public static void Write(string fileName, Molecule moleculeA, Molecule moleculeB, Transformation transform, float value)
{
new Output(fileName, moleculeA, moleculeB, transform, value);
}
public Grid(Molecule moleculeA, Molecule moleculeB)
{
scale = 1 / dimension;
maxDistanceSquared = maxDistance * maxDistance;
this.moleculeA = moleculeA;
this.moleculeB = moleculeB;
for (int i = 0; i < moleculeA.Size; i++)
{
Block block = GetBlock(moleculeA.GetAtom(i));
if (block.X < minX)
{
minX = block.X;
}
if (block.X > maxX)
{
maxX = block.X;
}
if (block.Y < minY)
{
minY = block.Y;
}
if (block.Y > maxY)
{
maxY = block.Y;
}
if (block.Z < minZ)
{
minZ = block.Z;
}
if (block.Z > maxZ)
{
maxZ = block.Z;
}
}
// Add small buffer to all edges
int edge = (int)Math.Ceiling(4 * maxDistance * scale);
minX -= edge;
minY -= edge;
minZ -= edge;
maxX += edge;
maxY += edge;
maxZ += edge;
rangeX = maxX - minX + 1;
rangeY = maxY - minY + 1;
rangeZ = maxZ - minZ + 1;
blocks = rangeX * rangeY * rangeZ;
atomsInBlock = new int[blocks];
blockStartIndex = new int[blocks];
int atomIndicesSize = 0;
forEachBlockAndAtom((block, atom) => {
atomsInBlock[GetIndex(block)]++;
atomIndicesSize++;
});
int pos = 0;
for (int i = 0; i < blocks; i++)
{
blockStartIndex[i] = pos;
pos += atomsInBlock[i];
atomsInBlock[i] = 0;
}
atomIndices = new int[atomIndicesSize];
forEachBlockAndAtom((block, atom) => {
int i = GetIndex(block);
atomIndices[blockStartIndex[i] + atomsInBlock[i]] = atom;
atomsInBlock[i]++;
});
}