def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk,
'Strip Matching Parameters')
t = tkutil.entry_row(self.top, 'Tolerances ',
(' 1H', '.02', 5),
(' 13C', '.2', 5),
(' 15N', '.2', 5))
t.frame.pack(side = 'top', anchor = 'w')
self.tolerances = {'1H': t.variables[0],
'13C': t.variables[1],
'15N': t.variables[2]}
e = tkutil.entry_field(self.top, 'Allow ', '0', 3, ' unmatched peaks')
e.frame.pack(side = 'top', anchor = 'w')
self.max_unmatched = e.variable
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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'ncIDP Repositioning Tool 1.2b/2nd DEC 2010')
cm = sputil.condition_menu(session, self.top, 'Condition: ')
cm.frame.pack(side = 'top', anchor = 'w')
self.condition_menu = cm
rr = tkutil.entry_row(self.top, 'Residues ',
('from', '', 3), ('to', '', 3))
self.range_variables = rr.variables
rr.frame.pack(side = 'top', anchor = 'w')
ol = tkutil.scrolling_list(self.top, '', 5)
ol.frame.pack(side = 'top', fill = 'both', expand = 1)
ol.listbox.bind('<ButtonRelease-1>', self.select_cb)
self.offset_list = ol
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Positions', self.positions_cb),
('Move', self.move_cb),
('Shifts', self.shifts_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Reposition'))
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
self.session = session
self.grid_widgets = []
tkutil.Dialog.__init__(self, session.tk, 'Read and write PCS values')
acqu_template = [("T{}-:".format(i + 1), "0.0", 6) for i in range(3)]
self.dia_menu = sputil.spectrum_menu(session, self.top,
'Diamagnetic Spectrum: ')
self.dia_menu.frame.pack(side='top', anchor='w')
self.dia_menu.add_callback(self.dia_spec_change)
self.dia_acqu = tkutil.entry_row(self.top, "Acqu Time:",
*acqu_template)
self.dia_acqu.frame.pack(side='top', anchor='w')
self.para_menu = sputil.spectrum_menu(session, self.top,
'Paramagnetic Spectrum: ')
self.para_menu.frame.pack(side='top', anchor='w')
self.para_menu.add_callback(self.para_spec_change)
self.para_acqu = tkutil.entry_row(self.top, "Acqu Time:",
*acqu_template)
self.para_acqu.frame.pack(side='top', anchor='w')
self.npc_write_path = tkutil.file_field(self.top,
'PCS save file: ',
'.npc',
save=1)
self.npc_write_path.frame.pack(side='top', anchor='e')
self.npc_write_path.set("pcsexp.npc")
self.npc_read_path = tkutil.file_field(self.top, 'PCS read file: ',
'.npc')
self.npc_read_path.frame.pack(side='top', anchor='e')
self.npc_read_path.set("pcscalc.npc")
self.message = Tkinter.Label(self.top)
self.message.pack(side='top', anchor='w')
self.message['text'] = "\n"
br = tkutil.button_row(self.top, ('Write PCS', self.write_npc_cb),
('Read PCS', self.read_npc_cb),
('Clear PCS', self.clear_peaks_cb),
('Close', self.close_cb))
br.frame.pack(side='top', anchor='w')
self.dia_spec_change()
self.para_spec_change()
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Create Corma Spectrum')
sm = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sm.frame.pack(side = 'top', anchor = 'w')
sm.add_callback(self.spectrum_cb)
self.spectrum_menu = sm
ms = tkutil.entry_row(self.top, 'Matrix size: ',
('w1', '0', 5), ('w2', '0', 5))
ms.frame.pack(side = 'top', anchor = 'w')
self.matrix_size = ms
lw = tkutil.entry_row(self.top, 'Default linewidth (hz): ',
('w1', '0', 5), ('w2', '0', 5))
lw.frame.pack(side = 'top', anchor = 'w')
self.default_linewidth = lw
cp = tkutil.file_field(self.top, 'Corma file: ', 'corma')
cp.frame.pack(side = 'top', anchor = 'w')
self.corma_path = cp
sp = tkutil.file_field(self.top, 'Save in file: ', 'spectrum', save = 1)
sp.frame.pack(side = 'top', anchor = 'w')
