def test_load_and_modify(self):
"""The modification of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe',
dir=status.install_path + sep + 'test_suite' +
sep + 'shared_data' + sep + 'saved_states')
# Add a new data pipe and some data to it.
ds.add('new', 'jw_mapping')
cdp.z = [None, None]
# Get the data pipes.
dp_orig = pipes.get_pipe('orig')
dp_new = pipes.get_pipe('new')
# Test the contents of the restored singleton (with subsequent data added).
self.assert_('orig' in ds)
self.assert_('new' in ds)
self.assertEqual(pipes.cdp_name(), 'new')
self.assertEqual(dp_orig.x, 1)
self.assertEqual(ds.y, 'Hello')
self.assertEqual(dp_new.z, [None, None])
def test_load_and_modify(self):
"""The modification of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'saved_states')
# Add a new data pipe and some data to it.
ds.add('new', 'jw_mapping')
cdp.z = [None, None]
# Get the data pipes.
dp_orig = pipes.get_pipe('orig')
dp_new = pipes.get_pipe('new')
# Test the contents of the restored singleton (with subsequent data added).
self.assert_('orig' in ds)
self.assert_('new' in ds)
self.assertEqual(pipes.cdp_name(), 'new')
self.assertEqual(dp_orig.x, 1)
self.assertEqual(ds.y, 'Hello')
self.assertEqual(dp_new.z, [None, None])
def action_spin_spin_copy(self, event):
"""Wrapper method.
@param event: The wx event.
@type event: wx event
"""
# Launch the user function wizard.
uf_store['spin.copy'](wx_parent=self.gui.spin_viewer,
pipe_from=cdp_name(),
spin_from=self.info['id'],
pipe_to=cdp_name())
def exists_data(pipe=None):
"""Determine if any interatomic data exists.
@keyword pipe: The data pipe in which the interatomic data will be checked for.
@type pipe: str
@return: The answer to the question about the existence of data.
@rtype: bool
"""
# The current data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Test the data pipe.
pipes.test(pipe)
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# The interatomic data structure is empty.
if dp.interatomic.is_empty():
return False
# Otherwise.
return True
def return_interatom_list(spin_id=None, pipe=None):
"""Return the list of interatomic data containers for the given spin.
@keyword spin_id: The spin ID string.
@type spin_id: str
@keyword pipe: The data pipe holding the container. This defaults to the current data pipe.
@type pipe: str or None
@return: The list of matching interatomic data containers, if any exist.
@rtype: list of data.interatomic.InteratomContainer instances
"""
# Check.
if spin_id == None:
raise RelaxError("The spin ID must be supplied.")
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Initialise.
interatoms = []
# Find and append all containers.
for i in range(len(dp.interatomic)):
if id_match(spin_id=spin_id, interatom=dp.interatomic[i], pipe=pipe) or id_match(spin_id=spin_id, interatom=dp.interatomic[i], pipe=pipe):
interatoms.append(dp.interatomic[i])
# Return the list of containers.
return interatoms
def check_structure_func(pipe_name=None):
"""Test if structural data is present.
@return: The initialised RelaxError object or nothing.
@rtype: None or RelaxError instance
"""
# Defaults.
if pipe_name == None:
pipe_name = cdp_name()
# Get the data pipe.
dp = get_pipe(pipe_name)
# Test if the structure exists.
if not hasattr(dp, 'structure'):
return RelaxError(
"No structural data is present in the current data pipe.")
# Check for models:
if not dp.structure.num_models():
return RelaxError(
"The structural object in the current data pipe contains no models."
)
# Check for molecules.
if not dp.structure.num_molecules():
return RelaxError(
"The structural object in the current data pipe contains no molecules."
)
def pipe_switch(self, pipe=None):
"""Switch the page to the given or current data pipe.
@keyword pipe: The pipe associated with the page to switch to. If not supplied, the current data pipe will be used.
@type pipe: str or None
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# No pipes to switch to.
if pipe == None:
return
# Find the page.
index = self.page_index_from_bundle(pipes.get_bundle(pipe))
# No matching page.
if index == None:
return
# The page is already active, so do nothing.
if self._current == index:
return
# Switch to the page.
self.switch_page(index)
# Notify the observers of the change.
status.observers.gui_analysis.notify()
def check_structure_func(pipe_name=None):
"""Test if structural data is present.
@return: The initialised RelaxError object or nothing.
@rtype: None or RelaxError instance
"""
# Defaults.
if pipe_name == None:
pipe_name = cdp_name()
# Get the data pipe.
dp = get_pipe(pipe_name)
# Test if the structure exists.
if not hasattr(dp, 'structure'):
return RelaxError("No structural data is present in the current data pipe.")
# Check for models:
if not dp.structure.num_models():
return RelaxError("The structural object in the current data pipe contains no models.")
# Check for molecules.
if not dp.structure.num_molecules():
return RelaxError("The structural object in the current data pipe contains no molecules.")
def exists_data(pipe=None):
"""Determine if any interatomic data exists.
@keyword pipe: The data pipe in which the interatomic data will be checked for.
@type pipe: str
@return: The answer to the question about the existence of data.
@rtype: bool
"""
# The current data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Test the data pipe.
check_pipe(pipe)
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# The interatomic data structure is empty.
if dp.interatomic.is_empty():
return False
# Otherwise.
return True
def return_interatom(spin_hash1=None, spin_hash2=None, pipe=None):
"""Return the list of interatomic data containers for the two spins.
@keyword spin_hash1: The unique spin hash for the first atom.
@type spin_hash1: str
@keyword spin_hash2: The unique spin hash for the second atom.
@type spin_hash2: str
@keyword pipe: The data pipe holding the container. Defaults to the current data pipe.
@type pipe: str or None
@return: The matching interatomic data container, if it exists.
@rtype: data.interatomic.InteratomContainer instance or None
"""
# Checks.
if spin_hash1 == None:
raise RelaxError("The first spin hash must be supplied.")
if spin_hash2 == None:
raise RelaxError("The second spin hash must be supplied.")
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Return the matching container.
for i in range(len(dp.interatomic)):
if spin_hash1 != spin_hash2 and spin_hash1 in [dp.interatomic[i]._spin_hash1, dp.interatomic[i]._spin_hash2] and spin_hash2 in [dp.interatomic[i]._spin_hash1, dp.interatomic[i]._spin_hash2]:
return dp.interatomic[i]
# No matchs.
return None
def return_interatom_list(spin_hash=None, pipe=None):
"""Return the list of interatomic data containers for the given spin.
