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emt.html
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<!doctype html>
<html>
<head>
<meta charset="UTF-8">
<title>Exact Mass Calculator</title>
<style>
*{
box-sizing: border-box;
user-select: none;
-webkit-user-select: none;
font-family: 'Helvetica', sans-serif;
}
html, body{
margin: 0;
height: 100%;
width: 100%;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
#3c3c3c
.rw{
width: 80%;
max-width: 1200px;
margin: 0 auto;
}
body.overlay::after{
content: "";
position: fixed;
top:0;
left: 0;
width: 100%;
height: 100%;
background: rgba(0, 0, 0, 0.5);
z-index: 100;
}
table{
border-collapse: collapse;
text-align: left;
}
tr:last-child td{
border-bottom:none;
}
th, td{
padding:10px;
padding-right: 15px;
min-width: 150px;
max-width: 300px;
}
th{
padding-bottom: 15px;
border-bottom: 2px solid black;
vertical-align: center;
}
td:first-child{
padding-bottom:20px;
}
td{
vertical-align: top;
border-bottom: 1px solid #afafaf;
}
input[type="number"]{
width: 3em;
}
#control_area{
position: fixed;
top:0;
background: #d6d6d6;
width:100%;
left:0;
padding: 10px;
padding-bottom:0;
z-index: 100;
}
#mode_select{
width: 12em;
margin-right: 15px;
}
#search_bar{
width: calc(100% - 29em - 30px);
padding: 3px;
margin-right: 15px;
}
#search_button{
width: 12em;
}
#search_bar:focus{
outline:2px solid black;
}
#input_area{
padding-bottom: 10px;
margin-bottom: 15px;
}
#button_bar button{
margin-right: 15px;
margin-bottom: 15px;
}
#control_area h1{
margin-bottom: 20px;
}
#mass_list{
margin-top:180px;
position: relative;
}
#mass_list img{
height: 90px;
width: 100%;
object-fit: cover;
transition:all 0.3s;
}
#candidate_list{
position: fixed;
background: rgba(47, 75, 130, 0.83);
z-index: 100;
border:1px solid black;
border-top: none;
color:white;
opacity: 0;
pointer-events: none;
}
#candidate_list div{
margin-bottom: 10px;
padding: 5px;
cursor: pointer;
}
#candidate_list div:hover{
background: white;
color:black;
font-weight: bold;
}
.show{
opacity: 1.0 !important;
pointer-events: all !important;
}
#copytext{
position: fixed;
top:-2000px;
}
#status_bar{
font-weight: lighter;
letter-spacing: 0.5px;
color:white;
padding:1em;
font-size: 14px;
width: 100%;
margin-bottom: 0.5em;
position: fixed;
top:-50px;
-webkit-transition: top 0.2s;
transition: top 0.2s;
z-index: 100000;
}
#status_bar.show{
top:0px;
}
#status_bar.success{
background: #4aa24a;
}
#status_bar.error{
background: #af4949;
}
#mass_list img:hover{
height:200px;
}
.clickcopy{
transition: all 0.15s;
transform-origin: center;
cursor: pointer;
}
.clickcopy.pop{
transform:translateY(-8px);
font-weight: bold;
font-size: 1.3em;
color: red;
}
*[data-mz].invalid{
color:red;
}
#fileupload{
visibility: hidden;
}
</style>
</head>
<body>
<div id = "control_area">
<h1 class="rw">Exact Mass Lookup</h1>
<div class="rw" id = "input_area">
mode:
<select id = "mode_select">
<option data-value = "ds">pubchem search</option>
<option data-value = "fc">formula calculation</option>
</select>
<input id = "search_bar" data-fc = "Enter a chemical formula to calculate its exact mass" data-ds = "Enter the name of a compound to search for it in Pubchem" type="text">
<div id = "candidate_list"></div>
<button id = "search_button">search</button>
</div>
<div class="rw" id = "button_bar">
<button id = "upload_search_list_button">upload search list</button>
