def create_script(file, model_type, algor):
"""Create the Dasha script file.
@param file: The opened file descriptor.
@type file: file object
@param model_type: The model-free model type.
@type model_type: str
@param algor: The optimisation algorithm to use. This can be the Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
"""
# Delete all data.
file.write("# Delete all data.\n")
file.write("del 1 10000\n")
# Nucleus type.
file.write("\n# Nucleus type.\n")
nucleus = None
for spin in spin_loop():
# Skip protons.
if spin.isotope == '1H':
continue
# Can only handle one spin type.
if nucleus and spin.isotope != nucleus:
raise RelaxError("The nuclei '%s' and '%s' do not match, relax can only handle one nucleus type in Dasha." % (nucleus, spin.isotope))
# Set the nucleus.
if not nucleus:
nucleus = spin.isotope
# Convert the name and write it.
if nucleus == '15N':
nucleus = 'N15'
elif nucleus == '13C':
nucleus = 'C13'
else:
raise RelaxError("Cannot handle the nucleus type '%s' within Dasha." % nucleus)
file.write("set nucl %s\n" % nucleus)
# Number of frequencies.
file.write("\n# Number of frequencies.\n")
file.write("set n_freq %s\n" % cdp.spectrometer_frq_count)
# Frequency values.
file.write("\n# Frequency values.\n")
count = 1
for frq in loop_frequencies():
file.write("set H1_freq %s %s\n" % (frq / 1e6, count))
count += 1
# Set the diffusion tensor.
file.write("\n# Set the diffusion tensor.\n")
if model_type != 'local_tm':
# Sphere.
if cdp.diff_tensor.type == 'sphere':
file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
# Spheroid.
elif cdp.diff_tensor.type == 'spheroid':
file.write('set tr %s\n' % (cdp.diff_tensor.tm / 1e-9))
# Ellipsoid.
elif cdp.diff_tensor.type == 'ellipsoid':
# Get the eigenvales.
Dx, Dy, Dz = diffusion_tensor.return_eigenvalues()
# Geometric parameters.
file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
file.write("set D1/D3 %s\n" % (Dx / Dz))
file.write("set D2/D3 %s\n" % (Dy / Dz))
# Orientational parameters.
file.write("set alfa %s\n" % (cdp.diff_tensor.alpha / (2.0 * pi) * 360.0))
file.write("set betta %s\n" % (cdp.diff_tensor.beta / (2.0 * pi) * 360.0))
file.write("set gamma %s\n" % (cdp.diff_tensor.gamma / (2.0 * pi) * 360.0))
# Reading the relaxation data.
file.write("\n# Reading the relaxation data.\n")
file.write("echo Reading the relaxation data.\n")
noe_index = 1
r1_index = 1
r2_index = 1
for ri_id in cdp.ri_ids:
# NOE.
if cdp.ri_type[ri_id] == 'NOE':
# Data set number.
number = noe_index
# Data type.
data_type = 'noe'
# Increment the data set index.
noe_index = noe_index + 1
# R1.
elif cdp.ri_type[ri_id] == 'R1':
# Data set number.
number = r1_index
# Data type.
data_type = '1/T1'
# Increment the data set index.
r1_index = r1_index + 1
# R2.
elif cdp.ri_type[ri_id] == 'R2':
# Data set number.
number = r2_index
# Data type.
data_type = '1/T2'
# Increment the data set index.
r2_index = r2_index + 1
# Set the data type.
if number == 1:
file.write("\nread < %s\n" % data_type)
else:
file.write("\nread < %s %s\n" % (data_type, number))
# The relaxation data.
for residue in residue_loop():
# Alias the spin.
spin = residue.spin[0]
# Skip deselected spins.
if not spin.select:
continue
# Skip and deselect spins for which relaxation data is missing.
if len(spin.ri_data) != len(cdp.ri_ids) or spin.ri_data[ri_id] == None:
spin.select = False
continue
# Data and errors.
file.write("%s %s %s\n" % (residue.num, spin.ri_data[ri_id], spin.ri_data_err[ri_id]))
# Terminate the reading.
file.write("exit\n")
# Individual residue optimisation.
if model_type == 'mf':
# Loop over the residues.
for residue in residue_loop():
# Alias the spin.
spin = residue.spin[0]
# Skip deselected spins.
if not spin.select:
continue
# Get the interatomic data containers.
interatoms = return_interatom_list(spin._spin_ids[0])
if len(interatoms) == 0:
raise RelaxNoInteratomError
elif len(interatoms) > 1:
raise RelaxError("Only one interatomic data container, hence dipole-dipole interaction, is supported per spin.")
