def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk, 'Peak List Settings')
fb = Tkinter.Frame(self.top, borderwidth=3, relief='groove')
fb.pack(side='top', fill='x')
#
# Create the checkbutton and extra widgets for each possible field
#
self.field_widgets = {}
for fc in field_classes:
self.field_widgets[fc] = fc.field_widgets(self.top, fc.name)
opt = Tkinter.Frame(self.top, borderwidth=3, relief='groove')
opt.pack(side='top', fill='x')
cb = tkutil.checkbutton(opt, 'Sort by assignment?', 1)
self.assignmentsort = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(opt, 'Pair crossdiagonal peaks?', 0)
self.crosspair = cb.variable
cb.button.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Pick Atoms')
cb = tkutil.checkbutton(self.top, 'Show atom labels?', 0)
self.show_label = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show distances?', 0)
self.show_distance = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show peaks?', 0)
self.show_peak = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show assigned atoms?', 0)
self.show_assigned = cb.variable
cb.button.pack(side='top', anchor='w')
cb.add_callback(pyutil.precompose(color_assigned_atoms, session))
self.status_line = Tkinter.Label(self.top, anchor='nw')
self.status_line.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'MidasPick')),
)
br.frame.pack(side='top', anchor='w')
self.pick_cb = self.atom_pick_cb
midas.process(self.session).add_atom_pick_callback(self.pick_cb)
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'View Constraints')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side = 'top', anchor = 'w')
self.mardi_file = tkutil.file_field(self.top,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show satisfied constraints?', 0)
self.satisfied = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show violated constraints?', 1)
self.violated = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Show', self.show_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session,
'MidasConstraints')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk, 'Peak List Settings')
fb = Tkinter.Frame(self.top, borderwidth = 3, relief = 'groove')
fb.pack(side = 'top', fill = 'x')
#
# Create the checkbutton and extra widgets for each possible field
#
self.field_widgets = {}
for fc in field_classes:
self.field_widgets[fc] = fc.field_widgets(self.top, fc.name)
opt = Tkinter.Frame(self.top, borderwidth = 3, relief = 'groove')
opt.pack(side = 'top', fill = 'x')
cb = tkutil.checkbutton(opt, 'Sort by assignment?', 1)
self.assignmentsort = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(opt, 'Pair crossdiagonal peaks?', 0)
self.crosspair = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Pick Atoms')
cb = tkutil.checkbutton(self.top, 'Show atom labels?', 0)
self.show_label = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show distances?', 0)
self.show_distance = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show peaks?', 0)
self.show_peak = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show assigned atoms?', 0)
self.show_assigned = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb.add_callback(pyutil.precompose(color_assigned_atoms, session))
self.status_line = Tkinter.Label(self.top, anchor = 'nw')
self.status_line.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'MidasPick')),
)
br.frame.pack(side = 'top', anchor = 'w')
self.pick_cb = self.atom_pick_cb
midas.process(self.session).add_atom_pick_callback(self.pick_cb)
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Table')
setup = Tkinter.Frame(self.top)
setup.pack(side='top', anchor='w')
# Choose Spectra
sbutton = tkutil.checkbutton(self.top, 'Choose Spectra', 1)
sbutton.button.pack(side='top', anchor='w')
schoice = Tkinter.Frame(self.top)
schoice.pack(side='top', anchor='w')
sc = sputil.spectrum_checkbuttons(session, schoice, '')
sc.frame.pack(side='top', anchor='w')
self.spectrum_list = sc.chosen_spectra
cb = tkutil.checkbutton(schoice, 'Noesy format?', 0)
self.noesy_format = cb.variable
cb.button.pack(side='top', anchor='w')
sbutton.map_widget(schoice)
# Peak list
pl = sputil.assignment_listbox(session, self.top)
pl.frame.pack(side='top', fill='both', expand=1)