@keyword spin_hash: The unique spin hash.
@type spin_hash: str
@keyword pipe: The data pipe holding the container. This defaults to the current data pipe.
@type pipe: str or None
@return: The list of matching interatomic data containers, if any exist.
@rtype: list of data.interatomic.InteratomContainer instances
"""
# Check.
if spin_hash == None:
raise RelaxError("The unique spin hash must be supplied.")
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Initialise.
interatoms = []
# Find and append all containers.
for i in range(len(dp.interatomic)):
if spin_hash in [dp.interatomic[i]._spin_hash1, dp.interatomic[i]._spin_hash2]:
interatoms.append(dp.interatomic[i])
# Return the list of containers.
return interatoms
def pipe_switch(self, pipe=None):
"""Switch the page to the given or current data pipe.
@keyword pipe: The pipe associated with the page to switch to. If not supplied, the current data pipe will be used.
@type pipe: str or None
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# No pipes to switch to.
if pipe == None:
return
# Find the page.
index = self.page_index_from_bundle(pipes.get_bundle(pipe))
# No matching page.
if index == None:
return
# The page is already active, so do nothing.
if self._current == index:
return
# Switch to the page.
self.switch_page(index)
# Notify the observers of the change.
status.observers.gui_analysis.notify()
def return_interatom(spin_id1=None, spin_id2=None, pipe=None):
"""Return the list of interatomic data containers for the two spins.
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
@keyword spin_id2: The spin ID string of the second atom.
@type spin_id2: str
@keyword pipe: The data pipe holding the container. Defaults to the current data pipe.
@type pipe: str or None
@return: The matching interatomic data container, if it exists.
@rtype: data.interatomic.InteratomContainer instance or None
"""
# Checks.
if spin_id1 == None:
raise RelaxError("The first spin ID must be supplied.")
if spin_id2 == None:
raise RelaxError("The second spin ID must be supplied.")
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Return the matching container.
for i in range(len(dp.interatomic)):
if id_match(spin_id=spin_id1, interatom=dp.interatomic[i], pipe=pipe) and id_match(spin_id=spin_id2, interatom=dp.interatomic[i], pipe=pipe):
return dp.interatomic[i]
# No matchs.
return None
def update_pipes(self, event=None):
"""Update the spin view data pipe selector.
@keyword event: The wx event.
@type event: wx event
"""
# Change the cursor to busy.
wx.BeginBusyCursor()
# Init.
pipe_switch = False
# The selected pipe.
if event:
# The name of the selected pipe.
pipe = gui_to_str(self.pipe_name.GetString(event.GetSelection()))
# A pipe change.
if pipe != cdp_name():
pipe_switch = True
else:
pipe = cdp_name()
if not pipe:
pipe = ''
# Clear the previous data.
self.pipe_name.Clear()
# The list of pipe names.
for name in pipe_names():
self.pipe_name.Append(str_to_gui(name))
# Switch.
if pipe_switch:
# Switch data pipes.
self.gui.interpreter.apply('pipe.switch', pipe)
# Update the tree view.
self.tree_panel.update()
# Set the pipe name to the cdp.
self.pipe_name.SetValue(str_to_gui(pipe))
# Reset the cursor.
if wx.IsBusy():
wx.EndBusyCursor()
def update_pipes(self, event=None):
"""Update the spin view data pipe selector.
@keyword event: The wx event.
@type event: wx event
"""
# Change the cursor to busy.
wx.BeginBusyCursor()
# Init.
pipe_switch = False
# The selected pipe.
if event:
# The name of the selected pipe.
pipe = gui_to_str(self.pipe_name.GetString(event.GetSelection()))
# A pipe change.
if pipe != cdp_name():
pipe_switch = True
else:
pipe = cdp_name()
if not pipe:
pipe = ''
# Clear the previous data.
self.pipe_name.Clear()
# The list of pipe names.
for name in pipe_names():
self.pipe_name.Append(str_to_gui(name))
# Switch.
if pipe_switch:
# Switch data pipes.
self.gui.interpreter.apply('pipe.switch', pipe)
# Update the tree view.
self.tree_panel.update()
# Set the pipe name to the cdp.
self.pipe_name.SetValue(str_to_gui(pipe))
# Reset the cursor.
if wx.IsBusy():
wx.EndBusyCursor()
def __init__(self, pipe_name=None, pipe_bundle=None, file_root='noe', results_dir=None, save_state=True):
"""Perform relaxation curve fitting.
To use this auto-analysis, a data pipe with all the required data needs to be set up. This data pipe should contain the following:
- All the spins loaded.
- Unresolved spins deselected.
- The NOE peak intensities from the saturated and reference spectra.
- Either the baseplane noise RMDS values should be set or replicated spectra loaded.
@keyword pipe_name: The name of the data pipe containing all of the data for the analysis.
@type pipe_name: str
@keyword pipe_bundle: The data pipe bundle to associate all spawned data pipes with.
@type pipe_bundle: str
@keyword file_root: File root of the output filea.
@type file_root: str
@keyword results_dir: The directory where results files are saved.
@type results_dir: str
@keyword save_state: A flag which if True will cause a relax save state to be created at the end of the analysis.
@type save_state: bool
"""
# Execution lock.
status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
# Set up the analysis status object.
status.init_auto_analysis(pipe_bundle, type='noe')
status.current_analysis = pipe_bundle
# Store the args.
self.save_state = save_state
self.pipe_name = pipe_name
self.pipe_bundle = pipe_bundle
self.file_root = file_root
self.results_dir = results_dir
if self.results_dir:
self.grace_dir = results_dir + sep + 'grace'
else:
self.grace_dir = 'grace'
# Data checks.
self.check_vars()
# Set the data pipe to the current data pipe.
if self.pipe_name != cdp_name():
switch(self.pipe_name)
# Load the interpreter.
self.interpreter = Interpreter(show_script=False, quit=False, raise_relax_error=True)
self.interpreter.populate_self()
self.interpreter.on(verbose=False)
# Execute.
self.run()
# Finish and unlock execution.
status.auto_analysis[self.pipe_bundle].fin = True
status.current_analysis = None
status.exec_lock.release()
def test_current(self):
"""Get the current data pipe.
The function used is pipe_control.pipes.cdp_name().
"""
# Test the current pipe.
self.assertEqual(pipes.cdp_name(), 'orig')
def test_switch(self):
"""Test the switching of the current data pipe.
