Author: bugman
Date: Thu Jan 13 11:08:47 2011
New Revision: 12282
URL: http://svn.gna.org/viewcvs/relax?rev=12282&view=rev
Log:
Modified the opt_tm2_grid.py model-free system test script to use the
abstracted opt_tm_fns.py fns.
Modified:
1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py
Modified: 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py?rev=12282&r1=12281&r2=12282&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py (original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py Thu Jan 13
11:08:47 2011
@@ -1,88 +1,51 @@
-"""Script for setting up the data pipe for testing optimisation."""
+###############################################################################
+#
#
+# 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
#
+#
#
+###############################################################################
-# Python module imports.
-from os import sep
+"""Set up the data pipe for testing optimisation against tm2 relaxation
data."""
# relax module imports.
-from status import Status; status = Status()
+from opt_tm_fns import create_sequence, opt_and_check, setup_data
-
-# Path of the files.
-path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm2_grid'
-
-# Create the sequence.
-molecule.create(mol_name='Polycarbonate')
-for i in range(3*3*3):
- 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(1.20 * 1e-10, 'bond_length')
-value.set(200 * 1e-6, 'csa')
-value.set('13C', 'heteronucleus')
-value.set('1H', 'proton')
-
-# Select the model-free model.
-model_free.select_model(model=cdp._model)
# The model-free parameters.
tm = [2e-9, 10e-9, 21e-9]
s2 = [0.2, 0.8, 0.95]
te = [2e-12, 40e-12, 1e-9]
-# Deselect all spins.
-deselect.spin()
+# Create the sequence.
+create_sequence(len(tm)*len(s2)*len(te))
+
+# Set up the data.
+setup_data(dir='tm2_grid')
# Residue index.
res_index = 0
-# Loop over te.
+# Loop over the parameters.
for te_index in range(3):
- # Loop over s2.
for s2_index in range(3):
- # Loop over tm.
for tm_index in range(3):
- # Alias the relevent spin container.
- spin = cdp.mol[0].res[res_index].spin[0]
+ # Optimise and validate.
+ opt_and_check(spin=cdp.mol[0].res[res_index].spin[0],
tm=tm[tm_index], s2=s2[s2_index], te=te[te_index])
- # Select the spin.
- spin.select = True
-
- # Set up the diffusion tensor.
- if cdp._model in ['m2', 'm4']:
- 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 cdp._model in ['tm2']:
- spin.local_tm = tm[tm_index] + 1e-11
- if cdp._model in ['tm2', 'm2', 'm4']:
- spin.s2 = s2[s2_index] - 0.01
- if cdp._model in ['tm2', 'm2', 'm4']:
- spin.te = te[te_index] + 1e-12
- if cdp._model in ['m4']:
- spin.rex = 0.1 / (2.0 * pi * spin.frq[0])**2
-
- # Minimise.
- minimise('newton', 'gmw', 'back', constraints=False)
-
- # Check the values.
- if cdp._model == 'm2':
- cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
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
r12282 - /1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py