<button id = "download_button">download</button>
<span style="margin-left: 50px;">C13 mass shift: </span>
<input style="margin-right: 50px;" id = "mass_shift_input" type = "number" min="0" value="0">
copy mode:
<select id = "copy_select">
<option data-value = "em">exact mass</option>
<option data-value = "emr">exact mass range (15ppm)</option>
</select>
</div>
</div>
<table class = "rw" id = "mass_list">
<tr class = "header_row">
<th>name</th>
<th>image</th>
<th>formula</th>
<th>fw(g/mol)</th>
<th>[M + <span class = "shift_n">0</span>]</th>
<th>[M + <span class = "shift_n">0</span>] - H</th>
<th>[M + <span class = "shift_n">0</span>] + H</th>
</tr>
</table>
<div id = "status_bar"></div>
<input id = "copytext" type="text">
<input id = "fileupload" type="file" accept=".csv">
<script src="https://code.jquery.com/jquery-3.5.1.min.js" integrity="sha256-9/aliU8dGd2tb6OSsuzixeV4y/faTqgFtohetphbbj0=" crossorigin="anonymous">
</script>
<script src = "https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.2.0/papaparse.min.js"></script>
<script src="massc2.js"></script>
<script>
const STATUS_BAR = $('#status_bar');
const SEARCH_BAR = $("#search_bar");
function FLASH_STATUS_BAR(status, message){
if(status == 'error'){
STATUS_BAR.removeClass("success");
STATUS_BAR.addClass("error");
}
else if(status == 'success'){
STATUS_BAR.removeClass("error");
STATUS_BAR.addClass("success");
}
STATUS_BAR.addClass("show");
STATUS_BAR.html(message);
setTimeout(function(){ STATUS_BAR.removeClass("show"); }, 600);
}
SEARCH_BAR.on("keypress", function(e){
if(e.key == "Enter"){
if(BAR_MODE == "ds"){
INITIATE_DATABASE_SEARCH_WITH_STRING($(this).val());
}
else{
CALCULATE_EXACT_MASS_FROM_STRING($(this).val());
}
}
});
$("#search_button").on("click", function(e){
if(BAR_MODE == "ds"){
INITIATE_DATABASE_SEARCH_WITH_STRING(SEARCH_BAR.val());
}
else{
CALCULATE_EXACT_MASS_FROM_STRING(SEARCH_BAR.val());
}
SEARCH_BAR.focus();
});
function INITIATE_DATABASE_SEARCH_WITH_STRING(str){
var text = str.trim();
if(text.length < 3) return;
GET_CANDIDATES_FOR_STRING(text, function(compounds){
DID_RECIEVE_CANDIDATE_COMPOUNDS(compounds);
});
}
function CALCULATE_EXACT_MASS_FROM_STRING(str){
var text = str.trim();
if(text.length < 1) return;
var rdata = {};
rdata.formula = text;
var mass_data = GET_MASS_DATA_FROM_FORMULA(text);
if(mass_data.m0 <= 0) {
FLASH_STATUS_BAR('error', 'The mass of the entered formula could not be calculated');
return;
}
for(var d in mass_data) rdata[d] = mass_data[d];
var new_row = GET_NEW_RESULT_ROW_FOR_DATA(rdata);
$("#mass_list").append(new_row);
UPDATE_MASS_SHIFTS();
}
function GET_CANDIDATES_FOR_STRING(str, f){
var url = 'https://pubchem.ncbi.nlm.nih.gov/rest/autocomplete/compound/';
url += str;
$.ajax({url:url, dataType:"json", success: function(result){
var compounds = result["dictionary_terms"]["compound"];
if(f != null) f.call(this, compounds);
},
error:function(){
FLASH_STATUS_BAR('error', 'The pubchem server could not be reached.');
}
});
}
function DID_RECIEVE_CANDIDATE_COMPOUNDS(compounds){
var search_string = SEARCH_BAR.val().trim().toLocaleLowerCase();
for(var c of compounds){
if(c.trim().toLowerCase() == search_string){
GET_DATA_FOR_COMPOUND(c, function(results){
SEARCH_BAR.val("");
DID_RECIEVE_DATA_FOR_COMPOUND(c, results);
});
return;
}
}
SHOW_CANDIDATE_COMPOUNDS(compounds);
}
function SHOW_CANDIDATE_COMPOUNDS(compounds){
