Author: bugman
Date: Thu Jul 28 11:44:06 2011
New Revision: 13947
URL: http://svn.gna.org/viewcvs/relax?rev=13947&view=rev
Log:
This should have been the commit message of the previous commit (r13946).
This change actually contains a trivial comment modification in the XYZ file
reading system tests.
Merged revisions
12937-12941,12943-12945,12947-12952,12954-12957,12959-12960,12965-12967,12969-12975,12982-13022,13028-13029,13045-13046,13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780,13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r12937 | bugman | 2011-06-09 17:52:04 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed a duplicated self.SetSize() call for the main GUI window.
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r12938 | bugman | 2011-06-09 17:53:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Changed the Frame.SetSize() call to SetMinSize() to prevent the main GUI
window becoming too small.
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r12939 | bugman | 2011-06-09 17:54:12 +0200 (Thu, 09 Jun 2011) | 5 lines
Both SetSize() and SetMinSize() are now used for the main GUI window.
This allows for a proper layout.
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r12940 | bugman | 2011-06-09 18:19:37 +0200 (Thu, 09 Jun 2011) | 3 lines
Simplified and localised a variable.
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r12941 | bugman | 2011-06-09 18:31:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Added a hard coded variable for the size of the graphical part of the
analysis frames.
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r12943 | bugman | 2011-06-09 19:06:49 +0200 (Thu, 09 Jun 2011) | 3 lines
The text controls are now horizontally expandable.
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r12944 | bugman | 2011-06-09 19:11:05 +0200 (Thu, 09 Jun 2011) | 3 lines
The model-free, Rx, and NOE frame main box sizers all expand horizontally
now.
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r12945 | bugman | 2011-06-09 19:33:23 +0200 (Thu, 09 Jun 2011) | 3 lines
A spacer is now used for add_text_sel_element() if no button is present to
fill the button space.
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r12947 | bugman | 2011-06-09 20:10:45 +0200 (Thu, 09 Jun 2011) | 5 lines
Big simplification by shifting the widths of the text selection GUI element
to hard coded variables.
These hard coded class variables are located in the base class.
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r12948 | bugman | 2011-06-09 20:16:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Added some horizontal spacing between the elements of the text selection
GUI element.
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r12949 | bugman | 2011-06-10 09:42:25 +0200 (Fri, 10 Jun 2011) | 5 lines
Created the setup_analysis_element() base method for laying out the main
analysis GUI element.
This currently adds a border of 10 px around each analysis.
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r12950 | bugman | 2011-06-10 09:43:01 +0200 (Fri, 10 Jun 2011) | 3 lines
The auto model-free analysis frame now uses the base
setup_analysis_element() method.
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r12951 | bugman | 2011-06-10 10:08:05 +0200 (Fri, 10 Jun 2011) | 7 lines
Split the auto model-free build_main_box() method into two.
The left hand box is now created by build_left_box(), to reflect the design
of build_right_box()
and to allow build_main_box() to be abstracted into a base class method for
all analysis frames to
use.
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r12952 | bugman | 2011-06-10 10:16:14 +0200 (Fri, 10 Jun 2011) | 3 lines
Shifted the model-free window build_main_box() method to the base class.
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r12954 | bugman | 2011-06-10 11:26:14 +0200 (Fri, 10 Jun 2011) | 5 lines
The NOE and Rx analysis windows now use the base class build_main_box()
method.
Their build_main_box() methods have been renamed to build_left_box() and
modified to suit.
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r12955 | bugman | 2011-06-10 11:31:40 +0200 (Fri, 10 Jun 2011) | 3 lines
The results tab now uses the base setup_analysis_element() method to add
borders.
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r12956 | bugman | 2011-06-10 11:58:32 +0200 (Fri, 10 Jun 2011) | 3 lines
The right hand box in the analysis windows now expands vertically with
window resizing.
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r12957 | bugman | 2011-06-10 12:09:07 +0200 (Fri, 10 Jun 2011) | 3 lines
Better layout for the base class static text, text control and button
addition.
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r12959 | bugman | 2011-06-10 12:17:13 +0200 (Fri, 10 Jun 2011) | 3 lines
The peak list grid GUI element now expands within the box it is given.
