Author: bugman
Date: Fri Mar 19 14:37:05 2010
New Revision: 11036
URL: http://svn.gna.org/viewcvs/relax?rev=11036&view=rev
Log:
test_suite.shared_data.diffusion_tensor.generate_data is now a module and
used by the ellipsoid.
Added:
1.3/test_suite/shared_data/__init__.py
- copied, changed from r11031, 1.3/test_suite/__init__.py
1.3/test_suite/shared_data/diffusion_tensor/__init__.py
- copied, changed from r11031, 1.3/test_suite/__init__.py
Modified:
1.3/test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py
1.3/test_suite/shared_data/diffusion_tensor/generate_data.py
Copied: 1.3/test_suite/shared_data/__init__.py (from r11031,
1.3/test_suite/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/__init__.py?p2=1.3/test_suite/shared_data/__init__.py&p1=1.3/test_suite/__init__.py&r1=11031&r2=11036&rev=11036&view=diff
==============================================================================
--- 1.3/test_suite/__init__.py (original)
+++ 1.3/test_suite/shared_data/__init__.py Fri Mar 19 14:37:05 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006, 2008 Edward d'Auvergne
#
+# Copyright (C) 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -21,11 +21,7 @@
###############################################################################
# Package docstring.
-"""The relax test-suite."""
+"""The relax test-suite shared data."""
-__all__ = ['formatting',
- 'relax_test_runner',
- 'system_tests',
- 'test_suite_runner',
- 'unit_tests']
+__all__ = []
Copied: 1.3/test_suite/shared_data/diffusion_tensor/__init__.py (from r11031,
1.3/test_suite/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/diffusion_tensor/__init__.py?p2=1.3/test_suite/shared_data/diffusion_tensor/__init__.py&p1=1.3/test_suite/__init__.py&r1=11031&r2=11036&rev=11036&view=diff
==============================================================================
--- 1.3/test_suite/__init__.py (original)
+++ 1.3/test_suite/shared_data/diffusion_tensor/__init__.py Fri Mar 19
14:37:05 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006, 2008 Edward d'Auvergne
#
+# Copyright (C) 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -21,11 +21,7 @@
###############################################################################
# Package docstring.
-"""The relax test-suite."""
+"""The relax test-suite shared diffusion tensor data."""
-__all__ = ['formatting',
- 'relax_test_runner',
- 'system_tests',
- 'test_suite_runner',
- 'unit_tests']
+__all__ = ['generate_data']
Modified:
1.3/test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py?rev=11036&r1=11035&r2=11036&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py
(original)
+++ 1.3/test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py
Fri Mar 19 14:37:05 2010
@@ -26,213 +26,10 @@
"""
# Python module imports.
-from math import sqrt
-from numpy import array, cross, dot, eye, float64, transpose, zeros
-from numpy.linalg import eig, inv, norm
+from numpy import array, float64
# relax module imports.
-from maths_fns.rotation_matrix import axis_angle_to_R, euler_to_R_zyz,
R_to_euler_zyz
-from generic_fns.structure.geometric import angles_uniform,
vect_dist_spherical_angles
-from generic_fns.structure.internal import Internal
-from relax_io import open_write_file
-
-
-def ri_data(Dx=None, Dy=None, Dz=None, vectors=None, frq_label=None,
wH=None, csa=None):
- """Calculate the relaxation data for the given vectors."""
-
- # Diff parameters.
- Diso = (Dx + Dy + Dz) / 3.0
- L2 = (Dx*Dy + Dx*Dz + Dy*Dz) / 3.0
- mux = (Dx - Diso) / sqrt(Diso**2 - L2)
- muy = (Dy - Diso) / sqrt(Diso**2 - L2)
- muz = (Dz - Diso) / sqrt(Diso**2 - L2)
-
- # The five time constants.
- tau = zeros(5, float64)
- tau[0] = 6 * (Diso - sqrt(Diso**2 - L2))
- tau[1] = 4*Dx + Dy + Dz
- tau[2] = Dx + 4*Dy + Dz
- tau[3] = Dx + Dy + 4*Dz
- tau[4] = 6 * (Diso + sqrt(Diso**2 - L2))
- tau = 1.0 / tau
- print("\nTime constants, tau: %s" % tau)
-
- # The dipolar constant.
- h = 6.62606876e-34 # Planck constant.
- h_bar = h / ( 2.0*pi ) # Dirac constant.
- mu0 = 4.0 * pi * 1e-7 # Permeability of free space.
- r = 1.02e-10 # NH bond length.
- gn = -2.7126e7 # 15N gyromagnetic ratio.
- gh = 26.7522212e7 # 1H gyromagnetic ratio.
- dip_const = 0.25 * (mu0/(4.0*pi))**2 * (gn * gh * h_bar)**2 / r**6 #
The dipolar constant.
