svn+ssh://bugman@.../svn/relax/1.3
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r12840 | bugman | 2011-05-31 14:47:37 +0200 (Tue, 31 May 2011) | 7 lines
Updates for the Dasha sample script.
The problem was identified by Shantanu Bhattacharyya <shantanu01 att cmu dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@...>).
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r12841 | semor | 2011-05-31 16:29:49 +0200 (Tue, 31 May 2011) | 7 lines
Updates for the diffusion tensor optimization sample script.
The problem was identified (for sample script "dasha.py")
by Shantanu Bhattacharyya <shantanu01 att cmu dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@...>).
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r12842 | bugman | 2011-05-31 18:43:18 +0200 (Tue, 31 May 2011) | 3 lines
Some fixes for the subprocess.Popen() calls on MS Windows.
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r12843 | bugman | 2011-06-03 17:46:57 +0200 (Fri, 03 Jun 2011) | 7 lines
Added the PDB reading parts of Scientific python to relax.
This is allowed as the CeCILL licence is GPL compatible. The Scientific python website is
https://sourcesup.cru.fr/projects/scientific-py/, but it hasn't been updated in a long time and
might be a dying project. Therefore the code is now part of relax so it can be used in the future.
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r12844 | bugman | 2011-06-03 17:48:05 +0200 (Fri, 03 Jun 2011) | 3 lines
The Scientific python PDB reading tests are no longer skipped if the module is not installed.
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r12845 | bugman | 2011-06-03 17:48:41 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the information printout from 'relax --info'.
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r12846 | bugman | 2011-06-03 17:51:24 +0200 (Fri, 03 Jun 2011) | 3 lines
Modified the Scientific python PDB reader relax module to use the internal module.
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r12847 | bugman | 2011-06-03 17:52:10 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the dependency checking.
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r12848 | bugman | 2011-06-03 17:54:51 +0200 (Fri, 03 Jun 2011) | 3 lines
The 'extern' package is now a proper package - the __init__.py file has been added!
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r12849 | bugman | 2011-06-03 17:57:07 +0200 (Fri, 03 Jun 2011) | 3 lines
Fixes for the Scientific python parts included with relax for the module path.
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r12850 | bugman | 2011-06-03 17:57:55 +0200 (Fri, 03 Jun 2011) | 3 lines
The dep_check.scientific_pdb_module flag was still being checked.
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r12851 | bugman | 2011-06-03 18:00:15 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed the dep_check checks and test disabling for the Scientific python system and unit tests.
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r12854 | bugman | 2011-06-03 18:34:07 +0200 (Fri, 03 Jun 2011) | 5 lines
Removed Scientific python and Numeric from the blacklisted modules.
This is for the docstring fetching script to generate the user function section of the user manual.
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r12855 | bugman | 2011-06-03 18:34:53 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the dependency list in the user manual.
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r12856 | michaelbieri | 2011-06-07 01:12:19 +0200 (Tue, 07 Jun 2011) | 2 lines
relax icon is not shown in window title if running on a Mac.
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r12857 | michaelbieri | 2011-06-07 01:14:31 +0200 (Tue, 07 Jun 2011) | 2 lines
Included copyright be the relax development team to main window.
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r12858 | michaelbieri | 2011-06-07 01:50:39 +0200 (Tue, 07 Jun 2011) | 2 lines
Peak lists and relaxation times are collected in data grid.
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r12859 | michaelbieri | 2011-06-07 01:55:37 +0200 (Tue, 07 Jun 2011) | 2 lines
Renamed load_peaklists() to add_pleaklists().
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r12860 | michaelbieri | 2011-06-07 02:10:21 +0200 (Tue, 07 Jun 2011) | 2 lines
Add peaklist button was added.
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r12861 | michaelbieri | 2011-06-07 02:42:27 +0200 (Tue, 07 Jun 2011) | 2 lines
Peak lists can be loaded into peak list grid.
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r12862 | michaelbieri | 2011-06-07 02:43:01 +0200 (Tue, 07 Jun 2011) | 2 lines
Allowed to load 50 peaklists.