pl.listbox.bind('<ButtonRelease-1>', self.select_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_assignment_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_assignment_cb)
self.peak_list = pl
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Save', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakTable')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Table')
setup = Tkinter.Frame(self.top)
setup.pack(side = 'top', anchor = 'w')
# Choose Spectra
sbutton = tkutil.checkbutton(self.top, 'Choose Spectra', 1)
sbutton.button.pack(side = 'top', anchor = 'w')
schoice = Tkinter.Frame(self.top)
schoice.pack(side = 'top', anchor = 'w')
sc = sputil.spectrum_checkbuttons(session, schoice, '')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_list = sc.chosen_spectra
cb = tkutil.checkbutton(schoice, 'Noesy format?', 0)
self.noesy_format = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
sbutton.map_widget(schoice)
# Peak list
pl = sputil.assignment_listbox(session, self.top)
pl.frame.pack(side = 'top', fill = 'both', expand = 1)
pl.listbox.bind('<ButtonRelease-1>', self.select_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_assignment_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_assignment_cb)
self.peak_list = pl
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Save', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakTable')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
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 __init__(self, session):
self.session = session
self.peak = None
tkutil.Dialog.__init__(self, session.tk, 'Peak Resonance Mover')
self.spectrum_menu = sputil.spectrum_menu(session, self.top,
'Spectrum: ')
self.spectrum_menu.frame.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'On / Off', 0)
cb.button.pack(side='top', anchor='w')
cb.add_callback(self.onoff_cb)
self.onoff = cb
self.will_drag_notice = None
self.dragged_notice = None
self.message = Tkinter.Label(self.top)
self.message.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ShiftRes')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
self.view_to_center = None
self.selection_notice = None
tkutil.Dialog.__init__(self, session.tk, 'View Center')
explain = ('Specify a view window to be centered\n' +
'by the cm or cp commands. The cm command\n' +
'centers the view at the point under the mouse\n'
'when the command is invoked in any window.\n' +
'The cp command centers the view on the selected\n' +
'peak.')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
add_command = pythonshell.add_command
add_command('cm', '', 'centerview', 'center_view_on_mouse', session)
add_command('cp', '', 'centerview', 'center_view_on_peak', session)
self.center_view = sputil.view_menu(session, self.top, 'View to center: ')
self.center_view.frame.pack(side = 'top', anchor = 'w')
ps = tkutil.checkbutton(self.top, 'Center when peak selected?', 0)
ps.button.pack(side = 'top', anchor = 'w')
self.peak_select = ps
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'CenterViews')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.peak = None
tkutil.Dialog.__init__(self, session.tk, 'Peak Resonance Mover')
self.spectrum_menu = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
self.spectrum_menu.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'On / Off', 0)
cb.button.pack(side = 'top', anchor = 'w')
cb.add_callback(self.onoff_cb)
self.onoff = cb
self.will_drag_notice = None
self.dragged_notice = None
self.message = Tkinter.Label(self.top)
self.message.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ShiftRes')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'MARDIGRAS Format')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_choice = sc
pl = sputil.peak_listbox(self.top)
pl.frame.pack(fill = 'both', expand = 1)
pl.heading['text'] = 'Peak list'
pl.listbox.bind('<ButtonRelease-1>', pl.select_peak_cb)
pl.listbox.bind('<ButtonRelease-2>', pl.goto_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', pl.goto_peak_cb)
self.peak_list = pl
ib = tkutil.checkbutton(self.top, 'Include unintegrated peaks?', 0)
ib.button.pack(side = 'top', anchor = 'w')
self.unintegrated = ib
nb = tkutil.checkbutton(self.top, 'Show peak notes?', 0)
nb.button.pack(side = 'top', anchor = 'w')
self.note = nb
eh = Tkinter.Label(self.top, text = 'Omit peak if note has a word from:')
