def set_dist(spin_id1=None, spin_id2=None, ave_dist=None, unit='meter'):
"""Set up the magnetic dipole-dipole interaction.
@keyword spin_id1: The spin identifier string of the first spin of the pair.
@type spin_id1: str
@keyword spin_id2: The spin identifier string of the second spin of the pair.
@type spin_id2: str
@keyword ave_dist: The r^-3 averaged interatomic distance.
@type ave_dist: float
@keyword unit: The measurement unit. This can be either 'meter' or 'Angstrom'.
@type unit: str
"""
# Check the units.
if unit not in ['meter', 'Angstrom']:
raise RelaxError("The measurement unit of '%s' must be one of 'meter' or 'Angstrom'." % unit)
# Unit conversion.
if unit == 'Angstrom':
ave_dist = ave_dist * 1e-10
# Generate the selection objects.
sel_obj1 = Selection(spin_id1)
sel_obj2 = Selection(spin_id2)
# Loop over the interatomic containers.
data = []
for interatom in interatomic_loop():
# Get the spin info.
mol_name1, res_num1, res_name1, spin1 = return_spin(spin_hash=interatom._spin_hash1, full_info=True)
mol_name2, res_num2, res_name2, spin2 = return_spin(spin_hash=interatom._spin_hash2, full_info=True)
# No match, either way.
if not (sel_obj1.contains_spin(spin_num=spin1.num, spin_name=spin1.name, res_num=res_num1, res_name=res_name1, mol=mol_name1) and sel_obj2.contains_spin(spin_num=spin2.num, spin_name=spin2.name, res_num=res_num2, res_name=res_name2, mol=mol_name2)) and not (sel_obj2.contains_spin(spin_num=spin1.num, spin_name=spin1.name, res_num=res_num1, res_name=res_name1, mol=mol_name1) and sel_obj1.contains_spin(spin_num=spin2.num, spin_name=spin2.name, res_num=res_num2, res_name=res_name2, mol=mol_name2)):
continue
# Store the averaged distance.
interatom.r = ave_dist
# Store the data for the printout.
data.append([repr(interatom.spin_id1), repr(interatom.spin_id2), repr(ave_dist)])
# No data, so fail!
if not len(data):
raise RelaxError("No data could be set.")
# Print out.
print("The following averaged distances have been set:\n")
write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2", "Ave_distance(meters)"], data=data)
def set_dist(spin_id1=None, spin_id2=None, ave_dist=None, unit='meter'):
"""Set up the magnetic dipole-dipole interaction.
@keyword spin_id1: The spin identifier string of the first spin of the pair.
@type spin_id1: str
@keyword spin_id2: The spin identifier string of the second spin of the pair.
@type spin_id2: str
@keyword ave_dist: The r^-3 averaged interatomic distance.
@type ave_dist: float
@keyword unit: The measurement unit. This can be either 'meter' or 'Angstrom'.
@type unit: str
"""
# Check the units.
if unit not in ['meter', 'Angstrom']:
raise RelaxError("The measurement unit of '%s' must be one of 'meter' or 'Angstrom'." % unit)
# Unit conversion.
if unit == 'Angstrom':
ave_dist = ave_dist * 1e-10
# Generate the selection objects.
sel_obj1 = Selection(spin_id1)
sel_obj2 = Selection(spin_id2)
# Loop over the interatomic containers.
data = []
for interatom in interatomic_loop():
# Get the spin info.
mol_name1, res_num1, res_name1, spin1 = return_spin(interatom.spin_id1, full_info=True)
mol_name2, res_num2, res_name2, spin2 = return_spin(interatom.spin_id2, full_info=True)
# No match, either way.
if not (sel_obj1.contains_spin(spin_num=spin1.num, spin_name=spin1.name, res_num=res_num1, res_name=res_name1, mol=mol_name1) and sel_obj2.contains_spin(spin_num=spin2.num, spin_name=spin2.name, res_num=res_num2, res_name=res_name2, mol=mol_name2)) and not (sel_obj2.contains_spin(spin_num=spin1.num, spin_name=spin1.name, res_num=res_num1, res_name=res_name1, mol=mol_name1) and sel_obj1.contains_spin(spin_num=spin2.num, spin_name=spin2.name, res_num=res_num2, res_name=res_name2, mol=mol_name2)):
continue
# Store the averaged distance.
interatom.r = ave_dist
# Store the data for the printout.
data.append([repr(interatom.spin_id1), repr(interatom.spin_id2), repr(ave_dist)])
# No data, so fail!
if not len(data):
raise RelaxError("No data could be set.")
