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 static Peptide PeptideFromSequence(AminoAcidSequence aminoAcidNameSequence, PeptideBuilderOptions options = null)
{
if (options == null)
{
options = new PeptideBuilderOptions();
}
if (options.BuildMolecule)
{
var aminoAcidReferences = aminoAcidNameSequence
.Select(sequenceItem => AminoAcidLibrary.Get(sequenceItem.AminoAcidName, sequenceItem.ResidueNumber));
return(PeptideFromAminoAcids(aminoAcidReferences));
}
else
{
var aminoAcidReferences = aminoAcidNameSequence
.Select((aa, idx) => new AminoAcidReference(aa.AminoAcidName, aa.ResidueNumber, null, new List <uint>(), 0, 0))
.ToList();
return(new Peptide(new MoleculeReference(new Molecule()), aminoAcidReferences));
}
}
public static Peptide PeptideFromSequence(
IEnumerable <AminoAcidName> aminoAcidNameSequence,
PeptideBuilderOptions options = null)
{
if (options == null)
{
options = new PeptideBuilderOptions();
}
if (options.BuildMolecule)
{
var aminoAcidReferences = aminoAcidNameSequence
.Select((aminoAcidName, idx) => AminoAcidLibrary.Get(aminoAcidName, options.FirstSequenceNumber + idx));
return(PeptideFromAminoAcids(aminoAcidReferences));
}
else
{
var aminoAcidReferences = aminoAcidNameSequence
.Select((aa, idx) => new AminoAcidReference(aa, options.FirstSequenceNumber + idx, null, new List <uint>(), 0, 0))
.ToList();
return(new Peptide(new MoleculeReference(new Molecule()), aminoAcidReferences));
}
}
