relax SVN archive

Merged revisions 24715-24717 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24715 | bugman | 2014-07-24 16:47:36 +0200 (Thu, 24 Jul 2014) | 5 lines

Turned on the optimisation in the Frame_order.test_cam_rigid system test.

This is to catch a number of failures in the frame order grid search.
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r24716 | bugman | 2014-07-24 16:50:44 +0200 (Thu, 24 Jul 2014) | 5 lines

Activated the grid search in the frame order system tests using the CaM synthetic data.

This is set to one increment so that the tests can complete in a reasonable time.
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r24717 | bugman | 2014-07-24 16:53:06 +0200 (Thu, 24 Jul 2014) | 6 lines

Fix for the specific_analyses.frame_order.optimisation.grid_row() function.

This can now handle the case of a single grid increment. The change is similar to r163 in the minfx
project (https://mail.gna.org/public/minfx-commits/2014-07/msg00015.html).
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Merged revisions 24709-24713 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24709 | bugman | 2014-07-24 15:11:29 +0200 (Thu, 24 Jul 2014) | 3 lines

Some more fixes for the optimisation user function changes.
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r24710 | bugman | 2014-07-24 16:02:59 +0200 (Thu, 24 Jul 2014) | 7 lines

Removed the parameter scaling for the pivot point frame order parameters.

These were already removed from the frame_order_cleanup branch in the assemble_scaling_matrix()
function, however they were reintroduced accidentally via the parameter object where this
information is now defined. So this removes the scaling a second time.
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r24711 | bugman | 2014-07-24 16:04:13 +0200 (Thu, 24 Jul 2014) | 6 lines

Fixes for the parameter scaling changes in the trunk.

The scaling flag is no longer part of the specific analysis API optimisation methods. Instead the
pre-assembled scaling matrices are passed into all three API optimisation methods.
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r24712 | bugman | 2014-07-24 16:21:47 +0200 (Thu, 24 Jul 2014) | 5 lines

Implemented the frame order specific analysis API method print_model_title().

This is simply aliased from the API common method _print_model_title_global().
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r24713 | bugman | 2014-07-24 16:24:53 +0200 (Thu, 24 Jul 2014) | 5 lines

Fix for the grid search in the frame order analysis.

This is a recently introduced problem due to the changes of the zooming_grid_search branch.
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Merged revisions 24560-24561,24585-24586,24666-24667 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24560 | bugman | 2014-07-18 10:26:01 +0200 (Fri, 18 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM free rotor isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24561 | bugman | 2014-07-18 10:30:09 +0200 (Fri, 18 Jul 2014) | 8 lines

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

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24585 | bugman | 2014-07-21 16:07:58 +0200 (Mon, 21 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM free rotor isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24586 | bugman | 2014-07-21 16:10:51 +0200 (Mon, 21 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM pseudo-ellipse test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24666 | bugman | 2014-07-23 08:57:12 +0200 (Wed, 23 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM torsionless isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24667 | bugman | 2014-07-23 08:58:29 +0200 (Wed, 23 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM pseudo-elliptic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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Merged revisions 24530-24534,24538-24539 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24530 | bugman | 2014-07-11 16:48:43 +0200 (Fri, 11 Jul 2014) | 7 lines

Sent the verbosity argument to the minfx.grid.grid_split() function for the frame order analysis.

This matches the relax trunk changes for the model-free analysis. The minfx function in the next
release (1.0.8) will now be more verbose, so this will help with user feedback when running the
model-free analysis on a cluster or multi-core system using MPI.
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r24531 | bugman | 2014-07-11 17:21:44 +0200 (Fri, 11 Jul 2014) | 9 lines

Improvements for the parallelised grid search for the frame order analysis.

As each grid point can take wildly different numbers of CPU cycles to calculate the chi-squared
value for, the result of subdividing the grid search was that some subdivisions where incredibly
quick while others required much larger amounts of time. To avoid this bad slave management, the
grid points are now randomised. This means that the subdivisions will require about the same amount
of time to optimise.
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r24532 | bugman | 2014-07-11 17:47:01 +0200 (Fri, 11 Jul 2014) | 10 lines

Moved the setup of the target function data structures in the frame order analysis.

This is for the grid_search and minimise user functions. The target function data setup function
has been renamed to target_fn_data_setup(). This is now called before the Frame_order_grid_command
and Frame_order_minimise_command multi-processor objects are initialised, and all of the data is now
passed into these functions. Although the code is uglier, this has the benefit that the
target_fn_data_setup() function will only be called once. This data setup requires a lot of time,
so for a large cluster, this can be a large time saving for the grid search.
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r24533 | bugman | 2014-07-14 12:17:07 +0200 (Mon, 14 Jul 2014) | 3 lines

Modified the frame_order_free_start.py script to better mimic the frame order auto-analysis.
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r24534 | bugman | 2014-07-15 11:14:39 +0200 (Tue, 15 Jul 2014) | 8 lines

Updated the frame order optimisation results for the 2nd CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24538 | bugman | 2014-07-16 11:32:25 +0200 (Wed, 16 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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r24539 | bugman | 2014-07-16 15:38:08 +0200 (Wed, 16 Jul 2014) | 8 lines

Updated the frame order optimisation results for the CaM missing data free rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.
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Merged revisions 24522-24524 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24522 | bugman | 2014-07-11 10:46:21 +0200 (Fri, 11 Jul 2014) | 12 lines

Parallelised the frame order grid search to run on clusters or multi-core systems via OpenMPI.