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r12863 | michaelbieri | 2011-06-07 02:44:15 +0200 (Tue, 07 Jun 2011) | 2 lines
Added R1 and R2 label to peak list title.
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r12864 | michaelbieri | 2011-06-07 02:52:01 +0200 (Tue, 07 Jun 2011) | 2 lines
Button in R1 to read relaxation delays from VD lists.
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r12865 | michaelbieri | 2011-06-07 02:53:18 +0200 (Tue, 07 Jun 2011) | 2 lines
Removed event.skip due to conflict with Windows.
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r12866 | michaelbieri | 2011-06-07 03:04:13 +0200 (Tue, 07 Jun 2011) | 2 lines
R1 delays can be imported from VD lists.
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r12867 | michaelbieri | 2011-06-07 03:12:32 +0200 (Tue, 07 Jun 2011) | 2 lines
Added import VC (variable counter) list function incl. space to sepcify counter time.
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r12868 | michaelbieri | 2011-06-07 03:38:15 +0200 (Tue, 07 Jun 2011) | 2 lines
R2 delax can be imported from variable counter (VC) list.
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r12869 | michaelbieri | 2011-06-07 04:29:04 +0200 (Tue, 07 Jun 2011) | 2 lines
Peak lists and relaxation delays are synchronized with relax data storage.
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r12870 | michaelbieri | 2011-06-07 06:17:52 +0200 (Tue, 07 Jun 2011) | 2 lines
Peak lists and relaxation times can be opened.
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r12871 | bugman | 2011-06-07 12:03:03 +0200 (Tue, 07 Jun 2011) | 5 lines
Copied all of Michael's code from the auto_rx_base module committed yesterday into the spectrum module.
This is to keep a clear code separation of the different elements in the R1 and R2 frames.
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r12872 | bugman | 2011-06-07 12:43:45 +0200 (Tue, 07 Jun 2011) | 3 lines
Partially reverted r12870 as the commenting out of link_data() broke the loading of the relax state!
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r12873 | bugman | 2011-06-07 12:44:36 +0200 (Tue, 07 Jun 2011) | 3 lines
Redesigned sync_ds() to handle the new wx.grid.Grid() object.
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r12874 | bugman | 2011-06-07 14:15:03 +0200 (Tue, 07 Jun 2011) | 3 lines
Capitalisation fix.
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r12875 | bugman | 2011-06-07 14:15:13 +0200 (Tue, 07 Jun 2011) | 3 lines
Spacing fix.
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r12876 | bugman | 2011-06-07 14:49:40 +0200 (Tue, 07 Jun 2011) | 3 lines
Double clicking on the peak list cells in the Rx frames now runs openfile().
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r12877 | bugman | 2011-06-07 15:47:04 +0200 (Tue, 07 Jun 2011) | 3 lines
Removed some unused variables.
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r12878 | bugman | 2011-06-07 16:19:42 +0200 (Tue, 07 Jun 2011) | 3 lines
Added a title and nicer spacing for the relaxation peak lists GUI element.
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r12879 | bugman | 2011-06-07 16:20:44 +0200 (Tue, 07 Jun 2011) | 3 lines
The 'Rx peak lists' column name is no longer plural.
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r12880 | bugman | 2011-06-07 16:41:43 +0200 (Tue, 07 Jun 2011) | 3 lines
Not selecting a peak list file also vetos the event so the cell is not editable.
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r12881 | bugman | 2011-06-07 16:46:06 +0200 (Tue, 07 Jun 2011) | 3 lines
Comment fix.
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r12882 | bugman | 2011-06-07 16:46:46 +0200 (Tue, 07 Jun 2011) | 5 lines
Fixes for the spin.copy() GUI user function element.
This still had remnants of the residue.copy() window.
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r12883 | bugman | 2011-06-07 17:22:47 +0200 (Tue, 07 Jun 2011) | 6 lines
Fix for the CSA value in the value.set() GUI wizard image.
This was reported by Seb at https://mail.gna.org/public/relax-devel/2011-06/msg00040.html
(Message-id: <4DEE3D12.4000406@...>).
