relax SVN archive

Merged revisions 21436-21453 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r21436 | bugman | 2013-11-13 22:06:46 +0100 (Wed, 13 Nov 2013) | 6 lines

Created the N_state_model.test_pyrotartaric_anhydride_mix system test.

This is used to demonstrate a bug in the N-state analysis using mixed RDC and long range absolute
J+D data.
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r21437 | bugman | 2013-11-14 10:48:08 +0100 (Thu, 14 Nov 2013) | 9 lines

Movement of N-state model specific code to the analysis neutral pipe_control package.

Many of the functions of the specific_analyses.n_state_model.data module relating to alignment
tensors, RDC data and PCS data have been shifted in to the pipe_control package modules
align_tensor, rdc, and pcs respectively. This allows these functions to be made more general and
allow the code to be shared with the frame order analysis or any future analysis using such data,
and hence remove some code duplication.
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r21438 | bugman | 2013-11-14 11:23:52 +0100 (Thu, 14 Nov 2013) | 3 lines

Create two new warnings RelaxNucleusWarning and RelaxSpinTypeWarning to match the equivalent errors.
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r21439 | bugman | 2013-11-14 11:34:18 +0100 (Thu, 14 Nov 2013) | 5 lines

Added some RDC data checks to the N_state_model.test_pyrotartaric_anhydride_rdcs system test.

This is to demonstrate a problem with the data assembly function pipe_control.rdc.return_rdc_data().
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r21440 | bugman | 2013-11-14 11:54:27 +0100 (Thu, 14 Nov 2013) | 6 lines

Clean ups and improvements for the pipe_control.rdc.check_rdcs() function.

Pseudo-atoms are now handled much better and correctly in all cases. And many RelaxErrors have been
converted to RelaxWarnings followed by a 'return False' statement.
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r21441 | bugman | 2013-11-14 11:56:30 +0100 (Thu, 14 Nov 2013) | 7 lines

Created the pipe_control.rdc.setup_pseudoatom_rdcs() function.

This is used to make sure that the pseudo-atom interatomic systems (the containers from heternucleus
to pseudo-atom and heteronucleus to pseudo-atom members) are properly set up. It will deselect the
interatomic containers if incorrectly set up or if they are not part of the main pair.
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r21442 | bugman | 2013-11-14 13:12:24 +0100 (Thu, 14 Nov 2013) | 3 lines

Typo fix in a warning message.
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r21443 | bugman | 2013-11-14 13:27:48 +0100 (Thu, 14 Nov 2013) | 3 lines

Removed a debugging printout.
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r21444 | bugman | 2013-11-14 13:34:07 +0100 (Thu, 14 Nov 2013) | 5 lines

Added quotation marks around a number of spin IDs with molecule names in some RDC data files.

This is for the N-state model population model data used in the test suite.
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r21445 | bugman | 2013-11-14 13:43:21 +0100 (Thu, 14 Nov 2013) | 6 lines

The rdc.read and j_coupling.read user functions now ignore all lines starting with the # character.

This is to remove all comment lines silently. Therefore if spin IDs are used which contain the
molecule name, then they should be wrapped in quotation marks.
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r21446 | bugman | 2013-11-14 13:44:17 +0100 (Thu, 14 Nov 2013) | 5 lines

Updated a number of RDC test suite data files to have quotation marks around the spin IDs.

This is to allow the molecule identifier to be present while not being mistaken for a comment line.
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r21447 | bugman | 2013-11-14 14:06:05 +0100 (Thu, 14 Nov 2013) | 6 lines

Updated some of the RDC data files used in the frame order system tests.

The spin IDs are now in quotation marks as the molecule name is included. This is to prevent the
line being removed as a comment.
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r21448 | bugman | 2013-11-14 14:38:19 +0100 (Thu, 14 Nov 2013) | 6 lines

Changes to the setup_pseudoatom_rdcs() function and renamed it to setup_pseudoatom_rdc().

The interatomic loop is now within the function to make sure that all is completed before the
containers are accessed.
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r21449 | bugman | 2013-11-14 14:39:13 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for the setup_pseudoatom_rdc() function which should have been part of r21448.
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r21450 | bugman | 2013-11-14 15:00:49 +0100 (Thu, 14 Nov 2013) | 8 lines

Started to add better pseudo-atom support for the PCS.

The new pipe_control.pcs.setup_pseudoatom_pcs() function has been added to deselect the spins which
are members of a pseudo-atom. The return_pcs_data() function in the same module now calls this
function and builds a list of pseudo-atom flags for use in the target function (though it is still
unused).
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r21451 | bugman | 2013-11-14 15:01:37 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for the N-state model _target_fn_setup() method for when no PCS data is present.
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r21452 | bugman | 2013-11-14 15:18:27 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for a recent bug in the pipe_control.rdc.setup_pseudoatom_rdc() function.
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r21453 | bugman | 2013-11-14 17:22:56 +0100 (Thu, 14 Nov 2013) | 5 lines

Finally eliminated the gui.paths module, replacing it with graphics.fetch_icon() calls.

The GUI was using a mix of the old gui.paths module and the fetch_icon() function.
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Finally eliminated the gui.paths module, replacing it with graphics.fetch_icon() calls.

The GUI was using a mix of the old gui.paths module and the fetch_icon() function.

Fix for a recent bug in the pipe_control.rdc.setup_pseudoatom_rdc() function.

Fix for the N-state model _target_fn_setup() method for when no PCS data is present.

Started to add better pseudo-atom support for the PCS.

The new pipe_control.pcs.setup_pseudoatom_pcs() function has been added to deselect the spins which
are members of a pseudo-atom. The return_pcs_data() function in the same module now calls this
function and builds a list of pseudo-atom flags for use in the target function (though it is still
unused).

Fix for the setup_pseudoatom_rdc() function which should have been part of r21448.

Changes to the setup_pseudoatom_rdcs() function and renamed it to setup_pseudoatom_rdc().

The interatomic loop is now within the function to make sure that all is completed before the
containers are accessed.

Updated some of the RDC data files used in the frame order system tests.

The spin IDs are now in quotation marks as the molecule name is included. This is to prevent the
line being removed as a comment.

Updated a number of RDC test suite data files to have quotation marks around the spin IDs.

This is to allow the molecule identifier to be present while not being mistaken for a comment line.

The rdc.read and j_coupling.read user functions now ignore all lines starting with the # character.

This is to remove all comment lines silently. Therefore if spin IDs are used which contain the
molecule name, then they should be wrapped in quotation marks.