def setup_data(self):
"""Function for setting up some data for the unit tests."""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first residue and add some data to its spin container.
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
dp.mol[0].name = 'Old mol'
# Create a second molecule.
dp.mol.add_item('New mol')
# Copy the residue to the new molecule.
copy_residue(res_from=':1', res_to='#New mol')
copy_residue(res_from='#Old mol:1', res_to='#New mol:5')
# Change the first residue's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
def setup_data(self):
"""Function for setting up some data for the unit tests."""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first residue and add some data to its spin container.
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
dp.mol[0].name = 'Old mol'
# Create a second molecule.
dp.mol.add_item('New mol')
# Copy the residue to the new molecule.
copy_residue(res_from=':1', res_to='#New mol')
copy_residue(res_from='#Old mol:1', res_to='#New mol:5')
# Change the first residue's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
def test_copy_molecule_within_pipe(self):
"""Test the copying of the molecule data within a single data pipe.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule a few times.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#2')
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='orig', mol_to='#3')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Copy the molecule once more.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#4')
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule 2.
self.assertEqual(dp.mol[1].name, '2')
self.assertEqual(dp.mol[1].res[0].num, 1)
self.assertEqual(dp.mol[1].res[0].name, 'Ala')
self.assertEqual(dp.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[1].res[0].spin[0].x, 1)
# Test the new molecule 3.
self.assertEqual(dp.mol[2].name, '3')
self.assertEqual(dp.mol[2].res[0].num, 1)
self.assertEqual(dp.mol[2].res[0].name, 'Ala')
self.assertEqual(dp.mol[2].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[2].res[0].spin[0].x, 1)
# Test the new molecule 4.
self.assertEqual(dp.mol[3].name, '4')
self.assertEqual(dp.mol[3].res[0].num, 1)
self.assertEqual(dp.mol[3].res[0].name, 'Ala')
self.assertEqual(dp.mol[3].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[3].res[0].spin[0].x, 2)
def test_copy_spin_between_pipes(self):
"""Test the copying of the spin data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_spin() and
prompt.spin.copy().
"""
# Copy the spin data.
self.spin_fns.copy(spin_from='#Old mol:1@C8', pipe_to='test')
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Change the first spin's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original spin.
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new spin.
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
def test_copy_spin_between_pipes(self):
"""Test the copying of the spin data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_spin() and
prompt.spin.copy().
"""
# Copy the spin data.
self.spin_fns.copy(spin_from='#Old mol:1@C8', pipe_to='test')
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Change the first spin's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original spin.
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new spin.
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
def test_copy_molecule_between_pipes(self):
"""Test the copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='test')
self.molecule_fns.copy(pipe_from='orig',
mol_from='#Old mol',
pipe_to='test',
mol_to='#New mol')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule.
self.assertEqual(dp_test.mol[0].name, 'Old mol')
self.assertEqual(dp_test.mol[0].res[0].num, 1)
self.assertEqual(dp_test.mol[0].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
# Test the second new molecule.
self.assertEqual(dp_test.mol[1].name, 'New mol')
self.assertEqual(dp_test.mol[1].res[0].num, 1)
self.assertEqual(dp_test.mol[1].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[1].res[0].spin[0].x, 1)
def test_copy_molecule_between_pipes(self):
"""Test the copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='test')
self.molecule_fns.copy(pipe_from='orig', mol_from='#Old mol', pipe_to='test', mol_to='#New mol')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule.
self.assertEqual(dp_test.mol[0].name, 'Old mol')
self.assertEqual(dp_test.mol[0].res[0].num, 1)
self.assertEqual(dp_test.mol[0].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
# Test the second new molecule.
self.assertEqual(dp_test.mol[1].name, 'New mol')
self.assertEqual(dp_test.mol[1].res[0].num, 1)
self.assertEqual(dp_test.mol[1].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[1].res[0].spin[0].x, 1)
def read(file='results', dir=None):
"""Function for reading the data out of a file."""
