This is a major feature and bugfix release which adds support for
reading 3D structures of organic molecules from Gaussian log files,
the new lib.periodic_table and lib.nmr modules, the 'NS MMQ 3-site
linear', 'NS MMQ 3-site', 'NS R1rho 3-site linear', and 'NS R1rho
3-site' relaxation dispersion models, R1rho dispersion data sets where
multiple offsets and multiple spin-lock fields have been collected for
each spin, the loading of spins directly from peak lists, and the
reading of NMRPipe seriesTab files. Due to the improvements and the
bugs fixed in the relaxation dispersion analysis, all users are
recommended to upgrade to this version.
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:
* 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. This follows the tutorial for
adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
* Added another Gaussian log file of strychnine, this time
with DFT structure optimisation. The file is bzip2 compressed to save
space.
* Created the Structure.test_read_gaussian_strychnine system
test. This will be used for implementing and testing the
structure.read_gaussian user function.
* Created the lib.periodic_table module for storing
information about the periodic table. This is via the periodic_table
object which will have different methods for obtaining different
information about an element.
* Implemented the structure.read_gaussian user function. This
will read the final structural data out of a Gaussian log file.
* Improved the checking of the
Structure.test_read_gaussian_strychnine system test. This now checks
all the atomic information loaded.
* Simple fix for the Relax_disp.test_korzhnev_2005_*_data
system tests. The CPMG frequencies are now being set up in the
setup_korzhnev_2005_data() method.
* Added support for the 'NS MMQ 3-site' model parameters to
the lib.text.gui module. This is for the 'NS MMQ 3-site' and 'NS MMQ
3-site (linear)' CPMG dispersion models. This follows the tutorial
for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
* Added the 'NS MMQ 3-site' models to the
relax_disp.select_model user function frontend. This is for the 'NS
MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This
follows the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
* Added support for the 'NS MMQ 3-site' models to the
relax_disp.select_model user function back end. This is for the 'NS
MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This
follows the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
* Added support for the new 3-site exchange dispersion
parameters. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site
(linear)' CPMG dispersion models. This follows the tutorial for
adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters.
* Removed the brackets from the 'NS MMQ 3-site (linear)'
dispersion model name.
* Renamed the Relax_disp.test_ns_mmq_3site_branched system
test to Relax_disp.test_ns_mmq_3site.
* Fixes for the loop_parameters() dispersion function for the
new 'NS MMQ 3-site' model parameters. The new parameters were not
being handled by this function.
* Created the target functions for the 'NS MMQ 3-site' models.
This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
* Added the R2eff calculating functions for the 'NS MMQ
3-site' models to the relax library. This is for the 'NS MMQ 3-site'
and 'NS MMQ 3-site linear' CPMG dispersion models. This follows the
tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
* Added the 'NS MMQ 3-site' models to the dispersion
auto-analysis. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site
linear' CPMG dispersion models. This follows the tutorial for adding
relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
* Added the 'NS MMQ 3-site' models to the GUI model list.
This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
* Updated the 'MMQ 2-site' model description in the manual.
The R2_DQ = R2_ZQ = R20 assumption is now explained.
* Added the 'NS MMQ 3-site' models to the relax user manual.
This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
* Completed the 'MMQ 2-site' documentation in the manual. The
equations for the numeric evolution of SQ, ZQ and DQ data was missing.
* Huge speed ups of the relaxation dispersion analysis. This
is due to the removal of huge inefficiencies in the loop_point(),
return_cpmg_frqs() and return_spin_lock_nu1() functions of the
specific_analysis.relax_disp.disp_data module. Two new functions
return_cpmg_frqs_single() and return_spin_lock_nu1_single() have been
introduces to pull out the nu_CPMG and spin-lock field strengths for a
given experiment and spectrometer frequency. This avoids calling the
loop_exp() and loop_frq() functions from within loop_point() which
itself is often called inside a loop_exp() and loop_frq() sequence.
* Added the results of cpmg_fit minimisation of the cpmg_fit
synthetic data for the 'NS MMQ 3-site' model.
* Fixes for the 'NS MMQ 3-site' dispersion models - the
evolution matrix is now correctly constructed.
