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.
check_pipe()
# 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))
# 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 read(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, sep=None, spin_id=None):
"""Read the molecule, residue, and/or spin sequence data from file.
@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
@keyword file_data: An alternative to 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 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.
check_pipe()
# Test if sequence data already exists.
if exists_mol_res_spin_data():
raise RelaxSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Generate the sequence.
for mol_name, res_num, res_name, spin_num, spin_name 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, sep=sep, spin_id=spin_id):
# Add the spin.
generate(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
# Append the new spin.
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)
# No data, so fail.
if not len(spin_names):
raise RelaxError("No sequence data could be loaded.")
# Write the data.
write_spin_data(sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)
def read(param=None, scaling=1.0, 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 spin specific data values from a file.
@keyword param: The name of the parameter to read.
@type param: str
@keyword scaling: A scaling factor by which all read values are multiplied by.
@type scaling: float
@keyword file: The name of the file to open.
@type file: str
@keyword dir: The directory containing the file (defaults to the current directory if None).
@type dir: str or None
@keyword file_data: An alternative to 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 RDC data in Hz.
@type data_col: int or None
@keyword error_col: The column containing the RDC 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.
@type spin_id: None or str
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Minimisation statistic flag.
min_stat = False
# Alias specific analysis API object method.
api = return_api()
return_value = api.return_value
# Specific set function.
set_fn = set
# Test data corresponding to param already exists.
for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
continue
# Get the value and error.
value, error = return_value(spin, param)
# Data exists.
if value != None or error != None:
raise RelaxValueError(param)
# Loop over the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
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, spin_id=spin_id):
# 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
# Set the value.
id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
set_fn(val=value, error=error, param=param, spin_id=id)
# Append the data for printout.
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)
# Print out.
write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values, data_name=param, error=errors, error_name='%s_error'%param)
# Reset the minimisation statistics.
if api.set(param) == 'min':
minimise.reset_min_stats()
def read(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, sep=None, spin_id=None):
"""Read the molecule, residue, and/or spin sequence data from file.
@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
@keyword file_data: An alternative to 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 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.
check_pipe()
# Test if sequence data already exists.
if exists_mol_res_spin_data():
raise RelaxSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Generate the sequence.
for mol_name, res_num, res_name, spin_num, spin_name 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, sep=sep, spin_id=spin_id):
# Add the spin.
generate(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
# Append the new spin.
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)
# No data, so fail.
if not len(spin_names):
raise RelaxError("No sequence data could be loaded.")
# Write the data.
write_spin_data(sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)
def sel_read(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, sep=None, spin_id=None, boolean='OR', change_all=False):
"""Select the spins contained in the given file.
@keyword file: The name of the file to open.
@type file: str
@keyword dir: The directory containing the file (defaults to the current
directory if None).
@type dir: str or None
@keyword 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 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
@param boolean: The boolean operator used to select the spin systems with. It
can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
This will be ignored if the change_all flag is set.
@type boolean: str
@keyword change_all: A flag which if True will cause all spins not specified in the
file to be deselected. Only the boolean operator 'OR' is
compatible with this flag set to True (all others will be
ignored).
@type change_all: bool
@raises RelaxNoSequenceError: If no molecule/residue/spins sequence data exists.
@raises RelaxError: If the boolean operator is unknown.
"""
# Test if the current data pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# First deselect all spins if the change_all flag is set.
if change_all:
# Loop over all spins.
for spin in spin_loop():
spin.select = False
# Then deselect the spins in the file.
ids = []
for id 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, sep=sep, spin_id=spin_id):
# Get the corresponding spin container.
spin = return_spin(spin_id=id)
# No spin.
if spin == None:
warn(RelaxNoSpinWarning(id))
continue
# Select the spin.
if change_all:
spin.select = True
# Boolean selections.
else:
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Store the spin ID for printouts.
if spin.select:
ids.append(id)
# Printout.
if not len(ids):
print("No spins selected.")
else:
print("The following spins were selected:")
for id in ids:
print(id)
def sel_read(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, sep=None, spin_id=None, boolean='OR', change_all=False):
"""Select the spins contained in the given file.
@keyword file: The name of the file to open.
@type file: str
@keyword dir: The directory containing the file (defaults to the current
directory if None).
