Relax 2.2.0 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-14T11:37:24Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Added keywords.

2015-10-22T18:05:37Z

Added keywords.

Bugman: Increased the sectioning depth.

2015-10-22T17:11:03Z

Increased the sectioning depth.

Bugman: Added the 'manual' parameter to {{infobox relax release}}.

2015-10-22T16:45:45Z

Added the 'manual' parameter to {{infobox relax release}}.

Bugman: Added an infobox.

2015-10-21T19:04:56Z

Added an infobox.

Bugman: /* See also */ Added a link to the API documentation.

2014-11-26T10:27:28Z

See also: Added a link to the API documentation.

Bugman: Link fix.

2014-09-11T19:00:23Z

Link fix.

Bugman: User function HTML manual links.

2014-09-11T18:58:17Z

User function HTML manual links.

Show changes

Bugman: Formatting of all symbols/parameters.

2014-09-11T18:52:09Z

Formatting of all symbols/parameters.

Bugman: Tracker links with full descriptions.

2014-09-11T18:49:49Z

Tracker links with full descriptions.

@@ Line 219: / Line 219: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_2.2.0 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2375 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2375|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/37 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00033.html Mail Archive]

@@ Line 2: / Line 2: @@
 {{infobox relax release
-| version = 2.2.0
+| version  = 2.2.0
-| prev    = 2.1.2
+| prev     = 2.1.2
-| next    = 2.2.1
+| next     = 2.2.1
-| type    = Major feature and bugfix
+| keywords = Ensemble analysis, N-state model analysis
-| date    = 27 January 2013
+| type     = Major feature and bugfix
-| manual  = yes
+| date     = 27 January 2013
 }}

@@ Line 10: / Line 10: @@
 }}
-= Description =
+== Description ==
 <section begin=description/>
@@ Line 16: / Line 16: @@
 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
@@ Line 22: / Line 22: @@
 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
@@ Line 30: / Line 30: @@
 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
@@ Line 47: / Line 47: @@
 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
@@ Line 167: / Line 167: @@
 <section end=changes/>
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
@@ Line 213: / Line 213: @@
 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
@@ Line 225: / Line 225: @@
 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/2.2/ The relax 2.2 API documentation]
 {{:relax release see also}}
 [[Category:N-state model analysis]]

@@ Line 7: / Line 7: @@
 | type    = Major feature and bugfix
 | date    = 27 January 2013
 }}

← Older revision		Revision as of 19:04, 21 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 2.2.0
		+	\| prev = 2.1.2
		+	\| next = 2.2.1
		+	\| type = Major feature and bugfix
		+	\| date = 27 January 2013
		+	}}

	= Description =		= Description =

@@ Line 64: / Line 64: @@
 *  Modified the [http://www.nmr-relax.com/manual/temperature.html temperature user function] - the value can be set twice if it is the same value.
 *  Modified the [http://www.nmr-relax.com/manual/frq_set.html frq.set user function] - the value can be set twice if it is the same value.
-*  The [http://www.nmr-relax.com/manual/rdc.back_calc.html rdc.back_calc user function] now handles absolute RDCs.
+*  The [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc user function] now handles absolute RDCs.
 *  Created the Align_tensor.test_copy system test to catch [https://gna.org/bugs/?20338 bug #20338].
 *  The [http://www.nmr-relax.com/manual/spin_create_pseudo.html spin.create_pseudo user function] 'members' argument is no longer read only in the GUI.  This allows the user to type in shorter spin IDs rather than selecting them from the list.

