+++ /dev/null
-/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson
-
- checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
-
- based on:
- *
- * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: hansonr@stolaf.edu
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
- * 02111-1307 USA.
- */
-
-// for documentation see www.jmol.org/jslibrary
-
-try{if(typeof(_jmol)!="undefined")exit()
-
-// place "?NOAPPLET" on your command line to check applet control action with a textarea
-// place "?JMOLJAR=xxxxx" to use a specific jar file
-
-// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
-// angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet
-// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
-// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
-// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
-// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
-// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
-// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
-// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
-// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
-// bob hanson -- fix for iframes not available for finding applet
-// bob hanson -- added applet fake ?NOAPPLET URL flag
-// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
-// used PRIOR to jmolApplet() or jmolAppletInline()
-// added 4th array element in jmolRadioGroup -- title
-// added <span> and id around link, checkbox, radio, menu
-// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
-// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
-// renamed Jmol.js for Jmol 11 distribution
-// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
-// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
-// bh -- jmolCommandInput()
-// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
-// bh -- minor fixes suggested by Angel
-// bh -- adds jmolSetSyncId() and jmolGetSyncId()
-// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()
-// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()
-// bh 6/2008 -- adds jmolSetAppletWindow()
-// Angel H. 6/2008 -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]
-// bh 7/2008 -- code fix "for(i..." not "for(var i..."
-// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
-// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
-
-// bh 5/2009 -- Support for XHTML using jmolSetXHTML(id)
-// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax
-// bh 11/2009 -- care in accessing top.document
-// bh 12/2009 -- added jmolSetParameter(name, value)
-// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line
-// bh 12/2009 -- overhaul of target checking
-// bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list
-// bh 1/2010 -- adds option to run a JavaScript function from any Jmol control.
-// This is accomplished by passing an array rather than a script:
-// jmolHref([myfunc,"my param 1", "my param 2"], "testing")
-// function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}
-// and allows much more flexibility with responding to controls
-// bh 4/2010 -- added jmolSetMemoryMb(nMb)
-// ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag;
-// fix of object tag (removed classid) accounts for change of behavior in Chrome
-// bh 3/2011 -- added jmolLoadAjax_STOLAF_NIH
-
-var defaultdir = "."
-var defaultjar = "JmolApplet.jar"
-
-
-// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:
-
-// JMOLJAR=xxxxx.jar on the URL for this page will override
-// the JAR file specified in the jmolInitialize() call.
-
-// The idea is that it can be very useful to test a web page with different JAR files
-// Or for an expert user to substitute a signed applet for an unsigned one
-// so as to use a broader range of models or to create JPEG files, for example.
-
-// If the JAR file is not in the current directory (has any sort of "/" in its name)
-// then the user is presented with a warning and asked whether it is OK to change Jar files.
-// The default action, if the user just presses "OK" is to NOT allow the change.
-// The user must type the word "yes" in the prompt box for the change to be approved.
-
-// If you don't want people to be able to switch in their own JAR file on your page,
-// simply set this next line to read "var allowJMOLJAR = false".
-
-
-var undefined; // for IE 5 ... wherein undefined is undefined
-
-////////////////////////////////////////////////////////////////
-// Basic Scripting infrastruture
-////////////////////////////////////////////////////////////////
-
-function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
- if (_jmol.initialized)
- return;
- _jmol.initialized = true;
- if(_jmol.jmoljar) {
- var f = _jmol.jmoljar;
- if (f.indexOf("/") >= 0) {
- alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")
- var ok = prompt("Do you want to use applet " + f + "? ","yes or no")
- if (ok == "yes") {
- codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
- fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
- } else {
- _jmolGetJarFilename(fileNameOrUseSignedApplet);
- alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
- }
- } else {
- fileNameOrUseSignedApplet = f;
- }
- }
- _jmolSetCodebase(codebaseDirectory);
- _jmolGetJarFilename(fileNameOrUseSignedApplet);
- _jmolOnloadResetForms();
-}
-
-function jmolSetTranslation(TF) {
- _jmol.params.doTranslate = ''+TF;
-}
-
-function _jmolGetJarFilename(fileNameOrFlag) {
- _jmol.archivePath =
- (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");
-}
-
-function jmolSetDocument(doc) {
- _jmol.currentDocument = doc;
-}
-
-function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
- _jmolInitCheck();
- _jmol.params.boxbgcolor = boxbgcolor;
- if (boxfgcolor)
- _jmol.params.boxfgcolor = boxfgcolor
- else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
- _jmol.params.boxfgcolor = "black";
- else
- _jmol.params.boxfgcolor = "white";
- if (progresscolor)
- _jmol.params.progresscolor = progresscolor;
- if (_jmol.debugAlert)
- alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
- " boxfgcolor=" + _jmol.params.boxfgcolor +
- " progresscolor=" + _jmol.params.progresscolor);
-}
-
-function jmolSetAppletWindow(w) {
- _jmol.appletWindow = w;
-}
-
-function jmolApplet(size, script, nameSuffix) {
- _jmolInitCheck();
- return _jmolApplet(size, null, script, nameSuffix);
-}
-
-////////////////////////////////////////////////////////////////
-// Basic controls
-////////////////////////////////////////////////////////////////
-
-// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)
-
-function jmolButton(script, label, id, title) {
- _jmolInitCheck();
- id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);
- label != undefined && label != null || (label = script.substring(0, 32));
- ++_jmol.buttonCount;
- var scriptIndex = _jmolAddScript(script);
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
- "' value='" + label +
- "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +
- ")' onmouseover='_jmolMouseOver(" + scriptIndex +
- ");return true' onmouseout='_jmolMouseOut()' " +
- _jmol.buttonCssText + " /></span>";
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
- labelHtml, isChecked, id, title) {
- _jmolInitCheck();
- id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);
- ++_jmol.checkboxCount;
- if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
- scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
- alert("jmolCheckbox requires two scripts");
- return;
- }
- if (labelHtml == undefined || labelHtml == null) {
- alert("jmolCheckbox requires a label");
- return;
- }
- var indexChecked = _jmolAddScript(scriptWhenChecked);
- var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
- var eospan = "</span>"
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
- "' onclick='_jmolCbClick(this," +
- indexChecked + "," + indexUnchecked + _jmol.targetText +
- ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +
- indexUnchecked +
- ");return true' onmouseout='_jmolMouseOut()' " +
- (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />"
- if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
- t += eospan
- eospan = "";
- }
- t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-function jmolStartNewRadioGroup() {
- ++_jmol.radioGroupCount;
-}
-
-function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
- /*
-
- array: [radio1,radio2,radio3...]
- where radioN = ["script","label",isSelected,"id","title"]
-
- */
-
- _jmolInitCheck();
- var type = typeof arrayOfRadioButtons;
- if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
- alert("invalid arrayOfRadioButtons");
- return;
- }
- separatorHtml != undefined && separatorHtml != null || (separatorHtml = " ");
- var len = arrayOfRadioButtons.length;
- jmolStartNewRadioGroup();
- groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
- var t = "<span id='"+(id ? id : groupName)+"'>";
- for (var i = 0; i < len; ++i) {
- if (i == len - 1)
- separatorHtml = "";
- var radio = arrayOfRadioButtons[i];
- type = typeof radio;
- if (type == "object") {
- t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);
- } else {
- t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
- }
- }
- t+="</span>"
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-
-function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
- _jmolInitCheck();
- if (_jmol.radioGroupCount == 0)
- ++_jmol.radioGroupCount;
- var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-function jmolLink(script, label, id, title) {
- _jmolInitCheck();
- id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);
- label != undefined && label != null || (label = script.substring(0, 32));
- ++_jmol.linkCount;
- var scriptIndex = _jmolAddScript(script);
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><a name='" + id + "' id='" + id +
- "' href='javascript:_jmolClick(this," + scriptIndex + _jmol.targetText + ");' onmouseover='_jmolMouseOver(" + scriptIndex +
- ");return true;' onmouseout='_jmolMouseOut()' " +
- _jmol.linkCssText + ">" + label + "</a></span>";
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-function jmolCommandInput(label, size, id, title) {
- _jmolInitCheck();
- id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);
- label != undefined && label != null || (label = "Execute");
- size != undefined && !isNaN(size) || (size = 60);
- ++_jmol.cmdCount;
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id +
- "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
-}
-
-function _jmolCommandKeyPress(e, id, target) {
- var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);
- if (keycode == 13) {
- var inputBox = document.getElementById(id)
- _jmolScriptExecute(inputBox, inputBox.value, target)
- }
-}
-
-function _jmolScriptExecute(element,script,target) {
- if (typeof(script) == "object")
- script[0](element, script, target)
- else
- jmolScript(script, target)
-}
-
-function jmolMenu(arrayOfMenuItems, size, id, title) {
- _jmolInitCheck();
- id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);
- ++_jmol.menuCount;
- var type = typeof arrayOfMenuItems;
- if (type != null && type == "object" && arrayOfMenuItems.length) {
- var len = arrayOfMenuItems.length;
- if (typeof size != "number" || size == 1)
- size = null;
- else if (size < 0)
- size = len;
- var sizeText = size ? " size='" + size + "' " : "";
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
- "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
- sizeText + _jmol.menuCssText + ">";
- for (var i = 0; i < len; ++i) {
- var menuItem = arrayOfMenuItems[i];
- type = typeof menuItem;
- var script, text;
- var isSelected = undefined;
- if (type == "object" && menuItem != null) {
- script = menuItem[0];
- text = menuItem[1];
- isSelected = menuItem[2];
- } else {
- script = text = menuItem;
- }
- text != undefined && text != null || (text = script);
- if (script=="#optgroup") {
- t += "<optgroup label='" + text + "'>";
- } else if (script=="#optgroupEnd") {
- t += "</optgroup>";
- } else {
- var scriptIndex = _jmolAddScript(script);
- var selectedText = isSelected ? "' selected='true'>" : "'>";
- t += "<option value='" + scriptIndex + selectedText + text + "</option>";
- }
- }
- t += "</select></span>";
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
- }
-}
-
-function jmolHtml(html) {
- return _jmolDocumentWrite(html);
-}
-
-function jmolBr() {
- return _jmolDocumentWrite("<br />");
-}
-
-////////////////////////////////////////////////////////////////
-// advanced scripting functions
-////////////////////////////////////////////////////////////////
-
-function jmolDebugAlert(enableAlerts) {
- _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
-}
-
-function jmolAppletInline(size, inlineModel, script, nameSuffix) {
- _jmolInitCheck();
- return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
- script, nameSuffix);
-}
-
-function jmolSetTarget(targetSuffix) {
- _jmol.targetSuffix = targetSuffix;
- _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";
-}
-
-function jmolScript(script, targetSuffix) {
- if (script) {
- _jmolCheckBrowser();
- if (targetSuffix == "all") {
- with (_jmol) {
- for (var i = 0; i < appletSuffixes.length; ++i) {
- var applet = _jmolGetApplet(appletSuffixes[i]);
- if (applet) applet.script(script);
- }
- }
- } else {
- var applet=_jmolGetApplet(targetSuffix);
- if (applet) applet.script(script);
- }
- }
-}
-
-function jmolLoadInline(model, targetSuffix) {
- if (!model)return "ERROR: NO MODEL"
- var applet=_jmolGetApplet(targetSuffix);
- if (!applet)return "ERROR: NO APPLET"
- if (typeof(model) == "string")
- return applet.loadInlineString(model, "", false);
- else
- return applet.loadInlineArray(model, "", false);
-}
-
-
-function jmolLoadInlineScript(model, script, targetSuffix) {
- if (!model)return "ERROR: NO MODEL"
- var applet=_jmolGetApplet(targetSuffix);
- if (!applet)return "ERROR: NO APPLET"
- return applet.loadInlineString(model, script, false);
-}
-
-
-function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
- if (!model)return "ERROR: NO MODEL"
- script || (script="")
- var applet=_jmolGetApplet(targetSuffix);
- if (!applet)return "ERROR: NO APPLET"
- try {
- return applet.loadInlineArray(ModelArray, script, false);
- } catch (err) {
- //IE 7 bug
- return applet.loadInlineString(ModelArray.join("\n"), script, false);
- }
-}
-
-function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
- if (!model)return "ERROR: NO MODEL"
- script || (script="")
- var applet=_jmolGetApplet(targetSuffix);
- if (!applet)return "ERROR: NO APPLET"
- try {
- return applet.loadInlineArray(ModelArray, script, true);
- } catch (err) {
- //IE 7 bug
- return applet.loadInlineString(ModelArray.join("\n"), script, true);
- }
-}
-
-function jmolAppendInlineScript(model, script, targetSuffix) {
- if (!model)return "ERROR: NO MODEL"
- var applet=_jmolGetApplet(targetSuffix);
- if (!applet)return "ERROR: NO APPLET"
- return applet.loadInlineString(model, script, true);
-}
-
-function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
- if (typeof action == "string") {
- action = action.toLowerCase();
- action == "alert" || action == "redirect" || action == "popup" || (action = null);
- }
- if (typeof action != "string")
- alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
- "action must be 'alert', 'redirect', or 'popup'");
- else {
- if (typeof urlOrMessage != "string")
- alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
- "urlOrMessage must be a string");
- else {
- _jmol.checkBrowserAction = action;
- _jmol.checkBrowserUrlOrMessage = urlOrMessage;
- }
- }
- if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
- _jmolCheckBrowser();
-}
-
-////////////////////////////////////////////////////////////////
-// Cascading Style Sheet Class support
-////////////////////////////////////////////////////////////////
-
-function jmolSetAppletCssClass(appletCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.appletCssClass = appletCssClass;
- _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
- }
-}
-
-function jmolSetButtonCssClass(buttonCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.buttonCssClass = buttonCssClass;
- _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
- }
-}
-
-function jmolSetCheckboxCssClass(checkboxCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.checkboxCssClass = checkboxCssClass;
- _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
- }
-}
-
-function jmolSetRadioCssClass(radioCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.radioCssClass = radioCssClass;
- _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
- }
-}
-
-function jmolSetLinkCssClass(linkCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.linkCssClass = linkCssClass;
- _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
- }
-}
-
-function jmolSetMenuCssClass(menuCssClass) {
- if (_jmol.hasGetElementById) {
- _jmol.menuCssClass = menuCssClass;
- _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
- }
-}
-
-////////////////////////////////////////////////////////////////
-// functions for INTERNAL USE ONLY which are subject to change
-// use at your own risk ... you have been WARNED!