eh.pack(side = 'top', anchor = 'w')
ef = tkutil.entry_field(self.top, ' ', width = 30)
ef.frame.pack(side = 'top', anchor = 'w')
self.note_words = ef
et = Tkinter.Label(self.top, text = '(space separated list of words)')
et.pack(side = 'top', anchor = 'w')
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Write Peaks', self.save_peaks_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session,
'MardigrasFormat')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'MARDIGRAS Format')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side='top', anchor='w')
self.spectrum_choice = sc
pl = sputil.peak_listbox(self.top)
pl.frame.pack(fill='both', expand=1)
pl.heading['text'] = 'Peak list'
pl.listbox.bind('<ButtonRelease-1>', pl.select_peak_cb)
pl.listbox.bind('<ButtonRelease-2>', pl.goto_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', pl.goto_peak_cb)
self.peak_list = pl
ib = tkutil.checkbutton(self.top, 'Include unintegrated peaks?', 0)
ib.button.pack(side='top', anchor='w')
self.unintegrated = ib
nb = tkutil.checkbutton(self.top, 'Show peak notes?', 0)
nb.button.pack(side='top', anchor='w')
self.note = nb
eh = Tkinter.Label(self.top, text='Omit peak if note has a word from:')
eh.pack(side='top', anchor='w')
ef = tkutil.entry_field(self.top, ' ', width=30)
ef.frame.pack(side='top', anchor='w')
self.note_words = ef
et = Tkinter.Label(self.top, text='(space separated list of words)')
et.pack(side='top', anchor='w')
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Write Peaks', self.save_peaks_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'MardigrasFormat')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
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 make_dialog(self):
tkutil.Dialog.__init__(self, self.session.tk, 'Mirror Assignment Checker')
self.top.bind('<Destroy>', self.window_destroyed_cb, 1)
w = self.make_noesy_table(self.top)
w.pack(side = 'top', anchor = 'w')
choices = ('Selected peaks',
'Peaks with assigned mirror peak',
'Peaks without assigned mirror peak',
'Unassigned with assigned mirror',
)
self.show_type = tkutil.option_menu(self.top, 'Show ',
choices, choices[0])
self.show_type.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top,
'Exclude mirrors with low signal/noise?', 0)
cb.button.pack(side = 'top', anchor = 'w')
self.exclude_mirrors = cb
f = Tkinter.Frame(self.top)
cb.map_widget(f)
e = tkutil.entry_field(f, 'C13 / N15 intensity ratio: ', '1', 3)
self.c13_n15_factor = e.variable
e.frame.pack(side = 'top', anchor = 'w')
e = tkutil.entry_field(f, 'Minimum mirror intensity factor: ', '.5', 3)
self.min_mirror_factor = e.variable
e.frame.pack(side = 'top', anchor = 'w')
pl = tkutil.scrolling_list(self.top, '', 5)
pl.frame.pack(side = 'top', fill = 'both', expand = 1)
pl.listbox.bind('<ButtonRelease-2>', self.select_peak_or_assignment_cb)
pl.listbox.bind('<ButtonRelease-1>', self.goto_peak_or_assignment_cb)
self.peak_list = pl
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Strips', self.strips_cb),
('Save', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(self.session,
'MirrorPeak')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
self.settings = self.get_settings()
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 __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Chemical Shift Plot')
self.top.columnconfigure(0, weight=1)
r = 0
self.condition_widget = sputil.condition_menu(session, self.top,
'Condition: ')
self.condition_widget.frame.grid(row=r, sticky='w')
r = r + 1
self.ppm_range_widget = [None, None]
er = tkutil.entry_row(self.top, 'PPM range: ', ('min', '0', 3),
('max', '12', 3), ('step', '1', 3))
(self.ppm_range_widget[0], self.ppm_range_widget[1],
self.ppm_step_widget) = er.variables
er.frame.grid(row=r, sticky='w')
r = r + 1
e = tkutil.entry_field(self.top, 'Atoms: ', '', 30)
self.atoms = e.variable
e.frame.grid(row=r, sticky='w')
r = r + 1
t = tkutil.checkbutton(self.top, 'Show typical amino acid shifts?', 0)
self.typical_range = t.variable
t.button.grid(row=r, sticky='w')
r = r + 1
c = tkutil.scrollable_canvas(self.top)
c.frame.grid(row=r, sticky='news')
self.top.rowconfigure(r, weight=1)
r = r + 1
self.canvas = c.canvas
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.grid(row=r, sticky='w')
r = r + 1
