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a);},"~N,~N,~N,~N");c(c$,"setColumnV",function(a,b){if(0==a)this.m00=b.x,this.m10=b.y,this.m20=b.z;else if(1==a)this.m01=b.x,this.m11=b.y,this.m21=b.z;else if(2==a)this.m02=b.x,this.m12=b.y,this.m22=b.z;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 2 and is "+a);},"~N,JU.V3");c(c$,"setColumnA",function(a,b){if(0==a)this.m00=b[0],this.m10=b[1],this.m20=b[2];else if(1==a)this.m01=b[0],this.m11=b[1],this.m21=b[2];else if(2==a)this.m02=b[0],this.m12=b[1],this.m22=b[2];else throw new ArrayIndexOutOfBoundsException("column must be 0 to 2 and is "+
a);},"~N,~A");c(c$,"getColumnV",function(a,b){if(0==a)b.x=this.m00,b.y=this.m10,b.z=this.m20;else if(1==a)b.x=this.m01,b.y=this.m11,b.z=this.m21;else if(2==a)b.x=this.m02,b.y=this.m12,b.z=this.m22;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 2 and is "+a);},"~N,JU.V3");c(c$,"getColumn",function(a,b){if(0==a)b[0]=this.m00,b[1]=this.m10,b[2]=this.m20;else if(1==a)b[0]=this.m01,b[1]=this.m11,b[2]=this.m21;else if(2==a)b[0]=this.m02,b[1]=this.m12,b[2]=this.m22;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 2 and is "+
a);},"~N,~A");c(c$,"add",function(a){this.m00+=a.m00;this.m01+=a.m01;this.m02+=a.m02;this.m10+=a.m10;this.m11+=a.m11;this.m12+=a.m12;this.m20+=a.m20;this.m21+=a.m21;this.m22+=a.m22},"JU.M3");c(c$,"sub",function(a){this.m00-=a.m00;this.m01-=a.m01;this.m02-=a.m02;this.m10-=a.m10;this.m11-=a.m11;this.m12-=a.m12;this.m20-=a.m20;this.m21-=a.m21;this.m22-=a.m22},"JU.M3");c(c$,"transpose",function(){var a=this.m01;this.m01=this.m10;this.m10=a;a=this.m02;this.m02=this.m20;this.m20=a;a=this.m12;this.m12=this.m21;
this.m21=a});c(c$,"transposeM",function(a){this.setM(a);this.transpose()},"JU.M3");c(c$,"setAA",function(a){this.setFromAxisAngle(a.x,a.y,a.z,a.angle)},"JU.A4");c(c$,"setFromAxisAngle",function(a,b,d,g){var c=Math.sqrt(a*a+b*b+d*d),c=1/c;a*=c;b*=c;d*=c;var f=Math.cos(g);g=Math.sin(g);c=1-f;this.m00=f+a*a*c;this.m11=f+b*b*c;this.m22=f+d*d*c;var f=a*b*c,j=d*g;this.m01=f-j;this.m10=f+j;f=a*d*c;j=b*g;this.m02=f+j;this.m20=f-j;f=b*d*c;j=a*g;this.m12=f-j;this.m21=f+j},"~N,~N,~N,~N");c(c$,"setM",function(a){this.m00=
a.m00;this.m01=a.m01;this.m02=a.m02;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M3");c(c$,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m10=a[3];this.m11=a[4];this.m12=a[5];this.m20=a[6];this.m21=a[7];this.m22=a[8]},"~A");c(c$,"invertM",function(a){this.setM(a);this.invert()},"JU.M3");c(c$,"invert",function(){var a=this.determinant();0!=a&&(a=1/a,this.set(this.m11*this.m22-this.m12*this.m21,this.m02*this.m21-this.m01*this.m22,
this.m01*this.m12-this.m02*this.m11,this.m12*this.m20-this.m10*this.m22,this.m00*this.m22-this.m02*this.m20,this.m02*this.m10-this.m00*this.m12,this.m10*this.m21-this.m11*this.m20,this.m01*this.m20-this.m00*this.m21,this.m00*this.m11-this.m01*this.m10),this.mulf(a))});c(c$,"determinant",function(){return this.m00*(this.m11*this.m22-this.m21*this.m12)-this.m01*(this.m10*this.m22-this.m20*this.m12)+this.m02*(this.m10*this.m21-this.m20*this.m11)});c(c$,"setScale",function(a){this.m00=a;this.m10=this.m02=
this.m01=0;this.m11=a;this.m21=this.m20=this.m12=0;this.m22=a},"~N");c(c$,"rotX",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=1;this.m10=this.m02=this.m01=0;this.m11=b;this.m12=-a;this.m20=0;this.m21=a;this.m22=b},"~N");c(c$,"rotY",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=b;this.m01=0;this.m02=a;this.m10=0;this.m11=1;this.m12=0;this.m20=-a;this.m21=0;this.m22=b},"~N");c(c$,"rotZ",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=b;this.m01=-a;this.m02=0;this.m10=a;this.m11=
b;this.m21=this.m20=this.m12=0;this.m22=1},"~N");c(c$,"mulf",function(a){this.m00*=a;this.m01*=a;this.m02*=a;this.m10*=a;this.m11*=a;this.m12*=a;this.m20*=a;this.m21*=a;this.m22*=a},"~N");c(c$,"mul",function(a){this.mul2(this,a)},"JU.M3");c(c$,"mul2",function(a,b){this.set(a.m00*b.m00+a.m01*b.m10+a.m02*b.m20,a.m00*b.m01+a.m01*b.m11+a.m02*b.m21,a.m00*b.m02+a.m01*b.m12+a.m02*b.m22,a.m10*b.m00+a.m11*b.m10+a.m12*b.m20,a.m10*b.m01+a.m11*b.m11+a.m12*b.m21,a.m10*b.m02+a.m11*b.m12+a.m12*b.m22,a.m20*b.m00+
a.m21*b.m10+a.m22*b.m20,a.m20*b.m01+a.m21*b.m11+a.m22*b.m21,a.m20*b.m02+a.m21*b.m12+a.m22*b.m22)},"JU.M3,JU.M3");h(c$,"equals",function(a){return!r(a,JU.M3)?!1:this.m00==a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m20==a.m20&&this.m21==a.m21&&this.m22==a.m22},"~O");h(c$,"hashCode",function(){return JU.T3.floatToIntBits0(this.m00)^JU.T3.floatToIntBits0(this.m01)^JU.T3.floatToIntBits0(this.m02)^JU.T3.floatToIntBits0(this.m10)^JU.T3.floatToIntBits0(this.m11)^
JU.T3.floatToIntBits0(this.m12)^JU.T3.floatToIntBits0(this.m20)^JU.T3.floatToIntBits0(this.m21)^JU.T3.floatToIntBits0(this.m22)});c(c$,"setZero",function(){this.m22=this.m21=this.m20=this.m12=this.m11=this.m10=this.m02=this.m01=this.m00=0});c(c$,"transform",function(a){this.transform2(a,a)},"JU.T3");c(c$,"transform2",function(a,b){b.set(this.m00*a.x+this.m01*a.y+this.m02*a.z,this.m10*a.x+this.m11*a.y+this.m12*a.z,this.m20*a.x+this.m21*a.y+this.m22*a.z)},"JU.T3,JU.T3");c(c$,"transformAdd",function(a,
b,d){d.x+=b*(this.m00*a.x+this.m01*a.y+this.m02*a.z);d.y+=b*(this.m10*a.x+this.m11*a.y+this.m12*a.z);d.z+=b*(this.m20*a.x+this.m21*a.y+this.m22*a.z)},"JU.T3,~N,JU.T3");c(c$,"toArrayD",function(){return[[this.m00,this.m01,this.m02],[this.m10,this.m11,this.m12],[this.m20,this.m21,this.m22]]});c(c$,"set",function(a,b,d,g,c,f,j,k,l){this.m00=a;this.m01=b;this.m02=d;this.m10=g;this.m11=c;this.m12=f;this.m20=j;this.m21=k;this.m22=l},"~N,~N,~N,~N,~N,~N,~N,~N,~N")}),p("JU"),t(null,"JU.M4",["java.lang.ArrayIndexOutOfBoundsException",
"JU.T3"],function(){c$=w(function(){this.m33=this.m32=this.m31=this.m30=this.m23=this.m22=this.m21=this.m20=this.m13=this.m12=this.m11=this.m10=this.m03=this.m02=this.m01=this.m00=0;u(this,arguments)},JU,"M4",null,java.io.Serializable);c$.newA=c(c$,"newA",function(a){var b=new JU.M4;b.m00=a[0];b.m01=a[1];b.m02=a[2];b.m03=a[3];b.m10=a[4];b.m11=a[5];b.m12=a[6];b.m13=a[7];b.m20=a[8];b.m21=a[9];b.m22=a[10];b.m23=a[11];b.m30=a[12];b.m31=a[13];b.m32=a[14];b.m33=a[15];return b},"~A");c$.newM=c(c$,"newM",
function(a){var b=new JU.M4;if(null==a)return b.setIdentity(),b;b.m00=a.m00;b.m01=a.m01;b.m02=a.m02;b.m03=a.m03;b.m10=a.m10;b.m11=a.m11;b.m12=a.m12;b.m13=a.m13;b.m20=a.m20;b.m21=a.m21;b.m22=a.m22;b.m23=a.m23;b.m30=a.m30;b.m31=a.m31;b.m32=a.m32;b.m33=a.m33;return b},"JU.M4");c$.newMV=c(c$,"newMV",function(a,b){var d=new JU.M4;d.setMV(a,b);return d},"JU.M3,JU.V3");c(c$,"setMV",function(a,b){this.setM3(a);this.setTranslation(b)},"JU.M3,JU.V3");c(c$,"setAA",function(a){this.setFromAxisAngle(a.x,a.y,a.z,
a.angle)},"JU.A4");c(c$,"setFromAxisAngle",function(a,b,d,g){var c=Math.sqrt(a*a+b*b+d*d),c=1/c;a*=c;b*=c;d*=c;var f=Math.cos(g);g=Math.sin(g);c=1-f;this.m00=f+a*a*c;this.m11=f+b*b*c;this.m22=f+d*d*c;var f=a*b*c,j=d*g;this.m01=f-j;this.m10=f+j;f=a*d*c;j=b*g;this.m02=f+j;this.m20=f-j;f=b*d*c;j=a*g;this.m12=f-j;this.m21=f+j},"~N,~N,~N,~N");c(c$,"setM",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m03=a.m03;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m13=a.m13;this.m20=a.m20;this.m21=
a.m21;this.m22=a.m22;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;this.m33=a.m33},"JU.M4");h(c$,"toString",function(){return"[\n  ["+this.m00+"\t"+this.m01+"\t"+this.m02+"\t"+this.m03+"]\n  ["+this.m10+"\t"+this.m11+"\t"+this.m12+"\t"+this.m13+"]\n  ["+this.m20+"\t"+this.m21+"\t"+this.m22+"\t"+this.m23+"]\n  ["+this.m30+"\t"+this.m31+"\t"+this.m32+"\t"+this.m33+"] ]"});c(c$,"setIdentity",function(){this.m00=1;this.m10=this.m03=this.m02=this.m01=0;this.m11=1;this.m21=this.m20=this.m13=
this.m12=0;this.m22=1;this.m32=this.m31=this.m30=this.m23=0;this.m33=1});c(c$,"setElement",function(a,b,d){if(0==a)if(0==b)this.m00=d;else if(1==b)this.m01=d;else if(2==b)this.m02=d;else if(3==b)this.m03=d;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+b);else if(1==a)if(0==b)this.m10=d;else if(1==b)this.m11=d;else if(2==b)this.m12=d;else if(3==b)this.m13=d;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+b);else if(2==a)if(0==b)this.m20=
d;else if(1==b)this.m21=d;else if(2==b)this.m22=d;else if(3==b)this.m23=d;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+b);else if(3==a)if(0==b)this.m30=d;else if(1==b)this.m31=d;else if(2==b)this.m32=d;else if(3==b)this.m33=d;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+b);else throw new ArrayIndexOutOfBoundsException("row must be 0 to 2 and is "+a);},"~N,~N,~N");c(c$,"getElement",function(a,b){switch(a){case 0:switch(b){case 0:return this.m00;
case 1:return this.m01;case 2:return this.m02;case 3:return this.m03}break;case 1:switch(b){case 0:return this.m10;case 1:return this.m11;case 2:return this.m12;case 3:return this.m13}break;case 2:switch(b){case 0:return this.m20;case 1:return this.m21;case 2:return this.m22;case 3:return this.m23}break;case 3:switch(b){case 0:return this.m30;case 1:return this.m31;case 2:return this.m32;case 3:return this.m33}}throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");},"~N,~N");
c(c$,"get",function(a){a.x=this.m03;a.y=this.m13;a.z=this.m23},"JU.V3");c(c$,"getRotationScale",function(a){a.m00=this.m00;a.m01=this.m01;a.m02=this.m02;a.m10=this.m10;a.m11=this.m11;a.m12=this.m12;a.m20=this.m20;a.m21=this.m21;a.m22=this.m22},"JU.M3");c(c$,"setRotationScale",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M3");c(c$,"setRow",function(a,b){if(0==a)this.m00=b[0],this.m01=b[1],this.m02=
b[2],this.m03=b[3];else if(1==a)this.m10=b[0],this.m11=b[1],this.m12=b[2],this.m13=b[3];else if(2==a)this.m20=b[0],this.m21=b[1],this.m22=b[2],this.m23=b[3];else if(3==a)this.m30=b[0],this.m31=b[1],this.m32=b[2],this.m33=b[3];else throw new ArrayIndexOutOfBoundsException("row must be 0 to 3 and is "+a);},"~N,~A");c(c$,"getRow",function(a,b){if(0==a)b[0]=this.m00,b[1]=this.m01,b[2]=this.m02,b[3]=this.m03;else if(1==a)b[0]=this.m10,b[1]=this.m11,b[2]=this.m12,b[3]=this.m13;else if(2==a)b[0]=this.m20,
b[1]=this.m21,b[2]=this.m22,b[3]=this.m23;else if(3==a)b[0]=this.m30,b[1]=this.m31,b[2]=this.m32,b[3]=this.m33;else throw new ArrayIndexOutOfBoundsException("row must be 0 to 3 and is "+a);},"~N,~A");c(c$,"setColumn4",function(a,b,d,g,c){if(0==a)this.m00=b,this.m10=d,this.m20=g,this.m30=c;else if(1==a)this.m01=b,this.m11=d,this.m21=g,this.m31=c;else if(2==a)this.m02=b,this.m12=d,this.m22=g,this.m32=c;else if(3==a)this.m03=b,this.m13=d,this.m23=g,this.m33=c;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+
a);},"~N,~N,~N,~N,~N");c(c$,"setColumn",function(a,b){if(0==a)this.m00=b[0],this.m10=b[1],this.m20=b[2],this.m30=b[3];else if(1==a)this.m01=b[0],this.m11=b[1],this.m21=b[2],this.m31=b[3];else if(2==a)this.m02=b[0],this.m12=b[1],this.m22=b[2],this.m32=b[3];else if(3==a)this.m03=b[0],this.m13=b[1],this.m23=b[2],this.m33=b[3];else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+a);},"~N,~A");c(c$,"getColumn",function(a,b){if(0==a)b[0]=this.m00,b[1]=this.m10,b[2]=this.m20,b[3]=
this.m30;else if(1==a)b[0]=this.m01,b[1]=this.m11,b[2]=this.m21,b[3]=this.m31;else if(2==a)b[0]=this.m02,b[1]=this.m12,b[2]=this.m22,b[3]=this.m32;else if(3==a)b[0]=this.m03,b[1]=this.m13,b[2]=this.m23,b[3]=this.m33;else throw new ArrayIndexOutOfBoundsException("column must be 0 to 3 and is "+a);},"~N,~A");c(c$,"sub",function(a){this.m00-=a.m00;this.m01-=a.m01;this.m02-=a.m02;this.m03-=a.m03;this.m10-=a.m10;this.m11-=a.m11;this.m12-=a.m12;this.m13-=a.m13;this.m20-=a.m20;this.m21-=a.m21;this.m22-=
a.m22;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31;this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(c$,"transpose",function(){var a=this.m01;this.m01=this.m10;this.m10=a;a=this.m02;this.m02=this.m20;this.m20=a;a=this.m03;this.m03=this.m30;this.m30=a;a=this.m12;this.m12=this.m21;this.m21=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(c$,"invertM",function(a){this.setM(a);this.invert()},"JU.M4");c(c$,"invert",function(){var a=this.determinant();0!=a&&(a=1/a,this.set(this.m11*
(this.m22*this.m33-this.m23*this.m32)+this.m12*(this.m23*this.m31-this.m21*this.m33)+this.m13*(this.m21*this.m32-this.m22*this.m31),this.m21*(this.m02*this.m33-this.m03*this.m32)+this.m22*(this.m03*this.m31-this.m01*this.m33)+this.m23*(this.m01*this.m32-this.m02*this.m31),this.m31*(this.m02*this.m13-this.m03*this.m12)+this.m32*(this.m03*this.m11-this.m01*this.m13)+this.m33*(this.m01*this.m12-this.m02*this.m11),this.m01*(this.m13*this.m22-this.m12*this.m23)+this.m02*(this.m11*this.m23-this.m13*this.m21)+
this.m03*(this.m12*this.m21-this.m11*this.m22),this.m12*(this.m20*this.m33-this.m23*this.m30)+this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22*(this.m00*this.m33-this.m03*this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+this.m20*(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*
this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-
this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*
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this.m12-this.m02*this.m11)*(this.m20*this.m33-this.m23*this.m30)-(this.m01*this.m13-this.m03*this.m11)*(this.m20*this.m32-this.m22*this.m30)+(this.m02*this.m13-this.m03*this.m12)*(this.m20*this.m31-this.m21*this.m30)});c(c$,"setM3",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m03=0;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m13=0;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22;this.m32=this.m31=this.m30=this.m23=0;this.m33=1},"JU.M3");c(c$,"setA",function(a,b){this.m00=a[b++];
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this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader",a),this.newAtomSet(b))}});c(c$,"processCtab",function(a){var b=null;a&&this.discardLinesUntilStartsWith("$CTAB");if(this.isV3000=null!=this.readLine()&&0<=this.line.indexOf("V3000"))this.is2D=this.dimension.equals("2D"),this.discardLinesUntilContains("COUNTS"),b=this.getTokens();if(null!=this.line){a=this.isV3000?this.parseIntStr(b[3]):this.parseIntRange(this.line,0,3);var b=this.isV3000?this.parseIntStr(b[4]):this.parseIntRange(this.line,
3,6),d=this.atomSetCollection.getAtomCount();this.readAtoms(a);this.readBonds(b);this.readUserData(d);this.isV3000&&this.discardLinesUntilContains("END CTAB");this.applySymmetryAndSetTrajectory()}},"~B");c(c$,"readAtoms",function(a){this.isV3000&&this.discardLinesUntilContains("BEGIN ATOM");for(var b=0;b<a;++b){this.readLine();var d=this.line.length,g,c,f,j,k=0,l=0,h=-2147483648;if(this.isV3000){this.checkLineContinuation();d=this.getTokens();h=this.parseIntStr(d[2]);g=d[3];if(g.equals("*"))continue;
c=this.parseFloatStr(d[4]);f=this.parseFloatStr(d[5]);j=this.parseFloatStr(d[6]);for(var n=7;n<d.length;n++){var q=d[n].toUpperCase();q.startsWith("CHG=")?k=this.parseIntStr(d[n].substring(4)):q.startsWith("MASS=")&&(l=this.parseIntStr(d[n].substring(5)))}1<l&&g.equals("H")&&(l=1-l)}else if(c=this.parseFloatRange(this.line,0,10),f=this.parseFloatRange(this.line,10,20),j=this.parseFloatRange(this.line,20,30),34>d)g=this.line.substring(31).trim();else if(g=this.line.substring(31,34).trim(),39<=d){d=
this.parseIntRange(this.line,36,39);1<=d&&7>=d&&(k=4-d);d=this.parseIntRange(this.line,34,36);if(0!=d&&-3<=d&&4>=d)switch(l=J.api.JmolAdapter.getNaturalIsotope(J.api.JmolAdapter.getElementNumber(g)),l){case 0:break;case 1:l=-d;break;default:l+=d}-2147483648==h&&this.haveAtomSerials&&(h=b+1)}switch(l){case 0:break;case -1:g="D";break;case -2:g="T";break;default:g=l+g}this.is2D&&0!=j&&(this.is2D=!1);l=new J.adapter.smarter.Atom;l.elementSymbol=g;l.formalCharge=k;this.setAtomCoordXYZ(l,c,f,j);-2147483648==
h?this.atomSetCollection.addAtom(l):(this.haveAtomSerials=!0,l.atomSerial=h,this.atomSetCollection.addAtomWithMappedSerialNumber(l))}this.isV3000&&this.discardLinesUntilContains("END ATOM")},"~N");c(c$,"checkLineContinuation",function(){for(;this.line.endsWith("-");){var a=this.line;this.readLine();this.line=a+this.line}});c(c$,"readBonds",function(a){this.isV3000&&this.discardLinesUntilContains("BEGIN BOND");for(var b=0;b<a;++b){this.readLine();var d,g,c,f=0;if(this.isV3000){this.checkLineContinuation();
var j=this.getTokens();c=this.parseIntStr(j[3]);d=this.parseIntStr(j[4]);g=this.parseIntStr(j[5]);for(var k=6;k<j.length;k++){var l=j[k].toUpperCase();if(l.startsWith("CFG=")){f=this.parseIntStr(j[k].substring(4));break}else if(l.startsWith("ENDPTS=")&&!(0>this.line.indexOf("ATTACH=ALL"))){j=J.adapter.smarter.AtomSetCollectionReader.getTokensAt(this.line,this.line.indexOf("ENDPTS=")+8);k=this.parseIntStr(j[0]);c=this.fixOrder(c,0);for(l=1;l<=k;l++)g=this.parseIntStr(j[l]),this.atomSetCollection.addNewBondWithMappedSerialNumbers(d,
g,c);break}}}else d=this.parseIntRange(this.line,0,3),g=this.parseIntRange(this.line,3,6),c=this.parseIntRange(this.line,6,9),this.is2D&&(1==c&&12<=this.line.length)&&(f=this.parseIntRange(this.line,9,12));c=this.fixOrder(c,f);this.haveAtomSerials?this.atomSetCollection.addNewBondWithMappedSerialNumbers(d,g,c):this.atomSetCollection.addNewBondWithOrder(this.iatom0+d-1,this.iatom0+g-1,c)}this.isV3000&&this.discardLinesUntilContains("END BOND")},"~N");c(c$,"fixOrder",function(a,b){switch(a){default:case 0:case -10:return 1;
case 1:switch(b){case 1:return 1025;case 3:case 6:return 1041}break;case 2:case 3:break;case 4:return 515;case 5:return 66;case 6:return 513;case 7:return 514;case 8:case 9:return 33}return a},"~N,~N")}),p("J.adapter.readers.molxyz"),t(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["java.lang.Float","J.util.Logger"],function(){c$=M(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);h(c$,"checkLine",function(){var a=this.parseIntStr(this.line);
if(-2147483648==a)return this.continuing=!1;this.vibrationNumber=++this.modelNumber;if(0>=this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):this.doGetVibration(this.vibrationNumber)){this.readLine();this.checkCurrentLineForScript();this.atomSetCollection.newAtomSet();var b=this.line;this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.atomSetCollection.setAtomSetName(b);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();
return!1});h(c$,"finalizeReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});c(c$,"skipAtomSet",function(a){for(this.readLine();0<=--a;)this.readLine()},"~N");c(c$,"readAtoms",function(a){for(var b=0;b<a;++b){this.readLine();var d=this.getTokens();if(4>d.length)J.util.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var g=this.atomSetCollection.addNewAtom();this.setElementAndIsotope(g,d[0]);g.x=this.parseFloatStr(d[1]);g.y=this.parseFloatStr(d[2]);g.z=this.parseFloatStr(d[3]);
if(Float.isNaN(g.x)||Float.isNaN(g.y)||Float.isNaN(g.z))J.util.Logger.warn("line cannot be read for XYZ atom data: "+this.line),g.set(0,0,0);var c=4;this.setAtomCoord(g);switch(d.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=d[4].indexOf("."))g.partialCharge=this.parseFloatStr(d[4]);else{var f=this.parseIntStr(d[4]);-2147483648!=f&&(g.formalCharge=f)}switch(d.length){case 5:continue;case 6:g.radius=this.parseFloatStr(d[5]);continue;case 9:g.atomSerial=this.parseIntStr(d[8])}c++;default:var f=
this.parseFloatStr(d[c++]),j=this.parseFloatStr(d[c++]),d=this.parseFloatStr(d[c++]);if(Float.isNaN(f)||Float.isNaN(j)||Float.isNaN(d))continue;this.atomSetCollection.addVibrationVector(g.index,f,j,d)}}}},"~N")}),p("J.adapter.smarter"),t(["JU.P3"],"J.adapter.smarter.Atom",["java.lang.Float","JU.AU","$.List","$.V3"],function(){c$=w(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=null;this.formalCharge=-2147483648;
this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.ignoreSymmetry=!1;u(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);c(c$,"addTensor",function(a,b,d){if(null==a)return null;if(d||null==this.tensors)this.tensors=new JU.List;this.tensors.addLast(a);null!=b&&a.setType(b);
return a},"J.util.Tensor,~S,~B");Da(c$,function(){this.set(NaN,NaN,NaN)});c(c$,"getClone",function(){var a=this.clone();null!=this.vib&&(a.vib=JU.V3.newV(a.vib));null!=this.anisoBorU&&(a.anisoBorU=JU.AU.arrayCopyF(this.anisoBorU,-1));if(null!=this.tensors){a.tensors=new JU.List;for(var b=this.tensors.size();0<=--b;)a.tensors.addLast(this.tensors.get(b).copyTensor())}return a});c(c$,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=this.atomName){for(var a=this.atomName.length,b=0,d=
String.fromCharCode(0);b<a&&!J.adapter.smarter.Atom.isValidFirstSymbolChar(d=this.atomName.charAt(b));)++b;switch(a-b){case 0:break;default:if(a=this.atomName.charAt(b+1),J.adapter.smarter.Atom.isValidElementSymbolNoCaseSecondChar2(d,a)){this.elementSymbol=""+d+a;break}case 1:J.adapter.smarter.Atom.isValidElementSymbol(d)&&(this.elementSymbol=""+d)}}return this.elementSymbol});c$.isValidElementSymbol=c(c$,"isValidElementSymbol",function(a){return"A"<=a&&"Z">=a&&0>J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-
65]},"~S");c$.isValidElementSymbol2=c(c$,"isValidElementSymbol2",function(a,b){return"A">a||"Z"<a||"a">b||"z"<b?!1:0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>b.charCodeAt(0)-97&1)},"~S,~S");c$.isValidElementSymbolNoCaseSecondChar2=c(c$,"isValidElementSymbolNoCaseSecondChar2",function(a,b){"A"<=b&&"Z">=b&&(b=String.fromCharCode(b.charCodeAt(0)+32));return"A">a||"Z"<a||"a">b||"z"<b?!1:0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>b.charCodeAt(0)-97&1)},"~S,~S");
c$.isValidFirstSymbolChar=c(c$,"isValidFirstSymbolChar",function(a){return"A"<=a&&"Z">=a&&0!=J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c$.isValidElementSymbolNoCaseSecondChar=c(c$,"isValidElementSymbolNoCaseSecondChar",function(a){if(null==a)return!1;var b=a.length;if(0==b)return!1;var d=a.charAt(0);if(1==b)return J.adapter.smarter.Atom.isValidElementSymbol(d);if(2<b)return!1;a=a.charAt(1);return J.adapter.smarter.Atom.isValidElementSymbolNoCaseSecondChar2(d,a)},"~S");c(c$,
"scaleVector",function(a){null==this.vib||Float.isNaN(this.vib.z)||this.vib.scale(a)},"~N");E(c$,"elementCharMasks",[1972292,-2147351151,-2146019271,-2130706430,1441792,-2147348464,25,-2147205008,-2147344384,0,-2147352576,1179905,548936,-2147434213,-2147221504,-2145759221,0,1056947,-2147339946,-2147477097,-2147483648,-2147483648,-2147483648,8388624,-2147483646,139264])}),p("J.adapter.smarter"),t(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["java.lang.Float","J.api.JmolAdapter"],
function(){c$=w(function(){this.iatom=0;this.atom=null;this.atomCount=0;this.bsAtoms=this.atoms=null;u(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);A(c$,function(a){this.atomCount=a.getAtomCount();this.atoms=a.getAtoms();this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");h(c$,"hasNext",function(){if(this.iatom==this.atomCount)return!1;for(;null==(this.atom=this.atoms[this.iatom++])||null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==
this.atomCount)return!1;this.atoms[this.iatom-1]=null;return!0});h(c$,"getAtomSetIndex",function(){return this.atom.atomSetIndex});h(c$,"getAtomSymmetry",function(){return this.atom.bsSymmetry});h(c$,"getAtomSite",function(){return this.atom.atomSite+1});h(c$,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});h(c$,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});h(c$,"getAtomName",
function(){return this.atom.atomName});h(c$,"getFormalCharge",function(){return this.atom.formalCharge});h(c$,"getPartialCharge",function(){return this.atom.partialCharge});h(c$,"getTensors",function(){return this.atom.tensors});h(c$,"getRadius",function(){return this.atom.radius});h(c$,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});h(c$,"getBfactor",function(){return Float.isNaN(this.atom.bfactor)&&null!=this.atom.anisoBorU?100*this.atom.anisoBorU[7]:
this.atom.bfactor});h(c$,"getOccupancy",function(){return y(100*this.atom.foccupancy)});h(c$,"getIsHetero",function(){return this.atom.isHetero});h(c$,"getAtomSerial",function(){return this.atom.atomSerial});h(c$,"getChainID",function(){return this.atom.chainID});h(c$,"getAlternateLocationID",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});h(c$,"getGroup3",function(){return this.atom.group3});h(c$,"getSequenceNumber",function(){return this.atom.sequenceNumber});
h(c$,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});h(c$,"getXYZ",function(){return this.atom})}),p("J.adapter.smarter"),t(["java.util.Hashtable","JU.P3"],"J.adapter.smarter.AtomSetCollection","java.lang.Boolean $.Float java.util.Collections $.Properties JU.AU $.BS $.List $.M3 $.M4 $.P3i $.PT $.SB $.V3 J.adapter.smarter.Atom $.Bond $.SmarterJmolAdapter J.api.Interface J.util.BSUtil $.Escape $.Logger".split(" "),function(){c$=w(function(){this.atomSetCollectionAuxiliaryInfo=
this.collectionName=this.fileTypeName=this.bsAtoms=null;this.atomCount=0;this.atoms=null;this.bondCount=0;this.bonds=null;this.structureCount=0;this.structures=null;this.atomSetCount=0;this.currentAtomSetIndex=-1;this.errorMessage=this.latticeCells=this.atomSetAuxiliaryInfo=this.atomSetBondCounts=this.atomSetAtomCounts=this.atomSetAtomIndexes=this.atomSetNumbers=null;this.isTrajectory=this.coordinatesAreFractional=!1;this.trajectoryStepCount=0;this.trajectoryNames=this.vibrationSteps=this.trajectorySteps=
null;this.doFixPeriodic=!1;this.notionalUnitCell=null;this.allowMultiple=!1;this.vConnect=this.readerList=this.reader=null;this.connectNextAtomSet=this.connectNextAtomIndex=0;this.bsStructuredModels=this.connectLast=null;this.symmetryRange=0;this.centroidPacked=this.doCentroidUnitCell=!1;this.symmetry=this.fmatSupercell=this.ptSupercell=null;this.haveUnitCell=!1;this.doNormalize=!0;this.doPackUnitCell=!1;this.rmaxz=this.rmaxy=this.rmaxx=this.rminz=this.rminy=this.rminx=0;this.maxXYZ0=this.minXYZ0=
this.maxXYZ=this.minXYZ=this.unitCellOffset=this.ptOffset=null;this.haveAnisou=!1;this.dtype=3;this.unitCellTranslations=null;this.baseSymmetryAtomCount=0;this.checkLatticeOnly=!1;this.latticeOp=0;this.latticeOnly=!1;this.bondIndex0=this.bondCount0=this.firstSymmetryAtom=this.noSymmetryCount=0;this.applySymmetryToBonds=!1;this.checkSpecial=!0;this.checkAll=!1;this.atomSymbolicMap=this.mTemp=this.ptTemp=null;this.haveMappedSerials=!1;u(this,arguments)},J.adapter.smarter,"AtomSetCollection");Q(c$,function(){this.atomSetCollectionAuxiliaryInfo=
new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=D(16,0);this.atomSetAtomIndexes=D(16,0);this.atomSetAtomCounts=D(16,0);this.atomSetBondCounts=D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.notionalUnitCell=O(6,0);this.ptOffset=new JU.P3;this.atomSymbolicMap=new java.util.Hashtable});c(c$,"getFileTypeName",function(){return this.fileTypeName});c(c$,"getCollectionName",function(){return this.collectionName});c(c$,"setCollectionName",
function(a){null!=a&&(a=a.trim(),0!=a.length&&(this.collectionName=a))},"~S");c(c$,"getAtomSetCollectionAuxiliaryInfoMap",function(){return this.atomSetCollectionAuxiliaryInfo});c(c$,"clearGlobalBoolean",function(a){this.atomSetCollectionAuxiliaryInfo.remove(J.adapter.smarter.AtomSetCollection.globalBooleans[a])},"~N");c(c$,"setGlobalBoolean",function(a){this.setAtomSetCollectionAuxiliaryInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a],Boolean.TRUE)},"~N");c(c$,"getGlobalBoolean",function(a){return this.getAtomSetCollectionAuxiliaryInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a])===
Boolean.TRUE},"~N");c(c$,"getAtomCount",function(){return this.atomCount});c(c$,"getHydrogenAtomCount",function(){for(var a=0,b=0;b<this.atomCount;b++)(1==this.atoms[b].elementNumber||this.atoms[b].elementSymbol.equals("H"))&&a++;return a});c(c$,"getAtoms",function(){return this.atoms});c(c$,"getAtom",function(a){return this.atoms[a]},"~N");c(c$,"getBondCount",function(){return this.bondCount});c(c$,"getBonds",function(){return this.bonds});c(c$,"getBond",function(a){return this.bonds[a]},"~N");c(c$,
"getStructureCount",function(){return this.structureCount});c(c$,"getStructures",function(){return this.structures});c(c$,"getAtomSetCount",function(){return this.atomSetCount});c(c$,"getCurrentAtomSetIndex",function(){return this.currentAtomSetIndex});c(c$,"setCurrentAtomSetIndex",function(a){this.currentAtomSetIndex=a},"~N");c(c$,"setDoFixPeriodic",function(){this.doFixPeriodic=!0});A(c$,function(a,b,d,g){this.fileTypeName=a;this.reader=b;this.allowMultiple=null==b||0>b.desiredVibrationNumber;a=
new java.util.Properties;a.put("PATH_KEY",".PATH");a.put("PATH_SEPARATOR",J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);this.setAtomSetCollectionAuxiliaryInfo("properties",a);if(null!=d){g=0;this.readerList=new JU.List;for(a=0;a<d.length;a++)(0<d[a].atomCount||null!=d[a].reader&&d[a].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(g++,d[a]);1<g&&this.setAtomSetCollectionAuxiliaryInfo("isMultiFile",Boolean.TRUE)}else null!=g&&(this.setAtomSetCollectionAuxiliaryInfo("isMultiFile",
Boolean.TRUE),this.appendAtomSetCollectionList(g))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.List");c(c$,"appendAtomSetCollectionList",function(a){var b=a.size();if(0==b)this.errorMessage="No file found!";else for(var d=0;d<b;d++){var g=a.get(d);r(g,JU.List)?this.appendAtomSetCollectionList(g):this.appendAtomSetCollection(d,g)}},"JU.List");c(c$,"setTrajectory",function(){this.isTrajectory||(this.trajectorySteps=new JU.List);this.isTrajectory=!0;this.addTrajectoryStep()});c(c$,"appendAtomSetCollection",
function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.atomCount;this.setAtomSetCollectionAuxiliaryInfo("loadState",b.getAtomSetCollectionAuxiliaryInfo("loadState"));if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var g=b.bsAtoms.nextSetBit(0);0<=g;g=b.bsAtoms.nextSetBit(g+1))this.bsAtoms.set(d+g)}for(var g=0,c=this.atomSetCount,f=0;f<b.atomSetCount;f++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.currentAtomSetIndex]=
b.atomSetAuxiliaryInfo[f]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=d);this.setAtomSetAuxiliaryInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(f));for(j=0;j<b.atomSetAtomCounts[f];j++){try{null!=this.bsAtoms&&this.bsAtoms.set(this.atomCount),this.newCloneAtom(b.atoms[g])}catch(k){if(C(k,Exception))this.errorMessage="appendAtomCollection error: "+k;else throw k;}g++}this.atomSetNumbers[this.currentAtomSetIndex]=0>a?this.currentAtomSetIndex+1:1E6*(a+1)+b.atomSetNumbers[f]}for(g=
0;g<b.bondCount;g++)f=b.bonds[g],this.addNewBondWithOrder(f.atomIndex1+d,f.atomIndex2+d,f.order);for(g=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--g;)b.getGlobalBoolean(g)&&this.setGlobalBoolean(g);for(g=0;g<b.structureCount;g++)d=b.structures[g],this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"setNoAutoBond",function(){this.setAtomSetCollectionAuxiliaryInfo("noAutoBond",Boolean.TRUE)});c(c$,"freeze",function(a){1==
this.atomSetCount&&null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setAtomSetAuxiliaryInfoForSet("initialAtomCount",Integer.$valueOf(this.atomSetAtomCounts[a]),a),this.setAtomSetAuxiliaryInfoForSet("initialBondCount",Integer.$valueOf(this.atomSetBondCounts[a]),a)},"~B");c(c$,"reverseAtomSets",function(){this.reverseArray(this.atomSetAtomIndexes);
this.reverseArray(this.atomSetNumbers);this.reverseArray(this.atomSetAtomCounts);this.reverseArray(this.atomSetBondCounts);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectorySteps);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectoryNames);J.adapter.smarter.AtomSetCollection.reverseList(this.vibrationSteps);this.reverseObject(this.atomSetAuxiliaryInfo);for(var a=0;a<this.atomCount;a++)this.atoms[a].atomSetIndex=this.atomSetCount-1-this.atoms[a].atomSetIndex;for(a=0;a<this.structureCount;a++){var b=
this.structures[a].modelStartEnd[0];0<=b&&(this.structures[a].modelStartEnd[0]=this.atomSetCount-1-this.structures[a].modelStartEnd[1],this.structures[a].modelStartEnd[1]=this.atomSetCount-1-b)}for(a=0;a<this.bondCount;a++)this.bonds[a].atomSetIndex=this.atomSetCount-1-this.atoms[this.bonds[a].atomIndex1].atomSetIndex;this.reverseSets(this.bonds,this.bondCount);for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),a=0;a<this.atomSetCount;a++)d[a]=new JU.List;for(a=0;a<this.atomCount;a++)d[this.atoms[a].atomSetIndex].addLast(this.atoms[a]);
for(var b=D(this.atomCount,0),g=this.atomCount,a=this.atomSetCount;0<=--a;)for(var c=d[a].size();0<=--c;){var f=this.atoms[--g]=d[a].get(c);b[f.index]=g;f.index=g}for(a=0;a<this.bondCount;a++)this.bonds[a].atomIndex1=b[this.bonds[a].atomIndex1],this.bonds[a].atomIndex2=b[this.bonds[a].atomIndex2];for(a=0;a<this.atomSetCount;a++)d=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),null!=d&&(d[0]=b[d[0]],d[1]=this.atomSetAtomCounts[a])});c(c$,"reverseSets",function(a,b){for(var d=
JU.AU.createArrayOfArrayList(this.atomSetCount),g=0;g<this.atomSetCount;g++)d[g]=new JU.List;for(g=0;g<b;g++){if(0>a[g].atomSetIndex)return;d[a[g].atomSetIndex].addLast(a[g])}for(g=this.atomSetCount;0<=--g;)for(var c=d[g].size();0<=--c;)a[--b]=d[g].get(c)},"~A,~N");c(c$,"reverseObject",function(a){for(var b=this.atomSetCount,d=s(b/2);0<=--d;)JU.AU.swap(a,d,b-1-d)},"~A");c$.reverseList=c(c$,"reverseList",function(a){null!=a&&java.util.Collections.reverse(a)},"JU.List");c(c$,"reverseArray",function(a){for(var b=
this.atomSetCount,d=s(b/2);0<=--d;)JU.AU.swapInt(a,d,b-1-d)},"~A");c(c$,"getList",function(a){var b;for(b=this.atomCount;0<=--b&&!(null!=this.atoms[b]&&"\x00"!=(a?this.atoms[b].altLoc:this.atoms[b].insertionCode)););if(!(0>b)){var d=Array(this.atomSetCount);for(b=0;b<this.atomSetCount;b++)d[b]="";var g;for(b=0;b<this.atomCount;b++)if(null!=this.atoms[b]){var c=a?this.atoms[b].altLoc:this.atoms[b].insertionCode;if("\x00"!=c&&0>d[g=this.atoms[b].atomSetIndex].indexOf(c))d[g]+=c}a=a?"altLocs":"insertionCodes";
for(b=0;b<this.atomSetCount;b++)0<d[b].length&&this.setAtomSetAuxiliaryInfoForSet(a,d[b],b)}},"~B");c(c$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetCollectionAuxiliaryInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=D(16,0);this.atomSymbolicMap=
new java.util.Hashtable;this.connectLast=this.bonds=null;this.currentAtomSetIndex=-1;this.symmetry=this.readerList=this.notionalUnitCell=this.latticeCells=null;this.structures=Array(16);this.structureCount=0;this.vConnect=this.vibrationSteps=this.trajectorySteps=null});c(c$,"discardPreviousAtoms",function(){for(var a=this.atomCount;0<=--a;)this.atoms[a]=null;this.atomCount=0;this.clearSymbolicMap();this.atomSetCount=0;this.currentAtomSetIndex=-1;for(a=this.atomSetAuxiliaryInfo.length;0<=--a;)this.atomSetAtomCounts[a]=
0,this.atomSetBondCounts[a]=0,this.atomSetAuxiliaryInfo[a]=null});c(c$,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,this.bsAtoms.setBits(0,this.atomCount));var b=this.atomSetAtomIndexes[a],d=b+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(b,d);for(b=d;b<this.atomCount;b++)this.atoms[b].atomSetIndex--;for(b=a+1;b<this.atomSetCount;b++)this.atomSetAuxiliaryInfo[b-1]=this.atomSetAuxiliaryInfo[b],this.atomSetAtomIndexes[b-1]=this.atomSetAtomIndexes[b],this.atomSetBondCounts[b-
1]=this.atomSetBondCounts[b],this.atomSetAtomCounts[b-1]=this.atomSetAtomCounts[b],this.atomSetNumbers[b-1]=this.atomSetNumbers[b];for(b=d=0;b<this.structureCount;b++){var g=this.structures[b];g.modelStartEnd[0]==a&&g.modelStartEnd[1]==a&&(this.structures[b]=null,d++)}if(0<d){a=Array(this.structureCount-d);for(d=b=0;b<this.structureCount;b++)null!=this.structures[b]&&(a[d++]=this.structures[b]);this.structures=a}for(b=0;b<this.bondCount;b++)this.bonds[b].atomSetIndex=this.atoms[this.bonds[b].atomIndex1].atomSetIndex;
this.atomSetAuxiliaryInfo[--this.atomSetCount]=null},"~N");c(c$,"removeCurrentAtomSet",function(){0>this.currentAtomSetIndex||(this.currentAtomSetIndex--,this.atomSetCount--)});c(c$,"newCloneAtom",function(a){a=a.getClone();this.addAtom(a);return a},"J.adapter.smarter.Atom");c(c$,"cloneFirstAtomSet",function(a){if(this.allowMultiple){this.newAtomSet();0==a&&(a=this.atomSetAtomCounts[0]);for(var b=0;b<a;++b)this.newCloneAtom(this.atoms[b])}},"~N");c(c$,"cloneFirstAtomSetWithBonds",function(a){if(this.allowMultiple){this.cloneFirstAtomSet(0);
for(var b=this.atomSetAtomCounts[0],d=0;d<a;d++){var g=this.bonds[this.bondCount-a];this.addNewBondWithOrder(g.atomIndex1+b,g.atomIndex2+b,g.order)}}},"~N");c(c$,"cloneLastAtomSet",function(){this.cloneLastAtomSetFromPoints(0,null)});c(c$,"cloneLastAtomSetFromPoints",function(a,b){if(this.allowMultiple){var d=0<a?a:this.getLastAtomSetAtomCount(),g=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<d;++c){var f=this.newCloneAtom(this.atoms[g++]);null!=b&&f.setT(b[c])}}},"~N,~A");c(c$,"getFirstAtomSetAtomCount",
function(){return this.atomSetAtomCounts[0]});c(c$,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.currentAtomSetIndex]});c(c$,"getLastAtomSetAtomIndex",function(){return this.atomCount-this.atomSetAtomCounts[this.currentAtomSetIndex]});c(c$,"addNewAtom",function(){var a=new J.adapter.smarter.Atom;this.addAtom(a);return a});c(c$,"addAtom",function(a){this.atomCount==this.atoms.length&&(this.atoms=2E5<this.atomCount?JU.AU.ensureLength(this.atoms,this.atomCount+5E4):JU.AU.doubleLength(this.atoms));
0==this.atomSetCount&&this.newAtomSet();a.index=this.atomCount;this.atoms[this.atomCount++]=a;a.atomSetIndex=this.currentAtomSetIndex;a.atomSite=this.atomSetAtomCounts[this.currentAtomSetIndex]++},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedName",function(a){this.addAtom(a);this.mapMostRecentAtomName()},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedSerialNumber",function(a){this.addAtom(a);this.mapMostRecentAtomSerialNumber()},"J.adapter.smarter.Atom");c(c$,"addNewBondWithOrder",function(a,
b,d){if(0>a||a>=this.atomCount||0>b||b>=this.atomCount)return null;a=new J.adapter.smarter.Bond(a,b,d);this.addBond(a);return a},"~N,~N,~N");c(c$,"addNewBondFromNames",function(a,b,d){return this.addNewBondWithOrder(this.getAtomIndexFromName(a),this.getAtomIndexFromName(b),d)},"~S,~S,~N");c(c$,"addNewBondWithMappedSerialNumbers",function(a,b,d){return this.addNewBondWithOrder(this.getAtomIndexFromSerial(a),this.getAtomIndexFromSerial(b),d)},"~N,~N,~N");c(c$,"addConnection",function(a){null==this.vConnect&&
(this.connectLast=null,this.vConnect=new JU.List);null!=this.connectLast&&a[0]==this.connectLast[0]&&a[1]==this.connectLast[1]&&2048!=a[2]?this.connectLast[2]++:this.vConnect.addLast(this.connectLast=a)},"~A");c(c$,"connectAllBad",function(a){for(var b=this.connectNextAtomIndex,d=this.connectNextAtomSet;d<this.atomSetCount;d++)this.setAtomSetAuxiliaryInfoForSet("PDB_CONECT_firstAtom_count_max",[b,this.atomSetAtomCounts[d],a],d),null!=this.vConnect&&(this.setAtomSetAuxiliaryInfoForSet("PDB_CONECT_bonds",
this.vConnect,d),this.setGlobalBoolean(3)),b+=this.atomSetAtomCounts[d];this.vConnect=null;this.connectNextAtomSet=this.currentAtomSetIndex+1;this.connectNextAtomIndex=b},"~N");c(c$,"connectAll",function(a,b){if(!(0>this.currentAtomSetIndex))if(b)this.connectAllBad(a);else if(this.setAtomSetAuxiliaryInfo("PDB_CONECT_firstAtom_count_max",[this.atomSetAtomIndexes[this.currentAtomSetIndex],this.atomSetAtomCounts[this.currentAtomSetIndex],a]),null!=this.vConnect){for(var d=this.connectNextAtomIndex,g=
this.connectNextAtomSet;g<this.atomSetCount;g++)this.setAtomSetAuxiliaryInfoForSet("PDB_CONECT_bonds",this.vConnect,g),this.setGlobalBoolean(3),d+=this.atomSetAtomCounts[g];this.vConnect=null;this.connectNextAtomSet=this.currentAtomSetIndex+1;this.connectNextAtomIndex=d}},"~N,~B");c(c$,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?J.util.Logger.debugging&&J.util.Logger.debug(">>>>>>BAD BOND:"+
a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):(this.bondCount==this.bonds.length&&(this.bonds=JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024)),this.bonds[this.bondCount++]=a,this.atomSetBondCounts[this.currentAtomSetIndex]++))},"J.adapter.smarter.Bond");c(c$,"finalizeStructures",function(){if(0!=this.structureCount){this.bsStructuredModels=new JU.BS;for(var a=new java.util.Hashtable,b=0;b<this.structureCount;b++){var d=this.structures[b];-1==d.modelStartEnd[0]&&(d.modelStartEnd[0]=0,d.modelStartEnd[1]=
this.atomSetCount-1);this.bsStructuredModels.setBits(d.modelStartEnd[0],d.modelStartEnd[1]+1);if(0!=d.strandCount){var d=d.structureID+" "+d.modelStartEnd[0],g=a.get(d),g=(null==g?0:g.intValue())+1;a.put(d,Integer.$valueOf(g))}}for(b=0;b<this.structureCount;b++)d=this.structures[b],1==d.strandCount&&(d.strandCount=a.get(d.structureID+" "+d.modelStartEnd[0]).intValue())}});c(c$,"addStructure",function(a){this.structureCount==this.structures.length&&(this.structures=JU.AU.arrayCopyObject(this.structures,
this.structureCount+32));this.structures[this.structureCount++]=a},"J.adapter.smarter.Structure");c(c$,"addVibrationVectorWithSymmetry",function(a,b,d,g,c){if(c){c=this.atoms[a].atomSite;for(var f=this.atoms[a].atomSetIndex;a<this.atomCount&&this.atoms[a].atomSetIndex==f;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,b,d,g)}else this.addVibrationVector(a,b,d,g)},"~N,~N,~N,~N,~B");c(c$,"addVibrationVector",function(a,b,d,g){this.allowMultiple||(a%=this.atomCount);this.atoms[a].vib=JU.V3.new3(b,
d,g)},"~N,~N,~N,~N");c(c$,"setAtomSetSpaceGroupName",function(a){this.setAtomSetAuxiliaryInfo("spaceGroup",a+"")},"~S");c(c$,"setCoordinatesAreFractional",function(a){this.coordinatesAreFractional=a;this.setAtomSetAuxiliaryInfo("coordinatesAreFractional",Boolean.$valueOf(a));a&&this.setGlobalBoolean(0)},"~B");c(c$,"setSymmetryRange",function(a){this.symmetryRange=a;this.setAtomSetCollectionAuxiliaryInfo("symmetryRange",Float.$valueOf(a))},"~N");c(c$,"setLatticeCells",function(a,b,d,g,c,f,j){this.latticeCells=
a;var k=555>=a[0]&&555<=a[1]&&(0==a[2]||1==a[2]||-1==a[2]);this.doNormalize=0!=a[0]&&(!k||1==a[2]);this.applySymmetryToBonds=b;this.doPackUnitCell=d;this.doCentroidUnitCell=g;this.centroidPacked=c;null!=f?this.setSuperCell(f):this.ptSupercell=j},"~A,~B,~B,~B,~B,~S,JU.P3");c(c$,"setSupercellFromPoint",function(a){this.ptSupercell=a;J.util.Logger.info("Using supercell "+J.util.Escape.eP(a))},"JU.P3");c(c$,"setSuperCell",function(a){null==this.fmatSupercell&&(this.fmatSupercell=O(16,0),null==this.getSymmetry().getMatrixFromString(a,
this.fmatSupercell,!0,0)?this.fmatSupercell=null:J.util.Logger.info("Using supercell \n"+JU.M4.newA(this.fmatSupercell)))},"~S");c(c$,"getSymmetry",function(){null==this.symmetry&&(this.symmetry=J.api.Interface.getOptionInterface("symmetry.Symmetry"));return this.symmetry});c(c$,"setNotionalUnitCell",function(a,b,d){this.notionalUnitCell=O(a.length,0);this.unitCellOffset=d;for(var g=0;g<a.length;g++)this.notionalUnitCell[g]=a[g];this.haveUnitCell=!0;this.setAtomSetAuxiliaryInfo("notionalUnitcell",
this.notionalUnitCell);this.setGlobalBoolean(2);this.getSymmetry().setUnitCell(this.notionalUnitCell);null!=d&&(this.symmetry.setOffsetPt(d),this.setAtomSetAuxiliaryInfo("unitCellOffset",d));null!=b&&(this.symmetry.setUnitCellOrientation(b),this.setAtomSetAuxiliaryInfo("matUnitCellOrientation",b))},"~A,JU.M3,JU.P3");c(c$,"addSpaceGroupOperation",function(a){this.getSymmetry().setSpaceGroup(this.doNormalize);return this.symmetry.addSpaceGroupOperation(a,0)},"~S");c(c$,"setLatticeParameter",function(a){this.getSymmetry().setSpaceGroup(this.doNormalize);
this.symmetry.setLattice(a)},"~N");c(c$,"applySymmetry",function(a,b){null!=a&&this.getSymmetry().setSpaceGroupS(a);this.applySymmetryLattice(b)},"J.api.SymmetryInterface,J.adapter.smarter.MSInterface");c(c$,"applySymmetryLattice",function(a){if(this.coordinatesAreFractional&&null!=this.getSymmetry().getSpaceGroup()){var b=this.latticeCells[0],d=this.latticeCells[1],g=Math.abs(this.latticeCells[2]);if(null!=this.fmatSupercell){this.rminz=this.rminy=this.rminx=3.4028235E38;this.rmaxz=this.rmaxy=this.rmaxx=
-3.4028235E38;var c=this.setSym(0,1,2),f=this.setSym(4,5,6),j=this.setSym(8,9,10);this.minXYZ=JU.P3i.new3(y(this.rminx),y(this.rminy),y(this.rminz));this.maxXYZ=JU.P3i.new3(y(this.rmaxx),y(this.rmaxy),y(this.rmaxz));this.applyAllSymmetry(a);for(var k=this.getLastAtomSetAtomIndex(),l=k;l<this.atomCount;l++)this.symmetry.toCartesian(this.atoms[l],!0);this.symmetry=null;this.setNotionalUnitCell([0,0,0,0,0,0,c.x,c.y,c.z,f.x,f.y,f.z,j.x,j.y,j.z],null,this.getAtomSetAuxiliaryInfoValue(-1,"unitCellOffset"));
this.setAtomSetSpaceGroupName("P1");this.getSymmetry().setSpaceGroup(this.doNormalize);this.symmetry.addSpaceGroupOperation("x,y,z",0);for(l=k;l<this.atomCount;l++)this.symmetry.toFractional(this.atoms[l],!0);this.haveAnisou=!1;this.atomSetAuxiliaryInfo[this.currentAtomSetIndex].remove("matUnitCellOrientation");this.doPackUnitCell=!1}this.minXYZ=new JU.P3i;this.maxXYZ=JU.P3i.new3(b,d,g);this.applyAllSymmetry(a);this.fmatSupercell=null}},"J.adapter.smarter.MSInterface");c(c$,"setSym",function(a,b,
d){var g=new JU.P3;g.set(this.fmatSupercell[a],this.fmatSupercell[b],this.fmatSupercell[d]);this.setSymmetryMinMax(g);this.symmetry.toCartesian(g,!1);return g},"~N,~N,~N");c(c$,"setSymmetryMinMax",function(a){this.rminx>a.x&&(this.rminx=a.x);this.rminy>a.y&&(this.rminy=a.y);this.rminz>a.z&&(this.rminz=a.z);this.rmaxx<a.x&&(this.rmaxx=a.x);this.rmaxy<a.y&&(this.rmaxy=a.y);this.rmaxz<a.z&&(this.rmaxz=a.z)},"JU.P3");c(c$,"isInSymmetryRange",function(a){return a.x>=this.rminx&&a.y>=this.rminy&&a.z>=this.rminz&&
a.x<=this.rmaxx&&a.y<=this.rmaxy&&a.z<=this.rmaxz},"JU.P3");c(c$,"isWithinCell",function(a,b,d,g,c,f,j,k,l){return b.x>d-l&&b.x<g+l&&(2>a||b.y>c-l&&b.y<f+l)&&(3>a||b.z>j-l&&b.z<k+l)},"~N,JU.P3,~N,~N,~N,~N,~N,~N,~N");c(c$,"setAnisoBorU",function(a,b,d){this.haveAnisou=!0;a.anisoBorU=b;b[6]=d},"J.adapter.smarter.Atom,~A,~N");c(c$,"getAnisoBorU",function(a){return a.anisoBorU},"J.adapter.smarter.Atom");c(c$,"setTensors",function(){if(this.haveAnisou){this.getSymmetry();for(var a=this.getLastAtomSetAtomIndex();a<
this.atomCount;a++)this.atoms[a].addTensor(this.symmetry.getTensor(this.atoms[a].anisoBorU),null,!1)}});c(c$,"setLatticeOnly",function(a){this.checkLatticeOnly=a},"~B");c(c$,"setBaseSymmetryAtomCount",function(a){this.baseSymmetryAtomCount=a},"~N");c(c$,"applyAllSymmetry",function(a){if(0!=this.atomCount){this.noSymmetryCount=0==this.baseSymmetryAtomCount?this.getLastAtomSetAtomCount():this.baseSymmetryAtomCount;this.firstSymmetryAtom=this.getLastAtomSetAtomIndex();this.setTensors();this.bondCount0=
this.bondCount;this.finalizeSymmetry(this.symmetry);var b=this.symmetry.getSpaceGroupOperationCount();this.dtype=y(this.symmetry.getUnitCellInfoType(6));this.symmetry.setMinMaxLatticeParameters(this.minXYZ,this.maxXYZ);this.doCentroidUnitCell&&this.setAtomSetCollectionAuxiliaryInfo("centroidMinMax",[this.minXYZ.x,this.minXYZ.y,this.minXYZ.z,this.maxXYZ.x,this.maxXYZ.y,this.maxXYZ.z,this.centroidPacked?1:0]);if(null!=this.ptSupercell)switch(this.setAtomSetAuxiliaryInfo("supercell",this.ptSupercell),
this.dtype){case 3:this.minXYZ.z*=y(Math.abs(this.ptSupercell.z)),this.maxXYZ.z*=y(Math.abs(this.ptSupercell.z));case 2:this.minXYZ.y*=y(Math.abs(this.ptSupercell.y)),this.maxXYZ.y*=y(Math.abs(this.ptSupercell.y));case 1:this.minXYZ.x*=y(Math.abs(this.ptSupercell.x)),this.maxXYZ.x*=y(Math.abs(this.ptSupercell.x))}if(this.doCentroidUnitCell||this.doPackUnitCell||0!=this.symmetryRange&&1==this.maxXYZ.x-this.minXYZ.x&&1==this.maxXYZ.y-this.minXYZ.y&&1==this.maxXYZ.z-this.minXYZ.z)switch(this.minXYZ0=
JU.P3.new3(this.minXYZ.x,this.minXYZ.y,this.minXYZ.z),this.maxXYZ0=JU.P3.new3(this.maxXYZ.x,this.maxXYZ.y,this.maxXYZ.z),null!=a&&(a.setMinMax0(this.minXYZ0,this.maxXYZ0),this.minXYZ.set(y(this.minXYZ0.x),y(this.minXYZ0.y),y(this.minXYZ0.z)),this.maxXYZ.set(y(this.maxXYZ0.x),y(this.maxXYZ0.y),y(this.maxXYZ0.z))),this.dtype){case 3:this.minXYZ.z--,this.maxXYZ.z++;case 2:this.minXYZ.y--,this.maxXYZ.y++;case 1:this.minXYZ.x--,this.maxXYZ.x++}for(var d=(this.maxXYZ.x-this.minXYZ.x)*(this.maxXYZ.y-this.minXYZ.y)*
(this.maxXYZ.z-this.minXYZ.z),g=this.checkSpecial?this.noSymmetryCount*b*d:0<this.symmetryRange?this.noSymmetryCount*b:1,c=Array(g),f=0;f<this.noSymmetryCount;f++)this.atoms[f+this.firstSymmetryAtom].bsSymmetry=J.util.BSUtil.newBitSet(b*(d+1));var f=0,j=D(d,0);this.unitCellTranslations=Array(d);var k=d=0,l=Math.abs(this.symmetryRange),h=0!=this.symmetryRange,n=0>this.symmetryRange,q=0<this.symmetryRange;h&&(this.rminz=this.rminy=this.rminx=3.4028235E38,this.rmaxz=this.rmaxy=this.rmaxx=-3.4028235E38);
var v=this.symmetry,x=v;this.latticeOp=v.getLatticeOp();this.checkAll=1==this.atomSetCount&&this.checkSpecial&&0<=this.latticeOp;this.latticeOnly=this.checkLatticeOnly&&0<=this.latticeOp;var N=v.getSpaceGroupOperation(0);this.doPackUnitCell&&this.ptOffset.set(0,0,0);for(var G=this.minXYZ.x;G<this.maxXYZ.x;G++)for(var s=this.minXYZ.y;s<this.maxXYZ.y;s++)for(var p=this.minXYZ.z;p<this.maxXYZ.z;p++)if(this.unitCellTranslations[d]=JU.V3.new3(G,s,p),j[d++]=555+100*G+10*s+p,!(0!=G||0!=s||0!=p||0==c.length)){for(f=
0;f<this.noSymmetryCount;f++){k=this.atoms[this.firstSymmetryAtom+f];null!=a&&(v=a.getAtomSymmetry(k,this.symmetry),v!==x&&(0==v.getSpaceGroupOperationCount()&&this.finalizeSymmetry(x=v),N=v.getSpaceGroupOperation(0)));var r=JU.P3.newP(k);N.transform(r);v.toCartesian(r,!1);this.doPackUnitCell&&(v.toUnitCell(r,this.ptOffset),k.setT(r),v.toFractional(k,!1));k.bsSymmetry.set(d*b);k.bsSymmetry.set(0);h&&this.setSymmetryMinMax(r);f<g&&(c[f]=r)}n&&(this.rminx-=l,this.rminy-=l,this.rminz-=l,this.rmaxx+=
l,this.rmaxy+=l,this.rmaxz+=l);k=f=this.symmetryAddAtoms(this.firstSymmetryAtom,this.noSymmetryCount,0,0,0,0,f,d*b,c,a)}q&&(this.rminx-=l,this.rminy-=l,this.rminz-=l,this.rmaxx+=l,this.rmaxy+=l,this.rmaxz+=l);d=0;for(G=this.minXYZ.x;G<this.maxXYZ.x;G++)for(s=this.minXYZ.y;s<this.maxXYZ.y;s++)for(p=this.minXYZ.z;p<this.maxXYZ.z;p++)if(d++,0!=G||0!=s||0!=p)f=this.symmetryAddAtoms(this.firstSymmetryAtom,this.noSymmetryCount,G,s,p,k,f,d*b,c,a);d*this.noSymmetryCount==this.atomCount-this.firstSymmetryAtom&&
this.appendAtomProperties(d);this.setSymmetryOps();this.setAtomSetAuxiliaryInfo("presymmetryAtomIndex",Integer.$valueOf(this.firstSymmetryAtom));this.setAtomSetAuxiliaryInfo("presymmetryAtomCount",Integer.$valueOf(this.noSymmetryCount));this.setAtomSetAuxiliaryInfo("latticeDesignation",v.getLatticeDesignation());this.setAtomSetAuxiliaryInfo("unitCellRange",j);this.setAtomSetAuxiliaryInfo("unitCellTranslations",this.unitCellTranslations);this.notionalUnitCell=O(6,0);this.coordinatesAreFractional=!1;
this.setAtomSetAuxiliaryInfo("hasSymmetry",Boolean.TRUE);this.setGlobalBoolean(1)}},"J.adapter.smarter.MSInterface");c(c$,"finalizeSymmetry",function(a){var b=this.getAtomSetAuxiliaryInfoValue(-1,"spaceGroup");a.setFinalOperations(b,this.atoms,this.firstSymmetryAtom,this.noSymmetryCount,this.doNormalize);(null==b||b.equals("unspecified!"))&&this.setAtomSetSpaceGroupName(a.getSpaceGroupName())},"J.api.SymmetryInterface");c(c$,"setSymmetryOps",function(){var a=this.symmetry.getSpaceGroupOperationCount();
if(0<a){for(var b=Array(a),d=0;d<a;d++)b[d]=""+this.symmetry.getSpaceGroupXyz(d,this.doNormalize);this.setAtomSetAuxiliaryInfo("symmetryOperations",b)}this.setAtomSetAuxiliaryInfo("symmetryCount",Integer.$valueOf(a))});c(c$,"setCheckSpecial",function(a){this.checkSpecial=a},"~B");c(c$,"symmetryAddAtoms",function(a,b,d,g,c,f,j,k,l,h){var n=0==f,q=this.bondCount0>this.bondIndex0&&this.applySymmetryToBonds,v=q?D(b,0):null;this.doPackUnitCell&&this.ptOffset.set(d,g,c);var x=this.symmetryRange*this.symmetryRange,
N=0>this.symmetryRange,G=0<this.symmetryRange,s=n&&G,G=(new Boolean(G&!n)).valueOf(),p=this.symmetry.getSpaceGroupOperationCount();1==p&&(this.checkSpecial=!1);var r=N||G,t=this.checkSpecial||r,y=this.checkSpecial||s,u=this.symmetry;N&&(f=b);b=a+b;for(var N=new JU.P3,w=0;w<p;w++)if(!(n&&0==w||this.latticeOnly&&0<w&&w!=this.latticeOp)){for(var B=this.checkSpecial?j:G?f:0,A=a;A<b;A++)if(!this.atoms[A].ignoreSymmetry&&(null==this.bsAtoms||this.bsAtoms.get(A))){null!=h&&(u=h.getAtomSymmetry(this.atoms[A],
this.symmetry));u.newSpaceGroupPoint(w,this.atoms[A],N,d,g,c);var C=null,z=JU.P3.newP(N);u.toCartesian(z,!1);if(this.doPackUnitCell&&(u.toUnitCell(z,this.ptOffset),N.setT(z),u.toFractional(N,!1),!this.isWithinCell(this.dtype,N,this.minXYZ0.x,this.maxXYZ0.x,this.minXYZ0.y,this.maxXYZ0.y,this.minXYZ0.z,this.maxXYZ0.z,0.02)))continue;s&&this.setSymmetryMinMax(z);if(t){var E=3.4028235E38;if(r&&!this.isInSymmetryRange(z))continue;for(var F=this.checkAll?this.atomCount:B;0<=--F;){var H=z.distanceSquared(l[F]);
if(this.checkSpecial&&1E-4>H){C=this.atoms[a+F];if(null==C.atomName||C.atomName.equals(this.atoms[A].atomName))break;C=null}G&&(F<f&&H<E)&&(E=H)}if(G&&E>x)continue}F=this.atoms[A].atomSite;if(null!=C)q&&(v[F]=C.index),C.bsSymmetry.set(k+w),C.bsSymmetry.set(w);else if(q&&(v[F]=this.atomCount),C=this.newCloneAtom(this.atoms[A]),C.setT(N),C.atomSite=F,C.bsSymmetry=J.util.BSUtil.newAndSetBit(k+w),C.bsSymmetry.set(w),y&&(l[j++]=z),null!=this.atoms[A].tensors){C.tensors=null;for(F=this.atoms[A].tensors.size();0<=
--F;)z=this.atoms[A].tensors.get(F),null!=z&&(1==p?C.addTensor(z.copyTensor(),null,!1):this.addRotatedTensor(C,z,w,!1,u))}}if(q)for(B=this.bondIndex0;B<this.bondCount0;B++)A=this.bonds[B],C=this.atoms[A.atomIndex1],z=this.atoms[A.atomIndex2],null==C||null==z||(C=v[C.atomSite],z=v[z.atomSite],(C>=b||z>=b)&&this.addNewBondWithOrder(C,z,A.order))}return j},"~N,~N,~N,~N,~N,~N,~N,~N,~A,J.adapter.smarter.MSInterface");c(c$,"addRotatedTensor",function(a,b,d,g,c){null==this.ptTemp&&(this.ptTemp=new JU.P3,
this.mTemp=new JU.M3);return a.addTensor(J.api.Interface.getOptionInterface("util.Tensor").setFromEigenVectors(c.rotateAxes(d,b.eigenVectors,this.ptTemp,this.mTemp),b.eigenValues,b.isIsotropic?"iso":b.type,b.id),null,g)},"J.adapter.smarter.Atom,J.util.Tensor,~N,~B,J.api.SymmetryInterface");c(c$,"applySymmetryBio",function(a,b,d,g){if(null!=this.latticeCells&&0!=this.latticeCells[0])J.util.Logger.error("Cannot apply biomolecule when lattice cells are indicated");else{var c=0<=g.indexOf("BYCHAIN")?
