(function(Clazz
,Clazz_newLongArray
,Clazz_doubleToByte
,Clazz_doubleToInt
,Clazz_doubleToLong
,Clazz_declarePackage
,Clazz_instanceOf
,Clazz_load
,Clazz_instantialize
,Clazz_decorateAsClass
,Clazz_floatToInt
,Clazz_makeConstructor
,Clazz_defineEnumConstant
,Clazz_exceptionOf
,Clazz_newIntArray
,Clazz_defineStatics
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_p0p
,Clazz_pu$h
,Clazz_newShortArray
,Clazz_innerTypeInstance
,Clazz_isClassDefined
,Clazz_prepareCallback
,Clazz_newArray
,Clazz_castNullAs
,Clazz_floatToShort
,Clazz_superCall
,Clazz_decorateAsType
,Clazz_newBooleanArray
,Clazz_newCharArray
,Clazz_implementOf
,Clazz_newDoubleArray
,Clazz_overrideConstructor
,Clazz_clone
,Clazz_doubleToShort
,Clazz_getInheritedLevel
,Clazz_getParamsType
,Clazz_isAF
,Clazz_isAI
,Clazz_isAS
,Clazz_isASS
,Clazz_isAP
,Clazz_isAFloat
,Clazz_isAII
,Clazz_isAFF
,Clazz_isAFFF
,Clazz_tryToSearchAndExecute
,Clazz_getStackTrace
,Clazz_inheritArgs
,Clazz_alert
,Clazz_defineMethod
,Clazz_overrideMethod
,Clazz_declareAnonymous
//,Clazz_checkPrivateMethod
,Clazz_cloneFinals
){
var $t$;
//var c$;
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "JmolPropertyManager");
Clazz_declarePackage ("JV");
Clazz_load (["J.api.JmolPropertyManager", "java.util.Hashtable"], "JV.PropertyManager", ["java.lang.Boolean", "$.Character", "$.Double", "$.Float", "java.util.Arrays", "$.Date", "$.Map", "JU.AU", "$.BArray", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.P3", "$.PT", "$.SB", "$.V3", "J.api.Interface", "JM.Atom", "$.BondSet", "$.LabelToken", "JS.SV", "$.T", "JU.BSUtil", "$.C", "$.Edge", "$.Elements", "$.Escape", "$.JmolMolecule", "$.Logger", "$.Txt", "JV.ActionManager", "$.JC", "$.Viewer", "JV.binding.Binding"], function () {
c$ = Clazz_decorateAsClass (function () {
this.vwr = null;
this.map = null;
Clazz_instantialize (this, arguments);
}, JV, "PropertyManager", null, J.api.JmolPropertyManager);
Clazz_prepareFields (c$, function () {
this.map =  new java.util.Hashtable ();
});
Clazz_makeConstructor (c$, 
function () {
});
Clazz_overrideMethod (c$, "setViewer", 
function (vwr) {
this.vwr = vwr;
for (var i = 0, p = 0; i < JV.PropertyManager.propertyTypes.length; i += 3) this.map.put (JV.PropertyManager.propertyTypes[i].toLowerCase (), Integer.$valueOf (p++));

}, "JV.Viewer");
Clazz_overrideMethod (c$, "getPropertyNumber", 
function (infoType) {
var n = this.map.get (infoType == null ? "" : infoType.toLowerCase ());
return (n == null ? -1 : n.intValue ());
}, "~S");
Clazz_overrideMethod (c$, "getDefaultPropertyParam", 
function (propID) {
return (propID < 0 ? "" : JV.PropertyManager.propertyTypes[propID * 3 + 2]);
}, "~N");
Clazz_overrideMethod (c$, "checkPropertyParameter", 
function (name) {
var propID = this.getPropertyNumber (name);
var type = JV.PropertyManager.getParamType (propID);
return (type.length > 0 && type !== "<atom selection>");
}, "~S");
Clazz_overrideMethod (c$, "getProperty", 
function (returnType, infoType, paramInfo) {
if (JV.PropertyManager.propertyTypes.length != 132) JU.Logger.warn ("propertyTypes is not the right length: " + JV.PropertyManager.propertyTypes.length + " != " + 132);
var info;
if (infoType.indexOf (".") >= 0 || infoType.indexOf ("[") >= 0) {
var args = this.getArguments (infoType);
info = this.extractProperty (this.getPropertyAsObject (args[0].asString (), paramInfo, null), args, 1, null, false);
} else {
info = this.getPropertyAsObject (infoType, paramInfo, returnType);
}if (returnType == null) return info;
var requestedReadable = returnType.equalsIgnoreCase ("readable");
if (requestedReadable) returnType = (JV.PropertyManager.isReadableAsString (infoType) ? "String" : "JSON");
if (returnType.equalsIgnoreCase ("String")) return (info == null ? "" : info.toString ());
if (requestedReadable) return JU.Escape.toReadable (infoType, info);
 else if (returnType.equalsIgnoreCase ("JSON")) return "{" + JU.PT.toJSON (infoType, info) + "}";
return info;
}, "~S,~S,~O");
Clazz_defineMethod (c$, "getArguments", 
 function (propertyName) {
var lc = propertyName.toLowerCase ();
var pt = -1;
while ((pt = lc.indexOf ("[select ", ++pt)) >= 0) {
var pt2 = lc.indexOf (" where ", pt);
var pt3 = lc.indexOf ("]", pt);
if (pt2 < 0 || pt2 > pt3) continue;
propertyName = propertyName.substring (0, pt2) + propertyName.substring (pt2, pt3).$replace ('.', '\1') + propertyName.substring (pt3);
}
propertyName = propertyName.$replace (']', '\0').$replace ('[', '\0').$replace ('.', '\0').$replace ('\1', '.');
propertyName = JU.PT.rep (propertyName, "\0\0", "\0");
var names = JU.PT.split (JU.PT.trim (propertyName, "\0"), "\0");
var args =  new Array (names.length);
for (var i = 0, n; i < names.length; i++) args[i] = (names[i].startsWith ("'") || names[i].startsWith ("\"") ? JS.SV.newS (JU.PT.trim (names[i], "'\"")) : (n = JU.PT.parseInt (names[i])) == -2147483648 ? JS.SV.newS (names[i]) : JS.SV.newI (n));

return args;
}, "~S");
Clazz_overrideMethod (c$, "extractProperty", 
function (prop, args, ptr, v2, isCompiled) {
if (ptr < 0) {
args = this.getArguments (args);
ptr = 0;
}if (ptr >= (args).length) return prop;
if (!isCompiled) args = this.compileSelect (args);
var pt;
var arg = (args)[ptr++];
var property = this.getObj (prop);
switch (arg.tok) {
case 2:
pt = arg.intValue - 1;
if (Clazz_instanceOf (property, JU.Lst)) {
var v = property;
if (pt < 0) pt += v.size ();
return (pt >= 0 && pt < v.size () ? this.extractProperty (v.get (pt), args, ptr, null, true) : "");
}if (Clazz_instanceOf (property, JU.M3)) {
var m = property;
var f = [[m.m00, m.m01, m.m02], [m.m10, m.m11, m.m12], [m.m20, m.m21, m.m22]];
if (pt < 0) pt += 3;
if (pt >= 0 && pt < 3) return this.extractProperty (f, args, --ptr, null, true);
return "";
}if (Clazz_instanceOf (property, JU.M4)) {
var m = property;
var f = [[m.m00, m.m01, m.m02, m.m03], [m.m10, m.m11, m.m12, m.m13], [m.m20, m.m21, m.m22, m.m23], [m.m30, m.m31, m.m32, m.m33]];
if (pt < 0) pt += 4;
if (pt >= 0 && pt < 4) return this.extractProperty (f, args, --ptr, null, true);
return "";
}if (JU.PT.isAI (property)) {
var ilist = property;
if (pt < 0) pt += ilist.length;
if (pt >= 0 && pt < ilist.length) return Integer.$valueOf (ilist[pt]);
return "";
}if (JU.PT.isAD (property)) {
var dlist = property;
if (pt < 0) pt += dlist.length;
if (pt >= 0 && pt < dlist.length) return Double.$valueOf (dlist[pt]);
return "";
}if (JU.PT.isAF (property)) {
var flist = property;
if (pt < 0) pt += flist.length;
if (pt >= 0 && pt < flist.length) return Float.$valueOf (flist[pt]);
return "";
}if (JU.PT.isAII (property)) {
var iilist = property;
if (pt < 0) pt += iilist.length;
if (pt >= 0 && pt < iilist.length) return this.extractProperty (iilist[pt], args, ptr, null, true);
return "";
}if (JU.PT.isAFF (property)) {
var fflist = property;
if (pt < 0) pt += fflist.length;
if (pt >= 0 && pt < fflist.length) return this.extractProperty (fflist[pt], args, ptr, null, true);
return "";
}if (JU.PT.isAS (property)) {
var slist = property;
if (pt < 0) pt += slist.length;
if (pt >= 0 && pt < slist.length) return slist[pt];
return "";
}if (Clazz_instanceOf (property, Array)) {
var olist = property;
if (pt < 0) pt += olist.length;
if (pt >= 0 && pt < olist.length) return olist[pt];
return "";
}break;
case 135280132:
case 4:
if (Clazz_instanceOf (property, java.util.Map)) {
var h = property;
var key;
if (arg.tok == 135280132) {
key = arg.myName;
if (!this.vwr.checkSelect (property, arg.value)) return "";
} else {
key = arg.asString ();
if (key.equalsIgnoreCase ("keys")) {
var keys =  new JU.Lst ();
for (var k, $k = h.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) keys.addLast (k);

