Author: bugman
Date: Sun Jun 16 10:59:27 2013
New Revision: 20141
URL: http://svn.gna.org/viewcvs/relax?rev=20141&view=rev
Log:
Epydoc docstring fixes for all of the modules of the lib.dispersion package.
Modified:
branches/relax_disp/lib/dispersion/cr72.py
branches/relax_disp/lib/dispersion/dpl94.py
branches/relax_disp/lib/dispersion/it99.py
branches/relax_disp/lib/dispersion/lm63.py
branches/relax_disp/lib/dispersion/m61.py
branches/relax_disp/lib/dispersion/m61b.py
Modified: branches/relax_disp/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/cr72.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/cr72.py (original)
+++ branches/relax_disp/lib/dispersion/cr72.py Sun Jun 16 10:59:27 2013
@@ -25,13 +25,14 @@
This module is for the function, gradient and Hessian of the CR72 model.
The model is named after the reference:
- Carver, J. P. and Richards, R. E. (1972). General 2-site solution for
chemical exchange produced dependence of T2 upon Carr-Purcell pulse
separation. J. Magn. Reson., 6, 89-105. (U{DOI:
10.1016/0022-2364(72)90090-X<http://dx.doi.org/10.1016/0022-2364(72)90090-X>}).
+ - Carver, J. P. and Richards, R. E. (1972). General 2-site solution for
chemical exchange produced dependence of T2 upon Carr-Purcell pulse
separation. J. Magn. Reson., 6, 89-105. (U{DOI:
10.1016/0022-2364(72)90090-X<http://dx.doi.org/10.1016/0022-2364(72)90090-X>}).
-The equation used is:
+The equation used is::
R2eff = 1/2 [ R2A0 + R2B0 + kex - 2.nu_cpmg.cosh^-1 (D+.cosh(eta+) -
D-.cos(eta-) ] ,
-where:
+where::
+
1 / Psi + 2delta_omega^2 \
D+/- = - | +/-1 + -------------------- | ,
2 \ sqrt(Psi^2 + zeta^2) /
@@ -44,11 +45,11 @@
zeta = 2delta_omega (R2A0 - R2B0 - pA.kex + pB.kex).
-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 in ppm. Importantly for the implementation of this model, it is
assumed that R2A0 and R2B0 are identical. This simplifies some of the
equations to:
+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 in ppm. Importantly for the implementation of this model, it is
assumed that R2A0 and R2B0 are identical. This simplifies some of the
equations to::
R2eff = R20 + kex/2 - nu_cpmg.cosh^-1 (D+.cosh(eta+) - D-.cos(eta-) ,
-where:
+where::
Psi = kex^2 - delta_omega^2 ,
@@ -78,7 +79,7 @@
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# The B population.
Modified: branches/relax_disp/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/dpl94.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/dpl94.py (original)
+++ branches/relax_disp/lib/dispersion/dpl94.py Sun Jun 16 10:59:27 2013
@@ -25,7 +25,7 @@
This module is for the function, gradient and Hessian of the DPL94 model.
The model is named after the reference:
- Davis, D. G., Perlman, M. E. and London, R. E. (1994). Direct
measurements of the dissociation-rate constant for inhibitor-enzyme complexes
via the T1rho and T2 (CPMG) methods. J. Magn. Reson, Series B, 104, 266-275.
(U{DOI: 10.1006/jmrb.1994.1084<http://dx.doi.org/10.1006/jmrb.1994.1084>})
+ - Davis, D. G., Perlman, M. E. and London, R. E. (1994). Direct
measurements of the dissociation-rate constant for inhibitor-enzyme complexes
via the T1rho and T2 (CPMG) methods. J. Magn. Reson, Series B, 104, 266-275.
(U{DOI: 10.1006/jmrb.1994.1084<http://dx.doi.org/10.1006/jmrb.1994.1084>})
The equation used is::
@@ -69,7 +69,7 @@
@keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to one of the spin-lock fields.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# Repetitive calculations (to speed up calculations).
Modified: branches/relax_disp/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/it99.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/it99.py (original)
+++ branches/relax_disp/lib/dispersion/it99.py Sun Jun 16 10:59:27 2013
@@ -25,7 +25,7 @@
This module is for the function, gradient and Hessian of the IT99 model.
The model is named after the reference:
- Ishima R. and Torchia D.A. (1999). Estimating the time scale of
chemical exchange of proteins from measurements of transverse relaxation
rates in solution. J. Biomol. NMR, 14, 369-372. (U{DOI:
10.1023/A:1008324025406<http://dx.doi.org/10.1023/A:1008324025406>}).
+ - Ishima R. and Torchia D.A. (1999). Estimating the time scale of
chemical exchange of proteins from measurements of transverse relaxation
rates in solution. J. Biomol. NMR, 14, 369-372. (U{DOI:
10.1023/A:1008324025406<http://dx.doi.org/10.1023/A:1008324025406>}).
