def write(file, dir=None, sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True, force=False):
"""Write the molecule, residue, and/or sequence data.
This calls the lib.io.write_spin_data() function to do most of the work.
@param file: The name of the file to write the data to.
@type file: str
@keyword dir: The directory to contain the file (defaults to the current directory if None).
@type dir: str or None
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@keyword force: A flag which if True will cause an existing file to be overwritten.
@type force: bin
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
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)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=file, dir=dir, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, force=force)
def write(file, dir=None, sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True, force=False):
"""Write the molecule, residue, and/or sequence data.
This calls the lib.io.write_spin_data() function to do most of the work.
@param file: The name of the file to write the data to.
@type file: str
@keyword dir: The directory to contain the file (defaults to the current directory if None).
@type dir: str or None
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@keyword force: A flag which if True will cause an existing file to be overwritten.
@type force: bin
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
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)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=file, dir=dir, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, force=force)
def display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True):
"""Display the current spin selections.
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@type spin_num_flag: bool
"""
# Test if the sequence data is loaded.
check_mol_res_spin_data()
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
selections = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True, skip_desel=False):
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)
selections.append(spin.select)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=sys.stdout, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=selections, data_name="selection")
def display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True):
"""Display the current spin selections.
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@type spin_num_flag: bool
"""
# Test if the sequence data is loaded.
check_mol_res_spin_data()
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
selections = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True, skip_desel=False):
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)
selections.append(spin.select)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=sys.stdout, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=selections, data_name="selection")
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(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 write_data(param=None, file=None, scaling=1.0, bc=False, return_value=None, return_data_desc=None, comment=None):
"""The function which actually writes the data.
@keyword param: The parameter to write.
@type param: str
@keyword file: The file to write the data to.
@type file: str
@keyword scaling: The value to scale the parameter by.
@type scaling: float
@keyword bc: A flag which if True will cause the back calculated values to be written.
@type bc: bool
@keyword return_value: An optional function which if supplied will override the default value returning function.
@type return_value: None or func
@keyword return_data_desc: An optional function which if supplied will override the default parameter description returning function.
@type return_data_desc: None or func
@keyword comment: Text which will be added to the start of the file as comments. All lines will be prefixed by '# '.
@type comment: str
"""
# The specific analysis API object.
api = return_api()
# Get the value and error returning function parameter description function if required.
if not return_value:
return_value = api.return_value
if not return_data_desc:
return_data_desc = api.return_data_desc
# Format string.
format = "%-30s%-30s"
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
# Get the parameter description and add it to the file.
desc = return_data_desc(param)
if desc:
file.write("# Parameter description: %s.\n" % desc)
file.write("#\n")
# The comments.
if comment:
# Split up the lines.
lines = comment.splitlines()
# Write out.
for line in lines:
file.write("# %s\n" % line)
file.write("#\n")
# Determine the data type, check the data, and set up the dictionary type data keys.
data_names = 'value'
error_names = 'error'
data_type = None
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Get the value and error.
value, error = return_value(spin, param, bc=bc)
# Dictionary type data.
if isinstance(value, dict):
# Sanity check.
if not data_type in [None, 'dict']:
raise RelaxError("Mixed data types.")
data_type = 'dict'
# Initialise the structures.
if not isinstance(data_names, list):
data_names = []
error_names = []
# Sort the keys.
keys = sorted(value.keys())
# Loop over the keys.
for key in keys:
# Add the data and error names if new.
if key not in data_names:
data_names.append(key)
error_names.append('sd(%s)' % key)
# List type data.
elif isinstance(value, list):
# Sanity check.
if not data_type in [None, 'list']:
raise RelaxError("Mixed data types.")
data_type = 'list'
# Initialise the structures.
if not isinstance(data_names, list):
data_names = []
error_names = []
# Check the length.
elif len(data_names) != len(value):
raise RelaxError("The list type data has an inconsistent number of elements between different spin systems.")
# Loop over the data.
for i in range(len(value)):
# The data and error names.
data_names.append('value_%s' % i)
error_names.append('error_%s' % i)
# None.
elif value == None:
pass
# Simple values.
else:
# Sanity check.
if not data_type in [None, 'value']:
raise RelaxError("Mixed data types.")
data_type = 'value'
# Pack the data.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Get the value and error.
value, error = return_value(spin, param, bc=bc)
# Append the spin data (scaled).
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)
# Dictionary type data.
if data_type == 'dict':
# Initialise the lists.
values.append([])
errors.append([])
# Loop over the keys.
for key in data_names:
# Append the scaled values and errors.
if value == None or key not in value:
values[-1].append(None)
else:
values[-1].append(scale(value[key], scaling))
if error == None or key not in error:
errors[-1].append(None)
else:
errors[-1].append(scale(error[key], scaling))
# List type data.
elif data_type == 'list':
# Initialise the lists.
values.append([])
errors.append([])
# Loop over the data.
for i in range(len(data_names)):
# Append the scaled values and errors.
if value == None:
values[-1].append(None)
else:
values[-1].append(scale(value[i], scaling))
if error == None:
errors[-1].append(None)
else:
errors[-1].append(scale(error[i], scaling))
# Simple values.
else:
# Append the scaled values and errors.
values.append(scale(value, scaling))
errors.append(scale(error, scaling))
# Replace all spaces " " with "_" in data_names list.
if isinstance(data_names, list):
for i, data_name in enumerate(data_names):
data_str = data_name.replace(" ", "_")
# Replace string.
data_names[i] = data_str
# Replace all spaces " " with "_" in error_names list.
if isinstance(error_names, list):
for i, error_name in enumerate(error_names):
error_str = error_name.replace(" ", "_")
# Replace string.
error_names[i] = error_str
# Write the data.
write_spin_data(file, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values, data_name=data_names, error=errors, error_name=error_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(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 write(align_id=None, file=None, dir=None, bc=False, force=False):
"""Display the PCS data corresponding to the alignment ID.
