def read_spins(file=None, dir=None, dim=1, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak intensities.
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword dim: The dimension of the peak list to associate the data with.
@type dim: int
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# Data checks.
check_pipe()
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Read the peak list data.
peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
# Loop over the peak_list.
created_spins = []
for assign in peak_list:
mol_name = assign.mol_names[dim-1]
res_num = assign.res_nums[dim-1]
res_name = assign.res_names[dim-1]
spin_num = assign.spin_nums[dim-1]
spin_name = assign.spin_names[dim-1]
# Generate the spin_id.
spin_id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_name=spin_name)
# Check if the spin already exist.
if return_spin(spin_id=spin_id) == None:
# Create the spin if not exist.
create_spin(spin_num=spin_num, spin_name=spin_name, res_num=res_num, res_name=res_name, mol_name=mol_name)
# Test that data exists.
check_mol_res_spin_data()
def read_spins(file=None,
dir=None,
dim=1,
spin_id_col=None,
mol_name_col=None,
res_num_col=None,
res_name_col=None,
spin_num_col=None,
spin_name_col=None,
sep=None,
spin_id=None,
verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak intensities.
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword dim: The dimension of the peak list to associate the data with.
@type dim: int
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# Data checks.
check_pipe()
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Read the peak list data.
peak_list = read_peak_list(file=file,
dir=dir,
spin_id_col=spin_id_col,
mol_name_col=mol_name_col,
res_num_col=res_num_col,
res_name_col=res_name_col,
spin_num_col=spin_num_col,
spin_name_col=spin_name_col,
sep=sep,
spin_id=spin_id)
# Loop over the peak_list.
created_spins = []
for assign in peak_list:
mol_name = assign.mol_names[dim - 1]
res_num = assign.res_nums[dim - 1]
res_name = assign.res_names[dim - 1]
spin_num = assign.spin_nums[dim - 1]
spin_name = assign.spin_names[dim - 1]
# Generate the spin_id.
spin_id = generate_spin_id_unique(mol_name=mol_name,
res_num=res_num,
res_name=res_name,
spin_name=spin_name)
# Check if the spin already exist.
if return_spin(spin_id=spin_id) == None:
# Create the spin if not exist.
create_spin(spin_num=spin_num,
spin_name=spin_name,
res_num=res_num,
res_name=res_name,
mol_name=mol_name)
# Test that data exists.
check_mol_res_spin_data()
def read(file=None,
dir=None,
spectrum_id=None,
dim=1,
int_col=None,
int_method=None,
spin_id_col=None,
mol_name_col=None,
res_num_col=None,
res_name_col=None,
spin_num_col=None,
spin_name_col=None,
sep=None,
spin_id=None,
ncproc=None,
verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file(s) containing the peak intensities.
@type file: str or list of str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword spectrum_id: The spectrum identification string.
@type spectrum_id: str or list of str
@keyword dim: The dimension of the peak list to associate the data with.
@type dim: int
@keyword int_col: The column containing the peak intensity data (used by the generic intensity file format).
@type int_col: int or list of int
@keyword int_method: The integration method, one of 'height', 'point sum' or 'other'.
@type int_method: str
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword ncproc: The Bruker ncproc binary intensity scaling factor.
@type ncproc: int or None
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# Data checks.
check_pipe()
check_mol_res_spin_data()
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Test that the intensity measures are identical.
if hasattr(cdp, 'int_method') and cdp.int_method != int_method:
raise RelaxError(
"The '%s' measure of peak intensities does not match '%s' of the previously loaded spectra."
% (int_method, cdp.int_method))
# Multiple ID flags.
flag_multi = False
flag_multi_file = False
flag_multi_col = False
if isinstance(spectrum_id, list) or spectrum_id == 'auto':
flag_multi = True
if isinstance(file, list):
flag_multi_file = True
if isinstance(int_col, list) or spectrum_id == 'auto':
flag_multi_col = True
# List argument checks.
if flag_multi:
# Too many lists.
if flag_multi_file and flag_multi_col:
raise RelaxError(
"If a list of spectrum IDs is supplied, the file names and intensity column arguments cannot both be lists."