This involved the creation of the Frame_order_grid_command class which is the multi-processor
Slave_command for performing the grid search. This was created by duplicating the
Frame_order_minimise_command class and then differentiating both classes.

For the subdivision of the grid search, the new minfx grid.grid_split_array() function is used in
the frame order grid() API method. The grid() method no longer calls the minimise() method but
instead obtains the processor box itself and adds the subdivided grid slaves to the processor. The
relax grid_search user function takes care of the rest.
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r24523 | bugman | 2014-07-11 12:01:20 +0200 (Fri, 11 Jul 2014) | 8 lines

Fixes for the parallelised grid search for the frame order analysis.

A chi-squared value check was added to the Frame_order_result_command.run() method to check if the
value is lower than the current when the result is returned to the master. Without this check, each
grid subdivision result will be stored as they are returned rather than storing the results from the
global minimum of the entire grid search.
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r24524 | bugman | 2014-07-11 15:38:59 +0200 (Fri, 11 Jul 2014) | 7 lines

Added a script for testing out the parameter nesting abilities of the frame order auto-analysis.

This script attempts to find the dynamics solution without knowing where the pivot is located.
Hence this will be as in the auto-analysis were this pivot point will be used as the base for all
other models.
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Merged revisions 24514-24520 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24514 | bugman | 2014-07-10 18:12:07 +0200 (Thu, 10 Jul 2014) | 5 lines

Changed the minimisation in the frame order system tests where optimisation is activated.

The number of iterations is now set to 1 for speed testing, and the constraints are turned on.
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r24515 | bugman | 2014-07-10 18:13:09 +0200 (Thu, 10 Jul 2014) | 5 lines

Turned on the optimisation flag for the Frame_order.test_cam_free_rotor system test.

This is to activate code paths currently not tested by the test suite.
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r24516 | bugman | 2014-07-10 18:27:10 +0200 (Thu, 10 Jul 2014) | 6 lines

Constraints are now properly turned off in the minimise user function for the frame order analysis.

The A and b matrices from linear_constraints() are now set to None if they are returned as empty
arrays.
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r24517 | bugman | 2014-07-10 19:04:37 +0200 (Thu, 10 Jul 2014) | 26 lines

Parallelised the frame order optimisation code to run on clusters or multi-core systems via OpenMPI.

The optimisation code has been split into the three standard parts of the multi-processor:

- Frame_order_memo is the new Memo object used to store data on the master for use when data is
returned from the slaves.

- Frame_order_minimise_command is the Slave_command which stored all required data for the
optimisation, is pickled and sent to a slave, sets up the target function, and then performs
optimisation.

- Frame_order_result_command is the Result_command initialised by the Slave_command on the slave for
pickling and returning results to the master.

To avoid pickling the target function class, which is not possible, the store_bc_data() and
target_fn_setup() functions of the specific_analyses.frame_order.optimisation module have been
redesigned to work with basic data structures rather than the target function class directly. The
target_fn_setup() function no longer returns an initialised target function class, but rather all
the data assembled prior to the initialisation. And the target function class was itself modified
so that pcs_theta and rdc_theta are always defined to allow the store_bc_data() function to be used
successfully.

This parallelisation currently only allows the Monte Carlo simulations to be run on slave
processors.
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r24518 | bugman | 2014-07-11 09:07:01 +0200 (Fri, 11 Jul 2014) | 21 lines

Reverted r24495 as this is rubbish.

The pivot point needs to be initially guessed to centre the grid search for the pivot to a
reasonable 20 Angstrom box in the PDB space.

The command used was:
svn merge -r24495:r24494 .

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r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines
Changed paths:
M /branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py

Modified the specific_analyses.frame_order.parameters.update_model() function.

The pivot parameters are now set to 0.0 if they do not currently exist. They were previously
excluded from this initialisation, but this is required for the frame order models if the pivot is
not initially fixed at a give location in the PDB space.
.....
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r24519 | bugman | 2014-07-11 10:14:45 +0200 (Fri, 11 Jul 2014) | 5 lines

The frame order linear_constraints() function now returns None if no constraints are present.

