def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'):
"""Create the ShereKhan input files.
@keyword spin_id: The spin ID string to restrict the file creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all pre-existing files to be overwritten.
@type force: bool
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@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
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# Directory creation.
if dir != None:
mkdir_nofail(dir, verbosity=0)
# Loop over the spin blocks.
cluster_index = 0
for spin_ids in loop_cluster():
# The spin containers.
spins = spin_ids_to_containers(spin_ids)
# Loop over the magnetic fields.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Loop over the time, and count it.
time_i = 0
for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True):
time_i += 1
# Check that not more than one time point is returned.
if time_i > 1:
raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i)
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (mi+1)
if dir != None:
dir_name = dir + sep + 'cluster%s' % (cluster_index+1)
else:
dir_name = 'cluster%s' % (cluster_index+1)
file = open_write_file(file_name=file_name, dir=dir_name, force=force)
# The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server).
file.write("%.10f\n" % abs(frq / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio('15N') / 1e6))
# The constant relaxation time for the CPMG experiment in seconds.
file.write("%s\n" % (time))
# The comment line.
file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error"))
# Loop over the spins of the cluster.
for i in range(len(spins)):
# Get the residue container.
res = return_residue(spin_ids[i])
# Name the residue if needed.
res_name = res.name
if res_name == None:
res_name = 'X'
# Initialise the lines to output (to be able to catch missing data).
lines = []
# The residue ID line.
lines.append("# %s%s\n" % (res_name, res.num))
# Loop over the dispersion points.
for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True):
# 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 spins[i].r2eff:
continue
# Store the data.
lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
# No data.
if len(lines) == 1:
continue
# Write out the data.
for line in lines:
file.write(line)
# Close the file.
file.close()
# Increment the cluster index.
cluster_index += 1
def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'):
"""Create the ShereKhan input files.
@keyword spin_id: The spin ID string to restrict the file creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all pre-existing files to be overwritten.
@type force: bool
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@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
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# Directory creation.
if dir != None:
mkdir_nofail(dir, verbosity=0)
# Loop over the spin blocks.
cluster_index = 0
for spin_ids in loop_cluster():
# The spin containers.
spins = spin_ids_to_containers(spin_ids)
# Loop over the magnetic fields.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Loop over the time, and count it.
time_i = 0
for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True):
time_i += 1
# Check that not more than one time point is returned.
if time_i > 1:
raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i)
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (mi+1)
if dir != None:
dir_name = dir + sep + 'cluster%s' % (cluster_index+1)
else:
dir_name = 'cluster%s' % (cluster_index+1)
file = open_write_file(file_name=file_name, dir=dir_name, force=force)
# The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server).
file.write("%.10f\n" % abs(frq / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio('15N') / 1e6))
# The constant relaxation time for the CPMG experiment in seconds.
file.write("%s\n" % (time))
# The comment line.
file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error"))
# Loop over the spins of the cluster.
for i in range(len(spins)):
# Get the residue container.
res = return_residue(spin_ids[i])
# Name the residue if needed.
res_name = res.name
if res_name == None:
res_name = 'X'
# Initialise the lines to output (to be able to catch missing data).
lines = []
# The residue ID line.
lines.append("# %s%s\n" % (res_name, res.num))
# Loop over the dispersion points.
for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True):
# 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 spins[i].r2eff:
continue
# Store the data.
lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
# No data.
if len(lines) == 1:
continue
# Write out the data.
for line in lines:
file.write(line)
# Close the file.
file.close()
# Increment the cluster index.
cluster_index += 1
exp_id = exp_ids[mi]
exp = exps[mi]
sfrq, time_T2, ncycs, r2eff_errs = exp
# Then loop over the spins.
for res_name, res_num, spin_name, params in cur_spins:
cur_spin_id = ":%i@%s"%(res_num, spin_name)
cur_spin = return_spin(spin_id=cur_spin_id)
## First do a fake R2eff structure.
# Define file name
file_name = "%s%s.txt" % (exp_id, cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_'))
file = open_write_file(file_name=file_name, dir=ds.tmpdir, force=True)
# Then loop over the points, make a fake R2eff value.
for offset, point, oi, di in loop_offset_point(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
string = "%.15f 1.0 %.3f\n"%(point, ds.r2eff_err)
file.write(string)
# Close file.
file.close()
