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)
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