This is a major feature and bugfix release. Features include the new
structure.pca user function for performing a principle component
analysis (PCA) of a set of structures, handling of replicated R2eff
data points in the dispersion analysis, improvements in the handling
of PDB structures, the protection against numpy ≥ 1.9 FutureWarnings
for a number of soon to change behaviours in numpy, and addition of a
deployment script for the Google Cloud Computing. Bugfixes include an
error when loading relaxation data, the CSA constant equation in the
manual, missing information in the relax state and results files,
loading of certain state files in the GUI, running relax with no
graphical display and using matplotlib, BMRB export failure when a
spin container is missing data or parameters.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.1 .
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:
* Many improvements for the compilation of the HTML version of
the relax manual (http://www.nmr-relax.com/manual/index.html).
* Updated relax to eliminate all FutureWarnings from numpy ≥
1.9, to future-proof relax against upcoming numpy behaviour changes.
* Ability to handle replicated R2eff data points by the
relax_disp.r2eff_read user function, but adding 0.001 to the frequency
value for the replicated point.
* A new sample script for loading a model-free results file
and back-calculating relaxation data.
* Improvements for the handling of PDB structural data.
* Implementation of the structure.pca user function for
performing principle component analyses (PCA) of an ensemble of
structures.
* Addition of a script for rapid deployment on the Google
Cloud Computing infrastructure.
Changes:
* Fix for the rigid frame order model 2nd degree frame order
matrix in the manual. The wrong symbol was being used.
* Removed the newparagraph and newsubparagraph definitions
from the LaTeX manual. These were causing conflicts with latex2html,
preventing the HTML version of the manual at
http://www.nmr-relax.com/manual/index.html from being compiled. These
definitions are unnecessary for the current set up of the sectioning
in the manual.
* Modified the short captions in the new frame models chapter
of the manual. The runic ᛞ character has been replaced simply by
'Daeg'. This is due to incompatibilities with latex2html which
prevents the HTML manual at http://www.nmr-relax.com/manual/index.html
from being compiled.
* Removal of the definition of a fixed-width table column from
the LaTeX manual preamble. This is required as the definition breaks
latex2html compatibility, causing a corruption in the figure numbering
resulting in the images in the HTML to be essentially randomised.
* Removal of the accents package to allow the HTML manual to
be compiled. The 'accents' LaTeX package is not compatible with
latex2html, so the easiest fix is to eliminate the package.
* Manually rotated the frame order matrix element EPS manual
figures, for latex2html compatibility. The '90 rotate' command has
been deleted and the bounding box permuted as 'a b c d' -> 'b -c d
-a'. This allows the angle argument in the \includegraphics{} command
to be dropped, as latex2html does not recognise this. It allows the
figures to be visible in the HTML version of the manual at
http://www.nmr-relax.com/manual/index.html .
* Redesign of the frame order parameter nesting table in the
manual for latex2html compatibility. The table uses the tikz package,
which is fatal for latex2html, even if not used. Therefore the table
in the docs/latex/frame_order/parameter_nesting.tex file has been
converted into a standalone LaTeX document to create a cropped
postscript version of the tikz formatted table. A compilation script
has been added as well. The resultant *.ps file is now included into
the PCS numerical integration section, rather than this section
creating the tikz table. All tikz preamble text has been removed to
allow latex2html to run.
* Workaround for latex2html not being able to handle the
allrunes package or associated font. In the preamble 'htmlonly'
environment, the frame order symbols are redefined using the text
'Daeg' instead of the runic character ᛞ.
* Fixes for sub and superscripts throughout the manual. This
introduces {} around all sub and superscripted \textrm{} instances.
This is not needed for the PDF version of the manual as the missing
bracket problem is avoided, but it affects the HTML version of the
manual compiled by latex2html, which requires the correct notation.
The fixes are for both the new frame order chapter as well as the
relaxation dispersion chapter.
* Editing and fixes for the relax 4.0.0 part of the CHANGES file.
* Updated and improved the wiki instructions in the relax
release checklist document.
* One more wiki instruction about checking for dead links in
the release checklist document.
* More minor changes to the 'Announcement' section of the
release checklist document.
* Updated the shell script for finding duplicated titles in
the LaTeX files of the manual.
* Converted the duplicate title finding shell script into a
Python script. The Python script is far more advanced and uses a
different logic to produce a table of replicated titles and their
count. The script also returns a failed exit status when replicates
exist.
* Converted the replicated title finding Python script to use
a class structure. This allows the script to be imported as a module.
The replicate finding has been shifted into a find() class method.
