Author: bugman
Date: Thu Jan 13 09:28:55 2011
New Revision: 12271
URL: http://svn.gna.org/viewcvs/relax?rev=12271&view=rev
Log:
Split out most of the code from the tm0 grid system test script into a
separate module.
This opt_tm_fns will be used for all of the model-free parameter grid system
tests.
Added:
1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py
Modified:
1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py
Modified: 1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py?rev=12271&r1=12270&r2=12271&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py (original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py Thu Jan 13
09:28:55 2011
@@ -1,95 +1,47 @@
+###############################################################################
+#
#
+# Copyright (C) 2011 Edward d'Auvergne
#
+#
#
+# 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
#
+#
#
+###############################################################################
+
"""Script for setting up the data pipe for testing optimisation."""
-# Python module imports.
-from os import sep
-from re import search
-
# relax module imports.
-from status import Status; status = Status()
+from opt_tm_fns import create_sequence, opt_and_check, setup_data
# The model-free parameters.
tm = [2e-9, 10e-9, 80e-9]
-# Path of the files.
-path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm0_grid'
+# Create the sequence.
+create_sequence(len(tm))
-# Create the sequence.
-molecule.create(mol_name='Polycarbonate')
-for i in range(len(tm)):
- spin.create(spin_num=1, spin_name='C1', res_num=i+1,
res_name='Bisphenol_A', mol_name='Polycarbonate')
-
-# The proton frequencies in MHz.
-frq = ['400', '500', '600', '700', '800', '900', '1000']
-
-# Load the relaxation data.
-for i in range(len(frq)):
- relax_data.read('NOE', frq[i], float(frq[i])*1e6, 'noe.%s.out' % frq[i],
dir=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)
- relax_data.read('R1', frq[i], float(frq[i])*1e6, 'r1.%s.out' % frq[i],
dir=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)
- relax_data.read('R2', frq[i], float(frq[i])*1e6, 'r2.%s.out' % frq[i],
dir=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)
-
-# Setup other values.
-value.set(1.04 * 1e-10, 'bond_length')
-value.set(-160 * 1e-6, 'csa')
-value.set('15N', 'heteronucleus')
-value.set('1H', 'proton')
-
-# Select the model-free model.
-model_free.select_model(model=cdp._model)
-
-# Deselect all spins.
-deselect.spin()
+# Set up the data.
+setup_data()
# Residue index.
res_index = 0
# Loop over tm.
for tm_index in range(len(tm)):
- # Default values for certain parameters.
- s2 = [1.0]
- s2_index = 0
- te = [0.0]
- te_index = 0
+ # Optimise and validate.
+ opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm,
tm_index=tm_index)
- # Alias the relevent spin container.
- spin = cdp.mol[0].res[res_index].spin[0]
-
- # Select the spin.
- spin.select = True
-
- # Set up the diffusion tensor.
- if search('^m', cdp._model):
- if res_index:
- diffusion_tensor.delete()
- diffusion_tensor.init(tm[tm_index])
-
- # Set up the initial model-free parameter values (bypass the grid search
for speed).
- if search('^t', cdp._model):
- spin.local_tm = tm[tm_index] + 1e-11
- if cdp._model in ['tm2', 'm1', 'm2']:
- spin.s2 = 0.98
- if cdp._model in ['tm2', 'm2']:
- spin.te = 1e-12
- if cdp._model in ['m3']:
- spin.rex = 0.1 / (2.0 * pi * spin.frq[0])**2
-
- # Minimise.
- minimise('newton', 'gmw', 'back', constraints=False)
-
- # Check the values.
- if cdp._model == 'm0':
- cdp._value_test(spin, chi2=0.0)
- elif cdp._model == 'm1':
- cdp._value_test(spin, s2=s2[s2_index], chi2=0.0)
- elif cdp._model == 'm2':
- cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
chi2=0.0)
- elif cdp._model == 'm3':
- cdp._value_test(spin, s2=s2[s2_index], rex=0.0, chi2=0.0)
- elif cdp._model == 'm4':
- cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
rex=0.0, chi2=0.0)
- elif cdp._model == 'tm2':
- cdp._value_test(spin, local_tm=tm[tm_index]*1e9, s2=s2[s2_index],
te=te[te_index]*1e12, chi2=0.0)
-
- # Increment the residue index and deselect the spin.