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r12884 | bugman | 2011-06-07 17:32:07 +0200 (Tue, 07 Jun 2011) | 3 lines
Updated the Bieri et al., 2011 reference as the relax GUI paper is now published.
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r12885 | bugman | 2011-06-07 17:56:24 +0200 (Tue, 07 Jun 2011) | 6 lines
Changed the "Help->Contact relaxGUI" to "Help->Mailing list contact".
This is because this sends an email to the relax users mailing list, and the user needs to be aware
that this is a public mailing list.
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r12886 | bugman | 2011-06-07 19:53:09 +0200 (Tue, 07 Jun 2011) | 6 lines
Renamed the "Relaxation time [s]" column to "Relaxation delay [s]" as this is a more correct desc.
Relaxation times are the inverse of the rates, not the delays causing relaxation in the pulse
sequence.
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r12887 | bugman | 2011-06-07 19:54:51 +0200 (Tue, 07 Jun 2011) | 3 lines
Widened the "Relaxation delay" column for the Rx tabs.
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r12888 | bugman | 2011-06-07 21:35:08 +0200 (Tue, 07 Jun 2011) | 3 lines
Deleted my ancient Melbourne Uni email address from the MEDLINE info!
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r12891 | bugman | 2011-06-08 12:13:37 +0200 (Wed, 08 Jun 2011) | 5 lines
Implemented the deletion of cell contents in the wx.grid element for Rx peak lists.
This requires a complex algorithm for handling wx.grid selections!
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r12892 | bugman | 2011-06-08 12:50:24 +0200 (Wed, 08 Jun 2011) | 3 lines
Better behaviour for the addition of peak list files to the Rx grid element.
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r12893 | semor | 2011-06-08 13:46:03 +0200 (Wed, 08 Jun 2011) | 3 lines
Fixed an alignment.
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r12894 | bugman | 2011-06-08 13:52:30 +0200 (Wed, 08 Jun 2011) | 3 lines
Shifted the button code into the add_buttons() method.
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r12895 | bugman | 2011-06-08 13:56:48 +0200 (Wed, 08 Jun 2011) | 3 lines
Shifted the grid construction code into the add_grid() method.
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r12896 | bugman | 2011-06-08 13:57:31 +0200 (Wed, 08 Jun 2011) | 3 lines
Renamed peak_list_header() to add_header().
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r12897 | bugman | 2011-06-08 13:58:59 +0200 (Wed, 08 Jun 2011) | 3 lines
Abstracted the grid GUI element by renaming self.peaklist to self.grid.
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r12899 | semor | 2011-06-08 14:49:50 +0200 (Wed, 08 Jun 2011) | 12 lines
relax icon is not shown in "Global relax settings" window if running on a Mac.
This is as in revision 12856:
http://svn.gna.org/viewcvs/relax?rev=12856&view=rev),
but for the button "Settings" / "Global relax settings".
This change creates a bug, as the opened window upon clicking this button,
when closed, will have relax gui crash (with no button responding). This
needs to be fixed...
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r12900 | bugman | 2011-06-08 20:44:28 +0200 (Wed, 08 Jun 2011) | 10 lines
Implemented the delay time TextCtrl and added the number of cycles column to the Rx peak list grid.
This implements what was discussed in https://mail.gna.org/public/relax-devel/2011-06/msg00036.html
(Message-id: <BANLkTi=8v-S=rO4NBcFVrxHorWaq34J5Jw@...>).
This is a big change. The changing of the number of cycles values or the delay time automatically
updates the relaxation times. These times are now read only cells. And the +, +VD, and +VC buttons
are gone as they are no longer needed.
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r12901 | bugman | 2011-06-08 20:55:02 +0200 (Wed, 08 Jun 2011) | 3 lines
Better spacing of the Rx tab elements.
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r12902 | bugman | 2011-06-09 08:43:04 +0200 (Thu, 09 Jun 2011) | 5 lines
Fixed the behaviour of the number of cycles column in the Rx tab grid.
Deleting or not entering a number was causing '1' to appear in the cell!
