def sel_domain(domain_id=None, boolean='OR', change_all=False):
"""Select all spins and interatomic data containers of the given domain.
@keyword domain_id: The domain ID string.
@type domain_id: str or None
@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 and interatomic data containers outside of the domain to be deselected.
@type change_all: bool
"""
# Test if the current data pipe exists.
pipes.test()
# Test if the domain is defined.
if not hasattr(cdp, 'domain') or domain_id not in cdp.domain:
raise RelaxNoDomainError(domain_id)
# The domain selection object.
domain = Selection(cdp.domain[domain_id])
# Loop over the spins and select as required.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Inside the domain.
if domain.contains_spin(spin_name=spin.name, spin_num=spin.num, res_name=res_name, res_num=res_num, mol=mol_name):
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Deselect spins outside of the domain.
elif change_all:
spin.select = False
# Interatomic data loop.
for interatom in interatomic_loop():
# Decode the spin ids.
mol_name1, res_num1, res_name1, spin_num1, spin_name1 = spin_id_to_data_list(interatom.spin_id1)
mol_name2, res_num2, res_name2, spin_num2, spin_name2 = spin_id_to_data_list(interatom.spin_id2)
# Inside the domain.
if domain.contains_spin(spin_name=spin_name1, spin_num=spin_num1, res_name=res_name1, res_num=res_num1, mol=mol_name1) or domain.contains_spin(spin_name=spin_name2, spin_num=spin_num2, res_name=res_name2, res_num=res_num2, mol=mol_name2):
interatom.select = boolean_select(current=interatom.select, boolean=boolean)
# Deselect containers outside of the domain.
elif change_all:
interatom.select = False
def sel_domain(domain_id=None, boolean='OR', change_all=False):
"""Select all spins and interatomic data containers of the given domain.
@keyword domain_id: The domain ID string.
@type domain_id: str or None
@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 and interatomic data containers outside of the domain to be deselected.
@type change_all: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Test if the domain is defined.
if not hasattr(cdp, 'domain') or domain_id not in cdp.domain:
raise RelaxNoDomainError(domain_id)
# The domain selection object.
domain = Selection(cdp.domain[domain_id])
# Loop over the spins and select as required.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Inside the domain.
if domain.contains_spin(spin_name=spin.name, spin_num=spin.num, res_name=res_name, res_num=res_num, mol=mol_name):
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Deselect spins outside of the domain.
elif change_all:
spin.select = False
# Interatomic data loop.
for interatom in interatomic_loop():
# Decode the spin ids.
mol_name1, res_num1, res_name1, spin_num1, spin_name1 = spin_id_to_data_list(interatom.spin_id1)
mol_name2, res_num2, res_name2, spin_num2, spin_name2 = spin_id_to_data_list(interatom.spin_id2)
# Inside the domain.
if domain.contains_spin(spin_name=spin_name1, spin_num=spin_num1, res_name=res_name1, res_num=res_num1, mol=mol_name1) or domain.contains_spin(spin_name=spin_name2, spin_num=spin_num2, res_name=res_name2, res_num=res_num2, mol=mol_name2):
interatom.select = boolean_select(current=interatom.select, boolean=boolean)
# Deselect containers outside of the domain.
elif change_all:
interatom.select = False
def read_spin_data(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, raise_flag=True):
"""Generator function for reading the spin specific data from file.
Description
===========
This function reads a columnar formatted file where each line corresponds to a spin system. Spin identification is either through a spin ID string or through columns containing the molecule name, residue name and number, and/or spin name and number.
@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 data.
@type data_col: int or None
@keyword error_col: The column containing the 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
@keyword raise_flag: A flag which if True will cause a RelaxError to be raised if no data can be found.
@type raise_flag: bool
@return: A list of the spin specific data is yielded. The format is a list consisting of the spin ID string, the data value (if data_col is give), and the error value (if error_col is given). If both data_col and error_col are None, then the spin ID string is simply yielded.
@rtype: str, list of [str, float], or list of [str, float, float]
"""
# Argument tests.
col_args = [spin_id_col, mol_name_col, res_name_col, res_num_col, spin_name_col, spin_num_col, data_col, error_col]
col_arg_names = ['spin_id_col', 'mol_name_col', 'res_name_col', 'res_num_col', 'spin_name_col', 'spin_num_col', 'data_col', 'error_col']
for i in range(len(col_args)):
if col_args[i] == 0:
raise RelaxError("The '%s' argument cannot be zero, column numbering starts at one." % col_arg_names[i])
if spin_id_col and (mol_name_col or res_name_col or res_num_col or spin_name_col or spin_num_col):
raise RelaxError("If the 'spin_id_col' argument has been supplied, then the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col must all be set to None.")
