relax Changelog

What's new in relax 4.1.2

Apr 26, 2019

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, R1?, 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.

New in relax 4.1.0 (Feb 20, 2019)

New in relax 4.0.3 (Oct 31, 2016)

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) = Iinf - I0 * exp(-R1 * t) whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).

New in relax 4.0.2 (May 21, 2016)

Features:
Addition of the new user functions system.cd and system.pwd to allow the working directory to be changed and displayed.
Addition of the structure.delete_ss user function to remove the helix and sheet information from the internal structural object.
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.
Bugfixes:
Fix for bug #24218, the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified. The logic for the labels was expanded from being only for all tensors to handling subsets.
Bug fix for the structure.read_pdb user function bug #24300, when the merge flag is True, and both multiple structures and multiple models are present, the structure.read_pdb user function would fail with a RelaxError. The problem was that the molecule index was simply not being updated correctly.
Fix for bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta. To handle the missing data, the peak intensity keys are now checked for in the spin container peak_intensities data structure. This is both for the R2eff model optimisation as well as the data back-calculation. A warning is given when the key is missing. The relaxation dispersion base_data_loop() method has been modified to now yield the spin ID string, as this is used in the warnings. In addition, the Grace plotting code in the relax library was also modified. When peak intensity keys are missing, some of the Grace plots will have no data. The code will now generate a plot for that data set, but detect the missing data and allow an empty plot to be created.

New in relax 4.0.1 (Dec 15, 2015)

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.
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.
Bug fixes:
Replicated titles in the HTML version of the relax manual, and hence replicated HTML file names overwriting earlier sections, have been eliminated.
Fix for bug #23933, the "NameError: global name 'ids' is not defined" problem when loading relaxation data. The bug was introduced back in November 2014, and is due to some incomplete error handling code. The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not been specified. Now the correct RelaxMultiSpinIDError is raised. The ids variable did not exist - it was code that was planned to be added, but never was and was forgotten.
Fix for the CSA constant equation in the model-free chapter of the manual. This was spotted by Christina Möller and reported on the relax-users mailing list.
Bug fix for the storage of the XML structural object in the state and results files. Previously any objects added to cdp.structure (or any structure object) would not be saved by the structural object to_xml() method unless the function is explicitly modified to store that object. Now all objects present will be converted to XML.
Fix for the relaxation dispersion analysis in the GUI, as caught by the Relax_disp.test_paul_schanda_nov_2015 GUI test. When loading from a script state file, the value of None can be present. This is now set to the standard values.
Fix for running relax at a server with no graphical display and using matplotlib. The error was found with the Relax_disp.test_repeat_cpmg system test. And the error generated was: QXcbConnection: Could not connect to display. Aborted (core dumped). The backend of matplotlib has to be changed.
Modified the behaviour of the bmrb.write user function backend for a model-free analysis (fix for bug #24131). This is in the bmrb_write() method of the model-free analysis API. Deselected spins are now skipped and a check has been added to be sure that spin data has been assembled.
Another fix for bug #24131, the BMRB export failure when the SpinContainer object has no S2 attribute. Now no data is stored in the BMRB file if a model-free model has not been set up for the spin. This allows the test suite to pass.
Bug fix to allow the Mf.test_bug_24131_missing_interaction system test to pass. This is part of bug #24131, the BMRB export failure with the SpinContainer object having no S2 value. The problem was when assembling the diffusion tensor data. The spin_loop() function was being called, as the diffusion tensor is reported for all residues. Therefore the skip_desel=True has been added to match the model-free part.

New in relax 4.0.0 (Oct 15, 2015)

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 an

New in relax 3.3.9 (Oct 5, 2015)

Changes:
Wrote a method to store parameter data and dispersion curves, for the protocol of repeated CPMG analysis. This is to prepare for analysis in other programs. The method loops through the data pipes, and writes the data out. It then writes a bash script that will concatenate the data in an matrix array style, for reading and processing in other programs. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Added to write out a collection script for ?2 and rate parameters. Task #7826: Write an Python class for the repeated analysis of dispersion data.
In the collection bash script, removes spins which have not been fitted. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Fix for use of " instead of ' in bash script. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Adding option to minimise class function, to perform Monte Carlo error analysis. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Printout when minimising Monte Carlo simulations. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Added additional test to system test Relax_disp.test_bug_23186_cluster_error_calc_dw() to prove that Bug #23619 is invalid. Bug #23619: Stored chi2 sim values from Monte Carlo simulations does not equal normal chi2 values.
Small fix for the shell script to collect data files, and not use the program "column" in the end. The line width becomes to large to handle for column. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Added a unit test that triggers the bug. Test added in test_delete_spin_all, and can be accessed with: relax -u _pipe_control.test_spin. Bug #23642: When deleting all spins for a residue, an empty placeholder is where select=True.
Added sample data and analysis script, that will eventually show that there is not much difference in the sample statistics used for comparing the output of two very similar datasets. This is a multiple comparison test with many T-tests at once, where the familywise error is controlled by the Holm method. Even if the values are close to equal, and within the standard deviation, this procedure will reject up to 20% of the null hypothesis. This is not deemed as a suitable method. Bug #23644: monte_carlo.error_analysis() does not update the mean value/expectation value from simulations.
Added Monte Carlo simulations to the N_state_model.test_absolute_T system test. This is to demonstrate a failure of the simulations in certain N-state model setups.
Added a missing call to monte_carlo.initial_values in the N_state_model.test_absolute_T system test. This fixes the N_state_model.test_absolute_T system test, showing that there is not a problem with the Monte Carlo simulations.
Added Monte Carlo and Bootstrap simulation support for the RDC and PCS Q factor calculations. The pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions have been modified to support Monte Carlo and Bootstrap simulations. The sim_index argument has been added to allow the Q factor for the given simulation number to be calculated. All of the Q factor data structures in the base data pipe now have *_sim equivalents for permanently storing the simulation values. For the simulation values, all the warnings have been silenced.
Added simulation support for the RDC and PCS Q factors in the N-state model analysis. This is for both Monte Carlo and Bootstrap simulation. The simulation RDC and PCS values, as well as the simulation back calculated values are now stored via the minimise_bc_data() function of specific_analyses.n_state_model.optimisation in the respective spin or interatomic data containers. The analysis specific API methods now send the sim_index value into minimise_bc_data(), as well as the pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions.
Silenced a warning in the N-state model optimisation if the verbosity is set to zero. This removes a repetitive warning from the Monte Carlo or Bootstrap simulations.
Huge speed up for the Monte Carlo simulations in the N-state model analyses. This speed up is also for Bootstrap simulations and the frame order analysis. The change affects the monte_carlo.initial_values user function. The alignment tensor _update_object() method was very inefficient when updating the Monte Carlo simulation data structures. For each simulation, each of the alignment tensor data structures were being updated for all simulations. Now only the current simulations is being updated. This speeds up the user function by many orders of magnitude.
Added functions for calculating the geometric mean and standard deviation to the relax library. These are the geometric_mean() and geometric_std() functions of the lib.statistics module. The implementation is designed to be fast, using numpy array arithmetic rather than Python loops.
Created a simple unit test for the new lib.statistics.geometric_mean() function.
Added a unit test for the new lib.statistics.geometric_std() function.
Made a summarize function to compare results. Task #7826: Write an Python class for the repeated analysis of dispersion data.
Bug fixes:
Fix committed, where an empty spin placeholder has the select flag set to False. Bug #23642: When deleting all spins for a residue, an empty placeholder is where select=True

New in relax 3.3.8 (Apr 2, 2015)

New in relax 3.3.7 (Mar 14, 2015)

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 (2Da^2(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:
Created the N_state_model.test_statistics system test. This system test will be used to implement the new statistics user function class consisting of the structure.model and structure.aic user functions for calculating and storing the [chi2, n, k] parameters and Akaike's Information Criterion statistic respectively.
Added the structure.align user function to the renaming translation table. This is so relax identifies structure.align user functions in scripts to raise an error saying that the structure.superimpose user function should be used instead.
Added the office-chart-pie set of Oxygen icons for use in the new statistics user function class.
Created the empty statistics user function class. This adds the infrastructure for creating the statistics user functions.
Small fix for the structure.add_model user function description.
Created the frontend for the statistics.model user function.
Created a wizard graphic for the statistics user functions. This is based on a number of Oxygen icons, as labelled in the SVG layer names.
The statistics.model user function now uses the new statistics wizard graphic.
Created the empty pipe_control.statistics module. This will be used for the backend of all of the statistics user functions.
Fixes for the EPS versions of some Oxygen icons used in the relax manual. This is the actions.document-preview-archive and actions.office-chart-pie Oxygen icons used for the user function icons. The files were not created correctly in the Gimp. The export to EPS requires the width and height to be both set to 6 mm, and the X and Y offsets to zero. This allows the icon bounding boxes and sizes to match the other EPS icons.
Implemented the backend of the statistics.model user function. The implementation heavily uses the specific analysis API, calling the calculate(), model_loop(), print_model_title(), model_statistics() and get_model_container() methods to do all of the work. The last of these API methods is yet to be implemented.
Fix for the statistics.model user function backend. The API methods are now called with the model_info argument set to a keyword argument so that it is always passed in as the correct argument.
Fix for the specific analysis API _print_model_title_global() common method. This method was horribly broken, as it was never used. The new statistics.model user function together with the N-state model uncovers this breakage.
Defined the get_model_container() specific analysis API method. This base method raises a RelaxImplementError, therefore each analysis type must implement its own method (or use an API common method).
Implemented the specific analysis API _get_model_container_cdp() commmon method. This is to be used for the get_model_container() for returning the current data pipe object as the model container. This is for the global models where the model information is stored in the pipe object rather than in spin containers.
The N-state model now uses the _get_model_container_cdp() method. This is aliased as the get_model_container() specific analysis API method.
Fix for the N_state_model.test_statistics system test - the probabilities were missing from k.
Expanded the printouts from the statistics.model user function to include the statistics.
Updated the N-state model num_data_points() function to use more modern integer incrementation.
Fix for the N_state_model.test_statistics system test. The deselected spins and interatomic data containers are now taken into account for the RDC and PCS data point counts.
Implementation of the statistics.aic user function. This is very similar to the statistics.model user function - the code was copied and only slightly modified. The new user function will calculate the current chi-squared value per model, obtain the model statistics, calculate the AIC value per model, and store the AIC value, chi-squared value and number of parameters in the appropriate location for the model in the relax data store.
Created the empty lib.plotting.veusz module for graphing using Veusz.
Shifted the lib.software.grace module to lib.plotting.grace. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7532 and http://thread.gmane.org/gmane.science.nmr.relax.devel/7536.
Created XY-data functions for the plotting API of the relax library. These are currently copies of the heads of the lib.plotting.grace functions write_xy_data() and write_xy_header(). These lib.plotting.api functions (write_xy_data() and write_xy_header()) are set up to use the grace functions.
Converted all of the Grace plotting in relax to use the plotting API of the relax library.
Shifted the pipe_control.grace.write() function. This is now the format independent pipe_control.plotting.write_xy() function. The format argument has been added and this defaults to 'grace'. The grace.write user function has been updated to use the new backend.
Updated the pcs.structural_noise user function to use the relax library plotting API.
Fixes for the new pipe_control.plotting.write_xy() function. This includes missing imports which should have moved from pipe_control.grace, as well as shifting the axis_setup() function from the pipe_control.grace module into the pipe_control.plotting module.
The rdc.corr_plot user function backend now uses the relax library plotting API. The write_xy_data() and write_xy_header() functions from lib.plotting.api are now uses instead of the equivalent pipe_control.grace functions which no longer exist.
More import fixes for the new pipe_control.plotting.write_xy() function.
Fix for the backend of the relax_disp.plot_disp_curves user function. The lib.plotting.api functions write_xy_data() and write_xy_header() require the format argument.
Updated the relative stereochemistry auto-analysis to use the relax library plotting API.
Huge speed up for the assembly of atomic coordinates from a large number of structures. The internal structural object validate_models() method was being called once for each structure when assembling the atomic coordinates. This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times. The problem was in lib.structure.internal.coordinates.assemble_atomic_coordinates(), in that the one_letter_codes() method, which calls validate_models(), was called for each molecule encountered. The solution was not to validate models in one_letter_codes().
Huge speed up of the internal structural object validate_models() method. The string formatting to create pseudo-PDB records and the large number of calls to the _translate() method for atomic information string formatting has been shifted to only be called when atomic information does not match. Instead the structural information is directly compared within a large if-else statement.
Created the Structure.test_atomic_fluctuations_no_match system test. This demonstrates a failure in the operation of the structure.atomic_fluctuations user function when the supplied atom ID matches no atoms.
Fix for the Structure.test_atomic_fluctuations_no_match system test. The structure.atomic_fluctuations user function will now raise a RelaxError when no data corresponding to the atom ID can be found, so the test now checks for this.
Created the unit test infrastructure for the lib.structure.internal.object module.
Created the Test_object.test_add_atom_sort unit test. This is from the _lib._structure._internal.test_object unit test module. The test will be used to implement the sorting of input data by residue number in the add_atom() internal structural object method. This will mean that added atoms will be placed in residue sequence order, so that output PDB files are correctly ordered.
Implementation of methods for sorting sequence data in the internal structural object. The information is sorted in the molecule container level using the new MolContainer._sort() private method. This uses the _sort_key() helper method which determines what the new order should be. This is used as the 'key' argument for the Python sort() method. Instead of list shuffling, new lists in the correct order are created. Although not memory efficient, this might be faster than shuffling.
The loading of structural data now sorts the data if the merge flag is True. The pack_structs() method for sorting the data will now call the new MolContainer._sort() function is the data is being merged. This is to ensure that the final structural data is correctly ordered.
Fixes for a number of Structure system tests for the sorted structural data changes.
Modified the structure.read_pdb user function backend to skip water molecules. All residues with the name 'HOH' are now skipped when loading PDB files. This is implemented in the MolContainer.fill_object_from_pdb() method, and a RelaxWarning is printed listing the residue numbers of all skipped waters.
Modified the Structure.test_read_pdb_1UBQ system test for the new water skipping feature. As the structure.read_pdb user function will now skip waters, the last atom in the structural object will now be the last ubiquitin atom and not the last water atom.
Modified the Test_object.test_add_atom_sort unit test to check atom connectivities. This is from the _lib._structure._internal.test_object unit test module. The problem is that the MolContainer._sort() method for sorting the structural data currently does not correctly update the bonded data structure.
Completed the implementation of the sorting of structural data in the internal structural object. The MolContainer._sort() private method now changes the connect atom indices in the bonded data structure to the new sorted indices.
Created new system tests for implementing new functionality for the structure.mean user function. This includes the Structure.test_mean_models and Structure.test_mean_molecules. The idea is to convert the user function to the new pipes/models/molecules/atom_id design. This will allow molecules with non-identical sequences and atomic compositions to be averaged. The set_mol_name and set_model_num arguments from the structure.read_pdb, structure.read_gaussian, and structure.read_xyz user functions will also be implemented to allow the mean structure to be stored alongside the other molecules.
Some fixes for the checks in the Structure.test_mean_molecules system test.
Fix for the structure.mean user function call in the Structure.test_mean_models system test.
Expanded the checking in all the Structure.test_mean* system tests to cover all atomic information. This includes the Structure.test_mean, Structure.test_mean_models, and Structure.test_mean_molecules system tests. All structural data is now carefully checked to make sure that the structure.mean user function operates correctly.
Converted the structure.mean user function to the new pipe/model/molecule/atom_id design. This allows the average structure calculation to work on atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend uses the new pipe_control.structure.main.assemble_structural_coordinates() function to assemble the common atom coordinates, molecule names, residue names, residue numbers, atom names and elements. All this information is then used to construct a new molecule container for storing the average structure in the internal structural object. To allow for the averaged structural data to be stored, the internal structural object method add_coordinates() has been created. This is modelled on the PDB, Gaussian, and XYZ format loading methods. The internal structural object mean() method is no longer used, but remains for anyone who might have interest in the future (though as it is untested, bit-rot will be a problem).
Small correction for the structure.read_pdb user function description.
Created the Structure.test_read_merge_simultaneous system test. This is to demonstrate a failure in the structure.read_pdb user function when merging multiple molecules from one file into one molecule simultaneously with a single user function call.
Added some error checking for the monte_carlo.setup user function. A RelaxError is now raised if the number of simulations is less than 3. This prevents Python errors when later calling the monte_carlo.error_analysis user function.
Test suite fixes for the error checking in the monte_carlo.setup user function. The number of simulations has been increased from either 1 or 2 in all tests to the minimal number of simulations (3).
Created the Structure.test_bug_23293_missing_hetatm system test. This is to catch bug #23293, the PDB HETATM loading error whereby the last HETATM record is sometimes not read from the PDB file.
Small fix for the chain IDs in the Structure.test_bug_23293_missing_hetatm system test.
Created the Structure.test_multi_model_and_multi_molecule system test. This is used to check the loading and writing of a multi-model and multi-molecule PDB file. The test shows that this functions correctly.
Modified the Structure.test_multi_model_and_multi_molecule test to check for model consistency. This is just for better test suite coverage of the handling of PDB structural data.
Created the Structure.test_bug_23294_multi_mol_automerge system test. This is used to catch bug #2329, the automatic merging of PDB molecules resulting in an IndexError. It reads in the 'in.pdb' PDB file attached to the bug report, now named 'bug_23294_multi_mol_automerge.pdb', to show the IndexError. The test also checks the structure.write_pdb user function to make sure that the output PDB file contains a single merged molecule.
Added the PDB file to the repository for the Structure.test_bug_23294_multi_mol_automerge system test.
Fix for the Structure.test_bug_23294_multi_mol_automerge system test. The MASTER PDB record has been added to the data to check for, as this will be produced by the structure.write_pdb user function.
Improved the RelaxWarning for missing atom numbers in the PDB CONECT records. This is for the structure.read_pdb user function. Now only one warning is given for the entire PDB file listing all of the missing atom numbers rather than one warning per missing atom. This can significantly compact the warnings, removing a lot of repetition.
Improved the quality of the printouts from the structure.read_pdb user function. This also affects the structure.read_gaussian and structure.read_xyz user functions. The messages about adding new molecules or merging with existing molecules has been significantly improved. The text with the model information is now only printed if the model number is present in the PDB file or has been supplied by the user.
Fixes for all of the PDB documentation HTML links in the docstrings. The PDB have shifted their documentation from http://www.wwpdb.org/documentation/format33/v3.3.html to http://www.wwpdb.org/documentation/file-format/format33/v3.3.html, stupidly without redirects. This will create dead links in the relax API documentation at http://www.nmr-relax.com/api/3.3/, as well as the older API documentation (http://www.nmr-relax.com/api/2.2/, http://www.nmr-relax.com/api/3.0/, http://www.nmr-relax.com/api/3.1/, http://www.nmr-relax.com/api/3.2/).
Created the Structure.test_bug_23295_ss_metadata_merge system test. This is to catch bug #23295, the PDB secondary structure HELIX and SHEET records not updated when merging molecules. This uses the '2BE6_secondary_structure.pdb' structure file and 'test.py' relax script contents as the test, checking the HELIX and SHEET records.
Added one more check to the Structure.test_bug_23295_ss_metadata_merge system test. The test would pass if no HELIX or SHEET records were to be written to the PDB file.
Fix for the Structure.test_bug_23295_ss_metadata_merge system test and additional printouts.
Fix for the Structure.test_pdb_combined_secondary_structure system test. The SHEET PDB record check was incorrect and was checking for the improperly formatted atom name field, which has now been fixed in relax.
Large speed up of the structure.web_of_motion user function. With the introduction of the _sort() internal structural object method and it being called by the add_atom(), the structure.web_of_motion user function was now painfully slow. As sorting the structural data is unnecessary for the backend of this user function, the add_atom() boolean argument 'sort' has been added to turn the sorting on and off, and the structure.web_of_motion backend now sets this to False.
Fix for the internal structural object unit test Test_object.test_add_atom_sort. This test of the _lib._structure._internal.test_object unit test module now requires the sort argument set to True when calling the add_atom() method.
Improvement for a RelaxError message when assembling structural data but no coordinates can be found.
Created a series of unit tests for implementing a new internal structural object feature. These tests check a new 'inv' argument for the selection() structural object method for allowing all atoms not matching the atom ID string to be selected.
Implemented the new 'inv' argument for the selection() structural object method. This allows for all atoms not matching the atom ID string to be selected. The unit tests for this argument now all pass, validating the implementation.
Improvement for the structure.mean user function. This can now be used to store an averaged structure in an empty data pipe. Previously structural data needed to be present in the current data pipe for the user function to work.
Created a system test to show a limitation of the rdc.copy user function. Currently, it cannot work when spin systems in two data pipes are different. The system test will be used to implement the support.
Simplification of the new Rdc.test_rdc_copy_different_spins system test. This no longer tests the deletion of interatomic data containers by the spin.delete user function, something which is not implemented.
Some more fixes for the Rdc.test_rdc_copy_different_spins system test. The residue.delete and not spin.delete user function is required to delete the sequence data.
Another small fix for the new Rdc.test_rdc_copy_different_spins system test. The rdc.copy user function requires the pipe_to argument to be supplied in this case.
Expansion of the Rdc.test_rdc_copy_different_spins system test. The interatomic data containers are now defined via the interatom.define user function, which requires the spin.element user function to set up the element information. A printout has also been added to demonstrate a failure in the pipe_control.interatomic.interatomic_loop() function in handling the correct data pipe.
Some more modifications for the Rdc.test_rdc_copy_different_spins system test. One of the interatomic data containers does not have RDC data, as it is not present in the original data pipe, hence this is checked for. And the printouts have more formatting.
Expanded the functionality of the rdc.copy user function. The user function will now operate on two data pipes with different spin sequences. If the interatomic data container is missing from the target data pipe, a warning is given. And if the interatomic data container is not present in the source data pipe, nothing will be copied.
Modified the rdc.copy user function to printout all copied RDC values and errors.
Created the Rdc.test_rdc_copy_back_calc system test. This will be used to implement the back_calc Boolean argument for the rdc.copy user function to allow not only measured, but also back-calculated RDC values to be copied.
Modified the rdc.copy printout of RDCs to occur for each alignment ID.
Implemented the back_calc argument for the rdc.copy user function. This allows the back-calculated RDCs to be additionally copied together with the real value and error.
Small formatting change for the rdc.copy user function printouts.
Created the Pcs.test_pcs_copy_different_spins system test. This will be used to show a limitation of the pcs.copy user function in that it cannot copy data between two data pipes with different molecule, residue, and spin sequences.
Added a printout of the alignment ID for the pcs.copy user function. This is to match the rdc.copy user function.
Created the Pcs.test_pcs_copy_back_calc system test. This will be used to implement the back_calc Boolean argument for the pcs.copy user function to allow not only measured, but also back-calculated PCS values to be copied. It matches the equivalent Rdc.test_rdc_copy_back_calc system test.
Implemented the back_calc argument for the pcs.copy user function. This allows the back-calculated PCSs to be additionally copied together with the real value and error. The implementation simply copies that of the rdc.copy user function.
Added full per-alignment data printouts to the pcs.copy user function to match rdc.copy. The feedback is important to know what was actually copied.
Modified the pcs.copy user function to handle different spin sequence between data pipes.
Fixes for the Pcs.test_pcs_copy_different_spins and Pcs.test_pcs_copy_back_calc system tests.
Fix for the pcs.copy user function for a recently introduced problem. The data pipe for the spin_loop() function must be supplied.
The pcs.copy user function now skips deselected spins.
Modified the N_state_model.test_data_copying system test to skip deselected spins.
Added more checks to the three Pcs.test_pcs_copy* system tests.
Added more checks to the three Rdc.test_rdc_copy* system tests.
Created the Rdc.test_calc_q_factors_no_tensor system test. This is to demonstrate a failure in the rdc.calc_q_factors user function when no alignment tensor is present. In addition, the test is also triggering an earlier problem of spin isotope information being missing. However the isotope is not required if the tensor is absent.
The Rdc.test_rdc_copy_* system tests now check for the 'rdc_data_types' data structure. This is in the Rdc.test_rdc_copy_different_spins and Rdc.test_rdc_copy_back_calc system tests and shows that the rdc.copy user function fails to duplicate this information.
The Rdc.test_rdc_copy_* system tests now check for the 'absolute_rdc' data structure. This is in the Rdc.test_rdc_copy_different_spins and Rdc.test_rdc_copy_back_calc system tests and shows that the rdc.copy user function fails to duplicate this information as well.
Expanded the rdc.copy user function to copy the RDC data type and absolute RDC flag information.
Created the Rdc.test_corr_plot system test to check the rdc.corr_plot user function. This shows that this poorly tested function works correctly.
Created the Pcs.test_corr_plot system test to check the pcs.corr_plot user function. This user function is poorly tested, and this test triggers a series of bugs.
Added the 'title' and 'subtitle' arguments to the pcs.corr_plot user function. This problem was detected by the new Pcs.test_corr_plot system test. The pcs.corr_plot user function now matches the rdc.corr_plot user function in terms of arguments.
Completed the Pcs.test_corr_plot system test. The file contents are now known and have been carefully checking in Grace.
Clarification of the RDC and PCS Q factors. This affects the rdc.calc_q_factors and pcs.calc_q_factors user functions, as well as all other operations involving the calculation of Q factors. The printouts have been modified to clarify if the normalisation is via the tensor size (2Da^2(4 + 3R)/5) or via the sum of data squared, and the separation of the two is now clearer. This allows for better RDC vs. PCS comparisons. In addition, the data pipe variable names have been updated to reflect the normalisation, so it is instantly known when looking at the XML contents of results or save files which was used. The backwards compatibility hooks have been modified to support the data pipe variable name changes.
The align_tensor.copy user function 'tensor_from' argument can now be None. This is to enable the copying of all alignment tensors from one data pipe to another.
Created the Align_tensor.test_copy_pipes system test. This is to show a problem in the align_tensor.copy user function when copying all tensors between data pipes.
Modified the pipe_control.align_tensor.align_data_exists() function to handle no tensor IDs. If no tensor ID is supplied, this will then return True if any alignment data exists.
Improvement for the align_tensor.copy user function. The user function has been modified to allow all alignment tensors to be copied between two data pipes. This allows the Align_tensor.test_copy_pipes system test to pass.
Fixes for the align_tensor.copy user function argument unit tests. The tensor_from and tensor_to arguments can now be None.
Created the Align_tensor.test_copy_pipes_sims system test. This demonstrates a failure of the align_tensor.copy user function when Monte Carlo simulated tensors are present.
Deleted the data_store.align_tensor.AlignTensorSimList.append() method. This replacement list method was proving fatal when copy.deepcopy() is called on the alignment tensor object. The change allows the Align_tensor.test_copy_pipes_sims system test to pass.
Huge speed up for loading results and state files with Monte Carlo simulation alignment tensors. The reading of the alignment tensor component of XML formatted results and state files has been modified. Previously the data_store.align_tensor.AlignTensorData._update_object() method for updating the alignment tensor object (for values, errors, simulations) was being called once for each Monte Carlo simulation. Now is it called only once for all simulations. In one test, the reading of the save file with 500 simulations dropped from 253.7 to 10.0 seconds.
Added an extra check for the assembly of RDC data. This is in the pipe_control.rdc.return_rdc_data() function and the check is for any unit vectors set to None, which is a fatal condition.
Improved the RelaxError message from the RDC assembly function when unit vectors are None.
Added a new warning to the interatom.unit_vectors user function if data is missing. This is to aid in detecting problems earlier before unit vectors of None are encountered by other parts of relax.
Modified the rdc.corr_plot user function to skip deselected interatomic data containers. This would normally happen as no back-calculated data is normally present. However, if data has been copied from elsewhere, this may not always be the case.
Created the Sequence.test_bug_23372_read_csv system test. This is to catch bug #23372, the sequence.read failure with CSV files. It uses a truncated version of the CSV data file attached to sr #3219.
Converted the lib.sequence.validate_sequence() to the checking function design. This is the checking function design documented at http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions. The validate_sequence() function has been renamed to check_sequence_func() and the checking object is called check_sequence. It removes the string processing hack to convert RelaxErrors to RelaxWarnings in the lib.sequence.read_spin_data() function, avoiding strange messages such at "RelaxWarning: ror: The sequence data in the line..." as seen in the Sequence.test_bug_23372_read_csv system test.
Small typo fix for the Sequence.test_bug_23372_read_csv system test.
Added the raise_flag argument to the lib.sequence.read_spin_data() function. This is to allow the missing data RelaxError to be deactivated.
Modified the spectrum.read_intensities user function backend to be more robust. This affects the generic formatted peak lists, via the lib.spectrum.peak_list.intensity_generic() function. The peak list reading will now continue reading the file after corrupted lines have been encountered.
Python 3 improvement for the rdc.corr_plot and pcs.corr_plot user functions. The world view is now set in floating point numbers. In Python 2, the math.ceil() and math.floor() functions return floats, whereas in Python 3 these functions return integers. The behaviour is now consistent in both Python versions, fixing a few system tests.
Modified the internal formatting of the data section of the Grace 2D graph files. This affects the lib.plotting.grace.write_xy_data() function. The formatting is now more consistent, with the X value now set to a fixed number of decimal places, and hence will no longer change between Python 2 and 3. The data is now all right justified as well, for easier reading. All affected system tests have been updated for the new format.
Epydoc documentation fix for the lib.structure.pdb_write._handle_atom_name() function.
Bugfixes:
Big bug fix for the N-state model num_data_points() function. This is from the specific_analyses.n_state_model.data module. This code was very much out of date. It was expecting an ancient behaviour where the spin container 'pcs' variable and interatomic data container 'rdc' where lists of floats. However these were converted many years ago to dictionaries with keys set to the alignment IDs. The result was that no RDCs nor PCSs were counted as a base data point, so the function would in most cases return a value of zero.
Fixes for the printout from the pipe_control.pcs.return_pcs_data() function. The number of PCSs printed out was including values of None when data was missing for one alignment. These values of None are no longer counted.
Fixes for the printout from the pipe_control.rdc.return_rdc_data() function. The number of RDCs printed out was including values of None when data was missing for one alignment. These values of None are no longer counted.
More fixes for the RDC and PCS count printouts from the corresponding data assembly functions. Sometimes the RDC or PCS value could be present as None. This is now detected and the count is not incremented.
More fixes for the PCS count printout from the pipe_control.pcs.return_pcs_data() function. The check for None values was incorrect.
Fixes for the N-state model num_data_points() function. The deselected interatomic data containers are no longer used for counting RDC data. And the skipping of deselected spin containers for the PCS is now via the spin_loop() skip_desel argument.
Fix for bug #23259, the broken user functions in the prompt UI with the RelaxError: The user function 'X' has been renamed to 'Y'. The problem was that the only the first part of the user function name, for example 'minimise' from 'minimise.calculate' was being checked in the user function name translation table. As the minimise user function has been renamed to minimise.execute, 'minimise' is in the translation table and hence minimise.calculate was being identified as the minimise user function. Now the full user function name is reconstructed before checking the translation table.
Fixes for the lib.structure.internal.coordinates.assemble_coord_array() function. The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The function can now handle no data being passed in.
Fixes for the pipe_control.structure.main.assemble_structural_coordinates() function. The function will now raise a RelaxError if no structural data matching the atom ID can be found. The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The fix affects the structure.atomic_fluctuations, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose, and structure.web_of_motion user functions.
Fix for bug #23265, the failure of the edit buttons in the user function GUI windows. The problem was that the column titles of the window opened by the edit button were being incorrectly handled if the dimensions of the window were not supplied.
Fix for bug #23288, the failure of the structure.read_pdb user function when simultaneously merging multiple molecules from one file. The set_mol_name and set_model_num arguments are now converted to lists equal to the length of the read_mol and read_model arguments simultaneously, if supplied.
Small fix for the structure.write_pdb user function for handling old relax state and results files.
Fix for bug #23293, the PDB HETATM loading error whereby the last HETATM record is sometimes not read from the PDB file. The problem was two-fold. Firstly the internal structural object _parse_mols_pdb() method for separating a PDB file into distinct molecules was terminating too early when a new molecule is found, so that the last PDB record is not appended to the records list for the molecule. Secondly the write_pdb() method was not handling the PDB sequential serial number correctly.
Fix for bug #23294, the automatic merging of PDB molecules resulting in an IndexError. Now if only a single molecule name is supplied, this will be used for all molecules in the PDB file. The result is that the structural data will all be automatically merged into a single molecule. This merging is communicated to the user via the current printouts.
Bug fix for the SHEET PDB records created by the structure.write_pdb user function. The current and previous atom parts of the record were not being correctly formatted. This was simply using the %4s formatting string. However the PDB atom format is rather more complicated. To handle this, the new _handle_atom_name() helper function has been added to the lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for consistently formatting the atom name field.
Fix for bug #23295, the PDB secondary structure HELIX and SHEET records not updating when merging molecules. The problem was that the algorithm for changing the molecule numbers for the helix and sheet metadata when calling the structure.read_pdb user function was far too simplistic. Therefore the logic has been completely rewritten. Now the helix and sheet metadata are stored in temporary data structures in the _parse_pdb_ss() method. As the molecules are being read from the PDB records, new data structures containing the original molecule numbers and new molecule numbers are created. The helix and sheet metadata is then stored in the internal structural object via the pack_structs() method, and the molecule indices of the metadata changed based on the two molecule number remapping data structures.
Python 3 fix for the new internal structural object MolContainer._sort() method. The list() builtin function is required to convert the output of the range() function into a true list in Python 3, so that the list.sort() method can be accessed.
Python 3 fix for the Test_msa.test_central_star unit test. This is from the _lib._sequence_alignment.test_msa unit test module. The logic of range() + range() does not work in Python 3, so the range function calls are now wrapped in list() function calls to convert to the correct data structure type.
Python 3 fix for the internal structural object MolContainer._sort_key() method. This method is used as the key for the sort() function. However in Python 3, the key cannot be None. So now if the residue number is None, the value of 0 is returned instead.
Python 3 fix for the pipe_control.structure.main.assemble_structural_coordinates() function. This affects most of the structure user functions. This was another case of requiring the list() built in function to create a list object from an iterator.
Another Python 3 list() fix for the structure user functions. This time the problem was in the pipe_control.structure.main.sequence_alignment() function.
Fix for a RelaxError message from the internal structural object when validating models.
Bug fix for the results.write user function when loading relax state files. The results.write user function can load not only the results file consisting of a single data pipe, but also relax state files if only a single pipe is present. However this was causing the current data pipe and other pipe-independent data (sequence alignments and the GUI) to be overwritten, just as when loading a state file. Now only the data from the data pipe will be loaded and the pipe independent data in the state file will be ignored.
Fix for the rdc.write user function. The check for the missing rdc_data_types variable in the interatomic containers is now more comprehensive and checks for the presence of the alignment ID.
Big bug fix for the pipe_control.interatomic.interatomic_loop() function. This was identified in the Rdc.test_rdc_copy_different_spins system test. The problem was that the pipe argument was being ignored when looking up the spin containers. Hence if the pipe being worked on was not the current data pipe, and the spin sequences were not identical, the function would fail. This mainly affects the rdc.copy user function.
Fix for the pcs.read user function. The problem was caught by the new Pcs.test_pcs_copy_different_spins system test. If the spin system does not exist in the current data pipe, but data for it is present in the PCS file, the pcs.read user function would terminate in a TypeError.
Fixes for the rdc.calc_q_factors user function for when no alignment tensor is present. This was caught by the Rdc.test_calc_q_factors_no_tensor system test. Now if no tensor is present, a warning is given and the 2Da^2(4 + 3R)/5 normalised Q factor is skipped. Also, if present but no spin isotope information is present, then RelaxSpinTypeError errors are raised.
Fix for the pcs.corr_plot user function when the spin containers have no element information.
Fix for bug #23372, the sequence.read failure with CSV files. The problem was that the sep argument was not being passed all the way to the backend lib.io.extract_data() function.

New in relax 3.3.6 (Feb 5, 2015)

