/// <summary>
/// Tries to saturate a bond by increasing its bond orders by 1.0.
/// </summary>
/// <returns>true if the bond could be increased</returns>
public bool SaturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer)
{
var atoms = BondManipulator.GetAtomArray(bond);
var atom = atoms[0];
var partner = atoms[1];
Debug.WriteLine(" saturating bond: ", atom.Symbol, "-", partner.Symbol);
var atomTypes1 = structgenATF.GetAtomTypes(atom.Symbol);
var atomTypes2 = structgenATF.GetAtomTypes(partner.Symbol);
foreach (var aType1 in atomTypes1)
{
Debug.WriteLine($" considering atom type: {aType1}");
if (CouldMatchAtomType(atomContainer, atom, aType1))
{
Debug.WriteLine($" trying atom type: {aType1}");
foreach (var aType2 in atomTypes2)
{
Debug.WriteLine($" considering partner type: {aType1}");
if (CouldMatchAtomType(atomContainer, partner, aType2))
{
Debug.WriteLine($" with atom type: {aType2}");
if (BondManipulator.IsLowerOrder(bond.Order, aType2.MaxBondOrder) &&
BondManipulator.IsLowerOrder(bond.Order, aType1.MaxBondOrder))
{
bond.Order = BondManipulator.IncreaseBondOrder(bond.Order);
Debug.WriteLine($"Bond order now {bond.Order}");
return(true);
}
}
}
}
}
return(false);
}
/// <summary>
/// Saturate atom by adjusting its bond orders.
/// This method is known to fail, especially on pyrrole-like compounds.
/// Consider using <see cref="Smiles.DeduceBondSystemTool"/>, which should work better
/// </summary>
public bool NewSaturate(IBond bond, IAtomContainer atomContainer)
{
var atoms = BondManipulator.GetAtomArray(bond);
var atom = atoms[0];
var partner = atoms[1];
Debug.WriteLine($" saturating bond: {atom.Symbol}-{partner.Symbol}");
var atomTypes1 = structgenATF.GetAtomTypes(atom.Symbol);
var atomTypes2 = structgenATF.GetAtomTypes(partner.Symbol);
bool bondOrderIncreased = true;
while (bondOrderIncreased && !IsSaturated(bond, atomContainer))
{
Debug.WriteLine("Can increase bond order");
bondOrderIncreased = false;
foreach (var aType1 in atomTypes1)
{
if (bondOrderIncreased)
{
break;
}
Debug.WriteLine($" considering atom type: {aType1}");
if (CouldMatchAtomType(atomContainer, atom, aType1))
{
Debug.WriteLine($" trying atom type: {aType1}");
foreach (var aType2 in atomTypes2)
{
if (bondOrderIncreased)
{
break;
}
Debug.WriteLine($" considering partner type: {aType1}");
if (CouldMatchAtomType(atomContainer, partner, aType2))
{
Debug.WriteLine($" with atom type: {aType2}");
if (!BondManipulator.IsLowerOrder(bond.Order, aType2.MaxBondOrder) ||
!BondManipulator.IsLowerOrder(bond.Order, aType1.MaxBondOrder))
{
Debug.WriteLine("Bond order not increased: atoms has reached (or exceeded) maximum bond order for this atom type");
}
else if (BondManipulator.IsLowerOrder(bond.Order, aType2.MaxBondOrder) &&
BondManipulator.IsLowerOrder(bond.Order, aType1.MaxBondOrder))
{
BondManipulator.IncreaseBondOrder(bond);
Debug.WriteLine($"Bond order now {bond.Order}");
bondOrderIncreased = true;
}
}
}
}
}
}
return(IsSaturated(bond, atomContainer));
}
/// <summary>
/// The method calculates the number of rotatable bonds of an atom container.
/// If the boolean parameter is set to <see langword="true"/>, terminal bonds are included.
/// </summary>
/// <returns>number of rotatable bonds</returns>
/// <param name="includeTerminals"><see langword="true"/> if terminal bonds are included</param>
/// <param name="excludeAmides"><see langword="true"/> if amide C-N bonds should be excluded</param>
public Result Calculate(IAtomContainer container, bool includeTerminals = false, bool excludeAmides = false)
{
container = (IAtomContainer)container.Clone();
IRingSet ringSet;
try
{
ringSet = new SpanningTree(container).GetBasicRings();
}
catch (NoSuchAtomException)
{
return(new Result(0));
}
foreach (var bond in container.Bonds)
{
if (ringSet.GetRings(bond).Count() > 0)
{
bond.IsInRing = true;
}
}
int rotatableBondsCount = 0;
foreach (var bond in container.Bonds)
{
var atom0 = bond.Atoms[0];
var atom1 = bond.Atoms[1];
if (atom0.AtomicNumber.Equals(AtomicNumbers.H) || atom1.AtomicNumber.Equals(AtomicNumbers.H))
{
continue;
}
if (bond.Order == BondOrder.Single)
{
if (BondManipulator.IsLowerOrder(container.GetMaximumBondOrder(atom0), BondOrder.Triple) &&
BondManipulator.IsLowerOrder(container.GetMaximumBondOrder(atom1), BondOrder.Triple))
{
if (!bond.IsInRing)
{
if (excludeAmides && (IsAmide(atom0, atom1, container) || IsAmide(atom1, atom0, container)))
{
continue;
}
// if there are explicit H's we should ignore those bonds
var degree0 = container.GetConnectedBonds(atom0).Count() - GetConnectedHCount(container, atom0);
var degree1 = container.GetConnectedBonds(atom1).Count() - GetConnectedHCount(container, atom1);
if ((degree0 == 1) || (degree1 == 1))
{
if (includeTerminals)
{
rotatableBondsCount += 1;
}
}
else
{
rotatableBondsCount += 1;
}
}
}
}
}
return(new Result(rotatableBondsCount));
}
