/// <summary>
/// set the active center for this molecule.
/// The active center will be those which correspond with X=Y.
/// </summary>
/// <param name="reactant">The molecule to set the activity</param>
private static void SetActiveCenters(IAtomContainer reactant)
{
if (AtomContainerManipulator.GetTotalCharge(reactant) != 0)
{
return;
}
foreach (var bondi in reactant.Bonds)
{
if (((bondi.Order == BondOrder.Double) || (bondi.Order == BondOrder.Triple)))
{
int chargeAtom0 = bondi.Begin.FormalCharge ?? 0;
int chargeAtom1 = bondi.End.FormalCharge ?? 0;
if (chargeAtom0 >= 0 && chargeAtom1 >= 0 &&
!reactant.GetConnectedSingleElectrons(bondi.Begin).Any() &&
!reactant.GetConnectedSingleElectrons(bondi.End).Any() &&
!reactant.GetConnectedLonePairs(bondi.Begin).Any() &&
!reactant.GetConnectedLonePairs(bondi.End).Any())
{
bondi.IsReactiveCenter = true;
bondi.Begin.IsReactiveCenter = true;
bondi.End.IsReactiveCenter = true;
}
}
}
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
IReactionProcess type = new SharingChargeDBReaction();
var setOfReactants = GetExampleReactants();
IAtomContainer molecule = setOfReactants[0];
/* initiate */
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter
{
IsSetParameter = false
};
paramList.Add(param);
type.ParameterList = paramList;
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
IAtomContainer product = setOfReactions[0].Products[0];
Assert.AreEqual(1, product.Atoms[1].FormalCharge.Value);
Assert.AreEqual(0, product.GetConnectedLonePairs(product.Atoms[1]).Count());
/* C[C+]O| */
IAtomContainer molecule2 = GetExpectedProducts()[0];
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(product);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, queryAtom));
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
/* Ionize(>C=O): C=CCC(=O)CC -> C=CCC(=O*)CC , set the reactive center */
IAtomContainer reactant = builder.NewAtomContainer();//CreateFromSmiles("C=CCC(=O)CC")
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("O"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.AddBond(reactant.Atoms[0], reactant.Atoms[1], BondOrder.Double);
reactant.AddBond(reactant.Atoms[1], reactant.Atoms[2], BondOrder.Single);
reactant.AddBond(reactant.Atoms[2], reactant.Atoms[3], BondOrder.Single);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[4], BondOrder.Double);
reactant.AddBond(reactant.Atoms[3], reactant.Atoms[5], BondOrder.Single);
reactant.AddBond(reactant.Atoms[5], reactant.Atoms[6], BondOrder.Single);
AddExplicitHydrogens(reactant);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
CDK.LonePairElectronChecker.Saturate(reactant);
foreach (var atom in reactant.Atoms)
{
if (reactant.GetConnectedLonePairs(atom).Count() > 0)
{
atom.IsReactiveCenter = true;
}
}
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
MakeSureAtomTypesAreRecognized(reactant);
IReactionProcess type = new ElectronImpactNBEReaction();
var paramList = new List <IParameterReaction>();
IParameterReaction param = new SetReactionCenter
{
IsSetParameter = true
};
paramList.Add(param);
type.ParameterList = paramList;
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
Assert.AreEqual(1, setOfReactions[0].Products.Count);
IAtomContainer molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[4].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[4]).Count());
Assert.IsTrue(setOfReactions[0].Mappings.Any());
}
/// <inheritdoc/>
public bool IsSaturated(IAtom atom, IAtomContainer ac)
{
var atomType = factory.GetAtomType(atom.AtomTypeName);
var lpCount = atomType.GetProperty <int>(CDKPropertyName.LonePairCount);
var foundLPCount = ac.GetConnectedLonePairs(atom).Count();
return(foundLPCount >= lpCount);
}
/// <summary>
/// set the active center for this molecule. The active center
/// will be heteroatoms which contain at least one group of
/// lone pair electrons.
