/// <summary>
/// Distribute the bonded atoms (neighbours) of an atom such that they fill the
/// remaining space around an atom in a geometrically nice way.
/// IMPORTANT: This method is not supposed to handle the
/// case of one or no place neighbor. In the case of
/// one placed neighbor, the chain placement methods
/// should be used.
/// </summary>
/// <param name="atom">The atom whose partners are to be placed</param>
/// <param name="placedNeighbours">The atoms which are already placed</param>
/// <param name="unplacedNeighbours">The partners to be placed</param>
/// <param name="bondLength">The standard bond length for the newly placed atoms</param>
/// <param name="sharedAtomsCenter">The 2D centre of the placed atoms</param>
public void DistributePartners(IAtom atom, IAtomContainer placedNeighbours, Vector2 sharedAtomsCenter, IAtomContainer unplacedNeighbours, double bondLength)
{
double occupiedAngle = 0;
IAtom[] sortedAtoms = null;
double startAngle = 0.0;
double addAngle = 0.0;
double radius = 0.0;
double remainingAngle = 0.0;
// calculate the direction away from the already placed partners of atom
var sharedAtomsCenterVector = sharedAtomsCenter;
var newDirection = atom.Point2D.Value;
var occupiedDirection = sharedAtomsCenter;
occupiedDirection = Vector2.Subtract(occupiedDirection, newDirection);
// if the placing on the centre atom we get NaNs just give a arbitrary direction the
// rest works it's self out
if (Math.Abs(occupiedDirection.Length()) < 0.001)
{
occupiedDirection = new Vector2(0, 1);
}
Debug.WriteLine("distributePartners->occupiedDirection.Lenght(): " + occupiedDirection.Length());
var atomsToDraw = new List <IAtom>();
Debug.WriteLine($"Number of shared atoms: {placedNeighbours.Atoms.Count}");
// IMPORTANT: This method is not supposed to handle the case of one or
// no place neighbor. In the case of one placed neighbor, the chain
// placement methods should be used.
if (placedNeighbours.Atoms.Count == 1)
{
Debug.WriteLine("Only one neighbour...");
for (int f = 0; f < unplacedNeighbours.Atoms.Count; f++)
{
atomsToDraw.Add(unplacedNeighbours.Atoms[f]);
}
addAngle = Math.PI * 2 / (unplacedNeighbours.Atoms.Count + placedNeighbours.Atoms.Count);
// IMPORTANT: At this point we need a calculation of the start
// angle. Not done yet.
IAtom placedAtom = placedNeighbours.Atoms[0];
double xDiff = placedAtom.Point2D.Value.X - atom.Point2D.Value.X;
double yDiff = placedAtom.Point2D.Value.Y - atom.Point2D.Value.Y;
Debug.WriteLine("distributePartners->xdiff: " + Vectors.RadianToDegree(xDiff));
Debug.WriteLine("distributePartners->ydiff: " + Vectors.RadianToDegree(yDiff));
startAngle = GeometryUtil.GetAngle(xDiff, yDiff);
Debug.WriteLine("distributePartners->angle: " + Vectors.RadianToDegree(startAngle));
PopulatePolygonCorners(atomsToDraw, atom.Point2D.Value, startAngle, addAngle, bondLength);
return;
}
else if (placedNeighbours.Atoms.Count == 0)
{
Debug.WriteLine("First atom...");
for (int f = 0; f < unplacedNeighbours.Atoms.Count; f++)
{
atomsToDraw.Add(unplacedNeighbours.Atoms[f]);
}
addAngle = Math.PI * 2.0 / unplacedNeighbours.Atoms.Count;
// IMPORTANT: At this point we need a calculation of the start
// angle. Not done yet.