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r12960 | bugman | 2011-06-10 12:23:41 +0200 (Fri, 10 Jun 2011) | 3 lines
Added a stretchable spacer to the NOE window so the execute relax button is
always at the bottom right.
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r12965 | bugman | 2011-06-10 14:48:51 +0200 (Fri, 10 Jun 2011) | 3 lines
Completely refactored the model-free model buttons code.
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r12966 | bugman | 2011-06-10 14:50:16 +0200 (Fri, 10 Jun 2011) | 3 lines
The model-free model buttons now expand to the correct width.
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r12967 | bugman | 2011-06-10 14:55:17 +0200 (Fri, 10 Jun 2011) | 3 lines
The add_mf_models() method is now using add_static_text() for the text.
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r12969 | bugman | 2011-06-10 15:24:59 +0200 (Fri, 10 Jun 2011) | 3 lines
Shifted the model-free add_execute_relax() method into the base class.
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r12970 | bugman | 2011-06-10 15:28:06 +0200 (Fri, 10 Jun 2011) | 3 lines
The method is now passed into add_execute_relax() to allow derived classes
to specify this.
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r12971 | bugman | 2011-06-10 15:30:20 +0200 (Fri, 10 Jun 2011) | 3 lines
Removed the SetName() call (it was for debugging).
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r12972 | bugman | 2011-06-10 15:32:49 +0200 (Fri, 10 Jun 2011) | 3 lines
Fixed the layout of the execute relax button GUI element.
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r12973 | bugman | 2011-06-10 15:35:58 +0200 (Fri, 10 Jun 2011) | 3 lines
The NOE and Rx frames are now using the base method add_execute_relax().
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r12974 | bugman | 2011-06-10 15:38:56 +0200 (Fri, 10 Jun 2011) | 3 lines
The left hand box of the analysis frames/windows now stretches vertically.
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r12975 | bugman | 2011-06-10 15:57:28 +0200 (Fri, 10 Jun 2011) | 3 lines
The peak intensity GUI element is now enclosed within a StaticBox.
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r12982 | bugman | 2011-06-14 12:56:01 +0200 (Tue, 14 Jun 2011) | 5 lines
Shifted the main GUI window layout to the start of the __init__() method.
This is to help with the sizing events.
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r12983 | bugman | 2011-06-14 14:17:01 +0200 (Tue, 14 Jun 2011) | 5 lines
Created the function gui.misc.add_border() for adding borders to generic
GUI elements.
The analysis tabs now use this method for their borders.
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r12984 | bugman | 2011-06-14 14:46:39 +0200 (Tue, 14 Jun 2011) | 5 lines
The gui.misc.add_border() function no longer packs the box in the parent
and detects orientation.
The parent argument has been replaced by a box sizer argument.
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r12985 | bugman | 2011-06-14 14:48:50 +0200 (Tue, 14 Jun 2011) | 3 lines
All the analysis tab GUI elements now use the new design of the
add_border() fn.
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r12986 | bugman | 2011-06-14 14:51:47 +0200 (Tue, 14 Jun 2011) | 5 lines
Added a method for catching resizing events.
It currently does nothing, allowing the event to continue.
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r12987 | bugman | 2011-06-14 14:58:50 +0200 (Tue, 14 Jun 2011) | 3 lines
Added an internal border to the relaxation peak list selection GUI element.
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r12988 | bugman | 2011-06-14 15:26:32 +0200 (Tue, 14 Jun 2011) | 3 lines
Added spacing above and below the peak list GUI element in the Rx tab GUI
elements.
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r12989 | bugman | 2011-06-14 15:43:19 +0200 (Tue, 14 Jun 2011) | 3 lines
The resize event is now bound to the grid and the first column now expands
with the window.
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r12990 | bugman | 2011-06-14 15:46:17 +0200 (Tue, 14 Jun 2011) | 3 lines
The Rx peak list grid cells can no longer be resized.
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r12991 | bugman | 2011-06-14 16:01:34 +0200 (Tue, 14 Jun 2011) | 3 lines
Horizontal scrolling is turned off in the relaxation peak list grid.
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r12992 | bugman | 2011-06-14 16:06:07 +0200 (Tue, 14 Jun 2011) | 3 lines
Switched the delay time and number of cycles columns in the peak list grid.
