relax SVN archive

The align_tensor.copy() tensor_to arg can now be None.

This is useful for copying between data pipes.

Created the align_tensor.fix() user function for fixing the alignment tensor during optimisation.

The alignment tensor optimisation is now optional within the population N-state model target fn.

Fix for the Grace write_xy_data() function for when data values of None are passed in.

Fix for the get_data() function - the returned data structure is dependent on the errors.

Instead of a list of x, y, error 1, error 2 with the errors set to None if non-existent, only the
required errors are returned.

Fix for the unit tests, the pseudo_ellipse module is now listed in maths_fns.__all__.

Fix for the relax_io.read_spin_data() function for when None is encountered.

The None values are now returned rather than skipped so that the calling code can decide what to do
with it.

The RDCs and PCSs can now be given optimisation weights.

Added a function for the pseudo-elliptical cosine function.

This is a numerical approximation generated by series expansion.

Merged revisions 11185-11189,11206-11210,11223-11224,11230-11233,11236,11240,11243-11245 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r11185 | bugman | 2010-05-11 16:48:07 +0200 (Tue, 11 May 2010) | 3 lines

Added some checks to properly inform the user as to what data is missing.
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r11186 | bugman | 2010-05-14 15:53:21 +0200 (Fri, 14 May 2010) | 3 lines

Docstring fix for the vect_dist_spherical_angles() function.
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r11187 | bugman | 2010-05-18 14:15:13 +0200 (Tue, 18 May 2010) | 5 lines

Added a check for the RDC RMS based Q-factor.

This is to check that relax matches both of Pales' Q-factors - which it does.
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r11188 | bugman | 2010-05-18 17:54:30 +0200 (Tue, 18 May 2010) | 3 lines

Broke some nasty circular import caused by importing the generic_fns.grace module.
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r11189 | bugman | 2010-05-18 18:32:14 +0200 (Tue, 18 May 2010) | 3 lines

Set names are now only written if they are not None.
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r11206 | bugman | 2010-05-19 10:49:53 +0200 (Wed, 19 May 2010) | 8 lines

Created the rdc.corr_plot() and pcs_corr_plot() user functions.

These are for creating correlation plots of measured vs. back-calculated RDCs and PCSs.

A couple of N-state model methods (return_grace_string() and return_units()) were added to allow the
user functions to work.
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r11207 | bugman | 2010-05-19 11:31:30 +0200 (Wed, 19 May 2010) | 6 lines

Added a maximum global iteration arg and check into the dauvergne_protocol.py module.

This was requested by Michael in the commit for r11194 at
https://mail.gna.org/public/relax-commits/2010-05/msg00022.html.
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r11208 | bugman | 2010-05-20 09:24:42 +0200 (Thu, 20 May 2010) | 16 lines

Bug fix for catching the looping around the universal solution in the dauvergne_protocol module.

This was first identified by Seb in the post at
https://mail.gna.org/public/relax-users/2007-09/msg00010.html (Message-id:
<46EEA6B2.90606@...>).

The problem was the automatic looping over optimisation cycles in the full_analysis.py script. This
code is now in the dauvergne_protocol auto_analyses module. The issue was a never-ending looping
around the universal solution (the optimisation minimum combined with Occam's razor or the model
selection minimum). This should now be caught and the protocol terminated at the end of the first
completed loop. The fix was to compare the chi2, selected models, diffusion tensor, and model-free
parameters to every iteration, starting from the first. This will not be optimal if the protocol is
interrupted in the middle of one such loop, but will just mean that a few extra iterations will be
required to complete the loop.
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r11209 | bugman | 2010-05-21 16:17:46 +0200 (Fri, 21 May 2010) | 3 lines

Modified the relax checklist to include minfx bundling.
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r11210 | bugman | 2010-05-21 16:59:46 +0200 (Fri, 21 May 2010) | 3 lines

More updates to the release checklist.
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r11223 | bugman | 2010-06-08 14:40:49 +0200 (Tue, 08 Jun 2010) | 3 lines

The RDC and PCS correlation plots now do not show deselected spins.
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r11224 | bugman | 2010-06-09 09:54:56 +0200 (Wed, 09 Jun 2010) | 5 lines

Small fix for the grace.write_xy_header() function.

The symbol numbers now range only between the legal values of 1 to 10.
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r11230 | bugman | 2010-06-11 13:46:02 +0200 (Fri, 11 Jun 2010) | 3 lines

Bug fix for the control of PyMOL (as a module).
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r11231 | bugman | 2010-06-11 14:02:28 +0200 (Fri, 11 Jun 2010) | 6 lines

Added a method for translating pymol.cmd.do() commands into specific pymol.cmd functions.

This prevents problems with commands being executed asynchronously. For example images were being
saved before ray-tracing was complete.
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r11232 | bugman | 2010-06-11 14:56:04 +0200 (Fri, 11 Jun 2010) | 6 lines

Reverted r11231 as this is not the best way to control pymol.

The command used was:
svn merge -r11231:11230 .
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r11233 | bugman | 2010-06-11 15:47:25 +0200 (Fri, 11 Jun 2010) | 5 lines

The PyMOL module pymol.cmd is now available within the pymol user function class.

This is accessible as pymol.cmd from the prompt/script interface.
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r11236 | bugman | 2010-06-12 17:33:38 +0200 (Sat, 12 Jun 2010) | 14 lines

Merged r11234 from the 1.3.5 tag into the 1.3 line.

The command used was:
svn merge -r11233:11234 svn+ssh://bugman@.../svn/relax/tags/1.3.5 .

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r11234 | bugman | 2010-06-12 17:23:16 +0200 (Sat, 12 Jun 2010) | 3 lines
Changed paths:
M /tags/1.3.5/scons/manuals.py

Excluded minfx from the API manual compilation.
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r11240 | bugman | 2010-06-12 18:17:47 +0200 (Sat, 12 Jun 2010) | 6 lines

Manually merged the 1.3.5 CHANGES file back into the main line.

The command used was:
svn merge -r11225:11226 svn+ssh://bugman@.../svn/relax/tags/1.3.5 .
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r11243 | bugman | 2010-06-15 16:51:24 +0200 (Tue, 15 Jun 2010) | 3 lines

Some function/method docstring epydoc formatting fixes.
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r11244 | bugman | 2010-06-15 16:56:43 +0200 (Tue, 15 Jun 2010) | 3 lines

The RDC and PCS correlation plots now also show the experimental errors.
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r11245 | bugman | 2010-06-15 17:05:56 +0200 (Tue, 15 Jun 2010) | 3 lines

Per point comments are now included in the Grace files.
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