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<!DOCTYPE html>
<html>
<head>
<title>OFraMP</title>
<meta charset="utf-8" />
<link rel="stylesheet" href="static/css/style.css" />
<link rel="stylesheet" href="static/css/OFraMP.css" />
<!--[if IE]><script type="text/javascript" src="static/js/lib/excanvas.js"></script><![endif]-->
<script type="text/javascript" src="static/js/compatibility/es5.js"></script>
<script type="text/javascript" src="static/js/compatibility/json3.min.js"></script>
<script type="text/javascript" src="static/js/compatibility/console.js"></script>
<script type="text/javascript" src="static/js/compatibility/Element.js"></script>
<script type="text/javascript" src="static/js/compatibility/Window.js"></script>
<script type="text/javascript" src="static/js/compatibility/base64.min.js"></script>
<script type="text/javascript" src="static/js/lib/BrowserDetect.js"></script>
<script type="text/javascript" src="static/js/lib/dat.gui.js"></script>
<script type="text/javascript" src="static/js/lib/URLParams.js"></script>
<script type="text/javascript" src="static/js/extensions/extensions.js"></script>
<script type="text/javascript" src="static/js/extensions/Array.js"></script>
<script type="text/javascript" src="static/js/extensions/CanvasRenderingContext2D.js"></script>
<script type="text/javascript" src="static/js/extensions/Color.js"></script>
<script type="text/javascript" src="static/js/extensions/Cookie.js"></script>
<script type="text/javascript" src="static/js/extensions/Date.js"></script>
<script type="text/javascript" src="static/js/extensions/DOM.js"></script>
<script type="text/javascript" src="static/js/extensions/MouseEvent.js"></script>
<script type="text/javascript" src="static/js/extensions/Number.js"></script>
<script type="text/javascript" src="static/js/extensions/Object.js"></script>
<script type="text/javascript" src="static/js/extensions/String.js"></script>
<script type="text/javascript" src="static/js/Tree/Tree.js"></script>
<script type="text/javascript" src="static/js/Tree/TreeVis.js"></script>
<script type="text/javascript" src="static/js/Cache/DummyCache.js"></script>
<script type="text/javascript" src="static/js/Cache/Cache.js"></script>
<script type="text/javascript" src="static/js/OFraMP/Atom.js"></script>
<script type="text/javascript" src="static/js/OFraMP/AtomList.js"></script>
<script type="text/javascript" src="static/js/OFraMP/Bond.js"></script>
<script type="text/javascript" src="static/js/OFraMP/BondList.js"></script>
<script type="text/javascript" src="static/js/OFraMP/Demo.js"></script>
<script type="text/javascript" src="static/js/OFraMP/Molecule.js"></script>
<script type="text/javascript" src="static/js/OFraMP/MoleculeViewer.js"></script>
<script type="text/javascript" src="static/js/OFraMP/OFraMP.js"></script>
<script type="text/javascript" src="static/js/OFraMP/SelectionArea.js"></script>
<script type="text/javascript" src="static/js/OFraMP/settings.js"></script>
<script type="text/javascript" src="static/js/OFraMP/Behavior.js"></script>
<script type="text/javascript" src="static/js/OFraMP/behaviors/NaiveBehavior.js"></script>
<script type="text/javascript" src="static/js/OFraMP/behaviors/SmartBehavior.js"></script>
<script type="text/javascript" src="static/js/OFraMP/behaviors/NaiveDemo.js"></script>
<script type="text/javascript" src="static/js/OFraMP/behaviors/SmartDemo.js"></script>
<script>
window.onload = function() {
var OAPoC_URL = "{{ base_server }}/{{ project_name_formatter('OAPoC') }}/generate/";
var OAPoC_LOAD_URL = "{{ base_server }}/{{ project_name_formatter('OAPoC') }}/loadATB/";
var FDB_URL = "{{ base_server }}/{{ project_name_formatter('FDB') }}/fragments/load/";
var FDB_REPO_URL = "{{ base_server }}/{{ project_name_formatter('FDB') }}/fragments/repos/";
