This major feature release introduces the new concept of a container
for data linking two atoms or spins - the interatomic data design.
This is for NMR data such as the magnetic dipole-dipole interaction
between two spins (including relaxation and RDC data) and NOESY data.
This design significantly extends relax's flexibility and opens up new
analysis type possibilities. As this is a highly invasive change,
touching almost all of the relax analysis types and modifying the GUI,
the minor version number has been incremented and all of the 2.0.x
version numbering has been skipped. Additional features and changes
include the update of the relax copyright license to GPLv3, support
for absolute or signless RDCs has been added, and elimination of many
GUI bugs in MS Windows. Due to the large number of improvements,
changes, and bug fixes, all users are recommended to upgrade.
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:
* Update of relax to the GNU General Public License version 3.
* Introduction of the interatomic data container design for
NMR data such as the magnetic dipole-dipole interaction between two
spins (including relaxation and RDC data) and NOESY data.
* Support for absolute or signless RDC values.
* Creation of a fast molecule, residue and spin data lookup
framework using private metadata.
Changes:
* Updated the journal reference for the published lactose
conformational search scripts.
* Shifted some of the sample scripts into the analysis
specific sub-directories.
* Increased the size of the test suite warning dialog for MS Windows.
* Improvements to the skipped test printout from the test
suite. Now all test categories (system, unit and GUI) are printed if
a module/package is missing. This allows for better debugging.
* Shifted all of the observer registration and unregistration
to observer_setup() in the pipe editor.
* Improved debugging print outs for the observer objects. The
method name is now stored and included in all the observer 'debug>'
printouts.
* Removed the notebook tab deletion from the GUI tests
tearDown() method. This should be performed when a relax reset
happens, so it is not needed in the tearDown() method just before the
reset() call.
* Merger of the absolute RDC branch (absolute_rdc).
* Added support for the absolute or signless RDCs to the
N-state model. This simply propagates the absolute flags into the
maths_fns.rdc module functions whereby the absolute RDC values and
gradients can be returned.
* The rdc.read user function backend is now storing the
absolute value flag in interatom.absolute_rdc.
* Converted the N-state model absolute_rdcs.py system test
script to the interatomic data design.
* Created an absolute value version of the synthetic CaM RDC
file for the test suite.
* The rdc.read user function backend now accepts the
'absolute' argument. This is used to signal that the RDCs are
signless absolute values.
* Created an initial system (and GUI) test for the absolute RDC
concept.
* Added the 'absolute' keyword arg to the rdc.read user
function definition. This will be used to mark RDCs as being
unsigned.
* Merger of the interatomic data container branch (interatomic).
* Added a new screenshot of the GUI model-free auto-analysis,
as it is now quite different.
* Added a wizard graphic (SVG form) for the 13C-1H dipole-dipole pair.
* A number of the generic_fns.mol_res_spin functions now
accept the pipe argument. These include name_spin(),
set_spin_element(), and set_spin_isotope() and this allows the
functions to operate on any data pipe.
* The dipole_pair.define user function backend now can handle
the pipe argument. This allows it to operate on an alternative data
pipe.
* The State.test_old_state_loading() GUI test now checks the
loaded data to a small extent.
* Better backwards compatibility of old relax results and
state XML files for the interatomic design. The
MoleculeContainer._back_compat_hook() method has been shifted into the
Relax_data_store._back_compat_hook() method. This allows the spin
containers with attached protons to be converted (with new spin
containers for the attached protons added) after loading of the XML
state.
* A small speed up for the model-free duplicate_data()
function. This is used in model selection.
* The generic_fns.mol_res_spin.index_molecule() function now
handles no molecule name given. If no name is given and only a single
molecule is in the current data pipe, then the index of 0 will be
returned.
* The sequence.attach_protons user function now ignores spins
with pre-existing attached protons.
* Improvement for the
generic_fns.interatomic.return_interatom_list() function. The spin ID
matching is now through the id_match() function, allowing unique but
different spin IDs to be used. This now matches the
return_interatom() behaviour.
