bugrelax - Bugs: bug #19887, Execution of relax_fit.py and the...

 
 
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bug #19887: Execution of relax_fit.py and the relaxation curve fitting failed

Submitted by:  None
Submitted on:  Mon 02 Jul 2012 08:27:01 AM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: RomelOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 2.0.0
Operating System: All systems

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Mon 02 Jul 2012 10:30:01 AM UTC, comment #11:

The problem was that relax was no longer catching the situation where the number of peak intensities for each spin is different (caused inconsistencies in the peaks between different peak lists). This was causing the setup of the C modules to fail. Now this is checked during the optimisation over-fitting checks prior to the execution of a grid search or minimisation, and if the number of peak intensities for a spin does not match the total number of peak lists loaded into relax, a RelaxError will be raised pointing to the offending spin.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:25:39 AM UTC, SVN revision 17122:

Merged revisions 16833-16839,16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r16833 | bugman | 2012-06-11 09:27:38 +0200 (Mon, 11 Jun 2012) | 5 lines

The Missing_data dialog can now have the parent wx element specified.

This is needed when launched from a child window such as the BMRB export window.
........
r16834 | bugman | 2012-06-11 09:30:51 +0200 (Mon, 11 Jun 2012) | 3 lines

Removed the word 'used' from the software and scripts GUI list element titles.
........
r16835 | bugman | 2012-06-11 09:31:41 +0200 (Mon, 11 Jun 2012) | 5 lines

Added checks to the BMRB export to make sure all necessary data has been input.

If not, then the Missing_data dialog will be presented to the user to explain what is required.
........
r16836 | bugman | 2012-06-11 10:05:58 +0200 (Mon, 11 Jun 2012) | 3 lines

The completion of the test suite in the GUI mode now sets the controller main gauge to 100%.
........
r16837 | bugman | 2012-06-11 10:15:21 +0200 (Mon, 11 Jun 2012) | 17 lines

Python 3 updates for the entire relax code base.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
........
r16838 | bugman | 2012-06-11 10:19:08 +0200 (Mon, 11 Jun 2012) | 3 lines

Used some colour for the relax GUI terminating print out asking for citations.
........
r16839 | bugman | 2012-06-11 11:48:27 +0200 (Mon, 11 Jun 2012) | 3 lines

Updated the release checklist document for the relax 2.0 development series.
........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Spun out the automatic column width formatting code from relax_io.write_spin_data() to write_data().

[...]

[...] The write_data() will be useful for many other columnar data printouts, and will write out to any

[...] file handles given to it.

[...]........

[...] r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Bug fix for a segmentation fault occurring during the model-free GUI test.

[...]

[...] Flushing of the interpreter queue object is needed as some parts of the interface use asynchronous

[...] user function calls.

[...]........

[...] r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!

[...]

[...] The command used was:

[...] svn merge -r16837:16836 .

[...]........

[...] r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class was in the wrong module!

[...]........

[...] r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Created a script for converting svn logs into the format for release messages.

[...]........

[...] r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

[...]

[...] The command used was:

[...] svn merge -r16887:r16888 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

[...]

[...] The command used was:

[...] svn merge -r16889:r16890 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.

[...]........

[...] r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Improved the debugging drawing for the about GUI elements.

[...]........

[...] r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

[...]

[...] Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

[...]

[...] To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window

[...] size exactly calculated in the first pass, and then used to set up the device context in the second.

[...] A space is also now added to the end to ensure the border is there.

[...]........

[...] r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

[...]

[...] This is a problem in at least GTK+ as scrolling is in increments of 20!

[...]........

[...] r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the grey about windows on MS Windows!

[...]

[...] All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!

[...]........

[...] r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

[...]

[...] The about model-free dialog no longer has grey at the bottom in MS Windows.

[...]

[...] The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the

[...] y scrolling is, and rounds up the virtual size based on that.

[...]........

[...] r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.

[...]........

[...] r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

[...]

[...] Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

[...]

[...] This function is required to handle alpha in bitmap on MS Windows so that regions with partial

[...] transparency are not blended into the default dark grey colour of Windows' windows.

[...]........

[...] r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Initialised a look up table in the cdp.mol structure for faster spin access.

[...]

[...] This look up table will be slowly transitioned to, and should significantly speed up certain

[...] operations.

[...]........

[...] r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

[...]

[...] Started to fill up the spin ID look up table.

[...]

[...] The index_molecule() and index_residue() functions have been added to determine the MoleculeList and

[...] ResidueList indices of given molecules and residues. These are used by the create_spin for

[...] efficiency and to allow the indices (together with the spin index and spin ID string) to be

[...] assembled into the look up table. This table is not used anywhere yet.

[...]........

[...] r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

[...]

[...] To support this, the return_residue() method now takes the 'indices' argument and returns the

[...] molecule and residue indices.

[...]........

[...] r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.

[...]........

[...] r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for return_residue() for a bug introduced at r16910.

[...]........

[...] r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!

[...]........

[...] r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

[...]

[...] This is to mimic the return_spin() function.

[...]........

[...] r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

[...]

[...] The slower return_spin() method will allow return_spin_from_id() to always be functional.

[...]........

[...] r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

[...]

[...] This shaves off a number of seconds from the system test - the look up table speed ups will come

[...] with support in the other mol_res_spin module functions.

[...]........

[...] r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines

[...]

[...] The generate_spin_id() function now choses to use the spin name instead of number by default.

[...]........

[...] r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines

[...]

[...] Created the generic_fns.mol_res_spin.return_spin_indices() function to return the index triplet.

[...]

[...] This allows a spin ID to be converted into the molecule, residue and spin indices.

[...]........

[...] r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Bug fix for the relax_data.copy user function - it can now handle spins without relaxation data.

[...]........

[...] r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Update and clean up of the model-free LaTeX table generation script.

[...]........

[...] r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.

[...]

[...] The selection object was using the wrong variable name, and the look up table fallback was always

[...] on!

[...]........

[...] r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

[...]

[...] The spin ID lookup table has been made private so that it is not included in the save files.

[...]........

[...] r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

[...]

[...] Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

[...]

[...] This is problematic only in certain edge cases, for example a multi-molecule entry.

[...]........

[...] r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

[...]

[...] This hack was for naming unnamed spins. But this is not needed as the

[...] generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.

[...]........

[...] r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

[...]

[...] This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the

[...] pack_data() function, this is a nasty hack which would have caused problems in the future.

[...]........

[...] r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

[...]

[...] Creation of a fast molecule, residue and spin data lookup framework using private metadata.

[...]

[...] This consists of two elements: The already existing private lookup table now at

[...] cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue

[...] and spin indices as values; and a set of private variables within the molecule, residue and spin

[...] containers which identify the parent container names, numbers and indices. As all data is private,

[...] it will not be visible to the user or be saved in the XML results and save files and should be

[...] considered volatile.

[...]

[...] All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions

[...] metadata_prune() and metadata_update(). For fast operation, these methods can update specific

[...] container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which

[...] modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin

[...] functions and test suite) call these two functions as needed. Two auxiliary functions

[...] spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin

[...] ID strings for a given spin (the second created IDs strings which should no longer exist).

[...]

[...] The speed ups from this change are significant. On one system, the system and unit tests decrease

[...] from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

[...]

[...] In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions

[...] create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule

[...] name will now always be a string! Previously this was allowed to be an integer. This is needed for

[...] the private metadata functions to operate correctly. A number of unit tests have been updated for

[...] the changes.

[...]........

[...] r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

[...]

[...] This is for better user feedback.

[...]........

[...] r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines

[...]

[...] Fix for the sequence.read user function for a problem with r17028.

