Merged revisions 9248-9271,9276-9288,9290,9292,9303-9311,9314,9317-9322,9324-9405,9411-9439,9454,9457-9526,9528-9658,9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3
Additionally, files 'prompt/grace.py' and 'specific_fns/__init__.py' were modified manually to
solve conflicts created by the merging process...
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r9248 | bugman | 2009-07-16 13:45:33 -0400 (Thu, 16 Jul 2009) | 5 lines
Bug fix for the write_pdb() method.
The MODEL record is now created for single structures if a model number exists.
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r9249 | bugman | 2009-07-19 19:16:52 -0400 (Sun, 19 Jul 2009) | 11 lines
Created functions for rank-4, 3D tensor transposes (and corresponding unit tests).
The new functions are:
maths_fns.kronecker_product.transpose_12()
maths_fns.kronecker_product.transpose_13()
maths_fns.kronecker_product.transpose_14()
maths_fns.kronecker_product.transpose_23()
maths_fns.kronecker_product.transpose_24()
maths_fns.kronecker_product.transpose_34()
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r9250 | bugman | 2009-07-20 08:02:30 -0400 (Mon, 20 Jul 2009) | 3 lines
Switched to the internal PDB reader for removal of the reliance on Scientific python.
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r9251 | bugman | 2009-07-21 09:09:18 -0400 (Tue, 21 Jul 2009) | 3 lines
Added some MC simulation data and errors for the diffusion tensor system tests.
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r9252 | bugman | 2009-07-21 09:19:03 -0400 (Tue, 21 Jul 2009) | 3 lines
Split the system test of structure.create_diff_tensor_pdb() into 3 tests for each diff type.
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r9253 | bugman | 2009-07-21 09:54:30 -0400 (Tue, 21 Jul 2009) | 3 lines
Removed trailing whitespace.
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r9254 | bugman | 2009-07-21 10:28:02 -0400 (Tue, 21 Jul 2009) | 5 lines
Changed the order of setting the MC simulation data for the diffusion tensor.
This should test things a bit better.
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r9255 | bugman | 2009-07-21 10:57:19 -0400 (Tue, 21 Jul 2009) | 3 lines
Modification of MC sim list elements is now also tested.
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r9256 | bugman | 2009-07-21 10:59:29 -0400 (Tue, 21 Jul 2009) | 6 lines
Bug fixes for the diffusion tensor MC simulation data structure updating.
The MC simulation structures were not being updated at all!!! This now works, allowing the
diffusion tensor PDB representation to be created.
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r9257 | bugman | 2009-07-21 11:03:21 -0400 (Tue, 21 Jul 2009) | 3 lines
The MC sim vectors for the diffusion tensor axes are now being properly created.
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r9258 | bugman | 2009-07-21 11:03:43 -0400 (Tue, 21 Jul 2009) | 3 lines
Removed some debugging code.
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r9259 | bugman | 2009-07-21 11:15:28 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the creation of the ellipsoid diffusion tensor PDB representation.
The axes are now labelled Dx, Dy, and Dz instead of all Dpar!
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r9260 | bugman | 2009-07-21 11:40:29 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the creation of the spheroid diff tensor PDB representation.
The simulation vectors should be initialised to a list.
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r9261 | bugman | 2009-07-21 11:47:23 -0400 (Tue, 21 Jul 2009) | 3 lines
The ellipsoid diff tensor PDB file is now being checked, line for line.
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r9262 | bugman | 2009-07-21 15:38:43 -0400 (Tue, 21 Jul 2009) | 3 lines
The diffusion tensor MC sim data is now properly set up.
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r9263 | bugman | 2009-07-21 15:39:44 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the diffusion tensor MC sim data structures.
All structures are now properly updated when a value for a single simulation changes.
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r9264 | bugman | 2009-07-21 16:31:06 -0400 (Tue, 21 Jul 2009) | 3 lines
The spherical diffusion tensor system tests are now properly set up.
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r9265 | bugman | 2009-07-21 16:32:04 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the __update_sim_append() method.
Now the diffusion tensor simulation structure appending works if the structure doesn't already exist.
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r9266 | bugman | 2009-07-21 19:10:56 -0400 (Tue, 21 Jul 2009) | 3 lines
Extended the test_copy() system test to properly check if a copy is made, rather than link.
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r9267 | bugman | 2009-07-21 19:20:52 -0400 (Tue, 21 Jul 2009) | 5 lines
Fix for the test_copy() system test.
The wrong indices were being checked.
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r9268 | bugman | 2009-07-21 20:00:13 -0400 (Tue, 21 Jul 2009) | 7 lines
Bug fix for the copying of diffusion tensors data structures.
The DiffTensorSimList objects in DiffTensorData were not being properly copied! This has been fixed
by writing class specific __deepcopy__() methods for both classes. The Element class has also been
subclassed from 'object'.
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r9269 | bugman | 2009-07-21 20:12:55 -0400 (Tue, 21 Jul 2009) | 5 lines
The test_create_diff_tensor_pdb_ellipsoid() system test has been made more vigorous.
The copy operations are now better tested.
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r9270 | bugman | 2009-07-22 03:40:26 -0400 (Wed, 22 Jul 2009) | 3 lines
The diffusion tensor copying system test is now more comprehensive.
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r9271 | bugman | 2009-07-22 05:23:10 -0400 (Wed, 22 Jul 2009) | 5 lines
Added comprehensive checks for the creation of the diffusion tensor PDB representations.
The sphere and spheroid PDB files are now checked, line for line.
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r9276 | bugman | 2009-08-12 07:06:51 -0400 (Wed, 12 Aug 2009) | 3 lines
Made the structure system tests more compatible with non-Unix operating systems.
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r9277 | bugman | 2009-08-12 07:11:27 -0400 (Wed, 12 Aug 2009) | 3 lines
Made get_file_path() and mkdir_nofail() compatible with non-Unix systems.
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r9278 | bugman | 2009-08-12 07:16:06 -0400 (Wed, 12 Aug 2009) | 3 lines
Made the full_analysis.py script more compatible with non-Unix operating systems.
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r9279 | bugman | 2009-08-12 07:18:30 -0400 (Wed, 12 Aug 2009) | 3 lines
Fix for test_load_scientific_results(). The Unix paths are used in the results file!
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r9280 | bugman | 2009-08-12 07:23:15 -0400 (Wed, 12 Aug 2009) | 3 lines
Non-Unix os fix.
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r9281 | bugman | 2009-08-12 07:54:53 -0400 (Wed, 12 Aug 2009) | 3 lines
Modified the unit tests to be more non-Unix operating system compatible.
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r9282 | bugman | 2009-08-12 08:25:49 -0400 (Wed, 12 Aug 2009) | 3 lines
Modified the system tests to be more non-Unix operating system compatible.
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r9283 | bugman | 2009-08-12 08:38:00 -0400 (Wed, 12 Aug 2009) | 4 lines
Modified the shared data scripts to be more non-Unix operating system compatible.
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r9284 | bugman | 2009-08-12 08:53:54 -0400 (Wed, 12 Aug 2009) | 3 lines
Removed the last '/' directory separators to be more non-Unix operating system compatible.
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r9285 | bugman | 2009-08-12 09:02:38 -0400 (Wed, 12 Aug 2009) | 3 lines
Removed a reference to the '..' dir.
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r9286 | bugman | 2009-08-12 09:05:03 -0400 (Wed, 12 Aug 2009) | 3 lines
Redid r9279! This was accidentally reverted by hand in r9282!!!
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r9287 | bugman | 2009-08-12 09:34:50 -0400 (Wed, 12 Aug 2009) | 3 lines
Caught a NaN problem in __q_factors_rdc() causing a system test to fail in Windows.
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r9288 | bugman | 2009-08-12 12:57:21 -0400 (Wed, 12 Aug 2009) | 7 lines
Massive clean up of the float module unit tests.
As a general clean up, the module has been converted to the relax coding conventions. Importantly
the floating point numbers defined as constants for the tests are now properly defined using the
packBytesAsPyFloat() function. This will allow these tests to pass on all machines!
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r9290 | bugman | 2009-08-12 14:04:53 -0400 (Wed, 12 Aug 2009) | 8 lines
Ported the CHANGES file for relax version 1.2.15 to the 1.3 line.
This was obviously forgotten when the release was made.
The command used was:
svn merge -r8033:8034 svn+ssh://bugman@.../svn/relax/tags/1.2.15 .
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r9292 | bugman | 2009-08-13 09:20:47 -0400 (Thu, 13 Aug 2009) | 5 lines
Updated the _off() and _on() user function echoing methods.
The flag is now a boolean, and the message has been reworded.
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r9303 | bugman | 2009-08-14 04:49:12 -0400 (Fri, 14 Aug 2009) | 3 lines
Updated the release checklist document to reflect Gna! and Freshmeat website changes.
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r9304 | bugman | 2009-08-14 04:51:09 -0400 (Fri, 14 Aug 2009) | 3 lines
Converted a number of flags from int to bool.
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r9305 | bugman | 2009-08-14 05:04:30 -0400 (Fri, 14 Aug 2009) | 3 lines
More changes to the release checklist document.
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r9306 | bugman | 2009-08-14 05:06:06 -0400 (Fri, 14 Aug 2009) | 3 lines
Added a script for running the full relax test suite against different Python versions.
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r9307 | bugman | 2009-08-14 05:19:20 -0400 (Fri, 14 Aug 2009) | 3 lines
Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test for Python 2.5.
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r9308 | bugman | 2009-08-14 05:25:29 -0400 (Fri, 14 Aug 2009) | 3 lines
Created a directory for holding miscellaneous scripts for developers.
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r9309 | bugman | 2009-08-14 05:25:55 -0400 (Fri, 14 Aug 2009) | 3 lines
Shifted the python version checking script.
