svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup
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r26671 | bugman | 2014-11-20 18:41:46 +0100 (Thu, 20 Nov 2014) | 7 lines
Completed the Frame_order.test_pdb_model_rotor system test.
This now sets the rotor axis to the z-axis (with a printout to be sure), sets the torsion angle to
zero for simplicity, creates a new data pipe and loads the PDB representation file, then checks all
of the key atom coordinates.
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r26673 | bugman | 2014-11-20 19:25:40 +0100 (Thu, 20 Nov 2014) | 9 lines
Fixes for the unit tests of the lib.frame_order_matrix_ops module for the free rotor isotropic cone.
The S1 order parameter has been eliminated due to angles > pi/2.0 causing the frame order matrix to
be incorrectly predicted. Therefore all unit tests have been converted to use the cone opening
angle theta instead. In addition, the test_compile_2nd_matrix_iso_cone_free_rotor_disorder had been
modified to pass with the incorrect frame order matrix by comparing to the half cone frame order
matrix rather than the identity frame order matrix.
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r26675 | bugman | 2014-11-21 08:44:35 +0100 (Fri, 21 Nov 2014) | 3 lines
Fix for inverted axes in the new Frame_order.test_pdb_model_rotor system test.
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r26676 | bugman | 2014-11-21 08:58:39 +0100 (Fri, 21 Nov 2014) | 12 lines
Huge bug fix for the frame_order.pdb_model user function - the single axis direction was incorrect.
In the PDB representation of the frame order motion for the rotor and isotropic cone models (rotor,
free rotor, isotropic cone, free rotor isotropic cone, and torsionless isotropic cone), the X and Z
axes were swapped. This is because the eigenframe of the motion was being incorrectly constructed
via the lib.geometry.rotations.two_vect_to_R() function.
For better control, the specific_analyses.frame_order.geometric.frame_from_axis() function has been
created. This constructs a full motional eigenframe from the Z-axis. The problem was detected via
the new Frame_order.test_pdb_model_rotor system test.
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r26677 | bugman | 2014-11-21 09:08:44 +0100 (Fri, 21 Nov 2014) | 9 lines
Size fix for the rotor representation from the frame_order.pdb_model user function.
The size problem was detected via the Frame_order.test_pdb_model_rotor system test. The rotors in
the PDB representation were all fixed in size, and ignored the 'size' argument of the
frame_order.pdb_model user function. The size argument is now passed into the add_rotors() function
of the specific_analyses.frame_order.geometric and passed on to the rotor() function of the
lib.structure.represent.rotor module.
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r26678 | bugman | 2014-11-21 09:41:51 +0100 (Fri, 21 Nov 2014) | 6 lines
Created the Frame_order.test_pdb_model_rotor2 system test to check for an offset pivot.
The pivot is set to [1, 0, 1] so that the rotor axis is tilted -45 degrees in the xz-plane. And the
size of the geometric object is set to 100 Angstrom for better testing of the sizes of the elements.
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r26680 | bugman | 2014-11-21 10:23:38 +0100 (Fri, 21 Nov 2014) | 5 lines
Simplification of the Frame_order.test_pdb_model_rotor system test.
The size is now programatically handled.
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r26683 | bugman | 2014-11-21 10:51:43 +0100 (Fri, 21 Nov 2014) | 6 lines
Created the Frame_order.test_pdb_model_iso_cone system test.
This is for checking the PDB representation of the isotropic cone frame order model created by the
frame_order.pdb_model user function. It checks both A and B representations.
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r26684 | bugman | 2014-11-21 10:55:28 +0100 (Fri, 21 Nov 2014) | 6 lines
Fix for the cone sized created by the frame_order.pdb_model user function.
The 'size' argument was not being used at all for the cone size. It is now passed into the
lib.structure.represent.cone.cone() function as the 'scale' argument.
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r26685 | bugman | 2014-11-21 10:59:22 +0100 (Fri, 21 Nov 2014) | 3 lines
Small fix for the Frame_order.test_pdb_model_iso_cone system test for the 'B' representation.
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r26686 | bugman | 2014-11-21 11:01:09 +0100 (Fri, 21 Nov 2014) | 6 lines
Fix for the representation label positions created by the frame_order.pdb_model user function.
The 'size' argument was not being used at all for the representation title
atoms. It is now passed into the add_titles() function as the displacement argument + 10 Angstrom.
