def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
self.par['ppm_to_rads_h'] = TWO_PI * self.par['h_larmor_frq']
self.par['ppm_to_rads'] = TWO_PI * self.par['h_larmor_frq'] * RATIO_N
temperature = self.par['temperature']
h_larmor_frq = self.par['h_larmor_frq']
resonance_id = self.par['resonance_id']
experiment_name = self.par['experiment_name']
assignment = parsing.parse_assignment(resonance_id)
index_1, residue_type_1, nucleus_type_1 = assignment[0]
index_2, residue_type_2, nucleus_type_2 = assignment[1]
nucleus_name_1 = residue_type_1 + str(index_1) + nucleus_type_1
nucleus_name_2 = residue_type_2 + str(index_2) + nucleus_type_2
nuclei_name = parsing.assignment_name(assignment)
self.par['_id'] = tuple((temperature, nucleus_name_2, h_larmor_frq))
args = (
self.par[arg]
for arg in getargspec(make_calc_observable.__wrapped__).args
)
self.calc_observable = make_calc_observable(*args)
self.short_long_par_names = (
('i0', ('i0', resonance_id, experiment_name)),
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw_h', ('dw', nucleus_name_2)),
('dw_n', ('dw', nucleus_name_1)),
('cs_h', ('cs', nucleus_name_2)),
('cs_n', ('cs', nucleus_name_1)),
('r_nxy', ('r_nxy', nucleus_name_1, h_larmor_frq, temperature)),
('dr_nxy', ('dr_nxy', nucleus_name_1, h_larmor_frq, temperature)),
('r_nz', ('r_nz', nucleus_name_1, h_larmor_frq, temperature)),
('r_hxy', ('r_hxy', nucleus_name_2, h_larmor_frq, temperature)),
('r_hz', ('r_hz', nucleus_name_2, h_larmor_frq, temperature)),
('r_2hznz', ('r_2hznz', nuclei_name, h_larmor_frq, temperature)),
(
'r_2hxynxy', ('r_2hxynxy', nuclei_name, h_larmor_frq, temperature)),
('etaxy', ('etaxy', nuclei_name, h_larmor_frq, temperature)),
('etaz', ('etaz', nuclei_name, h_larmor_frq, temperature)),
('j_hn', ('j_hn', nuclei_name, temperature)),
)
self.fitting_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit']
)
self.fixed_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix']
)
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
self.par['ppm_to_rads'] = TWO_PI * self.par['h_larmor_frq'] * RATIO_N
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
h_larmor_frq = self.par['h_larmor_frq']
experiment_name = self.par['experiment_name']
assignment = parse_assignment(resonance_id)
index_1, residue_type_1, nucleus_type_1 = assignment[0]
index_2, residue_type_2, nucleus_type_2 = assignment[1]
nucleus_name_1 = residue_type_1 + str(index_1) + nucleus_type_1
nucleus_name_2 = residue_type_2 + str(index_2) + nucleus_type_2
self.par['_id'] = tuple((temperature, nucleus_name_1, h_larmor_frq))
args = (self.par[arg]
for arg in getargspec(make_calc_observable.__wrapped__).args)
self.calc_observable = make_calc_observable(*args)
self.kwargs_default = {'ncyc': self.par['ncyc']}
self.short_long_par_names = (
('pb', ('pb', temperature)),
('pc', ('pc', temperature)),
('kex_ab', ('kex_ab', temperature)),
('kex_bc', ('kex_bc', temperature)),
('kex_ac', ('kex_ac', temperature)),
('dw_ab', ('dw_ab', nucleus_name_1)),
('dw_ac', ('dw_ac', nucleus_name_1)),
('cs', ('cs', nucleus_name_1, temperature)),
('i0', ('i0', resonance_id, experiment_name)),
('r_nxy', ('r_nxy', nucleus_name_1, h_larmor_frq, temperature)),
('dr_nxy_ab', ('dr_nxy_ab', nucleus_name_1, h_larmor_frq,
temperature)),
('dr_nxy_ac', ('dr_nxy_ac', nucleus_name_1, h_larmor_frq,
temperature)),
('r_nz', ('r_nz', nucleus_name_1, h_larmor_frq, temperature)),
('r_2hznz', ('r_2hznz', nucleus_name_1, nucleus_name_2,
h_larmor_frq, temperature)),
('etaxy', ('etaxy', nucleus_name_1, h_larmor_frq, temperature)),
('etaz', ('etaz', nucleus_name_1, h_larmor_frq, temperature)),
('j_hn', ('j_hn', nucleus_name_1, nucleus_name_2, temperature)),
('dj_hn_ab', ('dj_hn_ab', nucleus_name_1, nucleus_name_2,
temperature)),
('dj_hn_ac', ('dj_hn_ac', nucleus_name_1, nucleus_name_2,
temperature)),
)
self.fitting_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit'])
self.fixed_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix'])
def read_parameter_file(filename, par_name):
"""
Reads a file containing values associated with a nucleus name.