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r9310 | bugman | 2009-08-14 05:28:20 -0400 (Fri, 14 Aug 2009) | 3 lines
Shifted the code validation script from the website hidden location into the scripts directory.
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r9311 | bugman | 2009-08-14 05:37:47 -0400 (Fri, 14 Aug 2009) | 3 lines
Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test for all Python version.
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r9314 | bugman | 2009-08-14 05:44:34 -0400 (Fri, 14 Aug 2009) | 6 lines
Merged the relax 1.3.4 CHANGES file into the 1.3 line.
The command used was:
svn merge -r9296:9297 svn+ssh://bugman@.../svn/relax/tags/1.3.4 .
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r9317 | bugman | 2009-08-14 11:23:30 -0400 (Fri, 14 Aug 2009) | 3 lines
Docstring fix for the return_units() method.
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r9318 | bugman | 2009-08-14 11:28:03 -0400 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes.
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r9319 | bugman | 2009-08-14 11:54:39 -0400 (Fri, 14 Aug 2009) | 3 lines
Converted the function into a class object variable.
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r9320 | bugman | 2009-08-14 12:44:39 -0400 (Fri, 14 Aug 2009) | 7 lines
Epydoc docstring improvements/fixes.
The default_value(), return_data_name() and set_doc() method docstrings have been shifted into the
class variables default_value_doc, return_data_name_doc and set_doc, and proper epydoc docstrings
for the methods written.
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r9321 | bugman | 2009-08-14 12:55:04 -0400 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes for IO.__init__().
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r9322 | bugman | 2009-08-14 13:06:31 -0400 (Fri, 14 Aug 2009) | 5 lines
Bug fix for the return_data_name() method recently introduced.
This function takes the 'index' keyword argument.
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r9324 | bugman | 2009-08-18 07:57:40 -0400 (Tue, 18 Aug 2009) | 5 lines
Credited Wikipedia and added the quaternion to rotation matrix equation.
The reason is because Wikipedia looks like it has a mistake!
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r9325 | bugman | 2009-08-18 08:28:08 -0400 (Tue, 18 Aug 2009) | 6 lines
Bug fix for the quaternion_to_R() function.
The Wikipedia page was wrong (or at least misleading). The calculation of the rotation matrix is
now correct.
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r9326 | bugman | 2009-08-18 08:30:03 -0400 (Tue, 18 Aug 2009) | 3 lines
Character encoding fix - cannot use umlauts.
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r9327 | bugman | 2009-08-18 08:38:38 -0400 (Tue, 18 Aug 2009) | 3 lines
Fix for the user interface of frame_order.ref_domain().
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r9328 | bugman | 2009-08-18 08:42:41 -0400 (Tue, 18 Aug 2009) | 3 lines
Implemented the back end of the frame_order.ref_domain() user function.
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r9329 | bugman | 2009-08-18 09:00:14 -0400 (Tue, 18 Aug 2009) | 3 lines
The full_in_ref_frame arg is now accepted by __init_iso_cone().
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r9330 | bugman | 2009-08-18 09:00:56 -0400 (Tue, 18 Aug 2009) | 3 lines
Fix for the kron_prod() function, due to the new transpose_14() function.
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r9331 | bugman | 2009-08-18 09:03:43 -0400 (Tue, 18 Aug 2009) | 3 lines
Added checks for the __init_iso_cone() args.
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r9332 | bugman | 2009-08-18 09:17:37 -0400 (Tue, 18 Aug 2009) | 9 lines
Applied the patch to allow compilation on Mac OS X with Python 2.6.
This patch is from Jack Howarth <howarth att bromo dot med dot uc dot edu>, and was attached to the
post https://mail.gna.org/public/relax-users/2009-08/msg00036.html (Message-id:
<7f080ed10908180200m27620a30x7dc64731a9e02e87@...>). The parent of this thread is
https://mail.gna.org/public/relax-users/2009-08/msg00017.html (Message-id:
<20090816020851.GA29683@...>).
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r9333 | bugman | 2009-08-18 12:45:44 -0400 (Tue, 18 Aug 2009) | 5 lines
Fix for the kron_prod() function.
The transpose_14() function works on the given matrix and returns None!
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r9334 | bugman | 2009-08-19 04:19:26 -0400 (Wed, 19 Aug 2009) | 3 lines
Fix for the calls to transpose_14(). This operates on the matrix rather than returning a new one.
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r9335 | bugman | 2009-08-19 04:29:13 -0400 (Wed, 19 Aug 2009) | 3 lines
Added a unit test for the maths_fns.kronecker_product.kron_prod() function.
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r9336 | bugman | 2009-08-19 04:32:35 -0400 (Wed, 19 Aug 2009) | 3 lines
Expanded the test_kron_prod() to check all elements of the matrix.
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r9337 | bugman | 2009-08-19 04:43:51 -0400 (Wed, 19 Aug 2009) | 5 lines
Fix for the test_kron_prod() unit test.
The R2 matrix didn't match the tested real Kronecker product.
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r9338 | bugman | 2009-08-19 04:45:56 -0400 (Wed, 19 Aug 2009) | 6 lines
Bug fix for the kron_prod() function.
The T23 rather than T14 transpose should now be used! And the resultant matrix is now returned to
the correct, original rank-2 shape.
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r9339 | bugman | 2009-08-19 08:19:34 -0400 (Wed, 19 Aug 2009) | 7 lines
Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test.
The 2 different f and g count values on 64-bit GNU/Linux are now checked. This difference is
present even when the same Python and numpy versions are used, and is therefore likely to be gcc
or the blas/lapack libraries causing differences.
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r9340 | bugman | 2009-08-19 09:37:09 -0400 (Wed, 19 Aug 2009) | 10 lines
Replaced all instances of `x` with repr(x).
This was down with the python 2.x to 3.x script with the commands:
2to3 -f repr . -w
2to3 -f repr relax -w
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9341 | bugman | 2009-08-19 09:48:55 -0400 (Wed, 19 Aug 2009) | 5 lines
Bug fix for the relaxation curve-fitting difference plot script.
The spin_loop blocks were missing colons!
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r9342 | bugman | 2009-08-19 10:09:33 -0400 (Wed, 19 Aug 2009) | 9 lines
Removed all usages of the has_attr() dictionary method.
This was down with the python 2.x to 3.x script with the commands:
2to3 -f has_key relax . -w
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9343 | bugman | 2009-08-19 11:18:47 -0400 (Wed, 19 Aug 2009) | 9 lines
Converted all print statements into print() function calls.
This was down with the python 2.x to 3.x script with the commands:
2to3 -w -f print relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9344 | bugman | 2009-08-19 11:31:11 -0400 (Wed, 19 Aug 2009) | 9 lines
Modified the behaviour of raise statements according to http://www.python.org/dev/peps/pep-3109/.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f raise relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9345 | bugman | 2009-08-19 11:45:24 -0400 (Wed, 19 Aug 2009) | 3 lines
Renamed the pipe.list() user function to pipe.display().
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r9346 | bugman | 2009-08-19 12:47:50 -0400 (Wed, 19 Aug 2009) | 9 lines
The dictionary keys() return value is now converted into a list.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f dict relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9347 | bugman | 2009-08-20 11:48:36 -0400 (Thu, 20 Aug 2009) | 9 lines
The exec statement has been replaced with a call to the exec() function.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9348 | bugman | 2009-08-21 04:50:08 -0400 (Fri, 21 Aug 2009) | 18 lines
The execfile statement has been replaced with a call to the exec(compile()) function.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6. The syntax has changed from:
execfile(script_file, local)
to:
exec(compile(open(script_file).read(), script_file, 'exec'), local)
Hmmm, not much of a language simplification!
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r9349 | bugman | 2009-08-21 04:54:20 -0400 (Fri, 21 Aug 2009) | 3 lines
Added a text file documenting the changes in preparation for Python 3.x.
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r9350 | bugman | 2009-08-21 06:07:01 -0400 (Fri, 21 Aug 2009) | 16 lines
The Python 2.x idioms have been removed.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
The changes include:
1) The call to type() has been replaced with isinstance().
2) "while 1" has been replaced with "while True".
3) list sort methods x.sort() have been replaced with a call to sorted(x).
Booleans are instances of int, so the user function argument unit tests will be a massive mess!
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r9351 | bugman | 2009-08-21 10:54:29 -0400 (Fri, 21 Aug 2009) | 8 lines
Added a module containing functions for checking user function args.
So far this includes:
check.is_bool()
check.is_int()
check.is_str()
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r9352 | bugman | 2009-08-21 10:55:01 -0400 (Fri, 21 Aug 2009) | 3 lines
Updated the 2to3 checklist for the idioms.
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r9353 | bugman | 2009-08-21 11:23:56 -0400 (Fri, 21 Aug 2009) | 5 lines
Created a base class for the user function classes.
This defines the __init__() method for creating the relax help string.
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r9354 | bugman | 2009-08-21 11:25:00 -0400 (Fri, 21 Aug 2009) | 3 lines
Simplified the sequence user function class by using the check and base_class modules.
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r9355 | bugman | 2009-08-21 11:45:36 -0400 (Fri, 21 Aug 2009) | 3 lines
Removed the num_types module as this is redundant with the new check module.
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r9356 | bugman | 2009-08-21 12:27:29 -0400 (Fri, 21 Aug 2009) | 3 lines
Added a new error class, RelaxTupleNumError.
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r9357 | bugman | 2009-08-21 12:30:04 -0400 (Fri, 21 Aug 2009) | 3 lines
Added 2 more arg checking functions, is_float() and is_num_tuple().
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r9358 | bugman | 2009-08-21 12:32:25 -0400 (Fri, 21 Aug 2009) | 5 lines
Changed all the default can_be_none keywords to False.
