This relax version is a major feature and bugfix release. It adds the
new structure.add_model, structure.rmsd and structure.web_of_motion
user functions, enhances the structure.load_spins and
structure.find_pivot functions, and PDB support for the internal
structural object has been improved and updated. The new 'lib'
package is introduced which will, in the future, be extensive
collection of functions and special objects for all types of molecular
dynamics analyses. The relax controller in the relax GUI has been
improved with line wrapping to allow all messages to be seen. And
some major bugs affecting the model-free auto-analysis and PDB file
creation have been fixed. 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:
* Added the mol_name_target argument to the
structure.load_spins user function. This allows spins from different
molecules to be placed together in the same molecule container in the
relax data store.
* Addition of two new user functions - structure.add_model and
structure.rmsd.
* Created the structure.web_of_motion user function. This is
used to create a special PDB file which represents the atomic motions
between different structural models. Identical atoms of the selected
models are concatenated into one model, within a temporary internal
structural object, and linked together using PDB CONECT records.
* Better PDB support in the internal structural object with:
Improvements and fixes in reading/writing, an update of the format to
version 3.30, and faster PDB parsing.
* Creation of two new modules for better PDB support -
generic_fns.structure.pdb_read and generic_fns.structure.pdb_write.
* Improvements to the structure.find_pivot user function
including the addition of the func_tol argument to better control the
simplex optimisation and the use of the logarithmic barrier function
to prevent the pivot from heading to infinity when the solution is a
line.
* Initialised a new package called 'lib' - this will in the
future be an extensive collection of functions, methods, classes,
objects, etc. useful for the study of all types of molecular dynamics.
* Line wrapping has been turned on in the relax controller in
the GUI so that all text is visible.
Changes:
* The relax intro text now includes the repository URL for
checked out code. This is for preserving better debugging and logging
information, so that it is clear where the code comes from.
* Created the Structure.test_load_spins_mol_cat system test.
This will be used to test a new 'mol_name_target' argument to the
structure.load_spins user function.
* Created the Structure.test_delete_multi_pipe system test.
This is to check that the structure.delete user function is operating
on a single data pipe.
* Updated the Freecode instructions in the release checklist document.
* Created the simple Structure.test_delete_empty system test.
This is to demonstrate a failure of the structure.delete user function
when no structural data is present.
* Added a printout to structure.delete for when no structures
are present.
* Created the Structure.test_rmsd system test. This test
checks the currently unimplemented structure.add_model and
structure.rmsd user functions.
* The structural API num_molecules() method can now handle no
data being present.
* Implemented the structure.add_model user function.
* Added some more checks to the Structure.test_rmsd system test.
* Modified the structure.add_model calls in the
Structure.test_rmsd system test to include model nums.
* Added the 'model_num' argument to the structure.add_model
user function.
* Modified the structure.add_atom user function to allow the
position argument to be a rank-2 array. This allows a different
coordinate for each model to be specified.
* Spun out the atomic_rmsd() and calc_mean_structure()
functions into their own module. They were previously in the
generic_fns.structure.superimpose module but are now in the new
generic_fns.structure.statistics module.
* Added checks for the atomic information to the
Structure.test_rmsd system test. This demonstrates a failure of
structure.add_atom user function when specifying different positions
for the different models.
* Docstring addition for the
generic_fns.structure.statistics.atomic_rmsd() function.
* Implemented the structure.rmsd user function.
* Fixes for the Structure.test_rmsd system test - it now passes.
* Created a new float_object argument type which is used by
the 'pos' argument of structure.add_atom. A new
arg_check.float_object() function has been created to handle any float
object greater than rank-0.
* Created the Structure.test_rmsd_ubi system test to better
check the structure.rmsd user function. This uses the truncated
ubiquitin ensemble in the test suite shared data directories. The
RMSD matches the VMD 1.9.1 output.
* Added a new module generic_fns.structure.pdb_write for
generating the PDB records. This decouples the formatting code from
the internal structural obect. The PDB format has been updated to
version 3.30. There is one function for each PDB record, allowing
this to be easily extended and kept up to date.
* Created the generic_fns.structure.pdb_read module. This
replaces the internal structural object _parse_pdb_record() method
which was handling both ATOM+HETATM and CONECT records. It should
allow greater flexibility in reading data out of other PDB records in
the future. There is one function per PDB record type in this module.
