Clazz.declarePackage("J.render");
Clazz.load(["J.render.FontLineShapeRenderer", "JU.BS", "$.P3", "$.V3"], "J.render.SticksRenderer", ["JU.A4", "$.M3", "J.c.PAL", "JU.C", "$.Edge"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.showMultipleBonds = false;
this.multipleBondSpacing = 0;
this.multipleBondRadiusFactor = 0;
this.bondsPerp = false;
this.useBananas = false;
this.modeMultipleBond = 0;
this.isCartesian = false;
this.endcaps = 0;
this.ssbondsBackbone = false;
this.hbondsBackbone = false;
this.bondsBackbone = false;
this.hbondsSolid = false;
this.a = null;
this.b = null;
this.pa = null;
this.pb = null;
this.bond = null;
this.xA = 0;
this.yA = 0;
this.zA = 0;
this.xB = 0;
this.yB = 0;
this.zB = 0;
this.dx = 0;
this.dy = 0;
this.mag2d = 0;
this.bondOrder = 0;
this.wireframeOnly = false;
this.isAntialiased = false;
this.slabbing = false;
this.slabByAtom = false;
this.x = null;
this.y = null;
this.z = null;
this.p1 = null;
this.p2 = null;
this.bsForPass2 = null;
this.isPass2 = false;
this.isPymol = false;
this.strutsOnly = false;
this.xAxis1 = 0;
this.yAxis1 = 0;
this.xAxis2 = 0;
this.yAxis2 = 0;
this.dxStep = 0;
this.dyStep = 0;
this.rot = null;
this.a4 = null;
Clazz.instantialize(this, arguments);}, J.render, "SticksRenderer", J.render.FontLineShapeRenderer);
Clazz.prepareFields (c$, function(){
this.x =  new JU.V3();
this.y =  new JU.V3();
this.z =  new JU.V3();
this.p1 =  new JU.P3();
this.p2 =  new JU.P3();
this.bsForPass2 = JU.BS.newN(64);
});
Clazz.overrideMethod(c$, "render", 
function(){
var bonds = this.ms.bo;
if (bonds == null) return false;
this.isPass2 = this.vwr.gdata.isPass2;
if (!this.isPass2) this.bsForPass2.clearAll();
this.slabbing = this.tm.slabEnabled;
this.slabByAtom = this.vwr.getBoolean(603979939);
this.endcaps = 3;
this.dashDots = (this.vwr.getBoolean(603979893) ? J.render.FontLineShapeRenderer.sixdots : J.render.FontLineShapeRenderer.dashes);
this.isCartesian = (this.exportType == 1);
this.getMultipleBondSettings(0);
this.wireframeOnly = !this.vwr.checkMotionRendering(1677721602);
this.ssbondsBackbone = this.vwr.getBoolean(603979952);
this.hbondsBackbone = this.vwr.getBoolean(603979852);
this.bondsBackbone =  new Boolean (this.hbondsBackbone | this.ssbondsBackbone).valueOf();
this.hbondsSolid = this.vwr.getBoolean(603979854);
this.isAntialiased = this.g3d.isAntialiased();
this.strutsOnly = ((this.flags & 1) != 0);
var needTranslucent = false;
if (this.isPass2) {
for (var i = this.bsForPass2.nextSetBit(0); i >= 0; i = this.bsForPass2.nextSetBit(i + 1)) {
this.bond = bonds[i];
if (this.bond != null) this.renderBond(i);
}
} else {
for (var i = this.ms.bondCount; --i >= 0; ) {
this.bond = bonds[i];
if (this.bond != null && (this.bond.shapeVisibilityFlags & this.myVisibilityFlag) != 0 && this.renderBond(i)) {
needTranslucent = true;
this.bsForPass2.set(i);
}}
}return needTranslucent;
});
Clazz.defineMethod(c$, "renderBond", 
function(index){
var atomA0;
var atomB0;
this.a = atomA0 = this.bond.atom1;
this.b = atomB0 = this.bond.atom2;
var order = this.bond.order & 131071;
if (this.bondsBackbone) {
if (this.ssbondsBackbone && (order & 256) != 0) {
this.a = this.a.group.getLeadAtomOr(this.a);
this.b = this.b.group.getLeadAtomOr(this.b);
} else if (this.hbondsBackbone && JU.Edge.isOrderH(order)) {
this.a = this.a.group.getLeadAtomOr(this.a);
