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Created the model_directory() method for the frame order auto-analysis.

This is used to create the full path for saving model specific files. It replaces spaces with
underscores in the path and removes all commas. The commas in the path appear to be fatal for
certain PyMOL versions when viewing the frame order representation.

bugman 2014-08-29

changed /branches/frame_order_cleanup/auto_analyses/frame_order.py
/branches/frame_order_cleanup/auto_analyses/frame_order.py Diff Switch to side-by-side view
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