Author: bugman
Date: Fri Oct 2 13:44:48 2015
New Revision: 27950
URL: http://svn.gna.org/viewcvs/relax?rev=27950&view=rev
Log:
Merged revisions
25713-25715,25720-25723,25725-25741,25744-25747,25749-25754,25760-25769 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r25713 | bugman | 2014-09-09 14:24:13 +0200 (Tue, 09 Sep 2014) | 5 lines
Implemented the frame_order.permute_axes user function.
This is used to switch between local minima in the pseudo-elliptic frame
order models.
........
r25714 | bugman | 2014-09-09 14:25:41 +0200 (Tue, 09 Sep 2014) | 7 lines
Fix for the Frame_order.test_axis_permutation system test.
The motional eigenframe in the old log file was not exactly correct and did
not correspond exactly
to the Euler angles in the cam_pseudo_ellipse.bz2 results file in
test_suite/shared_data/frame_order/axis_permutations/.
........
r25715 | bugman | 2014-09-09 14:29:43 +0200 (Tue, 09 Sep 2014) | 6 lines
Extended the Frame_order.test_axis_permutation system test to check
frame_order.permute_axes twice.
This will check that two calls to the frame_order.permute_axes user
function will restore the
original parameter values.
........
r25720 | bugman | 2014-09-09 19:13:17 +0200 (Tue, 09 Sep 2014) | 5 lines
The frame_order.permute_axes user function can now handle the torsionless
pseudo-ellipse.
This model does not have the variable cdp.cone_sigma_max set.
........
r25721 | bugman | 2014-09-09 19:18:46 +0200 (Tue, 09 Sep 2014) | 5 lines
Fix for the frame_order.permute_axes user function for the torsionless
pseudo-ellipse.
This should have been part of the last commit.
........
r25722 | bugman | 2014-09-09 19:33:39 +0200 (Tue, 09 Sep 2014) | 8 lines
Added support for axis permutations in the frame order auto-analysis.
This is done by copying the data pipe of the already optimised
pseudo-elliptic models, permuting the
axes, and performing another optimisation using all RDC and PCS data. This
allows the second
solution for these pseudo-elliptic models to be found. The 2nd pipe is
included in the model
selection step to allow the best solution for the model to be found.
........
r25723 | bugman | 2014-09-09 19:39:36 +0200 (Tue, 09 Sep 2014) | 7 lines
Fix for the reading of old results files in the frame order auto-analysis.
The directory name is now processed by the model_directory() method. This
will convert the spaces
to '_' and remove commas. Without this the already created files could not
be found, if the model
name contains a space or comma.
........
r25725 | bugman | 2014-09-09 21:12:30 +0200 (Tue, 09 Sep 2014) | 6 lines
Made the pivot point in the frame order PDB representation fail-proof.
If the pivot position was outside of the bounds [-1000, 1000], the PDB file
creation would fail as
the record would be too long. So now the pivot is shifted to be in these
bounds.
........
r25726 | bugman | 2014-09-10 08:46:29 +0200 (Wed, 10 Sep 2014) | 5 lines
The axis permutation step in the frame order auto-analysis is now always
performed.
If an old results file was found, this step was accidentally skipped.
........
r25727 | bugman | 2014-09-10 09:22:20 +0200 (Wed, 10 Sep 2014) | 3 lines
Added extensive printouts to the frame_order.permute_axes user function.
........
r25728 | bugman | 2014-09-10 11:43:11 +0200 (Wed, 10 Sep 2014) | 7 lines
Redesigned the frame_order.permute_axes user function frontend.
Previously only cyclic permutations were considered, however non-cyclic
permutations are also
allowed when accompanied by an axis inversion. Therefore 3 combinations
exist with cone_theta_x <=
cone_theta_y, or 2 when the current combination is excluded.
........
r25729 | bugman | 2014-09-10 13:21:28 +0200 (Wed, 10 Sep 2014) | 10 lines
Created 6 system tests for the frame_order.permute_axes user function.
