Author: bugman
Date: Sun Aug 18 20:23:22 2013
New Revision: 20632
URL: http://svn.gna.org/viewcvs/relax?rev=20632&view=rev
Log:
Added the TSMFK01 model equations to the relax library:
lib/dispersion/tsmfk01.py
Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of
Tollinger/Kay dispersion model (2001)
Following the guide at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_
gmail_dot_com
Signed-off-by: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
Modified:
branches/relax_disp/lib/dispersion/__init__.py
branches/relax_disp/lib/dispersion/tsmfk01.py
Modified: branches/relax_disp/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=20632&r1=20631&r2=20632&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Sun Aug 18 20:23:22 2013
@@ -27,6 +27,7 @@
'dpl94',
'it99',
'lm63',
+ 'tsmfk01',
'lm63_3site',
'm61',
'm61b',
Modified: branches/relax_disp/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tsmfk01.py?rev=20632&r1=20631&r2=20632&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/tsmfk01.py (original)
+++ branches/relax_disp/lib/dispersion/tsmfk01.py Sun Aug 18 20:23:22 2013
@@ -1,7 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2009 Sebastien Morin
#
-# Copyright (C) 2013 Edward d'Auvergne
#
+# Copyright (C) 2013 Troels E. Linnet
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -21,41 +20,43 @@
###############################################################################
# Module docstring.
-"""The Luz and Meiboom (1963) 2-site fast exchange model.
+"""The Tollinger, Kay et al. (2001) 2-site very-slow exchange model, range
of microsecond to second time scale.
+Applicable in the limit of slow exchange, when |R20A-R2bj| << kA,kB <<
1/tau_CP. R20A is the transverse relaxation rate of site A in the absence of
exchange.
+2*tau_CP is is the time between successive 180 deg. pulses.
-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 TSMFK01 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>}).
+ - Martin Tollinger, Nikolai R. Skrynnikov, Frans A. A. Mulder, Julie D.
Forman-Kay and Lewis E. Kay., (2001) Slow Dynamics in Folded and Unfolded
States of an SH3 Domain, J. Am. Chem. Soc., 2001, 123 (46) (U{DOI:
10.1021/ja011300z<http://dx.doi.org/10.1021/ja011300z>}).
The equation used is::
- phi_ex / 4 * nu_cpmg / kex \ \
- R2eff = R20 + ------ * | 1 - ----------- * tanh | ----------- | | ,
- kex \ kex \ 4 * nu_cpmg / /
+ sin(delta_omega * tau_CP)
+ R2Aeff = R20A + kA - kA * ------------------------- ,
+ delta_omega * tau_CP
where::
- phi_ex = pA * pB * delta_omega^2 ,
+ tau_CP = 1.0/(4*nu_cpmg) ,
-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.
+R20A is the transverse relaxation rate of site A in the absence of exchange,
2*tau_CP is is the time between successive 180 deg. pulses, kA is the forward
chemical exchange rate constant, delta_omega is the chemical shift difference
between the two states.
"""
# Python module imports.
-from math import tanh
+from math import sin
-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_TSMFK01(r20a=None, dw=None, kA=None, cpmg_frqs=None,
back_calc=None, num_points=None):
+ """Calculate the R2eff values for the TSMFK01 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 r20a: The R20 parameter value of state A (R2 with no
exchange).
+ @type r20a: float
+ @keyword dw: The chemical exchange difference between states
A and B in rad/s.
+ @type dw: float
+ @keyword kA: The kA parameter value (the forward exchange
rate in rad/s).
+ @type kA: 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.
@@ -64,20 +65,32 @@
@type num_points: int
"""
- # Repetitive calculations (to speed up calculations).
- rex = phi_ex / kex
- kex_4 = 4.0 / kex
-
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
- # Catch zeros.
- if phi_ex == 0.0:
- back_calc[i] = r20
+ # Catch zeros (to avoid pointless mathematical operations).
+ if cpmg_frqs[i] == 0.0:
+ back_calc[i] = r20a
+ continue
+
+ # Repetitive calculations (to speed up calculations).
+ tau_CP = 1.0/(4*cpmg_frqs[i])
+
+ # The numerator.
+ numer = sin(dw * tau_CP)
+
+ # Catch zeros (to avoid pointless mathematical operations).
+ if numer == 0.0:
+ back_calc[i] = r20a + kA
+ continue
+
+ # Denominator.
+ denom = dw * tau_CP
# Avoid divide by zero.
- elif kex == 0.0:
+ if denom == 0.0:
back_calc[i] = 1e100
+ continue
# 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 + kA - kA * numer / denom
r20632 - in /branches/relax_disp/lib/dispersion: __init__.py tsmfk01.py