This allows the code using this to be simplified with respect to turning off the constraints.
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r24520 | bugman | 2014-07-11 10:33:48 +0200 (Fri, 11 Jul 2014) | 6 lines

Improvements for the printout at the start of optimisation of the frame order models.

This is in the target_fn_setup() frame order method. All the printouts are now in one place and
they are now better formatted and better controlled.
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Merged revisions 24433-24436,24441-24444,24449-24451,24455,24457-24459,24461-24499,24504,24506,24509 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r24433 | bugman | 2014-07-03 15:04:20 +0200 (Thu, 03 Jul 2014) | 8 lines

Redesign of the average domain position part of the frame_order.pdb_model user function.

The Monte Carlo simulations are now represented. If the file root is set to the default of
'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a compressed version. Each
simulation is in a different model, matching the geometric representation '*_sim.pdb' files. The
original structure is copied for each model, and then rotated to the MC simulation average position.
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r24434 | bugman | 2014-07-03 15:25:47 +0200 (Thu, 03 Jul 2014) | 6 lines

Change all of the domain user function calls in the frame order CaM test data scripts.

The domains are now identified by the molecule name rather than the range of residues. This allows
non-protein atoms, for example the Ca2+ atoms, to be rotated to the average domain position as well.
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r24435 | bugman | 2014-07-03 15:44:41 +0200 (Thu, 03 Jul 2014) | 8 lines

The PyMOL disable command is now used by the pymol.frame_order user function.

This is to first disable all PyMOL objects prior to loading anything, to hide the original
structures and any previous frame order representations, and then to hide all of the Monte Carlo
simulation representations. This is to simplify the picture initially presented to the user while
still allowing all elements to be easily found.
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r24436 | bugman | 2014-07-03 15:45:01 +0200 (Thu, 03 Jul 2014) | 3 lines

Removed a debugging printout.
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r24441 | bugman | 2014-07-03 17:16:15 +0200 (Thu, 03 Jul 2014) | 3 lines

The pymol.frame_order user function now centers and zooms on all objects.
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r24442 | bugman | 2014-07-03 17:48:36 +0200 (Thu, 03 Jul 2014) | 7 lines

Simplified the PyMOL view commands in all of the CaM test data optimisation scripts.

The pymol.view user function is not necessary as the PyMOL GUI will be launched by the
pymol.frame_order user function. And the pymol.command user function call for running the 'hide
all' command is also now redundant.
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r24443 | bugman | 2014-07-03 17:55:53 +0200 (Thu, 03 Jul 2014) | 6 lines

Removed all remaining uncompressed PDB files from the CaM test data directories.

These were complicating the debugging of the pymol.frame_order user function, as they were being
loaded on top of the compressed versions.
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r24444 | bugman | 2014-07-03 17:58:05 +0200 (Thu, 03 Jul 2014) | 5 lines

Removed some rotation files from the CaM frame order test data directories.

These files are no longer of any use and just take up large amounts of room for nothing.
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r24449 | bugman | 2014-07-04 10:34:56 +0200 (Fri, 04 Jul 2014) | 12 lines

Added titles to the frame order geometric representation PDB files from frame_order.pdb_model.

These are in the form of special Ti atoms placed 40 Angstrom away from the pivot along the z-axis of
the system, or shifted 3 more Angstrom for the Monte Carlo simulations. These are used to label the
alternative representations or the Monte Carlo simulation representations. The residue type is set
to TLE and this has been registered in the internal structural object.

The pymol.frame_order user function now calls the represent_titles() function to select these atoms,
hide them, and then add a long descriptive title. The atom name is used to distinguish between
different titles.
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r24450 | bugman | 2014-07-04 10:47:05 +0200 (Fri, 04 Jul 2014) | 12 lines

Changed the alternative representation names for the frame order geometric objects.

The aim is to put both representations on a more equal footing, as they are identical solutions.
Hence the inverted representation might be the correct representation of the domain motions. So
instead of calling these 'positive' and 'negative', the 'A' and 'B' notation will be used.

This affects the names of the files produced by the frame_order.pdb_model user function as well as
the internal titles. Instead of ending the files with "*_pos.*" and ""*_neg.*", these have been
changed to "*_A.*" and ""*_B.*". The atoms used for the titles have also been renamed, and the
pymol.frame_order user function now labels the titles using the 'A' and 'B' notation.
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r24451 | bugman | 2014-07-04 11:02:51 +0200 (Fri, 04 Jul 2014) | 7 lines

Changes to the rotor object in the frame order geometric representations.

For the isotropic and pseudo-elliptic cone models, the rotor is now halved. Instead of having two
axes radiating from the central pivot and terminating in the propeller blades, now only the positive
axis is shown lying in the centre of the cone.
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r24455 | bugman | 2014-07-04 12:00:51 +0200 (Fri, 04 Jul 2014) | 6 lines

Fixes for the MC simulation rotor objects in the frame order geometric representation.

