r6577 - in /1.3/test_suite/system_tests: model_free.py scripts/omp_model_free.py -- June 29, 2008 - 14:17

Author: bugman
Date: Sun Jun 29 14:17:09 2008
New Revision: 6577

URL: http://svn.gna.org/viewcvs/relax?rev=6577&view=rev
Log:
Wrote the test_omp_analysis() system test for testing a simple model-free 
analysis on the OMP data.


Added:
    1.3/test_suite/system_tests/scripts/omp_model_free.py
Modified:
    1.3/test_suite/system_tests/model_free.py

Modified: 1.3/test_suite/system_tests/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=6577&r1=6576&r2=6577&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Sun Jun 29 14:17:09 2008
@@ -154,6 +154,13 @@
         # Test the model.
         self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4')
         self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['S2', 'te', 
'Rex'])
+
+
+    def test_omp_analysis(self):
+        """Try a very minimal model-free analysis on the OMP relaxation 
data."""
+
+        # Execute the script.
+        self.relax.interpreter.run(script_file=sys.path[-1] + 
'/test_suite/system_tests/scripts/omp_model_free.py')
 
 
     def test_opendx_s2_te_rex(self):

Added: 1.3/test_suite/system_tests/scripts/omp_model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/omp_model_free.py?rev=6577&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/omp_model_free.py (added)
+++ 1.3/test_suite/system_tests/scripts/omp_model_free.py Sun Jun 29 14:17:09 
2008
@@ -1,0 +1,113 @@
+"""Script for performing a very minimal model-free analysis using the OMP 
relaxation data."""
+
+# Python module imports.
+import sys
+
+# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
+
+
+# Path of the relaxation data.
+DATA_PATH = sys.path[-1] + '/test_suite/shared_data/model_free/OMP'
+
+# Mini subset of local tm data pipes.
+LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2']
+
+# The bond length, CSA values, heteronucleus type, and proton type.
+BOND_LENGTH = 1.02 * 1e-10
+CSA = -172 * 1e-6
+HETNUC = '15N'
+PROTON = '1H'
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 3
+
+# The optimisation technique.
+MIN_ALGOR = 'simplex'
+
+
+class Main:
+    def __init__(self, relax):
+        """Execute the model-free analysis."""
+
+        # Setup.
+        self.relax = relax
+
+        # Read the results file to get the relaxation data from.
+        pipe.create('data', 'mf')
+        results.read(file='final_results_trunc_1.3', dir=DATA_PATH)
+
+
+        # MI - Local tm.
+        ################
+
+        # Sequential optimisation of all model-free models (function must be 
modified to suit).
+        self.multi_model(local_tm=True)
+
+        # Model selection data pipe.
+        pipe.create('aic', 'mf')
+
+        # Model selection.
+        self.model_selection(pipe='aic')
+
+
+    def model_selection(self, pipe=None):
+        """Model selection function."""
+
+        # Model elimination.
+        eliminate()
+
+        # Model selection.
+        model_selection(method='AIC', modsel_pipe=pipe, pipes=self.pipes)
+
+
+    def multi_model(self, local_tm=False):
+        """Function for optimisation of all model-free models."""
+
+        # Set the data pipe names (also the names of preset model-free 
models).
+        if local_tm:
+            self.pipes = LOCAL_TM_MODELS
+        else:
+            self.pipes = MF_MODELS
+
+        # Loop over the data pipes.
+        for name in self.pipes:
+            # Create the data pipe.
+            if ds.has_key(name):
+                pipe.delete(name)
+            pipe.create(name, 'mf')
+
+            # Copy the sequence.
+            sequence.copy('data')
+
+            # Select only 3 spins (residues 9, 10, and 11).
+            deselect.all()
+            select.spin(':9')
+            select.spin(':10')
+            select.spin(':11')
+
+            # Copy the relaxation data.
+            relax_data.copy('data')
+
+            # Copy the diffusion tensor from the 'opt' data pipe and prevent 
it from being minimised.
+            if not local_tm:
+                diffusion_tensor.copy('previous')
+                fix('diff')
+
+            # Set all the necessary values.
+            value.set(BOND_LENGTH, 'bond_length')
+            value.set(CSA, 'csa')
+            value.set(HETNUC, 'heteronucleus')
+            value.set(PROTON, 'proton')
+
+            # Select the model-free model.
+            model_free.select_model(model=name)
+
+            # Minimise.
+            grid_search(inc=GRID_INC)
+            minimise(MIN_ALGOR)
+
+
+
+# Execute the main class.
+Main(self.relax)