# Comment.
file.write("\n\n\n# Residue %s\n\n" % residue.num)
# Echo.
file.write("echo Optimisation of residue %s\n" % residue.num)
# Select the spin.
file.write("\n# Select the residue.\n")
file.write("set cres %s\n" % residue.num)
# The angle alpha of the XH vector in the spheroid diffusion frame.
if cdp.diff_tensor.type == 'spheroid':
file.write("set teta %s\n" % spin.alpha)
# The angles theta and phi of the XH vector in the ellipsoid diffusion frame.
elif cdp.diff_tensor.type == 'ellipsoid':
file.write("\n# Setting the spherical angles of the XH vector in the ellipsoid diffusion frame.\n")
file.write("set teta %s\n" % spin.theta)
file.write("set fi %s\n" % spin.phi)
# The 'jmode'.
if 'ts' in spin.params:
jmode = 3
elif 'te' in spin.params:
jmode = 2
elif 's2' in spin.params:
jmode = 1
# Chemical exchange.
if 'rex' in spin.params:
exch = True
else:
exch = False
# Anisotropic diffusion.
if cdp.diff_tensor.type == 'sphere':
anis = False
else:
anis = True
# Axial symmetry.
if cdp.diff_tensor.type == 'spheroid':
sym = True
else:
sym = False
# Set the jmode.
file.write("\n# Set the jmode.\n")
file.write("set def jmode %s" % jmode)
if exch:
file.write(" exch")
if anis:
file.write(" anis")
if sym:
file.write(" sym")
file.write("\n")
# Parameter default values.
file.write("\n# Parameter default values.\n")
file.write("reset jmode %s\n" % residue.num)
# Bond length.
file.write("\n# Bond length.\n")
file.write("set r_hx %s\n" % (interatoms[0].r / 1e-10))
# CSA value.
file.write("\n# CSA value.\n")
file.write("set csa %s\n" % (spin.csa / 1e-6))
# Fix the tf parameter if it isn't in the model.
if not 'tf' in spin.params and jmode == 3:
file.write("\n# Fix the tf parameter.\n")
file.write("fix tf 0\n")
# Optimisation of all residues.
file.write("\n\n\n# Optimisation of all residues.\n")
if algor == 'LM':
file.write("lmin %s %s" % (first_residue_num(), last_residue_num()))
elif algor == 'NR':
file.write("min %s %s" % (first_residue_num(), last_residue_num()))
# Show the results.
file.write("\n# Show the results.\n")
file.write("echo\n")
file.write("show all\n")
# Write the results.
file.write("\n# Write the results.\n")
file.write("write s2.out S\n")
file.write("write s2f.out Sf\n")
file.write("write s2s.out Ss\n")
file.write("write te.out te\n")
file.write("write tf.out tf\n")
file.write("write ts.out ts\n")
file.write("write rex.out rex\n")
file.write("write chi2.out F\n")
else:
raise RelaxError("Optimisation of the parameter set '%s' currently not supported." % model_type)
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)
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 create_script(file, model_type, algor):
"""Create the Dasha script file.
@param file: The opened file descriptor.
@type file: file object
@param model_type: The model-free model type.
@type model_type: str
@param algor: The optimisation algorithm to use. This can be the Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
"""
# Delete all data.
file.write("# Delete all data.\n")
file.write("del 1 10000\n")
# Nucleus type.
file.write("\n# Nucleus type.\n")
nucleus = None
for spin in spin_loop():
# Skip protons.
if spin.isotope == '1H':
continue
# Can only handle one spin type.
if nucleus and spin.isotope != nucleus:
raise RelaxError(
"The nuclei '%s' and '%s' do not match, relax can only handle one nucleus type in Dasha."
% (nucleus, spin.isotope))
# Set the nucleus.
if not nucleus:
nucleus = spin.isotope
# Convert the name and write it.
if nucleus == '15N':
nucleus = 'N15'
elif nucleus == '13C':
nucleus = 'C13'
else:
raise RelaxError("Cannot handle the nucleus type '%s' within Dasha." %
nucleus)
file.write("set nucl %s\n" % nucleus)
# Number of frequencies.
file.write("\n# Number of frequencies.\n")
file.write("set n_freq %s\n" % cdp.spectrometer_frq_count)
# Frequency values.
file.write("\n# Frequency values.\n")
count = 1
for frq in loop_frequencies():
file.write("set H1_freq %s %s\n" % (frq / 1e6, count))
count += 1
# Set the diffusion tensor.
file.write("\n# Set the diffusion tensor.\n")
if model_type != 'local_tm':
# Sphere.
if cdp.diff_tensor.type == 'sphere':
file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
# Spheroid.
elif cdp.diff_tensor.type == 'spheroid':
file.write('set tr %s\n' % (cdp.diff_tensor.tm / 1e-9))
# Ellipsoid.
elif cdp.diff_tensor.type == 'ellipsoid':
