Author: bugman
Date: Mon Jan 7 17:46:57 2008
New Revision: 4443
URL: http://svn.gna.org/viewcvs/relax?rev=4443&view=rev
Log:
Created a script containing the commands used in the N-state model system test.
The system test tries to execute the script. Work still needs to be done here
though.
Added:
branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py
Modified:
branches/N_state_model/test_suite/system_tests/n_state_model.py
Modified: branches/N_state_model/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/n_state_model.py?rev=4443&r1=4442&r2=4443&view=diff
==============================================================================
--- branches/N_state_model/test_suite/system_tests/n_state_model.py (original)
+++ branches/N_state_model/test_suite/system_tests/n_state_model.py Mon Jan 7
17:46:57 2008
@@ -49,6 +49,11 @@
State 5: {0, -pi/4, 0}
"""
+ # Execute the script '5_state_xz.py'.
+
self.relax.interpreter.script('test_suite/system_tests/scripts/5_state_xz.py')
+
+ return
+
# Create the data pipe.
self.relax.interpreter._Pipe.create('C domain', 'N-state')
Added: branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py?rev=4443&view=auto
==============================================================================
--- branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py (added)
+++ branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py Mon
Jan 7 17:46:57 2008
@@ -1,0 +1,55 @@
+"""A 5-state model in the xz-plane (no pivotting of alpha).
+
+The 5 states correspond to the Euler angles (z-y-z notation):
+ State 1: {0, pi/4, 0}
+ State 2: {0, pi/8, 0}
+ State 3: {0, 0, 0}
+ State 4: {0, -pi/8, 0}
+ State 5: {0, -pi/4, 0}
+"""
+
+# Create the data pipe.
+pipe.create('C domain', 'N-state')
+
+# Load the C-terminal alignment tensors..
+align_tensor.init(tensor='chi1', params=(-1/2., -1/2., 0., 0., 0.))
+align_tensor.init(tensor='chi2', params=(-1/8., -7/8., 0., 0., 0.))
+align_tensor.init(tensor='chi3', params=(-1/8., 1/16., 0., 0., -15/16.))
+align_tensor.init(tensor='chi4', params=(7/16., -7/8., 0., 9/16., 0.))
+align_tensor.init(tensor='chi5', params=(-1/2., -1/2., 3/8., 0., 0.))
+
+# Calculate the singular values.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
+
+# Calculate the angles between the matrices.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+
+# Create the data pipe.
+pipe.create('N domain', 'N-state')
+
+# Load the N-terminal alignment tensors.
+align_tensor.init(tensor='chi1', params=(1/4., -1/2., 0.,
3/4., 0.))
+align_tensor.init(tensor='chi2', params=(7/16., -7/8., 0.,
9/16., 0.))
+align_tensor.init(tensor='chi3', params=(-1/32., 1/16., -15/(16*sqrt(2)),
3/32., -15/(16*sqrt(2))))
+align_tensor.init(tensor='chi4', params=(1., -7/8., 0., 0.,
0.))
+align_tensor.init(tensor='chi5', params=(1/4., -1/2., 3/(8*sqrt(2)),
3/4., -3/(8*sqrt(2))))
+
+# Calculate the singular values.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
+
+# Calculate the angles between the matrices.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+# Grid search.
+minimisation.grid_search(inc=11)
+
+# Minimise.
+minimisation.minimise('simplex')
+
+# Finish.
+#results.write(file='devnull', force=1)
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