public static IReadOnlyList <IAtomContainer> PartitionIntoMolecules(IAtomContainer container, int[] components)
{
int maxComponentIndex = 0;
foreach (int component in components)
{
if (component > maxComponentIndex)
{
maxComponentIndex = component;
}
}
var containers = new IAtomContainer[maxComponentIndex + 1];
var componentsMap = new Dictionary <IAtom, IAtomContainer>(2 * container.Atoms.Count);
for (int i = 1; i < containers.Length; i++)
{
containers[i] = container.Builder.NewAtomContainer();
}
for (int i = 0; i < container.Atoms.Count; i++)
{
componentsMap.Add(container.Atoms[i], containers[components[i]]);
containers[components[i]].Atoms.Add(container.Atoms[i]);
}
foreach (var bond in container.Bonds)
{
var begComp = componentsMap[bond.Begin];
var endComp = componentsMap[bond.End];
if (begComp == endComp)
{
begComp.Bonds.Add(bond);
}
}
foreach (var electron in container.SingleElectrons)
{
componentsMap[electron.Atom].SingleElectrons.Add(electron);
}
foreach (var lonePair in container.LonePairs)
{
componentsMap[lonePair.Atom].LonePairs.Add(lonePair);
}
foreach (var stereo in container.StereoElements)
{
var focus = stereo.Focus;
switch (focus)
{
case IAtom atom:
if (componentsMap.ContainsKey(atom))
{
componentsMap[atom].StereoElements.Add(stereo);
}
break;
case IBond bond:
if (componentsMap.ContainsKey(bond.Begin))
{
componentsMap[bond.Begin].StereoElements.Add(stereo);
}
break;
default:
throw new InvalidOperationException("New stereo element not using an atom/bond for focus?");
}
}
// do not return IEnumerable, containers are modified above.
var containerSet = new List <IAtomContainer>(containers.Skip(1));
return(containerSet);
}