self.save_path = sp
progress_label = Tkinter.Label(self.top, anchor = 'nw', justify = 'left')
progress_label.pack(side = 'top', anchor = 'w')
self.spectrum_cb(self.spectrum_menu.get())
br = tkutil.button_row(self.top,
('Create Spectrum', self.create_spectrum_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'CormaSpectrum')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
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 tolerance_entry(self, parent):
t = tkutil.entry_row(parent, 'Tolerances (ppm)', (' 1H', '.02', 5),
(' 13C', '.4', 5), (' 15N', '.2', 5))
self.tolerances = {
'1H': t.variables[0],
'13C': t.variables[1],
'15N': t.variables[2]
}
return t.frame
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 tolerance_entry(self, parent):
t = tkutil.entry_row(parent, 'Tolerances (ppm)',
(' 1H', '.02', 5),
(' 13C', '.4', 5),
(' 15N', '.2', 5))
self.tolerances = {'1H': t.variables[0],
'13C': t.variables[1],
'15N': t.variables[2]}
return t.frame
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):
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, 'Possible Noesy Assignments')
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side='top', anchor='w')
self.spectrum_choice = sc
sc.add_callback(self.spectrum_cb)
er = tkutil.entry_row(self.top, 'PPM tolerance: ', ('w1', '.01', 4),
('w2', '.01', 4), ('w3', '.01', 4))
self.ppm_range = er.variables
self.w3_range_widget = er.entries[2].frame
er.frame.pack(side='top', anchor='w')
self.spectrum_cb(self.spectrum_choice.get())
t = tkutil.scrolling_text(self.top, height=32, width=60)
t.frame.pack(side='top', anchor='nw', fill='both', expand=1)
t.text['wrap'] = 'none'
self.text = t.text
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='nw')
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Diagram', self.diagram_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'NoesyAssign')),
)
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, '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, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk,
'Reposition Assigned Fragment')
cm = sputil.condition_menu(session, self.top, 'Condition: ')
cm.frame.pack(side='top', anchor='w')
self.condition_menu = cm
rr = tkutil.entry_row(self.top, 'Residues ', ('from', '', 3),
('to', '', 3))
self.range_variables = rr.variables
rr.frame.pack(side='top', anchor='w')
ol = tkutil.scrolling_list(self.top, '', 5)
ol.frame.pack(side='top', fill='both', expand=1)
ol.listbox.bind('<ButtonRelease-1>', self.select_cb)
self.offset_list = ol
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Positions', self.positions_cb),
('Move', self.move_cb),
('Shifts', self.shifts_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Reposition')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
self.sparky_session = session
tkutil.Settings_Dialog.__init__(self, session.tk, 'AutoAssign Setup')
sc = self.spectrum_choice_table(self.top)
sc.pack(side = 'top', anchor = 'w')
t = tkutil.entry_row(self.top, 'Tolerances (ppm)',
('HN', '', 4),
('N15', '', 4),
('CA', '', 4),
('CB', '', 4),
('HA', '', 4),
('CO', '', 4),
)
t.frame.pack(side = 'top', anchor = 'w')
self.tolerances = t.entries
td = tkutil.file_field(self.top, 'Temp directory for peak lists: ',
'autoassign', browse_button = 0, width = 30)
td.frame.pack(side = 'top', anchor = 'w')
self.temp_directory = td
m = Tkinter.Label(self.top, anchor = 'nw', justify = 'left')
m.pack(side = 'top', anchor = 'w')
self.message = m
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, 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 UpdateDialog(self):