* Renamed the replicate title finding script.
* Removed the duplicate LaTeX title finding shell script.
This is now handled by the far more advanced Python script.
* The Scons compilation of the PDF and HTML manuals now checks
for replicated titles. A new replicate_title_check target has been
added to the scons scripts. This calls the find() method of the
replicate LaTeX title finding script to determine if any titles are
replicated, and if so the scons target returns with a sys.exit(1)
call. This target is set at the start of the user_manual_pdf,
user_manual_pdf_nofetch, user_manual_html, user_manual_html_nofetch
scons targets. The result is that the manual cannot be compiled if
replicate titles exist, forcing the titles to be changed. The result
will be that the HTML pages at http://www.nmr-relax.com/manual/ will
all be unique, as replicated titles results in only one HTML page
being created for all the sections.
* Elimination of replicated titles in the LaTeX sources that
the new frame order chapters introduced.
* Removal of an old replicated title in the LaTeX sources for
the manual. This is the title 'Model-free analysis' which is used for
the entire specific analysis chapter as well as for the model-free
analysis section of the values, gradients, and Hessians for
optimisation chapter.
* Fixes and improved printouts for the replicate_title_check
scons target.
* Updated all of relax to protect against future changes
occurring in the numpy Python package. From numpy version 1.9, the
FutureWarning "__main__:1: FutureWarning: comparison to `None` will
result in an elementwise object comparison in the future." is seen in
a large percentage of all relax's user functions. This is caught and
turned into a RelaxWarning with the same message. The issue is that
the behaviour of the comparison operators '==' and '!=' will change
with future numpy versions. These have been replaced with 'is' and
'is not' throughout the relax code base. Changes have also been made
to the minfx and bmrblib packages to match.
* More future protection against numpy changes. The
FutureWarning is "`rank` is deprecated; use the `ndim` attribute or
function instead. To find the rank of a matrix see
`numpy.linalg.matrix_rank`." Therefore the N-state model target
function method paramag_info() has been updated to use the .ndim
attribute and longer use numpy.rank() function.
* Created the Mf.test_bug_23933_relax_data_read_ids system
test. This is designed to catch bug #23933
(https://gna.org/bugs/?23933), the "NameError: global name 'ids' is
not defined" problem when loading relaxation data. A truncated
version of the PDB file and relaxation data, the full versions of
which are attached to the bug report, consisting solely of residues
329, 330, and 331 have been added to the test suite shared data
directories, and the system test written to catch the NameError.
* Updated the Mf.test_bug_23933_relax_data_read_ids system
test to catch the RelaxMultiSpinIDError. This allows the system test
to pass, as a RelaxMultiSpinIDError is expected.
* Updated the minfx and bmrblib versions in the release
checklist document to 1.0.12 and 1.0.4. This is to remove the numpy
FutureWarning messages about the '== None' and '=! None' comparisons
to numpy data structures, which in the future will change in
behaviour.
* Increased the Gna! news item sectioning depth in the release
checklist document.
* Expanded the description of the sequence.attach_protons user
function. This follows from
http://thread.gmane.org/gmane.science.nmr.relax.user/1849/focus=1855 .
* Added initial data for testing data from Paul Schanda. This
will demonstrate that there are several possibilities to enhance the
r2eff point method.
* Added the Relax_disp.test_paul_schanda_nov_2015 system test.
This will catch the loaning of "nan" values.
* Made additional check in sequence reading, that "nan" values
are skipped.
* Making sure that the replicated 4000 Hz point fpr the 950
MHz experiment is not overwritten.
* In the Relax_disp.test_paul_schanda_nov_2015 system test,
added a test of counting the R2eff values. This shows that the
replicated R2eff at 950 MHz/4000 Hz point is overwritten. A solution
could be to change the dispersion frequency very little, to allow the
addition of the data point.
* Expanded a comment about why 1 is subtracted in a test.
* Added further tests to
Relax_disp.test_paul_schanda_nov_2015. This will show that replicates
of R2eff values is not handled well.
* In the function of r2eff_read, in data module of the
dispersion, added the possibilities to read r2eff values which are
replicated. This is done first checking if the dispersion key exists
in the r2eff dictionary. If it exists, continue add 0.001 to the
frequency until a new possibility exists. This should help handle
multiple R2eff points, as separate values and not taking any decision
to average them.
* Added the expectation of raising an relax error, if trying
to plot and no model information is stored.
* Raising an error if plotting dispersion curves, and no model is
saved.
* Changed example script for analysing data.
