[r10115]
by
bugman
Merged revisions 10108-10110 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10108 | bugman | 2010-01-05 19:10:19 +0100 (Tue, 05 Jan 2010) | 5 lines
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
........
r10109 | bugman | 2010-01-05 19:12:18 +0100 (Tue, 05 Jan 2010) | 9 lines
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
........
r10110 | bugman | 2010-01-05 19:14:09 +0100 (Tue, 05 Jan 2010) | 5 lines
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
........
|
2010-01-06 16:56:32
|
Tree
|
[r10114]
by
bugman
Merged revisions 10108-10110 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10108 | bugman | 2010-01-05 19:10:19 +0100 (Tue, 05 Jan 2010) | 5 lines
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
........
r10109 | bugman | 2010-01-05 19:12:18 +0100 (Tue, 05 Jan 2010) | 9 lines
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
........
r10110 | bugman | 2010-01-05 19:14:09 +0100 (Tue, 05 Jan 2010) | 5 lines
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
........
|
2010-01-06 16:56:30
|
Tree
|
[r10113]
by
bugman
Merged revisions 10108-10110 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10108 | bugman | 2010-01-05 19:10:19 +0100 (Tue, 05 Jan 2010) | 5 lines
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
........
r10109 | bugman | 2010-01-05 19:12:18 +0100 (Tue, 05 Jan 2010) | 9 lines
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
........
r10110 | bugman | 2010-01-05 19:14:09 +0100 (Tue, 05 Jan 2010) | 5 lines
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
........
|
2010-01-06 16:56:26
|
Tree
|
[r10112]
by
bugman
Merged revisions 10108-10110 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10108 | bugman | 2010-01-05 19:10:19 +0100 (Tue, 05 Jan 2010) | 5 lines
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
........
r10109 | bugman | 2010-01-05 19:12:18 +0100 (Tue, 05 Jan 2010) | 9 lines
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
........
r10110 | bugman | 2010-01-05 19:14:09 +0100 (Tue, 05 Jan 2010) | 5 lines
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
........
|
2010-01-06 16:55:35
|
Tree
|
[r10111]
by
bugman
Merged revisions 10108-10110 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10108 | bugman | 2010-01-05 19:10:19 +0100 (Tue, 05 Jan 2010) | 5 lines
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
........
r10109 | bugman | 2010-01-05 19:12:18 +0100 (Tue, 05 Jan 2010) | 9 lines
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
........
r10110 | bugman | 2010-01-05 19:14:09 +0100 (Tue, 05 Jan 2010) | 5 lines
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
........
|
2010-01-06 16:42:25
|
Tree
|
[r10110]
by
bugman
Bug fix for the euler_xyx_to_R() function.
The R[y, x] element was incorrect!!!
|
2010-01-05 18:14:09
|
Tree
|
[r10109]
by
bugman
The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
This is from Euler Angle Conversion. Graphics Gems IV. Paul Heckbert (ed.). Academic Press, 1994,
ISBN: 0123361567. pp. 222-229.
All of the R_to_euler_ijk() methods have been converted to call the new R_to_euler() method which
implements this.
|
2010-01-05 18:12:18
|
Tree
|
[r10108]
by
bugman
Fixes for all the test_R_to_euler_ijk() unit tests.
The print out has also been significantly improved.
|
2010-01-05 18:10:19
|
Tree
|
[r10107]
by
bugman
Merged revisions 10047-10084,10086-10091,10094-10102 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10047 | bugman | 2009-12-02 14:50:08 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 3 unit tests for the new maths_fns.rotation_matrix.reverse_euler_zyz() function.
This checks the double reversion to see if the original angles come back.
........
r10048 | bugman | 2009-12-02 14:52:56 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 6 more unit tests for the new maths_fns.rotation_matrix.reverse_euler_zyz() function.
This gives better coverage of the problematic areas.
........
r10049 | bugman | 2009-12-02 15:06:17 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 8 unit tests for maths_fns.rotation_matrix.R_to_euler_zyz().
