def pair_crossdiagonal_peaks(peaks, stoppable):
assignment_to_peak = {}
stoppable.stoppable_loop('finding crossdiagonal peaks', 200)
for peak in peaks:
stoppable.check_for_stop()
r = noesy.proton_resonances(peak)
assignment_to_peak[(r, peak.spectrum)] = peak
plist = []
peak_used = {}
stoppable.stoppable_loop('sorting crossdiagonal peaks', 200)
for peak in peaks:
stoppable.check_for_stop()
if not peak_used.has_key(peak):
plist.append(peak)
peak_used[peak] = 1
r = noesy.proton_resonances(peak)
if r:
tr = (r[1], r[0])
if assignment_to_peak.has_key((tr, peak.spectrum)):
tpeak = assignment_to_peak[(tr, peak.spectrum)]
if not peak_used.has_key(tpeak):
plist.append(tpeak)
peak_used[tpeak] = 1
return plist
def pair_crossdiagonal_peaks(peaks, stoppable):
assignment_to_peak = {}
stoppable.stoppable_loop('finding crossdiagonal peaks', 200)
for peak in peaks:
stoppable.check_for_stop()
r = noesy.proton_resonances(peak)
assignment_to_peak[(r, peak.spectrum)] = peak
plist = []
peak_used = {}
stoppable.stoppable_loop('sorting crossdiagonal peaks', 200)
for peak in peaks:
stoppable.check_for_stop()
if not peak_used.has_key(peak):
plist.append(peak)
peak_used[peak] = 1
r = noesy.proton_resonances(peak)
if r:
tr = (r[1], r[0])
if assignment_to_peak.has_key((tr, peak.spectrum)):
tpeak = assignment_to_peak[(tr, peak.spectrum)]
if not peak_used.has_key(tpeak):
plist.append(tpeak)
peak_used[tpeak] = 1
return plist
def distance_bounds(self, peak):
if peak.is_assigned:
res = noesy.proton_resonances(peak)
translate = self.atom_translations
return self.bounds(translate.resonance_number_atom(res[0]),
translate.resonance_number_atom(res[1]))
return None
def predicted_intensity(self, peak):
if peak.is_assigned:
res = noesy.proton_resonances(peak)
translate = self.atom_translations
return self.intensity(translate.resonance_number_atom(res[0]),
translate.resonance_number_atom(res[1]))
return None
def distance_bounds(self, peak):
if peak.is_assigned:
res = noesy.proton_resonances(peak)
translate = self.atom_translations
return self.bounds(translate.resonance_number_atom(res[0]),
translate.resonance_number_atom(res[1]))
return None
def predicted_intensity(self, peak):
if peak.is_assigned:
res = noesy.proton_resonances(peak)
translate = self.atom_translations
return self.intensity(translate.resonance_number_atom(res[0]),
translate.resonance_number_atom(res[1]))
return None
def noesy_distance(self, peak):
if peak.is_assigned:
res = noesy.proton_resonances(peak)
if res != None and len(res) == 2:
mol = peak.spectrum.molecule
return self.minimum_distance(res[0].atom, res[1].atom, mol)
return None
def assignment(self, peak):
if peak.is_assigned:
if self.noesy:
res = noesy.proton_resonances(peak)
else:
res = peak.resonances()
return sputil.group_atom_assignment(res)
return None
def assignment(self, peak):
if peak.is_assigned:
if self.noesy:
res = noesy.proton_resonances(peak)
else:
res = peak.resonances()
return sputil.group_atom_assignment(res)
return None
def peak_line(self, peak, bounds_text):
r1, r2 = noesy.proton_resonances(peak)
if r1 == None or r2 == None:
return None
if r1.group.number == None or r2.group.number == None:
return None
line = ('assign (residue %d and name %s) (residue %d and name %s) %s'
% (r1.group.number, r1.atom.name,
r2.group.number, r2.atom.name,
bounds_text))
return line
def peak_line(self, peak, show_note):
r1, r2 = noesy.proton_resonances(peak)
if r1 == None or r2 == None:
return ''
if r1.group.number == None or r2.group.number == None:
return ''
volume = peak.volume
if volume == None:
volume = 0
line = "%-4.4s%3d %-4.4s%3d %11.4e" % (r1.atom.name, r1.group.number,
r2.atom.name, r2.group.number,
volume)
if show_note and peak.note:
line = line + ' # ' + peak.note
return line
def peak_line(self, peak, show_note):
r1, r2 = noesy.proton_resonances(peak)
if r1 == None or r2 == None:
return ''
if r1.group.number == None or r2.group.number == None:
return ''
volume = peak.volume
if volume == None:
volume = 0
line = "%-4.4s%3d %-4.4s%3d %11.4e" % (r1.atom.name, r1.group.number,
r2.atom.name, r2.group.number,
volume)
if show_note and peak.note:
line = line + ' # ' + peak.note
return line