postscript_cb = pyutil.precompose(tkutil.postscript_cb, self.canvas)
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Postscript', postscript_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ChemShiftPlot')),
)
br.frame.grid(row=r, sticky='w')
r = r + 1
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def add_spectrum(self, spectrum, table, row):
pat_name, pat_axes = expectedpeaks.recall_pattern(spectrum)
# Make spectrum check button
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
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
def add_spectrum(self, spectrum, table, row):
onoff = self.default_onoff(spectrum)
b = tkutil.checkbutton(table.frame, spectrum.name, onoff)
b.button.grid(row = row, column = 0, sticky = 'nw')
ttext = self.default_time_parameter(spectrum)
e = tkutil.entry_field(table.frame, '', ttext)
e.frame.grid(row = row, column = 1, sticky = 'nw')
self.spectrum_widgets[spectrum] = (b, e)
def add_spect(self, spectrum, table, row):
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = spectrum_color(spectrum)
choose_cb = pyutil.precompose(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
def add_spect(self, spectrum, table, row):
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = spectrum_color(spectrum)
choose_cb = pyutil.precompose(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
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Chemical Shift Plot')
self.top.columnconfigure(0, weight = 1)
r = 0
self.condition_widget = sputil.condition_menu(session, self.top, 'Condition: ')
self.condition_widget.frame.grid(row = r, sticky = 'w')
r = r + 1
self.ppm_range_widget = [None, None]
er = tkutil.entry_row(self.top, 'PPM range: ',
('min', '0', 3), ('max', '12', 3), ('step', '1', 3))
(self.ppm_range_widget[0],
self.ppm_range_widget[1],
self.ppm_step_widget) = er.variables
er.frame.grid(row = r, sticky = 'w')
r = r + 1
e = tkutil.entry_field(self.top, 'Atoms: ', '', 30)
self.atoms = e.variable
e.frame.grid(row = r, sticky = 'w')
r = r + 1
t = tkutil.checkbutton(self.top, 'Show typical amino acid shifts?', 0)
self.typical_range = t.variable
t.button.grid(row = r, sticky = 'w')
r = r + 1
c = tkutil.scrollable_canvas(self.top)
c.frame.grid(row = r, sticky = 'news')
self.top.rowconfigure(r, weight = 1)
r = r + 1
self.canvas = c.canvas
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.grid(row = r, sticky = 'w')
r = r + 1
postscript_cb = pyutil.precompose(tkutil.postscript_cb, self.canvas)
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Postscript', postscript_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ChemShiftPlot')),
)
br.frame.grid(row = r, sticky = 'w')
r = r + 1
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk,
'Python Shell Preferences')
cb = tkutil.checkbutton(self.top, 'Show Python shell if error occurs?', 1)
cb.button.pack(side = 'top', anchor = 'nw')
self.raise_variable = cb.variable
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PythonShell')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Restricted Peak Pick')
m = sputil.view_menu(session, self.top, 'Find peaks in ')
m.frame.pack(side='top', anchor='w')
m.add_callback(self.chose_spectrum_cb)
self.pick_menu = m
m = sputil.spectrum_menu(session, self.top, 'Using peaks in ')
m.frame.pack(side='top', anchor='w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
b = tkutil.checkbutton(self.top, 'Use selected peaks only?', 0)
b.button.pack(side='top', anchor='w')
self.selected_only = b
lbl = Tkinter.Label(self.top, text='Axis match tolerances (ppm)')
lbl.pack(side='top', anchor='w')
self.axis_table_heading = lbl
f = Tkinter.Frame(self.top)
f.pack(side='top', anchor='w')
self.axis_table = f
self.range_entries = []
self.setup_axis_table()
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Pick peaks', self.pick_cb),
('Select peaks', self.select_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RestrictedPick')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk,
'Python Shell Preferences')
cb = tkutil.checkbutton(self.top, 'Show Python shell if error occurs?',
1)
cb.button.pack(side='top', anchor='nw')
self.raise_variable = cb.variable
br = tkutil.button_row(
self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PythonShell')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Restricted Peak Pick')
