/// <summary>
/// Calculate the accesible volume with 3 dye radii
/// </summary>
/// <param name="L">Linker length</param>
/// <param name="W">Linker width (diameter)</param>
/// <param name="R1">Dye radius 1</param>
/// <param name="R2">Dye radius 2</param>
/// <param name="R3">Dye radius 3</param>
/// <param name="atom_i">Atom ID (original number in the pdb file)</param>
public void Calculate3R(Double L, Double W, Double R1, Double R2, Double R3, Int32 atom_i)
{
// common grid
Double dg1 = Math.Min(L * _avGrid.GridSize, W * _avGrid.GridSize);
Double dg2 = Math.Min(R1 * 2.0 * _avGrid.GridSize, dg1);
dg1 = Math.Min(R2 * 2.0 * _avGrid.GridSize, dg2);
dg2 = Math.Min(R3 * 2.0 * _avGrid.GridSize, dg1);
Double dg = Math.Max(dg2, _avGrid.MinGridSize);
Double Rmax = Math.Max(R1, R2); Rmax = Math.Max(Rmax, R3);
Double x0 = mol.XLocal[atom_i], y0 = mol.YLocal[atom_i], z0 = mol.ZLocal[atom_i];
Double dx, dy, dz;
Int32 npm = (Int32)Math.Floor(L / dg);
Int32 ng = 2 * npm + 1, ng3 = ng * ng * ng, n;
Int32 offset;
Double[] xg = new Double[ng];
Double[] yg = new Double[ng];
Double[] zg = new Double[ng];
for (Int32 i = -npm; i <= npm; i++)
{
n = i + npm;
xg[n] = i * dg; yg[n] = i * dg; zg[n] = i * dg;
}
_density = new Byte[ng3];
n = FpsNativeWrapper.AvCalculate3R(L, W, R1, R2, R3, atom_i, dg, mol.XLocal, mol.YLocal, mol.ZLocal, mol.vdWR, mol.NAtoms,
AtomData.vdWRMax, _avGrid.LinkerInitialSphere, _avGrid.LinkSearchNodes, _density);
_r = new Vector3[n];
Double rn = 1.0 / (Double)n;
n = 0; dx = 0.0; dy = 0.0; dz = 0.0;
x0 += mol.CM.X; y0 += mol.CM.Y; z0 += mol.CM.Z;
for (Int32 ix = -npm; ix <= npm; ix++)
{
offset = ng * (ng * (ix + npm)) + npm;
for (Int32 iy = -npm; iy <= npm; iy++)
{
for (Int32 iz = -npm; iz <= npm; iz++)
{
for (Int32 dn = 0; dn < _density[iz + offset]; dn++)
{
_r[n].X = xg[ix + npm] + x0; dx += _r[n].X;
_r[n].Y = yg[iy + npm] + y0; dy += _r[n].Y;
_r[n].Z = zg[iz + npm] + z0; dz += _r[n++].Z;
}
}
offset += ng;
}
}
// other saves
_rmp.X = dx * rn; _rmp.Y = dy * rn; _rmp.Z = dz * rn;
_xGrid.Min = xg[0] + x0; _yGrid.Min = yg[0] + y0; _zGrid.Min = zg[0] + z0;
_xGrid.NNodes = ng; _yGrid.NNodes = ng; _zGrid.NNodes = ng;
_xGrid.Step = dg; _yGrid.Step = dg; _zGrid.Step = dg;
}