1:0<=g.indexOf("BYSYMOP")?2:0;this.doNormalize=!1;this.symmetry=null;var f=a.get("biomts");if(!(2>f.size())){Float.isNaN(b[0])||this.setNotionalUnitCell(b,null,this.unitCellOffset);this.getSymmetry().setSpaceGroup(this.doNormalize);this.addSpaceGroupOperation("x,y,z");a=a.get("name");this.setAtomSetSpaceGroupName(a);a=f.size();this.applySymmetryToBonds=d;this.bondCount0=this.bondCount;b=(d=this.bondCount0>this.bondIndex0&&d)?D(this.atomCount,0):null;this.firstSymmetryAtom=this.getLastAtomSetAtomIndex();
var j=this.atomCount,k=new java.util.Hashtable,l=0;switch(c){case 1:for(c=j;--c>=this.firstSymmetryAtom;){var h=Integer.$valueOf(this.atoms[c].chainID),n=k.get(h);null==n&&(l++,k.put(h,n=new JU.BS));n.set(c)}this.bsAtoms=new JU.BS;for(c=0;c<l;c++)this.bsAtoms.set(j+c),h=new J.adapter.smarter.Atom,h.set(0,0,0),h.radius=16,this.addAtom(h);for(var q=0,v,k=k.entrySet().iterator();k.hasNext()&&((v=k.next())||1);){h=this.atoms[j+q++];n=v.getValue();for(c=n.nextSetBit(0);0<=c;c=n.nextSetBit(c+1))h.add(this.atoms[c]);
h.scale(1/n.cardinality());h.atomName="Pt"+q;h.chainID=v.getKey().intValue()}this.firstSymmetryAtom=j;j+=l;break;case 2:this.bsAtoms=new JU.BS;this.bsAtoms.set(j);h=this.atoms[j]=new J.adapter.smarter.Atom;h.set(0,0,0);for(c=j;--c>=this.firstSymmetryAtom;)h.add(this.atoms[c]);h.scale(1/(j-this.firstSymmetryAtom));h.atomName="Pt";h.radius=16;this.firstSymmetryAtom=j++}0<=g.indexOf("#<")&&(a=Math.min(a,JU.PT.parseInt(g.substring(g.indexOf("#<")+2))-1),g=JU.PT.simpleReplace(g,"#<","_<"));for(v=this.firstSymmetryAtom;v<
j;v++)this.atoms[v].bsSymmetry=J.util.BSUtil.newAndSetBit(0);for(c=1;c<a;c++){if(0<=g.indexOf("!#")){if(0<=g.indexOf("!#"+(c+1)+";"))continue}else if(0<=g.indexOf("#")&&0>g.indexOf("#"+(c+1)+";"))continue;l=f.get(c);for(v=this.firstSymmetryAtom;v<j;v++)if(null==this.bsAtoms||this.bsAtoms.get(v))try{var x=this.atoms[v].atomSite,N;d&&(b[x]=this.atomCount);N=this.newCloneAtom(this.atoms[v]);null!=this.bsAtoms&&this.bsAtoms.set(N.index);N.atomSite=x;l.transform(N);N.bsSymmetry=J.util.BSUtil.newAndSetBit(c);
if(d)for(var G=this.bondIndex0;G<this.bondCount0;G++){var s=this.bonds[G],p=b[this.atoms[s.atomIndex1].atomSite],r=b[this.atoms[s.atomIndex2].atomSite];(p>=j||r>=j)&&this.addNewBondWithOrder(p,r,s.order)}}catch(t){if(C(t,Exception))this.errorMessage="appendAtomCollection error: "+t;else throw t;}0<c&&this.symmetry.addBioMoleculeOperation(l,!1)}this.noSymmetryCount=j-this.firstSymmetryAtom;this.setAtomSetAuxiliaryInfo("presymmetryAtomIndex",Integer.$valueOf(this.firstSymmetryAtom));this.setAtomSetAuxiliaryInfo("presymmetryAtomCount",
Integer.$valueOf(this.noSymmetryCount));this.setAtomSetAuxiliaryInfo("biosymmetryCount",Integer.$valueOf(a));this.setAtomSetAuxiliaryInfo("biosymmetry",this.symmetry);this.finalizeSymmetry(this.symmetry);this.setSymmetryOps();this.symmetry=null;this.coordinatesAreFractional=!1;this.setAtomSetAuxiliaryInfo("hasSymmetry",Boolean.TRUE);this.setGlobalBoolean(1)}}},"java.util.Map,~A,~B,~S");c(c$,"mapMostRecentAtomName",function(){if(0<this.atomCount){var a=this.atomCount-1,b=this.atoms[a].atomName;null!=
b&&this.atomSymbolicMap.put(b,Integer.$valueOf(a))}});c(c$,"clearSymbolicMap",function(){this.atomSymbolicMap.clear();this.haveMappedSerials=!1});c(c$,"mapMostRecentAtomSerialNumber",function(){if(0!=this.atomCount){var a=this.atomCount-1,b=this.atoms[a].atomSerial;-2147483648!=b&&this.atomSymbolicMap.put(Integer.$valueOf(b),Integer.$valueOf(a));this.haveMappedSerials=!0}});c(c$,"createAtomSerialMap",function(){if(!(this.haveMappedSerials||0>this.currentAtomSetIndex)){for(var a=this.getLastAtomSetAtomCount();a<
this.atomCount;a++){var b=this.atoms[a].atomSerial;-2147483648!=b&&this.atomSymbolicMap.put(Integer.$valueOf(b),Integer.$valueOf(a))}this.haveMappedSerials=!0}});c(c$,"getAtomIndexFromName",function(a){return this.getMapIndex(a)},"~S");c(c$,"getAtomIndexFromSerial",function(a){return this.getMapIndex(Integer.$valueOf(a))},"~N");c(c$,"getMapIndex",function(a){a=this.atomSymbolicMap.get(a);return null==a?-1:a.intValue()},"~O");c(c$,"setAtomSetCollectionAuxiliaryInfo",function(a,b){null==b?this.atomSetCollectionAuxiliaryInfo.remove(a):
this.atomSetCollectionAuxiliaryInfo.put(a,b)},"~S,~O");c(c$,"setAtomSetCollectionPartialCharges",function(a){if(!this.atomSetCollectionAuxiliaryInfo.containsKey(a))return!1;for(var b=this.atomSetCollectionAuxiliaryInfo.get(a),d=b.size();0<=--d;)this.atoms[d].partialCharge=b.get(d).floatValue();J.util.Logger.info("Setting partial charges type "+a);return!0},"~S");c(c$,"mapPartialCharge",function(a,b){this.atoms[this.getAtomIndexFromName(a)].partialCharge=b},"~S,~N");c(c$,"getAtomSetCollectionAuxiliaryInfo",
function(a){return this.atomSetCollectionAuxiliaryInfo.get(a)},"~S");c(c$,"addTrajectoryStep",function(){for(var a=Array(this.atomCount),b=0<this.atomCount&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),d=b?Array(this.atomCount):null,g=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0;c<this.atomCount;c++){var f=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=g&&(f=J.adapter.smarter.AtomSetCollection.fixPeriodic(f,g[c]));a[c]=f;b&&(d[c]=this.atoms[c].vib)}if(b){if(null==
this.vibrationSteps){this.vibrationSteps=new JU.List;for(c=0;c<this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(d)}this.trajectorySteps.addLast(a);this.trajectoryStepCount++});c$.fixPeriodic=c(c$,"fixPeriodic",function(a,b){a.x=J.adapter.smarter.AtomSetCollection.fixPoint(a.x,b.x);a.y=J.adapter.smarter.AtomSetCollection.fixPoint(a.y,b.y);a.z=J.adapter.smarter.AtomSetCollection.fixPoint(a.z,b.z);return a},"JU.P3,JU.P3");c$.fixPoint=c(c$,"fixPoint",function(a,
b){for(;0.9<a-b;)a-=1;for(;-0.9>a-b;)a+=1;return a},"~N,~N");c(c$,"finalizeTrajectoryAs",function(a,b){this.trajectorySteps=a;this.vibrationSteps=b;this.trajectoryStepCount=a.size();this.finalizeTrajectory()},"JU.List,JU.List");c(c$,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),b=null==this.vibrationSteps?null:this.vibrationSteps.get(0),d=new JU.V3;if(null!=this.vibrationSteps&&null!=b&&b.length<this.atomCount||a.length<this.atomCount)this.errorMessage=
"File cannot be loaded as a trajectory";else{for(var g=0;g<this.atomCount;g++)null!=this.vibrationSteps&&(this.atoms[g].vib=null==b?d:b[g]),null!=a[g]&&this.atoms[g].setT(a[g]);this.setAtomSetCollectionAuxiliaryInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setAtomSetCollectionAuxiliaryInfo("vibrationSteps",this.vibrationSteps)}}});c(c$,"newAtomSet",function(){this.newAtomSetClear(!0)});c(c$,"newAtomSetClear",function(a){!this.allowMultiple&&0<=this.currentAtomSetIndex&&
this.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.discardPreviousAtoms();this.currentAtomSetIndex=this.atomSetCount++;this.atomSetCount>this.atomSetNumbers.length&&(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));this.atomSetAtomIndexes[this.currentAtomSetIndex]=
this.atomCount;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?this.atomSetNumbers[this.currentAtomSetIndex+this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:this.atomSetNumbers[this.currentAtomSetIndex]=this.atomSetCount;a&&this.atomSymbolicMap.clear();this.setAtomSetAuxiliaryInfo("title",this.collectionName)},"~B");c(c$,"getAtomSetAtomIndex",function(a){return this.atomSetAtomIndexes[a]},
"~N");c(c$,"getAtomSetAtomCount",function(a){return this.atomSetAtomCounts[a]},"~N");c(c$,"getAtomSetBondCount",function(a){return this.atomSetBondCounts[a]},"~N");c(c$,"setAtomSetName",function(a){this.isTrajectory?this.setTrajectoryName(a):(this.setAtomSetAuxiliaryInfoForSet("name",a,this.currentAtomSetIndex),this.allowMultiple||this.setCollectionName(a))},"~S");c(c$,"setTrajectoryName",function(a){if(0!=this.trajectoryStepCount){null==this.trajectoryNames&&(this.trajectoryNames=new JU.List);for(var b=
this.trajectoryNames.size();b<this.trajectoryStepCount;b++)this.trajectoryNames.addLast(null);this.trajectoryNames.set(this.trajectoryStepCount-1,a)}},"~S");c(c$,"setAtomSetNames",function(a,b,d){for(var g=this.currentAtomSetIndex;0<=--b&&0<=g;--g)(null==d||!d.get(g))&&this.setAtomSetAuxiliaryInfoForSet("name",a,g)},"~S,~N,JU.BS");c(c$,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.currentAtomSetIndex+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(c$,"setAtomSetNumber",
function(a,b){this.atomSetNumbers[a]=b},"~N,~N");c(c$,"setAtomSetModelProperty",function(a,b){this.setAtomSetModelPropertyForSet(a,b,this.currentAtomSetIndex)},"~S,~S");c(c$,"setAtomSetModelPropertyForSet",function(a,b,d){var g=this.getAtomSetAuxiliaryInfoValue(d,"modelProperties");null==g&&this.setAtomSetAuxiliaryInfoForSet("modelProperties",g=new java.util.Properties,d);g.put(a,b)},"~S,~S,~N");c(c$,"setAtomSetAtomProperty",function(a,b,d){b.endsWith("\n")||(b+="\n");0>d&&(d=this.currentAtomSetIndex);
var g=this.getAtomSetAuxiliaryInfoValue(d,"atomProperties");null==g&&this.setAtomSetAuxiliaryInfoForSet("atomProperties",g=new java.util.Hashtable,d);g.put(a,b)},"~S,~S,~N");c(c$,"appendAtomProperties",function(a){var b=this.getAtomSetAuxiliaryInfoValue(-1,"atomProperties");if(null!=b)for(var d,g=b.entrySet().iterator();g.hasNext()&&((d=g.next())||1);){for(var c=d.getKey(),f=d.getValue(),j=new JU.SB,k=a;0<=--k;)j.append(f);b.put(c,j.toString())}},"~N");c(c$,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.currentAtomSetIndex].containsKey(a))return!1;
a=this.getAtomSetAuxiliaryInfoValue(this.currentAtomSetIndex,a);for(var b=a.size();0<=--b;)this.atoms[b].partialCharge=a.get(b).floatValue();return!0},"~S");c(c$,"getAtomSetAuxiliaryInfoValue",function(a,b){return this.atomSetAuxiliaryInfo[0<=a?a:this.currentAtomSetIndex].get(b)},"~N,~S");c(c$,"setAtomSetAuxiliaryInfo",function(a,b){this.setAtomSetAuxiliaryInfoForSet(a,b,this.currentAtomSetIndex)},"~S,~O");c(c$,"setAtomSetAuxiliaryInfoForSet",function(a,b,d){0>d||(null==this.atomSetAuxiliaryInfo[d]&&
(this.atomSetAuxiliaryInfo[d]=new java.util.Hashtable),null==b?this.atomSetAuxiliaryInfo[d].remove(a):this.atomSetAuxiliaryInfo[d].put(a,b))},"~S,~O,~N");c(c$,"setAtomSetPropertyForSets",function(a,b,d){for(var g=this.currentAtomSetIndex;0<=--d&&0<=g;--g)this.setAtomSetModelPropertyForSet(a,b,g)},"~S,~S,~N");c(c$,"cloneLastAtomSetProperties",function(){this.cloneAtomSetProperties(this.currentAtomSetIndex-1)});c(c$,"cloneAtomSetProperties",function(a){a=this.getAtomSetAuxiliaryInfoValue(a,"modelProperties");
null!=a&&this.setAtomSetAuxiliaryInfoForSet("modelProperties",a.clone(),this.currentAtomSetIndex)},"~N");c(c$,"getAtomSetNumber",function(a){return this.atomSetNumbers[a>=this.atomSetCount?0:a]},"~N");c(c$,"getAtomSetName",function(a){if(null!=this.trajectoryNames&&a<this.trajectoryNames.size())return this.trajectoryNames.get(a);a>=this.atomSetCount&&(a=this.atomSetCount-1);return this.getAtomSetAuxiliaryInfoValue(a,"name")},"~N");c(c$,"getAtomSetAuxiliaryInfo",function(a){return this.atomSetAuxiliaryInfo[a>=
this.atomSetCount?this.atomSetCount-1:a]},"~N");c(c$,"setAtomNames",function(a){if(null==a)return null;for(var b,d=0;d<this.atomCount;d++)if(null!=(b=a.getProperty(this.atoms[d].atomName)))this.atoms[d].atomName=b;return null},"java.util.Properties");c(c$,"setAtomSetEnergy",function(a,b){0>this.currentAtomSetIndex||(J.util.Logger.info("Energy for model "+(this.currentAtomSetIndex+1)+" = "+a),this.setAtomSetAuxiliaryInfo("EnergyString",a),this.setAtomSetAuxiliaryInfo("Energy",Float.$valueOf(b)),this.setAtomSetModelProperty("Energy",
""+b))},"~S,~N");c(c$,"setAtomSetFrequency",function(a,b,d,g){d+=" "+(null==g?"cm^-1":g);g=(null==b?"":b+" ")+d;this.setAtomSetName(g);this.setAtomSetModelProperty("Frequency",d);null!=b&&this.setAtomSetModelProperty("FrequencyLabel",b);this.setAtomSetModelProperty(".PATH",(null==a?"":a+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+"Frequencies")+"Frequencies");return g},"~S,~S,~S,~S");c(c$,"toCartesian",function(a){for(var b=this.getLastAtomSetAtomIndex();b<this.atomCount;b++)a.toCartesian(this.atoms[b],
!0)},"J.api.SymmetryInterface");c(c$,"getBondList",function(){for(var a=Array(this.bondCount),b=0;b<this.bondCount;b++)a[b]=[this.atoms[this.bonds[b].atomIndex1].atomName,this.atoms[this.bonds[b].atomIndex2].atomName,""+this.bonds[b].order];return a});c(c$,"centralize",function(){for(var a=new JU.P3,b=0;b<this.atomSetCount;b++){var d=this.atomSetAtomCounts[b],g=this.atomSetAtomIndexes[b];a.set(0,0,0);for(var c=g+d;--c>=g;)a.add(this.atoms[c]);a.scale(1/d);for(c=g+d;--c>=g;)this.atoms[c].sub(a)}});
c(c$,"mergeTrajectories",function(a){if(this.isTrajectory&&a.isTrajectory&&null==this.vibrationSteps){for(var b=0;b<a.trajectoryStepCount;b++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(b));this.setAtomSetCollectionAuxiliaryInfo("trajectorySteps",this.trajectorySteps)}},"J.adapter.smarter.AtomSetCollection");E(c$,"globalBooleans",["someModelsHaveFractionalCoordinates","someModelsHaveSymmetry","someModelsHaveUnitcells","someModelsHaveCONECT","isPDB"],"GLOBAL_FRACTCOORD",
0,"GLOBAL_SYMMETRY",1,"GLOBAL_UNITCELLS",2,"GLOBAL_CONECT",3,"GLOBAL_ISPDB",4,"notionalUnitcellTags","a b c alpha beta gamma".split(" "),"PARTICLE_NONE",0,"PARTICLE_CHAIN",1,"PARTICLE_SYMOP",2)}),p("J.adapter.smarter"),t(["JU.SB"],"J.adapter.smarter.AtomSetCollectionReader","java.io.BufferedReader java.lang.Boolean $.Character $.Float JU.BS $.List $.M3 $.P3 $.PT $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter $.JmolDocument J.util.BSUtil $.Logger $.Parser $.Quaternion".split(" "),
function(){c$=w(function(){this.isBinary=!1;this.next=this.prevline=this.line=this.trajectorySteps=this.htParams=this.readerName=this.doc=this.reader=this.atomSetCollection=null;this.ptLine=0;this.latticeCells=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=this.doProcessLines=!1;this.continuing=!0;this.viewer=null;this.isSequential=this.getHeader=this.doCheckUnitCell=this.applySymmetryToBonds=this.isTrajectory=this.ignoreFileSymmetryOperators=this.doApplySymmetry=!1;this.vibrationNumber=this.modelNumber=
this.templateAtomCount=0;this.desiredVibrationNumber=-2147483648;this.bsModels=null;this.havePartialChargeFilter=!1;this.calculationType="?";this.spaceGroup=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=!1;this.notionalUnitCell=null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=this.strSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=
this.doConvertToFractional=!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;this.desiredSpaceGroupIndex=-1;this.unitCellOffset=this.fileOffsetFractional=this.fileOffset=this.fileScaling=null;this.unitCellOffsetFractional=!1;this.fileName=this.filePath=null;this.stateScriptVersionInt=2147483647;this.haveModel=!1;this.previousUnitCell=this.previousSpaceGroup=null;this.nMatrixElements=0;this.filter=this.bsFilter=this.matUnitCellOrientation=null;this.filterAtomType=this.filterAtomName=
this.filterChain=this.filterGroup3=this.filterAltLoc=this.haveAtomFilter=!1;this.filterAtomTypeStr=null;this.filterAtomNameTerminator=";";this.filterEveryNth=this.filterHetero=this.filterElement=!1;this.nFiltered=this.filterN=0;this.reverseModels=this.doReadMolecularOrbitals=this.useAltNames=this.addVibrations=this.doCentralize=this.doSetOrientation=!1;this.nameRequired=null;this.centroidPacked=this.doCentroidUnitCell=!1;this.siteScript=this.previousScript=this.ms=this.matrixRotate=this.filter2=this.filter1=
null;u(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader");Q(c$,function(){this.next=D(1,0);this.loadNote=new JU.SB});c(c$,"setup",function(a,b,d){this.setupASCR(a,b,d)},"~S,java.util.Map,~O");c(c$,"setupASCR",function(a,b,d){null!=a&&(this.htParams=b,this.filePath=a.$replace("\\","/"),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+1),r(d,java.io.BufferedReader)?this.reader=d:r(d,J.api.JmolDocument)&&(this.doc=d))},"~S,java.util.Map,~O");c(c$,"readData",function(){this.initialize();
this.atomSetCollection=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);try{this.initializeReader();if(null==this.doc)for(null==this.line&&this.continuing&&this.readLine();null!=this.line&&this.continuing;)this.checkLine()&&this.readLine();else this.doc.setOutputChannel(this.out),this.processBinaryDocument(this.doc);this.finalizeReader()}catch(a){J.util.Logger.info("Reader error: "+a),this.viewer.isJS||a.printStackTrace(),this.setError(a)}null!=this.reader&&this.reader.close();
null!=this.doc&&this.doc.close();return this.finish()});c(c$,"fixBaseIndices",function(){try{var a=this.htParams.get("baseAtomIndex").intValue(),b=this.htParams.get("baseModelIndex").intValue(),a=a+this.atomSetCollection.getAtomCount(),b=b+this.atomSetCollection.getAtomSetCount();this.htParams.put("baseAtomIndex",Integer.$valueOf(a));this.htParams.put("baseModelIndex",Integer.$valueOf(b))}catch(d){if(!C(d,Exception))throw d;}});c(c$,"readDataObject",function(a){this.initialize();this.atomSetCollection=
new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(c$,"processDOM",function(){},"~O");c(c$,"processBinaryDocument",function(){},"J.api.JmolDocument");c(c$,"initializeReader",function(){});c(c$,"checkLine",function(){return!0});c(c$,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=!1;this.doProcessLines=!1;return!0});c(c$,"isLastModel",function(a){return 0<
this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(c$,"appendLoadNote",function(a){this.loadNote.append(a).append("\n");J.util.Logger.info(a);return a},"~S");c(c$,"initializeTrajectoryFile",function(){this.atomSetCollection.addAtom(new J.adapter.smarter.Atom);this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=new JU.List)});c(c$,"finalizeReader",function(){this.finalizeReaderASCR()});c(c$,"finalizeReaderASCR",
function(){this.applySymmetryAndSetTrajectory();this.setLoadNote();this.atomSetCollection.finalizeStructures();this.doCentralize&&this.atomSetCollection.centralize()});c(c$,"setLoadNote",function(){0<this.loadNote.length()&&this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("modelLoadNote",this.loadNote.toString())});c(c$,"setIsPDB",function(){this.atomSetCollection.setGlobalBoolean(4);this.atomSetCollection.setAtomSetAuxiliaryInfo("isPDB",Boolean.TRUE);null!=this.htParams.get("pdbNoHydrogens")&&
this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("pdbNoHydrogens",this.htParams.get("pdbNoHydrogens"));this.checkFilterKey("ADDHYDROGENS")&&this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("pdbAddHydrogens",Boolean.TRUE)});c(c$,"finish",function(){var a=this.htParams.get("loadState");this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("loadState",null==a?"":a);a=this.htParams.get("smilesString");null!=a&&this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("smilesString",
a);this.htParams.containsKey("templateAtomCount")||this.htParams.put("templateAtomCount",Integer.$valueOf(this.atomSetCollection.getAtomCount()));this.htParams.containsKey("bsFilter")&&this.htParams.put("filteredAtomCount",Integer.$valueOf(J.util.BSUtil.cardinalityOf(this.htParams.get("bsFilter"))));this.calculationType.equals("?")||this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("calculationType",this.calculationType);var b=a=this.atomSetCollection.getFileTypeName();0<=b.indexOf("(")&&(b=
b.substring(0,b.indexOf("(")));for(var d=this.atomSetCollection.getAtomSetCount();0<=--d;)this.atomSetCollection.setAtomSetAuxiliaryInfoForSet("fileName",this.filePath,d),this.atomSetCollection.setAtomSetAuxiliaryInfoForSet("fileType",b,d);this.atomSetCollection.freeze(this.reverseModels);if(null!=this.atomSetCollection.errorMessage)return this.atomSetCollection.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if(0==(null==this.atomSetCollection.bsAtoms?this.atomSetCollection.getAtomCount():this.atomSetCollection.bsAtoms.cardinality())&&
0>b.indexOf("DataOnly")&&null==this.atomSetCollection.getAtomSetCollectionAuxiliaryInfo("dataOnly"))return"No atoms found\nfor file "+this.filePath+"\ntype "+a;this.fixBaseIndices();return this.atomSetCollection});c(c$,"setError",function(a){var b;b=a.getMessage?a.getMessage():a.toString();this.atomSetCollection.errorMessage=null==this.line?"Error reading file at end of file \n"+b:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+b;this.viewer.isJS||a.printStackTrace()},"Throwable");
c(c$,"initialize",function(){var a=this.htParams.get("supercell");r(a,String)?this.strSupercell=a:this.ptSupercell=a;this.initializeSymmetry();this.viewer=this.htParams.remove("viewer");this.htParams.containsKey("stateScriptVersionInt")&&(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());this.merging=this.htParams.containsKey("merging");this.getHeader=this.htParams.containsKey("getHeader");this.isSequential=this.htParams.containsKey("isSequential");this.readerName=
this.htParams.get("readerName");this.htParams.containsKey("outputChannel")&&(this.out=this.htParams.get("outputChannel"));this.htParams.containsKey("vibrationNumber")?this.desiredVibrationNumber=this.htParams.get("vibrationNumber").intValue():this.htParams.containsKey("modelNumber")&&(this.desiredModelNumber=this.htParams.get("modelNumber").intValue());this.applySymmetryToBonds=this.htParams.containsKey("applySymmetryToBonds");this.bsFilter=this.htParams.get("bsFilter");this.setFilter(null);a=this.htParams.containsKey("ptFile")?
this.htParams.get("ptFile").intValue():-1;this.isTrajectory=this.htParams.containsKey("isTrajectory");0<a&&this.htParams.containsKey("firstLastSteps")?(a=this.htParams.get("firstLastSteps").get(a-1),r(a,JU.BS)?this.bsModels=a:this.firstLastStep=a):this.htParams.containsKey("firstLastStep")?this.firstLastStep=this.htParams.get("firstLastStep"):this.htParams.containsKey("bsModels")&&(this.bsModels=this.htParams.get("bsModels"));this.htParams.containsKey("templateAtomCount")&&(this.templateAtomCount=
this.htParams.get("templateAtomCount").intValue());if(null!=this.bsModels||null!=this.firstLastStep)this.desiredModelNumber=-2147483648;if(null==this.bsModels&&null!=this.firstLastStep){0>this.firstLastStep[0]&&(this.firstLastStep[0]=0);if(0==this.firstLastStep[2]||this.firstLastStep[1]<this.firstLastStep[0])this.firstLastStep[1]=-1;1>this.firstLastStep[2]&&(this.firstLastStep[2]=1);this.bsModels=J.util.BSUtil.newAndSetBit(this.firstLastStep[0]);if(this.firstLastStep[1]>this.firstLastStep[0])for(a=
this.firstLastStep[0];a<=this.firstLastStep[1];a+=this.firstLastStep[2])this.bsModels.set(a)}if(null!=this.bsModels&&(null==this.firstLastStep||-1!=this.firstLastStep[1]))this.lastModelNumber=this.bsModels.length();this.symmetryRange=this.htParams.containsKey("symmetryRange")?this.htParams.get("symmetryRange").floatValue():0;this.initializeSymmetryOptions();this.htParams.containsKey("spaceGroupIndex")&&(this.desiredSpaceGroupIndex=this.htParams.get("spaceGroupIndex").intValue(),-2==this.desiredSpaceGroupIndex&&
(this.spaceGroup=this.htParams.get("spaceGroupName")),this.ignoreFileSpaceGroupName=-2==this.desiredSpaceGroupIndex||0<=this.desiredSpaceGroupIndex,this.ignoreFileSymmetryOperators=-1!=this.desiredSpaceGroupIndex);this.htParams.containsKey("unitCellOffset")&&(this.fileScaling=JU.P3.new3(1,1,1),this.fileOffset=this.htParams.get("unitCellOffset"),this.fileOffsetFractional=JU.P3.newP(this.fileOffset),this.unitCellOffsetFractional=this.htParams.containsKey("unitCellOffsetFractional"));this.htParams.containsKey("unitcell")&&
(a=this.htParams.get("unitcell"),this.merging&&this.setFractionalCoordinates(!0),9==a.length?(this.addPrimitiveLatticeVector(0,a,0),this.addPrimitiveLatticeVector(1,a,3),this.addPrimitiveLatticeVector(2,a,6)):this.setUnitCell(a[0],a[1],a[2],a[3],a[4],a[5]),this.ignoreFileUnitCell=this.iHaveUnitCell,this.merging&&!this.iHaveUnitCell&&this.setFractionalCoordinates(!1))});c(c$,"initializeSymmetryOptions",function(){this.latticeCells=D(3,0);var a=this.htParams.get("lattice");this.forcePacked&&null==a&&
(a=JU.P3.new3(1,1,1));if(null!=a){this.latticeCells[0]=y(a.x);this.latticeCells[1]=y(a.y);this.latticeCells[2]=y(a.z);if((this.doCentroidUnitCell=this.htParams.containsKey("centroid"))&&(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.htParams.containsKey("packed");this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2])}this.doApplySymmetry=0<this.latticeCells[0]&&0<this.latticeCells[1];
this.doApplySymmetry||(this.latticeCells[0]=0,this.latticeCells[1]=0,this.latticeCells[2]=0)});c(c$,"doGetModel",function(a,b){if(null!=b&&null!=this.nameRequired&&0<this.nameRequired.length&&0>b.toUpperCase().indexOf(this.nameRequired))return!1;var d=null==this.bsModels?1>this.desiredModelNumber||a==this.desiredModelNumber:a>this.lastModelNumber?!1:0<a&&this.bsModels.get(a-1)||this.haveModel&&null!=this.firstLastStep&&0>this.firstLastStep[1]&&(2>this.firstLastStep[2]||0==(a-1-this.firstLastStep[0])%
this.firstLastStep[2]);d&&0==this.desiredModelNumber&&this.atomSetCollection.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|d)).valueOf();d&&(this.doProcessLines=!0);return d},"~N,~S");c(c$,"initializeSymmetry",function(){this.previousSpaceGroup=this.spaceGroup;this.previousUnitCell=this.notionalUnitCell;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.notionalUnitCell=O(25,0);for(var a=25;0<=--a;)this.notionalUnitCell[a]=NaN;null!=this.ptSupercell&&
(this.notionalUnitCell[22]=Math.max(1,y(this.ptSupercell.x)),this.notionalUnitCell[23]=Math.max(1,y(this.ptSupercell.y)),this.notionalUnitCell[24]=Math.max(1,y(this.ptSupercell.z)));this.symmetry=null}this.ignoreFileSpaceGroupName||(this.spaceGroup="unspecified!");this.doCheckUnitCell=!1});c(c$,"newAtomSet",function(a){0<=this.atomSetCollection.getCurrentAtomSetIndex()?(this.atomSetCollection.newAtomSet(),this.atomSetCollection.setCollectionName("<collection of "+(this.atomSetCollection.getCurrentAtomSetIndex()+
1)+" models>")):this.atomSetCollection.setCollectionName(a);this.atomSetCollection.setAtomSetAuxiliaryInfoForSet("name",a,Math.max(0,this.atomSetCollection.getCurrentAtomSetIndex()))},"~S");c(c$,"cloneLastAtomSet",function(a,b){var d=this.atomSetCollection.getLastAtomSetAtomCount();this.atomSetCollection.cloneLastAtomSetFromPoints(a,b);this.atomSetCollection.haveUnitCell&&(this.doCheckUnitCell=this.iHaveUnitCell=!0,this.spaceGroup=this.previousSpaceGroup,this.notionalUnitCell=this.previousUnitCell);
return d},"~N,~A");c(c$,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||(this.spaceGroup=a.trim(),J.util.Logger.info("Setting space group name to "+this.spaceGroup))},"~S");c(c$,"setSymmetryOperator",function(a){if(this.ignoreFileSymmetryOperators)return-1;this.setLatticeCells(!1);var b=this.atomSetCollection.addSpaceGroupOperation(a);0>b&&J.util.Logger.warn("Skipping symmetry operation "+a);this.iHaveSymmetryOperators=!0;return b},"~S");c(c$,"initializeCartesianToFractional",function(){for(var a=
0;16>a;a++)if(!Float.isNaN(this.notionalUnitCell[6+a]))return;for(a=0;16>a;a++)this.notionalUnitCell[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(c$,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=6;22>a;a++)this.notionalUnitCell[a]=NaN;this.checkUnitCell(6)}});c(c$,"setUnitCellItem",function(a,b){if(!this.ignoreFileUnitCell&&!(0==a&&1==b||3==a&&0==b))!Float.isNaN(b)&&(6<=a&&Float.isNaN(this.notionalUnitCell[6]))&&this.initializeCartesianToFractional(),this.notionalUnitCell[a]=b,J.util.Logger.debugging&&
J.util.Logger.debug("setunitcellitem "+a+" "+b),6>a||Float.isNaN(b)?this.iHaveUnitCell=this.checkUnitCell(6):12==++this.nMatrixElements&&this.checkUnitCell(22)},"~N,~N");c(c$,"setUnitCell",function(a,b,d,g,c,f){this.ignoreFileUnitCell||(this.clearUnitCell(),this.notionalUnitCell[0]=a,this.notionalUnitCell[1]=b,this.notionalUnitCell[2]=d,0!=g&&(this.notionalUnitCell[3]=g),0!=c&&(this.notionalUnitCell[4]=c),0!=f&&(this.notionalUnitCell[5]=f),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");
c(c$,"addPrimitiveLatticeVector",function(a,b,d){if(!this.ignoreFileUnitCell){if(0==a)for(var g=0;6>g;g++)this.notionalUnitCell[g]=0;a=6+3*a;this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a]=b[d];if(Float.isNaN(this.notionalUnitCell[0]))for(a=0;6>a;a++)this.notionalUnitCell[a]=-1;this.iHaveUnitCell=this.checkUnitCell(15)}},"~N,~A,~N");c(c$,"checkUnitCell",function(a){for(var b=0;b<a;b++)if(Float.isNaN(this.notionalUnitCell[b]))return!1;this.getSymmetry().setUnitCell(this.notionalUnitCell);
this.doApplySymmetry&&(this.doConvertToFractional=!this.fileCoordinatesAreFractional);this.checkUnitCellOffset();return!0},"~N");c(c$,"checkUnitCellOffset",function(){null==this.symmetry||null==this.fileOffsetFractional||(this.fileOffset.setT(this.fileOffsetFractional),this.unitCellOffsetFractional!=this.fileCoordinatesAreFractional&&(this.unitCellOffsetFractional?this.symmetry.toCartesian(this.fileOffset,!1):this.symmetry.toFractional(this.fileOffset,!1)))});c(c$,"getSymmetry",function(){return this.symmetry=
J.api.Interface.getOptionInterface("symmetry.Symmetry")});c(c$,"setFractionalCoordinates",function(a){this.iHaveFractionalCoordinates=this.fileCoordinatesAreFractional=a;this.checkUnitCellOffset()},"~B");c(c$,"setFilterAtomTypeStr",function(a){this.filterAtomTypeStr=a;this.filterAtomNameTerminator="\x00"},"~S");c(c$,"setFilter",function(a){null==a?a=this.htParams.get("filter"):this.bsFilter=null;null!=a&&(a=a.toUpperCase());this.filter=a;this.doSetOrientation=!this.checkFilterKey("NOORIENT");this.doCentralize=
!this.checkFilterKey("NOCENTER")&&this.checkFilterKey("CENTER");this.addVibrations=!this.checkFilterKey("NOVIB");this.doReadMolecularOrbitals=!this.checkFilterKey("NOMO");this.useAltNames=this.checkFilterKey("ALTNAME");this.reverseModels=this.checkFilterKey("REVERSEMODELS");this.checkFilterKey("NAME=")&&(this.nameRequired=this.filter.substring(this.filter.indexOf("NAME=")+5),this.nameRequired.startsWith("'")?this.nameRequired=JU.PT.split(this.nameRequired,"'")[1]:this.nameRequired.startsWith('"')&&
(this.nameRequired=JU.PT.split(this.nameRequired,'"')[1]),this.filter=JU.PT.simpleReplace(this.filter,this.nameRequired,""),this.filter=JU.PT.simpleReplace(this.filter,"NAME=",""));if(null!=this.filter&&(this.filterAtomName=this.checkFilterKey("*.")||this.checkFilterKey("!."),this.filterElement=this.checkFilterKey("_"),this.filterHetero=this.checkFilterKey("HETATM"),this.filterGroup3=this.checkFilterKey("["),this.filterChain=this.checkFilterKey(":"),this.filterAltLoc=this.checkFilterKey("%"),(this.filterEveryNth=
this.checkFilterKey("/="))?this.filterN=this.parseIntStr(this.filter.substring(this.filter.indexOf("/=")+2)):this.filterAtomType=this.checkFilterKey("="),-2147483648==this.filterN&&(this.filterEveryNth=!1),this.haveAtomFilter=this.filterAtomName||this.filterAtomType||this.filterElement||this.filterGroup3||this.filterChain||this.filterAltLoc||this.filterHetero||this.filterEveryNth||this.checkFilterKey("/="),null==this.bsFilter&&(this.bsFilter=new JU.BS,this.htParams.put("bsFilter",this.bsFilter),this.filter=
(";"+this.filter+";").$replace(",",";"),J.util.Logger.info("filtering with "+this.filter),this.haveAtomFilter&&(this.filter1=this.filter,0<=(a=this.filter.indexOf("|"))))))this.filter1=this.filter.substring(0,a).trim()+";",this.filter2=";"+this.filter.substring(a).trim()},"~S");c(c$,"getFilter",function(a){var b=null==this.filter?-1:this.filter.indexOf(a);return 0>b?null:this.filter.substring(b+a.length,this.filter.indexOf(";",b))},"~S");c(c$,"checkFilterKey",function(a){return null!=this.filter&&
0<=this.filter.indexOf(a)},"~S");c(c$,"filterAtom",function(a,b){if(!this.haveAtomFilter)return!0;var d=this.checkFilter(a,this.filter1);null!=this.filter2&&(d=(new Boolean(d|this.checkFilter(a,this.filter2))).valueOf());d&&this.filterEveryNth&&(d=0==this.nFiltered++%this.filterN);this.bsFilter.setBitTo(0<=b?b:this.atomSetCollection.getAtomCount(),d);return d},"J.adapter.smarter.Atom,~N");c(c$,"checkFilter",function(a,b){return(!this.filterGroup3||null==a.group3||!this.filterReject(b,"[",a.group3.toUpperCase()+
"]"))&&(!this.filterAtomName||this.allowAtomName(a.atomName,b))&&(null==this.filterAtomTypeStr||null==a.atomName||0<=a.atomName.toUpperCase().indexOf("\x00"+this.filterAtomTypeStr))&&(!this.filterElement||null==a.elementSymbol||!this.filterReject(b,"_",a.elementSymbol.toUpperCase()+";"))&&(!this.filterChain||0==a.chainID||!this.filterReject(b,":",""+this.viewer.getChainIDStr(a.chainID)))&&(!this.filterAltLoc||"\x00"==a.altLoc||!this.filterReject(b,"%",""+a.altLoc))&&(!this.filterHetero||!this.filterReject(b,
"HETATM",a.isHetero?"HETATM":"ATOM"))},"J.adapter.smarter.Atom,~S");c(c$,"rejectAtomName",function(a){return this.filterAtomName&&!this.allowAtomName(a,this.filter)},"~S");c(c$,"allowAtomName",function(a,b){return null==a||!this.filterReject(b,".",a.toUpperCase()+this.filterAtomNameTerminator)},"~S,~S");c(c$,"filterReject",function(a,b,d){return 0<=a.indexOf(b)&&(0<=a.indexOf("!"+b)?0<=a.indexOf(b+d):0>a.indexOf(b+d))},"~S,~S,~S");c(c$,"set2D",function(){this.atomSetCollection.setAtomSetCollectionAuxiliaryInfo("is2D",
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c[b]=e;if(null!=c[b].errorMessage)return c[b].errorMessage}catch(f){return J.util.Logger.error(""+f),""+f}if(d.containsKey("trajectorySteps")){a=c[0];try{a.finalizeTrajectoryAs(d.get("trajectorySteps"),d.get("vibrationSteps"))}catch(j){if(C(j,Exception))null==a.errorMessage&&(a.errorMessage=""+j);else throw j;}}else if(c[0].isTrajectory){a=c[0];for(b=1;b<c.length;b++)c[0].mergeTrajectories(c[b])}else a=new J.adapter.smarter.AtomSetCollection("Array",null,c,null);return null==a.errorMessage?a:a.errorMessage},
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d){this.pt=a;this.type=b;this.type2=d},"~N,~S,~S");c(c$,"getVdwLabel",function(){return null==this.type?this.type2:this.type});c$.getVdwType=c(c$,"getVdwType",function(a){if(null!=a)for(var b,d=0,c=J.constant.EnumVdw.values();d<c.length&&((b=c[d])||1);d++)if(a.equalsIgnoreCase(b.type))return b;return null},"~S");c$.getVdwType2=c(c$,"getVdwType2",function(a){if(null!=a)for(var b,d=0,c=J.constant.EnumVdw.values();d<c.length&&((b=c[d])||1);d++)if(a.equalsIgnoreCase(b.type2))return b;return null},"~S");
B(c$,"JMOL",0,[0,"Jmol",null]);B(c$,"BABEL",1,[1,"Babel",null]);B(c$,"RASMOL",2,[2,"RasMol",null]);B(c$,"BABEL21",3,[3,"Babel21",null]);B(c$,"AUTO_JMOL",4,[0,null,"Jmol"]);B(c$,"AUTO_BABEL",5,[1,null,"Babel"]);B(c$,"AUTO_RASMOL",6,[2,null,"RasMol"]);B(c$,"AUTO",7,[0,"Auto",null]);B(c$,"USER",8,[-1,"User",null]);B(c$,"ADPMAX",9,[-1,null,"adpmax"]);B(c$,"ADPMIN",10,[-1,null,"adpmin"]);B(c$,"HYDRO",11,[-1,null,"hydrophobic"]);B(c$,"IONIC",12,[-1,null,"ionic"]);B(c$,"TEMP",13,[-1,null,"temperature"]);
B(c$,"NOJMOL",14,[-1,null,null]);B(c$,"NADA",15,[-1,null,null])}),p("J.g3d"),t(null,"J.g3d.CylinderRenderer",["JU.AU","J.util.Shader"],function(){c$=w(function(){this.shader=this.line3d=this.g3d=null;this.colixB=this.colixA=0;this.shadesA=null;this.isScreenedA=!1;this.shadesB=null;this.isScreenedB=!1;this.dzBf=this.dyBf=this.dxBf=this.zAf=this.yAf=this.xAf=this.dzB=this.dyB=this.dxB=this.zA=this.yA=this.xA=0;this.tEvenDiameter=!1;this.endcaps=this.diameter=0;this.tEndcapOpen=!1;this.sinPhi=this.cosPhi=
this.cosTheta=this.radius2=this.radius=this.endcapShadeIndex=this.colixEndcap=this.argbEndcap=this.zEndcap=this.yEndcap=this.xEndcap=0;this.drawBackside=this.clipped=!1;this.rasterCount=this.zTip=this.yTip=this.xTip=0;this.fp8ShadeIndexUp=this.zRaster=this.yRaster=this.xRaster=this.tzRaster=this.tyRaster=this.txRaster=this.tRaster=null;this.zXMax=this.zXMin=this.xMax=this.xMin=this.yMax=this.yMin=0;u(this,arguments)},J.g3d,"CylinderRenderer");Q(c$,function(){this.tRaster=O(32,0);this.txRaster=O(32,
0);this.tyRaster=O(32,0);this.tzRaster=O(32,0);this.xRaster=D(32,0);this.yRaster=D(32,0);this.zRaster=D(32,0);this.fp8ShadeIndexUp=D(32,0)});A(c$,function(a){this.g3d=a;this.line3d=a.line3d;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,c,e,f,j,k,l,h,n,q){if(!(f>3*this.g3d.getRenderHeight())){this.isScreenedA=d;this.isScreenedB=c;var v=s(f/2)+1,x=this.g3d.clipCode3(j-v,k-v,l-v),N=this.g3d.clipCode3(j+v,k+v,l+v),G=this.g3d.clipCode3(h-v,n-v,q-v),v=this.g3d.clipCode3(h+v,n+v,
q+v);this.clipped=0!=(x|N|G|v);if(0==(x&v&N&G))if(this.dxB=h-j,this.dyB=n-k,this.dzB=q-l,1>=f)this.line3d.plotLineDelta(this.g3d.getColorArgbOrGray(a),d,this.g3d.getColorArgbOrGray(b),c,j,k,l,this.dxB,this.dyB,this.dzB,this.clipped);else{this.drawBackside=this.clipped||2==e||0==e;this.diameter=f;this.xA=j;this.yA=k;this.zA=l;this.endcaps=e;this.shadesA=this.g3d.getShades(this.colixA=a);this.shadesB=this.g3d.getShades(this.colixB=b);this.calcArgbEndcap(!0,!1);this.generateBaseEllipse();(2==e||4==e)&&
this.renderFlatEndcap(!0);this.g3d.setZMargin(5);for(a=this.rasterCount;0<=--a;)this.plotRaster(a);this.g3d.setZMargin(0);3==e&&this.renderSphericalEndcaps()}}},"~N,~N,~B,~B,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderBits",function(a,b,d,c,e,f,j,k,l,h,n,q){if(!(f>3*this.g3d.getRenderHeight())){this.isScreenedA=d;this.isScreenedB=c;var v=s(f/2)+1,x=Math.round(j),N=Math.round(k),G=Math.round(l),p=Math.round(h),r=Math.round(n),t=Math.round(q),u=this.g3d.clipCode3(x-v,N-v,G-v),x=this.g3d.clipCode3(x+v,N+v,
G+v),N=this.g3d.clipCode3(p-v,r-v,t-v),v=this.g3d.clipCode3(p+v,r+v,t+v);this.clipped=0!=(u|x|N|v);if(0==(u&v&x&N))if(this.dxBf=h-j,this.dyBf=n-k,this.dzBf=q-l,0==f||1==f)this.line3d.plotLineDelta(this.g3d.getColorArgbOrGray(a),d,this.g3d.getColorArgbOrGray(b),c,y(j),y(k),y(l),y(this.dxBf),y(this.dyBf),y(this.dzBf),this.clipped);else{0<f&&(this.diameter=f,this.xAf=j,this.yAf=k,this.zAf=l);this.drawBackside=!d&&!c&&(this.clipped||2==e||0==e);this.xA=y(this.xAf);this.yA=y(this.yAf);this.zA=y(this.zAf);
this.dxB=y(this.dxBf);this.dyB=y(this.dyBf);this.dzB=y(this.dzBf);this.shadesA=this.g3d.getShades(this.colixA=a);this.shadesB=this.g3d.getShades(this.colixB=b);this.endcaps=e;this.calcArgbEndcap(!0,!0);0<f&&this.generateBaseEllipsePrecisely(!1);2==e&&this.renderFlatEndcapPrecisely(!0);this.line3d.setLineBits(this.dxBf,this.dyBf);this.g3d.setZMargin(5);for(a=this.rasterCount;0<=--a;)this.plotRasterBits(a);this.g3d.setZMargin(0);3==e&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;
this.zAf+=this.dzBf}}},"~N,~N,~B,~B,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"plotRasterBits",function(a){var b=this.fp8ShadeIndexUp[a]>>8,d=b>>1,c=this.xRaster[a],e=this.yRaster[a];a=this.zRaster[a];this.tEndcapOpen&&0!=this.argbEndcap&&(this.clipped?(this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+c,this.yEndcap+e,this.zEndcap-a-1),this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-c,this.yEndcap-e,this.zEndcap+a-1)):(this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap+c,this.yEndcap+
e,this.zEndcap-a-1),this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap-c,this.yEndcap-e,this.zEndcap+a-1)));this.line3d.plotLineDeltaBits(this.shadesA,this.isScreenedA,this.shadesB,this.isScreenedB,b,this.xA+c,this.yA+e,this.zA-a,this.dxB,this.dyB,this.dzB,this.clipped);this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[d],this.isScreenedA,this.shadesB[d],this.isScreenedB,this.xA-c,this.yA-e,this.zA+a,this.dxB,this.dyB,this.dzB,this.clipped)},"~N");c(c$,"renderCone",function(a,b,
d,c,e,f,j,k,l,h,n,q){if(!(c>3*this.g3d.getRenderHeight()))if(this.dxBf=k-(this.xAf=e),this.dyBf=l-(this.yAf=f),this.dzBf=h-(this.zAf=j),this.xA=s(Math.floor(this.xAf)),this.yA=s(Math.floor(this.yAf)),this.zA=s(Math.floor(this.zAf)),this.dxB=s(Math.floor(this.dxBf)),this.dyB=s(Math.floor(this.dyBf)),this.dzB=s(Math.floor(this.dzBf)),this.xTip=k,this.yTip=l,this.zTip=h,this.colixA=a,this.isScreenedA=b,this.shadesA=this.g3d.getShades(a),a=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB),this.g3d.plotPixelClippedScreened(this.shadesA[a],
this.isScreenedA,y(k),y(l),y(h)),this.diameter=c,1>=c)1==c&&this.line3d.plotLineDelta(this.colixA,this.isScreenedA,this.colixA,this.isScreenedA,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=d;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(q);!q&&2==this.endcaps&&this.renderFlatEndcapPrecisely(!1);this.g3d.setZMargin(5);for(d=this.rasterCount;0<=--d;)this.plotRasterCone(d,n,q);this.g3d.setZMargin(0)}},"~N,~B,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"generateBaseEllipse",
function(){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;var a=this.dxB*this.dxB+this.dyB*this.dyB;if(0==a)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var b=Math.sqrt(a),a=Math.sqrt(a+this.dzB*this.dzB);this.cosTheta=this.dzB/a;this.cosPhi=this.dxB/b;this.sinPhi=this.dyB/b}this.calcRotatedPoint(0,0,!1);this.calcRotatedPoint(0.5,1,!1);this.calcRotatedPoint(1,2,!1);this.rasterCount=3;this.interpolate(0,1);this.interpolate(1,2)});c(c$,"generateBaseEllipsePrecisely",
function(a){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;var b=this.dxBf*this.dxBf+this.dyBf*this.dyBf;if(0==b)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var d=Math.sqrt(b),b=Math.sqrt(b+this.dzBf*this.dzBf);this.cosTheta=this.dzBf/b;this.cosPhi=this.dxBf/d;this.sinPhi=this.dyBf/d}a?(this.calcRotatedPoint(0,0,!0),this.calcRotatedPoint(0.5,1,!0),this.rasterCount=2,this.interpolatePrecisely(0,1)):(this.calcRotatedPoint(0,0,!0),this.calcRotatedPoint(0.5,
1,!0),this.calcRotatedPoint(1,2,!0),this.rasterCount=3,this.interpolatePrecisely(0,1),this.interpolatePrecisely(1,2));for(a=0;a<this.rasterCount;a++)this.xRaster[a]=s(Math.floor(this.txRaster[a])),this.yRaster[a]=s(Math.floor(this.tyRaster[a])),this.zRaster[a]=s(Math.floor(this.tzRaster[a]))},"~B");c(c$,"calcRotatedPoint",function(a,b,d){this.tRaster[b]=a;a*=3.141592653589793;var c=Math.sin(a)*this.cosTheta,e=Math.cos(a);a=this.radius*(c*this.cosPhi-e*this.sinPhi);c=this.radius*(c*this.sinPhi+e*this.cosPhi);
e=this.radius2-(a*a+c*c);e=0<e?Math.sqrt(e):0;d?(this.txRaster[b]=a,this.tyRaster[b]=c,this.tzRaster[b]=e):(this.tEvenDiameter?(this.xRaster[b]=s(a-0.5),this.yRaster[b]=s(c-0.5)):(this.xRaster[b]=s(a),this.yRaster[b]=s(c)),this.zRaster[b]=s(e+0.5));this.fp8ShadeIndexUp[b]=this.shader.getShadeFp8(a,c,e)},"~N,~N,~B");c(c$,"interpolate",function(a,b){var d=this.xRaster[b]-this.xRaster[a];0>d&&(d=-d);var c=this.yRaster[b]-this.yRaster[a];0>c&&(c=-c);if(!(1>=d+c)){for(var d=this.tRaster[a],c=this.tRaster[b],
e=this.allocRaster(!1),f=4;0<=--f;){var j=(d+c)/2;this.calcRotatedPoint(j,e,!1);if(this.xRaster[e]==this.xRaster[a]&&this.yRaster[e]==this.yRaster[a])this.fp8ShadeIndexUp[a]=this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[e]>>>1,d=j;else if(this.xRaster[e]==this.xRaster[b]&&this.yRaster[e]==this.yRaster[b])this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[e]>>>1,c=j;else{this.interpolate(a,e);this.interpolate(e,b);return}}this.xRaster[e]=this.xRaster[a];this.yRaster[e]=this.yRaster[b]}},
"~N,~N");c(c$,"interpolatePrecisely",function(a,b){var d=s(Math.floor(this.txRaster[b]))-s(Math.floor(this.txRaster[a]));0>d&&(d=-d);var c=s(Math.floor(this.tyRaster[b]))-s(Math.floor(this.tyRaster[a]));0>c&&(c=-c);if(!(1>=d+c)){for(var d=this.tRaster[a],c=this.tRaster[b],e=this.allocRaster(!0),f=4;0<=--f;){var j=(d+c)/2;this.calcRotatedPoint(j,e,!0);if(s(Math.floor(this.txRaster[e]))==s(Math.floor(this.txRaster[a]))&&s(Math.floor(this.tyRaster[e]))==s(Math.floor(this.tyRaster[a])))this.fp8ShadeIndexUp[a]=
this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[e]>>>1,d=j;else if(s(Math.floor(this.txRaster[e]))==s(Math.floor(this.txRaster[b]))&&s(Math.floor(this.tyRaster[e]))==s(Math.floor(this.tyRaster[b])))this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[e]>>>1,c=j;else{this.interpolatePrecisely(a,e);this.interpolatePrecisely(e,b);return}}this.txRaster[e]=this.txRaster[a];this.tyRaster[e]=this.tyRaster[b]}},"~N,~N");c(c$,"plotRaster",function(a){var b=this.fp8ShadeIndexUp[a]>>8,d=b>>1,c=
this.xRaster[a],e=this.yRaster[a];a=this.zRaster[a];this.tEndcapOpen&&0!=this.argbEndcap&&(this.clipped?(this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+c,this.yEndcap+e,this.zEndcap-a-1),this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-c,this.yEndcap-e,this.zEndcap+a-1)):(this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap+c,this.yEndcap+e,this.zEndcap-a-1),this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap-c,this.yEndcap-e,this.zEndcap+a-1)));this.line3d.plotLineDeltaA(this.shadesA,
this.isScreenedA,this.shadesB,this.isScreenedB,b,this.xA+c,this.yA+e,this.zA-a,this.dxB,this.dyB,this.dzB,this.clipped);this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[d],this.isScreenedA,this.shadesB[d],this.isScreenedB,this.xA-c,this.yA-e,this.zA+a,this.dxB,this.dyB,this.dzB,this.clipped)},"~N");c(c$,"allocRaster",function(a){for(;this.rasterCount>=this.xRaster.length;)this.xRaster=JU.AU.doubleLengthI(this.xRaster),this.yRaster=JU.AU.doubleLengthI(this.yRaster),this.zRaster=JU.AU.doubleLengthI(this.zRaster),
this.tRaster=JU.AU.doubleLengthF(this.tRaster);for(;this.rasterCount>=this.fp8ShadeIndexUp.length;)this.fp8ShadeIndexUp=JU.AU.doubleLengthI(this.fp8ShadeIndexUp);if(a)for(;this.rasterCount>=this.txRaster.length;)this.txRaster=JU.AU.doubleLengthF(this.txRaster),this.tyRaster=JU.AU.doubleLengthF(this.tyRaster),this.tzRaster=JU.AU.doubleLengthF(this.tzRaster);return this.rasterCount++},"~B");c(c$,"findMinMaxY",function(){this.yMin=this.yMax=this.yRaster[0];for(var a=this.rasterCount;0<--a;){var b=this.yRaster[a];
b<this.yMin?this.yMin=b:b>this.yMax?this.yMax=b:(b=-b,b<this.yMin?this.yMin=b:b>this.yMax&&(this.yMax=b))}});c(c$,"findMinMaxX",function(a){this.xMin=2147483647;this.xMax=-2147483648;for(var b=this.rasterCount;0<=--b;){if(this.yRaster[b]==a){var d=this.xRaster[b];d<this.xMin&&(this.xMin=d,this.zXMin=this.zRaster[b]);d>this.xMax&&(this.xMax=d,this.zXMax=this.zRaster[b])}this.yRaster[b]==-a&&(d=-this.xRaster[b],d<this.xMin&&(this.xMin=d,this.zXMin=-this.zRaster[b]),d>this.xMax&&(this.xMax=d,this.zXMax=
-this.zRaster[b]))}},"~N");c(c$,"renderFlatEndcap",function(a){if(0!=this.dzB&&this.g3d.setColix(this.colixEndcap)){var b=this.xA,d=this.yA,c=this.zA;if(a&&0>this.dzB){if(4==this.endcaps)return;b+=this.dxB;d+=this.dyB;c+=this.dzB}this.findMinMaxY();for(a=this.yMin;a<=this.yMax;++a){this.findMinMaxX(a);var e=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(e,b+this.xMin,d+a,c-this.zXMin-1,c-this.zXMax-1,null,null)}}},"~B");c(c$,"renderFlatEndcapPrecisely",
function(a){if(0!=this.dzBf&&this.g3d.setColix(this.colixEndcap)){var b=this.xAf,d=this.yAf,c=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,d+=this.dyBf,c+=this.dzBf);a=y(b);d=y(d);c=y(c);this.findMinMaxY();for(b=this.yMin;b<=this.yMax;++b){this.findMinMaxX(b);var e=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(e,a+this.xMin,d+b,c-this.zXMin-1,c-this.zXMax-1,null,null)}}},"~B");c(c$,"renderSphericalEndcaps",function(){0!=this.colixA&&this.g3d.setColix(this.colixA)&&
this.g3d.fillSphereXYZ(this.diameter,this.xA,this.yA,this.zA+1);0!=this.colixB&&this.g3d.setColix(this.colixB)&&this.g3d.fillSphereXYZ(this.diameter,this.xA+this.dxB,this.yA+this.dyB,this.zA+this.dzB+1)});c(c$,"plotRasterCone",function(a,b,d){var c=this.txRaster[a],e=this.tyRaster[a],f=this.tzRaster[a],j=this.xAf+c,k=this.yAf+e,l=this.zAf-f,c=this.xAf-c,e=this.yAf-e,f=this.zAf+f,h=this.shadesA[0];this.tEndcapOpen&&0!=this.argbEndcap&&(this.g3d.plotPixelClippedScreened(this.argbEndcap,this.isScreenedA,
y(j),y(k),y(l)),this.g3d.plotPixelClippedScreened(this.argbEndcap,this.isScreenedA,y(c),y(e),y(f)));a=this.fp8ShadeIndexUp[a]>>8;0!=h&&(this.line3d.plotLineDeltaA(this.shadesA,this.isScreenedA,this.shadesA,this.isScreenedA,a,y(j),y(k),y(l),s(Math.ceil(this.xTip-j)),s(Math.ceil(this.yTip-k)),s(Math.ceil(this.zTip-l)),!0),b&&(this.line3d.plotLineDeltaA(this.shadesA,this.isScreenedA,this.shadesA,this.isScreenedA,a,y(j),y(k)+1,y(l),s(Math.ceil(this.xTip-j)),s(Math.ceil(this.yTip-k))+1,s(Math.ceil(this.zTip-
l)),!0),this.line3d.plotLineDeltaA(this.shadesA,this.isScreenedA,this.shadesA,this.isScreenedA,a,y(j)+1,y(k),y(l),s(Math.ceil(this.xTip-j))+1,s(Math.ceil(this.yTip-k)),s(Math.ceil(this.zTip-l)),!0)),!d&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDelta(h,this.isScreenedA,h,this.isScreenedA,y(c),y(e),y(f),s(Math.ceil(this.xTip-c)),s(Math.ceil(this.yTip-e)),s(Math.ceil(this.zTip-f)),!0))},"~N,~B,~B");c(c$,"calcArgbEndcap",function(a,b){this.tEndcapOpen=!1;var d=b?this.dzBf:this.dzB;if(!(3==
this.endcaps||0==d)){this.xEndcap=this.xA;this.yEndcap=this.yA;this.zEndcap=this.zA;var c=b?this.dxBf:this.dxB,e=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-c,-e,d),this.colixEndcap=this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(c,e,-d),this.colixEndcap=this.colixB,d=this.shadesB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB);this.endcapShadeIndex>J.util.Shader.shadeIndexNoisyLimit&&(this.endcapShadeIndex=J.util.Shader.shadeIndexNoisyLimit);
this.argbEndcap=d[this.endcapShadeIndex];this.tEndcapOpen=1==this.endcaps}},"~B,~B")}),p("J.g3d"),S(J.g3d,"G3DRenderer"),p("J.g3d"),t(["J.api.JmolRendererInterface","J.util.GData","JU.V3","J.util.Normix"],"J.g3d.Graphics3D","java.lang.NullPointerException java.util.Arrays javajs.awt.Font JU.AU J.api.Interface J.constant.EnumStereoMode J.g3d.CylinderRenderer $.ImageRenderer $.LineRenderer $.Pixelator $.PixelatorShaded $.Platform3D $.SphereRenderer $.TextRenderer $.TextSorter $.TextString J.util.C $.Shader".split(" "),
function(){c$=w(function(){this.hermite3d=this.circle3d=this.triangle3d=this.cylinder3d=this.sphere3d=this.line3d=this.platform=null;this.antialias2=this.isFullSceneAntialiasingEnabled=!1;this.strings=null;this.stringCount=0;this.anaglyphChannelBytes=null;this.$haveTranslucentObjects=this.addAllPixels=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.isScreened=!1;this.argbNoisyDn=this.argbNoisyUp=
0;this.pixel=this.currentFont=null;this.zMargin=0;this.aobuf=null;this.saveDiffuse=this.saveAmbient=this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.$currentlyRendering=!1;this.shadeIndexes2Sided=this.shadeIndexes=this.transformedVectors=this.vectorNormal=this.vectorAC=this.vectorAB=null;u(this,arguments)},J.g3d,"Graphics3D",J.util.GData,J.api.JmolRendererInterface);Q(c$,function(){this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=new JU.V3;this.transformedVectors=
Array(J.g3d.Graphics3D.normixCount);for(var a=J.g3d.Graphics3D.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3;this.shadeIndexes=V(J.g3d.Graphics3D.normixCount,0);this.shadeIndexes2Sided=V(J.g3d.Graphics3D.normixCount,0)});h(c$,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});h(c$,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.platform=null});h(c$,"getGData",function(){return this});c(c$,"setZMargin",function(a){this.zMargin=
a},"~N");A(c$,function(){U(this,J.g3d.Graphics3D,[])});h(c$,"initialize",function(a){this.apiPlatform=a;this.platform=new J.g3d.Platform3D(a);this.graphicsForMetrics=this.platform.getGraphicsForMetrics();this.line3d=new J.g3d.LineRenderer(this);this.sphere3d=new J.g3d.SphereRenderer(this);this.cylinder3d=new J.g3d.CylinderRenderer(this)},"javajs.api.GenericPlatform");h(c$,"addRenderer",function(a){switch(a){case 1073741880:null==this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648147:null==
this.hermite3d&&(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"))}},"~N");c(c$,"getRenderer",function(a){return J.api.Interface.getOptionInterface("g3d."+a+"Renderer").set(this)},"~S");h(c$,"currentlyRendering",function(){return this.$currentlyRendering});h(c$,"setWindowParameters",function(a,b,d){this.setWinParams(a,b,d);this.$currentlyRendering&&this.endRendering()},"~N,~N,~B");h(c$,"checkTranslucent",function(a){a&&
(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.$isPass2==a},"~B");h(c$,"beginRendering",function(a,b,d,c){this.$currentlyRendering&&this.endRendering();this.renderLow=c;if(this.windowWidth!=this.newWindowWidth||this.windowHeight!=this.newWindowHeight||this.newAntialiasing!=this.isFullSceneAntialiasingEnabled)this.windowWidth=this.newWindowWidth,this.windowHeight=this.newWindowHeight,this.isFullSceneAntialiasingEnabled=this.newAntialiasing,this.releaseBuffers();this.setRotationMatrix(a);
this.antialiasEnabled=this.antialiasThisFrame=this.newAntialiasing;this.$currentlyRendering=!0;if(null!=this.strings)for(a=Math.min(this.strings.length,this.stringCount);0<=--a;)this.strings[a]=null;this.stringCount=0;this.twoPass=!0;this.$isPass2=!1;this.colixCurrent=0;this.$haveTranslucentObjects=!1;this.translucentCoverOnly=!b;this.addAllPixels=!0;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,d),this.pbuf=this.platform.pBuffer,this.zbuf=
this.platform.zBuffer,this.aobuf=null);this.setWidthHeight(this.antialiasThisFrame);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0)},"JU.M3,~B,~B,~B");h(c$,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(c$,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=this.pbuf=null;this.platform.releaseBuffers();this.line3d.clearLineCache()});h(c$,
"setPass2",function(a){if(!this.$haveTranslucentObjects||!this.$currentlyRendering)return!1;this.$isPass2=!0;this.colixCurrent=0;this.addAllPixels=!0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();return!0},"~B");h(c$,"endRendering",function(){if(this.$currentlyRendering){if(null!=
this.pbuf){if(this.$isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,this.pbufT[a],this.bgcolor);if(0!=this.ambientOcclusion){if(null==this.aobuf)this.aobuf=D(this.pbuf.length,0);else for(a=this.pbuf.length;0<=--a;)this.aobuf[a]=0;this.shader.occludePixels(this.pbuf,this.zbuf,this.aobuf,this.width,this.height,this.ambientOcclusion)}this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);
this.platform.notifyEndOfRendering();this.$currentlyRendering=!1}});c$.mergeBufferPixel=c(c$,"mergeBufferPixel",function(a,b,d,c){if(0!=d){var e=a[b];if(e!=d){0==e&&(e=c);c=e&16711935;var e=e&65280,f=d&16711935,j=d&65280;switch(d>>24&15){case 0:c=f;e=j;break;case 1:c=(f<<2)+(f<<1)+f+c>>3&16711935;e=(j<<2)+ +(j<<1)+j+e>>3&65280;break;case 2:c=(f<<1)+f+c>>2&16711935;e=(j<<1)+j+e>>2&65280;break;case 3:c=(f<<2)+f+(c<<1)+c>>3&16711935;e=(j<<2)+j+(e<<1)+e>>3&65280;break;case 4:c=c+f>>1&16711935;e=e+j>>
1&65280;break;case 5:c=(f<<1)+f+(c<<2)+c>>3&16711935;e=(j<<1)+j+(e<<2)+e>>3&65280;break;case 6:c=(c<<1)+c+f>>2&16711935;e=(e<<1)+e+j>>2&65280;break;case 7:c=(c<<2)+(c<<1)+c+f>>3&16711935,e=(e<<2)+(e<<1)+e+j>>3&65280}a[b]=4278190080|c|e}}},"~A,~N,~N,~N");h(c$,"getScreenImage",function(a){var b=this.platform.bufferedImage;a&&this.releaseBuffers();return b},"~B");h(c$,"applyAnaglygh",function(a,b){switch(a){case J.constant.EnumStereoMode.REDCYAN:this.applyCyanAnaglyph();break;case J.constant.EnumStereoMode.CUSTOM:this.applyCustomAnaglyph(b);
break;case J.constant.EnumStereoMode.REDBLUE:this.applyBlueAnaglyph();break;case J.constant.EnumStereoMode.REDGREEN:this.applyGreenAnaglyph()}},"J.constant.EnumStereoMode,~A");h(c$,"snapshotAnaglyphChannelBytes",function(){if(this.$currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=V(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=
--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});c(c$,"applyCustomAnaglyph",function(a){var b=a[0];a=a[1]&16777215;for(var d=this.anaglyphLength;0<=--d;){var c=this.anaglyphChannelBytes[d]&255,c=(c|(c|c<<8)<<8)&a;this.pbuf[d]=this.pbuf[d]&b|c}},"~A");c(c$,"applyGreenAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&4294901760|(this.anaglyphChannelBytes[a]&255)<<8});c(c$,"applyBlueAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&
4294901760|this.anaglyphChannelBytes[a]&255});c(c$,"applyCyanAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;){var b=this.anaglyphChannelBytes[a]&255;this.pbuf[a]=this.pbuf[a]&4294901760|b<<8|b}});h(c$,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});h(c$,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});c(c$,"setTempZSlab",function(a){this.zSlab=a},"~N");h(c$,"setZShade",function(a,b,d,c){a?(this.setZShade2(b,d,c),this.pixel=new J.g3d.PixelatorShaded(this)):
this.pixel=new J.g3d.Pixelator(this)},"~B,~N,~N,~N");c(c$,"downsampleFullSceneAntialiasing",function(a){var b=this.width,d=0,c=0,e=this.bgcolor;a&&(e+=255==(e&255)?-1:1);for(var f=this.pbuf.length;0<=--f;)0==this.pbuf[f]&&(this.pbuf[f]=e);e&=16777215;for(f=this.windowHeight;0<=--f;c+=b)for(var j=this.windowWidth;0<=--j;++d){var k=(this.pbuf[c]>>2&1061109567)+(this.pbuf[c++ +b]>>2&1061109567)+(this.pbuf[c]>>2&1061109567)+(this.pbuf[c++ +b]>>2&1061109567),k=k+((k&3233857728)>>6);this.pbuf[d]=k&16777215|
4278190080}if(a){d=c=0;for(f=this.windowHeight;0<=--f;c+=b)for(j=this.windowWidth;0<=--j;++d,++c)a=Math.min(this.zbuf[c],this.zbuf[c+b]),a=Math.min(a,this.zbuf[++c]),a=Math.min(a,this.zbuf[c+b]),2147483647!=a&&(a>>=1),this.zbuf[d]=this.pbuf[d]==e?2147483647:a;this.antialiasThisFrame=!1;this.setWidthHeight(!1)}},"~B");c(c$,"hasContent",function(){return this.platform.hasContent()});h(c$,"setColor",function(a){this.argbCurrent=this.argbNoisyUp=this.argbNoisyDn=a},"~N");h(c$,"setColix",function(a){var b=
J.util.C.isColixLastAvailable(a);if(!b&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var d=a&30720;if(16384==d)return!1;this.renderLow&&(d=0);var c=0!=d;this.isScreened=c&&30720==d;if(!this.checkTranslucent(c&&!this.isScreened))return!1;this.addAllPixels=this.$isPass2||!c;this.$isPass2?(this.translucencyMask=d<<13|16777215,this.translucencyLog=d>>11):this.translucencyLog=0;this.colixCurrent=a;b&&this.argbCurrent!=this.lastRawColor&&(0==this.argbCurrent&&(this.argbCurrent=4294967295),
this.lastRawColor=this.argbCurrent,this.shader.setLastColix(this.argbCurrent,this.inGreyscaleMode));this.shadesCurrent=this.getShades(a);this.currentShadeIndex=-1;this.setColor(this.getColorArgbOrGray(a));return!0},"~N");c(c$,"addPixel",function(a,b,d){this.pixel.addPixel(a,b,d)},"~N,~N,~N");c(c$,"clearPixel",function(a,b){this.pixel.clearPixel(a,b)},"~N,~N");h(c$,"drawFilledCircle",function(a,b,d,c,e,f){if(!this.isClippedZ(f)){var j=s((d+1)/2),j=c<j||c+j>=this.width||e<j||e+j>=this.height;if(!j||
!this.isClippedXY(d,c,e))0!=a&&this.setColix(a)&&(j?this.circle3d.plotCircleCenteredClipped(c,e,f,d):this.circle3d.plotCircleCenteredUnclipped(c,e,f,d)),0!=b&&this.setColix(b)&&(j?this.circle3d.plotFilledCircleCenteredClipped(c,e,f,d):this.circle3d.plotFilledCircleCenteredUnclipped(c,e,f,d))}},"~N,~N,~N,~N,~N,~N");h(c$,"volumeRender4",function(a,b,d,c){if(1==a)this.plotPixelClippedXYZ(b,d,c);else if(!this.isClippedZ(c)){var e=s((a+1)/2),e=b<e||b+e>=this.width||d<e||d+e>=this.height;if(!e||!this.isClippedXY(a,
b,d))e?this.circle3d.plotFilledCircleCenteredClipped(b,d,c,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,d,c,a)}},"~N,~N,~N,~N");h(c$,"fillSphereXYZ",function(a,b,d,c){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,b,d,c);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.addAllPixels,a,b,d,c,null,null,null,-1,null,this.addAllPixels)},"~N,~N,~N,~N");h(c$,"volumeRender",function(a){a?(this.saveAmbient=this.shader.ambientPercent,
this.saveDiffuse=this.shader.diffusePercent,this.setAmbientPercent(100),this.setDiffusePercent(0)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},"~B");h(c$,"fillSphereI",function(a,b){this.fillSphereXYZ(a,b.x,b.y,b.z)},"~N,JU.P3i");h(c$,"fillSphere",function(a,b){this.fillSphereXYZ(a,Math.round(b.x),Math.round(b.y),Math.round(b.z))},"~N,JU.P3");h(c$,"fillEllipsoid",function(a,b,d,c,e,f,j,k,l,h,n){switch(f){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,
c,e);return;case 0:return}f<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.addAllPixels,f,d,c,e,j,k,l,h,n,this.addAllPixels)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");h(c$,"drawRect",function(a,b,d,c,e,f){if(!(0!=c&&this.isClippedZ(c))){c=e-1;f-=1;e=a+c;var j=b+f;0<=b&&b<this.height&&this.drawHLine(a,b,d,c);0<=j&&j<this.height&&this.drawHLine(a,j,d,c);0<=a&&a<this.width&&this.drawVLine(a,b,d,f);0<=e&&e<this.width&&this.drawVLine(e,b,d,f)}},"~N,~N,~N,~N,~N,~N");
c(c$,"drawHLine",function(a,b,d,c){0>c&&(a+=c,c=-c);0>a&&(c+=a,a=0);a+c>=this.width&&(c=this.width-1-a);var e=a+this.width*b;if(this.addAllPixels)for(a=0;a<=c;a++)d<this.zbuf[e]&&this.addPixel(e,d,this.argbCurrent),e++;else{b=0!=((a^b)&1);for(a=0;a<=c;a++)(b=!b)&&d<this.zbuf[e]&&this.addPixel(e,d,this.argbCurrent),e++}},"~N,~N,~N,~N");c(c$,"drawVLine",function(a,b,d,c){0>c&&(b+=c,c=-c);0>b&&(c+=b,b=0);b+c>=this.height&&(c=this.height-1-b);var e=a+this.width*b;if(this.addAllPixels)for(a=0;a<=c;a++)d<
this.zbuf[e]&&this.addPixel(e,d,this.argbCurrent),e+=this.width;else{b=0!=((a^b)&1);for(a=0;a<=c;a++)(b=!b)&&d<this.zbuf[e]&&this.addPixel(e,d,this.argbCurrent),e+=this.width}},"~N,~N,~N,~N");h(c$,"fillRect",function(a,b,d,c,e,f){if(!this.isClippedZ(c)){if(0>a){e+=a;if(0>=e)return;a=0}if(a+e>this.width&&(e=this.width-a,0>=e))return;if(0>b){f+=b;if(0>=f)return;b=0}for(b+f>this.height&&(f=this.height-b);0<=--f;)this.plotPixelsUnclippedCount(e,a,b++,d)}},"~N,~N,~N,~N,~N,~N");h(c$,"drawString",function(a,
b,d,c,e,f,j){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(f)||this.drawStringNoSlab(a,b,d,c,e,j))},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");h(c$,"drawStringNoSlab",function(a,b,d,c,e,f){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var j=new J.g3d.TextString;j.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,J.util.C.isColixTranslucent(f)?this.getColorArgbOrGray(f)&16777215|(f&
30720)<<13:0,d,c,e);this.strings[this.stringCount++]=j}},"~S,javajs.awt.Font,~N,~N,~N,~N");h(c$,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&(J.g3d.Graphics3D.sort=new J.g3d.TextSorter),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var b=0;b<this.stringCount;b++){var d=this.strings[b];this.plotText(d.x,d.y,d.z,d.argb,d.bgargb,d.text,d.font,a)}this.strings=null;this.stringCount=0}},"~O");h(c$,"plotText",function(a,b,d,c,e,
f,j,k){J.g3d.TextRenderer.plot(a,b,d,c,e,f,j,this,k,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.api.JmolRendererInterface");h(c$,"drawImage",function(a,b,d,c,e,f,j,k){null==a||(0==j||0==k||this.isClippedZ(e))||this.plotImage(b,d,c,a,null,f,j,k)},"~O,~N,~N,~N,~N,~N,~N,~N");c(c$,"plotImage",function(a,b,d,c,e,f,j,k){this.setColix(f);this.$isPass2||(this.translucencyMask=-1);0==f&&(this.argbCurrent=0);J.g3d.ImageRenderer.plotImage(a,b,d,c,this,e,this.antialiasThisFrame,this.argbCurrent,
j,k)},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");h(c$,"setFontFid",function(a){this.currentFont=javajs.awt.Font.getFont3D(a)},"~N");h(c$,"setFont",function(a){this.currentFont=a},"javajs.awt.Font");h(c$,"getFont3DCurrent",function(){return this.currentFont});h(c$,"drawPixel",function(a,b,d){this.plotPixelClippedXYZ(a,b,d)},"~N,~N,~N");h(c$,"drawPoints",function(a,b,d){if(1<d)for(var c=0.8*d*d,e=-d;e<d;e++)for(var f=-d;f<d;f++)e*e+f*f>c||(this.plotPoints(a,b,e,f),this.plotPoints(a,b,e,f));
else this.plotPoints(a,b,0,0)},"~N,~A,~N");h(c$,"drawDashedLine",function(a,b,d,c){this.line3d.plotDashedLine(this.argbCurrent,!this.addAllPixels,a,b,d.x,d.y,d.z,c.x,c.y,c.z,!0)},"~N,~N,JU.P3i,JU.P3i");h(c$,"drawDottedLine",function(a,b){this.line3d.plotDashedLine(this.argbCurrent,!this.addAllPixels,2,1,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"drawLineXYZ",function(a,b,d,c,e,f){this.line3d.plotLine(this.argbCurrent,!this.addAllPixels,this.argbCurrent,!this.addAllPixels,a,b,d,c,e,f,!0)},
"~N,~N,~N,~N,~N,~N");h(c$,"drawLine",function(a,b,d,c,e,f,j,k){this.setColix(a)||(a=0);var l=!this.addAllPixels,h=this.argbCurrent;this.setColix(b)||(b=0);0==a&&0==b||this.line3d.plotLine(h,l,this.argbCurrent,!this.addAllPixels,d,c,e,f,j,k,!0)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"drawLineAB",function(a,b){this.line3d.plotLine(this.argbCurrent,!this.addAllPixels,this.argbCurrent,!this.addAllPixels,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"fillCylinderXYZ",function(a,b,d,c,e,f,j,k,l,h){this.setColix(a)||
(a=0);var n=!this.addAllPixels;this.setColix(b)||(b=0);0==a&&0==b||this.cylinder3d.render(a,b,n,!this.addAllPixels,d,c,e,f,j,k,l,h)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen",function(a,b,d,c,e,f,j,k){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.addAllPixels,!this.addAllPixels,a,b,d,c,e,f,j,k)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen3I",function(a,b,d,c){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.addAllPixels,!this.addAllPixels,
a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3i,JU.P3i,JU.P3,JU.P3,~N");h(c$,"fillCylinder",function(a,b,d,c){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.addAllPixels,!this.addAllPixels,a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3i,JU.P3i");h(c$,"fillCylinderBits",function(a,b,d,c){this.cylinder3d.renderBits(this.colixCurrent,this.colixCurrent,!this.addAllPixels,!this.addAllPixels,a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3,JU.P3");h(c$,"fillConeScreen",function(a,b,d,c,e){this.cylinder3d.renderCone(this.colixCurrent,
!this.addAllPixels,a,b,d.x,d.y,d.z,c.x,c.y,c.z,!1,e)},"~N,~N,JU.P3i,JU.P3i,~B");h(c$,"fillConeSceen3f",function(a,b,d,c){this.cylinder3d.renderCone(this.colixCurrent,!this.addAllPixels,a,b,d.x,d.y,d.z,c.x,c.y,c.z,!0,!1)},"~N,~N,JU.P3,JU.P3");h(c$,"drawHermite4",function(a,b,d,c,e){this.hermite3d.renderHermiteRope(!1,a,0,0,0,b,d,c,e)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawHermite7",function(a,b,d,c,e,f,j,k,l,h,n,q,v){if(0==v)this.hermite3d.renderHermiteRibbon(a,b,d,c,e,f,j,k,l,h,n,q,0);else{this.hermite3d.renderHermiteRibbon(a,
