/// <summary>
/// Determines if the atom can be of type <see cref="IAtomType"/>. That is, it sees if this
/// <see cref="IAtomType"/> only differs in bond orders, or implicit hydrogen count.
/// </summary>
private static bool CouldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type)
{
var bondOrderSum = container.GetBondOrderSum(atom);
var maxBondOrder = container.GetMaximumBondOrder(atom);
return(CouldMatchAtomType(atom, bondOrderSum, maxBondOrder, type));
}
public bool IsSaturated(IAtom atom, IAtomContainer container)
{
var type = atomTypeList.GetAtomType(atom.AtomTypeName);
if (type == null)
{
throw new CDKException($"Atom type is not a recognized CDK atom type: {atom.AtomTypeName}");
}
if (type.FormalNeighbourCount == null)
{
throw new CDKException($"Atom type is too general; cannot decide the number of implicit hydrogen to add for: {atom.AtomTypeName}");
}
if (type.GetProperty <object>(CDKPropertyName.PiBondCount) == null)
{
throw new CDKException($"Atom type is too general; cannot determine the number of pi bonds for: {atom.AtomTypeName}");
}
var bondOrderSum = container.GetBondOrderSum(atom);
var maxBondOrder = container.GetMaximumBondOrder(atom);
int?hcount = atom.ImplicitHydrogenCount == null ? 0 : atom.ImplicitHydrogenCount;
int piBondCount = type.GetProperty <int?>(CDKPropertyName.PiBondCount).Value;
int formalNeighborCount = type.FormalNeighbourCount.Value;
int typeMaxBondOrder = piBondCount + 1;
int typeBondOrderSum = formalNeighborCount + piBondCount;
if (bondOrderSum + hcount == typeBondOrderSum && maxBondOrder.Numeric() <= typeMaxBondOrder)
{
return(true);
}
return(false);
}
/// <summary>
/// Checks if the current atom has exceeded its bond order sum value.
/// </summary>
/// <param name="atom">The Atom to check</param>
/// <param name="ac">The atom container context</param>
/// <returns>oversaturated or not</returns>
public bool IsOverSaturated(IAtom atom, IAtomContainer ac)
{
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
if (!atomTypes.Any())
{
return(false);
}
var bondOrderSum = ac.GetBondOrderSum(atom);
var maxBondOrder = ac.GetMaximumBondOrder(atom);
var hcount = atom.ImplicitHydrogenCount ?? 0;
var charge = atom.FormalCharge ?? 0;
try
{
Debug.WriteLine($"*** Checking saturation of atom {ac.Atoms.IndexOf(atom)} ***");
Debug.WriteLine($"bondOrderSum: {bondOrderSum}");
Debug.WriteLine($"maxBondOrder: {maxBondOrder}");
Debug.WriteLine($"hcount: {hcount}");
}
catch (Exception)
{
}
foreach (var atomType in atomTypes)
{
if (bondOrderSum - charge + hcount > atomType.BondOrderSum)
{
Debug.WriteLine("*** Good ! ***");
return(true);
}
}
Debug.WriteLine("*** Bad ! ***");
return(false);
}
/// <summary>
/// Function to set up an array of integers corresponding to indicate how many free valencies need fulfilling for each atom through ring bonds.
/// </summary>
/// <returns>The List of free valencies available for extra ring bonding</returns>
private static List <int> GetFreeValenciesForRingGroup(IAtomContainer molecule, List <int> atomsToCheck, Matrix M, IRingSet rs)
{
List <int> fvtc = new List <int>();
for (int i = 0; i < atomsToCheck.Count; i++)
{
int j = atomsToCheck[i];
//Put in an implicit hydrogen atom for Planar3 C- atoms in 5-membered rings (it doesn't get put in by the Smiles parser)
if (string.Equals("C", molecule.Atoms[j].Symbol, StringComparison.Ordinal) &&
(molecule.Atoms[j].Hybridization == Hybridization.Planar3))
{
//Check that ring containing the atom is five-membered
foreach (var ac in rs)
{
if (ac.Contains(molecule.Atoms[j]))
{
if ((int)molecule.GetBondOrderSum(molecule.Atoms[j]) == 2 && ac.Atoms.Count == 5)
{
molecule.Atoms[j].ImplicitHydrogenCount = 1;
break;
}
}
}
}
int implicitH = 0;
if (!molecule.Atoms[j].ImplicitHydrogenCount.HasValue)
{
var ha = CDK.HydrogenAdder;
try
{
ha.AddImplicitHydrogens(molecule, molecule.Atoms[j]);
