public void TestGetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
IAtomContainer acyclicAlkane = TestMoleculeFactory.MakeAlkane(5);
foreach (var atom in benzene.Atoms)
{
atom.IsInRing = true;
}
foreach (var atom in acyclicAlkane.Atoms)
{
atom.IsAliphatic = true;
}
for (int j = 0; j < 3; j++)
{
benzene.Atoms[j].IsPlaced = true;
}
IAtom searchedatom1 = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(benzene);
Assert.IsNull(searchedatom1);
foreach (var atom in benzene.Atoms)
{
if (!atom.IsPlaced)
{
atom.IsPlaced = true;
}
}
IAtom searchedatom2 = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(benzene);
Assert.IsNull(searchedatom2);
for (int k = 0; k < 3; k++)
{
acyclicAlkane.Atoms[k].IsPlaced = true;
}
IAtom nextAtom = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(acyclicAlkane);
Assert.AreEqual(acyclicAlkane.Atoms[2], nextAtom);
}
/// <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);
}