# Test if the current data pipe exists.
check_pipe()
# Make sure that the data pipe is empty.
if not cdp.is_empty():
raise RelaxError("The current data pipe is not empty.")
# Get the full file path, for later use.
file_path = get_file_path(file_name=file, dir=dir)
# Open the file.
file = open_read_file(file_name=file_path)
# Determine the format of the file.
format = determine_format(file)
# XML results.
if format == 'xml':
ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
# Columnar results (for backwards compatibility with ancient relax results model-free files).
elif format == 'columnar':
# Extract the data from the file.
file_data = extract_data(file=file)
# Strip data.
file_data = strip(file_data)
# Do nothing if the file does not exist.
if not file_data:
raise RelaxFileEmptyError
# Read the results.
read_columnar_results(file_data)
# Unknown results file.
else:
raise RelaxError("The format of the results file " + repr(file_path) + " cannot be determined.")
# Update all of the required metadata structures.
mol_res_spin.metadata_update()
interatomic.metadata_update()
def setUp(self):
"""Set up some molecules, residues, and spins for testing."""
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Name the first molecule.
cdp.mol[0].name = 'Ap4Aase'
# Add a second molecule to the system.
cdp.mol.add_item(mol_name='RNA')
# Add two more residues to the first molecule (and set the residue number of the first).
cdp.mol[0].res[0].num = 1
cdp.mol[0].res.add_item(res_num=2, res_name='Glu')
cdp.mol[0].res.add_item(res_num=4, res_name='Pro')
# Add some spin info to this molecule.
cdp.mol[0].res[0].spin[0].name = 'NH'
cdp.mol[0].res[0].spin[0].num = 60
cdp.mol[0].res[1].spin[0].name = 'NH'
cdp.mol[0].res[1].spin[0].num = 63
# Add one more residue to the second molecule (and set the residue number of the first).
cdp.mol[1].res[0].num = -5
cdp.mol[1].res.add_item(res_num=-4)
# Add a second set of spins to the second molecule (naming the first set first).
cdp.mol[1].res[0].spin[0].name = 'C8'
cdp.mol[1].res[1].spin[0].name = 'C8'
cdp.mol[1].res[0].spin.add_item(spin_name='N5')
cdp.mol[1].res[1].spin.add_item(spin_name='N5')
cdp.mol[1].res[1].spin.add_item(spin_name='2H', spin_num=132)
# Deselect a number of spins.
cdp.mol[0].res[0].spin[0].select = 0
cdp.mol[0].res[2].spin[0].select = 0
cdp.mol[1].res[0].spin[0].select = 0
cdp.mol[1].res[1].spin[1].select = 0
# Update the metadata.
mol_res_spin.metadata_update()
def setUp(self):
"""Set up some molecules, residues, and spins for testing."""
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Name the first molecule.
cdp.mol[0].name = 'Ap4Aase'
# Add a second molecule to the system.
cdp.mol.add_item(mol_name='RNA')
# Add two more residues to the first molecule (and set the residue number of the first).
cdp.mol[0].res[0].num = 1
cdp.mol[0].res.add_item(res_num=2, res_name='Glu')
cdp.mol[0].res.add_item(res_num=4, res_name='Pro')
# Add some spin info to this molecule.
cdp.mol[0].res[0].spin[0].name = 'NH'
cdp.mol[0].res[0].spin[0].num = 60
cdp.mol[0].res[1].spin[0].name = 'NH'
cdp.mol[0].res[1].spin[0].num = 63
# Add one more residue to the second molecule (and set the residue number of the first).
cdp.mol[1].res[0].num = -5
cdp.mol[1].res.add_item(res_num=-4)
# Add a second set of spins to the second molecule (naming the first set first).
cdp.mol[1].res[0].spin[0].name = 'C8'
cdp.mol[1].res[1].spin[0].name = 'C8'
cdp.mol[1].res[0].spin.add_item(spin_name='N5')
cdp.mol[1].res[1].spin.add_item(spin_name='N5')
cdp.mol[1].res[1].spin.add_item(spin_name='2H', spin_num=132)