m = sputil.view_menu(session, self.top, 'Find peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.pick_menu = m
m = sputil.spectrum_menu(session, self.top, 'Using peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
b = tkutil.checkbutton(self.top, 'Use selected peaks only?', 0)
b.button.pack(side = 'top', anchor = 'w')
self.selected_only = b
lbl= Tkinter.Label(self.top, text = 'Axis match tolerances (ppm)')
lbl.pack(side = 'top', anchor = 'w')
self.axis_table_heading = lbl
f = Tkinter.Frame(self.top)
f.pack(side = 'top', anchor = 'w')
self.axis_table = f
self.range_entries = []
self.setup_axis_table()
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Pick peaks', self.pick_cb),
('Select peaks', self.select_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RestrictedPick')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.Settings_Dialog.__init__(self, session.tk, 'Show Peak Strips')
f = self.spectrum_choice_table(self.top)
f.pack(side = 'top', anchor = 'w')
sx = tkutil.checkbutton(self.top, 'Show spectrum name under each strip', 0)
sx.button.pack(side = 'top', anchor = 'w', padx = 10, pady = 10)
self.label_spectrum = sx
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'StripPlot')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk, 'AutoAssign Details')
se = tkutil.checkbutton(self.top,
'Use an already running AutoAssign server?', 0)
se.button.pack(side = 'top', anchor = 'w')
self.server_exists = se.variable
hp = tkutil.entry_row(self.top, 'Server on',
('host ', '', 25),
(' port ', '', 5),
)
hp.frame.pack(side = 'top', anchor = 'w')
self.server_host, self.server_port = hp.variables
sl = tkutil.entry_field(self.top,
'Sleep time after server startup (seconds): ',
initial = 1, width = 3)
sl.frame.pack(side = 'top', anchor = 'w')
self.server_lag = sl.variable
sp = tkutil.entry_field(self.top, 'Server program ', '', width = 25)
sp.frame.pack(side = 'top', anchor = 'w')
self.server_executable = sp.variable
cp = tkutil.entry_field(self.top, 'Client program ', '', width = 25)
cp.frame.pack(side = 'top', anchor = 'w')
self.client_executable = cp.variable
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AutoAssign')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, parent, name): cb = tkutil.checkbutton(parent, name, 0) cb.button.pack(side = 'top', anchor = 'w') self.checkbutton = cb
def __init__(self, session):
self.session = session
self.pdb_path = None
self.model = None
self.pseudobond_group = None
self.recenter_on_peak = 1
self.chimera_atom_to_num_atom = {}
self.num_atom_to_chimera_atom = {}
self.chimera_atom_to_resonance = {}
self.num_atom_pair_to_pseudobond = {}
self.selected_atoms = []
self.peak_selected_notice = None
self.bond_selection_trigger = None
self.chimera_quit_trigger = None
self.chimera_running = 0
tkutil.Dialog.__init__(self, session.tk, 'Chimera Model')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side='top', anchor='w')
colors = ('white', 'black', 'red', 'yellow', 'green', 'cyan', 'blue',
'magenta')
c = tkutil.option_menu(self.top, 'Color assigned atoms ', colors,
'yellow')
c.frame.pack(side='top', anchor='w')
self.assigned_atom_color = c
cb = tkutil.checkbutton(self.top,
'Selecting peak highlights assignment line?',
1)
cb.button.pack(side='top', anchor='w')
self.show_selected_peaks = cb
cb = tkutil.checkbutton(
self.top, 'Selecting assignment line recenters spectrum?', 1)
cb.button.pack(side='top', anchor='w')
self.show_selected_lines = cb
cb = tkutil.checkbutton(self.top,
'Selecting atoms recenters spectrum?', 1)
cb.button.pack(side='top', anchor='w')
self.show_selected_atoms = cb
c = tkutil.option_menu(self.top, 'Color lines for assignments ',
colors, 'blue')
c.frame.pack(side='top', anchor='w')
self.peak_line_color = c
cb = tkutil.checkbutton(self.top, 'Show contraint violations?', 0)
cb.button.pack(side='top', anchor='w')
self.show_constraints = cb
constraint_frame = Tkinter.Frame(self.top,
borderwidth=2,
relief='sunken')
cb.map_widget(constraint_frame)
self.mardi_file = tkutil.file_field(constraint_frame,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side='top', anchor='w')
cb = tkutil.checkbuttons(constraint_frame, 'top', '',
'Show satisfied constraints?',
'Show violated constraints?')