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r12993 | bugman | 2011-06-14 16:07:49 +0200 (Tue, 14 Jun 2011) | 14 lines
Reverted r12991, the disabling of horizontal scrolling.
The command used was:
svn merge -r12991:r12990 .
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r12991 | bugman | 2011-06-14 16:01:34 +0200 (Tue, 14 Jun 2011) | 3 lines
Changed paths:
M /1.3/gui/components/spectrum.py
Horizontal scrolling is turned off in the relaxation peak list grid.
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r12994 | bugman | 2011-06-14 16:20:30 +0200 (Tue, 14 Jun 2011) | 5 lines
The change_delay_down() and change_delay_up() methods are now bound again.
This allows only numbers in the delay time control and updates the grid
once changed.
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r12995 | bugman | 2011-06-14 16:21:37 +0200 (Tue, 14 Jun 2011) | 3 lines
Fixed update_grid() for the swapped columns.
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r12996 | bugman | 2011-06-14 16:22:13 +0200 (Tue, 14 Jun 2011) | 3 lines
Fixed sync_ds() for the swapped columns.
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r12997 | bugman | 2011-06-14 16:23:49 +0200 (Tue, 14 Jun 2011) | 3 lines
The relaxation delay time column is no longer read only.
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r12998 | bugman | 2011-06-14 16:34:20 +0200 (Tue, 14 Jun 2011) | 3 lines
Made the Rx peak list column a little smaller for better scrollbar handling.
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r12999 | bugman | 2011-06-14 16:47:09 +0200 (Tue, 14 Jun 2011) | 3 lines
The relaxation delay times are no longer reset if the number of cycles is
not set.
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r13000 | bugman | 2011-06-14 17:44:00 +0200 (Tue, 14 Jun 2011) | 3 lines
Better handling of changes in the relaxation peak list grid.
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r13001 | bugman | 2011-06-14 17:49:02 +0200 (Tue, 14 Jun 2011) | 3 lines
Removed a debugging printout.
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r13002 | bugman | 2011-06-14 17:51:12 +0200 (Tue, 14 Jun 2011) | 3 lines
The font for the grid is now set.
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r13003 | bugman | 2011-06-14 17:56:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Created a new font definition set to 10 pt and bold.
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r13004 | bugman | 2011-06-14 17:56:28 +0200 (Tue, 14 Jun 2011) | 3 lines
The grid fonts are now properly set.
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r13005 | bugman | 2011-06-14 18:04:33 +0200 (Tue, 14 Jun 2011) | 3 lines
The row heights are now set to match the delay time text control.
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r13006 | bugman | 2011-06-14 18:17:32 +0200 (Tue, 14 Jun 2011) | 3 lines
Improved layout of the model-free tab GUI element for resizing.
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r13007 | bugman | 2011-06-14 18:31:10 +0200 (Tue, 14 Jun 2011) | 6 lines
Created the analysis tab base class methods add_spin_control() and
add_spin_element().
These are similar to the text control and text selection elements
respectively, but use a SpinCtrl
instead.
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r13008 | bugman | 2011-06-14 18:31:51 +0200 (Tue, 14 Jun 2011) | 3 lines
The model-free analysis tab now uses the base class add_spin_element()
method for the max iterations.
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r13009 | bugman | 2011-06-14 18:43:49 +0200 (Tue, 14 Jun 2011) | 3 lines
Shifted the model-free list box in the results tab into the new
add_list_box() method.
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r13010 | bugman | 2011-06-14 18:50:17 +0200 (Tue, 14 Jun 2011) | 3 lines
The steady-state NOE results box now resizes.
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r13011 | bugman | 2011-06-14 18:50:48 +0200 (Tue, 14 Jun 2011) | 3 lines
Alphabetical ordering of methods.
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r13012 | bugman | 2011-06-14 18:53:46 +0200 (Tue, 14 Jun 2011) | 5 lines
All the result list boxes are now created by add_list_box().
The results tab now nicely resizes.
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r13013 | bugman | 2011-06-14 19:30:46 +0200 (Tue, 14 Jun 2011) | 9 lines
Complete redesign of the relax global settings window to fix the Mac OS X
crashing.
