Relax 4.0.3 - Revision history

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

2020-10-08T20:24:10Z

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

Bugman: Added a link to the next version of relax (4.1.0).

2019-02-19T19:36:57Z

Added a link to the next version of relax (4.1.0).

Bugman: Links to the API documentation.

2016-10-29T10:24:20Z

Links to the API documentation.

Bugman: More `tags.`


2016-10-28T19:42:53Z
More <code> tags.

				
				
				
				
				
				← Older revision
				Revision as of 19:42, 28 October 2016
				
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  * Added the MPI version information to the mpi4py information printout.   * Added the MPI version information to the mpi4py information printout.
  * Windows scons C module compilation now defaults to 32-bit.  This is because the default Python downloads are 32-bit.  And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit.  Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do.   * Windows scons C module compilation now defaults to 32-bit.  This is because the default Python downloads are 32-bit.  And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit.  Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do.
− * Added support in the information printout for Windows versions of the 'file' program.  This enables the C modules to be identified as 32 or 64-bit, if the 'file' program is installed. + * Added support in the information printout for Windows versions of the <code>file</code> program.  This enables the C modules to be identified as 32 or 64-bit, if the <code>file</code> program is installed.
  <section end=changes/>   <section end=changes/>



Bugman: Added some  tags.

2016-10-28T19:41:41Z
Added some <code> tags.

				
				
				
				
				
				← Older revision
				Revision as of 19:41, 28 October 2016
				
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  * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
  * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
− * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the {{:I0}} value in the script and system test has been changed from 30 to -30, so that the curves start as negative. + * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the <code>calc.py</code> Python script used to calculate the peak intensities in the <code>test_suite/shared_data/curve_fitting/inversion_recovery/*.list</code> files.  The script and Sparky files have been updated.  And the {{:I0}} value in the script and system test has been changed from 30 to -30, so that the curves start as negative.
  * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.   * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.
  * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].   * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].



Bugman: Another parameter template use.
2016-10-28T19:38:49Z
Another parameter template use.

				
				
				
				
				
				← Older revision
				Revision as of 19:38, 28 October 2016
				
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  * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
  * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
− * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I<sub>0</sub> value in the script and system test has been changed from 30 to -30, so that the curves start as negative. + * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the {{:I0}} value in the script and system test has been changed from 30 to -30, so that the curves start as negative.
  * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.   * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.
  * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].   * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].



Bugman: Converted all parameters to use parameter templates, and all symbols to use wiki markup.
2016-10-28T19:37:06Z
Converted all parameters to use parameter templates, and all symbols to use wiki markup.

				
				
				
				
				
				← Older revision
				Revision as of 19:37, 28 October 2016
				
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  * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
  * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].   * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
− * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative. + * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I<sub>0</sub> value in the script and system test has been changed from 30 to -30, so that the curves start as negative.
  * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.   * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.
  * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].   * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].
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  <section begin=bugfixes/>   <section begin=bugfixes/>
  * Fix for [https://gna.org/bugs/?24723 bug #24723].  This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.  The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix.   * Fix for [https://gna.org/bugs/?24723 bug #24723].  This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.  The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix.
− * Bug fix for the inversion recovery equations [https://gna.org/support/?3345 sr #3345].  The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t). + * Bug fix for the inversion recovery equations [https://gna.org/support/?3345 sr #3345].  The inversion recovery experiment was incorrectly implemented as I(t) = {{:Iinf}} - {{:I0}}e<sup>-{{:R1}}t</sup> whereas it should be I(t) = {{:Iinf}} - ({{:Iinf}} - {{:I0}})e<sup>-{{:R1}}t</sup>.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: Links to all of the relax manual user function pages.
2016-10-28T19:19:38Z
Links to all of the relax manual user function pages.

				
				
				
				
				
				← Older revision
				Revision as of 19:19, 28 October 2016
				
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  <section begin=description/>   <section begin=description/>
− This is a minor feature and bugfix release.  The structure.rmsd user function can now calculate per-atom RMSDs, structure superimposition is now orders of magnitude faster, the relax deployment scripts have been improved and expanded to cover other GNU/Linux systems, OpenMPI system testing scripts have been added, and the relax information printout has been improved.  Bugfixes include that the structure.rmsd user function now correctly calculates the RMSD value, and the inversion recovery relaxation curve-fitting equations are now correct. + This is a minor feature and bugfix release.  The [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function] can now calculate per-atom RMSDs, structure superimposition is now orders of magnitude faster, the relax deployment scripts have been improved and expanded to cover other GNU/Linux systems, OpenMPI system testing scripts have been added, and the relax information printout has been improved.  Bugfixes include that the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function] now correctly calculates the RMSD value, and the inversion recovery relaxation curve-fitting equations are now correct.
  <section end=description/>   <section end=description/>
    