This covers the problematic Euler angles of 0.
........
r10050 | bugman | 2009-12-02 16:18:53 +0100 (Wed, 02 Dec 2009) | 6 lines
Bug fix for maths_fns.rotation_matrix.R_to_euler_zyz() for the case where beta = 0.
This uses the sub-matrix components of the z rotation to put the full rotation into alpha (gamma
is zero).
........
r10051 | bugman | 2009-12-02 16:21:43 +0100 (Wed, 02 Dec 2009) | 3 lines
Expanded the maths_fns.rotation_matrix.R_to_euler_zyz() docstring to document the beta = 0 case.
........
r10052 | bugman | 2009-12-02 16:25:33 +0100 (Wed, 02 Dec 2009) | 3 lines
Fixed the Euler angle conversion unit tests for the beta = 0 degeneracy.
........
r10053 | bugman | 2009-12-03 17:51:22 +0100 (Thu, 03 Dec 2009) | 3 lines
Modified the alignment tensor print out to be more compact.
........
r10054 | bugman | 2009-12-04 15:55:05 +0100 (Fri, 04 Dec 2009) | 3 lines
Additional modifications to the alignment tensor print out to show more information.
........
r10055 | bugman | 2009-12-04 16:07:43 +0100 (Fri, 04 Dec 2009) | 18 lines
Expanded the alignment tensor object.
The 'tensor' and 'tensor_diag' objects are no more. New structures include:
A
A_5D
A_diag
eigvals
S
S_5D
S_diag
P
P_5D
P_diag
'Aii_unit', where i is one of x, y, or z has been renamed to 'unit_i'. 'rotation' has been renamed
to 'R'.
........
r10056 | bugman | 2009-12-04 16:10:57 +0100 (Fri, 04 Dec 2009) | 3 lines
Alphabetical reordering of the functions.
........
r10057 | bugman | 2009-12-04 17:16:57 +0100 (Fri, 04 Dec 2009) | 3 lines
Cut and paste bug fix for the alignment tensor diagonalisation function calc_A_diag().
........
r10058 | bugman | 2009-12-04 17:25:37 +0100 (Fri, 04 Dec 2009) | 3 lines
N-state model fix for the alignment tensor object renaming.
........
r10059 | bugman | 2009-12-04 17:26:39 +0100 (Fri, 04 Dec 2009) | 3 lines
Fixes for the alignment tensor unit tests (due to object renaming).
........
r10060 | bugman | 2009-12-04 17:41:09 +0100 (Fri, 04 Dec 2009) | 3 lines
Added the anisotropic Aa and rhombic Ar parameters to the alignment tensor object.
........
r10061 | bugman | 2009-12-04 17:44:21 +0100 (Fri, 04 Dec 2009) | 5 lines
Renamed the rotation matrix back to 'rotation'.
This is because R will be used as the 'R' alignment tensor parameter.
........
r10062 | bugman | 2009-12-04 17:56:26 +0100 (Fri, 04 Dec 2009) | 3 lines
Added the rhombicity R and asymmetry eta parameters to the alignment tensor object.
........
r10063 | bugman | 2009-12-04 18:18:52 +0100 (Fri, 04 Dec 2009) | 3 lines
Added geometric parameters to the align_tensor.display() print out.
........
r10064 | bugman | 2009-12-07 08:33:06 +0100 (Mon, 07 Dec 2009) | 3 lines
Bug fixes for the calculation of the anisotropic and rhombic alignment tensor parameters.
........
r10065 | bugman | 2009-12-07 10:57:35 +0100 (Mon, 07 Dec 2009) | 5 lines
Bug fix for the calc_rotation() function.
The axis permutation for | Azz | >= | Ayy | >= | Axx | is now correctly performed.
........
r10066 | bugman | 2009-12-07 19:41:44 +0100 (Mon, 07 Dec 2009) | 10 lines
Added all the 12 Euler angle notations to the rotation matrix module.