This is an attempt at fixing bug #18197 (https://gna.org/bugs/?18197).
The old code has been completely eliminated and replaced with a new set of
methods in the base
relax_gui class and a new Global_parameters class in gui.settings which is
of the same design as the
free file format settings window.
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r13014 | bugman | 2011-06-14 19:36:56 +0200 (Tue, 14 Jun 2011) | 3 lines
A minimum size is now set to prevent the settings windows from being
resized too small.
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r13015 | bugman | 2011-06-14 19:38:20 +0200 (Tue, 14 Jun 2011) | 3 lines
Fix for the global settings window - it needs to inherit from UF_window!
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r13016 | bugman | 2011-06-14 19:44:41 +0200 (Tue, 14 Jun 2011) | 3 lines
Brought the 'Execute relax' text inside the button.
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r13017 | bugman | 2011-06-14 19:53:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Added an icon to the 'Change' buttons throughout the GUI.
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r13018 | bugman | 2011-06-14 19:56:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Added the oxygen icons for opening folders.
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r13019 | bugman | 2011-06-14 19:59:06 +0200 (Tue, 14 Jun 2011) | 3 lines
Added the open folder icons to the paths module.
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r13020 | bugman | 2011-06-14 20:02:21 +0200 (Tue, 14 Jun 2011) | 3 lines
The open folder icons are now used for the 'Results directory' change
buttons.
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r13021 | bugman | 2011-06-14 20:03:30 +0200 (Tue, 14 Jun 2011) | 3 lines
Added a space between the relax icon and the text 'Execute relax' on the
button.
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r13022 | bugman | 2011-06-14 20:35:01 +0200 (Tue, 14 Jun 2011) | 5 lines
The settings windows are now derived from wx.Dialog rather than wx.Frame.
This is for better operation under MS Windows.
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r13028 | bugman | 2011-06-15 10:52:36 +0200 (Wed, 15 Jun 2011) | 3 lines
Added larger versions of the document-new.png Oxygen icons.
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r13029 | bugman | 2011-06-15 10:53:44 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the new document-new icons to the paths module.
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r13045 | bugman | 2011-06-15 16:29:43 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the document-close Oxygen icons.
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r13046 | bugman | 2011-06-15 16:32:19 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the document-close Oxygen icon to the paths module.
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r13153 | bugman | 2011-06-21 19:18:15 +0200 (Tue, 21 Jun 2011) | 5 lines
Removed a test for the sequence in the user function
structure.create_diff_tensor_pdb() backend.
The sequence data is not needed for this.
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r13258 | bugman | 2011-06-28 12:37:30 +0200 (Tue, 28 Jun 2011) | 6 lines
Bug fix for the NOE auto-analysis - the column numbers for the deselected
spins file are now assumed.
The residue number is assumed to be in the first column. This is a hack
until the spin selection
part is better designed.
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r13357 | bugman | 2011-07-01 13:33:41 +0200 (Fri, 01 Jul 2011) | 3 lines
Added support for old save files in the Peak_intensity.sync_ds() method.
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r13358 | bugman | 2011-07-01 13:35:09 +0200 (Fri, 01 Jul 2011) | 6 lines
Fix for the bug reported as sr #2764
(https://gna.org/support/index.php?2764).
The problem was that the sequence file is now in the variable sequence_file.
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r13359 | bugman | 2011-07-01 13:36:36 +0200 (Fri, 01 Jul 2011) | 5 lines
Another fix for the bug of sr #2764 (https://gna.org/support/?2764).
The sequence file variable is in self.data!!!
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r13411 | michaelbieri | 2011-07-04 01:15:43 +0200 (Mon, 04 Jul 2011) | 2
lines
Argument change_all for deselecting residues in the d'Auvergne protocol has
to be boolean.
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r13510 | bugman | 2011-07-08 08:58:14 +0200 (Fri, 08 Jul 2011) | 3 lines
Bug fix for the sequence.read() user function - the force flag is now being
passed on.
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r13511 | bugman | 2011-07-08 09:00:06 +0200 (Fri, 08 Jul 2011) | 5 lines
Another fix for the sequence.write() user function - the force flag is
passed to open_write_file().
This is from the relax_io.write_spin_data() function.
