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):
""" Initialization
"""
self.session = session
tkutil.Dialog.__init__(self, session.tk,
'Open & Autoreload Multiple Spectra')
proj = session.project
mfs = tkutil.multiple_file_selection(self.top, proj.sparky_directory)
mfs.frame.pack(side = 'top', anchor = 'nw', fill = 'both', expand = 1)
self.files = mfs
r = Tkinter.Label(self.top, justify = 'left')
r.pack(side = 'top', anchor = 'nw')
self.result = r
br = tkutil.button_row(self.top,
('Open', self.open_cb),
('Set Timer', self.set_timer),
('Toggle Autoreload', self.toggle_autoreload),
('Cancel', self.close_cb),
('Help',
sputil.help_cb(session,
'OpenAutoreloadSpectra')),
)
br.frame.pack(side = 'top', anchor = 'nw')
self.autoreload = True # if the spectrum files should be autoreloaded
self.paths = None # list of spectrum files to open
self.tslist = None # list of timestamps for the spectrum files
self.tth = None # threading.Timer instance
self.q = Queue.Queue(1)
def __init__(self, session):
self.session = session
self.title = 'Group dialog'
tkutil.Dialog.__init__(self, session.tk, self.title)
# modify things
# gid
# aatype, next, residue
# resonance
# merge
# atomtype
# use group_data.listbox.bind to add my own callbacks (see peaklist for an example)
self.group_data = tkutil.scrolling_list(self.top, 'Group data', 5)
self.group_data.frame.pack(side = 'top', fill = 'both', expand = 1)
self.group_data.listbox.bind('<ButtonRelease-1>', self.click_on_listbox)
# display things
# aatype, next, residue
# resonances in group
# aatype
# shift
# low, high shifts of peak dimensions
# when peak selection is changed, if the peak's resonances are all
# only assigned to a single group, make that the active group
br = tkutil.button_row(self.top,
('Refresh', self.reset),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
self.reset()
def __init__(self, session):
self.session = session
self.assignments = None
self.spin_graph_dialog = None
self.current_resonance = None
self.extender = None
self.shown_group_atoms = None
tkutil.Dialog.__init__(self, session.tk, 'Assignment Graph')
lb = self.peak_list_box(self.top)
lb.pack(side = 'top', fill = 'both', expand = 1)
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Assign', self.assign_cb),
('Unassign', self.unassign_cb),
('Strips...', self.strip_cb),
('Update', self.update_cb),
('Setup...', self.setup_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AssignGraph')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[5])
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.assignments = None
self.spin_graph_dialog = None
self.current_resonance = None
self.extender = None
self.shown_group_atoms = None
tkutil.Dialog.__init__(self, session.tk, 'Assignment Graph')
lb = self.peak_list_box(self.top)
lb.pack(side='top', fill='both', expand=1)
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Assign', self.assign_cb),
('Unassign', self.unassign_cb),
('Strips...', self.strip_cb),
('Update', self.update_cb),
('Setup...', self.setup_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AssignGraph')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[5])
def __init__(self, session):
self.session = session
self.view_to_center = None
self.selection_notice = None
tkutil.Dialog.__init__(self, session.tk, 'View Center')
explain = ('Specify a view window to be centered\n' +
'by the cm or cp commands. The cm command\n' +
'centers the view at the point under the mouse\n'
'when the command is invoked in any window.\n' +
'The cp command centers the view on the selected\n' +
'peak.')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.pack(side = 'top', anchor = 'w')
add_command = pythonshell.add_command
add_command('cm', '', 'centerview', 'center_view_on_mouse', session)
add_command('cp', '', 'centerview', 'center_view_on_peak', session)
self.center_view = sputil.view_menu(session, self.top, 'View to center: ')
self.center_view.frame.pack(side = 'top', anchor = 'w')
ps = tkutil.checkbutton(self.top, 'Center when peak selected?', 0)
ps.button.pack(side = 'top', anchor = 'w')
self.peak_select = ps
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'CenterViews')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
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):
self.session = session
self.peak = None
tkutil.Dialog.__init__(self, session.tk, 'Peak Resonance Mover')
self.spectrum_menu = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
