public List <IGlycoPeptide> Create(IGlycan glycan, IPeptide peptide) { List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>(); foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence())) { glycoPeptides.Add(new GeneralGlycoPeptide(peptide, glycan, pos)); } return(glycoPeptides); }
GenerateNewGlycoPeptide(IPeptide peptide, IGlycan glycan) { List <IAccumulatedGlycoPeptideMassProxy> glycos = new List <IAccumulatedGlycoPeptideMassProxy>(); foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence())) { SpecialGlycoPeptide <IAccumulatedGlycanMassProxy> g = new SpecialGlycoPeptide <IAccumulatedGlycanMassProxy>(peptide, glycan as IAccumulatedGlycanMassProxy, pos); glycos.Add(new GeneralAccumulatedGlycoPeptideMassProxy(g)); } return(glycos); }
public List <string> Generate(string sequence) { List <string> peptideList = new List <string>(); foreach (string s in generator.Generate(sequence)) { if (FindPTMPosition.ContainsOGlycanSite(s)) { peptideList.Add(s); } } return(peptideList); }
public List <IPeptide> Create(IProtein protein) { List <string> pepList = new List <string>(); foreach (string sequence in creator.GeneratePeptideSequences(protein)) { if (FindPTMPosition.ContainsOGlycanSite(sequence)) { pepList.Add(sequence); } } List <IPeptide> peptideList = creator.CreateNewPeptides(protein.GetID(), pepList); protein.SetPeptides(peptideList); return(peptideList); }
public List <IGlycoPeptide> Create(IGlycan glycan, IPeptide peptide) { List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>(); foreach (int pos in FindPTMPosition.FindNGlycanSite(peptide.GetSequence())) { try { IGlycoPeptideProxy glycoPeptideProxy = generator.Generate(glycan, peptide, pos); glycoPeptides.Add(glycoPeptideProxy); } catch (Exception e) { Console.WriteLine(e.Message); } } return(glycoPeptides); }