Author: bugman
Date: Sun Mar 24 10:35:28 2013
New Revision: 19098
URL: http://svn.gna.org/viewcvs/relax?rev=19098&view=rev
Log:
Updated the changes file for relax 2.2.5.
Modified:
tags/2.2.5/docs/CHANGES
Modified: tags/2.2.5/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/tags/2.2.5/docs/CHANGES?rev=19098&r1=19097&r2=19098&view=diff
==============================================================================
--- tags/2.2.5/docs/CHANGES (original)
+++ tags/2.2.5/docs/CHANGES Sun Mar 24 10:35:28 2013
@@ -1,3 +1,69 @@
+Version 2.2.5
+(24 March 2013, from /trunk)
+http://svn.gna.org/svn/relax/tags/2.2.5
+
+ Features:
+ * The files created by the value.write user function now include a
header describing the parameter.
+ * The relax internal structural object now supports the merger of
molecules. This can be useful if different domains of one system are in two
PDB files or are split in the one file.
+ * The structure.delete user function can now be used to delete parts
of molecules down to the level of individual atoms.
+ * Helix and sheet information from PDB files are now stored in the
internal structural object as metadata. The structure.read_pdb and
structure.write_pdb user functions will preserve this information.
+ * The numbers output by the value.display and value.write user
functions can now be scaled.
+ * The model-free auto-analysis now generates field strength
dependent Rex files for each field present.
+
+
+ Changes:
+ * Added a comment to the output from value.display and value.write
to describe the parameter. This idea is discussed at
http://thread.gmane.org/gmane.science.nmr.relax.user/1428. The idea is to
take the parameter description from the specific analysis API and add it to
the top of the file or output. This is to help understand what the Rex value
are. For example for the Rex parameter the first line would be: "# Parameter
description: Chemical exchange relaxation (sigma_ex = Rex / omega**2)."
+ * Created the Structure.test_read_merge system test to test a new
concept - merging of structures. The idea is to add the merge argument to
the structure.read_pdb user function to allow two different structures in two
PDB files to be merged. This is useful if structures of individual domains
have have been solved separately and are located in two PDB files. Then with
the merge flag, you will not need to use and external program or hand edit
PDB files to join them.
+ * Added the merge flag to the structure.read_pdb user function.
This currently does nothing.
+ * The merge flag for the structure.read_pdb user function is now
propagated to the pack_structs() method. This structure API method calls the
ModelList.merge_item() method which is yet to be implemented.
+ * The MolList.add_item() structural API method now returns the added
molecule container. This is used by the pack_structs() method to alias the
molecule, and will be required when structure merging is implemented.
+ * Whitespace fixes - replaced many instances of the tab character
'\t' with 4 spaces.
+ * Implemented the merging of structural objects. This allows the
merge flag of the structure.read_pdb user function to work.
+ * The printouts from the structure.read_pdb user function are now
different with the merge flag set. The text now says that the molecules are
being merged rather than added.
+ * Sections of molecules can now be deleted using the
structure.delete user function. The atom ID argument has been added and this
is now propagated into the internal structural object. This ID string can be
used to delete subsets of the 3D structural data in the relax data store.
+ * Created the Structure.test_read_write_pdb_1UBQ system test. This
is for checking the use of the structure.delete user function with the atom
ID argument.
+ * The Structure.test_read_write_pdb_1UBQ system test now checks for
HELIX and SHEET records. This is not implemented yet, but the idea is that
the structure.read_pdb and structure.write_pdb should preserve the helix and
sheet information present in the original PDB and that the internal
structural object should store this information.
+ * Created the internal structural object
_pdb_chain_id_to_mol_index() method. This will be used to convert PDB chain
IDs, which are used to indicate different molecules in the PDB, into molecule
indices for the internal structural object.
+ * HELIX PDB records are now read, stored, and written out by the
internal structural object. This affects the structure.read_pdb and
structure.write_pdb user functions. The helix is stored as a metadata type
object - its elements do not correspond to the atoms in the structural object.
+ * SHEET PDB records are now read, stored, and written out by the
internal structural object. This affects the structure.read_pdb and
structure.write_pdb user functions. The sheet is stored as a metadata type
object - its elements do not correspond to the atoms in the structural object.
+ * Created 13 unit tests of the Internal._trim_helix() internal
structural object method.
+ * Added the index_flag argument to all structural API atom_loop()
methods.
+ * Implemented the internal structural object _trim_helix() method.
This is used when the structure.delete user function is called to trim and
remove the helix metadata. For this to work, the additional method
_residue_data() was written to create a dictionary with residue numbers as
keys and the residue names as numbers. This dictionary is used by
_trim_helix() to change the residue names in the helix metadata.
+ * Created 13 unit tests of the Internal._trim_sheet() internal
structural object method. These are mirror the 13 unit tests of
Internal._trim_helix().
