Author: bugman
Date: Thu Aug 4 19:33:39 2011
New Revision: 14155
URL: http://svn.gna.org/viewcvs/relax?rev=14155&view=rev
Log:
Re-activated and redesigned the system test of the dauvergne_protocol.
Added:
branches/gui_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
- copied, changed from r14146,
branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py
Modified:
branches/gui_testing/test_suite/system_tests/model_free.py
Modified: branches/gui_testing/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/test_suite/system_tests/model_free.py?rev=14155&r1=14154&r2=14155&view=diff
==============================================================================
--- branches/gui_testing/test_suite/system_tests/model_free.py (original)
+++ branches/gui_testing/test_suite/system_tests/model_free.py Thu Aug 4
19:33:39 2011
@@ -211,19 +211,14 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['S2', 'te',
'Rex'])
- # FIXME!
- def xxx_test_dauvergne_protocol(self):
+ def test_dauvergne_protocol(self):
"""Check the execution of auto_analyses.dauvergne_protocol."""
# Create a temporary directory for dumping files.
ds.tmpdir = mkdtemp()
- # Copy the files into the temporary directory.
- path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data'+sep+'13259_bug_reproducing_data'
- copytree(path, ds.tmpdir + sep + 'data')
-
# Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'full_analysis_trunc.py')
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'dauvergne_protocol.py')
def test_generate_ri(self):
Copied:
branches/gui_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
(from r14146,
branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py?p2=branches/gui_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py&p1=branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py&r1=14146&r2=14155&rev=14155&view=diff
==============================================================================
--- branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py
(original)
+++
branches/gui_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
Thu Aug 4 19:33:39 2011
@@ -140,10 +140,13 @@
"""
# Python module imports.
+from os import sep
from time import asctime, localtime
# relax module imports.
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
+from data import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
# Analysis variables.
@@ -153,17 +156,17 @@
DIFF_MODEL = 'local_tm'
# The model-free models. Do not change these unless absolutely necessary,
the protocol is likely to fail if these are changed.
-MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
-LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
+MF_MODELS = ['m1', 'm2']
+LOCAL_TM_MODELS = ['tm0', 'tm1']
# The grid search size (the number of increments per dimension).
-GRID_INC = 11
+GRID_INC = 3
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
-MC_NUM = 500
+MC_NUM = 2
# Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
CONV_LOOP = True
@@ -179,27 +182,26 @@
name = "mf (%s)" % asctime(localtime())
pipe.create(name, 'mf')
+# The data path.
+data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' +
sep + 'model_free' + sep + 'sphere' + sep
+
# Load the sequence.
-sequence.read(file='noe.500.out', dir=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None)
+sequence.read(file='noe.500.out', dir=data_path, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5)
# Name the spins.
spin.name(name='N')
# Load the PDB file.
-structure.read_pdb('1f3y.pdb')
+structure.read_pdb('sphere.pdb', dir=data_path)
structure.vectors(attached='H')
# Load the relaxation data.
-relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6,
file='r1.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R2_600', ri_type='R2', frq=599.719*1e6,
file='r2.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=599.719*1e6,
file='noe.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R1_500', ri_type='R1', frq=500.208*1e6,
file='r1.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.208*1e6,
file='r2.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.208*1e6,
file='noe.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-
-# Deselect spins to be excluded (including unresolved and specifically
excluded spins).
-deselect.read(file='unresolved', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)
-deselect.read(file='exclude', spin_id_col=1)
+relax_data.read(ri_id='R1_900', ri_type='R1', frq=900*1e6,
file='r1.900.out', 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)
+relax_data.read(ri_id='R2_900', ri_type='R2', frq=900*1e6,
file='r2.900.out', 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)
+relax_data.read(ri_id='NOE_900', ri_type='NOE', frq=900*1e6,
file='noe.900.out', 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)
+relax_data.read(ri_id='R1_500', ri_type='R1', frq=500*1e6,
file='r1.500.out', 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)
+relax_data.read(ri_id='R2_500', ri_type='R2', frq=500*1e6,
file='r2.500.out', 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)
+relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500*1e6,
file='noe.500.out', 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 bond length, CSA values, heteronucleus type, and proton type.
value.set(1.02 * 1e-10, 'bond_length')
@@ -212,5 +214,5 @@
# Execution.
############
-# Do not change!
-dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
+for global_model in ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid',
'final']:
+ dAuvergne_protocol(pipe_name=name, results_dir=ds.tmpdir,
diff_model=global_model, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_sim_num=MC_NUM, conv_loop=CONV_LOOP)
r14155 - in /branches/gui_testing/test_suite/system_tests: model_free.py scripts/model_free/dauvergne_protocol.py