def initialize_shell(session, redirect_stdio=0):
session.redirect_stdio = redirect_stdio
sputil.the_dialog(python_shell_dialog, session) # setup Sparky stdio
args = (session, )
invoke_module_function(session, 'sparky_site', 'initialize_session', args)
invoke_module_function(session, 'sparky_init', 'initialize_session', args)
def initialize_shell(session, redirect_stdio = 0): session.redirect_stdio = redirect_stdio sputil.the_dialog(python_shell_dialog, session) # setup Sparky stdio args = (session,) invoke_module_function(session, 'sparky_site', 'initialize_session', args) invoke_module_function(session, 'sparky_init', 'initialize_session', args)
def show_sequence_dialog(session):
d = sputil.the_dialog(sequence_dialog, session)
s = session.selected_spectrum()
if s:
d.set_molecule(s.molecule)
d.show_window(1)
def setup_cb(self):
setup_dialog = sputil.the_dialog(relax_setup_dialog, self.session)
settings = {'spectrum-times': self.spectrum_times,
'error-estimate-trials': self.error_estimate_trials}
setup_dialog.set_parent_dialog(self, settings, self.set_params)
setup_dialog.show_window(1)
def show_details_cb(self):
details = sputil.the_dialog(autoassign_details_dialog, self.sparky_session)
settings = (self.server_exists, self.server_host,
self.server_port, self.server_lag,
self.server_executable, self.client_executable)
details.set_parent_dialog(self, settings, self.set_details)
details.show_window(1)
def show_setup_cb(self):
setup = sputil.the_dialog(autoassign_setup_dialog, self.sparky_session)
settings = {'type-spectrum-phase-list': self.tsp_list,
'tolerance-table': self.tolerances,
'temp-directory': self.temp_directory}
setup.set_parent_dialog(self, settings, self.set_spectra)
setup.show_window(1)
def molecule_sequence(molecule):
seq = has_molecule_sequence(molecule)
if seq == None:
d = sputil.the_dialog(sequence_dialog, molecule.session)
d.get_sequence(molecule)
return has_molecule_sequence(molecule)
def attached_proton_axis(spectrum, heavy_axis):
a = has_attached_proton_axis(spectrum, heavy_axis)
if a == None:
d = sputil.the_dialog(attached_proton_dialog, spectrum.session)
d.get_attached_axis(spectrum, heavy_axis)
return has_attached_proton_axis(spectrum, heavy_axis)
def show_attached_axis_dialog(session):
d = sputil.the_dialog(attached_proton_dialog, session)
spectrum = session.selected_spectrum()
if spectrum:
axes = heavy_atom_axes(spectrum)
if len(axes) == 1:
d.set_spectrum_heavy_axis(spectrum, axes[0])
d.show_window(1)
def setup_cb(self):
setup_dialog = sputil.the_dialog(assigner_setup_dialog, self.session)
if self.assignments:
asys = self.assignments.assignment_system
else:
asys = None
setup_dialog.set_parent_dialog(self, asys, self.update_assignment_system)
setup_dialog.show_window(1)
def update_assignment_system(self, assignment_system):
self.update_assignments(assignment_system)
self.update_graph_atoms()
self.update_graph_peaks()
setup_dialog = sputil.the_dialog(assigner_setup_dialog, self.session)
setup_dialog.show_settings(assignment_system)
self.progress_report('')
def setup_cb(self):
setup_dialog = sputil.the_dialog(assigner_setup_dialog, self.session)
if self.assignments:
asys = self.assignments.assignment_system
else:
asys = None
setup_dialog.set_parent_dialog(self, asys,
self.update_assignment_system)
setup_dialog.show_window(1)
def update_assignment_system(self, assignment_system):
self.update_assignments(assignment_system)
self.update_graph_atoms()
self.update_graph_peaks()
setup_dialog = sputil.the_dialog(assigner_setup_dialog, self.session)
setup_dialog.show_settings(assignment_system)
self.progress_report('')
def guess_atom_name_translations(session, name, group_atoms):
t = atom_name_translations(name)
galist = group_atoms
for trans in standard_translations():
if is_translation_applicable(trans, galist):
t.merge_translations(trans)
galist = map(lambda ga, f = trans.to_standard_name: apply(f, ga), galist)
d = sputil.the_dialog(translations_dialog, session)
d.add_translation(t, group_atoms)
return t
def guess_atom_name_translations(session, name, group_atoms):
t = atom_name_translations(name)
galist = group_atoms
for trans in standard_translations():