* Added the full 1UBQ PDB structure to the relax test-suite
shared data directories. This is a small, very quick to read
structure which will be used for validating the reading and writing of
different PDB record types.
* Changes to the internal structural object. The
_parse_models_pdb() method has been renamed to _parse_pdb_coord() and
the opening of the PDB file shifted into the base load_pdb() method.
This is in preparation for better parsing of PDB files to match the
main sections of the PDB format, see
http://www.wwpdb.org/documentation/format33/v3.3.html.
* Created the Structure.test_read_pdb_1UBQ to check the
complete parsing of the complex PDB file. The test is currently quite
basic and needs to check more of the internal structural object.
* Better checks for the atomic data in the
Structure.test_read_pdb_1UBQ system test.
* Added a series of _parse_pdb_*() methods to the internal
structural object. These correspond to each section of the PDB format
version 3.30 http://www.wwpdb.org/documentation/format33/v3.3.html.
The currently loop over the records of their section, returning the
remaining PDB records. The aim is for fast parsing and breaking into
sections.
* Faster PDB parsing by the removal of the use of the
re.search() function. Now line slices are directly compared instead.
* Added some more unit tests for the
generic_fns.structure.pdb_read module. These tests are not yet
complete, as it is unknown what these unimplemented functions will
return.
* Completed the unit test of the
generic_fns.structure.pdb_read.helix() function.
* Implemented the generic_fns.structure.pdb_read.helix() function.
* Created the Mf.test_bug_20531_molmol_macro_write_relaxfault
system test. This is an attempt at catching bug #20531. It creates
all of the m0-m9 and tm0-tm9 models, sets some parameter values, and
then attempts to create all of the Molmol macros, PyMOL macros, Grace
plots and parameter text files as present in the
auto_analysis.dauvergne_protocol module.
* The spectrometer frequency is now set in the
Mf.test_bug_20531_molmol_macro_write_relaxfault system test. This is
needed for the Rex scaling.
* The spin name, element and isotope is now set in
Mf.test_bug_20531_molmol_macro_write_relaxfault. This is required in
this system test so that the marco creation is not skipped.
* Added some work-arounds for the model-free specific code for
when no relaxation data is present. This is needed for the Rex
scaling, as the ID of the first relaxation data set was being used to
select the first frequency. As caught by the
Mf.test_bug_20531_molmol_macro_write_relaxfault system test, this
fails if no relaxation data is present.
* Expanded the unit test of the
generic_fns.structure.pdb_read.sheet() function.
* Implemented the PDB SHEET record parsing function
generic_fns.structure.pdb_read.sheet().
* Extended the PDB ATOM record reading unit test to be of 80
characters in length, as per the PDB definition.
* Created unit tests for the generic_fns.structure.pdb_write
module. This currently covers the atom(), helix() and sheet()
functions (the last 2 are not yet implemented).
* Implemented the PDB HELIX record writing function
generic_fns.structure.pdb_write.helix().
* Improved PDB writing capabilities. The functions of the
generic_fns.structure.pdb_write module now all use the _handle_none()
function to avoid the text "None" from appearing in the PDB file and
_record_validate() to be sure the record has not been corrupted with
bad input causing it to be either less or greater than 80 characters.
* The Mf.test_bug_20531_molmol_macro_write_relaxfault system
test now catches bug #20531. This now uses the results file attached
to the bug report https://gna.org/bugs/?20531.
* Implemented the PDB SHEET record writing function
generic_fns.structure.pdb_write.sheet().
* Created a unit test for the
generic_fns.structure.pdb_write.het() function.
* Created the generic_fns.structure.pdb_write._handle_text()
function. This private function is used to convert text into PDB
suitable format (uppercase and values of None converted to empty
strings).
* The diffusion tensor PDB files are now conform better to the
PDB standard. The HET records are now correct, only capitalised text
is present in the files, and trailing whitespace to character 80 has
been added.
* Epydoc docstring formatting for the
generic_fns.structure.pdb_write modules. These large changes improve
the API documentation at http://www.nmr-relax.com/api/.
* Created a unit test for the
generic_fns.structure.pdb_write.model() function.
