Author: bugman
Date: Wed Jul 1 13:05:09 2009
New Revision: 9167
URL: http://svn.gna.org/viewcvs/relax?rev=9167&view=rev
Log:
Reverted r9128 to r9133, the elimination of a Euler angle (maybe only
temporarily).
The command used was:
svn merge -r9134:9127 .
Modified:
branches/frame_order/generic_fns/monte_carlo.py
branches/frame_order/maths_fns/frame_order_matrix_ops.py
branches/frame_order/maths_fns/frame_order_models.py
branches/frame_order/specific_fns/frame_order.py
Modified: branches/frame_order/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/generic_fns/monte_carlo.py?rev=9167&r1=9166&r2=9167&view=diff
==============================================================================
--- branches/frame_order/generic_fns/monte_carlo.py (original)
+++ branches/frame_order/generic_fns/monte_carlo.py Wed Jul 1 13:05:09 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2005, 2007-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2005, 2007-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -51,6 +51,10 @@
# Test if simulations have been set up.
if not hasattr(cdp, 'sim_state'):
raise RelaxError, "Monte Carlo simulations have not been set up."
+
+ # Test if sequence data exists.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Test the method argument.
valid_methods = ['back_calc', 'direct']
Modified: branches/frame_order/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/maths_fns/frame_order_matrix_ops.py?rev=9167&r1=9166&r2=9167&view=diff
==============================================================================
--- branches/frame_order/maths_fns/frame_order_matrix_ops.py (original)
+++ branches/frame_order/maths_fns/frame_order_matrix_ops.py Wed Jul 1
13:05:09 2009
@@ -24,46 +24,39 @@
"""Module for the handling of Frame Order."""
# Python module imports.
-from math import cos, sin
-from numpy import cross, dot, transpose
-from numpy.linalg import norm
+from math import cos
+from numpy import dot, transpose
# relax module imports.
-from float import isNaN
from maths_fns.kronecker_product import kron_prod, transpose_14
-from maths_fns.rotation_matrix import R_2vect
-
-
-def compile_2nd_matrix_iso_cone(matrix, R, z_axis, cone_axis, theta_axis,
phi_axis, theta_cone):
+from maths_fns.rotation_matrix import R_euler_zyz
+
+
+def compile_2nd_matrix_iso_cone(matrix, R, alpha, beta, gamma, theta):
"""Generate the rotated 2nd degree Frame Order matrix.
- @param matrix: The Frame Order matrix, 2nd degree to be populated.
- @type matrix: numpy 9D, rank-2 array
- @param R: The rotation matrix to be populated.
- @type R: numpy 3D, rank-2 array
- @param z_axis: The molecular frame z-axis from which the cone axis
is rotated from.
- @type z_axis: numpy 3D, rank-1 array
- @param cone_axis: The storage structure for the cone axis.
- @type cone_axis: numpy 3D, rank-1 array
- @param theta_axis: The cone axis polar angle.
- @type theta_axis: float
- @param phi_axis: The cone axis azimuthal angle.
- @type phi_axis: float
- @param theta_cone: The cone angle in radians.
- @type theta_cone: float
- """
-
- # Generate the cone axis from the spherical angles.
- generate_vector(cone_axis, theta_axis, phi_axis)
+ @param matrix: The Frame Order matrix, 2nd degree to be populated.
+ @type matrix: numpy 9D, rank-2 array
+ @param R: The rotation matrix to be populated.
+ @type R: numpy 3D, rank-2 array
+ @param alpha: The alpha Euler angle in radians.
+ @type alpha: float
+ @param beta: The beta Euler angle in radians.
+ @type beta: float
+ @param gamma: The gamma Euler angle in radians.
+ @type gamma: float
+ @param theta: The cone angle in radians.