The methods added include:
axis_angle_to_euler_ijk(),
euler_ijk_to_axis_angle(),
euler_ijk_to_R(),
R_to_euler_ijk(),
reverse_euler_ijk().
........
r10067 | bugman | 2009-12-08 10:55:40 +0100 (Tue, 08 Dec 2009) | 5 lines
Converted all the R_to_euler_zyz() unit tests into one.
This will simplify the setup of the unit tests for the other Euler angle conventions.
........
r10068 | bugman | 2009-12-08 11:03:20 +0100 (Tue, 08 Dec 2009) | 3 lines
Wrote all the test_R_to_euler_ijk() unit tests to cover all Euler angle conventions.
........
r10069 | bugman | 2009-12-08 11:21:26 +0100 (Tue, 08 Dec 2009) | 3 lines
Modified the check_return_conversion() method to print out more information for debugging.
........
r10070 | bugman | 2009-12-08 14:05:08 +0100 (Tue, 08 Dec 2009) | 5 lines
Fix for the R_to_euler_zyx() function.
The beta = 0 problem point does not exist!
........
r10071 | bugman | 2009-12-08 15:44:24 +0100 (Tue, 08 Dec 2009) | 3 lines
The atomic position can now be directly supplied to pcs.centre().
........
r10072 | bugman | 2009-12-08 16:40:17 +0100 (Tue, 08 Dec 2009) | 3 lines
The arg_check.is_num_list() now will allow numpy arrays.
........
r10073 | bugman | 2009-12-08 16:40:42 +0100 (Tue, 08 Dec 2009) | 3 lines
The PCS centre can now be forcefully overwritten.
........
r10074 | bugman | 2009-12-08 16:43:17 +0100 (Tue, 08 Dec 2009) | 3 lines
The PCS centre position can now be a numpy array.
........
r10075 | bugman | 2009-12-09 10:21:33 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a verbosity arg to pcs.centre() to allow this thing to be silenced!
........
r10076 | bugman | 2009-12-09 11:21:30 +0100 (Wed, 09 Dec 2009) | 5 lines
Added more problematic test cases to the euler angle to rotation matrix and back again unit tests.
The problematic beta = -pi/2, pi/2, pi cases.
........
r10077 | bugman | 2009-12-09 11:25:36 +0100 (Wed, 09 Dec 2009) | 3 lines
Removed the beta = -pi/2 checks, as beta is between 0 and pi.
........
r10078 | bugman | 2009-12-09 11:25:58 +0100 (Wed, 09 Dec 2009) | 3 lines
Fixed the problem case for R_to_euler_zxy().
........
r10079 | bugman | 2009-12-09 12:01:01 +0100 (Wed, 09 Dec 2009) | 5 lines
Fix for the test_R_to_euler_zxy() unit test for beta = pi/2.
The alpha and gamma angles subtract in this case.
........
r10080 | bugman | 2009-12-09 19:05:08 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a check to test_R_to_euler_zyz() for negative beta angles.
........
r10081 | bugman | 2009-12-09 19:08:04 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a check to test_R_to_euler_zyz() for beta angles > pi.
........
r10082 | bugman | 2009-12-10 16:20:52 +0100 (Thu, 10 Dec 2009) | 3 lines
Fix for the PCS back calculation for when no weights are given.
........
r10083 | bugman | 2009-12-10 17:15:10 +0100 (Thu, 10 Dec 2009) | 6 lines
Big bug fix for the RDC and PCS calculations used in the fixed population N-state models.
The last weight, if supplied, was being converted to zero (1 - sum(weights)) hence the last
state/structure was not being included and the population sum was not 1!
........
r10084 | bugman | 2009-12-10 17:18:42 +0100 (Thu, 10 Dec 2009) | 3 lines
The temperature value is now converted into a float before storage.
........
r10086 | bugman | 2009-12-11 17:26:59 +0100 (Fri, 11 Dec 2009) | 3 lines
Added the back end to the rdc.back_calc() user function!