-////////////////////////////////////////////////////////////////
-var _jmol = {
- currentDocument: document,
-
- debugAlert: false,
-
- codebase: "",
- modelbase: ".",
-
- appletCount: 0,
- appletSuffixes: [],
- appletWindow: null,
- allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)
- /* By setting the _jmol.allowedJmolSize[] variable in the webpage
- before calling jmolApplet(), limits for applet size can be overriden.
- 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
- */
- buttonCount: 0,
- checkboxCount: 0,
- linkCount: 0,
- cmdCount: 0,
- menuCount: 0,
- radioCount: 0,
- radioGroupCount: 0,
-
- appletCssClass: null,
- appletCssText: "",
- buttonCssClass: null,
- buttonCssText: "",
- checkboxCssClass: null,
- checkboxCssText: "",
- java_arguments: "-Xmx512m",
- radioCssClass: null,
- radioCssText: "",
- linkCssClass: null,
- linkCssText: "",
- menuCssClass: null,
- menuCssText: "",
-
- targetSuffix: 0,
- targetText: ",0",
- scripts: [""],
- params: {
- syncId: ("" + Math.random()).substring(3),
- progressbar: "true",
- progresscolor: "blue",
- boxbgcolor: "black",
- boxfgcolor: "white",
- boxmessage: "Downloading JmolApplet ..."
- },
- ua: navigator.userAgent.toLowerCase(),
- // uaVersion: parseFloat(navigator.appVersion), // not used
-
- os: "unknown",
- browser: "unknown",
- browserVersion: 0,
- hasGetElementById: !!document.getElementById,
- isJavaEnabled: navigator.javaEnabled(),
- // isNetscape47Win: false, // not used, N4.7 is no longer supported even for detection
- useIEObject: false,
- useHtml4Object: false,
-
- windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
- windowsCabUrl:
- "http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab",
-
- isBrowserCompliant: false,
- isJavaCompliant: false,
- isFullyCompliant: false,
-
- initialized: false,
- initChecked: false,
-
- browserChecked: false,
- checkBrowserAction: "alert",
- checkBrowserUrlOrMessage: null,
-
- archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
-
- previousOnloadHandler: null,
-
- jmoljar: null,
- useNoApplet: false,
-
- ready: {}
-}
-
-with (_jmol) {
- function _jmolTestUA(candidate) {
- var ua = _jmol.ua;
- var index = ua.indexOf(candidate);
- if (index < 0)
- return false;
- _jmol.browser = candidate;
- _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
- return true;
- }
-
- function _jmolTestOS(candidate) {
- if (_jmol.ua.indexOf(candidate) < 0)
- return false;
- _jmol.os = candidate;
- return true;
- }
-
- _jmolTestUA("konqueror") ||
- _jmolTestUA("webkit") ||
- _jmolTestUA("omniweb") ||
- _jmolTestUA("opera") ||
- _jmolTestUA("webtv") ||
- _jmolTestUA("icab") ||
- _jmolTestUA("msie") ||
- (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); //Netscape, Mozilla, Seamonkey, Firefox and anything assimilated
-
- _jmolTestOS("linux") ||
- _jmolTestOS("unix") ||
- _jmolTestOS("mac") ||
- _jmolTestOS("win");
-
- /* not used:
- isNetscape47Win = (os == "win" && browser == "mozilla" &&
- browserVersion >= 4.78 && browserVersion <= 4.8);
- */
-
- if (os == "win") {
- isBrowserCompliant = hasGetElementById;
- } else if (os == "mac") { // mac is the problem child :-(
- if (browser == "mozilla" && browserVersion >= 5) {
- // miguel 2004 11 17
- // checking the plugins array does not work because
- // Netscape 7.2 OS X still has Java 1.3.1 listed even though
- // javaplugin.sf.net is installed to upgrade to 1.4.2
- eval("try {var v = java.lang.System.getProperty('java.version');" +
- " _jmol.isBrowserCompliant = v >= '1.4.2';" +
- " } catch (e) { }");
- } else if (browser == "opera" && browserVersion <= 7.54) {
- isBrowserCompliant = false;
- } else {
- isBrowserCompliant = hasGetElementById &&
- !((browser == "msie") ||
- (browser == "webkit" && browserVersion < 125.12));
- }
- } else if (os == "linux" || os == "unix") {
- if (browser == "konqueror" && browserVersion <= 3.3)
- isBrowserCompliant = false;
- else
- isBrowserCompliant = hasGetElementById;
- } else { // other OS
- isBrowserCompliant = hasGetElementById;
- }
-
- // possibly more checks in the future for this
- isJavaCompliant = isJavaEnabled;
-
- isFullyCompliant = isBrowserCompliant && isJavaCompliant;
-
- useIEObject = (os == "win" && browser == "msie" && browserVersion >= 5.5);
- useHtml4Object =
- (browser == "mozilla" && browserVersion >= 5) ||
- (browser == "opera" && browserVersion >= 8) ||
- (browser == "webkit" && browserVersion >= 412.2);
- try {
- if (top.location.search.indexOf("JMOLJAR=")>=0)
- jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];
- } catch(e) {
- // can't access top.location
- }
- try {
- useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);
- } catch(e) {
- // can't access top.document
- }
-}
-
-function jmolSetMemoryMb(nMb) {
- _jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"
-}
-
-function jmolSetParameter(name,value) {
- _jmol.params[name] = value
-}
-
-function jmolSetCallback(callbackName,funcName) {
- _jmol.params[callbackName] = funcName
-}
-
- try {
-// note this is done FIRST, so it cannot override a setting done by the developer
- if (top.location.search.indexOf("PARAMS=")>=0) {
- var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");
- for (var i = 0; i < pars.length; i++) {
- var p = pars[i].split(":");
- jmolSetParameter(p[0],p[1]);
- }
- }
- } catch(e) {
- // can't access top.location
- }
-
-function jmolSetSyncId(n) {
- return _jmol.params["syncId"] = n
-}
-
-function jmolGetSyncId() {
- return _jmol.params["syncId"]
-}
-
-function jmolSetLogLevel(n) {
- _jmol.params.logLevel = ''+n;
-}
-
- /* AngelH, mar2007:
- By (re)setting these variables in the webpage before calling jmolApplet(),
- a custom message can be provided (e.g. localized for user's language) when no Java is installed.
- */
-if (noJavaMsg==undefined) var noJavaMsg =
- "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
- "Check the warning message from your browser and/or enable Java applets in<br />\n" +
- "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
-if (noJavaMsg2==undefined) var noJavaMsg2 =
- "You do not have the<br />\n" +
- "Java Runtime Environment<br />\n" +
- "installed for applet support.<br />\n" +
- "Visit <a href='http://www.java.com'>www.java.com</a>";
-function _jmolApplet(size, inlineModel, script, nameSuffix) {
- /* AngelH, mar2007
- Fixed percent / pixel business, to avoid browser errors:
- put "px" where needed, avoid where not.
-
- Bob Hanson, 1/2010
- Fixed inline escape changing returns to |
- */
- with (_jmol) {
- nameSuffix == undefined && (nameSuffix = appletCount);
- appletSuffixes.push(nameSuffix);
- ++appletCount;
- script || (script = "select *");
- var sz = _jmolGetAppletSize(size);
- var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
- var tHeader, tFooter;
- codebase || jmolInitialize(".");
- if (useIEObject || useHtml4Object) {
- params.archive = archivePath;
- params.mayscript = 'true';
- params.codebase = codebase;
- params.code = 'JmolApplet';
- tHeader =
- "<object name='jmolApplet" + nameSuffix +
- "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
- widthAndHeight + "\n";
- tFooter = "</object>";
- }
- if (java_arguments)
- params.java_arguments = java_arguments;
- if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
- tHeader += " classid='" + windowsClassId + "'\n" +
- (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "") + ">\n";
- } else if (useHtml4Object) { // use HTML4 object tag
- tHeader += " type='application/x-java-applet'\n>\n";
- /* " classid='java:JmolApplet'\n" + AH removed this
- Chromium Issue 62076: Java Applets using an <object> with a classid paramater don't load.
- http://code.google.com/p/chromium/issues/detail?id=62076
- They say this is the correct behavior according to the spec, and there's no indication at this point
- that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.
- Removing the classid parameter seems to be well tolerated by all browsers (even IE!).
- */
- } else { // use applet tag
- tHeader =
- "<applet name='jmolApplet" + nameSuffix +
- "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
- widthAndHeight + "\n" +
- " code='JmolApplet'" +
- " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
- " mayscript='true'>\n";
- tFooter = "</applet>";
- }
- var visitJava;
- if (useIEObject || useHtml4Object) {
- var szX = "width:" + sz[0]
- if ( szX.indexOf("%")==-1 ) szX+="px"
- var szY = "height:" + sz[1]
- if ( szY.indexOf("%")==-1 ) szY+="px"
- visitJava =
- "<p style='background-color:yellow; color:black; " +
- szX + ";" + szY + ";" +
- // why doesn't this vertical-align work?
