def get_settings(self):
self.condition = self.condition_widget.condition()
if self.condition == None:
self.progress_report('Must select a condition.')
return 0
self.min_ppm = pyutil.string_to_float(self.ppm_range_widget[0].get())
self.max_ppm = pyutil.string_to_float(self.ppm_range_widget[1].get())
self.ppm_step = pyutil.string_to_float(self.ppm_step_widget.get())
if self.min_ppm == None or self.max_ppm == None or self.ppm_step == None:
self.progress_report('Must set ppm min, max, and step.')
return 0
self.atoms_per_line = 1
atoms = tuple(map(string.strip, string.split(self.atoms.get(), ',')))
if atoms == ('', ):
atoms = ()
self.atoms_to_show = atoms
self.show_aa_range = self.typical_range.get()
return 1
def get_settings(self):
self.spectrum = self.spectrum_widget.spectrum()
if self.spectrum == None:
self.progress_report('Must select a spectrum.')
return 0
anum = pyutil.string_to_int(self.axis_variable.get())
if anum == None:
self.progress_report('Must select a spectrum axis.')
return 0
else:
self.axis = anum - 1
self.min_linewidth = pyutil.string_to_float(self.lw_ranges[0].get())
self.max_linewidth = pyutil.string_to_float(self.lw_ranges[1].get())
self.linewidth_step = pyutil.string_to_float(self.lw_step.get())
if (self.min_linewidth == None or self.max_linewidth == None or
self.linewidth_step == None):
self.progress_report('Must select linewidth min, max, and step.')
return 0
self.atoms_per_line = 1
atoms = tuple(map(string.strip, string.split(self.atoms.get(), ',')))
if atoms == ('',):
atoms = ()
self.atoms_to_show = atoms
return 1
def get_settings(self):
self.spectrum = self.spectrum_widget.spectrum()
if self.spectrum == None:
self.progress_report('Must select a spectrum.')
return 0
anum = pyutil.string_to_int(self.axis_variable.get())
if anum == None:
self.progress_report('Must select a spectrum axis.')
return 0
else:
self.axis = anum - 1
self.min_linewidth = pyutil.string_to_float(self.lw_ranges[0].get())
self.max_linewidth = pyutil.string_to_float(self.lw_ranges[1].get())
self.linewidth_step = pyutil.string_to_float(self.lw_step.get())
if (self.min_linewidth == None or self.max_linewidth == None
or self.linewidth_step == None):
self.progress_report('Must select linewidth min, max, and step.')
return 0
self.atoms_per_line = 1
atoms = tuple(map(string.strip, string.split(self.atoms.get(), ',')))
if atoms == ('', ):
atoms = ()
self.atoms_to_show = atoms
return 1
def get_settings(self):
self.condition = self.condition_widget.condition()
if self.condition == None:
self.progress_report('Must select a condition.')
return 0
self.min_ppm = pyutil.string_to_float(self.ppm_range_widget[0].get())
self.max_ppm = pyutil.string_to_float(self.ppm_range_widget[1].get())
self.ppm_step = pyutil.string_to_float(self.ppm_step_widget.get())
if self.min_ppm == None or self.max_ppm == None or self.ppm_step == None:
self.progress_report('Must set ppm min, max, and step.')
