/// <summary>
/// Checks if <paramref name="atom1"/> and <paramref name="atom2"/> share membership in the same ring or ring system.
/// Membership in the same ring is checked if the RingSet contains the SSSR of a molecule; membership in
/// the same ring or same ring system is checked if the RingSet contains all rings of a molecule.
/// </summary>
/// <remarks>
/// <note type="important">
/// This method only returns meaningful results if <paramref name="atom1"/> and
/// <paramref name="atom2"/> are members of the same molecule for which the ring set was calculated!
/// </note>
/// </remarks>
/// <param name="ringSet">The collection of rings</param>
/// <param name="atom1">The first atom</param>
/// <param name="atom2">The second atom</param>
/// <returns><see langword="true"/> if <paramref name="atom1"/> and <paramref name="atom2"/> share membership of at least one ring or ring system, false otherwise</returns>
public static bool IsSameRing(IRingSet ringSet, IAtom atom1, IAtom atom2)
{
foreach (var atomContainer in ringSet)
{
IRing ring = (IRing)atomContainer;
if (ring.Contains(atom1) && ring.Contains(atom2))
{
return(true);
}
}
return(false);
}
/// <summary>
/// Partition the bonding partners of a given atom into ring atoms and non-ring atoms
/// </summary>
/// <param name="atom">The atom whose bonding partners are to be partitioned</param>
/// <param name="ring">The ring against which the bonding partners are checked</param>
/// <param name="ringAtoms">An AtomContainer to store the ring bonding partners</param>
/// <param name="nonRingAtoms">An AtomContainer to store the non-ring bonding partners</param>
public void PartitionNonRingPartners(IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms)
{
var atoms = Molecule.GetConnectedAtoms(atom);
foreach (var curAtom in atoms)
{
if (!ring.Contains(curAtom))
{
nonRingAtoms.Atoms.Add(curAtom);
}
else
{
ringAtoms.Atoms.Add(curAtom);
}
}
}
public static void FixAromaticityForXLogP(IAtomContainer m)
{
// need to find rings and aromaticity again since added H's
IRingSet rs = null;
try
{
AllRingsFinder arf = new AllRingsFinder();
rs = arf.FindAllRings(m);
// SSSRFinder s = new SSSRFinder(m);
// srs = s.FindEssentialRings();
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
try
{
// figure out which atoms are in aromatic rings:
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
Aromaticity.CDKLegacy.Apply(m);
// figure out which rings are aromatic:
RingSetManipulator.MarkAromaticRings(rs);
// figure out which simple (non cycles) rings are aromatic:
// HueckelAromaticityDetector.DetectAromaticity(m, srs);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is a part of
for (int i = 0; i <= m.Atoms.Count - 1; i++)
{
m.Atoms[i].IsAromatic = false;
for (int j = 0; j <= rs.Count - 1; j++)
{
//Debug.WriteLine(i+"\t"+j);
IRing r = (IRing)rs[j];
if (!r.IsAromatic)
{
goto continue_jloop;
}
bool haveatom = r.Contains(m.Atoms[i]);
//Debug.WriteLine("haveatom="+haveatom);
if (haveatom && r.Atoms.Count == 6)
{
m.Atoms[i].IsAromatic = true;
}
continue_jloop:
;
}
}
}