relax SVN archive

Merged revisions 24327-24334,24344-24346 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24327 | bugman | 2014-06-26 13:42:33 +0200 (Thu, 26 Jun 2014) | 7 lines

Small fix for the large angle CaM double rotor frame order model synthetic test data.

The way the rotation angle was calculated was slightly out due to integer truncation. The integers
are now converted to floats in the generate_distribution.py script and all of the PCS and RDC data
averaged over ~20 million states has been recalculated.
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r24328 | bugman | 2014-06-26 14:21:15 +0200 (Thu, 26 Jun 2014) | 8 lines

Added proper support for the double rotor frame order models to the system test scripts.

This is for the CaM synthetic data. The base script can now handle the current parameterisation of
the double rotor model with a single pivot, an eigenframe, and the second pivot defined by a
displacement along the z-axis. The scripts for the double_rotor and double_rotor_large_angle data
sets have been changed to use this parameterisation as well.
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r24329 | bugman | 2014-06-26 14:27:55 +0200 (Thu, 26 Jun 2014) | 5 lines

Attempt at implementing the 2nd degree frame order matrix for the double rotor model.

This is required for the RDC.
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r24330 | bugman | 2014-06-26 14:31:30 +0200 (Thu, 26 Jun 2014) | 6 lines

The second torsion angle is now printed out for the frame order system tests.

This is in the system test class mesg_opt_debug() method and allows for better debugging of the
double rotor models.
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r24331 | bugman | 2014-06-26 14:46:43 +0200 (Thu, 26 Jun 2014) | 5 lines

Fix for the Frame_order.test_cam_double_rotor_large_angle* system tests.

The system test script was pointing to the wrong data directory.
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r24332 | bugman | 2014-06-26 16:29:46 +0200 (Thu, 26 Jun 2014) | 6 lines

Fix for the double rotor frame order matrix assembly function.

The rotations where applied in reverse, hence the 2nd degree frame order matrix was the Kronecker
product transpose of the correct form.
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r24333 | bugman | 2014-06-26 16:32:23 +0200 (Thu, 26 Jun 2014) | 3 lines

The double rotor frame order system tests are no longer blacklisted.
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r24334 | bugman | 2014-06-26 16:40:02 +0200 (Thu, 26 Jun 2014) | 3 lines

Updated the chi-squared values being checked for the double rotor frame order system tests.
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r24344 | bugman | 2014-06-27 15:57:39 +0200 (Fri, 27 Jun 2014) | 5 lines

Shifted the frame order geometric representation functions into their own module.

This is the new specific_analyses.frame_order.geometric module.
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r24345 | bugman | 2014-06-27 16:07:16 +0200 (Fri, 27 Jun 2014) | 7 lines

The frame order geometric representation functions are no longer PDB specific.

Instead the format argument is accepted. This will allow different formats to be supported in the
future. Because of this change, all specific_analyses.frame_order.geometric.pdb_*() functions has
been renamed to create_*().
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r24346 | bugman | 2014-06-27 16:31:45 +0200 (Fri, 27 Jun 2014) | 7 lines

Created an auxiliary function for automatically generating the pivots of the frame order analysis.

This is the new specific_analyses.frame_order.data.generate_pivot() function. It will generate the
1st or 2nd pivot, hence supporting both the single motion models and the double motion double rotor
model.
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Merged revisions 23985,24015-24017,24090,24279,24284,24309-24314,24316-24318,24321-24322 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23985 | bugman | 2014-06-16 18:47:49 +0200 (Mon, 16 Jun 2014) | 5 lines

Updates for the Frame_order.test_rigid_data_to_pseudo_ellipse*_model system tests.

The chi-squared value now matches the rigid model.
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r24015 | bugman | 2014-06-17 09:52:10 +0200 (Tue, 17 Jun 2014) | 13 lines

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

In addition, the theta_x and theta_y angles have also been swapped so that the new constraint of
0 <= theta_x <= theta_y <= pi built into the analysis is satisfied.

