jsmol/simple.htm at main · openmopac/jsmol · GitHub

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<!DOCTYPE html>
<html>
<head>
<script type="text/javascript" src="JSmol.min.js"></script>

<script type="text/javascript">

// 1/21/2013 10:54:15 PM -- adds image handling

var jmolApplet0; // set up in HTML table, below

// logic is set by indicating order of USE -- default is HTML5 for this test page, though
var use = "HTML5" // JAVA HTML5 WEBGL IMAGE  are all otions
var s = document.location.search;


// Developers: The _debugCode flag is checked in j2s/core/core.z.js,
// and, if TRUE, skips loading the core methods, forcing those
// to be read from their individual directories. Set this
// true if you want to do some code debugging by inserting
// System.out.println, document.title, or alert commands
// anywhere in the Java or Jmol code.

Jmol._debugCode = (s.indexOf("debugcode") >= 0);

jmol_isReady = function(applet) {
	Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
}

var Styles = [];
Styles.push(["reset lighting; set cartoonsfancy off;set hermitelevel 0;set antialiasDisplay", "Jmol Fast Style"]);
Styles.push(["reset lighting; set cartoonsfancy; set hermitelevel 20;set antialiasDisplay;", "Jmol Fancy Style"]);
Styles.push(["set ambientpercent 25; set specularpower 100; set specularpercent 22; set specularexponent 4; set cartoonsfancy; set antialiasdisplay; set hermitelevel 20;","Chimera Style"]);

var xxxx = document.location.search
if (xxxx.indexOf("_USE=") > 0)xxxx = xxxx.substring(0, xxxx.indexOf("_USE=") - 1);
if (xxxx.length == 5 || xxxx.length == 0) {
	xxxx = (xxxx + "?1crn").substring(1,5)
	script = 'h2oOn=true;set animframecallback "jmolscript:if (!selectionHalos) {select model=_modelNumber}";'
     + ' set antialiasdisplay;'
	+'set errorCallback "myCallback";'
	+'set defaultloadscript "isDssp = false;set defaultVDW babel;if(!h2oOn){display !water}";'
	+'set zoomlarge false;set echo top left;echo loading XXXX...;refresh;'
	+'load "=XXXX";set echo top center;echo XXXX;'
	+'spacefill off;wireframe off;cartoons on;color structure;'
	script = script.replace(/XXXX/g, xxxx)
} else {
	script = unescape(xxxx.substring(1))
}


var Info = {
	width: 450,
	height: 450,
	debug: false,
	color: "white",
	addSelectionOptions: false,
	serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
	use: "HTML5",
	j2sPath: "j2s",
	readyFunction: jmol_isReady,
	script: script,
	//jarPath: "java",
	//jarFile: (useSignedApplet ? "JmolAppletSigned.jar" : "JmolApplet.jar"),
	//isSigned: useSignedApplet,
	//disableJ2SLoadMonitor: true,
	disableInitialConsole: true
	//defaultModel: "$dopamine",
	//console: "none", // default will be jmolApplet0_infodiv
}

Models = []

template = "xid='%1';load =%1|%2 (%1)"
function addModel(xxxx, text) {
 Models.push(template.replace(/\%1/g, xxxx).replace(/%2/g, text).split("|"))
}

addModel("1crn", "small")
addModel("1blu","Fe/S")
addModel("1bna","b-DNA")
addModel("1d66","transcription")

// these are conveniences that mimic behavior of Jmol.js

function jmolCheckbox(script1, script0,text,ischecked) {Jmol.jmolCheckbox(jmolApplet0,script1, script0, text, ischecked)}
function jmolButton(script, text) {Jmol.jmolButton(jmolApplet0, script,text)}
function jmolHtml(s) { document.write(s) };
function jmolBr() { jmolHtml("<br>") }
function jmolMenu(a) {Jmol.jmolMenu(jmolApplet0, a)}


</script>
</head>
<body onload="document.getElementsByTagName('form')[0].reset()">

<center>


<table><tr>
<td>
<i>set platformSpeed...</i>
<br>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 8')">8</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 7')">7</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 6')">6</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 5')">5</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 4')">4</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 3')">3</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 2')">2</a>
<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 1')">1</a>
</td>
<td align=center>

