relax SVN archive

Removal of the 'absolute_rdc' branch as all changes have been merged to the trunk.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/absolute_rdc

Merged revisions 17174 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17174 | bugman | 2012-07-04 09:32:35 +0200 (Wed, 04 Jul 2012) | 5 lines

Bug fix for the Palmer system tests for the changed spin ID syntax.

The spin Gly 2 can no longer be selected with ':2&:Gly', the '&' symbol is not allowed here.
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Merged revisions 16851,16856-16857,17187-17193,17195-17196 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/absolute_rdc

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r16851 | bugman | 2012-06-11 20:13:41 +0200 (Mon, 11 Jun 2012) | 5 lines

Added the 'absolute' keyword arg to the rdc.read user function definition.

This will be used to mark RDCs as being unsigned.
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r16856 | bugman | 2012-06-11 20:21:58 +0200 (Mon, 11 Jun 2012) | 3 lines

Created an initial system (and GUI) test for the absolute RDC concept.
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r16857 | bugman | 2012-06-11 20:23:02 +0200 (Mon, 11 Jun 2012) | 3 lines

Added the script for the system test of the last commit (r16856).
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r17187 | bugman | 2012-07-04 11:18:32 +0200 (Wed, 04 Jul 2012) | 5 lines

The rdc.read user function backend now accepts the 'absolute' argument.

This is used to signal that the RDCs are signless absolute values.
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r17188 | bugman | 2012-07-04 11:19:23 +0200 (Wed, 04 Jul 2012) | 3 lines

Created an absolute value version of the synthetic CaM RDC file for the test suite.
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r17189 | bugman | 2012-07-04 11:34:20 +0200 (Wed, 04 Jul 2012) | 3 lines

Whitespace fix.
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r17190 | bugman | 2012-07-04 11:34:43 +0200 (Wed, 04 Jul 2012) | 3 lines

Converted the N-state model absolute_rdcs.py system test script to the interatomic data design.
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r17191 | bugman | 2012-07-04 11:56:28 +0200 (Wed, 04 Jul 2012) | 3 lines

The rdc.read user function backend is now storing the absolute value flag in interatom.absolute_rdc.
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r17192 | bugman | 2012-07-04 11:58:44 +0200 (Wed, 04 Jul 2012) | 6 lines

Added support for the absolute or signless RDCs to the N-state model.

This simply propagates the absolute flags into the maths_fns.rdc module functions whereby the
absolute RDC values and gradients can be returned.
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r17193 | bugman | 2012-07-04 12:04:51 +0200 (Wed, 04 Jul 2012) | 9 lines

Fix for the absolute_rdcs.py system test script.

The signed and signless data are now loaded using the same alignment ID. A single RDC has been
removed from the test_suite/shared_data/align_data/CaM/synth_rdc_abs RDC file which is negative in
the corresponding synth_rdc file. The signed RDCs are first loaded followed by the signless RDCs
which overwrite the original RDCs - all except for the single negative value with the absolute flag
turned off. The single negative RDC allows the tensor negative and positive lobes to be defined.
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r17195 | bugman | 2012-07-04 12:24:44 +0200 (Wed, 04 Jul 2012) | 5 lines

Bug fix for the N_state_model _target_fn_setup() method for the absolute_rdc data structure.

This needs to be initialised to None for any analysis which doesn't include RDC data.
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r17196 | bugman | 2012-07-04 12:27:21 +0200 (Wed, 04 Jul 2012) | 6 lines

Bug fix for the N-state model _minimise_setup_rdcs() method for when the RDC data is incomplete.

The set up of the absolute RDC flag data structure can no handle the absence of the flag for certain
interatomic data containers or alignments.
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Merged revisions 17156 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17156 | bugman | 2012-07-03 14:20:16 +0200 (Tue, 03 Jul 2012) | 6 lines

Bug fix for the Value GUI input element for integer values.

This is only uncovered when remotely running the GUI - e.g. through the test suite - and an integer
value is set.
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Initialized merge tracking via "svnmerge" with revisions "1-16841" from
svn+ssh://bugman@.../svn/relax/branches/absolute_rdc

Bug fix for the N-state model _minimise_setup_rdcs() method for when the RDC data is incomplete.

The set up of the absolute RDC flag data structure can no handle the absence of the flag for certain
interatomic data containers or alignments.

Bug fix for the N_state_model _target_fn_setup() method for the absolute_rdc data structure.

This needs to be initialised to None for any analysis which doesn't include RDC data.

Merged revisions 17139,17142 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17139 | bugman | 2012-07-02 21:36:49 +0200 (Mon, 02 Jul 2012) | 6 lines

The spin container hidden objects are now replicated when the object is copied.

The old Prototype.__deepcopy__() method was skipping all hidden objects, but now only objects
starting with '__' are skipped.
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r17142 | bugman | 2012-07-02 22:07:41 +0200 (Mon, 02 Jul 2012) | 5 lines

Improvement for the RelaxNoVectorsError class - the data pipe name is now optional.

The print outs have been improved as well.
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Fix for the absolute_rdcs.py system test script.

The signed and signless data are now loaded using the same alignment ID. A single RDC has been
removed from the test_suite/shared_data/align_data/CaM/synth_rdc_abs RDC file which is negative in
the corresponding synth_rdc file. The signed RDCs are first loaded followed by the signless RDCs
which overwrite the original RDCs - all except for the single negative value with the absolute flag
turned off. The single negative RDC allows the tensor negative and positive lobes to be defined.