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 __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):
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.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):
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):
self.session = session
tkutil.Dialog.__init__(self, session.tk, 'Create Corma Spectrum')
sm = sputil.spectrum_menu(session, self.top, 'Spectrum: ')
sm.frame.pack(side = 'top', anchor = 'w')
sm.add_callback(self.spectrum_cb)
self.spectrum_menu = sm
ms = tkutil.entry_row(self.top, 'Matrix size: ',
('w1', '0', 5), ('w2', '0', 5))
ms.frame.pack(side = 'top', anchor = 'w')
self.matrix_size = ms
lw = tkutil.entry_row(self.top, 'Default linewidth (hz): ',
('w1', '0', 5), ('w2', '0', 5))
lw.frame.pack(side = 'top', anchor = 'w')
self.default_linewidth = lw
cp = tkutil.file_field(self.top, 'Corma file: ', 'corma')
cp.frame.pack(side = 'top', anchor = 'w')
self.corma_path = cp
sp = tkutil.file_field(self.top, 'Save in file: ', 'spectrum', save = 1)
sp.frame.pack(side = 'top', anchor = 'w')
self.save_path = sp
progress_label = Tkinter.Label(self.top, anchor = 'nw', justify = 'left')
progress_label.pack(side = 'top', anchor = 'w')
self.spectrum_cb(self.spectrum_menu.get())
br = tkutil.button_row(self.top,
('Create Spectrum', self.create_spectrum_cb),
('Stop', self.stop_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'CormaSpectrum')),
)
br.frame.pack(side = 'top', anchor = 'w')
tkutil.Stoppable.__init__(self, progress_label, br.buttons[1])
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Connect Ponderosa Analyzer')
cnt = tkutil.file_field(self.top, 'Connect file (sparky.cnt): ',
'Connect file')
cnt.frame.pack(side='top', anchor='w')
self.cnt_path = cnt
szCnt = os.getcwd() + os.sep + "sparky.cnt"
if os.path.isfile(szCnt):
self.cnt_path.set(szCnt)
spec1 = sputil.spectrum_menu(session, self.top, '15N-NOESY: ')
spec1.frame.pack(side='top', anchor='w')
self.nnoe = spec1
spec2 = sputil.spectrum_menu(session, self.top, '13C-NOESY(ali-): ')
spec2.frame.pack(side='top', anchor='w')
self.cnoe = spec2
spec3 = sputil.spectrum_menu(session, self.top, '13C-NOESY(aro-): ')
spec3.frame.pack(side='top', anchor='w')
self.aronoe = spec3
self.n15_ppms = [] # w1, w2, w3 chemical shifts
self.c15_ppms = [] # w1, w2, w3 chemical shifts
self.br = tkutil.button_row(
self.top,
('Update', self.update_cb),
('Move(15N-)', self.move_n_cb),
('Move(13C-)', self.move_c_cb),
('Close', self.close_cb),
)
self.br.frame.pack(side='top', anchor='w')
self.label_frame = Tkinter.Frame(self.top, width=500, height=100)
self.label_frame.pack(side='top', anchor='nw')
ll = modified_listbox(self.label_frame, 'Label List', 49, 8, "single")
ll.listbox.bind('<Double-ButtonRelease-1>', self.move_to_selected_cb)
ll.listbox.bind('<ButtonRelease-3>', self.move_to_selected_cb)
self.label_list = ll
self.label_list.frame.grid(sticky='news')
def __init__(self, session):
tkutil.Dialog.__init__(self, session.tk, 'Connect Ponderosa Analyzer')
cnt = tkutil.file_field(self.top, 'Connect file (sparky.cnt): ', 'Connect file')
cnt.frame.pack(side = 'top', anchor = 'w')
self.cnt_path = cnt
szCnt = os.getcwd() + os.sep + "sparky.cnt"
if os.path.isfile(szCnt):
self.cnt_path.set(szCnt)
spec1 = sputil.spectrum_menu(session, self.top, '15N-NOESY: ')
spec1.frame.pack(side = 'top', anchor = 'w')
self.nnoe = spec1
spec2 = sputil.spectrum_menu(session, self.top, '13C-NOESY(ali-): ')
spec2.frame.pack(side = 'top', anchor = 'w')
self.cnoe = spec2
spec3 = sputil.spectrum_menu(session, self.top, '13C-NOESY(aro-): ')
spec3.frame.pack(side = 'top', anchor = 'w')
self.aronoe = spec3
self.n15_ppms = [] # w1, w2, w3 chemical shifts
self.c15_ppms = [] # w1, w2, w3 chemical shifts
self.br = tkutil.button_row(self.top,
('Update', self.update_cb),
('Move(15N-)', self.move_n_cb),
('Move(13C-)', self.move_c_cb),
('Close', self.close_cb),
)
self.br.frame.pack(side = 'top', anchor = 'w')
self.label_frame = Tkinter.Frame(self.top, width = 500, height = 100)
self.label_frame.pack(side='top', anchor = 'nw')
ll = modified_listbox(self.label_frame, 'Label List', 49, 8, "single")
ll.listbox.bind('<Double-ButtonRelease-1>', self.move_to_selected_cb)
ll.listbox.bind('<ButtonRelease-3>', self.move_to_selected_cb)
self.label_list = ll
self.label_list.frame.grid(sticky='news')
def sequence_entry(self, parent):
f = Tkinter.Frame(parent)
h = Tkinter.Label(f, text = 'Sequence')
h.pack(side = 'top', anchor = 'w')
self.header = h
t = tkutil.scrolling_text(f)
t.text['wrap'] = 'char'
t.frame.pack(side = 'top', fill = 'x', expand = 1)
self.sequence_text = t
ff = tkutil.file_field(f, 'Sequence File', 'sequence')
ff.frame.pack(side = 'top', anchor = 'w')
self.file_field = ff
fr = tkutil.entry_field(f, 'First residue number', '1')
fr.frame.pack(side = 'top', anchor = 'w')
self.first_residue = fr
return f
def __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.sparky_session = session
tkutil.Settings_Dialog.__init__(self, session.tk, 'AutoAssign Setup')
sc = self.spectrum_choice_table(self.top)
sc.pack(side = 'top', anchor = 'w')
t = tkutil.entry_row(self.top, 'Tolerances (ppm)',
('HN', '', 4),
('N15', '', 4),
('CA', '', 4),
('CB', '', 4),
('HA', '', 4),
('CO', '', 4),
)
t.frame.pack(side = 'top', anchor = 'w')
self.tolerances = t.entries
td = tkutil.file_field(self.top, 'Temp directory for peak lists: ',
'autoassign', browse_button = 0, width = 30)
td.frame.pack(side = 'top', anchor = 'w')
self.temp_directory = td
m = Tkinter.Label(self.top, anchor = 'nw', justify = 'left')
m.pack(side = 'top', anchor = 'w')
self.message = m
br = tkutil.button_row(self.top,
('Ok', self.ok_cb),
('Apply', self.apply_cb),
('Close', self.close_cb),
('Help', sputil.help_cb(session, 'AutoAssign')),
)
br.frame.pack(side = 'top', anchor = 'w')
def __init__(self, parent, name): peak_list_field.field_widgets.__init__(self, parent, name) self.path_widget = tkutil.file_field(parent, 'File: ', 'corma') self.checkbutton.map_widget(self.path_widget.frame)
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, parent, name):
peak_list_field.field_widgets.__init__(self, parent, name)
self.path_widget = tkutil.file_field(parent, 'File: ', 'corma')
self.checkbutton.map_widget(self.path_widget.frame)
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')
