/// <summary>
/// Initiates the process for the given mechanism. The atoms to apply are mapped between
/// reactants and products.
/// </summary>
/// <param name="atomContainerSet"></param>
/// <param name="atomList">The list of atoms taking part in the mechanism. Only allowed two three.
/// The first atom is the atom which must contain the charge to be moved, the second
/// is the atom which is in the middle and the third is the atom which acquires the new charge
/// <param name="bondList">The list of bonds taking part in the mechanism. Only allowed two bond.</param>
/// The first bond is the bond to increase the order and the second is the bond
/// to decrease the order
/// It is the bond which is moved</param>
/// <returns>The Reaction mechanism</returns>
public IReaction Initiate(IChemObjectSet <IAtomContainer> atomContainerSet, IList <IAtom> atomList, IList <IBond> bondList)
{
var atMatcher = CDK.AtomTypeMatcher;
if (atomContainerSet.Count != 1)
{
throw new CDKException("RearrangementChargeMechanism only expects one IAtomContainer");
}
if (atomList.Count != 3)
{
throw new CDKException("RearrangementChargeMechanism expects three atoms in the List");
}
if (bondList.Count != 2)
{
throw new CDKException("RearrangementChargeMechanism only expect one bond in the List");
}
IAtomContainer molecule = atomContainerSet[0];
IAtomContainer reactantCloned;
reactantCloned = (IAtomContainer)molecule.Clone();
IAtom atom1 = atomList[0]; // Atom with the charge
IAtom atom1C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom1)];
IAtom atom3 = atomList[2]; // Atom which acquires the charge
IAtom atom3C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom3)];
IBond bond1 = bondList[0]; // Bond with single bond
int posBond1 = molecule.Bonds.IndexOf(bond1);
IBond bond2 = bondList[1]; // Bond with double bond
int posBond2 = molecule.Bonds.IndexOf(bond2);
BondManipulator.IncreaseBondOrder(reactantCloned.Bonds[posBond1]);
if (bond2.Order == BondOrder.Single)
{
reactantCloned.Bonds.Remove(reactantCloned.Bonds[posBond2]);
}
else
{
BondManipulator.DecreaseBondOrder(reactantCloned.Bonds[posBond2]);
}
//Depending of the charge moving (radical, + or -) there is a different situation
if (reactantCloned.GetConnectedSingleElectrons(atom1C).Any())
{
var selectron = reactantCloned.GetConnectedSingleElectrons(atom1C);
reactantCloned.SingleElectrons.Remove(selectron.Last());
reactantCloned.SingleElectrons.Add(bond2.Builder.NewSingleElectron(atom3C));
}
else if (atom1C.FormalCharge > 0)
{
int charge = atom1C.FormalCharge.Value;
atom1C.FormalCharge = charge - 1;
charge = atom3C.FormalCharge.Value;
atom3C.FormalCharge = charge + 1;
}
else if (atom1C.FormalCharge < 1)
{
int charge = atom1C.FormalCharge.Value;
atom1C.FormalCharge = charge + 1;
var ln = reactantCloned.GetConnectedLonePairs(atom1C);
reactantCloned.LonePairs.Remove(ln.Last());
atom1C.IsAromatic = false;
charge = atom3C.FormalCharge.Value;
atom3C.FormalCharge = charge - 1;
reactantCloned.LonePairs.Add(bond2.Builder.NewLonePair(atom3C));
atom3C.IsAromatic = false;
}
else
{
return(null);
}
atom1C.Hybridization = Hybridization.Unset;
atom3C.Hybridization = Hybridization.Unset;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.FindMatchingAtomType(reactantCloned, atom1C);
if (type == null || type.AtomTypeName.Equals("X", StringComparison.Ordinal))
{
return(null);
}
type = atMatcher.FindMatchingAtomType(reactantCloned, atom3C);
if (type == null || type.AtomTypeName.Equals("X", StringComparison.Ordinal))
{
return(null);
}
IReaction reaction = bond2.Builder.NewReaction();
reaction.Reactants.Add(molecule);
/* mapping */
foreach (var atom in molecule.Atoms)
{
IMapping mapping = bond2.Builder.NewMapping(atom,
reactantCloned.Atoms[molecule.Atoms.IndexOf(atom)]);
reaction.Mappings.Add(mapping);
}
if (bond2.Order != BondOrder.Single)
{
reaction.Products.Add(reactantCloned);
}
else
{
IChemObjectSet <IAtomContainer> moleculeSetP = ConnectivityChecker.PartitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.Count(); z++)
{
reaction.Products.Add((IAtomContainer)moleculeSetP[z]);
}
}
return(reaction);
}
/// <summary>
/// Initiates the process for the given mechanism. The atoms to apply are mapped between
/// reactants and products.