implicitH = molecule.Atoms[j].ImplicitHydrogenCount.Value;
}
catch (CDKException)
{
//No need to do anything because implicitH already set to 0
}
}
else
{
implicitH = molecule.Atoms[j].ImplicitHydrogenCount.Value;
}
fvtc.Add(molecule.Atoms[j].Valency.Value - (implicitH + (int)molecule.GetBondOrderSum(molecule.Atoms[j])) + M.SumOfRow(i));
}
return(fvtc);
}
// the Molecule tests
private static ValidationReport ValidateBondOrderSum(IAtom atom, IAtomContainer molecule)
{
var report = new ValidationReport();
var checkBondSum = new ValidationTest(atom, "The atom's total bond order is too high.");
try
{
var structgenATF = CDK.CdkAtomTypeFactory;
int bos = (int)molecule.GetBondOrderSum(atom);
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol).ToReadOnlyList();
if (atomTypes.Count == 0)
{
checkBondSum.Details = $"Cannot validate bond order sum for atom not in valency atom type list: {atom.Symbol}";
report.Warnings.Add(checkBondSum);
}
else
{
IAtomType failedOn = null;
bool foundMatchingAtomType = false;
foreach (var type in atomTypes)
{
if (atom.FormalCharge == type.FormalCharge)
{
foundMatchingAtomType = true;
if (bos == type.BondOrderSum)
{
// skip this atom type
}
else
{
failedOn = type;
}
}
}
if (foundMatchingAtomType)
{
report.OKs.Add(checkBondSum);
}
else
{
if (failedOn != null)
{
checkBondSum.Details = $"Bond order exceeds the one allowed for atom {atom.Symbol} for which the total bond order is {failedOn.BondOrderSum}";
}
else
{
}
report.Errors.Add(checkBondSum);
}
}
}
catch (Exception exception)
{
Trace.TraceError($"Error while performing atom bos validation: {exception.Message}");
Debug.WriteLine(exception);
}
return(report);
}
/// <summary>
/// Checks whether an atom is saturated by comparing it with known atom types.
/// </summary>
/// <returns><see langword="true"/> if the atom is an pseudo atom and when the element is not in the list.</returns>
public bool IsSaturated(IAtom atom, IAtomContainer container)
{
if (atom is IPseudoAtom)
{
Debug.WriteLine("don't figure it out... it simply does not lack H's");
return(true);
}
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
if (atomTypes.Any())
{
Trace.TraceWarning($"Missing entry in atom type list for {atom.Symbol}");
return(true);
}
var bondOrderSum = container.GetBondOrderSum(atom);
var maxBondOrder = container.GetMaximumBondOrder(atom);
var hcount = atom.ImplicitHydrogenCount.Value;
var charge = atom.FormalCharge.Value;
Debug.WriteLine($"Checking saturation of atom {atom.Symbol}");
Debug.WriteLine($"bondOrderSum: {bondOrderSum}");
Debug.WriteLine($"maxBondOrder: {maxBondOrder}");
Debug.WriteLine($"hcount: {hcount}");
Debug.WriteLine($"charge: {charge}");
bool elementPlusChargeMatches = false;
foreach (var type in atomTypes)
{
if (CouldMatchAtomType(atom, bondOrderSum, maxBondOrder, type))
{
if (bondOrderSum + hcount == type.BondOrderSum &&
!BondManipulator.IsHigherOrder(maxBondOrder, type.MaxBondOrder))
{
Debug.WriteLine($"We have a match: {type}");
Debug.WriteLine($"Atom is saturated: {atom.Symbol}");
return(true);
}
else
{
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches)
{
Debug.WriteLine("No, atom is not saturated.");
return(false);
}
// ok, the found atom was not in the list
Trace.TraceError("Could not find atom type!");
throw new CDKException($"The atom with element {atom.Symbol} and charge {charge} is not found.");
}
/// <summary>
/// Determines if the atom can be of atom type.
/// </summary>
private static bool CouldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)
{
Debug.WriteLine($" ... matching atom {atom.Symbol} vs {atomType}");
if (atomContainer.GetBondOrderSum(atom) + atom.ImplicitHydrogenCount < atomType.BondOrderSum)
{
Debug.WriteLine(" Match!");
return(true);
}
Debug.WriteLine(" No Match");
return(false);
}
/// <summary>
/// Checks whether an atom is saturated by comparing it with known atom types.