# Read in the R2eff file to create the structure.
# This is a trick, or else relax complains.
relax_disp.r2eff_read_spin(id=exp_id, spin_id=cur_spin_id, file=file_name, dir=ds.tmpdir, disp_point_col=1, data_col=2, error_col=3)
# Now back-calculate.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
exp_id = exp_ids[mi]
exp = exps[mi]
exp_id = exp_ids[mi]
exp = exps[mi]
sfrq, time_T2, ncycs, r2eff_errs = exp
# Then loop over the spins.
for res_name, res_num, spin_name, params in cur_spins:
cur_spin_id = ":%i@%s"%(res_num, spin_name)
cur_spin = return_spin(cur_spin_id)
## First do a fake R2eff structure.
# Define file name
file_name = "%s%s.txt" % (exp_id, cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_'))
file = open_write_file(file_name=file_name, dir=ds.tmpdir, force=True)
# Then loop over the points, make a fake R2eff value.
for offset, point, oi, di in loop_offset_point(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
string = "%.15f 1.0 %.3f\n"%(point, ds.r2eff_err)
file.write(string)
# Close file.
file.close()
# Read in the R2eff file to create the structure.
# This is a trick, or else relax complains.
relax_disp.r2eff_read_spin(id=exp_id, spin_id=cur_spin_id, file=file_name, dir=ds.tmpdir, disp_point_col=1, data_col=2, error_col=3)
# Now back-calculate.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
exp_id = exp_ids[mi]
exp = exps[mi]
def write_r2eff_files(input_dir=None, base_dir=None, force=False):
"""Create the CATIA R2eff input files.
@keyword input_dir: The special directory for the R2eff input files.
@type input_dir: str
@keyword base_dir: The base directory to place the files into.
@type base_dir: str
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Create the directory for the R2eff files for each field and spin.
dir = base_dir + sep + input_dir
mkdir_nofail(dir, verbosity=0)
# Determine the isotope information.
isotope = None
for spin in spin_loop(skip_desel=True):
if hasattr(spin, 'isotope'):
if isotope == None:
isotope = spin.isotope
elif spin.isotope != isotope:
raise RelaxError("CATIA only supports one spin type.")
if isotope == None:
raise RelaxError("The spin isotopes have not been specified.")
# Isotope translation.
if isotope == '1H':
isotope = 'H1'
elif isotope == '13C':
isotope = 'C13'
elif isotope == '15N':
isotope = 'N15'
# Loop over the frequencies.
for frq, mi in loop_frq(return_indices=True):
# The frequency string in MHz.
frq_string = int(frq * 1e-6)
# The set files.
file_name = "data_set_%i.inp" % frq_string
set_file = open_write_file(file_name=file_name,
dir=base_dir,
force=force)
id = frq_string
set_file.write("ID=%s\n" % id)
set_file.write("Sfrq = %s\n" % frq_string)
set_file.write("Temperature = %s\n" % 0.0)
set_file.write("Nucleus = %s\n" % isotope)
set_file.write("Couplednucleus = %s\n" % 'H1')
set_file.write("Time_equil = %s\n" % 0.0)
set_file.write("Pwx_cp = %s\n" % 0.0)
set_file.write("Taub = %s\n" % 0.0)
set_file.write("Time_T2 = %s\n" % cdp.relax_time_list[0])
set_file.write("Xcar = %s\n" % 0.0)
set_file.write("Seqfil = %s\n" % 'CW_CPMG')
set_file.write("Minerror = %s\n" % "(2.%;0.5/s)")
set_file.write("Basis = (%s)\n" % "Iph_7")
set_file.write("Format = (%i;%i;%i)\n" % (0, 1, 2))
set_file.write("DataDirectory = %s\n" % (dir + sep))
set_file.write("Data = (\n")
# Loop over the spins.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(
full_info=True, return_id=True, skip_desel=True):
# The file.
file_name = "spin%s_%i.cpmg" % (spin_id.replace('#', '_').replace(
':', '_').replace('@', '_'), frq_string)
spin_file = open_write_file(file_name=file_name,
dir=dir,
force=force)