return this.extractProperty (keys, args, ptr, null, true);
}}var isWild = (key.startsWith ("*") || key.endsWith ("*") || key.indexOf (",") >= 0);
if (isWild && v2 == null) v2 =  new JU.Lst ();
if (isWild && key.length == 1) {
if (ptr == (args).length) {
v2.addLast (property);
return v2;
}return this.extractProperty (property, args, ptr, v2, true);
}if (key.contains (",")) {
var mapNew = null;
mapNew =  new java.util.Hashtable ();
var tokens = JU.PT.split (key, ",");
for (var i = tokens.length; --i >= 0; ) JU.PT.getMapSubset (h, tokens[i], mapNew);

if (ptr == (args).length) {
v2.addLast (mapNew);
return v2;
}return this.extractProperty (mapNew, args, ptr, v2, true);
}key = this.checkMap (h, key, isWild, v2, args, ptr);
return (key != null && !isWild ? this.extractProperty (h.get (key), args, ptr, null, true) : isWild ? v2 : "");
}if (Clazz_instanceOf (property, JU.Lst)) {
var v = property;
if (v2 == null) v2 =  new JU.Lst ();
ptr--;
for (pt = 0; pt < v.size (); pt++) {
var o = v.get (pt);
if (Clazz_instanceOf (o, java.util.Map) || Clazz_instanceOf (o, JU.Lst) || (Clazz_instanceOf (o, JS.SV)) && ((o).getMap () != null || (o).getList () != null)) this.extractProperty (o, args, ptr, v2, true);
}
return v2;
}break;
}
return prop;
}, "~O,~O,~N,JU.Lst,~B");
Clazz_defineMethod (c$, "compileSelect", 
 function (args) {
var argsNew = null;
for (var i = args.length; --i >= 0; ) {
if (args[i].tok == 4) {
var key = args[i].value;
if (key.toUpperCase ().startsWith ("SELECT ")) {
if (argsNew == null) argsNew = JU.AU.arrayCopyObject (args, args.length);
key = key.substring (6).trim ();
if (key.toUpperCase ().startsWith ("WHERE ")) key = "* " + key;
var pt = key.toUpperCase ().indexOf (" WHERE ");
if (pt < 0) {
argsNew[i].value = key;
} else {
argsNew[i] = JS.SV.newV (135280132, this.vwr.compileExpr (key.substring (pt + 6).trim ()));
argsNew[i].myName = key.substring (0, pt).trim ();
}}}}
return (argsNew == null ? args : argsNew);
}, "~A");
Clazz_defineMethod (c$, "checkMap", 
 function (h, key, isWild, v2, args, ptr) {
var isOK = (v2 == null && h.containsKey (key));
if (!isOK) {
var lckey = (isWild ? key.toLowerCase () : null);
for (var k, $k = h.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
if (k.equalsIgnoreCase (key) || lckey != null && JU.PT.isLike (k.toLowerCase (), lckey)) {
if (v2 == null) return k;
v2.addLast (this.extractProperty (h.get (k), args, ptr, null, true));
if (!isWild) return null;
}}
}return (isOK ? key : null);
}, "java.util.Map,~S,~B,JU.Lst,~O,~N");
Clazz_defineMethod (c$, "getObj", 
 function (prop) {
return (Clazz_instanceOf (prop, JS.SV) ? JS.SV.oValue (prop) : prop);
}, "~O");
c$.getPropertyName = Clazz_defineMethod (c$, "getPropertyName", 
 function (propID) {
return (propID < 0 ? "" : JV.PropertyManager.propertyTypes[propID * 3]);
}, "~N");
c$.getParamType = Clazz_defineMethod (c$, "getParamType", 
 function (propID) {
return (propID < 0 ? "" : JV.PropertyManager.propertyTypes[propID * 3 + 1]);
}, "~N");
c$.isReadableAsString = Clazz_defineMethod (c$, "isReadableAsString", 
 function (infoType) {
for (var i = JV.PropertyManager.readableTypes.length; --i >= 0; ) if (infoType.equalsIgnoreCase (JV.PropertyManager.readableTypes[i])) return true;

return false;
}, "~S");
Clazz_defineMethod (c$, "getPropertyAsObject", 
 function (infoType, paramInfo, returnType) {
if (infoType.equals ("tokenList")) {
return JS.T.getTokensLike (paramInfo);
}var id = this.getPropertyNumber (infoType);
var iHaveParameter = (paramInfo != null && paramInfo.toString ().length > 0);
var myParam = (iHaveParameter ? paramInfo : this.getDefaultPropertyParam (id));
switch (id) {
case 0:
return this.getAppletInfo ();
case 5:
return this.getAnimationInfo ();
case 13:
return this.vwr.getAtomBitSetVector (myParam);
case 14:
return this.getAllAtomInfo (this.vwr.getAtomBitSet (myParam));
case 24:
return this.getAuxiliaryInfo (myParam);
case 15:
return this.getAllBondInfo (myParam);
case 25:
return this.getBoundBoxInfo ();
case 10:
return this.vwr.tm.getRotationCenter ();
case 16:
return this.getAllChainInfo (this.vwr.getAtomBitSet (myParam));
case 37:
return this.vwr.getProperty ("DATA_API", "consoleText", null);
case 26:
return this.vwr.getData (myParam.toString ());
case 33:
return this.vwr.getErrorMessageUn ();
case 28:
return this.vwr.evaluateExpression (myParam.toString ());
case 20:
return this.vwr.getModelExtract (myParam, true, false, "MOL");
case 32:
return JV.PropertyManager.getFileInfo (this.vwr.getFileData (), myParam.toString ());
case 1:
return this.vwr.getFullPathName (false);
case 2:
return this.vwr.getFileHeader ();
case 4:
case 3:
return (iHaveParameter ? this.vwr.getFileAsString (myParam.toString (), true) : this.vwr.getCurrentFileAsString ());
case 27:
var params = myParam.toString ().toLowerCase ();
return this.getImage (params, params.indexOf ("g64") < 0 && params.indexOf ("base64") < 0 && (returnType == null || returnType.equalsIgnoreCase ("java")));
case 35:
return this.vwr.getShapeProperty (24, "getInfo");
case 36:
return this.vwr.getShapeProperty (24, "getData");
case 40:
return this.vwr.getNMRCalculation ().getInfo (myParam.toString ());
case 41:
return this.getVariables (myParam.toString ());
case 21:
return this.vwr.getStatusChanged (myParam.toString ());
case 22:
return this.vwr;
case 38:
return this.vwr.getJspecViewProperties (myParam);
case 7:
return this.getLigandInfo (this.vwr.getAtomBitSet (myParam));
case 9:
return this.getMeasurementInfo ();
case 29:
return this.vwr.getMenu (myParam.toString ());
case 23:
return this.vwr.sm.getMessageQueue ();
case 30:
return this.vwr.getMinimizationInfo ();
case 6:
return this.getModelInfo (this.vwr.getAtomBitSet (myParam));
case 18:
return this.getMoleculeInfo (this.vwr.getAtomBitSet (myParam));
case 34:
return this.getMouseInfo ();
case 11:
return this.vwr.tm.getOrientationInfo ();
case 31:
return this.vwr.getPointGroupInfo (myParam);
case 17:
return this.getAllPolymerInfo (this.vwr.getAtomBitSet (myParam));
case 39:
return this.vwr.getScriptQueueInfo ();
case 8:
return this.getShapeInfo ();
case 19:
return this.vwr.getStateInfo3 (myParam.toString (), 0, 0);
case 12:
return this.vwr.tm.getMatrixRotate ();
case 42:
return this.getAnnotationInfo (myParam, 1073741925);
case 43:
return this.getAnnotationInfo (myParam, 1073742189);
}
var data =  new Array (44);
for (var i = 0; i < 44; i++) {
var paramType = JV.PropertyManager.getParamType (i);
var paramDefault = this.getDefaultPropertyParam (i);
var name = JV.PropertyManager.getPropertyName (i);
data[i] = (name.charAt (0) == 'X' ? "" : name + (paramType !== "" ? " " + JV.PropertyManager.getParamType (i) + (paramDefault !== "" ? " #default: " + this.getDefaultPropertyParam (i) : "") : ""));
}
java.util.Arrays.sort (data);
var info =  new JU.SB ();
info.append ("getProperty ERROR\n").append (infoType).append ("?\nOptions include:\n");
for (var i = 0; i < 44; i++) if (data[i].length > 0) info.append ("\n getProperty ").append (data[i]);