The function tested is pipe_control.pipes.switch().
"""
# Switch to the 'orig' data pipe.
pipes.switch('orig')
# Test the current data pipe.
self.assertEqual(pipes.cdp_name(), 'orig')
# Switch to the 'empty' data pipe.
pipes.switch('empty')
# Test the current data pipe.
self.assertEqual(pipes.cdp_name(), 'empty')
def test_current(self):
"""Get the current data pipe.
The function used is pipe_control.pipes.cdp_name().
"""
# Test the current pipe.
self.assertEqual(pipes.cdp_name(), 'orig')
def copy_frequencies(pipe_from=None, pipe_to=None, id=None):
"""Copy the frequency information from one data pipe to another.
@keyword pipe_from: The data pipe to copy the frequency information from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the frequency information to. This defaults to the current data pipe.
@type pipe_to: str
@param id: The experiment ID string.
@type id: str
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Test if the pipe_from and pipe_to data pipes exist.
check_pipe(pipe_from)
check_pipe(pipe_to)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
# Test if the pipe_from pipe has frequency data.
if not hasattr(dp_from, 'spectrometer_frq'):
raise RelaxNoFrqError(pipe_from)
elif id not in dp_from.spectrometer_frq:
raise RelaxNoFrqError(pipe_from, id=id)
# Set up the data structures if missing.
if not hasattr(dp_to, 'spectrometer_frq'):
dp_to.spectrometer_frq = {}
dp_to.spectrometer_frq_list = []
dp_to.spectrometer_frq_count = 0
# Copy the frequency.
dp_to.spectrometer_frq[id] = dp_from.spectrometer_frq[id]
# New frequency.
if dp_to.spectrometer_frq[id] not in dp_to.spectrometer_frq_list:
dp_to.spectrometer_frq_list.append(dp_to.spectrometer_frq[id])
dp_to.spectrometer_frq_count += 1
def test_switch(self):
"""Test the switching of the current data pipe.
The function tested is pipe_control.pipes.switch().
"""
# Switch to the 'orig' data pipe.
pipes.switch('orig')
# Test the current data pipe.
self.assertEqual(pipes.cdp_name(), 'orig')
# Switch to the 'empty' data pipe.
pipes.switch('empty')
# Test the current data pipe.
self.assertEqual(pipes.cdp_name(), 'empty')
def copy_frequencies(pipe_from=None, pipe_to=None, id=None):
"""Copy the frequency information from one data pipe to another.
@keyword pipe_from: The data pipe to copy the frequency information from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the frequency information to. This defaults to the current data pipe.
@type pipe_to: str
@param id: The experiment ID string.
@type id: str
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Test if the pipe_from and pipe_to data pipes exist.
check_pipe(pipe_from)
check_pipe(pipe_to)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
# Test if the pipe_from pipe has frequency data.
if not hasattr(dp_from, 'spectrometer_frq'):
raise RelaxNoFrqError(pipe_from)
elif id not in dp_from.spectrometer_frq:
raise RelaxNoFrqError(pipe_from, id=id)
# Set up the data structures if missing.
if not hasattr(dp_to, 'spectrometer_frq'):
dp_to.spectrometer_frq = {}
dp_to.spectrometer_frq_list = []
dp_to.spectrometer_frq_count = 0
# Copy the frequency.
dp_to.spectrometer_frq[id] = dp_from.spectrometer_frq[id]
# New frequency.
if dp_to.spectrometer_frq[id] not in dp_to.spectrometer_frq_list:
dp_to.spectrometer_frq_list.append(dp_to.spectrometer_frq[id])
dp_to.spectrometer_frq_count += 1
def load_spins_wizard(self, event=None):
"""The spin loading wizard.
@keyword event: The wx event.
@type event: wx event
"""
# No current data pipe.
if not cdp_name():
gui_raise(RelaxNoPipeError())
return
# Change the cursor to busy.
wx.BeginBusyCursor()
# Initialise a wizard.
self.wizard = Wiz_window(parent=self, size_x=1000, size_y=800, title="Load spins")
self.page_indices = {}
# The loading method page.
self.page_method = Load_method_page(self.wizard)
self.page_indices['method'] = self.wizard.add_page(self.page_method, apply_button=True, skip_button=False)
self.wizard.set_seq_next_fn(self.page_indices['method'], self.wizard_page_after_load_method)
# The sequence.read page.
page = uf_store['sequence.read'].create_page(self.wizard)
self.page_indices['sequence.read'] = self.wizard.add_page(page, skip_button=True)
self.wizard.set_seq_next_fn(self.page_indices['sequence.read'], self.wizard_page_after_sequence_read)
# The structure.read_pdb page.
page = uf_store['structure.read_pdb'].create_page(self.wizard)
self.page_indices['structure.read_pdb'] = self.wizard.add_page(page, skip_button=True)
self.wizard.set_seq_next_fn(self.page_indices['structure.read_pdb'], self.wizard_page_after_structure_read)
# The structure.read_xyz page.
page = uf_store['structure.read_xyz'].create_page(self.wizard)
self.page_indices['structure.read_xyz'] = self.wizard.add_page(page, skip_button=True)
self.wizard.set_seq_next_fn(self.page_indices['structure.read_xyz'], self.wizard_page_after_structure_read)
# The spectrum.read_spins page.
page = uf_store['spectrum.read_spins'].create_page(self.wizard)
self.page_indices['spectrum.read_spins'] = self.wizard.add_page(page, skip_button=True)
self.wizard.set_seq_next_fn(self.page_indices['spectrum.read_spins'], self.wizard_page_after_sequence_read)
# The structure.load_spins page.
page = uf_store['structure.load_spins'].create_page(self.wizard)
self.page_indices['structure.load_spins'] = self.wizard.add_page(page)
# The termination page.
page = Finish_page(self.wizard)
self.page_indices['fin'] = self.wizard.add_page(page, apply_button=False, skip_button=False)
# Reset the cursor.
if wx.IsBusy():
wx.EndBusyCursor()
# Run the wizard.
self.wizard.run()
def update_grid_safe(self):
"""Update the grid with the pipe data."""
