protected MacrocycleAnalysis(List <Atom> atoms, IEnumerable <Bond> bonds)
{
Atoms = atoms;
Bonds = bonds;
_guid = Guid.NewGuid();
//set special atoms
_cachedNeighbors = AtomUtil.BuildNeighborCache(Atoms, Bonds);
Alpha = Atoms.Where(IsAlpha).ToList();
Beta = Atoms.Where(s => Neighbors(s).Count == 2 && Neighbors(s).Count(IsAlpha) == 1).ToList();
N4Cavity = Atoms.Where(s => Neighbors(s).Where(IsAlpha).Count(n => DFSUtil.BackTrack(n, s, Neighbors, 5).Count == 5) == 2)
.ToList();
Meso = Atoms.Except(Alpha).Except(Beta).Except(N4Cavity).ToList();
}
