public MoleculeReference AddMolecule(MoleculeReference moleculeToBeAdded,
uint firstAtomId,
uint connectionAtomId,
BondMultiplicity bondMultiplicity = BondMultiplicity.Single)
{
return(AddMolecule(moleculeToBeAdded, firstAtomId, connectionAtomId, out _, bondMultiplicity));
}
public void Dispose()
{
MoleculeReference.Dispose();
AminoAcids.ForEach(aminoAcid => aminoAcid.Dispose());
Annotations.ForEach(annotation => annotation.Dispose());
AminoAcids.Clear();
Annotations.Clear();
}
public Peptide(MoleculeReference moleculeReference,
List <AminoAcidReference> aminoAcids,
List <PeptideAnnotation <AminoAcidReference> > annotations)
{
MoleculeReference = moleculeReference ?? throw new ArgumentNullException(nameof(moleculeReference));
AminoAcids = aminoAcids;
Annotations = annotations;
}
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 AminoAcidReference(AminoAcidName aminoAcidName, int sequenceNumber, MoleculeReference moleculeReference)
: this(aminoAcidName, sequenceNumber, moleculeReference.Molecule, moleculeReference.VertexIds, moleculeReference.FirstAtomId, moleculeReference.LastAtomId)
{
}
public Peptide(MoleculeReference moleculeReference,
List <AminoAcidReference> aminoAcids)
: this(moleculeReference, aminoAcids, new List <PeptideAnnotation <AminoAcidReference> >())
{
}
public void Add(AminoAcidReference aminoAcid)
{
MoleculeReference.Add(aminoAcid, out var aminoAcidReference);
AminoAcids.Add(new AminoAcidReference(aminoAcid.Name, aminoAcid.SequenceNumber, aminoAcidReference));
}