The axes of the Monte Carlo simulation rotors objects were being set to the original values and not
to the simulation values.
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r24457 | bugman | 2014-07-04 15:19:18 +0200 (Fri, 04 Jul 2014) | 5 lines

Fixes for the titles in the frame order geometric representation from frame_order.pdb_model.

There were a few bugs for a number of the frame order models preventing this code from working.
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r24458 | bugman | 2014-07-04 15:25:04 +0200 (Fri, 04 Jul 2014) | 3 lines

Added the geometric module to the specific_analyses.frame_order package __all__ list.
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r24459 | bugman | 2014-07-04 15:38:30 +0200 (Fri, 04 Jul 2014) | 16 lines

Redesign of the geometric representation of the cone structural objects to allow for models.

The old representation was not compatible with the PDB model concept whereby each model must have
the same number of atoms. To handle this situation, the cone objects have been simplified.
Specifically the cone cap.

The old behaviour was to remove all points outside of the cone when creating the cone cap, and then
to stitch the cap to the cone edge in a subsequent step. Now the behaviour is that all points
outside of the distribution are shifted to the cone edge. This avoids the need to stitch the cap to
the edge. This behaviour means that all cones with the same inc value will have the same number of
atoms.

The cones for the pseudo-ellipses are not as nice as the latitudinal lines are not strait at the
cone edge, but at least creating multiple models with different cone sizes is now possible.
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r24461 | bugman | 2014-07-05 14:39:55 +0200 (Sat, 05 Jul 2014) | 5 lines

Bug fix for the y-axis rotation matrix for the double rotor Sobol' integration points.

The matrix was inverted.
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r24462 | bugman | 2014-07-05 15:53:30 +0200 (Sat, 05 Jul 2014) | 17 lines

Reverted r24332 as this was incorrect - the data input was wrong, not the frame order matrix.

The command used was:
svn merge -r24332:r24331 .

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r24332 | bugman | 2014-06-26 16:29:46 +0200 (Thu, 26 Jun 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/lib/frame_order/double_rotor.py

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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r24463 | bugman | 2014-07-05 19:06:09 +0200 (Sat, 05 Jul 2014) | 9 lines

Converted all frame order target function data structures to float64.

This affects the vector data structures used for the PCS numeric integration. The float32
structures added for speed do not actually increase the speed. For the double rotor model, 10
target function calls took the pcs_pivot_motion_double_rotor() function 44.936 seconds using float32
and 44.105 seconds using all float64. The cumulative time is also longer. This must be because
other parts are float64, and therefore type conversions are happening during target function calls.
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r24464 | bugman | 2014-07-05 20:29:37 +0200 (Sat, 05 Jul 2014) | 3 lines

Updated the frame order system test chi-squared values for the fix of r24461.
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r24465 | bugman | 2014-07-05 20:37:38 +0200 (Sat, 05 Jul 2014) | 6 lines

Fixes for the double rotor frame order system tests for the CaM synthetic data.

The torsion angles needed to be swapped and the pivot point changed from the C terminal domain CoM
to the N domain CoM.
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r24466 | bugman | 2014-07-05 20:46:51 +0200 (Sat, 05 Jul 2014) | 5 lines

More fixes for the double rotor frame order system tests for the CaM synthetic data.

The eigensystem was inverted.
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r24467 | bugman | 2014-07-05 20:47:53 +0200 (Sat, 05 Jul 2014) | 5 lines

Updated the chi2 check for the large angle double rotor frame order system tests.

This is needed for the eigenframe fix.
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r24468 | bugman | 2014-07-05 20:51:40 +0200 (Sat, 05 Jul 2014) | 5 lines

Updates for the frame order system tests for the float32 to float64 change (r24463).

Some chi-squared values have slightly changed.
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r24469 | bugman | 2014-07-05 23:10:54 +0200 (Sat, 05 Jul 2014) | 6 lines

The CaM frame order test data optimisation scripts now save more state files.

The state of the true dynamics and the fixed pivot optimisation results are now stored as well.
This might be useful for extracting these results without redoing the calculations.
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r24470 | bugman | 2014-07-05 23:18:19 +0200 (Sat, 05 Jul 2014) | 5 lines

The script for representing the frame order dynamics for the CaM test data has been updated.

The domains of the system are now defined.
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r24471 | bugman | 2014-07-07 09:34:02 +0200 (Mon, 07 Jul 2014) | 13 lines

Changed the CaM frame order test data superimposition values.

Because the domains are now defined via the molecule name rather than the residue numbers, the
centroid of rotation set to the CoM has been shifted as now the Ca2+ ions are included in the CoM
calculation. Therefore the superimpose.py script has been updated to not delete the Ca atoms (this
reverts r23354).