@@ Line 30: / Line 30: @@
 *  Added the 'empty' flag to the [http://www.nmr-relax.com/manual/sequence_copy.html sequence.copy user function] to allow all the spin contents to be copied.
 *  Implemented the [http://www.nmr-relax.com/manual/pcs_structural_noise.html pcs.structural_noise user function].  This is used to determine the PCS error due to structural noise via simulation, and adds the error via variance addition to the experimental PCS error.
-*  The N-state model grid search optimises each tensor separately when only tensors are optimised.  This massively collapses the grid search size from inc**(5*N) to N*inc**5, where inc are the number of increments per dimension and N is the number of alignments, making a grid search possible.
+*  The N-state model grid search optimises each tensor separately when only tensors are optimised.  This massively collapses the grid search size from inc<sup>5*N</sup> to N*inc<sup>5</sup>, where inc are the number of increments per dimension and N is the number of alignments, making a grid search possible.
 *  Implemented the [http://www.nmr-relax.com/manual/rdc_set_errors.html rdc.set_errors] and [http://www.nmr-relax.com/manual/pcs_set_errors.html pcs.set_errors] user functions.
 *  Added Monte Carlo simulation support for the paramagnetic centre for PCSs in the N-state model.
@@ Line 154: / Line 154: @@
 *  The N-state model _check_rdcs() method now skips deselected interatomic data containers.  A FIXME comment has also been added to highlight a possible future problem.
 *  Added some consistency to the specific analysis API base class.  The return_data() method argument has been changed from 'spin' to 'data_id', as the data from the base_data_loop() methods are often not spin containers.
-*  Made the chi2 value check less stringent in the N_state_model.test_metal_pos_opt system test.  For some bizarre reason, the calc() call in the GUI is less precise.
+*  Made the &chi;<sup>2</sup> value check less stringent in the N_state_model.test_metal_pos_opt system test.  For some bizarre reason, the calc() call in the GUI is less precise.
 *  The N_state_model.test_populations system test has been made less stringent to allow MS Windows to pass.
 <section end=changes/>

