Author: bugman
Date: Fri Jul 19 15:14:25 2013
New Revision: 20410
URL: http://svn.gna.org/viewcvs/relax?rev=20410&view=rev
Log:
Added the 'LM63 3-site' R2eff calculating function to the relax library.
This is the Luz and Meiboom 1963 analytic model for three exchanging sites.
This commit follows step 3 of the relaxation dispersion model addition
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
Added:
branches/relax_disp/lib/dispersion/lm63_3site.py
- copied, changed from r20406,
branches/relax_disp/lib/dispersion/lm63.py
Modified:
branches/relax_disp/lib/dispersion/__init__.py
Modified: branches/relax_disp/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=20410&r1=20409&r2=20410&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Fri Jul 19 15:14:25 2013
@@ -27,6 +27,7 @@
'dpl94',
'it99',
'lm63',
+ 'lm63_3site',
'm61',
'm61b',
'ns_2site_3d',
Copied: branches/relax_disp/lib/dispersion/lm63_3site.py (from r20406,
branches/relax_disp/lib/dispersion/lm63.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/lm63_3site.py?p2=branches/relax_disp/lib/dispersion/lm63_3site.py&p1=branches/relax_disp/lib/dispersion/lm63.py&r1=20406&r2=20410&rev=20410&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/lm63.py (original)
+++ branches/relax_disp/lib/dispersion/lm63_3site.py Fri Jul 19 15:14:25 2013
@@ -21,41 +21,49 @@
###############################################################################
# Module docstring.
-"""The Luz and Meiboom (1963) 2-site fast exchange model.
+"""The Luz and Meiboom (1963) 3-site fast exchange model.
-This module is for the function, gradient and Hessian of the LM63 model.
The model is named after the reference:
+This module is for the function, gradient and Hessian of the 'LM63 3-site'
model. The model is named after the reference:
- Luz, S. and Meiboom S., (1963) Nuclear Magnetic Resonance study of
protolysis of trimethylammonium ion in aqueous solution - order of reaction
with respect to solvent, J. Chem. Phys. 39, 366-370 (U{DOI:
10.1063/1.1734254<http://dx.doi.org/10.1063/1.1734254>}).
+The phi_ex_i and kex_i factors for the 3-site model were derived in the
reference:
+
+
The equation used is::
- phi_ex / 4 * nu_cpmg / kex \ \
- R2eff = R20 + ------ * | 1 - ----------- * tanh | ----------- | | ,
- kex \ kex \ 4 * nu_cpmg / /
+ _3_
+ \ phi_ex_i / 4 * nu_cpmg / ki \
\
+ R2eff = R20 + > -------- * | 1 - ----------- * tanh | ----------- |
| .
+ /__ ki \ ki \ 4 * nu_cpmg /
/
+ i=2
-where::
+For deconvoluting the parameters, see the relax user manual or the reference:
- phi_ex = pA * pB * delta_omega^2 ,
+ - O'Connell, N. E., Grey, M. J., Tang, Y., Kosuri, P., Miloushev, V. Z.,
Raleigh, D. P., and Palmer, 3rd, A. G. (2009). Partially folded equilibrium
intermediate of the villin headpiece HP67 defined by 13C relaxation
dispersion. J. Biomol. NMR, 45(1-2), 85-98. (U{DOI:
10.1007/s10858-009-9340-0<http://dx.doi.org/10.1007/s10858-009-9340-0>}).
-kex is the chemical exchange rate constant, pA and pB are the populations of
states A and B, and delta_omega is the chemical shift difference between the
two states.
"""
# Python module imports.
from math import tanh
-def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None,
back_calc=None, num_points=None):
- """Calculate the R2eff values for the LM63 model.
+def r2eff_LM63_3site(r20=None, phi_ex=None, kex=None, cpmg_frqs=None,
back_calc=None, num_points=None):
+ """Calculate the R2eff values for the LM63 3-site model.
See the module docstring for details.
@keyword r20: The R20 parameter value (R2 with no exchange).
@type r20: float
- @keyword phi_ex: The phi_ex parameter value (pA * pB *
delta_omega^2).
- @type phi_ex: float
- @keyword kex: The kex parameter value (the exchange rate in
rad/s).
- @type kex: float
+ @keyword phi_ex_B: The phi_ex_B parameter value.
+ @type phi_ex_B: float
+ @keyword phi_ex_C: The phi_ex_C parameter value.
+ @type phi_ex_C: float
+ @keyword kB: Approximate chemical exchange rate constant
between sites A and B (the exchange rate in rad/s).
+ @type kB: float
+ @keyword kC: Approximate chemical exchange rate constant
between sites A and C (the exchange rate in rad/s).
+ @type kC: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: numpy rank-1 float array
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@@ -65,19 +73,23 @@
"""
# Repetitive calculations (to speed up calculations).
- rex = phi_ex / kex
- kex_4 = 4.0 / kex
+ rex_B = phi_ex_B / kB
+ rex_C = phi_ex_C / kC
+ kB_4 = 4.0 / kB
+ kC_4 = 4.0 / kC
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
# Catch zeros.
- if phi_ex == 0.0:
+ if phi_ex_B == 0.0 and phi_ex_C == 0.0:
back_calc[i] = r20
# Avoid divide by zero.
- elif kex == 0.0:
+ elif kA == 0.0 or kB == 0.0:
back_calc[i] = 1e100
# The full formula.
else:
- back_calc[i] = r20 + rex * (1.0 - kex_4 * cpmg_frqs[i] *
tanh(kex / (4.0 * cpmg_frqs[i])))
+ back_calc[i] = r20
+ back_calc[i] += rex_B * (1.0 - kB_4 * cpmg_frqs[i] * tanh(kB /
(4.0 * cpmg_frqs[i])))
+ back_calc[i] += rex_C * (1.0 - kC_4 * cpmg_frqs[i] * tanh(kC /
(4.0 * cpmg_frqs[i])))
r20410 - in /branches/relax_disp/lib/dispersion: __init__.py lm63_3site.py