/// <summary>
/// Initialize the surface, generating the points on the accessible surface
/// area of each atom as well as calculating the surface area of each atom.
/// </summary>
private void Init()
{
// invariants
foreach (var atom in atoms)
{
if (atom.Point3D == null)
{
throw new ArgumentException("One or more atoms had no 3D coordinate set");
}
}
// get r_f and geometric center
var cp = new Vector3(0, 0, 0);
double maxRadius = 0;
foreach (var atom in atoms)
{
var vdwr = PeriodicTable.GetVdwRadius(atom.Symbol).Value;
if (vdwr + solventRadius > maxRadius)
{
maxRadius = PeriodicTable.GetVdwRadius(atom.Symbol).Value + solventRadius;
}
cp.X = cp.X + atom.Point3D.Value.X;
cp.Y = cp.Y + atom.Point3D.Value.Y;
cp.Z = cp.Z + atom.Point3D.Value.Z;
}
cp.X = cp.X / atoms.Length;
cp.Y = cp.Y / atoms.Length;
cp.Z = cp.Z / atoms.Length;
// do the tesselation
var tess = new Tessellate("ico", tesslevel);
tess.DoTessellate();
Trace.TraceInformation($"Got tesselation, number of triangles = {tess.GetNumberOfTriangles()}");
// get neighbor list
var nbrlist = new NeighborList(atoms, maxRadius + solventRadius);
Trace.TraceInformation("Got neighbor list");
// loop over atoms and get surface points
this.surfPoints = new List <Vector3> [atoms.Length];
this.areas = new double[atoms.Length];
this.volumes = new double[atoms.Length];
for (int i = 0; i < atoms.Length; i++)
{
var pointDensity = tess.GetNumberOfTriangles() * 3;
var points = AtomicSurfacePoints(nbrlist, i, atoms[i], tess);
TranslatePoints(i, points, pointDensity, atoms[i], cp);
}
Trace.TraceInformation("Obtained points, areas and volumes");
}