var list = $("#candidate_list");
list.html("");
for(var c of compounds){
var item = $('<div>'+ c +'</div>');
item.click(function(){
var compound_name = $(this).html();
SEARCH_BAR.val(compound_name);
GET_DATA_FOR_COMPOUND(compound_name, function(results){
SEARCH_BAR.val("");
DID_RECIEVE_DATA_FOR_COMPOUND(compound_name, results);
});
list.removeClass("show");
})
list.append(item);
}
var rect = SEARCH_BAR[0].getBoundingClientRect();
list.css({top:rect.top + rect.height + "px", left:rect.left + "px", width:rect.width + "px"});
list.addClass("show");
}
function GET_DATA_FOR_COMPOUND(compound_name, f, ef){
var url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/";
url += compound_name;
url += "/property/MolecularFormula,MolecularWeight,IsomericSMILES/JSON";
url = encodeURI(url);
$.ajax({url: url, dataType: "json", success: function(result){
var props = result.PropertyTable.Properties[0];
if(f != null) f.call(this, props);
},
error:function(){
ERROR_DID_OCCUR_DURING_DATA_REQUEST();
if(ef != null) ef.call(this);
}
});
}
function DID_RECIEVE_DATA_FOR_COMPOUND(name, data){
var rdata = {};
rdata.name = name;
rdata.formula = data.MolecularFormula;
rdata.mw = data.MolecularWeight;
var mass_data = GET_MASS_DATA_FROM_FORMULA(rdata.formula);
for(var d in mass_data) rdata[d] = mass_data[d];
var new_row = GET_NEW_RESULT_ROW_FOR_DATA(rdata);
$("#mass_list").append(new_row);
UPDATE_MASS_SHIFTS();
SEARCH_BAR.focus();
}
function GET_MASS_DATA_FROM_FORMULA(formula){
var m0 = exact_mass(formula);
var m0mh = m0 - PROTON_MASS;
var m0ph = m0 + PROTON_MASS;
return {
m0:m0,
m0mh:m0mh,
m0ph:m0ph,
}
}
function GET_NEW_RESULT_ROW_FOR_DATA(data){
var row = '<tr class="content_row" ';
row += 'data-formula = "' + data.formula + '"';
row += '>';
if(data.name != undefined){
row += '<td>' + data.name + '</td>';
var id = new Date().getTime();
var src = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/";
src += data.name;
src += "/PNG";
row += '<td>' + '<img id ="' + id + '" src="' + encodeURI(src) + '">' + '</td>';
}
else{
row += '<td>MANUAL ENTRY:</td>';
row += '<td></td>';
}
row += '<td>' + data.formula + '</td>';
if(data.mw) row += '<td>' + data.mw + '</td>';
else row += '<td></td>';
row += '<td data-mz = "' + data.m0 +'" class="clickcopy Mn">' + data.m0.toFixed(4) + '</td>';
row += '<td data-mz = "' + data.m0mh + '" class="clickcopy Mn_minus_H">' + data.m0mh.toFixed(4) + '</td>';
row += '<td data-mz = "' + data.m0ph + '" class="clickcopy Mn_plus_H">' + data.m0ph.toFixed(4) +'</td>';
row += "</tr>";
var dom_row = $(row);
dom_row.find(".clickcopy").on("click", function(e){
var text = $(this).html();
var copy_mode = $("#copy_select").find("option:selected").attr("data-value");
if(copy_mode != 'em'){
var range = MZ_RANGE(parseFloat(text), 15);
text = range.min.toFixed(3) + '-' + range.max.toFixed(3);
}
COPY_TEXT_FROM_NODE(text, $(this));
})
return dom_row;
}
function ERROR_DID_OCCUR_DURING_DATA_REQUEST(){
FLASH_STATUS_BAR('error', 'An error occurred and the search could not be completed.');
}
$("#mass_shift_input").on("input", function(){
UPDATE_MASS_SHIFTS();
})
function COPY_TEXT_FROM_NODE(text, node){
var ct = $("#copytext");
ct.val(text)
ct[0].focus();
ct[0].select();
document.execCommand("copy");
node.addClass("pop");
setTimeout(function(){node.removeClass("pop")}, 130);
FLASH_STATUS_BAR('success', 'Value copied to clipboard.')