Changes:
Spelling fixes for the CHANGES document.
Created the Structure.test_align_molecules2 system test. This is to demonstrate a failure condition in the structure.align user function.
Large simplification of the atomic coordinate assembly code in the internal structural object. This is in the lib.structure.internal.coordinates.assemble_coord_array() function. The logic of the function has recently changed due to the introduction of the pairwise sequence alignments. This caused a lot of code to now be redundant, and also incorrect in certain cases. This simplification fixes the problem caught by the Structure.test_align_molecules2 system test.
Fix for the Structure.test_displacement system test - the molecule IDs needed updating.
Created the Structure.test_align_molecules_end_truncation system test. This is to demonstrate a failure of the common residue detection algorithm using multiple pairwise alignments in the backend of the structure.align and other multiple structure based user functions.
Created empty unit test infrastructure for testing the lib.structure.internal.coordinates module.
Created the Test_coordinates.test_common_residues unit test. This is from the _lib._structure._internal.test_coordinates unit test module. The test shows that the lib.structure.internal.coordinates.common_residues() function is working correctly. However the printout, which is not caught by the test, is incorrect.
Modified the lib.structure.internal.coordinates.common_residues() function. It now accepts the seq argument which will caused the gapped sequence strings to be returned. This is to allow for checking in the unit tests.
Created the Test_align_protein.test_align_multiple_from_pairwise unit test. This is in the _lib._sequence_alignment.test_align_protein unit test module. This test checks the operation of the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function, which does not yet exist.
Simplified the Test_coordinates.test_common_residues unit test by removing many residues. This is from the _lib._structure._internal.test_coordinates unit test module.
Expanded the docstring of the Test_align_protein.test_align_multiple_from_pairwise unit test. This is from the _lib._sequence_alignment.test_align_protein unit test module.
Attempt at fixing the lib.structure.internal.coordinates.common_residues() function. This function still does not work correctly.
Renamed the Test_align_protein.test_align_multiple_from_pairwise unit test. This is now the Test_msa.test_central_star unit test of the _lib._sequence_alignment.test_msa unit test module (it was originally in the _lib._sequence_alignment.test_align_protein unit test module). This is in preparation for converting the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function into the lib.sequence_alignment.msa.central_star() function.
Added the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function. This should have been committed earlier. The function is only partly implemented.
Initial lib.sequence_alignment.msa.central_star() function. This was moved from lib.sequence_alignment.align_protein.align_multiple_from_pairwise().
Import fix for the _lib._sequence_alignment.test_align_protein unit test module.
Added the verbosity argument to lib.sequence_alignment.align_protein.align_pairwise(). If set to zero, all printouts are suppressed.
The Needleman-Wunsch sequence alignment algorithm now calculates and returns an alignment score. This is in the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function. The score is calculated as the sum of the Needleman-Wunsch matrix elements along the traceback path.
The protein pairwise sequence alignment function now returns the alignment score. This is in the lib.sequence_alignment.align_protein.align_pairwise() function. The score from the Needleman-Wunsch sequence alignment algorithm is simply passed along.
Fix for the Test_msa.test_central_star unit test. This is from the _lib._sequence_alignment.test_msa unit test module. Some of the real gap matrix indices were incorrect.
Complete implementation of the central star multiple sequence alignment algorithm. This includes all the four major steps - pairwise alignment between all sequence pairs, finding the central sequence, iteratively aligning the sequences to the gapped central sequence, and introducing gaps in previous alignments during the iterative alignment. The correctness of the implementation is verified by the Test_msa.test_central_star unit test of the _lib._sequence_alignment.test_msa module.
Fixes for the unit tests of the _lib._sequence_alignment.test_align_protein module. The Test_align_protein.test_align_pairwise_PAM250 unit test was accidentally duplicated due to a copy and paste error. And the lib.sequence_alignment.align_protein.align_pairwise() function now also returns the alignment score.
Fixes for the unit tests of the _lib._sequence_alignment.test_needleman_wunsch module. The lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function now returns the alignment score.
The assemble_coord_array() function is now using the central star multiple sequence alignment. This is the function from the lib.structure.internal.coordinates module used to assemble common atomic coordinate information, 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. The non-functional lib.structure.internal.coordinates.common_residues() function has been removed as the lib.sequence_alignment.msa.central_star() function performs this functionality correctly.
Deleted the Test_coordinates.test_common_residues unit test. This is from the _lib._structure._internal.test_coordinates unit test module. The lib.structure.internal.coordinates.common_residues() function no longer exists.
Alphabetical ordering of all Structure system tests.
Better printout spacing in lib.sequence_alignment.msa.central_star().
Fixes for the Structure.test_align_molecules_end_truncation system test. This system test had only been partly converted from the old Structure.test_align_molecules2 system test it had been copied from.
Created the Internal_selection.count_atoms() internal structural object selection method. This counts the number of atoms in the current selection.
Added final printouts to the structure.rotate and structure.translate user function backends. This is to give feedback to the user as to how many atoms were translated or rotated, to aid in solving problems with the structure user functions. These backend functions are also used by the structure.align and structure.superimpose user functions.
Corrections for the Structure.test_align_CaM_BLOSUM62 system test. The CaM N and C domains can not be aligned together in a global MSA as they would align very well to themselves, causing the atomic coordinate assembly function to fail.
Improvement for the lib.sequence_alignment.msa.central_star() function. The strings and gap matrix returned by the function have been reordered to match the input sequences.
Modified the Structure.test_align_molecules_end_truncation system test. The calmodulin bound calciums are now deleted prior to the structure.align user function call. This prevents these being labelled as '*' residues and aligning with real amino acids via the central star multiple sequence alignment (MSA) algorithm.
Large speed up of the mol-res-spin selection object. The Selection.contains_mol(), Selection.contains_res() and Selection.contains_spin() methods of the lib.selection module have been redesigned for speed. Instead of setting a number of flags and performing bit operations at the end of the method to return the correct Boolean value, each of the multiple checks now simply returns a Boolean value, avoiding all subsequent checks. The check list order has also been rearranged so that the least expensive checks are to the top and the most time intensive checks are last.
Created the new relax data store object for saving sequence alignments. This is in the new data_store.seq_align module via the Sequence_alignments object, subclassed from RelaxListType, for holding all alignments and the Alignment Element object, subclassed from Element, for holding each individual alignment. The objects are currently unused.
Added the seq_align module to the data_store package __all__ list.
Created the Test_seq_align.test_alignment_addition unit test. This is in the _data_store.test_seq_align unit test module. This tests the setup of the sequence alignment object via the data_store.seq_align.Sequence_alignment.add() method.
Fixes for the data_store.seq_align.Alignment.generate_id() method. These problems were identified by the _data_store.test_seq_align module Test_seq_align.test_alignment_addition unit test.
Added the Test_seq_align.test_find_alignment and Test_seq_align.test_find_missing_alignment unit tests. These are in the _data_store.test_seq_align unit test module. They check the functionality of the currently unimplemented Sequence_alignment.find_alignment() method which will be used to return pre-existing alignments.
Code rearrangement in the _data_store.test_seq_align unit test module. The ID generation has been shifted into the generate_ids() method to be used by multiple tests.
Implemented the data_store.seq_align.Sequence_alignments.find_alignment() method. This will only return an alignment if all alignment input data and alignment settings match exactly.
Shifted the data_store.seq_align.Alignment.generate_id() method into the relax library. It has been converted into the lib.structure.internal.coordinates.generate_id() function to allow for greater reuse.
Created the Sequence.test_align_molecules system test. This will be used to implement the sequence.align user function which will be used for performing sequence alignments on structural data within the relax data store and storing the data in the data pipe independent sequence_alignments data store object (which will be an instance of data_store.seq_align.Sequence_alignments). The system test also checks the XML saving and loading of the ds.sequence_alignments data structure.
Renamed the Sequence.test_align_molecules system test to Structure.test_sequence_alignment_molecules. As the sequence alignment is dependent on the structural data in the relax data store, the user function for sequence alignment would be better named as structure.sequence_alignment. The sequence.align user function is not appropriate as all other sequence user functions relate to the molecule, residue, and spin data structure of each data pipe rather than to the structural data.
Modified the Structure.test_sequence_alignment_molecules system test. Changed and expanded the arguments to the yet to be implemented structure.sequence_alignment user function.
Important formatting improvement for the description in the GUI user function windows. Previously lists, item lists, and prompt items were spaced with one empty line at the top and two at the bottom. The two empty lines at the bottom was an accident caused by how the list text elements were built up. Now the final newline character is stripped so that the top and bottom of the lists only consist of one empty line. The change can give a lot more room in the GUI window.
Created the frontend for the structure.sequence_alignment user function. This is based on the structure.align user function with the 3D superimposition arguments removed and new arguments added for selecting the MSA algorithm and the pairwise alignment algorithm (despite only NW70 being currently implemented).
Modified the assemble_coordinates() function of the pipe_control.structure.main module. The function has been renamed to assemble_structural_objects(). The call to the lib.structure.internal.coordinates.assemble_coord_array() function has also been shifted out of assemble_structural_objects() to simplify the logic and decrease the amount of arguments passed around.
Spun out the atomic assembly code of the assemble_coord_array() function. The code from the lib.structure.internal.coordinates.assemble_coord_array() function has been shifted to the new assemble_atomic_coordinates(). This is to simplify assemble_coord_array() as well as to isolate the individual functionality for reuse.
Implemented the backend of the structure.sequence_alignment user function. This checks some of the input parameters, assembles the structural objects then the atomic coordinate information, performs the multiple sequence alignment, and then stores the results.
Fixes for the sequence alignment objects for the relax data store. The Sequence_alignments(RelaxListType) and Alignment(Element) classes were not being set up correctly. The container names and descriptions were missing.
The data store ds.sequence_alignment object is now being treated as special and is blacklisted. The object is now explicitly recreated in the data store from_xml() method.
Fixes for handling the sequence_alignments data store object.
Implemented the data store Sequence_alignments.from_xml() method. This method is required for being able to read RelaxListType objects from the XML file.
Modified the data returned by lib.structure.internal.coordinates.assemble_atomic_coordinates(). The function will now assemble simple lists of object IDs, model numbers and molecule names with each list element corresponding to a different structural model. This will be very useful for converting from the complicated pipes, models, and molecules user function arguments into relax data store independent flat lists.
Updates for the structure.sequence_alignment user function. This is for the changes to the lib.structure.internal.coordinates.assemble_atomic_coordinates() function return values. The new object ID, model, and molecule flat lists are used directly for storing the alignment results in the relax data store.
Updates for the Structure.test_sequence_alignment_molecules system test. This is required due to the changes in the backend of the structure.sequence_alignment user function.
Merger of the structure.align and structure.superimpose user functions. The final user function is called structure.superimpose. As the sequence alignment component of the structure.align user function has been shifted into the new structure.sequence_alignment user function and the information is now stored in ds.sequence_alignments relax data store object, the functionality of structure.align and structure.superimpose are now essentially the same. The sequence alignment arguments and documentation has also been eliminated. And the documentation has been updated to say that sequence alignments from structure.sequence_alignment will be used for superimposing the structures.
Updated the Structure system tests for the structure.align and structure.superimpose user function merger.
Fix for the structure.sequence_alignment user function. The alignment data should be stored in ds.sequence_alignments rather than ds.sequence_alignment.
Sequence alignments can now be retrieved without supplying the algorithm settings. This is in the data_store.seq_align.Sequence_alignments.find_alignment() method. The change allows for the retrieval of pre-existing sequence alignments at any stage.
Added a function for assemble the common atomic coordinates taking sequence alignments into account. This is the new pipe_control.structure.main.assemble_structural_coordinates() function. It takes the sequence alignment logic out of the lib.structure.internal.coordinates.assemble_coord_array() function so that sequence alignments in the relax data store can be used. The logic has also been redefined as: 1, use a sequence alignment from the relax data store if present; 2, use no sequence alignment if coordinates only come from structural models; 3, fall back to a residue number based alignment. The residue number based alignment is yet to be implemented. As a consequence, the lib.structure.internal.coordinates.assemble_coord_array() function has been greatly simplified. It no longer handles sequence alignments, but instead expects the residue skipping data structure, built from the alignment, as an argument. The seq_info_flag argument has also been eliminated in this function as well as the pipe_control.structure.main module.
Updated the structure.displacement user function for the changed atomic assembly logic. This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or the default of a residue number based alignment.
Updated the structure.find_pivot user function for the changed atomic assembly logic. This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or the default of a residue number based alignment.
Updated the structure.atomic_fluctuations user function for the changed atomic assembly logic. This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or the default of a residue number based alignment.
Updated the structure.rmsd user function for the changed atomic assembly logic. This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or the default of a residue number based alignment.
Updated the structure.web_of_motion user function for the changed atomic assembly logic. This now uses the assemble_structural_coordinates() function of the pipe_control.structure.main module to obtain the common coordinates based on pre-existing sequence alignments, no-alignment, or the default of a residue number based alignment.
Fix for the structure.superimpose user function if no data pipes are supplied. This reintroduces the pipes list construction.
Fix for the new pipe_control.structure.main.assemble_structural_coordinates() function. The atom_id argument is now passed into the assemble_atomic_coordinates() function of the lib.structure.internal.coordinates module so that atom subsets are once again recognised.
Another fix for the new pipe_control.structure.main.assemble_structural_coordinates() function. The logic for determining if only models will be superimposed was incorrect.
Implemented the residue number based alignment in the atomic assembly function. This is in the new pipe_control.structure.main.assemble_structural_coordinates() function. The code for creating the residue skipping data structure is now shared between the three sequence alignment options.
Implemented the multiple sequence alignment method based on residue numbers. This is the new msa_residue_numbers() function in the lib.sequence_alignment.msa module. The logic is rather basic in that the alignment is based on a residue number range from the lowest residue number to the highest - i.e. it does not take into account gaps in common between all input sequences.
The residue number based sequence alignment is now executed when assembling atomic coordinates. This is in the assemble_structural_coordinates() function of the pipe_control.structure.main module.
Modified the internal structural object one_letter_codes() method. This now validates the models to make sure all models match, and the method requires the selection object so that residue subsets can be handled.
The assemble_atomic_coordinates() function now calls one_letter_codes() with the selection object. This is the lib.structure.internal.coordinates module function.
Fix for the residue number based sequence alignment when assembling structural coordinates. This is in the assemble_structural_coordinates() function of the pipe_control.structure.main module. The sequences of the different molecules can be of different lengths.
Shifted the residue skipping data structure construction into the relax library. The code was originally in pipe_control.structure.main.assemble_structural_coordinates() but has been shifted into the new lib.sequence_alignment.msa.msa_residue_skipping() function. This will also for greater code reuse. The lib.sequence_alignment.msa module is also a better location for such functionality.
Renamed the Structure.test_sequence_alignment_molecules system test. The new name is Structure.test_sequence_alignment_central_star_nw70_blosum62, to better reflect what the test is doing.
Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62 system test. Some residues are now deleted so that the sequences are not identical.
Created the Structure.test_sequence_alignment_residue_number system test. This will be used to test the structure.sequence_alignment user function together with the 'residue number' MSA algorithm. This is simply a copy of the Structure.test_sequence_alignment_central_star_nw70_blosum62 system test with a few small changes.
Corrections and simplifications for the Structure.test_sequence_alignment_residue_number system test.
Modified the structure.sequence_alignment user function arguments. The pairwise_algorithm and matrix arguments can no be None, and they default to None.
Updated the Structure.test_align_CaM_BLOSUM62 system test script. The MSA algorithm and pairwise alignment algorithms are now specified in the structure.sequence_alignment user function calls.
Creation of the lib.sequence_alignment.msa.msa_general() function. This consists of code from the structure.sequence_alignment user function backend function pipe_control.structure.main.sequence_alignment() for selecting between the different sequence alignment methods.
The structure.sequence_alignment user function now sets some arguments to None before storage. This is for all arguments not used in the sequence alignment. For example the residue number based alignment does not use the gap penalties, pairwise alignment algorithm or the substitution matrices.
Fix for the lib.sequence_alignment.msa.msa_residue_skipping() function. The sequences argument for passing in the one letter codes has been removed. The per molecule loop should be over the alignment strings rather than one letter codes, otherwise the loop will be too short.
Fix for the internal structural object atomic coordinate assembly function. This is the pipe_control.structure.main.assemble_structural_coordinates() function. The case of no sequence alignment being required as only models are being handled is now functional. The strings and gaps data structures passed into the lib.sequence_alignment.msa.msa_residue_skipping() function for generating the residue skipping data structure are now set to the one letter codes and an empty structure of zeros respectively.
Test data directory renaming. The test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed to spheroid_prolate. This is in preparation for creating oblate spheroid diffusion relaxation data.
Creation of oblate spheroid diffusion relaxation data. This will be used in the Structure.test_create_diff_tensor_pdb_oblate system test.
Fix for the oblate spheroid diffusion relaxation data. The diffusion parameters are constrained as Dx ≤ Dy ≤ Dz.
More fixes for the Structure.test_create_diff_tensor_pdb_oblate system test. The initial Diso value is now set to the real final Diso, and the PDB file contents have been updated for the fixed oblate spheroidal diffusion relaxation data.
Updates for many of the Diffusion_tensor system tests. This is due to the changed directory names in test_suite/shared_data/diffusion_tensor/. The ds.diff_dir variable has been introduced to point to the correct data directory.
Large improvement for the GUI test tearDown() clean up method, fixing the tests on wxPython 2.8. The user function window destruction has been shifted into a new clean_up_windows() method which is executed via wx.CallAfter() to avoid racing conditions. In addition, the spin viewer window is destroyed between tests. The spin viewer window change allows the GUI tests to pass on wxPython 2.8 again. This also allows the GUI tests to progress much further on Mac OS X systems before they crash again for some other reason. This could simply be hiding a problem in the spin viewer window. However it is likely to be a racing problem only triggered by the super fast speed of the GUI tests and a normal user would never be able to operate the GUI on the millisecond timescale and hence may never see it.
Reverted the wxPython 2.8 warning printout when starting relax, introduced in relax 3.3.5.
Reverted the skipping of the GUI tests on wxPython 2.8, introduced in relax 3.3.5.
Reverted the General.test_bug_23187_residue_delete_gui GUI test disabling, introduced in relax 3.3.5. The 'Bus Error' on Mac OS X due to this test is no longer an issue, as the spin viewer window is now destroyed after each GUI test.
Created a special Destroy() method for the spin viewer window. This is for greater control of the spin viewer window destruction. First the methods registered with the observer objects are unregistered, then the children of the spin viewer window are destroyed, and finally the main spin viewer window is destroyed. This change saves a lot of GUI resources in the GUI tests (there is a large reduction in 'User Objects' and 'GDI Objects' used on MS Windows systems, hence an equivalent resource reduction on other operating systems).
Fix for the GUI test clean_up_windows() method called from tearDown(). The user function window (Wiz_window) must be closed before the user function page (Uf_page), so that the Wiz_window._handler_close() can still operate the methods of the Uf_page. This avoids a huge quantity of these errors: Traceback (most recent call last): __getattr__ wx._core.PyDeadObjectError: The C++ part of the Uf_page object has been deleted, attribute access no longer allowed.
Simplification of the Dead_uf_pages.test_mol_create GUI test. The RelaxError cannot be caught from the GUI user function window, therefore the try statement has been eliminated.
More memory saving improvements for the GUI test suite tearDown() method. The clean_up_windows() method now loops through all top level windows (frames, dialogs, panels, etc.) and calls their Destroy() method.
Created the gui.uf_objects.Uf_object.Destroy() method. This will be used to cleanly destroy the user function object.
Modified the GUI test suite _execute_uf() method. This user function execution method now calls the user function GUI object Destroy() method to clean up all GUI objects. This should save memory for GUI objects in the GUI test suite.
Modified the GUI test suite tearDown() method. The clean_up_windows() method called by tearDown() now prints out a lost of all of the living windows instead of trying to destroy them (which causes the running of the GUI tests in the GUI to cause the GUI to be destroyed). The printouts will be used for debugging purposes.
Fixes for the custom Wiz_window.Destroy() method. This will now first close the wizard window via the Close() method to make sure all of the wizard pages are properly updated. In the end the wizard DestroyChildren() method is called to clean up all child wx objects, and finally Destroy() is called to eliminate the wizard GUI object.
The GUI test suite tearDown() method now calls the user function GUI wizard Destroy() method. This is for better handling of user function elimination.
Fixes for the user function GUI object Destroy() method. This matches the code just deleted in the GUI test suite tearDown() method for handing the user function page object.
More fixes for the user function GUI object Destroy() method. This page GUI object is destroyed by the wizard window Destroy() method, so destroying again causes wxPython runtime errors.
Spacing printout for the list of still open GUI window elements. This is for the GUI test tearDown() method.
Shifted the printouts from the GUI tests suite clean_up_windows() method to the tearDown() method. This change means that the printouts are not within a wx.CallAfter() call, but rather at the end of the tearDown() method just prior to starting the next test.
Simplification of the GUI analysis post_reset() method. This now uses the delete_all() and hence delete_analysis() methods to clean up the GUI. The reset argument has been added to skip the manipulation of relax data store data, as the data store is empty after a reset. However the calling of the delete_analysis() method now ensures that the analysis specific delete() method is now called so that the GUI elements can be properly destroyed.
Proper destruction of the peak analysis wizard of the NOE GUI analysis. The peak wizard's Destroy() method is now called and the self.peak_wizard object deleted in the NOE GUI analysis delete() method.
Improved memory management in the NOE GUI analysis peak_wizard_launch() method. This method was just overwriting the self.peak_wizard object with a new object. However this does not destroy the wxPython window. Now if a peak wizard is detected, its Destroy() method is called before overwriting the object.
Improved GUI clean up when terminating GUI tests. The clean_up_windows() method, called from tearDown(), now also destroys the pipe editor window, the results viewer window, and the prompt window. This ensures that all of the major relax windows are destroyed between GUI tests.
Improved memory management in the relaxation curve-fitting GUI analysis. The peak intensity loading wizard is now properly destroyed. This is both via the delete() function for terminating the analysis calling the wizard Delete() method, and in the peak_wizard_launch() method calling the wizard Delete() method prior to overwriting the self.peak_wizard object with a new GUI wizard.
Improved memory management in the model-free GUI analysis. The dipole-dipole interaction wizard is now properly destroyed. This is both via the delete() function for terminating the analysis calling the wizard Delete() method, and in the setup_dipole_pair() method calling the wizard Delete() method prior to overwriting the self.dipole_wizard object with a new GUI wizard.
Improved memory management in the model-free GUI analysis. The analysis mode selection window (a wx.Dialog) is now being destroyed in the analysis delete() method. This appears to work on Linux, Windows, and Mac systems.
Improved memory management in the model-free GUI analysis. The local tm and model-free model windows are now destroyed in the GUI analysis delete() method.
Improved termination of the GUI tests. The clean_up_windows() method now calls the results viewer and pipe editor window handler_close() methods. This ensures that all observer objects are cleared out so that the methods of the dead windows can no longer be called.
Fix for the previous commit, calls to wx.Yield() are required to flush the calls on the observer objects after unregisteristing them and deleting the results and pipe editor windows.
Improved memory management in the relaxation dispersion GUI analysis. The peak intensity loading wizard is now properly destroyed. This is both via the delete() function for terminating the analysis calling the wizard Delete() method, and in the peak_wizard_launch() method calling the wizard Delete() method prior to overwriting the self.peak_wizard object with a new GUI wizard.
Created custom Destroy() methods for the pipe editor and results viewer GUI windows.
Improved memory management in the relaxation dispersion GUI analysis. The dispersion model list window is now destroyed in the GUI analysis delete() method.
Fixes for the custom Destroy() methods for the pipe editor and results viewer GUI windows. The event argument is now a keyword argument which defaults to None. This allows the Destroy() methods to be called without arguments.
Temporary disablement of the results viewer window destruction in the GUI tests. This currently, for some unknown reason, causes segfault crashes of the GUI tests on Linux systems.
Changes for how the main GUI windows are destroyed by the GUI test tearDown() method. These changes revert some of the code of previous commits. The recently introduced pipe editor and results viewer windows Delete() methods have been deleted. Instead the Close() methods are called in the tearDown() method to unregister the windows from the observer objects, followed by a wx.Yield() call to flush the wx events, and then the clean_up_windows() GUI test base method is called within a wx.CallAfter() call. This avoids the racing induced segfaults in the GUI tests.
Improved memory management in the spin viewer window. The spin loading wizard is now destroyed in the Destroy() method as well as before reinitialising the wizard in the load_spins_wizard() method.
The GUI tests tearDown() method now prints out the Wizard windows title, if not destroyed.
The Wizard window title is now being stored as a class instance variable.
Improved memory management in the relaxation data list GUI element, as well as the base list object. The relaxation data loading wizard is now destroyed in the Base_list.delete() method, or any wizard for that matter. In addition, the relaxation data loading wizard is destroyed before reinitialising the wizard in the wizard_exec() method.
Better memory management for the missing data dialog in the GUI analyses. The dialog is now stored as the class variable missing_data, and then is destroyed in the analysis delete() method. Without this, the wxPython dialog would remain in memory for the lifetime of the program.
Improved memory management for the Sequence and Sequence_2D input GUI elements. These are mainly used in the user function GUI windows. The dialogs are now destroyed before a second is opened.
Improved memory management for the GUI user function windows. The Destroy() method will now destroy any Sequence or Sequence_2D windows used for the user function arguments.
The relax prompt window is now being destroyed by the GUI test suite tearDown() method. The window is first closed in the tearDown() method and then destroyed in the clean_up_windows() method.
Added memory management checking to the GUI test suite tearDown() method. If any top level windows are present, excluding the main GUI window and the relax controller, then a RelaxError will be raised. Such a check will significantly help in future GUI coding, as now there will be feedback if not all windows are properly destroyed.
Popup menus are now properly destroyed in the GUI tests. In many instances, the wx.Menu.Destroy() method was only being called when the GUI is shown. This causes memory leaking in the GUI tests.
Changed the title for the user function GUI windows. To better help identify what the window is, the title is now the user function name together with text saying that it is a user function.
Removed the wx.CallAfter() call in the GUI tests tearDown() method. This was used to call the clean_up_windows() method. However the value of wx.Thread_IsMain() shows that the tearDown() method executes in the main GUI thread. Therefore the wx.CallAfter() call for avoiding racing conditions is not needed.
Fix for the GUI tests clean_up_windows() tearDown method. After destroying all of the main GUI windows, a wx.Yield() call is made to flush the wxPython event queue. This seems to help with the memory management.
Temporary disabling of the memory management check in the GUI tests tearDown() method. For some reason, it appears as if it is not possible to destroy wx Windows on MS Windows.
Created the relax GUI prompt Destroy() method. This is used to cleanly destroy the GUI prompt by first unregistering with the observer objects, destroying then deleting the wx.py.shell.Shell instance, and finally destroying the window.
Modified the manual_c_module.py developer script so that the path can be supplied on the command line.
Removed some unused imports, as found by devel_scripts/find_unused_imports.py.
Added a copyright notice to the memory_leak_test_relax_fit.py development script. This is to know how old the script is, to see how out of date it is in the future.
Created the memory_leak_test_GUI_uf.py development script. This is to help in tracking down memory leaks in the relax GUI user functions. Instead of using a debugging Python version and guppy (wxPython doesn't seem to work with these), the pympler Python package and its muppy module is used to produce a memory usage printout.
Clean up of the memory_leak_test_GUI_uf.py development script.
Created the new devel_scripts/memory_management/ directory. This will be used for holding all of the memory C module leak detection, GUI object leak detection, memory management, etc. development scripts.
Shifted the memory_leak_test_GUI_uf.py script to devel_scripts/memory_management/GUI_uf_minimise_execute.py.
Created a base class for the memory management scripts for the GUI user functions. The core of the GUI_uf_minimise_execute.py script has been converted into the GUI_base.py base class module. This will allow for new GUI user function testing scripts to be created.
Removal of unused imports from the GUI user function memory testing scripts.
Created a script for testing the memory management when calling the time GUI user function.
Large memory management improvement for the relax GUI wizards and GUI user functions. The pympler.muppy based memory management scripts in devel_scripts/memory_management for testing the GUI user function windows was showing that for each GUI user function call, 28 wx._core.BoxSizer elements were remaining in memory. This was traced back to the gui.wizards.wiz_objects.Wiz_window class, specifically the self._page_sizers and self._button_sizers lists storing wx.BoxSizer instances. The problem was that 16 page sizers and 16 button sizers were initialised each time for later use, however the add_page() method only added a small subset of these to the self._main_sizer wx.BoxSizer object. But the Destroy() method was only capable of destroying the wx.BoxSizer instances associated with another wxPython object. The fix was to add all page and button sizers to the self._main_sizer object upon initialisation. This will solve many memory issues in the GUI, especially in the GUI tests on Mac OS X systems causing 'memory error' or 'bus error' messages and on MS Windows due to 'USER Object' and 'GDI object' limitations.
The maximum number of pages in the GUI wizard is no longer hardcoded. The max_pages argument has been added to allow this value to be changed.
Fix for GUI wizards and GUI user functions. The recent memory management changes caused the wizard windows to have an incorrect layout so that the wizard pages were not visible. Reperforming a layout of the GUI elements did not help. The solution is to not initialise sets of max_pages of wx.BoxSizer elements in the wizard __init__() method, but to generate and append these dynamically via the add_page() method. The change now means that there are no longer multiple unused wx.BoxSizer instances generated for each wizard window created.
Fix for the GUI wizard _go_next() method. The way to determine if there are no more pages needs to be changed, as there are now no empty list elements at the end of the wizard storage objects.
Another fix for the now variable sized wizard page list. This time the fix is in the GUI user function __call__() method.
Created the Relax_fit.test_bug_23244_Iinf_graph system test. This is to catch bug #23244.
Bugfixes:
Bug fix for the structure.align user function. The addition of the molecule name to the displacement ID is now correctly performed.
Fix for the new Internal_selection.count_atoms() internal structural object selection method. The method was previously returning the total number of molecules, not the total number of atoms in the selection.
Printout fix for the backend of the structure.translate and structure.rotate user functions. Model numbers of zero were not correctly identified. This also affects the structure.align and structure.superimpose user functions which uses this backend code.
Another fix for the Internal_selection.count_atoms() internal structural object selection method.
Small fix for the lib.structure.internal.coordinates.assemble_coord_array() function. The termination condition for determining the residues in common between all structures was incorrect.
The Structure.test_create_diff_tensor_pdb_oblate system test now uses oblate diffusion relaxation data. This fixes bug #23232, the failure of this system test on Mac OS X. The problem was that the system test was previously using relaxation data for prolate spheroidal diffusion and fitting an oblate tensor to that data. This caused the solution to be slightly different on different CPUs, operating systems, Python versions, etc. and hence the PDB file representation of the diffusion would be slightly different.
Big bug fix for the GUI tests on MS Windows systems. On MS Windows systems, the GUI tests were unable to complete without crashing. This is because each GUI element requires one 'User object', and MS Windows has a maximum limit of 10,000 of these objects. The GUI tests were taking more than 10,000 and then Windows would say - relax, you die now. The solution is that after each GUI test, all user function windows are destroyed. The user function page is a wx.Panel object, so this requires a Destroy() call. But the window is a Uf_page instance which inherits from Wiz_page which inherits from wx.Dialog. Calling Destroy() on MS Windows and Linux works fine, but is fatal on Mac OS X systems. So the solution is to call Close() instead.
Fix for the default grid_inc argument for the relaxation curve-fitting auto-analysis. This needs to be an integer.
Fix for bug #23244. The relaxation curve-fitting auto-analysis now outputs text files and Grace graphs for the I0 parameter and the I∞ parameter if it exists.
Fixes for the package checking unit tests on MS Windows for the target_functions package. The compiled relaxation curve-fitting file is called target_functions\relax_fit.pyd on MS Windows. The package checking was only taking into account *.so compiled files and not *.pyd file.

New in relax 3.3.5 (Jan 28, 2015)

