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implemented mass lookup function
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@dominik-kopczynski
dominik-kopczynski committed Oct 9, 2023
1 parent d9559a7 commit dfc3fb7
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Showing 2 changed files with 85 additions and 120 deletions.
2 changes: 1 addition & 1 deletion LipidCreator/CreatorGUI.Designer.cs
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203 changes: 84 additions & 119 deletions LipidCreator/CreatorGUI.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -346,154 +346,44 @@ public CreatorGUI(string _inputParameters)
headgroup = headgroup.Substring(0, headgroup.Length - 2);
}

csgoslin.Headgroup hg = new csgoslin.Headgroup(headgroup);
switch(precursor.buildingBlockType)
{

case 0:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

for (int c = 8; c <= 120; c++)
{
for (int db = 0; db <= Math.Min(((c - 6 - 1) >> 1), 24); ++db)
{
int key = ((c - 2) << 20) + ((db + 1) << 5);
if (!fatty_acids.ContainsKey(key)) continue;
double mass = mass_hg + 3 * base_mass + fatty_acids[((c - 6) << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(kvp.Key + " " + fatty_acids[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
addLipidAssemblies(4, headgroup, fatty_acids);
break;
}

case 1:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

for (int c = 6; c <= 90; c++)
{
for (int db = 0; db <= Math.Min(((c - 4 - 1) >> 1), 18); ++db)
{
int key = ((c - 2) << 20) + ((db + 1) << 5);
if (!fatty_acids.ContainsKey(key)) continue;
double mass = mass_hg + 2 * base_mass + fatty_acids[((c - 4) << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(headgroup + " " + fatty_acids[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
addLipidAssemblies(3, headgroup, fatty_acids);
break;
}

case 2:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

if (plasmalogen)
{
for (int c = 4; c <= 60; c++)
{
for (int db = 0; db <= Math.Min(((c - 2 - 1) >> 1), 12); ++db)
{
int key = ((c - 2) << 20) + ((db + 1) << 5);
if (!fatty_acids_o.ContainsKey(key)) continue;
double mass = mass_hg + base_mass + fatty_acids_o[((c - 2) << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(headgroup + " " + fatty_acids_o[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
}
else
{
for (int c = 4; c <= 60; c++)
{
for (int db = 0; db <= Math.Min(((c - 2 - 1) >> 1), 12); ++db)
{
int key = ((c - 2) << 20) + ((db + 1) << 5);
if (!fatty_acids.ContainsKey(key)) continue;
double mass = mass_hg + base_mass + fatty_acids[((c - 2) << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(kvp.Key + " " + fatty_acids[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
}
if (plasmalogen) addLipidAssemblies(2, headgroup, fatty_acids_o);
else addLipidAssemblies(2, headgroup, fatty_acids);
break;
}

case 3:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);


if (plasmalogen)
{
for (int c = 2; c <= 30; c++)
{
for (int db = 0; db <= Math.Min((c >> 1), 6); ++db)
{
int key = (c << 20) + ((db + 1) << 5);
if (!fatty_acids_o.ContainsKey(key)) continue;
double mass = mass_hg + empty_mass + fatty_acids_o[(c << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(headgroup + " " + fatty_acids_o[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
}
else
{
for (int c = 2; c <= 30; c++)
{
for (int db = 0; db <= Math.Min(((c - 1) >> 1), 6); ++db)
{
int key = (c << 20) + ((db + 1) << 5);
if (!fatty_acids.ContainsKey(key)) continue;
double mass = mass_hg + empty_mass + fatty_acids[(c << 20) + ((db + 1) << 5)].mass;
searchLipids.Add(new LipidAssembly(kvp.Key + " " + fatty_acids[(c << 20) + ((db + 1) << 5)].name, mass));
}
}
}
if (plasmalogen) addLipidAssemblies(1, headgroup, fatty_acids_o);
else addLipidAssemblies(1, headgroup, fatty_acids);
break;
}

case 4:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

for (int c = 4; c <= 60; c++)
{
for (int db = 0; db <= Math.Min(((c - 2 - 1) >> 1), 12); ++db)
{
for (int oh = 2; oh <= 3; ++oh)
{
int key = (c << 20) + ((db + 1) << 5) + (oh + 1);
if (!long_chain_bases.ContainsKey(key)) continue;
double mass = mass_hg + base_mass + long_chain_bases[((c - 2) << 20) + ((db + 1) << 5) + (oh + 1)].mass;
searchLipids.Add(new LipidAssembly(kvp.Key + " " + long_chain_bases[(c << 20) + ((db + 1) << 5) + (oh + 1)].name, mass));
}
}
}
addLipidAssemblies(2, headgroup, long_chain_bases, true);
break;
}