+ @type theta: float
+ """
# Generate the rotation matrix.
- R_2vect(R, z_axis, cone_axis)
+ R_euler_zyz(R, alpha, beta, gamma)
# The outer product of R.
R_kron = kron_prod(R, R)
# Populate the Frame Order matrix in the eigenframe.
- populate_2nd_eigenframe_iso_cone(matrix, theta_cone)
+ populate_2nd_eigenframe_iso_cone(matrix, theta)
# Perform the T14 transpose to obtain the Kronecker product matrix!
matrix = transpose_14(matrix)
Modified: branches/frame_order/maths_fns/frame_order_models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/maths_fns/frame_order_models.py?rev=9167&r1=9166&r2=9167&view=diff
==============================================================================
--- branches/frame_order/maths_fns/frame_order_models.py (original)
+++ branches/frame_order/maths_fns/frame_order_models.py Wed Jul 1 13:05:09
2009
@@ -25,7 +25,7 @@
# Python module imports.
from copy import deepcopy
-from numpy import array, float64, ones, zeros
+from numpy import float64, ones, zeros
# relax module imports.
from generic_fns.frame_order import print_frame_order_2nd_degree
@@ -114,10 +114,6 @@
self.red_errors = red_errors
self.red_tensors_bc = zeros(self.num_tensors*5, float64)
- # The cone axis storage and molecular frame z-axis.
- self.cone_axis = zeros(3, float64)
- self.z_axis = array([0, 0, 1], float64)
-
# The rotation to the Frame Order eigenframe.
self.rot = zeros((3, 3), float64)
@@ -143,10 +139,6 @@
# The errors.
self.errors = ones((9, 9), float64)
- # The cone axis storage and molecular frame z-axis.
- self.cone_axis = zeros(3, float64)
- self.z_axis = array([0, 0, 1], float64)
-
# The rotation.
self.rot = zeros((3, 3), float64)
@@ -160,11 +152,12 @@
def func_iso_cone(self, params):
"""Target function for isotropic cone model optimisation using the
alignment tensors.
- This function optimises against alignment tensors. The cone axis
spherical angles theta and
- phi and the cone angle theta are the 3 parameters optimised in this
model.
-
- @param params: The vector of parameter values {theta, phi,
theta_cone} where the first two
- are the polar and azimuthal angles of the cone axis
theta_cone is the
+ This function optimises against alignment tensors. The Frame Order
eigenframe via the
+ alpha, beta, and gamma Euler angles, and the cone angle theta are
the 4 parameters optimised
+ in this model.
+
+ @param params: The vector of parameter values {alpha, beta, gamma,
theta} where the first
+ three are the Euler angles for the Frame Order
eigenframe and theta is the
isotropic cone angle.
@type params: list of float
@return: The chi-squared or SSE value.
@@ -172,10 +165,10 @@
"""
# Break up the parameters.
- theta, phi, theta_cone = params
+ alpha, beta, gamma, theta = params
# Generate the 2nd degree Frame Order super matrix.
- self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis,
self.cone_axis, theta, phi, theta_cone)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta,
gamma, theta)
# Back calculate the reduced tensors.
for i in range(self.num_tensors):
@@ -189,11 +182,11 @@
"""Target function for isotropic cone model optimisation using the
Frame Order matrix.
This function optimises by directly matching the elements of the 2nd
degree Frame Order
- super matrix. The cone axis spherical angles theta and phi and the
cone angle theta are the
- 3 parameters optimised in this model.
-
- @param params: The vector of parameter values {theta, phi,
theta_cone} where the first two
- are the polar and azimuthal angles of the cone axis
theta_cone is the
+ super matrix. The Frame Order eigenframe via the alpha, beta, and
gamma Euler angles, and
+ the cone angle theta are the 4 parameters optimised in this model.
+
+ @param params: The vector of parameter values {alpha, beta, gamma,
theta} where the first
+ three are the Euler angles for the Frame Order
eigenframe and theta is the
isotropic cone angle.
@type params: list of float
@return: The chi-squared or SSE value.
@@ -201,10 +194,10 @@
"""
# Break up the parameters.
- theta, phi, theta_cone = params
+ alpha, beta, gamma, theta = params
# Generate the 2nd degree Frame Order super matrix.
- self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, self.z_axis,
self.cone_axis, theta, phi, theta_cone)
+ self.frame_order_2nd =
compile_2nd_matrix_iso_cone(self.frame_order_2nd, self.rot, alpha, beta,
gamma, theta)
# Make the Frame Order matrix contiguous.
self.frame_order_2nd = self.frame_order_2nd.copy()
Modified: branches/frame_order/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/specific_fns/frame_order.py?rev=9167&r1=9166&r2=9167&view=diff
==============================================================================
--- branches/frame_order/specific_fns/frame_order.py (original)
+++ branches/frame_order/specific_fns/frame_order.py Wed Jul 1 13:05:09 2009
@@ -152,17 +152,20 @@
if cdp.model == 'iso cone':
# Set up the parameter arrays.
if not len(cdp.params):
- cdp.params.append('theta_axis')
- cdp.params.append('phi_axis')
- cdp.params.append('theta_cone')
-
- # Initialise the cone axis angles and cone angle values.