........
r10087 | bugman | 2009-12-14 11:38:04 +0100 (Mon, 14 Dec 2009) | 3 lines
Modified all the specific analysis overfit_deselect() methods to warn when spins are deselected.
........
r10088 | bugman | 2009-12-14 11:38:47 +0100 (Mon, 14 Dec 2009) | 3 lines
Missing 'warnings' import.
........
r10089 | bugman | 2009-12-14 11:42:51 +0100 (Mon, 14 Dec 2009) | 3 lines
Improved the warning messages for over-fit spin deselection.
........
r10090 | bugman | 2009-12-14 11:48:49 +0100 (Mon, 14 Dec 2009) | 7 lines
Fix for bug #14885 (https://gna.org/bugs/?14885).
This was reported by Tiago Pais (tpais att itqb dot unl dot pt).
The problem was a few missing user functions in the sample script.
........
r10091 | bugman | 2009-12-14 13:16:58 +0100 (Mon, 14 Dec 2009) | 3 lines
Fix for the call to spin.name(). The keyword arg must be specified as 'name'!
........
r10094 | bugman | 2009-12-14 17:25:31 +0100 (Mon, 14 Dec 2009) | 5 lines
Fixes for the overfit_deselect() methods.
The spin_id was not being returned by the spin_loop().
........
r10095 | bugman | 2009-12-14 17:53:08 +0100 (Mon, 14 Dec 2009) | 5 lines
Added a catch for bug #14941 (https://gna.org/bugs/index.php?14941) to the relax system tests.
This uses truncated data (first 2 residues), also randomised, to reproduce the bug.
........
r10096 | bugman | 2009-12-14 17:59:17 +0100 (Mon, 14 Dec 2009) | 9 lines
Fix for bug #14941 (https://gna.org/bugs/index.php?14941).
This was reported by Mikaela Stewart (mikaela dot stewart att gmail dot com).
The problem was that the global_flag variable was not being passed into the analysis specific API
duplicate_data() method so that only the first spin's data was being copied, all other spin
containers were empty.
........
r10097 | bugman | 2009-12-15 15:19:09 +0100 (Tue, 15 Dec 2009) | 5 lines
align_tensor.display() now prints the magnetic susceptibility tensor.
This only occurs if the field strength and temperature are given.
........
r10098 | bugman | 2010-01-04 17:14:23 +0100 (Mon, 04 Jan 2010) | 5 lines
Added a system test for catching bug #15050 (https://gna.org/bugs/index.php?15050).
This bug was submitted by Tiago Pais (https://gna.org/users/tpais).
........
r10099 | bugman | 2010-01-04 17:15:06 +0100 (Mon, 04 Jan 2010) | 3 lines
Shifted the bug #15050 system test script to the correct directory.
........
r10100 | bugman | 2010-01-04 17:21:20 +0100 (Mon, 04 Jan 2010) | 3 lines
Docstring fix for test_bug_15050().
........
r10101 | bugman | 2010-01-04 17:34:36 +0100 (Mon, 04 Jan 2010) | 9 lines
Fix for bug #15050 (https://gna.org/bugs/index.php?15050).
This bug was submitted by Tiago Pais (https://gna.org/users/tpais).
The _determine_model_type() method has been modified to return None when all parameters are fixed
(or if there no selected spins and no diffusion tensor). The model-free minimisation method has
also been modified to handle this.
........
r10102 | bugman | 2010-01-04 17:42:00 +0100 (Mon, 04 Jan 2010) | 3 lines
Copyright year updates.
........
|
2010-01-04 16:56:57
|
Tree
|
[r10106]
by
bugman
Merged revisions 10047-10084,10086-10091,10094-10102 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r10047 | bugman | 2009-12-02 14:50:08 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 3 unit tests for the new maths_fns.rotation_matrix.reverse_euler_zyz() function.
This checks the double reversion to see if the original angles come back.
