Author: bugman
Date: Sun Oct 9 14:29:22 2011
New Revision: 14814
URL: http://svn.gna.org/viewcvs/relax?rev=14814&view=rev
Log:
Created the N-state model test_monte_carlo_sims() system test for checking MC
sims with alignment data.
Added:
1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
- copied, changed from r14812,
1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py
Modified:
1.3/test_suite/system_tests/n_state_model.py
Modified: 1.3/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/n_state_model.py?rev=14814&r1=14813&r2=14814&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/n_state_model.py (original)
+++ 1.3/test_suite/system_tests/n_state_model.py Sun Oct 9 14:29:22 2011
@@ -387,6 +387,58 @@
self.assertAlmostEqual(cdp.q_pcs, 0.0)
+ def test_monte_carlo_sims(self):
+ """Test the Monte Carlo simulation data of fitting RDCs and PCSs."""
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'monte_carlo_testing.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000)
+ self.assertAlmostEqual(cdp.chi2, 1745860.0485368515)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+ self.assertAlmostEqual(cdp.q_pcs, 0.0)
+
+ # The tensor key.
+ key = 'synth'
+
+ # The spin data.
+ for spin in spin_loop():
+ # Print out.
+ print(spin)
+
+ # Check for simulation data.
+ self.assert_(hasattr(spin, 'rdc_sim'))
+ self.assert_(hasattr(spin, 'pcs_sim'))
+ self.assert_(spin.rdc_sim.has_key(key))
+ self.assert_(spin.pcs_sim.has_key(key))
+
+ # Check the values of the simulated data.
+ for i in range(cdp.sim_number):
+ self.assertAlmostEqual(spin.rdc[key], spin.rdc_sim[key][i])
+ self.assertAlmostEqual(spin.pcs[key], spin.pcs_sim[key][i])
+
+ # Test the optimised simluation values.
+ for i in range(cdp.sim_number):
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.351261/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000)
+ self.assertAlmostEqual(cdp.chi2, 1745860.0485368515)
+
+ # Test the tensor error values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx_err, 0.0)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy_err, 0.0)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy_err, 0.0)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz_err, 0.0)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz_err, 0.0)
+
+
def test_paramag_centre_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
Copied:
1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
(from r14812, 1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py?p2=1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py&p1=1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py&r1=14812&r2=14814&rev=14814&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py (original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
Sun Oct 9 14:29:22 2011
@@ -1,4 +1,4 @@
-"""Script for testing the fitting an alignment tensor to RDCs or PCSs."""
+"""Script for testing the Monte Carlo simulations of fitting an alignment
tensor to RDCs and PCSs."""
# Python module imports.
from os import sep
@@ -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'
-STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'monte_carlo_testing'
+STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'sphere'
# Create the data pipe.
-pipe.create('rdc', 'N-state')
+pipe.create('MC test', 'N-state')
-# 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'
-
-# Load the CaM structure.
-structure.read_pdb(file='bax_C_1J7P_N_H_Ca', dir=STRUCT_PATH)
+# Load the test structure.
+structure.read_pdb(file='sphere', dir=STRUCT_PATH)
# Load the spins.
structure.load_spins()
@@ -44,35 +32,33 @@
value.set('1H', 'proton', spin_id="@N")
# RDCs.
-if ds.mode in ['rdc', 'all']:
- rdc.read(align_id='synth', file=rdc_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)
+rdc.read(align_id='synth', file='synth_rdc', 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,
error_col=7)
# PCSs.
-if ds.mode in ['pcs', 'all']:
- 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)
+pcs.read(align_id='synth', file='synth_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,
error_col=7)
- # Set the paramagnetic centre.
- paramag.centre(atom_id=':1000@CA')
+# Set the paramagnetic centre.
+paramag.centre(pos=[10.0, 0.0, 0.0])
- # The temperature.
- temperature(id='synth', temp=303)
+# The temperature.
+temperature(id='synth', temp=303)
- # The frequency.
- frq.set(id='synth', frq=600.0 * 1e6)
+# The frequency.
+frq.set(id='synth', frq=600.0 * 1e6)
# Set up the model.
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
-
# Minimisation.
grid_search(inc=3)
minimise('simplex', constraints=False, max_iter=500)
+
+# Monte Carlo simulations.
+monte_carlo.setup(3)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise('simplex', constraints=False, max_iter=500)
+monte_carlo.error_analysis()
# Write out a results file.
results.write('devnull', force=True)
r14814 - in /1.3/test_suite/system_tests: n_state_model.py scripts/n_state_model/monte_carlo_testing.py