Author: bugman
Date: Tue Nov 26 18:11:50 2013
New Revision: 21649
URL: http://svn.gna.org/viewcvs/relax?rev=21649&view=rev
Log:
Backported the relax 3.0.2 CHANGES file addition to trunk.
The command used was:
svn merge -r21647:21648 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.0.2 .
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=21649&r1=21648&r2=21649&view=diff
==============================================================================
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Tue Nov 26 18:11:50 2013
@@ -1,3 +1,78 @@
+Version 3.0.2
+(26 November 2013, from /trunk)
+http://svn.gna.org/svn/relax/tags/3.0.2
+
+ Features:
+ * Much better pseudo-atom support, including not requiring
tetrahedral geometry.
+ * The value.write user function can now create files with
non-numeric data, such as the models for each spin.
+ * Improvements to the 2D Grace plotting from the grace.write user
function including full support for multiple graphs and the setting of the
axes to the zero point.
+
+
+ Changes:
+ * Updated the Release Checklist document rsync instructions to allow
resumed uploads. This is needed if the internet connection has been cut, as
uploading can take a long time.
+ * The test_suite.clean_up.deletion() function can now handle the
case of missing files and directories. This problem was occurring in the
relax_disp branch for some of the system tests.
+ * Created the is_int() and is_num() functions for the
lib.check_types module.
+ * The value.write user function can now properly handle non-numeric
data types. This allows the spin specific model name to be written to file,
or any other string defined in the specific analysis PARAMS data object.
+ * The multi-processor section of the manual is now labelled in the
correct position.
+ * Created a special GUI analysis element for floating point numbers.
This allows for user input of floating point numbers into one of the GUI
analysis tabs. If the input is not a number, the original value will be
restored.
+ * Created the new pipe_control.spectrum.add_spectrum_id() function.
This is used to handle the creation of spectrum ID strings in the data store.
This way new spectrum IDs can be created from different parts of relax in a
controlled way.
+ * Created the pipe_control.spectrometer.check_frequency() function
to standardise this check.
+ * Created the pipe_control.spectrometer.get_frequency() function for
returning the frequency for a given ID.
+ * The pipe_control.spectrum.add_spectrum_id() function now returns
silently if the ID already exists.
+ * Improvements to the pymol.view and molmol.view user functions for
finding the PDB files. Now the possibility that this is being run from a
results subdirectory is taken into consideration. If the file cannot be
found, the os.pardir parent directory is added to the start of the relative
path and the file checked for.
+ * The rdc.read user function will now skip all lines of the RDC file
starting with '#'. To include molecule identifiers at the start of the line
will now require quotation marks.
+ * Shifted the RDC and PCS assembly methods from the main class to
the data module for the N-state analysis.
+ * Created the pipe_control.mol_res_spin.is_pseudoatom() function to
simplify pseudo-atom handling.
+ * Created the pipe_control.mol_res_spin.pseudoatom_loop() function.
This is used to loop over the spin containers corresponding to a given
pseudo-atom.
+ * Added a PDB file and RDC values (and absolute J+D and J) for
propylene carbonate. This will be used for testing of pseudo-atoms in the
N-state model analysis.
+ * Renamed the propylene carbonate files to the correct name of
pyrotartaric anhydride.
+ * Created two new system tests based on the new pyrotarctic
anhydride long range (1J, 2J & 3J) RDC data. The first
(N_state_model.test_pyrotartaric_anhydride_rdcs) optimises an alignment
tensor using long range signed RDC data. The second
(N_state_model.test_pyrotartaric_anhydride_absT) optimises an alignment
tensor using long range absolute T (J+D) data. Both test long range data
together with methyl group pseudo-atom data.
+ * Added all of the pyrotartaric anhydride RDC generation scripts and
files. This is simply for reference and reproducibility.
+ * Modifications for the pyrotartaric anhydride system test script.
The grid search now is much quicker, and the RDC correlation plots are now
sent to DEVNULL.
+ * Added the return_id argument to the
pipe_control.mol_res_spin.pseudoatom_loop() function. This will then yield
both the spin container and spin ID string. This mimics the
spin_loop()function.
+ * Added proper pseudo-atom support for the RDCs in the N-state model
analysis. This involves a number of changes. The pseudo-atom specific
functions ave_rdc_tensor_pseudoatom() and
ave_rdc_tensor_pseudoatom_dDij_dAmn() have been added to the
lib.alignment.rdc module. These simply average the values from the
equivalent non-pseudo-atom functions. The return_rdc_data()function in the
specific_analyses.n_state_model.data module has been modified to assemble the
RDC constants and unit vectors for all members of the pseudo-atom and add
these to the returned structures, as well as a new list of flags specifying
if the interatom pair contains pseudo-atoms. The N-state model target
function and gradient have been updated to send the pseudo-atom data to the
new lib.alignment.rdc module functions.
+ * J couplings for the N-state analysis are now properly handled for
pseudo-atoms. The measured J couplings for the members of the pseudo-atom
should not be used, but rather that of the pseudo-atom spin itself (as the
former does not exist).
+ * Eliminated the old pseudo-atom handling in the N-state model
specific return_rdc_data() function. This was multiplying the RDCs by -3 to
handle the tetrahedral geometry of the 1J methyl RDCs. However this approach
is not valid for non-methyl pseudo-atoms or for 2J, 3J, etc. data.
+ * A RelaxError is now raised for the N-state model optimisation with
gradients when T = J+D data is used. The gradients for this data type are
not implemented yet, so it is better to prevent the user from using this.
+ * The N_state_model.test_pyrotartaric_anhydride_absT system test now
uses simplex optimisation to pass. The Newton algorithm cannot be used as
the gradients for T = J+D type data have not been implemented.
