public void ConnectAtoms(uint atomId1, uint atomId2, BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
var atom1 = GetAtom(atomId1);
var atom2 = GetAtom(atomId2);
var bonds = AtomConnector.CreateBonds(atom1, atom2, bondMultiplicity);
foreach (var bond in bonds)
{
var edge = (Edge <SimpleBond>)MoleculeStructure.ConnectVertices(atomId1, atomId2);
edge.Object = bond;
}
}
public MoleculeReference AddMolecule(MoleculeReference moleculeToBeAdded,
uint firstAtomId,
uint connectionAtomId,
out MoleculeReference convertedInputMoleculeReference,
BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
var mergeInfo = MoleculeStructure.AddGraph(moleculeToBeAdded.Molecule.MoleculeStructure);
var vertex1 = connectionAtomId;
var vertex2 = mergeInfo.VertexIdMap[moleculeToBeAdded.FirstAtomId];
var atom1 = MoleculeStructure.GetVertexFromId(vertex1).Object;
var atom2 = MoleculeStructure.GetVertexFromId(vertex2).Object;
var bonds = AtomConnector.CreateBonds(atom1, atom2, bondMultiplicity);
foreach (var bond in bonds)
{
var edge = (Edge <SimpleBond>)MoleculeStructure.ConnectVertices(vertex1, vertex2);
edge.Object = bond;
}
convertedInputMoleculeReference = new MoleculeReference(this,
moleculeToBeAdded.VertexIds.Select(oldVertexId => mergeInfo.VertexIdMap[oldVertexId]),
mergeInfo.VertexIdMap[moleculeToBeAdded.FirstAtomId],
mergeInfo.VertexIdMap[moleculeToBeAdded.LastAtomId]);
return(new MoleculeReference(this, firstAtomId, mergeInfo.VertexIdMap[moleculeToBeAdded.LastAtomId]));
}