* The relax_io.read_spin_data() function can now handle spin
IDs in quotes.
* The Scientific Python structural object are_bonded() now
uses 2.0 Angstrom as a cutoff radius.
* Added the are_bonded() and get_molecule() methods for the
Scientific Python PDB reader. This is now needed for defining
interatomic vectors in the interatomic data design.
* Expanded the Interatomic.test_manipulation system test to
demonstrate a few current failures.
* Some changes to the Interatomic.test_manipulation system
test to better test selection/deselection.
* The interatomic test suite scripts are now GUI tests as well.
* Created the new Interatomic system test class for testing
out the interatomic data containers.
* The rdc.read user function can now handle spin IDs in quotation
marks.
* Interatomic data containers can now be selected and
deselected. The user functions select.interatom and
deselect.interatom have been created mimicking the equivalent
select.spin and deselect.spin functions. Each interatomic data
container now has a select flag.
* Modified the interatomic_loop() function so that spin IDs
can be used to restrict the looping.
* Modified InteratomContainer.id_match() to handle a single
spin ID and to match to all unique IDs. This uses the spin container
_spin_ids list private metadata structure.
* Split the return_interatom() function into two. The new
return_interatom() function is used for returning single interatomic
data containers for perfect matches, whereas the
return_interatom_list() function is used to return a list of
containers matching a given spin. This simplifies the behaviour of
the module.
* The RelaxNucleusError and RelaxSpinTypeError can now have
the spin ID supplied.
* Bug fix for the dipole_pair.unit_vectors user function
positional checking. The arg_check.is_float() function needs the
raise_error flag turned off.
* dipole_pair.unit_vectors now raises a RelaxNoInteratomError
if not interatomic data is present.
* The specific API base skip_function() method now returns
False. This was previously raising a RelaxImplementError, but as
Monte Carlo simulations now require this function, but returning
always False, all analyses will be automatically supported.
* Eliminated all of the bond length and heteronucleus type
value.set units tests. These are no longer specific analysis
parameters.
* Removed all of the unit tests of the deleted
structure.vectors user function.
* The model-free data_init() method now sets boolean
parameters to the default of False. This excludes the selection flag
which is set to True. The data_init() method no longer uses the
data_names() API method but the self.PARAMS.loop() method for
returning the parameter names.
* Improvements for the reading of old 1.2 relax results files
for the attached proton spin containers.
* Improvements and fixes for the
generic_fns.relax_data.pack_data() function. This affects all the
relaxation data reading user functions.
* The structure.get_pos user function now prints out all data
and fails if nothing was extracted. This is to prevent the user from
going too far without realising that something is wrong.
* More print outs and better data loading checks in the
dipole_pair user functions.
* The relax_data.read user function now prints out all of the
data read in. This is to better inform the user that something has
happened.
* The return_spin_from_selection() function now lists all
matching spins in RelaxMultiSpinIDError.
* The return_spin() and return_spin_from_selection() functions
can now handle multiple spins. It the 'multi' flag is supplied, then
lists of spins (and associated data) will be returned, rather than a
RelaxMultiSpinIDError error raised.
* Created the list_to_text() RelaxError system function for
prettifying the output of RelaxMultiSpinIDError.
* Expanded RelaxMultiSpinIDError to be able to print out a
list of all the matching spin Ids.
* Improvements for the MoleculeContainer backwards
compatibility hook for the creation of proton spins. The proton
element and isotope type is now set to 'H' and '1H' respectively.
This now means that the old XML files require less work by the user to
convert to the new interatomic data design.
* Eliminated the RelaxProtonTypeError error and changed the
RelaxSpinTypeError message.
* The sequence.attach_protons user function now sets the
proton element and isotope types. This reduces the amount of work
required from the user.
* Rearranged the spin.element user function arguments.
* Created the sequence.attach_proton user function. This will
be useful for analyses which are missing structural data.
