def process(self):
"""Process the Bruker DC data already present in the section object."""
# Loop over the data.
for i in range(len(self._data)):
# The labelling.
if self._data[i][0] == 'Labelling:':
# The spin isotope.
self.isotope = self._data[i][1]
# The name of the spins.
self.spin_name = split('([A-Z]+)', self._data[i][1])[1]
# The atom name.
self.atom_name = element_from_isotope(self.isotope)
def read(ri_id=None, file=None, dir=None):
"""Read the DC data file and place all the data into the relax data store.
@keyword ri_id: The relaxation data ID string.
@type ri_id: str
@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
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Extract the data from the file.
values, errors, res_nums, int_type, frq, ri_type, spin_name, isotope, version = parse_file(
file=file, dir=dir)
# Name the spins if needed.
name_spin(name=spin_name, force=False)
# Modify the residue numbers by adding the heteronucleus name.
if isotope:
atom_name = element_from_isotope(isotope)
for i in range(len(res_nums)):
res_nums[i] += '@' + atom_name
# Pack the data.
pack_data(ri_id, ri_type, frq, values, errors, spin_ids=res_nums)
# Set the integration method.
peak_intensity_type(ri_id=ri_id, type=int_type)
# Set the DC as used software.
software_select('Bruker DC', version=version)
def read(ri_id=None, file=None, dir=None):
"""Read the DC data file and place all the data into the relax data store.
@keyword ri_id: The relaxation data ID string.
@type ri_id: str
@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
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Extract the data from the file.
values, errors, res_nums, int_type, frq, ri_type, spin_name, isotope, version = parse_file(file=file, dir=dir)
# Name the spins if needed.
name_spin(name=spin_name, force=False)
# Modify the residue numbers by adding the heteronucleus name.
if isotope:
atom_name = element_from_isotope(isotope)
for i in range(len(res_nums)):
res_nums[i] += '@' + atom_name
# Pack the data.
pack_data(ri_id, ri_type, frq, values, errors, spin_ids=res_nums)
# Set the integration method.
peak_intensity_type(ri_id=ri_id, type=int_type)
# Set the DC as used software.
software_select('Bruker DC', version=version)
def bmrb_write(star):
"""Generate the relaxation data saveframes for the NMR-STAR dictionary object.
@param star: The NMR-STAR dictionary object.
@type star: NMR_STAR instance
"""
# Get the current data pipe.
cdp = pipes.get_pipe()
# Initialise the spin specific data lists.
mol_name_list = []
res_num_list = []
res_name_list = []
atom_name_list = []
isotope_list = []
element_list = []
attached_atom_name_list = []
attached_isotope_list = []
attached_element_list = []
ri_data_list = []
ri_data_err_list = []
for i in range(len(cdp.ri_ids)):
ri_data_list.append([])
ri_data_err_list.append([])
# Relax data labels.
labels = cdp.ri_ids
exp_label = []
spectro_ids = []
spectro_labels = []
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(
full_info=True, return_id=True):
# Skip spins with no relaxation data.
if not hasattr(spin, 'ri_data'):
continue
# Check the data for None (not allowed in BMRB!).
if res_num == None:
raise RelaxError(
"For the BMRB, the residue of spin '%s' must be numbered." %
spin_id)
if res_name == None:
raise RelaxError(
"For the BMRB, the residue of spin '%s' must be named." %
spin_id)
if spin.name == None:
raise RelaxError("For the BMRB, the spin '%s' must be named." %
spin_id)
if spin.isotope == None:
raise RelaxError(
"For the BMRB, the spin isotope type of '%s' must be specified."
% spin_id)
# The molecule/residue/spin info.
mol_name_list.append(mol_name)
res_num_list.append(str(res_num))
res_name_list.append(str(res_name))
atom_name_list.append(str(spin.name))
# Interatomic info.
interatoms = return_interatom_list(spin_hash=spin._hash)
if len(interatoms) == 0:
raise RelaxError(
"No interatomic interactions are defined for the spin '%s'." %
spin_id)
if len(interatoms) > 1:
raise RelaxError(
"The BMRB only handles a signal interatomic interaction for the spin '%s'."
