CSMSL.IO.PepXML.PepXmlWriter.WriteModification C# (CSharp) Метод

        public void WriteModification(IMass modification, ModificationSites sites, bool fixedModification = true)
        {
            if (CurrentStage != Stage.SearchSummary)
                throw new ArgumentException("You must be in the Search Summary stage to write modifications");

            foreach (ModificationSites singleSite in sites.GetActiveSites())
            {
                double basemass = 0;
                if (singleSite >= ModificationSites.NPep)
                {
                    _writer.WriteStartElement("terminal_modification");
                    if (singleSite.HasFlag(ModificationSites.NPep) || singleSite.HasFlag(ModificationSites.NProt))
                    {
                        _writer.WriteAttributeString("terminus", "N");
                        basemass += AminoAcidPolymer.DefaultNTerminus.MonoisotopicMass;
                    }
                    else
                    {
                        _writer.WriteAttributeString("terminus", "C");
                        basemass += AminoAcidPolymer.DefaultCTerminus.MonoisotopicMass;
                    }

                    _writer.WriteAttributeString("protein_terminus", (singleSite.HasFlag(ModificationSites.NProt) || singleSite.HasFlag(ModificationSites.ProtC)) ? "Y" : "N");
                }
                else
                {
                    string letter = Enum.GetName(typeof (ModificationSites), singleSite);
                    AminoAcid aa = AminoAcid.GetResidue(letter);
                    _writer.WriteStartElement("aminoacid_modification");
                    _writer.WriteAttributeString("aminoacid", letter);
                    basemass += aa.MonoisotopicMass;
                }
                double massshift = modification.MonoisotopicMass;
                _writer.WriteAttributeString("variable", (fixedModification) ? "N" : "Y");
                _writer.WriteAttributeString("mass", (basemass + massshift).ToString());
                _writer.WriteAttributeString("massdiff", massshift.ToString());
                _writer.WriteAttributeString("description", modification.ToString());
                _writer.WriteEndElement();
            }
        }

        public static void WritePepXml()
        {
            string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");

            Console.WriteLine("Writting to " + filePath);
            using (PepXmlWriter writer = new PepXmlWriter(filePath))
            {
                writer.WriteSampleProtease(Protease.Trypsin);

                writer.StartSearchSummary("OMSSA", true, true);

                writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");

                writer.WriteSearchProtease(Protease.Trypsin, 3);

                writer.WriteModification(ModificationDictionary.GetModification("Acetyl"), ModificationSites.K | ModificationSites.NPep);
                writer.WriteModification(ModificationDictionary.GetModification("CAM"), ModificationSites.C);

                writer.WriteModification(ModificationDictionary.GetModification("Phospho"), ModificationSites.S | ModificationSites.T | ModificationSites.Y, false);

                writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);

                writer.StartSpectrum(15, 1.234, 523.4324, 3);

                PeptideSpectralMatch psm = new PeptideSpectralMatch(PeptideSpectralMatchScoreType.OmssaEvalue);
                psm.Score = 1.5e-5;
                Protein protein = new Protein("", "Test Protein");
                psm.Peptide = new Peptide("DEREK",protein);
                psm.Charge = 3;
                writer.WritePSM(psm);

                writer.EndSpectrum();
            }
        }