Author: bugman
Date: Sun Oct 29 03:53:37 2006
New Revision: 2682
URL: http://svn.gna.org/viewcvs/relax?rev=2682&view=rev
Log:
The diffusion tensor data structure now returns the matrices 'tensor' and
'tensor_diag'.
For spherical, spheroidal, and ellipsoidal diffusion, the diffusion tensor
data structure attributes
'tensor' and 'tensor_diag' now exist. These return the diffusion tensor in
the form of a matrix.
The object 'tensor_diag' returns the diffusion tensor defined within the
diffusion frame. The
object 'tensor' return the diffusion tensor defined within the structural
frame.
Modified:
branches/tensor_pdb/data.py
Modified: branches/tensor_pdb/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/data.py?rev=2682&r1=2681&r2=2682&view=diff
==============================================================================
--- branches/tensor_pdb/data.py (original)
+++ branches/tensor_pdb/data.py Sun Oct 29 03:53:37 2006
@@ -21,8 +21,9 @@
###############################################################################
-from Numeric import Float64, zeros
+from LinearAlgebra import inverse
from math import cos, pi, sin
+from Numeric import Float64, dot, identity, transpose, zeros
from re import match
from types import DictType, ListType
@@ -164,7 +165,7 @@
def __getattr__(self, name):
- """Function for calculating the parameters and unit vectors on the
fly.
+ """Function for calculating the parameters, unit vectors, and
tensors on the fly.
All tensor types
================
@@ -172,6 +173,22 @@
The equation for calculating Diso is
Diso = 1 / (6tm).
+
+
+ Spherical diffusion
+ ===================
+
+ The diagonalised spherical diffusion tensor is defined as
+
+ | Diso 0 0 |
+ tensor = | 0 Diso 0 |.
+ | 0 0 Diso |
+
+ The rotation matrix required to shift from the diffusion tensor
frame to the PDB frame is
+
+ | 1 0 0 |
+ R = | 0 1 0 |.
+ | 0 0 1 |
Spheroidal diffusion
@@ -191,6 +208,19 @@
Dpar_unit = | sin(theta) * sin(phi) |.
| cos(theta) |
+ The diagonalised spheroidal diffusion tensor is defined as
+
+ | Dper 0 0 |
+ tensor = | 0 Dper 0 |.
+ | 0 0 Dpar |
+
+ The rotation matrix required to shift from the diffusion tensor
frame to the PDB frame is
+ equal to
+
+ | cos(theta) * cos(phi) cos(theta) * sin(phi)
-sin(theta) |
+ R = | -sin(phi) cos(phi) 0
|.
+ | sin(theta) * cos(phi) sin(theta) * sin(phi)
cos(tehta) |
+
Ellipsoidal diffusion
=====================
@@ -221,6 +251,20 @@
Dz_unit = | sin(beta) * sin(gamma) |.
| cos(beta) |
+ The diagonalised ellipsoidal diffusion tensor is defined as
+
+ | Dx 0 0 |
+ tensor = | 0 Dy 0 |.
+ | 0 0 Dz |
+
+ The rotation matrix required to shift from the diffusion tensor
frame to the PDB frame is
+ equal to
+
+ R = | Dx_unit Dy_unit Dz_unit |,
+
+ | Dx_unit[0] Dy_unit[0] Dz_unit[0] |
+ = | Dx_unit[1] Dy_unit[1] Dz_unit[1] |.
+ | Dx_unit[2] Dy_unit[2] Dz_unit[2] |
"""
# All tensor types.
@@ -229,6 +273,23 @@
# Diso.
if name == 'Diso':
return 1.0 / (6.0 * self.tm)
+
+
+ # Spherical diffusion.
+ ######################
+
+ # The diffusion tensor.
+ if (name == 'tensor_diag' or name == 'tensor') and self.type ==
'sphere':
+ # Initialise the tensor.
+ tensor = zeros((3, 3), Float64)
+
+ # Populate the diagonal elements.
+ tensor[0, 0] = self.Diso
+ tensor[1, 1] = self.Diso
+ tensor[2, 2] = self.Diso
+
+ # Return the tensor.
+ return tensor
# Spheroidal diffusion.
@@ -259,6 +320,48 @@
# Return the unit vector.
return Dpar_unit
+ # The diffusion tensor (diagonalised).
+ if name == 'tensor_diag' and self.type == 'spheroid':
+ # Initialise the tensor.
+ tensor = zeros((3, 3), Float64)
+
+ # Populate the diagonal elements.
+ tensor[0, 0] = self.Dper
+ tensor[1, 1] = self.Dper
+ tensor[2, 2] = self.Dpar
+
+ # Return the tensor.
+ return tensor
+
+ # The diffusion tensor (within the structural frame).
+ if name == 'tensor' and self.type == 'spheroid':
+ # Initialise the tensor and the rotation matrix.
+ tensor = zeros((3, 3), Float64)
+ rotation = identity(3, Float64)
+
+ # Populate the diagonal elements.
+ tensor[0, 0] = self.Dper
+ tensor[1, 1] = self.Dper
+ tensor[2, 2] = self.Dpar
+
+ # First row of the rotation matrix.
+ rotation[0, 0] = cos(self.theta) * cos(self.phi)
+ rotation[0, 1] = cos(self.theta) * sin(self.phi)
+ rotation[0, 2] = -sin(self.theta)
+
+ # Second row of the rotation matrix.
+ rotation[1, 0] = -sin(self.phi)
+ rotation[1, 1] = cos(self.phi)
+
+ # Replace the last row of the rotation matrix with the Dpar unit
vector.
+ rotation[2] = self.Dpar_unit
+
+ # Rotation (R^T . tensor . R).
+ tensor = dot(transpose(rotation), dot(tensor, rotation))
+
+ # Return the tensor.
+ return tensor
+
# Ellipsoidal diffusion.
########################
@@ -313,6 +416,46 @@
# Return the unit vector.
return Dz_unit
+
+
+ # The diffusion tensor (diagonalised).
+ if name == 'tensor_diag' and self.type == 'ellipsoid':
+ # Initialise the tensor.
+ tensor = zeros((3, 3), Float64)
+
+ # Populate the diagonal elements.
+ tensor[0, 0] = self.Dx
+ tensor[1, 1] = self.Dy
+ tensor[2, 2] = self.Dz
+
+ # Return the tensor.
+ return tensor
+
+ # The diffusion tensor (within the structural frame).
+ if name == 'tensor' and self.type == 'ellipsoid':
+ # Initialise the tensor and the rotation matrix.
+ tensor = zeros((3, 3), Float64)
+ rotation = identity(3, Float64)
+
+ # Populate the diagonal elements.
+ tensor[0, 0] = self.Dx
+ tensor[1, 1] = self.Dy
+ tensor[2, 2] = self.Dz
+
+ # First column of the rotation matrix.
+ rotation[:, 0] = self.Dx_unit
+
+ # Second column of the rotation matrix.
+ rotation[:, 1] = self.Dy_unit
+
+ # Third column of the rotation matrix.
+ rotation[:, 2] = self.Dz_unit
+
+ # Rotation (R . tensor . R^T).
+ tensor = dot(rotation, dot(tensor, transpose(rotation)))
+
+ # Return the tensor.
+ return tensor
# The attribute asked for does not exist.
r2682 - /branches/tensor_pdb/data.py