Clazz.declarePackage("JM");
Clazz.load(["JM.Monomer"], "JM.CarbohydrateMonomer", ["J.c.STR"], function(){
var c$ = Clazz.declareType(JM, "CarbohydrateMonomer", JM.Monomer);
Clazz.overrideConstructor(c$, 
function(){
});
c$.validateAndAllocate = Clazz.defineMethod(c$, "validateAndAllocate", 
function(chain, group3, seqcode, firstIndex, lastIndex){
return  new JM.CarbohydrateMonomer().set2(chain, group3, seqcode, firstIndex, lastIndex, JM.CarbohydrateMonomer.alphaOffsets);
}, "JM.Chain,~S,~N,~N,~N");
Clazz.overrideMethod(c$, "isCarbohydrate", 
function(){
return true;
});
Clazz.overrideMethod(c$, "getProteinStructureType", 
function(){
return J.c.STR.CARBOHYDRATE;
});
Clazz.overrideMethod(c$, "isConnectedAfter", 
function(possiblyPreviousMonomer){
if (possiblyPreviousMonomer == null) return true;
for (var i = this.firstAtomIndex; i <= this.lastAtomIndex; i++) for (var j = possiblyPreviousMonomer.firstAtomIndex; j <= possiblyPreviousMonomer.lastAtomIndex; j++) {
var a = this.chain.model.ms.at[i];
var b = this.chain.model.ms.at[j];
if (a != null && b != null && a.getElementNumber() + b.getElementNumber() == 14 && a.distanceSquared(b) < 3.24) return true;
}

return false;
}, "JM.Monomer");
Clazz.overrideMethod(c$, "findNearestAtomIndex", 
function(x, y, closest, madBegin, madEnd){
var competitor = closest[0];
var anomericO = this.getLeadAtom();
var marBegin = (Clazz.doubleToInt(madBegin / 2));
if (marBegin < 1200) marBegin = 1200;
if (anomericO.sZ == 0) return;
var radiusBegin = Clazz.floatToInt(this.scaleToScreen(anomericO.sZ, marBegin));
if (radiusBegin < 4) radiusBegin = 4;
if (this.isCursorOnTopOf(anomericO, x, y, radiusBegin, competitor)) closest[0] = anomericO;
}, "~N,~N,~A,~N,~N");
Clazz.overrideMethod(c$, "isConnectedPrevious", 
function(){
if (this.monomerIndex <= 0) return false;
for (var i = this.firstAtomIndex; i <= this.lastAtomIndex; i++) if (this.getCrossLinkGroup(i, null, null, true, false, false)) return true;

return false;
});
c$.alphaOffsets =  Clazz.newByteArray(-1, [0]);
});
;//5.0.1-v7 Sun May 18 17:21:41 CDT 2025