- "text-align:center;vertical-align:middle;'>\n" +
- noJavaMsg +
- "</p>";
- } else {
- visitJava =
- "<table bgcolor='yellow'><tr>" +
- "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
- noJavaMsg2 +
- "</font></td></tr></table>";
- }
- params.loadInline = (inlineModel ? inlineModel : "");
- params.script = (script ? _jmolSterilizeScript(script) : "");
- var t = tHeader + _jmolParams() + visitJava + tFooter;
- jmolSetTarget(nameSuffix);
- ready["jmolApplet" + nameSuffix] = false;
- if (_jmol.debugAlert)
- alert(t);
- return _jmolDocumentWrite(t);
- }
-}
-
-function _jmolParams() {
- var t = "";
- for (var i in _jmol.params)
- if(_jmol.params[i]!="")
- t+=" <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
- return t
-}
-
-function _jmolInitCheck() {
- if (_jmol.initChecked)
- return;
- _jmol.initChecked = true;
- jmolInitialize(defaultdir, defaultjar)
-}
-
-function _jmolCheckBrowser() {
- with (_jmol) {
- if (browserChecked)
- return;
- browserChecked = true;
-
- if (isFullyCompliant)
- return true;
-
- if (checkBrowserAction == "redirect")
- location.href = checkBrowserUrlOrMessage;
- else if (checkBrowserAction == "popup")
- _jmolPopup(checkBrowserUrlOrMessage);
- else {
- var msg = checkBrowserUrlOrMessage;
- if (msg == null)
- msg = "Your web browser is not fully compatible with Jmol\n\n" +
- "browser: " + browser +
- " version: " + browserVersion +
- " os: " + os +
- " isBrowserCompliant: " + isBrowserCompliant +
- " isJavaCompliant: " + isJavaCompliant +
- "\n\n" + ua;
- alert(msg);
- }
- }
- return false;
-}
-
-function jmolSetXHTML(id) {
- _jmol.isXHTML = true
- _jmol.XhtmlElement = null
- _jmol.XhtmlAppendChild = false
- if (id){
- _jmol.XhtmlElement = document.getElementById(id)
- _jmol.XhtmlAppendChild = true
- }
-}
-
-function _jmolDocumentWrite(text) {
- if (_jmol.currentDocument) {
- if (_jmol.isXHTML && !_jmol.XhtmlElement) {
- var s = document.getElementsByTagName("script")
- _jmol.XhtmlElement = s.item(s.length - 1)
- _jmol.XhtmlAppendChild = false
- }
- if (_jmol.XhtmlElement) {
- _jmolDomDocumentWrite(text)
- } else {
- _jmol.currentDocument.write(text);
- }
- }
- return text;
-}
-
-function _jmolDomDocumentWrite(data) {
- var pt = 0
- var Ptr = []
- Ptr[0] = 0
- while (Ptr[0] < data.length) {
- var child = _jmolGetDomElement(data, Ptr)
- if (!child)break
- if (_jmol.XhtmlAppendChild)
- _jmol.XhtmlElement.appendChild(child)
- else
- _jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement);
- }
-}
-function _jmolGetDomElement(data, Ptr, closetag, lvel) {
- var e = document.createElement("span")
- e.innerHTML = data
- Ptr[0] = data.length
- return e
-
-//unnecessary?
-
- closetag || (closetag = "")
- lvel || (lvel = 0)
- var pt0 = Ptr[0]
- var pt = pt0
- while (pt < data.length && data.charAt(pt) != "<") pt++
- if (pt != pt0) {
- var text = data.substring(pt0, pt)
- Ptr[0] = pt
- return document.createTextNode(text)
- }
- pt0 = ++pt
- var ch
- while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++
- var tagname = data.substring(pt0, pt)
- var e = (tagname == closetag || tagname == "/" ? ""
- : document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
- : document.createElement(tagname));
- if (ch == ">") {
- Ptr[0] = ++pt
- return e
- }
- while (pt < data.length && (ch = data.charAt(pt)) != ">") {
- while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
- pt0 = pt
- while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++
- var attrname = data.substring(pt0, pt).toLowerCase()
- if (attrname && ch != "=")
- e.setAttribute(attrname, "true")
- while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
- if (ch == "/") {
- Ptr[0] = pt + 2
- return e
- } else if (ch == "=") {
- var quote = data.charAt(++pt)
- pt0 = ++pt
- while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++
- var attrvalue = data.substring(pt0, pt)
- e.setAttribute(attrname, attrvalue)
- pt++
- }
- }
- Ptr[0] = ++pt
- while (Ptr[0] < data.length) {
- var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)
- if (!child)break
- e.appendChild(child)
- }
- return e
-}
-
-function _jmolPopup(url) {
- var popup = window.open(url, "JmolPopup",
- "left=150,top=150,height=400,width=600," +
- "directories=yes,location=yes,menubar=yes," +
- "toolbar=yes," +
- "resizable=yes,scrollbars=yes,status=yes");
- if (popup.focus)
- poup.focus();
-}
-
-function _jmolReadyCallback(name) {
- if (_jmol.debugAlert)
- alert(name + " is ready");
- _jmol.ready["" + name] = true;
-}
-
-function _jmolSterilizeScript(script) {
- script = script.replace(/'/g, "'");
- if (_jmol.debugAlert)
- alert("script:\n" + script);
- return script;
-}
-
-function _jmolSterilizeInline(model) {
- model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'");
- if (_jmol.debugAlert)
- alert("inline model:\n" + model);
- return model;
-}
-
-function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
- ++_jmol.radioCount;
- groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
- if (!script)
- return "";
- labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));
- separatorHtml || (separatorHtml = "")
- var scriptIndex = _jmolAddScript(script);
- var eospan = "</span>"
- var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='"
- + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +
- scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +
- scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +
- (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"
- if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
- t += eospan
- eospan = "";
- }
- t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;
-
- return t;
-}
-
-function _jmolFindApplet(target) {
- // first look for the target in the current window
- var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);
- // THEN look for the target in child frames
- if (applet == undefined)
- applet = _jmolSearchFrames(window, target);
- // FINALLY look for the target in sibling frames
- if (applet == undefined)
- applet = _jmolSearchFrames(top, target); // look starting in top frame
- return applet;
-}
-
-function _jmolGetApplet(targetSuffix){
- var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
- var applet = _jmolFindApplet(target);
- if (applet) return applet
- _jmol.alerted || alert("could not find applet " + target);
- _jmol.alerted = true;
- return null
-}
-
-function _jmolSearchFrames(win, target) {
- var applet;
- var frames = win.frames;
- if (frames && frames.length) { // look in all the frames below this window
- try{
- for (var i = 0; i < frames.length; ++i) {
- applet = _jmolSearchFrames(frames[i], target);
- if (applet)
- return applet;
- }
- }catch(e) {
- if (_jmol.debugAlert)
- alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()")
- }
- }
- return applet = _jmolFindAppletInWindow(win, target)
-}
-
-function _jmolFindAppletInWindow(win, target) {
- var doc = win.document;
- if (doc.getElementById(target))
- return doc.getElementById(target);
- else if (doc.applets)
- return doc.applets[target];
- else
- return doc[target];
-}
-
-function _jmolAddScript(script) {
- if (!script)
- return 0;
- var index = _jmol.scripts.length;
- _jmol.scripts[index] = script;
- return index;
-}
-
-function _jmolClick(elementClicked, scriptIndex, targetSuffix) {
- _jmol.element = elementClicked;
- _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);
-}
-
-function _jmolMenuSelected(menuObject, targetSuffix) {
- var scriptIndex = menuObject.value;
- if (scriptIndex != undefined) {
- _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);
- return;
- }
- var len = menuObject.length;
- if (typeof len == "number") {
- for (var i = 0; i < len; ++i) {
- if (menuObject[i].selected) {
- _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);
- return;
- }
- }
- }
- alert("?Que? menu selected bug #8734");
-}
-
-
-_jmol.checkboxMasters = {};
-_jmol.checkboxItems = {};
-
-function jmolSetCheckboxGroup(chkMaster,chkBox) {
- var id = chkMaster;
- if(typeof(id)=="number")id = "jmolCheckbox" + id;
- chkMaster = document.getElementById(id);
- if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
- var m = _jmol.checkboxMasters[id] = {};
- m.chkMaster = chkMaster;
- m.chkGroup = {};
- for (var i = 1; i < arguments.length; i++){
- var id = arguments[i];
- if(typeof(id)=="number")id = "jmolCheckbox" + id;
- checkboxItem = document.getElementById(id);
- if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
- m.chkGroup[id] = checkboxItem;
- _jmol.checkboxItems[id] = m;
- }
-}
-
-function _jmolNotifyMaster(m){
- //called when a group item is checked
- var allOn = true;
- var allOff = true;
- for (var chkBox in m.chkGroup){
- if(m.chkGroup[chkBox].checked)
- allOff = false;
- else
- allOn = false;
- }
- if (allOn)m.chkMaster.checked = true;
- if (allOff)m.chkMaster.checked = false;
- if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])
- _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
-}
-
-function _jmolNotifyGroup(m, isOn){
- //called when a master item is checked
- for (var chkBox in m.chkGroup){
- var item = m.chkGroup[chkBox]
- item.checked = isOn;
- if (_jmol.checkboxMasters[item.id])
- _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
- }
-}
-
-function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
- _jmol.control = ckbox
- _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
- if(_jmol.checkboxMasters[ckbox.id])
- _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
- if(_jmol.checkboxItems[ckbox.id])
- _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
-}
-
-function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
- window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
-}
-
-function _jmolMouseOver(scriptIndex) {
- window.status = _jmol.scripts[scriptIndex];
-}
-
-function _jmolMouseOut() {
- window.status = " ";
- return true;
-}
-
-function _jmolSetCodebase(codebase) {
- _jmol.codebase = codebase ? codebase : ".";
- if (_jmol.debugAlert)
- alert("jmolCodebase=" + _jmol.codebase);
-}
-
-function _jmolOnloadResetForms() {
- // must be evaluated ONLY once
- _jmol.previousOnloadHandler = window.onload;
- window.onload =
- function() {
- with (_jmol) {
- if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
- var forms = document.forms;
- for (var i = forms.length; --i >= 0; )
- forms[i].reset();
- }
- if (previousOnloadHandler)
- previousOnloadHandler();
- }
- }
-}
-
-////////////////////////////////////
-/////extensions for getProperty/////
-////////////////////////////////////
-
-
-function _jmolEvalJSON(s,key){
- s=s+""
- if(!s)return []
- if(s.charAt(0)!="{"){
- if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")
- return s
- }
- var A = eval("("+s+")")
- if(!A)return
- if(key && A[key])A=A[key]
- return A
-}
-
-function _jmolEnumerateObject(A,key){
- var sout=""
- if(typeof(A) == "string" && A!="null"){
- sout+="\n"+key+"=\""+A+"\""
- }else if(!isNaN(A)||A==null){
- sout+="\n"+key+"="+(A+""==""?"null":A)
- }else if(A.length){
- sout+=key+"=[]"
- for(var i=0;i<A.length;i++){
- sout+="\n"
- if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
- sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
- }else{
- sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
- }
- }
- }else{
- if(key != ""){
- sout+=key+"={}"
- key+="."
