protected virtual void SetFixedMods(AminoAcidPolymer peptide)
{
foreach (Modification mod in _fixedMods)
{
peptide.SetModification(mod);
}
}
public Fragment(FragmentTypes type, int number, double monoisotopicMass, AminoAcidPolymer parent)
{
Type = type;
Number = number;
Parent = parent;
MonoisotopicMass = monoisotopicMass;
}
/// <summary>
/// Create a new peptide based on another amino acid polymer
/// </summary>
/// <param name="aminoAcidPolymer">The other amino acid polymer to copy</param>
/// <param name="includeModifications">Whether to copy the modifications to the new peptide</param>
public Peptide(AminoAcidPolymer aminoAcidPolymer, bool includeModifications = true)
: base(aminoAcidPolymer, includeModifications)
{
Parent = aminoAcidPolymer;
StartResidue = 0;
EndResidue = Length - 1;
}
internal IEnumerable <int> GetModifiableSites(AminoAcidPolymer peptide)
{
if (Sites == ModificationSites.None || peptide == null)
{
yield break;
}
if ((Sites & ModificationSites.NPep) == ModificationSites.NPep)
{
yield return(0);
}
int i = 1;
foreach (AminoAcid aa in peptide.AminoAcids)
{
if ((Sites & aa.Site) == aa.Site)
{
yield return(i);
}
i++;
}
if ((Sites & ModificationSites.PepC) == ModificationSites.PepC)
{
yield return(i);
}
}
/// <summary>
/// Parse and apply an omssa modification line to this current amino acid polymer
/// </summary>
/// <param name="aap"></param>
/// <param name="omssaModificationLine"></param>
/// <returns></returns>
public static AminoAcidPolymer SetModifications(this AminoAcidPolymer aap, string omssaModificationLine)
{
if (string.IsNullOrEmpty(omssaModificationLine))
{
return(aap);
}
foreach (Tuple <Modification, int> modPosition in OmssaModification.ParseModificationLine(omssaModificationLine))
{
int pos = modPosition.Item2;
if (pos == 0)
{
aap.NTerminusModification = modPosition.Item1;
}
else if (pos == aap.Length + 1)
{
aap.CTerminusModification = modPosition.Item1;
}
else
{
aap.SetModification(modPosition.Item1, pos);
}
}
return(aap);
}
public Peptide(AminoAcidPolymer aminoAcidPolymer, int firstResidue, int length, bool includeModifications = true)
: base(aminoAcidPolymer, firstResidue, length, includeModifications)
{
Parent = aminoAcidPolymer;
StartResidue = firstResidue;
EndResidue = firstResidue + length - 1;
PreviousAminoAcid = aminoAcidPolymer.GetResidue(StartResidue - 1);
NextAminoAcid = aminoAcidPolymer.GetResidue(EndResidue + 1);
}
protected virtual void SetVariableMods(AminoAcidPolymer peptide, string modname, int residue)
{
IMass mod;
if (_variableMods.TryGetValue(modname, out mod))
{
peptide.SetModification(mod, residue);
}
}
public void TestGetDigestionPointsWithMethionineAndSemiDigestion()
{
var ok = AminoAcidPolymer.GetDigestionPointsAndLengths("MDERLEK", new List <TestProtease> {
new TestProtease()
}, 0, 0, 10000, true, true).ToList();
IEqualityComparer <DigestionPointAndLength> jj = new OkComparer();
var yee = new HashSet <DigestionPointAndLength>(ok, jj);
Assert.AreEqual(1 + 3 + 1 + (8 - 1) + 1 + 1, yee.Count);
}
public static AminoAcidPolymer SetModifications(this AminoAcidPolymer aap, string mods)
{
if (string.IsNullOrEmpty(mods))
{
return(aap);
}
foreach (Tuple <Modification, int> modPosition in OmssaModification.ParseModificationLine(mods))
{
aap.SetModification(modPosition.Item1, modPosition.Item2);
}
return(aap);
}
public void TestGetDigestionPointsWithMethionine()
{
var ok = AminoAcidPolymer.GetDigestionPointsAndLengths("MDERLEKDERLE", new List <TestProtease> {
new TestProtease()
}, 0, 0, 10000, true, false).ToList();
Assert.AreEqual(1, ok[0].Index); // Methionine cleaved, digestion is at 1
Assert.AreEqual(4, ok[0].Length); // The test protease cleaves at index 4, so after L.