cb.frame.pack(side='top', anchor='w')
self.show_satisfied, self.show_violated = cb.variables
self.show_satisfied.set(0)
color_frame = Tkinter.Frame(constraint_frame)
color_frame.pack(side='top', anchor='w')
h = Tkinter.Label(color_frame, text='Constraint line colors:')
h.grid(row=0, column=0, columnspan=2, sticky='w')
self.constraint_colors = []
row = 1
for text, color in (('< 0.8 times lower bound',
'blue'), ('0.8-1.0 times lower bound', 'cyan'),
('satisfied constraint', 'green'),
('1.0-1.2 times upper bound',
'magenta'), ('> 1.2 times upper bound', 'red')):
c = tkutil.option_menu(color_frame, '', colors, color)
c.frame.grid(row=row, column=0, sticky='e', padx=10)
label = Tkinter.Label(color_frame, text=text)
label.grid(row=row, column=1, sticky='w')
row = row + 1
self.constraint_colors.append(c)
self.status_line = Tkinter.Label(self.top,
anchor='nw',
wraplength='15c',
justify='left')
self.status_line.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Show', self.show_cb),
('Erase', self.erase_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Chimera')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, parent, name):
cb = tkutil.checkbutton(parent, name, 0)
cb.button.pack(side='top', anchor='w')
self.checkbutton = cb
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'XPLOR Restraints')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_choice = sc
pl = sputil.peak_listbox(self.top)
pl.frame.pack(fill = 'both', expand = 1)
pl.heading['text'] = 'XPLOR Restraint list'
pl.listbox.bind('<ButtonRelease-1>', pl.select_peak_cb)
pl.listbox.bind('<ButtonRelease-2>', pl.goto_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', pl.goto_peak_cb)
self.peak_list = pl
bt = tkutil.entry_field(self.top, 'Bounds text ', width = 30)
bt.frame.pack(side = 'top', anchor = 'w')
self.bounds_text = bt
nb = tkutil.checkbutton(self.top, 'Show peak notes?', 0)
nb.button.pack(side = 'top', anchor = 'w')
self.note = nb
hb = tkutil.entry_row(self.top, 'Only peaks with height',
(' >= ', '', 8), (' and < ', '', 8))
hb.frame.pack(side = 'top', anchor = 'w')
self.height_min, self.height_max = hb.variables
vb = tkutil.entry_row(self.top, 'Only peaks with volume',
(' >= ', '', 8), (' and < ', '', 8))
vb.frame.pack(side = 'top', anchor = 'w')
self.volume_min, self.volume_max = vb.variables
eh1 = Tkinter.Label(self.top, text = 'Omit peak if note has a word from:')
eh1.pack(side = 'top', anchor = 'w')
ef1 = tkutil.entry_field(self.top, ' ', width = 30)
ef1.frame.pack(side = 'top', anchor = 'w')
self.exclude_note_words = ef1
eh2 = Tkinter.Label(self.top, text = 'or if it has no word from:')
eh2.pack(side = 'top', anchor = 'w')
ef2 = tkutil.entry_field(self.top, ' ', width = 30)
ef2.frame.pack(side = 'top', anchor = 'w')
self.require_note_words = ef2
et = Tkinter.Label(self.top, text = '(space separated list of words)')
et.pack(side = 'top', anchor = 'w')
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Write Restraints', self.save_peaks_cb),
('Append', self.append_peaks_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session,
'XplorFormat')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'DYANA / XEASY Format')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_choice = sc
sl = tkutil.scrolling_list(self.top, 'Chemical shift list', 5)
sl.frame.pack(fill = 'both', expand = 1)
sl.listbox.bind('<ButtonRelease-1>', self.resonance_cb)
self.shift_list = sl
pl = sputil.peak_listbox(self.top)
pl.frame.pack(fill = 'both', expand = 1)
pl.heading['text'] = 'Peak list'
pl.listbox.bind('<ButtonRelease-1>', pl.select_peak_cb)
pl.listbox.bind('<ButtonRelease-2>', pl.goto_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', pl.goto_peak_cb)
self.peak_list = pl
cy = tkutil.checkbutton(self.top, 'Cyana Formatting ?', 0)
cy.button.pack(side = 'top', anchor = 'w')
self.cyana = cy
hb = tkutil.checkbutton(self.top,
'Show peak heights instead of volumes?', 0)
hb.button.pack(side = 'top', anchor = 'w')
self.heights = hb
ib = tkutil.checkbutton(self.top, 'Include unintegrated peaks?', 0)
ib.button.pack(side = 'top', anchor = 'w')
self.unintegrated = ib
ab = tkutil.checkbutton(self.top, 'Include unassigned peaks?', 0)
ab.button.pack(side = 'top', anchor = 'w')
self.unassigned = ab
mb = tkutil.checkbutton(self.top,
'Include assignments without a residue number?', 0)
mb.button.pack(side = 'top', anchor = 'w')
self.unnumbered = mb
nb = tkutil.checkbutton(self.top, 'Show peak notes?', 0)
nb.button.pack(side = 'top', anchor = 'w')
self.note = nb
eh = Tkinter.Label(self.top, text = 'Omit peak if note has a word from:')