# Print out.
print("The following averaged distances have been set:\n")
write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2", "Ave_distance(meters)"], data=data)
def pack_data(ri_id,
ri_type,
frq,
values,
errors,
spin_ids=None,
mol_names=None,
res_nums=None,
res_names=None,
spin_nums=None,
spin_names=None,
spin_id=None,
gen_seq=False,
verbose=True):
"""Pack the relaxation data into the data pipe and spin containers.
The values, errors, and spin_ids arguments must be lists of equal length or None. Each element i corresponds to a unique spin.
@param ri_id: The relaxation data ID string.
@type ri_id: str
@param ri_type: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
@type ri_type: str
@param frq: The spectrometer proton frequency in Hz.
@type frq: float
@keyword values: The relaxation data for each spin.
@type values: None or list of float or float array
@keyword errors: The relaxation data errors for each spin.
@type errors: None or list of float or float array
@keyword spin_ids: The list of spin ID strings. If the other spin identifiers are given, i.e. mol_names, res_nums, res_names, spin_nums, and/or spin_names, then this argument is not necessary.
@type spin_ids: None or list of str
@keyword mol_names: The list of molecule names used for creating the spin IDs (if not given) or for generating the sequence data.
@type mol_names: None or list of str
@keyword res_nums: The list of residue numbers used for creating the spin IDs (if not given) or for generating the sequence data.
@type res_nums: None or list of str
@keyword res_names: The list of residue names used for creating the spin IDs (if not given) or for generating the sequence data.
@type res_names: None or list of str
@keyword spin_nums: The list of spin numbers used for creating the spin IDs (if not given) or for generating the sequence data.
@type spin_nums: None or list of str
@keyword spin_names: The list of spin names used for creating the spin IDs (if not given) or for generating the sequence data.
@type spin_names: None or list of str
@keyword gen_seq: A flag which if True will cause the molecule, residue, and spin sequence data to be generated.
@type gen_seq: bool
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# The number of spins.
N = len(values)
# Test the data.
if errors != None and len(errors) != N:
raise RelaxError(
"The length of the errors arg (%s) does not match that of the value arg (%s)."
% (len(errors), N))
if spin_ids and len(spin_ids) != N:
raise RelaxError(
"The length of the spin ID strings arg (%s) does not match that of the value arg (%s)."
% (len(mol_names), N))
if mol_names and len(mol_names) != N:
raise RelaxError(
"The length of the molecule names arg (%s) does not match that of the value arg (%s)."
% (len(mol_names), N))
if res_nums and len(res_nums) != N:
raise RelaxError(
"The length of the residue numbers arg (%s) does not match that of the value arg (%s)."
% (len(res_nums), N))
if res_names and len(res_names) != N:
raise RelaxError(
"The length of the residue names arg (%s) does not match that of the value arg (%s)."
% (len(res_names), N))
if spin_nums and len(spin_nums) != N:
raise RelaxError(
"The length of the spin numbers arg (%s) does not match that of the value arg (%s)."
% (len(spin_nums), N))
if spin_names and len(spin_names) != N:
raise RelaxError(
"The length of the spin names arg (%s) does not match that of the value arg (%s)."
% (len(spin_names), N))
# Generate some empty lists.
if not mol_names:
mol_names = [None] * N
if not res_nums:
res_nums = [None] * N
if not res_names:
res_names = [None] * N
if not spin_nums:
spin_nums = [None] * N
if not spin_names:
spin_names = [None] * N
if errors == None:
errors = [None] * N
# Generate the spin IDs.
if not spin_ids:
spin_ids = []
for i in range(N):
spin_ids.append(
generate_spin_id_unique(spin_num=spin_nums[i],
spin_name=spin_names[i],
res_num=res_nums[i],
res_name=res_names[i],
mol_name=mol_names[i]))
# Initialise the global data for the current pipe if necessary.
if not hasattr(cdp, 'ri_type'):
cdp.ri_type = {}
if not hasattr(cdp, 'ri_ids'):
cdp.ri_ids = []
# Set the spectrometer frequency.
set_frequency(id=ri_id, frq=frq)
# Update the global data.
cdp.ri_ids.append(ri_id)
cdp.ri_type[ri_id] = ri_type
# The selection object.
select_obj = None
if spin_id:
select_obj = Selection(spin_id)
# Loop over the spin data.
data = []
for i in range(N):