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r12903 | bugman | 2011-06-09 08:43:52 +0200 (Thu, 09 Jun 2011) | 3 lines
Fix for the Delay_num_cell_editor.Clone() method for cloning the grid editor class.
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r12904 | bugman | 2011-06-09 10:22:10 +0200 (Thu, 09 Jun 2011) | 3 lines
The delay time textctrl can now only have a single '.' char in the peak list grid.
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r12905 | bugman | 2011-06-09 10:28:03 +0200 (Thu, 09 Jun 2011) | 3 lines
Navigation keys are now allowed in the Rx tab delay time text field.
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r12906 | bugman | 2011-06-09 10:45:42 +0200 (Thu, 09 Jun 2011) | 5 lines
Better behaviour of the deletion of single cells in the Rx peak list grids.
The relaxation time is now cleared, rather than set to 0.0.
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r12907 | bugman | 2011-06-09 11:45:07 +0200 (Thu, 09 Jun 2011) | 6 lines
Normalisation of the text in the auto model-free analysis GUI tab.
The font sizes are now all the same, the text is not right aligned (not seen under Linux but very
ugly in Windows), and semicolon usage and capitalisation is normalised.
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r12908 | bugman | 2011-06-09 11:53:58 +0200 (Thu, 09 Jun 2011) | 5 lines
Shifted the model-free tab font formatting to be interface wide in self.gui.
This will help regularise the font throughout the GUI.
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r12909 | bugman | 2011-06-09 12:16:38 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularisation of the font formatting in the steady-state NOE GUI tab.
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r12910 | bugman | 2011-06-09 12:29:21 +0200 (Thu, 09 Jun 2011) | 5 lines
Shifted the title and subtitle creation for the NOE frame into a base class for all frames to use.
The formatting has also been regularised to improve the look of the GUI across operating systems.
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r12911 | bugman | 2011-06-09 12:29:52 +0200 (Thu, 09 Jun 2011) | 3 lines
Removal of empty lines.
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r12912 | bugman | 2011-06-09 12:32:27 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed some unused imports.
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r12913 | bugman | 2011-06-09 12:41:15 +0200 (Thu, 09 Jun 2011) | 3 lines
Spacing cleanup.
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r12914 | bugman | 2011-06-09 12:41:41 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularisation of the fonts, titles, and subtitles in the Rx auto-analysis frames.
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r12915 | bugman | 2011-06-09 12:52:56 +0200 (Thu, 09 Jun 2011) | 3 lines
The auto model-free frame is now using the add_title() base class method.
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r12916 | bugman | 2011-06-09 12:54:05 +0200 (Thu, 09 Jun 2011) | 3 lines
Rearrangement of the import statements.
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r12917 | bugman | 2011-06-09 13:05:45 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_subsubtitle() base class method for creating a sub-sub-title.
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r12918 | bugman | 2011-06-09 13:06:06 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised the text in the results tab.
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r12919 | bugman | 2011-06-09 13:08:58 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised the "Single delay cycle time [s]" text in the model-free frame.
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r12920 | bugman | 2011-06-09 13:10:19 +0200 (Thu, 09 Jun 2011) | 3 lines
Attempt to regularise the text in the text controls.
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r12921 | bugman | 2011-06-09 13:32:22 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_text_control() base class method for standardising the text controls.
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r12922 | bugman | 2011-06-09 13:33:48 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised all the stead-state NOE frame text controls.
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r12923 | bugman | 2011-06-09 13:57:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Fix for the base class add_text_control() method, the parent object is passed into the method!
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r12924 | bugman | 2011-06-09 13:58:24 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_static_text() base class method for all the GUI frames to use.
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r12925 | bugman | 2011-06-09 13:58:47 +0200 (Thu, 09 Jun 2011) | 3 lines
The NOE auto-analysis now uses the add_static_text() base class method for text.
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r12926 | bugman | 2011-06-09 14:35:27 +0200 (Thu, 09 Jun 2011) | 3 lines
Added the add_button_open() base class method for regularising the buttons across frames.
