Author: bugman
Date: Mon Jan 4 17:47:12 2010
New Revision: 10106
URL: http://svn.gna.org/viewcvs/relax?rev=10106&view=rev
Log:
Merged revisions 10047-10084,10086-10091,10094-10102 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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.
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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'.
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r10056 | bugman | 2009-12-04 16:10:57 +0100 (Fri, 04 Dec 2009) | 3 lines
Alphabetical reordering of the functions.
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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().
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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().
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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.
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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.
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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.
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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!
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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().
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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.
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r10073 | bugman | 2009-12-08 16:40:42 +0100 (Tue, 08 Dec 2009) | 3 lines
The PCS centre can now be forcefully overwritten.
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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.
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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!
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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.
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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.
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r10078 | bugman | 2009-12-09 11:25:58 +0100 (Wed, 09 Dec 2009) | 3 lines
Fixed the problem case for R_to_euler_zxy().
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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.
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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.
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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.
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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.
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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!
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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.
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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!
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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.
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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.
........
Added:
branches/j_couplings/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/
- copied from r10102,
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/
branches/j_couplings/test_suite/system_tests/scripts/model_free/
- copied from r10102, 1.3/test_suite/system_tests/scripts/model_free/
Modified:
branches/j_couplings/ (props changed)
branches/j_couplings/arg_check.py
branches/j_couplings/data/align_tensor.py
branches/j_couplings/generic_fns/align_tensor.py
branches/j_couplings/generic_fns/model_selection.py
branches/j_couplings/generic_fns/pcs.py
branches/j_couplings/generic_fns/rdc.py
branches/j_couplings/generic_fns/temperature.py
branches/j_couplings/maths_fns/pcs.py
branches/j_couplings/maths_fns/rdc.py
branches/j_couplings/maths_fns/rotation_matrix.py
branches/j_couplings/prompt/pcs.py
branches/j_couplings/relax
branches/j_couplings/sample_scripts/mf_multimodel.py
branches/j_couplings/specific_fns/api_common.py
branches/j_couplings/specific_fns/consistency_tests.py
branches/j_couplings/specific_fns/frame_order.py
branches/j_couplings/specific_fns/hybrid.py
branches/j_couplings/specific_fns/jw_mapping.py
branches/j_couplings/specific_fns/model_free/main.py
branches/j_couplings/specific_fns/model_free/mf_minimise.py
branches/j_couplings/specific_fns/n_state_model.py
branches/j_couplings/specific_fns/noe.py
branches/j_couplings/specific_fns/relax_fit.py
branches/j_couplings/test_suite/system_tests/model_free.py
branches/j_couplings/test_suite/unit_tests/_data/test_align_tensor.py
branches/j_couplings/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/j_couplings/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/arg_check.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/data/align_tensor.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/align_tensor.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/model_selection.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/pcs.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/rdc.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/generic_fns/temperature.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/temperature.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/maths_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/maths_fns/pcs.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/maths_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/maths_fns/rdc.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/maths_fns/rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/maths_fns/rotation_matrix.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/prompt/pcs.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/relax?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/sample_scripts/mf_multimodel.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/sample_scripts/mf_multimodel.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/api_common.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/consistency_tests.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/frame_order.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/hybrid.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/hybrid.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/jw_mapping.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/model_free/main.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/model_free/mf_minimise.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/n_state_model.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/noe.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/specific_fns/relax_fit.py?rev=10106&r1=10105&r2=10106&view=diff
Modified: branches/j_couplings/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/test_suite/system_tests/model_free.py?rev=10106&r1=10105&r2=10106&view=diff
Modified:
branches/j_couplings/test_suite/unit_tests/_data/test_align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/test_suite/unit_tests/_data/test_align_tensor.py?rev=10106&r1=10105&r2=10106&view=diff
Modified:
branches/j_couplings/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/j_couplings/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py?rev=10106&r1=10105&r2=10106&view=diff
r10106 - in /branches/j_couplings: ./ data/ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ specific_fns/model...