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. The algorithm for finding
suitable random domain positions within the motional limits has been changed as well by extracting
the theta and phi tilt angles from the random rotation, dropping the torsion angle sigma, and
reconstructing the rotation from just the tilt angles. This increases the speed of the data
generation script by minimally 5 orders of magnitude.
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r24016 | bugman | 2014-06-17 09:54:01 +0200 (Tue, 17 Jun 2014) | 6 lines

Changed the parameter values for the Frame_order.test_cam_pseudo_ellipse_torsionless* system tests.

The theta_x and theta_y angles are now swapped. The chi-squared values are now also lower in the
3 system tests as the data is now of much higher precision.
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r24017 | bugman | 2014-06-17 11:30:47 +0200 (Tue, 17 Jun 2014) | 7 lines

Speed up for the frame order analyses when only one domain is aligned.

When only one domain is aligned, the reverse Ln3+ to spin vectors for the PCS are no longer
calculated. For most analyses, this should significantly reduce the number of mathematical
operations required for the quasi-random Sobol' point numerical integration.
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r24090 | bugman | 2014-06-18 15:38:33 +0200 (Wed, 18 Jun 2014) | 12 lines

Support for the 3 vector system for double motions has been added to the frame order analysis.

This is used for the quasi-random Sobol' numeric integration of the PCS. The lanthanide to atom
vector is the sum of three parts: the 1st pivot to atom vector rotated by the 1st mode of motion;
the 2nd pivot to 1st pivot vector rotated by the 2nd mode of motion (together with the rotated 1st
pivot to atom vectors); and the lanthanide to second pivot vector.

All these vectors are passed into the lib.frame_order.double_rotor.pcs_numeric_int_double_rotor()
function, which passes them to the pcs_pivot_motion_double_rotor() function where they are rotated
and reconstructed into the Ln3+ to atom vectors.
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r24279 | bugman | 2014-06-24 14:52:58 +0200 (Tue, 24 Jun 2014) | 18 lines

Fully implemented the double rotor frame order model for PCS data.

Sobol' quasi-random points for the numerical integration are now generated separately for both
torsion angles, and two separate sets of rotation matrices for both angles for each Sobol' point are
now pre-calculated in the create_sobol_data() target function method. The calc_vectors() target
function method has also been modified as the lanthanide to pivot vector is to the second pivot in
the double rotor model rather than the first. The target function itself has been fixed as the two
pivots were mixed up - the 2nd pivot is optimised and the inter-pivot distance along the z-axis
gives the position of the 1st pivot.

For the lib.frame_order.double_rotor module, the second set of Sobol' point rotation matrices
corresponding to sigma2, the rotation about the second pivot, is now passed into the
pcs_numeric_int_double_rotor() function. These rotations are frame shifted into the eigenframe of
the motion, and then correctly passed into pcs_pivot_motion_double_rotor(). The elimination of
Sobol' points outside of the distribution has been fixed in the base pcs_numeric_int_double_rotor()
function and now both torsion angles are being checked.
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r24284 | bugman | 2014-06-24 16:10:00 +0200 (Tue, 24 Jun 2014) | 5 lines

Fix for the unpacking of the double rotor frame order parameters in the target function.

This is for when the pivot point is being optimised.
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r24309 | bugman | 2014-06-25 09:35:40 +0200 (Wed, 25 Jun 2014) | 8 lines

Created a new synthetic CaM data set for the double rotor frame order model.

This is the same as the test_suite/shared_data/frame_order/cam/double_rotor data except that the
angles have been increased from 11.5 and 10.5 degrees to 85.0 and 55.0 for the two torsion angles.
This is to help in debugging the double rotor model as the original test data is too close to the
rigid state to notice certain issues.
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r24310 | bugman | 2014-06-25 09:37:14 +0200 (Wed, 25 Jun 2014) | 6 lines

Corrected the printout from the CaM frame order data generation base script.

The number of states used in the distribution of domain positions is now correctly reported for the
models with multiple modes of motion.
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r24311 | bugman | 2014-06-25 09:47:33 +0200 (Wed, 25 Jun 2014) | 5 lines

Created a frame order optimisation script for the CaM double rotor test suite data.

This is the script used for testing the implementation, it will not be used in the test suite.
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r24312 | bugman | 2014-06-25 10:27:03 +0200 (Wed, 25 Jun 2014) | 6 lines

The pivot to atom vectors, and the reverse vectors, are no longer set up in the __init__() method.

