/// <summary>
/// Recursively performs a depth first search in a molecular graphs contained in
/// the AtomContainer molecule, starting at the root atom and returning when it
/// hits the target atom.
/// <para>
/// CAUTION: This recursive method sets the VISITED flag of each atom
/// does not reset it after finishing the search. If you want to do the
/// operation on the same collection of atoms more than once, you have
/// to set all the VISITED flags to false before each operation
/// by looping of the atoms and doing a
/// "atom.Flag = (CDKConstants.VISITED, false);"
/// </para>
/// <para>
/// Note that the path generated by the search will not contain the root atom,
/// but will contain the target atom
/// </para>
/// </summary>
/// <param name="molecule">The AtomContainer to be searched</param>
/// <param name="root">The root atom to start the search at</param>
/// <param name="target">The target</param>
/// <param name="path">An AtomContainer to be filled with the path</param>
/// <returns><see langword="true"/> if the target atom was found during this function call</returns>
public static bool DepthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path)
{
var bonds = molecule.GetConnectedBonds(root);
IAtom nextAtom;
root.IsVisited = true;
bool first = path.IsEmpty();
if (first)
{
path.Atoms.Add(root);
}
foreach (var bond in bonds)
{
nextAtom = bond.GetOther(root);
if (!nextAtom.IsVisited)
{
path.Atoms.Add(nextAtom);
path.Bonds.Add(bond);
if (nextAtom.Equals(target))
{
if (first)
{
path.Atoms.Remove(root);
}
return(true);
}
else
{
if (!DepthFirstTargetSearch(molecule, nextAtom, target, path))
{
// we did not find the target
path.Atoms.Remove(nextAtom);
path.Bonds.Remove(bond);
}
else
{
if (first)
{
path.Atoms.Remove(root);
}
return(true);
}
}
}
}
if (first)
{
path.Atoms.Remove(root);
}
return(false);
}
private static int[] DetermineComponents(IAtomContainer target, bool auto)
{
int[] components = null;
// no atoms -> no components
if (target.IsEmpty())
{
components = new int[0];
}
// defined by reaction grouping
if (components == null && target.Atoms[0].GetProperty <int?>(CDKPropertyName.ReactionGroup) != null)
{
int max = 0;
components = new int[target.Atoms.Count + 1];
for (int i = 0; i < target.Atoms.Count; i++)
{
var grp = target.Atoms[i].GetProperty <int?>(CDKPropertyName.ReactionGroup);
if (grp == null)
{
grp = 0;
}
components[i] = grp.Value;
if (grp > max)
{
max = grp.Value;
}
}
components[target.Atoms.Count] = max;
}
// calculate from connection table
if (components == null && auto)
{
int max = 0;
components = new int[target.Atoms.Count + 1];
int i = 0;
foreach (int grp in new ConnectedComponents(GraphUtil.ToAdjList(target)).GetComponents())
{
components[i++] = grp;
if (grp > max)
{
max = grp;
}
}
components[target.Atoms.Count] = max;
}
return(components);
}