The file should be formatted like sparky peak lists.
For example:
* To set G23N to 105.0 and G23H to 8.0:
G23N-H 105.0 8.0
* To set a parameter depending on multiple nuclei, eg. G23N and G23H, to 1.0:
G23N-H -93.0
"""
try:
raw_data = sp.genfromtxt(filename, dtype=None)
except IOError:
exit('The file \'{}\' is empty or does not exist!\n'.format(filename))
# Hack to solve the problem of 0d-array when 'filename' is a single line
# file
if raw_data.ndim == 0:
raw_data = sp.array([
raw_data,
])
parameters = []
for line in raw_data:
if line[0] in ['Assignment', '?-?']:
continue
assignment = parsing.parse_assignment(line[0])
if len(assignment) == len(line) - 1:
for index, an_assignment in enumerate(assignment, 1):
name = parsing.assignment_name([an_assignment])
full_par_name = par_name + [name]
parameters.append((full_par_name, line[index]))
elif len(line) == 2:
name = parsing.assignment_name(assignment)
full_par_name = par_name + [name]
parameters.append((full_par_name, line[1]))
else:
error_message = '\n'.join([
"Problem reading the parameter file '{}'.".format(filename),
"The number of columns does not match to the number of nuclei"
" contained in the assignment:"
])
exit(error_message)
return parameters
def read_parameter_file(filename, par_name):
"""
Reads a file containing values associated with a nucleus name.
The file should be formatted like sparky peak lists.
For example:
* To set G23N to 105.0 and G23H to 8.0:
G23N-H 105.0 8.0
* To set a parameter depending on multiple nuclei, eg. G23N and G23H, to 1.0:
G23N-H -93.0
"""
try:
raw_data = sp.genfromtxt(filename, dtype=None)
except IOError:
exit('The file \'{}\' is empty or does not exist!\n'.format(filename))
# Hack to solve the problem of 0d-array when 'filename' is a single line
# file
if raw_data.ndim == 0:
raw_data = sp.array([raw_data, ])
parameters = []
for line in raw_data:
if line[0] in ['Assignment', '?-?']:
continue
assignment = parsing.parse_assignment(line[0])
if len(assignment) == len(line) - 1:
for index, an_assignment in enumerate(assignment, 1):
name = parsing.assignment_name([an_assignment])
full_par_name = par_name + [name]
parameters.append((full_par_name, line[index]))
elif len(line) == 2:
name = parsing.assignment_name(assignment)
full_par_name = par_name + [name]
parameters.append((full_par_name, line[1]))
else:
error_message = '\n'.join(
["Problem reading the parameter file '{}'.".format(filename),
"The number of columns does not match to the number of nuclei"
" contained in the assignment:"])
exit(error_message)
return parameters
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
h_larmor_frq = self.par['h_larmor_frq']
experiment_name = self.par['experiment_name']
index, residue_type, nucleus_type = parse_assignment(resonance_id)[0]
nucleus_name = ''.join([residue_type, str(index), nucleus_type])
try:
self.par['ppm_to_rads'] = (
2.0 * pi * self.par['h_larmor_frq'] * xi_ratio[
nucleus_type[0].upper()]
)
except KeyError:
exit(
"Unknown nucleus type \"{}\" for peak \"{}\" in experiment "
"\"{}\""
.format(nucleus_type, resonance_id, experiment_name)
)
self.par['_id'] = ((temperature, nucleus_name, h_larmor_frq),)
args = (self.par[arg] for arg in
getargspec(make_calc_observable.__wrapped__).args)
self.calc_observable = make_calc_observable(*args)
self.kwargs_default = {'ncyc': self.par['ncyc']}
self.short_long_par_names = (
('i0', ('i0', resonance_id, experiment_name)),
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw', ('dw', nucleus_name)),
