r21432 - /trunk/pipe_control/rdc.py -- November 13, 2013 - 17:52

Author: bugman
Date: Wed Nov 13 17:52:22 2013
New Revision: 21432

URL: http://svn.gna.org/viewcvs/relax?rev=21432&view=rev
Log:
The pipe_control.rdc.q_factors() function now properly handles pseudo-atoms.

If pseudo-atoms are present, then 2Da^2(4 + 3R)/5 normalised Q factor is 
skipped.


Modified:
    trunk/pipe_control/rdc.py

Modified: trunk/pipe_control/rdc.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/rdc.py?rev=21432&r1=21431&r2=21432&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Wed Nov 13 17:52:22 2013
@@ -41,7 +41,7 @@
 from pipe_control import grace, pipes
 from pipe_control.align_tensor import get_tensor_index
 from pipe_control.interatomic import consistent_interatomic_data, 
create_interatom, interatomic_loop, return_interatom
-from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
+from pipe_control.mol_res_spin import exists_mol_res_spin_data, 
is_pseudoatom, return_spin
 
 
 def back_calc(align_id=None):
@@ -509,13 +509,19 @@
             g1 = return_gyromagnetic_ratio(spin1.isotope)
             g2 = return_gyromagnetic_ratio(spin2.isotope)
 
+            # Skip the 2Da^2(4 + 3R)/5 normalised Q factor if pseudo-atoms 
are present.
+            if  norm2_flag and (is_pseudoatom(spin1) or 
is_pseudoatom(spin2)):
+                warn(RelaxWarning("Pseudo-atoms are present, skipping the Q 
factor normalised with 2Da^2(4 + 3R)/5."))
+                norm2_flag = False
+
             # Calculate the RDC dipolar constant (in Hertz, and the 3 comes 
from the alignment tensor), and append it to the list.
-            dj_new = 3.0/(2.0*pi) * dipolar_constant(g1, g2, interatom.r)
-            if norm2_flag and dj != None and dj_new != dj:
-                warn(RelaxWarning("The dipolar constant is not the same for 
all RDCs, skipping the Q factor normalised with 2Da^2(4 + 3R)/5."))
-                norm2_flag = False
-            else:
-                dj = dj_new
+            if norm2_flag:
+                dj_new = 3.0/(2.0*pi) * dipolar_constant(g1, g2, interatom.r)
+                if dj != None and dj_new != dj:
+                    warn(RelaxWarning("The dipolar constant is not the same 
for all RDCs, skipping the Q factor normalised with 2Da^2(4 + 3R)/5."))
+                    norm2_flag = False
+                else:
+                    dj = dj_new
 
             # Increment the number of data sets.
             N = N + 1