b,d,c,e,f,j,k,l,h,n,q,1);var x=this.colixCurrent;this.setColix(v);this.hermite3d.renderHermiteRibbon(a,b,d,c,e,f,j,k,l,h,n,q,-1);this.setColix(x)}},"~B,~B,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,~N,~N");h(c$,"fillHermite",function(a,b,d,c,e,f,j,k){this.hermite3d.renderHermiteRope(!0,a,b,d,c,e,f,j,k)},"~N,~N,~N,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawTriangle3C",function(a,b,d,c,e,f,j){1==(j&1)&&this.drawLine(b,c,a.x,a.y,a.z,d.x,d.y,d.z);2==(j&2)&&this.drawLine(c,f,d.x,d.y,d.z,
e.x,e.y,e.z);4==(j&4)&&this.drawLine(b,f,a.x,a.y,a.z,e.x,e.y,e.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");h(c$,"drawTriangle3I",function(a,b,d,c){1==(c&1)&&this.line3d.plotLine(this.argbCurrent,!this.addAllPixels,this.argbCurrent,!this.addAllPixels,a.x,a.y,a.z,b.x,b.y,b.z,!0);2==(c&2)&&this.line3d.plotLine(this.argbCurrent,!this.addAllPixels,this.argbCurrent,!this.addAllPixels,b.x,b.y,b.z,d.x,d.y,d.z,!0);4==(c&4)&&this.line3d.plotLine(this.argbCurrent,!this.addAllPixels,this.argbCurrent,!this.addAllPixels,
a.x,a.y,a.z,d.x,d.y,d.z,!0)},"JU.P3i,JU.P3i,JU.P3i,~N");h(c$,"fillTriangleTwoSided",function(a,b,d,c,e,f,j,k,l,h){this.setColorNoisy(this.getShadeIndex(a));this.triangle3d.fillTriangleXYZ(b,d,c,e,f,j,k,l,h,!1)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillTriangle3f",function(a,b,d,c){var e=this.getShadeIndexP3(a,b,d);c?this.setColorNoisy(e):this.setColor(this.shadesCurrent[e]);this.triangle3d.fillTriangleP3f(a,b,d,!1)},"JU.P3,JU.P3,JU.P3,~B");h(c$,"fillTriangle3i",function(a,b,d){this.triangle3d.fillTriangleP3i(a,
b,d,!1)},"JU.P3i,JU.P3i,JU.P3i,JU.P3,JU.P3,JU.P3");h(c$,"fillTriangle",function(a,b,d,c,e,f,j,k,l,h){if(!this.$isPass2&&d==f&&d==l&&b==e&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,e,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(e)[this.getShadeIndex(f)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3if(a,c,j,h,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,~N");
h(c$,"fillTriangle3CN",function(a,b,d,c,e,f,j,k,l){if(!this.$isPass2&&d==f&&d==l&&b==e&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,e,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(e)[this.getShadeIndex(f)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3i(a,c,j,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");c(c$,"setTriangleColixAndShadeIndex",function(a,b){a==
this.colixCurrent&&this.currentShadeIndex==b||(this.currentShadeIndex=-1,this.setColix(a),this.setColorNoisy(b))},"~N,~N");c(c$,"setTriangleTranslucency",function(a,b,d){if(!this.$isPass2)return!0;a&=14336;b&=14336;d&=14336;this.translucencyMask=(J.util.GData.roundInt(s((a+b+d)/3))&30720)<<13|16777215;return!0},"~N,~N,~N");h(c$,"drawQuadrilateral",function(a,b,d,c,e){this.setColix(a);this.drawLineAB(b,d);this.drawLineAB(d,c);this.drawLineAB(c,e);this.drawLineAB(e,b)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");
h(c$,"fillQuadrilateral",function(a,b,d,c){this.setColorNoisy(this.getShadeIndexP3(a,b,d));this.triangle3d.fillTriangleP3f(a,b,d,!1);this.triangle3d.fillTriangleP3f(a,d,c,!1)},"JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"fillQuadrilateral3i",function(a,b,d,c,e,f,j,k,l,h,n,q){this.fillTriangle3CN(a,b,d,c,e,f,j,k,l);this.fillTriangle3CN(a,b,d,j,k,l,h,n,q)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");h(c$,"drawSurface",function(){},"J.util.MeshSurface,~N");c(c$,"plotPixelClippedXYZ",function(a,b,d){this.isClipped3(a,
b,d)||(a=b*this.width+a,d<this.zbuf[a]&&this.addPixel(a,d,this.argbCurrent))},"~N,~N,~N");h(c$,"plotPixelClippedP3i",function(a){this.plotPixelClippedXYZ(a.x,a.y,a.z)},"JU.P3i");c(c$,"plotPixelClippedArgb",function(a,b,d,c){this.isClipped3(b,d,c)||(b=d*this.width+b,c<this.zbuf[b]&&this.addPixel(b,c,a))},"~N,~N,~N,~N");h(c$,"plotImagePixel",function(a,b,d,c,e,f){this.isClipped(b,d)||(b=d*this.width+b,c<this.zbuf[b]&&this.shadeTextPixel(b,c,a,f,e))},"~N,~N,~N,~N,~N,~N");c(c$,"plotPixelClippedScreened",
function(a,b,d,c,e){!this.isClipped3(d,c,e)&&!(b&&0!=((d^c)&1))&&(b=c*this.width+d,e<this.zbuf[b]&&this.addPixel(b,e,a))},"~N,~B,~N,~N,~N");c(c$,"plotPixelUnclipped",function(a,b,d){a=b*this.width+a;d<this.zbuf[a]&&this.addPixel(a,d,this.argbCurrent)},"~N,~N,~N");c(c$,"plotPixelUnclippedArgb",function(a,b,d,c){b=d*this.width+b;c<this.zbuf[b]&&this.addPixel(b,c,a)},"~N,~N,~N,~N");c(c$,"plotPixelsClipped",function(a,b,d,c){if(!(0>d||d>=this.height||b>=this.width))if(0>b&&(a+=b,b=0),a+b>this.width&&
(a=this.width-b),!(0>=a)){var e=d*this.width+b;a=e+a;var f=1;this.addAllPixels||(f=2,0!=((b^d)&1)&&++e);for(;e<a;)c<this.zbuf[e]&&this.addPixel(e,c,this.argbCurrent),e+=f}},"~N,~N,~N,~N");c(c$,"plotPixelsClippedRaster",function(a,b,d,c,e,f,j){if(!(0>=a||0>d||d>=this.height||b>=this.width||c<this.slab&&e<this.slab||c>this.depth&&e>this.depth)){var k=(b<<16)+(d<<1)^858993459,l=(c<<10)+512;c=e-c;e=s(a/2);c=J.util.GData.roundInt(s(((c<<10)+(0<=c?e:-e))/a));if(0>b){b=-b;l+=c*b;a-=b;if(0>=a)return;b=0}a+
b>this.width&&(a=this.width-b);e=0!=((b^d)&1);b=d*this.width+b;if(null==f)for(;0<=--a;){if(this.addAllPixels||!0==(e=!e))j=l>>10,j>=this.slab&&(j<=this.depth&&j<this.zbuf[b])&&(k=(k<<16)+(k<<1)+k&2147483647,f=k>>16&7,this.addPixel(b,j,0==f?this.argbNoisyDn:1==f?this.argbNoisyUp:this.argbCurrent));++b;l+=c}else{k=f.rScaled<<8;d=s((j.rScaled-f.rScaled<<8)/a);var h=f.gScaled,n=s((j.gScaled-h)/a);f=f.bScaled;for(var q=s((j.bScaled-f)/a);0<=--a;){if(this.addAllPixels||(e=!e))j=l>>10,j>=this.slab&&(j<=
this.depth&&j<this.zbuf[b])&&this.addPixel(b,j,4278190080|k&16711680|h&65280|f>>8&255);++b;l+=c;k+=d;h+=n;f+=q}}}},"~N,~N,~N,~N,~N,J.util.Rgb16,J.util.Rgb16");c(c$,"plotPixelsUnclippedRaster",function(a,b,d,c,e,f,j){if(!(0>=a)){var k=((b<<16)+(d<<1)^858993459)&2147483647,l=0!=((b^d)&1),h=(c<<10)+512;c=e-c;e=s(a/2);c=J.util.GData.roundInt(s(((c<<10)+(0<=c?e:-e))/a));b=d*this.width+b;if(null==f)for(;0<=--a;){if(this.addAllPixels||(l=!l))j=h>>10,j<this.zbuf[b]&&(k=(k<<16)+(k<<1)+k&2147483647,f=k>>16&
7,this.addPixel(b,j,0==f?this.argbNoisyDn:1==f?this.argbNoisyUp:this.argbCurrent));++b;h+=c}else{k=f.rScaled<<8;d=J.util.GData.roundInt(s((j.rScaled-f.rScaled<<8)/a));e=f.gScaled;var n=J.util.GData.roundInt(s((j.gScaled-e)/a));f=f.bScaled;for(var q=J.util.GData.roundInt(s((j.bScaled-f)/a));0<=--a;){if(this.addAllPixels||(l=!l))j=h>>10,j<this.zbuf[b]&&this.addPixel(b,j,4278190080|k&16711680|e&65280|f>>8&255);++b;h+=c;k+=d;e+=n;f+=q}}}},"~N,~N,~N,~N,~N,J.util.Rgb16,J.util.Rgb16");c(c$,"plotPixelsUnclippedCount",
function(a,b,d,c){var e=d*this.width+b;if(this.addAllPixels)for(;0<=--a;)c<this.zbuf[e]&&this.addPixel(e,c,this.argbCurrent),++e;else if(a=e+a,!(0!=((b^d)&1)&&++e==a)){do c<this.zbuf[e]&&this.addPixel(e,c,this.argbCurrent),e+=2;while(e<a)}},"~N,~N,~N,~N");c(c$,"plotPoints",function(a,b,d,c){for(a*=3;0<a;){var e=b[--a],f=b[--a]+c,j=b[--a]+d;if(!this.isClipped3(j,f,e)){var k=f*this.width+j++;e<this.zbuf[k]&&this.addPixel(k,e,this.argbCurrent);this.antialiasThisFrame&&(k=f*this.width+j,!this.isClipped3(j,
f,e)&&e<this.zbuf[k]&&this.addPixel(k,e,this.argbCurrent),k=++f*this.width+j,!this.isClipped3(j,f,e)&&e<this.zbuf[k]&&this.addPixel(k,e,this.argbCurrent),k=f*this.width+--j,!this.isClipped3(j,f,e)&&e<this.zbuf[k]&&this.addPixel(k,e,this.argbCurrent))}}},"~N,~A,~N,~N");c(c$,"setColorNoisy",function(a){this.currentShadeIndex=a;this.argbCurrent=this.shadesCurrent[a];this.argbNoisyUp=this.shadesCurrent[a<J.util.Shader.shadeIndexLast?a+1:J.util.Shader.shadeIndexLast];this.argbNoisyDn=this.shadesCurrent[0<
a?a-1:0]},"~N");h(c$,"setNoisySurfaceShade",function(a,b,d){this.vectorAB.set(b.x-a.x,b.y-a.y,b.z-a.z);null==d?a=this.shader.getShadeIndex(-this.vectorAB.x,-this.vectorAB.y,this.vectorAB.z):(this.vectorAC.set(d.x-a.x,d.y-a.y,d.z-a.z),this.vectorAB.cross(this.vectorAB,this.vectorAC),a=0<=this.vectorAB.z?this.shader.getShadeIndex(-this.vectorAB.x,-this.vectorAB.y,this.vectorAB.z):this.shader.getShadeIndex(this.vectorAB.x,this.vectorAB.y,-this.vectorAB.z));a>J.util.Shader.shadeIndexNoisyLimit&&(a=J.util.Shader.shadeIndexNoisyLimit);
this.setColorNoisy(a)},"JU.P3i,JU.P3i,JU.P3i");c(c$,"getShadeIndexP3",function(a,b,d){this.vectorAB.sub2(b,a);this.vectorAC.sub2(d,a);this.vectorNormal.cross(this.vectorAB,this.vectorAC);return 0<=this.vectorNormal.z?this.shader.getShadeIndex(-this.vectorNormal.x,-this.vectorNormal.y,this.vectorNormal.z):this.shader.getShadeIndex(this.vectorNormal.x,this.vectorNormal.y,-this.vectorNormal.z)},"JU.P3,JU.P3,JU.P3");h(c$,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,
0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");h(c$,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"J.modelset.Atom");h(c$,"getExportType",function(){return 0});h(c$,"getExportName",function(){return null});c(c$,"canDoTriangles",function(){return!0});c(c$,"isCartesianExport",function(){return!1});h(c$,"initializeExporter",function(){return null},"J.viewer.Viewer,~N,J.util.GData,java.util.Map");h(c$,"finalizeOutput",function(){return null});h(c$,"drawBond",
function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");h(c$,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(c$,"getPrivateKey",function(){return 0});h(c$,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});h(c$,"getTransformedVertexVectors",function(){return this.transformedVectors});h(c$,"isDirectedTowardsCamera",function(a){return 0>a||0<this.transformedVectors[a].z},"~N");c(c$,"setRotationMatrix",function(a){for(var b=J.util.Normix.getVertexVectors(),d=J.g3d.Graphics3D.normixCount;0<=
--d;){var c=this.transformedVectors[d];a.transform2(b[d],c);this.shadeIndexes[d]=this.shader.getShadeB(c.x,-c.y,c.z);this.shadeIndexes2Sided[d]=0<=c.z?this.shadeIndexes[d]:this.shader.getShadeB(-c.x,c.y,-c.z)}},"JU.M3");c(c$,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");h(c$,"renderCrossHairs",function(a,b,d,c,e){b=this.isAntialiased();this.setColix(0>e?10:100<e?11:23);e=Math.max(Math.min(this.width,Math.round(c.x)),
0);d=Math.max(Math.min(this.height,Math.round(c.y)),0);var f=Math.round(c.z)+1,j=b?8:4,k=b?20:10;b=b?2:1;this.drawRect(e-j,d,f,0,k,b);this.drawRect(e,d-j,f,0,b,k);this.drawRect(e-j,d-j,f,0,k,k);j=k;k>>=1;this.setColix(a[1]<c.x?21:11);this.drawRect(e-j,d,f,0,k,b);this.setColix(a[0]>c.x?21:11);this.drawRect(e+k,d,f,0,k,b);this.setColix(a[3]<c.y?21:11);this.drawRect(e,d-j,f,0,b,k);this.setColix(a[2]>c.y?21:11);this.drawRect(e,d+k,f,0,b,k)},"~A,~N,~N,JU.P3,~N");h(c$,"initializeOutput",function(){return!1},
"J.viewer.Viewer,~N,J.util.GData,java.util.Map");c(c$,"shadeTextPixel",function(a,b,d,c,e){switch(e){case 8:this.addPixel(a,b,d);return}0!=c&&J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,c,this.bgcolor);e+=this.translucencyLog;7<e||(J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,d&16777215|e<<24,this.bgcolor),this.zbuf[a]=b)},"~N,~N,~N,~N,~N");E(c$,"sort",null);c$.normixCount=c$.prototype.normixCount=J.util.Normix.getNormixCount();E(c$,"nullShadeIndex",50)}),p("J.g3d"),c$=M(J.g3d,"ImageRenderer"),
c$.plotImage=c(c$,"plotImage",function(a,b,d,c,e,f,j,k,l,h){k=(j=-2147483648==a)?e.bgcolor:k;j&&(a=0,d=2147483646,l=e.width,h=e.height);0>=a+l||(a>=e.width||0>=b+h||b>=e.height)||(c=e.apiPlatform.drawImageToBuffer(null,e.platform.offscreenImage,c,l,h,j?k:0),null!=c&&(null!=f||0>a||a+l>e.width||0>b||b+h>e.height?J.g3d.ImageRenderer.plotImageClipped(a,b,d,e,f,l,h,c,k):J.g3d.ImageRenderer.plotImageUnClipped(a,b,d,e,l,h,c,k)))},"~N,~N,~N,~O,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B,~N,~N,~N"),c$.plotImageClipped=
c(c$,"plotImageClipped",function(a,b,d,c,e,f,j,k,l){null==e&&(e=c);for(var h=c=0;c<j;c++)for(var n=0;n<f;n++){var q=k[h++];e.plotImagePixel(q,a+n,b+c,d,8,l)}},"~N,~N,~N,J.g3d.Graphics3D,J.api.JmolRendererInterface,~N,~N,~A,~N"),c$.plotImageUnClipped=c(c$,"plotImageUnClipped",function(a,b,d,c,e,f,j){var k=c.zbuf,l=c.width;a=b*l+a;for(var h=b=0,n=0;b<f;){for(;h<e;)d<k[a]&&c.addPixel(a,d,j[n]),++n,++h,++a;++b;h-=e;a+=l-e}},"~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A,~N"),p("J.g3d"),t(["java.util.Hashtable"],
"J.g3d.LineRenderer",["java.lang.Float","J.util.BSUtil","$.Logger","$.Shader"],function(){c$=w(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nFound=this.nCached=this.nBits=0;this.slopeKey=this.lineCache=null;this.cc2=this.cc1=this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;u(this,arguments)},J.g3d,"LineRenderer");Q(c$,function(){this.lineCache=new java.util.Hashtable});A(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"setLineBits",
function(a,b){this.slope=0!=a?b/a:0<=b?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.getRenderWidth():this.g3d.getRenderHeight();if(!this.getCachedLine()){this.lineBits=J.util.BSUtil.newBitSet(this.nBits);b=Math.abs(b);a=Math.abs(a);if(b>a){var d=a;a=b;b=d}for(var d=0,c=a+a,e=b+b,f=0;f<this.nBits;f++)d+=e,d>a&&(this.lineBits.set(f),d-=c);this.lineCache.put(this.slopeKey,this.lineBits);this.nCached++}},"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear();
this.nCached=0});c(c$,"plotLine",function(a,b,d,c,e,f,j,k,l,h,n){this.x1t=e;this.x2t=k;this.y1t=f;this.y2t=l;this.z1t=j;this.z2t=h;if(n)switch(this.getTrimmedLine()){case 0:n=!1;break;case 2:return}this.plotLineClipped(a,b,d,c,e,f,j,k-e,l-f,h-j,n,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDelta",function(a,b,d,c,e,f,j,k,l,h,n){this.x1t=e;this.x2t=e+k;this.y1t=f;this.y2t=f+l;this.z1t=j;this.z2t=j+h;if(n)switch(this.getTrimmedLine()){case 2:return;case 0:n=!1}this.plotLineClipped(a,b,d,
c,e,f,j,k,l,h,n,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaA",function(a,b,d,c,e,f,j,k,l,h,n,q){this.x1t=f;this.x2t=f+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=k+n;if(q)switch(this.getTrimmedLine()){case 2:return;case 0:q=!1}this.plotLineClippedA(a,b,d,c,e,f,j,k,l,h,n,q,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaBits",function(a,b,d,c,e,f,j,k,l,h,n,q){this.x1t=f;this.x2t=f+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=k+n;q&&2==this.getTrimmedLine()||this.plotLineClippedBits(a,
b,d,c,e,f,j,k,l,h,n,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotDashedLine",function(a,b,d,c,e,f,j,k,l,h,n){this.x1t=e;this.x2t=k;this.y1t=f;this.y2t=l;this.z1t=j;this.z2t=h;if(n)switch(this.getTrimmedLine()){case 2:return;case 0:n=!1}this.plotLineClipped(a,b,a,b,e,f,j,k-e,l-f,h-j,n,d,c)},"~N,~B,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"getCachedLine",function(){this.slopeKey=Float.$valueOf(this.slope);if(!this.lineCache.containsKey(this.slopeKey))return!1;this.lineBits=this.lineCache.get(this.slopeKey);
J.util.Logger.debugging&&(this.nFound++,1E6==this.nFound&&J.util.Logger.debug("nCached/nFound lines: "+this.nCached+" "+this.nFound));return!0});c(c$,"getTrimmedLine",function(){this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t);this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(this.cc1|this.cc2))return 0;var a=this.g3d.xLast,b=this.g3d.yLast,d=this.g3d.slab,c=this.g3d.depth;do{if(0!=(this.cc1&this.cc2))return 2;var e=this.x2t-this.x1t,f=this.y2t-this.y1t,j=this.z2t-this.z1t;0!=
this.cc1?(0!=(this.cc1&8)?(this.y1t+=y(-this.x1t*f/e),this.z1t+=y(-this.x1t*j/e),this.x1t=0):0!=(this.cc1&4)?(this.y1t+=y((a-this.x1t)*f/e),this.z1t+=y((a-this.x1t)*j/e),this.x1t=a):0!=(this.cc1&2)?(this.x1t+=y(-this.y1t*e/f),this.z1t+=y(-this.y1t*j/f),this.y1t=0):0!=(this.cc1&1)?(this.x1t+=y((b-this.y1t)*e/f),this.z1t+=y((b-this.y1t)*j/f),this.y1t=b):0!=(this.cc1&32)?(this.x1t+=y((d-this.z1t)*e/j),this.y1t+=y((d-this.z1t)*f/j),this.z1t=d):(this.x1t+=y((c-this.z1t)*e/j),this.y1t+=y((c-this.z1t)*f/
j),this.z1t=c),this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(this.cc2&8)?(this.y2t+=y(-this.x2t*f/e),this.z2t+=y(-this.x2t*j/e),this.x2t=0):0!=(this.cc2&4)?(this.y2t+=y((a-this.x2t)*f/e),this.z2t+=y((a-this.x2t)*j/e),this.x2t=a):0!=(this.cc2&2)?(this.x2t+=y(-this.y2t*e/f),this.z2t+=y(-this.y2t*j/f),this.y2t=0):0!=(this.cc2&1)?(this.x2t+=y((b-this.y2t)*e/f),this.z2t+=y((b-this.y2t)*j/f),this.y2t=b):0!=(this.cc2&32)?(this.x2t+=y((d-this.z2t)*e/j),this.y2t+=y((d-this.z2t)*f/j),this.z2t=
d):(this.x2t+=y((c-this.z2t)*e/j),this.y2t+=y((c-this.z2t)*f/j),this.z2t=c),this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(this.cc1|this.cc2));return 1});c(c$,"plotLineClipped",function(a,b,d,c,e,f,j,k,h,m,n,q,v){var x=this.g3d.zbuf,N=this.g3d.getRenderWidth(),G=0;0==q&&(v=2147483647,q=1);var p=f*N+e,r=this.g3d.bufferSize,t=0!=((e^f)&1);0!=a&&(!n&&0<=p&&p<r&&j<x[p]&&(!b||(t=!t)))&&this.g3d.addPixel(p,j,a);if(!(0==k&&0==h)){n=1;var y=N;e+=k;var u=f+h;0>k&&(k=-k,n=-1);0>h&&(h=-h,
y=-N);N=k+k;f=h+h;j<<=10;if(h<=k){var w=k-1;0>m&&(w=-w);m=s(((m<<10)+w)/k);h=0;w=Math.abs(e-this.x2t)-1;e=Math.abs(e-this.x1t)-1;for(var u=k-1,C=s(u/2);--u>=w&&!(u==C&&(b=c,a=d,0==a));){p+=n;j+=m;h+=f;h>k&&(p+=y,h-=N,t=!t);if(0!=a&&u<e&&0<=p&&p<r&&G<v&&(!b||(t=!t))){var A=j>>10;A<x[p]&&this.g3d.addPixel(p,A,a)}G=(G+1)%q}}else{w=h-1;0>m&&(w=-w);m=s(((m<<10)+w)/h);k=0;w=Math.abs(u-this.y2t)-1;e=Math.abs(u-this.y1t)-1;u=h-1;for(C=s(u/2);--u>=w&&!(u==C&&(b=c,a=d,0==a));){p+=y;j+=m;k+=N;k>h&&(p+=n,k-=
f,t=!t);if(0!=a&&u<e&&0<=p&&p<r&&G<v&&(!b||(t=!t)))A=j>>10,A<x[p]&&this.g3d.addPixel(p,A,a);G=(G+1)%q}}}},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedA",function(a,b,d,c,e,f,j,k,h,m,n,q,v,x){var p=this.g3d.zbuf,G=this.g3d.getRenderWidth(),r=0;0==v&&(x=2147483647,v=1);var t=j*G+f,u=this.g3d.bufferSize,y=e<J.util.Shader.shadeIndexLast?e+1:e,w=0<e?e-1:e,A=a[y],C=a[w],B=d[e],y=d[y];d=d[w];a=a[e];e=b;var z=0!=((f^j)&1);0!=a&&(!q&&0<=t&&t<u&&k<p[t]&&(!e||(z=!z)))&&this.g3d.addPixel(t,
k,a);if(!(0==h&&0==m)){q=1;var w=G,D=f+h,E=j+m;0>h&&(h=-h,q=-1);0>m&&(m=-m,w=-G);j=h+h;f=m+m;k<<=10;if(m<=h){var F=h-1;0>n&&(F=-F);n=s(((n<<10)+F)/h);m=0;for(var F=Math.abs(D-this.x2t)-1,D=Math.abs(D-this.x1t)-1,E=h-1,H=s(E/2);--E>=F;){if(E==H){a=B;if(0==a)break;A=y;C=d;if((e=c)&&!b)var z=s(t/G),I=t%G,z=0==((I^z)&1)}t+=q;k+=n;m+=f;m>h&&(t+=w,m-=j,z=!z);if(0!=a&&E<D&&0<=t&&t<u&&r<x&&(!e||(z=!z)))if(I=k>>10,I<p[t]){var L=this.shader.nextRandom8Bit();this.g3d.addPixel(t,I,85>L?C:170<L?A:a)}r=(r+1)%v}}else{F=
m-1;0>n&&(F=-F);n=s(((n<<10)+F)/m);h=0;F=Math.abs(E-this.y2t)-1;D=Math.abs(E-this.y1t)-1;E=m-1;for(H=s(E/2);--E>=F;){if(E==H){a=B;if(0==a)break;A=y;C=d;if((e=c)&&!b)z=s(t/G),I=t%G,z=0==((I^z)&1)}t+=w;k+=n;h+=j;h>m&&(t+=q,h-=f,z=!z);if(0!=a&&E<D&&0<=t&&t<u&&r<x&&(!e||(z=!z)))I=k>>10,I<p[t]&&(L=this.g3d.shader.nextRandom8Bit(),this.g3d.addPixel(t,I,85>L?C:170<L?A:a));r=(r+1)%v}}}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedBits",function(a,b,d,c,e,f,j,k,h,m,n,q,v){var x=this.g3d.zbuf,
p=this.g3d.width,G=0;0==q&&(v=2147483647,q=1);var r=e<J.util.Shader.shadeIndexLast?e+1:e,t=0<e?e-1:e,u=a[e],w=a[r],A=a[t];e=d[e];r=d[r];d=d[t];var t=b,C=0!=((f^j)&1);a=j*p+f;var z=this.g3d.bufferSize,B,D,E,F,I;this.lineTypeX?(B=f,D=this.x1t,E=this.x2t,f+=s(h/2),F=j=0<=h?1:-1,I=0<=m?p:-p,h=n/Math.abs(h)):(B=j,D=this.y1t,E=this.y2t,f=j+s(m/2),j=0<=m?1:-1,F=0<=m?p:-p,I=0<=h?1:-1,h=n/Math.abs(m));m=!1;for(n=B;;n+=j,B+=j){n==D&&(m=!0);if(n==f){u=e;if(0==u)break;w=r;A=d;if((t=c)&&!b)C=s(a/p),C=0==((a%p^
C)&1)}if(0!=u&&(m&&0<=a&&a<z&&G<v&&(!t||(C=!C)))&&k<x[a]){var H=this.shader.nextRandom8Bit();this.g3d.addPixel(a,y(k),85>H?A:170<H?w:u)}if(n==E)break;G=(G+1)%q;for(a+=F;0>B;)B+=this.nBits;this.lineBits.get(B%this.nBits)&&(a+=I);k+=h}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~N,~N");E(c$,"VISIBILITY_UNCLIPPED",0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)}),p("J.g3d"),t(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=w(function(){this.g=null;u(this,arguments)},J.g3d,"Pixelator");A(c$,function(a){this.g=
a},"J.g3d.Graphics3D");c(c$,"clearPixel",function(a,b){!this.g.$isPass2&&this.g.zbuf[a]>b&&(this.g.zbuf[a]=2147483647)},"~N,~N");c(c$,"addPixel",function(a,b,d){this.addPixel1(a,b,d)},"~N,~N,~N");c(c$,"addPixel1",function(a,b,d){if(this.g.$isPass2){var c=this.g.zbufT[a];if(b<c){var e=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=e&&c-b>this.g.zMargin)&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,e,this.g.bgcolor);this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=c&&!this.g.translucentCoverOnly&&
b-c>this.g.zMargin&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,d&this.g.translucencyMask,this.g.bgcolor)}else this.g.zbuf[a]=b,this.g.pbuf[a]=d},"~N,~N,~N")}),p("J.g3d"),t(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=M(J.g3d,"PixelatorShaded",J.g3d.Pixelator);h(c$,"addPixel",function(a,b,d){if(!(b>this.g.zDepth)){if(b<=this.g.zDepth&&b>=this.g.zSlab){var c=(d&65280)>>8,e=(d&16711680)>>16,f=d&4278190080,j=(this.g.zDepth-b)/(this.g.zDepth-this.g.zSlab);if(1<this.g.zShadePower)for(var k=
0;k<this.g.zShadePower;k++)j*=j;d=this.g.zShadeR+y(j*((d&255)-this.g.zShadeR));c=this.g.zShadeG+y(j*(c-this.g.zShadeG));e=this.g.zShadeB+y(j*(e-this.g.zShadeB));d=e<<16|c<<8|d|f}this.addPixel1(a,b,d)}},"~N,~N,~N")}),p("J.g3d"),c$=w(function(){this.bufferSizeT=this.bufferSize=this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=
this.graphicsForTextOrImage=this.offscreenImage=null;u(this,arguments)},J.g3d,"Platform3D"),A(c$,function(a){this.apiPlatform=a},"javajs.api.GenericPlatform"),c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))}),c(c$,"allocateTBuffers",function(a){this.bufferSizeT=a?this.bufferSize:this.windowSize;this.zBufferT=D(this.bufferSizeT,0);this.pBufferT=D(this.bufferSizeT,0)},"~B"),c(c$,"allocateBuffers",function(a,b,d,c){this.windowWidth=a;this.windowHeight=
b;this.windowSize=a*b;d&&(a*=2,b*=2);this.bufferWidth=a;this.bufferHeight=b;this.bufferSize=this.bufferWidth*this.bufferHeight;this.zBuffer=D(this.bufferSize,0);this.pBuffer=D(this.bufferSize,0);this.bufferedImage=this.apiPlatform.allocateRgbImage(this.windowWidth,this.windowHeight,this.pBuffer,this.windowSize,J.g3d.Platform3D.backgroundTransparent,c)},"~N,~N,~B,~B"),c(c$,"releaseBuffers",function(){this.windowWidth=this.windowHeight=this.bufferWidth=this.bufferHeight=this.bufferSize=-1;null!=this.bufferedImage&&
(this.apiPlatform.flushImage(this.bufferedImage),this.bufferedImage=null);this.zBufferT=this.pBufferT=this.zBuffer=this.pBuffer=null}),c(c$,"hasContent",function(){for(var a=this.bufferSize;0<=--a;)if(2147483647!=this.zBuffer[a])return!0;return!1}),c(c$,"clearScreenBuffer",function(){for(var a=this.bufferSize;0<=--a;)this.zBuffer[a]=2147483647,this.pBuffer[a]=0}),c(c$,"setBackgroundColor",function(a){if(null!=this.pBuffer)for(var b=this.bufferSize;0<=--b;)0==this.pBuffer[b]&&(this.pBuffer[b]=a)},
"~N"),c(c$,"clearTBuffer",function(){for(var a=this.bufferSizeT;0<=--a;)this.zBufferT[a]=2147483647,this.pBufferT[a]=0}),c(c$,"clearBuffer",function(){this.clearScreenBuffer()}),c(c$,"clearScreenBufferThreaded",function(){}),c(c$,"notifyEndOfRendering",function(){this.apiPlatform.notifyEndOfRendering()}),c(c$,"getGraphicsForTextOrImage",function(a,b){if(a>this.widthOffscreen||b>this.heightOffscreen)null!=this.offscreenImage&&(this.apiPlatform.disposeGraphics(this.graphicsForTextOrImage),this.apiPlatform.flushImage(this.offscreenImage)),
a>this.widthOffscreen&&(this.widthOffscreen=a),b>this.heightOffscreen&&(this.heightOffscreen=b),this.offscreenImage=this.allocateOffscreenImage(this.widthOffscreen,this.heightOffscreen),this.graphicsForTextOrImage=this.apiPlatform.getStaticGraphics(this.offscreenImage,J.g3d.Platform3D.backgroundTransparent);return this.graphicsForTextOrImage},"~N,~N"),c(c$,"allocateOffscreenImage",function(a,b){return this.apiPlatform.newOffScreenImage(a,b)},"~N,~N"),c(c$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=
a},"~B"),E(c$,"backgroundTransparent",!1),p("J.g3d"),t(["JU.P3","J.util.Shader"],"J.g3d.SphereRenderer",["J.util.GData"],function(){c$=w(function(){this.shader=this.g3d=null;this.diameter=this.z=this.y=this.x=this.maxZ=this.minZ=this.maxY=this.minY=this.maxX=this.minX=0;this.tScreened=!1;this.mDeriv=this.coef=this.mat=this.zroot=this.shades=null;this.selectedOctant=0;this.octantPoints=null;this.planeShade=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.addAllPixels=
!1;this.dxyz=this.planeShades=this.ptTemp=null;this.z0=0;u(this,arguments)},J.g3d,"SphereRenderer");Q(c$,function(){this.zroot=ya(2,0);this.ptTemp=new JU.P3;this.planeShades=D(3,0);this.dxyz=O(3,3,0)});A(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,c,e,f,j,k,h,m,n,q){if(1!=f&&(this.width=this.g3d.width,this.height=this.g3d.height,49<d&&(d&=-2),!this.g3d.isClippedXY(d,c,e))){var v=d+1>>1;this.minX=c-v;this.maxX=c+v;this.minY=e-v;this.maxY=e+v;this.slab=
this.g3d.slab;this.depth=this.g3d.depth;this.minZ=f-v;this.maxZ=f+v;this.maxZ<this.slab||this.minZ>this.depth||(this.shader.nOut=this.shader.nIn=0,this.zbuf=this.g3d.zbuf,this.addAllPixels=q,this.offsetPbufBeginLine=this.width*e+c,this.x=c,this.y=e,this.z=f,this.diameter=d,this.tScreened=b,this.shades=a,this.mat=j,null!=j&&(this.coef=k,this.mDeriv=h,this.selectedOctant=m,this.octantPoints=n),null!=j||128<d?(this.renderLarge(),null!=j&&(this.octantPoints=this.mDeriv=this.coef=this.mat=null)):(a=this.getSphereShape(d),
0>this.minX||this.maxX>=this.width||0>this.minY||this.maxY>=this.height||this.minZ<this.slab||f>this.depth?this.renderShapeClipped(a):this.renderShapeUnclipped(a)),this.zbuf=this.shades=null)}},"~A,~B,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A,~B");c(c$,"getSphereShape",function(a){var b;return null==(b=this.shader.sphereShapeCache[a-1])?this.createSphereShape(a):b},"~N");c(c$,"createSphereShape",function(a){for(var b=0,d=0!=(a&1),c=a/2,e=c*c,f=s((a+1)/2),j=d?0:0.5,k=0;k<f;++k,++j)for(var h=j*j,m=d?0:0.5,n=
0;n<f;++n,++m){var q=m*m,q=e-h-q;0<=q&&++b}for(var b=D(b,0),v=0,j=d?0:0.5,k=0;k<f;++k,++j){h=j*j;m=d?0:0.5;for(n=0;n<f;++n,++m)if(q=m*m,q=e-h-q,0<=q){var x=Math.sqrt(q),q=y(x),p=this.shader.getShadeN(m,j,x,c),G=this.shader.getShadeN(-m,j,x,c),r=this.shader.getShadeN(m,-j,x,c),x=this.shader.getShadeN(-m,-j,x,c),q=q|p<<7|G<<13|r<<19|x<<25;b[v++]=q}b[v-1]|=2147483648}return this.shader.sphereShapeCache[a-1]=b},"~N");c(c$,"renderShapeUnclipped",function(a){var b=0,d=1-(this.diameter&1),c=this.offsetPbufBeginLine,
e=c-d*this.width,f=s((this.diameter+1)/2);if(this.tScreened){var j=(this.x^this.y)&1,k=j^d,j=j|(j^d)<<1|k<<2|(k^d)<<3;do{h=c;m=c-d;n=e;q=e-d;k=j=~j;do v=a[b++],x=this.z-(v&127),0!=(k&1)&&x<this.zbuf[h]&&this.g3d.addPixel(h,x,this.shades[v>>7&63]),0!=(k&2)&&x<this.zbuf[m]&&this.g3d.addPixel(m,x,this.shades[v>>13&63]),0!=(k&4)&&x<this.zbuf[n]&&this.g3d.addPixel(n,x,this.shades[v>>19&63]),0!=(k&8)&&x<this.zbuf[q]&&this.g3d.addPixel(q,x,this.shades[v>>25&63]),++h,--m,++n,--q,k=~k;while(0<=v);c+=this.width;
e-=this.width}while(0<--f)}else{do{var h=c,m=c-d,n=e,q=e-d,v;do{v=a[b++];var x=this.z-(v&127);x<this.zbuf[h]&&this.g3d.addPixel(h,x,this.shades[v>>7&63]);x<this.zbuf[m]&&this.g3d.addPixel(m,x,this.shades[v>>13&63]);x<this.zbuf[n]&&this.g3d.addPixel(n,x,this.shades[v>>19&63]);x<this.zbuf[q]&&this.g3d.addPixel(q,x,this.shades[v>>25&63]);++h;--m;++n;--q}while(0<=v);c+=this.width;e-=this.width}while(0<--f)}},"~A");c(c$,"renderShapeClipped",function(a){var b=0,d=1-(this.diameter&1),c=this.offsetPbufBeginLine,
e=c-d*this.width,f=s((this.diameter+1)/2),j=this.y,k=this.y-d,h=(this.x<<16)+(this.y<<1)^858993459,m=(this.x^this.y)&1,n=m^d,m=m|(m^d)<<1|n<<2|(n^d)<<3;do{var n=0<=j&&j<this.height,q=0<=k&&k<this.height,v=c,x=c-d,p=e,G=e-d,r,t=m=~m,u=this.x,w=this.x-d;do{var y=0<=w&&w<this.width,C=0<=u&&u<this.width;r=a[b++];var A;A=r&127;var z;this.z<this.slab?(z=this.z+A,A=z>=this.slab):(z=this.z-A,A=z<this.slab);A&&(z=this.slab);if(z>=this.slab&&z<=this.depth){if(n){if(C&&(this.addAllPixels||0!=(t&1))&&z<this.zbuf[v]){var B=
A?J.g3d.SphereRenderer.SHADE_SLAB_CLIPPED-3+(h>>7&7):r>>7&63;this.g3d.addPixel(v,z,this.shades[B])}if(y&&(this.addAllPixels||0!=(t&2))&&z<this.zbuf[x])B=A?J.g3d.SphereRenderer.SHADE_SLAB_CLIPPED-3+(h>>13&7):r>>13&63,this.g3d.addPixel(x,z,this.shades[B])}if(q){if(C&&(!this.tScreened||0!=(t&4))&&z<this.zbuf[p])B=A?J.g3d.SphereRenderer.SHADE_SLAB_CLIPPED-3+(h>>19&7):r>>19&63,this.g3d.addPixel(p,z,this.shades[B]);if(y&&(!this.tScreened||0!=(t&8))&&z<this.zbuf[G])B=A?J.g3d.SphereRenderer.SHADE_SLAB_CLIPPED-
3+(h>>25&7):r>>25&63,this.g3d.addPixel(G,z,this.shades[B])}}++v;--x;++p;--G;++u;--w;t=~t;A&&(h=(h<<16)+(h<<1)+h&2147483647)}while(0<=r);c+=this.width;e-=this.width;++j;--k}while(0<--f)},"~A");c(c$,"renderLarge",function(){null!=this.mat&&(null==this.shader.ellipsoidShades&&this.shader.createEllipsoidShades(),null!=this.octantPoints&&this.setPlaneDerivatives());this.renderQuadrant(-1,-1);this.renderQuadrant(-1,1);this.renderQuadrant(1,-1);this.renderQuadrant(1,1)});c(c$,"renderQuadrant",function(a,
b){var d=s(this.diameter/2),c=this.x+d*a,e=(0>this.x?-1:this.x<this.width?0:1)+(0>c?-2:c<this.width?0:2);-3==e||3==e||(c=this.y+d*b,c=(0>this.y?-1:this.y<this.height?0:1)+(0>c?-2:c<this.height?0:2),-3==c||3==c||(null==this.mat&&0==e&&0==c&&this.z-d>=this.slab&&this.z<=this.depth?this.renderQuadrantUnclipped(d,a,b):this.renderQuadrantClipped(d,a,b)))},"~N,~N");c(c$,"renderQuadrantUnclipped",function(a,b,d){for(var c=a*a,e=2*a+1,f=0==((this.x^this.y)&1),j=0>d?-this.width:this.width,k=this.offsetPbufBeginLine,
h=0,m=0;m<=c;m+=h+ ++h,k+=j)for(var n=k,q=f=!f,v=c-m,x=this.z-a,p=s((h*d+a<<8)/e),G=0,r=0;r<=v;r+=G+ ++G,n+=b)if((this.addAllPixels||(q=!q))&&!(this.zbuf[n]<=x))if(x=s(Math.sqrt(v-r)),x=this.z-x,!(this.zbuf[n]<=x)){var t=s((G*b+a<<8)/e);this.g3d.addPixel(n,x,this.shades[this.shader.sphereShadeIndexes[(p<<8)+t]])}},"~N,~N,~N");c(c$,"renderQuadrantClipped",function(a,b,d){for(var c=null!=this.mat,e=0<=this.selectedOctant,f=a*a,j=2*a+1,k=0>d?-this.width:this.width,h=this.offsetPbufBeginLine,m=(this.x<<
16)+(this.y<<1)^858993459,n=this.y,q=0,v=0,x=0,p=0;p<=f;p+=x+ ++x,h+=k,n+=d)if(0>n){if(0>d)break}else if(n>=this.height){if(0<d)break}else{var G=f-(c?0:p),r=this.x;c||(q=s((x*d+a<<8)/j));for(var m=(m<<16)+(m<<1)+m&2147483647,t=-1,u=1,w=h,y=0,A=0;A<=G;A+=y+ ++y,w+=b,r+=b)if(0>r){if(0>b)break}else if(r>=this.width){if(0<b)break}else if(!(this.tScreened&&0!=((r^n)&1))){var z;if(c){if(!J.g3d.SphereRenderer.getQuardricZ(r,n,this.coef,this.zroot)){if(0<=t)break;continue}t=this.z<this.slab?1:0;z=s(this.zroot[t]);
0==z&&(z=this.z);u=2;this.z0=z;if(e){this.ptTemp.set(r-this.x,n-this.y,z-this.z);this.mat.transform(this.ptTemp);J.util.GData.getScreenOctant(this.ptTemp)==this.selectedOctant&&(v=this.getPlaneShade(r,n,this.zroot),z=s(this.zroot[0]),u=3);var C=this.z<this.slab?z>=this.slab:z<this.slab;C&&(this.z0=z=this.slab,u=0)}if(z<this.slab||z>this.depth||this.zbuf[w]<=this.z0)continue}else{z=s(Math.sqrt(G-A));z=this.z+(this.z<this.slab?z:-z);if(C=this.z<this.slab?z>=this.slab:z<this.slab)z=this.slab,u=0;if(z<
this.slab||z>this.depth||this.zbuf[w]<=z)continue}switch(u){case 0:v=J.g3d.SphereRenderer.SHADE_SLAB_CLIPPED-3+(m>>8&7);m=(m<<16)+(m<<1)+m&2147483647;u=1;break;case 2:v=this.shader.getEllipsoidShade(r,n,this.zroot[t],a,this.mDeriv);break;case 3:this.g3d.clearPixel(w,this.z0);break;default:v=s((y*b+a<<8)/j),v=this.shader.sphereShadeIndexes[(q<<8)+v]}this.g3d.addPixel(w,z,this.shades[v])}m=(m+r+n|1)&2147483647}},"~N,~N,~N");c$.getQuardricZ=c(c$,"getQuardricZ",function(a,b,d,c){var e=(d[4]*a+d[5]*b+
d[8])/d[2]/2;a=e*e-(d[0]*a*a+d[1]*b*b+d[3]*a*b+d[6]*a+d[7]*b-1)/d[2];if(0>a)return!1;a=Math.sqrt(a);c[0]=-e-a;c[1]=-e+a;return!0},"~N,~N,~A,~A");c(c$,"setPlaneDerivatives",function(){this.planeShade=-1;for(var a=0;3>a;a++){var b=this.dxyz[a][0]=this.octantPoints[a].x-this.x,d=this.dxyz[a][1]=this.octantPoints[a].y-this.y,c=this.dxyz[a][2]=this.octantPoints[a].z-this.z;this.planeShades[a]=this.shader.getShadeIndex(b,d,-c);if(0==b&&0==d){this.planeShade=this.planeShades[a];break}}});c(c$,"getPlaneShade",
function(a,b,d){if(0<=this.planeShade)return this.planeShade;for(var c=3,e,f=3.4028235E38,j=0;3>j;j++)if(0!=(e=this.dxyz[j][2]))e=this.z+(-this.dxyz[j][0]*(a-this.x)-this.dxyz[j][1]*(b-this.y))/e,e<f&&(f=e,c=j);3==c&&(c=0,f=this.z);d[0]=f;return this.planeShades[c]},"~N,~N,~A");E(c$,"maxOddSizeSphere",49,"maxSphereDiameter",1E3,"maxSphereDiameter2",2E3);c$.SHADE_SLAB_CLIPPED=c$.prototype.SHADE_SLAB_CLIPPED=J.util.Shader.shadeIndexNormal-5}),p("J.g3d"),t(["java.util.Hashtable"],"J.g3d.TextRenderer",
["JU.CU"],function(){c$=w(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;u(this,arguments)},J.g3d,"TextRenderer");c$.clearFontCache=c(c$,"clearFontCache",function(){J.g3d.TextRenderer.working||(J.g3d.TextRenderer.htFont3d.clear(),J.g3d.TextRenderer.htFont3dAntialias.clear())});c$.plot=c(c$,"plot",function(a,b,d,c,e,f,j,k,h,m){if(0==f.length)return 0;if(0<=f.indexOf("<su")||0<=f.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,
b,d,c,e,f,j,k,h,m);var n=j.getAscent();b-=n;f=J.g3d.TextRenderer.getPlotText3D(a,b,k,f,j,m);if(f.isInvalid)return f.width;m&&0==(c&12632256)&&(c|=263172);null!=h||0>a||a+f.width>k.width||0>b||b+f.height>k.height?J.g3d.TextRenderer.plotClipped(a,b,d,c,e,k,h,f.mapWidth,f.height,f.tmap):J.g3d.TextRenderer.plotUnclipped(a,b,d,c,e,k,f.mapWidth,f.height,f.tmap);return f.width},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotByCharacter=c(c$,"plotByCharacter",
function(a,b,d,c,e,f,j,k,h,m){for(var n=0,q=f.length,v=Math.round(0.25*j.getHeight()),x=-Math.round(0.3*j.getHeight()),p=0,G=0;G<q;G++){if("<"==f.charAt(G)){if(G+5<q&&f.substring(G,G+6).equals("<color")){var p=c,r=f.indexOf(">",G);if(0>r)continue;c=JU.CU.getArgbFromString(f.substring(G+7,r).trim());G=r;continue}if(G+7<q&&f.substring(G,G+8).equals("</color>")){G+=7;c=p;continue}if(G+4<q&&f.substring(G,G+5).equals("<sub>")){G+=4;b+=v;continue}if(G+4<q&&f.substring(G,G+5).equals("<sup>")){G+=4;b+=x;
continue}if(G+5<q&&f.substring(G,G+6).equals("</sub>")){G+=5;b-=v;continue}if(G+5<q&&f.substring(G,G+6).equals("</sup>")){G+=5;b-=x;continue}}r=J.g3d.TextRenderer.plot(a+n,b,d,c,e,f.substring(G,G+1),j,k,h,m);n+=r}return n},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotUnclipped=c(c$,"plotUnclipped",function(a,b,d,c,e,f,j,k,h){var m=0,n=f.zbuf,q=f.width;a=b*q+a;for(b=0;b<k;b++){for(var v=0;v<j;v++){var x=h[m++];0!=x&&d<n[a]&&f.shadeTextPixel(a,d,c,e,x);
a++}a+=q-j}},"~N,~N,~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A");c$.plotClipped=c(c$,"plotClipped",function(a,b,d,c,e,f,j,k,h,m){null==j&&(j=f);for(var n=f=0;n<h;n++)for(var q=0;q<k;q++){var v=m[f++];0!=v&&j.plotImagePixel(c,a+q,b+n,d,v,e)}},"~N,~N,~N,~N,~N,J.g3d.Graphics3D,J.api.JmolRendererInterface,~N,~N,~A");A(c$,function(a,b){this.ascent=b.getAscent();this.height=b.getHeight();this.width=b.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,javajs.awt.Font");
c$.getPlotText3D=c(c$,"getPlotText3D",function(a,b,d,c,e,f){J.g3d.TextRenderer.working=!0;f=f?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var j=f.get(e),k=null,h=!1,m=!1;null!=j?k=j.get(c):(j=new java.util.Hashtable,h=!0);null==k&&(k=new J.g3d.TextRenderer(c,e),m=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=d.width||0>=b+k.height||b>=d.height;if(k.isInvalid)return k;h&&f.put(e,j);m&&(k.setTranslucency(c,e,d),j.put(c,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,javajs.awt.Font,~B");
c(c$,"setTranslucency",function(a,b,d){a=d.apiPlatform.getTextPixels(a,b,d.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),d.platform.offscreenImage,this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=V(this.size,0);for(b=a.length;0<=--b;)d=a[b]&255,0!=d&&(this.tmap[b]=J.g3d.TextRenderer.translucency[d>>5])}},"~S,javajs.awt.Font,J.g3d.Graphics3D");E(c$,"translucency",[7,6,5,4,3,2,1,8],"working",!1);c$.htFont3d=c$.prototype.htFont3d=new java.util.Hashtable;c$.htFont3dAntialias=
c$.prototype.htFont3dAntialias=new java.util.Hashtable}),p("J.g3d"),c$=M(J.g3d,"TextSorter",null,java.util.Comparator),h(c$,"compare",function(a,b){return null==a||null==b?0:a.z>b.z?-1:a.z<b.z?1:0},"J.g3d.TextString,J.g3d.TextString"),p("J.g3d"),t(["JU.P3i"],"J.g3d.TextString",null,function(){c$=w(function(){this.font=this.text=null;this.bgargb=this.argb=0;u(this,arguments)},J.g3d,"TextString",JU.P3i);c(c$,"setText",function(a,b,d,c,e,f,j){this.text=a;this.font=b;this.argb=d;this.bgargb=c;this.x=
e;this.y=f;this.z=j},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");c(c$,"toString",function(){return qa(this,J.g3d.TextString,"toString",[])+" "+this.text})}),p("J.g3d"),t(["J.g3d.G3DRenderer","J.util.Rgb16"],"J.g3d.TriangleRenderer",["J.util.GData"],function(){c$=w(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.az=this.ay=this.ax=this.g3d=null;u(this,arguments)},J.g3d,"TriangleRenderer",null,J.g3d.G3DRenderer);Q(c$,function(){this.ax=
D(3,0);this.ay=D(3,0);this.az=D(3,0);this.axW=D(64,0);this.azW=D(64,0);this.axE=D(64,0);this.azE=D(64,0);this.rgb16t1=new J.util.Rgb16;this.rgb16t2=new J.util.Rgb16});A(c$,function(){});h(c$,"set",function(a){try{this.rgb16sW=Array(64);this.rgb16sE=Array(64);for(var b=64;0<=--b;)this.rgb16sW[b]=new J.util.Rgb16,this.rgb16sE[b]=new J.util.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(b=3;0<=--b;)this.rgb16sGouraud[b]=new J.util.Rgb16}catch(d){if(!C(d,Exception))throw d;}return this},"J.api.JmolRendererInterface");
c(c$,"reallocRgb16s",function(a,b){var d=Array(b);System.arraycopy(a,0,d,0,a.length);for(var c=a.length;c<b;++c)d[c]=new J.util.Rgb16;return d},"~A,~N");c(c$,"setGouraud",function(a,b,d){this.rgb16sGouraud[0].setInt(a);this.rgb16sGouraud[1].setInt(b);this.rgb16sGouraud[2].setInt(d)},"~N,~N,~N");c(c$,"drawfillTriangle",function(a,b,d,c,e,f,j,k,h,m){this.ax[0]=a;this.ax[1]=c;this.ax[2]=j;this.ay[0]=b;this.ay[1]=e;this.ay[2]=k;this.az[0]=d;this.az[1]=f;this.az[2]=h;this.fillTriangleB(m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");
c(c$,"fillTriangleXYZ",function(a,b,d,c,e,f,j,k,h,m){this.ax[0]=a;this.ax[1]=c;this.ax[2]=j;this.ay[0]=b;this.ay[1]=e;this.ay[2]=k;this.az[0]=d;this.az[1]=f;this.az[2]=h;this.fillTriangleB(m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"fillTriangleP3i",function(a,b,d,c){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;this.fillTriangleB(c)},"JU.P3i,JU.P3i,JU.P3i,~B");c(c$,"fillTriangleP3f",function(a,b,d,c){this.ax[0]=
Math.round(a.x);this.ax[1]=Math.round(b.x);this.ax[2]=Math.round(d.x);this.ay[0]=Math.round(a.y);this.ay[1]=Math.round(b.y);this.ay[2]=Math.round(d.y);this.az[0]=Math.round(a.z);this.az[1]=Math.round(b.z);this.az[2]=Math.round(d.z);this.fillTriangleB(c)},"JU.P3,JU.P3,JU.P3,~B");c(c$,"fillTriangleP3if",function(a,b,d,c,e){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;J.g3d.TriangleRenderer.adjustVertex(this.ax,
c);J.g3d.TriangleRenderer.adjustVertex(this.ay,c);J.g3d.TriangleRenderer.adjustVertex(this.az,c);this.fillTriangleB(e)},"JU.P3i,JU.P3i,JU.P3i,~N,~B");c$.adjustVertex=c(c$,"adjustVertex",function(a,b){for(var d=(a[0]+a[1]+a[2])/3,c=0;3>c;c++)a[c]+=b*(d-a[c])},"~A,~N");c(c$,"fillTriangleB",function(a){if(!(1>=this.az[0]||1>=this.az[1]||1>=this.az[2])){var b=this.g3d.clipCode3(this.ax[0],this.ay[0],this.az[0]),d=this.g3d.clipCode3(this.ax[1],this.ay[1],this.az[1]),c=this.g3d.clipCode3(this.ax[2],this.ay[2],
this.az[2]),e=0!=(b|d|c);if(!(e&&0!=(b&d&c))){b=0;this.ay[1]<this.ay[b]&&(b=1);this.ay[2]<this.ay[b]&&(b=2);d=(b+1)%3;c=(b+2)%3;if(this.ay[d]>this.ay[c])var f=d,d=c,c=f;var j=this.ay[b],k=this.ay[d],h=this.ay[c],m=h-j+1;if(!(m>3*this.g3d.height)){m>this.axW.length&&this.reallocRasterArrays(m);var n,q;a?(n=this.rgb16sW,q=this.rgb16sE):n=q=null;f=k-j;0==f?(this.ax[d]<this.ax[b]&&(f=d,d=b,b=f),this.generateRaster(m,b,c,this.axW,this.azW,0,n),this.generateRaster(m,d,c,this.axE,this.azE,0,q)):k==h?(this.ax[c]<
this.ax[d]&&(f=d,d=c,c=f),this.generateRaster(m,b,d,this.axW,this.azW,0,n),this.generateRaster(m,b,c,this.axE,this.azE,0,q)):(k=this.ax[c]-this.ax[b],h=J.util.GData.roundInt(s(m/2)),0>k&&(h=-h),this.ax[b]+s((k*f+h)/m)<this.ax[d]?(this.generateRaster(m,b,c,this.axW,this.azW,0,n),this.generateRaster(f+1,b,d,this.axE,this.azE,0,q),this.generateRaster(m-f,d,c,this.axE,this.azE,f,q)):(this.generateRaster(f+1,b,d,this.axW,this.azW,0,n),this.generateRaster(m-f,d,c,this.axW,this.azW,f,n),this.generateRaster(m,
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function(){return this.clickabilityFlags});c(c$,"setClickable",function(a){this.clickabilityFlags=0==a?0:this.clickabilityFlags|a},"~N");c(c$,"isVisible",function(a){if(!this.isInFrame()||this.group.chain.model.modelSet.isAtomHidden(this.index))return!1;if(0!=a)return this.isShapeVisible(a);a=this.shapeVisibilityFlags;if(this.group.shapeVisibilityFlags!=J.modelset.Atom.BACKBONE_VISIBILITY_FLAG||this.isLeadAtom())a|=this.group.shapeVisibilityFlags;return 0!=(a&-2)},"~N");h(c$,"isLeadAtom",function(){return this.group.isLeadAtom(this.index)});
c(c$,"getGroupParameter",function(a){return this.group.getGroupParameter(a)},"~N");h(c$,"getChainID",function(){return this.group.chain.chainID});h(c$,"getChainIDStr",function(){return this.group.chain.getIDStr()});c(c$,"getSurfaceDistance100",function(){return this.group.chain.model.modelSet.getSurfaceDistance100(this.index)});c(c$,"getVibrationVector",function(){return this.group.chain.model.modelSet.getVibration(this.index,!1)});c(c$,"getVibrationCoord",function(a){return this.group.chain.model.modelSet.getVibrationCoord(this.index,
a)},"~S");c(c$,"getPolymerLength",function(){return this.group.getBioPolymerLength()});c(c$,"getPolymerIndexInModel",function(){return this.group.getBioPolymerIndexInModel()});c(c$,"getMonomerIndex",function(){return this.group.getMonomerIndex()});c(c$,"getSelectedGroupCountWithinChain",function(){return this.group.chain.selectedGroupCount});c(c$,"getSelectedGroupIndexWithinChain",function(){return this.group.getSelectedGroupIndex()});c(c$,"getSelectedMonomerCountWithinPolymer",function(){return this.group.getSelectedMonomerCount()});
c(c$,"getSelectedMonomerIndexWithinPolymer",function(){return this.group.getSelectedMonomerIndex()});c(c$,"getChain",function(){return this.group.chain});c(c$,"getModelNumberForLabel",function(){return this.group.chain.model.modelSet.getModelNumberForAtomLabel(this.modelIndex)});c(c$,"getModelNumber",function(){return this.group.chain.model.modelSet.getModelNumber(this.modelIndex)%1E6});c(c$,"getModelFileIndex",function(){return this.group.chain.model.fileIndex});c(c$,"getModelFileNumber",function(){return this.group.chain.model.modelSet.getModelFileNumber(this.modelIndex)});
h(c$,"getBioStructureTypeName",function(){return this.getProteinStructureType().getBioStructureTypeName(!0)});c(c$,"getProteinStructureType",function(){return this.group.getProteinStructureType()});c(c$,"getProteinStructureSubType",function(){return this.group.getProteinStructureSubType()});c(c$,"getStrucNo",function(){return this.group.getStrucNo()});c(c$,"getStructureId",function(){return this.group.getStructureId()});c(c$,"getProteinStructureTag",function(){return this.group.getProteinStructureTag()});
c(c$,"getGroupID",function(){return this.group.groupID});c(c$,"getSeqcodeString",function(){return this.group.getSeqcodeString()});c(c$,"getInsertionCode",function(){return this.group.getInsertionCode()});h(c$,"equals",function(a){return this===a},"~O");h(c$,"hashCode",function(){return this.index});c(c$,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var b=this.bonds.length;0<=--b;){var d=this.bonds[b],c=d.getOtherAtom(this);if(d.isAromatic()&&c.index!=a)return c}return null},
"~N");c$.atomPropertyInt=c(c$,"atomPropertyInt",function(a,b){switch(b){case 1095763969:return a.getAtomNumber();case 1095761922:return a.atomID;case 1095761923:return a.getIndex();case 1095761924:return a.getCovalentBondCount();case 1095761927:return a.group.chain.index+1;case 1766856708:return a.group.chain.model.modelSet.viewer.getColorArgbOrGray(a.getColix());case 1087375365:case 1095763978:return a.getElementNumber();case 1095761929:return a.atomicAndIsotopeNumber;case 1229984263:return a.getModelFileIndex()+
1;case 1632634891:return a.getFormalCharge();case 1095761932:return a.getGroupID();case 1095761933:return a.group.getGroupIndex();case 1095766030:return a.getModelNumber();case -1095766030:return a.getModelFileNumber();case 1095761935:return a.modelIndex;case 1095761936:return a.getMoleculeNumber(!0);case 1129318401:return a.getOccupancy100();case 1095761937:return a.getGroup().getBioPolymerIndexInModel()+1;case 1095761938:return a.getPolymerLength();case 1666189314:return a.getRasMolRadius();case 1095761939:return a.getResno();
case 1095761940:return a.getAtomSite();case 1641025539:return a.getProteinStructureType().getId();case 1238369286:return a.getProteinStructureSubType().getId();case 1095761941:return a.getStrucNo();case 1297090050:return a.getSymOp();case 1095763990:return a.getValence()}return 0},"J.modelset.Atom,~N");c(c$,"getSymOp",function(){return null==this.atomSymmetry?0:this.atomSymmetry.nextSetBit(0)+1});c$.atomPropertyFloat=c(c$,"atomPropertyFloat",function(a,b,d){switch(d){case 1666189314:return b.getRadius();
case 1114638363:return a.isAtomSelected(b.index)?1:0;case 1112539151:return b.group.chain.model.modelSet.getSurfaceDistanceMax(),b.getSurfaceDistance100()/100;case 1112541199:return b.getBfactor100()/100;case 1114638362:return b.getHydrophobicity();case 1313866249:return b.getVolume(a,J.constant.EnumVdw.AUTO);case 1112539137:return b.getADPMinMax(!0);case 1112539138:return b.getADPMinMax(!1);case 1112541185:case 1112541205:return b.x;case 1112541186:case 1112541206:return b.y;case 1112541187:case 1112541207:return b.z;
case 1112539140:return b.getCovalentRadiusFloat();case 1112541188:return b.getFractionalCoord("X",!0);case 1112541189:return b.getFractionalCoord("Y",!0);case 1112541190:return b.getFractionalCoord("Z",!0);case 1112541191:return b.getFractionalCoord("X",!1);case 1112541192:return b.getFractionalCoord("Y",!1);case 1112541193:return b.getFractionalCoord("Z",!1);case 1112539147:return b.sX;case 1112539148:return b.group.chain.model.modelSet.viewer.getScreenHeight()-b.sY;case 1112539149:return b.sZ;case 1112541195:return b.getBondingRadiusFloat();
case 1112539143:return b.getMass();case 1129318401:return b.getOccupancy100()/100;case 1112541196:return b.getPartialCharge();case 1112539145:case 1112539146:case 1112539144:if(b.group.chain.model.isJmolDataFrame&&b.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(d){case 1112539145:return b.getFractionalCoord("X",!1);case 1112539146:return b.getFractionalCoord("Y",!1);case 1112539144:if(b.group.chain.model.isJmolDataFrame&&b.group.chain.model.jmolFrameType.equals("plot ramachandran"))return a=
b.getFractionalCoord("Z",!1)-180,-180>a?360+a:a}return b.getGroupParameter(d);case 1112539141:case 1112539152:case 1112539150:return b.getGroupParameter(d);case 1113200651:return b.getRadius();case 1115297793:case 1113200642:case 1113198595:case 1113198596:case 1113198597:case 1113200646:case 1113200647:case 1113200649:case 1113200650:case 1113200652:case 1650071565:case 1113200654:return a.getAtomShapeValue(d,b.group,b.index);case 1112539153:return b.getFractionalUnitCoord("X");case 1112539154:return b.getFractionalUnitCoord("Y");
case 1112539155:return b.getFractionalUnitCoord("Z");case 1649412120:return b.getVanderwaalsRadiusFloat(a,J.constant.EnumVdw.AUTO);case 1112541202:return b.getVibrationCoord("X");case 1112541203:return b.getVibrationCoord("Y");case 1112541204:return b.getVibrationCoord("Z");case 1649410049:return b=b.getVibrationVector(),null==b?0:b.length()*a.getFloat(1649410049);case 1112539142:return a.getNMRCalculation().getMagneticShielding(b);case 1112539139:return a.getNMRCalculation().getChemicalShift(b)}return J.modelset.Atom.atomPropertyInt(b,
d)},"J.viewer.Viewer,J.modelset.Atom,~N");c(c$,"getMass",function(){var a=this.getIsotopeNumber();return 0<a?a:J.util.Elements.getAtomicMass(this.getElementNumber())});c$.atomPropertyString=c(c$,"atomPropertyString",function(a,b,d){switch(d){case 1087373315:return a=b.altloc,"\x00"==a?"":""+a;case 1087375362:return b.getAtomName();case 1087375361:return b.getAtomType();case 1087373316:return b.getChainIDStr();case 1087373320:return b.getGroup1("?");case 1087373319:return b.getGroup1("\x00");case 1087373318:return b.getGroup3(!1);
case 1087375365:return b.getElementSymbolIso(!0);case 1087373321:return b.getIdentity(!0);case 1087373322:return a=b.getInsertionCode(),"\x00"==a?"":""+a;case 1826248715:case 1288701960:return a=b.group.chain.model.modelSet.getAtomLabel(b.getIndex()),null==a&&(a=""),a;case 1641025539:return b.getProteinStructureType().getBioStructureTypeName(!1);case 1238369286:return b.getProteinStructureSubType().getBioStructureTypeName(!1);case 1087373324:return b.getStructureId();case 1087373323:return a.getHybridizationAndAxes(b.index,
null,null,"d");case 1087375373:return b.getElementSymbolIso(!1);case 1089470478:return b.getSymmetryOperatorList()}return""},"J.viewer.Viewer,J.modelset.Atom,~N");c$.atomPropertyTuple=c(c$,"atomPropertyTuple",function(a,b){switch(b){case 1146095627:return a.getFractionalCoordPt(!a.group.chain.model.isJmolDataFrame);case 1146095629:return a.getFractionalCoordPt(!1);case 1146093582:return a.group.chain.model.isJmolDataFrame?a.getFractionalCoordPt(!1):a.getFractionalUnitCoordPt(!1);case 1146095628:return JU.P3.new3(a.sX,
a.group.chain.model.modelSet.viewer.getScreenHeight()-a.sY,a.sZ);case 1146095631:var d=a.getVibrationVector();null==d&&(d=new JU.V3);return d;case 1146095626:return a;case 1766856708:return JU.CU.colorPtFromInt2(a.group.chain.model.modelSet.viewer.getColorArgbOrGray(a.getColix()))}return null},"J.modelset.Atom,~N");c(c$,"isWithinStructure",function(a){return this.group.isWithinStructure(a)},"J.constant.EnumStructure");h(c$,"getOffsetResidueAtom",function(a,b){return this.group.chain.model.modelSet.getGroupAtom(this,
b,a)},"~S,~N");h(c$,"isCrossLinked",function(a){return this.group.isCrossLinked(a.getGroup())},"J.util.JmolNode");h(c$,"getCrossLinkLeadAtomIndexes",function(a){return this.group.getCrossLinkLead(a)},"JU.List");h(c$,"toString",function(){return this.getInfo()});c(c$,"isWithinFourBonds",function(a){if(this.modelIndex!=a.modelIndex)return!1;if(this.isCovalentlyBonded(a))return!0;for(var b=a.bonds,d=0;d<b.length;d++){var c=b[d].getOtherAtom(a);if(this.isCovalentlyBonded(c))return!0;for(var e=0;e<this.bonds.length;e++)if(this.bonds[e].getOtherAtom(this).isCovalentlyBonded(c))return!0}return!1},
"J.modelset.Atom");h(c$,"findAtomsLike",function(a){return this.group.chain.model.modelSet.viewer.getAtomBitSet(a)},"~S");E(c$,"VIBRATION_VECTOR_FLAG",1,"IS_HETERO_FLAG",2,"FLAG_MASK",3,"RADIUS_MAX",16,"RADIUS_GLOBAL",16.1,"MAD_GLOBAL",32200);c$.BACKBONE_VISIBILITY_FLAG=c$.prototype.BACKBONE_VISIBILITY_FLAG=J.viewer.JC.getShapeVisibilityFlag(9)}),p("J.modelset"),t(["java.lang.Float","JU.BS","$.V3"],"J.modelset.AtomCollection","java.lang.Character java.util.Arrays $.Hashtable JU.A4 $.AU $.List $.M3 $.P3 $.PT J.api.Interface J.atomdata.RadiusData J.constant.EnumPalette $.EnumStructure $.EnumVdw J.modelset.Group J.script.T J.util.BSUtil $.Elements $.Escape $.Logger $.Measure $.Parser $.Txt $.Vibration J.viewer.JC".split(" "),
function(){c$=w(function(){this.atoms=this.g3d=this.viewer=null;this.atomCount=0;this.surfaceDistance100s=this.atomTensors=this.atomTensorList=this.hydrophobicities=this.ionicRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSerials=this.atomTypes=this.atomNames=null;this.haveStraightness=!1;this.labeler=this.bsHidden=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=!1;this.surfaceDistanceMax=this.bfactor100Hi=this.bfactor100Lo=0;
this.bsSurface=null;this.nSurfaceAtoms=0;this.bspf=null;this.preserveState=!0;this.tainted=null;this.canSkipLoad=!0;this.aaRet=this.bsFoundRectangle=this.bsEmpty=null;la("J.modelset.AtomCollection.AtomSorter")||J.modelset.AtomCollection.$AtomCollection$AtomSorter$();this.bsModulated=null;u(this,arguments)},J.modelset,"AtomCollection");Q(c$,function(){this.bsHidden=new JU.BS;this.bsEmpty=new JU.BS;this.bsFoundRectangle=new JU.BS});c(c$,"releaseModelSet",function(){this.releaseModelSetAC()});c(c$,"releaseModelSetAC",
function(){this.atomTensors=this.ionicRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=this.bspf=this.g3d=this.viewer=this.atoms=null});c(c$,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomSerials=a.atomSerials;this.vibrations=a.vibrations;this.occupancies=a.occupancies;this.bfactor100s=a.bfactor100s;this.ionicRadii=
a.ionicRadii;this.partialCharges=a.partialCharges;this.atomTensors=a.atomTensors;this.atomTensorList=a.atomTensorList;this.bsModulated=a.bsModulated;this.setHaveStraightness(!1);this.surfaceDistance100s=null},"J.modelset.AtomCollection");c(c$,"setHaveStraightness",function(a){this.haveStraightness=a},"~B");c(c$,"getHaveStraightness",function(){return this.haveStraightness});c(c$,"getAtomPointVector",function(a){var b=new JU.List;if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.addLast(this.atoms[d]);
return b},"JU.BS");c(c$,"getAtomCount",function(){return this.atomCount});c(c$,"modelSetHasVibrationVectors",function(){return null!=this.vibrations});c(c$,"getAtomTypes",function(){return this.atomTypes});c(c$,"getPartialCharges",function(){return this.partialCharges});c(c$,"getIonicRadii",function(){return this.ionicRadii});c(c$,"getBFactors",function(){return this.bfactor100s});c(c$,"getHydrophobicity",function(){return this.hydrophobicities});c(c$,"setBsHidden",function(a){this.bsHidden=a},"JU.BS");
c(c$,"isAtomHidden",function(a){return this.bsHidden.get(a)},"~N");c(c$,"getAtomInfo",function(a,b){return null==b?this.atoms[a].getInfo():this.getLabeler().formatLabel(this.viewer,this.atoms[a],b)},"~N,~S");c(c$,"getLabeler",function(){return null==this.labeler?this.labeler=J.api.Interface.getOptionInterface("modelset.LabelToken"):this.labeler});c(c$,"getAtomInfoXYZ",function(a,b){return this.atoms[a].getInfoXYZ(b)},"~N,~B");c(c$,"getElementSymbol",function(a){return this.atoms[a].getElementSymbol()},
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c(c$,"getAtomVdwRadius",function(a,b){return this.atoms[a].getVanderwaalsRadiusFloat(this.viewer,b)},"~N,J.constant.EnumVdw");c(c$,"getAtomColix",function(a){return this.atoms[a].getColix()},"~N");c(c$,"getAtomChain",function(a){return this.atoms[a].getChainIDStr()},"~N");c(c$,"getQuaternion",function(a,b){return 0>a?null:this.atoms[a].group.getQuaternion(b)},"~N,~S");c(c$,"getHelixData",function(a,b){var d=a.nextSetBit(0);return 0>d?"null":this.atoms[d].group.getHelixData(b,this.viewer.getQuaternionFrame(),
this.viewer.getInt(553648146))},"JU.BS,~N");c(c$,"getAtomIndexFromAtomNumber",function(a,b){for(var d=0;d<this.atomCount;d++){var c=this.atoms[d];if(c.getAtomNumber()==a&&b.get(c.modelIndex))return d}return-1},"~N,JU.BS");c(c$,"setFormalCharges",function(a,b){if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.atoms[d].setFormalCharge(b),this.taintAtom(d,4)},"JU.BS,~N");c(c$,"getAtomicCharges",function(){for(var a=O(this.atomCount,0),b=this.atomCount;0<=--b;)a[b]=this.atoms[b].getElementNumber();
return a});c(c$,"getRadiusVdwJmol",function(a){return J.util.Elements.getVanderwaalsMar(a.getElementNumber(),J.constant.EnumVdw.JMOL)/1E3},"J.modelset.Atom");c(c$,"getMaxVanderwaalsRadius",function(){1.4E-45==this.maxVanderwaalsRadius&&this.findMaxRadii();return this.maxVanderwaalsRadius});c(c$,"findMaxRadii",function(){for(var a=this.atomCount;0<=--a;){var b=this.atoms[a],d=b.getBondingRadiusFloat();d>this.maxBondingRadius&&(this.maxBondingRadius=d);b=b.getVanderwaalsRadiusFloat(this.viewer,J.constant.EnumVdw.AUTO);
b>this.maxVanderwaalsRadius&&(this.maxVanderwaalsRadius=b)}});c(c$,"clearBfactorRange",function(){this.hasBfactorRange=!1});c(c$,"calcBfactorRange",function(a){if(!this.hasBfactorRange){this.bfactor100Lo=2147483647;this.bfactor100Hi=-2147483648;if(null==a)for(var b=0;b<this.atomCount;b++)this.setBf(b);else for(b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.setBf(b);this.hasBfactorRange=!0}},"JU.BS");c(c$,"setBf",function(a){a=this.atoms[a].getBfactor100();a<this.bfactor100Lo?this.bfactor100Lo=a:
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b){var d=0;if(null!=a)for(var c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))d+=this.atoms[c].getVolume(this.viewer,b);return d},"JU.BS,J.constant.EnumVdw");c(c$,"getSurfaceDistance100",function(a){if(0==this.nSurfaceAtoms)return-1;null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistance100s[a]},"~N");c(c$,"calcSurfaceDistances",function(){this.calculateSurface(null,-1)});c(c$,"calculateSurface",function(a,b){0>b&&(b=3);var d=J.api.Interface.getOptionInterface("geodesic.EnvelopeCalculation").set(this.viewer,
this.atomCount,null);d.calculate(new J.atomdata.RadiusData(null,b,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,J.util.BSUtil.copyInvert(a,this.atomCount),!1,!1,!1,!0);var c=d.getPoints();this.surfaceDistanceMax=0;this.bsSurface=d.getBsSurfaceClone();this.surfaceDistance100s=D(this.atomCount,0);this.nSurfaceAtoms=J.util.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var d=3.4028235E38==b?0:b,e=0;e<this.atomCount;e++)if(this.bsSurface.get(e))this.surfaceDistance100s[e]=
0;else{for(var f=3.4028235E38,j=this.atoms[e],k=c.length;0<=--k;){var h=Math.abs(c[k].distance(j)-d);0>h&&J.util.Logger.debugging&&J.util.Logger.debug("draw d"+k+" "+J.util.Escape.eP(c[k])+' "'+h+" ? "+j.getInfo()+'"');f=Math.min(h,f)}h=this.surfaceDistance100s[e]=s(Math.floor(100*f));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,h)}return c},"JU.BS,~N");c(c$,"setAtomCoord2",function(a,b,d){var c=null,e=null,f=null,j=0,k=1;if(r(d,JU.P3))c=d;else if(r(d,JU.List)){f=d;if(0==(k=f.size()))return;
j=1}else if(JU.PT.isAP(d)){e=d;if(0==(k=e.length))return;j=2}else return;d=0;if(null!=a)for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){switch(j){case 1:if(d>=k)return;c=f.get(d++);break;case 2:if(d>=k)return;c=e[d++]}switch(b){case 1146095626:this.setAtomCoord(h,c.x,c.y,c.z);break;case 1146095627:this.atoms[h].setFractionalCoordTo(c,!0);this.taintAtom(h,2);break;case 1146095629:this.atoms[h].setFractionalCoordTo(c,!1);this.taintAtom(h,2);break;case 1146095631:this.setAtomVibrationVector(h,c)}}},
"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.atomCount)){var e=this.atoms[a];e.set(b,d,c);this.fixTrajectory(e);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"fixTrajectory",function(a){var b=a.modelIndex;if(this.isTrajectory(b)){var d=null!=this.unitCells&&this.unitCells[b].getCoordinatesAreFractional(),c=this.trajectorySteps.get(b)[a.index-this.models[b].firstAtomIndex];
c.set(a.x,a.y,a.z);d&&this.unitCells[b].toFractional(c,!0)}},"J.modelset.Atom");c(c$,"setAtomCoordRelative",function(a,b,d,c){if(!(0>a||a>=this.atomCount)){var e=this.atoms[a];e.x+=b;e.y+=d;e.z+=c;this.fixTrajectory(e);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"setAtomsCoordRelative",function(a,b,d,c){if(null!=a)for(var e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))this.setAtomCoordRelative(e,b,d,c)},"JU.BS,~N,~N,~N");c(c$,"setAPa",function(a,b,d,c,e,f,j){var k=0;if(!(null!=f&&0==f.length||null==a)){for(var h=
null!=f&&f.length==this.atomCount||null!=j&&j.length==this.atomCount,m=a.nextSetBit(0);0<=m;m=a.nextSetBit(m+1)){h&&(k=m);if(null!=f){if(k>=f.length)return;c=f[k++];d=y(c)}else if(null!=j){if(k>=j.length)return;e=j[k++]}var n=this.atoms[m];switch(b){case 1087375362:this.taintAtom(m,0);this.setAtomName(m,e);break;case 1095763969:this.taintAtom(m,13);this.setAtomNumber(m,d);break;case 1087375361:this.taintAtom(m,1);this.setAtomType(m,e);break;case 1112541185:case 1112541205:this.setAtomCoord(m,c,n.y,
n.z);break;case 1112541186:case 1112541206:this.setAtomCoord(m,n.x,c,n.z);break;case 1112541187:case 1112541207:this.setAtomCoord(m,n.x,n.y,c);break;case 1112541202:case 1112541203:case 1112541204:this.setVibrationVector2(m,b,c);break;case 1112541188:case 1112541189:case 1112541190:n.setFractionalCoord(b,c,!0);this.taintAtom(m,2);break;case 1112541191:case 1112541192:case 1112541193:n.setFractionalCoord(b,c,!1);this.taintAtom(m,2);break;case 1095763978:case 1087375365:this.setElement(n,d);break;case 1632634891:n.setFormalCharge(d);
this.taintAtom(m,4);break;case 1114638362:this.setHydrophobicity(m,c)&&this.taintAtom(m,5);break;case 1826248715:case 1288701960:this.viewer.setAtomLabel(e,m);break;case 1129318401:2>d&&(d=s(Math.floor(100*c)));this.setOccupancy(m,d)&&this.taintAtom(m,7);break;case 1112541196:this.setPartialCharge(m,c)&&this.taintAtom(m,8);break;case 1112541195:this.setIonicRadius(m,c)&&this.taintAtom(m,6);break;case 1666189314:case 1113200651:0>c?c=0:16<c&&(c=16.1);n.madAtom=oa(2E3*c);break;case 1114638363:this.viewer.setSelectedAtom(n.index,
0!=c);break;case 1112541199:this.setBFactor(m,c)&&this.taintAtom(m,9);break;case 1095763990:n.setValence(d);this.taintAtom(m,10);break;case 1649412120:n.setRadius(c)?this.taintAtom(m,11):this.untaint(m,11);break;default:J.util.Logger.error("unsettable atom property: "+J.script.T.nameOf(b))}}1114638363==b&&this.viewer.setSelectedAtom(-1,!1)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"setElement",function(a,b){this.taintAtom(a.index,3);a.setAtomicAndIsotopeNumber(b);a.setPaletteID(J.constant.EnumPalette.CPK.id);
a.setColixAtom(this.viewer.getColixAtomPalette(a,J.constant.EnumPalette.CPK.id))},"J.modelset.Atom,~N");c(c$,"getVibrationCoord",function(a,b){var d;if(null==this.vibrations||null==(d=this.vibrations[a]))return 0;switch(b){case "X":return d.x;case "Y":return d.y;default:return d.z}},"~N,~S");c(c$,"getVibration",function(a,b){var d=null==this.vibrations?null:this.vibrations[a];return null==d&&b?new J.util.Vibration:d},"~N,~B");c(c$,"setVibrationVector",function(a,b){if(!Float.isNaN(b.x)&&!Float.isNaN(b.y)&&
!Float.isNaN(b.z)){if(null==this.vibrations||this.vibrations.length<a)this.vibrations=Array(this.atoms.length);r(b,J.util.Vibration)?this.vibrations[a]=b:(null==this.vibrations[a]&&(this.vibrations[a]=new J.util.Vibration),this.vibrations[a].setT(b));this.atoms[a].setVibrationVector()}},"~N,JU.T3");c(c$,"setVibrationVector2",function(a,b,d){var c=this.getVibration(a,!0);switch(b){case 1112541202:c.x=d;break;case 1112541203:c.y=d;break;case 1112541204:c.z=d}this.setAtomVibrationVector(a,c)},"~N,~N,~N");
c(c$,"setAtomName",function(a,b){var d=J.viewer.JC.lookupSpecialAtomID(b);this.atoms[a].atomID=d;0<d&&this.models[this.atoms[a].modelIndex].isBioModel||(null==this.atomNames&&(this.atomNames=Array(this.atoms.length)),this.atomNames[a]=b)},"~N,~S");c(c$,"setAtomType",function(a,b){null==this.atomTypes&&(this.atomTypes=Array(this.atoms.length));this.atomTypes[a]=b},"~N,~S");c(c$,"setAtomNumber",function(a,b){null==this.atomSerials&&(this.atomSerials=D(this.atoms.length,0));this.atomSerials[a]=b;return!0},
"~N,~N");c(c$,"setOccupancy",function(a,b){if(null==this.occupancies){if(100==b)return!1;this.occupancies=V(this.atoms.length,0);for(var d=this.atoms.length;0<=--d;)this.occupancies[d]=100}this.occupancies[a]=255<b?255:0>b?0:b;return!0},"~N,~N");c(c$,"setPartialCharge",function(a,b){if(Float.isNaN(b))return!1;if(null==this.partialCharges){if(0==b&&!Float.$valueOf(b).equals(J.modelset.AtomCollection.MINUSZERO))return!1;this.partialCharges=O(this.atoms.length,0)}this.partialCharges[a]=b;return!0},"~N,~N");
c(c$,"setIonicRadius",function(a,b){if(Float.isNaN(b))return!1;null==this.ionicRadii&&(this.ionicRadii=O(this.atoms.length,0));this.ionicRadii[a]=b;return!0},"~N,~N");c(c$,"setBFactor",function(a,b){if(Float.isNaN(b))return!1;if(null==this.bfactor100s){if(0==b&&null==this.bfactor100s)return!1;this.bfactor100s=da(this.atoms.length,0)}this.bfactor100s[a]=Ja(100*(-327.68>b?-327.68:327.67<b?327.67:b)+(0>b?-0.5:0.5));return!0},"~N,~N");c(c$,"setHydrophobicity",function(a,b){if(Float.isNaN(b))return!1;
if(null==this.hydrophobicities){this.hydrophobicities=O(this.atoms.length,0);for(var d=0;d<this.atoms.length;d++)this.hydrophobicities[d]=J.util.Elements.getHydrophobicity(this.atoms[d].getGroupID())}this.hydrophobicities[a]=b;return!0},"~N,~N");c(c$,"setAtomData",function(a,b,d,c){var e=null,f=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;case 12:this.loadCoordinates(d,!0,!0);return;case 14:e=O(this.atomCount,0),f=J.util.BSUtil.newBitSet(this.atomCount)}c=J.util.Parser.markLines(d,";");
var j=0;try{for(var k=JU.PT.parseInt(d.substring(0,c[0]-1)),h=1;h<=k;h++){var m=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[h],c[h+1]-1))),n=JU.PT.parseInt(m[0])-1;if(!(0>n||n>=this.atomCount)){var q=this.atoms[n];j++;var v=m.length-1,x=JU.PT.parseFloat(m[v]);switch(a){case 14:e[n]=x;f.set(n);continue;case 13:this.setAtomNumber(n,y(x));break;case 0:this.setAtomName(n,m[v]);break;case 1:this.setAtomType(n,m[v]);break;case 3:q.setAtomicAndIsotopeNumber(y(x));q.setPaletteID(J.constant.EnumPalette.CPK.id);
q.setColixAtom(this.viewer.getColixAtomPalette(q,J.constant.EnumPalette.CPK.id));break;case 4:q.setFormalCharge(y(x));break;case 5:this.setHydrophobicity(n,x);break;case 6:this.setIonicRadius(n,x);break;case 8:this.setPartialCharge(n,x);break;case 9:this.setBFactor(n,x);break;case 10:q.setValence(y(x));break;case 11:q.setRadius(x)}this.taintAtom(n,a)}}14==a&&0<j&&this.viewer.setData(b,[b,e,f,Integer.$valueOf(1)],0,0,0,0,0)}catch(p){if(C(p,Exception))J.util.Logger.error("AtomCollection.loadData error: "+
p);else throw p;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,b,d){var c=J.util.Parser.markLines(a,";"),e=b?new JU.V3:null;try{for(var f=JU.PT.parseInt(a.substring(0,c[0]-1)),j=1;j<=f;j++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),h=JU.PT.parseInt(k[0])-1,m=JU.PT.parseFloat(k[3]),n=JU.PT.parseFloat(k[4]),q=JU.PT.parseFloat(k[5]);b?(e.set(m,n,q),this.setAtomVibrationVector(h,e)):(this.setAtomCoord(h,m,n,q),d||this.untaint(h,2))}}catch(v){if(C(v,Exception))J.util.Logger.error("Frame.loadCoordinate error: "+
