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tool2.html
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tool2.html
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<!DOCTYPE html>
<html>
<META HTTP-EQUIV="CACHE-CONTROL" CONTENT="NO-CACHE">
<META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE">
<head>
<title>homologyScanner Web Tool</title>
</head>
<body>
<div id="toolbar"></div>
<div id="slide-in-info">
<a id="slide-in-handle" href="#"><img class="arrowIcon" src="images/transparentImg.png"></img></a>
<div id="projectInfo" class="k-block">
<div class="k-header k-shadow">Project Information</div>
<div id="pInfo">
</div>
<div class="k-header k-shadow">Mutation Information</div>
<div id="mInfo">
<ol class="mut-name-value">
<li>
<label for="WTString">Wild Type</label>
<span id="WTString"></span>
</li>
<li>
<label for="status">status</label>
<!-- id= is used to modify contents with javascript -->
<span id="status"></span>
</li>
<li>
<label for="currentPdbId">PDB ID</label>
<!-- id= is used to modify contents with javascript -->
<span id="currentPdbId"></span>
</li>
</ol>
<!-- ol is ordered list. -->
<!-- class is used to set properties in a style sheet. can also be used by javascript to make changes. -->
<!--
<ol class="mut-name-value ddgOl">
<li>
<label for="ddg">ΔΔG</label>
<span id="ddg"></span>
</li>
</ol>
-->
</div>
<div class="k-header k-shadow">Highly similar mutants </div>
<div id="hInfo">
<table id="resultsTable" name="resultsTable" style=""></table>
<ol class="mut-name-value ddgOl">
<!--
<li>
<label for="ddg2">Average ΔΔG</label>
<span id="ddg2"></span>
</li>
-->
</ol>
</div>
</div>
</div>
<div id="jsmol-div"></div>
<div id="evalWindow">
Evaluation Notes:
<br>
<textarea class="k-textbox" id="eval-textarea" maxlength="300" placeholder="Optional Evaluation Notes up to 300 characters..."></textarea>
<input id="evaluationDD" name="evaluationDD"/>
<button class="k-button" id="eval-save-btn">Save</button>
</div>
<script>
var myJmol, loadscript, projectsCB, pdbIdsCB, mutationsCB, evalDD;
win = $("#evalWindow");
jmol_isReady = function(applet) {
//Jmol._getElement(applet, "appletdiv").style.border="1px solid lightblue";
//popupNotification.show("App Loaded", "info");
//$("#loading-img").fadeIn("slow");
}
var myInfo = {
width: "100%",
height: "100%",
debug: false,
color: "black",
addSelectionOptions: false,
serverURL: "http://pe1.scilifelab.se/jsmol.php",
//serverURL: "http://virtualchemistry.org/~mmb/jsmol.php",
use: "HTML5",
j2sPath: "j2s",
readyFunction: jmol_isReady,
disableInitialConsole: true,
loadStructCallback: "jsmolLoadStructCallback",
};
$("#toolbar").kendoToolBar({
items: [
// REDUNDANT SINCE PROJECT HAS BEEN HARDCODED TO homoScan.1
{
template: "<span style= 'visibility: hidden; display: none;'><label>Project:</label><input id='projectSelect' style='width: 220px;' /></span>",
overflow: "never",
hidden: true
},
//{ type: "separator" },
{
template: "<span><label>PDB ID:</label><input id='pdbIdSelect' style='width: 100px;' /></span>",
overflow: "never"
},
{ type: "separator" },
{
template: "<span><label>complex:</label><input id='complexSelect' style='width: 100px;' /></span>",
overflow: "never"
},
{ type: "separator" },
{
template: "<span><label>Mutation (renumbered):</label><input id='mutationSelect' style='width: 100px;' /></span>",
overflow: "never"
},
{ type: "separator" },
{ type: "button", text: "Load structure", id: "load-btn", enable: false, overflow: "never", click: load},
{ type: "separator" },
