relax SVN archive

Merged revisions 23632-23635 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23632 | bugman | 2014-06-04 10:56:18 +0200 (Wed, 04 Jun 2014) | 8 lines

Expanded the capabilities of the pymol.frame_order user function.

The isotropic and pseudo-elliptic cones are now represented as they used to be under the
pymol.cone_pdb user function. To avoid code duplication, the new represent_cone_axis(),
represent_cone_object() and represent_rotor_object() functions have been created to send the
commands into PyMOL.
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r23633 | bugman | 2014-06-04 11:24:12 +0200 (Wed, 04 Jun 2014) | 7 lines

Increased the precision of all of the CaM frame order system tests by 40 times.

The number of Sobol' integration points have been significantly increased while only increasing the
frame order system test timings by ~10%. This allows for checking for chi-squared values at the
minima much closer to zero, and is much better for demonstrating bugs.
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r23634 | bugman | 2014-06-04 13:54:40 +0200 (Wed, 04 Jun 2014) | 6 lines

Optimisation constraints are no longer turned off in the frame order auto-analysis.

Constraints are now supported by all frame order models, or automatically turned off for those which
do not have parameter constraints.
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r23635 | bugman | 2014-06-04 13:56:59 +0200 (Wed, 04 Jun 2014) | 5 lines

Fix for the frame order visualisation script created by the auto-analysis.

The call to pymol.frame_order is now correct for the current version of this user function.
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Merged revisions 23624-23627 via svnmerge from
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r23624 | bugman | 2014-06-03 18:09:00 +0200 (Tue, 03 Jun 2014) | 3 lines

The frame_order.num_int_pts user function now throws a RelaxWarning if not enough points are used.
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r23625 | bugman | 2014-06-03 18:12:00 +0200 (Tue, 03 Jun 2014) | 6 lines

Changed the creation of Sobol' points for numerical integration in the frame order target functions.

The points are now all created at once using the i4_sobol_generate() rather than i4_sobol() function
from the extern.sobol.sobol_lib module.
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r23626 | bugman | 2014-06-03 18:29:44 +0200 (Tue, 03 Jun 2014) | 6 lines

Increased the number of integration points from 50 or 100 to 5000.

This is for all CaM frame_order.py test data optimisation scripts. The higher number of points are
essential for optimising the frame order models and hence for checking the relax implementation.
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r23627 | bugman | 2014-06-04 09:04:34 +0200 (Wed, 04 Jun 2014) | 6 lines

Updated the frame_order.py optimisation script for the small angle CaM rotor frame order test data.

This now has the correct rotor torsion angle of 1 degree, and the spherical coordinates are now
converted to the axis alpha parameter.
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Merged revisions 23616-23622 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23616 | bugman | 2014-06-03 11:16:38 +0200 (Tue, 03 Jun 2014) | 6 lines

Created a new CaM frame order test data set.

This is for the rotor model with a very small torsion angle of 1 degree, and will be used as a
comparison to the rigid model and for testing the performance of the rotor model for an edge case.
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r23617 | bugman | 2014-06-03 11:18:44 +0200 (Tue, 03 Jun 2014) | 7 lines

Updated the frame order representations in all of the frame_order.py scripts for the CaM test data.

All PDB files are now gzipped to save space, the old pymol.cone_pdb user function calls replaced
with pymol.frame_order, and an average domain PDB file for the exact solution is now created in all
cases.
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r23618 | bugman | 2014-06-03 11:20:51 +0200 (Tue, 03 Jun 2014) | 3 lines

The minimisation constraints are now turned on for all CaM test data frame_order.py optimisation scripts.
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r23619 | bugman | 2014-06-03 11:24:59 +0200 (Tue, 03 Jun 2014) | 6 lines

Updated the rotor CaM test data frame_order.py script for the parameter reduction.

The rotor axis {theta, phi} polar angles have been replaced by the single axis alpha angle. This
now matches the script for the 2nd rotor model.
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r23620 | bugman | 2014-06-03 11:26:59 +0200 (Tue, 03 Jun 2014) | 3 lines

Fix for a fatal typo in r23618.
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r23621 | bugman | 2014-06-03 11:47:09 +0200 (Tue, 03 Jun 2014) | 7 lines

Updated the parameters in all of the frame_order.py scripts for the CaM test data.

