Class Frame_order

TestCase class for the functional tests of the frame order theories.

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

__init__(self, methodName='runTest')
Skip the tests if scipy is not installed.

setUp(self)
Set up for all the functional tests.

tearDown(self)
Clean up after the tests.

check_chi2(self, chi2=0.0, places=4)
Check the function evaluation.

check_pdb_model_representation(self, data=None, files=None)
Check the PDB model representation atom and residue names and numbers and coordinates.

flags(self, rdc=True, pcs=True, opt=False, quad_int=False)
Set a number of flags for the scripts.

str mesg_opt_debug(self)
Method for returning a string to help debug the minimisation.

numpy 3D, rank-1 array rotate_from_Z(self, origin=array([ 0., 0., 0.]), length=0.0, angle=0.0, axis=array([ 1., 0., 0.]), R=None, neg=False)
Rotate a vector along Z-axis around the origin.

setup_model(self, pipe_name='model', model=None, pivot=None, ave_pos_x=None, ave_pos_y=None, ave_pos_z=None, ave_pos_alpha=None, ave_pos_beta=None, ave_pos_gamma=None, pivot_disp=None, axis_alpha=None, axis_theta=None, axis_phi=None, eigen_alpha=None, eigen_beta=None, eigen_gamma=None, cone_theta=None, cone_theta_x=None, cone_theta_y=None, cone_sigma_max=None, cone_sigma_max_2=None)
Set up for the given frame order model.

space_probe(self, ref_chi2=None, params=None, delta=0.0523598775598)
Probe the space around the supposed minimum.

test_auto_analysis(self)
Test the frame order auto-analysis using the rigid CaM test data.

test_axis_perm_x_le_y_le_z_permA(self)
Test the operation of the frame_order.permute_axes user function for permutation 'A' when x <= y <= z.

test_axis_perm_x_le_y_le_z_permB(self)
Test the operation of the frame_order.permute_axes user function for permutation 'B' when x <= y <= z.

test_axis_perm_x_le_z_le_y_permA(self)
Test the operation of the frame_order.permute_axes user function for permutation 'A' when x <= z <= y.

test_axis_perm_x_le_z_le_y_permB(self)
Test the operation of the frame_order.permute_axes user function for permutation 'B' when x <= z <= y.

test_axis_perm_z_le_x_le_y_permA(self)
Test the operation of the frame_order.permute_axes user function for permutation 'A' when z <= x <= y.

test_axis_perm_z_le_x_le_y_permB(self)
Test the operation of the frame_order.permute_axes user function for permutation 'B' when z <= x <= y.

test_cam_qr_int_double_rotor(self)
Test the double rotor frame order model of CaM.

test_cam_qr_int_double_rotor_pcs(self)
Test the double rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_double_rotor_rdc(self)
Test the double rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_double_rotor_large_angle(self)
Test the double rotor frame order model of CaM.

test_cam_qr_int_double_rotor_large_angle_pcs(self)
Test the double rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_double_rotor_large_angle_rdc(self)
Test the double rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_free_rotor(self)
Test the free rotor frame order model of CaM.

test_cam_qr_int_free_rotor_missing_data(self)
Test the free rotor frame order model of CaM.

test_cam_qr_int_free_rotor_pcs(self)
Test the free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_free_rotor_rdc(self)
Test the free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_free_rotor2(self)
Test the second free rotor frame order model of CaM.

test_cam_qr_int_free_rotor2_pcs(self)
Test the second free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_free_rotor2_rdc(self)
Test the second free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_iso_cone(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_iso_cone_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_iso_cone_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_iso_cone_free_rotor(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_iso_cone_free_rotor_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_iso_cone_free_rotor_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_iso_cone_free_rotor2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_iso_cone_free_rotor2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_iso_cone_free_rotor2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_iso_cone_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_iso_cone_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_iso_cone_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_pseudo_ellipse(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_pseudo_ellipse_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_pseudo_ellipse_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_pseudo_ellipse2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_pseudo_ellipse2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_pseudo_ellipse2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_pseudo_ellipse_free_rotor(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_pseudo_ellipse_free_rotor_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_pseudo_ellipse_free_rotor_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_pseudo_ellipse_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_qr_int_pseudo_ellipse_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_pseudo_ellipse_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_rigid(self)
Test the rigid frame order model of CaM.