This covers the 3 starting conditions (x<y<z, x<z<y, z<x<y) and the two
permutations ('A' and 'B')
for each of these which do not include the starting permutation. They
replace the original
Frame_order.test_axis_permutation system test with the tests
Frame_order.test_axis_perm_x_le_y_le_z_permA,
Frame_order.test_axis_perm_x_le_y_le_z_permB,
Frame_order.test_axis_perm_x_le_z_le_y_permA,
Frame_order.test_axis_perm_x_le_z_le_y_permB,
Frame_order.test_axis_perm_z_le_x_le_y_permA, and
Frame_order.test_axis_perm_z_le_x_le_y_permB.
........
r25730 | bugman | 2014-09-10 13:41:33 +0200 (Wed, 10 Sep 2014) | 8 lines
Implemented the new frame_order.permute_axes backend.
The 3 starting conditions x<y<z, x<z<y, and z<x<y and the two permutations
'A' and 'B' (for each of
these which do not include the starting permutation) are now supported.
For these 6 combinations,
the axis and order parameter permutation and the z-axis inversion are
selected and applied to the
current system.
........
r25731 | bugman | 2014-09-10 13:43:41 +0200 (Wed, 10 Sep 2014) | 5 lines
Removed the second permutation from the 6 Frame_order.test_axis_perm_*
system tests.
A second identical permutation does not necessarily restore the original
state.
........
r25732 | bugman | 2014-09-10 13:49:20 +0200 (Wed, 10 Sep 2014) | 5 lines
Fix for the frame_order.permute_axes for the torsionless pseudo-ellipse
model.
The data structure cdp.cone_sigma_max does not exist in this model as
cone_sigma_max == 0.0.
........
r25733 | bugman | 2014-09-10 13:57:03 +0200 (Wed, 10 Sep 2014) | 7 lines
Modified the frame order auto-analysis axis permutation algorithm to handle
both permutations.
Instead of creating one additional data pipe for the permutations, two are
now created for the
permutations 'A' and 'B'. This allows all 3 solutions for the
pseudo-elliptic models to be
explored and included in the final model selection process.
........
r25734 | bugman | 2014-09-10 14:20:43 +0200 (Wed, 10 Sep 2014) | 5 lines
Fix for the Frame_order.test_axis_perm_x_le_z_le_y_permB system test.
The permuted z-axis needs to be inverted in the test.
........
r25735 | bugman | 2014-09-10 14:24:58 +0200 (Wed, 10 Sep 2014) | 8 lines
Many fixes for the frame_order.permute_axes user function.
The z-axis inversion is now encoded into a 3D numpy array as the index of
the new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max
parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the
cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be
reintroduced later).
........
r25736 | bugman | 2014-09-10 14:41:23 +0200 (Wed, 10 Sep 2014) | 6 lines
Fix for the axis permutation protocol in the frame order auto-analysis.
The pipe.copy user function does not switch pipes, therefore the
pipe.switch user function is now
being called so that the correct pipe is being permuted and optimised.
........
r25737 | bugman | 2014-09-10 18:46:29 +0200 (Wed, 10 Sep 2014) | 9 lines
Created some test data files for visualising the frame order axis
permutation.
This uses the CaM frame order synthetic data for the rotor model to
visualise the pseudo-ellipse
frame order model axis permutations. The initial conversion sets the
pseudo-ellipse torsion angle
cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic
cone opening to close to
zero. Then the axis permutations are performed. All three solutions are
optimised. PDB
representations before and after optimisation are included to illustrate
any problems.
........
r25738 | bugman | 2014-09-10 21:33:37 +0200 (Wed, 10 Sep 2014) | 7 lines
Bug fix for the new frame_order.permute_axes user function.
The cone and torsion angles were not being correctly permuted. Now the
direct permutation array is
being used. And the fact that cone_theta_x is a rotation along the y-axis
and cone_theta_y along
the x-axis is taken into account.
........
r25739 | bugman | 2014-09-11 13:43:37 +0200 (Thu, 11 Sep 2014) | 8 lines
Redesign of the axis permutation algorithm of the frame_order.permute_axes
user function.
Instead of tracking the fact that cone_theta_x is a rotation around the
y-axis and cone_theta_y is
about the x-axis, now two permutation arrays are created - one for the
three angles and one for the
axes. The permutation array values have also been completely changed as
previously the incorrect
inverse permutation was coded into the algorithm.
