relax releases

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This is a collection of all of the full release notes for each released relax version.

Contents

Version 5 of relax

relax 5.0 series

relax 5.0.0

Description

This is a major feature release that adds initial support for wxPython-Phoenix. It includes a large number of under the hood changes to support more modern Python versions and packages, a lot of polish of the relax text output, improved test suite control, and improved and modernised Travis CI support for automatically checking the integrity of the software.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 5.0.0
(24 August 2020, from master)
https://sourceforge.net/p/nmr-relax/code/ci/5.0.0/tree/


Features
  • Support for wxPython-Phoenix.
  • Bmrblib: This Python package is now once again optional and relax can run without it.
  • MS Windows builds are now 64-bit by default.
  • Major improvements to relax text output.


Changes
  • TestSuite: Skipped tests are no longer run when individual tests are supplied on the command line. The RelaxTestLoader.loadTestsFromNames() method has been implemented to gracefully handle the skipping of tests when only a single test is run.
  • Travis CI config: Fixes for PyPI numpy no longer being compatible with Python 2.7. Older versions of numpy now need to be manually specified for the Python 2.7 job.
  • Travis CI config: Attempt at making the MS Windows build job run again. The Travis CI infrastructure has changed yet again and the Windows job fails in the setup stage. These changes are just a guess to try to make this work again.
  • Travis CI config: 2nd attempt at making the MS Windows build job run again. Chocolatey was automatically installing the new Python 3.8.0 but the paths pointed to the 3.7 version. Now the 3.7.4 Python version is explicitly specified.
  • SCons: Change for the MS Windows build architecture from the default of 32-bit to 64-bit. Previously the default was 32-bit compilation on all Windows systems, via the WIN_TARGET_OVERRIDE flag, as official Python never used to release 64-bit builds for Windows systems. As this is no longer the case, the 32-bit override is now only set for the old Python 2 versions.
  • Travis CI config: Creation of a job for testing relax on an arm64 CPU. The system Python and its packages are used to avoid timeouts on arm64. Installing the Python packages via pip prior to running causes a Travis CI time out, as most of the 50 minutes allowed are used up by the compilation of SciPy. Despite the successful installation of the wxPython site-package on the system Python3, the GUI tests are not activated as there is a problem with xvfb on the arm64 Travis CI jobs.
  • N_state_model.test_populations system test: Loosened two of the checks to allow arm64 to pass.
  • wxPython: Added the dep_check.old_wx flag for differentiating between Classic and Phoenix.
  • wxPython-Phoenix: Fix for the wx.BoxSizer.AddSpacer() function calls. The old wxPython conversion of the size argument to (size, size) breaks the layout, so that the tuple arguments are essential. However tuple arguments are not allowed in wxPython-Phoenix. Therefore the dep_check.old_wx flag is used to differentiate the behaviour of the different wxPythons.
  • wxPython-Phoenix: Fix for the old wx.Sizer.DeleteWindows() method. This method no longer exists, so instead the Clear() method with the deleteWindows argument (or delete_windows in Phoenix) is used instead.
  • wxPython-Phoenix: Fix for the missing wx.SystemSettings_GetMetric() function. This has been switched to wx.SystemSettings.GetMetric() which is present in the original wxPython and Phoenix.
  • wxPython-Phoenix: Fixes for the relax gui About dialog. The wx.Frame.Center() function call only works if the window is shown (i.e. it is broken in the test suite), and the wx.DC.EndDrawing() function has been dropped in Phoenix.
  • wxPython-Phoenix: Fixes for the GUI sequence and file input elements. The wx.Frame.Center() function call only works if the window is shown (i.e. it is broken in the test suite).
  • wxPython-Phoenix: Support for the splash screen. The wx.SplashScreen and associated variables have shifted into wx.adv.
  • wxPython-Phoenix: Support for the relax icon. The wx.IconBundle.AddIconFromFile() function have been replaced by wx.IconBundle.AddIcon() in the current phoenix.
  • wxPython-Phoenix: Fix for the spin viewer window. The wx.Window.GetClientSizeTuple() function does not exist in Phoenix. However this can simply be replaced by wx.Window.GetClientSize() in the current code.
  • Deletion hack: The wx.Bitmap.HasAlpha() function is missing in current phoenix.
  • relax GUI: Fix for the window icons.
  • wxPython-Phoenix: Switch away from the depreciated wx.Menu.AppendItem() function. Classic still requires the calls to this function, but phoenix now uses wx.Menu.Append() instead.
  • wxPython: Renamed the dep_check.old_wx flag to dep_check.wx_classic.
  • wxPython-Phoenix: Prominent feedback warning the user about using unstable Phoenix versions. This includes both a RelaxWarning on start up and placing the warning text in red in the center of the blank relax GUI main window. Currently all Phoenix versions are labelled as unstable, however this can be changed in the future directly in the dep_check module.
  • wxPython-Phoenix: Switch away from the depreciated wx.ToolBar.AddLabelTool() function. This is still used for "Classic". For Phoenix, the wx.ToolBar.AddTool() function is used instead.
  • wxPython-Phoenix: Switch away from the depreciated wx.Window.SetToolTipString() function. Instead wx.Window.SetToolTip(wx.ToolTip(text)) is used for both "Classic" and Phoenix.
  • wxPython-Phoenix: Switch from wx.NamedColour() to wx.Colour() in the relax controller. "Classic" still uses the old function.
  • wxPython-Phoenix: Switch from the depreciated wx.Text.GetSizeTuple() to wx.Text.GetSize(). This seems to work on "Classic" as well.
  • wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.GetItemPyData() function. "Classic" is still using this function, but Phoenix is now using wx.TreeCtrl.GetItemData().
  • wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.SetDimensions() function. Instead SetSize() is now being used for Phoenix.
  • wxPython-Phoenix: Switch from the depreciated wx.TreeCtrl.SetPyData() function. "Classic" is still using this function, but Phoenix is now using wx.TreeCtrl.SetItemData().
  • wxPython-Phoenix: Switch from the depreciated wx.StockCursor() wrapper function. The overloaded wx.Cursor class can be used instead in Phoenix.
  • wxPython-Phoenix: Switch from the depreciated wx.EmptyBitmap() wrapper function. Instead Phoenix versions can simply use the overloaded wx.Bitmap class with the same arguments.
  • wxPython-Phoenix: Switch from wrapper to overloaded functions for the wx.ListCtrl elements.
  • Python 3.8 support: The platform.linux_distibution() function no longer exists. This is now replaced by the distro site-package. The lib.compat package deals with this difference.
  • Model-free analysis: Obscure syntax error bug fix for an issue highlighted by Python 3.8. The error in the set_xh_vect() function. This is only encountered when reading an ancient relax 1.2 model-free results file.
  • Travis CI config: Changes as suggested by the experimental Travis CI Build Config Explorer. The config text was pasted into https://config.travis-ci.com/explore and changed as suggested.
  • Travis CI config: Shifted the OpenMPI required packages into an apt addons section.
  • Travis CI config: Shifted the API doc build specific parts into the jobs matrix. This allows an environmental variable to be removed and a simplification of the script section.
  • Travis CI config: Shifted the FSF copyright validation specific parts into the jobs matrix. This allows an environmental variable to be removed and a simplification of the script section.
  • Travis CI config: Removal of the now unused TEST environmental variable.
  • Travis CI config: Simplification of the single processor and OpenMPI execution. The MPIRUN and RELAX_ARGS arguments have been introduced. These are normally unset but, for the OpenMPI jobs, they are set to mpirun -np 2 and --multi=mpi4py respectively. This allows the duplicated entries for the information printout and test suite execution to be collapsed into one.
  • Travis CI config: Removal of the pip upgraded package job. This job does not seem to be necessary for testing relax.
  • Travis CI config: Conversion of the Ubuntu Xenial job to Ubuntu Bionic.
  • Travis CI config: Removal of the language key in the jobs matrix when the value is python. This is a duplication as the language is set to Python outside of the matrix.
  • Multi-processor: Shifted the processor type checking into the initial command line parsing. This allows a non-zero error code to be returned to the shell.
  • Travis CI config: Shifted the echoing of environmental vars into a new before_script section. This allows the echoing to occur for all jobs.
  • Scons: Improvements to the string formatting and the printout for the C module compilation. This includes showing the target architecture for MS Windows compilation.
  • Scons: Document the environmental variables used.
  • Information printout: Improved output for Python3 compiled C modules. The bytesteam is now decoded.
  • Scons: The MS Windows binary target architecture is now determined by the Python binary arch.
  • Test suite: Implementation of a command line option for disabling IO capture. This was previously handled by using the debug command line option which simply prevented IO capture. This type of output is very hard to parse by eye, as the tests are not well separated and the debugging output is very verbose. Now the --no-capt or --no-capture option has been implement to disable the IO capture. The debug command line option no longer disables IO capture, rather it allows for finer control of the test suite in that verbose debugging output is now only shown for tests that do not pass. When IO capture is disabled, extra formatted output is used to provide clear separators, titles, descriptions and endings for each test.
  • Test suite: Argument reordering and better docstring documentation in the relax test suite runners.
  • Test suite: All adjustable widths are now set using the value of status.text_width. This include the separators for the tests and the test suite summary lines at the end.
  • Fix for Python 2.5 support.
  • Command line processing: Switch from the depreciated optparse Python module to argparse. The argument parsing code and help text has also been improved.
  • Travis CI config: Added the relax --test and --version modes.
  • Travis CI config: Alphabetical ordering of the environmental variable printouts.
  • Help: Improvements to the help printout, including new descriptions for the argument groups.
  • Status object: Improved logic for determining the ideal text width for relax.
  • Travis CI config: Added testing of the relax --help mode.
  • Test suite: Added text wrapping set to the relax text width for the test description. This is the description shown when running without IO capture.
  • Information printout: Improved formatting for MS Windows. The repr() function results in \\ for path separators rather than \, causing the formatting to be out.
  • Test suite: Addition of a new command line option for listing all of the test names. The new --list-tests option will cause the names of the tests to be printed out and not run any tests.
  • Travis CI config: Try to force a Py2 compatible version of kiwisolver, as needed by matplotlib.
  • Travis CI config: The virtual machines with Python2 now seem to require SCons be manually installed.
  • Test suite: Fixes for the Palmer.test_palmer_omp system test. The modelfree4 binary type linux-x86_64-gcc seems to now produce slightly different results with newer system libraries. The checks in this test have been updated to reflect this.


Bugfixes
  • GUI: Bug fix for the deletion of analysis tabs on Python 3. The value of None cannot be compared to an integer. This bug appears to only be triggered by another bug - a GUI tearDown() or deletion failure on MS Windows with wxPython-Phoenix and Python 3.
  • Bug fix: Restoration of the simple user function menus.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


Version 4 of relax

relax 4.1 series

relax 4.1.3

Description

This is a minor bugfix release that re-enables the reading of Bruker Dynamics Center NOE data files.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.1.3
(14 June 2019, from master)
https://sourceforge.net/p/nmr-relax/code/ci/4.1.3/tree/


Features

N/A


Changes
  • FSF Copyright Validation configuration: Blacklisted the PDF user manual. This allows the checking of relax tags to pass.
  • Release checklist document: Describe the relax fork of latex2html.
  • API manual: No longer raise errors when parsing the pystarlib docstrings.
  • Release checklist document: Minor improvements to match the practical aspects of the release.
  • User manual: Proper abbreviation of the "Quarterly Reviews of Biophysics" journal name.
  • Test suite: New system test to catch the failure of reading newer Bruker DC NOE data files. The system test is Bruker.test_bug_15_NOE_read_fail and it catches bug #15. The test uses truncated data from Stefano Ciurli as attached to the bug report.
  • Bruker DC: Silence the warnings about spin names already existing. The user does not need to see such warnings.
  • Travis CI config: Explicitly set trusty as the distribution name for the default images. In the support request titled Failure of GUI testing via xvfb, the Travis CI support staff suggested that we explicitly set dist: trusty.
  • Bruker DC: A different way to silence the warnings about spin names already existing. The previous attempt at setting the force flag to True was causing failures in a number of system tests. Therefore a new flag warn_flag has been added to pipe_control.mol_res_spin.name_spin() to allow warnings to be explicitly silenced.
  • Travis CI config: Use Xenial for running all tests on Linux and Python 2.7. This is from the support request titled Failure of GUI testing via xvfb.
  • Travis CI config: Manual support for old SciPy versions on Python 2.7. SciPy 1.3.0 now requires Python ≥ 3.5. Therefore the OLD_MATPLOTLIB variable has been renamed to OLD_PY2_PACKAGES and, when set, is now used to install old matplotlib and scipy versions when using Python 2.7.
  • Travis CI config: Deactivate the Mac OS X updates to avoid timeouts. The brew update and brew upgrade python3 take up half of the build time for the Mac OS X target. This large amount of time sometimes causes this build to hit the Travis CI time limits.


Bugfixes
  • Bruker DC: Support for handling newer versions of the NOE data file. This fixes bug #15, the failure to read newer versions of the Bruker DC NOE data files. This was simply a parsing issue as the NOE column is now NOE [ ] whereas previous DC versions used the text NOE or NOE [none].


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.1.2

Description

This is a minor feature and bugfix release. It includes tooltip improvements in the GUI for the user function windows and wizards, the addition of the newly published primary reference for the frame order analysis, and improved formatting for the bibliography and index of the relax manual.

There have also been improvements for the automated testing of relax by Travis CI. This includes the naming of the build jobs, the execution of the software verification tests, the installation of wxPython to enable GUI testing and the running of the whole test suite, the reordering of the system tests back before the unit tests to avoid hiding some nasty relaxation dispersion bugs, a fix for matplotlib on Mac OS X so that the tests will finally run on this OS, a new build job for the API documentation, and a new build job for the Free Software Foundation copyright validation script.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.1.2
(25 April 2019, from master)
https://sourceforge.net/p/nmr-relax/code/ci/4.1.2/tree/


Features
  • relax GUI: Improved tooltips for the buttons of the user function windows and wizards. This follows from the mailing list discussion.
  • User manual: Addition of the newly published frame order reference.
  • Formatting improvements for the user manual bibliography and index sections.


Changes
  • Development scripts: Improvements to the Python detection in the Python module seeking script.
  • Release checklist document: Updated the text to better match the new release process.
  • HTML manual: CSS fix for newer LaTeX2HTML versions. The text width in the HTML appears to now be fixed to a maximum width matching the text dimensions in the PDF. This looks bad together with the wider images and code snippets.
  • System tests: Added two tests to catch bug #12, the failure to catch the '#' character when setting the molecule name. The tests are Structure.test_bug_12_hash_in_mol_name_via_arg and Structure.test_bug_12_hash_in_mol_name_via_file. These cover the two ways a # character can enter a molecule name - via the file name or via the set_mol_name argument. Both the structure.read_pdb and structure.read_xyz user functions are checked.
  • Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files. The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch bug #13.
  • User function definitions: Clarifications for the bruker.read text.
  • User manual: Clean up of the bibliography entry titles. Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, R1ρ, R2, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.
  • User manual: Standardisation of the frame order indexing.
  • User manual: Standardisation of the relaxation dispersion indexing.
  • Travis CI config: Attempt at installing wxPython for Ubuntu and Python 2.7. This would allow for the whole test suite to be run on Travis CI on at least one OS. The instructions come from the stackoverflow response by dthor.
  • FSF Copyright Validation script: The script now returns an exit status.
  • Travis CI config: Avoid updating Conda. This seems to cause a breakage in installing matplotlib.
  • Travis CI: matplotlib is now manually installed to allow for older versions on Python 2.7. The current pip default of 3.0.3 is incompatible with Python 2.7. It is not clear how the installation of Conda (for wxPython support) caused the 3.0.3 version to be installed instead of the 2.2.4 version. So now the version is manually set in the Travis CI script.
  • Travis CI config: Enable xvfb to allow for wxPython and testing of the GUI.
  • Test suite: Restored the original test suite order to reveal relaxation dispersion bugs. The system tests should come first. This allows the maximum amount of code that might accidentally change read-only variables to run prior to the unit tests, where such changes are often subsequently picked up.
  • Test suite: The keyboard interrupt terminates the test suite once again.
  • FSF Copyright Validation script: The return status now starts at 0 to allow for early returns.
  • FSF Copyright Validation script: Support for saving and reading the committer information. This allows the committer information (file name, committer name, and copyright years) from older repositories to be saved and later read into the script. In this case, the old Subversion history has been read and the committer information placed into the fsfcv.svn_committer_info.bz2 file (in the devel_scripts/ directory). This compressed file is now specified in the fsfcv.conf.py configuration file. The result is that the fsfcv script can be run on the relax git repository without requiring a checkout of the old SVN repository.
  • Travis CI config: Improvements to the comments and spacing.
  • API manual: Scons compilation via epydoc now fails if a warning or error is found. This manually parses the epydoc output to skip the unavoidable wxPython warnings. Any error or warning will now cause an error to be raised. This results in a non-zero return code from scons to allow the api_manual_html target to be checked in scripts.
  • Travis CI config: Named all of the jobs.
  • Travis CI config: General clean up and execution of the software verification tests.
  • API manual: Scons compilation via epydoc now fails if an import error occurs.
  • Travis CI config: Alphabetical ordering of environmental variables and required Python packages.
  • Travis CI config: Creation of an API documentation build job.
  • Travis CI config: Fix for the Mac OS X build. This job passes, but the test suite fails with the following traceback message when trying to import matplotlib: "ImportError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.". The fix is simply to create $HOME/.matplotlib/matplotlibrc with the contents backend: TkAgg.
  • API manual: Greater filtering of the file list passed to epydoc. Now only relax modules ending in *.py are processed. That means that all base directory scripts, including sconstruct, are excluded from the API documentation.
  • API manual: More reliable parsing of the epydoc output to detect non-wxPython issues.
  • FSF Copyright Validation configuration: Improvements to the repository configuration section. The different configurations can now be chosen via a variable, rather than requiring code to be uncommented.
  • FSF Copyright Validation script: Sorted the years for the committer information output. This makes it easier to read the file and will help with compression.
  • FSF Copyright Validation script: A new file with all committer information up to 2018. This is to allow for much faster execution of the FSFCV script, by only looking at the git log from the start of 2019.
  • FSF Copyright Validation script: Support for skipping the first commit. This is for truncated history, where for example the git repository start date is set to a later date than the git repository migration or initial SVN commit, when the committer information up to a given date is read from a file.
  • FSF Copyright Validation script: Fix for tracking renames when saved committer information is used.
  • Travis CI config: Execution of the FSF copyright validation script as part of the testing. This is set to run only on a new Python 3.7 build job, simply to avoid unnecessary repetition. All of the git history needs to be fetched for the script to work, and the script requires the pytz Python module.
  • FSF Copyright Validation script: Addition of a repository configuration printout. This is to help in debugging, as it is otherwise not clear where the source of the copyright information comes from.
  • Release checklist document: Rewrote the 'preparation' instructions for Travis CI. All previous manual checking is now performed automatically by Travis CI for each push to the GitHub mirror repository.


Bugfixes
  • relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again. In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!". This was not present in wxPython-Phoenix 3. The Relax_icons class (a wx.IconBundle derived class) is no longer instantiated on import.
  • Structure loading: Fix for bug #12, the acceptance of the invalid '#' character in molecule names. A simple check has not been added to the load_pdb() and load_xyz() functions of the internal structural object in lib.structure.internal.object. This ensures that the # character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the structure.read_pdb or structure.read_xyz user functions.
  • Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions. This fixes bug #13, the failure of reading newer Bruker DC files. The backend has been resigned so that the relax library produces a complex Python object representation of the Bruker DC results file. This object now stores all of the data present within the Bruker DC file. The design is more flexible as precise column ordering no longer matters.
  • Fix for bug #14, the freezing of user functions in the GUI. The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor. These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter. Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in relax 4.1.0. These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.
  • GUI bug fix: Avoidance of the numpy depreciation of == None. This deprecation causes the GUI to fail with recent numpy versions.
  • Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification. These are now only used with copy.deepcopy(). This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'. The system tests add 'r1' and then the unit tests subsequently fail. This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.
  • Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm. This is the nesting_param() function of the specific_analyses.relax_disp.model module. The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are.
  • Dispersion auto-analysis: Bug fix for the plotting of the R1 parameter. The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of lib.dispersion.variables. Now the Model_class class from specific_analyses.relax_disp.model is being used to dynamically determine the parameters of the model.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.1.1

Description

This is a major bugfix release. The release fixes multiple issues with the relax GUI and with the relaxation dispersion analyses. Please see the notes below for details.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.1.1
(8 March 2019, from master)
https://sourceforge.net/p/nmr-relax/code/ci/4.1.1/tree/


Features
  • N/A.


Changes


Bugfixes
  • Fix for bug #2, the failure of the structure.read_pdb user function in the GUI. The problem was that the file selection argument was being set up incorrectly as two GUI elements - an inactive file selection element and a normal value setting GUI element. Only the second value input GUI element was active (due to the GUI elements being stored in a dictionary, with the first key value being overwritten by the second).
  • Fix for bug #3, the absence of user function argument validation within the GUI. The code for the user function argument validation in the prompt/script UIs was simply copied and slightly modified to fit into the GUI user function window execution. All arguments are now passed into the new lib.arg_check.validate_arg() function and are checked based on their user function definitions.
  • Fix for bug #4, the relax controller in the GUI not displaying text when required. Calls to the captured IO stream flush() methods are now been made in a number of places to allow the controller to show the text when required. This includes after printing out the intro text, after any captured and GUI handled errors, after clicking on the help→licence menu entry, after thread exceptions, and after a number of GUI message dialogs. The bug is only present in relax 4.1.0.
  • Typo fix in the description of the 'atomic' argument for the structure.rmsd user function.
  • Fix for bug #5, the incorrect numpy version check in the relaxation dispersion auto-analysis. The dep_check.version_comparison() function is now used for the version comparisons.
  • Dispersion: Fix for bug #7, the model list containing 'No Rex' twice. The MODEL_LIST_FULL variable contained the model 'No Rex' twice. The only manifestation of the bug is a RelaxError message showing the full list of models, when a user selects a non-existent dispersion model.
  • Dispersion: Fix for bug #6, the incorrect parameter counting for 3-site models with spin clustering. The issue was that the list of spin-specific parameters was incomplete. To resolve this, the parameter names have been shifted into the lib.dispersion.variables module lists PARAMS_R1, PARAMS_GLOBAL, and PARAMS_SPIN. By removing the parameter names from other parts of relax, the lib.dispersion.variables module will serve as a single point of failure and hence it will much easier to maintain the relaxation dispersion code when new models with new parameters are added.
  • Dispersion: Fix for bug #8, the accidental modification of the hardcoded variables. The MODEL_PARAMS lists in lib.dispersion.variables were accidentally being modified by the Model_class class in the specific_analyses.relax_disp.model module. The list for a given model was being set as the self.params list. This list would then have the 'r1' parameter pre-pended to it if that parameter is optimised for a model, and hence the lib.dispersion.variables list would be permanently modified. Now copy.deepcopy() is being used for all variables to avoid this issue. This bug was uncovered in the unit tests as the _specific_analyses._relax_disp.test_model tests were causing 'r1' to be added, and then the later _specific_analyses._relax_disp.test_parameters tests would fail as 'r1' should not be in those lists. This bug is highly unlikely to be encountered by users of relax. You would need to run two analyses, one after the other without closing relax, and the first analysis would need to have R1 optimised and the second not.
  • Dispersion: Fix for bug #9, the failure of the 3-site dispersion models when pB and pC are zero. When both are zero, for example during a comprehensive grid search when model nesting is not utilised, a divide by zero error occurs. This is now caught and large values (1e100) are set for the rates instead.
  • Dispersion: Fix for bug #11, the missing pC calculation for the 3-site R1ρ models. The models 'NS R1rho 3-site' and 'NS R1rho 3-site linear' were simply missing from the list of models for the pC parameter.
  • Dispersion: Fix for bug #10, the 3-site model failure of setting pC for Monte Carlo simulations. For this, the sim_init_values() function of the relaxation dispersion specific API has been completely rewritten. The specific_analyses.relax_disp.parameters.param_conversion() function is now called at the start to generate initial non-model parameters, and at the end to populate the simulation structures. The rest of the function has been stripped down and significantly simplified.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.1.0

Description

This is a major feature and bugfix release. This is also the first release after the permanent Gna! shutdown and the complete migration of relax's free software infrastructure to SourceForge, the first release after the complicated migration from the original Subversion version control repository to git for the relax source code and the relax website, and the first release after three years of development. In the meantime, a new demo repository has been created containing all the data and instructions required to perform and demonstrate different relax analyses.

Features of this release include the addition of a bash completion script, large speed improvements in the GUI and in the execution of many relax user functions, improved sample scripts, significant relax manual updates, support for newer NMRPipe SeriesTab files, improved Docker images, automated testing of relax via Travis-CI, the new user functions frame_order.decompose, structure.add_helix, and structure.add_sheet, and significant improvements for user function argument checking and user feedback via RelaxErrors.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.1.0
(14 February 2019, from master)
https://sourceforge.net/p/nmr-relax/code/ci/4.1.0/tree/


Features
  • Greater wxPython-Phoenix support while maintaining compatibility with wxPython-Classic.
  • Creation of a bash completion script for completing command line arguments with the tab key (docs/bash_completion.sh).
  • A significantly more responsive relax GUI.
  • Converted the steady-state NOE analysis sample script to use the auto-analysis.
  • Standardisation of initial and final printouts in the auto-analyses, including the elapsed time.
  • More of the GUI main menu entries are disabled during execution locking.
  • Safe execution of all of the auto-analyses.
  • Huge speed ups for many parts of relax with the addition of fast and temporary hash lookup tables and cross-referencing for the molecule, residue, spin and interatomic data containers.
  • Many improvements and updates throughout the relax manual.
  • Support for the new format of the NMRPipe SeriesTab files.
  • Improvements for the Docker container scripts and documentation in devel_scripts/Docker/.
  • Automated testing of relax via Travis-CI.
  • New frame_order.decompose user function for a new representation of the frame order analysis results.
  • Addition of the new user functions structure.add_helix and structure.add_sheet for manually defining secondary structure.
  • Speed up of the 'fit to first' algorithm in the structure.superimpose user function.
  • Significant improvements to the checking of arguments passed into user functions, and the resultant error messages for invalid arguments.
  • Improvements and fixes for the RelaxError messages to better explain user errors.
  • A large number of updates for the switch from the Subversion version control repository to git, and the move from the closed Gna! infrastructure to SourceForge.


Changes
  • Removal of the Mac OS X taskbar icon functionality. This code has been disabled since its deletion back in Jun 2012, as it does not work with wxPython 2.8 or 2.9. However with wxPython Phoenix, the disabled code fails as there is no wx.TaskBarIcon.
  • Keyword to positional argument conversion for the GUI wx.ListCtrl.SetStringItem() function calls. The keyword arguments for this function must exist for backwards compatibility with ancient wxPython versions. The current documentation lists them as positional arguments, and keyword arguments are not accepted by wxPython-Phoenix.
  • Keyword to positional argument conversion for the GUI wx.ScrolledWindow.EnableScrolling() calls. These function calls were using keyword arguments, however the old wxPython and Phoenix documentation say that these are not keyword arguments (this must have been for backwards compatibility with very old wxPython versions).
  • Keyword to positional argument conversion for a GUI wx.BoxSizer.Clear() call. This is for the spin containers in the spin viewer window. The keyword argument in wxPython classic is deleteWindows however in Phoenix it is delete_windows.
  • Decreased the precision of a check in the Rx.test_r1_analysis GUI test. This is to allow the test to pass on wxPython-Phoenix and Python 3.
  • Keyword to positional argument conversion for the GUI wx.Font() calls. A number of these were being called with keyword arguments, however the old wxPython and Phoenix documentation say that these are not keyword arguments (this must have been for backwards compatibility with very old wxPython versions).
  • Replacement of a wx.ListCtrl.DeleteAllColumns() function call from the spectrum GUI element. This function does not exist in wxPython-Phoenix. Instead the columns are looped over and wx.ListCtrl.DeleteColumn() is called instead.
  • Creation of an initial bash script for enabling bash completion.
  • Improvements for the bash completion relax script. Directories and relax scripts are now much better handled.
  • Fine tuning of the bash completion relax script. The option -o nospace for complete has been removed as spaces are not added for directories anyway. This means that a space is added after all options and scripts.
  • More precision decreases in the Rx.test_r1_analysis GUI test. This is to allow the test to pass on wxPython-Phoenix and Python 3.
  • Updates to the upload section of the release checklist document for sending files to SourceForge.
  • Added release instructions for creating the README.rst files for the download area. This is for using the custom html2rest to automatically generate the reStructuredText file from the wiki release notes.
  • Expanded the release checklist instructions for creating the README.rst files.
  • Updates to many frame order test suite shared data relax scripts. These scripts are used for data generation and display, and are not part of the test suite. The updates are for the frame_order.pdb_model and pymol.frame_order user functions which no longer support the dist keyword argument (this functionality was shifted into the frame_order.simulate user function).
  • First commit after the svn to git migration: Created a .gitignore file for the new git repository.
  • Documented the svn to git repository migration. All of the scripts used and detailed instructions have been included.
  • Standardisation of the section titles in a number of the documentation files.
  • The files auto-generated during the PDF user manual compilation are now ignored by git.
  • Git support for the repository version information. This is used in the relax introductory text, the manual compilation, and in the relax save states. The version.repo_revision variable has been renamed to version.repo_head to be repository type independent. For the repository URL, all of the git remotes are included.
  • C module blacklisting of the Relax_disp.test_bug_24601_r2eff_missing_data system test. The test is skipped if the C modules are not compiled.
  • Added .pyc and .so files to be ignored.
  • Fix for dep_check, when packages has an appended release candidate number. For example: numpy 1.8.0rc1.
  • Added a script to check for copyright notice compliance to the FSF standard.
  • Support for multiple git and svn repositories in the FSF copyright notice compliance checking script.
  • Collection of all commits to attribute to other authors. This is for the FSF copyright notice compliance checking script.
  • Collection of all commits to exclude by the FSF copyright notice compliance checking script.
  • FSF compliant copyright notices for all files in the documentation directory docs/devel/. This includes two README files with the copyright notices for all of the patches.
  • FSF compliant copyright notices for all files in the documentation directory docs/latex/. This includes a README file with the copyright notices for the binary graphics.
  • FSF compliant copyright notices for all files in the documentation directory docs/html/. This includes a README file with the copyright notices for latex2html-2008 icons. The copyright notice script has been updated to handle false negatives (significant git commits without copyright ownership), and additional copyrights not present in the git log.
  • FSF compliant copyright notices for all remaining files in the documentation directory.
  • Added the original oxygen icon AUTHORS and COPYING files and standardised the README file titles. The AUTHORS and COPYING files from the original svn repository svn://anonsvn.kde.org/home/kde/trunk/kdesupport/oxygen-icon have been added to the repository for better documentation of the copyright. The README file had also been updated with the origin information.
  • FSF compliant copyright notices for the entirety of the graphics/ directory.
  • FSF compliant copyright notices for the extern/ directory. The packages within this directory are skipped in the devel_scripts/copyright_notices.py copyright compliance checking script.
  • Update to FSF compliant copyright notices for all modules in the auto_analyses package.
  • Update to FSF compliant copyright notices for all modules in the data_store package.
  • FSF compliant copyright notices for the entirety of the devel_scripts/ directory.
  • Update to FSF compliant copyright notices for all modules in the gui package.
  • Update to FSF compliant copyright notices for all modules in the lib package.
  • Update to FSF compliant copyright notices for all modules in the multi package.
  • Update to FSF compliant copyright notices for all modules in the pipe_control package.
  • Update to FSF compliant copyright notices for all modules in the prompt package.
  • Update to FSF compliant copyright notices for all scripts in the sample_scripts/ directory.
  • Update to FSF compliant copyright notices for all modules in the scons package.
  • Update to FSF compliant copyright notices for all modules in the specific_analyses package.
  • Update to FSF compliant copyright notices for all modules in the target_functions package.
  • Update to FSF compliant copyright notices for all modules in the user_functions package.
  • Update to FSF compliant copyright notices for all modules and files in the base relax directory.
  • Update to FSF compliant copyright notices for all unit test modules.
  • Module docstring standardisation for the system test scripts.
  • Update to FSF compliant copyright notices for all system test modules and scripts.
  • Update to FSF compliant copyright notices for all verification test modules.
  • Update to FSF compliant copyright notices for all GUI test modules.
  • Update to FSF compliant copyright notices for the base test suite modules.
  • Support for automated copyright notice placement in README files. This is directly within the FSF copyright notice compliance checking script.
  • Update to FSF compliant copyright notices for all scripts in the test_suite/shared_data/ directory.
  • Self exclusion of the FSF compliant copyright notice commits.
  • Cosmetic change for the test___all__() unit test base class method. The files are now sorted.
  • Blacklisted missing files are now skipped in the test___all__() unit test base class method. This allows for the test_suite.unit_tests._target_functions.test___init__.Test___init__() unit test to pass when the relaxation curve-fitting C modules are not compiled.
  • Changed the relax state file name for the state.save user function calls in the sample scripts. This is to make it clearer what the files are. The old *save.bz2 notation has been removed and the files are now generally called state.bz2.
  • Update to FSF compliant copyright notices for the external Sobol package. An explicit README file has been added to clarify the copyright status of all files.
  • Added a trivial relax script to help regenerate the pec_diag.eps diagram.
  • Added the base Xmgrace data file for the generation of the NOE data plot. This is for regenerating graphics/screenshots/noe_analysis/grace.svg. The copyright notice checking script has been updated for this old 2004 file.
  • Changed a number of references to "Linux" to "GNU/Linux".
  • Replaced all references to "open source" in the manual with "free software".
  • Removed the ancient CIA.vc references in the development chapter of the manual.
  • Added a README file for the extern/numdifftools package. This is taken from the VC log and explains the origin, version, and licensing of the package.
  • Added the base Xmgrace data file for the generation of the R2 peak intensity data plot. This is for regenerating graphics/screenshots/xmgrace_peak_intensities.svg. The copyright notice checking script has been updated for this old 2004 file.
  • Copyright notice updates for the graphics/misc/relaxGUI_splash* files.
  • Fixes for the FSF copyright notice compliance checking script.
  • Update to FSF compliant copyright notices for the external numdifftools package. Explicit README files have been added to clarify the copyright status of all files.
  • Removal of the numdifftools extern package, as this can be easily installed in Python using pip.
  • Support for Grace-formatted units in the specific analysis parameter object. This is currently used by the relaxation curve-fitting analysis for the Rx parameters.
  • Created the Relax_fit.test_auto_analysis_pipe_name system test to catch a missing RelaxNoPipeError. This is to catch the error NameError: global name 'RelaxNoPipeError' is not defined.
  • Conversion of the relaxation curve-fitting sample script to use the auto-analysis.
  • Improved documentation for the DIFF_MODEL variable in the dauvergne_protocol.py sample script. The fact that it can be supplied as a list is now mentioned in the script docstring, and the default value is now a list with all of the global models.
  • Support for NMR proton pseudo-atom identification from PDB files in the internal structural object. The standard pseudo-atoms are now identified as being protons.
  • Removed a duplicated proton frequency check in the relax_data.read user function. This resulted duplicated RelaxWarnings being printed out.
  • Huge improvement for the responsiveness of the relax GUI. The relax controller window log panel was being updated with a wx.CallAfter() call after every write to the IO streams. If a relax analysis was proceeding very quickly, which is the case in most analyses, this created a huge backlog of GUI updates. The result was that the GUI would freeze, running at 100% CPU usage in its own thread, with the analysis running at 100% on another thread. The fix was to shift the log panel write() call to be triggered by the Timer already being used by the gauges, rather than by the IO stream write() methods. The text was already placed on a Queue object, so this change is very simple. Another small change was made to the log panel write() method to avoid a number of unneeded wx calls. This should also have a significant impact on the GUI updating.
  • Saved state file name change for the steady-state NOE and relaxation curve-fitting auto-analyses. The names are now simply state.bz2. This is so the file is easier to identify as being a relax state file that can be loaded with the state.load user function.
  • The relaxation curve-fitting sample script now timestamps the data pipe bundle name.
  • Redesign of Troels' grace2images.py script. The executable script creation has been shifted from the relaxation curve-fitting auto-analysis (auto_analyses.relax_fit) into the new function lib.plotting.grace.create_grace2images(). This is now also used by the steady-state NOE auto-analysis. The content of the script has also been shifted into the lib.plotting.grace.GRACE2IMAGES variable to allow for easier code editing. The grace2images.py script itself has been heavily modified: The script now uses Python3 by default; The depreciated optparse module has been changed to argparse; A copyright notice has been placed at the top of the script; The top comment has been converted into a docstring; The default format is now EPS rather than PNG, as PNG is often not supported as an output device; Bug fix in that all formats can now be created (supplying JPG previously did nothing); General code and comment cleanups.
  • The FSF copyright notice compliance checking script is no longer dependent on relax. The relevant lib.io relax module functions have been copied into the script, and modified with the assumptions of Python 3 only compatibility and less flexible input.
  • The relax status singleton now stores the time it was created as the program starting time. This is to allow for elapsed time calculations, which will be used in the auto-analyses for more detailed printouts.
  • Creation of the lib.timing.print_elapsed_time() function. This prints out an elapsed time value in day, hour, minute, and second format. A number of unit tests have been added to check the handling of different time values, including plurals.
  • Standardisation of initial and final printouts in the auto-analyses, including the elapsed time. The main auto-analyses now use lib.sectioning.title() for marking the start and the end of the analysis. And after the final title() printout, the lib.timing.print_elapsed_time() function is called to provide user feedback to how long relax had been running for.
  • Creation of the Relax_disp.test_bug_missing_replicates GUI test. This is to catch an Attribute error when the replicated spectra are specified via the spectrum list GUI element rather than the peak intensity loading wizard.
  • More of the GUI main menu entries are disabled during execution locking. This includes all of the Tools menu entries to block the free file format from changing mid-execution, the system information user function from being called, and the test suite from being run. The BMRB export menu entry is also disabled.
  • Safe execution of all of the auto-analyses (those that acquire the execution lock). The whole of the __init__() code of the auto-analyses is now wrapped within a try-finally set of statements. This is to be absolutely sure that the execution lock is released. This is not always the case, for example the Relax_fit.test_auto_analysis_pipe_name system test was not releasing the lock due to a RelaxError, and this was causing the later GUI tests to fail.
  • Updated the Rx.test_r1_analysis GUI test for the changed state file name in the auto-analysis.
  • Fix for the FSF copyright notice compliance checking script for lib/plotting/grace.py. The copyright notices within the grace2images.py script in the module variable are now ignored. This additionally required removing duplicate copyright notices as both the module and embedded script have "Copyright (C) 2013 Troels E. Linnet".
  • Unique and temporary hash support in the spin containers. These private data structures will allow for fast SpinContainer to InteratomContainer and reverse lookups. The hash is temporary and only created when a SpinContainer is created. It is not stored, so it is regenerated between relax sessions.
  • Unique and temporary hash support in the interatomic data containers. The interatomic data containers now have a unique and temporary private hash assigned to it, just as with the spin containers. They also now have the ability to store the unique spin container hashes. This is currently unused but will allow for fast SpinContainer to InteratomContainer and reverse lookups.
  • The interatomic data containers now store the SpinContainer hashes.
  • The InteratomContainer._hash value is now stored in the spin containers it refers to.
  • Bmrb system test fixes for the new SpinContainer private hash data structures. These structures are now blacklisted in the data pipe comparisons.
  • Speed up for the pipe_control.interatomic.define() function. The create_interatom() function will now accept the two spin containers as arguments. As the define() function already has these, they are now passed in avoid two calls to the pipe_control.mol_res_spin.return_spin() function.
  • Creation of the pipe_control.interatomic.hash_update() function. This is used when copying interatomic data containers (the pipe_control.interatomic.copy() function) to make sure that the spin hashes in the receiving data pipe are stored in the new interatomic data container.
  • Converted all pipe_control.mol_res_spin.return_spin() function calls to use keyword arguments. This is in preparation for adding support for the temporary spin hashes. The pipe_control.mol_res_spin module return_spin_from_selection() and return_spin_from_index() function calls have also been updated, just in case.
  • Support for a spin hash fast lookup table for the molecule, residue and spin data structures. The fast lookup table is stored as dp.mol._spin_hash_lookup. This matches the dp.mol._spin_id_lookup fast lookup table, but is a simpler table to maintain as there is only one hash ever per spin and that hash is unique. The table is maintained by the pipe_control.mol_res_spin module.
  • Conversion of all return_spin() calls with interatom spin IDs to use the spin_hash argument instead. This should slightly speed up the spin lookups.
  • Improved the formatting of the interatomic data container list to help with debugging. The data is now presented with the format_table() function of the lib.text.table module.
  • Data container hash cross-reference recreation. This is used by the model_selection, pipe.copy, results.read and state.load user functions. The cross referencing recreation is for both spin containers and interatomic data containers. The old pipe_control.mol_res_spin.metadata_update() and new pipe_control.interatomic.metadata_update() functions are called after the loading a results or state file, or a data pipe copy, so that the data structures properly cross-reference each other's hashes.
  • Huge speed up of the interatomic data container handling. The pipe_control.interatomic.create_interatom(), return_interatom(), and return_interatom_list() functions now operate with the unique spin hashes rather than spin IDs. This avoids the expensive calls to the now deleted pipe_control.interatomic.id_match() function.
  • Fixes for the copying of spin or interatomic data containers. The data_store.prototype methods Prototype.__clone__() and Prototype.__deepcopy__() will now regenerate the unique hash if a _generate_hash() function is present. This function has been added to SpinContainer and InteratomContainer.
  • Changed the spin ID printout for the rdc.read user function to be the unique ID rather than file ID. This is to help with debugging.
  • Bug fix for the N_state_model.test_CaM_IQ_tensor_fit system test. Some of the RDC data contained RDCs between two @N spins rather than an @N and @H spin. This bug was only uncovered by the switch to the spin and interatomic data container hashes for fast lookups.
  • Fix for the data store _back_compat_hook() method when creating interatomic data containers. The pipe_control.interatomic module define() function has been renamed to define_dipole_pair() for clarity and it now accepts two spin containers as arguments, overriding the spin ID arguments. This fixes the State.test_old_state_loading GUI test that was failing after the conversion to spin and interatomic data container hashes for fast lookups.
  • Printout fix for the check_read_results_1_3() method of the Mf system tests.
  • The interatomic_loop() function now uses the spin hash fast lookup table rather than spin IDs.
  • Redesign of the create_spin() function of the pipe_control.mol_res_spin module. This function is the backend of the spin.create user function and is also used throughout relax. Instead of creating a single residue or spin, if only a name and not number is supplied, now multiple spins are created. If the residue name is supplied but not the residue number, now all residues matching the given name will have new spins created. For example creating the spin with the name 'NE1' and only specifying the residue name 'TRP', then all tryptophans in all molecules will have NE1 indole side-chain spins created. This makes the operation of the spin.create user function more logical for the user.
  • Support for catching segfaults and other errors from Modelfree4. This allows for non-silent exiting from the Popen() class. All signals are now reported via RelaxErrors.
  • Added the text of the LGPLv3 licence to the extern.sobol package.
  • Added FSF recommended LGPLv3 licence notices to the top of all of the extern.sobol files. Excluded is the auto-generated test output file.
  • Renamed the LGPLv3 file in the extern.sobol package to COPYING.LESSER.
  • Updated all of the minfx project links from Gna! to the SourceForge site.
  • Updated all of the relax deployment scripts for the Gna! shutdown. These now use the SourceForge sites for relax, minfx, and bmrblib instead. The svn to git conversion is also taken into account, and git is used to pull in the latest relax code from the SourceForge mirror.
  • Converted a large number of Gna! links to point to the equivalent Web Archive URL. Most of these links should have had a snapshot made in the Internet Archive Wayback Machine.
  • Added some hyperlinks to the external programs listed in the intro chapter of the user manual.
  • Added the relaxation dispersion software support to the intro interfacing section.
  • The prompt UI is no longer referenced as the 'primary' interface in the intro chapter of the manual.
  • Added relaxation dispersion to the GUI features in the intro chapter.
  • Added relaxation dispersion to the list of all data pipe types in the intro chapter.
  • Improvements to the script UI text in the intro chapter.
  • Linked to the internal Gna! mailing list archives for the multi-processor announcement.
  • Added new sections to the infrastructure and development chapters about the Gna! shutdown. This is to warn that the information in these chapters of the manual is out of date.
  • Updated the NESSY link to point to the new SourceForge location for the project.
  • Changed the relax PDF manual link from Gna! to SourceForge for the HTML manual footers. This is in the latex2html configuration file so that the automatically created HTML manual pages point to a valid location.
  • Changed the relax PDF manual link from Gna! to SourceForge for the HTML manual headers. This is in the LaTeX header, so that the automatically created HTML manual pages point to a valid location.
  • Converted Gna! mail archive links in the manual to point to the copies at http://www.nmr-relax.com.
  • Rewrote the core design of relax development section of the relax manual. The code design figure has also been updated. All of the content was still written for the relax 1.3 releases.
  • Removed the dead Freshmeat/Freecode and Gmane text from the development chapter of the manual.
  • Copyright notice and FSF compliant copyright notice script updates.
  • Renamed the FSF Copyright Validator script to the acronym fsfcv.
  • Split the FSF Copyright Validation script into a configuration file and an executable script. The configuration part of the script has been retained but with all data stripped to be able to provide a blank template for a new configuration file. And the new mimetypes section has been converted into a variable rather than manipulating the mimetypes Python module so that the configuration script requires no Python imports.
  • Converted the whole FSF copyright notice validation script code into a class. This is in preparation for a number of major changes to the script.
  • The FSF copyright notice validation script now uses the argparse Python module. This is for more powerful command line argument processing. The new --blank-config option will now print out the blank configuration file, and the DEBUG variable has been replaced with the -d or --debug command line option.
  • Improved the documentation of the fsfcv configuration file.
  • Implementation of the configuration file parsing. This uses modern Python import mechanisms to load the blank config first for default values, followed by the user supplied configuration file.
  • Implemented the verbosity argument so per-file messages are only printed when activated.
  • The FSF Copyright Validation script will now add the current directory repository if not supplied. This allows the script to be executed without a configuration file.
  • New command line option for the FSF copyright validation script to only check for missing notices. This will only print out files with missing copyright notices. Files marked as valid may nevertheless have incorrect notices.
  • The capitalisation of "Copyright (C)" no longer matters for the FSF Copyright Validation script. This is for the copyright notices within the file. The configuration file has been updated for the lower case copyright notices (false positives).
  • Reactivated the user supplied binary mimetypes for the FSF Copyright Validation script.
  • More robust reading of copyright notices from binary files in the FSF Copyright Validation script. The reading of the text file will now return and empty list if a UnicodeDecodeError occurs.
  • Updated the fsfcv configuration file for the fsfcv script and configuration file itself.
  • Fixes for the extern/numpy_future.py copyright notices.
  • Support for multiple additional years in the FSF Copyright Validation script.
  • Added a progress meter, a simple spinner, to the FSF Copyright Validation script. This is taken directly from lib.text.progress, and the output is sent to STDERR. All other script output is now sent to STDOUT. It is only active if the verbose flag is off.
  • Separated the missing copyright notices from non-valid copyright notices in the fsfcv script. These are now counted separately and a different message printed out for the missing notice case.
  • Support added to the fsfcv script for handling content not within a version control repository. The untracked and non-valid copyright counting is turned off in this case.
  • Improved the feedback from the progress meter in the fsfcv script. This now says what the numbers are, using text such as "X files checked.".
  • Activated the link option for the epydoc API documentation. This allows for the navigation link to point to "/" rather than "http://www.nmr-relax.com". This is for SSL and https:// preparations, so that the http://www.nmr-relax.com part of the URL is not present in the local links.
  • Shifted the epydoc API documentation copyright notice insertion into the scons script. This notice was previously hardcoded into the devel_scripts/google_analytics.js script - as that is the GPLv3+ copyright notice of that script with the date of 2012. Instead the copyright notice in the Google analytics script is now skipped and the correct FDLv1.3 copyright notice with the current year programmatically inserted via the scons/manuals.py script.
  • Adding new format of NMRPipe SeriesTab which give errors.
  • Added the Relax_disp.test_bug_seriestab_format system test to check for the new format of NMRPipe SeriesTab.
  • Changes to lib.spectrum.nmrpipe to handle NMRPipe SeriesTab, when assignment has not been performed. Auto detecting the multiplier column.
  • Fixing for allowing renaming of SeriesTab spectrum ID.
  • Fix for help section in grace2images.py file. It was unclear how to get different types of images.
  • Extended the Relax_disp.test_bug_seriestab_format system test to include reading of several SeriesTab files, and selecting intensity column.
  • Modified lib.spectrum.nmrpipe in read_seriestab() to allow for selecting intensity column.
  • Allow for int_col to be a list to make a proper warning.
  • Initial try for running a Docker image with gedit. This is an attempt to try running OpenDX later.
  • Simplification of Dockerfile.
  • Removing dockerfile for gedit.
  • Adding a Dockerfile, which makes it easy to build an Ubuntu image and Launch OpenDX. This is very useful on a Mac.
  • If the current directory is mounted to home, then dx.map files is working.
  • Improved the help to settings in XQuartz when running Docker on a mac and accessing the OpenDX GUI.
  • Renamed the extern.sobol.sobol_lib-not_tested module to sobol_lib_untested. This is in preparation for updating to the newest upstream code.
  • Updated the extern.sobol package to the latest upstream code. This is the new MIT licensed code (which was previously LGPL licensed). The licence text has been modified to suit the licence change, and the LGPL copyright notices dropped from all files. The Python 3 updates to the relax version of the package have been transferred into the new code.
  • Added the MIT licence with copyright notices to the top of all files. The origin of all code was traced back through the MATLAB sources, FORTRAN90 sources, and FORTRAN77 sources. The original f77 code did not contain any shared lines of code with the f90 code, so no copyright statements for Bennett Fox were added. Comments were added to each function to document the history of all of the code.
  • Easier reading of the Dockerfile.
  • Extended the help section of running a Docker container, so now it is also possible to run a bash session in the container.
  • Fix for deploy script of relax to ubuntu. The version variables was wrongly set.
  • When running Docker with OpenDX, the current working directory is now mounted on $HOME/work instead of $HOME.
  • Made the Ultimate Docker file, which package relax and OpenDX together in one Dockerfile. Everything can now be packed together. This makes it an ultimate opportunity to easily ship the relax Docker image to run 'everywhere' easily.
  • Letting the default intensity column of SeriesTab be 'VOL'. This is the column SeriesTab uses. The 'HEIGHT' column is copied in from the nmrDraw test.tab file, and does not represent the measurement.
  • Fixes to sconstruct, when building with Python 3 and SCons. The current sconstruct caused an SyntaxError: invalid syntax when using ` in the file.
  • Fixes to sconstruct, when cleaning with Python 3 and SCons. This fix is to print the list represented.
  • Removed the Oxygen Icon directory from the skipped directory list of the fsfcv script.
  • Added copyright notices for every Oxygen Icon.
  • Small fix for the FSF Copyright Validation script (fsfcv).
  • Capitalised the copyright symbol in the Sobol' external library copyright notices. This is for easier handling by the FSF Copyright Validation script.
  • Fixes for the fsfcv script configuration for the Sobol' external package.
  • The alternative committer names are now better handled in the fsfcv script. The committer's names in the VC logs are now also translated from the alternative to the standard name.
  • Correct spelling of Troels Schwarz-Linnet in the copyright notices.
  • Troels' name is now handled differently in the fsfcv script configuration file. The text "Troels E. Linnet" is now the alternative name, and "Troels Schwarz-Linnet" the standard name.
  • MS Windows support for the FSF Copyright Validation script.
  • Cut and paste error fix for the Oxygen Icon licensing text in the README files. As stated in the COPYING file, the licence is LGPLv3+, not GPLv3+.
  • Updated the general relax copyright notice for 2018. This last copyright year is now stored as info.copyright_final_year.
  • Clarified the GPLv3+ licensing in the relax introduction string.
  • Manual: Addition of a GPLv3+ copyright notice to a second title page.
  • Another Oxygen Icon licensing text fix in the README files.
  • Improved the LGPLv3+ licensing text for the base directory of the Oxygen Icons.
  • Manual: Added the LGPLv3+ copyright notice for the Oxygen Icons to the second title page.
  • Documentation for the copyright and public domain notices for 3D structures. This is to explain why the strict format text files are not modified to include notices, hence they are placed in the README file, and detailing the public domain nature of the Protein Data Bank repository.
  • Updated the script for Docker images.
  • Adding Dockerfile for Ubuntu 18.04 LTS and development on Windows.
  • Fix for comparison of arrays to None. The use of x == None should be x is None.
  • Initial commit of travis-ci.
  • Setting sys.exit(1) in dep_check, to make Travis-ci fail the build on error.
  • Travis CI: Adding minfx to pip requirements file.
  • Travis CI: Fixing path to minfx for pip to install.
  • Travis CI: Adding PYTHON_INCLUDE_DIR.
  • Travis CI: Fix for getting Python.h.
  • Travis CI: Again trying to fix export variable to find Python.h.
  • Travis CI: Adding debug echo of path to Python.h.
  • Travis CI: Moving export to .travis.yml.
  • Travis CI: Adding unit test to travis.
  • Travis CI: Fix for executing relax from current folder.
  • Travis CI: Removing scons, since it should already be part of Compilers & Build toolchain in Trusty images.
  • Travis CI: Adding print of relax information.
  • Travis CI: Adding more packages to pip requirements.
  • Travis CI: Better reading of tests performed.
  • Travis CI config: Adding additional Python version to Travis and cleaning up.
  • Travis CI config: Adding Python 2.6 and 3.5 to the test matrix.
  • Travis CI config: Specific testing for Python 2.6.
  • Travis CI config: Trying to get pip conf file.
  • Travis CI config: Trying to add svwh.dl.sourceforge.net to trusted pip.
  • Travis CI config: Adding importlib for Python 2.6.
  • Travis CI config: Trying to add subprocess for Python 2.6.
  • Travis CI: Removed matplotlib from Python 2.6.
  • Travis CI: Remove test of Python 2.6.
  • Renamed README file to markdown.
  • Added travis build shield to README.
  • Adding system-tests to be executed with travis.
  • Creation of a large set of system tests for implementing the frame_order.decompose user function. The tests have been copied from Frame_order.test_distribute_* and include: Frame_order.test_decompose_free_rotor_z_axis, Frame_order.test_decompose_iso_cone_z_axis, Frame_order.test_decompose_iso_cone_xz_plane_tilt, Frame_order.test_decompose_iso_cone_free_rotor_z_axis, Frame_order.test_decompose_iso_cone_torsionless_z_axis, Frame_order.test_decompose_pseudo_ellipse_xz_plane_tilt, Frame_order.test_decompose_pseudo_ellipse_z_axis, Frame_order.test_decompose_pseudo_ellipse_free_rotor_z_axis, Frame_order.test_decompose_pseudo_ellipse_torsionless_z_axis, Frame_order.test_decompose_rotor_z_axis.
  • Creation of the frame_order.decompose user function front end.
  • Implementation of the frame_order.decompose user function backend.
  • Scons: Fixes for the manual compilation. The relax manual cannot be compiled if one of the sys.path values contains a docs/ directory. Instead of appending the relax docs/ path to sys.path, it is now prepended. The documentation Python module __all__ lists have also been filled out.
  • Renamed the relax default repository version from "repository checkout" to "repository commit". This general text is more appropriate for a git repository.
  • Manual: Removed a Gna! reference in the intro chapter.
  • Manual: Alias creation for the relax mailing lists. This is to allow for a centralised place for changing the mailing list name, if any changes occur to the mailing list in the future.
  • Manual, Ch. Infrastructure: Converted the Gna! shutdown note into a new 'History' section. A lot of the relax free software/open source infrastructure history is now documented.
  • Manual, Ch. Infrastructure: Removed the Gna! information from the relax website section.
  • Manual, Ch. Infrastructure: Updated the relax mailing list information from Gna! to SourceForge. This is now all through LaTeX aliases, so infrastructure changes should be easier to deal with in the future.
  • Manual, Ch. Infrastructure: Abstracted the bug reporting section using aliasing. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.
  • Manual, Ch. Infrastructure: Abstract the relax repository section and switch from svn to git. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.
  • Manual, Ch. Infrastructure: Removal of the news section, as this is not supported on SourceForge.
  • Manual, Ch. Infrastructure: Abstract the distribution archive section and switch from svn to git. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.
  • Manual, Ch. Installation: Abstraction of the bug tracker links. This replaces the dead Gna! links to the current SourceForge links.
  • Manual, Ch. N-state model: Abstraction of the relax-users mailing list.
  • Manual, Ch. Dispersion: Dead link and mailing list fixes. The mailing lists are now abstracted using aliases, some old dead links have been removed, and some Gna! support request links have been converted to Internet Archive links.
  • Manual, Ch. Development: Removal of the note about the Gna! shutdown. The chapter is about to be updated for the switch to SourceForge, so this note is no longer needed.
  • Manual, Ch. Development: Aliases for the mailing lists and addition of a cross reference.
  • Manual, Ch. Development: Converted the version control section from SVN to git.
  • Manual, Ch. Development: Minor edits to the coding conventions section.
  • Adding exit codes for the unit and system tests. This is for Travis to fail if these fail. In Windows these can be seen with: echo Exit Code is %errorlevel%
  • Manual, Ch. Development: Removal of the section describing creating and submitting patches.
  • Manual, Ch. Development: Section rearrangement in preparation for new text.
  • Manual, Ch. Development: svn to git and infrastructure abstraction in the Committers section. All references to svn have been changed to git. And the Gna! infrastructure has been abstracted to aliases in the main relax.tex file so that future infrastructure changes are easier to deal with. In addition, many edits of the text have been made.
  • Manual, Ch. Development: Expansion of the relax repository section.
  • Manual, Ch. Development: Minor edits to the relax repository git mirror section.
  • Manual, Ch. Development: Editing of the source code repository section.
  • Manual, Ch. Development: Added links to the web interfaces for all relax mirror sites.
  • Fixing the return value of execution of unit and system tests.
  • Manual, Ch. Development: New subsection and editing of the relax repository section. An initial section describing git version control and listing all relax repositories has been added.
  • Manual, Ch. Infrastructure: Updated the relax repository section to include the website and demo.
  • Manual, Ch. Development: Complete rewrite of the 'Submitting changes to the relax project' section. This converts the Subversion instructions to git, and switches from Gna! to the aliased primary relax infrastructure.
  • Manual, Ch. Development: Converted the SCons section from SVN to git, and removed Gna! references.
  • Manual, Ch. Development: Major editing of the 'Core design of relax' section. This section is now significantly improved. There was a lot of old information, some dating back to the pre-relax 3.0 designs. And a lot of new information has been added to expand on all of the descriptions.
  • Manual, Ch. Development: Minor editing of the tracker section.
  • Manual, Ch. Development: Updated the very out of date links section. This was incredibly out of date. The links have been updated to include everything listed at http://www.nmr-relax.com/links.html.
  • Manual, Index: Removed the no longer relevant svnmerge.py entry.
  • Simplify Travis file.
  • Added travis-ci support for Python 3.7 and OSX. Adding notifications from builds att travis-ci.com to nmr-relax-devel att lists.sourceforge.net. This is after inspiration from https://github.com/WeblateOrg/translation-finder/blob/master/.travis.yml. Windows can not be added due to unknown compile error.
  • Fixing a bug for running scons. This happens after a pip install -U numpy, where numpy is upgraded from 13.3 to 16.1.0. More to read here: https://docs.scipy.org/doc/numpy-1.15.0/reference/generated/numpy.set_printoptions.html; https://stackoverflow.com/questions/1987694/how-to-print-the-full-numpy-array; https://github.com/numpy/numpy/pull/12353.
  • Fix for building on Mac OSX Python 3.7. A possible solution was found here: https://stackoverflow.com/questions/31019854/typeerror-cant-use-a-string-pattern-on-a-bytes-like-object-in-re-findall.
  • Adding sending mails to nmr-relax-devel att lists.sourceforge.net. This introduces a spamming problem. Everyone who forks this project and have travis setup for their user will spam the develop mailing list. To limit this, there are options in travis: https://docs.travis-ci.com/user/notifications/; https://docs.travis-ci.com/user/conditional-builds-stages-jobs. Introducing a condition like if: branch = master seems not to be implemented yet: https://github.com/travis-ci/travis-ci/issues/1405. Travis has internal ticket to track this feature request.
  • SCons: Git support for the scons distribution targets. This was previously only set up for Subversion.
  • FSF Copyright Validation script: Support for tracking files renamed in later repositories. In this case, a file rename in the current git repository would not allow the file to be found in the SVN archive repository. The history of the later repository is now used to find all file renames after the end of the earlier repository. False git history is also correctly handled.
  • FSF Copyright Validation script: Bug fixes for recording the first VC commit as copyright ownership.
  • FSF Copyright Validation configuration: Updates for recent files and the script bug fixes. A lot false git history needed to be identified and blocked. And a lot of README files added for copyright identification needed to be manually included.
  • Python multiversion test suite script: Added Python 3.6 and 3.7 to the list to test.
  • Travis CI config: Minimise mailing list messages with successes only reported after fixing failures.
  • Test suite: Fix for the running of multiple test suite categories. Now all test categories will be run and the execution will not be terminated at the end of the category containing the first error/failure.
  • Activating MS Windows Python 3.7 32-bit for travis (64 bit does not work). Adding travis option for upgrading pip packages in one of the builds. This is to try to have pip packages where the versions numbers are normal/average and then where the packages have been upgraded to the newest. Adding check for Python 3.6, since this is the standard version in Ubuntu 16.04 and 18.04.
  • Added Python as overall language to travis.
  • System tests: Relax_disp.test_paul_schanda_nov_2015 is now skipped when Scipy is missing.
  • Devel scripts: Improved logic for finding Python.h in the manual C module building script.
  • SCons: Improved logic for finding Python.h for building the C modules.
  • Python multiversion test suite script: Removal of Python 2.3 and 2.4. These Python versions have not been supported since the first usage of from __future__ import absolute_import back in 2013.
  • Test suite: Graceful failure of the GUI tests when the wx app cannot be setup. This currently occurs when using wxPython-Phoenix.
  • Travis CI config: Adding Python 3.6 and adding test of mpirun.
  • .gitignore: Ignoring Windows C extensions.
  • Travis CI config: Trying to add MPI for Windows. It does not seem to work.
  • Travis CI config: Trying MPI on Windows does not work: The processor type 'mpi4py' is not supported.
  • GUI: Fix for a wxPython 2.9 issue found via the Relax_disp.test_bug_missing_replicates GUI test. The spectrum ID wx.ListCtrl element cannot be queried for item 0 when empty.
  • Development scripts: Rewrote the python_seek.py script to report all import errors.
  • Creation of a large set of system tests for expanding the frame_order.decompose user function. The tests have been copied from Frame_order.test_decompose_* and modified to include the new total, reverse, and mirror user function keywords. The tests include: Frame_order.test_decompose2_free_rotor_z_axis, Frame_order.test_decompose2_iso_cone_z_axis, Frame_order.test_decompose2_iso_cone_xz_plane_tilt, Frame_order.test_decompose2_iso_cone_free_rotor_z_axis, Frame_order.test_decompose2_iso_cone_torsionless_z_axis, Frame_order.test_decompose2_pseudo_ellipse_xz_plane_tilt, Frame_order.test_decompose2_pseudo_ellipse_z_axis, Frame_order.test_decompose2_pseudo_ellipse_free_rotor_z_axis, Frame_order.test_decompose2_pseudo_ellipse_torsionless_z_axis, Frame_order.test_decompose2_rotor_z_axis
  • User function frame_order.decompose: Implementation of the total, reverse and mirror params. This allows a fixed number of structures to be generated over the distribution, for the model order to be reversed, and for the models to step from the negative angle to positive angle and then return to the negative angle. The original code has been simplified by switching from numpy.arange() to numpy.linspace() for generating the range of angles. This function is far more reliable than arange() which has end point instability issues.
  • Creation of the Test_object.test_add_model unit test. This is within the _lib._structure._internal.test_object test module. The aim is to reveal issues with the model number accounting within the internal structural object.
  • System test: Addition of Structure.test_add_secondary_structure. This will be used to quickly implement the new structure.add_helix and structure.add_sheet user functions.
  • User function: Implementation of structure.add_helix for defining alpha helices.
  • User function: Implementation of structure.add_sheet for defining beta sheets.
  • Library: Implementation of the lib.arg_check.is_bool_or_bool_list() function. This is to allow for either Boolean values or lists of Booleans.
  • User functions: Registration of the bool_or_bool_list argument type.
  • User function frame_order.decompose: The argument reverse can now be a list of Booleans. This allows different modes to be selectively reversed.
  • User function structure.superimpose: Speed up of the 'fit to first' algorithm. The translation and rotation are now skipped for the first structure (as the translation is zero and the rotation matrix is the identity matrix).
  • User function structure.superimpose: Improved the documentation of the models arg.
  • RelaxErrors: Implementation of a number of new error types. This includes the RelaxBoolListBoolError, RelaxNoneBoolError, RelaxNoneBoolListBoolError, and RelaxNoneTupleNumError objects.
  • Unit tests: Complete checking of the lib.arg_check module.
  • lib.arg_check module: Missing RelaxError import for the new is_bool_or_bool_list() function. The lib.error import statement has also been spread across multiple lines and alphabetically sorted.
  • lib.arg_check module: Protection of the functions against future numpy depreciations. The code arg == None will not be supported by numpy in the future, if the arg being checked is a numpy object. Instead the arg is None syntax must be used.
  • RelaxErrors: Bug fix for the error message generation for list types. The simple_types and list_types variables are class rather than instance variables, but these were being unintentionally modified by the BaseArgError base class __init__() method.
  • lib.compat module: Implementation of the Python version independent from_iterable() function. This will be used to avoid directly using itertools.chain.from_iterable(), which was only introduced in Python 2.6 and later. For Python ≥ 2.6, the itertools.chain.from_iterable() function is used, otherwise the roughly equivalent lib.compat.from_iterable_pre_2_6() function is used.
  • lib.arg_check module: Redesign of the is_float_object() function to handle any data input. Previously the function could only handle max rank-2 Python lists (lists of lists), and max rank-2 numpy arrays. And only the first dimensionality was being checked. Now any rank list or numpy array is correctly handled.
  • lib.arg_check module: Addition of the can_be_none argument to the is_bool() function.
  • lib.arg_check module: Documentation fixes for the is_*() functions.
  • lib.arg_check module: Fix for the wrong RelaxErrors being used in the is_num_tuple() function.
  • lib.arg_check module: Fix for missing RelaxError imports for the is_list() function.
  • lib.arg_check module: Bug fix, Boolean or empty lists no longer evaluate as true in is_num_tuple().
  • lib.arg_check module: Bug fix, Boolean or empty lists no longer evaluate as true in is_num_list().
  • lib.arg_check module: Simplification of the is_list() function.
  • lib.arg_check module: Fixes to and simplification of the is_int_list() function. Boolean lists no longer evaluate as true.
  • RelaxErrors: Addition of more error objects in preparation for a new lib.arg_check function.
  • RelaxErrors: Expansion of the functionality of the BaseArgError base class. The docstring now documents the arguments. The dim and rank arguments have been added to allow for more control over the reported message for array-type objects. And the can_be_none argument has been added to append ', or None' to the message, negating the need for the RelaxNone*Error objects. For formatting the lists used in the BaseArgError class, the new function human_readable_list() has been added to the lib.text.string module.
  • lib.arg_check module: Creation of the generic validate_arg() function. A large number of associated unit tests have been added to test all combinations. The _lib.test_arg_check unit tests include: Test_arg_check.test_validate_arg_all_basic_types, Test_arg_check.test_validate_arg_all_basic_types_and_all_containers, Test_arg_check.test_validate_arg_all_containers, Test_arg_check.test_validate_arg_bool, Test_arg_check.test_validate_arg_bool_list, Test_arg_check.test_validate_arg_bool_list_rank2, Test_arg_check.test_validate_arg_bool_or_bool_list, Test_arg_check.test_validate_arg_float, Test_arg_check.test_validate_arg_float_list, Test_arg_check.test_validate_arg_float_list_rank2, Test_arg_check.test_validate_arg_float_or_float_list, Test_arg_check.test_validate_arg_func, Test_arg_check.test_validate_arg_int, Test_arg_check.test_validate_arg_int_list, Test_arg_check.test_validate_arg_int_list_rank2, Test_arg_check.test_validate_arg_int_or_int_list, Test_arg_check.test_validate_arg_list, Test_arg_check.test_validate_arg_list_or_numpy_array, Test_arg_check.test_validate_arg_number, Test_arg_check.test_validate_arg_number_array_rank1, Test_arg_check.test_validate_arg_number_array_rank2, Test_arg_check.test_validate_arg_number_array_rank3, Test_arg_check.test_validate_arg_number_list, Test_arg_check.test_validate_arg_number_list_rank2, Test_arg_check.test_validate_arg_number_list_rank3, Test_arg_check.test_validate_arg_number_numpy_array_rank1, Test_arg_check.test_validate_arg_number_numpy_array_rank2, Test_arg_check.test_validate_arg_number_numpy_array_rank3, Test_arg_check.test_validate_arg_number_or_number_tuple, Test_arg_check.test_validate_arg_number_tuple, Test_arg_check.test_validate_arg_number_tuple_rank2, Test_arg_check.test_validate_arg_number_tuple_rank3, Test_arg_check.test_validate_arg_numpy_float_array, Test_arg_check.test_validate_arg_numpy_float_matrix, Test_arg_check.test_validate_arg_numpy_float_rank3, Test_arg_check.test_validate_arg_numpy_int_array, Test_arg_check.test_validate_arg_numpy_int_matrix, Test_arg_check.test_validate_arg_numpy_int_rank3, Test_arg_check.test_validate_arg_str, Test_arg_check.test_validate_arg_str_list, Test_arg_check.test_validate_arg_str_list_rank2, Test_arg_check.test_validate_arg_str_or_file_object, Test_arg_check.test_validate_arg_str_or_str_list, Test_arg_check.test_validate_arg_tuple.
  • lib.arg_check module: Fixes for handling empty numpy arrays. This is for the is_float_array() and is_float_matrix() functions.
  • lib.arg_check module: Removal of the is_list_val_or_list_of_list_val() function. This was never completely implemented, and was only used by the point argument of the dx.map user function. The user function py_type "list_val_or_list_of_list_val" value has been renamed to 'num_list_or_num_list_of_lists' and the call to is_list_val_or_list_of_list_val() replaced by a call to validate_arg(). The dim argument for the point argument of the dx.map user function has been modified to match the validate_arg() function syntax.
  • User function definition redesign, increasing the argument setting flexibility. The py_type argument definition has been replaced by basic_types, container_types, and sometimes dim. This matches the new validate_arg() function in the lib.arg_check module and allows for far greater flexibility in defining a parameter together with more extensive parameter checking than previously possible.
  • specific_analyses.consistency_tests.api module: Missing RelaxWarning import.
  • User function definitions: Support for checking file lists (from arg_type='file sel multi'). The new RelaxStrFileListStrFileError object has been created for this check (and the RelaxStrListError also added for completeness).
  • User function definitions: Overrides for arguments with arg_type set. The arg_type argument is now fully documented in the user_functions.objects module Uf_container.add_keyarg() function docstring. The value is now checked, and a few unimplemented values have been eliminated. Overrides for the dim, basic_types, and container_types are now set for almost all arguments with arg_type set. And checks that these are not set in the user function definition have been added.
  • system.cd user function: Removal of the incorrect wiz_filesel_style argument in the definition.
  • User function definitions: Split of the 'file sel' arg_type value into readable and writable. The arg_type value is now either 'file sel read' or 'file sel write'. The 'file sel multi' value has also been split into 'file sel multi read' and 'file sel multi write'. This is used for checking if file objects supplied to the user function are correctly readable or writable. And it is used in the GUI to automatically set the file selection dialog style. Hence the redundant wiz_filesel_style argument has been removed from the user function definitions. The is_filetype_readable(), is_filetype_rw(), and is_filetype_writable() functions have been added to the lib.check_types module to check the file objects from within the lib.arg_check module validate_arg() function.
  • Test suite: Zero times reported on MS Windows with --time no longer have a negative sign.
  • python_seek.py development script: Added _tkinter to the all list for checking the Python install.
  • Test suite: Unit test times displayed with --time are now in milliseconds.
  • Python tempfile.mktemp(): Converted all usage of the function to tempfile.mkstemp(). The tempfile.mktemp() function was depreciated in Python 2.3. According to the Python documentation: "A historical way to create temporary files was to first generate a file name with the mktemp() function and then create a file using this name. Unfortunately this is not secure, because a different process may create a file with this name in the time between the call to mktemp() and the subsequent attempt to create the file by the first process. The solution is to combine the two steps and create the file immediately. This approach is used by mkstemp() and the other functions described above.". The Travis CI testing system was sometimes failing on files created with mktemp(), so hopefully mkstemp() will alleviate the issue.


