def __init__(self, session, gid=None, group_editor=None):
self.session = session
self.gid = gid
self.group_editor = group_editor
tkutil.Dialog.__init__(self, session.tk, 'Group editor -- ???')
e1 = tkutil.entry_field(self.top, 'GSS type:', '', 20)
e1.frame.pack(side='top', anchor='w')
self.aatype = e1.variable
e2 = tkutil.entry_field(self.top, 'Next GSS:', '', 20)
e2.frame.pack(side='top', anchor='w')
self.next_ = e2.variable
e3 = tkutil.entry_field(self.top, 'Residue:', '', 20)
e3.frame.pack(side='top', anchor='w')
self.residue = e3.variable
br = tkutil.button_row(self.top,
('Apply', self.update),
('Merge resonances', self.merge_resonances),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session, gid=None, group_editor=None):
self.session = session
self.gid = gid
self.group_editor = group_editor
tkutil.Dialog.__init__(self, session.tk, 'Group editor -- ???')
e1 = tkutil.entry_field(self.top, 'GSS type:', '', 20)
e1.frame.pack(side='top', anchor='w')
self.aatype = e1.variable
e2 = tkutil.entry_field(self.top, 'Next GSS:', '', 20)
e2.frame.pack(side='top', anchor='w')
self.next_ = e2.variable
e3 = tkutil.entry_field(self.top, 'Residue:', '', 20)
e3.frame.pack(side='top', anchor='w')
self.residue = e3.variable
br = tkutil.button_row(
self.top,
('Apply', self.update),
('Merge resonances', self.merge_resonances),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')
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 __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.g = GitRepo(model.project().sparky_directory)
self.session = session
self.title = 'Reproducibility'
tkutil.Dialog.__init__(self, session.tk, self.title)
br = tkutil.button_row(self.top, ('Make snapshot', self.make_snapshot))
br.frame.pack(side='top', anchor='w')
# TODO would like to get an enumerated list of these from somewhere
e = tkutil.entry_field(self.top, 'Deductive reason used:', '<enter reason>', 50)
e.frame.pack(side='top', anchor='w')
self.message = e.variable
br2 = tkutil.button_row(self.top, ('Set groups of selected peaks', self.set_group))
br2.frame.pack(side = 'top', anchor = 'w')
e2 = tkutil.entry_field(self.top, 'Group name:', '', 20, '(leave blank for name to be autogenerated)')
e2.frame.pack(side = 'top', anchor = 'w')
self.group = e2.variable
br4 = tkutil.button_row(self.top, ('Create new group for peak', self.create_new_group))
br4.frame.pack(side = 'top', anchor = 'w')
br5 = tkutil.button_row(self.top, ('Set selected peaks to noise', self.set_noise))
br5.frame.pack(side = 'top', anchor = 'w')
br6 = tkutil.button_row(self.top, ('Set selected peaks to artifact', self.set_artifact))
br6.frame.pack(side = 'top', anchor = 'w')
self.peaktype_spectrum = m1 = tkutil.option_menu(self.top, 'Select peaktype spectrum', peaktypes.spectra.keys())
m1.frame.pack(side='top', anchor='w')
m1.add_callback(self.set_peaktype_spectrum)
self.peaktype_dim_order = m3 = tkutil.option_menu(self.top, 'Peaktype dimension order', [])
self.dim_order = ','.join(map(str, peaktypes.orders[1][0]))
m3.frame.pack(side='top', anchor='w')
m3.add_callback(self.set_peaktype_dim_order)
self.peaktype = m2 = tkutil.option_menu(self.top, 'Assign peaktype', [])
m2.frame.pack(side='top', anchor='w')
m2.add_callback(self.assign_peaktype)
_spectrum_names = [sp.name for sp in model.spectra()]
self.select_signal_peaks_menu = m4 = tkutil.option_menu(self.top, 'Select signal peaks', _spectrum_names)
m4.frame.pack(side='top', anchor='w')
m4.add_callback(self.select_signal_peaks)
self.changed_callback = model.session().notify_me('selection changed', self.selection_changed)
br = tkutil.button_row(self.top,
('Open peak-GSS dialog', self.peaks_to_gss),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.title = 'Assign peaks into GSSs'
tkutil.Dialog.__init__(self, session.tk, self.title)
_spectrum_names = [sp.name for sp in model.spectra()]
self.spec_from = m1 = tkutil.option_menu(
self.top, 'Using selected peaks in spectrum:', _spectrum_names)
m1.frame.pack(side='top', anchor='w')
self.spec_to = m2 = tkutil.option_menu(
self.top, 'Assign peaks to GSSs in spectrum:', _spectrum_names)
m2.frame.pack(side='top', anchor='w')
_d3 = [1, 2, 3] # TODO do those values need to be strings?
