def create_menus(self, parent, session):
mbar = Tkinter.Frame(parent)
m = tkutil.menu(mbar, 'Show')
m.button.pack(side = 'left')
add_button = pyutil.precompose(self.add_menu_button, m)
add_button('Select strip spectra...', 'ss', select_strip_spectra)
add_button('Set strip width...', 'sw', choose_strip_width)
m.add_separator()
add_button('Add selected peak strips', 'sk', add_peak_strips)
add_button('All assigned strips', 'sn', add_assigned_strips)
m.add_separator()
add_button('Zoom strips in', 'si', zoom_in_strips)
add_button('Zoom strips out', 'so', zoom_out_strips)
add_button('Copy view strip options', 'sv', copy_view_options)
m.add_separator()
add_button('Delete selected strip', 'sd', delete_view_strip)
add_button('Delete all strips', 'sD', delete_all_strips)
m.add_separator()
m.add_button('Help', sputil.help_cb(self.session, 'StripPlot'))
m.add_button('Close', self.close_cb)
m = tkutil.menu(mbar, 'Find')
m.button.pack(side = 'left')
add_button = pyutil.precompose(self.add_menu_button, m)
add_button('Go to assigned peak strip', 'sj', goto_assigned_strip)
m.add_separator()
add_button('Strip matching tolerances...', 'sT', matching_strips_setup)
add_button('Add strips matching peaks', 'sm', add_matching_strips)
add_button('Delete matched strips', 'sM', delete_matched_strips)
return mbar
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 run_peaks2ucsf(self, save_path, msize, origin, nuclei, sfreq, swidth,
gaussians):
#
# Use my subprocess code instead of popen because I want to not block
# waiting for subprocess to finish and I want to be notified when it
# has finished
#
p2u_path = os.path.join(sparky.installation_path(), 'bin', 'peaks2ucsf')
proc = subprocess.subprocess(p2u_path, save_path)
p2u = proc.to_process
p2u.write('%d' % len(msize) + ' # dimension\n')
p2u.write(pyutil.sequence_string(msize, '%d ') + '# matrix size\n')
p2u.write(pyutil.sequence_string(origin, '%.6f ') + '# ppm origin\n')
p2u.write(pyutil.sequence_string(nuclei, '%s ') + '# nuclei\n')
p2u.write(pyutil.sequence_string(sfreq, '%.9f ') + '# spectometer freq\n')
p2u.write(pyutil.sequence_string(swidth, '%.3f ') + '# spectrum width\n')
for ppm_center, height, linewidth in gaussians:
p2u.write(pyutil.sequence_string(ppm_center, '%8.5f ') +
'%10.4g' % height +
pyutil.sequence_string(linewidth, '%8.2f ') +
'\n')
p2u.close()
message = ('%d unassigned resonances\n' % self.unassigned +
'%d unknown linewidths\n' % self.nolinewidth +
'Writing ' + os.path.basename(save_path))
report_finished = pyutil.precompose(self.report_finished, proc, message)
tkutil.call_me_when(self.top, report_finished, proc.exitted)
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 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 show_peaks(self):
self.noesy = self.noesy_format.get()
name_to_spect = pyutil.precompose(sputil.name_to_spectrum,
self.session)
peaks = self.assigned_peaks(self.spectrum_list)
self.show_assignments(peaks)
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 call_me_when(widget, callback, predicate):
ms_delay = 5000
def check(widget, predicate, callback):
if predicate():
callback()
else:
call_me_when(widget, callback, predicate)
cb = pyutil.precompose(check, widget, predicate, callback)
widget.after(ms_delay, cb)
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Linewidth Plot')
self.top.columnconfigure(0, weight=1)
r = 0
sw = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sw.frame.grid(row=r, sticky='w')
r = r + 1
self.spectrum_widget = sw
af = tkutil.entry_field(self.top, 'Spectrum axis: ', '1', 3)
af.frame.grid(row=r, sticky='w')
r = r + 1
self.axis_variable = af.variable
self.lw_ranges = [None, None]
er = tkutil.entry_row(self.top, 'Linewidth range (hz): ',
('min', '0', 3), ('max', '50', 3),
('step', '5', 3))
(self.lw_ranges[0], self.lw_ranges[1], self.lw_step) = 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
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, 'LinewidthPlot')),
)
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 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_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 call_me_when(widget, callback, predicate):
ms_delay = 5000
def check(widget, predicate, callback):
if predicate():
callback()
else:
call_me_when(widget, callback, predicate)
cb = pyutil.precompose(check, widget, predicate, callback)
widget.after(ms_delay, 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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Linewidth Plot')
self.top.columnconfigure(0, weight = 1)
r = 0
sw = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sw.frame.grid(row = r, sticky = 'w')
r = r + 1
self.spectrum_widget = sw
af = tkutil.entry_field(self.top, 'Spectrum axis: ', '1', 3)
af.frame.grid(row = r, sticky = 'w')