- }
-
- for(var i in A){
- sout+="\n"
- if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
- sout+=_jmolEnumerateObject(A[i],key+i)
- }else{
- sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
- }
- }
- }
- return sout
-}
-
-
-function _jmolSortKey0(a,b){
- return (a[0]<b[0]?1:a[0]>b[0]?-1:0)
-}
-
-function _jmolSortMessages(A){
- if(!A || typeof(A)!="object")return []
- var B = []
- for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]
- if(B.length == 0) return
- B=B.sort(_jmolSortKey0)
- return B
-}
-
-/////////additional extensions //////////
-
-
-function _jmolDomScriptLoad(URL){
- //open(URL) //to debug
- _jmol.servercall=URL
- var node = document.getElementById("_jmolScriptNode")
- if (node && _jmol.browser!="msie"){
- document.getElementsByTagName("HEAD")[0].removeChild(node)
- node=null
- }
- if (node) {
- node.setAttribute("src",URL)
- } else {
- node=document.createElement("script")
- node.setAttribute("id","_jmolScriptNode")
- node.setAttribute("type","text/javascript")
- node.setAttribute("src",URL)
- document.getElementsByTagName("HEAD")[0].appendChild(node)
- }
-}
-
-
-function _jmolExtractPostData(url){
- S=url.split("&POST:")
- var s=""
- for(var i=1;i<S.length;i++){
- KV=S[i].split("=")
- s+="&POSTKEY"+i+"="+KV[0]
- s+="&POSTVALUE"+i+"="+KV[1]
- }
- return "&url="+escape(S[0])+s
-}
-
-function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
- //called by server, but in client
- //overload this function to customize return
- _jmol.remoteURL=remoteURL
- isError && alert(errorMessage)
- jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
-}
-
-//////////user property/status functions/////////
-
-function jmolGetStatus(strStatus,targetSuffix){
- return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
-}
-
-function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
- return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
-}
-
-function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
- var applet = _jmolGetApplet(targetSuffix);
- sValue == undefined && (sValue="");
- return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
-}
-
-function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
- sValue == undefined && (sValue = "")
- var applet = _jmolGetApplet(targetSuffix);
- try {
- return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
- } catch(e) {
- return ""
- }
-}
-
-function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
- sValue == undefined && (sValue = "")
- var applet = _jmolGetApplet(targetSuffix);
- return (applet ? applet.getProperty(sKey,sValue) : null)
-}
-
-
-function jmolDecodeJSON(s) {
- return _jmolEnumerateObject(_jmolEvalJSON(s),"")
-}
-
-
-///////// synchronous scripting ////////
-
-function jmolScriptWait(script, targetSuffix) {
- targetSuffix == undefined && (targetSuffix="0")
- var Ret=jmolScriptWaitAsArray(script, targetSuffix)
- var s = ""
- for(var i=Ret.length;--i>=0;)
- for(var j=0;j< Ret[i].length;j++)
- s+=Ret[i][j]+"\n"
- return s
-}
-
-function jmolScriptWaitOutput(script, targetSuffix) {
- targetSuffix == undefined && (targetSuffix="0")
- var ret = ""
- try{
- if (script) {
- _jmolCheckBrowser();
- var applet=_jmolGetApplet(targetSuffix);
- if (applet) ret += applet.scriptWaitOutput(script);
- }
- }catch(e){
- }
- return ret;
-}
-
-function jmolEvaluate(molecularMath, targetSuffix) {
-
- //carries out molecular math on a model
-
- targetSuffix == undefined && (targetSuffix="0")
- var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
- var s = result.replace(/\-*\d+/,"")
- if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
- var s = result.replace(/\-*\d*\.\d*/,"")
- if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
- return result;
-}
-
-function jmolScriptEcho(script, targetSuffix) {
- // returns a newline-separated list of all echos from a script
- targetSuffix == undefined && (targetSuffix="0")
- var Ret=jmolScriptWaitAsArray(script, targetSuffix)
- var s = ""
- for(var i=Ret.length;--i>=0;)
- for(var j=Ret[i].length;--j>=0;)
- if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
- return s.replace(/ \| /g, "\n")
-}
-
-
-function jmolScriptMessage(script, targetSuffix) {
- // returns a newline-separated list of all messages from a script, ending with "script completed\n"
- targetSuffix == undefined && (targetSuffix="0")
- var Ret=jmolScriptWaitAsArray(script, targetSuffix)
- var s = ""
- for(var i=Ret.length;--i>=0;)
- for(var j=Ret[i].length;--j>=0;)
- if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
- return s.replace(/ \| /g, "\n")
-}
-
-
-function jmolScriptWaitAsArray(script, targetSuffix) {
- var ret = ""
- try{
- jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
- if (script) {
- _jmolCheckBrowser();
- var applet=_jmolGetApplet(targetSuffix);
- if (applet) ret += applet.scriptWait(script);
- ret = _jmolEvalJSON(ret,"jmolStatus")
- if(typeof ret == "object")
- return ret
- }
- }catch(e){
- }
- return [[ret]]
-}
-
-
-
-//////////// save/restore orientation /////////////
-
-function jmolSaveOrientation(id, targetSuffix) {
- targetSuffix == undefined && (targetSuffix="0")
- return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
-}
-
-function jmolRestoreOrientation(id, targetSuffix) {
- targetSuffix == undefined && (targetSuffix="0")
- var s=_jmol["savedOrientation"+id]
- if (!s || s == "")return
- s=s.replace(/1\.0/,"0")
- return jmolScriptWait(s,targetSuffix)
-}
-
-function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
- arguments.length < 2 && (delay=1)
- targetSuffix == undefined && (targetSuffix="0")
- var s=_jmol["savedOrientation"+id]
- if (!s || s == "")return
- s=s.replace(/1\.0/,delay)
- return jmolScriptWait(s,targetSuffix)
-}
-
-//////////// add parameter /////////////
-/*
- * for adding callbacks or other parameters. Use:
-
- jmolSetDocument(0)
- var s= jmolApplet(....)
- s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
- document.write(s)
- jmolSetDocument(document) // if you want to then write buttons and such normally
-
- */
-
-function jmolAppletAddParam(appletCode,name,value){
- return (value == "" ? appletCode : appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param"))
-}
-
-///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
-
-function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
-
- _jmol.thismodel || (_jmol.thismodel = "1crn")
- _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
- _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")
- _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")
- fileformat || (fileformat="PDB")
- pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))
- if(!pdbid || pdbid.length != 4)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
- fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=pdbid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-///////////////auto load NIH CACTVS data -- compound name or SMILES ///////////
-
-function jmolLoadAjax_STOLAF_NIH(compoundid,optionalscript,targetSuffix){
- _jmol.thismodel || (_jmol.thismodel = "aspirin")
- _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
- _jmol.defaultURL_NIH || (_jmol.defaultURL_NIH="http://cactus.nci.nih.gov/chemical/structure/FILE/file?format=sdf&get3d=True")
- compoundid || (compoundid=prompt("Enter a compound name or a SMILES string:",_jmol.thismodel))
- if(!compoundid)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- var url=_jmol.defaultURL_NIH.replace(/FILE/g,compoundid)
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=compoundid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-/////////////// St. Olaf College AJAX server -- ANY URL ///////////
-
-function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
- _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
- _jmol.thisurlANY || (_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol")
- url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))
- userid || (userid="0")
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- _jmol.optionalscript=optionalscript
- _jmol.thistargetsuffix=targetSuffix
- _jmol.modelArray = []
- _jmol.thisurl = url
- url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
- _jmolDomScriptLoad(url)
-}
-
-
-/////////////// Mineralogical Society of America (MSA) data /////////
-
-function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
-
- _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")
- _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")
- _jmol.ajaxURL_MSA || (_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs")
- key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))
- if(!key)return ""
- value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))
- if(!value)return ""
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- optionalscript == 1 && (optionalscript='load "" {1 1 1}')
- var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
- _jmol.optionalscript=optionalscript
- _jmol.thiskeyMSA=key
- _jmol.thismodelMSA=value
- _jmol.thistargetsuffix=targetSuffix
- _jmol.thisurl=url
- _jmol.modelArray = []
- loadModel=_jmolLoadModel
- _jmolDomScriptLoad(url)
- return url
-}
-
-
-
-function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
- userid || (userid="0")
- targetSuffix || (targetSuffix="0")
- optionalscript || (optionalscript="")
- _jmol.optionalscript=optionalscript
- _jmol.thismodel=userid
- _jmol.thistargetsuffix=targetSuffix
- _jmol.modelArray = []
- _jmol.thisurl = url
- url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
- _jmolDomScriptLoad(url)
-}
-
-
-//// in case Jmol library has already been loaded:
-
-}catch(e){}
-
-///////////////moving atoms //////////////
-
-// HIGHLY experimental!!
-
-function jmolSetAtomCoord(i,x,y,z,targetSuffix){
- _jmolCheckBrowser();
- var applet=_jmolGetApplet(targetSuffix);
- if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
-}
-
-function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
- _jmolCheckBrowser();
- var applet=_jmolGetApplet(targetSuffix);
- if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
-}
-
-
-///////////////applet fake for testing buttons/////////////
-
-
-if(_jmol.useNoApplet){
- jmolApplet = function(w){
- var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
- +"<td align=center valign=center style='background-color:white'>"
- +"Applet would be here"
- +"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
- +"</td></tr></table>"
- return _jmolDocumentWrite(s)
- }
-
- _jmolFindApplet = function(){return jmolApplet0}
-
- jmolApplet0 = {
- script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
- ,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}
- ,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
- }
-}
-
-
-///////////////////////////////////////////
-
- // This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility
- /*
- Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).
- targetSuffix is optional and defaults to zero (first applet in page).
- Both w and h are optional, but needed if you want to use targetSuffix.
- h defaults to w
- w defaults to 100% of window
- If either w or h is between 0 and 1, then it is taken as percent/100.
- If either w or h is greater than 1, then it is taken as a size (pixels).
- */
-function jmolResize(w,h,targetSuffix) {
- _jmol.alerted = true;
- var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0);
- var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);
- if (_jmol.browser=="msie") {
- var width=document.body.clientWidth;
- var height=document.body.clientHeight;
- } else {
- var netscapeScrollWidth=15;
- var width=window.innerWidth - netscapeScrollWidth;
- var height=window.innerHeight-netscapeScrollWidth;
- }
- var applet = _jmolGetApplet(targetSuffix);
- if(!applet)return;
- applet.style.width = (percentW ? width * percentW/100 : w)+"px";
- applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";
- //title=width + " " + height + " " + (new Date());
-}
-
-// 13 Jun 09 -- makes jmolResize() obsolete (kept for backwards compatibility)
-function jmolResizeApplet(size,targetSuffix) {
- // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]
- // Special case: an empty value for width or height is accepted, meaning no change in that dimension.
- _jmol.alerted = true;
- var applet = _jmolGetApplet(targetSuffix);
- if(!applet)return;
- var sz = _jmolGetAppletSize(size, "px");
- sz[0] && (applet.style.width = sz[0]);
- sz[1] && (applet.style.height = sz[1]);
-}
-
-function _jmolGetAppletSize(size, units) {
- /* Accepts single number or 2-value array, each one can be one of:
- percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
- [width, height] array of strings is returned, with units added if specified.
- Percent is relative to container div or element (which should have explicitly set size).
