public uint AddAtom(Atom atom, uint existingAtomId = uint.MaxValue, BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
// If no atoms in the molecule yet, just add the atom
if (!MoleculeStructure.Vertices.Any())
{
var firstVertex = new Vertex <Atom>(MoleculeStructure.GetUnusedVertexId())
{
Object = atom
};
MoleculeStructure.AddVertex(firstVertex);
return(firstVertex.Id);
}
if (!MoleculeStructure.HasVertex(existingAtomId))
{
throw new KeyNotFoundException("Adding atom to molecule failed, because the reference to an existing atom was not found");
}
var existingAtom = MoleculeStructure.GetVertexFromId(existingAtomId).Object;
var vertex = new Vertex <Atom>(MoleculeStructure.GetUnusedVertexId())
{
Object = atom
};
MoleculeStructure.AddVertex(vertex);
var bonds = AtomConnector.CreateBonds(atom, existingAtom, bondMultiplicity);
foreach (var bond in bonds)
{
var edge = new Edge <SimpleBond>(MoleculeStructure.GetUnusedEdgeId(), existingAtomId, vertex.Id)
{
Object = bond
};
MoleculeStructure.AddEdge(edge);
}
return(vertex.Id);
}
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]));
}
public Atom GetAtom(uint atomId)
{
return(MoleculeStructure.GetVertexFromId(atomId).Object);
}