[...]

[...] The sequence.generate() function was not returning the correct result as it didn't take into account

[...] the renaming and renumbering of empty spin containers. Now sequence.read will always print out the

[...] generated sequence and not result in a RelaxError for most of the system tests.

[...]........

[...] r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] Converted the consistency testing documentation strings to the Uf_tables and Desc_container design.

[...]

[...] This is needed to use the consistency testing documentation within the user function help system.

[...]........

[...] r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines

[...]

[...] Added the consistency testing documentation to the grace.write and value.* user functions.

[...]........

[...] r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines

[...]

[...] Modified the working of the n_state_model.elim_no_prob backend.

[...]

[...] This user function is not functional anyway and is not tested by the relax test suite, but will

[...] remain as it might be useful in the future.

[...]........

[...] r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

[...]

[...] Created a system test to replicate Romel Bobby's bug #19887.

[...]

[...] This is the bug report at https://gna.org/bugs/?19887.

[...]........

[...] r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

[...]

[...] Partial fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] The problem is that the number of peak height values was not the same for all spins!

[...]

[...] The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in

[...] incorrect values, causing relax to fail directly after the setup() call in

[...] specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but

[...] in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather

[...] than 5. Now the correct number is sent into setup().

[...]........

[...] r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

[...]

[...] A final fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This

[...] occurs in the relaxation curve-fitting overfit_deselect() method.

[...]........

[...]

[...]

(Browse SVN revision 17122)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:24:27 AM UTC, SVN revision 17121:

Merged revisions 16833-16839,16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r16833 | bugman | 2012-06-11 09:27:38 +0200 (Mon, 11 Jun 2012) | 5 lines

The Missing_data dialog can now have the parent wx element specified.

This is needed when launched from a child window such as the BMRB export window.
........
r16834 | bugman | 2012-06-11 09:30:51 +0200 (Mon, 11 Jun 2012) | 3 lines

Removed the word 'used' from the software and scripts GUI list element titles.
........
r16835 | bugman | 2012-06-11 09:31:41 +0200 (Mon, 11 Jun 2012) | 5 lines

Added checks to the BMRB export to make sure all necessary data has been input.

If not, then the Missing_data dialog will be presented to the user to explain what is required.
........
r16836 | bugman | 2012-06-11 10:05:58 +0200 (Mon, 11 Jun 2012) | 3 lines

The completion of the test suite in the GUI mode now sets the controller main gauge to 100%.
........
r16837 | bugman | 2012-06-11 10:15:21 +0200 (Mon, 11 Jun 2012) | 17 lines

Python 3 updates for the entire relax code base.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
........
r16838 | bugman | 2012-06-11 10:19:08 +0200 (Mon, 11 Jun 2012) | 3 lines

Used some colour for the relax GUI terminating print out asking for citations.
........
r16839 | bugman | 2012-06-11 11:48:27 +0200 (Mon, 11 Jun 2012) | 3 lines

Updated the release checklist document for the relax 2.0 development series.
........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Spun out the automatic column width formatting code from relax_io.write_spin_data() to write_data().

[...]

[...] The write_data() will be useful for many other columnar data printouts, and will write out to any

[...] file handles given to it.

[...]........

[...] r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Bug fix for a segmentation fault occurring during the model-free GUI test.

[...]

[...] Flushing of the interpreter queue object is needed as some parts of the interface use asynchronous

[...] user function calls.

[...]........

[...] r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!

[...]

[...] The command used was:

[...] svn merge -r16837:16836 .

[...]........

[...] r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class was in the wrong module!

[...]........

[...] r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Created a script for converting svn logs into the format for release messages.

[...]........

[...] r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

[...]

[...] The command used was:

[...] svn merge -r16887:r16888 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

[...]

[...] The command used was:

[...] svn merge -r16889:r16890 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.

[...]........

[...] r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Improved the debugging drawing for the about GUI elements.

[...]........

[...] r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

[...]

[...] Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

[...]

[...] To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window

[...] size exactly calculated in the first pass, and then used to set up the device context in the second.

[...] A space is also now added to the end to ensure the border is there.

[...]........

[...] r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

[...]

[...] This is a problem in at least GTK+ as scrolling is in increments of 20!

[...]........

[...] r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the grey about windows on MS Windows!

[...]

[...] All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!

[...]........

[...] r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

[...]

[...] The about model-free dialog no longer has grey at the bottom in MS Windows.

[...]

[...] The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the

[...] y scrolling is, and rounds up the virtual size based on that.

[...]........

[...] r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.

[...]........

[...] r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

[...]

[...] Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

[...]

[...] This function is required to handle alpha in bitmap on MS Windows so that regions with partial

[...] transparency are not blended into the default dark grey colour of Windows' windows.

[...]........

[...] r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Initialised a look up table in the cdp.mol structure for faster spin access.

[...]

[...] This look up table will be slowly transitioned to, and should significantly speed up certain

[...] operations.

[...]........

[...] r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

[...]

[...] Started to fill up the spin ID look up table.

[...]

[...] The index_molecule() and index_residue() functions have been added to determine the MoleculeList and

[...] ResidueList indices of given molecules and residues. These are used by the create_spin for

[...] efficiency and to allow the indices (together with the spin index and spin ID string) to be

[...] assembled into the look up table. This table is not used anywhere yet.

[...]........

[...] r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

[...]

[...] To support this, the return_residue() method now takes the 'indices' argument and returns the

[...] molecule and residue indices.

[...]........

[...] r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.

[...]........

[...] r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for return_residue() for a bug introduced at r16910.

[...]........

[...] r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!

[...]........

[...] r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

[...]

[...] This is to mimic the return_spin() function.

[...]........

[...] r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

[...]

[...] The slower return_spin() method will allow return_spin_from_id() to always be functional.

[...]........

[...] r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

[...]

[...] This shaves off a number of seconds from the system test - the look up table speed ups will come

[...] with support in the other mol_res_spin module functions.

[...]........

[...] r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines

[...]

[...] The generate_spin_id() function now choses to use the spin name instead of number by default.

[...]........

[...] r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines

[...]

[...] Created the generic_fns.mol_res_spin.return_spin_indices() function to return the index triplet.

[...]

[...] This allows a spin ID to be converted into the molecule, residue and spin indices.

[...]........

[...] r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Bug fix for the relax_data.copy user function - it can now handle spins without relaxation data.

[...]........

[...] r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Update and clean up of the model-free LaTeX table generation script.

[...]........

[...] r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.

[...]

[...] The selection object was using the wrong variable name, and the look up table fallback was always

[...] on!

[...]........

[...] r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

[...]

[...] The spin ID lookup table has been made private so that it is not included in the save files.

[...]........

[...] r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

[...]

[...] Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

[...]

[...] This is problematic only in certain edge cases, for example a multi-molecule entry.

[...]........

[...] r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

[...]

[...] This hack was for naming unnamed spins. But this is not needed as the

[...] generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.

[...]........

[...] r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

[...]

[...] This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the

[...] pack_data() function, this is a nasty hack which would have caused problems in the future.

[...]........

[...] r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

[...]

[...] Creation of a fast molecule, residue and spin data lookup framework using private metadata.

[...]

[...] This consists of two elements: The already existing private lookup table now at

[...] cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue

[...] and spin indices as values; and a set of private variables within the molecule, residue and spin

[...] containers which identify the parent container names, numbers and indices. As all data is private,

[...] it will not be visible to the user or be saved in the XML results and save files and should be

[...] considered volatile.

[...]

[...] All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions

[...] metadata_prune() and metadata_update(). For fast operation, these methods can update specific

[...] container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which

[...] modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin

[...] functions and test suite) call these two functions as needed. Two auxiliary functions

[...] spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin

[...] ID strings for a given spin (the second created IDs strings which should no longer exist).

