///// <summary>
///// Adds the element.
///// </summary>
///// <param name="element">The element.</param>
///// <param name="count">The count.</param>
//public void AddElement(IElement element, int count)
//{
// _elements.Add(new EntityCardinality<IElement>(element, count));
//}
/// <summary>
/// Waters the specified element provider.
/// </summary>
/// <param name="elementProvider">The element provider.</param>
/// <returns></returns>
public static ChemicalFormula Water(IElementProvider elementProvider)
{
return(new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(elementProvider.GetElement(1), 2),
new EntityCardinality <IElement>(elementProvider.GetElement(8), 1)
}));
}
/// <summary>
/// Initializes a new instance of the <see cref="ProteoformGroupFactory"/> class.
/// </summary>
/// <param name="elementProvider">The element provider.</param>
/// <param name="residueProvider">The residue provider.</param>
public ProteoformGroupFactory(IElementProvider elementProvider, IResidueProvider residueProvider)
{
_elementProvider = elementProvider;
_residueProvider = residueProvider;
_water = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement(1), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement(8), 1),
});
}
/// <summary>
/// Initializes a new instance of the <see cref="MockUnimodCompositionAtomProvider"/> class.
/// </summary>
/// <param name="elementProvider">The element provider.</param>
public MockUnimodCompositionAtomProvider(IElementProvider elementProvider)
{
_elementProvider = elementProvider;
_hydrogen = new UnimodCompositionAtom("H", "Hydrogen", new[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement(1), 1)
});
_carbon = new UnimodCompositionAtom("C", "Carbon", new[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement(6), 1)
});
}
/// <summary>
/// Gets the chemical formula.
/// </summary>
/// <param name="modification">The modification.</param>
/// <returns></returns>
protected override IChemicalFormula?GetChemicalFormula(UniprotModification modification)
{
string?formula = modification.CorrectionFormula;
if (string.IsNullOrEmpty(formula))
{
return(null);
}
string[] cells = formula.Split(' ');
var elements = new List <IEntityCardinality <IElement> >();
for (int i = 0; i < cells.Length; i++)
{
// Find last index for element name
int j = cells[i].Length - 1;
while (char.IsDigit(cells[i][j]) || cells[i][j] == '-')
{
j--;
}
string elementSymbol = cells[i].Substring(0, j + 1);
int count = Convert.ToInt32(cells[i].Substring(j + 1));
if (count != 0)
{
elements.Add(new EntityCardinality <IElement>(_elementProvider.GetElement(elementSymbol), count));
}
}
return(new ChemicalFormula(elements));
}
/// <summary>
/// Gets the unimod composition atom.
/// </summary>
/// <param name="symbol">The symbol.</param>
/// <returns></returns>
public UnimodCompositionAtom GetUnimodCompositionAtom(string symbol)
{
if (symbol == "H")
{
return(_hydrogen);
}
else if (symbol == "C")
{
return(_carbon);
}
else
{
try
{
IElement element = _elementProvider.GetElement(symbol);
if (element == null)
{
return(null);
}
else
{
return(new UnimodCompositionAtom(symbol, element.Symbol, new[]
{
new EntityCardinality <IElement>(element, 1)
}));
}
}
catch
{
return(null);
}
}
}
/// <summary>
/// Gets the chemical formula.
/// </summary>
/// <param name="modification">The modification.</param>
/// <returns></returns>
protected override IChemicalFormula?GetChemicalFormula(PsiModTerm modification)
{
string?formula = modification.DiffFormula;
if (string.IsNullOrEmpty(formula) || formula == "none")
{
return(null);
}
string[] cells = formula.Split(' ');
var elements = new List <IEntityCardinality <IElement> >();
for (int i = 0; i < cells.Length; i += 2)
{
if (cells[i] == "+")
{
continue;
}
int count = Convert.ToInt32(cells[i + 1]);
if (count != 0)
{
// Handle formal charge by adding or removing hydrogen atoms
if (modification.FormalCharge != 0 && cells[i] == "H")
{
count -= modification.FormalCharge;
}
if (cells[i][0] == '(') // Fixed isotope.