........
r25740 | bugman | 2014-09-11 14:58:38 +0200 (Thu, 11 Sep 2014) | 6 lines
Updated the frame order pseudo-ellipse motion permutation test data.
This is for the CaM frame order rotor model synthetic data. The correct
axis and cone angle
permutations of the frame_order.permute_axes user function are now being
used and optimised.
........
r25741 | bugman | 2014-09-11 14:59:42 +0200 (Thu, 11 Sep 2014) | 5 lines
Renamed the pseudo-ellipse permutation directory to
perm_pseudo_ellipse_x_le_y_le_z.
This is for the CaM frame order rotor model synthetic data.
........
r25744 | bugman | 2014-09-11 15:42:19 +0200 (Thu, 11 Sep 2014) | 5 lines
Fix for the frame_order.permute_axes user function.
One of the 6 permutations had the x and y axes switched (the x <= z <= y
condition, permutation A).
........
r25745 | bugman | 2014-09-11 17:17:05 +0200 (Thu, 11 Sep 2014) | 8 lines
Visualisation files for all of the pseudo-ellipse permutations by
frame_order.permute_axes.
This includes the x <= z <= y and z <= x <= y conditions (the previous
files were for x <= y <= z).
In all permutation combinations, optimisation has been performed to
demonstrate that these are all
local minima. These all approximate the rotor when using the CaM frame
order rotor model synthetic
data.
........
r25746 | bugman | 2014-09-11 19:16:52 +0200 (Thu, 11 Sep 2014) | 8 lines
Added support for the isotopic cone models to the frame_order.permute_axes
user function.
This is a simpler setup, but it uses the same permutation algorithm as
derived for the
pseudo-ellipse models. Instead of setting the x and y cone angles
separately, they are instead
averaged. And as the cone axis is undefined in the xy plane, the axis has
been randomly selected as
being the axis perpendicular to both the z-axis and the reference frame
x-axis.
........
r25747 | bugman | 2014-09-11 19:19:18 +0200 (Thu, 11 Sep 2014) | 7 lines
Created set of files showing the axis permutation problem for the isotopic
cone frame order model.
This shows that there are two minima. However one has a chi-squared value
of ~1, and the other a
value of ~150. Nevertheless, the optimisation could be trapped in the
non-global minimum so the
frame_order.permute_axes user function should be used for the isotopic
cones as well, just in case.
........
r25749 | bugman | 2014-09-11 19:37:44 +0200 (Thu, 11 Sep 2014) | 7 lines
Created the other isotropic cone condition z <= x = y.
As there are no constraints in this model, this condition should not result
in any major
differences, just the size of the cone being different and the optimisation
having to decrease the
cone angle significantly to mimic the rotor.
........
r25750 | bugman | 2014-09-11 19:43:45 +0200 (Thu, 11 Sep 2014) | 5 lines
Added the missing PDB files which should have been committed previously.
This are in
test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy.
........
r25751 | bugman | 2014-09-11 19:44:22 +0200 (Thu, 11 Sep 2014) | 5 lines
Added the missing PDB files which should have been committed previously.
This are in
test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/.
........
r25752 | bugman | 2014-09-11 19:52:47 +0200 (Thu, 11 Sep 2014) | 7 lines
Modified the frame order auto-analysis.
The axis permutation algorithm is now performed on all isotopic cone and
pseudo-ellipse models.
This is just in case the non-global minima was found in the original
optimisation. The isotropic
cone models possess two local minima whereas the pseudo-ellipse models
possess three local minima.
........
r25753 | bugman | 2014-09-11 19:57:46 +0200 (Thu, 11 Sep 2014) | 5 lines
Simplified the optimisation in the axis permutation part of the frame order
auto-analysis.
Only the last, highest quality setting is used for optimisation.
........
r25754 | bugman | 2014-09-11 20:30:12 +0200 (Thu, 11 Sep 2014) | 6 lines
Fix for the axis permutation protocol in the frame order auto-analysis.
This would fail if a results file for the permuted model already exists as
the pipe.copy user
function call was being performed too early.