This is for the frame order target functions. The structures are generated in the calc_vectors()
method via a dot product, and hence do not need to be initialised.
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r24313 | bugman | 2014-06-25 10:32:07 +0200 (Wed, 25 Jun 2014) | 17 lines

Reverted r24312 as the reverse vector data structure must exist in all cases.

The command used was:
svn merge -r24312:r24311 .

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r24312 | bugman | 2014-06-25 10:27:03 +0200 (Wed, 25 Jun 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/target_functions/frame_order.py

The pivot to atom vectors, and the reverse vectors, are no longer set up in the __init__() method.

This is for the frame order target functions. The structures are generated in the calc_vectors()
method via a dot product, and hence do not need to be initialised.
.....
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r24314 | bugman | 2014-06-25 10:56:37 +0200 (Wed, 25 Jun 2014) | 5 lines

Created the Frame_order.test_rigid_data_to_double_rotor_model system test.

This shows that the double rotor model works perfectly when the domains of the molecule are rigid.
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r24316 | bugman | 2014-06-25 16:41:20 +0200 (Wed, 25 Jun 2014) | 7 lines

Fix for the frame order target functions for when no PCS data is present.

In this case, the self.pivot structure was being created as an empty array rather than a rank-2
array with dimensions 1 and 3. This was causing the rotor models to fail, as this pivot is used to
recreate the rotation axis.
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r24317 | bugman | 2014-06-25 16:48:54 +0200 (Wed, 25 Jun 2014) | 6 lines

Fix for the CaM double rotor frame order system tests.

The torsion angle cone_sigma_max is a half angle, therefore the full angles from the data generation
script are now halved in the system test script.
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r24318 | bugman | 2014-06-25 16:53:16 +0200 (Wed, 25 Jun 2014) | 7 lines

Created 3 frame order system tests for the new large angle double rotor CaM synthetic data.

These are the Frame_order.test_cam_double_rotor_large_angle,
Frame_order.test_cam_double_rotor_large_angle_rdc, and
Frame_order.test_cam_double_rotor_large_angle_pcs system tests.
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r24321 | bugman | 2014-06-25 17:19:02 +0200 (Wed, 25 Jun 2014) | 5 lines

Added the full optimisation results for the torsionless pseudo-ellipse frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r24322 | bugman | 2014-06-25 17:21:13 +0200 (Wed, 25 Jun 2014) | 5 lines

Added the full optimisation results for the 2nd free rotor isotropic cone frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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Merged revisions 23935-23936,23943,23947-23948,23969-23983 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23935 | bugman | 2014-06-13 14:03:44 +0200 (Fri, 13 Jun 2014) | 12 lines

Added a script for timing different ways to calculate PCSs and RDCs for multiple vectors.

This uses the timeit module rather than profile to demonstrate the speed of 7 different ways to
calculate the RDCs or PCSs for an array of vectors using numpy. In the frame order analysis, this
is the bottleneck for the quasi-random numerical integration of the PCS.

The log file shows a potential 1 order of magnitude speed up between the 1st technique, which is
currently used in the frame order analysis, and the 7th and last technique. The first technique
loops over each vector, calculating the PCS. The last expands the PCS/RDC equation of the
projection of the vector into the alignment tensor, and calculates all PCSs simultaneously.
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r23936 | bugman | 2014-06-13 15:25:28 +0200 (Fri, 13 Jun 2014) | 8 lines

Added another timing script for RDC and PCS calculation timings.

This time, the calculation for multiple alignments is now being timed. An addition set of methods
for calculating the values via tensor projections have been added. For 5 alignments and 200
vectors, this demonstrates a potential 20x speed up for this part of the RDC/PCS calculation. Most
of this speed up should be obtainable for the numerical PCS integration in the frame order models.
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r23943 | bugman | 2014-06-13 17:43:50 +0200 (Fri, 13 Jun 2014) | 8 lines

Small speed up for all of the frame order models.