* Another fix for the 'NS MMQ 3-site' dispersion models. The
creation of the Z-matrix had a copy and paste error in that the
heteronuclear chemical shift sign was negated when it should be
positive. This was only in one of the two chemical shift numbers.
* Loosened the chi-squared check of the
Relax_disp.test_ns_mmq_3site system test to allow it to pass.
* Speed up of the Relax_disp.test_ns_mmq_3site system test.
The relax_disp.plot_disp_curves user function call is now skipped as
it takes too long.
* Renamed the 'ns_mmq_3site_branched' dispersion test data
directory to 'ns_mmq_3site'.
* Created the Relax_disp.test_ns_mmq_3site_linear system test
and modified Relax_disp.test_ns_mmq_3site. The
Relax_disp.test_ns_mmq_3site_linear system test uses the old data from
the directory test_suite/shared_data/dispersion/ns_mmq_3site/, as this
had kAC = 0, now copied into the ns_mmq_3site_linear/ directory. This
system test uses the 'NS MMQ 3-site linear' model. The base data
generated by cpmg_fit for the Relax_disp.test_ns_mmq_3site system test
was modified so that kAC is no longer 0, but set to 1000. This should
properly test the 'NS MMQ 3-site' model.
* Renamed the 'MMQ 2-site' model to 'NS MMQ 2-site'. This is
so that the name matches those of the 'NS MMQ 3-site linear' and 'NS
MMQ 3-site' models.
* Renamed all remaining instances of 'MMQ 2-site' to 'NS MMQ
2-site'. This is simply changing variable, method and module names.
* Removed the 'MMQ 3-site branched' and 'MMQ 3-site linear'
models from the to do list in the manual. These two dispersion models
are now implemented.
* Renamed the 'MQ CR72' dispersion model to 'MMQ CR72'. The
model is designed by Korzhnev et al., 2004 for proton-heteronuclear
SQ, ZQ, DQ, and MQ data (or MMQ data), so the change is logical as the
model is not just for MQ data.
* Clean up of the 'NS R1rho 3-site' model names in the manual.
The word 'branched' has been removed and the notation now matches the
'NS MMQ 3-site' models.
* Clean up of the parameter lists in the dispersion model
table of the manual.
* The pC parameter constraints are now implemented for the
3-site dispersion models. The new constraints are 0 <= pC <= pB.
* Editing of the introduction section of the dispersion
chapter of the manual.
* Added the 'NS MMQ 3-site' parameters to the optimisation
section of the dispersion chapter of the manual.
* Added some R1rho data from Dmitry Korzhnev's Fyn SH3 domain.
This originates from the cpmg_fit software and is published data.
* Small fix for the documentation of the
relax_disp.r2eff_read* user functions. This is for both
relax_disp.r2eff_read and relax_disp.r2eff_read_spin.
* Created the new lib.nmr relax library module. This
currently has a few simple functions for converting between ppm units
and Hertz or rad/s units.
* The relax_disp.spin_lock_offset user function now uses the
lib.nmr module. This is for converting between ppm and rad/s units.
* The relax_disp.r2eff_read_spin user function now can handle
offset data in the file. If the new offset_col argument is set and
disp_point_col is not, then the file being read can contain the
spin-lock offset information rather than the spin-lock field strength
values. This is only for R1rho-type data.
* Implemented GUI test which caches the bug #21076
(https://gna.org/bugs/?21076) - when loading a multi-spectra NMRPipe
seriesTab file through the GUI, several Error messages occur.
* Large redesign of the R2eff/R1rho data structures. The five
indices {Ei, Si, Mi, Oi, Di} for the experiment type, the spins of the
cluster, the magnetic field strengths, the pulse offsets, and the
dispersion points (nu_CPMG or nu1) respectively are now much better
defined. The Oi dimension is new and allows for support of R1rho-type
data whereby both different offsets and different spin-lock field
strengths have been collected. Previously only one or the other was
supported, but not both together. The offset information is now
included as part of the spin R2eff/R1rho key, even if not set. To
support this, the specific_analyses.relax_disp.disp_data module now
has the new functions loop_exp_frq_offset(),
loop_exp_frq_offset_point(), loop_exp_frq_offset_point_time(),
loop_frq_offset(), loop_frq_offset_point_key(), loop_offset(), and
loop_offset_point(). All of the {Ei, Si, Mi, Oi, Di} dispersion
indices throughout the source tree have been changed to ei, si, mi,oi,
and di respectively. And the time index ti has also been introduced.
