This is a minor feature and bugfix release. The new user functions
system.cd and system.pwd have been added to allow the working
directory to be changed and displayed. The time and sys_info user
functions have been renamed to system.time and system.sys_info. The
structure.delete_ss user function has been created to remove the helix
and sheet information from the internal structural object. For bugs,
the R2eff dispersion model can now handle missing peaks in subsets of
spectra, and the structure.read_pdb can now handle multiple structures
and multiple models with the merge flag set.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.2 .
The new relax versions can be downloaded from
http://www.nmr-relax.com/download.html. If binary distributions are
not yet available for your platform and you manage to compile the
binary modules, please consider contributing these to the relax
project (described in section 3.6 of the relax manual,
http://www.nmr-relax.com/manual/relax_distribution_archives.html).
The full list of changes is:
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 (www.nmr-relax.com/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.py. 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__.py, 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. This is the
failure of the optimisation of the 'R2eff' dispersion model when peaks
are missing from one spectrum, as reported by Petr Padrta at
https://gna.org/bugs/?24601. The test uses his data and script to
trigger the bug.
* Simplified the Relax_disp.test_bug_24601_r2eff_missing_data
system test. This is to allow the test to catch bug #24601 to
complete in a reasonable time (2 seconds on one system).
* Fix for the independence of the relax library. As
lib.system was using the status object, the library independence was
broken. To work around this, the module has simply been shifted into
the pipe_control package.
* Added some missing oxygen icons to allow the relax manual to
compile. These are the 128x128 EPS versions of the
places/folder-development.png and places/folder-favorites.png Oxygen
icons recently introduced. For completeness the 32x32, 48x48, and
128x128 PNG versions of the icons have also been added. To help
create these EPS icons in the future, the graphics/README file has
been added with a description of the *.eps.gz file creation.
* Some more details for the *.eps.gz icon creation process.
* Mac OS X fixes for the Structure.test_pca and
Structure.test_pca_observers system tests. The eigenvectors on this
OS are sometimes inverted. As the sign of the eigenvector is
irrelevant, the vectors hardcoded into the system tests are now
inverted as required.
Bugfixes:
* Fix for bug #24218 (https://gna.org/bugs/?24218). This is
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, https://gna.org/bugs/?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. This is the failure of the optimisation
of the 'R2eff' dispersion model when peaks are missing from one
spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601.
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.
relax version 4.0.2