This is so you have to explicitly say if None is allowed, rather than the other way around.
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r9359 | bugman | 2009-08-21 12:34:29 -0400 (Fri, 21 Aug 2009) | 3 lines
Fixed the calls to checks.is_*().
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r9360 | bugman | 2009-08-21 13:07:56 -0400 (Fri, 21 Aug 2009) | 3 lines
Fixed the capitalisation of the RelaxNoneListStrError error class.
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r9361 | bugman | 2009-08-21 13:12:46 -0400 (Fri, 21 Aug 2009) | 3 lines
Added the is_num_list() function.
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r9362 | bugman | 2009-08-21 13:13:58 -0400 (Fri, 21 Aug 2009) | 3 lines
Created the RelaxNoneListNumError error class.
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r9363 | bugman | 2009-08-21 13:14:49 -0400 (Fri, 21 Aug 2009) | 3 lines
Removed a dead import of num_types.
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r9364 | bugman | 2009-08-21 13:18:32 -0400 (Fri, 21 Aug 2009) | 3 lines
Created the is_str_list() function.
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r9365 | bugman | 2009-08-21 13:22:16 -0400 (Fri, 21 Aug 2009) | 3 lines
Migrated the user function class to the new 'check' and 'base_class' modules.
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r9366 | bugman | 2009-08-21 13:53:26 -0400 (Fri, 21 Aug 2009) | 3 lines
Bug fix for the is_str_list() function.
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r9367 | bugman | 2009-08-21 13:55:32 -0400 (Fri, 21 Aug 2009) | 3 lines
Missing imports.
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r9368 | bugman | 2009-08-21 14:20:54 -0400 (Fri, 21 Aug 2009) | 3 lines
Added the is_num() function and fixed the other number checking functions.
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r9369 | bugman | 2009-08-21 14:49:59 -0400 (Fri, 21 Aug 2009) | 3 lines
Created the crazy check.is_str_or_num_or_str_num_list() function.
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r9370 | bugman | 2009-08-21 15:07:30 -0400 (Fri, 21 Aug 2009) | 3 lines
Added the RelaxNumStrListNumStrError and RelaxNoneNumStrListNumStrError error classes.
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r9371 | bugman | 2009-08-21 15:08:00 -0400 (Fri, 21 Aug 2009) | 3 lines
Fixes for the test_set_argfail_param() unit test.
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r9372 | bugman | 2009-08-21 15:09:53 -0400 (Fri, 21 Aug 2009) | 3 lines
Fixes for the test_set_argfail_val() unit test.
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r9373 | bugman | 2009-08-21 15:11:20 -0400 (Fri, 21 Aug 2009) | 3 lines
Removed some unused imports.
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r9374 | bugman | 2009-08-21 15:12:18 -0400 (Fri, 21 Aug 2009) | 3 lines
Added is_str_or_str_list() and fixed the is_str_or_num_or_str_num_list() function.
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r9375 | bugman | 2009-08-21 15:19:45 -0400 (Fri, 21 Aug 2009) | 3 lines
Migrated a number of user function classes to the new 'check' and 'base_class' modules.
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r9376 | bugman | 2009-08-21 15:28:09 -0400 (Fri, 21 Aug 2009) | 3 lines
Fix for the test_set_argfail_val() unit test.
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r9377 | bugman | 2009-08-24 12:12:32 -0400 (Mon, 24 Aug 2009) | 7 lines
Converted the J(w) mapping sample script to the relax 1.3 design.
The problem of the old 1.2 line code was discovered by Leao Lagarto <dodgy_spin att yahoo ddot co
dot uk> in the thread starting at https://mail.gna.org/public/relax-devel/2009-08/msg00004.html
(Message-id: <44680.10570.qm@...>).
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r9378 | bugman | 2009-08-24 12:26:03 -0400 (Mon, 24 Aug 2009) | 5 lines
Fix for the is_num() function.
The wrong RelaxErrors were being raised.
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r9379 | bugman | 2009-08-24 13:08:12 -0400 (Mon, 24 Aug 2009) | 3 lines
Added the new function is_int_or_int_list().
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r9380 | bugman | 2009-08-24 13:08:55 -0400 (Mon, 24 Aug 2009) | 3 lines
Bug fixes for the is_num_list() and is_num_tuple() functions.
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r9381 | bugman | 2009-08-24 13:45:16 -0400 (Mon, 24 Aug 2009) | 3 lines
Added a length arg to RelaxListNumError and RelaxListStrError.
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r9382 | bugman | 2009-08-24 13:55:28 -0400 (Mon, 24 Aug 2009) | 3 lines
Added the length arg to RelaxNoneListNumError.
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r9383 | bugman | 2009-08-24 14:14:17 -0400 (Mon, 24 Aug 2009) | 3 lines
Modified is_num_list() to check for empty lists.
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r9384 | bugman | 2009-08-24 14:30:54 -0400 (Mon, 24 Aug 2009) | 3 lines
Cleaned up and simplified all the functions in prompt.check.
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r9385 | bugman | 2009-08-24 14:45:18 -0400 (Mon, 24 Aug 2009) | 3 lines
Created the RelaxNoneStrFileError error class.
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r9386 | bugman | 2009-08-24 15:02:55 -0400 (Mon, 24 Aug 2009) | 3 lines
Created the RelaxNumTupleNumError and RelaxNoneNumTupleNumError error classes.
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r9387 | bugman | 2009-08-24 15:12:34 -0400 (Mon, 24 Aug 2009) | 5 lines
Migrated many more user function classes to the new 'check' and 'base_class' modules.
All unit tests now pass, but not all user functions use the new modules (to be done later).
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r9388 | bugman | 2009-08-26 04:56:29 -0400 (Wed, 26 Aug 2009) | 5 lines
The is_str_or_inst() function now checks for the DummyFileObject object as well.
This fixes a system test.
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r9389 | bugman | 2009-08-26 04:57:24 -0400 (Wed, 26 Aug 2009) | 5 lines
Fix for the spin.number() user function.
The number can be None to reset the values. This is used in a system test.
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r9390 | bugman | 2009-08-26 05:12:43 -0400 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxNoneStrListNumError error class.
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r9391 | bugman | 2009-08-26 05:17:47 -0400 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxStrListNumError error class.
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r9392 | bugman | 2009-08-26 05:21:42 -0400 (Wed, 26 Aug 2009) | 5 lines
Wrote the is_str_or_num_list() argument checking function.
This is for arguments that can be a string or list of numbers.
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r9393 | bugman | 2009-08-26 05:26:41 -0400 (Wed, 26 Aug 2009) | 3 lines
Wrote 5 arg unit tests for the pymol.macro_exec() user function.
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r9394 | bugman | 2009-08-26 05:28:13 -0400 (Wed, 26 Aug 2009) | 3 lines
Wrote 5 arg unit tests for the molmol.macro_exec() user function.
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r9395 | bugman | 2009-08-26 08:10:22 -0400 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxNoneFunctionError error class.
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r9396 | bugman | 2009-08-26 09:32:27 -0400 (Wed, 26 Aug 2009) | 3 lines
Added the is_func() function.
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r9397 | bugman | 2009-08-26 09:44:06 -0400 (Wed, 26 Aug 2009) | 3 lines
All the user function classes have now been migrated to use the new 'check' and 'base_class' modules.
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r9398 | bugman | 2009-08-26 09:50:07 -0400 (Wed, 26 Aug 2009) | 3 lines
Created the Basic_class for simplifying all non-user function classes.
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r9399 | bugman | 2009-08-26 11:13:37 -0400 (Wed, 26 Aug 2009) | 3 lines
Added the is_tuple() function.
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r9400 | bugman | 2009-08-26 11:15:28 -0400 (Wed, 26 Aug 2009) | 3 lines
Fixes for the eliminate arg unit tests.
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r9401 | bugman | 2009-08-26 11:35:24 -0400 (Wed, 26 Aug 2009) | 3 lines
All the non user function classes have now been migrated to use the new 'check' and 'base_class' modules.
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r9402 | bugman | 2009-08-26 11:38:14 -0400 (Wed, 26 Aug 2009) | 3 lines
Removed a number of now unused RelaxError imports.
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r9403 | bugman | 2009-08-26 13:28:33 -0400 (Wed, 26 Aug 2009) | 6 lines
The argument RelaxError classes have been put into relative order compared to the previous chaos.
The RelaxNone* classes are now directly under the equivalent non-None class, and the simple types,
lists, tuples, and mixed classes separated into subcategories.
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r9404 | bugman | 2009-08-28 04:51:22 -0400 (Fri, 28 Aug 2009) | 3 lines
Started to redesign to simplify the argument RelaxError classes.
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r9405 | bugman | 2009-08-28 05:12:43 -0400 (Fri, 28 Aug 2009) | 3 lines
Simplified all the argument RelaxError classes using BaseArgError.
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r9411 | bugman | 2009-08-28 06:24:03 -0400 (Fri, 28 Aug 2009) | 3 lines
Added a check for the unimplemented constraints in the frame order code.
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r9412 | bugman | 2009-08-28 12:01:25 -0400 (Fri, 28 Aug 2009) | 3 lines
Created the 'rigid' frame order model.
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r9413 | bugman | 2009-08-31 11:49:38 -0400 (Mon, 31 Aug 2009) | 5 lines
Constraints are now automatically turned off, if the minimisation option is set to True.
These are not yet implemented!
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r9414 | bugman | 2009-08-31 11:52:41 -0400 (Mon, 31 Aug 2009) | 5 lines
Bug fix for the ref_domain() method.
This method now works if no domain names have been associated with the tensors.
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r9415 | bugman | 2009-08-31 12:08:22 -0400 (Mon, 31 Aug 2009) | 5 lines
Fix for the turning off of minimisation constraints.
