kabsch(name_from=None,
name_to=None,
coord_from=None,
coord_to=None,
centre_type=' centroid ' ,
elements=None,
centroid=None,
verbosity=1)
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Calculate the rotational and translational displacements between the
two given coordinate sets.
This uses the Kabsch algorithm.
- Parameters:
name_from (str) - The name of the starting structure, used for the printouts.
name_to (str) - The name of the ending structure, used for the printouts.
coord_from (numpy rank-2, Nx3 array) - The list of atomic coordinates for the starting structure.
coord_to (numpy rank-2, Nx3 array) - The list of atomic coordinates for the ending structure.
centre_type (str) - The type of centre to superimpose over. This can either be the
standard centroid superimposition or the CoM could be used
instead.
elements (list of str) - The list of elements corresponding to the atoms.
centroid (list of float or numpy rank-1, 3D array) - An alternative position of the centroid, used for studying
pivoted systems.
- Returns: numpy rank-1 3D array, float, numpy rank-2 3D array, numpy rank-1 3D
array, float, numpy rank-1 3D array
- The translation vector T, translation distance d, rotation matrix
R, rotation axis r, rotation angle theta, and the rotational
pivot defined as the centroid of the ending structure.
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