v);else throw v;}},"~S,~B,~B");c(c$,"validateBspf",function(a){null!=this.bspf&&this.bspf.validate(a)},"~B");c(c$,"validateBspfForModel",function(a,b){null!=this.bspf&&this.bspf.validateModel(a,b)},"~N,~B");c(c$,"setPreserveState",function(a){this.preserveState=a},"~B");c$.getUserSettableType=c(c$,"getUserSettableType",function(a){var b=0==a.indexOf("property_");a=b?a.substring(9):a;for(var d=0;14>d;d++)if(J.modelset.AtomCollection.userSettableValues[d].equalsIgnoreCase(a))return d;return b?14:-1},
"~S");c(c$,"getTaintedAtoms",function(a){return null==this.tainted?null:this.tainted[a]},"~N");c(c$,"taintAtoms",function(a,b){this.canSkipLoad=!1;if(this.preserveState)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.taintAtom(d,b)},"JU.BS,~N");c(c$,"taintAtom",function(a,b){this.preserveState&&(null==this.tainted&&(this.tainted=Array(14)),null==this.tainted[b]&&(this.tainted[b]=J.util.BSUtil.newBitSet(this.atomCount)),this.tainted[b].set(a),2==b&&this.validateBspfForModel(this.models[this.atoms[a].modelIndex].trajectoryBaseIndex,
!1))},"~N,~N");c(c$,"untaint",function(a,b){this.preserveState&&(null==this.tainted||null==this.tainted[b]||this.tainted[b].clear(a))},"~N,~N");c(c$,"setTaintedAtoms",function(a,b){this.preserveState&&(null==a?null!=this.tainted&&(this.tainted[b]=null):(null==this.tainted&&(this.tainted=Array(14)),null==this.tainted[b]&&(this.tainted[b]=J.util.BSUtil.newBitSet(this.atomCount)),J.util.BSUtil.copy2(a,this.tainted[b])))},"JU.BS,~N");c(c$,"unTaintAtoms",function(a,b){if(!(null==this.tainted||null==this.tainted[b])){for(var d=
a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.tainted[b].clear(d);0>this.tainted[b].nextSetBit(0)&&(this.tainted[b]=null)}},"JU.BS,~N");c(c$,"findNearest2",function(a,b,d,c,e){for(var f=null,j=this.atomCount;0<=--j;)if(!(null!=c&&c.get(j))){var k=this.atoms[j];k.isClickable()&&this.isCursorOnTopOf(k,a,b,e,f)&&(f=k)}d[0]=f},"~N,~N,~A,JU.BS,~N");c(c$,"isCursorOnTopOf",function(a,b,d,c,e){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(b,d,c,e)},"J.modelset.Atom,~N,~N,~N,J.modelset.Atom");
c(c$,"findAtomsInRectangle",function(a,b){this.bsFoundRectangle.and(this.bsEmpty);for(var d=this.atomCount;0<=--d;){var c=this.atoms[d];b.get(c.modelIndex)&&(c.isVisible(0)&&a.contains(c.sX,c.sY))&&this.bsFoundRectangle.set(d)}return this.bsFoundRectangle},"J.util.Rectangle,JU.BS");c(c$,"fillADa",function(a,b){a.atomXyz=this.atoms;a.atomCount=this.atomCount;a.atomicNumber=D(this.atomCount,0);var d=0!=(b&2);d&&(a.atomRadius=O(this.atomCount,0));for(var c=0!=(b&16),e=0;e<this.atomCount;e++){var f=this.atoms[e];
f.isDeleted()||!c&&0<=a.modelIndex&&f.modelIndex!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(e)):(a.atomicNumber[e]=f.getElementNumber(),a.lastModelIndex=f.modelIndex,d&&(a.atomRadius[e]=this.getWorkingRadius(f,a)))}},"J.atomdata.AtomData,~N");c(c$,"getWorkingRadius",function(a,b){var d=0,c=b.radiusData;switch(c.factorType){case J.atomdata.RadiusData.EnumType.ABSOLUTE:d=c.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:switch(c.vdwType){case J.constant.EnumVdw.IONIC:d=
a.getBondingRadiusFloat();break;case J.constant.EnumVdw.ADPMAX:d=a.getADPMinMax(!0);break;case J.constant.EnumVdw.ADPMIN:d=a.getADPMinMax(!1);break;default:d=a.getVanderwaalsRadiusFloat(this.viewer,b.radiusData.vdwType)}d=c.factorType===J.atomdata.RadiusData.EnumType.FACTOR?d*c.value:d+c.value}return d+c.valueExtended},"J.modelset.Atom,J.atomdata.AtomData");c(c$,"calculateHydrogens",function(a,b,d,c,e){var f=new JU.V3,j=new JU.V3,k=Array(this.atomCount),h=this.viewer.getDeletedAtoms(),m,n=0;if(null!=
a)for(var q=a.nextSetBit(0);0<=q;q=a.nextSetBit(q+1))if(!(null!=h&&h.get(q))){var v=this.atoms[q],x=v.getElementNumber();if(!(c&&6!=x)){var p=6>=x?1.1:10>=x?1:1.3;switch(x){case 7:case 8:p=1}if(!(d&&0<v.getCovalentHydrogenCount())&&(m=this.getImplicitHydrogenCount(v,!1),0!=m)){var r=this.aaRet[0],s=this.aaRet[2],t=this.aaRet[3];k[q]=Array(m);var u=0;if(0==t)switch(m){case 4:f.set(0.635,0.635,0.635),m=JU.P3.newP(f),m.add(v),k[q][u++]=m,null!=e&&e.addLast(v);case 3:f.set(-0.635,-0.635,0.635),m=JU.P3.newP(f),
m.add(v),k[q][u++]=m,null!=e&&e.addLast(v);case 2:f.set(-0.635,0.635,-0.635),m=JU.P3.newP(f),m.add(v),k[q][u++]=m,null!=e&&e.addLast(v);case 1:f.set(0.635,-0.635,-0.635),m=JU.P3.newP(f),m.add(v),k[q][u++]=m,null!=e&&e.addLast(v)}else switch(m){case 3:this.getHybridizationAndAxes(q,x,f,j,"sp3b",!1,!0);m=new JU.P3;m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);this.getHybridizationAndAxes(q,x,f,j,"sp3c",!1,!0);m=new JU.P3;m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);this.getHybridizationAndAxes(q,
x,f,j,"sp3d",!1,!0);m=new JU.P3;m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);break;case 2:s=2==s||5==x||1==t&&4==r||7==x&&this.isAdjacentSp2(v);this.getHybridizationAndAxes(q,x,f,j,s?"sp2b":3==r?"sp3c":"lpa",!1,!0);m=JU.P3.newP(f);m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);this.getHybridizationAndAxes(q,x,f,j,s?"sp2c":3==r?"sp3d":"lpb",!1,!0);m=JU.P3.newP(f);m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);break;case 1:switch(r-t){case 1:if(8==x&&v===v.getGroup().getCarbonylOxygenAtom()){k[q]=
null;continue}null!=this.getHybridizationAndAxes(q,x,f,j,2==s||5==x||7==x&&this.isAdjacentSp2(v)?"sp2c":"sp3d",!0,!1)?(m=JU.P3.newP(f),m.scaleAdd2(p,f,v),k[q][u++]=m,null!=e&&e.addLast(v)):k[q]=[];break;case 2:this.getHybridizationAndAxes(q,x,f,j,4==r?"sp2c":"sp2b",!1,!1);m=JU.P3.newP(f);m.scaleAdd2(p,f,v);k[q][u++]=m;null!=e&&e.addLast(v);break;case 3:this.getHybridizationAndAxes(q,x,f,j,"spb",!1,!0),m=JU.P3.newP(f),m.scaleAdd2(p,f,v),k[q][u++]=m,null!=e&&e.addLast(v)}}n+=u}}}b[0]=n;return k},"JU.BS,~A,~B,~B,JU.List");
c(c$,"isAdjacentSp2",function(a){for(var b=a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,e=0;e<c.length;e++)switch(c[e].order){case 515:case 514:case 2:case 3:return!0}return!1},"J.modelset.Atom");c(c$,"getImplicitHydrogenCount",function(a,b){var d=a.getTargetValence();if(0>d)return 0;var c=a.getFormalCharge();null==this.aaRet&&(this.aaRet=D(4,0));this.aaRet[0]=d;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();var e=this.models[a.modelIndex],e=e.isBioModel&&
!e.isPdbWithMultipleBonds?a.group.getGroup3():null;null!=e&&0==c&&J.viewer.JC.getAminoAcidValenceAndCharge(e,a.getAtomName(),this.aaRet)&&(d=this.aaRet[0],c=this.aaRet[1]);0!=c&&(d+=4==d?-Math.abs(c):c,this.aaRet[0]=d);d-=a.getValence();return 0>d&&!b?0:d},"J.modelset.Atom,~B");c(c$,"fixFormalCharges",function(a){for(var b=0,d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1)){var c=this.atoms[d],e=this.getImplicitHydrogenCount(c,!0);if(0!=e){var f=c.getFormalCharge(),e=f-e;c.setFormalCharge(e);this.taintAtom(d,
4);J.util.Logger.debugging&&J.util.Logger.debug("atom "+c+" formal charge "+f+" -> "+e);b++}}return b},"JU.BS");c(c$,"getHybridizationAndAxes",function(a,b,d,c,e,f,j){var k=0<e.length&&"-"==e.charAt(0)?e.substring(1):e;if(0<=e.indexOf("d")&&!e.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,d,c,k);var h=this.atoms[a];0==b&&(b=h.getElementNumber());var m=this.getAttached(h,4,f),n=m.length,q=k.charCodeAt(k.length-1)-97;if(0>q||6<q)q=0;d.set(0,0,0);c.set(0,0,0);for(var v=Array(4),x=0;x<n;x++)v[x]=
JU.V3.newVsub(h,m[x]),v[x].normalize(),d.add(v[x]);0<n&&c.setT(v[0]);x=!1;a=new JU.V3;3<=n&&(2.984513>c.angle(v[1])?a.cross(c,v[1]):a.cross(c,v[2]),a.normalize(),e=new JU.V3,2.984513>v[1].angle(v[2])?e.cross(v[1],v[2]):e.cross(c,v[2]),e.normalize(),x=0.95<=Math.abs(e.dot(a)));var p=0==k.indexOf("sp3"),r=!p&&0==k.indexOf("sp2"),s=!p&&!r&&0==k.indexOf("sp"),t=0==k.indexOf("p"),u=0==k.indexOf("lp");e=null;if(f){if(0==n)return null;if(p){if(3<q||4<n)return null}else if(r){if(2<q||3<n)return null}else if(s&&
(1<q||2<n))return null;switch(n){case 1:if(1==b&&!p)return null;if(p){e="sp3";break}switch(m[0].getCovalentBondCount()){case 1:if(2!=m[0].getValence()){e="sp";break}case 2:e=s?"sp":"sp2";break;case 3:if(!r&&!t)return null;e="sp2"}break;case 2:if(0.1>d.length()){if(0<=k.indexOf("2")||0<=k.indexOf("3"))return null;e="sp";break}e=p?"sp3":"sp2";if(0==k.indexOf("sp"))break;if(u){e="lp";break}e=k;break;default:if(x)e="sp2";else{if(u&&3==n){e="lp";break}e="sp3"}}if(null==e)return null;if(0==k.indexOf("p")){if("sp3"===
e)return null}else if(0>k.indexOf(e))return null}if(q<n&&!k.startsWith("p")&&!k.startsWith("l"))return d.sub2(m[q],h),d.normalize(),e;switch(n){case 0:k.equals("sp3c")||k.equals("sp2d")||k.equals("lpa")?d.set(-0.5,-0.7,1):k.equals("sp3b")||k.equals("lpb")?d.set(0.5,-0.7,-1):k.equals("sp3a")?d.set(0,1,0):d.set(0,0,1);c.set(1,0,0);break;case 1:a.setT(J.modelset.AtomCollection.vRef);c.cross(a,d);if(p){for(x=0;x<m[0].bonds.length;x++)if(m[0].bonds[x].isCovalent()&&m[0].getBondedAtomIndex(x)!=h.index&&
(c.sub2(m[0],m[0].bonds[x].getOtherAtom(m[0])),c.cross(d,c),0!=c.length())){c.cross(c,d);break}c.normalize();Float.isNaN(c.x)&&(c.setT(J.modelset.AtomCollection.vRef),c.cross(c,d));a.cross(d,c);a.normalize();d.normalize();c.scaleAdd2(2.828,c,d);3!=q&&(c.normalize(),b=JU.A4.new4(d.x,d.y,d.z,2.09439507*(2==q?1:-1)),j=JU.M3.newM(null),j.setAA(b),j.transform(c));d.setT(c);c.cross(a,d);break}a.cross(c,d);switch(m[0].getCovalentBondCount()){case 1:if(2!=m[0].getValence())break;case 2:j=m[0];c.setT(d);for(a.setT(J.modelset.AtomCollection.vRef);null!=
j&&2==j.getCovalentBondCount();){k=j.bonds;b=null;for(x=0;x<k.length;x++)if(k[x].isCovalent()&&(b=k[x].getOtherAtom(j),b!==h)){a.sub2(b,j);break}a.cross(a,c);if(0.1<a.length()||2!=b.getCovalentBondCount())break;h=j;j=b}0.1<a.length()?(d.cross(a,c),d.normalize(),1==q&&d.scale(-1),d.scale(J.modelset.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,c,d),t&&(a.cross(d,c),d.setT(a),a.setT(c)),c.cross(a,d)):(d.setT(c),c.cross(J.modelset.AtomCollection.vRef,c));break;case 3:this.getHybridizationAndAxes(m[0].index,
0,c,a,"pz",!1,j),a.setT(c),r?(c.cross(c,d),1==q&&c.scale(-1),c.scale(J.modelset.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,d,c)):(a.setT(d),d.setT(c)),c.cross(a,d)}break;case 2:if(0.1>d.length()){if(!k.equals("pz")){b=m[0];(h=3==b.getCovalentBondCount())||(h=3==(b=m[1]).getCovalentBondCount());if(h){this.getHybridizationAndAxes(b.index,0,c,d,"pz",!1,j);k.equals("px")&&c.scale(-1);d.setT(v[0]);break}a.setT(J.modelset.AtomCollection.vRef);d.cross(a,c);a.cross(d,c)}d.setT(c);c.cross(a,d);break}a.cross(d,
c);if(r){c.cross(d,a);break}if(p||u){a.normalize();d.normalize();k.equals("lp")||(0==q||2==q?d.scaleAdd2(-1.2,a,d):d.scaleAdd2(1.2,a,d));c.cross(d,a);break}c.cross(d,a);d.setT(a);0>d.z&&(d.scale(-1),c.scale(-1));break;default:if(p)break;if(!x){c.cross(d,c);break}d.setT(a);0>d.z&&j&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return e},"~N,~N,JU.V3,JU.V3,~S,~B,~B");c(c$,"getHybridizationAndAxesD",function(a,b,d,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&
(c="dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var e=c.startsWith("dsp3"),f=c.charCodeAt(c.length-1)-97;if(null!=b&&(!e&&(5<f||!c.startsWith("d2sp3"))||e&&4<f))return null;a=this.atoms[a];c=this.getAttached(a,6,!0);if(null==c)return null==b?null:"?";var j=c.length;if(3>j&&null!=b)return null;for(var k=f>=j,h=s(j*(j-1)/2),m=JU.AU.newInt2(h),n=D(3,0),h=D(3,h,0),q=0,v=0,x=0;x<j-1;x++)for(var p=x+1;p<j;p++){var r=J.util.Measure.computeAngleABC(c[x],a,c[p],!0),
r=105>r?0:150<=r?2:1;h[r][n[r]]=q;n[r]++;m[q++]=[x,p];0==x&&1==r&&v++}q=100*n[0]+10*n[1]+n[2];if(null==b)switch(q){default:return"";case 0:return"";case 1:return"linear";case 100:case 10:return"bent";case 111:case 201:return"T-shaped";case 30:case 120:case 210:case 300:return 162<Math.abs(J.util.Measure.computeTorsion(c[0],a,c[1],c[2],!0))?"trigonal planar":"trigonal pyramidal";case 330:return 1==v%2?"tetrahedral":"uncapped trigonal pyramid";case 60:case 150:case 240:return"tetrahedral";case 402:return"square planar";
case 411:case 501:return"see-saw";case 631:return"trigonal bipyramidal";case 802:return"uncapped square pyramid";case 1203:return"octahedral"}switch(q){default:return null;case 201:break;case 210:case 330:case 411:case 631:if(!e)return null;break;case 300:case 402:case 501:case 802:case 1203:if(e)return null}if(k)if(e)switch(n[1]){case 0:b.sub2(c[m[h[0][0]][0]],a);d.sub2(c[m[h[0][0]][1]],a);b.cross(b,d);b.normalize();4==f&&b.scale(-1);n=this.findNotAttached(j,m,h[2],n[2]);x=n.nextSetBit(0);d.sub2(c[x],
a);d.normalize();d.scale(0.5);b.scaleAdd2(J.modelset.AtomCollection.sqrt3_2,b,d);f=-1;break;case 1:4==f?(d=m[h[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),f=-1):(n=this.findNotAttached(j,m,h[1],n[1]),f=n.nextSetBit(0));break;default:n=this.findNotAttached(j,m,h[1],n[1]),f=n.nextSetBit(0)}else{q=!1;if(4==j)switch(n[2]){case 1:n=this.findNotAttached(j,m,h[2],n[2]);x=n.nextSetBit(0);f=4==f?x:n.nextSetBit(x+1);break;default:q=!0}else{n=this.findNotAttached(j,m,h[2],n[2]);x=n.nextSetBit(0);for(p=
j;p<f&&0<=x;p++)x=n.nextSetBit(x+1);-1==x?q=!0:f=x}q&&(b.sub2(c[m[h[0][0]][0]],a),d.sub2(c[m[h[0][0]][1]],a),b.cross(b,d),4==f&&b.scale(-1),f=-1)}0<=f&&b.sub2(c[f],a);k&&b.scale(-1);b.normalize();return e?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(c$,"getAttached",function(a,b,d){var c=a.getCovalentBondCount();if(c>b)return null;b=Array(c);if(0<c){for(var c=a.bonds,e=0,f=0;f<c.length;f++)c[f].isCovalent()&&(b[e++]=c[f].getOtherAtom(a));d&&java.util.Arrays.sort(b,ka(J.modelset.AtomCollection.AtomSorter,
this,null))}return b},"J.modelset.Atom,~N,~B");c(c$,"findNotAttached",function(a,b,d,c){var e=J.util.BSUtil.newBitSet(a);e.setBits(0,a);for(var f=0;f<a;f++)for(var j=0;j<c;j++){var k=b[d[j]];(k[0]==f||k[1]==f)&&e.clear(f)}return e},"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b){var d=new JU.BS,c,e,f=0;switch(a){case 1297090050:c=b.intValue();for(f=this.atomCount;0<=--f;)this.atoms[f].getSymOp()==c&&d.set(f);break;case 1095763969:c=b.intValue();for(f=this.atomCount;0<=--f;)this.atoms[f].getAtomNumber()==
c&&d.set(f);break;case 1087375362:c=","+b+",";for(f=this.atomCount;0<=--f;)e=this.atoms[f].getAtomName(),0<=c.indexOf(e)&&0<=c.indexOf(","+e+",")&&d.set(f);break;case 1087375361:c=","+b+",";for(f=this.atomCount;0<=--f;)e=this.atoms[f].getAtomType(),0<=c.indexOf(e)&&0<=c.indexOf(","+e+",")&&d.set(f);break;case 1048613:c=b.intValue();for(f=this.atomCount;0<=--f;)this.atoms[f].getGroupID()==c&&d.set(f);break;case 1048609:return J.util.BSUtil.copy(this.getChainBits(b.intValue()));case 1048614:return J.util.BSUtil.copy(this.getSeqcodeBits(b.intValue(),
!0));case 1613758470:for(f=this.atomCount;0<=--f;)this.atoms[f].isHetero()&&d.set(f);break;case 1613758476:for(f=this.atomCount;0<=--f;)1==this.atoms[f].getElementNumber()&&d.set(f);break;case 3145744:for(f=this.atomCount;0<=--f;)this.atoms[f].isProtein()&&d.set(f);break;case 3145764:for(f=this.atomCount;0<=--f;)this.atoms[f].isCarbohydrate()&&d.set(f);break;case 137363468:case 3145760:e=137363468==a?J.constant.EnumStructure.HELIX:J.constant.EnumStructure.SHEET;for(f=this.atomCount;0<=--f;)this.atoms[f].isWithinStructure(e)&&
d.set(f);break;case 3145742:for(f=this.atomCount;0<=--f;)this.atoms[f].isNucleic()&&d.set(f);break;case 3145732:for(f=this.atomCount;0<=--f;)this.atoms[f].isDna()&&d.set(f);break;case 3145750:for(f=this.atomCount;0<=--f;)this.atoms[f].isRna()&&d.set(f);break;case 3145746:for(f=this.atomCount;0<=--f;)this.atoms[f].isPurine()&&d.set(f);break;case 3145748:for(f=this.atomCount;0<=--f;)this.atoms[f].isPyrimidine()&&d.set(f);break;case 1087375365:c=b;e=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+
1))e.set(this.getElementNumber(f));for(f=this.atomCount;0<=--f;)e.get(this.getElementNumber(f))&&d.set(f);break;case 1095761940:c=b;e=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))e.set(this.atoms[f].atomSite);for(f=this.atomCount;0<=--f;)e.get(this.atoms[f].atomSite)&&d.set(f);break;case 1073741824:return this.getIdentifierOrNull(b);case 1048608:c=b.toUpperCase();0<=c.indexOf("\\?")&&(c=JU.PT.simpleReplace(c,"\\?","\u0001"));for(f=this.atomCount;0<=--f;)this.isAtomNameMatch(this.atoms[f],
c,!1)&&d.set(f);break;case 1048607:for(f=this.atomCount;0<=--f;)this.atoms[f].isAltLoc(b)&&d.set(f);break;case 1048612:return this.getSpecName(b)}if(0>f)return d;c=b;var j;e=c.nextSetBit(0);if(0>e)return d;f=0;switch(a){case 1087373318:for(f=e;0<=f;f=c.nextSetBit(f+1))e=this.atoms[f].getGroup().selectAtoms(d),e>f&&(f=e);break;case 1095766030:for(f=e;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.atoms[f].modelIndex;d.set(f);for(e=f;0<=--e;)if(this.atoms[e].modelIndex==j)d.set(e);else break;for(;++f<
this.atomCount;)if(this.atoms[f].modelIndex==j)d.set(f);else break}break;case 1087373316:c=J.util.BSUtil.copy(b);for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))this.atoms[f].getChain().setAtomBitSet(d),c.andNot(d);break;case 1095761937:for(f=e;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.atoms[f].getPolymerIndexInModel();d.set(f);for(e=f;0<=--e;)if(this.atoms[e].getPolymerIndexInModel()==j)d.set(e);else break;for(;++f<this.atomCount;)if(this.atoms[f].getPolymerIndexInModel()==j)d.set(f);else break}break;
case 1641025539:for(f=e;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.atoms[f].getGroup().getStructure();d.set(f);for(e=f;0<=--e;)if(this.atoms[e].getGroup().getStructure()===j)d.set(e);else break;for(;++f<this.atomCount;)if(this.atoms[f].getGroup().getStructure()===j)d.set(f);else break}}0==f&&J.util.Logger.error("MISSING getAtomBits entry for "+J.script.T.nameOf(a));return d},"~N,~O");c(c$,"getIdentifierOrNull",function(a){var b=this.getSpecNameOrNull(a,!1);0<=a.indexOf("\\?")&&(a=JU.PT.simpleReplace(a,
"\\?","\u0001"));if(null!=b||0<a.indexOf("?"))return b;if(0<a.indexOf("*"))return this.getSpecNameOrNull(a,!0);for(var d=a.length,c=0;c<d&&Character.isLetter(a.charAt(c));)++c;b=this.getSpecNameOrNull(a.substring(0,c),!1);if(c==d)return b;null==b&&(b=new JU.BS);for(var e=c;c<d&&Character.isDigit(a.charAt(c));)++c;var f=0;try{f=Integer.parseInt(a.substring(e,c))}catch(j){if(C(j,NumberFormatException))return null;throw j;}e=" ";c<d&&"^"==a.charAt(c)&&++c<d&&(e=a.charAt(c));f=J.modelset.Group.getSeqcodeFor(f,
e);f=this.getSeqcodeBits(f,!1);if(null==f){" "!=e&&(f=this.getSeqcodeBits(Character.toUpperCase(a.charAt(c)).charCodeAt(0),!1));if(null==f)return null;c++}b.and(f);if(c>=d)return b;if(c!=d-1)return null;b.and(this.getChainBits(a.charCodeAt(c)));return b},"~S");c(c$,"getSpecName",function(a){var b=this.getSpecNameOrNull(a,!1);if(null!=b)return b;0<a.indexOf("*")&&(b=this.getSpecNameOrNull(a,!0));return null==b?new JU.BS:b},"~S");c(c$,"getSpecNameOrNull",function(a,b){var d=null;a=a.toUpperCase();0<=
a.indexOf("\\?")&&(a=JU.PT.simpleReplace(a,"\\?","\u0001"));for(var c=this.atomCount;0<=--c;){var e=this.atoms[c].getGroup3(!0);if(null!=e&&0<e.length){if(J.util.Txt.isMatch(e,a,b,!0)){null==d&&(d=J.util.BSUtil.newBitSet(c+1));for(d.set(c);0<=--c&&this.atoms[c].getGroup3(!0).equals(e);)d.set(c);c++}}else this.isAtomNameMatch(this.atoms[c],a,b)&&(null==d&&(d=J.util.BSUtil.newBitSet(c+1)),d.set(c))}return d},"~S,~B");c(c$,"isAtomNameMatch",function(a,b,d){return J.util.Txt.isMatch(a.getAtomName().toUpperCase(),
b,d,!1)},"J.modelset.Atom,~S,~B");c(c$,"getSeqcodeBits",function(a,b){var d=new JU.BS,c=J.modelset.Group.getSeqNumberFor(a),e=2147483647!=c,f=!0,j=J.modelset.Group.getInsertionCodeChar(a);switch(j){case "?":for(var k=this.atomCount;0<=--k;){var h=this.atoms[k].getSeqcode();if(!e||c==J.modelset.Group.getSeqNumberFor(h)&&0!=J.modelset.Group.getInsertionCodeFor(h))d.set(k),f=!1}break;default:for(k=this.atomCount;0<=--k;)if(h=this.atoms[k].getSeqcode(),a==h||!e&&a==J.modelset.Group.getInsertionCodeFor(h)||
"*"==j&&c==J.modelset.Group.getSeqNumberFor(h))d.set(k),f=!1}return!f||b?d:null},"~N,~B");c(c$,"getChainBits",function(a){var b=256>a&&this.viewer.getBoolean(603979822);b||(a=J.modelset.AtomCollection.chainToUpper(a));for(var d=new JU.BS,c=J.util.BSUtil.newBitSet(this.atomCount),e,f=c.nextClearBit(0);f<this.atomCount;f=c.nextClearBit(f+1)){var j=this.atoms[f].getChain();a==(e=j.chainID)||!b&&a==J.modelset.AtomCollection.chainToUpper(e)?(j.setAtomBitSet(d),c.or(d)):j.setAtomBitSet(c)}return d},"~N");
c$.chainToUpper=c(c$,"chainToUpper",function(a){return String.fromCharCode(a).toUpperCase().charCodeAt(0)},"~N");c(c$,"getAtomIndices",function(a){for(var b=0,d=D(this.atomCount,0),c=a.nextSetBit(0);0<=c&&c<this.atomCount;c=a.nextSetBit(c+1))d[c]=++b;return d},"JU.BS");c(c$,"getAtomsWithin",function(a,b){for(var d=new JU.BS,c=this.atomCount;0<=--c;){var e=this.atoms[c],f=J.util.Measure.distanceToPlane(b,e);(0<a&&-0.1<=f&&f<=a||0>a&&0.1>=f&&f>=a||0==a&&0.01>Math.abs(f))&&d.set(e.index)}return d},"~N,JU.P4");
c(c$,"getAtomsWithinBs",function(a,b,d){var c=new JU.BS;if(0==b.length||null!=d&&0==d.cardinality())return c;null==d&&(d=J.util.BSUtil.setAll(b.length));for(var e=this.atomCount;0<=--e;)for(var f=this.atoms[e],j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(f.distance(b[j])<a){c.set(e);break}return c},"~N,~A,JU.BS");c(c$,"getVisibleSet",function(){for(var a=new JU.BS,b=this.atomCount;0<=--b;)this.atoms[b].isVisible(0)&&a.set(b);return a});c(c$,"getClickableSet",function(){for(var a=new JU.BS,b=this.atomCount;0<=
--b;)this.atoms[b].isClickable()&&a.set(b);return a});c(c$,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(c$,"deleteModelAtoms",function(a,b,d){this.atoms=JU.AU.deleteElements(this.atoms,a,b);this.atomCount=this.atoms.length;for(var c=a;c<this.atomCount;c++)this.atoms[c].index=c,this.atoms[c].modelIndex--;null!=this.bsModulated&&J.util.BSUtil.deleteBits(this.bsModulated,d);this.deleteAtomTensors(d);this.atomNames=JU.AU.deleteElements(this.atomNames,a,b);
this.atomTypes=JU.AU.deleteElements(this.atomTypes,a,b);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,b);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,b);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,b);this.partialCharges=JU.AU.deleteElements(this.partialCharges,a,b);this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,b);this.vibrations=JU.AU.deleteElements(this.vibrations,a,b);this.nSurfaceAtoms=0;this.surfaceDistance100s=this.bsSurface=
null;if(null!=this.tainted)for(a=0;14>a;a++)J.util.BSUtil.deleteBits(this.tainted[a],d)},"~N,~N,JU.BS");c(c$,"getAtomIdentityInfo",function(a,b){b.put("_ipt",Integer.$valueOf(a));b.put("atomIndex",Integer.$valueOf(a));b.put("atomno",Integer.$valueOf(this.getAtomNumber(a)));b.put("info",this.getAtomInfo(a,null));b.put("sym",this.getElementSymbol(a))},"~N,java.util.Map");c(c$,"getAtomTensorList",function(a){return 0>a||null==this.atomTensorList||a>=this.atomTensorList.length?null:this.atomTensorList[a]},
"~N");c(c$,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var b=new JU.List,d,c=this.atomTensors.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var e=this.atomTensors.get(d),f=e.size();0<=--f;){var j=e.get(f);(a.get(j.atomIndex1)||0<=j.atomIndex2&&a.get(j.atomIndex2))&&e.remove(f)}0==e.size()&&b.addLast(d)}for(f=b.size();0<=--f;)this.atomTensors.remove(b.get(f))}},"JU.BS");c(c$,"setAtomTensors",function(a,b){if(!(null==b||0==b.size())){null==this.atomTensors&&(this.atomTensors=
new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.atoms.length));this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.atoms.length);this.atomTensorList[a]=J.modelset.AtomCollection.getTensorList(b);for(var d=b.size();0<=--d;){var c=b.get(d);c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.atoms[a].modelIndex;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.List");c$.getTensorList=c(c$,"getTensorList",function(a){for(var b=
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"java.util.Map");E(c$,"NMR_NOT",0,"NMR_DC",1,"NMR_JC",2)}),p("J.modelset"),t(["J.api.JmolMeasurementClient"],"J.modelset.MeasurementData",["java.lang.Float","JU.BS","$.List","J.modelset.Measurement","J.util.BSUtil"],function(){c$=w(function(){this.points=this.measurements=this.measurementStrings=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=1060866;this.note=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=null;
this.mad=0;this.viewer=this.modelSet=this.minArray=this.units=this.atoms=this.text=this.thisID=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;u(this,arguments)},J.modelset,"MeasurementData",null,J.api.JmolMeasurementClient);A(c$,function(){});c(c$,"init",function(a,b,d){this.viewer=b;this.points=d;this.thisID=a;return this},"~S,J.viewer.Viewer,JU.List");c(c$,"setModelSet",function(a){this.modelSet=a;return this},"J.modelset.ModelSet");c(c$,"set",function(a,b,d,c,e,f,j,k,h,m,n,q,v){this.modelSet=
this.viewer.getModelSet();this.tokAction=a;2<=this.points.size()&&(r(this.points.get(0),JU.BS)&&r(this.points.get(1),JU.BS))&&(this.justOneModel=J.util.BSUtil.haveCommon(this.viewer.getModelBitSet(this.points.get(0),!1),this.viewer.getModelBitSet(this.points.get(1),!1)));this.htMin=b;this.radiusData=d;this.strFormat=c;this.units=e;this.tickInfo=f;this.mustBeConnected=j;this.mustNotBeConnected=k;this.intramolecular=h;this.isAll=m;this.mad=n;this.colix=q;this.text=v;return this},"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,J.modelset.TickInfo,~B,~B,Boolean,~B,~N,~N,J.modelset.Text");
c(c$,"processNextMeasure",function(a){var b=a.getMeasurement(null);if(!(null!=this.htMin&&!a.isMin(this.htMin)||null!=this.radiusData&&!a.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var d=this.minArray[this.iFirstAtom];a.value=b;b=a.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/d?b:Math.min(d,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(a.getStringUsing(this.viewer,this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(a.getMeasurement(null)))},
"J.modelset.Measurement");c(c$,"getMeasurements",function(a,b){if(b){this.minArray=O(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.modelSet);return this.minArray}if(a)return this.measurements=new JU.List,this.define(null,this.modelSet),this.measurements;this.measurementStrings=new JU.List;this.define(null,this.modelSet);return this.measurementStrings},"~B,~B");c(c$,"define",function(a,b){this.client=null==a?this:a;this.atoms=b.atoms;
var d=this.points.size();if(!(2>d)){var c=-1,e=Array(4),f=D(5,0),j=(new J.modelset.Measurement).setPoints(b,f,e,null);j.setCount(d);for(var k=-1,h=0;h<d;h++){var m=this.points.get(h);if(r(m,JU.BS)){k=m.cardinality();if(0==k)return;1<k&&(c=0);k=h;0==h&&(this.iFirstAtom=0);f[h+1]=m.nextSetBit(0)}else e[h]=m,f[h+1]=-2-h}this.nextMeasure(0,k,j,c)}},"J.api.JmolMeasurementClient,J.modelset.ModelSet");c(c$,"nextMeasure",function(a,b,d,c){if(a>b)d.isValid()&&((!this.mustBeConnected||d.isConnected(this.atoms,
a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var e=this.points.get(a),f=d.countPlusIndices,j=0==a?2147483647:f[a];if(0>j)this.nextMeasure(a+1,b,d,c);else{for(var k=!1,h=e.nextSetBit(0),m=0;0<=h;h=e.nextSetBit(h+1),m++)if(h!=j){var n=this.atoms[h].getModelIndex();if(0<=c&&this.justOneModel)if(0==a)c=n;else if(c!=n)continue;f[a+1]=h;0==a&&(this.iFirstAtom=
m);k=!0;this.nextMeasure(a+1,b,d,c)}k||this.nextMeasure(a+1,b,d,c)}}},"~N,~N,J.modelset.Measurement,~N")}),p("J.modelset"),t(["J.modelset.Measurement"],"J.modelset.MeasurementPending",null,function(){c$=w(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;u(this,arguments)},J.modelset,"MeasurementPending",J.modelset.Measurement);c(c$,"set",function(a){return this.setM(a,null,NaN,0,null,0)},"J.modelset.ModelSet");c(c$,"checkPoint",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==
-1-b&&0.01>this.pts[b-1].distance(a))return!1;return!0},"J.util.Point3fi");c(c$,"getIndexOf",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==a)return b;return 0},"~N");h(c$,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(c$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=
this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,J.util.Point3fi,~B")}),p("J.modelset"),t(["JU.BS","$.SB"],"J.modelset.Model",
["java.util.Hashtable","JU.AU","J.util.BSUtil"],function(){c$=w(function(){this.modelSet=null;this.hydrogenCount=this.fileIndex=this.modelIndex=0;this.hasRasmolHBonds=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.loadState="";this.loadScript=null;this.isModelKit=!1;this.dataFrames=null;this.dataSourceFrame=-1;this.jmolFrameType=this.jmolData=null;this.atomCount=this.firstAtomIndex=0;this.bsAtomsDeleted=this.bsAtoms=null;this.trajectoryBaseIndex=0;this.isTrajectory=!1;this.bondCount=this.selectedTrajectory=
-1;this.nInsertions=this.nAltLocs=this.moleculeCount=this.firstMoleculeIndex=0;this.groupCount=-1;this.chainCount=0;this.chains=null;this.biosymmetryCount=0;this.properties=this.auxiliaryInfo=null;this.defaultRotationRadius=0;this.orientation=this.biosymmetry=this.defaultStructure=null;this.isJmolDataFrame=this.structureTainted=!1;this.frameDelay=0;this.simpleCage=null;u(this,arguments)},J.modelset,"Model");Q(c$,function(){this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS;
this.chains=Array(8)});c(c$,"getModelSet",function(){return this.modelSet});c(c$,"isModelkit",function(){return this.isModelKit});c(c$,"getTrueAtomCount",function(){return this.bsAtoms.cardinality()-this.bsAtomsDeleted.cardinality()});c(c$,"setSelectedTrajectory",function(a){this.selectedTrajectory=a},"~N");c(c$,"getSelectedTrajectory",function(){return this.selectedTrajectory});c(c$,"resetBoundCount",function(){this.bondCount=-1});c(c$,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;
var a=this.modelSet.bonds;this.bondCount=0;for(var b=this.modelSet.bondCount;0<=--b;)a[b].atom1.modelIndex==this.modelIndex&&this.bondCount++;return this.bondCount});A(c$,function(a,b,d,c,e,f){this.modelSet=a;this.dataSourceFrame=this.modelIndex=b;this.trajectoryBaseIndex=(this.isTrajectory=0<=d)?d:b;null==f&&(f=new java.util.Hashtable);this.auxiliaryInfo=f;f.containsKey("biosymmetryCount")&&(this.biosymmetryCount=f.get("biosymmetryCount").intValue(),this.biosymmetry=f.get("biosymmetry"));this.properties=
e;null==c?this.jmolFrameType="modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,f.put("jmolData",c),f.put("title",c),this.jmolFrameType=0<=c.indexOf("ramachandran")?"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data")},"J.modelset.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(c$,"setNAltLocs",function(a){this.nAltLocs=a},"~N");c(c$,"setNInsertions",function(a){this.nInsertions=a},"~N");c(c$,"getModelNumberDotted",function(){return this.modelSet.getModelNumberDotted(this.modelIndex)});
c(c$,"getModelTitle",function(){return this.modelSet.getModelTitle(this.modelIndex)});c(c$,"isStructureTainted",function(){return this.structureTainted});c(c$,"getChains",function(){return this.chains});c(c$,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(c$,"getGroupCountHetero",function(a){for(var b=0,d=this.chainCount;0<=--d;)for(var c=this.chains[d].groupCount;0<=--c;)this.chains[d].groups[c].isHetero()==
a&&b++;return b},"~B");c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.chainCount;0<=--b;)this.chains[b].calcSelectedGroupsCount(a)},"JU.BS");c(c$,"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].getGroupCount()}return this.groupCount});c(c$,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(c$,"getChain",function(a){for(var b=this.chainCount;0<=--b;){var d=this.chains[b];if(d.chainID==
a)return d}return null},"~N");c(c$,"fixIndices",function(a,b,d){this.fixIndicesM(a,b,d)},"~N,~N,JU.BS");c(c$,"fixIndicesM",function(a,b,d){this.dataSourceFrame>a&&this.dataSourceFrame--;this.trajectoryBaseIndex>a&&this.trajectoryBaseIndex--;this.firstAtomIndex-=b;for(a=0;a<this.chainCount;a++)this.chains[a].fixIndices(b,d);J.util.BSUtil.deleteBits(this.bsAtoms,d);J.util.BSUtil.deleteBits(this.bsAtomsDeleted,d)},"~N,~N,JU.BS");c(c$,"freeze",function(){this.freezeM()});c(c$,"freezeM",function(){this.chains=
JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=-1;this.getGroupCount();for(var a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)});c(c$,"getPdbData",function(){},"J.viewer.Viewer,~S,~S,~B,JU.BS,JU.OC,~A,JU.SB,JU.BS");c(c$,"getDefaultLargePDBRendering",function(){},"JU.SB,~N");c(c$,"getBioBranches",function(a){return a},"JU.List");c(c$,"getGroupsWithin",function(){},"~N,JU.BS,JU.BS");c(c$,"getSequenceBits",function(){},
"~S,JU.BS,JU.BS");c(c$,"getRasmolHydrogenBonds",function(){},"JU.BS,JU.BS,JU.List,~B,~N,~B,JU.BS");c(c$,"clearRasmolHydrogenBonds",function(){},"JU.BS");c(c$,"clearBioPolymers",function(){});c(c$,"calcSelectedMonomersCount",function(){},"JU.BS");c(c$,"calculatePolymers",function(){},"~A,~N,~N,JU.BS,~B");c(c$,"getAllPolymerInfo",function(){},"JU.BS,java.util.Map,JU.List");c(c$,"getBioPolymerCount",function(){return 0});c(c$,"getPolymerPointsAndVectors",function(){},"JU.BS,JU.List,~B,~N");c(c$,"getPolymerLeadMidPoints",
function(){return null},"~N");c(c$,"recalculateLeadMidpointsAndWingVectors",function(){});c(c$,"calculateStructures",function(){return""},"~B,~B,~B,~B,~B");c(c$,"setStructureList",function(){},"java.util.Map");c(c$,"getChimeInfo",function(a,b){this.getChimeInfoM(a,b)},"JU.SB,~N");c(c$,"getChimeInfoM",function(a,b){a.append("\nNumber of Atoms ..... "+(this.modelSet.atomCount-b));0<b&&a.append(" ("+b+")");a.append("\nNumber of Bonds ..... "+this.modelSet.bondCount);a.append("\nNumber of Models ...... "+
this.modelSet.modelCount)},"JU.SB,~N");c(c$,"calculateStruts",function(){return 0},"J.modelset.ModelSet,JU.BS,JU.BS");c(c$,"calculateStraightness",function(){},"J.viewer.Viewer,~S,~S,~N");c(c$,"selectSeqcodeRange",function(){},"~N,~N,~N,JU.BS,~B");c(c$,"setConformation",function(){},"JU.BS");c(c$,"getPdbConformation",function(){return!1},"JU.BS,~N");c(c$,"getProteinStructureState",function(){return null},"JU.BS,~B,~B,~N");c(c$,"getFullPDBHeader",function(){return null})}),p("J.modelset"),t(["J.modelset.BondCollection",
"JU.BS","$.List","$.P3","J.util.BoxInfo"],"J.modelset.ModelCollection","java.lang.Boolean $.Character $.Float java.util.Date $.Hashtable JU.AU $.P4 $.PT $.SB $.V3 J.api.Interface $.JmolModulationSet J.bspt.Bspf J.constant.EnumPalette $.EnumVdw J.io.XmlUtil J.modelset.Atom $.AtomIteratorWithinModel $.AtomIteratorWithinModelSet $.Bond $.HBond $.LabelToken $.Model $.StateScript J.util.BSUtil $.Elements $.Escape $.JmolEdge $.JmolMolecule $.Logger $.Point3fi $.Quaternion $.Txt J.viewer.Viewer".split(" "),
function(){c$=w(function(){this.models=this.modelSetName=this.bsSymmetry=null;this.modelCount=0;this.unitCells=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=null;this.isPDB=this.isXYZ=!1;this.modelSetAuxiliaryInfo=this.modelSetProperties=null;this.someModelsHaveFractionalCoordinates=this.someModelsHaveAromaticBonds=this.someModelsHaveSymmetry=!1;this.averageAtomPoint=this.ptTemp=null;this.isBbcageDefault=
!1;this.stateScripts=this.boxInfo=this.bboxAtoms=this.bboxModels=null;this.thisStateModel=0;this.selectedMolecules=this.vibrationSteps=this.trajectorySteps=null;this.showRebondTimes=!0;this.ptTemp2=this.ptTemp1=this.shapeManager=this.bsAll=null;this.proteinStructureTainted=!1;this.triangulator=this.vOrientations=this.htPeaks=this.symTemp=null;u(this,arguments)},J.modelset,"ModelCollection",J.modelset.BondCollection);Q(c$,function(){this.models=Array(1);this.modelNumbers=D(1,0);this.modelFileNumbers=
D(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.ptTemp=new JU.P3;this.averageAtomPoint=new JU.P3;this.boxInfo=new J.util.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.stateScripts=new JU.List;this.selectedMolecules=new JU.BS;this.ptTemp1=new JU.P3;this.ptTemp2=new JU.P3});c(c$,"mergeModelArrays",function(a){this.atoms=a.atoms;this.bonds=a.bonds;this.stateScripts=a.stateScripts;
this.proteinStructureTainted=a.proteinStructureTainted;this.thisStateModel=-1;this.bsSymmetry=a.bsSymmetry;this.modelFileNumbers=a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=a.modelNumbers;this.frameTitles=a.frameTitles;this.mergeAtomArrays(a)},"J.modelset.ModelSet");h(c$,"releaseModelSet",function(){this.unitCells=this.bsAll=this.bsSymmetry=this.models=null;this.releaseModelSetBC()});c(c$,"getUnitCell",function(a){return!this.haveUnitCells||
0>a||a>=this.modelCount?null:null!=this.models[a].simpleCage?this.models[a].simpleCage:null==this.unitCells||a>=this.unitCells.length||!this.unitCells[a].haveUnitCell()?null:this.unitCells[a]},"~N");c(c$,"setModelCage",function(a,b){0>a||a>=this.modelCount||(this.models[a].simpleCage=b,this.haveUnitCells=!0)},"~N,J.api.SymmetryInterface");c(c$,"getPlaneIntersection",function(a,b,d,c,e){var f=null;switch(a){case 1614417948:if(null==e)return null;f=e.getCanonicalCopy(d,!0);break;case 1679429641:f=this.boxInfo.getCanonicalCopy(d)}a=
new JU.List;a.addLast(f);return this.intersectPlane(b,a,c)},"~N,JU.P4,~N,~N,J.api.SymmetryInterface");c(c$,"getModelName",function(a){return 1>this.modelCount?"":0<=a?this.modelNames[a]:this.modelNumbersForAtomLabel[-1-a]},"~N");c(c$,"getModelTitle",function(a){return this.getModelAuxiliaryInfoValue(a,"title")},"~N");c(c$,"getModelFileName",function(a){return this.getModelAuxiliaryInfoValue(a,"fileName")},"~N");c(c$,"getModelFileType",function(a){return this.getModelAuxiliaryInfoValue(a,"fileType")},
"~N");c(c$,"setFrameTitle",function(a,b){if(r(b,String))for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.frameTitles[d]=b;else for(var d=a.nextSetBit(0),c=0;0<=d;d=a.nextSetBit(d+1))c<b.length&&(this.frameTitles[d]=b[c++])},"JU.BS,~O");c(c$,"getFrameTitle",function(a){return 0<=a&&a<this.modelCount?this.frameTitles[a]:""},"~N");c(c$,"getModelNumberForAtomLabel",function(a){return this.modelNumbersForAtomLabel[a]},"~N");c(c$,"calculatePolymers",function(a,b,d,c){if(this.isPDB)for(var e=!this.viewer.getBoolean(603979892),
f=0;f<this.modelCount;f++)if((null==c||!c.get(f))&&this.models[f].isBioModel){this.models[f].calculatePolymers(a,b,d,c,e);break}},"~A,~N,~N,JU.BS");c(c$,"getGroups",function(){for(var a=0,b=0;b<this.modelCount;b++)a+=this.models[b].getGroupCount();for(var a=Array(a),d=b=0;b<this.modelCount;b++)for(var c=0;c<this.models[b].chainCount;c++)for(var e=0;e<this.models[b].chains[c].groupCount;e++)a[d]=this.models[b].chains[c].groups[e],a[d].groupIndex=d,d++;return a});c(c$,"getNotionalUnitcell",function(){var a=
this.getUnitCell(0);return null==a?null:a.getNotionalUnitCell()});c(c$,"setCrystallographicDefaults",function(){return!this.isPDB&&this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates});c(c$,"getAverageAtomPoint",function(){return this.averageAtomPoint});c(c$,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?new JU.P3:this.boxInfo.getBoundBoxCenter()},"~N");c(c$,"getBoundBoxCornerVector",function(){return this.boxInfo.getBoundBoxCornerVector()});c(c$,"getBboxVertices",
function(){return this.boxInfo.getBoundBoxVertices()});c(c$,"getBoundBoxInfo",function(){return this.boxInfo.getBoundBoxInfo()});c(c$,"getBoundBoxModels",function(){return this.bboxModels});c(c$,"setBoundBox",function(a,b,d,c){this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;this.boxInfo.setBoundBox(a,b,d,c)},"JU.P3,JU.P3,~B,~N");c(c$,"getBoundBoxCommand",function(a){if(!a&&null!=this.bboxAtoms)return"boundbox "+J.util.Escape.eBS(this.bboxAtoms);this.ptTemp.setT(this.boxInfo.getBoundBoxCenter());
var b=this.boxInfo.getBoundBoxCornerVector();a=a?"boundbox "+J.util.Escape.eP(this.ptTemp)+" "+J.util.Escape.eP(b)+"\n#or\n":"";this.ptTemp.sub(b);a+="boundbox corners "+J.util.Escape.eP(this.ptTemp)+" ";this.ptTemp.scaleAdd2(2,b,this.ptTemp);b=Math.abs(8*b.x*b.y*b.z);return a+=J.util.Escape.eP(this.ptTemp)+" # volume = "+b},"~B");c(c$,"getDefaultVdwType",function(a){return!this.models[a].isBioModel?J.constant.EnumVdw.AUTO_BABEL:0==this.models[a].hydrogenCount?J.constant.EnumVdw.AUTO_JMOL:J.constant.EnumVdw.AUTO_BABEL},
"~N");c(c$,"setRotationRadius",function(a,b){return this.isJmolDataFrameForModel(a)?(this.models[a].defaultRotationRadius=b,!1):!0},"~N,~N");c(c$,"calcRotationRadius",function(a,b){if(this.isJmolDataFrameForModel(a)){var d=this.models[a].defaultRotationRadius;return 0==d?10:d}for(var d=0,c=this.atomCount;0<=--c;)if(this.isJmolDataFrameForAtom(this.atoms[c]))for(a=this.atoms[c].modelIndex;0<=c&&this.atoms[c].modelIndex==a;)c--;else{var e=this.atoms[c],e=b.distance(e)+this.getRadiusVdwJmol(e);e>d&&
(d=e)}return 0==d?10:d},"~N,JU.P3");c(c$,"calcBoundBoxDimensions",function(a,b){null!=a&&0>a.nextSetBit(0)&&(a=null);null==a&&this.isBbcageDefault||2>this.atomCount||(this.bboxModels=this.getModelBitSet(this.bboxAtoms=J.util.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.atomCount&&(this.isBbcageDefault=!0),null==a&&(this.averageAtomPoint.setT(this.getAtomSetCenter(null)),null!=this.unitCells&&this.calcUnitCellMinMax()),this.boxInfo.setBbcage(b))},"JU.BS,~N");c(c$,"getBoxInfo",function(a,
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this.unitCells[a].getUnitCellVertices(),d=0;8>d;d++)this.boxInfo.addBoundBoxPoint(b[d])});c(c$,"calcRotationRadiusBs",function(a){for(var b=this.getAtomSetCenter(a),d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var e=this.atoms[c],e=b.distance(e)+this.getRadiusVdwJmol(e);e>d&&(d=e)}return 0==d?10:d},"JU.BS");c(c$,"getCenterAndPoints",function(a,b){for(var d,c,e=b?1:0,f=a.size();0<=--f;){var j=a.get(f);d=j[0];r(j[1],JU.BS)?(c=j[1],e+=Math.min(d.cardinality(),c.cardinality())):e+=Math.min(d.cardinality(),
j[1].length)}var k=ia(2,e,null);b&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(f=a.size();0<=--f;)if(j=a.get(f),d=j[0],r(j[1],JU.BS)){c=j[1];for(var j=d.nextSetBit(0),h=c.nextSetBit(0);0<=j&&0<=h;j=d.nextSetBit(j+1),h=c.nextSetBit(h+1))k[0][--e]=this.atoms[j],k[1][e]=this.atoms[h],b&&(k[0][0].add(this.atoms[j]),k[1][0].add(this.atoms[h]))}else{c=j[1];j=d.nextSetBit(0);for(h=0;0<=j&&h<c.length;j=d.nextSetBit(j+1),h++)k[0][--e]=this.atoms[j],k[1][e]=c[h],b&&(k[0][0].add(this.atoms[j]),k[1][0].add(c[h]))}b&&
(k[0][0].scale(1/(k[0].length-1)),k[1][0].scale(1/(k[1].length-1)));return k},"JU.List,~B");c(c$,"getAtomSetCenter",function(a){var b=JU.P3.new3(0,0,0),d=0;if(null!=a)for(var c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.atoms[c])||(d++,b.add(this.atoms[c]));0<d&&b.scale(1/d);return b},"JU.BS");c(c$,"setAPm",function(a,b,d,c,e,f,j){this.setAPa(a,b,d,c,e,f,j);switch(b){case 1095763990:case 1632634891:this.viewer.getBoolean(603979944)&&this.assignAromaticBonds()}},"JU.BS,~N,~N,~N,~S,~A,~A");
c(c$,"addStateScript",function(a,b,d,c,e,f,j){var k=this.viewer.getCurrentModelIndex();f?(this.thisStateModel!=k&&(a="frame "+(0>k?"all #"+k:this.getModelNumberDotted(k))+";\n  "+a),this.thisStateModel=k):this.thisStateModel=-1;a=new J.modelset.StateScript(this.thisStateModel,a,b,d,c,e,j);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(c$,"calculateStructuresAllExcept",function(a,b,d,c,e,f){this.freezeModels();var j="";a=J.util.BSUtil.copyInvert(a,this.modelCount);
e&&this.setDefaultStructure(a);for(var k=a.nextSetBit(0);0<=k;k=a.nextSetBit(k+1))j+=this.models[k].calculateStructures(b,d,c,e,f);e&&this.setStructureIndexes();return j},"JU.BS,~B,~B,~B,~B,~B");c(c$,"setDefaultStructure",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.models[b].isBioModel&&null==this.models[b].defaultStructure&&(this.models[b].defaultStructure=this.getProteinStructureState(this.models[b].bsAtoms,!1,!1,0))},"JU.BS");c(c$,"setProteinType",function(a,b){var d=-1,
c=-1,e=this.getModelBitSet(a,!1);this.setDefaultStructure(e);for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){c!=f-1&&(d=-1);var d=this.atoms[f].group.setProteinStructureType(b,d),j=this.atoms[f].modelIndex;this.proteinStructureTainted=this.models[j].structureTainted=!0;c=f=this.atoms[f].group.lastAtomIndex}d=D(this.modelCount,0);for(f=0;f<this.atomCount;)j=this.atoms[f].modelIndex,e.get(j)?(c=this.atoms[f].getStrucNo(),1E3>c&&c>d[j]&&(d[j]=c),f=this.atoms[f].group.lastAtomIndex+1):f=this.models[j].firstAtomIndex+
this.models[j].atomCount;for(f=0;f<this.atomCount;)j=this.atoms[f].modelIndex,e.get(j)?(1E3<this.atoms[f].getStrucNo()&&this.atoms[f].group.setStrucNo(++d[j]),f=this.atoms[f].group.lastAtomIndex+1):f=this.models[j].firstAtomIndex+this.models[j].atomCount},"JU.BS,J.constant.EnumStructure");c(c$,"freezeModels",function(){for(var a=this.modelCount;0<=--a;)this.models[a].freeze()});c(c$,"getStructureList",function(){return this.viewer.getStructureList()});c(c$,"setStructureList",function(a){for(var b=
this.modelCount;0<=--b;)this.models[b].setStructureList(a)},"java.util.Map");c(c$,"setConformation",function(a){for(var b=this.getModelBitSet(a,!1),d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.models[d].setConformation(a);return a},"JU.BS");c(c$,"getConformation",function(a,b,d){for(var c=new JU.BS,e=this.modelCount;0<=--e;)if(e==a||0>a){var f=this.getAltLocListInModel(e),j=this.getAltLocCountInModel(e);if(!(0<b&&b>=j)){var k=this.viewer.getModelUndeletedAtomsBitSet(e);if(0<=b&&!this.models[e].getPdbConformation(k,
b))for(;0<=--j;)j!=b&&k.andNot(this.getAtomBitsMDa(1048607,f.substring(j,j+1)));0<=k.nextSetBit(0)&&(c.or(k),d&&this.models[e].setConformation(k))}}return c},"~N,~N,~B");c(c$,"getHeteroList",function(a){for(var b=new java.util.Hashtable,d=!1,c=this.modelCount;0<=--c;)if(0>a||c==a){var e=this.getModelAuxiliaryInfoValue(c,"hetNames");if(null!=e)for(var d=!0,f,e=e.entrySet().iterator();e.hasNext()&&((f=e.next())||1);){var j=f.getKey();b.put(j,f.getValue())}}return d?b:this.getModelSetAuxiliaryInfoValue("hetNames")},
"~N");c(c$,"getModelSetProperties",function(){return this.modelSetProperties});c(c$,"getModelSetAuxiliaryInfo",function(){return this.modelSetAuxiliaryInfo});c(c$,"getModelSetProperty",function(a){return null==this.modelSetProperties?null:this.modelSetProperties.getProperty(a)},"~S");c(c$,"getModelSetAuxiliaryInfoValue",function(a){return null==this.modelSetAuxiliaryInfo?null:this.modelSetAuxiliaryInfo.get(a)},"~S");c(c$,"getModelSetAuxiliaryInfoBoolean",function(a){a=this.getModelSetAuxiliaryInfoValue(a);
return r(a,Boolean)&&a.booleanValue()},"~S");c(c$,"mergeTrajectories",function(a){if(null==this.trajectorySteps){if(!a)return 0;this.trajectorySteps=new JU.List}for(a=this.trajectorySteps.size();a<this.modelCount;a++)this.trajectorySteps.addLast(null);return this.modelCount},"~B");c(c$,"getTrajectoryIndex",function(a){return this.models[a].trajectoryBaseIndex},"~N");c(c$,"isTrajectory",function(a){return this.models[a].isTrajectory},"~N");c(c$,"isTrajectoryMeasurement",function(a){if(null==a)return!1;
for(var b=a[0],d,c=1;c<=b;c++)if(0<=(d=a[c])&&this.models[this.atoms[d].modelIndex].isTrajectory)return!0;return!1},"~A");c(c$,"getModelBitSet",function(a,b){for(var d=new JU.BS,c=0,e=null==a,c=e?0:a.nextSetBit(0);0<=c&&c<this.atomCount;c=e?c+1:a.nextSetBit(c+1)){d.set(c=this.atoms[c].modelIndex);if(b)for(var f=this.models[c].trajectoryBaseIndex,j=0;j<this.modelCount;j++)this.models[j].trajectoryBaseIndex==f&&d.set(j);c=this.models[c].firstAtomIndex+this.models[c].atomCount-1}return d},"JU.BS,~B");
c(c$,"getIterativeModels",function(a){for(var b=new JU.BS,d=0;d<this.modelCount;d++)(a||!this.isJmolDataFrameForModel(d))&&this.models[d].trajectoryBaseIndex==d&&b.set(d);return b},"~B");c(c$,"isTrajectorySubFrame",function(a){return this.models[a].isTrajectory&&this.models[a].trajectoryBaseIndex!=a},"~N");c(c$,"selectDisplayedTrajectories",function(a){for(var b=0;b<this.modelCount;b++)this.models[b].isTrajectory&&this.atoms[this.models[b].firstAtomIndex].modelIndex!=b&&a.clear(b);return a},"JU.BS");
c(c$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=D(this.atomCount,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var e=d.nextSetBit(0);0<=e;e=d.nextSetBit(e+1))a.atomMolecule[e]=c}}0!=(b&8)?(d=D(1,0),a.hAtomRadius=this.viewer.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,!1,!0,null),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==
a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.models[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.atomCount?0:this.atoms[a.firstAtomIndex].modelIndex,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"getModelNumberDotted",function(a){return 1>this.modelCount||a>=this.modelCount||0>a?"":J.util.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(c$,"getModelNumber",function(a){2147483647==
a&&(a=this.modelCount-1);return this.modelNumbers[a]},"~N");c(c$,"getModelFileNumber",function(a){return this.modelFileNumbers[a]},"~N");c(c$,"getModelProperties",function(a){return this.models[a].properties},"~N");c(c$,"getModelProperty",function(a,b){var d=this.models[a].properties;return null==d?null:d.getProperty(b)},"~N,~S");c(c$,"getModelAuxiliaryInfo",function(a){return 0>a?null:this.models[a].auxiliaryInfo},"~N");c(c$,"setModelAuxiliaryInfo",function(a,b,d){this.models[a].auxiliaryInfo.put(b,
d)},"~N,~O,~O");c(c$,"getModelAuxiliaryInfoValue",function(a,b){return 0>a?null:this.models[a].auxiliaryInfo.get(b)},"~N,~S");c(c$,"getModelAuxiliaryInfoBoolean",function(a,b){var d=this.models[a].auxiliaryInfo;return null!=d&&d.containsKey(b)&&d.get(b).booleanValue()},"~N,~S");c(c$,"getModelAuxiliaryInfoInt",function(a,b){var d=this.models[a].auxiliaryInfo;return null!=d&&d.containsKey(b)?d.get(b).intValue():-2147483648},"~N,~S");c(c$,"getModelAtomProperty",function(a,b){var d=this.getModelAuxiliaryInfoValue(a.modelIndex,
b);if(!r(d,Array))return"";var c=a.index-this.models[a.modelIndex].firstAtomIndex;return c<d.length?d[c].toString():""},"J.modelset.Atom,~S");c(c$,"getInsertionCountInModel",function(a){return this.models[a].nInsertions},"~N");c$.modelFileNumberFromFloat=c(c$,"modelFileNumberFromFloat",function(a){var b=s(Math.floor(a));for(a=s(Math.floor(1E4*(a-b+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*b+a},"~N");c(c$,"getAltLocCountInModel",function(a){return this.models[a].nAltLocs},"~N");c(c$,"getChainCount",
function(a){for(var b=0,d=this.modelCount;0<=--d;)b+=this.models[d].getChainCount(a);return b},"~B");c(c$,"getBioPolymerCount",function(){for(var a=0,b=this.modelCount;0<=--b;)this.isTrajectorySubFrame(b)||(a+=this.models[b].getBioPolymerCount());return a});c(c$,"getBioPolymerCountInModel",function(a){return 0>a?this.getBioPolymerCount():this.isTrajectorySubFrame(a)?0:this.models[a].getBioPolymerCount()},"~N");c(c$,"getPolymerPointsAndVectors",function(a,b,d,c){for(var e=0;e<this.modelCount;++e)this.models[e].getPolymerPointsAndVectors(a,
b,d,c)},"JU.BS,JU.List,~B,~N");c(c$,"recalculateLeadMidpointsAndWingVectors",function(a){if(0>a)for(a=0;a<this.modelCount;a++)this.isTrajectorySubFrame(a)||this.models[a].recalculateLeadMidpointsAndWingVectors();else this.models[a].recalculateLeadMidpointsAndWingVectors()},"~N");c(c$,"getPolymerLeadMidPoints",function(a,b){return this.models[a].getPolymerLeadMidPoints(b)},"~N,~N");c(c$,"getChainCountInModel",function(a,b){return 0>a?this.getChainCount(b):this.models[a].getChainCount(b)},"~N,~B");
c(c$,"getGroupCount",function(){for(var a=0,b=this.modelCount;0<=--b;)a+=this.models[b].getGroupCount();return a});c(c$,"getGroupCountInModel",function(a){return 0>a?this.getGroupCount():this.models[a].getGroupCount()},"~N");c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.modelCount;0<=--b;)this.models[b].calcSelectedGroupsCount(a)},"JU.BS");c(c$,"calcSelectedMonomersCount",function(a){for(var b=this.modelCount;0<=--b;)this.models[b].calcSelectedMonomersCount(a)},"JU.BS");c(c$,"calcRasmolHydrogenBonds",
function(a,b,d,c,e,f,j){for(var k=null==b||a.equals(b),h=this.modelCount;0<=--h;)this.models[h].isBioModel&&this.models[h].trajectoryBaseIndex==h&&(null==d&&(this.models[h].clearRasmolHydrogenBonds(a),k||this.models[h].clearRasmolHydrogenBonds(b)),this.models[h].getRasmolHydrogenBonds(a,b,d,c,e,f,j))},"JU.BS,JU.BS,JU.List,~B,~N,~B,JU.BS");c(c$,"calculateStraightness",function(){if(!this.getHaveStraightness()){for(var a=this.viewer.getQuaternionFrame(),b=this.viewer.getInt(553648146),d=this.modelCount;0<=
--d;)this.models[d].calculateStraightness(this.viewer,"S",a,b);this.setHaveStraightness(!0)}});c(c$,"getAtomGroupQuaternions",function(a,b,d){for(var c=0,e=new JU.List,f=a.nextSetBit(0);0<=f&&c<b;f=a.nextSetBit(f+1)){var j=this.atoms[f].group,k=j.getQuaternion(d);if(null==k&&(-2147483648==j.seqcode&&(k=j.getQuaternionFrame(this.atoms)),null==k))continue;c++;e.addLast(k);f=j.lastAtomIndex}return e.toArray(Array(e.size()))},"JU.BS,~N,~S");c(c$,"getPdbAtomData",function(a,b){if(0==this.atomCount||0>
a.nextSetBit(0))return"";null==b&&(b=this.viewer.getOutputChannel(null,null));var d=this.atoms[a.nextSetBit(0)].modelIndex,c=-1,e="%6.2Q%6.2b          ";if("PQR".equals(b.getType())){for(var e="%8.4P%7.4V       ",f=0,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1))f+=this.atoms[j].getPartialCharge();b.append("REMARK   1 PQR file generated by Jmol "+J.viewer.Viewer.getJmolVersion()).append("\nREMARK   1 created "+new java.util.Date).append("\nREMARK   1 Forcefield Used: unknown\nREMARK   1").append("\nREMARK   5").append("\nREMARK   6 Total charge on this protein: "+
f+" e\nREMARK   6\n")}for(var j=a.length()-1,k=(f=d!=this.atoms[j].modelIndex)?null:new JU.SB,d=this.models[d].isPdbWithMultipleBonds,h,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var m=this.atoms[j];f&&m.modelIndex!=c&&(-1!=c&&b.append("ENDMDL\n"),c=m.modelIndex,b.append("MODEL     "+(c+1)+"\n"));var n=m.getAtomName();h=2==m.getElementSymbol().length||4<=n.length||Character.isDigit(n.charAt(0));var q=this.models[m.modelIndex].isBioModel,n=m.isHetero();h=q?n?h?J.modelset.LabelToken.compile(this.viewer,
"HETATM%5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z"+e,"\x00",null):J.modelset.LabelToken.compile(this.viewer,"HETATM%5.-5i  %-3.3a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z"+e,"\x00",null):h?J.modelset.LabelToken.compile(this.viewer,"ATOM  %5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z"+e,"\x00",null):J.modelset.LabelToken.compile(this.viewer,"ATOM  %5.-5i  %-3.3a%1A%3.-3n %1c%4.-4R%1E   %8.3x%8.3y%8.3z"+e,"\x00",null):h?J.modelset.LabelToken.compile(this.viewer,"HETATM%5.-5i %-4.4a%1AUNK %1c   1%1E   %8.3x%8.3y%8.3z"+
e,"\x00",null):J.modelset.LabelToken.compile(this.viewer,"HETATM%5.-5i  %-3.3a%1AUNK %1c   1%1E   %8.3x%8.3y%8.3z"+e,"\x00",null);var v=m.getElementSymbolIso(!1).toUpperCase();b.append(J.modelset.LabelToken.formatLabelAtomArray(this.viewer,m,h,"\x00",null)).append(1==v.length?" "+v:v.substring(0,2)).append("  \n");if(!f&&(!q||n||d))if(q=m.getBonds(),null!=q)for(h=0;h<q.length;h++){var x=m.getAtomNumber(),p=q[h].getOtherAtom(m);if(a.get(p.index)&&(v=q[h].getCovalentOrder(),!(1==v&&d&&!n)))switch(p=
p.getAtomNumber(),v){case 2:case 3:if(p<x)continue;case 1:k.append("CONECT").append(J.util.Txt.formatStringI("%5i","i",x));for(x=0;x<v;x++)k.append(J.util.Txt.formatStringI("%5i","i",p));k.appendC("\n")}}}f?b.append("ENDMDL\n"):b.append(k.toString());return b.toString()},"JU.BS,JU.OC");c(c$,"getPdbData",function(a,b,d,c,e){this.isJmolDataFrameForModel(a)&&(a=this.getJmolDataSourceFrame(a));if(0>a)return"";var f=this.models[a].isBioModel;if(null==c&&!f)return null;var j=this.models[a];null==e&&(e=
this.viewer.getOutputChannel(null,null));var k=new JU.SB,h=0<=b.indexOf("draw"),m=null,n=new JU.BS,q="\x00",v=this.getLabeler().compile(this.viewer,"ATOM  %-6i%4a%1A%3n %1c%4R%1E   ","\x00",null);if(null==c)q=11<b.length&&0<=b.indexOf("quaternion ")?b.charAt(11):"R",j.getPdbData(this.viewer,b,q,h,d,e,v,k,n),m=this.viewer.getModelUndeletedAtomsBitSet(a);else{m=c[0];a=c[1];var j=c[2],x=c[3],p=null!=x,r=c[4],s=c[5],t=c[6];c=c[7];e.append("REMARK   6 Jmol PDB-encoded data: ").append(b).append(";\n");
e.append("REMARK   6 Jmol data").append(" min = ").append(J.util.Escape.eP(r)).append(" max = ").append(J.util.Escape.eP(s)).append(" unScaledXyz = xyz * ").append(J.util.Escape.eP(t)).append(" + ").append(J.util.Escape.eP(c)).append(";\n");b=null;c=m.nextSetBit(0);for(r=0;0<=c;c=m.nextSetBit(c+1),r++){var s=a[r],t=j[r],u=p?x[r]:0;if(!Float.isNaN(s)&&!Float.isNaN(t)&&!Float.isNaN(u)){var w=this.atoms[c];e.append(J.modelset.LabelToken.formatLabelAtomArray(this.viewer,w,v,"\x00",null));f&&n.set(c);
e.append(J.util.Txt.sprintf("%-8.2f%-8.2f%-10.2f    %6.3f          %2s    %s\n","ssF",[w.getElementSymbolIso(!1).toUpperCase(),"",[s,t,u,0]]));null!=b&&b.getPolymerIndexInModel()==w.getPolymerIndexInModel()&&k.append("CONECT").append(J.util.Txt.formatStringI("%5i","i",b.getAtomNumber())).append(J.util.Txt.formatStringI("%5i","i",w.getAtomNumber())).appendC("\n");b=w}}}e.append(k.toString());if(h)return e.toString();d.and(m);f&&e.append("\n\n"+this.getProteinStructureState(n,!1,"R"==q,1));return e.toString()},
"~N,~S,JU.BS,~A,JU.OC");c(c$,"isJmolDataFrameForModel",function(a){return 0<=a&&a<this.modelCount&&this.models[a].isJmolDataFrame},"~N");c(c$,"isJmolDataFrameForAtom",function(a){return this.models[a.modelIndex].isJmolDataFrame},"J.modelset.Atom");c(c$,"setJmolDataFrame",function(a,b,d){var c=this.models[null==a?this.models[d].dataSourceFrame:b];null==a&&(a=this.models[d].jmolFrameType);0<=b&&(null==c.dataFrames&&(c.dataFrames=new java.util.Hashtable),this.models[d].dataSourceFrame=b,this.models[d].jmolFrameType=
a,c.dataFrames.put(a,Integer.$valueOf(d)));a.startsWith("quaternion")&&0>a.indexOf("deriv")&&(a=a.substring(0,a.indexOf(" ")),c.dataFrames.put(a,Integer.$valueOf(d)))},"~S,~N,~N");c(c$,"getJmolDataFrameIndex",function(a,b){if(null==this.models[a].dataFrames)return-1;var d=this.models[a].dataFrames.get(b);return null==d?-1:d.intValue()},"~N,~S");c(c$,"clearDataFrameReference",function(a){for(var b=0;b<this.modelCount;b++){var d=this.models[b].dataFrames;if(null!=d)for(d=d.values().iterator();d.hasNext();)d.next().intValue()==
a&&d.remove()}},"~N");c(c$,"getJmolFrameType",function(a){return 0<=a&&a<this.modelCount?this.models[a].jmolFrameType:"modelSet"},"~N");c(c$,"getJmolDataSourceFrame",function(a){return 0<=a&&a<this.modelCount?this.models[a].dataSourceFrame:-1},"~N");c(c$,"saveModelOrientation",function(a,b){this.models[a].orientation=b},"~N,J.modelset.Orientation");c(c$,"getModelOrientation",function(a){return this.models[a].orientation},"~N");c(c$,"getPDBHeader",function(a){return this.models[a].isBioModel?this.models[a].getFullPDBHeader():
this.getFileHeader(a)},"~N");c(c$,"getFileHeader",function(a){if(0>a)return"";if(this.models[a].isBioModel)return this.models[a].getFullPDBHeader();a=this.getModelAuxiliaryInfoValue(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=a?a:"no header information found"},"~N");c(c$,"getAltLocIndexInModel",function(a,b){if("\x00"==b)return 0;var d=this.getAltLocListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,"getInsertionCodeIndexInModel",function(a,b){if("\x00"==b)return 0;
var d=this.getInsertionListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,"getAltLocListInModel",function(a){if(0>a)return"";a=this.getModelAuxiliaryInfoValue(a,"altLocs");return null==a?"":a},"~N");c(c$,"getInsertionListInModel",function(a){a=this.getModelAuxiliaryInfoValue(a,"insertionCodes");return null==a?"":a},"~N");c(c$,"getModelSymmetryCount",function(a){return 0<this.models[a].biosymmetryCount?this.models[a].biosymmetryCount:null==this.unitCells||null==this.unitCells[a]?0:this.unitCells[a].getSpaceGroupOperationCount()},
"~N");c(c$,"getSymmetryInfoString",function(a,b,d,c,e,f,j){a=this.getSymTemp(!0).getSpaceGroupInfo(this,a,b,d,c,e,f);return null==a?"":this.symTemp.getSymmetryInfoString(a,d,f,j)},"~N,~S,~N,JU.P3,JU.P3,~S,~B");c(c$,"getModelCellRange",function(a){return null==this.unitCells?null:this.unitCells[a].getCellRange()},"~N");c(c$,"getLastVibrationVector",function(a,b){if(null!=this.vibrations)for(var d=this.atomCount;0<=--d;)if((0>a||this.atoms[d].modelIndex==a)&&null!=this.vibrations[d]&&0<this.vibrations[d].length()&&
(0==b||1276121113==b==r(this.vibrations[d],J.api.JmolModulationSet)))return d;return-1},"~N,~N");c(c$,"getModulationList",function(a,b,d){var c=new JU.List;if(null!=this.vibrations)for(var e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))r(this.vibrations[e],J.api.JmolModulationSet)?c.addLast(this.vibrations[e].getModulation(b,d)):c.addLast(null);return c},"JU.BS,~S,JU.P3");c(c$,"getElementsPresentBitSet",function(a){if(0<=a)return this.elementsPresent[a];a=new JU.BS;for(var b=0;b<this.modelCount;b++)a.or(this.elementsPresent[b]);
return a},"~N");c(c$,"getSymmetryInfoAsStringForModel",function(a){a=this.getUnitCell(a);return null==a?"no symmetry information":a.getSymmetryInfoString()},"~N");c(c$,"getMoleculeIndex",function(a,b){0==this.moleculeCount&&this.getMolecules();for(var d=0;d<this.moleculeCount;d++)if(this.molecules[d].atomList.get(a))return b?this.molecules[d].indexInModel:d;return 0},"~N,~B");c(c$,"getMoleculeBitSet",function(a){0==this.moleculeCount&&this.getMolecules();var b=J.util.BSUtil.copy(a);a=J.util.BSUtil.copy(a);
for(var d=0,c=new JU.BS;0<=(d=a.length()-1);)c=this.getMoleculeBitSetForAtom(d),null==c?(a.clear(d),b.clear(d)):(a.andNot(c),b.or(c));return b},"JU.BS");c(c$,"getMoleculeBitSetForAtom",function(a){0==this.moleculeCount&&this.getMolecules();for(var b=0;b<this.moleculeCount;b++)if(this.molecules[b].atomList.get(a))return this.molecules[b].atomList;return null},"~N");c(c$,"getModelDipole",function(a){if(0>a)return null;var b=this.getModelAuxiliaryInfoValue(a,"dipole");null==b&&(b=this.getModelAuxiliaryInfoValue(a,
"DIPOLE_VEC"));return b},"~N");c(c$,"calculateMolecularDipole",function(a){if(null==this.partialCharges||0>a)return null;for(var b=0,d=0,c=0,e=0,f=new JU.V3,j=new JU.V3,k=0;k<this.atomCount;k++)if(this.atoms[k].modelIndex==a){var h=this.partialCharges[k];0>h?(d++,e+=h,j.scaleAdd2(h,this.atoms[k],j)):0<h&&(b++,c+=h,f.scaleAdd2(h,this.atoms[k],f))}if(0==d||0==b)return null;f.scale(1/c);j.scale(1/e);f.sub(j);J.util.Logger.warn("CalculateMolecularDipole: this is an approximate result -- needs checking");
f.scale(4.8*c);return f},"~N");c(c$,"getMoleculeCountInModel",function(a){var b=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var d=0;d<this.modelCount;d++)a==d&&(b+=this.models[d].moleculeCount);return b},"~N");c(c$,"calcSelectedMoleculesCount",function(a){0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var b=new JU.BS,d=0;d<this.moleculeCount;d++)J.util.BSUtil.copy2(a,b),b.and(this.molecules[d].atomList),0<b.length()&&
this.selectedMolecules.set(d)},"JU.BS");c(c$,"setCentroid",function(a,b){var d=this.getNotInCentroid(a,b);null!=d&&0<=d.nextSetBit(0)&&this.viewer.deleteAtoms(d,!1)},"JU.BS,~A");c(c$,"getNotInCentroid",function(a,b){var d=a.nextSetBit(0);if(0>d)return null;d=this.getUnitCell(this.atoms[d].modelIndex);return null==d?null:d.notInCentroid(this,a,b)},"JU.BS,~A");c(c$,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=
0;for(var a=null,b=Array(this.modelCount),d=null,c=0;c<this.modelCount;c++)b[c]=this.viewer.getModelUndeletedAtomsBitSet(c),a=this.models[c],a.moleculeCount=0,d=a.getBioBranches(d);this.molecules=J.util.JmolMolecule.getMolecules(this.atoms,b,d,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.models[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(c$,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isInitialized())){this.showRebondTimes&&
J.util.Logger.startTimer("build bspf");var a=new J.bspt.Bspf(3);J.util.Logger.debugging&&J.util.Logger.debug("sequential bspt order");for(var b=J.util.BSUtil.newBitSet(this.modelCount),d=this.atomCount;0<=--d;){var c=this.atoms[d];!c.isDeleted()&&!this.isTrajectorySubFrame(c.modelIndex)&&(a.addTuple(this.models[c.modelIndex].trajectoryBaseIndex,c),b.set(c.modelIndex))}this.showRebondTimes&&(J.util.Logger.checkTimer("build bspf",!1),a.stats());for(d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))a.validateModel(d,
!0);a.validate(!0);this.bspf=a}});c(c$,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||this.bspf.initialize(a,this.atoms,this.viewer.getModelUndeletedAtomsBitSet(a))},"~N");c(c$,"setIteratorForPoint",function(a,b,d,c){0>b?a.setCenter(d,c):(this.initializeBspt(b),a.setModel(this,b,this.models[b].firstAtomIndex,2147483647,d,c,null))},"J.api.AtomIndexIterator,~N,JU.P3,~N");c(c$,"setIteratorForAtom",function(a,b,d,c,e){0>b&&(b=this.atoms[d].modelIndex);b=this.models[b].trajectoryBaseIndex;
this.initializeBspt(b);a.setModel(this,b,this.models[b].firstAtomIndex,d,this.atoms[d],c,e)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(c$,"getSelectedAtomIterator",function(a,b,d,c,e){this.initializeBspf();if(e){e=this.getModelBitSet(a,!1);for(var f=e.nextSetBit(0);0<=f;f=e.nextSetBit(f+1))this.initializeBspt(f);e=new J.modelset.AtomIteratorWithinModelSet(e)}else e=new J.modelset.AtomIteratorWithinModel;e.initialize(this.bspf,a,b,d,c,this.viewer.isParallel());return e},"JU.BS,~B,~B,~B,~B");
h(c$,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.models[a].getBondCount()},"~N");c(c$,"calculateStruts",function(a,b){return this.calculateStrutsMC(a,b)},"JU.BS,JU.BS");c(c$,"calculateStrutsMC",function(a,b){this.makeConnections2(0,3.4028235E38,32768,12291,a,b,null,!1,!1,0);var d=a.nextSetBit(0);if(0>d)return 0;d=this.models[this.atoms[d].modelIndex];return d.isBioModel?d.calculateStruts(this,a,b):0},"JU.BS,JU.BS");c(c$,"getAtomCountInModel",function(a){return 0>a?this.atomCount:
this.models[a].atomCount},"~N");c(c$,"getModelAtomBitSetIncludingDeletedBs",function(a){var b=new JU.BS;null==a&&null==this.bsAll&&(this.bsAll=J.util.BSUtil.setAll(this.atomCount));if(null==a)b.or(this.bsAll);else for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.or(this.getModelAtomBitSetIncludingDeleted(d,!1));return b},"JU.BS");c(c$,"getModelAtomBitSetIncludingDeleted",function(a,b){var d=0>a?this.bsAll:this.models[a].bsAtoms;null==d&&(d=this.bsAll=J.util.BSUtil.setAll(this.atomCount));return b?
