Author: tlinnet
Date: Fri Mar 7 14:52:09 2014
New Revision: 22444
URL: http://svn.gna.org/viewcvs/relax?rev=22444&view=rev
Log:
Modified calc_rotating_frame_params() to operate on the level of spin
container and id.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
Modified:
trunk/specific_analyses/relax_disp/disp_data.py
Modified: trunk/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22444&r1=22443&r2=22444&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/disp_data.py (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py Fri Mar 7 14:52:09
2014
@@ -156,18 +156,25 @@
return intensity
-def calc_rotating_frame_params():
+def calc_rotating_frame_params(spin=None, spin_id=None):
"""Calculates and rotating frame parameters, calculated from:
- The spectrometer frequency.
- The spin-lock or hard pulse offset.
- The dispersion point data (the spin-lock field strength in Hz).
The return will be for each spin,
+ - Rotating frame tilt angle ( theta = arctan(w_1 / Omega) ) [rad]
- The average resonance offset in the rotating frame ( Domega =
w_{pop_ave} - w_rf ) [rad/s]
- - Rotating frame tilt angle ( theta = arctan(w_1 / Omega) ) [rad]
- Effective field in rotating frame ( w_eff = sqrt( Omega^2 + w_1^2 ) )
[rad/s]
Calculations are mentioned in the
U{manual<http://www.nmr-relax.com/manual/Dispersion_model_summary.html>}
+
+ @keyword spin: The spin system specific data container
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin ID string.
+ @type spin_id: None or str
+ @return: List with dict() of theta, Domega, w_eff and list of
dict() keys.
+ @rtype: List of dict()
"""
# Get the field count
field_count = cdp.spectrometer_frq_count
@@ -175,43 +182,32 @@
# 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, Delta_omega, w_eff =
return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids,
field_count=field_count, fields=spin_lock_nu1)
+ chemical_shifts, offsets, tilt_angles, Delta_omega, w_eff =
return_offset_data(spins=[spin], spin_ids=[spin_id], 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]
-
- 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]))
+ print("exp_type spin_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}")
+
+ si = 0
+ theta_spin_dic = dict()
+ Domega_spin_dic = dict()
+ w_eff_spin_dic = dict()
+ dic_key_list = []
+
+ 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, spin_id, frq, offset,
offsets[ei][si][mi][oi], ei, mi, oi, si, di, 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])
+ dic_key_list.append(dic_key)
+ theta_spin_dic["%s"%(dic_key)] = tilt_angles[ei][si][mi][oi][di]
+ Domega_spin_dic["%s"%(dic_key)] = Delta_omega[ei][si][mi][oi][di]
+ w_eff_spin_dic["%s"%(dic_key)] = w_eff[ei][si][mi][oi][di]
+
+ # Return the dic and list of keys
+ return [theta_spin_dic, Domega_spin_dic, w_eff_spin_dic, dic_key_list]
def count_exp():
r22444 - /trunk/specific_analyses/relax_disp/disp_data.py