self.spectrum_menu.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'On / Off', 0)
cb.button.pack(side = 'top', anchor = 'w')
cb.add_callback(self.onoff_cb)
self.onoff = cb
self.will_drag_notice = None
self.dragged_notice = None
self.message = Tkinter.Label(self.top)
self.message.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ShiftRes')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.title = 'Peak List'
self.spectrum = None
self.peaks = ()
self.settings = peak_list_settings()
tkutil.Dialog.__init__(self, session.tk, self.title)
pl = sputil.peak_listbox(self.top)
pl.frame.pack(side = 'top', fill = 'both', expand = 1)
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
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),
('Setup...', self.setup_cb),
('Save...', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakListPython')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
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, 'Peak List Settings')
fb = Tkinter.Frame(self.top, borderwidth = 3, relief = 'groove')
fb.pack(side = 'top', fill = 'x')
#
# Create the checkbutton and extra widgets for each possible field
#
self.field_widgets = {}
for fc in field_classes:
self.field_widgets[fc] = fc.field_widgets(self.top, fc.name)
opt = Tkinter.Frame(self.top, borderwidth = 3, relief = 'groove')
opt.pack(side = 'top', fill = 'x')
cb = tkutil.checkbutton(opt, 'Sort by assignment?', 1)
self.assignmentsort = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(opt, 'Pair crossdiagonal peaks?', 0)
self.crosspair = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Pick Atoms')
cb = tkutil.checkbutton(self.top, 'Show atom labels?', 0)
self.show_label = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show distances?', 0)
self.show_distance = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show peaks?', 0)
self.show_peak = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show assigned atoms?', 0)
self.show_assigned = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb.add_callback(pyutil.precompose(color_assigned_atoms, session))
self.status_line = Tkinter.Label(self.top, anchor = 'nw')
self.status_line.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'MidasPick')),
)
br.frame.pack(side = 'top', anchor = 'w')
self.pick_cb = self.atom_pick_cb
midas.process(self.session).add_atom_pick_callback(self.pick_cb)
def __init__(self, session):
""" Initialization
"""
self.session = session
tkutil.Dialog.__init__(self, session.tk, "Open & Reload Multiple Spectra")
proj = session.project
mfs = tkutil.multiple_file_selection(self.top, proj.sparky_directory)
mfs.frame.pack(side="top", anchor="nw", fill="both", expand=1)
self.files = mfs
r = Tkinter.Label(self.top, justify="left")
r.pack(side="top", anchor="nw")
self.result = r
br = tkutil.button_row(
self.top,
("Open", self.open_cb),
("Reload", self.reload_spectra),
("Cancel", self.close_cb),
("Help", sputil.help_cb(session, "OpenAutoreloadSpectra")),
)
br.frame.pack(side="top", anchor="nw")
self.paths = [] # list of spectrum files to open
self.spectra = [] # spectra already opened
# if there are opened windows, get the paths
for v in proj.view_list():
self.paths.append(v.spectrum.save_path)
self.spectra.append(v.spectrum)
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk, 'Peak List Settings')
fb = Tkinter.Frame(self.top, borderwidth=3, relief='groove')
fb.pack(side='top', fill='x')
#
# Create the checkbutton and extra widgets for each possible field
#
self.field_widgets = {}
for fc in field_classes:
self.field_widgets[fc] = fc.field_widgets(self.top, fc.name)
opt = Tkinter.Frame(self.top, borderwidth=3, relief='groove')
opt.pack(side='top', fill='x')
cb = tkutil.checkbutton(opt, 'Sort by assignment?', 1)
self.assignmentsort = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(opt, 'Pair crossdiagonal peaks?', 0)
self.crosspair = cb.variable
cb.button.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
tkutil.Settings_Dialog.__init__(self, session.tk,
'Assignment Graph Setup')
sc = self.spectrum_choice_table(self.top)
sc.pack(side='top', anchor='w')
te = self.tolerance_entry(self.top)
te.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,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AssignGraph')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
self.peak = None
tkutil.Dialog.__init__(self, session.tk, 'Peak Resonance Mover')
self.spectrum_menu = sputil.spectrum_menu(session, self.top,
