/// <summary>
/// Labels the Atom's and Bond's in each AtomContainer using the a1, a2, b1, b2
/// scheme often used in CML. It will also set id's for all AtomContainers, naming
/// them m1, m2, etc.
/// It will not the AtomContainerSet itself.
/// </summary>
private static void CreateIDsForAtomContainerSet(IChemObjectSet <IAtomContainer> containerSet, List <string> tabuList)
{
if (tabuList == null)
{
tabuList = AtomContainerSetManipulator.GetAllIDs(containerSet).ToList();
}
if (null == containerSet.Id)
{
atomContainerSetCount = SetId(ATOMCONTAINERSET_PREFIX, atomContainerSetCount, containerSet, tabuList);
}
if (policy == UniquePolicy.Object)
{
// start atom and bond indices within a container set always from 1
atomCount = 0;
bondCount = 0;
}
foreach (var ac in containerSet)
{
CreateIDsForAtomContainer(ac, tabuList);
}
}
internal IAtomContainer Generate2(IChemObjectSet <IAtomContainer> atomContainers)
{
int iteration = 0;
bool structureFound = false;
do
{
iteration++;
bool bondFormed;
do
{
bondFormed = false;
var atomContainersArray = atomContainers.ToList();
for (var atomContainersArrayIndex = 0; atomContainersArrayIndex < atomContainersArray.Count; atomContainersArrayIndex++)
{
var ac = atomContainersArray[atomContainersArrayIndex];
if (ac == null)
{
continue;
}
var atoms = ac.Atoms.ToList(); // ToList is required because some atoms are added to ac.Atoms in the loop.
foreach (var atom in atoms)
{
if (!satCheck.IsSaturated(atom, ac))
{
var partner = GetAnotherUnsaturatedNode(atom, ac, atomContainers);
if (partner != null)
{
var toadd = AtomContainerSetManipulator.GetRelevantAtomContainer(atomContainers, partner);
var cmax1 = satCheck.GetCurrentMaxBondOrder(atom, ac);
var cmax2 = satCheck.GetCurrentMaxBondOrder(partner, toadd);
var max = Math.Min(cmax1, cmax2);
var order = Math.Min(Math.Max(1, max), 3); //(double)Math.Round(Math.Random() * max)
Debug.WriteLine($"cmax1, cmax2, max, order: {cmax1}, {cmax2}, {max}, {order}");
if (toadd != ac)
{
var indexToRemove = atomContainersArray.IndexOf(toadd);
if (indexToRemove != -1)
{
atomContainersArray[indexToRemove] = null;
}
atomContainers.Remove(toadd);
ac.Add(toadd);
}
ac.Bonds.Add(ac.Builder.NewBond(atom, partner, BondManipulator.CreateBondOrder(order)));
bondFormed = true;
}
}
}
}
} while (bondFormed);
if (atomContainers.Count == 1 &&
satCheck.IsSaturated(atomContainers[0]))
{
structureFound = true;
}
} while (!structureFound && iteration < 5);
if (atomContainers.Count == 1 && satCheck.IsSaturated(atomContainers[0]))
{
structureFound = true;
}
if (!structureFound)
{
return(null);
}
return(atomContainers[0]);
}