return info.toString ();
}, "~S,~O,~S");
Clazz_defineMethod (c$, "getImage", 
 function (params, asBytes) {
var height = -1;
var width = -1;
var pt;
if ((pt = params.indexOf ("height=")) >= 0) height = JU.PT.parseInt (params.substring (pt + 7));
if ((pt = params.indexOf ("width=")) >= 0) width = JU.PT.parseInt (params.substring (pt + 6));
if (width < 0 && height < 0) height = width = -1;
 else if (width < 0) width = height;
 else height = width;
var type = "JPG";
if (params.indexOf ("type=") >= 0) type = JU.PT.getTokens (JU.PT.replaceWithCharacter (params.substring (params.indexOf ("type=") + 5), ";,", ' '))[0];
var errMsg =  new Array (1);
var bytes = this.vwr.getImageAsBytes (type.toUpperCase (), width, height, -1, errMsg);
return (errMsg[0] != null ? errMsg[0] : asBytes ?  new JU.BArray (bytes) : JU.Base64.getBase64 (bytes).toString ());
}, "~S,~B");
Clazz_defineMethod (c$, "getVariables", 
 function (name) {
return (name.toLowerCase ().equals ("all") ? this.vwr.g.getAllVariables () : this.vwr.evaluateExpressionAsVariable (name));
}, "~S");
c$.getFileInfo = Clazz_defineMethod (c$, "getFileInfo", 
function (objHeader, type) {
var ht =  new java.util.Hashtable ();
if (objHeader == null) return ht;
var haveType = (type != null && type.length > 0);
if (Clazz_instanceOf (objHeader, java.util.Map)) {
return (haveType ? (objHeader).get (type) : objHeader);
}var lines = JU.PT.split (objHeader, "\n");
if (lines.length == 0 || lines[0].length < 6 || lines[0].charAt (6) != ' ' || !lines[0].substring (0, 6).equals (lines[0].substring (0, 6).toUpperCase ())) {
ht.put ("fileHeader", objHeader);
return ht;
}var keyLast = "";
var sb =  new JU.SB ();
if (haveType) type = type.toUpperCase ();
var key = "";
for (var i = 0; i < lines.length; i++) {
var line = lines[i];
if (line.length < 12) continue;
key = line.substring (0, 6).trim ();
var cont = line.substring (7, 10).trim ();
if (key.equals ("REMARK")) {
key += cont;
}if (!key.equals (keyLast)) {
if (haveType && keyLast.equals (type)) return sb.toString ();
if (!haveType) {
ht.put (keyLast, sb.toString ());
sb =  new JU.SB ();
}keyLast = key;
}if (!haveType || key.equals (type)) sb.append (line).appendC ('\n');
}
if (!haveType) {
ht.put (keyLast, sb.toString ());
}if (haveType) return (key.equals (type) ? sb.toString () : "");
return ht;
}, "~O,~S");
Clazz_defineMethod (c$, "getMoleculeInfo", 
function (atomExpression) {
var bsAtoms = this.vwr.getAtomBitSet (atomExpression);
var molecules = this.vwr.ms.getMolecules ();
var V =  new JU.Lst ();
var bsTemp =  new JU.BS ();
for (var i = 0; i < molecules.length; i++) {
bsTemp = JU.BSUtil.copy (bsAtoms);
var m = molecules[i];
bsTemp.and (m.atomList);
if (bsTemp.length () > 0) {
var info =  new java.util.Hashtable ();
info.put ("mf", m.getMolecularFormula (false));
info.put ("number", Integer.$valueOf (m.moleculeIndex + 1));
info.put ("modelNumber", this.vwr.ms.getModelNumberDotted (m.modelIndex));
info.put ("numberInModel", Integer.$valueOf (m.indexInModel + 1));
info.put ("nAtoms", Integer.$valueOf (m.ac));
info.put ("nElements", Integer.$valueOf (m.nElements));
V.addLast (info);
}}
return V;
}, "~O");
Clazz_overrideMethod (c$, "getModelInfo", 
function (atomExpression) {
var bsModels = this.vwr.ms.getModelBS (this.vwr.getAtomBitSet (atomExpression), false);
var m = this.vwr.ms;
var info =  new java.util.Hashtable ();
info.put ("modelSetName", m.modelSetName);
info.put ("modelCount", Integer.$valueOf (m.mc));
info.put ("isTainted", Boolean.$valueOf (m.tainted != null));
info.put ("canSkipLoad", Boolean.$valueOf (m.canSkipLoad));
info.put ("modelSetHasVibrationVectors", Boolean.$valueOf (m.modelSetHasVibrationVectors ()));
if (m.modelSetProperties != null) {
info.put ("modelSetProperties", m.modelSetProperties);
}info.put ("modelCountSelected", Integer.$valueOf (JU.BSUtil.cardinalityOf (bsModels)));
info.put ("modelsSelected", bsModels);
var vModels =  new JU.Lst ();
m.getMolecules ();
for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) {
var model =  new java.util.Hashtable ();
model.put ("_ipt", Integer.$valueOf (i));
model.put ("num", Integer.$valueOf (m.getModelNumber (i)));
model.put ("file_model", m.getModelNumberDotted (i));
model.put ("name", m.getModelName (i));
var s = m.getModelTitle (i);
if (s != null) model.put ("title", s);
s = m.getModelFileName (i);
if (s != null) model.put ("file", s);
s = m.getInfo (i, "modelID");
if (s != null) model.put ("id", s);
model.put ("vibrationVectors", Boolean.$valueOf (this.vwr.modelHasVibrationVectors (i)));
var mi = m.am[i];
model.put ("atomCount", Integer.$valueOf (mi.ac));
model.put ("bondCount", Integer.$valueOf (mi.getBondCount ()));
model.put ("groupCount", Integer.$valueOf (mi.getGroupCount ()));
model.put ("moleculeCount", Integer.$valueOf (mi.moleculeCount));
model.put ("polymerCount", Integer.$valueOf (mi.getBioPolymerCount ()));
model.put ("chainCount", Integer.$valueOf (m.getChainCountInModelWater (i, true)));
if (mi.properties != null) {
model.put ("modelProperties", mi.properties);
}var energy = m.getInfo (i, "Energy");
if (energy != null) {
model.put ("energy", energy);
}model.put ("atomCount", Integer.$valueOf (mi.ac));
vModels.addLast (model);
}
info.put ("models", vModels);
return info;
}, "~O");
Clazz_overrideMethod (c$, "getLigandInfo", 
function (atomExpression) {
var bsAtoms = this.vwr.getAtomBitSet (atomExpression);
var bsSolvent = this.vwr.getAtomBitSet ("solvent");
var info =  new java.util.Hashtable ();
var ligands =  new JU.Lst ();
info.put ("ligands", ligands);
var ms = this.vwr.ms;
var bsExclude = JU.BSUtil.copyInvert (bsAtoms, ms.ac);
bsExclude.or (bsSolvent);
var atoms = ms.at;
for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) if (atoms[i].isProtein () || atoms[i].isNucleic ()) bsExclude.set (i);

var bsModelAtoms =  new Array (ms.mc);
for (var i = ms.mc; --i >= 0; ) {
bsModelAtoms[i] = this.vwr.getModelUndeletedAtomsBitSet (i);
bsModelAtoms[i].andNot (bsExclude);
}
var molList = JU.JmolMolecule.getMolecules (atoms, bsModelAtoms, null, bsExclude);
for (var i = 0; i < molList.length; i++) {
var bs = molList[i].atomList;
var ligand =  new java.util.Hashtable ();
ligands.addLast (ligand);
ligand.put ("atoms", JU.Escape.eBS (bs));
var names = "";
var sep = "";
var lastGroup = null;
var iChainLast = 0;
var sChainLast = null;
var reslist = "";
var model = "";
var resnolast = 2147483647;
var resnofirst = 2147483647;
for (var j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1)) {
var atom = atoms[j];
if (lastGroup === atom.group) continue;
lastGroup = atom.group;
var resno = atom.getResno ();
var chain = atom.getChainID ();
if (resnolast != resno - 1) {
if (reslist.length != 0 && resnolast != resnofirst) reslist += "-" + resnolast;
chain = -1;
resnofirst = resno;
}model = "/" + ms.getModelNumberDotted (atom.mi);
if (iChainLast != 0 && chain != iChainLast) reslist += ":" + sChainLast + model;
if (chain == -1) reslist += " " + resno;
resnolast = resno;
iChainLast = atom.getChainID ();
sChainLast = atom.getChainIDStr ();
names += sep + atom.getGroup3 (false);
sep = "-";
}
reslist += (resnofirst == resnolast ? "" : "-" + resnolast) + (iChainLast == 0 ? "" : ":" + sChainLast) + model;
ligand.put ("groupNames", names);
ligand.put ("residueList", reslist.substring (1));
}
return info;
}, "~O");
Clazz_overrideMethod (c$, "getSymmetryInfo", 
function (bsAtoms, xyz, op, pt, pt2, id, type) {
var iModel = -1;
if (bsAtoms == null) {
iModel = this.vwr.am.cmi;
if (iModel < 0) return "";
bsAtoms = this.vwr.getModelUndeletedAtomsBitSet (iModel);
}var iAtom = bsAtoms.nextSetBit (0);
if (iAtom < 0) return "";
iModel = this.vwr.ms.at[iAtom].mi;
var uc = this.vwr.ms.am[iModel].biosymmetry;
if (uc == null) uc = this.vwr.ms.getUnitCell (iModel);
if (uc == null) return "";
return uc.getSymmetryInfo (this.vwr.ms, iModel, iAtom, uc, xyz, op, pt, pt2, id, type);
}, "JU.BS,~S,~N,JU.P3,JU.P3,~S,~N");
Clazz_overrideMethod (c$, "getModelExtract", 
function (bs, doTransform, isModelKit, type) {
var asV3000 = type.equalsIgnoreCase ("V3000");
var asSDF = type.equalsIgnoreCase ("SDF");
var asXYZVIB = type.equalsIgnoreCase ("XYZVIB");
var asJSON = type.equalsIgnoreCase ("JSON") || type.equalsIgnoreCase ("CD");
var mol =  new JU.SB ();
var ms = this.vwr.ms;
if (!asXYZVIB && !asJSON) {
mol.append (isModelKit ? "Jmol Model Kit" : this.vwr.getFullPathName (false).$replace ('\\', '/'));
var version = JV.Viewer.getJmolVersion ();
mol.append ("\n__Jmol-").append (version.substring (0, 2));
var cMM;
var cDD;
var cYYYY;
var cHH;
var cmm;
{
var c = new Date();
cMM = c.getMonth();
cDD = c.getDate();
cYYYY = c.getFullYear();
cHH = c.getHours();
cmm = c.getMinutes();
}JU.Txt.rightJustify (mol, "_00", "" + (1 + cMM));
JU.Txt.rightJustify (mol, "00", "" + cDD);
mol.append (("" + cYYYY).substring (2, 4));
JU.Txt.rightJustify (mol, "00", "" + cHH);
JU.Txt.rightJustify (mol, "00", "" + cmm);
mol.append ("3D 1   1.00000     0.00000     0");
mol.append ("\nJmol version ").append (JV.Viewer.getJmolVersion ()).append (" EXTRACT: ").append (JU.Escape.eBS (bs)).append ("\n");
}var bsAtoms = JU.BSUtil.copy (bs);
var atoms = ms.at;
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) if (doTransform && atoms[i].isDeleted ()) bsAtoms.clear (i);