@type dir: str or None
@keyword 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 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
@param boolean: The boolean operator used to select the spin systems with. It
can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
This will be ignored if the change_all flag is set.
@type boolean: str
@keyword change_all: A flag which if True will cause all spins not specified in the
file to be deselected. Only the boolean operator 'OR' is
compatible with this flag set to True (all others will be
ignored).
@type change_all: bool
@raises RelaxNoSequenceError: If no molecule/residue/spins sequence data exists.
@raises RelaxError: If the boolean operator is unknown.
"""
# Test if the current data pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# First deselect all spins if the change_all flag is set.
if change_all:
# Loop over all spins.
for spin in spin_loop():
spin.select = False
# Then deselect the spins in the file.
ids = []
for id 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, sep=sep, spin_id=spin_id):
# Get the corresponding spin container.
spin = return_spin(id)
# No spin.
if spin == None:
warn(RelaxNoSpinWarning(id))
continue
# Select the spin.
if change_all:
spin.select = True
# Boolean selections.
else:
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Store the spin ID for printouts.
if spin.select:
ids.append(id)
# Printout.
if not len(ids):
print("No spins selected.")
else:
print("The following spins were selected:")
for id in ids:
print(id)
def read(align_id=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 the PCS data from file.
@param align_id: The alignment tensor ID string.
@type align_id: str
@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 PCS data in Hz.
@type data_col: int or None
@keyword error_col: The column containing the PCS 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
"""
# Check the pipe setup.
check_pipe_setup(sequence=True)
# Test if sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Either the data or error column must be supplied.
if data_col == None and error_col == None:
raise RelaxError("One of either the data or error column must be supplied.")
# Spin specific data.
#####################
# Loop over the PCS data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
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, spin_id=spin_id):
# 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
# Test the error value (cannot be 0.0).
if error == 0.0:
raise RelaxError("An invalid error value of zero has been encountered.")
# Get the corresponding spin container.
id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
spin = return_spin(id)
if spin == None and spin_id and spin_id[0] == '@': # Allow spin IDs of atom names to be used to specify multi column data.
spin = return_spin(id+spin_id)
if spin == None:
warn(RelaxNoSpinWarning(id))
continue
# Add the data.
if data_col:
# Initialise.
if not hasattr(spin, 'pcs'):
spin.pcs = {}
# Append the value.
spin.pcs[align_id] = value
# Add the error.
if error_col:
# Initialise.
if not hasattr(spin, 'pcs_err'):
spin.pcs_err = {}
# Append the error.
spin.pcs_err[align_id] = error
# Append the data for printout.
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)
# Print out.
write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values, data_name='PCSs', error=errors, error_name='PCS_error')
# Global (non-spin specific) data.
##################################
# No data, so return.
if not len(values):
return
# Initialise.
if not hasattr(cdp, 'align_ids'):
cdp.align_ids = []
if not hasattr(cdp, 'pcs_ids'):
cdp.pcs_ids = []
# Add the PCS id string.
if align_id not in cdp.align_ids:
cdp.align_ids.append(align_id)
if align_id not in cdp.pcs_ids:
cdp.pcs_ids.append(align_id)
def read(param=None, scaling=1.0, 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 spin specific data values from a file.
@keyword param: The name of the parameter to read.
@type param: str
@keyword scaling: A scaling factor by which all read values are multiplied by.
@type scaling: float
@keyword file: The name of the file to open.
@type file: str
@keyword dir: The directory containing the file (defaults to the current directory if None).
@type dir: str or None
@keyword file_data: An alternative to 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 RDC data in Hz.
@type data_col: int or None
@keyword error_col: The column containing the RDC 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.
@type spin_id: None or str
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Minimisation statistic flag.
min_stat = False
# Alias specific analysis API object method.
api = return_api()
return_value = api.return_value
# Specific set function.
set_fn = set
# Test data corresponding to param already exists.
for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
continue
# Get the value and error.
value, error = return_value(spin, param)
# Data exists.
if value != None or error != None:
raise RelaxValueError(param)
# Loop over the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
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, spin_id=spin_id):
# 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
# Set the value.
id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
set_fn(val=value, error=error, param=param, spin_id=id)
# Append the data for printout.
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)
# Print out.
write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values, data_name=param, error=errors, error_name='%s_error'%param)
# Reset the minimisation statistics.
if api.set(param) == 'min':
minimise.reset_min_stats()
def intensity_generic(
peak_list=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,
sep=None,
spin_id=None,
):
"""Extract the peak intensity information from the generic column formatted peak list.