- */
- var width, height;
- if ( (typeof size) == "object" && size != null ) {
- width = size[0]; height = size[1];
- } else {
- width = height = size;
- }
- return [_jmolFixDim(width, units), _jmolFixDim(height, units)];
-}
-
-function _jmolFixDim(x, units) {
- var sx = "" + x;
- return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])
- : sx.indexOf("%") == sx.length-1 ? sx
- : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"
- : (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]
- : x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]
- : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1]
- : x) + (units ? units : ""));
-}
-
-
-
-
-- MSIE and Safari cannot work with local pages\r
\r
*/\r
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+b._j2sPath+'/img/play_make_live.jpg" style="width:25px;height:25px;position:absolute;bottom:10px;left:10px;z-index:'+a._getZ(b,"coverImage")+';opacity:0.5;"'+d+" />",d='<div id="ID_coverdiv" style="background-color:red;z-index:'+a._getZ(b,"coverImage")+';width:100%;height:100%;display:inline;position:absolute;top:0px;left:0px"><image id="ID_coverimage" src="'+b._coverImage+'" style="width:100%;height:100%"'+d+"/>"+c+"</div>");c=a._appletCssText.replace(/\'/g,'"');c=0<=c.indexOf('style="')?c.split('style="')[1]:\r
+'" '+c;c='...<div id="ID_appletinfotablediv" style="width:Wpx;height:Hpx;position:relative;font-size:14px;text-align:left">IMG......<div id="ID_appletdiv" style="z-index:'+a._getZ(b,"header")+";width:100%;height:100%;position:absolute;top:0px;left:0px;"+c+">";var k=b._height,h=b._width;if("string"!==typeof k||0>k.indexOf("%"))k+="px";if("string"!==typeof h||0>h.indexOf("%"))h+="px";c=c.replace(/IMG/,d).replace(/Hpx/g,k).replace(/Wpx/g,h)}else c='......</div>......<div id="ID_2dappletdiv" style="position:absolute;width:100%;height:100%;overflow:hidden;display:none"></div>......<div id="ID_infotablediv" style="width:100%;height:100%;position:absolute;top:0px;left:0px">.........<div id="ID_infoheaderdiv" style="height:20px;width:100%;background:yellow;display:none"><span id="ID_infoheaderspan"></span><span id="ID_infocheckboxspan" style="position:absolute;text-align:right;right:1px;"><a href="javascript:Jmol.showInfo(ID,false)">[x]</a></span></div>.........<div id="ID_infodiv" style="position:absolute;top:20px;bottom:0px;width:100%;height:100%;overflow:auto"></div>......</div>...</div>';\r
+return c.replace(/\.\.\./g,"").replace(/[\n\r]/g,"").replace(/ID/g,b._id)};a._documentWrite=function(b){if(a._document){if(a._isXHTML&&!a._XhtmlElement){var e=document.getElementsByTagName("script");a._XhtmlElement=e.item(e.length-1);a._XhtmlAppendChild=!1}a._XhtmlElement?a._domWrite(b):a._document.write(b)}return b};a._domWrite=function(b){for(var e=[0];e[0]<b.length;){var c=a._getDomElement(b,e);if(!c)break;a._XhtmlAppendChild?a._XhtmlElement.appendChild(c):a._XhtmlElement.parentNode.insertBefore(c,\r
+_jmol.XhtmlElement)}};a._getDomElement=function(a,e){var c=document.createElement("span");c.innerHTML=a;e[0]=a.length;return c};a._setObject=function(b,e,c){b._id=e;b.__Info={};c.z&&c.zIndexBase&&(a._z=a._getZOrders(c.zIndexBase));for(var d in c)b.__Info[d]=c[d];(b._z=c.z)||c.zIndexBase&&(b._z=b.__Info.z=a._getZOrders(c.zIndexBase));b._width=c.width;b._height=c.height;b._noscript=!b._isJava&&c.noscript;b._console=c.console;b._cacheFiles=!!c.cacheFiles;b._viewSet=null==c.viewSet||b._isJava?null:"Set"+\r
+c.viewSet;null!=b._viewSet&&(a.View.__init(b),b._currentView=null);!a._fileCache&&b._cacheFiles&&(a._fileCache={});b._console||(b._console=b._id+"_infodiv");"none"==b._console&&(b._console=null);b._color=c.color?c.color.replace(/0x/,"#"):"#FFFFFF";b._disableInitialConsole=c.disableInitialConsole;b._noMonitor=c.disableJ2SLoadMonitor;a._j2sPath&&(c.j2sPath=a._j2sPath);b._j2sPath=c.j2sPath;b._coverImage=c.coverImage;b._isCovered=!!b._coverImage;b._deferApplet=c.deferApplet||b._isCovered&&b._isJava;b._deferUncover=\r
+c.deferUncover&&!b._isJava;b._coverScript=c.coverScript;b._coverTitle=c.coverTitle;b._coverTitle||(b._coverTitle=b._deferApplet?"activate 3D model":"3D model is loading...");b._containerWidth=b._width+(b._width==parseFloat(b._width)?"px":"");b._containerHeight=b._height+(b._height==parseFloat(b._height)?"px":"");b._info="";b._infoHeader=b._jmolType+' "'+b._id+'"';b._hasOptions=c.addSelectionOptions;b._defaultModel=c.defaultModel;b._readyScript=c.script?c.script:"";b._readyFunction=c.readyFunction;\r
+b._coverImage&&!b._deferApplet&&(b._readyScript+=";javascript "+e+"._displayCoverImage(false)");b._src=c.src};a._addDefaultInfo=function(b,e){for(var c in e)"undefined"==typeof b[c]&&(b[c]=e[c]);a._use&&(b.use=a._use);0<=b.use.indexOf("SIGNED")&&(0>b.jarFile.indexOf("Signed")&&(b.jarFile=b.jarFile.replace(/Applet/,"AppletSigned")),b.use=b.use.replace(/SIGNED/,"JAVA"),b.isSigned=!0)};a._syncedApplets=[];a._syncedCommands=[];a._syncedReady=[];a._syncReady=!1;a._isJmolJSVSync=!1;a._setReady=function(b){a._syncedReady[b]=\r
+1;for(var e=0,c=0;c<a._syncedApplets.length;c++){if(a._syncedApplets[c]==b._id)a._syncedApplets[c]=b,a._syncedReady[c]=1;else if(!a._syncedReady[c])continue;e++}e==a._syncedApplets.length&&a._setSyncReady()};a._setDestroy=function(b){a.featureDetection.allowDestroy&&a.$windowOn("beforeunload",function(){a._destroy(b)})};a._destroy=function(b){try{b._appletPanel&&b._appletPanel.destroy();b._applet=null;a._unsetMouse(b._canvas);b._canvas=null;for(var e=0,c=0;c<a._syncedApplets.length;c++)a._syncedApplets[c]==\r
+b&&(a._syncedApplets[c]=null),a._syncedApplets[c]&&e++;0<e||a._clearVars()}catch(d){}};a._setSyncReady=function(){a._syncReady=!0;for(var b="",e=0;e<a._syncedApplets.length;e++)a._syncedCommands[e]&&(b+="Jmol.script(Jmol._syncedApplets["+e+"], Jmol._syncedCommands["+e+"]);");setTimeout(b,50)};a._mySyncCallback=function(b,e){app=a._applets[b];if(app._viewSet)a.View.updateFromSync(app,e);else{if(!a._syncReady||!a._isJmolJSVSync)return 1;for(var c=0;c<a._syncedApplets.length;c++)0<=e.indexOf(a._syncedApplets[c]._syncKeyword)&&\r
+a._syncedApplets[c]._syncScript(e);return 0}};a._getElement=function(a,e){return document.getElementById(a._id+"_"+e)||{}};a._evalJSON=function(a,e){a+="";if(!a)return[];if("{"!=a.charAt(0))return 0<=a.indexOf(" | ")&&(a=a.replace(/\ \|\ /g,"\n")),a;var c=(new Function("return "+a))();return!c?null:e&&void 0!=c[e]?c[e]:c};a._sortMessages=function(a){function e(a,b){return a[0]<b[0]?1:a[0]>b[0]?-1:0}if(!a||"object"!=typeof a)return[];for(var c=[],d=a.length-1;0<=d;d--)for(var k=0,h=a[d].length;k<h;k++)c[c.length]=\r
+a[d][k];if(0!=c.length)return c=c.sort(e)};a._setMouseOwner=function(b,e){null==b||e?a._mouseOwner=b:a._mouseOwner==b&&(a._mouseOwner=null)};a._jsGetMouseModifiers=function(a){var e=0;switch(a.button){case 0:e=16;break;case 1:e=8;break;case 2:e=4}a.shiftKey&&(e+=1);a.altKey&&(e+=8);a.ctrlKey&&(e+=2);return e};a._jsGetXY=function(b,e){if(!b.applet._ready||a._touching&&0>e.type.indexOf("touch"))return!1;var c=a.$offset(b.id),d,k=e.originalEvent;e.pageX||(e.pageX=k.pageX);e.pageY||(e.pageY=k.pageY);\r
+a._mousePageX=e.pageX;a._mousePageY=e.pageY;k.targetTouches&&k.targetTouches[0]?(d=k.targetTouches[0].pageX-c.left,c=k.targetTouches[0].pageY-c.top):k.changedTouches?(d=k.changedTouches[0].pageX-c.left,c=k.changedTouches[0].pageY-c.top):(d=e.pageX-c.left,c=e.pageY-c.top);return void 0==d?null:[Math.round(d),Math.round(c),a._jsGetMouseModifiers(e)]};a._gestureUpdate=function(b,e){e.stopPropagation();e.preventDefault();var c=e.originalEvent;switch(e.type){case "touchstart":a._touching=!0;break;case "touchend":a._touching=\r
+!1}if(!c.touches||2!=c.touches.length)return!1;switch(e.type){case "touchstart":b._touches=[[],[]];break;case "touchmove":var d=a.$offset(b.id),k=b._touches[0],h=b._touches[1];k.push([c.touches[0].pageX-d.left,c.touches[0].pageY-d.top]);h.push([c.touches[1].pageX-d.left,c.touches[1].pageY-d.top]);c=k.length;3<c&&(k.shift(),h.shift());2<=c&&b.applet._processGesture(b._touches)}return!0};a._jsSetMouse=function(b){var e=function(a){return 0<=a.target.className.indexOf("swingjs-ui")};a.$bind(b,"mousedown touchstart",\r
+function(c){if(e(c))return!0;a._setMouseOwner(b,!0);c.stopPropagation();var d=c.target["data-UI"];(!d||!d.handleJSEvent(b,501,c))&&c.preventDefault();b.isDragging=!0;if("touchstart"==c.type&&a._gestureUpdate(b,c))return!!d;a._setConsoleDiv(b.applet._console);var k=a._jsGetXY(b,c);k&&(2!=c.button&&a.Swing.hideMenus(b.applet),b.applet._processEvent(501,k));return!!d});a.$bind(b,"mouseup touchend",function(c){if(e(c))return!0;a._setMouseOwner(null);c.stopPropagation();var d=c.target["data-UI"];(!d||\r
+!d.handleJSEvent(b,502,c))&&c.preventDefault();b.isDragging=!1;if("touchend"==c.type&&a._gestureUpdate(b,c))return!!d;(c=a._jsGetXY(b,c))&&b.applet._processEvent(502,c);return!!d});a.$bind(b,"mousemove touchmove",function(c){if(e(c))return!0;if(a._mouseOwner&&a._mouseOwner!=b&&a._mouseOwner.isDragging){if(!a._mouseOwner.mouseMove)return!0;a._mouseOwner.mouseMove(c);return!1}return a._drag(b,c)});a._drag=function(b,e){e.stopPropagation();e.preventDefault();if("touchmove"==e.type&&a._gestureUpdate(b,\r
