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

/* Jmol 11.7 script library Jmol.js  15:32 06.12.2008 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: [e-mail]
 *
 *  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%)
// 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

var defaultdir = "."
var defaultjar = "JmolApplet.jar"


// Note added 12:41 PM 9/21/2008 by Bob Hanson, [e-mail]:

// 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 allowJMOLJAR = true  


var undefined; // for IE 5 ... wherein undefined is undefined

////////////////////////////////////////////////////////////////
// Basic Scripting infrastruture
////////////////////////////////////////////////////////////////

function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
  if (_jmol.initialized)
    return;
  _jmol.initialized = true;
  if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {
    var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];
    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
////////////////////////////////////////////////////////////////

function jmolButton(script, label, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolButton" + _jmol.buttonCount;
  if (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(" + 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();
  if (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 " : "") + _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;
  }
  if (separatorHtml == undefined || separatorHtml == null)
    separatorHtml = "&nbsp; ";
  var len = arrayOfRadioButtons.length;
  jmolStartNewRadioGroup();
  if (!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();
  if (id == undefined || id == null)
    id = "jmolLink" + _jmol.linkCount;
  if (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(" + 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();
  if (id == undefined || id == null)
    id = "jmolCmd" + _jmol.cmdCount;
  if (label == undefined || label == null)
    label = "Execute";
  if (size == undefined || isNaN(size))
    size = 60;
  ++_jmol.cmdCount;
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + 
          "' size='"+size+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolMenu(arrayOfMenuItems, size, id, title) {
  _jmolInitCheck();
  if (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;
      }
      if (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>" : "'>";
        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 + "\"" : "";
}

function jmolScript(script, targetSuffix) {
  if (script) {
    _jmolCheckBrowser();