* Added a new PDB file with 3 models and a few atoms for
testing of the structure.web_of_motion user function.
* Created the Structure.test_web_of_motion_all system test.
This is to check the new structure.web_of_motion user function.
* The structure.web_of_motion user function can now handle
file objects as well as file names as input.
* Small fixes for the Structure.test_web_of_motion_all system test.
* Created the Structure.test_web_of_motion_12 system test to
show how model sets are currently ignored.
* Implemented the models argument for the
structure.web_of_motion user function. This was previously not being
used and was caught by the Structure.test_web_of_motion_12 system
test.
* Created the Structure.test_web_of_motion_13 system test.
This was just to be sure that the models argument was correctly
handled by the structure.web_of_motion user function.
* The structure.find_pivot user function now accepts the
func_tol argument. This is used to terminate the simplex optimisation
when this function tolerance value is reached.
* Shifted the ensemble pivot finding target function into the
maths_fns package.
* Added a sentence to the README file about the sample_scripts
directory.
* Added a document detailing the possible future layout of
relax's packages.
* The structure.find_pivot user function now uses the
logarithmic barrier function. This is for constrained optimisation
and requires the newest minfx code. The pivot position is constrained
within a box of +/- 1000 Angstroms from zero. This is needed for when
the solution is an infinite line - i.e. a rotation axis and not a
pivot point. Previously the simplex optimisation would head toward +
or - infinity. But now with a logarithmic barrier, the simplex
algorithm can stabilise and find a point on the axis very quickly,
long before reaching the edges of the box.
* The structure.find_pivot user function now accepts the
func_tol and box_limit arguments. This allows the function tolerance
for the simplex optimisation to be specified, as well as the size of
the box to constrain the pivot to be within.
* Initialised the lib.geometry package. This will be a
library of all mathematics functions relating to geometry.
* Added empty packages to the unit tests for the lib and
lib.geometry packages.
* Updated the maths_fns package __all__ list.
* Updated the test_suite.unit_tests package __all__ list to be
more modern.
* The n_state_model.number_of_states user function no longer
requires the N-state model to be defined. This was only needed to
update the model information, and is skipped if not set.
* The generic_fns.structure.superimpose.find_centroid()
function now prints out Euler angles as well.
* Large improvements to the checking for all the rdc and pcs
user functions. The new methods check_pipe_setup() have been added to
replace all other checking. This standardises all error checking and
provides much better coverage. The results is that you will be much
less likely to encounter a Python traceback when something is
forgotten, and will be told via a RelaxError what is missing.
* The rdc.back_calc and pcs.back_calc user functions now warn
if no data was calculated. This is to inform the user about problems
at the place that they occur instead of later on with, for example,
the creation of empty data files.
* Updated the float module to handle numpy floats. This makes
the floatToBinaryString() function compatible with the numpy.float16
type.
* Removed the prune parameter from the backend of the
monte_carlo.error_analysis user function. This was a dangerous
parameter used to mimic the 'Trim' parameter from the Modelfree4
program. The result is bad statistics. The probable reason for the
'Trim' parameter was the failure of model-free models in the
simulations, but this issue was solved using model elimination (see
http://www.nmr-relax.com/refs.html#dAuvergneGooley06).
* Created the Structure.test_read_xyz_strychnine system test
to demonstrate a bug in the XYZ parser. This is for the reading of
XYZ structure files.
* Created the lib.text package for text manipulation. The
first module will be the text formatting of tables.
* Created the lib.geometry.lines module for performing
geometric operations with lines. This has one stub of a function
lib.geometry.lines.closest_point() which will be used to find the
closest point on a line to a given point.
* Added the package checking unit tests for the lib package.
* Improved the base class unit test for the package __all__
list. Subpackages are now also checked.
* Blacklisted a number of files in the maths_fns package for
the package __all__ list unit test.
* Added a unit test for the lib.geometry package __all__ list.
* Created a unit test for the
lib.geometry.lines.closest_point() function.
* Created the lib.text.table module. This originates from the
prompt.uf_docstring module as most of that module is functions for
creating formatted text tables.
* Updated the lib package __all__ list for the lib.text package.
