Relax 1.3.14 - Revision history

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

2020-10-14T12:29:53Z

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

Bugman: /* Bugfixes */ Internal link to DASHA.

2015-12-15T15:12:19Z

Bugfixes: Internal link to DASHA.

Bugman: /* References */ Switched to a labelled section transclusion for the citations.

2015-11-03T17:17:13Z

References: Switched to a labelled section transclusion for the citations.

Bugman: Added an infobox.

2015-10-22T16:45:09Z

Added an infobox.

Bugman: Increased the sectioning depth.

2015-10-22T16:43:56Z

Increased the sectioning depth.

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

2014-11-26T10:24:13Z

See also: Added a link to the API documentation.

Bugman: /* Changes */ Symbol formatting.

2014-09-20T08:38:04Z

Changes: Symbol formatting.

Bugman: /* Links */ Removed the Gmane link as it does not exist.

2014-09-20T08:28:36Z

Links: Removed the Gmane link as it does not exist.

Bugman: Created a links section.

2014-09-20T08:27:31Z

Created a links section.

Bugman: User function HTML manual links.

2014-09-20T08:24:06Z

User function HTML manual links.

@@ Line 121: / Line 121: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_1.3.14 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2337 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2337|text=Gna! news item}}
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00025.html Mail archive]
 * [https://mail.gna.org/public/relax-announce/2012-03/msg00000.html Local archives]

@@ Line 107: / Line 107: @@
 *  Fix for a rare bug in the model-free analysis for when relaxation data of None is encountered.
 *  Fixes for the Dasha system test for the [https://gna.org/bugs/?19332 bug #19332] fix.
-*  Fixes for the Dasha use functions for file creation and data extraction - this should now handle relaxation data values of None, and also set the parameter values of deselected spins using the Dasha output files.
+*  Fixes for the Dasha use functions for file creation and data extraction - this should now handle relaxation data values of None, and also set the parameter values of deselected spins using the [[DASHA]] output files.
 *  Big bugfix for the [http://www.nmr-relax.com/manual/value_read.html value.read user function] - the wrong spin ID string was being used to set the parameter value so that all spins have the same value set for the parameter ([https://gna.org/bugs/?19332 bug #19332]).
 *  Bug fix for the consistency testing analysis for when relaxation data of None is encountered.

@@ Line 133: / Line 133: @@
 == References ==
-<section start=references/>
+* [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}
-* [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007).  Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm.  ''Mol. BioSyst.'', '''3'''(7), 483–494. (DOI: [http://dx.doi.org/10.1039/b702202f 10.1039/b702202f]).
+* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}
 <HarvardReferences />

← Older revision		Revision as of 16:45, 22 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 1.3.14
		+	\| prev = 1.3.13
		+	\| next = 1.3.15
		+	\| keywords = IO, memory, performance
		+	\| type = Major bugfix
		+	\| date = 19 March 2012
		+	\| manual = yes
		+	}}

	== Description ==		== Description ==

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 {{lowercase title}}
-= Description =
+== Description ==
 <section begin=description/>
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 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
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 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
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-== Features ==
+=== Features ===
 <section begin=features/>
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 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
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 <section end=changes/>
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
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 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
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 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= References =
+== References ==
 <section start=references/>
@@ Line 129: / Line 129: @@
 <HarvardReferences />
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
 {{:relax release see also}}

← Older revision		Revision as of 10:24, 26 November 2014
Line 131:		Line 131:
	= See also =		= See also =

		+	* [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
	{{:relax release see also}}		{{:relax release see also}}

@@ Line 66: / Line 66: @@
 *  Eliminated all usage of sys.__stdout__ and sys.__stderr__ in the multi-processor package - this returns full control of IO streams to the parent program.
 *  The float arg checks now checks against all the numpy float types (float16, float32, float64, float128).
-*  Added [http://www.nmr-relax.com/manual/value_write.html value.write user function] calls to the J(w) mapping system test script.
+*  Added [http://www.nmr-relax.com/manual/value_write.html value.write user function] calls to the J(&omega;) mapping system test script.
-*  Added some [http://www.nmr-relax.com/manual/value_write.html value.write user function]s to the J(w) mapping sample script.
+*  Added some [http://www.nmr-relax.com/manual/value_write.html value.write user function]s to the J(&omega;) mapping sample script.
-*  Modified the J(w) mapping test data to include relaxation values of None to trigger [https://gna.org/bugs/?19329 bug #19329].
+*  Modified the J(&omega;) mapping test data to include relaxation values of None to trigger [https://gna.org/bugs/?19329 bug #19329].
 *  Speed up for the generic_fns.relax_re.search() function.
 *  More speed ups for the Selection.__contains_mol_res_spin_containers() method.