@keyword align_id: The alignment tensor ID string.
@type align_id: str
@keyword file: The file name or object to write to.
@type file: str or file object
@keyword dir: The name of the directory to place the file into (defaults to the current directory).
@type dir: str
@keyword bc: The back-calculation flag which if True will cause the back-calculated rather than measured data to be written.
@type bc: bool
@keyword force: A flag which if True will cause any pre-existing file to be overwritten.
@type force: bool
"""
# Check the pipe setup.
check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
# Open the file for writing.
file = open_write_file(file, dir, force)
# Loop over the spins and collect the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Skip deselected spins.
if not spin.select:
continue
# Skip spins with no PCSs.
if not bc and (not hasattr(spin, 'pcs') or not align_id in spin.pcs):
continue
elif bc and (not hasattr(spin, 'pcs_bc') or align_id not in spin.pcs_bc):
continue
# Append the spin data.
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)
# The value.
if bc:
values.append(spin.pcs_bc[align_id])
else:
values.append(spin.pcs[align_id])
# The error.
if hasattr(spin, 'pcs_err') and align_id in spin.pcs_err:
errors.append(spin.pcs_err[align_id])
else:
errors.append(None)
# Write out.
write_spin_data(file=file, 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')
def write_data(param=None, file=None, scaling=1.0, bc=False, return_value=None, return_data_desc=None, comment=None):
"""The function which actually writes the data.
@keyword param: The parameter to write.
@type param: str
@keyword file: The file to write the data to.
@type file: str
@keyword scaling: The value to scale the parameter by.
@type scaling: float
@keyword bc: A flag which if True will cause the back calculated values to be written.
@type bc: bool
@keyword return_value: An optional function which if supplied will override the default value returning function.
@type return_value: None or func
@keyword return_data_desc: An optional function which if supplied will override the default parameter description returning function.
@type return_data_desc: None or func
@keyword comment: Text which will be added to the start of the file as comments. All lines will be prefixed by '# '.
@type comment: str
"""
# The specific analysis API object.
api = return_api()
# Get the value and error returning function parameter description function if required.
if not return_value:
return_value = api.return_value
if not return_data_desc:
return_data_desc = api.return_data_desc
# Format string.
format = "%-30s%-30s"
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
values = []
errors = []
# Get the parameter description and add it to the file.
desc = return_data_desc(param)
if desc:
file.write("# Parameter description: %s.\n" % desc)
file.write("#\n")
# The comments.
if comment:
# Split up the lines.
lines = comment.splitlines()
# Write out.
for line in lines:
file.write("# %s\n" % line)
file.write("#\n")
# Determine the data type, check the data, and set up the dictionary type data keys.
data_names = 'value'
error_names = 'error'
data_type = None
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Get the value and error.
value, error = return_value(spin, param, bc=bc)
# Dictionary type data.
if isinstance(value, dict):
# Sanity check.
if not data_type in [None, 'dict']:
raise RelaxError("Mixed data types.")
data_type = 'dict'
# Initialise the structures.
if not isinstance(data_names, list):
data_names = []
error_names = []
# Sort the keys.
keys = sorted(value.keys())
# Loop over the keys.
for key in keys:
# Add the data and error names if new.
if key not in data_names:
data_names.append(key)
error_names.append('sd(%s)' % key)
# List type data.
elif isinstance(value, list):
# Sanity check.
if not data_type in [None, 'list']:
raise RelaxError("Mixed data types.")
data_type = 'list'
# Initialise the structures.
if not isinstance(data_names, list):
data_names = []
error_names = []
# Check the length.
elif len(data_names) != len(value):
raise RelaxError("The list type data has an inconsistent number of elements between different spin systems.")
# Loop over the data.
for i in range(len(value)):
# The data and error names.
data_names.append('value_%s' % i)
error_names.append('error_%s' % i)
# None.
elif value == None:
pass
# Simple values.
else:
# Sanity check.
if not data_type in [None, 'value']:
raise RelaxError("Mixed data types.")
data_type = 'value'
# Pack the data.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Get the value and error.
value, error = return_value(spin, param, bc=bc)
# Append the spin data (scaled).
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)
# Dictionary type data.
if data_type == 'dict':
# Initialise the lists.
values.append([])
errors.append([])
# Loop over the keys.
for key in data_names:
# Append the scaled values and errors.
if value == None or key not in value:
values[-1].append(None)
else:
values[-1].append(scale(value[key], scaling))
if error == None or key not in error:
errors[-1].append(None)
else:
errors[-1].append(scale(error[key], scaling))
# List type data.
elif data_type == 'list':
# Initialise the lists.
values.append([])
errors.append([])
# Loop over the data.
for i in range(len(data_names)):
# Append the scaled values and errors.
if value == None:
values[-1].append(None)
else:
values[-1].append(scale(value[i], scaling))
if error == None:
errors[-1].append(None)
else:
errors[-1].append(scale(error[i], scaling))
# Simple values.
else:
# Append the scaled values and errors.
values.append(scale(value, scaling))
errors.append(scale(error, scaling))
# Replace all spaces " " with "_" in data_names list.
if isinstance(data_names, list):
for i, data_name in enumerate(data_names):
data_str = data_name.replace(" ", "_")
# Replace string.
data_names[i] = data_str
# Replace all spaces " " with "_" in error_names list.
if isinstance(error_names, list):
for i, error_name in enumerate(error_names):
error_str = error_name.replace(" ", "_")
# Replace string.
error_names[i] = error_str
# Write the data.
write_spin_data(file, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values, data_name=data_names, error=errors, error_name=error_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()