J.util.BSUtil.copy(d):d},"~N,~B");c(c$,"getAtomBitsMaybeDeleted",function(a,b){var d,c;switch(a){default:return this.getAtomBitsMDa(a,b);case 1678770178:case 1048585:return this.getAtomBitsMDb(a,b);case 1073741864:return this.getBasePairBits(b);case 1679429641:var e=this.getBoxInfo(b,1);c=this.getAtomsWithin(e.getBoundBoxCornerVector().length()+1E-4,e.getBoundBoxCenter(),null,-1);for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1))e.isWithin(this.atoms[d])||c.clear(d);return c;case 1095761925:c=new JU.BS;
d=b;this.ptTemp1.set(d[0]/1E3,d[1]/1E3,d[2]/1E3);e=!this.viewer.getBoolean(603979848);for(d=this.atomCount;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,e)&&c.set(d);return c;case 1095761926:c=J.util.BSUtil.newBitSet2(0,this.atomCount);d=b;e=[s(d[0]/1E3)-1,s(d[1]/1E3)-1,s(d[2]/1E3)-1,s(d[0]/1E3),s(d[1]/1E3),s(d[2]/1E3),0];for(d=this.modelCount;0<=--d;){var f=this.getUnitCell(d);null==f?J.util.BSUtil.andNot(c,this.models[d].bsAtoms):c.andNot(f.notInCentroid(this,this.models[d].bsAtoms,e))}return c;
case 1095761936:return this.getMoleculeBitSet(b);case 1087373320:return this.getSequenceBits(b,null);case 1048615:d=b;var e=d[0],f=d[1],j=d[2];c=new JU.BS;var k=this.viewer.getBoolean(603979822);0<=j&&(256>j&&!k)&&(j=J.modelset.AtomCollection.chainToUpper(j));for(d=this.modelCount;0<=--d;)this.models[d].isBioModel&&this.models[d].selectSeqcodeRange(e,f,j,c,k);return c;case 3145772:c=J.util.BSUtil.newBitSet(this.atomCount);e=-1;f=0;for(d=this.atomCount;0<=--d;)if(k=this.atoms[d],j=k.getAtomSymmetry(),
null!=j){if(k.modelIndex!=e){e=k.modelIndex;if(null==this.getModelCellRange(e))continue;f=this.getModelSymmetryCount(e)}for(var k=0,h=f;0<=--h;)if(j.get(h)&&1<++k){c.set(d);break}}return c;case 1089470478:return J.util.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=J.util.BSUtil.newBitSet(this.atomCount):this.bsSymmetry);case 1614417948:c=new JU.BS;if(null==this.viewer.getCurrentUnitCell())return c;this.ptTemp1.set(1,1,1);for(d=this.atomCount;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,
!1)&&c.set(d);return c}},"~N,~O");c(c$,"isInLatticeCell",function(a,b,d,c){var e=this.getUnitCell(this.atoms[a].modelIndex);d.setT(this.atoms[a]);return null!=e&&e.checkUnitCell(e,b,d,c)},"~N,JU.P3,JU.P3,~B");c(c$,"getAtomsWithinRD",function(a,b,d,c){var e=new JU.BS,f=this.getIterativeModels(!1);b=J.util.BSUtil.andNot(b,this.viewer.getDeletedAtoms());var j=this.getSelectedAtomIterator(null,!1,!1,!1,!1);if(d)for(d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))for(var k=this.modelCount;0<=--k;)f.get(k)&&
(0>a?this.getAtomsWithin(a,this.atoms[d].getFractionalUnitCoordPt(!0),e,-1):(this.setIteratorForAtom(j,k,d,a,c),j.addAtoms(e)));else{e.or(b);for(d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))0>a?this.getAtomsWithin(a,this.atoms[d],e,this.atoms[d].modelIndex):(this.setIteratorForAtom(j,-1,d,a,c),j.addAtoms(e))}j.release();return e},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,"getGroupsWithin",function(a,b){for(var d=this.getIterativeModels(!1),c=new JU.BS,e=this.modelCount;0<=--e;)d.get(e)&&this.models[e].isBioModel&&
this.models[e].getGroupsWithin(a,b,c);return c},"~N,JU.BS");c(c$,"getAtomsWithin",function(a,b,d,c){null==d&&(d=new JU.BS);if(0>a){a=-a;for(var e=this.atomCount;0<=--e;){var f=this.atoms[e];0<=c&&this.atoms[e].modelIndex!=c||!d.get(e)&&f.getFractionalUnitDistance(b,this.ptTemp1,this.ptTemp2)<=a&&d.set(f.index)}return d}c=this.getIterativeModels(!0);e=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(f=this.modelCount;0<=--f;)c.get(f)&&(this.setIteratorForAtom(e,-1,this.models[f].firstAtomIndex,-1,
null),e.setCenter(b,a),e.addAtoms(d));e.release();return d},"~N,JU.P3,JU.BS,~N");c(c$,"getBasePairBits",function(a){var b=new JU.BS;if(0!=a.length%2)return b;var d=null,c=null,b=new JU.List;if(0==a.length)d=c=this.viewer.getAllAtoms(),this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null);else for(var e=0;e<a.length;)d=this.getSequenceBits(a.substring(e,++e),null),0!=d.cardinality()&&(c=this.getSequenceBits(a.substring(e,++e),null),0!=c.cardinality()&&this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null));a=
new JU.BS;for(e=b.size();0<=--e;)d=b.get(e),a.set(d.atom1.index),a.set(d.atom2.index);return this.getAtomBitsMDb(1087373318,a)},"~S");c(c$,"getSequenceBits",function(a,b){null==b&&(b=this.viewer.getAllAtoms());var d=new JU.BS;if(0<a.length)for(var c=0;c<this.modelCount;++c)this.models[c].isBioModel&&this.models[c].getSequenceBits(a,b,d);return d},"~S,JU.BS");c(c$,"deleteBonds",function(a,b){if(!b)for(var d=new JU.BS,c=new JU.BS,e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1)){var f=this.bonds[e].atom1;
this.models[f.modelIndex].isModelKit||(d.clearAll(),c.clearAll(),d.set(f.index),c.set(this.bonds[e].getAtomIndex2()),this.addStateScript("connect ",null,d,c,"delete",!1,!0))}this.dBb(a,b)},"JU.BS,~B");c(c$,"makeConnections2",function(a,b,d,c,e,f,j,k,h,m){null==j&&(j=new JU.BS);var n=65535==d,q=131071==d;q&&(d=1);var v=J.modelset.Bond.isOrderH(d),x=!1,p=!1,r=!1,s=!1,t=a*a,u=b*b;switch(c){case 12291:return this.deleteConnections(a,b,d,e,f,k,q,t,u);case 603979874:case 1073741852:if(515!=d)return this.autoBond(e,
f,j,k,v,603979874==c);s=p=!0;break;case 1087373321:x=!0;break;case 1073742025:p=!0;break;case 1073741904:r=!0}this.defaultCovalentMad=this.viewer.getMadBond();c=0>a;q=0>b;c&&(a=-a);q&&(b=-b);for(var w=this.getDefaultMadFromOrder(d),y=0,z=0,A=null,C=k?1:this.atomCount,B=null,D=null,E=0,F=0,I=d|131072,H=e.nextSetBit(0);0<=H;H=e.nextSetBit(H+1)){if(k)A=this.bonds[H],B=A.atom1,D=A.atom2;else if(B=this.atoms[H],B.isDeleted())continue;for(var L=this.isModulated(H)?"\x00":B.altloc,K=k?C:f.nextSetBit(0);0<=
K;K=k?K-1:f.nextSetBit(K+1)){if(!k){if(K==H)continue;D=this.atoms[K];if(B.modelIndex!=D.modelIndex||D.isDeleted())continue;if("\x00"!=L&&L!=D.altloc&&"\x00"!=D.altloc)continue;A=B.getBond(D)}if(!(null==A&&(x||p)||null!=A&&r)){var O=B.distanceSquared(D);if(c||q)E=B.distance(D),F=B.getBondingRadiusFloat()+D.getBondingRadiusFloat();if(!(c?E<F*a:O<t)&&!(q?E>F*b:O>u))if(null!=A){if(!x&&!n&&(A.setOrder(d),this.bsAromatic.clear(A.index)),!x||n||d==A.order||I==A.order||v&&A.isHydrogen())j.set(A.index),z++}else j.set(this.bondAtoms(B,
D,d,w,j,m,h,!0).index),y++}}}s&&this.assignAromaticBondsBs(!0,j);x||this.shapeManager.setShapeSizeBs(1,-2147483648,null,j);return[y,z]},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"autoBondBs4",function(a,b,d,c,e,f){if(f)return this.autoBond_Pre_11_9_24(a,b,d,c,e);if(0==this.atomCount)return 0;0==e&&(e=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();f=this.viewer.getFloat(570425348);var j=this.viewer.getFloat(570425364),j=j*j,k=0;this.showRebondTimes&&J.util.Logger.startTimer("autobond");
var h=-1,m=null==a,n,q;m?(q=0,n=null):(a.equals(b)?n=a:(n=J.util.BSUtil.copy(a),n.or(b)),q=n.nextSetBit(0));for(var v=this.getSelectedAtomIterator(null,!1,!1,!0,!1);0<=q&&q<this.atomCount;q=m?q+1:n.nextSetBit(q+1)){var x=m||a.get(q),p=m||b.get(q),r=this.atoms[q];if(!r.isDeleted()){var s=r.modelIndex;if(s!=h&&(h=s,this.isJmolDataFrameForModel(s))){q=this.models[s].firstAtomIndex+this.models[s].atomCount-1;continue}s=r.getBondingRadiusFloat();if(0!=s){var t=null!=d&&d.get(q);for(this.setIteratorForAtom(v,
-1,q,s+this.maxBondingRadius+f,null);v.hasNext();){var u=this.atoms[v.next()];if(!u.isDeleted()){var w=u.index,y=m||a.get(w),z=m||b.get(w);!y&&!z||(!(x&&z||p&&y)||t&&d.get(w))||(w=J.modelset.BondCollection.getBondOrderFull(s,u.getBondingRadiusFloat(),v.foundDistance2(),j,f),0<w&&this.checkValencesAndBond(r,u,w,e,c)&&k++)}}v.release()}}}this.showRebondTimes&&J.util.Logger.checkTimer("autoBond",!1);return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B");c(c$,"autoBond_Pre_11_9_24",function(a,b,d,c,e){if(0==this.atomCount)return 0;
0==e&&(e=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var f=this.viewer.getFloat(570425348),j=this.viewer.getFloat(570425364),j=j*j,k=0;this.initializeBspf();for(var h=-1,m=this.atomCount;0<=--m;){var n=null==a||a.get(m),q=null==b||b.get(m);if(n||q){var v=this.atoms[m];if(!v.isDeleted()){var x=v.modelIndex;if(x!=h&&(h=x,this.isJmolDataFrameForModel(x))){for(;0<=--m&&this.atoms[m].modelIndex==x;);m++;continue}var p=v.getBondingRadiusFloat();if(0!=p){var r=p+this.maxBondingRadius+f;this.initializeBspt(x);
x=this.bspf.getCubeIterator(x);for(x.initialize(v,r,!0);x.hasMoreElements();)if(r=x.nextElement(),!(r===v||r.isDeleted())){var s=r.index,t=null==a||a.get(s),u=null==b||b.get(s);if(!(!t&&!u||null!=d&&d.get(s)&&d.get(m)))if(n&&u||q&&t)s=J.modelset.BondCollection.getBondOrderFull(p,r.getBondingRadiusFloat(),x.foundDistance2(),j,f),0<s&&this.checkValencesAndBond(v,r,s,e,c)&&k++}x.release()}}}}return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"autoBond",function(a,b,d,c,e,f){if(c){c=a;a=new JU.BS;b=new JU.BS;
for(var j=c.nextSetBit(0);0<=j;j=c.nextSetBit(j+1))a.set(this.bonds[j].atom1.index),b.set(this.bonds[j].atom2.index)}return[e?this.autoHbond(a,b,!1):this.autoBondBs4(a,b,null,d,this.viewer.getMadBond(),f),0]},"JU.BS,JU.BS,JU.BS,~B,~B,~B");c(c$,"autoHbond",function(a,b,d){if(d){for(var c=this.getModelBitSet(a,!1),e=c.nextSetBit(0);0<=e&&d;e=c.nextSetBit(e+1))d=!this.models[e].hasRasmolHBonds;if(d)return 0}d=!1;for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))if(1==this.atoms[e].getElementNumber()){d=
!0;break}c=new JU.BS;e=this.viewer.getBoolean(603979853);if(null==b||e&&!d)return J.util.Logger.info((null==b?"DSSP ":"RasMol")+" pseudo-hbond calculation"),this.calcRasmolHydrogenBonds(a,b,null,!1,2147483647,!1,c),-J.util.BSUtil.cardinalityOf(c);J.util.Logger.info(d?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var f=null;if(!d){f=new JU.BS;for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))switch(this.atoms[e].atomID){case 64:case 4:case 14:case 15:case 16:case 17:f.set(e)}}var j=this.viewer.getFloat(570425361),
k=3.141592653589793*this.viewer.getFloat(570425360)/180,h=j*j,m=J.modelset.ModelCollection.hbondMin*J.modelset.ModelCollection.hbondMin,n=j>J.modelset.ModelCollection.hbondMin?m:h,q=j>J.modelset.ModelCollection.hbondMin?J.modelset.ModelCollection.hbondMin:j,v=0,x=0,p=new JU.V3,r=new JU.V3;this.showRebondTimes&&J.util.Logger.debugging&&J.util.Logger.startTimer("hbond");var s=null,t=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1)){var u=this.atoms[e],
w=u.getElementNumber(),y=1==w;if(!(!y&&(d||7!=w&&8!=w)||y&&!d)){var z,A,B;if(y){w=u.bonds;if(null==w)continue;B=!1;for(z=0;z<w.length&&!B;z++)B=w[z].getOtherAtom(u).getElementNumber(),B=7==B||8==B;if(!B)continue;A=q;w=1;z=n;B=!1}else A=j,w=m,z=h,B=f.get(e);for(this.setIteratorForAtom(b,-1,u.index,A,null);b.hasNext();){A=this.atoms[b.next()];var C=A.getElementNumber();if(!(A===u||!y&&7!=C&&8!=C||y&&1==C||(x=b.foundDistance2())<w||x>z||B&&f.get(A.index)||u.isBonded(A))){if(0<k){p.sub2(u,A);if(null==
(t=J.modelset.ModelCollection.checkMinAttachedAngle(u,k,p,r,d)))continue;p.scale(-1);if(null==(s=J.modelset.ModelCollection.checkMinAttachedAngle(A,k,p,r,d)))continue}var C=0,D;y&&!Float.isNaN(s.x)&&!Float.isNaN(t.x)?(D=4096,C=J.modelset.HBond.getEnergy(Math.sqrt(x),s.distance(u),s.distance(t),A.distance(t))/1E3):D=2048;c.set(this.addHBond(u,A,D,C));v++}}}}b.release();this.shapeManager.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&J.util.Logger.checkTimer("hbond",!1);return d?v:-v},"JU.BS,JU.BS,~B");
c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,e){var f=a.bonds;if(null==f||0==f.length)return JU.P3.new3(NaN,0,0);for(var j=null,k=3.4028235E38,h=f.length;0<=--h;)if(f[h].isCovalent()){var m=f[h].getOtherAtom(a);if(e||1!=m.getElementNumber()){c.sub2(a,m);var n=c.angle(d);if(n<b)return null;n<k&&(j=m,k=n)}}return j},"J.modelset.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",function(){for(var a,b=0,d=-1,c=-1,e=-1,f=0;f<this.atomCount;f++){if((c=this.atoms[f].modelIndex)!=
e)b=0,e=c,d=-1;if((a=this.atoms[f].getStrucNo())!=d&&0!=a)this.atoms[f].getGroup().setStrucNo(++b),d=b}});c(c$,"getProteinStructureState",function(a,b,d,c){if(!this.isPDB)return"";for(var e=0;e<this.modelCount;e++)if(this.models[e].isBioModel)return this.models[e].getProteinStructureState(a,b,d,c);return""},"JU.BS,~B,~B,~N");c(c$,"getModelInfoAsString",function(){var a=(new JU.SB).append('<models count="');a.appendI(this.modelCount).append('" modelSetHasVibrationVectors="').append(this.modelSetHasVibrationVectors()+
'">\n<properties>');if(null!=this.modelSetProperties){for(var b=this.modelSetProperties.propertyNames();b.hasMoreElements();){var d=b.nextElement();a.append('\n <property name="').append(d).append('" value=').append(J.util.Escape.eS(this.modelSetProperties.getProperty(d))).append(" />")}a.append("\n</properties>")}for(b=0;b<this.modelCount;++b)a.append('\n<model index="').appendI(b).append('" n="').append(this.getModelNumberDotted(b)).append('" id=').append(J.util.Escape.eS(""+this.getModelAuxiliaryInfoValue(b,
"modelID"))),d=this.viewer.getJDXBaseModelIndex(b),d!=b&&a.append(" baseModelId=").append(J.util.Escape.eS(this.getModelAuxiliaryInfoValue(d,"jdxModelID"))),a.append(" name=").append(J.util.Escape.eS(this.getModelName(b))).append(" title=").append(J.util.Escape.eS(this.getModelTitle(b))).append(' hasVibrationVectors="').appendB(this.viewer.modelHasVibrationVectors(b)).append('" />');a.append("\n</models>");return a.toString()});c(c$,"getSymmetryInfoAsString",function(){for(var a=(new JU.SB).append("Symmetry Information:"),
b=0;b<this.modelCount;++b)a.append("\nmodel #").append(this.getModelNumberDotted(b)).append("; name=").append(this.getModelName(b)).append("\n").append(this.getSymmetryInfoAsStringForModel(b));return a.toString()});c(c$,"getAtomsConnected",function(a,b,d,c){for(var e=new JU.BS,f=D(this.atomCount,0),j,k=30720==d,h=65535==d,m=0;m<this.bondCount;m++){var n=this.bonds[m];if(h||n.is(d)||k&&n.isHydrogen())c.get(n.atom1.index)&&(f[j=n.atom2.index]++,e.set(j)),c.get(n.atom2.index)&&(f[j=n.atom1.index]++,
e.set(j))}d=0==a;for(j=this.atomCount;0<=--j;)c=f[j],c<a||c>b?e.clear(j):d&&0==c&&e.set(j);return e},"~N,~N,~N,JU.BS");c(c$,"getUnitCellInfoText",function(){var a=this.viewer.getCurrentModelIndex();if(0>a)return"no single current model";a=this.getUnitCell(a);return null==a?"not applicable":a.getUnitCellInfo()});c(c$,"getSymTemp",function(a){if(null==this.symTemp||a)this.symTemp=J.api.Interface.getOptionInterface("symmetry.Symmetry");return this.symTemp},"~B");c(c$,"createModels",function(a){a=this.modelCount+
a;var b=JU.AU.arrayCopyObject(this.models,a);this.validateBspf(!1);this.modelNumbers=JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,a);for(var d=s(this.getModelFileNumber(this.modelCount-1)/1E6)+1,c=this.modelCount,e=0;c<a;c++)this.modelNumbers[c]=c+this.modelCount,
this.modelFileNumbers[c]=1E6*d+ ++e,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=d+"."+e;this.thisStateModel=-1;d=this.getModelSetAuxiliaryInfoValue("group3Lists");null!=d&&(c=this.getModelSetAuxiliaryInfoValue("group3Counts"),d=JU.AU.arrayCopyS(d,a),c=JU.AU.arrayCopyII(c,a),this.modelSetAuxiliaryInfo.put("group3Lists",d),this.modelSetAuxiliaryInfo.put("group3Counts",c));this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.modelCount;c<a;c++)b[c]=new J.modelset.Model(this,c,-1,
null,null,null),b[c].loadState=" model create #"+c+";";this.models=b;this.modelCount=a},"~N");c(c$,"deleteModel",function(a,b,d,c,e){if(0>a)this.validateBspf(!1),this.bsAll=null,this.resetMolecules(),this.isBbcageDefault=!1,this.calcBoundBoxDimensions(null,1);else{this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,
a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var f=this.getModelSetAuxiliaryInfoValue("group3Lists"),j=this.getModelSetAuxiliaryInfoValue("group3Counts"),k=a+1;if(null!=f&&null!=f[k])for(var h=s(f[k].length/6);0<=--h;)0<j[k][h]&&(j[0][h]-=j[k][h],0==j[0][h]&&(f[0]=f[0].substring(0,6*h)+",["+f[0].substring(6*h+2)));null!=f&&(this.modelSetAuxiliaryInfo.put("group3Lists",JU.AU.deleteElements(f,a,1)),this.modelSetAuxiliaryInfo.put("group3Counts",JU.AU.deleteElements(j,
a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(h=this.stateScripts.size();0<=--h;)this.stateScripts.get(h).deleteAtoms(a,e,c)||this.stateScripts.remove(h);this.deleteModelAtoms(b,d,c);this.viewer.deleteModelAtoms(b,d,c)}},"~N,~N,~N,JU.BS,JU.BS");c(c$,"getMoInfo",function(a){for(var b=new JU.SB,d=0;d<this.modelCount;d++)if(!(0<=a&&d!=a)){var c=this.viewer.getModelAuxiliaryInfoValue(d,"moData");if(null!=c){var c=c.get("mos"),e=null==c?0:c.size();if(0!=e)for(;0<=
--e;){var f=c.get(e),j=f.get("type");null==j&&(j="");var k=f.get("energyUnits");null==k&&(k="");var h=f.get("occupancy");null!=h&&(j="occupancy "+h.floatValue()+" "+j);h=f.get("symmetry");null!=h&&(j+=h);h=""+f.get("energy");Float.isNaN(JU.PT.parseFloat(h))?b.append(J.util.Txt.sprintf("model %-2s;  mo %-2i # %s\n","sis",[this.getModelNumberDotted(d),Integer.$valueOf(e+1),j])):b.append(J.util.Txt.sprintf("model %-2s;  mo %-2i # energy %-8.3f %s %s\n","sifss",[this.getModelNumberDotted(d),Integer.$valueOf(e+
1),f.get("energy"),k,j]))}}}return b.toString()},"~N");c(c$,"assignAtom",function(a,b,d){null==b&&(b="C");var c=this.atoms[a],e=new JU.BS,f=1==c.getElementNumber(),e=J.util.Elements.elementNumberFromSymbol(b,!0),j=!1;if(0<e)this.setElement(c,e),this.viewer.setShapeSizeRD(0,this.viewer.getDefaultRadiusData(),J.util.BSUtil.newAndSetBit(a)),this.setAtomName(a,b+c.getAtomNumber()),this.models[c.modelIndex].isModelKit||this.taintAtom(a,0);else if(b.equals("Pl"))c.setFormalCharge(c.getFormalCharge()+1);
else if(b.equals("Mi"))c.setFormalCharge(c.getFormalCharge()-1);else if(b.equals("X"))j=!0;else if(!b.equals("."))return;this.removeUnnecessaryBonds(c,j);b=0;1==c.getCovalentBondCount()&&(f?b=1.5:!f&&1==e&&(b=1));0!=b&&(f=JU.V3.newVsub(c,this.atoms[c.getBondedAtomIndex(0)]),j=f.length(),f.normalize(),f.scale(b-j),this.setAtomCoordRelative(a,f.x,f.y,f.z));a=J.util.BSUtil.newAndSetBit(a);1!=e&&d&&(this.validateBspf(!1),e=this.getAtomsWithinRD(1,a,!1,null),e.andNot(a),0<=e.nextSetBit(0)&&this.viewer.deleteAtoms(e,
!1),e=this.viewer.getModelUndeletedAtomsBitSet(c.modelIndex),e.andNot(this.getAtomBitsMDa(1613758476,null)),this.makeConnections2(0.1,1.8,1,1073741904,a,e,null,!1,!1,0));this.viewer.addHydrogens(a,!1,!0)},"~N,~S,~B");c(c$,"deleteAtoms",function(a){if(null!=a){for(var b=new JU.BS,d=a.nextSetBit(0);0<=d&&d<this.atomCount;d=a.nextSetBit(d+1))this.atoms[d].deleteBonds(b);for(d=0;d<this.modelCount;d++)this.models[d].bsAtomsDeleted.or(a),this.models[d].bsAtomsDeleted.and(this.models[d].bsAtoms);this.deleteBonds(b,
!1)}},"JU.BS");c(c$,"getModelCml",function(a,b,d){var c=new JU.SB;if(0==J.util.BSUtil.cardinalityOf(a))return"";var e=J.api.Interface.getOptionInterface("io.XmlUtil");e.openTag(c,"molecule");e.openTag(c,"atomArray");for(var f=new JU.BS,j=a.nextSetBit(0);0<=j&&!(0>--b);j=a.nextSetBit(j+1)){var k=this.atoms[j],h=k.getAtomName();JU.PT.simpleReplace(h,'"',"''");f.set(k.index);e.appendTag(c,"atom/",["id","a"+(k.index+1),"title",k.getAtomName(),"elementType",k.getElementSymbol(),"x3",""+k.x,"y3",""+k.y,
"z3",""+k.z])}e.closeTag(c,"atomArray");if(d){e.openTag(c,"bondArray");for(j=0;j<this.bondCount;j++)a=this.bonds[j],b=a.atom2,f.get(a.atom1.index)&&f.get(b.index)&&(b=J.util.JmolEdge.getCmlBondOrder(a.order),null!=b&&e.appendTag(c,"bond/",["atomRefs2","a"+(a.atom1.index+1)+" a"+(a.atom2.index+1),"order",b]));e.closeTag(c,"bondArray")}e.closeTag(c,"molecule");return c.toString()},"JU.BS,~N,~B");c(c$,"adjustAtomArrays",function(a,b,d){this.atomCount=d;for(var c=b;c<d;c++){this.atoms[c]=this.atoms[a[c]];
this.atoms[c].index=c;var e=this.models[this.atoms[c].modelIndex];e.firstAtomIndex==a[c]&&(e.firstAtomIndex=c);e.bsAtoms.set(c)}if(null!=this.vibrations)for(c=b;c<d;c++)this.vibrations[c]=this.vibrations[a[c]];if(null!=this.occupancies)for(c=b;c<d;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.bfactor100s)for(c=b;c<d;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.partialCharges)for(c=b;c<d;c++)this.partialCharges[c]=this.partialCharges[a[c]];if(null!=this.atomTensorList)for(c=
b;c<d;c++)for(var e=this.atomTensorList[c]=this.atomTensorList[a[c]],f=e.length;0<=--f;){var j=e[f];null!=j&&(j.atomIndex1=a[j.atomIndex1])}if(null!=this.atomNames)for(c=b;c<d;c++)this.atomNames[c]=this.atomNames[a[c]];if(null!=this.atomTypes)for(c=b;c<d;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomSerials)for(c=b;c<d;c++)this.atomSerials[c]=this.atomSerials[a[c]]},"~A,~N,~N");c(c$,"growAtomArrays",function(a){this.atoms=JU.AU.arrayCopyObject(this.atoms,a);null!=this.vibrations&&(this.vibrations=
JU.AU.arrayCopyObject(this.vibrations,a));null!=this.occupancies&&(this.occupancies=JU.AU.arrayCopyByte(this.occupancies,a));null!=this.bfactor100s&&(this.bfactor100s=JU.AU.arrayCopyShort(this.bfactor100s,a));null!=this.partialCharges&&(this.partialCharges=JU.AU.arrayCopyF(this.partialCharges,a));null!=this.atomTensorList&&(this.atomTensorList=JU.AU.arrayCopyObject(this.atomTensorList,a));null!=this.atomNames&&(this.atomNames=JU.AU.arrayCopyS(this.atomNames,a));null!=this.atomTypes&&(this.atomTypes=
JU.AU.arrayCopyS(this.atomTypes,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a))},"~N");c(c$,"addAtom",function(a,b,d,c,e,f,j,k,h,m,n,q,v,x,p,r,s){f=(new J.modelset.Atom).setAtom(a,this.atomCount,j,k,s,f,d,m,p);this.models[a].atomCount++;this.models[a].bsAtoms.set(this.atomCount);J.util.Elements.isElement(d,1)&&this.models[a].hydrogenCount++;this.atomCount>=this.atoms.length&&this.growAtomArrays(this.atomCount+100);this.atoms[this.atomCount]=f;this.setBFactor(this.atomCount,
v);this.setOccupancy(this.atomCount,q);this.setPartialCharge(this.atomCount,n);null!=x&&this.setAtomTensors(this.atomCount,x);f.group=b;f.colixAtom=this.viewer.getColixAtomPalette(f,J.constant.EnumPalette.CPK.id);if(null!=c){if(0<=(a=c.indexOf("\x00")))null==this.atomTypes&&(this.atomTypes=Array(this.atoms.length)),this.atomTypes[this.atomCount]=c.substring(a+1),c=c.substring(0,a);f.atomID=r;0==r&&(null==this.atomNames&&(this.atomNames=Array(this.atoms.length)),this.atomNames[this.atomCount]=c.intern())}-2147483648!=
e&&(null==this.atomSerials&&(this.atomSerials=D(this.atoms.length,0)),this.atomSerials[this.atomCount]=e);null!=h&&this.setVibrationVector(this.atomCount,h);this.atomCount++;return f},"~N,J.modelset.Group,~N,~S,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.List,~B,~N,JU.BS");c(c$,"getInlineData",function(a){var b=null;if(0<=a)b=this.models[a].loadScript;else for(a=this.modelCount;0<=--a&&!(0<(b=this.models[a].loadScript).length()););a=b.lastIndexOf('data "');if(0>a)return null;a=b.indexOf2('"',a+7);var d=b.lastIndexOf('end "');
return d<a||0>a?null:b.substring2(a+2,d)},"~N");c(c$,"isAtomPDB",function(a){return 0<=a&&this.models[this.atoms[a].modelIndex].isBioModel},"~N");c(c$,"isAtomAssignable",function(a){return 0<=a&&this.atoms[a].modelIndex==this.modelCount-1},"~N");c(c$,"getGroupAtom",function(a,b,d){var c=a.group;a=c.getMonomerIndex();if(0>a)return-1;c=c.getGroups();a+=b;if(0<=a&&a<c.length){a=c[a];if(1==b&&!a.isConnectedPrevious())return-1;if("0".equals(d))return a.leadAtomIndex;for(b=a.firstAtomIndex;b<=a.lastAtomIndex;b++)if(null==
d||d.equalsIgnoreCase(this.atoms[b].getAtomName()))return b}return-1},"J.modelset.Atom,~N,~S");c(c$,"haveModelKit",function(){for(var a=0;a<this.modelCount;a++)if(this.models[a].isModelKit)return!0;return!1});c(c$,"getModelKitStateBitset",function(a,b){for(var d=J.util.BSUtil.copy(b),c=0;c<this.modelCount;c++)this.models[c].isModelKit||d.andNot(this.models[c].bsAtoms);return J.util.BSUtil.deleteBits(a,d)},"JU.BS,JU.BS");c(c$,"setAtomNamesAndNumbers",function(a,b,d){0>b&&(a=this.models[this.atoms[a].modelIndex].firstAtomIndex);
null==this.atomSerials&&(this.atomSerials=D(this.atomCount,0));null==this.atomNames&&(this.atomNames=Array(this.atomCount));for(var c=this.isXYZ&&this.viewer.getBoolean(603979978),e=2147483647,f=1;a<this.atomCount;++a){var j=this.atoms[a];j.modelIndex!=e&&(e=j.modelIndex,f=c?0:1);if(a>=-b){if(0==this.atomSerials[a]||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:f;if(null==this.atomNames[a]||0>b)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}(!this.models[e].isModelKit||0<j.getElementNumber()&&
!j.isDeleted())&&f++}},"~N,~N,J.modelset.AtomCollection");c(c$,"setUnitCellOffset",function(a,b,d){null!=a&&(null==b?a.setOffset(d):a.setOffsetPt(b))},"J.api.SymmetryInterface,JU.P3,~N");c(c$,"connect",function(a){this.resetMolecules();for(var b=new JU.BS,d=0;d<a.length;d++){var c=a[d];if(!(null==c||2>c.length)){var e=y(c[0]),f=0>e;f&&(e=-1-e);var j=y(c[1]);if(!(0>j||e>=this.atomCount||j>=this.atomCount)){var k=2<c.length?y(c[2]):1;0>k&&(k&=65535);var h=3<c.length?oa(1E3*a[d][3]):this.getDefaultMadFromOrder(k);
0==k||0==h&&32768!=k&&!J.modelset.Bond.isOrderH(k)?(c=this.atoms[e].getBond(this.atoms[j]),null!=c&&b.set(c.index)):this.bondAtoms(this.atoms[e],this.atoms[j],k,h,null,4<c.length?c[4]:0,f,!0)}}}0<=b.nextSetBit(0)&&this.deleteBonds(b,!1)},"~A");c(c$,"allowSpecAtom",function(){return 1!=this.modelCount||this.models[0].isBioModel});c(c$,"setFrameDelayMs",function(a,b){for(var d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.models[this.models[d].trajectoryBaseIndex].frameDelay=a},"~N,JU.BS");c(c$,"getFrameDelayMs",
function(a){return a<this.models.length&&0<=a?this.models[this.models[a].trajectoryBaseIndex].frameDelay:0},"~N");c(c$,"getModelIndexFromId",function(a){var b=0<=a.indexOf("#"),d=a.toLowerCase().endsWith(".basemodel");d&&(a=a.substring(0,a.length-10));for(var c=-1,e=null,f=0;f<this.modelCount;f++){var j=this.getModelAuxiliaryInfoValue(f,"modelID"),k=a.startsWith("~")?"~"+this.getModelNumberDotted(f):null;if(!(null==k&&null==j&&null==(j=this.getModelTitle(f)))){b&&(e=this.getModelFileName(f)+"#",j=
e+j);if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(k))return d?this.viewer.getJDXBaseModelIndex(f):f;null!=e&&a.startsWith(e)&&(c=-2)}}return null==e&&!b?-2:c},"~S");c(c$,"getAuxiliaryInfo",function(a){var b=this.modelSetAuxiliaryInfo;if(null==b)return null;for(var d=new JU.List,c=0;c<this.modelCount;++c)if(null==a||a.get(c)){var e=this.getModelAuxiliaryInfo(c);d.addLast(e)}b.put("models",d);return b},"JU.BS");c(c$,"getDihedralMap",function(a){for(var b=new JU.List,d=a.length,c=null,e=null,f=null,
j=null,k=d-1;0<=--k;)for(var h=d;--h>k;)if(c=this.atoms[a[k]],e=this.atoms[a[h]],c.isBonded(e))for(var m=d;0<=--m;)if(m!=k&&m!=h&&(f=this.atoms[a[m]]).isBonded(c))for(var n=d;0<=--n;)if(n!=k&&n!=h&&n!=m&&(j=this.atoms[a[n]]).isBonded(e)){var q=D(4,0);q[0]=f.index;q[1]=c.index;q[2]=e.index;q[3]=j.index;b.addLast(q)}d=b.size();a=JU.AU.newInt2(d);for(k=d;0<=--k;)a[d-k-1]=b.get(k);return a},"~A");c(c$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=new JU.BS;else if(null==
a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var e=this.viewer.getFloat(1276121113),f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var j=this.getVibration(f,!1);r(j,J.api.JmolModulationSet)&&(j.setModTQ(this.atoms[f],b,d,c,e),null!=this.bsModulated&&this.bsModulated.setBitTo(f,b))}},"JU.BS,~B,JU.P3,~B");c(c$,"getDynamicAtom",function(a,b){var d=this.getVibration(a,!1);if(null==d)return this.atoms[a];null==b&&(b=new J.util.Point3fi);b.setT(this.atoms[a]);b=this.viewer.getVibrationPoint(d,
b);b.sD=-1;return b},"~N,J.util.Point3fi");c(c$,"getBoundBoxOrientation",function(a,b){var d=b.nextSetBit(0);if(0>d)return"{0 0 0 1}";var c=null==this.vOrientations?0:this.vOrientations.length;if(0==c){for(var e=Array(3375),c=0,f=new JU.P4,j=-7;7>=j;j++)for(var k=-7;7>=k;k++)for(var h=0;14>=h;h++,c++)1<(e[c]=JU.V3.new3(j/7,k/7,h/14)).length()&&--c;this.vOrientations=Array(c);for(j=c;0<=--j;)h=Math.sqrt(1-e[j].lengthSquared()),Float.isNaN(h)&&(h=0),f.set(e[j].x,e[j].y,e[j].z,h),this.vOrientations[j]=
J.util.Quaternion.newP4(f)}for(var e=new JU.P3,f=3.4028235E38,m=null,n=null,j=0;j<c;j++){var h=this.vOrientations[j],q=new J.util.BoxInfo;q.setMargin(0);for(k=d;0<=k;k=b.nextSetBit(k+1))q.addBoundBoxPoint(h.transformP2(this.atoms[k],e));switch(a){default:case 1313866249:case 1073741863:k=(q.bbCorner1.x-q.bbCorner0.x)*(q.bbCorner1.y-q.bbCorner0.y)*(q.bbCorner1.z-q.bbCorner0.z);break;case 1112541205:k=q.bbCorner1.x-q.bbCorner0.x;break;case 1112541206:k=q.bbCorner1.y-q.bbCorner0.y;break;case 1112541207:k=
q.bbCorner1.z-q.bbCorner0.z}k<f&&(m=h,n=q,f=k)}if(1313866249!=a&&1073741863!=a)return m.toString();h=J.util.Quaternion.newQ(m);d=n.bbCorner1.x-n.bbCorner0.x;c=n.bbCorner1.y-n.bbCorner0.y;j=n.bbCorner1.z-n.bbCorner0.z;d<c&&(e.set(0,0,1),h=J.util.Quaternion.newVA(e,90).mulQ(h),k=d,d=c,c=k);c<j&&(j>d&&(e.set(0,1,0),h=J.util.Quaternion.newVA(e,90).mulQ(h),k=d,d=j,j=k),e.set(1,0,0),h=J.util.Quaternion.newVA(e,90).mulQ(h),k=c,c=j,j=k);return 1313866249==a?f+"\t{"+d+" "+c+" "+j+"}":0==h.getTheta()?"{0 0 0 1}":
h.toString()},"~N,JU.BS");c(c$,"intersectPlane",function(a,b,d){return(null==this.triangulator?this.triangulator=J.api.Interface.getOptionInterface("util.TriangleData"):this.triangulator).intersectPlane(a,b,d)},"JU.P4,JU.List,~N");c(c$,"getUnitCellForAtom",function(a){if(0>a||a>this.atomCount)return null;if(null!=this.bsModulated){var b=this.getVibration(a,!1);if(null!=b)return b.getUnitCell()}return this.getUnitCell(this.atoms[a].modelIndex)},"~N");E(c$,"hbondMin",2.5)}),p("J.modelset"),t(["java.util.Hashtable",
"JU.BS","J.viewer.JC"],"J.modelset.ModelLoader","java.lang.Boolean $.Float $.NullPointerException java.util.Arrays JU.AU $.List $.P3 $.PT $.SB $.V3 J.api.Interface J.modelset.Chain $.Group $.Model $.ModelSet J.util.BSUtil $.Elements $.JmolMolecule $.Logger".split(" "),function(){c$=w(function(){this.mergeModelSet=this.modelSet=this.viewer=null;this.appendNew=this.merging=!1;this.specialAtomIndexes=this.group3Counts=this.group3Lists=this.jmolData=null;this.doRemoveAddedHydrogens=this.doAddHydrogens=
this.doMinimize=this.isPyMOLsession=this.isTrajectory=this.isPDB=this.is2D=this.someModelsAreModulated=this.someModelsHaveUnitcells=!1;this.groups=this.jbr=this.fileHeader=null;this.groupCount=0;this.firstAtomIndexes=this.seqcodes=this.group3Of=this.chainOf=this.htAtomMap=null;this.currentModelIndex=0;this.currentModel=null;this.currentChainID=0;this.isNewChain=!1;this.currentChain=null;this.currentGroupSequenceNumber=0;this.currentGroupInsertionCode="\x00";this.nullGroup=this.currentGroup3=null;
this.adapterTrajectoryCount=this.adapterModelCount=this.baseTrajectoryCount=this.baseGroupIndex=this.baseAtomIndex=this.baseModelCount=this.baseModelIndex=0;this.modulationOn=this.noAutoBond=!1;this.$mergeGroups=null;this.iChain=0;this.structuresDefinedInFile=this.vStereo=null;u(this,arguments)},J.modelset,"ModelLoader");Q(c$,function(){this.specialAtomIndexes=D(J.viewer.JC.ATOMID_MAX,0);this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});A(c$,function(a,b,d,c,e,f){this.viewer=
a;this.modelSet=new J.modelset.ModelSet(a,b);var j=a.getModelAdapter();this.mergeModelSet=e;(this.merging=null!=this.mergeModelSet&&0<this.mergeModelSet.atomCount)?this.modelSet.canSkipLoad=!1:a.resetShapes(!1);this.modelSet.preserveState=a.getPreserveState();this.modelSet.showRebondTimes=a.getBoolean(603979934);null==f?(this.initializeInfo(b,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.modelSet.preserveState||(this.modelSet.canSkipLoad=!1),a=j.getAtomSetCollectionAuxiliaryInfo(c),
a.put("loadScript",d),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),a),this.createModelSet(j,c,f))},"J.viewer.Viewer,~S,JU.SB,~O,J.modelset.ModelSet,JU.BS");c(c$,"initializeInfo",function(a,b){this.modelSet.g3d=this.viewer.getGraphicsData();this.modelSet.modelSetTypeName=a;this.modelSet.isXYZ="xyz"===a;this.modelSet.modelSetAuxiliaryInfo=b;this.modelSet.modelSetProperties=this.modelSet.getModelSetAuxiliaryInfoValue("properties");if(this.isPDB=this.modelSet.isPDB=this.modelSet.getModelSetAuxiliaryInfoBoolean("isPDB"))try{this.jbr=
Class.forName("J.modelsetbio.Resolver").newInstance(),this.jbr.initialize(this)}catch(d){if(C(d,Exception))J.util.Logger.error("developer error: J.modelsetbio.Resolver could not be found");else throw d;}this.jmolData=this.modelSet.getModelSetAuxiliaryInfoValue("jmolData");this.fileHeader=this.modelSet.getModelSetAuxiliaryInfoValue("fileHeader");this.modelSet.trajectorySteps=this.modelSet.getModelSetAuxiliaryInfoValue("trajectorySteps");this.isTrajectory=null!=this.modelSet.trajectorySteps;this.isPyMOLsession=
this.modelSet.getModelSetAuxiliaryInfoBoolean("isPyMOL");this.doAddHydrogens=null!=this.jbr&&!this.isTrajectory&&!this.isPyMOLsession&&!this.modelSet.getModelSetAuxiliaryInfoBoolean("pdbNoHydrogens")&&(this.modelSet.getModelSetAuxiliaryInfoBoolean("pdbAddHydrogens")||this.viewer.getBooleanProperty("pdbAddHydrogens"));null!=b&&(b.remove("pdbNoHydrogens"),b.remove("pdbAddHydrogens"),b.remove("trajectorySteps"),this.isTrajectory&&(this.modelSet.vibrationSteps=b.remove("vibrationSteps")));this.modulationOn=
this.modelSet.getModelSetAuxiliaryInfoBoolean("modulationOn");this.noAutoBond=this.modelSet.getModelSetAuxiliaryInfoBoolean("noAutoBond");this.doMinimize=(this.is2D=this.modelSet.getModelSetAuxiliaryInfoBoolean("is2D"))&&this.modelSet.getModelSetAuxiliaryInfoBoolean("doMinimize");this.adapterTrajectoryCount=null==this.modelSet.trajectorySteps?0:this.modelSet.trajectorySteps.size();this.modelSet.someModelsHaveSymmetry=this.modelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveSymmetry");this.someModelsHaveUnitcells=
this.modelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveUnitcells");this.someModelsAreModulated=this.modelSet.getModelSetAuxiliaryInfoBoolean("someModelsAreModulated");this.modelSet.someModelsHaveFractionalCoordinates=this.modelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveFractionalCoordinates");this.merging&&(this.modelSet.isPDB=(new Boolean(this.modelSet.isPDB|this.mergeModelSet.isPDB)).valueOf(),this.modelSet.someModelsHaveSymmetry=(new Boolean(this.modelSet.someModelsHaveSymmetry|this.mergeModelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveSymmetry"))).valueOf(),
this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.mergeModelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveUnitcells"))).valueOf(),this.modelSet.someModelsHaveFractionalCoordinates=(new Boolean(this.modelSet.someModelsHaveFractionalCoordinates|this.mergeModelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveFractionalCoordinates"))).valueOf(),this.modelSet.someModelsHaveAromaticBonds=(new Boolean(this.modelSet.someModelsHaveAromaticBonds|this.mergeModelSet.someModelsHaveAromaticBonds)).valueOf(),
this.modelSet.modelSetAuxiliaryInfo.put("someModelsHaveSymmetry",Boolean.$valueOf(this.modelSet.someModelsHaveSymmetry)),this.modelSet.modelSetAuxiliaryInfo.put("someModelsHaveUnitcells",Boolean.$valueOf(this.someModelsHaveUnitcells)),this.modelSet.modelSetAuxiliaryInfo.put("someModelsHaveFractionalCoordinates",Boolean.$valueOf(this.modelSet.someModelsHaveFractionalCoordinates)),this.modelSet.modelSetAuxiliaryInfo.put("someModelsHaveAromaticBonds",Boolean.$valueOf(this.modelSet.someModelsHaveAromaticBonds)))},
"~S,java.util.Map");c(c$,"getGroup3",function(a){return a>=this.group3Of.length?null:this.group3Of[a]},"~N");c(c$,"getFirstAtomIndex",function(a){return this.firstAtomIndexes[a]},"~N");c(c$,"getAtomCount",function(){return this.modelSet.atomCount});c(c$,"createModelSet",function(a,b,d){var c=null==a?0:a.getAtomCount(b);0<c&&J.util.Logger.info("reading "+c+" atoms");this.adapterModelCount=null==a?1:a.getAtomSetCount(b);this.appendNew=!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||
this.viewer.getBoolean(603979792);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=D(32,0);this.firstAtomIndexes=D(32,0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.currentModelIndex=-1;this.currentModel=null;if(this.merging&&(this.baseModelCount=this.mergeModelSet.modelCount,this.baseTrajectoryCount=this.mergeModelSet.mergeTrajectories(this.isTrajectory),0<this.baseTrajectoryCount)){if(this.isTrajectory){if(null==
this.mergeModelSet.vibrationSteps){this.mergeModelSet.vibrationSteps=new JU.List;for(var e=this.mergeModelSet.trajectorySteps.size();0<=--e;)this.mergeModelSet.vibrationSteps.addLast(null)}for(e=0;e<this.modelSet.trajectorySteps.size();e++)this.mergeModelSet.trajectorySteps.addLast(this.modelSet.trajectorySteps.get(e)),this.mergeModelSet.vibrationSteps.addLast(null==this.modelSet.vibrationSteps?null:this.modelSet.vibrationSteps.get(e))}this.modelSet.trajectorySteps=this.mergeModelSet.trajectorySteps;
this.modelSet.vibrationSteps=this.mergeModelSet.vibrationSteps}this.initializeAtomBondModelCounts(c);null!=d&&(this.doMinimize||this.is2D)&&d.setBits(this.baseAtomIndex,this.baseAtomIndex+c);null==a?this.setModelNameNumberProperties(0,-1,"",1,null,null,null):(0<this.adapterModelCount&&(J.util.Logger.info("ModelSet: haveSymmetry:"+this.modelSet.someModelsHaveSymmetry+" haveUnitcells:"+this.someModelsHaveUnitcells+" haveFractionalCoord:"+this.modelSet.someModelsHaveFractionalCoordinates),J.util.Logger.info(this.adapterModelCount+
" model"+(1==this.modelSet.modelCount?"":"s")+' in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.')),e=this.modelSet.getModelSetAuxiliaryInfoValue("defaultOrientationQuaternion"),null!=e&&(J.util.Logger.info("defaultOrientationQuaternion = "+e),J.util.Logger.info('Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.')),this.iterateOverAllNewModels(a,b),this.iterateOverAllNewAtoms(a,
b),this.iterateOverAllNewBonds(a,b),this.merging&&!this.appendNew&&(e=a.getAtomSetAuxiliaryInfo(b,0),this.modelSet.setModelAuxiliaryInfo(this.baseModelIndex,"initialAtomCount",e.get("initialAtomCount")),this.modelSet.setModelAuxiliaryInfo(this.baseModelIndex,"initialBondCount",e.get("initialBondCount"))),this.initializeUnitCellAndSymmetry(),this.initializeBonding());this.finalizeGroupBuild();this.is2D&&this.doMinimize&&this.applyStereochemistry();this.doAddHydrogens&&this.jbr.finalizeHydrogens();
null!=a&&(this.modelSet.calculatePolymers(this.groups,this.groupCount,this.baseGroupIndex,null),null!=this.jbr&&this.jbr.iterateOverAllNewStructures(a,b));this.setDefaultRendering(this.viewer.getInt(553648170));var f=this.viewer.getDefaultRadiusData();d=this.modelSet.atomCount;c=this.modelSet.atoms;for(e=this.baseAtomIndex;e<d;e++)c[e].setMadAtom(this.viewer,f);f=this.modelSet.models;for(e=f[this.baseModelIndex].firstAtomIndex;e<d;e++)f[c[e].modelIndex].bsAtoms.set(e);this.freeze();this.finalizeShapes();
this.viewer.setModelSet(this.modelSet);this.setAtomProperties();null!=a&&a.finish(b);null!=this.mergeModelSet&&this.mergeModelSet.releaseModelSet();this.mergeModelSet=null},"J.api.JmolAdapter,~O,JU.BS");c(c$,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var b=new JU.SB,d=this.modelSet.modelCount,c=this.modelSet.models,e=this.baseModelIndex;e<d;e++)c[e].isBioModel&&c[e].getDefaultLargePDBRendering(b,a);0!=b.length()&&(b.append("select *;"),a=this.modelSet.getModelSetAuxiliaryInfoValue("jmolscript"),
null==a&&(a=""),b.append(a),this.modelSet.modelSetAuxiliaryInfo.put("jmolscript",b.toString()))}},"~N");c(c$,"setAtomProperties",function(){for(var a=this.modelSet.modelCount,b=this.baseModelIndex;b<a;b++){var d=this.modelSet.getModelAuxiliaryInfoValue(b,"atomProperties");if(null!=d)for(var c,d=d.entrySet().iterator();d.hasNext()&&((c=d.next())||1);){var e=c.getKey(),f=c.getValue(),j=this.modelSet.getModelAtomBitSetIncludingDeleted(b,!0);this.doAddHydrogens&&(f=this.jbr.fixPropertyValue(j,f));e="property_"+
e.toLowerCase();J.util.Logger.info("creating "+e+" for model "+this.modelSet.getModelName(b));this.viewer.setData(e,[e,f,j,Integer.$valueOf(0),Boolean.FALSE],this.modelSet.atomCount,0,0,2147483647,0)}}});c(c$,"initializeAtomBondModelCounts",function(a){var b=this.adapterTrajectoryCount;this.merging?(this.appendNew?(this.baseModelIndex=this.baseModelCount,this.modelSet.modelCount=this.baseModelCount+this.adapterModelCount):(this.baseModelIndex=this.viewer.getCurrentModelIndex(),0>this.baseModelIndex&&
(this.baseModelIndex=this.baseModelCount-1),this.modelSet.modelCount=this.baseModelCount),this.modelSet.atomCount=this.baseAtomIndex=this.mergeModelSet.atomCount,this.modelSet.bondCount=this.mergeModelSet.bondCount,this.$mergeGroups=this.mergeModelSet.getGroups(),this.groupCount=this.baseGroupIndex=this.$mergeGroups.length,this.modelSet.mergeModelArrays(this.mergeModelSet),this.modelSet.growAtomArrays(this.modelSet.atomCount+a)):(this.modelSet.modelCount=this.adapterModelCount,this.modelSet.atomCount=
0,this.modelSet.bondCount=0,this.modelSet.atoms=Array(a),this.modelSet.bonds=Array(250+a));this.doAddHydrogens&&this.jbr.initializeHydrogenAddition();1<b&&(this.modelSet.modelCount+=b-1);this.modelSet.models=JU.AU.arrayCopyObject(this.modelSet.models,this.modelSet.modelCount);this.modelSet.modelFileNumbers=JU.AU.arrayCopyI(this.modelSet.modelFileNumbers,this.modelSet.modelCount);this.modelSet.modelNumbers=JU.AU.arrayCopyI(this.modelSet.modelNumbers,this.modelSet.modelCount);this.modelSet.modelNumbersForAtomLabel=
JU.AU.arrayCopyS(this.modelSet.modelNumbersForAtomLabel,this.modelSet.modelCount);this.modelSet.modelNames=JU.AU.arrayCopyS(this.modelSet.modelNames,this.modelSet.modelCount);this.modelSet.frameTitles=JU.AU.arrayCopyS(this.modelSet.frameTitles,this.modelSet.modelCount);if(this.merging)for(a=0;a<this.mergeModelSet.modelCount;a++)(this.modelSet.models[a]=this.mergeModelSet.models[a]).modelSet=this.modelSet},"~N");c(c$,"mergeGroups",function(){var a=this.mergeModelSet.getAuxiliaryInfo(null),b=a.get("group3Lists"),
a=a.get("group3Counts");if(null!=b){for(var d=0;d<this.baseModelCount;d++)this.group3Lists[d+1]=b[d+1],this.group3Counts[d+1]=a[d+1],this.structuresDefinedInFile.set(d);this.group3Lists[0]=b[0];this.group3Counts[0]=a[0]}!this.appendNew&&this.isPDB&&this.structuresDefinedInFile.clear(this.baseModelIndex)});c(c$,"iterateOverAllNewModels",function(a,b){this.group3Lists=Array(this.modelSet.modelCount+1);this.group3Counts=JU.AU.newInt2(this.modelSet.modelCount+1);this.structuresDefinedInFile=new JU.BS;
this.merging&&this.mergeGroups();for(var d=this.isTrajectory?this.baseTrajectoryCount:-1,c=this.baseModelIndex,e=0;e<this.adapterModelCount;++e,++c){var f=a.getAtomSetNumber(b,e),j=a.getAtomSetName(b,e),h=a.getAtomSetAuxiliaryInfo(b,e);h.containsKey("modelID")&&h.put("modelID0",h.get("modelID"));var l=h.get("modelProperties");this.viewer.setStringProperty("_fileType",h.get("fileType"));null==j&&(j=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+
2,this.jmolData.indexOf(";")):this.appendNew?""+f%1E6:"");this.setModelNameNumberProperties(c,d,j,f,l,h,this.jmolData)&&(this.group3Lists[c+1]=J.viewer.JC.getGroup3List(),this.group3Counts[c+1]=D(J.viewer.JC.getGroup3Count()+10,0),null==this.group3Lists[0]&&(this.group3Lists[0]=J.viewer.JC.getGroup3List(),this.group3Counts[0]=D(J.viewer.JC.getGroup3Count()+10,0)));null!=this.modelSet.getModelAuxiliaryInfoValue(c,"periodicOriginXyz")&&(this.modelSet.someModelsHaveSymmetry=!0)}d=this.modelSet.models[this.baseModelIndex];
this.viewer.setSmilesString(this.modelSet.modelSetAuxiliaryInfo.get("smilesString"));e=this.modelSet.modelSetAuxiliaryInfo.remove("loadState");f=this.modelSet.modelSetAuxiliaryInfo.remove("loadScript");if(0>f.indexOf("Viewer.AddHydrogens")||!d.isModelKit){j=JU.PT.split(e,"\n");h=new JU.SB;for(e=0;e<j.length;e++)l=d.loadState.indexOf(j[e]),(0>l||l!=d.loadState.lastIndexOf(j[e]))&&h.append(j[e]).appendC("\n");d.loadState+=d.loadScript.toString()+h.toString();d.loadScript=new JU.SB;d.loadScript.append("  ").appendSB(f).append(";\n")}if(this.isTrajectory){e=
this.modelSet.modelCount-c+1;J.util.Logger.info(e+" trajectory steps read");this.modelSet.setModelAuxiliaryInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(e));d=this.adapterModelCount;for(e=c;e<this.modelSet.modelCount;e++,d++)this.modelSet.models[e]=this.modelSet.models[this.baseModelCount],this.modelSet.modelNumbers[e]=a.getAtomSetNumber(b,d),this.modelSet.modelNames[e]=a.getAtomSetName(b,d),this.structuresDefinedInFile.set(e)}this.finalizeModels(this.baseModelCount)},"J.api.JmolAdapter,~O");
c(c$,"setModelNameNumberProperties",function(a,b,d,c,e,f,j){var h=null!=f&&Boolean.TRUE===f.get("isPDB");this.appendNew?(this.modelSet.models[a]=h?this.jbr.getBioModel(a,b,j,e,f):new J.modelset.Model(this.modelSet,a,b,j,e,f),this.modelSet.modelNumbers[a]=c,this.modelSet.modelNames[a]=d):(b=f.get("PDB_CONECT_firstAtom_count_max"),null!=b&&this.modelSet.setModelAuxiliaryInfo(a,"PDB_CONECT_firstAtom_count_max",b));b=this.modelSet.models;c=this.modelSet.atoms;b[a].bsAtoms.set(c.length+1);b[a].bsAtoms.clear(c.length+
1);c=this.modelSet.getModelAuxiliaryInfoValue(a,"altLocs");b[a].setNAltLocs(null==c?0:c.length);null!=c&&(c=c.toCharArray(),java.util.Arrays.sort(c),c=String.valueOf(c),this.modelSet.setModelAuxiliaryInfo(a,"altLocs",c));c=this.modelSet.getModelAuxiliaryInfoValue(a,"insertionCodes");b[a].setNInsertions(null==c?0:c.length);d=null!=this.modelSet.modelSetName&&this.modelSet.modelSetName.startsWith("Jmol Model Kit")||d.startsWith("Jmol Model Kit")||"Jme".equals(this.modelSet.getModelAuxiliaryInfoValue(a,
"fileType"));b[a].isModelKit=d;return h},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(c$,"finalizeModels",function(a){var b=this.modelSet.modelCount;if(b!=a){var d,c=0,e=-1,f=this.modelSet.modelNumbers,j=this.modelSet.modelNames;if(this.isTrajectory)for(var h=a;++h<this.modelSet.modelCount;)f[h]=f[h-1]+1;if(0<a){if(1E6>f[0])for(h=0;h<a;h++)0==j[h].length&&(j[h]=""+f[h]),f[h]+=1E6,this.modelSet.modelNumbersForAtomLabel[h]="1."+(h+1);var l=f[a-1],l=l-l%1E6;1E6>f[a]&&(l+=1E6);for(h=a;h<b;h++)f[h]+=
l}for(var m=this.modelSet.models,h=a;h<b;++h)if(this.modelSet.setModelAuxiliaryInfo(h,"fileType",this.modelSet.modelSetTypeName),null!=this.fileHeader&&this.modelSet.setModelAuxiliaryInfo(h,"fileHeader",this.fileHeader),l=s(f[h]/1E6),l!=e&&(c=0,e=l),c++,0==l?(d=""+this.modelSet.getModelNumber(h),l=1):d=l+"."+c,this.modelSet.modelNumbersForAtomLabel[h]=d,m[h].fileIndex=l-1,this.modelSet.modelFileNumbers[h]=1E6*l+c,null==j[h]||0==j[h].length)j[h]=d;if(this.merging)for(h=0;h<a;h++)m[h].modelSet=this.modelSet;
for(h=0;h<b;h++)this.modelSet.setModelAuxiliaryInfo(h,"modelName",j[h]),this.modelSet.setModelAuxiliaryInfo(h,"modelNumber",Integer.$valueOf(f[h]%1E6)),this.modelSet.setModelAuxiliaryInfo(h,"modelFileNumber",Integer.$valueOf(this.modelSet.modelFileNumbers[h])),this.modelSet.setModelAuxiliaryInfo(h,"modelNumberDotted",this.modelSet.getModelNumberDotted(h)),a=this.modelSet.getModelAuxiliaryInfoValue(h,"altLocs"),null!=a&&J.util.Logger.info("model "+this.modelSet.getModelNumberDotted(h)+" alternative locations: "+
a)}},"~N");c(c$,"iterateOverAllNewAtoms",function(a,b){var d=-1,c=!1,e=!1,f=a.getAtomIterator(b),j=0,h=this.modelSet.models;0<this.modelSet.modelCount&&(this.nullGroup=(new J.modelset.Group).setGroup(new J.modelset.Chain(this.modelSet.models[this.baseModelIndex],32,-1),"",0,-1,-1));for(;f.hasNext();){j++;var l=f.getAtomSetIndex()+this.baseModelIndex;l!=d&&(this.iChain=0,this.currentModelIndex=l,this.currentModel=h[l],this.currentChainID=2147483647,this.isNewChain=!0,h[l].bsAtoms.clearAll(),c=h[l].isBioModel,
d=l,e=c&&this.doAddHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var l=f.getGroup3(),m=f.getChainID();this.checkNewGroup(a,m,l,f.getSequenceNumber(),f.getInsertionCode(),e,!1);m=f.getElementNumber();e&&1==J.util.Elements.getElementNumber(m)&&this.jbr.setHaveHsAlready(!0);var n=f.getAtomName(),q=e?this.getPdbCharge(l,n):f.getFormalCharge();this.addAtom(c,f.getAtomSymmetry(),f.getAtomSite(),f.getUniqueID(),m,n,q,f.getPartialCharge(),f.getTensors(),f.getOccupancy(),f.getBfactor(),f.getXYZ(),
f.getIsHetero(),f.getAtomSerial(),l,f.getVib(),f.getAlternateLocationID(),f.getRadius())}0<this.groupCount&&e&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);d=-1;c=null;e=this.modelSet.atoms;for(f=0;f<this.modelSet.atomCount;f++)e[f].modelIndex!=d&&(d=e[f].modelIndex,h[d].firstAtomIndex=f,l=this.modelSet.getDefaultVdwType(d),l!==c&&(J.util.Logger.info("Default Van der Waals type for model set to "+l.getVdwLabel()),c=l));J.util.Logger.info(j+" atoms created")},"J.api.JmolAdapter,~O");
c(c$,"getPdbCharge",function(a,b){return a.equals("ARG")&&b.equals("NH1")||a.equals("LYS")&&b.equals("NZ")||a.equals("HIS")&&b.equals("ND1")?1:0},"~S,~S");c(c$,"addAtom",function(a,b,d,c,e,f,j,h,l,m,n,q,v,x,p,r,s,t){var u=0;null!=f&&(a&&0<=f.indexOf("*")&&(f=f.$replace("*","'")),u=J.viewer.JC.lookupSpecialAtomID(f),a&&(2==u&&"CA".equalsIgnoreCase(p))&&(u=0));a=this.modelSet.addAtom(this.currentModelIndex,this.nullGroup,e,f,x,d,q,t,r,j,h,m,n,l,v,u,b);a.setAltLoc(s);this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.List,~N,~N,JU.P3,~B,~N,~S,JU.V3,~S,~N");
c(c$,"checkNewGroup",function(a,b,d,c,e,f,j){var h=null==d?null:d.intern();b!=this.currentChainID&&(this.currentChainID=b,this.currentChain=this.getOrAllocateChain(this.currentModel,b),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=-1,this.currentGroup3="xxxx",this.isNewChain=!0);if(c!=this.currentGroupSequenceNumber||e!=this.currentGroupInsertionCode||h!==this.currentGroup3){0<this.groupCount&&f&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?
