Clazz.declarePackage("JM");
Clazz.load(["JM.AlphaMonomer"], "JM.AminoMonomer", ["JU.A4", "$.BS", "$.M3", "$.P3", "$.PT", "$.Quat", "$.V3", "J.c.STR", "JU.Escape", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.nhChecked = false;
this.ptTemp = null;
Clazz.instantialize(this, arguments);}, JM, "AminoMonomer", JM.AlphaMonomer);
Clazz.overrideConstructor(c$, 
function(){
});
c$.validateAndAllocate = Clazz.defineMethod(c$, "validateAndAllocate", 
function(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms){
var offsets = JM.Monomer.scanForOffsets(firstAtomIndex, specialAtomIndexes, JM.AminoMonomer.interestingAminoAtomIDs);
if (offsets == null) return null;
JM.Monomer.checkOptional(offsets, 1, firstAtomIndex, specialAtomIndexes[5]);
if (atoms[firstAtomIndex].isHetero() && !JM.AminoMonomer.isBondedCorrectly(firstAtomIndex, offsets, atoms)) return null;
return  new JM.AminoMonomer().set2(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, offsets);
}, "JM.Chain,~S,~N,~N,~N,~A,~A");
c$.isBondedCorrectlyRange = Clazz.defineMethod(c$, "isBondedCorrectlyRange", 
function(offset1, offset2, firstAtomIndex, offsets, atoms){
var atomIndex1 = firstAtomIndex + (offsets[offset1] & 0xFF);
var atomIndex2 = firstAtomIndex + (offsets[offset2] & 0xFF);
return (atomIndex1 != atomIndex2 && atoms[atomIndex1].isBonded(atoms[atomIndex2]));
}, "~N,~N,~N,~A,~A");
c$.isBondedCorrectly = Clazz.defineMethod(c$, "isBondedCorrectly", 
function(firstAtomIndex, offsets, atoms){
return (JM.AminoMonomer.isBondedCorrectlyRange(2, 0, firstAtomIndex, offsets, atoms) && JM.AminoMonomer.isBondedCorrectlyRange(0, 3, firstAtomIndex, offsets, atoms) && (!JM.Monomer.have(offsets, 1) || JM.AminoMonomer.isBondedCorrectlyRange(3, 1, firstAtomIndex, offsets, atoms)));
}, "~N,~A,~A");
Clazz.overrideMethod(c$, "getNitrogenAtom", 
function(){
return this.getAtomFromOffsetIndex(2);
});
Clazz.defineMethod(c$, "getCarbonylCarbonAtom", 
function(){
return this.getAtomFromOffsetIndex(3);
});
Clazz.overrideMethod(c$, "getCarbonylOxygenAtom", 
function(){
return this.getWingAtom();
});
Clazz.overrideMethod(c$, "getInitiatorAtom", 
function(){
return this.getNitrogenAtom();
});
Clazz.overrideMethod(c$, "getTerminatorAtom", 
function(){
return this.getAtomFromOffsetIndex(JM.Monomer.have(this.offsets, 4) ? 4 : 3);
});
Clazz.defineMethod(c$, "hasOAtom", 
function(){
return JM.Monomer.have(this.offsets, 1);
});
Clazz.overrideMethod(c$, "isConnectedAfter", 
function(possiblyPreviousMonomer){
if (possiblyPreviousMonomer == null) return true;
var other = possiblyPreviousMonomer;
return other.getCarbonylCarbonAtom().isBonded(this.getNitrogenAtom());
}, "JM.Monomer");
Clazz.overrideMethod(c$, "findNearestAtomIndex", 
function(x, y, closest, madBegin, madEnd){
var competitor = closest[0];
var nitrogen = this.getNitrogenAtom();
var marBegin = (Clazz.doubleToInt(madBegin / 2));