- if not hasattr(cdp, 'theta_axis'):
- cdp.theta_axis = 0.0
- if not hasattr(cdp, 'phi_axis'):
- cdp.phi_axis = 0.0
- if not hasattr(cdp, 'theta_cone'):
- cdp.theta_cone = 0.0
+ cdp.params.append('alpha')
+ cdp.params.append('beta')
+ cdp.params.append('gamma')
+ cdp.params.append('theta')
+
+ # Initialise the Euler angle and cone angle values.
+ if not hasattr(cdp, 'alpha'):
+ cdp.alpha = 0.0
+ if not hasattr(cdp, 'beta'):
+ cdp.beta = 0.0
+ if not hasattr(cdp, 'gamma'):
+ cdp.gamma = 0.0
+ if not hasattr(cdp, 'theta'):
+ cdp.theta = 0.0
def __unpack_opt_results(self, results, sim_index=None):
@@ -192,20 +195,21 @@
# Isotropic cone model.
if cdp.model == 'iso cone':
# Disassemble the parameter vector.
- theta_axis, phi_axis, theta_cone = param_vector
+ alpha, beta, gamma, theta = param_vector
# Wrap the cone angle to be between 0 and pi.
- if theta_cone < 0.0:
- theta_cone = -theta_cone
- if theta_cone > pi:
- theta_cone = 2.0*pi - theta_cone
+ if theta < 0.0:
+ theta = -theta
+ if theta > pi:
+ theta = 2.0*pi - theta
# Monte Carlo simulation data structures.
if sim_index != None:
# Model parameters.
- cdp.theta_axis_sim[sim_index] = theta_axis
- cdp.phi_axis_sim[sim_index] = phi_axis
- cdp.theta_cone_sim[sim_index] = theta_cone
+ cdp.alpha_sim[sim_index] = alpha
+ cdp.beta_sim[sim_index] = beta
+ cdp.gamma_sim[sim_index] = gamma
+ cdp.theta_sim[sim_index] = theta
# Optimisation info.
cdp.chi2_sim[sim_index] = func
@@ -218,9 +222,10 @@
# Normal data structures.
else:
# Model parameters.
- cdp.theta_axis = theta_axis
- cdp.phi_axis = phi_axis
- cdp.theta_cone = theta_cone
+ cdp.alpha = alpha
+ cdp.beta = beta
+ cdp.gamma = gamma
+ cdp.theta = theta
# Optimisation info.
cdp.chi2 = func
@@ -509,12 +514,14 @@
# Set the grid search options.
for i in xrange(n):
- # Cone axis angles and cone angle.
- if cdp.params[i] == 'phi_axis':
+ # Euler angles.
+ if cdp.params[i] in ['alpha', 'gamma']:
+ grid_ops.append([inc[i], 0.0, 2*pi])
+ if cdp.params[i] == 'beta':
grid_ops.append([inc[i], 0.0, pi])
- if cdp.params[i] == 'theta_axis':
- grid_ops.append([inc[i], 0.0, pi])
- if cdp.params[i] == 'theta_cone':
+
+ # The cone angle.
+ if cdp.params[i] == 'theta':
grid_ops.append([inc[i], 0.0, pi])
# Lower bound (if supplied).
@@ -562,8 +569,8 @@
# Isotropic cone model.
if cdp.model == 'iso cone':
- # The initial parameter vector (the cone axis angles and the
cone angle).
- param_vector = array([cdp.theta_axis, cdp.phi_axis,
cdp.theta_cone], float64)
+ # The initial parameter vector (the Euler angles and the cone
angle).
+ param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta], float64)
# Get the data structures for optimisation using the tensors as
base data sets.
full_tensors, red_tensors, red_tensor_err =
self.__minimise_setup_tensors(sim_index)
r9167 - in /branches/frame_order: generic_fns/ maths_fns/ specific_fns/