private double calcSingleAsa(int i) {
Atom atom_i = atoms[i];
ArrayList<Integer> neighbor_indices = findNeighborIndices(i);
int n_neighbor = neighbor_indices.size();
int j_closest_neighbor = 0;
double radius = probe + radii[i];
int n_accessible_point = 0;
for (Point3d point : spherePoints) {
boolean is_accessible = true;
Point3d test_point =
new Point3d(
point.x * radius + atom_i.getX(),
point.y * radius + atom_i.getY(),
point.z * radius + atom_i.getZ());
int[] cycled_indices = new int[n_neighbor];
int arind = 0;
for (int ind = j_closest_neighbor; ind < n_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int ind = 0; ind < j_closest_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int j : cycled_indices) {
Atom atom_j = atoms[neighbor_indices.get(j)];
double r = radii[neighbor_indices.get(j)] + probe;
double diff_sq = test_point.distanceSquared(new Point3d(atom_j.getCoords()));
if (diff_sq < r * r) {
j_closest_neighbor = j;
is_accessible = false;
break;
}
}
if (is_accessible) {
n_accessible_point++;
}
}
return cons * n_accessible_point * radius * radius;
}