# Deselect a number of spins.
cdp.mol[0].res[0].spin[0].select = 0
cdp.mol[0].res[2].spin[0].select = 0
cdp.mol[1].res[0].spin[0].select = 0
cdp.mol[1].res[1].spin[1].select = 0
# Update the metadata.
mol_res_spin.metadata_update()
def test_copy_molecule_between_pipes_fail_no_pipe(self):
"""Test the failure of copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.assertRaises(RelaxNoPipeError, self.molecule_fns.copy, mol_from='#Old mol', pipe_to='test2')
def load_state(state=None, dir=None, verbosity=1, force=False):
"""Function for loading a saved program state.
@keyword state: The saved state file.
@type state: str
@keyword dir: The path of the state file.
@type dir: str
@keyword verbosity: The verbosity level.
@type verbosity: int
@keyword force: If True, the relax data store will be reset prior to state loading.
@type force: bool
"""
# Open the file for reading.
file = open_read_file(file_name=state, dir=dir, verbosity=verbosity)
# Reset.
if force:
reset()
# Make sure that the data store is empty.
if not ds.is_empty():
raise RelaxError("The relax data store is not empty.")
# Restore from the XML.
ds.from_xml(file)
# Update all of the required metadata structures.
for pipe, pipe_name in pipes.pipe_loop(name=True):
mol_res_spin.metadata_update(pipe=pipe_name)
interatomic.metadata_update(pipe=pipe_name)
# Signal a change in the current data pipe.
status.observers.pipe_alteration.notify()
# Signal the state loading
status.observers.state_load.notify()
def test_copy_molecule_between_pipes_fail_no_pipe(self):
"""Test the failure of copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.assertRaises(RelaxNoPipeError,
self.molecule_fns.copy,
mol_from='#Old mol',
pipe_to='test2')
def setUp(self):
"""Set up for all the spin unit tests.
The data contained within the 'orig' data pipe is:
ID Molecule Res number Res name Spin number Spin name
0,0,0 Old mol 1 Ala 111 C8
0,0,1 Old mol 1 Ala 6 C19
0,0,2 Old mol 1 Ala 7 C21
0,0,3 Old mol 1 Ala 8 C24
0,0,4 Old mol 1 Ala 9 C26
0,1,0 Old mol 2 Arg 78 NH
1,0,0 New mol 5 Lys 239 NH
1,1,0 New mol 6 Thr None None
1,1,1 New mol 6 Thr 3239 NH
The IDs correspond to the molecule, residue and spin indices.
"""
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Add a second data pipe for copying tests.
ds.add(pipe_name='test', pipe_type='mf')
# Set the current data pipe to 'orig'.
pipes.switch('orig')
# Name the first molecule.
cdp.mol[0].name = 'Old mol'
# Create the first residue and add some data to its spin container.
cdp.mol[0].res[0].num = 1
cdp.mol[0].res[0].name = 'Ala'
cdp.mol[0].res[0].spin[0].num = 111
cdp.mol[0].res[0].spin[0].name = 'C8'
cdp.mol[0].res[0].spin[0].x = 1
# Add some more spins.
cdp.mol[0].res[0].spin.add_item('C19', 6)
cdp.mol[0].res[0].spin.add_item('C21', 7)
cdp.mol[0].res[0].spin.add_item('C24', 8)
cdp.mol[0].res[0].spin.add_item('C26', 9)
# Create a second residue.
cdp.mol[0].res.add_item('Arg', 2)
cdp.mol[0].res[1].spin[0].num = 78
cdp.mol[0].res[1].spin[0].name = 'NH'
# Create a second molecule.
cdp.mol.add_item('New mol')
