private long[] Generate(IAtomContainer container, long[] seeds, IStereoEncoder encoder, int[][] graph)
{
Suppressed suppressed = suppression.Suppress(container);
// compute original values then find indices equivalent values
long[] original = simple.Generate(seeds, encoder, graph, suppressed);
var equivalentSet = finder.Find(original, container, graph);
var equivalents = equivalentSet.ToArray();
// size of the matrix we need to make
int n = original.Length;
int m = equivalents.Length;
// skip when there are no equivalent atoms
if (m < 2)
{
return(original);
}
// matrix of perturbed values and identity values
long[][] perturbed = Arrays.CreateJagged <long>(n, m + 1);
// set the original values in the first column
for (int i = 0; i < n; i++)
{
perturbed[i][0] = original[i];
}
// systematically perturb equivalent vertex
for (int i = 0; i < m; i++)
{
int equivalentIndex = equivalents[i];
// perturb the value and reset stereo configuration
original[equivalentIndex] = Rotate(original[equivalentIndex]);
encoder.Reset();
// compute new hash codes and copy the values a column in the matrix
long[] tmp = simple.Generate(Copy(original), encoder, graph, suppressed);
for (int j = 0; j < n; j++)
{
perturbed[j][i + 1] = tmp[j];
}
// reset value
original[equivalentIndex] = perturbed[equivalentIndex][0];
}
return(Combine(perturbed));
}
/// <summary>
/// reset the left and right encoders
/// </summary>
public void Reset()
{
left.Reset();
right.Reset();
}