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r26687 | bugman | 2014-11-21 11:04:19 +0100 (Fri, 21 Nov 2014) | 3 lines
Printout fix for the axis in the Frame_order.test_pdb_model_iso_cone system test.
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r26688 | bugman | 2014-11-21 13:46:14 +0100 (Fri, 21 Nov 2014) | 6 lines
Created the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test.
This checks the PDB file from the frame_order.pdb_model user function for the isotropic cone model
with a xz-plane tilt.
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r26689 | bugman | 2014-11-21 13:49:58 +0100 (Fri, 21 Nov 2014) | 3 lines
Renamed all of the Frame_order.test_pdb_model_* system tests to be more descriptive.
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r26690 | bugman | 2014-11-21 15:00:10 +0100 (Fri, 21 Nov 2014) | 7 lines
Improvements for all of the Frame_order.test_pdb_model_* system tests.
The rotate_from_Z() method has been introduced to simplify the determination of the 3D coordinates
expected for the PDB file. This will allow for more advanced testing of the PDB for the cone
models.
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r26691 | bugman | 2014-11-21 15:32:08 +0100 (Fri, 21 Nov 2014) | 3 lines
Fixes for the printouts from the Frame_order.test_pdb_model_rotor_* system tests.
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r26692 | bugman | 2014-11-21 16:37:00 +0100 (Fri, 21 Nov 2014) | 3 lines
Alphabetical ordering of the Frame_order system test methods.
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r26693 | bugman | 2014-11-21 17:45:39 +0100 (Fri, 21 Nov 2014) | 6 lines
Fixes for all of the Frame_order system tests - the temporary directories are now being deleted.
The system test base class tearDown() method is now being called to properly clean up after the
tests.
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r26694 | bugman | 2014-11-21 18:07:06 +0100 (Fri, 21 Nov 2014) | 6 lines
Created the Frame_order.test_pdb_model_pseudo_ellipse_z_axis system test.
This demonstrates the correct atom coordinates in the PDB file created by the frame_order.pdb_model
user function for the pseudo-ellipse model along the z-axis.
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r26695 | bugman | 2014-11-21 18:09:17 +0100 (Fri, 21 Nov 2014) | 6 lines
Fixes for the checks in the Frame_order.test_pdb_model_* system tests.
Atomic positions are now checked with self.assertAlmostEqual() to 3 places, and the residue and atom
names and numbers are checked with self.assertEqual().
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r26696 | bugman | 2014-11-21 19:19:53 +0100 (Fri, 21 Nov 2014) | 7 lines
Created the Frame_order.test_pdb_model_pseudo_ellipse_xz_plane_tilt system test.
This checks the PDB file created by the frame_order.pdb_model user function for the pseudo-ellipse
model with a xz-plane tilt. To properly construct the coordinates, the rotate_from_Z() method was
modified to accept a rotation matrix argument to allow the geometric shape to be rotated.
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r26697 | bugman | 2014-11-21 19:32:37 +0100 (Fri, 21 Nov 2014) | 6 lines
Modified the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test to have a cone angle.
The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB
file for a cone opening half-angle of 2.0.
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r26698 | bugman | 2014-11-21 19:51:14 +0100 (Fri, 21 Nov 2014) | 6 lines
Modified the Frame_order.test_pdb_model_iso_cone_z_axis system test to have a cone angle.
The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB
file for a cone opening half-angle of 2.0.
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r26717 | bugman | 2014-11-25 15:32:07 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new system tests for the free rotor PDB representation file.
This is the file from the frame_order.pdb_model user function. The two new unit tests are
Frame_order.test_pdb_model_free_rotor_z_axis and
Frame_order.test_pdb_model_free_rotor_xz_plane_tilt.
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r26718 | bugman | 2014-11-25 16:14:06 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new frame order system tests for the free rotor isotropic cone PDB representation file.
This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_iso_cone_free_rotor_z_axis and
Frame_order.test_pdb_model_iso_cone_free_rotor_xz_plane_tilt.
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r26719 | bugman | 2014-11-25 16:29:52 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new frame order system tests for the torsionless isotropic cone PDB representation file.
This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_iso_cone_torsionless_z_axis and
Frame_order.test_pdb_model_iso_cone_torsionless_xz_plane_tilt.
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r26720 | bugman | 2014-11-25 16:39:03 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new frame order system tests for the free rotor pseudo-ellipse PDB representation file.
