private void TranslatePoints(int atmIdx, Vector3[][] points, int pointDensity, IAtom atom, Vector3 cp)
{
var totalRadius = PeriodicTable.GetVdwRadius(atom.Symbol).Value + solventRadius;
var area = 4 * Math.PI * (totalRadius * totalRadius) * points.Length / pointDensity;
double sumx = 0.0;
double sumy = 0.0;
double sumz = 0.0;
foreach (var point in points)
{
var p = point[1];
sumx += p.X;
sumy += p.Y;
sumz += p.Z;
}
var vconst = 4.0 / 3.0 * Math.PI / (double)pointDensity;
var dotp1 = (atom.Point3D.Value.X - cp.X) * sumx
+ (atom.Point3D.Value.Y - cp.Y) * sumy
+ (atom.Point3D.Value.Z - cp.Z) * sumz;
var volume = vconst * (totalRadius * totalRadius) * dotp1 + (totalRadius * totalRadius * totalRadius) * points.Length;
this.areas[atmIdx] = area;
this.volumes[atmIdx] = volume;
var tmp = new List <Vector3>();
foreach (var point in points)
{
tmp.Add(point[0]);
}
this.surfPoints[atmIdx] = tmp;
}
/// <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");
}
/// <summary>
/// Method assigns the atoms of a biopolymer to the grid. For every atom
/// the corresponding grid point is identified and set to the value
/// of the proteinInterior variable.
/// The atom radius and solvent radius is accounted for with the variables:
/// double rAtom, and double rSolvent.
/// </summary>
/// <exception cref="Exception"></exception>
public void AssignProteinToGrid()
{
// 1. Step: Set all grid points to solvent accessible
this.Grid = GridGenerator.InitializeGrid(this.Grid, 0);
// 2. Step Grid points inaccessible to solvent are assigend a value of -1
// set grid points around (r_atom+r_solv) to -1
Vector3 gridPoint;
int checkGridPoints = 0;
double vdWRadius = 0;
int[] dim = gridGenerator.Dim;
int[] minMax = { 0, 0, 0, 0, 0, 0 };
foreach (var atom in Protein.Atoms)
{
var patom = (PDBAtom)atom;
if (patom.HetAtom.Value)
{
continue;
}
gridPoint = gridGenerator.GetGridPointFrom3dCoordinates(patom.Point3D.Value);
this.Grid[(int)gridPoint.X][(int)gridPoint.Y][(int)gridPoint.Z] = -1;
vdWRadius = PeriodicTable.GetVdwRadius(patom.Symbol).Value;
if (vdWRadius == 0)
{
vdWRadius = RAtom;
}
checkGridPoints = (int)(((vdWRadius + RSolvent) / gridGenerator.LatticeConstant) - AtomCheckRadius);
if (checkGridPoints < 0)
{
checkGridPoints = 0;
}
minMax[0] = (int)gridPoint.X - checkGridPoints;
minMax[1] = (int)gridPoint.X + checkGridPoints;
minMax[2] = (int)gridPoint.Y - checkGridPoints;
minMax[3] = (int)gridPoint.Y + checkGridPoints;
minMax[4] = (int)gridPoint.Z - checkGridPoints;
minMax[5] = (int)gridPoint.Z + checkGridPoints;
minMax = CheckBoundaries(minMax, dim);
for (int x = minMax[0]; x <= minMax[1]; x++)
{
for (int y = minMax[2]; y <= minMax[3]; y++)
{
for (int z = minMax[4]; z <= minMax[5]; z++)
{
this.Grid[x][y][z] = this.Grid[x][y][z] - 1;
}
}
}
}// for atoms.Length
}
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);
}
/// <summary>
/// This method calculate the van der Waals radius of an atom.
/// </summary>
/// <returns>The Van der Waals radius of the atom</returns>
public Result Calculate(IAtom atom)
{
var vdwradius = PeriodicTable.GetVdwRadius(atom.AtomicNumber);
return(new Result(vdwradius.Value));
}
