def rotate_3D(atom, source_atom):
"""
Rotates the ADP of 'atom' to match the orientation
of 'source_atom.
"""
from lauescript.cryst.match import get_transform
lst2 = [np.array([0, 0, 0]), source_atom.orientation[0], source_atom.orientation[1]]
lst1 = [np.array([0, 0, 0]), atom.orientation[0], atom.orientation[1]]
matrix = get_transform(lst1, lst2, matrix=True)
adp = source_atom.adp['cart_int']
atom.adp['cart_int'] = rotate_adp(adp, matrix)
def rotate_ADP_about_axis(ADP, angle, axisDirection):
"""
Rotates an ADP about an axis by a given angle.
:param ADP: list type containing six floats representing an ADP in XD format. (U11, U22, U33, U12, U13, U23)
:param angle: float representing the angle the point is about to be rotated in degree.
:param axisDirection: list type containing three floats representing the direction of the vector
the point is rotated about. (x, y, z)
:return: tuple containing six floats representing the rotated ADP.
"""
adp = get_adp_as_matrix(ADP)
u, v = np.linalg.eig(adp)
startPoints = [v[:, i].flatten().tolist()[0] for i in range(3)]
endPoints = [rotate_point_about_axis(point, angle, axisDirection, (0, 0, 0)) for point in startPoints]
rotMat = get_transform(startPoints, endPoints, matrix=True).transpose()
newadp = np.dot(rotMat.transpose(), np.dot(adp, rotMat))
return newadp[0, 0], newadp[1, 1], newadp[2, 2], newadp[0, 1], newadp[0, 2], newadp[1, 2]
def _trust_molecules(self):
cloud1 = self['exp'].coords()[:3]
cloud2 = self['micro'].coords()[:3]
transformation = get_transform(cloud1, cloud2, matrix=True)
for i, atom in enumerate(self['exp'].atoms):
atom.transfer_matched_ADP(self['micro'].atoms[i], transformation)
