relax SVN archive

STDOUT is now being restored after each stage.

STDOUT was being lost if logging was turned on!

The stereochem_analysis auto-analysis is now placing all generated files into the desired results dir.

The cwd is used if no results_dir arg is given.

A results directory can now be specified in the stereochem_analysis auto-analysis.

This is not being used yet.

Shifted the Gromacs phthalic acid structure.

Updated the package __all__ list to include all modules.

Added a directory to the test suite data for holding phthalic acid structures.

Missing import of pi.

The interpreter is now imported and set up. User function calls are now passed through this class.

Fix for the stereochem_analysis.py sample script - the instantiated class run() method must be run!