/// </summary>
public bool IsSaturated(IAtom atom, IAtomContainer ac)
{
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
if (!atomTypes.Any())
{
return(true);
}
double bondOrderSum = 0;
var maxBondOrder = BondOrder.Unset;
int hcount = 0;
int charge = 0;
bool isInited = false;
foreach (var atomType in atomTypes)
{
if (!isInited)
{
isInited = true;
bondOrderSum = ac.GetBondOrderSum(atom);
maxBondOrder = ac.GetMaximumBondOrder(atom);
hcount = atom.ImplicitHydrogenCount ?? 0;
charge = atom.FormalCharge ?? 0;
try
{
Debug.WriteLine($"*** Checking saturation of atom {atom.Symbol} {ac.Atoms.IndexOf(atom)} ***");
Debug.WriteLine($"bondOrderSum: {bondOrderSum}");
Debug.WriteLine($"maxBondOrder: {maxBondOrder}");
Debug.WriteLine($"hcount: {hcount}");
}
catch (Exception exc)
{
Debug.WriteLine(exc);
}
}
if (bondOrderSum - charge + hcount == atomType.BondOrderSum &&
!BondManipulator.IsHigherOrder(maxBondOrder, atomType.MaxBondOrder))
{
Debug.WriteLine("*** Good ! ***");
return(true);
}
}
Debug.WriteLine("*** Bad ! ***");
return(false);
}
private static double GetAtomScore(double score, IReadOnlyDictionary <IAtom, IAtom> atomMapMCS, IAtomContainer reactant, IAtomContainer product)
{
foreach (var mappings in atomMapMCS)
{
IAtom rAtom = mappings.Key;
IAtom pAtom = mappings.Value;
int rHCount = 0;
int pHCount = 0;
double rBO = reactant.GetBondOrderSum(rAtom);
double pBO = product.GetBondOrderSum(pAtom);
if (rAtom.ImplicitHydrogenCount != null)
{
rHCount = rAtom.ImplicitHydrogenCount.Value;
}
if (pAtom.ImplicitHydrogenCount != null)
{
pHCount = pAtom.ImplicitHydrogenCount.Value;
}
int hScore = Math.Abs(rHCount - pHCount);
double boScore = Math.Abs(rBO - pBO);
if (rHCount != pHCount)
{
score -= hScore;
}
else
{
score += hScore;
}
if (rBO != pBO)
{
score -= boScore;
}
else
{
score += boScore;
}
}
return(score);
}
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);
}
private void FixCarbonHCount(IAtomContainer mol)
{
// the following line are just a quick fix for this particluar
// carbon-only molecule until we have a proper hydrogen count
// configurator
double bondCount = 0;
IAtom atom;
for (int f = 0; f < mol.Atoms.Count; f++)
{
atom = mol.Atoms[f];
bondCount = mol.GetBondOrderSum(atom);
if (bondCount > 4)
{
Console.Out.WriteLine("bondCount: " + bondCount);
}
atom.ImplicitHydrogenCount = 4 - (int)bondCount - (int)(atom.Charge ?? 0);
}
}
/// <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;
}
/// <summary>
/// Returns the currently maximum bond order for this atom.
/// </summary>
/// <param name="atom">The atom to be checked</param>
/// <param name="ac">The AtomContainer that provides the context</param>
/// <returns>the currently maximum bond order for this atom</returns>
public double GetCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)
{
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
if (!atomTypes.Any())
{
return(0);
}
var bondOrderSum = ac.GetBondOrderSum(atom);
var hcount = atom.ImplicitHydrogenCount ?? 0;
double max = 0;
double current = 0;
foreach (var atomType in atomTypes)
{
current = hcount + bondOrderSum;
if (atomType.BondOrderSum - current > max)
{
max = atomType.BondOrderSum.Value - current;
}
}
return(max);
}
/// <summary>
/// The method is known to fail for certain compounds. For more information, see
/// cdk.test.limitations package.
/// This method is known to fail, especially on pyrrole-like compounds.
/// Consider using <see cref="Smiles.DeduceBondSystemTool"/>, which should work better
/// </summary>
public void Saturate(IAtomContainer atomContainer)
{
for (int i = 1; i < 4; i++)
{
// handle atoms with degree 1 first and then proceed to higher order
for (int f = 0; f < atomContainer.Atoms.Count; f++)
{
var atom = atomContainer.Atoms[f];
Debug.WriteLine($"symbol: {atom.Symbol}");
var atomTypes1 = structgenATF.GetAtomTypes(atom.Symbol);
var atomType1 = atomTypes1.FirstOrDefault();
if (atomType1 != null)
{
Debug.WriteLine($"first atom type: {atomType1}");
if (atomContainer.GetConnectedBonds(atom).Count() == i)
{
var hcount = atom.ImplicitHydrogenCount ?? 0;
if (atom.IsAromatic &&
atomContainer.GetBondOrderSum(atom) < atomType1.BondOrderSum - hcount)
{
var partners = atomContainer.GetConnectedAtoms(atom);
foreach (var partner in partners)
