This is a minor feature and bugfix release which includes improvements
to the relaxation dispersion chapter of the manual and the addition of
new infrastructure for R1rho data handling in the dispersion analysis.
More details are given below.
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:
* Large amounts of new infrastructure for the R1rho relaxation
dispersion analysis type.
* More hardware information printed out when using the
'--info' command line option.
* The user function relax_disp.write_disp_curves now produces
text files of R2eff verses the rotating frame tilt angle theta.
* Small improvements for the relaxation dispersion GUI
tutorial and citation chapter of the relax manual.
Changes:
* Added text file for the articles reference values from the
global fit in Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths. This is from optimisation of the Kjaergaard et al., 2013
Off-resonance R1rho relaxation dispersion experiments using the 'DPL'
model. This uses the data from Kjaergaard's paper at DOI:
http://dx.doi.org/10.1021/bi4001062.
* Replaced "_" with "-" in text file with global fit residues.
Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in
sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
* Sorted the reference values in residue order. Regarding bug
#21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired
R1rho dataset with missing combinations of time and spin-lock field
strengths.
* Added reference data and guess data for a global fit R1rho
analysis. Regarding bug #21344, (https://gna.org/bugs/?21344) -
Handling of in sparse acquired R1rho dataset with missing combinations
of time and spin-lock field strengths. This system test is setup
comparison with paper values, and will be turned off later to prevent
long running time.
* Redid dict() keys for unit test of find_intensity_keys(), to
pass on Python 3.2 and 3.3. Work in progress for Bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths. This is a response to message:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5132.
* Added ":" to dictionary keys to match return from spin_loop
in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug
#21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired
R1rho dataset with missing combinations of time and spin-lock field
strengths.
* Removed model 'No Rex' to be tested in system test
Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.
* Aliased spins in system test
Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.
* Set opt_func_tol = 1e-15 and opt_max_iterations = 100000 to
run system test Relax_disp.test_r1rho_kjaergaard faster. Regarding
bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse
acquired R1rho dataset with missing combinations of time and spin-lock
field strengths.
* Re-ordered code lines in system test
Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.
* Assigned guess values for system test
Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.
* Added a section at the start of the dispersion GUI analysis
tutorial about 'computation time'. This is for the dispersion chapter
of the manual.
* Removed alias of spins in system test
Relax_disp.test_r1rho_kjaergaard. Work in progress for Bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.
* Added fitted R1 values from paper to system test
Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff. This will be used to
test the output of calculating Omega_eff, as stated in
http://article.gmane.org/gmane.science.nmr.relax.devel/5148.
* Added reading of R1 values in system test
Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added full manual steps of analysis for system test
Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Modified the directory separator from "/" to os.sep in
system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Commented out the commands for writing of text files and
state files to speed up system test Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
* Added the testing of writing out theta values in system test
Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added the parameter "theta" to
specific_analyses/relax_disp/api.py. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Modified parameter py_type to dict() for the theta value.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
* Added parameter "theta" do description tables. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Made an assertion that spin contains attribute "theta" in
system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added unit test for return_offset_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff. This is development
according to thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/5157.
* Commented out the expectation of the attribute "theta" to
exist in system test Relax_disp.test_r1rho_kjaergaard. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Imported return_param_key_from_data to be used in unit test
return_offset_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* The relax information printout, from "relax -i" for example,
now includes detailed CPU information. This uses operating system
specific commands to obtain this information which is not available
from the platform Python module.
* Removed the dependence on subprocess.check_output() as this
is only for Python 2.7 and higher. This is for the relax information
printout about the CPU info recently introduced.
* The RAM in the relax information printout is now displayed
for Mac OS X. The 'sysctl' command is now being used to retrieve the
RAM size and total memory, and the swap is calculated as the
difference.
* Added the OMP relaxation rates and compressed PDB file to
the repository. This is to allow users to have a full data set to
perform a test model-free analysis with.
* Added a sample_script to generate theta values for R1rho
data. Regarding sr #3124, (https://gna.org/support/?3124) - Grace
graphs production for R1rho analysis with R2_eff as function of
Omega_eff. The script is explained at the wiki:
http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data
* Created a new citation for relax which concatenates both the
d'Auvergne and Gooley 2008 papers. This is to show to those who are
unaware of back-to-back paper concatenation rules how to cite both
papers using one reference, saving a lot of space.