'Spectrum: ')
self.spectrum_menu.frame.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'On / Off', 0)
cb.button.pack(side='top', anchor='w')
cb.add_callback(self.onoff_cb)
self.onoff = cb
self.will_drag_notice = None
self.dragged_notice = None
self.message = Tkinter.Label(self.top)
self.message.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ShiftRes')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Atom Name Translations')
self.trans_name = tkutil.option_menu(self.top, 'Atom set: ', ())
self.trans_name.frame.pack(side='top', anchor='w')
self.trans_name.add_callback(self.show_translation_cb)
st = tkutil.scrolling_list(self.top, 'Select applicable translations',
5)
st.frame.pack(side='top', anchor='w')
st.listbox['selectmode'] = 'multiple'
self.standard_trans = st
for t in standard_translations():
self.standard_trans.listbox.insert('end', t.name)
self.bad_names = tkutil.scrolling_list(self.top, 'Non standard names',
5)
self.bad_names.frame.pack(side='top', anchor='w', fill='y', expand=1)
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AtomNameTrans')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.session = session
self.title = 'Peak List'
self.spectrum = None
self.peaks = ()
self.settings = peak_list_settings()
tkutil.Dialog.__init__(self, session.tk, self.title)
pl = sputil.peak_listbox(self.top)
pl.frame.pack(side='top', fill='both', expand=1)
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
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),
('Setup...', self.setup_cb),
('Save...', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakListPython')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
self.session = session
self.drag_notice = None
tkutil.Dialog.__init__(self, session.tk, 'Region RMSD')
self.top.columnconfigure(0, weight = 1)
import Tkinter
explain = ('Dragging a box calculates the mean and RMSD\n'
'of data values for that spectrum region.')
w = Tkinter.Label(self.top, text = explain, justify = 'left')
w.grid(row = 0, column = 0, sticky = 'nw')
r = Tkinter.Label(self.top, justify = 'left')
r.grid(row = 1, column = 0, sticky = 'nw')
self.result_label = r
br = tkutil.button_row(self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RegionRMSD')),
)
br.frame.grid(row = 2, column = 0, sticky = 'nw')
self.register_callback(1)
self.top.bind('<Map>', lambda e, s=self: s.register_callback(1))
self.top.bind('<Unmap>', lambda e, s=self: s.register_callback(0))
def __init__(self, session):
self.session = session
tkutil.Settings_Dialog.__init__(self, session.tk, 'Assignment Graph Setup')
sc = self.spectrum_choice_table(self.top)
sc.pack(side = 'top', anchor = 'w')
te = self.tolerance_entry(self.top)
te.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,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AssignGraph')),
)
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, '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
tkutil.Dialog.__init__(self, session.tk, 'View Constraints')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side = 'top', anchor = 'w')
self.mardi_file = tkutil.file_field(self.top,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show satisfied constraints?', 0)
self.satisfied = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbutton(self.top, 'Show violated constraints?', 1)
self.violated = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Show', self.show_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session,
'MidasConstraints')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.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
tkutil.Dialog.__init__(self, session.tk, 'Pick Atoms')
cb = tkutil.checkbutton(self.top, 'Show atom labels?', 0)
self.show_label = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show distances?', 0)
self.show_distance = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show peaks?', 0)
self.show_peak = cb.variable
cb.button.pack(side='top', anchor='w')
cb = tkutil.checkbutton(self.top, 'Show assigned atoms?', 0)
self.show_assigned = cb.variable
cb.button.pack(side='top', anchor='w')
cb.add_callback(pyutil.precompose(color_assigned_atoms, session))
self.status_line = Tkinter.Label(self.top, anchor='nw')
self.status_line.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'MidasPick')),
)
br.frame.pack(side='top', anchor='w')
self.pick_cb = self.atom_pick_cb
midas.process(self.session).add_atom_pick_callback(self.pick_cb)