........
r10048 | bugman | 2009-12-02 14:52:56 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 6 more unit tests for the new maths_fns.rotation_matrix.reverse_euler_zyz() function.
This gives better coverage of the problematic areas.
........
r10049 | bugman | 2009-12-02 15:06:17 +0100 (Wed, 02 Dec 2009) | 5 lines
Added 8 unit tests for maths_fns.rotation_matrix.R_to_euler_zyz().
This covers the problematic Euler angles of 0.
........
r10050 | bugman | 2009-12-02 16:18:53 +0100 (Wed, 02 Dec 2009) | 6 lines
Bug fix for maths_fns.rotation_matrix.R_to_euler_zyz() for the case where beta = 0.
This uses the sub-matrix components of the z rotation to put the full rotation into alpha (gamma
is zero).
........
r10051 | bugman | 2009-12-02 16:21:43 +0100 (Wed, 02 Dec 2009) | 3 lines
Expanded the maths_fns.rotation_matrix.R_to_euler_zyz() docstring to document the beta = 0 case.
........
r10052 | bugman | 2009-12-02 16:25:33 +0100 (Wed, 02 Dec 2009) | 3 lines
Fixed the Euler angle conversion unit tests for the beta = 0 degeneracy.
........
r10053 | bugman | 2009-12-03 17:51:22 +0100 (Thu, 03 Dec 2009) | 3 lines
Modified the alignment tensor print out to be more compact.
........
r10054 | bugman | 2009-12-04 15:55:05 +0100 (Fri, 04 Dec 2009) | 3 lines
Additional modifications to the alignment tensor print out to show more information.
........
r10055 | bugman | 2009-12-04 16:07:43 +0100 (Fri, 04 Dec 2009) | 18 lines
Expanded the alignment tensor object.
The 'tensor' and 'tensor_diag' objects are no more. New structures include:
A
A_5D
A_diag
eigvals
S
S_5D
S_diag
P
P_5D
P_diag
'Aii_unit', where i is one of x, y, or z has been renamed to 'unit_i'. 'rotation' has been renamed
to 'R'.
........
r10056 | bugman | 2009-12-04 16:10:57 +0100 (Fri, 04 Dec 2009) | 3 lines
Alphabetical reordering of the functions.
........
r10057 | bugman | 2009-12-04 17:16:57 +0100 (Fri, 04 Dec 2009) | 3 lines
Cut and paste bug fix for the alignment tensor diagonalisation function calc_A_diag().
........
r10058 | bugman | 2009-12-04 17:25:37 +0100 (Fri, 04 Dec 2009) | 3 lines
N-state model fix for the alignment tensor object renaming.
........
r10059 | bugman | 2009-12-04 17:26:39 +0100 (Fri, 04 Dec 2009) | 3 lines
Fixes for the alignment tensor unit tests (due to object renaming).
........
r10060 | bugman | 2009-12-04 17:41:09 +0100 (Fri, 04 Dec 2009) | 3 lines
Added the anisotropic Aa and rhombic Ar parameters to the alignment tensor object.
........
r10061 | bugman | 2009-12-04 17:44:21 +0100 (Fri, 04 Dec 2009) | 5 lines
Renamed the rotation matrix back to 'rotation'.
This is because R will be used as the 'R' alignment tensor parameter.
........
r10062 | bugman | 2009-12-04 17:56:26 +0100 (Fri, 04 Dec 2009) | 3 lines
Added the rhombicity R and asymmetry eta parameters to the alignment tensor object.
........
r10063 | bugman | 2009-12-04 18:18:52 +0100 (Fri, 04 Dec 2009) | 3 lines
Added geometric parameters to the align_tensor.display() print out.
........
r10064 | bugman | 2009-12-07 08:33:06 +0100 (Mon, 07 Dec 2009) | 3 lines
Bug fixes for the calculation of the anisotropic and rhombic alignment tensor parameters.
........
r10065 | bugman | 2009-12-07 10:57:35 +0100 (Mon, 07 Dec 2009) | 5 lines
Bug fix for the calc_rotation() function.
