relax SVN archive

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

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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.
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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.

Merged revisions 22041-22045 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22041 | bugman | 2014-01-23 14:27:58 +0100 (Thu, 23 Jan 2014) | 5 lines

Created the lib.geometry.vectors.unit_vector_from_2point() function.

This is used to quickly calculate the unit vector between two points.
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r22042 | bugman | 2014-01-23 15:35:52 +0100 (Thu, 23 Jan 2014) | 5 lines

The lib.structure.represent.rotor.rotor_pdb() function can now handle multiple rotors.

Previously this function would fail if called twice with the same structural object.
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r22043 | bugman | 2014-01-23 15:37:00 +0100 (Thu, 23 Jan 2014) | 5 lines

Added the has_molecule() method to the relax internal structural object.

This is used to quickly check if a molecule name already exists in the structural object.
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r22044 | bugman | 2014-01-24 11:50:00 +0100 (Fri, 24 Jan 2014) | 5 lines

More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function.

The atom numbering is now better handled.
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r22045 | bugman | 2014-01-24 14:33:51 +0100 (Fri, 24 Jan 2014) | 11 lines

Better support for the writing out of multiple molecules by the structure.write_pdb user function.

This is for the internal structural object write_pdb() method. Now each molecule is assigned a
different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored.
The chain IDs should however be preserved when using structure.read_pdb followed by
structure.write_pdb, without storing the ID.

A number of the Structure system tests had to be updated, as now the relax generated PDB files will
always write out a chain ID.
........

Better support for the writing out of multiple molecules by the structure.write_pdb user function.

This is for the internal structural object write_pdb() method. Now each molecule is assigned a
different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored.
The chain IDs should however be preserved when using structure.read_pdb followed by
structure.write_pdb, without storing the ID.

A number of the Structure system tests had to be updated, as now the relax generated PDB files will
always write out a chain ID.

More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function.

The atom numbering is now better handled.