Features:
Improvements to the NMR spectral noise error analysis.
Addition of the new spectrum.error_analysis_per_field user function to quickly perform a per-NMR field spectrum error analysis.
Added spectrum.sn_ratio user function to calculate the signal to noise ration for all spins, and introduced the per-spin sn_ratio parameter for the NOE, relaxation curve-fitting and relaxation dispersion analyses.
Added the new select.sn_ratio and deselect.sn_ratio user functions to change the selection status of spins according to their signal to noise ratio.
Expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments.
Conversion of the structure.align, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a standardised pipes/models/molecules/atom_id argument design to allow the user functions to operate on different data pipes, different structural models and different molecules simultaneously and to restrict operation to a subset of all spins. This is also used by the new structure.atomic_fluctuations user function.
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 independently of the align_id atom ID for selecting atoms used in the superimposition.
Large improvement for the PDB molecule identification code affecting the structure.read_pdb user function allowing discontinuous ATOM and HETATM records with the same chain ID to be loaded as the same molecule.
Creation of the lib.plotting package for assembling all of the data plotting capabilities of relax into a unified software independent API.
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, measured as sample standard deviations, between different molecules.
The implementation of ordinary least squares fitting.
Improvements for the pcs.corr_plot and rdc.corr_plot user functions.
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 user function. The Needleman-Wunsch algorithm is implemented as in the EMBOSS software to allow for gap opening and extension penalties as well as end penalties. This is also used in all the other structure user functions dealing with multiple molecules - structure.atomic_fluctuations, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose, structure.web_of_motion.
Improved support for PDB secondary structure metadata for the structure.read_pdb and structure.write_pdb user functions.
Changes:
Added a sentence to the start of the citation chapter about http://www.nmr-relax.com links. This is to convince people to more freely use this URL. In that way, the relax search engine ranking should be significantly increased. And it will be easier for new users to get into relax.
Removing the automatic function for error analysis per field in the relaxation dispersion auto-analysis. This function is moved into pipe_control/spectrum.py.
Added the function pipe_control.spectrum.error_analysis_per_field(), as an automatic way of submitting subset IDs per field for error analysis.
For the pipe_control.spectrum.error_analysis_per_field(), added additional printout of subset IDs used for error analysis.
In the auto_analysis.relax_disp module, used the new spectrum.error_analysis_per_field user function to calculate the peak intensity errors.
Reinserted the error_analysis() function in the auto class of relaxation dispersion. This function only checks if the error analysis has not been be performed before, and then decides to call the spectrum.error_analysis_per_field user function. The implementation can be tested with the Relax_disp.test_estimate_r2eff_err_auto system test.
In pipe_control.spectrum.error_analysis_per_field() removed the checks which would stop the calculation of the errors. This function will now always run, which will make it possible for the user to try different error calculations.
Copy of the system test script peak_lists.py to spectrum.py. This is for the implementation of calculation of signal to noise ratio, selection and deselection.
Initialised first test in the Spectrum system test class. This is simply loading some intensity data, and checks data. The system test Spectrum.test_signal_noise_ratio will be expanded to test the calculation of the signal to noise ratio.
Added the Spectrum system test class to the init file, so these system tests can be executed.
Added the pipe_control.spectrum.signal_noise_ratio() backend function, for calculation of the signal to noise ratio per spin.
Added system test Spectrum.test_grace_int, to test plotting the intensity per residue. This is to prepare for a grace plotting of the signal to noise level per residue. Also added additional tests for signal to noise ratio calculation in the system test Spectrum.test_signal_noise_ratio.
Added system test Spectrum.test_grace_sn_ratio to help implement plotting the signal to noise ratio per residue.
Added the common API Parameter structure 'sn_ratio' in parameter_object.
For the specific analysis of "noe", "relax_disp", and "relax_fit", initialised the sn_ratio parameter structure.
Added float around values in signal_noise_ratio() function.
Made the spectrum.sn_ratio user function smaller.
Added two new system tests Spectrum.test_deselect_sn_ratio_all and Spectrum.test_deselect_sn_ratio_any. These test the deselect.sn_ratio user function, to deselect spins with a signal to noise ratio lower than the specified ratio.
Added function in pipe_control.spectrum.sn_ratio_deselection(), a function to deselect spins according to the signal to noise ratio. The function is flexible, since it possible to use different comparison operators. And the function can be switched, so a selection is made instead.
Added the new deselect.sn_ratio user function to deselect spins according to their signal to noise ratio.
Added new backend function in pipe_control.spectrum.sn_ratio_selection. This is to select spins with a signal to noise ratio, higher or lower than the specified ratio.
Added two new system tests Spectrum.test_select_sn_ratio_all and Spectrum.test_select_sn_ratio_any. These test the select.sn_ratio user function.
Added the new select.sn_ratio user function to select spins with signal to noise ratio above a specified ratio. The default ratio for signal to noise selection is 10.0. But should probably be 50-100 instead. The default of 'all_sn' is True, meaning that all signal to noise ratios for the spins needs to pass the test.
Small fix for standard values in deselect.sn_ratio user function. The standard values will deselect spins which have at least one signal to noise ratio which is lower than 10.0.
Small fix for the backend of spectrum sn_ratio_selection() and sn_ratio_deselection(). The standard values have been changed.
Fix for the window size in dx.map user function. The size of the windows was not compatible with the latest change.
Documentation fix in the manual for the lower and upper bonds for parameters in the grid search.
Documentation fix in the manual for the lower and upper bonds for parameters in the minimisation.
Documentation fix in the manual for the scaling values of parameters in the minimisation. The scaling helps the minimisers to make the same step size for all parameters when moving in the χ2 space.
Added a devel script which can quickly convert oxygen icons to the desired sizes.
Extended the devel script image size converter.
Adding new oxygen icon in all needed sizes.
Comment fix in user function select.sn_ratio and deselect.sn_ratio.
Important fix for the spectrum.error_analysis_per_field user function. This is for the compilation of the user manual. The possessive apostrophe should not be used in the text "spectrum ID's". This grammar error triggers an unfortunate bug in the docstring fetching script docs/latex/fetch_docstrings.py whereby the script thinks that ' is the start of a quote.
Added a compressed EPS version of the 128x128/actions/document-preview-archive Oxygen icon. The EPS bounding box was manually changed to 0 0 18 18 in a text editor. The scanline translation parameters were also fixed by changing them all to 18 as well. This allows the icon to be used in the relax manual.
Fix for the blacklist objects in data_store.data_classes.Element.to_xml(). The class blacklist variable was not being taken into account.
Added the norm_type argument to the grace.write user function. This is in response to http://thread.gmane.org/gmane.science.nmr.relax.devel/7392/focus=7438. This norm_type argument can either be 'first' or 'last' to allow different points of the plot to be the normalisation factor. The default of 'first' preserves the old behaviour of first point normalisation.
The relax_fit_saturation_recovery.py system test script now sets the norm_type argument. This is for testing out this new option for the grace.write user function.
The new grace.write user function norm_type argument has been activated. The argument is now passed from pipe_control.grace.write into the write_xy_data() function of the lib.software.grace module, and is used to select which point to use for the normalisation.
The relaxation exponential curve-fitting auto-analysis now sets the normalisation type. This is for the new grace.write user function. If the model for all spins is set to 'sat', then the norm_type will be set to 'last'. This allows for reasonable normalised curves for the saturation recovery R1 experiment types.
Change for norm_type variable in the relaxation exponential curve-fitting auto-analysis. This is now set to 'last', not only for the saturation recovery, but now also for the inversion recovery experiment types. This ensures that the normalisation point is the steady state magnetisation peak intensity.
Cleared the list of blacklisted objects for the cdp.exp_info data structure. The data_store.exp_info.ExpInfo class blacklist variable had previously not been used. But after recent changes, the list was now active. As all the contents of the container were blacklisted, the container was being initialised as being empty when reading the XML formatted state or results files. Therefore the blacklist is now set to an empty list.
Improvements for all of the tables of the relaxation dispersion chapter of the manual. The captions are now the full width (or height for rotated tables) of the page in the PDF version of the manual. The \latex{} command from the latex2html package has been used to improve the HTML versions of the tables by deactivating the landscape environment, the cmidrule command, and the caption width commands. This results in properly HTML formatted tables, rather than creating a PNG image for the whole table. These should significantly improve the tables in the webpages http://www.nmr-relax.com/manual/Comparison_of_dispersion_analysis_software.html, http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis.html, and http://www.nmr-relax.com/manual/Dispersion_model_summary.html.
Created the Structure.test_align_molecules system test. This will be used to extend the functionality of the structure.align user function to be able to align different molecules in the same data pipe, rather than requiring either models or identically named structures in different data pipes.
Modified the Structure.test_align_molecules system test. This now simultaneously checks both the pipes and molecules arguments to the structure.align user function.
More changes for the new Structure.test_align_molecules system test.
Some more fixes for the Structure.test_align_molecules system test.
Change to the Structure.test_align system test. The molecules argument for the structure.align user function has been changed to match the models argument, in that it now needs to be a list of lists with the first dimension matching the pipes argument. This change is to help with the implementation of the new structure.align functionality.
Implemented the new molecules argument for the structure.align user function. In addition to accepting the new argument, the user function backend has been redesigned for flexibility. The assembly of coordinates and final rotations and translations now consist of three loops over desired data pipes, all models, and all molecules. If the models or molecules arguments are supplied, then the models or molecules in the loop which do not match are skipped. This logic simplifies and cleans up the backend.
Created the Structure.test_rmsd_molecules system test. This will be used to implement a new molecules argument for the structure.rmsd user function so that the RMSD between different molecules rather than different models can be calculated.
Implemented the new molecules argument for the structure.rmsd user function. This allows the RMSD between different molecules rather than different models to be calculated, extending the functionality of this user function.
Created the Structure.test_displacement_molecules system test. This will be used to implement the new molecules argument for the structure.displacement user function.
Implemented the molecules argument for the structure.displacement user function. This allows the displacements (translations and rotations) to be calculated between different molecules rather than different models. This information is stored in the dictionaries of the cdp.structure.displacement object with the keys set to the molecule list indices.
Created the Structure.test_find_pivot system test. This is to check the structure.find_pivot user function as this algorithm is currently not being checked in the test suite.
Created the Structure.test_find_pivot_molecules system test. This will be used to implement support for a molecules argument in the structure.find_pivot user function so that different molecules rather than different models can be used in the analysis.
Increased the precision of pivot optimisation in the Structure.test_find_pivot_molecules system test.
Implemented the molecules argument for the structure.find_pivot user function. This allows the motional pivot optimisation between different molecules rather than different models.
Shifted the atomic assembly code from the structure.align user function into its own function. The new function assemble_coordinates() of the pipe_control.structure.main module will be used to standardise the process of assembling atomic coordinates for all of the structure user functions. This will improve the support for comparing different molecules rather than different models as missing atoms or divergent primary sequence are properly handled, and it has multi-pipe support.
Changed the argument order for the structure.align user function. The standardised order will now be pipes, models, molecules, atom_id, etc.
Converted the structure.find_pivot user function to the new pipes/models/molecules/atom_id design. This allows the motional pivot algorithm to work on atomic coordinates from different data pipes, different structural models, and different molecules. The change allows the Structure.test_find_pivot_molecules system test to now pass, as missing atomic data is now correctly handled. The user function backend uses the new pipe_control.structure.main.assemble_coordinates() function. The Structure.test_find_pivot and Structure.test_find_pivot_molecules system tests have been updated for the user function argument changes.
Shift of the atomic coordinate assembly code into the relax library. Most of the pipe_control.structure.main.assemble_coordinates() function has been shifted into the assemble_coord_array() function of the new lib.structure.internal.coordinates module. The pipe_control function now only checks the arguments and assembles the structural objects from the relax data store, and then calls assemble_coord_array() to do all of the work. This code abstraction increases the usefulness of the atomic coordinate assembly and allows it to be significantly expanded in the future, for example by being able to take sequence alignments into consideration.
Tooltip standardisation for the structure.align and structure.find_pivot user functions.
The coordinate assembly function now returns list of unique IDs. This is for each structural object, model and molecule.
Changed the structure ID strings returned by the assemble_coord_array() function. This is from the lib.structure.internal.coordinates module. The structural object name is only included if more than one structural object has been supplied.
More improvements for the structure ID strings returned by the assemble_coord_array() function.
Converted the internal structural displacement object to use unique IDs rather than model numbers. This allows the object to be much more flexible in what types of structures it can handle. This is in preparation for a change in the structure.displacement user function.
Converted the structure.displacement user function to the new pipes/models/molecules/atom_id design. This allows the displacements to be calculated between atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend has been hugely simplified as it now uses the new pipe_control.structure.main.assemble_coordinates() function. The Structure.test_displacement system test has been updated for the user function argument changes.
Another refinement for the structure ID strings returned by the assemble_coord_array() function.
Updated the Structure.test_displacement_molecules system test. This is for the changes to the structure.displacement user function.
Docstring spelling fixes for the steady-state NOE and relaxation curve-fitting auto-analyses.
Converted the structure.rmsd user function to the new pipes/models/molecules/atom_id design. This allows the RMSD calculation to work on atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend uses the new pipe_control.structure.main.assemble_coordinates() function. The Structure.test_rmsd_molecules system test has been updated for the user function argument changes.
Created the internal structural object model_list() method. This is to simplify the assembly of a list of all current models in the structural object.
Converted the structure.superimpose user function to the new pipes/models/molecules/atom_id design. The user function arguments have not changed, however the backend now uses the new pipe_control.structure.main.assemble_coordinates() function. This is to simply decrease the number of failure points possible in the structure user functions. The change has no effect on the user function use or results.
Documentation fix for the assemble_coord_array() function. The return values for lib.structure.internal.coordinates.assemble_coord_array() were incorrectly documented.
Modified the Structure.test_bug_22070_structure_superimpose_after_deletion system test. This now calls the structure.align user function after calling the structure.superimpose user function to better test a condition that can trigger bugs.
Fixes for the structure.superimpose and structure.align user functions. The fit_to_mean() and fit_to_first() functions of lib.structure.superimpose where being incorrectly called, in that they expect a list of elements and not lists of lists.
Code refactorisation for the structure.align user function backend. The looping over data pipes, model numbers, and molecule names, skipping those that don't match the function arguments, has been shifted into the new structure_loop() generator function of the pipe_control.structure.main module. This function assembles the data from the data store and then calls the new loop_coord_structures() generator function of the lib.structure.internal.coordinates module which does all of the work.
Some docstring expansions for the pipe_control.structure.main module functions.
Refactored the descriptions of a number of structure user functions. This includes the structure.align, structure.displacement, structure.find_pivot, structure.rmsd and structure.superimpose user functions. The paragraph_multi_struct and paragraph_atom_id module strings have been created and are shared as two paragraphs for each of these user function descriptions. This standardises the pipe/model/molecule/atom_id descriptions. The user function wizard page sizes have been updated for these changes.
Changed the design of the lib.structure.internal.coordinates.assemble_coord_array() function. The elements_flag argument has been renamed to seq_info_flag. If this is set, then in addition to the atomic elements, the molecule name, residue name, residue number, and atom name is now assembled and returned. This information is now the common information between the structures, hence the return values for the elements are a list of str rather than list of lists. All of the code in pipe_control.structure.main has been updated for the change.
Fix for the structure.align user function if no data pipes are supplied. The pipes list was no longer being created as it was shifted to the assemble_coordinates() function, however it is required for the translation and rotation function calls.
Converted the structure.web_of_motion user function to the new pipe/model/molecule/atom_id design. This allows the web of motion representation to work on atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend uses the new pipe_control.structure.main.assemble_coordinates() function to assemble the common atom coordinates, molecule names, residue names, residue numbers, atom names and elements. All this information is then used to construct the new web of motion PDB file. Therefore the entire backend has been rewritten. The Structure.test_web_of_motion_12, Structure.test_web_of_motion_13, and Structure.test_web_of_motion_all system tests have all been updated for the changed structure.web_of_motion user function arguments. In addition, the system tests Structure.test_web_of_motion_12_molecules, Structure.test_web_of_motion_13_molecules and Structure.test_web_of_motion_all_molecules have been created as a copy of the other tests but with the 3 structures loaded as different molecules.
Fix for the IDs returned by lib.structure.internal.coordinates.assemble_coord_array(). The list of unique structure IDs was being incorrectly constructed if multiple molecules are present but the molecules argument was not supplied. It would be of a different size to the coordinate data structure.
Fix for the Structure.test_displacement system test for the assemble_coord_array() function bugfix.
Modified the Structure.test_align system test to show a failure of the structure.align user function. The alignment causes all atoms in the structural object to be translated and rotated, whereas it should only operate on the atoms of the atom_id argument.
Modified the Structure.test_superimpose_fit_to_mean system test. This is also to demonstrate a bug, this time in the structure.superimpose user function, in which the algorithm causes a translation and rotation of all atoms rather than just those selected by the atom_id argument.
Modified some system tests of the structure.align and structure.superimpose user functions. The displace_id argument has been introduced for both of these user functions for finer control over which atoms are translated and rotated by the algorithm. This allows, for example, to align structures based on a set of backbone heavy atoms while the protons and side chains are displaced by default. Or if a domain is aligned, then just that domain can be displaced.
Added the displace_id argument to the structure.align and structure.superimpose user functions. This gives both of these user functions finer control over which atoms are translated and rotated by the algorithm. This allows, for example, to align structures based on a set of backbone heavy atoms while the protons and side chains are displaced by default. Or if a domain is aligned, then just that domain can be displaced.
Fixes for the Structure.test_superimpose_fit_to_mean system test for the displace_id argument.
Modified the Structure.test_align_molecules system test to catch a bug. This is the failure of the displace_id argument of the structure.align user function when the molecules argument is supplied - all atoms are being displaced instead of a subset.
Fix for the displace_id and molecules arguments of the structure.align user function. The atom ID used for the translations and rotations is now properly constructed from the molecule names in the molecules list and the displace_id string.
Changes for water in the PDB file created by the structure.write_pdb user function. The waters with the residue name 'HOH' are no longer output to HET records.
Improvement for the structure.read_pdb user function. The helix and sheet secondary structure reading now takes the real_mol argument into account to avoid reading in too much information.
Improvement for the merge argument of the structure.read_pdb user function. This argument is now overridden if the molecule to merge to does not exist. This allows the merge flag to be used together with read_mol and set_mol_name set to lists.
Fix for the selective secondary structure reading of the structure.read_pdb user function. The molecule index needs to incremented by 1 to be the molecule number.
Large improvement for the PDB molecule identification code. This affects the structure.read_pdb user function. Now the chain ID code, if present in the PDB file, is being used to determine which ATOM and HETATM records belong to which molecule. All of the records for each molecule are stored until the end, when they are all yielded. This allows for discontinuous chain IDs throughout the PDB file, something which occurs often with the HETATM records.
Expanded the displace_id argument for the structure.align user function. This can now be a list of atom IDs, so that any atoms can be rotated together with the structure being aligned. This is useful if the molecules argument is supplied.
Fix for the Noe.test_bug_21562_noe_replicate_fail system test. This is for the changed behaviour of the structure.read_pdb user function. The problem is that the PDB file read in this test has the chain ID set to X. This broken PDB causes molecule numbering problems.
Expanded the description of the structure.rmsd user function.
Changed the paragraph ordering in the documentation of a number of the structure user functions. This includes the structure.align, structure.displacement, and structure.find_pivot user functions.
Fix for the prompt examples documentation for the structure.align user function.
Improved the sizing layout of the structure.align user function GUI dialog.
Improved the sizing layout of the structure.superimpose user function GUI dialog.
Created the Structure.test_atomic_fluctuations system test. This will be used to implement the idea of the structure.atomic_fluctuations user function.
Implemented the structure.atomic_fluctuations user function. This is loosely based on the structure.web_of_motion user function and is related to it. The user function will write to file a correlation matrix of interatomic distance fluctuations.
Created 4 unit tests for the lib.io.swap_extension function. This is in preparation for implementing the function.
Implemented the lib.io.swap_extension() function. This is confirmed to be fully functional by its four unit tests.
Created the empty lib.plotting package. This follows from this thread. The package will be used for assembling all of the data plotting capabilities of relax. It will make support for different plotting software - Grace, OpenDX, matplotlib, gnuplot, etc - more coherent. This will be used to create a software independent API for plotting in relax. I.e. the plotting software is chosen by the user and then the data output by the user function passes into the lib.plotting API which is then passed into the software dependent backend in lib.plotting.
Created the Structure.test_atomic_fluctuations_gnuplot system test. This checks the operation of the structure.atomic_fluctuations user function when the output format is set to 'gnuplot'. This will be used to implement this option. The current gnuplot script expected by this test is just a very basic starting script for now.
Created the lib.plotting API function correlation_matrix(). This is the lib.plotting.api.correlation_matrix() function. It will be used for the visualisation of rank-2 correlation matrices. The current basic API design here uses a dictionary of backend functions (currently empty) for calling the backend.
Implemented a very basic gnuplot backend for the correlation_matrix() plotting API function. This is in the new lib.plotting.gnuplot module. It creates an incredibly basic gnuplot script for visualising the correlation matrix, assuming a text file has already been created.
Enabled the gnuplot format for the structure.atomic_fluctuations user function. This uses the plotting API correlation_matrix() function for visualisation. The change allows the Structure.test_atomic_fluctuations_gnuplot system test to pass.
Shifted the matrix output of the structure.atomic_fluctuations user function into lib.plotting.text. The new lib.plotting.text module will be used by the relax library plotting API to output data into plain text format. The current correlation_matrix() function, which has been added to the API correlation_matrix() function dictionary, simply has the file writing code of the structure.atomic_fluctuations user function. This significantly simplifies the user function.
More simplifications for the structure.atomic_fluctuations user function backend.
Fix for the structure.atomic_fluctuations user function backend. The pipe_control.structure.main.atomic_fluctuations() function no longer opens the output file.
The gnuplot correlation_matrix() plotting API function now creates a text file of the data. The lib.plotting.gnuplot.correlation_matrix() function now calls the lib.plotting.text.correlation_matrix() function prior to creating the gnuplot script.
Significantly expanded the gnuplot script from via the correlation_matrix() plotting API function. This is for the structure.atomic_fluctuations user function. The output terminal is now set to EPS, the colour map changed from the default to a blue-red map, labels have been added, the plot is now square, and comments are now included throughout the script to help a user hand modify it after creation.
Improvement in the comments from the gnuplot correlation_matrix() plotting API function.
Updated the Structure.test_atomic_fluctuations_gnuplot system test. This is for the gnuplot correlation_matrix() plotting API changes which affect the structure.atomic_fluctuations user function.
Docstring fixes for the Structure.test_atomic_fluctuations_gnuplot system test. This was pointing to the structure.rmsd user function instead of structure.atomic_fluctuations.
Fixes and improvements for the gnuplot correlation_matrix() plotting API function. This is for the structure.atomic_fluctuations user function. The "pm3d map" plot type is incorrect for such data type, so instead of using 'splot', 'plot' is being used instead. The resultant EPS file is now much smaller. The colour map has also been changed to one of the inbuilt ones for higher contrast.
Forced the gnuplot correlation_matrix plot to be square. This is for the correlation_matrix() plotting API function used by the new structure.atomic_fluctuations user function.
Updated the Structure.test_atomic_fluctuations_gnuplot system test. This is for the changes of the gnuplot correlation_matrix() plotting API function used by the structure.atomic_fluctuations user function.
Docstring fix for the Structure.test_atomic_fluctuations system test.
Another docstring fix for the Structure.test_atomic_fluctuations system test.
Created the Structure.test_atomic_fluctuations_angle system test. This will be used to implement the mapping of inter-atomic vector angular fluctuations between structures via a new 'measure' keyword argument for the structure.atomic_fluctuations user function.
Implemented angular fluctuations for the structure.atomic_fluctuations user function. This adds the measure argument to the user function to allow either the default of 'distance' or the 'angle' setting to be chosen. The implementation is confirmed by the Structure.test_atomic_fluctuations_angle system test which now passes.
Clean ups and speed ups of the structure.atomic_fluctuations user function. Duplicate calculations are now avoided, as the SD matrix is symmetric.
Description improvements and GUI layout fixes for the structure.atomic_fluctuations user function.
Added the 'parallax shift' measure to the structure.atomic_fluctuations user function. The parallax shift is defined as the length of the average vector minus the interatomic vector. It is similar to the angle measure however, importantly, it is independent of the distance between the two atoms.
Updated the gnuplot scripts to be executable. These are the scripts created by the gnuplot specific correlation_matrix() plotting API function. The file is made executable and the script now starts with "#!/usr/bin/env gnuplot".
Created the Structure.test_atomic_fluctuations_parallax system test. This is to demonstrate that the parallax shift fluctuations are not implemented correctly.
Fix for the Structure.test_atomic_fluctuations_parallax system test. The distance shifts need to be numbers, not vectors.
Proper implementation of the 'parallax shift' for the structure.atomic_fluctuations user function.
Improved the structure.atomic_fluctuations user function documentation. The fluctuation categories are now better explained. And the 'parallax shift' option is now available in the GUI.
Fix for the parallax shift description in the structure.atomic_fluctuations user function. The parallax shift is not quite orthogonal to the distance fluctuations.
Implemented ordinary_least_squares function the repeated auto-analysis. Inspection of statistics books, shows that several authors does not recommend using regression through the origin (RTO). From Joseph G. Eisenhauer, Regression through the Origin: RTO residuals will usually have a nonzero mean, because forcing the regression line through the origin is generally inconsistent with the best fit; R square measures (for RTO) the proportion of the variability in the dependent variable "about the origin" explained by regression. This cannot be compared to R square for models which include an intercept. From "Experimental design and data analysis for biologists", G. P. Quinn, M. J. Keough: Minimum observed xi rarely extends to zero, and forcing our regression line through the origin not only involves extrapolating the regression line outside our data range but also assuming the relationship is linear outside this range (Cade & Terrell 1997, Neter et al. 1996); We recommend that it is better to have a model that fits the observed data well than one that goes through the origin but provides a worse fit to the observed data; residuals from the no-intercept model no longer sum to zero; usual partition of SSTotal into SSRegression and SSResidual does not work.
Added save state for test of bug 23186. Bug #23186: Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.
Added the system test Relax_disp.test_bug_23186_cluster_error_calc_dw which shows the failure of Monte Carlo simulations error calculations. Bug #23186: Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.
Added additional test for the r2a parameter. Bug #23186: Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.
Attempt to implement the GUI test General.test_bug_23187_residue_delete_gui. This will NOT catch the error. Bug #23187: Deleting residue in GUI, and then open spin viewer crashes relax.
Added test for spin independent error of kAB. Bug #23186: Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.
Fix for the showing of the spin viewer window in the GUI tests. The show_tree() method of the main GUI window class was not calling the custom self.spin_viewer.Show() method, as required to set up the observer objects required to keep the spin viewer window updated. The value of status.show_gui was blocking this. Instead the show argument of this Show() method is being set to status.show_gui to allow the method to always be executed.
Updated the main relax copyright notices for 2015.
The copyright notice in the GUI now uses the info box object. This is for the status bar at the bottom of the GUI window. This removes one place where copyright notices needs to be updated each year. This status text will then be updated whenever the info.py file has been updated.
Updated the copyright notice for 2015 in the GUI splash screen graphic.
Racing fixes for the General.test_bug_23187_residue_delete_gui GUI test. Some GUI interpreter flush() calls have been added to avoid racing in the GUI. The GUI tests are so quick that the asynchronous user function call will be processed at the same time as the spin viewer window is being created, causing fatal segmentation faults in the test suite.
More robustness for the spin viewer GUI window prune_*() methods. When no spin data exists, the self.tree.GetItemPyData(key) call can return None. This is now being checked for and such None values are being skipped in the prune_mol(), prune_res() and prune_spin() methods. The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command: for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
More robustness for the spin viewer GUI window update_*() methods. When no spin data exists, the self.tree.GetItemPyData(key) call can return None. This is now being checked for and such None values are being skipped in the update_mol(), update_res() and update_spin() methods. The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command: for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
More robustness for the spin viewer GUI window prune_*() methods. The data returned from the self.tree.GetItemPyData(key) call can in rare racing cases not contain the 'id' key. This is now being checked for and are being skipped in the prune_mol(), prune_res() and prune_spin() methods. The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command: for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
More robustness for the spin viewer GUI window update_*() methods. The data returned from the self.tree.GetItemPyData(key) call can in rare racing cases not contain the 'id' key. This is now being checked for and are being skipped in the update_mol(), update_res() and update_spin() methods. The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command: for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
Created a development document for catching segfaults and other errors in the GUI tests. This is needed as not all wxPython errors can be caught in the Python unittest framework.
Small whitespace formatting fix for the titles printed by the [http://www.nmr-relax.com/manual/align_tensor_display.html alig
Small whitespace formatting fix for the titles printed by the align_tensor.display user function.
Improvements for the plots created by the pcs.corr_plot user function. The axes now have labels, and have the range and number of ticks set to reasonable values.
Improvements for the pcs.corr_plot user function - the plot range is now determined by the data.
Improvements for the rdc.corr_plot user function - the plot range is now determined by the data.
Added save state for testing implementation of error analysis. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Simplification of system test Relax_disp.test_task_7882_monte_carlo_std_residual, to just test the creation of Monte-Carlo data where errors are drawn from the reduced χ2 distribution. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Extension of the monte_carlo.create_data user function to draw errors from the reduced χ2 Gauss distribution as found by best fit. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Adding to backend of pipe_control.error_analysis(), to modify data point as error drawn from the reduced χ2 Gauss distribution. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Adding empty API method to return errors from the reduced χ2 distribution. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Added API function in relaxation dispersion to return error structure from the reduced χ2 distribution. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Temporary test of making a confidence interval as described in fitting guide. This is system test Relax_disp.x_test_task_7882_kex_conf, which is not activated by default. Running the test, interestingly shows, there is a possibility for a lower global kex. But the value only differ from kex=1826 to kex=1813. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Change to system test Relax_disp.x_test_task_7882_kex_conf(). This is just a temporary system test, to check for local minima. This is method in regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf Page: 109-111. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Raising an error, if the http://wiki.nmr-relax.com/R2eff model is used, and drawing errors from the fit. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
To system test Relax_disp.test_task_7882_monte_carlo_std_residual(), adding test for raise of errors, if the http://wiki.nmr-relax.com/R2eff model is selected. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Added test of argument "distribution" in pipe_control.error_analysis.monte_carlo_create_data(). This is to make sure that a wrong argument is not passed into the function. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Extended the monte_carlo.create_data user function, to allow for the definition of the STD to use in Gauss distribution. This is for creation of Monte-Carlo simulations, where one has perhaps gained information about the expected errors of the data points, which is not measured. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
In backend pipe_control.error_analysis.monte_carlo_create_data() added the argument 'fixed_error' to allow for fixed input of error to the Gauss distribution. Inserted a range of checks, to make sure function behaves as expected. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Added to pipe_control.error_analysis.monte_carlo_create_data() the creation of data points for a fixed distribution. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
To system test Relax_disp.test_task_7882_monte_carlo_std_residual(), added tests for creation of Monte-Carlo data by different methods. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
In pipe_control.error_analysis.monte_carlo_create_data(), if data is of list type or ndarray, then modify the data point according to the fixed error if the distribution is set to 'fixed'. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Expanded the STD acronym, to the meaning of standard deviation. This is in the monte_carlo.create_data user function. Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals.
Added a RelaxWarning printout to the dep_check module if wxPython 2.8 or less is encountered. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. The warning text is simply written to STDERR as relax starts.
Updated the wxPython version in the relax manual to be 2.9 or higher. This is in the section http://www.nmr-relax.com/manual/Dependencies.html.
The GUI tests are now skipped for wxPython version < = 2.8 due to bugs causing fatal segfaults. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. These wxPython versions are simply too buggy.
Fix for the Relax_disp.test_bug_23186_cluster_error_calc_dw system test on 32-bit and Python < = 2.5 systems.
Better error handling in the structure.align user function. If no common atoms can be found between the structures, a RelaxError is now raised for better user feedback.
Created an empty lib.sequence_alignment relax library package. This may be used in the future for implementing more advanced structural alignments (the current method is simply to skip missing atoms, sequence numbering changes are not handled).
Added the sequence_alignment package to the lib package _all_ list.
Added the unit testing infrastructure for the new lib.sequence_alignment package.
Implementation of the Needleman-Wunsch sequence alignment algorithm. This is located in the lib.sequence_alignment.needleman_wunsch module. This is implemented as described in the Wikipedia article https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm.
Created a unit test for checking the Needleman-Wunsch sequence alignment algorithm. This uses the DNA data from the example in the Wikipedia article at https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm. The test shows that the implementation of the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function is correct.
Created the lib.sequence_alignment.substitution_matrices module. This is for storing substitution matrices for use in sequence alignment. The module currently only includes the BLOSSUM62 matrix.
Corrected the spelling of the BLOSUM62 matrix in lib.sequence_alignment.substitution_matrices.
Fix for the lib.sequence_alignment.substitution_matrices.BLOSUM62_SEQ string.
Modification of the Needleman-Wunsch sequence alignment algorithm implementation. This is in the lib.sequence_alignment.needleman_wunsch functions. Scoring matrices are now supported, as well as a user supplied non-integer gap penalty. The algorithm for walking through the traceback matrix has been fixed for a bug under certain conditions.
Created the lib.sequence_alignment.align_protein module for the sequence alignment of proteins. This general module currently implements the align_pairwise() function for the pairwise alignment of protein sequences. It provides the infrastructure for specifying gap starting and extension penalties, choosing the alignment algorithm (currently only the Needleman-Wunsch sequence alignment algorithm as 'NW70'), and choosing the substitution matrix (currently only BLOSUM62). The function provides lots of printouts for user feedback.
Created a unit test for lib.sequence_alignment.align_protein.align_pairwise(). This is to test the pairwise alignment of two protein sequences using the Needleman-Wunsch sequence alignment algorithm, BLOSUM62 substitution matrix, and gap penalty of 10.0.
Added more printouts to the Test_align_protein.test_align_pairwise unit test. This is the test of the module _lib._sequence_alignment.test_align_protein.
Fix for the Needleman-Wunsch sequence alignment algorithm when the substitution matrix is absent.
The lib.sequence_alignment.align_protein.align_pairwise() function now returns data. This includes both alignment strings as well as the gap matrix.
Annotated the BLOSUM62 substitution matrix with the amino acid codes for easy reading.
Updated the gap penalties in the Test_align_protein.test_align_pairwise unit test. This is from the unit test module _lib._sequence_alignment.test_align_protein.
Modified the Needleman-Wunsch sequence alignment algorithm. The previous attempt was buggy. The algorithm has been modified to match the logic of the GPL licenced EMBOSS software to allow for gap opening and extension penalties, as well as end penalties. No code was copied, rather the algorithm for creating the scoring and penalty matrices, as well as the traceback matrix.
Added a DNA similarity matrix to lib.sequence_alignment.substitution_matrices.
Added sanity checks to the Needleman-Wunsch sequence alignment algorithm. The residues of both sequences are now checked in needleman_wunsch_align() to make sure that they are present in the substitution matrix.
Added the NUC 4.4 nucleotide substitution matrix from ftp://ftp.ncbi.nih.gov/blast/matrices/. Uracil was added to the table as a copy to T.
Added the header from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62. This is to document the BLOSUM62 substitution matrix.
Added the PAM 250 amino acid substitution matrix. This was taken from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM250 and added to lib.sequence_alignment.substitution_matrices.PAM250.
Modified the Test_needleman_wunsch.test_needleman_wunsch_align_DNA unit test to pass. This is from the unit test module _lib._sequence_alignment.test_needleman_wunsch. The DNA sequences were simplified so that the behaviour can be better predicted.
Created the Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4 unit test. This is in the unit test module _lib._sequence_alignment.test_needleman_wunsch. This tests the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.
Created a unit test for demonstrating a failure in the Needleman-Wunsch sequence alignment algorithm. The test is Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4b from the _lib._sequence_alignment.test_needleman_wunsch module. The problem is that the start of the alignment is truncated if any gaps are present.
Fix for the Needleman-Wunsch sequence alignment algorithm. The start of the sequences are no longer truncated when starting gaps are encountered.
The needleman_wunsch_align() function now accepts the end gap penalty arguments. These are passed onto the needleman_wunsch_matrix() function.
Added the end gap penalty arguments to lib.sequence_alignment.align_protein.align_pairwise().
Created the Structure.test_align_CaM_BLOSUM62 system test. This will be used for expanding the functionality of the structure.align user function to perform true sequence alignment via the new lib.sequence_alignment package. The test aligns 3 calmodulin (CaM) structures from different organisms, hence the sequence numbering is different and the current structure.align user function design fails. The structure.align user function has been expanded in the test to include a number of arguments for advanced sequence alignment.
Added support for the PAM250 substitution matrix to the protein pairwise sequence alignment function. This is the function lib.sequence_alignment.align_protein.align_pairwise().
Bug fix for the Needleman-Wunsch sequence alignment algorithm. Part of the scoring system was functioning incorrectly when the gap penalty scores were non-integer, as some scores were being stored in an integer array. Now the array is a float array.
Created the Test_align_protein.test_align_pairwise_PAM250 unit test. This is in the unit test module _lib._sequence_alignment.test_align_protein. It checks the protein alignment function lib.sequence_alignment.align_protein.align_pairwise() together with the PAM250 substitution matrix.
Small docstring expansion for lib.sequence_alignment.align_protein.align_pairwise().
Added the sequence alignment arguments to the structure.align user function front end. This includes the 'matrix', 'gap_open_penalty', 'gap_extend_penalty', 'end_gap_open_penalty', and 'end_gap_extend_penalty' arguments. The 'algorithm' argument has not been added to save room, as there is only one choice of 'NW70'. A paragraph has been added to the user function description to explain the sequence alignment part of the user function.
Added the sequence alignment arguments to the back end of the structure.align user function. This is to allow the code in trunk to be functional before the sequence alignment before superimposition has been implemented.
Removed the 'algorithm' argument from the Structure.test_align_CaM_BLOSUM62 system test script. This is for the structure.align user function. The argument has not been implemented to save room in the GUI, and as 'NW70' is currently the only choice.
The sequence alignment arguments are now passed all the way to the internal structural object backend. These are the arguments of the structure.align user function.
Created the lib.sequence.aa_codes_three_to_one() function. The lib.sequence module now contains the AA_CODES dictionary which is a translation table for the 3 letter amino acid codes to the one letter codes. The new aa_codes_three_to_one() function performs the conversion.
Implemented the internal structural object MolContainer.loop_residues() method. This generator method is used to quickly loop over all residues of the molecule.
Implemented the internal structural object one_letter_codes() method. This will create a string of one letter residue codes for the given molecule. Only proteins are currently supported. This method uses the new lib.sequence.aa_codes_three_to_one() relax library function.
Sequence alignment is now performed in lib.structure.internal.coordinates.assemble_coord_array(). This is a pairwise alignment to the first molecule of the list. The alignments are not yet used for anything. The assemble_coord_array() function is used by the structure.align user function, as well as a few other structure user functions.
Fix for the lib.sequence.aa_codes_three_to_one() function. Non-standard residues are now converted to the '*' code. The value of 'X' prevents any type of alignment of a stretch of X residues as X to X in both the BLOSUM62 and PAM250 substitution matrices are set to -1.
Modified the gap penalty arguments for the structure.align user function. These now must always be supplied, as None is not handled by the backend lib.sequence_alignment.needleman_wunsch module. The previous defaults of None are now set to 0.0.
Updated the artificial diffusion tensor test suite data. This is the data in test_suite/shared_data/diffusion_tensor. The residues in the PDB files are now proper amino acids, so the HETATM records are now ATOM records, and the CONECT records have been eliminated.
Another update for the artificial diffusion tensor test suite data. The number of increments on the sphere has been increased from 5 to 6, to make the vector distribution truly uniform. All PDB files and relaxation data has been updated.
Changed the synthetic PDB for the artificial diffusion tensor test suite data. The nitrogen and proton positions are now shifted 10 Angstrom along the distribution vectors. This is to avoid having all nitrogens positioned at the origin which causes the internal structural object algorithm for determining which atoms are connected to fail.
Reintroduced the CONECT PDB records into the artificial diffusion tensor test suite data. The uniform vector distributions have overlapping vectors. This causes the internal structural object atom connection determining algorithm to fail, as this is distance-based rather than using the PDB amino acid definitions for now.
Updates for the Structure.test_create_diff_tensor_pdb_sphere system test. The test now uses the sphere synthetic relaxation data rather than the ellipsoid data, and the PDB checking has been updated for the new data.
Updates for the Structure.test_create_diff_tensor_pdb_prolate system test. The test now uses the spheroid synthetic relaxation data rather than the ellipsoid data, and the PDB checking has been updated for the new data.
Updates for the Structure.test_create_diff_tensor_pdb_oblate system test. The test now uses the spheroid synthetic relaxation data rather than the ellipsoid data, and the PDB checking has been updated for the new data. The oblate tensor is now forced in the system test script.
Updates for the Structure.test_create_diff_tensor_pdb_ellipsoid system test. The PDB checking has been updated for the new data.
Updated the Structure.test_delete_atom system test for the changed PDB structures. The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the atomic positions are different.
Updated the Structure.test_align system test for the changed PDB structures. The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the atomic positions are different.
Updated the Structure.test_align_molecules system test for the changed PDB structures. The test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb file now has more residues, and the atomic positions are different.
Python 3 fix for the lib.sequence module. The string.upper() function no longer exists.
Python 3 fix for the lib.sequence_alignment.align_protein module. The string.upper() function no longer exists.
Modified the generate_data.py diffusion tensor to relaxation data creation script. The NH vectors are no longer truncated to match the PDB.
Python 3 fix for the generate_data.py diffusion tensor to relaxation data creation script. The string.upper() function no longer exists.
Reintroduced the simulated PDB truncation into the artificial diffusion tensor test suite data. This is different to the previous implementation which was deleted recently. It now simulates the truncation of both the N and H positions in the PDB and reconstructs the expected vector.
Updates for some of the Structure.test_create_diff_tensor_pdb_* system tests. This includes Structure.test_create_diff_tensor_pdb_ellipsoid, Structure.test_create_diff_tensor_pdb_oblate, and Structure.test_create_diff_tensor_pdb_prolate. The new simulated PDB truncation in the test data causes the PDB files created in these tests to be slightly different.
The pairwise sequence alignment is now active in the structure.align user function. This is implemented in the lib.structure.internal.coordinates.assemble_coord_array() function for assembling atomic coordinates. It will also automatically be used by many of the structure user functions which operate on multiple structures. The atomic coordinate assembly logic has been completely changed. Instead of grouping atomic information by the molecule, it is now grouped per residue. This allows the residue based sequence alignments to find matching coordinate information. The assemble_coord_array() function will also handle the algorithm argument set to None and assume that the residue sequences are identical between the structures, but this should be avoided. A new function, common_residues() has been created as a work-around for not having a multiple sequence alignment implementation. It will take the pairwise sequence alignment information and construct a special data structure specifying which residues are present in all structures. The logic for skipping missing atoms remains in place, but it now operates on the residue rather than molecule level and simply uses the atom name rather than atom ID to identify common atoms.
Changed the gap opening penalty to 10 in the N-state model structure_align.py system test script.
Docstring update for the pipe_control.structure.main.assemble_coordinates() function. This is for the algorithm argument which can now be set to None.
Fix for the sequence alignment for assembling atomic coordinates. This caused the Structure.test_superimpose_fit_to_mean system test to fail. The problem was in the new logic of the lib.structure.internal.coordinates.assemble_coord_array() function. The coordinate assembly now terminates when either the end of the first molecule or the current molecule is reached.
Bug fixes for the new lib.structure.internal.coordinates.common_residues() function. This function for determining the common residues between multiple sets of pairwise alignments was failing in quite a number of cases. The logic has been updated to handle these.
Another fix for the lib.structure.internal.coordinates.common_residues() function. The wrong index was being used to skip residues in the second sequence.
Created the Structure.test_pdb_combined_secondary_structure system test. This is used to demonstrate a problem in the handling of secondary structure metadata when combining multiple PDB structures. It appears as if the chain ID is preserved as the original ID and is not updated to match the new IDs in the output PDB.
Updated the Structure.test_metadata_xml system test for the changed PDB metadata handling. The helix and sheets IDs are now molecule indices.
Disabled the General.test_bug_23187_residue_delete_gui GUI test. This is essential as a wxPython bug in Mac OS X systems causes this test to trigger a 'Bus Error' every time the GUI tests are run, killing relax.
Bugfixes:
Bug fix for the lib.arg_check.is_int_list() function for checking a list of lists. This is used to check user function arguments, but was causing a RelaxError to be raised for all integer list of lists user function arguments when a valid value is supplied. The function has been updated to match the is_str_list() function which does not suffer from this bug.
Fix in dispersion API, to set error value for clustered values. Bug #23186: Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.
Fix for bug #23187, the problem whereby opening the spin viewer window, deleting a residue, and then reopening the spin viewer crashes relax. This change completes the spin viewer update_*() functions. The prune_list variable was initialised but not used. Now it is used to store the keys of the items to delete, and then the items are deleted at the end in a new loop so that the loop over the dictionary keys is not corrupted.
Fix for the rdc.corr_plot user function. The Y-axis is now set to the measured RDC, as the RDC errors are plotted as dY errors. This matches the behaviour of the pcs.corr_plot user function.
Bug fix for the printouts from the relax_data.read user function. This problem was introduced in the last relax release. The problem is that the spin ID in the loaded relaxation data printout is the same for all data, being the spin ID of the first spin. This has no effect on how relax runs, it is only incorrect feedback.
Bug fix for the PDB secondary sheet handling when combining multiple PDB structures. The helix and sheet metadata now converts the original chain IDs into molecule indices, shifted to new values based on the currently loaded data, when the structure.read_pdb user function is executed. When the structure.write_pdb user function is executed, the molecule indices are converted into new chain IDs. This allows the chain IDs in the HELIX and SHEET records to match those of the ATOM and HETATOM records.
Bug fix for the structure.read_pdb user function parsing of CONECT records. CONECT records pointing to ATOM records were not being read by the user function. As ATOM records should not require CONECT records by their definition, this is only a minor problem affecting synthetic edge cases.

New in relax 3.3.4 (Dec 4, 2014)

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:
Small updates for the wiki section of the release checklist document.
Fixes for the links at the bottom of all HTML manual pages. This is for the automatically generated documentation, created using latex2html. The links all require double quotes, and some a trailing '/'. The links fixed are http://www.nmr-relax.com, http://www.nmr-relax.com/manual/ and http://download.gna.org/relax/manual/relax.pdf.
Removed the repository backup file text from the relax manual. The gzipped repository dump file has not been created by Gna! for many, many years. The problem was identified by the W3C link checker.
Updated all of the http://www.nmr-relax.com/manual/ links in the lib.dispersion package. This is for all of the individual model pages in the HTML manual.
Improved the description for the relax_fit.select_model user function.
A small code rearrangement to create the new target_functions.relax_fit_wrapper module. This follows from the idea at https://gna.org/task/?7415#comment6. The *func_wrapper() functions of the specific_analyses.relax_fit.optimisation module have been shifted out and converted to class methods to create the target_functions.relax_fit_wrapper module. This will be used to abstract away all of the C code, and will form the infrastructure to allow new exponential curves to be quickly supported. The modules of the specific_analyses.relax_fit and specific_analyses.relax_disp packages now import the target_functions.relax_fit_wrapper.Relax_fit_opt target function class and use that instead.
Shifted the C code Jacobian functions into the new target_functions.relax_fit_wrapper module. This shifts all of the relaxation curve-fitting C code access into the target_functions.relax_fit_wrapper module so that the rest of relax does not need to handle the C code. This will allow for new models to be very easily supported, as they would all be set up in this target function module.
Updated the formula in the description of the relax_fit.select_model user function.
Modified the printouts from the structure.write_pdb user function if models are present. Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each model, the header 'MODEL records' is printed followed by a single '.' character for each model. For structures with many models, this results in a huge speed up of the user function which is strongly limited by how fast the terminal can display text.
Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository. These files were created by Andras Boeszoermenyi. They are attached to task #7415 as the Relax_sym.tar.gz file. They were created for the formula I0(1 - e^(−R1.t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of a basic system test. This system test could then be used to implement the saturation-recovery experiment equations in relax.
Updated the target_functions package _all_ list to include the relax_fit* modules.
Modified the package _all_ list checking unit test to accept *.so C modules.
Removal of an unused import in the relax_fit_zooming_grid.py system test script.
Added a system test script for testing the saturation-recovery R1 experiment. This was created by Andras Boeszoermenyi. The file was taken from the saturation_recovery.tar.gaz file attached to task #7415. The only difference with the original script is that the grace.view user function calls have been removed, as these cannot be used in a system test.
Modified the relax_fit_saturation_recovery.py script to work as a system test. This is the script from Andras Boeszoermenyi. The change follows from the discussion of http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369. The status.install_path variable is now used to point to the location of the files. The relax data store ds.tmpdir variable is used for outputting all files. And commented out user functions have been deleted.
Added a copyright notice for Andras Boeszoermenyi for the newly added saturation-recovery R1 script. This change follows the discussion in the message http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
Created the Relax_fit.test_saturation_recovery system test. This follows from the discussion of http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
Added the saturation recovery experiment to the relax_fit.select_model user function. This simply adds a new option and sets up a different parameter set [Rx, Iinf].
Modified the Relax_fit.test_saturation_recovery system test script. The relax_fit.select_model user function call now selects the 'sat' model.
Fix for the relax_fit.select_model user function backend for the 'sat' model.
The exponential model name is now being passed into the target function class. The model as specified by the relax_fit.select_model user function is now finally being sent into the target function, in this case the target_functions.relax_fit_wrapper.Relax_fit_opt Relax_fit_opt class in target_functions.relax_fit_wrapper.
Small fix for the relax_fit.select_model user function.
Renamed all of the relaxation curve-fitting target functions. This includes all of the C functions which are model specific, by appending '_exp' to the current names to now be func_exp, dfunc_exp, http://www.nmr-relax.com/api/3.3/target_functions.relax_fit-module.html#d2func_exp d2func_exp], jacobian_exp, and jacobian_chi2_exp. And all of the target_functions.relax_fit_wrapper.Relax_fit_opt Relax_fit_opt target function class *_wrapper() methods to _exp(). The target function class is now only aliasing the _exp() methods when the model is set to 'exp'.
Alphabetical ordering of the C function imports in the target_functions.relax_fit_wrapper module.
Modified the Relax_fit.test_saturation_recovery system test to check for Iinf instead of I0.
Added support for the saturation recovery experiment to parameter disassembly function. This is in the disassemble_param_vector() function of the specific_analyses.relax_fit.parameters module. This function requires each experiment to be handled separately.
Implemented the target functions for the saturation recovery exponential curve. In the target_functions.relax_fit_wrapper.Relax_fit_opt Python target function class Relax_fit_opt, the new func_sat(), dfunc_sat() and d2func_sat() methods have been created as wrappers for the new C functions. These are aliased to func(), dfunc() and d2func() in the _init_() method. In the target_functions/exponential.c C file, the functions exponential_sat(), exponential_sat_dIinf(), exponential_sat_dR(), exponential_sat_dIinf2(), exponential_sat_dR_dIinf() and exponential_sat_dR2() have been created to implement the function, gradient, and Hessian for the equation I(t) = Iinf(1 - e^(-R.t)). In the target_functions/relax_fit.c file, the functions func_sat(), dfunc_sat(), d2func_sat(), jacobian_sat() and jacobian_chi2_sat() have been created as duplications of the _exp() functions, but pointing to the exponential_sat*() functions and using Iinf instead of I0.
Split the saturation recovery exponential equations and partial derivatives into their own C file.
Expansion and improvements for the relax_fit.select_model user function documentation and printouts.
The relax_fit.relax_time and relax_fit.select_model user functions now have wizard graphics. The R1 graphic from graphics/analyses/r1_200x200.png is now being used.
Added support for the inversion recovery experiment to parameter disassembly function. This matches the change for the saturation recovery experiment. This is in the disassemble_param_vector() function of the specific_analyses.relax_fit.parameters module. This function requires each experiment to be handled separately.
Expanded the relax_fit_saturation_recovery.py system test script. This now calls the error_analysis.covariance_matrix user function to test that code path.
Updated the relaxation curve-fitting covariance_matrix() API method to handle all models. The check for the 'exp' model type has been eliminated, and the parameter vector is assembled using the flexible assemble_param_vector() function rather than manually constructing the vector.
The errors in the Relax_fit.test_saturation_recovery system test are now reasonable. They have been set to 5% of Iinf so that the chi-squared value during optimisation is more realistic.
Updated the relaxation curve-fitting get_param_names() API method to handle all models. This now simply returns the spin container 'params' list, allowing all models to be properly supported.
Big bug fix for the error_analysis.covariance_matrix user function. The model_info structure is now being passed into the get_param_names() API method, as required by the API.
Another change for the relaxation curve-fitting covariance_matrix() API method to handle all models. The scaling matrix diagonalised list of 1.0 values now has the same number of elements as there are parameters.
Implemented the target functions for the inversion recovery exponential curve. In the target_functions.relax_fit_wrapper.Relax_fit_opt Python target function class Relax_fit_opt, the new func_inv(), dfunc_inv() and d2func_inv() methods have been created as wrappers for the new C functions. These are aliased to func(), dfunc() and d2func() in the _init_() method. The target_functions/exponential_inv.c C file has been created with the functions exponential_inv(), exponential_inv_d0(), exponential_inv_dIinf(), exponential_inv_dR(), exponential_inv_dI02(), exponential_inv_dIinf2(), exponential_inv_dI0_dIinf(), exponential_inv_dR_dI0(), exponential_inv_dR_dIinf() and exponential_inv_dR2() have been created to implement the function, gradient, and Hessian for the equation I(t) = Iinf - I0e^(-R.t). In the target_functions/relax_fit.c file, the functions func_inv(), dfunc_inv(), d2func_inv(), jacobian_inv() and jacobian_chi2_inv() have been created as duplications of the _exp() functions, but pointing to the exponential_inv*() functions and adding the Iinf dimension.
More editing of the relax_fit.select_model user function. The IR and SR abbreviations have been added, and a lot of text cleaned up.
Improvement for the relax_fit.select_model user function in the GUI. Unicode text is now being used to display the parameters as R_x and I_0 and to show an infinity symbol in the Iinf parameter. The Rx and Iinf parameters have been added to lib.text.gui to allow this.
Expanded the relaxation curve-fitting chapter of the manual to include descriptions of the models. A new section at the start of this chapter has been added to explain the different models and their equations. This was taken from the script mode section and expanded to include the new saturation recovery experiment.
Removed the relax_fit.select_model user function call from the relax_fit auto-analysis. This is to allow the user in a script, or in the GUI, to choose the model themselves.
Added a button to the R1 and R2 GUI analyses for executing the relax_fit.select_model user function. This is just after the peak list GUI element and before the optimisation settings. It allows different curve types to be selected for the analysis.
Created the new specific_analyses.relax_fit.checks module. This creates the check_model_setup Check object, following the check_*() function design at http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions. This will be used to make sure that the exponential curve model is set prior to executing certain user functions.
Improved the checking in the relaxation curve-fitting analysis. The new specific_analyses.relax_fit.checks.check_model_setup() function is now called prior to minimisation and in the get_param_names() API method to prevent Python errors from occurring due to missing data structures. In addition, the pipe_control.mol_res_spin module function exists_mol_res_spin_data() has been replaced with check_mol_res_spin_data().
Fix for the recently broken Relax_fit.test_curve_fitting_height_estimate_error system test. The relax_fit.select_model user function is now called as this is no longer performed in the auto-analysis.
Removed the text that the inversion recovery experiment is not implemented yet. This is in the documentation for the relax_fit.select_model user function and is in preparation for completing this.
Added the checks module to the specific_analyses.relax_fit package _all_ list.
Fixes for the relaxation dispersion analysis for the recent relaxation curve-fitting analysis changes. The target_functions.relax_fit_wrapper.Relax_fit_opt Relax_fit_opt target function class requires the model argument to be supplied to be correctly set up.
Fixes for the unit tests of the target_functions.relax_fit C module. This is for the recent renaming of all the C functions based on the model type.
Fix for the Rx.test_r1_analysis GUI test. A click on the relax_fit.select_model user function button is now being simulated.
Created a directory for holding synthetic inversion recovery R1 data.
Copied synthetic inversion recovery Sparky peak lists from Sébastien Morin's inversion-recovery branch.
Created a system test script for the inversion-recovery function. This is based on a copy of the script 'relax_fit_exp_2param_neg.py'.
The 3-parameter curve fitting test script now uses the corresponding peak lists.
Prepared the "exp_3param" test for inclusion of artificial data.
Added missing delays in the list. The duplicates had been omitted...
Manually fix the script based on changes made during branch updating. This is as discussed by Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-01/msg00001.html.
Updated Séb's relax_fit_exp_3param_inv_neg.py system test script to work with the current relax design.
Added a script for calculating the expected peak intensities for an inversion recovery curve. This is based on the values used by Sébastien Morin in his inversion-recovery branch, as the check_curve_fitting_exp_3param_inv_neg() function of the test_suite/system_tests/relax_fit.py file.
Increased the precision of the printout from the calc.py script of the last commit.
Changed the peak intensities for Gly 4 in the synthetic inversion recovery Sparky lists. The values have been changed to match that determined from the calc.py script. The replicate spectra intensities are simply the calculated intensity +/-1, to preserve the average.
Created the Relax_fit.test_inversion_recovery system test. This simply calls Sébastien Morin's relax_fit_exp_3param_inv_neg.py system test script, ported from the inversion-recovery branch, and then checks the parameter values for the single optimised spin.
Updated the manual_c_module.py C module compilation development script for the recent changes. The exponential_inv.c and exponential_sat.c files need to be compiled as well.
Python 3 fix for the relax_fit_exp_3param_inv_neg.py system test script. The xrange() function does not exist in Python 3, so was replaced by range().
Updated the memory_leak_test_relax_fit.py development script for the C module changes. This is only the docstring description which changed.
Epydoc docstring fixes for the lib.io module - keyword arguments were not correctly identified. These were identified by Troels in the post at http://thread.gmane.org/gmane.science.nmr.relax.scm/24565/focus=7384.
Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test. This is to catch bug #23017, the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files. This test checks a rank-2 float64 numpy array stored in the current data pipe against what the IEEE 754 int list should be for it.
Grammar fix for a warning from the pymol.frame_order user function.
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.