)
# Not enough lists.
if not flag_multi_file and not flag_multi_col:
raise RelaxError(
"If a list of spectrum IDs is supplied, either the file name or intensity column arguments must be a list of equal length."
)
# List lengths for multiple files.
if flag_multi_file and len(spectrum_id) != len(file):
raise RelaxError(
"The file list %s and spectrum ID list %s do not have the same number of elements."
% (file, spectrum_id))
# List lengths for multiple intensity columns.
if flag_multi_col and spectrum_id != 'auto' and len(
spectrum_id) != len(int_col):
raise RelaxError(
"The spectrum ID list %s and intensity column list %s do not have the same number of elements."
% (spectrum_id, int_col))
# More list argument checks (when only one spectrum ID is supplied).
else:
# Multiple files.
if flag_multi_file:
raise RelaxError(
"If multiple files are supplied, then multiple spectrum IDs must also be supplied."
)
# Multiple intensity columns.
if flag_multi_col:
raise RelaxError(
"If multiple intensity columns are supplied, then multiple spectrum IDs must also be supplied."
)
# Intensity column checks.
if spectrum_id != 'auto' and not flag_multi and flag_multi_col:
raise RelaxError(
"If a list of intensity columns is supplied, the spectrum ID argument must also be a list of equal length."
)
# Check the intensity measure.
if not int_method in ['height', 'point sum', 'other']:
raise RelaxError(
"The intensity measure '%s' is not one of 'height', 'point sum', 'other'."
% int_method)
# Set the peak intensity measure.
cdp.int_method = int_method
# Convert the file argument to a list if necessary.
if not isinstance(file, list):
file = [file]
# Loop over all files.
for file_index in range(len(file)):
# Read the peak list data.
peak_list = read_peak_list(file=file[file_index],
dir=dir,
int_col=int_col,
spin_id_col=spin_id_col,
mol_name_col=mol_name_col,
res_num_col=res_num_col,
res_name_col=res_name_col,
spin_num_col=spin_num_col,
spin_name_col=spin_name_col,
sep=sep,
spin_id=spin_id)
# Automatic spectrum IDs.
if spectrum_id == 'auto':
spectrum_id = peak_list[0].intensity_name
# Loop over the assignments.
data = []
data_flag = False
for assign in peak_list:
# Generate the spin_id.
spin_id = generate_spin_id_unique(res_num=assign.res_nums[dim - 1],
spin_name=assign.spin_names[dim -
1])
# Convert the intensity data to a list if needed.
intensity = assign.intensity
if not isinstance(intensity, list):
intensity = [intensity]
# Loop over the intensity data.
for int_index in range(len(intensity)):
# Sanity check.
if intensity[int_index] == 0.0:
warn(
RelaxWarning(
"A peak intensity of zero has been encountered for the spin '%s' - this could be fatal later on."
% spin_id))
# Get the spin container.
spin = return_spin(spin_id=spin_id)
if not spin:
warn(RelaxNoSpinWarning(spin_id))
continue
# Skip deselected spins.
if not spin.select:
continue
# Initialise.
if not hasattr(spin, 'peak_intensity'):
spin.peak_intensity = {}
# Intensity scaling.
if ncproc != None:
intensity[int_index] = intensity[int_index] / float(2**
ncproc)
# Add the data.
if flag_multi_file:
id = spectrum_id[file_index]
elif flag_multi_col:
id = spectrum_id[int_index]
else:
id = spectrum_id
spin.peak_intensity[id] = intensity[int_index]
# Switch the flag.
data_flag = True
# Append the data for printing out.
data.append([spin_id, repr(intensity[int_index])])
# Add the spectrum id (and ncproc) to the relax data store.
spectrum_ids = spectrum_id
if isinstance(spectrum_id, str):
spectrum_ids = [spectrum_id]
if ncproc != None and not hasattr(cdp, 'ncproc'):
cdp.ncproc = {}
for i in range(len(spectrum_ids)):
add_spectrum_id(spectrum_ids[i])
if ncproc != None:
cdp.ncproc[spectrum_ids[i]] = ncproc
# No data.
if not data_flag:
# Delete all the data.
delete(spectrum_id)
# Raise the error.
raise RelaxError("No data could be loaded from the peak list")
# Printout.
if verbose:
print(
"\nThe following intensities have been loaded into the relax data store:\n"
)
write_data(out=sys.stdout,
headings=["Spin_ID", "Intensity"],
data=data)
print('')
def read(file=None, dir=None, spectrum_id=None, dim=1, int_col=None, int_method=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None, verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file(s) containing the peak intensities.
