public void Ctor()
{
{
#region 1
IAtomContainer methane = new AtomContainer();
IAtom carbon = new Atom("C");
methane.Atoms.Add(carbon);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.GetInstance();
foreach (var atom in methane.Atoms)
{
IAtomType type = matcher.FindMatchingAtomType(methane, atom);
AtomTypeManipulator.Configure(atom, type);
}
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(methane);
#endregion
}
{
#region 2
IAtomContainer ethane = new AtomContainer();
IAtom carbon1 = new Atom("C");
IAtom carbon2 = new Atom("C");
ethane.Atoms.Add(carbon1);
ethane.Atoms.Add(carbon2);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.GetInstance();
IAtomType type = matcher.FindMatchingAtomType(ethane, carbon1);
AtomTypeManipulator.Configure(carbon1, type);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(ethane, carbon1);
#endregion
}
}
/// <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 receives the charge and the second the single electron</param>
/// <param name="bondList">The list of bonds taking part in the mechanism. Only allowed one bond</param>
/// <returns>The Reaction mechanism</returns>
public IReaction Initiate(IChemObjectSet <IAtomContainer> atomContainerSet, IList <IAtom> atomList, IList <IBond> bondList)
{
var atMatcher = CDKAtomTypeMatcher.GetInstance(CDKAtomTypeMatcher.Mode.RequireExplicitHydrogens);
if (atomContainerSet.Count != 1)
{
throw new CDKException("RemovingSEofBMechanism only expects one IAtomContainer");
}
if (atomList.Count != 2)
{
throw new CDKException("RemovingSEofBMechanism expects two atoms in the List");
}
if (bondList.Count != 1)
{
throw new CDKException("RemovingSEofBMechanism only expects one bond in the List");
}
var molecule = atomContainerSet[0];
var reactantCloned = (IAtomContainer)molecule.Clone();
var atom1 = atomList[0];
var atom1C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom1)];
var atom2 = atomList[1];
var atom2C = reactantCloned.Atoms[molecule.Atoms.IndexOf(atom2)];
var bond1 = bondList[0];
var posBond1 = molecule.Bonds.IndexOf(bond1);
if (bond1.Order == BondOrder.Single)
{
reactantCloned.Bonds.Remove(reactantCloned.Bonds[posBond1]);
}
else
{
BondManipulator.DecreaseBondOrder(reactantCloned.Bonds[posBond1]);
}
var charge = atom1C.FormalCharge.Value;
atom1C.FormalCharge = charge + 1;
reactantCloned.SingleElectrons.Add(atom1C.Builder.NewSingleElectron(atom2C));
// check if resulting atom type is reasonable
atom1C.Hybridization = Hybridization.Unset;
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactantCloned);
var 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);
}
var reaction = atom1C.Builder.NewReaction();
reaction.Reactants.Add(molecule);
/* mapping */
foreach (var atom in molecule.Atoms)
{
IMapping mapping = atom1C.Builder.NewMapping(atom,
reactantCloned.Atoms[molecule.Atoms.IndexOf(atom)]);
reaction.Mappings.Add(mapping);
}
if (bond1.Order != BondOrder.Single)
{
reaction.Products.Add(reactantCloned);
}
else
{
var moleculeSetP = ConnectivityChecker.PartitionIntoMolecules(reactantCloned);
foreach (var moleculeP in moleculeSetP)
{
reaction.Products.Add(moleculeP);
}
}
return(reaction);
}
