Author: bugman
Date: Fri Jan 31 12:14:57 2014
New Revision: 22097
URL: http://svn.gna.org/viewcvs/relax?rev=22097&view=rev
Log:
Backported the relax 3.1.4 CHANGES file addition to trunk.
The command used was:
svn merge -r22095:22096 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.1.4 .
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=22097&r1=22096&r2=22097&view=diff
==============================================================================
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Fri Jan 31 12:14:57 2014
@@ -1,3 +1,47 @@
+Version 3.1.4
+(31 January 2014, from /trunk)
+http://svn.gna.org/svn/relax/tags/3.1.4
+
+ Features:
+ * The structure.write_pdb user function now supports multiple
molecules being present.
+ * Large speed optimisations for the internal structural object when
multiple models are present.
+ * Improved support for replicated spectra in the NOE analysis.
+
+
+ Changes:
+ * Created the Frame_order.test_generate_rotor2_distribution system
test. This is to test the Frame Order distribution generating base script,
used for creating the synthetic Frame Order test data, and to demonstrate a
failure in handling back-calculated RDC data. To implement this, the
test_suite/shared_data/frame_order/cam/ path has been converted into a Python
package (with the addition of the __init__.py files). The base data
generation script test_suite/shared_data/frame_order/cam/generate_base.py has
also been modified to use the absolute path for the data files and its run()
method now accepts the save_path argument to allow the files to be saved into
a temporary directory.
+ * Fixes for the Frame_order.test_generate_rotor2_distribution system
test. The test_suite/shared_data/frame_order/cam/generate_base.py script now
saves the program state files into the self.save_path directory, preventing
the system test from attempting to save files into the relax test suite
directories.
+ * Another fix for the Frame_order.test_generate_rotor2_distribution
system test. The test_suite/shared_data/frame_order/cam/generate_base.py
script no longer prints its progress indicator to sys.__stderr__ but to
sys.stderr instead. This avoids the progress text from appearing during the
relax test suite execution.
+ * Created the Structure.test_bug_21522_master_record_atom_count
system test. This is designed to catch bug #21522
(https://gna.org/bugs/?21522), the structure.write_pdb user function creating
an incorrect MASTER record. This hence also catches bug #21520
(https://gna.org/bugs/?21520), the failure of the structure.write_pdb user
function when creating the MASTER record due to too many ATOM and HETATM
records being present. The test simply creates two structural models, adds
one atom, and writes out a PDB file, checking its contents.
+ * The structure.write_pdb user function can now handle a file
instance for the file argument. This is for the
Structure.test_bug_21522_master_record_atom_count system test, to allow a
dummy file object to be used. This can also be useful for power users.
+ * Created the lib.geometry.vectors.unit_vector_from_2point()
function. This is used to quickly calculate the unit vector between two
points.
+ * The lib.structure.represent.rotor.rotor_pdb() function can now
handle multiple rotors. Previously this function would fail if called twice
with the same structural object.
+ * Added the has_molecule() method to the relax internal structural
object. This is used to quickly check if a molecule name already exists in
the structural object.
+ * More improvements for handling multiple rotors in the
lib.structure.represent.rotor.rotor_pdb() function. The atom numbering is
now better handled.
+ * Better support for the writing out of multiple molecules by the
structure.write_pdb user function. This is for the internal structural
object write_pdb() method. Now each molecule is assigned a different chain
ID in the PDB file, and the chain IDs loaded into the structural object are
ignored. The chain IDs should however be preserved when using
structure.read_pdb followed by structure.write_pdb, without storing the ID.
A number of the Structure system tests had to be updated, as now the relax
generated PDB files will always write out a chain ID.
+ * Large speed up for the internal structural object for when many
models are present. The new ModelList.current_models object keeps track of
all the models already present in the structural object. This simplifies the
checks of the pack_structs() internal structural object method by removing
expensive looping. This allows the loading of PDB files to continue to be
fast even with many tens or hundreds of thousands of models already loaded.
+ * More speed ups for the internal structural object when huge
numbers of models are present. Another loop over the structural_data object
has been eliminated from the PDB reading load_pdb() method.