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r12927 | bugman | 2011-06-09 14:39:25 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised all of the auto NOE analysis frame buttons.
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r12928 | bugman | 2011-06-09 15:28:44 +0200 (Thu, 09 Jun 2011) | 5 lines
Added the add_text_sel_element() base class method for creating one of the basic frame elements.
This element consists of text, a text control, and an optional button.
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r12929 | bugman | 2011-06-09 15:45:25 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the NOE frame code by the use of the add_text_sel_element() base method.
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r12930 | bugman | 2011-06-09 15:53:09 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the Rx frame code by the use of the add_text_sel_element() base method.
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r12931 | bugman | 2011-06-09 15:59:58 +0200 (Thu, 09 Jun 2011) | 3 lines
The Rx peak list grid GUI element now also uses the add_text_sel_element() base method.
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r12932 | bugman | 2011-06-09 16:13:13 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the model-free frame code by the use of the add_text_sel_element() base method.
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r12933 | bugman | 2011-06-09 16:32:40 +0200 (Thu, 09 Jun 2011) | 3 lines
With debugging turned on, the size of the GUI main frame can be changed.
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r12934 | bugman | 2011-06-09 17:15:10 +0200 (Thu, 09 Jun 2011) | 6 lines
Added a simple XYZ structure file for the test suite.
This was attached to task #7404 (https://gna.org/task/?7404) by Han. The directory for the file was
given at https://mail.gna.org/public/relax-devel/2011-06/msg00083.html.
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r12935 | bugman | 2011-06-09 17:18:10 +0200 (Thu, 09 Jun 2011) | 5 lines
Eliminated the __set_properties() and __do_layout() methods.
The code has been shifted into __init__() and some variables shifted to hardcoded class variables.
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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.
The flag was previously not sent to the method so that the creation of a new data pipe always
resulted in a switch to that pipe. This bug is normally harmless.
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r13835 | bugman | 2011-07-22 16:30:29 +0200 (Fri, 22 Jul 2011) | 6 lines
Fix for the model-free _determine_model_type() method when the spin container has no 'local_tm'.
This code was failing in certain rare circumstances (when the setting up of the diffusion tensor was
forgotten).
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r13836 | bugman | 2011-07-22 16:57:05 +0200 (Fri, 22 Jul 2011) | 3 lines
Created a script for byte compiling the Python source files.
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r13845 | bugman | 2011-07-25 10:07:31 +0200 (Mon, 25 Jul 2011) | 5 lines
Added some old 2004 scripts for creating a uniform vector distribution and calculating relaxation data.
This will be used in the end to build a quick test for the dauvergne_protocol auto-analysis.
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r13846 | bugman | 2011-07-25 10:13:27 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the spherical vector distribution script in preparation for Python 3.
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r13847 | bugman | 2011-07-25 10:15:19 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the script to only have 3 incs.
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r13848 | bugman | 2011-07-25 10:15:51 +0200 (Mon, 25 Jul 2011) | 3 lines
Created the PDB representation of the spherical vector distribution for 9 vectors.
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r13849 | bugman | 2011-07-25 10:37:49 +0200 (Mon, 25 Jul 2011) | 3 lines
Converted the relaxation data generation script from relax 1.0 format to relax 1.3.
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r13850 | bugman | 2011-07-25 12:02:17 +0200 (Mon, 25 Jul 2011) | 9 lines
Added initial support for determining protein connectivities in the internal structural reader.
This is currently only for intra-residue connectivities in the protein backbone. A number of new
methods have been added:
_mol_type()
_protein_connect()
_protein_intra_connect()
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r13851 | bugman | 2011-07-25 12:20:43 +0200 (Mon, 25 Jul 2011) | 5 lines
Fixes for the test suite relaxation data creation script.
The code was not fully compatible with the relax 1.3 design.
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r13852 | bugman | 2011-07-25 12:21:13 +0200 (Mon, 25 Jul 2011) | 3 lines
Fixes to the relaxation data generation sample script based on the changes of r13851.
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r13853 | bugman | 2011-07-25 12:22:22 +0200 (Mon, 25 Jul 2011) | 5 lines
The relaxation data is now for 500 and 900 MHz.