% spin_id)
# Get the attached spin.
spin_attached = return_spin(spin_hash=interatoms[0]._spin_hash1)
if id(spin_attached) == id(spin):
spin_attached = return_spin(spin_hash=interatoms[0]._spin_hash2)
# The attached atom info.
if hasattr(spin_attached, 'name'):
attached_atom_name_list.append(str(spin_attached.name))
else:
attached_atom_name_list.append(None)
if hasattr(spin_attached, 'isotope'):
attached_element_list.append(
element_from_isotope(spin_attached.isotope))
attached_isotope_list.append(
str(number_from_isotope(spin_attached.isotope)))
else:
attached_element_list.append(None)
attached_isotope_list.append(None)
# The relaxation data.
used_index = -ones(len(cdp.ri_ids))
for i in range(len(cdp.ri_ids)):
# Data exists.
if cdp.ri_ids[i] in spin.ri_data:
ri_data_list[i].append(str(spin.ri_data[cdp.ri_ids[i]]))
ri_data_err_list[i].append(str(
spin.ri_data_err[cdp.ri_ids[i]]))
else:
ri_data_list[i].append(None)
ri_data_err_list[i].append(None)
# Other info.
isotope_list.append(int(spin.isotope.strip(string.ascii_letters)))
element_list.append(spin.element)
# Convert the molecule names into the entity IDs.
entity_ids = zeros(len(mol_name_list), int32)
mol_names = get_molecule_names()
for i in range(len(mol_name_list)):
for j in range(len(mol_names)):
if mol_name_list[i] == mol_names[j]:
entity_ids[i] = j + 1
# Check the temperature control methods.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info,
'temp_calibration'):
raise RelaxError(
"The temperature calibration methods have not been specified.")
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info,
'temp_control'):
raise RelaxError(
"The temperature control methods have not been specified.")
# Check the peak intensity type.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info,
'peak_intensity_type'):
raise RelaxError(
"The peak intensity types measured for the relaxation data have not been specified."
)
# Loop over the relaxation data.
for i in range(len(cdp.ri_ids)):
# Alias.
ri_id = cdp.ri_ids[i]
ri_type = cdp.ri_type[ri_id]
# Convert to MHz.
frq = cdp.spectrometer_frq[ri_id] * 1e-6
# Get the temperature control methods.
temp_calib = cdp.exp_info.temp_calibration[ri_id]
temp_control = cdp.exp_info.temp_control[ri_id]
# Get the peak intensity type.
peak_intensity_type = cdp.exp_info.peak_intensity_type[ri_id]
# Check.
if not temp_calib:
raise RelaxError(
"The temperature calibration method for the '%s' relaxation data ID string has not been specified."
% ri_id)
if not temp_control:
raise RelaxError(
"The temperature control method for the '%s' relaxation data ID string has not been specified."
% ri_id)
# Add the relaxation data.
star.relaxation.add(data_type=ri_type,
frq=frq,
entity_ids=entity_ids,
res_nums=res_num_list,
res_names=res_name_list,
atom_names=atom_name_list,
atom_types=element_list,
isotope=isotope_list,
entity_ids_2=entity_ids,
res_nums_2=res_num_list,
res_names_2=res_name_list,
atom_names_2=attached_atom_name_list,
atom_types_2=attached_element_list,
isotope_2=attached_isotope_list,
data=ri_data_list[i],
errors=ri_data_err_list[i],
temp_calibration=temp_calib,
temp_control=temp_control,
peak_intensity_type=peak_intensity_type)
# The experimental label.
if ri_type == 'NOE':
exp_name = 'steady-state NOE'
else:
exp_name = ri_type
exp_label.append("%s MHz %s" % (frq, exp_name))
# Spectrometer info.
frq_num = 1
for frq in loop_frequencies():
if frq == cdp.spectrometer_frq[ri_id]:
break
frq_num += 1
spectro_ids.append(frq_num)
spectro_labels.append("$spectrometer_%s" % spectro_ids[-1])
# Add the spectrometer info.
num = 1
for frq in loop_frequencies():
star.nmr_spectrometer.add(name="$spectrometer_%s" % num,
manufacturer=None,
model=None,
frq=int(frq / 1e6))
num += 1
# Add the experiment saveframe.
star.experiment.add(name=exp_label,
spectrometer_ids=spectro_ids,
spectrometer_labels=spectro_labels)
def bmrb_write(star):
"""Generate the relaxation data saveframes for the NMR-STAR dictionary object.
@param star: The NMR-STAR dictionary object.
@type star: NMR_STAR instance
"""
# Get the current data pipe.
cdp = pipes.get_pipe()
# Initialise the spin specific data lists.
mol_name_list = []
res_num_list = []
res_name_list = []
atom_name_list = []
isotope_list = []
element_list = []
attached_atom_name_list = []
attached_isotope_list = []
attached_element_list = []
ri_data_list = []
ri_data_err_list = []
for i in range(len(cdp.ri_ids)):
ri_data_list.append([])
ri_data_err_list.append([])
# Relax data labels.
labels = cdp.ri_ids
exp_label = []
spectro_ids = []
spectro_labels = []
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True):
# Skip spins with no relaxation data.
if not hasattr(spin, 'ri_data'):
continue
# Check the data for None (not allowed in BMRB!).
if res_num == None:
raise RelaxError("For the BMRB, the residue of spin '%s' must be numbered." % spin_id)
if res_name == None:
raise RelaxError("For the BMRB, the residue of spin '%s' must be named." % spin_id)
if spin.name == None:
raise RelaxError("For the BMRB, the spin '%s' must be named." % spin_id)
if spin.isotope == None:
raise RelaxError("For the BMRB, the spin isotope type of '%s' must be specified." % spin_id)