+ # Increment the residue index.
res_index += 1
- spin.select = False
Added: 1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py?rev=12271&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py (added)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py Thu Jan 13
09:28:55 2011
@@ -1,0 +1,132 @@
+###############################################################################
+#
#
+# Copyright (C) 2011 Edward d'Auvergne
#
+#
#
+# 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
#
+#
#
+###############################################################################
+
+"""Functions for the local tm grid optimisation tests."""
+
+# Python module imports.
+from os import sep
+from re import search
+
+# relax module imports.
+from prompt.interpreter import Interpreter
+from status import Status; status = Status()
+
+
+# Initialise the interpreter.
+interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
+interpreter.populate_self()
+
+
+def create_sequence(num_res):
+ """Generate the required sequence.
+
+ @param num_res: The total number of residues to create.
+ @type num_res: int
+ """
+
+ # Create the molecule.
+ interpreter.molecule.create(mol_name='Polycarbonate')
+
+ # Create the spins and residues.
+ for i in range(num_res):
+ interpreter.spin.create(spin_num=1, spin_name='C1', res_num=i+1,
res_name='Bisphenol_A', mol_name='Polycarbonate')
+
+
+def opt_and_check(spin=None, tm=None, tm_index=None):
+ """Optimise the given model-free model, residue by residue.
+
+ @keyword spin: The spin container to validate.
+ @type spin: SpinContainer instance
+ """
+
+ # Default values for certain parameters.
+ s2 = [1.0]
+ s2_index = 0
+ te = [0.0]
+ te_index = 0
+
+ # Select the spin.
+ spin.select = True
+
+ # Set up the diffusion tensor.
+ if search('^m', cdp._model):
+ if hasattr(cdp, 'diffusion_tensor'):
+ diffusion_tensor.delete()
+ diffusion_tensor.init(tm[tm_index])
+
+ # Set up the initial model-free parameter values (bypass the grid search
for speed).
+ if search('^t', cdp._model):
+ spin.local_tm = tm[tm_index] + 1e-11
+ if cdp._model in ['tm2', 'm1', 'm2']:
+ spin.s2 = 0.98
+ if cdp._model in ['tm2', 'm2']:
+ spin.te = 1e-12
+ if cdp._model in ['m3']:
+ spin.rex = 0.1 / (2.0 * pi * spin.frq[0])**2
+
+ # Minimise.
+ interpreter.minimise('newton', 'gmw', 'back', constraints=False)
+
+ # Check the values.
+ if cdp._model == 'm0':
+ cdp._value_test(spin, chi2=0.0)
+ elif cdp._model == 'm1':
+ cdp._value_test(spin, s2=s2[s2_index], chi2=0.0)
+ elif cdp._model == 'm2':
+ cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
chi2=0.0)
+ elif cdp._model == 'm3':
+ cdp._value_test(spin, s2=s2[s2_index], rex=0.0, chi2=0.0)
+ elif cdp._model == 'm4':
+ cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
rex=0.0, chi2=0.0)
+ elif cdp._model == 'tm2':
+ cdp._value_test(spin, local_tm=tm[tm_index]*1e9, s2=s2[s2_index],
te=te[te_index]*1e12, chi2=0.0)
+
+ # Deselect the spin.
+ spin.select = False
+
+
+def setup_data():
+ """Set up all the relevant data prior to optimisation."""
+
+ # Path of the files.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm0_grid'
+
+ # The proton frequencies in MHz.
+ frq = ['400', '500', '600', '700', '800', '900', '1000']
+
+ # Load the relaxation data.
+ for i in range(len(frq)):
+ interpreter.relax_data.read('NOE', frq[i], float(frq[i])*1e6,
'noe.%s.out' % frq[i], dir=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)
+ interpreter.relax_data.read('R1', frq[i], float(frq[i])*1e6,
'r1.%s.out' % frq[i], dir=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)
+ interpreter.relax_data.read('R2', frq[i], float(frq[i])*1e6,
'r2.%s.out' % frq[i], dir=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)
+
+ # Setup other values.
+ interpreter.value.set(1.04 * 1e-10, 'bond_length')
+ interpreter.value.set(-160 * 1e-6, 'csa')
+ interpreter.value.set('15N', 'heteronucleus')
+ interpreter.value.set('1H', 'proton')
+
+ # Select the model-free model.
+ interpreter.model_free.select_model(model=cdp._model)
+
+ # Deselect all spins.
+ interpreter.deselect.spin()
r12271 - in /1.3/test_suite/system_tests/scripts/model_free: opt_tm0_grid.py opt_tm_fns.py