public static AminoAcidReference Arginine(int sequenceNumber)
{
var sideChain1Builder = new MoleculeBuilder();
var sideChain11Builder = new MoleculeBuilder();
sideChain11Builder.Start
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen, ElementName.Hydrogen);
var sideChain12Builder = new MoleculeBuilder();
sideChain12Builder.Start
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen);
sideChain1Builder.Start
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen, ElementName.Hydrogen)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen, ElementName.Hydrogen)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen, ElementName.Hydrogen)
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon)
.AddSideChain(sideChain11Builder.Start)
.AddSideChain(sideChain12Builder.Start, BondMultiplicity.Double);
var moduleBuilder = new MoleculeBuilder();
var moleculeReference = moduleBuilder.Start
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon).AddSideChain(sideChain1Builder.Start)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Oxygen, BondMultiplicity.Double);
return(new AminoAcidReference(AminoAcidName.Arginine, sequenceNumber, moleculeReference));
}
public static AminoAcidReference Tyrosine(int sequenceNumber)
{
var sideChain1Builder = new MoleculeBuilder();
var benzolReferences = sideChain1Builder.Start
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen, ElementName.Hydrogen)
.AddBenzolRing(3);
benzolReferences.Single().Add(ElementName.Oxygen, ElementName.Hydrogen);
var moduleBuilder = new MoleculeBuilder();
var moleculeReference = moduleBuilder.Start
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon).AddSideChain(sideChain1Builder.Start).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Oxygen, BondMultiplicity.Double);
return(new AminoAcidReference(AminoAcidName.Tyrosine, sequenceNumber, moleculeReference));
}
public static AminoAcidReference Histidine(int sequenceNumber)
{
var sideChain1Builder = new MoleculeBuilder();
var ringBuilder = new MoleculeBuilder();
var ringEnd = ringBuilder.Start
.Add(ElementName.Carbon)
.Add(ElementName.Nitrogen)
.Add(ElementName.Carbon, BondMultiplicity.Double)
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen);
ringBuilder.Start.ConnectTo(ringEnd, BondMultiplicity.Double);
sideChain1Builder.Start
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Hydrogen)
.AddSideChain(ringBuilder.Start);
var moduleBuilder = new MoleculeBuilder();
var moleculeReference = moduleBuilder.Start
.Add(ElementName.Nitrogen).AddToCurrentAtom(ElementName.Hydrogen)
.Add(ElementName.Carbon).AddSideChain(sideChain1Builder.Start)
.Add(ElementName.Carbon).AddToCurrentAtom(ElementName.Oxygen, BondMultiplicity.Double);
return(new AminoAcidReference(AminoAcidName.Histidine, sequenceNumber, moleculeReference));
}
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);
}