New in relax 3.3.3 (Nov 24, 2014)

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:
Basic Epydoc fix for the data_store.exp_info module.
Epydoc fix for the name_pipe() method of the relaxation dispersion auto-analysis for repeated data
Fixes for the HTML user manual compilation. The index.html file was not being created as the main page has changed from 'relax_user_manual.html' to 'The_relax_user_manual.html'.
Added a line to the release checklist document about updating the wiki release links. These are for the combined release notes pages at http://wiki.nmr-relax.com/Relax_releases, http://wiki.nmr-relax.com/Relax_release_descriptions, http://wiki.nmr-relax.com/Relax_release_metadata, http://wiki.nmr-relax.com/Relax_release_features, http://wiki.nmr-relax.com/Relax_release_changes, http://wiki.nmr-relax.com/Relax_release_bugfixes, http://wiki.nmr-relax.com/Relax_release_links.
Updates for the release announcement section of the release checklist document.
Created a system test to catch a rare relaxation data loading problem.
Created the Mf.test_dauvergne_protocol_sphere system test. This catches bug #22963: Using '@N*' to define the interatomic interactions for a model-free analysis fails when using non-backbone 15N spins.
Set more reasonable default values for the lib.structure.pdb_write functions atom() and hetatm(). The occupancy now defaults to 1.0 instead of '', and the temperature factor to 0.0 instead of ''. This avoid painful errors when using these functions, as these arguments must be floating point numbers at all times, hence the default value of '' causes a TypeError.
Updated the PDB file in the test_suite/shared_data/model_free/sphere/ directory. The relax library is now being used to create the PDB file. Additional TER and CONECT records are now being created so the result is a more correct PDB file.
Converted all ATOM records to HETATM in the sphere.pdb file.
Renamed vector_angle() to vector_angle_normal() in the lib.geometry.vectors module. This is to standardise the naming as there are now the standard vector angle formula implemented as the vector_angle_acos() and vector_angle_atan2() functions.
Added 6 unit tests for the lib.geometry.vectors.vector_angle_acos() function. These are similar to those of the vector_angle_normal() function but unsigned angles are checked for.
Created 6 unit tests for the lib.geometry.vectors.vector_angle_atan2() function.
Created a script and log file to demonstrate differences between alignment tensor basis sets. This shows that the inter-tensor angles and condition numbers are dependent on the basis set used.
Improved the printouts from the align_tensor.svd user function by including the basis set text.
Updated the log file for comparing different alignment tensor basis sets for align_tensor.svd changes.
Implemented a new default basis set for the align_tensor.matrix_angles user function. This is uses standard definition of the inter-matrix angle using the Euclidean inner product of the two matrices divided by the product of the Frobenius norm of each matrix. As this is a linear map, it should produce the correct definition of inter-tensor angles.
Improvements to the description of the align_tensor.matrix_angles user function.
Updated the test_matrix_angles_identity() unit test for pipe_control.align_tensor.matrix_angles(). This is the test in the _prompt.test_align_tensor.Test_align_tensor module. The basis set has been set back to the now non-default value of 0, and the value checks have been converted from assertEqual() to assertAlmostEqual() to allow for small truncation errors.
Conversion of the basis_set argument for the align_tensor.matrix_angles user function. The argument is now a string that accepts the values of 'matrix', 'unitary 5D', and 'geometric 5D' to select between the different matrix angles techniques. This has been updated in the test suite as well.
Added a check for the values of the basis_set argument. This is to the align_tensor.matrix_angles user function backend.
Printout improvements clarifying the align_tensor.matrix_angles user function.
Conversion of the basis_set argument for the align_tensor.svd user function. The argument is now a string that accepts the values of 'unitary 9D', 'unitary 5D', and 'geometric 5D' to select between the different SVD matrices. This has been updated in the test suite as well.
Expanded the N_state_model.test_5_state_xz system test. This now covers the new 'unitary 9D' basis set for the align_tensor.svd user function and the new 'matrix' basis set for the align_tensor.matrix_angles user function.
Expansion of the align_tensor.matrix_angles user function. The new basis set 'unitary 9D' has been introduced. This creates vectors as {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} and computes the inter-vector angles. These match the 'matrix' basis set whereby the Euclidean inner product divided by the Frobenius norms is used to calculate the inter-tensor angles. In addition, the user function documentation and printouts have been improved. And the backend code has been simplified.
Updated the script and log file for demonstrating differences between alignment tensor basis sets. This now handles the changes to the basis_set arguments used in the align_tensor.matrix_angles and align_tensor.svd user functions, and includes the new basis sets.
Added the irreducible tensor notation of {A-2, A-1, A0, A1, A2} to the alignment tensor object. This follows from the definition of Sass et al, J. Am. Chem. Soc. 1999, 121, 2047-2055, DOI: 10.1021/ja983887w. The equations of (2) were converted using Gaussian elimination to obtain a reduced row echelon form, so that the equations in terms of {A-2, A-1, A0, A1, A2} were derived. These have been coded into the alignment tensor object calc_Am2, calc_Am1, calc_A0, calc_A1 and calc_A2 methods respectively, and the values can be obtained by accessing the Am2, Am1, A0, A1, and A2 objects. To check that the implementation is correct, a unit test has been created to compare the calculated values with those determined using Pales.
Expanded the unit test of the alignment tensor {A-2, A-1, A0, A1, A2} parameters to cover all values.
Created functions in the relax library for calculating the inter-vector angle for complex vectors. This is in the lib.geometry.vectors module. The [function http://www.nmr-relax.com/api/3.3/lib.geometry.vectors-module.html#vector_angle_complex_conjugate vector_angle_complex_conjugate()] has been created to calculate the angle between two complex vectors. This uses the new auxiliary function complex_inner_product() to calculate .
Added the 'irreducible 5D' basis set option to the align_tensor.matrix_angles user function. This is for the inter-tensor vector angle for the irreducible 5D basis set {S-2, S-1, S0, S1, S2}. Its results match that of the standard tensor angle as well as the 'unitary 9D' basis sets.
Added the 'irreducible 5D' basis set option to the align_tensor.svd user function. This is for the inter-tensor vector angle for the irreducible 5D basis set {A-2, A-1, A0, A1, A2}. Its results match that of the 'unitary 9D' basis set.
Editing of the description for the 'irreducible 5D' alignment tensor basis set. This is for the align_tensor.matrix_angles and align_tensor.svd user functions. All Sm element have been converted to Am.
Editing of the description for the align_tensor.matrix_angles user function.
Editing of the align_tensor.svd user function description.
Updated the script and log file for demonstrating differences between alignment tensor basis sets. The 'irreducible 5D' basis set in now used for both the align_tensor.matrix_angles and align_tensor.svd user functions.
Fix for a spelling mistake in the align_tensor.matrix_angles user function printouts.
Small fix for the align_tensor.matrix_angles user function documentation.
Expanded the N_state_model.test_5_state_xz system test for more alignment tensor basis sets. The align_tensor.matrix_angles and align_tensor.svd user functions are now being called with the additional 'irreducible 5D', and 'unitary 9D' basis sets, to make sure these work correctly.
Created the Align_tensor.test_align_tensor_matrix_angles system test. This is to check the angles calculated by the align_tensor.matrix_angles user function. As there are no external references, this essentially fixes the angles to the currently calculated values to catch any accidental changes in the future.
Created the Align_tensor.test_align_tensor_svd system test. This is to check the angles calculated by the align_tensor.svd user function. As there are no external references, this essentially fixes the singular values and condition numbers to the currently calculated values to catch any accidental changes in the future.
Fixes for the proportions of the align_tensor.matrix_angles user function GUI wizard.
Expanded the 'irreducible 5D' text in the align_tensor.matrix_angles and align_tensor.svd user functions. This now explains that these are the coefficients for the spherical harmonic decomposition.
Improved the text for the irreducible tensor notation in the align_tensor.display user function.
Formatting fix for the magnetic susceptibility tensor part of the align_tensor.display user function.
More improvements for the align_tensor.matrix_angles user function description.
Epydoc docstring fixes and expansion for the lib.io.sort_filenames() function.
Epydoc docstring fixes for the lib.spectrum.nmrpipe module. This is for the API documentation. The show_apod_rmsd_to_file() and show_apod_rmsd_dir_to_files() function docstrings have both been modified.
Epydoc docstring fixes for the pipe_control.opendx.map() function. The fixes include whitespace and textwrapping changes.
Python 2.5 fix for the align_tensor.display user function. The new irreducible spherical tensor coefficient printout was failing as the float.real variable was introduced from Python 2.6 onwards.
Shifted the structure checks into their own module. This shifts the special check_structure Check object from pipe_control.structure.main into the new checks module. It allows the check to be performed by other modules in the pipe_control.structure package.
Added the missing_error keyword argument to the pipe_centre_of_mass() function. This is from the pipe_control.structure.mass module. The new keyword controls what happens with the absence of structural data. The pipe_control.structure.checks.check_structure() function is now being used to either throw a warning and return [0, 0, 0] or to raise a RelaxError.
Fix for the new unit tests - Python 2.5 floats do not have a 'real' property.
Bugfixes:
Fix for bug #22961, the failure of relaxation data loading with the message "IndexError: list index out of range". The bug was found by Julien Orts. It is triggered by loading relaxation data from a file containing spin name information and supplying the spin ID using the spin name to restrict data loading to a spin subset. To solve the problem, the pipe_control.relax_data.pack_data() function has been redesigned. Now the selection union concept of Chris MacRaild's selection object is being used by joining the spin ID constructed from the data file and the user supplied spin ID with '&', and using this to isolate the correct spin system.
Big Python 3 bug fix for the dep_check module for the detection of the NMRPipe showApod software. The showApod program was falsely detected as always not being present when using Python 3. This is because the output of the program was being tested using string comparisons. However the output from programs obtained from the subprocess module is no longer strings but rather byte-arrays in Python 3. Therefore the byte-array is not being converted to text if Python 3 is being used, allowing the showApod software to be detected.
Python 3 bug fix for the lib.spectrum.nmrpipe.show_apod_extract() function. The subprocess module output from the showApod program, or any software, is a byte array in Python 3 rather than text. This is now detected and the byte array converted to text before any processing.
Bug fix for the lib.structure.angles.angles_*() functions for odd increments. This affects the PDB representations of the diffusion tensor and frame order when the number of increments in the respective user functions is set to an odd number. It really only affects the frame_order.pdb_model user function, as the number of increments cannot be set in any of the other user functions (structure.create_diff_tensor_pdb, structure.create_rotor_pdb, structure.create_vector_dist, n_state_model.cone_pdb).

New in relax 3.3.2 (Nov 14, 2014)

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 chi2 values, when creating a dx_map. Task #7860: When dx_map is issued, create a parameter file which maps parameters to chi2 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 chi2 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 chi2 value. Bug #22754: The minimise.calculate() does not calculate chi2 value for clustered residues. Task #7860: When dx_map is issued, create a parameter file which maps parameters to chi2 value.
Renamed test scripts and files for producing surface chi2 plots.
Renamed sample scripts making surface maps.
Added scripts to make surface plots of spin independents parameters dw and R2a.
Added example surface chi2 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 chi2 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 chi2 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 chi2 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 chi2 value. For each map, it creates a projected 3d map of the parameters and the chi2 value, and a heat map for the contours. It also scatters the minimum chi2 value, the 4 smallest chi2 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 chi2 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 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 R2a, 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:
Fix for the latex2html tags in the model-free chapter of the relax manual. This bug may affect the compilation of both the PDF and HTML version (http://www.nmr-relax.com/manual/) of the manual.
Formatting improvements for the user function chapter of the HTML manual. This will hopefully fix the horrible formatting whereby all text is wrapped in the HTML tags text.
Big bug fix for the text size formatting of the HTML manual. The previous fix for the user function chapter of the HTML manual (http://www.nmr-relax.com/manual/Alphabetical_listing_user_functions.html) did not fix the problem. The issue was with the {exampleenv} defined using a \newenvironment command in the preamble. The command \footnotesize was bing used in the start, but nothing was changing the font size at the end. In LaTeX, the ending of the environment appears to reset the font size, whereas in latex2html it does not. Therefore all text after this environment is prepended by in the HTML manual and this keeps adding to the text after each new exampleenv environment.
Fix for the poorly written User_functions.test_structure_add_atom GUI test. This fixes one part of 2 of the bug #22772, the modelfree4 binary issue and the User_functions GUI tests with wxPython 2.9 failures of the test suite. The problem was that a list element was being set in the GUI test, but that element did not exist yet. Somehow this worked in wxPython 2.8. But the bad code failed on wxPython 2.9.
Updated the Palmer.test_palmer_omp system test for the 64-bit Linux Modelfree 4.20 GCC binary file. This fixes the second part and last part of the bug #22772, the modelfree4 binary issue and the User_functions GUI tests with wxPython 2.9 failures of the test suite. The problem is that the 64-bit GNU/Linux GCC compiled binary of Modelfree 4.20 produces different results as previous versions. These are now caught by the system test and correctly checked.
Removal the use of OrderedDict(). OrderedDict is first available in python 2.7, and is not essential functionality. The functionality is replaced with looping over a list of dictionary keys instead, which is picked up under analysis. Bug #22798: Failure of relax to start due to an OrderedDict ImportError on Python 2.6 and earlier.
Fix for the find next bug in the relax controller window. This is bug #22815, the failure of find next using F3 (or Ctrl-G on Mac OS X) in the relax controller window if search text has already been set. The fix was simple, as the required flags are in the self.find_data class object (an instance of wx.FindReplaceData).
Fix for find dialog in the relax controller window. This is for bug #22816, the find functionality of the relax controller window does not find text when using wxPython >= 2.9. The find wxPython events are now bound to the find dialog rather than the relax controller window LogCtrl element for displaying the relax messages. This works on all wxPython versions.
Bug fix for the structure.align user function for when no data pipes are supplied.
Bug fix for the N-state model grid search when only alignment tensor parameters are optimised. The algorithm for splitting up the grid search to optimise each tensor separately, hence massively collapsing the dimensionality of the problem, was being performed incorrectly. The grid_search() API method inc, lower, and upper arguments are lists of lists, but were only being treated as lists.
Final fix for bug #22849, the failure of the N-state model analysis when optimising only alignment tensors using RDCs and/or PCSs. The alignment tensor is no longer initialised to zero values. This is to allow the skip_preset argument for the minimise.grid_search user function to be operational for the N-state model, a feature introduced with the zooming grid search. The solution was to check for the uninitialised tensor in the minimise_setup_fixed_tensors() method of the specific_analyses.n_state_model.optimisation module.
Bug fix for the lib.arg_check.is_float_matrix() function. The check for a numpy.ndarray data structure type was incorrect so that lists of numpy arrays were failing in this function. Rank-2 arrays were not affected.
Fix for the structure.com user function. This fixes bug #22860, the failure of the structure.com user function after calling structure.delete. The number of models in cdp.structure is now counted and if set to zero, RelaxNoPdbError will be raised.
The structure.write_pdb user function can now handle empty molecules. This fixes bug #22861, the chain IDs in the structure.write_pdb user function PDB files are incorrect after calling structure.delete. To handle this consistently, the internal structural object ModelContainer.mol_loop() generator method has been created. This loops over the molecules, yielding those that are not empty. The MolContainer.is_empty() method has been fixed by not checking for the molecule name, as that remains after the structure.delete user function call while all other information has been removed. And finally the write_pdb() structural object method has been modified to use the mol_loop() method rather than performing the loop itself.
Fix for the structure.delete user function for molecule metadata once no more data exists. This relates to bug #22861, the chain IDs in the structure.write_pdb user function PDB files are incorrect after calling structure.delete. The metadata, when it exists, is now deleted for the molecule once no more data is present.
Fix for system test Relax_disp.test_bug_atul_srivastava. The call to the expected RelaxError needed to be performed differently for erlier python versions that 2.7.
Fix for bug #22937, the failure of the Relax_disp.test_estimate_r2eff_err_auto system test on Python 2.5. The test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py simply required a newline character at the end of the file so that it can be executed in Python 2.5.
Fix for bug #22938, the failure of the test suite in the relax GUI. The problem was that the status.skip_blacklisted_tests variable did not exist - it was only initialised if relax is started in test suite mode. Now the value is always set from within the status module and defaults to True.
Python 3 fixes for the relax codebase. These changes were made using the command: 2to3 -j 4 -w -f buffer -f idioms -f set_literal -f ws_comma -x except -x import -x imports -x long -x numliterals -x xrange .
Python 3 fixes throughout relax, as identified by the 2to3 script. The command used was: 2to3 -j 4 -w -f except -f import -f imports -f long -f numliterals -f xrange .
Python 3 fixes - eliminated all usage of the dictionary iteritems() calls as this no longer exists.
Python 3 fixes using 2to3 for the extern.numdifftools package (mainly spacing fixes). The command used was: 2to3 -j 4 -w -f buffer -f idioms -f set_literal -f ws_comma -x except -x import -x imports -x long -x numliterals -x xrange .
Python 3 fixes using 2to3 for the extern.numdifftools package. The command used was: 2to3 -j 4 -w -f except -f import -f imports -f long -f numliterals -f xrange .
Python 3 fixes for all print statements in the extern.numdifftools package. The print statements have been manually converted into print() functions.
Python 3 fixes via 2to3 - elimination of all map and lambda usage in relax. The command used was: 2to3 -j 4 -w -f map .
Python 3 fixes via 2to3 - replacement of all `x` with repr(x). The command used was: 2to3 -j 4 -w -f repr .
Manual Python 3 fixes for the dict.key() function which returns a list or iterator in Python 2 or 3. This involves a number of changes. The biggest is the conversion of the "x in y.keys()" statements to "x in y". For code which requires a list of keys, the function calls "list(y.keys())" or preferably "sorted(y.keys())" are used throughout (sorted() ensures that the list will be of the same order on all operating systems and Python implementations). A number of "x in list(y.keys())" statements were simplified to "x in y", some list() calls changed to sorted(), and some unnecessary list() calls were removed.
Python 3 fixes via 2to3 - elimination of all apply() calls. This only affects the GUI which cannot run in Python 3 yet as wxPython is not Python 3 compatible yet. The command used was: 2to3 -j 4 -w -f apply .
Python 3 fixes via 2to3 - proper handling of the dict.items() and dict.values() functions. These are now all wrapped in list() function calls to ensure that the Python 3 iterators are converted to list objects before they are accessed. The command used was: 2to3 -j 4 -w -f dict .
Python 3 fixes via 2to3 - the execfile() function does not exist in Python 3. The command used was: 2to3 -j 4 -w -f execfile .
Python 3 fixes via 2to3 - the filter() function in Python 3 now returns an iterator. The command used was: 2to3 -j 4 -w -f filter .

New in relax 3.3.1 (Oct 10, 2014)

Features:
Initial auto-analysis support for a highly repetitive protocol for analysing relaxation dispersion data.
Addition of the docs/user_function_changes.txt file which documents all user function changes from relax 1.0.1 to 3.3.1 to help with upgrading scripts to newer relax versions.
Updated the translation table used to identify no longer existing user functions and explain what the new user function is called for all relax versions from 1.3.1 to 3.3.1.
The structure.delete user function can now delete individual models as well as select atoms in individual models.
Addition of the error_analysis.covariance_matrix user function for determining parameter errors via the covariance matrix. This is currently only implemented for the relaxation curve-fitting analysis.
Bundling of the Numdifftools 0.6.0 package with relax for numerically testing implementations of gradients, Hessians, and Jacobians.
Implementation of the internal structural object collapse_ensemble() method to allow for all but one model to be deleted.
Massive speed up of the internal structural object by pre-processing the atom ID string into a special atom selection object. This speeds up the interatom.define, structure.delete, structure.rotate, structure.translate and many other user functions which loop over structural data.
Many orders of magnitude speed up of the structure.add_model user function.
Implementation of the structure.mean user function to calculate the mean structure from the atomic coordinates of all loaded models.
Implementation of the structure.align user function for aligning and superimposing different but related structures. This is similar to the structure.superimpose user function but allows for missing atomic information or small sequence changes. Only atoms with the same residue name and number and atom name are used in the superimposition.
Expanded the structure.com user function to accept the atom_id argument to allow the centre of mass of a subset of atoms to be determined.
Improvements for the running of the relax test suite.
Changes:
Epydoc docstring fix for the dep_check.version_comparison() function.
Removed ZZ and HD exchange from the dispersion chapter of the relax manual. These would probably require completely new analysis types added to relax to analyse such data.
Updated the 'Announcement' section of the release checklist document. This now includes details about initially composing the message using the relax wiki, and then how that text and the CHANGES file are used for the email announcement and the Gna! news item.
Small changes for the Gna! news item in the release checklist document.
Modified the announcement section of the release checklist document. Text about removing wiki markup has been added.
More expansion of the release checklist document. Added text about creating internal and external links for the wiki release notes.
Modified system test Relax_disp.test_show_apod_extract that test output from showApod. The output can be different according to NMRPipe version. The 'Noise Std Dev' is though the same.
Fix for comments to dependency check of showApod.
Fix for raising error when calling showApod, and subprocess module not available.
Fix for the dependency check for showApod in system tests.
Further extended the protocol for repeated dispersion analysis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Extended the system test for the protocol for repeated dispersion analysis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added a relaxation dispersion model profiling log file for relax version 3.3.0 vs. 3.2.3. This is the output from the dispersion model profiling master script. These numbers will be used for the 3.3.0 release notes.
Fixes for the 3.3.0 vs. 3.2.3 dispersion model profiling log file. The numeric model numbers were incorrectly scaled and a factor of 10 too high.
Fixes for the scaling factors in the dispersion model super profiling script.
Editing of the 3.3.0 features section of the CHANGES file. This will be used for the release notes.
Added more test data for the repeated analysis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Updated the Baldwin 2014 reference in the relax manual. The pybliographic software was used to format this BibTeX entry. This was updated as volume and page number information is now available.
Updated the Morin et al, 2014 paper (the relax relaxation dispersion paper) reference in the manual. The paper now has volume and page information.
Added some more user function ranamings to the translation table. These were identified while preparing the release notes on the wiki (http://wiki.nmr-relax.com/Category:Release_Notes, http://wiki.nmr-relax.com/Release_notes).
Stored a frequency dependent dictionary with spectrum IDs and repeated PMG frequencies in setup pipe. This information will progress out through children pipes. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Further extended methods in the class for repeated analysis of dispersion data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Updated the release checklist document, including adding a section about cross-linking. The cross-linking is important for search engine indexing.
Created a simple script for printing out the names of all user functions.
Added listings of all user functions from relax version 2.0.0 all the way to 3.3.0. This will be used to look at how the user function names have changed with time.
Added a script and log file for comparing relax user function differences between versions.
Created a document for relax users which follows the changes to the user function names.
For the spin.display user function, added the print out of spin ID and status for selection. This is to help with showing the spin ID string for selection, and the current status of selection. Task #7826: Write a Python class for the repeated analysis of dispersion data.
To the back-end of display pipes, added functionality to sort the pipe names before printing. Also added the return of the list of pipes, with its associated information about pipe type, and pipe_bundle. This is to help with getting a better overview for multiple pipes in data store. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Parsed the force flag from front end of value.set to back end. Bug #22598. Back end of value.set does not respect force=False flag.
Broke optimisation function into smaller functions. This is to help selecting spins, do particular grid search and minimise. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Modified system test to follow the new functions in the auto analysis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Shifted the user function listing script into the test suite directory where the results are.
Created a script for printing out relax 1.3 user functions.
Stripped out all of the relax intro and script printouts from the user function listing files. This allows the diff.py script to be simplified.
Updated the relax 1.3 user function printout script and added many printouts. The printouts are for relax versions 1.3.5 to 1.3.16. The earlier relax versions used the relax 1.2 user function setup.
Created a script for printing out all user functions for relax 1.2 versions. This also includes the 1.3.0 to 1.3.4 versions.
Added the 1.3.0 to 1.3.4 user function printouts.
Changed the behaviour of the script for showing user function difference between relax versions. The relax versions are now reversed so the oldest version is at the bottom of the difference printout.
Added the 1.0.1 to 1.2.15 user function printouts. The diff.log file has also been updated with all of these versions.
Updated the user_function_changes.txt document. This now lists all changes in the user function naming from relax version 1.0.1 all the way to 3.3.0.
Added all remaining user function ranamings since 2.0.0 to the translation table. These were taken directly from the docs/user_function_changes.txt document.
Added all user function ranamings since 1.3.1 to the translation table. These were taken directly from the docs/user_function_changes.txt document. Earlier relax versions are far too different, so this will be the earliest relax version for this translation table. The relax 1.2 and earlier (and 1.3.0) versions used the run argument throughout and the scripting was so different, that telling the user how to upgrade to new user functions is pointless. And the release date of 1.2.15, the last of these old designs was in November 2008.
Changed the order of the two relax versions being compared for user function changes. This is in the diff.py script and log file and the user_function_changes.txt document.
Changed the organisation of the files in the docs/ directory. A new docs/devel directory has been created and the 2to3_checklist, Mac_framework_build_3way, package_layout, and prompt_screenshot.txt documents shifted into it. This is to hide or abstract away the development documents so that relax users do not see them when looking into docs/. This should make the directory less intimidating.
Shifted the Release_Checklist document into docs/devel/ to hide it from users.
Correction for the noe.read to spectrum.read_intensities user function change. This is for the translation table used to catch old user function calls.
Initial try to implement plotting in the repeated auto analysis protocol. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Small improvement of the matplotlib plotting of data in the repeated analysis protocol. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Fix for calling correct folder with test intensities. Task #7826: Write a Python class for the repeated analysis of dispersion data.
For the class of repeated analysis, implemented method to collect peak intensity, and function to plot the correlation. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added system test Relax_disp.test_repeat_cpmg to be skipped, if no matplotlib module exists. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added the Gimp XCF file for the logo of the relax wiki.
Added system test Relax_fit.test_curve_fitting_height_estimate_error() for the manual and automated analysis of exponential fit. This is to prepare for new methods in the auto analysis protocol.
In the auto analysis of exponential fitting, changed the minimisation method from simplex to Newton, to speed-up the fitting. This is for master Monte Carlo simulations.
In the system test Relax_fit.test_curve_fitting_height_estimate_error(), moved the auto-detection of replicated spectra into the manual method. This is to prepare for auto-mated detection of replicates.
Implemented a method to automatically find duplicates of spectrum in exponential fit. This is to ease the user intervention for error analysis, if this has been forgotten.
Implemented the writing out of a "grace2images.py" script file, when performing auto analysis of exponential fits.
Created the Structure.test_delete_model system test. This is in preparation for extending the structure.delete user function to be able to delete individual structural models. The test will only pass once this functionality is in place.
Expanded the wiki instructions in the release checklist document. This includes a number of steps for significantly improving the release notes: External links to the Gna! trackers with full descriptions, external links to the HTML user manual for all user functions, internal links to release notes of other relax versions, internal links to wiki pages for all models from all theories, and HTML formatting of all symbols/parameters/etc.
Introduction of the model argument to the structure.delete user function. This argument is passed all the way into the internal structural object, but is not used yet.
The model argument in the structure.delete user function is now operational. In the internal object, it has two functions. When the atom_id argument is none, then new ModelList.delete_model() function is being called to remove the entire model from the list of structural models. When the atom_id argument is supplied, then only the corresponding atoms in the given model will be deleted.
Expanded the checking in the Structure.test_delete_model system test. Now a number of structural model loading and deletion scenarios are tested.
Implemented back-end function to estimate Rx and I0 errors from Jacobian matrix. This is to prepare for user function in relax_fit, to estimate errors.
Implemented user function relax_fit.rx_err_estimate in relax_fit to estimate Rx and I0 errors from the Jacobian Co-variance matrix.
Extended system test Relax_fit.test_curve_fitting_height_estimate_error() to test the error estimation method from the Co-variance matrix. The results seems very similar, if increasing to 2000 Monte Carlo simulations.
Renamed the pipe_control.monte_carlo module to pipe_control.error_analysis. This is in preparation for the module to handle all error analysis techniques: Monte Carlo simulations, covariance matrix, Jackknife simulations, Bootstrapping (which is currently via the Monte Carlo functions), etc. All current functions are now prepended with 'monte_carlo_*()'.
Fix for the old relax 1.2 model-free results file reading. This is due to the pipe_control.monte_carlo to pipe_control.error_analysis module renaming.
Implemented the pipe_control.error_analysis.covariance_matrix() function. This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/23526/focus=7096. It will be used by a new error_analysis.covariance_matrix user function. And it calls the specific API methods model_loop(), covariance_matrix(), and set_error() and the relax library lib.statistics.multifit_covar() function do to most of the work.
Modified the Relax_fit.test_curve_fitting_height_estimate_error system test. The call to relax_fit.rx_err_estimate has been replaced by the yet-to-be implemented error_analysis.covariance_matrix user function.
Creation of the error_analysis.covariance_matrix user function. This is simply a code rearrangement. The relax_fit user function module was duplicated and relax_fit.rx_err_estimate renamed to error_analysis.covariance_matrix. References to the specific analysis have been removed.
Created the specific analysis base API method covariance_matrix(). This defines the arguments required and what is returned by the method. It raises the RelaxImplementError for all analyses which do not implement this method.
Modified pipe_control.error_analysis.covariance_matrix(). The call to the API covariance_matrix() method now has the model_info argument passed into it. For the relaxation curve-fitting, this allows the loop over spin systems to be skipped.
Shifted the contents of the specific_analysis.relax_fit.estimate_rx_err module into the API. The estimate_rx_err() function is now the covariance_matrix() method of the specific API. The code for calculating the covariance matrix and errors are now in the function pipe_control.error_analysis.covariance_matrix(), so this has been removed. And the error setting is performed by the set_errors() API method, so that code has been deleted as well.
Removed the specific_analyses.relax_fit.estimate_rx_err module import. The module has been merged into the specific API module.
Fix for the pipe_control.error_analysis.covariance_matrix() function. The set_error() API method is parameter specific, so a loop over the parameters using the get_param_names() API method has been added.
Removed the estimate_rx_err module from the specific_analyses.relax_fit.__all__ list. This module was deleted after merger into the api module.
Improved the plotting of correlation plot for intensity. Now the intensity to error is plotted, which is the correct measure of this data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented a correlation plot for Reff2 values to be plotted for different pipes. This has the Reff2/σReff2 plotted, which is the best way to represent this data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Further improved the plotting of data in repeated analysis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added the Relax_disp.test_show_apod_rmsd_dir_to_files system test to the blacklist. This is if the showApod program is not installed on the machine and allows the test suite to pass.
Extended the printout for the skipped tests in the test suite. As tests using the NMRPipe showApod software are skipped and listed in this table, the text now includes 'software' in the list.
Shifted the checks for the Dasha and Modelfree4 software into the system test _init_() method. This is to bring this into the same design as the relaxation dispersion tests which require the NMRPipe showApod software. Now the test suite will list either Dasha or Modelfree4 in the skipped test table if they are not installed.
Adding another statistic method to plot for multi-data sets. Task #7826: Write a Python class for the repeated analysis of dispersion data.
More adding of matplotlib snippets for plotting intermediate data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Changing the range of plotting for statistics. Task #7826: Write a Python class for the repeated analysis of dispersion data.
More changes to plotting for statistics. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Fix for axis limits when plotting stats. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Fix for globing, to prevent incidentally taking wrong intensity file. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Correction to figure limits. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented writing out of statistics to file. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Adding writing out of PNG files from matplotlib, when looking at statistics. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Another math domain checking, if ref intensity is set to 0.0, then points are skipped, rather than raising an Error. This can happen for extremely bad dispersion data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Trying implementing flexibility, when data expected data is missing. This can be due failing of processing data, where a whole run of data is randomly skipped. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Better check for math domain error in intensity proportionality. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Removal of initialised of dictionary, before data existence have been checked. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Small fix for correct check of missing of data. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Imported the Numdifftools 0.6.0 package into the relax source tree. This package is extremely useful for testing the implementation of gradients, Hessians, and Jacobians for all relax target functions. The numerical values from numdifftools can be compared to the directly calculated values. And for analysis types where the partial derivatives with respect to each model parameter are too complicated to calculated, or the derivatives are very complicated and hence slow, numdifftools can be used to provide a numerical estimate for direct use in the optimisation. The Numdifftools package is from https://pypi.python.org/pypi/Numdifftools and https://code.google.com/p/numdifftools/. The current version 0.6.0 has been placed into extern/numdifftools. This is only the numdifftools package within the official distribution files and the Python package setup.py file and associated files and directories have not been included. The package uses the New BSD licence (the revised licence with no advertising clause) which is compatible with the GPL v3 licence.
Reordered functions in repeated analysis protocol. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added more check of methods to the system test Relax_disp.test_repeat_cpmg(). This actually shows, that user function relax_disp.r20_from_min_r2eff maybe is broken. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Fix for the testing of method is finished when called. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Turned on minimisation in system test Relax_disp.test_repeat_cpmg(). Task #7826: Write a Python class for the repeated analysis of dispersion data.
The lib.spectrum.nmrpipe module has been made independent of the relax source code. This was discussed at http://thread.gmane.org/gmane.science.nmr.relax.scm/23357/focus=7103. The change allows the software verification tests pass. The dep_check module cannot be used in the relax lib package. Only modules from within lib are allowed to be imported into modules of lib. The fix now allows the full test suite to pass and hence new relax releases are once again possible.
Created a document which explains how missing copyrights can be found.
Even more improvements to the shell command for finding missing copyrights.
Updated the copyright notice for 2014 for all files changed by Edward d'Auvergne. These were identified using the command in the find_missing_copyrights document.
Added numdifftools to the extern package _all_ list.
Updated the find_missing_copyrights document. The matching is now more precise and skips all svnmerge operations.
Added the 2014 copyright notice for Troels Linnet to many relax source files. These were identified as being edited by Troels using the command listed in the find_missing_copyrights document. The changes include adding "Copyright 2014 Troels E. Linnet" to many files not containing Troels' copyright notice, and extending the 2013 copyright to 2014.
Implemented correlation plot of minimisation values. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Changed the missing package/module/software table in the test suite. This is to allow all names to fit and to update the column titles for software packages.
Decreased the accuracy of a check in the Relax_disp.test_estimate_r2eff_err_auto system test. This is to allow the test to pass on my Windows 7 VM.
Added Troels E. Linnet to the COMMITTERS file, which has not been updated in almost 3 years.
Created the Structure.test_get_model system test. This demonstrates that the internal structural object get_model() method is not working as it should.
Added a few more checks to the Structure.test_get_model system test.
Created the Structure.test_collapse_ensemble system test. This is used to test a planned feature of the internal structural object. The collapse_ensemble() method will be created to remove all but one model in the structural ensemble.
Modified the Structure.test_collapse_ensemble system test to check the initial values. This is for sanity reasons as the test coverage of the structure.add_atom user function is poor.
Implemented the internal structural object collapse_ensemble() method. This allows the Structure.test_collapse_ensemble system test to pass.
Created a basic text based progress meter in the new lib.text.progress module. This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.
Modifications to the User_functions.test_structure_add_atom GUI test. As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI is now significantly different. Therefore many checks have been removed from the GUI test.
Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the dep_check module. This newest version handles infinite target function values preventing optimisation from continuing forever. The 1.0.10 version is also useful as there is full support for gradients and Hessians in the log-barrier constraint algorithm.
Shifted the specific_analyses.relax_disp.variables module into lib.dispersion. This is both to minimise circular dependencies, as previously the specific_analyses.relax_disp modules import from target_functions.relax_disp and vice-versa, and to allow the relax library functions to have access to these variables. This follows from a similar change to the frame order analysis in the frame_order_cleanup branch.
Dependency fix for the auto_analyses.relax_disp_repeat_cpmg module. This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused relax to not start if scipy was not installed. This was detected by testing relax with PyPy.
Implemented writing out of particular correlation plots to file. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Created a special internal structural object selection object. This will be used for massively speeding up the internal structural object. The use of the lib.selection module by the internal structural object is currently very slow as a huge number of calls to re.search() are required. The idea is to avoid this by using lib.selection once to populate this new selection object, and then reusing this object to loop over molecules and atoms.
Added the selection() method to the internal structural object. This parses the atom ID string using the lib.selection module, loops over the molecules and atoms, performs matches using re.search() via lib.selection, and populates and returns the new Internal_selection object. This can be used to pre-process the atom ID string to save huge amounts of time.
The internal structural object validate_models() method now accepts the verbosity argument. This is used to silence printouts.
Fixes for the new structural object Internal_selection object. The atom indices are not stored via the molecule index.
Converted the rotate() and translate() structural object methods to use the new selection object. The atom_id arguments have been replaced with selection arguments. Therefore all parts of relax which call these methods must first call selection() to obtain the Internal_selection instance.
Created the structural object Internal_selection.mol_loop() method. This is to simply quickly loop over all molecule indices of the selection object.
Converted all structural object methods to use the selection object rather that atom ID strings. This should have a significant impact on the speed of certain operations within relax. The most obvious effect will be a huge speed up of the interatom.define user function. There should be speed ups with a number of other user functions relating to structural information. All parts of relax have been updated for the change.
Implemented the sampling sparseness instead of NI on the graph axis. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Massive speed up of the internal structural object add_model() method. This speeds up the structure.add_model user function, as well as many internal relax operations on the structural object. Instead of using the copy.deepcopy() function to duplicate an already existing structural model, now new molecule container objects are created and then the individual elements of the original molecule container data lists are copied one by one. This avoids copying a lot of internal Python junk and hence the copying operation is now orders of magnitude faster.
Created the new --no-skip relax command line option. This is a debugging option specifically designed for relax developers. It allows all blacklisted tests to be executed, i.e. all blacklists are ignored. These tests would normally be skipped, however this option enables them.
Fix for the test suite summary printout function for the new --no-skip option. The relax status object was clashing with a variable of the same name.
Reactivated the Relax_disp.test_m61b_data_to_m61b system test, but blacklisted it. This will allow the test to be executed if the --no-skip command line option is used.
Created the Bmrb.test_bug_22703_display_empty system and GUI test. This system test catches bug #22703, the failure of the bmrb.display user function with an AttributeError when no data is present. It is simultaneously a system and GUI test, as the GUI test class inherits directly from the system test class.
Created the pipe_control.spectrometer.check_setup() function. This follows the design on the wiki page http://wiki.nmr-relax.com/Relax_source_design. This is for checking if spectrometer information has been set up.
Created the RelaxNoFrqWarning warning class for warning that no spectrometer information is present.
Renamed the pipe_control.spectrometer.check_setup() function to check_spectrometer_setup(). This is so it can be used without confusion outside of the module.
Fix for a broken elif block in the new pipe_control.spectrometer.check_spectrometer_setup() function.
The model-free bmrb_write() API method now checks for spectrometer information. This is via a call to thepipe_control.spectrometer.check_spectrometer_setup() function.
Modified the Bmrb.test_bug_22703_display_empty system/GUI test to catch the RelaxNoFrqError.
Created a special Check class based on the strategy design pattern. This is in the new lib.checks module. The class will be used to simplify and unify all of the check_*() functions in the pipe_control and specific_analyses packages.
Converted the pipe_control.spectrometer.check_*() functions to the strategy design pattern. These are now passed into the lib.checks.Check object, and the original functions are now instances of this class.
Alphabetical ordering of all functions in the pipe_control.pipes module.
Changed the design of the Check object in lib.checks. The design of the checking function to call has been modified - it should now return either None if the check passes or an instantiated RelaxError object if not. This is then used to determine if the _call_() method should return True (when None is received). Otherwise if escalate is set to 1, the text from the RelaxError object is sent into a RelaxWarning and False is returned. And if escalate is set to 2, then the error object is simply raised.
Updated the pipe_control.spectrometer.check_*_func() functions to use the new design.
Implemented the writing out of parameter values between comparison of NI level. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Fixes for the lib.checks.Check object. The _call_() method keyword arguments **kargs needs to be processed inside the method to strip out the escalate argument.
The default value of the escalate argument of the Check.__call__() method is now 2. This will cause the calls to the check_*() function/objects to default to raising RelaxErrors.
Changed the behaviour of the lib.checks.Check object again. This time the registered function is stored rather than converted into a class instance method. That way the check_*() function-like objects do not need to accept the unused 'self' argument.
The data pipe testing function has been converted to the strategy design pattern of the Check object. The function pipe_control.pipes.test() has also been renamed to check_pipe().
Created the Bmrb.test_bug_22704_corrupted_state_file system test. This is to catch bug #22704, the corrupted relax state files after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions.
Implemented getting the statistics for parameters and comparing to init NI. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented writing and plotting of statistics for individual and clustered fitting, comparing to full NI. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added checks to the Bmrb.test_bug_22704_corrupted_state_file system test. This is to see if the cdp.exp_info data structure has been correctly restored from the save file.
Uncommented some checks in the Bmrb.test_bug_22704_corrupted_state_file system test.
For relaxation dispersion, modified that the grid search and linear constraints for parameter kAB is between 0-100. The parameter is only used in the TSMFK01 model. The kAB parameter is only for very slow forward exchange rate. The expected values should according to the reference paper: Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., and Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an sh3 domain. J. Am. Chem. Soc., 123(46), 11341-11352. (10.1021/ja011300z) The paper concerns values of kAB in the region 0.1 to 5.0. If the exchange rate is any higher value of this, then another model should be used for the analysis.
Set the default insignificance value to 0.0 instead of 1.0. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Modified the grid search limits for parameter kAB to be between 0.1 and 20.0 rad.s-1. This is for the TSMFK01 model, where values much above 10/20 is not expected.
Implemented counting of outliers for statistics. This is to get a better feeling why some statistics are very much different between NI. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Created the Structure.test_mean system test. This is to test the functionality of a planned new feature, the structure.mean user function. This is an analysis aid that will calculate the mean structure from all loaded models.
Implemented the structure.mean user function frontend. The backend is currently just a stub function.
Fixes and simplifications for the pipe_control.pipes.check_pipe() checking object. One of the RelaxError classes were not initialised and the docstring was incorrect.
Created the pipe_control.structure.main.check_structure() checking object. This will be used for providing much more detailed feedback for when structural information is missing.
Converted all of the pipe_control.structure.main functions to use the check_structure() object. This standardises and improves all of the checks.
Some fixes and additional checks for the Structure.test_mean system test.
Implemented the backend of the structure.mean user function. This primarily occurs within the internal structural object in the new mean() method. The pipe_control.structure.main.mean() function simply checks if the current data pipe is correctly set up and then calls the structural object mean() method.
Created the Structure.test_align system test. This will be used to test the yet to be implemented structure.align user function. This user function will be similar to the structure.superimpose user function but will be designed so that structures with different primary and atomic sequences can be superimposed.
Created the frontend of the structure.align user function. This is almost the same as that of the structure.superimpose user function except that the pipes argument has been added and the titles and description changed to indicate the differences.
Registered the new user function argument type 'int_list_of_lists' in the prompt UI. This is to allow for lists of lists of integers, as used for the model argument in the new structure.align user function.
Modified the lib.arg_check.is_int_list() function to accept the list_of_lists Boolean argument. This updates the function to have the same functionality as is_str_list(), allows for lists of lists of int to be checked.
Extended the Structure.test_align system test to throughly check the structural data. This includes changing the structure.align user function call to use 'fit to first' and carefully checking the new atomic coordinates.
Modified the Structure.test_align system test so that translations and rotations match the algorithm. This allows the output of the structure.align user function to be checked to see if the rotation matrix and translation vector found match that used to shift the original structures.
Implemented the structure.align user function backend. This is similar to the structure.superimpose user function, however the coordinate data structure only contains atoms which are in common to all structures.
The pipe_control.structure.main functions translate() and rotate() now accept the pipe_name argument. This is used to translate and rotate structures in different data pipes, as required by the structure.align user function.
The pipe_control.structure.main.check_structure() checking object now accepts the pipe_name argument. This allows structural data to be checked for in different data pipes without having to switch to them.
Modified the Structure.test_align system test to call the structure.write_pdb user function. This sets the file name to sys.stdout so that the original structure and the final aligned structures are output to STDOUT for debugging purposes.
Created the Structure.test_delete_atom system test. This is used to test the deletion of a single atom using the structure.delete user function.
Expanded the Structure.test_delete_atom system test. This is to show that the structure.write_pdb user function fails after a call to the structure.delete user function to delete individual atoms.
Fix for the new structure.align user function. The translation and rotation of the structures at the end to the aligned positions was being incorrectly performed.
Loosened some checks in the Structure.test_align system test to allow it to pass. Some self.assertEqual() checks for the atomic coordinates have been replaced by self.assertAlmostEqual() to allow for small machine precision differences.
Modified the lib.arg_check.is_str_or_inst() function to handle cStringIO objects. This allows sys.stdout to be used as a file object in the relax test suite.
Modified the lib.arg_check.is_str_or_inst() function to work with Python 3. Instead of checking for cStringIO.OutputType, which does not exist in Python 3, the argument is simply checked to see if it has a write() method.
Print out of the number of all Reff2 points, if they are different between analysis. This can become an issue if a single intensity point has slipped into noise, due to low quality of spectrum reconstruction. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented statistics for Reff2 values. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added data checks and printouts to the structure.align user function. The data checks are to prevent the user from attempting an alignment with differently named molecules, as this will not work.
Implemented writing out intensity and error correlations plot. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented writing out of intensity statistics. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Expanded the structure.com user function to accept the atom_id argument. This allows the centre of mass (CoM) calculation to be restricted to a certain subset of atoms. The backend already had support for this feature, but now it is exposed in the frontend. The user function docstring has been slightly modified as well.
Skipping of intensity calculation, if the intensity pipe does not exists. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Added example CPMG data, which could possibly be sent for BMRB submission. The data is un-published CPMG data, related to the paper: Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE (2011). Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. Proteins: Struct., Funct., Bioinf. 79(3), 685-702, DOI 10.1002/prot.22886. Task #7858: Make it possible to submit CPMG experiments for BMRB.
Added system test Relax_disp.test_bmrb_sub_cpmg() to try calling the bmrb functions in relax. Task #7858: Make it possible to submit CPMG experiments for BMRB.
Implemented the initial part of the API, to collect data for BMRB submission. Task #7858: Make it possible to submit CPMG experiments for BMRB.
Inserted a "RelaxImplementError" when trying to call bmrb_write from a relaxation dispersion analysis. To implement the function, it would require a re-write of the relax_data bmrb_write(star) function, and proper handling of cdp.ri_ids. It was also not readily possible to find examples of submitted CPMG data in the BMRB database. This makes it hard to develop, and even ensure that BMRB would accept the format. Task #7858: Make it possible to submit CPMG experiments for BMRB.
Removed the system test Relax_disp.test_bmrb_sub_cpmg() to be tested in the test-suite. This test will not be implemented, as it requires a large re-write of data structures. Task #7858: Make it possible to submit CPMG experiments for BMRB.
Removed the showing of Matplotlib figures in the test suite. Task #7826: Write a Python class for the repeated analysis of dispersion data.
Implemented system test Relax_disp.test_dx_map_clustered to catch the missing creation of a point file. Bug #22753: dx.map does not work when only 1 point is used.
Inserted a check in system test Relax_disp.test_dx_map_clustered, that a call to minimise.calculate should be the same as the file stored with the clustered χ2 value. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Made initial preparation to loop over clustered spins and IDs for the minimise.calculate user function call. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Implemented looping over spin-clusters when issuing a minimise.calculate. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Made back_calc_r2eff() in optimisation module use the spin and ID list instead. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Fix for graph plotting functionality to send spins as list of one spins. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Fix for calling back_calc_r2eff with the new argument keywords, and use list of spin and spin IDs. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Fix for synthetic script calling back_calc_r2eff() with old arguments and to use list of spin containers and IDs. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Inserted last test in test_dx_map_clustered, to check out the written χ2 values are as expected. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Moved the looping over cluster spin IDs into its own function in the API. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Added the selection string for all the cluster IDs to be parsed back as well. Bug #22754: The minimise.calculate user function does not calculate χ2 value for clustered residues.
Made the value set function, set values to all spins, if it is a global parameter.

