/// <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($"Bond order now {bond.Order}");
return(true);
}
}
}
}
}
return(false);
}
public bool HasPerfectConfiguration(IAtom atom, IAtomContainer ac)
{
var bondOrderSum = ac.GetBondOrderSum(atom);
var maxBondOrder = ac.GetMaximumBondOrder(atom);
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
if (!atomTypes.Any())
{
return(true);
}
Debug.WriteLine("*** Checking for perfect configuration ***");
try
{
Debug.WriteLine($"Checking configuration of atom {ac.Atoms.IndexOf(atom)}");
Debug.WriteLine($"Atom has bondOrderSum = {bondOrderSum}");
Debug.WriteLine($"Atom has max = {bondOrderSum}");
}
catch (Exception)
{
}
foreach (var atomType in atomTypes)
{
if (bondOrderSum == atomType.BondOrderSum && maxBondOrder == atomType.MaxBondOrder)
{
try
{
Debug.WriteLine($"Atom {ac.Atoms.IndexOf(atom)} has perfect configuration");
}
catch (Exception)
{
}
return(true);
}
}
try
{
Debug.WriteLine($"*** Atom {ac.Atoms.IndexOf(atom)} has imperfect configuration ***");
}
catch (Exception)
{
}
return(false);
}
/// <summary>
/// Finds the AtomType matching the Atom's element symbol, formal charge and
/// hybridization state.
/// </summary>
/// <param name="atomContainer">AtomContainer</param>
/// <param name="atom">the target atom</param>
/// <exception cref="CDKException">Exception thrown if something goes wrong</exception>
/// <returns>the matching AtomType</returns>
public IEnumerable <IAtomType> PossibleAtomTypes(IAtomContainer atomContainer, IAtom atom)
{
var bondOrderSum = atomContainer.GetBondOrderSum(atom);
var maxBondOrder = atomContainer.GetMaximumBondOrder(atom);
var charge = atom.FormalCharge.Value;
var hcount = atom.ImplicitHydrogenCount.Value;
var types = factory.GetAtomTypes(atom.Symbol);
foreach (var type in types)
{
Debug.WriteLine(" ... matching atom ", atom, " vs ", type);
if (bondOrderSum - charge + hcount <= type.BondOrderSum &&
!BondManipulator.IsHigherOrder(maxBondOrder, type.MaxBondOrder))
{
yield return(type);
}
}
Debug.WriteLine(" No Match");
yield break;
}
private static bool CreateBondsWithRebondTool(IAtomContainer molecule)
{
var tool = new RebondTool(2.0, 0.5, 0.5);
try
{
foreach (var atom in molecule.Atoms)
{
try
{
var types = factory.GetAtomTypes(atom.Symbol);
var type = types.FirstOrDefault();
if (type != null)
{
// just pick the first one
AtomTypeManipulator.Configure(atom, type);
}
else
{
Trace.TraceWarning("Could not configure atom with symbol: " + atom.Symbol);
}
}
catch (Exception e)
{
Trace.TraceWarning("Could not configure atom (but don't care): " + e.Message);
Debug.WriteLine(e);
}
}
tool.Rebond(molecule);
}
catch (Exception e)
{
Trace.TraceError($"Could not rebond the polymer: {e.Message}");
Debug.WriteLine(e);
}
return(true);
}