Trees | Indices | Help |
|
---|
|
|
|||
DiffTensorData An empty data container for the diffusion tensor elements. |
|||
DiffTensorSimList Empty data container for Monte Carlo simulation diffusion tensor data. |
|
|||
float |
|
||
float |
|
||
numpy array |
|
||
float |
|
||
float |
|
||
float |
|
||
numpy array |
|
||
float |
|
||
numpy array |
|
||
float |
|
||
numpy array |
|
||
numpy 3x3 array |
|
||
str |
|
||
numpy 3x3 array |
|
||
numpy 3x3 array |
|
||
|
|
|||
__package__ =
|
Imports: deepcopy, search, cos, sin, array, float64, dot, identity, transpose, zeros, ListType, Element, spherical_to_cartesian, two_vect_to_R, RelaxError, fill_object_contents, xml_to_object
|
Function for calculating the Diso value. The equation for calculating the parameter is: Diso = 1 / (6tm).
|
Function for calculating the Dpar value. The equation for calculating the parameter is: Dpar = Diso + 2/3 Da.
|
Function for calculating the Dpar unit vector. The unit vector parallel to the unique axis of the diffusion tensor is: | sin(theta) * cos(phi) | Dpar_unit = | sin(theta) * sin(phi) |. | cos(theta) |
|
Function for calculating the Dper value. The equation for calculating the parameter is: Dper = Diso - 1/3 Da.
|
Function for calculating the Dratio value. The equation for calculating the parameter is: Dratio = Dpar / Dper.
|
Function for calculating the Dx value. The equation for calculating the parameter is: Dx = Diso - 1/3 Da(1 + 3Dr).
|
Function for calculating the Dx unit vector. The unit Dx vector is: | -sin(alpha) * sin(gamma) + cos(alpha) * cos(beta) * cos(gamma) | Dx_unit = | -sin(alpha) * cos(gamma) - cos(alpha) * cos(beta) * sin(gamma) |. | cos(alpha) * sin(beta) |
|
Function for calculating the Dy value. The equation for calculating the parameter is: Dy = Diso - 1/3 Da(1 - 3Dr),
|
Function for calculating the Dy unit vector. The unit Dy vector is: | cos(alpha) * sin(gamma) + sin(alpha) * cos(beta) * cos(gamma) | Dy_unit = | cos(alpha) * cos(gamma) - sin(alpha) * cos(beta) * sin(gamma) |. | sin(alpha) * sin(beta) |
|
Function for calculating the Dz value. The equation for calculating the parameter is: Dz = Diso + 2/3 Da.
|
Function for calculating the Dz unit vector. The unit Dz vector is: | -sin(beta) * cos(gamma) | Dz_unit = | sin(beta) * sin(gamma) |. | cos(beta) |
|
Function for calculating the rotation matrix. Spherical diffusionAs the orientation of the diffusion tensor within the structural frame is undefined when the molecule diffuses as a sphere, the rotation matrix is simply the identity matrix: | 1 0 0 | R = | 0 1 0 |. | 0 0 1 | Spheroidal diffusionThe rotation matrix required to shift from the diffusion tensor frame to the structural frame is generated from the unique axis of the diffusion tensor. Ellipsoidal diffusionThe rotation matrix required to shift from the diffusion tensor frame to the structural 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] |
|
Determine the spheroid type.
|
Function for calculating the diffusion tensor (in the structural frame). The diffusion tensor is calculated using the diagonalised tensor and the rotation matrix through the equation: R . tensor_diag . R^T.
|
Function for calculating the diagonalised diffusion tensor. The diagonalised spherical diffusion tensor is defined as: | Diso 0 0 | tensor = | 0 Diso 0 |. | 0 0 Diso | The diagonalised spheroidal tensor is defined as: | Dper 0 0 | tensor = | 0 Dper 0 |. | 0 0 Dpar | The diagonalised ellipsoidal diffusion tensor is defined as: | Dx 0 0 | tensor = | 0 Dy 0 |. | 0 0 Dz |
|
Generator for the automatic updating the diffusion tensor data structures. The order of the yield statements is important!
|
Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Wed Apr 10 13:30:28 2013 | http://epydoc.sourceforge.net |