}
function GET_ACTIVE_MASS_SHIFT(){
var v = $("#mass_shift_input").val();
if(v.trim().length == 0) return 0;
return C_NEUTRON_MASS*parseInt(v);
}
function UPDATE_MASS_SHIFTS(){
var c13n = parseInt($("#mass_shift_input").val());
$(".shift_n").html(c13n);
var shift = GET_ACTIVE_MASS_SHIFT();
$("*[data-mz]").each(function(){
var mz = parseFloat($(this).attr("data-mz"));
$(this).html((mz + shift).toFixed(4));
var num_c = formula_from_str($(this).parent().attr("data-formula"))["C"];
if(num_c == undefined && c13n != 0){
$(this).addClass("invalid");
}
else if(c13n > num_c){
$(this).addClass("invalid");
}
else{
$(this).removeClass("invalid");
}
})
}
var BAR_MODE = 'ds';
SEARCH_BAR.attr("placeholder", SEARCH_BAR.attr("data-" + BAR_MODE));
$('#mode_select').on('input', function(){
SWITCH_BAR_MODE();
});
function SWITCH_BAR_MODE(){
BAR_MODE = BAR_MODE == 'ds'? 'fc': 'ds';
SEARCH_BAR.attr("placeholder", SEARCH_BAR.attr("data-" + BAR_MODE));
$("#candidate_list").removeClass("show");
SEARCH_BAR.val('');
SEARCH_BAR.focus();
}
SEARCH_BAR.focus();
$("#upload_search_list_button").on("click", function(){
$("#fileupload").click();
});
$("#fileupload").on('change', function(e){
var file = this.files[0];
var reader = new FileReader();
reader.readAsText(file);
reader.onload = function(e) {
Papa.parse(e.target.result, {
header: false,
dynamicTyping: true,
complete: function(results) {
COMPOUND_NAME_FILE_WAS_UPLOADED(results.data);
}
});
}
});
function COMPOUND_NAME_FILE_WAS_UPLOADED(rows){
var names = [];
for(var row of rows) names.push(row[0]);
SEARCH_FOR_FIRST_ITEM(names);
}
function SEARCH_FOR_FIRST_ITEM(items){
if(items.length == 0) return;
GET_DATA_FOR_COMPOUND(items[0], function(results){
DID_RECIEVE_DATA_FOR_COMPOUND(items[0], results);
items.shift();
SEARCH_FOR_FIRST_ITEM(items);
}, function(){
items.shift();
SEARCH_FOR_FIRST_ITEM(items);
})
}
$("#download_button").on("click", function(){
DOWNLOAD_TABLE();
});
function DOWNLOAD_TABLE(){
var rows = [];
var n = $("#mass_shift_input").val();
rows.push(["name", "formula", "fw", "M" + n, "M" + n + "-H", "M" + n+ "+H"]);
$("#mass_list").find(".content_row").each(function(){
var row_values = [];
var row = $(this);
row.find("td").each(function(){
if($(this).children().length > 0) return;
row_values.push($(this).html());
});
rows.push(row_values);
});
var csv = Papa.unparse(rows);
var link = document.createElement('a');
link.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(csv));
link.setAttribute('download', "exact_mass_results_" + new Date().toISOString().slice(0,10) + ".csv");
link.style.display = 'none';
document.body.appendChild(link);
link.click();
document.body.removeChild(link);
}
</script>
</body>
</html>