this.b = this.b.group.getLeadAtomOr(this.b);
}}if (!this.isPass2 && (!this.a.isVisible(9) || !this.b.isVisible(9) || !this.g3d.isInDisplayRange(this.a.sX, this.a.sY) || !this.g3d.isInDisplayRange(this.b.sX, this.b.sY))) return false;
if (this.slabbing) {
var ba = this.vwr.gdata.isClippedZ(this.a.sZ);
if (ba && this.vwr.gdata.isClippedZ(this.b.sZ) || this.slabByAtom && (ba || this.vwr.gdata.isClippedZ(this.b.sZ))) return false;
}this.zA = this.a.sZ;
this.zB = this.b.sZ;
if (this.zA == 1 || this.zB == 1) return false;
this.colixA = atomA0.colixAtom;
this.colixB = atomB0.colixAtom;
if (((this.colix = this.bond.colix) & -30721) == 2) {
this.colix = (this.colix & 30720);
this.colixA = JU.C.getColixInherited((this.colix | this.vwr.cm.getColixAtomPalette(atomA0, J.c.PAL.CPK.id)), this.colixA);
this.colixB = JU.C.getColixInherited((this.colix | this.vwr.cm.getColixAtomPalette(atomB0, J.c.PAL.CPK.id)), this.colixB);
} else {
this.colixA = JU.C.getColixInherited(this.colix, this.colixA);
this.colixB = JU.C.getColixInherited(this.colix, this.colixB);
}var needTranslucent = false;
var skip = false;
this.bondOrder = order & 131071;
var isStrut = (this.bondOrder == 32768);
if (this.strutsOnly != isStrut) {
if (isStrut) {
(this.shape).haveStrutPoints = true;
if (!this.isPass2) {
this.a.group.unsetStrutPoint();
this.b.group.unsetStrutPoint();
}}skip = true;
}if (!this.isExport && !this.isPass2) {
var doA = !JU.C.renderPass2(this.colixA);
var doB = !JU.C.renderPass2(this.colixB);
if (!doA || !doB) {
if (isStrut || !doA && !doB) {
skip = true;
}this.g3d.setC(!doA ? this.colixB : this.colixA);
needTranslucent = true;
}}if (skip) return needTranslucent;
var isPartial = this.bond.isPartial();
if (!isPartial) {
if ((this.bondOrder & 256) != 0) this.bondOrder &= -257;
if ((this.bondOrder & 1023) != 0) {
if (!this.showMultipleBonds || (this.modeMultipleBond == 2 && this.mad > 1000) || (this.bondOrder & 98304) == 65536) {
this.bondOrder = 1;
}}}this.pa = this.a;
this.pb = this.b;
var mask = 0;
switch (this.bondOrder) {
case 1025:
case 1041:
case 1057:
this.bondOrder = 1;
case 1:
case 2:
case 3:
case 4:
case 5:
case 6:
break;
case 17:
case 513:
this.bondOrder = 1;
mask = (order == 513 ? 0 : 1);
break;
case 515:
case 514:
this.bondOrder = 2;
mask = (order == 515 ? this.getAromaticDottedBondMask() : 0);
break;
default:
if ((this.bondOrder & 98304) == 98304) {
this.getMultipleBondSettings(this.bondOrder);
this.bondOrder &= 3;
mask = -2;
} else if (isPartial) {
this.bondOrder = JU.Edge.getPartialBondOrder(order);
mask = JU.Edge.getPartialBondDotted(order);
} else if (JU.Edge.isOrderH(this.bondOrder)) {
this.bondOrder = 1;
if (!this.hbondsSolid) mask = -1;
} else if (isStrut) {
this.bondOrder = 1;
var p1 = this.a.group.strutPoint;
var p2 = this.b.group.strutPoint;
this.pa = this.setStrutPoint(p1, this.pa);
this.pb = this.setStrutPoint(p2, this.pb);
this.zA = this.pa.sZ;
this.zB = this.pb.sZ;
}}
this.xA = this.pa.sX;
this.yA = this.pa.sY;
this.xB = this.pb.sX;
this.yB = this.pb.sY;
this.mad = this.bond.mad;
if (this.multipleBondRadiusFactor > 0 && this.bondOrder > 1) this.mad *= this.multipleBondRadiusFactor;
this.dx = this.xB - this.xA;
this.dy = this.yB - this.yA;
this.width = Clazz.floatToInt(this.vwr.tm.scaleToScreen(Clazz.doubleToInt((this.zA + this.zB) / 2), this.mad));
if (this.wireframeOnly && this.width > 0) this.width = 1;