The PCS averaging in the quasi-random numerical integration functions now uses the multiply() and
divide() numpy methods to eliminate a loop over the alignments. For this, a new dimension over the
spins was added to the PCS constant calculated in the target function __init__() method. In one
test of the pseudo-ellipse, the time dropped from 191 seconds to 172.
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r23947 | bugman | 2014-06-13 19:51:26 +0200 (Fri, 13 Jun 2014) | 6 lines

Added another timing script for helping with speeding up the frame order analysis.

This is for the part where the rotation matrix for each Sobol' integration point is shifted into the
eigenframe.
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r23948 | bugman | 2014-06-13 19:54:40 +0200 (Fri, 13 Jun 2014) | 3 lines

Python 3 fix for the CaM frame order system test base script.
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r23969 | bugman | 2014-06-16 09:02:19 +0200 (Mon, 16 Jun 2014) | 5 lines

Added the full optimisation results for the torsionless isotropic cone frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r23970 | bugman | 2014-06-16 11:05:28 +0200 (Mon, 16 Jun 2014) | 12 lines

Small speed ups for all of the frame order models in the quasi-random numerical PCS integration.

These changes result in an ~10% speed up. Testing via the func_pseudo_ellipse() target function
using the relax profiling flag, the time for one optimisation decreased from 158 to 146 seconds.

The changes consist of pre-calculating all rotations of the rotation matrix into the motional
eigenframe in one mathematical operation rather than one operation per Sobol' point rotation,
unpacking the Sobol' points into the respective angles prior to looping over the points, and taking
the absolute value of the torsion angle and testing if it is out of the bounds rather than checking
both the negative and positive values.
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r23971 | bugman | 2014-06-16 11:07:44 +0200 (Mon, 16 Jun 2014) | 8 lines

Attempt at speeding up the torsionless pseudo-ellipse frame order model.

The check if the Sobol' point is outside of an isotropic cone defined by the largest angle theta_y
is now performed to avoid many unnecessary calls to the tmax_pseudo_ellipse() function.

This however reveals a problem with the test suite data for this model.
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r23972 | bugman | 2014-06-16 11:11:13 +0200 (Mon, 16 Jun 2014) | 7 lines

Updated all of the CaM frame order system tests for the recent speed up (r23970).

The speed up switched to the use of numpy.tensordot() for shifting each Sobol' rotation into the
eigenframe rather than the previous numpy.dot(). Strangely this affects the precision and hence the
chi-squared value calculated for each system test - both increasing and decreasing it randomly.
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r23973 | bugman | 2014-06-16 11:40:37 +0200 (Mon, 16 Jun 2014) | 5 lines

The frame order target function calc_vectors() method arguments have all been converted to keywords.

This is in preparation for handling a second pivot argument for the double rotor model.
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r23974 | bugman | 2014-06-16 11:49:10 +0200 (Mon, 16 Jun 2014) | 7 lines

Updated the double rotor frame order model to be in a pseudo-functional state.

Bugs in the target function method have been removed, the calc_vectors() target function now accepts
the pivot2 argument (but does nothing with it yet), and the lib.frame_order.double_rotor module has
been updated to match the logic used in all other lib.frame_order modules.
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r23975 | bugman | 2014-06-16 12:05:39 +0200 (Mon, 16 Jun 2014) | 3 lines

The frame_order.pdb_model user function no longer tries to create a cone object for the double rotor.
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r23976 | bugman | 2014-06-16 16:03:55 +0200 (Mon, 16 Jun 2014) | 3 lines

Added a timeit script and log file for different ways of checking a binary numpy array.
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r23977 | bugman | 2014-06-16 17:08:10 +0200 (Mon, 16 Jun 2014) | 8 lines

Modified the rigid_test.py system test script to really be the rigid case.

This is used in all of the Frame_order.test_rigid_data_to_*_model system tests. Previously the
parameters of the dynamics were set to being close to zero, to catch the cases were a few Sobol'
PCS integration points were accepted. But now the case were no Sobol' points can be used is being
tested. This checks a code path currently untested in the test suite, demonstrating many failures.
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r23978 | bugman | 2014-06-16 17:30:30 +0200 (Mon, 16 Jun 2014) | 7 lines

Fix for the frame order matrix calculation for a pseudo-elliptic cone with angles of zero degrees.