{
Debug.WriteLine($"Atom has {partners.Count()} partners");
var atomType2 = structgenATF.GetAtomTypes(partner.Symbol).FirstOrDefault();
if (atomType2 == null)
{
return;
}
hcount = partner.ImplicitHydrogenCount ?? 0;
if (atomContainer.GetBond(partner, atom).IsAromatic &&
atomContainer.GetBondOrderSum(partner) < atomType2.BondOrderSum - hcount)
{
Debug.WriteLine($"Partner has {atomContainer.GetBondOrderSum(partner)}, may have: {atomType2.BondOrderSum}");
var bond = atomContainer.GetBond(atom, partner);
Debug.WriteLine($"Bond order was {bond.Order}");
BondManipulator.IncreaseBondOrder(bond);
Debug.WriteLine($"Bond order now {bond.Order}");
break;
}
}
}
var bondOrderSum = atomType1.BondOrderSum ?? 0;
var hydrogenCount = atom.ImplicitHydrogenCount ?? 0;
var atomContainerBondOrderSum = atomContainer.GetBondOrderSum(atom);
if (atomContainerBondOrderSum < bondOrderSum - hydrogenCount)
{
Debug.WriteLine("Atom has " + atomContainerBondOrderSum + ", may have: " + bondOrderSum);
var partners = atomContainer.GetConnectedAtoms(atom);
foreach (var partner in partners)
{
Debug.WriteLine("Atom has " + partners.Count() + " partners");
var atomType2 = structgenATF.GetAtomTypes(partner.Symbol).FirstOrDefault();
if (atomType2 == null)
{
return;
}
var bos2 = atomType2.BondOrderSum ?? 0;
var hc2 = partner.ImplicitHydrogenCount ?? 0;
var acbos2 = atomContainer.GetBondOrderSum(partner);
if (acbos2 < bos2 - hc2)
{
Debug.WriteLine($"Partner has {acbos2}, may have: {bos2}");
var bond = atomContainer.GetBond(atom, partner);
Debug.WriteLine($"Bond order was {bond.Order}");
BondManipulator.IncreaseBondOrder(bond);
Debug.WriteLine($"Bond order now {bond.Order}");
break;
}
}
}
}
}
}
}
}
public int CalculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
{
return(this.CalculateNumberOfImplicitHydrogens(atom, container.GetBondOrderSum(atom), container.GetMaximumBondOrder(atom), container.GetConnectedBonds(atom).Count()));
}
private static int GetBadCount(IAtomContainer atomContainer, IRingSet ringSet)
{
// finds count of nitrogens in the rings that have 4 bonds
// to non hydrogen atoms and one to hydrogen
// or nitrogens with 2 double bonds to atoms in the ringset
// or have S atom with more than 2 bonds
// these arent necessarily bad- just unlikely
int count = 0;
for (int j = 0; j <= atomContainer.Atoms.Count - 1; j++)
{
var atom = atomContainer.Atoms[j];
if (InRingSet(atom, ringSet))
{
if (atom.AtomicNumber.Equals(AtomicNumbers.N))
{
if (atom.FormalCharge == 0)
{
if (atomContainer.GetBondOrderSum(atom) == 4)
{
count++; //
}
else if (atomContainer.GetBondOrderSum(atom) == 5)
{
// check if have 2 double bonds to atom in ring
int doublebondcount = 0;
var ca = atomContainer.GetConnectedAtoms(atom);
foreach (var a in ca)
{
if (atomContainer.GetBond(atom, a).Order == BondOrder.Double)
{
if (InRingSet(a, ringSet))
{
doublebondcount++;
}
}
}
if (doublebondcount == 2)
{
count++;
}
}
}
else if (atom.FormalCharge == 1)
{
if (atomContainer.GetBondOrderSum(atom) == 5)
{
count++;
}
}
}
else if (atom.AtomicNumber.Equals(AtomicNumbers.S))
{
if (atomContainer.GetBondOrderSum(atom) > 2)
{
count++;
}
}
}
}
return(count);
}
/// <summary>
/// Proposes a structure which can be accepted or rejected by an external
/// entity. If rejected, the structure is not used as a starting point
/// for the next random move in structure space.
/// </summary>
/// <returns>A proposed molecule</returns>
public IAtomContainer ProposeStructure()
{
Debug.WriteLine("RandomGenerator->ProposeStructure() Start");
do
{
trial = (IAtomContainer)Molecule.Clone();
Mutate(trial);
Debug.WriteLine("BondCounts: " + string.Join(" ", trial.Atoms.Select(n => trial.GetConnectedBonds(n).Count())));
Debug.WriteLine("BondOrderSums: " + string.Join(" ", trial.Atoms.Select(n => trial.GetBondOrderSum(n))));
} while (trial == null || !ConnectivityChecker.IsConnected(trial));
proposedStructure = trial;
return(proposedStructure);
}
public int CalculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, bool throwExceptionForUnknowAtom)
{
return(this.CalculateNumberOfImplicitHydrogens(atom, container.GetBondOrderSum(atom),
container.GetConnectedSingleElectrons(atom).Count(), container.GetConnectedBonds(atom),
throwExceptionForUnknowAtom));
}