* Implemented the closest_point() and closest_point_ax()
functions of lib.geometry.lines. These two functions do the same
thing - find the closest point on a line to any given point - but take
different arguments to define the line.
* Improved the package __all__ list base unit test by skipping
all hidden files and directories.
* Refactored the lib.text.table module. The create_table()
function is now called format_table() and the table_line() function
has been made private. All references to the user function tables and
the relax status object have been removed and replaced by arguments to
format_table().
* The prompt.uf_docstring module now uses
lib.text.table.format_table(). This significantly simplifies the
module.
* Removed a number of unused imports in prompt.uf_docstring.
* Deleted prompt.uf_docstring.table_line() as this is now a
private function of lib.text.table.
* Fix for lib.text.table.format_table() as table_line() is now
private.
* Added the spacing argument to lib.text.table.format_table().
This removes the reference to the user function table spacing
variable from this function and shifts it to the
prompt.uf_docstring.create_table() function.
* Created the framework for the unit tests of the lib.text package.
* Created two unit tests for the lib.text.table.format_table()
function.
* Updates to the unit tests of the
lib.text.table.format_table() function.
* Many improvements to the lib.text.table module. The
format_table() function now accepts arguments for text to prefix and
postfix to each line,the text padding to the left and right inside the
table, and the text used to separate the columns. The _blank() and
_rule() private functions have been added to create distinct table
elements.
* Created the lib.text.table.MULTI_COL constant for defining
cells spanning multiple columns. This is not used yet.
* Modified the Mf.test_mf_auto_analysis GUI test to catch bug
#20603 (https://gna.org/bugs/?20603).
* Created a unit test for the lib.text.table.format_table()
function to test multiple column support. Support for content
spanning multiple cells is yet to be implemented.
* Implemented multi-column support in lib.text.table.format_table().
* Spacing between heading rows is now functional in
lib.text.table.format_table().
* Created a new unit test of lib.text.table.format_table() to
check for non-string type data.
* The table contents are now all converted to strings in
lib.text.table.format_table(). This uses the _convert_to_string()
private function.
* Converted the test_format_table4() unit test of
lib.text.table.format_table() to check justification. The right
justification of cells with numbers will be implemented to match these
changes.
* Numbers are now right justified in cells in the
lib.text.table.format_table() function.
* Modified the test_format_table4() unit test of
lib.text.table.format_table(). This change is to test the currently
unimplemented custom_format argument. This will be used to allow
special formatting in the table. For example using '%.3f' for a
float.
* Implemented the custom_format argument for
lib.text.table.format_table(). This allows cell contents to be
formatted as the user asks. It defaults to standard string conversion
is the custom conversion fails.
* Rounding error fix for the test_format_table4() unit test of
lib.text.table.format_table().
* Python 3 fix for the test_format_table4() unit test of
lib.text.table.format_table(). The string representation of the
builtin list object is different in Python 2 vs. 3.
* Created the test_format_table5() unit test for
lib.text.table.format_table(). This test checks what happens if no
header is given to format_table(). This currently fails.
* The lib.text.table.format_table() function can now create a
table without headers.
* Added column number checks for the data input into
lib.text.table.format_table().
* Created the test_format_table6() unit test for
lib.text.table.format_table(). This test shows a problem with more
than one multi-column cells defined, as well as problems when a
multi-column cell is wider than the sum of the widths of the columns
it spans.
* Fix for lib.text.table.format_table() when more than one
multi-column cell per row is encountered. The algorithm for
determining the total width of the multi-column cell in _table_line()
was not checking if the end of the span was being reached.
* The lib.text.table.format_table() function now handles
overfull multi-column cells. The _determine_widths() private function
has been created to better handle the determination of the table
column widths. It will now extend the width of the last column to
allow overfull multi-column cells to fit.
* Modified the test_format_table5() unit test of
lib.text.table.format_table() to check bool types.
* The lib.text.table.format_table() function now handles boolean
types.
* Booleans are not numbers, so do not right justify them in
lib.text.table.format_table().
* The minfx.__version__ value is now read for the version in
the relax information printout.
* The bmrblib.__version__ value is now read for the version in
the relax information printout.
* All of the specific API data and error returning common
methods can now handle missing data/errors. This affects the
_return_data_relax_data() and _return_value_general() methods.