if is_translation_applicable(trans, galist):
t.merge_translations(trans)
galist = map(lambda ga, f=trans.to_standard_name: apply(f, ga),
galist)
d = sputil.the_dialog(translations_dialog, session)
d.add_translation(t, group_atoms)
return t
def read_peak_list(session): sputil.the_dialog(read_peaks_dialog,session).show_window(1)
def show_dialog(session): sputil.the_dialog(hc_peak_dialog,session).show_window(1)
def matching_strips_setup(self):
msd = sputil.the_dialog(match_settings_dialog, self.session)
settings = (self.match_tolerances, self.max_unmatched)
msd.set_parent_dialog(self, settings, self.set_match_tolerances)
msd.show_window(1)
def select_noesy_spectra(session): sputil.the_dialog(mirror_assignment_dialog,session).show_window(1)
def show_pine_graph(session): sputil.the_dialog(pine_graph, session).show_window(1)
def show_chimera_dialog(session):
sputil.the_dialog(noeshow_dialog, session).show_window(1)
def Graph(self):
self.peak.selected = 1
sputil.the_dialog(pinegraph.pine_graph, self.session).show_window(1)
return
def read_write_pcs_files(session):
sputil.the_dialog(ReadWritePCSFiles, session).show_window(1)
def show_file_dialog(session):
d = sputil.the_dialog(open_spectra_dialog, session)
d.show_window(1)
def connect_ponderosa_analyzer(session):
sputil.the_dialog(connect_ponderosa_dialog, session).show_window(1)
def show_constraint_dialog(session): sputil.the_dialog(midas_constraint_dialog,session).show_window(1)
def show_repositioner(session):
sputil.the_dialog(reposition_dialog, session).show_window(1)
def show_region_rmsd_dialog(session): sputil.the_dialog(region_rmsd_dialog,session).show_window(1)
def setup_cb(self):
psd = sputil.the_dialog(peak_list_settings_dialog, self.session)
psd.set_parent_dialog(self, self.settings, self.new_settings)
psd.top.title(self.title + ' settings')
psd.show_window(1)
def best_assign(session):
setup_dialog = sputil.the_dialog(base_prob, session)
setup_dialog.show_window(1)
def show_corma_spectrum(session): sputil.the_dialog(corma_spectrum_dialog,session).show_window(1)
def show_peak_grouper_dialog(session):
d = sputil.the_dialog(Peak_grouper_dialog, session)
d.show_window(1)
def show_file_dialog(session): d = sputil.the_dialog(open_spectra_dialog, session) d.show_window(1)
def select_strip_spectra(self):
sd = sputil.the_dialog(choose_strips_dialog, self.session)
settings = (self.chosen_spectra, self.spectrum_axis_orders, self.spectrum_label)
sd.set_parent_dialog(self, settings, self.set_spectra)
sd.show_window(1)
def show_snapshot_dialog(session):
d = sputil.the_dialog(Snapshot_dialog, session)
d.show_window(1)
def show_mirror_peak(session): sputil.the_dialog(mirror_assignment_dialog,session).show_mirror_peak()
def strip_dialog(session): return sputil.the_dialog(strip_plot, session)
def show_dialog(session):
sputil.the_dialog(restricted_pick_dialog, session).show_window(1)
def choose_strip_width(self):
sd = sputil.the_dialog(strip_plot_settings, self.session)
settings = (self.strip_width, self.strip_gap)
sd.set_parent_dialog(self, settings, self.set_strip_width)
sd.show_window(1)
def show_fit(session, heading, fit, callback = None): d = sputil.the_dialog(fit_display, session) d.show_window(1) d.plot_fit(heading, fit, callback)
def show_file_dialog(session):
d = sputil.the_dialog(OpenReloadDialog, session)
d.show_window(1)
def show_linewidth_dialog(session): sputil.the_dialog(linewidth_plot_dialog,session).show_window(1)
def show_peak_table(session): sputil.the_dialog(peak_table_dialog,session).show_window(1)
def send_command(session, command): sputil.the_dialog(python_shell_dialog,session).send_command(command)
def show_pine_assigner(session):
sputil.the_dialog(pine_dialog, session).show_window(1)
def show_python_shell(session): sputil.the_dialog(python_shell_dialog,session).show_window(1)
def read_peak_list(session):
sputil.the_dialog(read_peaks_dialog, session).show_window(1)
def preferences_cb(self):
pd = sputil.the_dialog(shell_preferences_dialog, self.session)
settings = {'raise-on-error': self.raise_on_error}
pd.set_parent_dialog(self, settings, self.set_preferences)
pd.show_window(1)
