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
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.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 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 add_spectrum(self, spectrum, table, row):
pat_name, pat_axes = expectedpeaks.recall_pattern(spectrum)
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = sputil.spectrum_color(spectrum)
choose_cb = pyutil.precompose(sputil.choose_spectrum_cb, spectrum,
table.chosen_spectra)
cb.add_callback(choose_cb)
cb.button.grid(row=row, column=0, sticky='w')
if pat_name:
cb.set_state(1)
table.spectrum_to_checkbutton[spectrum] = cb
#
# Make peak pattern menu
#
epeak_types = expectedpeaks.expected_peak_descriptions.keys()
pm = tkutil.option_menu(table.frame, '', epeak_types)
pm.frame.grid(row=row, column=1, sticky='w')
table.spectrum_epeak_menus[spectrum] = pm
#
# Get default spectrum peak pattern and axis order
#
if pat_name == None:
pat_name = expectedpeaks.default_spectrum_pattern_name(spectrum)
if pat_name == None:
pat_name = pm.get()
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
pat_axes = pyutil.order(pat_nuclei, spectrum.nuclei)
#
# Make axis order menu
#
aom = axes.axis_order_menu(table.frame,
spectrum.nuclei,
initial_order=pat_axes)
aom.frame.grid(row=row, column=2, sticky='w')
table.axis_order_menu[spectrum] = aom
#
# Register a callback to limit the menu choices for axis order.
#
def restrict_axis_order_cb(pat_name, aom=aom):
import expectedpeaks
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
aom.restrict_menu_permutations(pat_nuclei)
pm.add_callback(restrict_axis_order_cb)
pm.set(pat_name)
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, 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 add_spectrum(self, spectrum, table, row):
pat_name, pat_axes = expectedpeaks.recall_pattern(spectrum)
#
# Make spectrum checkbutton
#
cb = tkutil.checkbutton(table.frame, spectrum.name, 0)
cb.button['selectcolor'] = sputil.spectrum_color(spectrum)
choose_cb = pyutil.precompose(sputil.choose_spectrum_cb, spectrum,
table.chosen_spectra)
cb.add_callback(choose_cb)
cb.button.grid(row = row, column = 0, sticky = 'w')
if pat_name:
cb.set_state(1)
table.spectrum_to_checkbutton[spectrum] = cb
#
# Make peak pattern menu
#
epeak_types = expectedpeaks.expected_peak_descriptions.keys()
pm = tkutil.option_menu(table.frame, '', epeak_types)
pm.frame.grid(row = row, column = 1, sticky = 'w')
table.spectrum_epeak_menus[spectrum] = pm
#
# Get default spectrum peak pattern and axis order
#
if pat_name == None:
pat_name = expectedpeaks.default_spectrum_pattern_name(spectrum)
if pat_name == None:
pat_name = pm.get()
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
pat_axes = pyutil.order(pat_nuclei, spectrum.nuclei)
#
# Make axis order menu
#
aom = axes.axis_order_menu(table.frame, spectrum.nuclei,
initial_order = pat_axes)
aom.frame.grid(row = row, column = 2, sticky = 'w')
table.axis_order_menu[spectrum] = aom
#
# Register a callback to limit the menu choices for axis order.
#
def restrict_axis_order_cb(pat_name, aom=aom):
import expectedpeaks
pat_list = expectedpeaks.expected_peak_descriptions[pat_name]
pat_nuclei = expectedpeaks.pattern_nuclei(pat_list[0])
aom.restrict_menu_permutations(pat_nuclei)
pm.add_callback(restrict_axis_order_cb)
pm.set(pat_name)
def __init__(self, session):
self.session = session
self.title = 'Assign peaks into GSSs'
tkutil.Dialog.__init__(self, session.tk, self.title)
_spectrum_names = [sp.name for sp in model.spectra()]
self.spec_from = m1 = tkutil.option_menu(
self.top, 'Using selected peaks in spectrum:', _spectrum_names)
m1.frame.pack(side='top', anchor='w')
self.spec_to = m2 = tkutil.option_menu(
self.top, 'Assign peaks to GSSs in spectrum:', _spectrum_names)
m2.frame.pack(side='top', anchor='w')
_d3 = [1, 2, 3] # TODO do those values need to be strings?
