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')