// { type: "button", text: "Evaluate", id: "eval-btn", enable: false, overflow: "never", click: winOpen},
// { type: "separator" },
]
});
/* REDUNDANT SINCE PROJECT HAS BEEN HARDCODED TO homoScan.1
function getProjectInfo(projectName) {
$.ajax({
type: "POST",
url: "calls.php",
dataType: 'json',
data: {restcall: 'getJobInfo', arguments: [projectName]},
success: function(projectInfo_data) {
$("#maxMutants").html(projectInfo_data.maxMutants);
$("#generationSize").html(projectInfo_data.generationSize);
$("#maxGenerations").html(projectInfo_data.maxGenerations);
$("#reportingInterval").html(projectInfo_data.reportingInterval);
$("#integratorAccuracy").html(projectInfo_data.integratorAccuracy);
$("#temperature").html(projectInfo_data.temperature);
//projectInfo.maximize();
},
error: function(projectInfo_jqXHR, projectInfo_textStatus, projectInfo_errorThrown) {
popupNotification.show("Error receiving Project Information: " + projectInfo_jqXHR.responseText, "error");
}
});
}
*/
function setMutationInfo(mutIndex) {
console.log("mutIndex : ", mutIndex);
console.log(mutationsCB.dataItem(mutIndex) );
console.log("PDB ID : ",mutationsCB.dataItem(mutIndex).pdbId );
$("#WTString").html(mutationsCB.dataItem(mutIndex).WTString);
$("#status").html(mutationsCB.dataItem(mutIndex).status);
$("#ddg").html(mutationsCB.dataItem(mutIndex).ddg.toFixed(3));
$("#currentPdbId").html(pdbIdsCB.pdbIdCache);
$("#ddg2").html("Calculating..");
populateResultsTable(mutIndex);
}
function populateResultsTable(mutIndex){
var myTable = document.getElementById("resultsTable");
var xhttp = new XMLHttpRequest(); // May need variant to handle old IE browsers https://www.w3schools.com/js/js_ajax_http.asp
console.log("check 1 ");
xhttp.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200){
console.log("check 2 ");
console.log("check 2.1 ");
console.log(this.responseText);
console.log("check 2.1.1 ");
console.log(JSON.parse(this.responseText)) ; // results of mysql query
console.log("check 2.2 ");
var myResultsArray = []; // casting these as arrays
var myResultsArray = JSON.parse(this.responseText);
console.log("check 2.3 ");
console.log(myResultsArray);
console.log(myResultsArray.length);
var averageDDG = 0.0;
$("#resultsTable tr").remove();
for (var i = 0; i< myResultsArray.length; i++){
console.log("check 2.2 ");
myRow = myTable.insertRow(0);
myCell = myRow.insertCell(0);
myCell.innerHTML = myResultsArray[i].DDGhomolog.toFixed(3);
myCell = myRow.insertCell(0);
myCell.innerHTML = myResultsArray[i].mutationStringHomolog;
myCell = myRow.insertCell(0);
myCell.innerHTML = myResultsArray[i].pdbHomolog;
averageDDG += myResultsArray[i].DDGhomolog / myResultsArray.length;
}
var myRow = myTable.insertRow(0);
var myCell = myRow.insertCell(0);
myCell.innerHTML = "FoldX ΔΔG <br>(kcal/mol)"
var myCell = myRow.insertCell(0);
myCell.innerHTML = "mutation <br>(renumbered residues)"
var myCell = myRow.insertCell(0);
myCell.innerHTML = "PDB ID" ;
var myRow = myTable.insertRow(-1);
var myCell = myRow.insertCell(0);
//myCell.color = #F4AF03;
myCell.innerHTML = "<font color=#F4AF03><big> " + averageDDG.toFixed(3) + "</big></font>";// averageDDG.toFixed(3);
var myCell = myRow.insertCell(0);
myCell.innerHTML = ""
var myCell = myRow.insertCell(0);
myCell.innerHTML = "Average";
//$("#ddg2").html(averageDDG.toFixed(3));
} else {
console.log("check 3 ");
console.log(this.status) ;
}
};
xhttp.open("POST", "calls.php", true ); // Going with asynchronous as I don't want to move on until the chains are ready. Revisit this decision later.
