Author: tlinnet
Date: Thu Mar 6 22:45:21 2014
New Revision: 22424
URL: http://svn.gna.org/viewcvs/relax?rev=22424&view=rev
Log:
Added a sample_script to generate theta values for R1rho data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
The script is explained at the wiki:
http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data
Added:
trunk/sample_scripts/relax_disp/return_offset_data.py
Added: trunk/sample_scripts/relax_disp/return_offset_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/relax_disp/return_offset_data.py?rev=22424&view=auto
==============================================================================
--- trunk/sample_scripts/relax_disp/return_offset_data.py (added)
+++ trunk/sample_scripts/relax_disp/return_offset_data.py Thu Mar 6
22:45:21 2014
@@ -0,0 +1,77 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+"""Script for returning off-resonance R1rho-type data."""
+
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from pipe_control.mol_res_spin import find_index, get_spin_ids,
index_molecule, index_residue, return_spin, spin_loop
+from specific_analyses.relax_disp.disp_data import loop_exp_frq_offset,
return_offset_data, return_param_key_from_data, return_spin_lock_nu1
+
+def generate_theta_dic():
+ # Get the field count
+ field_count = cdp.spectrometer_frq_count
+
+ # Get the spin_lock_field points
+ spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+
+ # Initialize data containers
+ all_spin_ids = get_spin_ids()
+
+ # Containers for only selected spins
+ cur_spin_ids = []
+ cur_spins = []
+ for curspin_id in all_spin_ids:
+ # Get the spin
+ curspin = return_spin(curspin_id)
+
+ # Check if is selected
+ if curspin.select == True:
+ cur_spin_ids.append(curspin_id)
+ cur_spins.append(curspin)
+
+ # The offset and R1 data.
+ chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids,
field_count=field_count, fields=spin_lock_nu1)
+
+ # Loop over the index of spins, then exp_type, frq, offset
+ print("Printing the following")
+ print("exp_type curspin_id frq offset{ppm}
offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm}
chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz}
tilt_angles[ei][si][mi][oi]{rad}")
+ for si in range(len(cur_spin_ids)):
+ theta_spin_dic = dict()
+ curspin_id = cur_spin_ids[si]
+ cur_spin = cur_spins[si]
+ for exp_type, frq, offset, ei, mi, oi in
loop_exp_frq_offset(return_indices=True):
+ # Loop over the dispersion points.
+ spin_lock_fields = spin_lock_nu1[ei][mi][oi]
+ for di in range(len(spin_lock_fields)):
+ print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i
%7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset,
offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift,
chemical_shifts[ei][si][mi], spin_lock_fields[di],
tilt_angles[ei][si][mi][oi][di]))
+ dic_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, offset=offset, point=spin_lock_fields[di])
+ theta_spin_dic["%s"%(dic_key)] =
tilt_angles[ei][si][mi][oi][di]
+ # Store the data
+ cur_spin.theta = theta_spin_dic
+
+ print("\nThe theta data now resides in")
+ for curspin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ spin_index = find_index(selection=spin_id, global_index=False)
+ print("%s cdp.mol[%i].res[%i].spin[%i].theta"%(spin_id,
spin_index[0], spin_index[1], spin_index[2]))
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Re: r22424 - /trunk/sample_scripts/relax_disp/return_offset_data.py