var bsBonds = JV.PropertyManager.getCovalentBondsForAtoms (ms.bo, ms.bondCount, bsAtoms);
if (!asXYZVIB && bsAtoms.cardinality () == 0) return "";
var isOK = true;
var q = (doTransform ? this.vwr.tm.getRotationQuaternion () : null);
if (asSDF) {
var header = mol.toString ();
mol =  new JU.SB ();
var bsModels = this.vwr.ms.getModelBS (bsAtoms, true);
for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) {
mol.append (header);
var bsTemp = JU.BSUtil.copy (bsAtoms);
bsTemp.and (ms.getModelAtomBitSetIncludingDeleted (i, false));
bsBonds = JV.PropertyManager.getCovalentBondsForAtoms (ms.bo, ms.bondCount, bsTemp);
if (!(isOK = this.addMolFile (mol, bsTemp, bsBonds, false, false, q))) break;
mol.append ("$$$$\n");
}
} else if (asXYZVIB) {
var tokens1 = JM.LabelToken.compile (this.vwr, "%-2e %10.5x %10.5y %10.5z %10.5vx %10.5vy %10.5vz\n", '\0', null);
var tokens2 = JM.LabelToken.compile (this.vwr, "%-2e %10.5x %10.5y %10.5z\n", '\0', null);
var bsModels = this.vwr.ms.getModelBS (bsAtoms, true);
var ptTemp =  new JU.P3 ();
for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) {
var bsTemp = JU.BSUtil.copy (bsAtoms);
bsTemp.and (ms.getModelAtomBitSetIncludingDeleted (i, false));
if (bsTemp.cardinality () == 0) continue;
mol.appendI (bsTemp.cardinality ()).appendC ('\n');
var props = ms.am[i].properties;
mol.append ("Model[" + (i + 1) + "]: ");
if (ms.frameTitles[i] != null && ms.frameTitles[i].length > 0) {
mol.append (ms.frameTitles[i].$replace ('\n', ' '));
} else if (props == null) {
mol.append ("Jmol " + JV.Viewer.getJmolVersion ());
} else {
var sb =  new JU.SB ();
var e = props.propertyNames ();
var path = null;
while (e.hasMoreElements ()) {
var propertyName = e.nextElement ();
if (propertyName.equals (".PATH")) path = props.getProperty (propertyName);
 else sb.append (";").append (propertyName).append ("=").append (props.getProperty (propertyName));
}
if (path != null) sb.append (";PATH=").append (path);
path = sb.substring (sb.length () > 0 ? 1 : 0);
mol.append (path.$replace ('\n', ' '));
}mol.appendC ('\n');
for (var j = bsTemp.nextSetBit (0); j >= 0; j = bsTemp.nextSetBit (j + 1)) mol.append (JM.LabelToken.formatLabelAtomArray (this.vwr, atoms[j], (ms.getVibration (j, false) == null ? tokens2 : tokens1), '\0', null, ptTemp));

}
} else {
isOK = this.addMolFile (mol, bsAtoms, bsBonds, asV3000, asJSON, q);
}return (isOK ? mol.toString () : "ERROR: Too many atoms or bonds -- use V3000 format.");
}, "JU.BS,~B,~B,~S");
Clazz_defineMethod (c$, "addMolFile", 
 function (mol, bsAtoms, bsBonds, asV3000, asJSON, q) {
var nAtoms = bsAtoms.cardinality ();
var nBonds = bsBonds.cardinality ();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999)) return false;
var ms = this.vwr.ms;
var atomMap =  Clazz_newIntArray (ms.ac, 0);
var pTemp =  new JU.P3 ();
if (asV3000) {
mol.append ("  0  0  0  0  0  0            999 V3000");
} else if (asJSON) {
mol.append ("{\"mol\":{\"createdBy\":\"Jmol " + JV.Viewer.getJmolVersion () + "\",\"a\":[");
} else {
JU.Txt.rightJustify (mol, "   ", "" + nAtoms);
JU.Txt.rightJustify (mol, "   ", "" + nBonds);
mol.append ("  0  0  0  0              1 V2000");
}if (!asJSON) mol.append ("\n");
if (asV3000) {
mol.append ("M  V30 BEGIN CTAB\nM  V30 COUNTS ").appendI (nAtoms).append (" ").appendI (nBonds).append (" 0 0 0\n").append ("M  V30 BEGIN ATOM\n");
}var ptTemp =  new JU.P3 ();
for (var i = bsAtoms.nextSetBit (0), n = 0; i >= 0; i = bsAtoms.nextSetBit (i + 1)) this.getAtomRecordMOL (ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp, ptTemp, asV3000, asJSON);

if (asV3000) {
mol.append ("M  V30 END ATOM\nM  V30 BEGIN BOND\n");
} else if (asJSON) {
mol.append ("],\"b\":[");
}for (var i = bsBonds.nextSetBit (0), n = 0; i >= 0; i = bsBonds.nextSetBit (i + 1)) this.getBondRecordMOL (mol, ++n, ms.bo[i], atomMap, asV3000, asJSON);

if (asV3000) {
mol.append ("M  V30 END BOND\nM  V30 END CTAB\n");
}if (asJSON) mol.append ("]}}");
 else {
mol.append ("M  END\n");
}if (!asJSON && !asV3000) {
var pc = ms.getPartialCharges ();
if (pc != null) {
mol.append ("> <JMOL_PARTIAL_CHARGES>\n").appendI (nAtoms).appendC ('\n');
for (var i = bsAtoms.nextSetBit (0), n = 0; i >= 0; i = bsAtoms.nextSetBit (i + 1)) mol.appendI (++n).append (" ").appendF (pc[i]).appendC ('\n');

