pyvibdmc.analysis.rotator

Classes

MolRotator

A helper class that will rotate a stack of molecules and generate 3D rotation matrices using vectorized

Module Contents

class pyvibdmc.analysis.rotator.MolRotator

A helper class that will rotate a stack of molecules and generate 3D rotation matrices using vectorized numpy operations.

static rotate_geoms(rot_mats, geoms)

Takes in a stack of rotation matrices and applies it to a stack of geometries.

static rotate_vec(rot_mats, vecc)

Takes in a stack of rotation matrices and applies it to a stack of vector

static gen_rot_mats(theta, xyz_int)

Generates the 3D rotation matrix about X, Y, or Z by theta radians

static rotate_to_xy_plane(geoms, orig, xax, xyp, return_mat=False)

Rotate geometries to XY plane, placing one atom at the origin, one on the xaxis, and one on the xyplane. Done through successive rotations about the X-axis, Z-axis then X-axis again.

static gen_eulers(xyz, XYZ)

Takes in cartesian vectors and gives you the 3 euler angles that bring xyz to XYZ based on a ‘ZYZ’ rotation

static extract_eulers(rot_mats)

From a rotation matrix, calculate the three euler angles theta,phi and Chi. This is based on a ‘ZYZ’ euler rotation