('r_ixy', ('r_ixy', nucleus_name, h_larmor_frq, temperature)),
('dr_ixy', ('dr_ixy', nucleus_name, h_larmor_frq, temperature)),
)
self.fitting_parameter_names.update(long_name
for short_name, long_name in
self.short_long_par_names
if short_name in PAR_DICT['fit'])
self.fixed_parameter_names.update(long_name
for short_name, long_name in
self.short_long_par_names
if short_name in PAR_DICT['fix'])
def group_data(data):
"""Groups the data resonance specifically"""
data_grouped = dict()
for data_pt in data:
resonance_id = data_pt.par['resonance_id']
assignment = parse_assignment(resonance_id)
index = int(assignment[0][0])
data_grouped.setdefault((index, resonance_id), []).append(data_pt)
return data_grouped
def group_data(dataset):
"""Groups the data resonance specifically"""
data_grouped = dict()
for data_pt in dataset:
id_ = data_pt.par['resonance_id']
assignment = parse_assignment(id_)
index = int(assignment[0][0])
data_grouped.setdefault((index, id_), []).append(data_pt)
return data_grouped
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'], plot_data)
self.par['ppm_to_rads'] = TWO_PI * self.par['h_larmor_frq'] * RATIO_C
self.kwargs_default = dict()
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
h_larmor_frq = self.par['h_larmor_frq']
experiment_name = self.par['experiment_name']
assignment = parse_assignment(resonance_id)
index, residue_type, nucleus_type = assignment[0]
nucleus_name = ''.join([residue_type, str(index), nucleus_type])
couplings = J_COUPLINGS[residue_type][nucleus_type]
self.par['multiplet'] = calc_multiplet(couplings)
self.par['_id'] = tuple((temperature, nucleus_name, h_larmor_frq))
args = (self.par[arg] for arg in getargspec(make_calc_observable.__wrapped__).args)
self.calc_observable = make_calc_observable(*args)
self.short_long_par_names = (
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw', ('dw', nucleus_name)),
('cs', ('cs', nucleus_name, temperature)),
('i0', ('i0', resonance_id, experiment_name)),
('r_cxy', ('r_cxy', nucleus_name, h_larmor_frq, temperature)),
('dr_cxy', ('dr_cxy', nucleus_name, h_larmor_frq, temperature)),
('r_cz', ('r_cz', nucleus_name, h_larmor_frq, temperature)),
)
self.fitting_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit']
)
self.fixed_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix']
)
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
self.par['ppm_to_rads'] = TWO_PI * self.par['h_larmor_frq'] * RATIO_C
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
h_larmor_frq = self.par['h_larmor_frq']
experiment_name = self.par['experiment_name']
assignment = parse_assignment(resonance_id)
index, residue_type, nucleus_type = assignment[0]
nucleus_name = ''.join([residue_type, str(index), nucleus_type])
self.par['_id'] = tuple((temperature, nucleus_name, h_larmor_frq))
args = (self.par[arg] for arg in
getargspec(make_calc_observable.__wrapped__).args)
self.calc_observable = make_calc_observable(*args)
self.kwargs_default = {'ncyc': self.par['ncyc']}
self.short_long_par_names = (
('i0', ('i0', resonance_id, experiment_name)),
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw', ('dw', nucleus_name)),
('cs', ('cs', nucleus_name, temperature)),
('r_cxy', ('r_cxy', nucleus_name, h_larmor_frq, temperature)),
('dr_cxy', ('dr_cxy', nucleus_name, h_larmor_frq, temperature)),
('r_cz', ('r_cz', nucleus_name, h_larmor_frq, temperature)),
)