# A selection union.
select_id = spin_ids[i]
if spin_id != None:
select_id = "%s&%s" % (select_id, spin_id)
# Get the corresponding spin container.
match_mol_names, match_res_nums, match_res_names, spins = return_spin_from_selection(
selection=select_id, full_info=True, multi=True)
# No spin.
if len(spins) == 0:
continue
# Check that multiple spins are not present.
if len(spins) > 1:
# Generate the list of spin IDs.
new_ids = []
for j in range(len(spins)):
new_ids.append(
generate_spin_id_unique(mol_name=match_mol_names[j],
res_num=match_res_nums[j],
res_name=match_res_names[j],
spin_num=spins[j].num,
spin_name=spins[j].name))
# Raise the error.
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
# Check that at least one spin is present.
if len(spins) == 0:
raise RelaxNoSpinError(spin_ids[i])
# Loop over the spins.
for j in range(len(spins)):
# No match to the selection.
if select_obj and not select_obj.contains_spin(
spin_num=spins[j].num,
spin_name=spins[j].name,
res_num=res_nums[j],
res_name=res_names[j],
mol=mol_names[j]):
continue
# Initialise the spin data if necessary.
if not hasattr(spins[j], 'ri_data') or spins[j].ri_data == None:
spins[j].ri_data = {}
if not hasattr(spins[j],
'ri_data_err') or spins[j].ri_data_err == None:
spins[j].ri_data_err = {}
# Update all data structures.
spins[j].ri_data[ri_id] = values[i]
spins[j].ri_data_err[ri_id] = errors[i]
# Append the data for printing out.
data.append([spin_ids[i], repr(values[i]), repr(errors[i])])
# Print out.
if verbose:
print(
"\nThe following %s MHz %s relaxation data with the ID '%s' has been loaded into the relax data store:\n"
% (frq / 1e6, ri_type, ri_id))
write_data(out=sys.stdout,
headings=["Spin_ID", "Value", "Error"],
data=data)
def interatomic_loop(selection1=None, selection2=None, pipe=None, skip_desel=True):
"""Generator function for looping over all the interatomic data containers.
@keyword selection1: The optional spin ID selection of the first atom.
@type selection1: str
@keyword selection2: The optional spin ID selection of the second atom.
@type selection2: str
@keyword pipe: The data pipe containing the spin. Defaults to the current data pipe.
@type pipe: str
@keyword skip_desel: A flag which if True will cause only selected interatomic data containers to be returned.
@type skip_desel: bool
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Parse the spin ID selection strings.
select_obj = None
select_obj1 = None
select_obj2 = None
if selection1 and selection2:
select_obj1 = Selection(selection1)
select_obj2 = Selection(selection2)
elif selection1:
select_obj = Selection(selection1)
elif selection2:
select_obj = Selection(selection2)
# Loop over the containers, yielding them.
for i in range(len(dp.interatomic)):
# Skip deselected containers.
if skip_desel and not dp.interatomic[i].select:
continue
# Aliases.
interatom = dp.interatomic[i]
mol_index1, res_index1, spin_index1 = dp.mol._spin_hash_lookup[interatom._spin_hash1]
mol_index2, res_index2, spin_index2 = dp.mol._spin_hash_lookup[interatom._spin_hash2]
mol1 = dp.mol[mol_index1]
res1 = dp.mol[mol_index1].res[res_index1]
spin1 = dp.mol[mol_index1].res[res_index1].spin[spin_index1]
mol2 = dp.mol[mol_index2]
res2 = dp.mol[mol_index2].res[res_index2]
spin2 = dp.mol[mol_index2].res[res_index2].spin[spin_index2]
# The different selection combinations.
if select_obj:
sel1 = select_obj.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel2 = select_obj.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
if select_obj1:
sel11 = select_obj1.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel12 = select_obj1.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
if select_obj2:
sel21 = select_obj2.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel22 = select_obj2.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
# Check that the selections are met.
if select_obj:
if not sel1 and not sel2:
continue
if select_obj1:
if not (sel11 or sel12):
continue
if select_obj2:
if not (sel21 or sel22):
continue
# Return the container.
yield interatom
def pack_data(ri_id, ri_type, frq, values, errors, spin_ids=None, mol_names=None, res_nums=None, res_names=None, spin_nums=None, spin_names=None, spin_id=None, gen_seq=False, verbose=True):
"""Pack the relaxation data into the data pipe and spin containers.
The values, errors, and spin_ids arguments must be lists of equal length or None. Each element i corresponds to a unique spin.
