public void TestGetCarbonRange()
{
string peptide = "MAAHRRWLLMSFLFLEVILLEAAK";
Aminoacids aas = new Aminoacids();
double residueMass = aas.MonoResiduesMass(peptide);
int expect = aas.AtomCount(peptide, Atom.C);
CarbonRange carbonRange = new ProteinCarbonRangePredictor().GetCarbonRange(residueMass);
Assert.Greater(expect, carbonRange.Min);
Assert.Less(expect, carbonRange.Max);
}
public void TestGetCarbonPercentAminoacid()
{
Aminoacids aas = new Aminoacids();
Aminoacid maxAA = aas.GetMaxCarbonPercentAminoacid();
Assert.AreEqual("Phe", maxAA.ThreeName);
Aminoacid minAA = aas.GetMinCarbonPercentAminoacid();
Assert.AreEqual("Cys", minAA.ThreeName);
}
//(STY* +79.96633) (M# +15.99492) (ST@ -18.00000) C=160.16523 Enzyme:Trypsin(KR) (1)
public static Aminoacids ParseModificationFromOutFileLine(string line)
{
Dictionary <char, double> map = ModificationUtils.ParseFromOutFileLine(line);
var result = new Aminoacids();
foreach (char c in map.Keys)
{
result[c].ResetMass(map[c], map[c]);
}
return(result);
}
public void TestBuildInfo()
{
var aas = new Aminoacids();
var addedMass1 = 20.3847;
var addedMass2 = 40.3847;
aas['*'].ResetMass(addedMass1, addedMass1);
aas['#'].ResetMass(addedMass2, addedMass2);
var s1 = aas.BuildInfo("R.A#D*K.L");
Assert.AreEqual(3, s1.Count);
Assert.AreEqual('A', s1[0].Aminoacid);
Assert.AreEqual(aas['A'].MonoMass + addedMass2, s1[0].Mass, 0.0001);
Assert.AreEqual(aas['D'].MonoMass + addedMass1, s1[1].Mass, 0.0001);
Assert.AreEqual(aas['K'].MonoMass, s1[2].Mass, 0.0001);
}
public void TestPeptideAtomCompositionCalculator()
{
AtomComposition nterm = new AtomComposition("H");
AtomComposition cterm = new AtomComposition("OH");
Aminoacids aas = new Aminoacids();
PeptideAtomCompositionCalculator calc = new PeptideAtomCompositionCalculator(nterm, cterm, aas);
//Terminal only
IPeptideInfo terminalInfo = new IdentifiedPeptideInfo("", 0.0, 0);
AtomComposition terminalActual = calc.GetAtomComposition(terminalInfo);
Assert.AreEqual(2, terminalActual[Atom.H]);
Assert.AreEqual(1, terminalActual[Atom.O]);
//A:C3H5NO
IPeptideInfo peptideInfo = new IdentifiedPeptideInfo("A", 0.0, 0);
AtomComposition peptideActual = calc.GetAtomComposition(peptideInfo);
Assert.AreEqual(3, peptideActual[Atom.C]);
Assert.AreEqual(7, peptideActual[Atom.H]);
Assert.AreEqual(1, peptideActual[Atom.N]);
Assert.AreEqual(2, peptideActual[Atom.O]);
}
public Aminoacids(Aminoacids source)
{
this.mAminoacids = source.mAminoacids;
}
public PeptideWeightFilter(Aminoacids aminoacids, double minWeight, double maxWeight)
{
this.aminoacids = aminoacids;
this.minWeight = minWeight;
this.maxWeight = maxWeight;
}
public AveragePeptideMassCalculator(Aminoacids aas)
: base(NTERM, CTERM)
{
this.aas = aas;
}
public AveragePeptideMassCalculator(Aminoacids aas, double nterm, double cterm)
: base(nterm, cterm)
{
this.aas = aas;
}
public MonoisotopicPeptideMassCalculator(Aminoacids aas)
: base(NTERM, CTERM)
{
this.aas = aas;
}
public MonoisotopicPeptideMassCalculator(Aminoacids aas, double nterm, double cterm)
: base(nterm, cterm)
{
this.aas = aas;
}