public override void TestGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeAlkane(7);
for (int j = 0; j < 5; j++)
{
molecule.Atoms[j].IsPlaced = true;
}
IAtom atom2 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[1], molecule.Atoms[0]);
IAtom atom3 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[2], molecule.Atoms[1]);
IAtom nullAtom = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[0], molecule.Atoms[1]);
Assert.AreEqual(atom2, molecule.Atoms[2]);
Assert.AreEqual(atom3, molecule.Atoms[3]);
Assert.IsNull(nullAtom);
}
/// <summary>
/// Layout all aliphatic chains with ZMatrix.
/// </summary>
/// <param name="startAtoms">AtomContainer of possible start atoms for a chain</param>
private void PlaceLinearChains3D(IAtomContainer molecule, IAtomContainer startAtoms, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** PLACE LINEAR CHAINS ******");
IAtom dihPlacedAtom = null;
IAtom thirdPlacedAtom = null;
IAtomContainer longestUnplacedChain = molecule.Builder.NewAtomContainer();
if (startAtoms.Atoms.Count == 0)
{
//no branch points ->linear chain
//Debug.WriteLine("------ LINEAR CHAIN - FINISH ------");
}
else
{
for (int i = 0; i < startAtoms.Atoms.Count; i++)
{
//Debug.WriteLine("FOUND BRANCHED ALKAN");
//Debug.WriteLine("Atom NOT NULL:" + molecule.Atoms.IndexOf(startAtoms.GetAtomAt(i)));
thirdPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, startAtoms.Atoms[i]);
dihPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, thirdPlacedAtom, startAtoms.Atoms[i]);
longestUnplacedChain.Atoms.Add(dihPlacedAtom);
longestUnplacedChain.Atoms.Add(thirdPlacedAtom);
longestUnplacedChain.Atoms.Add(startAtoms.Atoms[i]);
longestUnplacedChain.Add(AtomPlacer.GetLongestUnplacedChain(molecule, startAtoms.Atoms[i]));
SetAtomsToUnVisited(molecule);
if (longestUnplacedChain.Atoms.Count < 4)
{
//di,third,sec
//Debug.WriteLine("------ Single BRANCH METHYLTYP ------");
//break;
}
else
{
//Debug.WriteLine("LongestUnchainLength:"+longestUnplacedChain.Atoms.Count);
ap3d.PlaceAliphaticHeavyChain(molecule, longestUnplacedChain);
ap3d.ZMatrixChainToCartesian(molecule, true);
SearchAndPlaceBranches(molecule, longestUnplacedChain, ap3d, atlp3d, atomPlacer);
}
longestUnplacedChain.RemoveAllElements();
}//for
}
//Debug.WriteLine("****** HANDLE ALIPHATICS END ******");
}
public override void TestGetPlacedHeavyAtom_IAtomContainer_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeCyclohexane();
// For(IAtom a : m.Atoms) a.IsPlaced = true;
for (int i = 0; i < 3; i++)
{
molecule.Atoms[i].IsPlaced = true;
}
IAtom atom1 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[0]);
Assert.AreEqual(atom1, molecule.Atoms[1]);
IAtom atom2 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[2]);
Assert.AreEqual(atom2, molecule.Atoms[1]);
IAtom atom3 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[4]);
Assert.IsNull(atom3);
}
/// <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;
}