* Added lib.rotating_frame module containing functions related
to rotating frame NMR calculations. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added rotating_frame to lib.__init__.py. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Added unit test file _lib.test_rotating_frame.py to
__init__.py. Regarding sr #3124, (https://gna.org/support/?3124) -
Grace graphs production for R1rho analysis with R2_eff as function of
Omega_eff.
* Added unit test file _lib.test_rotating_frame(). Regarding
sr #3124, (https://gna.org/support/?3124) - Grace graphs production
for R1rho analysis with R2_eff as function of Omega_eff. These unit
test will be used to calculate and return dictionaries of tilt_angles,
Delta_omega and omega_eff. Some of the R1rho data mentioned in:
http://www.nmr-relax.com/manual/Dispersion_model_summary.html.
* Added link to manual for calculating NMR parameters in the
doctring for lib.rotating_frame.py. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Renamed function "calc_tilt_angle" to
"calc_rotating_frame_params" in lib.rotating_frame. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff. This is to
reflect, that the function should return and store spin values of both
tilt_angles, Delta_omega and omega_eff.
* Replaced with calc_rotating_frame_params in unit test, to
reflect function renaming. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Improved docstring in lib.rotating_frame. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Rearranged the citations in the citations chapter. The
references for relax are now far more prominent.
* Implemented the return of Delta_omega = "average resonance
offset in the rotating frame" in
specific_analysis.relax_disp.return_offset_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Fixed unpacking of return from function calls of
return_offset_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Made specific_analysis.relax_disp.return_offset_data return
"w_eff" - the effective field in rotating frame in rad/s. Regarding
sr #3124, (https://gna.org/support/?3124) - Grace graphs production
for R1rho analysis with R2_eff as function of Omega_eff.
* Fixed unpacking of return from function calls of
return_offset_data, since w_eff is now also returned. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Moved calc_rotating_frame_params() to
specific_analysis.relax_disp.disp_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff. This is in a response
to message: http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
* Started unit test for
_specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is in response to message:
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
* Removed lib.test_rotating_frame.py and the associated unit
test. Regarding sr #3124, (https://gna.org/support/?3124) - Grace
graphs production for R1rho analysis with R2_eff as function of
Omega_eff. This is in response to
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
* Made calc_rotating_frame_params take spin "The spin system
specific data container" as input. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Modified calc_rotating_frame_params() to operate on the
level of spin container and ID. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Modified unit test test_calc_rotating_frame_params to use
spin container and ID in test. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Epydoc docstring fix for the
Structure.test_bug_21522_master_record_atom_count system test. This
is for the API documentation at
http://www.nmr-relax.com/api/3.1/index.html.
* Epydoc docstring fix for the SetValue() method of the File
input GUI element. This is for the API documentation at
http://www.nmr-relax.com/api/3.1/index.html.
* Removed the test_suite/shared_data directory from the API
documentation scanning. This is to avoid trying to import the frame
order relax scripts which cannot be imported into Python.
* Added epydoc information about dimensions for w_e in
function return_offset_data. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added verbosity flag to calc_rotating_frame_params() to
allow switching of print information. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added unit test for use of value.write to write theta values
calculated from calc_rotating_frame_params(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Extended unit test for use of value.write to write
intensities file. This is to test that changing of the API function
will retain its function. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Replaced API function in specific_analysis.relax_disp.api to
calculate and return values for parameter theta when this is
requested. Regarding sr #3124, (https://gna.org/support/?3124) -
Grace graphs production for R1rho analysis with R2_eff as function of
Omega_eff. Implemented according to
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05082.html.
* Extended API function in specific_analysis.relax_disp.api to
calculate and return values for parameter theta when this is
requested. Regarding sr #3124, (https://gna.org/support/?3124) -
Grace graphs production for R1rho analysis with R2_eff as function of
Omega_eff. Implemented according to
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05082.html.
* Variable renaming and closing of files in unit test
test_value_write_calc_rotating_frame_params(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Extended unit test
test_value_write_calc_rotating_frame_params() to also test writing of
w_eff values. Regarding sr #3124, (https://gna.org/support/?3124) -
Grace graphs production for R1rho analysis with R2_eff as function of
Omega_eff.