{
int endIsotopeIndex = cells[i].IndexOf(')');
string isotopeStr = cells[i].Substring(1, endIsotopeIndex - 1);
int fixedIsotope = Convert.ToInt32(isotopeStr);
elements.Add(new EntityCardinality <IElement>(_elementProvider.GetElement(cells[i].Substring(endIsotopeIndex + 1), fixedIsotope), count));
}
else
{
elements.Add(new EntityCardinality <IElement>(_elementProvider.GetElement(cells[i]), count));
}
}
}
return(new ChemicalFormula(elements));
}
private BrnoModification[] CreateModificationArray(IElementProvider elementProvider)
{
var mods = new BrnoModification[7];
var h = elementProvider.GetElement(1);
var c = elementProvider.GetElement(6);
var o = elementProvider.GetElement(8);
var p = elementProvider.GetElement(15);
mods[0] = new BrnoModification("B:ac", new[]
{
new EntityCardinality <IElement>(c, 2),
new EntityCardinality <IElement>(h, 2),
new EntityCardinality <IElement>(o, 1)
});
mods[1] = new BrnoModification("B:me1", new[]
{
new EntityCardinality <IElement>(c, 1),
new EntityCardinality <IElement>(h, 2)
});
var me2 = new[]
{
new EntityCardinality <IElement>(c, 2),
new EntityCardinality <IElement>(h, 4)
};
mods[2] = new BrnoModification("B:me2s", me2);
mods[3] = new BrnoModification("B:me2a", me2);
mods[4] = new BrnoModification("B:me2", me2);
mods[5] = new BrnoModification("B:me3", new[]
{
new EntityCardinality <IElement>(c, 3),
new EntityCardinality <IElement>(h, 6)
});
mods[6] = new BrnoModification("B:ph", new[]
{
new EntityCardinality <IElement>(h, 1),
new EntityCardinality <IElement>(o, 3),
new EntityCardinality <IElement>(p, 1),
});
return(mods);
}
private void AddElement(Dictionary <string, UnimodCompositionAtom> atoms, IElementProvider elementProvider,
string symbol, string name, string elementSymbol, int?fixedIsotopeNumber = null)
{
IElement element = elementProvider.GetElement(elementSymbol, fixedIsotopeNumber);
atoms.Add(symbol, new UnimodCompositionAtom(symbol, name, new[]
{
new EntityCardinality <IElement>(element, 1)
}));
}
private void AddElement(Dictionary <string, UnimodCompositionAtom> atoms, IElementProvider elementProvider,
string symbol, string name)
{
IElement element = elementProvider.GetElement(symbol);
atoms.Add(symbol, new UnimodCompositionAtom(symbol, name, new[]
{
new EntityCardinality <IElement>(element, 1)
}));
}
public void FormulaLookup()
{
string formulaString = "C2H2O";
ProFormaDescriptor proFormaDescriptor = new ProFormaDescriptor(ProFormaKey.Formula, formulaString);
ChemicalFormula chemicalFormula = new ChemicalFormula(new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("H"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 1),
});
var proteoformModification = _formulaLookup.GetModification(proFormaDescriptor);
Assert.IsInstanceOf(typeof(IHasChemicalFormula), proteoformModification);
var formulaMod = (IHasChemicalFormula)proteoformModification;
Assert.AreEqual(chemicalFormula, formulaMod.GetChemicalFormula());
}
/// <summary>
/// Gets the chemical formula.