# Create the first and second residue of the second molecule and add some data to its spin container.
cdp.mol[1].res[0].num = 5
cdp.mol[1].res[0].name = 'Lys'
cdp.mol[1].res[0].spin[0].num = 239
cdp.mol[1].res[0].spin[0].name = 'NH'
cdp.mol[1].res.add_item('Thr', 6)
cdp.mol[1].res[1].spin.add_item(None, 1433)
cdp.mol[1].res[1].spin.add_item('NH', 3239)
# Create a third molecule.
cdp.mol.add_item('3rd')
# Create the first residue of the 3rd molecule and add some data to its spin container.
cdp.mol[2].res[0].num = 13
cdp.mol[2].res[0].name = 'Gly'
cdp.mol[2].res[0].spin[0].x = 'hello'
# Update the metadata.
metadata_update()
def test_sim_init_values(self):
"""Test the specific_analyses.relax_disp.api.sim_init_values() function for a cluster of 2 spins."""
# Test parameter values.
fixed_values = {
'r1': 2.2,
'r2eff': 10.0,
'r2': 15.0,
'r2a': 12.0,
'r2b': 18.0,
'pA': 0.80,
'pB': 0.15,
'k_AB': 0.001,
'k_BA': 0.003,
'kex': 0.01,
'kex_AB': 0.015,
'kex_BC': 0.017,
'kex_AC': 0.016,
'kB': 0.005,
'kC': 0.004,
'tex': 50.0,
'dw': 1.0,
'dw_AB': 1.02,
'dw_BC': 1.03,
'dwH': 0.1,
'dwH_AB': 0.12,
'dwH_BC': 0.13,
'phi_ex': 0.5,
'phi_ex_B': 0.4,
'phi_ex_C': 0.3,
}
# Loop over all models.
print(
"Checking the parameter conversion and setting for a cluster of 2 spins."
)
for model in MODEL_LIST_FULL:
# Printout.
print(" Model '%s'." % model)
# Set up the data store.
ds.add(pipe_name=model, pipe_type='relax_disp')
if model == MODEL_R2EFF:
cdp.model_type = 'R2eff'
else:
cdp.model_type = 'disp'
cdp.exp_type_list = [self.exp_type[model]]
cdp.spectrometer_frq_list = [1e6]
cdp.sim_number = 2
# Set up the spin systems.
cdp.mol.add_item(mol_name="sim test")
cdp.mol[0].res[0].num = 1
cdp.mol[0].res.add_item(res_num=2)
mol_res_spin.metadata_update()
spins = [cdp.mol[0].res[0].spin[0], cdp.mol[0].res[1].spin[0]]
for spin in spins:
spin.model = model
if model == MODEL_R2EFF:
spin.params = ['r2eff']
else:
spin.params = deepcopy(MODEL_PARAMS[model])
spin.chi2 = 1000.0
spin.iter = 20
spin.f_count = 300
spin.g_count = 200
spin.h_count = 100
spin.warning = None
spin.isotope = '15N'
# Set the ordinary parameter values, as these are copied into the simulation structures.
for name, param_index, spin_index, R20_key in loop_parameters(
spins):
# R1/R2 parameters.
if name in ['r1', 'r2', 'r2a', 'r2b']:
key = "%s - %.8f MHz" % (cdp.exp_type_list[0],
cdp.spectrometer_frq_list[0] /
1e6)
print(" Setting spin %i parameter %s['%s'] to %s." %
(spin_index, name, key, fixed_values[name]))
setattr(spins[spin_index], name, {key: fixed_values[name]})
# Global parameters.
elif spin_index == None:
print(" Setting global parameter %s to %s." %
(name, fixed_values[name]))
setattr(spins[0], name, fixed_values[name])
setattr(spins[1], name, fixed_values[name])
# Spin parameters.
else:
print(" Setting spin %i parameter %s to %s." %
(spin_index, name, fixed_values[name]))
setattr(spins[spin_index], name, fixed_values[name])
# MC simulation setup.
api = Relax_disp()
api.sim_init_values()
# Checks.
for i in range(cdp.sim_number):
print(" Simulation %i." % i)
# Check the probabilities.
if 'pB' in MODEL_PARAMS[model]:
print(" Checking parameter pC.")