# Get the eigenvales.
Dx, Dy, Dz = diffusion_tensor.return_eigenvalues()
# Geometric parameters.
file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
file.write("set D1/D3 %s\n" % (Dx / Dz))
file.write("set D2/D3 %s\n" % (Dy / Dz))
# Orientational parameters.
file.write("set alfa %s\n" % (cdp.diff_tensor.alpha /
(2.0 * pi) * 360.0))
file.write("set betta %s\n" % (cdp.diff_tensor.beta /
(2.0 * pi) * 360.0))
file.write("set gamma %s\n" % (cdp.diff_tensor.gamma /
(2.0 * pi) * 360.0))
# Reading the relaxation data.
file.write("\n# Reading the relaxation data.\n")
file.write("echo Reading the relaxation data.\n")
noe_index = 1
r1_index = 1
r2_index = 1
for ri_id in cdp.ri_ids:
# NOE.
if cdp.ri_type[ri_id] == 'NOE':
# Data set number.
number = noe_index
# Data type.
data_type = 'noe'
# Increment the data set index.
noe_index = noe_index + 1
# R1.
elif cdp.ri_type[ri_id] == 'R1':
# Data set number.
number = r1_index
# Data type.
data_type = '1/T1'
# Increment the data set index.
r1_index = r1_index + 1
# R2.
elif cdp.ri_type[ri_id] == 'R2':
# Data set number.
number = r2_index
# Data type.
data_type = '1/T2'
# Increment the data set index.
r2_index = r2_index + 1
# Set the data type.
if number == 1:
file.write("\nread < %s\n" % data_type)
else:
file.write("\nread < %s %s\n" % (data_type, number))
# The relaxation data.
for residue in residue_loop():
# Alias the spin.
spin = residue.spin[0]
# Skip deselected spins.
if not spin.select:
continue
# Skip and deselect spins for which relaxation data is missing.
if len(spin.ri_data) != len(
cdp.ri_ids) or spin.ri_data[ri_id] == None:
spin.select = False
continue
# Data and errors.
file.write(
"%s %s %s\n" %
(residue.num, spin.ri_data[ri_id], spin.ri_data_err[ri_id]))
# Terminate the reading.
file.write("exit\n")
# Individual residue optimisation.
if model_type == 'mf':
# Loop over the residues.
for residue in residue_loop():
# Alias the spin.
spin = residue.spin[0]
# Skip deselected spins.
if not spin.select:
continue
# Get the interatomic data containers.
interatoms = return_interatom_list(spin_hash=spin._hash)
if len(interatoms) == 0:
raise RelaxNoInteratomError
elif len(interatoms) > 1:
raise RelaxError(
"Only one interatomic data container, hence dipole-dipole interaction, is supported per spin."
)
# Comment.
file.write("\n\n\n# Residue %s\n\n" % residue.num)
# Echo.
file.write("echo Optimisation of residue %s\n" % residue.num)
# Select the spin.
file.write("\n# Select the residue.\n")
file.write("set cres %s\n" % residue.num)
# The angle alpha of the XH vector in the spheroid diffusion frame.
if cdp.diff_tensor.type == 'spheroid':
file.write("set teta %s\n" % spin.alpha)
# The angles theta and phi of the XH vector in the ellipsoid diffusion frame.
elif cdp.diff_tensor.type == 'ellipsoid':
file.write(
"\n# Setting the spherical angles of the XH vector in the ellipsoid diffusion frame.\n"
)
file.write("set teta %s\n" % spin.theta)
file.write("set fi %s\n" % spin.phi)
# The 'jmode'.
if 'ts' in spin.params:
jmode = 3
elif 'te' in spin.params:
jmode = 2
elif 's2' in spin.params:
jmode = 1
# Chemical exchange.
if 'rex' in spin.params:
exch = True
else:
exch = False
# Anisotropic diffusion.
if cdp.diff_tensor.type == 'sphere':
anis = False
else:
anis = True
# Axial symmetry.
if cdp.diff_tensor.type == 'spheroid':
sym = True
else:
sym = False
# Set the jmode.
file.write("\n# Set the jmode.\n")
file.write("set def jmode %s" % jmode)
if exch:
file.write(" exch")
if anis:
file.write(" anis")
if sym:
file.write(" sym")
file.write("\n")
# Parameter default values.
file.write("\n# Parameter default values.\n")
file.write("reset jmode %s\n" % residue.num)
# Bond length.
file.write("\n# Bond length.\n")
file.write("set r_hx %s\n" % (interatoms[0].r / 1e-10))
# CSA value.
file.write("\n# CSA value.\n")
file.write("set csa %s\n" % (spin.csa / 1e-6))
# Fix the tf parameter if it isn't in the model.
if not 'tf' in spin.params and jmode == 3:
file.write("\n# Fix the tf parameter.\n")
file.write("fix tf 0\n")
# Optimisation of all residues.
file.write("\n\n\n# Optimisation of all residues.\n")
if algor == 'LM':
file.write("lmin %s %s" %
(first_residue_num(), last_residue_num()))
elif algor == 'NR':
file.write("min %s %s" % (first_residue_num(), last_residue_num()))
# Show the results.
file.write("\n# Show the results.\n")
file.write("echo\n")
file.write("show all\n")
# Write the results.
file.write("\n# Write the results.\n")
file.write("write s2.out S\n")
file.write("write s2f.out Sf\n")
file.write("write s2s.out Ss\n")
file.write("write te.out te\n")
file.write("write tf.out tf\n")
file.write("write ts.out ts\n")
file.write("write rex.out rex\n")
file.write("write chi2.out F\n")
else:
raise RelaxError(
"Optimisation of the parameter set '%s' currently not supported." %
model_type)