+e))return!1;var d=a._jsGetXY(b,e);if(!d)return!1;b.isDragging||(d[2]=0);var k=e.target["data-UI"];b.isdragging&&(!k||k.handleJSEvent(b,506,e));b.applet._processEvent(b.isDragging?506:503,d);return!!k};a.$bind(b,"DOMMouseScroll mousewheel",function(c){if(e(c))return!0;c.stopPropagation();c.preventDefault();b.isDragging=!1;var d=c.originalEvent,d=d.detail?d.detail:("mac"==a.featureDetection.os?1:-1)*d.wheelDelta;c=a._jsGetMouseModifiers(c);b.applet._processEvent(-1,[0>d?-1:1,0,c]);return!1});a.$bind(b,\r
+"contextmenu",function(){return!1});a.$bind(b,"mouseout",function(c){if(e(c))return!0;a._mouseOwner&&!a._mouseOwner.mouseMove&&a._setMouseOwner(null);b.applet._appletPanel&&b.applet._appletPanel.startHoverWatcher(!1);a._jsGetXY(b,c);return!1});a.$bind(b,"mouseenter",function(c){if(e(c))return!0;b.applet._appletPanel&&b.applet._appletPanel.startHoverWatcher(!0);if(0===c.buttons||0===c.which){b.isDragging=!1;c=a._jsGetXY(b,c);if(!c)return!1;b.applet._processEvent(504,c);b.applet._processEvent(502,c);\r
+return!1}});a.$bind(b,"mousemoveoutjsmol",function(c,d,k){if(e(k))return!0;if(b==a._mouseOwner&&b.isDragging)return a._drag(b,k)});b.applet._is2D&&a.$resize(function(){b.applet&&b.applet._resize()});a.$bind("body","mouseup touchend",function(c){if(e(c))return!0;b.applet&&(b.isDragging=!1);a._setMouseOwner(null)})};a._jsUnsetMouse=function(b){b.applet=null;a.$bind(b,"mousedown touchstart mousemove touchmove mouseup touchend DOMMouseScroll mousewheel contextmenu mouseout mouseenter",null);a._setMouseOwner(null)};\r
+a.Swing={count:0,menuInitialized:0,menuCounter:0,htDialogs:{}};var r=a.Swing;SwingController=r;r.setDraggable=function(b){b=b.prototype;b.setContainer||(b.setContainer=function(b){this.container=b;b.obj=this;this.ignoreMouse=this.isDragging=!1;var c=this;b.bind("mousedown touchstart",function(b){if(c.ignoreMouse)return c.ignoreMouse=!1,!0;a._setMouseOwner(c,!0);c.isDragging=!0;c.pageX=b.pageX;c.pageY=b.pageY;return!1});b.bind("mousemove touchmove",function(b){if(c.isDragging&&a._mouseOwner==c)return c.mouseMove(b),\r
+!1});b.bind("mouseup touchend",function(b){c.mouseUp(b);a._setMouseOwner(null)})},b.mouseUp=function(b){if(this.isDragging&&a._mouseOwner==this)return this.pageX0+=b.pageX-this.pageX,this.pageY0+=b.pageY-this.pageY,this.isDragging=!1;a._setMouseOwner(null)},b.setPosition=function(){if(null===a._mousePageX){var b=a.$offset(this.applet._id+"_"+(this.applet._is2D?"canvas2d":"canvas"));a._mousePageX=b.left;a._mousePageY=b.top}this.pageX0=a._mousePageX;this.pageY0=a._mousePageY;this.container.css({top:a._mousePageY+\r
+"px",left:a._mousePageX+"px"})},b.mouseMove=function(b){if(this.isDragging&&a._mouseOwner==this){this.timestamp=System.currentTimeMillis();var c=this.pageX0+(b.pageX-this.pageX);b=this.pageY0+(b.pageY-this.pageY);a._mousePageX=c;a._mousePageY=b;this.container.css({top:b+"px",left:c+"px"})}},b.dragBind=function(b){this.applet._ignoreMouse=!b;this.container.unbind("mousemoveoutjsmol");this.container.unbind("touchmoveoutjsmol");this.container.unbind("mouseupoutjsmol");this.container.unbind("touchendoutjsmol");\r
+a._setMouseOwner(null);if(b){var c=this;this.container.bind("mousemoveoutjsmol touchmoveoutjsmol",function(a,b,d){c.mouseMove(d)});this.container.bind("mouseupoutjsmol touchendoutjsmol",function(a,b,d){c.mouseUp(d)})}})};r.JSDialog=function(){};r.setDraggable(r.JSDialog);r.getScreenDimensions=function(a){a.width=l(window).width();a.height=l(window).height()};r.dispose=function(b){a.$remove(b.id+"_mover");delete r.htDialogs[b.id];b.container.obj.dragBind(!1)};r.register=function(a,d){a.id=d+ ++r.count;\r
+r.htDialogs[a.id]=a};r.setDialog=function(b){a._setMouseOwner(null);a.$remove(b.id);var d=b.id+"_mover",c=a._$(d),k;c[0]?(c.html(b.html),k=c[0].jd):(a.$after("body","<div id='"+d+"' style='position:absolute;left:0px;top:0px;'>"+b.html+"</div>"),k=new r.JSDialog,c=a._$(d),b.container=c,k.applet=b.manager.vwr.html5Applet,k.setContainer(c),k.dialog=b,k.setPosition(),k.dragBind(!0),c[0].jd=k);a.$bind("#"+b.id+" .JButton","mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JComboBox",\r
+"mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JCheckBox","mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JTextField","mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JTable","mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JScrollPane","mousedown touchstart",function(){k.ignoreMouse=!0});a.$bind("#"+b.id+" .JEditorPane","mousedown touchstart",function(){k.ignoreMouse=!0})};r.setSelected=function(b){a.$prop(b.id,\r
+"checked",!!b.selected)};r.setSelectedIndex=function(b){a.$prop(b.id,"selectedIndex",b.selectedIndex)};r.setText=function(b){a.$prop(b.id,"value",b.text)};r.setVisible=function(b){a.$setVisible(b.id,b.visible)};r.setEnabled=function(b){a.$setEnabled(b.id,b.enabled)};r.click=function(b,d){var c=r.htDialogs[b.id];if(c){var k=c.toString();if(0<=k.indexOf("JCheck"))c.selected=b.checked;else if(0<=k.indexOf("JCombo"))c.selectedIndex=b.selectedIndex;else if(null!=c.text&&(c.text=b.value,d&&13!=(d.charCode||\r
+d.keyCode)))return}k=r.htDialogs[a.$getAncestorDiv(b.id,"JDialog").id];k.manager.actionPerformed(c?c.name:k.registryKey+"/"+b.id)};r.setFront=function(b){var d=b.manager.vwr.html5Applet;b.zIndex!=a._getZ(d,"dialog")&&(b.zIndex=a._incrZ(d,"dialog"));b.container&&((b.container[0]||b.container).style.zIndex=b.zIndex)};r.hideMenus=function(a){if(a=a._menus)for(var d in a)a[d].visible&&r.hideMenu(a[d])};r.windowClosing=function(b){b=r.htDialogs[a.$getAncestorDiv(b.id,"JDialog").id];b.registryKey?b.manager.processWindowClosing(b.registryKey):\r
+b.dispose()};a._track=function(b){if(a._tracker){try{var d='<iframe style="display:none" width="0" height="0" frameborder="0" tabindex="-1" src="'+(a._tracker+"&applet="+b._jmolType+"&version="+a._version+"&appver="+a.___JmolVersion+"&url="+encodeURIComponent(document.location.href))+'"></iframe>';a.$after("body",d)}catch(c){}delete a._tracker}return b};a.getProfile=function(){window["j2s.doProfile"]=!0;if(self.Clazz&&self.JSON)return Clazz._profile||(Clazz._profile={}),Clazz.getProfile()};a._getInChIKey=\r
+function(a,d){0<=d.indexOf("MOL=")&&d.split("MOL=")[1].split('"')};a._getAttr=function(a,d){var c=a.indexOf(d+"=");return 0<=c&&0<=(c=a.indexOf('"',c))?a.substring(c+1,a.indexOf('"',c+1)):null};a.User={viewUpdatedCallback:null};a.View={count:0,applets:{},sets:{}};(function(b){b.updateView=function(d,c){if(null!=d._viewSet){c.chemID||(d._searchQuery=null);c.data||(c.data="N/A");c.type=d._viewType;if(null==(d._currentView=b.__findView(d._viewSet,c)))d._currentView=b.__createViewSet(d._viewSet,c.chemID,\r
+c.viewID||c.chemID);d._currentView[c.type].data=c.data;d._currentView[c.type].smiles=d._getSmiles();a.User.viewUpdatedCallback&&a.User.viewUpdatedCallback(d,"updateView");b.__setView(d._currentView,d,!1)}};b.updateFromSync=function(d,c){d._updateMsg=c;var k=a._getAttr(c,"sourceID")||a._getAttr(c,"file");if(k){var h=b.__findView(d._viewSet,{viewID:k});if(null==h)return a.updateView(d,c);h!=d._currentView&&b.__setView(h,d,!0);var n=(k=a._getAttr(c,"atoms"))&&0<=c.indexOf("selectionhalos ON")?eval("["+\r
+k+"]"):[];setTimeout(function(){d._currentView==h&&b.updateAtomPick(d,n)},10);a.User.viewUpdatedCallback&&a.User.viewUpdatedCallback(d,"updateFromSync")}};b.updateAtomPick=function(b,c){var d=b._currentView;if(null!=d){for(var k in d)"info"!=k&&d[k].applet!=b&&d[k].applet._updateAtomPick(c);a.User.viewUpdatedCallback&&a.User.viewUpdatedCallback(b,"updateAtomPick")}};b.dumpViews=function(a){var c=b.sets[a];if(c){var d="View set "+a+":\n";a=b.applets[a];for(var k in a)d+="\napplet "+a[k]._id+" currentView="+\r
+(a[k]._currentView?a[k]._currentView.info.viewID:null);for(k=c.length;0<=--k;){a=c[k];var d=d+("\n\n<b>view="+k+" viewID="+a.info.viewID+" chemID="+a.info.chemID+"</b>\n"),h,n;for(n in a)"info"!=n&&(d+="\nview="+k+" type="+n+" applet="+((h=a[n]).applet?h.applet._id:null)+" SMILES="+h.smiles+"\n atomMap="+JSON.stringify(h.atomMap)+"\n data=\n"+h.data+"\n")}return d}};b.__init=function(a){var c=a._viewSet,d=b.applets;d[c]||(d[c]={});d[c][a._viewType]=a};b.__findView=function(a,c){var d=b.sets[a];null==\r
+d&&(d=b.sets[a]=[]);for(var k=d.length;0<=--k;){var h=d[k];if(c.viewID){if(h.info.viewID==c.viewID)return h}else{if(null!=c.chemID&&c.chemID==h.info.chemID)return h;for(var n in h)if("info"!=n&&(null!=c.data&&null!=h[n].data?c.data==h[n].data:c.type==n))return h}}return null};b.__createViewSet=function(d,c,k){b.count++;c={info:{chemID:c,viewID:k||"model_"+b.count}};for(var h in a._applets)k=a._applets[h],k._viewSet==d&&(c[k._viewType]={applet:k,data:null});b.sets[d].push(c);return c};b.__setView=\r
+function(a,b,d){for(var k in a)if("info"!=k){var h=a[k],n=h.applet,s=d||null!=n&&"<modified>"==n._molData;if(!(null==n||n==b&&!s)){var l=null==h.data,r=null!=n._currentView;n._currentView=a;if(!r||!(a[k].data==h.data&&!l&!s))if(n._loadModelFromView(a),l)break}}}})(a.View);a.Cache={fileCache:{}};a.Cache.get=function(b){return a.Cache.fileCache[b]};a.Cache.put=function(b,d){a.Cache.fileCache[b]=d};a.Cache.setDragDrop=function(b){a.$appEvent(b,"appletdiv","dragover",function(a){a=a.originalEvent;a.stopPropagation();\r
