Author: bugman
Date: Thu Sep 12 20:59:44 2013
New Revision: 20992
URL: http://svn.gna.org/viewcvs/relax?rev=20992&view=rev
Log:
The relax_disp.catia_input user function now creates the main CATIA input
file and all R2eff data files.
Modified:
branches/relax_disp/specific_analyses/relax_disp/catia.py
Modified: branches/relax_disp/specific_analyses/relax_disp/catia.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/catia.py?rev=20992&r1=20991&r2=20992&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/catia.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/catia.py Thu Sep 12
20:59:44 2013
@@ -22,11 +22,16 @@
# Module docstring.
"""Functions for interfacing with Flemming Hansen's CATIA program."""
+# Python module imports.
+from os import sep
+
# relax module imports.
-from lib.io import mkdir_nofail
+from lib.errors import RelaxError
+from lib.io import mkdir_nofail, open_write_file
from pipe_control import pipes
-from pipe_control.mol_res_spin import check_mol_res_spin_data
+from pipe_control.mol_res_spin import check_mol_res_spin_data, spin_loop
from specific_analyses.relax_disp.checks import check_model_type,
check_spectra_id_setup
+from specific_analyses.relax_disp.disp_data import loop_frq, loop_point,
return_param_key_from_data
def catia_input(file='Fit.catia', dir=None, force=False):
@@ -46,6 +51,172 @@
check_spectra_id_setup()
check_model_type()
+ # Check that this is CPMG data.
+ for id in cdp.spectrum_ids:
+ if cdp.exp_type[id] != 'CPMG':
+ raise RelaxError("Only CPMG type data is supported.")
+
# Directory creation.
if dir != None:
mkdir_nofail(dir, verbosity=0)
+
+ # Create the R2eff files.
+ write_r2eff_files(base_dir=dir, force=force)
+
+ # Create the main execution file.
+ write_main_file(file=file, dir=dir, force=force)
+
+
+def write_main_file(file=None, dir=None, f_tol=1e-25, max_iter=10000000,
r1=False, force=False):
+ """Create the main CATIA execution file.
+
+ @keyword file: The main CATIA execution file.
+ @type file: str
+ @keyword dir: The directory to place the files into.
+ @type dir: str or None
+ @keyword r1: A flag which if True will cause the R1 data to be
used for off-resonance effets.
+ @type r1: bool
+ @keyword force: A flag which if True will cause a pre-existing file
to be overwritten.
+ @type force: bool
+ """
+
+ # The file.
+ catia_in = open_write_file(file_name=file, dir=dir, force=force)
+
+ # The R2eff input sets.
+ for frq in loop_frq():
+ frq_label = int(frq*1e-6)
+ file_name = "data_set_%i.inp" % frq_label
+ catia_in.write("ReadDataset(%s)\n" % file_name)
+
+ # Write out the data.
+ catia_in.write("ReadParam_Global(ParamGlobal.inp)\n")
+ catia_in.write("ReadParam_Local(ParamSet1.inp)\n")
+ catia_in.write("\n")
+
+ # The R1 data for off-resonance effects.
+ if r1:
+ catia_in.write("ReadParam(Omega;%s;0;1)\n" % shift_file)
+ for frq in loop_frq():
+ frq_label = int(frq*1e-6)
+ param = "R1iph_%s" % frq_label
+ r1_file = "R1_%s.out" % frq_label
+ catia_in.write("ReadParam(%s;%s;0;1)\n" % (param, r1_file))
+ catia_in.write("\n")
+
+ # Fix these parameters.
+ catia_in.write("FreeLocalParam(all;Omega;false)\n")
+ for frq in loop_frq():
+ frq_label = int(frq*1e-6)
+ param = "R1iph_%s" % frq_label
+ catia_in.write("FreeLocalParam(all;%s;false)\n" % param)
+ catia_in.write("\n")
+
+ # Minimisation.
+ catia_in.write("Minimize(print=y;tol=%s;maxiter=%i)\n" % (f_tol,
max_iter))
+ catia_in.write("\n")
+
+ # Plotting.
+ catia_in.write("PrintParam(output/GlobalParam.fit;global)\n")
+ catia_in.write("PrintParam(output/DeltaOmega.fit;DeltaO)\n")
+ catia_in.write("PrintData(output/)\n")
+ catia_in.write("\n")
+
+ # Calculate the chi-squared value (not sure why, it's calculated in the
minimisation).
+ catia_in.write("ChiSq(all;all)\n")
+
+ # Exit the program.
+ catia_in.write("exit(0)\n")
+
+
+def write_r2eff_files(input_dir='input_r2eff', 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 in loop_frq():
+ # 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)
+ 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)
+ file = open_write_file(file_name=file_name, dir=dir, force=force)
+
+ # Write the header.
+ file.write("# %18s %20s %20s\n" % ("nu_cpmg(Hz)", "R2(1/s)",
"Esd(R2)"))
+
+ # Loop over the dispersion points.
+ for point in loop_point(exp_type='CPMG'):
+ # The key.
+ key = return_param_key_from_data(frq=frq, point=point)
+
+ # No data.
+ if key not in spin.r2eff:
+ continue
+
+ # Write out the data.
+ file.write("%20.15f %20.15f %20.15f\n" % (point,
spin.r2eff[key], spin.r2eff_err[key]))
+
+ # Close the file.
+ 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()
r20992 - /branches/relax_disp/specific_analyses/relax_disp/catia.py