These changes hugely simplify the code.
* The relax_disp.plot_disp_curves user function can now
support 150 sets per Grace graph.
* The relax_disp.plot_disp_curves user function can now
support 3000 sets per Grace graph.
* System test for sequence read expanded to include assertions
of correct data. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added some more files for the Fyn SH3 R1rho test data. This
includes the cpmg_fit input and output files, R1 data files for relax
as R1 cannot optimised yet, and a relax script.
* Added system test for reading spins from a Sparky list.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added interpreter.spectrum.read_spins function. Work in
progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Created the back end function for the read_spins function.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Fix for system test. Work in progress for Support Request
#3044 (https://gna.org/support/index.php?3044) - load spins from
Sparky list.
* Extended reading of Sparky files to include residue names.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Expanded system test and made it pass for user function
spectrum.read_spins. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Updated the GUI test to check for first ID in list. Fix for
bug #21076, (https://gna.org/bugs/?21076) - When loading a
multi-spectra NMRPipe seriesTab file through the GUI, several Error
messages occur.
* Added keyword dim to frontend function for
spectrum.read_spins(). Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list. This is associate data with the spins of up to two dimensions.
* Implemented system test for reading spins from NMRPipe
SeriesTab formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Extended reading of spin residue names from NMRPipe
SeriesTab formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified NMRPipe SeriesTab to read residue numbers and name
for two-dimensional list. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Insert check if spin already exist before creating it. Work
in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Issuing a warning instead of error when loading spins from
Sparky list where residue names are not present. Work in progress for
Support Request #3044 (https://gna.org/support/index.php?3044) - load
spins from Sparky list.
* Issued a warning instead of error when loading spin residue
names from a NMRPipe SeriesTab formatted file. Work in progress for
Support Request #3044 (https://gna.org/support/index.php?3044) - load
spins from Sparky list.
* Changed to use return_spin for testing presence of spin.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented another system test for reading NMRPipe
SeriesTab files. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Fix for issuing a warning in reading spins from a NMRPipe
SeriesTab formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Fix for issuing a warning when reading spins from a Sparky
formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented system test for reading spin IDs from NMRView
formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Made reading of NMRView formatted file return the residue
number as integer instead of string. Work in progress for Support
Request #3044 (https://gna.org/support/index.php?3044) - load spins
from Sparky list.
* Fix for calling the warn() function. Work in progress for
Support Request #3044 (https://gna.org/support/index.php?3044) - load
spins from Sparky list.
* Extended the error description for reading NMRView files.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented system test for reading spins from a NMRPipe
SeriesTab formatted file whereby the assignments for second dimension
is missing. This will be a typically export from Sparky, converted to
NMRPipe format, and processed with SeriesTab. Work in progress for
Support Request #3044 (https://gna.org/support/index.php?3044) - load
spins from Sparky list.
* Fixed for reading spins from a NMRPipe SeriesTab formatted
file whereby dimension 2 misses residue number and residue name. Work
in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Expanded the warning message for a system test. Work in
progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified system test for reading an assignment whereby the
second dimension is missing. Work in progress for Support Request
#3044 (https://gna.org/support/index.php?3044) - load spins from
Sparky list.
* If dimension 2 in a SeriesTab formatted file does not
contain residue number+name, it defaults to the dimension 1. Work in
progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented system test for reading spins from an XEasy
file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified XEasy reading function to pass residue names back.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Copied a SeriesTab file for the implementation of double
assignments in Sparky files.
* Redesign of the CPMG frequency and spin-lock field strength
data structures. These now have an extra dimension for the offset so
that the values are now experiment, magnetic field strength and offset
dependent. If many offsets are present but are variable for each
dispersion point, then this saves a lot of calculation time. This
mainly affects R1rho-type data. To better handle this, all of the
specific_analyses.relax_disp.disp_data.loop_*() functions have been
modified to accept data values rather than indices.
* Improved the printout of the relax_disp.r2eff_read_spin user
function for the R2eff keys.
* Extended the system test for reading spins from Sparky files
with empty residue name+number second dimension assignment. Work in
progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified the Sparky peak list for two dimensional assignment
example. This will typically be the export from CcpNmr Analysis.
Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented a system test for using double assignments in
Sparky formatted files. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Extended reading of spins from Sparky files for up to two
dimensional assignments. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added example of CcpNmr analysis exported Sparky file. Work
in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added system test for reading CcpNmr Analysis exported
Sparky file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified the reading of Sparky files when exported from
CcpNmr Analysis. The keyword 'Data' is not present here. Work in
progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added a system test for using generic file for reading
spins. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Modified the generic list to also return spin information
when intensity is not present. Work in progress for Support Request
#3044 (https://gna.org/support/index.php?3044) - load spins from
Sparky list.
* Added another system test for returning spins from a generic
file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added residue 4 to the R2eff files for the truncated CPMG
data from Flemming Hansen.
* Added cpmg_fit results to the software comparison table for
Flemming Hansen's CPMG data. The cpmg_fit input and log files have
been added as well.
* Shifted the software comparison down a directory so it can
be used for all the different data.
* Added system test for reading chemical shift from NMRPipe
SeriesTab file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Implemented reading of chemical shifts from NMRPipe
SeriesTab formatted files. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Additional chemical shift reading test for SeriesTab
formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Improvements for the find_intensity_keys() dispersion
analysis function. This now handles the reference point None being
converted to NaN in numpy arrays and the logic is now clearer.
* Changed some warnings in the dispersion analysis so they
only show if R1rho data is loaded. This is for missing chemical
shifts and R1 data.
* Increased the size of the grid search in the
Relax_disp.test_m61_exp_data_to_m61 system test. This should increase
the stability of this test.
* Introduced the eliminate argument for the dispersion
auto-analysis. This flag allows model and Monte Carlo simulation
elimination to be deactivated.
* Updated two dispersion scripts in the test data directories
to work with the current design.
* Updated more test suite scripts to call the
relax_disp.cpmg_frq user function.
* The 'CR72' and 'MMQ CR72' models are now classified as
nested in the dispersion auto-analysis. The grid search for the 'MMQ
CR72' model will therefore be skipped and the parameters taken from
the 'CR72' model. This will however rarely, if ever, be used.
* Fix for the relax_disp.plot_disp_curves user function. The
interpolated curves now have all invalid points of 1e100 removed from
the graph. This allows for reasonable graph scaling.
* The 'LM63' and 'LM63 3-site' models are now classified as
nested in the dispersion auto-analysis. The grid search for the 'LM63
3-site' model is therefore skipped and the starting parameters for
optimisation are set to those of the optimised 'LM63' model.
* Updated the relax results for the truncated CPMG data from
Flemming Hansen. This includes the new results for the 'MMQ CR72'
model. The analysis uses more model nesting. And the Grace plots now
include the interpolation graphs (hence the plots are now bzip2
compressed).
* Updated the NESSY results for the truncated CPMG data from
Flemming Hansen. This now uses the data from all residues to allow
for a proper error analysis so the results are comparable to all the
other software.
* Updated and reformatted the dispersion software comparison document.
* Made a system test test pass on Mac OS 10.9.
* Complete reworking of the 'NS R1rho 2-site' dispersion
model. The original code of Nikolai Skrynnikov and Martin Tollinger
has been modified to match the behaviour of Dmitry Korzhnev's cpmg_fit
software. The equations from Korzhnev et al., JACS 2005
(http://dx.doi.org/10.1021/ja0446855) have been used for the initial
magnetisation and the R1rho' calculation. All equations have been
added to the manual to clarify the model.
* Both relax and cpmg_fit input and output files for the Fyn
SH3 R1rho data have been added. This is for the 'TP02' model and 'NS
R1rho 2-site' models. The cpmg_fit results include source code
modifications to show the differences between the various
'corrections'. The dispersion software comparison file has been
updated to include this data and to show the cpmg_fit verses relax
differences.
* Updated the Relax_disp.test_tp02_data_to_ns_r1rho_2site
system test. This is for the fixes of the 'NS R1rho 2-site'
dispersion model.
* Added the Korzhnev 2005 R1rho constant time correction to
the 'To do' section of the dispersion chapter of the user manual.
* Removed the 'CR72' model for cpmg_fit from the dispersion
software comparison table in the dispersion chapter of the user
manual.