Bugfixes
  • Bug fix for the pcs.structural_noise user function. The user function now uses a real multivariate normal distribution for sampling atomic positions. The previous random unit vector + univariate Gaussian sampling does not correctly reproduce the multivariate normal distribution.
  • Python 3 bugfix for the Relax_disp.test_bug_24601_r2eff_missing_data system test. Tab characters rather than spaces made the system test script unloadable in Python 3.
  • Python 3 fixes for the gui.misc module. This is for text formatting using the "x"*num logic. In Python 3, num is often a float so this does not work and an explicit int() function call is required.
  • Python 3 fix for the combo list sequence elements. Comparison of integers to values of None are not allowed.
  • Bug fix for Tools→System information GUI menu item. The user function has been renamed from sys_info to system.sys_info.
  • Python ≥ 3.4 fix by removing an unused types.ListType import.
  • Bug fix allowing for spaces in file paths in the GUI open_file() function. This used by the file preview buttons and the results viewer window.
  • Minor fixes for the relaxation curve-fitting sample script.
  • Another small fix for trp indole 15N spins in the relaxation curve-fitting sample script.
  • Fix for the relaxation curve-fitting auto-analysis for when the data pipe name is incorrect. This was simply a missing import.
  • Bug fix for the relaxation dispersion GUI analysis when specifying replicated spectra. This is for the Attribute error when the replicated spectra are specified via the spectrum list GUI element rather than the peak intensity loading wizard. The GUI test Relax_disp.test_bug_missing_replicates now passes.
  • Bug fix by redesigning the GUI pipe editor pop up menu. The menu now uses IDs to associate menu items with the correct method to call. Previously all menu entries were calling the method of the last menu entry, which was in most cases the pipe switching method. As the pipe deletion method is now properly exposed, the Question dialog was increased in size to be able to see all the text.
  • MS Windows fixes for running relax from git and git-svn repositories. Multiple commands on MS Windows need to be separated by && and not ;.
  • Bug fix: Removal of '\u' escape sequences from the latex_mf_table.py test suite script docstring. This fixes Bug #1 reported on the new SourceForge infrastructure, and allows the script to be used with Python 3.
  • Bug fix for the model number tracking with the addition of new models. If a single model is present without a model number, this is now correctly renumbered.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.0 series

relax 4.0.3

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.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.0.3
(28 October 2016, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.3


Features
  • Per-atom RMSD calculation by the structure.rmsd user function.
  • Much faster superimposition of structures.
  • More relax deployment scripts for Google Cloud for different GNU/Linux distributions.
  • Addition of OpenMPI testing scripts.
  • Improved relax information printout.


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.
  • 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.
  • Implemented the per-atom RMSD calculation for the 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.
  • 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.
  • Moving fedora to redhat. Google Cloud does not offer fedora images.
  • Adding deploy script for RHEL 6.
  • Added initial script for testing OpenMPI.
  • Making a redhat 6 deploy script, which will upgrade Python from 2.6 to 2.7 The normal installation through yum will have Python 2.6 and only numpy 2.4. This is not good.
  • Moved deploy scripts. There would probably have to be a deploy script for each system.
  • Renamed the Ubuntu deploy script.
  • Adding scripts to test OpenMPI installation and deploy in redhat.
  • Change to pip install command, to source Python first.
  • Adding installation of matplotlib to Redhat 6, Python 2.7.
  • More changing to deploy scripts.
  • Small change to deploy script to build wxPython.
  • More changing to deployment scripts.
  • Moving test script of OpenMPI to bash version.
  • Made a copy of OpenMPI test script for tcsh shell.
  • Again small changes to deployment scripts.
  • Changed more to OpenMPI script.
  • Altering test OpenMPI script to an alias function.
  • Change to bash OpenMPI test script.
  • Last changes to testing of OpenMPI.
  • Small change to test OpenMPI script for bash
  • Back to function in bash script for OpenMPI.
  • Made a deployment script for CentOS 6.
  • Scons on CentOS finds python2.6 instead of python2.7
  • Try to make the script for tcsh and OpenMPI working on all versions of tcsh.
  • 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.
  • 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.


Bugfixes
  • Fix for 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) = I∞ - I0e-R1t whereas it should be I(t) = I∞ - (I∞ - I0)e-R1t.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.0.2

Description

This is a minor feature and bugfix release. The new user functions system.cd and system.pwd have been added to allow the working directory to be changed and displayed. The time and sys_info user functions have been renamed to system.time and system.sys_info. The structure.delete_ss user function has been created to remove the helix and sheet information from the internal structural object. For bugs, the R2eff dispersion model can now handle missing peaks in subsets of spectra, and the structure.read_pdb can now handle multiple structures and multiple models with the merge flag set.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.0.2
(13 May 2016, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.2


Features


Changes
  • Improved formatting for the \yes LaTeX command for the HTML manual. This now inputs the raw HTML character for a tick.
  • The replicate title finding script now processes short titles as well. This shows that the Frame_order.html file will be conflicting and overwritten.
  • Avoidance of a replicated title in the frame order chapter of the manual.
  • Added some unicode characters for improved formatting of the CHANGES file.
  • A number of updates for the release checklist document. This should make it easier to replicate the full release process.
  • Update the release checklist document. The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release.
  • Added a check for the total argument for the frame_order.distribute user function. The maximum value is 9999, as the PDB format cannot accept more models.
  • Creation of the structure.delete_ss user function. This simply resets the helices and sheets data structures in the internal structural object to [].
  • Updated the copyright notices for 2016.
  • Created a short Info_box copyright string for displaying in the main GUI window. This shows the full range of copyright dates.
  • Added the spin_num boolean argument to the structure.load_spins user function. Setting this flag to False will cause the spin number information to be ignored when creating the spin containers. This allows for better support of homologous structures but with different PDB atom numbering. The default flag value is True, preserving the old behaviour.
  • Added support for concatenating atomic positions in the structure.load_spins user function. Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering. The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.
  • Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument.
  • In the GUI the user functions sys_info and time are now grouped into a system subclass. This is to prepare for other system related functions.
  • Added a new 16x16 icon for the oxygen folder-favorites icon.
  • Adding a new file at lib.system. This file will contain different functions related to Python os and system related functions. For example changing directory or printing working directory.
  • In lib.__init__, adding the filename for system.py.
  • Renaming the folder-favorites icon.
  • Deleting the old folder-favorites icon.
  • Adding a new graphics variable: WIZARD_OXYGEN_PATH, to use oxygen icons with size of 200px.
  • Adding the new user function system.cd. This is to change the current working directory.
  • Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image.
  • Adding a user function translation for: This is to catch the new naming of these functions.
  • Adding a new lib.system.pwd() function, to print and return the current working directory.
  • Adding a new user function system.pwd to print/display the current working directory.
  • Adding new 16x16 px and 200px of the oxygen icon folder-development. This icon is used for displaying the current working directory.
  • Adding a relax GUI menu for changing the current working directory.
  • Adding a menu item for changing the current working directory.
  • Adding a verbose True/False for the lib.system.pwd() function.
  • Storing the current working directory as a GUI variable.
  • Adding a toolbar button for changing the current working directory.
  • Adding a verbose flag to lib.system.pwd() function.
  • Changing to a filedialog for the user function system.cd.
  • Adding an observer for current working directory.
  • Modifying the user function system.cd not to show the result to STDOUT.
  • Letting the lib.system.cd function notify the observer, when changing directory.
  • Letting the current working directory be printed in the statusbar in the bottom.
  • Updating self.system_cwd_path when a directory change is observed.
  • For the four auto-analysis methods, the default results directory is now the current working directory instead of the launch directory.
  • Changing the keyboard shortcut for changing the working directory to Ctrl+W. Since Ctrl+C is often used for copying (from the terminal).
  • Fix for GUI prompt bug, where ANSI escape characters should not be printed when interpreter is inherited from wxPython.
  • Added a newline character after printing the script.
  • Optimising the width of the statusbar.
  • When the user function script is called, a notification of pipe_alteration is made. This will force the GUI to update, and make sure that it is up to date.
  • Updated the frame order auto-analysis for the time → system.time user function change.
  • Fix for the GUI status bar element widths. Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window. Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.
  • Created a system test for catching bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta. The test uses his data and script to trigger the bug.
  • Simplified the Relax_disp.test_bug_24601_r2eff_missing_data system test. This is to allow the test to catch bug #24601 to complete in a reasonable time (2 seconds on one system).
  • Fix for the independence of the relax library. As lib.system was using the status object, the library independence was broken. To work around this, the module has simply been shifted into the pipe_control package.
  • Added some missing oxygen icons to allow the relax manual to compile. These are the 128x128 EPS versions of the places/folder-development.png and places/folder-favorites.png Oxygen icons recently introduced. For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added. To help create these EPS icons in the future, the graphics/README file has been added with a description of the *.eps.gz file creation.
  • Some more details for the *.eps.gz icon creation process.
  • Mac OS X fixes for the Structure.test_pca and Structure.test_pca_observers system tests. The eigenvectors on this OS are sometimes inverted. As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.0.1

Description

This is a major feature and bugfix release. Features include the new structure.pca user function for performing a principle component analysis (PCA) of a set of structures, handling of replicated R2,eff data points in the dispersion analysis, improvements in the handling of PDB structures, the protection against numpy ≥ 1.9 FutureWarnings for a number of soon to change behaviours in numpy, and addition of a deployment script for the Google Cloud Computing. Bugfixes include an error when loading relaxation data, the CSA constant equation in the manual, missing information in the relax state and results files, loading of certain state files in the GUI, running relax with no graphical display and using matplotlib, BMRB export failure when a spin container is missing data or parameters.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.0.1
(14 December 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.1


Features
  • Many improvements for the compilation of the HTML version of the relax manual.
  • Updated relax to eliminate all FutureWarnings from numpy ≥ 1.9, to future-proof relax against upcoming numpy behaviour changes.
  • Ability to handle replicated R2,eff data points by the relax_disp.r2eff_read user function, but adding 0.001 to the frequency value for the replicated point.
  • A new sample script for loading a model-free results file and back-calculating relaxation data.
  • Improvements for the handling of PDB structural data.
  • Implementation of the structure.pca user function for performing principle component analyses (PCA) of an ensemble of structures.
  • Addition of a script for rapid deployment on the Google Cloud Computing infrastructure.


Changes
  • Fix for the rigid frame order model 2nd degree frame order matrix in the manual. The wrong symbol was being used.
  • Removed the newparagraph and newsubparagraph definitions from the LaTeX manual. These were causing conflicts with latex2html, preventing the HTML version of the manual from being compiled. These definitions are unnecessary for the current set up of the sectioning in the manual.
  • Modified the short captions in the new frame models chapter of the manual. The runic ᛞ character has been replaced simply by 'Daeg'. This is due to incompatibilities with latex2html which prevents the HTML manual from being compiled.
  • Removal of the definition of a fixed-width table column from the LaTeX manual preamble. This is required as the definition breaks latex2html compatibility, causing a corruption in the figure numbering resulting in the images in the HTML to be essentially randomised.
  • Removal of the accents package to allow the HTML manual to be compiled. The accents LaTeX package is not compatible with latex2html, so the easiest fix is to eliminate the package.
  • Manually rotated the frame order matrix element EPS manual figures, for latex2html compatibility. The '90 rotate' command has been deleted and the bounding box permuted as a b c d → b -c d -a. This allows the angle argument in the \includegraphics{} command to be dropped, as latex2html does not recognise this. It allows the figures to be visible in the HTML version of the manual.
  • Redesign of the frame order parameter nesting table in the manual for latex2html compatibility. The table uses the tikz package, which is fatal for latex2html, even if not used. Therefore the table in the docs/latex/frame_order/parameter_nesting.tex file has been converted into a standalone LaTeX document to create a cropped postscript version of the tikz formatted table. A compilation script has been added as well. The resultant *.ps file is now included into the PCS numerical integration section, rather than this section creating the tikz table. All tikz preamble text has been removed to allow latex2html to run.
  • Workaround for latex2html not being able to handle the allrunes package or associated font. In the preamble htmlonly environment, the frame order symbols are redefined using the text 'Daeg' instead of the runic character ᛞ.
  • Fixes for sub and superscripts throughout the manual. This introduces {} around all sub and superscripted \textrm{} instances. This is not needed for the PDF version of the manual as the missing bracket problem is avoided, but it affects the HTML version of the manual compiled by latex2html, which requires the correct notation. The fixes are for both the new frame order chapter as well as the relaxation dispersion chapter.
  • Editing and fixes for the relax 4.0.0 part of the CHANGES file.
  • Updated and improved the wiki instructions in the relax release checklist document.
  • One more wiki instruction about checking for dead links in the release checklist document.
  • More minor changes to the 'Announcement' section of the release checklist document.
  • Updated the shell script for finding duplicated titles in the LaTeX files of the manual.
  • Converted the duplicate title finding shell script into a Python script. The Python script is far more advanced and uses a different logic to produce a table of replicated titles and their count. The script also returns a failed exit status when replicates exist.
  • Converted the replicated title finding Python script to use a class structure. This allows the script to be imported as a module. The replicate finding has been shifted into a find() class method.
  • Renamed the replicate title finding script.
  • Removed the duplicate LaTeX title finding shell script. This is now handled by the far more advanced Python script.
  • The Scons compilation of the PDF and HTML manuals now checks for replicated titles. A new replicate_title_check target has been added to the scons scripts. This calls the find() method of the replicate LaTeX title finding script to determine if any titles are replicated, and if so the scons target returns with a sys.exit(1) call. This target is set at the start of the user_manual_pdf, user_manual_pdf_nofetch, user_manual_html, user_manual_html_nofetch scons targets. The result is that the manual cannot be compiled if replicate titles exist, forcing the titles to be changed. The result will be that the HTML pages will all be unique, as replicated titles results in only one HTML page being created for all the sections.
  • Elimination of replicated titles in the LaTeX sources that the new frame order chapters introduced.
  • Removal of an old replicated title in the LaTeX sources for the manual. This is the title 'Model-free analysis' which is used for the entire specific analysis chapter as well as for the model-free analysis section of the values, gradients, and Hessians for optimisation chapter.
  • Fixes and improved printouts for the replicate_title_check scons target.
  • Updated all of relax to protect against future changes occurring in the numpy Python package. From numpy version 1.9, the FutureWarning __main__:1: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future. is seen in a large percentage of all relax's user functions. This is caught and turned into a RelaxWarning with the same message. The issue is that the behaviour of the comparison operators == and != will change with future numpy versions. These have been replaced with is and is not throughout the relax code base. Changes have also been made to the minfx and bmrblib packages to match.
  • More future protection against numpy changes. The FutureWarning is `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. Therefore the N-state model target function method paramag_info() has been updated to use the .ndim attribute and longer use numpy.rank() function.
  • Created the Mf.test_bug_23933_relax_data_read_ids system test. This is designed to catch bug #23933, the "NameError: global name 'ids' is not defined" problem when loading relaxation data. A truncated version of the PDB file and relaxation data, the full versions of which are attached to the bug report, consisting solely of residues 329, 330, and 331 have been added to the test suite shared data directories, and the system test written to catch the NameError.
  • Updated the Mf.test_bug_23933_relax_data_read_ids system test to catch the RelaxMultiSpinIDError. This allows the system test to pass, as a RelaxMultiSpinIDError is expected.
  • Updated the minfx and bmrblib versions in the release checklist document to 1.0.12 and 1.0.4. This is to remove the numpy FutureWarning messages about the == None and =! None comparisons to numpy data structures, which in the future will change in behaviour.
  • Increased the Gna! news item sectioning depth in the release checklist document.
  • Expanded the description of the sequence.attach_protons user function. This follows from http://thread.gmane.org/gmane.science.nmr.relax.user/1849/focus=1855.
  • Added initial data for testing data from Paul Schanda. This will demonstrate that there are several possibilities to enhance the R2,eff point method.
  • Added the Relax_disp.test_paul_schanda_nov_2015 system test. This will catch the loaning of nan values.
  • Made additional check in sequence reading, that nan values are skipped.
  • Making sure that the replicated 4000 Hz point for the 950 MHz experiment is not overwritten.
  • In the Relax_disp.test_paul_schanda_nov_2015 system test, added a test of counting the R2,eff values. This shows that the replicated R2,eff at 950 MHz/4000 Hz point is overwritten. A solution could be to change the dispersion frequency very little, to allow the addition of the data point.
  • Added further tests to Relax_disp.test_paul_schanda_nov_2015. This will show that replicates of R2,eff values is not handled well.
  • In the function of r2eff_read in data module of the dispersion, added the possibilities to read R2,eff values which are replicated. This is done first checking if the dispersion key exists in the R2,eff dictionary. If it exists, continue add 0.001 to the frequency until a new possibility exists. This should help handle multiple R2,eff points, as separate values and not taking any decision to average them.
  • Added the expectation of raising an relax error, if trying to plot and no model information is stored.
  • Raising an error if plotting dispersion curves, and no model is saved.
  • Changed example script for analysing data.
  • Extended the Relax_disp.test_paul_schanda_nov_2015 system test to include auto-analysis and clustered fits. This should show that the analysis is now possible.
  • Added a temporary state and a script for GUI setup to the data Paul Schanda.
  • Added the Relax_disp.test_paul_schanda_nov_2015 GUI test. This will show that loading a state will create a problem. Traceback (most recent call last): TypeError: int() argument must be a string or a number, not 'NoneType'.
  • Added a sample script for back-calculating relaxation data from a model-free results file. This is useful when the results file is not the final model, as these results file do not contain the back-calculated data. This is in response to Christina Möller's support request #3303.
  • Using Gary's lib.float.isNaN() instead of math.isnan(), to have backwards compatibility with python 2.5.
  • Fix for spelling mistake and documenting the new behavior of relax_disp.r2eff_read, when reading R2,eff points with the same frequency. If the spin-container already contain R2,eff values with the 'frequency of the CPMG pulse' or 'spin-lock field strength', the frequency will be changed by a infinitesimal small value of + 0.001 Hz. This allow for duplicates or more of the same frequency.
  • Modified the internal structural object to be less influenced by the format of the PDB. The PDB serial number is now intelligently handled, in that it is reset to 1 when a new model is created. This information is still kept for supporting the logic of the reading of the CONECT records, and will be eliminated in the future. The chain ID information is now no longer stored in the internal structural object, as this information is recreated by the structure.write_pdb user function based on how the internal structural object has been created.
  • Updates to the Noe and Structure system test classes for the internal structural object changes. The serial number can now be reset, and the chain ID information is no longer stored.
  • Added a file to the test suite shared data to help implement the PCA structural analysis. This is the N-domain of the CaM-IQ complex used in a frame order analysis. It is the first 5 structures from a call to the frame_order.distribute user function, with the different rigid-bodies merged back together into a single molecule.
  • Created the structure.pca user function front end. This is currently modelled on the structure.rmsd user function framework.
  • Basic implementation of the structure.pca user function back end. This is the new pca() function of the pipe_control.structure.main module. It simply performs some checks, assembles the atomic coordinates, and the passes control to the relax library pca_analysis() function of the currently unimplemented lib.structure.pca module.
  • Partial implemented of the PCA analysis in the relax library. This is for the new structure.pca user function. The lib.structure.pca module has been created, and the pca_analysis() function created to calculate the structure covariance matrix, via the calc_covariance_matrix() function, and then calculate the eigenvalues and eigenvectors of the covariance matrix, sorting them and truncating to the desired number of PCA modes.
  • Added the algorithm and num_modes arguments to the structure.pca user function. These are passed all the way into the relax library backend.
  • Implemented the SVD algorithm for the PCA analysis in the relax library. This simply calls numpy.linalg.svd().
  • The PCA analysis in the relax library now calculates the per structure projections along the PCs.
  • The PCA analysis function in the relax library is now returning data. This includes the PCA values and vectors, and the per structure projections.
  • The PCA values and vectors, and the per structure projections are now being stored. This is in the structure.pca user function backend in the pipe_control.structure.main module.
  • Added the format and dir arguments to the structure.pca user function. This is to the front and back ends.
  • Modified the assemble_structural_coordinates() method to return more information. This is from the pipe_control.structure.main module. The lists boolean argument is now accepted which will cause the function to additionally return the object ID list per molecule, the model number list per molecule, and the molecule name list per molecule.
  • The structure.pca user function now creates graphs of the PC projections. This includes PC1 vs. PC2, PC2 vs. PC3, etc.
  • Added the Gromacs PCA results for the distribution.pdb file. This includes a script used to execute all parts of Gromacs and all output files.
  • Updated the Gromacs PCA results for the newest 5.1.1 Gromacs version.
  • Created an initial Structure.test_pca system test. This executes the new structure.pca user function, and checks if data is stored in cdp.structure.
  • Improved the graphs in the backend of the structure.pca user function. The graphs are now clustered so that different models of the same structure in the same data pipe are within one graph set. The graph header has also been improved.
  • Expanded the Structure.test_pca system test checks to compare to the values from Gromacs.
  • A weighted mean structure can now be calculated. This is for the calc_mean_structure() function of the relax library module lib.structure.statistics. Weights can now be supplied for each structure to allow for a weighted mean to be calculated and returned.
  • Added support for observer structures in the structure.pca user function. This allows a subset of the structures used in the PC analysis to have zero weight so that these structures can be used for comparison purposes. The obs_pipes, obs_models, and obs_molecules arguments have been added to the user function front end. The backend uses this to create an array of weights for each structure. And the lib.structure.pca functions use the zero weights to remove the observer structures from the PC mode calculations.
  • Created the Structure.test_pca_observers system test. This is for testing the new observer structures concept of the structure.pca user function.
  • Improved the printouts from the relax library principle component analysis. This is in the pca_analysis() function of the lib.structure.pca module.
  • Fixes and improvements for the graphs produced by the structure.pca user function. The different sets are now correctly created, and are now labelled in the plots.
  • Adding a testing deploy script, for rapid deployment on Google Cloud Computing. This is for an intended install in Ubuntu 14.04 LTS.
  • Expanding script for installation.
  • Putting installation into functions in deploy script.
  • Splitting deploy script into several small functions.
  • Adding checking statements to install script.
  • When sourcing the scripts, several functions can be performed instead.
  • Added spaces to install script for better printing.
  • Adding a tutorial script.
  • Adding 2 tutorial scripts.
  • Fix for small spin ID error in tutorial script.
  • Created a system test for catching bug #24131, the BMRB export failure when the SpinContainer object has no S2 attribute, as reported by Martin Ballaschk.
  • Modified the Mf.test_bug_24131_bmrb_deposition system test to check for the RelaxError. The test results in a RelaxError, as the results file contains no selected spins.
  • Added the Mf.test_bug_24131_missing_interaction system test to catch another problem. This is part of bug #24131, the BMRB export failure with the SpinContainer object having no S2 value. However the previous fix of skipping deselected spins introduced a new problem of relax still searching for the interatomic interactions for that deselected spin.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 4.0.0

Description

This is a major feature release for a new analysis type labelled 'frame order'. The frame order theory aims to unify all rotational molecular physics data sources via a single mechanical model. It is a bridging physics theory for rigid body motions based on the statistical mechanical ordering of reference frames. The previous analysis of the same name was an early iteration of this theory that was however rudamentary and non-functional. Its current implementation is for analysing RDC and PCS data from an internal alignment to interpret domain or other rigid body motions within a molecule or molecular complex.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 4.0.0
(7 October 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.0


Features
  • The final, complete, and correct implementation of the frame order theory for studying rigid body motions. This is currently for analysing RDC and PCS data from internally aligned systems.