The axis permutation for | Azz | >= | Ayy | >= | Axx | is now correctly performed.
........
r10066 | bugman | 2009-12-07 19:41:44 +0100 (Mon, 07 Dec 2009) | 10 lines
Added all the 12 Euler angle notations to the rotation matrix module.
The methods added include:
axis_angle_to_euler_ijk(),
euler_ijk_to_axis_angle(),
euler_ijk_to_R(),
R_to_euler_ijk(),
reverse_euler_ijk().
........
r10067 | bugman | 2009-12-08 10:55:40 +0100 (Tue, 08 Dec 2009) | 5 lines
Converted all the R_to_euler_zyz() unit tests into one.
This will simplify the setup of the unit tests for the other Euler angle conventions.
........
r10068 | bugman | 2009-12-08 11:03:20 +0100 (Tue, 08 Dec 2009) | 3 lines
Wrote all the test_R_to_euler_ijk() unit tests to cover all Euler angle conventions.
........
r10069 | bugman | 2009-12-08 11:21:26 +0100 (Tue, 08 Dec 2009) | 3 lines
Modified the check_return_conversion() method to print out more information for debugging.
........
r10070 | bugman | 2009-12-08 14:05:08 +0100 (Tue, 08 Dec 2009) | 5 lines
Fix for the R_to_euler_zyx() function.
The beta = 0 problem point does not exist!
........
r10071 | bugman | 2009-12-08 15:44:24 +0100 (Tue, 08 Dec 2009) | 3 lines
The atomic position can now be directly supplied to pcs.centre().
........
r10072 | bugman | 2009-12-08 16:40:17 +0100 (Tue, 08 Dec 2009) | 3 lines
The arg_check.is_num_list() now will allow numpy arrays.
........
r10073 | bugman | 2009-12-08 16:40:42 +0100 (Tue, 08 Dec 2009) | 3 lines
The PCS centre can now be forcefully overwritten.
........
r10074 | bugman | 2009-12-08 16:43:17 +0100 (Tue, 08 Dec 2009) | 3 lines
The PCS centre position can now be a numpy array.
........
r10075 | bugman | 2009-12-09 10:21:33 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a verbosity arg to pcs.centre() to allow this thing to be silenced!
........
r10076 | bugman | 2009-12-09 11:21:30 +0100 (Wed, 09 Dec 2009) | 5 lines
Added more problematic test cases to the euler angle to rotation matrix and back again unit tests.
The problematic beta = -pi/2, pi/2, pi cases.
........
r10077 | bugman | 2009-12-09 11:25:36 +0100 (Wed, 09 Dec 2009) | 3 lines
Removed the beta = -pi/2 checks, as beta is between 0 and pi.
........
r10078 | bugman | 2009-12-09 11:25:58 +0100 (Wed, 09 Dec 2009) | 3 lines
Fixed the problem case for R_to_euler_zxy().
........
r10079 | bugman | 2009-12-09 12:01:01 +0100 (Wed, 09 Dec 2009) | 5 lines
Fix for the test_R_to_euler_zxy() unit test for beta = pi/2.
The alpha and gamma angles subtract in this case.
........
r10080 | bugman | 2009-12-09 19:05:08 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a check to test_R_to_euler_zyz() for negative beta angles.
........
r10081 | bugman | 2009-12-09 19:08:04 +0100 (Wed, 09 Dec 2009) | 3 lines
Added a check to test_R_to_euler_zyz() for beta angles > pi.
........
r10082 | bugman | 2009-12-10 16:20:52 +0100 (Thu, 10 Dec 2009) | 3 lines
Fix for the PCS back calculation for when no weights are given.
........
r10083 | bugman | 2009-12-10 17:15:10 +0100 (Thu, 10 Dec 2009) | 6 lines
Big bug fix for the RDC and PCS calculations used in the fixed population N-state models.