* Updated the release checklist to include information about
updating the FSF directory.
* Modified the release checklist document to use the stable
release tags of minfx and bmrblib. This is instead of the code in
trunk which may not always be in a stable state.
* Redesign of the generic_fns.mol_res_spin.generate_spin_id()
function. The function now tries to generate a unique ID based on the
spin information in the specified data pipe. This is to attempt to
fix a bug uncovered by the Structure.test_read_xyz_internal2 system
test. Defaulting in all cases to the spin name rather than spin
number will often fail for a small organic molecule, as the name in
XYZ files is the atomic symbol and hence will almost never be unique.
* Created the
generic_fns.mol_res_spin.return_molecule_by_name() function. This
will be used in the future as it is much faster than
generic_fns.mol_res_spin.return_molecule()if the molecule name is
already known.
* Missing import affecting the
generic_fns.interatomic.create_interatom() function.
* Reverted the last revision (r18737) as it was not correct
and RelaxErrors should be used instead. The command used was:svn
merge -r18737:18736 .
* Fix for the generic_fns.interatomic.create_interatom()
function. RelaxNoSpinWarning has been replaced with RelaxNoSpinError.
* Fixes for the metadata update of the residue and spin name
and number counts.
* Created the
generic_fns.mol_res_spin.generate_spin_id_unique() function. This
will return a truly unique spin ID string based on the current
molecule, residue, and spin data structure.
* The spin_loop() function now uses generate_spin_id_unique()
when the return_id flag is set. This ensures that the caller received
a unique spin ID which can be used to retrieve the corresponding spin
container.
* Improved the
generic_fns.mol_res_spin.generate_spin_id_unique() function. This can
now work with molecule, residue, and spin names and numbers
alternatively to the containers supplied as arguments. For this to
work, the return_molecule_by_name() function has been improved and the
functions return_residue_by_info() and return_spin_by_info() have been
added.
* The pcs.read user function backend now uses
generic_fns.mol_res_spin.generate_spin_id_unique(). This allows the
matching spin container to always be returned for storing the data.
* Large speed ups of the Bmrb system tests by the deletion of
most of the residues. On one system, this cuts the time for all 3
Bmrb tests from 70 to ~12 seconds.
* Added the profile flag keyword argument to the relax startup
script for Unix-like systems. This is to simplify the switching on of
profiling.
* Large cleanup and bugfixes for the molecule, residue, and
spin data structure metadata maintenance. The bugs fixed are
important for non-protein molecules. For example is the spin name is
not unique per residue, or per molecule if no residues are defined,
many parts of relax would fail. All of the metadata_*() and
spin_id_variants*() functions have been redesigned. It was also
identified that metadata_prune() was being used by different parts of
relax for two different purposes - the removal or pruning of metadata
prior to the deletion of a data structure and the clean up of no
longer valid metadata. These two goals conflicted resulting in
unpredictable behaviour. Therefore the new metadata_cleanup() and
spin_id_variants_cleanup() functions have been created and the two
behaviours separated.
* Fix for the bmrb.read user function for the recent molecule,
residue and spin metadata improvements. The
generic_fns.bmrb.generate_sequence() function now calls
generic_fns.mol_res_spin.metadata_clean()to be sure that the metadata
is correct. The problem is the structure of the BMRB file with no
spin information in the entity record, hence the residues are created
first and the spins much later in generate_sequence().
* Removed unused imports in the generic_fns.rdc module.
* The generic_fns.mol_res_spin.generate_spin_id_unique()
function now handles missing spin containers. Previously if this
function was used to generate a spin ID string of a spin not in the
data store,it would fail. Now it generates an ID by defaulting to
generate_spin_id().
* Converted many calls to
generic_fns.mol_res_spin.generate_spin_id() to
generate_spin_id_unique(). This will allow many future bugs to be
avoided, as the spin ID string is most often used to retrieve spin
containers. By using the generate_spin_id_unique() function, the
returning of spin containers will always be correct.
* Created the Mf.test_bug_20563_missing_ri_error system test
to catch bug #20563. The bug report is at
https://gna.org/bugs/?20563. The data added to the test suite is a
highly truncated data set of a analysis completed using the data
attached to the bug report.