The parameters are now specified at the top of the script as variables. All scripts now handle the
change to the translation + CoM rotation for the average domain position rather than having a pure
rotation about a fixed pivot, which is no longer supported.
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r23622 | bugman | 2014-06-03 11:49:00 +0200 (Tue, 03 Jun 2014) | 3 lines

Fix for a missing import in the isotropic cone CaM test data frame_order.py scripts.
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Merged revisions 23613-23615 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23613 | bugman | 2014-06-03 08:53:25 +0200 (Tue, 03 Jun 2014) | 5 lines

Optimisation of the rotor model to the rigid CaM frame order test data.

The optimisation script and all results files have been added to the repository.
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r23614 | bugman | 2014-06-03 09:00:25 +0200 (Tue, 03 Jun 2014) | 4 lines

Increased the grid search bounds for the frame order average domain translation.

Instead of being a 10 Angstrom box centred at {0, 0, 0}, now the translation search has been
increased to a 100 Angstrom box.
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r23615 | bugman | 2014-06-03 09:16:09 +0200 (Tue, 03 Jun 2014) | 8 lines

Proper edge case handling and slight speed up of the frame order PCS integration functions.

The case whereby no Sobol' points in the numerical integration lie within the motional distribution
is now caught and the rotation matrix set to the motional eigenframe to simulate the rigid state.
As the code for averaging the PCS was changed, it was also simplified by removing an unnecessary
loop over all spins. This should speed up the PCS integration by a tiny amount.
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Merged revisions 23612 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23612 | bugman | 2014-05-30 12:49:16 +0200 (Fri, 30 May 2014) | 3 lines

Preformed a frame order analysis on the rigid CaM test data set.

This is to demonstrate that everything is operating correctly.
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Merged revisions 23611 via svnmerge from
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r23611 | bugman | 2014-05-30 11:48:40 +0200 (Fri, 30 May 2014) | 4 lines

Preformed a frame order analysis on a number of the CaM test data sets.

This includes the rotor, isotropic cone, and pseudo-ellipse, and the analyses demonstrate a common
bug between all these models.
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Merged revisions 23544 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23544 | bugman | 2014-05-28 17:47:55 +0200 (Wed, 28 May 2014) | 7 lines

Attempt to speed up the pseudo-elliptic frame order models.

The quasi-random numerical integration of the PCS for the pseudo-ellipse has been modified so that
the torsion angle check for each Sobol' point is preformed before the tmax_pseudo_ellipse() function
call. A new check that the tilt angle is less than cone_theta_y, the larger of the two cone angles,
has also been added to avoid tmax_pseudo_ellipse() when the theta tilt angle is outside of an
isotropic cone defined by cone_theta_y.
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Merged revisions 23427-23430,23466-23467 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23427 | bugman | 2014-05-26 17:00:03 +0200 (Mon, 26 May 2014) | 3 lines

The minimisation verbosity flag now effects the frame order RelaxWarning about turning constraints off.
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r23428 | bugman | 2014-05-26 18:15:06 +0200 (Mon, 26 May 2014) | 3 lines

Preformed a frame order analysis on the 2nd CaM free-rotor model test data.

This is to check that everything is operating as expected.
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r23429 | bugman | 2014-05-26 19:07:55 +0200 (Mon, 26 May 2014) | 4 lines

Small speed up for the frame order target functions for most models.

The rotation matrix corresponding to each Sobol' point for the numerical integration is now
pre-calculated during target function initialisation rather than once for each function call.
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r23430 | bugman | 2014-05-26 19:08:02 +0200 (Mon, 26 May 2014) | 5 lines

Updates for some of the frame order system tests for the rotation matrix pre-calculation change.

As the rotation matrix is being pre-calculated, one consequence is that the Sobol' angles are now
full 64-bit precision rather than 32-bit. Therefore this changes the chi-squared value a little,
requiring updates to the tests.
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r23466 | bugman | 2014-05-27 13:54:09 +0200 (Tue, 27 May 2014) | 3 lines

Preformed a frame order analysis on the CaM free-rotor mode test data set.