........
r25760 | bugman | 2014-09-11 21:56:47 +0200 (Thu, 11 Sep 2014) | 3 lines
Created set of files for the axis permutation of the torsionless isotopic
cone frame order model.
........
r25761 | bugman | 2014-09-12 09:35:32 +0200 (Fri, 12 Sep 2014) | 7 lines
Created an initial Frame_order.test_frame_order_pdb_model_ensemble system
test.
This is to check the operation of the frame_order.pdb_model user function
when an ensemble of
structures is encountered. However as this uses a very minimal number of
user functions to set up
the system, a number of other minor bugs will probably be uncovered.
........
r25762 | bugman | 2014-09-12 09:45:00 +0200 (Fri, 12 Sep 2014) | 6 lines
Added printouts to the
specific_analyses.frame_order.parameters.update_model() function.
This is to make it easier to understand why certain things fail due to the
system not being fully
set up.
........
r25763 | bugman | 2014-09-12 09:49:37 +0200 (Fri, 12 Sep 2014) | 6 lines
Simplified the operation of the frame_order.select_model user function.
This is by removing the check of PCS data from the
specific_analyses.frame_order.data.pivot_fixed()
function using the base_data_types() function call. This allows the model
to be set up more easily.
........
r25764 | bugman | 2014-09-12 09:54:31 +0200 (Fri, 12 Sep 2014) | 5 lines
Modified the frame order check_pivot() function to operate on any data pipe.
The function now accepts the pipe_name argument so that checks can happen
on any data pipe.
........
r25765 | bugman | 2014-09-12 09:57:12 +0200 (Fri, 12 Sep 2014) | 5 lines
Missing imports in the specific_analyses.frame_order.checks module.
This is from the recent pipe_name argument addition in the check_pivot()
function.
........
r25766 | bugman | 2014-09-12 09:58:37 +0200 (Fri, 12 Sep 2014) | 6 lines
The frame order generate_pivot() function can now handle no pivot being
present.
At the start of this specific_analyses.frame_order.data module function,
the check_pivot() function
is being called to make sure that a pivot is present.
........
r25767 | bugman | 2014-09-12 10:08:13 +0200 (Fri, 12 Sep 2014) | 6 lines
Added a call to check_pivot() to the frame_order.select_model user function.
This is to prevent this user function from being called before the pivot
has been set, as otherwise
the parameter vector will be incorrectly set up.
........
r25768 | bugman | 2014-09-12 10:12:00 +0200 (Fri, 12 Sep 2014) | 5 lines
Modified the Frame_order.test_frame_order_pdb_model_ensemble system test so
it is set up correctly.
The pivot point and moving domain are now specified.
........
r25769 | bugman | 2014-09-12 10:14:16 +0200 (Fri, 12 Sep 2014) | 7 lines
Added Monte Carlo simulations to the
Frame_order.test_frame_order_pdb_model_ensemble system test.
This is only setting up Monte Carlo simulation data structures via the
monte_carlo.setup user
function. This demonstrates a failure of the frame_order.pdb_model user
function when an ensemble
of structures is present with Monte Carlo simulations.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_torsionless_xy_le_z/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_torsionless_xy_le_z/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_y_le_z/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_y_le_z/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_z_le_y/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_z_le_y/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y/
trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y_alt/
- copied from r25769,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y_alt/
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/specific_analyses/frame_order/checks.py
trunk/specific_analyses/frame_order/data.py
trunk/specific_analyses/frame_order/geometric.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.py
trunk/test_suite/system_tests/frame_order.py
trunk/user_functions/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27950&r1=27949&r2=27950&view=diff
Modified: trunk/specific_analyses/frame_order/checks.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/checks.py?rev=27950&r1=27949&r2=27950&view=diff
Modified: trunk/specific_analyses/frame_order/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/data.py?rev=27950&r1=27949&r2=27950&view=diff
Modified: trunk/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/geometric.py?rev=27950&r1=27949&r2=27950&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=27950&r1=27949&r2=27950&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=27950&r1=27949&r2=27950&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=27950&r1=27949&r2=27950&view=diff
Modified: trunk/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/frame_order.py?rev=27950&r1=27949&r2=27950&view=diff
r27950 - in /trunk: ./ auto_analyses/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/rotor/perm_iso_c...