* Removed the 'CR72' model for GUARDD from the dispersion
software comparison table in the dispersion chapter of the user
manual. This software, like cpmg_fit, only supports the 'MMQ CR72'
model which gives slightly different results to the original 'CR72'
model when using only SQ CPMG-type data. Hence supporting 'MMQ CR72'
does not automatically mean that the 'CR72' model can be optimised.
* Updated the ShereKhan error estimation technique in the
dispersion software comparison table. This is for the dispersion
chapter of the user manual. Adam Mazur communicated that errors are
estimated using the covariance matrix in a private mail.
* Large rearrangements in the dispersion chapter of the user
manual. The MMQ CPMG-type experiments now follow from the SQ
CPMG-type experiments, hence the R1rho models are now listed last.
* Added a to do entry for the 3-site and N-site analytic R1rho
models listed in Palmer and Massi 2006. This is for the 'To do'
section of the dispersion chapter of the user manual.
* Updated the lib.dispersion.ns_r1rho_2site module docstring
to explain the origin of the equations. This includes the Korzhnev
2005 reference where the modifications come from.
* Created some synthetic data for the 'NS R1rho 3-site linear'
dispersion model using cpmg_fit.
* Added cpmg_fit results for the Fyn SH3 R1rho test suite data
using the 3-site numeric solution.
* Created the Relax_disp.test_ns_r1rho_3site_linear system
test. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear'
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
* Added the 'NS R1rho 3-site' models to the dispersion
variables. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site
linear' dispersion models. This follows the tutorial for adding
relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
* Added the 'NS R1rho 3-site' models to the
relax_disp.select_model user function frontend. This is for the 'NS
R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This
follows the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
* Changed the order of the experiment types in the
relax_disp.select_model user function frontend. The R1rho-type models
have been shifted to the end so that the MMQ CPMG-type models are just
after the SQ CPMG-type models.
* Changed the 'CPMG-type' to 'SQ CPMG-type' in the
relax_disp.select_model user function frontend.
* Added support for the 'NS R1rho 3-site' models to the
relax_disp.select_model user function back end. This is for the 'NS
R1rho 3-site' and 'NS R1rho 3-site linear' CPMG dispersion models.
This follows the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
* Decreased the amount of synthetic data in the
ns_r1rho_3site_linear test suite shared data directory. The number of
offsets for this 'NS R1rho 3-site linear' model synthetic data has
been decreased from 81 points to 21. This is because the large
quantities of data slow the test suite down too much.
* Added a GUI test for reading spins from a spectrum formatted
file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added the GUI key 'new spectrum' to point to
'spectrum.read_spins'. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added the spectrum.read_spins GUI page for reading spins
from a spectrum formatted file. Work in progress for Support Request
#3044 (https://gna.org/support/index.php?3044) - load spins from
Sparky list.
* Added radio button for reading spins from a spectrum
formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Further added to the GUI test for reading spins from
spectrum formatted file. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Speed up of the Relax_disp.test_ns_r1rho_3site_linear system
test. Half of the data has been commented out, as too much data was
being loaded for the test.
* Created the target functions for the 'NS R1rho 3-site'
models. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site
linear' dispersion models. This follows the tutorial for adding
relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
* Added the R2eff calculating functions for the 'NS R1rho
3-site' models to the relax library. This is for the 'NS R1rho
3-site' and 'NS R1rho 3-site linear' dispersion models. This follows
the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
* Fix for GUI text string for the select radio button for
reading spins from a spectrum formatted file. Work in progress for
Support Request #3044 (https://gna.org/support/index.php?3044) - load
spins from Sparky list.
* Bug fix for the new 'NS R1rho 3-site' dispersion models -
the Y and Z initial magnetisations were switched. This is for the 'NS
R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This
follows the tutorial for adding relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added cpmg_fit results for the program modified to turn off
the PEAK_SHIFT flag. These are the results which should most closely
match the relax results. This is for the simulated R1rho data for the
'NS R1rho 3-site linear' model.
* Fix for the MODEL_NS_R1RHO_3SITE_LINEAR dispersion variable.
The model name was not correct.
* Turned off the dw dispersion parameter constraints for the
'NS R1rho 3-site' models.