/// </summary>
/// <param name="reactant">The molecule to set the activity</param>
private static void SetActiveCenters(IAtomContainer reactant)
{
foreach (var atom in reactant.Atoms)
{
if (reactant.GetConnectedLonePairs(atom).Any() && !reactant.GetConnectedSingleElectrons(atom).Any())
{
atom.IsReactiveCenter = true;
}
}
}
internal IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents, string atomSymbol)
{
CheckInitiateParams(reactants, agents);
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant);
}
if (AtomContainerManipulator.GetTotalCharge(reactant) > 0)
{
return(setOfReactions);
}
foreach (var atomi in reactant.Atoms)
{
if (atomi.IsReactiveCenter &&
(atomi.FormalCharge ?? 0) <= 0 &&
reactant.GetConnectedLonePairs(atomi).Any() &&
!reactant.GetConnectedSingleElectrons(atomi).Any())
{
var atomList = new List <IAtom> {
atomi
};
IAtom atomH = reactant.Builder.NewAtom(atomSymbol);
atomH.FormalCharge = 1;
atomList.Add(atomH);
var moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IAtomContainer adduct = reactant.Builder.NewAtomContainer();
adduct.Atoms.Add(atomH);
moleculeSet.Add(adduct);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, null);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
return(setOfReactions);
}
/// <inheritdoc/>
public void Saturate(IAtom atom, IAtomContainer ac)
{
Trace.TraceInformation("Saturating atom by adjusting lone pair electrons...");
var atomType = factory.GetAtomType(atom.AtomTypeName);
var lpCount = atomType.GetProperty <int>(CDKPropertyName.LonePairCount);
var missingLPs = lpCount - ac.GetConnectedLonePairs(atom).Count();
for (int j = 0; j < missingLPs; j++)
{
var lp = atom.Builder.NewLonePair(atom);
ac.LonePairs.Add(lp);
}
}
/// <summary>
/// Performs a BreadthFirstSearch in an AtomContainer starting with a
/// particular sphere, which usually consists of one start atom. While
/// searching the graph, the method marks each visited atom. It then puts all
/// the atoms connected to the atoms in the given sphere into a new vector
/// which forms the sphere to search for the next recursive method call. All
/// atoms that have been visited are put into a molecule container. This
/// BreadthFirstSearch does thus find the connected graph for a given start
/// atom.
/// <para>IMPORTANT: this method does not reset the VISITED flags, which must be
/// done if calling this method twice!
/// </para>
/// </summary>
/// <param name="atomContainer">The AtomContainer to be searched</param>
/// <param name="sphere">A sphere of atoms to start the search with</param>
/// <param name="molecule">A molecule into which all the atoms and bonds are stored that are found during search</param>
/// <param name="max">max</param>
public static void BreadthFirstSearch(IAtomContainer atomContainer, IEnumerable <IAtom> sphere, IAtomContainer molecule, int max)
{
IAtom nextAtom;
List <IAtom> newSphere = new List <IAtom>();
foreach (var atom in sphere)
{
molecule.Atoms.Add(atom);
// first copy LonePair's and SingleElectron's of this Atom as they need
// to be copied too
var lonePairs = atomContainer.GetConnectedLonePairs(atom);
foreach (var lonePair in lonePairs)
{
molecule.LonePairs.Add(lonePair);
}
var singleElectrons = atomContainer.GetConnectedSingleElectrons(atom);
foreach (var singleElectron in singleElectrons)
{
molecule.SingleElectrons.Add(singleElectron);
}
// now look at bonds
var bonds = atomContainer.GetConnectedBonds(atom);
foreach (var bond in bonds)
{
nextAtom = bond.GetOther(atom);