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  <section begin=features/>   <section begin=features/>
− * Per-atom RMSD calculation by the structure.rmsd user function. + * Per-atom RMSD calculation by the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
  * Much faster superimposition of structures.   * Much faster superimposition of structures.
  * More relax deployment scripts for Google Cloud for different GNU/Linux distributions.   * More relax deployment scripts for Google Cloud for different GNU/Linux distributions.
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  <section begin=changes/>   <section begin=changes/>
− * Addition of the atomic boolean argument to the structure.rmsd user function front end.  This will be used to enable the calculation of per-atom RMSDs. + * Addition of the atomic boolean argument to the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function] front end.  This will be used to enable the calculation of per-atom RMSDs.
− * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the structure.rmsd user function. + * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation.  This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
− * Implemented the per-atom RMSD calculation for the structure.rmsd user function. + * Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
  * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative.   * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative.
  * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.   * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.



Bugman: Converted all of the tracker links to wiki format.
2016-10-28T16:02:50Z
Converted all of the tracker links to wiki format.

				
				
				
				
				
				← Older revision
				Revision as of 16:02, 28 October 2016
				
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  * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative.   * Fixes for the Relax_fit.test_inversion_recovery system test.  The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.  The script and Sparky files have been updated.  And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative.
  * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.   * Huge speed up for the superimposition of a large number of structures.  The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object.  This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times.  Therefore selection() method no longer calls validate_models().  This may speed up quite a number of internal structure object methods when large numbers of structures are present.
− * Copying deployment script of Ubuntu to a Fedora version.  This is a response to bug #25084 (https://gna.org/bugs/?25084). + * Copying deployment script of Ubuntu to a Fedora version.  This is a response to [https://gna.org/bugs/?25084 bug #25084].
  * Moving fedora to redhat.  Google Cloud does not offer fedora images.   * Moving fedora to redhat.  Google Cloud does not offer fedora images.
  * Adding deploy script for RHEL 6.   * Adding deploy script for RHEL 6.
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  <section begin=bugfixes/>   <section begin=bugfixes/>
− * Fix for bug #24723 (https://gna.org/bugs/?24723).  This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.  The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix. + * Fix for [https://gna.org/bugs/?24723 bug #24723].  This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.  The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix.
− * Bug fix for the inversion recovery equations (sr #3345).  The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t). + * Bug fix for the inversion recovery equations [https://gna.org/support/?3345 sr #3345].  The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: /* Bugfixes */ Copied the bugfix list from the CHANGES file.
2016-10-28T15:53:46Z
Bugfixes:  Copied the bugfix list from the CHANGES file.

				
				
				
				
				
				← Older revision
				Revision as of 15:53, 28 October 2016
				
Line 81:
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  <section begin=bugfixes/>   <section begin=bugfixes/>
  + * Fix for bug #24723 (https://gna.org/bugs/?24723).  This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.  The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix.
  + * Bug fix for the inversion recovery equations (sr #3345).  The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
  <section end=bugfixes/>   <section end=bugfixes/>

@@ Line 92: / Line 92: @@
 * [http://wiki.nmr-relax.com/Relax_4.0.3 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2540 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2540|text=Gna! news item}}.
 * [https://www.mail-archive.com/relax-announce@gna.org/msg00061.html Mail Archive]
 * [https://mail.gna.org/public/relax-announce/2016-10/msg00000.html Local archives].

@@ Line 4: / Line 4: @@
 | version  = 4.0.3
 | prev     = 4.0.2
 | keywords = Fast superimposition, Google Cloud deployment scripts, OpenMPI, per-atom RMSDs
 | type     = Minor feature and bugfix

← Older revision		Revision as of 15:53, 28 October 2016
Line 81:		Line 81:

	<section begin=bugfixes/>		<section begin=bugfixes/>
		+	* Fix for bug #24723 (https://gna.org/bugs/?24723). This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean. The quadratic mean and quadratic standard deviation are now correctly calculated, and the structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi system tests have been updated for the fix.
		+	* Bug fix for the inversion recovery equations (sr #3345). The inversion recovery experiment was incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
	<section end=bugfixes/>		<section end=bugfixes/>

Relax 4.0.3 - Revision history

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

Bugman: Added a link to the next version of relax (4.1.0).

Bugman: Links to the API documentation.

Bugman: More tags.

Bugman: Added some tags.

Bugman: Another parameter template use.

Bugman: Converted all parameters to use parameter templates, and all symbols to use wiki markup.

Bugman: Links to all of the relax manual user function pages.

Bugman: Converted all of the tracker links to wiki format.

Bugman: /* Bugfixes */ Copied the bugfix list from the CHANGES file.

Bugman: More `tags.`

Bugman: Added some `tags.`