* Added the 'NS R1rho 3-site' models to the dispersion
auto-analysis. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site
linear' dispersion models. This follows the tutorial for adding
relaxation dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
* Added the 'NS R1rho 3-site' models to the GUI model list.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear'
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
* Removed the pC <= pB constraint from the 3-site dispersion
models. This is important for the linear models where a violation of
this constraint is reasonable. This has been replaced by the pC <= pA
constraint.
* Added the 'NS R1rho 3-site' models to the relax user manual.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear'
dispersion models. This follows the tutorial for adding relaxation
dispersion models at
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
* Transposed some of the 'NS R1rho 3-site' model evolution
matrix elements. These now match the 'NS R1rho 2-site' model.
* Last fixes for the 'NS R1rho 3-site' dispersion models.
These now behave identically to the cpmg_fit program with the
PEAK_SHIFT flag disabled. The tilt angle for the initial
magnetisation is no longer that for the average offset but that of
state A.
* Fixes for swapped indices in the relaxation evolution matrix
for the 'NS R1rho 3-site' dispersion models.
* Docstring fix for the lib.dispersion.ns_r1rho_3site module.
* Added the Omega_A,B,C resonance offset parameter definitions
to the dispersion chapter of the manual.
* Updated the relax results for the synthetic data of the 'NS
R1rho 3-site linear' dispersion model.
* Modified the 'NS R1rho 2-site' dispersion model to match the
'NS R1rho 3-site' models. The 6D evolution matrix indices have been
rearranged to match the 9D matrix indices. The tilt angle for the
initial magnetisation is no longer that for the average offset but
that of state A, as was changed for the 'NS R1rho 3-site' models
earlier. The system test was therefore updated for the slightly
different behaviour.
* Updated the relax results for the Fyn SH3 R1rho dispersion
data. This is for the recent changes to the 'NS R1rho 2-site'
dispersion model.
* Updated the Relax_disp.test_ns_r1rho_3site_linear system
test so it now passes. The chi-squared value is not exactly zero as
there are numerical differences between relax and cpmg_fit due to
different approaches being used.
* Added the RMSD determined via showApod for the 69
experiments. Work in progress for Support Request #3083,
(https://gna.org/support/index.php?3083) - Addition of Data-set for
R1rho analysis.
* Added system test for the analysis of optimisation of the
Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion
experiments using the 'DPL' model. Work in progress for Support
Request #3083, (https://gna.org/support/index.php?3083) - Addition of
Data-set for R1rho analysis.
* Modified analysis script for example data of R1rho. Work in
progress for Support Request #3083,
(https://gna.org/support/index.php?3083) - Addition of Data-set for
R1rho analysis.
* Created synthetic R1rho dispersion data for the 'NS R1rho
3-site' model. This is a simple modification of the data for the 'NS
R1rho 3-site linear' model. The k_AC parameter was simply changed
from 0 to 1000. The cpmg_fit software was used to create the data.
Both cpmg_fit and relax results have been updated to the new model.
* Created the new Relax_disp.test_ns_r1rho_3site system test.
This was copied from the Relax_disp.test_ns_r1rho_3site_linear test
and modified to use the new 'NS R1rho 3-site' model synthetic data.
* Fix for wrong use of relax_fit.relax_time instead of
relax_disp.relax_time. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Added the ns_r1rho_3site module to the lib.dispersion
package __all__ list. This allows the unit tests to pass.
* turned off a system test until the release of relax 3.1.1 is
over. Work in progress for Support Request #3044
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
* Fix for the Relax_disp.test_bug_21076_multi_col_peak_list
GUI test. The peak intensity wizard is now closed at the end of the
test so that subsequent tests can cleanly operate. Without closing
this wizard, launching it a second time in another test will always
fail.
* Capitalised 'Python' in the IO redirection messages.
* Epydoc docstring fix for the
lib.dispersion.ns_mmq_3site.r2eff_ns_mmq_3site_sq_dq_zq() function.
This allows the API to be compiled correctly.
* Bug fix for the dispersion grid_search_setup() optimisation
function. This function was not updated for the recent addition of
the spin-lock or hard pulse offset dimension in the
specific_analyses.relax_disp.disp_data module (and hence all
structures used by the dispersion target functions). The
loop_exp_frq_point() function call has been replaced by a
loop_exp_frq_offset_point() function call to allow the 'R2eff' model
parameters to be looped over. For more details, see the thread
http://thread.gmane.org/gmane.science.nmr.relax.scm/19685. This
solution was mentioned at
http://thread.gmane.org/gmane.science.nmr.relax.scm/19685/focus=4859.