New in relax 3.3.0 (Oct 10, 2014)

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 2**zoom_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 R1rho 2D graph plotting in the relax_disp.plot_disp_curves user function as the X-axis can now be the nu1 value, the effective field omega_eff, or the rotating frame title angle. 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/R1rho 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:
Improved model handling for the internal structural object. The set_model() method has been added to allow either a model number to be set to the first unnumbered model (in preparation for adding new models) or to allow models to be renumbered. The logic of the add_model() has also been changed. Rather than looping over all atoms of the first model and copying them, which does not work due to the model validity checks, the entire MolList (molecule list) data structure is copied using copy.deepcopy() to make a perfect copy of the structural data. The ModelList.add_item() method has also been modified to return the newly added or numbered model. This is used by the add_model() structural object method to obtain the model object.
Updated the Mac OS X framework setting up instruction document. New sections have been added for the nose and matplotlib Python packages, as nose is needed for the numpy and scipy testing frameworks and matplotlib might be a useful optional dependency in the future. The mpy4py section has been updated to avoid the non-framework fink version of mpicc which cannot produce universal binaries. A few other parts also have small edits.
Removed the Freecode section from the release checklist as Freecode has been permanently shut down. The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead (http://freecode.com/about).
Fix for the internal structural object MolContainer.last_residue() method. This can now operate when no structural information is present, returning 0 instead of resulting in an IndexError.
Updated the script for finding unused imports in the relax source code. Now the file name is only printed for Python files which have unused imports.
Completely removed all mentions of Freecode from the release document. The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead (http://freecode.com/about).
Updated the minfx version in the release checklist document to 1.0.8. This version has not been released yet, but it will include important fixes and additions for constrained parallelised grid searches.
Fix for a broken link in the development chapter of the relax manual.
Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax manual. The B14 model links to http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken as the B in B14 was capitalised.
Sent in the verbosity argument value to the minfx.grid.grid_split() function. 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.
The time user function now uses the chronometer Oxygen icon in the GUI.
Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings. This is for the pipe_control.minimise module.
More docstring line wrapping removal from pipe_control.minimise.
Bug fix for the parameter units descriptions. This only affects a few rare parameters. The specific analysis API parameter object units() method was incorrectly checking if the units value is a function - it was checking the parameter conversion factor instead.
Modified the align_tensor.init user function so that the parameters are now optional. This allows alignment tensors to be initialised without specifying the parameter values for that tensor.
Modified profiling script to have different number of NCYC points per frequency. This is to complicate the data, so any erroneous reshaping of data is discovered. It is expected, that experiments can have different number of NCYC points per spectrometer frequency. Task #7807: Speed-up of dispersion models for clustered analysis.
Initial try to alter the target function calc_CR72_chi2. This is the first test to restructure the arrays, to allow for higher dimensional computation. All numpy arrays have to have same shape to allow to multiply together. The dimensions should be [ei][si][mi][oi][di]. [Experiment][spins][spec. frq][offset][disp points]. This is complicated with number of disp point can change per spectrometer frequency. Task #7807: Speed-up of dispersion models for clustered analysis. This implementation brings a high overhead. The first test shows no winning of time. The creation of arrays takes all the time.
Temporary changed the lib/dispersion/cr72.py function to unsafe state. This change turns-off all the safety measures, since they have to be re-implemented for higher dimensional structures.
Altered profiling script to report cumulative timings and save to temporary files. Task #7807: Speed-up of dispersion models for clustered analysis. This indeed shows that the efficiency has gone down.
Added print out of chi2 to profile script. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the creation of special numpy structures outside target function. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified profiling script to calculate correct values when setting up R2eff values. This is to test, that the return of chi2 gets zero. Task #7807: Speed-up of dispersion models for clustered analysis.
Removing looping over exp and offset indices in calc_chi2. They are always 0 anyway. This brings a little speed. Task #7807: Speed-up of dispersion models for clustered analysis.
In profiling script, moved up the calculation of values one level. This is to better see the output of the profiling iterations for CR72.py. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for calculation of the Larmor frequency per spin in profiling script. The frq loop should also be up-shifted. It was now extracted as 0.0. Task #7807: Speed-up of dispersion models for clustered analysis.
Re-inserted safety checks in lin/dispersion/CR72.py file. This is re-inserted for the rank_1 cases. This makes the unit-tests pass again. Task #7807: Speed-up of dispersion models for clustered analysis.
Important fix for extracting the correct shape to create new arrays. If using just one field, or having the same number of dispersion points, the shape would extend to the dispersion number. It would report [ei][si][mi][oi][di] when calling ndarray.shape. Shape always has to be reported as: [ei][si][mi][oi]. Task #7807: Speed-up of dispersion models for clustered analysis.
Made it easier to switch between single and cluster reporting in profiling script. Task #7807: Speed-up of dispersion models for clustered analysis.
Important fix for the creation of the multi dimensional pA numpy array. It should be created as numpy.zeros([ei][si][mi][oi]) instead of numpy.ones([ei][si][mi][oi]). This allows for rapid testing of all dimensions with np.allclose(pA, numpy.ones(dw.shape)). pA can have missing filled out values, when the number of dispersion points are different per spectrometer frequency. Task #7807: Speed-up of dispersion models for clustered analysis.
Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation. This is implemented for one field. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Task #7807: Speed-up of dispersion models for clustered analysis.
Re-implemented safety checks in lib/dispersion/cr72.py. This is now implemented for both rank-1 float array and of higher dimensions. This makes the unit tests pass for multi dimensional computing. Task #7807: Speed-up of dispersion models for clustered analysis.
Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation. This is implemented for three fields. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: Task #7807: Speed-up of dispersion models for clustered analysis.
Changed that special numpy structure is also created for "CR72". This makes most system tests pass. Task #7807: Speed-up of dispersion models for clustered analysis.
Critical fix for the slicing of values in target function. This makes system test: Relax_disp.test_sod1wt_t25_to_cr72 pass. Task #7807: Speed-up of dispersion models for clustered analysis.
Added self.has_missing keyword in initialization of the Dispersion class. This is to test once, per spin or cluster. This saves a looping over the dispersion points, when collection the data. Task #7807: Speed-up of dispersion models for clustered analysis.
Created multi dimensional error and value numpy arrays. This is to calculate the chi2 sum much faster. Reordered the loop over missing data points, so it is only initiated if missing points is detected. Task #7807: Speed-up of dispersion models for clustered analysis.
Switch the looping from spin->frq to frq->spin. Since the number of dispersion points are the same for all spins, this allows to move the calculation of pA and kex array one level up. This saves a lot of computation. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed all the creation of special numpy arrays to be of float64 type. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the data filling of special numpy array errors and values, to initialization of Dispersion class. These values does not change, and can safely be stored outside. Task #7807: Speed-up of dispersion models for clustered analysis.
Just a tiny little more speed, by removing temporary storage of chi2 calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Made copies of numpy arrays instead of creating from new. Task #7807: Speed-up of dispersion models for clustered analysis.
Added a self.frqs_a as a multidimensional numpy array. Task #7807: Speed-up of dispersion models for clustered analysis.
Small fix for the indices to the errors and values numpy array. Task #7807: Speed-up of dispersion models for clustered analysis.
Lowered the number of iterations to the profiling scripts. This is to use the profiling script as bug finder. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the calculation of dw_frq out of spin and spectrometer loop. This is done by having a special 1/0 spin numpy array, which turns on or off the values in the numpy array multiplication. The multiplication needs to first axis expand dw, and then tile the arrays according to the numpy structure. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the calculation of pA and kex out off all loops. This was done by having two special 1/0 spin structure arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed dw_frq_a numpy array, as it was not necessary. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed all looping over spin and spectrometer frequency. This is the last loop! Wuhu. Task #7807: Speed-up of dispersion models for clustered analysis.
Reordered arrays for beauty of code. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the back_calc array be initiated as copy of the values array. Task #7807: Speed-up of dispersion models for clustered analysis.
Small edit to profiling script, to help bug finding. Task #7807: Speed-up of dispersion models for clustered analysis.
Fixed that arrays are correctly initiated with one or zero values. Task #7807: Speed-up of dispersion models for clustered analysis.
Very important fix, for only replacing part of data array which have Nan values. Before, all values were replaced, which was wrong. Task #7807: Speed-up of dispersion models for clustered analysis.
Needed to increase the relative tolerance when testing if pA array is 1. Now system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis passes. Also added some comments lines, to prepare for mask replace of values. For example if only some of etapos values should be replaced. Task #7807: Speed-up of dispersion models for clustered analysis.
Restored profiling script to normal. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the logic and comments much clearer about how to reshape, expand axis, and tile numpy arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented a masked array search for where "missing" array is equal 1. This makes it possible to replace all values with this mask, from the value array. This eliminates the last loops over the missing values. It took over 4 hours to figure out, that the mask should be called with mask.mask, to return the same fulls structure, Task #7807: Speed-up of dispersion models for clustered analysis.
Yet another small improvement for the profiling script. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed the multi dimensional structure of pA. pA is not multi-dimensional, and can just be multiplied with numpy arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for testing of pA in lib function, when pA is just float. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified unit tests, so pA is sent to target function as float instead of array. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed the multi dimensional structure of kex. kex is not multi-dimensional, and can just be multiplied with numpy arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for testing of kex in lib function, when kex is just float. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified unit tests, so kex is sent to target function as float instead of array. Task #7807: Speed-up of dispersion models for clustered analysis.
Important fix for replacing values if eta_pos > 700 is violated. This fixes system test: Relax_disp.test_sod1wt_t25_to_cr72, which failed after making kex to a numpy float. The trick is to make a numpy mask which stores the position where to replace the values. Then replace the values just before last return. This makes sure, that not all values are changed. Task #7807: Speed-up of dispersion models for clustered analysis.
Increased the kex speed to 1e7 in clustered unit tests cases. This is to demonstrate where there will be no excange. Task #7807: Speed-up of dispersion models for clustered analysis.
Added a multi-dimensional numpy array chi2 value calculation function. Task #7807: Speed-up of dispersion models for clustered analysis.
Called the newly created chi2 function to calculate for multi dimensional numpy arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Renamed chi2_ND to chi2_rankN. This is a better name for representing multiple axis calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Made special ei, si, mi, and oi numpy structure array. This is for rapid speed-up of numpy array creation in target function. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced self.spins_a with self.disp_struct. Task #7807: Speed-up of dispersion models for clustered analysis.
Made initialisation structures for dw. Task #7807: Speed-up of dispersion models for clustered analysis.
Initial try to reshape dw faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Switched to use self.ei, self.si, self.mi, self.oi, self.di. This is for better reading of code. Task #7807: Speed-up of dispersion models for clustered analysis.
Comment out the sys.exit(), which would make the code fail for wrong calculation of dw. Task #7807: Speed-up of dispersion models for clustered analysis.
Copied profiling script for CPMG model CR72 to R1rho DPL94 model. The framework of the script will be the same, but the data a little different. Task #7807: Speed-up of dispersion models for clustered analysis.
Started converting profiling script to DPL94. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced self.(ei,si,mi,oi,di) with self.(NE,NS,NM,NO,ND). These numbers represents the maximum number of dimensions, instead of index. Task #7807: Speed-up of dispersion models for clustered analysis.
Added the ei index, when creating the first dw_mask. Task #7807: Speed-up of dispersion models for clustered analysis.
Reordered how the structures dw init structures are created. Task #7807: Speed-up of dispersion models for clustered analysis.
Clearing the dw_struct before calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Started using the new way of constructing dw. This is for running system tests. Note, somewhere in the dw array, the frequencies will be different between the two implementations. But apparently, this does not matter. Task #7807: Speed-up of dispersion models for clustered analysis.
Inserted temporary method to switch for profiling. Task #7807: Speed-up of dispersion models for clustered analysis.
First try to speed-up the old dw structure calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Simplified calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Yet another try to implement a fast dw structure method. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented the fastest way to calculate the dw structure. This uses the numpy ufunc multiply.outer function to create the outer array, and then multiply with the frqs_structure. Task #7807: Speed-up of dispersion models for clustered analysis.
Renamed dw temporary structure to generic structure. Task #7807: Speed-up of dispersion models for clustered analysis.
Restructured the calculation of R20A and R20B to the most efficient way. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the lib/CR72.py to a numpy multi dimensional numpy array calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the catching when dw is zero, to use masked array. Implemented backwards compatibility with unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Bugfix for testing if kex is zero. It was tested if kex was equal 1.0. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented masked replacement if fact is less that 1.0. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced isnan mask with function that catches all invalid values.
Removed the masked replacement if fact is less than 1.0. This is very strange, but otherwise system test: Relax_disp.test_hansen_cpmg_data_missing_auto_analysis would fail. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed the slow allclose() function to test if R20A and R20B is equal. It is MUCH faster to just subtract and check sum is not 0.0. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced the temporary variable R2eff with back_calc, and used numpy subtract to speed up. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the lib function into a pure numpy array calculation. This requires, that r20a, r20b and dw has same dimension as the dispersion points. Task #7807: Speed-up of dispersion models for clustered analysis.
Changes too unit tests, so data is sent to target function in numpy array format. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed the creation of an unnecessary structure by using numpy multiply. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the mask which finds where to replace values into the _init_ function. Task #7807: Speed-up of dispersion models for clustered analysis.
Copied profiling script for CR72 to B14 model. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified profiling script for the B14 model. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified model B14 lib file to faster numpy multidimensional mode. The implementations comes almost directly from the CR72 model file. Task #7807: Speed-up of dispersion models for clustered analysis.
Reverted the use of the mask "mask_set_blank". It did not work, and many system tests started failing. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the target function to handle the B14 model for faster numpy computation. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed unit test for B14 to match numpy input requirement. Task #7807: Speed-up of dispersion models for clustered analysis.
Added additional tests in b14, when math errors can occur. This is very easy with a conditional masked search in arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Comment fix for finding when E0 is above 700 in lib function of B14. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed use of "asarray", since the variables are already arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed target function for model CR72. To CR72 is now also the input of the parameters of R20A, R20B and dw. dw is tested for zero, to return flat lines. It is faster to search in the smaller numpy array, than the 5 dimensional dw array. This is for speed-up. R20A and R20B is also subtracted, to see if the full model should be used. In the same way, it is faster to subtract the smaller array. These small tricks are expected to give 5-10 pct. speeed-up. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the lib function of CR72 accept the R20A, R20B and dw of the original array. This is for speed-up. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed unit-tests, to send in the original R20A, R20B and dw_orig to the testing of the lib function CR72. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed profiling script to send R20A, R20B and dw, as original parameters to the lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed target function for model B14. To B14 now also send the input of the original parameters dw. dw is tested for zero, to return flat lines. It is faster to search in the smaller numpy array, than the 5 dimensional dw array. This is for speed-up. These small tricks are expected to give 5-10 pct. speed-up. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the lib function of B14 accept dw of the original array. This is for speed-up. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed unit-tests, to send in the original dw_orig to the testing of the lib function B14. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed profiling script to send dw as original parameters to the lib function B14. Task #7807: Speed-up of dispersion models for clustered analysis.
Copied profiling script for CR72 model to TSMFK01 model. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified profiling script to be used for model TSMFK01. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified target function for model TSMFK01, to send in dw as original parameter. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified lib function for model TSMFK01 to accept dw_orig as input and replaced functions to find math domain errors into maske replacements. Task #7807: Speed-up of dispersion models for clustered analysis.
Made unit tests for model TSMFK01 send in R20A and dw as a numpy array. Task #7807: Speed-up of dispersion models for clustered analysis.
Large increase in speed for model TSMFK01 by changing target functions to use multidimensional numpy arrays in calculation. This is done by restructuring data into multidimensional arrays of dimension [NE][NS][NM][NO][ND], which are number of spins, number of magnetic field strength, number of offsets, maximum number of dispersion point. The speed comes from using numpy ufunc operations. The new version is 2.4X as fast per spin calculation, and 54X as fast for clustered analysis.
Replacing math domain checking in model DPL94, with masked array replacement. Task #7807: Speed-up of dispersion models for clustered analysis.
First try to speed up model DPL94. This has not succeeded, since system test: Relax_disp.test_dpl94_data_to_dpl94 still fails. Task #7807: Speed-up of dispersion models for clustered analysis.
Trying to move some of the structures into its own part. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for forgetting to multiply frqs to power 2. This was found by inspecting all print out before and after implementation. New implementation of DPL94 now passes all system and unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the expansion of the R1 structure out of the for loops. This is to speed-up the _init_ of the class of the target function. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the packing of errors and values out of for loop in the _init_ class of target function. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the multi dimensional expansion of inv_relax_times out of for loop. This can be done for all structures, which does not have missing points. Task #7807: Speed-up of dispersion models for clustered analysis.
For inv_relax_times, expanded one axis, and tiled up to NR spins, before reshaping and blowing up to full structure. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the expansion of frqs out of for loops. Task #7807: Speed-up of dispersion models for clustered analysis.
Documentation fix for description of input arrays to lib functions. Task #7807: Speed-up of dispersion models for clustered analysis.
Converted TAP03 model to use multi dimensional numpy arrays. Task #7807: Speed-up of dispersion models for clustered analysis.
Made dw in unit tests of TAP03 be of numpy array. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced the loop structure in target function of TAP03 with numpy arrays. This makes the model faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Reordered the initialization structure of the special numpy arrays. This was done in the init part of the target function of relaxation dispersion. Task #7807: Speed-up of dispersion models for clustered analysis.
Added model MODEL_TSMFK01 also get self.tau_cpmg calculated in init part. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model TP02, has been replaced with numpy masks. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in dw as numpy array in unit tests of model TP02. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model TP02, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for adding model TP02 to part of init class to initialize preparation of higher dimension numpy structures. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the NOREX model a faster numpy array calculation. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed an unnecessary frq_struct in init of target function. frqs can just be expanded, and back_calc is cleaned afterwards with disp_struct. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model M61, has been replaced with numpy masks. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in r1rho_prime and phi_ex_scaled as numpy array in unit tests of model M61. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model M61, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model M61b, has been replaced with numpy masks. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in r1rho_prime and dw as numpy array in unit tests of model M61b. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model M61b, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points to be send to lib function of model TSMFK01. These are not used anymore. Also removed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points and pB to be send to lib function of model TP02. Number of points are not used anymore. pB is calculated in lib function instead. Also removed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points and pB to send to lib function of model TP02. pB is calculated in lib function instead. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, pB, k_AB, k_BA to be send to lib function of model B14. Number of points are not used anymore. pB is calculated in lib function instead. k_AB, and k_BA are calculated in lib functions instead. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending number of points in target function of TSMFK01. This was removed in lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, pB, to be send to lib function of model TAP03. Number of points are not used anymore. pB is calculated in lib function instead. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, to be send to lib function of model CR72. Number of points are not used anymore. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, to be send to lib function of model DPL94. Number of points are not used anymore. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, to be send to lib function of model M61. Number of points are not used anymore. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points, to be send to lib function of model M61b. Number of points are not used anymore. Fixed in target function. Fixed in lib function. Fixed in corresponding unit tests. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model MP05, has been replaced with numpy masks. Number of points has been removed, as the masks utility replaces this. Calculation of pB, has been moved to lib function for simplicity. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in dw as numpy array in unit tests of model MP05. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model MP05, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model LM63, has been replaced with numpy masks. Number of points has been removed, as the masks utility replaces this. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in number of points in unit tests of model LM63. Task #7807: Speed-up of dispersion models for clustered analysis. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model LM63, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for replacement of values with mask, when phi_ex is zero. This can be spin specific. System test: Relax_disp.test_hansen_cpmg_data_to_lm63 starts to fail: Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in r20 and phi_ex as numpy array in unit tests of LM63. This is after using masks as replacement. Task #7807: Speed-up of dispersion models for clustered analysis.
1 digit decrease in parameter check in system test: Relax_disp.test_hansen_cpmg_data_to_lm63. It is unknown, why this has occurred. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model IT99, has been replaced with numpy masks. Number of points has been removed, as the masks utility replaces this. pB is now moved to be calculated inside. This makes the lib function simpler. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in r20 and dw as numpy array in unit tests of IT99. This is after using masks as replacement. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model IT99, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model ns_cpmg_2site_expanded, has been replaced with numpy masks. Number of points has been removed, as the masks utility replaces this. pB is now moved to be calculated inside. This makes the lib function simpler. k_AB and k_BA is also now calculated here. Documentation is also fixed. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for sending in r20 and dw as numpy array in unit tests of ns_cpmg_2site_expanded. This is after using masks as replacement. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced target function for model ns_cpmg_2site_expanded, to use higher dimensional numpy array structures. That makes the model much faster. I cannot get system test: Relax_disp.test_cpmg_synthetic_dx_map_points to pass. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for system test Relax_disp.test_cpmg_synthetic_dx_map_points. By just copying self.back_calc_a to self.back_calc, problem was solved. In specific_analysis.relax_disp.optimisation in function back_calc_r2eff(), the function gets the last values stores in the class function. This is in "class Disp_result_command(Result_command)" with self.back_calc = back_calc. And back_calc_r2eff() have return model.back_calc. Task #7807: Speed-up of dispersion models for clustered analysis.
Methods to replace math domain errors in model ns_cpmg_2site_3d, has been replaced with numpy masks. Number of points has been removed, as the masks utility replaces this. pB is now moved to be calculated inside. This makes the lib function simpler. k_AB and k_BA is also now calculated here. Magnetization vector is also now filled in lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for unit tests of model NS CPMG 2-site 3D to the reduced input to the lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Change to the target function to the model NS CPMG 2-site 3D to use the reduced input to the lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed linked matrix/vector inner products into chained dot expressions. Task #7807: Speed-up of dispersion models for clustered analysis.
Wrote the essential dot matrix up to be initiated earlier. Task #7807: Speed-up of dispersion models for clustered analysis.
Lowered the number of dot iterations, by pre-prepare the dot matrix another round. Task #7807: Speed-up of dispersion models for clustered analysis.
Turned Mint vector into a 7,1 matrix, so dimensions fit with evolution matrix. Task #7807: Speed-up of dispersion models for clustered analysis.
Lowered the number of dot operations, by pre-preparing the evolution matrix another round. The power is in system tests always even. The trick to removing this for loop, would be to make a general multi dot function. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the bulk operation of model NS CPMG 2-site 3D into the lib file. This is to keep the API clean. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the unit test of NS CPMG 2-site 3D, after the input to the function has changed. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the target function for NS CPMG 2-site 3D. This reflects the new API layout. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the lib function of NS CPMG 2-site star, to get input of dw and r20a+r20b of higher dimensional type. This is to move the main operations from the target function to the lib function, and make the API code clean and consistent. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the target function of NS CPMG 2-site star, to reflect the input to the function. Task #7807: Speed-up of dispersion models for clustered analysis.
Made the dot evolution structure faster for NS CPMG 2-site 3D. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented the BLAS method of dot product, which should be faster. I cannot get the "out" argument to work. Task #7807: Speed-up of dispersion models for clustered analysis.
Small fix for the dot method. But the out argument does not work. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented the dot method via blas. This needs a array with one more axis. Task #7807: Speed-up of dispersion models for clustered analysis.
Last try to use the out argument. In the last dotting loop, the out argument wont work, no matter what I do. Task #7807: Speed-up of dispersion models for clustered analysis.
Inner product fix in model NS CPMG 2-site 3D. Fix for system tests: Relax_disp.test_cpmg_synthetic_ns3d_to_b14, Relax_disp.test_cpmg_synthetic_ns3d_to_CR72, Relax_disp.test_cpmg_synthetic_ns3d_to_CR72_noise_cluster. The number of dotting with Mint, should correspond to the power. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced the temporary structure self.frqs_a to self.frqs, which works for all target functions. Task #7807: Speed-up of dispersion models for clustered analysis.
Replaced the temporary structure self.cpmg_frqs_a to self.cpmg_frqs, which works for all target functions. Task #7807: Speed-up of dispersion models for clustered analysis.
Restructured all data structures into higher dimension in target function. Fix for the input to the different models. Restructured how to detect the number of offset and dispersion points. Task #7807: Speed-up of dispersion models for clustered analysis.
Various index fixes, after the data structures have been reordered. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for unit test, where the dimension of points has to be one lower. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for plotting, since the back_calc now can hold more data points that cpmg frequencies. This is because the numpy array has been expanded to the maximum number of points. Task #7807: Speed-up of dispersion models for clustered analysis.
Implemented a frqs_squared calculation in the init of target function. This is to speed up the calculations. Task #7807: Speed-up of dispersion models for clustered analysis.
Restructured frqs_H to higher dimension in target function. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the calculation of dw and dwH out of for loops for model MMQ CR72. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed looping over spin and frequencies for model MMQ CR72. Task #7807: Speed-up of dispersion models for clustered analysis.
Temporary removed check for dw = 0.0 in MMQ CR72. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed number of points to be parsed to model MMQ CR72. Task #7807: Speed-up of dispersion models for clustered analysis.
Removed power to be parsed to MMQ CR72, since it is not used. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed MMQ CR72 to use multi dimensional data. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed unit test of MMQ CR72 to pass. dw needs to be of numpy structure. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the calculation of dw out of for loops for model NS MMQ 2-site. Task #7807: Speed-up of dispersion models for clustered analysis.
Modified lib function for NS MMQ 2-site, to have looping over spins and frequencies inside lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Fixed the use of higher dimensional data in NS MMQ 2-site SQ DQ ZQ. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for documentation in NS MMQ 2-site/SQ/DQ/ZQ/MQ. Now explains which dimension data should be in. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the reshaping of dw and dwH, since it is not dependent on experiment. Task #7807: Speed-up of dispersion models for clustered analysis.
Changed the calculation of inner product in model NS CPMG 2-site 3D. The out argument of numpy.dot is buggy, and should not be used. Task #7807: Speed-up of dispersion models for clustered analysis.
Added missing instances of cleaning the data. Task #7807: Speed-up of dispersion models for clustered analysis.
Bug fix for model LM63 3-site. The index si has to be used to extract data to lib function. Task #7807: Speed-up of dispersion models for clustered analysis.
Temporary added system test: test_korzhnev_2005_all_data_disp_speed_bug. This makes a minimisation with 1 iteration, and so will give the chi2 value at the preset parameter values. This is chi2 value should give 162.5, but gives 74.7104. Task #7807: Speed-up of dispersion models for clustered analysis.
Updated documentation on dimensionality of numpy array num_points. They are in dimension [NE][NS][[NM][NO], where oi gives the number of dispersion points at that offset. Task #7807: Speed-up of dispersion models for clustered analysis.
Fix for system test: test_korzhnev_2005_all_data. The masking for replacing values was wrong. Task #7807: Speed-up of dispersion models for clustered analysis.
Moved the cleaning of data points and replacing of values of out loop for model NS MMQ 2-site. Task #7807: Speed-up of dispersion models for clustered analysis.

New in relax 3.2.3 (Jul 3, 2014)

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 (https://gna.org/users/jlec) 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 R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: Unpacking of R2A and R2B 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 R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE 3D full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE STAR full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
Added synthetic data generator script which created the data to test against. Bug #22146: Unpacking of R2A and R2B 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 R2A and R2B 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 R2A and R2B 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 chi2 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 dw 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/[email protected]/msg06288.html, http://www.mail-archive.com/[email protected]/msg06289.html, http://www.mail-archive.com/[email protected]/msg06327.html, and http://www.mail-archive.com/[email protected]/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.record() 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

New in relax 3.2.0 (May 21, 2014)