return 0
self.atoms_per_line = 1
atoms = tuple(map(string.strip, string.split(self.atoms.get(), ',')))
if atoms == ('',):
atoms = ()
self.atoms_to_show = atoms
self.show_aa_range = self.typical_range.get()
return 1
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 parse_peak_line(self, line, dim):
fields = string.split(line, None, dim + 1)
if len(fields) < dim + 1:
return None
assignment = sputil.parse_assignment(fields[0])
if assignment == None or len(assignment) != dim:
self.unreadable.listbox.insert('end', line)
return None
frequency = []
for a in range(dim):
f = pyutil.string_to_float(fields[a+1])
if f == None:
self.unreadable.listbox.insert('end', line)
return None
frequency.append(f)
if len(fields) > dim + 1:
note = fields[dim + 1]
else:
note = ''
return (assignment, frequency, note)
def parse_peak_line(self, line, dim):
fields = string.split(line, None, dim + 1)
if len(fields) < dim + 1:
return None
assignment = sputil.parse_assignment(fields[0])
if assignment == None or len(assignment) != dim:
self.unreadable.listbox.insert('end', line)
return None
frequency = []
for a in range(dim):
f = pyutil.string_to_float(fields[a + 1])
if f == None:
self.unreadable.listbox.insert('end', line)
return None
frequency.append(f)
if len(fields) > dim + 1:
note = fields[dim + 1]
else:
note = ''
return (assignment, frequency, note)
def read_tolerances(self):
tolerances = {}
for e in self.tolerances:
atom_name = e.label['text']
tolerance = pyutil.string_to_float(e.variable.get(), 0)
tolerances[atom_name] = tolerance
tolerances['{CA CB }'] = min(tolerances['CA'], tolerances['CB'])
return tolerances
def get_settings(self):
match_tolerances = {}
for nucleus in ('1H', '13C', '15N'):
tol = pyutil.string_to_float(self.tolerances[nucleus].get(), 0)
match_tolerances[nucleus] = tol
max_unmatched = pyutil.string_to_int(self.max_unmatched.get(), 0)
return (match_tolerances, max_unmatched)
def spectrum_times(self):
st = []
for s, (b, e) in self.spectrum_widgets.items():
if b.variable.get():
ttext = e.variable.get()
t = pyutil.string_to_float(ttext)
st.append((s, t))
s.save_value('relaxation_time_parameter', ttext)
st.sort(self.spectrum_time_order)
return tuple(st)
def parse_mardi_line(line):
atom1 = string.strip(line[0:4])
n1 = pyutil.string_to_int(line[4:7])
atom2 = string.strip(line[8:12])
n2 = pyutil.string_to_int(line[12:15])
if n1 == None or n2 == None:
return None
bounds = string.split(line[15:])
if len(bounds) < 2:
return None
lower = pyutil.string_to_float(bounds[0])
upper = pyutil.string_to_float(bounds[1])
if lower == None or upper == None:
return None
return n1, atom1, n2, atom2, lower, upper
def set_resonance_shift(self, symbol, number, atom_name, sequence,
shift_text, rtable):
shift = pyutil.string_to_float(shift_text)
if shift == None:
return
r = sequence.resonance(number, symbol, atom_name)
if r == None:
return
rtable[r] = shift
def parse_mardi_line(line):
atom1 = string.strip(line[0:4])
n1 = pyutil.string_to_int(line[4:7])
atom2 = string.strip(line[8:12])
n2 = pyutil.string_to_int(line[12:15])
if n1 == None or n2 == None:
return None
bounds = string.split(line[15:])
if len(bounds) < 2:
return None
lower = pyutil.string_to_float(bounds[0])
upper = pyutil.string_to_float(bounds[1])
if lower == None or upper == None:
return None
return n1, atom1, n2, atom2, lower, upper
def show_settings(self, settings):
match_tolerances, max_unmatched = settings
for nucleus, tol in match_tolerances.items():
var = self.tolerances[nucleus]
cur_tol = pyutil.string_to_float(var.get(), 0)
new_tol = match_tolerances[nucleus]
if new_tol != cur_tol:
var.set('%.3g' % new_tol)
self.max_unmatched.set('%d' % max_unmatched)
def show_settings(self, settings):
stimes = {}