* The dipole_pair user functions now fail if nothing could be
done. This is for the dipole_pair.define, dipole_pair.read_dist, and
dipole_pair.set_dist user functions.
* The Monte Carlo select_all_sims() function is now using the
specific skip_function(). This is needed for recreating model-free
simulations as deselected proton spin containers now exist.
* The MoleculeContainer XML backwards compatibility hook now
deletes the spin 'r_err' and 'r_sim' vars.
* Added a backwards compatibility hook for converting old XML
files to the interatomic data design. This will convert the variable
names, deleting the old, and create proton spins and interatomic data
containers populating them with the old spin parameters.
* Added a verbose flag to the generic_fns.dipole_pair.define()
function.
* Added a check to the model-free overfit_deselect() to see if
a relaxation mechanism is present.
* Expanded the functionality of the generic_fns.interatomic
module. The copy() and exists_data() functions have been added to
copy all interatomic data from one data pipe to another and to check
if interatomic data exists within a data pipe respectively. The
create_interatom() function now also accepts a 'pipe' argument so that
non-current pipes can be used.
* Created the RelaxInteratomError and RelaxNoInteratomError
classes for interatomic data errors.
* The interatomic data container now has the dipole_pair flag
initialised to False.
* Expanded the return_interatom() function to handle a single
spin ID. This function now returns a list of matching interatomic
data containers.
* Modified the check_args() method of the dauvergne_protocol
model-free auto-analysis for the new data. The heteronuc_type and
proton_type are now in the spin's isotope variable, and the bond
length 'r' is now the interatomic distance variable 'r'. All spin
containers and interatomic data containers are being checked.
* Expanded the RelaxNoValueError to handle one or two spin IDs
as arguments. This is to better identify which spins or interatomic
data containers are deficient.
* The nuclear isotope is now defined via spin.isotope.
* Eliminated a number of the specific API parameters relating
to dipole-dipole interactions. These are now provided by the
spin.isotope user function and the dipole_pair user functions. The
eliminated parameters are: 'r' - replaced by dipole_pair.set_dist or
dipole_pair.read_dist, 'xh_vect' - replaced by
dipole_pair.unit_vectors, 'heteronuc_type' - replaced by spin.isotope,
'proton_type' - replaced by spin.isotope, and 'attached_proton' -
replaced by dipole_pair.define.
* Created the spin.isotope user function. This is designed to
be a permanent replacement for the specific analysis API
'heteronuc_type' and 'proton_type' parameters.
* Added the nuclear symbol as a wizard graphic.
* Added a set of icons for nuclear or isotope related usage.
* Deletion of the structure.vectors user function as it has
been superseded by dipole_pair.unit_vectors. Only the user function
definition has deleted - the backend code will remain so that it can
be used internally.
* Implemented the dipole_pair.unit_vectors user function
backend. This code originates from the
generic_fns.structure.main.vectors() function (the structure.vectors
user function backend). The dipole_pair.unit_vectors user function is
designed to replace structure.vectors.
* Created the dipole_pair.unit_vectors user function definition.
* Created the backend of the dipole_pair.read_dist user function.
* Created the dipole_pair.read_dist user function definitions.
This new user function is for simplifying the loading of many
different interatomic distances into relax.
* Created a set of icons for the dipole_pair user functions.
* Shifted the relax_data.dipole_pair user function into the
new dipole_pair user function class. This has also been split into
two new user functions: dipole_pair.define used to set up the
magnetic dipole-dipole interactions, and dipole_pair.set_dist used to
set up the r^-3 averaged interatomic distances.
* The relax_data.dipole_pair backend now uses the direct_bond flag.
* Added CONECT records to the sphere.pdb file to allow
connectivities to be more easily determined. This is for the internal
reader, as the current algorithm for finding attached atoms is
distance based, and as all N atoms of all residues are at [0, 0, 0],
this algorithm fails.
* Implemented the are_bonded() structural API method for the
internal structural object.
