public virtual void TestRemoveAtomContainer_IAtomContainer()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
T ac1 = NewContainerObject();
T ac2 = NewContainerObject();
som.Add(ac1);
som.Add(ac2);
som.Remove(ac1);
Assert.AreEqual(1, som.Count);
Assert.AreEqual(ac2, som[0]);
}
private static void filterInorganicsFromIterator(IChemObjectSet <IAtomContainer> rxnIt)
{
for (int i = rxnIt.Count - 1; i >= 0; --i)
{
var sub = rxnIt[i];
var formula = MolecularFormulaManipulator.GetMolecularFormula(sub);
if (!MolecularFormulaManipulator.ContainsElement(formula, ChemicalElement.C))
{
rxnIt.Remove(sub);
}
}
}
public virtual void TestBug2679343()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
T ac1 = NewContainerObject();
T ac2 = NewContainerObject();
som.Add(ac1);
som.Add(ac2);
som.Add(ac2);
Assert.AreEqual(3, som.Count);
som.Remove(ac2);
Assert.AreEqual(1, som.Count);
}
public static void RemoveElectronContainer(IChemObjectSet <IAtomContainer> set, IElectronContainer electrons)
{
foreach (var atomContainer in set)
{
if (atomContainer.Contains(electrons))
{
atomContainer.Remove(electrons);
var molecules = ConnectivityChecker.PartitionIntoMolecules(atomContainer);
if (molecules.Count > 1)
{
set.Remove(atomContainer);
for (int k = 0; k < molecules.Count; k++)
{
set.Add(molecules[k]);
}
}
return;
}
}
}
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]);
}