Author: bugman
Date: Thu Dec 13 17:47:10 2012
New Revision: 18133
URL: http://svn.gna.org/viewcvs/relax?rev=18133&view=rev
Log:
Created the N_state_model.test_paramag_align_fit system test to check the
paramagnetic data.
This test check the alignment tensor optimisation of the RDC and PCS data in
test_suite/shared_data/align_data/paramagnetic/, loading both alignment data
sets but only
optimising one tensor.
Added:
trunk/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py
- copied, changed from r18125,
trunk/test_suite/system_tests/scripts/n_state_model/align_fit.py
Modified:
trunk/test_suite/system_tests/n_state_model.py
Modified: trunk/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/n_state_model.py?rev=18133&r1=18132&r2=18133&view=diff
==============================================================================
--- trunk/test_suite/system_tests/n_state_model.py (original)
+++ trunk/test_suite/system_tests/n_state_model.py Thu Dec 13 17:47:10 2012
@@ -580,6 +580,25 @@
self.assertAlmostEqual(cdp.align_tensors[0].Ayz_err, 0.0)
+ def test_paramag_align_fit(self):
+ """Test the use of RDCs and PCSs to find the alignment tensor."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'paramag_align_fit.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[1].Axx, 0.001414718232784)
+ self.assertAlmostEqual(cdp.align_tensors[1].Ayy, 0.001530457843766)
+ self.assertAlmostEqual(cdp.align_tensors[1].Axy, 0.001689957281873)
+ self.assertAlmostEqual(cdp.align_tensors[1].Axz, 0.000838692329704)
+ self.assertAlmostEqual(cdp.align_tensors[1].Ayz, -0.000984302159683)
+ self.assertAlmostEqual(cdp.q_factors_rdc['Er'], 0.0, 7)
+ self.assertAlmostEqual(cdp.q_factors_rdc_norm2['Er'], 0.0, 7)
+ self.assertAlmostEqual(cdp.q_factors_pcs['Er'], 0.0, 7)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0, 7)
+ self.assertAlmostEqual(cdp.q_pcs, 0.0, 7)
+
+
def test_paramag_centre_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
Copied:
trunk/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py
(from r18125,
trunk/test_suite/system_tests/scripts/n_state_model/align_fit.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py?p2=trunk/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py&p1=trunk/test_suite/system_tests/scripts/n_state_model/align_fit.py&r1=18125&r2=18133&rev=18133&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/align_fit.py
(original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/paramag_align_fit.py
Thu Dec 13 17:47:10 2012
@@ -11,26 +11,14 @@
# Path of the alignment data and structure.
-DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'CaM'
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'paramagnetic'
STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
# Create the data pipe.
-self._execute_uf('rdc', 'N-state', uf_name='pipe.create')
-
-# Set the mode, if not specified by the system test.
-if not hasattr(ds, 'mode'):
- ds.mode = 'all'
-
-# The data to use.
-if hasattr(ds, 'rand') and ds.rand:
- rdc_file = 'synth_rdc_rand'
- pcs_file = 'synth_pcs_rand'
-else:
- rdc_file = 'synth_rdc'
- pcs_file = 'synth_pcs'
+self._execute_uf('paramagnetic alignment', 'N-state', uf_name='pipe.create')
# Load the CaM structure.
-self._execute_uf(uf_name='structure.read_pdb', file='bax_C_1J7P_N_H_Ca',
dir=STRUCT_PATH)
+self._execute_uf(uf_name='structure.read_pdb', file='bax_C_1J7P_N_H_Ca',
dir=STRUCT_PATH, set_mol_name='CaM')
# Load the spins.
self._execute_uf(uf_name='structure.load_spins')
@@ -45,42 +33,37 @@
self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H')
# RDCs.
-if ds.mode in ['rdc', 'all']:
- self._execute_uf(uf_name='rdc.read', align_id='synth', file=rdc_file,
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=None)
+self._execute_uf(uf_name='rdc.read', align_id='Dy', file='dy_700_rdc',
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=None)
+self._execute_uf(uf_name='rdc.read', align_id='Er', file='er_900_rdc',
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=None)
+
+# The frequency.
+self._execute_uf(uf_name='frq.set', id='Dy', frq=700.0 * 1e6)
+self._execute_uf(uf_name='frq.set', id='Er', frq=900.0 * 1e6)
# PCSs.
-if ds.mode in ['pcs', 'all']:
- self._execute_uf(uf_name='pcs.read', align_id='synth', file=pcs_file,
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6)
+self._execute_uf(uf_name='pcs.read', align_id='Dy', file='dy_pcs',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6)
+self._execute_uf(uf_name='pcs.read', align_id='Er', file='er_pcs',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6)
- # Set the paramagnetic centre.
- self._execute_uf(uf_name='paramag.centre', atom_id=':1000@CA')
+# Set the paramagnetic centre.
+self._execute_uf(uf_name='paramag.centre', atom_id=':1000@CA')
- # The temperature.
- self._execute_uf(uf_name='temperature', id='synth', temp=303)
-
- # The frequency.
- self._execute_uf(uf_name='frq.set', id='synth', frq=600.0 * 1e6)
+# The temperature.
+self._execute_uf(uf_name='temperature', id='Dy', temp=303)
+self._execute_uf(uf_name='temperature', id='Er', temp=303)
# Set up the model.
self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
-# Set the tensor elements.
-#cdp.align_tensors[0].Axx = -0.351261/2000
-#cdp.align_tensors[0].Ayy = 0.556994/2000
-#cdp.align_tensors[0].Axy = -0.506392/2000
-#cdp.align_tensors[0].Axz = 0.560544/2000
-#cdp.align_tensors[0].Ayz = -0.286367/2000
+# Set up the alignment tensors (for faster optimisation in the test suite)
+self._execute_uf(uf_name='align_tensor.init', tensor='Dy', params=(0.00037,
-0.00017, 0.00016, 0.00060, -0.00019))
+self._execute_uf(uf_name='align_tensor.init', tensor='Er', params=(0.00141,
0.00153, 0.00169, 0.00084, -0.00098))
-# Minimisation.
-self._execute_uf(uf_name='grid_search', inc=3)
+# Minimisation of only the Er tensor.
+self._execute_uf(uf_name='align_tensor.fix', id='Dy', fixed=True)
self._execute_uf('simplex', constraints=False, max_iter=500,
uf_name='minimise')
# Write out a results file.
-self._execute_uf('devnull', force=True, uf_name='results.write')
-
-# Show the tensors.
-self._execute_uf(uf_name='align_tensor.display')
+self._execute_uf('devnull', dir=None, force=True, uf_name='results.write')
# Print the contents of the current data pipe (for debugging Q-values).
print(cdp)
-print(cdp.align_tensors[0])
r18133 - in /trunk/test_suite/system_tests: n_state_model.py scripts/n_state_model/paramag_align_fit.py