/// <summary> Converts a RingSet to an AtomContainer.
///
/// </summary>
/// <param name="ringSet"> The RingSet to be converted.
/// </param>
/// <returns> The AtomContainer containing the bonds and atoms of the ringSet.
/// </returns>
public static IAtomContainer convertToAtomContainer(IRingSet ringSet)
{
IRing ring = (IRing)ringSet.getAtomContainer(0);
if (ring == null)
{
return(null);
}
IAtomContainer ac = ring.Builder.newAtomContainer();
for (int i = 0; i < ringSet.AtomContainerCount; i++)
{
ring = (IRing)ringSet.getAtomContainer(i);
for (int r = 0; r < ring.getBondCount(); r++)
{
IBond bond = ring.getBondAt(r);
if (!ac.contains(bond))
{
for (int j = 0; j < bond.AtomCount; j++)
{
ac.addAtom(bond.getAtomAt(j));
}
ac.addBond(bond);
}
}
}
return(ac);
}
public static bool replaceAtomByAtom(IAtomContainer container, IAtom atom, IAtom newAtom)
{
if (!container.contains(atom))
{
// it should complain
return(false);
}
else
{
container.setAtomAt(container.getAtomNumber(atom), newAtom);
IElectronContainer[] electronContainers = container.ElectronContainers;
for (int i = 0; i < electronContainers.Length; i++)
{
if (electronContainers[i] is IBond)
{
IBond bond = (IBond)electronContainers[i];
if (bond.contains(atom))
{
for (int j = 0; j < bond.AtomCount; j++)
{
if (atom.Equals(bond.getAtomAt(j)))
{
bond.setAtomAt(newAtom, j);
}
}
}
}
else if (electronContainers[i] is ILonePair)
{
ILonePair lonePair = (ILonePair)electronContainers[i];
if (atom.Equals(lonePair.Atom))
{
lonePair.Atom = newAtom;
}
}
}
return(true);
}
}
public static void removeElectronContainer(ISetOfAtomContainers set_Renamed, IElectronContainer electrons)
{
IAtomContainer[] acs = set_Renamed.AtomContainers;
for (int i = 0; i < acs.Length; i++)
{
IAtomContainer container = acs[i];
if (container.contains(electrons))
{
container.removeElectronContainer(electrons);
IMolecule[] molecules = ConnectivityChecker.partitionIntoMolecules(container).Molecules;
if (molecules.Length > 1)
{
set_Renamed.removeAtomContainer(container);
for (int k = 0; k < molecules.Length; k++)
{
set_Renamed.addAtomContainer(molecules[k]);
}
}
return;
}
}
}
public static bool replaceAtomByAtom(IAtomContainer container, IAtom atom, IAtom newAtom)
{
if (!container.contains(atom))
{
// it should complain
return false;
}
else
{
container.setAtomAt(container.getAtomNumber(atom), newAtom);
IElectronContainer[] electronContainers = container.ElectronContainers;
for (int i = 0; i < electronContainers.Length; i++)
{
if (electronContainers[i] is IBond)
{
IBond bond = (IBond)electronContainers[i];
if (bond.contains(atom))
{
for (int j = 0; j < bond.AtomCount; j++)
{
if (atom.Equals(bond.getAtomAt(j)))
{
bond.setAtomAt(newAtom, j);
}
}
}
}
else if (electronContainers[i] is ILonePair)
{
ILonePair lonePair = (ILonePair)electronContainers[i];
if (atom.Equals(lonePair.Atom))
{
lonePair.Atom = newAtom;
}
}
}
return true;
}
}