def __init__(self, session, 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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Atom Name Translations')
self.trans_name = tkutil.option_menu(self.top, 'Atom set: ', ())
self.trans_name.frame.pack(side = 'top', anchor = 'w')
self.trans_name.add_callback(self.show_translation_cb)
st = tkutil.scrolling_list(self.top, 'Select applicable translations', 5)
st.frame.pack(side = 'top', anchor = 'w')
st.listbox['selectmode'] = 'multiple'
self.standard_trans = st
for t in standard_translations():
self.standard_trans.listbox.insert('end', t.name)
self.bad_names = tkutil.scrolling_list(self.top, 'Non standard names', 5)
self.bad_names.frame.pack(side = 'top', anchor = 'w',
fill = 'y', expand = 1)
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AtomNameTrans')),
)
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.grid_widgets = []
tkutil.Dialog.__init__(self, session.tk, 'Fit Delta-Chi Tensor to PCS')
self.dia_menu = sputil.spectrum_menu(session, self.top, 'Diamagnetic Spectrum: ')
self.dia_menu.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.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')
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.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
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 CreateButtonList(self, parent):
self.br = tkutil.button_row(parent,
('<<', self.FastPrev),
('<', self.Prev),
('>', self.Next),
('>>', self.FastNext),
('Update', self.UpdateDialog),
('Assign', self.Assign),
('UnAssign', self.UnAssign),
('Close', self.close_cb),
)
self.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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Chemical Shift Plot')
self.top.columnconfigure(0, weight = 1)
r = 0
self.condition_widget = sputil.condition_menu(session, self.top, 'Condition: ')
self.condition_widget.frame.grid(row = r, sticky = 'w')
r = r + 1
self.ppm_range_widget = [None, None]
er = tkutil.entry_row(self.top, 'PPM range: ',
('min', '0', 3), ('max', '12', 3), ('step', '1', 3))
(self.ppm_range_widget[0],
self.ppm_range_widget[1],
self.ppm_step_widget) = er.variables
er.frame.grid(row = r, sticky = 'w')
r = r + 1
e = tkutil.entry_field(self.top, 'Atoms: ', '', 30)
self.atoms = e.variable
e.frame.grid(row = r, sticky = 'w')
r = r + 1
t = tkutil.checkbutton(self.top, 'Show typical amino acid shifts?', 0)
self.typical_range = t.variable
t.button.grid(row = r, sticky = 'w')
r = r + 1
c = tkutil.scrollable_canvas(self.top)
c.frame.grid(row = r, sticky = 'news')
self.top.rowconfigure(r, weight = 1)
r = r + 1
self.canvas = c.canvas
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.grid(row = r, sticky = 'w')
r = r + 1
postscript_cb = pyutil.precompose(tkutil.postscript_cb, self.canvas)
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Postscript', postscript_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'ChemShiftPlot')),
)
br.frame.grid(row = r, sticky = 'w')
r = r + 1
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Table')
setup = Tkinter.Frame(self.top)
setup.pack(side='top', anchor='w')
# Choose Spectra
sbutton = tkutil.checkbutton(self.top, 'Choose Spectra', 1)
sbutton.button.pack(side='top', anchor='w')
schoice = Tkinter.Frame(self.top)
schoice.pack(side='top', anchor='w')
sc = sputil.spectrum_checkbuttons(session, schoice, '')
sc.frame.pack(side='top', anchor='w')
self.spectrum_list = sc.chosen_spectra
cb = tkutil.checkbutton(schoice, 'Noesy format?', 0)
self.noesy_format = cb.variable
cb.button.pack(side='top', anchor='w')
sbutton.map_widget(schoice)
# Peak list
pl = sputil.assignment_listbox(session, self.top)
pl.frame.pack(side='top', fill='both', expand=1)
pl.listbox.bind('<ButtonRelease-1>', self.select_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_assignment_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_assignment_cb)
self.peak_list = pl
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Save', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakTable')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Peak Table')
setup = Tkinter.Frame(self.top)
setup.pack(side = 'top', anchor = 'w')
# Choose Spectra
sbutton = tkutil.checkbutton(self.top, 'Choose Spectra', 1)
sbutton.button.pack(side = 'top', anchor = 'w')
schoice = Tkinter.Frame(self.top)
schoice.pack(side = 'top', anchor = 'w')
sc = sputil.spectrum_checkbuttons(session, schoice, '')
sc.frame.pack(side = 'top', anchor = 'w')
self.spectrum_list = sc.chosen_spectra