# matching dimension 1
self.match1_from = m3 = tkutil.option_menu(
self.top, 'Matching dimension 1: from:', _d3)
m3.frame.pack(side='top', anchor='w')
self.match1_to = m4 = tkutil.option_menu(self.top,
'Matching dimension 1: to:',
_d3)
m4.frame.pack(side='top', anchor='w')
self.tol1 = tkutil.entry_field(
self.top, 'Matching dimension 1: tolerance (PPM):', '0.2', 20)
self.tol1.frame.pack(side='top', anchor='w')
# matching dimension 2
self.match2_from = tkutil.option_menu(self.top,
'Matching dimension 2: from:',
_d3)
self.match2_from.frame.pack(side='top', anchor='w')
self.match2_to = tkutil.option_menu(self.top,
'Matching dimension 2: to:', _d3)
self.match2_to.frame.pack(side='top', anchor='w')
self.tol2 = tkutil.entry_field(
self.top, 'Matching dimension 2: tolerance (PPM):', '0.2', 20)
self.tol2.frame.pack(side='top', anchor='w')
# TODO check that the nuclei match
# TODO are 2 matching dimensions enough?
br = tkutil.button_row(
self.top,
('Assign peaks', self.execute),
('Close', self.close_cb),
)
br.frame.pack(side='top', anchor='w')
def __init__(self, session):
self.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.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
self.title = 'Assign peaks into GSSs'
tkutil.Dialog.__init__(self, session.tk, self.title)
_spectrum_names = [sp.name for sp in model.spectra()]
self.spec_from = m1 = tkutil.option_menu(self.top, 'Using selected peaks in spectrum:', _spectrum_names)
m1.frame.pack(side='top', anchor='w')
self.spec_to = m2 = tkutil.option_menu(self.top, 'Assign peaks to GSSs in spectrum:', _spectrum_names)
m2.frame.pack(side='top', anchor='w')
_d3 = [1, 2, 3] # TODO do those values need to be strings?
# matching dimension 1
self.match1_from = m3 = tkutil.option_menu(self.top, 'Matching dimension 1: from:', _d3)
m3.frame.pack(side='top', anchor='w')
self.match1_to = m4 = tkutil.option_menu(self.top, 'Matching dimension 1: to:', _d3)
m4.frame.pack(side='top', anchor='w')
self.tol1 = tkutil.entry_field(self.top, 'Matching dimension 1: tolerance (PPM):', '0.2', 20)
self.tol1.frame.pack(side = 'top', anchor = 'w')
# matching dimension 2
self.match2_from = tkutil.option_menu(self.top, 'Matching dimension 2: from:', _d3)
self.match2_from.frame.pack(side='top', anchor='w')
self.match2_to = tkutil.option_menu(self.top, 'Matching dimension 2: to:', _d3)
self.match2_to.frame.pack(side='top', anchor='w')
self.tol2 = tkutil.entry_field(self.top, 'Matching dimension 2: tolerance (PPM):', '0.2', 20)
self.tol2.frame.pack(side = 'top', anchor = 'w')
# TODO check that the nuclei match
# TODO are 2 matching dimensions enough?
br = tkutil.button_row(self.top,
('Assign peaks', self.execute),
('Close', self.close_cb),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.pdb_path = None
self.model = None
self.pseudobond_group = None
self.recenter_on_peak = 1
self.chimera_atom_to_num_atom = {}
self.num_atom_to_chimera_atom = {}
self.chimera_atom_to_resonance = {}
self.num_atom_pair_to_pseudobond = {}
self.selected_atoms = []
self.peak_selected_notice = None
self.bond_selection_trigger = None
self.chimera_quit_trigger = None
self.chimera_running = 0
tkutil.Dialog.__init__(self, session.tk, 'Chimera Model')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side = 'top', anchor = 'w')
colors = ('white', 'black', 'red', 'yellow',
'green', 'cyan', 'blue', 'magenta')
c = tkutil.option_menu(self.top, 'Color assigned atoms ',
colors, 'yellow')
c.frame.pack(side = 'top', anchor = 'w')
self.assigned_atom_color = c
cb = tkutil.checkbutton(self.top,
'Selecting peak highlights assignment line?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_peaks = cb
cb = tkutil.checkbutton(self.top,
'Selecting assignment line recenters spectrum?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_lines = cb
cb = tkutil.checkbutton(self.top, 'Selecting atoms recenters spectrum?', 1)
cb.button.pack(side = 'top', anchor = 'w')
self.show_selected_atoms = cb
c = tkutil.option_menu(self.top, 'Color lines for assignments ',
colors, 'blue')
c.frame.pack(side = 'top', anchor = 'w')
self.peak_line_color = c
cb = tkutil.checkbutton(self.top, 'Show contraint violations?', 0)
cb.button.pack(side = 'top', anchor = 'w')
self.show_constraints = cb
constraint_frame = Tkinter.Frame(self.top, borderwidth = 2,
relief = 'sunken')
cb.map_widget(constraint_frame)
self.mardi_file = tkutil.file_field(constraint_frame,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side = 'top', anchor = 'w')
cb = tkutil.checkbuttons(constraint_frame, 'top', '',
'Show satisfied constraints?',
'Show violated constraints?')