The algorithm needs to also change.
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r9416 | bugman | 2009-08-31 12:08:39 -0400 (Mon, 31 Aug 2009) | 3 lines
Changed a flag to a bool type.
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r9417 | bugman | 2009-08-31 13:07:18 -0400 (Mon, 31 Aug 2009) | 6 lines
Added __description__ strings to the user function class relax help strings.
The __strip_lead() method has been added to User_fn_class to remove leading whitespace from the
__description__ strings.
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r9418 | bugman | 2009-09-01 04:15:08 -0400 (Tue, 01 Sep 2009) | 6 lines
Rearrangement of the handling of frame order models.
The tensor rotation Euler angles are now model independent, the 'rigid' model is better supported,
and a clear isolation of the isotropic cone model has been made.
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r9419 | bugman | 2009-09-01 05:15:17 -0400 (Tue, 01 Sep 2009) | 3 lines
Added a missing alias for the current data pipe.
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r9420 | bugman | 2009-09-01 05:52:51 -0400 (Tue, 01 Sep 2009) | 3 lines
Added a system test for the frame order 'rigid' model with no tensor rotations and no motion.
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r9421 | bugman | 2009-09-01 07:48:39 -0400 (Tue, 01 Sep 2009) | 5 lines
Large code refactorisation - the current data pipe is now in __builtin__.cdp.
The result is the removal of 484 calls to generic_fns.pipes.get_pipe() to get the current data pipe.
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r9422 | bugman | 2009-09-01 10:02:48 -0400 (Tue, 01 Sep 2009) | 3 lines
Created the new maths_fns.rotation_matrix.R_to_euler_zyz() function and associated unit test.
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r9423 | bugman | 2009-09-01 10:38:26 -0400 (Tue, 01 Sep 2009) | 3 lines
The frame order minimisation now first checks if the tensor reductions have been specified.
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r9424 | bugman | 2009-09-01 10:40:49 -0400 (Tue, 01 Sep 2009) | 5 lines
Fix for the script() user function.
The function intro flag at the end of executing an external script was not being restored.
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r9425 | bugman | 2009-09-01 10:44:00 -0400 (Tue, 01 Sep 2009) | 3 lines
Added a function intro text for the script() user function.
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r9426 | bugman | 2009-09-02 08:09:02 -0400 (Wed, 02 Sep 2009) | 8 lines
Improvements to the optimisation tests and fixes for bug #14173, bug #14174, bug #14175, bug #14176, bug #14177, bug #14182.
The bugs were reported by Jack Howarth (https://gna.org/users/jhowarth) and Seb
(https://gna.org/users/semor).
The architecture info and optimisation stats for a number of systems have been added to the file for reference.
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r9427 | bugman | 2009-09-02 08:10:30 -0400 (Wed, 02 Sep 2009) | 6 lines
Created a script to test optimisation on various systems.
This just runs the optimisation system tests, collecting and printing the architecture info and
optimisation stats.
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r9428 | bugman | 2009-09-02 09:15:13 -0400 (Wed, 02 Sep 2009) | 3 lines
Added a unit test checking the generic_fns.structure.__all__ list.
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r9429 | bugman | 2009-09-02 09:21:46 -0400 (Wed, 02 Sep 2009) | 3 lines
Tidying up of the docstrings and printouts of the Test___init__ test class.
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r9430 | bugman | 2009-09-02 09:37:30 -0400 (Wed, 02 Sep 2009) | 3 lines
Shifted the test___all__() method into the PackageTestCase base class.
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r9431 | bugman | 2009-09-02 09:43:16 -0400 (Wed, 02 Sep 2009) | 3 lines
Added many more checks for the package __all__ lists.
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r9432 | bugman | 2009-09-02 09:48:17 -0400 (Wed, 02 Sep 2009) | 3 lines
Added a check for the __all__ list of the data package.
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r9433 | bugman | 2009-09-02 13:53:15 -0400 (Wed, 02 Sep 2009) | 3 lines
Comment fixes.
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r9434 | bugman | 2009-09-02 14:15:21 -0400 (Wed, 02 Sep 2009) | 3 lines
Updated the package __all__ lists.
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r9435 | bugman | 2009-09-02 14:24:47 -0400 (Wed, 02 Sep 2009) | 3 lines
Added a check for non-existent modules, and updated the __all__ lists.
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r9436 | bugman | 2009-09-02 16:11:08 -0400 (Wed, 02 Sep 2009) | 7 lines
Made the profile module optional, removing the dependency on the Python development packages.
This was in response to Tiago Pais's <tpais att itqb dot unl dot pt> message at
https://mail.gna.org/public/relax-users/2009-08/msg00040.html (Message-id:
<A3A9E765436240CDA75B3045C405BED6@...>).
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r9437 | bugman | 2009-09-03 07:42:16 -0400 (Thu, 03 Sep 2009) | 11 lines
The whitespace after commas has been enforced (for Python 3.x).
This was done with the python 2.x to 3.x script with the command:
2to3 -w -f ws_comma relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6. All commas now have whitespace after them.
The docs/2to3_checklist file has also been updated with all the 2to3 changes.
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r9438 | bugman | 2009-09-03 07:52:25 -0400 (Thu, 03 Sep 2009) | 3 lines
Removed some debugging code.
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r9439 | bugman | 2009-09-03 08:06:49 -0400 (Thu, 03 Sep 2009) | 9 lines
Some more print statement updates for Python 3.x.
This was down with the python 2.x to 3.x script with the commands:
2to3 -w -f print relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6.
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r9454 | bugman | 2009-09-03 09:23:45 -0400 (Thu, 03 Sep 2009) | 3 lines
Updated the non-dangerous Python3k update command.
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r9457 | bugman | 2009-09-03 11:53:41 -0400 (Thu, 03 Sep 2009) | 3 lines
Created a sub-directory for frame order test scripts.
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r9458 | bugman | 2009-09-03 12:18:51 -0400 (Thu, 03 Sep 2009) | 3 lines
Shifted the rigid frame order system test into the sub-directory.
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r9459 | bugman | 2009-09-03 12:31:23 -0400 (Thu, 03 Sep 2009) | 3 lines
Added another rigid frame order system test.
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r9460 | bugman | 2009-09-03 12:32:10 -0400 (Thu, 03 Sep 2009) | 3 lines
Renamed a frame order system test.
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r9461 | bugman | 2009-09-03 13:05:02 -0400 (Thu, 03 Sep 2009) | 3 lines
Specific architecture and optimisation details are now printed if the frame order system tests fail.
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r9462 | bugman | 2009-09-03 13:17:08 -0400 (Thu, 03 Sep 2009) | 3 lines
Fix for the new frame order system test - the results file goes to devnull.
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r9463 | bugman | 2009-09-03 13:25:01 -0400 (Thu, 03 Sep 2009) | 3 lines
The beta angle for the tensor rotations is now folded to be between 0 and pi.
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r9464 | bugman | 2009-09-04 04:24:52 -0400 (Fri, 04 Sep 2009) | 5 lines
Added a function for converting the frame order matrix to the rotational superoperator.
The function is called daeg_to_rotational_superoperator().
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r9465 | bugman | 2009-09-04 05:21:28 -0400 (Fri, 04 Sep 2009) | 5 lines
Fix for the new daeg_to_rotational_superoperator() function.
The frame order matrix shape is now restored.
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r9466 | bugman | 2009-09-04 10:12:31 -0400 (Fri, 04 Sep 2009) | 5 lines
The print_frame_order_2nd_degree() function now accepts the epsilon arg.
This allows zero to be defined differently making the printout nicer.
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r9467 | bugman | 2009-09-07 13:28:57 -0400 (Mon, 07 Sep 2009) | 6 lines
Improved and expanded the output of the print_frame_order_2nd_degree() function.
The print out can now be in integer form, dots can replace zeros, and commas between elements are
now optional. Matrix forms are also converted to array forms.
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r9468 | bugman | 2009-09-07 13:31:49 -0400 (Mon, 07 Sep 2009) | 5 lines
Fix for the __update_model() method.
The theta_axis, phi_axis, and theta_cone params were not being added to the parameter array!
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r9469 | bugman | 2009-09-08 05:14:08 -0400 (Tue, 08 Sep 2009) | 5 lines
Added some unit tests for the R_euler_zyz() function.
This tests some basic axis rotations.
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r9470 | bugman | 2009-09-08 05:26:37 -0400 (Tue, 08 Sep 2009) | 3 lines
Fixes for the R_euler_zyz() unit tests.
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r9471 | bugman | 2009-09-08 05:27:23 -0400 (Tue, 08 Sep 2009) | 5 lines
Fix for the R_euler_zyz() function.
The rotations were being performed in the opposite direction?!?
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r9472 | bugman | 2009-09-08 08:38:05 -0400 (Tue, 08 Sep 2009) | 3 lines
Removed the incorrect part of the R_euler_zyz() docstring.
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r9473 | bugman | 2009-09-08 08:40:37 -0400 (Tue, 08 Sep 2009) | 5 lines
Bug fix for the R_to_euler_zyz() function.
This matches the important bug fix in the R_euler_zyz() function.
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r9474 | bugman | 2009-09-08 08:43:47 -0400 (Tue, 08 Sep 2009) | 5 lines
Fixes for the test_func3() and test_func4() unit tests.
The rotations were backwards because of the R_euler_zyz() fix!
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r9475 | bugman | 2009-09-08 09:11:17 -0400 (Tue, 08 Sep 2009) | 6 lines
Fix to the frame order system tests.
This corresponds to the fixes in R_euler_zyz() where the rotation matrices were in the left-handed
universe and hence the rotation was back to front.
