private static List <IAtomContainer> MakeCut(IBond cut, IAtomContainer mol, Dictionary <IAtom, int> idx, int[][] adjlist)
{
var beg = cut.Begin;
var end = cut.End;
var bvisit = new LinkedHashSet <IAtom>();
var evisit = new LinkedHashSet <IAtom>();
var queue = new ArrayDeque <IAtom>();
bvisit.Add(beg);
evisit.Add(end);
queue.Add(beg);
bvisit.Add(end); // stop visits
while (queue.Any())
{
var atom = queue.Poll();
bvisit.Add(atom);
foreach (var w in adjlist[idx[atom]])
{
var nbr = mol.Atoms[w];
if (!bvisit.Contains(nbr))
{
queue.Add(nbr);
}
}
}
bvisit.Remove(end);
queue.Add(end);
evisit.Add(beg); // stop visits
while (queue.Any())
{
var atom = queue.Poll();
evisit.Add(atom);
foreach (var w in adjlist[idx[atom]])
{
var nbr = mol.Atoms[w];
if (!evisit.Contains(nbr))
{
queue.Add(nbr);
}
}
}
evisit.Remove(beg);
var bldr = mol.Builder;
var bfrag = bldr.NewAtomContainer();
var efrag = bldr.NewAtomContainer();
int diff = bvisit.Count - evisit.Count;
if (diff < -10)
{
evisit.Clear();
}
else if (diff > 10)
{
bvisit.Clear();
}
if (bvisit.Any())
{
bfrag.Atoms.Add(bldr.NewPseudoAtom());
foreach (var atom in bvisit)
{
bfrag.Atoms.Add(atom);
}
bfrag.AddBond(bfrag.Atoms[0], bfrag.Atoms[1], cut.Order);
bfrag.Bonds[0].SetProperty(PropertyName_CutBond, cut);
}
if (evisit.Any())
{
efrag.Atoms.Add(bldr.NewPseudoAtom());
foreach (var atom in evisit)
{
efrag.Atoms.Add(atom);
}
efrag.AddBond(efrag.Atoms[0], efrag.Atoms[1], cut.Order);
efrag.Bonds[0].SetProperty(PropertyName_CutBond, cut);
}
foreach (var bond in mol.Bonds)
{
var a1 = bond.Begin;
var a2 = bond.End;
if (bvisit.Contains(a1) && bvisit.Contains(a2))
{
bfrag.Bonds.Add(bond);
}
else if (evisit.Contains(a1) && evisit.Contains(a2))
{
efrag.Bonds.Add(bond);
}
}
var res = new List <IAtomContainer>();
if (!bfrag.IsEmpty())
{
res.Add(bfrag);
}
if (!efrag.IsEmpty())
{
res.Add(efrag);
}
return(res);
}