Author: bugman
Date: Mon Dec 9 12:33:31 2013
New Revision: 21899
URL: http://svn.gna.org/viewcvs/relax?rev=21899&view=rev
Log:
Added the R2eff calculating functions for the 'NS R1rho 3-site' models to the
relax library.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
Added:
trunk/lib/dispersion/ns_r1rho_3site.py
- copied, changed from r21888, trunk/lib/dispersion/ns_r1rho_2site.py
Modified:
trunk/lib/dispersion/ns_matrices.py
Modified: trunk/lib/dispersion/ns_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_matrices.py?rev=21899&r1=21898&r2=21899&view=diff
==============================================================================
--- trunk/lib/dispersion/ns_matrices.py (original)
+++ trunk/lib/dispersion/ns_matrices.py Mon Dec 9 12:33:31 2013
@@ -160,6 +160,96 @@
return temp
+def rr1rho_3d_3site(matrix=None, R1=None, r1rho_prime=None, pA=None,
pB=None, pC=None, wA=None, wB=None, wC=None, w1=None, k_AB=None, k_BA=None,
k_BC=None, k_CB=None, k_AC=None, k_CA=None):
+ """Definition of the 3D exchange matrix.
+
+ @keyword matrix: The matrix to fill.
+ @type matrix: numpy rank-2 9D array
+ @keyword R1: The longitudinal, spin-lattice relaxation rate.
+ @type R1: float
+ @keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate
in the absence of exchange.
+ @type r1rho_prime: float
+ @keyword pA: The population of state A.
+ @type pA: float
+ @keyword pB: The population of state B.
+ @type pB: float
+ @keyword pC: The population of state C.
+ @type pC: float
+ @keyword wA: The chemical shift offset of state A from the
spin-lock.
+ @type wA: float
+ @keyword wB: The chemical shift offset of state B from the
spin-lock.
+ @type wB: float
+ @keyword wC: The chemical shift offset of state C from the
spin-lock.
+ @type wC: float
+ @keyword w1: The spin-lock field strength in rad/s.
+ @type w1: float
+ @keyword k_AB: The forward exchange rate from state A to state
B.
+ @type k_AB: float
+ @keyword k_BA: The reverse exchange rate from state B to state
A.
+ @type k_BA: float
+ @keyword k_BC: The forward exchange rate from state B to state
C.
+ @type k_BC: float
+ @keyword k_CB: The reverse exchange rate from state C to state
B.
+ @type k_CB: float
+ @keyword k_AC: The forward exchange rate from state A to state
C.
+ @type k_AC: float
+ @keyword k_CA: The reverse exchange rate from state C to state
A.
+ @type k_CA: float
+ """
+
+ # The AB auto-block.
+ matrix[0, 0] = -r1rho_prime - k_AB - k_AC
+ matrix[0, 1] = -wA
+ matrix[1, 0] = wA
+ matrix[1, 1] = -r1rho_prime - k_AB - k_AC
+ matrix[1, 2] = -w1
+ matrix[2, 1] = w1
+ matrix[2, 2] = -R1 - k_AB - k_AC
+
+ # The AC auto-block.
+ matrix[3, 3] = -r1rho_prime - k_BA - k_BC
+ matrix[3, 4] = -wB
+ matrix[4, 3] = wB
+ matrix[4, 4] = -r1rho_prime - k_BA - k_BC
+ matrix[4, 5] = -w1
+ matrix[5, 4] = w1
+ matrix[5, 5] = -R1 - k_BA - k_BC
+
+ # The BC auto-block.
+ matrix[6, 6] = -r1rho_prime - k_CA - k_CB
+ matrix[6, 7] = -wC
+ matrix[7, 6] = wC
+ matrix[7, 7] = -r1rho_prime - k_CA - k_CB
+ matrix[7, 8] = -w1
+ matrix[8, 7] = w1
+ matrix[8, 8] = -R1 - k_CA - k_CB
+
+ # The AB cross-block.