This larger difference should hopefully speed up optimisation in the test suite.
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r13854 | bugman | 2011-07-25 12:23:36 +0200 (Mon, 25 Jul 2011) | 3 lines
Added the relaxation data.
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r13855 | bugman | 2011-07-25 13:45:04 +0200 (Mon, 25 Jul 2011) | 5 lines
Added the argument 'bc' to the relax_data.write() user function front end.
This currently doesn't do anything.
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r13856 | bugman | 2011-07-25 14:33:28 +0200 (Mon, 25 Jul 2011) | 5 lines
The 'bc' arg is now part of the value.write() user function, and all of the return_value functions.
The arg is also propagated to the back-end of the relax_data.write() user function.
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r13857 | bugman | 2011-07-25 14:34:12 +0200 (Mon, 25 Jul 2011) | 3 lines
The back calculated data is now written out to file in the synthetic relaxation data script.
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r13904 | bugman | 2011-07-26 21:40:15 +0200 (Tue, 26 Jul 2011) | 5 lines
Added the data_type() method to the specific functions API.
This will be used to determine the type that a given parameter from data_names() should be.
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r13905 | bugman | 2011-07-26 21:52:58 +0200 (Tue, 26 Jul 2011) | 3 lines
Modified the specific functions API method data_type() so that Python type objects should be returned.
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r13906 | bugman | 2011-07-26 21:55:53 +0200 (Tue, 26 Jul 2011) | 3 lines
Implemented the model-free version of the data_type() API method.
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r13909 | bugman | 2011-07-26 22:18:51 +0200 (Tue, 26 Jul 2011) | 3 lines
The data_type() API method is now exposed.
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r13919 | bugman | 2011-07-27 09:37:48 +0200 (Wed, 27 Jul 2011) | 3 lines
The heteronucleus and proton type parameters can now be specified by their parameter names aas well.
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r13926 | bugman | 2011-07-27 16:01:22 +0200 (Wed, 27 Jul 2011) | 5 lines
The create_molecule, create_residue, and create_spin functions now returned the created container.
This should not affect any of the current code using these, as normally None would be returned.
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r13927 | bugman | 2011-07-27 16:05:49 +0200 (Wed, 27 Jul 2011) | 6 lines
Invisible fix for the test_opendx_theta_phi_da() system test.
The spins are extracted from the structure, so they don't need to be read from the relaxation data
file as well. This is causing problems in the xyz branch, but is not an issue in the main line.
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r13929 | bugman | 2011-07-27 16:15:41 +0200 (Wed, 27 Jul 2011) | 3 lines
Modified the create_spin() function to overwrite the first spin if empty.
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r13932 | bugman | 2011-07-27 17:54:24 +0200 (Wed, 27 Jul 2011) | 13 lines
Redesign of the structure.load_spins user function back end.
This redesign is required due to problems encountered by Han in the xyz branch. See the thread
starting at https://mail.gna.org/public/relax-devel/2011-07/msg00021.html.
This commit consists of a number of changes:
- The combine_models argument has been removed as it is a relic, and isn't used at all.
- The spins are now created in the standard way via the generic_fns.mol_res_spin.create_spin()
function, eliminating all of the issues and complications of the old code.
- The atomic positions are now converted to numpy arrays.
- Only the created spins are included in the print out, and not replicated for each model.
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r13951 | bugman | 2011-07-28 15:14:55 +0200 (Thu, 28 Jul 2011) | 7 lines
Redesign of the main relax module.
The module has been renamed to 'relax.py', and the original file 'relax' is now a very basic python
script which simply loads the module and runs the new start() function for launching relax. The MS
Windows BAT file has also been updated to feed the module into python.
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r13956 | bugman | 2011-07-28 16:26:16 +0200 (Thu, 28 Jul 2011) | 3 lines
The relax mode normally specified by the command line can now be overridden.
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r13958 | bugman | 2011-07-28 16:35:58 +0200 (Thu, 28 Jul 2011) | 3 lines
Removed the executable svn property on the info module.
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