Changes
  • Deletion of the frame_order.average_position user function and all of the associated backend code. This user function allowed the user to specify five different types of displacement to the average moving domain position: a pure rotation, with no translation, about the pivot of the motion in the system; a rotation about the pivot of the motion of the system together with a translation; a pure translation with no rotation; a rotation about the centre of mass of the moving domain with no translation; a rotation about the centre of mass of the moving domain together with a translation. Now the last option will be the default and only option. This option is equivalent to the standard superimposition algorithm (the Kabsch algorithm) to a hypothetical structure at the real average position. The other four are due to the history of the development of the theory. These limit the usefulness of the theory and will only cause confusion.
  • Clean up of the frame order target function code. This matches the previous change of the deletion of the frame_order.average_position user function. The changes include the removal of the translation optimisation flag as this is now always performed, and the removal of the flag which causes the average domain rotation pivot point to match the motional pivot point as these are now permanently decoupled.
  • Alphabetical ordering of functions in the lib.frame_order.pseudo_ellipse module.
  • Eliminated all of the 'line' frame order models, as they are not implemented yet. This is just frontend code - the backend does not exist.
  • Updated the isotropic cone CaM frame order test model optimisation script. Due to all of the changes in the frame order analysis, the old script was no longer functional.
  • Created a script for the CaM frame order test models for finding the average domain position. As the rotation about a fixed pivot has been eliminated, the shift from 1J7P_1st_NH_rot.pdb to 1J7P_1st_NH.pdb has to be converted into a translation and rotation about the CoM. This script will be used to replace the pivot rotation Euler angles with the translation vector and CoM rotation Euler angles. However the structure.superimpose user function will need to be modified to handle both the standard centroid superimposition as well as a CoM superimposition.
  • Updated the CaM frame order test model superimposition script. The structure.superimpose user function is now correctly called. The output log file has been added to the repository as it contains the correct translation and Euler rotation information needed for the test models.
  • Parameter update for the isotropic cone CaM frame order test model optimisation script. The Euler angles for the rotation about the motional pivot have been replaced by the translation vector and Euler angle CoM rotation parameters.
  • Fix for a number of the frame order models which do not have parameter constraints. The linear_constraint() function was returning A, b = [], [] for these models, but these empty numpy arrays were causing the minfx library to fail. These values are now caught and the constraint algorithm turned off in the minimise() specific API method.
  • Increased the precision of all the data in the CaM frame order test data generation base script. These have all been converted from float16 to float64 numpy types.
  • Fix for the RDC error setting in the CaM frame order test data generation base script. The rdc_err data structure is located in the interatomic data containers, no the spin containers.
  • Modification of the structure loading part of the CaM frame order data generation base script. The structures are now only loaded if the DIST_PDB flag is set, as they are only used for generating the 3D distribution of structures. This saves a lot of time and computer memory.
  • Huge speedup of the CaM frame order test data generation base script. By using multidimensional numpy arrays to store the atomic positions and XH unit vectors of all spins, and performing the rotations on these structures using numpy.tensordot(), the calculations are now a factor of 10 times faster. The progress meter had to be changed to show every 1000 rather than 100 iterations. The rotations of the positions and vectors are now performed sequentially, accidentally fixing a bug with the double motion models (i.e. the 'double rotor' model).
  • Modified the CaM frame order test data generation base script to conserve computer RAM. The XH vector and atomic position data structures for all N rotations are now of the numpy.float32 rather than numpy.float64 type. The main change is to calculate the averaged RDCs and averaged PCSs separately, deleting the N-sized data structures once the data files are written.
  • Complete redesign of the CaM frame order data generation base script for speed and memory savings. Although the rotated XH bond vector and atomic position code was very fast, the amount of memory needed to store these in the spin containers and interatomic data containers was huge when N > 1e6. The subsequent rdc.back_calc and pcs.back_calc user function calls would also take far too long. Therefore the base script has been redesigned. The _create_distribution() method has been split into four: _calculate_pcs(), _calculate_rdc(), _create_distribution(), and _pipe_setup(). The _pipe_setup() method is called first to set up the data pipe with all required data. Then the _calculate_rdc() and _calculate_pcs() methods, and finally _create_distribution() if the DIST_PDB flag is set. The calls to the rdc.back_calc and pcs.back_calc user functions have been eliminated. Instead the _calculate_rdc() and _calculate_pcs() methods calculate the averaged RDC and PCS themselves as numpy array structures. Rather than storing the huge rotated vectors and atomic positions data structures, the RDCs and PCSs are summed. These are then divided by self.N at the end to average the values. Compared to the old code, when N is set to 20 million the RAM usage drops from ~20 GB to ~65 MB. The total run time is also decreased on one system from a few days to a few hours (an order or two of magnitude).
  • Changed the progress meter updating for the CaM frame order test data generation base script. The spinner was far too fast, updating every 5 increments, and is now updated every 250. And the total number is now only printed every 10,000 increments.
  • Improvements to the progress meter for the CaM frame order test data generation base script. Commas are now printed between the thousands and the numbers are now right justified.
  • Large increase in accuracy of the RDC and PCS averaging. This is for the CaM frame order test data generation base script. By summing the RDCs and PCSs into 1D numpy.float128 arrays (for this, a 64-bit system is required), and then dividing by N at the end, the average value can be calculated with a much higher accuracy. As N becomes larger, the numerical averaging introduces greater and greater amounts of truncation artifacts. So this change alleviates this.
  • Fix for the RDC and PCS averaging in the CaM frame order test data generation base script. For the double rotor model, or any multiple motional mode model, the averaging was incorrect. Instead of dividing by N, the values should be divided by NM, where M is the number of motional modes.
  • Huge increase in precision for the CaM frame order free rotor model test data. The higher precision is because the number structures in the distribution is now twenty million rather than one million, and the much higher precision numpy.float128 averaging of the updated data generation base script has been used. This data should allow for a much better estimate of the β and γ average domain position parameter values for the free rotor models which are affected by the collapse of the α parameter to zero.
  • Huge increase in precision for the CaM frame order double rotor model test data. The higher precision is because the number structures in the distribution is now over twenty million (45002) rather than a quarter of a million (5002). And the much higher precision numpy.float128 averaging of the updated data generation base script has been used.
  • Fix for the constraint deactivation in the frame order minimisation when no constraints are present.
  • Huge increase in precision for the CaM frame order rotor model test data. The higher precision is because the number structures in the distribution is now 20 million rather than 166,666, and the numpy.float128 data averaging has been used.
  • Large increase in precision for the 2nd CaM frame order rotor model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1,000,001 and the numpy.float128 data averaging has been used.
  • Parameter update for the 2nd rotor CaM frame order test model optimisation script. The Euler angles for the rotation about the motional pivot have been replaced by the translation vector and Euler angle CoM rotation parameters.
  • Large increase in precision for the 2nd CaM frame order free rotor model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 999,999 and the numpy.float128 data averaging has been used.
  • Updated the CaM frame order test model superimposition script. The Ca2+ atoms are now deleted from the structures before superimposition so that the centroid matches that used in the frame order analysis.
  • The average domain rotation centroid is printed out when setting up the frame order target functions. This is to help the user understand what is happening in the analysis.
  • Faster clearing of numpy arrays in the lib.frame_order modules. The x[:] = 0.0 notation is now used to set all elements to zero, rather than nested looping over all dimensions. This however has a negligible effect on the test suite timings.
  • Large increase in precision for the CaM frame order pseudo-ellipse model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Improved the value setting in the optimisation() method of the CaM frame order system tests. This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
  • Changed the average domain position parameter values in the CaM frame order system tests. This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/. The translation vector coordinates are now set, as well as the CoM Euler angle rotations. These come from the log file of the test_suite/shared_data/frame_order/cam/superimpose.py script, and are needed due to the simplification of the average domain position mechanics now mimicking the Kabsch superimposition algorithm.
  • The CaM frame order system test mesg_opt_debug() method now prints out the translation vector. This is printed out at the end of all CaM frame order system tests to help with debugging when the test fails.
  • Change for how the CaM frame order system test scripts handle the average domain position rotation. The trick of pre-rotating the 3D coordinates was used to solve the {α, β, γ} -> {0, β', γ'} angle conversion problem in the rotor models no longer works now that the average domain position mechanics has been simplified. Instead, high precision optimised β' and γ' values are now set, and the ave_pos_alpha value set to None. The high precision parameters were obtained with the frame_order.py script located in the directory test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target function was modified so that the translation vector is hard-coded to [-20.859750185691549, -2.450606987447843, -2.191854570352916] and the axis θ and φ angles to 0.96007997859534299767 and 4.0322755062196229403. These parameters were then commented out for the model in the module specific_analyses.frame_order.parameters so only β' and γ' were optimised. Iterative optimisation was used with increasing precision, ending up with high precision using 10,000 Sobol' points.
  • Updated a number of the CaM frame order system tests for the higher precision data. The new data results in chi-squared values at the real solution to be much closer to zero.
  • Change for how the CaM frame order free-rotor pseudo-ellipse test script handle the average position.
  • Added FIXME comments to the 2nd free-rotor CaM frame order model system test scripts. These explain the steps required to obtain the correct β' and γ' average domain position rotation angles.
  • Large increase in precision for the CaM frame order isotropic cone model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Large increase in precision for the CaM frame order free-rotor, isotropic cone model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Updated the CaM frame order free-rotor model test data set for testing for missing data. This is the data in test_suite/shared_data/frame_order/cam/free_rotor_missing_data. To simplify the copying of data from test_suite/shared_data/frame_order/cam/free_rotor and then the deletion of data, the missing.py script was created to automate the process. The generate_distribution.py script and some of the files it creates were removed from the repository so it is clearer how the data has been created.
  • Large increase in precision for the 2nd CaM frame order free-rotor, isotropic cone model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Large increase in precision for the CaM frame order free-rotor, pseudo-ellipse model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Large increase in precision for the CaM frame order pseudo-ellipse model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used.
  • Updated a number of the CaM frame order system tests for the higher precision data. The new data results in chi-squared values at the real solution to be much closer to zero. The free-rotor pseudo-ellipse models might need investigation however as the chi-squared values have increased.
  • Elimination of the error_flag variable from the frame order analysis. This flag is used to activate some old code paths which have now been deleted as they are never used.
  • Optimisation of the average domain position for the CaM frame order free-rotor models. The log file that shows the optimisation of the average domain position for the free-rotor models has been added to the repository for reference. This is for the simple free-rotor model, but the optimised position holds for the isotropic cone and pseudo-ellipse model data too. To perform the optimisation, the axis_theta and axis_phi parameters were removed from the model and hardcoded into the target function. As the rotor axis is know, this allows the average domain position to be optimised in isolation. Visual inspection of the results confirmed the position to be correct.
  • Fixes for the 2nd frame order free-rotor system tests. The average domain position parameters are now set to the correct values, matching those in the relax log file frame_order_ave_pos_opt.log in test_suite/shared_data/frame_order/cam/free_rotor2.
  • Updated the 2nd CaM free-rotor frame order system tests for the correct average domain position. The chi-squared values are now significantly lower.
  • Increased the precision of the chi-squared value testing in the CaM frame order system tests. The check_chi2 method has been modified so that the chi-squared value is no longer scaled, and the precision has been increased from 1 significant figure to 4. All of the tests have been updated to match.
  • The minimisation verbosity flag now effects the frame order RelaxWarning about turning constraints off.
  • Preformed a frame order analysis on the 2nd CaM free-rotor model test data. This is to check that everything is operating as expected.
  • Small speedup for the frame order target functions for most models. The rotation matrix corresponding to each Sobol' point for the numerical integration is now pre-calculated during target function initialisation rather than once for each function call.
  • Updates for some of the frame order system tests for the rotation matrix pre-calculation change. As the rotation matrix is being pre-calculated, one consequence is that the Sobol' angles are now full 64-bit precision rather than 32-bit. Therefore this changes the chi-squared value a little, requiring updates to the tests.
  • Preformed a frame order analysis on the CaM free-rotor mode test data set. This is to demonstrate that everything is operating correctly.
  • Preformed a frame order analysis on the CaM free-rotor mode test data set with missing data. This is to demonstrate that everything is operating correctly.
  • Attempt to speed up the pseudo-elliptic frame order models. The quasi-random numerical integration of the PCS for the pseudo-ellipse has been modified so that the torsion angle check for each Sobol' point is preformed before the tmax_pseudo_ellipse() function call. A new check that the tilt angle is less than cone_theta_y, the larger of the two cone angles, has also been added to avoid tmax_pseudo_ellipse() when the θ tilt angle is outside of an isotropic cone defined by cone_theta_y.
  • Preformed a frame order analysis on a number of the CaM test data sets. This includes the rotor, isotropic cone, and pseudo-ellipse, and the analyses demonstrate a common bug between all these models.
  • Preformed a frame order analysis on the rigid CaM test data set. This is to demonstrate that everything is operating correctly.
  • Optimisation of the rotor model to the rigid CaM frame order test data. The optimisation script and all results files have been added to the repository.
  • Increased the grid search bounds for the frame order average domain translation. Instead of being a 10 Angstrom box centred at {0, 0, 0}, now the translation search has been increased to a 100 Angstrom box.
  • Proper edge case handling and slight speedup of the frame order PCS integration functions. The case whereby no Sobol' points in the numerical integration lie within the motional distribution is now caught and the rotation matrix set to the motional eigenframe to simulate the rigid state. As the code for averaging the PCS was changed, it was also simplified by removing an unnecessary loop over all spins. This should speed up the PCS integration by a tiny amount.
  • Created a new CaM frame order test data set. This is for the rotor model with a very small torsion angle of 1 degree, and will be used as a comparison to the rigid model and for testing the performance of the rotor model for an edge case.
  • Updated the frame order representations in all of the frame_order.py scripts for the CaM test data. All PDB files are now gzipped to save space, the old pymol.cone_pdb user function calls replaced with pymol.frame_order, and an average domain PDB file for the exact solution is now created in all cases.
  • The minimisation constraints are now turned on for all CaM test data frame_order.py optimisation scripts.
  • Updated the rotor CaM test data frame_order.py script for the parameter reduction. The rotor axis {θ, φ} polar angles have been replaced by the single axis α angle. This now matches the script for the 2nd rotor model.
  • Updated the parameters in all of the frame_order.py scripts for the CaM test data. The parameters are now specified at the top of the script as variables. All scripts now handle the change to the translation + CoM rotation for the average domain position rather than having a pure rotation about a fixed pivot, which is no longer supported.
  • The frame_order.num_int_pts user function now throws a RelaxWarning if not enough points are used.
  • Changed the creation of Sobol' points for numerical integration in the frame order target functions. The points are now all created at once using the i4_sobol_generate() rather than i4_sobol() function from the extern.sobol.sobol_lib module.
  • Increased the number of integration points from 50 or 100 to 5000. This is for all CaM frame_order.py test data optimisation scripts. The higher number of points are essential for optimising the frame order models and hence for checking the relax implementation.
  • Updated the frame_order.py optimisation script for the small angle CaM rotor frame order test data. This now has the correct rotor torsion angle of 1 degree, and the spherical coordinates are now converted to the axis α parameter.
  • Expanded the capabilities of the pymol.frame_order user function. The isotropic and pseudo-elliptic cones are now represented as they used to be under the pymol.cone_pdb user function. To avoid code duplication, the new represent_cone_axis(), represent_cone_object() and represent_rotor_object() functions have been created to send the commands into PyMOL.
  • Increased the precision of all of the CaM frame order system tests by 40 times. The number of Sobol' integration points have been significantly increased while only increasing the frame order system test timings by ~10%. This allows for checking for chi-squared values at the minima much closer to zero, and is much better for demonstrating bugs.
  • Optimisation constraints are no longer turned off in the frame order auto-analysis. Constraints are now supported by all frame order models, or automatically turned off for those which do not have parameter constraints.
  • Fix for the frame order visualisation script created by the auto-analysis. The call to pymol.frame_order is now correct for the current version of this user function.
  • Removed a terrible hack for handling the frame order analysis without constraints. This is no longer needed as the log-barrier method is now used to constrain the optimisation, so that the torsion angle can no longer be negative.
  • Constraints are now implemented in the frame order grid search. This is useful for the pseudo-elliptic models as the cone θx < θy constraint halves the optimisation space.
  • Expanded the CaM rotor test data frame_order.py optimisation script. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower. The results of the new optimisation are included.
  • Expanded the CaM pseudo-ellipse test data frame_order.py optimisation script. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower. The results of the new optimisation are included.
  • Added one more iteration for the zooming optimisation of the frame order auto-analysis. This is to improve the speed of optimisation when all RDC and PCS data is being used. The previous iterations where with [100, 1000, 200000] Sobol' integration points and [1e-2, 1e-3, 1e-4] function tolerances. This has been increased to [100, 1000, 10000, 100000] and [1e-2, 1e-3, 5e-3, 1e-4]. The final number of points has been decreased as that level of accuracy does not appear to be necessary. These are also only default values that the user can change for themselves.
  • Updated the CaM frame order data generation base script to print out more information. This is for the first axis system so that the same amount of information as the second system is printed.
  • Expanded the CaM isotropic cone test data frame_order.py optimisation script and added the results. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower.
  • Important fix for the 2nd rotor model of the CaM frame order test data. The tilt angle was not set, and therefore the old data matched the non-tilted 1st rotor model. All PCS and RDC data has been regenerated to the highest quality using 20,000,000 structures.
  • Updated the 3 Frame_order.test_cam_rotor2* system tests for the higher quality data.
  • Expanded the 2nd CaM pseudo-ellipse test data frame_order.py optimisation script. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower. The results of the new optimisation have been added to the repository.
  • Expanded the CaM free-rotor isotropic cone test data frame_order.py optimisation script. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower. The results of the new optimisation have been added to the repository.
  • Expanded all remaining CaM test data frame_order.py optimisation scripts. The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy of the quasi-random numerical integration together with an decrease of the function tolerance cutoff for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the accuracy of the initial grid search and the Monte Carlo simulations is now much lower.
  • Updated the CaM 2-site to rotor model frame_order.py optimisation script for the parameter reduction. The rotor frame order model axis spherical angles have now been converted to a single α angle.
  • Fix for a number of the frame order models which do not have parameter constraints. This change to the grid_search() API method is similar to the previous fix for the minimise() method. The linear_constraint() function was returning A, b = [], [] for these models, but these empty numpy arrays were causing the dot product with A to fail in the grid_search() API method. These values are now caught and the constraint algorithm turned off.
  • Converted the 'free rotor' frame order model to the new axis_alpha parameter system. The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle α. The α parameter defines the rotor axis angle from the xy-plane.
  • Parameter conversion for all of the CaM free rotor test data frame_order.py optimisation scripts. The rotor axis spherical angles have been replaced by the axis α angle defining the rotor with respect to the xy-plane.
  • Modified the CaM frame order base system test script to catch a bug in the free rotor model. The axis spherical angles are no longer set for the rotor or free rotor models, as they use the α angle instead and the lack of the θ and φ parameters triggers the bug. The PDB representation of the frame order motions is also now tested for all frame order models, as it was turned off for the rigid, rotor and free rotor models and this is where the bug lies.
  • Fix for the failure of the frame_order.pdb_model user function for the free rotor frame order model. This is due to the recent parameter conversion to the axis α angle.
  • Eliminated the average position α Euler angle parameter from the free-rotor pseudo-ellipse model. As this frame order model is a free-rotor, the average domain position is therefore undefined and it can freely rotate about the rotor axis. One of the Euler angles for rotating to the average position can therefore be removed, just as in the free rotor and free rotor isotropic cone models.
  • Eliminated the ave_pos_alpha parameter from the free rotor psuedo-ellipse model target function. The average domain position α Euler angle has already been removed from the specific analyses code and this change brings the target function into line with these changes.
  • Added the full optimisation results for the 2nd rotor frame order model for the CaM test data. This is from the new frame_order.py optimisation script and the results demonstrate the stability of the rotor model.
  • Added the full optimisation results for the small angle rotor CaM frame order test data. This is from the new frame_order.py optimisation script and the results demonstrate the stability of the rotor model, even when the rotor is as small as 1 degree.
  • Fix for the free rotor PDB representation created by the frame_order.pdb_model user function. The simulation axes were being incorrectly generated from the θ and φ angles, which no longer exist as they have been replaced by the α angle.
  • Added the full optimisation results for the free rotor pseudo-ellipse frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added the full optimisation results for the rotor frame order model. This is for the 2-site CaM test data using the new frame_order.py optimisation script.
  • The CaM frame order data generation base script now uses lib.compat.norm(). This is to allow the test suite to pass on systems with old numpy versions whereby the numpy.linalg.norm() function does not support the new axis argument.
  • Modified the pymol.cone_pdb and pymol.frame_order user functions to use PyMOL IDs. The PyMOL IDs are used to select individual objects in PyMOL rather than all objects so that the subsequent PyMOL commands will only be applied to that object. This allows for multiple objects to be handled simultaneously.
  • Added the full optimisation results for the free rotor frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added the full optimisation results for the 2nd free rotor frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added the full optimisation results for the free rotor frame order model with missing data. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added a script for recreating the frame order PDB representation and displaying it in PyMOL. This is for the optimised results.
  • Fixes for the rotor object created by the frame_order.pdb_model user function. The rotor is now also shown for the free rotor pseudo-ellipse, despite it being a useless model, and the propeller blades are no longer staggered for all the free rotor models so that two circles are no longer produced.
  • Updated the free rotor and 2nd free rotor PDB representations using the represent_frame_order.py script. This is for the CaM frame order test data.
  • Reparameterisation of the double rotor frame order model. The two axes defined by spherical angles have been replaced by a full eigenframe and the second pivot has been replaced by a single displacement along the z-axis of the eigenframe.
  • Removed the 2nd pivot point infrastructure from the frame order analysis. The 2nd pivot is now defined via the pivot_disp parameter.
  • Added the 2nd rotor axis torsion angle to the list of frame order parameters. This is for the double rotor model.
  • Comment fixes for the eigenframe reconstruction in the frame order target functions.
  • Converted the double rotor frame order model target function to use the new parameterisation.
  • Fix for the PDB representation generated by frame_order.pdb_model for the free rotor pseudo-ellipse.
  • Fix for the Frame_order.test_rigid_data_to_free_rotor_model system test. As the free rotor has undergone a reparameterisation, the chi-squared value is now higher. The value is reasonable as the free rotor can never model the rigid system.
  • Removed the structure loading and transformation from the CaM frame order system tests. This was mimicking the old behaviour of the auto-analysis. However as that behaviour has been shifted into the backend of the frame_order.pdb_model user function, which is called by these system tests as well, the code is now redundant and is wasting test suite time.
  • Removed the setting of the second pivot point in the CaM frame order system tests. The second pivot point has been removed from the double rotor frame order model to eliminate parameter redundancy, so no models now have a conventional second pivot.
  • Modified the CaM frame order system test base script to test alternative code paths. This pivot point was fixed in all tests, so the code in the target functions behind the pivot_opt flag was not being tested. Now for those system tests whereby the calc rather than minimise user function is called, the pivot is no longer fixed to execute this code.
  • Simplification and clean up of the RDC and PCS flags in the frame order target functions. The per-alignment flags have been removed and replaced by a global flag for all data. This accidentally fixes a bug when only RDCs are present, as the calc_vectors() method was being called when it should not have been.
  • Speedup and simplifications for the vector calculations used for the PCS numerical integration. This has a minimal effect on the total speed as the target function calc_vectors() method is not the major bottleneck - the slowest part is the quasi-random numerical integration. However the changes may be useful for speeding up the integration later on. The 3D pivot point, average domain rotation pivot, and paramagnetic centre position arrays are now converted into rank-2 arrays in __init__() where the first dimension corresponds to the spin. Each element is a copy of the 3D array. These are then used for the calculation of the pivot to atom vectors, eliminating the looping over spins. The numpy add() and subtract() ufuncs are used together with the out argument for speed and to avoid temporary data structure creation and deletion. The end result is that the calculated vector structure is transposed, so the first dimension are the spins. The changes required minor updates to a number of system tests. The target functions themselves had to be modified so that the pivot is converted to the larger structure when optimised, or aliased.
  • Added a script for timing different ways to calculate PCSs and RDCs for multiple vectors. This uses the timeit module rather than profile to demonstrate the speed of 7 different ways to calculate the RDCs or PCSs for an array of vectors using numpy. In the frame order analysis, this is the bottleneck for the quasi-random numerical integration of the PCS. The log file shows a potential 1 order of magnitude speedup between the 1st technique, which is currently used in the frame order analysis, and the 7th and last technique. The first technique loops over each vector, calculating the PCS. The last expands the PCS/RDC equation of the projection of the vector into the alignment tensor, and calculates all PCSs simultaneously.
  • Added another timing script for RDC and PCS calculation timings. This time, the calculation for multiple alignments is now being timed. An addition set of methods for calculating the values via tensor projections have been added. For 5 alignments and 200 vectors, this demonstrates a potential 20x speedup for this part of the RDC/PCS calculation. Most of this speedup should be obtainable for the numerical PCS integration in the frame order models.
  • Small speedup for all of the frame order models. The PCS averaging in the quasi-random numerical integration functions now uses the multiply() and divide() numpy methods to eliminate a loop over the alignments. For this, a new dimension over the spins was added to the PCS constant calculated in the target function __init__() method. In one test of the pseudo-ellipse, the time dropped from 191 seconds to 172.
  • Added another timing script for helping with speeding up the frame order analysis. This is for the part where the rotation matrix for each Sobol' integration point is shifted into the eigenframe.
  • Python 3 fix for the CaM frame order system test base script.
  • Added the full optimisation results for the torsionless isotropic cone frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Small speedups for all of the frame order models in the quasi-random numerical PCS integration. These changes result in an ~10% speedup. Testing via the func_pseudo_ellipse() target function using the relax profiling flag, the time for one optimisation decreased from 158 to 146 seconds. The changes consist of pre-calculating all rotations of the rotation matrix into the motional eigenframe in one mathematical operation rather than one operation per Sobol' point rotation, unpacking the Sobol' points into the respective angles prior to looping over the points, and taking the absolute value of the torsion angle and testing if it is out of the bounds rather than checking both the negative and positive values.
  • Attempt at speeding up the torsionless pseudo-ellipse frame order model. The check if the Sobol' point is outside of an isotropic cone defined by the largest angle θy is now performed to avoid many unnecessary calls to the tmax_pseudo_ellipse() function. This however reveals a problem with the test suite data for this model.
  • Updated all of the CaM frame order system tests for the recent speedup. The speedup switched to the use of numpy.tensordot() for shifting each Sobol' rotation into the eigenframe rather than the previous numpy.dot(). Strangely this affects the precision and hence the chi-squared value calculated for each system test - both increasing and decreasing it randomly.
  • The frame order target function calc_vectors() method arguments have all been converted to keywords. This is in preparation for handling a second pivot argument for the double rotor model.
  • Updated the double rotor frame order model to be in a pseudo-functional state. Bugs in the target function method have been removed, the calc_vectors() target function method now accepts the pivot2 argument (but does nothing with it yet), and the lib.frame_order.double_rotor module has been updated to match the logic used in all other lib.frame_order modules.
  • The frame_order.pdb_model user function no longer tries to create a cone object for the double rotor.
  • Added a timeit script and log file for different ways of checking a binary numpy array.
  • Modified the rigid_test.py system test script to really be the rigid case. This is used in all of the Frame_order.test_rigid_data_to_*_model system tests. Previously the parameters of the dynamics were set to being close to zero, to catch the cases were a few Sobol' PCS integration points were accepted. But now the case were no Sobol' points can be used is being tested. This checks a code path currently untested in the test suite, demonstrating many failures.
  • Fix for the frame order matrix calculation for a pseudo-elliptic cone with angles of zero degrees. The lib.frame_order.pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless() function has been changed to prevent a divide by zero failure. The surface area normalisation factor now defaults to 0.0.
  • Fixes for all PCS numeric integration for all frame order models in the rigid case. The exact PCS values for the rigid state are now correctly calculated when no Sobol' points lie within the motional model. The identity matrix is used to set the rotation to zero, and the PCS values are now multiplied by the constant.
  • Updates for the chi-squared value in all the Frame_order.test_rigid_data_to_*_model system tests. This is now much reduced as the true rigid state is now being tested for.
  • The rigid frame order matrix for the pseudo-ellipse models is now correctly handled. This allows the rigid case RDCs to be correctly calculated for both the pseudo-ellipse and torsionless pseudo-ellipse models. The previous catch of the θx cone angle of zero was incorrectly recreating the frame order matrix, which really should be the identity matrix. However truncation artifacts due to the quadratic SciPy integration still cause the model to be ill-conditioned near the rigid case. The rigid case is correctly handled, but a tiny shift of the parameters off zero cause a discontinuity.
  • Updates for the Frame_order.test_rigid_data_to_pseudo_ellipse*_model system tests. The chi-squared value now matches the rigid model.
  • Large increase in precision for the CaM frame order torsionless pseudo-ellipse model test data set. In addition, the θx and θy angles have also been swapped so that the new constraint of 0 ≤ θx ≤ θy ≤ π built into the analysis is satisfied. The higher precision is because the number structures in the distribution is now 20 million rather than 1 million and the numpy.float128 data averaging has been used. The algorithm for finding suitable random domain positions within the motional limits has been changed as well by extracting the θ and φ tilt angles from the random rotation, dropping the torsion angle σ, and reconstructing the rotation from just the tilt angles. This increases the speed of the data generation script by minimally 5 orders of magnitude.
  • Changed the parameter values for the Frame_order.test_cam_pseudo_ellipse_torsionless* system tests. The θx and θy angles are now swapped. The chi-squared values are now also lower in the 3 system tests as the data is now of much higher precision.
  • Speedup for the frame order analyses when only one domain is aligned. When only one domain is aligned, the reverse Ln3+ to spin vectors for the PCS are no longer calculated. For most analyses, this should significantly reduce the number of mathematical operations required for the quasi-random Sobol' point numerical integration.
  • Support for the 3 vector system for double motions has been added to the frame order analysis. This is used for the quasi-random Sobol' numeric integration of the PCS. The lanthanide to atom vector is the sum of three parts: the 1st pivot to atom vector rotated by the 1st mode of motion; the 2nd pivot to 1st pivot vector rotated by the 2nd mode of motion (together with the rotated 1st pivot to atom vectors); and the lanthanide to second pivot vector. All these vectors are passed into the lib.frame_order.double_rotor.pcs_numeric_int_double_rotor() function, which passes them to the pcs_pivot_motion_double_rotor() function where they are rotated and reconstructed into the Ln3+ to atom vectors.
  • Fully implemented the double rotor frame order model for PCS data. Sobol' quasi-random points for the numerical integration are now generated separately for both torsion angles, and two separate sets of rotation matrices for both angles for each Sobol' point are now pre-calculated in the create_sobol_data() target function method. The calc_vectors() target function method has also been modified as the lanthanide to pivot vector is to the second pivot in the double rotor model rather than the first. The target function itself has been fixed as the two pivots were mixed up - the 2nd pivot is optimised and the inter-pivot distance along the z-axis gives the position of the 1st pivot. For the lib.frame_order.double_rotor module, the second set of Sobol' point rotation matrices corresponding to sigma2, the rotation about the second pivot, is now passed into the pcs_numeric_int_double_rotor() function. These rotations are frame shifted into the eigenframe of the motion, and then correctly passed into pcs_pivot_motion_double_rotor(). The elimination of Sobol' points outside of the distribution has been fixed in the base pcs_numeric_int_double_rotor() function and now both torsion angles are being checked.
  • Fix for the unpacking of the double rotor frame order parameters in the target function. This is for when the pivot point is being optimised.
  • Created a new synthetic CaM data set for the double rotor frame order model. This is the same as the test_suite/shared_data/frame_order/cam/double_rotor data except that the angles have been increased from 11.5 and 10.5 degrees to 85.0 and 55.0 for the two torsion angles. This is to help in debugging the double rotor model as the original test data is too close to the rigid state to notice certain issues.
  • Corrected the printout from the CaM frame order data generation base script. The number of states used in the distribution of domain positions is now correctly reported for the models with multiple modes of motion.
  • Created a frame order optimisation script for the CaM double rotor test suite data. This is the script used for testing the implementation, it will not be used in the test suite.
  • Created the Frame_order.test_rigid_data_to_double_rotor_model system test. This shows that the double rotor model works perfectly when the domains of the molecule are rigid.
  • Fix for the frame order target functions for when no PCS data is present. In this case, the self.pivot structure was being created as an empty array rather than a rank-2 array with dimensions 1 and 3. This was causing the rotor models to fail, as this pivot is used to recreate the rotation axis.
  • Fix for the CaM double rotor frame order system tests. The torsion angle cone_sigma_max is a half angle, therefore the full angles from the data generation script are now halved in the system test script.
  • Created 3 frame order system tests for the new large angle double rotor CaM synthetic data. These are the Frame_order.test_cam_double_rotor_large_angle, Frame_order.test_cam_double_rotor_large_angle_rdc, and Frame_order.test_cam_double_rotor_large_angle_pcs system tests.
  • Added the full optimisation results for the torsionless pseudo-ellipse frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added the full optimisation results for the 2nd free rotor isotropic cone frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Small fix for the large angle CaM double rotor frame order model synthetic test data. The way the rotation angle was calculated was slightly out due to integer truncation. The integers are now converted to floats in the generate_distribution.py script and all of the PCS and RDC data averaged over ~20 million states has been recalculated.
  • Added proper support for the double rotor frame order models to the system test scripts. This is for the CaM synthetic data. The base script can now handle the current parameterisation of the double rotor model with a single pivot, an eigenframe, and the second pivot defined by a displacement along the z-axis. The scripts for the double_rotor and double_rotor_large_angle data sets have been changed to use this parameterisation as well.
  • Attempt at implementing the 2nd degree frame order matrix for the double rotor model. This is required for the RDC.
  • The second torsion angle is now printed out for the frame order system tests. This is in the system test class mesg_opt_debug() method and allows for better debugging of the double rotor models.
  • Fix for the Frame_order.test_cam_double_rotor_large_angle* system tests. The system test script was pointing to the wrong data directory.
  • The double rotor frame order system tests are no longer blacklisted.
  • Updated the chi-squared values being checked for the double rotor frame order system tests.
  • Shifted the frame order geometric representation functions into their own module. This is the new specific_analyses.frame_order.geometric module.
  • The frame order geometric representation functions are no longer PDB specific. Instead the format argument is accepted. This will allow different formats to be supported in the future. Because of this change, all specific_analyses.frame_order.geometric.pdb_*() functions has been renamed to create_*().
  • Created an auxiliary function for automatically generating the pivots of the frame order analysis. This is the new specific_analyses.frame_order.data.generate_pivot() function. It will generate the 1st or 2nd pivot, hence supporting both the single motion models and the double motion double rotor model.
  • Shifted the rotor generation for the frame order geometric representation into its own function. This is the specific_analyses.frame_order.geometric.add_rotors() function which adds the rotors are new structures to a given internal structural object. The code has been extended to add support for the double rotor model.
  • Fix for the pivots created by the specific_analyses.frame_order.data.generate_pivot() function. This is for the double rotor model where the 1st mode of motion is about the 2nd pivot, and the 2nd mode of motion about the 1st pivot.
  • Fixes for the cone geometric representation in the internal structural object. The representation can now be created if the given MoleculeContainer object is empty.
  • Refactored the frame order geometric motional representation code. The code of the specific_analyses.frame_order.geometric.create_geometric_rep() function has been spun out into 3 new functions: add_rotors(), add_axes(), and add_cones(). This is to better isolate the various elements to allow for better control. Each function now adds the atoms for its geometric representation to a separate molecule called 'axes' or 'cones'. The add_rotors() does not create a molecule as the lib.structure.represent.rotor.rotor_pdb() function creates its own. As part of the rafactorisation, the neg_cone flag has been eliminated.
  • Renamed the residues of the rotor geometric object representation. The rotor axis atoms now belong to the RTX residue and the propeller blades to the RTB residue. The 'RT' at the start represents the rotor and this will allow all the geometric objects to be better isolated.
  • Improvements to the internal structural object _get_chemical_name() method. This now uses a translation table to convert the hetID or residue name into a description, for example as used in the PDB HETNAM records to give a human readable description of the residue inside the PDB file itself. The new rotor RTX and RTB residue names have been added to the table as well.
  • Renaming of the residues of the cone geometric representation. The cone apex or centre is now the CNC residue, the cone axis is now CNX and the cone edge is now CNE. These used to be APX, AXE, and EDG respectively. The aim is to make these names 100% specific to the cone object so that they can be more easily selected for manipulating the representation and so that they are more easily identifiable. The internal structural object _get_chemical_name() function now returns a description for each of these. Note that the main cone object is still named CON.
  • The motional pivots for the frame order models are now labelled in the geometric representation. The pivot points are now added as a new molecule called 'pivots' in the frame_order.pdb_model user function. The atoms all belong to the PIV residue. The pymol.frame_order user function now selects this residue, hides its atoms, and then shows the atom name 'Piv' as the label. For the double rotor model, the atom names 'Piv1' and 'Piv2' are used to differentiate the pivots.
  • Renamed the lib.structure.represent.rotor.rotor_pdb() function to rotor(). This function is not PDB specific and it just creates a 3D structural representation of a rotor object.
  • Added support for labels in the rotor geometric object for the internal structural object. The labels are created by the frame_order.pdb_model user function backend. For the double rotor model, these are 'x-ax' and 'y-ax'. For all other models, the label is 'z-ax'. The labels are then sent into the lib.structure.represent.rotor.rotor() function via the new label argument. This function adds two new atoms to the rotor molecule which are 2 Angstrom outside of the rotor span and lying on the rotor axis. These then have their atom name set to the label. The residue name is set to the new RTL name which has been added to the internal structural object _get_chemical_name() method to describe the residue in the PDB file for the user. Finally the pymol.frame_order user function selects these atoms, hides them and then labels them using the atom name (x-ax, y-ax, or z-ax).
  • Modified the rotor representation generated by the pymol.frame_order user function. This is to make the object less bulky.
  • Redesign of the axis geometric representation for the frame order motions. This is now much more model dependent to avoid clashes with the rotor objects and other representations: For the torsionless isotropic cone, a single z-axis is created; For the double rotor, a single z-axis is produced connecting the two pivots, from pivot2 to pivot1; For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are created; For the torsionless pseudo-ellipse, all three x, y and z-axes are created; For all other models, no axis system is produced as this has been made redundant by the rotor objects.
  • Fixes for the cone geometric object created by the frame_order.pdb_model user function. This was broken by the code refactoring and now works again for the pseudo-ellipse models.
  • Fix for the pymol.frame_order user function. The representation function for the rotor objects was hiding all parts of the representation, hence the pivot labels where being hidden. To fix this, the hiding of the geometric object now occurs in the base frame_order_geometric() function prior to setting up the representations for the various objects.
  • Started to redesign the frame_order.pdb_model user function. Instead of having the positive and negative representations in different PDB models, and the Monte Carlo simulations in different molecules, these will now all be shifted into separate files. For this to be possible, the file root rather than file names must now be supplied to the frame_order.pdb_model user function. To allow for different file compression, the compress_type argument is now used. The backend code correctly handles the file root change, but the multiple files are not created yet.
  • Python 3 fixes using the 2to3 script. Fatal changes to the multi.processor module were reverted.
  • Improvements to the lib.structure.represent.rotor.rotor() function for handling models. The 'rotor', 'rotor2', or 'rotor3' molecule name determination is now also model specific.
  • The frame order generate_pivot() function can now return the pivots for Monte Carlo simulations. This is the specific_analyses.frame_order.data.generate_pivot() function. The sim_index argument has been added to the function which will allow the pivots from the Monte Carlo simulations to be returned. If the pivot was fixed, then the original pivot will be returned instead.
  • Test suite fixes for the recent redesign of the frame_order.pdb_model user function.
  • Fixes for the frame_order.pdb_model user function for the rotor and free rotor models.
  • Redesign of the geometric object representation part of the frame_order.pdb_model user function. The positive and negative representations of the frame order motions have been separated out into two PDB files rather than being two models of one PDB file. This will help the user understand that there are two identical representations of the motions, as both will now be displayed rather than having to understand the model concept of PyMOL. The file root is taken, for example 'frame_order', and the files 'frame_order_pos.pdb' and 'frame_order_neg.pdb' are created. If no inverse representation exists for the model, the file 'frame_order.pdb' will be created instead. The Monte Carlo simulations are now also treated differently. Rather than showing multiple vectors in the axes representation component within one molecule in the same file as the frame order representation, these are now in their own file and each simulation is now a different model. If an inverse representation is present, then the positive representation will go into the file 'frame_order_sim_pos.pdb', for example, and the negative representation into the file 'frame_order_sim_neg.pdb'. Otherwise the file 'frame_order_sim.pdb' will be created.
  • Clean up of the frame_order.pdb_model user function definitions. Some elements were no longer of use, and some descriptions have been updated.
  • Redesign of the pymol.frame_order user function to match the redesign of frame_order.pdb_model. The file names are no longer given but rather the file root. Then all PDB files matching that file root in the given directory will be loaded into PyMOL.
  • Updated all of the frame order scripts for the frame_order.pdb_model and pymol.frame_order changes. These are the scripts for the CaM frame order test data.
  • Redesign of the average domain position part of the frame_order.pdb_model user function. The Monte Carlo simulations are now represented. If the file root is set to the default of 'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a compressed version. Each simulation is in a different model, matching the geometric representation '*_sim.pdb' files. The original structure is copied for each model, and then rotated to the MC simulation average position.
  • Change all of the domain user function calls in the frame order CaM test data scripts. The domains are now identified by the molecule name rather than the range of residues. This allows non-protein atoms, for example the Ca2+ atoms, to be rotated to the average domain position as well.
  • The PyMOL disable command is now used by the pymol.frame_order user function. This is to first disable all PyMOL objects prior to loading anything, to hide the original structures and any previous frame order representations, and then to hide all of the Monte Carlo simulation representations. This is to simplify the picture initially presented to the user while still allowing all elements to be easily found.
  • The pymol.frame_order user function now centers and zooms on all objects.
  • Simplified the PyMOL view commands in all of the CaM test data optimisation scripts. The pymol.view user function is not necessary as the PyMOL GUI will be launched by the pymol.frame_order user function. And the pymol.command user function call for running the 'hide all' command is also now redundant.
  • Removed all remaining uncompressed PDB files from the CaM test data directories. These were complicating the debugging of the pymol.frame_order user function, as they were being loaded on top of the compressed versions.
  • Removed some rotation files from the CaM frame order test data directories. These files are no longer of any use and just take up large amounts of room for nothing.
  • Added titles to the frame order geometric representation PDB files from frame_order.pdb_model. These are in the form of special Ti atoms placed 40 Angstrom away from the pivot along the z-axis of the system, or shifted 3 more Angstrom for the Monte Carlo simulations. These are used to label the alternative representations or the Monte Carlo simulation representations. The residue type is set to TLE and this has been registered in the internal structural object. The pymol.frame_order user function now calls the represent_titles() function to select these atoms, hide them, and then add a long descriptive title. The atom name is used to distinguish between different titles.
  • Changed the alternative representation names for the frame order geometric objects. The aim is to put both representations on a more equal footing, as they are identical solutions. Hence the inverted representation might be the correct representation of the domain motions. So instead of calling these 'positive' and 'negative', the 'A' and 'B' notation will be used. This affects the names of the files produced by the frame_order.pdb_model user function as well as the internal titles. Instead of ending the files with "*_pos.*" and "*_neg.*", these have been changed to "*_A.*" and "*_B.*". The atoms used for the titles have also been renamed, and the pymol.frame_order user function now labels the titles using the 'A' and 'B' notation.
  • Changes to the rotor object in the frame order geometric representations. For the isotropic and pseudo-elliptic cone models, the rotor is now halved. Instead of having two axes radiating from the central pivot and terminating in the propeller blades, now only the positive axis is shown lying in the centre of the cone.
  • Fixes for the MC simulation rotor objects in the frame order geometric representation. The axes of the Monte Carlo simulation rotors objects were being set to the original values and not to the simulation values.
  • Fixes for the titles in the frame order geometric representation from frame_order.pdb_model. There were a few bugs for a number of the frame order models preventing this code from working.
  • Redesign of the geometric representation of the cone structural objects to allow for models. The old representation was not compatible with the PDB model concept whereby each model must have the same number of atoms. To handle this situation, the cone objects have been simplified. Specifically the cone cap. The old behaviour was to remove all points outside of the cone when creating the cone cap, and then to stitch the cap to the cone edge in a subsequent step. Now the behaviour is that all points outside of the distribution are shifted to the cone edge. This avoids the need to stitch the cap to the edge. This behaviour means that all cones with the same inc value will have the same number of atoms. The cones for the pseudo-ellipses are not as nice as the latitudinal lines are not strait at the cone edge, but at least creating multiple models with different cone sizes is now possible.
  • Bug fix for the y-axis rotation matrix for the double rotor Sobol' integration points. The matrix was inverted.
  • Updated the frame order system test chi-squared values for the previous fix.
  • Fixes for the double rotor frame order system tests for the CaM synthetic data. The torsion angles needed to be swapped and the pivot point changed from the C terminal domain CoM to the N domain CoM.
  • More fixes for the double rotor frame order system tests for the CaM synthetic data. The eigensystem was inverted.
  • Updated the χ2 check for the large angle double rotor frame order system tests. This is needed for the eigenframe fix.
  • Updates for the frame order system tests for the float32 to float64 change. Some chi-squared values have slightly changed.
  • The CaM frame order test data optimisation scripts now save more state files. The state of the true dynamics and the fixed pivot optimisation results are now stored as well. This might be useful for extracting these results without redoing the calculations.
  • The script for representing the frame order dynamics for the CaM test data has been updated. The domains of the system are now defined.
  • Changed the CaM frame order test data superimposition values. Because the domains are now defined via the molecule name rather than the residue numbers, the centroid of rotation set to the CoM has been shifted as now the Ca2+ ions are included in the CoM calculation. Therefore the superimpose.py script has been updated to not delete the Ca atoms. All of the frame order optimisation scripts have been updated with the new rotation Euler angles and translation vector. To match this, the system test base script for the CaM frame order test data has also had its rotations and translations updates, and the domain user function call changed to use molecule names.
  • Updated all of the CaM frame order system test chi-squared values. These have changed slightly due to the rotation and translation changes.
  • Added support for the 'pivot_disp' frame order parameter to the grid search. This is required for the double rotor model.
  • Changed some of the default values for the frame order auto-analysis. The number of Sobol' quasi-random integration points were far too low to obtain any reasonable results.
  • Simplified the PyMOL visualisation relax script created by the frame order auto-analysis. This now consists of a single pymol.frame_order user function call. The other pymol user function calls were unnecessary.
  • Added the full optimisation results for the large angle double rotor frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Added model support for the rotor geometric object. This is the structural object used in the frame order analysis to create PDB representations of rotor motions. The number of atoms created for the rotor is now constant, allowing for models whereby the atom number and connectivity must be preserved between all models.
  • Changed the grid search pivot displacement frame order parameter. Instead of searching from 0 to 50 Angstroms, the search is now from 10 to 50. This is to avoid the edge case of pivot_disp = 0.0 from which the optimisation cannot escape.
  • Speedup of the PCS component of the rigid frame order model. The lanthanide to atom vectors are now being calculated outside of the alignment tensor and spin loops, as well as the inverse vector lengths to the 5th power. This increases the speed by a factor of 1.216 (from 38.133 to 31.368 seconds for 23329 calls of the func_rigid() target function).
  • Added the full optimisation results for the rigid frame order model. This is for the CaM test data using the new frame_order.py optimisation script.
  • Numpy ≤ 1.6 fixes for the frame order PCS code. The numpy.linalg.norm function does not have an axis argument in numpy 1.6, therefore the lib.compat.norm() function is now used instead. This function was created exactly for this axis argument problem.
  • Created the new specific_analyses.frame_order.variables module. This currently contains variables for all of the frame order model names, as well as various lists of these models. The rest of the frame order specific analysis code as well as the frame order user functions have been converted to use these model variables exclusively rather than having the model name strings hardcoded throughout the codebase.
  • Added the full optimisation results for the double rotor test data. This is for the CaM frame order test data using the new frame_order.py optimisation script.
  • Added a script for profiling the target function calls of the pseudo-ellipse frame order model.
  • Added a timeit script and log file showing how numpy.cos() is 10 times slower than math.cos(). This is for single floats.
  • Shifted the calculation of the θmax cone opening for the pseudo-ellipse outside of all loops. This is infrastructure change for potentially eliminating all of the looping for the PCS numeric integration in the future. It however slightly speeds up the pseudo-ellipse frame order model. Using 500 target function calls in the profiling_pseudo_ellipse.py script in test_suite/shared_data/frame_order/timings/, the time spent in the pcs_pivot_motion_full_qrint() function decreases from 20.849 to 20.719 seconds.
  • Converted the torsionless pseudo-ellipse model to also use the tmax_pseudo_ellipse_array() function. This allows the calculation of the pseudo-elliptic cone opening θmax to be shifted outside of all loops.
  • Created a profiling script and log file for the isotropic cone frame order model. This shows where the slow points of the model are, using 2000 target function calls.
  • Increased the function call number to 500 in the pseudo-ellipse frame order model profiling script. The profiling log file has also been added to show where the slowness is - specifically that the numeric PCS integration takes almost the same amount of time as the RDC frame order matrix construction using the scipy.integrate.quad() function.
  • Created the specific_analyses.frame_order.checks.check_pivot() function. This is to check that the pivot point has been set.
  • The frame order grid search is now checking if the pivot point has been set.
  • Added a profiling script and log file for the free rotor frame order model.
  • Updated the frame order optimisation results for the CaM isotropic cone test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository and the old ones removed.
  • Modified the script for recreating the frame order PDB representation and displaying it in PyMOL. The state loading, domain redefinition, and representation creation parts have all been removed, as these will soon all be redundant as the frame order analysis for all models is being redone. All that remains are the pymol.frame_order() function calls for displaying all the representations.
  • The pivot point parameters in the frame order analysis are no longer scaled by 100. This is to match the average domain position translation which is also not scaled.
  • The specific_analyses.frame_order.variables module is now used throughout the frame order code. The target function code, auto-analysis, and test suite now all use the variables defined in this module rather than having hardcoded strings. The MODEL_LIST_NONREDUNDANT variable has been created to exclude the redundant free rotor pseudo-ellipse which cannot be optimised, and this is used by the auto-analysis.
  • Removal of many unused imports in the frame_order_cleanup branch. These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find all unused imports. The false positives also present in the trunk were ignored. And the unused imports in the dispersion code were also left for clean up the disp_spin_speed branch.
  • Changed the minimisation in the frame order system tests where optimisation is activated. The number of iterations is now set to 1 for speed testing, and the constraints are turned on.
  • Turned on the optimisation flag for the Frame_order.test_cam_free_rotor system test. This is to activate code paths currently not tested by the test suite.
  • Constraints are now properly turned off in the minimise user function for the frame order analysis. The A and b matrices from linear_constraints() are now set to None if they are returned as empty arrays.
  • Parallelised the frame order optimisation code to run on clusters or multi-core systems via OpenMPI. The optimisation code has been split into the three standard parts of the multi-processor: 1) Frame_order_memo is the new Memo object used to store data on the master for use when data is returned from the slaves. 2) Frame_order_minimise_command is the Slave_command which stored all required data for the optimisation, is pickled and sent to a slave, sets up the target function, and then performs optimisation. 3) Frame_order_result_command is the Result_command initialised by the Slave_command on the slave for pickling and returning results to the master. To avoid pickling the target function class, which is not possible, the store_bc_data() and target_fn_setup() functions of the specific_analyses.frame_order.optimisation module have been redesigned to work with basic data structures rather than the target function class directly. The target_fn_setup() function no longer returns an initialised target function class, but rather all the data assembled prior to the initialisation. And the target function class was itself modified so that pcs_theta and rdc_theta are always defined to allow the store_bc_data() function to be used successfully. This parallelisation currently only allows the Monte Carlo simulations to be run on slave processors.
  • The frame order linear_constraints() function now returns None if no constraints are present. This allows the code using this to be simplified with respect to turning off the constraints.
  • Improvements for the printout at the start of optimisation of the frame order models. This is in the target_fn_setup() frame order method. All the printouts are now in one place and they are now better formatted and better controlled.
  • Parallelised the frame order grid search to run on clusters or multi-core systems via OpenMPI. This involved the creation of the Frame_order_grid_command class which is the multi-processor Slave_command for performing the grid search. This was created by duplicating the Frame_order_minimise_command class and then differentiating both classes. For the subdivision of the grid search, the new minfx grid.grid_split_array() function is used in the frame order grid() API method. The grid() method no longer calls the minimise() method but instead obtains the processor box itself and adds the subdivided grid slaves to the processor. The relax grid_search user function takes care of the rest.
  • Fixes for the parallelised grid search for the frame order analysis. A chi-squared value check was added to the Frame_order_result_command.run() method to check if the value is lower than the current when the result is returned to the master. Without this check, each grid subdivision result will be stored as they are returned rather than storing the results from the global minimum of the entire grid search.
  • Added a script for testing out the parameter nesting abilities of the frame order auto-analysis. This script attempts to find the dynamics solution without knowing where the pivot is located. Hence this will be as in the auto-analysis were this pivot point will be used as the base for all other models.
  • Sent the verbosity argument to the minfx.grid.grid_split() function for the frame order analysis. This matches the relax trunk changes for the model-free analysis. The minfx function in the next release (1.0.8) will now be more verbose, so this will help with user feedback when running the model-free analysis on a cluster or multi-core system using MPI.
  • Improvements for the parallelised grid search for the frame order analysis. As each grid point can take wildly different numbers of CPU cycles to calculate the chi-squared value for, the result of subdividing the grid search was that some subdivisions where incredibly quick while others required much larger amounts of time. To avoid this bad slave management, the grid points are now randomised. This means that the subdivisions will require about the same amount of time to optimise.
  • Moved the setup of the target function data structures in the frame order analysis. This is for the grid_search and minimise user functions. The target function data setup function has been renamed to target_fn_data_setup(). This is now called before the Frame_order_grid_command and Frame_order_minimise_command multi-processor objects are initialised, and all of the data is now passed into these functions. Although the code is uglier, this has the benefit that the target_fn_data_setup() function will only be called once. This data setup requires a lot of time, so for a large cluster, this can be a large time saving for the grid search.
  • Modified the frame_order_free_start.py script to better mimic the frame order auto-analysis.
  • Updated the frame order optimisation results for the 2nd CaM free rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM free rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM missing data free rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM free rotor isotropic cone test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM small angle rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the 2nd CaM free rotor isotropic cone test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM pseudo-ellipse test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM torsionless isotropic cone test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the 2nd CaM pseudo-elliptic cone test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Some more fixes for the optimisation user function changes.
  • Removed the parameter scaling for the pivot point frame order parameters. These were already removed from the frame_order_cleanup branch in the assemble_scaling_matrix() function, however they were reintroduced accidentally via the parameter object where this information is now defined. So this removes the scaling a second time.
  • Fixes for the parameter scaling changes in the trunk. The scaling flag is no longer part of the specific analysis API optimisation methods. Instead the pre-assembled scaling matrices are passed into all three API optimisation methods.
  • Implemented the frame order specific analysis API method print_model_title(). This is simply aliased from the API common method _print_model_title_global().
  • Fix for the grid search in the frame order analysis. This is a recently introduced problem due to the changes of the zooming_grid_search branch.
  • Turned on the optimisation in the Frame_order.test_cam_rigid system test. This is to catch a number of failures in the frame order grid search.
  • Activated the grid search in the frame order system tests using the CaM synthetic data. This is set to one increment so that the tests can complete in a reasonable time.
  • Fix for the specific_analyses.frame_order.optimisation.grid_row() function. This can now handle the case of a single grid increment. The change is similar to r163 in the minfx project.
  • Converted the frame_order_free_start.py script to use the zooming grid search.
  • Added lots of calls to the time user function to the frame_order_free_start.py. This will be used to fine tune the frame order analysis on a cluster.
  • Increased the default grid bounds for the pivot parameters of the frame order models. The pivot point is now searched for in a 50 Angstrom box and the pivot displacement for the double motion models from 10 to 60 Angstroms. These were originally a 20 Angstrom box and 10 to 50 Angstroms. The larger grid is possible when combined with the new zooming grid search.
  • Updated the frame order optimisation results for the 2-site CaM test data fitting to the rotor model. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the 2nd CaM rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Fixes for the CaM free-rotor pseudo-ellipse frame order model test data set. This is for the constraint 0 ≤ θx ≤ θy ≤ π, as the old data was created with θx > θy. The new data is also of high quality using 20 million structures and numpy.float128 data averaging.
  • Created the lib.frame_order.rotor_axis.convert_axis_alpha_to_spherical() function. This will convert the axis α angle to the equivalent spherical angles θ and φ.
  • Renamed the lib.frame_order.rotor_axis module to lib.frame_order.conversions. This module will be used for all sorts of frame order parameter conversions.
  • Added the pipe_name argument to the specific_analyses.frame_order.data.generate_pivot() function. This allows the pivot from data pipes other than the current one to be assembled and returned.
  • Updated the frame order optimisation results for the CaM free rotor, pseudo-ellipse test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Updated the frame order optimisation results for the CaM torsionless, pseudo-ellipse test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
  • Fix for the Frame_order.test_cam_pseudo_ellipse_free_rotor system test. This is for the change of the X and Y cone opening angles.
  • Redesign and expansion of the nested model parameter copying in the frame order auto-analysis. The nested parameter protocol used to allow the analysis to complete in under 1,000,000 years was no longer functional due to the switching to the axis α parameter to decrease parameter number and redundancy. The copying of the average domain position for the free rotor models was also incorrect as the dropping of the α Euler angle cause the translation parameters and β and γ angles to change drastically. The new protocol has been split into four methods for the average domain position, the pivot point, the motional eigenframe and the parameters of ordering. These use the fact that the free rotor and torsionless models are the two extrema of the models where the torsion angle is restricted. The pivot copying is a new addition.
  • Created the Frame_order.test_auto_analysis system test. This will be an extremely quick run through of the frame order auto-analysis as this is not currently tested. 1 Sobol' quasi-random integration point will be used for all models for speed. The system test uses the rigid CaM test data to perform a full analysis.
  • Alphabetical ordering of the imports in the frame order auto-analysis module.
  • Fixes for the backend script of the Frame_order.test_auto_analysis system test. This includes a missing import and the removal of a long ago deleted user function.
  • Fix for the frame order auto-analysis for the call to the grid search user function. This user function has been renamed to minimise.grid_search, however not all parts of the analysis had been converted to the new name.
  • Created a method in the frame order auto-analysis to reorder the models. This is needed as the nested model parameter copying protocol requires the simpler models to be optimised first.
  • The Frame_order.test_auto_analysis system test now writes all files to the directory of ds.tmpdir. This is to prevent the system test from dumping files in the current directory.
  • Modified the specific_analyses.frame_order.parameters.update_model() function. This will no longer set all parameters to 0.0, excluding the pivot point.
  • Modified the specific_analyses.frame_order.parameters.assemble_param_vector() function. This can now handle the case of no parameters being present. The corresponding elements of the numpy array will consist of NaN values.
  • Better handling of unset parameters in the frame order optimisation functions. The specific_analyses.frame_order.optimisation.target_fn_data_setup() and specific_analyses.frame_order.parameters.assemble_param_vector() function both now accept the unset_fail argument. This is set in both the calculate() and minimise() API methods. When set, a RelaxError will be raised in the assemble_param_vector() function when a parameter has not been set yet. This together with previous changes will prevent the frame order analysis from using 0.0 as a starting value for unset parameters.
  • Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests. The base script now sets all parameter values so that the minimise.calculate user function can operate. The two free rotor model chi-squared values have been updated as these are sensitive to the motional eigenframe parameter values - these models can never approximate a rigid state.
  • Modified the optimisation of the rigid model in the frame order auto-analysis. The grid search is now implemented as a zooming grid search.
  • Updates and fixes for the frame order auto-analysis. The custom grid setup now works for the new reduced parameter set models and the double rotor model is now also included. The cone axis α angle to spherical angle conversion has had a bug removed. And some of the printouts are now more detailed.
  • Redesigned the Frame_order.test_auto_analysis system test. This now uses a hypothetical new Optimisation_settings object from the frame order auto-analysis module for holding all of the grid search, zooming grid search and minimisation settings. This will allow for far greater user control of the settings and hugely simplify the auto-analysis interface by decreasing the number of input arguments. It should also be less confusing.
  • Implementation of the Optimisation_settings object in the frame order auto-analysis. This object holds all of the grid search, zooming grid search, and minimisation settings. It provides the add_grid() and add_min() methods to allow the user to add successive iterations of optimisation and settings to the object. The loop_grid() and loop_min() methods are used to loop over each iteration of each method. And the get_grid_inc(), get_grid_num_int_pts(), get_grid_zoom_level(), get_min_algor(), get_min_func_tol() and get_min_num_int_pts() methods are used to access the user defined settings. The auto-analysis has been redesigned around this new concept. All of the optimisation arguments have been replaced. Instead there are the opt_rigid, opt_subset, opt_full, and opt_mc arguments which are expected to be instances of the Optimisation_settings object. The optimisation in the auto-analysis is now more advanced in that more user optimisation settings are now available and active.
  • Added linear constraints for the pivot and average domain translation frame order parameters. The pivot coordinates are constrained between -999 and 999 Angstrom and the translation between -500 and 500 Angstrom. This allows the frame_order.pdb_model user function to operate in the case of failed models - often the free rotors fitting to torsionally restricted data - by preventing the PDB coordinates from being out of the PDB format range. It should also speed up optimisation by stopping the optimisation of failed models earlier.
  • The frame order auto-analysis Optimisation_settings object now handles the maximum iterations. The new max_iter argument has been added to the add_min() method, and the new get_min_max_iter() method added to fetch the value. This is used in the auto-analysis to set the maximum number of optimisation iterations in the minimise.execute user function calls. Limiting this will be of greatest benefit for the test suite.
  • Speedup of the Frame_order.test_auto_analysis system test. This involves limiting the maximum number of optimisation steps to 20 for most parts (the rigid model excluded so the average domain position is correctly found), and using the PCS subset data for the full data set.
  • Updated the full_analysis.py script for the CaM frame order test data. This is for the recent changes to the auto-analysis with the Optimisation_settings object and for the changes of this branch.
  • Removed the RDC data checks from the frame order optimisation. This is in the minimise_setup_rdcs() and store_bc_data() functions of the specific_analyses.frame_order.optimisation module, called before and after all optimisation. The reason was identified by profiling - this check was adding significant amounts of time to the setup and results unpacking parts of the optimisation. Specifically the interatomic_loop() function was identified via profiling as the function requiring the most amount of cumulative time in the Frame_order.test_auto_analysis system test (17 seconds out of a total of ~60 seconds).
  • Fixes for the removal of the RDC data checks from the frame order optimisation functions. The specific analysis API method overfit_deselect() has now been created to deselect spins which do not have PCS data or interatomic data containers missing RDC data. The handling of deselected spins and interatomic data containers is now also correctly handled throughout the frame order specific code.
  • Enabled pivot optimisation in the full_analysis.py script for the CaM frame order test data.
  • The frame order auto-analysis now calls the time user function. This is used at the start of each model section, as well as at the very start and very end of the analysis. This feedback is needed for the user to be able to optimise the optimisation settings.
  • Major bugfix for the frame order auto-analysis. The algorithm of using a PCS data subset of a few selected residues to find an initial parameter estimate followed by using all PCS data was badly implemented. The use of the PCS subset caused most spin systems to be deselected, however they remained deselected once all data was being used. So the result was that only the spin subset was ever being used in the analysis.
  • Fix for the recent lib.period_table and lib.physical_constants module changes.
  • Created the model_directory() method for the frame order auto-analysis. This is used to create the full path for saving model specific files. It replaces spaces with underscores in the path and removes all commas. The commas in the path appear to be fatal for certain PyMOL versions when viewing the frame order representation.
  • The frame order auto-analysis results printout has been extended to include the pivot point.
  • Change to the parameter nesting in the frame order auto-analysis. The pivot is now taken from the rotor model for all other models. Taking the pivot point from the isotropic cone model is not a good idea as there are situations where the pivot point optimisation catastrophically fails, sending the point many tens or hundreds of Angstrom away from the molecule.
  • Copied a frame order results file for testing axis permutations. This is from the test_suite/shared_data/frame_order/cam/pseudo_ellipse/ directory. The optimisation results were identified to have failed, in that it found the alternative minimum. The pseudo-ellipse model as two minima in the space, and in this case the global minimum was missed.
  • Created the Frame_order.test_axis_permutation system test. This is to test the operation of the yet-to-be implemented frame_order.permute_axes user function.
  • Implemented the frame_order.permute_axes user function. This is used to switch between local minima in the pseudo-elliptic frame order models.
  • Fix for the Frame_order.test_axis_permutation system test. The motional eigenframe in the old log file was not exactly correct and did not correspond exactly to the Euler angles in the cam_pseudo_ellipse.bz2 results file in test_suite/shared_data/frame_order/axis_permutations/.
  • Extended the Frame_order.test_axis_permutation system test to check frame_order.permute_axes twice. This will check that two calls to the frame_order.permute_axes user function will restore the original parameter values.
  • The frame_order.permute_axes user function can now handle the torsionless pseudo-ellipse. This model does not have the variable cdp.cone_sigma_max set.
  • Added support for axis permutations in the frame order auto-analysis. This is done by copying the data pipe of the already optimised pseudo-elliptic models, permuting the axes, and performing another optimisation using all RDC and PCS data. This allows the second solution for these pseudo-elliptic models to be found. The 2nd pipe is included in the model selection step to allow the best solution for the model to be found.
  • Fix for the reading of old results files in the frame order auto-analysis. The directory name is now processed by the model_directory() method. This will convert the spaces to '_' and remove commas. Without this the already created files could not be found, if the model name contains a space or comma.
  • Made the pivot point in the frame order PDB representation fail-proof. If the pivot position was outside of the bounds [-1000, 1000], the PDB file creation would fail as the record would be too long. So now the pivot is shifted to be in these bounds.
  • The axis permutation step in the frame order auto-analysis is now always performed. If an old results file was found, this step was accidentally skipped.
  • Added extensive printouts to the frame_order.permute_axes user function.
  • Redesigned the frame_order.permute_axes user function frontend. Previously only cyclic permutations were considered, however non-cyclic permutations are also allowed when accompanied by an axis inversion. Therefore 3 combinations exist with cone_theta_x ≤ cone_theta_y, or 2 when the current combination is excluded.
  • Created 6 system tests for the frame_order.permute_axes user function. This covers the 3 starting conditions (x<y<z, x<z<y, z<x<y) and the two permutations ('A' and 'B') for each of these which do not include the starting permutation. They replace the original Frame_order.test_axis_permutation system test with the tests Frame_order.test_axis_perm_x_le_y_le_z_permA, Frame_order.test_axis_perm_x_le_y_le_z_permB, Frame_order.test_axis_perm_x_le_z_le_y_permA, Frame_order.test_axis_perm_x_le_z_le_y_permB, Frame_order.test_axis_perm_z_le_x_le_y_permA, and Frame_order.test_axis_perm_z_le_x_le_y_permB.
  • Implemented the new frame_order.permute_axes backend. The 3 starting conditions x<y<z, x<z<y, and z<x<y and the two permutations 'A' and 'B' (for each of these which do not include the starting permutation) are now supported. For these 6 combinations, the axis and order parameter permutation and the z-axis inversion are selected and applied to the current system.
  • Removed the second permutation from the 6 Frame_order.test_axis_perm_* system tests. A second identical permutation does not necessarily restore the original state.
  • Fix for the frame_order.permute_axes for the torsionless pseudo-ellipse model. The data structure cdp.cone_sigma_max does not exist in this model as cone_sigma_max == 0.0.
  • Modified the frame order auto-analysis axis permutation algorithm to handle both permutations. Instead of creating one additional data pipe for the permutations, two are now created for the permutations 'A' and 'B'. This allows all 3 solutions for the pseudo-elliptic models to be explored and included in the final model selection process.
  • Fix for the Frame_order.test_axis_perm_x_le_z_le_y_permB system test. The permuted z-axis needs to be inverted in the test.
  • Many fixes for the frame_order.permute_axes user function. The z-axis inversion is now encoded into a 3D numpy array as the index of the new z-axis position needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max parameters are now permuted in reverse 'perm' data structure by calling its index() method. And the cone_theta_x - cone_theta_y to y-axis - x-axis switch has been removed (this may need to be reintroduced later).
  • Fix for the axis permutation protocol in the frame order auto-analysis. The pipe.copy user function does not switch pipes, therefore the pipe.switch user function is now being called so that the correct pipe is being permuted and optimised.
  • Created some test data files for visualising the frame order axis permutation. This uses the CaM frame order synthetic data for the rotor model to visualise the pseudo-ellipse frame order model axis permutations. The initial conversion sets the pseudo-ellipse torsion angle cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic cone opening to close to zero. Then the axis permutations are performed. All three solutions are optimised. PDB representations before and after optimisation are included to illustrate any problems.
  • Bug fix for the new frame_order.permute_axes user function. The cone and torsion angles were not being correctly permuted. Now the direct permutation array is being used. And the fact that cone_theta_x is a rotation along the y-axis and cone_theta_y along the x-axis is taken into account.
  • Redesign of the axis permutation algorithm of the frame_order.permute_axes user function. Instead of tracking the fact that cone_theta_x is a rotation around the y-axis and cone_theta_y is about the x-axis, now two permutation arrays are created - one for the three angles and one for the axes. The permutation array values have also been completely changed as previously the incorrect inverse permutation was coded into the algorithm.
  • Updated the frame order pseudo-ellipse motion permutation test data. This is for the CaM frame order rotor model synthetic data. The correct axis and cone angle permutations of the frame_order.permute_axes user function are now being used and optimised.
  • Renamed the pseudo-ellipse permutation directory to perm_pseudo_ellipse_x_le_y_le_z. This is for the CaM frame order rotor model synthetic data.
  • Fix for the frame_order.permute_axes user function. One of the 6 permutations had the x and y axes switched (the x ≤ z ≤ y condition, permutation A).
  • Visualisation files for all of the pseudo-ellipse permutations by frame_order.permute_axes. This includes the x ≤ z ≤ y and z ≤ x ≤ y conditions (the previous files were for x ≤ y ≤ z). In all permutation combinations, optimisation has been performed to demonstrate that these are all local minima. These all approximate the rotor when using the CaM frame order rotor model synthetic data.
  • Added support for the isotopic cone models to the frame_order.permute_axes user function. This is a simpler setup, but it uses the same permutation algorithm as derived for the pseudo-ellipse models. Instead of setting the x and y cone angles separately, they are instead averaged. And as the cone axis is undefined in the xy plane, the axis has been randomly selected as being the axis perpendicular to both the z-axis and the reference frame x-axis.
  • Created set of files showing the axis permutation problem for the isotopic cone frame order model. This shows that there are two minima. However one has a chi-squared value of ~1, and the other a value of ~150. Nevertheless, the optimisation could be trapped in the non-global minimum so the frame_order.permute_axes user function should be used for the isotopic cones as well, just in case.
  • Created the other isotropic cone condition z ≤ x = y. As there are no constraints in this model, this condition should not result in any major differences, just the size of the cone being different and the optimisation having to decrease the cone angle significantly to mimic the rotor.
  • Modified the frame order auto-analysis. The axis permutation algorithm is now performed on all isotopic cone and pseudo-ellipse models. This is just in case the non-global minima was found in the original optimisation. The isotropic cone models possess two local minima whereas the pseudo-ellipse models possess three local minima.
  • Simplified the optimisation in the axis permutation part of the frame order auto-analysis. Only the last, highest quality setting is used for optimisation.
  • Fix for the axis permutation protocol in the frame order auto-analysis. This would fail if a results file for the permuted model already exists as the pipe.copy user function call was being performed too early.
  • Created set of files for the axis permutation of the torsionless isotopic cone frame order model.
  • Created an initial Frame_order.test_frame_order_pdb_model_ensemble system test. This is to check the operation of the frame_order.pdb_model user function when an ensemble of structures is encountered. However as this uses a very minimal number of user functions to set up the system, a number of other minor bugs will probably be uncovered.
  • Added printouts to the specific_analyses.frame_order.parameters.update_model() function. This is to make it easier to understand why certain things fail due to the system not being fully set up.
  • Simplified the operation of the frame_order.select_model user function. This is by removing the check of PCS data from the specific_analyses.frame_order.data.pivot_fixed() function using the base_data_types() function call. This allows the model to be set up more easily.
  • Modified the frame order check_pivot() function to operate on any data pipe. The function now accepts the pipe_name argument so that checks can happen on any data pipe.
  • Missing imports in the specific_analyses.frame_order.checks module. This is from the recent pipe_name argument addition in the check_pivot() function.
  • The frame order generate_pivot() function can now handle no pivot being present. At the start of this specific_analyses.frame_order.data module function, the check_pivot() function is being called to make sure that a pivot is present.
  • Modified the Frame_order.test_frame_order_pdb_model_ensemble system test so it is set up correctly. The pivot point and moving domain are now specified.
  • Added Monte Carlo simulations to the Frame_order.test_frame_order_pdb_model_ensemble system test. This is only setting up Monte Carlo simulation data structures via the monte_carlo.setup user function. This demonstrates a failure of the frame_order.pdb_model user function when an ensemble of structures is present with Monte Carlo simulations.
  • Added support for the model argument for the frame_order.pdb_model user function. This argument is used to specify which of the models in an ensemble will be used to represent the average domain position Monte Carlo simulations, as each simulation is encoded as a model, as well as for the distribution of structures simulating the motion of the system. The argument is therefore passed into the create_ave_pos() and create_distribution() functions of the specific_analyses.frame_order.geometric module. To handle all models being used in the non Monte Carlo simulation PDB file and only one in this file, the internal structural object is copied twice. The second copy for the MC sims has all but the chosen model deleted out of it.
  • Fix for the Frame_order.test_frame_order_pdb_model_ensemble system test. More needed to be done to set up the Monte Carlo simulations - the monte_carlo.initial_values user function call was required.
  • Modified the frame order sim_init_values() API method to handle missing optimisation data. The monte_carlo.initial_values user function was failing if optimisation had not been performed. This is now caught and handled correctly.
  • Created the Frame_order.test_frame_order_pdb_model_failed_pivot system test. This simply shows how the frame_order.pdb_model user function currently fails if the optimised pivot point is outside of the PDB coordinate limits of "%8.3f".
  • The frame_order.pdb_model user function can now properly handle a failed pivot optimisation. This is when the pivot point optimises to a coordinate outside of the PDB limits. Now all calls to specific_analyses.frame_order.data.generate_pivot() from the module specific_analyses.frame_order.geometric set the pdb_limit flag to True. This allows all representation objects to be within the PDB limits. The algorithm in generate_pivot() has been extended to allow higher positive values, as the real PDB limits are [-999.999, 9999.999]. And a RelaxWarning is called when the pivot is outside to tell the user about it.
  • Modified the frame order auto-analysis to be more fail-safe. Almost all of the protocol is now within a try-finally block so that the execution lock will always be released.
  • Fix for the specific_analyses.frame_order.data.pivot_fixed() function. This was recently introduced when the check for PCS data was removed from this function. To fix the problem, instead of calling base_data_types() to see if PCS data is present, the cdp.pcs_ids data structure is checked instead.
  • Fix for the model argument for the frame_order.pdb_model user function. The deletion of structural models for the Monte Carlo simulations in the average domain position representation now only happen if more than one model exists.
  • Modified the Frame_order.test_frame_order_pdb_model_failed_pivot system test. This is to show that the frame_order.pdb_model user function fails if the pivot is close to but still within the PDB coordinate limits.
  • Modified the pivot position checking in specific_analyses.frame_order.data.generate_pivot(). Now the pivot is shifted to be within the limits shrunk by 100 Angstrom. This allows any PDB representation created by the frame_order.pdb_model user function to be within the PDB limits.
  • Fix for the axis permutation protocol in the frame order auto-analysis. If a results file was found for one of the permutations, a return from the function would occur. The result is that the other permutations would not be loaded or optimised.
  • Fix for the RelaxError raised by the frame_order.select_model user function. This is the error if the model name is incorrect.
  • Created the Frame_order.test_pseudo_ellipse_zero_cone_angle system test. This is to catch a bug in optimisation when the cone_theta_x is set to zero in the pseudo-ellipse models.
  • Bug fix for the lib.frame_order.pseudo_ellipse.tmax_pseudo_ellipse_array() function. The problem was that when θx or θy were zero, the floating point value of 0.0 would be returned. This is the incorrect behaviour as the returned value must be an array matching the dimensions of the φ angle array argument.
  • Fix for the Pseudo_elliptic cone object for when the cone angles are zero. The Pseudo_elliptic.phi_max() method now avoids a divide by zero error.
  • Updates for all of the Frame_order.test_axis_perm_* system tests. The axis permutations and angle permutations are now performed correctly within the tests themselves. This allows the tests to pass.
  • Modified the Frame_order.test_pseudo_ellipse_zero_cone_angle system test to be quick. Now that the test passes, the optimisation needs to be short. So a maximum of two iterations are now set. Otherwise the test would take hours to complete.
  • Small speedup of the Frame_order.test_auto_analysis system test.
  • Alphabetical ordering of most of the Frame_order system tests.
  • Created the very simple Frame_order.test_num_int_points system test. This simply creates a data pipe and calls the frame_order.num_int_pts user function to test its operation. This is to increase the test suite coverage of this user function.
  • Created the Frame_order.test_num_int_pts2 system test. This checks the operation of the frame_order.num_int_pts user function when only the model has been chosen.
  • Renamed the Frame_order.test_num_int_points system test to Frame_order.test_num_int_pts.
  • Created the check_domain() function for the frame order analysis. This is in the specific_analyses.frame_order.checks module. The function checks that the reference domain has been specified.
  • Created the check_model() function for the frame order analysis. This is in the specific_analyses.frame_order.checks module. The function checks that the frame order model has been selected via the frame_order.select_model user function.
  • The frame_order.ref_domain user function backend now uses the check_domain() function.
  • Created the check_parameters() function for the frame order analysis. This is in the specific_analyses.frame_order.checks module. The function checks that the frame order parameters have been set up and have values.
  • Created the Frame_order.test_num_int_pts3 system test. This checks the operation of the frame_order.num_int_pts user function when the model has been and the frame order parameters have been set up.
  • Created the Frame_order.test_count_sobol_points system test. This will test that the frame_order.num_int_pts user function can correctly count the number of Sobol' integration points used for the current set of parameter values. This frame_order.num_int_pts functionality does not exist yet.
  • Implementation of the specific_analyses.frame_order.optimisation.count_sobol_points() function. This is used by the frame_order.num_int_pts user function to provide a printout of the number of Sobol' integration points used for the current parameter values. This is to provide user feedback so that it is know if enough Sobol' points have been used.
  • Modified the Frame_order.test_count_sobol_points system test. The number of points has been massively decreased as generating Sobol' points takes a long time, and the check for the number of used Sobol' points has been set to the real value.
  • Created the Frame_order.test_count_sobol_points2 system test. This checks the operation of the frame_order.count_sobol_points user function. As this user function has not been implemented yet, the test currently fails.
  • Created the frame_order.count_sobol_points user function. This is simply a frontend to the new specific_analyses.frame_order.optimisation.count_sobol_points() function.
  • Updated the Frame_order.test_count_sobol_points2 system test for the correct number of Sobol' points.
  • Created the Frame_order.test_count_sobol_points_rigid system test. This is to demonstrate a failure of the frame_order.test_count_sobol_points user function when applied to the rigid frame order model.
  • Fix for the frame_order.count_sobol_points user function for the rigid model. This model is now caught at the start, a message printed out, and the function exited.
  • Fix for the Frame_order.test_count_sobol_points_rigid system test. This now checks that cdp.used_sobol_points does not exist for the rigid frame order model after a call to the frame_order.count_sobol_points user function.
  • Created the Frame_order.test_count_sobol_points_rotor system test. This is to test the frame_order.count_sobol_points user function for the rotor model.
  • Fix for the frame_order.count_sobol_points user function for the rotor model. The σ angles unpacking required a dimensionality collapse in the Sobol' angle data structure.
  • Updated the number of points to allow the Frame_order.test_count_sobol_points_rotor system test to pass.
  • The frame order count_sobol_points() function is now being called by all of minimise user functions. This occurs at the end of the minimise.calculate, minimise.grid_search, and minimise.execute user function backends to provide more feedback to the user as to the quality of the optimisation. To avoid initialising the target function twice, the count_sobol_points() function now accepts the initialised target function as an optional argument.
  • Created the Frame_order.test_count_sobol_points_free_rotor system test. This is to demonstrate that the frame_order.count_sobol_points user function currently fails for the free-rotor model.
  • Fix for the frame_order.count_sobol_points user function for the free-rotor models. The torsion angle is now correctly handled as the 3 free-rotor models do not have cdp.cone_sigma_max set.
  • Updated the number of points in the Frame_order.test_count_sobol_points_free_rotor system test. This is to allow the test to pass.
  • Fix for the frame order count_sobol_points() function. The checks for the model, parameter and domain set up must come first, before cdp.model is accessed. Otherwise the frame_order.num_int_pts user function will often fail.
  • Fix for the frame order count_sobol_points() function. The free-rotor isotropic cone model was incorrectly handled, as the cone parameter is 'cone_s1' and not 'cone_theta'. The order parameter is now converted to an angle before checking if the Sobol' point is outside of the cone or not.
  • More fixes for the frame order count_sobol_points() function. The torsion angle for the torsionless models is no longer accessed, and the cone_theta parameter is only accessed for models with this parameter.
  • Created the Frame_order.test_count_sobol_points_iso_cone_free_rotor system test. This is to test the frame_order.count_sobol_points user function for the free-rotor isotropic cone model.
  • Fix for the frame order count_sobol_points() function. The torsion angle ranges from -π to π, so the absolute value needs to be checked, just as in the lib.frame_order modules.
  • Updates for the number of Sobol' points in the Frame_order.test_count_sobol_points_* system tests. This is simply to allow all Frame_order system tests to pass.
  • Redesigned the frame_order.num_int_pts user function frontend for the oversampling idea. The use of the quasi-random Sobol' sequence for numerical PCS integration will be modified to use the concept of oversampling. Instead of specifying the exact number of points in the Sobol' sequence and then removing points outside of the current parameter values, the algorithm will oversample as N * Ov * 10M, where N is the maximum number of Sobol' points to be used for the integration, Ov is the oversampling factor, and M is the number of dimensions or torsion-tilt angles used in the system. The aim is to try to use the maximum number of points N for all frame order models and all ranges of dynamics.
  • Renamed the frame_order.num_int_pts user function to frame_order.sobol_setup. The user function no longer specifies the number of integration points. Instead it now specifies the maximum number of points N and oversampling factor Ov used to generate the oversampled Sobol' sequence.
  • Implemented the Sobol' sequence oversampling in the frame order target function class.
  • Converted all of the specific_analyses.frame_order package to the Sobol' point oversampling design. The correct values are now sent into the target function and all references to cdp.num_int_pts has been replaced with the cdp.sobol_max_points and cdp.sobol_oversample pair of variables. The frame_order.count_sobol_points user function backend has also been updated to show the total number of oversampling points and the number of points used.
  • The frame_order.count_sobol_points user function now shows more information. The maximum number and oversampling factors are now also printed out for maximum user feedback.
  • Improved the printout formatting for the count_sobol_points() frame order function.
  • The frame order target function now passes the maximum number of Sobol' points to the relax library. The value is being passed into the lib.frame_order.*.pcs_numeric_int_*() functions, though it is not used set.
  • Fix for the percentage calculation for the frame order count_sobol_points() function.
  • Changed the creation of the Sobol' points in the frame order target function. For increased accuracy of the numerical PCS integration, the first 1000 points of the Sobol' sequence are now skipped to avoid any bias. For speed, the axis order of the Sobol' torsion-tilt angles has been swapped so that the numpy.swapaxes() function call is no longer required in the lib.frame_order.*.pcs_numeric_int_*() functions.
  • Updated the frame order count_sobol_points() function to handle the swapped axis order.
  • Huge speedup for the generation of the Sobol' sequence data in the frame order target function. The new Sobol_data class has been created and is instantiated in the module namespace as target_function.frame_order.sobol_data. This is used to store all of the Sobol' sequence associated data, including the torsion-tilt angles and all corresponding rotation matrices. When initialising the target function, if the Sobol_data container holds the data for the same model and same total number of Sobol' points, then the pre-existing data will be used rather than regenerating all the data. This can save a huge amount of time.
  • Updated the frame order count_sobol_points() function to use the new Sobol_data container. The Sobol' sequence data generated by the target function is now located at target_functions.frame_order.sobol_data.
  • Updated all the lib.frame_order.*.pcs_numeric_int_*() functions for the new Sobol' point algorithm. The functions now all accept the max_points argument and terminate the loop over the Sobol' points once the maximum number of points has been reached. The calls to numpy.swapaxes() have also been removed as this is now pre-performed by the target function initialisation.
  • Changed the default oversampling factor from 100 to 1 in the frame_order.sobol_setup user function.
  • Converted the frame order auto-analysis to use the new frame_order.sobol_setup user function design. The auto-analysis Optimisation_settings object has also been modified so that all num_int_pts arguments and internal structures have been split into the two new sobol_max_points and sobol_oversample names and objects.
  • Fix for the rigid frame order model for the recent frame_order.sobol_setup user function changes. For this model, the number of Sobol' points normally is does not exist. This is now correctly handled.
  • Created the sobol_setup() method for the frame order auto-analysis. This is used to correctly handle the new design of the frame_order.sobol_setup user function consistently throughout the protocol.
  • Updated the Frame_order.test_auto_analysis system test script. This now uses the new auto-analysis Optimisation_settings object design.
  • Updated the Frame_order.test_count_sobol_points system test. The call to the frame_order.num_int_pts user function was changed to frame_order.sobol_setup.
  • Fixes for the Frame_order.test_count_sobol_points2 system test. The test_suite/shared_data/frame_order/axis_permutations/cam_pseudo_ellipse.bz2 relax state file has been manual edited to change the num_int_pts data pipe structure to sobol_max_points and to add the new sobol_oversample variable.
  • Added a backwards compatibility hook for state and results files for the Sobol' sequence changes. The data pipe num_int_pts variable is now renamed to sobol_max_points when present, and the sobol_oversample variable is created and set to 1.
  • Updates to all of the Frame_order.test_count_sobol_points_* system tests. The frame_order.sobol_setup user function is used to set a small maximum number of points (20) to allow the tests to be fast. The value of 20 is also checked for to allow the tests to pass.
  • Renamed the cdp.used_sobol_points variable to sobol_points_used. This is created by the count_sobol_points() frame order function. The name change is to match the sobol_max_points and sobol_oversample variable names.
  • Renamed all the Frame_order.test_num_int_pts* system tests to Frame_order.test_sobol_setup*. These system tests where for checking the operation of the old frame_order.num_int_pts user function. But this is now the frame_order.sobol_setup user function.
  • Fix for all of the Frame_order.test_rigid_data_to_*_model system tests. The frame_order.num_int_pts user function call was changed to frame_order.sobol_setup.
  • Updated the χ2 check in the Frame_order.test_rigid_data_to_free_rotor_model system test. This value has changed due to the first 1000 points of the Sobol' sequence being skipped.
  • Fixes for all of the lib.frame_order.*.pcs_numeric_int_*_qrint() functions. The loop over the Sobol' points was broken. As numpy.swapaxes() has been applied to the points argument already, the loop needs to be over the second dimension of the points data structure.
  • Updates for all of the Frame_order.test_cam_* system tests. The NUM_INT_PTS variable in the system tests scripts is now passed into the frame_order.sobol_setup user function as the max_num argument. This number has also been changed so that the tests take a reasonable amount of time. All χ2 value checks were updated. These were validated by increasing the number of integration points and watching the χ2 value of the Frame_order.test_cam_*_pcs version of the system tests head to zero.
  • Another update for the χ2 check in the Frame_order.test_rigid_data_to_free_rotor_model system test. The previous commit used an incorrect value for the χ2. This new value is now much closer to the original.
  • Turned down the verbosity of the update_model() frame order function. The verbosity flag is now accepted and set to zero by the get_param_names() API method and specific_analyses.frame_order.parameters.param_num() function. This removes a lot of useless printouts from many different user functions.
  • Introduced the verbosity argument to the count_sobol_points() frame order function. This is used to turn the printouts on or off. The optimisation code now calls this function with the verbosity argument sent into the minimise.grid_search and minimise.execute user functions. Hence the printouts are suppressed for Monte Carlo simulations.
  • Removed the axis system printout from the frame_order.pdb_model user function. This is for the geometric representation of the frame order dynamics. The axis system is printed out as the rotation matrix used for the lib.structure.geometric.generate_vector_residues() function later on anyway. The change is to simplify the printouts.
  • Editing of the docstring of the frame_order.sobol_setup user function.
  • Fix for the frame order system test optimisation printouts. The cdp.num_int_pts variable is now called cdp.sobol_max_points.
  • The starting time of the axis permutation model optimisations is now output. This is in the frame order auto-analysis. This call to the time user function occurred for the normal models, so extending it to the permuted axes models makes the output more consistent.
  • Simplified the atomic position averaging warning in the frame order analysis. Instead of throwing a warning for each spin, one warning for all spins is now given. This should make the output a lot less verbose.
  • The frame order minimise_setup_atomic_pos() function now accepts the verbosity argument. This is used to silence the warnings in user functions such as frame_order.sobol_setup.
  • Improvements for the frame order overfit_deselect() API method. Three changes have been made: The print statements have been converted to RelaxWarnings; The spin IDs or spin ID pairs are now stored in a list and one RelaxWarning for the missing PCS data and one for the missing RDC data is now given; And the verbose flag is now used to determine if a RelaxWarning will be given.
  • Change to the position averaging warning in the minimise_setup_atomic_pos() frame order function.
  • Improvements for the printout from the update_model() frame order function. A list of updated parameters is now created and everything is printed on a single line at the end. The printout is therefore much more compact.
  • Spun out part of the frame_order.pdb_model user function into the new frame_order.simulate user function. The new user function arguments required for properly creating the pseudo-Brownian dynamics simulation would have made the frame_order.pdb_model user function too complicated. Therefore this part has been spun out into the new frame_order.simulate user function. The frame_order.simulate frontend fully describes the algorithm that will be used to simulate the dynamic content of the PCS and RDC data, and warns that not all modes of motion are visible and present.
  • Updated the frame order auto-analysis to call the new frame_order.simulate user function. Although not implemented yet, this allows the user function to create the simulation PDB file in the future.
  • Small fix for the new frame_order.simulate user function backend.
  • Updated the base script for the Frame_order.test_cam_* system tests. The frame_order.simulate user function is now called directly after the frame_order.pdb_model user function.
  • Created the backend framework for the frame_order.simulate user function. The backend specific_analyses.frame_order.uf.simulate() function performs all data checks required, prepares the output file object, assembles the frame order parameter values and pivot point, and creates a copy of the structural object object with the ensemble collapsed into a single model. All this data is then passed into the new lib.frame_order.simulation.brownian() function. This initialises all required data structures and the structural object. The main loop of the simulation is also implemented, taking snapshots at every fixed number of steps and terminating the loop once the total number of snapshots are reached. The snapshot consists of copying the original unrotated structural model and rotating it into the new position. The rotation is currently the identity matrix. The old specific_analyses.frame_order.geometric.create_distribution() stub function has been deleted.
  • Decreased the time required for the Frame_order.test_cam_* system tests. The frame_order.simulate user function now only creates a total of 20 snapshots rather than 1000.
  • Added new arguments to the frame order auto-analysis for the frame_order.simulate user function. These are the brownian_step_size, brownian_snapshot and brownian_total arguments which are passed directly into the frame_order.simulate user function. This gives the user more control, as well as allowing the test suite to speed up this part of the analysis.
  • Huge speedup for the Frame_order.test_auto_analysis system test. The pseudo-Brownian dynamics simulation via the frame_order.simulate user function has been massively sped up to allow the test to be almost as fast as before.
  • Spun out the code for shifting to the average frame order position into a new function. The old code of the create_ave_pos() of the specific_analyses.frame_order.geometric module has been shifted into the new average_position() function. This will allow the code to be reused by other parts of relax to obtain the average frame order structures.
  • Implemented the shifting to the average position for the frame_order.simulate user function backend. This simply sends the structural object into the new average_position() function of the specific_analyses.frame_order.geometric module.
  • Improvements for the frame_order.simulate user function. The rigid model is now skipped, the PDB file closed, and some printouts for better user feedback have been added.
  • Changed the default PDB file name for the frame_order.simulate user function to 'simulate.pdb'. The '*.bz2' extension has been dropped so that the file is quicker to create and does not need to be decompressed for loading into molecular viewers.
  • Created the specific_analyses.frame_order.geometric.generate_axis_system() function. This is now used by most parts of the frame order analysis to generate the full 3D eigenframe of the motions. Previously this was implemented each time the frame or major axis was required. This replicated and highly inconsistent code has been eliminated.
  • Fix for the new specific_analyses.frame_order.geometric.generate_axis_system() function. The rotor and free rotor models were not correctly handled and the returned eigenframe was the zero matrix.
  • Implemented the pseudo-Brownian frame order dynamics simulation for the single motion models. This uses the same logic as in the test_suite/shared_data/frame_order/cam/*/generate_distribution.py scripts which were used to generate all of the test suite data. However rather than using a random rotation matrix, a random 3D vector is used to rotate a fixed angle. And the rotation is used to rotate the current state to state i+1. The rotation for the state is decomposed into torsion-tilt angles once shifted into the motional eigenframe, the violations checked for as the state shifted to the boundary, then the new state reconstructed from the corrected torsion-tilt angles, and then it is shifted from the motional eigenframe to the PDB frame.
  • Shifted the specific_analyses.frame_order.variables module into the lib.frame_order package. This is both to minimise circular dependencies, as previously the specific_analyses.frame_order modules import from target_functions.frame_order and vice-versa, and to allow the relax library functions to have access to these variables.
  • Implemented the frame_order.simulate user function backend for the double rotor frame order model. This involved extending the algorithm to loop over N states, where N=2 for the double rotor and N=1 for all other models. To handle the rotations being about the x and y-axes, an axis permutation algorithm is used to shift these axes to z prior to decomposing to the torsion-tilt angles. The reverse permutation is used to shift the axes back after correcting for being outside of the allowed angles.
  • Fixes for the specific_analyses.frame_order.geometric.average_position() function. The recent trunk changes with the structural object Internal_selection class required a change in this function.
  • Updated the lib.frame_order.simulation.brownian() function. This now uses the internal structural object selection object logic - the selection() method is called to obtain the Internal_selection object, and this is then passed into the rotation() method.
  • The quad_int argument for the frame order target function class now defaults to False. This is so that quasi-random Sobol' numerical integration will be used by default.
  • The cdp.quad_int flag is now passed into the target function for the frame order calculate() method. This is for the minimise.calculate user function backend.
  • Fixes for the missing cdp.quad_int flag. If the cdp.quad_int flag is missing, this is now set to False before setting up the target function class. The previous behaviour was that the frame_order.quad_int user function must be called prior to optimisation. Now it is optional for turning this flag on and off.
  • The RDC only optimisation now defaults to the *_qrint() frame order target functions. This restores the earlier behaviour prior to the restoration of the SciPy quadratic integration.
  • Clean up for the frame order target function aliasing. The Scipy quadratic integration and the quasi-random Sobol' integration target functions are now aliased using the getattr() Python method to programmatically choose one or the other. The rigid model has been removed from the list as it is not a numeric model, and the func_double_rotor() target function has been renamed to func_double_rotor_qrint() to make it consistent with the naming of the other target functions.
  • Renaming of all the frame order target functions and PCS integration functions. For consistency, all quasi-random Sobol' integration functions now use the 'qr_int' tag whereas the SciPy quadratic integration functions use the 'quad_int' tag. This is not only in the target function names but also the PCS integration functions in lib.frame_order.
  • Duplicated all Frame_order.test_cam_* system tests for testing the SciPy quadratic integration. The Frame_order.test_cam_* system tests have all been renamed to Frame_order.test_cam_qr_int_*. These have been duplicated and renamed to Frame_order.test_cam_quad_int_*. The flag() system test method has been extended to include the quad_int flag which is then stored in the status object and used in the base CaM frame order system test script to activate the frame_order.quad_int user function.
  • Activated the quad_int flag for a number of the Frame_order.test_cam_quad_int_* system tests. The quad_int argument for the flags() test suite method had been missed for a few of these tests.
  • Updated the χ2 check in the Frame_order.test_cam_qr_int_pseudo_ellipse_free_rotor_rdc system test. This test is not normally run as it blacklisted and duplicates the coverage of other tests. However its chi-squared value check had not been updated for a while and hence the test fails when explicitly run.
  • The Sobol' point counting is now turned off for the frame order optimisation functions if none exist. If the cdp.quad_int flag is set, then there will be no Sobol' points to count. This count_sobol_point() user feedback function will therefore not be called by the minimise.calculate, minimise.grid_search and minimise.execute user functions.
  • Turned off optimisation for all of the Frame_order.test_cam_quad_int_* system tests. The SciPy quadratic integration is far too slow to be used in the test suite. The simple call to the minimise.calculate user function is sufficient for checking these target functions.
  • Updated all of the Scipy quadratic integration frame order target functions. A number of the data structures in the target function class have been redesigned since these target functions were deleted. All of the func_*_quad_int*() target functions have been updated for these changes.
  • Updated all of the χ2 value checks for the Frame_order.test_cam_quad_int_* system tests. This is only for those tests which use PCS data - the RDC only test χ2 values are the same as in the Frame_order.test_cam_qr_int_* system tests. In all cases, the χ2 value is lower for the more accurate SciPy quadratic integration as compared to the quasi-random Sobol' integration, as expected.
  • Implemented the SciPy quadratic integration target function for the double rotor frame order model. This simply follows from what all the other quadratic integration target functions and lib.frame_order module functions do.
  • Changed the χ2 value checks in the Frame_order.test_cam_quad_int_double_rotor* system tests. These were the values for the quasi-random Sobol' integration and needed updating for the SciPy quadratic integration.
  • Removed the skip_tests argument for the Frame_order system tests __init__() method. This argument, which was used to manually turn on or off the blacklisted tests, is no longer needed due to the new --no-skip relax command line flag which will enable all blacklisted tests.
  • The [http://www.nmr-relax.com/api/4.0/auto_analyses.frame_order-module.html frame order auto-analysis Optimisation_settings object now supports the quad_int flag. This is for activating the SciPy quadratic integration. It is accepted as an argument for the add_grid() and add_min() methods, and it returned by the new get_grid_quad_int() and get_min_quad_int() methods.
  • Added the ability to specify a pre-run directory in the frame order auto-analysis. This will be used for refinement purposes. If the new pre_run_dir argument, modelled on the relaxation dispersion auto-analysis, is supplied then results files will be loaded from this directory and the base data pipe copying and PCS subset optimisation steps will be skipped. The model nesting algorithm is also deactivated.
  • Activated the SciPy quadratic integration in the frame order auto-analysis. If the Optimisation_settings object has been set up with the quad_int flag, then the auto-analysis will skip the sobol_setup() method and instead directly call the frame_order.quad_int user function. Optimisation will then use the SciPy quadratic integration rather than the quasi-random Sobol' integration.
  • Improvements for the usage of the frame_order.quad_int user function in the auto-analysis. The frame_order.quad_int user function is now called even when the Optimisation_settings object quad_int flag is False. This allows for switching between the SciPy quadratic integration and the quasi-random Sobol' integration, as the SciPy quadratic integration can now be turned off.
  • Additions to the frame order auto-analysis documentation.
  • Incorporated the contents of the summarise.py script into the frame order auto-analysis module. This has been converted into the summarise() function which will generate a results summary table as the analysis is still running.
  • Improved logic in the auto_analyses.frame_order.summarise() function. The model names, directories and titles are now being auto-generated from the full list of frame order models in lib.frame_order.variables.MODEL_LIST. To create a common mechanism for determining the model directory name, the Frame_order_analysis.model_directory() method has been converted into a module function.
  • The frame order auto-analysis now calls the summarise() function at the end to create a summary table.
  • Shifted the final state saving in the frame order auto-analysis to be within the safety of the try block.
  • Turned off the final state saving in the Frame_order.test_auto_analysis system test. This almost halves the time required for the test. A private class variable _final_state has been added to the auto_analyses.frame_order.Frame_order_analysis class which when False will cause the state saving step to be skipped.
  • The summarise() function call is now after saving the final state in the frame order auto-analysis. This is needed because the summarise() function will create a new set of data pipes, loading the results which already exist under a different pipe name in the relax data store. Otherwise the final state file is twice as big as it should be.
  • Incorporated the contents of count_sobol_points.py into the frame order auto-analysis module. The analysis script has been converted into the count_sobol_points() function which will generate a summary table of the number of quasi-random Sobol' points used for the PCS numerical integration.
  • The frame order auto-analysis now calls the count_sobol_points() function at the end. This is to automatically create the Sobol' point summary table.
  • Fixes for the auto_analyses.frame_order.summarise() function. If the count_sobol_points() function is called followed by summarise(), a RelaxError will be raised as the data pipe already exists. The summarise() function has been modified to switch to the data pipe if it already exists.
  • Expanded the frame order auto-analysis documentation. This adds a description for the summarise() and count_sobol_points() functions.
  • Elimination of most of the Frame_order.fixme_test_* system tests and associated data. These tests are from a very early stage of the development of the frame order theory back when the base data was the full and reduced alignment tensors for the each domain calculated from the RDC data. They do not fit into the current analysis where the base data is the RDCs and PCSs for the moving domain. There is no point upgrading the tests as it will be far too much effort and it will only duplicate the coverage of the Frame_order.test_cam_* system tests.
  • Renamed the Frame_order.fixme_test_opendx_map system test to Frame_order.test_opendx_map to activate it.
  • Upgraded the Frame_order.test_opendx_map system test. To upgrade from the ancient design to the current design so that the test is functional and relevant, this now uses the same setup as the Frame_order.test_cam_qr_int_rigid system test. Instead of performing optimisation, the test calls the dx.map user function.
  • Fix for the frame order specific API calculate() method. This was caught by the Frame_order.test_opendx_map system test. The scaling matrix was not being specified by the dx.map user function backend and this was causing the method to fail. Instead of passing the non-existent scaling matrix into the target function, the argument is simply ignored. The scaling matrix has no effect on the minimise.calculate user function so it is not necessary.
  • The verbosity flag is now being respected by the frame order specific API calculate() method. This silences the method when executing the dx.map user function. The χ2 value printout is suppressed and the verbosity argument is being sent into the frame order count_sobol_points() function.
  • Added a section printout to the frame order auto-analysis when summary tables are created.
  • The frame_order.simulate user function now defaults to creating a gzipped PDB file. This is to save room, and because most molecular viewers will automatically read gzipped PDB files.
  • Fix for the change of the pipe_control.pipes.test() function to check_pipe().
  • Small change in the title of the summary table of the frame order auto-analysis. 'Order parameters' has been replaced by 'Cone half angles' to clarify what the values really are.
  • Fix for the frame order optimisation target setup printouts. The 'Numerical integration: ' printout was fixed to 'Quasi-random Sobol' sequence'. This now changes to 'SciPy quadratic integration' if cdp.quad_int is set. The text 'PCS' has also been added for clarification.
  • Removed the call to the frame_order.simulate user function for the rigid model in the auto-analysis. There is no motion to simulate in the rigid model, so the frame_order.simulate user function has no use.
  • Improvements, fixes, and expansion of the results and data visualisation file creation. This is for the frame order auto-analysis. The visualisation() method has been renamed to results_output() and its scope expanded. The function previously only called the frame_order.pdb_model and frame_order.simulate user functions for creating PDB representations of the frame order motions and performing a pseudo-Brownian frame order dynamics simulate. This has been extended to also call the results.write user function for outputting results files and the rdc.corr_plot and pcs.corr_plot for generating correlation plots of the measured vs. back-calculated data. All parts of the auto-analysis were output files are required now call this method. This ensures that all output files are always created, and are placed into the correct directories.
  • Improvements for the sectioning printouts for the frame order auto-analysis. The sections now use the lib.text.formatting subtitle() and subsubtitle() functions to distinguish them from the output of all the user functions, which use the section(), subsection() and subsubsection() functions. New sectioning printouts have been added for clarity.
  • Possible fixes for the frame order auto-analysis. This is just in case a user decides to not perform the optimisation starting with a PCS subset. In this case, the analysis will now execute correctly.
  • Improvements to the summary table for the frame order auto-analysis. The rotor and free rotor model motional eigenframe parameter axis_alpha is now being converted into spherical angles and reported in the table. This allows the motional eigenframe of all models to be easily compared in the table.
  • Created a directory and base PDB system for testing out the PCS information content. The base PDB system consists of Ad Bax's CaM domain structures superimposed onto the open CaM structure, the N-domain CoM shifted to the origin, and the C-domain CoM shifted to the z-axis.
  • Modified the PCS content testing base system. The paramagnetic centre is now shifted to the origin, as this is the real centre of the PCS physics.
  • Intermediate optimisation results are now stored by the frame order auto-analysis. The results from each minimise.grid_search and minimise.execute user function call are now stored in specially named directories located in the 'intermediate_results' directory, which itself is located in the auto-analysis results_dir directory. This allows intermediate results to be more easily analysed later on, which can be useful for optimising the optimisation steps. These directories can also be used for the pre_run_dir auto-analysis argument for subsequent refinements from earlier steps in the optimisation. The results stored include everything from the results_output() method and the count_sobol_points() and summarise() functions. To allow this to work, the auto-analysis functions count_sobol_points() and summarise() required modification. Results files are now always loaded into a temporary data pipe, rather switching to the corresponding pipe, and the temporary data pipe is deleted after the data has been extracted. The original data pipe name is also stored and a switch back to that pipe occurs at the end of each function.
  • The simulation is now turned of for intermediate results in the frame order auto-analysis. The intermediate results are only for checking, so for these the full pseudo-Brownian dynamics simulations are not required. The simulation flag has been introduced into the results_output() method of the auto-analysis to control this.
  • The splitting of the rigid model grid search into rotation and translation parts is now optional. In the frame order auto-analysis, the rigid_grid_split argument has been introduced. The alternating algorithm of performing a grid search over the rotational space followed by translation is now optional and turned off by default. The reason is because the global minimum is sometimes missed with this shortcut algorithm.
  • Speedup of the Frame_order.test_auto_analysis system test. The splitting of the rigid model grid search into rotation and translation parts has been reactivated.
  • Created the Optimisation.has_grid() method for the frame order auto-analysis. This is used to test if the optimisation settings object has a grid search defined.
  • The grid search can now be skipped for the rigid model in the frame order auto-analysis. If the input 3D structures are close to the real solution, the grid search over the translational and rotation parameters of the rigid model could be skipped. This speeds up the analysis and can help find the real solution in problematic cases.
  • The intermediate results storing can now be turned off in the frame order auto-analysis. The new store_intermediate Boolean argument has been added to the analysis to allow the storage of these results to be turned on or off.
  • The intermediate results are no longer stored in the Frame_order.test_auto_analysis system test. This drops the test timing on one system from ~190 seconds to ~50 seconds.
  • The compression level for results files can now be set in the frame order auto-analysis. This is via the new argument results_compress_type, which is used to set the compress_type argument of the results.write user function. The results reading parts of the auto-analysis have been updated to allow uncompressed, bzip2 compressed, and gzip compressed files to be handled.
  • Added a printout of the frame order model in the target function setup function. This is printed out when the minimise.calculate, minimise.grid_search, or minimise.execute user functions are called, and is for better feedback, especially in the auto-analysis where the repetitive optimisations can be confusing.
  • Updated the frame order analysis for the structure.load_spins user function changes. The minimise_setup_atomic_pos() function of the specific_analyses.frame_order.optimisation module now handles the mixed type spin.pos variable correctly.
  • The data pipe containing a PCS subset is now optional in the frame order auto-analysis. This is for systems which have so little data that a subset makes no sense.
  • Redesigned the optimisation steps for the frame order auto-analysis. The code has been significantly simplified as the optimisation for the PCS subset and full data set was the same. The code duplication has been eliminated by combining it into the new optimisation() method. The check for the PCS subset has also been expanded so that it is skipped if the subset data pipe is not supplied, even if an optimisation object for the subset has been (this should prevent strange errors when the auto-analysis is incorrectly used). A side effect of this code merger is that the zooming grid search has now been activated for the full PCS data set. This is of great benefit when a PCS subset is not being used.
  • The minimise.execute user function skip_preset flag is now False in the frame order auto-analysis. This is for the main model optimisation. Without this flag set, the grid search for the pivot point position for the rotor model was being skipped at the first zoom level.
  • The pivot point can now be excluded from the grid search in the frame order auto-analysis. If the initial pivot point is known to be reasonable, then it may be possible to skip it in the grid search for the rotor frame order model. This can lead to a speedup of the analysis and can help with stability. The pivot_search argument has been added to the auto-analysis Optimisation.add_grid() method to enable this. The get_grid_pivot_search() method has also been added to allow the auto-analysis to query this and turn it off if desired.
  • Updated the description of the frame_order.permute_axes user function. This now includes the isotopic cone.
  • Replaced the table in the frame_order.permute_axes user function. The original table was an old and incorrect version. This has been replaced by the correct permutation table.
  • Added some old relax scripts for both simulating and predicting the frame order matrix elements. These were used for the initial implementation of the pseudo-ellipse frame order model back in July 2010. The scripts will be extended for all frame order models. The simulated values could then be used in unit tests of the frame order matrix code in lib.frame_order.
  • Updated the frame_order_simulate.py script for simulating frame order matrix elements. The MODEL variable has been added in preparation for supporting all model types, and this is now added to the file name. The Grace header is now also being automatically generated.
  • Improvements for the Grace files produced by the frame_order_simulate.py script. The model name is now set as a variable and is used for the subheading.
  • Updated the frame_order_solution.py script for directly calculating the frame order matrix elements. The MODEL variable has been added in preparation for supporting all model types, and this is now added to the file name. The Grace header is now also being automatically generated and this matches that for the frame_order_simulation.py script.
  • Zero values can now be handled in the pseudo-ellipse 1st degree frame order matrix function. This is in lib.frame_order.pseudo_ellipse.compile_1st_matrix_pseudo_ellipse().
  • Removed some unused code in the pseudo-ellipse 2nd degree frame order matrix function. This is the compile_2nd_matrix_pseudo_ellipse() function in the lib.frame_order.pseudo_ellipse module. The change should make the RDC part of the frame order analysis for the pseudo-ellipse model slightly faster.
  • Modified the rotate_daeg() function as this is independent of the degree of the frame order matrix. This is the lib.frame_order.matrix_ops.rotate_daeg() function.
  • Fix for the compile_1st_matrix_pseudo_ellipse() function. This function of the lib.frame_order.pseudo_ellipse module now can rotate the 1st degree frame order matrix out of its eigenframe and into the PDB frame.
  • Created an executable Python script for mass converting the frame order matrix Grace graphs. The script converts the *.agr files to EPS and PNG files.
  • Modified the frame order matrix Grace graph to EPS/PNG format conversion script. The binary being called is now 'grace' rather than 'xmgrace'. This allows different Grace versions to be used.
  • Modified the frame order matrix Grace graph to EPS/PNG format conversion script. Grace is now used to create a PostScript file and then the ps2eps program is called to convert to EPS. This produces much better EPS files for inclusion into LaTeX documents.
  • Redesign of the frame_order_solution.py script for calculating the frame order matrix elements. This script now loops over all models, all motional frame orientations, and all order parameters to generate the Grace graphs of all 1st and 2nd degree frame order matrix elements. Therefore the script only needs to be executed once. The script also now calculates a point at zero (slightly shifted to 0.01 to avoid artifacts).
  • Added all of the Grace graphs produced by the frame_order_solution.py script. These are the graphs of the 1st and 2nd degree frame order matrix elements, calculated using the functions in lib.frame_order.
  • Updated frame_order_simulate.py to be much faster in simulating the frame order matrix elements. The script also matches the Grace file output of the frame_order_solution.py script. The inside() method has been renamed for the pseudo-ellipse and the infrastructure for adding support for the other frame order models has been added. By shifting calculations outside of the loops, the script is now many orders of magnitude faster.
  • Implemented the compile_1st_matrix_rotor() function. This is for the lib.frame_order.rotor module. The function will calculate the 1st degree in-frame frame order matrix for the rotor model.
  • Created the Grace graphs for the rotor model 1st degree frame order matrix elements. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Implemented the compile_1st_matrix_free_rotor() function. This is for the lib.frame_order.free_rotor module. The function will calculate the 1st degree in-frame frame order matrix for the free rotor model.
  • Created the Grace graphs for the free rotor model 1st degree frame order matrix elements. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Implemented the compile_1st_matrix_iso_cone() function. This is for the lib.frame_order.iso_cone module. The function will calculate the 1st degree in-frame frame order matrix for the isotropic cone model.
  • Created the Grace graphs for the isotropic cone model 1st degree frame order matrix elements. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Implemented the compile_1st_matrix_iso_cone_torsionless() function. This is for the lib.frame_order.iso_cone_torsionless module. The function will calculate the 1st degree in-frame frame order matrix for the torsionless isotropic cone model.
  • Created the Grace graphs for the torsionless isotropic cone 1st degree frame order matrix elements. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Implemented the compile_1st_matrix_iso_cone_free_rotor() function. This is for the lib.frame_order.iso_cone_free_rotor module. The function will calculate the 1st degree in-frame frame order matrix for the free rotor isotropic cone model.
  • Created the Grace graphs for the free rotor isotropic cone 1st degree frame order matrix elements. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Docstring fixes for the new compile_1st_matrix_iso_cone() function.
  • A minor speedup for the frame_order_simulate.py script. The angles are now being calculated at the very start prior to the main loop, removing repetitive calculations.
  • The frame_order_simulate.py script now uses lib.text.progress.progress_meter(). This script for simulating the frame order matrix elements now uses the standard progress meter in relax to simplify the script. This should also speed up the calculations as the progress printouts were slowing down the calculations.
  • Simulation of the pseudo-ellipse frame order matrix elements. This is for a simulation of 1,000,000 states for each angle increment, and includes in-frame and out-of-frame and varying of θ X, Y, and Z. The resultant Grace graphs have been added to the repository.
  • The frame order matrix element simulation script now uses the Kronecker outer product. This allows the frame order matrix to be in the same notation as that used internally in relax. It will cause the colours of the Sijkl_* curves to match between the simulation and solution scripts.
  • Added the rotor model to the frame order matrix element simulation script. The generated in-frame and out-of-frame Grace graphs containing the matrix values for 1,000,000 simulation values have been added to the repository. The script was modified so that the rotation is generated by special rotation_*() methods which are aliased depending on the model.
  • Added the free rotor model to the frame order matrix element simulation script. The generated in-frame and out-of-frame Grace graphs containing the matrix values for 1,000,000 simulation values have been added to the repository. The inside_free_rotor() method has been added to always return True for the rotation generated by rotation_z_axis().
  • Simplifications and fixes for the 1st degree frame order matrix calculation for the pseudo-ellipse. The compile_1st_matrix_pseudo_ellipse() function of the lib.frame_order.pseudo_ellipse module has been significantly simplified by shifting a lot of maths outside of the quadratic integration.
  • Updated all the calculated 1st degree frame order matrix graphs for the pseudo-ellipse. The changes are due to the fixes in the lib.frame_order.pseudo_ellipse module.
  • Simplifications for all of the torsionless pseudo-ellipse frame order matrix equations.
  • Implemented the compile_1st_matrix_pseudo_ellipse_torsionless() function. This is for the lib.frame_order.pseudo_ellipse_torsionless module. The function will calculate the 1st degree in-frame frame order matrix for the torsionless pseudo-ellipse model.
  • Created the Grace graphs for the torsionless pseudo-ellipse model 1st degree frame order matrix. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Added the isotropic cone model to the frame order matrix element simulation script. The generated in-frame and out-of-frame Grace graphs for the torsion angle cone_sigma_max, containing the matrix values for 1,000,000 simulation values have been added to the repository. The inside_iso_cone() method has been created to check for the θx and θz angle violations from the rotation_hypersphere() method.
  • Simplifications for the inside_*() methods of the frame order matrix element simulation script. The limit() method is now called only once outside of these methods and the maximum cone half-angles passed into the inside_*() methods. Although only slightly faster, this is mainly to simplify the code.
  • Alphabetical ordering of methods in the frame order matrix element simulation script.
  • Simplification of some of the pseudo-ellipse 2nd degree frame order matrix equations.
  • More simplifications of the pseudo-ellipse 2nd degree frame order matrix equations.
  • Integer to float conversions in part_int_daeg2_pseudo_ellipse_13(). This avoid integer to float conversion during execution, saving a little time for the pseudo-ellipse 2nd degree frame order matrix compilation.
  • Removal of many repetitive calculations in the pseudo-ellipse 2nd degree frame order matrix equations.
  • Simplifications of pseudo-ellipse 1st degree frame order matrix functions. The xx, yy, and zz have been renamed to 00, 11, and 22 for consistency. And all sigma_max arguments have been dropped as they are not used.
  • Small numerical changes for the pseudo-ellipse 2nd degree frame order matrix graphs. These are only for the first point close to zero and the changes are minimal, caused by the recent simplifications of the code.
  • Created the Grace graphs for the free rotor pseudo-ellipse model 1st degree frame order matrix. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Implemented the compile_1st_matrix_pseudo_ellipse_free_rotor() function. This is for the lib.frame_order.pseudo_ellipse_free_rotor module. The function will calculate the 1st degree in-frame frame order matrix for the free_rotor pseudo-ellipse model.
  • Speedups and simplifications of the free rotor pseudo-ellipse 2nd degree frame order matrix equations.
  • Added the torsionless isotropic cone model to the frame order matrix element simulation script.
  • Implemented the compile_1st_matrix_double_rotor() function. This is for the lib.frame_order.double_rotor module. The function will calculate the 1st degree frame order matrix for the double_rotor model.
  • Created the Grace graphs for the double rotor model 1st degree frame order matrix. These are the values calculated directly from the lib.frame_order modules. The graphs were previously all zeros.
  • Recreated all of the simulated pseudo-ellipse frame order matrix element graphs. These are now in the Kronecker product notation so that they will match the graphs calculated using the relax lib.frame_order.pseudo_ellipse module.
  • Fix for the pseudo-ellipse 1st degree frame order matrix ᛞ22 element.
  • Updated all of the pseudo-ellipse 1st degree frame order matrix graphs for the recent fix.
  • Converted the Sobol' rotation matrices to float32 in the frame order target function. This is to conserve huge amounts of memory to allow for more Sobol' points to be used. For example for the models which use 3D Sobol' points (isotropic cone and pseudo-ellipse), a maximum of 50000 Sobol' points requires 50000000 to be created, using about 15 Gb of RAM.
  • A few Frame_order system test updates for the float64 to float32 memory saving changes. The chi-squared value of 3 tests was slightly different.
  • Bug fix for the activation of quadratic integration in the frame order auto-analysis. The calls to the frame_order.quad_int user function in the optimisation() method did not supply an argument so the user function was defaulting to False rather than the True value required.
  • The frame order auto-analysis summary functions are now more robust. If the data pipe already exists for some reason, it is deleted prior to the new one being created.
  • Changed the frame_order.quad_int user function argument default to True. This means that calling the user function without arguments will activate the quadratic integration rather than turning it off.
  • Added the isotropic cone model frame order matrix simulation graphs for the cone opening angle θx.
  • Created and added all of the torsionless isotropic cone simulated frame order matrix element graphs.
  • Added the free rotor isotropic cone model to the frame order matrix element simulation script. The generated Grace graphs containing the matrix values for 1,000,000 simulation values have been added to the repository. The self.torsion_check variable has been created to allow the inside_iso_cone() method to skip the torsion angle check when its value is False.
  • Added the torsionless pseudo-ellipse model to the frame order matrix element simulation script. The generated Grace graphs containing the matrix values for 1,000,000 simulation values have been added to the repository. The rotations are generated by the rotation_hypersphere_torsionless() method and the angle violations checked using the inside_pseudo_ellipse() method.
  • Bug fix for the torsionless pseudo-ellipse 1st degree frame order matrix. The 11 element was of the wrong sign.
  • Fixes for the torsionless pseudo-ellipse 1st degree frame order matrix element graphs.
  • Added the free rotor pseudo-ellipse model to the frame order matrix element simulation script. This only required the self.torsion_check variable to be set to False. The model uses the inside_pseudo_ellipse() and rotation_hypersphere() methods.
  • Fixes for free rotor isotropic cone 1st degree frame order matrix graphs calculated using relax. The 1st degree function accepts the cone opening angle θ rather than the order parameter S.
  • Added the frame order matrix element graphs for the in-frame free rotor pseudo-ellipse model.
  • Added the frame order matrix element graphs for the out-of-frame free rotor pseudo-ellipse model.
  • Added support for the double rotor model to the frame order matrix element simulation script. The double rotation is constructed in the new rotation_double_xy_axes() method, and the checks for the violation of the two torsion angles in the inside_double_rotor() method. In the main loop, the θ, φ and σ angles correspond to sigma1, sigma2, and nothing.
  • Fixes for all of the calculated double rotor model frame order matrix graphs. The X and Y angles were mixed up. The first torsion half-angle sigma1 corresponds to a y-axis rotation and the second sigma2 corresponds to a x-axis rotation.
  • Added the frame order matrix element graphs for the double rotor model.
  • A divide by zero fix for the torsionless pseudo-ellipse. This is in the compile_2nd_matrix_pseudo_ellipse_torsionless() relax library function.
  • A divide by zero fix for the free rotor pseudo-ellipse. This is in the compile_2nd_matrix_pseudo_ellipse_free_rotor() relax library function.
  • The 1st angle for the calculated frame order matrix graphs is 0 for all non pseudo-ellipse models. This is for the frame_order_solution.py script. Only the pseudo-ellipse models where numerical integration is required fail for the angle of 0.0. Therefore the changing of the first angle from 0.0 to 0.01 only occurs for the pseudo-ellipse models. All graphs have been updated.
  • The 1st pseudo-ellipse torsion angle value in the frame order matrix graphs is now 0.0. Only the cone opening angles set to 0.0 cause a failure in the pseudo-ellipse models, so the torsion angle is now allowed to start at exactly zero.
  • Clean up of the frame order matrix element simulation script.
  • Redesign of the free rotor isotropic cone frame order model - the order parameter has been replaced. From the frame order matrix element graphs in test_suite/shared_data/frame_order/sim_vs_pred_matrix, specifically Sijkl_iso_cone_free_rotor_in_frame_theta_x_calc.agr, Sijkl_iso_cone_free_rotor_axis2_1_3_theta_x_calc.agr, and Sijkl_iso_cone_free_rotor_out_of_frame_theta_x_calc.agr, it is clear that the symmetry of the order parameter after 120 degrees causes the 2nd degree frame order matrix to be incorrectly estimated. Therefore the S1 order parameter has been replaced with the original cone opening angle cone_theta. All parts of relax have been updated for this large conversion.
  • Updated the frame order matrix element graphs for the free rotor isotropic cone fixes. The cone S1 parameter has been converted back to the original cone θ opening half-angle, allowing the 2nd degree frame order matrix elements to be properly calculated for all motions.
  • Eliminated the lib.frame_order.iso_cone.populate_*() functions. The populate_1st_eigenframe_iso_cone() function was unused and incorrect, so it was deleted. The contents of the populate_2nd_eigenframe_iso_cone() function have been shifted compile_2nd_matrix_iso_cone() as a separate function is unnecessary. This now matches all the other lib.frame_order modules.
  • Bug fix for the frame_order.simulate user function. The incorrect model number was being specified and hence the simulation was not starting from the optimised average domain position but rather the arbitrary position of the original structure.
  • Manual Python 3 fixes for the dict.key() function which returns a list or iterator in Python 2 or 3. This matches r26519 in trunk.
  • Python 3 fixes via 2to3 - the "while 1" construct has been replaces with "while True". The command used was: 2to3 -j 4 -w -f idioms .
  • Python 3 fixes via 2to3 - the spacing around commas has been fixed. The command used was: 2to3 -j 4 -w -f ws_comma .
  • Python 3 fixes via 2to3 - the xrange() function has been replaced by range(). The command used was: 2to3 -j 4 -w -f xrange .
  • Started to create the Frame_order.test_pdb_model_rotor system test. This will be used to check that the PDB representations of the frame order motions are correct.
  • Modified the frame_order.pdb_model user function backend to handle missing structural data. The create_ave_pos() function of the specific_analyses.frame_order.geometric module now checks that cdp.structure exists, and if not a warning is given and the PDB file creating is skipped.
  • Fixes for the frame_order.pdb_model user function backend for when no data is present. The pipe_centre_of_mass() function of pipe_control.structure.mass module is now called with the missing_error flag set to False so that the PDB generation can continue with the CoM set to [0, 0, 0].
  • The geometric representation part of the frame_order.pdb_model user function now checks parameters. This calls the specific_analyses.frame_order.checks.check_parameters Check object to make sure that all necessary parameters for the model exist.
  • Completed the Frame_order.test_pdb_model_rotor system test. This now sets the rotor axis to the z-axis (with a printout to be sure), sets the torsion angle to zero for simplicity, creates a new data pipe and loads the PDB representation file, then checks all of the key atom coordinates.
  • Fixes for the unit tests of the lib.frame_order.matrix_ops module for the free rotor isotropic cone. The S1 order parameter has been eliminated due to angles > π/2.0 causing the frame order matrix to be incorrectly predicted. Therefore all unit tests have been converted to use the cone opening angle θ instead. In addition, the test_compile_2nd_matrix_iso_cone_free_rotor_disorder had been modified to pass with the incorrect frame order matrix by comparing to the half cone frame order matrix rather than the identity frame order matrix.
  • Fix for inverted axes in the new Frame_order.test_pdb_model_rotor system test.
  • Huge bug fix for the frame_order.pdb_model user function - the single axis direction was incorrect. In the PDB representation of the frame order motion for the rotor and isotropic cone models (rotor, free rotor, isotropic cone, free rotor isotropic cone, and torsionless isotropic cone), the X and Z axes were swapped. This is because the eigenframe of the motion was being incorrectly constructed via the lib.geometry.rotations.two_vect_to_R() function. For better control, the specific_analyses.frame_order.geometric.frame_from_axis() function has been created. This constructs a full motional eigenframe from the Z-axis. The problem was detected via the new Frame_order.test_pdb_model_rotor system test.
  • Size fix for the rotor representation from the frame_order.pdb_model user function. The size problem was detected via the Frame_order.test_pdb_model_rotor system test. The rotors in the PDB representation were all fixed in size, and ignored the 'size' argument of the frame_order.pdb_model user function. The size argument is now passed into the add_rotors() function of the specific_analyses.frame_order.geometric module and passed on to the rotor() function of the lib.structure.represent.rotor module.
  • Created the Frame_order.test_pdb_model_rotor2 system test to check for an offset pivot. The pivot is set to [1, 0, 1] so that the rotor axis is tilted -45 degrees in the xz-plane. And the size of the geometric object is set to 100 Angstrom for better testing of the sizes of the elements.
  • Simplification of the Frame_order.test_pdb_model_rotor system test. The size is now programatically handled.
  • Created the Frame_order.test_pdb_model_iso_cone system test. This is for checking the PDB representation of the isotropic cone frame order model created by the frame_order.pdb_model user function. It checks both A and B representations.
  • Fix for the cone sized created by the frame_order.pdb_model user function. The 'size' argument was not being used at all for the cone size. It is now passed into the lib.structure.represent.cone.cone() function as the 'scale' argument.
  • Small fix for the Frame_order.test_pdb_model_iso_cone system test for the 'B' representation.
  • Fix for the representation label positions created by the frame_order.pdb_model user function. The 'size' argument was not being used at all for the representation title atoms. It is now passed into the add_titles() function as the displacement argument + 10 Angstrom.
  • Printout fix for the axis in the Frame_order.test_pdb_model_iso_cone system test.
  • Created the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test. This checks the PDB file from the frame_order.pdb_model user function for the isotropic cone model with a xz-plane tilt.
  • Renamed all of the Frame_order.test_pdb_model_* system tests to be more descriptive.
  • Improvements for all of the Frame_order.test_pdb_model_* system tests. The rotate_from_Z() method has been introduced to simplify the determination of the 3D coordinates expected for the PDB file. This will allow for more advanced testing of the PDB for the cone models.
  • Fixes for the printouts from the Frame_order.test_pdb_model_rotor_* system tests.
  • Alphabetical ordering of the Frame_order system test methods.
  • Fixes for all of the Frame_order system tests - the temporary directories are now being deleted. The system test base class tearDown() method is now being called to properly clean up after the tests.
  • Created the Frame_order.test_pdb_model_pseudo_ellipse_z_axis system test. This demonstrates the correct atom coordinates in the PDB file created by the frame_order.pdb_model user function for the pseudo-ellipse model along the z-axis.
  • Fixes for the checks in the Frame_order.test_pdb_model_* system tests. Atomic positions are now checked with self.assertAlmostEqual() to 3 places, and the residue and atom names and numbers are checked with self.assertEqual().
  • Created the Frame_order.test_pdb_model_pseudo_ellipse_xz_plane_tilt system test. This checks the PDB file created by the frame_order.pdb_model user function for the pseudo-ellipse model with a xz-plane tilt. To properly construct the coordinates, the rotate_from_Z() method was modified to accept a rotation matrix argument to allow the geometric shape to be rotated.
  • Modified the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test to have a cone angle. The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB file for a cone opening half-angle of 2.0.
  • Modified the Frame_order.test_pdb_model_iso_cone_z_axis system test to have a cone angle. The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB file for a cone opening half-angle of 2.0.
  • Created two new system tests for the free rotor PDB representation file. This is the file from the frame_order.pdb_model user function. The two new unit tests are Frame_order.test_pdb_model_free_rotor_z_axis and Frame_order.test_pdb_model_free_rotor_xz_plane_tilt.
  • Created two new frame order system tests for the free rotor isotropic cone PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_iso_cone_free_rotor_z_axis and Frame_order.test_pdb_model_iso_cone_free_rotor_xz_plane_tilt.
  • Created two new frame order system tests for the torsionless isotropic cone PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_iso_cone_torsionless_z_axis and Frame_order.test_pdb_model_iso_cone_torsionless_xz_plane_tilt.
  • Created two new frame order system tests for the free rotor pseudo-ellipse PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_z_axis and Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_xz_plane_tilt.
  • Created two new frame order system tests for the torsionless pseudo-ellipse PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_pseudo_ellipse_torsionless_z_axis and Frame_order.test_pdb_model_pseudo_ellipse_torsionless_xz_plane_tilt.
  • Created two new frame order system tests for the double rotor PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_double_rotor_z_axis and Frame_order.test_pdb_model_double_rotor_xz_plane_tilt.
  • Added relax scripts and PDB files which match the Frame_order.test_test_pdb_model_* system tests. These were used to construct and visually check the tests in a molecular viewer. These could be a useful reference, so have been added to the repository.
  • Simplified all of the Frame_order.test_pdb_model_* system tests. The atom, residue and 3D coordinate checking in all these methods has been shifted into the common check_pdb_model_representation() method. This dramatically decreases the amount of code in the system test file.
  • Simplification for all of the Frame_order.test_pdb_model_* system tests. The model setup in all of these tests has been merged into the common setup_model() method. This not only removes a large quantity of repetitive code, but the new method can also be used for constructing future tests, for example for checking the frame_order.simulate user function.
  • Created an initial version of the Frame_order.test_simulate_rotor_z_axis system test. This is to check the frame_order.simulate user function rotor model along the z-axis. It currently fails due to a bug in the user function.
  • Fixes for the Frame_order.test_simulate_rotor_z_axis system test. Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at [1, 0, 0] so that the axis α angle of π/2 creates an axis parallel to Z. The origin to atom distance check has also been loosened due to the PDB truncation artifact.
  • Fix for the Frame_order.test_pdb_model_free_rotor_xz_plane_tilt system test. This was broken while implementing the Frame_order.test_simulate_rotor_z_axis system test. Instead of shifting the 6 atom structure so its CoM is the pivot of the motion when creating the atoms, now the Frame_order.test_simulate_rotor_z_axis system test sets the average domain translation vector to the pivot to achieve the same result. This preserves the z-axis orientation of the rotor models.
  • Created the Frame_order.test_simulate_free_rotor_z_axis system test. This is to check the frame_order.simulate user function for the free rotor model along the z-axis.
  • Created the Frame_order.test_simulate_iso_cone_z_axis system test. This is to check the frame_order.simulate user function for the isotropic cone model along the z-axis.
  • Created the Frame_order.test_simulate_iso_cone_free_rotor_z_axis system test. This is to check the frame_order.simulate user function for the free rotor isotropic cone model along the z-axis.
  • Created the Frame_order.test_simulate_iso_cone_torsionless_z_axis system test. This is to check the frame_order.simulate user function for the torsionless isotropic cone model along the z-axis.
  • Created the Frame_order.test_simulate_pseudo_ellipse_z_axis system test. This is to check the frame_order.simulate user function for the pseudo-ellipse model along the z-axis.
  • Created the Frame_order.test_simulate_iso_cone_xz_plane_tilt system test. This is to check the frame_order.simulate user function for the torsionless isotropic cone model with a xz-plane tilt.
  • Created the Frame_order.test_simulate_pseudo_ellipse_free_rotor_z_axis system test. This is to check the frame_order.simulate user function for the free rotor pseudo-ellipse model along the z-axis.
  • Created the Frame_order.test_simulate_pseudo_ellipse_xy_plane_tilt system test. This is to check the frame_order.simulate user function for the pseudo-ellipse model with a xz-plane tilt.
  • Created the Frame_order.test_simulate_pseudo_ellipse_torsionless_z_axis system test. This is to check the frame_order.simulate user function for the torsionless pseudo-ellipse model along the z-axis.
  • Fix for the Frame_order.test_simulate_pseudo_ellipse_xz_plane_tilt system test name. This was mislabelled as Frame_order.test_simulate_pseudo_ellipse_xy_plane_tilt.
  • Redesign of the pymol.frame_order user function. This user function was still fitting to the old design in the relax trunk. It has been updated for the frame_order_cleanup branch whereby the frame_order.pdb_model user function has been split up and the positional distribution has been replaced by the Brownian simulation user function frame_order.simulate.
  • Better checking for the non-moving domain setup. The frame_order.pdb_model user function will now raise a RelaxError if the frame_order.ref_domain user function has not been called to set up the non-moving domain.
  • Updated the frame_order.ref_domain user function for the current branch design. This user function was quite out of date. The alignment tensor checks have been removed, to allow this to be used in the absence of base data. And the user function description has been updated.
  • Updated all frame order system tests for the frame_order.ref_domain user function requirement.
  • Expanded all of the Frame_order.test_simulate_* system tests. Two atoms have been added to the origin [0, 0, 0], one in the moving domain, the other in the reference non-moving domain. The positions of these atoms are checked to make sure that the domain systems are correctly handled.
  • Expanded the double rotor model description in the frame_order.select_model user function.
  • Added the pipe_name argument to the frame order check_model() function. This is for the specific_analyses.frame_order.checks module.
  • Converted the specific_analyses.frame_order.checks module to the new Check object design. This follows from http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions and the changes significantly simplify the checking objects.
  • Improved checking for the frame order generate_pivot() function. The check_model() checking object is now called to make sure the frame order model has been specified, as this is essential for this function.
  • Created two system tests for the frame_order.simulate user function for the double rotor model. These are Frame_order.test_simulate_double_rotor_mode1_z_axis and Frame_order.test_simulate_double_rotor_mode2_z_axis.
  • Created two system tests for the frame_order.simulate user function for the double rotor model. These are Frame_order.test_simulate_double_rotor_mode1_xz_plane_tilt and Frame_order.test_simulate_double_rotor_mode2_xz_plane_tilt.
  • Added relax scripts which match the Frame_order.test_test_simulate_* system tests. These are the tests of the frame_order.simulate user function. These were used to construct and visually check the Brownian simulation and PDB model representation in a molecular viewer. These could be a useful reference, so have been added to the repository.
  • Fix for the frame order auto-analysis when only the 'rigid' model is optimised. The final summary table printout for the number of Sobol' points used was failing as there were no models in the table. The table is now only printed out if non rigid models are present in the model list.
  • Introduced the nested_params_ave_dom_pos argument to the frame order auto-analysis. This allows the average domain position to be set to no rotations and translations rather than taking the average position from the rotor or free-rotor model. This can be useful when large motions are present causing the rigid model to have unreasonable domain positions.
  • Fix for the frame_order.permute_axes user function description to allow the manual to be compiled. The table caption containing the user function name was causing the LaTeX compilation to fail. Therefore the captions have been rewritten to avoid the user function name.
  • Modified the frame order system test check_chi2() method to test the statistics.model user function. This causes all of the Frame_order.test_cam_* system tests to fail, as the user function backend is not implemented for the frame order analysis.
  • Implemented the frame order analysis backend for the statistics.model and statistics.aic user functions. This simply required aliasing the specific analysis API common _get_model_container_cdp() method to get_model_container().
  • Bug fix for the frame order specific analysis API base_data_loop() method. This was looping over non-existent PCS and RDC data. Now the alignment ID is checked for in the interatomic data container 'rdc' data structure and the spin container 'pcs' data structure, as well as values of None, before yielding the data.
  • Created a large set of system tests for implementing the frame_order.distribute user function. This user function will be similar to frame_order.simulate. However instead of creating a PDB file with models from a pseudo-Brownian simulation, the frame_order.distribute user function will generate a PDB file of models forming a uniform distribution of structures covering the full frame order motional space. The new system tests are: Frame_order.test_distribute_double_rotor_mode1_xz_plane_tilt, Frame_order.test_distribute_double_rotor_mode1_z_axis, Frame_order.test_distribute_double_rotor_mode2_xz_plane_tilt, Frame_order.test_distribute_double_rotor_mode2_z_axis, Frame_order.test_distribute_free_rotor_z_axis, Frame_order.test_distribute_iso_cone_z_axis, Frame_order.test_distribute_iso_cone_xz_plane_tilt, Frame_order.test_distribute_iso_cone_torsionless_z_axis, Frame_order.test_distribute_pseudo_ellipse_xz_plane_tilt, Frame_order.test_distribute_pseudo_ellipse_z_axis, Frame_order.test_distribute_pseudo_ellipse_free_rotor_z_axis, Frame_order.test_distribute_pseudo_ellipse_torsionless_z_axis, Frame_order.test_distribute_rotor_z_axis. These are aliases for the equivalent Frame_order.test_simulate_* system tests which have had the 'type' keyword argument added, defaulting to 'sim', which allows to switch between the frame_order.simulate and frame_order.distribute user functions. The concept behind these system tests are the same for both user functions, so the code is shared.
  • Created the front-end of the frame_order.distribute user function. This is a copy and modification of the frame_order.simulate user function, as the concepts are similar.
  • Small modification of the frame_order.simulate user function. The GUI file opening dialog wildcard selectors are now set to all PDB file types (plain text, bzip2 compressed, and gzip compressed).
  • Added the frame_order.distribute user function to the auto-analysis results output. This will allow both the pseudo-Brownian simulation and uniform distribution PDB files to be available to the user in all results directories (excluding the intermediate results for speed).
  • Implemented the back-end of the frame_order.distribute user function. This follows the design of the pseudo-Brownian simulation frame_order.simulate user function. The specific_analyses.frame_order.uf.distribute() function has been created as a modified copy of the simulate() function of the same module. This simply performs checks and assembles the data, passing into the new lib.frame_order.simulate.uniform_distribution() function, which itself is a modified copy of the brownian() function in the same module.
  • Introduced the max_rotations argument into the frame_order.distribute user function. This is used to prevent the user function from running forever. This happens whenever a cone opening angle or torsion angle is zero, and hence the random sampling of the rotational space will never find rotations within the motional distribution.
  • Improved control of the frame_order.distribute user function in the frame order auto-analysis. The maximum number of rotations can now be set, and the argument for the total states for the distribution has been shortened.
  • Speedup of the Frame_order.test_auto_analysis system test. After the introduction of the frame_order.distribute user function into the auto-analysis, the test was taking far too long to complete. Now the distribution arguments are set to low values to allow the test to pass in under a minute.
  • Changed the default relax results compression type to bzip2 in the frame order auto-analysis. This was set to no compression for speeding up some system tests, however the system tests can set this for themselves.
  • The Frame_order.test_auto_analysis system test now sets the results file compression type to bzip2.
  • Changed the default max_rotations argument value to 100,000 in the frame_order.distribute user function. This decrease from one million is so the user function completes in a reasonable amount of time.
  • The frame_order.distribute user function now warns when the maximum rotations are reached.
  • Deleted a number of Frame_order.test_distribute* system tests. These are the four double rotor model tests. The frame_order.distribute user function cannot operate on these test cases as one of the two torsion angles are set to zero in the tests.
  • Fix to allow Monte Carlo simulations to be repeated in the frame order analysis. The code for checking for pre-existing Monte Carlo simulation data structures and raising a RelaxError if anything is found has been deleted.
  • Fix of a fatal bug preventing the frame order analysis to be run on a multi-processor system. The multi-processor code was calling the count_sobol_points() function of the specific_analyses.frame_order.optimisation module to give feedback when calling the minimise.execute or minimise.calculate user functions. However this was run in the slave command run() method, hence would be executed on the slave. The problem is that count_sobol_points() performs a number of checks on the current data pipe, however the slaves do not have any data pipes set up.
  • Added the new 'atom_id' argument to the frame_order.distribute user function. This uses the new inverse selection functionality recently introduced into the trunk to delete all structural data not matching the atom_id from the copy of the loaded structural data string prior to generating the distribution of structures.
  • Bug fix for the frame order target function (introduced recently). The copy.deepcopy() function is now used for all numpy input data to avoid the data from being modified between function calls. This is important for missing RDC and PCS data which is sent in as NaN values. In the target function __init__() method, the NaN values are replaced by 0.0 after the self.missing_rdc and self.missing_pcs structures have been by checking for NaN values. However the recent specific_analyses.frame_order.optimisation change in the Frame_order_minimise_command slave command to printout the number of integration points resulted in the target function being initialised twice, causing all NaN values to be 0.0 in the second initialisation. Hence all missing data was being treated as real data with values of 0.0.
  • Created a new skeleton chapter in the relax manual for the frame order analysis.
  • Added a theory section to the new frame order chapter. This is taken from an in-preparation supplement.
  • Rearrangement of the frame order chapter in the manual. The theory section has been spun out into its own frame_order_theory.tex LaTeX file for better organisation.
  • Added two more sections to the frame order chapter of the manual. This includes a frame order modelling section and PCS numerical integration section. Both are from a supplement from an in-preparation manuscript.
  • Added a DOI and ISBN number to the bibliography.
  • Moved the frame_order_theory.tex LaTeX file into the frame_order directory.
  • Shifted the frame order model derivations into their own 'Advanced topics' chapter.
  • Added the frame order sample scripts used in the CaM-IQ analysis.
  • Added an introduction for the frame order chapter of the manual.
  • Added a 'Data analysis' section to the frame order chapter of the manual. This includes the N-state and frame order analysis scripts required to perform a full analysis.
  • Editing of the data analysis section of the frame order chapter of the manual. A PCS structural error figure has been added, all the text improved, and the scripts made to match those in sample_scripts/frame_order/.
  • Added a section to the end of the frame order chapter about the long computation times.
  • The 'scons clean' target now removes all LaTeX *.aux files. The docs/latex/frame_order/ directory is now also being checked for *.aux files.
  • Removed many unnecessary references to relax.
  • Removed lots of useless comments about book references.
  • Added some images missing from the frame order chapter of the manual.
  • Avoided a doubly defined label in the manual.
  • Removed some duplicated text in the frame order models chapter of the manual. This is duplicated from the frame order analysis chapter.
  • Indentation fix for allowing the API documentation to be properly compiled.
  • Added a patch file for fixing Epydoc version 3.0.1. This is needed to allow the dot graph files names to be unique (by no longer truncating to 30 characters), and to allow epydoc to handle newer Graphvis versions.
  • Improvements for the release checklist document. The backporting of the CHANGES file to trunk is now more obvious, and instructions for fixing Epydoc have been added.
  • Clean up of some of the release instructions (for using vim).
  • Added error catching to the find_unused_imports.py developer script.
  • Fix for the error catching in the find_unused_imports.py developer script. The numerous pylint warnings are also sent to STDERR.
  • Removed the printout of pylint STDERR messages in the find_unused_imports.py developer script.
  • Elimination of a number of wildcard imports from some frame order timing scripts. This is to avoid excessive function imports.
  • Removal of an unused import from the user_functions.frame_order module.
  • Removal of unused imports from the test_suite/shared_data/frame_order/simulation scripts.
  • Updated some unused frame order scripts to use the new minimise user function design.
  • Unused import clean up in the test_suite/shared_data/curve_fitting/numeric_topology directory. All the scripts in this directory have been cleaned up to remove unused imports. In one case, commented out code was replaced with an 'if 0:' statement to silence the unused import warnings from the devel_scripts/find_unused_imports.py script.
  • Unused import clean up in the test_suite/shared_data/curve_fitting/profiling directory. The scripts in this directory have been cleaned up to remove unused imports.
  • Added an exception system to the find_unused_imports.py developer script. Sometimes pylint will give an "Unused import" warning for imports that are needed by the module. Therefore an exception list of the file name and module has been created to skip these warnings. The list covers the dep_check module and all of the profiling_*.py scripts in the directory test_suite/shared_data/dispersion/profiling/.
  • Added a copyright notice to the find_unused_imports.py development script. This is mainly to indicate how out of date the script will be in the future.
  • A directory can now be supplied on the command line for the find_unused_imports.py devel script.
  • Changed the imports in the test_monte_carlo_mean.py script. This inconsequential change is to avoid false positives from the find_unused_imports.py devel script.
  • Modifications of the test suite script for calculating synthetic CPMG data. The imports in cpmg_synthetic.py are now all used, rather than being commented out. This allows the find_unused_imports.py devel script to pass.
  • Unused import cleanup of all scripts in the test_suite/shared_data/dispersion/ directories. This both removes unused imports, or uncomments but deactivates temporarily unused code.
  • Removed unused imports from the scripts in the test_suite/shared_data/frame_order subdirectories.
  • Removed unused imports from the spectrum system test base module.
  • Removed unused imports from the relax_disp system test base module.
  • Clean up of all unused imports in the system test scripts.
  • Removed unused imports from the structure system test base module.
  • Changed how the import of lib.regex in the test_regex unit tests is used. The module is no longer stored in the TestCase class namespace, but is rather called directly within the unit test.
  • Changed the import of pipe_control.state in the test_state unit test module.
  • Removed unused imports from the unit tests.
  • Added another exception to the find_unused_imports.py devel script. This is for the test_suite.unit_tests._lib._geometry.test_rotations module which programatically obtains the imports using globals().
  • Added a workaround or hack for exceptions for circular imports in the find_unused_imports.py script. This is currently for the test_suite.unit_tests._lib.test___init__ and test_suite.unit_tests._lib._geometry.test___init__ modules.
  • Removal of unused imports from the GUI test modules.
  • Removed all unused imports from the pipe_control package.
  • Added import exceptions for the lib.compat module in the find_unused_imports.py devel script.
  • Added import exceptions for the lib.xml module in the find_unused_imports.py devel script. These are needed because of eval() function calls on XML stored Python data structures.
  • Removed all unused imports from the relax library package.
  • Removed all unused imports from the target_functions package.
  • Removed unused imports from the developer scripts.
  • Removed all unused imports from the specific_analyses package.
  • Removed all unused imports from the auto_analyses package.
  • Removed all unused imports from the numdifftools extern package.
  • Removal of the last unused import from the target_functions package.
  • Fix for the PCS system tests on old Python versions. The self.assertAlmostEqual() function cannot compare None values in earlier Python versions.
  • MS Windows fix for the Frame_order.test_generate_rotor2_distribution system test. The locale.setlocale() function call for correctly setting up a spinning progress meter was failing on MS Windows. The error is now caught and the local setting skipped.
  • Added Python 3.5 to the manual C module compilation script.
  • Added Python 3.5 to the Python multiversion test suite script.
  • Changes to the introduction of the frame order theory chapter of the manual.