* Fixed typo and removed grace string for parameter
description of theta. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added parameter 'w_eff', the effective field in rotating
frame calculation to dispersion API. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added handling of calculating w_eff in dispersion API.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
* Added unit to parameter description of theta and w_eff.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
* Fix for field count and added check for R1rho type in
calc_rotating_frame_params(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added grace string to parameter description of theta and
w_eff. Regarding sr #3124, (https://gna.org/support/?3124) - Grace
graphs production for R1rho analysis with R2_eff as function of
Omega_eff.
* Fixed code duplication in relax_disp API, for calculation of
theta and w_eff. Regarding sr #3124, (https://gna.org/support/?3124)
- Grace graphs production for R1rho analysis with R2_eff as function
of Omega_eff.
* Removed unused lines of code in unit test
test_return_offset_data(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Moved unit test of value writing of
calc_rotating_frame_params() into separate system tests. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Added system test
Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is to test the auto_analysis value.write function to write theta
and w_eff values for an R1rho setup.
* Added writing of parameters theta and w_eff for an
auto-analysis if model in MODEL_LIST_R1RHO_FULL. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added return of None values for function
calc_rotating_frame_params() if spin is not selected. Regarding sr
#3124, (https://gna.org/support/?3124) - Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
* Extended system test
Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis()
to test the writing of theta values. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Hardcoded the writing of R2eff as function of the tilt angle
Theta, when using the user function relax_disp.write_disp_curves.
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
Theta values per spin will be written if the spin.model is in the list
MODEL_LIST_R1RHO_FULL.
* Fix for return of None tuble in
calc_rotating_frame_params(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Fix for correct use of assertNotEqual or assertEqual in
Relax_disp system tests. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Hardcoded contents of writing of parameters theta and w_eff
in system test
Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().
Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is to better support testing of key ordering and different
architectures, etc.
* Fixed code duplication in
specific_analysis.relax_disp.disp_data.write_disp_curves(). Regarding
sr #3124, (https://gna.org/support/?3124) - Grace graphs production
for R1rho analysis with R2_eff as function of Omega_eff.
* Modified system test of hardcoded values of theta and w_eff
to match precision to 14 digits. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Fix for handling the writing of theta.out and w_eff.out in
relax_disp auto_analysis, when model is not of R1rho type. Regarding
sr #3124, (https://gna.org/support/?3124) - Grace graphs production
for R1rho analysis with R2_eff as function of Omega_eff. This was
discovered using the system tests.
* Fix for calculating the theta angle describing the tilted
rotating frame relative to the laboratory, when omega1 / Delta_omega
is negative. Regarding sr #3124, (https://gna.org/support/?3124) -
Grace graphs production for R1rho analysis with R2_eff as function of
Omega_eff. This follows discussion in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
* Modified unit and system test to reflect new calculation of
rotating frame tilt angle Theta. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff. This was discussed in
thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
* Added interpolation calculation of theta and w_eff, when
dispersion points are interpolated. Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
* Added printout of Omega, the average resonance offset, in
calc_rotating_frame_params(). Regarding sr #3124,
(https://gna.org/support/?3124) - Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
Bugfixes:
* Typo fix for text in the model-free GUI auto-analysis. The
maximum iterations for the protocol was misspelled in the GUI. This
was spotted by Hessam Nasrollah.
* Fix for one of the frame order system tests when using the
Mac OS X application binary. The problem was that the 'shared_data'
directory could not be found as it was not included in the test_suite
package __all__ list.
* Fix for bug #21754 (https://gna.org/bugs/?21754). This is
the failure of the grace.view user function on MS Windows in opening a
file in qtgrace when the path includes spaces, as reported by Mengjun
Xue (mengjun dott xue att mailbox dott tu-berlin dott de). The fix
was to run the program with the file name in double quotes.
* Fix for bug #21763 (https://gna.org/bugs/?21763). This is
the problem of the chi2 value not being visible in the parameter list
of the grace.write and value.write user functions in the GUI. The
problem was that when asking for the parameter name list, the
minimisation parameters were not being asked for.
relax version 3.1.7.