console.log(this.status) ;
xhttp.setRequestHeader("Content-Type", "application/x-www-form-urlencoded"); // this turns out to be crucial!
var pdbId = mutationsCB.dataItem(mutIndex).pdbId ;
console.log("check 3.5");
console.log(mutIndex);
console.log(mutationsCB.dataItem(mutIndex).pdbId);
var mutationString = (mutationsCB.dataItem(mutIndex).mutationString);
console.log(mutationsCB.dataItem(mutIndex).mutationString);
console.log("check 3.6");
console.log(mutationString);
xhttp.send("restcall=getSynopsisTableFromHomolog&arguments[0]=" + pdbIdsCB.pdbIdCache + "&arguments[1]=" + mutationString + "&arguments[2]=" + complexCB.complexCache + "&arguments[3]=" + "homoScan.1");
console.log("check 4 ");
}
/* REDUNDANT SINCE PROJECT HAS BEEN HARDCODED TO homoScan.1
function onProjectSelect(e) {
pdbIdsCB.enable(true);
pdbIdsCB.value("");
var dataSource = new kendo.data.DataSource({
transport: {
read: {
type: "POST",
url: "calls.php",
dataType: "json",
//data: {restcall: 'getMutInfo' ,arguments: [e.item.text()]}
// SCF modified:
data: {restcall: 'getDistinctPdbIdsForProject' ,arguments: [(e).item.text()]}
//data: {restcall: 'getDistinctPdbIdsForProject' ,arguments: [$("#projectSelect").getKendoComboBox().dataTextField ]}
// trying:
//data: {restcall: 'getDistinctPdbIdsForProject' ,arguments: [$("#animal").projectCB.text()]}
}
}
});
pdbIdsCB.setDataSource(dataSource);
getProjectInfo(e.item.text());
pdbIdsCB.jobNameCache = e.item.text();
$("#WTString").html("");
$("#status").html("");
$("#ddg").html("");
win.data("kendoWindow").close();
$("#toolbar").data("kendoToolBar").enable("#eval-btn", false);
$("#toolbar").data("kendoToolBar").enable("#load-btn", false);
}
*/
function onPdbIdSelect(e) {
mutationsCB.enable(false);
mutationsCB.value("");
complexCB.enable(true);
complexCB.value("Select..");
pdbIdsCB.jobNameCache = "homoScan.1";
pdbIdsCB.pdbIdCache = (e).item.text();
console.log((e).item.index());
console.log((e).item.text());
console.log((e).item.index());
console.log(" pdbIdCache = ",pdbIdsCB.pdbIdCache);
console.log("jobNameCache = ",pdbIdsCB.jobNameCache);
//$("#toolbar").data("kendoToolBar").enable("#load-btn");
$("#toolbar").data("kendoToolBar").enable("#eval-btn",false);
$("#toolbar").data("kendoToolBar").enable("#load-btn",false);
var dataSource2 = new kendo.data.DataSource({
transport: {
read: {
type: "POST",
url: "calls.php",
dataType: "json",
data: {restcall: 'getComplexesFromPdb' ,arguments: [ pdbIdsCB.pdbIdCache]}
}
}
});
console.log("check 9");
console.log(dataSource2);
complexCB.setDataSource(dataSource2);
/*
complexCB.index = 0 ;
complexCB.select(1) ;
complexCB.trigger("change");*/
if (visible == true) {
$("#slide-in-handle").click();
}
}
function onComplexSelect(e) {
mutationsCB.enable(true);
mutationsCB.value("");
complexCB.complexCache = (e).item.text();
console.log((e).item.index());
console.log((e).item.text());
console.log((e).item.index());
console.log(" complexCache = ",complexCB.complexCache);
console.log("check 18");
var dataSource = new kendo.data.DataSource({
transport: {
read: {
type: "POST",
url: "calls.php",
dataType: "json",
data: {restcall: 'getMutInfoFromHomologPdbAndComplex' ,arguments: [pdbIdsCB.jobNameCache, pdbIdsCB.pdbIdCache, complexCB.complexCache]}
}
}
});
//data: {restcall: 'getMutInfoFromProjectAndPdb' ,arguments: [pdbIdsCB.jobNameCache, pdbIdsCB.pdbIdCache]}
mutationsCB.setDataSource(dataSource);
$("#toolbar").data("kendoToolBar").enable("#eval-btn",false);
$("#toolbar").data("kendoToolBar").enable("#load-btn",false);
}
function onMutationSelect(e) {
console.log("check 12");
win.data("kendoWindow").close();
//win.data("kendoWindow").open();
console.log("check 13");
win.data("kendoWindow").title("Evaluation for " + e.item.text());
console.log("check 14");
setMutationInfo(e.item.index());
console.log("check 15");
//getCurEval(e.item.text()); // temporarily disabling. Having trouble with the queries.
