This is a major feature and bugfix release. It fixes a failure when
loading relaxation data and adds Python 3 support for using the
NMRPipe showApod software. Features include a large expansion for the
align_tensor.matrix_angles and align_tensor.svd user functions to
support the standard inter-matrix angles, the unitary 9D vector
notation {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}, and the
irreducible spherical tensor 5D basis set of {A-2, A-1, A0, A1, A2}
for correctly calculating the inter-tensor angles, singular values and
condition numbers.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.3.
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:
* 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 (https://gna.org/bugs/?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,
http://dx.doi.org/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
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 <v1|v2>.
* 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_angle
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 at
http://www.nmr-relax.com/api/index.html. 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. This is for
http://www.nmr-relax.com/api/3.3/pipe_control.opendx-module.html#map.
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 (https://gna.org/bugs/?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 functions, 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).
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