[...]

[...] The speed ups from this change are significant. On one system, the system and unit tests decrease

[...] from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

[...]

[...] In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions

[...] create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule

[...] name will now always be a string! Previously this was allowed to be an integer. This is needed for

[...] the private metadata functions to operate correctly. A number of unit tests have been updated for

[...] the changes.

[...]........

[...] r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

[...]

[...] This is for better user feedback.

[...]........

[...] r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines

[...]

[...] Fix for the sequence.read user function for a problem with r17028.

[...]

[...] The sequence.generate() function was not returning the correct result as it didn't take into account

[...] the renaming and renumbering of empty spin containers. Now sequence.read will always print out the

[...] generated sequence and not result in a RelaxError for most of the system tests.

[...]........

[...] r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] Converted the consistency testing documentation strings to the Uf_tables and Desc_container design.

[...]

[...] This is needed to use the consistency testing documentation within the user function help system.

[...]........

[...] r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines

[...]

[...] Added the consistency testing documentation to the grace.write and value.* user functions.

[...]........

[...] r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines

[...]

[...] Modified the working of the n_state_model.elim_no_prob backend.

[...]

[...] This user function is not functional anyway and is not tested by the relax test suite, but will

[...] remain as it might be useful in the future.

[...]........

[...] r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

[...]

[...] Created a system test to replicate Romel Bobby's bug #19887.

[...]

[...] This is the bug report at https://gna.org/bugs/?19887.

[...]........

[...] r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

[...]

[...] Partial fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] The problem is that the number of peak height values was not the same for all spins!

[...]

[...] The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in

[...] incorrect values, causing relax to fail directly after the setup() call in

[...] specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but

[...] in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather

[...] than 5. Now the correct number is sent into setup().

[...]........

[...] r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

[...]

[...] A final fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This

[...] occurs in the relaxation curve-fitting overfit_deselect() method.

[...]........

[...]

[...]

(Browse SVN revision 17121)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:21:45 AM UTC, SVN revision 17120:

Merged revisions 16833-16839,16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r16833 | bugman | 2012-06-11 09:27:38 +0200 (Mon, 11 Jun 2012) | 5 lines

The Missing_data dialog can now have the parent wx element specified.

This is needed when launched from a child window such as the BMRB export window.
........
r16834 | bugman | 2012-06-11 09:30:51 +0200 (Mon, 11 Jun 2012) | 3 lines

Removed the word 'used' from the software and scripts GUI list element titles.
........
r16835 | bugman | 2012-06-11 09:31:41 +0200 (Mon, 11 Jun 2012) | 5 lines

Added checks to the BMRB export to make sure all necessary data has been input.

If not, then the Missing_data dialog will be presented to the user to explain what is required.
........
r16836 | bugman | 2012-06-11 10:05:58 +0200 (Mon, 11 Jun 2012) | 3 lines

The completion of the test suite in the GUI mode now sets the controller main gauge to 100%.
........
r16837 | bugman | 2012-06-11 10:15:21 +0200 (Mon, 11 Jun 2012) | 17 lines

Python 3 updates for the entire relax code base.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
........
r16838 | bugman | 2012-06-11 10:19:08 +0200 (Mon, 11 Jun 2012) | 3 lines

Used some colour for the relax GUI terminating print out asking for citations.
........
r16839 | bugman | 2012-06-11 11:48:27 +0200 (Mon, 11 Jun 2012) | 3 lines

Updated the release checklist document for the relax 2.0 development series.
........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Spun out the automatic column width formatting code from relax_io.write_spin_data() to write_data().

[...]

[...] The write_data() will be useful for many other columnar data printouts, and will write out to any

[...] file handles given to it.

[...]........

[...] r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Bug fix for a segmentation fault occurring during the model-free GUI test.

[...]

[...] Flushing of the interpreter queue object is needed as some parts of the interface use asynchronous

[...] user function calls.

[...]........

[...] r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!

[...]

[...] The command used was:

[...] svn merge -r16837:16836 .

[...]........

[...] r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class was in the wrong module!

[...]........

[...] r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Created a script for converting svn logs into the format for release messages.

[...]........

[...] r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

[...]

[...] The command used was:

[...] svn merge -r16887:r16888 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

[...]

[...] The command used was:

[...] svn merge -r16889:r16890 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.

[...]........

[...] r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Improved the debugging drawing for the about GUI elements.

[...]........

[...] r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

[...]

[...] Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

[...]

[...] To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window

[...] size exactly calculated in the first pass, and then used to set up the device context in the second.

[...] A space is also now added to the end to ensure the border is there.

[...]........

[...] r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

[...]

[...] This is a problem in at least GTK+ as scrolling is in increments of 20!

[...]........

[...] r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the grey about windows on MS Windows!

[...]

[...] All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!

[...]........

[...] r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

[...]

[...] The about model-free dialog no longer has grey at the bottom in MS Windows.

[...]

[...] The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the

[...] y scrolling is, and rounds up the virtual size based on that.

[...]........

[...] r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.

[...]........

[...] r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

[...]

[...] Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

[...]

[...] This function is required to handle alpha in bitmap on MS Windows so that regions with partial

[...] transparency are not blended into the default dark grey colour of Windows' windows.

[...]........

[...] r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Initialised a look up table in the cdp.mol structure for faster spin access.

[...]

[...] This look up table will be slowly transitioned to, and should significantly speed up certain

[...] operations.

[...]........

[...] r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

[...]

[...] Started to fill up the spin ID look up table.

[...]

[...] The index_molecule() and index_residue() functions have been added to determine the MoleculeList and

[...] ResidueList indices of given molecules and residues. These are used by the create_spin for

[...] efficiency and to allow the indices (together with the spin index and spin ID string) to be

[...] assembled into the look up table. This table is not used anywhere yet.

[...]........

[...] r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

[...]

[...] To support this, the return_residue() method now takes the 'indices' argument and returns the

[...] molecule and residue indices.

[...]........

[...] r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.

[...]........

[...] r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for return_residue() for a bug introduced at r16910.

[...]........

[...] r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!

[...]........

[...] r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

[...]

[...] This is to mimic the return_spin() function.

[...]........

[...] r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

[...]

[...] The slower return_spin() method will allow return_spin_from_id() to always be functional.

[...]........

[...] r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

[...]

[...] This shaves off a number of seconds from the system test - the look up table speed ups will come

[...] with support in the other mol_res_spin module functions.

[...]........

[...] r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines

[...]

[...] The generate_spin_id() function now choses to use the spin name instead of number by default.

[...]........

[...] r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines

[...]

[...] Created the generic_fns.mol_res_spin.return_spin_indices() function to return the index triplet.

[...]

[...] This allows a spin ID to be converted into the molecule, residue and spin indices.

[...]........

[...] r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Bug fix for the relax_data.copy user function - it can now handle spins without relaxation data.

[...]........

[...] r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Update and clean up of the model-free LaTeX table generation script.

[...]........

[...] r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.

[...]

[...] The selection object was using the wrong variable name, and the look up table fallback was always

[...] on!

[...]........

[...] r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

[...]

[...] The spin ID lookup table has been made private so that it is not included in the save files.

[...]........

[...] r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

[...]

[...] Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

[...]

[...] This is problematic only in certain edge cases, for example a multi-molecule entry.

[...]........

[...] r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

[...]

[...] This hack was for naming unnamed spins. But this is not needed as the

[...] generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.

[...]........

[...] r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

[...]

[...] This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the

[...] pack_data() function, this is a nasty hack which would have caused problems in the future.