# First freeze the grid, so that the GUI element doesn't update until the end.
self.grid.Freeze()
# Acquire the pipe lock.
status.pipe_lock.acquire('pipe editor window')
# Delete the rows, leaving a single row.
self.grid.DeleteRows(numRows=self.grid.GetNumberRows()-1)
# Clear the contents of the first row.
for i in range(self.grid.GetNumberCols()):
self.grid.SetCellValue(0, i, str_to_gui(""))
# The data pipes.
pipe_list = pipe_names()
n = len(pipe_list)
# Append the appropriate number of rows.
if n >= 1:
self.grid.AppendRows(numRows=n-1)
# Loop over the data pipes.
for i in range(n):
# Set the pipe name.
self.grid.SetCellValue(i, 0, str_to_gui(pipe_list[i]))
# Set the pipe type.
self.grid.SetCellValue(i, 1, str_to_gui(get_type(pipe_list[i])))
# Set the pipe bundle.
self.grid.SetCellValue(i, 2, str_to_gui(get_bundle(pipe_list[i])))
# Set the current pipe.
if pipe_list[i] == cdp_name():
self.grid.SetCellValue(i, 3, str_to_gui("cdp"))
# Set the tab the pipe belongs to.
self.grid.SetCellValue(i, 4, str_to_gui(self.gui.analysis.page_name_from_bundle(get_bundle(pipe_list[i]))))
# Set the grid properties once finalised.
for i in range(self.grid.GetNumberRows()):
# Row properties.
self.grid.SetRowSize(i, 27)
# Loop over the columns.
for j in range(self.grid.GetNumberCols()):
# Cell properties.
self.grid.SetReadOnly(i, j)
# Release the lock.
status.pipe_lock.release('pipe editor window')
# Unfreeze.
self.grid.Thaw()
def update_grid_safe(self):
"""Update the grid with the pipe data."""
# First freeze the grid, so that the GUI element doesn't update until the end.
self.grid.Freeze()
# Acquire the pipe lock.
status.pipe_lock.acquire('pipe editor window')
# Delete the rows, leaving a single row.
self.grid.DeleteRows(numRows=self.grid.GetNumberRows()-1)
# Clear the contents of the first row.
for i in range(self.grid.GetNumberCols()):
self.grid.SetCellValue(0, i, str_to_gui(""))
# The data pipes.
pipe_list = pipe_names()
n = len(pipe_list)
# Append the appropriate number of rows.
if n >= 1:
self.grid.AppendRows(numRows=n-1)
# Loop over the data pipes.
for i in range(n):
# Set the pipe name.
self.grid.SetCellValue(i, 0, str_to_gui(pipe_list[i]))
# Set the pipe type.
self.grid.SetCellValue(i, 1, str_to_gui(get_type(pipe_list[i])))
# Set the pipe bundle.
self.grid.SetCellValue(i, 2, str_to_gui(get_bundle(pipe_list[i])))
# Set the current pipe.
if pipe_list[i] == cdp_name():
self.grid.SetCellValue(i, 3, str_to_gui("cdp"))
# Set the tab the pipe belongs to.
self.grid.SetCellValue(i, 4, str_to_gui(self.gui.analysis.page_name_from_bundle(get_bundle(pipe_list[i]))))
# Set the grid properties once finalised.
for i in range(self.grid.GetNumberRows()):
# Row properties.
self.grid.SetRowSize(i, 27)
# Loop over the columns.
for j in range(self.grid.GetNumberCols()):
# Cell properties.
self.grid.SetReadOnly(i, j)
# Release the lock.
status.pipe_lock.release('pipe editor window')
# Unfreeze.
self.grid.Thaw()
def update_mf(self):
"""Update the model-free specific elements."""
# The analysis key.
key = self.analysis_key()
if not key:
return
# Loaded a finished state, so fill all gauges and return.
elif not key in status.auto_analysis and cdp_name() == 'final':
wx.CallAfter(self.mc_gauge_mf.SetValue, 100)
wx.CallAfter(self.progress_gauge_mf.SetValue, 100)
wx.CallAfter(self.main_gauge.SetValue, 100)
return
# Nothing to do.
if not key in status.auto_analysis:
wx.CallAfter(self.mc_gauge_mf.SetValue, 0)
wx.CallAfter(self.progress_gauge_mf.SetValue, 0)
wx.CallAfter(self.main_gauge.SetValue, 0)
return
# Set the diffusion model.
wx.CallAfter(self.global_model_mf.SetValue, str_to_gui(status.auto_analysis[key].diff_model))
# Update the progress gauge for the local tm model.
if status.auto_analysis[key].diff_model == 'local_tm':
if status.auto_analysis[key].current_model:
# Current model.
no = int(status.auto_analysis[key].current_model[2:])
# Total selected models.
total_models = len(status.auto_analysis[key].local_tm_models)
# Update the progress bar.
percent = int(100 * no / float(total_models))
wx.CallAfter(self.progress_gauge_mf.SetValue, percent)
# Sphere to ellipsoid Models.
elif status.auto_analysis[key].diff_model in ['sphere', 'prolate', 'oblate', 'ellipsoid']:
# Check that the round has been set.
if status.auto_analysis[key].round == None:
wx.CallAfter(self.progress_gauge_mf.SetValue, 0)
else:
# The round as a percentage.
percent = int(100 * (status.auto_analysis[key].round + 1) / (status.auto_analysis[key].max_iter + 1))
# Update the progress bar.
wx.CallAfter(self.progress_gauge_mf.SetValue, percent)
# Monte Carlo simulations.
if status.auto_analysis[key].mc_number:
# The simulation number as a percentage.
percent = int(100 * (status.auto_analysis[key].mc_number + 1) / cdp.sim_number)
# Update the progress bar.
wx.CallAfter(self.mc_gauge_mf.SetValue, percent)
def write(file="results", dir=None, force=False, compress_type=1, verbosity=1):
"""Create the results file."""
# Test if the current data pipe exists.
check_pipe()
# The special data pipe name directory.
if dir == 'pipe_name':
dir = pipes.cdp_name()
# Open the file for writing.
results_file = open_write_file(file_name=file, dir=dir, force=force, compress_type=compress_type, verbosity=verbosity)
# Write the results.
ds.to_xml(results_file, pipes=pipes.cdp_name())
# Close the results file.
results_file.close()
def write(file="results", dir=None, force=False, compress_type=1, verbosity=1):
"""Create the results file."""
# Test if the current data pipe exists.
check_pipe()
# The special data pipe name directory.
if dir == 'pipe_name':
dir = pipes.cdp_name()
# Open the file for writing.
results_file = open_write_file(file_name=file, dir=dir, force=force, compress_type=compress_type, verbosity=verbosity)
# Write the results.
ds.to_xml(results_file, pipes=pipes.cdp_name())
# Close the results file.
results_file.close()
def action_spin_spin_copy(self, event):
"""Wrapper method.