@type file: str or list of str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword spectrum_id: The spectrum identification string.
@type spectrum_id: str or list of str
@keyword dim: The dimension of the peak list to associate the data with.
@type dim: int
@keyword int_col: The column containing the peak intensity data (used by the generic intensity file format).
@type int_col: int or list of int
@keyword int_method: The integration method, one of 'height', 'point sum' or 'other'.
@type int_method: str
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword ncproc: The Bruker ncproc binary intensity scaling factor.
@type ncproc: int or None
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# Data checks.
check_pipe()
check_mol_res_spin_data()
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Test that the intensity measures are identical.
if hasattr(cdp, 'int_method') and cdp.int_method != int_method:
raise RelaxError("The '%s' measure of peak intensities does not match '%s' of the previously loaded spectra." % (int_method, cdp.int_method))
# Multiple ID flags.
flag_multi = False
flag_multi_file = False
flag_multi_col = False
if isinstance(spectrum_id, list) or spectrum_id == 'auto':
flag_multi = True
if isinstance(file, list):
flag_multi_file = True
if isinstance(int_col, list) or spectrum_id == 'auto':
flag_multi_col = True
# List argument checks.
if flag_multi:
# Too many lists.
if flag_multi_file and flag_multi_col:
raise RelaxError("If a list of spectrum IDs is supplied, the file names and intensity column arguments cannot both be lists.")
# Not enough lists.
if not flag_multi_file and not flag_multi_col:
raise RelaxError("If a list of spectrum IDs is supplied, either the file name or intensity column arguments must be a list of equal length.")
# List lengths for multiple files.
if flag_multi_file and len(spectrum_id) != len(file):
raise RelaxError("The file list %s and spectrum ID list %s do not have the same number of elements." % (file, spectrum_id))
# List lengths for multiple intensity columns.
if flag_multi_col and spectrum_id != 'auto' and len(spectrum_id) != len(int_col):
raise RelaxError("The spectrum ID list %s and intensity column list %s do not have the same number of elements." % (spectrum_id, int_col))
# More list argument checks (when only one spectrum ID is supplied).
else:
# Multiple files.
if flag_multi_file:
raise RelaxError("If multiple files are supplied, then multiple spectrum IDs must also be supplied.")
# Multiple intensity columns.
if flag_multi_col:
raise RelaxError("If multiple intensity columns are supplied, then multiple spectrum IDs must also be supplied.")
# Intensity column checks.
if spectrum_id != 'auto' and not flag_multi and flag_multi_col:
raise RelaxError("If a list of intensity columns is supplied, the spectrum ID argument must also be a list of equal length.")
# Check the intensity measure.
if not int_method in ['height', 'point sum', 'other']:
raise RelaxError("The intensity measure '%s' is not one of 'height', 'point sum', 'other'." % int_method)
# Set the peak intensity measure.
cdp.int_method = int_method
# Convert the file argument to a list if necessary.
if not isinstance(file, list):
file = [file]
# Loop over all files.
for file_index in range(len(file)):
# Read the peak list data.
peak_list = read_peak_list(file=file[file_index], dir=dir, int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
# Automatic spectrum IDs.
if spectrum_id == 'auto':
spectrum_id = peak_list[0].intensity_name
# Loop over the assignments.
data = []
data_flag = False
for assign in peak_list:
# Generate the spin_id.
spin_id = generate_spin_id_unique(res_num=assign.res_nums[dim-1], spin_name=assign.spin_names[dim-1])
# Convert the intensity data to a list if needed.
intensity = assign.intensity
if not isinstance(intensity, list):
intensity = [intensity]
# Loop over the intensity data.
for int_index in range(len(intensity)):
# Sanity check.
if intensity[int_index] == 0.0:
warn(RelaxWarning("A peak intensity of zero has been encountered for the spin '%s' - this could be fatal later on." % spin_id))