All of the frame order optimisation scripts have been updated with the new rotation Euler angles and
translation vector. To match this, the system test base script for the CaM frame order test data
has also had its rotations and translations updates, and the domain user function call changed to
use molecule names.
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r24472 | bugman | 2014-07-07 09:58:19 +0200 (Mon, 07 Jul 2014) | 5 lines

Updated all of the CaM frame order system test chi-squared values.

These have changed slightly due to the rotation and translation changes (r24471).
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r24473 | bugman | 2014-07-07 16:28:29 +0200 (Mon, 07 Jul 2014) | 5 lines

Added support for the 'pivot_disp' frame order parameter to the grid search.

This is required for the double rotor model.
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r24474 | bugman | 2014-07-07 16:57:24 +0200 (Mon, 07 Jul 2014) | 6 lines

Changed some of the default values for the frame order auto-analysis.

The number of Sobol' quasi-random integration points were far too low to obtain any reasonable
results.
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r24475 | bugman | 2014-07-07 18:20:15 +0200 (Mon, 07 Jul 2014) | 6 lines

Simplified the PyMOL visualisation relax script created by the frame order auto-analysis.

This now consists of a single pymol.frame_order user function call. The other pymol user function
calls were unnecessary.
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r24476 | bugman | 2014-07-08 11:26:46 +0200 (Tue, 08 Jul 2014) | 5 lines

Added the full optimisation results for the large angle double rotor frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r24477 | bugman | 2014-07-08 11:36:31 +0200 (Tue, 08 Jul 2014) | 3 lines

Removal of some accidentally committed debugging code.
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r24478 | bugman | 2014-07-08 12:08:28 +0200 (Tue, 08 Jul 2014) | 7 lines

Added model support for the rotor geometric object.

This is the structural object used in the frame order analysis to create PDB representations of
rotor motions. The number of atoms created for the rotor is now constant, allowing for models
whereby the atom number and connectivity must be preserved between all models.
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r24479 | bugman | 2014-07-08 12:17:48 +0200 (Tue, 08 Jul 2014) | 6 lines

Changed the grid search pivot displacement frame order parameter.

Instead of searching from 0 to 50 Angstroms, the search is now from 10 to 50. This is to avoid the
edge case of pivot_disp = 0.0 from which the optimisation cannot escape.
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r24480 | bugman | 2014-07-08 14:21:23 +0200 (Tue, 08 Jul 2014) | 7 lines

Speed up of the PCS component of the rigid frame order model.

The lanthanide to atom vectors are now being calculated outside of the alignment tensor and spin
loops, as well as the inverse vector lengths to the 5th power. This increases the speed by a factor
of 1.216 (from 38.133 to 31.368 seconds for 23329 calls of the func_rigid() target function).
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r24481 | bugman | 2014-07-08 15:57:43 +0200 (Tue, 08 Jul 2014) | 5 lines

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

This is for the CaM test data using the new frame_order.py optimisation script.
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r24482 | bugman | 2014-07-08 17:07:24 +0200 (Tue, 08 Jul 2014) | 7 lines

Numpy <= 1.6 fixes for the frame order PCS code.

The numpy.linalg.norm function does not have an axis argument in numpy 1.6, therefore the
lib.compat.norm() function is now used instead. This function was created exactly for this axis
argument problem.
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r24483 | bugman | 2014-07-09 10:03:17 +0200 (Wed, 09 Jul 2014) | 8 lines

Created the new specific_analyses.frame_order.variables module.

This currently contains variables for all of the frame order model names, as well as various lists
of these models. The rest of the frame order specific analysis code as well as the frame order user
functions have been converted to use these model variables exclusively rather than having the
model name strings hardcoded throughout the codebase.
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r24484 | bugman | 2014-07-09 10:05:34 +0200 (Wed, 09 Jul 2014) | 5 lines

Added the full optimisation results for the double rotor test data.

This is for the CaM frame order test data using the new frame_order.py optimisation script.
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r24485 | bugman | 2014-07-09 10:40:09 +0200 (Wed, 09 Jul 2014) | 3 lines

Added a script for profiling the target function calls of the pseudo-ellipse frame order model.
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r24486 | bugman | 2014-07-09 10:59:03 +0200 (Wed, 09 Jul 2014) | 5 lines

Added a timeit script and log file showing how numpy.cos() is 10 times slower than math.cos().

This is for single floats.
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r24487 | bugman | 2014-07-09 11:39:08 +0200 (Wed, 09 Jul 2014) | 9 lines

Shifted the calculation of the theta_max cone opening for the pseudo-ellipse outside of all loops.

This is infrastructure change for potentially eliminating all of the looping for the PCS numeric
integration in the future. It however slightly speeds up the pseudo-ellipse frame order model.
Using 500 target function calls in the profiling_pseudo_ellipse.py script in
test_suite/shared_data/frame_order/timings/, the time spent in the pcs_pivot_motion_full_qrint()
function decreases from 20.849 to 20.719 seconds.
........
r24488 | bugman | 2014-07-09 11:52:30 +0200 (Wed, 09 Jul 2014) | 6 lines

Converted the torsionless pseudo-ellipse model to also use the tmax_pseudo_ellipse_array() function.