test_cam_qr_int_rigid_pcs(self)
Test the rigid frame order model of CaM (with only PCS data).

test_cam_qr_int_rigid_rdc(self)
Test the rigid frame order model of CaM (with only RDC data).

test_cam_qr_int_rotor(self)
Test the rotor frame order model of CaM.

test_cam_qr_int_rotor_pcs(self)
Test the rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_rotor_rdc(self)
Test the rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_rotor_2_state(self)
Test the 2-state rotor frame order model of CaM.

test_cam_qr_int_rotor_2_state_pcs(self)
Test the 2-state rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_rotor_2_state_rdc(self)
Test the 2-state rotor frame order model of CaM (with only RDC data).

test_cam_qr_int_rotor2(self)
Test the second rotor frame order model of CaM.

test_cam_qr_int_rotor2_pcs(self)
Test the second rotor frame order model of CaM (with only PCS data).

test_cam_qr_int_rotor2_rdc(self)
Test the second rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_double_rotor(self)
Test the double rotor frame order model of CaM.

test_cam_quad_int_double_rotor_pcs(self)
Test the double rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_double_rotor_rdc(self)
Test the double rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_double_rotor_large_angle(self)
Test the double rotor frame order model of CaM.

test_cam_quad_int_double_rotor_large_angle_pcs(self)
Test the double rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_double_rotor_large_angle_rdc(self)
Test the double rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_free_rotor(self)
Test the free rotor frame order model of CaM.

test_cam_quad_int_free_rotor_missing_data(self)
Test the free rotor frame order model of CaM.

test_cam_quad_int_free_rotor_pcs(self)
Test the free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_free_rotor_rdc(self)
Test the free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_free_rotor2(self)
Test the second free rotor frame order model of CaM.

test_cam_quad_int_free_rotor2_pcs(self)
Test the second free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_free_rotor2_rdc(self)
Test the second free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_iso_cone(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_iso_cone_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_iso_cone_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_iso_cone_free_rotor(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_iso_cone_free_rotor_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_iso_cone_free_rotor_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_iso_cone_free_rotor2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_iso_cone_free_rotor2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_iso_cone_free_rotor2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_iso_cone_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_iso_cone_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_iso_cone_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_pseudo_ellipse(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_pseudo_ellipse_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_pseudo_ellipse_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_pseudo_ellipse2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_pseudo_ellipse2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_pseudo_ellipse2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_pseudo_ellipse_free_rotor(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_pseudo_ellipse_free_rotor_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_pseudo_ellipse_free_rotor_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_pseudo_ellipse_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_quad_int_pseudo_ellipse_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_pseudo_ellipse_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_rigid(self)
Test the rigid frame order model of CaM.

test_cam_quad_int_rigid_pcs(self)
Test the rigid frame order model of CaM (with only PCS data).

test_cam_quad_int_rigid_rdc(self)
Test the rigid frame order model of CaM (with only RDC data).

test_cam_quad_int_rotor(self)
Test the rotor frame order model of CaM.

test_cam_quad_int_rotor_pcs(self)
Test the rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_rotor_rdc(self)
Test the rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_rotor_2_state(self)
Test the 2-state rotor frame order model of CaM.

test_cam_quad_int_rotor_2_state_pcs(self)
Test the 2-state rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_rotor_2_state_rdc(self)
Test the 2-state rotor frame order model of CaM (with only RDC data).

test_cam_quad_int_rotor2(self)
Test the second rotor frame order model of CaM.

test_cam_quad_int_rotor2_pcs(self)
Test the second rotor frame order model of CaM (with only PCS data).

