jmol.js

Jmol是一个使用java语言编写的开源的免费三维分子显示工具,用于分子模型的浏览和编辑

    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"
  if (!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"
  if (!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();
    if (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,
  
  buttonCount: 0,
  checkboxCount: 0,
  linkCount: 0,
  cmdCount: 0,
  menuCount: 0,
  radioCount: 0,
  radioGroupCount: 0,
  
  appletCssClass: null,
  appletCssText: "",
  buttonCssClass: null,
  buttonCssText: "",
  checkboxCssClass: null,
  checkboxCssText: "",
  radioCssClass: null,
  radioCssText: "",
  linkCssClass: null,
  linkCssText: "",
  menuCssClass: null,
  menuCssText: "",
  
  targetSuffix: 0,
  targetText: "",
  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),
  
  os: "unknown",
  browser: "unknown",
  browserVersion: 0,
  hasGetElementById: !!document.getElementById,
  isJavaEnabled: navigator.javaEnabled(),
  isNetscape47Win: false,
  isIEWin: false,
  useIEObject: false,
  useHtml4Object: false,
  
  windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
  windowsCabUrl:
   "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-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,
  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("safari") ||
  _jmolTestUA("omniweb") ||
  _jmolTestUA("opera") ||
  _jmolTestUA("webtv") ||
  _jmolTestUA("icab") ||
  _jmolTestUA("msie") ||
  (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));
  
  _jmolTestOS("linux") ||
  _jmolTestOS("unix") ||
  _jmolTestOS("mac") ||
  _jmolTestOS("win");

  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 == "safari" && 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;

  // IE5.5 works just fine ... but let's push them to Sun Java
  isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);
  useIEObject = isIEWin;
  useHtml4Object =
   (os != "mac" && browser == "mozilla" && browserVersion >= 5) ||
   (os == "win" && browser == "opera" && browserVersion >= 8) ||
   (os == "mac" && browser == "safari" && browserVersion >= 412.2);

 doTranslate = true;
 haveSetTranslate = false;
}


function jmolSetCallback(callbackName,funcName) {
  _jmol.params[callbackName] = funcName
}

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.		
	*/
  with (_jmol) {
    if (! nameSuffix)
      nameSuffix = appletCount;
    appletSuffixes.push(nameSuffix);
    ++appletCount;
    if (! script)
      script = "select *";
    var sz = _jmolGetAppletSize(size);
    var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
    var tHeader, tFooter;
    if (!codebase)
	jmolInitialize(".");
    if (useIEObject || useHtml4Object) {
      params.name = 'jmolApplet' + nameSuffix;
      params.archive = archivePath;
      params.mayscript = 'true';
      params.codebase = codebase;
    }
    if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
      winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
      params.code = 'JmolApplet';
      tHeader = 
        "<object name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
      tFooter = "</object>";
    } else if (useHtml4Object) { // use HTML4 object tag
      tHeader = 
        "<object name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
	" classid='java:JmolApplet'\n" +
        " type='application/x-java-applet'\n" +
        widthAndHeight + ">\n";
      tFooter = "</object>";
    } else { // use applet tag
      tHeader = 
        "<applet name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix +
        "' " + appletCssText +
        " code='JmolApplet'" +
        " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
		widthAndHeight +
        " mayscript='true'>\n";
      tFooter = "</applet>";
    }
    var visitJava;
    if (isIEWin || 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; " +