# matching dimension 1
self.match1_from = m3 = tkutil.option_menu(
self.top, 'Matching dimension 1: from:', _d3)
m3.frame.pack(side='top', anchor='w')
self.match1_to = m4 = tkutil.option_menu(self.top,
'Matching dimension 1: to:',
_d3)
m4.frame.pack(side='top', anchor='w')
self.tol1 = tkutil.entry_field(
self.top, 'Matching dimension 1: tolerance (PPM):', '0.2', 20)
self.tol1.frame.pack(side='top', anchor='w')
# matching dimension 2
self.match2_from = tkutil.option_menu(self.top,
'Matching dimension 2: from:',
_d3)
self.match2_from.frame.pack(side='top', anchor='w')
self.match2_to = tkutil.option_menu(self.top,
'Matching dimension 2: to:', _d3)
self.match2_to.frame.pack(side='top', anchor='w')
self.tol2 = tkutil.entry_field(
self.top, 'Matching dimension 2: tolerance (PPM):', '0.2', 20)
self.tol2.frame.pack(side='top', anchor='w')
# TODO check that the nuclei match
# TODO are 2 matching dimensions enough?
br = tkutil.button_row(
self.top,
('Assign peaks', self.execute),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')
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):
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):
tkutil.Settings_Dialog.__init__(self, session.tk, 'Relaxation Spectra')
headings = ('Spectrum ', 'Time parameter')
st = sputil.spectrum_table(session, self.top, headings,
self.add_spectrum, self.remove_spectrum)
st.frame.pack(side = 'top', anchor = 'w')
self.spectrum_widgets = {}
spectra = session.project.spectrum_list()
def time_param(s, self=self):
return pyutil.string_to_float(self.default_time_parameter(s), 0)
spectra = pyutil.sort_by_function_value(spectra, time_param)
for spectrum in spectra:
st.add_spectrum(spectrum)
e = tkutil.entry_field(self.top, 'Use ', '5', 3,
' random trials for error estimates.')
e.frame.pack(side = 'top', anchor = 'w')
self.trials = e
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RelaxFit')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.title = 'Assign peaks into GSSs'
tkutil.Dialog.__init__(self, session.tk, self.title)
_spectrum_names = [sp.name for sp in model.spectra()]
self.spec_from = m1 = tkutil.option_menu(self.top, 'Using selected peaks in spectrum:', _spectrum_names)
m1.frame.pack(side='top', anchor='w')
self.spec_to = m2 = tkutil.option_menu(self.top, 'Assign peaks to GSSs in spectrum:', _spectrum_names)
m2.frame.pack(side='top', anchor='w')
_d3 = [1, 2, 3] # TODO do those values need to be strings?
# matching dimension 1
self.match1_from = m3 = tkutil.option_menu(self.top, 'Matching dimension 1: from:', _d3)
m3.frame.pack(side='top', anchor='w')
self.match1_to = m4 = tkutil.option_menu(self.top, 'Matching dimension 1: to:', _d3)
m4.frame.pack(side='top', anchor='w')
self.tol1 = tkutil.entry_field(self.top, 'Matching dimension 1: tolerance (PPM):', '0.2', 20)
self.tol1.frame.pack(side = 'top', anchor = 'w')
# matching dimension 2
self.match2_from = tkutil.option_menu(self.top, 'Matching dimension 2: from:', _d3)
self.match2_from.frame.pack(side='top', anchor='w')
self.match2_to = tkutil.option_menu(self.top, 'Matching dimension 2: to:', _d3)
self.match2_to.frame.pack(side='top', anchor='w')
self.tol2 = tkutil.entry_field(self.top, 'Matching dimension 2: tolerance (PPM):', '0.2', 20)
self.tol2.frame.pack(side = 'top', anchor = 'w')