# The molecule/residue/spin info.
mol_name_list.append(mol_name)
res_num_list.append(str(res_num))
res_name_list.append(str(res_name))
atom_name_list.append(str(spin.name))
# Interatomic info.
interatoms = return_interatom_list(spin_id)
if len(interatoms) == 0:
raise RelaxError("No interatomic interactions are defined for the spin '%s'." % spin_id)
if len(interatoms) > 1:
raise RelaxError("The BMRB only handles a signal interatomic interaction for the spin '%s'." % spin_id)
# Get the attached spin.
spin_attached = return_spin(interatoms[0].spin_id1)
if id(spin_attached) == id(spin):
spin_attached = return_spin(interatoms[0].spin_id2)
# The attached atom info.
if hasattr(spin_attached, 'name'):
attached_atom_name_list.append(str(spin_attached.name))
else:
attached_atom_name_list.append(None)
if hasattr(spin_attached, 'isotope'):
attached_element_list.append(element_from_isotope(spin_attached.isotope))
attached_isotope_list.append(str(number_from_isotope(spin_attached.isotope)))
else:
attached_element_list.append(None)
attached_isotope_list.append(None)
# The relaxation data.
used_index = -ones(len(cdp.ri_ids))
for i in range(len(cdp.ri_ids)):
# Data exists.
if cdp.ri_ids[i] in list(spin.ri_data.keys()):
ri_data_list[i].append(str(spin.ri_data[cdp.ri_ids[i]]))
ri_data_err_list[i].append(str(spin.ri_data_err[cdp.ri_ids[i]]))
else:
ri_data_list[i].append(None)
ri_data_err_list[i].append(None)
# Other info.
isotope_list.append(int(spin.isotope.strip(string.ascii_letters)))
element_list.append(spin.element)
# Convert the molecule names into the entity IDs.
entity_ids = zeros(len(mol_name_list), int32)
mol_names = get_molecule_names()
for i in range(len(mol_name_list)):
for j in range(len(mol_names)):
if mol_name_list[i] == mol_names[j]:
entity_ids[i] = j+1
# Check the temperature control methods.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_calibration'):
raise RelaxError("The temperature calibration methods have not been specified.")
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_control'):
raise RelaxError("The temperature control methods have not been specified.")
# Check the peak intensity type.
if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'peak_intensity_type'):
raise RelaxError("The peak intensity types measured for the relaxation data have not been specified.")
# Loop over the relaxation data.
for i in range(len(cdp.ri_ids)):
# Alias.
ri_id = cdp.ri_ids[i]
ri_type = cdp.ri_type[ri_id]
# Convert to MHz.
frq = cdp.spectrometer_frq[ri_id] * 1e-6
# Get the temperature control methods.
temp_calib = cdp.exp_info.temp_calibration[ri_id]
temp_control = cdp.exp_info.temp_control[ri_id]
# Get the peak intensity type.
peak_intensity_type = cdp.exp_info.peak_intensity_type[ri_id]
# Check.
if not temp_calib:
raise RelaxError("The temperature calibration method for the '%s' relaxation data ID string has not been specified." % ri_id)
if not temp_control:
raise RelaxError("The temperature control method for the '%s' relaxation data ID string has not been specified." % ri_id)
# Add the relaxation data.
star.relaxation.add(data_type=ri_type, frq=frq, entity_ids=entity_ids, res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list, atom_types=element_list, isotope=isotope_list, entity_ids_2=entity_ids, res_nums_2=res_num_list, res_names_2=res_name_list, atom_names_2=attached_atom_name_list, atom_types_2=attached_element_list, isotope_2=attached_isotope_list, data=ri_data_list[i], errors=ri_data_err_list[i], temp_calibration=temp_calib, temp_control=temp_control, peak_intensity_type=peak_intensity_type)
# The experimental label.
if ri_type == 'NOE':
exp_name = 'steady-state NOE'
else:
exp_name = ri_type
exp_label.append("%s MHz %s" % (frq, exp_name))
# Spectrometer info.
frq_num = 1
for frq in loop_frequencies():
if frq == cdp.spectrometer_frq[ri_id]:
break
frq_num += 1
spectro_ids.append(frq_num)
spectro_labels.append("$spectrometer_%s" % spectro_ids[-1])
# Add the spectrometer info.
num = 1
for frq in loop_frequencies():
star.nmr_spectrometer.add(name="$spectrometer_%s" % num, manufacturer=None, model=None, frq=int(frq/1e6))
num += 1
# Add the experiment saveframe.
star.experiment.add(name=exp_label, spectrometer_ids=spectro_ids, spectrometer_labels=spectro_labels)