+ * Implemented the Internal._trim_sheet() internal structural object
method. This is also now used by the structure.delete user function to
remove sheet metadata for residues which no longer exist.
+ * Modified the ScientificPython structural object atom_loop() method
to match the internal object. If only one element is returned from the
atom_loop(), then this is returned as a single item rather than a tuple of
length 1.
+ * Lots of fixes for the change to the structural API atom_loop()
method. This method when returning a single item now returns a single item
rather than a tuple of length 1.
+ * The index_flag argument to the ScientificPython structural object
atom_loop() method is now used.
+ * Created the Structure.test_metadata_xml system test. This is used
to check that the structural metadata (currently helices and sheets) are
stored in the relax XML save files and then can be read back into relax again.
+ * The helix and sheet metadata is now stored in and read from relax
XML state files.
+ * Added the scaling argument to the value.display and value.write
user functions. The idea comes from a suggestion by Angelo Figueiredo <am
dott figueiredo att fct dott unl dott pt> and was discussed at
http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. This
allows the user to scale parameters to any value, for example scaling the Rex
value to the field strength dependent value.
+ * The model-free auto-analysis (the dauvergne_protocol) now
generates field strength dependent Rex files. The idea comes from a
suggestion by Angelo Figueiredo <am dott figueiredo att fct dott unl dott pt>
and was discussed at
http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. One
file per field strength is generated and named 'rex_600' for 600 MHz, for
example. The new scaling argument of the value.write user function is being
used to scale the tiny field strength independent value used internally in
relax to the Rex value in rad.s^-1 that you would see in an R2 data set.
+ * Added the new 'comment' argument to the value.write user function.
This is used to add user comments to the top of the file.
+ * The model-free auto-analysis (the dauvergne_protocol module) now
adds comments to the Rex files. This is through the new comment argument of
the value.write user function. These comments explain that the Rex values
are scaled to the stated field strength.
+ * Modified the Mf.test_dauvergne_protocol system test to check for
all the files and directories created.
+ * Created the new lib.text.sectioning module for formatting titles,
subtitles and other sectioning text. The two functions title() and
subtitle() have been implemented.
+ * Created unit tests for the title() and subtitle() functions of the
lib.text.sectioning module.
+ * Expansion of the lib.text.sectioning module. The following new
functions have been added: box(), section(), subsection(),
subsubsection(),subtitle(), subsubtitle(), underline().
+ * Expanded the unit testing of the lib.text.sectioning module to
cover all title and section functions.
+ * Added prespace and postspace arguments to the *section() and
*title() functions of lib.text.sectioning. Through these arguments, the
amount of spacing above and below the section text can be controlled.
+ * Split the generic_fns.structure.geometric.create_rotor_pdb()
function. The non-relax specific code has been shifted into the rotor_pdb()
function.
+ * Initialised the lib.structure package - this is currently empty.
+ * Shifted the rotor creation components from
generic_fns.structure.geometric to lib.structure.rotor. The
create_rotor_pdb() function remains in place as this is the user function
backend which checks for data pipes and updates the status object, but the
rotor_pdb() and create_rotor_propellers() functions have been moved into the
relax library. The create_rotor_propellers() function has been renamed to
lib.structure.rotor.rotor_propellers().
+ * Converted links in all docstrings to use the Epydoc hyperlink
notation. This will allow links to be clickable for the API documentation
(http://www.nmr-relax.com/api/).
+ * Added Epydoc hyperlink markup for the bug tracker in the system
test docstring where missing. This is for a better API documentation
(http://www.nmr-relax.com/api/).
+ * The lib.structure.rotor.rotor_pdb() rotor_angle argument should
now be in radians. This does not affect the structure.create_rotor_pdb()
user function as the generic_fns.structure.geometric.create_rotor_pdb()
function converts the value to radians prior to calling the rotor_pdb()
function.
+ * The lib.structure.rotor.rotor_pdb() function can now handle
structural models. The model number argument has been added to allow the
rotor structure to be added to a single model, or to all models if not
supplied.
+
+
+ Bugfixes:
+ * Fix for a copy and paste error in the Structure.test_read_merge
system test.
+ * Fixes for all the Ap4Aase truncated PDB files. The atom numbers
are now sequential, as defined by the PDB standard.
+ * Bug fix for the structural data consistency test in the
pack_structs() structural API method. The index was not correct causing
failures in certain rare cases.
+ * Python 3 fix for an import into the generic_fns.structure.internal
module.
+ * Python 3 fixes for the relax version information for code checked
out from the relax repository. The subversion version.revision() and
version.url() functions now handle the Python 3 issue of Popen working with
byte arrays instead of normal strings.
+
+
+
Version 2.2.4
(17 March 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.4
r19098 - /tags/2.2.5/docs/CHANGES