1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=e;for(this.currentGroup3=h;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),this.firstAtomIndexes=JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.modelSet.atomCount;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=
d;this.seqcodes[this.groupCount]=J.modelset.Group.getSeqcodeFor(c,e);++this.groupCount}},"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");c(c$,"getOrAllocateChain",function(a,b){var d=a.getChain(b);if(null!=d)return d;a.chainCount==a.chains.length&&(a.chains=JU.AU.doubleLength(a.chains));return a.chains[a.chainCount++]=new J.modelset.Chain(a,b,0==b||32==b?-1:this.iChain++)},"J.modelset.Model,~N");c(c$,"iterateOverAllNewBonds",function(a,b){var d=a.getBondIterator(b);if(null!=d){var c=this.viewer.getMadBond();
this.modelSet.defaultCovalentMad=null==this.jmolData?c:0;for(var e=!1;d.hasNext();){var f=d.getEncodedOrder(),j=f,h=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),j);null!=h&&(1<j&&(1025!=j&&1041!=j)&&(e=!0),j=d.getRadius(),0<j&&h.setMad(oa(2E3*j)),j=d.getColix(),0<=j&&h.setColix(j),h.order|=f&65536)}e&&(this.modelSet.someModelsHaveSymmetry&&!this.viewer.getBoolean(603979794))&&J.util.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.');
this.modelSet.defaultCovalentMad=c}},"J.api.JmolAdapter,~O");c(c$,"bondAtoms",function(a,b,d){var c=this.htAtomMap.get(a);if(null==c)return J.util.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(b);if(null==a)return J.util.Logger.error("bondAtoms cannot find atomUid2?:"+b),null;if(c.isBonded(a))return null;1025==d||1041==d?(b=this.modelSet.bondMutually(c,a,this.is2D?d:1,this.modelSet.getDefaultMadFromOrder(1),0),null==this.vStereo&&(this.vStereo=new JU.List),this.vStereo.addLast(b)):
(b=this.modelSet.bondMutually(c,a,d,this.modelSet.getDefaultMadFromOrder(d),0),b.isAromatic()&&(this.modelSet.someModelsHaveAromaticBonds=!0));this.modelSet.bondCount==this.modelSet.bonds.length&&(this.modelSet.bonds=JU.AU.arrayCopyObject(this.modelSet.bonds,this.modelSet.bondCount+250));this.modelSet.setBond(this.modelSet.bondCount++,b);return b},"~O,~O,~N");c(c$,"initializeUnitCellAndSymmetry",function(){this.someModelsAreModulated&&null==this.modelSet.bsModulated&&(this.modelSet.bsModulated=new JU.BS);
if(this.someModelsHaveUnitcells){this.modelSet.unitCells=Array(this.modelSet.modelCount);this.modelSet.haveUnitCells=!0;for(var a=null!=this.mergeModelSet&&null!=this.mergeModelSet.unitCells,b=0;b<this.modelSet.modelCount;b++)a&&b<this.baseModelCount?this.modelSet.unitCells[b]=this.mergeModelSet.unitCells[b]:(this.modelSet.unitCells[b]=J.api.Interface.getOptionInterface("symmetry.Symmetry"),this.modelSet.unitCells[b].setSymmetryInfo(b,this.modelSet.getModelAuxiliaryInfo(b)))}if(this.appendNew&&this.modelSet.someModelsHaveSymmetry){this.modelSet.getAtomBits(1089470478,
null);for(var a=this.modelSet.atoms,b=this.baseAtomIndex,d=-1,c=0;b<this.modelSet.atomCount;b++)a[b].modelIndex!=d&&(d=a[b].modelIndex,c=this.baseAtomIndex+this.modelSet.getModelAuxiliaryInfoInt(d,"presymmetryAtomIndex")+this.modelSet.getModelAuxiliaryInfoInt(d,"presymmetryAtomCount")),b>=c&&this.modelSet.bsSymmetry.set(b)}if(this.appendNew&&this.modelSet.someModelsHaveFractionalCoordinates){a=this.modelSet.atoms;c=-1;d=null;for(b=this.baseAtomIndex;b<this.modelSet.atomCount;b++)a[b].modelIndex!=
c&&(c=a[b].modelIndex,d=this.modelSet.getUnitCell(c)),null!=d&&d.getCoordinatesAreFractional()&&(d=a[b].getUnitCell(),d.toCartesian(d.toSupercell(a[b]),!1));for(a=this.baseModelIndex;a<this.modelSet.modelCount;a++)if(this.modelSet.isTrajectory(a)&&(d=this.modelSet.getUnitCell(a),null!=d&&d.getCoordinatesAreFractional()&&d.isSupercell())){c=this.modelSet.trajectorySteps.get(a);for(b=c.length;0<=--b;)null!=c[b]&&d.toSupercell(c[b])}}});c(c$,"initializeBonding",function(){var a=null==this.modelSet.getModelSetAuxiliaryInfoValue("someModelsHaveCONECT")?
null:new JU.BS;null!=a&&this.modelSet.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,a);var b=0,d=this.viewer.getBoolean(603979794),c=this.viewer.getBoolean(603979798),e=this.viewer.getBoolean(603979846),f=null,j=!1,h=this.modelSet.modelCount,l=this.modelSet.models;if(!this.noAutoBond)for(var m=this.baseModelIndex;m<h;m++){var b=l[m].bsAtoms.cardinality(),n=this.modelSet.getModelAuxiliaryInfoInt(m,"initialBondCount"),q=l[m].isBioModel;0>n&&(n=this.modelSet.bondCount);var v=this.modelSet.getModelAuxiliaryInfoBoolean(m,
"hasSymmetry");if(e||c&&(0==n||q&&null==this.jmolData&&(this.modelSet.getModelSetAuxiliaryInfoBoolean("havePDBHeaderName")||n<s(b/2))||v&&!d&&!this.modelSet.getModelAuxiliaryInfoBoolean(m,"hasBonds")))if(j=!0,this.merging||1<h)null==f&&(f=J.util.BSUtil.newBitSet(this.modelSet.atomCount)),(m==this.baseModelIndex||!this.isTrajectory)&&f.or(l[m].bsAtoms)}j?(this.modulationOn&&this.modelSet.setModulation(null,!0,null,!1),this.modelSet.autoBondBs4(f,f,a,null,this.modelSet.defaultCovalentMad,this.viewer.getBoolean(603979874)),
J.util.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):(this.modelSet.initializeBspf(),J.util.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation"))});c(c$,"finalizeGroupBuild",function(){this.groups=Array(this.groupCount);if(this.merging)for(var a=0;a<this.$mergeGroups.length;a++)this.groups[a]=this.$mergeGroups[a],this.groups[a].setModelSet(this.modelSet);for(a=this.baseGroupIndex;a<this.groupCount;++a)this.distinguishAndPropagateGroup(a,
this.chainOf[a],this.group3Of[a],this.seqcodes[a],this.firstAtomIndexes[a],a==this.groupCount-1?this.modelSet.atomCount:this.firstAtomIndexes[a+1]);if(null!=this.group3Lists&&null!=this.modelSet.modelSetAuxiliaryInfo){this.modelSet.modelSetAuxiliaryInfo.put("group3Lists",this.group3Lists);this.modelSet.modelSetAuxiliaryInfo.put("group3Counts",this.group3Counts);for(a=0;a<this.group3Counts.length;a++)null==this.group3Counts[a]&&(this.group3Counts[a]=D(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,
b,d,c,e,f){var j=f-1;if(j<e)throw new NullPointerException;var h=this.modelSet.atoms[e].modelIndex,l=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,e,f,h,this.specialAtomIndexes,this.modelSet.atoms);null==l?(l=(new J.modelset.Group).setGroup(b,d,c,e,j),c="o>"):c=l.isProtein()?"p>":l.isNucleic()?"n>":l.isCarbohydrate()?"c>":"o>";null!=d&&this.countGroup(h,c,d);this.addGroup(b,l);this.groups[a]=l;l.setGroupIndex(a);for(a=f;--a>=e;)this.modelSet.atoms[a].setGroup(l)},"~N,J.modelset.Chain,~S,~N,~N,~N");
c(c$,"addGroup",function(a,b){a.groupCount==a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));a.groups[a.groupCount++]=b},"J.modelset.Chain,J.modelset.Group");c(c$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var e=(d+"   ").substring(0,3),f=this.group3Lists[c].indexOf(e);0>f&&(this.group3Lists[c]+=",["+e+"]",f=this.group3Lists[c].indexOf(e),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][s(f/
6)]++;f=this.group3Lists[c].indexOf(",["+e);0<=f&&(this.group3Lists[c]=this.group3Lists[c].substring(0,f)+b+this.group3Lists[c].substring(f+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"freeze",function(){this.htAtomMap.clear();this.modelSet.atomCount<this.modelSet.atoms.length&&this.modelSet.growAtomArrays(this.modelSet.atomCount);this.modelSet.bondCount<this.modelSet.bonds.length&&(this.modelSet.bonds=JU.AU.arrayCopyObject(this.modelSet.bonds,this.modelSet.bondCount));for(var a=5;0<--a;){this.modelSet.numCached[a]=
0;for(var b=this.modelSet.freeBonds[a],d=b.length;0<=--d;)b[d]=null}this.modelSet.setAtomNamesAndNumbers(0,this.baseAtomIndex,this.mergeModelSet);this.findElementsPresent();this.modelSet.resetMolecules();this.currentChain=this.currentModel=null;!this.isPDB||this.isPyMOLsession?this.modelSet.freezeModels():(a=this.viewer.getBoolean(603979825),a=this.modelSet.calculateStructuresAllExcept(this.structuresDefinedInFile,a,!1,!0,!0,a),0<a.length&&J.util.Logger.info(a))});c(c$,"findElementsPresent",function(){this.modelSet.elementsPresent=
Array(this.modelSet.modelCount);for(var a=0;a<this.modelSet.modelCount;a++)this.modelSet.elementsPresent[a]=J.util.BSUtil.newBitSet(64);for(a=this.modelSet.atomCount;0<=--a;){var b=this.modelSet.atoms[a].getAtomicAndIsotopeNumber();b>=J.util.Elements.elementNumberMax&&(b=J.util.Elements.elementNumberMax+J.util.Elements.altElementIndexFromNumber(b));this.modelSet.elementsPresent[this.modelSet.atoms[a].modelIndex].set(b)}});c(c$,"applyStereochemistry",function(){this.set2dZ(this.baseAtomIndex,this.modelSet.atomCount);
if(null!=this.vStereo){var a=new JU.BS;a.setBits(this.baseAtomIndex,this.modelSet.atomCount);for(var b=this.vStereo.size();0<=--b;){var d=this.vStereo.get(b),c=1025==d.order?3:-3;d.order=1;d.atom2.z!=d.atom1.z&&0>c==d.atom2.z<d.atom1.z&&(c/=3);var e=J.util.JmolMolecule.getBranchBitSet(this.modelSet.atoms,d.atom2.index,a,null,d.atom1.index,!1,!0);e.set(d.atom2.index);for(var f=e.nextSetBit(0);0<=f;f=e.nextSetBit(f+1))this.modelSet.atoms[f].z+=c;d.atom2.x=(d.atom1.x+d.atom2.x)/2;d.atom2.y=(d.atom1.y+
d.atom2.y)/2}this.vStereo=null}this.is2D=!1});c(c$,"set2dZ",function(a,b){var d=J.util.BSUtil.newBitSet(b),c=new JU.BS,e=new JU.V3,f=JU.V3.new3(0,1,0),j=new JU.V3,h=new JU.BS;h.setBits(a,b);for(var l=a;l<b;l++)!d.get(l)&&!c.get(l)&&(c=this.getBranch2dZ(l,-1,h,c,e,f,j),d.or(c))},"~N,~N");c(c$,"getBranch2dZ",function(a,b,d,c,e,f,j){c=J.util.BSUtil.newBitSet(this.modelSet.atomCount);if(0>a)return c;var h=new JU.BS;h.or(d);0<=b&&h.clear(b);J.modelset.ModelLoader.setBranch2dZ(this.modelSet.atoms[a],c,
h,e,f,j);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setBranch2dZ=c(c$,"setBranch2dZ",function(a,b,d,c,e,f){var j=a.index;if(d.get(j)&&(d.clear(j),b.set(j),null!=a.bonds))for(j=a.bonds.length;0<=--j;){var h=a.bonds[j];h.isHydrogen()||(h=h.getOtherAtom(a),J.modelset.ModelLoader.setAtom2dZ(a,h,c,e,f),J.modelset.ModelLoader.setBranch2dZ(h,b,d,c,e,f))}},"J.modelset.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setAtom2dZ=c(c$,"setAtom2dZ",function(a,b,d,c,e){d.sub2(b,a);d.z=0;d.normalize();e.cross(c,
d);d=Math.acos(d.dot(c));b.z=a.z+0.8*Math.sin(4*d)},"J.modelset.Atom,J.modelset.Atom,JU.V3,JU.V3,JU.V3");c(c$,"finalizeShapes",function(){this.modelSet.shapeManager=this.viewer.getShapeManager();this.modelSet.shapeManager.setModelSet(this.modelSet);this.modelSet.setBsHidden(this.viewer.getHiddenSet());this.merging||this.modelSet.shapeManager.resetShapes();this.modelSet.shapeManager.loadDefaultShapes(this.modelSet);this.modelSet.someModelsHaveAromaticBonds&&this.viewer.getBoolean(603979944)&&this.modelSet.assignAromaticBondsBs(!1,
null);this.merging&&1==this.baseModelCount&&this.modelSet.shapeManager.setShapePropertyBs(6,"clearModelIndex",null,null)});c(c$,"undeleteAtom",function(a){this.modelSet.atoms[a].valence=0},"~N");c(c$,"deleteAtoms",function(a){this.doRemoveAddedHydrogens=!0;for(var b=D(this.modelSet.atomCount,0),d=D(this.modelSet.atomCount-a.cardinality(),0),c=this.baseAtomIndex,e=this.modelSet.models,f=this.modelSet.atoms,j=this.baseAtomIndex;j<this.modelSet.atomCount;j++)e[f[j].modelIndex].bsAtoms.clear(j),e[f[j].modelIndex].bsAtomsDeleted.clear(j),
a.get(j)?(b[j]=c-1,e[f[j].modelIndex].atomCount--):(d[c]=j,b[j]=c++);this.modelSet.modelSetAuxiliaryInfo.put("bsDeletedAtoms",a);for(j=this.baseGroupIndex;j<this.groups.length;j++)a=this.groups[j],a.firstAtomIndex>=this.baseAtomIndex&&(a.firstAtomIndex=b[a.firstAtomIndex],a.lastAtomIndex=b[a.lastAtomIndex],0<=a.leadAtomIndex&&(a.leadAtomIndex=b[a.leadAtomIndex]));this.modelSet.adjustAtomArrays(d,this.baseAtomIndex,c);this.modelSet.calcBoundBoxDimensions(null,1);this.modelSet.resetMolecules();this.modelSet.validateBspf(!1)},
"JU.BS");c$.createAtomDataSet=c(c$,"createAtomDataSet",function(a,b,d,c,e){if(null!=c){var f=a.getModelAdapter(),j=new JU.P3,h=b.atoms,l=a.getFloat(570425363);if(null!=b.unitCells)for(var m=e.nextSetBit(0);0<=m;m=e.nextSetBit(m+1))if(null!=h[m].getAtomSymmetry()){l=-l;break}for(var m=-1,n=0,q=J.util.BSUtil.cardinalityOf(e)==a.getAtomCount(),v=f.getAtomIterator(c);v.hasNext();){var x=v.getXYZ();if(!Float.isNaN(x.x+x.y+x.z))if(1146095626==d){m=e.nextSetBit(m+1);if(0>m)break;n++;J.util.Logger.debugging&&
J.util.Logger.debug("atomIndex = "+m+": "+h[m]+" --\x3e ("+x.x+","+x.y+","+x.z);b.setAtomCoord(m,x.x,x.y,x.z)}else{j.setT(x);x=J.util.BSUtil.newBitSet(b.atomCount);b.getAtomsWithin(l,j,x,-1);x.and(e);if(q)if(n=J.util.BSUtil.cardinalityOf(x),0==n){J.util.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<n&&J.util.Logger.debugging&&J.util.Logger.debug("createAtomDataSet: "+n+" atoms found at position "+j);switch(d){case 1146095631:var p=v.getVib();if(null==p)continue;J.util.Logger.debugging&&
J.util.Logger.debug("xyz: "+j+" vib: "+p);b.setAtomCoords(x,1146095631,p);break;case 1129318401:b.setAtomProperty(x,d,v.getOccupancy(),0,null,null,null);break;case 1112541196:b.setAtomProperty(x,d,0,v.getPartialCharge(),null,null,null);break;case 1112541199:b.setAtomProperty(x,d,0,v.getBfactor(),null,null,null)}}}switch(d){case 1146095631:b=f.getAtomSetName(c,0);J.util.Logger.info("_vibrationName = "+b);a.setStringProperty("_vibrationName",b);break;case 1146095626:J.util.Logger.info(n+" atom positions read"),
b.recalculateLeadMidpointsAndWingVectors(-1)}}},"J.viewer.Viewer,J.modelset.ModelSet,~N,~O,JU.BS");E(c$,"defaultGroupCount",32)}),p("J.modelset"),t(["J.modelset.ModelCollection","JU.M3","$.M4","$.V3"],"J.modelset.ModelSet","java.lang.Boolean java.util.Hashtable JU.A4 $.BS $.List $.P3 $.SB J.api.Interface J.atomdata.RadiusData J.util.BSUtil $.JmolMolecule $.Measure $.Quaternion J.viewer.JC".split(" "),function(){c$=w(function(){this.echoShapeActive=this.selectionHaloEnabled=!1;this.vTemp=this.mat4t=
this.mat4=this.matInv=this.matTemp=this.pointGroup=this.closest=this.modelSetTypeName=null;u(this,arguments)},J.modelset,"ModelSet",J.modelset.ModelCollection);Q(c$,function(){this.closest=Array(1);this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=new JU.M4;this.vTemp=new JU.V3});A(c$,function(a,b){U(this,J.modelset.ModelSet,[]);this.viewer=a;this.modelSetName=b},"J.viewer.Viewer,~S");c(c$,"releaseModelSet",function(){this.models=null;this.closest[0]=null;qa(this,J.modelset.ModelSet,
"releaseModelSet",[])});c(c$,"setSelectionHaloEnabled",function(a){this.selectionHaloEnabled=a},"~B");c(c$,"getSelectionHaloEnabled",function(){return this.selectionHaloEnabled});c(c$,"getEchoStateActive",function(){return this.echoShapeActive});c(c$,"setEchoStateActive",function(a){this.echoShapeActive=a},"~B");c(c$,"getModelSetTypeName",function(){return this.modelSetTypeName});c(c$,"getModelNumberIndex",function(a,b,d){if(b){for(b=0;b<this.modelCount;b++)if(this.modelNumbers[b]==a||1E6>a&&this.modelNumbers[b]==
1E6+a)return b;return-1}for(b=0;b<this.modelCount;b++)if(this.modelFileNumbers[b]==a)return d&&this.isTrajectory(b)&&this.setTrajectory(b),b;return-1},"~N,~B,~B");c(c$,"getBitSetTrajectories",function(){if(null==this.trajectorySteps)return null;for(var a=new JU.BS,b=this.modelCount;0<=--b;){var d=this.models[b].getSelectedTrajectory();0<=d&&(a.set(d),b=this.models[b].trajectoryBaseIndex)}return a});c(c$,"setTrajectoryBs",function(a){for(var b=0;b<this.modelCount;b++)a.get(b)&&this.setTrajectory(b)},
"JU.BS");c(c$,"setTrajectory",function(a){if(!(0>a)&&this.isTrajectory(a)&&this.atoms[this.models[a].firstAtomIndex].modelIndex!=a){var b=this.models[a].trajectoryBaseIndex;this.models[b].setSelectedTrajectory(a);this.setAtomPositions(b,a,this.trajectorySteps.get(a),null,0,null==this.vibrationSteps?null:this.vibrationSteps.get(a),!0);b=this.viewer.getCurrentModelIndex();0<=b&&(b!=a&&this.models[b].fileIndex==this.models[a].fileIndex)&&this.viewer.setCurrentModelIndexClear(a,!1)}},"~N");c(c$,"morphTrajectories",
function(a,b,d){if(!(0>a||0>b||!this.isTrajectory(a)||!this.isTrajectory(b)))if(0==d)this.setTrajectory(a);else if(1==d)this.setTrajectory(b);else{var c=this.models[a].trajectoryBaseIndex;this.models[c].setSelectedTrajectory(a);this.setAtomPositions(c,a,this.trajectorySteps.get(a),this.trajectorySteps.get(b),d,null==this.vibrationSteps?null:this.vibrationSteps.get(a),!0);b=this.viewer.getCurrentModelIndex();0<=b&&(b!=a&&this.models[b].fileIndex==this.models[a].fileIndex)&&this.viewer.setCurrentModelIndexClear(a,
!1)}},"~N,~N,~N");c(c$,"setAtomPositions",function(a,b,d,c,e,f,j){var h=new JU.BS,l=new JU.V3,m=this.models[a].firstAtomIndex,n=m+this.getAtomCountInModel(a);if(0==e)for(var q=0;m<n&&q<d.length;m++,q++)this.atoms[m].modelIndex=b,null!=d[q]&&(j?this.atoms[m].setFractionalCoordTo(d[q],!0):this.atoms[m].setT(d[q]),null!=this.vibrationSteps&&(null!=f&&null!=f[q]&&(l=f[q]),this.setVibrationVector(m,l)),h.set(m));else{f=new JU.P3;l=Math.min(d.length,c.length);for(q=0;m<n&&q<l;m++,q++)this.atoms[m].modelIndex=
b,null==d[q]||null==c[q]||(f.sub2(c[q],d[q]),f.scaleAdd2(e,f,d[q]),j?this.atoms[m].setFractionalCoordTo(f,!0):this.atoms[m].setT(f),h.set(m))}this.initializeBspf();this.validateBspfForModel(a,!1);this.recalculateLeadMidpointsAndWingVectors(a);this.shapeManager.refreshShapeTrajectories(a,h,null);this.models[a].hasRasmolHBonds&&(this.models[a].clearRasmolHydrogenBonds(null),this.models[a].getRasmolHydrogenBonds(h,h,null,!1,2147483647,!1,null))},"~N,~N,~A,~A,~N,~A,~B");c(c$,"getFrameOffsets",function(a){if(null==
a)return null;for(var b=Array(this.modelCount),d=0;d<this.modelCount;d++)b[d]=new JU.P3;for(var c=0,e=0,f=b[0],j=null!=this.trajectorySteps&&this.trajectorySteps.size()==this.modelCount,h=j?this.modelCount:1,l=0;l<h;l++){j&&this.setTrajectory(l);for(d=0;d<=this.atomCount;d++){if(d==this.atomCount||this.atoms[d].modelIndex!=c){0<e&&(f.scale(-1/e),0!=c&&f.sub(b[0]),e=0);if(d==this.atomCount)break;c=this.atoms[d].modelIndex;f=b[c]}a.get(d)&&(f.add(this.atoms[d]),e++)}}b[0].set(0,0,0);return b},"JU.BS");
c(c$,"getAtomBits",function(a,b){switch(a){default:return J.util.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,b),this.viewer.getDeletedAtoms());case 1048610:var d=b.intValue(),c=this.getModelNumberIndex(d,!0,!0);return 0>c&&0<d?new JU.BS:this.viewer.getModelUndeletedAtomsBitSet(c)}},"~N,~O");c(c$,"getAtomLabel",function(a){return this.viewer.getShapePropertyIndex(5,"label",a)},"~N");c(c$,"findNearestAtomIndex",function(a,b,d,c){if(0==this.atomCount)return-1;this.closest[0]=null;this.g3d.isAntialiased()&&
(a<<=1,b<<=1);this.findNearest2(a,b,this.closest,d,c);this.shapeManager.findNearestShapeAtomIndex(a,b,this.closest,d);a=null==this.closest[0]?-1:this.closest[0].index;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(c$,"calculateStructures",function(a,b,d,c){var e=new JU.BS;a=J.util.BSUtil.copyInvert(this.modelsOf(a,e),this.modelCount);if(!c)return this.calculateStructuresAllExcept(a,b,!0,d,!1,!1);for(c=0;c<this.modelCount;c++)a.get(c)||this.models[c].clearBioPolymers();this.calculatePolymers(null,
0,0,a);b=this.calculateStructuresAllExcept(a,b,!0,d,!0,!1);this.viewer.resetBioshapes(e);this.setStructureIndexes();return b},"JU.BS,~B,~B,~B");c(c$,"calculatePointGroup",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!1,null,0,0)},"JU.BS");c(c$,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!0,null,0,0)},"JU.BS");c(c$,"getPointGroupAsString",function(a,b,d,c,e){return this.calculatePointGroupForFirstModel(a,!0,b,!1,d,c,e)},"JU.BS,~B,~S,~N,~N");
c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,e,f,j){var h=this.viewer.getCurrentModelIndex(),l=null==a?-1:a.nextSetBit(0);0>h&&0<=l&&(h=this.atoms[l].getModelIndex());0>h&&(h=this.viewer.getVisibleFramesBitSet().nextSetBit(0),a=null);var m=this.viewer.getModelUndeletedAtomsBitSet(h);null!=a&&m.and(a);l=m.nextSetBit(0);0>l&&(m=this.viewer.getModelUndeletedAtomsBitSet(h),l=m.nextSetBit(0));a=this.viewer.getShapePropertyIndex(18,"mad",l);a=null!=a&&0!=a.intValue()||this.viewer.isVibrationOn();
this.pointGroup=J.api.Interface.getOptionInterface("symmetry.Symmetry").setPointGroup(this.pointGroup,this.atoms,m,a,this.viewer.getFloat(570425382),this.viewer.getFloat(570425384));if(!b&&!c)return this.pointGroup.getPointGroupName();b=this.pointGroup.getPointGroupInfo(h,d,c,e,f,j);return c?b:(1<this.modelCount?"frame "+this.getModelNumberDotted(h)+"; ":"")+b},"JU.BS,~B,~B,~B,~S,~N,~N");c(c$,"modelsOf",function(a,b){for(var d=J.util.BSUtil.newBitSet(this.modelCount),c=null==a,e=c?this.atomCount-
1:a.nextSetBit(0);0<=e;e=c?e-1:a.nextSetBit(e+1)){var f=this.models[this.atoms[e].modelIndex].trajectoryBaseIndex;this.isJmolDataFrameForModel(f)||(d.set(f),b.set(e))}return d},"JU.BS,JU.BS");c(c$,"getDefaultStructure",function(a,b){for(var d=this.modelsOf(a,b),c=new JU.SB,e=d.nextSetBit(0);0<=e;e=d.nextSetBit(e+1))this.models[e].isBioModel&&null!=this.models[e].defaultStructure&&c.append(this.models[e].defaultStructure);return c.toString()},"JU.BS,JU.BS");c(c$,"makeConnections",function(a,b,d,c,
e,f,j,h,l,m){if(1073741852==c&&2048!=d){var n="connect ";0.1!=a&&(n+=a+" ");1E8!=b&&(n+=b+" ");this.addStateScript(n,h?e:null,h?null:e,h?null:f," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,e,f,j,h,l,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"setPdbConectBonding",function(a,b,d){for(var c=this.viewer.getMadBond();b<this.modelCount;b++){var e=this.getModelAuxiliaryInfoValue(b,"PDB_CONECT_bonds");if(null!=e){var f=e.size();this.setModelAuxiliaryInfo(b,"initialBondCount",
Integer.$valueOf(f));for(var j=this.getModelAuxiliaryInfoValue(b,"PDB_CONECT_firstAtom_count_max"),h=j[0]+a,l=h+j[1],j=j[2],m=D(j+1,0),n=h;n<l;n++)if(0<(h=this.atomSerials[n]))m[h]=n+1;for(l=0;l<f;l++){var n=e.get(l),q=n[0],h=n[1],n=n[2];0>q||(0>h||q>j||h>j)||(q=m[q]-1,h=m[h]-1,0>q||0>h||(null!=d&&(this.atoms[q].isHetero()&&d.set(q),this.atoms[h].isHetero()&&d.set(h)),this.checkValencesAndBond(this.atoms[q],this.atoms[h],n,2048==n?1:c,null)))}}}},"~N,~N,JU.BS");c(c$,"deleteAllBonds",function(){this.moleculeCount=
0;for(var a=this.stateScripts.size();0<=--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.remove(a);this.deleteAllBonds2()});c(c$,"includeAllRelatedFrames",function(a){for(var b,d=0;d<this.modelCount;d++)if(a.get(d)){if(this.isTrajectory(d)&&!a.get(b=this.models[d].trajectoryBaseIndex)){a.set(b);this.includeAllRelatedFrames(a);break}}else(this.isTrajectory(d)&&a.get(this.models[d].trajectoryBaseIndex)||this.isJmolDataFrameForModel(d)&&a.get(this.models[d].dataSourceFrame))&&a.set(d)},"JU.BS");
c(c$,"deleteModels",function(a){this.moleculeCount=0;a=this.getModelBitSet(a,!1);this.includeAllRelatedFrames(a);var b=J.util.BSUtil.cardinalityOf(a);if(0==b)return null;for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.clearDataFrameReference(d);if(b==this.modelCount)return b=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.viewer.zap(!0,!1,!1),b;this.validateBspf(!1);for(var c=Array(this.modelCount-b),e=this.models,b=new JU.BS,f=d=0;d<this.modelCount;d++)a.get(d)?(this.getAtomCountInModel(d),
b.or(this.getModelAtomBitSetIncludingDeleted(d,!1))):(this.models[d].modelIndex=f,c[f++]=this.models[d]);this.models=c;var j=this.modelCount,h=this.getBondsForSelectedAtoms(b,!0);this.deleteBonds(h,!0);for(f=d=0;d<j;d++)if(a.get(d)){var l=e[d].atomCount;if(0!=l){var m=e[d].bsAtoms,n=e[d].firstAtomIndex;J.util.BSUtil.deleteBits(this.bsSymmetry,m);this.deleteModel(f,n,l,m,h);for(var q=j;--q>d;)e[q].fixIndices(f,l,m);this.viewer.deleteShapeAtoms([c,this.atoms,[f,n,l]],m);this.modelCount--}}else f++;
this.deleteModel(-1,0,0,null,null);return b},"JU.BS");c(c$,"setAtomProperty",function(a,b,d,c,e,f,j){switch(b){case 1115297793:case 1113200642:case 1113200647:case 1113200649:case 1113200650:case 1650071565:case 1113200654:if(4<c&&(c=4),null!=f){d=O(this.atomCount,0);e=a.nextSetBit(0);for(j=0;0<=e;e=a.nextSetBit(e+1))d[e]=f[j++];f=d}case 1113200646:case 1113200652:d=null;e=0;null==f?(16<c&&(c=16.1),0>c&&(c=0),e=s(Math.floor(2E3*c))):d=new J.atomdata.RadiusData(f,0,null,null);this.shapeManager.setShapeSizeBs(J.viewer.JC.shapeTokenIndex(b),
e,d,a);return}this.setAPm(a,b,d,c,e,f,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getFileData",function(a){if(0>a)return"";var b=this.getModelAuxiliaryInfoValue(a,"fileData");if(null!=b)return b;if(!this.getModelAuxiliaryInfoBoolean(a,"isCIF"))return this.getPDBHeader(a);b=this.viewer.getCifData(a);this.setModelAuxiliaryInfo(a,"fileData",b);return b},"~N");h(c$,"calculateStruts",function(a,b){this.viewer.setModelVisibility();return this.calculateStrutsMC(a,b)},"JU.BS,JU.BS");c(c$,"addHydrogens",function(a,
b){var d=this.modelCount-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.models[d].getGroupCount())return c;this.growAtomArrays(this.atomCount+b.length);for(var e=this.viewer.getDefaultRadiusData(),f=this.getDefaultMadFromOrder(1),j=0,h=this.models[d].atomCount+1;j<a.size();j++,h++){var l=a.get(j),m=this.addAtom(d,l.group,1,"H"+h,h,h,b[j],NaN,null,0,0,100,NaN,null,!1,0,null);m.setMadAtom(this.viewer,e);c.set(m.index);this.bondAtoms(l,m,1,f,null,0,!1,!1)}this.shapeManager.loadDefaultShapes(this);return c},
"JU.List,~A");c(c$,"setAtomCoordsRelative",function(a,b){this.setAtomsCoordRelative(b,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(b,this.mat4)},"JU.T3,JU.BS");c(c$,"setAtomCoords",function(a,b,d){this.setAtomCoord2(a,b,d);switch(b){case 1112541202:case 1112541203:case 1112541204:case 1146095631:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(c$,"invertSelected",function(a,
b,d,c,e){if(null!=a)for(var f=e.nextSetBit(0);0<=f;f=e.nextSetBit(f+1)){d=2*(a.x-this.atoms[f].x);c=2*(a.y-this.atoms[f].y);var j=2*(a.z-this.atoms[f].z);this.setAtomCoordRelative(f,d,c,j)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var h=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),f=e.nextSetBit(0);0<=f;f=e.nextSetBit(f+1))j=2*-J.util.Measure.distanceToPlaneD(b,h,this.atoms[f]),d=a.x*j,c=a.y*j,j*=a.z,this.setAtomCoordRelative(f,d,c,j)}else if(0<=d&&(b=this.atoms[d],a=b.bonds,null!=a)){e=
new JU.BS;j=new JU.List;h=this.viewer.getModelUndeletedAtomsBitSet(b.modelIndex);for(f=0;f<a.length;f++){var l=a[f].getOtherAtom(b);c.get(l.index)?e.or(J.util.JmolMolecule.getBranchBitSet(this.atoms,l.index,h,null,d,!0,!0)):j.addLast(l)}0!=j.size()&&(a=J.util.Measure.getCenterAndPoints(j)[0],f=JU.V3.newVsub(b,a),f=J.util.Quaternion.newVA(f,180),this.moveAtoms(null,f.getMatrix(),null,e,b,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS,JU.BS");c(c$,"setDihedrals",function(a,b,d){var c=s(a.length/6);1<d&&(d=1);for(var e=
0,f=0;e<c;e++,f+=6){var j=b[e];if(!(null==j||j.isEmpty())){var h=this.atoms[y(a[f+1])],l=JU.V3.newVsub(this.atoms[y(a[f+2])],h),l=JU.A4.newVA(l,-((a[f+5]-a[f+4])*d)/57.29577951308232);this.matTemp.setAA(l);this.ptTemp.setT(h);for(h=j.nextSetBit(0);0<=h;h=j.nextSetBit(h+1))this.atoms[h].sub(this.ptTemp),this.matTemp.transform(this.atoms[h]),this.atoms[h].add(this.ptTemp),this.taintAtom(h,2)}}},"~A,~A,~N");c(c$,"moveAtoms",function(a,b,d,c,e,f,j){if(!j){null==a?this.matTemp.setM(b):(this.matInv.setM(b),
this.matInv.invert(),this.ptTemp.set(0,0,0),this.matTemp.mul2(a,b),this.matTemp.mul2(this.matInv,this.matTemp));f?(this.vTemp.setT(e),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setM3(this.matTemp),this.mat4.mulM4(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),this.mat4.mulM4(this.mat4t)):this.mat4.setM3(this.matTemp);for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))f?this.mat4.transform(this.atoms[a]):(this.ptTemp.add(this.atoms[a]),
this.mat4.transform(this.atoms[a]),this.ptTemp.sub(this.atoms[a])),this.taintAtom(a,2);f||(this.ptTemp.scale(1/c.cardinality()),null==d&&(d=new JU.V3),d.add(this.ptTemp))}if(null!=d){for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))this.atoms[a].add(d);j||(this.mat4t.setIdentity(),this.mat4t.setTranslation(d),this.mat4.mul2(this.mat4t,this.mat4))}this.recalculatePositionDependentQuantities(c,this.mat4)},"JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(c$,"recalculatePositionDependentQuantities",function(a,
b){this.getHaveStraightness()&&this.calculateStraightness();this.recalculateLeadMidpointsAndWingVectors(-1);for(var d=this.getModelBitSet(a,!1),c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))this.shapeManager.refreshShapeTrajectories(c,a,b)},"JU.BS,JU.M4");c(c$,"getBsBranches",function(a){for(var b=s(a.length/6),d=Array(b),c=new java.util.Hashtable,e=0,f=0;e<b;e++,f+=6)if(!(1>Math.abs(a[f+5]-a[f+4]))){var j=y(a[f+1]),h=y(a[f+2]),l=""+j+"_"+h;if(!c.containsKey(l)){c.put(l,Boolean.TRUE);for(var l=this.viewer.getBranchBitSet(h,
j,!0),m=this.atoms[j].bonds,j=this.atoms[j],n=0;n<m.length;n++){var q=m[n];if(q.isCovalent()&&(q=q.getOtherAtom(j).index,q!=h&&l.get(q))){l=null;break}}d[e]=l}}return d},"~A");c(c$,"getSymMatrices",function(a){var b=this.getModelSymmetryCount(a);if(0==b)return null;var d=Array(b),c=this.models[a].biosymmetry;null==c&&(c=this.viewer.getModelUnitCell(a));for(a=b;0<=--a;)d[a]=c.getSpaceGroupOperation(a);return d},"~N")}),p("J.modelset"),t(["JU.M3","$.P3"],"J.modelset.Orientation",["J.util.Escape"],function(){c$=
w(function(){this.rotationMatrix=this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.viewer=this.pymolView=this.moveToText=null;u(this,arguments)},J.modelset,"Orientation");Q(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});A(c$,function(a,b,d){this.viewer=a;null!=d?(this.pymolView=
d,this.moveToText="moveTo -1.0 PyMOL "+J.util.Escape.eAF(d)):(a.finalizeTransformParameters(),b?(b=a.getModelSetAuxiliaryInfoValue("defaultOrientationMatrix"),null==b?this.rotationMatrix.setIdentity():this.rotationMatrix.setM(b)):a.getRotation(this.rotationMatrix),this.xTrans=a.getTranslationXPercent(),this.yTrans=a.getTranslationYPercent(),this.zoom=a.getZoomSetting(),this.center.setT(a.getRotationCenter()),this.windowCenteredFlag=a.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=
a.getBoolean(603979887),this.moveToText=a.getMoveToText(-1),this.navigationMode&&(this.xNav=a.getNavigationOffsetPercent("X"),this.yNav=a.getNavigationOffsetPercent("Y"),this.navDepth=a.getNavigationDepthPercent(),this.navCenter=JU.P3.newP(a.getNavigationCenter())),0!=a.getCamera().z&&(this.cameraDepth=a.getCameraDepth(),this.cameraX=a.getCamera().x,this.cameraY=a.getCamera().y))},"J.viewer.Viewer,~B,~A");c(c$,"getMoveToText",function(a){return a?"   "+this.moveToText+"\n  save orientation "+J.util.Escape.eS(this.saveName.substring(12))+
";\n":this.moveToText},"~B");c(c$,"restore",function(a,b){b?(this.viewer.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.viewer.setBooleanProperty("navigationMode",this.navigationMode),null==this.pymolView?this.viewer.moveTo(this.viewer.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.viewer.movePyMOL(this.viewer.eval,a,this.pymolView)):
this.viewer.setRotationMatrix(this.rotationMatrix);return!0},"~N,~B")}),p("J.modelset"),t(null,"J.modelset.StateScript",["JU.SB","J.util.BSUtil","$.Escape"],function(){c$=w(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;u(this,arguments)},J.modelset,"StateScript");A(c$,function(a,b,d,c,e,f,j){this.modelIndex=a;this.script1=b;this.bsBonds=J.util.BSUtil.copy(d);this.bsAtoms1=J.util.BSUtil.copy(c);this.bsAtoms2=J.util.BSUtil.copy(e);
this.script2=f;this.inDefinedStateBlock=j},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");c(c$,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});h(c$,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(J.util.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(J.util.Escape.eBS(this.bsAtoms1));
null!=this.bsAtoms2&&a.append(" ").append(J.util.Escape.eBS(this.bsAtoms2));null!=this.script2&&a.append(" ").append(this.script2);a=a.toString();a.endsWith(";")||(a+=";");return a});c(c$,"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(c$,"deleteAtoms",function(a,b,d){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;J.util.BSUtil.deleteBits(this.bsBonds,b);J.util.BSUtil.deleteBits(this.bsAtoms1,d);J.util.BSUtil.deleteBits(this.bsAtoms2,d);return this.isValid()},"~N,JU.BS,JU.BS");
c(c$,"setModelIndex",function(a){this.modelIndex=a},"~N")}),p("J.modelset"),c$=w(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;u(this,arguments)},J.modelset,"TickInfo"),A(c$,function(a){this.ticks=a},"JU.P3"),p("J.render"),t(["J.render.ShapeRenderer"],"J.render.BallsRenderer",["J.shape.Shape"],function(){c$=M(J.render,"BallsRenderer",J.render.ShapeRenderer);h(c$,"render",function(){var a=!1;if(this.isExport||
this.viewer.checkMotionRendering(1141899265))for(var b=this.modelSet.atoms,d=this.shape.colixes,c=this.viewer.getRenderableBitSet(),e=c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1)){var f=b[e];0<f.sD&&0!=(f.getShapeVisibilityFlags()&this.myVisibilityFlag)&&(this.g3d.setColix(null==d?f.getColix():J.shape.Shape.getColix(d,e,f))?this.g3d.drawAtom(f):a=!0)}return a})}),p("J.render"),t(["J.render.ShapeRenderer","JU.P3","$.P3i","$.V3"],"J.render.FontLineShapeRenderer",["java.lang.Float","J.constant.EnumAxesMode",
"J.util.Txt"],function(){c$=w(function(){this.imageFontScaling=0;this.tickInfo=this.vectorT3=this.vectorT2=this.vectorT=this.pointT3=this.pointT2=this.pointT=this.s2=this.s1=this.pt2i=this.pt1i=this.pt0i=this.font3d=this.atomB=this.atomA=null;this.draw000=!0;this.width=0;this.endcap=3;this.colixB=this.colixA=0;this.dotsOrDashes=!1;this.dashDots=null;this.asLineOnly=!1;u(this,arguments)},J.render,"FontLineShapeRenderer",J.render.ShapeRenderer);Q(c$,function(){this.pt0i=new JU.P3i;this.pt1i=new JU.P3i;
this.pt2i=new JU.P3i;this.s1=new JU.P3i;this.s2=new JU.P3i;this.pointT=new JU.P3;this.pointT2=new JU.P3;this.pointT3=new JU.P3;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.vectorT3=new JU.V3});c(c$,"getDiameter",function(a,b){var d;d=20<b;switch(this.exportType){case 1:d=d?b:s(Math.floor(1E3*this.viewer.unscaleToScreen(a,2*b)));break;default:d?d=y(this.viewer.scaleToScreen(a,b)):(this.g3d.isAntialiased()&&(b+=b),d=b)}return d},"~N,~N");c(c$,"renderLine",function(a,b,d,c,e,f){c.set(s(Math.floor(a.x)),
s(Math.floor(a.y)),s(Math.floor(a.z)));e.set(s(Math.floor(b.x)),s(Math.floor(b.y)),s(Math.floor(b.z)));0>d?this.g3d.drawDottedLine(c,e):this.g3d.fillCylinder(this.endcap,d,c,e);f&&null!=this.tickInfo&&(this.atomA.sX=c.x,this.atomA.sY=c.y,this.atomA.sZ=c.z,this.atomB.sX=e.x,this.atomB.sY=e.y,this.atomB.sZ=e.z,this.drawTicks(this.atomA,this.atomB,d,!0))},"JU.P3,JU.P3,~N,JU.P3i,JU.P3i,~B");c(c$,"drawTicks",function(a,b,d,c){Float.isNaN(this.tickInfo.first)&&(this.tickInfo.first=0);this.drawTicks2(a,
b,this.tickInfo.ticks.x,8,d,!c?null:null==this.tickInfo.tickLabelFormats?["%0.2f"]:this.tickInfo.tickLabelFormats);this.drawTicks2(a,b,this.tickInfo.ticks.y,4,d,null);this.drawTicks2(a,b,this.tickInfo.ticks.z,2,d,null)},"J.util.Point3fi,J.util.Point3fi,~N,~B");c(c$,"drawTicks2",function(a,b,d,c,e,f){if(0!=d&&(this.g3d.isAntialiased()&&(c*=2),this.vectorT2.set(b.sX,b.sY,0),this.vectorT.set(a.sX,a.sY,0),this.vectorT2.sub(this.vectorT),!(50>this.vectorT2.length()))){var j=this.tickInfo.signFactor;this.vectorT.sub2(b,
a);var h=this.vectorT.length();if(null!=this.tickInfo.scale)if(Float.isNaN(this.tickInfo.scale.x)){var l=this.viewer.getUnitCellInfo(0);Float.isNaN(l)||this.vectorT.set(this.vectorT.x/l,this.vectorT.y/this.viewer.getUnitCellInfo(1),this.vectorT.z/this.viewer.getUnitCellInfo(2))}else this.vectorT.set(this.vectorT.x*this.tickInfo.scale.x,this.vectorT.y*this.tickInfo.scale.y,this.vectorT.z*this.tickInfo.scale.z);l=this.vectorT.length()+1E-4*d;if(!(l<d)){this.vectorT.scale(d/l*h/l);b=(b.sZ-a.sZ)/(l/d);
l+=this.tickInfo.first;h=s(Math.floor(this.tickInfo.first/d))*d-this.tickInfo.first;this.pointT.scaleAdd2(h/d,this.vectorT,a);h+=this.tickInfo.first;a=a.sZ;0>e&&(e=1);this.vectorT2.set(-this.vectorT2.y,this.vectorT2.x,0);this.vectorT2.scale(c/this.vectorT2.length());c=this.tickInfo.reference;null==c?(this.pointT3.setT(this.viewer.getBoundBoxCenter()),this.viewer.getAxesMode()===J.constant.EnumAxesMode.BOUNDBOX&&(this.pointT3.x+=1,this.pointT3.y+=1,this.pointT3.z+=1)):this.pointT3.setT(c);this.viewer.transformPtScr(this.pointT3,
this.pt2i);c=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var m=!c,n=!c&&0>this.vectorT2.x,q=null!=f&&0<f.length,v,p,r=Array(1),t=this.draw000?0:-1;h<l;){if(h>=this.tickInfo.first&&(this.pointT2.setT(this.pointT),this.viewer.transformPt3f(this.pointT2,this.pointT2),this.drawLine(s(Math.floor(this.pointT2.x)),s(Math.floor(this.pointT2.y)),y(a),v=s(Math.floor(this.pointT2.x+this.vectorT2.x)),p=s(Math.floor(this.pointT2.y+this.vectorT2.y)),y(a),e),q&&(this.draw000||0!=h))){r[0]=Float.$valueOf(0==
h?0:h*j);var u=J.util.Txt.sprintf(f[t%f.length],"f",r);this.drawString(v,p,y(a),4,n,c,m,s(Math.floor(this.pointT2.y)),u)}this.pointT.add(this.vectorT);h+=d;a+=b;t++}}}},"J.util.Point3fi,J.util.Point3fi,~N,~N,~N,~A");c(c$,"drawLine",function(a,b,d,c,e,f,j){return this.drawLine2(a,b,d,c,e,f,j)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawLine2",function(a,b,d,c,e,f,j){this.pt0i.set(a,b,d);this.pt1i.set(c,e,f);if(this.dotsOrDashes)null!=this.dashDots&&this.drawDashed(a,b,d,c,e,f,this.dashDots);else{if(0>j)return this.g3d.drawDashedLine(4,
2,this.pt0i,this.pt1i),1;this.g3d.fillCylinder(2,j,this.pt0i,this.pt1i)}return s((j+1)/2)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawString",function(a,b,d,c,e,f,j,h,l){if(null!=l){var m=this.font3d.stringWidth(l),n=this.font3d.getAscent();a=e?a-(s(c/2)+2+m):f?a-(s(c/2)+2+s(m/2)):a+(s(c/2)+2);e=b;e=j?e+s(n/2):0==h||h<b?e+n:e-s(c/2);b=d-c-2;1>b&&(b=1);this.g3d.drawString(l,this.font3d,a,e,b,b,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");c(c$,"drawDashed",function(a,b,d,c,e,f,j){if(!(null==j||0>this.width)){var h=j[0];
c-=a;e-=b;f-=d;var l=0,m=j===J.render.FontLineShapeRenderer.ndots,n=m||j===J.render.FontLineShapeRenderer.sixdots;if(n){var q=(c*c+e*e)/(this.width*this.width);m?(h=Math.sqrt(q)/1.5,l=y(h)+3):8>q?j=J.render.FontLineShapeRenderer.twodots:32>q&&(j=J.render.FontLineShapeRenderer.fourdots)}var q=j[1],v=j[2],p=this.colixA,r=0==v?this.colixB:this.colixA;0==l&&(l=j.length);for(var t=0,u=3;u<l;u++){var t=m?t+1:j[u],w=s(Math.floor(a+c*t/h)),z=s(Math.floor(b+e*t/h)),A=s(Math.floor(d+f*t/h));if(n)this.s1.set(w,
z,A),u==q?this.g3d.setColix(this.colixA):u==v&&this.g3d.setColix(this.colixB),this.g3d.fillSphereI(this.width,this.s1);else{u==q&&(p=this.colixB);t=j[++u];u==v&&(r=this.colixB);var B=s(Math.floor(a+c*t/h)),C=s(Math.floor(b+e*t/h)),D=s(Math.floor(d+f*t/h));this.fillCylinder(p,r,2,this.width,w,z,A,B,C,D)}}}},"~N,~N,~N,~N,~N,~N,~A");c(c$,"fillCylinder",function(a,b,d,c,e,f,j,h,l,m){this.asLineOnly?this.g3d.drawLine(a,b,e,f,j,h,l,m):this.g3d.fillCylinderXYZ(a,b,d,!this.isExport||1==this.mad?c:this.mad,
e,f,j,h,l,m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");E(c$,"dashes",[12,0,0,2,5,7,10],"hDashes",[10,7,6,1,3,4,6,7,9],"ndots",[0,3,1E3],"sixdots",[12,3,6,1,3,5,7,9,11],"fourdots",[13,3,5,2,5,8,11],"twodots",[12,3,4,3,9])}),p("J.render"),t(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["J.util.C"],function(){c$=M(J.render,"FrankRenderer",J.render.ShapeRenderer);h(c$,"render",function(){var a=this.shape,b=this.viewer.getBooleanProperty("allowKeyStrokes"),d=this.viewer.getBoolean(603979883);this.colix=
d?20:this.viewer.isSignedApplet()?b||this.viewer.isJS&&!this.viewer.isWebGL?5:10:b?7:12;if(this.isExport||!this.viewer.getShowFrank())return!1;if(!this.g3d.setColix(J.util.C.getColixTranslucent3(this.colix,this.g3d.haveTranslucentObjects(),0.5)))return!0;b=this.viewer.getImageFontScaling();a.getFont(b);var b=y(a.frankWidth+4*b),c=a.frankDescent;this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.g3d.getRenderWidth()-b,this.g3d.getRenderHeight()-c,0,0);d&&this.g3d.fillRect(0,0,0,0,2*c,s(3*b/2));
return!1})}),p("J.render"),t(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.util.Logger","J.viewer.JC"],function(){c$=w(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.viewer=null;this.holdRepaint=0;this.repaintPending=!1;u(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);Q(c$,function(){this.bsTranslucent=JU.BS.newN(36)});A(c$,function(){});h(c$,"set",function(a,b){this.viewer=a;this.shapeManager=b},"J.viewer.Viewer,J.viewer.ShapeManager");
h(c$,"isRepaintPending",function(){return this.repaintPending});h(c$,"pushHoldRepaint",function(){++this.holdRepaint},"~S");h(c$,"popHoldRepaint",function(a,b){--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(b)))},"~B,~S");h(c$,"requestRepaintAndWait",function(){"undefined"!=typeof Jmol&&Jmol._repaint&&Jmol._repaint(this.viewer.applet,!1);this.repaintDone()},"~S");h(c$,"repaintIfReady",function(a){if(this.repaintPending)return!1;this.repaintPending=
!0;0==this.holdRepaint&&this.repaintNow(a);return!0},"~S");c(c$,"repaintNow",function(){this.viewer.haveDisplay&&"undefined"!=typeof Jmol&&Jmol._repaint&&Jmol._repaint(this.viewer.applet,!0)},"~S");h(c$,"repaintDone",function(){this.repaintPending=!1});h(c$,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=0;36>a;++a)this.renderers[a]=null},"~N");c(c$,"getRenderer",function(a){if(null!=this.renderers[a])return this.renderers[a];var b=J.viewer.JC.getShapeClassName(a,
!0)+"Renderer";try{var d=Class.forName(b).newInstance();d.setViewerG3dShapeID(this.viewer,a);return this.renderers[a]=d}catch(c){if(C(c,Exception))return J.util.Logger.errorEx("Could not instantiate renderer:"+b,c),null;throw c;}},"~N");h(c$,"render",function(a,b,d,c){var e=this.viewer.getBoolean(603979934);try{a.renderBackground(null);if(d){this.bsTranslucent.clearAll();null!=c&&a.renderCrossHairs(c,this.viewer.getScreenWidth(),this.viewer.getScreenHeight(),this.viewer.getNavigationOffset(),this.viewer.getNavigationDepthPercent());
var f=this.viewer.getRubberBandSelection();null!=f&&a.setColix(this.viewer.getColixRubberband())&&a.drawRect(f.x,f.y,0,0,f.width,f.height)}null==this.renderers&&(this.renderers=Array(36));c=null;for(f=0;36>f&&a.currentlyRendering();++f){var j=this.shapeManager.getShape(f);null!=j&&(e&&(c="rendering "+J.viewer.JC.getShapeClassName(f,!1),J.util.Logger.startTimer(c)),(d||this.bsTranslucent.get(f))&&this.getRenderer(f).renderShape(a,b,j)&&this.bsTranslucent.set(f),e&&J.util.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(h){if(C(h,
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this.hbondsBackbone=this.viewer.getBoolean(603979852);this.bondsBackbone=(new Boolean(this.hbondsBackbone|this.ssbondsBackbone)).valueOf();this.hbondsSolid=this.viewer.getBoolean(603979854);this.isAntialiased=this.g3d.isAntialiased();var b=!1;if(!this.isExport&&this.isPass2)for(var d=this.bsForPass2.nextSetBit(0);0<=d;d=this.bsForPass2.nextSetBit(d+1))this.bond=a[d],this.renderBond();else for(d=this.modelSet.bondCount;0<=--d;)this.bond=a[d],0!=(this.bond.getShapeVisibilityFlags()&this.myVisibilityFlag)&&
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this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB);a>>=1;if(0>=--this.bondOrder)break;this.stepAxisCoordinates()}}}}},"~N");c(c$,"resetAxisCoordinates",function(){var a=this.mag2d>>3;-1!=this.multipleBondSpacing&&0>this.multipleBondSpacing&&(a*=-this.multipleBondSpacing);a=this.width+a;this.dxStep=s(a*this.dy/this.mag2d);this.dyStep=s(a*-this.dx/this.mag2d);
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arguments)},J.script,"ScriptContext"),A(c$,function(){this.id=++J.script.ScriptContext.contextCount}),E(c$,"contextCount",0),p("J.script"),t(["java.lang.Exception"],"J.script.ScriptException",null,function(){c$=w(function(){this.untranslated=this.message=this.eval=null;u(this,arguments)},J.script,"ScriptException",Exception);A(c$,function(a,b,d,c){U(this,J.script.ScriptException,[]);this.eval=a;this.message=b;c&&this.eval.setException(this,b,d)},"J.api.JmolScriptEvaluator,~S,~S,~B");c(c$,"getErrorMessageUntranslated",
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function(){c$=w(function(){this.myMask=0;this.reportAll=!1;this.ptXY=this.selectedBonds=this.bsOrderSet=null;u(this,arguments)},J.shape,"Sticks",J.shape.Shape);Q(c$,function(){this.ptXY=new JU.P3i});c(c$,"initShape",function(){qa(this,J.shape.Sticks,"initShape",[]);this.myMask=1023;this.reportAll=!1});h(c$,"setSize",function(a,b){if(2147483647==a)this.selectedBonds=J.util.BSUtil.copy(b);else if(-2147483648==a)null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS),this.bsOrderSet.or(b);else{null==this.bsSizeSet&&
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new JU.BS);a=b.shortValue();for(d=null!=this.selectedBonds?this.modelSet.getBondIterator(this.selectedBonds):this.modelSet.getBondIteratorForType(65535,d);d.hasNext();)this.bsOrderSet.set(d.nextIndex()),d.next().setOrder(a)}else if("color"===a)if(null==this.bsColixSet&&(this.bsColixSet=new JU.BS),a=J.util.C.getColixO(b),b=r(b,J.constant.EnumPalette)?b:null,b===J.constant.EnumPalette.TYPE||b===J.constant.EnumPalette.ENERGY){var c=b===J.constant.EnumPalette.ENERGY;for(d=null!=this.selectedBonds?this.modelSet.getBondIterator(this.selectedBonds):
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h(c$,"getShapeState",function(){return this.viewer.getBondState(this,this.bsOrderSet,this.reportAll)});h(c$,"checkObjectHovered",function(a,b,d){var c=new JU.P3;a=this.findPickedBond(a,b,d,c);if(null==a)return!1;this.viewer.highlightBond(a.index,!0);return!0},"~N,~N,JU.BS");h(c$,"checkObjectClicked",function(a,b,d,c){d=new JU.P3;a=this.findPickedBond(a,b,c,d);if(null==a)return null;b=a.getAtom1().modelIndex;c=a.getIdentity();var e=new java.util.Hashtable;e.put("pt",d);e.put("index",Integer.$valueOf(a.index));
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c(c$,"addPoint",function(a,b,d,c){a.x-c<b.x&&(b.x=a.x-c);a.x+c>d.x&&(d.x=a.x+c);a.y-c<b.y&&(b.y=a.y-c);a.y+c>d.y&&(d.y=a.y+c);a.z-c<b.z&&(b.z=a.z-c);a.z+c>d.z&&(d.z=a.z+c)},"JU.P3,JU.P3,JU.P3,~N");c$.addPointXYZ=c(c$,"addPointXYZ",function(a,b,d,c,e,f){a-f<c.x&&(c.x=a-f);a+f>e.x&&(e.x=a+f);b-f<c.y&&(c.y=b-f);b+f>e.y&&(e.y=b+f);d-f<c.z&&(c.z=d-f);d+f>e.z&&(e.z=d+f)},"~N,~N,~N,JU.P3,JU.P3,~N");c(c$,"setBbcage",function(a){this.isScaleSet=!0;this.bbCenter.add2(this.bbCorner0,this.bbCorner1);this.bbCenter.scale(0.5);
this.bbVector.sub2(this.bbCorner1,this.bbCenter);0<a?this.bbVector.scale(a):(this.bbVector.x-=a/2,this.bbVector.y-=a/2,this.bbVector.z-=a/2);for(a=8;0<=--a;){var b=this.bbVertices[a];b.setT(J.util.BoxInfo.unitBboxPoints[a]);b.x*=this.bbVector.x;b.y*=this.bbVector.y;b.z*=this.bbVector.z;b.add(this.bbCenter)}this.bbCorner0.setT(this.bbVertices[0]);this.bbCorner1.setT(this.bbVertices[7])},"~N");c(c$,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&
a.y>=this.bbCorner0.y&&a.y<=this.bbCorner1.y&&a.z>=this.bbCorner0.z&&a.z<=this.bbCorner1.z},"JU.P3");E(c$,"bbcageTickEdges","z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""),"uccageTickEdges","zyx\x00\x00\x00\x00\x00\x00\x00\x00\x00".split(""),"edges",[0,1,0,2,0,4,1,3,1,5,2,3,2,6,3,7,4,5,4,6,5,7,6,7]);c$.unitCubePoints=c$.prototype.unitCubePoints=[JU.P3.new3(0,0,0),JU.P3.new3(0,0,1),JU.P3.new3(0,1,0),JU.P3.new3(0,1,1),JU.P3.new3(1,0,0),JU.P3.new3(1,0,1),JU.P3.new3(1,1,0),JU.P3.new3(1,1,1)];c$.facePoints=
c$.prototype.facePoints=[JU.P3i.new3(4,0,6),JU.P3i.new3(4,6,5),JU.P3i.new3(5,7,1),JU.P3i.new3(1,3,0),JU.P3i.new3(6,2,7),JU.P3i.new3(1,0,5)];E(c$,"toCanonical",[0,3,4,7,1,2,5,6]);c$.cubeVertexOffsets=c$.prototype.cubeVertexOffsets=[JU.P3i.new3(0,0,0),JU.P3i.new3(1,0,0),JU.P3i.new3(1,0,1),JU.P3i.new3(0,0,1),JU.P3i.new3(0,1,0),JU.P3i.new3(1,1,0),JU.P3i.new3(1,1,1),JU.P3i.new3(0,1,1)];c$.unitBboxPoints=c$.prototype.unitBboxPoints=Array(8)}),p("J.util"),t(["JU.BS"],"J.util.BSUtil",null,function(){c$=M(J.util,
"BSUtil");c$.newAndSetBit=c(c$,"newAndSetBit",function(a){var b=J.util.BSUtil.newBitSet(a+1);b.set(a);return b},"~N");c$.areEqual=c(c$,"areEqual",function(a,b){return null==a||null==b?null==a&&null==b:a.equals(b)},"JU.BS,JU.BS");c$.haveCommon=c(c$,"haveCommon",function(a,b){return null==a||null==b?!1:a.intersects(b)},"JU.BS,JU.BS");c$.cardinalityOf=c(c$,"cardinalityOf",function(a){return null==a?0:a.cardinality()},"JU.BS");c$.newBitSet2=c(c$,"newBitSet2",function(a,b){var d=J.util.BSUtil.newBitSet(b);
d.setBits(a,b);return d},"~N,~N");c$.setAll=c(c$,"setAll",function(a){var b=J.util.BSUtil.newBitSet(a);b.setBits(0,a);return b},"~N");c$.andNot=c(c$,"andNot",function(a,b){null!=b&&null!=a&&a.andNot(b);return a},"JU.BS,JU.BS");c$.copy=c(c$,"copy",function(a){return null==a?null:a.clone()},"JU.BS");c$.copy2=c(c$,"copy2",function(a,b){if(null==a||null==b)return null;b.clearAll();b.or(a);return b},"JU.BS,JU.BS");c$.copyInvert=c(c$,"copyInvert",function(a,b){return null==a?null:J.util.BSUtil.andNot(J.util.BSUtil.setAll(b),
a)},"JU.BS,~N");c$.invertInPlace=c(c$,"invertInPlace",function(a,b){return J.util.BSUtil.copy2(J.util.BSUtil.copyInvert(a,b),a)},"JU.BS,~N");c$.toggleInPlace=c(c$,"toggleInPlace",function(a,b){a.equals(b)?a.clearAll():0==J.util.BSUtil.andNot(J.util.BSUtil.copy(b),a).length()?J.util.BSUtil.andNot(a,b):a.or(b);return a},"JU.BS,JU.BS");c$.deleteBits=c(c$,"deleteBits",function(a,b){if(null==a||null==b)return a;var d=b.nextSetBit(0);if(0>d)return a;var c=a.length(),e=Math.min(c,b.length()),f;for(f=b.nextClearBit(d);f<
e&&0<=f;f=b.nextClearBit(f+1))a.setBitTo(d++,a.get(f));for(f=e;f<c;f++)a.setBitTo(d++,a.get(f));d<c&&a.clearBits(d,c);return a},"JU.BS,JU.BS");c$.newBitSet=c(c$,"newBitSet",function(a){return JU.BS.newN(a)},"~N");c$.offset=c(c$,"offset",function(a,b,d){if(null!=a){for(var c=JU.BS.newN(a.length()+d),e=a.nextSetBit(0);e>=b;e=a.nextSetBit(e+1))c.set(e+d);J.util.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");c$.setMapBitSet=c(c$,"setMapBitSet",function(a,b,d,c){var e;a.containsKey(c)?e=a.get(c):a.put(c,e=new JU.BS);
e.setBits(b,d+1)},"java.util.Map,~N,~N,~S");c$.emptySet=c$.prototype.emptySet=new JU.BS}),p("J.util"),t(["J.util.Int2IntHash"],"J.util.C","java.lang.Byte $.Float JU.AU $.CU $.PT $.SB J.constant.EnumPalette J.util.Escape $.Logger".split(" "),function(){c$=M(J.util,"C");A(c$,function(){});c$.getColix=c(c$,"getColix",function(a){if(0==a)return 0;var d=0;-16777216!=(a&4278190080)&&(d=J.util.C.getTranslucentFlag(a>>24&255),a|=4278190080);var c=J.util.C.colixHash.get(a);3==(c&3)&&(d=0);return(0<c?c:J.util.C.allocateColix(a))|
d},"~N");c$.allocateColix=c(c$,"allocateColix",function(a){for(var d=J.util.C.colixMax;4<=--d;)if((a&16777215)==(J.util.C.argbs[d]&16777215))return d;J.util.C.colixMax==J.util.C.argbs.length&&(d=2*J.util.C.colixMax,2048<d&&(d=2048),J.util.C.argbs=JU.AU.arrayCopyI(J.util.C.argbs,d),null!=J.util.C.argbsGreyscale&&(J.util.C.argbsGreyscale=JU.AU.arrayCopyI(J.util.C.argbsGreyscale,d)));J.util.C.argbs[J.util.C.colixMax]=a;null!=J.util.C.argbsGreyscale&&(J.util.C.argbsGreyscale[J.util.C.colixMax]=JU.CU.toFFGGGfromRGB(a));
J.util.C.colixHash.put(a,J.util.C.colixMax);return 2047>J.util.C.colixMax?J.util.C.colixMax++:J.util.C.colixMax},"~N");c$.setLastGrey=c(c$,"setLastGrey",function(a){J.util.C.calcArgbsGreyscale();J.util.C.argbsGreyscale[2047]=JU.CU.toFFGGGfromRGB(a)},"~N");c$.calcArgbsGreyscale=c(c$,"calcArgbsGreyscale",function(){if(null==J.util.C.argbsGreyscale){for(var a=D(J.util.C.argbs.length,0),d=J.util.C.argbs.length;4<=--d;)a[d]=JU.CU.toFFGGGfromRGB(J.util.C.argbs[d]);J.util.C.argbsGreyscale=a}});c$.getArgbGreyscale=
c(c$,"getArgbGreyscale",function(a){null==J.util.C.argbsGreyscale&&J.util.C.calcArgbsGreyscale();return J.util.C.argbsGreyscale[a&-30721]},"~N");c$.getColixO=c(c$,"getColixO",function(a){if(null==a)return 0;if(r(a,J.constant.EnumPalette))return a===J.constant.EnumPalette.NONE?0:2;if(r(a,Integer))return J.util.C.getColix(a.intValue());if(r(a,String))return J.util.C.getColixS(a);if(r(a,Byte))return 0==a.byteValue()?0:2;J.util.Logger.debugging&&J.util.Logger.debug("?? getColix("+a+")");return 22},"~O");
c$.getTranslucentFlag=c(c$,"getTranslucentFlag",function(a){return 0==a?0:0>a?30720:Float.isNaN(a)||255<=a||1==a?16384:(s(Math.floor(1>a?256*a:9>=a?s(Math.floor(a-1))<<5:15>a?256:a))>>5&15)<<11},"~N");c$.isColixLastAvailable=c(c$,"isColixLastAvailable",function(a){return 0<a&&2047==(a&2047)},"~N");c$.getArgb=c(c$,"getArgb",function(a){return J.util.C.argbs[a&-30721]},"~N");c$.isColixColorInherited=c(c$,"isColixColorInherited",function(a){switch(a){case 0:case 1:return!0;default:return 1==(a&-30721)}},
"~N");c$.getColixInherited=c(c$,"getColixInherited",function(a,d){switch(a){case 0:return d;case 1:return d&-30721;default:return 1==(a&-30721)?d&-30721|a&30720:a}},"~N,~N");c$.isColixTranslucent=c(c$,"isColixTranslucent",function(a){return 0!=(a&30720)},"~N");c$.getChangeableColixIndex=c(c$,"getChangeableColixIndex",function(a){return 0<=a?-1:a&2047},"~N");c$.getColixTranslucent3=c(c$,"getColixTranslucent3",function(a,d,c){a&=-30721;0==a&&(a=1);return d?a|J.util.C.getTranslucentFlag(c):a},"~N,~B,~N");
c$.copyColixTranslucency=c(c$,"copyColixTranslucency",function(a,d){return J.util.C.getColixTranslucent3(d,J.util.C.isColixTranslucent(a),J.util.C.getColixTranslucencyLevel(a))},"~N,~N");c$.getColixTranslucencyFractional=c(c$,"getColixTranslucencyFractional",function(a){a=J.util.C.getColixTranslucencyLevel(a);return-1==a?0.5:0==a?0:255==a?1:a/256},"~N");c$.getColixTranslucencyLevel=c(c$,"getColixTranslucencyLevel",function(a){a=a>>11&15;switch(a){case 0:return 0;case 1:case 2:case 3:case 4:case 5:case 6:case 7:return a<<
5;case 15:return-1;default:return 255}},"~N");c$.getColixS=c(c$,"getColixS",function(a){var d=JU.CU.getArgbFromString(a);return 0!=d?J.util.C.getColix(d):"none".equalsIgnoreCase(a)?0:"opaque".equalsIgnoreCase(a)?1:2},"~S");c$.getColixArray=c(c$,"getColixArray",function(a){if(null==a||0==a.length)return null;a=JU.PT.getTokens(a);for(var d=da(a.length,0),c=0;c<a.length;c++)if(d[c]=J.util.C.getColix(JU.CU.getArgbFromString(a[c])),0==d[c])return null;return d},"~S");c$.getHexCode=c(c$,"getHexCode",function(a){return J.util.Escape.escapeColor(J.util.C.getArgb(a))},
"~N");c$.getHexCodes=c(c$,"getHexCodes",function(a){if(null==a)return null;for(var d=new JU.SB,c=0;c<a.length;c++)d.append(0==c?"":" ").append(J.util.C.getHexCode(a[c]));return d.toString()},"~A");c$.getColixTranslucent=c(c$,"getColixTranslucent",function(a){var d=a>>24&255;return 255==d?J.util.C.getColix(a):J.util.C.getColixTranslucent3(J.util.C.getColix(a),!0,d/255)},"~N");c$.getBgContrast=c(c$,"getBgContrast",function(a){return 128>(JU.CU.toFFGGGfromRGB(a)&255)?8:4},"~N");E(c$,"INHERIT_ALL",0,
"INHERIT_COLOR",1,"USE_PALETTE",2,"RAW_RGB",3,"SPECIAL_COLIX_MAX",4,"colixMax",4,"argbs",D(128,0),"argbsGreyscale",null);c$.colixHash=c$.prototype.colixHash=new J.util.Int2IntHash(256);E(c$,"RAW_RGB_INT",3,"UNMASK_CHANGEABLE_TRANSLUCENT",2047,"CHANGEABLE_MASK",32768,"LAST_AVAILABLE_COLIX",2047,"TRANSLUCENT_SHIFT",11,"ALPHA_SHIFT",13,"TRANSLUCENT_MASK",30720,"TRANSLUCENT_SCREENED",30720,"TRANSPARENT",16384,"OPAQUE_MASK",-30721,"BLACK",4,"ORANGE",5,"PINK",6,"BLUE",7,"WHITE",8,"CYAN",9,"RED",10,"GREEN",
11,"GRAY",12,"SILVER",13,"LIME",14,"MAROON",15,"NAVY",16,"OLIVE",17,"PURPLE",18,"TEAL",19,"MAGENTA",20,"YELLOW",21,"HOTPINK",22,"GOLD",23,"predefinedArgbs",[4278190080,4294944E3,4294951115,4278190335,4294967295,4278255615,4294901760,4278222848,4286611584,4290822336,4278255360,4286578688,4278190208,4286611456,4286578816,4278222976,4294902015,4294967040,4294928820,4294956800]);for(var a=0;a<J.util.C.predefinedArgbs.length;++a)J.util.C.getColix(J.util.C.predefinedArgbs[a])}),p("J.util"),t(null,"J.util.ColorEncoder",
"java.lang.Boolean $.Float java.util.Hashtable JU.AU $.CU $.List $.PT J.constant.EnumPalette J.util.C $.Escape $.Logger J.viewer.JC".split(" "),function(){c$=w(function(){this.argbsAmino=this.argbsShapely=this.argbsRwb=this.argbsRoygb=this.argbsCpk=this.paletteFriendly=this.paletteWB=this.paletteBW=null;this.ihalf=0;this.schemes=null;this.currentPalette=0;this.currentSegmentCount=1;this.isTranslucent=!1;this.hi=this.lo=0;this.isReversed=!1;this.thisScale=this.userScale=null;this.thisName="scheme";
this.isColorIndex=!1;this.propertyColorEncoder=null;u(this,arguments)},J.util,"ColorEncoder");Q(c$,function(){this.userScale=[-8355712];this.thisScale=[-8355712]});A(c$,function(a){null==a?(this.schemes=new java.util.Hashtable,this.argbsCpk=J.constant.EnumPalette.argbsCpk,this.argbsRoygb=J.viewer.JC.argbsRoygbScale,this.argbsRwb=J.viewer.JC.argbsRwbScale,this.argbsShapely=J.viewer.JC.argbsShapely,this.argbsAmino=J.viewer.JC.argbsAmino,this.ihalf=s(J.viewer.JC.argbsRoygbScale.length/3),this.propertyColorEncoder=
this):(this.propertyColorEncoder=a,this.schemes=a.schemes)},"J.util.ColorEncoder");c$.getSchemeIndex=c(c$,"getSchemeIndex",function(a){for(var b=0;b<J.util.ColorEncoder.colorSchemes.length;b++)if(J.util.ColorEncoder.colorSchemes[b].equalsIgnoreCase(a))return 16<=b?b-16:13>b?b:-b;return-1},"~S");c$.fixName=c(c$,"fixName",function(a){if(a.equalsIgnoreCase("byelement"))return"byelement_jmol";var b=J.util.ColorEncoder.getSchemeIndex(a);return 0<=b?J.util.ColorEncoder.colorSchemes[b]:a.toLowerCase()},
"~S");c(c$,"makeColorScheme",function(a,b,d){a=J.util.ColorEncoder.fixName(a);if(null==b){this.schemes.remove(a);a=this.createColorScheme(a,!1,d);if(d)switch(a){case 12:this.paletteFriendly=this.getPaletteAC();break;case 10:this.paletteBW=this.getPaletteBW();break;case 11:this.paletteWB=this.getPaletteWB();break;case 0:case 1:this.argbsRoygb=J.viewer.JC.argbsRoygbScale;break;case 6:case 7:this.argbsRwb=J.viewer.JC.argbsRwbScale;break;case 2:this.argbsCpk=J.constant.EnumPalette.argbsCpk;break;case 3:J.util.ColorEncoder.getRasmolScale();
break;case 5:this.argbsAmino=J.viewer.JC.argbsAmino;break;case 4:this.argbsShapely=J.viewer.JC.argbsShapely}return 2147483647==a?0:a}this.schemes.put(a,b);this.setThisScheme(a,b);a=this.createColorScheme(a,!1,d);if(d)switch(a){case 10:this.paletteBW=this.thisScale;break;case 11:this.paletteWB=this.thisScale;break;case 0:case 1:this.argbsRoygb=this.thisScale;this.ihalf=s(this.argbsRoygb.length/3);break;case 6:case 7:this.argbsRwb=this.thisScale;break;case 2:this.argbsCpk=this.thisScale;break;case 5:this.argbsAmino=
this.thisScale;break;case 4:this.argbsShapely=this.thisScale}return-1},"~S,~A,~B");c(c$,"createColorScheme",function(a,b,d){a=a.toLowerCase();if(a.equals("inherit"))return 15;var c=Math.max(a.indexOf("="),a.indexOf("["));if(0<=c){b=JU.PT.replaceAllCharacters(a.substring(0,c)," =","");0<b.length&&(d=!0);var e=0;a.length>c+1&&!a.contains("[")&&(a="["+a.substring(c+1).trim()+"]",a=JU.PT.simpleReplace(a.$replace("\n"," "),"  "," "),a=JU.PT.simpleReplace(a,", ",",").$replace(" ",","),a=JU.PT.simpleReplace(a,
",","]["));for(c=-1;0<=(c=a.indexOf("[",c+1));)e++;if(0==e)return this.makeColorScheme(b,null,d);for(var f=D(e,0),e=0;0<=(c=a.indexOf("[",c+1));){var j=a.indexOf("]",c);0>j&&(j=a.length-1);var h=JU.CU.getArgbFromString(a.substring(c,j+1));0==h&&(h=JU.CU.getArgbFromString(a.substring(c+1,j).trim()));if(0==h)return J.util.Logger.error("error in color value: "+a.substring(c,j+1)),0;f[e++]=h}return b.equals("user")?(this.setUserScale(f),-13):this.makeColorScheme(b,f,d)}a=J.util.ColorEncoder.fixName(a);
d=J.util.ColorEncoder.getSchemeIndex(a);return this.schemes.containsKey(a)?(this.setThisScheme(a,this.schemes.get(a)),d):-1!=d?d:b?0:2147483647},"~S,~B,~B");c(c$,"setUserScale",function(a){this.propertyColorEncoder.userScale=a;this.makeColorScheme("user",a,!1)},"~A");c(c$,"getColorSchemeArray",function(a){switch(a){case -1:return this.thisScale;case 0:return this.propertyColorEncoder.argbsRoygb;case 1:return JU.AU.arrayCopyRangeRevI(this.propertyColorEncoder.argbsRoygb,0,-1);case 8:return JU.AU.arrayCopyRangeI(this.propertyColorEncoder.argbsRoygb,
0,this.propertyColorEncoder.ihalf);case 9:var b=JU.AU.arrayCopyRangeI(this.propertyColorEncoder.argbsRoygb,this.propertyColorEncoder.argbsRoygb.length-2*this.propertyColorEncoder.ihalf,-1);a=D(this.propertyColorEncoder.ihalf,0);for(var d=a.length,c=b.length;0<=--d&&0<=--c;)a[d]=b[c--];return a;case 12:return this.getPaletteAC();case 10:return this.getPaletteBW();case 11:return this.getPaletteWB();case 6:return this.propertyColorEncoder.argbsRwb;case 7:return JU.AU.arrayCopyRangeRevI(this.propertyColorEncoder.argbsRwb,
0,-1);case 2:return this.propertyColorEncoder.argbsCpk;case 3:return J.util.ColorEncoder.getRasmolScale();case 4:return this.propertyColorEncoder.argbsShapely;case 5:return this.propertyColorEncoder.argbsAmino;case -13:return this.propertyColorEncoder.userScale;case -14:return JU.AU.arrayCopyRangeRevI(this.propertyColorEncoder.userScale,0,-1);default:return null}},"~N");c(c$,"getColorIndexFromPalette",function(a,b,d,c,e){c=J.util.C.getColix(this.getArgbFromPalette(a,b,d,c));e&&(a=(d-a)/(d-b),1<a?