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 https://gna.org/projects/minfx/ 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 Baldwin 2014 paper at http://dx.doi.org/10.1016/j.jmr.2014.02.023).
Large improvements to the relax HTML manual at http://www.nmr-relax.com/manual/index.html 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:
Shifted two functions from pipe_control.angles into the new lib.geometry.angles module. This is the fold_spherical_angles() and wrap_angles() functions which are not related to the relax data store and hence can be made independent.
Replaced function atan(omega1 / Delta_omega) with atan2(omega1 , Delta_omega), to make sure returned theta values are between 0 and pi. This was done in the function return_offset_data() in the specific_analyses of relax_disp. This was discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5210.
Changed a unit test and system test, where a change from the atan to atan2 function to calculate theta can give differences to the 15 decimal.
Replaced how a global analysis average results from a previous run to instead take the median. This is to prevent averaging extreme outliers, and instead take the median of the previous result. This was discussed in: https://mail.gna.org/public/relax-devel/2013-10/msg00009.html.
Modified system test Relax_disp.test_r1rho_kjaergaard to use input guess values of phi_ex in units of ppm^2 instead of rad^2/s^2.
Small change to system test Relax_disp.test_r1rho_kjaergaard. The outcome of kex from system test is in the area of 4-5000. The expected value is 13000. A deeer analysis of the input is needed, to judge what is the correct value.
Created the Structure.test_bug_21814_pdb_no_80_space_padding system test. This is for catching bug #21814, the PDB reading failure when the PDB records are not padded to 80 spaces. The PDB file used for the test is the same file as attached to the bug report.
The verbosity flag is now used in the centre of mass calculations. The pipe_control.structure.mass.pipe_centre_of_mass() function now passes the verbosity argument into the lib.structure.mass.centre_of_mass() function.
Created the new vector_angle() library function. This is located in the lib.geometry.vectors module. The function will calculate the angle between two vectors with sign or direction using the atan2() function.
Addition of a number of unit tests for the new lib.geometry.vectors.vector_angle() function.
Changes to the lib.geometry.vectors.vector_angle() function. This now expects the normal of the plane in which the angle is defined. The original logic was not functional, therefore the angle is forced to be negative if the cross product between the two vectors points in the opposite direction as the normal.
Improvements for the log converter script. This is for the script used to convert SVN messages into a format for the relax release announcement. The script now handles spacing better. Multi-line messages are now concatenated into a single line using a double space between separate sentences and a single space in all other cases.
Improvements for the pipe_control.mol_res_spin.generate_spin_id_unique() function. The unique spin ID now takes into account if the molecule is named or not (for single molecules). This allows the function to be used when dealing with the structural data rather than the molecule, residue, and spin data structure.
Removed the full stop from the printout of the test names in the test suite. This allows for quicker copying and pasting of the test name when running with the --time option and then selecting a single test to run.
Modified the Noe.test_noe_analysis system test to catch bug #21863. This is the failure to create the ref and sat Grace 2D plots in the NOE analysis.
Improved the user feedback when executing a user function in the GUI. The busy cursor is now turned on at the start of the user function wizard page method _apply() and turned off again at the end. This would avoid user confusion, thinking that the program has frozen (as was the case in bug #21862.
Changed the Noe.test_noe_analysis system test to handle the peak intensities correctly. This relates to bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot.
Changed the Noe analysis sample script to properly handle the peak intensity Grace plots. This relates to bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot. These changes match those of the test suite.
Fix for the line numbering for the NOE analysis sample script in the user manual. The line numbering for the code snippets did not match that of the full sample script shown at the start of that section of the NOE chapter.
Added a simple shell script to quickly grep the entire source tree while excluding .svn directories. This will only work on POSIX systems (Linux and Macs).
Fix for the Noe.test_bug_21562_noe_replicate_fail system test. The 'ref' and 'sat' parameters do not exist. Therefore the grace.write user function calls in the system test script have been modified to output the 'intensities' parameter instead.
Complete rearrangement of the specific analysis code for the steady-state NOE. This brings the code into line with the recent specific analysis code rearrangements, specifically in the specific_analyses.relax_disp package.
Changed the Noe auto-analysis to properly handle the peak intensity Grace plots. This relates to bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py. Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter. The reference and saturated intensities will appear as two graph sets within that plot.
Redesign and standardisation of the peak intensity data structure throughout all analyses in relax. The various structures 'intensities', 'intensity_err', 'intensity_sim', 'sim_intensity', and 'intensity_bc' have all been renamed. The new structures are called 'peak_intensity', 'peak_intensity_err', 'peak_intensity_sim' and 'peak_intensity_bc'. This allows the structure to be processed as a standard parameter in the specific analysis API. One very visible consequence is that plots of peak intensities, as well as value files, will now have peak intensity errors. For backwards compatibility, the relax data store method _back_compat_hook() has been modified to catch all previous peak intensity object variants and to standardise and rename these to the new object names. As the parameter is now called 'peak_intensity' rather than 'intensities', all calls to the grace.write and value.write for this parameter have been changed in the auto-analyses, the sample scripts, the test suite and the manual.
Fix for the Noe.test_noe_analysis system test. The grace plots of the peak intensities now have error bars.
The legends in Grace plots are now turned on by default, if the legend flags are not specified. The Noe.test_noe_analysis system test has been updated for the change.
Added matplotlib detection to the dep_check module. This follows step 1 from the planning document at http://thread.gmane.org/gmane.science.nmr.relax.devel/5278.
Added matplotlib to the info module. This follows step 1 from the planning document at http://thread.gmane.org/gmane.science.nmr.relax.devel/5278.
Modified the python_multiversion_test_suite.py script to run the relax information printout. This is to test out the info module on multiple Python versions and to have a record of the setup of each Python version.
Python 3 fixes for the info module. The new processor_name() function was not compatible with Python 3 as the text read from STDOUT needs to be 'decoded'.
The variables in the relax_fit.h file are now all static.
Added the new exp_mc_sim_num argument to the relaxation dispersion auto-analysis. This is in preparation for fixing bug #21869. This argument allows for a different number of Monte Carlo simulations for the 'R2eff' model when exponential curves are fit. It will mainly be useful in the test suite to improve the accuracy of the R2eff errors, while still running a low number of simulations for the other models to allow optimisation to be quick.
Modifications to the Relax_disp.test_m61_exp_data_to_m61 system test. This is to fix bug #21869, the failure of this system test. The number of Monte Carlo simulation for the 'R2eff' model has been increased from 3 to 25 using the new exp_mc_sim_num argument to the dispersion auto-analysis. To keep the test fast, only a single spin is optimised.
Redesign and major clean up of the specific_analyses.jw_mapping package. The code has been broken up into separate modules.
Fix for the default value table documentation in the specific_analyses.jw_mapping package. This was broken in the last commit.
Updates for the rest of relax for the redesign of the specific_analyses.jw_mapping package.
Redesign and major clean up of the specific_analyses.consistency_tests package. The code has been broken up into separate modules. This matches the similar specific_analyses.jw_mapping package.
Redesign and major clean up of the specific_analyses.relax_fit package. The code has been broken up into separate modules. The rest of relax has been updated to handle the changes.
Removed the empty documentation strings from the specific analysis API base class. These are being gradually shifted into the specific_analyses.*.uf modules, so do not belong in the API object.
The specific analysis API classes are now all singletons. This change will reduce the amount of memory used, as these classes are initialised multiple times throughout relax, especially in the test suite. The API objects are not used for local storage so the multiple instance verses singleton design change will make no difference. The singleton design pattern code has been added to the base class specific_analyses.api_base.Api_base so that all classes inherit the _new_() method which implements the singleton.
Shifted the NOE analysis specific user function documentation from the API object to the uf module.
More code refactorisation of the specific_analyses.n_state_model package into new modules. The API object is now in the 'api' module, the remaining private methods have been shifted into the 'optimisation' and 'uf' modules, and the user function documentation moved to the 'uf' module.
Added units tests for package consistency testing for all of the remaining specific analyses.
Fixes for the unit tests for the N-state model specific analysis package changes.
Updated the package _all_ lists for a number of the specific analyses.
Shifted all of the private methods for optimisation from the relaxation dispersion API object. These are now functions of the specific_analyses.relax_disp.optimisation module.
Created the new specific_analyses.relax_disp.uf module. This consists of the private methods of the relaxation dispersion API object which act as the back end for the user functions, as well as the user function documentation, all shifted from the 'api' module.
Shifted the model-free analysis specific API object to the specific_analyses.model_free.api module.
Fixes for the new specific_analyses.model_free.api module.
Created the new specific_analyses.model_free.uf module. This consists of the private methods from the 'main' module which act as the back end for the user functions as well as the user function documentation.
Created the new specific_analyses.model_free.parameters module. This consists of the private methods from the 'main' and 'mf_minimise'. All class methods have been converted into functions.
Created the new specific_analyses.model_free.optimisation module. This consists of the merger of the 'mf_minimise' and 'multi_processor_commands' modules. All the private class methods have been converted into functions.
Shifted all of the model-free specific analysis API methods into specific_analyses.model_free.api.
Clean up and refactoring of the specific_analyses.model_free.bmrb module. The class methods have all been converted into functions, the deleted class is no longer a base class for the specific analysis API class.
The read_columnar_results() method has been removed from the specific analysis API. This is only for backwards compatibility with ancient relax 1.2 and earlier model-free results files, so will never be used by any other analysis.
Converted all of the class methods in specific_analyses.model_free.results to functions. This class has been removed from the API as well.
Renamed specific_analyses.model_free.results to back_compat. This is to make the purpose of the module clearer, to avoid developer confusion.
Shifted the model-free classic_style_doc user function documentation to the 'uf' module.
Shifted the last private method out of the model-free specific analysis API class. It has been converted into a function of the new 'data' module, for lack of a better name.
Shifted some of the specific_analyses.model_free.parameters functions into the new 'model' module.
Removed the test_grid_ops() method from the specific analysis API. This has been shifted into the new lib.optimisation module and converted into a function, breaking a number of circular import kludges.
Fixes for the specific analysis API unit tests. The 'instance' variable used for the singleton design pattern is skipped in the method and object checks.
Redesign of the specific analysis API. All parts of relax using this API now work with the API objects directly. The specific_analyses.setup module has been renamed to specific_analyses.api and the get_specific_fn() function has been eliminated. Instead of calling this, the different parts of relax now obtain the API object by calling the new return_api() function. This results in a large cleanup of the API - method names are no longer changed to a different name.
Fix for the new singleton design of the specific analysis API objects. The use of the class namespace as a storage space has been eliminated. This was causing test suite failures when checking the API objects. For some reason, some of the target function objects were being placed in 'self'.
Created a directory for holding the CaM double rotor frame order synthetic data.
Capitalised the pivot and CoM variables in the base frame order distribution generation script.
Reintroduced the distribution PDB file creation to the frame order test data generation script. This is the generate_base.py script in the test_suite/shared_data/frame_order/cam directory. The ability to create the distribution.pdb file was long lost in this script, and can now be activated using the DIST_PDB class variable.
The Frame Order test data generation base script now loads all structures before rotating them. This allows the progress printout to function correctly by not having any user function printouts as the rotations are occurring.
Created a simple double rotor geometric system to used for this frame order test data generation. The system_create.py script creates the geometric system based on the CoMs of both domains in the parent directory and two perpendicular rotation axes passing through both CoMs. A PDB file of the representation is created by the script.
Improvements and expansion of the frame order test data generation base script. More of the class variables are now defined in this base class and dummy methods are provided to allow certain operations to be skipped (print_axis_system(), axes_to_pdb() and build_axes()). Importantly, the script can now handle multiple modes of motion with the introduction of the key _multi_system() and _state_loop() methods.
Fixes for the calculation of the frame order matrix in the test data generation base script. The matrix generation now handles multiple modes of motion correctly. The total rotation matrix is constructed when looping over the modes by using the dot product of the individual rotation to the total, and then this is used to create the outer product, summed over all states.
The frame order test data generation base script now outputs the frame order matrix to 8 places.
Introduced the ROT_FILE flag to the frame order test data generation base script. This allows the 'rotations.bz2' file creation to be skipped, if set to False. This file takes time to create and is of limited use.
Removed a duplicated state.save call in the frame order test data generation base script.
The save file created by the frame order test data generation base script can now be bypassed. When loading 1,000,000 PDB structures as models into the relax data store, the RAM usage can go over 10 Gb. When trying to save this into a relax state file with the state.save user function, the time required can be over a day. Therefore the SAVE_STATE class variable has been introduced to allow the state.save call to be bypassed.
Created the RDC and PCS back calculated test data for the CaM double rotor frame order model. This consists of a uniform distribution over both rotors, the first centred in the C-domain and the second in the N-domain, and the two axes being perpendicular to each other along the CoM-CoM axis. The distribution consists of 250000 rotated structures. The frame order matrix for this model is also given.
Created a distribution of structures for the CaM double rotor frame order model. This is only for a distribution of 100 structures, to keep the file size to a reasonable size. A PyMOL *.pse file is also included to show the distribution together with the rotor system and the domain positions.
Updated the rotation() method of all the CaM frame order test data generation scripts. The motion_index argument is now accepted by all of the methods to allow the base script to execute correctly.
Fix for the Frame_order.test_generate_rotor2_distribution system test. The rotation() method now must accept the motion_index keyword argument.
Created the Frame_order.test_cam_double_rotor system test for the CaM synthetic data. This will be used to implement the frame order double rotor model.
The CaM double rotor frame order test RDC data now has single quotes around the spin IDs. This allows the data to be loaded in the Frame_order.test_cam_double_rotor system test.
Created subsets of the CaM double rotor frame order test PCS data. This consists of data for only 5 spins, and matches those of the other CaM frame order test data.
Large refactorisation of the frame order package. The private methods of the frame order package specific_analyses.frame_order have now all been shifted into modules. This is to simplify the package by not having huge quantities of code in the _init_ module. Now the code resides in the api, checks, data, optimisation, parameters, and user_functions modules.
Added the double rotor frame order model to the frame_order.select_model user function.
Better support for the parameters of the double rotor frame order model.
Initial implementation of the double rotor frame order model target function. The target function func_double_rotor() has been created as a copy of the func_rotor_qrint() method, modified for the double rotor model. Modifications will likely be needed as the compile_2nd_matrix_double_rotor() and pcs_numeric_int_double_rotor() functions are implemented.
Initial implementation of the lib.frame_order.double_rotor module. This module implements the functions needed to solve the frame order analysis for the RDC (via the frame order matrix) and PCS (numerically). The interfaces have been updated for the double rotor but most of the code still implements the basic rotor model from which it derives.
Fix for the double rotor frame order model when only RDCs are used. The target function was not being aliased when no PCS data was present.
Changed the precision of the deactivated Frame_order.test_cam_double_rotor_pcs system test. This test will run with the command "relax -s Frame_order.test_cam_double_rotor_pcs" and, because of the small angle of the test model, the chi-squared value differences for just the PCS were too small for the previous precision of 1 decimal place.
The double rotor system is now truly perpendicular. This is for the CaM frame order synthetic test data. The two axes were not perpendicular whereas for the model they should be.
Updated the double rotor distribution PDB file for the perpendicular axes. This is for the CaM frame order double rotor synthetic data. The number of structures in this distribution is set to 100 (10 per motional mode). The PyMOL *.pse file has also been updated.
Updated the CaM frame order double rotor synthetic test data for the perpendicular axes. The RDC and PCS data has been recalculated for 250,000 structures, this time with the axes being truly perpendicular.
Added a simple script for analysing the eigensystem of the CaM frame order double rotor test model.
Capitalised the class variables of all of the CaM frame order system test scripts.
Class variable cleanup for the CaM frame order system test scripts. The variables are now all defined in the base script and only overwritten when needed by the individual tests.
Changed the handling of the pivot point in the CaM frame order system tests. The pivot point is now a class variable, rather than being hardcoded into a function. The handling of a second pivot has also been added.
Updated the CaM frame order double rotor system test script to have the correct two pivots.
Changes to the frame_order.pivot user function. The 'order' argument has been added to allow for multiple pivots to be present. The user function backend will store these as cdp.pivot, cdp.pivot2, cdp.pivot3, etc. The 'fix' argument is now defaulting to False to make sure it is always boolean.
The second pivot is now being passed into the frame order target function class.
Simplified the CaM frame order system test base script. The class variables are now always defined, so checking for their existence is pointless. The CONE_S1 is now also defined in the base script as a class variable.
Added support for the new axis_alpha frame order parameter to the specific_analyses.frame_order package.
Implemented the new frame order rotor model parameters in the target function. The parameters {axis_theta, axis_phi} have been replaced by the single axis_alpha. To support the new model construct, the CoM of the entire system is now passed into the target function.
The AXIS_ALPHA parameter is now initialised in the CaM frame order system test base script. The base script was broken a while back due to AXIS_ALPHA not being defined but being checked for.
Improvements for the centre of mass calculation for the frame order model optimisation. This is now only calculated for the rotor models. The CoM is also printed out for better user feedback.
The CaM frame order system tests for the rotor models are converted to the new axis_alpha parameter. 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 alpha.
The CaM frame order system test base script is now using lib.geometry.vectors.vector_angle(). This is for correctly calculating the alpha axis angle for the rotor models.
Fixes for the rotor axis alpha angle conversion in the CaM frame order system test base script. The pivot point is now the point on the rotor axis closest to the reference point (the CoM). Therefore the closest point is now calculated from the pivot point on the axis and the axis vector. This closest point is needed for defining the new minimal parameter set for the rotor models.
Changes for the convert_rotor() method of the CaM frame order system test base script. The method now sets the alpha angle rather than returning it. The method now also resets the pivot point to the point on the rotation axis closest to the CoM.
Fixes for the rotor axis reconstruction in the func_rotor_qrint() frame order target function. This is for the rotor model. The axis alpha angle is now correctly converted into the rotor axis using the CoM and pivot point.
Optimisation is now turned on for the Frame_order.test_cam_rotor2 system test. This is to reveal deficiencies in the handling of the new axis alpha parameter.
The frame order optimisation results unpacking function now supports the axis alpha parameter. This is in the function specific_analyses.frame_order.optimisation.unpack_opt_results().
Updated the chi2 value check in some of the CaM frame order system tests for the rotor model. The chi2 value is slightly different due to truncation and conversion artifacts of the parameter set reduction.
Shifted all of the code for calculating the frame order rotor axis into lib.frame_order.rotor_axis. The new frame_order.rotor_axis module consists of three function for creating a unit vector or the rotor axis using either the axis alpha angle, the two spherical angles or the three Euler angles.
Renamed the specific_analyses.frame_order.user_functions module to uf.
Fix for the optimised chi-squared value check in the Frame_order.test_cam_rotor system test. The reduced parameter set results in a slightly different chi2 value.
Shifted the frame order average domain position info check from the 'optimisation' to 'checks' module.
Fix for the CaM frame order system tests. The axis alpha angle and pivot shifting to the closest point to the CoM in the base system test script now only happens for the 'rotor' and 'free rotor' models. This allows the tests for the isotropic cone models to pass again.
Fixes for all of the CaM frame order optimisation scripts in the test data directories. The frame_order.average_position user function is now essential.
The centre of mass printout in the frame order target function setup now uses the verbosity argument. This means that the printout is not shown for the Monte Carlo simulation optimisation.
Correction for the nu_CPMG to tau_CPMG conversion formula in the dispersion chapter of the manual. In relax, the conversion nu_CPMG = 0.25 * tau_CPMG is used and not nu_CPMG = 0.5 * tau_CPMG.
Merged the Van't Hoff and Arrhenius lines of the dispersion software comparison table of the manual.
Renamed the specific_analyses.relax_disp.disp_data module to specific_analyses.relax_disp.data. This is to match the module naming convention used in the other specific analyses, and as detailed in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/5294.
Updated all of the frame order optimisation scripts for the CaM test suite data. These simple testing scripts were very much out of date and non-function for the current code. Half of the code in these scripts is now implemented in the concise frame_order.pdb_model user function.
Updated the ancient test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py script. This now matches the script of its parent directory.
Simplified all of the CaM frame order optimisation testing scripts. These are for the synthetic test suite data. The unnecessary class structure of the scripts has been eliminated.
The frame_order.pivot user function can now be used to turn the pivot optimisation on and off. If the pivot point is not given, this user function will now just set the fixed flag and nothing else, allowing the optimisation status of a pre-set pivot to be changed.
Added the axis alpha angle to the frame order return_units() API method.
The frame order axis alpha angle is now defined in the grid search from -pi to pi.
Replaced the 'elif' statements with 'if' in the frame order update_model() function. This is to avoid possible future bugs as the logic was not consistent.
Renamed the specific_analyses.api_objects module to parameter_object to better reflect what it is. This contains a single object for the parameter list object and therefore does not need to be generalised for additional types of objects for the specific analysis API.
Updated the module docstring of specific_analyses.parameter_object to match its purpose.
Created a parameter list object for the relaxation dispersion analysis. Instead of using the parameter list object from the base class, the dispersion analysis now defines its own.
Docstring improvements for the add_min_data() parameter list base class method.
Created two new parameter list methods from the relaxation dispersion code. The add_model_info() and add_peak_intensity() base class methods have been created from the relaxation dispersion code. These are just aliases for setting up a number of parameters via add() in a standard way.
The frame order specific analysis API object is now truly a singleton. This should help eliminate some bugs.
Standardised all of the parameter list objects for the specific analyses. All of the specific_analyses packages now contain a parameter_object module which defines all of the parameters. The ordering of these is now consistent between the analyses, the result of which will be more consistent ordering of element in the relax XML state files. The new Param_list.add_csa() base class method has been added to standardise the CSA parameter. And the capabilities of the add_model_info() method has been expanded.
The parameter list objects in the specific analysis API are now singletons. This has no immediate benefit as these classes are only instantiated once. But it will allow for efficient reuse of these objects in the future and for expansions of the specific analysis API.
The frame order pivot points are now stored differently in the current data pipe. Instead of being stored as a list or array of numbers in cdp.pivot, the point is now stored as cdp.pivot_x, cdp.pivot_y and cdp.pivot_z. The second pivot cdp.pivot2 is now stored as cdp.pivot_x_2, cdp.pivot_y_2 and cdp.pivot_z_2. This is to simplify the automated handling of optimisation parameters. Rather than having to convert the pivot_x, pivot_y, and pivot_z parameters to and from a list, the same mechanisms can now be used for all of the optimised frame order parameters. This will be used to hugely simplify many of the functions in the specific_analyses.frame_order.parameters module and eliminate a large source of bugs.
Temporary deactivation of the Frame_order.test_cam_double_rotor system test.
Huge simplification of the specific_analyses.frame_order.parameters.assemble_param_vector() function. The parameters are now assembled in a generic way by looping over cdp.params. The simpler code should also be faster.
Huge simplification of specific_analyses.frame_order.parameters.param_num(). This now simply calls update_model() and then returns the length of cdp.params.
Clean up of the specific_analyses.frame_order.parameters module. The unused and terribly designed assemble_limit_arrays() function has been deleted. And unused imports have been removed.
Simplification of the specific_analyses.frame_order.optimisation.unpack_opt_results() function. Looping over the cdp.params parameter list is now used to minimise the amount of replicated code.
The frame order analysis is now using the special frame order parameter object.
Elimination of the specific_analyses.frame_order.checks.check_rdcs() function. This function duplicates the functionality of pipe_control.rdc.check_rdcs() while not being as comprehensive. Switching to the pipe_control.rdc version minimises the amount of code in the frame order analysis, decreasing the potential for bugs.
Simplified the assemble_scaling_matrix() frame order function. The data_type argument no longer does anything, so has been eliminated.
Clean up of the base_data_types() frame order function and it use. The propagation of the data type list around the frame order code is now greatly reduced. And the alignment tensors and NOESY data have been removed from the base_data_types() function - these are not used.
Docstring fixes for the frame order specific analysis API object. A number of the methods were referring to the base data as being alignment tensors, but this has changed to RDCs and PCSs a long time ago.
Clean up and fixes for the frame order model_statistics() API method. The number of data points 'n' was incorrectly calculated using the original alignment tensor base data.
Eliminated the specific analysis API object base _init_() method. This is no longer needed as the parameter list object is now analysis specific and set up by each analysis type separately. The calls to this method from the derived classes have therefore also been deleted.
Shifted the frame order specific API deselect() method into the Api_common base class. The method has been renamed to _deselect_global() and extended to handle Monte Carlo simulations.
The specific API PARAMS object is now private. Apart from fixing a number of unit tests, these aliased singletons should not be accessed by the rest of relax.
Created the specific analysis API common method _is_spin_param_false(). This simply returns False. The is_spin_param() frame order method has been deleted and this common method is now used instead.
Replaced the frame order specific API model_loop() method. The base method _model_loop_single_global() is used instead.
Replaced the frame order API model_type() method with the base _model_type_global() method. The two methods were identical anyway.
Fixes for the units of the ave_pos_x, ave_pos_y, and ave_pos_z frame order parameters.
Removed the frame order API return_units() method. This method has been superseded by the parameter list object.
Added the PCS and RDC as parameters for the frame order and N-state model analyses. These are now defined in the respective parameter list objects. The base method add_align_data() has been created to avoid code duplication.
Eliminated the last of the specific analysis API return_units() methods. This functionality is now provided by the parameter list object.
Eliminated the model-free specific analysis API data_type() method. This functionality is now provided by the parameter list object.
Converted the N_state_model.test_5_state_xz system test to use a new way to set parameters. Instead of using pseudo-parameters for the value.set user function such as 'p0', 'p1', etc. for the probabilities, which are then converted into the 'probs' parameter with the index taken from the name, instead the index is now directly given. The value.set user function will need to be modified to handle this. The aim is to standardise the parameter list object for the N-state model analysis.
Converted the remaining N-state model system tests to use the new value.set index argument.
Converted all of the N-state model parameters to use the parameter list object. The default_value(), return_data_name() and return_grace_string() API methods have also been deleted as these have been superseded by the parameter list object.
Clean up of the N-state model user function docstrings. The pseudo-parameter names such as 'p0', 'p1', etc. no longer exist.
The new index argument for the value.set user function now defaults to zero. This is for backwards compatibility as the default value of None was not handled by the user function backend.
Fix for one of the value.set user function unit tests. The 'alpha2' N-state model parameter no longer exists, and the '2' is now supplied as index=2.
Shifted the core of the data_names() specific analysis API method into the parameter list object.
Renamed many of the specific analysis parameter list object methods to match the API names. This is to prepare for a decoupling of the parameter list object from the API object.
Updated the relaxation dispersion citation for relax as this is now officially published.
All of the add*() methods of the parameter list object have been made private. This is to prepare the object to be accessible to the rest of relax, so that it can be decoupled from the specific API object.
Shifted the minimisation Grace strings and units into the parameter list object. The return_grace_string() and return_units() functions of the pipe_control.minimise module have been deleted and their contents shifted into the specific analysis parameter list object.
Simplified the pipe_control.minimise.minimise() function. The specific API object only needs to be fetched once.
Eliminated the return_data_name() concept from the specific analysis API. The parameter names can now only have one value, i.e. 's2' is different from 'S2'. In addition, a number of related functions have been deleted form the pipe_control.minimise module as these are now handled by the parameter list object. The deleted functions are return_conversion_factor() and return_value().
Shifted the Brownian rotational diffusion tensor parameters into the parameter list object. This only affects the model-free analysis. The pipe_control.diffusion_tensor module functions default_value(), return_conversion_factor(), return_data_name() and return_units() have been eliminated. These functions have been merged together with the diffusion parameter self._add() calls in the model-free specific parameter list into the new parameter list base class _add_diffusion_params() method. To allow the model-free analysis code to differentiate between diffusion and model-free parameters, the new scope() parameter list base class method has been created. Diffusion parameters return 'global' whereas model-free parameters return 'spin'. The model-free specific API methods default_value() and is_spin_param() have been deleted as these are now provided fully by the parameter list object. The is_spin_param() method has been newly implemented in the parameter list object to check the parameter scope.
Eliminated a lot of unused code from the pipe_control.align_tensor module. This includes the functions data_names(), default_value(), map_bounds(), map_labels(), return_conversion_factor(), return_data_name() and return_units() as well as the unused and very old user function documentation _default_value_prompt_doc_, _return_data_name_prompt_doc_ and _set_prompt_doc_. These are all remnants from the origin of the module - the copying of the diffusion_tensor module. But they have never been used.
Changed the values of the set argument for the parameter list object. The 'generic' value has been renamed to 'fixed' and is now for all permanently fixed parameters of the model - for example the CSA value in a number of analyses. The default set argument value of the _add() method has been changed to 'all' so that any parameters registered via that method are not placed in a special set (unless specified otherwise).
Clean up and fixes for the parameter definitions in the consistency testing analysis. The fixed and calculated parameters are now defined in the correct sets, and the description for tc has been expanded and improved.
Added the ability to automatically create the parameter tables for the user function documentation. These are the tables used in many of the user function docstrings. This has been added to the parameter list base class. The section title is pre-specified by the new _set_uf_title() method, and the table caption and LaTeX label by the _set_uf_table() method. The documentation is generated by calling the uf_doc() method. This uses the new type_string() method to add a compact parameter type string representation to the table. The aim is to eliminate all of the hard-coded tables in the specific analyses which are always very quickly outdated. By automatically creating the tables, this simplifies the codebase and simplifies the addition of new analysis types.
The parameter tables are now properly initialised in all of the specific analyses. This will allow the tables to now be used in the user function documentation.
The auto-generated user function tables can now display the base units.
Spacing fix for one of the diffusion tensor parameter descriptions.
The label and caption for the parameter list user function documentation is now supplied to uf_doc(). This allows different types of tables to be generated, for example the default value is useful for the value.set user function but not value.write, while allowing tables to still be shared.
Expanded the steady-state NOE parameter description.
Expanded the reduced spectral density mapping parameter descriptions.
The default scope for the parameter list object uf_doc() method is now 'spin'. Most of the parameter tables are for setting spin parameters, so this will minimise code.
Fixes for the specific analysis parameter list singleton object. These objects are now really singleton objects and are only initialised once.
Fixes for some of the NOE system tests - the NOE parameter description is now different.
Shifted the user function documentation creation into the parameter list objects. The uf_doc() method will now return the pre-created documentation object, and the original base class method for creating the documentation has been renamed to _uf_param_table().
Shifted all of the user functions to use the auto-generated parameter tables. All of the specific analysis default_value_doc and return_data_name_doc documentation objects have been deleted and replaced with the auto-generated ones. This results in a big code clean up and removes synchronisation issues with the user function documentation quickly becoming out of date when parameters change.
Expansion of the dx.map user function documentation. This now includes tables of the N-state model and relaxation dispersion parameters. A new auto-generated model-free parameter table including the diffusion parameters has been created and is now used instead of the separate diffusion tensor and model-free parameter tables.
Deleted the diffusion tensor _return_data_name_doc_ documentation object. This is no longer used, being redundant with the new parameter list objects.
The frame order parameter tables for the user function documentation are now created.
The dx.map user function documentation now included the frame order parameters.
Different parameter sets can now be specified when creating the parameter tables. This is for the analysis specific parameter list objects and the auto-generated user function documentation.
Clean up of the grace.write user function documentation. The minimisation statistics table has been removed and instead the minimisation statistics are included in the parameter tables of the specific analyses, when appropriate.
Code clean up - deleted the return_data_name_doc and set_doc pipe.control.minimise objects. These user function documentation objects are no longer used. They were also extremely out of date.
Created the parameter list object base class _uf_doc_loop() method. This will be used to loop over all or subsets of the user function documentation parameter tables.
The model-free parameter setting documentation has been shifted into the parameter list object. As the text was quite out of date, it has been updated to the current relax design.
The J(w) mapping parameter setting documentation has been shifted into the parameter list object. This has also been updated to reflect the current design of relax.
The consistency testing parameter setting documentation has been shifted into the parameter list object. This has also been updated to reflect the current design of relax.
The relaxation dispersion parameter setting documentation has been shifted into the parameter list object. The documentation has also been rewritten as it originates from Sebastien Morin back in 2009 and is now very much out of date.
Deleted the relaxation curve-fitting parameter setting documentation. This really didn't say anything.
The N-state model parameter setting documentation has been shifted into the parameter list object.
Updated the two_domain.py N-state model sample script. The value setting for the N-state model is now handled differently.
More updates of the N-state model sample scripts for the value.set user function changes.
Deleted the diffusion tensor parameter setting documentation from the value.set user function. These values have not been able to be set by the value.set user function for over half a decade. Therefore this documentation can only lead to user confusion.
Deletion of the user function documentation in the pipe_control.diffusion tensor module. The _default_value_doc_ and _set_doc_ documentation objects are out of date and no longer used anywhere in relax, so they have been eliminated.
Shifted the model-free parameter writing documentation to the parameter list object.
Rearranged the parameter table ordering in the value user functions. The order now better matches that of the chapters of the user manual and is consistent between the functions.
More reordering of the parameter tables for the value user functions.
Removed all of the prompt.doc_string.regexp_doc documentation objects from the user functions. This is the regular expression documentation which no longer has a purpose. It was for specifying multiple parameters simultaneously in user functions such as value.set, but this functionality has been removed.
Created parameter tables with no additional trailing text. This is used in a few of the user functions.
Updated the value.copy user function documentation for the frame order theory. The value.copy title has been changed to not be spin specific and a table of the frame order parameters has been added.
Improvements for the value.display user function documentation. The N-state model parameter table has been removed as these parameters are not spin specific and cannot be used. And the title has been modified.
Improvements for the value.read user function documentation. The N-state model parameter table has been removed as these parameters are not spin specific and cannot be read from a file. And the title has been modified.
Updated the value.set user function documentation for the frame order theory. The value.set title has been changed to not be spin specific and a table of the frame order parameters has been added. The spin ID documentation has also been rewritten.
Changed the title in the value.write user function documentation.
Changed the title for the value user function class.
Docstring update for the relaxation dispersion linear_constraints() function.
The pivot point x, y and z coordinates are now registered as parameters of the frame order analysis. These are stored as the parameters pivot_x, pivot_y and pivot_z.
Docstring fix in the relaxation curve-fitting linear_constraints() function.
Converted the status.escalate variable into module variables for lib.errors and lib.warnings. This variable is set by the command line flag '-e' or '--escalate'. By converting it into a module variable, the lib.errors and lib.warnings warnings are now independent of relax.
Created the lib.warnings.TRACEBACK variable. When True, this will cause stack-traceback to be printed out with the warning. This is to decouple the traceback printout from the warning to error escalation.
Created the new '-r' or '--traceback' relax command line option. If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors. This allows for finer debugging control.
Clean up of the debugging command line options. The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised. This gives greater control of a powerful feature added to relax by Chris MacRaild. The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
Reordered the debugging command line options and removed the '-r' shortcut.
The lib.errors module is now really independent of relax - the compat module is no longer used. Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
Decreased the amount of newlines around the printout from the '--error-state' command line option.
Improved support for printing stack tracebacks with RelaxWarnings. The '--traceback' command line option will now show a full traceback. A replacement warnings.showwarning() function has been written to write out the traceback before the warnings.formatwarning() replacement function is called.
Divide by zero avoidance fix for the rotor frame order model module lib.frame_order.rotor.
Removed the dependency on the relax dep_check module from the relax library. This is to further decouple the library from relax.
Added a script for testing the independence of the relax library.
Removal of all unused imports in the lib.dispersion package.
Improvements to the test_library_independence.py development script. This script for checking the independence of the relax library will now recursively import all packages and modules in the library and report at the end a list of all failures.
Shifted the Python 2 and 3 compatibility module 'compat' into the relax library.
Shifted the pipe_control.sequence.validate_sequence() function into the relax library. For this, the new lib.sequence module has been created. This change is for better library independence. A circular import with lib.io and lib.arg_check has also been resolved.
Shifted the read_spin_data() and write_spin_data() functions from lib.io to lib.sequence.
Removed the dependence on the relax 'dep_check' module from the lib.frame_order package. This is for more independence of the relax library.
Added the missing Bioinformatics journal to the bibtex file journal name aliases.
Huge clean up of all unused imports in relax. These were found using the find_unused_imports.py development script. A number of these changes significantly decrease the possibilities of circular imports appearing in the future. And this also makes the relax library more independent from the rest of relax.
Shifted the data_store.relax_xml module into the relax library as lib.xml. This module contains a couple of functions which are used for converting Python objects into an XML representation and back again. These are used not only by the relax data store, but also a number of the structural objects in the relax library (which are themselves placed in the relax data store). This makes the relax library more independent from the rest of relax.
Shifted many of the pipe_control.structure.geometric functions into the relax library. All but two functions from the pipe_control.structure.geometric module are independent of the relax data store. These have been shifted into the new lib.structure.geometric module. This removes most of the remaining relax dependencies in the relax library.
Removed the automatic axis labelling in the lib.software.grace.write_xy_header() function. This is the automatic labelling based on the parameter Grace strings and units of the specific analysis type. This is now preformed by the specific analyses themselves so the automatic code is not needed or used. This allows the dependence on the pipe_control.pipes module and the specific analysis API to be removed making the relax library now 100% independent from the rest of relax.
Editing of the relax command line option descriptions.
Created a new test category for the relax test suite - the software verification tests. This is part of the full test suite or can be run by itself using the new --verification-tests command line option. Such tests are best described by https://en.wikipedia.org/wiki/Verification_and_validation_(software). These tests will be used to make sure that the design aims of the relax source code are satisfied. For example that the relax library is independent from the rest of relax. Or that the package _all_ lists actually contain all modules and sub-packages (these tests are currently part of the unit tests).
Shifted the relax library independence developer script into the software verification tests. The functionality of the devel_scripts/test_library_independence.py script is now within the Library.test_library_independence software verification test. Therefore the script has been deleted.
Updated the text for the software verification tests in the test suite.
The relaxation dispersion auto-analysis now outputs the R20, R20A, R20B, and R1rho0 parameters. This includes both text files and 2D Grace plots.
Python 3 fix for one of the old scripts in the test suite directories.
Improved error messages for when the GUI is launched but the wxPython installation is broken. Now the case of a broken wxPython installation is handled rather than just a missing installation. The dep_check module will store the import error message, and relax will now report that back to the user.
Python 2.5 and 2.6 compatibility for the Library.test_library_independence verification test. The importlib package is not available in these Python versions, but the code in the Python 2.7 library file importlib/__init__.py is compatible all the way back to Python 2.3. Therefore the importlib functions have been copied directly into the system test script and the importlib dependency removed.
Updated one of the OMP model-free results files for the different ordering of parameters in the XML. The changes to the parameter setup for the model-free analysis means that the XML files are now ordered differently.
Fix for the Test_data.test_count_relax_times_r1rho relaxation dispersion unit test for Python 3.2+. The '%s' representation of floating point numbers is different on these Python versions - the number of decimal places used are different by default.
Added Python 3.4 support to some of the development scripts.
Added 4 more relaxation dispersion system tests to the blacklist for when C modules are missing. This allows these 4 tests to be skipped in the system test rather than failing with "RelaxError: The exponential curve-fitting C module cannot be found.".
Changed the backward compatibility hook for old state files for the spectrometer frequency. The behaviour has been changed so that the data pipe structure spectrometer_frq_list is now sorted. This simply allows a number of tests to pass on Python 3.3+, a user would not notice any differences.
Fixes for two relaxation curve-fitting system tests for Python 3.3+. These are the Relax_fit.test_curve_fitting_height and Relax_fit.test_curve_fitting_volume system tests which fail due to accuracy differences and a bad call to the UnitTest method assertEqaul() which should have been an assertAlmostEqual() call.
Added the matplotlib module to the Python binary and module seeking script.
Added dataset for system test. System test for CPMG dataset, (http://dx.doi.org/10.1073/pnas.0907387106) Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 SOD1-WT at 25 C.
Added system test to analyse data. System test for CPMG dataset, (http://dx.doi.org/10.1073/pnas.0907387106) Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 SOD1-WT at 25 C.
The debugging command line option no longer turns on RelaxWarning tracebacks. These tracebacks can be separately turned on with the --traceback command line option.
Made name for system test shorter and moved data to shorter folder name. Regarding bug #21953 - weird performance of grid search.
Modified system test for cleaner implementation of tests. Regarding bug #21953 - weird performance of grid search.
Lowered range for grid search by factor 10 for kex to now between 1-10000. Regarding bug #21953 - weird performance of grid search.
Changes to system test Relax_disp.test_hansen_cpmg_data_auto_analysis. Regarding bug #21953 - weird performance of grid search. The grid search needed to be increased by +1 and lowering of some results by one digit.
Lowering of precision in Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric. Regarding bug #21953 - weird performance of grid search.
Changes to system test Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff. Regarding bug #21953 - weird performance of grid search. The grid search needed to be increased by +1 and lowering of some results by one digit.
Changes to system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis. Regarding bug #21953 - weird performance of grid search. The grid search needed to be increased by +1 and changes of some results.
Modified system test Relax_disp.test_sod1wt_t25_to_cr72. Regarding bug #21953 - weird performance of grid search.
Modified dw and kex in system test Relax_disp.test_tp02_data_to_tap03. Regarding bug #21953 - weird performance of grid search.
Split system test Relax_disp.sod1wt_t25_to_cr72 into part as setup and test part. Regarding bug #21953 - weird performance of grid search.
Started implementation of error analysis bug. Regarding bug #21954 - Order of spectrum.error_analysis is important.
Small edit of the relax command line option descriptions.
Undid the modification of dw and kex in system test Relax_disp.test_tp02_data_to_tap03. Regarding bug #21953 - weird performance of grid search. The number of iterations needed to be increased from 2000 to 2500 to allow the values to be found.
Further extended system test Relax_disp.test_sod1wt_t25_bug_21954_order_error_analysis. Regarding bug #21954 - order of spectrum.error_analysis is important.
Extended --gui-tests Relax_disp.test_hansen_trunc_data. Regarding bug #21954 - order of spectrum.error_analysis is important. To catch errors in this dataset.
This time the blacklisted relaxation dispersion system tests have been correctly reduced. Only one blacklisted test did not require the C modules to be compiled.
Shifted all of the dispersion model descriptions and parameter lists to the variables module. The descriptions and parameter lists which were part of the relax_disp.select_model user function backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables. The descriptions have also all been standardised. The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
The General.test_bug_21720_pipe_switching_with_tab_closure GUI test now works without compiled C modules.
Updated the release checklist for the new minfx version 1.0.6 release. See https://gna.org/forum/forum.php?forum_id=2456 and https://freecode.com/projects/minfx.
Fixes for the specific API _set_param_values_spin() method for lists and dictionaries. This is for the value.set user function to allow it to handle parameters of different types. For example the 'R2' parameter in the relaxation dispersion analysis. This API common method now sets all dictionary elements, list elements, or the variable to the given value.
Created the new specific_analyses.relax_disp.variables.PARAMS_R20 list. This variable is a list of all R20 parameters of the dispersion models. It has been shifted out of the parameters module.
Created a relaxation dispersion specific API set_param_values() method. This originates from the base _set_param_values_spin() method from the api_common module. The method has been extended to handle the R20 parameter types - generating the current dictionary keys as needed.
Expanded the relaxation dispersion auto-analysis to allow the grid search to be turned off. By setting the grid_inc argument to None, the grid search will be turned off. As a replacement, the value.set user function is used for all model parameters to set them to their default values prior to minimisation. This design is for speed as optimisation from the defaults is often - though not always - good enough. It can be used, for example, in the test suite to make the system tests much faster.
Changed the default R20 relaxation rate from 15 to 10 rad.s^-1. This is probably closer to the average rate expected for molecules studied by NMR.
The R2eff dispersion parameter now also defaults to 10 rad.s^-1.
Expanded the dispersion specific API set_param_values() method for the 'r2eff' and 'i0' parameters. This now sets these parameter values correctly if the value sent into the method is

New in relax 3.1.5 (Feb 6, 2014)

New in relax 3.1.4 (Feb 6, 2014)

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, as reported by Martin Ballaschk (https://gna.org/users/mab). This catches the failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present.
Added the truncated data for creating a system test to catch bug #21562. This bug was reported by Dhanas Muthu (https://gna.org/users/dhanas) and is the failure of the NOE analysis when spectra are replicated. 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, reported by Dhanas Muthu (https://gna.org/users/dhanas). This is the failure of the NOE analysis when spectra are replicated. 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:
Fix for bug #21499, the failure of the rdc.write user function. The rdc.write user function fails for back-calculated RDC data. The fix was to handle the missing interatom.rdc_data_types variable.
Fix for bug #21522 and bug #21520. These bugs are the structure.write_pdb user function creating an incorrect MASTER record and 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 counts for the ATOM, HETATM, and TER records are now only for a single model, rather than being the sum for all models together.
Fix for bug #21561, the structure.create_diff_tensor_pdb user function failure with no simulations. Bug #21561 was reported by Martin Ballaschk (https://gna.org/users/mab). The problem was that the simulation axes of the tensor PDB file were not being initialised correctly when no Monte Carlo simulations had been run.
Fix for bug #21562, the failure of the NOE analysis when spectra are replicated. This bug was reported by Dhanas Muthu (https://gna.org/users/dhanas). The problem was that the NOE overfit_deselect() method was deselecting all spins which do not have exactly 2 intensity values. This is incompatible with replicated spectra as the number will be greater than two. The check has been modified to deselect spins only when the number of intensity values are zero or one.

New in relax 3.1.3 (Jan 18, 2014)

Changes:
Fix for the parameters listed for the IT99 dispersion model in the manual
Improvements and addition of many links to the lib.dispersion.cr72 API documentation.
Spacing fix for the lib.dispersion.cr72 module docstring
Improvements and addition of many links to the lib.dispersion.dpl94 API documentation.
Improvements and addition of many links to the lib.dispersion.it99 API documentation.
Improvements and addition of many links to the lib.dispersion.lm63_3site API documentation.
Improvements and addition of many links to the lib.dispersion.lm63 API documentation.
Improvements and addition of many links to the lib.dispersion.m61b API documentation.
Improvements and addition of many links to the lib.dispersion.m61 API documentation.
Improvements and addition of many links to the lib.dispersion.mmq_cr72 API documentation.
Improvements and addition of many links to the lib.dispersion.mp05 API documentation.
Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_3d API documentation.
Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_expanded API documentation.
Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_star API documentation.
Added the 'NS CPMG 2-site 3D full' model to the lib.dispersion.ns_cpmg_2site_3d module docstring
Improvements and addition of many links to the lib.dispersion.ns_mmq_2site API documentation.
Improvements and addition of many links to the lib.dispersion.ns_mmq_3site API documentation.
Improvements and addition of many links to the lib.dispersion.ns_r1rho_2site API documentation.
Improvements and addition of many links to the lib.dispersion.ns_r1rho_3site API documentation.
Small docstring edit for the lib.dispersion.mp05 module
Improvements and addition of many links to the lib.dispersion.tap03 API documentation.
Improvements and addition of many links to the lib.dispersion.tp02 API documentation.
Epydoc URL simplifications in the lib.dispersion.mp05 module
Epydoc docstring edit in the lib.dispersion.mmq_cr72 module
Improvements and addition of many links to the lib.dispersion.tsmfk01 API documentation.
Copyright notice updates for the lib.dispersion modules changed today
Added links to the relax wiki, API documentation, and relax website to all dispersion models in the manual. This is to make it easier to find additional information about each of the models
Updated the author list for the submitted paper for the relaxation dispersion analysis
Added the primary reference for relaxation dispersion in relax to the dispersion chapter of the manual. This is the paper which is not published yet
Removed the single quantum R1rho-type data reference in the introduction of the dispersion chapter of the manual. This is redundant as R1rho data is always single quantum

New in relax 3.1.2 (Jan 18, 2014)

Changes:
The average_intensity() dispersion function now accepts the offset argument. This is for better support of combined offset and spin-lock varied R1rho-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 sr #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:
Partial fix for bug #21338 - the bad sRGB profile in some PNGs. This is only partial as some files are still to be converted (the original Bruker logo, and the 16x16, 22x22 and 32x32 sized Bruker icons).
Fix for bug #21460, the failure of relaxation dispersion due to incorrect spectrometer information. There was only one place in the dispersion analysis which failed due to a spectrometer frequency not containing any relaxation data - in the insignificance testing in the auto-analysis.
Loosened the chi2 check in the Relax_disp.test_korzhnev_2005_15n_mq_data system test. This is to allow the test to pass on a 32-bit Linux (Mageia 1) test system.

New in relax 3.1.1 (Jan 18, 2014)

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, dw_AB, dw_BC, dwH_AB, dwH_BC, kex_AB, kex_BC}.
The 'NS MMQ 3-site' numeric model - the model for 3-site exchange using 3D magnetisation vectors with the parameters {R20, ..., pA, pB, dw_AB, dw_BC, dwH_AB, dwH_BC, kex_AB, kex_BC, kex_AC}.
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 {R1rho', ..., pA, pB, dw_AB, dw_BC, kex_AB, kex_BC}.
The 'NS R1rho 3-site' numeric model - the model for 3-site exchange using 3D magnetisation vectors with the parameters {R1rho', ..., pA, pB, dw_AB, dw_BC, kex_AB, kex_BC, kex_AC}.
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. /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.
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.
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.
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.
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.
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.
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.
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.
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

New in relax 3.1.0 (Jan 18, 2014)