This is to demonstrate that everything is operating correctly.
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r23467 | bugman | 2014-05-27 13:54:14 +0200 (Tue, 27 May 2014) | 3 lines

Preformed a frame order analysis on the CaM free-rotor mode test data set with missing data.

This is to demonstrate that everything is operating correctly.
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Merged revisions 23394-23407,23411,23421-23424 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23394 | bugman | 2014-05-24 09:11:48 +0200 (Sat, 24 May 2014) | 5 lines

Improved the value setting in the optimisation() method of the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
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r23395 | bugman | 2014-05-24 09:14:53 +0200 (Sat, 24 May 2014) | 9 lines

Changed the average domain position parameter values in the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
The translation vector coordinates are now set, as well as the CoM Euler angle rotations. These
come from the log file of the test_suite/shared_data/frame_order/cam/superimpose.py script, and are
needed due to the simplification of the average domain position mechanics now mimicking the Kabsch
superimposition algorithm.
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r23396 | bugman | 2014-05-24 09:16:28 +0200 (Sat, 24 May 2014) | 6 lines

The CaM frame order system test mesg_opt_debug() method not prints out the translation vector.

This is printed out at the end of all CaM frame order system tests to help with debugging when the
test fails.
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r23397 | bugman | 2014-05-24 09:32:21 +0200 (Sat, 24 May 2014) | 16 lines

Change for how the CaM frame order system test scripts handle the average domain position rotation.

The trick of pre-rotating the 3D coordinates was used to solve the {a, b, g} -> {0, b', g'} angle
conversion problem in the rotor models no longer works now that the average domain position
mechanics has been simplified. Instead, high precision optimised b' and g' values are now set, and
the ave_pos_alpha value set to None.

The high precision parameters were obtained with the frame_order.py script located in the directory
test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target function was modified so
that the translation vector is hard-coded to [-20.859750185691549, -2.450606987447843,
-2.191854570352916] and the axis theta and phi angles to 0.96007997859534299767 and
4.0322755062196229403. These parameters were then commented out for the model in the module
specific_analyses.frame_order.parameters so only b' and g' were optimised. Iterative optimisation
was used with increasing precision, ending up with high precision using 10,000 Sobol' points.
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r23398 | bugman | 2014-05-24 10:03:22 +0200 (Sat, 24 May 2014) | 5 lines

Updated a number of the CaM frame order system tests for the higher precision data.

The new data results in chi-squared values at the real solution to be much closer to zero.
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r23399 | bugman | 2014-05-24 10:09:39 +0200 (Sat, 24 May 2014) | 5 lines

Change for how the CaM frame order free-rotor pseudo-ellipse test script handle the average position.

This should have been updated earlier (r23397).
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r23400 | bugman | 2014-05-24 10:10:46 +0200 (Sat, 24 May 2014) | 6 lines

Added FIXME comments to the 2nd free-rotor CaM frame order model system test scripts.

These explain the steps required to obtain the correct b' and g' average domain position rotation
angles.
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r23401 | bugman | 2014-05-24 11:47:05 +0200 (Sat, 24 May 2014) | 4 lines

Large increase in precision for the CaM frame order isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23402 | bugman | 2014-05-25 08:49:33 +0200 (Sun, 25 May 2014) | 4 lines

Large increase in precision for the CaM frame order free-rotor, isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23403 | bugman | 2014-05-25 09:39:39 +0200 (Sun, 25 May 2014) | 7 lines

Updated the CaM frame order free-rotor model test data set for testing for missing data.

This is the data in test_suite/shared_data/frame_order/cam/free_rotor_missing_data. To simplify the
copying of data from test_suite/shared_data/frame_order/cam/free_rotor and then the deletion of
data, the missing.py script was created to automate the process. The generate_distribution.py
script and some of the files it creates were removed from the repository so it is clearer how the
data has been created.
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r23404 | bugman | 2014-05-26 09:05:05 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the 2nd CaM frame order free-rotor, isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23405 | bugman | 2014-05-26 09:05:09 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the CaM frame order free-rotor, pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23406 | bugman | 2014-05-26 09:05:12 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the CaM frame order pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23407 | bugman | 2014-05-26 09:48:42 +0200 (Mon, 26 May 2014) | 5 lines

Updated a number of the CaM frame order system tests for the higher precision data.