self.assertAlmostEqual(spins[0].pC_sim[i], 0.05)
self.assertAlmostEqual(spins[1].pC_sim[i], 0.05)
elif 'pA' in MODEL_PARAMS[model]:
print(" Checking parameter pB.")
self.assertAlmostEqual(spins[0].pB_sim[i], 0.20)
self.assertAlmostEqual(spins[1].pB_sim[i], 0.20)
# Check the kex-tex pair.
if 'kex' in MODEL_PARAMS[model]:
print(" Checking parameter tex.")
self.assertAlmostEqual(spins[0].tex_sim[i], 100.0)
self.assertAlmostEqual(spins[1].tex_sim[i], 100.0)
elif 'tex' in MODEL_PARAMS[model]:
print(" Checking parameter kex.")
self.assertAlmostEqual(spins[0].kex_sim[i], 0.02)
self.assertAlmostEqual(spins[1].kex_sim[i], 0.02)
# Check the rates.
if 'kex' in MODEL_PARAMS[model] and 'pA' in MODEL_PARAMS[model]:
print(" Checking parameter k_AB.")
self.assertAlmostEqual(spins[0].k_AB_sim[i], 0.002)
self.assertAlmostEqual(spins[1].k_AB_sim[i], 0.002)
print(" Checking parameter k_BA.")
self.assertAlmostEqual(spins[0].k_BA_sim[i], 0.008)
self.assertAlmostEqual(spins[1].k_BA_sim[i], 0.008)
def test_copy_molecule_within_pipe(self):
"""Test the copying of the molecule data within a single data pipe.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule a few times.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#2')
self.molecule_fns.copy(mol_from='#Old mol',
pipe_to='orig',
mol_to='#3')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Copy the molecule once more.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#4')
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule 2.
self.assertEqual(dp.mol[1].name, '2')
self.assertEqual(dp.mol[1].res[0].num, 1)
self.assertEqual(dp.mol[1].res[0].name, 'Ala')
self.assertEqual(dp.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[1].res[0].spin[0].x, 1)
# Test the new molecule 3.
self.assertEqual(dp.mol[2].name, '3')
self.assertEqual(dp.mol[2].res[0].num, 1)
self.assertEqual(dp.mol[2].res[0].name, 'Ala')
self.assertEqual(dp.mol[2].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[2].res[0].spin[0].x, 1)
# Test the new molecule 4.
self.assertEqual(dp.mol[3].name, '4')
self.assertEqual(dp.mol[3].res[0].num, 1)
self.assertEqual(dp.mol[3].res[0].name, 'Ala')
self.assertEqual(dp.mol[3].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[3].res[0].spin[0].x, 2)
def setUp(self):
"""Set up for all the spin unit tests.
The data contained within the 'orig' data pipe is:
ID Molecule Res number Res name Spin number Spin name
0,0,0 Old mol 1 Ala 111 C8
0,0,1 Old mol 1 Ala 6 C19
0,0,2 Old mol 1 Ala 7 C21
0,0,3 Old mol 1 Ala 8 C24
0,0,4 Old mol 1 Ala 9 C26
0,1,0 Old mol 2 Arg 78 NH
1,0,0 New mol 5 Lys 239 NH
1,1,0 New mol 6 Thr None None
1,1,1 New mol 6 Thr 3239 NH
The IDs correspond to the molecule, residue and spin indices.
