relax SVN archive

The save file created by the frame order test data generation base script can now be bypassed.

When loading 1,000,000 PDB structures as models into the relax data store, the RAM usage can go over
10 Gb. When trying to save this into a relax state file with the state.save user function, the time
required can be over a day. Therefore the SAVE_STATE class variable has been introduced to allow
the state.save call to be bypassed.

Removed a duplicated state.save call in the frame order test data generation base script.

Introduced the ROT_FILE flag to the frame order test data generation base script.

This allows the 'rotations.bz2' file creation to be skipped, if set to False. This file takes time
to create and is of limited use.

The frame order test data generation base script now outputs the frame order matrix to 8 places.

Fix for the frame order test data generation base script for when the distribution of structures is not created.

Fixes for the calculation of the frame order matrix in the test data generation base script.

The matrix generation now handles multiple modes of motion correctly. The total rotation matrix is
constructed when looping over the modes by using the dot product of the individual rotation to the
total, and then this is used to create the outer product, summed over all states.

The frame order matrix printing function can now output the matrix to any precision.

The lib.frame_order.format.print_frame_order_2nd_degree() function now accepts the 'places' argument
which allows for higher precision printouts.

Merged revisions 22051-22053 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22051 | bugman | 2014-01-27 19:23:47 +0100 (Mon, 27 Jan 2014) | 6 lines

More speed ups for the internal structural object when huge numbers of models are present.

Another loop over the structural_data object has been eliminated from the PDB reading load_pdb()
method.
........
r22052 | bugman | 2014-01-27 20:42:01 +0100 (Mon, 27 Jan 2014) | 6 lines

Another optimisation for the internal structural object for large numbers of models.

The ModelList.add_item() method no longer loops over all models to check if a model is already
present, instead using the new current_models list.
........
r22053 | bugman | 2014-01-27 21:49:32 +0100 (Mon, 27 Jan 2014) | 8 lines

Yet more optimisation for handling large quantities of models in the internal structural model.

Now when adding new models to the object, the model_indices and model_list objects are no longer
created. This saves much time as the large model_list is now not sorted. A number of structural
object methods have been updated to handle the change by switching to the model_loop() method for
looping over the models, rather than using the model_indices and model_list objects.
........

Yet more optimisation for handling large quantities of models in the internal structural model.

Now when adding new models to the object, the model_indices and model_list objects are no longer
created. This saves much time as the large model_list is now not sorted. A number of structural
object methods have been updated to handle the change by switching to the model_loop() method for
looping over the models, rather than using the model_indices and model_list objects.

Another optimisation for the internal structural object for large numbers of models.

The ModelList.add_item() method no longer loops over all models to check if a model is already
present, instead using the new current_models list.