- print("Dipolar constant: %s" % dip_const)
-
- # The five frequencies.
- wN = wH * gn/gh
- w = zeros(5, float64)
- w[0] = 0
- w[1] = wN
- w[2] = wH - wN
- w[3] = wH
- w[4] = wH + wN
- print("\nFrequencies, w: %s" % w)
-
- # CSA constant.
- csa_const = (wN * csa)**2 / 3.0
- print("CSA constant: %s" % csa_const)
-
- # The files.
- R1_file = open('R1.%s.out' % frq_label, 'w')
- R2_file = open('R2.%s.out' % frq_label, 'w')
- NOE_file = open('NOE.%s.out' % frq_label, 'w')
-
- # Loop over the vectors.
- c = zeros(5, float64)
- for i in range(len(vectors)):
- print("\ni: %s" % i)
- print("vector: %s" % vectors[i])
-
- # Direction cosines.
- delta_x, delta_y, delta_z = vectors[i]
-
- # The d and e factors.
- d = 3.0 * (delta_x**4 + delta_y**4 + delta_z**4) - 1.0
- e = mux * (delta_x**4 + 2.0*delta_y**2 * delta_z**2)
- e = e + muy * (delta_y**4 + 2.0*delta_x**2 * delta_z**2)
- e = e + muz * (delta_z**4 + 2.0*delta_x**2 * delta_y**2)
-
- # The weights.
- c[0] = (d + e) / 4.0
- c[1] = 3 * delta_y**2 * delta_z**2
- c[2] = 3 * delta_x**2 * delta_z**2
- c[3] = 3 * delta_x**2 * delta_y**2
- c[4] = (d - e) / 4.0
- print("Weights, c: %s" % c)
-
- # The spectral density function.
- Jw = zeros(5, float64)
- for frq_index in range(5):
- for k in range(5):
- Jw[frq_index] = Jw[frq_index] + 0.4 * c[k] * tau[k] / (1.0
+ (w[frq_index]*tau[k])**2)
- print("Jw: %s" % Jw)
-
- # The relaxation data.
- R1 = dip_const * (Jw[2] + 3.0*Jw[1] + 6.0*Jw[4]) + csa_const *
Jw[1]
- R2 = dip_const/2.0 * (4.0*Jw[0] + Jw[2] + 3.0*Jw[1] + 6.0*Jw[3] +
6.0*Jw[4]) + csa_const/6.0 * (4.0*Jw[0] + 3.0*Jw[1])
- sigma_noe = dip_const * (6.0*Jw[4] - Jw[2])
- NOE = 1.0 + gh/gn * sigma_noe / R1
- print("R1: %s" % R1)
- print("R2: %s" % R2)
- print("NOE: %s" % NOE)
-
- # Write the data.
- R1_file.write("%s %s %s\n" % (i+1, R1, 0.05*R1))
- R2_file.write("%s %s %s\n" % (i+1, R2, 0.05*R2))
- NOE_file.write("%s %s %s\n" % (i+1, NOE, 0.04))
-
-
-def tensor_setup(Dx=None, Dy=None, Dz=None, alpha=None, beta=None,
gamma=None):
- """Set up the diffusion tensor according to the correct Euler angle
convention."""
-
- # Print out.
- print("\n\n")
- print("# Angles to diff tensor.")
- print("########################")
-
- # Init.
- ROT = False
-
- # The rotation matrix (in the rotating axis system).
- R = zeros((3, 3), float64)
- R_rev = zeros((3, 3), float64)
- euler_to_R_zyz(gamma, beta, alpha, R)
- R_rev = transpose(R)
- print("\nEuler angels: [%s, %s, %s]" % (alpha, beta, gamma))
- print("R:\n%s" % R)
- print("R_rev:\n%s" % R_rev)
- print("X x Y: %s" % cross(R[:, 0], R[:, 1]))
-
- # Axis rotations.
- if ROT:
- R_x180 = zeros((3, 3), float64)
- R_y180 = zeros((3, 3), float64)
- R_z180 = zeros((3, 3), float64)
- axis_angle_to_R(R_rev[:, 0], pi, R_x180)
- axis_angle_to_R(R_rev[:, 1], pi, R_y180)
- axis_angle_to_R(R_rev[:, 2], pi, R_z180)
- print("\nR (x 180):\n%s" % R_x180)
- print("\nR (y 180):\n%s" % R_y180)
- print("\nR (z 180):\n%s" % R_z180)
-
- # A test vector.
- mu = array([1, 2, -3], float64)
- mu = mu / norm(mu)
-
- # Tensor in eigenframe.
- D_prime = zeros((3, 3), float64)
- D_prime[0, 0] = 1e7
- D_prime[1, 1] = 2e7
- D_prime[2, 2] = 3e7
- print("\nD':\n%s" % D_prime)
-
- # Rotate tensor from the eigenframe to the ref frame.