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r13512 | bugman | 2011-07-08 09:01:05 +0200 (Fri, 08 Jul 2011) | 5 lines
Bug fix for the sequence.write() user function when the column separator is
not whitespace.
The column widths are no longer fixed is the separator is not whitespace.
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r13577 | bugman | 2011-07-13 11:44:38 +0200 (Wed, 13 Jul 2011) | 5 lines
Many bug fixes for the functions of the generic_fns.mol_res_spin module.
These fixes are for when a data pipe other than the current data pipe is
used.
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r13631 | bugman | 2011-07-14 18:38:10 +0200 (Thu, 14 Jul 2011) | 5 lines
Bug fix for the relax save states - the current data pipe is now saved and
restored.
The info about the cdp was being blacklisted, so was not stored in the
relax save file.
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r13632 | bugman | 2011-07-14 20:09:47 +0200 (Thu, 14 Jul 2011) | 7 lines
Fix for the loading of saved state files prior to r13631 - the cdp is now
set to the last pipe.
The earlier saved state files did not store the current data pipe info, so
the current data pipe was
set by default to the last data pipe. This behaviour was broken with
r13631 but is now restored for
the old state files.
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r13641 | bugman | 2011-07-15 12:25:21 +0200 (Fri, 15 Jul 2011) | 3 lines
Fix for the new relax save state with current pipe info - the cdp ojbect is
now set after loading.
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r13655 | bugman | 2011-07-15 16:37:34 +0200 (Fri, 15 Jul 2011) | 3 lines
Bug fix for the atomic position check in the spin.create_pseudo user
function.
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r13660 | bugman | 2011-07-15 19:50:44 +0200 (Fri, 15 Jul 2011) | 6 lines
Bug fix for pseudo-atom support when only a single structure is loaded.
Pseudo-atom support was only working correctly for when multiple models
were loaded and atomic
positions were not averaged.
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r13683 | bugman | 2011-07-18 14:00:29 +0200 (Mon, 18 Jul 2011) | 6 lines
Bug fix for the spectrum.read_intensities int_method argument for volumes.
Volume integration should be called 'point sum', but the back end code was
checking against the
string 'volume'.
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r13686 | bugman | 2011-07-18 14:24:00 +0200 (Mon, 18 Jul 2011) | 3 lines
Bug fix in one of the relaxation curve-fitting system tests - 'volume'
should have been 'point sum'.
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r13706 | bugman | 2011-07-18 20:13:04 +0200 (Mon, 18 Jul 2011) | 6 lines
Fix for the PCS back-calculation function - divide by zero is now avoided.
The PCS back-calculation function was calculating the normalised bond
vector between the lanthanide
atom and itself. The normalisation in this case is now avoided.
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r13742 | bugman | 2011-07-19 17:02:29 +0200 (Tue, 19 Jul 2011) | 6 lines
Changed the order of some of the replicated spectra in the
test_curve_fitting_height system test.
This triggers a bug in the spectra.error_analysis user function which looks
like the replicated
spectra list is order dependent (when it shouldn't be).
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r13743 | bugman | 2011-07-19 17:18:49 +0200 (Tue, 19 Jul 2011) | 7 lines
Bug fix for the spectrum user functions for when the ID order does not
match those loaded.
If the order of IDs sent to spectrum.replicated did not match the order
they were loaded by
spectrum.read_intensities, then the spectrum.error_analysis user function
would fail. The order is
no longer important.
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r13748 | bugman | 2011-07-19 17:58:00 +0200 (Tue, 19 Jul 2011) | 5 lines
The relax_fit overfit_deselect() method now skips deselected spins.
This prevents unnecessary warnings about missing data for deselected spins.
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r13749 | bugman | 2011-07-19 18:00:13 +0200 (Tue, 19 Jul 2011) | 3 lines
All of the overfit_deselect() methods now skip deselected spins, avoiding
confusing warnings.
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r13780 | bugman | 2011-07-20 15:56:27 +0200 (Wed, 20 Jul 2011) | 6 lines
Bug fix - the pipe switching flag is now propagated all the way to the data
store add() method.
[... 144 lines stripped ...]
r13947 - /branches/xyz/test_suite/system_tests/structure.py