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 R1rho-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 R1rho 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, ..., phi_ex, kex}.
The 'LM63 3-site' SQ CPMG-type analytic model - the original Luz and Meiboom 1963 3-site fast exchange equation with parameters {R20, ..., phi_exB, k_B, phi_exC, k_C}.
The 'CR72' SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R20A = R20B is assumed with the parameters {R20, ..., pA, dw, kex}.
The 'CR72 full' SQ CPMG-type analytic model - the full Carver and Richards 1972 2-site equation for most time scales with parameters {R20A, R20B, ..., pA, dw, kex}.
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, ..., phi_ex, pA.dw^2, kex}.
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 {R20A, ..., dw, k_AB}.
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, dw, 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 R20A = R20B is assumed with the parameters {R20, ..., pA, dw, 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 {R20A, R20B, ..., pA, dw, 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 R20A = R20B is assumed with the parameters {R20, ..., pA, dw, 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 {R20A, R20B, ..., pA, dw, kex}.
The 'M61' R1rho-type analytic model - the Meiboom 1961 2-site fast exchange equation for on-resonance data with parameters {R1rho', ..., phi_ex, kex}.
The 'M61 skew' R1rho-type analytic model - the Meiboom 1961 2-site equation for all time scales with pA >> pB and with parameters {R1rho', ..., pA, dw, kex}.
The 'DPL94' R1rho-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the 'M61' model for off-resonance data with parameters {R1rho', ..., phi_ex, kex}.
The 'TP02' R1rho-type analytic model - the Trott and Palmer 2002 2-site equation for all time scales with pA >> pB and with parameters {R1rho', ..., pA, dw, kex}.
The 'TAP03' R1rho-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 {R1rho', ..., pA, dw, kex}.
The 'MP05' R1rho-type analytic model - the Miloushev and Palmer 2005 off-resonance 2-site equation for all time scales with parameters {R1rho', ..., pA, dw, kex}.
The 'NS R1rho 2-site' R1rho numeric model - the model for 2-site exchange using 3D magnetisation vectors with the parameters {R1rho', ..., pA, dw, 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, dw, dwH, kex}.
The 'MMQ 2-site' MMQ-type numeric model - the model for 2-site exchange whereby the simplification R20A = R20B is assumed with the parameters {R20, ..., pA, dw, dwH, 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:
Started to implement the framework for relaxation dispersion system tests.
Copied 'test_suite/system_tests/relax_fit.py' for relaxation dispersion.
Started to implement relaxation dispersion system tests.
Created the user_functions.relax_disp module by copying user_functions.relax_fit. This file now needs to be modified to suit the needs of relaxation dispersion.
Manually created the relax_disp user functions. This is equivalent to Seb's commit for the prompt.relax_disp module. The equivalent changes to the user_functions.relax_disp were hand edited. Added functions to select the experiment type and mathematical model used. These functions allow the user to select the experiment type (cpmg or r1rho) as well as the mathematical model to fit the data (fast or slow).
Copied the 'relax_fit.py' script to 'relax_disp.py'. This file, obviously, will need to be modified to suit the needs of the relaxation dispersion code.
Modified the script so it will test for fast-exchange curve fitting from CPMG data. Data and functions to treat it are still missing.
Added a test for CPMG data in slow-exchange and changed the name of the test for fast-exchange.
Copied the 'relax_fit.py' specific functions to 'relax_disp.py'. The code will now need many many many changes to suit the needs of relaxation dispersion.
Made a few changes towards a functional relaxation dispersion code. This includes several modifications as well as the addition of the exp_type() function.
Moved the relax_time() function to cpmg_frq() and made other small changes. Still much (!) work is needed for this code to be complete.
Renamed 'cdp.frq' to 'cdp.cpmg_frqs' so it is not confusing with the spectrometer frequency. Indeed, 'cdp.cpmg_frqs' points to the CPMG pulse train frequency (nu_cpmg).
Changed all instances of 'relax_times' to 'cpmg_frqs' and made other small changes.
Changed 'relax_time' instances to 'cpmg_frq'.
Changed the index name and description. The description might change later to be more appropriate when the code is more mature...
Included the setting of the spectrometer frequency and uncommented a few lines of code. Of course, this won't work until the sample data has been introduced and the right names for the different files be input in the system test script...
Fixed many formatting errors and made the 'relax_disp' code accessible (pipes, interpreter, etc.). These changes also include a coming back to using the C code 'math_fns/relax_fit.py' since there is still no such code associated to relaxation dispersion. This will allow working in the code without relax crashing and complaining about the lack of a C module name 'relax_disp.py'.
Added the user function cpmg_delayT() which allows setting the CPMG constant time delay T used for the analysed dataset. This follows a post at https://mail.gna.org/public/relax-devel/2009-01/msg00027.html.
Made a few changes so the cpmg_delayT() function now works.
Added the user function cpmg_frq() and added examples to the user function cpmg_delayT().
Corrected remaining frq instances to cpmg_frq when appropriate to avoid confusion and corrected a few related things in the system test script.
Made the cpmg_frq() function accept only None for the reference spectrum and corrected a typo.
Added the parameters for the slow- and fast-exchange regime.
Added the parameters for the slow- and fast-exchange regime in the function data_names().
Corrected a few formatting issues and still added parameters for the slow- and fast-exchange regime.
Corrected a few formatting issues and still added parameters for the slow- and fast-exchange regime. Formatting issues corrected were spotted by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00045.html.
A bit more changes to introduce parameters for CPMG relaxation dispersion.
Introduced CPMG parameters into the function return_grace_string() and corrected formatting issues.
Introduced relaxation dispersion parameters in the function return_data_name().
Changed the default cpmg_frq value in cpmg_frq() from 0 to None.
Added a relaxation dispersion dataset in the system-test. This was kindly provided by Dr Flemming Hansen (flemming AT pound DOT med DOT utoronto DOT ca) and was previously published in Hansen, Vallurupalli & Kay (2008) J. Phys. Chem. B, 112, 5898-5904. The original format was different and was modified to better suit the way relax handles datasets. Finally, the information contained here were written in a 'readme' file placed in the same directory as the dataset itself to allow referencing and acknowledgments.
Added 'Sparky' formatted files to the system-test so the files can be input and development of the branch continued.
Changed the format of the CPMG frequency and corrected the names of some input files.
Added an unresolved file to meet the script requirements.
Copied the script for the fast-exchange regime to the slow-exchange regime.
Modified the newly copied script so it is effectively for the slow-exchange regime.
Added details to the readme file and changed the directory name where the sample data is located. The directory is now named 'dataset_1-a'. This contains data recorded at 500 MHz. Data recorded at 800 MHz will be put in a directory called 'dataset_1-b'.
Created a directory for the data recorded at 800 MHz and put a readme file explaining its origin.
Added the relaxation dispersion dataset recorded at 800 MHz in the system-test. This was kindly provided by Dr Flemming Hansen (flemming AT pound DOT med DOT utoronto DOT ca) and was previously published in Hansen, Vallurupalli & Kay (2008) J. Phys. Chem. B, 112, 5898-5904. The original format was different and two formats were made ('generic' and 'sparky'), as for the dataset recorded at 500 MHz.
Renamed the directories containing the sample datasets provided by Flemming Hansen. The names are now more obvious as to their content...
Added an 'unresolved' file to the 800 MHz data and moved (and modified) some files (sequence and readme) so there is only one copy for the 500 and 800 MHz data. This prevents duplicated files.
Changed the object names so they are lower case as they should be, based on the rest of the code. Made the equivalent change in the function assemble_param_vector() to allow the system-test to go further..
Corrected capitalisation issues for param names.
Rearranged commands in the scripts. The experiment type and exchange regime will have to be input before the cpmg pulse train delay T.
Introduced a RelaxError when chosing 'r1rho' as experiment type as this won't be implemented now. Efforts will be concentrated on the CPMG code first, then on the R1rho code.
Added tests, print statements and other code to the relaxation dispersion specific functions.
Started to implement a function for calculating the effective transversal relaxation rate (R2eff).
Converted the function linear_constraints() for relaxation dispersion needs.
Started to implement the scaling matrix for scaling the 'R2eff' values. This might change in the future as other possible curve fitting parameters ('R2', 'Rex', 'kex', 'R2A', 'kA', 'dw') might need some scaling.
Completed the scaling matrix code.
Imported relaxation dispersion in grace user functions.
Added a missing quote which prevented the user manual to be sconstructed.
Started to implement a function for reading 'R2eff' values directly.
Started to put equations and references in the user function docstrings and also corrected a small typo.
Corrected the way the scaling matrix is assembled.
The scaling values are now based on the default values for the different parameters which were slightly modified. The only parameter for which the average is still used (as for intensities in the 'relax_fit.py' code) is 'R2eff'.
Continued to implement the user function calc_r2eff(). This follows a discussion at https://mail.gna.org/public/relax-devel/2009-01/msg00067.html.
Copied 'test_relax_fit.py' to 'test_relax_disp.py'. This will allow the design of a few unit tests for the relaxation dispersion code.
Added two unit tests for the relaxation dispersion code and fixed errors in the corresponding code. More unit tests will be added soon to help debugging and developing.
Added two more unit tests.
One more unit test.
One more unit test for the relaxation dispersion code.
Added more unit tests and tried to debug what was uncovered by these tests. Still more work is needed for debugging...
A few fixes based on the unit tests problems.
Changed the default value for 'int_cpmg' to avoid an impossible mathematical situation: ln(0).
Fixed a bug where the 'id' argument was not set. This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00127.html.
Started to make changes for multiple field relaxation dispersion analysis. This seems necessary, so maybe we should not support single field analysis of relaxation dispersion at all. -> Kovrigin et al. (2006) JMagRes, 180: 93-104. The changes made here are only a first draft and may not work. In particular, maybe the spectrum.read_intensities(), relax_disp.cpmg_frq(), spectrum.replicated(), spectrum.error_analysis(), and deselect.read() functions will need to know the magnetic field to which the particular dataset is associated... In fact, the different datasets should be input first and their R2eff calculated independently. In a second step, the actual relaxation dispersion curve fitting should be made with all data.
Fixed a bug which prevented the manual pdf to be compiled. The problem was caused by a ':' character in the references (after the volume number, as usual). This was changed for a '.' character. Equations were fine.. Moreover, a better formatting was done by adding ':' characters after the word 'are' before enumerations.
Fixed the unit tests. This is as proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00132.html.
Started to implement the reading of 'r2eff' by relax_data.read() by first writing a system test.
Updated a few dosctrings and tried to improve the system test.
Removed the obsolete function 'relax_disp.r2eff_read()'. R2eff values will be read directly by 'relax_data.read()'.
Reordered a few functions for alphabetical reasons.
A small fix to the system test. However, is this fix the solution or is there something wrong with the reading of data (such as 'R2eff') by relax_data.read()? Shouldn't the data, for example 'R2eff', be available in 'cdp.mol[0].res[0].spin[0].R2eff_val[0]' or 'cdp.mol[0].res[0].spin[0].R2eff[0]' for the 1st spin of the 1st residue in the 1st molecule?
Fixed an import (as well as a few comments). This however introduces an error concerning the 'chi2' being undefined in the C module for relaxation dispersion...
Solved an issue created during the merge process concerning the 'return_data_name_doc' call. The solution is based on the code in 'specific_fns/relax_fit.py'.
Brought the relaxation dispersion branch into sync with the 1.3 line. There were many design changes within the 1.3 line that required that the old relaxation dispersion code be updated.
Fixes for the relaxation dispersion system tests. The install path is now in the status object, and not in _main_.
GPLv3 license updates for all files not found in the trunk.
Import fixes for the specific_analyses.relax_disp due to the recent trunk package layout redesign.
Made the non-API methods of the specific_analyses.relax_disp.Relax_disp class private.
Improvements for the GUI representation of the relax_disp user functions.
More import fixes for the new package layout.
Fix for the relax_data.read user function call in the Relax_disp.test_read_r2eff system test. The column numbers must be supplied.
Some more fixes to make the Relax_disp.test_read_r2eff system test pass. These are again changes needed due to the trunk now being very different.
The cpmg_frq argument of the relax_disp.cpmg_frq user function can now be None.
The cpmg_frq argument of the relax_disp.cpmg_frq user function can now be an integer as well as a float.
Updates for the relaxation dispersion system test scripts for the newer design of relax. A number of changes were required as the code was quite old.
Created the lib.dispersion.equations module. This is a translation of Sebastien Morin's C code in the old relax_disp branch.
Created a very basic initial target function class for relaxation dispersion. This code is a translation of Sebastien Morin's C code in the old relax_disp branch.
The relaxation dispersion specific analysis code now uses the Python target function rather than the C.
Fix for the Relax_disp.test_curve_fitting_cpmg_fast system test variable names.
Added the model argument to the dispersion target function class to select between different equations.
The relaxation dispersion target function class now imports the equations from lib.dispersion.equations.
The relaxation dispersion target function class raises a RelaxError when the model is not implemented.
Modified all the relaxation dispersion test data Sparky files at 800 MHz. The last three lines of the files were not properly formatted.
Converted all of the raising of RelaxErrors in the specific_analyses.relax_disp to the new standard. This is for Python 3 support.
Converted all print statements in specific_analyses.relax_disp to function calls. This is for Python 3 compatibility.
Converted the prompt unit tests for relaxation dispersion to the current relax design.
Updated the target_functions package _all_ list for the relax_disp module.
Another fix for the prompt argument unit tests of the relax_disp user functions.
Big changes to the front end of the relax_disp.select_model user function. The model strings have been changed and are now programmatically added to the user function documentation. The main text has also been redesigned. And the new model 'exp_fit' has been added which allows just the exponential curves to be fit.
Python 3 import fix for the specific_analyses.relax_disp module.
Updated the documentation in specific_analyses.relax_disp to use the user_functions package design. The user_functions.objects.Desc_container and user_functions.data.Uf_tables objects are now used to construct the relaxation dispersion documentation.
The relax_disp.select_model backend now handles the 'exp_fit' model.
Removed all aliasing of the current data pipe in specific_analyses.relax_disp as this is in _builtin_.
The specific_analyses.relax_disp module now uses the parameter list object to define parameters. This allows the now unused methods data_names(), default_value(), return_data_name(), and return_grace_string() to be deleted and their contents copied into the parameter definitions in the class _init_() method.
Alphabetical arrangement of methods in the specific_analyses.relax_disp module.
Docstring cleanups for the specific_analyses.relax_disp module.
The relaxation dispersion specific analysis now aliases API base methods for a number of methods.
Import cleanup in the specific_analyses.relax_disp module.
The relaxation dispersion specific analysis module is now using the base _data_init_spin() method. This is aliased to data_init() and replaces the old non-functional method.
Created the relax_disp.spin_lock_field user function. This is used to set the spin-lock field strength of a given R1rho spectrum.
Created the relax_disp.relax_time user function. This is almost a direct copy of the relax_fit.relax_time user function, but has been modernised.
Fix for the printout from the relax_disp.relax_time user function - the time is no longer divided by 1k.
Expanded the dispersion model parameters to include the exponential curve parameters.
Clean up of some of the old relax_disp user functions - many argument types are now numbers rather than floats.
Unit test fixes for the prompt relax_disp user function argument checks.
Added the specific_analyses.relax_disp module to the unit test checking of the specific API.
Big cleanup of the relaxation dispersion code to match the analysis specific API. All methods not belonging to the API have been made private. The arguments and keyword arguments for the API methods now match the API.
Completely redesigned the minimisation parts of the specific_analyses.relax_disp module. Instead of dealing with the optimisation of individual spins, groups of spins are now optimised together. This allows for the clustering analysis of relaxation dispersion. The method _block_loop() has been created to loop over spin blocks, but it currently only returns individual spins. However with the rest of the code designed to handle this loop, only this function needs to be modified to enable clustering. The method _param_num() has also been added to determine the total parameter number per spin block. The data structures sent into the Dispersion target function class have also been redesigned to handle spin blocks instead of individual spins.
Modified the relax_disp.cpmg_frq user function to match relax_disp.spin_lock_field. Both the front and back ends now use the same logic as the relax_disp.spin_lock_field user function and will allow some sanity to the analysis specific code.
The relax_disp.cpmg_frq and relax_disp.spin_lock_field user functions now create cdp.curve_count. This is an integer which indicates the number of exponential curves which are to be optimised per spin block.
The relaxation dispersion analysis specific _param_num() method now takes the number of curves into account.
Better setup checking for the relaxation dispersion specific analysis minimise() method.
Renamed cdp.curve_type to cdp.model to better explain the variable.
Fixes for the dispersion specific analysis separating R2eff from R2. There is one R2eff parameter per exponential curve, but only one R2 per model. The code now better handles this.
The dispersion specific methods now handle one R2eff and I0 parameter per exponential curve.
Better management of the global relaxation dispersion data. The user functions relax_disp.cpmg_frq, relax_disp.spin_lock_nu1, and relax_disp.relax_time now maintain data structures in the current data pipe of the unique frequencies, fields, and times (sorted) as well as the number of frequencies, fields, and times. This data is used by the minimise user function back end to set up the target function, and will be required by many other parts of the analysis.
The dispersion specific _assemble_param_vector() method now handles multiple R2eff and I0 values. These spin structures are dictionaries holding multiple values.
Created the dispersion specific _exp_curve_loop() method for looping over each exponential curve. This yields the index and key for each curve, simplifying the handling of this data.
Expanded the relax_disp.select_model user function documentation to cover R2eff and I0. These parameters and how they are optimised are now better described.
Updated the relaxation dispersion target function class to handle the recent changes.
First attempt at a target function for fitting exponential curves for relaxation dispersion.
Added some synthetic data to test the 'exp_fit' relaxation dispersion model fitting. These are just basic synthetic exponential curves. R2eff and I0 should be very easy to find.
The lib.software.sparky.read_list_intensity() function can now handle lowercase in the residue names.
Created the Relax_disp.test_exp_fit system test for checking the relaxation dispersion 'exp_fit' model.
The specific_analyses.relax_disp module is now using minfx correctly. The minfx grid search is no longer part of generic_minimise() and must be called separately.
The relax_disp function _grid_search_setup() now operates in the same way as the relax_fit code. This function originates from the 'relax_fit' specific analysis code, but that code has since evolved. The 'relax_disp' code now mimics the new code, returning lists of grid search increments and upper and lower limits.
The scaling flag is now initialised in the relaxation dispersion target function class.
Created the lib.curve_fit package and associated unit tests. This will be used for holding modules such as for exponential curve-fitting required for the relaxation dispersion analysis.
Created the new lib.curve_fit.exponential module for exponential curve-fitting. This contains the single exponential_2param_neg() function which will be used for the relaxation dispersion target functions. This is based on Sebastien Morin's function exp_2param_neg in maths_fns.exponential.c in his dormant inversion-recovery branch.
Typo fix for the new lib.curve_fit.exponential.exponential_2param_neg() function.
The relaxation dispersion func_exp_fit() target function now uses exponential_2param_neg(). This is from the lib.curve_fit.exponential module.
Fix for the relaxation dispersion specific _assemble_scaling_matrix() method. The values were all inverted - the matrix should hold values on the same order as the parameter values.
Fix for the func_exp_fit() relaxation dispersion target function. The parameter index was not correctly calculated.
The 'exp_fit' relaxation dispersion model now uses the minfx.grid sparseness argument. This is used to skip all parts of the grid search belonging to a different exponential curve or different spin. If the number of curves is N and the number of spins M, the grid size decreases from inc*(2NM) to (inc2)N*M. For lots of spins and curves, this is a huge decrease.
The relaxation dispersion specific _disassemble_param_vector() method is now functional. This should allow the minimise user function to complete.
Fixes for the dispersion specific _assemble_param_vector() method. The R2eff and I0 spin dictionary structures are now checked for their keys before pulling the value out.
Fix for the relaxation dispersion grid search. The lower and upper bounds are no longer continually scaled with each optimisation.
Increased the speed of the Relax_disp.test_exp_fit system test by using a smaller grid search.
The relaxation dispersion target function class back_calc variable now matches the values variable. Instead of being a temporary structure which is overwritten for each spin and each exponential curve, the structure now matches the dimensions of the values variable and hence is persistent per function call. This allows external code to access the structure - for example for data back calculation in the relaxation dispersion specific analysis module.
Fixes for the dispersion specific _back_calc() method. This method still has a long way to go before it is of any use.
Created a custom base_data_loop() method for the relaxation dispersion analysis. This defines the base data as the peak intensities of a single exponential curve and yields the spin container and exponential curve key identifying the individual curves.
Activated Monte Carlo simulations for the relaxation dispersion analysis. This required a bit of work. The key parts were renaming _block_loop() to the API method model_loop() as that is exactly what the model_loop() method is supposed to do, converting a bunch of API common spin-based methods to handle dispersion clustering, and to modify existing methods from Seb's original branch to handle the base_data_loop() method. The following methods have been added or modified. _back_calc(): This method has been modified to handle clustering and the returning of peak intensities from only one exponential curve. _exp_curve_index_from_key(): This new method is used to convert exponential curve key into the corresponding index. _intensity_key(): This new method is for converting an exponential curve key and relaxation time into the corresponding intensity key. create_mc_data(): This method is now functional and handles the data from the base_data_loop() method. return_error(): This method now handles the data from the base_data_loop() method. set_selected_sim(): This new method has been modified from the common _set_selected_sim_spin() method but modified for the model_loop() method. sim_pack_data(): This method now handles the data from the base_data_loop() method. sim_return_param(): This new method has been modified from the common _sim_return_param_spin() method to suit the model_loop(). sim_return_selected(): This new method has been modified from the common _sim_return_selected_spin() method again to suit the model_loop().
Modified the Relax_disp.test_exp_fit system test to be faster and not create plots which it cannot.
The Relax_disp.test_exp_fit system test now checks some of the final results.
The relaxation dispersion parameter errors from Monte Carlo simulations are now stored. Previously MC simulations could run, but the errors were not being calculated and stored. The sim_return_param() method was empty. This method is now complete. In addition the set_error() method has been created for setting the parameter errors. And the _exp_curve_key_from_index() and _param_index_to_param_info() auxiliary methods added to facilitate data access.
Expanded the checking in the Relax_disp.test_exp_fit system test.
Converted all relaxation dispersion parameters to lowercase. This is so the variable names match the parameter names identically, avoiding problems with some of the shared methods of the specific analysis API.
The spin parameters are now set up last by the relax_disp.select_model user function back end.
Added 'spin_lock_nu1' as a dictionary type parameter of the relaxation dispersion specific analysis.
Rearrangements of the 2 system tests of Fleming Hansen's CPMG data. The system tests are now called Relax_disp.test_hansen_cpmg_data_fast_2site and Relax_disp.test_hansen_cpmg_data_slow_2site, and the system test scripts are now all in test_suite/system_tests/scripts/relax_disp/.
Created a basic initial auto-analysis script for relaxation dispersion. This currently only supports the optimisation of the 'exp_fit' diffusion model, but has all of the infrastructure set up to make it easy to add other models.
Added the relaxation dispersion module to the auto_analyses package _all_ list.
The relaxation dispersion system test class now imports the auto-analysis. This fixes an import order error.
The Relax_disp.test_exp_fit system test now uses the auto_analyses.relax_disp analysis.
Fix for the relaxation dispersion auto-analysis. The exponential fit model is now selected prior to optimisation.
Removed the relax_disp.select_model user function call from the exp_fit dispersion system test script. This is performed by the auto-analysis and not during setup.
Added testing for spin clustering to the Relax_disp.test_exp_fit system test. This includes calls to the new relax_disp.cluster user function and the checking of pipe variables holding the clustering information.
Fix for the spin ID string for the relax_disp.cluster user function. This is for the exp_fit.py relaxation dispersion system test script.
Implemented the relax_disp.cluster user function. This is for clustering spins together for a dispersion analysis.
Clustering is now enabled for relaxation dispersion. The model_loop() analysis specific API method now loops over the spin clusterings, allowing a cluster of spins to be optimised simultaneously to one set of model parameters.
Fixes for the spin clustering for relaxation dispersion. Both optimisation and Monte Carlo simulations were affected by these bugs.
Speed up of the Relax_disp.test_exp_fit system test by cutting the grid size down to 3 increments.
Expanded the write_results() method of the relaxation dispersion auto-analysis. More Grace graphs are now being produced, and the Rex file creation is now model dependent.
Fix for the relax_disp.cluster user function. The 'free spins' category is now not deleted when empty.
Created an icon set for relaxation dispersion.
Renamed the relaxation dispersion test suite data directory to 'dispersion'.
Changed the relax_disp.cpmg_frq user function id argument to spectrum_id. All the relax_disp user functions now operate with the spectrum IDs instead of experiment IDs.
The relax_disp.cpmg_delayT user function backend now uses the spectrum ID rather than experiment ID.
Expanded the relax_disp.exp_type user function to include the fixed period CPMG experiments.
The relax_disp.cpmg_delayT backend can now handle the 'cpmg fixed' experiment type.
The relax_disp.cpmg_frq user function can now handle values of None. The float function is no longer used if the value of None is encountered.
Updated the dispersion system test script for Flemming Hansen's data. This script should now be close to the final form for a relaxation dispersion analysis of CPMG data with a fixed relaxation time period.
Combined all the system test scripts of Flemming Hansen's fixed time period CPMG data. For details of this data, see http://thread.gmane.org/gmane.science.nmr.relax.devel/3790/focus=3827.
Fixes for the renaming of the relaxation dispersion test suite shared data directory.
Started to redesign how R2eff is handled in the relaxation dispersion analysis. Instead of being part of the optimisation of the dispersion model, it will itself be the model named 'R2eff' (converted from the 'exp_fit' model). This model will either use the calc user function to determine R2eff when the fixed relaxation period experiment is selected, or fit exponential curves using the relax_fit C module for the variable relaxation period experiments. The R2eff values will then be copied over for each dispersion model in the auto-analysis using the value.copy user function.
Created the relax_disp.plot_exp_curves user function. This is to be used to create 2D graphs of the exponential curves (relaxation time verses peak intensity) as the grace.write user function plots are not very nice - the curves from each spectrometer field strength and dispersion point are mixed into one curve.
The relaxation dispersion auto-analysis is now created plots of the exponential curves.
The R2eff model now works for the variable time relaxation period and exponential curve-fitting.
The relax_disp.select_model user function now checks for the compiled C module when required.
Expanded the new analysis wizard in the GUI to accommodate the relaxation dispersion auto-analysis. Now the buttons are a matrix of 4x2 with the NOE, R1, R2, and model-free analyses at the top and two new blank buttons have been added to the bottom. One will be used for the dispersion analysis.
Created some basic graphics for the relaxation dispersion analysis fur use in the GUI.
Added the correct sized graphic for the relaxation dispersion button in the new analysis wizard.
Created the relaxation dispersion button in the new analysis wizard.
Created the initial version of the relaxation dispersion auto-analysis GUI frame. This is built from copying lots of code from the NOE, R1, and R2 analyses. The dispersion specific parts will be added later.
The relaxation dispersion GUI analysis now has an element for selecting the models to be optimised.
Removed some unneeded checks in the relax_disp.exp_type user function.
Added a GUI element to the relaxation dispersion auto-analysis for selecting the experiment type.
The relax_disp.exp_type user function has been shifted to the new analysis wizard. Instead of being one of the elements on the relaxation dispersion analysis frame, it is now placed between the analysis selection page and the data pipe page of the new analysis wizard. The user function execution is delayed until the set up of the frame, just after the execution of the pipe.create user function. This will allow the frame to be set up differently for each experiment type.
Extended the tooltip for the experiment type GUI element in the relaxation dispersion frame.
Improvements to the tooltips in the relaxation dispersion analysis frame of the GUI.
Changed the peak intensity wizard for the relaxation dispersion frame to match the other analyses.
Unused import removal from the gui.analyses.auto_relax_disp module.
Missing import in the gui.analyses.auto_relax_disp module.
Added support for all the relaxation dispersion user functions in the Peak_intensity_wizard object.
Modified how the fixed time period is specified in the Flemming Hansen data system test. Instead of using relax_disp.cpmg_delayT user function, the relax_disp.relax_time user function will be used. The functionality is duplicated and relax_disp.cpmg_delayT is not needed.
Modified the Spectra_list GUI element to handle relaxation dispersion data.
The relaxation dispersion GUI analysis now uses the dispersion parts of the peak intensity elements. This includes activating the dispersion parts of the Spectra_list GUI element for displaying the spectrum ID with associated metadata and the dispersion parts of the Peak_intensity_wizard for loading the data.
The relaxation dispersion auto-analysis is now correctly executed from the GUI. The GUI data gathering is also now complete in the assemble_data() method.
Added some more module variables to specific_analyses.relax_disp for the experiment types.
The relaxation dispersion auto-analysis now performs the peak intensity error analysis. This is essential for when the GUI is used.
More Unicode characters are now used in the relaxation dispersion GUI analysis frame. The model parameter lists have also been improved.
Removed the spectrum.error_analysis user function call in the exp_fit.py dispersion system test script. This is now performed by the auto-analysis.
Fixed for the error_analysis() method of the relaxation dispersion auto-analysis. The method can now handle missing spectrometer field strength data.
More fixed for the peak intensity error analysis method of the relaxation dispersion auto-analysis. The fixed relaxation time period type experiments can now be handled.
Elimination of the relax_disp.cpmg_delayT user function. This user function is not necessary as the relax_disp.relax_time user function serves the same purpose. The use of relax_disp.relax_time instead allows for code sharing between the fixed and variable time period relaxation dispersion experiment types.
Elimination of the relax_disp.calc_r2eff user function. This user function, which is non-functional anyway, is not needed. The calculation of the R2eff values will occur with the optimisation of the 'R2eff' model (with a call to the calc user function for the fixed time period experiment types) so direct calculation through a specific user function is not needed.
Improvements to the GUI text subscripting in the relaxation dispersion analysis frame.
Removed the temporary relaxation dispersion SVG graphic for the GUI analysis.
Redesign of the graphic for the relaxation dispersion analysis. This is a modification of the r1.svg graphic to show roughly the graphic as in "Protein NMR Spectroscopy, Principles and Practice" by Cavanagh, Fairbrother, Palmer and Skelton.
Editing of the relaxation dispersion analysis graphic.
Added the relaxation dispersion graphic to all of the dispersion GUI user functions missing a graphic.
Redesign of the relaxation dispersion models in the relax_disp.select_model user function front-end. The models have been renamed and better defined based on the experiment type (CPMG or R1rho).
The relaxation dispersion scaling matrix assembly now uses lib.mathematics.round_to_next_order(). This allows the printed out I0 values for the optimisation of the exponential curves to be easier to scale back to the real value.
The Relax_disp.test_hansen_cpmg_data_fast_2site system test now uses the R2eff model. The equivalent slow exchange system test also uses the model. This model will be used to find the R2eff values from the fixed relaxation time period data.
Fix for some RelaxError printouts in the relaxation dispersion specific code.
The relaxation dispersion class variables for the experiment types are now used for all comparisons. This should avoid random bugs.
Fix for the calculation part of the relaxation dispersion auto-analysis. This is for the fixed relaxation period data types.
The 2D Grace plots of the exponential curves are now skipped for the fixed relaxation period data types. This is in the relaxation dispersion auto-analysis.
Started to implement the relaxation dispersion analysis specific calculate() method. This will be used to calculate the R2eff/R1rho values for the fixed relaxation time period data types and is equivalent to Sebastien Morin's relax_disp.calc_r2eff user function which was deleted (see http://thread.gmane.org/gmane.science.nmr.relax.scm/17336).
Converted the specific_analyses.relax_disp module into its own package. This is to allow the code to be broken up into separate modules to simplify the analysis.
Shifted out all of the variables and dispersion data specific code into separate modules. The dispersion data private methods have been converted into functions of the specific_analyses.relax_disp.disp_data module. The package variables have also been shifted into the specific_analyses.relax_disp.variables module to avoid circular imports.
Alphabetical ordering of the functions of the specific_analyses.relax_disp.disp_data module.
Created the specific_analyses.relax_disp.disp_data.loop_all_data() function. This is to loop over all possible base relaxation dispersion data (spectrometer frequencies then dispersion points).
Updates for the dispersion user functions for the changes in specific_fns.relax_disp.
Typo fix in the new loop_all_data() function.
Created the lib.dispersion.calc_two_point_r2eff() function. This is for calculating the R2eff/R1rho value for the fixed relaxation time data.
Improvements to the specific_analysis.relax_disp.disp_data module. The function loop_all_data() has been expanded to include the relaxation time period into the loop. The functions return_intensity() and return_key() have been added to return peak intensities and the key corresponding to the data returned by loop_all_data().
Fixes for some latent bugs in the specific_analyses.relax_disp.disp_data module. The checks for the CPMG-data type in a number of functions now uses the CPMG_EXP list instead of fixed strings.
Completed the relaxation dispersion calculate() method. This allows the R2eff/R1rho values to be calculated for the fixed relaxation time period experiments through the calc user function.
Created a script for running a full relaxation dispersion analysis on Flemming Hansen's data. This is located in the shared data directories and is not part of the test suite as a full analysis will take far too long.
Updated the models in the script for the full relaxation dispersion analysis of Hansen's data.
Updated the backend of the relax_disp.select_model to handle the new model names.
Spun out a number of dispersion methods into the new specific_analyses.relax_disp.parameters module. This is a module of functions relating to the parameters of the relaxation dispersion models.
More spacing before the sectioning printouts in the relaxation dispersion auto-analysis.
Modified the printouts of the relax_disp.select_model user function.
Fix for the relaxation dispersion auto-analysis. The data pipes created for each model optimised are now switched to prior to any operations on the pipe.
Changed the phi_ex parameter in the LM63 model back to rex.
Changed the Grace string for the rex parameter to be phi_ex.
Converted all of the specific_analyses.relax_disp.parameters module to handle different models. The R2eff and I0 parameters are now only part of the 'R2eff' model and all other standard parameters belong to all of the other models.
Shifted all of the constant relaxation dispersion variables into the specific module. All of the dispersion code now uses the variables of specific_analyses.relax_disp.variables.
Renamed the lib.dispersion.equations.fast_2site() function to r2eff_LM63(). The number of relaxation times has also been replaced by the number of dispersion points.
Added the return_cpmg_frqs() and return_spin_lock_nu1() functions to specific_analyses.relax_disp.disp_data.
Updates to the relaxation dispersion auto-analysis. The Grace plots created are now more dependent on the current model, so that dispersion curves are only created for the 'R2eff' model. The specific_analyses.relax_disp.variables module is now also being used.
Started to redesign the relaxation dispersion target function class. The input data is now expected to be R2eff/R1rho data and all mentions of exponential curves have been eliminated. The func_exp_fit() target function has been deleted as it is not used - as now the _minimise_r2eff() method in the dispersion specific analysis class is used instead. And the func_fast_2site() target function has been renamed to func_LM63().
Redesigned the optimisation code of the dispersion analysis specific class for the new target functions. This includes the assembling of R2eff/R1rho values instead of peak heights, and a number of small fixes.
Shifted the LM63 dispersion model functions into the new lib.dispersion.lm63 module.
The reference spectrum is now not included when counting the number of dispersion points.
Fix for the lib.dispersion.lm63 module and parameters of zero are now gracefully handled.
Fixes for the func_LM63() dispersion target function.
Shifted the R2eff/R1rho value and error assembly into specific_analyses.relax_disp.disp_data. This is in the new return_r2eff_arrays() function. The code has also been debugged and made functional.
Added support for handling missing data in the relaxation dispersion analysis. This support was mentioned in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3835.
Added a FIXME to a comment about the hardcoded Bootstrap number for relaxation dispersion.
Started to add support for Monte Carlo simulations for the relaxation dispersion models. This is for all models except 'R2eff'. The changes are extensive but incomplete. The new functions disp_point_key_from_index() and disp_point_index_from_key() have been added to the specific_analyses.relax_disp.disp_data module, but the disp_point_index_from_key() function still needs work. The _back_calc() method of the specific_analyses.relax_disp.Relax_disp class has been redesigned, as well as base_data_loop() method and all methods which depend on it.
Updated the relaxation dispersion system tests of the Hansen CPMG data for the new models. The models are now 'LM63' and 'CR72', and the tests have been renamed to Relax_disp.test_hansen_cpmg_data_LM63 and Relax_disp.test_hansen_cpmg_data_CR72.
Update of the specific_analyses.relax_disp package docstring.
Fix for the linear constraints setup of the 'R2eff' relaxation dispersion model. There are no constraints, so the specific_analyses.relax_disp.parameters.linear_constraints() function now returns A and b values of None.
Basic fix for the _back_calc_r2eff() relaxation dispersion method. A variable was misnamed.
Major redesign of the relaxation dispersion data model in the relax data store. The data model now revolves around the three concepts of the spectrometer frequency, the dispersion points, and the relaxation times. Peak intensity data is now handled through averaging using the new specific_analyses.relax_disp.disp_data.average_intensity() function. R2eff/R1rho values are now referenced by a key generated from the spectrometer frequency and nu_CPMG frequency or nu1 spin-lock field strength. All of the specific_analyses.relax_disp package has been standardised around these concepts. This simplifies all of the modules of the package and removes a large number of latent bugs.
A number of fixes to partly enable Monte Carlo simulations for the non 'R2eff' dispersion models.
Finally Monte Carlo simulations for the relaxation dispersion models now work. This was a simple fix for the specific_analyses.relax_disp.parameters.param_index_to_param_info() function.
Created truncated data files of the Hansen CPMG data. This consists of residues 70 and 71 and will be used to massively speed up the system tests.
The truncated Hansen CPMG data is now in the form of Sparky peak lists.
Now all of the Hansen CPMG data is present as truncated Sparky peak lists.
Speedup for the relaxation dispersion system tests which use Flemming Hansen's CPMG data. The system test script now reads the truncated data files (of only residues 70 and 71) to minimise the time required to read the data and store it in the relax data store.
Added a script to the test suite shared data for analysing the truncated Hansen CPMG data.
Fixes for the LM63 dispersion CPMG model. The 'r2' model parameter is now an array as there is one R2 value per magnetic field strength. And the 'rex' parameter has been renamed to 'phi_ex' and is scaled quadratically with the field strength within the optimisation target function.
Fix for the setup of the relaxation dispersion GUI analysis. The base method add_execute_relax() has been renamed to add_execute_analysis().
Added support for interfacing with Art Palmer's CPMGFit program. The two new user functions relax_disp.cpmgfit_input and relax_disp.cpmgfit_execute have been created to interface with CPMGFit. The first creates the per spin system CPMGFit input files as well as a batch script for executing CPMGFit with all the input files. The second bypasses the batch script and allows CPMGFit to be executed from within relax. This mimics the palmer and dasha user functions. The back end code is in the new specific_analyses.relax_disp.cpmgfit module.
Created the Relax_disp.test_hansen_cpmgfit_input system test. This is for checking the operation of the relax_disp.cpmgfit_input user function conversion of Flemming Hansen's CPMG R2eff values into input files for CPMGFit. A relax state file containing the results of an analysis of an 'R2eff' model analysis of the truncated data has been added to the test suite data to speed up the test and to check the loading of dispersion state files.
Created a directory for the results of the CPMGFit program using Hansen's truncated CPMG data. The script 'cpmgfit.py' has been added to create the input files for CPMGFit and execute the program. The input and batch files have been added to the repository as well.
Added the results from NESSY of the analysis of Flemming Hansen's truncated CPMG data. This is only for the truncated data of residues 70 and 71. All files, except for the PNG graphics, have been added to the repository. The 'summary' file has been created to hold the data from NESSY's summary tab, as this is not stored in the NESSY saved state and is permanently lost after closing NESSY.
A dispersion saved state from the prompt or script UI can now be associated with a GUI analysis.
Created the Relax_disp.test_hansen_trunc_data GUI test for checking the GUI dispersion auto-analysis. This checks the full operation of the relaxation dispersion GUI analysis, without checking the final results (to be added later).
Fixes for the change to the new spectrometer.frequency user function and associated data structures.
Removed the preview button from the file selection GUI element of the CPMGFit user functions. These are the relax_disp.cpmgfit_execute and relax_disp.cpmgfit_input user functions.
The relaxation dispersion specific code now uses the changes of the spectrometer.frequency user function. This simplifies the handling of magnetic field strength data.
More fixes to the relax_disp branch for the changes of the spectrometer.frequency user function.
Changes to the CPMGFit input files due to the new spectrometer.frequency user function.
The relax_disp.cpmgfit_execute user function now correctly calls CPMGFit. The -grid command line option has been added and the output for each spin is sent to a special output file.
Updated the input files and added the output files for the CPMGFit program with Hansen's CPMG data. This is for the data truncated to residues 70 and 71.
Fixes for the relax_disp branch for the spectrometer.frequency user function changes.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test. This is for the recent spectrometer.frequency user function changes.
The specific_analyses.relax_disp.disp_data.loop_frq() function can now handle missing data. This allows the loop to yield a single value of None when the spectrometer information has not been loaded and enables R1rho analyses at a single field strength.
Fix for the LM63 dispersion model target function - the scaled Phi_ex value is now used for the R2.
Fixes for the relaxation dispersion auto-analysis for the LM63 model. The Rex parameter is now the phi_ex parameter.
Added printouts of the optimised parameters to the Relax_disp.test_hansen_cpmg_data_LM63 system test. This includes the conversion to the equivalent CPMGFit parameters.
Massively increased the precision of the R2eff error analysis. The hard-coded simulation number variable is now set to 100000. This appears to be necessary for reliably reproducing results in the subsequent dispersion models.
Created the specific_analyses.relax_disp.disp_data.spin_has_frq_data() function. This is for determining if a spin has peak intensity for the given spectrometer field strength.
Updates some scripts for the spectrometer.frequency user function change.
Created a script to calculate the R2eff rate errors extremely precisely for Hansen's CPMG data. This uses 1 million Bootstrap simulations for calculating the errors. The 'r2eff_values.bz2' is saved after deleting the spin specific r2eff_sim structures so that the file drops from 388 Mb in size to 7.3 kb.
The CPMGFit script for Hansen's CPMG data now starts with the high precision error r2eff_values.bz2 file. This ensures consistency between comparisons between relax, NESSY, CPMGFit, etc.
Removed the '_trunc' part of the nessy_results directory from the NESSY final save file.
The relaxation dispersion loop_point() function can now return the reference point. This is enabled via the skip_ref argument.
Created the relax_disp.nessy_input user function front and backends. This user function takes the data in the relax data store and creates a NESSY save file to be opened within NESSY. The backend is the new specific_analyses.relax_disp.nessy module. For the GUI frontend, graphics for icons and the wizard have been taken from the NESSY repository file pics/nessy_new.png@r1088 in the trunk.
A script has been added to create the NESSY input for Flemming Hansen's CPMG data.
Updated the NESSY results for Flemming Hansen's CPMG data for the R2eff values with high precision errors. A file containing the log or printouts from NESSY has been added for reference.
Updated the NESSY log from the Hansen CPMG data of residue 70 to remove the NESSY errors. These were removed with the commit r1090 to the NESSY trunk.
Split up the r2eff_values.bz2 save file into the results files for each data pipe. This is for Flemming Hansen's CPMG data truncated to residues 70 and 71. This is to simplify the system tests which use this data.
Large simplification of the Relax_disp system tests using Hansen's CPMG data. Instead of calculating the R2eff values in the test, these are read from the high error precision results files in test_suite/shared_data/dispersion/Hansen. This allows the model parameters to be consistently found and to be identical between different runs of the test.
Added a file which compares the results for the LM63 model with Hansen's CPMG data between all programs. This currently includes relax, NESSY and CPMGFit.
Added a printout to the specific_analyses.relax_disp.cpmgfit.translate_model() function.
The dispersion system test script for Hansen's CPMG data can now run stand-alone.
The log barrier constraint algorithm is now used for the relaxation dispersion optimisation. This is to allow constraints in the absence of gradient target functions. The constraints have been turned on by default in the auto-analysis.
Changed the dispersion GUI tab to use the model names from specific_analyses.relax_disp.variables.
The spectrum wizard now uses the spectrometer.frequency user function rather than frq.set. The frq.set user function is now called spectrometer.frequency.
An upper limit of 200 rad/s has been added to the linear constraints for the R2 dispersion parameters.
Fixes for the checking in the Relax_disp.test_hansen_cpmgfit_input system test.
The relaxation dispersion auto-analysis now calls the relax_disp.plot_disp_curves user function. This user function is not implemented yet, but will be used to create plots of the dispersion curves.
Implemented a basic graph for the relax_disp.plot_disp_curves user function. This simply plots out the nu_CPMG value or spin-lock field verses the R2eff/R1rho values from the experiment. The graph of the back calculated R2eff/R1rho values from the model fit is still to be added.
Fix for the linear constraints for the 'R2eff' model. The A and b matrices are no longer set to None, as this kills the auto-analysis or any analysis when constraints are turned on. Now the constraints 0

New in relax 3.0.2 (Nov 27, 2013)

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 2Da^2(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.

New in relax 3.0.1 (Nov 27, 2013)

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 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 w2 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 w2.
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 w1, the indirect dimension in a 2D experiment. The description has also been fixed.
Fixes for all of the peak intensity reading functions - the w1 and w2 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 omega 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 (https://gna.org/projects/minfx/) bug (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 tau 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 tau 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 (https://gna.org/users/mab).
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:
Bibtex fixes required for proper latex2html compilation.
Fix for the Palmer.test_palmer_omp for the different Modelfree4 binaries. The gcc and pdf binaries are now properly detected and the slightly different results are now correctly checked for.
The graphics.fetch_icon() function can now return either the absolute or relative path to the icon. This is a partial solution for bug #21042.
Fix for bug #21042. The docs/latex/fetch_docstrings.py now asks the graphics.fetch_icon() function for the relative path to the icon rather than the absolute path.
The fetch_docstrings.py script now asks for the Unix '/' separator through graphics.fetch_icon(). This is a final fix for bug 21042. The graphics.fetch_icon() function now accepts the 'sep' argument. This defaults to os.sep. But the docs/latex/fetch_docstrings.py script uses the Unix '/' separator to obtain a LaTeX correct path on MS Windows.
Modified the create_mc_data() method to partly fix bug #21079. Some spins with local tm models remain selected despite not containing any data. These are handled explicitly. Instead of a RelaxNoModelError being raised, the method returns None to indicate that something went wrong.
Final fix for bug #21079. This is the failure of the dauvergne_protocol auto-analysis when the "local tm" global model is selected. The Monte Carlo create_data() method not skips data from the base_data_loop() if the create_mc_data() method returns None.
Fix for bug #21097. This was a simple typo. It has not been encountered before because it is in a rarely encountered RelaxError.
Fix for bibtex warning 'Warning--string name "mb" is undefined'. Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
Fix for latex bibtex string 'cp' instead of 'cj'. Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
Another fix for bibtex string 'cp' instead of 'cj'. Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
Fix for bug #21187 - the corrupted PDB issue with protons atom numbers of zero. The bug was reported by Martin Ballaschk (https://gna.org/users/mab). The fix was to allow for spin containers in the relax data store to have the same atom number, as long as the atom names are different.
Modified the Monte Carlo simulation printout behaviour for the minimisation related user functions. This is to help in fixing bug #21190. This includes the calculate, grid_search, and minimise user functions. The new multi-processor is_queued() method is used to determine if the optimisation code of the specific analysis has queued rather than run the calculations. If queued, the 'Simulation X' text will not be printed out. This avoids printing out all the text at the start before anything has happened. The specific multi-processor optimisation code must provide it's own printouts when each calculation is complete.

New in relax 3.0.0 (Nov 27, 2013)

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 enviroment.
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 .
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(w) mapping analysis. This now reveals the same bug but for the J(w) 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 . 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(w) 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 (http://gna.org/bugs/?20873). This is from Troels E. Linnet (http://gna.org/users/tlinnet). 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 (http://gna.org/users/tlinnet).
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(w) 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 . 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(w) 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 . 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 (http://gna.org/users/tlinnet) 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 (https://gna.org/users/tlinnet). 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 (http://gna.org/bugs/?20873). This was reported by Troels E. Linnet (http://gna.org/users/tlinnet). 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

New in relax 2.2.5 (Mar 29, 2013)

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 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) now generates field strength dependent Rex files. The idea comes from a suggestion by Angelo Figueiredo 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) 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 (http://www.nmr-relax.com/api/).
Added Epydoc hyperlink markup for the bug tracker in the system test docstring where missing. This is for a better API documentation (http://www.nmr-relax.com/api/).
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.

New in relax 2.2.4 (Mar 18, 2013)

New in relax 2.2.3 (Mar 12, 2013)

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.
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 https://gna.org/bugs/?20531.
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 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.seq user function units argument is no longer read-only. This is needed for some of the GUI tests in the frame_order_testing branch.
Bugfixes:
Fixes for the structure.delete user function. This can now handle no data being present, the spin and interatomic data containers are now have their structural data properly deleted, and printouts have been added so the user knows what has happened.
Bug fix for the arg_check.is_float_matrix() function for when the dimensions are not given.
Fix for the structure.add_atom user function for the internal structural object. The atomic positions for each model are now correctly set.
Formatting fixes for the generic_fns.structure.pdb_write module.
Fix for the classic_style() method of the model-free specific Macro class. This was identified by the new Mf.test_bug_20531_molmol_macro_write_relaxfault system test, but would probably never be encountered by relax users. It is not related to the bug this test is trying to catch. The problem is if spins have model-free parameters set up but there is no model-free model initialised - then the Molmol and PyMOL macro creation would fail.
Fix for bug #20531. This is the bug of the RelaxFault during the final stages of the auto_analysis.dauvergne_protocol model-free analysis when the Molmol and PyMOL macros are being created. The problem was caused by model m9 (just the Rex parameter) when trying to determine what the order parameter for fast (< 200ps) motions is. The code was assuming that the model-free model would always contain an order parameter.
Fix for the generic_fns.structure.pdb_write.het() function - the record now has trailing whitespace. The PDB records require trailing whitespace to the 80th character position.
Fixes for many of the generic_fns.structure.pdb_write functions. The PDB records are now all filled with whitespace up to the 80th character.
Fix for the creation of HET PDB records in the internal structural object. The residue name and chain ID were mixed up.
Fix for the generic_fns.structure.pdb_write.ter() function. Whitespace to character 80 is now being added to the TER PDB records.
Fix for the creation of the FORMUL PDB records by the internal structural object. The component number is now set to the index of the hetrogen plus one. This number should have been a sequential number starting at 1 and is not related to the residue number in any way.
Fix for the generic_fns.structure.pdb_write.model() function. The correct amount of whitespace is now added to the end of the record.
Fix for the internal PDB reading - the MASTER record was being marked as a molecule. Now this record is checked for and the molecule loop terminated.
Bug fix for the XYZ 3D structure file reader. The atom name is now correctly set up for each atom in the file. The element type setting has also been simplified.
Fix for bug #20603, the relaxation data right click menu failure. The problem was that there was that the last menu item specified had no contents. This item has been removed.
Fix for bug #20563, the end failure of the model-free auto-analysis. This was reported by Stanislava Panova (https://gna.org/users/stacy). The problem was related to the Monte Carlo simulations. The generic_fns.monte_carlo.create_data() function is now asking for the errors associated with a certain data point, even if that data point does not exist. The solution was to check if the relaxation data ID string is present in spin.ri_data_err before accessing the key-value pair (in the specific API _return_error_relax_data() common method).
Bug fix for the maintenance of the spin ID lookup table metadata. This is important for small molecules. Non-unique IDs were being placed into the lookup table,resulting in incorrect spin containers being sometimes used. Now the molecule container has the _res_name_count and _res_num_count metadata and the residue container the _spin_name_count and _spin_num_count structures. These are updated via metadata_update() and are used by the spin_id_variants() function to create a list of purely unique spin IDs.
The spin_id argument to the residue.delete user function is no longer read-only. This allows spin ranges or other complicated IDs to be specified. This is needed for the Bmrb GUI tests to pass.
Fix for the package _all_ list checking unit tests - *.pyc files are now skipped.
Fix for one of the RelaxError messages from the SpinList.add_item() method.