* Created the structural API base are_bonded() method - this
is for determining if 2 atoms are bonded. This is a method stub which
raises a RelaxImplementError.
* Started to add the backend of the relax_data.dipole_pair
user function.
* Shifted the dipole-dipole graphics to the Wizard directory,
as this is a wizard graphic.
* Created graphics for the magnetic dipole-dipole interaction.
* Removed the bond length from the model-free parameter list.
* The bond length setting via value.set has no been merged
into relax_data.dipole_pair. This averaged length is dipole-dipole
distance and does not need to be a model-free parameter.
* Added the definition for the new relax_data.dipole_pair user
function.
* Started to change the structure.vectors backend to handle
two spin IDs.
* Expanded the description of the negative gyromagnetic ratio
flag for the rdc.read user function.
* Created the generic_fns.interatomic.interatomic_loop()
generator function.
* The generic_fns.interatomic.create_interatom() function now
returns the created container. This comes from the
InteratomicContainer.add_item() method which now also returns the
container.
* Renamed the interatomic function return_container() to
return_interatom(). This is to make the name more unique.
* Shifted some code from InteratomList.add_item() to
generic_fns.interatomic.create_interatom(). This is to break a
circular import problem.
* The rdc.read user function backend is now adding the RDCs to
the interatomic data containers.
* Created the generic_fns.interatomic.create_interatom()
function for creating interatomic data containers.
* Added checks to the InteratomList.add_item() method to make
sure that the spin IDs already exist.
* Created the generic_fns.interatomic module and added the
return_container() method.
* Created the InteratomContainer.id_match() method for
checking the spin IDs in both directions for a match.
* Created the interatomic data list and containers, and added
these to the data pipe structures. This is modelled on the
molecule/residue/spin structures. The new containers have is_empty(),
from_xml() and to_xml() methods and should be fully functional with
the relax infrastructure.
* Improvement for the RelaxNoVectorsError class - the data
pipe name is now optional. The print outs have been improved as well.
* The spin container hidden objects are now replicated when
the object is copied. The old Prototype.__deepcopy__() method was
skipping all hidden objects, but now only objects starting with '__'
are skipped.
* Created a system test to replicate Romel Bobby's bug #19887.
This is the bug report at https://gna.org/bugs/?19887.
* Modified the working of the n_state_model.elim_no_prob
backend. This user function is not functional anyway and is not
tested by the relax test suite, but will remain as it might be useful
in the future.
* Added the consistency testing documentation to the
grace.write and value.* user functions.
* Converted the consistency testing documentation strings to
the Uf_tables and Desc_container design. This is needed to use the
consistency testing documentation within the user function help
system.
* The sequence.read user function now fails with a RelaxError
if no sequence data was loaded. This is for better user feedback.
* Creation of a fast molecule, residue and spin data lookup
framework using private metadata. This consists of two elements: The
already existing private lookup table now at cdp.mol._spin_id_lookup
which is a dictionary with spin IDs as keys and a list of molecule,
residue and spin indices as values; and a set of private variables
within the molecule, residue and spin containers which identify the
parent container names, numbers and indices. As all data is
private,it will not be visible to the user or be saved in the XML
results and save files and should be considered volatile. All this
private metadata is kept up to date via the two new
generic_fns.mol_res_spin functions metadata_prune() and
metadata_update(). For fast operation, these methods can update
specific container subsets via the mol_index, res_index and spin_index
arguments. All parts of relax which modify the data pipe's molecule,
residue and spin data structure (the generic_fns.mol_res_spin
functions and test suite) call these two functions as needed. Two
auxiliary functions spin_id_variants() and spin_id_variants_elim()
have been added to create all possible matching spin ID strings for a
given spin (the second created IDs strings which should no longer
exist). The speed ups from this change are significant. On one
system, the system and unit tests decrease from 492.8s/26.4s to
434.3s/25.1s. On another the decrease is from 330.7s/17.4s to
258.9s/15.4s. In addition, the pipe argument has been added to the
generic_fns.mol_res_spin functions create_molecule(),
create_residue(), create_pseudo_spin() and create_spin(). Also, the
molecule name will now always be a string. Previously this was
allowed to be an integer. This is needed for the private metadata
functions to operate correctly. A number of unit tests have been
updated for the changes.