@@ Line 44: / Line 44: @@
 *  Small syntax fix in the release checklist document.
 *  Added the MARC archive links to the development chapter of the relax user manual.  These links are:  http://marc.info/?l=relax-announce&r=1&w=2, http://marc.info/?l=relax-users&r=1&w=2, http://marc.info/?l=relax-devel&r=1&w=2, and http://marc.info/?l=relax-commits&r=1&w=2.
-*  The model-free overfit deselection algorithm now fails with a RelaxError when no spins are selected.  This is to avoid situations such as bug #20277 (https://gna.org/bugs/?20277).
+*  The model-free overfit deselection algorithm now fails with a RelaxError when no spins are selected.  This is to avoid situations such as [https://gna.org/bugs/?20277 bug #20277].
 *  The pipe.display user function now uses relax_io.write_data() for better output formatting.
 *  Created the N_state_model.test_data_copying system test for the rdc.copy and pcs.copy user functions.  These user functions do not exist yet, but this test will be used to implement them.
@@ Line 61: / Line 61: @@
 *  Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.  This is a test of the long range, absolute RDCs for menthol.
 *  Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
-*  Modified the N_state_model.test_populations system test to catch bug #20335.  This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and PCS data.
+*  Modified the N_state_model.test_populations system test to catch [https://gna.org/bugs/?20335 bug #20335].  This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and PCS data.
 *  Modified the temperature user function - the value can be set twice if it is the same value.
 *  Modified the frq.set user function - the value can be set twice if it is the same value.
 *  The rdc.back_calc user function now handles absolute RDCs.
-*  Created the Align_tensor.test_copy system test to catch bug #20338 (https://gna.org/bugs/?20338).
+*  Created the Align_tensor.test_copy system test to catch [https://gna.org/bugs/?20338 bug #20338].
 *  The spin.create_pseudo user function 'members' argument is no longer read only in the GUI.  This allows the user to type in shorter spin IDs rather than selecting them from the list.
 *  Shifted and renamed the arg_check.check_float() function to check_types.is_float().
@@ Line 97: / Line 97: @@
 *  The frq.set user function now warns if the frequency is lower than 100 MHz or higher than 2 GHz.
 *  Updated the diffusion tensor minimisation sample script as the code is very old and useless.
-*  Created the State.test_align_tensor_with_mc_sims system test to catch bug #20414.  The report is at http://gna.org/bugs/?20414.
+*  Created the State.test_align_tensor_with_mc_sims system test to catch [http://gna.org/bugs/?20414 bug #20414].
 *  Modified the align_tensor_mc.bz2 save file to catch a strange and rare bug.  This is caught by the State.test_align_tensor_with_mc_sims system test.
 *  Spun out the maths_fns.rotation_matrix.random_rot_axis() function into its own module.  The function is now called maths_fns.vectors.random_unit_vector().
@@ Line 169: / Line 169: @@
 *  Fix for the relax_io.write_data() function - it can now handle no data being sent in.
 *  Bugfix for the use of pseudo-atoms for RDCs in the N-state model analysis.  If the second atom of the pair in the intermolecular data container holding the RDC data was a pseudo-atom, then the N-state model optimisation setup would fail.  Now both the first and second atoms being pseudo-atoms is supported.
-*  Fix for bug #20335 (https://gna.org/bugs/?20335).  The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
+*  Fix for [https://gna.org/bugs/?20335 bug #20335].  The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
-*  Fix for bug #20338 (https://gna.org/bugs/?20338), the new tensor name is now set.
+*  Fix for [https://gna.org/bugs/?20338 bug #20338], the new tensor name is now set.
 *  Bugfix for the catching of errors in the GUI user functions - the sys module import was missing.
 *  Bugfix for the GUI combo_list input element SetValue() method.  Values not belonging to the combo lists can now be set.  This fixes the spin.create_pseudo user function in the test suite, a bug triggered by the N_state_model.test_absolute_rdc_menthol GUI test.
@@ Line 178: / Line 178: @@
 *  Bugfix for the RelaxNoAlignError error class - the printout statement was broken.
 *  Bugfix for the rdc.copy user function - it is now functional.  The code was old and untested, and still assumed that the RDC values were held in spin containers rather than the interatomic data containers.
-*  Partial fix for bug #20378 (https://gna.org/bugs/?20378).  The gui_raise() function was operating differently under the command line run test suite and the GUI run test suite.  The operation of the function is now consistent, and no RelaxError is raised (unless the raise_flag argument is set).
+*  Partial fix for [https://gna.org/bugs/?20378 bug #20378].  The gui_raise() function was operating differently under the command line run test suite and the GUI run test suite.  The operation of the function is now consistent, and no RelaxError is raised (unless the raise_flag argument is set).
-*  Full fix for bug #20378 (https://gna.org/bugs/?20378).  As no RelaxError is no longer raised in this Bruker.test_bug_20152_read_dc_file GUI test (well only in the command line operation of the GUI tests), instead the current data pipe is checked to make sure no relaxation data was loaded.
+*  Full fix for [https://gna.org/bugs/?20378 bug #20378].  As no RelaxError is no longer raised in this Bruker.test_bug_20152_read_dc_file GUI test (well only in the command line operation of the GUI tests), instead the current data pipe is checked to make sure no relaxation data was loaded.
-*  Fix for bug #20414 (http://gna.org/bugs/?20414).  The variable for the number of simulations in the AlignmentTensorList object is now set prior to setting the simulation parameter values.
+*  Fix for [https://gna.org/bugs/?20414 bug #20414].  The variable for the number of simulations in the AlignmentTensorList object is now set prior to setting the simulation parameter values.
-*  Fix for bug #20417 (https://gna.org/bugs/?20417).  The backwards compatibility hook for the loading of old relax state and results files can now handle the presence of proton spins.  The data structures are now correctly converted to the current data pipe design.  This is only the case for old files containing PCS data.
+*  Fix for [https://gna.org/bugs/?20417 bug #20417].  The backwards compatibility hook for the loading of old relax state and results files can now handle the presence of proton spins.  The data structures are now correctly converted to the current data pipe design.  This is only the case for old files containing PCS data.
-*  Fix for bug #20420 (https://gna.org/bugs/?20420).  The problem was in the generic_fns.mol_res_spin.create_spin() function.  The index_molecule() and index_residue() functions where not taking alternative, non-current data pipes into account.
+*  Fix for [https://gna.org/bugs/?20420 bug #20420].  The problem was in the generic_fns.mol_res_spin.create_spin() function.  The index_molecule() and index_residue() functions where not taking alternative, non-current data pipes into account.
-*  Fix for bug #20421 (https://gna.org/bugs/?20421).  The loading of relax state files was only updating the spin ID metadata structures for the current data pipe.  Now all loaded data pipes are updated.
+*  Fix for [https://gna.org/bugs/?20421 bug #20421].  The loading of relax state files was only updating the spin ID metadata structures for the current data pipe.  Now all loaded data pipes are updated.
 *  RDC data fix for the _back_compat_hook() method for converting old relax state and results files.  The RDC data was not being shifted into the corresponding interatomic data container and remained in the spin containers.
 *  Fix for the bug caught by the N_state_model.test_mc_sim_failure system test.  If no RDC error is present, then the returned error from the N-state model analysis specific method return_error() is None.