public CompositeCompoundList(string tableCompType, string tableSumCompName, string tableMolCompName, string tableToDeleteInMolComp, string tableConstPart, string tableConstMod, string radical1, string radical2, string radical3, string radical4, Dictionary <string, BuildingBlockList> allBuildingBlocks)
{
int limitR1R2; int limitR2R3; int limitR3R4;
BuildingBlockList R1 = allBuildingBlocks[radical1];
for (int i = 0; i < R1.Count; i++)
{
BuildingBlockList R2 = allBuildingBlocks[radical2];
if (radical1 == radical2)
{
limitR1R2 = i + 1;
}
else
{
limitR1R2 = R2.Count;
}
for (int j = 0; j < limitR1R2; j++)
{
BuildingBlockList R3 = allBuildingBlocks[radical3];
if (radical2 == radical3)
{
limitR2R3 = j + 1;
}
else
{
limitR2R3 = R3.Count;
}
for (int g = 0; g < limitR2R3; g++)
{
BuildingBlockList R4 = allBuildingBlocks[radical4];
if (radical3 == radical4)
{
limitR3R4 = g + 1;
}
else
{
limitR3R4 = R4.Count;
}
for (int f = 0; f < limitR3R4; f++)
{
string totalElemComp = R1[i].Composition + "+" + R2[j].Composition + "+" + R3[g].Composition + "+" + R4[f].Composition + "+" + tableConstMod;
totalElemComp = totalElemComp.Replace("+0", "");
totalElemComp = totalElemComp.Replace("+", "");
int totalX = R1[i].X + R2[j].X + R3[g].X + R4[f].X;
int totalY = R1[i].Y + R2[j].Y + R3[g].Y + R4[f].Y;
int totalZ = R1[i].Z + R2[j].Z + R3[g].Z + R4[f].Z;
this.Add(new CompositeCompound(tableCompType, tableSumCompName, tableMolCompName, tableToDeleteInMolComp, totalElemComp, R1[i].Name, R2[j].Name, R3[g].Name, R4[f].Name, totalX, totalY, totalZ));
}
}
}
}
}
/// <summary>
/// Generates expected lipid compounds.
/// </summary>
///
public IList <LipidCompound> GenerateLipids()
{
// init timer
var timer = Stopwatch.StartNew();
// init container
var expectedLipids = new List <LipidCompound>();
//generates FA building blocks
#region Make building bloks
BuildingBlockList NAN = new BuildingBlockList("", "", "0", "", "", "");
BuildingBlockList FAdb = new BuildingBlockList("FAdb", "FA x:y", "c*x + h*(x-y)*2 + o*2", "12-22", "y=function", "");
BuildingBlockList SPH = new BuildingBlockList("SPH", "d18:1", "c*18 + h*35 + o*1 + n", "18", "1", "2");
BuildingBlockList FA = new BuildingBlockList("", "", "", "", "", "");
FA.RemoveAt(0);
foreach (var bb in FattyAcyl.Values)
{
FA.Add(FAdb.Find(x => x.Name.Contains(bb)));
}
var allBB = new Dictionary <string, BuildingBlockList>
{
[""] = NAN,
["FAdb"] = FAdb,
["FA"] = FA,
["SPH"] = SPH
};
#endregion
#region Generate List of Candidates
CompositeCompoundList classPC = new CompositeCompoundList("PC", "PC x:y", "PC r1-r2", "FA ", "", "C8H16O4NP", "FA", "FA", "", "", allBB);
CompositeCompoundList classPCO = new CompositeCompoundList("PC O", "PC O-x:y", "PC O-r1-r2", "FA ", "", "C8H18O3NP", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPC = new CompositeCompoundList("LPC", "LPC x:y", "LPC r1", "FA ", "", "C8H18O5NP", "FA", "", "", "", allBB);
CompositeCompoundList classLPCO = new CompositeCompoundList("LPC O", "LPC O-x:y", "LPC O-r1", "FA ", "", "C8H20O4NP", "FA", "", "", "", allBB);
CompositeCompoundList classPE = new CompositeCompoundList("PE", "PE x:y", "PE r1-r2", "FA ", "", "C5H10O4NP", "FA", "FA", "", "", allBB);
CompositeCompoundList classPEO = new CompositeCompoundList("PE O", "PE O-x:y", "PE O-r1-r2", "FA ", "", "C5H12O3NP", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPE = new CompositeCompoundList("LPE", "LPE x:y", "LPE r1", "FA ", "", "C5H12O5NP", "FA", "", "", "", allBB);
CompositeCompoundList classLPEO = new CompositeCompoundList("LPE O", "LPE O-x:y", "LPE O-r1", "FA ", "", "C5H14NO4P", "FA", "", "", "", allBB);
