Re: r22440 - /trunk/specific_analyses/relax_disp/disp_data.py -- March 07, 2014

Hi,

I have a recommendation for the print statements for this function.
There are quite a lot, and most users will probably not be interested
in seeing them.  Therefore you could set a verbosity argument for the
function which defaults to False.  If it is set to True, then the
print statements are activated:

    # Loop over the index of spins, then exp_type, frq, offset
    if verbosity:
        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}")

You can see how often I use this trick with:

$ grep -r verbosity . --exclude-dir=.svn

That way you can have print statements that can be turned on and off
at any time.

Regards,

Edward


On 7 March 2014 13:21,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Fri Mar  7 13:21:33 2014
New Revision: 22440

URL: http://svn.gna.org/viewcvs/relax?rev=22440&view=rev
Log:
Moved calc_rotating_frame_params() to 
specific_analysis.relax_disp.disp_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.

This is in a response to message: 
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.

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=22440&r1=22439&r2=22440&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/disp_data.py     (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py     Fri Mar  7 13:21:33 
2014
@@ -68,7 +68,7 @@
 from lib.software.grace import write_xy_data, write_xy_header, 
script_grace2images
 from lib.warnings import RelaxWarning, RelaxNoSpinWarning
 from pipe_control import pipes
-from pipe_control.mol_res_spin import check_mol_res_spin_data, 
exists_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop
+from pipe_control.mol_res_spin import check_mol_res_spin_data, 
exists_mol_res_spin_data, find_index, generate_spin_id_unique, 
get_spin_ids, return_spin, spin_loop
 from pipe_control.result_files import add_result_file
 from pipe_control.selection import desel_spin
 from pipe_control.sequence import return_attached_protons
@@ -154,6 +154,64 @@

     # Return the value.
     return intensity
+
+
+def calc_rotating_frame_params():
+    """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,
+    - 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>}
+    """
+    # 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, Delta_omega, w_eff = 
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]
+
+    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]))


 def count_exp():


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Re: r22440 - /trunk/specific_analyses/relax_disp/disp_data.py

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