Author: semor
Date: Mon Jul 28 21:36:19 2008
New Revision: 6993
URL: http://svn.gna.org/viewcvs/relax?rev=6993&view=rev
Log:
Started to add system tests for model-free analysis using Modelfree4.
Added:
1.3/test_suite/system_tests/palmer.py
1.3/test_suite/system_tests/scripts/palmer.py
Modified:
1.3/test_suite/system_tests/__init__.py
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=6993&r1=6992&r2=6993&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Mon Jul 28 21:36:19 2008
@@ -41,6 +41,7 @@
from model_selection import Modsel
from n_state_model import N_state_model
from nmrview import NMRView
+from palmer import Palmer
from pipe_create import Pipe_create
from relax_fit import Relax_fit
from results import Results
@@ -57,6 +58,7 @@
'model_selection',
'n_state_model',
'nmrview',
+ 'palmer',
'pipe_create',
'relax_fit',
'results',
@@ -89,6 +91,7 @@
suite_array.append(TestLoader().loadTestsFromTestCase(Load_spins))
suite_array.append(TestLoader().loadTestsFromTestCase(Mf))
suite_array.append(TestLoader().loadTestsFromTestCase(Modsel))
+ suite_array.append(TestLoader().loadTestsFromTestCase(Palmer))
suite_array.append(TestLoader().loadTestsFromTestCase(Relax_fit))
suite_array.append(TestLoader().loadTestsFromTestCase(Results))
suite_array.append(TestLoader().loadTestsFromTestCase(Sequence))
Added: 1.3/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/palmer.py?rev=6993&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/palmer.py (added)
+++ 1.3/test_suite/system_tests/palmer.py Mon Jul 28 21:36:19 2008
@@ -1,0 +1,39 @@
+###############################################################################
+#
#
+# Copyright (C) 2008 Sebastien Morin
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Python module imports.
+import sys
+from unittest import TestCase
+
+
+class Palmer(TestCase):
+ """Class for testing various aspects specific to model-free analysis
using the program
+ 'Modelfree4'.
+ """
+
+ def test_palmer_stage_1(self):
+ """Test a complete model-free analysis using the program
'Modelfree4'."""
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/palmer.py')
+
+
Added: 1.3/test_suite/system_tests/scripts/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/palmer.py?rev=6993&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/palmer.py (added)
+++ 1.3/test_suite/system_tests/scripts/palmer.py Mon Jul 28 21:36:19 2008
@@ -1,0 +1,136 @@
+# Script for model-free analysis using the program 'Modelfree4'.
+
+# Python module imports.
+import sys
+
+# The RelaxError system.
+from relax_errors import RelaxError
+
+# Set the stage of analysis.
+#
+# The three stages in this script are:
+# Stage 1: Initial model-free minimisation.
+# Stage 2: Model-free model selection.
+# Stage 3: Final optimisation of diffusion tensor parameters together
with model-free parameters.
+
+
+# Functions.
+
+def exec_stage_1(runs):
+ """Stage 1 function.
+
+ Initial model-free minimisation.
+ """
+
+ # Loop over the runs.
+ for name in runs:
+ # Create the run.
+ print "\n\n# " + name + " #"
+ pipe.create(name, 'mf')
+
+ # Load the sequence.
+ sequence.read(sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+ # PDB.
+ #structure.read_pdb(name, 'Ap4Aase_new_3.pdb')
+
+ # Load the relaxation data.
+ relax_data.read('R1', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/R1.dat')
+ relax_data.read('R2', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/R2.dat')
+ relax_data.read('NOE', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+ # Setup other values.
+ diffusion_tensor.init(1e-8)
+ value.set(NUCLEI, 'heteronucleus')
+ value.set(1.02 * 1e-10, 'bond_length')
+ value.set(-172 * 1e-6, 'csa')
+
+ # Select the model-free model.
+ model_free.select_model(model=name)
+
+ # Create the Modelfree4 files.
+ palmer.create(force=True, sims=0)
+
+ # Run Modelfree4.
+ palmer.execute(force=True)
+
+ # Save the program state.
+ state.save('stage1.save', force=True)
+
+
+def exec_stage_2(runs):
+ """Stage 2 function.
+
+ Model-free model selection.
+ """
+
+ # Load the saved state from stage 1.
+ state.load('stage1.save')
+
+ # Print out.
+ print "\n\nLoading all the Modelfree 4 data."
+
+ # Extract the Modelfree4 data from the 'mfout' files.
+ for name in runs:
+ palmer.extract()
+
+ # Print out.
+ print "\n\nModel selection."
+
+ # Create the model selection run.
+ name = 'aic'
+ pipe.create(name, 'mf')
+
+ # Model selection.
+ model_selection(method='AIC', modsel_run=name)
+
+ # Write the results.
+ results.write(file='results', force=True)
+
+ # Save the program state.
+ state.save('stage2.save', force=True)
+
+
+def exec_stage_3():
+ """Stage 3 function.
+
+ Final optimisation of diffusion tensor parameters together with
model-free parameters.
+ """
+
+ # Load the saved state from stage 2.
+ state.load('stage2.save')
+
+ # Set the run name.
+ name = 'aic'
+
+ # Let the diffusion tensor parameters be optimised.
+ fix(name, 'diff', 0)
+
+ # Create the Modelfree4 files (change sims as needed, see below).
+ palmer.create(dir='final', force=True, sims=0)
+
+ # Run Modelfree4.
+ palmer.execute(dir='final', force=True)
+
+ # Extract the Modelfree4 data from the 'mfout' file.
+ palmer.extract(dir='final')
+
+ # Save the program state.
+ state.save('stage3.save', force=True)
+
+
+# Main section of the script.
+#############################
+
+# Nuclei type.
+NUCLEI = '15N'
+
+# Set the run name (also the name of a preset model-free model).
+runs = ['m1', 'm2', 'm3']
+
+# Run the stages.
+exec_stage_1(runs)
+exec_stage_2(runs)
+exec_stage_3()
+
+# Either repeat all the above with the optimised diffusion tensor or run
Monte Carlo simulations on the final results.
r6993 - in /1.3/test_suite/system_tests: __init__.py palmer.py scripts/palmer.py