def fix_cyclopropenyl(atoms: Atoms, mol: pybel.Molecule) -> Atoms:
"""Detect cyclopropenyl groups and assure they are planar.
Args:
atoms: Object holding the 3D positions
mol: Object holidng the bonding information
Returns:
Version of atoms with the rings flattened
"""
# Find cyclopropenyl groups
smarts = pybel.Smarts('C1=C[C+]1')
rings = smarts.findall(mol)
if len(rings) == 0:
return atoms # no changes
# For each ring, flatten it
atoms = atoms.copy()
g = get_bonding_graph(mol)
for ring in rings:
ring = tuple(x - 1 for x in rings[0]) # Pybel is 1-indexed
# Get the normal of the ring
normal = np.cross(*np.subtract(atoms.positions[ring[:2], :],
atoms.positions[ring[2], :]))
normal /= np.linalg.norm(normal)
# Adjust the groups attached to each member of the ring
for ring_atom in ring:
# Get the ID of the group bonded to it
bonded_atom = next(r for r in g[ring_atom] if r not in ring)
# Determine the atoms that are part of that functional group
h = g.copy()
h.remove_edge(ring_atom, bonded_atom)
a, b = nx.connected_components(h)
mask = np.zeros((len(atoms), ), dtype=bool)
if bonded_atom in a:
mask[list(a)] = True
else:
mask[list(b)] = True
# Get the rotation angle
bond_vector = atoms.positions[bonded_atom, :] - atoms.positions[
ring_atom, :]
angle = np.dot(bond_vector, normal) / np.linalg.norm(bond_vector)
rot_angle = np.arccos(angle) - np.pi / 2
logger.debug(f'Rotating by {rot_angle} radians')
# Perform the rotation
rotation_axis = np.cross(bond_vector, normal)
atoms._masked_rotate(atoms.positions[ring_atom], rotation_axis,
rot_angle, mask)
# make the atom at a 150 angle with the the ring too
another_ring = next(r for r in ring if r != ring_atom)
atoms.set_angle(another_ring,
ring_atom,
bonded_atom,
150,
mask=mask)
assert np.isclose(
atoms.get_angle(another_ring, ring_atom, bonded_atom),
150).all()
# Make sure it worked
bond_vector = atoms.positions[bonded_atom, :] - atoms.positions[
ring_atom, :]
angle = np.dot(bond_vector, normal) / np.linalg.norm(bond_vector)
final_angle = np.arccos(angle)
assert np.isclose(final_angle, np.pi / 2).all()
logger.info(
f'Detected {len(rings)} cyclopropenyl rings. Ensured they are planar.'
)
return atoms
