def read_settings(self): atof = pyutil.string_to_float settings = pyutil.generic_class() settings.spectrum = self.spectrum_choice.spectrum() settings.fit_default_error = None if self.fit_default.get(): settings.fit_default_error = atof(self.fit_default_error.get()) settings.box_default_error = None if self.box_default.get(): settings.box_default_error = atof(self.box_default_error.get()) settings.near_diagonal_range = None settings.near_diagonal_error = None if self.near_diagonal.get(): settings.near_diagonal_range = atof(self.near_diagonal_range.get()) settings.near_diagonal_error = atof(self.near_diagonal_error.get()) settings.nearby_peaks = {} settings.nearby_error = {} if self.nearby_peaks.get(): range = (atof(self.nearby_range['w1 range'].get()), atof(self.nearby_range['w2 range'].get())) if range[0] != None and range[1] != None: plist = settings.spectrum.peak_list() settings.nearby_peaks = nearby_peak_table(plist, range, self) for range in ('< .5', '.5 - 2', '> 2', 'unintegrated'): e = atof(self.nearby_error[range].get(), 0) settings.nearby_error[range] = e return settings
def show_linewidths(self, ap_pairs): p = pyutil.generic_class() p.top_yspace = 30 p.name_xspace = 70 p.name_yspace = 18 p.atom_yspace = p.name_yspace / self.atoms_per_line p.tick_size = p.atom_yspace / 2 p.label_gap = 15 p.left_xspace = 20 p.names_xspace = p.left_xspace + self.atoms_per_line * p.name_xspace p.plot_range = (p.names_xspace, p.names_xspace + 500) p.linewidth_range = (self.min_linewidth, self.max_linewidth) p.line = 0 self.canvas.delete('all') self.plot_linewidths(ap_pairs, p) self.plot_grid(p) box = self.canvas.bbox('all') self.canvas['width'] = box[2] self.canvas['scrollregion'] = box tkutil.set_canvas_corner(self.canvas, 0, 0)
def get_settings(self): settings = pyutil.generic_class() settings.c13_spectrum = self.c13_spect.spectrum() settings.n15_spectrum = self.n15_spect.spectrum() settings.c13_ppm_range = tkutil.float_variable_values(self.c13_ppm_range) settings.n15_ppm_range = tkutil.float_variable_values(self.n15_ppm_range) settings.show_type = self.show_type.get() settings.exclude_mirrors = self.exclude_mirrors.state() if settings.exclude_mirrors: ftext = self.c13_n15_factor.get() settings.c13_n15_factor = pyutil.string_to_float(ftext, 1) ftext = self.min_mirror_factor.get() settings.min_mirror_factor = pyutil.string_to_float(ftext, 0) return settings
def get_settings(self): settings = pyutil.generic_class() settings.spectrum = self.spectrum_choice.spectrum() settings.noesy_hsqc = noesy.is_noesy_hsqc(settings.spectrum) settings.pdb_paths = list(self.pdb_paths.path_list) settings.max_distance = pyutil.string_to_float(self.max_dist.get()) if settings.spectrum: dim = settings.spectrum.dimension settings.ppm_range = tkutil.float_variable_values(self.ppm_range)[:dim] else: settings.ppm_range = None settings.show_type = self.show_type.get() settings.show_dist = self.show_dist.get() return settings
def get_settings(self): settings = pyutil.generic_class() settings.spectrum = self.spectrum_choice.spectrum() settings.noesy_hsqc = noesy.is_noesy_hsqc(settings.spectrum) settings.pdb_paths = list(self.pdb_paths.path_list) settings.max_distance = pyutil.string_to_float(self.max_dist.get()) if settings.spectrum: dim = settings.spectrum.dimension settings.ppm_range = tkutil.float_variable_values( self.ppm_range)[:dim] else: settings.ppm_range = None settings.show_type = self.show_type.get() settings.show_dist = self.show_dist.get() return settings
def get_settings(self): settings = pyutil.generic_class() Labels = [] for (resi,resn) in self.sequence: Labels.append(resn + str(resi)) spectra = self.spectrum_table.chosen_spectra settings.spectrum_list=[spectrum for spectrum in spectra] settings.pdb_path = self.pdb_path.get() settings.chains = self.chains.get().replace(',','') settings.labeling = self.labeling.get() settings.sequence = self.sequence settings.ref_spectrum = self.sc_ref_spectrum.spectrum() settings.spectrum_2 = self.sc_spectrum_2.spectrum() settings.Htol = float(self.ppm_range.variables[0].get()) settings.Ctol = float(self.ppm_range.variables[1].get()) settings.Labels = Labels return settings
def get_settings(self): settings = pyutil.generic_class() settings.ref_spectrum = self.ref_menu.spectrum() if settings.ref_spectrum == None: self.progress_report('Spectrum %s not found' % self.ref_menu.get()) return None settings.pick_view = self.pick_menu.view() if settings.pick_view == None: self.progress_report('View %s not found' % self.pick_menu.get()) return None settings.selected_only = self.selected_only.state() settings.ranges = [] for ref_axis, pick_axis, ef in self.range_entries: rtext = ef.variable.get() r = pyutil.string_to_float(rtext) if r != None: settings.ranges.append((ref_axis, pick_axis, r)) return settings
def show_intervals(self, slist): p = pyutil.generic_class() p.top_yspace = 30 p.name_xspace = 70 p.name_yspace = 18 p.atom_yspace = p.name_yspace / self.atoms_per_line p.tick_size = p.atom_yspace / 2 p.label_gap = 15 p.left_xspace = 20 p.names_xspace = p.left_xspace + self.atoms_per_line * p.name_xspace p.plot_range = (p.names_xspace + 500, p.names_xspace) p.ppm_range = (self.min_ppm, self.max_ppm) self.canvas.delete('all') self.plot_grid(p, len(slist)) self.plot_shifts(slist, p) box = self.canvas.bbox('all') self.canvas['width'] = box[2] self.canvas['scrollregion'] = box tkutil.set_canvas_corner(self.canvas, 0, 0)