@param event: The wx event.
@type event: wx event
"""
# Launch the user function wizard.
uf_store['spin.copy'](wx_parent=self.gui.spin_viewer, pipe_from=cdp_name(), spin_from=self.info['id'], pipe_to=cdp_name())
def create(algor='LM', dir=None, force=False):
"""Create the Dasha script file 'dasha_script' for controlling the program.
@keyword algor: The optimisation algorithm to use. This can be the Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
@keyword dir: The optional directory to place the script into.
@type dir: str or None
@keyword force: A flag which if True will cause any pre-existing file to be overwritten.
@type force: bool
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Determine the parameter set.
model_type = determine_model_type()
# Test if diffusion tensor data for the data_pipe exists.
if model_type != 'local_tm' and not hasattr(cdp, 'diff_tensor'):
raise RelaxNoTensorError('diffusion')
# Test if the PDB file has been loaded (for the spheroid and ellipsoid).
if model_type != 'local_tm' and cdp.diff_tensor.type != 'sphere' and not hasattr(
cdp, 'structure'):
raise RelaxNoPdbError
# Test the optimisation algorithm.
if algor not in ['LM', 'NR']:
raise RelaxError(
"The Dasha optimisation algorithm '%s' is unknown, it should either be 'LM' or 'NR'."
% algor)
# Deselect certain spins.
__deselect_spins()
# Directory creation.
if dir == None:
dir = pipes.cdp_name()
mkdir_nofail(dir, verbosity=0)
# Calculate the angle alpha of the XH vector in the spheroid diffusion frame.
if cdp.diff_tensor.type == 'spheroid':
angles.spheroid_frame()
# Calculate the angles theta and phi of the XH vector in the ellipsoid diffusion frame.
elif cdp.diff_tensor.type == 'ellipsoid':
angles.ellipsoid_frame()
# The 'dasha_script' file.
script = open_write_file(file_name='dasha_script', dir=dir, force=force)
create_script(script, model_type, algor)
script.close()
def check_pipe_setup(pipe=None, pcs_id=None, sequence=False, N=False, tensors=False, pcs=False, paramag_centre=False):
"""Check that the current data pipe has been setup sufficiently.
@keyword pipe: The data pipe to check, defaulting to the current pipe.
@type pipe: None or str
@keyword pcs_id: The PCS ID string to check for in cdp.pcs_ids.
@type pcs_id: None or str
@keyword sequence: A flag which when True will invoke the sequence data check.
@type sequence: bool
@keyword N: A flag which if True will check that cdp.N is set.
@type N: bool
@keyword tensors: A flag which if True will check that alignment tensors exist.
@type tensors: bool
@keyword pcs: A flag which if True will check that PCSs exist.
@type pcs: bool
@keyword paramag_centre: A flag which if True will check that the paramagnetic centre has been set.
@type paramag_centre: bool
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Test if the current data pipe exists.
check_pipe(pipe)
# Test if sequence data exists.
if sequence and not exists_mol_res_spin_data(pipe):
raise RelaxNoSequenceError(pipe)
# Check for dp.N.
if N and not hasattr(dp, 'N'):
raise RelaxError("The number of states N has not been set.")
# Check that alignment tensors are present.
if tensors and (not hasattr(dp, 'align_tensors') or len(dp.align_tensors) == 0):
raise RelaxNoTensorError('alignment')
# Test for the alignment ID.
if pcs_id and (not hasattr(dp, 'align_ids') or pcs_id not in dp.align_ids):
raise RelaxNoAlignError(pcs_id, pipe)
# Test if PCS data exists.
if pcs and not hasattr(dp, 'align_ids'):
raise RelaxNoAlignError()
if pcs and not hasattr(dp, 'pcs_ids'):
raise RelaxNoPCSError()
elif pcs and pcs_id and pcs_id not in dp.pcs_ids:
raise RelaxNoPCSError(pcs_id)
# Test if the paramagnetic centre is set.
if paramag_centre and not hasattr(cdp, 'paramagnetic_centre'):
raise RelaxError("The paramagnetic centre has not been defined.")
def copy(pipe_from=None, pipe_to=None):
"""Copy the J coupling data from one data pipe to another.
@keyword pipe_from: The data pipe to copy the J coupling data from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the J coupling data to. This defaults to the current data pipe.
@type pipe_to: str
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Check the pipe setup.
check_pipe_setup(pipe=pipe_from, sequence=True, j=True)
check_pipe_setup(pipe=pipe_to, sequence=True)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
# Test that the interatomic data is consistent between the two data pipe.
consistent_interatomic_data(pipe1=pipe_to, pipe2=pipe_from)
# Loop over the interatomic data.
for i in range(len(dp_from.interatomic)):
# Alias the containers.
interatom_from = dp_from.interatomic[i]
interatom_to = dp_to.interatomic[i]
# No data or errors.
if not hasattr(interatom_from, 'j_coupling') or not hasattr(interatom_from, 'j_coupling_err'):
continue
# Copy the value and error from pipe_from.
if hasattr(interatom_from, 'j_coupling'):
interatom_to.j_coupling = interatom_from.j_coupling
if hasattr(interatom_from, 'j_coupling_err'):
interatom_to.j_coupling_err = interatom_from.j_coupling_err
def copy(pipe_from=None, pipe_to=None):
"""Copy the J coupling data from one data pipe to another.
@keyword pipe_from: The data pipe to copy the J coupling data from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the J coupling data to. This defaults to the current data pipe.
@type pipe_to: str
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Check the pipe setup.
check_pipe_setup(pipe=pipe_from, sequence=True, j=True)
check_pipe_setup(pipe=pipe_to, sequence=True)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
# Test that the interatomic data is consistent between the two data pipe.
consistent_interatomic_data(pipe1=pipe_to, pipe2=pipe_from)
# Loop over the interatomic data.
for i in range(len(dp_from.interatomic)):
# Alias the containers.
interatom_from = dp_from.interatomic[i]
interatom_to = dp_to.interatomic[i]
# No data or errors.
if not hasattr(interatom_from, 'j_coupling') or not hasattr(interatom_from, 'j_coupling_err'):
continue
# Copy the value and error from pipe_from.
if hasattr(interatom_from, 'j_coupling'):
interatom_to.j_coupling = interatom_from.j_coupling
if hasattr(interatom_from, 'j_coupling_err'):
interatom_to.j_coupling_err = interatom_from.j_coupling_err
def create_interatom(spin_id1=None, spin_id2=None, spin1=None, spin2=None, pipe=None, verbose=False):
"""Create and return the interatomic data container for the two spins.