if (marBegin < 1200) marBegin = 1200;
if (nitrogen.sZ == 0) return;
var radiusBegin = Clazz.floatToInt(this.scaleToScreen(nitrogen.sZ, marBegin));
if (radiusBegin < 4) radiusBegin = 4;
var ccarbon = this.getCarbonylCarbonAtom();
var marEnd = (Clazz.doubleToInt(madEnd / 2));
if (marEnd < 1200) marEnd = 1200;
var radiusEnd = Clazz.floatToInt(this.scaleToScreen(nitrogen.sZ, marEnd));
if (radiusEnd < 4) radiusEnd = 4;
var alpha = this.getLeadAtom();
if (this.isCursorOnTopOf(alpha, x, y, Clazz.doubleToInt((radiusBegin + radiusEnd) / 2), competitor) || this.isCursorOnTopOf(nitrogen, x, y, radiusBegin, competitor) || this.isCursorOnTopOf(ccarbon, x, y, radiusEnd, competitor)) closest[0] = alpha;
}, "~N,~N,~A,~N,~N");
Clazz.defineMethod(c$, "resetHydrogenPoint", 
function(){
this.nhChecked = false;
this.nitrogenHydrogenPoint = null;
});
Clazz.defineMethod(c$, "getNitrogenHydrogenPoint", 
function(){
if (this.nitrogenHydrogenPoint == null && !this.nhChecked) {
this.nhChecked = true;
this.nitrogenHydrogenPoint = this.getExplicitNH();
}return this.nitrogenHydrogenPoint;
});
Clazz.defineMethod(c$, "getExplicitNH", 
function(){
var nitrogen = this.getNitrogenAtom();
var h = null;
var bonds = nitrogen.bonds;
if (bonds != null) for (var i = 0; i < bonds.length; i++) if ((h = bonds[i].getOtherAtom(nitrogen)).getElementNumber() == 1) return h;

return null;
});
Clazz.defineMethod(c$, "getNHPoint", 
function(aminoHydrogenPoint, vNH, jmolHPoint, dsspIgnoreHydrogens){
if (this.monomerIndex <= 0 || this.groupID == 15) return false;
var nitrogenPoint = this.getNitrogenAtom();
var nhPoint = this.getNitrogenHydrogenPoint();
if (nhPoint != null && !dsspIgnoreHydrogens) {
vNH.sub2(nhPoint, nitrogenPoint);
aminoHydrogenPoint.setT(nhPoint);
return true;
}var prev = this.bioPolymer.monomers[this.monomerIndex - 1];
if (jmolHPoint) {
vNH.sub2(nitrogenPoint, this.getLeadAtom());
vNH.normalize();
var v = JU.V3.newVsub(nitrogenPoint, prev.getCarbonylCarbonAtom());
v.normalize();
vNH.add(v);
} else {
var oxygen = prev.getCarbonylOxygenAtom();
if (oxygen == null) return false;
vNH.sub2(prev.getCarbonylCarbonAtom(), oxygen);
}vNH.normalize();
aminoHydrogenPoint.add2(nitrogenPoint, vNH);
this.nitrogenHydrogenPoint = JU.P3.newP(aminoHydrogenPoint);
if (JU.Logger.debugging) JU.Logger.debug("draw ID \"pta" + this.monomerIndex + "_" + nitrogenPoint.i + "\" " + JU.Escape.eP(nitrogenPoint) + JU.Escape.eP(aminoHydrogenPoint) + " # " + nitrogenPoint);
return true;
}, "JU.P3,JU.V3,~B,~B");
Clazz.overrideMethod(c$, "getQuaternionFrameCenter", 
function(qType){
if (this.monomerIndex < 0) return null;
switch ((qType).charCodeAt(0)) {
default:
case 97:
case 98:
case 99:
case 67:
return this.getQuaternionFrameCenterAlpha(qType);
case 110:
return this.getNitrogenAtom();
case 112:
case 80:
return this.getCarbonylCarbonAtom();
case 113:
if (this.monomerIndex == this.bioPolymer.monomerCount - 1) return null;
var mNext = (this.bioPolymer.monomers[this.monomerIndex + 1]);
var pt =  new JU.P3();
pt.ave(this.getCarbonylCarbonAtom(), mNext.getNitrogenAtom());
return pt;
}
}, "~S");
Clazz.overrideMethod(c$, "getQuaternion", 
function(qType){
if (this.monomerIndex < 0) return null;
var ptC = this.getCarbonylCarbonAtom();
var ptCa = this.getLeadAtom();
var vA =  new JU.V3();
var vB =  new JU.V3();
var vC = null;
switch ((qType).charCodeAt(0)) {
case 97:
case 110:
if (this.monomerIndex == 0 || this.groupID == 15) return null;
vC =  new JU.V3();
if (this.ptTemp == null) this.ptTemp =  new JU.P3();
this.getNHPoint(this.ptTemp, vC, true, false);
vB.sub2(ptCa, this.getNitrogenAtom());
vB.cross(vC, vB);
 new JU.M3().setAA(JU.A4.newVA(vB, -0.29670596)).rotate(vC);
vA.cross(vB, vC);
break;
case 98:
return this.getQuaternionAlpha('b');
case 99:
vA.sub2(ptC, ptCa);
vB.sub2(this.getNitrogenAtom(), ptCa);
break;
case 112:
case 120:
if (this.monomerIndex == this.bioPolymer.monomerCount - 1) return null;
vA.sub2(ptCa, ptC);
vB.sub2((this.bioPolymer.monomers[this.monomerIndex + 1]).getNitrogenAtom(), ptC);
break;
case 113:
if (this.monomerIndex == this.bioPolymer.monomerCount - 1) return null;
var mNext = (this.bioPolymer.monomers[this.monomerIndex + 1]);
vB.sub2(mNext.getLeadAtom(), mNext.getNitrogenAtom());
vA.sub2(ptCa, ptC);
break;
default:
return null;
}
return JU.Quat.getQuaternionFrameV(vA, vB, vC, false);
}, "~S");
Clazz.overrideMethod(c$, "getStructureId", 
function(){
if (this.proteinStructure == null || this.proteinStructure.structureID == null) return "";
return this.proteinStructure.structureID;
});
Clazz.overrideMethod(c$, "getProteinStructureTag", 
function(){
if (this.proteinStructure == null || this.proteinStructure.structureID == null) return null;
var tag = "%3N %3ID";
tag = JU.PT.formatStringS(tag, "N", this.proteinStructure.serialID);
tag = JU.PT.formatStringS(tag, "ID", this.proteinStructure.structureID);
if (this.proteinStructure.type === J.c.STR.SHEET) tag += JU.PT.formatStringI("%2SC", "SC", this.proteinStructure.strandCount);
return tag;
});
Clazz.overrideMethod(c$, "getBSSideChain", 
function(){
var bs =  new JU.BS();
this.setAtomBits(bs);
this.clear(bs, this.getLeadAtom(), true);
this.clear(bs, this.getCarbonylCarbonAtom(), false);
this.clear(bs, this.getCarbonylOxygenAtom(), false);
this.clear(bs, this.getNitrogenAtom(), true);
return bs;
});
Clazz.defineMethod(c$, "clear", 
function(bs, a, andH){
if (a == null) return;
bs.clear(a.i);
if (!andH) return;
var b = a.bonds;
var h;
for (var j = b.length; --j >= 0; ) if ((h = b[j].getOtherAtom(a)).getElementNumber() == 1) bs.clear(h.i);

}, "JU.BS,JM.Atom,~B");
c$.interestingAminoAtomIDs =  Clazz.newByteArray(-1, [2, -5, 1, 3, -65]);
});
;//5.0.1-v7 Thu Jun 04 11:07:16 CDT 2026
