Clazz.declarePackage("JV");
Clazz.load(["JV.JmolChimeMessenger"], "JV.ChimeMessenger", ["java.util.Hashtable", "J.c.CBK", "$.STR", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
Clazz.instantialize(this, arguments);}, JV, "ChimeMessenger", null, JV.JmolChimeMessenger);
/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set", 
function(vwr){
this.vwr = vwr;
return this;
}, "JV.Viewer");
Clazz.overrideMethod(c$, "getInfoXYZ", 
function(a){
var group3 = a.getGroup3(true);
var chainID = a.group.chain.chainID;
return "Atom: " + (group3 == null ? a.getElementSymbol() : a.getAtomName()) + " " + a.getAtomNumber() + (group3 != null && group3.length > 0 ? (a.isHetero() ? " Hetero: " : " Group: ") + group3 + " " + a.getResno() + (chainID != 0 && chainID != 32 ? " Chain: " + a.group.chain.getIDStr() : "") : "") + " Model: " + a.getModelNumber() + " Coordinates: " + a.x + " " + a.y + " " + a.z;
}, "JM.Atom");
Clazz.overrideMethod(c$, "showHash", 
function(outputBuffer, s){
if (s == null) return;
if (outputBuffer == null) {
if (!this.vwr.isPrintOnly) JU.Logger.warn(s);
this.vwr.scriptStatus(s);
} else {
outputBuffer.append(s).appendC('\n');
}}, "JU.SB,~S");
Clazz.overrideMethod(c$, "reportSelection", 
function(n){
this.vwr.reportSelection((n == 0 ? "No atoms" : n == 1 ? "1 atom" : n + " atoms") + " selected!");
}, "~N");
Clazz.overrideMethod(c$, "update", 
function(msg){
if (msg == null) msg = "script <exiting>";
 else msg = "Requesting " + msg;
this.vwr.scriptStatus(msg);
}, "~S");
Clazz.overrideMethod(c$, "scriptCompleted", 
function(sm, statusMessage, strErrorMessageUntranslated){
var data =  Clazz.newArray(-1, [null, "script <exiting>", statusMessage, Integer.$valueOf(-1), strErrorMessageUntranslated]);
if (sm.notifyEnabled(J.c.CBK.SCRIPT)) sm.cbl.notifyCallback(J.c.CBK.SCRIPT, data);
sm.processScript(data);
return "Jmol script completed.";
}, "JV.StatusManager,~S,~S");
Clazz.overrideMethod(c$, "getAllChimeInfo", 
function(sb){
var nHetero = 0;
var nH = -1;
var nS = 0;
var nT = 0;
var ms = this.vwr.ms;
if (ms.haveBioModels) {
var n = 0;
var models = ms.am;
var modelCount = ms.mc;
var ac = ms.ac;
var atoms = ms.at;
sb.append("\nMolecule name ....... " + ms.getInfoM("COMPND"));
sb.append("\nSecondary Structure . PDB Data Records");
sb.append("\nBrookhaven Code ..... " + ms.modelSetName);
for (var i = modelCount; --i >= 0; ) n += models[i].getChainCount(false);

sb.append("\nNumber of Chains .... " + n);
var ng = 0;
var ngHetero = 0;
var map =  new java.util.Hashtable();
var id;
var lastid = -1;
nH = 0;
for (var i = ac; --i >= 0; ) {
var a = atoms[i];
if (a == null) continue;
var isHetero = a.isHetero();
if (isHetero) nHetero++;
var g = a.group;
if (!map.containsKey(g)) {
map.put(g, Boolean.TRUE);
if (isHetero) ngHetero++;
 else ng++;
}if (a.mi == 0) {
if ((id = g.getStrucNo()) != lastid && id != 0) {
lastid = id;
switch (g.getProteinStructureType()) {
case J.c.STR.HELIX:
nH++;
break;
case J.c.STR.SHEET:
nS++;
break;
case J.c.STR.TURN:
nT++;
break;
}
}}}
sb.append("\nNumber of Groups .... " + ng);
if (ngHetero > 0) sb.append(" (" + ngHetero + ")");
}sb.append("\nNumber of Atoms ..... " + (ms.ac - nHetero));
if (nHetero > 0) sb.append(" (" + nHetero + ")");
sb.append("\nNumber of Bonds ..... " + ms.bondCount);
sb.append("\nNumber of Models ...... " + ms.mc);
if (nH >= 0) {
sb.append("\nNumber of Helices ... " + nH);
sb.append("\nNumber of Strands ... " + nS);
sb.append("\nNumber of Turns ..... " + nT);
}}, "JU.SB");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