# Clear objects
if self.spectrum_text <> None:
self.spectrum_text.frame.destroy()
if self.peak_text <> None:
self.peak_text.frame.destroy()
if self.label_box <> None:
self.label_box.destroy()
if self.br <> None:
self.br.frame.destroy()
if self.br2 <> None:
self.br2.frame.destroy()
if self.progress_label <> None:
self.progress_label.destroy()
# Set up selected spectrum
self.spectrum = self.session.selected_spectrum()
# There should be selected spectrum
if self.spectrum == None:
self.close_cb()
# There should be one selected peak
peaks = self.spectrum.selected_peaks()
if len(peaks) > 0:
self.peak = peaks[0]
else:
self.close_cb()
# Create label object for showing spectrum name
t = tkutil.entry_row(self.top, 'Selected Spectrum: ' + self.spectrum.name)
t.frame.pack(side = 'top', anchor = 'w')
self.spectrum_text = t
# Dunno why 'len(peaks) > 0' is not working
if self.peak <> None:
if self.spectrum.dimension == 2:
u = tkutil.entry_row(self.top, 'Selected Peak: %7.3f,%7.3f' % (self.peak.position[0],self.peak.position[1]) )
else:
u = tkutil.entry_row(self.top, 'Selected Peak: %7.3f,%7.3f,%7.3f' % (self.peak.position[0],self.peak.position[1],self.peak.position[2]) )
u.frame.pack(side = 'top', anchor = 'w')
self.peak_text = u
# Create listbox object for showing labels
lbLabel = self.label_list_box(self.top) # List box
lbLabel.pack(side = 'top', fill = 'both', expand = 1)
self.label_box = lbLabel
self.LabelBox() # Set up label list box
# Create Buttons
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
self.progress_label = progress_label
self.br = tkutil.button_row(self.top,
('Update', self.UpdateDialog), # Func
('Assign', self.Assign), # Func
('Best Prob.', self.AssignTheBest),
('UnAssign', self.UnAssign), # Func
)
self.br2 = tkutil.button_row(self.top,
('Floating Labels', self.FloatingLabel),
('Graph...', self.Graph), # Func
('Stop', self.stop_cb),
('Close', self.close_cb),
#('Help', sputil.Help(session, 'PineAssign')),
)
self.br.frame.pack(side = 'top', anchor = 'w')
self.br2.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, self.br2.buttons[2])
def __init__(self, session):
self.session = session
self.selection_notice = None
tkutil.Dialog.__init__(self, session.tk, 'Assignment Distances')
self.top.bind('<Destroy>', self.window_destroyed_cb, 1)
self.pdb_paths = tkutil.file_choices(self.top, 'PDB files: ', 'pdb')
self.pdb_paths.frame.pack(side='top', anchor='w', fill='x')
self.spectrum_choice = sputil.spectrum_menu(session, self.top,
'Spectrum: ')
self.spectrum_choice.frame.pack(side='top', anchor='w')
self.spectrum_choice.add_callback(self.spectrum_cb)
er = tkutil.entry_row(self.top, 'PPM tolerance: ', ('w1', '.01', 4),
('w2', '.01', 4), ('w3', '.01', 4))
self.ppm_range = er.variables
self.w3_range_widget = er.entries[2].frame
er.frame.pack(side='top', anchor='w')
self.line_format = '%15s %s %7s %s'
self.spectrum_cb(self.spectrum_choice.get())
e = tkutil.entry_field(self.top, 'Max atom distance: ', '', 5)
self.max_dist = e.variable
e.frame.pack(side='top', anchor='w')
tchoices = ('Assignments with far atoms',
'Peaks with multiple assignments',
'Close atoms with no peak',
'Assignments for unassigned peaks', 'Unassignable peaks',
'Assignments for selected peaks')
initial = tchoices[5]
self.show_type = tkutil.option_menu(self.top, 'Show: ', tchoices,
initial)
self.show_type.frame.pack(side='top', anchor='w')
dchoices = ('shortest', 'all', 'min, ave, max')
self.show_dist = tkutil.option_menu(self.top, 'Show model distances: ',
dchoices)
self.show_dist.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-1>', self.select_peak_or_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_peak_or_assignment_cb)