if (!this.isCartesian) {
this.asLineOnly = (this.width <= 1);
if (this.asLineOnly && (this.isAntialiased)) {
this.width = 3;
this.asLineOnly = false;
}}var renderD = (!this.isExport || this.mad == 1 ? this.width : this.mad);
switch (mask) {
case -2:
this.drawBond(0);
this.getMultipleBondSettings(0);
break;
case -1:
J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d, this.xA, this.yA, this.zA, this.xB, this.yB, this.zB, J.render.FontLineShapeRenderer.hDashes, this.width, this.colixA, this.colixB, renderD, this.asLineOnly, this.s1);
break;
default:
switch (this.bondOrder) {
case 4:
{
this.bondOrder = 2;
var f = this.multipleBondRadiusFactor;
if (f == 0 && this.width > 1) this.width = Clazz.doubleToInt(this.width * 0.5);
var m = this.multipleBondSpacing;
if (m < 0) this.multipleBondSpacing = 0.30;
this.drawBond(mask);
this.bondsPerp = !this.bondsPerp;
this.bondOrder = 2;
this.drawBond(mask >> 2);
this.bondsPerp = !this.bondsPerp;
this.multipleBondSpacing = m;
this.isPymol = false;
}break;
case 5:
{
this.bondOrder = 3;
var f = this.multipleBondRadiusFactor;
if (f == 0 && this.width > 1) this.width = Clazz.doubleToInt(this.width * 0.5);
var m = this.multipleBondSpacing;
if (m < 0) this.multipleBondSpacing = 0.20;
this.drawBond(mask);
this.bondsPerp = !this.bondsPerp;
this.bondOrder = 2;
this.multipleBondSpacing *= 1.5;
this.drawBond(mask >> 3);
this.bondsPerp = !this.bondsPerp;
this.multipleBondSpacing = m;
this.isPymol = false;
}break;
case 6:
{
this.bondOrder = 4;
var f = this.multipleBondRadiusFactor;
if (f == 0 && this.width > 1) this.width = Clazz.doubleToInt(this.width * 0.5);
var m = this.multipleBondSpacing;
if (m < 0) this.multipleBondSpacing = 0.15;
this.drawBond(mask);
this.bondsPerp = !this.bondsPerp;
this.bondOrder = 2;
this.multipleBondSpacing *= 1.5;
this.drawBond(mask >> 4);
this.bondsPerp = !this.bondsPerp;
this.multipleBondSpacing = m;
this.isPymol = false;
}break;
default:
this.drawBond(mask);
}
break;
}
return needTranslucent;
}, "~N");
Clazz.defineMethod(c$, "setStrutPoint", 
function(p, a){
if (p.sX == -2147483648) return a;
var pi = this.vwr.tm.transformPt(p);
p.sX = pi.x;
p.sY = pi.y;
p.sZ = pi.z;
return p;
}, "JU.Point3fi,JU.Point3fi");
Clazz.defineMethod(c$, "getMultipleBondSettings", 
function(pymolBondOrder){
this.isPymol = (pymolBondOrder != 0);
if (this.isPymol) {
this.bondsPerp = false;
var scale = ((pymolBondOrder >> 2) & 0x3F) / 50;
this.showMultipleBonds = (scale != 0);
var n = (pymolBondOrder & 3);
this.multipleBondRadiusFactor = scale * 2 / (3 * n - 1);
this.multipleBondSpacing = this.multipleBondRadiusFactor * 3 / 2 * (Clazz.doubleToInt(this.bond.mad / 1000));
} else {
this.useBananas = (this.vwr.getBoolean(603979886) && !this.isPymol);
this.multipleBondSpacing = this.vwr.getFloat(570425370);
this.multipleBondRadiusFactor = this.vwr.getFloat(570425369);
this.bondsPerp = (this.useBananas || this.multipleBondSpacing > 0 && this.multipleBondRadiusFactor < 0);
if (this.useBananas) this.multipleBondSpacing = (this.multipleBondSpacing < 0 ? -this.multipleBondSpacing * 0.4 : this.multipleBondSpacing);
this.multipleBondRadiusFactor = Math.abs(this.multipleBondRadiusFactor);
if (this.multipleBondSpacing == 0 && this.isCartesian) this.multipleBondSpacing = 0.2;
}this.modeMultipleBond = this.vwr.g.modeMultipleBond;