@@ Line 48: / Line 48: @@
 *  Elimination of all relax dependencies from the multi-processor package.
 *  Added support for the memory size on MS Windows to the relax info print out.
-*  Updated the value.set user function unknown parameter error message to list the known ones.
+*  Updated the [http://www.nmr-relax.com/manual/value_set.html value.set user function] unknown parameter error message to list the known ones.
 *  For Unix and GNU/Linux systems, the relax info printout now shows the ram and swap size.
 *  Expansion and improvement of the information printed out by 'relax --info'.
@@ Line 66: / Line 66: @@
 *  Eliminated all usage of sys.__stdout__ and sys.__stderr__ in the multi-processor package - this returns full control of IO streams to the parent program.
 *  The float arg checks now checks against all the numpy float types (float16, float32, float64, float128).
-*  Added value.write user function calls to the J(w) mapping system test script.
+*  Added [http://www.nmr-relax.com/manual/value_write.html value.write user function] calls to the J(w) mapping system test script.
-*  Added some value.write user functions to the J(w) mapping sample script.
+*  Added some [http://www.nmr-relax.com/manual/value_write.html value.write user function]s to the J(w) mapping sample script.
 *  Modified the J(w) mapping test data to include relaxation values of None to trigger [https://gna.org/bugs/?19329 bug #19329].
 *  Speed up for the generic_fns.relax_re.search() function.
@@ Line 76: / Line 76: @@
 *  Removal of a number of debugging print out statements.
 *  Significant speed ups of the return_spin() and return_residue() functions.
-*  Added a print out for the diffusion_tensor.init user function to inform the user of an angle unit change - this is in response to [https://gna.org/bugs/?19323 bug #19323] to make it clearer that a parameter conversion has occurred.
+*  Added a print out for the [http://www.nmr-relax.com/manual/diffusion_tensor_init.html diffusion_tensor.init user function] to inform the user of an angle unit change - this is in response to [https://gna.org/bugs/?19323 bug #19323] to make it clearer that a parameter conversion has occurred.
 *  Created a special specific API object called SPIN_PARAMS - this will be used to handle all operations to do with model parameters.  The object Param_list has methods for parameter initialisation and handling (where all info is specified such as Grace string, units, default value, etc) and for determining if a parameter exists.
 *  Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data structures.  The parameters are now all lowercase, for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex'].  The follow parameters are now converted throughout relax: 'bond_length' to 'r', 'CSA' to 'csa', 'heteronucleus' to 'heteronuc_type', 'proton' to 'proton_type'.
-*  Created a new algorithm for finding the pivot of motion between different structural models - this is available through the structure.find_pivot user function.
+*  Created a new algorithm for finding the pivot of motion between different structural models - this is available through the [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot user function].
 *  Added the validate_models() method to the structural API - this is used to check that the models are 100% consistent.
-*  Added the centroid argument to the structure.superimpose user function - this allows for the superimposition of structures assuming a pivoted motion.
+*  Added the centroid argument to the [http://www.nmr-relax.com/manual/structure_superimpose.html structure.superimpose user function] - this allows for the superimposition of structures assuming a pivoted motion.
 <section end=changes/>
@@ Line 98: / Line 98: @@
 *  Fixes for the Dasha system test for the [https://gna.org/bugs/?19332 bug #19332] fix.
 *  Fixes for the Dasha use functions for file creation and data extraction - this should now handle relaxation data values of None, and also set the parameter values of deselected spins using the Dasha output files.
-*  Big bugfix for the value.read user function - the wrong spin ID string was being used to set the parameter value so that all spins have the same value set for the parameter ([https://gna.org/bugs/?19332 bug #19332]).
+*  Big bugfix for the [http://www.nmr-relax.com/manual/value_read.html value.read user function] - the wrong spin ID string was being used to set the parameter value so that all spins have the same value set for the parameter ([https://gna.org/bugs/?19332 bug #19332]).
 *  Bug fix for the consistency testing analysis for when relaxation data of None is encountered.
 *  The spin is now deselected if there is really less than three data points, excluding data points of None ([https://gna.org/bugs/?19329 bug #19329]).
 *  Bug fix for the arg_check.is_none() function - the RelaxNoneError was not imported!
-*  Fix for the numbering of the TER record and subsequence HETATM records in the PDB file creation.  The structure.write_pdb user function now creates the correct TER record after the ATOM records, and the HETATM records are renumbered if needed.
+*  Fix for the numbering of the TER record and subsequence HETATM records in the PDB file creation.  The [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] now creates the correct TER record after the ATOM records, and the HETATM records are renumbered if needed.
 *  Bug fix for the compilation of the user manual.  The molecule user function class used the temporary variable i, which was causing the fetch_docstrings script to fail.
 <section end=bugfixes/>