}}return true;
}, "JU.SB,JU.BS,JU.BS,~B,~B,JU.Quat");
c$.getCovalentBondsForAtoms = Clazz_defineMethod (c$, "getCovalentBondsForAtoms", 
 function (bonds, bondCount, bsAtoms) {
var bsBonds =  new JU.BS ();
for (var i = 0; i < bondCount; i++) {
var bond = bonds[i];
if (bsAtoms.get (bond.atom1.i) && bsAtoms.get (bond.atom2.i) && bond.isCovalent ()) bsBonds.set (i);
}
return bsBonds;
}, "~A,~N,JU.BS");
Clazz_defineMethod (c$, "getAtomRecordMOL", 
 function (ms, mol, n, a, q, pTemp, ptTemp, asV3000, asJSON) {
if (ms.am[a.mi].isTrajectory) a.setFractionalCoordPt (ptTemp, ms.trajectorySteps.get (a.mi)[a.i - ms.am[a.mi].firstAtomIndex], true);
 else pTemp.setT (a);
if (q != null) q.transformP2 (pTemp, pTemp);
var elemNo = a.getElementNumber ();
var sym = (a.isDeleted () ? "Xx" : JU.Elements.elementSymbolFromNumber (elemNo));
var iso = a.getIsotopeNumber ();
var charge = a.getFormalCharge ();
if (asV3000) {
mol.append ("M  V30 ").appendI (n).append (" ").append (sym).append (" ").appendF (pTemp.x).append (" ").appendF (pTemp.y).append (" ").appendF (pTemp.z).append (" 0");
if (charge != 0) mol.append (" CHG=").appendI (charge);
if (iso != 0) mol.append (" MASS=").appendI (iso);
mol.append ("\n");
} else if (asJSON) {
if (n != 1) mol.append (",");
mol.append ("{");
if (a.getElementNumber () != 6) mol.append ("\"l\":\"").append (a.getElementSymbol ()).append ("\",");
if (charge != 0) mol.append ("\"c\":").appendI (charge).append (",");
if (iso != 0 && iso != JU.Elements.getNaturalIsotope (elemNo)) mol.append ("\"m\":").appendI (iso).append (",");
mol.append ("\"x\":").appendF (a.x).append (",\"y\":").appendF (a.y).append (",\"z\":").appendF (a.z).append ("}");
} else {
mol.append (JU.Txt.sprintf ("%10.5p%10.5p%10.5p", "p", [pTemp]));
mol.append (" ").append (sym);
if (sym.length == 1) mol.append (" ");
if (iso > 0) iso -= JU.Elements.getNaturalIsotope (a.getElementNumber ());
mol.append (" ");
JU.Txt.rightJustify (mol, "  ", "" + iso);
JU.Txt.rightJustify (mol, "   ", "" + (charge == 0 ? 0 : 4 - charge));
mol.append ("  0  0  0  0\n");
}}, "JM.ModelSet,JU.SB,~N,JM.Atom,JU.Quat,JU.P3,JU.P3,~B,~B");
Clazz_defineMethod (c$, "getBondRecordMOL", 
 function (mol, n, b, atomMap, asV3000, asJSON) {
var a1 = atomMap[b.atom1.i];
var a2 = atomMap[b.atom2.i];
var order = b.getValence ();
if (order > 3) order = 1;
switch (b.order & -131073) {
case 515:
order = (asJSON ? -3 : 4);
break;
case 66:
order = (asJSON ? -3 : 5);
break;
case 513:
order = (asJSON ? 1 : 6);
break;
case 514:
order = (asJSON ? 2 : 7);
break;
case 33:
order = (asJSON ? -1 : 8);
break;
}
if (asV3000) {
mol.append ("M  V30 ").appendI (n).append (" ").appendI (order).append (" ").appendI (a1).append (" ").appendI (a2).appendC ('\n');
} else if (asJSON) {
if (n != 1) mol.append (",");
mol.append ("{\"b\":").appendI (a1 - 1).append (",\"e\":").appendI (a2 - 1);
if (order != 1) {
mol.append (",\"o\":");
if (order < 0) {
mol.appendF (-order / 2);
} else {
mol.appendI (order);
}}mol.append ("}");
} else {
JU.Txt.rightJustify (mol, "   ", "" + a1);
JU.Txt.rightJustify (mol, "   ", "" + a2);
mol.append ("  ").appendI (order).append ("  0  0  0\n");
}}, "JU.SB,~N,JM.Bond,~A,~B,~B");
Clazz_overrideMethod (c$, "getChimeInfo", 
function (tok, bs) {
switch (tok) {
case 1073741982:
break;
case 1073741864:
return this.getBasePairInfo (bs);
default:
return this.getChimeInfoA (this.vwr.ms.at, tok, bs);
}
var sb =  new JU.SB ();
this.vwr.ms.am[0].getChimeInfo (sb, 0);
return sb.appendC ('\n').toString ().substring (1);
}, "~N,JU.BS");
Clazz_defineMethod (c$, "getChimeInfoA", 
 function (atoms, tok, bs) {
var info =  new JU.SB ();
info.append ("\n");
var s = "";
var clast = null;
var glast = null;
var modelLast = -1;
var n = 0;
if (bs != null) for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
var a = atoms[i];
switch (tok) {
default:
return "";
case 1114638363:
s = a.getInfo ();
break;
case 1141899265:
s = "" + a.getAtomNumber ();
break;
case 1087373318:
s = a.getGroup3 (false);
break;
case 1087373316:
case 1073742120:
case 1087373320:
case 1087373319:
var id = a.getChainID ();
s = (id == 0 ? " " : a.getChainIDStr ());
if (id > 255) s = JU.PT.esc (s);
switch (tok) {
case 1073742120:
s = "[" + a.getGroup3 (false) + "]" + a.getSeqcodeString () + ":" + s;
break;
case 1087373320:
case 1087373319:
if (a.getModelIndex () != modelLast) {
info.appendC ('\n');
n = 0;
modelLast = a.getModelIndex ();
info.append ("Model " + a.getModelNumber ());
glast = null;
clast = null;
}if (a.getChain () !== clast) {
info.appendC ('\n');
n = 0;
clast = a.getChain ();
info.append ("Chain " + s + ":\n");
glast = null;
}var g = a.getGroup ();
if (g !== glast) {
glast = g;
if (tok == 1087373319) {
info.append (a.getGroup1 ('?'));
} else {
if ((n++) % 5 == 0 && n > 1) info.appendC ('\n');
JU.Txt.leftJustify (info, "          ", "[" + a.getGroup3 (false) + "]" + a.getResno () + " ");
}}continue;
}
break;
}
if (info.indexOf ("\n" + s + "\n") < 0) info.append (s).appendC ('\n');
}
if (tok == 1087373320) info.appendC ('\n');
return info.toString ().substring (1);
}, "~A,~N,JU.BS");
Clazz_overrideMethod (c$, "getModelFileInfo", 
function (frames) {
var ms = this.vwr.ms;
var sb =  new JU.SB ();
for (var i = 0; i < ms.mc; ++i) {
if (frames != null && !frames.get (i)) continue;
var s = "[\"" + ms.getModelNumberDotted (i) + "\"] = ";
sb.append ("\n\nfile").append (s).append (JU.PT.esc (ms.getModelFileName (i)));
var id = ms.getInfo (i, "modelID");
if (id != null) sb.append ("\nid").append (s).append (JU.PT.esc (id));
sb.append ("\ntitle").append (s).append (JU.PT.esc (ms.getModelTitle (i)));
sb.append ("\nname").append (s).append (JU.PT.esc (ms.getModelName (i)));
sb.append ("\ntype").append (s).append (JU.PT.esc (ms.getModelFileType (i)));
}
return sb.toString ();
}, "JU.BS");
Clazz_defineMethod (c$, "getAllAtomInfo", 
function (bs) {
var V =  new JU.Lst ();
var ptTemp =  new JU.P3 ();
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
V.addLast (this.getAtomInfoLong (i, ptTemp));
}
return V;
}, "JU.BS");
Clazz_defineMethod (c$, "getAtomInfoLong", 
 function (i, ptTemp) {
var ms = this.vwr.ms;
var atom = ms.at[i];
var info =  new java.util.Hashtable ();
ms.getAtomIdentityInfo (i, info, ptTemp);
info.put ("element", ms.getElementName (i));
info.put ("elemno", Integer.$valueOf (ms.getElementNumber (i)));
info.put ("x", Float.$valueOf (atom.x));
info.put ("y", Float.$valueOf (atom.y));
info.put ("z", Float.$valueOf (atom.z));
info.put ("coord", JU.P3.newP (atom));
if (ms.vibrations != null && ms.vibrations[i] != null) ms.vibrations[i].getInfo (info);
info.put ("bondCount", Integer.$valueOf (atom.getCovalentBondCount ()));
info.put ("radius", Float.$valueOf ((atom.getRasMolRadius () / 120.0)));
info.put ("model", atom.getModelNumberForLabel ());
var shape = JM.Atom.atomPropertyString (this.vwr, atom, 1087373323);
if (shape != null) info.put ("shape", shape);
info.put ("visible", Boolean.$valueOf (atom.checkVisible ()));
info.put ("clickabilityFlags", Integer.$valueOf (atom.clickabilityFlags));
info.put ("visibilityFlags", Integer.$valueOf (atom.shapeVisibilityFlags));
info.put ("spacefill", Float.$valueOf (atom.getRadius ()));
var strColor = JU.Escape.escapeColor (this.vwr.getColorArgbOrGray (atom.colixAtom));
if (strColor != null) info.put ("color", strColor);
info.put ("colix", Integer.$valueOf (atom.colixAtom));
var isTranslucent = atom.isTranslucent ();
if (isTranslucent) info.put ("translucent", Boolean.$valueOf (isTranslucent));
info.put ("formalCharge", Integer.$valueOf (atom.getFormalCharge ()));
info.put ("partialCharge", Float.$valueOf (atom.getPartialCharge ()));
var d = atom.getSurfaceDistance100 () / 100;
if (d >= 0) info.put ("surfaceDistance", Float.$valueOf (d));
if (ms.am[atom.mi].isBioModel) {
info.put ("resname", atom.getGroup3 (false));
var insCode = atom.getInsertionCode ();
var seqNum = atom.getResno ();
if (seqNum > 0) info.put ("resno", Integer.$valueOf (seqNum));
if (insCode.charCodeAt (0) != 0) info.put ("insertionCode", "" + insCode);
info.put ("name", ms.getAtomName (i));
info.put ("chain", atom.getChainIDStr ());
info.put ("atomID", Integer.$valueOf (atom.atomID));
info.put ("groupID", Integer.$valueOf (atom.getGroupID ()));
if (atom.altloc != '\0') info.put ("altLocation", "" + atom.altloc);
info.put ("structure", Integer.$valueOf (atom.getProteinStructureType ().getId ()));
info.put ("polymerLength", Integer.$valueOf (atom.getPolymerLength ()));
info.put ("occupancy", Integer.$valueOf (atom.getOccupancy100 ()));
var temp = atom.getBfactor100 ();
info.put ("temp", Integer.$valueOf (Clazz_doubleToInt (temp / 100)));
}return info;
}, "~N,JU.P3");
Clazz_defineMethod (c$, "getAllBondInfo", 
function (bsOrArray) {
var v =  new JU.Lst ();
var ms = this.vwr.ms;
var bondCount = ms.bondCount;
var bonds = ms.bo;
var bs1;
if (Clazz_instanceOf (bsOrArray, String)) {
bsOrArray = this.vwr.getAtomBitSet (bsOrArray);
}var ptTemp =  new JU.P3 ();
if (Clazz_instanceOf (bsOrArray, Array)) {
bs1 = (bsOrArray)[0];
var bs2 = (bsOrArray)[1];
for (var i = 0; i < bondCount; i++) {
var ia = bonds[i].atom1.i;
var ib = bonds[i].atom2.i;
if (bs1.get (ia) && bs2.get (ib) || bs2.get (ia) && bs1.get (ib)) v.addLast (this.getBondInfo (i, ptTemp));
}
} else if (Clazz_instanceOf (bsOrArray, JM.BondSet)) {
bs1 = bsOrArray;
for (var i = bs1.nextSetBit (0); i >= 0 && i < bondCount; i = bs1.nextSetBit (i + 1)) v.addLast (this.getBondInfo (i, ptTemp));