This allows the calculation of the pseudo-elliptic cone opening theta_max to be shifted outside of
all loops.
........
r24489 | bugman | 2014-07-09 11:59:05 +0200 (Wed, 09 Jul 2014) | 5 lines

Created a profiling script and log file for the isotropic cone frame order model.

This shows where the slow points of the model are, using 2000 target function calls.
........
r24490 | bugman | 2014-07-09 12:02:55 +0200 (Wed, 09 Jul 2014) | 7 lines

Increased the function call number to 500 in the pseudo-ellipse frame order model profiling script.

The profiling log file has also been added to show where the slowness is - specifically that the
numeric PCS integration takes almost the same amount of time as the RDC frame order matrix
construction using the scipy.integrate.quad() function.
........
r24491 | bugman | 2014-07-09 12:04:11 +0200 (Wed, 09 Jul 2014) | 3 lines

Removal of unused imports from the lib.frame_order.rotor module as identified using pylint.
........
r24492 | bugman | 2014-07-09 14:23:48 +0200 (Wed, 09 Jul 2014) | 3 lines

Added the new variables module to the specific_analyses.frame_order package __all__ list.
........
r24493 | bugman | 2014-07-09 14:59:32 +0200 (Wed, 09 Jul 2014) | 5 lines

Created the specific_analyses.frame_order.checks.check_pivot() function.

This is to check that the pivot point has been set.
........
r24494 | bugman | 2014-07-09 14:59:58 +0200 (Wed, 09 Jul 2014) | 3 lines

The frame order grid search is now checking if the pivot point has been set.
........
r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines

Modified the specific_analyses.frame_order.parameters.update_model() function.

The pivot parameters are now set to 0.0 if they do not currently exist. They were previously
excluded from this initialisation, but this is required for the frame order models if the pivot is
not initially fixed at a give location in the PDB space.
........
r24496 | bugman | 2014-07-09 16:20:51 +0200 (Wed, 09 Jul 2014) | 3 lines

Added a profiling script and log file for the free rotor frame order model.
........
r24497 | bugman | 2014-07-09 16:36:14 +0200 (Wed, 09 Jul 2014) | 5 lines

Added the log file which should have been committed at r24496.

The number of function calls has also been decreased to 100.
........
r24498 | bugman | 2014-07-09 17:09:10 +0200 (Wed, 09 Jul 2014) | 7 lines

Updated the frame order optimisation results for the CaM isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository and the old ones removed.
........
r24499 | bugman | 2014-07-09 17:19:52 +0200 (Wed, 09 Jul 2014) | 7 lines

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

The state loading, domain redefinition, and representation creation parts have all been removed, as
these will soon all be redundant as the frame order analysis for all models is being redone. All
that remains are the pymol.frame_order() function calls for displaying all the representations.
........
r24504 | bugman | 2014-07-09 19:52:00 +0200 (Wed, 09 Jul 2014) | 5 lines

The pivot point parameters in the frame order analysis are no longer scaled by 100.

This is to match the average domain position translation which is also not scaled.
........
r24506 | bugman | 2014-07-10 10:36:20 +0200 (Thu, 10 Jul 2014) | 8 lines

The specific_analyses.frame_order.variables module is now used throughout the frame order code.

The target function code, auto-analysis, and test suite now all use the variables defined in this
module rather than having hardcoded strings. The MODEL_LIST_NONREDUNDANT variable has been created
to exclude the redundant free rotor pseudo-ellipse which cannot be optimised, and this is used by
the auto-analysis.
........
r24509 | bugman | 2014-07-10 11:43:53 +0200 (Thu, 10 Jul 2014) | 7 lines

Removal of many unused imports in the frame_order_cleanup branch.

These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find
all unused imports. The false positives also present in the trunk were ignored. And the unused
imports in the dispersion code were also left for clean up the disp_spin_speed branch.
........

Merged revisions 24352,24358,24366-24379,24385,24397,24402-24406,24409-24411 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

........
r24352 | bugman | 2014-06-27 17:47:15 +0200 (Fri, 27 Jun 2014) | 7 lines

Shifted the rotor generation for the frame order geometric representation into its own function.

This is the specific_analyses.frame_order.geometric.add_rotors() function which adds the rotors are
new structures to a given internal structural object. The code has been extended to add support for
the double rotor model.
........
r24358 | bugman | 2014-06-27 18:36:44 +0200 (Fri, 27 Jun 2014) | 6 lines

Removed unused imports.

This is from the splitting of the specific_analyses.frame_order.uf module into the new geometric
module.
........
r24366 | bugman | 2014-07-01 09:13:39 +0200 (Tue, 01 Jul 2014) | 6 lines

Fix for the pivots created by the specific_analyses.frame_order.data.generate_pivot() function.

