def get_normal(building_block):
"""
Get a normal to a plane crossing the building block.
The normal is defined by the plane of best fit to the placer atoms
of the building block. It is defined such that the it always forms
an acute angle with the vector running from the centroid of the
placer atoms to the centroid of the building block.
Parameters
----------
building_block : :.BuildingBlock`
The building block whose normal should be calculated.
Returns
-------
:class:`numpy.ndarray`
The normal of `building_block`.
"""
placer_centroid = building_block.get_centroid(
atom_ids=building_block.get_placer_ids(),
)
normal = stk.get_acute_vector(
reference=building_block.get_centroid() - placer_centroid,
vector=building_block.get_plane_normal(
atom_ids=building_block.get_placer_ids(),
),
)
if np.allclose(normal, [0, 0, 1], atol=1e-13):
return np.array([0, 0, 1])
if np.allclose(normal, [0, 0, -1], atol=1e-13):
return np.array([0, 0, -1])
return normal
def functional_group_angle(building_block):
fg0 = next(building_block.get_functional_groups(0))
fg0_position = building_block.get_centroid(
atom_ids=fg0.get_placer_ids(),
)
placer_centroid = building_block.get_centroid(
atom_ids=building_block.get_placer_ids(),
)
fg0_direction = fg0_position - placer_centroid
centroid = building_block.get_centroid(
atom_ids=building_block.get_placer_ids(),
)
normal = stk.get_acute_vector(
reference=building_block.get_centroid() - placer_centroid,
vector=building_block.get_plane_normal(
atom_ids=building_block.get_placer_ids(),
),
)
axis = -np.cross(normal, fg0_direction)
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
return inner
def get_plane_normal(building_block):
macrocycle = max(
rdkit.GetSymmSSSR(building_block.to_rdkit_mol()),
key=len,
)
centroid = building_block.get_centroid()
atom1_position, = building_block.get_atomic_positions(0)
normal = -stk.get_acute_vector(
reference=atom1_position - centroid,
vector=building_block.get_plane_normal(macrocycle),
)
if np.allclose(normal, [1, 0, 0], atol=1e-13):
return np.array([1, 0, 0], dtype=np.float64)
elif np.allclose(normal, [-1, 0, 0], atol=1e-13):
return np.array([-1, 0, 0], dtype=np.float64)
return normal