test_cam_quad_int_rotor2_rdc(self)
Test the second rotor frame order model of CaM (with only RDC data).

test_count_sobol_points(self)
Test the ability of the frame_order.sobol_setup user function to be able to count the number of Sobol' points used for the current parameter values.

test_count_sobol_points2(self)
Test the frame_order.count_sobol_points user function.

test_count_sobol_points_free_rotor(self)
Test the frame_order.count_sobol_points user function for the free-rotor model.

test_count_sobol_points_iso_cone_free_rotor(self)
Test the frame_order.count_sobol_points user function for the free-rotor isotropic cone model.

test_count_sobol_points_rigid(self)
Test the frame_order.count_sobol_points user function for the rigid model.

test_count_sobol_points_rotor(self)
Test the frame_order.count_sobol_points user function for the rotor model.

test_decompose_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor model along the z-axis.

test_decompose_iso_cone_z_axis(self)
Check the frame_order.decompose user function PDB file for the isotropic cone model along the z-axis.

test_decompose_iso_cone_xz_plane_tilt(self)
Check the frame_order.decompose user function PDB file for the isotropic cone model with a xz-plane tilt.

test_decompose_iso_cone_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor isotropic cone model along the z-axis.

test_decompose_iso_cone_torsionless_z_axis(self)
Check the frame_order.decompose user function PDB file for the torsionless isotropic cone model along the z-axis.

test_decompose_pseudo_ellipse_xz_plane_tilt(self)
Check the frame_order.decompose user function PDB file for the pseudo-ellipse model with a xz-plane tilt.

test_decompose_pseudo_ellipse_z_axis(self)
Check the frame_order.decompose user function PDB file for the pseudo-ellipse model along the z-axis.

test_decompose_pseudo_ellipse_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor pseudo-ellipse model along the z-axis.

test_decompose_pseudo_ellipse_torsionless_z_axis(self)
Check the frame_order.decompose user function PDB file for the torsionless pseudo-ellipse model along the z-axis.

test_decompose_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the rotor model along the z-axis.

test_decompose2_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor model along the z-axis.

test_decompose2_iso_cone_z_axis(self)
Check the frame_order.decompose user function PDB file for the isotropic cone model along the z-axis.

test_decompose2_iso_cone_xz_plane_tilt(self)
Check the frame_order.decompose user function PDB file for the isotropic cone model with a xz-plane tilt.

test_decompose2_iso_cone_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor isotropic cone model along the z-axis.

test_decompose2_iso_cone_torsionless_z_axis(self)
Check the frame_order.decompose user function PDB file for the torsionless isotropic cone model along the z-axis.

test_decompose2_pseudo_ellipse_xz_plane_tilt(self)
Check the frame_order.decompose user function PDB file for the pseudo-ellipse model with a xz-plane tilt.

test_decompose2_pseudo_ellipse_z_axis(self)
Check the frame_order.decompose user function PDB file for the pseudo-ellipse model along the z-axis.

test_decompose2_pseudo_ellipse_free_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the free rotor pseudo-ellipse model along the z-axis.

test_decompose2_pseudo_ellipse_torsionless_z_axis(self)
Check the frame_order.decompose user function PDB file for the torsionless pseudo-ellipse model along the z-axis.

test_decompose2_rotor_z_axis(self)
Check the frame_order.decompose user function PDB file for the rotor model along the z-axis.

test_distribute_free_rotor_z_axis(self)
Check the frame_order.distribute user function PDB file for the free rotor model along the z-axis.

test_distribute_iso_cone_z_axis(self)
Check the frame_order.distribute user function PDB file for the isotropic cone model along the z-axis.

test_distribute_iso_cone_xz_plane_tilt(self)
Check the frame_order.distribute user function PDB file for the isotropic cone model with a xz-plane tilt.

test_distribute_iso_cone_torsionless_z_axis(self)
Check the frame_order.distribute user function PDB file for the torsionless isotropic cone model along the z-axis.

