def read(ri_id=None, ri_type=None, frq=None, file=None, dir=None, file_data=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, data_col=None, error_col=None, sep=None, spin_id=None):
"""Read R1, R2, or NOE, or R2eff relaxation data from a file.
@param ri_id: The relaxation data ID string.
@type ri_id: str
@param ri_type: The relaxation data type, ie 'R1', 'R2', 'NOE', or 'R2eff'.
@type ri_type: str
@param frq: The spectrometer proton frequency in Hz.
@type frq: float
@param file: The name of the file to open.
@type file: str
@param dir: The directory containing the file (defaults to the current directory if None).
@type dir: str or None
@param file_data: An alternative opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
@type file_data: list of lists
@keyword spin_id_col: The column containing the spin ID strings. 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. 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. 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. 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. 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. If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword data_col: The column containing the relaxation data.
@type data_col: int or None
@keyword error_col: The column containing the relaxation data errors.
@type error_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.
@type spin_id: None or str
"""
# Test if the current data pipe exists.
pipes.test()
# Test if sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Test if the ri_id already exists.
if hasattr(cdp, 'ri_ids') and ri_id in cdp.ri_ids:
raise RelaxError("The relaxation ID string '%s' already exists." % ri_id)
# Check if the type is valid.
if ri_type not in VALID_TYPES:
raise RelaxError("The relaxation data type '%s' must be one of %s." % (ri_type, VALID_TYPES))
# Frequency checks.
frequency_checks(frq)
# Loop over the file data to create the data structures for packing.
values = []
errors = []
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
for data in read_spin_data(file=file, dir=dir, file_data=file_data, 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, data_col=data_col, error_col=error_col, sep=sep):
# Unpack.
if data_col and error_col:
mol_name, res_num, res_name, spin_num, spin_name, value, error = data
elif data_col:
mol_name, res_num, res_name, spin_num, spin_name, value = data
error = None
else:
mol_name, res_num, res_name, spin_num, spin_name, error = data
value = None
# No data.
if value == None and error == None:
continue
# Store all the info.
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(spin_num)
spin_names.append(spin_name)
values.append(value)
errors.append(error)
# Pack the data.
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id)
def back_calc(ri_id=None, ri_type=None, frq=None):
"""Back calculate the relaxation data.
If no relaxation data currently exists, then the ri_id, ri_type, and frq args are required.
@keyword ri_id: The relaxation data ID string. If not given, all relaxation data will be back calculated.
@type ri_id: None or str
@keyword ri_type: The relaxation data type. This should be one of 'R1', 'R2', or 'NOE'.
@type ri_type: None or str
@keyword frq: The spectrometer proton frequency in Hz.
@type frq: None or float
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Check that ri_type and frq are supplied if no relaxation data exists.
if ri_id and (not hasattr(cdp, 'ri_ids') or ri_id
not in cdp.ri_ids) and (ri_type == None or frq == None):
raise RelaxError(
"The 'ri_type' and 'frq' arguments must be supplied as no relaxation data corresponding to '%s' exists."
% ri_id)
# Check if the type is valid.
if ri_type and ri_type not in VALID_TYPES:
raise RelaxError("The relaxation data type '%s' must be one of %s." %
(ri_type, VALID_TYPES))
# Frequency checks.
frequency_checks(frq)
# Initialise the global data for the current pipe if necessary.
if not hasattr(cdp, 'ri_type'):
cdp.ri_type = {}
if not hasattr(cdp, 'ri_ids'):
cdp.ri_ids = []
# Update the global data if needed.
if ri_id and ri_id not in cdp.ri_ids:
cdp.ri_ids.append(ri_id)
cdp.ri_type[ri_id] = ri_type
set_frequency(id=ri_id, frq=frq)
# The specific analysis API object.
api = return_api()
# The IDs to loop over.
if ri_id == None:
ri_ids = cdp.ri_ids
else:
ri_ids = [ri_id]
# The data types.
if ri_type == None:
ri_types = cdp.ri_type
else:
ri_types = {ri_id: ri_type}
# The frequencies.
if frq == None:
frqs = cdp.spectrometer_frq
else:
frqs = {ri_id: frq}
# Loop over the spins.
for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
# The global index.
spin_index = find_index(spin_id)
# Initialise the spin data if necessary.
if not hasattr(spin, 'ri_data_bc'):
spin.ri_data_bc = {}
# Back-calculate the relaxation value.
for ri_id in ri_ids:
spin.ri_data_bc[ri_id] = api.back_calc_ri(spin_index=spin_index,
ri_id=ri_id,
ri_type=ri_types[ri_id],
frq=frqs[ri_id])
def back_calc(ri_id=None, ri_type=None, frq=None):
"""Back calculate the relaxation data.
If no relaxation data currently exists, then the ri_id, ri_type, and frq args are required.
@keyword ri_id: The relaxation data ID string. If not given, all relaxation data will be back calculated.
@type ri_id: None or str
@keyword ri_type: The relaxation data type. This should be one of 'R1', 'R2', or 'NOE'.
@type ri_type: None or str
@keyword frq: The spectrometer proton frequency in Hz.
@type frq: None or float
"""
# Test if the current pipe exists.
pipes.test()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Check that ri_type and frq are supplied if no relaxation data exists.
if ri_id and (not hasattr(cdp, 'ri_ids') or ri_id not in cdp.ri_ids) and (ri_type == None or frq == None):
raise RelaxError("The 'ri_type' and 'frq' arguments must be supplied as no relaxation data corresponding to '%s' exists." % ri_id)
# Check if the type is valid.
if ri_type and ri_type not in VALID_TYPES:
raise RelaxError("The relaxation data type '%s' must be one of %s." % (ri_type, VALID_TYPES))
# Frequency checks.
frequency_checks(frq)
# Initialise the global data for the current pipe if necessary.
if not hasattr(cdp, 'ri_type'):
cdp.ri_type = {}
if not hasattr(cdp, 'ri_ids'):
cdp.ri_ids = []
# Update the global data if needed.
if ri_id and ri_id not in cdp.ri_ids:
cdp.ri_ids.append(ri_id)
cdp.ri_type[ri_id] = ri_type
set_frequency(id=ri_id, frq=frq)
# Specific Ri back calculate function setup.
back_calculate = specific_analyses.setup.get_specific_fn('back_calc_ri', pipes.get_type())
# The IDs to loop over.
if ri_id == None:
ri_ids = cdp.ri_ids
else:
ri_ids = [ri_id]
# The data types.
if ri_type == None:
ri_types = cdp.ri_type
else:
ri_types = {ri_id: ri_type}
# The frequencies.
if frq == None:
frqs = cdp.spectrometer_frq
else:
frqs = {ri_id: frq}
# Loop over the spins.
for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
# The global index.
spin_index = find_index(spin_id)
# Initialise the spin data if necessary.
if not hasattr(spin, 'ri_data_bc'):
spin.ri_data_bc = {}
# Back-calculate the relaxation value.
for ri_id in ri_ids:
spin.ri_data_bc[ri_id] = back_calculate(spin_index=spin_index, ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id])