/// <summary>
/// Layout the molecule, starts with ring systems and than aliphatic chains.
/// </summary>
/// <param name="ringSetMolecule">ringSystems of the molecule</param>
private void LayoutMolecule(IReadOnlyList <IRingSet> ringSetMolecule, IAtomContainer molecule, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** LAYOUT MOLECULE MAIN *******");
IAtomContainer ac = null;
int safetyCounter = 0;
IAtom atom = null;
//Place rest Chains/Atoms
do
{
safetyCounter++;
atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedRingNeighbour(molecule);
if (atom != null)
{
//Debug.WriteLine("layout RingSystem...");
var unplacedAtom = ap3d.GetUnplacedRingHeavyAtom(molecule, atom);
var ringSetA = GetRingSetOfAtom(ringSetMolecule, unplacedAtom);
var ringSetAContainer = RingSetManipulator.GetAllInOneContainer(ringSetA);
templateHandler.MapTemplates(ringSetAContainer, ringSetAContainer.Atoms.Count);
if (CheckAllRingAtomsHasCoordinates(ringSetAContainer))
{
}
else
{
throw new IOException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout. Sorry");
}
Vector3 firstAtomOriginalCoord = unplacedAtom.Point3D.Value;
Vector3 centerPlacedMolecule = ap3d.GeometricCenterAllPlacedAtoms(molecule);
SetBranchAtom(molecule, unplacedAtom, atom, ap3d.GetPlacedHeavyAtoms(molecule, atom), ap3d, atlp3d);
LayoutRingSystem(firstAtomOriginalCoord, unplacedAtom, ringSetA, centerPlacedMolecule, atom, ap3d);
SearchAndPlaceBranches(molecule, ringSetAContainer, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("Ready layout Ring System");
ringSetA = null;
unplacedAtom = null;
}
else
{
//Debug.WriteLine("layout chains...");
SetAtomsToUnVisited(molecule);
atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(molecule);
if (atom != null)
{
ac = atom.Builder.NewAtomContainer();
ac.Atoms.Add(atom);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
ac = null;
}
}
} while (!ap3d.AllHeavyAtomsPlaced(molecule) || safetyCounter > molecule.Atoms.Count);
}
public override void TestGeometricCenterAllPlacedAtoms_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeAlkane(2);
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = true;
}
molecule.Atoms[0].Point3D = new Vector3(-1.0, 0.0, 0.0);
molecule.Atoms[1].Point3D = new Vector3(1.0, 0.0, 0.0);
Vector3 center = atmplacer.GeometricCenterAllPlacedAtoms(molecule);
Assert.AreEqual(0.0, center.X, 0.01);
Assert.AreEqual(0.0, center.Y, 0.01);
Assert.AreEqual(0.0, center.Z, 0.01);
}
/// <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;
}
