def _assemble_experiment(self):
"""Assemble the experimental data."""
# Get the spectrometer info.
frq_Hz = get_frequencies(units='MHz')
frq_T = get_frequencies(units='T')
# Loop over all data points.
for exp_type, frq, point, time, ei, mi, di, ti in loop_exp_frq_point_time(return_indices=True):
# The frequency data.
self.cpmg_delay[mi] = str(time)
# Loop over the experiments.
for i in range(cdp.spectrometer_frq_count):
# Spectrometer info.
self.spec_frq[i] = str(frq_Hz[i] / g1H * g15N)
self.B0[i] = str(frq_T[i])
def _assemble_experiment(self):
"""Assemble the experimental data."""
# Get the spectrometer info.
frq_Hz = get_frequencies(units='MHz')
frq_T = get_frequencies(units='T')
# Loop over all data points.
for exp_type, frq, point, time, ei, mi, di, ti in loop_exp_frq_point_time(
return_indices=True):
# The frequency data.
self.cpmg_delay[mi] = str(time)
# Loop over the experiments.
for i in range(cdp.spectrometer_frq_count):
# Spectrometer info.
self.spec_frq[i] = str(frq_Hz[i] /
periodic_table.gyromagnetic_ratio('1H') *
periodic_table.gyromagnetic_ratio('15N'))
self.B0[i] = str(frq_T[i])
def create_spin_input(function=None, spin=None, spin_id=None, dir=None):
"""Generate the CPMGFit file for the given spin.
@keyword function: The CPMGFit model or function name.
@type function: str
@keyword spin: The spin container to generate the input file for.
@type spin: SpinContainer instance
@keyword spin_id: The spin ID string corresponding to the spin container.
@type spin_id: str
@keyword dir: The directory to place the file into.
@type dir: str or None
@return: The name of the file created.
@rtype: str
"""
# The output file.
file_name = spin_file_name(spin_id=spin_id)
file = open_write_file(file_name=file_name, dir=dir, force=True)
# The title.
file.write("title %s\n" % spin_id)
# The proton frequencies.
frq = get_frequencies(units='T')
# The frequency info.
file.write("fields %s" % len(frq))
for i in range(len(frq)):
file.write(" %.10f" % frq[i])
file.write("\n")
# The function and parameters.
if function == 'CPMG':
# Function.
file.write("function CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex 0 100.0 100\n")
file.write("Tau 0 10.0 100\n")
# The function and parameters.
elif function == 'Full_CPMG':
# Function.
file.write("function Full_CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("papb 0.01 0.49 20\n")
file.write("dw 0 10.0 100\n")
file.write("kex 0.1 1.0 100\n")
# The function and parameters.
elif function == "Ishima":
# Function.
file.write("function Ishima\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex 0 100.0 50\n")
file.write("PaDw 2 10.0 50\n")
file.write("Tau 0.1 10.0 50\n")
# The function and parameters.
if function == '3-site_CPMG':
# Function.
file.write("function 3-site_CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex1 0 100.0 20\n")
file.write("Tau1 0 10.0 20\n")
file.write("Rex2 0 100.0 20\n")
file.write("Tau2 0 10.0 20\n")
# The Grace setup.
file.write("xmgr\n")
file.write("@ xaxis label \"1/tcp (1/ms)\"\n")
file.write("@ yaxis label \"R2(tcp) (rad/s)\"\n")
file.write("@ xaxis ticklabel format decimal\n")
file.write("@ yaxis ticklabel format decimal\n")
file.write("@ xaxis ticklabel char size 0.8\n")
file.write("@ yaxis ticklabel char size 0.8\n")
file.write("@ world xmin 0.0\n")
# The data.
file.write("data\n")
for exp_type, frq, offset, point in loop_exp_frq_offset_point():
# The parameter key.
param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point)
# No data.
if param_key not in spin.r2eff:
continue
# Tesla units.
B0 = frq * 2.0 * pi / periodic_table.gyromagnetic_ratio('1H')
# The X value of 1/tcp (or 1/tau_CPMG) in ms. This assumes Art's usage of the definition that nu_CPMG = 1 / (2 * tau_CPMG).
x = 2.0 * point / 1000.0
# Write out the data and error.
file.write("%-20f %-20f %-20f %-20f\n" % (x, spin.r2eff[param_key], spin.r2eff_err[param_key], B0))
# Close the file and return its name.
file.close()
return file_name
def create_spin_input(function=None, spin=None, spin_id=None, dir=None):
"""Generate the CPMGFit file for the given spin.
@keyword function: The CPMGFit model or function name.
@type function: str
@keyword spin: The spin container to generate the input file for.
@type spin: SpinContainer instance
@keyword spin_id: The spin ID string corresponding to the spin container.
@type spin_id: str
@keyword dir: The directory to place the file into.
@type dir: str or None
@return: The name of the file created.
