Author: bugman
Date: Mon Oct 24 12:11:07 2011
New Revision: 14893
URL: http://svn.gna.org/viewcvs/relax?rev=14893&view=rev
Log:
Created the Frame_order.test_cam_rigid system test and optimisation script.
Added:
1.3/test_suite/system_tests/scripts/frame_order/cam/
1.3/test_suite/system_tests/scripts/frame_order/cam/rigid.py
Modified:
1.3/test_suite/system_tests/frame_order.py
Modified: 1.3/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/frame_order.py?rev=14893&r1=14892&r2=14893&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/frame_order.py (original)
+++ 1.3/test_suite/system_tests/frame_order.py Mon Oct 24 12:11:07 2011
@@ -157,6 +157,21 @@
setattr(cdp, param, curr)
+ def test_cam_rigid(self):
+ """Test the rigid frame order model of CaM."""
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rigid.py')
+
+ # Check the average structure atomic positions (to only one decimal
point as the PDB file accuracy isn't great).
+ ave_pos = ds['ave pos'].structure.structural_data[0].mol[0]
+ orig_pos = ds['orig pos'].structure.structural_data[0].mol[0]
+ for i in range(len(ave_pos.atom_name)):
+ self.assertAlmostEqual(ave_pos.x[i], orig_pos.x[i], 1)
+ self.assertAlmostEqual(ave_pos.y[i], orig_pos.y[i], 1)
+ self.assertAlmostEqual(ave_pos.z[i], orig_pos.z[i], 1)
+
+
def test_model_free_rotor(self):
"""Test the free rotor frame order model."""
Added: 1.3/test_suite/system_tests/scripts/frame_order/cam/rigid.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/frame_order/cam/rigid.py?rev=14893&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/frame_order/cam/rigid.py (added)
+++ 1.3/test_suite/system_tests/scripts/frame_order/cam/rigid.py Mon Oct 24
12:11:07 2011
@@ -1,0 +1,100 @@
+# Script for optimising the rigid frame order test model of CaM.
+
+# Python module imports.
+from numpy import array, float64, transpose, zeros
+from os import sep
+
+# relax module imports.
+from maths_fns.rotation_matrix import euler_to_R_zyz
+from status import Status; status = Status()
+
+
+# Some variables.
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep
+
+
+class Analysis:
+ def __init__(self):
+ """Execute the frame order analysis."""
+
+ # Optimise.
+ self.optimisation()
+
+ # The rotation matrix.
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
+ print("Rotation matrix:\n%s\n" % R)
+ R = transpose(R)
+ print("Inverted rotation:\n%s\n" % R)
+
+ # Load the original structure.
+ self.original_structure()
+
+ # Domain transformation.
+ self.transform(R, array([ 37.254, 0.5, 16.7465]))
+
+
+ def optimisation(self):
+ """Optimise the frame order model."""
+
+ # The file paths.
+ PATH_N_DOM = DATA_PATH
+ PATH_C_DOM = PATH_N_DOM+sep+'rigid'+sep
+
+ # Create the data pipe.
+ pipe.create(pipe_name='frame order', pipe_type='frame order')
+
+ # Load the tensors.
+ script(PATH_N_DOM + 'tensors.py')
+ script(PATH_C_DOM + 'tensors.py')
+
+ # The tensor domains and reductions.
+ full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
+ red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
+ for i in range(len(full)):
+ align_tensor.set_domain(tensor=full[i], domain='N')
+ align_tensor.set_domain(tensor=red[i], domain='C')
+ align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
+
+ # Select the model.
+ frame_order.select_model('rigid')
+
+ # Set the reference domain.
+ frame_order.ref_domain('N')
+
+ # Optimise.
+ grid_search(inc=3)
+ minimise('simplex', constraints=False)
+
+ # Write the results.
+ results.write('devnull', dir=None, force=True)
+
+
+ def original_structure(self):
+ """Load the original structure into a dedicated data pipe."""
+
+ # Create a special data pipe for the original rigid body position.
+ pipe.create(pipe_name='orig pos', pipe_type='frame order')
+
+ # Load the structure.
+ structure.read_pdb(DATA_PATH+'1J7P_1st_NH.pdb')
+
+
+ def transform(self, R, pivot):
+ """Transform the domain to the average position."""
+
+ # Create a special data pipe for the average rigid body position.
+ pipe.create(pipe_name='ave pos', pipe_type='frame order')
+
+ # Load the structure.
+ structure.read_pdb(DATA_PATH+'1J7P_1st_NH_rot.pdb')
+
+ # Rotate all atoms.
+ structure.rotate(R=R, origin=pivot)
+
+ # Write out the new PDB.
+ structure.write_pdb('devnull')
+
+
+# Execute the analysis.
+Analysis()
r14893 - in /1.3/test_suite/system_tests: frame_order.py scripts/frame_order/cam/ scripts/frame_order/cam/rigid.py