[...]........

[...] r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

[...]

[...] Creation of a fast molecule, residue and spin data lookup framework using private metadata.

[...]

[...] This consists of two elements: The already existing private lookup table now at

[...] cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue

[...] and spin indices as values; and a set of private variables within the molecule, residue and spin

[...] containers which identify the parent container names, numbers and indices. As all data is private,

[...] it will not be visible to the user or be saved in the XML results and save files and should be

[...] considered volatile.

[...]

[...] All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions

[...] metadata_prune() and metadata_update(). For fast operation, these methods can update specific

[...] container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which

[...] modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin

[...] functions and test suite) call these two functions as needed. Two auxiliary functions

[...] spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin

[...] ID strings for a given spin (the second created IDs strings which should no longer exist).

[...]

[...] The speed ups from this change are significant. On one system, the system and unit tests decrease

[...] from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

[...]

[...] In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions

[...] create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule

[...] name will now always be a string! Previously this was allowed to be an integer. This is needed for

[...] the private metadata functions to operate correctly. A number of unit tests have been updated for

[...] the changes.

[...]........

[...] r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

[...]

[...] This is for better user feedback.

[...]........

[...] r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines

[...]

[...] Fix for the sequence.read user function for a problem with r17028.

[...]

[...] The sequence.generate() function was not returning the correct result as it didn't take into account

[...] the renaming and renumbering of empty spin containers. Now sequence.read will always print out the

[...] generated sequence and not result in a RelaxError for most of the system tests.

[...]........

[...] r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] Converted the consistency testing documentation strings to the Uf_tables and Desc_container design.

[...]

[...] This is needed to use the consistency testing documentation within the user function help system.

[...]........

[...] r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines

[...]

[...] Added the consistency testing documentation to the grace.write and value.* user functions.

[...]........

[...] r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines

[...]

[...] Modified the working of the n_state_model.elim_no_prob backend.

[...]

[...] This user function is not functional anyway and is not tested by the relax test suite, but will

[...] remain as it might be useful in the future.

[...]........

[...] r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

[...]

[...] Created a system test to replicate Romel Bobby's bug #19887.

[...]

[...] This is the bug report at https://gna.org/bugs/?19887.

[...]........

[...] r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

[...]

[...] Partial fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] The problem is that the number of peak height values was not the same for all spins!

[...]

[...] The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in

[...] incorrect values, causing relax to fail directly after the setup() call in

[...] specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but

[...] in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather

[...] than 5. Now the correct number is sent into setup().

[...]........

[...] r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

[...]

[...] A final fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This

[...] occurs in the relaxation curve-fitting overfit_deselect() method.

[...]........

[...]

[...]

(Browse SVN revision 17120)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:21:40 AM UTC, SVN revision 17119:

Merged revisions 16833-16839,16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r16833 | bugman | 2012-06-11 09:27:38 +0200 (Mon, 11 Jun 2012) | 5 lines

The Missing_data dialog can now have the parent wx element specified.

This is needed when launched from a child window such as the BMRB export window.
........
r16834 | bugman | 2012-06-11 09:30:51 +0200 (Mon, 11 Jun 2012) | 3 lines

Removed the word 'used' from the software and scripts GUI list element titles.
........
r16835 | bugman | 2012-06-11 09:31:41 +0200 (Mon, 11 Jun 2012) | 5 lines

Added checks to the BMRB export to make sure all necessary data has been input.

If not, then the Missing_data dialog will be presented to the user to explain what is required.
........
r16836 | bugman | 2012-06-11 10:05:58 +0200 (Mon, 11 Jun 2012) | 3 lines

The completion of the test suite in the GUI mode now sets the controller main gauge to 100%.
........
r16837 | bugman | 2012-06-11 10:15:21 +0200 (Mon, 11 Jun 2012) | 17 lines

Python 3 updates for the entire relax code base.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
........
r16838 | bugman | 2012-06-11 10:19:08 +0200 (Mon, 11 Jun 2012) | 3 lines

Used some colour for the relax GUI terminating print out asking for citations.
........
r16839 | bugman | 2012-06-11 11:48:27 +0200 (Mon, 11 Jun 2012) | 3 lines

Updated the release checklist document for the relax 2.0 development series.
........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Spun out the automatic column width formatting code from relax_io.write_spin_data() to write_data().

[...]

[...] The write_data() will be useful for many other columnar data printouts, and will write out to any

[...] file handles given to it.

[...]........

[...] r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines

[...]

[...] Bug fix for a segmentation fault occurring during the model-free GUI test.

[...]

[...] Flushing of the interpreter queue object is needed as some parts of the interface use asynchronous

[...] user function calls.

[...]........

[...] r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!

[...]

[...] The command used was:

[...] svn merge -r16837:16836 .

[...]........

[...] r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class was in the wrong module!

[...]........

[...] r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

[...]

[...] Created a script for converting svn logs into the format for release messages.

[...]........

[...] r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

[...]

[...] The command used was:

[...] svn merge -r16887:r16888 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

[...]

[...] Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

[...]

[...] The command used was:

[...] svn merge -r16889:r16890 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0

[...]........

[...] r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.

[...]........

[...] r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Improved the debugging drawing for the about GUI elements.

[...]........

[...] r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

[...]

[...] Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

[...]

[...] To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window

[...] size exactly calculated in the first pass, and then used to set up the device context in the second.

[...] A space is also now added to the end to ensure the border is there.

[...]........

[...] r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

[...]

[...] This is a problem in at least GTK+ as scrolling is in increments of 20!

[...]........

[...] r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the grey about windows on MS Windows!

[...]

[...] All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!

[...]........

[...] r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

[...]

[...] The about model-free dialog no longer has grey at the bottom in MS Windows.

[...]

[...] The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the

[...] y scrolling is, and rounds up the virtual size based on that.

[...]........

[...] r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.

[...]........

[...] r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

[...]

[...] Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

[...]

[...] This function is required to handle alpha in bitmap on MS Windows so that regions with partial

[...] transparency are not blended into the default dark grey colour of Windows' windows.

[...]........

[...] r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Initialised a look up table in the cdp.mol structure for faster spin access.

[...]

[...] This look up table will be slowly transitioned to, and should significantly speed up certain

[...] operations.

[...]........

[...] r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

[...]

[...] Started to fill up the spin ID look up table.

[...]

[...] The index_molecule() and index_residue() functions have been added to determine the MoleculeList and

[...] ResidueList indices of given molecules and residues. These are used by the create_spin for

[...] efficiency and to allow the indices (together with the spin index and spin ID string) to be

[...] assembled into the look up table. This table is not used anywhere yet.

[...]........

[...] r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

[...]

[...] To support this, the return_residue() method now takes the 'indices' argument and returns the

[...] molecule and residue indices.

[...]........

[...] r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.

[...]........

[...] r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for return_residue() for a bug introduced at r16910.

[...]........

[...] r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!

[...]........

[...] r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

[...]

[...] This is to mimic the return_spin() function.

[...]........

[...] r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

[...]

[...] The slower return_spin() method will allow return_spin_from_id() to always be functional.

[...]........

[...] r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

[...]

[...] This shaves off a number of seconds from the system test - the look up table speed ups will come

[...] with support in the other mol_res_spin module functions.

[...]........

[...] r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines

[...]

[...] The generate_spin_id() function now choses to use the spin name instead of number by default.

[...]........

[...] r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines

[...]

[...] Created the generic_fns.mol_res_spin.return_spin_indices() function to return the index triplet.

[...]

[...] This allows a spin ID to be converted into the molecule, residue and spin indices.

[...]........

