public static List <MoleculeReference> AddBenzolRing(this MoleculeReference moleculeReference, params int[] referencePositions)
{
var sideChainReference = moleculeReference;
var references = new List <MoleculeReference>();
MoleculeReference firstCarbonReference = null;
for (var carbonIdx = 0; carbonIdx < 6; carbonIdx++)
{
var bondMultiplicity = carbonIdx.IsEven() ? BondMultiplicity.Double : BondMultiplicity.Single;
sideChainReference = sideChainReference.Add(ElementName.Carbon, bondMultiplicity);
if (carbonIdx == 0)
{
firstCarbonReference = sideChainReference;
}
if (referencePositions.Contains(carbonIdx))
{
references.Add(sideChainReference);
}
else
{
sideChainReference.AddToCurrentAtom(ElementName.Hydrogen);
}
}
firstCarbonReference.ConnectTo(sideChainReference);
return(references);
}
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 Peptide PeptideFromAminoAcids(IEnumerable <AminoAcidReference> aminoAcidReferences)
{
var aminoAcids = new List <AminoAcidReference>();
MoleculeReference moleculeReference = null;
foreach (var aminoAcid in aminoAcidReferences)
{
MoleculeReference aminoAcidReference;
if (moleculeReference != null)
{
moleculeReference = moleculeReference.Add(aminoAcid, out aminoAcidReference);
}
else
{
moleculeReference = aminoAcid;
aminoAcidReference = new MoleculeReference(
aminoAcid.Molecule,
aminoAcid.VertexIds,
aminoAcid.FirstAtomId,
aminoAcid.LastAtomId);
}
aminoAcids.Add(new AminoAcidReference(aminoAcid.Name, aminoAcid.SequenceNumber, aminoAcidReference));
}
return(new Peptide(moleculeReference, aminoAcids));
}
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, MoleculeReference otherMoleculeReference)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
return(moleculeReference.Molecule.AddMolecule(otherMoleculeReference,
moleculeReference.FirstAtomId,
moleculeReference.LastAtomId));
}
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));
}
public static void MarkBackbone(this Molecule molecule, MoleculeReference moleculeReference)
{
var pathsFromFirstAtom = GraphAlgorithms.ShortestPaths(molecule.MoleculeStructure, moleculeReference.FirstAtomId);
var pathToLastAtom = pathsFromFirstAtom.PathTo(molecule.MoleculeStructure.GetVertexFromId(moleculeReference.LastAtomId));
var pathVertices = pathToLastAtom.Path
.SelectMany(edge => new[] { edge.Vertex1Id, edge.Vertex2Id })
.Distinct()
.Select(vId => molecule.MoleculeStructure.GetVertexFromId(vId))
.Select(v => v.Object);
pathVertices.ForEach(atom => atom.IsBackbone = true);
}
public static MoleculeReference AddToCurrentAtom(this MoleculeReference moleculeReference, params ElementName[] elements)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
foreach (var element in elements)
{
var atom = Atom.FromStableIsotope(element);
moleculeReference.Molecule.AddAtom(atom, moleculeReference.LastAtomId);
}
return(moleculeReference);
}
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 static MoleculeReference AddSideChain(this MoleculeReference moleculeReference, params ElementName[] sideChainElements)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
var sideChainBuilder = new MoleculeBuilder();
var sideChainReference = sideChainBuilder.Start.Add(sideChainElements);
moleculeReference.Molecule.AddMolecule(sideChainReference,
moleculeReference.FirstAtomId,
moleculeReference.LastAtomId);
return(moleculeReference);
}
public static MoleculeReference Add(this MoleculeReference moleculeReference, params ElementName[] elements)
{
var lastAtomId = moleculeReference.LastAtomId;
foreach (var element in elements)
{
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));
}