if (!bond.IsVisited)
{
molecule.Atoms.Add(nextAtom);
molecule.Bonds.Add(bond);
bond.IsVisited = true;
}
if (!nextAtom.IsVisited)
{
newSphere.Add(nextAtom);
nextAtom.IsVisited = true;
}
}
if (max > -1 && molecule.Atoms.Count > max)
{
return;
}
}
if (newSphere.Count > 0)
{
BreadthFirstSearch(atomContainer, newSphere, molecule, max);
}
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <param name="reactants">Reactants of the reaction</param>
/// <param name="agents">Agents of the reaction (Must be in this case null)</param>
/// <exception cref="CDKException"> Description of the Exception</exception>
public IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents)
{
Debug.WriteLine("initiate reaction: ElectronImpactNBEReaction");
if (reactants.Count != 1)
{
throw new CDKException("ElectronImpactNBEReaction only expects one reactant");
}
if (agents != null)
{
throw new CDKException("ElectronImpactNBEReaction don't expects agents");
}
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
// if the parameter hasActiveCenter is not fixed yet, set the active centers
IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant);
}
foreach (var atom in reactant.Atoms)
{
if (atom.IsReactiveCenter && reactant.GetConnectedLonePairs(atom).Any() &&
!reactant.GetConnectedSingleElectrons(atom).Any())
{
var atomList = new List <IAtom>
{
atom
};
IChemObjectSet <IAtomContainer> moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, null);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
return(setOfReactions);
}
private static void SetActiveCenters(IAtomContainer reactant)
{
if (AtomContainerManipulator.GetTotalCharge(reactant) > 0)
{
return;
}
foreach (var atomi in reactant.Atoms)
{
if ((atomi.FormalCharge ?? 0) <= 0 &&
reactant.GetConnectedLonePairs(atomi).Any() &&
!reactant.GetConnectedSingleElectrons(atomi).Any())
{
atomi.IsReactiveCenter = true;
}
}
}
/// <summary>
/// Calculate the electronegativity of orbitals pi.
/// </summary>
/// <param name="ac"></param>
/// <param name="atom">atom for which effective atom electronegativity should be calculated</param>
/// <param name="maxIterations">The maximal number of Iteration</param>
/// <param name="maxResonStruc">The maximal number of Resonance Structures</param>
/// <returns>Electronegativity of orbitals pi.</returns>
public double CalculatePiElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
{
MaxIterations = maxIterations;
MaxResonanceStructures = maxResonStruc;
double electronegativity = 0;
try
{
if (!ac.Equals(acOldP))
{
molPi = ac.Builder.NewAtomContainer(ac);
peoe = new GasteigerMarsiliPartialCharges();
peoe.AssignGasteigerMarsiliSigmaPartialCharges(molPi, true);
var iSet = ac.Builder.NewAtomContainerSet();
iSet.Add(molPi);
iSet.Add(molPi);
gasteigerFactors = pepe.AssignrPiMarsilliFactors(iSet);
acOldP = ac;
}
IAtom atomi = molPi.Atoms[ac.Atoms.IndexOf(atom)];
int atomPosition = molPi.Atoms.IndexOf(atomi);
int stepSize = pepe.StepSize;
int start = (stepSize * (atomPosition) + atomPosition);
double q = atomi.Charge.Value;
if (molPi.GetConnectedLonePairs(molPi.Atoms[atomPosition]).Any() ||
molPi.GetMaximumBondOrder(atomi) != BondOrder.Single || atomi.FormalCharge != 0)
{
return((gasteigerFactors[1][start]) + (q * gasteigerFactors[1][start + 1]) + (gasteigerFactors[1][start + 2] * (q * q)));
}
}
catch (Exception e)
{
Trace.TraceError(e.StackTrace);
}
return(electronegativity);
}
/// <summary>
/// Check an Atom whether it may be conjugated or not.