+ matrix[3, 0] = k_AB
+ matrix[4, 1] = k_AB
+ matrix[5, 2] = k_AB
+ matrix[0, 3] = k_BA
+ matrix[1, 4] = k_BA
+ matrix[2, 5] = k_BA
+
+ # The AC cross-block.
+ matrix[6, 0] = k_AC
+ matrix[7, 1] = k_AC
+ matrix[8, 2] = k_AC
+ matrix[0, 6] = k_CA
+ matrix[1, 7] = k_CA
+ matrix[2, 8] = k_CA
+
+ # The BC cross-block.
+ matrix[6, 3] = k_BC
+ matrix[7, 4] = k_BC
+ matrix[8, 5] = k_BC
+ matrix[3, 6] = k_CB
+ matrix[4, 7] = k_CB
+ matrix[5, 8] = k_CB
+
+
+
def rr1rho_3d(R1A=None, R1=None, Rinf=None, pA=None, pB=None, wA=None,
wB=None, w1=None, k_AB=None, k_BA=None):
"""Definition of the 3D exchange matrix.
Copied: trunk/lib/dispersion/ns_r1rho_3site.py (from r21888,
trunk/lib/dispersion/ns_r1rho_2site.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?p2=trunk/lib/dispersion/ns_r1rho_3site.py&p1=trunk/lib/dispersion/ns_r1rho_2site.py&r1=21888&r2=21899&rev=21899&view=diff
==============================================================================
--- trunk/lib/dispersion/ns_r1rho_2site.py (original)
+++ trunk/lib/dispersion/ns_r1rho_3site.py Mon Dec 9 12:33:31 2013
@@ -22,15 +22,13 @@
###############################################################################
# Module docstring.
-"""This function performs a numerical fit of 2-site Bloch-McConnell
equations for R1rho-type experiments.
+"""This function performs a numerical fit of 3-site Bloch-McConnell
equations for R1rho-type experiments.
-This is the model of the numerical solution for the 2-site Bloch-McConnell
equations. It originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
+This is the model of the numerical solution for the 3-site Bloch-McConnell
equations. It originates from the funNumrho.m file from the Skrynikov &
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
The solution has been modified to use the from presented in:
- - Korzhnev, D. M., Orekhov, V. Y., and Kay, L. E. (2005). Off-resonance
R(1rho) NMR
-studies of exchange dynamics in proteins with low spin-lock fields: an
application to a
-Fyn SH3 domain. J. Am. Chem. Soc., 127, 713-721. (U{DOI:
10.1021/ja0446855<http://dx.doi.org/10.1021/ja0446855>}).
+ - Korzhnev, D. M., Orekhov, V. Y., and Kay, L. E. (2005). Off-resonance
R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock
fields: an application to a Fyn SH3 domain. J. Am. Chem. Soc., 127,
713-721. (U{DOI: 10.1021/ja0446855<http://dx.doi.org/10.1021/ja0446855>}).
"""
# Dependency check module.
@@ -41,19 +39,21 @@
from numpy import dot
# relax module imports.
-from lib.dispersion.ns_matrices import rr1rho_3d
+from lib.dispersion.ns_matrices import rr1rho_3d_3site
from lib.float import isNaN
from lib.linear_algebra.matrix_exponential import matrix_exponential
-def ns_r1rho_2site(M0=None, r1rho_prime=None, omega=None, offset=None,
r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None,
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None,
num_points=None):
- """The 2-site numerical solution to the Bloch-McConnell equation for
R1rho data.
+def ns_r1rho_3site(M0=None, matrix=None, r1rho_prime=None, omega=None,
offset=None, r1=0.0, pA=None, pB=None, pC=None, dw_AB=None, dw_AC=None,
k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None,
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None,
num_points=None):
+ """The 3-site numerical solution to the Bloch-McConnell equation for
R1rho data.
This function calculates and stores the R1rho values.
@keyword M0: This is a vector that contains the initial
magnetizations corresponding to the A and B state transverse magnetizations.
