Author: bugman Date: Fri Nov 28 08:50:00 2014 New Revision: 26796 URL: http://svn.gna.org/viewcvs/relax?rev=26796&view=rev Log: 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. Modified: branches/frame_order_cleanup/test_suite/system_tests/frame_order.py Modified: branches/frame_order_cleanup/test_suite/system_tests/frame_order.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/frame_order.py?rev=26796&r1=26795&r2=26796&view=diff ============================================================================== --- branches/frame_order_cleanup/test_suite/system_tests/frame_order.py (original) +++ branches/frame_order_cleanup/test_suite/system_tests/frame_order.py Fri Nov 28 08:50:00 2014 @@ -389,19 +389,14 @@ # Create a data pipe. self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame order') - # Convert the pivot to a numpy array. - pivot = array(pivot) - - # The 3 atomic positions. + # Create a 6 atom structure with the CoM at [0, 0, 0]. atom_pos = 100.0 * eye(3) - - # Create a 6 atom structure. - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='X', res_num=1, pos=atom_pos[0]+pivot, element='N') - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='Y', res_num=2, pos=atom_pos[1]+pivot, element='N') - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='Z', res_num=3, pos=atom_pos[2]+pivot, element='N') - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nX', res_num=4, pos=-atom_pos[0]+pivot, element='N') - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nY', res_num=5, pos=-atom_pos[1]+pivot, element='N') - self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nZ', res_num=6, pos=-atom_pos[2]+pivot, element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='X', res_num=1, pos=atom_pos[0], element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='Y', res_num=2, pos=atom_pos[1], element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='Z', res_num=3, pos=atom_pos[2], element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nX', res_num=4, pos=-atom_pos[0], element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nY', res_num=5, pos=-atom_pos[1], element='N') + self.interpreter.structure.add_atom(mol_name='axes', atom_name='N', res_name='nZ', res_num=6, pos=-atom_pos[2], element='N') # Set up the moving domain. self.interpreter.domain(id='X', spin_id=':1') @@ -3193,7 +3188,7 @@ print("Rotor apex (100*axis + [1, 0, 0]):\n %s" % (l*axis + pivot)) # Set up. - self.setup_model(pipe_name='PDB model', model='rotor', pivot=pivot, ave_pos_x=0.0, ave_pos_y=0.0, ave_pos_z=0.0, ave_pos_alpha=0.0, ave_pos_beta=0.0, ave_pos_gamma=0.0, axis_alpha=axis_alpha, cone_sigma_max=cone_sigma_max) + self.setup_model(pipe_name='PDB model', model='rotor', pivot=pivot, ave_pos_x=pivot[0], ave_pos_y=pivot[1], ave_pos_z=pivot[2], ave_pos_alpha=0.0, ave_pos_beta=0.0, ave_pos_gamma=0.0, axis_alpha=axis_alpha, cone_sigma_max=cone_sigma_max) # Create the PDB. self.interpreter.frame_order.simulate(file='simulation.pdb', dir=ds.tmpdir, step_size=10.0, snapshot=10, total=sim_num)