private UnitVector3D FindPositionVector(
AminoAcidReference aminoAcid,
AminoAcidReference secondAminoAcid)
{
var firstCarbonAlpha = aminoAcid.GetAtomFromName("CA");
if (firstCarbonAlpha == null)
{
throw new KeyNotFoundException("Could not find carbon alpha in first amino acid");
}
var secondCarbonAlpha = secondAminoAcid.GetAtomFromName("CA");
if (secondCarbonAlpha == null)
{
throw new KeyNotFoundException("Could not find carbon alpha in second amino acid");
}
return(firstCarbonAlpha.Position.VectorTo(secondCarbonAlpha.Position));
}
public Peptide GetBackbone()
{
var aminoAcids = new List <AminoAcidReference>();
foreach (var approximatedAminoAcid in approximatePeptide.AminoAcids)
{
var moleculeBuilder = new MoleculeBuilder();
var aminoAcidReference = moleculeBuilder.Start
.Add(ElementName.Nitrogen, ElementName.Carbon, ElementName.Carbon);
var aminoAcid = new AminoAcidReference(approximatedAminoAcid.Name, approximatedAminoAcid.SequenceNumber, aminoAcidReference);
var nitrogen = aminoAcid.VertexIds
.Select(aminoAcid.Molecule.GetAtom)
.Single(atom => atom.Element == ElementName.Nitrogen);
nitrogen.Position = approximatedAminoAcid.NitrogenPosition;
nitrogen.IsPositionFixed = true;
var carbonAlpha = aminoAcid.VertexIds
.Select(aminoAcid.Molecule.GetAtom)
.First(atom => atom.Element == ElementName.Carbon);
carbonAlpha.Position = approximatedAminoAcid.CarbonAlphaPosition;
carbonAlpha.IsPositionFixed = true;
var carbon = aminoAcid.VertexIds
.Select(aminoAcid.Molecule.GetAtom)
.Last(atom => atom.Element == ElementName.Carbon);
carbon.Position = approximatedAminoAcid.CarbonPosition;
carbon.IsPositionFixed = true;
aminoAcids.Add(aminoAcid);
}
var peptide = PeptideBuilder.PeptideFromAminoAcids(aminoAcids);
return(peptide);
}