@keyword peak_list: The peak list object to place all data into.
@type peak_list: lib.spectrum.objects.Peak_list instance
@keyword file_data: The data extracted from the file converted into a list of lists.
@type file_data: list of lists of 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 data_col: The column containing the peak intensities.
@type data_col: int or list of int
@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
@raises RelaxError: When the expected peak intensity is not a float.
"""
# Strip the data.
file_data = strip(file_data)
# Check the intensity column argument.
data_present = True
if data_col == None:
warn(RelaxWarning("The data column argument has not been supplied, and function will only return spin data."))
data_present = False
# Convert the the data_col argument to a list if needed.
if not isinstance(data_col, list):
data_col = [data_col]
# Loop over the file data.
for line in file_data:
# Loop over the intensity columns, storing the data.
intensity = []
data_flag = False
for i in range(len(data_col)):
# Extract the data for the single line (loop of a single element).
for values in read_spin_data(
file_data=[line],
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[i],
sep=sep,
spin_id=spin_id,
raise_flag=False,
):
# The data flag.
data_flag = True
# Check the values.
if len(values) != 6 and data_present:
raise RelaxError(
"The molecule name, residue number and name, spin number and name, and value columns could not be found in the data %s."
% repr(values)
)
# Unpack when peak data is present
elif data_present:
# Unpack.
mol_name, res_num, res_name, spin_num, spin_name, value = values
# Store the intensity.
intensity.append(value)
# Unpack when peak data is not present.
elif not data_present:
# Unpack.
mol_name, res_num, res_name, spin_num, spin_name = values
# Add the assignment to the peak list object.
if data_flag:
peak_list.add(
mol_names=[mol_name, mol_name],
res_nums=[res_num, res_num],
res_names=[res_name, res_name],
spin_nums=[spin_num, spin_num],
spin_names=[spin_name, spin_name],
intensity=intensity,
)
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.
check_pipe()
# 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 intensity_generic(peak_list=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,
sep=None,
spin_id=None):
"""Extract the peak intensity information from the generic column formatted peak list.
@keyword peak_list: The peak list object to place all data into.
@type peak_list: lib.spectrum.objects.Peak_list instance
@keyword file_data: The data extracted from the file converted into a list of lists.
@type file_data: list of lists of 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 data_col: The column containing the peak intensities.
@type data_col: int or list of int
@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
@raises RelaxError: When the expected peak intensity is not a float.
"""
# Strip the data.
file_data = strip(file_data)
# Check the intensity column argument.
data_present = True
if data_col == None:
warn(
RelaxWarning(
"The data column argument has not been supplied, and function will only return spin data."
))
data_present = False
# Convert the the data_col argument to a list if needed.
if not isinstance(data_col, list):
data_col = [data_col]
# Loop over the file data.
for line in file_data:
# Loop over the intensity columns, storing the data.
intensity = []
data_flag = False
for i in range(len(data_col)):
# Extract the data for the single line (loop of a single element).
for values in read_spin_data(file_data=[line],
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[i],
sep=sep,
spin_id=spin_id,
raise_flag=False):
# The data flag.
data_flag = True
# Check the values.
if len(values) != 6 and data_present:
raise RelaxError(
"The molecule name, residue number and name, spin number and name, and value columns could not be found in the data %s."
% repr(values))
# Unpack when peak data is present
elif data_present:
# Unpack.
mol_name, res_num, res_name, spin_num, spin_name, value = values
# Store the intensity.
intensity.append(value)
# Unpack when peak data is not present.
elif not data_present:
# Unpack.
mol_name, res_num, res_name, spin_num, spin_name = values
# Add the assignment to the peak list object.
if data_flag:
peak_list.add(mol_names=[mol_name, mol_name],
res_nums=[res_num, res_num],
res_names=[res_name, res_name],
spin_nums=[spin_num, spin_num],
spin_names=[spin_name, spin_name],
intensity=intensity)