@param ri_id: The relaxation data ID string.
@type ri_id: str
@param ri_type: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
@type ri_type: str
@param frq: The spectrometer proton frequency in Hz.
@type frq: float
@keyword values: The relaxation data for each spin.
@type values: None or list of float or float array
@keyword errors: The relaxation data errors for each spin.
@type errors: None or list of float or float array
@keyword spin_ids: The list of spin ID strings. If the other spin identifiers are given, i.e. mol_names, res_nums, res_names, spin_nums, and/or spin_names, then this argument is not necessary.
@type spin_ids: None or list of str
@keyword mol_names: The list of molecule names used for creating the spin IDs (if not given) or for generating the sequence data.
@type mol_names: None or list of str
@keyword res_nums: The list of residue numbers used for creating the spin IDs (if not given) or for generating the sequence data.
@type res_nums: None or list of str
@keyword res_names: The list of residue names used for creating the spin IDs (if not given) or for generating the sequence data.
@type res_names: None or list of str
@keyword spin_nums: The list of spin numbers used for creating the spin IDs (if not given) or for generating the sequence data.
@type spin_nums: None or list of str
@keyword spin_names: The list of spin names used for creating the spin IDs (if not given) or for generating the sequence data.
@type spin_names: None or list of str
@keyword gen_seq: A flag which if True will cause the molecule, residue, and spin sequence data to be generated.
@type gen_seq: bool
@keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out.
@type verbose: bool
"""
# The number of spins.
N = len(values)
# Test the data.
if errors != None and len(errors) != N:
raise RelaxError("The length of the errors arg (%s) does not match that of the value arg (%s)." % (len(errors), N))
if spin_ids and len(spin_ids) != N:
raise RelaxError("The length of the spin ID strings arg (%s) does not match that of the value arg (%s)." % (len(mol_names), N))
if mol_names and len(mol_names) != N:
raise RelaxError("The length of the molecule names arg (%s) does not match that of the value arg (%s)." % (len(mol_names), N))
if res_nums and len(res_nums) != N:
raise RelaxError("The length of the residue numbers arg (%s) does not match that of the value arg (%s)." % (len(res_nums), N))
if res_names and len(res_names) != N:
raise RelaxError("The length of the residue names arg (%s) does not match that of the value arg (%s)." % (len(res_names), N))
if spin_nums and len(spin_nums) != N:
raise RelaxError("The length of the spin numbers arg (%s) does not match that of the value arg (%s)." % (len(spin_nums), N))
if spin_names and len(spin_names) != N:
raise RelaxError("The length of the spin names arg (%s) does not match that of the value arg (%s)." % (len(spin_names), N))
# Generate some empty lists.
if not mol_names:
mol_names = [None] * N
if not res_nums:
res_nums = [None] * N
if not res_names:
res_names = [None] * N
if not spin_nums:
spin_nums = [None] * N
if not spin_names:
spin_names = [None] * N
if errors == None:
errors = [None] * N
# Generate the spin IDs.
if not spin_ids:
spin_ids = []
for i in range(N):
spin_ids.append(generate_spin_id_unique(spin_num=spin_nums[i], spin_name=spin_names[i], res_num=res_nums[i], res_name=res_names[i], mol_name=mol_names[i]))
# Initialise the global data for the current pipe if necessary.
if not hasattr(cdp, 'ri_type'):
cdp.ri_type = {}
if not hasattr(cdp, 'ri_ids'):
cdp.ri_ids = []
# Set the spectrometer frequency.
set_frequency(id=ri_id, frq=frq)
# Update the global data.
cdp.ri_ids.append(ri_id)
cdp.ri_type[ri_id] = ri_type
# The selection object.
select_obj = None
if spin_id:
select_obj = Selection(spin_id)
# Loop over the spin data.
data = []
for i in range(N):
# Get the corresponding spin container.
match_mol_names, match_res_nums, match_res_names, spins = return_spin_from_selection(spin_ids[i], full_info=True, multi=True)
if spins in [None, []]:
raise RelaxNoSpinError(spin_ids[i])