cb = tkutil.checkbutton(schoice, 'Noesy format?', 0)
self.noesy_format = cb.variable
cb.button.pack(side = 'top', anchor = 'w')
sbutton.map_widget(schoice)
# Peak list
pl = sputil.assignment_listbox(session, self.top)
pl.frame.pack(side = 'top', fill = 'both', expand = 1)
pl.listbox.bind('<ButtonRelease-1>', self.select_assignment_cb)
pl.listbox.bind('<ButtonRelease-2>', self.goto_assignment_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_assignment_cb)
self.peak_list = pl
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Save', self.peak_list.save_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PeakTable')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
self.molecule = None
tkutil.Dialog.__init__(self, session.tk, 'Sequence Entry')
se = self.sequence_entry(self.top)
se.pack(side = 'top', anchor = 'w', fill = 'x', expand = 1)
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Cancel', self.close_cb),
('Help', sputil.help_cb(session, 'Sequence')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk,
'Python Shell Preferences')
cb = tkutil.checkbutton(self.top, 'Show Python shell if error occurs?', 1)
cb.button.pack(side = 'top', anchor = 'nw')
self.raise_variable = cb.variable
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PythonShell')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session, 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):
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.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):
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.spectrum = None
self.heavy_axis = None
tkutil.Dialog.__init__(self, session.tk, 'Attached Proton')
am = tkutil.option_menu(self.top, 'Attached proton axis: ', ())
am.frame.pack(side = 'top')
self.axis_menu = am
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Cancel', self.close_cb),
('Help', sputil.help_cb(session, 'LabelledAxis')),
)
br.frame.pack(side = 'top', anchor = 'w')
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, 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):
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, gid=None, group_editor=None):
self.session = session
self.gid = gid
self.group_editor = group_editor
tkutil.Dialog.__init__(self, session.tk, 'merge resonances -- ???')
self.rid1 = m1 = tkutil.option_menu(self.top, 'Resonance 1', [])
m1.frame.pack(side='top', anchor='w')
self.rid2 = m2 = tkutil.option_menu(self.top, 'Resonance 2', [])
m2.frame.pack(side='top', anchor='w')
br = tkutil.button_row(self.top,
('Merge', self.merge_resonances),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
tkutil.Settings_Dialog.__init__(self, session.tk,
'Python Shell Preferences')
cb = tkutil.checkbutton(self.top, 'Show Python shell if error occurs?',
1)
cb.button.pack(side='top', anchor='nw')
self.raise_variable = cb.variable
br = tkutil.button_row(
self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PythonShell')),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session, num_range):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Noesy Assignment Diagram')
c = Tkinter.Canvas(self.top, width=700, height=700)
c.pack(fill='both', expand=1)
self.canvas = c
br = tkutil.button_row(
self.top,
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'NoesyAssign')),
)
br.frame.pack(side='top', anchor='w')
self.draw_circle(num_range)
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Restricted Peak Pick')
m = sputil.view_menu(session, self.top, 'Find peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.pick_menu = m
m = sputil.spectrum_menu(session, self.top, 'Using peaks in ')
m.frame.pack(side = 'top', anchor = 'w')
m.add_callback(self.chose_spectrum_cb)
self.ref_menu = m
b = tkutil.checkbutton(self.top, 'Use selected peaks only?', 0)
b.button.pack(side = 'top', anchor = 'w')
self.selected_only = b
lbl= Tkinter.Label(self.top, text = 'Axis match tolerances (ppm)')
lbl.pack(side = 'top', anchor = 'w')
self.axis_table_heading = lbl
f = Tkinter.Frame(self.top)
f.pack(side = 'top', anchor = 'w')
self.axis_table = f
self.range_entries = []
self.setup_axis_table()
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Pick peaks', self.pick_cb),
('Select peaks', self.select_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RestrictedPick')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[2])
def __init__(self, session):
tkutil.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')