The lib.frame_order.pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless()
function has been changed to prevent a divide by zero failure. The surface area normalisation
factor now defaults to 0.0.
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r23979 | bugman | 2014-06-16 17:39:25 +0200 (Mon, 16 Jun 2014) | 7 lines

Fixes for all PCS numeric integration for all frame order models in the rigid case.

The exact PCS values for the rigid state are now correctly calculated when no Sobol' points lie
within the motional model. The identity matrix is used to set the rotation to zero, and the PCS
values are now multiplied by the constant.
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r23980 | bugman | 2014-06-16 17:40:42 +0200 (Mon, 16 Jun 2014) | 5 lines

Updates for the chi-squared value in all the Frame_order.test_rigid_data_to_*_model system tests.

This is now much reduced as the true rigid state is now being tested for.
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r23981 | bugman | 2014-06-16 17:53:11 +0200 (Mon, 16 Jun 2014) | 3 lines

Fix for the fix of r23978, the theta_x angle should be checked for zero as it is the smallest.
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r23982 | bugman | 2014-06-16 18:10:07 +0200 (Mon, 16 Jun 2014) | 10 lines

The rigid frame order matrix for the pseudo-ellipse models is now correctly handled.

This allows the rigid case RDCs to be correctly calculated for both the pseudo-ellipse and
torsionless pseudo-ellipse models. The previous catch of the theta_x cone angle of zero was
incorrectly recreating the frame order matrix, which really should be the identity matrix. However
truncation artifacts due to the quadratic SciPy integration still cause the model to be
ill-conditioned near the rigid case. The rigid case is correctly handled, but a tiny shift of the
parameters off zero cause a discontinuity.
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r23983 | bugman | 2014-06-16 18:28:49 +0200 (Mon, 16 Jun 2014) | 3 lines

Fix for the rigid frame order model broken at r23973.
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Merged revisions 23856-23863,23878-23879,23883-23887 via svnmerge from
svn+ssh://bugman@.../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.
........

Merged revisions 23807-23812 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23807 | bugman | 2014-06-11 08:07:03 +0200 (Wed, 11 Jun 2014) | 5 lines

Added the full optimisation results for the free rotor frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r23808 | bugman | 2014-06-11 08:07:50 +0200 (Wed, 11 Jun 2014) | 5 lines

Added the full optimisation results for the 2nd free rotor frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r23809 | bugman | 2014-06-11 08:08:17 +0200 (Wed, 11 Jun 2014) | 5 lines

Removed a PDB file from the free rotor CaM frame order test data directory.

This is now present as a *.gz file, so the uncompressed file can go.
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r23810 | bugman | 2014-06-11 08:10:02 +0200 (Wed, 11 Jun 2014) | 5 lines

Added the full optimisation results for the free rotor frame order model with missing data.

This is for the CaM test data using the new frame_order.py optimisation script.
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r23811 | bugman | 2014-06-11 08:19:22 +0200 (Wed, 11 Jun 2014) | 5 lines

Added a script for recreating the frame order PDB representation and displaying it in PyMOL.

This is for the optimised results.
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r23812 | bugman | 2014-06-11 08:21:48 +0200 (Wed, 11 Jun 2014) | 7 lines

Fixes for the rotor object created by the frame_order.pdb_model user function.

The rotor is now also shown for the free rotor pseudo-ellipse, despite it being a useless model, and
the propeller blades are no longer staggered for all the free rotor models so that two circles are
no longer produced.
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Merged revisions 23713-23714,23717,23771-23773,23778,23783 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23713 | bugman | 2014-06-06 18:09:59 +0200 (Fri, 06 Jun 2014) | 6 lines

Added the full optimisation results for the small angle rotor CaM frame order test data.

This is from the new frame_order.py optimisation script and the results demonstrate the stability of
the rotor model, even when the rotor is as small as 1 degree.
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r23714 | bugman | 2014-06-06 18:11:08 +0200 (Fri, 06 Jun 2014) | 5 lines

Removed some files from the 2nd rotor CaM frame order test data directory.

These are now present as *.gz files, so the uncompressed files can go.
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r23717 | bugman | 2014-06-06 18:26:14 +0200 (Fri, 06 Jun 2014) | 5 lines

Removed a PDB file from the 2nd rotor CaM frame order test data directory.