startAngle = 0.0;
PopulatePolygonCorners(atomsToDraw, atom.Point2D.Value, startAngle, addAngle, bondLength);
return;
}
if (DoAngleSnap(atom, placedNeighbours))
{
int numTerminal = 0;
foreach (var unplaced in unplacedNeighbours.Atoms)
{
if (Molecule.GetConnectedBonds(unplaced).Count() == 1)
{
numTerminal++;
}
}
if (numTerminal == unplacedNeighbours.Atoms.Count)
{
var a = NewVector(placedNeighbours.Atoms[0].Point2D.Value, atom.Point2D.Value);
var b = NewVector(placedNeighbours.Atoms[1].Point2D.Value, atom.Point2D.Value);
var d1 = GeometryUtil.GetAngle(a.X, a.Y);
var d2 = GeometryUtil.GetAngle(b.X, b.Y);
var sweep = Vectors.Angle(a, b);
if (sweep < Math.PI)
{
sweep = 2 * Math.PI - sweep;
}
startAngle = d2;
if (d1 > d2 && d1 - d2 < Math.PI || d2 - d1 >= Math.PI)
{
startAngle = d1;
}
sweep /= (1 + unplacedNeighbours.Atoms.Count);
PopulatePolygonCorners(unplacedNeighbours.Atoms,
atom.Point2D.Value, startAngle, sweep, bondLength);
MarkPlaced(unplacedNeighbours);
return;
}
else
{
atom.RemoveProperty(MacroCycleLayout.MACROCYCLE_ATOM_HINT);
}
}
// if the least hindered side of the atom is clearly defined (bondLength / 10 is an arbitrary value that seemed reasonable)
//newDirection.Sub(sharedAtomsCenterVector);
sharedAtomsCenterVector -= newDirection;
newDirection = sharedAtomsCenterVector;
newDirection = Vector2.Normalize(newDirection);
newDirection = newDirection * bondLength;
newDirection = -newDirection;
Debug.WriteLine($"distributePartners->newDirection.Lenght(): {newDirection.Length()}");
var distanceMeasure = atom.Point2D.Value;
distanceMeasure += newDirection;
// get the two sharedAtom partners with the smallest distance to the new center
sortedAtoms = placedNeighbours.Atoms.ToArray();
GeometryUtil.SortBy2DDistance(sortedAtoms, distanceMeasure);
var closestPoint1 = sortedAtoms[0].Point2D.Value;
var closestPoint2 = sortedAtoms[1].Point2D.Value;
closestPoint1 -= atom.Point2D.Value;
closestPoint2 -= atom.Point2D.Value;
occupiedAngle = Vectors.Angle(closestPoint1, occupiedDirection);
occupiedAngle += Vectors.Angle(closestPoint2, occupiedDirection);
var angle1 = GeometryUtil.GetAngle(
sortedAtoms[0].Point2D.Value.X - atom.Point2D.Value.X,
sortedAtoms[0].Point2D.Value.Y - atom.Point2D.Value.Y);
var angle2 = GeometryUtil.GetAngle(
sortedAtoms[1].Point2D.Value.X - atom.Point2D.Value.X,
sortedAtoms[1].Point2D.Value.Y - atom.Point2D.Value.Y);
var angle3 = GeometryUtil.GetAngle(
distanceMeasure.X - atom.Point2D.Value.X,
distanceMeasure.Y - atom.Point2D.Value.Y);
if (debug)
{
try
{
Debug.WriteLine($"distributePartners->sortedAtoms[0]: {(Molecule.Atoms.IndexOf(sortedAtoms[0]) + 1)}");
Debug.WriteLine($"distributePartners->sortedAtoms[1]: {(Molecule.Atoms.IndexOf(sortedAtoms[1]) + 1)}");
Debug.WriteLine($"distributePartners->angle1: {Vectors.RadianToDegree(angle1)}");
Debug.WriteLine($"distributePartners->angle2: {Vectors.RadianToDegree(angle2)}");
}
catch (Exception exc)
{
Debug.WriteLine(exc);
}
}
IAtom startAtom = null;
if (angle1 > angle3)
{
if (angle1 - angle3 < Math.PI)
{
startAtom = sortedAtoms[1];
}
else
{
// 12 o'clock is between the two vectors
startAtom = sortedAtoms[0];
}
}
else
{
if (angle3 - angle1 < Math.PI)
{
startAtom = sortedAtoms[0];
}
else
{
// 12 o'clock is between the two vectors
startAtom = sortedAtoms[1];
}
}
remainingAngle = (2 * Math.PI) - occupiedAngle;
addAngle = remainingAngle / (unplacedNeighbours.Atoms.Count + 1);
if (debug)
{
try
{
Debug.WriteLine($"distributePartners->startAtom: {(Molecule.Atoms.IndexOf(startAtom) + 1)}");
Debug.WriteLine($"distributePartners->remainingAngle: {Vectors.RadianToDegree(remainingAngle)}");
Debug.WriteLine($"distributePartners->addAngle: {Vectors.RadianToDegree(addAngle)}");
Debug.WriteLine($"distributePartners-> partners.Atoms.Count: {unplacedNeighbours.Atoms.Count}");
}
catch (Exception exc)
{
Debug.WriteLine(exc);
}
}
for (int f = 0; f < unplacedNeighbours.Atoms.Count; f++)
{
atomsToDraw.Add(unplacedNeighbours.Atoms[f]);
}
radius = bondLength;
startAngle = GeometryUtil.GetAngle(startAtom.Point2D.Value.X - atom.Point2D.Value.X, startAtom.Point2D.Value.Y - atom.Point2D.Value.Y);
Debug.WriteLine($"Before check: distributePartners->startAngle: {startAngle}");
Debug.WriteLine($"After check: distributePartners->startAngle: {startAngle}");
PopulatePolygonCorners(atomsToDraw, atom.Point2D.Value, startAngle, addAngle, radius);
}
