def test_molecule_loop(self):
"""Test the proper operation of the molecule loop with molecule selection.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Loop over the molecules.
for mol in mol_res_spin.molecule_loop('#RNA'):
# Test the molecule name.
self.assertEqual(mol.name, 'RNA')
# Test loop length.
self.assertEqual(len(list(mol_res_spin.molecule_loop('#RNA'))), 1)
def test_molecule_loop(self):
"""Test the proper operation of the molecule loop with molecule selection.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Loop over the molecules.
for mol in mol_res_spin.molecule_loop('#RNA'):
# Test the molecule name.
self.assertEqual(mol.name, 'RNA')
# Test loop length.
self.assertEqual(len(list(mol_res_spin.molecule_loop('#RNA'))), 1)
def update(self, pipe_name=None):
"""Update the tree view using the given data pipe."""
# Acquire the pipe and spin locks.
status.pipe_lock.acquire('spin viewer window')
status.spin_lock.acquire('spin viewer window')
try:
# The data pipe.
if not pipe_name:
pipe = cdp
else:
pipe = get_pipe(pipe_name)
# No data pipe, so delete everything and return.
if not pipe:
self.tree.DeleteChildren(self.root)
return
# Update the molecules.
for mol, mol_id in molecule_loop(return_id=True):
self.update_mol(mol, mol_id)
# Remove any deleted molecules.
self.prune_mol()
# Release the locks.
finally:
status.pipe_lock.release('spin viewer window')
status.spin_lock.release('spin viewer window')
def update(self, pipe_name=None):
"""Update the tree view using the given data pipe."""
# Acquire the pipe and spin locks.
status.pipe_lock.acquire('spin viewer window')
status.spin_lock.acquire('spin viewer window')
try:
# The data pipe.
if not pipe_name:
pipe = cdp
else:
pipe = get_pipe(pipe_name)
# No data pipe, so delete everything and return.
if not pipe:
self.tree.DeleteChildren(self.root)
return
# Update the molecules.
for mol, mol_id in molecule_loop(return_id=True):
self.update_mol(mol, mol_id)
# Remove any deleted molecules.
self.prune_mol()
# Release the locks.
finally:
status.pipe_lock.release('spin viewer window')
status.spin_lock.release('spin viewer window')
def update_data(self):
"""Method called from self.build_element_safe() to update the list data."""
# Expand the number of rows to match the number of molecules, and add the data.
i = 0
for mol, mol_id in molecule_loop(return_id=True):
# Set the index.
self.element.InsertStringItem(i, str_to_gui(mol_id))
# Set the molecule name.
if mol.name != None:
self.element.SetStringItem(i, 1, str_to_gui(mol.name))
# Set the molecule type.
if hasattr(mol, 'type'):
self.element.SetStringItem(i, 2, str_to_gui(mol.type))
# Set the thiol state.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info,
'thiol_state'):
self.element.SetStringItem(
i, 3, str_to_gui(cdp.exp_info.thiol_state))
# Increment the counter.
i += 1
def is_complete(self):
"""Determine if the data input is complete.
@return: A list of all the missing components.
@rtype: list of str
"""
# Initialise.
missing = []
# Relaxation data metadata.
if hasattr(cdp, 'ri_ids'):
# Loop over the data.
for i in range(len(cdp.ri_ids)):
# Check the peak intensity types.
if not hasattr(cdp, 'exp_info') or not hasattr(
cdp.exp_info, 'peak_intensity_type'
) or not cdp.ri_ids[i] in cdp.exp_info.peak_intensity_type:
missing.append(
"The peak intensity type for the relaxation data ID '%s'."
% cdp.ri_ids[i])
# Check the temperature calibration methods.
if not hasattr(cdp, 'exp_info') or not hasattr(
cdp.exp_info, 'temp_calibration'
) or not cdp.ri_ids[i] in cdp.exp_info.temp_calibration:
missing.append(
"The temperature calibration method for the relaxation data ID '%s'."
% cdp.ri_ids[i])
# Check the temperature control methods.
if not hasattr(cdp, 'exp_info') or not hasattr(
cdp.exp_info, 'temp_control'
) or not cdp.ri_ids[i] in cdp.exp_info.temp_control:
missing.append(
"The temperature control method for the relaxation data ID '%s'."
