public MoleculeReference AddMolecule(MoleculeReference moleculeToBeAdded,
uint firstAtomId,
uint connectionAtomId,
BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
return(AddMolecule(moleculeToBeAdded, firstAtomId, connectionAtomId, out _, bondMultiplicity));
}
public static MoleculeReference ConnectTo(this MoleculeReference moleculeReference, MoleculeReference otherReference,
BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
if (!otherReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Side chain molecule reference is not initialized");
}
var lastAtomInOtherReference = otherReference.Molecule.GetAtom(otherReference.LastAtomId);
var matchingConnectionAtom = moleculeReference.Molecule.Atoms
.SingleOrDefault(a => a.Equals(lastAtomInOtherReference));
if (matchingConnectionAtom == null)
{
moleculeReference.Molecule.AddMolecule(otherReference,
moleculeReference.FirstAtomId,
moleculeReference.LastAtomId,
bondMultiplicity);
}
else
{
var connectionAtomVertexId = moleculeReference.Molecule.MoleculeStructure.Vertices
.Single(v => v.Object.Equals(matchingConnectionAtom));
moleculeReference.Molecule.ConnectAtoms(moleculeReference.LastAtomId, connectionAtomVertexId.Id, bondMultiplicity);
}
return(moleculeReference);
}
public static IEnumerable <SimpleBond> CreateBonds(Atom atom1, Atom atom2, BondMultiplicity bondMultiplicity)
{
if (atom1 is AtomWithOrbitals && atom2 is AtomWithOrbitals)
{
return(CreateOrbitalBonds((AtomWithOrbitals)atom1, (AtomWithOrbitals)atom2, (int)bondMultiplicity));
}
return(CreateSimpleBonds(atom1, atom2, (int)bondMultiplicity));
}
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 static MoleculeReference AddSideChain(this MoleculeReference moleculeReference, MoleculeReference sideChainReference,
BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
moleculeReference.Molecule.AddMolecule(sideChainReference,
moleculeReference.FirstAtomId,
moleculeReference.LastAtomId,
bondMultiplicity);
return(moleculeReference);
}
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 static MoleculeReference AddToCurrentAtom(this MoleculeReference moleculeReference, ElementName element, BondMultiplicity bondMultiplicity)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
var atom = Atom.FromStableIsotope(element);
moleculeReference.Molecule.AddAtom(atom, moleculeReference.LastAtomId, bondMultiplicity);
return(moleculeReference);
}
public static MoleculeReference Add(this MoleculeReference moleculeReference, ElementName element, BondMultiplicity bondMultiplicity)
{
var lastAtomId = moleculeReference.LastAtomId;
var atom = Atom.FromStableIsotope(element);
lastAtomId = moleculeReference.Molecule.AddAtom(atom, lastAtomId);
if (!moleculeReference.IsInitialized)
{
moleculeReference.FirstAtomId = lastAtomId;
}
return(new MoleculeReference(moleculeReference.Molecule, moleculeReference.FirstAtomId, lastAtomId));
}