# Minimum number of columns.
min_col_num = max([_f for _f in [spin_id_col, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, data_col, error_col] if _f])
# Extract the data from the file.
if not file_data:
# Extract.
file_data = extract_data(file, dir, sep=sep)
# Strip the data of all comments and empty lines.
if spin_id_col != None:
file_data = strip(file_data, comments=False)
else:
file_data = strip(file_data)
# No data!
if not file_data:
warn(RelaxFileEmptyWarning(file))
return
# Yield the data, spin by spin.
missing_data = True
for line in file_data:
# Convert the spin IDs.
if spin_id_col != None and line[spin_id_col-1][0] in ["\"", "\'"]:
line[spin_id_col-1] = eval(line[spin_id_col-1])
# Convert.
# Validate the sequence.
if not check_sequence(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, error_col=error_col, escalate=1):
continue
# Get the spin data from the ID.
if spin_id_col:
# Invalid spin ID.
if line[spin_id_col-1] == '#':
warn(RelaxWarning("Invalid spin ID, skipping the line %s" % line))
continue
mol_name, res_num, res_name, spin_num, spin_name = spin_id_to_data_list(line[spin_id_col-1])
# Convert the spin data.
else:
# The molecule.
mol_name = None
if mol_name_col != None and line[mol_name_col-1] != 'None':
mol_name = line[mol_name_col-1]
# The residue number, catching bad values.
res_num = None
if res_num_col != None:
try:
if line[res_num_col-1] == 'None':
res_num = None
else:
res_num = int(line[res_num_col-1])
except ValueError:
warn(RelaxWarning("Invalid residue number, skipping the line %s" % line))
continue
# The residue name.
res_name = None
if res_name_col != None and line[res_name_col-1] != 'None':
res_name = line[res_name_col-1]
# The spin number, catching bad values.
spin_num = None
if spin_num_col != None:
try:
if line[spin_num_col-1] == 'None':
spin_num = None
else:
spin_num = int(line[spin_num_col-1])
except ValueError:
warn(RelaxWarning("Invalid spin number, skipping the line %s" % line))
continue
# The spin name.
spin_name = None
if spin_name_col != None and line[spin_name_col-1] != 'None':
spin_name = line[spin_name_col-1]
# Convert the data.
value = None
if data_col != None:
try:
# None.
if line[data_col-1] == 'None':
value = None
# A float.
else:
value = float(line[data_col-1])
# If it a float, test if is nan.
if not isFinite(value):
warn(RelaxWarning("The value is not finite, skipping the line %s" % line))
continue
# Bad data.
except ValueError:
warn(RelaxWarning("Invalid data, skipping the line %s" % line))
continue
# Convert the errors.
error = None
if error_col != None:
try:
# None.
if line[error_col-1] == 'None':
error = None
# A float.
else:
error = float(line[error_col-1])
# If it a float, test if is nan.
if not isFinite(error):
warn(RelaxWarning("The error is not finite, skipping the line %s" % line))
continue
# Bad data.
except ValueError:
warn(RelaxWarning("Invalid errors, skipping the line %s" % line))
continue
# Right, data is OK and exists.
missing_data = False
# Yield the data.
if data_col and error_col:
yield mol_name, res_num, res_name, spin_num, spin_name, value, error
elif data_col:
yield mol_name, res_num, res_name, spin_num, spin_name, value
elif error_col:
yield mol_name, res_num, res_name, spin_num, spin_name, error
else:
yield mol_name, res_num, res_name, spin_num, spin_name
# Hmmm, no data!
if raise_flag and missing_data:
raise RelaxError("No corresponding data could be found within the file.")
def read_spin_data(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, raise_flag=True):
"""Generator function for reading the spin specific data from file.
Description
===========
This function reads a columnar formatted file where each line corresponds to a spin system. Spin identification is either through a spin ID string or through columns containing the molecule name, residue name and number, and/or spin name and number.
@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 data.
@type data_col: int or None
@keyword error_col: The column containing the 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
@keyword raise_flag: A flag which if True will cause a RelaxError to be raised if no data can be found.
@type raise_flag: bool
@return: A list of the spin specific data is yielded. The format is a list consisting of the spin ID string, the data value (if data_col is give), and the error value (if error_col is given). If both data_col and error_col are None, then the spin ID string is simply yielded.