"""
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Add a second data pipe for copying tests.
ds.add(pipe_name='test', pipe_type='mf')
# Set the current data pipe to 'orig'.
pipes.switch('orig')
# Name the first molecule.
cdp.mol[0].name = 'Old mol'
# Create the first residue and add some data to its spin container.
cdp.mol[0].res[0].num = 1
cdp.mol[0].res[0].name = 'Ala'
cdp.mol[0].res[0].spin[0].num = 111
cdp.mol[0].res[0].spin[0].name = 'C8'
cdp.mol[0].res[0].spin[0].x = 1
# Add some more spins.
cdp.mol[0].res[0].spin.add_item('C19', 6)
cdp.mol[0].res[0].spin.add_item('C21', 7)
cdp.mol[0].res[0].spin.add_item('C24', 8)
cdp.mol[0].res[0].spin.add_item('C26', 9)
# Create a second residue.
cdp.mol[0].res.add_item('Arg', 2)
cdp.mol[0].res[1].spin[0].num = 78
cdp.mol[0].res[1].spin[0].name = 'NH'
# Create a second molecule.
cdp.mol.add_item('New mol')
# Create the first and second residue of the second molecule and add some data to its spin container.
cdp.mol[1].res[0].num = 5
cdp.mol[1].res[0].name = 'Lys'
cdp.mol[1].res[0].spin[0].num = 239
cdp.mol[1].res[0].spin[0].name = 'NH'
cdp.mol[1].res.add_item('Thr', 6)
cdp.mol[1].res[1].spin.add_item(None, 1433)
cdp.mol[1].res[1].spin.add_item('NH', 3239)
# Create a third molecule.
cdp.mol.add_item('3rd')
# Create the first residue of the 3rd molecule and add some data to its spin container.
cdp.mol[2].res[0].num = 13
cdp.mol[2].res[0].name = 'Gly'
cdp.mol[2].res[0].spin[0].x = 'hello'
# Update the metadata.
metadata_update()
def select(method=None, modsel_pipe=None, bundle=None, pipes=None):
"""Model selection function.
@keyword method: The model selection method. This can currently be one of:
- 'AIC', Akaike's Information Criteria.
- 'AICc', Small sample size corrected AIC.
- 'BIC', Bayesian or Schwarz Information Criteria.
- 'CV', Single-item-out cross-validation.
None of the other model selection techniques are currently supported.
@type method: str
@keyword modsel_pipe: The name of the new data pipe to be created by copying of the selected data pipe.
@type modsel_pipe: str
@keyword bundle: The optional data pipe bundle to associate the newly created pipe with.
@type bundle: str or None
@keyword pipes: A list of the data pipes to use in the model selection.
@type pipes: list of str
"""
# Test if the pipe already exists.
if has_pipe(modsel_pipe):
raise RelaxPipeError(modsel_pipe)
# Use all pipes.
if pipes == None:
# Get all data pipe names from the relax data store.
pipes = pipe_names()
# Select the model selection technique.
if method == 'AIC':
print("AIC model selection.")
formula = aic
elif method == 'AICc':
print("AICc model selection.")
formula = aicc
elif method == 'BIC':
print("BIC model selection.")
formula = bic
elif method == 'CV':
print("CV model selection.")
raise RelaxError("The model selection technique " + repr(method) + " is not currently supported.")
else:
raise RelaxError("The model selection technique " + repr(method) + " is not currently supported.")
# No pipes.
if len(pipes) == 0:
raise RelaxError("No data pipes are available for use in model selection.")
# Initialise.
function_type = {}
model_loop = {}
model_type = {}
duplicate_data = {}
model_statistics = {}
skip_function = {}
modsel_pipe_exists = False
# Cross validation setup.
if isinstance(pipes[0], list):
# No pipes.
if len(pipes[0]) == 0:
raise RelaxError("No pipes are available for use in model selection in the array " + repr(pipes[0]) + ".")
# Loop over the data pipes.
for i in range(len(pipes)):
for j in range(len(pipes[i])):
# The specific analysis API object.
api = return_api(pipe_name=pipes[i][j])
# Store the specific functions.
model_loop[pipes[i][j]] = api.model_loop
model_type[pipes[i][j]] = api.model_type
duplicate_data[pipes[i][j]] = api.duplicate_data
model_statistics[pipes[i][j]] = api.model_statistics
skip_function[pipes[i][j]] = api.skip_function
# The model loop should be the same for all data pipes!
for i in range(len(pipes)):
for j in range(len(pipes[i])):
if model_loop[pipes[0][j]] != model_loop[pipes[i][j]]:
raise RelaxError("The models for each data pipes should be the same.")