# Get the spin container.
spin = return_spin(spin_id)
if not spin:
warn(RelaxNoSpinWarning(spin_id))
continue
# Skip deselected spins.
if not spin.select:
continue
# Initialise.
if not hasattr(spin, 'peak_intensity'):
spin.peak_intensity = {}
# Intensity scaling.
if ncproc != None:
intensity[int_index] = intensity[int_index] / float(2**ncproc)
# Add the data.
if flag_multi_file:
id = spectrum_id[file_index]
elif flag_multi_col:
id = spectrum_id[int_index]
else:
id = spectrum_id
spin.peak_intensity[id] = intensity[int_index]
# Switch the flag.
data_flag = True
# Append the data for printing out.
data.append([spin_id, repr(intensity[int_index])])
# Add the spectrum id (and ncproc) to the relax data store.
spectrum_ids = spectrum_id
if isinstance(spectrum_id, str):
spectrum_ids = [spectrum_id]
if ncproc != None and not hasattr(cdp, 'ncproc'):
cdp.ncproc = {}
for i in range(len(spectrum_ids)):
add_spectrum_id(spectrum_ids[i])
if ncproc != None:
cdp.ncproc[spectrum_ids[i]] = ncproc
# No data.
if not data_flag:
# Delete all the data.
delete(spectrum_id)
# Raise the error.
raise RelaxError("No data could be loaded from the peak list")
# Printout.
if verbose:
print("\nThe following intensities have been loaded into the relax data store:\n")
write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"], data=data)
print('')
def read(file=None, dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak intensities.
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword verbose: A flag which if True will cause all chemical shift data loaded to be printed out.
@type verbose: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Read the peak list data.
peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
# Loop over the assignments.
data = []
data_flag = False
for assign in peak_list:
# Loop over the dimensions of the peak list.
for i in range(peak_list.dimensionality):
# Generate the spin_id.
spin_id = generate_spin_id_unique(res_num=assign.res_nums[i], spin_name=assign.spin_names[i])
# Get the spin container.
spin = return_spin(spin_id)
if not spin:
warn(RelaxNoSpinWarning(spin_id))
continue
# Skip deselected spins.
if not spin.select:
continue
# Store the shift.
spin.chemical_shift = assign.shifts[i]
# Switch the flag.
data_flag = True
# Append the data for printing out.
data.append([spin_id, repr(spin.chemical_shift)])
# No data.
if not data_flag:
raise RelaxError("No chemical shifts could be loaded from the peak list")
# Print out.
if verbose:
print("\nThe following chemical shifts have been loaded into the relax data store:\n")
write_data(out=sys.stdout, headings=["Spin_ID", "Chemical shift"], data=data)
def read(file=None, dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, verbose=True):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak intensities.
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type mol_name_col: int or None
@keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_name_col: int or None
@keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type res_num_col: int or None
@keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_name_col: int or None
@keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to whitespace.
@type sep: str or None
@keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai.
@type spin_id: None or str
@keyword verbose: A flag which if True will cause all chemical shift data loaded to be printed out.
@type verbose: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Check the file name.
if file == None:
raise RelaxError("The file name must be supplied.")
# Read the peak list data.
peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
# Loop over the assignments.
data = []
data_flag = False
for assign in peak_list:
# Loop over the dimensions of the peak list.
for i in range(peak_list.dimensionality):
# Generate the spin_id.
spin_id = generate_spin_id_unique(res_num=assign.res_nums[i], spin_name=assign.spin_names[i])
# Get the spin container.
spin = return_spin(spin_id=spin_id)
if not spin:
warn(RelaxNoSpinWarning(spin_id))
continue
# Skip deselected spins.
if not spin.select:
continue
# Store the shift.
spin.chemical_shift = assign.shifts[i]
# Switch the flag.
data_flag = True
# Append the data for printing out.
data.append([spin_id, repr(spin.chemical_shift)])
# No data.
if not data_flag:
raise RelaxError("No chemical shifts could be loaded from the peak list")
# Print out.
if verbose:
print("\nThe following chemical shifts have been loaded into the relax data store:\n")
write_data(out=sys.stdout, headings=["Spin_ID", "Chemical shift"], data=data)