# TODO check that the nuclei match
# TODO are 2 matching dimensions enough?
br = tkutil.button_row(self.top,
('Assign peaks', self.execute),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
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, 'Show Peak Strips')
sw = tkutil.entry_field(self.top, 'Strip width (screen pixels): ', '', 4)
sw.frame.pack(side = 'top', anchor = 'w')
self.strip_width = sw.variable
gp = tkutil.entry_field(self.top, 'Gap between strips (screen pixels): ',
'', 4)
gp.frame.pack(side = 'top', anchor = 'w')
self.strip_gap = gp.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 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 __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, '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, gid=None, rid=None, group_editor=None):
self.gid = gid
self.rid = rid
self.group_editor = group_editor
tkutil.Dialog.__init__(self, session.tk, 'Resonance editor --- ???')
e1 = tkutil.entry_field(self.top, 'Atom type:', '', 20)
e1.frame.pack(side='top', anchor='w')
self.atomtype = e1.variable
br = tkutil.button_row(self.top,
('Apply', self.update),
('Close', self.close_cb),
)
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, gid=None, rid=None, group_editor=None):
self.gid = gid
self.rid = rid
self.group_editor = group_editor
tkutil.Dialog.__init__(self, session.tk, 'Resonance editor --- ???')
e1 = tkutil.entry_field(self.top, 'Atom type:', '', 20)
e1.frame.pack(side='top', anchor='w')
self.atomtype = e1.variable
br = tkutil.button_row(
self.top,
('Apply', self.update),
('Close', self.close_cb),
)
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 sequence_entry(self, parent):
f = Tkinter.Frame(parent)
h = Tkinter.Label(f, text = 'Sequence')
h.pack(side = 'top', anchor = 'w')
self.header = h
t = tkutil.scrolling_text(f)
t.text['wrap'] = 'char'
t.frame.pack(side = 'top', fill = 'x', expand = 1)
self.sequence_text = t
ff = tkutil.file_field(f, 'Sequence File', 'sequence')
ff.frame.pack(side = 'top', anchor = 'w')
self.file_field = ff
fr = tkutil.entry_field(f, 'First residue number', '1')
fr.frame.pack(side = 'top', anchor = 'w')
self.first_residue = fr
return f
def setup_axis_table(self):
for w in self.axis_table.grid_slaves():
w.destroy()
ref_spectrum = self.ref_menu.spectrum()
pick_view = self.pick_menu.view()
if ref_spectrum == None or pick_view == None:
return
heading = ('\nAxis match tolerances (ppm)\n%s \ %s' %
(ref_spectrum.name, pick_view.name))
self.axis_table_heading['text'] = heading
column = 1
pick_nuclei = pick_view.spectrum.nuclei
for nucleus in pick_nuclei:
lbl = Tkinter.Label(self.axis_table, text=nucleus)
lbl.grid(row=1, column=column)
column = column + 1
row = 2
ref_nuclei = ref_spectrum.nuclei
for nucleus in ref_nuclei:
lbl = Tkinter.Label(self.axis_table, text=nucleus)
lbl.grid(row=row, column=0, sticky='w')
row = row + 1
self.range_entries = []
for r in range(len(ref_nuclei)):
for p in range(len(pick_nuclei)):
if ref_nuclei[r] == pick_nuclei[p]:
if ref_nuclei[r] == '1H':
rtext = '.02'
else:
rtext = '.2'
e = tkutil.entry_field(self.axis_table, '', rtext, 4)
e.frame.grid(row=r + 2, column=p + 1, sticky='w')
self.range_entries.append((r, p, e))
def setup_axis_table(self):
for w in self.axis_table.grid_slaves():
w.destroy()
ref_spectrum = self.ref_menu.spectrum()
pick_view = self.pick_menu.view()
if ref_spectrum == None or pick_view == None:
return
heading = ('\nAxis match tolerances (ppm)\n%s \ %s' % (ref_spectrum.name,
pick_view.name))
self.axis_table_heading['text'] = heading
column = 1
pick_nuclei = pick_view.spectrum.nuclei
for nucleus in pick_nuclei:
lbl= Tkinter.Label(self.axis_table, text = nucleus)
lbl.grid(row = 1, column = column)
column = column + 1
row = 2
ref_nuclei = ref_spectrum.nuclei
for nucleus in ref_nuclei:
lbl= Tkinter.Label(self.axis_table, text = nucleus)
