/// <summary> We define the heaviest ring as the one with the highest number of double bonds.
/// Needed for example for the placement of in-ring double bonds.
///
/// </summary>
/// <param name="bond"> A bond which must be contained by the heaviest ring
/// </param>
/// <returns> The ring with the higest number of double bonds connected to a given bond
/// </returns>
public static IRing getHeaviestRing(IRingSet ringSet, IBond bond)
{
System.Collections.IList rings = ringSet.getRings(bond);
IRing ring = null;
int maxOrderSum = 0;
for (int i = 0; i < rings.Count; i++)
{
if (maxOrderSum < ((IRing)rings[i]).OrderSum)
{
ring = (IRing)rings[i];
maxOrderSum = ring.OrderSum;
}
}
return(ring);
}
private bool preprocessMolecule(IAtomContainer original)
{
//prepare atom weights
var atomWeightCanBeCalculated = prepareAtomWeights(original);
// If the SDF contains an "R" or something, we don't know its mass, so this whole endevour is fruitless
// (since we won't be able to match the fragment masses to the peaks).
if (!atomWeightCanBeCalculated)
{
return false;
}
//mark all the bonds and atoms with numbers --> identify them later on
originalMolecule = markAllBonds(original);
//do ring detection with the original molecule
var allRingsFinder = new AllRingsFinder();
// Steve: Set a really large timeout, because we don't want to crash just because it took a long time.
// The size limit of 7 below should stop it looping forever.
allRingsFinder.setTimeout(int.MaxValue);
// TODO: Steve: The 7 is a max ring size - I added this to prevent it getting in to infinite loops (7 comes from MetFrag
// where it is used in some other random class). Don't know if we need to change this??
allRings = allRingsFinder.findAllRings(originalMolecule, Integer.valueOf(7));
aromaticBonds = new List<IBond>();
CDKHueckelAromaticityDetector.detectAromaticity(originalMolecule);
foreach (var bond in originalMolecule.bonds().ToWindowsEnumerable<IBond>())
{
//lets see if it is a ring and aromatic
var rings = allRings.getRings(bond);
//don't split up aromatic rings...see constructor for option
for (var i = 0; i < rings.getAtomContainerCount(); i++)
{
var aromatic = AromaticityCalculator.isAromatic((IRing)rings.getAtomContainer(i), originalMolecule);
if (aromatic)
{
aromaticBonds.Add(bond);
break;
}
}
}
return true;
}
/// <summary> We define the heaviest ring as the one with the highest number of double bonds.
/// Needed for example for the placement of in-ring double bonds.
///
/// </summary>
/// <param name="bond"> A bond which must be contained by the heaviest ring
/// </param>
/// <returns> The ring with the higest number of double bonds connected to a given bond
/// </returns>
public static IRing getHeaviestRing(IRingSet ringSet, IBond bond)
{
System.Collections.IList rings = ringSet.getRings(bond);
IRing ring = null;
int maxOrderSum = 0;
for (int i = 0; i < rings.Count; i++)
{
if (maxOrderSum < ((IRing)rings[i]).OrderSum)
{
ring = (IRing)rings[i];
maxOrderSum = ring.OrderSum;
}
}
return ring;
}