/// </summary>
/// <param name="modification">The modification.</param>
/// <returns></returns>
protected override IChemicalFormula?GetChemicalFormula(ResidModification modification)
{
string?formula = modification.DiffFormula;
if (string.IsNullOrEmpty(formula))
{
return(null);
}
string[] cells = formula.Split(' ');
var elements = new List <IEntityCardinality <IElement> >();
for (int i = 0; i < cells.Length; i += 2)
{
if (cells[i] == "+")
{
continue;
}
int count = Convert.ToInt32(cells[i + 1]);
if (count != 0)
{
// Handle formal charge by adding or removing hydrogen atoms
if (modification.FormalCharge != 0 && cells[i] == "H")
{
count -= modification.FormalCharge;
}
elements.Add(new EntityCardinality <IElement>(_elementProvider.GetElement(cells[i]), count));
}
}
return(new ChemicalFormula(elements));
}
private Dictionary <string, UnimodCompositionAtom> CreateDictionary(IElementProvider elementProvider)
{
var atoms = new Dictionary <string, UnimodCompositionAtom>();
var h = elementProvider.GetElement(1);
var c = elementProvider.GetElement(6);
var n = elementProvider.GetElement(7);
var o = elementProvider.GetElement(8);
var s = elementProvider.GetElement(16);
this.AddElement(atoms, elementProvider, "13C", "Carbon 13", "C", 13);
this.AddElement(atoms, elementProvider, "15N", "Nitrogen 15", "N", 15);
this.AddElement(atoms, elementProvider, "18O", "Oxygen 18", "O", 18);
this.AddElement(atoms, elementProvider, "2H", "Deuterium", "H", 2);
atoms.Add("Ac", new UnimodCompositionAtom("Ac", "Acetate", new[]
{
new EntityCardinality <IElement>(c, 2),
new EntityCardinality <IElement>(h, 3),
new EntityCardinality <IElement>(o, 2),
}));
this.AddElement(atoms, elementProvider, "Ag", "Silver");
this.AddElement(atoms, elementProvider, "Al", "Aluminium");
this.AddElement(atoms, elementProvider, "As", "Arsenic");
this.AddElement(atoms, elementProvider, "Au", "Gold");
this.AddElement(atoms, elementProvider, "B", "Boron");
this.AddElement(atoms, elementProvider, "Br", "Bromine");
this.AddElement(atoms, elementProvider, "C", "Carbon");
this.AddElement(atoms, elementProvider, "Ca", "Calcium");
this.AddElement(atoms, elementProvider, "Cd", "Cadmium");
this.AddElement(atoms, elementProvider, "Cl", "Chlorine");
this.AddElement(atoms, elementProvider, "Co", "Cobalt");
this.AddElement(atoms, elementProvider, "Cr", "Chromium");
this.AddElement(atoms, elementProvider, "Cu", "Copper");
atoms.Add("dHex", new UnimodCompositionAtom("dHex", "Deoxy-hexose", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 10),
new EntityCardinality <IElement>(o, 4),
}));
this.AddElement(atoms, elementProvider, "F", "Fluorine");
this.AddElement(atoms, elementProvider, "Fe", "Iron");
this.AddElement(atoms, elementProvider, "H", "Hydrogen");
atoms.Add("Hep", new UnimodCompositionAtom("Hep", "Heptose", new[]
{
new EntityCardinality <IElement>(c, 7),
new EntityCardinality <IElement>(h, 12),
new EntityCardinality <IElement>(o, 6),
}));
atoms.Add("Hex", new UnimodCompositionAtom("Hex", "Hexose", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 10),
new EntityCardinality <IElement>(o, 5),
}));
// Not sure about C6H8O6
atoms.Add("HexA", new UnimodCompositionAtom("HexA", "Hexuronic acid", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 8),
new EntityCardinality <IElement>(o, 6),
}));
// Not sure about C6H11O4N
atoms.Add("HexN", new UnimodCompositionAtom("HexN", "Hexosamine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 11),
new EntityCardinality <IElement>(o, 4),
new EntityCardinality <IElement>(n, 1),
}));
atoms.Add("HexNAc", new UnimodCompositionAtom("HexNAc", "N-Acetyl Hexosamine", new[]
{
new EntityCardinality <IElement>(c, 8),
new EntityCardinality <IElement>(h, 13),
new EntityCardinality <IElement>(o, 5),
new EntityCardinality <IElement>(n, 1),
}));
this.AddElement(atoms, elementProvider, "Hg", "Mercury");