[...] r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Bug fix for the relax_data.copy user function - it can now handle spins without relaxation data.

[...]........

[...] r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Update and clean up of the model-free LaTeX table generation script.

[...]........

[...] r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.

[...]

[...] The selection object was using the wrong variable name, and the look up table fallback was always

[...] on!

[...]........

[...] r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

[...]

[...] The spin ID lookup table has been made private so that it is not included in the save files.

[...]........

[...] r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

[...]

[...] Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

[...]

[...] This is problematic only in certain edge cases, for example a multi-molecule entry.

[...]........

[...] r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

[...]

[...] This hack was for naming unnamed spins. But this is not needed as the

[...] generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.

[...]........

[...] r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

[...]

[...] This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the

[...] pack_data() function, this is a nasty hack which would have caused problems in the future.

[...]........

[...] r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

[...]

[...] Creation of a fast molecule, residue and spin data lookup framework using private metadata.

[...]

[...] This consists of two elements: The already existing private lookup table now at

[...] cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue

[...] and spin indices as values; and a set of private variables within the molecule, residue and spin

[...] containers which identify the parent container names, numbers and indices. As all data is private,

[...] it will not be visible to the user or be saved in the XML results and save files and should be

[...] considered volatile.

[...]

[...] All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions

[...] metadata_prune() and metadata_update(). For fast operation, these methods can update specific

[...] container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which

[...] modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin

[...] functions and test suite) call these two functions as needed. Two auxiliary functions

[...] spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin

[...] ID strings for a given spin (the second created IDs strings which should no longer exist).

[...]

[...] The speed ups from this change are significant. On one system, the system and unit tests decrease

[...] from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

[...]

[...] In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions

[...] create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule

[...] name will now always be a string! Previously this was allowed to be an integer. This is needed for

[...] the private metadata functions to operate correctly. A number of unit tests have been updated for

[...] the changes.

[...]........

[...] r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

[...]

[...] This is for better user feedback.

[...]........

[...] r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines

[...]

[...] Fix for the sequence.read user function for a problem with r17028.

[...]

[...] The sequence.generate() function was not returning the correct result as it didn't take into account

[...] the renaming and renumbering of empty spin containers. Now sequence.read will always print out the

[...] generated sequence and not result in a RelaxError for most of the system tests.

[...]........

[...] r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] Converted the consistency testing documentation strings to the Uf_tables and Desc_container design.

[...]

[...] This is needed to use the consistency testing documentation within the user function help system.

[...]........

[...] r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines

[...]

[...] Added the consistency testing documentation to the grace.write and value.* user functions.

[...]........

[...] r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines

[...]

[...] Modified the working of the n_state_model.elim_no_prob backend.

[...]

[...] This user function is not functional anyway and is not tested by the relax test suite, but will

[...] remain as it might be useful in the future.

[...]........

[...] r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

[...]

[...] Created a system test to replicate Romel Bobby's bug #19887.

[...]

[...] This is the bug report at https://gna.org/bugs/?19887.

[...]........

[...] r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

[...]

[...] Partial fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] The problem is that the number of peak height values was not the same for all spins!

[...]

[...] The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in

[...] incorrect values, causing relax to fail directly after the setup() call in

[...] specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but

[...] in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather

[...] than 5. Now the correct number is sent into setup().

[...]........

[...] r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

[...]

[...] A final fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This

[...] occurs in the relaxation curve-fitting overfit_deselect() method.

[...]........

[...]

[...]

(Browse SVN revision 17119)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:21:06 AM UTC, SVN revision 17118:

Merged revisions 17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

Created a system test to replicate Romel Bobby's bug #19887.

This is the bug report at https://gna.org/bugs/?19887.
........
r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

Partial fix for bug #19887 (https://gna.org/bugs/?19887).

The problem is that the number of peak height values was not the same for all spins!

The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in
incorrect values, causing relax to fail directly after the setup() call in
specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but
in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather
than 5. Now the correct number is sent into setup().
........
r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

A final fix for bug #19887 (https://gna.org/bugs/?19887).

Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This
occurs in the relaxation curve-fitting overfit_deselect() method.
........

(Browse SVN revision 17118)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:19:52 AM UTC, SVN revision 17117:

Merged revisions 16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines

Spun out the automatic column width formatting code from relax_io.write_spin_data() to write_data().

The write_data() will be useful for many other columnar data printouts, and will write out to any
file handles given to it.
........
r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines

Bug fix for a segmentation fault occurring during the model-free GUI test.

Flushing of the interpreter queue object is needed as some parts of the interface use asynchronous
user function calls.
........
r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines

Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!

The command used was:
svn merge -r16837:16836 .
........
r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines

Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class was in the wrong module!
........
r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

Created a script for converting svn logs into the format for release messages.
........
r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

The command used was:
svn merge -r16887:r16888 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0
........
r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

The command used was:
svn merge -r16889:r16890 svn+ssh://bugman@svn.gna.org/svn/relax/tags/2.0.0
........
r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.
........

[...] r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Improved the debugging drawing for the about GUI elements.

[...]........

[...] r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

[...]

[...] Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

[...]

[...] To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window

[...] size exactly calculated in the first pass, and then used to set up the device context in the second.

[...] A space is also now added to the end to ensure the border is there.

[...]........

[...] r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

[...]

[...] This is a problem in at least GTK+ as scrolling is in increments of 20!

[...]........

[...] r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

[...]

[...] Bug fix for the grey about windows on MS Windows!

[...]

[...] All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!

[...]........

[...] r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

[...]

[...] The about model-free dialog no longer has grey at the bottom in MS Windows.

[...]

[...] The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the

[...] y scrolling is, and rounds up the virtual size based on that.

[...]........

[...] r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

[...]

[...] Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.

[...]........

[...] r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

[...]

[...] Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

[...]

[...] This function is required to handle alpha in bitmap on MS Windows so that regions with partial

[...] transparency are not blended into the default dark grey colour of Windows' windows.

[...]........

[...] r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Initialised a look up table in the cdp.mol structure for faster spin access.

[...]

[...] This look up table will be slowly transitioned to, and should significantly speed up certain

[...] operations.

[...]........

[...] r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

[...]

[...] Started to fill up the spin ID look up table.

[...]

[...] The index_molecule() and index_residue() functions have been added to determine the MoleculeList and

[...] ResidueList indices of given molecules and residues. These are used by the create_spin for

[...] efficiency and to allow the indices (together with the spin index and spin ID string) to be

[...] assembled into the look up table. This table is not used anywhere yet.

[...]........

[...] r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

[...]

[...] To support this, the return_residue() method now takes the 'indices' argument and returns the

[...] molecule and residue indices.

[...]........

[...] r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.

[...]........

[...] r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for return_residue() for a bug introduced at r16910.

[...]........

[...] r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

[...]

[...] Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!

[...]........

[...] r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

[...]

[...] This is to mimic the return_spin() function.

[...]........

[...] r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

[...]

[...] return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

[...]

[...] The slower return_spin() method will allow return_spin_from_id() to always be functional.

[...]........

[...] r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

[...]

[...] Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

[...]

[...] This shaves off a number of seconds from the system test - the look up table speed ups will come

[...] with support in the other mol_res_spin module functions.

[...]........

[...] r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines

[...]

[...] The generate_spin_id() function now choses to use the spin name instead of number by default.

[...]........

[...] r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines

[...]

[...] Created the generic_fns.mol_res_spin.return_spin_indices() function to return the index triplet.

[...]

[...] This allows a spin ID to be converted into the molecule, residue and spin indices.

[...]........

[...] r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Bug fix for the relax_data.copy user function - it can now handle spins without relaxation data.

[...]........

