/// <summary>
/// Search and place branches of a chain or ring.
/// </summary>
/// <param name="chain">AtomContainer if atoms in an aliphatic chain or ring system</param>
private void SearchAndPlaceBranches(IAtomContainer molecule, IAtomContainer chain, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** SEARCH AND PLACE ****** Chain length: "+chain.Atoms.Count);
IAtomContainer branchAtoms = molecule.Builder.NewAtomContainer();
IAtomContainer connectedAtoms = molecule.Builder.NewAtomContainer();
for (int i = 0; i < chain.Atoms.Count; i++)
{
var atoms = molecule.GetConnectedAtoms(chain.Atoms[i]);
foreach (var atom in atoms)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.H) & !atom.IsPlaced & !atom.IsInRing)
{
connectedAtoms.Add(ap3d.GetPlacedHeavyAtoms(molecule, chain.Atoms[i]));
try
{
SetBranchAtom(molecule, atom, chain.Atoms[i], connectedAtoms, ap3d, atlp3d);
}
catch (CDKException ex2)
{
Trace.TraceError($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms due to {ex2.ToString()}");
throw new CDKException($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms: {ex2.Message}", ex2);
}
branchAtoms.Atoms.Add(atom);
connectedAtoms.RemoveAllElements();
}
}
}//for ac.getAtomCount
PlaceLinearChains3D(molecule, branchAtoms, ap3d, atlp3d, atomPlacer);
}
public override void TestGetPlacedHeavyAtoms_IAtomContainer_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeBenzene();
for (int j = 0; j < 3; j++)
{
(molecule.Atoms[j]).IsPlaced = true;
}
IAtomContainer placedAndConnectedTo1 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[1]);
IAtomContainer placedAndConnectedTo2 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[2]);
IAtomContainer placedAndConnectedTo4 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[4]);
Assert.AreEqual(2, placedAndConnectedTo1.Atoms.Count);
Assert.AreEqual(1, placedAndConnectedTo2.Atoms.Count);
Assert.AreEqual(0, placedAndConnectedTo4.Atoms.Count);
}
/// <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);
}
