Author: bugman
Date: Fri Oct 2 10:49:41 2015
New Revision: 27936
URL: http://svn.gna.org/viewcvs/relax?rev=27936&view=rev
Log:
Merged revisions
23985,24015-24017,24090,24279,24284,24309-24314,24316-24318,24321-24322 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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 .
.....
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.
.....
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/
- copied from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos_true.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order_fixed_piv.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order_true.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.bz2
- copied unchanged from r24017,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.bz2
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.py
- copied unchanged from r24322,
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.py
Modified:
trunk/ (props changed)
trunk/lib/frame_order/double_rotor.py
trunk/lib/frame_order/matrix_ops.py
trunk/lib/frame_order/rotor.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/rdc_tm.txt
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_torsionless.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27936&r1=27935&r2=27936&view=diff
Modified: trunk/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=27936&r1=27935&r2=27936&view=diff
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27936&r1=27935&r2=27936&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27936&r1=27935&r2=27936&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.bz2?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.log.bz2?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/axis.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/axis.pdb?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_matrix
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_matrix?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.log.bz2?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy.txt?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_dy_subset.txt?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er.txt?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_er_subset.txt?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tb.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tb.txt?rev=27936&r1=27935&r2=27936&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/pcs_tb_subset.txt
[... 29 lines stripped ...]
r27936 - in /trunk: ./ lib/frame_order/ target_functions/ test_suite/shared_data/frame_order/cam/ test_suite/shared_data/fra...