} else if (Clazz_instanceOf (bsOrArray, JU.BS)) {
bs1 = bsOrArray;
var thisAtom = (bs1.cardinality () == 1 ? bs1.nextSetBit (0) : -1);
for (var i = 0; i < bondCount; i++) {
if (thisAtom >= 0 ? (bonds[i].atom1.i == thisAtom || bonds[i].atom2.i == thisAtom) : bs1.get (bonds[i].atom1.i) && bs1.get (bonds[i].atom2.i)) v.addLast (this.getBondInfo (i, ptTemp));
}
}return v;
}, "~O");
Clazz_defineMethod (c$, "getBondInfo", 
 function (i, ptTemp) {
var bond = this.vwr.ms.bo[i];
var atom1 = bond.atom1;
var atom2 = bond.atom2;
var info =  new java.util.Hashtable ();
info.put ("_bpt", Integer.$valueOf (i));
var infoA =  new java.util.Hashtable ();
this.vwr.ms.getAtomIdentityInfo (atom1.i, infoA, ptTemp);
var infoB =  new java.util.Hashtable ();
this.vwr.ms.getAtomIdentityInfo (atom2.i, infoB, ptTemp);
info.put ("atom1", infoA);
info.put ("atom2", infoB);
info.put ("order", Float.$valueOf (JU.PT.fVal (JU.Edge.getBondOrderNumberFromOrder (bond.order))));
info.put ("type", JU.Edge.getBondOrderNameFromOrder (bond.order));
info.put ("radius", Float.$valueOf ((bond.mad / 2000.)));
info.put ("length_Ang", Float.$valueOf (atom1.distance (atom2)));
info.put ("visible", Boolean.$valueOf (bond.shapeVisibilityFlags != 0));
var strColor = JU.Escape.escapeColor (this.vwr.getColorArgbOrGray (bond.colix));
if (strColor != null) info.put ("color", strColor);
info.put ("colix", Integer.$valueOf (bond.colix));
if (JU.C.isColixTranslucent (bond.colix)) info.put ("translucent", Boolean.TRUE);
return info;
}, "~N,JU.P3");
Clazz_defineMethod (c$, "getAllChainInfo", 
function (bs) {
var finalInfo =  new java.util.Hashtable ();
var modelVector =  new JU.Lst ();
var modelCount = this.vwr.ms.mc;
for (var i = 0; i < modelCount; ++i) {
var modelInfo =  new java.util.Hashtable ();
var info = this.getChainInfo (i, bs);
if (info.size () > 0) {
modelInfo.put ("modelIndex", Integer.$valueOf (i));
modelInfo.put ("chains", info);
modelVector.addLast (modelInfo);
}}
finalInfo.put ("models", modelVector);
return finalInfo;
}, "JU.BS");
Clazz_defineMethod (c$, "getChainInfo", 
 function (modelIndex, bs) {
var model = this.vwr.ms.am[modelIndex];
var nChains = model.getChainCount (true);
var infoChains =  new JU.Lst ();
var ptTemp =  new JU.P3 ();
for (var i = 0; i < nChains; i++) {
var chain = model.getChainAt (i);
var infoChain =  new JU.Lst ();
var nGroups = chain.getGroupCount ();
var arrayName =  new java.util.Hashtable ();
for (var igroup = 0; igroup < nGroups; igroup++) {
var group = chain.getGroup (igroup);
if (bs.get (group.firstAtomIndex)) infoChain.addLast (group.getGroupInfo (igroup, ptTemp));
}
if (!infoChain.isEmpty ()) {
arrayName.put ("residues", infoChain);
infoChains.addLast (arrayName);
}}
return infoChains;
}, "~N,JU.BS");
Clazz_defineMethod (c$, "getAllPolymerInfo", 
 function (bs) {
var finalInfo =  new java.util.Hashtable ();
var modelVector =  new JU.Lst ();
var modelCount = this.vwr.ms.mc;
var models = this.vwr.ms.am;
for (var i = 0; i < modelCount; ++i) if (models[i].isBioModel) models[i].getAllPolymerInfo (bs, finalInfo, modelVector);

