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
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 = '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):
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, '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):
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 peak_list_box(self, parent):
pl = tkutil.scrolling_list(parent, 'Possible resonance assignments', 5)
pl.listbox.bind('<ButtonRelease-1>', self.select_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_peak_cb)
self.peak_list = pl
return pl.frame
def peak_list_box(self, parent):
pl = tkutil.scrolling_list(parent, 'Possible resonance assignments', 5)
pl.listbox.bind('<ButtonRelease-1>', self.select_peak_cb)
pl.listbox.bind('<Double-ButtonRelease-1>', self.goto_peak_cb)
self.peak_list = pl
return pl.frame
def label_list_box(self, parent):
pl = tkutil.scrolling_list(parent, 'Choose possible resonance assignments by PINE', 8)
pl.listbox.bind('<Double-ButtonRelease-1>', self.Assign_cb) # Func
pl.listbox.bind('<ButtonRelease-3>', self.Assign_cb) # Func
self.label_list = pl
return pl.frame
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 label_list_box(self, parent):
pl = tkutil.scrolling_list(
parent, 'Choose possible resonance assignments by PINE', 8)
pl.listbox.bind('<Double-ButtonRelease-1>', self.Assign_cb) # Func
pl.listbox.bind('<ButtonRelease-3>', self.Assign_cb) # Func
self.label_list = pl
return pl.frame
def __init__(self, session):
self.session = session
self.spectrum_times = []
self.last_spectrum_times = []
self.error_estimate_trials = 5
tkutil.Dialog.__init__(self, session.tk, 'Relaxation Peak Heights')
pl = tkutil.scrolling_list(self.top, heading = '', height = 5)
pl.frame.pack(side = 'top', fill = 'both', expand = 1)
pl.listbox.bind('<ButtonRelease-1>', self.show_fit_cb)
pl.listbox.bind('<KeyPress-Delete>', pl.delete_selected_cb)
# The following is needed so key press is received by list box.
pl.listbox.bind('<ButtonPress-1>', pl.set_focus_cb)
self.peak_list = pl
md = tkutil.option_menu(self.top, 'Use ',
(self.HEIGHTS_MODE,
self.ASSIGNED_HEIGHTS_MODE,
self.ASSIGNED_HEIGHTS_ONLY_MODE,
self.VOLUMES_MODE))
md.frame.pack(side = 'top', anchor = 'w')
self.mode = md.variable
progress_label = Tkinter.Label(self.top, anchor = 'nw')
progress_label.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Setup...', self.setup_cb),
('Save', self.peak_list.save_cb),
('Append', self.peak_list.append_cb),
('Clear', self.clear_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'RelaxFit')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[4])
def __init__(self, session):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'PDB Atom Name Check')
cm = sputil.condition_menu(session, self.top, 'Condition: ')
cm.frame.pack(side = 'top', anchor = 'w')
self.condition_menu = cm
pf = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
pf.frame.pack(side = 'top', anchor = 'w')
self.pdb_path = pf
al = tkutil.scrolling_list(self.top, 'Resonances w/o PDB atoms', 5)
al.frame.pack(fill = 'both', expand = 1)
self.atom_list = al
br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'PDBNames')),
)
br.frame.pack(side = 'top', anchor = 'w')
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
tkutil.Dialog.__init__(self, session.tk,
'Reposition Assigned Fragment')
cm = sputil.condition_menu(session, self.top, 'Condition: ')
cm.frame.pack(side='top', anchor='w')
self.condition_menu = cm
rr = tkutil.entry_row(self.top, 'Residues ', ('from', '', 3),
('to', '', 3))
self.range_variables = rr.variables
rr.frame.pack(side='top', anchor='w')
ol = tkutil.scrolling_list(self.top, '', 5)
ol.frame.pack(side='top', fill='both', expand=1)
ol.listbox.bind('<ButtonRelease-1>', self.select_cb)
self.offset_list = ol
progress_label = Tkinter.Label(self.top, anchor='nw')
progress_label.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Positions', self.positions_cb),
('Move', self.move_cb),
('Shifts', self.shifts_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Reposition')),
)
br.frame.pack(side='top', anchor='w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[3])
def __init__(self, session):
self.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):
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.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])