public void Rank_all_equiv()
{
InvariantRanker ranker = new InvariantRanker(6);
long[] prev = new long[] { 1, 1, 1, 1, 1, 1 };
long[] curr = new long[] { 42, 42, 42, 42, 42, 42 };
// no we leave extra space
int[] vs = new int[] { 0, 1, 2, 3, 4, 5 };
int[] ws = new int[6];
int ranks = ranker.Rank(vs, ws, 6, curr, prev);
Assert.AreEqual(1, ranks);
// assigned ranks (note: unique assigned first)
Assert.IsTrue(Compares.AreEqual(new long[] { 1, 1, 1, 1, 1, 1 }, prev));
// remaining non-unique vertices
Assert.IsTrue(Compares.AreEqual(new int[] { 0, 1, 2, 3, 4, 5 }, ws));
}
public void Rank_all_unique()
{
InvariantRanker ranker = new InvariantRanker(7);
long[] prev = new long[] { 1, 1, 1, 1, 1, 1, 1 };
long[] curr = new long[] { 7, 3, 1, 0, 91, 32, 67 };
// no we leave extra space
int[] vs = new int[] { 0, 1, 2, 3, 4, 5, 6 };
int[] ws = new int[7];
int ranks = ranker.Rank(vs, ws, 7, curr, prev);
Assert.AreEqual(7, ranks);
// assigned ranks (note: unique assigned first)
Assert.IsTrue(Compares.AreEqual(new long[] { 4, 3, 2, 1, 7, 5, 6 }, prev));
// no non-unique vertices
Assert.IsTrue(Compares.AreEqual(new int[] { -1, 0, 0, 0, 0, 0, 0 }, ws));
}
/// <summary>
/// Internal - refine invariants to a canonical labelling and symmetry classes.
/// </summary>
/// <param name="invariants">the invariants to refine (canonical labelling gets written here)</param>
/// <param name="hydrogens">binary vector of terminal hydrogens</param>
/// <returns>the symmetry classes</returns>
private long[] Refine(long[] invariants, bool[] hydrogens)
{
int ord = g.Length;
InvariantRanker ranker = new InvariantRanker(ord);
// current/next vertices, these only hold the vertices which are
// equivalent
int[] currVs = new int[ord];
int[] nextVs = new int[ord];
// fill with identity (also set number of non-unique)
int nnu = ord;
for (int i = 0; i < ord; i++)
{
currVs[i] = i;
}
long[] prev = invariants;
long[] curr = Arrays.CopyOf(invariants, ord);
// initially all labels are 1, the input invariants are then used to
// refine this coarse partition
Arrays.Fill(prev, 1L);
// number of ranks
int n = 0, m = 0;
// storage of symmetry classes
long[] symmetry = null;
while (n < ord)
{
// refine the initial invariants using product of primes from
// adjacent ranks
while ((n = ranker.Rank(currVs, nextVs, nnu, curr, prev)) > m && n < ord)
{
nnu = 0;
for (int i = 0; i < ord && nextVs[i] >= 0; i++)
{
int v = nextVs[i];
currVs[nnu++] = v;
curr[v] = hydrogens[v] ? prev[v] : PrimeProduct(g[v], prev, hydrogens);
}
m = n;
}
if (symmetry == null)
{
// After symmetry classes have been found without hydrogens we add
// back in the hydrogens and assign ranks. We don't refine the
// partition until the next time round the while loop to avoid
// artificially splitting due to hydrogen representation, for example
// the two hydrogens are equivalent in this SMILES for ethane '[H]CC'
for (int i = 0; i < g.Length; i++)
{
if (hydrogens[i])
{
curr[i] = prev[g[i][0]];
hydrogens[i] = false;
}
}
n = ranker.Rank(currVs, nextVs, nnu, curr, prev);
symmetry = Arrays.CopyOf(prev, ord);
// Update the buffer of non-unique vertices as hydrogens next
// to discrete heavy atoms are also discrete (and removed from
// 'nextVs' during ranking.
nnu = 0;
for (int i = 0; i < ord && nextVs[i] >= 0; i++)
{
currVs[nnu++] = nextVs[i];
}
}
// partition is discrete or only symmetry classes are needed
if (symOnly || n == ord)
{
return(symmetry);
}
// artificially split the lowest cell, we perturb the value
// of all vertices with equivalent rank to the lowest non-unique
// vertex
int lo = nextVs[0];
for (int i = 1; i < ord && nextVs[i] >= 0 && prev[nextVs[i]] == prev[lo]; i++)
{
prev[nextVs[i]]++;
}
// could also swap but this is cleaner
Array.Copy(nextVs, 0, currVs, 0, nnu);
}
return(symmetry);
}