$("#toolbar").data("kendoToolBar").enable("#eval-btn",false);// this does not seem to work at the moment. Fix and reinstate.
$("#toolbar").data("kendoToolBar").enable("#load-btn");
if (visible == false) {
$("#slide-in-handle").click();
}
}
$("#projectSelect").kendoComboBox({
dataTextField: "jobName",
dataValueField: "jobName",
placeholder: "Select Project...",
filter: "contains",
dataSource: {
transport: {
read: {
type: "POST",
url: "calls.php",
dataType: "json",
data: {restcall: 'getJobNames',arguments: [user]}
}
}
},
//select: onProjectSelect
});
projectsCB = $("#projectSelect").data("kendoComboBox");
projectsCB.value("homoScan.1");
$("#pdbIdSelect").kendoComboBox({
//dataTextField: "jobName",
//dataValueField: "jobName",
dataTextField: "pdbId",
dataValueField: "pdbId",
placeholder: "PDB ID...",
filter: "contains",
dataSource: {
transport: {
read: {
type: "POST",
url: "calls.php",
dataType: "json",
data: {restcall: 'getDistinctPdbIdsForProject' ,arguments: ["homoScan.1"]}
}
}
},
select: onPdbIdSelect,
enable: true,
});
pdbIdsCB = $("#pdbIdSelect").data("kendoComboBox");
pdbIdsCB.pdbIdCache = "howdy1"; // Just a flag to make sure this gets overriden later
pdbIdsCB.jobNameCache = "howdy2";
$("#complexSelect").kendoComboBox({
dataTextField: "complexHomolog",
dataValueField: "complexHomolog",
placeholder: "Complex...",
filter: "contains",
select: onComplexSelect,
enable: false,
});
complexCB = $("#complexSelect").data("kendoComboBox");
complexCB.complexCache = "complexCB.complexCache : This cache has not been set"; // Just a flag to make sure this gets overriden later
$("#mutationSelect").kendoComboBox({
dataTextField: "mutationString",
dataValueField: "mutationString",
placeholder: "Mutation...",
filter: "contains",
select: onMutationSelect,
enable: false
});
mutationsCB = $("#mutationSelect").data("kendoComboBox");
$("#evaluationDD").kendoDropDownList({
dataTextField: "status",
dataValueField: "id",
dataSource: evalData,
index: 1
});
evalDD = $("#evaluationDD").data("kendoDropDownList");
$("#eval-save-btn").click(function() {
if ($("#eval-textarea").val().length > 300) {
popupNotification.show("Please keep the note up to 300 characters.", "warning");
return false;
}
$("#loading-img").fadeIn("slow");
$(this).prop("disabled",true);
$.ajax({
type: "POST",
url: "calls.php",
dataType: 'json',
// SCF update to include pdbId :
data: {restcall: 'submitEval', arguments: [user, projectsCB.value(), mutationsCB.value(), evalDD.value(), $("#eval-textarea").val()]},
success: function(submitEval_data) {
$("#loading-img").fadeOut("slow");
$("#eval-save-btn").prop('disabled', false);
popupNotification.show("Evaluation saved, Thank you.", "success");
},
error: function(submitEval_jqXHR, submitEval_textStatus, submitEval_errorThrown) {
popupNotification.show("Error saving evaluation: " + submitEval_jqXHR.responseText, "error");
$("#loading-img").fadeOut("slow");
$("#eval-save-btn").prop('disabled', false);
}
});
});
function getCurEval(mutName) {
$.ajax({
type: "POST",
url: "calls.php",
dataType: 'json',
data: {restcall: 'getEval', arguments: [user, projectsCB.value(),pdbIdsCB.pdbIdCache, mutName]},