for s, t in settings['spectrum-times']:
stimes[s] = t
for s, (b, e) in self.spectrum_widgets.items():
b.variable.set(stimes.has_key(s))
if (stimes.has_key(s) and
pyutil.string_to_float(e.variable.get()) != stimes[s]):
e.variable.set('%.5g' % stimes[s])
self.trials.variable.set('%d' % settings['error-estimate-trials'])
def update_cb(self):
spectrum = self.spectrum_choice.spectrum()
if spectrum == None:
return
show_note = self.note.state()
bounds_text = self.bounds_text.variable.get()
hmin = pyutil.string_to_float(self.height_min.get())
hmax = pyutil.string_to_float(self.height_max.get())
vmin = pyutil.string_to_float(self.volume_min.get())
vmax = pyutil.string_to_float(self.volume_max.get())
exclude_note_words = string.split(self.exclude_note_words.variable.get())
exculde_note_words = filter(lambda w: len(w) > 0, exclude_note_words)
require_note_words = string.split(self.require_note_words.variable.get())
require_note_words = filter(lambda w: len(w) > 0, require_note_words)
peaks = sputil.sort_peaks_by_assignment(spectrum.peak_list(), self)
self.stoppable_call(self.show_peaks, peaks, show_note,
hmin, hmax, vmin, vmax,
exclude_note_words, require_note_words,
bounds_text)
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 show_settings(self, asys):
st = self.spectrum_table
s2cb = st.spectrum_to_checkbutton
for cb in s2cb.values():
cb.set_state(0)
if asys:
s2epm = st.spectrum_epeak_menus
s2aom = st.axis_order_menu
for asp in asys.assignable_spectra:
s = asp.spectrum
if s2cb.has_key(s):
s2cb[s].set_state(1)
if hasattr(asp, 'expected_peak_pattern_name'):
s2epm[s].set(asp.expected_peak_pattern_name)
if hasattr(asp, 'pattern_axis_order'):
s2aom[s].set_axis_order(asp.pattern_axis_order)
for axis in range(s.dimension):
var = self.tolerances[s.nuclei[axis]]
cur_tol = pyutil.string_to_float(var.get(), 0)
new_tol = asp.tolerances[axis]
if new_tol != cur_tol:
var.set('%.3g' % new_tol)
def show_settings(self, settings):
tsp_list = settings['type-spectrum-phase-list']
if tsp_list:
types = {}
for type, spectrum, phase in tsp_list:
if sparky.object_exists(spectrum):
self.type_to_spectrum_menu[type].set(spectrum.name)
self.type_to_phase[type].set(phase)
types[type] = 1
for type in self.type_to_spectrum_menu.keys():
if not types.has_key(type):
self.type_to_spectrum_menu[type].set('')
ttable = settings['tolerance-table']
for e in self.tolerances:
atom_name = e.label['text']
if ttable.has_key(atom_name):
new_tol = ttable[atom_name]
current_tol = pyutil.string_to_float(e.variable.get(), 0)
if new_tol != current_tol:
e.variable.set('%.3g' % new_tol)
self.temp_directory.set(settings['temp-directory'])
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_settings(self, asys):
st = self.spectrum_table
s2cb = st.spectrum_to_checkbutton
for cb in s2cb.values():
cb.set_state(0)
if asys:
s2epm = st.spectrum_epeak_menus
s2aom = st.axis_order_menu
for asp in asys.assignable_spectra:
s = asp.spectrum
if s2cb.has_key(s):
s2cb[s].set_state(1)
if hasattr(asp, 'expected_peak_pattern_name'):
s2epm[s].set(asp.expected_peak_pattern_name)
if hasattr(asp, 'pattern_axis_order'):
s2aom[s].set_axis_order(asp.pattern_axis_order)
for axis in range(s.dimension):
var = self.tolerances[s.nuclei[axis]]
cur_tol = pyutil.string_to_float(var.get(), 0)
new_tol = asp.tolerances[axis]
if new_tol != cur_tol:
var.set('%.3g' % new_tol)
def read_tolerances(self):
ttable = {}
for nucleus, tol in self.tolerances.items():
ttable[nucleus] = pyutil.string_to_float(tol.get(), 0)
return ttable
def read_tolerances(self):
ttable = {}
for nucleus, tol in self.tolerances.items():
ttable[nucleus] = pyutil.string_to_float(tol.get(), 0)
return ttable
def time_param(s, self=self): return pyutil.string_to_float(self.default_time_parameter(s), 0)