pl.listbox.bind('<Double-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='nw')
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, 'AssignmentDistance')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
self.settings = self.get_settings()
def __init__(self, session):
self.session = session
self.selection_notice = None
tkutil.Dialog.__init__(self, session.tk, 'Assignment Distances')
self.top.bind('<Destroy>', self.window_destroyed_cb, 1)
self.pdb_paths = tkutil.file_choices(self.top, 'PDB files: ', 'pdb')
self.pdb_paths.frame.pack(side = 'top', anchor = 'w', fill = 'x')
self.spectrum_choice = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
self.spectrum_choice.frame.pack(side = 'top', anchor = 'w')
self.spectrum_choice.add_callback(self.spectrum_cb)
er = tkutil.entry_row(self.top, 'PPM tolerance: ',
('w1', '.01', 4), ('w2', '.01', 4), ('w3', '.01', 4))
self.ppm_range = er.variables
self.w3_range_widget = er.entries[2].frame
er.frame.pack(side = 'top', anchor = 'w')
self.line_format = '%15s %s %7s %s'
self.spectrum_cb(self.spectrum_choice.get())
e = tkutil.entry_field(self.top, 'Max atom distance: ', '', 5)
self.max_dist = e.variable
e.frame.pack(side = 'top', anchor = 'w')
tchoices = ('Assignments with far atoms',
'Peaks with multiple assignments',
'Close atoms with no peak',
'Assignments for unassigned peaks',
'Unassignable peaks',
'Assignments for selected peaks')
initial = tchoices[5]
self.show_type = tkutil.option_menu(self.top, 'Show: ', tchoices, initial)
self.show_type.frame.pack(side = 'top', anchor = 'w')
dchoices = ('shortest', 'all', 'min, ave, max')
self.show_dist = tkutil.option_menu(self.top, 'Show model distances: ', dchoices)
self.show_dist.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-1>', self.select_peak_or_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_peak_or_assignment_cb)
pl.listbox.bind('<Double-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 = 'nw')
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,
'AssignmentDistance')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
self.settings = self.get_settings()
def UpdateDialog(self):
# Clear objects
if self.spectrum_text <> None:
self.spectrum_text.frame.destroy()
if self.peak_text <> None:
self.peak_text.frame.destroy()
if self.label_box <> None:
self.label_box.destroy()
if self.br <> None:
self.br.frame.destroy()
if self.br2 <> None:
self.br2.frame.destroy()
if self.progress_label <> None:
self.progress_label.destroy()
# Set up selected spectrum
self.spectrum = self.session.selected_spectrum()
# There should be selected spectrum
if self.spectrum == None:
self.close_cb()
# There should be one selected peak
peaks = self.spectrum.selected_peaks()
if len(peaks) > 0:
self.peak = peaks[0]
else:
self.close_cb()
# Create label object for showing spectrum name
t = tkutil.entry_row(self.top,
'Selected Spectrum: ' + self.spectrum.name)
t.frame.pack(side='top', anchor='w')
self.spectrum_text = t
# Dunno why 'len(peaks) > 0' is not working
if self.peak <> None:
if self.spectrum.dimension == 2:
u = tkutil.entry_row(
self.top, 'Selected Peak: %7.3f,%7.3f' %
(self.peak.position[0], self.peak.position[1]))
else:
u = tkutil.entry_row(
self.top, 'Selected Peak: %7.3f,%7.3f,%7.3f' %
(self.peak.position[0], self.peak.position[1],
self.peak.position[2]))
u.frame.pack(side='top', anchor='w')
self.peak_text = u
# Create listbox object for showing labels
lbLabel = self.label_list_box(self.top) # List box
lbLabel.pack(side='top', fill='both', expand=1)
self.label_box = lbLabel