* Removed a hack from the generic_fns.relax_data.pack_data()
function for the BMRB support. This calls the
generic_fns.bmrb.generate_sequence() function. As non-BMRB code paths
access the pack_data() function, this is a nasty hack which would have
caused problems in the future.
* Removal of a hack from the
generic_fns.bmrb.generate_sequence() function. This hack was for
naming unnamed spins. But this is not needed as the
generic_fns.mol_res_spin.create_spin() function already does this but
with many more safety checks.
* The spin ID lookup table has been made private so that it is
not included in the save files.
* Update and clean up of the model-free LaTeX table generation script.
* Created the generic_fns.mol_res_spin.return_spin_indices()
function to return the index triplet. This allows a spin ID to be
converted into the molecule, residue and spin indices.
* The generate_spin_id() function now choses to use the spin
name instead of number by default.
* Renamed return_spin_from_id() to return_spin(), and
return_spin() to return_spin_from_selection(). This shaves off a
number of seconds from the system test - the look up table speed ups
will come with support in the other mol_res_spin module functions.
* return_spin_from_id() now defaults to return_spin() when the
spin ID is not in the lookup table. The slower return_spin() method
will allow return_spin_from_id() to always be functional.
* Added the 'pipe' argument to
generic_fns.mol_res_spin.return_spin_from_id(). This is to mimic the
return_spin() function.
* Created generic_fns.mol_res_spin.return_spin_from_id() for
returning spin containers from spin IDs.
* generic_fns.mol_res_spin.create_pseudo_spin() is now adding
data to the spin ID look up table. To support this, the
return_residue() method now takes the 'indices' argument and returns
the molecule and residue indices.
* Started to fill up the spin ID look up table. The
index_molecule() and index_residue() functions have been added to
determine the MoleculeList and ResidueList indices of given molecules
and residues. These are used by the create_spin for efficiency and to
allow the indices (together with the spin index and spin ID string) to
be assembled into the look up table. This table is not used anywhere
yet.
* Initialised a look up table in the cdp.mol structure for
faster spin access. This look up table will be slowly transitioned
to, and should significantly speed up certain operations.
* Created the gui.misc.bitmap_setup() function for handling
bitmap alpha correctly on operating systems. This function is
required to handle alpha in bitmap on MS Windows so that regions with
partial transparency are not blended into the default dark grey colour
of Windows' windows.
* Added the status/weather-snow-scattered-night Oxygen icon as
a wizard graphic for the temperature uf.
* The about model-free dialog no longer has grey at the bottom
in MS Windows. The wx.ScrolledWindow.GetScrollPixelsPerUnit()
function is now used to determine how many pixels the y scrolling is,
and rounds up the virtual size based on that.
* Improved the debugging drawing for the about GUI elements.
* Hack for the relax_fit C module compilation to detect
supported CPUs for Mac OS X cross compilation.
Bugfixes:
* Bug fix for the model-free GUI auto-analysis GUI test on MS
Windows - the wizards for the CSA value and nuclear isotopes were
experiencing racing conditions on MS Windows.
* Bug fix for MS Windows for the deletion of temporary files
in the system tests. For certain Windows/Python combinations, a
WindowsError was being raised saying that the file cannot be deleted
as it is being used by another process.
* Fix for the reporting of skipped GUI tests. The Frame_order
tests skipped because of the missing Scipy module were been labelled
as system rather than GUI tests.
* The GUI show_pipe_editor() method is now the place where the
methods are registered with the observers. This is a partial bug fix
for the GUI tests. The hiding mechanism of the window with
unregistration requires this.
* Bug fix for the pipe editor window hiding and restoring.