case 5:
{
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

for (int c = 2; c <= 30; c++)
{
for (int db = 0; db <= Math.Min(((c - 1) >> 1), 6); ++db)
{
for (int oh = 2; oh <= 3; ++oh)
{
int key = (c << 20) + ((db + 1) << 5) + (oh + 1);
if (!long_chain_bases.ContainsKey(key)) continue;
double mass = mass_hg + long_chain_bases[(c << 20) + ((db + 1) << 5) + (oh + 1)].mass;
searchLipids.Add(new LipidAssembly(kvp.Key + " " + long_chain_bases[(c << 20) + ((db + 1) << 5) + (oh + 1)].name, mass));
}
}
}
addLipidAssemblies(1, headgroup, long_chain_bases, true);
break;
}

Expand All @@ -515,11 +405,77 @@ public CreatorGUI(string _inputParameters)
}
}

Dictionary<AdductType, double> adducts = new Dictionary<AdductType, double>();
foreach (KeyValuePair<AdductType, Adduct> kvp in Lipid.ALL_ADDUCTS)
{
ElementDictionary elements = kvp.Value.elements;
double mass = 0;
for (int m = 0; m < elements.Count; ++m)
{
mass += elements[m] * MS2Fragment.ALL_ELEMENTS[(Molecule)m].mass;
}
adducts.Add(kvp.Key, mass);
}

int num = searchLipids.Count;
for (int i = 0; i < num; ++i)
{
foreach (KeyValuePair<AdductType, double> kvp in adducts)
{
Adduct adduct = Lipid.ALL_ADDUCTS[kvp.Key];
double charge = adduct.charge;
double mass = searchLipids[i].mass + kvp.Value;
mass = (mass - charge * LipidCreator.ELECTRON_REST_MASS) / Math.Abs(charge);

searchLipids.Add(new LipidAssembly(searchLipids[i].name, mass, adduct.visualization));
}
}

searchLipids = searchLipids.Where(x => x.adduct.Length > 0).ToList();

searchLipids.Sort(delegate(LipidAssembly x, LipidAssembly y){
return x.mass < y.mass ? -1 : 1;
});
}




private void addLipidAssemblies(int fa, string headgroup, Dictionary<int, FattyAcidAssembly> chain_dict, bool isLCB = false)
{
csgoslin.Headgroup hg = new csgoslin.Headgroup(headgroup);
ElementTable elements = hg.get_elements();
double mass_hg = csgoslin.StringFunctions.get_mass(elements);

LipidClassMeta meta = LipidClasses.lipid_classes[hg.lipid_class];
int additional_fa = meta.possible_num_fa;
int remaining_H = meta.max_num_fa - additional_fa;
mass_hg += (fa - 1) * MS2Fragment.ALL_ELEMENTS[Molecule.O].mass;
mass_hg -= (-remaining_H + fa - 1) * MS2Fragment.ALL_ELEMENTS[Molecule.H].mass;

Console.WriteLine(searchLipids[0].mass + " " + searchLipids[0].name);
for (int c = 2 * fa; c <= 30 * fa; c++)
{
for (int db = 0; db <= Math.Min(((c - 1) >> 1), 6 * fa); ++db)
{
if (isLCB)
{
for (int oh = 2; oh <= 3; ++oh)
{
int key = (c << 20) + ((db + 1) << 5) + (oh + 1);
if (!chain_dict.ContainsKey(key)) continue;
double mass = mass_hg + chain_dict[key].mass;
searchLipids.Add(new LipidAssembly(headgroup + " " + chain_dict[key].name, mass));
}
}
else
{
int key = (c << 20) + ((db + 1) << 5);
if (!chain_dict.ContainsKey(key)) continue;
double mass = mass_hg + chain_dict[key].mass;
searchLipids.Add(new LipidAssembly(headgroup + " " + chain_dict[key].name, mass));
}
}
}
}


Expand Down Expand Up @@ -688,6 +644,15 @@ private void searchFragmentsComplete(object sender, DataGridViewBindingCompleteE
}


private void searchLipidsComplete(object sender, DataGridViewBindingCompleteEventArgs e)
{
searchlipidsGridview.Columns[0].Width = (int)Math.Floor(searchfragmentsGridview.Size.Width * 0.2);
searchlipidsGridview.Columns[1].Width = (int)Math.Floor(searchfragmentsGridview.Size.Width * 0.2);
searchlipidsGridview.Columns[2].Width = (int)Math.Floor(searchfragmentsGridview.Size.Width * 0.4);
searchlipidsGridview.Columns[3].Width = (int)Math.Floor(searchfragmentsGridview.Size.Width * 0.2);
}





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