This is for the double rotor model where the 1st mode of motion is about the 2nd pivot, and the 2nd
mode of motion about the 1st pivot.
........
r24367 | bugman | 2014-07-01 11:11:25 +0200 (Tue, 01 Jul 2014) | 5 lines

Fixes for the cone geometric representation in the internal structural object.

The representation can now be created if the given MoleculeContainer object is empty.
........
r24368 | bugman | 2014-07-01 11:40:21 +0200 (Tue, 01 Jul 2014) | 10 lines

Refactored the frame order geometric motional representation code.

The code of the specific_analyses.frame_order.geometric.create_geometric_rep() function has been
spun out into 3 new functions: add_rotors(), add_axes(), and add_cones(). This is to better isolate
the various elements to allow for better control. Each function now adds the atoms for its
geometric representation to a separate molecule called 'axes' or 'cones'. The add_rotors() does not
create a molecule as the lib.structure.represent.rotor.rotor_pdb() function creates its own. As
part of the rafactorisation, the neg_cone flag has been eliminated.
........
r24369 | bugman | 2014-07-01 11:46:58 +0200 (Tue, 01 Jul 2014) | 7 lines

Renamed the residues of the rotor geometric object representation.

The rotor axis atoms now belong to the RTX residue and the propeller blades to the RTB residue. The
'RT' at the start represents the rotor and this will allow all the geometric objects to be better
isolated.
........
r24370 | bugman | 2014-07-01 11:59:05 +0200 (Tue, 01 Jul 2014) | 7 lines

Improvements to the internal structural object _get_chemical_name() method.

This now uses a translation table to convert the hetID or residue name into a description, for
example as used in the PDB HETNAM records to give a human readable description of the residue inside
the PDB file itself. The new rotor RTX and RTB residue names have been added to the table as well.
........
r24371 | bugman | 2014-07-01 12:04:41 +0200 (Tue, 01 Jul 2014) | 3 lines

Typo fix for r24368, the 'cones' molecule was mistyped.
........
r24372 | bugman | 2014-07-01 12:18:03 +0200 (Tue, 01 Jul 2014) | 10 lines

Renaming of the residues of the cone geometric representation.

The cone apex or centre is now the CNC residue, the cone axis is now CNX and the cone edge is now
CNE. These used to be APX, AXE, and EDG respectively. The aim is to make these names 100% specific
to the cone object so that they can be more easily selected for manipulating the representation and
so that they are more easily identifiable. The internal structural object _get_chemical_name()
function now returns a description for each of these. Note that the main cone object is still named
CON.
........
r24373 | bugman | 2014-07-01 12:42:41 +0200 (Tue, 01 Jul 2014) | 8 lines

The motional pivots for the frame order models are now labelled in the geometric representation.

The pivot points are now added as a new molecule called 'pivots' in the frame_order.pdb_model user
function. The atoms all belong to the PIV residue. The pymol.frame_order user function now selects
this residue, hides its atoms, and then shows the atom name 'Piv' as the label. For the double
rotor model, the atom names 'Piv1' and 'Piv2' are used to differentiate the pivots.
........
r24374 | bugman | 2014-07-01 12:51:23 +0200 (Tue, 01 Jul 2014) | 6 lines

Renamed the lib.structure.represent.rotor.rotor_pdb() function to rotor().

This function is not PDB specific and it just creates a 3D structural representation of a rotor
object.
........
r24375 | bugman | 2014-07-01 13:49:54 +0200 (Tue, 01 Jul 2014) | 15 lines

Added support for labels in the rotor geometric object for the internal structural object.

The labels are created by the frame_order.pdb_model user function backend. For the double rotor
model, these are 'x-ax' and 'y-ax'. For all other models, the label is 'z-ax'.

The labels are then sent into the lib.structure.represent.rotor.rotor() function via the new label
argument. This function adds two new atoms to the rotor molecule which are 2 Angstrom outside of
the rotor span and lying on the rotor axis. These then have their atom name set to the label. The
residue name is set to the new RTL name which has been added to the internal structural object
_get_chemical_name() method to describe the residue in the PDB file for the user.

Finally the pymol.frame_order user function selects these atoms, hides them and then labels them
using the atom name (x-ax, y-ax, or z-ax).
........
r24376 | bugman | 2014-07-01 14:20:02 +0200 (Tue, 01 Jul 2014) | 5 lines

Modified the rotor representation generated by the pymol.frame_order user function.

This is to make the object less bulky.
........
r24377 | bugman | 2014-07-01 16:17:10 +0200 (Tue, 01 Jul 2014) | 17 lines

Redesign of the axis geometric representation for the frame order motions.

This is now much more model dependent to avoid clashes with the rotor objects and other
representations:

- For the torsionless isotropic cone, a single z-axis is created.