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
@keyword spin_id2: The spin ID string of the second atom.
@type spin_id2: str
@keyword spin1: The optional spin container for the first atom. This is for speeding up the interatomic data container creation, if the spin containers are already available in the calling function.
@type spin1: str
@keyword spin2: The optional spin container for the second atom. This is for speeding up the interatomic data container creation, if the spin containers are already available in the calling function.
@type spin2: str
@keyword pipe: The data pipe to create the interatomic data container for. This defaults to the current data pipe if not supplied.
@type pipe: str or None
@keyword verbose: A flag which if True will result printouts.
@type verbose: bool
@return: The newly created interatomic data container.
@rtype: data.interatomic.InteratomContainer instance
"""
# Printout.
if verbose:
print("Creating an interatomic data container between the spins '%s' and '%s'." % (spin_id1, spin_id2))
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Check that the spin IDs exist.
if spin1 == None:
spin1 = return_spin(spin_id=spin_id1, pipe=pipe)
if spin1 == None:
raise RelaxNoSpinError(spin_id1)
if spin2 == None:
spin2 = return_spin(spin_id=spin_id2, pipe=pipe)
if spin2 == None:
raise RelaxNoSpinError(spin_id2)
# Check if the two spin IDs have already been added.
for i in range(len(dp.interatomic)):
if spin1._hash != spin2._hash and spin1._hash in [dp.interatomic[i]._spin_hash1, dp.interatomic[i]._spin_hash2] and spin2._hash in [dp.interatomic[i]._spin_hash1, dp.interatomic[i]._spin_hash2]:
raise RelaxError("The spin pair %s and %s have already been added." % (spin_id1, spin_id2))
# Add the data.
interatom = dp.interatomic.add_item(spin_id1=spin_id1, spin_id2=spin_id2, spin_hash1=spin1._hash, spin_hash2=spin2._hash)
# Store the interatom hash in the spin containers.
spin1._interatomic_hashes.append(interatom._hash)
spin2._interatomic_hashes.append(interatom._hash)
# Return the interatomic data container.
return interatom
def update_pipes(self):
"""Update the data pipe list."""
# Clear the previous data pipe.
self.pipe_name.Clear()
# The list of data pipes.
for pipe in pipe_names():
self.pipe_name.Append(str_to_gui(pipe))
# Set the name to the current data pipe.
self.pipe_name.SetValue(str_to_gui(cdp_name()))
def update_pipes(self):
"""Update the data pipe list."""
# Clear the previous data pipe.
self.pipe_name.Clear()
# The list of data pipes.
for pipe in pipe_names():
self.pipe_name.Append(str_to_gui(pipe))
# Set the name to the current data pipe.
self.pipe_name.SetValue(str_to_gui(cdp_name()))
def create(algor='LM', dir=None, force=False):
"""Create the Dasha script file 'dasha_script' for controlling the program.
@keyword algor: The optimisation algorithm to use. This can be the Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
@keyword dir: The optional directory to place the script into.
@type dir: str or None
@keyword force: A flag which if True will cause any pre-existing file to be overwritten.
@type force: bool
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Determine the parameter set.
model_type = determine_model_type()
# Test if diffusion tensor data for the data_pipe exists.
if model_type != 'local_tm' and not hasattr(cdp, 'diff_tensor'):
raise RelaxNoTensorError('diffusion')
# Test if the PDB file has been loaded (for the spheroid and ellipsoid).
if model_type != 'local_tm' and cdp.diff_tensor.type != 'sphere' and not hasattr(cdp, 'structure'):
raise RelaxNoPdbError
# Test the optimisation algorithm.
if algor not in ['LM', 'NR']:
raise RelaxError("The Dasha optimisation algorithm '%s' is unknown, it should either be 'LM' or 'NR'." % algor)
# Deselect certain spins.
__deselect_spins()
# Directory creation.
if dir == None:
dir = pipes.cdp_name()
mkdir_nofail(dir, verbosity=0)
# Calculate the angle alpha of the XH vector in the spheroid diffusion frame.
if cdp.diff_tensor.type == 'spheroid':
angles.spheroid_frame()
# Calculate the angles theta and phi of the XH vector in the ellipsoid diffusion frame.
elif cdp.diff_tensor.type == 'ellipsoid':
angles.ellipsoid_frame()
# The 'dasha_script' file.
script = open_write_file(file_name='dasha_script', dir=dir, force=force)
create_script(script, model_type, algor)
script.close()
def test_load_and_reset(self):
"""The resetting of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'saved_states')
# Reset relax.
reset()
# Test that there are no contents in the reset singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
def test_load(self):
"""The unpickling and restoration of the relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'saved_states')
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Test the contents of the restored singleton.
self.assertEqual(list(ds.keys()), ['orig'])
self.assertEqual(pipes.cdp_name(), 'orig')
self.assertEqual(dp.x, 1)
self.assertEqual(ds.y, 'Hello')
def check_pipe_setup(pipe=None, rdc_id=None, sequence=False, N=False, tensors=False, rdc=False):
"""Check that the current data pipe has been setup sufficiently.
@keyword pipe: The data pipe to check, defaulting to the current pipe.
@type pipe: None or str
@keyword rdc_id: The RDC ID string to check for in cdp.rdc_ids.
@type rdc_id: None or str
@keyword sequence: A flag which when True will invoke the sequence data check.
@type sequence: bool
@keyword N: A flag which if True will check that cdp.N is set.
@type N: bool
@keyword tensors: A flag which if True will check that alignment tensors exist.
@type tensors: bool
@keyword rdc: A flag which if True will check that RDCs exist.
@type rdc: bool
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Test if the current data pipe exists.
pipes.test(pipe)
# Test if sequence data exists.
if sequence and not exists_mol_res_spin_data(pipe):
raise RelaxNoSequenceError(pipe)
# Check for dp.N.
if N and not hasattr(dp, 'N'):
raise RelaxError("The number of states N has not been set.")