Bugfixes
  • Fix for the alignment tensor MC simulation objects in the data store for Python 3.1. The sim_indices object was sometimes created with the range() method, however the returned iterator does not possess an index() function in Python 3.1. Therefore it was converted to a standard list.
  • Cosmetic bug fix for the running of the test suite in the GUI. The list of skipped tests in the status object was not being reinitialised for each run of the test suite. This only affects the GUI where the tests can be run multiple times. The result was that the list of skipped tests was always being printed out, even if no tests were skipped.
  • Fix for the numpy version number checking in the dep_check module. The version_comparison() function is now being used to compare numbers, replacing the previous hack.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


Version 3 of relax

relax 3.3 series

relax 3.3.9

Description

This is a minor feature release with improvements to the automatic relaxation dispersion protocol for repeated CPMG data, support for Monte Carlo or Bootstrap simulating RDC and PCS Q factors, a huge speedup of Monte Carlo simulations in the N-state model analysis, and geometric mean and standard deviation functions added to the relax library.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.9
(30 September 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.9


Features
  • Improvements to the automatic relaxation dispersion protocol for repeated CPMG data.
  • Support for Monte Carlo or Bootstrap simulating the RDC and PCS Q factors.
  • Huge speedup of Monte Carlo simulations in the N-state model analysis.
  • Geometric mean and standard deviation functions added to the relax library.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.8

Description

This is a minor bugfix release which allows the relax GUI to be used on screens with the low resolution of 1024x768 pixels.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.8
(2 April 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.8


Features

N/A


Changes


Bugfixes
  • Resized all fixed-sized GUI wizards to fit on 1024x768 pixel wide displays. The problem was reported by Lora Picton in the thread starting at http://thread.gmane.org/gmane.science.nmr.relax.user/1813. Both the spin loading wizard of the spin viewer window and the relaxation data loading wizard used currently in the model-free analysis tab and BMRB export page were fixed. These both had the y-dimension set to 800 pixels, hence parts of the window would be out of view.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.7

Description

This is a major feature and bugfix release. New features include the statistics.aic and statistics.model user functions, plotting API advancements, huge speed ups for the assembly of atomic coordinates from a large number of structures, the sorting of sequence data in the internal structural object for better structural consistency, conversion of the structure.mean user function to the new pipe/model/molecule/atom_id design, and improvements to the rdc.copy and pcs.copy user functions. Bugs fixed include the incorrect pre-scanning of old scripts identifying the minimise.calculate user function as the old minimise user function, Python 3 fixes, and the failure in reading CSV files in the sequence.read user function. Many more features and bugfixes are listed below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.7
(13 March 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.7


Features
  • Creation of the statistics.aic and statistics.model user functions for calculating and printing out different statistics.
  • Addition of new infrastructure for future support for plotting data using Veusz.
  • Huge speed up for the assembly of atomic coordinates from a large number of structures.
  • Sequence data in the internal structural object can now be sorted for better structural consistency.
  • The structure.read_pdb user function now skips water molecules, avoiding the creation of hundreds of new molecules when reading X-ray structures.
  • Conversion of the structure.mean user function to the new pipes/models/molecules/atom_id design and the addition of the set_mol_name and set_model_num arguments to allow the mean structure to be stored alongside the other molecules.
  • The monte_carlo.setup user function now raises a RelaxError if the number of simulations is less than 3, avoiding subsequent errors.
  • Expanded the functionality of the rdc.copy and pcs.copy user functions, allowing for the operation on two data pipes with different spin sequences, skipping deselected spins and interatomic data containers, printing out all copied data for better feedback, and copying all alignment metadata.
  • The sequence.attach_protons user function now lists all the newly created spins.
  • Clarification of the RDC and PCS Q factors with the printouts and XML file variable names modified to indicate if the normalisation is via the tensor size (2Da2(4 + 3R)/5) or via the sum of data squared to allow for clearer RDC vs. PCS comparisons.
  • Expansion of the align_tensor.copy user function to allow all tensors to be copied between different data pipes.
  • Huge speed up for loading results and state files with Monte Carlo simulation alignment tensors.
  • Improvements for the rdc.weight and pcs.weight user functions. The spin_id argument can now be set to None to allow all spins or interatomic data containers to be set.
  • Improvements for the pcs.structural_noise user function. The check for the presence of PCS data for points to skip now includes checking for PCS values of None. And the output Grace file now also includes the spin ID string as a string or comment value which can be displayed in the plot when desired.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.6

Description

This is a minor feature and bugfix release. It includes the addition of the new structure.sequence_alignment user function which can use the 'Central Star' multiple sequence alignment algorithm or align based on residue numbers, saving the results in the relax data store. The assembly of structural coordinates used by the structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and structure.web_of_motion user functions has been redesigned around this new user function. It will use any pre-existing sequence alignments for the molecules of interest, use no sequence alignment if only structural models are selected, and default to a residue number based alignment if the structure.sequence_alignment user function has not been used. Bug fixes include a system test failure on Mac OS X, and I∞ parameter text files and Grace graphs are now produced by the relaxation curve-fitting auto-analysis for the inversion recovery and saturation recovery experiment types. Many more details are given below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.6
(4 February 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.6


Features


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.5

Description

This is a major feature and bugfix release. It fixes an important bug in the Monte Carlo simulation error analysis in the relaxation dispersion analysis. Features include improvements to the NMR spectral noise error analysis, expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments, the implementation of Needleman-Wunsch pairwise sequence alignment algorithm using the BLOSUM62, PAM250 and NUC 4.4 substitution matrices for more advanced 3D structural alignments via the structure.align and structure.superimpose user functions as well as any of the other structure user functions dealing with multiple molecules, conversion of the structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a new pipes/models/molecules/atom_id design to allow the user functions to operate on different data pipes, different structural models and different molecules, addition of the displace_id argument to the structure.align and structure.superimpose user functions to allow finer control over which atoms are translated and rotated by the algorithm, large improvement for the PDB molecule identification code affecting the structure.read_pdb user function, creation of the lib.plotting package for assembling all of the data plotting capabilities of relax, implementation of the new structure.atomic_fluctuations user function for creating text output or Gnuplot graphs of the correlation matrix of interatomic distance, angle or parallax shift fluctuations, the implementation of ordinary least squares fitting, and improvements for the pcs.corr_plot and rdc.corr_plot user functions. Many more features and bugfixes are listed below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.5
(27 January 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.5


Features


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.4

Description

This is a major feature and bugfix release, finally adding support for the saturation recovery and inversion recovery R1 experiments and including a major bug fix for storing multi-dimensional numpy data structures as IEEE 754 byte arrays in the XML output of the relax state and results files.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.4
(3 December 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.4


Features
  • Numerous improvements for the relax_fit.select_model user function.
  • Support for the saturation recovery experiment in the relaxation exponential curve-fitting analysis.
  • Support for the inversion recovery experiment in the relaxation exponential curve-fitting analysis.
  • Added a section to the start of the relaxation curve-fitting chapter of the manual to include descriptions of all supported models.
  • Addition of a button to the R1 and R2 GUI analyses for selecting the desired exponential curve model via the relax_fit.select_model user function.