% cdp.ri_ids[i])
# Loop over the molecules.
for mol, mol_id in molecule_loop(return_id=True):
# No name.
if mol.name == None:
missing.append("The name of the molecule for %s." % mol_id)
continue
# No molecule type.
if not hasattr(mol, 'type') or mol.type == None:
missing.append("The type of the molecule %s." % mol_id)
# No thiol state.
if not hasattr(cdp, 'exp_info') or not hasattr(
cdp.exp_info, 'thiol_state'):
missing.append("The thiol state of the molecule %s." % mol_id)
# Return the list of missing data.
return missing
def test_molecule_loop_no_selection(self):
"""Test the proper operation of the molecule loop when no selection is present.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Molecule data.
name = ['Ap4Aase', 'RNA']
# Loop over the molecules.
i = 0
for mol in mol_res_spin.molecule_loop():
# Test the molecule names.
self.assertEqual(mol.name, name[i])
# Increment i.
i = i + 1
# Test loop length.
self.assertEqual(len(list(mol_res_spin.molecule_loop())), 2)
def test_molecule_loop_no_selection(self):
"""Test the proper operation of the molecule loop when no selection is present.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Molecule data.
name = ['Ap4Aase', 'RNA']
# Loop over the molecules.
i = 0
for mol in mol_res_spin.molecule_loop():
# Test the molecule names.
self.assertEqual(mol.name, name[i])
# Increment i.
i = i + 1
# Test loop length.
self.assertEqual(len(list(mol_res_spin.molecule_loop())), 2)
def is_complete(self):
"""Determine if the data input is complete.
@return: A list of all the missing components.
@rtype: list of str
"""
# Initialise.
missing = []
# Relaxation data metadata.
if hasattr(cdp, 'ri_ids'):
# Loop over the data.
for i in range(len(cdp.ri_ids)):
# Check the peak intensity types.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'peak_intensity_type') or not cdp.ri_ids[i] in cdp.exp_info.peak_intensity_type.keys():
missing.append("The peak intensity type for the relaxation data ID '%s'." % cdp.ri_ids[i])
# Check the temperature calibration methods.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_calibration') or not cdp.ri_ids[i] in cdp.exp_info.temp_calibration.keys():
missing.append("The temperature calibration method for the relaxation data ID '%s'." % cdp.ri_ids[i])
# Check the temperature control methods.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_control') or not cdp.ri_ids[i] in cdp.exp_info.temp_control.keys():
missing.append("The temperature control method for the relaxation data ID '%s'." % cdp.ri_ids[i])
# Loop over the molecules.
for mol, mol_id in molecule_loop(return_id=True):
# No name.
if mol.name == None:
missing.append("The name of the molecule for %s." % mol_id)
continue
# No molecule type.
if not hasattr(mol, 'type') or mol.type == None:
missing.append("The type of the molecule %s." % mol_id)
# No thiol state.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'):
missing.append("The thiol state of the molecule %s." % mol_id)
# Return the list of missing data.
return missing
def test_molecule_loop_no_data(self):
"""Test the proper operation of the molecule loop when no data is present.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Loop over the molecules.
i = 0
for molecule in mol_res_spin.molecule_loop():
i = i + 1
# Test loop length.
self.assertEqual(i, 0)
def test_molecule_loop_no_data(self):
"""Test the proper operation of the molecule loop when no data is present.
The function tested is pipe_control.mol_res_spin.molecule_loop().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Loop over the molecules.
i = 0
for molecule in mol_res_spin.molecule_loop():
i = i + 1
# Test loop length.
self.assertEqual(i, 0)
def update_data(self):
"""Method called from self.build_element_safe() to update the list data."""
# Expand the number of rows to match the number of molecules, and add the data.
i = 0
for mol, mol_id in molecule_loop(return_id=True):
# Set the index.
self.element.InsertStringItem(i, str_to_gui(mol_id))
# Set the molecule name.
if mol.name != None:
self.element.SetStringItem(i, 1, str_to_gui(mol.name))
# Set the molecule type.
if hasattr(mol, 'type'):
self.element.SetStringItem(i, 2, str_to_gui(mol.type))
# Set the thiol state.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'thiol_state'):
self.element.SetStringItem(i, 3, str_to_gui(cdp.exp_info.thiol_state))
# Increment the counter.
i += 1
def is_complete(self):
"""Determine if the data input is complete.
@return: The answer to the question.
@rtype: bool
"""
# Loop over the molecules.
for mol in molecule_loop():
# No name.
if mol.name == None:
return False
# No molecule type.
if not hasattr(mol, 'type') or mol.type == None:
return False
# No thiol state.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'):
return False
# Data input is complete.
return True
def is_complete(self):
"""Determine if the data input is complete.
@return: The answer to the question.
@rtype: bool
"""
# Loop over the molecules.
for mol in molecule_loop():
# No name.
if mol.name == None:
return False
# No molecule type.
if not hasattr(mol, 'type') or mol.type == None:
return False
# No thiol state.
if not hasattr(cdp, 'exp_info') or not hasattr(
cdp.exp_info, 'thiol_state'):
return False
# Data input is complete.
return True
def fail_test():
for molecule in mol_res_spin.molecule_loop():
pass
def fail_test():
for molecule in mol_res_spin.molecule_loop():
pass