Assert.AreEqual(0, ok[1].Index); // Regular digestion 1
Assert.AreEqual(5, ok[1].Length); // Regular digestion 1
Assert.AreEqual(5, ok[2].Index); // Regular digestion 2
Assert.AreEqual(1, ok[2].Length); // Regular digestion 2
Assert.AreEqual(6, ok[3].Index); // Regular digestion 3
Assert.AreEqual(6, ok[3].Length); // Regular digestion 3
}
public void CleavageIndicesTest()
{
IEnumerable <IProtease> proteases = new List <TestProtease> {
new TestProtease()
};
var ok1 = AminoAcidPolymer.GetCleavageIndexes("ACDEFG", proteases, true).ToList();
var ok2 = AminoAcidPolymer.GetCleavageIndexes("ACDEFG", proteases, false).ToList();
var ok3 = AminoAcidPolymer.GetCleavageIndexes("ACDE", proteases, true).ToList();
var ok4 = AminoAcidPolymer.GetCleavageIndexes("ACDE", proteases, false).ToList();
Assert.AreEqual(3, ok1.Count());
Assert.AreEqual(2, ok2.Count());
Assert.AreEqual(4, ok3.Count());
Assert.AreEqual(2, ok4.Count());
}
public Peptide(string sequence, AminoAcidPolymer parent, int startResidue)
: base(sequence)
{
Parent = parent;
StartResidue = startResidue;
EndResidue = startResidue + Length - 1;
if (parent != null)
{
if (StartResidue > 0)
PreviousAminoAcid = parent.AminoAcids[StartResidue - 1];
if (EndResidue < parent.Length - 1)
NextAminoAcid = parent.AminoAcids[EndResidue + 1];
}
}
public static string WriteModificationString(AminoAcidPolymer polymer)
{
IMass[] mods = polymer.GetModifications();
int count = mods.Length;
StringBuilder sb = new StringBuilder();
for (int i = 0; i < count; i++)
{
if (mods[i] == null)
{
continue;
}
sb.Append(mods[i].ToString());
sb.Append(":");
sb.Append(i);
sb.Append(',');
}
if (sb.Length > 0)
{
sb.Remove(sb.Length - 1, 1);
}
return(sb.ToString());
}
public ChemicalFormulaFragment(FragmentTypes type, int number, ChemicalFormula formula, AminoAcidPolymer parent)
: base(type, number, formula.MonoisotopicMass, parent)
{
ChemicalFormula = new ChemicalFormula(formula);
}
public new bool Equals(AminoAcidPolymer other)
{
return(base.Equals(other));
}
public ChemicalFormulaFragment(FragmentTypes type, int number, ChemicalFormula formula, AminoAcidPolymer parent)
: base(type, number, formula.MonoisotopicMass, parent)
{
ChemicalFormula = new ChemicalFormula(formula);
}
public ChemicalFormulaFragment(FragmentTypes type, int number, string chemicalFormula, AminoAcidPolymer parent)
: this(type, number, new ChemicalFormula(chemicalFormula), parent)
{
}
private void SetDynamicMods(AminoAcidPolymer peptide, string modifications)
{
if (peptide == null || string.IsNullOrEmpty(modifications))
return;
foreach (string modification in modifications.Split(',',';'))
{
string[] modParts = modification.Trim().Split(':');
int location = 0;
if (int.TryParse(modParts[1], out location))
{
SetVariableMods(peptide, modParts[0], location);
OmssaModification omssaModification;
if (OmssaModification.TryGetModification(modParts[0], out omssaModification))
{
peptide.SetModification(omssaModification, location);
}
else
{
throw new ArgumentException("Could not find the following OMSSA modification: " + modParts[0]);
}
}
else
{
throw new ArgumentException("Could not parse the residue position for the following OMSSA modification: " + modification);
}
}
}
public int MissedCleavages(AminoAcidPolymer aminoAcidSequence)
{
throw new NotImplementedException();
}
public IEnumerable <int> GetDigestionSites(AminoAcidPolymer aminoAcidSequence)
{
return(GetDigestionSites(aminoAcidSequence.BaseSequence));
}
public Peptide(string sequence, AminoAcidPolymer parent)
: this(sequence, parent, 0)
{
}
protected virtual void SetVariableMods(AminoAcidPolymer peptide, string modname, int residue)
{
IMass mod;
if (_variableMods.TryGetValue(modname, out mod))
{
peptide.SetModification(mod, residue);
}
}
public void DigestionTest()
{
IProtease protease = new TestProtease();
Assert.AreEqual(6, AminoAcidPolymer.Digest(_mockPeptideEveryAminoAcid, protease).Count());
}
protected virtual void SetFixedMods(AminoAcidPolymer peptide)
{
foreach (Modification mod in _fixedMods)
{
peptide.SetModification(mod);
}
}
public static string WriteModificationString(AminoAcidPolymer polymer)
{
IMass[] mods = polymer.GetModifications();
int count = mods.Length;
StringBuilder sb = new StringBuilder();
for (int i = 0; i < count; i++)
{
if (mods[i] == null)
continue;
sb.Append(mods[i].ToString());
sb.Append(":");
sb.Append(i);
sb.Append(',');
}
if(sb.Length > 0) {
sb.Remove(sb.Length - 1, 1);
}
return sb.ToString();
}
public ChemicalFormulaFragment(FragmentTypes type, int number, string chemicalFormula, AminoAcidPolymer parent)
: this(type, number, new ChemicalFormula(chemicalFormula), parent)
{
}
public FragmentCollection(IEnumerable <Fragment> fragments, AminoAcidPolymer parent = null)
{
_fragments = new List <Fragment>(fragments);
_parent = parent;
}
public FragmentCollection(AminoAcidPolymer parent = null)
{
_fragments = new List <Fragment>();
_parent = parent;
}