# Check that alignment tensors are present.
if tensors and (not hasattr(dp, 'align_tensors') or len(dp.align_tensors) == 0):
raise RelaxNoTensorError('alignment')
# Test for the alignment ID.
if rdc_id and (not hasattr(dp, 'align_ids') or rdc_id not in dp.align_ids):
raise RelaxNoAlignError(rdc_id, pipe)
# Test if RDC data exists.
if rdc and not hasattr(dp, 'align_ids'):
raise RelaxNoAlignError()
if rdc and not hasattr(dp, 'rdc_ids'):
raise RelaxNoRDCError()
elif rdc and rdc_id and rdc_id not in dp.rdc_ids:
raise RelaxNoRDCError(rdc_id)
def test_load_and_reset(self):
"""The resetting of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe',
dir=status.install_path + sep + 'test_suite' +
sep + 'shared_data' + sep + 'saved_states')
# Reset relax.
reset()
# Test that there are no contents in the reset singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
def action_export_bmrb(self, event=None):
"""Export the contents of the current data pipe for BMRB deposition.
@keyword event: The wx event.
@type event: wx event
"""
# No current data pipe.
if not cdp_name():
gui_raise(RelaxNoPipeError())
return
# Open the export window.
Export_bmrb_window(self)
def update_status_bar(self):
"""Update the status bar info."""
# Set the current data pipe info.
pipe = cdp_name()
# No data pipe.
if pipe == None:
pipe = ''
# Set the status.
wx.CallAfter(self.status_bar.SetStatusText, "(C) 2001-2013 the relax development team", 0)
wx.CallAfter(self.status_bar.SetStatusText, "Current data pipe:", 1)
wx.CallAfter(self.status_bar.SetStatusText, pipe, 2)
def test_creation(self):
"""Test the creation of a data pipe.
The function used is pipe_control.pipes.create().
"""
# Create a new model-free data pipe.
name = 'new'
pipes.create(name, 'mf')
# Test that the data pipe exists.
self.assert_(name in ds)
# Test that the current pipe is the new pipe.
self.assertEqual(pipes.cdp_name(), name)
def test_creation(self):
"""Test the creation of a data pipe.
The function used is pipe_control.pipes.create().
"""
# Create a new model-free data pipe.
name = 'new'
pipes.create(name, 'mf')
# Test that the data pipe exists.
self.assert_(name in ds)
# Test that the current pipe is the new pipe.
self.assertEqual(pipes.cdp_name(), name)
def test_load(self):
"""The unpickling and restoration of the relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe',
dir=status.install_path + sep + 'test_suite' +
sep + 'shared_data' + sep + 'saved_states')
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Test the contents of the restored singleton.
self.assertEqual(list(ds.keys()), ['orig'])
self.assertEqual(pipes.cdp_name(), 'orig')
self.assertEqual(dp.x, 1)
self.assertEqual(ds.y, 'Hello')
def test_pipe_bundle(self):
"""Test the pipe bundle concepts."""
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'pipe_bundle.py')
# Checks.
self.assertEqual(pipes.cdp_name(), None)
self.assertEqual(pipes.has_bundle('test bundle 1'), True)
self.assertEqual(pipes.has_bundle('test bundle 2'), True)
self.assertEqual(pipes.has_bundle('test bundle 3'), False)
bundles = sorted(pipes.bundle_names())
self.assertEqual(bundles, ['test bundle 1', 'test bundle 2'])
for pipe, name in pipes.pipe_loop(name=True):
self.assert_(name in ['test pipe 1', 'test pipe 2', 'test pipe 3', 'test pipe 4', 'test pipe 5', 'test pipe 6'])
self.assert_(pipes.get_bundle(name) in ['test bundle 1', 'test bundle 2'])
def test_bug_20480(self):
"""Catch U{bug #20480<https://web.archive.org/web/https://gna.org/bugs/?20480>}, the failure to load a relax state in the GUI.
This was reported by U{Stanislava Panova<https://web.archive.org/web/https://gna.org/users/stacy>}.
"""
# Simulate the 'Open relax state' menu entry.
file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'saved_states' + sep + 'bug_20480.bz2'
self.app.gui.state_load(file_name=file)
# Check that the data has been loaded.
self.assertEqual(cdp_name(), "aic - mf (Mon Feb 4 13:30:01 2013)")
self.assertEqual(cdp.spectrometer_frq['NOE_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R1_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R2_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R2_600'], 599999000.0)
def test_bug_20480(self):
"""Catch U{bug #20480<https://gna.org/bugs/?20480>}, the failure to load a relax state in the GUI.
This was reported by U{Stanislava Panova<https://gna.org/users/stacy>}.
"""
# Simulate the 'Open relax state' menu entry.
file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'saved_states' + sep + 'bug_20480.bz2'
self.app.gui.state_load(file_name=file)
# Check that the data has been loaded.
self.assertEqual(cdp_name(), "aic - mf (Mon Feb 4 13:30:01 2013)")
self.assertEqual(cdp.spectrometer_frq['NOE_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R1_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R2_800'], 800000031.0)
self.assertEqual(cdp.spectrometer_frq['R2_600'], 599999000.0)
def test_bug_21720_pipe_switching_with_tab_closure(self):
"""Catch U{bug #20479<https://web.archive.org/web/https://gna.org/bugs/?20479>}, the failure to switch pipes when closing non-last tabs."""
# NOE tab: Simulate the new analysis wizard.
analysis = self.new_analysis_wizard(analysis_type='noe', analysis_name='NOE test', pipe_name='noe', pipe_bundle='noe bundle')
# Mf tab: Simulate the new analysis wizard.
analysis = self.new_analysis_wizard(analysis_type='mf', analysis_name='Mf test', pipe_name='mf', pipe_bundle='mf bundle')
# NOE tab: Switch back.
self.app.gui.analysis.switch_page(index=0)
# NOE tab: Closure.
self.app.gui.analysis.delete_analysis(0)
# Check that the Mf data pipe is now the current pipe.
self.assertEqual(cdp_name(), 'mf')
def test_bug_21720_pipe_switching_with_tab_closure(self):
"""Catch U{bug #20479<https://gna.org/bugs/?20479>}, the failure to switch pipes when closing non-last tabs."""