Changes


Bugfixes
  • Bug fix for the pymol.view user function for when no PDB file exists. The user function would fail with an AttributeError when the currently loaded data does not exist as a PDB file. This is now caught and the non-existent PDB is no longer displayed. A better solution might be to dump all the current structural data into a temporary file and load that, all within a try-finally statement to be sure to delete the temporary file. This solution may not be what the user is interested in anyway.
  • Simple fix for bug #23017, the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files. The problem was a relatively recent regression caused by a change to the is_float_matrix() function of the lib.arg_check module. It was simply that the default dims keyword argument value was changed from None to (3, 3). Therefore any call to the function without supplying the dims argument would fail if the matrix was not of the (3, 3) shape.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.3

Description

This is a major feature and bugfix release. It fixes a failure when loading relaxation data and adds Python 3 support for using the NMRPipe showApod software. Features include a large expansion for the align_tensor.matrix_angles and align_tensor.svd user functions to support the standard inter-matrix angles, the unitary 9D vector notation {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}, and the irreducible spherical tensor 5D basis set of {A-2, A-1, A0, A1, A2} for correctly calculating the inter-tensor angles, singular values and condition numbers.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.3
(24 November 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.3


Features
  • Implemented the lib.geometry.vectors.vector_angle_atan2() relax library function. This is for calculating the inter-vector angle using the more numerically stable atan2() formula.
  • Implemented the lib.geometry.vectors.vector_angle_acos() relax library function. This is used to calculate the inter-vector angle using the arccos of the dot product formula. The function has been introduced into the relax library as the calculation is repeated throughout relax.
  • Expanded the basis sets for the align_tensor.matrix_angles user function to allow the correct inter-tensor angles to be calculated. This includes the standard inter-matrix angles via the arccos of the Euclidean inner product of the alignment matrices in rank-2, 3D form divided by the Frobenius norm of the matrices, irreducible spherical tensor 5D basis set {A-2, A-1, A0, A1, A2}, and the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} (all of which produce the same result).
  • Expanded the basis sets for the align_tensor.svd user function to allow the correct singular values and condition number to be calculated. This includes the irreducible spherical tensor 5D basis set {A-2, A-1, A0, A1, A2} and the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} (both of which produce the same result).
  • Added the angle_units and precision arguments to the align_tensor.matrix_angles user function to allow either degrees or radians to be output and the number of decimal points to be specified.
  • Added the precision argument to the align_tensor.svd user function to allow the number of decimal points for the singular values and condition number to be specified.
  • Updated the align_tensor.display user function to output the irreducible spherical harmonic weights. This is the alignment tensor in the {A-2, A-1, A0, A1, A2} notation.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.2

Description

This is a minor feature and bugfix release. It includes improvements to the readability of the HTML version of the manual, improved printouts throughout the program, numerous GUI enhancements, and far greater Python 3 support. Please see below for a full listing of all the new features and bugfixes.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.2
(13 November 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.2


Features
  • Many improvements for the HTML version of the manual.
  • Improved sectioning printouts in the model-free dauvergne_protocol auto-analysis.
  • Significant improvements for the relax controller window.
  • All wizards and user functions in the relax GUI now have focus so that keyboard is active without requiring a mouse click.
  • The ESC key will now close the relax controller window and all user function windows.
  • The structure.load_spins user function can now load spins from multiple non-identical molecules and merge them into one molecule allowing missing atoms and differential atom numbering to be handled.
  • Improvements to the printouts for many user functions.


Changes
  • Updated the minfx version in the release checklist document to version 1.0.11.
  • Updated the relax version in the release checklist document to be more modern.
  • Spelling fixes for the CHANGES file.
  • Updates for the release checklist document. This is mainly because the main release notes are now the relax wiki, for example for the current version at http://wiki.nmr-relax.com/Relax_3.3.1.
  • Spelling fixed throughout the CHANGES document.
  • Removed a few triple spaces in the CHANGES document.
  • Added periods to the end of all items in the CHANGES document.
  • Fix for an 'N/A' in the CHANGES document.
  • Converted a number of single spaces between sentences to double spaces in the CHANGES document.
  • More updates for the announcement section of the release checklist document.
  • The HTML version of the manual is now compiled with Unicode character support. It allows Greek symbols, for example, to be represented as text rather than LaTeX generated PNG images. This fixes titles and massively decreases the number of images required by the HTML pages.
  • Removal of many dual LaTeX and latex2html section titles in the manual. As the HTML manual is now compiled with Unicode support, the Greek characters in the titles are now supported. Therefore in the model-free and the values, gradients, and Hessians chapters, the dual LaTeX and latex2html section titles could be collapsed to the standard LaTeX section title. This will result in better formatting of the manual and its links.
  • Added instructions and a build script for creating a useful version of latex2html. This version is essential for building the HTML version of the manual. The build script downloads the Debian latex2html-2008 sources as well as all Debian patches for latex2html. It then applies a number of patches for fixing and improving the relax documentation. The program is then compiled and can be installed as the root user into /usr/local/.
  • Extended the number of words used in the HTML webpage file names. This is to hopefully prevent files from being overwritten by multiple files having the same name.
  • Added the write out of parameters and χ2 values, when creating a dx_map. Task #7860: When dx_map is issued, create a parameter file which maps parameters to χ2 value.
  • Created system test Relax_disp.test_dx_map_clustered_create_par_file, which must show that relax is not able to find the local minimum under clustered conditions. When creating the map, the map contain χ2 values, which are lower than the clustered fitted values. This should not be the case. Running a larger map with larger bounds and more increments, which should show that there exist a minimum in the minimisation space with a lower χ2 value. Bug #22754: The minimise.calculate() does not calculate χ2 value for clustered residues. Task #7860: When dx_map is issued, create a parameter file which maps parameters to χ2 value.
  • Renamed test scripts and files for producing surface χ2 plots.
  • Renamed sample scripts making surface maps.
  • Added scripts to make surface plots of spin independents parameters δω and Ra2.
  • Added example surface χ2 values for plots. Task #7826: Write an python class for the repeated analysis of dispersion data.
  • Added example save state for more surface plotting.
  • Added boolean argument to dx.map user function, to specify the creation of a parameter and associated χ2 values file. For very very special situations, the creation of this file is not desired.
  • Modified that structure of points in dx.map is always a list of numpy arrays with 3 values.
  • When issuing dx.map user function with points, implemented the writing out of parameter file, with associated calculated χ2 values.
  • Improved the feedback in the User_functions.test_structure_add_atom GUI test. It is now clearer what the input and output data is.
  • The devel_scripts/python_multiversion_test_suite.py script now runs relax with the --time flag. This is for quicker identification of failure points. It will also force the sys.stdout buffer to be flushed more often on Python 2.5 so that it does not appear as if the tests have frozen.
  • Added check to system test Relax_disp.test_cpmg_synthetic_dx_map_points for the creation of a matplotlib surface command plot file.
  • Added the write out of a matplotlib command file, to plot surfaces of a dx map. It uses the minimum χ2 value in the map space, to define surface definitions. It creates a X,Y; X,Z; Y,Z map, where the values in the missing dimension has been cut at the minimum χ2 value. For each map, it creates a projected 3d map of the parameters and the χ2 value, and a heat map for the contours. It also scatters the minimum χ2 value, the 4 smallest χ2 values, and maps any points in the point file, to a scatter point. Mapping the points from file to map points, is done by finding the shortest Euclidean distance in the space from the points to any map points.
  • Fix for testing the raise of expected errors in system tests. The system test will not be tested, if Python version is under version 2.7. Bug #22801: Failure of the relax test suite on Python 2.5.
  • Inserted a z_axis limit for the plotting of 2D surfaces in matplotlib.
  • Added better figure control of χ2 values on z-axis for surface plots.
  • Narrowed in dx_map in system test Relax_disp.test_dx_map_clustered_create_par_file. This is to illustrate the failure of relax finding the global minimum. It seems there is a shallow barrier, which relax failed to climb over, in order to find the minimum value.
  • Added the verbosity argument to the pipe_control.minimise.reset_min_stats() function. All of the minimisation code which calls this now send in their verbosity arguments. This allows the text "Resetting the minimisation statistics." to be suppressed.
  • Added the verbosity argument to the pipe_control.value.set() function. This is passed into the pipe_control.minimise.reset_min_stats() function so its printouts can be silenced.
  • The pipe_control.opendx space mapping code now calls the value.set() function with verbosity=0. This is to silence the very repetitive statistics resetting messages when executing the dx.map user function.
  • Added more checks to the determine_rnd() of the dauvergne_protocol model-free auto-analysis. This is to try to catch bizarre situations such as bug #22730, model-free auto-analysis - relax stops and quits at the polate step. The following additional fatal conditions are now checked for: A file with the same name as the base model directory already exists; The base model directory is not readable; The base model directory is not writable. The last two could be caused by file system corruptions. In addition, the presence of the base model directory is checked for using os.path.isdir() rather than catching errors coming out of the os.listdir() function. These changes should make the analysis more robust in the presence of 'strangeness'.
  • Added an additional check to determine_rnd() of the dauvergne_protocol model-free auto-analysis. This is to try to catch bizarre situations such as bug #22730, model-free auto-analysis - relax stops and quits at the polate step. The additional check is that if the base model directory is not executable, a RelaxError is raised.
  • Added printouts to the determine_rnd() function of the dauvergne_protocol model-free auto-analysis. This is for better user feedback in the log files as to what is happening. It may help in debugging bug #22730: Model-free auto-analysis - relax stops and quits at the polate step.
  • Alphabetical ordering of imports in the dauvergne_protocol model-free auto-analysis.
  • Changed the model-free single spin optimisation title printouts. The specific_analyses.model_free.optimisation.spin_print() function has been deleted. It has instead been replaced by a call to lib.text.sectioning.subtitle(). This is to match the grid search setup title printouts and to differentiate these titles from those printed out by minfx being underlined by '~' characters.
  • Added extensive sectioning printouts to the dauvergne_protocol model-free auto-analysis. The lib.text.sectioning functions title() and subtitle() are now used to mark out all parts of the auto-analysis. This will allow for a much better understanding of the log files produced by this auto-analysis.
  • Complete redesign of the following of text in the relax controller window in the GUI. The current design for some reason no longer worked very often, and there would be many situations where the scrolling to follow the text output would stop and could never be recovered. Therefore this feature has been redesigned. In the LogCtrl element of the relax controller, which displays the relax output messages, the at_end class boolean variable has been introduced. It defaults to True. The following events will turn it off: Arrow keys, Home key, End key, Ctrl-Home key, Mouse button clicks, Mouse wheel scrolling, Window thumbtrack scrolling (the side scrollbar), finding text, the pop up menu 'Go to start', and Select all (menu or Ctrl-A). It will only be turned on in two cases: The pop up menu 'Go to end', and if the caret is on the final line (caused by Ctrl-End, Mouse wheel scrolling, Page Down, Down arrow, Window thumbtrack scrolling, etc.). Three new methods have been introduced to handle certain events: capture_mouse() for mouse button clicks, capture_mouse_wheel() for mouse wheel scrolling, and capture_scroll for window thumbtrack scrolling.
  • Improvements for selecting all text in the relax controller window. Selecting text using the pop up menu or [Ctrl-A] now shifted the caret to line 1 before selecting all text. This deactivates the following of the end of text, if active, as the text following feature causes the text selection to be lost.
  • Modified the behaviour of the relax controller window so that pressing escape closes the window. This involves setting the initial focus on the LogCtrl, and catching the ESC key press in the LogCtrl as well as all relax controller read only wx.Field elements and calling the parent controller handle_close() method.
  • Replaced the hardcoded integer keycodes in the relax controller with the wx variables. This is for the LogCtrl.capture_keys() handler method for dealing with key presses.
  • Improvement for all wizards and user functions in the relax GUI. The focus is now set on the currently displayed page of the wizard. This allows the keyboard to be active without requiring a mouse click. Now text can be instantly input into the first text control and the tab key can jump between elements. As the GUI user functions are wizards with a single page, this is a significant usability improvement for the GUI.
  • The ESC character now closes all wizards and user functions in the relax GUI. By using an accelerator table set to the entire wizard window to catch the ESC keyboard event, the ESC key will cause the _handler_escape() method to be called which then calls the windows Close() method to close the window.
  • Changed the logic for how the new analysis wizard in the GUI is destroyed. This relates to bug #22818, the GUI test suite failures in MS Windows - PyAssertionError: C++ assertion "Assert failure". The Destroy() method has been added to the Analysis_wizard class to properly close all elements of the wizard. This is now called from the menu_new() method of the Analysis_controller class, which is the target of the menu item and toolbar button. To allow the test suite to use this, the menu_new() method now accepts the destroy boolean argument. The test suite can set this to False and then access the GUI elements after calling the method (however the Destroy() method must be called by the test suite).
  • Resign of how the new analysis wizard is handled in the GUI tests. This relates to bug #22818, the GUI test suite failures in MS Windows - PyAssertionError: C++ assertion "Assert failure". The GUI test base class method new_analysis_wizard() has been created to simplify the process. When a new analysis is desired, this method should be called. It will return the analysis page GUI element for use in the test. The method standardises the execution of the new analysis wizard and sets up the analysis in the GUI. It also properly destroys the wizard to avoid the memory leaking issues such as bug #22818. All GUI tests have been converted to use new_analysis_wizard(). This allows the GUI tests to pass on MS Windows. However there are still significant sources of memory leaks (the USER Objects count) visible in the Windows Task Manager.
  • Fix for the gui.fonts module to allow it to be used outside of the GUI.
  • Updated all of the scripts in devel_scripts/gui/. These have been non-functional since the merger of the relax bieri_gui branch back in January 2011.
  • The gui.misc.bitmap_setup() function can now be used outside of the GUI.
  • Fix for the GUI test base class new_analysis_wizard() method for relaxation dispersion analyses.
  • Modified the pipe_control.pipes.get_bundle() function to operate when no pipe is supplied. In this case, the pipe bundle that the current data pipe belongs to will be returned.
  • Created the Periodic_table.has_element() method for the lib.periodic_table module. This is used to simply check if a given symbol exists as an atom in the periodic table.
  • Added 4 unit tests to the _lib.test_periodic_table module for the Periodic_table.has_element() method.
  • Modified the internal structural object backend for the structure.read_pdb user function. The MolContainer._det_pdb_element() method for handling PDB files with missing element information has been updated to use the Periodic_table.has_element() method to check if the PDB atom name corresponds to any atoms in the periodic table. This allows for far greater support for HETATOMS and all of the metals.
  • Created the Structure.test_load_spins_multi_mol system test. This is to test yet to be implemented functionality of the structure.load_spins user function. This is the loading of spin information similar, but not necessarily identical molecules all loaded into the same structural model. For this, the from_mols argument will be added.
  • Fixes for the Structure.test_load_spins_multi_mol system test. The call to the structure.load_spins user function has also been modified so that all 3 spins are loaded at the same time.
  • Implemented the multiple molecule merging functionality of the structure.load_spins user function. The argument has been added to the user function frontend and a description added for this new functionality. In the backend, the pipe_control.structure.main.load_spins() function will now call the load_spins_multi_mol() function if from_mols is supplied. This alternative function is required to handle missing atoms and differential atom numbering.
  • Modified the N_state_model.test_populations system test to test the grid search code paths. This performs a grid search of one increment after minimisation, then switches to the 'fixed' N-state model and performs a second grid search of one increment. This now tests currently untested code paths in the grid_search() API method behind the minimise.grid_search user function. The test demonstrates a bug in the N-state model which was not uncovered in the test suite.
  • Created the N_state_model.test_CaM_IQ_tensor_fit system test. This is for catching bug #22849, the failure of the N-state model analysis when optimising only alignment tensors using RDCs and/or PCSs. This new test checks code paths unchecked in the rest of the test suite, and is therefore of high value.
  • Modified the atomic position handling in pipe_control.structure.main.load_spins_multi_mol(). The multiple molecule merging functionality of the structure.load_spins user function now handles missing atomic positions differently. The aim is that the length of the spin container position variable is fixed for all spins to the number of structures, as the N-state model analysis assumes this equal length for all spins. When data is missing, the atomic position for that structure is now set to None. This will require other modifications in relax to support this new design.
  • Modified the interatom.unit_vectors user function backend to handle missing atomic positions. This is to match the structure.load_spins user function change whereby missing atomic positions are now set to the value of None.
  • Fix for the atomic position handling in pipe_control.structure.main.load_spins_multi_mol(). The dimensionality of the position structure returned by the structural object atom_loop() method needed to be reduced.
  • The structure.load_spins user function now stores the number of states in cdp.N. This is to help the specific analyses which handle ensembles of structures. With the introduction of the from_mols argument to the structure.load_spins user function, the number of states is now not equal to the number of structural models, as the states can now come from different structures of the same model. Therefore the user function will now explicitly set cdp.N to the number of states depending on how the spins were loaded.
  • Clean up and speed up of the N_state_model.test_CaM_IQ_tensor_fit system test. All output files are now set to 'devnull' so that the system test no longer creates any files within the relax source directories. And the optimisation settings have been decreased to hugely speed up the system test.
  • Expanded the lib.arg_check.is_float_matrix() function by adding the none_elements argument. This matches a number of the other module functions, and allows for entire rows of the matrix to be None.
  • Lists of lists containing rows of None are now better supported by the lib.xml functions. The object_to_xml() function will now convert the float parts to IEEE-754 byte arrays, and the None parts will be stored as None in the <ieee_754_byte_array> list node. The matching xml_to_object() function has also been modified to read in this new node format. This affects the results.write and state.save user functions (as well as the results.read and state.load user functions).
  • Added spacing after the minimise.grid_search user function setup printouts. This is for better spacing for the next messages from the specific analysis.
  • Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test. This test is however still far too slow.
  • Added printouts to pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data(). These functions now accept the verbosity argument which if greater than 0 will activate printouts of how many RDCs or PCSs have been assembled for each alignment. This will be useful for user feedback as the spin verses interatomic data container selections can be difficult to understand.
  • The verbosity argument for the N-state model optimisation is now propagated for more printouts. The argument for the calculate() and minimise() API methods is now sent into specific_analyses.n_state_model.optimisation.target_fn_setup(), and from there into the pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data() functions. That way the number of RDCs and PCSs used in the N-state model is reported back to the user for better feedback.
  • Updated the N_state_model.test_CaM_IQ_tensor_fit system test so it operates correctly as a GUI test. All user functions are now executed through the special self._execute_uf() method to allow either the prompt interpreter or the GUI to execute the user function.
  • Modified the N_state_model.test_CaM_IQ_tensor_fit system/GUI test for implementing a new feature. The 'spin_selection' argument has been added to the interatom.define user function. This will be used to carry the spin selections over into the interatomic data containers.
  • Implemented the spin_selection Boolean argument for the interatom.define user function. This has been added to the frontend with a description, and to the backend. When set, it allows the spin selections to define the interatomic data container selection.
  • Changed the spin_selection argument default in the interatom.define user function backend. This now defaults to False to allow other parts of relax which call this function to operate as previously. The default for the interatom.define user function is however still True.
  • Modified the Structure.test_load_spins_multi_mol system test for the spin.pos variable changes. The atomic position for an ensemble of structures is now set to None rather than being missing, so the system test has been updated to check for this.
  • The align_tensor.display user function now has more consistent section formatting. The section() and subsection() functions of the lib.text.sectioning module are now being used to standardise these custom printouts with the rest of relax.
  • Modifications to the new N_state_model.test_CaM_IQ_tensor_fit system test. The system test now checks all of the optimised values to make sure the correct values have been found. That will block any future regressions in this N-state model code path. The system test is now also faster. And the pcs.structural_noise user function RMSD value has been set to 0.0 so that the test no longer has a random component affecting the final optimised values.
  • Added printouts for the rdc.calc_q_factors and pcs.calc_q_factors user functions. These are activated by the new verbosity user function argument which defaults to 1. If the value is greater than 0, then the backend will print out all the calculated Q factors.
  • The verbosity argument of the RDC and PCS q_factors() functions now defaults to 1. This causes the Q factors to be printed out at the end of all N-state model optimisations.
  • Created the Structure.test_bug_22860_CoM_after_deletion system test. This is to catch bug #22860, the failure of the structure.com user function after calling structure.delete.
  • Fix for the checks in the new Structure.test_load_spins_multi_mol system test. A spin index was incorrect.
  • Fix for the structure.load_spins user function when the from_mols argument is used. The load_spins_multi_mol() function of the pipe_control.structure.main module was incorrectly handling the atomic position returned by the internal structural object atom_loop() method. This position is a list of lists when multiple models are present. But when only a single model is present, it returns a simple list.
  • Modified the Structure.test_bug_22860_CoM_after_deletion system test to expect a RelaxNoPdbError. This tests that the structure.com user function raises RelaxNoPdbError after deleting all of the structural information from the current data pipe.
  • The mol_name argument is now exposed in the structure.add_atom user function. This has been added as the first argument of the user function to allow new molecules to be created or to allow the atom to be placed into a specific molecule container. The functionality was already implemented in the backend, so it has been exposed by simply adding a new argument definition to the user function.
  • Created the Structure.test_bug_22861_PDB_writing_chainID_fail system test. This is to catch bug #22861, the chain IDs in the structure.write_pdb user function PDB files are incorrect after calling structure.delete.
  • Small modification of the Structure.test_bug_22861_PDB_writing_chainID_fail system test. File metadata is now being set to demonstrate that the structure.delete user function does not remove this once there is no more data left for the molecule.
  • Small indexing fixes for the dispersion chapter of the relax manual.
  • Fix for system test Relax_disp.test_cpmg_synthetic_dx_map_points. Another import line was written to the matplotlib script.
  • Speedup and fix for system test Relax_disp.test_dx_map_clustered_create_par_file. The following test was taken out, since this a particular interesting case. There exist a double minimum, where relax has not found the global minimum. This is due to not grid searching for Ra2, but using the minimum value.
  • Removed debugging code from the N_state_model.test_CaM_IQ_tensor_fit system test. This was an accidentally introduced state.save user function used to catch the system test state. It would results in the 'x.bz2' file being dumped in the current directory.
  • Loosened the checks in the Relax_disp.test_baldwin_synthetic_full system test. This is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit GNU/Linux system.
  • Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test for certain systems. This change is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit GNU/Linux system. This may be related to 32-bit numpy 1.6.2 verses later numpy versions causing precision differences.
  • Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test for certain systems. The optimisation precision has been increased, and the value checking precision has been decreased. This change is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit GNU/Linux system. This may be related to 32-bit numpy 1.6.2 verses later numpy versions causing precision differences.
  • Converted all the extern.numdifftools modules using the dos2unix program.
  • Updated the Python 2 to Python 3 migration document to be more current.
  • Small edit of the docs/devel/2to3_checklist document.
  • Expanded the Python 2 to 3 conversion document to list the 2to3 command individually.
  • The ImportErrors in unit tests are now correctly handled by the relax test suite. If an ImportError occurred, this was previously killing the entire test suite.
  • The target_function.relax_fit module unit tests are now skipped if the C module is not compiled.
  • Expanded the Python 2 to 3 conversion document.
  • Small update to the 2to3_checklist document - the print statement conversion has been added.
  • The lib.errors module is now importing lib.compat.pickle for better Python 2 and 3 support. This shifts the compatibility code from lib.errors into lib.compat so that the 2to3 program will not touch the lib.errors module.
  • Better Python 3 compatibility in some test suite shared data profiling scripts. These changes invert the logic, importing the Python 3 builtins module and aliasing xrange() to range(), and passing if an ImporError occurs. The code will now no longer be modified by the 2to3 program.
  • Unicode fixes for the "\u" string in "\usepackage" in the module docstring. This requires escaping as "\\usepackage" to avoid the unicode character '\u'.
  • The lib.check_types module now imports io.IOBase from the lib.compat module. This is to shift more Python 2 vs. 3 compatibility into lib.compat and out of all other modules.
  • Python 3 improvements - changed how the Python 3 absent builtins.unicode() function is handled. The aliased builtins.str() function is now referenced as lib.compat.unicode(). The Python 2 __builtin__.unicode() function is also aliased to lib.compat.unicode(). The GUI using this function now import it from lib.compat.
  • Removed the writable base directory check in the dauvergne_protocol auto-analysis. This check was causing the system test to fail if the user does not have write access to the installed relax directory.
  • Expanded the Mac_framework_build_3way document to include matplotlib.
  • Important bug fix for racing causing the GUI to freeze. This is really only seen in the GUI tests on MS Windows systems, as a user could never be fast enough with the mouse. The GUI interpreter flush() method for ensuring that all user functions in the queue have been cleared now calls wx.Yield() to force all wxPython events to also be flushed. This change will avoid random freezing of the relax test suite.
  • Bug fix for the Mf.test_bug_21615_incomplete_setup_failure GUI test on MS Windows systems. The GUI interpreter flush() method needs to be called between the two structure.load_spins user function calls. Without this, the test will freeze on MS Windows. The freezing behaviour is however not 100% reproducible and is dependent on the Windows version and wxPython version.
  • Shifted a number of wx.NewId() calls to the module namespace to conserve IDs. These are for the menus in the main window and in the spin view window.
  • Shifted the wx.NewId() calls for the spectrum list GUI element to the module namespace. These IDs are used for the pop up menus. The change avoids repetitive calls to wx.NewId() every time a right click occurs, conserving wx IDs so that they are not exhausted when running the test suite or running the GUI for a long time.
  • More shifting of wx.NewId() calls for popup menus to module namespaces to conserve IDs.
  • Converted all of the GUI wizard button IDs to -1, as they are currently unused. This should conserve wx IDs, especially in the test suite.
  • Shifted the main GUI window toolbar button wx IDs to the module namespace. This has no effect apart from better organising the code.
  • Shifted the relax controller window popup menu wx IDs to the module namespace. This is simply to better organise the code to match the other GUI module changes.
  • Menus created by the gui.components.menu.build_menu_item() now default to the wx ID of -1. This is to conserve wx IDs. If the calling code does not provide the ID, there is no need to grab one from the small pool of IDs.
  • Shifted the spin viewer GUI window toolbar button wx IDs to the module namespace. This should conserve wx IDs as the window is created and destroyed, as only 2 IDs will be taken from the small pool for the entire lifetime of the program.
  • Shifted all of the wx.NewId() calls for the new analysis wizard into the module namespace. This will hugely save the number of wx IDs used by the GUI, especially in the test suite. Instead of grabbing 8 IDs from the small pool every time the new analysis wizard is created, only 8 IDs for the lifetime of the program will be used.
  • Another large wx ID saving change. The ID associated with the special accelerator table that allows the ESC button to close relax wizards is now initialised once in the module namespace, and not each time a wizard is created.
  • A small wx ID conserving change - the 'Execute' button in the analysis tabs now uses the ID of -1. A unique ID is not necessary and is unused.
  • The user function class menus no longer have unique wx IDs, as these are unnecessary. This conserves the small pool of unique wx IDs, as the spin viewer window is created and destroyed.
  • Bug fix for the structure.load_spins user function new from_mols argument. This was incorrectly using the pipe_control.pipes.pipe_names() function to obtain its default values in the GUI (although this is not currently uesd). The result was a non-fatal error message on Mac OS X systems of "Python[1065:1d03] *** __NSAutoreleaseNoPool(): Object 0x3a3944c of class NSCFString autoreleased with no pool in place - just leaking".
  • Added a debugging Python version check to the devel_scripts/memory_leak_test_relax_fit.py script. This prevents the script from being executed with a normal Python binary.
  • Created the blacklisted Noe.test_noe_analysis_memory_leaks GUI test. This long test can be manually run to help chase down memory leaks. This can be monitored using the MS Windows task manager, once the 'USER Objects' column is shown. If the USER Objects count reaches 10,000 in Windows, then no more GUI elements can be created and the user will see errors.
  • Added a printout to the Noe.test_noe_analysis_memory_leaks GUI test to help with debugging.
  • Improved debugging printouts for the Noe.test_noe_analysis_memory_leaks GUI test.
  • Small fix for the GUI analysis deletion method to prevent racing in the GUI tests.
  • Redesigned how wizards are destroyed in the GUI. The relax wizard Destroy() method is now overridden. This allows the buttons in the wizard to be properly destroyed, as well as all wizard pages. This should remove a lot of GUI memory leaks.
  • Created the General.test_new_analysis_wizard_memory_leak blacklisted GUI test. This will be used to check for memory leaks in the new analysis wizard.
  • Removed an unused dictionary from the GUI wizard object.
  • Added a wx.Yield() before destroying the new analysis wizard via menu_new(). This is to avoid racing which can be triggered in the test suite.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.1

Description

This is a minor feature and bugfix release. It includes the addition of the error_analysis.covariance_matrix, structure.align, and structure.mean user functions and expanded functionality for the structure.com and structure.delete user functions. Many operations involving the internal structural object are now orders of magnitude faster, with the interatom.define user function showing the greatest speed ups. There are also improvements for helping to upgrade relax scripts to newer relax versions. The numdifftools package is now bundled with relax for allowing numerical gradient, Hessian and Jacobian matrices to be calculated. And the release includes the start of a new protocol for iteratively analysing repetitive relaxation dispersion experiments.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.1
(9 October 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.1


Features


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.3.0

Description

This is a major feature release which includes a huge number of changes, as can be seen below. The most important change is an incredible speed up of all relaxation dispersion models. See the table below for a comparison to the previous relax 3.2.3 release. The maximum possible advantage of linear algebra operations are used to eliminate all of the slow Python looping and to obtain the ultimate algorithms for speed. As this is using NumPy, conversion to C or FORTRAN will not result in any significant speed advantage. With these huge speed ups, relax should now be one of the fastest software packages for analysing relaxation dispersion phenomena.

Other important features include the implementation of a zooming grid search algorithm for use in all analysis types, expanded plotting capabilities for R1ρ values in the relaxation dispersion analysis, the ability to optimise the R1 parameter in all off-resonance dispersion models, proper minimisation statistics resetting by the minimisation user functions, and a large expansion of the periodic table information for all elements in the relax library for correctly estimating molecular masses. Additional features are that there is better tab completion support in the prompt UI for Mac OS X, the addition of the time user function for printing the current date and time, the value.copy user function accepting a force argument for overwriting values, model nesting in the dispersion auto-analysis has been extended, the spin-lock offset is now shown in the dispersion analysis in the GUI, the relax_disp.r2eff_estimate user function has been added for fast R2eff and I0 parameter value and error estimation, and gradient and Hessian functions have been added to the exponential curve-fitting C module allowing for more advanced optimisation in the relaxation curve-fitting and dispersion analyses.

Note that this new 3.3 relax series breaks compatibility with old relax scripts. The important change, which is the main reason for starting the relax 3.3.x line, is the renaming of the calc, grid_search and minimise user functions to minimise.calculate, minimise.grid_search and minimise.execute respectively. Please update your scripts appropriately. A new relax feature is that old user function calls are detected in the prompt and script UIs and a RelaxError raised explaining what to rename the user function to.

Important bugfixes in this release include that relax can run on MS Windows systems again, numerous Python 3 fixes, the ability to load Bruker DC files when the file format has corrupted whitespace, the GUI "close all analyses" feature works and no longer raises an error, structure.create_diff_tensor_pdb user function now works when no structural data is present, the geometric prolate diffusion 3D PDB representation in a model-free analysis now aligns with the axis in the PDB as it was previously rotated by 90 degrees, and the Monte Carlo simulations in the relaxation dispersion analysis for exponential curve-fitting for R2eff/R1ρ parameter errors is now correct and no longer underestimating the errors by half. For more details about the new features and the bug fixes, please see below. For fully formatted and easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.0.

To demonstrate the huge speeds ups in the relaxation dispersion analysis, the following table compares the speed of dispersion models in relax 3.2.3 compared to the new 3.3.0 version:

100 single spins analysis (times in seconds):
Dispersion model relax 3.2.3 timings relax 3.3.0 timings Speed change
No Rex 0.824±0.017 0.269±0.016 3.068x faster.
LM63 1.616±0.017 0.749±0.008 2.157x faster.
LM63 3-site 3.218±0.039 0.996±0.013 3.230x faster.
CR72 2.639±0.042 1.536±0.019 1.718x faster.
CR72 full 2.808±0.027 1.689±0.075 1.663x faster.
IT99 1.838±0.032 0.868±0.011 2.118x faster.
TSMFK01 1.643±0.033 0.718±0.011 2.289x faster.
B14 5.841±0.050 3.747±0.044 1.559x faster.
B14 full 5.942±0.053 3.841±0.044 1.547x faster.
NS CPMG 2-site expanded 8.309±0.066 4.070±0.073 2.041x faster.
NS CPMG 2-site 3D 245.180±2.162 45.410±0.399 5.399x faster.
NS CPMG 2-site 3D full 237.217±2.582 45.177±0.415 5.251x faster.
NS CPMG 2-site star 183.423±1.966 36.542±0.451 5.020x faster.
NS CPMG 2-site star full 183.622±1.326 36.788±0.343 4.991x faster.
MMQ CR72 5.920±0.105 4.078±0.105 1.452x faster.
NS MMQ 2-site 363.659±2.610 82.588±1.197 4.403x faster.
NS MMQ 3-site linear 386.798±4.480 92.060±0.754 4.202x faster.
NS MMQ 3-site 391.195±3.442 93.025±0.829 4.205x faster.
M61 1.576±0.022 0.862±0.009 1.828x faster.
DPL94 22.794±0.517 1.101±0.008 20.705x faster.
TP02 19.892±0.363 1.232±0.007 16.152x faster.
TAP03 31.701±0.378 1.936±0.017 16.377x faster.
MP05 24.918±0.572 1.428±0.015 17.454x faster.
NS R1rho 2-site 244.604±2.493 35.125±0.202 6.964x faster.
NS R1rho 3-site linear 287.181±2.939 68.245±0.536 4.208x faster.
NS R1rho 3-site 290.486±3.614 70.449±0.686 4.123x faster.
Cluster of 100 spins analysis (times in seconds):
Dispersion model relax 3.2.3 timings relax 3.3.0 timings Speed change
No Rex 0.818±0.016 0.008±0.001 97.333x faster.
LM63 1.593±0.018 0.037±0.000 43.401x faster.
LM63 3-site 3.134±0.039 0.067±0.001 47.128x faster.
CR72 2.610±0.047 0.115±0.001 22.732x faster.
CR72 full 2.679±0.034 0.122±0.005 22.017x faster.
IT99 1.807±0.025 0.063±0.001 28.687x faster.
TSMFK01 1.636±0.036 0.039±0.001 42.170x faster.
B14 5.799±0.054 0.488±0.010 11.879x faster.
B14 full 5.803±0.043 0.484±0.006 11.990x faster.
NS CPMG 2-site expanded 8.326±0.081 0.685±0.012 12.160x faster.
NS CPMG 2-site 3D 244.869±2.382 41.217±0.467 5.941x faster.
NS CPMG 2-site 3D full 236.760±2.575 41.001±0.466 5.775x faster.
NS CPMG 2-site star 183.786±2.089 30.896±0.417 5.948x faster.
NS CPMG 2-site star full 183.243±1.615 30.898±0.343 5.931x faster.
MMQ CR72 5.978±0.094 0.847±0.007 7.061x faster.
NS MMQ 2-site 363.138±3.041 75.906±0.845 4.784x faster.
NS MMQ 3-site linear 384.978±5.402 83.703±0.773 4.599x faster.
NS MMQ 3-site 388.557±3.261 84.702±0.762 4.587x faster.
M61 1.555±0.021 0.034±0.001 45.335x faster.
DPL94 22.837±0.494 0.140±0.002 163.004x faster.
TP02 19.958±0.407 0.167±0.002 119.222x faster.
TAP03 31.698±0.424 0.287±0.003 110.484x faster.
MP05 25.009±0.683 0.187±0.007 133.953x faster.
NS R1rho 2-site 242.096±1.483 32.043±0.157 7.555x faster.
NS R1rho 3-site linear 280.778±2.589 62.866±0.616 4.466x faster.
NS R1rho 3-site 282.192±5.195 63.174±0.816 4.467x faster.

Full details of this comparison can be seen in the test_suite/shared_data/dispersion/profiling directory. For information about each of these models, please see the links: http://wiki.nmr-relax.com/No_Rex, http://wiki.nmr-relax.com/LM63, http://wiki.nmr-relax.com/LM63_3-site, http://wiki.nmr-relax.com/CR72, http://wiki.nmr-relax.com/CR72_full, http://wiki.nmr-relax.com/IT99, http://wiki.nmr-relax.com/TSMFK01, http://wiki.nmr-relax.com/B14, http://wiki.nmr-relax.com/B14_full, http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded, http://wiki.nmr-relax.com/NS_CPMG_2-site_3D, http://wiki.nmr-relax.com/NS_CPMG_2-site_3D_full, http://wiki.nmr-relax.com/NS_CPMG_2-site_star, http://wiki.nmr-relax.com/NS_CPMG_2-site_star_full, http://wiki.nmr-relax.com/MMQ_CR72, http://wiki.nmr-relax.com/NS_MMQ_2-site, http://wiki.nmr-relax.com/NS_MMQ_3-site_linear, http://wiki.nmr-relax.com/NS_MMQ_3-site, http://wiki.nmr-relax.com/M61, http://wiki.nmr-relax.com/DPL94, http://wiki.nmr-relax.com/TP02, http://wiki.nmr-relax.com/TAP03, http://wiki.nmr-relax.com/MP05, http://wiki.nmr-relax.com/NS_R1rho_2-site, http://wiki.nmr-relax.com/NS_R1rho_3-site_linear, http://wiki.nmr-relax.com/NS_R1rho_3-site.

For CPMG statistics: 3 fields, each with 20 CPMG points. Total number of dispersion points per spin is 60.

For R1ρ experiments: 3 fields, each with 10 spin lock offsets, and each offset has been measured at 5 different spin lock fields. Per field there is 50 dispersion points. Total number of dispersion points per spin is 150.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.0
(3 September 2014, from /trunk)
https://sourceforge.net/p/nmr-relax/code/ci/3.3.0/tree/


Features
  • Huge speed ups for all of the relaxation dispersion models ranging from 1.452x to 163.004x times faster. The speed ups for the clustered spin analysis are far greater than for the single spin analysis.
  • Implementation of a zooming grid search algorithm for optimisation in all analyses. This includes the addition of the minimise.grid_zoom user function to set the zoom level. The grid width will be divided by 2zoom_level and centred at the current parameter values. If the new grid is outside of the bounds of the original grid, the entire grid will be translated so that it lies entirely within the original.
  • Increased the amount of user feedback for the minimise.grid_search user function. Now a comment for each parameter is included in the printed grid search setup table. This includes if the lower or upper bounds, or both, have been supplied and if a preset value has been used instead.
  • Expanded support for R1ρ 2D graph plotting in the relax_disp.plot_disp_curves user function as the X-axis can now be the ν1 value, the effective field ωeff, or the rotating frame title angle θ. And the plots are interpolation over the spin-lock offset.
  • Ability to optimise the R1 relaxation rate parameter in the off-resonance relaxation dispersion models.
  • Creation of the relax_disp.r1_fit user function for activating and deactivating R1 fitting in the dispersion analysis.
  • Better tab completion support in the prompt UI for Mac OS X users. For some Python versions, the Mac supplied libedit library is used rather than GNU readline. But this library uses a completely different language and hence tab completion was non-functional on these systems. The library difference is now detected and the correct language sent into libedit to activate tab completion.
  • Created the time user function. This is just a shortcut for printing out the output of the time.asctime() function.
  • The value.copy user function now accepts the force flag to allow destination values to be overwritten.
  • Expanded model nesting capabilities in the relaxation dispersion auto-analysis to speed up the protocol.
  • The spin-lock offset is now included in the spectra list GUI element for the relaxation dispersion analysis.
  • Creation of the relax_disp.r2eff_estimate user function for the fast estimation of R2eff/R1ρ values and errors when full exponential curves have been collected. This experimental feature uses linearisation to estimate the R2eff and I0 parameters and the covariance matrix to estimate parameter errors.
  • Gradients and Hessians are implemented for the exponential curve-fitting, hence all optimisation algorithms and constraint algorithms are now available for this analysis type. Using Newton optimisation instead of Nelder-Mead Simplex can save over an order of magnitude in computation time. This is also available in the relaxation dispersion analysis.
  • The minimisation statistics are now being reset for all analysis types. The minimise.calculate, minimise.grid_search, and minimise.execute user functions now all reset the minimisation statistics for either the model or the Monte Carlo simulations prior to performing any optimisation. This is required for both parallelised grid searches and repetitive optimisation schemes to allow the result to overwrite an old result in all situations, as sometimes the original chi-squared value is lower and the new result hence is rejected.
  • Large expansion of the periodic table information in the relax library to include all elements, the IUPAC 2011 standard atomic weights for all elements, mass numbers and atomic masses for all stable isotopes, and gyromagnetic ratios.
  • Significant improvements to the structure centre of mass calculations by using the new periodic table information - all elements are now supported and exact masses are now used.
  • Added a button to the spectra list GUI element for the spectrum.error_analysis user function. This is placed after the 'Add' and 'Delete' buttons and is used in the NOE, R1 and R2 curve-fitting and relaxation dispersion analyses.
  • RelaxErrors are now raised in the prompt or script UI if an old user function is called, printing out the names of the old and new user functions. This is for help in upgrading old scripts and is currently for the calc(), grid_search(), and minimise() user function calls.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.2 series

relax 3.2.3

Description

This is a major bugfix release and the first requiring numpy ≥ 1.6 to allow for faster calculations for certain analyses. There have been improvements to the GUI user functions, the ^[[?1034h escape code is finally suppressed on Linux systems, and the structure.com user function has been added. Bugfixes include the proper handling of R2A0 and R2B0 parameters in the relaxation dispersion models, the IT99 dispersion model tex parameter was incorrectly handled, the LM63 3-site dispersion models had a fatal mistake in its equations, files with multiple extensions (for example *.pdb.gz) are now correctly handled, and closing the free file format window in Mac OS X systems caused the GUI to freeze. Full details can be found below.

For this release, the Mac OS X framework used to build the universal 3-way (ppc, i386, x86_64) binaries for the stand-alone relax application has been updated. The relax application now bundles Python 2.7.8, numpy 1.8.1, scipy 0.14.0, nose 1.3.3, wxPython 2.9.3.1 osx-cocoa (classic), matplotlib 1.3.1, epydoc 3.0.1, mpi4py 1.3.1 and py2app 0.8.1. This should result in better formatted relax state and results files and give access to more advanced packages for power users to take advantage of.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.2.3
(1 July 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.3


Features
  • Improvements for a number of GUI elements used in the user function windows.
  • The ^[[?1034h escape code should now no longer be emitted by GNU readline on Linux systems.
  • Created the very basic structure.com user function for calculating the centre of mass. This is to simply allow an easy interface to the pipe_control.structure.mass.pipe_centre_of_mass() function.
  • Expansion of the REMARK section of the PDB file created for the internal structural object. This is visible when using the structure.write_pdb user function, as well as the many other user functions which create PDB files. The relax version as well as the file creation date are now recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK section improve the formatting.


Changes
  • Added proper sectioning to the release checklist document.
  • Added the upload script to the release checklist document.
  • Modified the Sequence GUI input element used for the user function list arguments. The first column is now of fixed with when titles are supplied. Previously when supplying titles, the width would be tiny and no text would be visible.
  • Added titles for all 3D coordinate user function arguments. This is for the Sequence GUI input element, and affects the frame_order.average_position, n_state_model.CoM and paramag.centre user functions.
  • The compilation of the C modules now respects the user defined environment. This is the patch from Justin attached to bug #22145. It has been modified to include a comment and remove a double empty line.
  • Bug fix for the compilation of the C modules now respects the user defined environment. The problem was that on Mac OS X (as well as other systems), that these environmental variables were not defined and hence the scons commands would all fail with a KeyError and traceback. Now the keys in the os.environ dictionary are being searched for before they are set.
  • Fix for the wxPython link in the installation chapter of the manual. This was pointing to the scipy website for some reason.
  • Changed the Python readline link for MS Windows in the installation chapter of the manual. This now points to https://pypi.python.org/pypi/pyreadline as the iPython link is broken.
  • Implemented system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster. This is to catch the wrong unpacking of R2A0 and R2B0 when performing a clustered full dispersion model analysis. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for B14 full model. This is to catch the wrong unpacking of R2A0 and R2B0 when performing a clustered full dispersion model analysis. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2-site 3D full model. This is to catch the wrong unpacking of R2A0 and R2B0 when performing a clustered full dispersion model analysis. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2-site star full model. This is to catch the wrong unpacking of R2A0 and R2B0 when performing a clustered full dispersion model analysis. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Added synthetic data generator script which created the data to test against. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Split system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster up in different tests. A setup function which is: setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None): And then the tests: test_bug_22146_unpacking_r2a_r2b_cluster_B14 test_bug_22146_unpacking_r2a_r2b_cluster_CR72 test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Modified profiling script to get closer to the implementation in relax. An additional test function is setup to figure out how to reshape the numpy arrays in the target function. Bug #22146 Unpacking of R2A0 and R2B0 is performed wrong for clustered "full" dispersion models.
  • Updated profiling text for CR72 model. Now it is tested for 3 fields. This is related to: Task #7807: Speed-up of dispersion models for Clustered analysis.
  • Added searching for environment variable PYTHON_INCLUDE_DIR if Python.h is not found in standard Python library. This can be very handsome, if one has a Python virtual environment for multiple users. This relates to the wiki page: http://wiki.nmr-relax.com/Epd_canopy.
  • The lib.compat.norm() replacement function for numpy.linalg.norm() now handles no axis argument. This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while providing compatibility with the axis argument and all numpy versions.
  • Fix for the scons target for compiling the relax manual when using a repository checkout copy. The method for compiling the relax manual was calling the version.revision() function, however this has been replaced a while ago by the version.repo_revision variable.
  • Created two unit tests for the lib.io.file_root() function. The second of the tests demonstrate a failure of the function if multiple file extensions are present.
  • Lowered χ2 value test in system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. This is due to the data produced on 32 bit machine, and tested on 64 bit machines. The error was: AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places. The reason for this is due to truncation artifacts.
  • Fix for wrong path testing of Python.h. Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h and not in PYTHON_PREFIX/include/Python.h.
  • Better handling of the control-C keyboard interrupt signal in the relax test suite. This includes two changes. The Python 2.7 and higher unittest.installHandler() function is now called, when present, to terminate all tests using the unittest module control-C handler. The second change is that the keyboard interrupt signal is caught in a try-except statement, a message printed out, and the tests terminated. This should be an improvement for all systems.
  • Adding last profiling information for model CR72.
  • Added system test for model LM63 3-site. According to results folder in test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site. This should pass, but it doesn't.
  • Created an initial Relax_disp.test_lm63_3site_synthetic system test. This should have been set up a long time ago. It uses the synthetic noise-free data in the test_suite/shared_data/dispersion/lm63_3site directory which was created for a system test but never converted into one. The test still needs modifications to allow it to pass.
  • Modifications for the Relax_disp.test_lm63_3site_synthetic system test. The r2eff_values.bz2 saved state file has been updated, as it was too old to use in the test. The test has also had a typo bug fixed and the data pipe name updated. The test now also checks all of the optimised values.
  • Removed system test test_hansen_cpmg_data_to_lm63_3site. This was a temporary implementation and has been replaced with system test Relax_disp.test_lm63_3site_synthetic.
  • Fixes for all of the relaxation dispersion system tests which were failing with the new minfx code. Due to the tuning of the log barrier constraint algorithm in minfx in the commit at http://article.gmane.org/gmane.science.mathematics.minfx.scm/25, many system tests needed to be slightly adjusted. Two of the Relax_disp.test_tp02_data_to_* system tests were also failing as the optimisation can no longer move out of the minimum at pA = 0.5 for one spin (due to the low quality grid search in the auto-analysis).
  • Updated the release checklist document for the new 1.0.7 release of minfx.
  • Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. The pA parameter is no longer tested for one spin as it moves to random values on different operating systems and 32 vs. 64-bit systems. This is because this spin experiences no exchange, both Δω and kex are zero.
  • Decreased the value checking precision in the Relax_disp.test_hansen_cpmg_data_to_lm63 system test. This is to allow the test to pass on certain operating systems and 32-bit systems.
  • Modified the precision of the output from the relax_disp.sherekhan_input user function. This is simply to allow the Relax_disp.test_sod1wt_t25_to_sherekhan_input system test to pass on certain 32-bit systems, as the float output to 15 decimal places is not always the same. This system test has been updated for the change.
  • Modified the Relax_disp.test_sprangers_data_to_mmq_cr72 system test to pass on certain systems. This test fails on 32-bit Linux (and probably other systems as well). To fix the test, the kex values are all divided by 100 before checking them to 4 decimal places of accuracy.
  • Improved how the relax installation path is determined in the status object. If the path cannot be found, the current working directory is then checked if it is where relax is installed. This is needed when importing modules outside of relax.
  • Hack to permanently eliminate the ^[[?1034h escape code being produced on Linux systems. This is produced by importing the readline module. The escape code will be sent to STDOUT every time relax is executed, so it will be present in all log files. The problem is the TERM environmental variable being set to 'xterm'. The hack simply sets TERM to an empty string.
  • More hacks for permanently eliminating the ^[[?1034h escape code being produced on Linux systems. This is a nasty feature of the GNU readline library. It is now also turned off in the dep_check module, suppressing ^[[?1034h in Python scripts which import only parts of relax.
  • Numpy version 1.6 or higher is now required to be able to run relax. This follows from the series of messages: http://www.mail-archive.com/relax-devel@gna.org/msg06288.html, http://www.mail-archive.com/relax-devel@gna.org/msg06289.html, http://www.mail-archive.com/relax-devel@gna.org/msg06327.html, and http://www.mail-archive.com/relax-devel@gna.org/msg06335.html. If too many users complain, maybe this change can be reverted later. This minimal numpy version is needed for many of the speed ups going in the relaxation dispersion and frame order analyses. It is required for the numpy ufunc out arguments and for the numpy.eigsum() function. These will likely be used in other analyses in the future for improving the speed of relax, so it might affect users of other analyses later on.
  • Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.
  • Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded module docstring. This is to better separate the original scripts used to document the code evolution.
  • Empty lines are now handled by the lib.structure.pdb_write.remark() function. By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file. This can be used for nicer formatting.
  • Fixes for the Diffusion_tensor system tests due to the recent PDB file changes. Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.
  • Fixes for all system tests failing due to the expanded and improved PDB REMARK section. The system tests now remove all REMARK records prior to comparing file contents. The special strip_remarks() system test method has been created to simplify the stripping process.
  • Fix for the software verification tests. The recent expansion and improvements of the REMARK records created by the internal structural object PDB writing method imported the relax version to place this information into the PDB files. However this breaks the relax library design, as shown by the verification tests. Instead the relax version information is being taken from the lib.structure.internal.object.RELAX_VERSION variable. This defaults to None, however the version module now sets this variable directly when it is imported so that it is always set to the current relax version when running relax.
  • General Python 3 fixes via the 2to3 script.
  • Removed the lib.compat.sorted() function which was providing Python2.3 compatibility. For a while now, relax has been unable to run on Python versions less than 2.5. Therefore there is no use for having this replacement function for Python ≤ 2.3 which was being placed into the builtins module.
  • Python 3 fixes for the entire codebase using the 2to3 script. The command used was: 2to3 -j 4 -w -f xrange .
  • The internal structural object add_molecule() and has_molecule() methods are now model specific. This allows for finer control of structural object.
  • Created the new lib.structure.files module. This currently contains the single find_pdb_files() function which will be used to find all *.pdb, *.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
  • Fix for the breakage of the relax help system. This was reported at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481. The problem was that the TERM environmental variable was turned off to avoid the GNU readline library on Linux systems emitting the ^[[?1034h escape code. See the message at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for more details. However the Python help system obviously requires this environmental variable. Now only if the TERM variable is set to 'xterm' will it be reset, and to 'linux' instead of the blank string "". This does not affect any relax releases.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.2.2

Description

This is a major feature and bugfix release. It includes a large speed up of all analytic relaxation dispersion models, the correct handling of edge case failures in all models of the dispersion analysis, a number of fixes for the handling of list-type data in the GUI user function windows including the fatal GUI crashes on Mac OS X systems, and many other bug fixes. Please see below for a full list of features, changes and bugfixes. All users of the dispersion analysis, the relax GUI, or Mac OS X systems are recommended to upgrade to this newest version.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.2.2
(5 June 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.2


Features
  • Large speedups of all analytical relaxation dispersion models by converting the R2eff calculations and value error checking from single values to numpy arrays.
  • Edge cases where function failures occur are now properly handled for all analytical relaxation dispersion models.
  • Completion of the frame_order.pdb_model user function backend for the frame order PDB representation.
  • relax will now detect when files with *.gz or *.bz2 file extensions are being created and automatically gzip or bzip compress the file.