/// </summary>
/// <param name="ac">The AtomContainer containing currentAtom</param>
/// <param name="currentAtom">The Atom to check</param>
/// <returns>-1 if isolated, 0 if conjugated, 1 if cumulative db</returns>
private static int CheckAtom(IAtomContainer ac, IAtom currentAtom)
{
int check = -1;
var atoms = ac.GetConnectedAtoms(currentAtom).ToReadOnlyList();
var bonds = ac.GetConnectedBonds(currentAtom).ToReadOnlyList();
if (currentAtom.IsAromatic)
{
check = 0;
}
else if (currentAtom.FormalCharge == 1)
/* && currentAtom.Symbol.Equals("C") */
{
check = 0;
}
else if (currentAtom.FormalCharge == -1)
{
//// NEGATIVE CHARGES WITH A NEIGHBOOR PI BOND ////
int counterOfPi = 0;
foreach (var atom in atoms)
{
if (ac.GetMaximumBondOrder(atom) != BondOrder.Single)
{
counterOfPi++;
}
}
if (counterOfPi > 0)
{
check = 0;
}
}
else
{
int se = ac.GetConnectedSingleElectrons(currentAtom).Count();
if (se == 1)
{
check = 0; //// DETECTION of radicals
}
else if (ac.GetConnectedLonePairs(currentAtom).Any()
/* && (currentAtom.Symbol.Equals("N") */)
{
check = 0; //// DETECTION of lone pair
}
else
{
int highOrderBondCount = 0;
for (int j = 0; j < atoms.Count; j++)
{
var bond = bonds[j];
if (bond == null || bond.Order != BondOrder.Single)
{
highOrderBondCount++;
}
else
{
}
}
if (highOrderBondCount == 1)
{
check = 0;
}
else if (highOrderBondCount > 1)
{
check = 1;
}
}
}
return(check);
}
/// <summary>
/// Initiate process.
/// It is needed to call the addExplicitHydrogensToSatisfyValency
/// from the class tools.HydrogenAdder.
/// </summary>
/// <exception cref="CDKException"> Description of the Exception</exception>
/// <param name="reactants">reactants of the reaction</param>
/// <param name="agents">agents of the reaction (Must be in this case null)</param>
public IReactionSet Initiate(IChemObjectSet <IAtomContainer> reactants, IChemObjectSet <IAtomContainer> agents)
{
Debug.WriteLine("initiate reaction: " + GetType().Name);
if (reactants.Count != 1)
{
throw new CDKException(GetType().Name + " only expects one reactant");
}
if (agents != null)
{
throw new CDKException(GetType().Name + " don't expects agents");
}
IReactionSet setOfReactions = reactants.Builder.NewReactionSet();
IAtomContainer reactant = reactants[0];
// if the parameter hasActiveCenter is not fixed yet, set the active centers
IParameterReaction ipr = base.GetParameterClass(typeof(SetReactionCenter));
if (ipr != null && !ipr.IsSetParameter)
{
SetActiveCenters(reactant);
}
if (AtomContainerManipulator.GetTotalCharge(reactant) != 0)
{
return(setOfReactions);
}
foreach (var bondi in reactant.Bonds)
{
if (bondi.IsReactiveCenter &&
((bondi.Order == BondOrder.Double) || (bondi.Order == BondOrder.Triple)) &&
bondi.Begin.IsReactiveCenter &&
bondi.End.IsReactiveCenter)
{
int chargeAtom0 = bondi.Begin.FormalCharge ?? 0;
int chargeAtom1 = bondi.End.FormalCharge ?? 0;
if (chargeAtom0 >= 0 && chargeAtom1 >= 0 &&
!reactant.GetConnectedSingleElectrons(bondi.Begin).Any() &&
!reactant.GetConnectedSingleElectrons(bondi.End).Any() &&
!reactant.GetConnectedLonePairs(bondi.Begin).Any() &&
!reactant.GetConnectedLonePairs(bondi.End).Any())
{
for (int j = 0; j < 2; j++)
{
var atomList = new List <IAtom>();
if (j == 0)
{
atomList.Add(bondi.Begin);
atomList.Add(bondi.End);
}
else
{
atomList.Add(bondi.End);
atomList.Add(bondi.Begin);
}
IAtom atomH = reactant.Builder.NewAtom("H");
atomH.FormalCharge = 1;
atomList.Add(atomH);
var bondList = new List <IBond>
{
bondi
};
IChemObjectSet <IAtomContainer> moleculeSet = reactant.Builder.NewAtomContainerSet();
moleculeSet.Add(reactant);
IAtomContainer adduct = reactant.Builder.NewAtomContainer();
adduct.Atoms.Add(atomH);
moleculeSet.Add(adduct);
IReaction reaction = Mechanism.Initiate(moleculeSet, atomList, bondList);
if (reaction == null)
{
continue;
}
else
{
setOfReactions.Add(reaction);
}
}
}
}
}
return(setOfReactions);
}