CompositeCompoundList classPS = new CompositeCompoundList("PS", "PS x:y", "PS r1-r2", "FA ", "", "C6H10NO6P", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPS = new CompositeCompoundList("LPS", "LPS x:y", "LPS r1", "FA ", "", "C6H12NO7P", "FA", "", "", "", allBB);
CompositeCompoundList classPI = new CompositeCompoundList("PI", "PI x:y", "PI r1-r2", "FA ", "", "C9H15O9P", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPI = new CompositeCompoundList("LPI", "LPI x:y", "LPI r1", "FA ", "", "C9H17O10P", "FA", "", "", "", allBB);
CompositeCompoundList classPA = new CompositeCompoundList("PA", "PA x:y", "PA r1-r2", "FA ", "", "C3H5O4P", "FA", "FA", "", "", allBB);
CompositeCompoundList classPAO = new CompositeCompoundList("PA O", "PA O-x:y", "PA O-r1-r2", "FA ", "", "C3H7O3P", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPA = new CompositeCompoundList("LPA", "LPA x:y", "LPA r1", "FA ", "", "C3H7O5P", "FA", "", "", "", allBB);
CompositeCompoundList classLPAO = new CompositeCompoundList("LPA O", "LPA O-x:y", "LPAO r1", "FA ", "", "C3H9O4P", "FA", "", "", "", allBB);
CompositeCompoundList classPG = new CompositeCompoundList("PG", "PG x:y", "PG r1-r2", "FA ", "", "C6H11O6", "FA", "FA", "", "", allBB);
CompositeCompoundList classLPG = new CompositeCompoundList("LPG", "LPG x:y", "LPG r1", "FA ", "", "C6H13O7P", "FA", "", "", "", allBB);
CompositeCompoundList classCL = new CompositeCompoundList("CL", "CL x:y", "CL r1-r2-r3-r4", "FA ", "", "C9H14O9P2", "FA", "FA", "FA", "FA", allBB);
CompositeCompoundList classCer = new CompositeCompoundList("Cer", "Cer dx:y", "Cer r1-r2", "SPH", "", "", "SPH", "FA", "", "", allBB);
CompositeCompoundList classSM = new CompositeCompoundList("SM", "SM dx:y", "SM r1-r2", "SPH", "", "C5H12N2O3P", "SPH", "FA", "", "", allBB);
CompositeCompoundList classHexCer = new CompositeCompoundList("HexCer", "HexCer dx:y", "HexCer r1-r2", "SPH", "", "C6H10O5", "SPH", "FA", "", "", allBB);
CompositeCompoundList classTAG = new CompositeCompoundList("TAG", "TAG x:y", "TAG r1-r2-r3", "FA ", "", "C3H2", "FA", "FA", "FA", "", allBB);
CompositeCompoundList classDAG = new CompositeCompoundList("DAG", "DAG x:y", "DAG r1-r2", "FA ", "", "C3H4O", "FA", "FA", "", "", allBB);
CompositeCompoundList classMAG = new CompositeCompoundList("MAG", "MAG x:y", "MAG r1", "FA ", "", "C3H4O", "FA", "", "", "", allBB);
var allClasses = new Dictionary <string, CompositeCompoundList>
{
["PC"] = classPC,
["PC O"] = classPCO,
["LPC"] = classLPC,
["LPC O"] = classLPCO,
["PE"] = classPE,
["PE O"] = classPEO,
["LPE"] = classLPE,
["LPE O"] = classLPEO,
["PS"] = classPS,
["LPS"] = classLPS,
["PI"] = classPI,
["LPI"] = classLPI,
["PA"] = classPA,
["PA O"] = classPAO,
["LPA"] = classLPA,
["LPA O"] = classLPAO,
["PG"] = classLPG,
["LPG"] = classLPG,
["CL"] = classCL,
["TAG"] = classTAG,
["DAG"] = classDAG,
["MAG"] = classMAG,
["Cer"] = classCer,
["HexCer"] = classHexCer,
["SM"] = classSM
};
foreach (var key in LipidCLass.Values)
{
CompositeCompoundList tempClass = allClasses[key];
foreach (var lipid in tempClass)
{
if (!expectedLipids.Exists(x => x.Name == lipid.SumComp))
{
LipidCompound temp = new LipidCompound(lipid.Composition, -1);
temp.Name = lipid.SumComp;
temp.Class = lipid.Type;
expectedLipids.Add(temp);
}
}
}
#endregion
foreach (var species in expectedLipids)
{
SendAndLogVerboseMessage(MessageLevel.Info, $"Lipid {species.Name} with {species.ElementalCompositionFormula} on the list of candidates.");
}
timer.Stop();
SendAndLogVerboseMessage(MessageLevel.Info, $"Generating {expectedLipids.Count} expected lipids took {StringHelper.GetDisplayString(timer.Elapsed)}.");
return(expectedLipids);
}
