MediaWiki:GlycosphingolipidMassCalculator.js
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/*
Last-Update: 2023/01/24
*/
class GlycosphingolipidMassCalculator
{
constructor()
{
// recalculate
document.getElementById("cs_average").onchange = function(){
gVar.gsMassCalc.calculateGlycosphingolipid();
}
// setLactoneMax
document.getElementById("cs_neuac").onchange = function(){
gVar.gsMassCalc.setLactoneMax();
}
document.getElementById("cs_neugc").onchange = function(){
gVar.gsMassCalc.setLactoneMax();
}
document.getElementById("cs_hexua").onchange = function(){
gVar.gsMassCalc.setLactoneMax();
}
document.getElementById("cs_lactone").onchange = function(){
gVar.gsMassCalc.setLactoneMax();
}
// setFattyAcidMax
document.getElementById("cs_fa_carbonno").onchange = function(){
gVar.gsMassCalc.setFattyAcidMax();
}
document.getElementById("cs_fa_unsaturation").onchange = function(){
gVar.gsMassCalc.setFattyAcidMax();
}
document.getElementById("cs_fa_hydroxygroup").onchange = function(){
gVar.gsMassCalc.setFattyAcidMax();
}
// setLongChainBases
document.getElementById("cs_lcb_carbonno").onchange = function(){
gVar.gsMassCalc.setLongChainBasesMax("cs_lcb_carbonno", document.getElementById("cs_lcb_carbonno").min);
}
document.getElementById("cs_lcb_hydroxygroup").onchange = function(){
gVar.gsMassCalc.setLongChainBasesMax("cs_lcb_hydroxygroup", document.getElementById("cs_lcb_hydroxygroup").min);
}
// Polarity
document.getElementById("cs_polarity").onchange = function(){
gVar.gsMassCalc.switchCharge();
}
document.getElementById("cs_charge").onchange = function(){
gVar.gsMassCalc.checkCharge();
}
// calculate button
document.getElementById("calculate_glycosphingolipid_button").onclick = function(){
gVar.gsMassCalc.calculateGlycosphingolipid();
}
// sample button
// Ganglioside GM1 of FA 18:0, LCB d20:1
document.getElementById("ex_ganglioside").onclick = function(){
gVar.gsMassCalc.setExampleNumbers({"cs_hexose":3,
"cs_hexnac":1,
"cs_neuac":1,
"cs_fa_carbonno":18,
"cs_lcb_carbonno":20,
"cs_lcb_unsaturation":1,
"cs_lcb_hydroxygroup":2});
gVar.gsMassCalc.calculateGlycosphingolipid();
}
// Sulfatide of FA 24:1, LCB d18:1
document.getElementById("ex_sulfatide").onclick = function(){
gVar.gsMassCalc.setExampleNumbers({"cs_hexose":1,
"cs_fa_carbonno":24,
"cs_fa_unsaturation":1,
"cs_lcb_carbonno":18,
"cs_lcb_unsaturation":1,
"cs_lcb_hydroxygroup":2,
"cs_sulfate":1});
gVar.gsMassCalc.calculateGlycosphingolipid();
}
// Lactotetraosylceramide of FA 16:0, LCB t18:0
document.getElementById("ex_lactotetraosylceramide").onclick = function(){
gVar.gsMassCalc.setExampleNumbers({"cs_hexose":3,
"cs_hexnac":1,
"cs_fa_carbonno":16,
"cs_fa_hydroxygroup":1,
"cs_lcb_carbonno":18,
"cs_lcb_hydroxygroup":3});
gVar.gsMassCalc.calculateGlycosphingolipid();
}
}
setExampleNumbers(values)
{
// clear
document.getElementById("cs_hexose" ).value = 0;
document.getElementById("cs_fucose" ).value = 0;
document.getElementById("cs_hexua" ).value = 0;
document.getElementById("cs_hexnac" ).value = 0;
document.getElementById("cs_neuac" ).value = 0;
document.getElementById("cs_neugc" ).value = 0;
document.getElementById("cs_methyl" ).value = 0;
document.getElementById("cs_acetyl" ).value = 0;
document.getElementById("cs_nmethylamide" ).value = 0;
document.getElementById("cs_fa_carbonno" ).value = 0;
document.getElementById("cs_fa_unsaturation" ).value = 0;
document.getElementById("cs_fa_hydroxygroup" ).value = 0;
document.getElementById("cs_lcb_carbonno" ).value = 0;
