void forEachBlockAndAtom(Action <Block, int> callback)
{
int radius = (int)Math.Ceiling(maxDistance * scale);
float radiusSquared = maxDistance * maxDistance + dimension * dimension;
for (int i = 0; i < moleculeA.Size; i++)
{
Vector vector = moleculeA.GetAtom(i);
Block block = GetBlock(vector);
for (int x = block.X - radius; x <= block.X + radius; x++)
{
for (int y = block.Y - radius; y <= block.Y + radius; y++)
{
for (int z = block.Z - radius; z <= block.Z + radius; z++)
{
Block current = new Block(x, y, z);
if (vector.DistanceSquared(BlockCenter(current)) <= radiusSquared)
{
callback(current, i);
}
}
}
}
}
}
private Output(string fileName, Molecule moleculeA, Molecule moleculeB, Transformation transform, float value)
{
writer = new StreamWriter(File.Open(fileName, FileMode.Create));
addRemark(new string [] { "Binding of " + moleculeA.FileName, "with " + moleculeB.FileName });
addRemark(new string [] { "Energy between molecules: " + Utils.FloatToString(value) });
addRemark(new string [] {
"Transformation:",
"rotate " + transform.RotationString(),
"transpose "
+ Utils.FloatToString(transform.Transpose.X)
+ ", " + Utils.FloatToString(transform.Transpose.Y)
+ ", " + Utils.FloatToString(transform.Transpose.Z)
});
for (int i = 0; i < moleculeA.Size; i++)
{
addAtom(
moleculeA.IsHetAtm[i],
moleculeA.AtomId[i],
moleculeA.AtomNames[i],
moleculeA.AminoAcids[i],
'A',
moleculeA.AminoAcidIds[i],
moleculeA.X[i],
moleculeA.Y[i],
moleculeA.Z[i],
moleculeA.Charge[i],
moleculeA.Diameter[i]
);
}
for (int i = 0; i < moleculeB.Size; i++)
{
Vector vector = transform.Transform(moleculeB.GetAtom(i));
addAtom(
moleculeB.IsHetAtm[i],
moleculeA.MaxAtomId + moleculeB.AtomId[i],
moleculeB.AtomNames[i],
moleculeB.AminoAcids[i],
'B',
moleculeA.MaxAminoAcidId + moleculeB.AminoAcidIds[i],
vector.X,
vector.Y,
vector.Z,
moleculeB.Charge[i],
moleculeB.Diameter[i]
);
}
for (int i = 0; i < moleculeA.Connections.Length; i++)
{
addConnect(moleculeA.Connections[i], 0);
}
for (int i = 0; i < moleculeB.Connections.Length; i++)
{
addConnect(moleculeB.Connections[i], moleculeA.MaxAtomId);
}
writer.Write("END");
writer.Flush();
}
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]++;
});
}