* Extended the Relax_disp.test_paul_schanda_nov_2015 system
test to include auto-analysis and clustered fits. This should show
that the analysis is now possible.
* Added a temporary state and a script for GUI setup to the
data Paul Schanda.
* Added the Relax_disp.test_paul_schanda_nov_2015 GUI test.
This will show that loading a state will create a problem. Traceback
(most recent call last): TypeError: int() argument must be a string or
a number, not 'NoneType'.
* Added a sample script for back-calculating relaxation data
from a model-free results file. This is useful when the results file
is not the final model, as these results file do not contain the
back-calculated data. This is in response to Christina Möller's sr
#3303 support request (https://gna.org/support/?3303).
* Using Gary's lib.float.isNaN() instead of math.isnan(), to
have backwards compatibility with python 2.5.
* Fix for spelling mistake and documenting the new behavior of
relax_disp.r2eff_read(), when reading r2eff points with the same
frequency. If the spin-container already contain r2eff values with
the 'frequency of the CPMG pulse' or 'spin-lock field strength', the
frequency will be changed by a infinitesimal small value of + 0.001
Hz. This allow for duplicates or more of the same frequency.
* Modified the internal structural object to be less
influenced by the format of the PDB. The PDB serial number is now
intelligently handled, in that it is reset to 1 when a new model is
created. This information is still kept for supporting the logic of
the reading of the CONECT records, and will be eliminated in the
future. The chain ID information is now no longer stored in the
internal structural object, as this information is recreated by the
structure.write_pdb user function based on how the internal structural
object has been created.
* Updates to the Noe and Structure system test classes for the
internal structural object changes. The serial number can now be
reset, and the chain ID information is no longer stored.
* Added a file to the test suite shared data to help implement
the PCA structural analysis. This is the N-domain of the CaM-IQ
complex used in a frame order analysis. It is the first 5 structures
from a call to the frame_order.distribute user function, with the
different rigid-bodies merged back together into a single molecule.
* Created the structure.pca user function front end. This is
currently modelled on the structure.rmsd user function framework.
* Basic implementation of the structure.pca user function back
end. This is the new pca() function of the
pipe_control.structure.main module. It simply performs some checks,
assembles the atomic coordinates, and the passes control to the relax
library pca_analysis() function of the currently unimplemented
lib.structure.pca module.
* Partial implemented of the PCA analysis in the relax
library. This is for the new structure.pca user function. The
lib.structure.pca module has been created, and the pca_analysis()
function created to calculate the structure covariance matrix, via the
covariance() function, and then calculate the eigenvalues and
eigenvectors of the covariance matrix, sorting them and truncating to
the desired number of PCA modes.
* Added the 'algorithm' and 'num_modes' arguments to the
structure.pca user function. These are passed all the way into the
relax library backend.
* Implemented the SVD algorithm for the PCA analysis in the
relax library. This simply calls numpy.linalg.svd().
* The PCA analysis in the relax library now calculates the per
structure projections along the PCs.
* The PCA analysis function in the relax library is now
returning data. This includes the PCA values and vectors, and the per
structure projections.
* The PCA values and vectors, and the per structure
projections are now being stored. This is in the structure.pca user
function backend in the pipe_control.structure.main module.
* Added the 'format' and 'dir' arguments to the structure.pca
user function. This is to the front and back ends.
* Modified the assemble_structural_coordinates() method to
return more information. This is from the pipe_control.structure.main
module. The 'lists' boolean argument is now accepted which will cause
the function to additionally return the object ID list per molecule,
the model number list per molecule, and the molecule name list per
molecule.
* The structure.pca user function now creates graphs of the PC
projections. This includes PC1 vs. PC2, PC2 vs. PC3, etc.
* Added the Gromacs PCA results for the distribution.pdb file.
This includes a script used to execute all parts of Gromacs and all
output files.
* Updated the Gromacs PCA results for the newest Gromacs
version (5.1.1).
* Created an initial Structure.test_pca system test. This
executes the new structure.pca user function, and checks if data is
stored in cdp.structure.
* Improved the graphs in the backend of the structure.pca user
function. The graphs are now clustered so that different models of
the same structure in the same data pipe are within one graph set.
The graph header has also been improved.
* Expanded the Structure.test_pca system test checks to
compare to the values from Gromacs.
* A weighted mean structure can now be calculated. This is
for the calc_mean_structure() function of the relax library module
lib.structure.statistics. Weights can now be supplied for each
structure to allow for a weighted mean to be calculated and returned.