self.fitting_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit']
)
self.fixed_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix']
)
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
h_larmor_frq = self.par['h_larmor_frq']
experiment_name = self.par['experiment_name']
index, residue_type, nucleus_type = parse_assignment(resonance_id)[0]
nucleus_name = ''.join([residue_type, str(index), nucleus_type])
try:
self.par['ppm_to_rads'] = (2.0 * pi * self.par['h_larmor_frq'] *
xi_ratio[nucleus_type[0].upper()])
except KeyError:
exit("Unknown nucleus type \"{}\" for peak \"{}\" in experiment "
"\"{}\"".format(nucleus_type, resonance_id, experiment_name))
self.par['_id'] = ((temperature, nucleus_name, h_larmor_frq), )
args = (self.par[arg]
for arg in getargspec(make_calc_observable.__wrapped__).args)
self.calc_observable = make_calc_observable(*args)
self.kwargs_default = {'ncyc': self.par['ncyc']}
self.short_long_par_names = (
('i0', ('i0', resonance_id, experiment_name)),
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw', ('dw', nucleus_name)),
('r_ixy', ('r_ixy', nucleus_name, h_larmor_frq, temperature)),
('dr_ixy', ('dr_ixy', nucleus_name, h_larmor_frq, temperature)),
)
self.fitting_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit'])
self.fixed_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix'])
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
self.par['ppm_to_rads_h'] = TWO_PI * self.par['h_larmor_frq']
self.par['ppm_to_rads_n'] = TWO_PI * self.par['h_larmor_frq'] * RATIO
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
assignment = parse_assignment(resonance_id)
index_1, residue_type_1, nucleus_type_1 = assignment[0]
index_2, residue_type_2, nucleus_type_2 = assignment[1]
nucleus_name_1 = residue_type_1 + str(index_1) + nucleus_type_1
nucleus_name_2 = residue_type_2 + str(index_2) + nucleus_type_2
self.calc_observable = calc_observable
self.kwargs_default = {
'ppm_to_rads_h': self.par['ppm_to_rads_h'],
'ppm_to_rads_n': self.par['ppm_to_rads_n'],
}
self.short_long_par_names = (
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw_n', ('dw', nucleus_name_1)),
('dw_h', ('dw', nucleus_name_2)),
)
self.fitting_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit']
)
self.fixed_parameter_names.update(
long_name
for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix']
)
def __init__(self, val, err, par):
BaseDataPoint.__init__(self, val, err, par, PAR_DICT['par_conv'],
plot_data)
self.par['ppm_to_rads_h'] = TWO_PI * self.par['h_larmor_frq']
self.par['ppm_to_rads_n'] = TWO_PI * self.par['h_larmor_frq'] * RATIO
temperature = self.par['temperature']
resonance_id = self.par['resonance_id']
assignment = parse_assignment(resonance_id)
index_1, residue_type_1, nucleus_type_1 = assignment[0]
index_2, residue_type_2, nucleus_type_2 = assignment[1]
nucleus_name_1 = residue_type_1 + str(index_1) + nucleus_type_1
nucleus_name_2 = residue_type_2 + str(index_2) + nucleus_type_2
self.calc_observable = calc_observable
self.kwargs_default = {
'ppm_to_rads_h': self.par['ppm_to_rads_h'],
'ppm_to_rads_n': self.par['ppm_to_rads_n'],
}
self.short_long_par_names = (
('pb', ('pb', temperature)),
('kex', ('kex', temperature)),
('dw_n', ('dw', nucleus_name_1)),
('dw_h', ('dw', nucleus_name_2)),
)
self.fitting_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fit'])
self.fixed_parameter_names.update(
long_name for short_name, long_name in self.short_long_par_names
if short_name in PAR_DICT['fix'])