document.getElementById("cs_lcb_unsaturation").value = 0;
document.getElementById("cs_lcb_hydroxygroup").value = 0;
document.getElementById("cs_phosphate" ).value = 0;
document.getElementById("cs_nh4" ).value = 0;
document.getElementById("cs_na" ).value = 0;
document.getElementById("cs_k" ).value = 0;
document.getElementById("cs_sulfate" ).value = 0;
document.getElementById("cs_lactone" ).value = 0;
document.getElementById("cs_polarity").selectedIndex = 0;
gVar.gsMassCalc.switchCharge();
// set values
for(var key in values){
document.getElementById(key).value = values[key];
}
}
setLactoneMax()
{
var neuac = getGlycosphingolipidNum("cs_neuac", 0, 0);
var hexua = getGlycosphingolipidNum("cs_hexua", 0, 0);
var neugc = getGlycosphingolipidNum("cs_neugc", 0, 0);
var lactoneMax = neuac + hexua + neugc;
var lactone = document.getElementById("cs_lactone");
lactone.max = lactoneMax;
if(lactoneMax < lactone.value)
lactone.value = lactoneMax;
}
setFattyAcidMax()
{
var saturationDOM = document.getElementById("cs_fa_unsaturation");
var hydroxyDOM = document.getElementById("cs_fa_hydroxygroup");
var carbonno = getGlycosphingolipidNum("cs_fa_carbonno", 0, 0);
if(carbonno < 3){
saturationDOM.max = 0;
saturationDOM.value = '0';
} else {
saturationDOM.max = carbonno-2;
var saturation = getGlycosphingolipidNum("cs_fa_unsaturation", 0, 0);
if(carbonno-2 < saturation)
saturationDOM.value = carbonno-2;
}
if(carbonno < 2)
hydroxyDOM.value = '0';
else {
hydroxyDOM.max = carbonno-1;
var hydroxy = getGlycosphingolipidNum("cs_fa_hydroxygroup", 0, 0);
if(carbonno-1 < hydroxy)
hydroxyDOM.value = carbonno-1;
}
}
setLongChainBasesMax(id, min)
{
gVar.gsMassCalc.getGlycosphingolipidNum(id, min, 0);
}
switchCharge()
{
var display = document.getElementById("cs_polarity").selectedIndex == 0 ? 'none' : 'block';
document.getElementById("div_charge").style.cssText = 'display: ' + display;
}
checkCharge()
{
var charge = Number(document.getElementById("cs_charge").value);
if(charge == 0)
charge = 1;
else if(charge < 0)
charge = -charge;
document.getElementById("cs_charge").value = charge;
}
getGlycosphingolipidNum(id, min, max)
{
var dom = document.getElementById(id);
var num = dom.value;
if(num == null || !isFinite(num)){
dom.value = 0;
return 0;
}
num = Number(num);
if(max != 0 && max < num){
dom.value = max;
return max;
}
if(num < min){
dom.value = min;
return min;
}
return num;
}
checkFormulaNums(atom, count)
{
var str = "";
if(count > 0){
str = atom;
if(count > 1)
str += count;
}
return str;
}
calculateGlycosphingolipid()
{
var hexose = gVar.gsMassCalc.getGlycosphingolipidNum("cs_hexose", 0, 0);
var fucose = gVar.gsMassCalc.getGlycosphingolipidNum("cs_fucose", 0, 0);
var hexua = gVar.gsMassCalc.getGlycosphingolipidNum("cs_hexua", 0, 0);
var hexnac = gVar.gsMassCalc.getGlycosphingolipidNum("cs_hexnac", 0, 0);
var neuac = gVar.gsMassCalc.getGlycosphingolipidNum("cs_neuac", 0, 0);
var neugc = gVar.gsMassCalc.getGlycosphingolipidNum("cs_neugc", 0, 0);
var methyl = gVar.gsMassCalc.getGlycosphingolipidNum("cs_methyl", -99, 0);
var acetyl = gVar.gsMassCalc.getGlycosphingolipidNum("cs_acetyl", -99, 0);
var nma = gVar.gsMassCalc.getGlycosphingolipidNum("cs_nmethylamide", 0, 0);
var fac = gVar.gsMassCalc.getGlycosphingolipidNum("cs_fa_carbonno", 0, 0);
var faus = gVar.gsMassCalc.getGlycosphingolipidNum("cs_fa_unsaturation", 0, fac-2 < 0 ? 0 : fac-2);
var faoh = gVar.gsMassCalc.getGlycosphingolipidNum("cs_fa_hydroxygroup", 0, fac-1 < 0 ? 0 : fac-1);