var FDB_GENERATE_URL = "{{ base_server }}/{{ project_name_formatter('FDB') }}/fragments/generate/";
var FDB_MISSING_URL = "{{ base_server }}/{{ project_name_formatter('FDB') }}/fragments/missing/";
var FDB_COORDINATES_URL = "{{ base_server }}/{{ project_name_formatter('FDB') }}/fragments/coordinates/";
var ATB_API_URL = "{{ atb_api_url }}/";
var DEFAULT_REPO = "ATB3";
var DEFAULT_SHELL = 2;
var MAX_SHELL = 5;
$ext.dom.remove(document.getElementById("loader"));
var oframp = new OFraMP(NaiveBehavior, "oframp", {
oapoc : {
url : OAPoC_URL,
loadUrl : OAPoC_LOAD_URL
},
omfraf: {
url: FDB_URL,
repoUrl: FDB_REPO_URL,
generateUrl: FDB_GENERATE_URL,
missingUrl: FDB_MISSING_URL,
coordsUrl: FDB_COORDINATES_URL,
},
atb: {
api_url: ATB_API_URL,
},
defaults: {
repo: DEFAULT_REPO,
defaultShell: DEFAULT_SHELL,
maxShell: MAX_SHELL
}
});
window.onresize = function() {
oframp.setMVSize(document.documentElement.clientWidth, document.documentElement.clientHeight);
};
var zi = document.getElementById("zoomin");
zi.onclick = function() {
oframp.zoom(1.1);
};
var zo = document.getElementById("zoomout");
zo.onclick = function() {
oframp.zoom(.9);
};
var zp = document.getElementById("zoom");
zp.onclick = function(e, x, y, z) {
switch(zp.value) {
case 'min':
oframp.minimize();
break;
case 'max':
oframp.maximize();
break;
case 'avg':
oframp.idealize();
break;
case 'fit':
oframp.bestFit();
break;
}
zp.value = 'pre';
};
var rp = document.getElementById("reset");
rp.onclick = function() {
oframp.resetPositions();
};
var dl = document.getElementById("download");
dl.onclick = function(e) {
var data = oframp.getMVDataURI('image/png');
data = data.replace(/^data:image\/png;base64,/, '');
var date = $ext.date.format(new Date(), "%Y%m%d%H%M%S");
var fname = "OFraMP-" + date + ".png";
$ext.sendDataForm("save.php", {
data: data,
fname: fname,
bd: "image/png"
}, "post", "_blank");
if(e.preventDefault) {
e.preventDefault();
} else {
return false;
}
};
var nm = document.getElementById("new");
$ext.dom.onMouseClick(nm, newMolecule, $ext.mouse.LEFT);
function newMolecule() {
oframp.showInsertMoleculePopup();
}
var of = document.getElementById("open");
$ext.dom.onMouseClick(of, openFile, $ext.mouse.LEFT);
function openFile() {
oframp.showInsertMoleculePopup();
var lb = document.getElementById("load_oss");
lb.click();
}
var sb = document.getElementById("snap");
$ext.dom.onMouseClick(sb, saveMolecule, $ext.mouse.LEFT);
function saveMolecule() {
var data = oframp.getDataURI();
data = data.replace(/^data:application\/octet-stream;base64,/, '');
var date = $ext.date.format(new Date(), "%Y%m%d%H%M%S");
var fname = "OFraMP-" + date + ".oss";
$ext.sendDataForm("save.php", {
data: data,
fname: fname
}, "post", "_blank");
}
var sv = document.getElementById("save");
$ext.dom.onMouseClick(sv, downloadLGF, $ext.mouse.LEFT);
function downloadLGF() {
oframp.mv.molecule.downloadLGF();
}
var atb_missing_button = document.getElementById("atb_missing");
$ext.dom.onMouseClick(atb_missing_button, transfer_missing, $ext.mouse.LEFT);
function transfer_missing() {
oframp.mv.molecule.transfer_missing(oframp.settings.atb.api_url, oframp.off, oframp.settings.omfraf.version);
}
var atb_button = document.getElementById("atb");
$ext.dom.onMouseClick(atb_button, transfer_charges, $ext.mouse.LEFT);
function transfer_charges() {
oframp.mv.molecule.transfer_charges(oframp.settings.atb.api_url);
}
var ub = document.getElementById("undo");
$ext.dom.onMouseClick(ub, function() {
undo();
});
function undo() {
if(!oframp.checkpoints) {
return;
}
if(oframp.activeCheckpoint > 0) {
oframp.previousCheckpoint();
}
}
var rb = document.getElementById("redo");
$ext.dom.onMouseClick(rb, function() {
redo();
});
function redo() {
if(!oframp.checkpoints) {
return;
}