New in relax 2.2.2 (Feb 14, 2013)

Features:
Improvements to the relax API documentation
Changes:
Updated the release checklist to include the devel_scripts/log_converter.py script usage.
Modified the relax manual subtitle as this is no longer only for relaxation analysis.
Docstring fix for the maths_fns.vectors.random_unit_vector() function (this is for the API documentation at http://www.nmr-relax.com/api/).
Epydoc docstring fix for the dfunc_standard() N-state model target function (this is for the API documentation at http://www.nmr-relax.com/api/).
Epydoc docstring fixes for the diffusion tensor objects of the relax data store.
Added and edited a number of module docstrings.
Module and package docstrings additions/improvements for the SCons scripts.
Lots of module and package docstring updates for the analysis specific code.
Module docstring additions and improvements for the relax data store modules.
Addition of the generic_fns package docstring.
Added a module docstring for the main relax module.
Created the State.test_bug_20480 system test to catch bug #20480, the failure to load a saved relax model-free state in the GUI. This bug was reported by Stanislava Panova (https://gna.org/users/stacy).
Created the Mf.test_bug_20479_gui_final_pipe GUI test to catch bug #20479, the model-free analysis failure in the GUI after setting the protocol mode to local tm. This bug was reported by Stanislava Panova (https://gna.org/users/stacy).
Added a printout to the GUI test case base check_exceptions() method to explain what is happening.
Large expansion of the Mf.test_bug_20479_gui_final_pipe GUI test. Instead of loading the bug #20480 state file, now the entire GUI analysis starting from scratch and using the relaxation data files is performed remotely by the test. This is necessary because the result of the bug is present in the state file.
Added spherical diffusion to the optimisation in the Mf.test_bug_20479_gui_final_pipe GUI test.
Added a global model print out to the Mf.test_bug_20479_gui_final_pipe GUI test. This is to help identify where failures occur.
Proper handling of the dipole interaction wizard in the Mf.test_bug_20479_gui_final_pipe GUI test. This was causing the subsequent GUI tests to fail as the observer objects from the wizard were not all being unregistered.
Added skips for some GUI tests when wxPython version '2.9.4.1 gtk2 (classic)' is used. There are a number of bugs in this version which cannot be worked around in certain GUI tests, so they must be skipped.
More wxPython version '2.9.4.1 gtk2 (classic)' bug avoidances in the GUI tests. Now the auto-analyses do not check the gauges in the relax controller at the end of the auto NOE, Rx, and model-free analyses, as reading gauge values is faulty in this version. The Rx test is no longer skipped for this wxPython version.
Improved the printout from the align_tensor.matrix_angles user function. The relax_io.write_data() function is being used and the tensors are now identified by name rather than index.
Improved the printouts from the align_tensor.svd user function.
The relax program introduction now includes the revision number for subversion checked out copied. This allows for better identification of the code base being used.
Fixes for the Pcs.test_structural_noise system test. As this is based on random functions, sometimes, though rarely, the test fails. Now the simulation accuracy has been increased and the tests are less rigorous.
Spacing fixes as identified by the Python 2to3 conversion program.
Bugfixes:
Epydoc documentation fix - a circular import in the GUI code paths has been broken. This affects the API documentation at http://www.nmr-relax.com/api/.
Fix for the failed loading of states in the GUI. This problem was caught by the State.test_bug_20480 GUI test. If the loading of a state file fails,sometimes the relax data store can contain partial information from that file. Now if the loading fails in the GUI, relax is reset.
Fix for bug #20480, the failure to load a saved relax model-free state in the GUI. This was reported by Stanislava Panova (https://gna.org/users/stacy). The problem was that the state file was saved after a RelaxError occurred during the model-free analysis. The GUI data store information states that the active data pipe is called 'final'. But an error occurred prior to the 'final' data pipe being created. The fix was to allow the state to be loaded even if the GUI data store information has been corrupted.
Fix for bug #20479 - the failure of non-fully automated model-free analyses in the GUI. This bug was reported by Stanislava Panova (https://gna.org/users/stacy). The problem is GUI specific and was when running each diffusion model one after the other. The GUI was setting the base data pipe to the 'final' data pipe, which is a clear error.
Fix for bug #20481. This is the bug where the dauvergne_protocol model-free auto-analysis expects the prolate and oblate spheroids and ellipsoid to be optimised. It was caught by the Mf.test_bug_20479_gui_final_pipe GUI test.
Bug fix for the diffusion tensor PDB creation in the dauvergne_protocol model-free auto-analysis. The call to the structure.create_diff_tensor_pdb user function now only occurs if structural data is present.

New in relax 2.2.1 (Feb 14, 2013)

Changes
Replaced a reference to freshmeat with Freecode in the Release checklist document. Freshmeat no longer exists and is now called Freecode (http://freecode.com/projects/nmr-relax).
Created the Mf.test_bug_20464_missing_ri_data system test to catch bug #20464. The data comes from the bug report submitted by Stanislava Panova (stpanova att gmail dot com).
Created the Structure.test_bug_sr_2998_broken_conect_records system test. This is to catch the bug reported as service request #2998 (https://gna.org/support/?2998) and is for corrupted PDB files with broken CONECT records.
Created the Structure.test_bug_20469_scientific_parser_xray_records system test. This is to catch bug #20469.
Created the Structure.test_bug_20470_alternate_location_indicator system test to catch bug #20470.
Created the Structure.test_alt_loc_missing system test. This is to test that the internal relax PDB reader raises an error when a PDB file is encountered with alternate location indicators but the alt_loc argument has not been specified.
Created the Bmrb.test_bug_20471_structure_present to catch bug #20471.
Modified the bmrb.read documentation to make it clearer that the data pipe must be empty.
Bugfixes:
Python 3 fix for a print statement in the metal_pos_opt.py N-state model system test script.
Python 3 fix for the part of ScientificPython distributed with relax (for the PDB parser).
Python 3 import fixes for the GUI.
Python 3 fixes for the list sort() method - this has been replaced by the builtin sorted() function.
Fix for bug #20464 - the model-free analysis failure with missing relaxation data. The problem was the previously missing data had a value of None whereas now the dictionary element can be missing. Checks have been added to make sure the spin specific relaxation data structures have the key corresponding to the data.
Fix for the N_state_model.test_monte_carlo_sims system test. On certain systems, the chi2 check is too stringent.
Fix for the bug reported as the support request sr #2998 (https://gna.org/support/?2998). CONECT records pointing to non-existent atoms can now be handled.
Fix for bug #20469. This is the Failure in reading X-ray PDB files using the ScientificPython parser. The ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra imports in the Geometry.TensorModule in newly used code paths have been fixed as well.
Fix for bug #20470. The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate location indicator to read. This is used by the internal PDB reader. The bug was caught by the Structure.test_bug_20470_alternate_location_indicator system test.
Fix for bug #20471 - the is_empty() AttributeError when reading BMRB files. The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present.

New in relax 2.2.0 (Feb 14, 2013)

Features:
Implementation of the rdc.copy and pcs.copy user functions.
Improved printouts from the model_selection, pipe.display, rdc.read user functions.
Implemented the interatomic.copy and interatomic.create user functions
Added the 'units' argument to the frq.set user function to allow values other than Hz to be input.
Added the 'empty' flag to the sequence.copy user function to allow all the spin contents to be copied.
Implemented the pcs.structural_noise user function. This is used to determine the PCS error due to structural noise via simulation, and adds the error via variance addition to the experimental PCS error.
The N-state model grid search optimises each tensor separately when only tensors are optimised. This massively collapses the grid search size from inc*(5N) to Ninc*5, where inc are the number of increments per dimension and N is the number of alignments, making a grid search possible.
Implemented the rdc.set_errors and pcs.set_errors user functions.
Added Monte Carlo simulation support for the paramagnetic centre for PCSs in the N-state model.
The paramagnetic centre position for the PCS can now be optimised using algorithms other than simplex, such as BFGS, as the gradients of the PCS equations have been implemented. This allows for huge speedups as the simplex optimiser is not suited to such a problem.
The probabilities and paramagnetic position can now be simultaneously optimised in the N-state model. Such a combination would have previously failed to unpack the parameters correctly.
Constraints are now allowed for the paramagnetic position optimisation in the N-state model. This is because the gradients are implemented and functional.
Changes:
The relax HTML user manual footer has been modified to remove the name of the person who compiled it. This is for http://www.nmr-relax.com/manual/index.html, and now contains links for relax (http://www.nmr-relax.com), the manual (http://www.nmr-relax.com/manual) and the PDF version of the manual (http://download.gna.org/relax/manual/relax.pdf).
Small syntax fix in the release checklist document.
Added the MARC archive links to the development chapter of the relax user manual. These links are: http://marc.info/?l=relax-announce&r=1&w=2, http://marc.info/?l=relax-users&r=1&w=2, http://marc.info/?l=relax-devel&r=1&w=2, and http://marc.info/?l=relax-commits&r=1&w=2.
The model-free overfit deselection algorithm now fails with a RelaxError when no spins are selected. This is to avoid situations such as bug #20277.
The pipe.display user function now uses relax_io.write_data() for better output formatting.
Created the N_state_model.test_data_copying system test for the rdc.copy and pcs.copy user functions. These user functions do not exist yet, but this test will be used to implement them.
Reactivated the rdc.copy and pcs.copy user function front-ends. The backends are missing, so relax is currently broken.
Created the RelaxNoAlignError error class for use by rdc.copy and pcs.copy.
Created the RelaxAlignError error class for use by the rdc.copy and pcs.copy user functions.
Implemented the rdc.copy and pcs.copy user function backends. This code is copied from the relax_data.copy user function and has been tailored to the different data types.
Modified the RDC and PCS data copying system test script to check overwriting. The rdc.copy and pcs.copy user function should support the overwriting of existent values.
The rdc.copy and pcs.copy user functions now support overwriting pre-existing data.
Removed some debugging printouts.
The N_state_model.test_data_copying system test now checks the spin RDC and PCS data.
The model_selection user function is now using relax_io.write_data() for its printouts. This allows for clean formatting when data pipes have long names.
The rdc.write and pcs.write user functions now skip deselected spins.
The axis for PDB geometric cone can now be turned off in the create_cone_pdb() function. The axis_flag keyword argument is now accepted and if False will cause the axis to be excluded. This is useful for the frame order cones for example as its own {x,y,z}-axis system is created.
Many docstring fixes for the functions of the generic_fns.structure.geometric module.
Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure. This is a test of the long range, absolute RDCs for menthol.
Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
Modified the N_state_model.test_populations system test to catch bug #20335. This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and PCS data.
Modified the temperature user function - the value can be set twice if it is the same value.
Modified the frq.set user function - the value can be set twice if it is the same value.
The rdc.back_calc user function now handles absolute RDCs.
Created the Align_tensor.test_copy system test to catch bug #20338.
The spin.create_pseudo user function 'members' argument is no longer read only in the GUI. This allows the user to type in shorter spin IDs rather than selecting them from the list.
Shifted and renamed the arg_check.check_float() function to check_types.is_float().
The relax_io.write_spin_data() function now formats floating point numbers better. This affects the printouts of many data loading user functions.
Better printouts from the rdc.read user function - the numbers are now formatted.
Created the interatomic.copy and interatomic.create user functions. This is simply new front ends for the user for the functions of generic_fns.interatomic.
The generic_fns.interatomic.copy() function now accepts spin IDs as arguments to partially copy the data.
Expanded the RelaxNoSpinError class to accept the data pipe name for the error printout.
Created the Interatomic.test_copy system test to check the interatomic.copy user function.
Expanded the Interatomic.test_copy system test to check interatomic.copy without spin IDs.
Added a test for the presence of target sequence data in generic_fns.interatomic.copy().
Spun out code from generic_fns.pipes.create() into the new check_type() function. This code will be reused in a new pipe user function.
Created the Pipes.test_change_type system test to check the non-existent pipe.change_type user function.
Implemented the pipe.change_type user function front and back ends.
Created the Align_tensor.test_fix() system test to check the operation of align_tensor.fix.
Created some synthetic paramagnetically aligned RDC and PCS data to the test suite. This will be used in later system tests.
Fixes for the PCS values of the paramagnetic alignment test suite data. The data generation script output and results file have been added to the repository as well.
Created the N_state_model.test_paramag_align_fit system test to check the paramagnetic data. This test check the alignment tensor optimisation of the RDC and PCS data in test_suite/shared_data/align_data/paramagnetic/, loading both alignment data sets but only optimising one tensor.
The RelaxErrors when calling user functions in the prompt/script interface are now more informative. The user function is now stated. This is to better help the user work out where the problem is.
Created the Rdc.test_rdc_copy system test to demonstrate the failure of the rdc.copy user function.
Created the Pcs.test_pcs_load and Pcs.test_pcs_copy system tests to check some of the PCS user functions. The Pcs system test class is new, and these tests check untested areas of relax.
Created RelaxInteratomInconsistentError for when the data is inconsistent between two data pipes.
Created the generic_fns.interatomic.consistent_interatomic_data() function for checking data consistency.
The rdc.copy user function now uses the new consistent_interatomic_data() function prior to copying. To copy the RDC data, the interatomic data containers must be identical between the two data pipes.
Fix for the N_state_model.test_data_copying system test. The interatomic data is now copied prior to copying the RDC data.
Created 4 unit tests to demonstrate the failure of the selection object with spin IDs.
The molecule, residue and spin selection object now works with spin IDs.
Docstring consistency editing for all parts of the generic_fns.mol_res_spin module.
Created the Selection system test class. This currently has the test Selection.test_deselect_all for checking the deselect.all user function. The number of tests will be expanded in the future to cover interatomic data containers and the operation of all the select and deselect user functions.
Shifted the boolean selection operations of the generic_fns.selection module into two new functions. These are the boolean_select() and boolean_deselect() functions. The change removes much duplicated code which could be a source of bugs in the future.
The frq.set user function now warns if the frequency is lower than 100 MHz or higher than 2 GHz.
Updated the diffusion tensor minimisation sample script as the code is very old and useless.
Created the State.test_align_tensor_with_mc_sims system test to catch bug #20414. The report is at http://gna.org/bugs/?20414.
Modified the align_tensor_mc.bz2 save file to catch a strange and rare bug. This is caught by the State.test_align_tensor_with_mc_sims system test.
Spun out the maths_fns.rotation_matrix.random_rot_axis() function into its own module. The function is now called maths_fns.vectors.random_unit_vector().
Added a second data pipe with data to the 'align_tensor_mc.bz2' saved state to catch a bug. This bug was recently introduced.
Added checks for the RDC data in the State.test_align_tensor_with_mc_sims system test. This is to be sure that the data is properly converted from the old design.
Added the 'empty' flag to the sequence.copy user function to allow all the spin contents to be copied. The user function was only copying the basic empty molecule, residue and spin containers, in contrast to the interatomic.copy user function which copies all of the container contents as well. This new flag is for backwards compatibility - it allows old scripts to operate as before while enabling the new functionality.
Removed the check for the 3D structural data in the paramag.centre user function. This check is not needed.
Created the Pcs.test_structural_noise system test for the new pcs.structural_noise user function.
Created the N_state_model.test_mc_sim_failure system test to demonstrate a bug in the N-state model. This appears to be a problem with Monte Carlo simulations when data is missing.
Modified the N_state_model.test_mc_sim_failure system test to include missing PCS data. This is to catch another bug.
Modified the missing data system test script to include Monte Carlo simulations. This is to cover untested code paths.
Added calls to rdc.set_errors and pcs.set_errors in the missing data N-state model system test script. These user functions currently do not exist, but are needed as the data files contain no errors.
Modified all generic_fns.mol_res_spin.get_*() functions to handle no data pipes being present. These functions were previously raising RelaxErrors as no pipes were present. They now return empty lists instead. This allows many of the GUI user functions to open in the GUI when no data is present, allowing better debugging and less confusion for the user.
The Pipes.test_change_type system test is skipped if the required scipy module is not installed.
Python 3 fix for the new pcs.structural_noise user function. There was a string/unicode problem in the Grace plot creation code.
Created the Pcs.test_load_multi_col_data system test to demonstrate a failure of PCS data loading. This is a problem when 15N data is in one column and 1H data is in another, and the spin_id argument is used to specify which is which.
Added some printouts to the Pcs.test_load_multi_col_data system test.
Created the Pcs.test_grace_plot system test to check the pcs.corr_plot user function.
Created the Pcs.test_load_multi_col_data2 system test to catch a bug with the molecule name. This is the same as the Pcs.test_load_multi_col_data system test but the spins have the molecule name set.
Created the Mol_res_spin.test_prune_metadata system test to catch a bug in the spin ID lookup table. Spin IDs appear not to be correctly removed from the lookup table.
Added some more checks to the Mol_res_spin.test_prune_metadata system test to demonstrate more bugs.
Activated the Monte Carlo simulations in the metal_pos_opt.py system test script. This is to test the combination of Monte Carlo simulations and paramagnetic centre position optimisation.
Added Monte Carlo simulations to the N_state_model.test_paramag_centre_fit system test. This is to better test the code paths.
Modified the N_state_model.test_mc_sim_failure to demonstrate a failure in paramagnetic centre code. The failure is for the combination of paramagnetic centre optimisation and Monte Carlo simulations.
Modified the paramag.centre user function printouts for the 'fix' flag.
The alignment tensor objects in the relax data store now support sequential Monte Carlo analyses. The AlignTensorData.set_sim_num() method was preventing a second Monte Carlo error analysis from being performed by throwing a RelaxError. The check for previous simulations has been killed.
Added checks to the N-state model for the paramagnetic centre optimisation. Only simplex optimisation without constraints is allowed for the paramagnetic centre position as the PCS gradients and Hessians are not yet implemented for the coordinate parameters.
Improved the RDC and PCS Q factor calculation warnings to be more informative. These warnings sometimes appear at the end of the N-state model optimisation, but it is not clear where they come from.
Clean up of some of the logic in N-state model analysis specific code. The following methods have been added: _opt_tensor(), _opt_uses_align_data(), _opt_uses_pcs(), and _opt_uses_rdc(). These are used through the class to determine what is needed for or used during optimisation,making a lot of checking code more consistent (hence removing latent bugs).
Added some more checks to the metal_pos_opt.py N-state model system test script.
First attempt at implementing the paramagnetic centre position gradient in the N-state model. This will be used for faster optimisation of the lanthanide position. Two new functions have been added: maths_fns.pcs.ave_pcs_tensor_ddeltaij_dc() and maths_fns.pcs.pcs_constant_grad(). These are used by the dfunc_*() methods of the N-state model target function class.
Major code simplification of the N-state model target functions. The func_tensor_opt(), dfunc_tensor_opt(), and d2func_tensor_opt() methods have been merged with the func_population(), dfunc_population(), and d2func_population() methods into the new func_standard(),dfunc_standard(), and d2func_standard() methods. This halves the amount of code required to be maintained and debugged. For the merger, the new probs_fixed class instance variable has been created to determine when the probabilities need to be unpacked from the parameter vector.
Removed the unused parameter scaling in the N-state model gradient and Hessian target functions.
Added a RelaxError to the N-state model Hessian for the optimisation of the paramagnetic position. This is because these equations are not derived or coded yet.
Expanded the N-state model target function func_standard() docstring to include the xi derivative. This is the partial derivative with respect to the paramagnetic centre position.
Comment fixes in the ave_pcs_tensor_ddeltaij_dc() and pcs_constant_grad() functions.
Modified the N-state model metal_pos_opt.py system test script. This is to test optimisation with the new paramagnetic position gradients.
BFGS optimisation is now being used for the N_state_model.test_mc_sim_failure system test. This is to have better test coverage of the paramagnetic centre position optimisation gradient code paths.
Simplified the parameter unpacking in the func_standard() N-state model target function.
Improved the comments in the _disassemble_param_vector() N-state model method.
Modified the populations.py N-state model system test script to better test optimisation. The probability of the 2nd state has been slightly shifted to make sure the original value can be found.
Modified the metal_pos_opt.py N-state model system test script to demonstrate some failures.
Improved the checks of the metal_pos_opt.py N-state model system test script.
Modified the metal_pos_opt.py N-state model system test script to catch yet another bug.
Added Monte Carlo simulations to the align_fit.py N-state model system test script. This is to increase the very low coverage of Monte Carlo simulation testing for the N-state model.
Modified the metal_pos_opt.py N-state model system test script to test the bootstrapping code path. This converts the Monte Carlo simulations into bootstrapping to make sure this method also functions correctly.
Implemented the N-state model specific return_data() method. This is needed for bootstrapping.
Fixes for the N-state model return_data() method.
Modified the RelaxNoRDCError and RelaxNoPCSError to accept no alignment ID. This is then used to indicate the complete absence of data.
Modified the initial testing of the rdc.set_errors and pcs.set_errors user functions. This is to better indicate to the user what the problem is and why the user function cannot operate.
Fixes for the align_fit.py N-state model system test script. The recently introduced Monte Carlo simulations and associated RDC and PCS error setting was failing when RDC or PCS data was missing. The script now checks the mode of operation and only sets errors if the corresponding data is present.
The N_state_model.test_align_fit system test now checks the simulation PCS values.
Fix for the metal_pos_opt.py N-state model system test script. The moving interatomic data containers are now also deselected.
Added extensive data checks to the N_state_model.test_metal_pos_opt system test script.
Added new checks in the N_state_model.test_metal_pos_opt system test. These are for structures which should not be in the deselected spins and interatomic containers
The N-state model _check_rdcs() method now skips deselected interatomic data containers. A FIXME comment has also been added to highlight a possible future problem.
Added some consistency to the specific analysis API base class. The return_data() method argument has been changed from 'spin' to 'data_id', as the data from the base_data_loop() methods are often not spin containers.
Made the chi2 value check less stringent in the N_state_model.test_metal_pos_opt system test. For some bizarre reason, the calc() call in the GUI is less precise.
The N_state_model.test_populations system test has been made less stringent to allow MS Windows to pass.
Bugfixes:
Scons fix for MS Windows. A bug was introduced in the previous version which causes scons to fail on MS Windows. This has to do with the ctypes.Structure object but strangely led to a AttributeError importing scipy when initialising scons.
Another attempt at fixing the scons failure in MS Windows due to scipy and ctypes killing each other.
Work around for a numpy bug triggered by scons and the import of Scientific.Visualization.VMD. For details, see the thread started by Jack Howarth (howarth att bromo dot med dot uc dot edu) started at http://thread.gmane.org/gmane.science.nmr.relax.devel/3663 (Message ID:).
Fix for a fatal bug in the multi-processor code (https://gna.org/bugs/?20253). The Queue module is now imported as 'queue' for Python 3 support, so the code was referring to the wrong object name.
Bugfix for the grid_search user function. The elements of the list of integers can be None to indicate that no grid search in that dimension is to be performed.
Fix for model elimination in the modsel.py model-free sample script. The eliminate user function should be applied to each data pipe separately.
Fix for the relax_io.write_data() function - it can now handle no data being sent in.
Bugfix for the use of pseudo-atoms for RDCs in the N-state model analysis. If the second atom of the pair in the intermolecular data container holding the RDC data was a pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second atoms being pseudo-atoms is supported.
Fix for bug #20335. The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
Fix for bug #20338, the new tensor name is now set.
Bugfix for the catching of errors in the GUI user functions - the sys module import was missing.
Bugfix for the GUI combo_list input element SetValue() method. Values not belonging to the combo lists can now be set. This fixes the spin.create_pseudo user function in the test suite, a bug triggered by the N_state_model.test_absolute_rdc_menthol GUI test.
Fixes for the align_tensor.copy user function for when the tensor_to argument is not supplied. Now it is assumed that the new tensor will have the same name as the old. The new tensor is also properly initialised.
Bugfix for the N-state model with PCSs and the temperature or spectrometer frequency are not set. Previously the missing value was set to 0 K or 1e-10 Hz, but this was causing optimisation to fail. Now a RelaxError is produced if the value is missing and optimisation is attempted.
Fixes for the calculation of RDC and PCS Q factors for when fixed alignment tensors are present. If a tensor is fixed, then there will be no back-calculated data. Therefore instead of returning from the function, a continue statement is used to skip just that alignment.
Bugfix for the RelaxNoAlignError error class - the printout statement was broken.
Bugfix for the rdc.copy user function - it is now functional. The code was old and untested, and still assumed that the RDC values were held in spin containers rather than the interatomic data containers.
Partial fix for bug #20378. The gui_raise() function was operating differently under the command line run test suite and the GUI run test suite. The operation of the function is now consistent, and no RelaxError is raised (unless the raise_flag argument is set).
Full fix for bug #20378. As no RelaxError is no longer raised in this Bruker.test_bug_20152_read_dc_file GUI test (well only in the command line operation of the GUI tests), instead the current data pipe is checked to make sure no relaxation data was loaded.
Fix for bug #20414. The variable for the number of simulations in the AlignmentTensorList object is now set prior to setting the simulation parameter values.
Fix for bug #20417. The backwards compatibility hook for the loading of old relax state and results files can now handle the presence of proton spins. The data structures are now correctly converted to the current data pipe design. This is only the case for old files containing PCS data.
Fix for bug #20420. The problem was in the generic_fns.mol_res_spin.create_spin() function. The index_molecule() and index_residue() functions where not taking alternative, non-current data pipes into account.
Fix for bug #20421. The loading of relax state files was only updating the spin ID metadata structures for the current data pipe. Now all loaded data pipes are updated.
RDC data fix for the _back_compat_hook() method for converting old relax state and results files. The RDC data was not being shifted into the corresponding interatomic data container and remained in the spin containers.
Fix for the bug caught by the N_state_model.test_mc_sim_failure system test. If no RDC error is present, then the returned error from the N-state model analysis specific method return_error() is None.
Fix for the missing PCS data in the N-state model Monte Carlo simulations. This was caught by the N_state_model.test_mc_sim_failure system test.
Fix for the N_state_model.test_mc_sim_failure GUI test - the relax data store was not empty at the start.
Bugfix for the loading of PCS data from a file with different spin types in different columns. This was caught by the Pcs.test_load_multi_col_data system test which now passes.
Bugfix for generic_fns.mol_res_spin.metadata_prune(). Non-unique molecules and residues are now removed from the spin ID lookup table.
Proper bugfix for the spin ID metadata lookup table pruning. The Mol_res_spin.test_prune_metadata system test now passes. The previous fix was not complete, and it should have been in the spin_id_variants_elim() function rather than metadata_prune().
Python 3 fix for the Pcs.test_grace_plot system test.
Fix for the N-state model _minimise_setup_atomic_pos() method for the paramagnetic centre. The cdp.paramagnetic_centre_sim may not exist prior to Monte Carlo simulations.
Fix for the Monte Carlo initialisation of the paramagnetic centre position in the N-state model. The simulation positions are now initialised to the optimised position.
Fix for the N-state model Monte Carlo simulations for when the paramagnetic centre is fixed.
Bugfix for the N-state model optimisation of populations and paramagnetic position. The gradient from dfunc_standard() is now correctly calculated when both are optimised.
Fix for the assembly of the N-state model linear constraints. These were not set up correctly when the populations and paramagnetic position are optimised together.
Bugfix for the N-state model Hessian d2func_standard() method. An index variable name was incorrect causing the population model to fail with Newton optimisation.
Bugfixes for the _opt_uses_pcs() and _opt_uses_rdc() N-state model methods. These now check that the populations are optimised as well.
Fix for a bug caught by the N_state_model.test_metal_pos_opt system test. The problem was that uninitialised probability arrays of None from cdp.probs was always sent into the target function, whereas None should be sent in instead.
Big data store clean up fix for the N-state model. The N-state model specific base_data_loop() method now skips deselected interatomic data containers and spins. This prevents a lot of junk data being created in the data pipe, for example back calculated and Monte Carlo simulation RDC and PCS data.
Fixes for the relaxation curve-fitting specific return_data() method. Strangely it appears as if this method is never used.

New in relax 2.1.2 (Feb 14, 2013)

Features:
Python 2.3 to 3.3 support, including large changes throughout the code to be able to run on Python 3.
Improvements to the GUI tutorial in the model-free chapter of the relax manual.
A number of bugfixes.
Small improvements overall.
Changes:
The scons 'clean' target now removes the Python 3 _pycache_ directories.
Small edit to the installation chapter of the user manual.
Decreased the Python version dependency from 2.5 to 2.3 in the installation chapter of the user manual.
More error checking for the associate_auto() method of the data pipe editor window.
Added data pipe bundle error checking for the GUI pipe editor window associate_auto() method.
Added some error checking for the data pipe bundle in the auto model-free analysis GUI code.
Added some special RelaxErrors for data pipe bundles.
Added some bug catching code for the observer objects. In some rare cases a registered method's key was set to None. This is now caught and a RelaxError thrown to prevent later indecipherable errors.
The setup.py application building script now complains if the Python setuptools are not installed.
Updated the relax prompt mode figure in the intro chapter of the user manual to the more modern prompt.
Improvements to the API documentation compilation. The excluded files and directories, as well as hidden ones, are no longer included in the list of files/directories to add to the documentation.
Added a file with the relax user functions used for the prompt screenshots. This is for the manual and the website.
Added the public domain LaTeX nth.sty style file for the user manual. Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing the PDF manual to compile on more systems.
Fixes for weird print statements with double brackets generated by the 2to3 Python conversion script.
Removed a debugging printout.
Python 3 fixes for one of the test data scripts - print statement with function call replacements.
Python 3 fixes for non-used Python code - converted print statements to function calls.
Python 3 fixes for the script for generating plots of magnetic field lines.
Another print statement to function Python 3 fix for the user manual.
The Python print statements in the user manual are now function calls to be Python 3 compatible.
Python 3 fix for the generic_fns.structure.geometric.angles_regular() function. Integer divisions no longer produce integers.
Better formatting of the test suite summary.
The text relax controller log is no longer cleared when a reset occurs. This allows the test suite results to still be presented in GUI mode.
Even cleaner exiting of the GUI - the interpreter thread is terminated by the exit_gui() method.
The GUI is now cleanly exited with a call to wx.App.ExitMainLoop rather than wx.Exit.
Python 3 fix for the compat module - the Queue2 object needs to always be defined.
Added support for Python 2.2 and earlier for the compilation of the C modules.
Removed an unused import of the Queue module from the multi-processor.
Python 3 fix for the ScientificPython PDB reader unit tests. The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to comparison.
Redesigned the reset user function backend. This now no only clears out the relax data store, but it also resets the GUI if present. Some of the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI window are closed and the relax controller gauges are set to zero and the log window text cleared. These changes should allow GUI tests after an error or failure to pass, something which is currently problematic.
Disabled the initial relax intro printout from the GUI when running the test suite. This prevents the intro text from appearing in the first failed test.
Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2. The object comparison method no longer converts dictionaries to strings for the comparison, as the string version is different in different Python versions.
Fix for the Mf.test_write_results() system test for the Python 3 versions. The logic for determining Python 3 versions was broken and the incorrect files was used for Python 3.1.
Better Python 2.3 support. The compat module is now imported at the very start to allow the builtins to be set before any other imports. The sorted() builtin method is now mimicked and the os.devnull string set for Python 2.3 and earlier.
Fix for the Mf.test_write_results() system test for Python 3.1. The XML version in Python 3.1 is the old style. Therefore the old results file is being used to check this Python 3.1 result.
Small improvements to the multiple Python version test suite testing script.
Reactivated support for Python 2.3. This mainly skips the missing 'subprocess' module. This however decreases relax's functionality a little.
Created a special script for testing out relax with Python versions 1.0 all the way to 3.3. This builds the C modules for each Python version in ~/bin and then runs the test suite, outputting everything to log files.
The Results system tests are no longer dependent on the relaxation curve-fitting C modules. This allows these tests to run when the module cannot be imported.
Python 2.5 and lower fix for the test_write_protein_sequence() unit test. The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the code without failing, and the byte array comparison is now only used for Python 3+.
All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails. This removes a pile of useless error messages from the test suite and presents a table of skipped tests at the end.
More Python 3 fixes for the use of now non-existent string module functions.
Python 3 fix for the model-free BMRB export - many string module methods no longer exist.
Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensor. This large set of changes matches all of those revisions for the diffusion tensor already committed. The alignment tensor data structures are now read only, and can only be modified via the set() method. This is a much simplified design which works on all Python versions.
Small clean ups of the diffusion tensor data structure code.
Deleted the now unused _update_sim_set() method of the diffusion tensor data structure.
Removed the now unused _update_sim_append() method from the diffusion tensor data structure.
Cleaned up the docstring of the diffusion tensor data object _setattr_() method.
Updated all of the diffusion tensor unit tests to the new design.
Fix for the reading of model-free results files from relax 1.2 when simulation data is missing.
Fix for the reading of relax 1.2 model-free results files for the diffusion tensor structure redesign.
Another fix for the fold_angles() diffusion tensor function - again an incomplete design conversion.
Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.
Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.
Another fix for the diffusion_tensor.init user function - it was not completely converted.
Fix for the fixing of parameters in the model-free analyses. The diffusion tensor set_fixed() method is now used.
Fix for the XML output of the diffusion tensor - only the modifiable parameters are output. This was the previous behaviour and is needed for the test suite to pass.
Converted the palmer.extract user function to use the new diffusion tensor design.
The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().
The fix user function now uses the diffusion tensor set_fixed() method.
Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.
Fix for the model-free specific analysis duplicate_data() method for the new design. The diffusion tensor _mod_attr_ object is now called _mod_attr.
Fix for the diffusion tensor to_xml() method for the new design. For some reason the methods of the Element class are no longer blacklisted.
Converted the diffusion tensor data structure from_xml() method to the new tensor design.
Fix for the Diffusion_tensor.test_copy system test - the simulation parameters are now read-only. Instead, the diffusion tensor set() method needs to be called.
The setting of list values for the DiffTensorSimList object now works correctly. The private _set() method now works correctly by calling the base class method, and the normal setting of diffusion tensor simulation values produces a RelaxError.
Fix for the diffusion tensor _deepcopy_() replacement method for the new design.
The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.
Modified the setUp() method for the diffusion tensor system tests to use the new design.
Redesigned how diffusion tensor simulation structures are handled. The design is now much cleaner and works with all Python versions.
Removed all the unused imports from specific_fns.model_free.main.
A number of private diffusion tensor objects and methods have switched to the single leading '_' format.
Improvements to the diffusion tensor set() method. The parameters, errors and simulations are now properly differentiated and stored.
Converted the old diffusion tensor _setattr_() method into the set() method. This is the only way in which diffusion tensor parameters, errors and simulations can be set.
Renamed the diffusion tensor data structure type() method to set_type(). This is because the type is stored as the 'type' object, clashing with the method name.
Created the diffusion tensor data structure type() method for setting the tensor type. This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of relax, as the structure is now read only.
The new diffusion tensor fixed() method has been created to allow the fixed flag to be changed.
Fix for the initialisation of the diffusion tensor data structure, now that it is read-only.
The diffusion tensor data structure has been completely converted into a read-only structure. The _setattr_() method now will always raise a RelaxError, and the diffusion tensor simulation data structure objects _setitem_() method will raise the same error.
Updated the relax version numbers and 'trunk' used relax user manual. For example the information about checking out the main development line was still talking about 1.3 rather than the trunk.
Python 3 fix for the setting of diffusion and alignment tensor simulation values. The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.
Python 3 fix for the model-free results file reading tests. The ordering of dictionaries is different in Python 3, so now these are properly converted from strings to dictionaries before comparison. This was not happening because of the XML changes from Python 2.7.3 onwards.
The relaxation curve-fitting system tests are now skipped if the module is missing or broken. This improves the printouts from the test suite and shows a summary of skipped tests rather than a pile of traceback messages and errors.
The message about skipping the GUI tests due to wxPython being missing is now more specific. This was being shown for all runs of the test suite when it only needs to appear if GUI tests have been run.
Added a Python 3 version of the truncated OMP model-free results file. This was created with trunk.
Removed the Python 3 byte array hack which should have been removed earlier.
The OMP model-free results file generation script now outputs for any relax version.
Python 3 fix for the Mf.test_latex_table system test. The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw string format r"""Text""" is now used.
Python 3 support for Modelfree4 and Dasha. The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python objects are now interconverted when the Python 3 encode() and decode() methods are detected.
Removed the pickle format information and arguments from the state user function definitions.
Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.
Removed the ability to save and restore states using the pickle module. A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now everything defaults to the XML formatted output.
Python 3 fix - removed the use of the string module from generic_fns.spectrum.
Python 3 fix for the relax_io.open_write_file() function. This now matches the behaviour of open_read_file() in that there are three different behaviours for opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as open_write_file() is for creating text files.
Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.
For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places. This increased precision will only be of use in the relax test suite.
Python 3 fix for the Pipes.test_pipe_bundle() system test. The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.
The C module compilation testing script now accepts the Python version as a first argument.
The relax_io.open_read_file() now supports all Python versions over 2.4. This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped around io.TextIOWrapper().
Added the IO module to the relax information printout and dependency checks.
The manual C module compilation script is now executable.
Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.
Finished off the C module compilation testing script.
Added a script for testing out the C module compilation on multiple Python targets.
The relax_fit specific analysis module now supports both Python 2 and 3.
The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.
Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.
The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213. The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report. The PDB now only contains Asp47, the optimisation parameters have been made almost insignificant, and all models but 'tm0' have been removed from the analysis.
The Python 3 dictionary values() method no longer returns a list, so a list() call is needed.
Python 3 bug fix for the geometric structure module - another integer division to float problem.
The Mf.test_write_results system test can now select the correct file to compare against in Python 3. The algorithm for determining if the 'final_results_trunc_1.3_v2' or 'final_results_trunc_1.3_pre_py2.7.3_v2' file should be used could not handle Python 3.
Python 3 fix for the format detection of results and save files.
Python 3 import fixes for the generic_fns.structure package using relative paths.
Python 3 fix - removed the use of the string.lower() function in the OpenDX mapping code.
Python 3 fix for the frame order system tests. As float to string conversions behave differently, the %.1f formatting is used to force only a single decimal place float.
Python 3 fix for the frame order system tests - float to string conversions behave differently. Now the explicit %.1f formatting is used to force only a single decimal place float.
Python 3 integer division to float fix for the frame order analysis.
Python 3 bug fix for the frame order analysis - another int division problem.
Python 3 fixes - eliminated all usage of the dictionary has_key() calls as they are no longer present.
Python 2 and 3 support in the generic_fns.relax_data module using 2to3. One print call was fixed after running 2to3.
Python 3 bug fix for the Structure.test_read_pdb_mol_2_model_scientific system tests. This is again an integer division problem returning a float.
Python 3 fix for the test_write_protein_sequence() unit test. This is again a string verses byte verses unicode problem.
Python 3 fix for the user function docstring creation in the prompt UI mode. Again this is the problem of a division now returning a float rather than an int.
Python 3 bug fix for the N-state model target function setup. The num_tensors variable needs to be an integer, but the Python 3 division will create a float type.
Python 3 fix for the results.read user function matching that of state.load.
Python 3 bug fix for the relax_io.read_spin_data() function. The built in max() function cannot handle the value of None, therefore the filter() function is used to remove all instances of None from the list.
Python 3 bug fix for the state.load user function. The header line of pickled states (rather than the standard XML states) is of the b'' byte format. This is now converted to a string, and the search expression is comparing it to the raw string r"

New in relax 1.3.14 (Mar 21, 2012)

Features:
an expanded system information printout (from 'relax -i').
improvements to the multi-processor implementation, including creation of a public api and a reference implementation.
overhaul of the multi-processor stream capture design - the slave io streams are now properly redirected to the master processor and the master no longer overrides stream capture by the relax user interfaces.
numpy data structures are now supported in relax save files.
implemented the rdc.Delete and pcs.Delete user functions.
speed ups of a number of user functions involved in looping over atomic or spin specific data - this can be significant if a lot of structural operations are performed, or a large number of structures are required.
redesigned how spin parameters are handled in the specific analyses (which includes parameter name changes).
Changes:
the ms windows text wrapping width has been changed from 80 to 79 - this now fits the cmd prompt.
the program intro print out and prompt ui help system is using the new status.Text_width variable to wrap text.
the model-free constraint matrix a is now of numpy.Int8 type - this is to decrease virtual memory usage and increase the scaling efficiency on clusters.
changed all relax website links to http://www.Nmr-relax.Com for consistency.
the setup.Py script can now be imported for the epydoc api documentation system.
the extern and minfx.Scipy_subset relax packages are excluded form the api documentation.
added the ability to skip scripts in the package __all__ list unit test checks.
added some code to detect the bit version of ms windows in the information print out (to better distinguish 32 vs. 64-bit versions).
added some documentation about master processors on linux 2.6 eating 100% of one cpu core (in the mpi4py multi-processor fabric).
added a reference implementation to the multi-processor package - this is to demonstrate to users of the package how an implementation is created via the public api.
elimination of all relax dependencies from the multi-processor package.
added support for the memory size on ms windows to the relax info print out.
updated the value.Set user function unknown parameter error message to list the known ones.
for unix and gnu/linux systems, the relax info printout now shows the ram and swap size.
expansion and improvement of the information printed out by 'relax --info'.
expansion of the multi-processor api documentation.
expansion of the multi-processor package documentation with a step by step usage guide - this should increase the usability of the package by clarifying how one should use it.
expansion and improvements to the multi-processor package and module docstrings.
the finish button in the new analysis wizard has been renamed to "start".
created a special verbosity singleton for controlling the multi-processor package print outs.
future proofed the relax codebase by replacing all ''' with """ in the docstrings.
removed the unnecessary try statement in the model-free slave_command.Run() method as exception handling is correctly performed on the slave and master.
shifted the memo object into its own module (multi package).
simplification and abstraction of the slave_command.Run() method to shift all exception handling into the package. Therefore program code no longer needs to handle the multi-processor specific errors.
created a new module 'multi.Misc' for holding miscellaneous functions used throughout the multi package.
created a public api for the multi-processor package, available via multi.__init__.
the load_multiprocessor() function is no longer a static method of the processor base class. This function loads the correct processor class, so doesn't need to be a method of the base class and operates cleanly and more clearly as a stand alone function.
clean up of the processor io module (multi package).
eliminated all usage of sys.__stdout__ and sys.__stderr__ in the multi-processor package - this returns full control of io streams to the parent program.
the float arg checks now checks against all the numpy float types (float16, float32, float64, float128).
added value.Write user function calls to the j(w) mapping system test script.
added some value.Write user functions to the j(w) mapping sample script.
modified the j(w) mapping test data to include relaxation values of none to trigger bug #19329.
speed up for the generic_fns.Relax_re.Search() function.
more speed ups for the selection.__contains_mol_res_spin_containers() method.
reordered the checks in selection.__contains_mol_res_spin_containers() - this cuts the number of function calls down by avoiding relax_re.Search() calls if residue or spin numbers match.
simplified the generic_fns.Relax_re.Search() function - this is to minimise the number of isinstance() calls when dealing with the relax mol-res-spin sequence data.
updates for python 3.0 using 2to3.
removal of a number of debugging print out statements.
significant speed ups of the return_spin() and return_residue() functions.
added a print out for the diffusion_tensor.Init user function to inform the user of an angle unit change - this is in response to bug #19323 to make it clearer that a parameter conversion has occurred.
created a special specific api object called spin_params - this will be used to handle all operations to do with model parameters. The object param_list has methods for parameter initialisation and handling (where all info is specified such as grace string, units, default value, etc) and for determining if a parameter exists.
mass conversion to the new global_params and spin_params specific api data structures. The parameters are now all lowercase, for example ['s2', 'te', 'rex'] is now ['s2', 'te', 'rex']. The follow parameters are now converted throughout relax: 'bond_length' to 'r', 'csa' to 'csa', 'heteronucleus' to 'heteronuc_type', 'proton' to 'proton_type'.
created a new algorithm for finding the pivot of motion between different structural models - this is available through the structure.Find_pivot user function.
added the validate_models() method to the structural api - this is used to check that the models are 100% consistent.
added the centroid argument to the structure.Superimpose user function - this allows for the superimposition of structures assuming a pivoted motion.
Bugfixes:
fix for the title of the analysis selection wizard gui element.
fix for the memoryerror during the "final" run of d'auvergne protocol affecting 32-bit systems (bug #19528).
epydoc docstring fixes for the api documentation.
bug fix for old numpy versions missing the float16 object.
the relax prompt mode now prints the intro message to sys.Stdout - this fixes this mode with the logging option or in the mpi4py multiprocessor mode.
fix for the storage of numpy data structures in the relax save files - if special structures are created by the user, these were not correctly stored. The precision was often too low (printed at the numpy default of a precision of 8), and if one dimension had more than 1000 elements, ellipses would be stored instead (the ellipses would cause the save file to be unreadable by relax).
created the splitio.Flush() method so that a flush() call now works with the -t and -l command line args - this simply calls the flush() methods of both streams.
the relax data store __repr__() method now prints out all objects within the base object.
fix for a rare bug in the model-free analysis for when relaxation data of none is encountered.
fixes for the dasha system test for the bug #19332 fix.
fixes for the dasha use functions for file creation and data extraction - this should now handle relaxation data values of none, and also set the parameter values of deselected spins using the dasha output files.
big bugfix for the value.Read user function - the wrong spin id string was being used to set the parameter value so that all spins have the same value set for the parameter(bug #19332).
bug fix for the consistency testing analysis for when relaxation data of none is encountered.
the spin is now deselected if there is really less than three data points, excluding data points of none (bug #19329).
bug fix for the arg_check.Is_none() function - the relaxnoneerror was not imported!
fix for the numbering of the ter record and subsequence hetatm records in the pdb file creation. The structure.Write_pdb user function now creates the correct ter record after the atom records, and the hetatm records are renumbered if needed.
bug fix for the compilation of the user manual. The molecule user function class used the temporary variable i, which was causing the fetch_docstrings script to fail.