relax SVN archive

Made the structure system tests more compatible with non-Unix operating systems.

Merged revisions 9236-9246,9248-9271 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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.
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r9237 | bugman | 2009-07-15 17:39:16 +0200 (Wed, 15 Jul 2009) | 3 lines

Modified return_spin() to handle multiple spin ID strings.
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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.
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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().
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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!
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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.
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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.
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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.
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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.
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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.
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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.
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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.
........

Created the bmrblib.kinetics.general_relaxation module.

Much work is still to be done.

Reverted r9272 as this was a mistake! It was a mix of svnmerge and other changes.

The command used was:
svn merge -r9272:9271 .

Merged revisions 9236-9246,9248-9271 via svnmerge from
svn+ssh://bugman@.../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.
........
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.
........
r9244 | bugman | 2009-07-15 19:20:10 +0200 (Wed, 15 Jul 2009) | 3 lines

Fix for the N-state model when N = 1.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........

Added comprehensive checks for the creation of the diffusion tensor PDB representations.

The sphere and spheroid PDB files are now checked, line for line.

The diffusion tensor copying system test is now more comprehensive.

The test_create_diff_tensor_pdb_ellipsoid() system test has been made more vigorous.

The copy operations are now better tested.

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'.

Fix for the test_copy() system test.

The wrong indices were being checked.