public void Run()
{
ITableNGlycan glycan = new ComplexNGlycan(new int[24]);
Console.WriteLine(glycan.GetName());
//glycan.SetNGlycanTable(0, 1);
ITableNGlycanProxy glycanProxy = new GeneralTableNGlycanMassProxy(glycan);
ITableNGlycanProxyGenerator generator = new GeneralTableNGlycanMassProxyGenerator();
IGlycanCreator glycanCreator = new GeneralTableNGlycanCreator(generator, glycanProxy);
List <IGlycan> glycans = glycanCreator.Create();
//foreach(IGlycan g in glycans)
//{
// Console.WriteLine(string.Join(" ", g.GetStructure()));
//}
IGlycoPeptideProxyGenerator glycoPeptideProxyGenerator = new GeneralTableNGlycoPeptideMassProxyGenerator();
IGlycoPeptideCreator glycoPeptideCreator = new GeneralNGlycoPeptideSingleSiteCreator(glycoPeptideProxyGenerator);
IPeptide peptide = new GeneralPeptide("test3", "ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAK");
foreach (IGlycan g in glycans)
{
List <IGlycoPeptide> glycoPeptides = glycoPeptideCreator.Create(g, peptide);
//Console.WriteLine(glycoPeptides.Count);
foreach (IGlycoPeptide glyco in glycoPeptides)
{
//Console.WriteLine(glyco.GetGlycan().GetName());
//Console.WriteLine(glyco.GetPosition());
}
}
Console.Read();
}
public IGlycoPeptide createGlyco()
{
int[] structTable = new int[24];
structTable[0] = 1;
IPeptide peptide = new GeneralPeptide("test3", "ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAK");
IGlycoPeptide glycoPeptide = new GeneralGlycoPeptide(new ComplexNGlycan(structTable), peptide, 0);
return(glycoPeptide);
}
public override List <IPeptide> CreateNewPeptides(string id, List <string> pepList)
{
List <IPeptide> peptideList = new List <IPeptide>();
foreach (string sequence in pepList)
{
GeneralPeptide peptide = new GeneralPeptide(id, sequence);
peptideList.Add(peptide);
}
return(peptideList);
}
public List <IPeptide> Create(IProtein protein)
{
List <IPeptide> peptideList = new List <IPeptide>();
List <string> sequences = generator.Generate(protein.GetSequence());
foreach (string seq in sequences)
{
GeneralPeptide peptide = new GeneralPeptide(protein.GetID(), seq);
peptideList.Add(peptide);
}
protein.SetPeptides(peptideList);
return(peptideList);
}
public void Run()
{
//AccumulatedStructBruteForceNGlycanCreator creator = new AccumulatedStructBruteForceNGlycanCreator();
//creator.Generate();
////http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html
IPeptide peptide = new GeneralPeptide("test", "VVLHPNYSQVD");
//IPeptide peptide = new GeneralPeptide("test", "SRNLTK");
//IPeptide peptide = new GeneralPeptide("test", "LCPDCPLLAPLNDSR");
ICalcMass calculator = UtilMass.Instance;
ICalcMassOption option = UtilMassOption.Instance;
//double mass = calculator.CalcPeptideMass(peptide, option); //1154.63213937
//
//double mass = calculator.CalcPeptideMass(peptide, option);
//double mass = calculator.CalcPeptideIonMass("CHS", IonType.xIon, option);
//Console.WriteLine(mass);
//double mass = calculator.CalcPeptideIonMass("VVLHPNYSQV", IonType.cIon, option);
//Console.WriteLine(mass);
//mass = calculator.CalcPeptideIonMass("CHS", IonType.zIon, option);
//Console.WriteLine(mass);
//IGlycan glycan = new GeneralGlycan(6, 7, 2, 3, 0);
IGlycan glycan = new GeneralGlycan(1, 0, 0, 0, 0);
//option.SetPermethylation(true);
double mass = calculator.CalcPeptideMass(peptide, option);
mass += calculator.CalcGlycanMass(glycan, option);
//mass = calculator.CalcGlycanYIonMass(glycan, option);
//peptide = new GeneralPeptide("1", "EPTIDE");
//mass = calculator.CalcPeptideIonMass(peptide, IonType.xIon, option);
//Console.WriteLine((mass+Hydrogen)/1);
//peptide = new GeneralPeptide("1", "TIDE");
//mass = calculator.CalcPeptideIonMass(peptide, IonType.xIon, option);
//Console.WriteLine((mass+Hydrogen)/1);
//2322.82285937
Console.WriteLine(mass);
Console.WriteLine(mass / 1.0 + Hydrogen);
//Console.WriteLine(calculator.CalcPPM(mass, 329.09256));
Console.Read();
}