The last weight, if supplied, was being converted to zero (1 - sum(weights)) hence the last
state/structure was not being included and the population sum was not 1!
........
r10084 | bugman | 2009-12-10 17:18:42 +0100 (Thu, 10 Dec 2009) | 3 lines
The temperature value is now converted into a float before storage.
........
r10086 | bugman | 2009-12-11 17:26:59 +0100 (Fri, 11 Dec 2009) | 3 lines
Added the back end to the rdc.back_calc() user function!
........
r10087 | bugman | 2009-12-14 11:38:04 +0100 (Mon, 14 Dec 2009) | 3 lines
Modified all the specific analysis overfit_deselect() methods to warn when spins are deselected.
........
r10088 | bugman | 2009-12-14 11:38:47 +0100 (Mon, 14 Dec 2009) | 3 lines
Missing 'warnings' import.
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r10089 | bugman | 2009-12-14 11:42:51 +0100 (Mon, 14 Dec 2009) | 3 lines
Improved the warning messages for over-fit spin deselection.
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r10090 | bugman | 2009-12-14 11:48:49 +0100 (Mon, 14 Dec 2009) | 7 lines
Fix for bug #14885 (https://gna.org/bugs/?14885).
This was reported by Tiago Pais (tpais att itqb dot unl dot pt).
The problem was a few missing user functions in the sample script.
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r10091 | bugman | 2009-12-14 13:16:58 +0100 (Mon, 14 Dec 2009) | 3 lines
Fix for the call to spin.name(). The keyword arg must be specified as 'name'!
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r10094 | bugman | 2009-12-14 17:25:31 +0100 (Mon, 14 Dec 2009) | 5 lines
Fixes for the overfit_deselect() methods.
The spin_id was not being returned by the spin_loop().
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r10095 | bugman | 2009-12-14 17:53:08 +0100 (Mon, 14 Dec 2009) | 5 lines
Added a catch for bug #14941 (https://gna.org/bugs/index.php?14941) to the relax system tests.
This uses truncated data (first 2 residues), also randomised, to reproduce the bug.
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r10096 | bugman | 2009-12-14 17:59:17 +0100 (Mon, 14 Dec 2009) | 9 lines
Fix for bug #14941 (https://gna.org/bugs/index.php?14941).
This was reported by Mikaela Stewart (mikaela dot stewart att gmail dot com).
The problem was that the global_flag variable was not being passed into the analysis specific API
duplicate_data() method so that only the first spin's data was being copied, all other spin
containers were empty.
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r10097 | bugman | 2009-12-15 15:19:09 +0100 (Tue, 15 Dec 2009) | 5 lines
align_tensor.display() now prints the magnetic susceptibility tensor.
This only occurs if the field strength and temperature are given.
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r10098 | bugman | 2010-01-04 17:14:23 +0100 (Mon, 04 Jan 2010) | 5 lines
Added a system test for catching bug #15050 (https://gna.org/bugs/index.php?15050).
This bug was submitted by Tiago Pais (https://gna.org/users/tpais).
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r10099 | bugman | 2010-01-04 17:15:06 +0100 (Mon, 04 Jan 2010) | 3 lines
Shifted the bug #15050 system test script to the correct directory.
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r10100 | bugman | 2010-01-04 17:21:20 +0100 (Mon, 04 Jan 2010) | 3 lines
Docstring fix for test_bug_15050().
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r10101 | bugman | 2010-01-04 17:34:36 +0100 (Mon, 04 Jan 2010) | 9 lines
Fix for bug #15050 (https://gna.org/bugs/index.php?15050).
This bug was submitted by Tiago Pais (https://gna.org/users/tpais).
The _determine_model_type() method has been modified to return None when all parameters are fixed
(or if there no selected spins and no diffusion tensor). The model-free minimisation method has
also been modified to handle this.
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r10102 | bugman | 2010-01-04 17:42:00 +0100 (Mon, 04 Jan 2010) | 3 lines
Copyright year updates.
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2010-01-04 16:47:12
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