r = r + 1
self.axis_variable = af.variable
self.lw_ranges = [None, None]
er = tkutil.entry_row(self.top, 'Linewidth range (hz): ',
('min', '0', 3), ('max', '50', 3), ('step', '5', 3))
(self.lw_ranges[0], self.lw_ranges[1], self.lw_step) = 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
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, 'LinewidthPlot')),
)
br.frame.grid(row = r, sticky = 'w')
r = r + 1
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
# Initialize variables
self.session = session
self.canvas = None
self.selected_group = None
self.selected_atom = None
self.selected_groupatom = None
self.selected_group_prev = None
self.selected_group_next = None
self.selected_spectrum = self.session.selected_spectrum()
self.selected_index = -1
self.sequences = []
self.groups = []
self.label_list = None
self.selected_atom_obj = None
tkutil.Dialog.__init__(self, session.tk, 'Pine Graph Assigner')
keypress_cb = pyutil.precompose(sputil.command_keypress_cb, session)
self.top.bind('<KeyPress>', keypress_cb)
self.InitSequences()
# set selected
# spectrum
self.InitSpectrum()
# group&atom
self.InitGroupAtom()
# Setting up locations for each component
self.canvas_frame = Tkinter.Frame(self.top, width = 600, height = 400)
self.canvas_frame.pack(side='top', anchor='w')
self.CreateCanvas(self.canvas_frame) # Create Scrollable Canvas
self.spectra_frame = Tkinter.Frame(self.top, width = 120, height = 200)
self.spectra_frame.pack(side='left', anchor = 'nw')
self.CreateSpectraList(self.spectra_frame) # Create check boxes for spectra
self.button_frame = Tkinter.Frame(self.top, width = 480, height = 30)
self.button_frame.pack(side='top', anchor = 'nw')
self.CreateButtonList(self.button_frame) # Create buttons
self.label_frame = Tkinter.Frame(self.top, width = 480, height = 170)
self.label_frame.pack(side='top', anchor = 'nw')
self.CreateLabelList(self.label_frame) # Create peak lists
# Updating components
self.UpdateCanvas()
self.UpdateSpectraList()
self.UpdateLabelList()
def __init__(self, session):
# Initialize variables
self.peak = None
self.graph_dialog = None
self.spectrum_text = None
self.peak_text = None
self.label_box = None
self.label_list = None
self.br = None
self.br2 = None
self.progress_label = None
tkutil.Dialog.__init__(self, session.tk, 'Pine Assigner')
#self.top.grab_set()
#self.top.focus_set()
keypress_cb = pyutil.precompose(sputil.command_keypress_cb, session)
self.top.bind('<KeyPress>', keypress_cb)
self.session = session
self.UpdateDialog()
def __init__(self, session):
# Initialize variables
self.peak = None
self.graph_dialog = None
self.spectrum_text = None
self.peak_text = None
self.label_box = None
self.label_list = None
self.br = None
self.br2 = None
self.progress_label = None
tkutil.Dialog.__init__(self, session.tk, 'Pine Assigner')
#self.top.grab_set()
#self.top.focus_set()
keypress_cb = pyutil.precompose(sputil.command_keypress_cb, session)
self.top.bind('<KeyPress>', keypress_cb)
self.session = session
self.UpdateDialog()
def add_menu_button(self, menu, menu_text, accel, func):
cb = pyutil.precompose(func, self.session)
menu.add_button(menu_text + (' (%s)' % accel), cb)
self.session.add_command(accel, '', cb)
def add_command(accel, menu_text, module_name, func_name, session):
cb = pyutil.precompose(invoke_module_function, session, module_name,
func_name, (session, ))
session.add_command(accel, menu_text, cb)
def add_entry(self, name):
set_variable_cb = pyutil.precompose(self.variable.set, name)
self.menu.add_command(label=name, command=set_variable_cb)
def map_widget(self, popup):
self.add_callback(pyutil.precompose(self.show_widget_cb, popup))
def variable_set_callback(widget, variable, callback):
python_cb = pyutil.precompose(variable_set_cb, variable, callback)
tcl_cb_name = widget._register(python_cb)
variable._tk.call('trace', 'variable', str(variable), 'w', tcl_cb_name)
def add_command(accel, menu_text, module_name, func_name, session):
cb = pyutil.precompose(invoke_module_function, session,
module_name, func_name, (session,))
session.add_command(accel, menu_text, cb)
def variable_set_callback(widget, variable, callback):
python_cb = pyutil.precompose(variable_set_cb, variable, callback)
tcl_cb_name = widget._register(python_cb)
variable._tk.call('trace', 'variable', str(variable), 'w', tcl_cb_name)
def show_peaks(self):
self.noesy = self.noesy_format.get()
name_to_spect = pyutil.precompose(sputil.name_to_spectrum, self.session)
peaks = self.assigned_peaks(self.spectrum_list)
self.show_assignments(peaks)
def add_entry(self, name): set_variable_cb = pyutil.precompose(self.variable.set, name) self.menu.add_command(label = name, command = set_variable_cb)
def map_widget(self, popup):
self.add_callback(pyutil.precompose(self.show_widget_cb, popup))
