/// <summary>
/// Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
/// The first Atom end up in the origin, the second on on the x axis, and the third
/// one in the XY plane. The rest is added by applying the Zmatrix distances, angles
/// and dihedrals. Assign coordinates directly to the atoms.
/// </summary>
/// <param name="molecule">the molecule to be placed in 3D</param>
/// <param name="flagBranched">marks branched chain</param>
// @author: egonw,cho
public virtual void ZMatrixChainToCartesian(IAtomContainer molecule, bool flagBranched)
{
Vector3?result = null;
for (int index = 0; index < distances.Length; index++)
{
if (index == 0)
{
result = new Vector3(0d, 0d, 0d);
}
else if (index == 1)
{
result = new Vector3(distances[1], 0d, 0d);
}
else if (index == 2)
{
result = new Vector3(-Math.Cos((angles[2] / 180) * Math.PI) * distances[2] + distances[1],
Math.Sin((angles[2] / 180) * Math.PI) * distances[2], 0);
}
else
{
var cd = molecule.Atoms[thirdAtoms[index]].Point3D.Value
- molecule.Atoms[secondAtoms[index]].Point3D.Value;
var bc = molecule.Atoms[secondAtoms[index]].Point3D.Value
- molecule.Atoms[firstAtoms[index - 3]].Point3D.Value;
var n1 = Vector3.Cross(cd, bc);
n1 = Vector3.Normalize(n1);
Vector3 n2;
if (index == 3 && flagBranched)
{
n2 = AtomTetrahedralLigandPlacer3D.Rotate(n1, bc, DIHEDRAL_BRANCHED_CHAIN);
}
else
{
n2 = AtomTetrahedralLigandPlacer3D.Rotate(n1, bc, dihedrals[index]);
}
n2 = Vector3.Normalize(n2);
Vector3 ba = new Vector3();
if (index == 3 && flagBranched)
{
ba = AtomTetrahedralLigandPlacer3D.Rotate(cd, n2, (-angles[index] / 180) * Math.PI);
ba = AtomTetrahedralLigandPlacer3D.Rotate(ba, cd, (-angles[index] / 180) * Math.PI);
}
else
{
ba = AtomTetrahedralLigandPlacer3D.Rotate(cd, n2, (-angles[index] / 180) * Math.PI);
}
ba = Vector3.Normalize(ba);
Vector3 ban = ba;
ban *= distances[index];
result = molecule.Atoms[firstAtoms[index - 1]].Point3D.Value + ban;
}
IAtom atom = molecule.Atoms[firstAtoms[index]];
if ((atom.Point3D == null || !atom.IsPlaced) &&
!atom.IsInRing && IsHeavyAtom(atom))
{
atom.Point3D = result;
atom.IsPlaced = true;
}
}
}
/// <summary>
/// Layout the ring system, rotate and translate the template.
/// </summary>
/// <param name="originalCoord">coordinates of the placedRingAtom from the template</param>
/// <param name="placedRingAtom">placedRingAtom</param>
/// <param name="ringSet">ring system which placedRingAtom is part of</param>
/// <param name="centerPlacedMolecule">the geometric center of the already placed molecule</param>
/// <param name="atomB">placed neighbour atom of placedRingAtom</param>
private static void LayoutRingSystem(Vector3 originalCoord, IAtom placedRingAtom, IRingSet ringSet,
Vector3 centerPlacedMolecule, IAtom atomB, AtomPlacer3D ap3d)
{
//Debug.WriteLine("****** Layout ring System ******");Console.Out.WriteLine(">around atom:"+molecule.Atoms.IndexOf(placedRingAtom));
IAtomContainer ac = RingSetManipulator.GetAllInOneContainer(ringSet);
Vector3 newCoord = placedRingAtom.Point3D.Value;
Vector3 axis = new Vector3(atomB.Point3D.Value.X - newCoord.X, atomB.Point3D.Value.Y - newCoord.Y, atomB.Point3D.Value.Z - newCoord.Z);
TranslateStructure(originalCoord, newCoord, ac);
//Rotate Ringsystem to farthest possible point
Vector3 startAtomVector = new Vector3(newCoord.X - atomB.Point3D.Value.X, newCoord.Y - atomB.Point3D.Value.Y, newCoord.Z - atomB.Point3D.Value.Z);
IAtom farthestAtom = ap3d.GetFarthestAtom(placedRingAtom.Point3D.Value, ac);
Vector3 farthestAtomVector = new Vector3(farthestAtom.Point3D.Value.X - newCoord.X, farthestAtom.Point3D.Value.Y - newCoord.Y, farthestAtom.Point3D.Value.Z - newCoord.Z);
Vector3 n1 = Vector3.Cross(axis, farthestAtomVector);
n1 = Vector3.Normalize(n1);
double lengthFarthestAtomVector = farthestAtomVector.Length();
Vector3 farthestVector = startAtomVector;
farthestVector = Vector3.Normalize(farthestVector);
farthestVector *= startAtomVector.Length() + lengthFarthestAtomVector;
double dotProduct = Vector3.Dot(farthestAtomVector, farthestVector);
double angle = Math.Acos(dotProduct / (farthestAtomVector.Length() * farthestVector.Length()));
Vector3 ringCenter = new Vector3();
for (int i = 0; i < ac.Atoms.Count; i++)
{
if (!(ac.Atoms[i].IsPlaced))
{
ringCenter.X = (ac.Atoms[i].Point3D).Value.X - newCoord.X;
ringCenter.Y = (ac.Atoms[i].Point3D).Value.Y - newCoord.Y;
ringCenter.Z = (ac.Atoms[i].Point3D).Value.Z - newCoord.Z;
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, n1, angle);
ac.Atoms[i].Point3D =
new Vector3(ringCenter.X + newCoord.X, ringCenter.Y + newCoord.Y, ringCenter.Z + newCoord.Z);
//ac.GetAtomAt(i).IsPlaced = true;
}
}
//Rotate Ring so that geometric center is max from placed center
//Debug.WriteLine("Rotate RINGSYSTEM");
Vector3 pointRingCenter = GeometryUtil.Get3DCenter(ac);
double distance = 0;
double rotAngleMax = 0;
angle = 1 / 180 * Math.PI;
ringCenter = new Vector3(pointRingCenter.X, pointRingCenter.Y, pointRingCenter.Z);
ringCenter.X = ringCenter.X - newCoord.X;
ringCenter.Y = ringCenter.Y - newCoord.Y;
ringCenter.Z = ringCenter.Z - newCoord.Z;
for (int i = 1; i < 360; i++)
{
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, axis, angle);
if (Vector3.Distance(centerPlacedMolecule, new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z)) > distance)
{
rotAngleMax = i;
distance = Vector3.Distance(centerPlacedMolecule, new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z));
}
}
//rotate ring around axis with best angle
rotAngleMax = (rotAngleMax / 180) * Math.PI;
for (int i = 0; i < ac.Atoms.Count; i++)
{
if (!(ac.Atoms[i].IsPlaced))
{
ringCenter.X = (ac.Atoms[i].Point3D).Value.X;
ringCenter.Y = (ac.Atoms[i].Point3D).Value.Y;
ringCenter.Z = (ac.Atoms[i].Point3D).Value.Z;
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, axis, rotAngleMax);
ac.Atoms[i].Point3D = new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z);
ac.Atoms[i].IsPlaced = true;
}
}
}