# Write the header.
spin_file.write("# %18s %20s %20s\n" %
("nu_cpmg(Hz)", "R2(1/s)", "Esd(R2)"))
# Loop over the dispersion points.
for offset, point, oi, di in loop_offset_point(
exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
# The key.
key = return_param_key_from_data(exp_type=EXP_TYPE_CPMG_SQ,
frq=frq,
offset=offset,
point=point)
# No data.
if key not in spin.r2eff:
continue
# Write out the data.
spin_file.write("%20.15f %20.15f %20.15f\n" %
(point, spin.r2eff[key], spin.r2eff_err[key]))
# Close the file.
spin_file.close()
# Add the file name to the set.
catia_spin_id = "%i%s" % (res_num, spin.name)
set_file.write(" [%s;%s];\n" % (catia_spin_id, file_name))
# Terminate the set file.
set_file.write(")\n")
set_file.close()
def write_r2eff_files(input_dir=None, base_dir=None, force=False):
"""Create the CATIA R2eff input files.
@keyword input_dir: The special directory for the R2eff input files.
@type input_dir: str
@keyword base_dir: The base directory to place the files into.
@type base_dir: str
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Create the directory for the R2eff files for each field and spin.
dir = base_dir + sep + input_dir
mkdir_nofail(dir, verbosity=0)
# Determine the isotope information.
isotope = None
for spin in spin_loop(skip_desel=True):
if hasattr(spin, 'isotope'):
if isotope == None:
isotope = spin.isotope
elif spin.isotope != isotope:
raise RelaxError("CATIA only supports one spin type.")
if isotope == None:
raise RelaxError("The spin isotopes have not been specified.")
# Isotope translation.
if isotope == '1H':
isotope = 'H1'
elif isotope == '13C':
isotope = 'C13'
elif isotope == '15N':
isotope = 'N15'
# Loop over the frequencies.
for frq, mi in loop_frq(return_indices=True):
# The frequency string in MHz.
frq_string = int(frq*1e-6)
# The set files.
file_name = "data_set_%i.inp" % frq_string
set_file = open_write_file(file_name=file_name, dir=base_dir, force=force)
id = frq_string
set_file.write("ID=%s\n" % id)
set_file.write("Sfrq = %s\n" % frq_string)
set_file.write("Temperature = %s\n" % 0.0)
set_file.write("Nucleus = %s\n" % isotope)
set_file.write("Couplednucleus = %s\n" % 'H1')
set_file.write("Time_equil = %s\n" % 0.0)
set_file.write("Pwx_cp = %s\n" % 0.0)
set_file.write("Taub = %s\n" % 0.0)
set_file.write("Time_T2 = %s\n"% cdp.relax_time_list[0])
set_file.write("Xcar = %s\n" % 0.0)
set_file.write("Seqfil = %s\n" % 'CW_CPMG')
set_file.write("Minerror = %s\n" % "(2.%;0.5/s)")
set_file.write("Basis = (%s)\n" % "Iph_7")
set_file.write("Format = (%i;%i;%i)\n" % (0, 1, 2))
set_file.write("DataDirectory = %s\n" % (dir+sep))
set_file.write("Data = (\n")
# Loop over the spins.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# The file.
file_name = "spin%s_%i.cpmg" % (spin_id.replace('#', '_').replace(':', '_').replace('@', '_'), frq_string)
spin_file = open_write_file(file_name=file_name, dir=dir, force=force)
# Write the header.
spin_file.write("# %18s %20s %20s\n" % ("nu_cpmg(Hz)", "R2(1/s)", "Esd(R2)"))
# Loop over the dispersion points.
for offset, point, oi, di in loop_offset_point(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
# The key.
key = return_param_key_from_data(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, offset=offset, point=point)
# No data.
if key not in spin.r2eff:
continue
# Write out the data.
spin_file.write("%20.15f %20.15f %20.15f\n" % (point, spin.r2eff[key], spin.r2eff_err[key]))
# Close the file.
spin_file.close()
# Add the file name to the set.
catia_spin_id = "%i%s" % (res_num, spin.name)
set_file.write(" [%s;%s];\n" % (catia_spin_id, file_name))
# Terminate the set file.
set_file.write(")\n")
set_file.close()