Clazz.declarePackage("JM");
Clazz.load(["JM.ProteinStructure"], "JM.Helix", ["JU.Measure", "$.P3", "$.V3", "J.c.STR"], function(){
var c$ = Clazz.declareType(JM, "Helix", JM.ProteinStructure);
Clazz.makeConstructor(c$, 
function(apolymer, monomerIndex, monomerCount, subtype){
Clazz.superConstructor (this, JM.Helix, []);
this.setupPS(apolymer, J.c.STR.HELIX, monomerIndex, monomerCount);
this.subtype = subtype;
}, "JM.AlphaPolymer,~N,~N,J.c.STR");
Clazz.overrideMethod(c$, "calcAxis", 
function(){
if (this.axisA != null) return;
var points =  new Array(this.nRes + 1);
for (var i = 0; i <= this.nRes; i++) this.apolymer.getLeadMidPoint(this.monomerIndexFirst + i, points[i] =  new JU.P3());

this.axisA =  new JU.P3();
this.axisUnitVector =  new JU.V3();
JU.Measure.calcBestAxisThroughPoints(points, points.length, this.axisA, this.axisUnitVector, this.vectorProjection, 4);
this.axisB = JU.P3.newP(points[this.nRes]);
JU.Measure.projectOntoAxis(this.axisB, this.axisA, this.axisUnitVector, this.vectorProjection);
});
});
;//5.0.1-v7 Mon Jul 21 08:59:16 CDT 2025