lbl.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.range_entries = []
for r in range(len(ref_nuclei)):
for p in range(len(pick_nuclei)):
if ref_nuclei[r] == pick_nuclei[p]:
if ref_nuclei[r] == '1H':
rtext = '.02'
else:
rtext = '.2'
e = tkutil.entry_field(self.axis_table, '', rtext, 4)
e.frame.grid(row = r + 2, column = p + 1, sticky = 'w')
self.range_entries.append((r,p,e))
def spectrum_choice_table(self, parent):
f = Tkinter.Frame(parent, borderwidth = 5)
self.type_to_spectrum_menu = {}
self.type_to_phase = {}
count = 0
entries_per_column = 5
row = 1
column = 0
for type in spectrum_types:
column = 4 * (count / entries_per_column)
row = 1 + (count % entries_per_column)
if row == 1:
lbl = Tkinter.Label(f, text = ' ')
lbl.grid(row = 0, column = column)
lbl = Tkinter.Label(f, text = 'Spectrum')
lbl.grid(row = 0, column = column + 2)
lbl = Tkinter.Label(f, text = 'Phase')
lbl.grid(row = 0, column = column + 3)
lbl = Tkinter.Label(f, text = type)
lbl.grid(row = row, column = column + 1, sticky = 'w')
m = sputil.spectrum_menu(self.sparky_session, f, '', allow_no_choice = 1)
m.frame.grid(row = row, column = column + 2, sticky = 'w')
self.type_to_spectrum_menu[type] = m
p = tkutil.entry_field(f, '', width = 6)
p.frame.grid(row = row, column = column + 3, sticky = 'w')
self.type_to_phase[type] = p.variable
count = count + 1
return f
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
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):
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 __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
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')
def __init__(self, session):
self.g = GitRepo(model.project().sparky_directory)
self.session = session
self.title = 'Reproducibility'
tkutil.Dialog.__init__(self, session.tk, self.title)
br = tkutil.button_row(self.top, ('Make snapshot', self.make_snapshot))
br.frame.pack(side='top', anchor='w')
# TODO would like to get an enumerated list of these from somewhere
e = tkutil.entry_field(self.top, 'Deductive reason used:',
'<enter reason>', 50)
e.frame.pack(side='top', anchor='w')
self.message = e.variable
br2 = tkutil.button_row(
self.top, ('Set groups of selected peaks', self.set_group))
br2.frame.pack(side='top', anchor='w')
e2 = tkutil.entry_field(self.top, 'Group name:', '', 20,
'(leave blank for name to be autogenerated)')
e2.frame.pack(side='top', anchor='w')
self.group = e2.variable
br4 = tkutil.button_row(
self.top, ('Create new group for peak', self.create_new_group))
br4.frame.pack(side='top', anchor='w')
br5 = tkutil.button_row(
self.top, ('Set selected peaks to noise', self.set_noise))
br5.frame.pack(side='top', anchor='w')
br6 = tkutil.button_row(
self.top, ('Set selected peaks to artifact', self.set_artifact))
br6.frame.pack(side='top', anchor='w')
self.peaktype_spectrum = m1 = tkutil.option_menu(
self.top, 'Select peaktype spectrum', peaktypes.spectra.keys())
m1.frame.pack(side='top', anchor='w')
m1.add_callback(self.set_peaktype_spectrum)
self.peaktype_dim_order = m3 = tkutil.option_menu(
self.top, 'Peaktype dimension order', [])
self.dim_order = ','.join(map(str, peaktypes.orders[1][0]))
m3.frame.pack(side='top', anchor='w')
m3.add_callback(self.set_peaktype_dim_order)
self.peaktype = m2 = tkutil.option_menu(self.top, 'Assign peaktype',
[])
m2.frame.pack(side='top', anchor='w')
m2.add_callback(self.assign_peaktype)
_spectrum_names = [sp.name for sp in model.spectra()]
self.select_signal_peaks_menu = m4 = tkutil.option_menu(
self.top, 'Select signal peaks', _spectrum_names)
m4.frame.pack(side='top', anchor='w')
m4.add_callback(self.select_signal_peaks)
self.changed_callback = model.session().notify_me(
'selection changed', self.selection_changed)
br = tkutil.button_row(
self.top,
('Open peak-GSS dialog', self.peaks_to_gss),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')