Author: bugman
Date: Fri Aug 14 11:42:11 2009
New Revision: 9313
URL: http://svn.gna.org/viewcvs/relax?rev=9313&view=rev
Log:
Merged revisions 9232-9312 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9236 | bugman | 2009-07-15 17:38:43 +0200 (Wed, 15 Jul 2009) | 3 lines
The rdc.read() user function now accepts the spin_id arg.
........
r9237 | bugman | 2009-07-15 17:39:16 +0200 (Wed, 15 Jul 2009) | 3 lines
Modified return_spin() to handle multiple spin ID strings.
........
r9238 | bugman | 2009-07-15 17:45:07 +0200 (Wed, 15 Jul 2009) | 3 lines
The pcs.read() user function also now accepts the spin_id argument.
........
r9239 | bugman | 2009-07-15 17:46:36 +0200 (Wed, 15 Jul 2009) | 5 lines
Removed the checks to see if the RDC or PCS data is already loaded.
Now data can be loaded sequentially by a few calls to rdc.read() and
pcs.read().
........
r9240 | bugman | 2009-07-15 18:00:33 +0200 (Wed, 15 Jul 2009) | 5 lines
Large improvements to the align_tensor.display() user function.
Now much more information is provided.
........
r9241 | bugman | 2009-07-15 18:25:39 +0200 (Wed, 15 Jul 2009) | 3 lines
Added the method names() to return a list of alignment tensor names.
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r9242 | bugman | 2009-07-15 18:26:17 +0200 (Wed, 15 Jul 2009) | 5 lines
Removed a check for the presence of the alignment tensor.
Now align_tensor.init() can be used to reset the tensor values.
........
r9243 | bugman | 2009-07-15 18:27:37 +0200 (Wed, 15 Jul 2009) | 3 lines
Only add a new tensor object if the tensor doesn't already exist.
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r9244 | bugman | 2009-07-15 19:20:10 +0200 (Wed, 15 Jul 2009) | 3 lines
Fix for the N-state model when N = 1.
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r9245 | bugman | 2009-07-15 20:13:25 +0200 (Wed, 15 Jul 2009) | 3 lines
Added the Saupe element eigenvalues to the align_tensor.display() print out.
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r9246 | bugman | 2009-07-15 20:25:23 +0200 (Wed, 15 Jul 2009) | 3 lines
The matrix_angles() function now avoids NaN problems through arccos of
numbers > 1.
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r9248 | bugman | 2009-07-16 19:45:33 +0200 (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.
........
r9249 | bugman | 2009-07-20 01:16:52 +0200 (Mon, 20 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()
........
r9250 | bugman | 2009-07-20 14:02:30 +0200 (Mon, 20 Jul 2009) | 3 lines
Switched to the internal PDB reader for removal of the reliance on
Scientific python.
........
r9251 | bugman | 2009-07-21 15:09:18 +0200 (Tue, 21 Jul 2009) | 3 lines
Added some MC simulation data and errors for the diffusion tensor system
tests.
........
r9252 | bugman | 2009-07-21 15:19:03 +0200 (Tue, 21 Jul 2009) | 3 lines
Split the system test of structure.create_diff_tensor_pdb() into 3 tests
for each diff type.
........
r9253 | bugman | 2009-07-21 15:54:30 +0200 (Tue, 21 Jul 2009) | 3 lines
Removed trailing whitespace.
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r9254 | bugman | 2009-07-21 16:28:02 +0200 (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.
........
r9255 | bugman | 2009-07-21 16:57:19 +0200 (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 16:59:29 +0200 (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.
........
r9257 | bugman | 2009-07-21 17:03:21 +0200 (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 17:03:43 +0200 (Tue, 21 Jul 2009) | 3 lines
Removed some debugging code.
........
r9259 | bugman | 2009-07-21 17:15:28 +0200 (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!
........
r9260 | bugman | 2009-07-21 17:40:29 +0200 (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.
........
r9261 | bugman | 2009-07-21 17:47:23 +0200 (Tue, 21 Jul 2009) | 3 lines
The ellipsoid diff tensor PDB file is now being checked, line for line.
........
r9262 | bugman | 2009-07-21 21:38:43 +0200 (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 21:39:44 +0200 (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.
........
r9264 | bugman | 2009-07-21 22:31:06 +0200 (Tue, 21 Jul 2009) | 3 lines
The spherical diffusion tensor system tests are now properly set up.
........
r9265 | bugman | 2009-07-21 22:32:04 +0200 (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.