test_distribute_pseudo_ellipse_xz_plane_tilt(self)
Check the frame_order.distribute user function PDB file for the pseudo-ellipse model with a xz-plane tilt.

test_distribute_pseudo_ellipse_z_axis(self)
Check the frame_order.distribute user function PDB file for the pseudo-ellipse model along the z-axis.

test_distribute_pseudo_ellipse_free_rotor_z_axis(self)
Check the frame_order.distribute user function PDB file for the free rotor pseudo-ellipse model along the z-axis.

test_distribute_pseudo_ellipse_torsionless_z_axis(self)
Check the frame_order.distribute user function PDB file for the torsionless pseudo-ellipse model along the z-axis.

test_distribute_rotor_z_axis(self)
Check the frame_order.distribute user function PDB file for the rotor model along the z-axis.

test_frame_order_pdb_model_ensemble(self)
Test the operation of the frame_order.pdb_model user function when an ensemble of structures are loaded.

test_frame_order_pdb_model_failed_pivot(self)
Test the operation of the frame_order.pdb_model user function when the pivot is outside of the PDB limits.

test_generate_rotor2_distribution(self)
Generate the rotor2 distribution of CaM.

test_opendx_map(self)
Test the mapping of the Euler angle parameters for OpenDx viewing.

test_pdb_model_double_rotor_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the rotor model along the z-axis.

test_pdb_model_double_rotor_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the rotor model along the z-axis.

test_pdb_model_free_rotor_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the rotor model with a xz-plane tilt.

test_pdb_model_free_rotor_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the free rotor model along the z-axis.

test_pdb_model_iso_cone_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the isotropic cone model with a xz-plane tilt.

test_pdb_model_iso_cone_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the isotropic cone model along the z-axis.

test_pdb_model_iso_cone_free_rotor_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the free rotor isotropic cone model with a xz-plane tilt.

test_pdb_model_iso_cone_free_rotor_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the free rotor isotropic cone model along the z-axis.

test_pdb_model_iso_cone_torsionless_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the torsionless isotropic cone model with a xz-plane tilt.

test_pdb_model_iso_cone_torsionless_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the torsionless isotropic cone model along the z-axis.

test_pdb_model_pseudo_ellipse_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the pseudo-ellipse model with a xz-plane tilt.

test_pdb_model_pseudo_ellipse_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the pseudo-ellipse model along the z-axis.

test_pdb_model_pseudo_ellipse_free_rotor_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the free rotor pseudo-ellipse model with a xz-plane tilt.

test_pdb_model_pseudo_ellipse_free_rotor_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the free rotor pseudo-ellipse model along the z-axis.

test_pdb_model_pseudo_ellipse_torsionless_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the torsionless pseudo-ellipse model with a xz-plane tilt.

test_pdb_model_pseudo_ellipse_torsionless_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the torsionless pseudo-ellipse model along the z-axis.

test_pdb_model_rotor_xz_plane_tilt(self)
Check the frame_order.pdb_model user function PDB file for the rotor model with a xz-plane tilt.

test_pdb_model_rotor_z_axis(self)
Check the frame_order.pdb_model user function PDB file for the rotor model along the z-axis.

test_pseudo_ellipse_zero_cone_angle(self)
Catch for a bug in optimisation when the cone_theta_x is set to zero in the pseudo-ellipse models.

test_rigid_data_to_double_rotor_model(self)
Test the double rotor target function for the data from a rigid test molecule.

test_rigid_data_to_free_rotor_model(self)
Test the free rotor target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_free_rotor_model(self)
Test the iso cone, free rotor target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_model(self)
Test the iso cone target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_torsionless_model(self)
Test the iso cone, torsionless target function for the data from a rigid test molecule.

test_rigid_data_to_pseudo_ellipse_model(self)
Test the pseudo-ellipse target function for the data from a rigid test molecule.

test_rigid_data_to_pseudo_ellipse_torsionless_model(self)
Test the pseudo-ellipse, torsionless target function for the data from a rigid test molecule.