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r9476 | bugman | 2009-09-08 10:40:16 -0400 (Tue, 08 Sep 2009) | 3 lines
Created 3 unit tests of the maths_fns.rotation_matrix.quaternion_to_R() function.
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r9477 | bugman | 2009-09-08 11:07:06 -0400 (Tue, 08 Sep 2009) | 5 lines
Created 3 unit tests of the maths_fns.rotation_matrix.R_axis_angle() function.
These are almost identical to those of quaternion_to_R().
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r9478 | bugman | 2009-09-08 11:42:48 -0400 (Tue, 08 Sep 2009) | 3 lines
Added a unit test for maths_fns.rotation_matrix.R_to_axis_angle() using R = I.
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r9479 | bugman | 2009-09-08 11:43:36 -0400 (Tue, 08 Sep 2009) | 5 lines
Bug fix for R_to_axis_angle().
All vector elements were NaN when the angle is 0. Now the zero vector is not normalised by zero.
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r9480 | bugman | 2009-09-08 11:47:59 -0400 (Tue, 08 Sep 2009) | 3 lines
Added another unit test for maths_fns.rotation_matrix.R_axis_angle().
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r9481 | bugman | 2009-09-08 12:20:08 -0400 (Tue, 08 Sep 2009) | 5 lines
Function renaming and argument order changes in the maths_fns.rotation_matrix module.
The naming scheme is now more logical (as well as the argument order).
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r9482 | bugman | 2009-09-08 12:27:50 -0400 (Tue, 08 Sep 2009) | 3 lines
Alphabetical reordering of functions.
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r9483 | bugman | 2009-09-08 12:52:54 -0400 (Tue, 08 Sep 2009) | 3 lines
Huge simplifications to the unit tests for the maths_fns.rotation_matrix package.
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r9484 | bugman | 2009-09-08 13:17:29 -0400 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9485 | bugman | 2009-09-08 13:51:14 -0400 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function.
This is accompanied by 2 unit tests.
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r9486 | bugman | 2009-09-08 14:20:34 -0400 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.R_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9487 | bugman | 2009-09-08 15:07:41 -0400 (Tue, 08 Sep 2009) | 13 lines
Added a unit test to bounce around all the conversion functions in maths_fns.rotation_matrix.
This bounces through:
1) euler_zyz_to_R().
2) R_to_axis_angle().
3) axis_angle_to_quaternion().
4) quaternion_to_axis_angle().
5) axis_angle_to_R().
6) R_to_quaternion().
7) quaternion_to_R().
8) R_to_euler_zyz().
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r9488 | bugman | 2009-09-09 10:04:40 -0400 (Wed, 09 Sep 2009) | 5 lines
Added a unit test to check if all the maths_fns.kronecker_product.transpose_*() functions revert.
Calling the function twice should return the matrix to the original state.
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r9489 | bugman | 2009-09-10 08:33:33 -0400 (Thu, 10 Sep 2009) | 3 lines
Renamed the data pipes system tests module.
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r9490 | bugman | 2009-09-10 10:51:39 -0400 (Thu, 10 Sep 2009) | 3 lines
Wrote a system test for the writing and re-reading of data pipes.
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r9491 | bugman | 2009-09-10 10:53:06 -0400 (Thu, 10 Sep 2009) | 3 lines
Shifted the valid types private function variable into a module variable.
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r9492 | bugman | 2009-09-10 10:54:55 -0400 (Thu, 10 Sep 2009) | 3 lines
The test_write_read_pipes() system test is now using the VALID_TYPES module variable to get all pipes.
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r9493 | bugman | 2009-09-10 11:01:39 -0400 (Thu, 10 Sep 2009) | 3 lines
Deleted the __init__() class methods as these were empty, and shifted the docstring to that of the class.
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r9494 | bugman | 2009-09-10 11:02:22 -0400 (Thu, 10 Sep 2009) | 3 lines
Removed an empty line.
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r9495 | bugman | 2009-09-10 11:20:21 -0400 (Thu, 10 Sep 2009) | 5 lines
Added a very basic, and completely empty module and class for SRLS analysis.
This is to allow the data pipe to be created.
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r9496 | bugman | 2009-09-10 11:37:16 -0400 (Thu, 10 Sep 2009) | 3 lines
Updated the specific_fns module __all__ list for the SRLS module.
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r9497 | bugman | 2009-09-10 11:38:20 -0400 (Thu, 10 Sep 2009) | 5 lines
Shifted the test_write_read_pipes() system test to the 'state' test module.
The program state is now being saved as the results file is for just one data pipe.
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r9498 | bugman | 2009-09-10 12:07:22 -0400 (Thu, 10 Sep 2009) | 3 lines
A few fixes for the test_write_read_pipes() system test.
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r9499 | bugman | 2009-09-10 12:32:31 -0400 (Thu, 10 Sep 2009) | 7 lines
Redesign of the relax state loading for adding support for a XML formatted state file.
Half of the load_state() is now in load_pickle(), and a new function load_xml() added.
The determine_format() function will tell if the file is a pickle or XML file, and then
load_pickle() will run the appropriate loading function.
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r9500 | bugman | 2009-09-10 12:36:40 -0400 (Thu, 10 Sep 2009) | 5 lines
Added the pickle flag to save_state().
This defaults to True to prevent relax failures during the XML file implementation.
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r9501 | bugman | 2009-09-10 13:01:25 -0400 (Thu, 10 Sep 2009) | 5 lines
The save_state() function now calls the relax data store to_xml() method.
This method is currently only for one data pipe, and is used by the results writing user function.
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r9502 | bugman | 2009-09-10 13:24:30 -0400 (Thu, 10 Sep 2009) | 6 lines
The relax data store to_xml() method now can add all data pipes to the XML file (or a subset).
The results.write() method now asks to_xml() for just the current pipe to be stored, whereas
state.save() supplies no 'pipes' argument to have all pipes stored.
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r9503 | bugman | 2009-09-10 13:26:22 -0400 (Thu, 10 Sep 2009) | 5 lines
Shifted the results.write() force arg to the end.
Bool args should be last!
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r9504 | bugman | 2009-09-10 13:37:33 -0400 (Thu, 10 Sep 2009) | 3 lines
Removed trailing whitespace.
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r9505 | bugman | 2009-09-10 13:56:32 -0400 (Thu, 10 Sep 2009) | 3 lines
Updates to the load_xml() function. This now does something!
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r9506 | bugman | 2009-09-10 14:04:05 -0400 (Thu, 10 Sep 2009) | 3 lines
Created the relax data store is_empty() method.
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r9507 | bugman | 2009-09-11 04:06:05 -0400 (Fri, 11 Sep 2009) | 6 lines
Added the pickle arg to state.save().
This allows the relax state - the contents of the relax data store - to either be saved as XML or as
a pickled object.
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r9508 | bugman | 2009-09-11 04:07:11 -0400 (Fri, 11 Sep 2009) | 3 lines
Added a warning to the state.save() user function about the pickle format compatibility.
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r9509 | bugman | 2009-09-11 04:16:04 -0400 (Fri, 11 Sep 2009) | 6 lines
Absorbed the load_xml() function into load_state().
After shifting the data store check to load_state() for all formats, the function only had one
statement.
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r9510 | bugman | 2009-09-11 04:29:08 -0400 (Fri, 11 Sep 2009) | 3 lines
Docstring clarification of the dir arg.
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r9511 | bugman | 2009-09-11 05:12:30 -0400 (Fri, 11 Sep 2009) | 3 lines
Updated the relax data store from_xml() method for support of the loading of the XML state file.
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r9512 | bugman | 2009-09-11 05:31:44 -0400 (Fri, 11 Sep 2009) | 5 lines
Added the force flag to the state.load() user function.
When True, this causes the relax data store to be reset prior to state loading.
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r9513 | bugman | 2009-09-11 05:36:02 -0400 (Fri, 11 Sep 2009) | 5 lines
Duplicated the test_state() system test into test_state_pickle() and test_state_xml().
This tests both formats.
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r9514 | bugman | 2009-09-11 05:39:53 -0400 (Fri, 11 Sep 2009) | 6 lines
Fixes for load_pickle().
The ds.__reset__() call has been removed because of redundancy and the new ds.is_empty() has been
blacklisted.
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r9515 | bugman | 2009-09-11 05:48:17 -0400 (Fri, 11 Sep 2009) | 3 lines
Changed the default save state to XML.
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r9516 | bugman | 2009-09-11 07:43:34 -0400 (Fri, 11 Sep 2009) | 3 lines
Added a dir arg to a state.save() call in test_state_pickle().
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r9517 | bugman | 2009-09-11 07:52:36 -0400 (Fri, 11 Sep 2009) | 5 lines
Renamed the state.load() and state.save() directory argument from dir_name to dir.
This is to bring it in line with the rest of relax.
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r9518 | bugman | 2009-09-11 08:44:41 -0400 (Fri, 11 Sep 2009) | 3 lines
Fixes for print_frame_order_2nd_degree() for when NaN is encountered.
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r9519 | bugman | 2009-09-11 08:46:04 -0400 (Fri, 11 Sep 2009) | 5 lines
Fix for the print_frame_order_2nd_degree().
The NaN fix was partly incorrect.
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r9520 | bugman | 2009-09-11 09:04:15 -0400 (Fri, 11 Sep 2009) | 3 lines
Made the integer printout 4 char wide.
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r9521 | bugman | 2009-09-11 09:31:42 -0400 (Fri, 11 Sep 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The T23 and not T14 transpose should be performed!
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r9522 | bugman | 2009-09-11 09:59:04 -0400 (Fri, 11 Sep 2009) | 2 lines
Reordered the relax debugging save state so that the format is yyyymmdd_hhmmss rather than yyyyddmm_hhmmss.
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r9523 | bugman | 2009-09-11 11:55:23 -0400 (Fri, 11 Sep 2009) | 3 lines
Added a check for the setting of the domain the tensor corresponds to.
