Author: bugman
Date: Tue Jul 16 17:16:09 2013
New Revision: 20338
URL: http://svn.gna.org/viewcvs/relax?rev=20338&view=rev
Log:
Converted the 'NS 2-site' model to 'NS 2-site 3D' to be more specific.
This might change again in the future.
Added:
branches/relax_disp/lib/dispersion/ns_2site_3d.py
- copied unchanged from r20335,
branches/relax_disp/lib/dispersion/ns_2site.py
Removed:
branches/relax_disp/lib/dispersion/ns_2site.py
Modified:
branches/relax_disp/lib/dispersion/__init__.py
branches/relax_disp/specific_analyses/relax_disp/variables.py
branches/relax_disp/target_functions/relax_disp.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=20338&r1=20337&r2=20338&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Tue Jul 16 17:16:09 2013
@@ -29,7 +29,7 @@
'lm63',
'm61',
'm61b',
- 'ns_2site',
+ 'ns_2site_3d',
'ns_2site_star',
'ns_matrices',
'two_point'
Removed: branches/relax_disp/lib/dispersion/ns_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_2site.py?rev=20337&view=auto
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_2site.py (original)
+++ branches/relax_disp/lib/dispersion/ns_2site.py (removed)
@@ -1,101 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2010-2013 Paul Schanda (https://gna.org/users/pasa)
#
-# Copyright (C) 2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""This function performs a numerical fit of 2-site Bloch-McConnell
equations for CPMG-type experiments.
-
-The function uses an explicit matrix that contains relaxation, exchange and
chemical shift terms. It does the 180deg pulses in the CPMG train. The
approach of Bloch-McConnell can be found in chapter 3.1 of Palmer, A. G. Chem
Rev 2004, 104, 3623-3640. This function was written, initially in MATLAB, in
2010.
-
-This is the model of the numerical solution for the 2-site Bloch-McConnell
equations. It originates as optimization function number 1 from the
fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and
Dominique Marion (see
http://thread.gmane.org/gmane.science.nmr.relax.devel/4138,
https://gna.org/task/?7712#comment2 and
https://gna.org/support/download.php?file_id=18262).
-"""
-
-# Dependency check module.
-import dep_check
-
-# Python module imports.
-from math import fabs, log
-if dep_check.scipy_module:
- from scipy.linalg import expm
-
-# relax module imports.
-from lib.dispersion.ns_matrices import r180x_3d, rcpmg_3d
-
-
-def r2eff_ns_2site_3D(M0=None, r10a=0.0, r10b=0.0, r20a=None, r20b=None,
pA=None, dw=None, k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
- """The 2-site numerical solution to the Bloch-McConnell equation.
-
- This function calculates and stores the R2eff 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, 2D array
- @keyword r10a: The R1 value for state A.
- @type r10a: float
- @keyword r10b: The R1 value for state B.
- @type r10b: float
- @keyword r20a: The R2 value for state A in the absence of
exchange.
- @type r20a: float
- @keyword r20b: The R2 value for state B in the absence of
exchange.
- @type r20b: float
- @keyword pA: The population of state A.
- @type pA: float
- @keyword dw: The chemical exchange difference between states
A and B in rad/s.
- @type dw: 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 inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
- @type inv_tcpmg: float
- @keyword tcp: The tau_CPMG times (1 / 4.nu1).
- @type tcp: 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.
- @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 tcp and back_calc arguments.
- @type num_points: int
- @keyword power: The matrix exponential power array.
- @type power: numpy int16, rank-1 array
- """
-
- # The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
- R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b, df=dw, k_AB=k_AB,
k_BA=k_BA)
-
- # Loop over the time points, back calculating the R2eff values.
- for i in range(num_points):
- # Initial magnetisation.
- Mint = M0
-
- # This matrix is a propagator that will evolve the magnetization
with the matrix R for a delay tcp.
- Rexpo = expm(R*tcp[i])
-
- # Loop over the CPMG elements, propagating the magnetisation.
- for j in range(2*power[i]):
- Mint = Rexpo * Mint
- Mint = r180x_3d() * Mint
- Mint = Rexpo * Mint
-
- # The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
- Mgx = fabs((Mint[1])/pA)
- if Mgx == 0.0:
- back_calc[i] = 1e99
- else:
- back_calc[i]= -inv_tcpmg * log(Mgx)
Modified: branches/relax_disp/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/variables.py?rev=20338&r1=20337&r2=20338&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/variables.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/variables.py Tue Jul 16
17:16:09 2013
@@ -67,8 +67,8 @@
# The Numerical model names.
-MODEL_NS_2SITE = 'NS 2-site'
-"""The numerical solution for the 2-site Bloch-McConnell equations."""
+MODEL_NS_2SITE_3D = 'NS 2-site 3D'
+"""The numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors."""
MODEL_NS_2SITE_STAR_RED = 'NS 2-site star red'
"""The numerical solution for the 2-site Bloch-McConnell equations using
complex conjugate matrices, whereby the simplification R20A = R20B is
assumed."""
@@ -78,16 +78,16 @@
# The model lists.
-MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED, MODEL_CR72,
MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_NS_2SITE,
MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
+MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED, MODEL_CR72,
MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_NS_2SITE_3D,
MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
"""The list of all dispersion models (excluding the R2eff model)."""
-MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED,
MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_NS_2SITE,
MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
+MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED,
MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B,
MODEL_NS_2SITE_3D, MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
"""The list of the R2eff model together with all dispersion models."""
-MODEL_LIST_CPMG = [MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED, MODEL_CR72,
MODEL_IT99, MODEL_NS_2SITE, MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
+MODEL_LIST_CPMG = [MODEL_NOREX, MODEL_LM63, MODEL_CR72_RED, MODEL_CR72,
MODEL_IT99, MODEL_NS_2SITE_3D, MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
"""The list of all dispersion models specifically for CPMG-type experiments
(excluding the R2eff model)."""
-MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63,
MODEL_CR72_RED, MODEL_CR72, MODEL_IT99, MODEL_NS_2SITE,
MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
+MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63,
MODEL_CR72_RED, MODEL_CR72, MODEL_IT99, MODEL_NS_2SITE_3D,
MODEL_NS_2SITE_STAR_RED, MODEL_NS_2SITE_STAR]
"""The list of the R2eff model together with all dispersion models
specifically for CPMG-type experiments."""
MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_M61, MODEL_DPL94, MODEL_M61B]
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=20338&r1=20337&r2=20338&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Tue Jul 16 17:16:09
2013
@@ -33,7 +33,7 @@
from lib.dispersion.lm63 import r2eff_LM63
from lib.dispersion.m61 import r1rho_M61
from lib.dispersion.m61b import r1rho_M61b
-from lib.dispersion.ns_2site import r2eff_ns_2site_3D
+from lib.dispersion.ns_2site_3d import r2eff_ns_2site_3D
from lib.dispersion.ns_2site_star import r2eff_ns_2site_star
from lib.errors import RelaxError
from target_functions.chi2 import chi2
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=20338&r1=20337&r2=20338&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Tue Jul 16 17:16:09 2013
@@ -39,7 +39,7 @@
from specific_analyses.relax_disp.disp_data import cpmg_frq,
plot_disp_curves, plot_exp_curves, relax_time, spin_lock_field
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.sherekhan import sherekhan_input
-from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_RED, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61, MODEL_M61B,
MODEL_NOREX, MODEL_R2EFF, MODEL_NS_2SITE, MODEL_NS_2SITE_STAR,
MODEL_NS_2SITE_STAR_RED
+from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_RED, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61, MODEL_M61B,
MODEL_NOREX, MODEL_R2EFF, MODEL_NS_2SITE_3D, MODEL_NS_2SITE_STAR,
MODEL_NS_2SITE_STAR_RED
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -443,7 +443,7 @@
"%s: {R20, ..., pA, dw, kex}" % MODEL_CR72_RED,
"%s: {R20A, R20B, ..., pA, dw, kex}" % MODEL_CR72,
"%s: {R20, ..., phi_ex, padw2, kex}" % MODEL_IT99,
- "%s: {R20A, R20B, ..., pA, dw, kex}" % MODEL_NS_2SITE,
+ "%s: {R20A, R20B, ..., pA, dw, kex}" % MODEL_NS_2SITE_3D,
"%s: {R20, ..., pA, dw, kex}" % MODEL_NS_2SITE_STAR_RED,
"%s: {R20A, R20B, ..., pA, dw, kex}" % MODEL_NS_2SITE_STAR,
"%s: {R1rho', ..., phi_ex, kex}" % MODEL_M61,
@@ -457,7 +457,7 @@
MODEL_CR72_RED,
MODEL_CR72,
MODEL_IT99,
- MODEL_NS_2SITE,
+ MODEL_NS_2SITE_3D,
MODEL_NS_2SITE_STAR_RED,
MODEL_NS_2SITE_STAR,
MODEL_M61,
@@ -490,7 +490,7 @@
uf.desc[-1].add_paragraph("The Bloch-McConnell equations can also be solved
numerically. The numeric models are also dependent upon whether the data
originates from a CPMG-type or R1rho-type experiment. For the CPMG-type
experiments, the currently supported models are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the model
used to determine the R2eff values and errors required as the base data for
all other models,")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX, "This is the model
for no chemical exchange being present,")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_2SITE, "The numerical
solution for the 2-site Bloch-McConnell equations with parameters {R20A,
R20B, ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_2SITE_3D, "The numerical
solution for the 2-site Bloch-McConnell equations using 3D magnetisation
vectors. Its parameters are {R20A, R20B, ..., pA, dw, kex}.")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_2SITE_STAR_RED, "The
numerical solution for the 2-site Bloch-McConnell equations using complex
conjugate matrices whereby the simplification R20A = R20B is assumed. It has
the parameters {R20, ..., pA, dw, kex}.")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_2SITE_STAR, "The
numerical solution for the 2-site Bloch-McConnell equations using complex
conjugate matrices with parameters {R20A, R20B, ..., pA, dw, kex}.")
uf.desc[-1].add_paragraph("For the R1rho-type experiment, only the base
models are currently supported:")
r20338 - in /branches/relax_disp: lib/dispersion/ specific_analyses/relax_disp/ target_functions/ user_functions/