* Added support for 'observer' structures in the structure.pca
user function. This allows a subset of the structures used in the PC
analysis to have zero weight so that these structures can be used for
comparison purposes. The obs_pipes, obs_models, and obs_molecules
arguments have been added to the user function front end. The backend
uses this to create an array of weights for each structure. And the
lib.structure.pca functions use the zero weights to remove the
observer structures from the PC mode calculations.
* Created the Structure.test_pca_observers system test. This
is for testing the new observer structures concept of the
structure.pca user function.
* Improved the printouts from the relax library principle
component analysis. This is in the pca_analysis() function of the
lib.structure.pca module.
* Fixes and improvements for the graphs produced by the
structure.pca user function. The different sets are now correctly
created, and are now labelled in the plots.
* Adding a testing deploy script, for rapid deployment on
Google Cloud Computing. This is for an intended install in Ubuntu
14.04 LTS.
* Expanding script for installation.
* Putting installation into functions in deploy script.
* Splitting deploy script into several small functions.
* Adding checking statements to install script.
* When sourcing the scripts, several functions can be performed
instead.
* Added spaces to install script for better printing.
* Adding a tutorial script.
* Adding 2 tutorial scripts.
* Fix for small spin ID error in tutorial script.
* Created a system test for catching bug #24131. This is the
BMRB export failure when the SpinContainer object has no s2 attribute,
as reported by Martin Ballaschk at https://gna.org/bugs/?24131.
* Modified the Mf.test_bug_24131_bmrb_deposition system test
to check for the RelaxError. The test results in a RelaxError, as the
results file contains no selected spins.
* Added the Mf.test_bug_24131_missing_interaction system test
to catch another problem. This is part of bug #24131
(https://gna.org/bugs/?24131), the BMRB export failure with the
SpinContainer object having no s2 value. However the previous fix of
skipping deselected spins introduced a new problem of relax still
searching for the interatomic interactions for that deselected spin.
Bugfixes:
* Replicated titles in the HTML version of the relax manual
(http://www.nmr-relax.com/manual/index.html), and hence replicated
HTML file names overwriting earlier sections, have been eliminated.
* Fix for bug #23933 (https://gna.org/bugs/?23933). This is
the "NameError: global name 'ids' is not defined" problem when loading
relaxation data. The bug was introduced back in November 2014, and is
due to some incomplete error handling code. The problem is that the
spin type that the relaxation data belongs to (@N vs. @H) has not been
specified. Now the correct RelaxMultiSpinIDError is raised. The
'ids' variable did not exist - it was code that was planned to be
added, but never was and was forgotten.
* Fix for the CSA constant equation in the model-free chapter
of the manual. This was spotted by Christina Möller and reported on
the relax-users mailing list at
https://mail-archive.com/relax-users%40gna.org/msg01776.html .
* Bug fix for the storage of the XML structural object in the
state and results files. Previously any objects added to
cdp.structure (or any structure object) would not be saved by the
structural object to_xml() method unless the function is explicitly
modified to store that object. Now all objects present will be
converted to XML.
* Fix for the relaxation dispersion analysis in the GUI, as
caught by the Relax_disp.test_paul_schanda_nov_2015 GUI test. When
loading from a script state file, the value of "None" can be present.
This is now set to the standard values.
* Fix for running relax at a server with no graphical display
and using matplotlib. The error was found with the
Relax_disp.test_repeat_cpmg system test. And the error generated was:
"QXcbConnection: Could not connect to display. Aborted (core dumped)".
The backend of matplotlib has to be changed. This is for example
described in:
http://stackoverflow.com/questions/2766149/possible-to-use-pyplot-without-display
http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib.
* Modified the behaviour of the bmrb.write user function
backend for a model-free analysis (fix for bug #24131,
https://gna.org/bugs/?24131). This is in the bmrb_write() method of
the model-free analysis API. Deselected spins are now skipped and a
check has been added to be sure that spin data has been assembled.
* Another fix for bug #24131 (https://gna.org/bugs/?24131).
This is the BMRB export failure when the SpinContainer object has no
s2 attribute. Now no data is stored in the BMRB file if a model-free
model has not been set up for the spin. This allows the test suite to
pass.
* Bug fix to allow the Mf.test_bug_24131_missing_interaction
system test to pass. This is part of bug #24131
(https://gna.org/bugs/?24131), the BMRB export failure with the
SpinContainer object having no s2 value. The problem was when
assembling the diffusion tensor data. The spin_loop() function was
being called, as the diffusion tensor is reported for all residues.
Therefore the skip_desel=True has been added to match the model-free
part.
relax version 4.0.1.