/// <summary>
/// Produces a HOSE code for Atom <paramref name="root"/> in the <see cref="IAtomContainer"/> <paramref name="ac"/>. The HOSE
/// code is produced for the number of spheres given by <paramref name="noOfSpheres"/>.
/// </summary>
/// <remarks>
/// <note type="important">
/// If you want aromaticity to be included in the code, you need
/// to apply <see cref="Aromaticities.Aromaticity.Apply(IAtomContainer)"/> to <paramref name="ac"/> prior to
/// using <see cref="GetHOSECode(IAtomContainer, IAtom, int, bool)"/>. This method only gives proper results if the molecule is
/// fully saturated (if not, the order of the HOSE code might depend on atoms in higher spheres).
/// This method is known to fail for protons sometimes.
/// </note>
/// <note type="important">
/// Your molecule must contain implicit or explicit hydrogens
/// for this method to work properly.
/// </note>
/// </remarks>
/// <param name="ac">The IAtomContainer with the molecular skeleton in which the root atom resides</param>
/// <param name="root">The root atom for which to produce the HOSE code</param>
/// <param name="noOfSpheres">The number of spheres to look at</param>
/// <param name="ringsize">The size of the Ring(s) it is in is included in center atom code</param>
/// <returns>The HOSECode value</returns>
/// <exception cref="CDKException">Thrown if something is wrong</exception>
public string GetHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, bool ringsize)
{
var canLabler = new CanonicalLabeler();
canLabler.CanonLabel(ac);
centerCode = "";
this.atomContainer = ac;
maxSphere = noOfSpheres;
spheres = new List <TreeNode> [noOfSpheres + 1];
for (int i = 0; i < ac.Atoms.Count; i++)
{
ac.Atoms[i].IsVisited = false;
}
root.IsVisited = true;
rootNode = new TreeNode(this, root.Symbol, null, root, (double)0, atomContainer.GetConnectedBonds(root).Count(), 0);
// All we need to observe is how the ranking of substituents in the
// subsequent spheres of the root nodes influences the ranking of the
// first sphere, since the order of a node in a sphere depends on the
// order the preceding node in its branch
HOSECode = new StringBuilder();
CreateCenterCode(root, ac, ringsize);
BreadthFirstSearch(root, true);
CreateCode();
FillUpSphereDelimiters();
Debug.WriteLine($"HOSECodeGenerator -> HOSECode: {HOSECode}");
return(HOSECode.ToString());
}
public int[] GetCanonicalPermutation(IAtomContainer container)
{
CanonicalLabeler labeler = new CanonicalLabeler();
labeler.CanonLabel(container);
int n = container.Atoms.Count;
int[] perm = new int[n];
for (int i = 0; i < n; i++)
{
IAtom a = container.Atoms[i];
int x = (int)a.GetProperty <long>(InvPair.CanonicalLabelPropertyKey);
perm[i] = x - 1;
}
return(perm);
}