a=1:0.125>a&&(a=0.125),c=J.util.C.getColixTranslucent3(c,!0,a));return c},"~N,~N,~N,~N,~B");c(c$,"getPaletteColorCount",function(a){switch(a){case -1:return this.thisScale.length;case 10:case 11:return this.getPaletteBW().length;case 0:case 1:return this.propertyColorEncoder.argbsRoygb.length;case 8:case 9:return this.propertyColorEncoder.ihalf;case 6:case 7:return this.propertyColorEncoder.argbsRwb.length;case -13:case -14:return this.propertyColorEncoder.userScale.length;case 2:return this.argbsCpk.length;
case 3:return J.util.ColorEncoder.getRasmolScale().length;case 4:return this.propertyColorEncoder.argbsShapely.length;case 5:return this.propertyColorEncoder.argbsAmino.length;case 12:return this.getPaletteAC().length;default:return 0}},"~N");c(c$,"getArgbFromPalette",function(a,b,d,c){if(Float.isNaN(a))return-8355712;var e=this.getPaletteColorCount(c);switch(c){case -1:return this.isColorIndex&&(b=0,d=this.thisScale.length),this.thisScale[J.util.ColorEncoder.quantize(a,b,d,e)];case 10:return this.getPaletteBW()[J.util.ColorEncoder.quantize(a,
b,d,e)];case 11:return this.getPaletteWB()[J.util.ColorEncoder.quantize(a,b,d,e)];case 0:return this.propertyColorEncoder.argbsRoygb[J.util.ColorEncoder.quantize(a,b,d,e)];case 1:return this.propertyColorEncoder.argbsRoygb[J.util.ColorEncoder.quantize(-a,-d,-b,e)];case 8:return this.propertyColorEncoder.argbsRoygb[J.util.ColorEncoder.quantize(a,b,d,e)];case 9:return this.propertyColorEncoder.argbsRoygb[this.propertyColorEncoder.ihalf+2*J.util.ColorEncoder.quantize(a,b,d,e)];case 6:return this.propertyColorEncoder.argbsRwb[J.util.ColorEncoder.quantize(a,
b,d,e)];case 7:return this.propertyColorEncoder.argbsRwb[J.util.ColorEncoder.quantize(-a,-d,-b,e)];case -13:return 0==this.propertyColorEncoder.userScale.length?-8355712:this.propertyColorEncoder.userScale[J.util.ColorEncoder.quantize(a,b,d,e)];case -14:return 0==this.propertyColorEncoder.userScale.length?-8355712:this.propertyColorEncoder.userScale[J.util.ColorEncoder.quantize(-a,-d,-b,e)];case 2:return this.propertyColorEncoder.argbsCpk[J.util.ColorEncoder.colorIndex(a,e)];case 3:return J.util.ColorEncoder.getRasmolScale()[J.util.ColorEncoder.colorIndex(a,
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c(c$,"getColorSchemeName",function(a){var b=Math.abs(a);return-1==a?this.thisName:b<J.util.ColorEncoder.colorSchemes.length&&0<=b?J.util.ColorEncoder.colorSchemes[b]:null},"~N");c$.getColorSchemeList=c(c$,"getColorSchemeList",function(a){if(null==a)return"";for(var b="",d=0;d<a.length;d++)b+=(0==d?"":" ")+J.util.Escape.escapeColor(a[d]);return b},"~A");c$.getRasmolScale=c(c$,"getRasmolScale",function(){if(null!=J.util.ColorEncoder.rasmolScale)return J.util.ColorEncoder.rasmolScale;J.util.ColorEncoder.rasmolScale=
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b){return s(Math.floor(0>=a||a>=b?0:a))},"~N,~N");c$.colorIndexRepeat=c(c$,"colorIndexRepeat",function(a,b){return s(Math.floor(0>=a?0:a))%b},"~N,~N");c(c$,"getColorScheme",function(){return(this.isTranslucent?"translucent ":"")+(0>this.currentPalette?J.util.ColorEncoder.getColorSchemeList(this.getColorSchemeArray(this.currentPalette)):this.getColorSchemeName(this.currentPalette))});c$.RGBtoHSL=c(c$,"RGBtoHSL",function(a,b,d,c){a/=255;b/=255;d/=255;1<a&&(a=1);1<b&&(b=1);1<d&&(d=1);var e=Math.min(a,
Math.min(b,d)),f=Math.max(a,Math.max(b,d)),j=0;f==e?j=0:f==a?j=(60*(b-d)/(f-e)+360)%360:f==b?j=60*(d-a)/(f-e)+120:f==d&&(j=60*(a-b)/(f-e)+240);a=(f+e)/2;c[0]=j/360;c[1]=f==e?0:0.5>=a?(f-e)/(f+e):(f-e)/(2-f-e);c[2]=a},"~N,~N,~N,~A");E(c$,"GRAY",4286611584,"BYELEMENT_PREFIX","byelement","BYRESIDUE_PREFIX","byresidue");c$.BYELEMENT_JMOL=c$.prototype.BYELEMENT_JMOL="byelement_jmol";c$.BYELEMENT_RASMOL=c$.prototype.BYELEMENT_RASMOL="byelement_rasmol";c$.BYRESIDUE_SHAPELY=c$.prototype.BYRESIDUE_SHAPELY=
"byresidue_shapely";c$.BYRESIDUE_AMINO=c$.prototype.BYRESIDUE_AMINO="byresidue_amino";E(c$,"CUSTOM",-1,"ROYGB",0,"BGYOR",1,"JMOL",2,"RASMOL",3,"SHAPELY",4,"AMINO",5,"RWB",6,"BWR",7,"LOW",8,"HIGH",9,"BW",10,"WB",11,"FRIENDLY",12,"USER",-13,"RESU",-14,"INHERIT",15,"ALT",16);c$.colorSchemes=c$.prototype.colorSchemes="roygb bgyor byelement_jmol byelement_rasmol byresidue_shapely byresidue_amino rwb bwr low high bw wb friendly user resu inherit rgb bgr jmol rasmol byresidue".split(" ");E(c$,"rasmolScale",
null)}),p("J.util"),t(null,"J.util.CommandHistory",["JU.List"],function(){c$=w(function(){this.commandList=null;this.maxSize=100;this.cursorPos=this.nextCommand=0;this.isOn=!0;u(this,arguments)},J.util,"CommandHistory");A(c$,function(){this.reset(100)});c(c$,"clear",function(){this.reset(this.maxSize)});c(c$,"reset",function(a){this.maxSize=a;this.commandList=new JU.List;this.nextCommand=0;this.commandList.addLast("");this.cursorPos=0},"~N");c(c$,"setMaxSize",function(a){if(a!=this.maxSize){for(2>
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case 1:return this.getCommandDown();default:if(0>a)return this.setMaxSize(-2-a),"";a=Math.max(this.nextCommand-a,0)}for(var b="";a<this.nextCommand;a++)this.commandList.get(a).toUpperCase().startsWith("WRITE HISTORY")||(b+=this.commandList.get(a)+"\n");return b},"~N");c(c$,"removeCommand",function(){return this.removeCommand(this.nextCommand-1)});c(c$,"removeCommand",function(a){if(0>a||a>=this.nextCommand)return"";a=this.commandList.remove(a);this.nextCommand--;return a},"~N");c(c$,"addCommandLine",
function(a){if(!(null==a||0==a.length)&&!a.endsWith("#--"))this.nextCommand>=this.maxSize&&(this.commandList.remove(0),this.nextCommand=this.maxSize-1),this.commandList.add(this.nextCommand,a),this.nextCommand++,this.cursorPos=this.nextCommand,this.commandList.add(this.nextCommand,"")},"~S");E(c$,"ERROR_FLAG","#??","NOHISTORYLINE_FLAG","#--","NOHISTORYATALL_FLAG","#----","DEFAULT_MAX_SIZE",100)}),p("J.util"),t(["J.util.LoggerInterface"],"J.util.DefaultLogger",["J.util.Logger"],function(){c$=M(J.util,
"DefaultLogger",null,J.util.LoggerInterface);c(c$,"log",function(a,b,d,c){a===System.err&&System.out.flush();if(null!=a&&(null!=d||null!=c))if(a.println((J.util.Logger.logLevel()?"["+J.util.Logger.getLevel(b)+"] ":"")+(null!=d?d:"")+(null!=c?": "+c.toString():"")),null!=c&&(b=c.getStackTrace(),null!=b))for(d=0;d<b.length;d++)a.println(b[d].getClassName()+" - "+b[d].getLineNumber()+" - "+b[d].getMethodName());a===System.err&&System.err.flush()},"java.io.PrintStream,~N,~S,Throwable");h(c$,"debug",function(a){this.log(System.out,
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"J.util.Elements",["java.lang.Character","java.util.Hashtable","JU.PT","J.util.Logger"],function(){c$=M(J.util,"Elements");c$.getAtomicMass=c(c$,"getAtomicMass",function(a){return 1>a||a>=J.util.Elements.atomicMass.length?0:J.util.Elements.atomicMass[a]},"~N");c$.elementNumberFromSymbol=c(c$,"elementNumberFromSymbol",function(a,d){if(null==J.util.Elements.htElementMap){for(var c=new java.util.Hashtable,e=J.util.Elements.elementNumberMax;0<=--e;){var f=J.util.Elements.elementSymbols[e],j=Integer.$valueOf(e);
c.put(f,j);2==f.length&&c.put(f.toUpperCase(),j)}for(e=J.util.Elements.altElementMax;4<=--e;)f=J.util.Elements.altElementSymbols[e],j=Integer.$valueOf(J.util.Elements.altElementNumbers[e]),c.put(f,j),2==f.length&&c.put(f.toUpperCase(),j);J.util.Elements.htElementMap=c}if(null==a)return 0;c=J.util.Elements.htElementMap.get(a);if(null!=c)return c.intValue();if(Character.isDigit(a.charAt(0))&&(f=a.length-2,0<=f&&Character.isDigit(a.charAt(f))&&f++,c=0<f?JU.PT.parseInt(a.substring(0,f)):0,0<c&&(f=J.util.Elements.elementNumberFromSymbol(a.substring(f),
!0),0<f)))return c=J.util.Elements.getAtomicAndIsotopeNumber(f,c),J.util.Elements.htElementMap.put(a.toUpperCase(),Integer.$valueOf(c)),c;d||J.util.Logger.error("'"+a+"' is not a recognized symbol");return 0},"~S,~B");c$.elementSymbolFromNumber=c(c$,"elementSymbolFromNumber",function(a){var d=0;if(a>=J.util.Elements.elementNumberMax){for(d=J.util.Elements.altElementMax;0<=--d;)if(a==J.util.Elements.altElementNumbers[d])return J.util.Elements.altElementSymbols[d];d=J.util.Elements.getIsotopeNumber(a);
return""+d+J.util.Elements.getElementSymbol(a%128)}return J.util.Elements.getElementSymbol(a)},"~N");c$.getElementSymbol=c(c$,"getElementSymbol",function(a){if(0>a||a>=J.util.Elements.elementNumberMax)a=0;return J.util.Elements.elementSymbols[a]},"~N");c$.elementNameFromNumber=c(c$,"elementNameFromNumber",function(a){if(a>=J.util.Elements.elementNumberMax){for(var d=J.util.Elements.altElementMax;0<=--d;)if(a==J.util.Elements.altElementNumbers[d])return J.util.Elements.altElementNames[d];a%=128}if(0>
a||a>=J.util.Elements.elementNumberMax)a=0;return J.util.Elements.elementNames[a]},"~N");c$.altElementNameFromIndex=c(c$,"altElementNameFromIndex",function(a){return J.util.Elements.altElementNames[a]},"~N");c$.altElementNumberFromIndex=c(c$,"altElementNumberFromIndex",function(a){return J.util.Elements.altElementNumbers[a]},"~N");c$.altElementSymbolFromIndex=c(c$,"altElementSymbolFromIndex",function(a){return J.util.Elements.altElementSymbols[a]},"~N");c$.altIsotopeSymbolFromIndex=c(c$,"altIsotopeSymbolFromIndex",
function(a){a=J.util.Elements.altElementNumbers[a];return(a>>7)+J.util.Elements.elementSymbolFromNumber(a&127)},"~N");c$.altIsotopeSymbolFromIndex2=c(c$,"altIsotopeSymbolFromIndex2",function(a){a=J.util.Elements.altElementNumbers[a];return J.util.Elements.elementSymbolFromNumber(a&127)+(a>>7)},"~N");c$.getElementNumber=c(c$,"getElementNumber",function(a){return a&127},"~N");c$.getIsotopeNumber=c(c$,"getIsotopeNumber",function(a){return a>>7},"~N");c$.getAtomicAndIsotopeNumber=c(c$,"getAtomicAndIsotopeNumber",
function(a,d){return(0>a?0:a)+(0>=d?0:d<<7)},"~N,~N");c$.altElementIndexFromNumber=c(c$,"altElementIndexFromNumber",function(a){for(var d=0;d<J.util.Elements.altElementMax;d++)if(J.util.Elements.altElementNumbers[d]==a)return d;return 0},"~N");c$.getNaturalIsotope=c(c$,"getNaturalIsotope",function(a){for(var d=0;d<J.util.Elements.naturalIsotopeMasses.length;d+=2)if(J.util.Elements.naturalIsotopeMasses[d]==a)return J.util.Elements.naturalIsotopeMasses[++d];return 0},"~N");c$.isNaturalIsotope=c(c$,
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d,c){d=(a<<4)+(d+4);for(var e=0,f=0,j=0,h=s(c.length/2);j!=h;)if(f=s((j+h)/2),e=c[f<<1],e>d)h=f;else if(e<d)j=f+1;else return c[(f<<1)+1]/1E3;e>d&&f--;e=c[f<<1];a!=e>>4&&f++;return c[(f<<1)+1]/1E3},"~N,~N,~A");c$.getVanderwaalsMar=c(c$,"getVanderwaalsMar",function(a,d){return J.util.Elements.vanderwaalsMars[((a&127)<<2)+d.pt%4]},"~N,J.constant.EnumVdw");c$.getHydrophobicity=c(c$,"getHydrophobicity",function(a){return 1>a||a>=J.util.Elements.hydrophobicities.length?0:J.util.Elements.hydrophobicities[a]},
"~N");c$.getAllredRochowElectroNeg=c(c$,"getAllredRochowElectroNeg",function(a){return 0<a&&a<J.util.Elements.electroNegativities.length?J.util.Elements.electroNegativities[a]:0},"~N");c$.isElement=c(c$,"isElement",function(a,d){return(a&127)==d},"~N,~N");E(c$,"elementSymbols","Xx H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt".split(" "),
"atomicMass",[0,1.008,4.003,6.941,9.012,10.81,12.011,14.007,15.999,18.998,20.18,22.99,24.305,26.981,28.086,30.974,32.07,35.453,39.948,39.1,40.08,44.956,47.88,50.941,52,54.938,55.847,58.93,58.69,63.55,65.39,69.72,72.61,74.92,78.96,79.9,83.8,85.47,87.62,88.91,91.22,92.91,95.94,98.91,101.07,102.91,106.42,107.87,112.41,114.82,118.71,121.75,127.6,126.91,131.29,132.91,137.33,138.91,140.12,140.91,144.24,144.9,150.36,151.96,157.25,158.93,162.5,164.93,167.26,168.93,173.04,174.97,178.49,180.95,183.85,186.21,
190.2,192.22,195.08,196.97,200.59,204.38,207.2,208.98,210,210,222,223,226.03,227.03,232.04,231.04,238.03,237.05,239.1,243.1,247.1,247.1,252.1,252.1,257.1,256.1,259.1,260.1,261,262,263,262,265,268]);c$.elementNumberMax=c$.prototype.elementNumberMax=J.util.Elements.elementSymbols.length;E(c$,"htElementMap",null,"elementNames","unknown hydrogen helium lithium beryllium boron carbon nitrogen oxygen fluorine neon sodium magnesium aluminum silicon phosphorus sulfur chlorine argon potassium calcium scandium titanium vanadium chromium manganese iron cobalt nickel copper zinc gallium germanium arsenic selenium bromine krypton rubidium strontium yttrium zirconium niobium molybdenum technetium ruthenium rhodium palladium silver cadmium indium tin antimony tellurium iodine xenon cesium barium lanthanum cerium praseodymium neodymium promethium samarium europium gadolinium terbium dysprosium holmium erbium thulium ytterbium lutetium hafnium tantalum tungsten rhenium osmium iridium platinum gold mercury thallium lead bismuth polonium astatine radon francium radium actinium thorium protactinium uranium neptunium plutonium americium curium berkelium californium einsteinium fermium mendelevium nobelium lawrencium rutherfordium dubnium seaborgium bohrium hassium meitnerium".split(" "),
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a.size(),d=Array(b+1);d[0]=new JU.P3;if(0<b){for(var c=0;c<b;c++)d[0].add(d[c+1]=a.get(c));d[0].scale(1/b)}return d},"JU.List");c$.getTransformMatrix4=c(c$,"getTransformMatrix4",function(a,b,d,c){a=J.util.Measure.getCenterAndPoints(a);var e=J.util.Measure.getCenterAndPoints(b);b=O(2,0);var f=J.util.Measure.calculateQuaternionRotation([a,e],b,!0),e=JU.V3.newVsub(e[0],a[0]);d.setMV(f.getMatrix(),e);null!=c&&c.setT(a[0]);return b[1]},"JU.List,JU.List,JU.M4,JU.P3");c$.calculateQuaternionRotation=c(c$,
"calculateQuaternionRotation",function(a,b,d){b[1]=NaN;var c=new J.util.Quaternion;if(1==a[0].length||a[0].length!=a[1].length)return c;var e=a[0].length-1;if(d)for(var f=1;f<=e;f++){var j=a[0][f],h=a[1][f];if(r(j,J.modelset.Atom)&&r(h,J.modelset.Atom))J.util.Logger.info(" atom 1 "+j.getInfo()+"\tatom 2 "+h.getInfo());else break}if(2>e)return c;for(var l=d=0,m=0,n=0,q=0,p=0,x=0,s=0,t=0,u=new JU.P3,w=new JU.P3,f=e+1;1<=--f;)j=a[0][f],h=a[1][f],u.sub2(j,a[0][0]),w.sub2(h,a[0][1]),d+=u.x*w.x,l+=u.x*
w.y,m+=u.x*w.z,n+=u.y*w.x,q+=u.y*w.y,p+=u.y*w.z,x+=u.z*w.x,s+=u.z*w.y,t+=u.z*w.z;b[0]=J.util.Measure.getRmsd(a,c);c=ya(4,4,0);c[0][0]=d+q+t;c[0][1]=c[1][0]=p-s;c[0][2]=c[2][0]=x-m;c[0][3]=c[3][0]=l-n;c[1][1]=d-q-t;c[1][2]=c[2][1]=l+n;c[1][3]=c[3][1]=x+m;c[2][2]=-d+q-t;c[2][3]=c[3][2]=p+s;c[3][3]=-d-q+t;c=J.api.Interface.getOptionInterface("util.Eigen").newM(c).getEigenvectorsFloatTransposed()[3];c=J.util.Quaternion.newP4(JU.P4.new4(c[1],c[2],c[3],c[0]));b[1]=J.util.Measure.getRmsd(a,c);return c},
"~A,~A,~B");c$.getRmsd=c(c$,"getRmsd",function(a,b){for(var c=0,g=a[0],e=a[1],f=g[0],j=e[0],h=g.length-1,l=new JU.P3,m=h+1;1<=--m;)l.sub2(g[m],f),b.transformP2(l,l).add(j),c+=l.distanceSquared(e[m]);return Math.sqrt(c/h)},"~A,J.util.Quaternion");c$.transformPoints=c(c$,"transformPoints",function(a,b,c){for(var g=new JU.List,e=0;e<a.size();e++){var f=JU.P3.newP(a.get(e));f.sub(c);b.transform2(f,f);f.add(c);g.addLast(f)}return g},"JU.List,JU.M4,JU.P3");c$.isInTetrahedron=c(c$,"isInTetrahedron",function(a,
b,c,g,e,f,j,h,l,m){J.util.Measure.getPlaneThroughPoints(g,e,b,j,h,l,f);var n=0<=J.util.Measure.distanceToPlane(f,a);J.util.Measure.getPlaneThroughPoints(b,e,c,j,h,l,f);if(n!=0<=J.util.Measure.distanceToPlane(f,a))return!1;J.util.Measure.getPlaneThroughPoints(c,e,g,j,h,l,f);if(n!=0<=J.util.Measure.distanceToPlane(f,a))return!1;J.util.Measure.getPlaneThroughPoints(b,c,g,j,h,l,f);a=J.util.Measure.distanceToPlane(f,a);if(m)return n==0<=a;e=J.util.Measure.distanceToPlane(f,e);return 0>=e*a||Math.abs(e)>
Math.abs(a)},"JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P4,JU.V3,JU.V3,JU.V3,~B");c$.getIntersectionPP=c(c$,"getIntersectionPP",function(a,b){var c=a.x,g=a.y,e=a.z,f=a.w,j=b.x,h=b.y,l=b.z,m=b.w,n=JU.V3.new3(c,g,e),q=JU.V3.new3(j,h,l),p=new JU.V3;p.cross(n,q);var n=Math.abs(p.x),q=Math.abs(p.y),x=Math.abs(p.z);switch(n>q?n>x?1:3:q>x?2:3){case 1:n=0;q=g*l-h*e;if(0.01>Math.abs(q))return null;e=(e*m-l*f)/q;c=(h*f-m*g)/q;break;case 2:q=c*l-j*e;if(0.01>Math.abs(q))return null;n=(e*m-l*f)/q;e=0;c=(j*f-m*c)/q;break;
default:q=c*h-j*g;if(0.01>Math.abs(q))return null;n=(g*m-h*f)/q;e=(j*f-m*c)/q;c=0}g=new JU.List;g.addLast(JU.P3.new3(n,e,c));p.normalize();g.addLast(p);return g},"JU.P4,JU.P4");c$.getIntersection=c(c$,"getIntersection",function(a,b,c,g,e,f){J.util.Measure.getPlaneProjection(a,c,g,e);e.set(c.x,c.y,c.z);e.normalize();null==b&&(b=JU.V3.newV(e));c=b.dot(e);if(0.01>Math.abs(c))return null;f.sub2(g,a);g.scaleAdd2(f.dot(e)/c,b,a);return g},"JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");E(c$,"radiansPerDegree",0.017453292519943295)}),
p("J.util"),t(null,"J.util.MeshSurface","java.lang.Float java.util.Hashtable JU.AU $.BS $.List $.P3 $.P4 $.PT $.SB J.util.BSUtil $.BoxInfo $.C $.Escape $.Geodesic $.Measure $.TempArray".split(" "),function(){c$=w(function(){this.meshType=this.spanningVectors=null;this.vertexCount=0;this.vertexSource=this.vertexValues=this.vertices=null;this.polygonCount=0;this.polygonTranslucencies=this.polygonIndexes=null;this.haveQuads=this.isTriangleSet=!1;this.colixBack=this.colix=0;this.isColorSolid=!0;this.normalsTemp=
this.normals=this.vertexColixes=this.polygonColixes=this.altVertices=this.offset=null;this.normixCount=this.normalCount=0;this.vertexSets=this.surfaceSet=this.mat4=this.bsPolygons=null;this.nSets=0;this.checkCount=2;this.vertexCount0=this.polygonCount0=this.iC=this.iB=this.iA=this.lastColix=this.lastColor=0;this.bsTransPolygons=this.bsSlabGhost=this.bsSlabDisplay=null;this.slabColix=this.slabMeshType=0;this.slabOptions=this.bsDisplay=null;this.doCap=this.doGhost=this.doClear=!1;this.mergePolygonCount0=
this.mergeVertexCount0=this.iE=this.iD=0;this.isMerged=!1;u(this,arguments)},J.util,"MeshSurface");A(c$,function(){});c$.newMesh=c(c$,"newMesh",function(a,b,c,g,e,f){var j=new J.util.MeshSurface;j.polygonIndexes=g;a?j.altVertices=b:j.vertices=b;j.vertexCount=0==c?b.length:c;j.normals=e;j.normalCount=0==f&&null!=e?e.length:f;return j},"~B,~A,~N,~A,~A,~N");c$.newSlab=c(c$,"newSlab",function(a,b,c,g,e,f){var j=new J.util.MeshSurface;j.vertices=a;j.vertexValues=c;j.vertexCount=b;j.polygonIndexes=g;j.polygonCount=
e;j.checkCount=f;return j},"~A,~N,~A,~A,~N,~N");c(c$,"getVertices",function(){return null==this.altVertices?this.vertices:this.altVertices});c(c$,"getFaces",function(){return this.polygonIndexes});c(c$,"setColix",function(a){this.colix=a},"~N");c(c$,"setColixBack",function(a){this.colixBack=a},"~N");c(c$,"addV",function(a){0==this.vertexCount?this.vertices=Array(25):this.vertexCount==this.vertices.length&&(this.vertices=JU.AU.doubleLength(this.vertices));this.vertices[this.vertexCount]=JU.P3.newP(a);
return this.vertexCount++},"JU.P3");c(c$,"addTriangle",function(a,b,c){this.addPolygon([a,b,c],null)},"~N,~N,~N");c(c$,"addQuad",function(a,b,c,g){this.haveQuads=!0;this.addPolygon([a,b,c,g],null)},"~N,~N,~N,~N");c(c$,"setPolygonCount",function(a){this.polygonCount=a;if(!(0>a)&&(null==this.polygonIndexes||a>this.polygonIndexes.length))this.polygonIndexes=JU.AU.newInt2(a)},"~N");c(c$,"addVCVal",function(a,b){0==this.vertexCount?this.vertexValues=O(25,0):this.vertexCount>=this.vertexValues.length&&
(this.vertexValues=JU.AU.doubleLengthF(this.vertexValues));this.vertexValues[this.vertexCount]=b;return this.addV(a)},"JU.P3,~N");c(c$,"addTriangleCheck",function(a,b,c,g,e,f){return null==this.vertices||null!=this.vertexValues&&(Float.isNaN(this.vertexValues[a])||Float.isNaN(this.vertexValues[b])||Float.isNaN(this.vertexValues[c]))||Float.isNaN(this.vertices[a].x)||Float.isNaN(this.vertices[b].x)||Float.isNaN(this.vertices[c].x)?-1:this.addPolygonV3(a,b,c,g,e,f,null)},"~N,~N,~N,~N,~N,~N");c(c$,"addPolygonV3",
function(a,b,c,g,e,f,j){return 2==this.checkCount?this.addPolygonC([a,b,c,g,e],f,j):this.addPolygon([a,b,c,g],j)},"~N,~N,~N,~N,~N,~N,JU.BS");c(c$,"addPolygonC",function(a,b,c){if(0!=b){if(null==this.polygonColixes||0==this.polygonCount)this.lastColor=0;b=b==this.lastColor?this.lastColix:this.lastColix=J.util.C.getColix(this.lastColor=b);this.setPolygonColix(this.polygonCount,b)}return this.addPolygon(a,c)},"~A,~N,JU.BS");c(c$,"addPolygon",function(a,b){var c=this.polygonCount;0==this.polygonCount?
this.polygonIndexes=JU.AU.newInt2(25):this.polygonCount==this.polygonIndexes.length&&(this.polygonIndexes=JU.AU.doubleLength(this.polygonIndexes));null!=b&&b.set(this.polygonCount);this.polygonIndexes[this.polygonCount++]=a;return c},"~A,JU.BS");c(c$,"setPolygonColix",function(a,b){null==this.polygonColixes?this.polygonColixes=da(25,0):a>=this.polygonColixes.length&&(this.polygonColixes=JU.AU.doubleLengthShort(this.polygonColixes));this.polygonColixes[a]=b},"~N,~N");c(c$,"invalidatePolygons",function(){for(var a=
this.polygonCount;--a>=this.mergePolygonCount0;)if((null==this.bsSlabDisplay||this.bsSlabDisplay.get(a))&&!this.setABC(a))this.polygonIndexes[a]=null});c(c$,"setABC",function(a){if(null!=this.bsSlabDisplay&&!this.bsSlabDisplay.get(a)&&(null==this.bsSlabGhost||!this.bsSlabGhost.get(a)))return!1;a=this.polygonIndexes[a];if(null==a||3>a.length)return!1;this.iA=a[0];this.iB=a[1];this.iC=a[2];return null==this.vertexValues||!(Float.isNaN(this.vertexValues[this.iA])||Float.isNaN(this.vertexValues[this.iB])||
Float.isNaN(this.vertexValues[this.iC]))},"~N");c(c$,"setTranslucentVertices",function(){},"JU.BS");c(c$,"setSlab",function(a,b,c,g,e){this.bsSlabDisplay=a;this.bsSlabGhost=b;this.slabMeshType=c.equalsIgnoreCase("mesh")?1073742018:1073741938;this.slabColix=J.util.C.getColixTranslucent3(J.util.C.getColixS(g),!0,e)},"JU.BS,JU.BS,~S,~S,~N");c(c$,"getSlabColor",function(){return null==this.bsSlabGhost?null:J.util.C.getHexCode(this.slabColix)});c(c$,"getSlabTranslucency",function(){return null==this.bsSlabGhost?
null:""+J.util.C.getColixTranslucencyFractional(this.slabColix)});c(c$,"getSlabType",function(){return null!=this.bsSlabGhost&&1073742018==this.slabMeshType?"mesh":null});c(c$,"resetTransPolygons",function(){for(var a=J.util.C.isColixTranslucent(this.colix),b=J.util.C.getColixTranslucencyFractional(this.colix),c=0;c<this.polygonCount;c++)this.bsTransPolygons.get(c)&&this.setABC(c)&&(this.vertexColixes[this.iA]=J.util.C.getColixTranslucent3(this.vertexColixes[this.iA],a,b),this.vertexColixes[this.iB]=
J.util.C.getColixTranslucent3(this.vertexColixes[this.iB],a,b),this.vertexColixes[this.iC]=J.util.C.getColixTranslucent3(this.vertexColixes[this.iC],a,b));this.polygonTranslucencies=this.bsTransPolygons=null});c(c$,"resetSlab",function(){this.slabPolygons(J.util.TempArray.getSlabObjectType(1048587,null,!1,null),!1)});c$.getCapSlabObject=c(c$,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var c=JU.PT.split(a.substring(6,a.length-1),",");return J.util.TempArray.getSlabObjectType(1679429641,
[J.util.Escape.uP(c[0]),J.util.Escape.uP(c[1]),J.util.Escape.uP(c[2]),J.util.Escape.uP(c[3])],b,null)}var g=J.util.Escape.uP(a);if(r(g,JU.P4))return J.util.TempArray.getSlabObjectType(135266319,g,b,null)}catch(e){if(!C(e,Exception))throw e;}return null},"~S,~B");c(c$,"slabPolygonsList",function(a,b){for(var c=0;c<a.size()&&this.slabPolygons(a.get(c),b);c++);},"JU.List,~B");c(c$,"slabPolygons",function(a,b){if(0>this.polygonCount0)return!1;var c=a[0].intValue();if(1048587==c||1073741872==c){if(null!=
this.bsSlabDisplay&&(0!=this.polygonCount0||0!=this.vertexCount0))this.polygonCount=this.polygonCount0,this.vertexCount=this.vertexCount0,this.polygonCount0=this.vertexCount0=0,this.normixCount=this.isTriangleSet?this.polygonCount:this.vertexCount,this.bsSlabDisplay.setBits(0,0==this.polygonCount?this.vertexCount:this.polygonCount),this.slabOptions=(new JU.SB).append(this.meshType+" slab none"),this.bsSlabGhost=null,this.slabMeshType=1048587;if(1048587==c)return!1}var g=a[1],e=a[2].booleanValue()&&
1073741872!=c;if(e&&!b)return!1;var f=a[3],j=null!=f;if(null==this.bsSlabDisplay||0==this.polygonCount0&&0==this.vertexCount0){if(this.polygonCount0=this.polygonCount,this.vertexCount0=this.vertexCount,this.bsSlabDisplay=J.util.BSUtil.setAll(0==this.polygonCount?this.vertexCount:this.polygonCount),this.bsSlabGhost=null,0==this.polygonCount&&0==this.vertexCount)return!1}else this.isMerged&&(0==this.polygonCount?this.bsSlabDisplay.setBits(this.mergeVertexCount0,this.vertexCount):this.bsSlabDisplay.setBits(this.mergePolygonCount0,
this.polygonCount));j&&(null==this.bsSlabGhost&&(this.bsSlabGhost=new JU.BS),this.slabMeshType=f[0].intValue(),this.slabColix=f[1].shortValue(),e=!1,this.colix=J.util.C.getColixTranslucent3(this.colix,!1,0));f=new JU.SB;f.append(e?" cap ":" slab ");if(j){f.append("translucent ").appendF(J.util.C.getColixTranslucencyFractional(this.slabColix)).append(" ");var h=J.util.C.getHexCode(this.slabColix);null!=h&&f.append(h).append(" ");1073742018==this.slabMeshType&&f.append("mesh ")}switch(c){case 1073741872:f.append("brillouin");
this.slabBrillouin(g);break;case 3:this.getIntersection(0,null,null,null,null,g,null,e,!1,3,j);break;case 135266319:f.append(J.util.Escape.eP4(g));this.getIntersection(0,g,null,null,null,null,null,e,!1,135266319,j);break;case 1614417948:case 1679429641:f.append("within ").append(J.util.Escape.eAP(g));g=J.util.BoxInfo.getFacesFromCriticalPoints(g);for(h=0;h<g.length;h++)this.getIntersection(0,g[h],null,null,null,null,null,e,!1,135266319,j);break;case 135270407:this.getIntersection(0,null,null,null,
g,null,null,!1,!1,32,j);break;case 135266325:case 1073742114:case 1073742018:switch(h=g[0].floatValue(),c){case 135266325:c=g[1];g=g[2];f.append("within ").appendF(h).append(null==g?J.util.Escape.e(c):J.util.Escape.e(g));this.getIntersection(h,null,c,null,null,null,null,e,!1,0<h?1276118018:1073742154,j);break;case 1073742114:if(null==this.vertexValues)return!1;c=g[1].floatValue();f.append("within range ").appendF(h).append(" ").appendF(c);g=c<h?J.util.BSUtil.copy(this.bsSlabDisplay):null;this.getIntersection(h,
null,null,null,null,null,null,e,!1,32,j);h=null==g?null:J.util.BSUtil.copy(this.bsSlabDisplay);J.util.BSUtil.copy2(g,this.bsSlabDisplay);this.getIntersection(c,null,null,null,null,null,null,e,!1,64,j);null!=h&&this.bsSlabDisplay.or(h);break;case 1073742018:this.getIntersection(0,null,null,null,null,null,g[1],e,!1,0>h?32:64,j)}}e=f.toString();null==this.slabOptions&&(this.slabOptions=new JU.SB);0>this.slabOptions.indexOf(e)&&this.slabOptions.append(0<this.slabOptions.length()?"; ":"").append(this.meshType).append(e);
return!0},"~A,~B");c(c$,"slabBrillouin",function(){},"~A");c(c$,"addIntersectionVertex",function(a,b,c,g,e,f,j){j=f>j?j+"_"+f:f+"_"+j;if(0<=f&&(f=e.get(j),null!=f))return f.intValue();null!=this.vertexSource&&(this.vertexCount>=this.vertexSource.length&&(this.vertexSource=JU.AU.doubleLengthI(this.vertexSource)),this.vertexSource[this.vertexCount]=c);null!=this.vertexSets&&(this.vertexCount>=this.vertexSets.length&&(this.vertexSets=JU.AU.doubleLengthI(this.vertexSets)),this.vertexSets[this.vertexCount]=
g);a=this.addVCVal(a,b);e.put(j,Integer.$valueOf(a));return a},"JU.P3,~N,~N,~N,java.util.Map,~N,~N");c(c$,"getIntersection",function(a,b,c,g,e,f,j,h,l,m,n){var q=null==g,p=null;if(null==e)if(3==m&&null!=f){e=O(this.vertexCount,0);for(j=0;j<this.vertexCount;j++)-1==(e[j]=this.vertexSource[j])&&System.out.println("meshsurface hmm")}else e=this.vertexValues;var x=new java.util.Hashtable;if(null!=c||n)h=!1;var r=O(2,0),s=O(2,0),t=Math.abs(a),u,w,y,z,A,B,C=0,E=0,F=0,H=0,I=h?new JU.List:null;if(0==this.polygonCount)for(j=
this.mergeVertexCount0;j<this.vertexCount;j++)(Float.isNaN(e[j])||0<J.util.MeshSurface.checkSlab(m,this.vertices[j],e[j],a,b,c,f))&&this.bsSlabDisplay.clear(j);else{var L=this.polygonCount;for(j=this.mergePolygonCount0;j<L;j++)if(this.setABC(j)){var K=null!=this.bsSlabGhost&&this.bsSlabGhost.get(j)?this.bsSlabGhost:this.bsSlabDisplay,M=this.polygonIndexes[j][3],P=2==this.checkCount?this.polygonIndexes[j][4]:0,Q=this.vertices[this.iA],R=this.vertices[this.iB],S=this.vertices[this.iC];z=e[this.iA];
A=e[this.iB];B=e[this.iC];null!=this.vertexSource&&(C=this.vertexSource[this.iA],E=this.vertexSource[this.iB],F=this.vertexSource[this.iC]);null!=this.vertexSets&&(H=this.vertexSets[this.iA]);u=J.util.MeshSurface.checkSlab(m,Q,z,null==f?a:C,b,c,f);w=J.util.MeshSurface.checkSlab(m,R,A,null==f?a:E,b,c,f);y=J.util.MeshSurface.checkSlab(m,S,B,null==f?a:F,b,c,f);var T=(0!=u&&0>u?1:0)+(0!=w&&0>w?2:0)+(0!=y&&0>y?4:0);switch(T){case 1:case 6:p=null==c?[J.util.MeshSurface.interpolatePoint(Q,R,-u,w,z,A,r,s,
0),J.util.MeshSurface.interpolatePoint(Q,S,-u,y,z,B,r,s,1)]:[this.interpolateSphere(Q,R,-u,-w,t,z,A,r,s,0),this.interpolateSphere(Q,S,-u,-y,t,z,B,r,s,1)];break;case 2:case 5:p=null==c?[J.util.MeshSurface.interpolatePoint(R,Q,-w,u,A,z,r,s,1),J.util.MeshSurface.interpolatePoint(R,S,-w,y,A,B,r,s,0)]:[this.interpolateSphere(R,Q,-w,-u,t,A,z,r,s,1),this.interpolateSphere(R,S,-w,-y,t,A,B,r,s,0)];break;case 3:case 4:p=null==c?[J.util.MeshSurface.interpolatePoint(S,Q,-y,u,B,z,r,s,0),J.util.MeshSurface.interpolatePoint(S,
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c$.setInverseNormixes=c(c$,"setInverseNormixes",function(){if(null==J.util.Normix.inverseNormixes){J.util.Normix.getNormixCount();J.util.Normix.getVertexVectors();J.util.Normix.inverseNormixes=da(J.util.Normix.normixCount,0);for(var a=new JU.BS,b=J.util.Normix.normixCount;0<=--b;){var c=J.util.Normix.vertexVectors[b];J.util.Normix.inverseNormixes[b]=J.util.Normix.getNormix(-c.x,-c.y,-c.z,3,a)}}});c$.getInverseNormix=c(c$,"getInverseNormix",function(a){return J.util.Normix.inverseNormixes[a]},"~N");
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b,c,g,e){var f,j;0<=c?(f=0,j=c-1):(f=11,j=c- -1);e.clearAll();e.set(f);J.util.Normix.getVertexVectors();J.util.Normix.getNeighborVertexArrays();j=a*a+b*b+j*j;for(var h=0;h<=g;++h)for(var l=J.util.Normix.neighborVertexesArrays[h],m=6*f,n=m+(12>f?5:6);--n>=m;){var q=l[n];if(!e.get(q)){e.set(q);var p=J.util.Normix.vertexVectors[q],r;r=p.x-a;var s=r*r;s>=j||(r=p.y-b,s+=r*r,s>=j||(r=p.z-c,s+=r*r,s>=j||(f=q,j=s)))}}return f},"~N,~N,~N,~N,JU.BS");E(c$,"NORMIX_GEODESIC_LEVEL",3,"normixCount",0,"vertexVectors",
null,"inverseNormixes",null,"neighborVertexesArrays",null,"NORMIX_NULL",9999)}),p("J.util"),t(null,"J.util.Parser",["java.lang.Float","JU.AU","$.PT"],function(){c$=M(J.util,"Parser");c$.parseStringInfestedFloatArray=c(c$,"parseStringInfestedFloatArray",function(a,b,c){return J.util.Parser.parseFloatArrayBsData(JU.PT.getTokens(a),b,c)},"~S,JU.BS,~A");c$.parseFloatArrayBsData=c(c$,"parseFloatArrayBsData",function(a,b,c){for(var g=c.length,e=a.length,f=0,j=0,h=null!=b,l=h?b.nextSetBit(0):0;0<=l&&l<g&&
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J.util.Parser.fixDataString(a);var b=J.util.Parser.markLines(a,"\n"),c=b.length,g=JU.PT.getTokens(a.substring(0,b[0]));if(3!=g.length)return O(0,0,0,0);var e=JU.PT.parseInt(g[0]),f=JU.PT.parseInt(g[1]),j=JU.PT.parseInt(g[2]);if(1>e||1>f||1>j)return O(1,1,1,0);for(var h=JU.AU.newFloat3(e,f),l=0,m=0,n=1,g=b[0];n<c&&l<e;g=b[n++])g=JU.PT.getTokens(a.substring(g,b[n])),g.length<j||(JU.PT.parseFloatArrayData(g,h[l][m]=O(g.length,0)),++m==f&&(l++,m=0));return l!=e?(System.out.println("Error reading 3D data -- nX = "+
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c(c$,"copy",function(){try{return this.clone()}catch(a){if(C(a,CloneNotSupportedException))return null;throw a;}})}),p("J.util"),t(["JU.P4"],"J.util.Quaternion","java.lang.Float JU.A4 $.M3 $.P3 $.V3 J.util.Escape $.Logger $.Txt".split(" "),function(){c$=w(function(){this.q3=this.q2=this.q1=this.q0=0;this.mat=null;u(this,arguments)},J.util,"Quaternion");A(c$,function(){this.q0=1});c$.newQ=c(c$,"newQ",function(a){var b=new J.util.Quaternion;b.set(a);return b},"J.util.Quaternion");c$.newVA=c(c$,"newVA",
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c}},"JU.T3,~N");c(c$,"setAA",function(a){a=JU.A4.newAA(a);0==a.angle&&(a.y=1);var b=new JU.M3;b.setAA(a);this.setM(b)},"JU.A4");c(c$,"setM",function(a){this.mat=a;var b=a.m00+a.m11+a.m22,c,g,e;0.5<=b?(b=Math.sqrt(1+b),c=(a.m21-a.m12)/b,g=(a.m02-a.m20)/b,e=(a.m10-a.m01)/b):0.5<=(c=a.m00+a.m00-b)?(c=Math.sqrt(1+c),b=(a.m21-a.m12)/c,g=(a.m10+a.m01)/c,e=(a.m20+a.m02)/c):0.5<=(c=a.m11+a.m11-b)||a.m11>a.m22?(g=Math.sqrt(1+c),b=(a.m02-a.m20)/g,c=(a.m10+a.m01)/g,e=(a.m21+a.m12)/g):(e=Math.sqrt(1+a.m22+a.m22-
b),b=(a.m10-a.m01)/e,c=(a.m20+a.m02)/e,g=(a.m21+a.m12)/e);this.q0=0.5*b;this.q1=0.5*c;this.q2=0.5*g;this.q3=0.5*e},"JU.M3");c(c$,"setRef",function(a){null==a?this.mul(this.getFixFactor()):0<=this.dot(a)||(this.q0*=-1,this.q1*=-1,this.q2*=-1,this.q3*=-1)},"J.util.Quaternion");c$.getQuaternionFrame=c(c$,"getQuaternionFrame",function(a,b,c){b=JU.V3.newV(b);c=JU.V3.newV(c);null!=a&&(b.sub(a),c.sub(a));return J.util.Quaternion.getQuaternionFrameV(b,c,null,!1)},"JU.P3,JU.T3,JU.T3");c$.getQuaternionFrameV=
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2*this.q1*this.q2-2*this.q0*this.q3;this.mat.m02=2*this.q1*this.q3+2*this.q0*this.q2;this.mat.m10=2*this.q1*this.q2+2*this.q0*this.q3;this.mat.m11=this.q0*this.q0-this.q1*this.q1+this.q2*this.q2-this.q3*this.q3;this.mat.m12=2*this.q2*this.q3-2*this.q0*this.q1;this.mat.m20=2*this.q1*this.q3-2*this.q0*this.q2;this.mat.m21=2*this.q2*this.q3+2*this.q0*this.q1;this.mat.m22=this.q0*this.q0-this.q1*this.q1-this.q2*this.q2+this.q3*this.q3});c(c$,"add",function(a){return J.util.Quaternion.newVA(this.getNormal(),
this.getTheta()+a)},"~N");c(c$,"mul",function(a){return 1==a?J.util.Quaternion.new4(this.q0,this.q1,this.q2,this.q3):J.util.Quaternion.newVA(this.getNormal(),this.getTheta()*a)},"~N");c(c$,"mulQ",function(a){return J.util.Quaternion.new4(this.q0*a.q0-this.q1*a.q1-this.q2*a.q2-this.q3*a.q3,this.q0*a.q1+this.q1*a.q0+this.q2*a.q3-this.q3*a.q2,this.q0*a.q2+this.q2*a.q0+this.q3*a.q1-this.q1*a.q3,this.q0*a.q3+this.q3*a.q0+this.q1*a.q2-this.q2*a.q1)},"J.util.Quaternion");c(c$,"div",function(a){return this.mulQ(a.inv())},
"J.util.Quaternion");c(c$,"divLeft",function(a){return this.inv().mulQ(a)},"J.util.Quaternion");c(c$,"dot",function(a){return this.q0*a.q0+this.q1*a.q1+this.q2*a.q2+this.q3*a.q3},"J.util.Quaternion");c(c$,"inv",function(){return J.util.Quaternion.new4(this.q0,-this.q1,-this.q2,-this.q3)});c(c$,"negate",function(){return J.util.Quaternion.new4(-this.q0,-this.q1,-this.q2,-this.q3)});c(c$,"getFixFactor",function(){return 0>this.q0||0==this.q0&&(0>this.q1||0==this.q1&&(0>this.q2||0==this.q2&&0>this.q3))?
-1:1});c(c$,"getVector",function(a){return this.getVectorS(a,1)},"~N");c(c$,"getVectorS",function(a,b){if(-1==a)return b*=this.getFixFactor(),JU.V3.new3(this.q1*b,this.q2*b,this.q3*b);null==this.mat&&this.setMatrix();var c=new JU.V3;this.mat.getColumnV(a,c);1!=b&&c.scale(b);return c},"~N,~N");c(c$,"getNormal",function(){var a=J.util.Quaternion.getRawNormal(this);a.scale(this.getFixFactor());return a});c$.getRawNormal=c(c$,"getRawNormal",function(a){a=JU.V3.new3(a.q1,a.q2,a.q3);if(0==a.length())return JU.V3.new3(0,
0,1);a.normalize();return a},"J.util.Quaternion");c(c$,"getTheta",function(){return 360*Math.acos(Math.abs(this.q0))/3.141592653589793});c(c$,"getThetaRadians",function(){return 2*Math.acos(Math.abs(this.q0))});c(c$,"getNormalDirected",function(a){var b=this.getNormal();0>b.x*a.x+b.y*a.y+b.z*a.z&&b.scale(-1);return b},"JU.V3");c(c$,"get3dProjection",function(a){a.set(this.q1,this.q2,this.q3);return a},"JU.V3");c(c$,"getThetaDirected",function(a){var b=this.getTheta(),c=this.getNormal();0>a.x*this.q1+
a.y*this.q2+a.z*this.q3&&(c.scale(-1),b=-b);a.set(c.x,c.y,c.z,b);return a},"JU.P4");c(c$,"getThetaDirectedV",function(a){var b=this.getTheta(),c=this.getNormal();0>a.x*this.q1+a.y*this.q2+a.z*this.q3&&(c.scale(-1),b=-b);return b},"JU.V3");c(c$,"toPoint4f",function(){return JU.P4.new4(this.q1,this.q2,this.q3,this.q0)});c(c$,"toAxisAngle4f",function(){var a=2*Math.acos(Math.abs(this.q0)),b=Math.sin(a/2),c=this.getNormal();0>b&&(c.scale(-1),a=3.141592653589793-a);return JU.A4.newVA(c,a)});c(c$,"transformPt",
function(a){null==this.mat&&this.setMatrix();a=JU.P3.newP(a);this.mat.transform(a);return a},"JU.P3");c(c$,"transformP2",function(a,b){null==this.mat&&this.setMatrix();this.mat.transform2(a,b);return b},"JU.T3,JU.T3");c(c$,"transform",function(a){null==this.mat&&this.setMatrix();a=JU.V3.newV(a);this.mat.transform(a);return a},"JU.V3");c(c$,"leftDifference",function(a){a=0>this.dot(a)?a.negate():a;return this.inv().mulQ(a)},"J.util.Quaternion");c(c$,"rightDifference",function(a){a=0>this.dot(a)?a.negate():
a;return this.mulQ(a.inv())},"J.util.Quaternion");c(c$,"getInfo",function(){var a=this.toAxisAngle4f();return J.util.Txt.sprintf("%10.6f%10.6f%10.6f%10.6f  %6.2f  %10.5f %10.5f %10.5f","F",[[this.q0,this.q1,this.q2,this.q3,180*a.angle/3.141592653589793,a.x,a.y,a.z]])});c(c$,"draw",function(a,b,c,g){c=" VECTOR "+J.util.Escape.eP(c)+" ";0==g&&(g=1);return"draw "+a+"x"+b+c+J.util.Escape.eP(this.getVectorS(0,g))+" color red\ndraw "+a+"y"+b+c+J.util.Escape.eP(this.getVectorS(1,g))+" color green\ndraw "+
a+"z"+b+c+J.util.Escape.eP(this.getVectorS(2,g))+" color blue\n"},"~S,~S,JU.P3,~N");h(c$,"toString",function(){return"{"+this.q1+" "+this.q2+" "+this.q3+" "+this.q0+"}"});c$.div=c(c$,"div",function(a,b,c,g){var e;if(null==a||null==b||0==(e=Math.min(a.length,b.length)))return null;0<c&&e>c&&(e=c);c=Array(e);for(var f=0;f<e;f++){if(null==a[f]||null==b[f])return null;c[f]=g?a[f].divLeft(b[f]):a[f].div(b[f])}return c},"~A,~A,~N,~B");c$.sphereMean=c(c$,"sphereMean",function(a,b,c){if(null==a||0==a.length)return new J.util.Quaternion;
null==b&&(b=O(1,0));if(1==a.length)return b[0]=0,J.util.Quaternion.newQ(a[0]);for(var g=3.4028235E38,e=3.4028235E38,f=J.util.Quaternion.simpleAverage(a),j=0;g>c&&0!=e&&100>j;)f=J.util.Quaternion.newMean(a,f),b[0]=J.util.Quaternion.stdDev(a,f),g=Math.abs(b[0]-e),e=b[0],J.util.Logger.info(++j+" sphereMean "+f+" stddev="+e+" diff="+g);return f},"~A,~A,~N");c$.simpleAverage=c(c$,"simpleAverage",function(a){var b=JU.V3.new3(0,0,1),c=a[0].getNormal();b.add(c);for(var g=a.length;0<=--g;)b.add(a[g].getNormalDirected(b));
b.sub(c);b.normalize();for(var e=0,g=a.length;0<=--g;)e+=Math.abs(a[g].get3dProjection(c).dot(b));0!=e&&b.scale(e/a.length);e=Math.sqrt(1-b.lengthSquared());Float.isNaN(e)&&(e=0);return J.util.Quaternion.newP4(JU.P4.new4(b.x,b.y,b.z,e))},"~A");c$.newMean=c(c$,"newMean",function(a,b){for(var c=new JU.V3,g,e,f=a.length;0<=--f;)g=a[f],e=g.div(b),g=e.getNormal(),g.scale(e.getTheta()),c.add(g);c.scale(1/a.length);return J.util.Quaternion.newVA(c,c.length()).mulQ(b)},"~A,J.util.Quaternion");c$.stdDev=c(c$,
"stdDev",function(a,b){for(var c=0,g=a.length,e=g;0<=--e;)var f=a[e].div(b).getTheta(),c=c+f*f;return Math.sqrt(c/g)},"~A,J.util.Quaternion");c(c$,"getEulerZYZ",function(){var a,b,c;a=Math.atan2(2*(this.q2*this.q3-this.q0*this.q1),2*(this.q1*this.q3+this.q0*this.q2));b=Math.acos(this.q3*this.q3-this.q2*this.q2-this.q1*this.q1+this.q0*this.q0);c=Math.atan2(2*(this.q2*this.q3+this.q0*this.q1),2*(this.q0*this.q2-this.q1*this.q3));return[a/0.017453292519943295,b/0.017453292519943295,c/0.017453292519943295]});
c(c$,"getEulerZXZ",function(){var a,b,c;a=Math.atan2(2*(this.q1*this.q3+this.q0*this.q2),2*(this.q0*this.q1-this.q2*this.q3));b=Math.acos(this.q3*this.q3-this.q2*this.q2-this.q1*this.q1+this.q0*this.q0);c=Math.atan2(2*(this.q1*this.q3-this.q0*this.q2),2*(this.q2*this.q3+this.q0*this.q1));return[a/0.017453292519943295,b/0.017453292519943295,c/0.017453292519943295]});c$.qZero=c$.prototype.qZero=new JU.P4;E(c$,"RAD_PER_DEG",0.017453292519943295)}),p("J.util"),c$=w(function(){this.height=this.width=this.y=
this.x=0;u(this,arguments)},J.util,"Rectangle"),c(c$,"contains",function(a,b){return a>=this.x&&b>=this.y&&a-this.x<this.width&&b-this.y<this.height},"~N,~N"),p("J.util"),t(null,"J.util.Rgb16",["JU.SB"],function(){c$=w(function(){this.bScaled=this.gScaled=this.rScaled=0;u(this,arguments)},J.util,"Rgb16");A(c$,function(){});c$.newI=c(c$,"newI",function(a){var b=new J.util.Rgb16;b.setInt(a);return b},"~N");c(c$,"setInt",function(a){this.rScaled=a>>8&65280|128;this.gScaled=a&65280|128;this.bScaled=a<<
8&65280|128},"~N");c(c$,"setRgb",function(a){this.rScaled=a.rScaled;this.gScaled=a.gScaled;this.bScaled=a.bScaled},"J.util.Rgb16");c(c$,"diffDiv",function(a,b,c){this.rScaled=s((a.rScaled-b.rScaled)/c);this.gScaled=s((a.gScaled-b.gScaled)/c);this.bScaled=s((a.bScaled-b.bScaled)/c)},"J.util.Rgb16,J.util.Rgb16,~N");c(c$,"setAndIncrement",function(a,b){this.rScaled=a.rScaled;a.rScaled+=b.rScaled;this.gScaled=a.gScaled;a.gScaled+=b.gScaled;this.bScaled=a.bScaled;a.bScaled+=b.bScaled},"J.util.Rgb16,J.util.Rgb16");
c(c$,"getArgb",function(){return 4278190080|this.rScaled<<8&16711680|this.gScaled&65280|this.bScaled>>8});h(c$,"toString",function(){return(new JU.SB).append("Rgb16(").appendI(this.rScaled).appendC(",").appendI(this.gScaled).appendC(",").appendI(this.bScaled).append(" -> ").appendI(this.rScaled>>8&255).appendC(",").appendI(this.gScaled>>8&255).appendC(",").appendI(this.bScaled>>8&255).appendC(")").toString()})}),p("J.util"),t(["JU.AU","$.V3"],"J.util.Shader",["JU.CU","J.util.C"],function(){c$=w(function(){this.zLight=
this.yLight=this.xLight=0;this.lightSource=null;this.specularOn=!0;this.usePhongExponent=!1;this.ambientPercent=45;this.diffusePercent=84;this.specularExponent=6;this.specularPercent=22;this.specularPower=40;this.phongExponent=64;this.specularFactor=this.intenseFraction=this.diffuseFactor=this.ambientFraction=0;this.ashadesGreyscale=this.ashades=null;this.celOn=!1;this.celPower=10;this.celZ=this.celRGB=0;this.useLight=!1;this.sphereShadeIndexes=null;this.seed=305419897;this.ellipsoidShades=this.sphereShapeCache=
null;this.nIn=this.nOut=0;u(this,arguments)},J.util,"Shader");Q(c$,function(){this.lightSource=new JU.V3;this.ambientFraction=this.ambientPercent/100;this.diffuseFactor=this.diffusePercent/100;this.intenseFraction=this.specularPower/100;this.specularFactor=this.specularPercent/100;this.ashades=JU.AU.newInt2(128);this.sphereShadeIndexes=V(65536,0);this.sphereShapeCache=JU.AU.newInt2(128)});A(c$,function(){this.setLightSource(-1,-1,2.5)});c(c$,"setLightSource",function(a,b,c){this.lightSource.set(a,
b,c);this.lightSource.normalize();this.xLight=this.lightSource.x;this.yLight=this.lightSource.y;this.zLight=this.lightSource.z},"~N,~N,~N");c(c$,"setCel",function(a,b,c){a=a&&0!=b;c=J.util.C.getArgb(J.util.C.getBgContrast(c));c=4278190080==c?4278453252:-1==c?-2:c+1;this.celOn==a&&this.celRGB==c&&this.celPower==b||(this.celOn=a,this.celPower=b,this.useLight=!this.celOn||0<b,this.celZ=1-Math.pow(2,-Math.abs(b)/10),this.celRGB=c,this.flushCaches())},"~B,~N,~N");c(c$,"flushCaches",function(){this.flushShades();
this.flushSphereCache()});c(c$,"setLastColix",function(a,b){J.util.C.allocateColix(a);this.checkShades();b&&J.util.C.setLastGrey(a);this.ashades[2047]=this.getShades2(a,!1)},"~N,~B");c(c$,"getShades",function(a){this.checkShades();a&=-30721;var b=this.ashades[a];null==b&&(b=this.ashades[a]=this.getShades2(J.util.C.argbs[a],!1));return b},"~N");c(c$,"getShadesG",function(a){this.checkShades();a&=-30721;null==this.ashadesGreyscale&&(this.ashadesGreyscale=JU.AU.newInt2(this.ashades.length));var b=this.ashadesGreyscale[a];
null==b&&(b=this.ashadesGreyscale[a]=this.getShades2(J.util.C.argbs[a],!0));return b},"~N");c(c$,"checkShades",function(){null!=this.ashades&&this.ashades.length==J.util.C.colixMax||(this.ashades=JU.AU.arrayCopyII(this.ashades,J.util.C.colixMax),null!=this.ashadesGreyscale&&(this.ashadesGreyscale=JU.AU.arrayCopyII(this.ashadesGreyscale,J.util.C.colixMax)))});c(c$,"flushShades",function(){this.checkShades();for(var a=J.util.C.colixMax;0<=--a;)this.ashades[a]=null;this.calcSphereShading()});c(c$,"getShades2",
function(a,b){var c=D(J.util.Shader.shadeIndexMax,0);if(0==a)return c;for(var g=a>>16&255,e=a>>8&255,f=a&255,j=0,h=0,l=0,m=this.ambientFraction;;)if(j=g*m+0.5,h=e*m+0.5,l=f*m+0.5,0<m&&4>j&&4>h&&4>l)g++,e++,f++,0.1>m&&(m+=0.1),a=JU.CU.rgb(s(Math.floor(g)),s(Math.floor(e)),s(Math.floor(f)));else break;var n=0,m=(1-m)/J.util.Shader.shadeIndexNormal,g=g*m,e=e*m,f=f*m;if(this.celOn){var m=s(J.util.Shader.shadeIndexMax/2),q=JU.CU.rgb(s(Math.floor(j)),s(Math.floor(h)),s(Math.floor(l)));if(0<=this.celPower)for(;n<
m;++n)c[n]=q;h+=e*m;l+=f*m;for(q=JU.CU.rgb(s(Math.floor(j+g*m)),s(Math.floor(h)),s(Math.floor(l)));n<J.util.Shader.shadeIndexMax;n++)c[n]=q;c[0]=c[1]=this.celRGB}else{for(;n<J.util.Shader.shadeIndexNormal;++n)c[n]=JU.CU.rgb(s(Math.floor(j)),s(Math.floor(h)),s(Math.floor(l))),j+=g,h+=e,l+=f;c[n++]=a;m=this.intenseFraction/(J.util.Shader.shadeIndexMax-n);g=(255.5-j)*m;e=(255.5-h)*m;for(f=(255.5-l)*m;n<J.util.Shader.shadeIndexMax;n++)j+=g,h+=e,l+=f,c[n]=JU.CU.rgb(s(Math.floor(j)),s(Math.floor(h)),s(Math.floor(l)))}if(b)for(;0<=
--n;)c[n]=JU.CU.toFFGGGfromRGB(c[n]);return c},"~N,~B");c(c$,"getShadeIndex",function(a,b,c){var g=Math.sqrt(a*a+b*b+c*c);return Math.round(this.getShadeF(a/g,b/g,c/g)*J.util.Shader.shadeIndexLast)},"~N,~N,~N");c(c$,"getShadeB",function(a,b,c){return Math.round(this.getShadeF(a,b,c)*J.util.Shader.shadeIndexLast)},"~N,~N,~N");c(c$,"getShadeFp8",function(a,b,c){var g=Math.sqrt(a*a+b*b+c*c);return s(Math.floor(256*this.getShadeF(a/g,b/g,c/g)*J.util.Shader.shadeIndexLast))},"~N,~N,~N");c(c$,"getShadeF",
function(a,b,c){b=this.useLight?a*this.xLight+b*this.yLight+c*this.zLight:c;if(0>=b)return 0;a=b*this.diffuseFactor;if(this.specularOn&&(b=2*b*c-this.zLight,0<b)){if(this.usePhongExponent)b=Math.pow(b,this.phongExponent);else for(var g=this.specularExponent;0<=--g&&1E-4<b;)b*=b;a+=b*this.specularFactor}return this.celOn&&c<this.celZ?0:1<a?1:a},"~N,~N,~N");c(c$,"getShadeN",function(a,b,c,g){b=s(Math.floor(256*this.getShadeF(a/g,b/g,c/g)*J.util.Shader.shadeIndexLast));a=b>>8;if(!this.useLight)return a;
(b&255)>this.nextRandom8Bit()&&++a;b=this.seed&65535;21845>b&&0<a?--a:43690<b&&a<J.util.Shader.shadeIndexLast&&++a;return a},"~N,~N,~N,~N");c(c$,"calcSphereShading",function(){for(var a=-127.5,b=0;256>b;++a,++b)for(var c=-127.5,g=a*a,e=0;256>e;++c,++e){var f=0,j=16900-g-c*c;0<j&&(f=Math.sqrt(j),f=this.getShadeN(a,c,f,130));this.sphereShadeIndexes[(e<<8)+b]=f}});c(c$,"nextRandom8Bit",function(){var a=this.seed;this.seed=a=(a<<16)+(a<<1)+a&2147483647;return a>>23});c(c$,"getEllipsoidShade",function(a,
b,c,g,e){var f=e.m00*a+e.m01*b+e.m02*c+e.m03,j=e.m10*a+e.m11*b+e.m12*c+e.m13;a=e.m20*a+e.m21*b+e.m22*c+e.m23;g=Math.min(g/2,45)/Math.sqrt(f*f+j*j+a*a);f=y(-f*g);j=y(-j*g);g=y(a*g);if(a=-20>f||20<=f||-20>j||20<=j||0>g||40<=g){for(;0==f%2&&0==j%2&&0==g%2&&0<f+j+g;)f>>=1,j>>=1,g>>=1;a=-20>f||20<=f||-20>j||20<=j||0>g||40<=g}a?this.nOut++:this.nIn++;return a?this.getShadeIndex(f,j,g):this.ellipsoidShades[f+20][j+20][g]},"~N,~N,~N,~N,JU.M4");c(c$,"createEllipsoidShades",function(){this.ellipsoidShades=
V(40,40,40,0);for(var a=0;40>a;a++)for(var b=0;40>b;b++)for(var c=0;40>c;c++)this.ellipsoidShades[a][b][c]=this.getShadeIndex(a-20,b-20,c)});c(c$,"flushSphereCache",function(){for(var a=128;0<=--a;)this.sphereShapeCache[a]=null;this.ellipsoidShades=null});c(c$,"occludePixels",function(a,b,c,g,e){a=b.length;for(var f=c=0,j=0;j<a;j++){var h=Math.min(b[j]>>5,0);if(0!=h){for(var l=Math.min(g,c+h),m=Math.min(e,f+h),n=Math.max(0,c-h);n<l;n++)for(var q=Math.max(0,f-h);q<m;q++);++c==g&&(c=0,f++)}}},"~A,~A,~A,~N,~N,~N");
E(c$,"shadeIndexMax",64);c$.shadeIndexLast=c$.prototype.shadeIndexLast=J.util.Shader.shadeIndexMax-1;E(c$,"shadeIndexNormal",52,"shadeIndexNoisyLimit",56,"SLIM",20,"SDIM",40,"maxSphereCache",128)}),p("J.util"),t(null,"J.util.SimpleUnitCell",["java.lang.Float","JU.AU","$.M4","$.V3"],function(){c$=w(function(){this.matrixFractionalToCartesian=this.matrixCartesianToFractional=this.notionalUnitcell=null;this.dimension=this.c_=this.b_=this.a_=this.cB_=this.cA_=this.volume=this.sinGamma=this.cosGamma=this.sinBeta=
this.cosBeta=this.sinAlpha=this.cosAlpha=this.gamma=this.beta=this.alpha=this.c=this.b=this.a=this.nc=this.nb=this.na=0;this.matrixFtoCAbsolute=this.matrixCtoFAbsolute=null;u(this,arguments)},J.util,"SimpleUnitCell");c(c$,"isSupercell",function(){return 1<this.na||1<this.nb||1<this.nc});c$.isValid=c(c$,"isValid",function(a){return null!=a&&(0<a[0]||14<a.length&&!Float.isNaN(a[14]))},"~A");A(c$,function(){});c$.newA=c(c$,"newA",function(a){var b=new J.util.SimpleUnitCell;b.set(a);return b},"~A");c(c$,
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a[13],a[14]);this.a=b.length();this.b=c.length();this.c=g.length();if(0==this.a)return;0==this.b?this.b=this.c=-1:0==this.c&&(this.c=-1);this.alpha=0>this.b||0>this.c?90:c.angle(g)/0.017453292;this.beta=0>this.c?90:b.angle(g)/0.017453292;this.gamma=0>this.b?90:b.angle(c)/0.017453292;0>this.c&&(a=JU.AU.arrayCopyF(a,-1),0>this.b&&(c.set(0,0,1),c.cross(c,b),0.001>c.length()&&c.set(0,1,0),c.normalize(),a[9]=c.x,a[10]=c.y,a[11]=c.z),0>this.c&&(g.cross(b,c),g.normalize(),a[12]=g.x,a[13]=g.y,a[14]=g.z))}this.a*=
this.na;0>=this.b?this.dimension=this.b=this.c=1:0>=this.c?(this.c=1,this.b*=this.nb,this.dimension=2):(this.b*=this.nb,this.c*=this.nc,this.dimension=3);this.cosAlpha=Math.cos(0.017453292*this.alpha);this.sinAlpha=Math.sin(0.017453292*this.alpha);this.cosBeta=Math.cos(0.017453292*this.beta);this.sinBeta=Math.sin(0.017453292*this.beta);this.cosGamma=Math.cos(0.017453292*this.gamma);this.sinGamma=Math.sin(0.017453292*this.gamma);b=Math.sqrt(this.sinAlpha*this.sinAlpha+this.sinBeta*this.sinBeta+this.sinGamma*
this.sinGamma+2*this.cosAlpha*this.cosBeta*this.cosGamma-2);this.volume=this.a*this.b*this.c*b;this.cA_=(this.cosAlpha-this.cosBeta*this.cosGamma)/this.sinGamma;this.cB_=b/this.sinGamma;this.a_=this.b*this.c*this.sinAlpha/this.volume;this.b_=this.a*this.c*this.sinBeta/this.volume;this.c_=this.a*this.b*this.sinGamma/this.volume;if(21<a.length&&!Float.isNaN(a[21])){b=O(16,0);for(c=0;16>c;c++){switch(c%4){case 0:g=this.na;break;case 1:g=this.nb;break;case 2:g=this.nc;break;default:g=1}b[c]=a[6+c]*g}this.matrixCartesianToFractional=
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c(c$,"getUnitCellAsArray",function(a){var b=this.matrixFractionalToCartesian;return a?[b.m00,b.m10,b.m20,b.m01,b.m11,b.m21,b.m02,b.m12,b.m22]:[this.a,this.b,this.c,this.alpha,this.beta,this.gamma,b.m00,b.m10,b.m20,b.m01,b.m11,b.m21,b.m02,b.m12,b.m22,this.dimension,this.volume]},"~B");c(c$,"getInfo",function(a){switch(a){case 0:return this.a;case 1:return this.b;case 2:return this.c;case 3:return this.alpha;case 4:return this.beta;case 5:return this.gamma;case 6:return this.dimension}return NaN},"~N");
c$.ijkToPoint3f=c(c$,"ijkToPoint3f",function(a,b,c){c-=5;b.x=s(a/100)+c;b.y=s(a%100/10)+c;b.z=a%10+c},"~N,JU.P3,~N");E(c$,"toRadians",0.017453292,"INFO_DIMENSIONS",6,"INFO_GAMMA",5,"INFO_BETA",4,"INFO_ALPHA",3,"INFO_C",2,"INFO_B",1,"INFO_A",0)}),p("J.util"),t(null,"J.util.TempArray",["java.lang.Boolean","$.Float","JU.P3","$.P3i"],function(){c$=w(function(){this.freeEnum=this.lengthsFreeEnum=this.freeScreens=this.lengthsFreeScreens=this.freePoints=this.lengthsFreePoints=null;u(this,arguments)},J.util,
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a)},"~A");c$.getSlabWithinRange=c(c$,"getSlabWithinRange",function(a,b){return[Integer.$valueOf(1073742114),[Float.$valueOf(a),Float.$valueOf(b)],Boolean.FALSE,null]},"~N,~N");c$.getSlabObjectType=c(c$,"getSlabObjectType",function(a,b,c,g){return[Integer.$valueOf(a),b,Boolean.$valueOf(c),g]},"~N,~O,~B,~O");E(c$,"freePointsSize",6,"freeScreensSize",6,"freeEnumSize",2)}),p("J.util"),t(null,"J.util.Txt",["java.lang.Character","$.Double","$.Float","JU.PT","$.SB"],function(){c$=M(J.util,"Txt");c$.formatStringS=
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function(){c$=w(function(){this.viewer=null;this.haveMultiTouchInput=!1;this.predragBinding=this.rasmolBinding=this.dragBinding=this.pfaatBinding=this.jmolBinding=this.binding=null;this.LEFT_DRAGGED=this.LEFT_CLICKED=0;this.hoverWatcherThread=null;la("J.viewer.ActionManager.MotionPoint")||J.viewer.ActionManager.$ActionManager$MotionPoint$();this.dragGesture=null;la("J.viewer.ActionManager.Gesture")||J.viewer.ActionManager.$ActionManager$Gesture$();this.atomPickingMode=1;this.pickingStyleSelect=this.pickingStyle=
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this.dragAtomIndex=-1;this.rubberbandSelectionMode=!1;this.rectRubber=null;this.isAltKeyReleased=!0;this.isMultiTouchServer=this.isMultiTouchClient=this.keyProcessing=!1;this.clickAction=this.dragAction=this.pressAction=0;this.measurementQueued=null;this.selectionWorking=!1;u(this,arguments)},J.viewer,"ActionManager",null,javajs.api.EventManager);Q(c$,function(){this.dragGesture=ka(J.viewer.ActionManager.Gesture,this,null,20);this.current=new J.viewer.MouseState("current");this.moved=new J.viewer.MouseState("moved");
this.clicked=new J.viewer.MouseState("clicked");this.pressed=new J.viewer.MouseState("pressed");this.dragged=new J.viewer.MouseState("dragged");this.rectRubber=new J.util.Rectangle});c(c$,"setViewer",function(a){this.viewer=a;this.setBinding(this.jmolBinding=new J.viewer.binding.JmolBinding);this.LEFT_CLICKED=J.viewer.binding.Binding.getMouseAction(1,16,2);this.LEFT_DRAGGED=J.viewer.binding.Binding.getMouseAction(1,16,1)},"J.viewer.Viewer,~S");c(c$,"checkHover",function(){if(!this.viewer.getInMotion(!0)&&
!this.viewer.getSpinOn()&&!this.viewer.getNavOn()&&!this.viewer.checkObjectHovered(this.current.x,this.current.y)){var a=this.viewer.findNearestAtomIndex(this.current.x,this.current.y);if(!(0>a)){var b=2==this.getAtomPickingMode()&&this.isBound(J.viewer.binding.Binding.getMouseAction(this.clickedCount,this.moved.modifiers,1),10);this.viewer.hoverOn(a,b)}}});c(c$,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(c$,"isBound",function(a,b){return this.binding.isBound(a,b)},"~N,~N");c(c$,
"bindAction",function(a,b){var c=J.viewer.ActionManager.getActionFromName(b),g=J.viewer.binding.Binding.getMouseActionStr(a);0!=g&&(0<=c?this.binding.bindAction(g,c):this.binding.bindName(g,b))},"~S,~S");c(c$,"clearBindings",function(){this.setBinding(this.jmolBinding=new J.viewer.binding.JmolBinding);this.rasmolBinding=this.dragBinding=this.pfaatBinding=null});c(c$,"unbindAction",function(a,b){if(null==a&&null==b)this.clearBindings();else{var c=J.viewer.ActionManager.getActionFromName(b),g=J.viewer.binding.Binding.getMouseActionStr(a);
0<=c?this.binding.unbindAction(g,c):0!=g&&this.binding.unbindName(g,b);null==b&&this.binding.unbindUserAction(a)}},"~S,~S");c$.newAction=c(c$,"newAction",function(a,b,c){J.viewer.ActionManager.actionInfo[a]=c;J.viewer.ActionManager.actionNames[a]=b},"~N,~S,~S");c$.getActionName=c(c$,"getActionName",function(a){return a<J.viewer.ActionManager.actionNames.length?J.viewer.ActionManager.actionNames[a]:null},"~N");c$.getActionFromName=c(c$,"getActionFromName",function(a){for(var b=0;b<J.viewer.ActionManager.actionNames.length;b++)if(J.viewer.ActionManager.actionNames[b].equalsIgnoreCase(a))return b;
return-1},"~S");c(c$,"getBindingInfo",function(a){return this.binding.getBindingInfo(J.viewer.ActionManager.actionInfo,J.viewer.ActionManager.actionNames,a)},"~S");c(c$,"setBinding",function(a){this.binding=a},"J.viewer.binding.Binding");c$.getPickingModeName=c(c$,"getPickingModeName",function(a){return 0>a||a>=J.viewer.ActionManager.pickingModeNames.length?"off":J.viewer.ActionManager.pickingModeNames[a]},"~N");c$.getPickingMode=c(c$,"getPickingMode",function(a){for(var b=J.viewer.ActionManager.pickingModeNames.length;0<=
--b;)if(a.equalsIgnoreCase(J.viewer.ActionManager.pickingModeNames[b]))return b;return-1},"~S");c(c$,"getAtomPickingMode",function(){return this.atomPickingMode});c(c$,"setPickingMode",function(a){var b=!1;switch(a){case -1:b=!0;this.bondPickingMode=35;a=1;break;case 35:case 34:case 33:this.viewer.setBooleanProperty("bondPicking",!0);this.bondPickingMode=a;return;case 8:this.bondPickingMode=a;if(this.viewer.getBondPicking())return;b=!0}b=(new Boolean(b|this.atomPickingMode!=a)).valueOf();this.atomPickingMode=
a;b&&this.resetMeasurement()},"~N");c(c$,"setAtomPickingOption",function(a){switch(this.atomPickingMode){case 32:this.pickAtomAssignType=a,this.isPickAtomAssignCharge=this.pickAtomAssignType.equals("Pl")||this.pickAtomAssignType.equals("Mi")}},"~S");c(c$,"setBondPickingOption",function(a){switch(this.bondPickingMode){case 33:this.pickBondAssignType=Character.toLowerCase(a.charAt(0))}},"~S");c$.getPickingStyleName=c(c$,"getPickingStyleName",function(a){return 0>a||a>=J.viewer.ActionManager.pickingStyleNames.length?