test_rigid_data_to_rigid_model(self)
Test the rigid target function for the data from a rigid test molecule.

test_rigid_data_to_rotor_model(self)
Test the rotor target function for the data from a rigid test molecule.

test_simulate_double_rotor_mode1_xz_plane_tilt(self, type='sim')
Check the frame_order.simulate user function PDB file for the double rotor model with a xz-plane tilt for the first rotation mode.

test_simulate_double_rotor_mode1_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the double rotor model along the z-axis for the first rotation mode.

test_simulate_double_rotor_mode2_xz_plane_tilt(self, type='sim')
Check the frame_order.simulate user function PDB file for the double rotor model with a xz-plane tilt for the second rotation mode.

test_simulate_double_rotor_mode2_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the double rotor model along the z-axis for the second rotation mode.

test_simulate_free_rotor_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the free rotor model along the z-axis.

test_simulate_iso_cone_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the isotropic cone model along the z-axis.

test_simulate_iso_cone_xz_plane_tilt(self, type='sim')
Check the frame_order.simulate user function PDB file for the isotropic cone model with a xz-plane tilt.

test_simulate_iso_cone_free_rotor_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the free rotor isotropic cone model along the z-axis.

test_simulate_iso_cone_torsionless_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the torsionless isotropic cone model along the z-axis.

test_simulate_pseudo_ellipse_xz_plane_tilt(self, type='sim')
Check the frame_order.simulate user function PDB file for the pseudo-ellipse model with a xz-plane tilt.

test_simulate_pseudo_ellipse_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the pseudo-ellipse model along the z-axis.

test_simulate_pseudo_ellipse_free_rotor_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the free rotor pseudo-ellipse model along the z-axis.

test_simulate_pseudo_ellipse_torsionless_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the torsionless pseudo-ellipse model along the z-axis.

test_simulate_rotor_z_axis(self, type='sim')
Check the frame_order.simulate user function PDB file for the rotor model along the z-axis.

test_sobol_setup(self)
Check the basic operation of the frame_order.sobol_setup user function.

test_sobol_setup2(self)
Check the operation of the frame_order.sobol_setup user function with just the model specified.

test_sobol_setup3(self)
Check the operation of the frame_order.sobol_setup user function with the model and parameters set up.

Inherited from base_classes.SystemTestCase: script_exec

Inherited from unittest.case.TestCase: __call__, __eq__, __hash__, __ne__, __repr__, __str__, addCleanup, addTypeEqualityFunc, assertAlmostEqual, assertAlmostEquals, assertDictContainsSubset, assertDictEqual, assertEqual, assertEquals, assertFalse, assertGreater, assertGreaterEqual, assertIn, assertIs, assertIsInstance, assertIsNone, assertIsNot, assertIsNotNone, assertItemsEqual, assertLess, assertLessEqual, assertListEqual, assertMultiLineEqual, assertNotAlmostEqual, assertNotAlmostEquals, assertNotEqual, assertNotEquals, assertNotIn, assertNotIsInstance, assertNotRegexpMatches, assertRaises, assertRaisesRegexp, assertRegexpMatches, assertSequenceEqual, assertSetEqual, assertTrue, assertTupleEqual, assert_, countTestCases, debug, defaultTestResult, doCleanups, fail, failIf, failIfAlmostEqual, failIfEqual, failUnless, failUnlessAlmostEqual, failUnlessEqual, failUnlessRaises, id, run, shortDescription, skipTest

Inherited from unittest.case.TestCase (private): _addSkip, _baseAssertEqual, _deprecate, _formatMessage, _getAssertEqualityFunc, _truncateMessage

Inherited from object: __delattr__, __format__, __getattribute__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Methods

Inherited from unittest.case.TestCase: setUpClass, tearDownClass

Class Variables

Inherited from unittest.case.TestCase: longMessage, maxDiff

Inherited from unittest.case.TestCase (private): _classSetupFailed, _diffThreshold

Properties

Inherited from object: __class__

Method Details

__init__(self, methodName='runTest')
(Constructor)

Skip the tests if scipy is not installed.

