def get_stk_bond_angle(mol, atom1_id, atom2_id, atom3_id):
# TODO: Fill in the doc string for this including defintiions.
atom1_pos, = mol.get_atomic_positions(atom_ids=atom1_id)
atom2_pos, = mol.get_atomic_positions(atom_ids=atom2_id)
atom3_pos, = mol.get_atomic_positions(atom_ids=atom3_id)
v1 = atom1_pos - atom2_pos
v2 = atom3_pos - atom2_pos
return stk.vector_angle(v1, v2)
def inner(functional_group):
position = building_block.get_centroid(
atom_ids=functional_group.get_placer_ids(), )
fg_direction = position - centroid
theta = stk.vector_angle(fg0_direction, fg_direction)
projection = fg_direction @ axis
if theta > 0 and projection < 0:
return 2 * np.pi - theta
return theta
def is_rotated(original, rotated, angle):
"""
Check that `rotated` is `original` with a rotation of `angle`.
Parameters
----------
original : :class:`numpy.ndarray`
The position matrix of a molecule before rotation.
rotated : :class:`numpy.ndarray`
The position matrix of a molecule after rotation.
angle : :class:`float`
The rotational angle.
Returns
-------
None : :class:`NoneType`
"""
for atom_id in range(max(len(original), len(rotated))):
# No rotation is expected if the atom was located at the
# origin of the rotation.
if np.allclose(original[atom_id], [0, 0, 0], 1e-13):
assert np.allclose(
a=original[atom_id],
b=rotated[atom_id],
atol=1e-13,
)
else:
applied_rotation = stk.vector_angle(
vector1=original[atom_id],
vector2=rotated[atom_id],
)
assert abs(abs(angle) - applied_rotation) < 1e-13
def inner(fg_id):
fg = bb.func_groups[fg_id]
fg_vector = (bb.get_centroid(fg.get_bonder_ids()) -
bb.get_centroid(bb.get_bonder_ids()))
return stk.vector_angle(fg_vector, edge_vector)