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r9524 | bugman | 2009-09-14 07:59:44 -0400 (Mon, 14 Sep 2009) | 3 lines
Renamed the frame order target function module.
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r9525 | bugman | 2009-09-14 08:07:40 -0400 (Mon, 14 Sep 2009) | 3 lines
Bug fix, the func_iso_cone_elements() method was been replaced with func_iso_cone().
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r9526 | bugman | 2009-09-14 08:23:10 -0400 (Mon, 14 Sep 2009) | 5 lines
Fix for r9525.
The func_iso_cone() was now not being set up.
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r9528 | bugman | 2009-09-18 08:04:52 -0400 (Fri, 18 Sep 2009) | 3 lines
Created the euler_zyz_to_axis_angle() conversion function.
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r9529 | bugman | 2009-09-18 08:28:37 -0400 (Fri, 18 Sep 2009) | 6 lines
Created axis_angle_to_euler_zyz().
The test_euler_zyz_to_euler_zyz() unit test now checks both euler_zyz_to_axis_angle() and
axis_angle_to_euler_zyz().
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r9530 | bugman | 2009-09-18 11:38:27 -0400 (Fri, 18 Sep 2009) | 12 lines
Final 1.3 line redesigns of the relax_io module.
The log() and tee() functions have been renamed to io_streams_log() and io_streams_tee(), and the
old IO.logging_off() class method has been converted to the io_streams_restore() function. The
io_streams_restore() function is also differently designed, using the true original IO streams
(sys.__stdin__, sys.__stdout__, and sys.__stderr__).
The IO.delete() method has been converted to a module function.
The IO class has been eliminated.
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r9531 | bugman | 2009-09-18 12:19:26 -0400 (Fri, 18 Sep 2009) | 6 lines
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This checks the dumping and
reloading of alignment tensors into an XML file.
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r9532 | bugman | 2009-09-18 12:26:40 -0400 (Fri, 18 Sep 2009) | 5 lines
Bug fix for the delete function.
The function was failing if the file was missing!
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r9533 | bugman | 2009-09-18 12:28:05 -0400 (Fri, 18 Sep 2009) | 6 lines
Bug fix for the test suite.
The temporary files were not always deleted if a .bz2 extension was added! Now relax_io.delete() is
being called to fix this.
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r9534 | bugman | 2009-09-18 12:28:56 -0400 (Fri, 18 Sep 2009) | 3 lines
Reactivated the system tests turned off in r9533.
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r9535 | bugman | 2009-09-18 12:32:41 -0400 (Fri, 18 Sep 2009) | 5 lines
Fix for the data_names() method for when no model has been setup.
This allows the frame order data pipe to be written out prior to the model setup.
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r9536 | bugman | 2009-09-18 12:43:02 -0400 (Fri, 18 Sep 2009) | 3 lines
Expansion of the test_to_and_from_xml() system test to check more data structures.
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r9537 | bugman | 2009-09-18 12:47:49 -0400 (Fri, 18 Sep 2009) | 3 lines
The data structures of the AlignTensorList class are now packed into the XML file.
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r9538 | bugman | 2009-09-18 13:11:30 -0400 (Fri, 18 Sep 2009) | 3 lines
Added the blacklist arg to xml_to_object().
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r9539 | bugman | 2009-09-18 13:15:06 -0400 (Fri, 18 Sep 2009) | 6 lines
Reverted r9538. The wrong file was committed!
The command used was:
svn merge -r9538:9537 .
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r9540 | bugman | 2009-09-18 13:15:40 -0400 (Fri, 18 Sep 2009) | 3 lines
Try again: Added the blacklist arg to xml_to_object().
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r9541 | bugman | 2009-09-18 13:18:14 -0400 (Fri, 18 Sep 2009) | 3 lines
Bug fix, the blacklist args now default to [].
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r9542 | bugman | 2009-09-18 13:19:39 -0400 (Fri, 18 Sep 2009) | 3 lines
Fix for the test_to_and_from_xml() check of the 'reduction' data structure.
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r9543 | bugman | 2009-09-18 13:20:15 -0400 (Fri, 18 Sep 2009) | 3 lines
The 'reduction' data structure is now properly created from the XML file.
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r9544 | bugman | 2009-09-21 07:25:14 -0400 (Mon, 21 Sep 2009) | 6 lines
Modified the frame order grid search.
The angle end points are now avoided (as they are the same as the start points) and the beta Euler
angle increments are halved, as the search is half of that of alpha and gamma (0 to pi).
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r9545 | bugman | 2009-09-21 07:53:39 -0400 (Mon, 21 Sep 2009) | 5 lines
Removed the end point of the cone angle from the grid search.
This is unrestricted motion, so is physically not possible.
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r9546 | bugman | 2009-09-21 08:03:55 -0400 (Mon, 21 Sep 2009) | 5 lines
Also halved the number of theta polar angle increments in the frame order grid search.
This is to match the cone axis azimuthal angle phi.
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r9547 | bugman | 2009-09-21 10:20:58 -0400 (Mon, 21 Sep 2009) | 6 lines
Fix for the missing PDB file error.
The extension '.pdb' was being added to the end so if the missing file '1F3Y.pdb' was specified,
the RelaxError would say that '1F3Y.pdb.pdb' was missing.
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r9548 | bugman | 2009-09-21 12:44:14 -0400 (Mon, 21 Sep 2009) | 7 lines
Complete redesign of the grid_search() method.
The grid ops structure is no longer created, rather the grid is directly created to be passed to the
grid search algorithm. The __grid_row() method has been added to create the row of the grid
corresponding to a certain parameter.
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r9549 | bugman | 2009-09-21 13:37:50 -0400 (Mon, 21 Sep 2009) | 3 lines
Implemented the acos grid search for angular parameters of the frame order theories.
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r9550 | bugman | 2009-09-21 13:39:41 -0400 (Mon, 21 Sep 2009) | 3 lines
Fixed the call to the grid search.
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r9551 | bugman | 2009-09-21 14:25:52 -0400 (Mon, 21 Sep 2009) | 5 lines
Fix for the __unpack_opt_results() for the new direct calling of the grid search.
The returned results are different.
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r9552 | bugman | 2009-09-22 05:50:31 -0400 (Tue, 22 Sep 2009) | 3 lines
Added a false, deliberately broken Xplor line to test the parsing of Xplor NOE files.
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r9553 | bugman | 2009-09-22 06:04:37 -0400 (Tue, 22 Sep 2009) | 3 lines
Bug fix for the reading of Xplor NOE data when a line starts with '#'.
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r9554 | bugman | 2009-09-22 07:15:40 -0400 (Tue, 22 Sep 2009) | 5 lines
Fix for the test_opt_rigid_rand_rot() system test.
The changes to the frame order grid search broke this test.
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r9555 | bugman | 2009-09-22 08:28:03 -0400 (Tue, 22 Sep 2009) | 3 lines
Added a series of checks to the test_curve_fitting() system test.
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r9556 | bugman | 2009-09-22 08:29:24 -0400 (Tue, 22 Sep 2009) | 3 lines
Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
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r9557 | bugman | 2009-09-22 08:38:58 -0400 (Tue, 22 Sep 2009) | 3 lines
A bit of a clean up of the relaxation curve fitting minimise() method.
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r9558 | bugman | 2009-09-22 08:52:46 -0400 (Tue, 22 Sep 2009) | 3 lines
Redesigned the N-state model grid search setup around the new minfx interface.
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r9559 | bugman | 2009-09-22 09:00:03 -0400 (Tue, 22 Sep 2009) | 3 lines
Added a comment line.
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r9560 | bugman | 2009-09-22 09:00:25 -0400 (Tue, 22 Sep 2009) | 3 lines
Another clean out of the grid search setup.
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r9561 | bugman | 2009-09-22 09:16:24 -0400 (Tue, 22 Sep 2009) | 3 lines
Removed some trailing whitespace.
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r9562 | bugman | 2009-09-22 12:18:55 -0400 (Tue, 22 Sep 2009) | 3 lines
Redesigned the model-free grid search setup around the new minfx interface.
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r9563 | bugman | 2009-09-22 13:35:05 -0400 (Tue, 22 Sep 2009) | 3 lines
Modified the grid search calls due to changes in minfx.
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r9564 | bugman | 2009-10-05 04:25:33 -0400 (Mon, 05 Oct 2009) | 10 lines
Bug fix: Added the function __deselect_spins() to remove spins with too little data.
This fixes bug #14428 (http://gna.org/bugs/?14428) reported by Pierre-Yves Savard <pierre-yves dott
savard at bcm dot ulaval dot ca>.
The new function is almost identical to that used in the model-free analysis performed by relax in
that spins with no or too little data, or those which would be over-fit are removed from the
analysis.
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r9565 | bugman | 2009-10-05 04:26:24 -0400 (Mon, 05 Oct 2009) | 3 lines
Fix for the system test of Art Palmer's Modelfree4 program for the new __deselect_spins() fn.
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r9566 | bugman | 2009-10-05 05:34:48 -0400 (Mon, 05 Oct 2009) | 3 lines
Added a script for creating Molmol macros to represent the model-free motions.
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r9567 | bugman | 2009-10-05 06:15:51 -0400 (Mon, 05 Oct 2009) | 3 lines
Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
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r9568 | bugman | 2009-10-06 05:22:21 -0400 (Tue, 06 Oct 2009) | 6 lines
Added the spin_id_col arg to the rdc.read() user function.
This allows 2 different formats for spin identification - spin ID string or mol name, res name and
num, and spin name and num.
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r9569 | bugman | 2009-10-06 05:25:10 -0400 (Tue, 06 Oct 2009) | 3 lines
Removed some empty lines.