Parameters:

• methodName (str) - The name of the test.

Overrides: object.__init__

setUp(self)

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

tearDown(self)

Clean up after the tests.

Overrides: unittest.case.TestCase.tearDown

check_pdb_model_representation(self, data=None, files=None)

Check the PDB model representation atom and residue names and numbers and coordinates.

Propeller blade atoms with the name 'BLD' are skipped, as well as the cone interior residues with the name 'CON'.

Parameters:

• data (list of list of lists) - The list of data to check. The first dimension is for the representation, and the second for each atom. The lists of each atom consist of the residue number, residue name, atom number, atom name, and the 3D position.
• files (list of str) - The list of files for each representation.

mesg_opt_debug(self)

Method for returning a string to help debug the minimisation.

Returns: str

The debugging string.

rotate_from_Z(self, origin=array([ 0., 0., 0.]), length=0.0, angle=0.0, axis=array([ 1., 0., 0.]), R=None, neg=False)

Rotate a vector along Z-axis around the origin.

Parameters:

• origin (numpy 3D, rank-1 array) - The origin of the final vector.
• length (float) - The length of the Z-vector to rotate.
• angle (float) - The angle in rad to rotate by.
• axis (numpy 3D, rank-1 array) - The direction in the xy-plane to rotate the vector along.
• R (numpy 3D, rank-2 array) - A rotation matrix to be used before adding the origin.
• neg (bool) - A flag which if True causes the negative Z-axis to be used.

Returns: numpy 3D, rank-1 array

The final rotated vector shifted by the origin.

setup_model(self, pipe_name='model', model=None, pivot=None, ave_pos_x=None, ave_pos_y=None, ave_pos_z=None, ave_pos_alpha=None, ave_pos_beta=None, ave_pos_gamma=None, pivot_disp=None, axis_alpha=None, axis_theta=None, axis_phi=None, eigen_alpha=None, eigen_beta=None, eigen_gamma=None, cone_theta=None, cone_theta_x=None, cone_theta_y=None, cone_sigma_max=None, cone_sigma_max_2=None)

Set up for the given frame order model.

This will execute the following user functions:

• pipe.create to set up a data pipe for the model.
• frame_order.select_model.
• value.set for all given parameters.
• frame_order.pivot to define the pivot point.

Parameters:

• pipe_name (str) - The name of the new data pipe.
• model (str) - The frame order model to setup.
• pivot (list of float) - The pivot to setup.
• ave_pos_x (None or float) - The average domain position X coordinate.
• ave_pos_y (None or float) - The average domain position Y coordinate.
• ave_pos_z (None or float) - The average domain position Z coordinate.
• ave_pos_alpha (None or float) - The average domain position alpha Euler rotation angle.
• ave_pos_beta (None or float) - The average domain position beta Euler rotation angle.
• ave_pos_gamma (None or float) - The average domain position gamma Euler rotation angle.
• pivot_disp (None or float) - The pivot displacement parameter.
• axis_alpha (None or float) - The motional eigenframe axis alpha angle.
• axis_theta (None or float) - The motional eigenframe axis theta spherical angle.
• axis_phi (None or float) - The motional eigenframe axis phi spherical angle.
• eigen_alpha (None or float) - The motional eigenframe alpha Euler rotation angle.
• eigen_beta (None or float) - The motional eigenframe beta Euler rotation angle.
• eigen_gamma (None or float) - The motional eigenframe gamma Euler rotation angle.
• cone_theta (None or float) - The isotropic cone opening half angle.
• cone_theta_x (None or float) - The x-axis half cone angle.
• cone_theta_y (None or float) - The y-axis half cone angle.
• cone_sigma_max (None or float) - The maximum torsion angle.
• cone_sigma_max_2 (None or float) - The second maximum torsion angle.