+ * Another optimisation for the internal structural object for large
numbers of models. The ModelList.add_item() method no longer loops over all
models to check if a model is already present, instead using the new
current_models list.
+ * Yet more optimisation for handling large quantities of models in
the internal structural model. Now when adding new models to the object, the
model_indices and model_list objects are no longer created. This saves much
time as the large model_list is now not sorted. A number of structural
object methods have been updated to handle the change by switching to the
model_loop() method for looping over the models, rather than using the
model_indices and model_list objects.
+ * The frame order matrix printing function can now output the matrix
to any precision. The lib.frame_order.format.print_frame_order_2nd_degree()
function now accepts the 'places' argument which allows for higher precision
printouts.
+ * The behaviour of the rdc.write user function has been changed to
output spin ID strings in single quotes. This is to avoid problems with the
'#' molecule identifier and the '#' comment character.
+ * Fix for the diffusion_tensor.init user function reference in the
intro chapter of the manual. This was using a very old and now
non-functional syntax.
+ * Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure
system test. This is to catch bug #21561 (https://gna.org/bugs/?21561), as
reported by Martin Ballaschk (https://gna.org/users/mab). This catches the
failure of the structure.create_diff_tensor_pdb user function for
non-spherical diffusion tensors when no Monte Carlo simulations are present.
+ * Added the truncated data for creating a system test to catch bug
#21562. This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu
(https://gna.org/users/dhanas) and is the failure of the NOE analysis when
spectra are replicated. This consists of the Sparky peak lists attached to
the bug report and the modified 2AT7 PDB file. The data has been truncated
to only include residues :12, :13, and :14.
+ * Shifted the NOE system test script into the new 'noe' directory.
+ * Created the Noe.test_bug_21562_noe_replicate_fail system test.
This is to catch bug #21562 (https://gna.org/bugs/?21562), reported by Dhanas
Muthu (https://gna.org/users/dhanas). This is the failure of the NOE
analysis when spectra are replicated. This uses the truncated data taken
from the files attached to the bug report. The NOE output file is checked to
see if the contents are correct.
+ * Better support for replicated spectra in the NOE analysis. The
saturated and reference peak intensity and error are now properly averaged.
Previously averaging was not used as the number of replicates N are cancelled
in the ratios used for the NOE and error calculation. However this fails
when the number of replicates for the saturated spectrum does not match the
number of replicates for the reference spectrum. Now any data combination is
possible.
+ * Another fix for the NOE analysis for when replicated spectra have
been collected. Variance averaging rather than error averaging is now used
for the peak intensity errors. This is important if the errors for each
replicated spectra are different - a case which is rarely encountered as the
replicates are almost always used to determine one error for all the
replicates.
+
+
+ Bugfixes:
+ * Fix for bug #21499 (https://gna.org/bugs/?21499), the failure of
the rdc.write user function. The rdc.write user function fails for
back-calculated RDC data. The fix was to handle the missing
interatom.rdc_data_types variable.
+ * Fix for bug #21522 (https://gna.org/bugs/?21522) and bug #21520
(https://gna.org/bugs/?21520). These bugs are the structure.write_pdb user
function creating an incorrect MASTER record and the failure of the
structure.write_pdb user function when creating the MASTER record due to too
many ATOM and HETATM records being present. The counts for the ATOM, HETATM,
and TER records are now only for a single model, rather than being the sum
for all models together.
+ * Fix for bug #21561, the structure.create_diff_tensor_pdb user
function failure with no simulations. Bug #21561
(https://gna.org/bugs/?21561) was reported by Martin Ballaschk
(https://gna.org/users/mab). The problem was that the simulation axes of the
tensor PDB file were not being initialised correctly when no Monte Carlo
simulations had been run.
+ * Fix for bug #21562, the failure of the NOE analysis when spectra
are replicated. This bug (https://gna.org/bugs/?21562) was reported by
Dhanas Muthu (https://gna.org/users/dhanas). The problem was that the NOE
overfit_deselect() method was deselecting all spins which do not have exactly
2 intensity values. This is incompatible with replicated spectra as the
number will be greater than two. The check has been modified to deselect
spins only when the number of intensity values are zero or one.
+
+
+
Version 3.1.3
(16 January 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.3
r22097 - /trunk/docs/CHANGES