/// <summary> /// Parses a string sequence of amino acids characters into a peptide object /// </summary> /// <param name="sequence"></param> /// <returns></returns> private void ParseSequence(string sequence) { bool inMod = false; bool cterminalMod = false; // n or c terminal modification int index = 0; double monoMass = 0; StringBuilder modSb = new StringBuilder(10); foreach (char letter in sequence) { if (inMod) { if (letter == ']') { inMod = false; // end the modification phase string modString = modSb.ToString(); modSb.Clear(); IHasMass modification; try { modification = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula(modString)); } catch (MzLibException) { if (double.TryParse(modString, out double mass)) { modification = new ModWithOnlyMass(mass); } else { throw new MzLibException("Unable to correctly parse the following modification: " + modString); } } monoMass += modification.MonoisotopicMass; if (_modifications == null) { _modifications = new IHasMass[Length + 2]; } if (cterminalMod) { _modifications[index + 1] = modification; } else { _modifications[index] = modification; } cterminalMod = false; } else { modSb.Append(letter); } } else { //char upperletter = char.ToUpper(letter); // moved to amino acid dictionary if (Residue.TryGetResidue(letter, out Residue residue)) { residues[index++] = residue; monoMass += residue.MonoisotopicMass; } else { switch (letter) { case '[': // start of a modification inMod = true; break; case '-': // End of an n-terminus mod or start of a c-terminus mod cterminalMod = (index > 0); break; default: throw new MzLibException(string.Format(CultureInfo.InvariantCulture, "Amino Acid Letter {0} does not exist in the Amino Acid Dictionary. {0} is also not a valid character", letter)); } } } } if (inMod) { throw new MzLibException("Couldn't find the closing ] for a modification in this sequence: " + sequence); } Length = index; MonoisotopicMass += monoMass; Array.Resize(ref residues, Length); if (_modifications != null) { Array.Resize(ref _modifications, Length + 2); } }
public OldSchoolChemicalFormulaModification(OldSchoolChemicalFormulaModification other) : this(ChemicalFormula.ParseFormula(other.ThisChemicalFormula.Formula), other.Name, other.Sites) { }