finalInfo.put ("models", modelVector);
return finalInfo;
}, "JU.BS");
Clazz_defineMethod (c$, "getBasePairInfo", 
 function (bs) {
var info =  new JU.SB ();
var vHBonds =  new JU.Lst ();
this.vwr.ms.calcRasmolHydrogenBonds (bs, bs, vHBonds, true, 1, false, null);
for (var i = vHBonds.size (); --i >= 0; ) {
var b = vHBonds.get (i);
JV.PropertyManager.getAtomResidueInfo (info, b.atom1);
info.append (" - ");
JV.PropertyManager.getAtomResidueInfo (info, b.atom2);
info.append ("\n");
}
return info.toString ();
}, "JU.BS");
c$.getAtomResidueInfo = Clazz_defineMethod (c$, "getAtomResidueInfo", 
 function (info, atom) {
info.append ("[").append (atom.getGroup3 (false)).append ("]").append (atom.getSeqcodeString ()).append (":");
var id = atom.getChainID ();
info.append (id == 0 ? " " : atom.getChainIDStr ());
}, "JU.SB,JM.Atom");
Clazz_defineMethod (c$, "getAppletInfo", 
 function () {
var info =  new java.util.Hashtable ();
info.put ("htmlName", this.vwr.htmlName);
info.put ("syncId", this.vwr.syncId);
info.put ("fullName", this.vwr.fullName);
info.put ("codeBase", "" + JV.Viewer.appletCodeBase);
if (this.vwr.isApplet ()) {
info.put ("documentBase", JV.Viewer.appletDocumentBase);
info.put ("registry", this.vwr.sm.getRegistryInfo ());
}info.put ("version", JV.JC.version);
info.put ("date", JV.JC.date);
info.put ("javaVendor", JV.Viewer.strJavaVendor);
info.put ("javaVersion", JV.Viewer.strJavaVersion + (!this.vwr.isJS ? "" : this.vwr.isWebGL ? "(WebGL)" : "(HTML5)"));
info.put ("operatingSystem", JV.Viewer.strOSName);
return info;
});
Clazz_defineMethod (c$, "getAnimationInfo", 
 function () {
var am = this.vwr.am;
var info =  new java.util.Hashtable ();
info.put ("firstModelIndex", Integer.$valueOf (am.firstFrameIndex));
info.put ("lastModelIndex", Integer.$valueOf (am.lastFrameIndex));
info.put ("animationDirection", Integer.$valueOf (am.animationDirection));
info.put ("currentDirection", Integer.$valueOf (am.currentDirection));
info.put ("displayModelIndex", Integer.$valueOf (am.cmi));
if (am.animationFrames != null) {
info.put ("isMovie", Boolean.TRUE);
info.put ("frames", JU.Escape.eAI (am.animationFrames));
info.put ("currentAnimationFrame", Integer.$valueOf (am.caf));
}info.put ("displayModelNumber", this.vwr.getModelNumberDotted (am.cmi));
info.put ("displayModelName", (am.cmi >= 0 ? this.vwr.getModelName (am.cmi) : ""));
info.put ("animationFps", Integer.$valueOf (am.animationFps));
info.put ("animationReplayMode", am.animationReplayMode.name ());
info.put ("firstFrameDelay", Float.$valueOf (am.firstFrameDelay));
info.put ("lastFrameDelay", Float.$valueOf (am.lastFrameDelay));
info.put ("animationOn", Boolean.$valueOf (am.animationOn));
info.put ("animationPaused", Boolean.$valueOf (am.animationPaused));
return info;
});
Clazz_defineMethod (c$, "getBoundBoxInfo", 
 function () {
var pts = this.vwr.ms.getBoxInfo (null, 1).getBoundBoxPoints (true);
var info =  new java.util.Hashtable ();
info.put ("center", JU.P3.newP (pts[0]));
info.put ("vector", JU.V3.newV (pts[1]));
info.put ("corner0", JU.P3.newP (pts[2]));
info.put ("corner1", JU.P3.newP (pts[3]));
return info;
});
Clazz_defineMethod (c$, "getShapeInfo", 
 function () {
var info =  new java.util.Hashtable ();
var commands =  new JU.SB ();
var shapes = this.vwr.shm.shapes;
if (shapes != null) for (var i = 0; i < 36; ++i) {
var shape = shapes[i];
if (shape != null) {
var shapeType = JV.JC.shapeClassBases[i];
var shapeDetail = shape.getShapeDetail ();
if (shapeDetail != null) info.put (shapeType, shapeDetail);
}}
if (commands.length () > 0) info.put ("shapeCommands", commands.toString ());
return info;
});
Clazz_defineMethod (c$, "getAuxiliaryInfo", 
 function (atomExpression) {
return this.vwr.ms.getAuxiliaryInfo (this.vwr.ms.getModelBS (this.vwr.getAtomBitSet (atomExpression), false));
}, "~O");
Clazz_defineMethod (c$, "getAnnotationInfo", 
 function (atomExpression, type) {
var bsAtoms = this.vwr.getAtomBitSet (atomExpression);
var iModel = this.vwr.ms.getModelBS (bsAtoms, false).nextSetBit (0);
if (iModel < 0) return null;
var modelinfo = this.vwr.ms.getModelAuxiliaryInfo (iModel);
var objAnn = modelinfo.get (type == 1073741925 ? "domains" : "validation");
if (objAnn == null || objAnn.tok != 6) return null;
this.vwr.getAnnotationParser ().initializeAnnotation (objAnn, type, iModel);
return objAnn.getMap ().get ("_list");
}, "~O,~N");
Clazz_defineMethod (c$, "getMeasurementInfo", 
 function () {
return this.vwr.getShapeProperty (6, "info");
});
Clazz_defineMethod (c$, "getMouseInfo", 
 function () {
if (!this.vwr.haveDisplay) return null;
var info =  new java.util.Hashtable ();
var list =  new JU.Lst ();
var am = this.vwr.actionManager;
for (var obj, $obj = am.b.getBindings ().values ().iterator (); $obj.hasNext () && ((obj = $obj.next ()) || true);) {
if (Clazz_instanceOf (obj, Boolean)) continue;
if (JU.PT.isAI (obj)) {
var binding = obj;
obj = [JV.binding.Binding.getMouseActionName (binding[0], false), JV.ActionManager.getActionName (binding[1])];
}list.addLast (obj);
}
info.put ("bindings", list);
info.put ("bindingName", am.b.name);
info.put ("actionNames", JV.ActionManager.actionNames);
info.put ("actionInfo", JV.ActionManager.actionInfo);
info.put ("bindingInfo", JU.PT.split (am.getBindingInfo (null), "\n"));
return info;
});
Clazz_overrideMethod (c$, "getPdbAtomData", 
function (bs, out) {
if (this.vwr.ms.ac == 0 || bs.nextSetBit (0) < 0) return "";
if (out == null) out = this.vwr.getOutputChannel (null, null);
var atoms = this.vwr.ms.at;
var models = this.vwr.ms.am;
var iModel = atoms[bs.nextSetBit (0)].mi;
var iModelLast = -1;
var isPQR = "PQR".equals (out.getType ());
var occTemp = "%6.2Q%6.2b          ";
if (isPQR) {
occTemp = "%8.4P%7.4V       ";
var charge = 0;
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) charge += atoms[i].getPartialCharge ();

out.append ("REMARK   1 PQR file generated by Jmol " + JV.Viewer.getJmolVersion ()).append ("\nREMARK   1 " + "created " + ( new java.util.Date ())).append ("\nREMARK   1 Forcefield Used: unknown\nREMARK   1").append ("\nREMARK   5").append ("\nREMARK   6 Total charge on this protein: " + charge + " e\nREMARK   6\n");
}var lastAtomIndex = bs.length () - 1;
var showModels = (iModel != atoms[lastAtomIndex].mi);
var sbCONECT = (showModels ? null :  new JU.SB ());
var isMultipleBondPDB = models[iModel].isPdbWithMultipleBonds;
var tokens;
var ptTemp =  new JU.P3 ();
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
var a = atoms[i];
if (showModels && a.mi != iModelLast) {
if (iModelLast != -1) out.append ("ENDMDL\n");
iModelLast = a.mi;
out.append ("MODEL     " + (iModelLast + 1) + "\n");
}var sa = a.getAtomName ();
var leftJustify = (a.getElementSymbol ().length == 2 || sa.length >= 4 || Character.isDigit (sa.charAt (0)));
var isBiomodel = models[a.mi].isBioModel;
var isHetero = a.isHetero ();
if (!isBiomodel) tokens = (leftJustify ? JM.LabelToken.compile (this.vwr, "HETATM%5.-5i %-4.4a%1AUNK %1c   1%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null) : JM.LabelToken.compile (this.vwr, "HETATM%5.-5i  %-3.3a%1AUNK %1c   1%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null));
 else if (isHetero) tokens = (leftJustify ? JM.LabelToken.compile (this.vwr, "HETATM%5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null) : JM.LabelToken.compile (this.vwr, "HETATM%5.-5i  %-3.3a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null));
 else tokens = (leftJustify ? JM.LabelToken.compile (this.vwr, "ATOM  %5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null) : JM.LabelToken.compile (this.vwr, "ATOM  %5.-5i  %-3.3a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z" + occTemp, '\0', null));
var XX = a.getElementSymbolIso (false).toUpperCase ();
out.append (JM.LabelToken.formatLabelAtomArray (this.vwr, a, tokens, '\0', null, ptTemp)).append (XX.length == 1 ? " " + XX : XX.substring (0, 2)).append ("  \n");
if (!showModels && (!isBiomodel || isHetero || isMultipleBondPDB)) {
var bonds = a.getBonds ();
if (bonds != null) for (var j = 0; j < bonds.length; j++) {
var iThis = a.getAtomNumber ();
var a2 = bonds[j].getOtherAtom (a);
if (!bs.get (a2.i)) continue;
var n = bonds[j].getCovalentOrder ();
if (n == 1 && isMultipleBondPDB && !isHetero) continue;
var iOther = a2.getAtomNumber ();
switch (n) {
case 2:
case 3:
if (iOther < iThis) continue;
case 1:
sbCONECT.append ("CONECT").append (JU.Txt.formatStringI ("%5i", "i", iThis));
for (var k = 0; k < n; k++) sbCONECT.append (JU.Txt.formatStringI ("%5i", "i", iOther));