[...] r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines

[...]

[...] Update and clean up of the model-free LaTeX table generation script.

[...]........

[...] r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.

[...]

[...] The selection object was using the wrong variable name, and the look up table fallback was always

[...] on!

[...]........

[...] r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

[...]

[...] The spin ID lookup table has been made private so that it is not included in the save files.

[...]........

[...] r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

[...]

[...] Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

[...]

[...] This is problematic only in certain edge cases, for example a multi-molecule entry.

[...]........

[...] r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

[...]

[...] This hack was for naming unnamed spins. But this is not needed as the

[...] generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.

[...]........

[...] r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

[...]

[...] Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

[...]

[...] This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the

[...] pack_data() function, this is a nasty hack which would have caused problems in the future.

[...]........

[...] r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

[...]

[...] Creation of a fast molecule, residue and spin data lookup framework using private metadata.

[...]

[...] This consists of two elements: The already existing private lookup table now at

[...] cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue

[...] and spin indices as values; and a set of private variables within the molecule, residue and spin

[...] containers which identify the parent container names, numbers and indices. As all data is private,

[...] it will not be visible to the user or be saved in the XML results and save files and should be

[...] considered volatile.

[...]

[...] All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions

[...] metadata_prune() and metadata_update(). For fast operation, these methods can update specific

[...] container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which

[...] modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin

[...] functions and test suite) call these two functions as needed. Two auxiliary functions

[...] spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin

[...] ID strings for a given spin (the second created IDs strings which should no longer exist).

[...]

[...] The speed ups from this change are significant. On one system, the system and unit tests decrease

[...] from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

[...]

[...] In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions

[...] create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule

[...] name will now always be a string! Previously this was allowed to be an integer. This is needed for

[...] the private metadata functions to operate correctly. A number of unit tests have been updated for

[...] the changes.

[...]........

[...] r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

[...]

[...] This is for better user feedback.

[...]........

[...] r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines

[...]

[...] Fix for the sequence.read user function for a problem with r17028.

[...]

[...] The sequence.generate() function was not returning the correct result as it didn't take into account

[...] the renaming and renumbering of empty spin containers. Now sequence.read will always print out the

[...] generated sequence and not result in a RelaxError for most of the system tests.

[...]........

[...] r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines

[...]

[...] Converted the consistency testing documentation strings to the Uf_tables and Desc_container design.

[...]

[...] This is needed to use the consistency testing documentation within the user function help system.

[...]........

[...] r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines

[...]

[...] Added the consistency testing documentation to the grace.write and value.* user functions.

[...]........

[...] r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines

[...]

[...] Modified the working of the n_state_model.elim_no_prob backend.

[...]

[...] This user function is not functional anyway and is not tested by the relax test suite, but will

[...] remain as it might be useful in the future.

[...]........

[...] r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines

[...]

[...] Created a system test to replicate Romel Bobby's bug #19887.

[...]

[...] This is the bug report at https://gna.org/bugs/?19887.

[...]........

[...] r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines

[...]

[...] Partial fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] The problem is that the number of peak height values was not the same for all spins!

[...]

[...] The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in

[...] incorrect values, causing relax to fail directly after the setup() call in

[...] specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but

[...] in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather

[...] than 5. Now the correct number is sent into setup().

[...]........

[...] r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines

[...]

[...] A final fix for bug #19887 (https://gna.org/bugs/?19887).

[...]

[...] Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This

[...] occurs in the relaxation curve-fitting overfit_deselect() method.

[...]........

[...]

[...]

(Browse SVN revision 17117)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:17:23 AM UTC, SVN revision 17116:

A final fix for bug #19887 (https://gna.org/bugs/?19887).

Now a RelaxError is raised if the number of peak intensities is not the same for all spins. This
occurs in the relaxation curve-fitting overfit_deselect() method.

(Browse SVN revision 17116)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 10:03:02 AM UTC, SVN revision 17115:

Partial fix for bug #19887 (https://gna.org/bugs/?19887).

The problem is that the number of peak height values was not the same for all spins!

The error message was being caused by the math_fns.relax_fit C object 'setup' function being feed in
incorrect values, causing relax to fail directly after the setup() call in
specific_fns.relax_fit.minimise(). The number of points was being taken from cdp.relax_times, but
in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins has 4 points rather
than 5. Now the correct number is sent into setup().

(Browse SVN revision 17115)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 09:16:10 AM UTC, comment #2:

This was first discussed on the relax-users mailing list at the threads starting at:

https://mail.gna.org/public/relax-users/2012-06/msg00011.html

and:

https://mail.gna.org/public/relax-users/2012-07/msg00000.html

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 09:14:28 AM UTC, SVN revision 17114:

Created a system test to replicate Romel Bobby's bug #19887.

This is the bug report at https://gna.org/bugs/?19887.

(Browse SVN revision 17114)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 02 Jul 2012 08:27:01 AM UTC, original submission:

Dear all,

I've been trying to use the curve fitting routine for R1 and R2 in relax using the sample script relax_fit.py. I managed to read in the spectra and obtain a value for the uncertainty. However, once it gets to the point of performing a grid_search that's where it fails (see below). Has anyone had a similar problem?

[?1034h

relax 2.0.0

Molecular dynamics by NMR data analysis

Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2012 the relax development team

This is free software which you are welcome to modify and redistribute under the conditions of the
GNU General Public License (GPL). This program, including all modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within the relax prompt.

Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within
the prompt.

Processor fabric: Uni-processor.

script = 'relax_fit.py'
----------------------------------------------------------------------------------------------------
###############################################################################
# #
# Copyright (C) 2004-2012 Edward d'Auvergne #
# #
# This file is part of the program relax. #
# #
# relax is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation; either version 2 of the License, or #
# (at your option) any later version. #
# #
# relax is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with relax; if not, write to the Free Software #
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA #
# #
###############################################################################

"""Script for relaxation curve fitting."""

# Create the 'rx' data pipe.
pipe.create('rx', 'relax_fit')

# Load the backbone amide 15N spins from a PDB file.
structure.read_pdb('IL6_mf.pdb')
structure.load_spins(spin_id='@N')

# Spectrum names.
names = [
'T1_1204.04',
'T1_1504.04',
'T1_1804.04',
'T1_2104.04',
'T1_2404.04',
'T1_2754.04',
'T1_304.04',
'T1_304.040',
'T1_54.04',
'T1_604.04',
'T1_604.040',
'T1_904.04',
]

# Relaxation times (in seconds).
times = [
1.204,
1.504,
1.804,
2.104,
2.404,
2.754,
0.304,
0.304,
0.054,
0.604,
0.604,
0.904
]

# Loop over the spectra.
for i in xrange(len(names)):
# Load the peak intensities.
spectrum.read_intensities(file=names[i]+'.list', dir='', spectrum_id=names[i], int_method='height')

# Set the relaxation times.
relax_fit.relax_time(time=times[i], spectrum_id=names[i])

# Specify the duplicated spectra.
spectrum.replicated(spectrum_ids=['T1_304.04', 'T1_304.040'])
spectrum.replicated(spectrum_ids=['T1_604.04', 'T1_604.040'])

# Peak intensity error analysis.
spectrum.error_analysis()

# Deselect unresolved spins.
# deselect.read(file='unresolved', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5)

# Set the relaxation curve type.
relax_fit.select_model('inv')

# Grid search.
grid_search(inc=11)

# Minimise.
minimise('simplex', scaling=False, constraints=False)

# Monte Carlo simulations.
monte_carlo.setup(number=500)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise('simplex', scaling=False, constraints=False)
monte_carlo.error_analysis()

# Save the relaxation rates.
value.write(param='rx', file='rx.out', force=True)

# Save the results.
results.write(file='results', force=True)

# Create Grace plots of the data.
grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised chi-squared value.
grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak intensity.
grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation rate.
grace.write(x_data_type='relax_times', y_data_type='intensities', file='intensities.agr', force=True) # Average peak intensities.
grace.write(x_data_type='relax_times', y_data_type='intensities', norm=True, file='intensities_norm.agr', force=True) # Average peak intensities (normalised).