@type M0: numpy float64, rank-1, 7D array
+ @keyword matrix: A numpy array to be populated to create the
evolution matrix.
+ @type matrix: numpy rank-2, 2D complex64 array
@keyword r1rho_prime: The R1rho_prime parameter value (R1rho with
no exchange).
@type r1rho_prime: float
@keyword omega: The chemical shift for the spin in rad/s.
@@ -66,12 +66,24 @@
@type pA: float
@keyword pB: The population of state B.
@type pB: float
- @keyword dw: The chemical exchange difference between
states A and B in rad/s.
- @type dw: float
+ @keyword pC: The population of state C.
+ @type pC: float
+ @keyword dw_AB: The chemical exchange difference between
states A and B in rad/s.
+ @type dw_AB: float
+ @keyword dw_AC: The chemical exchange difference between
states A and C in rad/s.
+ @type dw_AC: float
@keyword k_AB: The rate of exchange from site A to B
(rad/s).
@type k_AB: float
@keyword k_BA: The rate of exchange from site B to A
(rad/s).
@type k_BA: float
+ @keyword k_BC: The rate of exchange from site B to C
(rad/s).
+ @type k_BC: float
+ @keyword k_CB: The rate of exchange from site C to B
(rad/s).
+ @type k_CB: float
+ @keyword k_AC: The rate of exchange from site A to C
(rad/s).
+ @type k_AC: float
+ @keyword k_CA: The rate of exchange from site C to A
(rad/s).
+ @type k_CA: float
@keyword spin_lock_fields: The R1rho spin-lock field strengths (in
rad.s^-1).
@type spin_lock_fields: numpy rank-1 float array
@keyword relax_time: The total relaxation time period for each
spin-lock field strength (in seconds).
@@ -85,25 +97,27 @@
"""
# Repetitive calculations (to speed up calculations).
- Wa = omega # Larmor frequency [s^-1].
- Wb = omega + dw # Larmor frequency [s^-1].
- W = pA*Wa + pB*Wb # Population-averaged Larmor frequency
[s^-1].
+ Wa = omega # Larmor frequency for state A [s^-1].
+ Wb = omega + dw_AB # Larmor frequency for state B [s^-1].
+ Wc = omega + dw_AC # Larmor frequency for state C [s^-1].
+ W = pA*Wa + pB*Wb + pC*Wc # Population-averaged Larmor frequency
[s^-1].
dA = Wa - offset # Offset of spin-lock from A.
dB = Wb - offset # Offset of spin-lock from B.
+ dC = Wc - offset # Offset of spin-lock from C.
d = W - offset # Offset of spin-lock from
population-average.
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
- # The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
- R = rr1rho_3d(R1=r1, Rinf=r1rho_prime, pA=pA, pB=pB, wA=dA, wB=dB,
w1=spin_lock_fields[i], k_AB=k_AB, k_BA=k_BA)
+ # The matrix that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
+ rr1rho_3d_3site(matrix=matrix, R1=r1, r1rho_prime=r1rho_prime,
pA=pA, pB=pB, pC=pC, wA=dA, wB=dB, wC=dC, w1=spin_lock_fields[i], k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA)
# The following lines rotate the magnetization previous to spin-lock
into the weff frame.
theta = atan(spin_lock_fields[i]/d)
M0[0] = sin(theta)
- M0[4] = cos(theta)
+ M0[1] = cos(theta)
# This matrix is a propagator that will evolve the magnetization
with the matrix R.
- Rexpo = matrix_exponential(R*relax_time)
+ Rexpo = matrix_exponential(matrix*relax_time)
# Magnetization evolution.
MA = dot(M0, dot(Rexpo, M0))
@@ -113,5 +127,3 @@
back_calc[i] = 1e99
else:
back_calc[i]= -inv_relax_time * log(MA)
-
-
r21899 - in /trunk/lib/dispersion: ns_matrices.py ns_r1rho_3site.py