<script type="text/javascript">

jmolApplet0 = Jmol.getApplet("jmolApplet0", Info)

</script>
</td><td rowspan=2>
<form><!-- (FORM tag is important to automatically set checkbox off when page reloads) -->
<script type="text/javascript">
Jmol.setButtonCss(null,"style='width:160px'")
Jmol.setMenuCss(null,"style='width:160px'")
jmolButton("if (!xid) { xid = '1crn'};var x = prompt('Enter a four-digit PDB ID',xid);if (!x) { quit }; xid = x; load @{'=' + x}","Load PDB by ID")
jmolBr()
jmolCheckbox("set pdbAddHydrogens TRUE","set pdbAddHydrogens FALSE","with hydrogens",false)
jmolBr()
jmolCheckbox("set defaultLoadFilter 'biomolecule 1'","set defaultLoadFilter ''","biomolecule 1",false)
jmolBr()
jmolHtml("Examples:")
jmolBr()
jmolMenu(Models)
jmolBr()
jmolButton("if (!molname) { molname = 'tylenol'};var x = prompt('Enter the name or identifier (SMILES, InChI, CAS) of a molecule',molname);if (!x) { quit }; molname = x; load @{'$' + molname}","Load MOL by NAME")
jmolBr()
jmolButton("load ?","Load URL")
jmolBr()
jmolButton("load file://?","Load FILE")
jmolBr()
jmolButton("script ?.spt","Load SCRIPT")
jmolBr()
jmolBr()
jmolCheckbox("if (getproperty('shapeInfo.isosurface').length){isosurface on} else {isosurface @{'='+_modelName};}","isosurface off","show electron density",false)
jmolBr()
jmolBr()
jmolMenu(Styles)
jmolBr()
jmolCheckbox("set antialiasdisplay TRUE","set antialiasdisplay FALSE","antialiasDisplay",true)
jmolBr()
jmolCheckbox("h2oOn=true;display *","h2oOn=false;display !water","display water",true)
jmolBr()
jmolCheckbox("set zshade true","set zshade false","zshade (fog)",false)
jmolBr()
jmolCheckbox("background black","background white","background black",false)
jmolBr()
jmolBr()
jmolButton("write FILE ?","Save FILE")
jmolBr()
jmolButton("write IMAGE jsmol.jpg","Save JPG")
jmolBr()
jmolButton("write IMAGE jsmol.png","Save PNG")
jmolBr()
jmolButton("write jsmol.jmol","Save Jmol")
jmolBr()
jmolButton("write PNGJ jsmol.png","Save PNG+Jmol")
jmolBr()
jmolButton("write STATE jsmol.spt","Save STATE")
jmolBr()


</script>
</form>
</td></tr>
<tr>
<td></td>
<td align=center>


<script type="text/javascript">
jmolBr()
Jmol.setButtonCss(null,"style='width:120px'")
jmolButton("color cpk")
jmolButton("color group")
jmolButton("color amino")
jmolButton("color structure")
jmolBr()
Jmol.setButtonCss(null,"style='width:96px'")
jmolButton("backbone only", "backbone")
jmolButton("trace only", "trace")
jmolButton("cartoon only", "cartoon")
jmolButton("spacefill only", "spacefill")
jmolButton("spacefill only;spacefill 23%;wireframe 0.15","ball&stick")
jmolBr()
Jmol.setButtonCss(null,"style='width:60px'")
jmolButton("Model")
Jmol.setButtonCss(null,"style='width:50px'")
jmolButton("model; if (!isDssp) { save structure s1; isDssp = true; calculate structure DSSP;cartoons only;color structure}", "DSSP")
Jmol.setButtonCss(null,"style='width:50px'")
jmolButton("model; if (isDssp) { restore structure s1; isDssp = false; cartoons only;color structure}", "Auth")
Jmol.setButtonCss(null,"style='width:160px'")
jmolButton("Ramachandran relative")
jmolButton("Quaternion difference")
jmolBr()
Jmol.setButtonCss(null,"style='width:100px'")
jmolButton("console")
Jmol.jmolCommandInput(jmolApplet0)
</script>

</td></tr></table>

</body>
</html>