Clazz.declarePackage("JM");
Clazz.load(["JM.Monomer", "J.c.STR"], "JM.PhosphorusMonomer", ["JU.Quat", "$.V3"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.dssrSubType = null;
this.basepairSubType = null;
Clazz.instantialize(this, arguments);}, JM, "PhosphorusMonomer", JM.Monomer);
Clazz.prepareFields (c$, function(){
this.dssrSubType = J.c.STR.NONE;
this.basepairSubType = J.c.STR.NONE;
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JM.PhosphorusMonomer, []);
});
Clazz.overrideMethod(c$, "isNucleic", 
function(){
return true;
});
c$.validateAndAllocateP = Clazz.defineMethod(c$, "validateAndAllocateP", 
function(chain, group3, seqcode, firstIndex, lastIndex, specialAtomIndexes){
return (firstIndex != lastIndex || specialAtomIndexes[13] != firstIndex ? null :  new JM.PhosphorusMonomer().set2(chain, group3, seqcode, firstIndex, lastIndex,  Clazz.newByteArray (1, 0)));
}, "JM.Chain,~S,~N,~N,~N,~A");
Clazz.overrideMethod(c$, "isDna", 
function(){
return this.isDnaByID();
});
Clazz.overrideMethod(c$, "isRna", 
function(){
return this.isRnaByID();
});
Clazz.overrideMethod(c$, "isPurine", 
function(){
return this.isPurineByID();
});
Clazz.overrideMethod(c$, "isPyrimidine", 
function(){
return this.isPyrimidineByID();
});
Clazz.overrideMethod(c$, "getStructure", 
function(){
return this.chain;
});
Clazz.overrideMethod(c$, "getBioStructureType", 
function(){
return J.c.STR.NONE;
});
Clazz.overrideMethod(c$, "isConnectedAfter", 
function(possiblyPreviousMonomer){
return this.isCA2(possiblyPreviousMonomer);
}, "JM.Monomer");
Clazz.defineMethod(c$, "isCA2", 
function(possiblyPreviousMonomer){
if (possiblyPreviousMonomer == null) return true;
var distance = this.getLeadAtom().distance(possiblyPreviousMonomer.getLeadAtom());
return distance <= JM.PhosphorusMonomer.MAX_ADJACENT_PHOSPHORUS_DISTANCE;
}, "JM.Monomer");
Clazz.overrideMethod(c$, "getQuaternion", 
function(qType){
return this.getQuaternionP();
}, "~S");
Clazz.defineMethod(c$, "getQuaternionP", 
function(){
var i = this.monomerIndex;
if (i <= 0 || i >= this.bioPolymer.monomerCount - 1) return null;
var ptP = this.bioPolymer.monomers[i].getAtomFromOffsetIndex(0);
var ptA;
var ptB;
ptA = this.bioPolymer.monomers[i + 1].getAtomFromOffsetIndex(0);
ptB = this.bioPolymer.monomers[i - 1].getAtomFromOffsetIndex(0);
if (ptP == null || ptA == null || ptB == null) return null;
var vA =  new JU.V3();
var vB =  new JU.V3();
vA.sub2(ptA, ptP);
vB.sub2(ptB, ptP);
return JU.Quat.getQuaternionFrameV(vA, vB, null, false);
});
Clazz.overrideMethod(c$, "getQuaternionFrameCenter", 
function(qType){
return this.getAtomFromOffsetIndex(0);
}, "~S");
Clazz.overrideMethod(c$, "getHelixData", 
function(tokType, qType, mStep){
return this.getHelixData2(tokType, qType, mStep);
}, "~N,~S,~N");
Clazz.overrideMethod(c$, "getBioStructureSubType", 
function(dssx){
switch (dssx) {
case 1111490651:
return this.dssrSubType;
case 1073741863:
return this.basepairSubType;
}
return J.c.STR.NONE;
}, "~N");
Clazz.overrideMethod(c$, "setDSSRStructureSubType", 
function(type){
this.dssrSubType = type;
}, "J.c.STR");
c$.MAX_ADJACENT_PHOSPHORUS_DISTANCE = 8.0;
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