The equation used is::
@@ -34,7 +34,7 @@
1 + omega_a^2*tex^2
phi_ex = pA * pB * delta_omega^2 ,
-
+
omega_a^2 = sqrt(omega_1eff^4 + pA^2*delta_omega^4) ,
R2eff = R20 + Rex ,
@@ -71,7 +71,7 @@
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# Repetitive calculations (to speed up calculations).
Modified: branches/relax_disp/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/lm63.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/lm63.py (original)
+++ branches/relax_disp/lib/dispersion/lm63.py Sun Jun 16 10:59:27 2013
@@ -25,15 +25,15 @@
This module is for the function, gradient and Hessian of the LM63 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>}).
+ - 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 equation used is:
+The equation used is::
phi_ex / 4 * nu_cpmg / kex \ \
R2eff = R20 + ------ * | 1 - ----------- * tanh | ----------- | | ,
kex \ kex \ 4 * nu_cpmg / /
-where:
+where::
phi_ex = pA * pB * delta_omega^2 ,
@@ -61,7 +61,7 @@
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# Repetitive calculations (to speed up calculations).
Modified: branches/relax_disp/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/m61.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/m61.py (original)
+++ branches/relax_disp/lib/dispersion/m61.py Sun Jun 16 10:59:27 2013
@@ -25,19 +25,19 @@
This module is for the function, gradient and Hessian of the M61 model. The
model is named after the reference:
- Meiboom S. (1961). Nuclear magnetic resonance study of the proton
transfer in water. J. Chem. Phys., 34, 375-388. (U{DOI:
10.1063/1.1700960<http://dx.doi.org/10.1063/1.1700960>}).
+ - Meiboom S. (1961). Nuclear magnetic resonance study of the proton
transfer in water. J. Chem. Phys., 34, 375-388. (U{DOI:
10.1063/1.1700960<http://dx.doi.org/10.1063/1.1700960>}).
-The equation used is:
+The equation used is::
- phi_ex * kex
- R1rho = R1rho' + sin^2(theta) * ----------------- ,
- kex^2 + omega_e^2
+ phi_ex * kex
+ R1rho = R1rho' + ----------------- ,
+ kex^2 + omega_1^2
-where R1rho' is the R1rho value in the absence of exchange, theta is the
rotating frame tilt angle,
+where::
phi_ex = pA * pB * delta_omega^2 ,
-kex is the chemical exchange rate constant, pA and pB are the populations of
states A and B, delta_omega is the chemical shift difference between the two
states, and omega_e is the effective field in the rotating frame.
+R1rho' is the R1rho value in the absence of exchange, kex is the chemical
exchange rate constant, pA and pB are the populations of states A and B,
delta_omega is the chemical shift difference between the two states, and
omega_1 is the spin-lock field strength.
"""
# Python module imports.
@@ -65,22 +65,20 @@
@keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to one of the spin-lock fields.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# Repetitive calculations (to speed up calculations).
kex2 = kex**2
- sin_theta2 = sin(theta)**2
- R1_R2 = R1 * cos(theta)**2 + r1rho_prime * sin(theta)**2
# The numerator.
- numer = sin_theta2 * phi_ex * kex
+ numer = phi_ex * kex
# Loop over the dispersion points, back calculating the R1rho values.
for i in range(num_points):
# Catch zeros (to avoid pointless mathematical operations).
if numer == 0.0:
- back_calc[i] = R1_R2
+ back_calc[i] = r1rho_prime
continue
# Denominator.
@@ -92,4 +90,4 @@
continue
# R1rho calculation.
- back_calc[i] = R1_R2 + numer / denom
+ back_calc[i] = r1rho_prime + numer / denom
Modified: branches/relax_disp/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/m61b.py?rev=20141&r1=20140&r2=20141&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/m61b.py (original)
+++ branches/relax_disp/lib/dispersion/m61b.py Sun Jun 16 10:59:27 2013
@@ -25,9 +25,9 @@
This module is for the function, gradient and Hessian of the M61 skew model.
The model is named after the reference:
- Meiboom S. (1961). Nuclear magnetic resonance study of the proton
transfer in water. J. Chem. Phys., 34, 375-388. (U{DOI:
10.1063/1.1700960<http://dx.doi.org/10.1063/1.1700960>}).
+ - Meiboom S. (1961). Nuclear magnetic resonance study of the proton
transfer in water. J. Chem. Phys., 34, 375-388. (U{DOI:
10.1063/1.1700960<http://dx.doi.org/10.1063/1.1700960>}).
-The equation used is:
+The equation used is::
pA^2.pB.delta_omega^2.kex
R1rho = R1rho' + -------------------------------------- ,
@@ -59,7 +59,7 @@
@keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to one of the spin-lock fields.
@type back_calc: numpy rank-1 float array
@keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields and back_calc arguments.
- @type num_poinst: int
+ @type num_points: int
"""
# The B population.
r20141 - in /branches/relax_disp/lib/dispersion: cr72.py dpl94.py it99.py lm63.py m61.py m61b.py