//data: {restcall: 'getEval', arguments: [user, projectsCB.value(), mutName]},
success: function(getEval_data) {
if (JSON.stringify(getEval_data) != "false") {
evalDD.select(getEval_data.status - 1);
$("#eval-textarea").val(getEval_data.note);
}else {
evalDD.select(0);
$("#eval-textarea").val("");
}
},
error: function(getEval_jqXHR, getEval_textStatus, getEval_errorThrown) {
popupNotification.show(" Retrieving current mutation evaluation: " + getEval_jqXHR.responseText, "warning");
}
});
}
function load() {
$("#loading-img").fadeIn("slow");
$.ajax({
type: "POST",
url: "calls.php",
dataType: 'json',
// SCF update to include pdbId :
data: {restcall: 'getPdb', arguments: [projectsCB.value(), pdbIdsCB.value(),complexCB.value(), mutationsCB.value(), sID]},
success: function(getPdb_data) {
popupNotification.show("File transfer successful", "success");
if (user != "Guest") {
$("#toolbar").data("kendoToolBar").enable("#eval-btn");
}
loadJsMol();
},
error: function(getPdb_jqXHR, getPdb_textStatus, getPdb_errorThrown) {
popupNotification.show("Error in File tranfer: " + getPdb_jqXHR.responseText, "error");
$("#loading-img").fadeOut("slow");
}
});
}
function loadJsMol() {
console.log(mutationsCB.value());
var selectionString = "A-163-A.A-166-R";// mutationsCB.value();
var selectionString = mutationsCB.value();
selectionString = selectionString.replace(/\-.\./g,".");
console.log("check 19");
console.log(selectionString);
selectionString = selectionString.slice(0, -2);
console.log(selectionString);
selectionString = selectionString.replace(/\./g,") or (:");
console.log(selectionString);
selectionString = selectionString.replace(/\-/g," and " );
console.log(selectionString);
selectionString = " select (:" + selectionString + ") ; color cpk; wireframe 0.5; spacefill off; ";
console.log(selectionString);
//var selectionString = "select (:A and 163) or (:A and 166); color cpk; wireframe 0.4; spacefill off;"
xxxx = projectsCB.value().replace("/", "_") + "_" + mutationsCB.value();
loadscript = 'h2oOn=true;set animframecallback "jmolscript:if (!selectionHalos) {select model=_modelNumber}";'
+'set errorCallback "errorCallback";'
+'set defaultloadscript "isDssp = false;set defaultVDW babel;if(!h2oOn){display !water}";'
+'set zoomlarge false;color echo orange;set echo top left;echo Loading ' + mutationsCB.value() + '...;refresh;'
+'load "http://pe1.scilifelab.se//temp/' + sID + '/XXXX.pdb";color echo orange;set echo top center;echo ' + mutationsCB.value() + ';'
+'spacefill off;wireframe off;cartoons on;color chain;'
+selectionString
loadscript = loadscript.replace(/XXXX/g, xxxx)
Jmol.script(myJmol, loadscript);
}
function jsmolLoadStructCallback() {
$("#loading-img").fadeOut("slow");
}
var slide = kendo.fx($("#slide-in-info")).slideIn("left"),visible = false ;
$("#slide-in-handle").click(function(e) {
console.log("check 16");
if (!visible) {
slide.reverse();
} else {
slide.play();
}
visible = !visible;
e.preventDefault();
});
win.kendoWindow({
width : "300px",
height : "200px",
visible: false,
draggable: false,
resizable: false
});