* Modified the dauvergne_protocol model-free auto-analysis to
aid in debugging. The write_results_dir argument has been added to
allow the test suite to read from one directory in test suite shared
data directories and redirect output to a temporary directory.
* The files from the Mf.test_bug_20563_missing_ri_error system
test are now placed in a temporary directory. This is essential for
the test suite to prevent files from going everywhere.
* The frq.seq user function units argument is no longer
read-only. This is needed for some of the GUI tests in the
frame_order_testing branch.
Bugfixes:
* Fixes for the structure.delete user function. This can now
handle no data being present, the spin and interatomic data containers
are now have their structural data properly deleted, and printouts
have been added so the user knows what has happened.
* Bug fix for the arg_check.is_float_matrix() function for
when the dimensions are not given.
* Fix for the structure.add_atom user function for the
internal structural object. The atomic positions for each model are
now correctly set.
* Formatting fixes for the generic_fns.structure.pdb_write module.
* Fix for the classic_style() method of the model-free
specific Macro class. This was identified by the new
Mf.test_bug_20531_molmol_macro_write_relaxfault system test, but would
probably never be encountered by relax users. It is not related to
the bug this test is trying to catch. The problem is if spins have
model-free parameters set up but there is no model-free model
initialised - then the Molmol and PyMOL macro creation would fail.
* Fix for bug #20531 (https://gna.org/bugs/?20531). This is
the bug of the RelaxFault during the final stages of the
auto_analysis.dauvergne_protocol model-free analysis when the Molmol
and PyMOL macros are being created. The problem was caused by model
m9 (just the Rex parameter) when trying to determine what the order
parameter for fast (< 200ps) motions is. The code was assuming that
the model-free model would always contain an order parameter.
* Fix for the generic_fns.structure.pdb_write.het() function -
the record now has trailing whitespace. The PDB records require
trailing whitespace to the 80th character position.
* Fixes for many of the generic_fns.structure.pdb_write
functions. The PDB records are now all filled with whitespace up to
the 80th character.
* Fix for the creation of HET PDB records in the internal
structural object. The residue name and chain ID were mixed up.
* Fix for the generic_fns.structure.pdb_write.ter() function.
Whitespace to character 80 is now being added to the TER PDB records.
* Fix for the creation of the FORMUL PDB records by the
internal structural object. The component number is now set to the
index of the hetrogen plus one. This number should have been a
sequential number starting at 1 and is not related to the residue
number in any way.
* Fix for the generic_fns.structure.pdb_write.model()
function. The correct amount of whitespace is now added to the end of
the record.
* Fix for the internal PDB reading - the MASTER record was
being marked as a molecule. Now this record is checked for and the
molecule loop terminated.
* Bug fix for the XYZ 3D structure file reader. The atom name
is now correctly set up for each atom in the file. The element type
setting has also been simplified.
* Fix for bug 20603 (https://gna.org/bugs/?20603), the
relaxation data right click menu failure. The problem was that there
was that the last menu item specified had no contents. This item has
been removed.
* Fix for bug #20563 (https://gna.org/bugs/?20563), the end
failure of the model-free auto-analysis. This was reported by
Stanislava Panova (https://gna.org/users/stacy). The problem was
related to the Monte Carlo simulations. The
generic_fns.monte_carlo.create_data() function is now asking for the
errors associated with a certain data point, even if that data point
does not exist. The solution was to check if the relaxation data ID
string is present in spin.ri_data_err before accessing the key-value
pair (in the specific API _return_error_relax_data() common method).
* Bug fix for the maintenance of the spin ID lookup table
metadata. This is important for small molecules. Non-unique IDs were
being placed into the lookup table,resulting in incorrect spin
containers being sometimes used. Now the molecule container has the
_res_name_count and _res_num_count metadata and the residue container
the _spin_name_count and _spin_num_count structures. These are
updated via metadata_update() and are used by the spin_id_variants()
function to create a list of purely unique spin IDs.
* The spin_id argument to the residue.delete user function is
no longer read-only. This allows spin ranges or other complicated IDs
to be specified. This is needed for the Bmrb GUI tests to pass.
* Fix for the package __all__ list checking unit tests - *.pyc
files are now skipped.
* Fix for one of the RelaxError messages from the
SpinList.add_item() method.
relax version 2.2.3.