if(oframp.activeCheckpoint < oframp.checkpoints.length - 1) {
oframp.nextCheckpoint();
}
}
var op = document.getElementById("opti");
$ext.dom.onMouseClick(op, function() {
oframp.settingsUI.toggle();
}, $ext.mouse.LEFT);
var hb = document.getElementById("help");
$ext.dom.onMouseClick(hb, openHelp, $ext.mouse.LEFT);
function openHelp() {
window.open('help.html', '_blank').focus();
}
$ext.dom.addEventListener(oframp.container, 'historychanged', function() {
if(oframp.activeCheckpoint === 0) {
ub.disabled = "disabled";
} else {
ub.disabled = "";
}
if(oframp.activeCheckpoint === oframp.checkpoints.length - 1) {
rb.disabled = "disabled";
} else {
rb.disabled = "";
}
});
var controlsInitialized = false;
var header = document.getElementById("header");
var controls = document.getElementById("controls");
var extraControls = document.getElementById("extra_controls");
var fragmentControls = document.getElementById("fragment_controls");
var toggle = document.getElementById("extra_controls_toggle");
var extraControlsVisible = false;
function initControls() {
controls.style.display = "inline-block";
extraControls.style.display = "inline-block";
fragmentControls.style.display = "block";
if($ext.onBrokenIE()) {
var logo = document.getElementById("logo");
logo.style.position = "absolute";
logo.style.marginLeft = "-120px";
header.style.paddingLeft = "120px";
}
var set_toggle = function() {
if(extraControlsVisible) {
header.style.height = "30px";
toggle.style.backgroundImage = "url('static/img/double_arrow_down.png')";
extraControlsVisible = false;
} else {
header.style.height = "70px";
toggle.style.backgroundImage = "url('static/img/double_arrow_up.png')";
extraControlsVisible = true;
}
};
$ext.dom.onMouseClick(toggle, set_toggle, $ext.mouse.LEFT);
set_toggle();
$ext.dom.addEventListener(window, 'keydown', function(evt) {
if(!evt.altKey) {
return;
}
var keyCode = evt.keyCode || evt.charCode;
if(keyCode > 26) {
keyCode -= 64;
}
if(keyCode === 26) {
if(evt.shiftKey) {
redo();
} else {
undo();
}
} else if(keyCode === 25) {
redo();
} else if(keyCode === 14) {
newMolecule();
} else if(keyCode === 15) {
openFile();
} else if(keyCode === 19) {
saveMolecule();
} else if(keyCode === 12) {
downloadLGF();
} else if(keyCode === 8) {
openHelp();
}
});
controlsInitialized = true;
}
$ext.dom.addEventListener(oframp.container, 'moleculeentered', function() {
if (controlsInitialized) {
controls.style.display = "none";
extraControls.style.display = "none";
fragmentControls.style.display = "none";
}
});
$ext.dom.addEventListener(oframp.container, 'moleculedisplayed', function() {
if (!controlsInitialized) {
initControls();
} else {
controls.style.display = "inline-block";
extraControls.style.display = "inline-block";
fragmentControls.style.display = "block";
}
});
// Hide broken stuff on IE
if(BrowserDetect.browser === "Explorer") {
if(BrowserDetect.version < 10) {
of.remove();
sb.remove();
}
if(BrowserDetect.version < 9) {
dl.remove();
op.remove();
}
}
if (URLParams) {
if (URLParams.mds) {
oframp.submitMDS(URLParams.mds);
} else if (URLParams.atb_id) {
oframp.submitMDS(URLParams.atb_id);
} else if (URLParams.oss) {
oframp.loadOSS(URLParams.oss);
}
}
if (URLParams && URLParams.user_token && URLParams.atb_id) {
}
else {
alert(
"No ATB user_token was found in the HTTP request. This means that OFraMP will work, but the charges generated will not be saved in the ATB and won't be available to populate topology templates.\n\nTo get an ATB user token, go to the ATB (https://atb.uq.edu.au), log in to your ATB account and go to the ATB page of the molecule of interest. " +
"Then, click the 'Fragment-Based Parametrisation with OFraMP' button at the top of the page.\n\n If you don't have an ATB account, you can register for one (free for academic use)."