var lcbc = gVar.gsMassCalc.getGlycosphingolipidNum("cs_lcb_carbonno", 5, 0);
var lcbus = gVar.gsMassCalc.getGlycosphingolipidNum("cs_lcb_unsaturation", 0, 0);
var lcboh = gVar.gsMassCalc.getGlycosphingolipidNum("cs_lcb_hydroxygroup", 2, 0);
var hpo3 = gVar.gsMassCalc.getGlycosphingolipidNum("cs_phosphate", 0, 0);
var nh4 = gVar.gsMassCalc.getGlycosphingolipidNum("cs_nh4", 0, 0);
var sod = gVar.gsMassCalc.getGlycosphingolipidNum("cs_na", 0, 0);
var pot = gVar.gsMassCalc.getGlycosphingolipidNum("cs_k", 0, 0);
var so3 = gVar.gsMassCalc.getGlycosphingolipidNum("cs_sulfate", 0, 0);
var lactone = gVar.gsMassCalc.getGlycosphingolipidNum("cs_lactone", 0, neuac+neugc+hexua);
var charge = gVar.gsMassCalc.getGlycosphingolipidNum("cs_charge", 0, 0);
var pol = document.getElementById("cs_polarity").value;
switch(pol){
case 'NON': pol = 0; break;
case 'NEG': pol = -1; break;
case 'POS': pol = 1; break;
}
// struct formula
var formulaNums = [];
formulaNums[0] = (hexose + fucose + hexua)*6 + hexnac*8 + (neuac + neugc)*11 +
methyl + acetyl*2 + nma + fac + lcbc; // C
formulaNums[1] = 2 + (hexose + fucose)*10 + hexnac*13 + (neuac + neugc)*17 +
hexua*8 + hpo3 + (methyl + acetyl - lcbus)*2 +
nma*3 + (lcbc*2+1) + nh4*3 - sod - pot + (pol * charge); // H
if(fac != 0)
formulaNums[1] = formulaNums[1] + (fac-1)*2 - faus*2;
formulaNums[2] = 1 + (hexose + hexnac)*5 + fucose*4 + neuac*8 + neugc*9 +
hexua*6 + (so3 + hpo3)*3 + acetyl - nma + (lcboh-1); // O
if(fac != 0)
formulaNums[2] = formulaNums[2] + 1 + faoh;
formulaNums[3] = 1 + hexnac + neuac + neugc + nh4 + nma; // N
formulaNums[4] = so3; // S
formulaNums[5] = hpo3; // P
formulaNums[6] = sod; // Na
formulaNums[7] = pot; // K
// formulaNums[8] = cal; // Ca
formulaNums[1] = formulaNums[1] - lactone*2;
formulaNums[2] = formulaNums[2] - lactone;
var formula = 'C' + formulaNums[0];
formula += 'H' + formulaNums[1];
formula += 'N';
if(formulaNums[3] > 1)
formula += formulaNums[3];
formula += gVar.gsMassCalc.checkFormulaNums('O', formulaNums[2]);
formula += gVar.gsMassCalc.checkFormulaNums('P', formulaNums[5]);
formula += gVar.gsMassCalc.checkFormulaNums('S', formulaNums[4]);
// formula += gVar.gsMassCalc.checkFormulaNums('Ca', formulaNums[8]);
formula += gVar.gsMassCalc.checkFormulaNums('K', formulaNums[7]);
formula += gVar.gsMassCalc.checkFormulaNums('Na', formulaNums[6]);
document.getElementById("cs_formula").value = formula;
var EXACT = {
"C": 12.0,
"H": 1.0078250322,
"Li": 7.01600344,
"O": 15.994914620,
"N": 14.003074004,
"S": 31.972071174,
"P": 30.973761998,
"Na": 22.98976928,
"K": 38.96370649,
"Ca": 39.9625909
}
var electron = 0.00054857990;
// 質量計算
// var mass = calculateMassFromFormula(formula, document.getElementById("cs_average").value === 'true');
var mass = formulaNums[0] * EXACT["C"] + formulaNums[1] * EXACT["H"] + formulaNums[2] * EXACT["O"] +
formulaNums[3] * EXACT["N"] + formulaNums[4] * EXACT["S"] + formulaNums[5] * EXACT["P"] +
formulaNums[6] * EXACT["Na"] + formulaNums[7] * EXACT["K"];
var nominal = formulaNums[0]*12 +formulaNums[1] +formulaNums[2]*16
+formulaNums[3]*14 +formulaNums[4]*32 +formulaNums[5]*31
+formulaNums[6]*23 +formulaNums[7]*39;
if(charge != 0 && pol != 0){
if(pol > 0)
mass = mass / charge - electron;
else if(pol < 0)
mass = mass / charge + electron;
nominal /= charge;
}
if(Math.floor(nominal) == nominal)
nominal = nominal.toFixed(0);
else
nominal = nominal.toFixed(2);
document.getElementById("cs_mass").value = mass.toFixed(6);
document.getElementById("cs_nominalmass").value = nominal;
}
}