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r9570 | bugman | 2009-10-06 05:38:20 -0400 (Tue, 06 Oct 2009) | 9 lines
Changes to the pcs.read() and rdc.read() user function interfaces.
Columns are now numbered from 1 - note this will break many things! The spin_id_col is now accepted
and the spin_id arg is explained.
The docstrings have also been modified all over these user function classes to replace
'identification string' with 'ID string'.
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r9571 | bugman | 2009-10-06 05:39:22 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixed the call from the prompt to the generic fns.
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r9572 | bugman | 2009-10-06 06:18:35 -0400 (Tue, 06 Oct 2009) | 6 lines
Created the read_spin_data_file() generator function.
This is designed to replace quite a few inconsistent functions throughout the generic function code
base. It reads a columnar formatted file with a spin per line.
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r9573 | bugman | 2009-10-06 06:20:20 -0400 (Tue, 06 Oct 2009) | 3 lines
Modified generate_spin_id_data_array() so that column numbering starts at 1.
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r9574 | bugman | 2009-10-06 06:28:13 -0400 (Tue, 06 Oct 2009) | 3 lines
Modified generic_fns.rdc.read() to use the new relax_io.read_spin_data_file().
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r9575 | bugman | 2009-10-06 06:32:17 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixes for the unit tests of generic_fns.mol_res_spin.generate_spin_id_data_array().
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r9576 | bugman | 2009-10-06 06:52:42 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixed the calls to rdc.read() and pcs.read() in the system tests.
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r9577 | bugman | 2009-10-06 06:56:53 -0400 (Tue, 06 Oct 2009) | 3 lines
Added a check to see if the file is empty to read_spin_data_file().
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r9578 | bugman | 2009-10-06 07:01:06 -0400 (Tue, 06 Oct 2009) | 5 lines
Converted value.read() to use the new relax_io.read_spin_data_file() function.
This converts the user function to the 1.3 line design as well.
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r9579 | bugman | 2009-10-06 07:19:44 -0400 (Tue, 06 Oct 2009) | 3 lines
Docstring modification better explaining spin_id.
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r9580 | bugman | 2009-10-06 07:20:57 -0400 (Tue, 06 Oct 2009) | 5 lines
Converted spectrum.read_intensities() to use the new relax_io.read_spin_data_file() function.
This is only for the generic formatted file.
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r9581 | bugman | 2009-10-06 07:22:23 -0400 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of relax_io.read_spin_data_file().
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r9582 | bugman | 2009-10-06 09:26:28 -0400 (Tue, 06 Oct 2009) | 5 lines
Bug fix for the relax_io.read_spin_data_file() function.
The column number check was incorrect due to the column renumbering.
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r9583 | bugman | 2009-10-06 09:46:25 -0400 (Tue, 06 Oct 2009) | 6 lines
The relax_io.read_spin_data_file() function now calls generic_fns.sequence.validate_sequence().
This is a more advanced check of the sequence information. The validate_sequence() function has
also been modified to handle single data lines.
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r9584 | bugman | 2009-10-06 10:07:58 -0400 (Tue, 06 Oct 2009) | 3 lines
Wrote spin_id_to_data_list() to convert a single spin ID into a list of mol, res, and spin names and numbers.
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r9585 | bugman | 2009-10-06 10:13:53 -0400 (Tue, 06 Oct 2009) | 3 lines
Converted the sequence.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9586 | bugman | 2009-10-06 10:14:54 -0400 (Tue, 06 Oct 2009) | 5 lines
Fix for the spin_id_to_data_list() function.
The spin ID string was incorrectly named.
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r9587 | bugman | 2009-10-06 10:21:16 -0400 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line!
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r9588 | bugman | 2009-10-06 10:22:55 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixed some calls to sequence.read() in the unit tests.
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r9589 | bugman | 2009-10-06 11:25:41 -0400 (Tue, 06 Oct 2009) | 5 lines
Rewrote the tokenise() function to allow for the '&' boolean operator for residues and spins.
This allows ':1&:GLY' or '@453&@N' to be parsed.
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r9590 | bugman | 2009-10-06 11:35:51 -0400 (Tue, 06 Oct 2009) | 3 lines
Modified parse_token() to handle multiple tokens simultaneously.
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r9591 | bugman | 2009-10-06 11:38:48 -0400 (Tue, 06 Oct 2009) | 3 lines
Some fixes for the spin_id_to_data_list() function.
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r9592 | bugman | 2009-10-06 11:45:44 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixes for spin_id_to_data_list(), and now it returns a tuple rather than a list.
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r9593 | bugman | 2009-10-06 12:06:03 -0400 (Tue, 06 Oct 2009) | 3 lines
Some more fixes for spin_id_to_data_list().
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r9594 | bugman | 2009-10-06 12:11:12 -0400 (Tue, 06 Oct 2009) | 3 lines
Fix for the read() function. The arguments are now properly sent to generate().
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r9595 | bugman | 2009-10-06 12:19:45 -0400 (Tue, 06 Oct 2009) | 5 lines
Fix for the test_read() system test.
The residue columns must now be specified.
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r9596 | bugman | 2009-10-06 12:36:04 -0400 (Tue, 06 Oct 2009) | 3 lines
Yet another fix for the new read_spin_data_file() function - hopefully this will be the last!
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r9597 | bugman | 2009-10-06 12:37:01 -0400 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of read_spin_data_file().
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r9598 | bugman | 2009-10-06 12:40:24 -0400 (Tue, 06 Oct 2009) | 5 lines
Fix for the validate_sequence().
The shifted column numbers were not being taken into account.
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r9599 | bugman | 2009-10-06 12:42:51 -0400 (Tue, 06 Oct 2009) | 3 lines
Removed the test for error values of zero, as this was killing Dasha!
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r9600 | bugman | 2009-10-06 12:43:38 -0400 (Tue, 06 Oct 2009) | 3 lines
Fixed all the calls to sequence.read() where the default residue columns were being relied upon.
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r9601 | bugman | 2009-10-06 12:53:57 -0400 (Tue, 06 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9602 | bugman | 2009-10-06 13:07:51 -0400 (Tue, 06 Oct 2009) | 3 lines
Reverted some accidental commenting out of system tests.
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r9603 | bugman | 2009-10-06 13:21:42 -0400 (Tue, 06 Oct 2009) | 3 lines
Converted select.read() and deselect.read() to use the new relax_io.read_spin_data_file() function.
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r9604 | bugman | 2009-10-06 13:37:39 -0400 (Tue, 06 Oct 2009) | 3 lines
Additions to the select.read() and deselect.read() docstrings.
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r9605 | bugman | 2009-10-06 13:57:12 -0400 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9606 | bugman | 2009-10-06 14:07:29 -0400 (Tue, 06 Oct 2009) | 3 lines
Converted the relax_data.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9607 | bugman | 2009-10-06 14:13:44 -0400 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9608 | bugman | 2009-10-06 14:22:15 -0400 (Tue, 06 Oct 2009) | 3 lines
Converted the pcs.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9609 | bugman | 2009-10-06 14:27:10 -0400 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9610 | bugman | 2009-10-06 14:28:02 -0400 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9611 | bugman | 2009-10-06 14:29:46 -0400 (Tue, 06 Oct 2009) | 3 lines
Header realignment.
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r9612 | bugman | 2009-10-07 03:43:42 -0400 (Wed, 07 Oct 2009) | 5 lines
Bug fixes for the RDC and PCS read() functions.
The alignment tensor ID had the same variable name as the spin ID!
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r9613 | bugman | 2009-10-07 03:53:40 -0400 (Wed, 07 Oct 2009) | 3 lines
Renamed all the alignment ID args and variables 'id' to 'align_id' in the RDC and PCS user fns.
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r9614 | bugman | 2009-10-07 03:55:26 -0400 (Wed, 07 Oct 2009) | 3 lines
Docstring spelling mistake fix - 'spid_id_col' should be 'spin_id_col'!
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r9615 | bugman | 2009-10-07 04:08:32 -0400 (Wed, 07 Oct 2009) | 3 lines
Fixes for the system tests to use the new 'align_id' args.
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r9616 | bugman | 2009-10-07 04:18:37 -0400 (Wed, 07 Oct 2009) | 6 lines
Removed some unneeded files.
The relaxation delays will be placed into the script itself, and the generic_intensity2.txt file
will replace generic_intensity.txt.
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r9617 | bugman | 2009-10-07 04:19:57 -0400 (Wed, 07 Oct 2009) | 3 lines
Renamed generic_intensity2.txt to generic_intensity.txt.
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r9618 | bugman | 2009-10-07 04:28:59 -0400 (Wed, 07 Oct 2009) | 3 lines
Redesigned the test_read_peak_list_generic() system test.
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r9619 | bugman | 2009-10-07 04:29:47 -0400 (Wed, 07 Oct 2009) | 5 lines
Deleted the test_read_peak_list_generic2() system test.
This was just duplicating test_read_peak_list_generic().
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r9620 | bugman | 2009-10-07 04:30:21 -0400 (Wed, 07 Oct 2009) | 3 lines
Commented out the header.
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r9621 | bugman | 2009-10-07 05:25:42 -0400 (Wed, 07 Oct 2009) | 3 lines
Added the new error class RelaxArgNotNoneError for when an argument should be None.
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r9622 | bugman | 2009-10-07 05:28:35 -0400 (Wed, 07 Oct 2009) | 6 lines
Complete redesign of the generic_fns.spectrum module.
This significantly simplifies the code base (much less jumping between functions) and prepares for
the generically formatted file support.
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r9623 | bugman | 2009-10-07 05:35:45 -0400 (Wed, 07 Oct 2009) | 3 lines
Fixes for the test_read_peak_list_generic() system test.
