relax SVN archive

Converted the rotate() and translate() structural object methods to use the new selection object.

The atom_id arguments have been replaced with selection arguments. Therefore all parts of relax
which call these methods must first call selection() to obtain the Internal_selection instance.

Fixes for the new structural object Internal_selection object.

The atom indices are not stored via the molecule index.

Indentation fix for the internal structural object validate_model() method.

Missing import of the Internal_selection class.

The internal structural object validate_models() method now accepts the verbosity argument.

This is used to silence printouts.

Added the selection() method to the internal structural object.

This parses the atom ID string using the lib.selection module, loops over the molecules and atoms,
performs matches using re.search() via lib.selection, and populates and returns the new
Internal_selection object. This can be used to pre-process the atom ID string to save huge amounts
of time.

Created a special internal structural object selection object.

This will be used for massively speeding up the internal structural object. The use of the
lib.selection module by the internal structural object is currently very slow as a huge number of
calls to re.search() are required. The idea is to avoid this by using lib.selection once to
populate this new selection object, and then reusing this object to loop over molecules and atoms.

Implemented the frame_order.simulate user function backend for the double rotor frame order model.

This involved extending the algorithm to loop over N states, where N=2 for the double rotor and N=1
for all other models. To handle the rotations being about the x and y-axes, an axis permutation
algorithm is used to shift these axes to z prior to decomposing to the torsion-tilt angles. The
reverse permutation is used to shift the axes back after correcting for being outside of the allowed
angles.

Merged revisions 25967-25968 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25967 | bugman | 2014-09-23 13:59:05 +0200 (Tue, 23 Sep 2014) | 6 lines

Dependency fix for the auto_analyses.relax_disp_repeat_cpmg module.

This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused
relax to not start if scipy was not installed. This was detected by testing relax with PyPy.
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r25968 | tlinnet | 2014-09-23 14:41:49 +0200 (Tue, 23 Sep 2014) | 3 lines

Implemented writing out of particular correlation plots to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
........

Implemented writing out of particular correlation plots to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.