public ProductMassesMightHave ProductMassesMightHaveDuplicatesAndNaNs(List <ProductType> productTypes)
{
int massLen = 0;
bool containsAdot = productTypes.Contains(ProductType.Adot);
bool containsB = productTypes.Contains(ProductType.B);
bool containsBnoB1 = productTypes.Contains(ProductType.BnoB1ions);
bool containsC = productTypes.Contains(ProductType.C);
bool containsX = productTypes.Contains(ProductType.X);
bool containsY = productTypes.Contains(ProductType.Y);
bool containsZdot = productTypes.Contains(ProductType.Zdot);
if (containsAdot)
{
throw new NotImplementedException();
}
if (containsBnoB1)
{
massLen += compactPeptide.NTerminalMasses.Length - 1;
}
if (containsB)
{
massLen += compactPeptide.NTerminalMasses.Length;
}
if (containsC)
{
massLen += compactPeptide.NTerminalMasses.Length;
}
if (containsX)
{
throw new NotImplementedException();
}
if (containsY)
{
massLen += compactPeptide.CTerminalMasses.Length;
}
if (containsZdot)
{
massLen += compactPeptide.CTerminalMasses.Length;
}
ProductMassesMightHave productMassMightHave = new ProductMassesMightHave(massLen);
int i = 0;
int ib = 0;
int ic = 0;
for (int j = 0; j < compactPeptide.NTerminalMasses.Length; j++)
{
var hm = compactPeptide.NTerminalMasses[j];
if (containsBnoB1)
{
if (j > 0)
{
productMassMightHave.ProductMz[i] = hm;
productMassMightHave.ProductName[i] = "b" + (ib + 2).ToString();
i++;
ib++;
}
}
if (containsB)
{
productMassMightHave.ProductMz[i] = hm;
productMassMightHave.ProductName[i] = "b" + (ib + 1).ToString();
i++;
ib++;
}
if (containsC)
{
productMassMightHave.ProductMz[i] = hm + nitrogenAtomMonoisotopicMass + 3 * hydrogenAtomMonoisotopicMass;
productMassMightHave.ProductName[i] = "c" + (ic + 1).ToString();
i++;
ic++;
}
}
int iy = compactPeptide.CTerminalMasses.Length - 1;
int iz = compactPeptide.CTerminalMasses.Length - 1;
for (int j = 0; j < compactPeptide.CTerminalMasses.Length; j++)
{
var hm = compactPeptide.CTerminalMasses[j];
if (containsY)
{
productMassMightHave.ProductMz[i] = hm + waterMonoisotopicMass;
productMassMightHave.ProductName[i] = "y" + (compactPeptide.CTerminalMasses.Length - iy).ToString();
i++;
iy--;
}
if (containsZdot)
{
productMassMightHave.ProductMz[i] = hm + oxygenAtomMonoisotopicMass - nitrogenAtomMonoisotopicMass;
productMassMightHave.ProductName[i] = "z" + (compactPeptide.CTerminalMasses.Length - iz).ToString();
i++;
iz--;
}
}
return(productMassMightHave);
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMasses(PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
foreach (var ipos in linkPos)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = ipos;
List <double> x = new List <double>();
List <string> y = new List <string>();
if (crosslinker.Cleavable)
{
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort);
y.Add("PepS");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort) / 2);
y.Add("PepS2");
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong);
y.Add("PepL");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong) / 2);
y.Add("PepL2");
}
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'b')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2b" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3b" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'c')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2c" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3c" + nm.ToString());
}
}
if ((cr == 'y' || cr == 'z') && nm < length - ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'y')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2y" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3y" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'z')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2z" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3z" + nm.ToString());
}
}
if (cr == 'b' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2b" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3b" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sb" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lb" + nm.ToString());
}
}
if (cr == 'c' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2c" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3c" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sc" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lc" + nm.ToString());
}
}
if (cr == 'y' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2y" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3y" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sy" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("ly" + nm.ToString());
}
}
if (cr == 'z' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2z" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3z" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sz" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lz" + nm.ToString());
}
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
return(pmmhList);
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMassesForLoopCrosslink(PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
if (linkPos.Count() >= 2)
{
for (int ipos = 0; ipos < linkPos.Count() - 1; ipos++)
{
for (int jpos = ipos + 1; jpos < linkPos.Count(); jpos++)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = linkPos[ipos];
pmmhCurr.XlPos2 = linkPos[jpos];
List <double> x = new List <double>();
List <string> y = new List <string>();
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < linkPos[ipos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if ((cr == 'y' || cr == 'z') && nm < length - linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if (cr == 'b' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
}
if (cr == 'c' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
}
if (cr == 'y' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
}
if (cr == 'z' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
}
}
return(pmmhList);
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static ProductMassesMightHave XlCalculateTotalProductMassesForSingle(PsmCross psmCross, List <ProductType> lp, bool Charge_2_3_PrimeFragment)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
var pmmhCurr = new ProductMassesMightHave();
List <double> x = new List <double>();
List <string> y = new List <string>();
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm <= length + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'b')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2b" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3b" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'c')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2c" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3c" + nm.ToString());
}
}
if ((cr == 'y' || cr == 'z') && nm <= length + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'y')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2y" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3y" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'z')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2z" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3z" + nm.ToString());
}
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
return(pmmhCurr);
}