def spectrum_names(self):
spectra = self.session.project.spectrum_list()
names = pyutil.attribute_values(spectra, 'name')
if self.allow_no_choice:
names = ('', ) + names
return names
def spectrum_names(self):
spectra = self.session.project.spectrum_list()
names = pyutil.attribute_values(spectra, 'name')
if self.allow_no_choice:
names = ('',) + names
return names
def set_volume_error(self, peak):
if peak.volume == None or peak.volume_error_method == 'manual':
return
method = peak.volume_method
settings = self.settings
e = 0
if settings.fit_default_error:
if method == 'gaussian' or method == 'lorentzian':
e = e + settings.fit_default_error
elif method == 'peak-group':
methods = pyutil.attribute_values(peak.peaklets(), 'volume_method')
if 'gaussian' in methods or 'lorentzian' in methods:
e = e + settings.fit_default_error
if settings.box_default_error:
if method == 'box' or method == 'ellipse':
e = e + settings.box_default_error
elif method == 'peak-group':
methods = pyutil.attribute_values(peak.peaklets(), 'volume_method')
if 'box' in methods or 'ellipse' in methods:
e = e + settings.box_default_error
if settings.near_diagonal_error and settings.near_diagonal_range:
f = peak.frequency
if abs(f[0] - f[1]) <= settings.near_diagonal_range:
e = e + settings.near_diagonal_error
if settings.nearby_peaks:
vol = peak.volume
for p in settings.nearby_peaks[peak]:
pvol = p.volume
if pvol == None:
e = e + settings.nearby_error['unintegrated']
elif pvol < .5 * vol:
e = e + settings.nearby_error['< .5']
elif pvol < 2 * vol:
e = e + settings.nearby_error['.5 - 2']
else:
e = e + settings.nearby_error['> 2']
if e > 0:
peak.volume_error = e / 100.0
peak.volume_error_method = 'auto'
def spectrum_names(self):
Names = []
spectra = self.session.project.spectrum_list()
for spectrum in spectra:
if spectrum.dimension == 2:
Names.append(spectrum)
names = pyutil.attribute_values(Names, 'name')
if self.allow_no_choice:
names = ('',) + names
return names
def sort_alternative_assignments(self, peak, alist):
dim = peak.spectrum.dimension
pfreq = peak.frequency
scale = self.settings.ppm_range
offsets = {}
for assignment in alist:
afreq = pyutil.attribute_values(assignment, 'frequency')
offset2 = 0
for k in range(dim):
diff = afreq[k] - pfreq[k]
if scale[k] != 0:
w = diff / scale[k]
offset2 = offset2 + w*w
offsets[assignment] = offset2
return pyutil.sort_keys_by_value(offsets)
def sort_alternative_assignments(self, peak, alist):
dim = peak.spectrum.dimension
pfreq = peak.frequency
scale = self.settings.ppm_range
offsets = {}
for assignment in alist:
afreq = pyutil.attribute_values(assignment, 'frequency')
offset2 = 0
for k in range(dim):
diff = afreq[k] - pfreq[k]
if scale[k] != 0:
w = diff / scale[k]
offset2 = offset2 + w * w
offsets[assignment] = offset2
return pyutil.sort_keys_by_value(offsets)
def update_graph_atoms(self):
sgd = self.spin_graph()
if sgd == None:
return
sgd.show_window(1)
asys = self.assignments.assignment_system
if asys.sequence == None:
return
galist = pyutil.attribute_values(asys.assignable_resonances, 'group_atom')
if galist != self.shown_group_atoms:
self.shown_group_atoms = galist
self.progress_report('Showing spin graph atoms')
groups_per_row = asys.sequence.last_residue_number + 1
sgd.set_graph(galist, groups_per_row, 0, None)
sgd.graph.update_what_to_show(show_line_label = 0,
lines_to_groups = 0,
shade_by_range = 0)
sgd.graph.show_atoms(1)
sgd.graph.full_view('y')
def update_graph_atoms(self):
sgd = self.spin_graph()
if sgd == None:
return
sgd.show_window(1)
asys = self.assignments.assignment_system
if asys.sequence == None:
return
galist = pyutil.attribute_values(asys.assignable_resonances,
'group_atom')
if galist != self.shown_group_atoms:
self.shown_group_atoms = galist
self.progress_report('Showing spin graph atoms')
groups_per_row = asys.sequence.last_residue_number + 1
sgd.set_graph(galist, groups_per_row, 0, None)
sgd.graph.update_what_to_show(show_line_label=0,
lines_to_groups=0,
shade_by_range=0)
sgd.graph.show_atoms(1)
sgd.graph.full_view('y')
def view_names(self):
views = self.session.project.view_list()
return pyutil.attribute_values(views, 'name')
def assignment_position(assignment, spectrum): freq = pyutil.attribute_values(assignment, 'frequency') return alias_onto_spectrum(freq, spectrum)
def view_names(self):
views = self.session.project.view_list()
return pyutil.attribute_values(views, 'name')
def assignment_position(assignment, spectrum):
freq = pyutil.attribute_values(assignment, 'frequency')
return alias_onto_spectrum(freq, spectrum)