@rtype: str, list of [str, float], or list of [str, float, float]
"""
# Argument tests.
col_args = [spin_id_col, mol_name_col, res_name_col, res_num_col, spin_name_col, spin_num_col, data_col, error_col]
col_arg_names = ['spin_id_col', 'mol_name_col', 'res_name_col', 'res_num_col', 'spin_name_col', 'spin_num_col', 'data_col', 'error_col']
for i in range(len(col_args)):
if col_args[i] == 0:
raise RelaxError("The '%s' argument cannot be zero, column numbering starts at one." % col_arg_names[i])
if spin_id_col and (mol_name_col or res_name_col or res_num_col or spin_name_col or spin_num_col):
raise RelaxError("If the 'spin_id_col' argument has been supplied, then the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col must all be set to None.")
# Minimum number of columns.
min_col_num = max([_f for _f in [spin_id_col, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, data_col, error_col] if _f])
# Extract the data from the file.
if not file_data:
# Extract.
file_data = extract_data(file, dir, sep=sep)
# Strip the data of all comments and empty lines.
if spin_id_col != None:
file_data = strip(file_data, comments=False)
else:
file_data = strip(file_data)
# No data!
if not file_data:
warn(RelaxFileEmptyWarning(file))
return
# Yield the data, spin by spin.
missing_data = True
for line in file_data:
# Convert the spin IDs.
if spin_id_col != None and line[spin_id_col-1][0] in ["\"", "\'"]:
line[spin_id_col-1] = eval(line[spin_id_col-1])
# Convert.
# Validate the sequence.
if not check_sequence(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, error_col=error_col, escalate=1):
continue
# Get the spin data from the ID.
if spin_id_col:
# Invalid spin ID.
if line[spin_id_col-1] == '#':
warn(RelaxWarning("Invalid spin ID, skipping the line %s" % line))
continue
mol_name, res_num, res_name, spin_num, spin_name = spin_id_to_data_list(line[spin_id_col-1])
# Convert the spin data.
else:
# The molecule.
mol_name = None
if mol_name_col != None and line[mol_name_col-1] != 'None':
mol_name = line[mol_name_col-1]
# The residue number, catching bad values.
res_num = None
if res_num_col != None:
try:
if line[res_num_col-1] == 'None':
res_num = None
else:
res_num = int(line[res_num_col-1])
except ValueError:
warn(RelaxWarning("Invalid residue number, skipping the line %s" % line))
continue
# The residue name.
res_name = None
if res_name_col != None and line[res_name_col-1] != 'None':
res_name = line[res_name_col-1]
# The spin number, catching bad values.
spin_num = None
if spin_num_col != None:
try:
if line[spin_num_col-1] == 'None':
spin_num = None
else:
spin_num = int(line[spin_num_col-1])
except ValueError:
warn(RelaxWarning("Invalid spin number, skipping the line %s" % line))
continue
# The spin name.
spin_name = None
if spin_name_col != None and line[spin_name_col-1] != 'None':
spin_name = line[spin_name_col-1]
# Convert the data.
value = None
if data_col != None:
try:
# None.
if line[data_col-1] == 'None':
value = None
# A float.
else:
value = float(line[data_col-1])
# If it a float, test if is nan.
if isnan(value):
warn(RelaxWarning("The value is 'nan', skipping the line %s" % line))
continue
# Bad data.
except ValueError:
warn(RelaxWarning("Invalid data, skipping the line %s" % line))
continue
# Convert the errors.
error = None
if error_col != None:
try:
# None.
if line[error_col-1] == 'None':
error = None
# A float.
else:
error = float(line[error_col-1])
# If it a float, test if is nan.
if isnan(error):
warn(RelaxWarning("The error is 'nan', skipping the line %s" % line))
continue
# Bad data.
except ValueError:
warn(RelaxWarning("Invalid errors, skipping the line %s" % line))
continue
# Right, data is OK and exists.
missing_data = False
# Yield the data.
if data_col and error_col:
yield mol_name, res_num, res_name, spin_num, spin_name, value, error
elif data_col:
yield mol_name, res_num, res_name, spin_num, spin_name, value
elif error_col:
yield mol_name, res_num, res_name, spin_num, spin_name, error
else:
yield mol_name, res_num, res_name, spin_num, spin_name
# Hmmm, no data!
if raise_flag and missing_data:
raise RelaxError("No corresponding data could be found within the file.")