# NOE tab: Simulate the new analysis wizard.
analysis = self.new_analysis_wizard(analysis_type='noe', analysis_name='NOE test', pipe_name='noe', pipe_bundle='noe bundle')
# Mf tab: Simulate the new analysis wizard.
analysis = self.new_analysis_wizard(analysis_type='mf', analysis_name='Mf test', pipe_name='mf', pipe_bundle='mf bundle')
# NOE tab: Switch back.
self.app.gui.analysis.switch_page(index=0)
# NOE tab: Closure.
self.app.gui.analysis.delete_analysis(0)
# Check that the Mf data pipe is now the current pipe.
self.assertEqual(cdp_name(), 'mf')
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 test_deletion(self):
"""Test the deletion of a data pipe.
The function tested is pipe_control.pipes.delete()
"""
# Set the current pipe to the 'orig' data pipe.
name = 'orig'
pipes.switch(name)
# Delete the 'orig' data pipe.
pipes.delete(name)
# Test that the data pipe no longer exists.
self.assert_(name not in ds)
# Test that the current pipe is None (as the current pipe was deleted).
self.assertEqual(pipes.cdp_name(), None)
def test_deletion(self):
"""Test the deletion of a data pipe.
The function tested is pipe_control.pipes.delete()
"""
# Set the current pipe to the 'orig' data pipe.
name = 'orig'
pipes.switch(name)
# Delete the 'orig' data pipe.
pipes.delete(name)
# Test that the data pipe no longer exists.
self.assert_(name not in ds)
# Test that the current pipe is None (as the current pipe was deleted).
self.assertEqual(pipes.cdp_name(), None)
def switch_page(self, index):
"""Switch to the given page.
@param index: The index of the page to switch to.
@type index: int
"""
# Set the current page number.
self._current = index
# Switch to the major data pipe of the page if not the current one.
if pipes.cdp_name() != ds.relax_gui.analyses[self._current].pipe_name:
self.gui.interpreter.apply('pipe.switch', ds.relax_gui.analyses[self._current].pipe_name)
# Switch to the page.
wx.CallAfter(self.notebook.SetSelection, self._current)
# Notify the observers of the change.
wx.CallAfter(status.observers.gui_analysis.notify)
def generate(mol_name=None, res_num=None, res_name=None, spin_num=None, spin_name=None, pipe=None, select=True, verbose=True):
"""Generate the sequence item-by-item by adding a single molecule/residue/spin container as necessary.
@keyword mol_name: The molecule name.
@type mol_name: str or None
@keyword res_num: The residue number.
@type res_num: int or None
@keyword res_name: The residue name.
@type res_name: str or None
@keyword spin_num: The spin number.
@type spin_num: int or None
@keyword spin_name: The spin name.
@type spin_name: str or None
@keyword pipe: The data pipe in which to generate the sequence. This defaults to the current data pipe.
@type pipe: str
@keyword select: The spin selection flag.
@type select: bool
@keyword verbose: A flag which if True will cause info about each spin to be printed out as the sequence is generated.
@type verbose: bool
"""
# The current data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# A new molecule.
if not return_molecule(generate_spin_id(mol_name=mol_name), pipe=pipe):
create_molecule(mol_name=mol_name, pipe=pipe)
# A new residue.
curr_res = return_residue(generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name), pipe=pipe)
if not curr_res or ((res_num != None and curr_res.num != res_num) or (res_name != None and curr_res.name != res_name)):
create_residue(mol_name=mol_name, res_num=res_num, res_name=res_name, pipe=pipe)
# A new spin.
curr_spin = return_spin(spin_id=generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name), pipe=pipe)
if not curr_spin or ((spin_num != None and curr_spin.num != spin_num) or (spin_name != None and curr_spin.name != spin_name)):
# Add the spin.
curr_spin = create_spin(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name, pipe=pipe)[0]
# Set the selection flag.
curr_spin.select = select
def update_controller(self):
"""Update the relax controller."""
# Set the current data pipe info.
pipe = cdp_name()
if pipe == None:
pipe = ''
wx.CallAfter(self.cdp.SetValue, str_to_gui(pipe))
# Set the current GUI analysis info.
name = self.gui.analysis.current_analysis_name()
if name == None:
name = ''
wx.CallAfter(self.name.SetValue, str_to_gui(name))
# The analysis type.
type = self.gui.analysis.current_analysis_type()
# Rx fitting auto-analysis.
if type in ['R1', 'R2']:
if status.show_gui:
wx.CallAfter(self.panel_rx.Show)
wx.CallAfter(self.update_rx)
else:
if status.show_gui:
wx.CallAfter(self.panel_rx.Hide)
# Model-free auto-analysis.
if type == 'model-free':
if status.show_gui:
wx.CallAfter(self.panel_mf.Show)
wx.CallAfter(self.update_mf)
else:
if status.show_gui:
wx.CallAfter(self.panel_mf.Hide)
# Update the main gauge.
wx.CallAfter(self.update_gauge)
# Re-layout the window.
wx.CallAfter(self.main_panel.Layout)
def spin_count(self):
"""Count the number of loaded spins, returning a string formatted as 'xxx spins loaded'.
@return: The number of loaded spins in the format 'xxx spins loaded'.
@rtype: str
"""
# The data pipe.
if hasattr(self.data, 'pipe_name'):
pipe = self.data.pipe_name
else:
pipe = cdp_name()
# The count.
if not has_pipe(pipe):
num = 0
else:
num = count_spins(pipe=pipe)
# Return the formatted string.
return "%s spins loaded and selected" % num
def check_pivot_func(pipe_name=None):
"""Check that the pivot point has been set.
@keyword pipe_name: The data pipe to check the pivot for. This defaults to the current data pipe if not set.
@type pipe_name: str
@return: The initialised RelaxError object if the pivot point has not been set, or nothing.
@rtype: None or RelaxError instance
"""
# The data pipe.
if pipe_name == None:
pipe_name = cdp_name()
# Get the data pipe.
dp = get_pipe(pipe_name)
# Check for the pivot_x parameter.
if not hasattr(dp, 'pivot_x'):
return RelaxError(
"The pivot point has not been set, please use the frame_order.pivot user function to define the point."
)
def check_model_func(pipe_name=None):
"""Check if the frame order model has been set up.
@keyword pipe_name: The data pipe to check for, if not the current pipe.
@type pipe_name: None or str
@return: The initialised RelaxError object if the model is not set up, or nothing.
@rtype: None or RelaxError instance
"""
# The data pipe.
if pipe_name == None:
pipe_name = cdp_name()
# Get the data pipe.
dp = get_pipe(pipe_name)
# Check that the model is set up.
if not hasattr(dp, 'model'):
return RelaxError(
"The frame order model has not been set up, please use the frame_order.select_model user function."
)