........
r9266 | bugman | 2009-07-22 01:10:56 +0200 (Wed, 22 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 | 2009-07-22 01:20:52 +0200 (Wed, 22 Jul 2009) | 5 lines
Fix for the test_copy() system test.
The wrong indices were being checked.
........
r9268 | bugman | 2009-07-22 02:00:13 +0200 (Wed, 22 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'.
........
r9269 | bugman | 2009-07-22 02:12:55 +0200 (Wed, 22 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.
........
r9270 | bugman | 2009-07-22 09:40:26 +0200 (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 11:23:10 +0200 (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.
........
r9276 | bugman | 2009-08-12 13:06:51 +0200 (Wed, 12 Aug 2009) | 3 lines
Made the structure system tests more compatible with non-Unix operating
systems.
........
r9277 | bugman | 2009-08-12 13:11:27 +0200 (Wed, 12 Aug 2009) | 3 lines
Made get_file_path() and mkdir_nofail() compatible with non-Unix systems.
........
r9278 | bugman | 2009-08-12 13:16:06 +0200 (Wed, 12 Aug 2009) | 3 lines
Made the full_analysis.py script more compatible with non-Unix operating
systems.
........
r9279 | bugman | 2009-08-12 13:18:30 +0200 (Wed, 12 Aug 2009) | 3 lines
Fix for test_load_scientific_results(). The Unix paths are used in the
results file!
........
r9280 | bugman | 2009-08-12 13:23:15 +0200 (Wed, 12 Aug 2009) | 3 lines
Non-Unix os fix.
........
r9281 | bugman | 2009-08-12 13:54:53 +0200 (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 14:25:49 +0200 (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 14:38:00 +0200 (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 14:53:54 +0200 (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 15:02:38 +0200 (Wed, 12 Aug 2009) | 3 lines
Removed a reference to the '..' dir.
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r9286 | bugman | 2009-08-12 15:05:03 +0200 (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 15:34:50 +0200 (Wed, 12 Aug 2009) | 3 lines
Caught a NaN problem in __q_factors_rdc() causing a system test to fail in
Windows.
........
r9288 | bugman | 2009-08-12 18:57:21 +0200 (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!
........
r9290 | bugman | 2009-08-12 20:04:53 +0200 (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@xxxxxxxxxxx/svn/relax/tags/1.2.15 .
........
r9292 | bugman | 2009-08-13 15:20:47 +0200 (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.
........
r9303 | bugman | 2009-08-14 10:49:12 +0200 (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 10:51:09 +0200 (Fri, 14 Aug 2009) | 3 lines
Converted a number of flags from int to bool.
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r9305 | bugman | 2009-08-14 11:04:30 +0200 (Fri, 14 Aug 2009) | 3 lines
More changes to the release checklist document.
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r9306 | bugman | 2009-08-14 11:06:06 +0200 (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 11:19:20 +0200 (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.
........
r9308 | bugman | 2009-08-14 11:25:29 +0200 (Fri, 14 Aug 2009) | 3 lines
Created a directory for holding miscellaneous scripts for developers.
........
r9309 | bugman | 2009-08-14 11:25:55 +0200 (Fri, 14 Aug 2009) | 3 lines
Shifted the python version checking script.
........
r9310 | bugman | 2009-08-14 11:28:20 +0200 (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 11:37:47 +0200 (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.
........
Added:
branches/cst/scripts/
- copied from r9311, 1.3/scripts/
branches/cst/test_suite/shared_data/structures/diff_tensors/
- copied from r9311, 1.3/test_suite/shared_data/structures/diff_tensors/
branches/cst/test_suite/unit_tests/_maths_fns/test_kronecker_product.py
- copied unchanged from r9311,
1.3/test_suite/unit_tests/_maths_fns/test_kronecker_product.py
Modified:
branches/cst/ (props changed)
branches/cst/data/align_tensor.py
branches/cst/data/data_classes.py
branches/cst/data/diff_tensor.py
branches/cst/docs/CHANGES
branches/cst/docs/Release_Checklist
branches/cst/generic_fns/align_tensor.py
branches/cst/generic_fns/dasha.py
branches/cst/generic_fns/mol_res_spin.py
branches/cst/generic_fns/palmer.py
branches/cst/generic_fns/pcs.py
branches/cst/generic_fns/rdc.py
branches/cst/generic_fns/structure/geometric.py
branches/cst/generic_fns/structure/internal.py
branches/cst/maths_fns/kronecker_product.py
branches/cst/maths_fns/n_state_model.py
branches/cst/prompt/interpreter.py
branches/cst/prompt/pcs.py
branches/cst/prompt/rdc.py
branches/cst/relax_io.py
branches/cst/sample_scripts/full_analysis.py
branches/cst/sample_scripts/xh_vector_dist.py
branches/cst/scons/manuals.py
branches/cst/specific_fns/n_state_model.py
branches/cst/test_suite/shared_data/align_data/CaM/generate_data.py
branches/cst/test_suite/shared_data/align_data/CaM/pre_bleach.py
branches/cst/test_suite/shared_data/saved_states/create_peak_heights_T2_ncyc1.py
