def add_spectrum(self, spectrum, table, row):
if spectrum.dimension != 3:
return
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = sputil.spectrum_color(spectrum)
choose_cb = pyutil.precompose(sputil.choose_spectrum_cb, spectrum,
table.chosen_spectra)
cb.add_callback(choose_cb)
cb.button.grid(row = row, column = 0, sticky = 'w')
table.spectrum_to_checkbutton[spectrum] = cb
#
# Make axis order menu. Set default xyz axis order for triple
# resonance spectra to HCN.
#
hcn_order = pyutil.order(('1H', '13C', '15N'), spectrum.nuclei)
aom = axes.axis_order_menu(table.frame, spectrum.nuclei,
initial_order = hcn_order)
aom.frame.grid(row = row, column = 1, sticky = 'w')
table.axis_order_menu[spectrum] = aom
def place_peaks(self, spectrum):
hc_axes = pyutil.order(('1H', '13C'), spectrum.nuclei)
if spectrum.dimension != 2 or hc_axes == None:
self.progress_report('Spectrum must 2D with H and C axes.')
return
molecule = spectrum.molecule
condition = spectrum.condition
self.stoppable_loop('resonances', 50)
for rH in condition.resonance_list():
self.check_for_stop()
if rH.atom.nucleus == '1H':
catom = atoms.attached_heavy_atom(rH.atom, molecule)
if catom and catom.nucleus == '13C':
rC = condition.find_resonance(catom)
if rC:
assignment = pyutil.permute((rH, rC), hc_axes)
if not spectrum.find_peak(assignment):
freq = pyutil.permute((rH.frequency, rC.frequency), hc_axes)
pos = sputil.alias_onto_spectrum(freq, spectrum)
peak = spectrum.place_peak(pos)
peak.assign(hc_axes[0], rH.group.name, rH.atom.name)
peak.assign(hc_axes[1], rC.group.name, rC.atom.name)
if freq != pos:
peak.alias = pyutil.subtract_tuples(freq, pos)
peak.show_assignment_label()
def add_spectrum(self, spectrum, table, row):
pat_name, pat_axes = expectedpeaks.recall_pattern(spectrum)
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = sputil.spectrum_color(spectrum)
choose_cb = pyutil.precompose(sputil.choose_spectrum_cb, spectrum,
table.chosen_spectra)
cb.add_callback(choose_cb)
cb.button.grid(row=row, column=0, sticky='w')
if pat_name:
cb.set_state(1)
table.spectrum_to_checkbutton[spectrum] = cb
#
# Make peak pattern menu
#
epeak_types = expectedpeaks.expected_peak_descriptions.keys()
pm = tkutil.option_menu(table.frame, '', epeak_types)
pm.frame.grid(row=row, column=1, sticky='w')
table.spectrum_epeak_menus[spectrum] = pm
#
# Get default spectrum peak pattern and axis order
#
if pat_name == None:
pat_name = expectedpeaks.default_spectrum_pattern_name(spectrum)
if pat_name == None:
pat_name = pm.get()
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
pat_axes = pyutil.order(pat_nuclei, spectrum.nuclei)
#
# Make axis order menu
#
aom = axes.axis_order_menu(table.frame,
spectrum.nuclei,
initial_order=pat_axes)
aom.frame.grid(row=row, column=2, sticky='w')
table.axis_order_menu[spectrum] = aom
#
# Register a callback to limit the menu choices for axis order.
#
def restrict_axis_order_cb(pat_name, aom=aom):
import expectedpeaks
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
aom.restrict_menu_permutations(pat_nuclei)
pm.add_callback(restrict_axis_order_cb)
pm.set(pat_name)
def add_spectrum(self, spectrum, table, row):
pat_name, pat_axes = expectedpeaks.recall_pattern(spectrum)
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = sputil.spectrum_color(spectrum)
choose_cb = pyutil.precompose(sputil.choose_spectrum_cb, spectrum,
table.chosen_spectra)
cb.add_callback(choose_cb)
cb.button.grid(row = row, column = 0, sticky = 'w')
if pat_name:
cb.set_state(1)
table.spectrum_to_checkbutton[spectrum] = cb
#
# Make peak pattern menu
#
epeak_types = expectedpeaks.expected_peak_descriptions.keys()
pm = tkutil.option_menu(table.frame, '', epeak_types)
pm.frame.grid(row = row, column = 1, sticky = 'w')
table.spectrum_epeak_menus[spectrum] = pm
#
# Get default spectrum peak pattern and axis order
#
if pat_name == None:
pat_name = expectedpeaks.default_spectrum_pattern_name(spectrum)
if pat_name == None:
pat_name = pm.get()
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
pat_axes = pyutil.order(pat_nuclei, spectrum.nuclei)
#
# Make axis order menu
#
aom = axes.axis_order_menu(table.frame, spectrum.nuclei,
initial_order = pat_axes)
aom.frame.grid(row = row, column = 2, sticky = 'w')
table.axis_order_menu[spectrum] = aom
#
# Register a callback to limit the menu choices for axis order.
#
def restrict_axis_order_cb(pat_name, aom=aom):
import expectedpeaks
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
aom.restrict_menu_permutations(pat_nuclei)
pm.add_callback(restrict_axis_order_cb)
pm.set(pat_name)
def default_axis_orders(self):
axis_orders = {}
spectra = self.session.project.spectrum_list()
for spectrum in spectra:
if spectrum.dimension == 3:
order = pyutil.order(('1H', '13C', '15N'), spectrum.nuclei)
if order == None:
order = (0, 1, 2)
axis_orders[spectrum] = order
return axis_orders
def autoassign_assignment_system(self, tsp_list, tolerances):
asp_list = []
for type, spectrum, phase in tsp_list:
axis_names = self.autoassign_axis_names(spectrum, type)
tol = pyutil.table_values(tolerances, axis_names)
self.progress_report('Calculating expected peaks for ' + spectrum.name)
pat_name = self.type_to_pattern_name[type]
if spectrum.dimension == 3:
pat_axes = axes.amide_axes(spectrum)
else:
pat_axes = pyutil.order(('1H', '15N'), spectrum.nuclei)
asp = expectedpeaks.assignable_spectrum_from_pattern(spectrum, tol,
pat_name, pat_axes,
self)
asp.autoassign_type = type
asp.autoassign_phase = phase
asp_list.append(asp)
return expectedpeaks.assignment_system(asp_list)