);
}
};
</script>
{% if google_analytics_id %}
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
ga('create', '{{ google_analytics_id }}', 'auto');
ga('send', 'pageview');
</script>
{% endif %}
</head>
<body>
<div id="header">
<div id="logo">
<span id="logo_o">O</span><span id="logo_fra">Fra</span><span id="logo_m">M</span><span id="logo_p">P</span>
</div>
<div id="controls">
<div class="bgroup">
<button id="new" class="border_box" title="Submit another molecule (Alt+N)">
New molecule
</button>
<button id="open" class="border_box" title="Open a saved molecule (Alt+O)">
Open
</button>
<button id="snap" class="border_box" title="Save the current state (Alt+S)">
Save
</button>
</div>
<div class="bgroup">
<button id="undo" class="border_box" title="Undo last action (Alt+Z)">
Undo
</button>
<button id="redo" class="border_box" title="Redo last action (Alt+Y / Alt+Shift+Z)">
Redo
</button>
</div>
<div class="bgroup">
<button id="save" class="border_box" title="Download LGF file">
Download LGF
</button>
</div>
<div class="bgroup">
<button id="atb_missing" class="border_box" title="Transfer missing fragments to the ATB">
Send missing to ATB
</button>
<button id="atb" class="border_box" title="Transfer charges to the ATB">
Send charges to ATB
</button>
</div>
<div class="bgroup">
<button id="help" class="border_box" title="Open OFraMP Help (Alt+H)">
Help
</button>
</div>
<div class="bgroup">
<button id="extra_controls_toggle" class="border_box" title="Show/Hide advanced controls">
</button>
</div>
</div>
<div id="extra_controls">
<div class="bgroup">
<button id="zoomin" class="border_box" title="Zoom in">
Zoom +
</button>
<button id="zoomout" class="border_box" title="Zoom out">
Zoom -
</button>
<select id="zoom" class="border_box" title="Zoom to a predefined level">
<option value="pre" disabled="disabled" selected="selected">Predefined</option>
<option value="min">Minimal</option>
<option value="avg">Ideal</option>
<option value="max">Maximal</option>
<option value="fit">Best fit</option>
</select>
</div>
<div class="bgroup">
<button id="reset" class="border_box" title="Reset the atom positions">
Reset positions
</button>
</div>
<div class="bgroup">
<a id="download" class="border_box" href="" title="Download the molecule as an image">
Download image
</a>
</div>
<div class="bgroup">
<button id="opti" class="border_box" title="Settings">
Settings
</button>
</div>
</div>
</div>
<div id="fragment_controls">
</div>
<div id="legend">
<b>Legend</b>
</div>
<div id="copyright">
© 2013-2018 jimivdw | CWI
</div>
<div id="oframp"></div>
<div id="loader">
<p>Please be patient as the Online tool for Fragment-based Molecule Parameterisation is being loaded.</p>
<div class='loader'></div>
</div>
</body>
</html>