Author: bugman
Date: Fri Jun 14 19:13:56 2013
New Revision: 20136
URL: http://svn.gna.org/viewcvs/relax?rev=20136&view=rev
Log:
Created the N_state_model.test_absolute_T system test.
This is for checking the optimisation of absolute T=J+D values to find
alignment tensors.
Added:
trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
(with props)
trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py
Modified:
trunk/test_suite/system_tests/n_state_model.py
Added:
trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt?rev=20136&view=auto
==============================================================================
--- trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
(added)
+++ trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
Fri Jun 14 19:13:56 2013
@@ -1,0 +1,23 @@
+# Spin_ID1 Spin_ID2 T=J+D error J error Sign of J distan
+
+ @14 @35 195.2 0.27 158.2 0.12 1 1.083939
+ @11 @32 205.9 0.17 168.1 0.04 1 1.078456
+ @23 @45 109.4 1.64 149.4 0.11 1 1.096979
+ @8 @30 113.8 0.32 124.8 0.06 1 1.096844
+ @9 @31 127.4 0.21 144.9 0.007 1 1.091030
+ @21 @42 156.0 0.36 158.8 0.01 1 1.086156
+ @7 @29 92.1 3.16 130.8 0.08 1 1.096312
+ @5 @26 173.2 0.17 148.1 0.12 1 1.094863
+ @13 @34 183.0 0.16 160.2 0.12 1 1.083164
+ @12 @33 174.3 0.11 158.6 0.14 1 1.083601
+ @24 @46 152.2 0.27 135.3 0.05 1 1.087948
+ @24 @47 97.3 1.99 125.6 0.14 1 1.094413
+ @6 @27 136.0 1.44 129.7 0.14 1 1.091609
+ @6 @28 129.2 0.83 130.8 0.24 1 1.092415
+ @18 @38 145.5 0.31 148.2 0.28 1 1.093127
+ @18 @39 156.0 0.24 130.5 0.39 1 1.098294
+ @19 @40 121.6 0.39 130.4 0.03 1 1.090714
+ @19 @41 128.0 3.17 138.2 0.07 1 1.094526
+ @22 @44 154.5 0.18 145.5 0.02 1 1.090005
+ @22 @43 94.2 0.35 136.8 0.05 1 1.098353
+
Propchange:
trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
------------------------------------------------------------------------------
svn:eol-style = native
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=20136&r1=20135&r2=20136&view=diff
==============================================================================
--- trunk/test_suite/system_tests/n_state_model.py (original)
+++ trunk/test_suite/system_tests/n_state_model.py Fri Jun 14 19:13:56 2013
@@ -213,6 +213,65 @@
self.assertAlmostEqual(cdp.q_rdc_norm2, 0.81262759306400001)
+ def test_absolute_T(self):
+ """Test the fitting of signless T values (J+D)."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'absolute_T.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -1.436586299657e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, -5.004443735044e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -5.017832275009e-05)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 1.366097786433e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -1.614772175671e-04)
+ self.assertAlmostEqual(cdp.chi2, 311.70348701353225)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+ self.assertAlmostEqual(cdp.q_rdc_norm2, 0.086891848854541404)
+
+ # The signless T data.
+ T = [195.2, 205.9, 109.4, 113.8, 127.4, 156.0, 92.1, 173.2, 183.0,
174.3, 152.2, 97.3, 136.0, 129.2, 145.5, 156.0, 121.6, 128.0, 154.5, 94.2]
+ T_bc = [
+ 195.009353539915281,
+ 205.456622836526037,
+ 112.285085032859712,
+ 113.628896345578610,
+ 127.440986667041187,
+ 155.505017063790831,
+ 94.332271833299316,
+ 172.408496922639102,
+ 181.972859458051403,
+ 173.655640981746103,
+ 153.402585241137388,
+ 92.115389822570464,
+ 139.743303992644570,
+ 131.399101601878243,
+ 146.219317894376132,
+ 153.945261372587538,
+ 119.541444938794172,
+ 126.620471670822312,
+ 155.940753902549545,
+ 90.813638474619523
+ ]
+
+ # Back calc.
+ self.interpreter.rdc.back_calc('Gel')
+
+ # Check the spin data.
+ i = 0
+ for interatom in interatomic_loop():
+ # No PCS.
+ if not hasattr(interatom, 'rdc'):
+ continue
+
+ # Check the loaded and back-calculated absolute values.
+ self.assertAlmostEqual(interatom.rdc['Gel'], T[i])
+ self.assertAlmostEqual(interatom.rdc_bc['Gel'], T_bc[i])
+
+ # Increment the spin index.
+ i += 1
+
+
def test_align_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
Added: trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py?rev=20136&view=auto
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py (added)
+++ trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py Fri Jun
14 19:13:56 2013
@@ -1,0 +1,51 @@
+"""Script for testing the fitting of signless T data (J+D)."""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+
+# Path of the alignment data and structure.
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'
+STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+# Create the data pipe.
+self._execute_uf(uf_name='pipe.create', pipe_name='1J RDCs',
pipe_type='N-state')
+
+# Load the structure.
+self._execute_uf(uf_name='structure.read_xyz', file='strychnine.xyz',
dir=STRUCT_PATH)
+
+# Set up the 13C and 1H spins information.
+self._execute_uf(uf_name='structure.load_spins', spin_id='@C*',
ave_pos=False)
+self._execute_uf(uf_name='structure.load_spins', spin_id='@H*',
ave_pos=False)
+
+# Define the nuclear isotopes of all spins.
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
+
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='interatom.read_dist',
file='one_bond_RDC_data_strychnine.txt', dir=DATA_PATH, unit='Angstrom',
spin_id1_col=1, spin_id2_col=2, data_col=8)
+self._execute_uf(uf_name='interatom.unit_vectors', ave=False)
+
+# Load the J and J+D data.
+self._execute_uf(uf_name='rdc.read', align_id='Gel',
file='one_bond_RDC_data_strychnine.txt', dir=DATA_PATH, data_type='T',
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4, absolute=True)
+self._execute_uf(uf_name='j_coupling.read',
file='one_bond_RDC_data_strychnine.txt', dir=DATA_PATH, spin_id1_col=1,
spin_id2_col=2, data_col=5, error_col=6, sign_col=7)
+
+# Set up the model.
+self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
+
+# Minimisation.
+self._execute_uf(uf_name='grid_search', inc=3)
+self._execute_uf(uf_name='minimise', min_algor='simplex')
+
+# Show the tensors.
+self._execute_uf(uf_name='align_tensor.display')
+
+# Create a correlation plot.
+self._execute_uf(uf_name='rdc.corr_plot', file='devnull', force=True)
+
+# Print out.
+print(cdp)
r20136 - in /trunk/test_suite: shared_data/align_data/ system_tests/ system_tests/scripts/n_state_model/