program trusting __del__() to get the on-disk files in synch could be badly surprised. The race has been repaired. A sync() method was also added so that shelve can guarantee data is written to disk. The close() me...
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