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 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 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)
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)