Author: bugman
Date: Tue Mar 3 16:49:03 2015
New Revision: 27756
URL: http://svn.gna.org/viewcvs/relax?rev=27756&view=rev
Log:
Fixes for the rdc.calc_q_factors user function for when no alignment tensor is
present.
This was caught by the Rdc.test_calc_q_factors_no_tensor system test. Now if
no tensor is present,
a warning is given and the 2Da^2(4 + 3R)/5 normalised Q factor is skipped.
Also, if present but no
spin isotope information is present, then RelaxSpinTypeError errors are raised.
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=27756&r1=27755&r2=27756&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Tue Mar 3 16:49:03 2015
@@ -734,17 +734,29 @@
else:
D2_sum = D2_sum + interatom.rdc[align_id]**2
- # Gyromagnetic ratios.
- g1 = periodic_table.gyromagnetic_ratio(spin1.isotope)
- g2 = periodic_table.gyromagnetic_ratio(spin2.isotope)
+ # Skip the 2Da^2(4 + 3R)/5 normalised Q factor if no tensor is
present.
+ if norm2_flag and not hasattr(cdp, 'align_tensors'):
+ warn(RelaxWarning("No alignment tensors are present, skipping
the Q factor normalised with 2Da^2(4 + 3R)/5."))
+ norm2_flag = False
# 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)):
+ 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.
if norm2_flag:
+ # Data checks.
+ if not hasattr(spin1, 'isotope'):
+ raise RelaxSpinTypeError(spin_id=interatom.spin_id1)
+ if not hasattr(spin2, 'isotope'):
+ raise RelaxSpinTypeError(spin_id=interatom.spin_id2)
+
+ # Gyromagnetic ratios.
+ g1 = periodic_table.gyromagnetic_ratio(spin1.isotope)
+ g2 = periodic_table.gyromagnetic_ratio(spin2.isotope)
+
+ # Calculate the dipolar constant.
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."))
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