# Display the Grace plots.
grace.view(file='chi2.agr')
grace.view(file='i0.agr')
grace.view(file='rx.agr')
grace.view(file='intensities.agr')
grace.view(file='intensities_norm.agr')

# Save the program state.
state.save('rx.save', force=True)
----------------------------------------------------------------------------------------------------

relax> pipe.create(pipe_name='rx', pipe_type='relax_fit', bundle=None)

relax> structure.read_pdb(file='IL6_mf.pdb', dir=None, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, parser='internal')

Internal relax PDB parser.
Opening the file 'IL6_mf.pdb' for reading.
Adding molecule 'IL6_mf_mol1' to model None (from the original molecule number 1 of model None)

relax> structure.load_spins(spin_id='@N', ave_pos=True)
Adding the following spins to the relax data store.

# mol_name res_num res_name spin_num spin_name
IL6_mf_mol1 20 LEU 1 N
IL6_mf_mol1 21 THR 20 N
IL6_mf_mol1 22 SER 34 N
IL6_mf_mol1 23 SER 45 N
IL6_mf_mol1 24 GLU 56 N
IL6_mf_mol1 25 ARG 71 N
IL6_mf_mol1 26 ILE 95 N
IL6_mf_mol1 27 ASP 114 N
IL6_mf_mol1 28 LYS 126 N
IL6_mf_mol1 29 GLN 148 N
IL6_mf_mol1 30 ILE 165 N
IL6_mf_mol1 31 ARG 184 N
IL6_mf_mol1 32 TYR 208 N
IL6_mf_mol1 33 ILE 229 N
IL6_mf_mol1 34 LEU 248 N
IL6_mf_mol1 35 ASP 267 N
IL6_mf_mol1 36 GLY 279 N
IL6_mf_mol1 37 ILE 286 N
IL6_mf_mol1 38 SER 305 N
IL6_mf_mol1 39 ALA 316 N
IL6_mf_mol1 40 LEU 326 N
IL6_mf_mol1 41 ARG 345 N
IL6_mf_mol1 42 LYS 369 N
IL6_mf_mol1 43 GLU 391 N
IL6_mf_mol1 44 THR 406 N
IL6_mf_mol1 45 CYS 420 N
IL6_mf_mol1 46 ASN 430 N
IL6_mf_mol1 47 LYS 444 N
IL6_mf_mol1 48 SER 466 N
IL6_mf_mol1 49 ASN 477 N
IL6_mf_mol1 50 MET 491 N
IL6_mf_mol1 51 CYS 508 N
IL6_mf_mol1 52 GLU 518 N
IL6_mf_mol1 53 SER 533 N
IL6_mf_mol1 54 SER 544 N
IL6_mf_mol1 55 LYS 555 N
IL6_mf_mol1 56 GLU 577 N
IL6_mf_mol1 57 ALA 592 N
IL6_mf_mol1 58 LEU 602 N
IL6_mf_mol1 59 ALA 621 N
IL6_mf_mol1 60 GLU 631 N
IL6_mf_mol1 61 ASN 646 N
IL6_mf_mol1 62 ASN 660 N
IL6_mf_mol1 63 LEU 674 N
IL6_mf_mol1 64 ASN 693 N
IL6_mf_mol1 65 LEU 707 N
IL6_mf_mol1 66 PRO 726 N
IL6_mf_mol1 67 LYS 740 N
IL6_mf_mol1 68 MET 762 N
IL6_mf_mol1 69 ALA 779 N
IL6_mf_mol1 70 GLU 789 N
IL6_mf_mol1 71 LYS 804 N
IL6_mf_mol1 72 ASP 826 N
IL6_mf_mol1 73 GLY 838 N
IL6_mf_mol1 74 CYS 845 N
IL6_mf_mol1 75 PHE 855 N
IL6_mf_mol1 76 GLN 875 N
IL6_mf_mol1 77 SER 892 N
IL6_mf_mol1 78 GLY 903 N
IL6_mf_mol1 79 PHE 910 N
IL6_mf_mol1 80 ASN 930 N
IL6_mf_mol1 81 GLU 944 N
IL6_mf_mol1 82 GLU 959 N
IL6_mf_mol1 83 THR 974 N
IL6_mf_mol1 84 CYS 988 N
IL6_mf_mol1 85 LEU 998 N
IL6_mf_mol1 86 VAL 1017 N
IL6_mf_mol1 87 LYS 1033 N
IL6_mf_mol1 88 ILE 1055 N
IL6_mf_mol1 89 ILE 1074 N
IL6_mf_mol1 90 THR 1093 N
IL6_mf_mol1 91 GLY 1107 N
IL6_mf_mol1 92 LEU 1114 N
IL6_mf_mol1 93 LEU 1133 N
IL6_mf_mol1 94 GLU 1152 N
IL6_mf_mol1 95 PHE 1167 N
IL6_mf_mol1 96 GLU 1187 N
IL6_mf_mol1 97 VAL 1202 N
IL6_mf_mol1 98 TYR 1218 N
IL6_mf_mol1 99 LEU 1239 N
IL6_mf_mol1 100 GLU 1258 N
IL6_mf_mol1 101 TYR 1273 N
IL6_mf_mol1 102 LEU 1294 N
IL6_mf_mol1 103 GLN 1313 N
IL6_mf_mol1 104 ASN 1330 N
IL6_mf_mol1 105 ARG 1344 N
IL6_mf_mol1 106 PHE 1368 N
IL6_mf_mol1 107 GLU 1388 N
IL6_mf_mol1 108 SER 1403 N
IL6_mf_mol1 109 SER 1414 N
IL6_mf_mol1 110 GLU 1425 N
IL6_mf_mol1 111 GLU 1440 N
IL6_mf_mol1 112 GLN 1455 N
IL6_mf_mol1 113 ALA 1472 N
IL6_mf_mol1 114 ARG 1482 N
IL6_mf_mol1 115 ALA 1506 N
IL6_mf_mol1 116 VAL 1516 N
IL6_mf_mol1 117 GLN 1532 N
IL6_mf_mol1 118 MET 1549 N
IL6_mf_mol1 119 SER 1566 N
IL6_mf_mol1 120 THR 1577 N
IL6_mf_mol1 121 LYS 1591 N
IL6_mf_mol1 122 VAL 1613 N
IL6_mf_mol1 123 LEU 1629 N
IL6_mf_mol1 124 ILE 1648 N
IL6_mf_mol1 125 GLN 1667 N
IL6_mf_mol1 126 PHE 1684 N
IL6_mf_mol1 127 LEU 1704 N
IL6_mf_mol1 128 GLN 1723 N
IL6_mf_mol1 129 LYS 1740 N
IL6_mf_mol1 130 LYS 1762 N
IL6_mf_mol1 131 ALA 1784 N
IL6_mf_mol1 132 LYS 1794 N
IL6_mf_mol1 133 ASN 1816 N
IL6_mf_mol1 134 LEU 1830 N
IL6_mf_mol1 135 ASP 1849 N
IL6_mf_mol1 136 ALA 1861 N
IL6_mf_mol1 137 ILE 1871 N
IL6_mf_mol1 138 THR 1890 N
IL6_mf_mol1 139 THR 1904 N
IL6_mf_mol1 140 PRO 1918 N
IL6_mf_mol1 141 ASP 1932 N
IL6_mf_mol1 142 PRO 1944 N
IL6_mf_mol1 143 THR 1958 N
IL6_mf_mol1 144 THR 1972 N
IL6_mf_mol1 145 ASN 1986 N
IL6_mf_mol1 146 ALA 2000 N
IL6_mf_mol1 147 SER 2010 N
IL6_mf_mol1 148 LEU 2021 N
IL6_mf_mol1 149 LEU 2040 N
IL6_mf_mol1 150 THR 2059 N
IL6_mf_mol1 151 LYS 2073 N
IL6_mf_mol1 152 LEU 2095 N
IL6_mf_mol1 153 GLN 2114 N
IL6_mf_mol1 154 ALA 2131 N
IL6_mf_mol1 155 GLN 2141 N
IL6_mf_mol1 156 ASN 2158 N
IL6_mf_mol1 157 GLN 2172 N
IL6_mf_mol1 158 TRP 2189 N
IL6_mf_mol1 159 LEU 2213 N
IL6_mf_mol1 160 GLN 2232 N
IL6_mf_mol1 161 ASP 2249 N
IL6_mf_mol1 162 MET 2261 N
IL6_mf_mol1 163 THR 2278 N
IL6_mf_mol1 164 THR 2292 N
IL6_mf_mol1 165 HIS 2306 N
IL6_mf_mol1 166 LEU 2323 N
IL6_mf_mol1 167 ILE 2342 N
IL6_mf_mol1 168 LEU 2361 N
IL6_mf_mol1 169 ARG 2380 N
IL6_mf_mol1 170 SER 2404 N
IL6_mf_mol1 171 PHE 2415 N
IL6_mf_mol1 172 LYS 2435 N
IL6_mf_mol1 173 GLU 2457 N
IL6_mf_mol1 174 PHE 2472 N
IL6_mf_mol1 175 LEU 2492 N
IL6_mf_mol1 176 GLN 2511 N
IL6_mf_mol1 177 SER 2528 N
IL6_mf_mol1 178 SER 2539 N
IL6_mf_mol1 179 LEU 2550 N
IL6_mf_mol1 180 ARG 2569 N
IL6_mf_mol1 181 ALA 2593 N
IL6_mf_mol1 182 LEU 2603 N
IL6_mf_mol1 183 ARG 2622 N
IL6_mf_mol1 184 GLN 2646 N
IL6_mf_mol1 185 MET 2663 N