/// </summary>
/// <param name="atomContainerSet"></param>
/// <param name="atomList">
/// The list of atoms taking part in the mechanism. Only allowed two atoms.
/// The first atom is the atom which contains the ISingleElectron and the second
/// third is the atom which will be removed
/// the first atom</param>
/// <param name="bondList">The list of bonds taking part in the mechanism. Only allowed one bond.
/// It is the bond which is moved</param>
/// <returns>The Reaction mechanism</returns>
public IReaction Initiate(IChemObjectSet <IAtomContainer> atomContainerSet, IList <IAtom> atomList, IList <IBond> bondList)
{
var atMatcher = CDK.AtomTypeMatcher;
if (atomContainerSet.Count != 1)
{
throw new CDKException("RadicalSiteIonizationMechanism only expects one IAtomContainer");
}
if (atomList.Count != 3)
{
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the List");
}
if (bondList.Count != 2)
{
throw new CDKException("RadicalSiteIonizationMechanism only expect one bond in the List");
}
IAtomContainer molecule = atomContainerSet[0];
IAtomContainer reactantCloned;
reactantCloned = (IAtomContainer)molecule.Clone();
IAtom atom1 = atomList[0]; // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom1)];
IAtom atom2 = atomList[1]; // Atom
IAtom atom2C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom2)];
IAtom atom3 = atomList[2]; // Atom to be saved
IAtom atom3C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom3)];
IBond bond1 = bondList[0]; // Bond to increase the order
int posBond1 = molecule.Bonds.IndexOf(bond1);
IBond bond2 = bondList[1]; // Bond to remove
int posBond2 = molecule.Bonds.IndexOf(bond2);
BondManipulator.IncreaseBondOrder(reactantCloned.Bonds[posBond1]);
reactantCloned.Bonds.Remove(reactantCloned.Bonds[posBond2]);
var selectron = reactantCloned.GetConnectedSingleElectrons(atom1C);
reactantCloned.SingleElectrons.Remove(selectron.Last());
atom1C.Hybridization = Hybridization.Unset;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.FindMatchingAtomType(reactantCloned, atom1C);
if (type == null || type.AtomTypeName.Equals("X", StringComparison.Ordinal))
{
return(null);
}
atom2C.Hybridization = Hybridization.Unset;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.FindMatchingAtomType(reactantCloned, atom2C);
if (type == null || type.AtomTypeName.Equals("X", StringComparison.Ordinal))
{
return(null);
}
reactantCloned.SingleElectrons.Add(atom2C.Builder.NewSingleElectron(atom3C));
atom3C.Hybridization = Hybridization.Unset;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.FindMatchingAtomType(reactantCloned, atom3C);
if (type == null || type.AtomTypeName.Equals("X", StringComparison.Ordinal))
{
return(null);
}
IReaction reaction = atom2C.Builder.NewReaction();
reaction.Reactants.Add(molecule);
/* mapping */
foreach (var atom in molecule.Atoms)
{
IMapping mapping = atom2C.Builder.NewMapping(atom,
reactantCloned.Atoms[molecule.Atoms.IndexOf(atom)]);
reaction.Mappings.Add(mapping);
}
IChemObjectSet <IAtomContainer> moleculeSetP = ConnectivityChecker.PartitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.Count(); z++)
{
reaction.Products.Add((IAtomContainer)moleculeSetP[z]);
}
return(reaction);
}