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();
}
}
static void Main(string[] args)
{
Loaders.LoadElements("ok.txt");
List <char> aminoAcidsToConsider = new List <char>()
{
'G', 'A', 'S', 'P', 'V', 'T', 'C', 'I', 'L', 'N', 'D', 'Q', 'K', 'E', 'M', 'H', 'F', 'R', 'Y', 'W'
};
List <Tuple <AminoAcid, AminoAcid, double> > tuples = new List <Tuple <AminoAcid, AminoAcid, double> >();
foreach (var ok in aminoAcidsToConsider)
{
var aa1 = AminoAcid.GetResidue(ok);
foreach (var ok2 in aminoAcidsToConsider)
{
var aa2 = AminoAcid.GetResidue(ok2);
var diff = aa2.MonoisotopicMass - aa1.MonoisotopicMass;
var tuple = new Tuple <AminoAcid, AminoAcid, double>(aa1, aa2, diff);
tuples.Add(tuple);
}
}
// IGNORE ALL ZERO MASSES AND SUBSTITUTIONS TO ISOLEUCINE
tuples = tuples.OrderBy(b => b.Item3).Where(b => b.Item3 != 0).ToList();
Console.WriteLine("FOR EXCEL");
double prevDiff = double.MinValue;
foreach (var ok in tuples)
{
if (prevDiff > ok.Item3 - tol && prevDiff < ok.Item3 + tol)
{
Console.Write(" or " + ok.Item1.Name + "->" + ok.Item2.Name);
}
else
{
Console.Write("\n" + ok.Item3 + ";" + ok.Item1.Name + "->" + ok.Item2.Name);
prevDiff = ok.Item3;
}
}
Console.WriteLine("\n\nFOR PTMLIST");
foreach (var ok in tuples)
{
Console.WriteLine("ID " + ok.Item1.Name + "->" + ok.Item2.Name);
Console.WriteLine("FT MOD_RES");
Console.WriteLine("TG " + ok.Item1.Name);
Console.WriteLine("PP Anywhere");
Console.WriteLine("MM " + ok.Item3);
Console.WriteLine("//");
}
Console.WriteLine("\n\nFOR EXCEL");
aminoAcidsToConsider.Reverse();
foreach (var ok in aminoAcidsToConsider)
{
var aa1 = AminoAcid.GetResidue(ok);
Console.WriteLine(-aa1.MonoisotopicMass + ";" + aa1.Name + " not here");
}
Console.WriteLine("\n\nFOR PTMLIST");
foreach (var ok in aminoAcidsToConsider)
{
var aa1 = AminoAcid.GetResidue(ok);
Console.WriteLine("ID " + aa1.Name + " not here");
Console.WriteLine("FT MOD_RES");
Console.WriteLine("TG " + aa1.Name);
Console.WriteLine("PP Anywhere");
Console.WriteLine("MM -" + aa1.MonoisotopicMass);
Console.WriteLine("//");
}
Console.Read();
}
public void GetResidueBy3LetterSymbol()
{
AminoAcid aa = AminoAcid.GetResidue("Ala");
Assert.AreEqual(aa.Name, "Alanine");
}
public void GetResidueByName()
{
AminoAcid aa = AminoAcid.GetResidue("Alanine");
Assert.AreEqual(aa.Name, "Alanine");
}
public void GetResidueByCharacterString()
{
AminoAcid aa = AminoAcid.GetResidue("A");
Assert.AreEqual(aa.Name, "Alanine");
}
