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);
        }
Beispiel #2
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        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);
        }
Beispiel #4
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        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;
 }