This is now present as a *.gz file, so the uncompressed file can go.
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r23771 | bugman | 2014-06-10 09:15:53 +0200 (Tue, 10 Jun 2014) | 6 lines

Fix for the free rotor PDB representation created by the frame_order.pdb_model user function.

The simulation axes were being incorrectly generated from the theta and phi angles, which no longer
exist as they have been replaced by the alpha angle.
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r23772 | bugman | 2014-06-10 09:27:41 +0200 (Tue, 10 Jun 2014) | 5 lines

Added the full optimisation results for the free rotor pseudo-ellipse frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r23773 | bugman | 2014-06-10 09:29:19 +0200 (Tue, 10 Jun 2014) | 5 lines

Added the full optimisation results for the rotor frame order model.

This is for the 2-site CaM test data using the new frame_order.py optimisation script.
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r23778 | bugman | 2014-06-10 09:48:07 +0200 (Tue, 10 Jun 2014) | 6 lines

The CaM frame order data generation base script now uses lib.compat.norm().

This is to allow the test suite to pass on systems with old numpy versions whereby the
numpy.linalg.norm() function does not support the new axis argument.
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r23783 | bugman | 2014-06-10 10:21:27 +0200 (Tue, 10 Jun 2014) | 7 lines

Modified the pymol.cone_pdb and pymol.frame_order user functions to use PyMOL IDs.

The PyMOL IDs are used to select individual objects in PyMOL rather than all objects so that the
subsequent PyMOL commands will only be applied to that object. This allows for multiple objects to
be handled simultaneously.
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Merged revisions 23682-23687,23690-23691,23709 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23682 | bugman | 2014-06-06 10:10:00 +0200 (Fri, 06 Jun 2014) | 8 lines

Fix for a number of the frame order models which do not have parameter constraints.

This change to the grid_search() API method is similar to the change for the minimise() method
(r23211). The linear_constraint() function was returning A, b = [], [] for these models, but these
empty numpy arrays were causing the dot product with A to fail in the grid_search() API method.
These values are now caught and the constraint algorithm turned off.
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r23683 | bugman | 2014-06-06 10:26:20 +0200 (Fri, 06 Jun 2014) | 7 lines

Converted the 'free rotor' frame order model to the new axis_alpha parameter system.

The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle
alpha. The alpha parameter defines the rotor axis angle from the xy-plane.
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r23684 | bugman | 2014-06-06 10:30:45 +0200 (Fri, 06 Jun 2014) | 6 lines

Parameter conversion for all of the CaM free rotor test data frame_order.py optimisation scripts.

The rotor axis spherical angles have been replaced by the axis alpha angle defining the rotor with
respect to the xy-plane.
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r23685 | bugman | 2014-06-06 10:36:24 +0200 (Fri, 06 Jun 2014) | 8 lines

Modified the CaM frame order base system test script to catch a bug in the free rotor model.

The axis spherical angles are no longer set for the rotor or free rotor models, as they use the
alpha angle instead and the lack of the theta and phi parameters triggers the bug. The PDB
representation of the frame order motions is also now tested for all frame order models, as it was
turned off for the rigid, rotor and free rotor models and this is where the bug lies.
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r23686 | bugman | 2014-06-06 10:37:29 +0200 (Fri, 06 Jun 2014) | 5 lines

Fix for the failure of the frame_order.pdb_model user function for the free rotor frame order model.

This is due to the recent parameter conversion to the axis alpha angle.
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r23687 | bugman | 2014-06-06 10:46:02 +0200 (Fri, 06 Jun 2014) | 3 lines

Removed a debugging printout.
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r23690 | bugman | 2014-06-06 14:08:23 +0200 (Fri, 06 Jun 2014) | 7 lines

Eliminated the average position alpha Euler angle parameter from the free-rotor pseudo-ellipse model.

As this frame order model is a free-rotor, the average domain position is therefore undefined and it
can freely rotate about the rotor axis. One of the Euler angles for rotating to the average
position can therefore be removed, just as in the free rotor and free rotor isotropic cone models.
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r23691 | bugman | 2014-06-06 14:11:04 +0200 (Fri, 06 Jun 2014) | 6 lines

Eliminated the free rotor psuedo-ellipse model ave_pos_alpha parameter from the target function.

