def attack_cost(reactant, subst_centres, attacking_mol_idx,
a=1.0, b=1.0, c=1.0, d=10.0):
"""
Calculate the 'attack cost' for a molecule attacking in e.g. a
substitution or elimination reaction::
C = Σ_ac a * (r_ac - r^0_ac)^2 + Σ_acx b * (1 - cos(θ)) +
Σ_acx c*(1 + cos(φ)) + Σ_ij d/r_ij^4
where::
cos(θ) = (v_ann • v_cx / |v_ann||v_cx|)
cos(φ) = (v_ca • v_cx / |v_ca||v_cx|)
Returns:
(float): Cost
"""
coords = reactant.get_coordinates()
cost = 0
for subst_centre in subst_centres:
r_ac = reactant.get_distance(atom_i=subst_centre.a_atom,
atom_j=subst_centre.c_atom)
cost += a * (r_ac - subst_centre.r0_ac)**2
# Attack vector is the average of all the nearest neighbour atoms,
# unless it is flat
a_nn_coords = [coords[atom_index] - coords[subst_centre.a_atom] for atom_index in subst_centre.a_atom_nn]
if len(a_nn_coords) == 0:
# The attacking atom has no nearest neighbours thus take the
# attack vector to be a unit vector
v_ann = np.array([1.0, 0.0, 0.0])
else:
v_ann = -np.average(np.array(a_nn_coords), axis=0)
if length(v_ann) < 1E-1:
# Attacking atom is planar. Compute the perpendicular from two
# nearest neighbours
v_ann = np.cross(coords[subst_centre.a_atom] - coords[subst_centre.a_atom_nn[0]],
coords[subst_centre.a_atom] - coords[subst_centre.a_atom_nn[1]])
v_cx = coords[subst_centre.x_atom] - coords[subst_centre.c_atom]
# b(1 - cos(θ))
cost += b * (1 - np.dot(v_ann, v_cx) / (length(v_ann) * length(v_cx)))
v_ca = coords[subst_centre.a_atom] - coords[subst_centre.c_atom]
# c(1 + cos(φ))
cost += c * (1 + np.dot(v_ca, v_cx) / (length(v_ca) * length(v_cx)))
repulsion = reactant.calc_repulsion(mol_index=attacking_mol_idx)
cost += d * repulsion
return cost
def add_dummy_atom(reactant, bond_rearrangement):
"""
Add a dummy atom above or below the plane of the reactant as a temporary
X atom
Arguments:
reactant (autode.complex.ReactantComplex):
bond_rearrangement (autode.bond_rearrangement.BondRearrangement):
"""
logger.info('Adding dummy X atom so a substitution center can be found')
fbond = bond_rearrangement.fbonds[0]
bbond = bond_rearrangement.bbonds[0]
components = connected_components(reactant.graph)
if len(components) != 2:
raise NotImplementedError('Must have two components for dummy add')
mol1_idxs, mol2_idxs = components
# Find the central atom as the atom index that is in the forming bond but
# also contains all indexes of the breaking bond
if fbond[0] in mol1_idxs and all(idx in mol2_idxs for idx in bbond):
c_atom = fbond[1]
else:
c_atom = fbond[0]
# Nearest neighbours to the central atom used to generate the normal
# along which the dummy atom is placed
c_atom_nns = list(reactant.graph.neighbors(c_atom))
if len(c_atom_nns) < 2:
raise NotImplementedError('Cannot place dummy atom')
cn1, cn2 = c_atom_nns[:2]
coords = reactant.get_coordinates()
# Calculate the normal from the vectors to two of the neighbours
position = np.cross(coords[cn1] - coords[c_atom],
coords[cn2] - coords[c_atom])
position /= length(position)
# Add the dummy atom to a position on the top/bottom face
logger.warning('Adding a dummy atom to the set of atoms')
reactant.atoms.append(DummyAtom(*position))
# Add the breaking bond to the bond rearrangement temporarily
bond_rearrangement.bbonds.append([c_atom, len(reactant.atoms) - 1])
return None
def get_distance(self, atom_i, atom_j):
"""Get the distance between two atoms in the species"""
return length(self.atoms[atom_i].coord - self.atoms[atom_j].coord)
def test_length():
assert geom.length(np.ones(3)) == np.linalg.norm(np.ones(3))
def test_length():
assert geom.length(np.array([1.0, 1.0, 1.0])) == np.linalg.norm(
np.array([1.0, 1.0, 1.0]))