def calculate_asa(atoms, probe, n_sphere_point=960):
"""
Returns list of accessible surface areas of the atoms, using the probe
and atom radius to define the surface.
"""
sphere_points = generate_sphere_points(n_sphere_point)
points = np.array([ [a.pos.x, a.pos.y, a.pos.z] for a in atoms ]) #, dtype=np.float16)
radii = np.array([a.radius for a in atoms]) #, dtype=np.float16)
const = 4.0 * math.pi / len(sphere_points)
test_point = Vector3d()
areas = []
for i, atom_i in enumerate(atoms):
neighbor_indices = find_neighbor_indices(points, radii, probe, i)
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.x = point[0]*radius + atom_i.pos.x
test_point.y = point[1]*radius + atom_i.pos.y
test_point.z = point[2]*radius + atom_i.pos.z
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
diff_sq = pos_distance_sq(atom_j.pos, test_point)
if diff_sq < 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(atoms, probe, n_sphere_point=960):
"""
Returns list of accessible surface areas of the atoms, using the probe
and atom radius to define the surface.
"""
sphere_points = generate_sphere_points(n_sphere_point)
const = 4.0 * math.pi / len(sphere_points)
test_point = Vector3d()
areas = []
for i, atom_i in enumerate(atoms):
neighbor_indices = find_neighbor_indices(atoms, probe, i)
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.x = point[0] * radius + atom_i.pos.x
test_point.y = point[1] * radius + atom_i.pos.y
test_point.z = point[2] * radius + atom_i.pos.z
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
diff_sq = pos_distance_sq(atom_j.pos, test_point)
if diff_sq < 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