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