private void WipeMoleculeRings()
{
Rings.RemoveAll();
//first set all atoms to side chains
foreach (var a in Atoms)
{
a.Rings.RemoveAll();
_sortedRings = null;
}
}
/// <summary>
/// Rebuilds the molecule without trashing it totally
/// </summary>
/// <param name="seed">start Atom for refresh operation</param>
private void Refresh(Atom seed = null)
{
//keep a list of the atoms to refer to later when rebuilding
List <Atom> checklist = new List <Atom>();
//set the parent to null but keep a list of all atoms
foreach (Atom atom in Atoms)
{
atom.Parent = null;
checklist.Add(atom);
}
//clear the associated collections
Atoms.RemoveAll();
AllAtoms.RemoveAll();
foreach (Bond bond in Bonds)
{
bond.Parent = null;
}
Bonds.RemoveAll();
AllBonds.RemoveAll();
Rings.RemoveAll();
//if we've been provided with a seed atom, use that
//else use the first atom in the checklist
if (seed == null)
{
seed = checklist[0];
}
//now traverse the tree as far as it will go
DepthFirstTraversal(seed,
operation: atom =>
{
Atoms.Add(atom);
foreach (Bond b in atom.Bonds.Where(b => b.Parent == null))
{
Bonds.Add(b);
}
if (checklist.Contains(atom))
{
checklist.Remove(atom);
}
},
isntProcessed: atom => atom.Parent == null);
//only if the molecule has rings do we rebuild it
RebuildRings();
//now we check to see whether there are any more unconnected regions lurking around
while (checklist.Count > 0)//means we haven't yet accounted for all the original atoms
{
seed = checklist[0];
Molecule addnlMol = new Molecule();
DepthFirstTraversal(seed,
operation: atom =>
{
addnlMol.Atoms.Add(atom);
foreach (Bond b in atom.Bonds.Where(b => b.Parent == null))
{
addnlMol.Bonds.Add(b);
}
if (checklist.Contains(atom))
{
checklist.Remove(atom);
}
},
isntProcessed: atom => atom.Parent == null);
//only if the molecule has rings do we rebuild it
addnlMol.RebuildRings();
this.Parent.Molecules.Add(addnlMol);
}
}