This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_xz_plane_tilt.
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r26721 | bugman | 2014-11-25 16:56:10 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new frame order system tests for the torsionless pseudo-ellipse PDB representation file.
This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_torsionless_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_torsionless_xz_plane_tilt.
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r26722 | bugman | 2014-11-25 19:39:46 +0100 (Tue, 25 Nov 2014) | 7 lines
Created two new frame order system tests for the double rotor PDB representation file.
This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_double_rotor_z_axis and
Frame_order.test_pdb_model_double_rotor_xz_plane_tilt.
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r26764 | bugman | 2014-11-26 14:35:38 +0100 (Wed, 26 Nov 2014) | 6 lines
Added relax scripts and PDB files which match the Frame_order.test_test_pdb_model_* system tests.
These were used to construct and visually check the tests in a molecular viewer. These could be a
useful reference, so have been added to the repository.
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r26767 | bugman | 2014-11-26 15:55:07 +0100 (Wed, 26 Nov 2014) | 7 lines
Simplified all of the Frame_order.test_pdb_model_* system tests.
The atom, residue and 3D coordinate checking in all these methods has been shifted into the common
check_pdb_model_representation() method. This dramatically decreases the amount of code in the
system test file.
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r26773 | bugman | 2014-11-27 10:54:56 +0100 (Thu, 27 Nov 2014) | 7 lines
Simplification for all of the Frame_order.test_pdb_model_* system tests.
The model setup in all of these tests has been merged into the common setup_model() method. This
not only removes a large quantity of repetitive code, but the new method can also be used for
constructing future tests, for example for checking the frame_order.simulate user function.
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r26784 | bugman | 2014-11-27 16:27:21 +0100 (Thu, 27 Nov 2014) | 6 lines
Created an initial version of the Frame_order.test_simulate_rotor_z_axis system test.
This is to check the frame_order.simulate user function rotor model along the z-axis. It currently
fails due to a bug in the user function.
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r26789 | bugman | 2014-11-27 17:56:25 +0100 (Thu, 27 Nov 2014) | 8 lines
Fixes for the Frame_order.test_simulate_rotor_z_axis system test.
Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is
required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at
[1, 0, 0] so that the axis alpha angle of pi/2 creates an axis parallel to Z. The origin to atom
distance check has also been loosened due to the PDB truncation artifact.
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r26796 | bugman | 2014-11-28 08:50:00 +0100 (Fri, 28 Nov 2014) | 8 lines
Fix for the Frame_order.test_pdb_model_free_rotor_xz_plane_tilt system test.
This was broken while implementing the Frame_order.test_simulate_rotor_z_axis system test. Instead
of shifting the 6 atom structure so its CoM is the pivot of the motion when creating the atoms, now
the Frame_order.test_simulate_rotor_z_axis system test sets the average domain translation vector to
the pivot to achieve the same result. This preserves the z-axis orientation of the rotor models.
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r26797 | bugman | 2014-11-28 08:55:30 +0100 (Fri, 28 Nov 2014) | 5 lines
Created the Frame_order.test_simulate_free_rotor_z_axis system test.
This is to check the frame_order.simulate user function for the free rotor model along the z-axis.
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r26800 | bugman | 2014-11-28 12:15:34 +0100 (Fri, 28 Nov 2014) | 6 lines
Created the Frame_order.test_simulate_iso_cone_z_axis system test.
This is to check the frame_order.simulate user function for the isotropic cone model along the
z-axis.
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r26801 | bugman | 2014-11-28 12:17:42 +0100 (Fri, 28 Nov 2014) | 6 lines
Created the Frame_order.test_simulate_iso_cone_free_rotor_z_axis system test.
This is to check the frame_order.simulate user function for the free rotor isotropic cone model
along the z-axis.
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r26802 | bugman | 2014-11-28 12:20:00 +0100 (Fri, 28 Nov 2014) | 6 lines
Created the Frame_order.test_simulate_iso_cone_torsionless_z_axis system test.
This is to check the frame_order.simulate user function for the torsionless isotropic cone model
along the z-axis.
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r26809 | bugman | 2014-11-28 15:36:21 +0100 (Fri, 28 Nov 2014) | 6 lines
Created the Frame_order.test_simulate_pseudo_ellipse_z_axis system test.
This is to check the frame_order.simulate user function for the pseudo-ellipse model along the
z-axis.
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