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r9624 | bugman | 2009-10-07 05:36:44 -0400 (Wed, 07 Oct 2009) | 5 lines
Rewrote the intensity_generic() function.
This is now much simpler (5 lines of code).
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r9625 | bugman | 2009-10-07 05:39:24 -0400 (Wed, 07 Oct 2009) | 3 lines
More fixes for the test_read_peak_list_generic(). It now passes!
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r9626 | bugman | 2009-10-07 06:44:06 -0400 (Wed, 07 Oct 2009) | 3 lines
Removed some unused imports.
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r9627 | bugman | 2009-10-07 08:29:55 -0400 (Wed, 07 Oct 2009) | 6 lines
Wrote the relax_io.write_spin_data_file() function.
This writes spin specific data to a file (can be STDOUT). It will replace the write_header()
and write_body() functions of generic_fns.sequence.
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r9628 | bugman | 2009-10-07 08:31:29 -0400 (Wed, 07 Oct 2009) | 5 lines
Deleted the write_body(), write_header(), and write_line() functions from generic_fns.sequence.
This should accelerate the switch to relax_io.write_spin_data_file().
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r9629 | bugman | 2009-10-07 08:34:52 -0400 (Wed, 07 Oct 2009) | 3 lines
Import fixes by shifting to relax_io.write_spin_data_file().
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r9630 | bugman | 2009-10-07 08:41:02 -0400 (Wed, 07 Oct 2009) | 3 lines
Renamed read_spin_data_file() to read_spin_data() and write_spin_data_file() to write_spin_data().
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r9631 | bugman | 2009-10-07 08:59:07 -0400 (Wed, 07 Oct 2009) | 3 lines
Removed all dependence on write_body() and write_header() from the sequence module.
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r9632 | bugman | 2009-10-07 09:04:47 -0400 (Wed, 07 Oct 2009) | 3 lines
Converted the load_spins() function to use relax_io.write_spin_data().
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r9633 | bugman | 2009-10-07 09:07:56 -0400 (Wed, 07 Oct 2009) | 3 lines
Spacing fixes for write_spin_data().
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r9634 | bugman | 2009-10-07 09:17:25 -0400 (Wed, 07 Oct 2009) | 3 lines
Modified write_spin_data() to dynamically modify the spin ID column widths if the data is too long.
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r9635 | bugman | 2009-10-07 11:49:06 -0400 (Wed, 07 Oct 2009) | 3 lines
Missing import.
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r9636 | bugman | 2009-10-07 11:53:33 -0400 (Wed, 07 Oct 2009) | 3 lines
Converted the file keyword args to read_ and write_spin_data() to normal args.
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r9637 | bugman | 2009-10-07 11:56:40 -0400 (Wed, 07 Oct 2009) | 5 lines
Fixed the write_spin_data() from read().
The file arg must be given, and now as this is set to sys.stdout, STDOUT redirection works again.
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r9638 | bugman | 2009-10-07 12:00:19 -0400 (Wed, 07 Oct 2009) | 5 lines
Fix for the test_write_protein_sequence() unit test.
The output file format is now a little different.
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r9639 | bugman | 2009-10-07 12:16:52 -0400 (Wed, 07 Oct 2009) | 3 lines
Converted value.write() to user relax_io.write_spin_data().
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r9640 | bugman | 2009-10-07 12:18:11 -0400 (Wed, 07 Oct 2009) | 5 lines
Converted the read_spin_data() file arg back to a keyword.
The file_data arg can be used instead!
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r9641 | bugman | 2009-10-07 12:21:07 -0400 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (http://gna.org/bugs/?14464).
The problem fix here (only one of a few) was the new design of the user function classes. This was
breaking the docstring fetching script used to generate the relax manual.
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r9642 | bugman | 2009-10-07 12:24:40 -0400 (Wed, 07 Oct 2009) | 3 lines
Modified the output of the user function docstring parsing.
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r9643 | bugman | 2009-10-07 12:48:19 -0400 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (https://gna.org/bugs/?14464).
Fix for the PDF manual compilation - os.rename() is being used instead of shutil.move(). No idea
why shutil.move() was no longer working?!?
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r9644 | bugman | 2009-10-07 13:32:19 -0400 (Wed, 07 Oct 2009) | 3 lines
Fixed a call to write_spin_data() which should pass in sys.stdout as the file.
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r9645 | bugman | 2009-10-07 13:33:53 -0400 (Wed, 07 Oct 2009) | 3 lines
Prevented __find_bonded_atoms() from connecting protons in the internal PDB reader.
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r9646 | bugman | 2009-10-07 13:46:04 -0400 (Wed, 07 Oct 2009) | 5 lines
Fix for the retrieval of bond vectors for the N-state model.
The object could also be called 'bond_vect' rather than 'xh_vect'.
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r9647 | bugman | 2009-10-07 13:56:59 -0400 (Wed, 07 Oct 2009) | 3 lines
More fixes for the N-state model for the 'xh_vect' and 'bond_vect' mix up.
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r9648 | bugman | 2009-10-07 13:57:27 -0400 (Wed, 07 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9649 | semor | 2009-10-07 14:30:34 -0400 (Wed, 07 Oct 2009) | 7 lines
Modified the sequence.read() entries in order to reflect the new design.
The sequence.read() function now absolutely needs an argument for res_num_col. Hence, this argument
is now shown in the sample script in order to avoid the users lose time figuring out where their
script went bad...
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r9650 | semor | 2009-10-07 14:37:57 -0400 (Wed, 07 Oct 2009) | 8 lines
Modified the relax_data.read() entries in order to reflect the new design.
The relax_data.read() function now absolutely needs arguments for 'res_num_col', 'data_col' and
'error_col'. Hence, this argument is now shown in the sample script in order to avoid the users
lose time figuring out where their script went bad...
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r9651 | bugman | 2009-10-08 03:24:50 -0400 (Thu, 08 Oct 2009) | 8 lines
Significant improvements to the __find_bonded_atoms() method.
The maximum number of bonds an element can have is now taken into account so that protons are not
thought to be attached to 2 carbons within a 2 Angstrom radius! The atoms closest to the atom of
interest are now connected. Geometry constraints or other advanced techniques are not yet
implemented.
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r9652 | bugman | 2009-10-08 03:45:46 -0400 (Thu, 08 Oct 2009) | 3 lines
Modified the message printed by RelaxInvalidSeqError.
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r9653 | bugman | 2009-10-08 03:46:39 -0400 (Thu, 08 Oct 2009) | 3 lines
read_spin_data() now gives a warning rather than an error if the sequence data in a line is bad.
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r9654 | bugman | 2009-10-08 04:01:18 -0400 (Thu, 08 Oct 2009) | 6 lines
Improvements to the read_spin_data() function.
The data checks now occur during the yield loop. This allows for invalid lines to be skipped while
those with real data are used.
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r9655 | bugman | 2009-10-08 04:24:34 -0400 (Thu, 08 Oct 2009) | 6 lines
Bug fix for __find_bonded_atoms().
The loop over the maximum number of connect atoms was failing if the number of 'connected' atoms was
less.
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r9656 | bugman | 2009-10-08 04:49:12 -0400 (Thu, 08 Oct 2009) | 3 lines
Removed some debugging print statements.
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r9657 | bugman | 2009-10-08 06:30:16 -0400 (Thu, 08 Oct 2009) | 3 lines
Created the structure.delete() user function for deleting all structural information from the cdp.
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r9658 | bugman | 2009-10-08 06:42:22 -0400 (Thu, 08 Oct 2009) | 3 lines
Modified the structure.delete() user function to remove all spin specific structural data.
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r9696 | semor | 2009-10-09 08:44:40 -0400 (Fri, 09 Oct 2009) | 10 lines
Improved the error handling for AICc model selection.
The code now tells users with too small datasets (n<=k) why AICc model selection does not work in
their situation.
This follows a discussion started at:
https://mail.gna.org/public/relax-devel/2009-10/msg00015.html
(# Message-id: <4ACD6F60.7060102@...>)
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r9700 | bugman | 2009-10-09 12:00:30 -0400 (Fri, 09 Oct 2009) | 3 lines
Added a copyright notice and a function for returning the SVN revision number to the version module.
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r9706 | bugman | 2009-10-09 12:47:13 -0400 (Fri, 09 Oct 2009) | 3 lines
Added a function to get the SVN URL.
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r9709 | bugman | 2009-10-09 14:06:21 -0400 (Fri, 09 Oct 2009) | 3 lines
Comment fix.
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r9747 | bugman | 2009-10-12 10:00:39 -0400 (Mon, 12 Oct 2009) | 3 lines
__linear_ave() is no longer a private function.
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r9794 | bugman | 2009-10-27 05:59:25 -0400 (Tue, 27 Oct 2009) | 7 lines
Added user variable checking to the full_analysis.py script.
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-10/msg00009.html (Message-id:
<E45CDDF4A4E54B34A36BFBA62E6BFF20@...>).
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r9799 | bugman | 2009-10-27 10:24:25 -0400 (Tue, 27 Oct 2009) | 3 lines
Fix for the frame order grid search.
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r9800 | bugman | 2009-10-27 10:25:08 -0400 (Tue, 27 Oct 2009) | 3 lines
Created the structure.get_pos() user function for extracting atomic positions.
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r9829 | bugman | 2009-10-28 06:47:59 -0400 (Wed, 28 Oct 2009) | 3 lines
Added functions for determining the element name and isotope number from an isotope name.
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r9831 | bugman | 2009-10-28 06:51:19 -0400 (Wed, 28 Oct 2009) | 3 lines
Bug fix for the new isotope functions.
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r9834 | bugman | 2009-10-28 08:48:59 -0400 (Wed, 28 Oct 2009) | 3 lines
Added checks for insufficient or single field strength relaxation data.
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