tfep.utils.geometry

Math and geometry utility functions to manipulate coordinates.

Functions

batchwise_rotate(x, rotation_matrices[, inverse])	Rotate a batch of configurations with their respective rotation matrix.
cartesian_to_polar(x, y[, return_log_det_J])	Transform Cartesian coordinates into polar.
get_axis_from_name(name)	Return the 3D vector representation of an axis.
pdist(x[, pairs, return_diff])	Compute p-norm distances between pairs of row vectors.
polar_to_cartesian(r, angle[, return_log_det_J])	Transform polar coordinates into Cartesian.
proper_dihedral_angle(x1, x2, x3)	Compute the proper dihedral angle between the plane x1-x2 and x2-x3.
reference_frame_rotation_matrix(...[, ...])	Return the rotation matrix required to rotate the frame of reference based on two atoms.
rotation_matrix_3d(angles, directions)	Return the matrix rotating vectors for the given angle about a direction.
vector_plane_angle(x, plane)	Return the angle in radians between a batch of vectors and another vector.
vector_vector_angle(x1, x2)	Return the angle in radians between a two vectors.