Author: bugman
Date: Fri Dec 14 17:00:41 2012
New Revision: 18139
URL: http://svn.gna.org/viewcvs/relax?rev=18139&view=rev
Log:
Created the N_state_model.test_frame_order_align_fit to demonstrate a rare
bug.
This bug is when alignment tensors, RDC and PCS data is copied from a frame
order data pipe to a
N-state model data pipe and a single tensor is optimised.
Added:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py
- copied, changed from r18137,
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
Modified:
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
Modified:
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/n_state_model.py?rev=18139&r1=18138&r2=18139&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/n_state_model.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/n_state_model.py Fri
Dec 14 17:00:41 2012
@@ -439,6 +439,33 @@
self.assertEqual(spin_orig.pcs[id], spin_new.pcs[id])
+ def test_frame_order_align_fit(self):
+ """Test the use of alignment tensors, RDCs and PCSs from a frame
order data pipe for the N-state model."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'frame_order_align_fit.py')
+
+ # The actual tensors.
+ A_5D = []
+ A_5D.append([1.42219822168827662867e-04,
-1.44543001566521341940e-04, -7.07796211648713973798e-04,
-6.01619494082773244303e-04, 2.02008007072950861996e-04])
+ A_5D.append([3.56720663040924505435e-04,
-2.68385787902088840916e-04, -1.69361406642305853832e-04,
1.71873715515064501074e-04, -3.05790155096090983822e-04])
+ A_5D.append([2.32088908680377300801e-07, 2.08076808579168379617e-06,
-2.21735465435989729223e-06, -3.74311563209448033818e-06,
-2.40784858070560310370e-06])
+ A_5D.append([-2.62495279588228071048e-04,
7.35617367964106275147e-04, 6.39754192258981332648e-05,
6.27880171180572523460e-05, 2.01197582457700226708e-04])
+
+ # Check the tensors.
+ for i in range(1):
+ self.assertAlmostEqual(cdp.align_tensors[i].Axx, A_5D[i][0])
+ self.assertAlmostEqual(cdp.align_tensors[i].Ayy, A_5D[i][1])
+ self.assertAlmostEqual(cdp.align_tensors[i].Axy, A_5D[i][2])
+ self.assertAlmostEqual(cdp.align_tensors[i].Axz, A_5D[i][3])
+ self.assertAlmostEqual(cdp.align_tensors[i].Ayz, A_5D[i][4])
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.chi2, 0.0)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+ self.assertAlmostEqual(cdp.q_pcs, 0.0)
+
+
def test_lactose_n_state_fixed(self):
"""The 4-state model analysis of lactose using RDCs and PCSs."""
Copied:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py
(from r18137,
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/missing_data_test.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py?p2=branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py&p1=branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/missing_data_test.py&r1=18137&r2=18139&rev=18139&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/frame_order_align_fit.py
Fri Dec 14 17:00:41 2012
@@ -12,7 +12,7 @@
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'missing_data'
# Create the data pipe.
-self._execute_uf(uf_name='pipe.create', pipe_name='missing_data_test',
pipe_type='N-state')
+self._execute_uf(uf_name='pipe.create', pipe_name='orig', pipe_type='frame
order')
# Load the structure.
self._execute_uf(uf_name='structure.read_pdb', file='LE_trunc.pdb',
dir=str_path, set_mol_name='LE')
@@ -51,17 +51,36 @@
# The frequency.
self._execute_uf(uf_name='frq.set', id=align_list[i], frq=799.75376122 *
1e6)
+ # Initialise an alignment tensor.
+ self._execute_uf(uf_name='align_tensor.init', tensor=align_list[i],
align_id=align_list[i], params=(0, 0, 0, 0, 0))
+
# Set the paramagnetic centre.
self._execute_uf(uf_name='paramag.centre', pos=[1, 2, -30])
+
+# Create a new data pipe by copying the old, and switch to it.
+self._execute_uf(uf_name='pipe.copy', pipe_to='copy')
+self._execute_uf(uf_name='pipe.switch', pipe_name='copy')
+
+# Change the data pipe type.
+self._execute_uf(uf_name='pipe.change_type', pipe_type='N-state')
+
+# Delete all the alignment data.
+self._execute_uf(uf_name='rdc.delete')
+self._execute_uf(uf_name='pcs.delete')
+self._execute_uf(uf_name='align_tensor.delete')
+
+# Copy the tensor back.
+self._execute_uf(uf_name='align_tensor.copy', pipe_from='orig',
tensor_from='Dy')
+
+# Copy the alignment data.
+self._execute_uf(uf_name='rdc.copy', pipe_from='orig', align_id='Dy')
+self._execute_uf(uf_name='pcs.copy', pipe_from='orig', align_id='Dy')
# Set up the model.
self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
# Minimisation.
-self._execute_uf(uf_name='minimise', min_algor='bfgs', constraints=True)
+self._execute_uf(uf_name='minimise', min_algor='newton', constraints=True)
# Write out a results file.
self._execute_uf(uf_name='results.write', file='devnull', force=True)
-
-# Show the tensors.
-self._execute_uf(uf_name='align_tensor.display')
r18139 - in /branches/frame_order_testing/test_suite/system_tests: ./ scripts/n_state_model/