this.showMultipleBonds = (this.multipleBondSpacing != 0 && this.modeMultipleBond != 0 && this.vwr.getBoolean(603979928));
}, "~N");
Clazz.defineMethod(c$, "drawBond", 
function(dottedMask){
var isDashed = (dottedMask & 1) != 0;
var endcaps = ((this.colixA & 30720) == 16384 || (this.colixB & 30720) == 16384 ? 2 : this.endcaps);
if (this.isCartesian && this.bondOrder == 1 && !isDashed) {
this.g3d.drawBond(this.pa, this.pb, this.colixA, this.colixB, endcaps, this.mad, -1);
return;
}var isEndOn = (this.dx == 0 && this.dy == 0);
if (isEndOn && this.asLineOnly && !this.isCartesian) return;
var renderD = (!this.isExport || this.mad == 1 ? this.width : this.mad);
var doFixedSpacing = (this.bondOrder > 1 && (this.isPymol || this.multipleBondSpacing > 0));
var isPiBonded = doFixedSpacing && (this.vwr.getHybridizationAndAxes(this.a.i, this.z, this.x, "pz") != null || this.vwr.getHybridizationAndAxes(this.b.i, this.z, this.x, "pz") != null) && !Float.isNaN(this.x.x);
if (isEndOn && !doFixedSpacing) {
var space = Clazz.doubleToInt(this.width / 8) + 3;
var step = this.width + space;
var y = this.yA - Clazz.doubleToInt((this.bondOrder - 1) * step / 2);
do {
J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.xA, y, this.zA, this.xB, y, this.zB, renderD, this.asLineOnly);
y += step;
} while (--this.bondOrder > 0);
return;
}if (this.bondOrder == 1) {
if (isDashed) J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d, this.xA, this.yA, this.zA, this.xB, this.yB, this.zB, this.dashDots, this.width, this.colixA, this.colixB, renderD, this.asLineOnly, this.s1);
 else J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.xA, this.yA, this.zA, this.xB, this.yB, this.zB, renderD, this.asLineOnly);
return;
}if (doFixedSpacing) {
if (!isPiBonded) this.z.setT(JU.P3.getUnlikely());
this.x.sub2(this.b, this.a);
this.y.cross(this.x, this.z);
this.y.normalize();
if (Float.isNaN(this.y.x)) {
this.z.setT(JU.P3.getUnlikely());
this.y.cross(this.x, this.z);
this.y.cross(this.y, this.x);
this.y.normalize();
}if (this.bondsPerp) this.y.cross(this.y, this.x);
this.y.scale(this.multipleBondSpacing);
this.x.setT(this.y);
this.x.scale((this.bondOrder - 1) / 2);
if (this.useBananas) {
this.drawBanana(this.a, this.b, this.x, 0);
switch (this.bondOrder) {
case 4:
this.drawBanana(this.a, this.b, this.x, 90);
this.drawBanana(this.a, this.b, this.x, -90);
case 2:
default:
this.drawBanana(this.a, this.b, this.x, 180);
break;
case 3:
this.drawBanana(this.a, this.b, this.x, 120);
this.drawBanana(this.a, this.b, this.x, -120);
break;
}
return;
}this.p1.sub2(this.a, this.x);
this.p2.sub2(this.b, this.x);
while (true) {
if (this.isCartesian) {
this.g3d.drawBond(this.p1, this.p2, this.colixA, this.colixB, endcaps, this.mad, -2);
} else {
this.tm.transformPtScr(this.p1, this.s1);
this.tm.transformPtScr(this.p2, this.s2);
if (isDashed) J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d, this.s1.x, this.s1.y, this.s1.z, this.s2.x, this.s2.y, this.s2.z, this.dashDots, this.width, this.colixA, this.colixB, renderD, this.asLineOnly, this.s1);
 else J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.s1.x, this.s1.y, this.s1.z, this.s2.x, this.s2.y, this.s2.z, renderD, this.asLineOnly);
}dottedMask >>= 1;
isDashed = (dottedMask & 1) != 0;
if (--this.bondOrder <= 0) break;
this.p1.add(this.y);
this.p2.add(this.y);
this.stepAxisCoordinates();
