public Peptide GetFullPeptide()
{
var aminoAcids = new List <AminoAcidReference>();
foreach (var approximatedAminoAcid in approximatePeptide.AminoAcids)
{
var aminoAcid = AminoAcidLibrary.Get(approximatedAminoAcid.Name, approximatedAminoAcid.SequenceNumber);
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
var nitrogen = aminoAcid.GetAtomFromName("N");
nitrogen.Position = approximatedAminoAcid.NitrogenPosition;
nitrogen.IsPositionFixed = true;
var carbonAlpha = aminoAcid.GetAtomFromName("CA");
carbonAlpha.Position = approximatedAminoAcid.CarbonAlphaPosition;
carbonAlpha.IsPositionFixed = true;
var carbon = aminoAcid.GetAtomFromName("C");
carbon.Position = approximatedAminoAcid.CarbonPosition;
carbon.IsPositionFixed = true;
aminoAcid.Molecule.PositionAtoms();
aminoAcids.Add(aminoAcid);
}
var peptide = PeptideBuilder.PeptideFromAminoAcids(aminoAcids);
peptide.Molecule.PositionAtoms();
return(peptide);
}
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);
}