* Removed a printout from the Relax_disp.test_r1rho_kjaergaard
GUI test as this is fatal for Python 3.
* Python 3 fixes for the relax_disp.r2eff_read_spin user
function. The check for the dispersion point column now only runs if
that argument is set. In addition, the offset column is now also
being checked.
Bugfixes:
* Fix for the sample_scripts/relax_disp/R1rho_analysis.py
sample script. This was identified by Justin Lecher <jlec att gentoo
doot org> in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/4748
(Message-ID:<52984043.3030808@xxxxxxxxxx>), or the threaded view
http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4748.
The problem was some extra commas which should not have been there.
* Bug fixes for the non-functional R1rho_analysis.py
relaxation dispersion sample script. This script was horribly broken,
but it should now work. It can even be executed from the base relax
directory or from within the sample_scripts/relax_disp/ directory and
perform the full analysis (assuming write access to the relax source
directory).
* Fix for a number of PNG files for NESSY and Bruker icons for
broken IDAT entries. This problem was identified by Justin Lecher
<jlec att gentoo doot org> in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/4750
(Message-ID:<5298572C.5010409@xxxxxxxxxx>), or in the threaded view
http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4750.
As a result those icons are missing in the GUI. This was fixed using
the pngcrush tool.
* Fix for a typo in a model name in the cpmg_analysis.py
relaxation dispersion sample script.
* Fix for bug #21309, the 'R2eff' dispersion model failure
when peak intensity data is missing. The bug is reported at
https://gna.org/bugs/?21309. The problem was that the check for
missing data in the _calculate_r2eff() private API method was
accidentally deleted in the relax_disp branch. See the commit at
http://article.gmane.org/gmane.science.nmr.relax.scm/19261 and the
accidental deletion at
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?view=diff&r1=21504&r2=21505&pathrev=21505.
* Another fix for bug #21309, the 'R2eff' dispersion model
failure when peak intensity data is missing. The bug is reported at
https://gna.org/bugs/?21309. This second problem is only for the
numeric CPMG models for when all data at one magnetic field strength
is missing. When the relaxation dispersion target function is being
set up, the creation of the self.power data structure holding the
number of CPMG blocks fails. The problem is that the relaxation time
for the missing field strength is set to NaN. This is now caught
using lib.float.isNaN().
* Loosened a check in the
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test.
This is to allow this test to pass on certain Mac OS X machines. It
was reported by Troels in the post
http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
* Basic fix for the Relax_disp.test_r2eff_read_spin system
test - the CPMG frequencies are now set. This was identified in the
post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
* Fixes for the parameters in the Relax_disp.test_ns_mmq_3site
system test script.
* Fix for optimisation of Dr. Flemming Hansen's CPMG data to
the 'NS CPMG 2-site star' dispersion model. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Adjusted pA,
dw, kex, chi2.
* Fix for optimisation of the Korzhnev et al., 2005 15N DQ
CPMG data using the 'MMQ 2-site' model. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
* Fix for optimisation of the Korzhnev et al., 2005 15N MQ
CPMG data using the 'MMQ 2-site' model. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
* Fix for optimisation of the Korzhnev et al., 2005 15N ZQ
CPMG data using the 'MMQ 2-site' model. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
* Fix for optimisation of all the Korzhnev et al., 2005 CPMG
data using the 'MMQ 2-site' model. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
* Fix for optimisation of Dr. Flemming Hansen's CPMG data to
the 'NS CPMG 2-site star' dispersion model. Changed so
assertAlmostEqual matches 2 digits. Fix for bug #21322,
(https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0,
reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
* Bug fixes for the dispersion analysis when certain data sets
are completely missing.
* Fix for loading a seriesTab formatted intensity, and getting
the ID for the following GUI elements. Fix for bug #21076,
(https://gna.org/bugs/?21076) - when loading a multi-spectra NMRPipe
seriesTab file through the GUI, several Error messages occur.
* Fix for the relax_disp.r2eff_read_spin user function. The
offsets are now converted to ppm prior to finding the R2eff/R1rho key.
relax version 3.1.1.