relax SVN archive

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

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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.
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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.
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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.

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.

Merged revisions 22049 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22049 | bugman | 2014-01-27 18:54:08 +0100 (Mon, 27 Jan 2014) | 8 lines

Large speed up for the internal structural object for when many models are present.

The new ModelList.current_models object keeps track of all the models already present in the
structural object. This simplifies the checks of the pack_structs() internal structural object
method by removing expensive looping. This allows the loading of PDB files to continue to be fast
even with many tens or hundreds of thousands of models already loaded.
........

Large speed up for the internal structural object for when many models are present.

The new ModelList.current_models object keeps track of all the models already present in the
structural object. This simplifies the checks of the pack_structs() internal structural object
method by removing expensive looping. This allows the loading of PDB files to continue to be fast
even with many tens or hundreds of thousands of models already loaded.

Improvements and expansion of the frame order test data generation base script.

More of the class variables are now defined in this base class and dummy methods are provided to
allow certain operations to be skipped (print_axis_system(), axes_to_pdb() and build_axes()).
Importantly, the script can now handle multiple modes of motion with the introduction of the key
_multi_system() and _state_loop() methods.

Created a simple double rotor geometric system to used for this frame order test data generation.

The system_create.py script creates the geometric system based on the CoMs of both domains in the
parent directory and two perpendicular rotation axes passing through both CoMs. A PDB file of the
representation is created by the script.