The average domain position alpha Euler angle has already been removed from the specific analyses
code and this change brings the target function into line with these changes.
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r23709 | bugman | 2014-06-06 18:00:28 +0200 (Fri, 06 Jun 2014) | 6 lines

Added the full optimisation results for the 2nd rotor frame order model for the CaM test data.

This is from the new frame_order.py optimisation script and the results demonstrate the stability of
the rotor model.
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Merged revisions 23650,23668-23673 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23650 | bugman | 2014-06-05 13:15:07 +0200 (Thu, 05 Jun 2014) | 8 lines

Expanded the CaM isotropic cone test data frame_order.py optimisation script and added the results.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.
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r23668 | bugman | 2014-06-05 19:00:23 +0200 (Thu, 05 Jun 2014) | 6 lines

Important fix for the 2nd rotor model of the CaM frame order test data.

The tilt angle was not set, and therefore the old data matched the non-tilted 1st rotor model. All
PCS and RDC data has been regenerated to the highest quality using 20,000,000 structures.
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r23669 | bugman | 2014-06-05 19:05:20 +0200 (Thu, 05 Jun 2014) | 3 lines

Updated the 3 Frame_order.test_cam_rotor2* system tests for the higher quality data.
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r23670 | bugman | 2014-06-06 08:38:25 +0200 (Fri, 06 Jun 2014) | 10 lines

Expanded the 2nd CaM pseudo-ellipse test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation have been added to the repository.
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r23671 | bugman | 2014-06-06 08:39:27 +0200 (Fri, 06 Jun 2014) | 10 lines

Expanded the CaM free-rotor isotropic cone test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation have been added to the repository.
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r23672 | bugman | 2014-06-06 08:59:05 +0200 (Fri, 06 Jun 2014) | 8 lines

Expanded all remaining CaM test data frame_order.py optimisation scripts.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.
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r23673 | bugman | 2014-06-06 09:01:17 +0200 (Fri, 06 Jun 2014) | 5 lines

Updated the CaM 2-site to rotor model frame_order.py optimisation script for the parameter reduction.

The rotor frame order model axis spherical angles have now been converted to a single alpha angle.
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Merged revisions 23641-23646 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23641 | bugman | 2014-06-04 19:21:24 +0200 (Wed, 04 Jun 2014) | 6 lines

Removed a terrible hack for handling the frame order analysis without constraints.

This is no longer needed as the log-barrier method is now used to constrain the optimisation, so
that the torsion angle can no longer be negative.
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r23642 | bugman | 2014-06-04 19:36:43 +0200 (Wed, 04 Jun 2014) | 6 lines

Constraints are now implemented in the frame order grid search.

This is useful for the pseudo-elliptic models as the cone theta_x < theta_y constraint halves the
optimisation space.
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r23643 | bugman | 2014-06-05 08:36:47 +0200 (Thu, 05 Jun 2014) | 10 lines

Expanded the CaM rotor test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation are included.
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r23644 | bugman | 2014-06-05 08:51:23 +0200 (Thu, 05 Jun 2014) | 10 lines

Expanded the CaM pseudo-ellipse test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation are included.
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r23645 | bugman | 2014-06-05 10:28:34 +0200 (Thu, 05 Jun 2014) | 9 lines

Added one more iteration for the zooming optimisation of the frame order auto-analysis.

This is to improve the speed of optimisation when all RDC and PCS data is being used. The previous
iterations where with [100, 1000, 200000] Sobol' integration points and [1e-2, 1e-3, 1e-4] function
tolerances. This has been increased to [100, 1000, 10000, 100000] and [1e-2, 1e-3, 5e-3, 1e-4].
The final number of points has been decreased as that level of accuracy does not appear to be
necessary. These are also only default values that the user can change for themselves.
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r23646 | bugman | 2014-06-05 10:50:12 +0200 (Thu, 05 Jun 2014) | 6 lines

Updated the CaM frame order data generation base script to print out more information.

This is for the first axis system so that the same amount of information as the second system is
printed.
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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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