def place_peaks(self, spectrum):
hc_axes = pyutil.order(('1H', '13C'), spectrum.nuclei)
if spectrum.dimension != 2 or hc_axes == None:
self.progress_report('Spectrum must 2D with H and C axes.')
return
molecule = spectrum.molecule
condition = spectrum.condition
self.stoppable_loop('resonances', 50)
for rH in condition.resonance_list():
self.check_for_stop()
if rH.atom.nucleus == '1H':
catom = atoms.attached_heavy_atom(rH.atom, molecule)
if catom and catom.nucleus == '13C':
rC = condition.find_resonance(catom)
if rC:
assignment = pyutil.permute((rH, rC), hc_axes)
if not spectrum.find_peak(assignment):
freq = pyutil.permute((rH.frequency, rC.frequency), hc_axes)
pos = sputil.alias_onto_spectrum(freq, spectrum)
peak = spectrum.place_peak(pos)
peak.assign(hc_axes[0], rH.group.name, rH.atom.name)
peak.assign(hc_axes[1], rC.group.name, rC.atom.name)
if freq != pos:
peak.alias = pyutil.subtract_tuples(freq, pos)
peak.show_assignment_label()
def mirror_assignment(assignment, spectrum, c13_spectrum, n15_spectrum):
aH, aCN, aH2 = noesy.noesy_hsqc_axes(spectrum)
labelled_proton = assignment[aH].atom
unlabelled_proton = assignment[aH2].atom
mol = spectrum.molecule
other_heavy_atom = atoms.attached_heavy_atom(unlabelled_proton, mol)
if other_heavy_atom == None:
hname = atoms.attached_heavy_atom_name(unlabelled_proton, mol)
if hname == None:
raise AttachedAtomUnknown, unlabelled_proton
else:
raise AtomUnknown, (unlabelled_proton.group.name, hname)
nucleus = other_heavy_atom.nucleus
if nucleus == '13C':
mirror_spectrum = c13_spectrum
elif nucleus == '15N':
mirror_spectrum = n15_spectrum
else:
raise NoHeavyAtomSpectrum, other_heavy_atom
a = noesy.noesy_hsqc_assignment(mirror_spectrum, unlabelled_proton,
labelled_proton, other_heavy_atom)
if a == None:
raise AtomUnassigned, other_heavy_atom
return (a, mirror_spectrum)
def nearby_noesy_hsqc_assignments(spectrum, position, ppm_range):
res_lists = nearby_resonances(spectrum, position, ppm_range)
aH, aCN, aH2 = noesy_hsqc_axes(spectrum)
rH = res_lists[aH]
rCN = res_lists[aCN]
rH2 = res_lists[aH2]
rHCN = []
m = spectrum.molecule
c = spectrum.condition
for r in rH:
cnatom = atoms.attached_heavy_atom(r.atom, m)
if cnatom != None:
rheavy = c.find_resonance(cnatom)
if rheavy != None and rheavy in rCN:
rHCN.append((r, rheavy))
alist = []
for rh, rcn in rHCN:
for rh2 in rH2:
a = [None, None, None]
a[aH] = rh
a[aCN] = rcn
a[aH2] = rh2
alist.append(tuple(a))
return tuple(alist)
def atom_pairs_to_hsqc_assignments(spectrum, atom_pairs):
heavy_nucleus = spectrum.nuclei[spectrum.heavy_atom_axis]
alist = []
for h, h2 in atom_pairs:
cn = atoms.attached_heavy_atom(h, spectrum.molecule)
if cn and cn.nucleus == heavy_nucleus:
assignment = noesy_hsqc_assignment(spectrum, h, h2, cn)
if assignment:
alist.append(assignment)
return tuple(alist)
def identify_hsqc_axes(spectrum):
mol = spectrum.molecule
a1, a2 = axes.proton_axes(spectrum)
aCN = axes.heavy_atom_axes(spectrum)[0]
for p in spectrum.peak_list():
if p.is_assigned:
res = p.resonances()
h1 = atoms.attached_heavy_atom(res[a1].atom, mol)
h2 = atoms.attached_heavy_atom(res[a2].atom, mol)
if h1 and h2 and h1 != h2:
if h1 == res[aCN].atom:
set_noesy_hsqc_axes(spectrum, a1, aCN, a2)
return
elif h2 == res[aCN].atom:
set_noesy_hsqc_axes(spectrum, a2, aCN, a1)
return
aH = axes.attached_proton_axis(spectrum, aCN)
if aH == None:
aH = 2
aH2 = axes.second_nucleus_axis(spectrum, '1H', aH)
set_noesy_hsqc_axes(spectrum, aH, aCN, aH2)
def extend_noesy_assignment(spectrum, hres):
if hres and spectrum.dimension == 3:
heavy = atoms.attached_heavy_atom(hres[0].atom, spectrum.molecule)
if heavy == None:
return None
aH, aCN, aH2 = noesy_hsqc_axes(spectrum)
if heavy.nucleus == spectrum.nuclei[aCN]:
return noesy_hsqc_assignment(spectrum, hres[0].atom, hres[1].atom,
heavy)
else:
return None
return hres