@rtype: str
"""
# The output file.
file_name = spin_file_name(spin_id=spin_id)
file = open_write_file(file_name=file_name, dir=dir, force=True)
# The title.
file.write("title %s\n" % spin_id)
# The proton frequencies.
frq = get_frequencies(units='T')
# The frequency info.
file.write("fields %s" % len(frq))
for i in range(len(frq)):
file.write(" %.10f" % frq[i])
file.write("\n")
# The function and parameters.
if function == 'CPMG':
# Function.
file.write("function CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex 0 100.0 100\n")
file.write("Tau 0 10.0 100\n")
# The function and parameters.
elif function == 'Full_CPMG':
# Function.
file.write("function Full_CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("papb 0.01 0.49 20\n")
file.write("dw 0 10.0 100\n")
file.write("kex 0.1 1.0 100\n")
# The function and parameters.
elif function == "Ishima":
# Function.
file.write("function Ishima\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex 0 100.0 50\n")
file.write("PaDw 2 10.0 50\n")
file.write("Tau 0.1 10.0 50\n")
# The function and parameters.
if function == '3-site_CPMG':
# Function.
file.write("function 3-site_CPMG\n")
# Parameters.
file.write("R2 1 10 20\n")
file.write("Rex1 0 100.0 20\n")
file.write("Tau1 0 10.0 20\n")
file.write("Rex2 0 100.0 20\n")
file.write("Tau2 0 10.0 20\n")
# The Grace setup.
file.write("xmgr\n")
file.write("@ xaxis label \"1/tcp (1/ms)\"\n")
file.write("@ yaxis label \"R2(tcp) (rad/s)\"\n")
file.write("@ xaxis ticklabel format decimal\n")
file.write("@ yaxis ticklabel format decimal\n")
file.write("@ xaxis ticklabel char size 0.8\n")
file.write("@ yaxis ticklabel char size 0.8\n")
file.write("@ world xmin 0.0\n")
# The data.
file.write("data\n")
for exp_type, frq, offset, point in loop_exp_frq_offset_point():
# The parameter key.
param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point)
# No data.
if param_key not in spin.r2eff:
continue
# Tesla units.
B0 = frq * 2.0 * pi / periodic_table.gyromagnetic_ratio('1H')
# The X value of 1/tcp (or 1/tau_CPMG) in ms. This assumes Art's usage of the definition that nu_CPMG = 1 / (2 * tau_CPMG).
x = 2.0 * point / 1000.0
# Write out the data and error.
file.write("%-20f %-20f %-20f %-20f\n" % (x, spin.r2eff[param_key], spin.r2eff_err[param_key], B0))
# Close the file and return its name.
file.close()
return file_name
def write_results(self):
"""Create Grace plots of the final model-free results."""
# Save the results file.
dir = self.write_results_dir + 'final'
self.interpreter.results.write(file='results', dir=dir, force=True)
# The Grace plots.
dir = self.write_results_dir + 'final' + sep + 'grace'
self.interpreter.grace.write(x_data_type='res_num', y_data_type='s2', file='s2.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='s2f', file='s2f.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='s2s', file='s2s.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='te', file='te.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='tf', file='tf.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='ts', file='ts.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='res_num', y_data_type='rex', file='rex.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='s2', y_data_type='te', file='s2_vs_te.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='s2', y_data_type='rex', file='s2_vs_rex.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='te', y_data_type='rex', file='te_vs_rex.agr', dir=dir, force=True)
# Write the values to text files.
dir = self.write_results_dir + 'final'
self.interpreter.value.write(param='s2', file='s2.txt', dir=dir, force=True)
self.interpreter.value.write(param='s2f', file='s2f.txt', dir=dir, force=True)
self.interpreter.value.write(param='s2s', file='s2s.txt', dir=dir, force=True)
self.interpreter.value.write(param='te', file='te.txt', dir=dir, force=True)
self.interpreter.value.write(param='tf', file='tf.txt', dir=dir, force=True)
self.interpreter.value.write(param='ts', file='ts.txt', dir=dir, force=True)
self.interpreter.value.write(param='rex', file='rex.txt', dir=dir, force=True)
self.interpreter.value.write(param='local_tm', file='local_tm.txt', dir=dir, force=True)
frqs = spectrometer.get_frequencies()
for i in range(len(frqs)):
comment = "This is the Rex value with units rad.s^-1 scaled to a magnetic field strength of %s MHz." % (frqs[i]/1e6)
self.interpreter.value.write(param='rex', file='rex_%s.txt'%int(frqs[i]/1e6), dir=dir, scaling=(2.0*pi*frqs[i])**2, comment=comment, force=True)
# Create the PyMOL macros.
dir = self.write_results_dir + 'final' + sep + 'pymol'
self.interpreter.pymol.macro_write(data_type='s2', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='s2f', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='s2s', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='amp_fast', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='amp_slow', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='te', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='tf', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='ts', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='time_fast', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='time_slow', dir=dir, force=True)
self.interpreter.pymol.macro_write(data_type='rex', dir=dir, force=True)
# Create the Molmol macros.
dir = self.write_results_dir + 'final' + sep + 'molmol'
self.interpreter.molmol.macro_write(data_type='s2', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='s2f', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='s2s', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='amp_fast', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='amp_slow', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='te', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='tf', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='ts', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='time_fast', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='time_slow', dir=dir, force=True)
self.interpreter.molmol.macro_write(data_type='rex', dir=dir, force=True)
# Create a diffusion tensor representation of the tensor, if a PDB file is present and the local tm global model has not been selected.
if hasattr(cdp, 'structure') and hasattr(cdp, 'diff_tensor'):
dir = self.write_results_dir + 'final'
self.interpreter.structure.create_diff_tensor_pdb(file="tensor.pdb", dir=dir, force=True)