- For the double rotor, a single z-axis is produced connecting the two pivots, from pivot2 to pivot1.

- For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are created.

- For the torsionless pseudo-ellipse, all three x, y and z-axes are created.

- For all other models, no axis system is produced as this has been made redundant by the rotor
objects.
........
r24378 | bugman | 2014-07-01 16:26:41 +0200 (Tue, 01 Jul 2014) | 5 lines

Fixes for the cone geometric object created by the frame_order.pdb_model user function.

This was broken by the code refactoring and now works again for the pseudo-ellipse models.
........
r24379 | bugman | 2014-07-01 16:46:08 +0200 (Tue, 01 Jul 2014) | 8 lines

Fix for the pymol.frame_order user function.

The representation function for the rotor objects was hiding all parts of the representation, hence
the pivot labels where being hidden. To fix this, the hiding of the geometric object now occurs in
the base frame_order_geometric() function prior to setting up the representations for the various
objects.
........
r24385 | bugman | 2014-07-01 18:08:30 +0200 (Tue, 01 Jul 2014) | 11 lines

Started to redesign the frame_order.pdb_model user function.

Instead of having the positive and negative representations in different PDB models, and the Monte
Carlo simulations in different molecules, these will now all be shifted into separate files.

For this to be possible, the file root rather than file names must now be supplied to the
frame_order.pdb_model user function. To allow for different file compression, the compress_type
argument is now used. The backend code correctly handles the file root change, but the multiple
files are not created yet.
........
r24397 | bugman | 2014-07-02 09:54:00 +0200 (Wed, 02 Jul 2014) | 19 lines

Python 3 fixes using the 2to3 script.

Fatal changes to the multi.processor module were reverted.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.
........
r24402 | bugman | 2014-07-02 11:57:18 +0200 (Wed, 02 Jul 2014) | 5 lines

Improvements to the lib.structure.represent.rotor.rotor() function for handling models.

The 'rotor', 'rotor2', or 'rotor3' molecule name determination is now also model specific.
........
r24403 | bugman | 2014-07-02 11:59:23 +0200 (Wed, 02 Jul 2014) | 7 lines

The frame order generate_pivot() function can now return the pivots for Monte Carlo simulations.

This is the specific_analyses.frame_order.data.generate_pivot() function. The sim_index argument
has been added to the function which will allow the pivots from the Monte Carlo simulations to be
returned. If the pivot was fixed, then the original pivot will be returned instead.
........
r24404 | bugman | 2014-07-02 13:40:45 +0200 (Wed, 02 Jul 2014) | 3 lines

Test suite fixes for the recent redesign of the frame_order.pdb_model user function.
........
r24405 | bugman | 2014-07-02 13:42:36 +0200 (Wed, 02 Jul 2014) | 3 lines

Fixes for the frame_order.pdb_model user function for the rotor and free rotor models.
........
r24406 | bugman | 2014-07-02 13:59:36 +0200 (Wed, 02 Jul 2014) | 17 lines

Redesign of the geometric object representation part of the frame_order.pdb_model user function.

The positive and negative representations of the frame order motions have been separated out into
two PDB files rather than being two models of one PDB file. This will help the user understand that
there are two identical representations of the motions, as both will now be displayed rather than
having to understand the model concept of PyMOL. The file root is taken, for example 'frame_order',
and the files 'frame_order_pos.pdb' and 'frame_order_neg.pdb' are created. If no inverse
representation exists for the model, the file 'frame_order.pdb' will be created instead.

The Monte Carlo simulations are now also treated differently. Rather than showing multiple vectors
in the axes representation component within one molecule in the same file as the frame order
representation, these are now in their own file and each simulation is now a different model. If an
inverse representation is present, then the positive representation will go into the file
'frame_order_sim_pos.pdb', for example, and the negative representation into the file
'frame_order_sim_neg.pdb'. Otherwise the file 'frame_order_sim.pdb' will be created.
........
r24409 | bugman | 2014-07-02 14:51:29 +0200 (Wed, 02 Jul 2014) | 5 lines

Clean up of the frame_order.pdb_model user function definitions.

Some elements were no longer of use, and some descriptions have been updated.
........
r24410 | bugman | 2014-07-02 14:53:21 +0200 (Wed, 02 Jul 2014) | 6 lines

Redesign of the pymol.frame_order user function to match the redesign of frame_order.pdb_model.

The file names are no longer given but rather the file root. Then all PDB files matching that file
root in the given directory will be loaded into PyMOL.
........
r24411 | bugman | 2014-07-02 15:19:46 +0200 (Wed, 02 Jul 2014) | 5 lines

Updated all of the frame order scripts for the frame_order.pdb_model and pymol.frame_order changes.

These are the scripts for the CaM frame order test data.
........

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

........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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_*().
........
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.
........

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

........
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.
........