def add_bond(a, a1, a2, conn, d_max):
'''
If distance between atoms a1 and a2 is less than d_max (neighboring atoms),
add atoms a1 and a2 in adjacency list conn to each other
'''
atom1 = a[a1]
atom2 = a[a2]
if v3.mag2(atom1.pos - atom2.pos) <= d_max * d_max: # connected
conn[a1].append(a2)
conn[a2].append(a1)
def add_bond(a, a1, a2, conn, d_max):
'''
If distance between atoms a1 and a2 is less than d_max (neighboring atoms),
add atoms a1 and a2 in adjacency list conn to each other
'''
atom1 = a[a1]
atom2 = a[a2]
if v3.mag2(atom1.pos - atom2.pos) <= d_max * d_max: # connected
conn[a1].append(a2)
conn[a2].append(a1)
def find_neighbor_indices_modified(atoms, indices, probe, k):
"""
Returns list of indices of atoms within probe distance to atom k.
"""
neighbor_indices = []
atom_k = atoms[k]
radius = atom_k.radius + probe + probe
for i in indices:
if i == k: continue
atom_i = atoms[i]
dist2 = v3.mag2(atom_k.pos - atom_i.pos) # ToAn
if dist2 < (radius + atom_i.radius) ** 2: # ToAn
neighbor_indices.append(i)
return neighbor_indices
def find_neighbor_indices_modified(atoms, indices, probe, k):
"""
Returns list of indices of atoms within probe distance to atom k.
"""
neighbor_indices = []
atom_k = atoms[k]
radius = atom_k.radius + probe + probe
for i in indices:
if i == k: continue
atom_i = atoms[i]
dist2 = v3.mag2(atom_k.pos - atom_i.pos) # ToAn
if dist2 < (radius + atom_i.radius)**2: # ToAn
neighbor_indices.append(i)
return neighbor_indices
def calculate_asa_optimized(atoms, probe, n_sphere_point=960):
"""
Returns the accessible-surface areas of the atoms, by rolling a
ball with probe radius over the atoms with their radius
defined.
"""
sphere_points = generate_sphere_points(n_sphere_point)
const = 4.0 * math.pi / len(sphere_points)
areas = []
neighbor_list = adjacency_list(
atoms, 2 * (probe + max(atoms, key=lambda p: p.radius).radius))
for i, atom_i in enumerate(atoms):
neighbor_indices = [neig for neig in neighbor_list[i]]
neighbor_indices = find_neighbor_indices_modified(
atoms, neighbor_indices, probe, i) # even further narrow diapazon
n_neighbor = len(neighbor_indices)
j_closest_neighbor = 0
radius = probe + atom_i.radius
n_accessible_point = 0
for point in sphere_points:
is_accessible = True
test_point = v3.scale(point, radius) + atom_i.pos
cycled_indices = range(j_closest_neighbor, n_neighbor)
cycled_indices.extend(range(j_closest_neighbor))
for j in cycled_indices:
atom_j = atoms[neighbor_indices[j]]
r = atom_j.radius + probe
diff2 = v3.mag2(atom_j.pos - test_point)
if diff2 < r * r:
j_closest_neighbor = j
is_accessible = False
break
if is_accessible:
n_accessible_point += 1
area = const * n_accessible_point * radius * radius
areas.append(area)
return areas
def calculate_asa_optimized(atoms, probe, n_sphere_point=960):
"""
Returns the accessible-surface areas of the atoms, by rolling a
ball with probe radius over the atoms with their radius
defined.
"""
sphere_points = generate_sphere_points(n_sphere_point)
const = 4.0 * math.pi / len(sphere_points)
areas = []
neighbor_list = adjacency_list(atoms, 2 * (probe + max(atoms, key=lambda p: p.radius).radius))
for i, atom_i in enumerate(atoms):
neighbor_indices = [neig for neig in neighbor_list[i]]
neighbor_indices = find_neighbor_indices_modified(atoms, neighbor_indices, probe, i) # even further narrow diapazon
n_neighbor = len(neighbor_indices)
j_closest_neighbor = 0
radius = probe + atom_i.radius
n_accessible_point = 0
for point in sphere_points:
is_accessible = True
test_point = v3.scale(point, radius) + atom_i.pos
cycled_indices = range(j_closest_neighbor, n_neighbor)
cycled_indices.extend(range(j_closest_neighbor))
for j in cycled_indices:
atom_j = atoms[neighbor_indices[j]]
r = atom_j.radius + probe
diff2 = v3.mag2(atom_j.pos - test_point)
if diff2 < r*r:
j_closest_neighbor = j
is_accessible = False
break
if is_accessible:
n_accessible_point += 1
area = const*n_accessible_point*radius*radius
areas.append(area)
return areas