eh.pack(side = 'top', anchor = 'w')
ef = tkutil.entry_field(self.top, ' ', width = 30)
ef.frame.pack(side = 'top', anchor = 'w')
self.note_words = ef
et = Tkinter.Label(self.top, text = '(space separated list of words)')
et.pack(side = 'top', anchor = 'w')
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Write Shifts', self.save_shifts_cb),
('Write Peaks', self.save_peaks_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'XEASYFormat')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Set Volume Errors')
self.spectrum_choice = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
self.spectrum_choice.frame.pack(side = 'top', anchor = 'w')
f = Tkinter.Frame(self.top)
f.pack(side = 'top', anchor = 'w')
r = 0
w = Tkinter.Label(f, text = 'Error (%)')
w.grid(row = r, column = 1)
r = r + 1
cb = tkutil.checkbutton(f, 'Default fit', 1)
self.fit_default = cb.variable
cb.button.grid(row = r, column = 0, sticky = 'w')
e = tkutil.entry_field(f, '', '10', 4)
self.fit_default_error = e.variable
e.frame.grid(row = r, column = 1)
r = r + 1
cb = tkutil.checkbutton(f, 'Default box / ellipse', 1)
self.box_default = cb.variable
cb.button.grid(row = r, column = 0, sticky = 'w')
e = tkutil.entry_field(f, '', '20', 4)
self.box_default_error = e.variable
e.frame.grid(row = r, column = 1)
r = r + 1
cb = tkutil.checkbutton(f, 'Near diagonal', 0)
self.near_diagonal = cb.variable
cb.button.grid(row = r, column = 0, sticky = 'w')
e = tkutil.entry_field(f, '', '20', 4)
self.near_diagonal_error = e.variable
e.frame.grid(row = r, column = 1)
tkutil.grid_labels(f, ('Range (ppm)', r, 2))
e = tkutil.entry_field(f, '|w1-w2| ', '.1', 4)
self.near_diagonal_range = e.variable
e.frame.grid(row = r+1, column = 2)
r = r + 2
cb = tkutil.checkbutton(f, 'Near other peaks', 0)
self.nearby_peaks = cb.variable
cb.button.grid(row = r, column = 0, sticky = 'w')
tkutil.grid_labels(f,
('Relative volume', r+1, 0),
('< .5', r+2, 0),
('.5 - 2', r+3, 0),
('> 2', r+4, 0),
('unintegrated', r+5, 0))
self.nearby_error = {}
(self.nearby_error['< .5'],
self.nearby_error['.5 - 2'],
self.nearby_error['> 2'],
self.nearby_error['unintegrated']
) = tkutil.grid_entries(f, 4,
('5', r+2, 1),
('10', r+3, 1),
('20', r+4, 1),
('20', r+5, 1))
self.nearby_range = {}
tkutil.grid_labels(f, ('Range (ppm)', r+1, 2))
e = tkutil.entry_field(f, 'w1 ', '.05', 4)
self.nearby_range['w1 range'] = e.variable
e.frame.grid(row = r+2, column = 2)
e = tkutil.entry_field(f, 'w2 ', '.05', 4)
self.nearby_range['w2 range'] = e.variable
e.frame.grid(row = r+3, column = 2)
r = r + 6
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Set Volume Errors', self.update_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'VolumeErrors')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
def __init__(self, session):
self.session = session
self.pdb_path = None
self.model = None
self.pseudobond_group = None
self.recenter_on_peak = 1
self.chimera_atom_to_num_atom = {}
self.num_atom_to_chimera_atom = {}
self.chimera_atom_to_resonance = {}
self.num_atom_pair_to_pseudobond = {}
self.selected_atoms = []
self.peak_selected_notice = None
self.bond_selection_trigger = None
self.chimera_quit_trigger = None
self.chimera_running = 0
tkutil.Dialog.__init__(self, session.tk, 'Chimera Model')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side = 'top', anchor = 'w')
colors = ('white', 'black', 'red', 'yellow',
'green', 'cyan', 'blue', 'magenta')
c = tkutil.option_menu(self.top, 'Color assigned atoms ',
colors, 'yellow')
c.frame.pack(side = 'top', anchor = 'w')
self.assigned_atom_color = c
cb = tkutil.checkbutton(self.top,
'Selecting peak highlights assignment line?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_peaks = cb
cb = tkutil.checkbutton(self.top,
'Selecting assignment line recenters spectrum?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_lines = cb
cb = tkutil.checkbutton(self.top, 'Selecting atoms recenters spectrum?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_atoms = cb
c = tkutil.option_menu(self.top, 'Color lines for assignments ',
colors, 'blue')
c.frame.pack(side = 'top', anchor = 'w')
self.peak_line_color = c
cb = tkutil.checkbutton(self.top, 'Show contraint violations?', 0)
cb.button.pack(side = 'top', anchor = 'w')
self.show_constraints = cb
constraint_frame = Tkinter.Frame(self.top, borderwidth = 2,
relief = 'sunken')
cb.map_widget(constraint_frame)
self.mardi_file = tkutil.file_field(constraint_frame,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbuttons(constraint_frame, 'top', '',
'Show satisfied constraints?',
'Show violated constraints?')
