Package lib :: Package structure :: Package represent :: Module diffusion_tensor
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Module diffusion_tensor

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Functions [hide private]
 
diffusion_tensor(mol=None, tensor=None, tensor_diag=None, diff_type=None, rotation=None, axes=None, sim_axes=None, com=None, scale=1.8e-06)
Create the structural representation of the diffusion tensor.
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Variables [hide private]
  __package__ = 'lib.structure.represent'

Imports: array, dot, float64, transpose, generate_vector_dist, generate_vector_residues


Function Details [hide private]

diffusion_tensor(mol=None, tensor=None, tensor_diag=None, diff_type=None, rotation=None, axes=None, sim_axes=None, com=None, scale=1.8e-06)

source code 

Create the structural representation of the diffusion tensor.

Parameters:
  • mol (MolContainer instance) - The molecule container.
  • tensor (numpy rank-2, 3D array) - The diffusion tensor.
  • tensor_diag (numpy rank-2, 3D array) - The diagonalised diffusion tensor in tensor frame.
  • diff_type (str) - The type of diffusion tensor. This can be one of 'sphere', 'oblate', 'prolate', 'ellipsoid'.
  • rotation (numpy rank-2, 3D array) - The diffusion tensor rotation matrix.
  • axes (list of numpy rank-1, 3D arrays) - The axis system of the tensor. For the spheroids this is one vector, for the ellipsoid it should be three vectors.
  • sim_axes (None or list of lists of numpy rank-1, 3D arrays) - The axis systems of the tensor for each simulation. For the spheroids this is one vector, for the ellipsoid it should be three vectors. The first dimension is the axis type (x, y, or z), the second is the simulation, and the third is the vector.
  • com (numpy rank-1, 3D array) - The centre of mass of the diffusion structure.
  • scale (float) - The scaling factor for the diffusion tensor.