Changes
  • Small speed up for all the isotropic cone and pseudo-elliptic cone frame order models. The vector length calculation for the numeric PCS integration has been simplified and shifted outside of a loop to take advantage of the speed of numpy.
  • All three file arguments for the pymol.frame_order user function are now optional.
  • Updated all the API documentation links in the dispersion chapter of the manual. These were pointing to http://www.nmr-relax.com/api/3.1/ whereas they should now be point to http://www.nmr-relax.com/api/3.2/.
  • Modified a printout in the 'devel_scripts/code_validator' script. This is to clarify that the first method of a class does not need two preceding empty lines.
  • Shifted some functions from lib.structure.geometric into their own modules. The angles_regular() and angles_uniform() functions are now in the lib.structure.angles module, and the get_proton_names in lib.structure.conversion.
  • Deletion of the pipe_control.structure.main.create_cone_pdb() function. This is only used in the frame order analysis, but has been made redundant by the lib.structure.represent.cone.cone() function.
  • Completed the frame_order.pdb_model user function backend for the frame order PDB representation. Most of this backend, including the axes and cone representations, had been broken for quite a while and were being skipped with an early return statement. This has now been made functional and a few fixes have been made. For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model is produced in the final frame order PDB representation file. For all other models, the rotor representation is no longer centred to the point on axis closest to the centre of mass, as the pivot is unambiguously defined. The rotor representation has also been made larger in these models so that it is outside of the cone, and the propeller blades are now staggered.
  • Modified py_type from "list" to "float_array" in uf_object type in user function dx.map. Bug #22035 The dx.map user function is broken in the GUI.
  • Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects. Bug #22035 The dx.map user function is broken in the GUI.
  • Modified the frame order constraints so that coneθx ≤ coneθy. The linear_constraints() function docstring has been updated to include this constraint.
  • Set dim=4 when setting chi surface level in user function dx.map.
  • Fix for the n_state_model.cone_pdb user function for the recent internal structural object changes. The cone arguments should now be called cone_obj.
  • Renamed the relax_disp.set_grid_r20_from_min_r2eff user function to relax_disp.r20_from_min_r2eff. This follows from the proposal at http://thread.gmane.org/gmane.science.nmr.relax.devel/5957.
  • Modification to the Sequence_2D GUI element used for some user function windows. The selection_win_show() method has been redefined, as the parent method from the Sequence element is specific for the 1D sequence module. The open_dialog() method has also been modified to use the new selection_win_show(), as well as the parent Sequence class selection_win_data() method.
  • Created the User_functions.test_structure_rotate GUI tests. This is to catch bug #22100, the rotation argument for the structure.rotate user function cannot be changed in the GUI, as an AttributeError is raised.
  • Moved py_type "list_val_or_list_of_list_val" to 2D sequence types.
  • Added dim dimensions to match the {x, y, z} positions for GUI input in user function dx.map.
  • Modified the User_functions.test_structure_rotate GUI test to change and check the rotation matrix.
  • Some more fixes for the User_functions.test_structure_rotate GUI test. The open_dialog() method cannot be used, as it deletes the window at the end. Instead the selection_win_show() and selection_win_data() method combination is used.
  • Expanded the User_functions.test_structure_rotate GUI test. This is to more extensively check the 'float_matrix' user function argument type in the GUI.
  • Modified the dim dimensions to (None, 3) to allow the user to change number of points in the GUI. This is for the user function dx.map.
  • Simplified the User_functions GUI tests. The exec_uf_pipe_create() method has been created to simplify the data pipe creation in the tests.
  • Expanded the User_functions.test_structure_rotate GUI test. The rotation matrix argument checks for the Sequence_2D GUI element have been expanded to check that setting nothing (blank element) returns nothing (None). The other checks have also been slightly modified.
  • Expanded the User_functions.test_structure_rotate GUI test to catch more problems. Now the rotation matrix value in the user function window is set to a series of invalid values to test if the Sequence_2D GUI element will handle the rubbish input. This is to mimic user errors.
  • Created the is_list() and is_list_of_lists() functions for the lib.check_types module.
  • Clean up of the User_functions.test_structure_rotate GUI test. The invalid value check is simpler and the Sequence_2D GUI object return value is now checked to be None.
  • Expanded the User_functions.test_structure_rotate GUI once more. This time the setting of invalid values in the Sequence_2D element itself is now checked. For example for the rotation matrix of the structure.rotate user function, if a matrix element is set to a string, a NameError is raised.
  • Created the User_functions.test_dx_map GUI test. This extensively checks the 'point' argument for the dx.map user function GUI window. This is to catch bug #22102, the point argument of the dx.map user function being incorrect in the GUI.
  • Modified the User_functions.test_dx_map GUI test to catch another problem with the Sequence_2D element.
  • Fixes for the frame order PDB presentation in the frame_order.pdb_model user function backend.
  • Expanded the User_functions.test_dx_map GUI test once again. The new test is to set 2 valid points in the wizard, open and close the Sequence_2D window (twice), and check that the points come back.
  • Increased the width of the first column of the Sequence_2D GUI element for variable lists. This is so the column title "Number" will fit.
  • Added list titles for the dx.map user function point argument. This is so that the Sequence_2D GUI element will have column titles of 'X coordinate', 'Y coordinate', and 'Z coordinate'.
  • The self.variable_length flag is now used throughout the Sequence GUI element.
  • The self.variable_length flag is used in one more spot in the Sequence_2D GUI element.
  • Created the User_functions.test_structure_add_atom GUI test. This is used to check the operation of the Sequence GUI element via the 'pos' argument of the structure.add_atom user function. This is a list fixed to 3 elements.
  • Titles are now handled and set in the Sequence GUI element. The titles will replace the numbering of 1 onwards in the first column of the GUI element.
  • Small fix for switched indices in the new User_functions.test_structure_add_atom GUI test.
  • Modified the 'pos' argument of the structure.add_atom user function. The argument is now a list of fixed length of 3, and it has the titles 'X coordinate', 'Y coordinate', and 'Z coordinate' which are shown in the GUI.
  • Created the User_functions.test_spectrum_read_intensities GUI test to catch bug #22105. The problem is that a single file name is split up into many files when the file selection button is clicked, one for each character of the file name.
  • Fix for the User_functions.test_spectrum_read_intensities GUI test. A valid value was being checked as invalid.
  • Shifted all wildcards used in GUI file selection dialogs into the new user_functions.wildcard module. These have now all been standardised, and expanded to include more capitalisation combinations and to include more *.* options.
  • Created a file selection wildcard for use in the GUI for selecting peak lists. This is used in the four user functions which read peak lists.
  • Changed all *.* GUI file selection wildcards to *.
  • Huge speedup for model CR72. Task #7793 Speedup of dispersion models. The system test Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster changes from 7 seconds to 4.5 seconds. This is won by not checking single values in the R2eff array for math domain errors, but calculating all steps, and in one single round check for finite values. If just one non-finite value is found, the whole array is returned with a large penalty of 1e100. This makes all calculations be the fastest numpy array way.
  • Fix for system test test_cpmg_synthetic_dx_map_points. Task #7793 Speedup of dispersion models.
  • Critical fixes for system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis. Task #7793 Speedup of dispersion models. It is suspected that when relax have touched boundary values which made math domain errors, the error catching have created local minima or interfered with the simplex search algorithm.
  • Speedup of model TSMFK01. Task #7793 Speedup of dispersion models. This is won by not checking single values in the R2eff array for math domain errors, but calculating all steps, and in one single round check for finite values. If just one non-finite value is found, the whole array is returned with a large penalty of 1e100. This makes all calculations be the fastest numpy array way.
  • Huge speedup of model B14. Task #7793 Speedup of dispersion models. Time test for system tests: test_baldwin_synthetic 2.626s -> 1.990s, test_baldwin_synthetic_full 18.326s -> 13.742s. This is won by not checking single values in the R2eff array for math domain errors, but calculating all steps, and in one single round check for finite values. If just one non-finite value is found, the whole array is returned with a large penalty of 1e100. This makes all calculations be the fastest numpy array way.
  • Speedup of model TP02. Task #7793 Speedup of dispersion models. The change for running system test is: test_curve_type_r1rho_fixed_time 0.057s -> 0.049s, test_tp02_data_to_ns_r1rho_2site 10.539s -> 10.456s, test_tp02_data_to_tp02 8.608s -> 5.727s. This is won by not checking single values in the R1ρ array for math domain errors, but calculating all steps, and in one single round check for finite values. If just one non-finite value is found, the whole array is returned with a large penalty of 1e100. This makes all calculations be the fastest numpy array way.
  • Huge speedup for model TAP03. Task #7793 Speedup of dispersion models. The change for running system test is: test_tp02_data_to_tap03 13.869s -> 7.263s. This is won by not checking single values in the R1ρ array for math domain errors, but calculating all steps, and in one single round check for finite values. If just one non-finite value is found, the whole array is returned with a large penalty of 1e100. This makes all calculations be the fastest numpy array way.
  • Speedup of model MP05. Task #7793 Speedup of dispersion models. The change in system test is: test_tp02_data_to_mp05 10.750s -> 6.644s.
  • Speedup of model MMQ CR72. Task #7793 Speedup of dispersion models. Change in system test: test_sprangers_data_to_mmq_CR72 9.892s -> 4.121s.
  • Speedup for model M61. Task #7793 Speedup of dispersion models. Change in speed is: test_m61_data_to_m61 6.692s -> 3.480s.
  • Speedup of model LM63. Task #7793 Speedup of dispersion models. Change in system test was: test_hansen_cpmg_data_auto_analysis 13.731s -> 9.971s, test_hansen_cpmg_data_auto_analysis_r2eff 13.370s -> 9.510s, test_hansen_cpmg_data_to_lm63 3.254s -> 2.080s.
  • Speedup of model IT99. Task #7793 Speedup of dispersion models. Change in speed is: test_hansen_cpmg_data_auto_analysis 9.74s -> 8.330s, test_hansen_cpmg_data_to_it99 4.928s -> 3.138s.
  • Speedup of model DPL94. Task #7793 Speedup of dispersion models. Change in speed is: test_dpl94_data_to_dpl94 19.412s -> 4.427s.
  • Math-domain catching for model B14. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model CR72. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model: NS CPMG 2-site expanded. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model CR72. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. The skipping of test when num_points > 0, is a bad implementation. If such a case should show, it is best to catch the wrong input for the calculations. This is best done with a check before running the calculations.
  • Math-domain catching for model TSMFK01. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model TP02. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model TAP03. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model DPL94. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model TAP03. Another check for division with 0 inserted.
  • Math-domain catching for model MP05. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model IT99. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Removed class object "back_calc" being updated per time point for model LM63. Task #7793 Speedup of dispersion models. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model M61. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Math-domain catching for model MMQ CR72. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Align math-domain catching for model CR72 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model DPL94 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model IT99 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model LM63 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model M61 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model MP05 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model TAP03 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model TP02 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Align math-domain catching for model TSMFK01 with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Removing unnecessary math-domain catching for model IT99. Task #7793 Speedup of dispersion models. The denominator is always positive.
  • Align math-domain catching for model NS CPMG 2-site expanded with trunk implementation. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of errors have to be more careful.
  • Modified unit tests demonstrating edge case 'no Rex' failures of the model NS CPMG 2-site expanded. This is to align with the current return of data in the disp_speed branch. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0.
  • Added 7 unit tests demonstrating edge case 'no Rex' failures of the model DPL94. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0.
  • Unit test _lib/test_ns_cpmg_2site_expanded.py copied to _/test_lm63.py. They are both of CPMG type.
  • Added 7 unit tests demonstrating edge case 'no Rex' failures of the model LM63. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0.
  • Unit test _lib/_dispersion/test_ns_cpmg_2site_expanded.py copied to _lib/_dispersion/b14.py. They are both of CPMG type, and can be re-used.
  • Added 7 unit tests demonstrating edge case 'no Rex' failures of the model B14. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0.
  • Removed unnecessary math domain checking in model B14. They are slowing down the code. There is now protection for edge cases, and a last final check, before returning values. That should be sufficient.
  • Unit test _lib/_dispersion/test_b14.py copied to _lib/_dispersion/test_CR72.py. They are both of CPMG type, and can be re-used.
  • Copied unit test _lib/_dispersion/* to be reused for other models.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model CR72. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e5.
  • Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model B14. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e5.
  • Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model LM63. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Small fix for 8 unit tests demonstrating edge case 'no Rex' failures of the model 'ns cpmg_2site_expanded'. The comparison of R2eff is now divided into a special case for kex having large values.
  • Deleted unit test case for lm63 3site.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model M61. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model DPL94. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange:
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model M61b. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Math-domain catching for model M61b. Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These can be found via the --numpy-raise function to the system tests. To make the code look clean, the class object "back_calc" is no longer being updated per time point, but is updated in the relax_disp target function in one go.
  • Modified script to be able to run system test Relax_disp.xxx_test_m61b_data_to_m61b.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model IT99. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e19.
  • Added 9 unit tests demonstrating edge case 'no Rex' failures of the model MMQ CR72. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e5; ΔωH = 0.0.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model MP05. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model TAP03. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model TP02. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e20.
  • Added 7 unit tests demonstrating edge case 'no Rex' failures of the model TSMFK01. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0.
  • Copied unit test test_b14.py to test_ns_cpmg_2site_3d.py.
  • Added 8 unit tests demonstrating edge case 'no Rex' failures of the model NS CPMG 2-site 3D. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e7.
  • Modified unit tests demonstrating edge cases 'no Rex' failures of the model TP02. The catching of errors for off-resonance R1ρ models was implemented wrong. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0; kex = 1e5.
  • Critical fix for the math domain catching of model TP02. The catching of errors for off-resonance R1ρ models was implemented wrong. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
  • Modified unit tests demonstrating edge cases 'no Rex' failures of the model DPL94. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
  • Modified unit tests demonstrating edge cases 'no Rex' failures of the model MP05. The catching of errors for off-resonance R1ρ models was implemented wrong. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model MP05. The catching of errors for off-resonance R1ρ models was implemented wrong. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
  • Modified unit tests demonstrating edge cases 'no Rex' failures of the model TAP03. The catching of errors for off-resonance R1ρ models was implemented wrong. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938. And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models.
  • Critical fix for the math domain catching of model TAP03. The catching of errors for off-resonance R1ρ models was implemented wrong. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938. And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944.
  • Modified unit tests demonstrating edge cases 'no Rex' failures of the model MMQ CR72. This was pointed out in post http://article.gmane.org/gmane.science.nmr.relax.devel/5940. And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models.
  • Small fix for the math domain catching of model MMQ CR72. This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5940. And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946.
  • Various spacing fixes in unit test files _lib/_dispersion. This is the preparation for merging back disp_speed branch into trunk. This follows post http://article.gmane.org/gmane.science.nmr.relax.devel/5948. Usin the code validator script './devel_scripts/code_validator'.
  • Modified that unit tests having different r20a and r20b values is checking if the correct one is returned. This is the preparation for merging back disp_speed branch into trunk. This follows post http://article.gmane.org/gmane.science.nmr.relax.devel/5948.
  • Modified unit test to have standard population of pA = 0.95, and a correctly calculation of Δω in ppm to rad/s. This is related to Task #7793 Speedup of dispersion models.
  • Small fix in parameter calculation in unit test _dispersion/test_ns_cpmg_2site_expanded.
  • Increased max kex to value 1e18 for unit test of lin/ns_cpmg_2site_expanded.py.
  • Increased max kex to value 1e20 for unit test of lib/ns_cpmg_2site_3d.py.
  • Fix for looking for negative values, when all values where converted to positive in matrix in ns_cpmg_2site_3d.py. This is to implement catching of math domain errors, before they occur. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models.
  • Removed nested looping of returning back_calc in lib/ns_cpmg_2site_3d.
  • Removed the 8th unit test for model NS CPMG 2-site 3D. This was the catching of errors when kex = 1e20. The model cannot handle this situations, and we need to let it fail.
  • Removed the 8th unit test for model NS CPMG 2-site expanded. This was the catching of errors when kex has high values. The model cannot handle this situations, and we need to let it fail.
  • Fix for differences in system tests which are different from trunk. These were found with the command: diff -bur disp_speed/test_suite/ relax_trunk/test_suite/ | grep -v "Binary files" > diff.txt.
  • Converting back to having back_calc as a function argument to model B14. This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model CR72: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model DPL94: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model IT99: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model LM63: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model M61: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model M61b: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model MMQ CR72: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model MP05: This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model NS CPMG 2-site expanded. This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model TAP03. This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model TP02. This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Converting back to having back_calc as a function argument to model TSMFK01. This is to clean up the API. There can be bo no partial measures/implementations in the relax trunk. The problem is, that many numerical models can't be optimised further, since they evolve the spin-magnetisation in a matrix. That spin evolution can't be put into a larger numpy array. This is related to Task #7793 Speedup of dispersion models.
  • Created the lib.compat.norm() compatibility function for numpy.linalg.norm(). For numpy 1.8 and higher, the numpy.linalg.norm() function has introduced the 'axis' argument. This is an incredibly fast way of determining the norm of an array of vectors. This is used by the frame order analysis. However for older numpy versions, this causes the frame order analysis, and many corresponding system and GUI tests to fail. Therefore this new lib.compat.norm() function has been designed to default to numpy.linalg.norm() if the axis argument is supported, or to switch to the much slower numpy.apply_along_axis(numpy.linalg.norm, axis, x) call which is supported by older numpy.
  • The frame order analysis now uses the lib.compat.norm() replacement for numpy.linalg.norm(). This is to allow for the axis argument on numpy versions before version 1.8, though these older versions will result in slower optimisation of the frame order models.
  • The built in Python range() function is no longer being replaced by xrange(). Replacing builtin.range() with builtin.xrange() on Python 2 was causing problems with Python site-packages which were not Python 3 compliant. This includes old numpy versions. The original overwriting of range() with xrange() was for both speed and memory conservation. However profiling the system tests, the time for all tests did not change significantly. This change may cause problems in certain places in relax on memory constrained computer systems, so it may need to be reverted in the future.
  • The lib.io.open_write_file() function now automatically determines the compression type. This is used by many user functions which create files. The end result for a user is that if they supply a '.gz' or '.bz2' file extension, a gzipped or bzipped file will be produced.
  • Removal of the docstring text wrapping in the lib.io module.
  • Expanded and improved the docstring for the relax_disp.r20_from_min_r2eff user function. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/5957. The documentation now covers a number of the uses for this user function. The text has also been lightly edited. To fit all the text into the GUI user function window, the size of the dialog and the text high settings have been changed.
  • Large improvements for the detection of cross-compilation on Mac OS X systems. The tests for different architecture support now follows the ideas discussed in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/5785/focus=5820. In summary, for each architecture a simple C file is created, compiled with 'gcc -arch xyz', and the resultant binary file tested. To support 64-bit compilation on 32-bit systems, all previously successful architectures are also included in the gcc command. The change allows the 'ppc64' architecture to be reintroduced.
  • Fixed the docstring for the det_arch() method of the sconstruct script. This is for the true cross-compilation detection on Mac OS X.


Bugfixes
  • Fix for the lib.geometry.lines.closest_point_ax() function for when the two points are the same. If the point on the line and point in the 3D space are the same, then this function used to return an array of NaN values. This situation is now caught and the point in the 3D space is returned.
  • Fix for the heterogen section of the internal structural object write_pdb() method. A number of checks were performed to see if the PDB heterogen records were the same for all structures, but this is meaningless as the structures can of course be different.
  • Fixes for the lib.structure.represent.cone module. The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with the cone() function in the module namespace.
  • Fix for the lib.structure.geometric.generate_vector_residues() function. The atom numbers are no longer read from the internal structural object, as these are not reliable. If another geometric representation exists in the object, then the atom numbers could be None. Or loading structures from multiple PDB files can cause the numbering to be repeated or out of order.
  • Fix for the frame_order.pdb_model user function for the rotor models. The rotor axis is no longer defined by spherical angles and therefore needs to be recreated using the create_rotor_axis_alpha() rather than create_rotor_axis_spherical() function from lib.frame_order.rotor_axis.
  • Partial fix for bug #22100, the rotation argument for the structure.rotate user function cannot be changed in the GUI, as an AttributeError is raised. The append_row() method call has been replaced by the correct add_element() call.
  • Bug fix for the Sequence_2D GUI element. This is used for the user function windows in the GUI for setting lists of lists or matrices. The GUI element GetValue() method will now return None if nothing is set. This prevents a list of lists of None being added to the main user function window.
  • Fixes for the Sequence and Sequence_2D GUI elements for handling invalid input data. These elements used by the user function windows previously raised all sorts of errors if the data was not what they expected (lists or lists of lists respectively). These situations are now caught and the input data is ignored, so blank Sequence and Sequence_2D elements are presented to the user.
  • Bug fix for the Sequence_2D GUI element. This is used for handling list of lists user function arguments in the user function GUI windows. The setting of invalid values directly in the Sequence_2D GUI element is now detected. These values are now replaced with None.
  • Fix for bug #22102, the point argument of the dx.map user function failing in the GUI. The Sequence_2D GUI element used for all list of lists arguments in the user function GUI windows now correctly handles variable length lists. The first column which shows a count of the elements is now properly taken into account in the SetValue(), GetValue() and add_item() methods, via a new self.offset variable. The self.variable_length variable has also been fixed so it is not overwritten by the parent Sequence GUI element.
  • Bug fixes for the Sequence GUI element used for lists in the user function windows. Invalid values input into the Sequence GUI window are now ignored rather than raising different types of error. And invalid input lists for fixed dimension arguments are also ignored. This allows the User_functions.test_structure_add_atom GUI test to pass.
  • Bug fix for the lib.arg_check.is_float_object() function. The dim argument can sometimes be an integer rather than a tuple, but this was not handled by the function. Now integer dim arguments are pre-converted to lists before performing all the checks.
  • Fix for bug #22105, the failure spectrum.read_intensities GUI user function whereby a file name is turned into lists of characters. A few changes were made to allow the Selector_file_multiple GUI element to operate correctly.
  • Critical fix for the math domain catching of model LM63. This was discovered with the added 7 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model B14. This was discovered with the added 7 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model CR72. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. When kex is large, e.g. kex = 1e5, the values of etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs will exceed possible numerical representation. The catching of these occurrences needed to be re-written.
  • Critical fix for the math domain catching of model B14. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. When kex is large, e.g. kex = 1e5, "nan" values where produced, which were replaced with 1e100. The catching of these occurrences needed to be re-written.
  • Critical fix for the math domain catching of model CR72. Removed the test for kex ≥ 1e5. This catching should rather be performed on the math functions instead.
  • Critical fix for the math domain catching of model B14. Removed the test for kex ≥ 1e5. This catching should rather be performed on the math functions instead. In this case, it is the catching of sinh(), not evaluating values above 710.
  • Critical fix for the math domain catching of model MMQ CR72. This was discovered with the added 9 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model IT99. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of these occurrences needed to be re-written.
  • Critical fix for the math domain catching of model TAP03. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model TP02. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Critical fix for the math domain catching of model TSMFK01. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur. The catching of these occurrences needed to be re-written.
  • Critical fix for the math domain catching of model NS CPMG 2-site 3D. This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to Task #7793 Speedup of dispersion models. This is to implement catching of math domain errors, before they occur.
  • Fix for bug #22112, the GUI failure when setting list values via the sequence windows, launched from user function windows fails on Mac OS X. The problem was two fold. First the Sequence and Sequence_2D windows from wx.Dialog should not be terminated via the Destroy() method, as wx.Dialog.Destroy() appears to be horribly broken on Macs.
  • Another fix for bug #22112, the GUI failure when setting list values via the sequence windows, launched from user function windows fails on Mac OS X. This change is for the multiple file selection window and matches the previous change by replacing the Mac OS X fatal wx.Dialog.Destroy() call with wx.Dialog.Close().
  • Fix for the relax start up detection of missing Python packages. The dep_check module is now imported first, as it used to be. This is required to check if all required modules are installed and to present understandable messages to the user rather than cryptic ImportError messages with tracebacks.
  • Fix for bug #22033, the inability to use other optimisation algorithms in the dispersion analysis. As mentioned in comment #2, the solution is to raise a RelaxError explaining that only 'simplex' optimisation is possible for the dispersion analysis as the gradients are not derived and implemented in relax.


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.2.1

Description

This is a major bugfix release which includes the equations for the B14 and B14 full relaxation dispersion models [Baldwin 2014] introduced with relax version 3.2.0, now being calculated correctly, the NS CPMG 2-site expanded model correctly handling edge cases where no exchange is expected, and the structure.delete user function correctly operating when multiple models are loaded into the data store.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.2.1
(23 May 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.1


Features
  • N/A


Changes
  • Punctuation fixes throughout the CHANGES document.
  • Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug #22017: LinAlgError, for all numerical CPMG models. System test was renamed from test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to reflect which model create the data and which model fits the data.
  • Modified cpmg_synthetic script to first create all time structures before doing back-calculation. Bug #22017: LinAlgError, for all numerical CPMG models. The numerical models need all time points which are defined in setup to be present when calculating.
  • Renamed system test to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster. The model that creates the data has been changed to numerical model. Bug #22017: LinAlgError, for all numerical CPMG models.
  • Implemented system test Relax_disp.test_cpmg_synthetic_ns3d_to_b14. Bug #22021: model B14 shows bad fitting to data. This is to catch model B14 showing bad fitting behaviour.
  • Parameter precision increase for system test Relax_disp.test_baldwin_synthetic. The correct implementation of the trigonometric functions allow for higher precision. Bug #22021: model B14 shows bad fitting to data. Duplicate line codes were also removed.
  • Code cleanup in system test Relax_disp.test_baldwin_synthetic_full. Bug #22021: model B14 shows bad fitting to data. The precision could also be increased by 1 digit.
  • Code cleanup in system test Relax_disp.test_baldwin_synthetic. Bug #22021: model B14 shows bad fitting to data. Removing many unnecessary lines of code.
  • Added 7 unit tests demonstrating edge case 'no Rex' failures of the NS CPMG 2-site expanded model. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. These tests cover all parameter value combinations which result in no exchange: Δω = 0.0; pA = 1.0; kex = 0.0; Δω = 0.0 and pA = 1.0; Δω = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; Δω = 0.0, pA = 1.0, and kex = 0.0. Such tests should be replicated for all dispersion models.
  • Created the Structure.test_bug_22069_structure_delete_helix_attribute system test. This is to catch bug #22069, the failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'".
  • Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test. This is to catch bug #22070, the failure of the structure.superimpose user function after deleting atoms with structure.delete.
  • Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test. These tests reveal the real problem - that the atoms of the second model have not been removed by the structure.delete user function.
  • Added git-svn support for the relax version information module. This allows the subversion revision number and repository URL to be displayed on program startup, so that it is stored in log files. This is very useful for debugging purposes.
  • Improvements for the git-svn support in the relax version module. Python 3 is now correctly handled and the URL is properly extracted from the git repository.
  • Improvement for the unit test printouts when run with the --time command line option. The full unit test name is now printed out, reverting to the old behaviour. However the shortened test names are preserved for the other test suite categories.
  • Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test. This is a demonstration, showing the NS CPMG 2-site expanded model with no exchange when kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used for all dispersion models to make sure that they model this edge case correctly as well. This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5906.
  • Attempt at fixing bug #22071, the relax unit test and system test not functioning. The fix here is that the git commands to show the current subversion revision number only works when run from the relax base directory, or one of the subdirectories. This should now be fixed, as the pipe running the command will first 'cd' to the relax base directory.
  • Another attempt at fixing bug #22071, the relax unit test and system test not functioning. This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been replaced with "cd %s; git svn info".
  • Changed most default dispersion parameter values to avoid edge cases where there is no exchange. The Δω parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever used for an optimisation starting point - which it never should, apart from development, test suite, and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away from the no exchange condition of pA = 1.0. This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
  • Fixes for 3 dispersion system tests for the change in default parameter values. The default values are used in the auto-analysis in the test suite to avoid the grid search. The changed values affected the optimisation of two spins from Flemming Hansen's data located at test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue 70 used as an example where data is only available at one field. The system test Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these default values.
  • Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test. This uses the default parameter values to start the optimisation, therefore the recent change away from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly optimised.
  • Speed up for the version module when using a repository copy of the code. The repository revision and URL and now stored as module variables, so that the 'svn info' and 'git svn info' commands are only run twice, once for the revision() function and once for the url() function.
  • Large speed up for the relax start up times for svn and git-svn copies of the relax repository. The 'svn info' and 'git svn info' commands are now only executed once when the version module is first imported. The revision() and url() functions have been merged into the repo_info() function and this is called when the module is imported. This repo_info() function stores the repository revision and URL as the version.repo_revision and version.repo_url module variables. It also catches if these variables are already set, so that multiple imports of the module do not cause the repository information to be looked up each time. Previously the revision() and url() functions where called every time a relax state or result file was created, hence for repository copies the 'svn info' or 'git svn info' commands were being called each time. The functions were also called for each interpreter object instantiated, and for each import of the version module.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.2.0

Description

This is a major feature release. It includes the addition of the new B14 and B14 full relaxation dispersion models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new user functions, documentation improvements including the addition of a new chapter to the manual for the N-state model or ensemble analysis, and numerous of other features. This is also a major bugfix release, so all users are recommended to upgrade. This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected. See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.2.0
(20 May 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.0


Features
  • Addition of the vector_angle() relax library function for calculating the signed or directional angle between two vectors.
  • Huge speed up of the interatom.define user function.
  • For improved feedback, a busy cursor is shown in the GUI when executing user functions.
  • The steady-state NOE auto-analysis now produces a 2D Grace plot of the reference and saturated spectra peak intensity values.
  • Complete redesign of the specific analyses backend, simplifying and cleaning up this internal API and making it easier for users to add completely new analysis types to relax.
  • Parametric reduction of the rotor frame order model, eliminating one redundant parameter hence simplifying optimisation.
  • Large improvement for the lib.software.grace module. The '*_err' and '*_bc' parameter names for the parameter error and back-calculated parameters respectively are now supported, allowing these values to be easily plotted.
  • Expansion of the value.set user function to handle parameters which consist of lists of values. The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
  • Improvements for the parameter definitions in all analysis types. This allows for better output in 2D plots and text files.
  • Implemented linear constraints for the frame order analysis. This uses the log-barrier constraint algorithm in the minfx library to provide constraints without requiring gradients.
  • Improved and expanded the relax command line options for debugging.
  • Full independence of the relax library so that it can be used outside of relax.
  • The addition of a relaxation dispersion user function for setting the R20 values to the minimum R2eff value.
  • Expanded capabilities for the relax_disp.sherekhan_input user function.
  • Implementation of the B14 and B14 full relaxation dispersion CPMG models for 2-site exchange for all time scales (from the new paper [Baldwin 2014] at http://dx.doi.org/10.1016/j.jmr.2014.02.023).
  • Large improvements to the relax HTML manual including fixes for URLs, bibliography entries, links, and tables.
  • Support for multiple point creation for the OpenDX chi-squared space mapping user function.
  • Automatic determination of reasonable initial contour levels for the OpenDX mapping user function.
  • Addition of a new chapter to the manual for the N-state model or ensemble analysis.
  • Creation of the new pymol.frame_order user function for visualising results.
  • Expansion of the Grace 2D data plotting capabilities.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1 series

relax 3.1.7

Description

This is a minor feature and bugfix release which includes improvements to the relaxation dispersion chapter of the manual and the addition of new infrastructure for R1ρ data handling in the dispersion analysis. More details are given below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.7
(17 March 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.7


Features


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1.6

Description

This is a major feature and bugfix release. A comprehensive tutorial has been added to the relaxation dispersion chapter of the manual which shows, step-by-step, the dispersion analysis in the GUI using screenshots. Other changes include improved PDB chain ID support, a new mode for running a relax script and then entering the prompt UI mode, multiple file reading by the spectrum.read_intensities user function, and improvements to the relaxation dispersion analysis. A number of major bugs in the dispersion analysis concerning different relaxation delay times for different experiments and for improved handling of the offset have also been fixed. A number of important GUI bugs have also been fixed. All users are recommended to upgrade to this version of relax.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.6
(28 February 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.6


Features
  • Full support for PDB chain IDs in the internal structural object.
  • Improvements for the devel_scripts/python_seek.py for finding all installed Python versions and modules. Individual modules can now be specified on the command line.
  • The pedantic command line option -p, --pedantic has been renamed to -e, --escalate.
  • The new prompt command line option -p, --prompt causes the relax prompt mode to launch after running a script to allow relax to be inspected interactively.
  • Better organisation of the relax command line options into groups, as shown by running 'relax -h'.
  • A tutorial for using the relaxation dispersion analysis in the GUI has been added to the manual. This includes step-by-step instructions with many screenshots.
  • Improvements to the manual including better and consistent line breaking for the GUI menu item text, user functions, file and directory paths, and Python module paths.
  • The spectrum.read_intensities user function can now load multiple files simultaneously, allowing for simplified use in the GUI.
  • Addition of a new GUI window element for loading multiple files.
  • Improvements to the sequence data input GUI window including the item count being displayed and a 'Delete' button to remove the last element.
  • Improvement for the relaxation dispersion auto-analysis - the names of the automatically created data pipes are now unique by appending the name of the data pipe bundle to the end. This allows multiple dispersion auto-analyses to exist simultaneously in the GUI or within one relax state file.
  • The relaxation dispersion analysis now handles deselected spins.
  • Improved colour coding of relax log messages in the relax manual.
  • The relaxation dispersion auto-analysis now creates the chi2.out text file. This is for more easily comparing the chi-squared values between analyses.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1.5

Description

This is a major bugfix release which fixes the complete failure of the NOE analysis for most users, a bug introduced in the last relax release. All users of relax 3.1.4 should upgrade to this version.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.5
(4 February 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.5


Features

N/A


Changes
  • Updated the interatom.unit_vectors user function description to add the text '3D structure'. This is in response to the http://thread.gmane.org/gmane.science.nmr.relax.user/1547 relax-users mailing list message and the change is to clarify the usage of the user function.
  • Created the Noe.test_bug_21591_noe_calculation_fail system test. This is to catch bug #21591 submitted by Martin Ballaschk. This is the complete failure of the NOE analysis. The peak lists attached to the bug report have been included in the test suite to create the system test.
  • Improvements for the steady-state NOE analysis overfit_deselect() method. The spin deselection which occurs at the start of the calc user function call, used to calculate the NOE, is now clearer. Each deselection condition is now explained in detail and the text is now far more informative. In addition, the special condition of all spins being deselected is now caught. If this happens, a RelaxError is raised to prevent the user from going forwards. This should remove confusion as to why the output file is empty.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1.4

Description

This is a minor feature and bugfix release which has improvements for the handling of structural data involving multiple molecules or models and improved support in the NOE analysis for replicated spectra. Included are fixes for the failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present and for the failure of the rdc.write user function for back calculated RDC data. Full details are given below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.4
(31 January 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.4


Features
  • The structure.write_pdb user function now supports multiple molecules being present.
  • Large speed optimisations for the internal structural object when multiple models are present.
  • Improved support for replicated spectra in the NOE analysis.


Changes
  • Created the Frame_order.test_generate_rotor2_distribution system test. This is to test the Frame Order distribution generating base script, used for creating the synthetic Frame Order test data, and to demonstrate a failure in handling back-calculated RDC data. To implement this, the test_suite/shared_data/frame_order/cam/ path has been converted into a Python package (with the addition of the __init__.py files). The base data generation script test_suite/shared_data/frame_order/cam/generate_base.py has also been modified to use the absolute path for the data files and its run() method now accepts the save_path argument to allow the files to be saved into a temporary directory.
  • Fixes for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script now saves the program state files into the self.save_path directory, preventing the system test from attempting to save files into the relax test suite directories.
  • Another fix for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script no longer prints its progress indicator to sys.__stderr__ but to sys.stderr instead. This avoids the progress text from appearing during the relax test suite execution.
  • Created the Structure.test_bug_21522_master_record_atom_count system test. This is designed to catch bug #21522, the structure.write_pdb user function creating an incorrect MASTER record. This hence also catches bug #21520, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present. The test simply creates two structural models, adds one atom, and writes out a PDB file, checking its contents.
  • The structure.write_pdb user function can now handle a file instance for the file argument. This is for the Structure.test_bug_21522_master_record_atom_count system test, to allow a dummy file object to be used. This can also be useful for power users.
  • Created the lib.geometry.vectors.unit_vector_from_2point() function. This is used to quickly calculate the unit vector between two points.
  • The lib.structure.represent.rotor.rotor_pdb() function can now handle multiple rotors. Previously this function would fail if called twice with the same structural object.
  • Added the has_molecule() method to the relax internal structural object. This is used to quickly check if a molecule name already exists in the structural object.
  • More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function. The atom numbering is now better handled.
  • Better support for the writing out of multiple molecules by the structure.write_pdb user function. This is for the internal structural object write_pdb() method. Now each molecule is assigned a different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored. The chain IDs should however be preserved when using structure.read_pdb followed by structure.write_pdb, without storing the ID. A number of the Structure system tests had to be updated, as now the relax generated PDB files will always write out a chain ID.
  • Large speed up for the internal structural object for when many models are present. The new ModelList.current_models object keeps track of all the models already present in the structural object. This simplifies the checks of the pack_structs() internal structural object method by removing expensive looping. This allows the loading of PDB files to continue to be fast even with many tens or hundreds of thousands of models already loaded.
  • More speed ups for the internal structural object when huge numbers of models are present. Another loop over the structural_data object has been eliminated from the PDB reading load_pdb() method.
  • Another optimisation for the internal structural object for large numbers of models. The ModelList.add_item() method no longer loops over all models to check if a model is already present, instead using the new current_models list.
  • Yet more optimisation for handling large quantities of models in the internal structural model. Now when adding new models to the object, the model_indices and model_list objects are no longer created. This saves much time as the large model_list is now not sorted. A number of structural object methods have been updated to handle the change by switching to the model_loop() method for looping over the models, rather than using the model_indices and model_list objects.
  • The frame order matrix printing function can now output the matrix to any precision. The lib.frame_order.format.print_frame_order_2nd_degree() function now accepts the 'places' argument which allows for higher precision printouts.
  • The behaviour of the rdc.write user function has been changed to output spin ID strings in single quotes. This is to avoid problems with the '#' molecule identifier and the '#' comment character.
  • Fix for the diffusion_tensor.init user function reference in the intro chapter of the manual. This was using a very old and now non-functional syntax.
  • Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure system test. This is to catch bug #21561, failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present, as reported by Martin Ballaschk.
  • Added the truncated data for creating a system test to catch bug #21562, the failure of the NOE analysis when spectra are replicated. This bug was reported by Dhanas Muthu. This consists of the Sparky peak lists attached to the bug report and the modified 2AT7 PDB file. The data has been truncated to only include residues :12, :13, and :14.
  • Shifted the NOE system test script into the new 'noe' directory.
  • Created the Noe.test_bug_21562_noe_replicate_fail system test. This is to catch bug #21562, the failure of the NOE analysis when spectra are replicated, reported by Dhanas Muthu. This uses the truncated data taken from the files attached to the bug report. The NOE output file is checked to see if the contents are correct.
  • Better support for replicated spectra in the NOE analysis. The saturated and reference peak intensity and error are now properly averaged. Previously averaging was not used as the number of replicates N are cancelled in the ratios used for the NOE and error calculation. However this fails when the number of replicates for the saturated spectrum does not match the number of replicates for the reference spectrum. Now any data combination is possible.
  • Another fix for the NOE analysis for when replicated spectra have been collected. Variance averaging rather than error averaging is now used for the peak intensity errors. This is important if the errors for each replicated spectra are different - a case which is rarely encountered as the replicates are almost always used to determine one error for all the replicates.


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1.3

Description

This is a minor documentation release which includes small improvements to the documentation of the relaxation dispersion analysis in the manual as well as the API documentation for the lib.dispersion package. As the manual is available from http://download.gna.org/relax/manual/relax.pdf, installing this newer version of relax is not necessary.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.3
(16 January 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.3


Features

N/A


Changes


Bugfixes

N/A


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


relax 3.1.2

Description

This relax version is a minor bugfix release which repairs a number of icons on newer operating systems and a solves a problem caused by accidentally setting an incorrect spectrometer frequency.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.2
(13 January 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.2


Features

N/A


Changes
  • The average_intensity() dispersion function now accepts the offset argument. This is for better support of combined offset and spin-lock varied R1ρ-type data. The argument is then passed into the find_intensity_keys() function.
  • Improved the DPL94 dispersion model description in the manual.
  • Copied a Sparky peak list to be modified to be a Sparky file without intensity column.
  • Modified the Sparky file to have no columns with intensity values.
  • Implemented to read spins from a SPARKY list, when no intensity column is present. Addition to Support Request #3044 - load spins from Sparky list.
  • Created the Relax_disp.test_bug_21460_disp_cluster_fail system test. This is to catch bug #21460 reported by Min-Kyu Cho. The save file added to the repository consists solely of the data for the first residue.
  • Speed ups for the Relax_disp.test_bug_21460_disp_cluster_fail system test. The optimisation precision is not important for demonstrating this bug.
  • Updated the main copyright notice for 2014.
  • Fix for the main copyright notice.
  • Updated the copyright notice visible to the user to 2014.
  • Updated the copyright for the relax GUI splash screen for 2014.
  • Improvement for the relax test suite printout with the --time command line argument flag. The tests printed out now have the package and module names removed, so that one the test name remains. This removes a large amount of text, simplifying the printout.


Bugfixes


Links

For reference, the following links are also part of the announcement for this release:


relax 3.1.1

Description

This is a major feature and bugfix release which adds support for reading 3D structures of organic molecules from Gaussian log files, the new lib.periodic_table and lib.nmr modules, the NS MMQ 3-site linear, NS MMQ 3-site, NS R1rho 3-site linear, and NS R1rho 3-site relaxation dispersion models, R1ρ dispersion data sets where multiple offsets and multiple spin-lock fields have been collected for each spin, the loading of spins directly from peak lists, and the reading of NMRPipe seriesTab files. Due to the improvements and the bugs fixed in the relaxation dispersion analysis, all users are recommended to upgrade to this version.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.1
(10 December 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.1


Features
  • Support for reading 3D structures of organic molecules from Gaussian log files using the new structure.read_gaussian user function.
  • Addition of the lib.periodic_table module for storing information about the periodic table.
  • Addition of the lib.nmr module for basic NMR related functions. It currently has functions for converting between ppm, Hz, and rad.s-1 units.
  • Many improvements to the relaxation dispersion chapter of the user manual.
  • The NS MMQ 3-site linear numeric model - the model for 3-site exchange using 3D magnetisation vectors linearised with kAC = kCA = 0 with the parameters {R20, ..., pA, pB, ΔωAB, ΔωBC, ΔωHAB, ΔωHBC, kexAB, kexBC}.
  • The NS MMQ 3-site numeric model - the model for 3-site exchange using 3D magnetisation vectors with the parameters {R20, ..., pA, pB, ΔωAB, ΔωBC, ΔωHAB, ΔωHBC, kexAB, kexBC, kexAC}.
  • The NS R1rho 3-site linear numeric model - the model for 3-site exchange using 3D magnetisation vectors linearised with kAC = kCA = 0 with the parameters {R1ρ', ..., pA, pB, ΔωAB, ΔωBC, kexAB, kexBC}.
  • The NS R1rho 3-site numeric model - the model for 3-site exchange using 3D magnetisation vectors wit'h the parameters {R1ρ', ..., pA, pB, ΔωAB, ΔωBC, kexAB, kexBC, kexAC}.
  • More model nesting in the relaxation dispersion auto-analysis (CR72 and MMQ CR72, LM63 and LM63 3-site).
  • Large speed up of the TP02 and NS R1rho 2-site dispersion models by minimising repetitive calculations.
  • Support for the loading of spins directly from peak lists.
  • Support for the reading of peak intensities from NMRPipe seriesTab formatted files (*.ser).


Changes
  • Small improvement for the devel_scripts/log_converter.py script for detecting commit boundaries.
  • Added many small details to the release checklist document. This is for the formatting and editing of the CHANGES file, which is used for the release announcements. Some additional details about the API documentation at http://www.nmr-relax.com/api have been added too.
  • Added sectioning printouts for the relaxation dispersion auto-analysis. This simply tells the user which part of the protocol is currently being performed.
  • Setup for testing the sample_scripts/relax_disp/R1rho_analysis.py sample script. The script was copied into the test_suite/shared_data/dispersion/r1rho_off_res_tp02/ data directory where it will be tested on real data. The 'fake_sequence.in' and 'unresolved' files have been created to allow the script to run. And the script itself has been heavily debugged.
  • All of the relaxation dispersion auto-analysis options are now exposed by the sample scripts. This included the pre_run_dir argument for specifying a directory of results from a non-clustered analysis and the flag for running MC simulations for all models.
  • Added the DATA_PATH variable to the cpmg_analysis.py dispersion sample script. This allows the user to more easily specify a different directory for the files.
  • Docstring improvement for the test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1rho_analysis.py script.
  • Synchronised the test_suite/shared_data/dispersion/Hansen/relax_disp.py with the sample script. This script now matches very closely with the sample_scripts/relax_disp/cpmg_analysis.py sample script. This is for sample script debugging purposes.
  • Created a base data pipe for Flemming Hansen's truncated CPMG data for testing out missing data. The :4 spin is missing just a few data points, whereas the :71 spin is missing all 800 MHz data.
  • Created the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. This is used to demonstrate a failure in the R2eff model when some data is missing.
  • Expansion and fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. The parameters for spin :4 are now being checked, and all the checks updated for the changed data. The parameter values are slightly different as data is now missing and because only 3 spins are used for the error analysis whereas in all other Hansen CPMG data sets the more accurate errors are from all spins.
  • The lib.dispersion.cr72.r2eff_CR72() function is now more robust. Values less than 1.0 are now caught to avoid passing it into the numpy.arccosh() function. This avoids many warning messages on Mac OS X.
  • Added a Gaussian DFT optimisation log file to the shared data directories. This will be used to test the reading of structural data from Gaussian files.
  • Modified the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test to catch another failure. This is the failure of all numeric models when all data from one magnetic field strength is missing for a spin.
  • Created data for a NS MMQ 3-site (branched) model using cpmg_fit from Dmitry Korzhnev.
  • The relax_disp.r2eff_read_spin user function now really strips comments and empty lines from the file.
  • A big change to the usage of the relax_disp.r2eff_read_spin user function. Now the nu_CPMG frequency or the spin-lock field strength must be set prior to calling this user function. This allows for more flexibility as often the experiment IDs and frequency values in the files do not match to the same number of decimal places. The frequency is no longer read from the file but must be preset.
  • Created a relax script for back calculating R2eff values for the same parameters as cpmg_fit. This is for the NS MMQ 3-site (branched) CPMG dispersion model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
  • Created the Relax_disp.test_ns_mmq_3site_branched system test. This is for the NS MMQ 3-site (branched) CPMG dispersion model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
  • Added the NS MMQ 3-site models to the dispersion variables. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
  • Added another Gaussian log file of strychnine, this time with DFT structure optimisation. The file is bzip2 compressed to save space.
  • Created the Structure.test_read_gaussian_strychnine system test. This will be used for implementing and testing the structure.read_gaussian user function.
  • Created the lib.periodic_table module for storing information about the periodic table. This is via the periodic_table object which will have different methods for obtaining different information about an element.
  • Implemented the structure.read_gaussian user function. This will read the final structural data out of a Gaussian log file.
  • Improved the checking of the Structure.test_read_gaussian_strychnine system test. This now checks all the atomic information loaded.
  • Simple fix for the Relax_disp.test_korzhnev_2005_*_data system tests. The CPMG frequencies are now being set up in the setup_korzhnev_2005_data() method.
  • Added support for the NS MMQ 3-site model parameters to the lib.text.gui module. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
  • Added the NS MMQ 3-site models to the relax_disp.select_model user function frontend. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
  • Added support for the NS MMQ 3-site models to the relax_disp.select_model user function back end. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
  • Added support for the new 3-site exchange dispersion parameters. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters.
  • Removed the brackets from the NS MMQ 3-site (linear) dispersion model name.
  • Renamed the Relax_disp.test_ns_mmq_3site_branched system test to Relax_disp.test_ns_mmq_3site.
  • Fixes for the loop_parameters() dispersion function for the new NS MMQ 3-site model parameters. The new parameters were not being handled by this function.
  • Created the target functions for the NS MMQ 3-site models. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
  • Added the R2eff calculating functions for the NS MMQ 3-site models to the relax library. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
  • Added the NS MMQ 3-site models to the dispersion auto-analysis. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
  • Added the NS MMQ 3-site models to the GUI model list. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
  • Updated the MMQ 2-site model description in the manual. The R2_DQ = R2_ZQ = R20 assumption is now explained.
  • Added the NS MMQ 3-site models to the relax user manual. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
  • Completed the MMQ 2-site documentation in the manual. The equations for the numeric evolution of SQ, ZQ and DQ data was missing.
  • Huge speed ups of the relaxation dispersion analysis. This is due to the removal of huge inefficiencies in the loop_point(), return_cpmg_frqs() and return_spin_lock_nu1() functions of the specific_analysis.relax_disp.disp_data module. Two new functions return_cpmg_frqs_single() and return_spin_lock_nu1_single() have been introduces to pull out the nu_CPMG and spin-lock field strengths for a given experiment and spectrometer frequency. This avoids calling the loop_exp() and loop_frq() functions from within loop_point() which itself is often called inside a loop_exp() and loop_frq() sequence.
  • Added the results of cpmg_fit minimisation of the cpmg_fit synthetic data for the NS MMQ 3-site model.
  • Fixes for the NS MMQ 3-site dispersion models - the evolution matrix is now correctly constructed.
  • Another fix for the NS MMQ 3-site dispersion models. The creation of the Z-matrix had a copy and paste error in that the heteronuclear chemical shift sign was negated when it should be positive. This was only in one of the two chemical shift numbers.
  • Loosened the chi-squared check of the Relax_disp.test_ns_mmq_3site system test to allow it to pass.
  • Speed up of the Relax_disp.test_ns_mmq_3site system test. The relax_disp.plot_disp_curves user function call is now skipped as it takes too long.
  • Renamed the 'ns_mmq_3site_branched' dispersion test data directory to 'ns_mmq_3site'.
  • Created the Relax_disp.test_ns_mmq_3site_linear system test and modified Relax_disp.test_ns_mmq_3site. The Relax_disp.test_ns_mmq_3site_linear system test uses the old data from the directory test_suite/shared_data/dispersion/ns_mmq_3site/, as this had kAC = 0, now copied into the ns_mmq_3site_linear/ directory. This system test uses the NS MMQ 3-site linear model. The base data generated by cpmg_fit for the Relax_disp.test_ns_mmq_3site system test was modified so that kAC is no longer 0, but set to 1000. This should properly test the NS MMQ 3-site model.
  • Renamed the MMQ 2-site model to NS MMQ 2-site. This is so that the name matches those of the NS MMQ 3-site linear and NS MMQ 3-site models.
  • Renamed all remaining instances of MMQ 2-site to NS MMQ 2-site. This is simply changing variable, method and module names.
  • Removed the MMQ 3-site branched and MMQ 3-site linear models from the to do list in the manual. These two dispersion models are now implemented.
  • Renamed the MQ CR72 dispersion model to MMQ CR72. The model is designed by Korzhnev et al., 2004 for proton-heteronuclear SQ, ZQ, DQ, and MQ data (or MMQ data), so the change is logical as the model is not just for MQ data.
  • Clean up of the NS R1rho 3-site model names in the manual. The word 'branched' has been removed and the notation now matches the NS MMQ 3-site models.
  • Clean up of the parameter lists in the dispersion model table of the manual.
  • The pC parameter constraints are now implemented for the 3-site dispersion models. The new constraints are 0 ≤ pC ≤ pB.
  • Editing of the introduction section of the dispersion chapter of the manual.
  • Added the NS MMQ 3-site parameters to the optimisation section of the dispersion chapter of the manual.
  • Added some R1ρ data from Dmitry Korzhnev's Fyn SH3 domain. This originates from the cpmg_fit software and is published data.
  • Small fix for the documentation of the relax_disp.r2eff_read* user functions. This is for both relax_disp.r2eff_read and relax_disp.r2eff_read_spin.
  • Created the new lib.nmr relax library module. This currently has a few simple functions for converting between ppm units and Hertz or rad/s units.
  • The relax_disp.spin_lock_offset user function now uses the lib.nmr module. This is for converting between ppm and rad/s units.
  • The relax_disp.r2eff_read_spin user function now can handle offset data in the file. If the new offset_col argument is set and disp_point_col is not, then the file being read can contain the spin-lock offset information rather than the spin-lock field strength values. This is only for R1ρ-type data.
  • Implemented GUI test which caches the bug #21076 - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
  • Large redesign of the R2eff/R1ρ data structures. The five indices {Ei, Si, Mi, Oi, Di} for the experiment type, the spins of the cluster, the magnetic field strengths, the pulse offsets, and the dispersion points (nu_CPMG or nu1) respectively are now much better defined. The Oi dimension is new and allows for support of R1ρ-type data whereby both different offsets and different spin-lock field strengths have been collected. Previously only one or the other was supported, but not both together. The offset information is now included as part of the spin R2eff/R1ρ key, even if not set. To support this, the specific_analyses.relax_disp.disp_data module now has the new functions loop_exp_frq_offset(), loop_exp_frq_offset_point(), loop_exp_frq_offset_point_time(), loop_frq_offset(), loop_frq_offset_point_key(), loop_offset(), and loop_offset_point(). All of the {Ei, Si, Mi, Oi, Di} dispersion indices throughout the source tree have been changed to ei, si, mi,oi, and di respectively. And the time index ti has also been introduced. These changes hugely simplify the code.
  • The relax_disp.plot_disp_curves user function can now support 150 sets per Grace graph.
  • The relax_disp.plot_disp_curves user function can now support 3000 sets per Grace graph.
  • System test for sequence read expanded to include assertions of correct data. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added some more files for the Fyn SH3 R1ρ test data. This includes the cpmg_fit input and output files, R1 data files for relax as R1 cannot optimised yet, and a relax script.
  • Added system test for reading spins from a Sparky list. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added interpreter.spectrum.read_spins function. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Created the back end function for the read_spins function. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fix for system test. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Extended reading of Sparky files to include residue names. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Expanded system test and made it pass for user function spectrum.read_spins. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Updated the GUI test to check for first ID in list. Fix for bug #21076 - When loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
  • Added keyword dim to frontend function for spectrum.read_spins(). Work in progress for Support Request #3044 - load spins from Sparky list. This is associate data with the spins of up to two dimensions.
  • Implemented system test for reading spins from NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Extended reading of spin residue names from NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified NMRPipe SeriesTab to read residue numbers and name for two-dimensional list. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Insert check if spin already exist before creating it. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Issuing a warning instead of error when loading spins from Sparky list where residue names are not present. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Issued a warning instead of error when loading spin residue names from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Changed to use return_spin for testing presence of spin. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented another system test for reading NMRPipe SeriesTab files. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fix for issuing a warning in reading spins from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fix for issuing a warning when reading spins from a Sparky formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented system test for reading spin IDs from NMRView formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Made reading of NMRView formatted file return the residue number as integer instead of string. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fix for calling the warn() function. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Extended the error description for reading NMRView files. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented system test for reading spins from a NMRPipe SeriesTab formatted file whereby the assignments for second dimension is missing. This will be a typically export from Sparky, converted to NMRPipe format, and processed with SeriesTab. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fixed for reading spins from a NMRPipe SeriesTab formatted file whereby dimension 2 misses residue number and residue name. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Expanded the warning message for a system test. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified system test for reading an assignment whereby the second dimension is missing. Work in progress for Support Request #3044 - load spins from Sparky list.
  • If dimension 2 in a SeriesTab formatted file does not contain residue number+name, it defaults to the dimension 1. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented system test for reading spins from an XEasy file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified XEasy reading function to pass residue names back. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Copied a SeriesTab file for the implementation of double assignments in Sparky files.
  • Redesign of the CPMG frequency and spin-lock field strength data structures. These now have an extra dimension for the offset so that the values are now experiment, magnetic field strength and offset dependent. If many offsets are present but are variable for each dispersion point, then this saves a lot of calculation time. This mainly affects R1ρ-type data. To better handle this, all of the specific_analyses.relax_disp.disp_data.loop_*() functions have been modified to accept data values rather than indices.
  • Improved the printout of the relax_disp.r2eff_read_spin user function for the R2eff keys.
  • Extended the system test for reading spins from Sparky files with empty residue name+number second dimension assignment. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified the Sparky peak list for two dimensional assignment example. This will typically be the export from CcpNmr Analysis. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented a system test for using double assignments in Sparky formatted files. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Extended reading of spins from Sparky files for up to two dimensional assignments. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added example of CcpNmr analysis exported Sparky file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added system test for reading CcpNmr Analysis exported Sparky file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified the reading of Sparky files when exported from CcpNmr Analysis. The keyword 'Data' is not present here. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added a system test for using generic file for reading spins. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Modified the generic list to also return spin information when intensity is not present. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added another system test for returning spins from a generic file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added residue 4 to the R2eff files for the truncated CPMG data from Flemming Hansen.
  • Added cpmg_fit results to the software comparison table for Flemming Hansen's CPMG data. The cpmg_fit input and log files have been added as well.
  • Shifted the software comparison down a directory so it can be used for all the different data.
  • Added system test for reading chemical shift from NMRPipe SeriesTab file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Implemented reading of chemical shifts from NMRPipe SeriesTab formatted files. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Additional chemical shift reading test for SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Improvements for the find_intensity_keys() dispersion analysis function. This now handles the reference point None being converted to NaN in numpy arrays and the logic is now clearer.
  • Changed some warnings in the dispersion analysis so they only show if R1ρ data is loaded. This is for missing chemical shifts and R1 data.
  • Increased the size of the grid search in the Relax_disp.test_m61_exp_data_to_m61 system test. This should increase the stability of this test.
  • Introduced the eliminate argument for the dispersion auto-analysis. This flag allows model and Monte Carlo simulation elimination to be deactivated.
  • Updated two dispersion scripts in the test data directories to work with the current design.
  • Updated more test suite scripts to call the relax_disp.cpmg_frq user function.
  • The CR72 and MMQ CR72 models are now classified as nested in the dispersion auto-analysis. The grid search for the MMQ CR72 model will therefore be skipped and the parameters taken from the CR72 model. This will however rarely, if ever, be used.
  • Fix for the relax_disp.plot_disp_curves user function. The interpolated curves now have all invalid points of 1e100 removed from the graph. This allows for reasonable graph scaling.
  • The LM63 and LM63 3-site models are now classified as nested in the dispersion auto-analysis. The grid search for the LM63 3-site model is therefore skipped and the starting parameters for optimisation are set to those of the optimised LM63 model.
  • Updated the relax results for the truncated CPMG data from Flemming Hansen. This includes the new results for the MMQ CR72 model. The analysis uses more model nesting. And the Grace plots now include the interpolation graphs (hence the plots are now bzip2 compressed).
  • Updated the NESSY results for the truncated CPMG data from Flemming Hansen. This now uses the data from all residues to allow for a proper error analysis so the results are comparable to all the other software.
  • Updated and reformatted the dispersion software comparison document.
  • Made a system test test pass on Mac OS 10.9.
  • Complete reworking of the NS R1rho 2-site dispersion model. The original code of Nikolai Skrynnikov and Martin Tollinger has been modified to match the behaviour of Dmitry Korzhnev's cpmg_fit software. The equations from Korzhnev et al., JACS 2005 (http://dx.doi.org/10.1021/ja0446855) have been used for the initial magnetisation and the R1ρ' calculation. All equations have been added to the manual to clarify the model.
  • Both relax and cpmg_fit input and output files for the Fyn SH3 R1ρ data have been added. This is for the TP02 model and NS R1rho 2-site models. The cpmg_fit results include source code modifications to show the differences between the various 'corrections'. The dispersion software comparison file has been updated to include this data and to show the cpmg_fit verses relax differences.
  • Updated the Relax_disp.test_tp02_data_to_ns_r1rho_2site system test. This is for the fixes of the NS R1rho 2-site dispersion model.
  • Added the Korzhnev 2005 R1ρ constant time correction to the 'To do' section of the dispersion chapter of the user manual.
  • Removed the CR72 model for cpmg_fit from the dispersion software comparison table in the dispersion chapter of the user manual.
  • Removed the CR72 model for GUARDD from the dispersion software comparison table in the dispersion chapter of the user manual. This software, like cpmg_fit, only supports the MMQ CR72 model which gives slightly different results to the original CR72 model when using only SQ CPMG-type data. Hence supporting MMQ CR72 does not automatically mean that the CR72 model can be optimised.
  • Updated the ShereKhan error estimation technique in the dispersion software comparison table. This is for the dispersion chapter of the user manual. Adam Mazur communicated that errors are estimated using the covariance matrix in a private mail.
  • Large rearrangements in the dispersion chapter of the user manual. The MMQ CPMG-type experiments now follow from the SQ CPMG-type experiments, hence the R1ρ models are now listed last.
  • Added a to do entry for the 3-site and N-site analytic R1ρ models listed in Palmer and Massi 2006. This is for the 'To do' section of the dispersion chapter of the user manual.
  • Updated the lib.dispersion.ns_r1rho_2site module docstring to explain the origin of the equations. This includes the Korzhnev 2005 reference where the modifications come from.
  • Created some synthetic data for the NS R1rho 3-site linear dispersion model using cpmg_fit.
  • Added cpmg_fit results for the Fyn SH3 R1ρ test suite data using the 3-site numeric solution.
  • Created the Relax_disp.test_ns_r1rho_3site_linear system test. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
  • Added the NS R1rho 3-site models to the dispersion variables. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
  • Added the NS R1rho 3-site models to the relax_disp.select_model user function frontend. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
  • Changed the order of the experiment types in the relax_disp.select_model user function frontend. The R1ρ-type models have been shifted to the end so that the MMQ CPMG-type models are just after the SQ CPMG-type models.
  • Changed the 'CPMG-type' to 'SQ CPMG-type' in the relax_disp.select_model user function frontend.
  • Added support for the NS R1rho 3-site models to the relax_disp.select_model user function back end. This is for the NS R1rho 3-site and NS R1rho 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
  • Decreased the amount of synthetic data in the ns_r1rho_3site_linear test suite shared data directory. The number of offsets for this NS R1rho 3-site linear model synthetic data has been decreased from 81 points to 21. This is because the large quantities of data slow the test suite down too much.
  • Added a GUI test for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added the GUI key 'new spectrum' to point to 'spectrum.read_spins'. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added the spectrum.read_spins GUI page for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added radio button for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Further added to the GUI test for reading spins from spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Speed up of the Relax_disp.test_ns_r1rho_3site_linear system test. Half of the data has been commented out, as too much data was being loaded for the test.
  • Created the target functions for the NS R1rho 3-site models. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
  • Added the R2eff calculating functions for the NS R1rho 3-site models to the relax library. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
  • Fix for GUI text string for the select radio button for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Bug fix for the new NS R1rho 3-site dispersion models - the Y and Z initial magnetisations were switched. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
  • Added cpmg_fit results for the program modified to turn off the PEAK_SHIFT flag. These are the results which should most closely match the relax results. This is for the simulated R1ρ data for the NS R1rho 3-site linear model.
  • Fix for the MODEL_NS_R1RHO_3SITE_LINEAR dispersion variable. The model name was not correct.
  • Turned off the Δω dispersion parameter constraints for the NS R1rho 3-site models.
  • Added the NS R1rho 3-site models to the dispersion auto-analysis. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
  • Added the NS R1rho 3-site models to the GUI model list. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
  • Removed the pC ≤ pB constraint from the 3-site dispersion models. This is important for the linear models where a violation of this constraint is reasonable. This has been replaced by the pC ≤ pA constraint.
  • Added the NS R1rho 3-site models to the relax user manual. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
  • Transposed some of the NS R1rho 3-site model evolution matrix elements. These now match the NS R1rho 2-site model.
  • Last fixes for the NS R1rho 3-site dispersion models. These now behave identically to the cpmg_fit program with the PEAK_SHIFT flag disabled. The tilt angle for the initial magnetisation is no longer that for the average offset but that of state A.
  • Fixes for swapped indices in the relaxation evolution matrix for the NS R1rho 3-site dispersion models.
  • Docstring fix for the lib.dispersion.ns_r1rho_3site module.
  • Added the Omega_A,B,C resonance offset parameter definitions to the dispersion chapter of the manual.
  • Updated the relax results for the synthetic data of the NS R1rho 3-site linear dispersion model.
  • Modified the NS R1rho 2-site dispersion model to match the NS R1rho 3-site models. The 6D evolution matrix indices have been rearranged to match the 9D matrix indices. The tilt angle for the initial magnetisation is no longer that for the average offset but that of state A, as was changed for the NS R1rho 3-site models earlier. The system test was therefore updated for the slightly different behaviour.
  • Updated the relax results for the Fyn SH3 R1ρ dispersion data. This is for the recent changes to the NS R1rho 2-site dispersion model.
  • Updated the Relax_disp.test_ns_r1rho_3site_linear system test so it now passes. The chi-squared value is not exactly zero as there are numerical differences between relax and cpmg_fit due to different approaches being used.
  • Added the RMSD determined via showApod for the 69 experiments. Work in progress for Support Request #3083 - Addition of Data-set for R1ρ analysis.
  • Added system test for the analysis of optimisation of the Kjaergaard et al., 2013 Off-resonance R1ρ relaxation dispersion experiments using the DPL model. Work in progress for Support Request #3083 - Addition of Data-set for R1ρ analysis.
  • Modified analysis script for example data of R1ρ. Work in progress for Support Request #3083 - Addition of Data-set for R1ρ analysis.
  • Created synthetic R1ρ dispersion data for the NS R1rho 3-site model. This is a simple modification of the data for the NS R1rho 3-site linear model. The k_AC parameter was simply changed from 0 to 1000. The cpmg_fit software was used to create the data. Both cpmg_fit and relax results have been updated to the new model.
  • Created the new Relax_disp.test_ns_r1rho_3site system test. This was copied from the Relax_disp.test_ns_r1rho_3site_linear test and modified to use the new NS R1rho 3-site model synthetic data.
  • Fix for wrong use of relax_fit.relax_time instead of relax_disp.relax_time. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Added the ns_r1rho_3site module to the lib.dispersion package __all__ list. This allows the unit tests to pass.
  • turned off a system test until the release of relax 3.1.1 is over. Work in progress for Support Request #3044 - load spins from Sparky list.
  • Fix for the Relax_disp.test_bug_21076_multi_col_peak_list GUI test. The peak intensity wizard is now closed at the end of the test so that subsequent tests can cleanly operate. Without closing this wizard, launching it a second time in another test will always fail.
  • Capitalised 'Python' in the IO redirection messages.
  • Epydoc docstring fix for the lib.dispersion.ns_mmq_3site.r2eff_ns_mmq_3site_sq_dq_zq() function. This allows the API to be compiled correctly.
  • Bug fix for the dispersion grid_search_setup() optimisation function. This function was not updated for the recent addition of the spin-lock or hard pulse offset dimension in the specific_analyses.relax_disp.disp_data module (and hence all structures used by the dispersion target functions). The loop_exp_frq_point() function call has been replaced by a loop_exp_frq_offset_point() function call to allow the R2eff model parameters to be looped over. For more details, see the thread http://thread.gmane.org/gmane.science.nmr.relax.scm/19685. This solution was mentioned at http://thread.gmane.org/gmane.science.nmr.relax.scm/19685/focus=4859.
  • Removed a printout from the Relax_disp.test_r1rho_kjaergaard GUI test as this is fatal for Python 3.
  • Python 3 fixes for the relax_disp.r2eff_read_spin user function. The check for the dispersion point column now only runs if that argument is set. In addition, the offset column is now also being checked.


