public void OrderTest()
{
Partition p = new Partition(new int[][] { new[] { 1, 3 }, new[] { 0, 2 } });
p.Order();
SortedSet <int> cell0 = p.GetCell(0);
SortedSet <int> cell1 = p.GetCell(1);
Assert.IsTrue(cell0.First() < cell1.First());
Assert.IsTrue(cell0.Last() < cell1.Last());
}
/// <summary>
/// The automorphism partition is a partition of the elements of the group.
///
/// <returns>a partition of the elements of group</returns>
/// </summary>
public Partition GetAutomorphismPartition()
{
int n = group.Count;
DisjointSetForest forest = new DisjointSetForest(n);
group.Apply(new AutomorphismPartitionBacktracker(n, forest));
// convert to a partition
Partition partition = new Partition();
foreach (var set in forest.GetSets())
{
partition.AddCell(set);
}
// necessary for comparison by string
partition.Order();
return(partition);
}
/// <summary>
/// Get the bond partition, based on the element types of the atoms at either end
/// of the bond, and the bond order.
/// </summary>
/// <returns>a partition of the bonds based on the element types and bond order</returns>
public Partition GetInitialPartition()
{
var bondCount = atomContainer.Bonds.Count;
var cellMap = new Dictionary <string, SortedSet <int> >();
// make mini-'descriptors' for bonds like "C=O" or "C#N" etc
for (int bondIndex = 0; bondIndex < bondCount; bondIndex++)
{
var bond = atomContainer.Bonds[bondIndex];
var el0 = bond.Atoms[0].Symbol;
var el1 = bond.Atoms[1].Symbol;
string boS;
if (ignoreBondOrders)
{
// doesn't matter what it is, so long as it's constant
boS = "1";
}
else
{
var isArom = bond.IsAromatic;
var orderNumber = isArom ? 5 : bond.Order.Numeric();
boS = orderNumber.ToString(NumberFormatInfo.InvariantInfo);
}
string bondString;
if (string.CompareOrdinal(el0, el1) < 0)
{
bondString = el0 + boS + el1;
}
else
{
bondString = el1 + boS + el0;
}
SortedSet <int> cell;
if (cellMap.ContainsKey(bondString))
{
cell = cellMap[bondString];
}
else
{
cell = new SortedSet <int>();
cellMap[bondString] = cell;
}
cell.Add(bondIndex);
}
// sorting is necessary to get cells in order
var bondStrings = new List <string>(cellMap.Keys);
bondStrings.Sort();
// the partition of the bonds by these 'descriptors'
var bondPartition = new Partition();
foreach (string key in bondStrings)
{
var cell = cellMap[key];
bondPartition.AddCell(cell);
}
bondPartition.Order();
return(bondPartition);
}