Author: bugman
Date: Fri Nov 15 19:14:55 2013
New Revision: 21454
URL: http://svn.gna.org/viewcvs/relax?rev=21454&view=rev
Log:
Merged revisions 21436-21453 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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.
........
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.
........
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().
........
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.
........
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.
........
r21442 | bugman | 2013-11-14 13:12:24 +0100 (Thu, 14 Nov 2013) | 3 lines
Typo fix in a warning message.
........
r21443 | bugman | 2013-11-14 13:27:48 +0100 (Thu, 14 Nov 2013) | 3 lines
Removed a debugging printout.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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).
........
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.
........
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.
........
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.
........
Added:
branches/relax_disp/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range
- copied unchanged from r21453,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range
branches/relax_disp/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range
- copied unchanged from r21453,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range
Removed:
branches/relax_disp/gui/paths.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/gui/analyses/auto_model_free.py
branches/relax_disp/gui/analyses/auto_noe.py
branches/relax_disp/gui/analyses/auto_rx_base.py
branches/relax_disp/gui/analyses/base.py
branches/relax_disp/gui/analyses/elements/model_list.py
branches/relax_disp/gui/analyses/elements/text_element.py
branches/relax_disp/gui/components/free_file_format.py
branches/relax_disp/gui/controller.py
branches/relax_disp/gui/input_elements/combo_list.py
branches/relax_disp/gui/input_elements/file.py
branches/relax_disp/gui/input_elements/sequence.py
branches/relax_disp/gui/menu.py
branches/relax_disp/gui/message.py
branches/relax_disp/gui/pipe_editor.py
branches/relax_disp/gui/relax_gui.py
branches/relax_disp/gui/results_viewer.py
branches/relax_disp/gui/spin_viewer/tree.py
branches/relax_disp/gui/wizards/wiz_objects.py
branches/relax_disp/lib/warnings.py
branches/relax_disp/pipe_control/align_tensor.py
branches/relax_disp/pipe_control/j_coupling.py
branches/relax_disp/pipe_control/pcs.py
branches/relax_disp/pipe_control/rdc.py
branches/relax_disp/specific_analyses/n_state_model/__init__.py
branches/relax_disp/specific_analyses/n_state_model/data.py
branches/relax_disp/specific_analyses/n_state_model/parameters.py
branches/relax_disp/target_functions/n_state_model.py
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_0
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_2
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_3
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_0
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_2
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_3
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_0
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_2
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_3
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_dy.txt
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_er.txt
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_ho.txt
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tb.txt
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tm.txt
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_yb.txt
branches/relax_disp/test_suite/system_tests/n_state_model.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/gui/analyses/auto_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/auto_model_free.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/analyses/auto_noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/auto_noe.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/analyses/auto_rx_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/auto_rx_base.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/analyses/base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/base.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/analyses/elements/model_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/elements/model_list.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/analyses/elements/text_element.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/analyses/elements/text_element.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/components/free_file_format.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/components/free_file_format.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/controller.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/controller.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/input_elements/combo_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/input_elements/combo_list.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/input_elements/file.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/input_elements/file.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/input_elements/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/input_elements/sequence.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/menu.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/menu.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/message.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/message.py?rev=21454&r1=21453&r2=21454&view=diff
Removed: branches/relax_disp/gui/paths.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/paths.py?rev=21453&view=auto
Modified: branches/relax_disp/gui/pipe_editor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/pipe_editor.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/relax_gui.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/results_viewer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/results_viewer.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/spin_viewer/tree.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/spin_viewer/tree.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/gui/wizards/wiz_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/wizards/wiz_objects.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/lib/warnings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/warnings.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/align_tensor.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/pipe_control/j_coupling.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/j_coupling.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/pcs.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/rdc.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/specific_analyses/n_state_model/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model/__init__.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/specific_analyses/n_state_model/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model/data.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/specific_analyses/n_state_model/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model/parameters.py?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/n_state_model.py?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_0
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_0?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_2
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_2?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_3
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/metal_pos_opt/missing_rdc_3?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_0
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_0?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_2
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_2?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_3
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/missing_data/missing_rdc_3?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_0
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_0?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_2
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_2?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_3
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/population_model/missing_rdc_3?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_dy.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_dy.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_er.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_er.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_ho.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_ho.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tb.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tb.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tm.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_tm.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_yb.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/displacements/rdc_yb.txt?rev=21454&r1=21453&r2=21454&view=diff
Modified: branches/relax_disp/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/n_state_model.py?rev=21454&r1=21453&r2=21454&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py?rev=21454&r1=21453&r2=21454&view=diff
r21454 - in /branches/relax_disp: ./ gui/ gui/analyses/ gui/analyses/elements/ gui/components/ gui/input_elements/ gui/spin_...