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

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<!DOCTYPE html>
<html>
<head>
<title>Jmol CIP Demo</title>
<meta charset="utf-8" />
<script type="text/javascript" src="JSmol.min.js"></script>
<script type="text/javascript" src="js/JSmolJME.js"></script>
<script type="text/javascript" language="javascript" src="jsme/jsme/jsme.nocache.js"></script>

<script type="text/javascript">

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


calcscript = ";select *;calculate chirality;set labelfor {*} \"%[chirality]\";"
styleYellow = ";select *;font label 20;set labeloffset 10 10; background label yellow;color labels black;set labelfor {*} \"%[chirality]\";"
style2 = ";select *;font label 20;set labelfront;set labeloffset 0 0;display remove _H;background labels none;set labelfor {chirality == ''} \"\";select {chirality == ''};spacefill off;set labelfor {*} \"%a %[chirality]\";"
style3 = ";select *;font label 20;set labelfront;set labeloffset 0 0;display remove _H;background labels none;set labelfor {chirality == ''} \"\";select {chirality == ''};spacefill off;set labelfor {chirality != ''} \"%a %[chirality]\";"

var jmol="jmol";
var jme = "jme";

var defaultScript = "set zoomlarge false; "
if (document.location.href.indexOf("model=") >= 0) {
 defaultScript = "set zoomlarge false; load \"$" + document.location.href.split("model=")[1].split("&")[0] + "\";"
} else if (document.location.href.indexOf("load=") >= 0) {
 defaultScript = "set zoomlarge false;load \"" + document.location.href.split("load=")[1].split("&")[0] + "\";"
                + styleYellow
}

var JmolInfo = {
	width: 1000,
	height: 600,
	debug: false,
	color: "black",
	use: "HTML5",
  addSelectionOptions: true,
	serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
  disableJ2SLoadMonitor: true,
  disableInitialConsole: true,
  jarPath: "java",
	jarFile: "JmolAppletSigned.jar",
  j2sPath: "j2s",
	isSigned: true,
  defaultModel: "",
	script: defaultScript + ";calculate chirality;label %[chirality];"
	+"background label yellow;color labels black;set antialiasdisplay;"
	+"set atomMovedCallback 'jmolScript:calculate Chirality;label %[chirality]';"
}

var JMEInfo = {
	use: "HTML5"
  ,visible: true
  ,divId: "jmediv"
  ,options : "autoez;nocanonize"
	//,jarPath: "jme",
	//,jarFile: "JME.jar"
  //optional parameters
  //,"jme" : startingStructure
}

//Jmol.setGrabberOptions([[":", "PubChem"]])
//Jmol.setGrabberOptions([["$", "NCI"]])


function showSmiles(from3d) {
  $("#jsmolsmiles").html(jmol._getSmiles("/opensmiles/"));
  $("#jsmesmiles").html(jme._getSmiles());
}

</script>
</head>
<body>
<table width=1000 cellpadding=10>
<tr>
<td>
<H3>Cahn-Ingold-Prelog Stereochemistry Page</H3>
Draw compounds in 2D and convert them to 3D or search for models in 3D, then show Jmol's
calculation of the <a target=_blank href=https://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules>CIP descriptors</a>
for that compound. You can save your work as an <a target=_blank href=https://en.wikipedia.org/wiki/Chemical_table_file#SDF>SDF model file</a>
 or as a <a target=_blank href=http://wiki.jmol.org/index.php/File_formats/Compressed#PNGJ>PNG+Jmol image/model</a> (droppable back into this page or into Jmol).
<br><br>

<br>
<br>

<div id="jmediv" style="position:relative;width:350px;height:300px;"></div></td>
<td>
<input type="button" onclick="Jmol.show2d(jmol, false);showSmiles(false)" value="&#8594" />
<br>
<input type="button" onclick="Jmol.show2d(jmol, true);showSmiles(true)" value="&#8592" />
</td>
<td>

<a href="javascript:Jmol.showInfo(jmol, true)">info</a>
<a href="javascript:Jmol.clearConsole(jmol)">clear</a>
<a href="javascript:Jmol.showInfo(jmol, false)">no info</a>
<br>
<script>
jmol = Jmol.getApplet(jmol, JmolInfo)
jme = Jmol.getJMEApplet(jme, JMEInfo, jmol);

//Jmol.jmolButton(jmol, "load $glucose;" + calcscript + //styleYellow, "glucose");
Jmol.jmolHtml("<center>")
Jmol.jmolHtml("<br>")
Jmol.jmolButton(jmol, calcscript + styleYellow,"show R/S")
Jmol.jmolButton(jmol, calcscript + "set labelfor {chirality != ''} \"%[chirality](%[cipRule])\"","show CIP rule")
Jmol.jmolButton(jmol, "if(picking != 'identify'){set picking identify" + calcscript + ";prompt 'picking set to IDENTIFY'}else{set picking invertstereo; prompt 'picking set to INVERTSTEREO - click on an atom to invert it'};set labelfor {!_H} \"%a\"","toggle select/invert center")
Jmol.jmolHtml("<br>")
Jmol.jmolButton(jmol, styleYellow,"display style 1")
Jmol.jmolButton(jmol, style2,"display style 2")
Jmol.jmolButton(jmol, style3,"display style 3")
Jmol.jmolHtml("<br>")
Jmol.jmolButton(jmol, "select *;invertselected plane xy;" + calcscript,"invert all chirality")
Jmol.jmolButton(jmol, "set modelkitmode @{!modelkitmode}","toggle modelKitMode")
Jmol.jmolHtml("<br>")
Jmol.jmolButton(jmol, "select *; write coord test.sdf","save SDF")
Jmol.jmolButton(jmol, "select *; write test.pngj","save PNG+Jmol")
Jmol.jmolButton(jmol, "console","open console")
Jmol.jmolHtml("</center>")
</script>
</tr>
</table>
<br>
JSME SMILES: <span id="jsmesmiles"></span>
<br>
JSmol OpenSMILES: <span id="jsmolsmiles"></span>
</body>
</html>