public void TestGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_Double_double()
{
IAtom atom1 = new Atom("C")
{
Point3D = new Vector3(1, 1, 1)
};
IAtom atom2 = new Atom("H");
IAtom atom3 = new Atom("H");
IAtom atom4 = new Atom("H");
IAtom atom5 = new Atom("H");
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom1, atom3);
IBond bond3 = new Bond(atom1, atom4);
IBond bond4 = new Bond(atom1, atom5);
IAtomContainer ac = atom1.Builder.NewAtomContainer();
ac.Atoms.Add(atom1);
ac.Atoms.Add(atom2);
ac.Atoms.Add(atom3);
ac.Atoms.Add(atom4);
ac.Atoms.Add(atom5);
atom1.FormalNeighbourCount = 4;
atom2.FormalNeighbourCount = 1;
atom3.FormalNeighbourCount = 1;
atom4.FormalNeighbourCount = 1;
atom5.FormalNeighbourCount = 1;
ac.Bonds.Add(bond1);
ac.Bonds.Add(bond2);
ac.Bonds.Add(bond3);
ac.Bonds.Add(bond4);
IAtomContainer noCoords = AtomTetrahedralLigandPlacer3D.GetUnsetAtomsInAtomContainer(atom1, ac);
IAtomContainer withCoords = AtomTetrahedralLigandPlacer3D.GetPlacedAtomsInAtomContainer(atom1, ac);
var placer = new AtomTetrahedralLigandPlacer3D();
Vector3[] newPoints = placer.Get3DCoordinatesForLigands(atom1, noCoords, withCoords, null, 4, placer.DefaultBondLengthH, -1);
for (int j = 0; j < noCoords.Atoms.Count; j++)
{
if (newPoints[j] == null)
{
Assert.Fail("No coordinates generated for atom " + j);
}
IAtom ligand = noCoords.Atoms[j];
ligand.Point3D = newPoints[j];
}
ModelBuilder3DTest.CheckAverageBondLength(ac);
}
/// <summary>
/// Sets a branch atom to a ring or aliphatic chain.
/// </summary>
/// <param name="unplacedAtom">The new branchAtom</param>
/// <param name="atomA">placed atom to which the unplaced atom is connected</param>
/// <param name="atomNeighbours">placed atomNeighbours of atomA</param>
private static void SetBranchAtom(IAtomContainer molecule, IAtom unplacedAtom, IAtom atomA, IAtomContainer atomNeighbours,
AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d)
{
//Debug.WriteLine("****** SET Branch Atom ****** >"+molecule.Atoms.IndexOf(unplacedAtom));
IAtomContainer noCoords = molecule.Builder.NewAtomContainer();
noCoords.Atoms.Add(unplacedAtom);
Vector3 centerPlacedMolecule = ap3d.GeometricCenterAllPlacedAtoms(molecule);
IAtom atomB = atomNeighbours.Atoms[0];
string atypeNameA = atomA.AtomTypeName;
string atypeNameB = atomB.AtomTypeName;
string atypeNameUnplaced = unplacedAtom.AtomTypeName;
double length = ap3d.GetBondLengthValue(atypeNameA, atypeNameUnplaced);
double angle = (ap3d.GetAngleValue(atypeNameB, atypeNameA, atypeNameUnplaced)) * Math.PI / 180;
// Console.Out.WriteLine("A:"+atomA.Symbol+" "+atomA.AtomTypeName+
// " B:"+atomB.Symbol+" "+atomB.AtomTypeName
// +" unplaced Atom:"
// +unplacedAtom.AtomTypeName+" BL:"+length+" Angle:"+angle
// +" FormalNeighbour:"
// +atomA.FormalNeighbourCount+" HYB:"+atomA.getFlag
// (CDKConstants.HYBRIDIZATION_SP2)
// +" #Neigbhours:"+atomNeighbours.Atoms.Count);
IAtom atomC = ap3d.GetPlacedHeavyAtom(molecule, atomB, atomA);
Vector3[] branchPoints = atlp3d.Get3DCoordinatesForLigands(atomA, noCoords, atomNeighbours, atomC,
(atomA.FormalNeighbourCount.Value - atomNeighbours.Atoms.Count), length, angle);
double distance = 0;
int farthestPoint = 0;
for (int i = 0; i < branchPoints.Length; i++)
{
if (Math.Abs(Vector3.Distance(branchPoints[i], centerPlacedMolecule)) > Math.Abs(distance))
{
distance = Vector3.Distance(branchPoints[i], centerPlacedMolecule);
farthestPoint = i;
}
}
int stereo = -1;
IBond unplacedBond = molecule.GetBond(atomA, unplacedAtom);
if (atomA.StereoParity != 0 ||
(unplacedBond.Stereo == BondStereo.Up || unplacedBond.Stereo == BondStereo.Down) &&
molecule.GetMaximumBondOrder(atomA) == BondOrder.Single)
{
if (atomNeighbours.Atoms.Count > 1)
{
stereo = AtomTetrahedralLigandPlacer3D.MakeStereocenter(atomA.Point3D.Value, molecule.GetBond(atomA, unplacedAtom),
(atomNeighbours.Atoms[0]).Point3D.Value, (atomNeighbours.Atoms[1]).Point3D.Value,
branchPoints);
}
}
if (stereo != -1)
{
farthestPoint = stereo;
}
unplacedAtom.Point3D = branchPoints[farthestPoint];
unplacedAtom.IsPlaced = true;
}