this.AddElement(atoms, elementProvider, "I", "Iodine");
this.AddElement(atoms, elementProvider, "K", "Potassium");
// Should be Hex(2) + HexA
atoms.Add("Kdn", new UnimodCompositionAtom("Kdn", "3-deoxy-d-glycero-D-galacto-nonulosonic acid", new[]
{
new EntityCardinality <IElement>(c, 18),
new EntityCardinality <IElement>(h, 28),
new EntityCardinality <IElement>(o, 16),
}));
// Never used
//atoms.Add("Kdo", new UnimodCompositionAtom("13C", "2-keto-3-deoxyoctulosonic acid", new[]
//{
// new EntityCardinality<IElement>(c, 0),
// new EntityCardinality<IElement>(h, 0),
// new EntityCardinality<IElement>(o, 0),
//}));
this.AddElement(atoms, elementProvider, "Li", "Lithium");
atoms.Add("Me", new UnimodCompositionAtom("Me", "Methyl", new[]
{
new EntityCardinality <IElement>(c, 1),
new EntityCardinality <IElement>(h, 2),
}));
this.AddElement(atoms, elementProvider, "Mg", "Magnesium");
this.AddElement(atoms, elementProvider, "Mn", "Manganese");
this.AddElement(atoms, elementProvider, "Mo", "Molybdenum");
this.AddElement(atoms, elementProvider, "N", "Nitrogen");
this.AddElement(atoms, elementProvider, "Na", "Sodium");
atoms.Add("NeuAc", new UnimodCompositionAtom("NeuAc", "N-acetyl neuraminic acid", new[]
{
new EntityCardinality <IElement>(c, 11),
new EntityCardinality <IElement>(h, 17),
new EntityCardinality <IElement>(o, 8),
new EntityCardinality <IElement>(n, 1),
}));
atoms.Add("NeuGc", new UnimodCompositionAtom("NeuGc", "N-glycoyl neuraminic acid", new[]
{
new EntityCardinality <IElement>(c, 11),
new EntityCardinality <IElement>(h, 17),
new EntityCardinality <IElement>(o, 9),
new EntityCardinality <IElement>(n, 1),
}));
this.AddElement(atoms, elementProvider, "Ni", "Nickel");
this.AddElement(atoms, elementProvider, "O", "Oxygen");
this.AddElement(atoms, elementProvider, "P", "Phosphorous");
this.AddElement(atoms, elementProvider, "Pd", "Palladium");
atoms.Add("Pent", new UnimodCompositionAtom("Pent", "Pentose", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 8),
new EntityCardinality <IElement>(o, 4),
}));
// Never used
//atoms.Add("Phos", new UnimodCompositionAtom("13C", "Phosphate", new[]
//{
// new EntityCardinality<IElement>(c, 0),
// new EntityCardinality<IElement>(h, 0),
// new EntityCardinality<IElement>(o, 0),
// new EntityCardinality<IElement>(n, 0),
//}));
this.AddElement(atoms, elementProvider, "Pt", "Platinum");
this.AddElement(atoms, elementProvider, "Ru", "Ruthenium");
this.AddElement(atoms, elementProvider, "S", "Sulphur");
this.AddElement(atoms, elementProvider, "Se", "Selenium");
atoms.Add("Sulf", new UnimodCompositionAtom("Sulf", "Sulphate", new[]
{
new EntityCardinality <IElement>(s, 1),
new EntityCardinality <IElement>(o, 3),
}));
atoms.Add("Water", new UnimodCompositionAtom("Water", "Water", new[]
{
new EntityCardinality <IElement>(h, 2),
new EntityCardinality <IElement>(o, 1),
}));
this.AddElement(atoms, elementProvider, "Zn", "Zinc");
return(atoms);
}
private static IEntityCardinality <IElement> GetElement(ReadOnlySpan <char> symbol, int?isotope, int count, IElementProvider elementProvider)
{
return(new EntityCardinality <IElement>(elementProvider.GetElement(symbol, isotope), count));
}
private IResidue[] CreateResideArray(IElementProvider elementProvider)
{
var aaMass = new AminoAcid[26];
var h = elementProvider.GetElement(1);
var c = elementProvider.GetElement(6);
var n = elementProvider.GetElement(7);
var o = elementProvider.GetElement(8);
var s = elementProvider.GetElement(16);
aaMass[0] = new AminoAcid('A', "Alanine", new[]
{
new EntityCardinality <IElement>(c, 3),
new EntityCardinality <IElement>(h, 5),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[17] = new AminoAcid('R', "Arginine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 12),
new EntityCardinality <IElement>(n, 4),
new EntityCardinality <IElement>(o, 1),
});
aaMass[13] = new AminoAcid('N', "Asparagine", new[]
{
