private IEnumerable <IList <char> > FindPeptides(double mass, char[] ignoreAA) { int index = (int)(mass / Precision); string[] combinations = emptyArray; if (Dictionary.ContainsKey(index)) { combinations = Dictionary[index].Split(','); } foreach (string comb in combinations) { bool keepIt = true; foreach (char c in comb) { if (ignoreAA.Contains(c)) { keepIt = false; } } if (keepIt) { double SeqMass = AminoAcidMasses.GetMass(comb); if (Math.Abs(SeqMass - mass) < Precision) { foreach (IList <char> str in new Permutations <char>(new List <char>(comb), GenerateOption.WithoutRepetition)) { yield return(str); } } } } }
public void TestAminoAcidMassesDefaultLysine() { var MassesList1 = new AminoAcidMasses(true, true); Assert.AreEqual(136.109162, MassesList1.AA_Masses['K']); var MassesList2 = new AminoAcidMasses(true, false); Assert.Less(MassesList2.AA_Masses['K'], 136.109162); }
public double GetMonoisotopicMassShift(char aa) { if (aa == AminoAcid) { return(MonoisotopicMassShift + AminoAcidMasses.GetMonoisotopicMass(aa)); } else { return(0); } }
public void TestAminoAcidMassesConstructor() { var MassesList1 = new AminoAcidMasses(true, false); Assert.AreEqual(131.040485, MassesList1.AA_Masses['M']); Assert.AreEqual(160.030649, MassesList1.AA_Masses['C']); var MassesList2 = new AminoAcidMasses(false, false); Assert.AreEqual(131.040485, MassesList2.AA_Masses['M']); Assert.AreEqual(103.009185, MassesList2.AA_Masses['C']); }
public List <string> GetPermutations(double mass) { List <string> results = new List <string>(); int index = (int)(mass / Precision); string[] combinations = emptyArray; if (Dictionary.ContainsKey(index)) { combinations = Dictionary[index].Split(','); } foreach (string comb in combinations) { double SeqMass = AminoAcidMasses.GetMass(comb); if (Math.Abs(SeqMass - mass) < Precision) { foreach (IList <char> str in new Permutations <char>(new List <char>(comb), GenerateOption.WithoutRepetition)) { results.Add(string.Concat(str)); } } } return(results); }
public List <PeptideView> GetPeptides(Spectrum spectrum, DBOptions options) { char[] ignoreAA = GetFixedModAA(options.fixedModifications); List <PeptideView> results = new List <PeptideView>(); //Modless and Single variable mod peptides List <Modification> allMods = new List <Modification>(options.variableModifications); foreach (Modification mod in options.fixedModifications) { allMods.Add(mod); } allMods.Add(null); foreach (Modification mod in allMods) { IEnumerable <IList <char> > enumeration; if (mod == null) { enumeration = FindPeptides(spectrum.PrecursorMass, ignoreAA); } else { enumeration = FindPeptidesWithMods(spectrum.PrecursorMass, mod); } foreach (IList <char> str in enumeration) { string sequence = string.Concat(str); double[] masses = new double[sequence.Length]; for (int i = 0; i < sequence.Length; i++) { masses[i] = AminoAcidMasses.GetMonoisotopicMass(sequence[i]); } if (mod != null) { for (int i = 0; i < sequence.Length; i++) { if (sequence[i] == mod.AminoAcid) { double[] modMasses = new List <double>(masses).ToArray(); modMasses[i] += mod.MonoisotopicMassShift; double score = DotNetMHC.Analysis.PeptideCoverage.PSMScoreMatch(modMasses, sequence.Length, spectrum.PrecursorCharge, spectrum, options); if (score > 0) { results.Add(new PeptideView(sequence, modMasses, spectrum.PrecursorMass, score, mod, i)); } } } } else { double score = DotNetMHC.Analysis.PeptideCoverage.PSMScoreMatch(masses, sequence.Length, spectrum.PrecursorCharge, spectrum, options); if (score > 0) { results.Add(new PeptideView(sequence, masses, spectrum.PrecursorMass, score)); } } } } return(results); }
public static bool Run() { //TODO test GPU instead DBOptions dbOptions = MhcSample.CreateOptions(""); Dictionary <string, int> sequences = new Dictionary <string, int>(); List <Protein> proteins = Propheus.ReadProteomeFromFasta(Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "UnitTest", "proteins.fasta"), false, dbOptions);//ETLPAMCNVYYVNCMAPLTE string sequence = proteins[0].BaseSequence; double[] proteinMasses = new double[sequence.Length]; List <double> precursors = new List <double>(); for (int i = 0; i < sequence.Length; i++) { for (int j = i + dbOptions.MinimumPeptideLength - 1; j < sequence.Length; j++) { int size = j - i + 1; if (size <= dbOptions.MaximumPeptideLength) { string subStr = sequence.Substring(i, j - i + 1); if (!sequences.ContainsKey(subStr)) { sequences.Add(subStr, 1); } else { sequences[subStr]++; } double mass = Constants.WATER_MONOISOTOPIC_MASS; for (int k = 0; k < subStr.Length; k++) { mass += AminoAcidMasses.GetMonoisotopicMass(subStr[k]); } precursors.Add(mass); } } proteinMasses[i] = AminoAcidMasses.GetMonoisotopicMass(sequence[i]); } precursors.Sort(); Queries queries = new Queries(dbOptions, precursors.ToArray()); Digestion ps = new Digestion(dbOptions); List <Protein> lProt = new List <Protein>(); lProt.Add(proteins[0]); //for each protein, build matrix of mass //Trinity_Gpu.ProteinDigest pg = new Trinity_Gpu.ProteinDigest(precursors.ToArray(), sequence.Length); //Test twice to test that precursor list stays in gpu memory for (int iter = 0; iter < 2; iter++) { Dictionary <string, int> sequencesTmp = new Dictionary <string, int>(sequences); foreach (Tuple <Peptide, int> item in ps.DigestProteomeOnTheFlyNoEnzyme(lProt, queries)) { sequencesTmp[item.Item1.BaseSequence] -= 1;//TODO add modifications } /* * foreach (Trinity_Gpu.ProteinPrecursorMatch match in pg.Execute(proteinMasses, 0.00005, 10000000))//TODO compute correct tolerance window * { * int size = match.proteinEndPos - match.proteinStartPos; * string str = sequence.Substring(match.proteinStartPos, size); * if (size >= dbOptions.MinimumPeptideLength) * { * sequencesTmp[str] -= 1;//TODO add modifications * } * }//*/ foreach (int val in sequencesTmp.Values) { if (val != 0) { return(false);//*/ } } } //pg.Dispose(); return(true); }