sbCONECT.appendC ('\n');
break;
}
}
}}
if (showModels) out.append ("ENDMDL\n");
 else out.append (sbCONECT.toString ());
return out.toString ();
}, "JU.BS,JU.OC");
Clazz_overrideMethod (c$, "getPdbData", 
function (modelIndex, type, bsSelected, parameters, out, addStructure) {
if (this.vwr.ms.isJmolDataFrameForModel (modelIndex)) modelIndex = this.vwr.ms.getJmolDataSourceFrame (modelIndex);
if (modelIndex < 0) return "";
var model = this.vwr.ms.am[modelIndex];
var isPDB = model.isBioModel;
if (parameters == null && !isPDB) return null;
if (out == null) out = this.vwr.getOutputChannel (null, null);
var pdbCONECT =  new JU.SB ();
var isDraw = (type.indexOf ("draw") >= 0);
var bsAtoms = null;
var bsWritten =  new JU.BS ();
var ctype = '\u0000';
var tokens = this.vwr.ms.getLabeler ().compile (this.vwr, "ATOM  %-6i%4a%1A%3n %1c%4R%1E   ", '\0', null);
if (parameters == null) {
ctype = (type.length > 11 && type.indexOf ("quaternion ") >= 0 ? type.charAt (11) : 'R');
model.getPdbData (this.vwr, type, ctype, isDraw, bsSelected, out, tokens, pdbCONECT, bsWritten);
bsAtoms = this.vwr.getModelUndeletedAtomsBitSet (modelIndex);
} else {
bsAtoms = parameters[0];
var dataX = parameters[1];
var dataY = parameters[2];
var dataZ = parameters[3];
var haveZ = (dataZ != null);
var minXYZ = parameters[4];
var maxXYZ = parameters[5];
var factors = parameters[6];
var center = parameters[7];
out.append ("REMARK   6 Jmol PDB-encoded data: ").append (type).append (";\n");
out.append ("REMARK   6 Jmol data").append (" min = ").append (JU.Escape.eP (minXYZ)).append (" max = ").append (JU.Escape.eP (maxXYZ)).append (" unScaledXyz = xyz * ").append (JU.Escape.eP (factors)).append (" + ").append (JU.Escape.eP (center)).append (";\n");
var strExtra = "";
var atomLast = null;
var atoms = this.vwr.ms.at;
var ptTemp =  new JU.P3 ();
for (var i = bsAtoms.nextSetBit (0), n = 0; i >= 0; i = bsAtoms.nextSetBit (i + 1), n++) {
var x = dataX[n];
var y = dataY[n];
var z = (haveZ ? dataZ[n] : 0);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) continue;
var a = atoms[i];
out.append (JM.LabelToken.formatLabelAtomArray (this.vwr, a, tokens, '\0', null, ptTemp));
if (isPDB) bsWritten.set (i);
out.append (JU.Txt.sprintf ("%-8.2f%-8.2f%-10.2f    %6.3f          %2s    %s\n", "ssF", [a.getElementSymbolIso (false).toUpperCase (), strExtra, [x, y, z, 0]]));
if (atomLast != null && atomLast.getPolymerIndexInModel () == a.getPolymerIndexInModel ()) pdbCONECT.append ("CONECT").append (JU.Txt.formatStringI ("%5i", "i", atomLast.getAtomNumber ())).append (JU.Txt.formatStringI ("%5i", "i", a.getAtomNumber ())).appendC ('\n');
atomLast = a;
}
}out.append (pdbCONECT.toString ());
if (isDraw) return out.toString ();
bsSelected.and (bsAtoms);
if (isPDB && addStructure) out.append ("\n\n" + this.vwr.ms.getProteinStructureState (bsWritten, false, ctype == 'R', 1));
return out.toString ();
}, "~N,~S,JU.BS,~A,JU.OC,~B");
Clazz_overrideMethod (c$, "getModelCml", 
function (bs, atomsMax, addBonds) {
var sb =  new JU.SB ();
var nAtoms = JU.BSUtil.cardinalityOf (bs);
if (nAtoms == 0) return "";
J.api.Interface.getInterface ("JU.XmlUtil");
JU.XmlUtil.openTag (sb, "molecule");
JU.XmlUtil.openTag (sb, "atomArray");
var bsAtoms =  new JU.BS ();
var atoms = this.vwr.ms.at;
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
if (--atomsMax < 0) break;
var atom = atoms[i];
var name = atom.getAtomName ();
JU.PT.rep (name, "\"", "''");
bsAtoms.set (atom.i);
JU.XmlUtil.appendTag (sb, "atom/", ["id", "a" + (atom.i + 1), "title", atom.getAtomName (), "elementType", atom.getElementSymbol (), "x3", "" + atom.x, "y3", "" + atom.y, "z3", "" + atom.z]);
}
JU.XmlUtil.closeTag (sb, "atomArray");
if (addBonds) {
JU.XmlUtil.openTag (sb, "bondArray");
var bondCount = this.vwr.getBondCount ();
var bonds = this.vwr.ms.bo;
for (var i = 0; i < bondCount; i++) {
var bond = bonds[i];
var a1 = bond.atom1;
var a2 = bond.atom2;
if (!bsAtoms.get (a1.i) || !bsAtoms.get (a2.i)) continue;
var order = JU.Edge.getCmlBondOrder (bond.order);
if (order == null) continue;
JU.XmlUtil.appendTag (sb, "bond/", ["atomRefs2", "a" + (bond.atom1.i + 1) + " a" + (bond.atom2.i + 1), "order", order]);
}
JU.XmlUtil.closeTag (sb, "bondArray");
}JU.XmlUtil.closeTag (sb, "molecule");
return sb.toString ();
}, "JU.BS,~N,~B");
Clazz_defineStatics (c$,
"atomExpression", "<atom selection>");
c$.propertyTypes = c$.prototype.propertyTypes = ["appletInfo", "", "", "fileName", "", "", "fileHeader", "", "", "fileContents", "<pathname>", "", "fileContents", "", "", "animationInfo", "", "", "modelInfo", "<atom selection>", "{*}", "ligandInfo", "<atom selection>", "{*}", "shapeInfo", "", "", "measurementInfo", "", "", "centerInfo", "", "", "orientationInfo", "", "", "transformInfo", "", "", "atomList", "<atom selection>", "(visible)", "atomInfo", "<atom selection>", "(visible)", "bondInfo", "<atom selection>", "(visible)", "chainInfo", "<atom selection>", "(visible)", "polymerInfo", "<atom selection>", "(visible)", "moleculeInfo", "<atom selection>", "(visible)", "stateInfo", "<state type>", "all", "extractModel", "<atom selection>", "(visible)", "jmolStatus", "statusNameList", "", "jmolViewer", "", "", "messageQueue", "", "", "auxiliaryInfo", "<atom selection>", "{*}", "boundBoxInfo", "", "", "dataInfo", "<data type>", "types", "image", "<width=www,height=hhh>", "", "evaluate", "<expression>", "", "menu", "<type>", "current", "minimizationInfo", "", "", "pointGroupInfo", "<atom selection>", "(visible)", "fileInfo", "<type>", "", "errorMessage", "", "", "mouseInfo", "", "", "isosurfaceInfo", "", "", "isosurfaceData", "", "", "consoleText", "", "", "JSpecView", "<key>", "", "scriptQueueInfo", "", "", "nmrInfo", "<elementSymbol> or 'all' or 'shifts'", "all", "variableInfo", "<name>", "all", "domainInfo", "<atom selection>", "{visible}", "validationInfo", "<atom selection>", "{visible}"];
Clazz_defineStatics (c$,
"PROP_APPLET_INFO", 0,
"PROP_FILENAME", 1,
"PROP_FILEHEADER", 2,
"PROP_FILECONTENTS_PATH", 3,
"PROP_FILECONTENTS", 4,
"PROP_ANIMATION_INFO", 5,
"PROP_MODEL_INFO", 6,
"PROP_LIGAND_INFO", 7,
"PROP_SHAPE_INFO", 8,
"PROP_MEASUREMENT_INFO", 9,
"PROP_CENTER_INFO", 10,
"PROP_ORIENTATION_INFO", 11,
"PROP_TRANSFORM_INFO", 12,
"PROP_ATOM_LIST", 13,
"PROP_ATOM_INFO", 14,
"PROP_BOND_INFO", 15,
"PROP_CHAIN_INFO", 16,
"PROP_POLYMER_INFO", 17,
"PROP_MOLECULE_INFO", 18,
"PROP_STATE_INFO", 19,
"PROP_EXTRACT_MODEL", 20,
"PROP_JMOL_STATUS", 21,
"PROP_JMOL_VIEWER", 22,
"PROP_MESSAGE_QUEUE", 23,
"PROP_AUXILIARY_INFO", 24,
"PROP_BOUNDBOX_INFO", 25,
"PROP_DATA_INFO", 26,
"PROP_IMAGE", 27,
"PROP_EVALUATE", 28,
"PROP_MENU", 29,
"PROP_MINIMIZATION_INFO", 30,
"PROP_POINTGROUP_INFO", 31,
"PROP_FILE_INFO", 32,
"PROP_ERROR_MESSAGE", 33,
"PROP_MOUSE_INFO", 34,
"PROP_ISOSURFACE_INFO", 35,
"PROP_ISOSURFACE_DATA", 36,
"PROP_CONSOLE_TEXT", 37,
"PROP_JSPECVIEW", 38,
"PROP_SCRIPT_QUEUE_INFO", 39,
"PROP_NMR_INFO", 40,
"PROP_VAR_INFO", 41,
"PROP_DOM_INFO", 42,
"PROP_VAL_INFO", 43,
"PROP_COUNT", 44,
"readableTypes", ["", "stateinfo", "extractmodel", "filecontents", "fileheader", "image", "menu", "minimizationInfo"]);
});
})(Clazz
,Clazz.newLongArray
,Clazz.doubleToByte
,Clazz.doubleToInt
,Clazz.doubleToLong
,Clazz.declarePackage
,Clazz.instanceOf
,Clazz.load
,Clazz.instantialize
,Clazz.decorateAsClass
,Clazz.floatToInt
,Clazz.makeConstructor
,Clazz.defineEnumConstant
,Clazz.exceptionOf
,Clazz.newIntArray
,Clazz.defineStatics
,Clazz.newFloatArray
,Clazz.declareType
,Clazz.prepareFields
,Clazz.superConstructor
,Clazz.newByteArray
,Clazz.declareInterface
,Clazz.p0p
,Clazz.pu$h
,Clazz.newShortArray
,Clazz.innerTypeInstance
,Clazz.isClassDefined
,Clazz.prepareCallback
,Clazz.newArray
,Clazz.castNullAs
,Clazz.floatToShort
,Clazz.superCall
,Clazz.decorateAsType
,Clazz.newBooleanArray
,Clazz.newCharArray
,Clazz.implementOf
,Clazz.newDoubleArray
,Clazz.overrideConstructor
,Clazz.clone
,Clazz.doubleToShort
,Clazz.getInheritedLevel
,Clazz.getParamsType
,Clazz.isAF
,Clazz.isAI
,Clazz.isAS
,Clazz.isASS
,Clazz.isAP
,Clazz.isAFloat
,Clazz.isAII
,Clazz.isAFF
,Clazz.isAFFF
,Clazz.tryToSearchAndExecute
,Clazz.getStackTrace
,Clazz.inheritArgs
,Clazz.alert
,Clazz.defineMethod
,Clazz.overrideMethod
,Clazz.declareAnonymous
//,Clazz.checkPrivateMethod
,Clazz.cloneFinals
);