def read_range(self):
condition = self.condition_menu.condition()
residue_range = (pyutil.string_to_int(self.range_variables[0].get()),
pyutil.string_to_int(self.range_variables[1].get()))
if residue_range[0] == None or residue_range[1] == None:
self.progress_report('Must select residue range.')
return 0
reslist = self.range_resonances(condition, residue_range)
if len(reslist) == 0:
self.progress_report('No residues in selected range.')
return 0
seq = sequence.molecule_sequence(condition.molecule)
if seq == None:
self.progress_report('Molecule sequence unknown.')
return 0
self.residue_range = residue_range
self.resonances = reslist
self.sequence = seq
return 1
def start_session(self, write_peak_lists = 1,
start_server = 1, start_client = 1):
if self.tsp_list == None:
return None
session = autoassign_session(self.tsp_list, self.tolerances,
self.progress_report, self.sparky_session)
if write_peak_lists:
self.progress_report('Writing peak lists')
session.write_autoassign_input_files(self.tolerances,
self.temp_directory)
server_port = pyutil.string_to_int(self.server_port, default_server_port)
if start_server:
self.progress_report('Running AutoAssign server')
server_lag = pyutil.string_to_int(self.server_lag, 0)
session.start_server(self.server_host, server_port,
self.server_executable, server_lag)
if start_client:
self.progress_report('Running AutoAssign client')
session.start_client(self.client_executable, self.server_host,
server_port)
table_path = os.path.join(self.temp_directory, 'table.aat')
init_script = 'Execute (Initialize, %s)\n' % table_path
output = session.run_script(init_script)
self.show_output(output)
self.progress_report('')
return session
def read_range(self):
condition = self.condition_menu.condition()
residue_range = (pyutil.string_to_int(self.range_variables[0].get()),
pyutil.string_to_int(self.range_variables[1].get()))
if residue_range[0] == None or residue_range[1] == None:
self.progress_report('Must select residue range.')
return 0
reslist = self.range_resonances(condition, residue_range)
if len(reslist) == 0:
self.progress_report('No residues in selected range.')
return 0
seq = sequence.molecule_sequence(condition.molecule)
if seq == None:
self.progress_report('Molecule sequence unknown.')
return 0
self.residue_range = residue_range
self.resonances = reslist
self.sequence = seq
# Compute global ncIDP-based random coil chemical shifts
self.RC_prediction = shiftstats_ncIDP.resonance_statistics(reslist)
return 1
def read_range(self):
condition = self.condition_menu.condition()
residue_range = (pyutil.string_to_int(self.range_variables[0].get()),
pyutil.string_to_int(self.range_variables[1].get()))
if residue_range[0] == None or residue_range[1] == None:
self.progress_report('Must select residue range.')
return 0
reslist = self.range_resonances(condition, residue_range)
if len(reslist) == 0:
self.progress_report('No residues in selected range.')
return 0
seq = sequence.molecule_sequence(condition.molecule)
if seq == None:
self.progress_report('Molecule sequence unknown.')
return 0
self.residue_range = residue_range
self.resonances = reslist
self.sequence = seq
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 has_attached_proton_axis(spectrum, heavy_axis):
key = 'w%d_attached_proton_axis' % (heavy_axis + 1)
a = spectrum.saved_value(key)
if a:
a = pyutil.string_to_int(a)
return a
def chosen_axis(self):
axis_text = self.get()
if len(axis_text) >= 2:
anum = pyutil.string_to_int(axis_text[1])
if anum != None:
axis = anum - 1
return axis
return None
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 has_molecule_sequence(molecule):
if not hasattr(molecule, 'sequence'):
s = molecule.saved_value('sequence')
f = molecule.saved_value('first_residue_number')
if s == None or f == None:
molecule.sequence = None
else:
f = pyutil.string_to_int(f)
molecule.sequence = sequence(s, f)
return molecule.sequence
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 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 read_sequence(self):
path = self.file_field.get()
if path:
seqfile = open(path, 'r')
seq = seqfile.read()
seqfile.close()
self.sequence_text.text.delete('0.0', 'end')
self.sequence_text.text.insert('0.0', seq)
aa_sequence = self.sequence_text.text.get('0.0', 'end')
first_residue_number = pyutil.string_to_int(self.first_residue.variable.get(), 1)
s = sequence(aa_sequence, first_residue_number)
return s
def get_settings(self):
swidth = pyutil.string_to_int(self.strip_width.get(), 52)
sgap = pyutil.string_to_int(self.strip_gap.get(), 8)
return (swidth, sgap)
def get_settings(self):
trials = pyutil.string_to_int(self.trials.variable.get(), 0)
settings = {'spectrum-times': self.spectrum_times(),
'error-estimate-trials': trials}
return settings