def noesy_table_row(self, table, row, atom_name):
t = Tkinter.Label(table, text = atom_name + ' ')
t.grid(row = row, column = 0)
spectrum = sputil.spectrum_menu(self.session, table,
'', allow_no_choice = 1)
spectrum.frame.grid(row = row, column = 1)
ppm_range = []
for a in range(3):
v = Tkinter.StringVar(table)
v.set('.02')
e = Tkinter.Entry(table, textvariable = v, width = 5)
e.grid(row = row, column = 2 + a)
ppm_range.append(v)
spectra = self.session.project.spectrum_list()
s = noesy.noesy_hsqc_spectrum(spectra, atom_name)
if s:
spectrum.set(s.name)
heavy_axis = axes.unique_nucleus_axis(s, atom_name)
ppm_range[heavy_axis].set('.2')
return spectrum, ppm_range
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Read Peak List')
plp = tkutil.file_field(self.top, 'Peak file: ', 'peaklist')
plp.frame.pack(side = 'top', anchor = 'w')
self.peak_list_path = plp
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, 'Unreadable lines', 5)
sl.frame.pack(side = 'top', anchor = 'w', fill = 'both', expand = 1)
self.unreadable = sl
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Create peaks', self.read_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ReadPeaks')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
def __init__(self, session):
self.session = session
self.peak = None
tkutil.Dialog.__init__(self, session.tk, 'Peak Resonance Mover')
self.spectrum_menu = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
self.spectrum_menu.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'On / Off', 0)
cb.button.pack(side = 'top', anchor = 'w')
cb.add_callback(self.onoff_cb)
self.onoff = cb
self.will_drag_notice = None
self.dragged_notice = None
self.message = Tkinter.Label(self.top)
self.message.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ShiftRes')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Place HC Peaks from Resonances')
explain = ('Create and label peaks on a 2D C13 HSQC spectrum\n' +
'for all protons attached to carbons, if both proton\n' +
'and carbon resonances are assigned and labeled\n'
'correctly.\n')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
m = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
m.frame.pack(side = 'top', anchor = 'w')
self.spectrum_menu = m
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Place peaks', self.place_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'HCPeaks')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Connect Ponderosa Analyzer')
cnt = tkutil.file_field(self.top, 'Connect file (sparky.cnt): ', 'Connect file')
cnt.frame.pack(side = 'top', anchor = 'w')
self.cnt_path = cnt
szCnt = os.getcwd() + os.sep + "sparky.cnt"
if os.path.isfile(szCnt):
self.cnt_path.set(szCnt)
spec1 = sputil.spectrum_menu(session, self.top, '15N-NOESY: ')
spec1.frame.pack(side = 'top', anchor = 'w')
self.nnoe = spec1
spec2 = sputil.spectrum_menu(session, self.top, '13C-NOESY(ali-): ')
spec2.frame.pack(side = 'top', anchor = 'w')
self.cnoe = spec2
spec3 = sputil.spectrum_menu(session, self.top, '13C-NOESY(aro-): ')
spec3.frame.pack(side = 'top', anchor = 'w')
self.aronoe = spec3
self.n15_ppms = [] # w1, w2, w3 chemical shifts
self.c15_ppms = [] # w1, w2, w3 chemical shifts
self.br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Move(15N-)', self.move_n_cb),
('Move(13C-)', self.move_c_cb),
('Close', self.close_cb),
)
self.br.frame.pack(side = 'top', anchor = 'w')
self.label_frame = Tkinter.Frame(self.top, width = 500, height = 100)
self.label_frame.pack(side='top', anchor = 'nw')
ll = modified_listbox(self.label_frame, 'Label List', 49, 8, "single")
ll.listbox.bind('<Double-ButtonRelease-1>', self.move_to_selected_cb)
ll.listbox.bind('<ButtonRelease-3>', self.move_to_selected_cb)
self.label_list = ll
self.label_list.frame.grid(sticky='news')
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, 'Align Spectrum')
m = sputil.spectrum_menu(session, self.top, 'Align spectrum ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.align_menu = m
m = sputil.spectrum_menu(session, self.top, 'using peak in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
lbl = Tkinter.Label(self.top, text = 'Match axes')
lbl.pack(side = 'top', anchor = 'w')
f = Tkinter.Frame(self.top)
f.pack(side = 'top', anchor = 'w')
self.axis_table = f
self.axis_menus = []
self.setup_axis_table()
m = Tkinter.Label(self.top)
m.pack(side = 'top', anchor = 'w')
self.message = m
br = tkutil.button_row(self.top,
('Align', self.align_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AlignSpectrum')),
)
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):
self.session = session
self.selection_notice = None
tkutil.Dialog.__init__(self, session.tk, 'Read Cyana peak list')
tspectra=('2D','3D')
initial=tspectra[0]
self.spectratype = tkutil.option_menu(self.top, "Select spectra dimension", tspectra, initial)
self.spectratype.frame.pack(side = 'top', anchor = 'w')
order=('xy','yx','xyz','xzy','yxz','yzx','zxy','zyx')
initial=order[0]
self.order = tkutil.option_menu(self.top, "Select output order", order, initial)
self.order.frame.pack(side = 'top', anchor = 'w')
self.plp = tkutil.file_field(self.top, 'Cyana output peak file: ', 'peaklist')
self.plp.frame.pack(side = 'top', anchor = 'e')
self.peak_list_path = self.plp
self.pl = tkutil.file_field(self.top, 'Cyana output proton file:', 'protlist')
self.pl.frame.pack(side = 'top', anchor = 'e')
self.proton_list_path = self.pl
self.sl = tkutil.file_field(self.top, 'Sequence file: ', 'seqlist')
self.sl.frame.pack(side = 'top', anchor = 'e')
self.sequence_list_path = self.sl
sc = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_choice = sc
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Create peaks', self.read_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ReadPeaks')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Restricted Peak Pick')
m = sputil.view_menu(session, self.top, 'Find peaks in ')
m.frame.pack(side='top', anchor='w')
m.add_callback(self.chose_spectrum_cb)
self.pick_menu = m
m = sputil.spectrum_menu(session, self.top, 'Using peaks in ')
m.frame.pack(side='top', anchor='w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
b = tkutil.checkbutton(self.top, 'Use selected peaks only?', 0)
b.button.pack(side='top', anchor='w')
self.selected_only = b
lbl = Tkinter.Label(self.top, text='Axis match tolerances (ppm)')
lbl.pack(side='top', anchor='w')
self.axis_table_heading = lbl
f = Tkinter.Frame(self.top)
f.pack(side='top', anchor='w')
self.axis_table = f
self.range_entries = []
self.setup_axis_table()
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Pick peaks', self.pick_cb),
('Select peaks', self.select_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RestrictedPick')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Restricted Peak Pick')
m = sputil.view_menu(session, self.top, 'Find peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.pick_menu = m
m = sputil.spectrum_menu(session, self.top, 'Using peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
b = tkutil.checkbutton(self.top, 'Use selected peaks only?', 0)
b.button.pack(side = 'top', anchor = 'w')
self.selected_only = b
lbl= Tkinter.Label(self.top, text = 'Axis match tolerances (ppm)')
lbl.pack(side = 'top', anchor = 'w')
self.axis_table_heading = lbl
f = Tkinter.Frame(self.top)
f.pack(side = 'top', anchor = 'w')
self.axis_table = f
self.range_entries = []
self.setup_axis_table()
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Pick peaks', self.pick_cb),
('Select peaks', self.select_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RestrictedPick')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.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, '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 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
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):
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, '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):
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])