}
return;
}var dxB = this.dx * this.dx;
var dyB = this.dy * this.dy;
this.mag2d = Math.round(Math.sqrt(dxB + dyB));
this.resetAxisCoordinates();
if (this.isCartesian && this.bondOrder == 3) {
J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.xAxis1, this.yAxis1, this.zA, this.xAxis2, this.yAxis2, this.zB, renderD, this.asLineOnly);
this.stepAxisCoordinates();
this.x.sub2(this.b, this.a);
this.x.scale(0.05);
this.p1.sub2(this.a, this.x);
this.p2.add2(this.b, this.x);
this.g3d.drawBond(this.p1, this.p2, this.colixA, this.colixB, endcaps, this.mad, -2);
this.stepAxisCoordinates();
J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.xAxis1, this.yAxis1, this.zA, this.xAxis2, this.yAxis2, this.zB, renderD, this.asLineOnly);
return;
}while (true) {
if ((dottedMask & 1) != 0) J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d, this.xAxis1, this.yAxis1, this.zA, this.xAxis2, this.yAxis2, this.zB, this.dashDots, this.width, this.colixA, this.colixB, renderD, this.asLineOnly, this.s1);
 else J.render.FontLineShapeRenderer.fillCylinder(this.g3d, this.colixA, this.colixB, endcaps, this.xAxis1, this.yAxis1, this.zA, this.xAxis2, this.yAxis2, this.zB, renderD, this.asLineOnly);
dottedMask >>= 1;
if (--this.bondOrder <= 0) break;
this.stepAxisCoordinates();
}
}, "~N");
Clazz.defineMethod(c$, "resetAxisCoordinates", 
function(){
var space = this.mag2d >> 3;
if (this.multipleBondSpacing != -1 && this.multipleBondSpacing < 0) space *= -this.multipleBondSpacing;
var step = this.width + space;
this.dxStep = Clazz.doubleToInt(step * this.dy / this.mag2d);
this.dyStep = Clazz.doubleToInt(step * -this.dx / this.mag2d);
this.xAxis1 = this.xA;
this.yAxis1 = this.yA;
this.xAxis2 = this.xB;
this.yAxis2 = this.yB;
var f = (this.bondOrder - 1);
this.xAxis1 -= Clazz.doubleToInt(this.dxStep * f / 2);
this.yAxis1 -= Clazz.doubleToInt(this.dyStep * f / 2);
this.xAxis2 -= Clazz.doubleToInt(this.dxStep * f / 2);
this.yAxis2 -= Clazz.doubleToInt(this.dyStep * f / 2);
});
Clazz.defineMethod(c$, "stepAxisCoordinates", 
function(){
this.xAxis1 += this.dxStep;
this.yAxis1 += this.dyStep;
this.xAxis2 += this.dxStep;
this.yAxis2 += this.dyStep;
});
Clazz.defineMethod(c$, "getAromaticDottedBondMask", 
function(){
var atomC = this.b.findAromaticNeighbor(this.a.i);
if (atomC == null) return 1;
var dxAC = atomC.sX - this.xA;
var dyAC = atomC.sY - this.yA;
return ((this.dx * dyAC - this.dy * dxAC) < 0 ? 2 : 1);
});
Clazz.defineMethod(c$, "drawBanana", 
function(a, b, x, deg){
this.g3d.addRenderer(553648143);
this.vectorT.sub2(b, a);
if (this.rot == null) {
this.rot =  new JU.M3();
this.a4 =  new JU.A4();
}this.a4.setVA(this.vectorT, (deg * 3.141592653589793 / 180));
this.rot.setAA(this.a4);
this.pointT.setT(a);
this.pointT3.setT(b);
this.pointT2.ave(a, b);
this.rot.rotate2(x, this.vectorT);
this.pointT2.add(this.vectorT);
this.tm.transformPtScrT3(a, this.pointT);
this.tm.transformPtScrT3(this.pointT2, this.pointT2);
this.tm.transformPtScrT3(b, this.pointT3);
var w = Math.max(this.width, 1);
this.g3d.setC(this.colixA);
this.g3d.fillHermite(5, w, w, w, this.pointT, this.pointT, this.pointT2, this.pointT3);
this.g3d.setC(this.colixB);
this.g3d.fillHermite(5, w, w, w, this.pointT, this.pointT2, this.pointT3, this.pointT3);
}, "JM.Atom,JM.Atom,JU.V3,~N");
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