self.LabelBox() # Set up label list box
# Create Buttons
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
self.progress_label = progress_label
self.br = tkutil.button_row(
self.top,
('Update', self.UpdateDialog), # Func
('Assign', self.Assign), # Func
('Best Prob.', self.AssignTheBest),
('UnAssign', self.UnAssign), # Func
)
self.br2 = tkutil.button_row(
self.top,
('Floating Labels', self.FloatingLabel),
('Graph...', self.Graph), # Func
('Stop', self.stop_cb),
('Close', self.close_cb),
#('Help', sputil.Help(session, 'PineAssign')),
)
self.br.frame.pack(side='top', anchor='w')
self.br2.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, self.br2.buttons[2])
def __init__(self, session):
self.session = session
try:
persist_path = self.session.project.save_path + '.seq'
except:
persist_path = ''
sequence = []
## If the session.project.save_path + '.seq' file exist then produce sequence = [(idx, szA)]
if os.path.exists(persist_path):
pszLines =[line.rstrip() for line in open(persist_path).readlines() if line.rstrip() and ">" not in line and "#" not in line]
for line in pszLines:
if line.split()[0] in AAA_dict.keys():
sequence.append((int(line.split()[1]), AAA_dict[line.split()[0]]))
if not os.path.exists(persist_path):
tkMessageBox.showinfo('Input Error', "No Sequence file was found\n Please load a sequence using 'sq' command\nSave the project and relaunch MAGIC-Act")
return self.close_cb
self.sequence = sequence
self.selection_notice = None
self.save_file = session.project.save_path.split('/')[-1].replace('.proj', '_pymol.txt')
tkutil.Dialog.__init__(self, session.tk, 'MAGIC-View')
explain = ('Pymol Visualization and Assignment Accuracy Statistics\n')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
explain = ('PDB does NOT need H')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
ep = tkutil.file_field2(self.top, 'PDB file', 'Browse...', file_type=[('Protein Data Bank File', '.pdb')], default_ext='.pdb')
self.pdb_path = ep.variable
ep.frame.pack(side = 'top', anchor = 'w')
lb = tkutil.entry_field(self.top, 'Labeled Methyls: ', 'ILVMAT', 10)
lb.frame.pack(side = 'top', anchor = 'w')
self.labeling = lb.variable
explain = ('Specify which chain should be used')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
ch = tkutil.entry_field(self.top, 'Use Chain(s): ', 'A', 5)
self.chains = ch.variable
ch.frame.pack(side = 'top', anchor = 'w')
explain = ('Select 2D spectra that contain assignments')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
self.sc = self.spectrum_choice_table(self.top)
self.sc.pack(side = 'top', anchor = 'w')
# Compare Assignments Box
self.lf2 = Tkinter.LabelFrame(self.top, text='Compare Assignments')
self.lf2.pack(fill=X, pady=5)
self.pmframe= Tkinter.Frame(self.lf2)
self.pmframe.pack(pady=5)
# First Spectrum
self.sc_ref_spectrum = spectrum_menu(session, self.pmframe, 'Ref Spectrum: ')
self.sc_ref_spectrum.frame.pack(side ='top',padx=3)
# Second Spectrum
self.sc_spectrum_2 = spectrum_menu(session, self.pmframe, 'Query Spectrum: ')
self.sc_spectrum_2.frame.pack(side = 'top', anchor = 'w')
sl = tkutil.scrolling_list(self.top, 'Assignment Report', 10)
sl.frame.pack(fill = 'both', expand = 1)
self.summary_list = sl
# PPM Tolerances for filtering noesy and finding geminal pairs
er = tkutil.entry_row(self.top, 'PPM tolerance: ',
('1H', '0.01', 5),
('13C', '0.10', 5))
er.frame.pack(side = 'top', anchor = 'w',padx=2)
self.ppm_range = er
br = tkutil.button_row(self.top,
('Compare', self.show_summary),
('Save', self.save_pymol_cb),
('Close', self.close_cb))
br.frame.pack(side = 'top', anchor = 'w')