+a.preventDefault();a.dataTransfer.dropEffect="copy"});a.$appEvent(b,"appletdiv","drop",function(d){var c=d.originalEvent;c.stopPropagation();c.preventDefault();var k=c.dataTransfer.files[0];if(null==k)try{k=""+c.dataTransfer.getData("text"),(0==k.indexOf("file:/")||0==k.indexOf("http:/"))&&b._scriptLoad(k)}catch(h){}else c=new FileReader,c.onloadend=function(c){if(c.target.readyState==FileReader.DONE){var h="cache://DROP_"+k.name;c=a._toBytes(c.target.result);h.endsWith(".spt")||b._appletPanel.cacheFileByName("cache://DROP_*",\r
+!1);"JSV"==b._viewType||h.endsWith(".jdx")?a.Cache.put(h,c):b._appletPanel.cachePut(h,c);(c=a._jsGetXY(b._canvas,d))&&(!b._appletPanel.setStatusDragDropped||b._appletPanel.setStatusDragDropped(0,c[0],c[1],h))&&b._appletPanel.openFileAsyncSpecial(h,1)}},c.readAsArrayBuffer(k)})}})(Jmol,jQuery);Jmol._debugCode=!1;\r
+(function(a){a._isAsync=!1;a._asyncCallbacks={};a._coreFiles=[];var l=!1,k=[],h=[],d=0,n=[],s=[],r=function(b){arguments.length||(b=!0);delete d;for(var e;0<h.length&&"done"==(e=h[0])[4];)h.shift();if(0!=h.length)if(!a._isAsync&&!b)setTimeout(r,10);else{e.push("done");var n="JSmol exec "+e[0]._id+" "+e[3]+" "+e[2];self.System&&System.out.println(n);self.console&&console.log(n+" -- OK");k.push(n);e[1](e[0],e[2])}},b=function(b){l?r():(l=!0,LoadClazz(),b._noMonitor&&(Clazz._LoaderProgressMonitor.showStatus=\r
+function(){}),LoadClazz=null,b.__Info.uncompressed&&Clazz.loadClass(),Clazz._Loader.onGlobalLoaded=function(){Clazz._LoaderProgressMonitor.showStatus("Application loaded.",!0);if(!a._debugCode||!a.haveCore)a.haveCore=!0,r()},Clazz._Loader.loadPackageClasspath("java",null,!0,r))},e=function(a,b){Clazz._Loader.loadClass(b,function(){r()})};a.showExecLog=function(){return k.join("\n")};a._addExec=function(a){a[1]||(a[1]=e);var b="JSmol load "+a[0]._id+" "+a[3];self.console&&console.log(b+"...");k.push(b);\r
+h.push(a)};a._addCoreFile=function(b,d,e){b=b.toLowerCase().split(".")[0];if(!(0<=n.join("").indexOf(b))){n.push(b);n.sort();a._coreFiles=[d+"/core/core"+n.join("")+".z.js"];if(e&&(e=e.split(" ")))for(b=0;b<e.length;b++)0>s.join("").indexOf(e[b])&&s.push(d+"/core/core"+e[b]+".z.js");for(b=0;b<s.length;b++)a._coreFiles.push(s[b])}};a._Canvas2D=function(b,d,e,k){this._uniqueId=(""+Math.random()).substring(3);this._id=b;this._is2D=!0;this._isJava=!1;this._jmolType="Jmol._Canvas2D ("+e+")";this._isLayered=\r
+d._isLayered||!1;this._isSwing=d._isSwing||!1;this._isJSV=d._isJSV||!1;this._isAstex=d._isAstex||!1;this._platform=d._platform||"";if(k)return this;window[b]=this;this._createCanvas(b,d);if(!a._document||this._deferApplet)return this;this._init();return this};a._setAppletParams=function(b,d,e,k){for(var h in e)if(!b||0<=b.indexOf(";"+h.toLowerCase()+";"))null==e[h]||"language"==h&&!a.featureDetection.supportsLocalization()||(k?d.put(h,!0===e[h]?Boolean.TRUE:!1===e[h]?Boolean.FALSE:e[h]):d[h]=e[h])};\r
+a._jsSetPrototype=function(c){c._init=function(){this._setupJS();this._showInfo(!0);this._disableInitialConsole&&this._showInfo(!1)};c._createCanvas=function(b,c,d){a._setObject(this,b,c);d&&(this._GLmol=d,this._GLmol.applet=this,this._GLmol.id=this._id);d=a._getWrapper(this,!0);this._deferApplet||(a._document?(a._documentWrite(d),this._newCanvas(!1),d=""):(this._deferApplet=!0,d+='<script type="text/javascript">'+b+"._cover(false)\x3c/script>"));d+=a._getWrapper(this,!1);c.addSelectionOptions&&(d+=\r
+a._getGrabberOptions(this));a._debugAlert&&!a._document&&alert(d);this._code=a._documentWrite(d)};c._newCanvas=function(a){this._is2D?this._createCanvas2d(a):this._GLmol.create()};c._getHtml5Canvas=function(){return this._canvas};c._getWidth=function(){return this._canvas.width};c._getHeight=function(){return this._canvas.height};c._getContentLayer=function(){return a.$(this,"contentLayer")[0]};c._repaintNow=function(){a._repaint(this,!1)};c._createCanvas2d=function(){var b=a.$(this,"appletdiv");\r
+try{b[0].removeChild(this._canvas),this._canvas.frontLayer&&b[0].removeChild(this._canvas.frontLayer),this._canvas.rearLayer&&b[0].removeChild(this._canvas.rearLayer),this._canvas.contentLayer&&b[0].removeChild(this._canvas.contentLayer),a._jsUnsetMouse(this._mouseInterface)}catch(c){}var d=Math.round(b.width()),e=Math.round(b.height()),k=document.createElement("canvas");k.applet=this;this._canvas=k;k.style.width="100%";k.style.height="100%";k.width=d;k.height=e;k.id=this._id+"_canvas2d";b.append(k);\r
+a._$(k.id).css({"z-index":a._getZ(this,"main")});if(this._isLayered){var h=document.createElement("div");k.contentLayer=h;h.id=this._id+"_contentLayer";b.append(h);a._$(h.id).css({zIndex:a._getZ(this,"image"),position:"absolute",left:"0px",top:"0px",width:(this._isSwing?d:0)+"px",height:(this._isSwing?e:0)+"px",overflow:"hidden"});this._isSwing?(b=document.createElement("div"),b.id=this._id+"_swingdiv",a._$(this._id+"_appletinfotablediv").append(b),a._$(b.id).css({zIndex:a._getZ(this,"rear"),position:"absolute",\r
+left:"0px",top:"0px",width:d+"px",height:e+"px",overflow:"hidden"}),this._mouseInterface=k.contentLayer,k.contentLayer.applet=this):this._mouseInterface=this._getLayer("front",b,d,e,!1)}else this._mouseInterface=k;a._jsSetMouse(this._mouseInterface)};c._getLayer=function(b,c,d,e,k){var h=document.createElement("canvas");this._canvas[b+"Layer"]=h;h.style.width="100%";h.style.height="100%";h.id=this._id+"_"+b+"Layer";h.width=d;h.height=e;c.append(h);h.applet=this;a._$(h.id).css({background:k?"rgb(0,0,0,1)":\r
+"rgb(0,0,0,0.001)","z-index":a._getZ(this,b),position:"absolute",left:"0px",top:"0px",overflow:"hidden"});return h};c._setupJS=function(){window["j2s.lib"]={base:this._j2sPath+"/",alias:".",console:this._console,monitorZIndex:a._getZ(this,"monitorZIndex")};0==h.length&&a._addExec([this,b,null,"loadClazz"]);this._addCoreFiles();a._addExec([this,this.__startAppletJS,null,"start applet"]);this._isSigned=!0;this._ready=!1;this._applet=null;this._canScript=function(){return!0};this._savedOrientations=\r
+[];d&&clearTimeout(d);d=setTimeout(r,100)};c.__startAppletJS=function(b){0==a._version.indexOf("$Date: ")&&(a._version=(a._version.substring(7)+" -").split(" -")[0]+" (JSmol/j2s)");var c=Clazz._4Name("java.util.Hashtable").newInstance();a._setAppletParams(b._availableParams,c,b.__Info,!0);c.put("appletReadyCallback","Jmol._readyCallback");c.put("applet",!0);c.put("name",b._id);c.put("syncId",a._syncId);a._isAsync&&c.put("async",!0);b._color&&c.put("bgcolor",b._color);b._startupScript&&c.put("script",\r
+b._startupScript);a._syncedApplets.length&&c.put("synccallback","Jmol._mySyncCallback");c.put("signedApplet","true");c.put("platform",b._platform);b._is2D&&c.put("display",b._id+"_canvas2d");c.put("documentBase",document.location.href);var d=b._j2sPath+"/";if(0>d.indexOf("://")){var e=document.location.href.split("#")[0].split("?")[0].split("/");0==d.indexOf("/")?e=[e[0],d.substring(1)]:e[e.length-1]=d;d=e.join("/")}c.put("codePath",d);a._registerApplet(b._id,b);try{b._newApplet(c)}catch(k){System.out.println((a._isAsync?\r
+"normal async abort from ":"")+k);return}b._jsSetScreenDimensions();r()};c._restoreState||(c._restoreState=function(){});c._jsSetScreenDimensions=function(){if(this._appletPanel){var b=a._getElement(this,this._is2D?"canvas2d":"canvas");this._appletPanel.setScreenDimension(b.width,b.height)}};c._show=function(b){a.$setVisible(a.$(this,"appletdiv"),b);b&&a._repaint(this,!0)};c._canScript=function(){return!0};c.equals=function(a){return this==a};c.clone=function(){return this};c.hashCode=function(){return parseInt(this._uniqueId)};\r
+c._processGesture=function(a){return this._appletPanel.processTwoPointGesture(a)};c._processEvent=function(a,b){this._appletPanel.processMouseEvent(a,b[0],b[1],b[2],System.currentTimeMillis())};c._resize=function(){var b="__resizeTimeout_"+this._id;a[b]&&clearTimeout(a[b]);var c=this;a[b]=setTimeout(function(){a._repaint(c,!0);a[b]=null},100)};return c};a._repaint=function(b,d){if(b&&b._appletPanel){var e=a.$(b,"appletdiv"),k=Math.round(e.width()),e=Math.round(e.height());if(b._is2D&&(b._canvas.width!=\r
+k||b._canvas.height!=e))b._newCanvas(!0),b._appletPanel.setDisplay(b._canvas);b._appletPanel.setScreenDimension(k,e);k=function(){b._appletPanel.paint?b._appletPanel.paint(null):b._appletPanel.update(null)};d?setTimeout(k):k()}};a._getHiddenCanvas=function(a,b,d,e){b=a._id+"_"+b;a=document.createElement("canvas");a.width=a.style.width=d;a.height=a.style.height=e;a.id=b;return a};a._loadImage=function(b,d,e,k,h){var n=d[1];if(null==h&&(h=new Image,null==e?h.onload=function(){a._loadImage(b,d,null,\r
+k,h)}:(e=JU.Base64.getBase64(e).toString(),n=n.substring(n.lastIndexOf("/")+1),n="data:"+(0<=n.indexOf(".png")?"image/png":0<=n.indexOf(".jpg")?"image/jpg":"")+";base64,"+e),h.src=n,null==e))return;e=h.width;var s=h.height,l="echo_"+d[0],r=a._getHiddenCanvas(b.vwr.html5Applet,l,e,s,!0);r.imageWidth=e;r.imageHeight=s;r.id=l;r.image=h;a._setCanvasImage(r,e,s);k(r,n)};a._setCanvasImage=function(a,b,d){a.buf32=null;a.width=b;a.height=d;a.getContext("2d").drawImage(a.image,0,0,b,d)}})(Jmol);\r
+(function(a,l){a._Applet=function(d,k,h){window[d]=this;this._jmolType="Jmol._Applet"+(k.isSigned?" (signed)":"");this._viewType="Jmol";this._isJava=!0;this._syncKeyword="Select:";this._availableParams=";progressbar;progresscolor;boxbgcolor;boxfgcolor;allowjavascript;boxmessage;\t\t\t\t\t\t\t\t\t;messagecallback;pickcallback;animframecallback;appletreadycallback;atommovedcallback;\t\t\t\t\t\t\t\t\t;echocallback;evalcallback;hovercallback;language;loadstructcallback;measurecallback;\t\t\t\t\t\t\t\t\t;minimizationcallback;resizecallback;scriptcallback;statusform;statustext;statustextarea;\t\t\t\t\t\t\t\t\t;synccallback;usecommandthread;syncid;appletid;startupscript;menufile;";\r
