public static HashSet <Atom>[] BuildRigids(Universe univ)
{
List <HashSet <Atom> > rigidgroups;
{
rigidgroups = new List <HashSet <Atom> >();
//List<Atom[]> rigidgroups = univ.FindRigidUnits();
foreach (Atom[] atoms in univ.FindRigidUnits())
{
HashSet <Atom> rigidgroup = new HashSet <Atom>(atoms);
{
/// When rigid group is "ghij" and its rigid structure is same to the below,
/// add "f","c","k" also (which are the bonded atoms of "ghij") into the rigid group.
///
/// def klm
/// \ /
/// abc---ghij
///
foreach (Atom atom in atoms)
{
foreach (Bond bond in atom.Bonds)
{
rigidgroup.Add(bond.atoms[0]);
rigidgroup.Add(bond.atoms[1]);
}
}
}
rigidgroups.Add(rigidgroup);
}
}
HashSet <Atom>[] rigids = new HashSet <Atom> [univ.size];
foreach (HashSet <Atom> rigidgroup in rigidgroups)
{
foreach (Atom atom in rigidgroup)
{
if (rigids[atom.ID] == null)
{
rigids[atom.ID] = rigidgroup;
}
else
{
/// When the case of "g", it is belonged to three rigid groups "abc", "def", and "ghij".
/// In this case, the atom "g" has a unique rigid groups, which combines all them.
IEnumerable <Atom> union = Enumerable.Union(rigids[atom.ID], rigidgroup);
rigids[atom.ID] = new HashSet <Atom>(union);
}
}
}
return(rigids);
}