All of the Pipe_editor.Show() method has been shifted into the GUI
show_pipe_editor() method. This is needed for the technique of
unregistering with the observer objects when the window is closed via
a Hide() call.
* Fix for the State.test_load_state_no_gui() GUI test for
handling pipe bundles.
* Redesign of the setUp() and tearDown() methods of the GUI
tests. This is needed as the current design does not work under MS
Windows. Instead of created a new wx app for each test (this dies in
Windows as it looks like only a limited number of toolbars can be
created), only one app is created and is recycled. This design better
mimics GUI usage anyway. This change uncovers a few GUI bugs not
caught by the previous design.
* Bug fix for the GUI test suite setUp() method. The observer
objects are reset at the start to get around a bug when the setUp()
method fails for a previous test.
* Bug fix for the running of the GUI tests on Mac OS X - the
relax GUI 'app' needs to be deleted after each test.
* Bug fix for the Dead_uf_pages.test_mol_create() GUI test for
MS Windows. The _execute_uf() method is now used instead of
simulating _ok() calls.
* Bug fix for the GUI tests on MS Windows. The
GuiTestCase._execute_uf() method now prevents the wizard from running
when calling the GUI user function by setting the wx_wizard_run
argument to False. This allows the wizard _ok() call to function on
Windows.
* Bug fix for the Palmer system tests for the changed spin ID
syntax. The spin Gly 2 can no longer be selected with ':2&:Gly', the
'&' symbol is not allowed here.
* Bug fix for the Value GUI input element for integer values.
This is only uncovered when remotely running the GUI - e.g. through
the test suite - and an integer value is set.
* A final fix for bug #19887 (https://gna.org/bugs/?19887).
Now a RelaxError is raised if the number of peak intensities is not
the same for all spins. This occurs in the relaxation curve-fitting
overfit_deselect() method.
* Partial fix for bug #19887 (https://gna.org/bugs/?19887).
The problem is that the number of peak height values was not the same
for all spins. The error message was being caused by the
math_fns.relax_fit C object 'setup' function being feed in incorrect
values, causing relax to fail directly after the setup() call in
specific_fns.relax_fit.minimise(). The number of points was being
taken from cdp.relax_times, but in the
Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3 spins
has 4 points rather than 5. Now the correct number is sent into
setup().
* Fix for reading of BMRB CSA saveframe data - spin IDs
generated from the data now have molecule info. This is problematic
only in certain edge cases, for example a multi-molecule entry.
* Bug fox for the
generic_fns.mol_res_spin.return_spin_indices() function. The
selection object was using the wrong variable name, and the look up
table fallback was always on.
* Bug fix for the relax_data.copy user function - it can now
handle spins without relaxation data.
* Bug fix for the grey about windows on MS Windows. All the
about windows were grey. The temporary wxPython 2.9.3.1 fix was
breaking the Windows GUI.
* Bug fix for the model-free analysis tab about window -
sometimes a grey region would appear at the bottom. This is a problem
in at least GTK+ as scrolling is in increments of 20.
* Bug fix for sizing of the GUI about dialogs - the virtual
sizes are now accurately calculated. To do this, the window contents
(a wx.BufferedDC instance) is created twice, with the virtual window
size exactly calculated in the first pass, and then used to set up the
device context in the second. A space is also now added to the end to
ensure the border is there.
* Fixes for the spin.create user function for GUI usage.
* Fixes for the J(w) mapping and consistency testings scripts
so they can run as GUI tests.
* Fix for the spin.copy user function for GUI use.
* Bug fix for the return_spin_from_selection() function for
the 'multi' flag. This function needs to handle the case of no spins
matching the selection!
* Bug fix - the spin_id arg for the relax_data.read user
function now actually does something. This argument is passed into
the pack_data() function, where it is used to match against the spins
matching each file line. Only if there is a match, is the relaxation
data loaded for that spin.
* Fixes for the reading of relax 1.2 results files. The new
'H' spin containers are now deselected, and the simulation structure
creation has been reverted.
relax version 2.1.0.