private Vector3[][] AtomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, IAtom atom, Tessellate tess)
{
double totalRadius = PeriodicTable.GetVdwRadius(atom.Symbol).Value + solventRadius;
double totalRadius2 = totalRadius * totalRadius;
double twiceTotalRadius = 2 * totalRadius;
int[] nlist = nbrlist.GetNeighbors(currAtomIdx);
double[][] data = Arrays.CreateJagged <double>(nlist.Length, 4);
for (int i = 0; i < nlist.Length; i++)
{
double x12 = atoms[nlist[i]].Point3D.Value.X - atom.Point3D.Value.X;
double y12 = atoms[nlist[i]].Point3D.Value.Y - atom.Point3D.Value.Y;
double z12 = atoms[nlist[i]].Point3D.Value.Z - atom.Point3D.Value.Z;
double d2 = x12 * x12 + y12 * y12 + z12 * z12;
double tmp = PeriodicTable.GetVdwRadius(atoms[nlist[i]].Symbol).Value + solventRadius;
tmp = tmp * tmp;
double thresh = (d2 + totalRadius2 - tmp) / twiceTotalRadius;
data[i][0] = x12;
data[i][1] = y12;
data[i][2] = z12;
data[i][3] = thresh;
}
Vector3[] tessPoints = tess.GetTessAsPoint3ds();
List <Vector3[]> points = new List <Vector3[]>();
for (int i = 0; i < tessPoints.Length; i++)
{
Vector3 pt = tessPoints[i];
bool buried = false;
for (int j = 0; j < data.Length; j++)
{
if (data[j][0] * pt.X + data[j][1] * pt.Y + data[j][2] * pt.Z > data[j][3])
{
buried = true;
break;
}
}
if (buried == false)
{
Vector3[] tmp = new Vector3[2];
tmp[0] = new Vector3(totalRadius * pt.X + atom.Point3D.Value.X, totalRadius * pt.Y
+ atom.Point3D.Value.Y, totalRadius * pt.Z + atom.Point3D.Value.Z);
tmp[1] = pt;
points.Add(tmp);
}
}
// the first column contains the transformed points
// and the second column contains the points from the
// original unit tesselation
Vector3[][] ret = Arrays.CreateJagged <Vector3>(points.Count, 2);
for (int i = 0; i < points.Count; i++)
{
Vector3[] tmp = points[i];
ret[i][0] = tmp[0];
ret[i][1] = tmp[1];
}
return(ret);
}