function evalWindowRelocate() {
var h,w;
if ($(window).height() > $("html").css("min-height").slice(0,-2)) {
h = $(window).height();
}else {
h = $("html").css("min-height").slice(0,-2);
}
if ($(window).width() > $("html").css("min-width").slice(0,-2)) {
w = $(window).width();
}else {
w = $("html").css("min-width").slice(0,-2);
}
win.data("kendoWindow").setOptions({
position: {
top: h - 250,
left: w - 310
}
});
}
function winOpen() {
if (mutationsCB.value() != "") {
if (win.data("kendoWindow").element.is(":hidden")) {
evalWindowRelocate();
win.data("kendoWindow").open();
}else {
win.data("kendoWindow").toFront();
}
}else {
popupNotification.show("Please select a Mutation first.", "warning");
}
}
$(document).on('dblclick','.k-window-titlebar',function(e){
e.preventDefault();
});
window.onresize = function(event) {
evalWindowRelocate();
};
$(document).ready(function() {
setTimeout(function() {
Jmol.setDocument(0);
Jmol.getApplet("myJmol", myInfo);
$("#jsmol-div").html(Jmol.getAppletHtml(myJmol));
}, 50);
});
</script>
<style>
html {
min-width: 800px;
min-height: 600px;
font-family: Arial, Helvetica, sans-serif;
}
html,body {
height: 100%;
width: 100%;
margin: 0;
padding: 0;
}
#toolbar {
font-size: 75%;
line-height: 28px;
height: 30px;
}
.menuBtns {
font-size: 75%;
}
.arrowIcon {
width: 16px;
height: 28px;
background: url("styles/Moonlight/sprite_2x.png") 318px 287px;
}
#jsmol-div {
height: calc(100% - 32px);
width: 100%;
overflow: hidden;
}
#slide-in-info {
position: absolute;
top: 80px;
left: 0;
width: 250px;
margin-left: -252px;
border: solid #171E28;
border-width: 1px 1px 0px 0;
background-color: #212A33;
color: white;
z-index: 10000;
}
#slide-in-handle {
position: absolute;
top: calc(50% - 26px);
left: 250px;
width: 14px;
height: 40px;
background-color: #212A33;
padding: 12px 4px 0 4px;
border-radius: 0 5px 5px 0;
}
#projectInfo {
font-size: 90%;
}
.k-header.k-shadow {
text-align: center;
margin-bottom: 5px;
}
#pInfo,#mInfo {
padding: 0 3% 0 3%;
margin: 0 0 10px 0;
}
ol.proj-name-value {
width: 100%;
list-style: none;
display: table;
padding: 0;
margin: 0;
line-height: 1.4;
}
ol.proj-name-value li {
display: table-row;
}
ol.proj-name-value li label {
display: table-cell;
width: 80%;
}
ol.proj-name-value li span {
display: table-cell;
width: 20%;
color: #F4AF03;
}
ol.mut-name-value {
width: 100%;
list-style: none;
display: table;
padding: 0;
margin: 0;
line-height: 1.4;
}
ol.mut-name-value li {
display: table-row;
}
ol.mut-name-value li label {
display: table-cell;
width: 50%;
}
ol.mut-name-value li span {
display: table-cell;
width: 50%;
color: #F4AF03;
}
ol.mut-name-value.ddgOl label {
display: table-cell;
width: 30%;
}
ol.mut-name-value.ddgOl span {
display: table-cell;
width: 75%;
color: #F4AF03;
}
.k-window-titlebar {
font-size: 95% !important;
font-weight: bold;
}
#evalWindow {
font-size: 90%;
margin: 0;
padding: 5px;
}
#eval-textarea {
resize: none;
width: 290px;
height: 130px;
margin-bottom: 5px;
}
#evaluationDD {
float: left;
width: 195px;
}
#eval-save-btn {
width: 90px;
height: 31px;
font-size: 14px;
font-weight: bold;
float: right;
}
</style>
</body>
</html>