Bugfixes


Links

For reference, the following links are also part of the announcement for this release:


relax 3.1.0

Description

After four years of development by numerous NMR spectroscopists, the relaxation dispersion analysis in relax is finally ready for release [Morin et al., 2014]! This support is complete and includes almost all analytic and numeric dispersion models in existence. These have been labelled as R2eff, No Rex, LM63 [Luz and Meiboom 1963], LM63 3-site [Luz and Meiboom 1963], CR72 [Carver and Richards 1972], IT99 [Ishima and Torchia 1999], TSMFK01 [Tollinger et al., 2001], NS CPMG 2-site expanded, NS CPMG 2-site 3D, NS CPMG 2-site star, M61 [Meiboom 1961], DPL94 [Davis et al., 1994], TP02 [Trott and Palmer 2002], TAP03 [Trott et al., 2003], MP05 [Miloushev and Palmer 2005], NS R1rho 2-site, MQ CR72, and MMQ 2-site, mainly named after the authors and publication date. It includes support for single, zero, double, and multiple quantum CPMG data, including combined proton-heteronuclear data, and off-resonance R1ρ data. An automated protocol has been developed to simplify the analysis and a GUI has been designed around this auto-analysis. Calculations have been parallelised at the spin cluster and Monte Carlo simulation level for speed.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.1.0
(28 November 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.0


Features
  • Full support for the analysis of relaxation dispersion data in the prompt, scripting, and graphical user interfaces.
  • Support for single quantum (SQ), zero quantum (ZQ), double quantum (DQ), and multiple quantum (MQ) CPMG-type data.
  • Support for R1ρ-type data.
  • Support for combined proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG-type data (multiple-MQ or MMQ data).
  • The R2eff model - used to determine the R2eff or R1ρ values and errors required as the base data for all other models.
  • The No Rex model - the model for no chemical exchange being present.
  • The LM63 SQ CPMG-type analytic model - the original Luz and Meiboom 1963 2-site fast exchange equation with parameters {R20, …, φex, kex} [Luz and Meiboom 1963].
  • The LM63 3-site SQ CPMG-type analytic model - the original Luz and Meiboom 1963 3-site fast exchange equation with parameters {R20, …, φex,B, kB, φex,C, kC} [Luz and Meiboom 1963].
  • The CR72 SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R2A0 = R2B0 is assumed with the parameters {R20, …, pA, δω, kex} [Carver and Richards 1972].
  • The CR72 full SQ CPMG-type analytic model - the full Carver and Richards 1972 2-site equation for most time scales with parameters {R2A0, R2B0, …, pA, δω, kex} [Carver and Richards 1972].
  • The IT99 SQ CPMG-type analytic model - the Ishima and Torchia 1999 2-site model for all time scales with pA ≫ pB and with parameters {R20, …, φex, pA.δω2, kex} [Ishima and Torchia 1999].
  • The TSMFK01 SQ CPMG-type analytic model - the Tollinger et al., 2001 2-site very-slow exchange model for time scales within range of microsecond to second time scale with parameters are {R2A0, …, δω, kAB} [Tollinger et al., 2001].
  • The NS CPMG 2-site expanded SQ CPMG-type numeric model - A model for 2-site exchange expanded using Maple by Nikolai Skrynnikov (Tollinger et al., 2001) with the parameters {R20, …, pA, δω, kex}.
  • The NS CPMG 2-site 3D SQ CPMG-type numeric model - the reduced model for 2-site exchange using 3D magnetisation vectors whereby the simplification R2A0 = R2B0 is assumed with the parameters {R20, …, pA, δω, kex}.
  • The NS CPMG 2-site 3D full SQ CPMG-type numeric model - the full model for 2-site exchange using 3D magnetisation vectors with parameters {R2A0, R2B0, …, pA, δω, kex}.
  • The NS CPMG 2-site star SQ CPMG-type numeric model - the reduced model for 2-site exchange using complex conjugate matrices whereby the simplification R2A0 = R2B0 is assumed with the parameters {R20, …, pA, δω, kex}.
  • The NS CPMG 2-site star full SQ CPMG-type numeric model - the full model for 2-site exchange using complex conjugate matrices with parameters {R2A0, R2B0, …, pA, δω, kex}.
  • The M61 R1ρ-type analytic model - the Meiboom 1961 2-site fast exchange equation for on-resonance data with parameters {R1ρ', …, φex, kex} [Meiboom 1961].
  • The M61 skew R1ρ-type analytic model - the Meiboom 1961 2-site equation for all time scales with pA ≫ pB and with parameters {R1ρ', …, pA, δω, kex} [Meiboom 1961].
  • The DPL94 R1ρ-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the M61 model for off-resonance data with parameters {R1ρ', …, φex, kex} [Davis et al., 1994].
  • The TP02 R1ρ-type analytic model - the Trott and Palmer 2002 2-site equation for all time scales with pA ≫ pB and with parameters {R1ρ', …, pA, δω, kex} [Trott and Palmer 2002].
  • The TAP03 R1ρ-type analytic model - the Trott et al., 2003 off-resonance 2-site equation for all time scales with the weak condition pA ≫ pB and with parameters {R1ρ', …, pA, δω, kex} [Trott et al., 2003].
  • The MP05 R1ρ-type analytic model - the Miloushev and Palmer 2005 off-resonance 2-site equation for all time scales with parameters {R1ρ', …, pA, δω, kex} [Miloushev and Palmer 2005].
  • The NS R1rho 2-site R1ρ numeric model - the model for 2-site exchange using 3D magnetisation vectors with the parameters {R1ρ', …, pA, δω, kex}.
  • The MQ CR72 MMQ-type analytic model - the Carver and Richards 1972 2-site model for most time scales expanded for MMQ CPMG data by Korzhnev et al., 2004 with the parameters {R20, …, pA, δω, δωH, kex}.
  • The MMQ 2-site MMQ-type numeric model - the model for 2-site exchange whereby the simplification R2A0 = R2B0 is assumed with the parameters {R20, …, pA, δω, δωH, kex}.
  • An automated protocol for relaxation dispersion which includes sequential optimisation of the models, fixed model elimination rules to remove failed models and failed MC simulations increasing both parameter reliability and accuracy [d'Auvergne and Gooley 2006], and a final run whereby AIC model selection is used to judge statistical significance.
  • Additional methods to speed up the auto-analysis by skipping the grid search: Model nesting, the more complex model starts with the optimised parameters of the simpler; Model equivalence, when two models have the same parameters; And spin clustering, the analysis starts with the averaged parameter values from a completed non-clustered analysis.
  • Parallelisation of the dispersion analysis at the level of the spin cluster and Monte Carlo simulation for fast optimisation on computer clusters using OpenMPI.


Changes

#lst:relax 3.1.0

Bugfixes
  • Bug fixes for a number of broken Oxygen icon lookups in the GUI.
  • Bug fixes for the molecule.delete, residue.delete and spin.delete user functions. The molecule, residue, and spin metadata in the relax data store was not being updated correctly after these user function calls so that any subsequent operations on this data was failing. This metadata problem was not noticed before as it disappears if the state is saved and reloaded into relax after a restart.


Links

For reference, the following links are also part of the announcement for this release:


relax 3.0 series

relax 3.0.2

Description

This version is a minor feature and bugfix release which includes better pseudo-atom support, support of the value.write user function to allow model information to be written to file, improvements to the 2D Grace plots, and fixes for missing log messages when running on a cluster using OpenMPI.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.0.2
(26 November 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.0.2


Features
  • Much better pseudo-atom support, including not requiring tetrahedral geometry.
  • The value.write user function can now create files with non-numeric data, such as the models for each spin.
  • Improvements to the 2D Grace plotting from the grace.write user function including full support for multiple graphs and the setting of the axes to the zero point.


Changes
  • Updated the Release Checklist document rsync instructions to allow resumed uploads. This is needed if the internet connection has been cut, as uploading can take a long time.
  • The test_suite.clean_up.deletion() function can now handle the case of missing files and directories. This problem was occurring in the relax_disp branch for some of the system tests.
  • Created the is_int() and is_num() functions for the lib.check_types module.
  • The value.write user function can now properly handle non-numeric data types. This allows the spin specific model name to be written to file, or any other string defined in the specific analysis PARAMS data object.
  • The multi-processor section of the manual is now labelled in the correct position.
  • Created a special GUI analysis element for floating point numbers. This allows for user input of floating point numbers into one of the GUI analysis tabs. If the input is not a number, the original value will be restored.
  • Created the new pipe_control.spectrum.add_spectrum_id() function. This is used to handle the creation of spectrum ID strings in the data store. This way new spectrum IDs can be created from different parts of relax in a controlled way.
  • Created the pipe_control.spectrometer.check_frequency() function to standardise this check.
  • Created the pipe_control.spectrometer.get_frequency() function for returning the frequency for a given ID.
  • The pipe_control.spectrum.add_spectrum_id() function now returns silently if the ID already exists.
  • Improvements to the pymol.view and molmol.view user functions for finding the PDB files. Now the possibility that this is being run from a results subdirectory is taken into consideration. If the file cannot be found, the os.pardir parent directory is added to the start of the relative path and the file checked for.
  • The rdc.read user function will now skip all lines of the RDC file starting with '#'. To include molecule identifiers at the start of the line will now require quotation marks.
  • Shifted the RDC and PCS assembly methods from the main class to the data module for the N-state analysis.
  • Created the pipe_control.mol_res_spin.is_pseudoatom() function to simplify pseudo-atom handling.
  • Created the pipe_control.mol_res_spin.pseudoatom_loop() function. This is used to loop over the spin containers corresponding to a given pseudo-atom.
  • Added a PDB file and RDC values (and absolute J+D and J) for propylene carbonate. This will be used for testing of pseudo-atoms in the N-state model analysis.
  • Renamed the propylene carbonate files to the correct name of pyrotartaric anhydride.
  • Created two new system tests based on the new pyrotarctic anhydride long range (1J, 2J & 3J) RDC data. The first (N_state_model.test_pyrotartaric_anhydride_rdcs) optimises an alignment tensor using long range signed RDC data. The second (N_state_model.test_pyrotartaric_anhydride_absT) optimises an alignment tensor using long range absolute T (J+D) data. Both test long range data together with methyl group pseudo-atom data.
  • Added all of the pyrotartaric anhydride RDC generation scripts and files. This is simply for reference and reproducibility.
  • Modifications for the pyrotartaric anhydride system test script. The grid search now is much quicker, and the RDC correlation plots are now sent to DEVNULL.
  • Added the return_id argument to the pipe_control.mol_res_spin.pseudoatom_loop() function. This will then yield both the spin container and spin ID string. This mimics the spin_loop()function.
  • Added proper pseudo-atom support for the RDCs in the N-state model analysis. This involves a number of changes. The pseudo-atom specific functions ave_rdc_tensor_pseudoatom() and ave_rdc_tensor_pseudoatom_dDij_dAmn() have been added to the lib.alignment.rdc module. These simply average the values from the equivalent non-pseudo-atom functions. The return_rdc_data()function in the specific_analyses.n_state_model.data module has been modified to assemble the RDC constants and unit vectors for all members of the pseudo-atom and add these to the returned structures, as well as a new list of flags specifying if the interatom pair contains pseudo-atoms. The N-state model target function and gradient have been updated to send the pseudo-atom data to the new lib.alignment.rdc module functions.
  • J couplings for the N-state analysis are now properly handled for pseudo-atoms. The measured J couplings for the members of the pseudo-atom should not be used, but rather that of the pseudo-atom spin itself (as the former does not exist).
  • Eliminated the old pseudo-atom handling in the N-state model specific return_rdc_data() function. This was multiplying the RDCs by -3 to handle the tetrahedral geometry of the 1J methyl RDCs. However this approach is not valid for non-methyl pseudo-atoms or for 2J, 3J, etc. data.
  • A RelaxError is now raised for the N-state model optimisation with gradients when T = J+D data is used. The gradients for this data type are not implemented yet, so it is better to prevent the user from using this.
  • The N_state_model.test_pyrotartaric_anhydride_absT system test now uses simplex optimisation to pass. The Newton algorithm cannot be used as the gradients for T = J+D type data have not been implemented.
  • An RDC error of 0.0 will now deselect the corresponding interatomic data container. This can be used for simpler pseudo-atom handling.
  • Updated the menthol long range RDC data file to include pseudo-atom member distances.
  • Renamed the interatomic_loop() function 'selected' argument to 'skip_desel'. This is to match the spin_loop() function arguments.
  • The interatom.unit_vectors user function now calculates the unit vectors for deselected containers. This is useful for pseudo-atom handling where the interatomic containers to the pseudo-atom members have already been deselected.
  • Updated the value checking for the N_state_model.test_absolute_rdc_menthol system test. The pseudo-atoms are now properly handled so the result is now much better.
  • The stereochemistry auto-analysis can now accept a file of interatomic distances. This is for better pseudo-atom support.
  • The N-state model specific check_rdcs() function now properly handles pseudo-atoms.
  • The pipe_control.rdc.q_factors() function now properly handles pseudo-atoms. If pseudo-atoms are present, then 2Da2(4 + 3R)/5 normalised Q factor is skipped.
  • Created the N_state_model.test_pyrotartaric_anhydride_mix system test. This is used to demonstrate a bug in the N-state analysis using mixed RDC and long range absolute J+D data.
  • Movement of N-state model specific code to the analysis neutral pipe_control package. Many of the functions of the specific_analyses.n_state_model.data module relating to alignment tensors, RDC data and PCS data have been shifted in to the pipe_control package modules align_tensor, rdc, and pcs respectively. This allows these functions to be made more general and allow the code to be shared with the frame order analysis or any future analysis using such data, and hence remove some code duplication.
  • Create two new warnings RelaxNucleusWarning and RelaxSpinTypeWarning to match the equivalent errors.
  • Added some RDC data checks to the N_state_model.test_pyrotartaric_anhydride_rdcs system test. This is to demonstrate a problem with the data assembly function pipe_control.rdc.return_rdc_data().
  • Clean ups and improvements for the pipe_control.rdc.check_rdcs() function. Pseudo-atoms are now handled much better and correctly in all cases. And many RelaxErrors have been converted to RelaxWarnings followed by a 'return False' statement.
  • Created the pipe_control.rdc.setup_pseudoatom_rdcs() function. This is used to make sure that the pseudo-atom interatomic systems (the containers from heternucleus to pseudo-atom and heteronucleus to pseudo-atom members) are properly set up. It will deselect the interatomic containers if incorrectly set up or if they are not part of the main pair.
  • Added quotation marks around a number of spin IDs with molecule names in some RDC data files. This is for the N-state model population model data used in the test suite.
  • The rdc.read and j_coupling.read user functions now ignore all lines starting with the # character. This is to remove all comment lines silently. Therefore if spin IDs are used which contain the molecule name, then they should be wrapped in quotation marks.
  • Updated a number of RDC test suite data files to have quotation marks around the spin IDs. This is to allow the molecule identifier to be present while not being mistaken for a comment line.
  • Updated some of the RDC data files used in the frame order system tests. The spin IDs are now in quotation marks as the molecule name is included. This is to prevent the line being removed as a comment.
  • Changes to the setup_pseudoatom_rdcs() function and renamed it to setup_pseudoatom_rdc(). The interatomic loop is now within the function to make sure that all is completed before the containers are accessed.
  • Started to add better pseudo-atom support for the PCS. The new pipe_control.pcs.setup_pseudoatom_pcs() function has been added to deselect the spins which are members of a pseudo-atom. The return_pcs_data() function in the same module now calls this function and builds a list of pseudo-atom flags for use in the target function (though it is still unused).
  • Finally eliminated the gui.paths module, replacing it with graphics.fetch_icon() calls. The GUI was using a mix of the old gui.paths module and the fetch_icon() function.
  • Created the pipe_control.sequence.return_attached_protons() function. This is used to return a list of proton spin containers attached to the given spin.
  • Improved Grace graph scaling and arrangement when multiple graphs are present. The lib.software.grace.write_xy_data() function now executes the 'autoscale' command for each graph and executes the 'arrange' to layout the graphs automatically.
  • The Grace plotting (via lib.software.grace) now fully supports the plotting of multiple graphs.
  • Improvements to the lib.software.grace module. The set colours are now applied to all set objects. And the axis label and tick sizes are now much smaller.
  • Created the --numpy-raise command line option. When this is set, all numpy warnings will be converted to errors. This is to aid in debugging to locate where the warning messages are coming from. These appear as RelaxWarnings, but there is no indication as to where the problem is.
  • The lib.software.grace module now supports setting the X and Y axes at zero.
  • Modified the model list GUI window. This can now be resized and it uses a scrolled panel to allow the contents of the window to be bigger than the window size.


Bugfixes
  • Fix for bug #21233 - the missing mpi4py multi-processor messages. When multiple commands were being sent to one slave, the captured IO was being overwritten by each executed command. Therefore the slave would only return the printouts from the last command.
  • Fix for a fatal bug in the rarely used structure.add_atom user function. The position argument in the user function definitions was incorrectly defined causing the user function to be non-functional. The 'float_object' argument type is now supported in the GUI.
  • Fix for the N-state model _target_fn_setup() method for when no PCS data is present.
  • Bug fix for the lib.structure.mass.centre_of_mass() function warning when the element is not known. This warning was buggy and resulted tracebacks.


Links

For reference, the following links are also part of the announcement for this release:


relax 3.0.1

Description

This version is a minor feature and bugfix release. The handling of peak lists has been enhanced and chemical shifts can now be read into relax, there are a number of improvements throughout the GUI, and a number of minor bugs have been solved. If these changes affect you, please upgrade to this latest version.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.0.1
(17 October 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.0.1


Features
  • Improved handling of peak lists.
  • Simplification of the user function GUI elements for those associated with the free file format.
  • Support for the reading of chemical shifts into the relax data store with the new chemical_shift.read user function.
  • Improvements to the appearance of the GUI by using more unicode.
  • Redesign of the model list GUI element used in the model-free analysis.


Changes
  • The font size is no longer set for the latex2html compiled user manual.
  • A number of updates and improvements to the document explaining how to setup a Mac OS X framework. This Framework Python setup is used to build the binary distribution files.
  • Updated the Mac Framework testing script to handled 4-way binaries (ppc74 included).
  • Better support for 4-way binaries in the Mac OS X Framework detection script.
  • Added support for the 'current ar archive random library' file type in the Mac OS X Framework testing script.
  • Added py2app to the Mac OS X Framework setup instructions.
  • Shifted code from pipe_control.spectrum to the new lib.spectrum.peak_list relax library module. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/3972/focus=4347.
  • Added a special script for locating all Python versions and printing out the installed modules.
  • Large change to the free file format GUI element for the user functions. The GUI element used in the user function wizard windows has been modified to have both a 'default' form, which is the previous design, and a 'mini' form which is now used for the user functions. This mini form only uses 1 row, rather than the default of 6 or 8. It is a read only text element with a button that launches the free file format window. The amount of space saved is huge.
  • Improved the text for the mini free file format GUI element.
  • Updated all of the user function GUI window sizes for the 'mini' free file format GUI element. This allows much more text of the description to be displayed.
  • Updated the Mac Framework setup document to help with scipy compilation problems.
  • Improved the Python seeking and module version print out script for symlinks. This should now be much more capable of finding all Python versions on a system.
  • Added support for the Mac OS X Modelfree4 binary results to the Palmer.* system tests. The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In the Mac binaries, the results are instead written out to 4 significant figures. Therefore the number of decimal places are much less than the Linux results.
  • Syntax error fix for one of the unused scripts in the relax test suite shared data directories. This problem was encountered by Jack Howarth <howarth att bromo dott med dott uc dott edu> and communicated in a private message. The issue was found by fink. This script is never used and will never be used again - it is only there for reference.
  • Modification of the spectrum.read_intensities user function front end. The heteronuc and proton arguments have been eliminated. Instead the new dim argument is used to associate the data with the spins of any dimension in the peak list.
  • Replaced the 'heteronuc' and 'proton' arguments of the spectrum.read_intensities user function backend with 'dim'.
  • Created the new lib.spectrum.objects module. This will hold temporary data structures for representing peak lists and other spectral data. The module currently contains the Peak_list class which is used to hold peak list data.
  • Started to shift the spectrum.read_intensities user function backend to use lib.spectrum.peak_list.
  • The pipe_control.spectrum.read_intensities() function now works with the Peak_list object.
  • The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function.
  • The lib.software.sparky.read_list_intensity() function now operates on the Peak_list object.
  • Changed the spectrum.read_intensities dim argument default to ω2 and improved the long description.
  • Fix for the assignment handling in the lib.software.sparky.read_peak_list() function. The first element is usually the indirect dimension or ω2.
  • Fix for many of the Peak_list system tests for the user function argument changes. The heteronuc and proton arguments have been replaced by the dim argument.
  • The lib.software.xeasy.read_list_intensity() function now operates on the Peak_list object.
  • The lib.software.nmrview.read_list_intensity() function now operates on the Peak_list object.
  • The lib.spectrum.peak_list.intensity_generic() function now operates on the Peak_list object.
  • Fixes for the pipe_control.spectrum.read() function. An error was referencing a now non-existent variable and the docstring has been fixed.
  • The Peak_list object can now store peak intensity names. This is for peak lists such as from NMRPipe seriersTab files where the peak list covers multiple spectra.
  • The NMRPipe seriesTab peak lists are now supported through the Peak_list object.
  • Unit test fixes for the spectrum.read_intensities user function argument changes.
  • Fixes for a few system tests for the spectrum.read_intensities user function argument changes.
  • Fixes for a few GUI tests for the spectrum.read_intensities user function argument changes.
  • Changes for the spectrum.read_intensities user function dim argument. The default is now ω1, the indirect dimension in a 2D experiment. The description has also been fixed.
  • Fixes for all of the peak intensity reading functions - the ω1 and ω2 dimensions were swapped.
  • Updates to the sample scripts for the spectrum.read_intensities user function argument changes.
  • Updates to the user manual for the spectrum.read_intensities user function argument changes.
  • Created the Chemical_shift.test_read_sparky system test for the reading of chemical shifts. This is for the reading of shifts from a Sparky peak list. It tests the currently non-existent chemical_shift.read user function.
  • Created some incredibly basic icons for the chemical shift user functions. These are simply an ω symbol and will need to be replaced by something better in the future.
  • Created the chemical_shift.read user function. This includes both the front and back end code.
  • Shifted all the modules from lib.software to do with peak lists to lib.spectrum. This is for a more logical organisation, as these modules are solely used by the lib.spectrum.peak_list module.
  • Renamed all of read_*() functions of the lib.spectrum modules for consistency. These functions will now be used to read all types of data from a peak list, from the assignments to chemical shifts to peak intensities, and everything in between.
  • Modified the peak list object. The peak list dimensionality variable is no longer private, and many values of None are now converted to lists of None so that the peak list data is easier to handle.
  • Fix for the proton name in the new Chemical_shift.test_read_sparky system test.
  • Expanded the functionality of the lib.spectrum.sparky.read_list() function. Now the dimensionality of the peak list is automatically determined, and all peak lists from 1D to 4D are supported. The chemical shifts are also automatically detected and extracted from the list and placed into the peak list object. The peak intensity data is also automatically detected,therefore the int_col argument is no longer used.
  • The lib.spectrum.sparky.read_list() function can now auto-detect the peak volume column and use it for intensities.
  • Created the Chemical_shift.test_read_xeasy system test. This is for checking the reading of chemical shifts from a 2D XEasy peak list.
  • Implemented the reading of chemical shifts in the lib.spectrum.xeasy.read_list() function.
  • Created the Chemical_shift.test_read_nmrview system test. This, if not obvious from the name, is for checking the reading of chemical shifts from an NMRView peak list.
  • Implemented the reading of chemical shifts in the lib.spectrum.nmrview.read_list() function.
  • Assignments can now contain lowercase letters in Sparky and NMRPipe seriesTab peak lists.
  • Fix for the unit test for the reading of intensities from Sparky peak lists.
  • Updated the nmrPipe processing script in the relax user manual. This is in response to the post by Troels Linnet at http://thread.gmane.org/gmane.science.nmr.relax.user/1520. The text has also been expanded to better explain spectral processing.
  • Improvements for the description of the NMRPipe processing script in the R1/R2 chapter of the user manual.
  • LaTeX fix for the curvefit chapter of the user manual.
  • The isInf() and isNan() functions of lib.float can now handle values of None. If None is encountered, the functions simply return False.
  • The model-free optimisation code now handles minfx returning nothing. This is due to the fix of bug #21001 in relax, which is really a fix for an upstream minfx bug #21090.
  • Created the Mf.test_bug_21079_local_tm_global_selection system test. This is to catch bug #21079.
  • Extended the Mf.bug_21079_local_tm_global_selection system test for all Monte Carlo simulation steps.
  • The model_free.select_model user function GUI element now uses unicode for the model parameters. The τ character is now used for the tm, te, tf, and ts parameters. And a superscript 2 is used for the order parameters.
  • The model lists in the model-free GUI auto-analysis now use unicode for the S2 parameters.
  • The peak intensity wizard in the GUI is now more robust. The wizard_update_ids() method can now better handle missing data. This is encountered if a user skips the first elements of the wizard.
  • Created Wiz_window.setup_page() for user function wizard pages to allow for simpler GUI tests. This method can be used to setup any user function wizard page with all its arguments set. It accepts all keyword arguments and sets these for the wizard page, translating to GUI strings as needed. This should save a lot of lines in the GUI tests.
  • Simplified the Noe.test_noe_analysis GUI test by using the new Wiz_window.setup_page() method.
  • Python 3 fixes for all of the unicode strings in relax. Instead of using the u"xyz" notation, now unicode("xyz") is being used. This works as the relax compat module sets the builtin unicode() function to str() for Python 3, as all strings in Python 3 are unicode and hence both the Python 2 u"xyz" and unicode() code are undefined in Python 3.
  • Defined two new functions called u() in the compat module for better unicode string support. The two functions are defined differently for Python2 and Python3. The Python3 function simply returns the text unmodified, as all strings are unicode. The Python2 function converts the str type to a unicode type.
  • The new compat.u() function is now being used for all unicode strings.
  • All "local tm" text in the GUI now uses a subscript m unicode character as well as the τ character.
  • Created the pipe_control.spectrum.test_spectrum_id() function for checking if a spectrum ID exists.
  • Renamed pipe_control.spectrum.test_spectrum_id() to check_spectrum_id(). A bug in the function was also removed, and the other code in the module now uses this function.
  • Created the pipe_control.mol_res_spin.check_mol_res_spin_data() function. This will check for the existence of molecule, residue and spin data and raise a RelaxError if none exists.
  • Simplification of the data checks in the pipe_control.spectrum module. This is using the new pipe_control.*.check*() functions.
  • Huge speed up of the GUI tests by the removal of the N_state_model.test_populations test. This problem was identified by running the GUI tests with the '--time' flag. One one test machine, this single test took ~142 seconds to complete when the entire GUI tests took ~242 seconds (i.e. this one test took up to 60% of the whole test suite). This test comes directly from a system test, but the equivalent system test only takes about 6 seconds to complete. The difference is due to the slow generation of the user function GUI pages.
  • Created the new RelaxNoPeakIntensityError error object.
  • The compat.SYSTEM variable is now set to 'Windows' when 'Microsoft' is detected. This is for easier identification of MS Windows systems, as either string could be used.
  • Created the new gui.text module for holding all of the unicode text for the GUI. This module contains unicode strings for the various analysis types, which are then all defined in one location. This is for consistency.
  • Converted the model-free user function definitions to use the new gui.text module strings.
  • Shifted the gui.text module to lib.text.gui to avoid a fatal circular import in the GUI.
  • MS Windows fixes for the GUI for missing unicode font glyphs.
  • Added some Mac OS X GUI string fixes for missing unicode characters to lib.text.gui.
  • The size of the model list GUI window can now be changed.
  • Redesign of the model list GUI element. The wx.ListCtrl element has been replaced by a wx.FlexGridSizer combined with wx.CheckBox and wx.StaticText. The result is a much nicer formatting of the element. The checkboxes in the old element displayed slight rendering problems on all operating systems and did not look neat. The new design is also more flexible in that models of None are now treated as separators in the window.
  • The model list GUI element can now display an optional model description column.
  • Added model descriptions and adjusted the size of the model-free model list GUI elements.
  • Refinements for the model list GUI window. The font for all text elements is now set. And the elements of the wx.FlexGridSizer are now vertically centred so that the text of the checkboxes and text elements line up perfectly.
  • The size of the model list GUI window is now automatically set to the best fit.
  • The model list GUI element is now centred after the autosizing.
  • The titles in the model list GUI window now use a smaller font size.
  • Update of the description of the interatom.define user function.
  • Added multi-processor support for Monte Carlo simulations. This simply involves accessing the multi-processor box singleton and running the processor.run_queue() method within the pipe_control.minimise.minimise() function. This currently does nothing as the processor queue is always empty. But if the code in the specific_analyses package is modified to add slave commands to the processor but not execute the run_queue() method, then the Monte Carlo simulations will be automatically parallelised.
  • Updated the spectrum.error_analysis user function backend to use the lib.statistics.std() function. This simplifies the code. It affects only the peak intensity error analysis when spectra have been replicated.
  • Created the Structure.test_bug_21187_corrupted_pdb system test to catch bug #21187. The bug was reported by Martin Ballaschk.
  • Bug fix for the specific analysis API _data_init_spin() method. This is used for the API init_spin() method. This is a latent bug which does not affect any of the current analyses in relax. It was discovered in the relaxation dispersion branch.
  • Addded a new is_queued() method to the Processor object of the multi package. This allows the Processor object for the uni and mpi4py multi-processor to be queried to see if any slave commands have been queued.
  • Created a unit test for the lib.linear_algebra.matrix_exponential module. This module does not exist yet, but it will be used to replace the scipy.linalg.expm() function use in the relaxation dispersion branch.
  • Loosened the lib.linear_algebra.matrix_exponential.matrix_exponential() unit test checks.
  • Implemented the lib.linear_algebra.matrix_exponential.matrix_exponential() function. This handles square matrices in either complex or real form.
  • Created the lib.check_types.is_complex() function. This is used to determine if a number is a Python or numpy complex type.
  • The lib.linear_algebra.matrix_exponential.matrix_exponential() function now uses lib.check_types.is_complex(). This fixes the function for complex matrices.
  • Created a new unit test for lib.linear_algebra.matrix_exponential.matrix_exponential() for complex matrices.
  • Fix for the new lib.linear_algebra.matrix_exponential.matrix_exponential() function. This function now returns a numpy array type rather than matrix type.


Bugfixes


Links

For reference, the following links are also part of the announcement for this release:


relax 3.0.0

Description

This is the first release of the new relax 3 series. This release marks a major shift of relax towards becoming a scientific computing environment specialised for the study of molecular dynamics using experimental biophysical data. It is designed to be a replacement for numerical computational environments such as GNU Octave, MATLAB, Mathematica, Maple, etc. From the perspective of a user, however, not much has changed. There are only a few modifications to the prompt, script, or graphical user interfaces. Most changes are for the power user as they are rather in the backend. The infrastructure changes are comprehensive and include the reorganisation of most of the relax code base, a large expansion of the relax library, and general improvements and fixes to the user manual, the GUI, and the whole code base. The huge number of changes can be seen below.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.0.0
(6 August 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.0.0


Features
  • Huge amounts of code throughout the relax codebase has been shifted into independent functions in the relax library.
  • Many new functions added to the relax library.
  • Complete rearrangement of the relax package and module layout.
  • Clean up and improvements to the relaxation curve-fitting C module including the removal of a severe memory leak eating up all the RAM when lots of spins are analysed simultaneously.
  • Complete redesign of the 2D graphing code for improved data visualisation and to allow expansion to software other than Grace.
  • Polishing of the GUI - many bug fixes and improvements throughout the GUI.
  • Addition of the --time command line option for the relax test suite.
  • Large speed ups of the relax test suite.
  • Merger of the dipole_pair and interatomic user function classes into the new interatom user function class.
  • Added support for J couplings.
  • Import cleanups throughout relax, avoiding potential future bugs and making the code much cleaner.
  • Addition of many new scripts for use by the relax developers.
  • Support for the NMRPipe SeriesTab format in the spectrum.read_intensities user function.
  • Improvements for all code examples in the relax user manual including much better fonts, formatting, line wrapping, line numbering, and colouring using the lstlisting LaTeX environment.
  • Created the relax language definition for the lstlisting LaTeX environment for better colouring of relax scripts in the user manual.
  • Converted the Citations chapter of the relax user manual into a preface chapter.
  • Overhaul of the indexing in the relax user manual.
  • Higher level structuring of the user manual into parts.
  • Creation of the optimisation chapter of the relax user manual.
  • General improvements throughout the user manual.


Changes
  • Some small clarifications and reordering of the release checklist document.
  • Shifted the pipe_control.structure.superimpose module to lib.structure.superimpose.
  • Shifted the pipe_control.structure.statistics module to lib.structure.statistics.
  • Created the unit test infrastructure for the lib.structure package.
  • Shifted the pipe_control.structure.pdb_read and pipe_control.structure.pdb_write modules to lib.structure.
  • Shifted the pipe_control.structure.cones module to lib.structure.cones.
  • Split the pipe_control.structure.mass module into two with the CoM code going to lib.structure.mass.
  • Removed the data pipe checks from the internal structural object. This decoupling from the relax data store is in preparation for moving into the lib.structure package.
  • More decoupling of the internal structural object from the relax data store. Removed the ability of the internal structural object to determine if two atoms are connected by consulting the relax data store.
  • Created the empty lib.structure.internal package for holding the internal structural object.
  • Shifted part of the internal structural object into the lib.structure.internal.models module. This contains the two classes ModelList and ModelContainer from the pipe_control.structure.api_base module.
  • Shifted part of the internal structural object into the lib.structure.internal.molecules module. This contains the class MolList from the pipe_control.structure.api_base module.
  • Shifted the MolContainer class from pipe_control.structure.internal into lib.structure.internal.molecules. This is in preparation for shifting the internal structural object to lib.structure.internal and for the elimination of the unused and no longer useful ScientificPython structural object.
  • Created the empty lib.structure.represent package. This will be used to hold modules which generate 3D structures as geometric representations of abstract ideas such as tensors, cones, frames, etc.
  • Shifted the lib.structure.rotor module to lib.structure.represent.rotor.
  • Total elimination of the ScientificPython PDB object. Maintaining this reader was too much effort and the internal structural object has now surpassed the capabilities of the ScientificPython PDB object (for example the internal object is not PDB specific). And ScientificPython is very much a dead project, largely replaced by the more successful scipy.
  • Merged the structural API base module api_base into pipe_control.structure.internal. The API base class is no longer needed as the ScientificPython PDB reader has been eliminated.
  • Deleted the unit tests of the structural API base class.
  • Moved the residual pipe_control.structure.api_base module to lib.structure.internal.displacements. This is because the base module still contained the Displacements class.
  • Docstring consistency in the internal structural object.
  • Shifted the pipe_control.structure.internal module to lib.structure.internal.object. This is the new location of the internal structural object.
  • Shifted the selection object out of pipe_control.mol_res_spin and into the new lib.selection module. The dependence on the MoleculeContainer, ResidueContainer and SpinContainer objects have been removed, as this is part of the relax data store. Therefore all of the private methods (__contains__, __contains_mol_res_spin_containers, and __contains_spin_id) have been deleted. The contains_*() will need to be used instead.
  • The pipe_control.mol_res_spin functions no longer use the selection object __contains__() method. All functions now use the contains_*() methods of the lib.selection.Selection object.
  • Shifted parse_token() and tokenise() from pipe_control.mol_res_spin to lib.selection.
  • The lib.selection.parse_token() function is using the new Python way of splitting strings. This is via the string's split() method.
  • Removed the no longer used parser argument for reading PDB files from some unit tests.
  • Removed the unit test of the parser argument of the structure.read_pdb user function. The argument no longer exists.
  • Shifted the cone geometric object representation functions to lib.structure.represent.cone. The structure.create_cone_pdb user function first calls pipe_control.structure.main.create_cone_pdb() which then calls lib.structure.represent.cone.cone(). This allows the pipe_control function to write out the file and add it to the data pipe's results file list.
  • Fixed some name classes in the namespace of pipe_control.structure.mass.
  • Shifted the diffusion tensor structural object code to lib.structure.represent.diffusion_tensor. The user function routes to pipe_control.structure.main.create_diff_tensor_pdb(), which pulls the tensor info out of the data store, and then calls the diffusion_tensor() function of lib.structure.represent.diffusion_tensor to create the representation, writes out a PDB file, and finally adds the file to the data pipe's results file list.
  • More removals of the now dead parser argument for the structure.read_pdb user function.
  • Removed the parser argument from structure.read_pdb in the stereochemistry auto-analysis.
  • Restored the selection object __contains_spin_id() method as contains_spin_id(). This will allow for faster checks for matches to spin ID strings.
  • Speed ups for the interatom_loop() by restoring some of the code previously deleted. This spin ID lookup table is being used again, as this is much faster than the string parsing of spin IDs.
  • The frame order analysis is now using the correct centre of mass function.
  • Shifted calc_chi_tensor() and kappa() from pipe_control.align_tensor to lib.alignment.alignment_tensor.
  • Shifted some of the pipe_control.diffusion_tensor functions to lib.diffusion.main.
  • Created the empty lib.software package. This will be for functions which create input, read output, or control external programs.
  • Shifted and decoupled some of the grace code into lib.software.grace. This includes most of the write_xy_header() and write_xy_data() functions. The data store specific part of write_xy_header() has been shifted into pipe_control.grace.axis_setup().
  • Missing import fix for the lib.alignment.alignment_tensor module.
  • Shifted the lib.opendx package to lib.software.opendx.
  • Shifted the lib.xplor module into the lib.software package.
  • Shifted the Bruker Dynamics Centre parsing code into the new lib.software.bruker_dc module.
  • Deleted the completely unused pipe_control.spectrum.Bruker_import class. This was added by Michael Bieri in Oct 2011, but the code has never been used. Other, simpler code has replaced its functionality.
  • Created the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de> at https://gna.org/bugs/?20674.
  • Decreased the number of Monte Carlo simulations in the Ct.test_bug_20674_ct_analysis_failure system test.
  • Created the Jw.bug_20674_jw_mapping system test. This is a modification of the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674. The test script was duplicated and the small modifications made to convert it into the J(ω) mapping analysis. This now reveals the same bug but for the J(ω) mapping analysis.
  • System test speed ups - decreased the number of Monte Carlo simulations in many tests. Running 500 simulation optimisations in a system test is a total waste of time!
  • Converted the bug_20674_jw_mapping.py system test script to use the self._execute_uf() interface. This allows the script to be used in the GUI.
  • Created the Mf.test_bug_20683_bdc_inf_values system test. This is for catching bug #20683 reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The problem is due to infinite and NaN values in the Bruker Dynamics Centre file.
  • Ported the changes of r19302 to the consistency testing and J(ω) mapping analyses. This is the code for checking for infinite relaxation rates imported from Bruker Dynamics Centre files.
  • Missing imports of the lib.float.isInf() function.
  • Modified the bug_20674_ct_analysis_failure.py system test script to use self._execute_uf(). This allows the test to operate as a GUI test, which was failing.
  • Created the specific API common method _data_init_spin(). This will be used as a general method for aliasing to data_init() for initialising spin parameters.
  • Added printouts for the select.read and deselect.read user functions to identify the spins affected.
  • Created the new lib.list module with the function count_unique_elements(). This function will be used to determine the unique number of elements in a list.
  • Shifted the Sparky peak intensity reading code to lib.software.sparky.read_list_intensity(). This new function comes from the old pipe_control.spectrum.intensity_sparky() function, but with the spin ID code removed.
  • Shifted the XEasy peak intensity reading code to lib.software.xeasy.read_list_intensity(). This new function comes from the old pipe_control.spectrum.intensity_xeasy() function, but with the spin ID code removed.
  • Docstring fix for the lib.software.xeasy.read_list_intensity() function.
  • Shifted the NMRView peak intensity reading code to lib.software.nmrview.read_list_intensity(). This new function comes from the old pipe_control.spectrum.intensity_nmrview() function, but with the spin ID code removed.
  • Created the lib.software.sparky.write_list() function and associated unit test. This will be used to create simple Sparky .list files.
  • The relaxation curve-fitting analysis parameters are now all lowercase. This is to match the other analysis types so that the parameter names are identical to the corresponding variable name. This is assumed by some of the specific analysis API methods.
  • Removal of junk code in the _assemble_scaling_matrix() relaxation curve-fitting method.
  • Parameter scaling is now functional in the target_function.relax_fit.c code. Previously the scaling was not being used and the Python to C conversion was broken.
  • The scaling matrix is now converted into a usable list of diagonal elements for the relax_fit C module.
  • Simplified the code of the relax_fit C module.
  • The common spin methods of the specific analysis API now ignore parameters not in the model. This affects the _data_init_spin(), _sim_init_values_spin(), and _sim_return_param_spin() methods. The result is that the spin containers no longer hold parameter variables set to None for non-model parameters.
  • Created the pipe_control.plotting module. This will be used as a base for the plotting of all types of data. This includes the current OpenDX and Grace modules, as well as future modules. The determine_functions() function has been added and is used to simplify the pipe_control.grace.get_data() function.
  • The grace.write user function data type argument sequence values have changed. Instead of 'spin', this can now be 'res_num' or 'spin_num' to specify that either the residue number or spin number should be plotted on the desired axis. The x_data_type now defaults to 'res_num'.
  • Created the pipe_control.mol_res_spin.count_max_spins_per_residue() function. This will be used by the plotting module to determine if more than one spin per residue exists.
  • Fixes for the change of the grace.write user function data type 'spin' to 'res_num'.
  • Updated the pipe_control.plotting.determine_functions() function.
  • Added the skip_desel flag to the important pipe_control.mol_res_spin.spin_loop() generator function. This is used to skip deselected spins within the loop. As must of the code in relax using the spin_loop() does this anyway, this can be used to simplify many of the spin looping elements in relax.
  • Expanded the relax_fit system test script to produce all types of currently supported Grace graphs. This is to more extensively test the grace.write user function.
  • Large redesign of the 2D graphing code in relax. This currently affects only the grace.write user function, but the new infrastructure will make it much easier to expand the graphing abilities and to support other 2D graphing software. The plotting code has also been significantly simplified. The pipe_control.grace.get_data() function has been shifted into the pipe_control.plotting module. It has been split up into the base assemble_data() function with the data assembly shifted to assemble_data_scatter(), assemble_data_seq_value() and assemble_data_series_series(). This split massively simplifies the code by not packing all different graph and set combinations into one. In addition the auxiliary functions classify_graph_2D(), fetch_1D_data(), get_functions(), and get_data_type() have been created to maximise code sharing between the different assemble_*() functions.
  • Modified the relax_fit system test script to generate a new type of graph. This is the residue number sequence verses the peak intensity series data (and vice versa) via the grace.write user function. This is to help in the implementation of this graph type.
  • Created the pipe_control.plotting.assemble_data_seq_series() function. This is to allow the residue or spin numbering to be plotted against any series type data (lists or dictionaries), or vice versa.
  • Added a link to the PDF user manual from the HTML user manual. This will affect all pages at http://www.nmr-relax.com/manual/ by adding an icon to the navigation bar pointing to the PDF manual at http://download.gna.org/relax/manual/relax.pdf.
  • The plotting of residue or spin numbers verses values now handles multiple spin types properly. This is in the pipe_control.plotting.assemble_data_seq_value() function. The spin name is being used to identify different spin types for the graph sets.
  • The pipe_control.mol_res_spin.count_max_spins_per_residue() function now accepts a spin ID argument. This can be used to restrict the spins to count.
  • The spin ID string is now being used by the plotting functions. The spin ID was not being passed into the assemble_data_*() functions.
  • Changed how pipe_control.plotting.assemble_data_seq_value() determines the number of graph sets. Instead of counting the maximum number of spins per residue, different spin names are now checked across the sequence. This is needed as a single residue could have a different type of spin. This was caught by the Mf.test_dauvergne_protocol system test.
  • Modified pipe_control.plotting.assemble_data_series_series() to handle dictionaries with keys as values. This will be useful in, for example, relaxation dispersion for plotting the dispersion curves. In this case, the R2eff values are in a dictionary where the keys are the values to plot against. This is different from the current case where the X and Y data dictionaries are required to have the same keys. These changes expand the capabilities of the grace.write user function.
  • Formatting change for the auto_analyses __all__ package list.
  • Removed the import of the auto-analysis modules into the auto_analyses package __init__ module. This import is not needed.
  • The N-state model system test module now imports the auto-analysis to fix an import order error.
  • Added a warning for the spectrum.read user function if a peak intensity of zero is encountered. This value can cause singular matrix failures in certain optimisation algorithms.
  • The spectrum.error_analysis user function can now be performed on a subset of all spectra. The subset argument has been added to allow the error analysis to be restricted to a subset of all loaded spectral data.
  • Created the lib.list.unique_elements() function for returning a list with duplicates removed.
  • Shifted the standard deviation code from the Monte Carlo error_analysis() function to the lib package. The new function lib.stats.std() is now used to simplify the error_analysis() function and allow the code to be reused. This will be useful for expanding the pipe_control.monte_carlo.error_analysis() function to handle parameters which are dictionaries, for example as in the relax_disp branch.
  • The Monte Carlo error_analysis() function now handles dictionary type parameters.
  • Renamed the new lib.stats module to lib.statistics.
  • Spun out the model list GUI element from the model-free auto-analysis into its own module. This GUI element is now the gui.analyses.model_list.Model_list class. This code has been spun out as the GUI element will be used by the relaxation dispersion branch.
  • The gui.analyses.model_list.Model_list GUI element now can have tooltips via the tooltip class variable.
  • Rearrangements of the gui.analyses package. The new gui.analyses.elements package has been created and the model list and text and spin GUI elements have all been shifted into the package.
  • Spun out the Spin_ctrl analysis GUI element into its own module in gui.analyses.elements.
  • The relaxation time part of the spectra list GUI element can now be turned on or off.
  • The execution of the user function GUI pages can now be delayed. The create_page() execute flag has been added to disable execution. This can be later forced with the new on_execute() force_execute flag.
  • Modified the GUI new analysis wizard to return a list of user function on_execute methods. This will be used in the relax_disp branch and in the future for when a special user function page is added to the new analysis wizard. This allows the use of user function pages with execution delayed until the analysis __init__() method is being run.
  • Standardisation of the text of the GUI elements of the analysis frames and expansion of the tooltips. All the text parts of the Spin_ctrl and Text_ctrl elements now end in a colon. Tooltips are now present on all elements and have been expanded and improved.
  • The Text_ctrl analysis frame GUI elements now have separate tooltips for the buttons. This is to give a hint to the user as to what the button does.
  • The model selection GUI analysis element can now have a different tooltip for the button.
  • Added tooltips to the model-free model list GUI elements in the model-free analysis frame.
  • Created the gui.wizards package for holding all of the relax wizards. The gui.wizard module is now called gui.wizards.wiz_objects.
  • Shifted and merged the NOE and Rx peak intensity wizards into a new module. The wizards were separate and a part of the analysis frame class objects. The two wizards have been merged into the gui.wizards.peak_intensity.Peak_intensity_wizard class as most of the code is shared. This one wizard class will be useful for reusing in the relaxation dispersion branch.
  • The peak intensity wizard class now inherits from Wiz_window. This allows the class to be a wizard window instead of launching a wizard window from within the class.
  • Small rearrangements in the gui.wizards.peak_intensity module.
  • Alphabetical ordering of the methods in the gui.wizards.peak_intensity module.
  • Simplified all of the peak analysis wizard wizard_update_*() methods. They now all defer to the wizard_update_ids() method which updates the spectrum ID fields.
  • Simplified the wizard_update_noe_spectrum_type() method as in the previous commit.
  • Fixes for the frq.set user function in the GUI. The ID list is now set to the spectrum IDs, and the frequency units are no longer all fused into one string.
  • Unicode is now used for the tau symbol in the model-free model parameter lists in the GUI. This is only when modifying the models to optimise, which shouldn't be changed anyway.
  • Removed the 'string' from 'Spectrum ID string' in the spectrum list GUI element. This is a GUI - the word string is meaningless here!
  • The delay times column string now specifies seconds in the spectrum list GUI element.
  • Formatting improvements for the relaxation data list GUI element. The data type column entries are now descriptive and use subscript.
  • More unicode strings are used for the GUI for subscripts and Greek letters.
  • Fixes for the R1 and R2 GUI analyses for the recently introduced unicode subscript characters. There is now self.label for a pure string version and self.gui_label for the fancier unicode version.
  • The frq.set user function 'id' argument is no longer read only - this was causing test suite failures.
  • Removed a nasty kludge for releasing the execution lock on failure. This kludge, after the bug fix for https://gna.org/bugs/?20756, was causing failures in the test suite.
  • Changed the 'Execute relax' button in all analyses in the GUI to 'Execute analysis'. It makes no sense to execute relax as relax has been executing during the analysis initialisation and the user setting up all the data for the analysis. This is a remnant of ancient design of Michael Bieri's GUI being a separate program to relax, which would execute relax with the click of this button.
  • Restored the Py_INCREF() function call in the relaxation curve-fitting C module. This was deleted at r12632 along with Py_XDECREF() and Py_DECREF() calls. The absence of a Py_INCREF() function call causes the module to crash the Python interpreter under certain conditions. The problem was found in the relax_disp branch.
  • Clean up of unused headers and declarations in the exponential curve C module.
  • The relax_fit C module setup() function now uses the Py_RETURN_NONE macro to terminate. This macro does exactly what the old code does anyway.
  • Removed an unused declaration in the relax_fit C module setup() function.
  • Increased the maximum number of relaxation times for the relax_fit C module to 50.
  • Shifted the C array creation to the relax_fit C module header. The params, values, sd, relax_times, and scaling_matrix C arrays are now declared and allocated in the header file rather than using malloc() calls in the setup() function. This is to attempt to remove a memory leak. The arrays are now of fixed length and reused for each setup() call. These, as well as the other variables declared in the header, are no longer declared in the functions.
  • Improved the Python and C documentation of the functions of the relax_fit C module.
  • Converted the Py_BuildValue() calls to PyFloat_FromDouble() in the relax_fit C module. This doesn't change much.
  • Documentation improvements for the back_calc_I() function of the relax_fit C module.
  • The exponential C file now uses the exp() function from math.h rather than Python.h. This file is independent from Python.
  • The numpy include is no longer used for the compilation of the C modules. Numpy is not used at all in the C modules, so this just adds an annoying dependency for those who need to compile the module themselves.
  • Removed some bad calls to status.exec_lock.release(). This commit may have to be reverted in the future. The problem is that the execution lock is not being held when these calls are made. The calls were added as a kludge to handle certain situations where the execution lock was not released. There may be cases were this behaviour is still needed.
  • Added a developer script for testing of memory leaks in the relax_fit C modules.
  • Removed the numpy dependence from the manual C module compilation script.
  • Created the lib.mathematics relax library module. This currently contains two functions, order_of_magnitude() and round_to_next_order().
  • Added unit tests for the lib.mathematics module.
  • The relax_fit analysis now uses lib.mathematics.round_to_next_order() for the scaling matrix. This allows the optimised I0 value to be better understandable in the printouts.
  • Created the new Value system test class with the first test Value.test_value_copy. This test demonstrates some pretty large bugs in the value.copy user function.
  • Modified the Value.test_value_copy system test to check the copying of errors as well.
  • Added the error flag argument to all of the specific analysis API set_param_values() methods. This will allow parameter errors as well as values to be set.
  • The Value.test_value_copy system test now checks all of the values and errors.
  • Added the error flag argument to the value.set user function. This will allow for parameter errors to be set by the user.
  • The specific analysis API _return_value_general() method now returns errors even when values are missing.
  • The internal structural object PDF file creation now writes out http://www.nmr-relax.com. Previously the link http://nmr-relax.com was written out.
  • Diffusion tensor PDB file fixes for the internal structural object changes. This is because the relax website link is now written into the PDB file as http://www.nmr-relax.com rather than http://nmr-relax.com. This fixes the diffusion tensor system tests.
  • Converted all of the specific analysis modules into packages. The model-free and steady-state NOE analyses were already packages, and this now brings all other analyses in line with the package design of specific_analyses. The only change is that the files specific_analyses/x.py have been shifted to specific_analyses/x/__init__.py and the __all__ package variable added.
  • Epydoc docstring fixes for the compat module.
  • The peak intensity wizard can now function remotely when the spins are not named. This will be needed for the GUI tests to allow the Question() call to be bypassed and still adding the spin.name user function as the first page of the wizard. The key for spin.name page has also been fixed so that the page can be accessed.
  • The timing of individual tests in the relax test suite can now be printed out. The new command line argument --time has been added which, when supplied with one of the test suite arguments, will cause the time required to complete each individual test to be displayed. Instead of just printing the characters '.', 'F', and 'E' for each test, now these characters are postfixed with the time in seconds, the name of the test and ending in a newline character.
  • Big speed up of the test suite by skipping a large number of redundant Frame Order system tests. These are tests of using only PCS or only RDC data. These tests are still active for the pseudo-ellipse just to make sure that a whole missing data type can be handled.
  • Suppressed the reporting of skipped tests in the test suite if the module is set to None.
  • The preview button in the file selection elements of the user function windows can now be disabled. This is via the new wiz_filesel_preview argument being set to False.
  • Merged the frq.set and temperature user functions into the new spectrometer user function class. The frq.set user function is now called spectrometer.frequency and temperature is now spectrometer.temperature. To match these changes, the cdp.frq variable is now called cdp.spectrometer_frq.
  • Modified the spectrometer.frequency user function so that a frequency list and count is stored. These are the new cdp.spectrometer_frq_list and cdp.spectrometer_frq_count variables. This will allow various parts of relax which assemble frequency information to be simplified and made more consistent.
  • Created basic SVG and PNG graphics for the spectrometer user function class. The spectrometer is black so as not to offend Bruker, Varian, or Jeol users by avoiding a colour from one of these companies.
  • The pipe_control.spectrometer.get_frequencies() function can now return MHz or Tesla units.
  • Renamed the functions of the pipe_control.spectrometer module. The frequency() and temperature() functions are now called set_frequency() and set_temperature().
  • Added backwards compatibility support for the spectrometer frequency list and count. This is needed for old relax state files.
  • A whitelist is now being used to limit the number of frame order GUI tests to 1.
  • Shifted all frequency data handling associated with relaxation data to pipe_control.spectrometer. This includes the deletion of the relax_data.frq user function as this replicates the behaviour of spectrometer.frequency. A number of functions from the pipe_control.relax_data module have changed: frq() has been deleted as it is replaced by pipe_control.spectrometer.set_frequencies(); frq_checks() has been shifted to pipe_control.spectrometer.frequency_checks(); frq_loop() has been shifted to pipe_control.spectrometer.loop_frequencies(); num_frq() has been deleted as the new variable cdp.spectrometer_frq_count contains this info. Two new functions in the pipe_control.spectrometer module have been added to remove the functionality from pipe_control.relax_data. These are copy_frequencies() and delete_frequencies().
  • The molmol.macro_run user function file argument now has a description.
  • Huge speed up of the system tests for the loading and creation of model-free saved states. The OMP files used for the system test have been truncated from 134 to 7 spins, changing the timing of 6 system tests from 11-13 seconds to less than 0.5 seconds each.
  • All of the binary file arguments for the user functions now are file selection GUI elements. The GUI user function wizard pages now have file selection buttons for selecting the executable to run. These all have the preview button disabled. The results.read and state.load GUI elements also have the preview button disabled.
  • The user function 'prompt' description elements as now displayed in the GUI wizard page.
  • The monte_carlo.error_analysis user function can now handle parameters which are lists.
  • Added the ability for specific analyses to override the optimisation constraint algorithm. The default is still the 'Method of Multipliers', but if the constraint_algorithm() method returns a different string, then that will be used to select the algorithm. This allows the 'Log Barrier' method in minfx to be used.
  • The value.display and value.write user functions can now handle list and dictionary type parameters.
  • Added two methods to the specific analysis common API class. These are the _model_type_global() and _model_type_local() methods for always specifying that the model type is global (i.e. at the level of the data pipe) or local (i.e. there can be multiple clusters of models).
  • Added some more functions to the lib.statistics module. These include the bucket() function for creating a discrete distribution from a list of floating point numbers, and the gaussian() function for calculating the probability of a point on a Gaussian distribution.
  • Added a directory and files for testing the white noise in relaxation data. This includes scripts and graphs.
  • The initial parameters are now the real parameter rather than the optimised ones. This is for the script for testing white noise in relaxation data.
  • The spectrum.peak_intensities is now more robust when reading in a generic formatted file. Firstly there is a check that the intensity column number has been supplied. And then there is a checks that all relevant data could be extracted from each row of the file. This replaces traceback errors with RelaxErrors explaining the problem if the user inputs bad data or forgets the intensity column argument.
  • Changed the "Execute analysis" button text back to the original "Execute" text of the old relax GUI.
  • Added the 'test.seq' file from bug report #20873. This is from Troels E. Linnet. The bug report and link to http://thread.gmane.org/gmane.science.nmr.relax.user/1452 explains the contents. The file will be used to construct a system test to catch the bug.
  • Created the Peak_lists.test_bug_20873_peak_lists system test to catch bug #20873. This was reported by Troels E. Linnet. The test has been created by copying the user function calls from the original bug report and slightly modifying them to suite a 'relax_fit' analysis type.
  • Fix for the Peak_lists.test_bug_20873_peak_lists system test. The spectrum IDs are now strings.
  • Added checks of the peak intensities to the Peak_lists.test_bug_20873_peak_lists system test.
  • The spectrum.integration_points page in the peak analysis GUI wizard has been fixed. It is only shown when volume integration is selected with no replicated spectra.
  • Removed a debugging printout which is killing the relax unit tests in Python 3.
  • Added an EPS version of the 128x128 pixel spectrometer icon. This is for use in the relax manual.
  • Added a README file for the relax 128x128 icons describing how the EPS files should be created.
  • Updated the spectrometer 128x128 icon to be of the correct size and colour.
  • Added a README file to the graphic/analyses directory describing how to create the EPS files.
  • Merger of the dipole_pair and interatomic user function classes. The functionality of these two classes overlaps significantly. And the dipole_pair user functions are not related to magnetic dipole-dipole interactions. Therefore all the user functions from both classes were shifted into the new interatom user function class. This change will affect almost all relax scripts but, as this will form part of the relax 3 release, script breakage should be expected anyway.
  • Removed the pipe_control.dipole_pair module as its contents is now in pipe_control.interatomic.
  • Removed the dipole_pair module from the pipe_control package __all__ list.
  • Merged the interatom.create user function into interatom.define. These user functions had overlapping functionality which would be confusing for a user.
  • Added polish to all of the interatom user function docstrings.
  • Improved the functionality of the interatom.read_dist user function. The file data is now stripped using lib.io.strip to remove comments and blank lines. And now if the iteratomic data container cannot be found, it is created instead of raising a RelaxError.
  • Improvements to the RelaxZeroVectorWarning - the warning message was terribly out of date.
  • Polish for the rdc.read user function. Comment lines and blank lines are now removed to suppress useless warning messages about these lines containing no valid data.
  • Added some basic initial relax icons for J couplings.
  • Created some basic initial GUI wizard graphics for J couplings.
  • Modified the titles of all the auto-analysis GUI elements. The text 'Setup for' has been removed as it is meaningless.
  • Added more emphasis on the titles of the auto-analysis GUI elements. There is now more space below the title, and a different font (16pt roman italic) is being used.
  • Removed some now irrelevant information from the rdc.read user function docstring.
  • Removed a false prompt example from the rdc.read user function docstring.
  • Created an entire new user function class for handling J couplings in the relax data store. This derives from the RDC user function modules. The following functions have been created: j_coupling.copy, j_coupling.delete, j_coupling.display, j_coupling.read, and j_coupling.write.
  • Added a check for the RDC data type to the rdc.read user function.
  • The rdc.read user function can now handle T = J+D type data. Support for this in the specific analyses is yet to be added.
  • Fixed for the rdc.read, j_coupling.read and interatomic.read_dist user functions. Comment lines are no longer removed, as it is impossible to tell a comment line from a spin ID string.
  • Split up the specific_analyses.n_state_model package into modules. The new data and parameter modules have been created by shifting out method from the __init__ module and converting them into functions of the two new modules. This is to simplify the package.
  • Shifted another method from the N_state_model class to the specific_analyses.n_state_model.data module.
  • Added support for the T = J+D RDC data type to the N-state model target function. The J couplings are sent into the target function class when the 'T' RDC data type is encountered. These measured values are then added to the back-calculated RDC values to produced T(theta) which is then compared to T via the chi-squared function.
  • Fix for the new specific_analyses.n_state_model.data.opt_uses_j_couplings() function. The cdp.rdc_data_types appears not to have all alignments IDs within it.
  • Removed the check for Numeric Python in the dep_check module. This Python module not been used within relax for the better part of a decade. This check is not needed.
  • Added the j_coupling module to the pipe_control __all__ list.
  • Fix for the pipe_control.rdc.q_factors() for T = J+D type data. The Q factor normalisation was incorrect, as the J coupling should be subtracted from T first.
  • Unit test fixes for the N-state model. This is needed due to the recent package rearrangements.
  • Removed the absolute argument for all of the lib.alignment.rdc functions. This should be performed at the level of the target function, as mathematical operations may be required prior to taking the absolute value.
  • Fixes for the N-state model target functions for the lib.alignment.rdc changes. The absolute value is now calculated within the target function rather than when back calculating the RDCs.
  • Errors are now handled correctly for the N-state model when T = J+D values are used for the RDCs. The error is the square root of the average variance of the RDC error and J coupling error.
  • The RDC back-calculation function now supports T = J+D values.
  • Created the N_state_model.test_absolute_T system test. This is for checking the optimisation of absolute T=J+D values to find alignment tensors.
  • Epydoc docstring fix for the RelaxTestResult.write_time() method.
  • Created a script to look through the entire relax source tree for unused imports.
  • Removed a large amount of unused imports throughout the relax code base. These were identified by the new ./devel_scripts/find_unused_imports.py script together with pylint.
  • Fixes for the pipe_control.rdc module for when the structure cdp.rdc_data_types is missing.
  • Improvements to the devel_scripts/find_unused_imports.py script.
  • More cleanups of unused imports throughout relax.
  • Fixes for how the devel_scripts/find_unused_imports.py script runs pylint.
  • More cleanups of unused imports throughout relax.
  • Fixes and expansion of the test_suite.unit_tests._lib package __all__ list.
  • Fixes and improvements to Gary Thompson's unit_test_runner.py script. The printouts have been improved and the script can now handle more than 3 levels of directories for a package.
  • The unit_test_runner.py script now defaults to verbose mode.
  • More cleanups of the unit_test_runner.py script.
  • Added a printout to the unit_test_runner.py if the TestCase class cannot be found. This normally continued the test loading silently without warning that the TestCase class name is missing or incorrect.
  • Missing import in the unit test module for the lib.frame_order.matrix_ops module.
  • Shifted the spin_id_to_data_list() function from pipe_control.selection to lib.selection. This is because the selection object requires this function, and the function has nothing to do with the relax data store.
  • Lots of import cleanups including removal of '*' imports, missing imports, and unused imports.
  • Small change to the find_unused_imports.py printouts.
  • Large removal of unused imports throughout relax found using the devel_scripts/find_unused_imports.py script.
  • Clean up of all the imports in the relax code base. This is mainly alphabetical reordering of the imports required due to the huge layout changes in the trunk.
  • Shifted the user function initalisation. This is from the import of the user_functions package to the package initialise() function. This is for saner importing dependencies in the relax sources.
  • The lib.io.open_write_file() function now catches file names of None and raises a RelaxError. This is useful for the GUI if the user forgets to select a file name.
  • The rdc.corr_plot user function can now handled T=J+D type data.
  • The N-state model analysis can now handle RDC data of mixed D and T=J+D.
  • Added support for mixed RDC data types per alignment. This is to allow, for example, one bond RDC values of the 'D' data type and two bond RDC values of the T = J+D data type to be loaded for the same alignment ID. This is now handled in the N-state or ensemble analysis by handling a different RDC data type per RDC value.
  • The Peak_lists.test_bug_20873_peak_lists system test is now skipped if the C modules are not compiled. This test requires the presence of the C modules.
  • Added a completely empty PNG image to use in the new analysis GUI wizard for blank buttons. This will be used in the relax_disp branch to eliminate a Mac OS X only bug.
  • Added the scripts for backing up the relax SVN repository and mailing lists to the repository. This is to make it easier for others to set up the backups on their systems.
  • Added comments to the backup scripts to make it easier to use them.
  • Added the listings package to the relax user manual LaTeX file. This will be used to improve the formatting and look of relax scripts in the manual.
  • Started to convert the relax user manual to use the lstlisting environment for scripts. This is to prettify the scripts in the manual.
  • Improvements to the script UI section of the NOE chapter of the user manual. The lstlisting environments now have the correct numbering to match the script at the start,comments have been copied into the split up script elements, and a few comments improved.
  • The NMRPipe script in the relaxation curve-fitting chapter of the manual now uses lstlisting. The language has been explicitly set to csh to override the global default of Python.
  • Converted all of the relaxation curve-fitting chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
  • Converted all of the model-free chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
  • Converted all of the J(ω) mapping chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
  • Converted all of the Consistency testing chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
  • Created a new listings language definition for relax for the user manual. This is for better highlighting of relax scripts and code in the relax manual.
  • Added an EPS version of the 128x128 J coupling icon for use in the relax user manual.
  • Removed some junk text from the relax script text in section 6.3.8 of the user manual.
  • The relax language definition is now auto-generated by the fetch_docstrings.py script. This is for use in the relax user manual using the listings package. The fetch_docstrings.py script now creates the docs/latex/script_definition.tex file. This is used by the relax.tex file via an \include{} statement. This setup allows all of the relax user functions to be dynamically set as keywords for the relax language definition.
  • Converted all of the Development chapter of the user manual to use the listing package. This is for all of the code examples, which are now much more colourful.
  • Small typo fix for the relaxation curve-fitting chapter of the user manual.
  • Fixed some out of date script code for the relaxation curve-fitting chapter of the user manual.
  • Added a section label to the relaxation curve-fitting chapter of the user manual.
  • Adding a test data file in NMRPipe SeriesTab format. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. A file in NMRPipe SeriesTab format is added to the test-suite for further development.
  • Test function for NMRPipe SeriesTab format implemented. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. An assertEqual test is implemented for the reading of NMRPipe SeriesTab format. The standalone call is: relax -s Peak_lists.test_read_peak_list_NMRPipe_seriesTab.
  • Adding a NMRPipe function file in the folder lib\software\nmrpipe.py. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. Initial file for: lib\software\nmrpipe.py. This file will hold the function calls handling NMRPipe SeriesTab format.
  • Fix for commit (http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The spin naming was wrong. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. 'spin_id' keywords should be supplied different. Ex: spin.name(name='NE1', spin_id=':62').
  • Autodetect format implemented for NMRPipe SeriesTab format implemented. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK SeriesTab.
  • Update of the rotation matrix example in the intro chapter of the user manual. The function is now in lib.geometry.rotations.euler_to_R_zyz(). The example has also been converted to the lstlisting environment for better formatting.
  • The relax prompt strings and help system are now keywords for the relax listings package definition. The prompt strings "relax>" and "relax|" are now recognised as keywords and are coloured blue. The help system has been added as a normal Python keyword for highlighting.
  • Converted all relax prompt examples in the intro chapter of the manual to the lstlisting environment. This is simply for a more colourful representation.
  • The prompt examples in the user function chapter of the manual now use the listing environment. This is via the fetch_docstrings.py script and results in much better formatting of these subsections.
  • Added function destination for auto-detected NMRPipe SeriesTab format. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. Auto-detected NMRPipe SeriesTab format make function calls to the file: lib\software\nmrpipe.py in function nmrpipe.read_list_intensity_seriestab().
  • Imported the missing lib.software.nmrpipe module into pipe_control.spectrum. Progress sr #3043 - Support for NMRPipe seriesTab format *.ser. Expected modules for use in lib\software\nmrpipe.py is imported.
  • Release checklist minfx and bmrblib version update to the newest versions.
  • Spacing fix in an import statement (found using the 2to3 conversion program).
  • Added the relax wiki backup script for dumping the MySQL database contents locally. This is from http://article.gmane.org/gmane.science.nmr.relax.devel/4163.
  • Added the script from Troels Linnet for backing up the relax wiki via FTP. This is from the post http://article.gmane.org/gmane.science.nmr.relax.devel/4168.
  • Added a link to Troels' post to the relax-devel mailing list to the relax wiki FTP backup script. The link is http://article.gmane.org/gmane.science.nmr.relax.devel/4168
  • The relax info printout now works in the absence of the bmrblib module.
  • Added some Oxygen icons for a boolean GUI input element. The media-record-relax-green.png files are the media-record.png files with the hue set to 117.
  • Created a boolean input element for the auto-analyses of the GUI. This simply turns on and off.
  • The boolean GUI auto-analysis input element now has a SetValue() method.
  • Completed NMRPipe SeriesTab reader. Progress sr #3043 - support for NMRPipe seriesTab format *.ser. Completed NMRPipe SeriesTab reader for assignment according to SPARKY format. Changes implemented according to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.
  • Extraction of NMRPipe SeriesTab changed. Progress sr #3043 - support for NMRPipe seriesTab format *.ser. The Extraction of NMRPipe SeriesTab data is changed in pipe_control/spectrum.py in the read() function.
  • Added flag for single or multiple extraction of spectrum. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Flag change added to reading of NMRPipe SeriesTab. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Some small edits to the intro chapter of the relax user manual.
  • Many improvements to the indexing in the relax user manual.
  • Removed the flag for single_spectrum. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Fixed wrong reference to Sparky format. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Modfied the intensity list to handle intensities for all spectra per spin. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Fixed the extraction of NMRPipe seriestab data in pipe_control.spectrum.read(). Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Adding NMR seriesTab data file for a multiple column / multiple spectrum formatted file. This file is from https://gna.org/support/download.php?file_id=18618 attached to the support request https://gna.org/support/?3043 by Troels Linnet. This is if the command "seriesTab -in ../../peaks.dat -out seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1" where nmrfiles.list contains file reference to 10 .ft2 files.
  • Fix for unit test of nmrpipe. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Replacing a pointer-reference structure to an empty creation of list of lists. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • The ID of spins in seriesTab_multi.ser was not formatted correctly to SPARKY format. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Added system test for reading of a multi column formatted NMRPipe seriesTab file. Progress sr #3043 - support for NMRPipe seriesTab format *.ser. Generated the reference data in Excel, for the system test. The spectrum ID's are auto generated by supplying the keyword spectrum_id='auto'. The first few tests was matched against integers rather than floats. Adding '.0' to the end of each number. Spaces added after the commas in the self.assertAlmostEqual() calls. The 2to3 conversion program (for Python 2 to Python 3 conversion) highlights this issue.
  • Added check for number of supplied spectra ID's and the number of returned intensity columns. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Made it possible to autogenerate spectrum ID's, if spectrum_id='auto'. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Remove from datalist where empty list starts. These are created where spins are skipped for ID = '?-?'. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Moved checks for matching length of spectrum IDs and intensities columns. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Moved the adding function of adding the spectrum id (and ncproc) to the relax data store. Progress sr #3043 - support for NMRPipe seriesTab format *.ser. Shifting it to later will prevent the cdp.spectrum_ids list to be populated after the user calls the user function incorrectly.
  • Added epydoc documentation in pipe_controlspectrum.read() when supplying keyword 'auto'. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Added GUI description for when supplying 'auto' to the spectrum_id. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Added a stub GUI describtion in the File formats, for NMRPipe seriesTab. Progress sr #3043 - support for NMRPipe seriesTab format *.ser.
  • Fix for two spaces are used after a period in documentation. Progress sr #3043 - support for NMRPipe seriesTab format *.ser. relax uses the double space for easier for the eyes to pick up the sentence structure.
  • The relax user manual is now broken into parts. The higher level LaTeX part command is now used to group related chapters. This should make it easier for users to navigate this huge thing.
  • Creation of the optimisation chapter of the relax user manual. The main text of this chapter originates as part of the model-free chapter. As this most of this text was not model-free specific, it has been spun out as its own chapter. Text has also been taken from the "Optimisation of relaxation data – values, gradients, and Hessians" chapter. The indexing for the optimisation topics has also been improved.
  • Changed the chapter layout of the relax user manual. The development chapter has been moved forwards.
  • Fix for the spectrum.read_intensities user function docstring. Grammatically, the text "spectrum ID's" should be "spectrum IDs". The problem though was that this text was strangely causing the user manual compilation to fail.
  • Added subsubindexing for the optimisation algorithm index entries.
  • Added extensive cross-referencing to the index of the relax user manual.
  • Added some hyphenation rules for better formatting in the user manual. For this, the external hyphenation.tex has been created.
  • Better indexing in the relax user manual. The imakeidx LaTeX package is now used instead of makeidx, and the hyphenation has been improved.
  • Lots of spelling fixes for the relax user manual.
  • Updated the minimum Python version from 2.3 to 2.5 in the user manual.
  • Epydoc docstring fix for the pipe_control.spectrum.read() function. The text "Z_A{i}" causes problems when compiling the API documentation, so it has been changed to "Z_Ai".
  • Python 3 fix for the new test_suite.clean_up module. The exceptions Python module does not exist in Python 3, so instead the relax compat.builtins object is being used to store the WindowsError variable of None.
  • Added a paragraph to the installation chapter of the manual about not supporting the EPD.


