Author: bugman
Date: Wed Nov 20 17:30:11 2013
New Revision: 21549
URL: http://svn.gna.org/viewcvs/relax?rev=21549&view=rev
Log:
Created the relax_disp.write_disp_curves user function.
This is based on feedback from Nikolai Skrynnikov. The user function will
generate one file per
spin system and dump all of the R2eff values (measured, back calculated, and
errors) into the file.
Modified:
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=21549&r1=21548&r2=21549&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Wed Nov 20
17:30:11 2013
@@ -2452,3 +2452,86 @@
# Printout.
print("Setting the '%s' spectrum spin-lock offset to %s ppm." %
(spectrum_id, cdp.spin_lock_offset[spectrum_id]))
+
+
+def write_disp_curves(dir=None, force=None):
+ """Write out the dispersion curves to text files.
+
+ One file will be created per spin system.
+
+
+ @keyword dir: The optional directory to place the file into.
+ @type dir: str
+ @param force: If True, the files will be overwritten if they
already exists.
+ @type force: bool
+ """
+
+ # Checks.
+ pipes.test()
+ check_mol_res_spin_data()
+
+ # The formatting strings.
+ format_head = "# %-18s %-20s %-20s %-20s %-20s %-20s\n"
+ format = "%-20s %20s %20s %20s %20s %20s\n"
+
+ # Loop over each spin.
+ for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ continue
+
+ # MMQ flags.
+ proton_sq_flag = has_proton_sq_cpmg()
+ proton_mq_flag = has_proton_mq_cpmg()
+ proton_mmq_flag = proton_sq_flag or proton_mq_flag
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
+ # The unique file name.
+ file_name = "disp%s.out" % spin_id.replace('#', '_').replace(':',
'_').replace('@', '_')
+
+ # Open the file for writing.
+ file_path = get_file_path(file_name, dir)
+ file = open_write_file(file_name, dir, force)
+
+ # Write a header.
+ file.write(format_head % ("Experiment_name", "Field_strength_(MHz)",
"Disp_point_(Hz)", "R2eff_(measured)", "R2eff_(back_calc)", "R2eff_errors"))
+
+ # Loop over the dispersion points.
+ for exp_type, frq, point, exp_type_index, frq_index, point_index in
loop_exp_frq_point(return_indices=True):
+ # Alias the correct spin.
+ current_spin = spin
+ if exp_type in [EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_PROTON_MQ]:
+ current_spin = proton
+
+ # The data key.
+ key = return_param_key_from_data(exp_type=exp_type, frq=frq,
point=point)
+
+ # Format the R2eff data.
+ r2eff = "-"
+ if key in current_spin.r2eff:
+ r2eff = "%.15f" % current_spin.r2eff[key]
+
+ # Format the R2eff back calc data.
+ r2eff_bc = "-"
+ if hasattr(current_spin, 'r2eff_bc') and key in
current_spin.r2eff_bc:
+ r2eff_bc = "%.15f" % current_spin.r2eff_bc[key]
+
+ # Format the R2eff errors.
+ r2eff_err = "-"
+ if key in current_spin.r2eff_err:
+ r2eff_err = "%.15f" % current_spin.r2eff_err[key]
+
+ # Write out the data.
+ frq_text = "%.3f" % frq
+ point_text = "%.6f" % point
+ file.write(format % (repr(exp_type), frq_text, point_text,
r2eff, r2eff_bc, r2eff_err))
+
+ # Close the file.
+ file.close()
+
+ # Add the file to the results file list.
+ add_result_file(type='text', label='Text', file=file_path)
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=21549&r1=21548&r2=21549&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Wed Nov 20 17:30:11 2013
@@ -38,7 +38,7 @@
from pipe_control.mol_res_spin import get_spin_ids
from specific_analyses.relax_disp.catia import catia_execute, catia_input
from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute,
cpmgfit_input
-from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, r2eff_read, r2eff_read_spin, relax_time,
set_exp_type, spin_lock_field, spin_lock_offset
+from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, r2eff_read, r2eff_read_spin, relax_time,
set_exp_type, spin_lock_field, spin_lock_offset, write_disp_curves
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
@@ -962,3 +962,32 @@
uf.menu_text = "spin_lock_&offset"
uf.wizard_size = (800, 500)
uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+
+
+# The relax_disp.write_disp_curves user function.
+uf = uf_info.add_uf('relax_disp.write_disp_curves')
+uf.title = "Create text files of the dispersion curves for each spin system."
+uf.title_short = "Dispersion curve writing."
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir sel",
+ desc_short = "directory name",
+ desc = "The directory name to place all of the spin system files into.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "force",
+ default = False,
+ py_type = "bool",
+ desc_short = "force flag",
+ desc = "A flag which, if set to True, will cause the files to be
overwritten."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This is used to created text files of the
dispersion curves of R2eff/R1rho values, both measured and back calculated
from the optimised dispersion model. The columns of the text file will be
the experiment name, the magnetic field strength (as the proton frequency in
MHz), dispersion point (nu_CPMG or the spin-lock field strength), the
experimental R2eff value, the back-calculated R2eff value, and the
experimental R2eff error. One file will be created per spin system with the
name 'disp_x.out', where x is the spin ID string.")
+uf.backend = write_disp_curves
+uf.menu_text = "&write_disp_curves"
+uf.gui_icon = "oxygen.actions.document-save"
+uf.wizard_size = (700, 500)
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
r21549 - in /branches/relax_disp: specific_analyses/relax_disp/disp_data.py user_functions/relax_disp.py