# Remove non-matching spins.
if select_obj:
new_spins = []
new_mol_names = []
new_res_nums = []
new_res_names = []
new_ids = []
for j in range(len(spins)):
if select_obj.contains_spin(spin_num=spins[j].num, spin_name=spins[j].name, res_num=match_res_nums[j], res_name=match_res_names[j], mol=match_mol_names[j]):
new_spins.append(spins[j])
new_mol_names.append(match_mol_names[j])
new_res_nums.append(match_res_nums[j])
new_res_names.append(match_res_names[j])
new_ids.append(generate_spin_id_unique(mol_name=mol_names[i], res_num=res_nums[i], res_name=res_names[i], spin_num=spins[j].num, spin_name=spins[j].name))
new_id = new_ids[0]
# Aliases for normal operation.
else:
new_spins = spins
new_mol_names = match_mol_names
new_res_nums = match_res_nums
new_res_names = match_res_names
new_id = spin_ids[i]
new_ids = None
# Check that only a singe spin is present.
if len(new_spins) > 1:
if new_ids:
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
else:
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
if len(new_spins) == 0:
raise RelaxNoSpinError(spin_ids[i])
# Loop over the spins.
for j in range(len(new_spins)):
# No match to the selection.
if select_obj and not select_obj.contains_spin(spin_num=new_spins[j].num, spin_name=new_spins[j].name, res_num=new_res_nums[j], res_name=new_res_names[j], mol=new_mol_names[j]):
continue
# Initialise the spin data if necessary.
if not hasattr(new_spins[j], 'ri_data') or new_spins[j].ri_data == None:
new_spins[j].ri_data = {}
if not hasattr(new_spins[j], 'ri_data_err') or new_spins[j].ri_data_err == None:
new_spins[j].ri_data_err = {}
# Update all data structures.
new_spins[j].ri_data[ri_id] = values[i]
new_spins[j].ri_data_err[ri_id] = errors[i]
# Append the data for printing out.
data.append([new_id, repr(values[i]), repr(errors[i])])
# Print out.
if verbose:
print("\nThe following %s MHz %s relaxation data with the ID '%s' has been loaded into the relax data store:\n" % (frq/1e6, ri_type, ri_id))
write_data(out=sys.stdout, headings=["Spin_ID", "Value", "Error"], data=data)
def interatomic_loop(selection1=None, selection2=None, pipe=None, skip_desel=True):
"""Generator function for looping over all the interatomic data containers.
@keyword selection1: The optional spin ID selection of the first atom.
@type selection1: str
@keyword selection2: The optional spin ID selection of the second atom.
@type selection2: str
@keyword pipe: The data pipe containing the spin. Defaults to the current data pipe.
@type pipe: str
@keyword skip_desel: A flag which if True will cause only selected interatomic data containers to be returned.
@type skip_desel: bool
"""
# The data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# Get the data pipe.
dp = pipes.get_pipe(pipe)
# Parse the spin ID selection strings.
select_obj = None
select_obj1 = None
select_obj2 = None
if selection1 and selection2:
select_obj1 = Selection(selection1)
select_obj2 = Selection(selection2)
elif selection1:
select_obj = Selection(selection1)
elif selection2:
select_obj = Selection(selection2)
# Loop over the containers, yielding them.
for i in range(len(dp.interatomic)):
# Skip deselected containers.
if skip_desel and not dp.interatomic[i].select:
continue
# Aliases.
interatom = dp.interatomic[i]
mol_index1, res_index1, spin_index1 = cdp.mol._spin_id_lookup[interatom.spin_id1]
mol_index2, res_index2, spin_index2 = cdp.mol._spin_id_lookup[interatom.spin_id2]
mol1 = cdp.mol[mol_index1]
res1 = cdp.mol[mol_index1].res[res_index1]
spin1 = cdp.mol[mol_index1].res[res_index1].spin[spin_index1]
mol2 = cdp.mol[mol_index2]
res2 = cdp.mol[mol_index2].res[res_index2]
spin2 = cdp.mol[mol_index2].res[res_index2].spin[spin_index2]
# The different selection combinations.
if select_obj:
sel1 = select_obj.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel2 = select_obj.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
if select_obj1:
sel11 = select_obj1.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel12 = select_obj1.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
if select_obj2:
sel21 = select_obj2.contains_spin(spin_name=spin1.name, spin_num=spin1.num, res_name=res1.name, res_num=res1.num, mol=mol1.name)
sel22 = select_obj2.contains_spin(spin_name=spin2.name, spin_num=spin2.num, res_name=res2.name, res_num=res2.num, mol=mol2.name)
# Check that the selections are met.
if select_obj:
if not sel1 and not sel2:
continue
if select_obj1:
if not (sel11 or sel12):
continue
if select_obj2:
if not (sel21 or sel22):
continue
# Return the container.
yield interatom