relax SVN archive

svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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

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

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

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

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

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

The rotor axis spherical angles have been replaced by the axis alpha angle defining the rotor with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

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

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

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

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

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

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

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

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

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

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

This is from the new frame_order.py optimisation script and the results demonstrate the stability of
the rotor model.
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