+ * An RDC error of 0.0 will now deselect the corresponding
interatomic data container. This can be used for simpler pseudo-atom
handling.
+ * Updated the menthol long range RDC data file to include
pseudo-atom member distances.
+ * Renamed the interatomic_loop() function 'selected' argument to
'skip_desel'. This is to match the spin_loop() function arguments.
+ * The interatom.unit_vectors user function now calculates the unit
vectors for deselected containers. This is useful for pseudo-atom handling
where the interatomic containers to the pseudo-atom members have already been
deselected.
+ * Updated the value checking for the
N_state_model.test_absolute_rdc_menthol system test. The pseudo-atoms are
now properly handled so the result is now much better.
+ * The stereochemistry auto-analysis can now accept a file of
interatomic distances. This is for better pseudo-atom support.
+ * The N-state model specific check_rdcs() function now properly
handles pseudo-atoms.
+ * The pipe_control.rdc.q_factors() function now properly handles
pseudo-atoms. If pseudo-atoms are present, then 2Da^2(4 + 3R)/5 normalised Q
factor is skipped.
+ * Created the N_state_model.test_pyrotartaric_anhydride_mix system
test. This is used to demonstrate a bug in the N-state analysis using mixed
RDC and long range absolute J+D data.
+ * Movement of N-state model specific code to the analysis neutral
pipe_control package. Many of the functions of the
specific_analyses.n_state_model.data module relating to alignment tensors,
RDC data and PCS data have been shifted in to the pipe_control package
modules align_tensor, rdc, and pcs respectively. This allows these functions
to be made more general and allow the code to be shared with the frame order
analysis or any future analysis using such data, and hence remove some code
duplication.
+ * Create two new warnings RelaxNucleusWarning and
RelaxSpinTypeWarning to match the equivalent errors.
+ * Added some RDC data checks to the
N_state_model.test_pyrotartaric_anhydride_rdcs system test. This is to
demonstrate a problem with the data assembly function
pipe_control.rdc.return_rdc_data().
+ * Clean ups and improvements for the pipe_control.rdc.check_rdcs()
function. Pseudo-atoms are now handled much better and correctly in all
cases. And many RelaxErrors have been converted to RelaxWarnings followed by
a 'return False' statement.
+ * Created the pipe_control.rdc.setup_pseudoatom_rdcs() function.
This is used to make sure that the pseudo-atom interatomic systems (the
containers from heternucleus to pseudo-atom and heteronucleus to pseudo-atom
members) are properly set up. It will deselect the interatomic containers if
incorrectly set up or if they are not part of the main pair.
+ * Added quotation marks around a number of spin IDs with molecule
names in some RDC data files. This is for the N-state model population model
data used in the test suite.
+ * The rdc.read and j_coupling.read user functions now ignore all
lines starting with the # character. This is to remove all comment lines
silently. Therefore if spin IDs are used which contain the molecule name,
then they should be wrapped in quotation marks.
+ * Updated a number of RDC test suite data files to have quotation
marks around the spin IDs. This is to allow the molecule identifier to be
present while not being mistaken for a comment line.
+ * Updated some of the RDC data files used in the frame order system
tests. The spin IDs are now in quotation marks as the molecule name is
included. This is to prevent the line being removed as a comment.
+ * Changes to the setup_pseudoatom_rdcs() function and renamed it to
setup_pseudoatom_rdc(). The interatomic loop is now within the function to
make sure that all is completed before the containers are accessed.
+ * Started to add better pseudo-atom support for the PCS. The new
pipe_control.pcs.setup_pseudoatom_pcs() function has been added to deselect
the spins which are members of a pseudo-atom. The return_pcs_data() function
in the same module now calls this function and builds a list of pseudo-atom
flags for use in the target function (though it is still unused).
+ * Finally eliminated the gui.paths module, replacing it with
graphics.fetch_icon() calls. The GUI was using a mix of the old gui.paths
module and the fetch_icon() function.
+ * Created the pipe_control.sequence.return_attached_protons()
function. This is used to return a list of proton spin containers attached
to the given spin.
+ * Improved Grace graph scaling and arrangement when multiple graphs
are present. The lib.software.grace.write_xy_data() function now executes
the 'autoscale' command for each graph and executes the 'arrange' to layout
the graphs automatically.
+ * The Grace plotting (via lib.software.grace) now fully supports the
plotting of multiple graphs.
+ * Improvements to the lib.software.grace module. The set colours
are now applied to all set objects. And the axis label and tick sizes are
now much smaller.
+ * Created the --numpy-raise command line option. When this is set,
all numpy warnings will be converted to errors. This is to aid in debugging
to locate where the warning messages are coming from. These appear as
RelaxWarnings, but there is no indication as to where the problem is.
+ * The lib.software.grace module now supports setting the X and Y
axes at zero.
+ * Modified the model list GUI window. This can now be resized and
it uses a scrolled panel to allow the contents of the window to be bigger
than the window size.
+
+
+ Bugfixes:
+ * Fix for bug #21233 (https://gna.org/bugs/?21233) - the missing
mpi4py multi-processor messages. When multiple commands were being sent to
one slave, the captured IO was being overwritten by each executed command.
Therefore the slave would only return the printouts from the last command.
+ * Fix for a fatal bug in the rarely used structure.add_atom user
function. The position argument in the user function definitions was
incorrectly defined causing the user function to be non-functional. The
'float_object' argument type is now supported in the GUI.
+ * Fix for the N-state model _target_fn_setup() method for when no
PCS data is present.
+ * Bug fix for the lib.structure.mass.centre_of_mass() function
warning when the element is not known. This warning was buggy and resulted
tracebacks.
+
+
+
Version 3.0.1
(17 October 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.0.1
r21649 - /trunk/docs/CHANGES