+if(h)return this;this._isSigned=k.isSigned;this._readyFunction=k.readyFunction;this._ready=!1;this._isJava=!0;this._isInfoVisible=!1;this._applet=null;this._memoryLimit=k.memoryLimit||512;this._canScript=function(){return!0};this._savedOrientations=[];this._initialize=function(d,b){var e=!1;a._jarFile&&(b=a._jarFile);if(this._jarFile){var c=this._jarFile;0<=c.indexOf("/")?(alert("This web page URL is requesting that the applet used be "+c+". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network."),\r
+"yes"==prompt("Do you want to use applet "+c+"? ","yes or no")?(d=c.substring(0,c.lastIndexOf("/")),b=c.substring(c.lastIndexOf("/")+1)):e=!0):b=c;this_isSigned=k.isSigned=0<=b.indexOf("Signed")}this._jarPath=k.jarPath=d||".";this._jarFile=k.jarFile="string"==typeof b?b:(b?"JmolAppletSigned":"JmolApplet")+"0.jar";e&&alert("The web page URL was ignored. Continuing using "+this._jarFile+' in directory "'+this._jarPath+'"');void 0==a.controls||a.controls._onloadResetForms()};this._create(d,k);return this};\r
+var k=a._Applet,h=a._Applet.prototype;k._get=function(d,h,l){l||(l=!1);h||(h={});a._addDefaultInfo(h,{color:"#FFFFFF",width:300,height:300,addSelectionOptions:!1,serverURL:"http://your.server.here/jsmol.php",defaultModel:"",script:null,src:null,readyFunction:null,use:"HTML5",jarPath:"java",jarFile:"JmolApplet0.jar",isSigned:!1,j2sPath:"j2s",coverImage:null,coverTitle:"",coverCommand:"",deferApplet:!1,deferUncover:!1,disableJ2SLoadMonitor:!1,disableInitialConsole:!1,debug:!1});a._debugAlert=h.debug;\r
+h.serverURL&&(a._serverUrl=h.serverURL);for(var r=!1,b=null,e=h.use.toUpperCase().split("#")[0].split(" "),c=0;c<e.length;c++){switch(e[c]){case "JAVA":r=!0;a.featureDetection.supportsJava()&&(b=new k(d,h,l));break;case "WEBGL":b=k._getCanvas(d,h,l,!0);break;case "HTML5":a.featureDetection.allowHTML5?b=k._getCanvas(d,h,l,!1):e.push("JAVA");break;case "IMAGE":b=new a._Image(d,h,l)}if(null!=b)break}null==b&&(l||!r?b={_jmolType:"none"}:r&&(b=new k(d,h)));return l?b:a._registerApplet(d,b)};k._getCanvas=\r
+function(d,h,l,r){h._isLayered=!1;h._platform="J.awtjs2d.Platform";return r&&a.featureDetection.supportsWebGL()?(a._Canvas3D.prototype=a.GLmol.extendApplet(a._jsSetPrototype(new k(d,h,!0))),new a._Canvas3D(d,h,"Jmol",l)):!r?(a._Canvas2D.prototype=a._jsSetPrototype(new k(d,h,!0)),new a._Canvas2D(d,h,"Jmol",l)):null};k._noJavaMsg="Either you do not have Java applets enabled in your web<br />browser or your browser is blocking this applet.<br />\t\t\tCheck the warning message from your browser and/or enable Java applets in<br />\t\t\tyour web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a>";\r
+k._setCommonMethods=function(a){a._showInfo=h._showInfo;a._search=h._search;a._getName=h._getName;a._readyCallback=h._readyCallback};k._createApplet=function(d,h,s){d._initialize(h.jarPath,h.jarFile);var r=d._jarFile;a._isFile&&(r=r.replace(/0\.jar/,".jar"));var b=0<=d._containerWidth.indexOf("px")?d._containerWidth:"100%",e=0<=d._containerHeight.indexOf("px")?d._containerHeight:"100%",b=' style="width:'+b+";height:"+e+'" ',e="name='"+d._id+"_object' id='"+d._id+"_object' \n"+b+"\n";s.codebase=d._jarPath;\r
+s.codePath=s.codebase+"/";if(0>s.codePath.indexOf("://")){var c=l.location.href.split("#")[0].split("?")[0].split("/");c[c.length-1]=s.codePath;s.codePath=c.join("/")}s.archive=r;s.mayscript="true";s.java_arguments="-Xmx"+Math.round(h.memoryLimit||d._memoryLimit)+"m";s.permissions=d._isSigned?"all-permissions":"sandbox";s.documentLocation=l.location.href;s.documentBase=l.location.href.split("#")[0].split("?")[0];s.jarPath=h.jarPath;a._syncedApplets.length&&(s.synccallback="Jmol._mySyncCallback");\r
+d._startupScript&&(s.script=d._startupScript);var c="\n",q;for(q in s)s[q]&&(c+=" <param name='"+q+"' value='"+s[q]+"' />\n");c=a.featureDetection.useIEObject||a.featureDetection.useHtml4Object?"<object "+e+(a.featureDetection.useIEObject?" classid='clsid:8AD9C840-044E-11D1-B3E9-00805F499D93' codebase='http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab'>":" type='application/x-java-applet'>")+c+"<p style='background-color:yellow;"+b.split('"')[1]+";text-align:center;vertical-align:middle;'>\n"+\r
+k._noJavaMsg+"</p></object>\n":"<applet "+e+" code='"+s.code+"' codebase='"+d._jarPath+"' archive='"+r+"' mayscript='true'>\n"+c+"<table bgcolor='yellow'><tr><td align='center' valign='middle' "+b+">\n"+k._noJavaMsg+"</td></tr></table></applet>\n";d._deferApplet&&(d._javaCode=c,c="");c=a._getWrapper(d,!0)+c+a._getWrapper(d,!1)+(h.addSelectionOptions?a._getGrabberOptions(d):"");a._debugAlert&&alert(c);d._code=a._documentWrite(c)};h._newApplet=function(a){this._is2D||a.put("script",(a.get("script")||\r
+"")+";set multipleBondSpacing 0.35;");this._viewerOptions=a;return new J.appletjs.Jmol(a)};h._addCoreFiles=function(){a._addCoreFile("jmol",this._j2sPath,this.__Info.preloadCore);this._is2D||a._addExec([this,null,"J.export.JSExporter","load JSExporter"]);a._debugCode&&a._addExec([this,null,"J.appletjs.Jmol","load Jmol"])};h._create=function(d,h){a._setObject(this,d,h);var l={syncId:a._syncId,progressbar:"true",progresscolor:"blue",boxbgcolor:this._color||"black",boxfgcolor:"white",boxmessage:"Downloading JmolApplet ...",\r
+script:this._color?'background "'+this._color+'"':"",code:"JmolApplet.class"};a._setAppletParams(this._availableParams,l,h);var r;h.inlineModel?(r=h.inlineModel,r=r.replace(/\r|\n|\r\n/g,0<=r.indexOf("|")?"\\/n":"|").replace(/'/g,"'"),a._debugAlert&&alert("inline model:\n"+r)):r="";l.loadInline=r;l.appletReadyCallback="Jmol._readyCallback";a._syncedApplets.length&&(l.synccallback="Jmol._mySyncCallback");l.java_arguments="-Xmx"+Math.round(h.memoryLimit||this._memoryLimit)+"m";this._initialize(h.jarPath,\r
+h.jarFile);k._createApplet(this,h,l)};h._restoreState=function(d,k){System.out.println("\n\nasynchronous restore state for "+d+" "+k);var h=this,l=h._applet&&h._applet.viewer;switch(k){case "setOptions":return function(){h.__startAppletJS(h)};case "render":return function(){setTimeout(function(){l.refresh(2)},10)};default:switch(d){case "J.shape.Balls":case "J.shape.Sticks":case "J.shape.Frank":return null}if(l&&l.isScriptExecuting&&l.isScriptExecuting()){if(a._asyncCallbacks[d])return System.out.println("...ignored"),\r
+1;var b=l.getEvalContextAndHoldQueue(l.eval),e=b.pc-1;b.asyncID=d;a._asyncCallbacks[d]=function(a){b.pc=a;System.out.println("sc.asyncID="+b.asyncID+" sc.pc = "+b.pc);l.eval.resumeEval(b)};l.eval.pc=l.eval.pcEnd;System.out.println("setting resume for pc="+b.pc+" "+d+" to "+a._asyncCallbacks[d]+"//");return function(){System.out.println("resuming "+d+" "+a._asyncCallbacks[d]);a._asyncCallbacks[d](e)}}System.out.println(d+"?????????????????????"+k);return function(){setTimeout(function(){l.refresh(2)},\r
+10)}}};h._readyCallback=function(d,k,h){h&&(a._setDestroy(this),this._ready=!0,d=this._readyScript,this._defaultModel?a._search(this,this._defaultModel,d?";"+d:""):d?this._script(d):this._src&&this._script('load "'+this._src+'"'),this._showInfo(!0),this._showInfo(!1),a.Cache.setDragDrop(this),this._readyFunction&&this._readyFunction(this),a._setReady(this),(d=this._2dapplet)&&(d._isEmbedded&&d._ready&&d.__Info.visible)&&this._show2d(!0))};h._showInfo=function(d){d&&this._2dapplet&&this._2dapplet._show(!1);\r
+a.$html(a.$(this,"infoheaderspan"),this._infoHeader);this._info&&a.$html(a.$(this,"infodiv"),this._info);if(!this._isInfoVisible!=!d){this._isInfoVisible=d;if(this._isJava){var k=d?2:"100%";a.$setSize(a.$(this,"appletdiv"),k,k)}a.$setVisible(a.$(this,"infotablediv"),d);a.$setVisible(a.$(this,"infoheaderdiv"),d);this._show(!d)}};h._show2d=function(a){this._2dapplet._show2d(a);this._2dapplet._isEmbedded&&(this._showInfo(!1),this._show(!a),this._2dapplet.__showContainer(!0,!0))};h._getAtomCorrelation=\r
+function(a){this._loadMolData(a,"atommap = compare({1.1} {2.1} 'MAP' 'H'); zap 2.1",!0);a=jmol._evaluate("atommap");for(var k=jmol._evaluate("{*}.count"),h=[],l=[],b=0;b<a.length;b++){var e=a[b];h[e[0]+1]=e[1]-k+1;l[e[1]-k+1]=e[0]+1}return{fromJmol:h,toJmol:l}};h._show=function(d){var k=!d?2:"100%";a.$setSize(a.$(this,"object"),k,k);this._isJava||a.$setVisible(a.$(this,"appletdiv"),d)};h._clearConsole=function(){this._console==this._id+"_infodiv"&&(this.info="");self.Clazz&&(a._setConsoleDiv(this._console),\r
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\r
Jmol.Info = { \r
// uncomment one or more of these next lines only if you want to override jmolInitialize()\r
//jarPath: "java", \r
//jarFile: "JmolAppletSigned0.jar", \r
//j2sPath: "j2s", \r
- use: "HTML5", // could be JAVA or HTML5\r
+ use: "JAVA", // could be JAVA or HTML5\r
// the serverURL path is only used to load binary files in Safari, Chrome, and MSIE\r
- serverURL: "http://your.server.here/jsmol.php", // required for binary file loading (Spartan, .gz, .map, etc.)\r
+ serverURL: "http://www.jalview.org/jsmol.php", // required for binary file loading (Spartan, .gz, .map, etc.)\r
disableJ2SLoadMonitor: false,\r
disableInitialConsole: true\r
\r
git://source.jalview.org / jalview.git / commitdiff