/// <summary>
/// Makes an array containing the morgan numbers of the atoms of
/// atomContainer. These number are the extended connectivity values and not
/// the lexicographic smallest labelling on the graph.
/// </summary>
/// <param name="molecule">the molecule to analyse.</param>
/// <returns>The morgan numbers value.</returns>
public static long[] GetMorganNumbers(IAtomContainer molecule)
{
int order = molecule.Atoms.Count;
long[] currentInvariants = new long[order];
long[] previousInvariants = new long[order];
int[][] graph = Arrays.CreateJagged <int>(order, InitialDegree);
int[] degree = new int[order];
// which atoms are the non-hydrogens.
int[] nonHydrogens = new int[order];
for (int v = 0; v < order; v++)
{
nonHydrogens[v] = molecule.Atoms[v].AtomicNumber.Equals(AtomicNumbers.H) ? 0 : 1;
}
// build the graph and initialise the current connectivity
// value to the number of connected non-hydrogens
foreach (var bond in molecule.Bonds)
{
int u = molecule.Atoms.IndexOf(bond.Begin);
int v = molecule.Atoms.IndexOf(bond.End);
graph[u] = Ints.EnsureCapacity(graph[u], degree[u] + 1, InitialDegree);
graph[v] = Ints.EnsureCapacity(graph[v], degree[v] + 1, InitialDegree);
graph[u][degree[u]++] = v;
graph[v][degree[v]++] = u;
currentInvariants[u] += nonHydrogens[v];
currentInvariants[v] += nonHydrogens[u];
}
// iteratively sum the connectivity values for each vertex
for (int i = 0; i < order; i++)
{
Array.Copy(currentInvariants, 0, previousInvariants, 0, order);
for (int u = 0; u < order; u++)
{
currentInvariants[u] = 0;
// for each of the vertices adjacent to <paramref name="u"/> sum their
// previous connectivity value
int[] neighbors = graph[u];
for (int j = 0; j < degree[u]; j++)
{
int v = neighbors[j];
currentInvariants[u] += previousInvariants[v] * nonHydrogens[v];
}
}
}
return(currentInvariants);
}