branches/cst/test_suite/shared_data/structures/generate_str_scientific_results.py
branches/cst/test_suite/system_tests/angles.py
branches/cst/test_suite/system_tests/consistency_tests.py
branches/cst/test_suite/system_tests/dasha.py
branches/cst/test_suite/system_tests/diffusion_tensor.py
branches/cst/test_suite/system_tests/generic.py
branches/cst/test_suite/system_tests/jw_mapping.py
branches/cst/test_suite/system_tests/load_spins.py
branches/cst/test_suite/system_tests/model_elimination.py
branches/cst/test_suite/system_tests/model_free.py
branches/cst/test_suite/system_tests/model_selection.py
branches/cst/test_suite/system_tests/n_state_model.py
branches/cst/test_suite/system_tests/noe.py
branches/cst/test_suite/system_tests/noe_restraints.py
branches/cst/test_suite/system_tests/palmer.py
branches/cst/test_suite/system_tests/peak_lists.py
branches/cst/test_suite/system_tests/relax_fit.py
branches/cst/test_suite/system_tests/results.py
branches/cst/test_suite/system_tests/scripts/1UBQ_relax_fit.py
branches/cst/test_suite/system_tests/scripts/align_fit.py
branches/cst/test_suite/system_tests/scripts/angles.py
branches/cst/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
branches/cst/test_suite/system_tests/scripts/consistency_tests.py
branches/cst/test_suite/system_tests/scripts/create_m4.py
branches/cst/test_suite/system_tests/scripts/dasha.py
branches/cst/test_suite/system_tests/scripts/jw_mapping.py
branches/cst/test_suite/system_tests/scripts/lactose_n_state.py
branches/cst/test_suite/system_tests/scripts/latex_mf_table.py
branches/cst/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
branches/cst/test_suite/system_tests/scripts/local_tm_model_elimination.py
branches/cst/test_suite/system_tests/scripts/noe.py
branches/cst/test_suite/system_tests/scripts/omp_model_free.py
branches/cst/test_suite/system_tests/scripts/opendx_s2_te_rex.py
branches/cst/test_suite/system_tests/scripts/opt_setup_S2_0_970_te_2048_Rex_0_149.py
branches/cst/test_suite/system_tests/scripts/palmer.py
branches/cst/test_suite/system_tests/scripts/palmer_omp.py
branches/cst/test_suite/system_tests/scripts/phthalic_acid_noes.py
branches/cst/test_suite/system_tests/scripts/relax_fit.py
branches/cst/test_suite/system_tests/scripts/tylers_peptide.py
branches/cst/test_suite/system_tests/scripts/xh_vector_dist.py
branches/cst/test_suite/system_tests/sequence.py
branches/cst/test_suite/system_tests/structure.py
branches/cst/test_suite/system_tests/unit_vectors.py
branches/cst/test_suite/test_suite_runner.py
branches/cst/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
branches/cst/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
branches/cst/test_suite/unit_tests/_maths_fns/__init__.py
branches/cst/test_suite/unit_tests/_specific_fns/_model_free/test_main.py
branches/cst/test_suite/unit_tests/relax_data_testing_base.py
branches/cst/test_suite/unit_tests/sequence_testing_base.py
branches/cst/test_suite/unit_tests/state_testing_base.py
branches/cst/test_suite/unit_tests/test_float.py
branches/cst/test_suite/unit_tests/test_relax_io.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/cst/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/data/align_tensor.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/data/data_classes.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/data/diff_tensor.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/CHANGES?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/Release_Checklist?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/align_tensor.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/dasha.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/mol_res_spin.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/palmer.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/pcs.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/rdc.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/structure/geometric.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/structure/internal.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/maths_fns/kronecker_product.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/kronecker_product.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/n_state_model.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/interpreter.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/pcs.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/rdc.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/relax_io.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/sample_scripts/full_analysis.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/sample_scripts/xh_vector_dist.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/sample_scripts/xh_vector_dist.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/scons/manuals.py?rev=9313&r1=9312&r2=9313&view=diff
Modified: branches/cst/specific_fns/n_state_model.py
[... 170 lines stripped ...]
r9313 - in /branches/cst: ./ data/ docs/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ scons/ scrip...