The new data results in chi-squared values at the real solution to be much closer to zero. The
free-rotor pseudo-ellipse models might need investigation however as the chi-squared values have
increased.
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r23411 | bugman | 2014-05-26 11:43:18 +0200 (Mon, 26 May 2014) | 6 lines

Elimination of the error_flag variable from the frame order analysis.

This flag is used to activate some old code paths which have now been deleted as they are never
used.
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r23421 | bugman | 2014-05-26 15:20:04 +0200 (Mon, 26 May 2014) | 10 lines

Optimisation of the average domain position for the CaM frame order free-rotor models.

The log file that shows the optimisation of the average domain position for the free-rotor models
has been added to the repository for reference. This is for the simple free-rotor model, but the
optimised position holds for the isotropic cone and pseudo-ellipse model data too.

To perform the optimisation, the axis_theta and axis_phi parameters were removed from the model and
hardcoded into the target function. As the rotor axis is know, this allows the average domain
position to be optimised in isolation. Visual inspection of the results confirmed the position to
be correct.
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r23422 | bugman | 2014-05-26 15:23:37 +0200 (Mon, 26 May 2014) | 6 lines

Fixes for the 2nd frame order free-rotor system tests.

The average domain position parameters are now set to the correct values, matching those in the
relax log file frame_order_ave_pos_opt.log in test_suite/shared_data/frame_order/cam/free_rotor2.
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r23423 | bugman | 2014-05-26 15:37:55 +0200 (Mon, 26 May 2014) | 3 lines

Updated the 2nd CaM free-rotor frame order system tests for the correct average domain position.

The chi-squared values are now significantly lower.
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r23424 | bugman | 2014-05-26 16:24:42 +0200 (Mon, 26 May 2014) | 5 lines

Increased the precision of the chi-squared value testing in the CaM frame order system tests.

The check_chi2 method has been modified so that the chi-squared value is no longer scaled, and the
precision has been increased from 1 significant figure to 4. All of the tests have been updated to
match.
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Merged revisions 23326,23347,23354-23355,23387-23388,23391 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23326 | bugman | 2014-05-22 12:13:26 +0200 (Thu, 22 May 2014) | 4 lines

Parameter update for the 2nd rotor CaM frame order test model optimisation script.

The Euler angles for the rotation about the motional pivot have been replaced by the translation
vector and Euler angle CoM rotation parameters.
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r23347 | bugman | 2014-05-22 18:26:47 +0200 (Thu, 22 May 2014) | 4 lines

Large increase in precision for the 2nd CaM frame order free rotor model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 999,999 and the numpy.float128 data averaging has been used.
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r23354 | bugman | 2014-05-22 18:37:42 +0200 (Thu, 22 May 2014) | 4 lines

Updated the CaM frame order test model superimposition script.

The Ca2+ atoms are now deleted from the structures before superimposition so that the centroid
matches that used in the frame order analysis.
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r23355 | bugman | 2014-05-22 18:46:51 +0200 (Thu, 22 May 2014) | 5 lines

The average domain rotation centroid is printed out when setting up the frame order target functions.

This is to help the user understand what is happening in the analysis.
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r23387 | bugman | 2014-05-23 16:55:52 +0200 (Fri, 23 May 2014) | 6 lines

Faster clearing of numpy arrays in the lib.frame_order modules.

The x[:] = 0.0 notation is now used to set all elements to zero, rather than nested looping over all
dimensions. This however has a negligible effect on the test suite timings.
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r23388 | bugman | 2014-05-23 17:38:34 +0200 (Fri, 23 May 2014) | 4 lines

Large increase in precision for the CaM frame order pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23391 | bugman | 2014-05-23 20:09:10 +0200 (Fri, 23 May 2014) | 3 lines

Missing import from the trunk merge.
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