relax> spectrum.read_intensities(file='T1_1204.04.list', dir='', spectrum_id='T1_1204.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_1204.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=1.204, spectrum_id='T1_1204.04')

relax> spectrum.read_intensities(file='T1_1504.04.list', dir='', spectrum_id='T1_1504.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_1504.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=1.504, spectrum_id='T1_1504.04')

relax> spectrum.read_intensities(file='T1_1804.04.list', dir='', spectrum_id='T1_1804.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_1804.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=1.804, spectrum_id='T1_1804.04')

relax> spectrum.read_intensities(file='T1_2104.04.list', dir='', spectrum_id='T1_2104.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_2104.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=2.104, spectrum_id='T1_2104.04')

relax> spectrum.read_intensities(file='T1_2404.04.list', dir='', spectrum_id='T1_2404.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_2404.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=2.404, spectrum_id='T1_2404.04')

relax> spectrum.read_intensities(file='T1_2754.04.list', dir='', spectrum_id='T1_2754.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_2754.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=2.754, spectrum_id='T1_2754.04')

relax> spectrum.read_intensities(file='T1_304.04.list', dir='', spectrum_id='T1_304.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_304.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.304, spectrum_id='T1_304.04')

relax> spectrum.read_intensities(file='T1_304.040.list', dir='', spectrum_id='T1_304.040', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_304.040.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.304, spectrum_id='T1_304.040')

relax> spectrum.read_intensities(file='T1_54.04.list', dir='', spectrum_id='T1_54.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_54.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.054, spectrum_id='T1_54.04')

relax> spectrum.read_intensities(file='T1_604.04.list', dir='', spectrum_id='T1_604.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_604.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.604, spectrum_id='T1_604.04')

relax> spectrum.read_intensities(file='T1_604.040.list', dir='', spectrum_id='T1_604.040', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_604.040.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.604, spectrum_id='T1_604.040')

relax> spectrum.read_intensities(file='T1_904.04.list', dir='', spectrum_id='T1_904.04', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
Opening the file 'T1_904.04.list' for reading.
Sparky formatted data file.

Number of header lines found: 1

relax> relax_fit.relax_time(time=0.904, spectrum_id='T1_904.04')

relax> spectrum.replicated(spectrum_ids=['T1_304.04', 'T1_304.040'])

relax> spectrum.replicated(spectrum_ids=['T1_604.04', 'T1_604.040'])

relax> spectrum.error_analysis()
Intensity measure: Peak heights.
Replicated spectra: Yes.
All spectra replicated: No.

Replicated spectra: ['T1_304.04', 'T1_304.040']
Standard deviation: 54707.6690901

Replicated spectra: ['T1_604.04', 'T1_604.040']
Standard deviation: 49975.7017454

Variance averaging over all spectra.
Standard deviation for all spins: 52395.132513514036

relax> relax_fit.select_model(model='inv')
Three parameter inversion recovery fit.

relax> grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1)

Over-fit spin deselection.

Fitting to spin '#IL6_mf_mol1:24@56'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/usr/local/relax/multi/processor.py", line 480, in run
self.callback.init_master(self)
File "/usr/local/relax/multi/__init__.py", line 319, in default_init_master
self.master.run()
File "/usr/local/relax/relax.py", line 183, in run
self.interpreter.run(self.script_file)
File "/usr/local/relax/prompt/interpreter.py", line 280, in run
return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 570, in run_script
return console.interact(intro, local, script_file, quit, show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 455, in interact_script
exec_script(script_file, local)
File "/usr/local/relax/prompt/interpreter.py", line 329, in exec_script
runpy.run_module(module, globals)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in <module>
grid_search(inc=11)
File "/usr/local/relax/prompt/uf_objects.py", line 220, in _call_
self._backend(*new_args, **uf_kargs)
File "/usr/local/relax/generic_fns/minimise.py", line 141, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity)
File "/usr/local/relax/specific_fns/relax_fit.py", line 609, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/usr/local/relax/specific_fns/relax_fit.py", line 716, in minimise
if constraints and not match('^[Gg]rid', min_algor):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py", line 137, in match
return _compile(pattern, flags).match(string)
TypeError: bad argument type for built-in operation

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file #15952:  relax_fit.tar.gz added by None (128kB - application/x-gzip)
file #15953:  relax_info.txt added by None (6kB - text/plain)
file #15954:  relax_fit.log added by None (25kB - application/octet-stream)

 

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Items that depend on this one: None found

 

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  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by None (Submitted the item)
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    Follow 10 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 02 Jul 2012 10:30:01 AM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Mon 02 Jul 2012 08:52:19 AM UTCbugmanCategoryrelax sample scripts=>relax's source code
      StatusIn Progress=>Confirmed
      Operating SystemMac OS X (Intel)=>All systems
    Mon 02 Jul 2012 08:39:14 AM UTCbugmanStatusNone=>In Progress
      Assigned toNone=>bugman
    Mon 02 Jul 2012 08:27:02 AM UTCNoneAttached File-=>Added relax_fit.tar.gz, #15952
      Attached File-=>Added relax_info.txt, #15953
      Attached File-=>Added relax_fit.log, #15954
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