new EntityCardinality <IElement>(c, 4),
new EntityCardinality <IElement>(h, 6),
new EntityCardinality <IElement>(n, 2),
new EntityCardinality <IElement>(o, 2),
});
aaMass[3] = new AminoAcid('D', "Aspartic Acid", new[]
{
new EntityCardinality <IElement>(c, 4),
new EntityCardinality <IElement>(h, 5),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 3),
});
aaMass[2] = new AminoAcid('C', "Cysteine", new[]
{
new EntityCardinality <IElement>(c, 3),
new EntityCardinality <IElement>(h, 5),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
new EntityCardinality <IElement>(s, 1),
});
aaMass[4] = new AminoAcid('E', "Glutamic acid", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 7),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 3),
});
aaMass[16] = new AminoAcid('Q', "Glutamine", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 8),
new EntityCardinality <IElement>(n, 2),
new EntityCardinality <IElement>(o, 2),
});
aaMass[6] = new AminoAcid('G', "Glycine", new[]
{
new EntityCardinality <IElement>(c, 2),
new EntityCardinality <IElement>(h, 3),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[7] = new AminoAcid('H', "Histidine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 7),
new EntityCardinality <IElement>(n, 3),
new EntityCardinality <IElement>(o, 1),
});
aaMass[8] = new AminoAcid('I', "Isoleucine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 11),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[11] = new AminoAcid('L', "Leucine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 11),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[10] = new AminoAcid('K', "Lysine", new[]
{
new EntityCardinality <IElement>(c, 6),
new EntityCardinality <IElement>(h, 12),
new EntityCardinality <IElement>(n, 2),
new EntityCardinality <IElement>(o, 1),
});
aaMass[12] = new AminoAcid('M', "Methionine", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 9),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
new EntityCardinality <IElement>(s, 1),
});
aaMass[5] = new AminoAcid('F', "Phenylalanine", new[]
{
new EntityCardinality <IElement>(c, 9),
new EntityCardinality <IElement>(h, 9),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[15] = new AminoAcid('P', "Proline", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 7),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
aaMass[14] = new AminoAcid('O', "Pyrrolysine", new[]
{
new EntityCardinality <IElement>(c, 12),
new EntityCardinality <IElement>(h, 19),
new EntityCardinality <IElement>(n, 3),
new EntityCardinality <IElement>(o, 2),
});
aaMass[20] = new AminoAcid('U', "Selenocysteine", new[]
{
new EntityCardinality <IElement>(c, 3),
new EntityCardinality <IElement>(h, 5),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
new EntityCardinality <IElement>(elementProvider.GetElement("Se"), 1),
});
aaMass[18] = new AminoAcid('S', "Serine", new[]
{
new EntityCardinality <IElement>(c, 3),
new EntityCardinality <IElement>(h, 5),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 2),
});
aaMass[19] = new AminoAcid('T', "Threonine", new[]
{
new EntityCardinality <IElement>(c, 4),
new EntityCardinality <IElement>(h, 7),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 2),
});
aaMass[22] = new AminoAcid('W', "Tryptophan", new[]
{
new EntityCardinality <IElement>(c, 11),
new EntityCardinality <IElement>(h, 10),
new EntityCardinality <IElement>(n, 2),
new EntityCardinality <IElement>(o, 1),
});
aaMass[24] = new AminoAcid('Y', "Tyrosine", new[]
{
new EntityCardinality <IElement>(c, 9),
new EntityCardinality <IElement>(h, 9),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 2),
});
aaMass[21] = new AminoAcid('V', "Valine", new[]
{
new EntityCardinality <IElement>(c, 5),
new EntityCardinality <IElement>(h, 9),
new EntityCardinality <IElement>(n, 1),
new EntityCardinality <IElement>(o, 1),
});
return(aaMass);
}