cb.frame.pack(side = 'top', anchor = 'w')
self.show_satisfied, self.show_violated = cb.variables
self.show_satisfied.set(0)
color_frame = Tkinter.Frame(constraint_frame)
color_frame.pack(side = 'top', anchor = 'w')
h = Tkinter.Label(color_frame, text = 'Constraint line colors:')
h.grid(row = 0, column = 0, columnspan = 2, sticky = 'w')
self.constraint_colors = []
row = 1
for text, color in (('< 0.8 times lower bound', 'blue'),
('0.8-1.0 times lower bound', 'cyan'),
('satisfied constraint', 'green'),
('1.0-1.2 times upper bound', 'magenta'),
('> 1.2 times upper bound', 'red')):
c = tkutil.option_menu(color_frame, '', colors, color)
c.frame.grid(row = row, column = 0, sticky = 'e', padx = 10)
label = Tkinter.Label(color_frame, text = text)
label.grid(row = row, column = 1, sticky = 'w')
row = row + 1
self.constraint_colors.append(c)
self.status_line = Tkinter.Label(self.top, anchor = 'nw',
wraplength = '15c', justify = 'left')
self.status_line.pack(side = 'top', anchor = 'w')
br = tkutil.button_row(self.top,
('Show', self.show_cb),
('Erase', self.erase_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Chimera')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, session):
self.session = session
self.pdb_path = None
self.model = None
self.pseudobond_group = None
self.recenter_on_peak = 1
self.chimera_atom_to_num_atom = {}
self.num_atom_to_chimera_atom = {}
self.chimera_atom_to_resonance = {}
self.num_atom_pair_to_pseudobond = {}
self.selected_atoms = []
self.peak_selected_notice = None
self.bond_selection_trigger = None
self.chimera_quit_trigger = None
self.chimera_running = 0
tkutil.Dialog.__init__(self, session.tk, 'Chimera Model')
self.pdb_file = tkutil.file_field(self.top, 'PDB File: ', 'pdb')
self.pdb_file.frame.pack(side='top', anchor='w')
colors = ('white', 'black', 'red', 'yellow', 'green', 'cyan', 'blue',
'magenta')
c = tkutil.option_menu(self.top, 'Color assigned atoms ', colors,
'yellow')
c.frame.pack(side='top', anchor='w')
self.assigned_atom_color = c
cb = tkutil.checkbutton(self.top,
'Selecting peak highlights assignment line?',
1)
cb.button.pack(side='top', anchor='w')
self.show_selected_peaks = cb
cb = tkutil.checkbutton(
self.top, 'Selecting assignment line recenters spectrum?', 1)
cb.button.pack(side='top', anchor='w')
self.show_selected_lines = cb
cb = tkutil.checkbutton(self.top,
'Selecting atoms recenters spectrum?', 1)
cb.button.pack(side='top', anchor='w')
self.show_selected_atoms = cb
c = tkutil.option_menu(self.top, 'Color lines for assignments ',
colors, 'blue')
c.frame.pack(side='top', anchor='w')
self.peak_line_color = c
cb = tkutil.checkbutton(self.top, 'Show contraint violations?', 0)
cb.button.pack(side='top', anchor='w')
self.show_constraints = cb
constraint_frame = Tkinter.Frame(self.top,
borderwidth=2,
relief='sunken')
cb.map_widget(constraint_frame)
self.mardi_file = tkutil.file_field(constraint_frame,
'Mardigras Constraint File: ',
'mardigras')
self.mardi_file.frame.pack(side='top', anchor='w')
cb = tkutil.checkbuttons(constraint_frame, 'top', '',
'Show satisfied constraints?',
'Show violated constraints?')
cb.frame.pack(side='top', anchor='w')
self.show_satisfied, self.show_violated = cb.variables
self.show_satisfied.set(0)
color_frame = Tkinter.Frame(constraint_frame)
color_frame.pack(side='top', anchor='w')
h = Tkinter.Label(color_frame, text='Constraint line colors:')
h.grid(row=0, column=0, columnspan=2, sticky='w')
self.constraint_colors = []
row = 1
for text, color in (('< 0.8 times lower bound',
'blue'), ('0.8-1.0 times lower bound', 'cyan'),
('satisfied constraint', 'green'),
('1.0-1.2 times upper bound',
'magenta'), ('> 1.2 times upper bound', 'red')):
c = tkutil.option_menu(color_frame, '', colors, color)
c.frame.grid(row=row, column=0, sticky='e', padx=10)
label = Tkinter.Label(color_frame, text=text)
label.grid(row=row, column=1, sticky='w')
row = row + 1
self.constraint_colors.append(c)
self.status_line = Tkinter.Label(self.top,
anchor='nw',
wraplength='15c',
justify='left')
self.status_line.pack(side='top', anchor='w')
br = tkutil.button_row(
self.top,
('Show', self.show_cb),
('Erase', self.erase_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'Chimera')),
)
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.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()