cb.frame.pack(side = 'top', anchor = 'w')
self.show_satisfied, self.show_violated = cb.variables
self.show_satisfied.set(0)
color_frame = Tkinter.Frame(constraint_frame)
color_frame.pack(side = 'top', anchor = 'w')
h = Tkinter.Label(color_frame, text = 'Constraint line colors:')
h.grid(row = 0, column = 0, columnspan = 2, sticky = 'w')
self.constraint_colors = []
row = 1
for text, color in (('< 0.8 times lower bound', 'blue'),
('0.8-1.0 times lower bound', 'cyan'),
('satisfied constraint', 'green'),
('1.0-1.2 times upper bound', 'magenta'),
('> 1.2 times upper bound', 'red')):
c = tkutil.option_menu(color_frame, '', colors, color)
c.frame.grid(row = row, column = 0, sticky = 'e', padx = 10)
label = Tkinter.Label(color_frame, text = text)
label.grid(row = row, column = 1, sticky = 'w')
row = row + 1
self.constraint_colors.append(c)
self.status_line = Tkinter.Label(self.top, anchor = 'nw',
wraplength = '15c', justify = 'left')
self.status_line.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Show', self.show_cb),
('Erase', self.erase_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Chimera')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'DYANA / XEASY Format')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side='top', anchor='w')
self.spectrum_choice = sc
sl = tkutil.scrolling_list(self.top, 'Chemical shift list', 5)
sl.frame.pack(fill='both', expand=1)
sl.listbox.bind('<ButtonRelease-1>', self.resonance_cb)
self.shift_list = sl
pl = sputil.peak_listbox(self.top)
pl.frame.pack(fill='both', expand=1)
pl.heading['text'] = 'Peak list'
pl.listbox.bind('<ButtonRelease-1>', pl.select_peak_cb)
pl.listbox.bind('<ButtonRelease-2>', pl.goto_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', pl.goto_peak_cb)
self.peak_list = pl
cy = tkutil.checkbutton(self.top, 'Cyana Formatting ?', 0)
cy.button.pack(side='top', anchor='w')
self.cyana = cy
hb = tkutil.checkbutton(self.top,
'Show peak heights instead of volumes?', 0)
hb.button.pack(side='top', anchor='w')
self.heights = hb
ib = tkutil.checkbutton(self.top, 'Include unintegrated peaks?', 0)
ib.button.pack(side='top', anchor='w')
self.unintegrated = ib
ab = tkutil.checkbutton(self.top, 'Include unassigned peaks?', 0)
ab.button.pack(side='top', anchor='w')
self.unassigned = ab
mb = tkutil.checkbutton(
self.top, 'Include assignments without a residue number?', 0)
mb.button.pack(side='top', anchor='w')
self.unnumbered = mb
nb = tkutil.checkbutton(self.top, 'Show peak notes?', 0)
nb.button.pack(side='top', anchor='w')
self.note = nb
eh = Tkinter.Label(self.top, text='Omit peak if note has a word from:')
eh.pack(side='top', anchor='w')
ef = tkutil.entry_field(self.top, ' ', width=30)
ef.frame.pack(side='top', anchor='w')
self.note_words = ef
et = Tkinter.Label(self.top, text='(space separated list of words)')
et.pack(side='top', anchor='w')
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Write Shifts', self.save_shifts_cb),
('Write Peaks', self.save_peaks_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'XEASYFormat')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