# Alias some function from the specific API of the first data pipe.
api = return_api(pipe_name=pipes[0][0])
model_loop = api.model_loop
model_desc = api.model_desc
# Global vs. local models.
global_flag = False
for i in range(len(pipes)):
for j in range(len(pipes[i])):
if model_type[pipes[i][j]]() == 'global':
global_flag = True
# All other model selection setup.
else:
# Loop over the data pipes.
for i in range(len(pipes)):
# The specific analysis API object.
api = return_api()
# Store the specific functions.
model_loop[pipes[i]] = api.model_loop
model_type[pipes[i]] = api.model_type
duplicate_data[pipes[i]] = api.duplicate_data
model_statistics[pipes[i]] = api.model_statistics
skip_function[pipes[i]] = api.skip_function
# Alias some function from the specific API of the first data pipe.
api = return_api(pipe_name=pipes[0])
model_loop = api.model_loop
model_desc = api.model_desc
# Global vs. local models.
global_flag = False
for j in range(len(pipes)):
if model_type[pipes[j]]() == 'global':
global_flag = True
# Loop over the base models.
for model_info in model_loop():
# Print out.
print("\n")
desc = model_desc(model_info)
if desc:
print(desc)
# Initial model.
best_model = None
best_crit = 1e300
data = []
# Loop over the pipes.
for j in range(len(pipes)):
# Single-item-out cross validation.
if method == 'CV':
# Sum of chi-squared values.
sum_crit = 0.0
# Loop over the validation samples and sum the chi-squared values.
for k in range(len(pipes[j])):
# Alias the data pipe name.
pipe = pipes[j][k]
# Switch to this pipe.
switch(pipe)
# Skip function.
if skip_function[pipe](model_info):
continue
# Get the model statistics.
k, n, chi2 = model_statistics[pipe](model_info)
# Missing data sets.
if k == None or n == None or chi2 == None:
continue
# Chi2 sum.
sum_crit = sum_crit + chi2
# Cross-validation criterion (average chi-squared value).
crit = sum_crit / float(len(pipes[j]))
# Other model selection methods.
else:
# Reassign the pipe.
pipe = pipes[j]
# Switch to this pipe.
switch(pipe)
# Skip function.
if skip_function[pipe](model_info):
continue
# Get the model statistics.
k, n, chi2 = model_statistics[pipe](model_info, global_stats=global_flag)
# Missing data sets.
if k == None or n == None or chi2 == None:
continue
# Calculate the criterion value.
crit = formula(chi2, float(k), float(n))
# Store the values for a later printout.
data.append([pipe, repr(k), repr(n), "%.5f" % chi2, "%.5f" % crit])
# Select model.
if crit < best_crit:
best_model = pipe
best_crit = crit
# Write out the table.
write_data(out=sys.stdout, headings=["Data pipe", "Num_params_(k)", "Num_data_sets_(n)", "Chi2", "Criterion"], data=data)
# Duplicate the data from the 'best_model' to the model selection data pipe.
if best_model != None:
# Print out of selected model.
print("The model from the data pipe " + repr(best_model) + " has been selected.")
# Switch to the selected data pipe.
switch(best_model)
# Duplicate.
duplicate_data[best_model](best_model, modsel_pipe, model_info, global_stats=global_flag, verbose=False)
# Model selection pipe now exists.
modsel_pipe_exists = True
# No model selected.
else:
# Print out of selected model.
print("No model has been selected.")
# Switch to the model selection pipe.
if modsel_pipe_exists:
switch(modsel_pipe)
# Bundle the data pipe.
if bundle:
pipe_control.pipes.bundle(bundle=bundle, pipe=modsel_pipe)
# Update all of the required metadata structures.
mol_res_spin.metadata_update()
interatomic.metadata_update()
