Author: bugman
Date: Fri Oct 2 09:29:12 2015
New Revision: 27934
URL: http://svn.gna.org/viewcvs/relax?rev=27934&view=rev
Log:
Merged revisions 23856-23863,23878-23879,23883-23887 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
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r23856 | bugman | 2014-06-12 10:42:55 +0200 (Thu, 12 Jun 2014) | 5 lines
Updated the free rotor and 2nd free rotor PDB representations using the
represent_frame_order.py script.
This is for the CaM frame order test data.
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r23857 | bugman | 2014-06-12 10:44:38 +0200 (Thu, 12 Jun 2014) | 5 lines
Removed some debugging code from the frame order system tests.
This was used to activate all tests.
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r23858 | bugman | 2014-06-12 10:47:31 +0200 (Thu, 12 Jun 2014) | 6 lines
Reparameterisation of the double rotor frame order model.
The two axes defined by spherical angles have been replaced by a full
eigenframe and the second
pivot has been replaced by a single displacement along the z-axis of the
eigenframe.
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r23859 | bugman | 2014-06-12 10:53:55 +0200 (Thu, 12 Jun 2014) | 6 lines
Removed the 2nd pivot point infrastructure from the frame order analysis.
This change is almost the same as reverting r22177 of the deleted
double_rotor branch. The 2nd
pivot is now defined via the pivot_disp parameter.
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r23860 | bugman | 2014-06-12 10:57:21 +0200 (Thu, 12 Jun 2014) | 5 lines
Added the 2nd rotor axis torsion angle to the list of frame order
parameters.
This is for the double rotor model.
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r23861 | bugman | 2014-06-12 10:58:26 +0200 (Thu, 12 Jun 2014) | 3 lines
Fix for the previous commit - the parameter name was not correct.
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r23862 | bugman | 2014-06-12 11:23:22 +0200 (Thu, 12 Jun 2014) | 3 lines
Comment fixes for the eigenframe reconstruction in the frame order target
functions.
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r23863 | bugman | 2014-06-12 12:12:19 +0200 (Thu, 12 Jun 2014) | 3 lines
Converted the double rotor frame order model target function to use the new
parameterisation.
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r23878 | bugman | 2014-06-12 13:52:26 +0200 (Thu, 12 Jun 2014) | 3 lines
Fix for the PDB representation generated by frame_order.pdb_model for the
free rotor pseudo-ellipse.
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r23879 | bugman | 2014-06-12 13:55:35 +0200 (Thu, 12 Jun 2014) | 6 lines
Fix for the Frame_order.test_rigid_data_to_free_rotor_model system test.
As the free rotor has undergone a reparameterisation, the chi-squared value
is now higher. The
value is reasonable as the free rotor can never model the rigid system.
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r23883 | bugman | 2014-06-12 15:57:22 +0200 (Thu, 12 Jun 2014) | 7 lines
Removed the structure loading and transformation from the CaM frame order
system tests.
This was mimicking the old behaviour of the auto-analysis. However as that
behaviour has been
shifted into the backend of the frame_order.pdb_model user function, which
is called by these system
tests as well, the code is now redundant and is wasting test suite time.
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r23884 | bugman | 2014-06-12 16:00:22 +0200 (Thu, 12 Jun 2014) | 6 lines
Removed the setting of the second pivot point in the CaM frame order system
tests.
The second pivot point has been removed from the double rotor frame order
model to eliminate
parameter redundancy, so no models now have a conventional second pivot.
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r23885 | bugman | 2014-06-12 16:40:15 +0200 (Thu, 12 Jun 2014) | 7 lines
Modified the CaM frame order system test base script to test alternative
code paths.
This pivot point was fixed in all tests, so the code in the target
functions behind the pivot_opt
flag was not being tested. Now for those system tests whereby the calc
rather than minimise user
function is called, the pivot is no longer fixed to execute this code.
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r23886 | bugman | 2014-06-12 18:47:36 +0200 (Thu, 12 Jun 2014) | 7 lines
Simplification and clean up of the RDC and PCS flags in the frame order
target functions.
The per-alignment flags have been removed and replaced by a global flag for
all data. This
accidentally fixes a bug when only RDCs are present, as the calc_vectors()
method was being called
when it should not have been.
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r23887 | bugman | 2014-06-12 19:44:47 +0200 (Thu, 12 Jun 2014) | 19 lines
Speed up and simplifications for the vector calculations used for the PCS
numerical integration.
This has a minimal effect on the total speed as the target function
calc_vectors() method is not the
major bottleneck - the slowest part is the quasi-random numerical
integration. However the changes
may be useful for speeding up the integration later on.
The 3D pivot point, average domain rotation pivot, and paramagnetic centre
position arrays are now
converted into rank-2 arrays in __init__() where the first dimension
corresponds to the spin. Each
element is a copy of the 3D array.
These are then used for the calculation of the pivot to atom vectors,
eliminating the looping over
spins. The numpy add() and subtract() ufuncs are used together with the
out argument for speed and
to avoid temporary data structure creation and deletion. The end result is
that the calculated
vector structure is transposed, so the first dimension are the spins.
The changes required minor updates to a number of system tests. The target
functions themselves had
to be modified so that the pivot is converted to the larger structure when
optimised, or aliased.
........
Modified:
trunk/ (props changed)
trunk/lib/frame_order/matrix_ops.py
trunk/lib/frame_order/rotor.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameter_object.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/specific_analyses/frame_order/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameter_object.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27934&r1=27933&r2=27934&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/ave_pos.pdb.gz?rev=27934&r1=27933&r2=27934&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.pdb.gz?rev=27934&r1=27933&r2=27934&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/ave_pos.pdb.gz?rev=27934&r1=27933&r2=27934&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.pdb.gz?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27934&r1=27933&r2=27934&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27934&r1=27933&r2=27934&view=diff
r27934 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_data/frame_order/...