- D = dot(R_rev, dot(D_prime, transpose(R_rev)))
- print("\nD:\n%s" % D)
- print("\n\n")
-
- # Return the forward and reverse rotation, and the diffusion tensors.
- return R, R_rev, D_prime, D
-
-
-def pdb(R=eye(3), r=1.02, file_name='uniform.pdb', inc=None):
- """Create the bond vector distribution and save the PDB file."""
-
- # Create the structural object.
- structure = Internal()
-
- # Add a molecule.
- structure.add_molecule(name='dist')
-
- # Alias the single molecule from the single model.
- mol = structure.structural_data[0].mol[0]
-
- # Get the polar and azimuthal angles for the distribution.
- phi, theta = angles_uniform(inc)
-
- # Get the uniform vector distribution.
- vectors = vect_dist_spherical_angles(inc=inc, distribution='uniform')
-
- # Loop over the radial array of vectors (change in longitude).
- atom_num = 1
- for i in range(len(theta)):
- # Loop over the vectors of the radial array (change in latitude).
- for j in range(len(phi)):
- # Rotate the vector into the diffusion frame.
- vector = dot(R, vectors[i + j*len(theta)])
-
- # Scale the vector.
- vector = vector * r
-
- # Residue number.
- res = (atom_num + 1) / 2
-
- # Add the vector as a N-H atom pair.
- mol.atom_add(pdb_record='HETATM', atom_num=atom_num,
atom_name='N', res_name='NH', res_num=res, pos=zeros(3), element='N')
- mol.atom_add(pdb_record='HETATM', atom_num=atom_num+1,
atom_name='H', res_name='NH', res_num=res, pos=vector, element='H')
-
- # Connect.
- mol.atom_connect(atom_num-1, atom_num)
-
- # Move 2 atoms forwards.
- atom_num += 2
-
- # The PDB file.
- file = open_write_file(file_name, force=True)
- structure.write_pdb(file)
- file.close()
-
- # Return the vectors in the diffusion frame.
- return vectors
+from test_suite.shared_data.diffusion_tensor import generate_data
# The tensor values.
@@ -249,11 +46,11 @@
csa = -172e-6
# The tensor.
-R, R_rev, D_prime, D = tensor_setup(Dx, Dy, Dz, alpha, beta, gamma)
+R, R_rev, D_prime, D = generate_data.tensor_setup(Dx, Dy, Dz, alpha, beta,
gamma)
# The bond vector distribution.
-vectors = pdb(R=R, file_name='uniform.pdb', inc=5)
+vectors = generate_data.pdb(R=R, file_name='uniform.pdb', inc=5)
# The relaxation data.
for i in range(len(frq)):
- ri_data(Dx=Dx, Dy=Dy, Dz=Dz, vectors=vectors,
frq_label=str(int(frq[i])), wH=wH[i], csa=csa)
+ generate_data.ri_data(Dx=Dx, Dy=Dy, Dz=Dz, vectors=vectors,
frq_label=str(int(frq[i])), wH=wH[i], csa=csa)
Modified: 1.3/test_suite/shared_data/diffusion_tensor/generate_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/diffusion_tensor/generate_data.py?rev=11036&r1=11035&r2=11036&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/diffusion_tensor/generate_data.py (original)
+++ 1.3/test_suite/shared_data/diffusion_tensor/generate_data.py Fri Mar 19
14:37:05 2010
@@ -26,7 +26,7 @@
"""
# Python module imports.
-from math import sqrt
+from math import pi, sqrt
from numpy import array, cross, dot, eye, float64, transpose, zeros
from numpy.linalg import eig, inv, norm
@@ -233,27 +233,3 @@
# Return the vectors in the diffusion frame.
return vectors
-
-
-# The tensor values.
-Dx = 1e7
-Dy = 2e7
-Dz = 3e7
-alpha = 1.0
-beta = 2.0
-gamma = 0.5
-
-# Other data.
-frq = array([500, 600, 700, 800], float64)
-wH = frq * 1e6 * 2*pi
-csa = -172e-6
-
-# The tensor.
-R, R_rev, D_prime, D = tensor_setup(Dx, Dy, Dz, alpha, beta, gamma)
-
-# The bond vector distribution.
-vectors = pdb(R=R, file_name='uniform.pdb', inc=5)
-
-# The relaxation data.
-for i in range(len(frq)):
- ri_data(Dx=Dx, Dy=Dy, Dz=Dz, vectors=vectors,
frq_label=str(int(frq[i])), wH=wH[i], csa=csa)
r11036 - in /1.3/test_suite/shared_data: ./ diffusion_tensor/ diffusion_tensor/ellipsoid/