Bugfixes
  • Fix for bug #20674 - the failure of the consistency testing analysis. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The problem was that the first residue did not have a single proton 'H' in the PDB file, and therefore the dipolar relaxation interaction was not set up. The overfit_deselect() method of the consistency testing specific API was not checking for this. The method is now much more like that of the model-free specific analysis.
  • Fix for the model-free analysis specific overfit_deselect() method. The tests for the presence of dipolar relaxation was not correct and was non-functional.
  • Fix for the J(ω) mapping analysis matching that for the consistency testing. The overfit_deselect() method is now identical to that of the consistency testing analysis.
  • Fix for bug #20683 - the infinite and NaN data in Bruker DC files. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The model-free specific overfit_deselect() method now checks for infinite relaxation data and deselects the spin if such data is encountered.
  • Fix for the analysis specific API common method _data_init_spin(). The data types are now correctly checked - they are not strings but types.
  • Fix for the relaxation curve-fitting _assemble_scaling_matrix() method. The intensity scaling was never activated before due to a lower vs. uppercase parameter name mismatch. This scaling is now correctly set up as the previous code assumed cdp.relax_times was a list whereas it has been a dictionary since the early 1.3 releases.
  • The grid search bounds for the relaxation curve-fitting are no longer affected by scaling. The parameter scaling recently activated revealed a bug in the lower and upper data structures for the grid search in that these were continuously scaled down.
  • Fix for the target_functions.relax_fit C module - the scaling was incorrectly performed.
  • Fix for the relaxation curve-fitting _back_calc() method for the changes to the C module. The setup() method requires that the scaling matrix is converted to a list of the diagonal elements.
  • Fix for the analysis specific API common _return_value_general() method. The value of None is now handled properly when a simulation value is asked for.
  • Restored the default behaviour of the spin_loop(). The skip_desel flag is now functional and defaults to False.
  • Fix for the relax_times and intensities parameter definitions for specific_analyses.relax_fit. These are dictionaries, not lists.
  • Fix for the spectrum.error_analysis user function for replicated spectra and subsets. A second call to spectrum.error_analysis was removing the results from the first call. This is now avoided.
  • Bug fix for the right click popup menu in the spectra list GUI element. This affects the NOE, R1, and R2 analyses. The actions of the menu items were all mixed up.
  • Fix for the nasty bug #20756. The problem was that the global execution lock was not always released by a relax script when certain errors are raised during the script execution. This does not occur for all types of error though. Now the release of the lock has been shifted into the 'finally' statement to absolutely force lock release.
  • Big bug fix for a memory leak in the relaxation curve-fitting C module. Proper reference counting is used for the temporary 'element' Python objects used in the conversion between Python and C objects. The use of the Py_CLEAR() macro removes the memory leak. However the number of references as seen by sys.gettotalrefcount() in a debugging Python version keeps rising and might be a problem in the future.
  • Big bug fix for the value.copy user function - it is now functional again.
  • Bug fix for the value.copy user function. The user function can now handle parameter errors, and the values are set in the correct data pipe.
  • Bug fix for an incorrect print statement in the N_state_model.test_paramag_centre_fit system test. This is in the script, and was uncovered using WinPython by Troels E. Linnet via the relax system tests at http://thread.gmane.org/gmane.science.nmr.relax.devel/3863. The Python bug was detailed at http://thread.gmane.org/gmane.science.nmr.relax.devel/3863/focus=3867.
  • Fix for the package checking as part of the unit tests. This was identified from the bug report #20820 submitted by Troels E. Linnet. The problem was that on some systems, the full path is required for checking the presence of the directories which are the sub-packages of the main package being checked. The result was that checking for the package in the __all__ list was skipped. Note that this change does not fix the bug reported.
  • Fixes for the Jw.test_calc system test - the spectral density value comparison is now significant.
  • Bug fix for the pipe_control.spectrometer.get_frequencies() function. The units argument was incorrectly referenced.
  • Fix for bug #20820. Solution found - 'software' was not mentioned in __init__.py, and failed at import.
  • Partial fix for bug #20873. The spectrum_id argument for the spectrum.read_intensities user function can now be both a string and a list of strings.
  • Fix for bug #20873. This was reported by Troels E. Linnet. The ability to load multiple peak intensities from a single generic formatted file has been correctly implemented. This involves added checks to make sure that the user supplies reasonable arguments and to then loop over the intensity column argument.
  • Python 3 fixes via the 2to3 program.
  • Bug fix for the value.write user function for list or dictionary type data. This is for the case where the variable of one spin is set to None rather than a list or dictionary type.
  • Bug fix for the Sequence GUI input element. This complete the removal of bug #20873. The problem was that the gui_to_str() function was not failing to convert the string into a string list, so the list was deemed as a single string. Now the first character of '[' or '(' for lists or tuples are now searched for instead of relying on the conversion to trigger an error.
  • Fixes for the value.write user function for simple parameter values of None. This is a recently introduced bug which causes a complete failure of the user function is the parameter for any spin is None.
  • Fix for bug #20888, the autoscaling of Grace graphs. This solution was mentioned in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3920/focus=3930. Instead of using minimum and maximum values for the axes in the Grace graphs produced by the lib.software.grace module, which was the old solution for having the graphs scaled to reasonable values, instead the '@autoscale' command is appended to the end of all graphs. This is performed by the write_xy_data() function.
  • Bug fix for the running of the test suite in the relax GUI. The fix of r19727 was extended to apply to the GUI as well. Too many arguments were being sent into TextTestRunner Python class on certain Python versions (3.1 and ≤ 2.6).
  • Big bug fix - the relax execution lock now truly supports nesting. This fixes bug #20891 reported by Troels Linnet. Scripts can now be executed from the GUI. Note that this is a very dangerous fix.
  • Completed the fix for bug #20889. The problem was that the spectrum.read_intensities user function was incorrectly updating the cdp.spectrum_ids list when the spectrum_id argument is set to a list. The list of IDs was being set as a single element of cdp.spectrum_ids, causing problems with the GUI when updating the ComboBox choices and then subsequent setting of the spectrum IDs. This bug and fix is independent of the relax_disp branch, despite being uncovered there and being caught by the Relax_disp.test_bug_20889_multi_col_peak_list GUI test in that branch.
  • Bug fix for the GUI element for the interatom.define user function. The special spin ID GUI elements can not be set to the get_spin_ids() function as then SetValue can no longer work for IDs not in the list.
  • Fixes for the TestCase class names for a number of lib package modules. As the test class name was incorrect, previously the test suite was skipping these silently. This was dangerous.
  • Fixes for the unit tests of the lib.selection module. The contains_*() methods now should be used. And the test_Selection_ful_spin_id() unit test has been completely deleted as this way of checking the selection object is no longer valid.
  • Fix for bug #20910 - the broken grace.write GUI interface. The problem was that the Value GUI input element was not detecting list-type data returned by the wiz_combo_iter method.
  • Fix for [ (https://gna.org/bugs/?20915 bug #2091 - Failure of Grace opening in MS Windows]. Troels E. Linnet provided this patch, and was discovered during work on a Windows 7 system: telinnet aaattt bio_dot_ku_dot_dk. This is a small fix for a wrong call to "raise RelaxMissingBinaryError(binary)", when issuing an external call to xmgrace. The "path_sep" would be equal = [\/], and the RE search would not find(True) the full path specified for the xmgrace file. This is now shifted to python: os.path.isfile http://docs.python.org/2/library/os.path.html. Another fix, is that as a standard the command "xmgrace" is provided. This will work fine through windows cmd, but the true name for program in windows is "xmgrace.exe", and so an additional search for +".exe" is also performed.
  • Fix for the N_state_model.test_absolute_T system test for Mac OS X. The precision of the check needed to be decreased.
  • Fix for bug #20918, the hanging of the data pipe editor. This was reported by Troels Linnet and is an MS Windows only problem. The problem is in the wxMSW part of wxPython, and it may be fixed in newer wxPython versions. The issue is nevertheless now avoided by calling the GUI user function store objects with the arguments wx_wizard_sync=True and wx_wizard_modal=True. This appears to solve the problem.
  • Decreased the precision of the check in the Frame_order.test_rigid_data_to_rigid_model system test. This is to allow the test to pass on a MS Windows 7 test machine.
  • More MS Windows fixes, this time a nasty kludge, for the relax system tests. This is strangely needed for the relax_disp branch and not the trunk for a 64-bit MS Windows 7 test system. The reason why this WindowsError is triggered by the base tearDown() method in the relax_disp branch and not trunk is a total mystery. Actually why Windows refuses to complete the file close() operations of the results.write and state.save user functions before calling the tearDown() method is the greater mystery.
  • Bug fix for the batch file permissions for executing Art Palmer's Modelfree4 program. This was identified in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. The file was set to be executable, but on Unix systems it would end up with the permissions "---x------".
  • Small comment fix in the sample_scripts/consistency_tests.py script.
  • Fix for the scons fetch_docstrings target. The user functions need to be explicitly initialised in the fetch_docstrings script as this is not running through relax.
  • Fix for bug #20921, the GUI tests freezing in MS Windows. The problem was that the dipolar interaction wizard in the model-free auto-analysis GUI element was calling its user functions asynchronously. This can lead to racing conditions. The commit r80084 (http://article.gmane.org/gmane.science.nmr.relax.scm/17840) somehow randomly triggers this racing on MS Windows systems only together with the Mf.test_mf_auto_analysis GUI test. Now all user functions are called synchronously.
  • Fix for the relax GUI splash screen. On certain systems, the GUI was failing due to the splash screen. It is now shown after the main wxPython window has been created.
  • Fix for the new analysis wizard when running the GUI tests. If the create_button() method is called without a function argument, the wizard is still created. This is triggered in the relax_disp branch on certain systems.
  • Bug fix for the spin parameter array always being converted to lowercase. The is in the data_store.mol_res_spin.SpinContainer._back_compat_hook() method. It always calls the _back_compat_hook_mf_data() method which converts the spin 'params' list all to lowercase. Now the _back_compat_hook() method first checks that the data pipe is that of a model-free analysis.
  • Proper bug fix for the spin parameter array always being converted to lowercase. The previous fix was causing failures in certain cases. One system test and one GUI test were failing. Now the spin container is checked for the presence 'equation' variable to determine if this is a model free data pipe.
  • Fix for the relax version file for the relax user manual construction. This was causing 'scons user_manual_pdf' and related targets to fail when a local git repository is used (via git-svn).
  • Bug fix for the page numbers in the index - these were often out by a few pages. The makeindex command was being run too early in the repetitive LaTeX compilation chain, causing the page numbers to be incorrect. It is now run twice to fix the problem.
  • Fix for the spectrum.read_intensities user function in the GUI. The menu string was truncated to spectrum.read.
  • Python 3 fix for the lib.software.nmrpipe.read_list_intensity_seriestab() function. The inbuilt Python filter() function does not return a list in Python 3, as previously, but rather a filter object. Therefore a call to list() is required to properly convert the data.
  • An attempt at better handling MS Windows not releasing the file handle on time in the test suite. The system and unit tests tearDown() method should now be resilient to the strange MS Windows behaviour of not releasing the relax state files. The tearDown() method should now complete even when this error occurs. A delay of 3 seconds has been added when the WindowsError occurs to give the OS some time before attempting to delete the file again. If this fails, then the file deletion operation is skipped.
  • Better handling of temporary file and directory removal in the relax test suite. The new test_suite.clean_up.deletion() function has been created from the recent method of the same name. This is used by the tearDown() method of the system, unit, and GUI tests. It should prevent rare MS Windows errors from appearing due to the OS not releasing a temporary file after a close() call.


Links

For reference, the following links are also part of the announcement for this release:


Version 2 of relax

relax 2.2 series

relax 2.2.5

Description

This is a minor feature release. Improvements include the creation of Rex value files scaled to all spectrometer frequencies for the model-free auto-analysis [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] and some new capabilities in the structural API. Feel free to upgrade if you wish to use these new features.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 2.2.5
(24 March 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.5


Features
  • The files created by the value.write user function now include a header describing the parameter.
  • The relax internal structural object now supports the merger of molecules. This can be useful if different domains of one system are in two PDB files or are split in the one file.
  • The structure.delete user function can now be used to delete parts of molecules down to the level of individual atoms.
  • Helix and sheet information from PDB files are now stored in the internal structural object as metadata. The structure.read_pdb and structure.write_pdb user functions will preserve this information.
  • The numbers output by the value.display and value.write user functions can now be scaled.
  • The model-free auto-analysis now generates field strength dependent Rex files for each field present.


Changes
  • Added a comment to the output from value.display and value.write to describe the parameter. This idea is discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428. The idea is to take the parameter description from the specific analysis API and add it to the top of the file or output. This is to help understand what the Rex value are. For example for the Rex parameter the first line would be: "# Parameter description: Chemical exchange relaxation (sigma_ex = Rex / omega**2)."
  • Created the Structure.test_read_merge system test to test a new concept - merging of structures. The idea is to add the merge argument to the structure.read_pdb user function to allow two different structures in two PDB files to be merged. This is useful if structures of individual domains have have been solved separately and are located in two PDB files. Then with the merge flag, you will not need to use and external program or hand edit PDB files to join them.
  • Added the merge flag to the structure.read_pdb user function. This currently does nothing.
  • The merge flag for the structure.read_pdb user function is now propagated to the pack_structs() method. This structure API method calls the ModelList.merge_item() method which is yet to be implemented.
  • The MolList.add_item() structural API method now returns the added molecule container. This is used by the pack_structs() method to alias the molecule, and will be required when structure merging is implemented.
  • Whitespace fixes - replaced many instances of the tab character '\t' with 4 spaces.
  • Implemented the merging of structural objects. This allows the merge flag of the structure.read_pdb user function to work.
  • The printouts from the structure.read_pdb user function are now different with the merge flag set. The text now says that the molecules are being merged rather than added.
  • Sections of molecules can now be deleted using the structure.delete user function. The atom ID argument has been added and this is now propagated into the internal structural object. This ID string can be used to delete subsets of the 3D structural data in the relax data store.
  • Created the Structure.test_read_write_pdb_1UBQ system test. This is for checking the use of the structure.delete user function with the atom ID argument.
  • The Structure.test_read_write_pdb_1UBQ system test now checks for HELIX and SHEET records. This is not implemented yet, but the idea is that the structure.read_pdb and structure.write_pdb should preserve the helix and sheet information present in the original PDB and that the internal structural object should store this information.
  • Created the internal structural object _pdb_chain_id_to_mol_index() method. This will be used to convert PDB chain IDs, which are used to indicate different molecules in the PDB, into molecule indices for the internal structural object.
  • HELIX PDB records are now read, stored, and written out by the internal structural object. This affects the structure.read_pdb and structure.write_pdb user functions. The helix is stored as a metadata type object - its elements do not correspond to the atoms in the structural object.
  • SHEET PDB records are now read, stored, and written out by the internal structural object. This affects the structure.read_pdb and structure.write_pdb user functions. The sheet is stored as a metadata type object - its elements do not correspond to the atoms in the structural object.
  • Created 13 unit tests of the Internal._trim_helix() internal structural object method.
  • Added the index_flag argument to all structural API atom_loop() methods.
  • Implemented the internal structural object _trim_helix() method. This is used when the structure.delete user function is called to trim and remove the helix metadata. For this to work, the additional method _residue_data() was written to create a dictionary with residue numbers as keys and the residue names as numbers. This dictionary is used by _trim_helix() to change the residue names in the helix metadata.
  • Created 13 unit tests of the Internal._trim_sheet() internal structural object method. These are mirror the 13 unit tests of Internal._trim_helix().
  • Implemented the Internal._trim_sheet() internal structural object method. This is also now used by the structure.delete user function to remove sheet metadata for residues which no longer exist.
  • Modified the ScientificPython structural object atom_loop() method to match the internal object. If only one element is returned from the atom_loop(), then this is returned as a single item rather than a tuple of length 1.
  • Lots of fixes for the change to the structural API atom_loop() method. This method when returning a single item now returns a single item rather than a tuple of length 1.
  • The index_flag argument to the ScientificPython structural object atom_loop() method is now used.
  • Created the Structure.test_metadata_xml system test. This is used to check that the structural metadata (currently helices and sheets) are stored in the relax XML save files and then can be read back into relax again.
  • The helix and sheet metadata is now stored in and read from relax XML state files.
  • Added the scaling argument to the value.display and value.write user functions. The idea comes from a suggestion by Angelo Figueiredo <am dott figueiredo att fct dott unl dott pt> and was discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. This allows the user to scale parameters to any value, for example scaling the Rex value to the field strength dependent value.
  • The model-free auto-analysis (the dauvergne_protocol [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]) now generates field strength dependent Rex files. The idea comes from a suggestion by Angelo Figueiredo <am dott figueiredo att fct dott unl dott pt> and was discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. One file per field strength is generated and named 'rex_600' for 600 MHz, for example. The new scaling argument of the value.write user function is being used to scale the tiny field strength independent value used internally in relax to the Rex value in rad.s-1 that you would see in an R2 data set.
  • Added the new 'comment' argument to the value.write user function. This is used to add user comments to the top of the file.
  • The model-free auto-analysis (the dauvergne_protocol module [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]) now adds comments to the Rex files. This is through the new comment argument of the value.write user function. These comments explain that the Rex values are scaled to the stated field strength.
  • Modified the Mf.test_dauvergne_protocol system test to check for all the files and directories created.
  • Created the new lib.text.sectioning module for formatting titles, subtitles and other sectioning text. The two functions title() and subtitle() have been implemented.
  • Created unit tests for the title() and subtitle() functions of the lib.text.sectioning module.
  • Expansion of the lib.text.sectioning module. The following new functions have been added: box(), section(), subsection(), subsubsection(),subtitle(), subsubtitle(), underline().
  • Expanded the unit testing of the lib.text.sectioning module to cover all title and section functions.
  • Added prespace and postspace arguments to the *section() and *title() functions of lib.text.sectioning. Through these arguments, the amount of spacing above and below the section text can be controlled.
  • Split the generic_fns.structure.geometric.create_rotor_pdb() function. The non-relax specific code has been shifted into the rotor_pdb() function.
  • Initialised the lib.structure package - this is currently empty.
  • Shifted the rotor creation components from generic_fns.structure.geometric to lib.structure.rotor. The create_rotor_pdb() function remains in place as this is the user function backend which checks for data pipes and updates the status object, but the rotor_pdb() and create_rotor_propellers() functions have been moved into the relax library. The create_rotor_propellers() function has been renamed to lib.structure.rotor.rotor_propellers().
  • Converted links in all docstrings to use the Epydoc hyperlink notation. This will allow links to be clickable for the API documentation.
  • Added Epydoc hyperlink markup for the bug tracker in the system test docstring where missing. This is for a better API documentation.
  • The lib.structure.rotor.rotor_pdb() rotor_angle argument should now be in radians. This does not affect the structure.create_rotor_pdb user function as the generic_fns.structure.geometric.create_rotor_pdb() function converts the value to radians prior to calling the rotor_pdb() function.
  • The lib.structure.rotor.rotor_pdb() function can now handle structural models. The model number argument has been added to allow the rotor structure to be added to a single model, or to all models if not supplied.


Bugfixes
  • Fix for a copy and paste error in the Structure.test_read_merge system test.
  • Fixes for all the Ap4Aase truncated PDB files. The atom numbers are now sequential, as defined by the PDB standard.
  • Bug fix for the structural data consistency test in the pack_structs() structural API method. The index was not correct causing failures in certain rare cases.
  • Python 3 fix for an import into the generic_fns.structure.internal module.
  • Python 3 fixes for the relax version information for code checked out from the relax repository. The subversion version.revision() and version.url() functions now handle the Python 3 issue of Popen working with byte arrays instead of normal strings.


Links

For reference, the following links are also part of the announcement for this release:


relax 2.2.4

Description

This is a major bugfix release. System and unit test bugs in the Mac OS X application have been eliminated, the RMSD related functions for systems with old Numpy versions installed have been fixed, the system information printout when the relax path contains spaces now works, Python 3 fixes have been made throughout, problems with the last steps of the model-free auto-analysis under certain conditions have been resolved, and the value.write and value.display user functions no longer present a list of zero values when very small number are encountered (for example the field-strength independent Rex values from a model-free analysis). Upgrading is recommended.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 2.2.4
(17 March 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.4


Features


Changes
  • Updated the release checklist document to include the correct instructions for minfx and bmrblib. These are the packages bundled with relax (https://sourceforge.net/projects/minfx/ and https://sourceforge.net/projects/bmrblib/)
  • Improvements for Python 2 and 3 compatibility. Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and different Python 3 version compatibility, code has been shifted into the compat module. The different parts of relax now import from the compat module for modules/packages with different import semantics for different Python versions. In addition the different handling of the bz2 and gzip module for reading and writing files has been shifted from 'relax_io' into 'compat'.
  • Updated the 2to3 checklist document to include multiple threads for faster operation.
  • Eliminated the os.devnull import flag dep_check.devnull_import. This is not needed as the compat relax module defines os.devnull for Python ≤ 2.3. The devnull module is no longer part of the relax information printout.
  • Added a more informative error message if the platform module is missing. This is for Python ≤ 2.2. The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can simply be copied into the lib/pythonX.X/ directory to fix this.
  • Slight change to the message printed if the platform module is missing.
  • Modified the script for running the relax test-suite on multiple Python versions. The pre-2.2 Python versions are now commented out as well as the abortive Python 3.0.
  • Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test to catch bug #20613. This was reported by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt>. This test is a direct copy of the Mf.test_bug_20563_missing_ri_error system test. The only change is that the local tm global model results file (in the local_tm/aic/ directory) has been modified. This results were read into relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb loaded into the data pipe, and the results saved again. This triggers the bug as the problem is the presence of structural data with the local tm global model being selected in the auto-analysis.
  • Shifted all of the model-free specific analysis class documentation variables to the top. This is simply for better organisation of the code.
  • Created the model-free write_doc class variable talking about the field strength independent Rex value. This has been added to the value.display and value.write user functions to explain that Rex values are very small and that the user needs to scale them up.
  • Shifted all of the documentation variables to the top of the specific API_base class. This is for better organisation.
  • Added the write_doc class variable to the specific analysis API class as a empty string. This is to fix the unit tests.
  • Created the front end for the new structure.create_rotor_pdb user function. This will be used to create a PDB representation of a rotor motional model.
  • Added file, directory and overwrite force arguments to the structure.create_rotor_pdb user function.
  • Started to implement the backend of the structure.create_rotor_pdb user function.
  • The internal structural object MolContainer.add_atom() method now returns the index of the new atom.
  • Created the internal structural object MolContainer.last_residue() method.
  • Fully implemented the structure.create_rotor_pdb user function. For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created.


Bugfixes
  • Fix for the system tests in the Mac OS X application binary. The Mf.test_bug_20563_missing_ri_error system test fails in the Mac OS X application binary. The problem is that the py2app extension used to build the Mac application decides that empty directories are not to be included in the app, so naturally the test fails when checking for these. Now empty results files have been added to these directories to trick py2app to include them.
  • Fixes for the unit test package __all__ list checking. Now only *.py files and directories are checked. In some cases other files could be present in the packages, for example the object files when compiling the C modules. These would cause the unit tests to fail unnecessarily.
  • Fixes for the unit test __all__ list checking for the lib package for the Mac OS X application. For some reason the py2app extension which creates the app merges the Python installation directory Resources/lib/python2.7 and the relax lib package into Resources/lib. Now 'python2.7' is blacklisted when checking the lib package so that the parasitic Python install location is ignored.
  • Bug fix for the structure RMSD function for when old numpy versions are present. Older numpy versions do not have the ddof argument for the std() standard deviation function,therefore relax now catches this, calculates the biased standard deviation formula, and then multiplies the value by a correction factor to obtain the non-biased estimator.
  • Bug fix for the info relax system information module for when spaces are present in the relax path. If relax is placed into a directory containing spaces, then the determination of the architecture of the compiled C modules fails.
  • Python 3 fixes for the model-free analysis specific code. This was causing errors "AttributeError: 'dict_values' object has no attribute 'sort'".
  • Python 3 updates and fixes using the 2to3 program.
  • Bug fix for the external Scientific Python Geometry package. This is a strange Python 3 issue only triggered when the epydoc Python package is installed.
  • Fix for bug #20613, the failure of the diffusion tensor PDB creation. This was reported by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt>. The problem was that the diffusion tensor PDB representation structure.create_diff_tensor_pdb user function was being called even when the local tm global model was selected. This naturally failed as there is no global diffusion tensor. Now this user function is avoided for the local tm global model.
  • Fix for the value.write user function for very small parameter values (Rex for example). This was reported by Martin Ballaschk <ballaschk att fmp-berlin dott de> in the thread http://thread.gmane.org/gmane.science.nmr.relax.user/1397/focus=1402 and by by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt> in the unrelated bug report at https://gna.org/bugs/?20613. The formatting string "20.15f" has been changed to "20.15g" to allow Python to decide if the normal decimal or exponential form of the number should be printed.
  • Fix for a strange and extremely rare typo bug in the model-free specific analysis code. This was identified by Manish Chaubey <manish dott chaubey att tuebingen dott mpg dott de> in the message at http://thread.gmane.org/gmane.science.nmr.relax.user/1422. This only occurs if a relaxation data error of zero is encountered and is a bug in the RelaxError message explaining the problem with the data.


Links

For reference, the following links are also part of the announcement for this release:


relax 2.2.3

Description

This relax version is a major feature and bugfix release. It adds the new structure.add_model, structure.rmsd and structure.web_of_motion user functions, enhances the structure.load_spins and structure.find_pivot functions, and PDB support for the internal structural object has been improved and updated. The new 'lib' package is introduced which will, in the future, be extensive collection of functions and special objects for all types of molecular dynamics analyses. The relax controller in the relax GUI has been improved with line wrapping to allow all messages to be seen. And some major bugs affecting the model-free auto-analysis and PDB file creation have been fixed. All users are recommended to upgrade.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 2.2.3
(11 March 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.3


Features
  • Added the mol_name_target argument to the structure.load_spins user function. This allows spins from different molecules to be placed together in the same molecule container in the relax data store.
  • Addition of two new user functions - structure.add_model and structure.rmsd.
  • Created the structure.web_of_motion user function. This is used to create a special PDB file which represents the atomic motions between different structural models. Identical atoms of the selected models are concatenated into one model, within a temporary internal structural object, and linked together using PDB CONECT records.
  • Better PDB support in the internal structural object with: Improvements and fixes in reading/writing, an update of the format to version 3.30, and faster PDB parsing.
  • Creation of two new modules for better PDB support - generic_fns.structure.pdb_read and generic_fns.structure.pdb_write.
  • Improvements to the structure.find_pivot user function including the addition of the func_tol argument to better control the simplex optimisation and the use of the logarithmic barrier function to prevent the pivot from heading to infinity when the solution is a line.
  • Initialised a new package called 'lib' - this will in the future be an extensive collection of functions, methods, classes, objects, etc. useful for the study of all types of molecular dynamics.
  • Line wrapping has been turned on in the relax controller in the GUI so that all text is visible.


Changes
  • The relax intro text now includes the repository URL for checked out code. This is for preserving better debugging and logging information, so that it is clear where the code comes from.
  • Created the Structure.test_load_spins_mol_cat system test. This will be used to test a new 'mol_name_target' argument to the structure.load_spins user function.
  • Created the Structure.test_delete_multi_pipe system test. This is to check that the structure.delete user function is operating on a single data pipe.
  • Updated the Freecode instructions in the release checklist document.
  • Created the simple Structure.test_delete_empty system test. This is to demonstrate a failure of the structure.delete user function when no structural data is present.
  • Added a printout to structure.delete for when no structures are present.
  • Created the Structure.test_rmsd system test. This test checks the currently unimplemented structure.add_model and structure.rmsd user functions.
  • The structural API num_molecules() method can now handle no data being present.
  • Implemented the structure.add_model user function.
  • Added some more checks to the Structure.test_rmsd system test.
  • Modified the structure.add_model calls in the Structure.test_rmsd system test to include model nums.
  • Added the 'model_num' argument to the structure.add_model user function.
  • Modified the structure.add_atom user function to allow the position argument to be a rank-2 array. This allows a different coordinate for each model to be specified.
  • Spun out the atomic_rmsd() and calc_mean_structure() functions into their own module. They were previously in the generic_fns.structure.superimpose module but are now in the new generic_fns.structure.statistics module.
  • Added checks for the atomic information to the Structure.test_rmsd system test. This demonstrates a failure of structure.add_atom user function when specifying different positions for the different models.
  • Docstring addition for the generic_fns.structure.statistics.atomic_rmsd() function.
  • Implemented the structure.rmsd user function.
  • Fixes for the Structure.test_rmsd system test - it now passes.
  • Created a new float_object argument type which is used by the 'pos' argument of structure.add_atom. A new arg_check.float_object() function has been created to handle any float object greater than rank-0.
  • Created the Structure.test_rmsd_ubi system test to better check the structure.rmsd user function. This uses the truncated ubiquitin ensemble in the test suite shared data directories. The RMSD matches the VMD 1.9.1 output.
  • Added a new module generic_fns.structure.pdb_write for generating the PDB records. This decouples the formatting code from the internal structural obect. The PDB format has been updated to version 3.30. There is one function for each PDB record, allowing this to be easily extended and kept up to date.
  • Created the generic_fns.structure.pdb_read module. This replaces the internal structural object _parse_pdb_record() method which was handling both ATOM+HETATM and CONECT records. It should allow greater flexibility in reading data out of other PDB records in the future. There is one function per PDB record type in this module.
  • Added the full 1UBQ PDB structure to the relax test-suite shared data directories. This is a small, very quick to read structure which will be used for validating the reading and writing of different PDB record types.
  • Changes to the internal structural object. The _parse_models_pdb() method has been renamed to _parse_pdb_coord() and the opening of the PDB file shifted into the base load_pdb() method. This is in preparation for better parsing of PDB files to match the main sections of the PDB format, see http://www.wwpdb.org/documentation/format33/v3.3.html.
  • Created the Structure.test_read_pdb_1UBQ to check the complete parsing of the complex PDB file. The test is currently quite basic and needs to check more of the internal structural object.
  • Better checks for the atomic data in the Structure.test_read_pdb_1UBQ system test.
  • Added a series of _parse_pdb_*() methods to the internal structural object. These correspond to each section of the PDB format version 3.30 http://www.wwpdb.org/documentation/format33/v3.3.html. The currently loop over the records of their section, returning the remaining PDB records. The aim is for fast parsing and breaking into sections.
  • Faster PDB parsing by the removal of the use of the re.search() function. Now line slices are directly compared instead.
  • Added some more unit tests for the generic_fns.structure.pdb_read module. These tests are not yet complete, as it is unknown what these unimplemented functions will return.
  • Completed the unit test of the generic_fns.structure.pdb_read.helix() function.
  • Implemented the generic_fns.structure.pdb_read.helix() function.
  • Created the Mf.test_bug_20531_molmol_macro_write_relaxfault system test. This is an attempt at catching bug #20531. It creates all of the m0-m9 and tm0-tm9 models, sets some parameter values, and then attempts to create all of the Molmol macros, PyMOL macros, Grace plots and parameter text files as present in the auto_analysis.dauvergne_protocol module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
  • The spectrometer frequency is now set in the Mf.test_bug_20531_molmol_macro_write_relaxfault system test. This is needed for the Rex scaling.
  • The spin name, element and isotope is now set in Mf.test_bug_20531_molmol_macro_write_relaxfault. This is required in this system test so that the marco creation is not skipped.
  • Added some work-arounds for the model-free specific code for when no relaxation data is present. This is needed for the Rex scaling, as the ID of the first relaxation data set was being used to select the first frequency. As caught by the Mf.test_bug_20531_molmol_macro_write_relaxfault system test, this fails if no relaxation data is present.
  • Expanded the unit test of the generic_fns.structure.pdb_read.sheet() function.
  • Implemented the PDB SHEET record parsing function generic_fns.structure.pdb_read.sheet().
  • Extended the PDB ATOM record reading unit test to be of 80 characters in length, as per the PDB definition.
  • Created unit tests for the generic_fns.structure.pdb_write module. This currently covers the atom(), helix() and sheet() functions (the last 2 are not yet implemented).
  • Implemented the PDB HELIX record writing function generic_fns.structure.pdb_write.helix().
  • Improved PDB writing capabilities. The functions of the generic_fns.structure.pdb_write module now all use the _handle_none() function to avoid the text "None" from appearing in the PDB file and _record_validate() to be sure the record has not been corrupted with bad input causing it to be either less or greater than 80 characters.
  • The Mf.test_bug_20531_molmol_macro_write_relaxfault system test now catches bug #20531. This now uses the results file attached to the bug report.
  • Implemented the PDB SHEET record writing function generic_fns.structure.pdb_write.sheet().
  • Created a unit test for the generic_fns.structure.pdb_write.het() function.
  • Created the generic_fns.structure.pdb_write._handle_text() function. This private function is used to convert text into PDB suitable format (uppercase and values of None converted to empty strings).
  • The diffusion tensor PDB files are now conform better to the PDB standard. The HET records are now correct, only capitalised text is present in the files, and trailing whitespace to character 80 has been added.
  • Epydoc docstring formatting for the generic_fns.structure.pdb_write modules. These large changes improve the API documentation at http://www.nmr-relax.com/api/.
  • Created a unit test for the generic_fns.structure.pdb_write.model() function.
  • Added a new PDB file with 3 models and a few atoms for testing of the structure.web_of_motion user function.
  • Created the Structure.test_web_of_motion_all system test. This is to check the new structure.web_of_motion user function.
  • The structure.web_of_motion user function can now handle file objects as well as file names as input.
  • Small fixes for the Structure.test_web_of_motion_all system test.
  • Created the Structure.test_web_of_motion_12 system test to show how model sets are currently ignored.
  • Implemented the models argument for the structure.web_of_motion user function. This was previously not being used and was caught by the Structure.test_web_of_motion_12 system test.
  • Created the Structure.test_web_of_motion_13 system test. This was just to be sure that the models argument was correctly handled by the structure.web_of_motion user function.
  • The structure.find_pivot user function now accepts the func_tol argument. This is used to terminate the simplex optimisation when this function tolerance value is reached.
  • Shifted the ensemble pivot finding target function into the maths_fns package.
  • Added a sentence to the README file about the sample_scripts directory.
  • Added a document detailing the possible future layout of relax's packages.
  • The structure.find_pivot user function now uses the logarithmic barrier function. This is for constrained optimisation and requires the newest minfx code. The pivot position is constrained within a box of +/- 1000 Angstroms from zero. This is needed for when the solution is an infinite line - i.e. a rotation axis and not a pivot point. Previously the simplex optimisation would head toward + or - infinity. But now with a logarithmic barrier, the simplex algorithm can stabilise and find a point on the axis very quickly, long before reaching the edges of the box.
  • The structure.find_pivot user function now accepts the func_tol and box_limit arguments. This allows the function tolerance for the simplex optimisation to be specified, as well as the size of the box to constrain the pivot to be within.
  • Initialised the lib.geometry package. This will be a library of all mathematics functions relating to geometry.
  • Added empty packages to the unit tests for the lib and lib.geometry packages.
  • Updated the maths_fns package __all__ list.
  • Updated the test_suite.unit_tests package __all__ list to be more modern.
  • The n_state_model.number_of_states user function no longer requires the N-state model to be defined. This was only needed to update the model information, and is skipped if not set.
  • The generic_fns.structure.superimpose.find_centroid() function now prints out Euler angles as well.
  • Large improvements to the checking for all the rdc and pcs user functions. The new methods check_pipe_setup() have been added to replace all other checking. This standardises all error checking and provides much better coverage. The results is that you will be much less likely to encounter a Python traceback when something is forgotten, and will be told via a RelaxError what is missing.
  • The rdc.back_calc and pcs.back_calc user functions now warn if no data was calculated. This is to inform the user about problems at the place that they occur instead of later on with, for example, the creation of empty data files.
  • Updated the float module to handle numpy floats. This makes the floatToBinaryString() function compatible with the numpy.float16 type.
  • Removed the prune parameter from the backend of the monte_carlo.error_analysis user function. This was a dangerous parameter used to mimic the 'Trim' parameter from the Modelfree4 program. The result is bad statistics. The probable reason for the 'Trim' parameter was the failure of model-free models in the simulations, but this issue was solved using model elimination (see http://www.nmr-relax.com/refs.html#dAuvergneGooley06).
  • Created the Structure.test_read_xyz_strychnine system test to demonstrate a bug in the XYZ parser. This is for the reading of XYZ structure files.
  • Created the lib.text package for text manipulation. The first module will be the text formatting of tables.
  • Created the lib.geometry.lines module for performing geometric operations with lines. This has one stub of a function lib.geometry.lines.closest_point() which will be used to find the closest point on a line to a given point.
  • Added the package checking unit tests for the lib package.
  • Improved the base class unit test for the package __all__ list. Subpackages are now also checked.
  • Blacklisted a number of files in the maths_fns package for the package __all__ list unit test.
  • Added a unit test for the lib.geometry package __all__ list.
  • Created a unit test for the lib.geometry.lines.closest_point() function.
  • Created the lib.text.table module. This originates from the prompt.uf_docstring module as most of that module is functions for creating formatted text tables.
  • Updated the lib package __all__ list for the lib.text package.
  • Implemented the closest_point() and closest_point_ax() functions of lib.geometry.lines. These two functions do the same thing - find the closest point on a line to any given point - but take different arguments to define the line.
  • Improved the package __all__ list base unit test by skipping all hidden files and directories.
  • Refactored the lib.text.table module. The create_table() function is now called format_table() and the table_line() function has been made private. All references to the user function tables and the relax status object have been removed and replaced by arguments to format_table().
  • The prompt.uf_docstring module now uses lib.text.table.format_table(). This significantly simplifies the module.
  • Removed a number of unused imports in prompt.uf_docstring.
  • Deleted prompt.uf_docstring.table_line() as this is now a private function of lib.text.table.
  • Fix for lib.text.table.format_table() as table_line() is now private.
  • Added the spacing argument to lib.text.table.format_table(). This removes the reference to the user function table spacing variable from this function and shifts it to the prompt.uf_docstring.create_table() function.
  • Created the framework for the unit tests of the lib.text package.
  • Created two unit tests for the lib.text.table.format_table() function.
  • Updates to the unit tests of the lib.text.table.format_table() function.
  • Many improvements to the lib.text.table module. The format_table() function now accepts arguments for text to prefix and postfix to each line,the text padding to the left and right inside the table, and the text used to separate the columns. The _blank() and _rule() private functions have been added to create distinct table elements.
  • Created the lib.text.table.MULTI_COL constant for defining cells spanning multiple columns. This is not used yet.
  • Modified the Mf.test_mf_auto_analysis GUI test to catch bug #20603.
  • Created a unit test for the lib.text.table.format_table() function to test multiple column support. Support for content spanning multiple cells is yet to be implemented.
  • Implemented multi-column support in lib.text.table.format_table().
  • Spacing between heading rows is now functional in lib.text.table.format_table().
  • Created a new unit test of lib.text.table.format_table() to check for non-string type data.
  • The table contents are now all converted to strings in lib.text.table.format_table(). This uses the _convert_to_string() private function.
  • Converted the test_format_table4() unit test of lib.text.table.format_table() to check justification. The right justification of cells with numbers will be implemented to match these changes.
  • Numbers are now right justified in cells in the lib.text.table.format_table() function.
  • Modified the test_format_table4() unit test of lib.text.table.format_table(). This change is to test the currently unimplemented custom_format argument. This will be used to allow special formatting in the table. For example using '%.3f' for a float.
  • Implemented the custom_format argument for lib.text.table.format_table(). This allows cell contents to be formatted as the user asks. It defaults to standard string conversion is the custom conversion fails.
  • Rounding error fix for the test_format_table4() unit test of lib.text.table.format_table().
  • Python 3 fix for the test_format_table4() unit test of lib.text.table.format_table(). The string representation of the builtin list object is different in Python 2 vs. 3.
  • Created the test_format_table5() unit test for lib.text.table.format_table(). This test checks what happens if no header is given to format_table(). This currently fails.
  • The lib.text.table.format_table() function can now create a table without headers.
  • Added column number checks for the data input into lib.text.table.format_table().
  • Created the test_format_table6() unit test for lib.text.table.format_table(). This test shows a problem with more than one multi-column cells defined, as well as problems when a multi-column cell is wider than the sum of the widths of the columns it spans.
  • Fix for lib.text.table.format_table() when more than one multi-column cell per row is encountered. The algorithm for determining the total width of the multi-column cell in _table_line() was not checking if the end of the span was being reached.
  • The lib.text.table.format_table() function now handles overfull multi-column cells. The _determine_widths() private function has been created to better handle the determination of the table column widths. It will now extend the width of the last column to allow overfull multi-column cells to fit.
  • Modified the test_format_table5() unit test of lib.text.table.format_table() to check bool types.
  • The lib.text.table.format_table() function now handles boolean types.
  • Booleans are not numbers, so do not right justify them in lib.text.table.format_table().
  • The minfx.__version__ value is now read for the version in the relax information printout.
  • The bmrblib.__version__ value is now read for the version in the relax information printout.
  • All of the specific API data and error returning common methods can now handle missing data/errors. This affects the _return_data_relax_data() and _return_value_general() methods.
  • Updated the release checklist to include information about updating the FSF directory.
  • Modified the release checklist document to use the stable release tags of minfx and bmrblib. This is instead of the code in trunk which may not always be in a stable state.
  • Redesign of the generic_fns.mol_res_spin.generate_spin_id() function. The function now tries to generate a unique ID based on the spin information in the specified data pipe. This is to attempt to fix a bug uncovered by the Structure.test_read_xyz_internal2 system test. Defaulting in all cases to the spin name rather than spin number will often fail for a small organic molecule, as the name in XYZ files is the atomic symbol and hence will almost never be unique.
  • Created the generic_fns.mol_res_spin.return_molecule_by_name() function. This will be used in the future as it is much faster than generic_fns.mol_res_spin.return_molecule()if the molecule name is already known.
  • Missing import affecting the generic_fns.interatomic.create_interatom() function.
  • Reverted the last revision (r18737) as it was not correct and RelaxErrors should be used instead. The command used was:svn merge -r18737:18736 .
  • Fix for the generic_fns.interatomic.create_interatom() function. RelaxNoSpinWarning has been replaced with RelaxNoSpinError.
  • Fixes for the metadata update of the residue and spin name and number counts.
  • Created the generic_fns.mol_res_spin.generate_spin_id_unique() function. This will return a truly unique spin ID string based on the current molecule, residue, and spin data structure.
  • The spin_loop() function now uses generate_spin_id_unique() when the return_id flag is set. This ensures that the caller received a unique spin ID which can be used to retrieve the corresponding spin container.
  • Improved the generic_fns.mol_res_spin.generate_spin_id_unique() function. This can now work with molecule, residue, and spin names and numbers alternatively to the containers supplied as arguments. For this to work, the return_molecule_by_name() function has been improved and the functions return_residue_by_info() and return_spin_by_info() have been added.
  • The pcs.read user function backend now uses generic_fns.mol_res_spin.generate_spin_id_unique(). This allows the matching spin container to always be returned for storing the data.
  • Large speed ups of the Bmrb system tests by the deletion of most of the residues. On one system, this cuts the time for all 3 Bmrb tests from 70 to ~12 seconds.
  • Added the profile flag keyword argument to the relax startup script for Unix-like systems. This is to simplify the switching on of profiling.
  • Large cleanup and bugfixes for the molecule, residue, and spin data structure metadata maintenance. The bugs fixed are important for non-protein molecules. For example is the spin name is not unique per residue, or per molecule if no residues are defined, many parts of relax would fail. All of the metadata_*() and spin_id_variants*() functions have been redesigned. It was also identified that metadata_prune() was being used by different parts of relax for two different purposes - the removal or pruning of metadata prior to the deletion of a data structure and the clean up of no longer valid metadata. These two goals conflicted resulting in unpredictable behaviour. Therefore the new metadata_cleanup() and spin_id_variants_cleanup() functions have been created and the two behaviours separated.
  • Fix for the bmrb.read user function for the recent molecule, residue and spin metadata improvements. The generic_fns.bmrb.generate_sequence() function now calls generic_fns.mol_res_spin.metadata_clean()to be sure that the metadata is correct. The problem is the structure of the BMRB file with no spin information in the entity record, hence the residues are created first and the spins much later in generate_sequence().
  • Removed unused imports in the generic_fns.rdc module.
  • The generic_fns.mol_res_spin.generate_spin_id_unique() function now handles missing spin containers. Previously if this function was used to generate a spin ID string of a spin not in the data store,it would fail. Now it generates an ID by defaulting to generate_spin_id().
  • Converted many calls to generic_fns.mol_res_spin.generate_spin_id() to generate_spin_id_unique(). This will allow many future bugs to be avoided, as the spin ID string is most often used to retrieve spin containers. By using the generate_spin_id_unique() function, the returning of spin containers will always be correct.
  • Created the Mf.test_bug_20563_missing_ri_error system test to catch bug #20563. The data added to the test suite is a highly truncated data set of a analysis completed using the data attached to the bug report.
  • Modified the dauvergne_protocol model-free auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] to aid in debugging. The write_results_dir argument has been added to allow the test suite to read from one directory in test suite shared data directories and redirect output to a temporary directory.
  • The files from the Mf.test_bug_20563_missing_ri_error system test are now placed in a temporary directory. This is essential for the test suite to prevent files from going everywhere.
  • The frq.set user function units argument is no longer read-only. This is needed for some of the GUI tests in the frame_order_testing branch.


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(12 February 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.2


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