"toggle":J.viewer.ActionManager.pickingStyleNames[a]},"~N");c$.getPickingStyleIndex=c(c$,"getPickingStyleIndex",function(a){for(var b=J.viewer.ActionManager.pickingStyleNames.length;0<=--b;)if(a.equalsIgnoreCase(J.viewer.ActionManager.pickingStyleNames[b]))return b;return-1},"~S");c(c$,"getPickingState",function(){var a=";set modelkitMode "+this.viewer.getBoolean(603979883)+";set picking "+J.viewer.ActionManager.getPickingModeName(this.atomPickingMode);32==this.atomPickingMode&&(a+="_"+this.pickAtomAssignType);
a+=";";0!=this.bondPickingMode&&(a+="set picking "+J.viewer.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.pickBondAssignType);return a+";"});c(c$,"getPickingStyle",function(){return this.pickingStyle});c(c$,"setPickingStyle",function(a){this.pickingStyle=a;4<=a?(this.pickingStyleMeasure=a,this.resetMeasurement()):(3>a&&(this.rootPickingStyle=a),this.pickingStyleSelect=a);this.rubberbandSelectionMode=!1;switch(this.pickingStyleSelect){case 2:this.binding.name.equals("extendedSelect")||
this.setBinding(null==this.pfaatBinding?this.pfaatBinding=J.viewer.binding.Binding.newBinding("Pfaat"):this.pfaatBinding);break;case 3:this.binding.name.equals("drag")||this.setBinding(null==this.dragBinding?this.dragBinding=J.viewer.binding.Binding.newBinding("Drag"):this.dragBinding);this.rubberbandSelectionMode=!0;break;case 1:this.binding.name.equals("selectOrToggle")||this.setBinding(null==this.rasmolBinding?this.rasmolBinding=J.viewer.binding.Binding.newBinding("Rasmol"):this.rasmolBinding);
break;default:this.binding!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.binding.name.equals("drag")||(this.predragBinding=this.binding)},"~N");c(c$,"getMouseInfo",function(){for(var a=new java.util.Hashtable,b=new JU.List,c,g=this.binding.getBindings().values().iterator();g.hasNext()&&((c=g.next())||1);)r(c,Boolean)||(JU.PT.isAI(c)&&(c=[J.viewer.binding.Binding.getMouseActionName(c[0],!1),J.viewer.ActionManager.getActionName(c[1])]),b.addLast(c));a.put("bindings",b);a.put("bindingName",
this.binding.name);a.put("actionNames",J.viewer.ActionManager.actionNames);a.put("actionInfo",J.viewer.ActionManager.actionInfo);a.put("bindingInfo",JU.PT.split(this.getBindingInfo(null),"\n"));return a});c(c$,"setGestureSwipeFactor",function(a){this.gestureSwipeFactor=a},"~N");c(c$,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(c$,"setMouseWheelFactor",function(a){this.mouseWheelFactor=a},"~N");c(c$,"setCurrent",function(a,b,c,g){this.viewer.hoverOff();this.current.set(a,b,c,g)},
"~N,~N,~N,~N");c(c$,"getCurrentX",function(){return this.current.x});c(c$,"getCurrentY",function(){return this.current.y});c(c$,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=this.viewer.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.atomPickingMode){default:return;case 32:this.measuresEnabled=!this.isPickAtomAssignCharge;return;case 4:this.drawMode=!0;this.measuresEnabled=!1;break;case 2:this.labelMode=!0;this.measuresEnabled=
!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(c$,"clearMouseInfo",function(){this.pressedCount=this.clickedCount=0;this.dragGesture.setAction(0,0);this.exitMeasurementMode(null)});c(c$,"isMTClient",function(){return this.isMultiTouchClient});c(c$,"isMTServer",function(){return this.isMultiTouchServer});c(c$,"dispose",function(){this.clear()});c(c$,"clear",function(){this.startHoverWatcher(!1);null!=this.predragBinding&&
(this.binding=this.predragBinding);this.viewer.setPickingMode(null,1);this.viewer.setPickingStyle(null,this.rootPickingStyle);this.isAltKeyReleased=!0});c(c$,"startHoverWatcher",function(a){if(!this.viewer.isPreviewOnly())try{a?null==this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread=new J.thread.HoverWatcherThread(this,this.current,this.moved,this.viewer)):null!=this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread.interrupt(),this.hoverWatcherThread=null)}catch(b){if(!C(b,
Exception))throw b;}},"~B");c(c$,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");h(c$,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.viewer.hoverOff();this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.viewer.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.dragged.modifiers|=1;this.moved.modifiers|=1;break;case 17:this.moved.modifiers|=
2;break;case 27:this.exitMeasurementMode("escape")}var c=8464|this.moved.modifiers;!this.labelMode&&!this.binding.isUserAction(c)&&this.checkMotionRotateZoom(c,this.current.x,0,0,!1);if(this.viewer.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:case 32:case 46:this.viewer.navigate(a,b)}this.keyProcessing=!1;return!0},"~N,~N");h(c$,"keyReleased",function(a){switch(a){case 18:this.dragSelectedMode&&this.viewer.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1);
this.isAltKeyReleased=!0;this.moved.modifiers&=-9;break;case 16:this.moved.modifiers&=-2;break;case 17:this.moved.modifiers&=-3}0==this.moved.modifiers&&this.viewer.setCursor(0);if(this.viewer.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:this.viewer.navigate(0,0)}},"~N");h(c$,"mouseEnterExit",function(a,b,c,g){this.setCurrent(a,b,c,0);g&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(c$,"setMouseActions",function(a,b,c){this.pressAction=J.viewer.binding.Binding.getMouseAction(a,
b,c?5:4);this.dragAction=J.viewer.binding.Binding.getMouseAction(a,b,1);this.clickAction=J.viewer.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");h(c$,"mouseAction",function(a,b,c,g,e,f){if(this.viewer.getMouseEnabled())switch(J.util.Logger.debuggingHigh&&0!=a&&this.viewer.showString("mouse action: "+a+" "+f+" "+J.viewer.binding.Binding.getMouseActionName(J.viewer.binding.Binding.getMouseAction(e,f,a),!1),!1),a){case 0:this.setCurrent(b,c,g,f);this.moved.setCurrent(this.current,0);if(null!=this.measurementPending||
this.hoverActive){this.clickAction=J.viewer.binding.Binding.getMouseAction(this.clickedCount,f,0);this.checkClickAction(c,g,b,0);break}if(this.isZoomArea(c)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.viewer.getCursor()&&this.viewer.setCursor(0);break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(0,0,0,f,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.viewer.checkInMotion(1),this.setCurrent(b,c,g,f));this.pressAction=J.viewer.binding.Binding.getMouseAction(this.pressedCount,
f,4);this.viewer.setCursor(12);this.pressed.setCurrent(this.current,1);this.dragged.setCurrent(this.current,1);this.viewer.setFocus();this.dragGesture.setAction(this.dragAction,b);this.checkPressedAction(c,g,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,f,!1);a=c-this.dragged.x;e=g-this.dragged.y;this.setCurrent(b,c,g,f);this.dragged.setCurrent(this.current,-1);32!=this.atomPickingMode&&this.exitMeasurementMode(null);this.dragGesture.add(this.dragAction,c,g,b);this.checkDragWheelAction(this.dragAction,
c,g,a,e,b,1);break;case 5:this.setMouseActions(this.pressedCount,f,!0);this.setCurrent(b,c,g,f);this.viewer.spinXYBy(0,0,0);f=!this.pressed.check(this.xyRange,c,g,f,b,9223372036854775E3);this.checkReleaseAction(c,g,b,f);break;case 3:if(this.viewer.isApplet()&&!this.viewer.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,f);this.checkDragWheelAction(J.viewer.binding.Binding.getMouseAction(0,f,3),this.current.x,this.current.y,0,g,b,3);break;case 2:this.setMouseMode();this.clickedCount=
1<e?e:this.clicked.check(0,0,0,f,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,c,g,f);this.setMouseActions(this.clickedCount,f,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.viewer.setFocus();if(9!=this.atomPickingMode&&this.isBound(J.viewer.binding.Binding.getMouseAction(1,f,4),31))break;this.clickAction=J.viewer.binding.Binding.getMouseAction(this.clickedCount,f,2);this.checkClickAction(c,g,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(c$,"checkPressedAction",
function(a,b,c){var g=J.viewer.binding.Binding.getButtonMods(this.pressAction),e=this.isBound(J.viewer.binding.Binding.getMouseAction(1,g,4),31);if(0!=g){this.pressAction=this.viewer.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;g=J.viewer.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,g,!1);J.util.Logger.debugging&&J.util.Logger.debug(J.viewer.binding.Binding.getMouseActionName(this.pressAction,!1));if(this.drawMode&&(this.isBound(this.dragAction,
8)||this.isBound(this.dragAction,9))||this.labelMode&&this.isBound(this.dragAction,10))this.viewer.checkObjectDragged(-2147483648,0,a,b,this.dragAction);else{this.checkUserAction(this.pressAction,a,b,0,0,c,4);c=!1;switch(this.atomPickingMode){case 32:c=this.isBound(this.clickAction,0);break;case 28:c=this.isBound(this.dragAction,7)||this.isBound(this.dragAction,14);break;case 26:case 36:case 27:c=this.isBound(this.dragAction,7)||this.isBound(this.dragAction,27)||this.isBound(this.dragAction,14);break;
case 29:c=this.isBound(this.dragAction,11)||this.isBound(this.dragAction,14);break;case 30:c=this.isBound(this.dragAction,12)||this.isBound(this.dragAction,27)||this.isBound(this.dragAction,14)}if(c){if(this.dragAtomIndex=this.viewer.findNearestAtomIndexMovable(a,b,!0),0<=this.dragAtomIndex&&(32==this.atomPickingMode||31==this.atomPickingMode)&&this.viewer.isAtomAssignable(this.dragAtomIndex))this.enterMeasurementMode(this.dragAtomIndex),this.measurementPending.addPoint(this.dragAtomIndex,null,!1)}else this.isBound(this.pressAction,
23)?(e="j",this.viewer.getBoolean(603979883)&&(e=this.viewer.checkObjectClicked(a,b,this.LEFT_CLICKED),e=null!=e&&"bond".equals(e.get("type"))?"b":0<=this.viewer.findNearestAtomIndex(a,b)?"a":"m"),this.viewer.popupMenu(a,b,e)):this.dragSelectedMode?(this.haveSelection=!0,e&&(this.haveSelection=0<=this.viewer.findNearestAtomIndexMovable(a,b,!0)),this.haveSelection&&(this.isBound(this.dragAction,13)||this.isBound(this.dragAction,14))&&this.viewer.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,
null,!1,!1)):(this.viewer.global.useArcBall&&this.viewer.rotateArcBall(a,b,0),this.checkMotionRotateZoom(this.dragAction,a,0,0,!0))}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,c,g,e,f,j){var h=J.viewer.binding.Binding.getButtonMods(a);if(0!=h){h=this.viewer.notifyMouseClicked(b,c,J.viewer.binding.Binding.getMouseAction(this.pressedCount,h,j),j);if(0==h)return;0<h&&(a=h)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.viewer.refresh(3,"rubberBand selection");else if(!this.checkUserAction(a,
b,c,g,e,f,j)){if(0<=this.viewer.getRotateBondIndex()){if(this.isBound(a,26)){this.viewer.moveSelected(g,e,-2147483648,b,c,null,!1,!1);return}this.isBound(a,25)||this.viewer.setRotateBondIndex(-1)}f=null;if(0<=this.dragAtomIndex)switch(this.atomPickingMode){case 26:this.setMotion(13,!0);this.isBound(a,27)&&this.viewer.getBoolean(603979785)?this.viewer.rotateSelected(this.getDegrees(g,0),this.getDegrees(e,1),null):this.viewer.moveSelected(g,e,this.isBound(a,14)?-e:-2147483648,-2147483648,-2147483648,
null,!0,!1);return;case 36:case 27:case 30:f=this.viewer.getAtomBits(1095761936,J.util.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.atomPickingMode&&f.and(this.viewer.getAtomBitSet("ligand"));case 28:case 29:1==this.dragGesture.getPointCount()&&this.viewer.undoMoveActionClear(this.dragAtomIndex,2,!0);this.setMotion(13,!0);if(this.isBound(a,27))this.viewer.rotateSelected(this.getDegrees(g,0),this.getDegrees(e,1),f);else{switch(this.atomPickingMode){case 36:case 27:case 30:this.viewer.select(f,
!1,0,!0)}this.viewer.moveAtomWithHydrogens(this.dragAtomIndex,g,e,this.isBound(a,14)?-e:-2147483648,f)}return}0<=this.dragAtomIndex&&1==j&&this.isBound(this.clickAction,0)&&32==this.atomPickingMode?(e=this.viewer.findNearestAtomIndexMovable(b,c,!1),0<=e?(null!=this.measurementPending?this.measurementPending.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(e),this.addToMeasurement(e,null,!0),this.measurementPending.colix=20):null!=this.measurementPending&&(this.measurementPending.setCount(1),
this.measurementPending.colix=23),null!=this.measurementPending&&(this.measurementPending.traceX=b,this.measurementPending.traceY=c,this.viewer.refresh(3,"assignNew"))):!this.drawMode&&!this.labelMode&&this.isBound(a,45)?this.viewer.translateXYBy(g,e):this.dragSelectedMode&&this.haveSelection&&(this.isBound(a,13)||this.isBound(a,27))?(b=this.viewer.getSelectionSet(!1).nextSetBit(0),0>b||(1==this.dragGesture.getPointCount()?this.viewer.undoMoveActionClear(b,2,!0):this.viewer.moveSelected(2147483647,
0,-2147483648,-2147483648,-2147483648,null,!1,!1),this.setMotion(13,!0),this.isBound(a,27)&&this.viewer.getBoolean(603979785)?this.viewer.rotateSelected(this.getDegrees(g,0),this.getDegrees(e,1),null):this.viewer.moveSelected(g,e,-2147483648,-2147483648,-2147483648,null,!0,!1))):this.drawMode&&(this.isBound(a,8)||this.isBound(a,9))||this.labelMode&&this.isBound(a,10)?(this.setMotion(13,!0),this.viewer.checkObjectDragged(this.dragged.x,this.dragged.y,b,c,a)):this.checkMotionRotateZoom(a,b,g,e,!0)?
this.viewer.getSlabEnabled()&&this.checkSlideZoom(a)?this.viewer.slabDepthByPixels(e):this.viewer.zoomBy(e):this.isBound(a,25)?(a=this.getDegrees(g,0),e=this.getDegrees(e,1),this.viewer.global.useArcBall?this.viewer.rotateArcBall(b,c,this.mouseDragFactor):this.viewer.rotateXYBy(a,e)):this.isBound(a,29)?0==g&&1<Math.abs(e)?(this.setMotion(8,!0),this.viewer.zoomBy(e+(0<e?-1:1))):0==e&&1<Math.abs(g)&&(this.setMotion(13,!0),this.viewer.rotateZBy(-g+(0<g?1:-1),2147483647,2147483647)):this.isBound(a,46)?
this.zoomByFactor(e,2147483647,2147483647):this.isBound(a,28)?(this.setMotion(13,!0),this.viewer.rotateZBy(-g,2147483647,2147483647)):this.viewer.getSlabEnabled()&&(this.isBound(a,6)?this.viewer.depthByPixels(e):this.isBound(a,38)?this.viewer.slabByPixels(e):this.isBound(a,39)&&this.viewer.slabDepthByPixels(e))}},"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkReleaseAction",function(a,b,c,g){J.util.Logger.debugging&&J.util.Logger.debug(J.viewer.binding.Binding.getMouseActionName(this.pressAction,!1));this.viewer.checkInMotion(0);
this.viewer.setInMotion(!1);this.viewer.setCursor(0);this.dragGesture.add(this.dragAction,a,b,c);g&&this.viewer.setRotateBondIndex(-2147483648);0<=this.dragAtomIndex&&(29==this.atomPickingMode||30==this.atomPickingMode)&&this.minimize(!0);if(32==this.atomPickingMode&&this.isBound(this.clickAction,0))null==this.measurementPending||0>this.dragAtomIndex||this.assignNew(a,b);else if(this.dragAtomIndex=-1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=
this.binding.name.equals("drag"),this.rectRubber.x=2147483647,g&&this.viewer.notifyMouseClicked(a,b,J.viewer.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.drawMode&&(this.isBound(this.dragAction,8)||this.isBound(this.dragAction,9))||this.labelMode&&this.isBound(this.dragAction,10))this.viewer.checkObjectDragged(2147483647,0,a,b,this.dragAction);else if(this.dragSelectedMode&&(this.isBound(this.dragAction,13)&&this.haveSelection)&&this.viewer.moveSelected(2147483647,0,-2147483648,-2147483648,
-2147483648,null,!1,!1),(!g||!this.checkUserAction(this.pressAction,a,b,0,0,c,5))&&this.viewer.getBoolean(603979780)&&this.isBound(this.dragAction,44))a=this.getExitRate(),0<a&&this.viewer.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.viewer.global.logGestures&&this.viewer.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");c(c$,"checkClickAction",function(a,b,c,g){if(this.viewer.haveModelSet()){if(0<g){if(this.checkUserAction(this.clickAction,
a,b,0,0,c,32768))return;this.clickAction=this.viewer.notifyMouseClicked(a,b,this.clickAction,32768);if(0==this.clickAction)return}J.util.Logger.debugging&&J.util.Logger.debug(J.viewer.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.isBound(this.clickAction,2)&&this.viewer.frankClicked(a,b))this.viewer.popupMenu(-a,b,"j");else if(this.isBound(this.clickAction,2)&&this.viewer.frankClickedModelKit(a,b))this.viewer.popupMenu(0,0,"m");else{c=null;var e=!1,f=!1,j=null;this.drawMode||(j=
this.viewer.checkObjectClicked(a,b,this.clickAction),null!=j&&(e="bond".equals(j.get("type")),f="isosurface".equals(j.get("type")),c=this.getPoint(j)));e&&(g=1);if(!(null!=c&&Float.isNaN(c.x))){var h=this.findNearestAtom(a,b,c,0<g);if(0==g&&32!=this.atomPickingMode)null!=this.measurementPending&&((null!=c||0==this.measurementPending.getIndexOf(h))&&this.measurementPending.addPoint(h,c,!1),this.measurementPending.haveModified&&this.viewer.setPendingMeasurement(this.measurementPending),this.viewer.refresh(3,
"measurementPending"));else if(this.setMouseMode(),this.isBound(this.clickAction,43)&&this.viewer.stopMotion(),this.viewer.getBoolean(603979887)&&23==this.atomPickingMode&&this.isBound(this.clickAction,21))this.viewer.navTranslatePercent(100*a/this.viewer.getScreenWidth()-50,100*b/this.viewer.getScreenHeight()-50);else{if(e){if(this.isBound(this.clickAction,34==this.bondPickingMode||33==this.bondPickingMode?0:5)){this.bondPicked(j.get("index").intValue());return}}else{if(f)return;if(32!=this.atomPickingMode&&
null!=this.measurementPending&&this.isBound(this.clickAction,20)){this.atomOrPointPicked(h,c);4==this.addToMeasurement(h,c,!1)&&this.toggleMeasurement();return}if(this.isBound(this.clickAction,37)){null!=this.measurementPending?(this.addToMeasurement(h,c,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(h),this.addToMeasurement(h,c,!0));this.atomOrPointPicked(h,c);return}}this.isSelectAction(this.clickAction)?
f||this.atomOrPointPicked(h,c):this.isBound(this.clickAction,24)&&0>h&&this.reset()}}}}},"~N,~N,~N,~N");c(c$,"checkUserAction",function(a,b,c,g,e,f,j){if(!this.binding.isUserAction(a))return!1;for(var h=!1,l,m=this.binding.getBindings(),n=a+"\t",q,p=m.keySet().iterator();p.hasNext()&&((q=p.next())||1);)if(0==q.indexOf(n)&&JU.PT.isAS(l=m.get(q))){var r=l[1],s=null;if(0<=r.indexOf("_ATOM")){var t=this.findNearestAtom(b,c,null,!0),r=JU.PT.simpleReplace(r,"_ATOM","({"+(0<=t?""+t:"")+"})");0<=t&&(r=JU.PT.simpleReplace(r,
"_POINT",J.util.Escape.eP(this.viewer.getModelSet().atoms[t])))}if(!this.drawMode&&(0<=r.indexOf("_POINT")||0<=r.indexOf("_OBJECT")||0<=r.indexOf("_BOND"))){t=this.viewer.checkObjectClicked(b,c,a);if(null!=t&&null!=(s=t.get("pt")))t.get("type").equals("bond")&&(r=JU.PT.simpleReplace(r,"_BOND","[{"+t.get("index")+"}]")),r=JU.PT.simpleReplace(r,"_POINT",J.util.Escape.eP(s)),r=JU.PT.simpleReplace(r,"_OBJECT",J.util.Escape.escapeMap(t));r=JU.PT.simpleReplace(r,"_BOND","[{}]");r=JU.PT.simpleReplace(r,
"_OBJECT","{}")}r=JU.PT.simpleReplace(r,"_POINT","{}");r=JU.PT.simpleReplace(r,"_ACTION",""+a);r=JU.PT.simpleReplace(r,"_X",""+b);r=JU.PT.simpleReplace(r,"_Y",""+(this.viewer.getScreenHeight()-c));r=JU.PT.simpleReplace(r,"_DELTAX",""+g);r=JU.PT.simpleReplace(r,"_DELTAY",""+e);r=JU.PT.simpleReplace(r,"_TIME",""+f);r=JU.PT.simpleReplace(r,"_MODE",""+j);r.startsWith("+:")&&(h=!0,r=r.substring(2));this.viewer.evalStringQuiet(r)}return!h},"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,
b,c,g,e){b=this.checkSlideZoom(a);var f=this.isBound(a,25),j=this.isBound(a,29);if(!b&&!f&&!j)return!1;a=(c=j&&(0==c||Math.abs(g)>5*Math.abs(c)))||this.isZoomArea(this.moved.x)||this.isBound(a,46)?8:f||j?13:this.isBound(a,1)?12:0;this.setMotion(a,e);return c||b},"~N,~N,~N,~N,~B");c(c$,"getExitRate",function(){return 10<this.dragGesture.getTimeDifference(2)?0:this.dragGesture.getSpeedPixelsPerMillisecond(4,2)});c(c$,"isRubberBandSelect",function(a){a=a&-8193|32768;return this.rubberbandSelectionMode&&
(this.isBound(a,35)||this.isBound(a,34)||this.isBound(a,32))},"~N");c(c$,"getRubberBand",function(){return!this.rubberbandSelectionMode||2147483647==this.rectRubber.x?null:this.rectRubber});c(c$,"calcRectRubberBand",function(){var a=this.viewer.isAntialiased()?2:1;this.current.x<this.pressed.x?(this.rectRubber.x=this.current.x*a,this.rectRubber.width=(this.pressed.x-this.current.x)*a):(this.rectRubber.x=this.pressed.x*a,this.rectRubber.width=(this.current.x-this.pressed.x)*a);this.current.y<this.pressed.y?
(this.rectRubber.y=this.current.y*a,this.rectRubber.height=(this.pressed.y-this.current.y)*a):(this.rectRubber.y=this.pressed.y*a,this.rectRubber.height=(this.current.y-this.pressed.y)*a)});c(c$,"getDegrees",function(a,b){var c=0==b?this.viewer.getScreenWidth():this.viewer.getScreenHeight();500<c&&(c=500);return 180*(a/c)*this.mouseDragFactor},"~N,~N");c(c$,"checkSlideZoom",function(a){return this.isBound(a,40)&&this.isZoomArea(this.pressed.x)},"~N");c(c$,"isZoomArea",function(a){return a>98*this.viewer.getScreenWidth()*
(this.viewer.isStereoDouble()?2:1)/100},"~N");c(c$,"getPoint",function(a){var b=new J.util.Point3fi;b.setT(a.get("pt"));b.modelIndex=a.get("modelIndex").intValue();return b},"java.util.Map");c(c$,"findNearestAtom",function(a,b,c,g){a=this.drawMode||null!=c?-1:this.viewer.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(g||null==this.measurementPending)&&!this.viewer.isInSelectionSubset(a)?-1:a},"~N,~N,J.util.Point3fi,~B");c(c$,"isSelectAction",function(a){return this.isBound(a,17)||!this.drawMode&&
!this.labelMode&&1==this.atomPickingMode&&this.isBound(a,1)||this.dragSelectedMode&&(this.isBound(this.dragAction,27)||this.isBound(this.dragAction,13))||this.isBound(a,22)||this.isBound(a,35)||this.isBound(a,32)||this.isBound(a,34)||this.isBound(a,36)||this.isBound(a,30)},"~N");c(c$,"enterMeasurementMode",function(a){this.viewer.setPicked(-1);this.viewer.setPicked(a);this.viewer.setCursor(1);this.viewer.setPendingMeasurement(this.measurementPending=this.viewer.getMP());this.measurementQueued=this.measurementPending},
"~N");c(c$,"addToMeasurement",function(a,b,c){if(-1==a&&null==b||null==this.measurementPending)return this.exitMeasurementMode(null),0;var g=this.measurementPending.count;-2147483648!=this.measurementPending.traceX&&2==g&&this.measurementPending.setCount(g=1);return 4==g&&!c?g:this.measurementPending.addPoint(a,b,!0)},"~N,J.util.Point3fi,~B");c(c$,"resetMeasurement",function(){this.exitMeasurementMode(null);this.measurementQueued=this.viewer.getMP()});c(c$,"exitMeasurementMode",function(a){null!=
this.measurementPending&&(this.viewer.setPendingMeasurement(this.measurementPending=null),this.viewer.setCursor(0),null!=a&&this.viewer.refresh(3,a))},"~S");c(c$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);0>a||0>b||(a=this.viewer.getSmiles(a,b,null,!0,!1,!1,!1),this.viewer.setStatusMeasuring("measureSequence",-2,a,0))});c(c$,"minimize",function(a){this.viewer.stopMinimization();var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1);
a=0==this.viewer.getMotionFixedAtoms().cardinality()?this.viewer.getAtomBits(this.viewer.isAtomPDB(b)?1087373318:1095761936,J.util.BSUtil.newAndSetBit(b)):J.util.BSUtil.setAll(this.viewer.getAtomCount());this.viewer.minimize(2147483647,0,a,null,0,!1,!1,!1,!1)},"~B");c(c$,"queueAtom",function(a,b){var c=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.viewer.setStatusAtomPicked(a,"Atom #"+c+":"+this.viewer.getAtomInfo(a));return c},"~N,J.util.Point3fi");c(c$,"setMotion",function(a,b){switch(this.viewer.getCursor()){case 3:break;
default:this.viewer.setCursor(a)}b&&this.viewer.setInMotion(!0)},"~N,~B");c(c$,"zoomByFactor",function(a,b,c){0!=a&&(this.setMotion(8,!0),this.viewer.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,c),this.viewer.setInMotion(!1))},"~N,~N,~N");c(c$,"runScript",function(a){this.viewer.script(a)},"~S");c(c$,"atomOrPointPicked",function(a,b){if(0>a){this.resetMeasurement();if(this.isBound(this.clickAction,33)){this.runScript("select none");return}if(5!=this.atomPickingMode&&6!=this.atomPickingMode)return}var c=
2;switch(this.atomPickingMode){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var g=8==this.atomPickingMode,c=25==this.atomPickingMode;if(!this.isBound(this.clickAction,g?5:3))return;if(null==this.measurementQueued||0==this.measurementQueued.count||2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);if(2!=this.queueAtom(a,b))return;g=g||this.measurementQueued.isConnected(this.viewer.getModelSet().atoms,2)?" DELETE":c?"STRUTS":
"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+g);this.resetMeasurement();return;case 21:c++;case 20:c++;case 18:case 19:case 22:if(!this.isBound(this.clickAction,20))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>c)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);g=this.measurementQueued.count;1==g&&(this.viewer.setPicked(-1),this.viewer.setPicked(a));if(g<
c)return;22==this.atomPickingMode?this.getSequence():(this.viewer.setStatusMeasuring("measurePicked",c,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.atomPickingMode||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}g=null!=this.measurementPending&&1!=this.atomPickingMode?1:this.atomPickingMode;switch(g){case 3:if(!this.isBound(this.clickAction,17))return;null==b?this.zoomTo(a):
this.runScript("zoomTo "+J.util.Escape.eP(b));return;case 5:case 6:this.isBound(this.clickAction,17)&&this.checkTwoAtomAction(b,a)}if(null==b){switch(g){case 1:!this.drawMode&&!this.labelMode&&this.isBound(this.clickAction,1)?this.zoomTo(a):this.isBound(this.clickAction,17)&&this.viewer.setStatusAtomPicked(a,null);return;case 2:this.isBound(this.clickAction,19)&&(this.runScript("set labeltoggle {atomindex="+a+"}"),this.viewer.setStatusAtomPicked(a,null));return;case 31:if(this.isBound(this.clickAction,
0)){var c=this.viewer.getAtomBitSet("connected(atomIndex="+a+") and !within(SMARTS,'[r50,R]')"),e=c.cardinality();switch(e){case 0:case 1:return;case 3:case 4:for(var f=D(e,0),j=D(e,0),h=0,g=c.nextSetBit(0);0<=g;g=c.nextSetBit(g+1),h++)f[h]=this.viewer.getBranchBitSet(g,a,!0).cardinality(),j[h]=g;for(h=0;h<e-2;h++){for(var l=-2147483648,m=0,g=0;g<e;g++)f[g]>=l&&c.get(j[g])&&(m=j[g],l=f[g]);c.clear(m)}}this.viewer.undoMoveActionClear(a,2,!0);this.viewer.invertSelected(null,null,a,c);this.viewer.setStatusAtomPicked(a,
"inverted: "+J.util.Escape.eBS(c))}return;case 7:this.isBound(this.clickAction,4)&&(c=J.util.BSUtil.newAndSetBit(a),this.viewer.deleteAtoms(c,!1),this.viewer.setStatusAtomPicked(a,"deleted: "+J.util.Escape.eBS(c)));return}g="atomindex="+a;switch(this.atomPickingMode){default:return;case 9:this.selectAtoms(g);break;case 10:this.selectAtoms("within(group, "+g+")");break;case 11:this.selectAtoms("within(chain, "+g+")");break;case 13:this.selectAtoms("within(polymer, "+g+")");break;case 14:this.selectAtoms("within(structure, "+
g+")");break;case 12:this.selectAtoms("within(molecule, "+g+")");break;case 16:this.selectAtoms("within(model, "+g+")");break;case 17:this.selectAtoms("visible and within(element, "+g+")");break;case 15:this.selectAtoms("visible and within(site, "+g+")")}this.viewer.clearClickCount();this.viewer.setStatusAtomPicked(a,null)}},"~N,J.util.Point3fi");c(c$,"assignNew",function(a,b){if(2==this.measurementPending.count)this.viewer.undoMoveActionClear(-1,4146,!0),this.runScript("assign connect "+this.measurementPending.getMeasurementScript(" ",
!1));else if(this.pickAtomAssignType.equals("Xx"))this.exitMeasurementMode("bond dropped");else if(this.pressed.inRange(this.xyRange,this.dragged.x,this.dragged.y)){var c="assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'"';this.isPickAtomAssignCharge?(c+=";{atomindex="+this.dragAtomIndex+"}.label='%C'; ",this.viewer.undoMoveActionClear(this.dragAtomIndex,4,!0)):this.viewer.undoMoveActionClear(-1,4146,!0);this.runScript(c)}else this.isPickAtomAssignCharge||(this.viewer.undoMoveActionClear(-1,
4146,!0),c=this.viewer.getModelSet().atoms[this.dragAtomIndex],1==c.getElementNumber()?this.runScript("assign atom ({"+this.dragAtomIndex+'}) "X"'):(c=JU.P3.new3(a,b,c.sZ),this.viewer.unTransformPoint(c,c),this.runScript("assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'" '+J.util.Escape.eP(c))));this.exitMeasurementMode(null)},"~N,~N");c(c$,"bondPicked",function(a){33==this.bondPickingMode&&this.viewer.undoMoveActionClear(-1,4146,!0);switch(this.bondPickingMode){case 33:this.runScript("assign bond [{"+
a+'}] "'+this.pickBondAssignType+'"');break;case 34:this.viewer.setRotateBondIndex(a);break;case 8:this.viewer.deleteBonds(J.util.BSUtil.newAndSetBit(a))}},"~N");c(c$,"checkTwoAtomAction",function(a,b){var c=5==this.atomPickingMode;if(this.viewer.getSpinOn()||this.viewer.getNavOn()||null!=this.viewer.getPendingMeasurement())this.resetMeasurement(),this.viewer.getSpinOn()&&this.runScript("spin off");else{2<=this.measurementQueued.count&&this.resetMeasurement();var g=this.measurementQueued.count;if(1==
g)if(null==a){if(this.measurementQueued.getAtomIndex(1)==b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=b||null!=a)g=this.queueAtom(b,a);2>g?c?this.viewer.scriptStatus(1==g?J.i18n.GT._("pick one more atom in order to spin the model around an axis"):J.i18n.GT._("pick two atoms in order to spin the model around an axis")):this.viewer.scriptStatus(1==g?J.i18n.GT._("pick one more atom in order to display the symmetry relationship"):J.i18n.GT._("pick two atoms in order to display the symmetry relationship between them")):
(g=this.measurementQueued.getMeasurementScript(" ",!1),c?this.runScript("spin"+g+" "+this.viewer.getInt(553648157)):this.runScript("draw symop"+g+";show symop"+g))}},"J.util.Point3fi,~N");c(c$,"reset",function(){this.runScript("!reset")});c(c$,"selectAtoms",function(a){if(!(null!=this.measurementPending||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.isBound(this.clickAction,35)?"selected and not ("+a+") or (not selected) and ":this.isBound(this.clickAction,
32)?"selected and not ":this.isBound(this.clickAction,34)?"selected or ":0==this.clickAction||this.isBound(this.clickAction,36)?"selected tog ":this.isBound(this.clickAction,30)?"":null;if(null!=b)try{var c=this.viewer.getAtomBitSetEval(null,b+("("+a+")"));this.viewer.select(c,!1,0,!1);this.viewer.refresh(3,"selections set")}catch(g){if(!C(g,Exception))throw g;}this.selectionWorking=!1}},"~S");c(c$,"selectRb",function(a){var b=this.viewer.findAtomsInRectangle(this.rectRubber);0<b.length()&&(b=J.util.Escape.eBS(b),
this.isBound(a,34)?this.runScript("selectionHalos on;select selected or "+b):this.isBound(a,32)?this.runScript("selectionHalos on;select selected and not "+b):this.runScript("selectionHalos on;select selected tog "+b));this.viewer.refresh(3,"mouseReleased")},"~N");c(c$,"toggleMeasurement",function(){if(null!=this.measurementPending){var a=this.measurementPending.count;2<=a&&4>=a&&this.runScript("!measure "+this.measurementPending.getMeasurementScript(" ",!0));this.exitMeasurementMode(null)}});c(c$,
"zoomTo",function(a){this.runScript("zoomTo (atomindex="+a+")");this.viewer.setStatusAtomPicked(a,null)},"~N");h(c$,"keyTyped",function(){return!1},"~N,~N");c$.$ActionManager$MotionPoint$=function(){fa();c$=w(function(){ma(this,arguments);this.time=this.y=this.x=this.index=0;u(this,arguments)},J.viewer.ActionManager,"MotionPoint");c(c$,"set",function(a,b,c,g){this.index=a;this.x=b;this.y=c;this.time=g},"~N,~N,~N,~N");h(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+
" ]"});c$=ea()};c$.$ActionManager$Gesture$=function(){fa();c$=w(function(){ma(this,arguments);this.action=0;this.nodes=null;this.time0=this.ptNext=0;u(this,arguments)},J.viewer.ActionManager,"Gesture");A(c$,function(a){this.nodes=Array(a);for(var b=0;b<a;b++)this.nodes[b]=ka(J.viewer.ActionManager.MotionPoint,this,null)},"~N");c(c$,"setAction",function(a,b){this.action=a;this.ptNext=0;this.time0=b;for(var c=0;c<this.nodes.length;c++)this.nodes[c].index=-1},"~N,~N");c(c$,"add",function(a,b,c,g){this.action=
a;this.getNode(this.ptNext).set(this.ptNext,b,c,g-this.time0);this.ptNext++;return this.ptNext},"~N,~N,~N,~N");c(c$,"getTimeDifference",function(a){a=this.getPointCount2(a,0);if(2>a)return 0;var b=this.getNode(this.ptNext-1);a=this.getNode(this.ptNext-a);return b.time-a.time},"~N");c(c$,"getSpeedPixelsPerMillisecond",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),g=this.getNode(this.ptNext-a-b),e=360*((c.x-g.x)/this.b$["J.viewer.ActionManager"].viewer.getScreenWidth()),
f=360*((c.y-g.y)/this.b$["J.viewer.ActionManager"].viewer.getScreenHeight());return Math.sqrt(e*e+f*f)/(c.time-g.time)},"~N,~N");c(c$,"getDX",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),g=this.getNode(this.ptNext-a-b);return c.x-g.x},"~N,~N");c(c$,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),g=this.getNode(this.ptNext-a-b);return c.y-g.y},"~N,~N");c(c$,"getPointCount",function(){return this.ptNext});
c(c$,"getPointCount2",function(a,b){a>this.nodes.length-b&&(a=this.nodes.length-b);for(var c=a+1;0<=--c&&!(0<=this.getNode(this.ptNext-c-b).index););return c},"~N,~N");c(c$,"getNode",function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");h(c$,"toString",function(){return 0==this.nodes.length?""+this:J.viewer.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]});c$=ea()};E(c$,"ACTION_assignNew",0,"ACTION_center",1,
"ACTION_clickFrank",2,"ACTION_connectAtoms",3,"ACTION_deleteAtom",4,"ACTION_deleteBond",5,"ACTION_depth",6,"ACTION_dragAtom",7,"ACTION_dragDrawObject",8,"ACTION_dragDrawPoint",9,"ACTION_dragLabel",10,"ACTION_dragMinimize",11,"ACTION_dragMinimizeMolecule",12,"ACTION_dragSelected",13,"ACTION_dragZ",14,"ACTION_multiTouchSimulation",15,"ACTION_navTranslate",16,"ACTION_pickAtom",17,"ACTION_pickIsosurface",18,"ACTION_pickLabel",19,"ACTION_pickMeasure",20,"ACTION_pickNavigate",21,"ACTION_pickPoint",22,"ACTION_popupMenu",
23,"ACTION_reset",24,"ACTION_rotate",25,"ACTION_rotateBranch",26,"ACTION_rotateSelected",27,"ACTION_rotateZ",28,"ACTION_rotateZorZoom",29,"ACTION_select",30,"ACTION_selectAndDrag",31,"ACTION_selectAndNot",32,"ACTION_selectNone",33,"ACTION_selectOr",34,"ACTION_selectToggle",35,"ACTION_selectToggleExtended",36,"ACTION_setMeasure",37,"ACTION_slab",38,"ACTION_slabAndDepth",39,"ACTION_slideZoom",40,"ACTION_spinDrawObjectCCW",41,"ACTION_spinDrawObjectCW",42,"ACTION_stopMotion",43,"ACTION_swipe",44,"ACTION_translate",
45,"ACTION_wheelZoom",46,"ACTION_count",47);c$.actionInfo=c$.prototype.actionInfo=Array(47);c$.actionNames=c$.prototype.actionNames=Array(47);J.viewer.ActionManager.newAction(0,"_assignNew",J.i18n.GT.o(J.i18n.GT._("assign/new atom or bond (requires {0})"),"set picking assignAtom_??/assignBond_?"));J.viewer.ActionManager.newAction(1,"_center",J.i18n.GT._("center"));J.viewer.ActionManager.newAction(2,"_clickFrank",J.i18n.GT._("pop up recent context menu (click on Jmol frank)"));J.viewer.ActionManager.newAction(4,
"_deleteAtom",J.i18n.GT.o(J.i18n.GT._("delete atom (requires {0})"),"set picking DELETE ATOM"));J.viewer.ActionManager.newAction(5,"_deleteBond",J.i18n.GT.o(J.i18n.GT._("delete bond (requires {0})"),"set picking DELETE BOND"));J.viewer.ActionManager.newAction(6,"_depth",J.i18n.GT.o(J.i18n.GT._("adjust depth (back plane; requires {0})"),"SLAB ON"));J.viewer.ActionManager.newAction(7,"_dragAtom",J.i18n.GT.o(J.i18n.GT._("move atom (requires {0})"),"set picking DRAGATOM"));J.viewer.ActionManager.newAction(8,
"_dragDrawObject",J.i18n.GT.o(J.i18n.GT._("move whole DRAW object (requires {0})"),"set picking DRAW"));J.viewer.ActionManager.newAction(9,"_dragDrawPoint",J.i18n.GT.o(J.i18n.GT._("move specific DRAW point (requires {0})"),"set picking DRAW"));J.viewer.ActionManager.newAction(10,"_dragLabel",J.i18n.GT.o(J.i18n.GT._("move label (requires {0})"),"set picking LABEL"));J.viewer.ActionManager.newAction(11,"_dragMinimize",J.i18n.GT.o(J.i18n.GT._("move atom and minimize molecule (requires {0})"),"set picking DRAGMINIMIZE"));
J.viewer.ActionManager.newAction(12,"_dragMinimizeMolecule",J.i18n.GT.o(J.i18n.GT._("move and minimize molecule (requires {0})"),"set picking DRAGMINIMIZEMOLECULE"));J.viewer.ActionManager.newAction(13,"_dragSelected",J.i18n.GT.o(J.i18n.GT._("move selected atoms (requires {0})"),"set DRAGSELECTED"));J.viewer.ActionManager.newAction(14,"_dragZ",J.i18n.GT.o(J.i18n.GT._("drag atoms in Z direction (requires {0})"),"set DRAGSELECTED"));J.viewer.ActionManager.newAction(15,"_multiTouchSimulation",J.i18n.GT._("simulate multi-touch using the mouse)"));
J.viewer.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT._("translate navigation point (requires {0} and {1})"),["set NAVIGATIONMODE","set picking NAVIGATE"]));J.viewer.ActionManager.newAction(17,"_pickAtom",J.i18n.GT._("pick an atom"));J.viewer.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT._("connect atoms (requires {0})"),"set picking CONNECT"));J.viewer.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT._("pick an ISOSURFACE point (requires {0}"),
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"set pickingStyle DRAG/EXTENDEDSELECT"));J.viewer.ActionManager.newAction(35,"_selectToggle",J.i18n.GT.o(J.i18n.GT._("toggle selection (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL"));J.viewer.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT._("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG"));J.viewer.ActionManager.newAction(37,"_setMeasure",J.i18n.GT._("pick an atom to initiate or conclude a measurement"));
J.viewer.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT._("adjust slab (front plane; requires {0})"),"SLAB ON"));J.viewer.ActionManager.newAction(39,"_slabAndDepth",J.i18n.GT.o(J.i18n.GT._("move slab/depth window (both planes; requires {0})"),"SLAB ON"));J.viewer.ActionManager.newAction(40,"_slideZoom",J.i18n.GT._("zoom (along right edge of window)"));J.viewer.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT._("click on two points to spin around axis counterclockwise (requires {0})"),
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4,"PICKINGSTYLE_MEASURE_OFF",5,"pickingStyleNames","toggle selectOrToggle extendedSelect drag measure measureoff".split(" "),"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1)}),p("J.viewer"),t(["JU.BS","J.constant.EnumAnimationMode"],"J.viewer.AnimationManager",["J.api.Interface","J.util.BSUtil"],function(){c$=w(function(){this.viewer=this.animationThread=
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c$.getMouseActionName=c(c$,"getMouseActionName",function(a,b){var c=new JU.SB;if(0==a)return"";var g=J.viewer.binding.Binding.includes(a,8)&&!J.viewer.binding.Binding.includes(a,16)&&!J.viewer.binding.Binding.includes(a,4),e="      ".toCharArray();J.viewer.binding.Binding.includes(a,2)&&(c.append("CTRL+"),e[5]="C");!g&&J.viewer.binding.Binding.includes(a,8)&&(c.append("ALT+"),e[4]="A");J.viewer.binding.Binding.includes(a,1)&&(c.append("SHIFT+"),e[3]="S");J.viewer.binding.Binding.includes(a,16)?(e[2]=
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32768)&&(c.append("+click"),e[0]="4");return b?String.instantialize(e)+":"+c.toString():c.toString()},"~N,~B");c(c$,"getBindings",function(){return this.bindings});A(c$,function(){});c(c$,"bindAction",function(a,b){this.addBinding(a+"\t"+b,[a,b])},"~N,~N");c(c$,"bindName",function(a,b){this.addBinding(a+"\t",Boolean.TRUE);this.addBinding(a+"\t"+b,[J.viewer.binding.Binding.getMouseActionName(a,!1),b])},"~N,~S");c(c$,"unbindAction",function(a,b){0==a?this.unbindJmolAction(b):this.removeBinding(null,
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J.util.Logger.debug("removing binding "+b);null==a?this.bindings.remove(b):a.remove()},"java.util.Iterator,~S");c(c$,"unbindUserAction",function(a){var b=this.bindings.keySet().iterator();for(a="\t"+a;b.hasNext();){var c=b.next();c.endsWith(a)&&this.removeBinding(b,c)}},"~S");c(c$,"unbindMouseAction",function(a){var b=this.bindings.keySet().iterator();for(a+="\t";b.hasNext();){var c=b.next();c.startsWith(a)&&this.removeBinding(b,c)}},"~N");c(c$,"isBound",function(a,b){return this.bindings.containsKey(a+
"\t"+b)},"~N,~N");c(c$,"isUserAction",function(a){return this.bindings.containsKey(a+"\t")},"~N");c(c$,"getBindingInfo",function(a,b,c){var g=new JU.SB;c=null==c||c.equalsIgnoreCase("all")?null:c.toLowerCase();for(var e=Array(a.length),f=new JU.List,j,h=this.bindings.values().iterator();h.hasNext()&&((j=h.next())||1);)if(JU.PT.isAI(j)){var l=j,m=l[1];null==e[m]&&(e[m]=new JU.List);l=J.viewer.binding.Binding.getMouseActionName(l[0],!0);(null==c||0<=(b[m]+";"+a[m]+";"+l).toLowerCase().indexOf(c))&&
e[m].addLast(l)}else JU.PT.isAS(j)&&(m=j[0],l=j[1],(null==c||0<=c.indexOf("user")||0<=m.indexOf(c)||0<=l.indexOf(c))&&f.addLast(j));for(m=0;m<a.length;m++){var n;null==e[m]||0==(n=e[m].size())||this.addInfo(g,e[m].toArray(Array(n)),b[m],a[m])}for(m=0;m<f.size();m++)l=f.get(m),this.addInfo(g,["USER:::"+l[0]],"user-defined",l[1]);return g.toString()},"~A,~A,~S");c(c$,"addInfo",function(a,b,c,g){java.util.Arrays.sort(b);J.util.Txt.leftJustify(a,"                      ",c);a.append("\t");c="";for(var e=
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20,"BUTTON_MASK",28,"BUTTON_MODIFIER_MASK",63,"SINGLE",256,"DOUBLE",512,"COUNT_MASK",768,"DOWN",4096,"DRAG",8192,"UP",16384,"CLICK",32768,"MODE_MASK",61440)}),p("J.viewer.binding"),t(["J.viewer.binding.JmolBinding"],"J.viewer.binding.DragBinding",null,function(){c$=M(J.viewer.binding,"DragBinding",J.viewer.binding.JmolBinding);A(c$,function(){U(this,J.viewer.binding.DragBinding,[]);this.set("drag")});h(c$,"setSelectBindings",function(){this.bindAction(33040,30);this.bindAction(33041,35);this.bindAction(33048,
34);this.bindAction(33049,32);this.bindAction(4368,31);this.bindAction(8464,13);this.bindAction(33040,17)})}),p("J.viewer.binding"),t(["J.viewer.binding.Binding"],"J.viewer.binding.JmolBinding",null,function(){c$=M(J.viewer.binding,"JmolBinding",J.viewer.binding.Binding);A(c$,function(){U(this,J.viewer.binding.JmolBinding,[]);this.set("toggle")});c(c$,"set",function(a){this.name=a;this.setGeneralBindings();this.setSelectBindings()},"~S");c(c$,"setSelectBindings",function(){this.bindAction(33296,30);
this.bindAction(33040,36)});c(c$,"setGeneralBindings",function(){this.bindAction(8474,45);this.bindAction(8454,45);this.bindAction(8721,45);this.bindAction(8712,45);this.bindAction(8464,25);this.bindAction(8472,28);this.bindAction(8453,28);this.bindAction(8465,29);this.bindAction(8456,29);this.bindAction(288,46);this.bindAction(8464,40);this.bindAction(8464,16);this.bindAction(4370,23);this.bindAction(4356,23);this.bindAction(33040,2);this.bindAction(8467,38);this.bindAction(8723,6);this.bindAction(8475,
39);this.bindAction(8464,44);this.bindAction(8464,41);this.bindAction(8465,42);this.bindAction(8473,13);this.bindAction(8465,14);this.bindAction(8472,27);this.bindAction(8465,26);this.bindAction(8465,10);this.bindAction(8472,9);this.bindAction(8465,8);this.bindAction(33297,24);this.bindAction(33288,24);this.bindAction(33296,43);this.bindAction(8464,7);this.bindAction(8464,11);this.bindAction(8464,12);this.bindAction(33040,17);this.bindAction(33040,22);this.bindAction(33040,19);this.bindAction(33040,
20);this.bindAction(33296,37);this.bindAction(33040,18);this.bindAction(33043,21);this.bindAction(33040,4);this.bindAction(33040,5);this.bindAction(33040,3);this.bindAction(33040,0);this.bindAction(33043,1)})}),p("J.viewer"),t(["J.util.ColorEncoder"],"J.viewer.ColorManager","java.lang.Float JU.AU J.constant.EnumPalette J.util.C $.Elements $.Logger J.viewer.JC".split(" "),function(){c$=w(function(){this.colorData=this.altArgbsCpk=this.argbsCpk=this.g3d=this.viewer=this.propertyColorEncoder=null;this.isDefaultColorRasmol=
!1;this.colixRubberband=22;this.colixBackgroundContrast=0;u(this,arguments)},J.viewer,"ColorManager");Q(c$,function(){this.propertyColorEncoder=new J.util.ColorEncoder(null)});A(c$,function(a,b){this.viewer=a;this.g3d=b;this.argbsCpk=J.constant.EnumPalette.argbsCpk;this.altArgbsCpk=JU.AU.arrayCopyRangeI(J.viewer.JC.altArgbsCpk,0,-1)},"J.viewer.Viewer,J.util.GData");c(c$,"clear",function(){});c(c$,"getDefaultColorRasmol",function(){return this.isDefaultColorRasmol});c(c$,"resetElementColors",function(){this.setDefaultColors(!1)});
c(c$,"setDefaultColors",function(a){a?(this.isDefaultColorRasmol=!0,this.argbsCpk=JU.AU.arrayCopyI(J.util.ColorEncoder.getRasmolScale(),-1)):(this.isDefaultColorRasmol=!1,this.argbsCpk=J.constant.EnumPalette.argbsCpk);this.altArgbsCpk=JU.AU.arrayCopyRangeI(J.viewer.JC.altArgbsCpk,0,-1);this.propertyColorEncoder.createColorScheme(a?"Rasmol=":"Jmol=",!0,!0);for(a=J.constant.EnumPalette.argbsCpk.length;0<=--a;)this.g3d.changeColixArgb(a,this.argbsCpk[a]);for(a=J.viewer.JC.altArgbsCpk.length;0<=--a;)this.g3d.changeColixArgb(J.util.Elements.elementNumberMax+
a,this.altArgbsCpk[a])},"~B");c(c$,"setRubberbandArgb",function(a){this.colixRubberband=0==a?0:J.util.C.getColix(a)},"~N");c(c$,"setColixBackgroundContrast",function(a){this.colixBackgroundContrast=J.util.C.getBgContrast(a)},"~N");c(c$,"getColixBondPalette",function(a,b){switch(b){case 19:return this.propertyColorEncoder.getColorIndexFromPalette(a.getEnergy(),-2.5,-0.5,7,!1)}return 10},"J.modelset.Bond,~N");c(c$,"getColixAtomPalette",function(a,b){var c=0,g;switch(b){case 84:return null==this.colorData||
a.index>=this.colorData.length?12:this.getColixForPropertyValue(this.colorData[a.index]);case 0:case 1:c=a.getAtomicAndIsotopeNumber();if(c<J.util.Elements.elementNumberMax)return this.g3d.getChangeableColix(c,this.argbsCpk[c]);g=c;c=J.util.Elements.altElementIndexFromNumber(c);return 0==c?(c=J.util.Elements.getElementNumber(g),this.g3d.getChangeableColix(c,this.argbsCpk[c])):this.g3d.getChangeableColix(J.util.Elements.elementNumberMax+c,this.altArgbsCpk[c]);case 2:return c=J.util.ColorEncoder.quantize(a.getPartialCharge(),
-1,1,J.viewer.JC.PARTIAL_CHARGE_RANGE_SIZE),this.g3d.getChangeableColix(J.viewer.JC.PARTIAL_CHARGE_COLIX_RED+c,J.viewer.JC.argbsRwbScale[c]);case 3:return c=a.getFormalCharge()- -4,this.g3d.getChangeableColix(J.viewer.JC.FORMAL_CHARGE_COLIX_RED+c,J.viewer.JC.argbsFormalCharge[c]);case 68:case 5:return 68==b?(c=this.viewer.getModelSet(),g=c.getBfactor100Lo(),c=c.getBfactor100Hi()):(g=0,c=1E4),this.propertyColorEncoder.getColorIndexFromPalette(a.getBfactor100(),g,c,7,!1);case 86:return this.propertyColorEncoder.getColorIndexFromPalette(a.getGroupParameter(1112539150),
-1,1,7,!1);case 70:return c=this.viewer.getSurfaceDistanceMax(),this.propertyColorEncoder.getColorIndexFromPalette(a.getSurfaceDistance100(),0,c,7,!1);case 8:return this.propertyColorEncoder.getColorIndexFromPalette(a.getGroupID(),0,0,5,!1);case 9:return this.propertyColorEncoder.getColorIndexFromPalette(a.getGroupID(),0,0,4,!1);case 75:return this.propertyColorEncoder.getColorIndexFromPalette(a.getSelectedGroupIndexWithinChain(),0,a.getSelectedGroupCountWithinChain()-1,1,!1);case 87:return c=this.viewer.getModelSet().models[a.modelIndex],
this.propertyColorEncoder.getColorIndexFromPalette(a.getPolymerIndexInModel(),0,c.getBioPolymerCount()-1,1,!1);case 76:return this.propertyColorEncoder.getColorIndexFromPalette(a.getSelectedMonomerIndexWithinPolymer(),0,a.getSelectedMonomerCountWithinPolymer()-1,1,!1);case 77:return c=this.viewer.getModelSet(),this.propertyColorEncoder.getColorIndexFromPalette(c.getMoleculeIndex(a.getIndex(),!0),0,c.getMoleculeCountInModel(a.getModelIndex())-1,0,!1);case 14:return c=this.viewer.getModelSet(),g=a.getModelIndex(),
this.propertyColorEncoder.getColorIndexFromPalette(c.getAltLocIndexInModel(g,a.getAlternateLocationID()),0,c.getAltLocCountInModel(g),0,!1);case 15:return c=this.viewer.getModelSet(),g=a.getModelIndex(),this.propertyColorEncoder.getColorIndexFromPalette(c.getInsertionCodeIndexInModel(g,a.getInsertionCode()),0,c.getInsertionCountInModel(g),0,!1);case 16:c=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(c,1073741992);break;case 17:c=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(c,
1073742116);break;case 7:c=a.getProteinStructureSubType().getColor();break;case 10:c=a.getChainID(),c=((0>c?0:256<=c?c-256:c)&31)%J.viewer.JC.argbsChainAtom.length,c=(a.isHetero()?J.viewer.JC.argbsChainHetero:J.viewer.JC.argbsChainAtom)[c]}return 0==c?22:J.util.C.getColix(c)},"J.modelset.Atom,~N");c(c$,"getJmolOrRasmolArgb",function(a,b){switch(b){case 1073741992:if(a>=J.util.Elements.elementNumberMax)break;return this.propertyColorEncoder.getArgbFromPalette(a,0,0,2);case 1073742116:if(a>=J.util.Elements.elementNumberMax)break;
return this.propertyColorEncoder.getArgbFromPalette(a,0,0,3);default:return b}return J.viewer.JC.altArgbsCpk[J.util.Elements.altElementIndexFromNumber(a)]},"~N,~N");c(c$,"setElementArgb",function(a,b){1073741992==b&&this.argbsCpk===J.constant.EnumPalette.argbsCpk||(b=this.getJmolOrRasmolArgb(a,b),this.argbsCpk===J.constant.EnumPalette.argbsCpk&&(this.argbsCpk=JU.AU.arrayCopyRangeI(J.constant.EnumPalette.argbsCpk,0,-1),this.altArgbsCpk=JU.AU.arrayCopyRangeI(J.viewer.JC.altArgbsCpk,0,-1)),a<J.util.Elements.elementNumberMax?
(this.argbsCpk[a]=b,this.g3d.changeColixArgb(a,b)):(a=J.util.Elements.altElementIndexFromNumber(a),this.altArgbsCpk[a]=b,this.g3d.changeColixArgb(J.util.Elements.elementNumberMax+a,b)))},"~N,~N");c(c$,"getPropertyColorRange",function(){return this.propertyColorEncoder.isReversed?[this.propertyColorEncoder.hi,this.propertyColorEncoder.lo]:[this.propertyColorEncoder.lo,this.propertyColorEncoder.hi]});c(c$,"setPropertyColorRangeData",function(a,b,c){this.colorData=a;this.propertyColorEncoder.currentPalette=
this.propertyColorEncoder.createColorScheme(c,!0,!1);this.propertyColorEncoder.hi=-3.4028235E38;this.propertyColorEncoder.lo=3.4028235E38;if(null!=a){c=null==b;for(var g,e=c?a.length-1:b.nextSetBit(0);0<=e;e=c?e-1:b.nextSetBit(e+1))if(!Float.isNaN(g=a[e]))this.propertyColorEncoder.hi=Math.max(this.propertyColorEncoder.hi,g),this.propertyColorEncoder.lo=Math.min(this.propertyColorEncoder.lo,g);this.setPropertyColorRange(this.propertyColorEncoder.lo,this.propertyColorEncoder.hi)}},"~A,JU.BS,~S");c(c$,
"setPropertyColorRange",function(a,b){this.propertyColorEncoder.setRange(a,b,a>b);J.util.Logger.debugging&&J.util.Logger.debug('ColorManager: color "'+this.propertyColorEncoder.getCurrentColorSchemeName()+'" range '+a+" "+b)},"~N,~N");c(c$,"setPropertyColorScheme",function(a,b,c){var g=0==a.length;g&&(a="=");var e=this.getPropertyColorRange();this.propertyColorEncoder.currentPalette=this.propertyColorEncoder.createColorScheme(a,!0,c);g||this.setPropertyColorRange(e[0],e[1]);this.propertyColorEncoder.isTranslucent=
b},"~S,~B,~B");c(c$,"setUserScale",function(a){this.propertyColorEncoder.setUserScale(a)},"~A");c(c$,"getColorSchemeList",function(a){a=null==a||0==a.length?this.propertyColorEncoder.currentPalette:this.propertyColorEncoder.createColorScheme(a,!0,!1);return J.util.ColorEncoder.getColorSchemeList(this.propertyColorEncoder.getColorSchemeArray(a))},"~S");c(c$,"getColixForPropertyValue",function(a){return this.propertyColorEncoder.getColorIndex(a)},"~N");c(c$,"getColorEncoder",function(a){if(null==a||
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function(){c$=w(function(){this.viewer=null;this.pathForAllFiles="";this.nameAsGiven="zapped";this.lastFullPathName=this.fullPathName=null;this.lastNameAsGiven="zapped";this.cache=this.spardirCache=this.pngjCache=this.appletProxy=this.appletDocumentBaseURL=this.fileName=null;u(this,arguments)},J.viewer,"FileManager",null,javajs.api.BytePoster);Q(c$,function(){this.cache=new java.util.Hashtable});A(c$,function(a){this.viewer=a;this.clear()},"J.viewer.Viewer");c(c$,"clear",function(){this.setFileInfo([this.viewer.getZapName()]);
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(this.lastNameAsGiven=this.nameAsGiven,this.lastFullPathName=this.fullPathName)},"~A");c(c$,"getFileInfo",function(){return[this.fullPathName,this.fileName,this.nameAsGiven]});c(c$,"getFullPathName",function(a){var b=null!=this.fullPathName?this.fullPathName:this.nameAsGiven;return!a||!b.equals("zapped")?b:null!=this.lastFullPathName?this.lastFullPathName:this.lastNameAsGiven},"~B");c(c$,"getFileName",function(){return null!=this.fileName?this.fileName:this.nameAsGiven});c(c$,"getAppletDocumentBase",
function(){return null==this.appletDocumentBaseURL?"":this.appletDocumentBaseURL.toString()});c(c$,"setAppletContext",function(a){try{System.out.println('setting document base to "'+a+'"'),this.appletDocumentBaseURL=0==a.length?null:new java.net.URL(na("java.net.URL"),a,null)}catch(b){if(C(b,java.net.MalformedURLException))System.out.println("error setting document base to "+a);else throw b;}},"~S");c(c$,"setAppletProxy",function(a){this.appletProxy=null==a||0==a.length?null:a},"~S");c(c$,"createAtomSetCollectionFromFile",
function(a,b,c){null==b.get("atomDataOnly")&&this.setLoadState(b);a=this.viewer.resolveDatabaseFormat(a);var g=a.indexOf("::"),e=0<=g?a.substring(g+2):a,g=0<=g?a.substring(0,g):null;J.util.Logger.info("\nFileManager.getAtomSetCollectionFromFile("+e+")"+(a.equals(e)?"":" //"+a));var f=this.classifyName(e,!0);if(1==f.length)return f[0];a=f[0];f=f[1];b.put("fullPathName",(null==g?"":g+"::")+a.$replace("\\","/"));this.viewer.getBoolean(603979880)&&this.viewer.getBoolean(603979824)&&this.viewer.scriptStatus("Requesting "+
a);b=new J.io.FileReader(this,this.viewer,f,a,e,g,null,b,c);b.run();return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(c$,"createAtomSetCollectionFromFiles",function(a,b,c){this.setLoadState(b);for(var g=Array(a.length),e=Array(a.length),f=Array(a.length),j=0;j<a.length;j++){var h=a[j].indexOf("::"),l=0<=h?a[j].substring(h+2):a[j],h=0<=h?a[j].substring(0,h):null,m=this.classifyName(l,!0);if(1==m.length)return m[0];g[j]=m[0];a[j]=m[0].$replace("\\","/");f[j]=h;e[j]=l}b.put("fullPathNames",g);
b.put("fileTypes",f);a=this.newFilesReader(g,e,f,null,b,c);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(c$,"createAtomSetCollectionFromString",function(a,b,c){this.setLoadState(b);var g=0<=a.indexOf("Viewer.AddHydrogens")?this.getFileInfo():null;b=new J.io.FileReader(this,this.viewer,"string","string","string",null,J.io.JmolBinary.getBR(a),b,c);b.run();null!=g&&this.setFileInfo(g);!c&&!r(b.getAtomSetCollection(),String)&&(this.viewer.zap(!1,!0,!1),this.setFileInfo(["5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63"===
a?"Jmol Model Kit":"string"]));return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(c$,"createAtomSeCollectionFromStrings",function(a,b,c,g){if(!c.containsKey("isData")){var e='"'+this.viewer.getDataSeparator()+'"',f='"'+(g?"append":"model")+' inline"',j=new JU.SB;j.append('set dataSeparator "~~~next file~~~";\ndata ').append(f);for(var h=0;h<a.length;h++)0<h&&j.append("~~~next file~~~"),j.append(a[h]);j.append("end ").append(f).append(";set dataSeparator ").append(e);b.appendSB(j)}this.setLoadState(c);
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}else throw g;}return null==c?"":J.io.JmolBinary.fixUTF(c)},"~S,~A");E(c$,"URL_LOCAL",3,"urlPrefixes",["http:","https:","ftp:","file:"]);c$.scriptFilePrefixes=c$.prototype.scriptFilePrefixes=['/*file*/"','FILE0="','FILE1="']}),p("J.viewer"),t(["java.util.Hashtable","JU.P3","J.constant.EnumAxesMode","$.EnumCallback"],"J.viewer.GlobalSettings","java.lang.Boolean $.Float JU.BS $.DF $.List J.constant.EnumStructure J.script.SV J.util.BSUtil $.Escape $.Logger $.Txt J.viewer.JC $.StateManager $.Viewer".split(" "),
function(){c$=w(function(){this.databases=this.htUserVariables=this.htPropertyFlagsRemoved=this.htBooleanParameterFlags=this.htNonbooleanParameterValues=this.viewer=null;this.ambientPercent=45;this.diffusePercent=84;this.specular=!0;this.specularExponent=6;this.phongExponent=64;this.specularPercent=22;this.specularPower=40;this.zDepth=0;this.zShadePower=3;this.zSlab=50;this.slabByAtom=this.slabByMolecule=!1;this.appendNew=this.allowEmbeddedScripts=!0;this.appletProxy="";this.applySymmetryToBonds=
!1;this.atomTypes="";this.autoBond=!0;this.axesOrientationRasmol=!1;this.bondRadiusMilliAngstroms=150;this.bondTolerance=0.45;this.defaultDirectory="";this.defaultStructureDSSP=!0;this.ptDefaultLattice=null;this.defaultLoadFilter=this.defaultLoadScript="";this.defaultDropScript="zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == '' && defaultLoadScript == '' && _filetype == 'Pdb') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";
this.fractionalRelative=this.forceAutoBond=!1;this.inlineNewlineChar="|";this.pubChemFormat=this.nihResolverFormat=this.smilesUrlFormat=this.nmrPredictFormat=this.nmrUrlFormat=this.loadLigandFormat=this.loadFormat=null;this.edsUrlFormat="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";this.edsUrlCutoff="load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]";this.edsUrlOptions="within 2.0 {*}";this.minBondDistance=0.4;this.minPixelSelRadius=
6;this.pdbSequential=this.pdbGetHeader=this.pdbAddHydrogens=!1;this.percentVdwAtom=23;this.smallMoleculeMaxAtoms=4E4;this.smartAromatic=!0;this.allowMoveAtoms=this.allowRotateSelected=this.legacyHAddition=this.legacyAutoBonding=this.zeroBasedXyzRasmol=!1;this.defaultPerspectiveDepth=!0;this.visualRange=5;this.solventOn=!1;this.defaultTorsionLabel=this.defaultDistanceLabel=this.defaultAngleLabel="%VALUE %UNITS";this.measureAllModels=this.justifyMeasurements=!1;this.minimizationSteps=100;this.minimizationRefresh=
!0;this.minimizationSilent=!1;this.minimizationCriterion=0.001;this.antialiasDisplay=!1;this.displayCellParameters=this.antialiasTranslucent=this.imageState=this.antialiasImages=!0;this.dotsSelectedOnly=!1;this.dotSurface=!0;this.dotDensity=3;this.meshScale=this.dotScale=1;this.isosurfaceKey=this.greyscaleRendering=!1;this.isosurfacePropertySmoothing=!0;this.isosurfacePropertySmoothingPower=7;this.platformSpeed=10;this.repaintWaitMs=1E3;this.showHiddenSelectionHalos=!1;this.showMeasurements=this.showKeyStrokes=
!0;this.showTiming=!1;this.zoomLarge=!0;this.zoomHeight=!1;this.backgroundImageFileName=null;this.hbondsBackbone=this.bondModeOr=this.partialDots=!1;this.hbondsAngleMinimum=90;this.hbondsDistanceMaximum=3.25;this.hbondsRasmol=!0;this.hbondsSolid=!1;this.modeMultipleBond=2;this.showMultipleBonds=this.showHydrogens=!0;this.ssbondsBackbone=!1;this.multipleBondSpacing=-1;this.multipleBondRadiusFactor=0;this.chainCaseSensitive=this.cartoonLadders=this.cartoonFancy=this.cartoonRockets=this.cartoonBaseEdges=
!1;this.hermiteLevel=0;this.rangeSelected=this.highResolutionFlag=!1;this.rasmolHeteroSetting=this.rasmolHydrogenSetting=!0;this.ribbonAspectRatio=16;this.rocketBarrels=this.ribbonBorder=!1;this.sheetSmoothing=1;this.translucent=this.traceAlpha=!0;this.allowGestures=this.twistedSheets=!1;this.allowMultiTouch=this.allowModelkit=!0;this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=null;this.axesScale=2;this.starScale=0.05;this.bondPicking=!1;this.defaultCameraDepth=
3;this.celShading=!1;this.celShadingPower=10;this.dataSeparator="~~~";this.debugScript=!1;this.defaultDrawArrowScale=0.5;this.defaultLabelXYZ="%a";this.defaultLabelPDB="%m%r";this.defaultTranslucent=0.5;this.delayMaximumMs=0;this.dipoleScale=1;this.drawFontSize=14;this.drawPicking=this.drawHover=this.dragSelected=this.disablePopupMenu=!1;this.dsspCalcHydrogen=!0;this.energyUnits="kJ";this.exportScale=1;this.helpPath="http://chemapps.stolaf.edu/jmol/docs/index.htm";this.fontScaling=!1;this.fontCaching=
!0;this.forceField="MMFF";this.helixStep=1;this.hideNameInPopup=!1;this.hoverDelayMs=500;this.loadAtomDataTolerance=0.01;this.logGestures=this.logCommands=!1;this.measureDistanceUnits="nanometers";this.measurementLabels=!0;this.monitorEnergy=this.messageStyleChime=!1;this.modulationScale=1;this.multiProcessor=!0;this.particleRadius=20;this.pickingSpinRate=10;this.pickLabel="";this.pointGroupDistanceTolerance=0.2;this.pointGroupLinearTolerance=8;this.preserveState=!0;this.propertyColorScheme="roygb";
this.quaternionFrame="p";this.saveProteinStructureState=!0;this.solventProbeRadius=1.2;this.scriptDelay=0;this.statusReporting=this.selectAllModels=!0;this.strandCountForStrands=5;this.strandCountForMeshRibbon=7;this.strutSpacing=6;this.strutLengthMaximum=7;this.strutDefaultRadius=0.3;this.useArcBall=this.strutsMultiple=!1;this.waitForMoveTo=this.useScriptQueue=this.useNumberLocalization=this.useMinimizationThread=!0;this.vectorScale=1;this.vectorSymmetry=!1;this.vibrationScale=this.vibrationPeriod=
1;this.navigationPeriodic=this.navigationMode=this.hideNavigationPoint=this.wireframeRotation=!1;this.navigationSpeed=5;this.showNavigationPointAlways=!1;this.stereoState=null;this.modelKitMode=!1;this.objMad=this.objStateOn=this.objColors=null;this.ellipsoidFill=this.ellipsoidArrows=this.ellipsoidArcs=this.ellipsoidDots=this.ellipsoidAxes=!1;this.ellipsoidBall=!0;this.ellipsoidDotCount=200;this.ellipsoidAxisDiameter=0.02;this.testFlag4=this.testFlag3=this.testFlag2=this.testFlag1=!1;this.structureList=
null;this.haveSetStructureList=!1;this.userDatabases=null;u(this,arguments)},J.viewer,"GlobalSettings");Q(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.axesMode=J.constant.EnumAxesMode.BOUNDBOX;this.objColors=D(8,0);this.objStateOn=ua(8,!1);this.objMad=D(8,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.constant.EnumStructure.TURN,[30,90,-15,95]);this.structureList.put(J.constant.EnumStructure.SHEET,[-180,-10,70,180,-180,-45,
-180,-130,140,180,90,180]);this.structureList.put(J.constant.EnumStructure.HELIX,[-160,0,-100,45])});A(c$,function(a,b,c){this.viewer=a;this.registerAllValues(b,c)},"J.viewer.Viewer,J.viewer.GlobalSettings,~B");c(c$,"clear",function(){for(var a=this.htUserVariables.keySet().iterator();a.hasNext();){var b=a.next();("@"==b.charAt(0)||b.startsWith("site_"))&&a.remove()}this.setPicked(-1);this.setI("_atomhovered",-1);this.setS("_pickinfo","");this.setB("selectionhalos",!1);this.setB("hidenotselected",
!1);this.setB("measurementlabels",this.measurementLabels=!0);this.setB("drawHover",this.drawHover=!1);this.viewer.saveScene("DELETE",null)});c(c$,"registerAllValues",function(a,b){this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;null!=a&&(b||(this.htUserVariables=a.htUserVariables),this.debugScript=a.debugScript,this.disablePopupMenu=a.disablePopupMenu,this.messageStyleChime=a.messageStyleChime,
this.defaultDirectory=a.defaultDirectory,this.allowGestures=a.allowGestures,this.allowModelkit=a.allowModelkit,this.allowMultiTouch=a.allowMultiTouch,this.allowKeyStrokes=a.allowKeyStrokes,this.legacyAutoBonding=a.legacyAutoBonding,this.legacyHAddition=a.legacyHAddition,this.platformSpeed=a.platformSpeed,this.useScriptQueue=a.useScriptQueue,this.useArcBall=a.useArcBall,this.databases=a.databases,this.showTiming=a.showTiming,this.wireframeRotation=a.wireframeRotation);null==this.databases&&(this.databases=
new java.util.Hashtable,this.getDataBaseList(J.viewer.JC.databases),this.getDataBaseList(this.userDatabases));this.loadFormat=this.databases.get("pdb");this.loadLigandFormat=this.databases.get("ligand");this.nmrUrlFormat=this.databases.get("nmr");this.nmrPredictFormat=this.databases.get("nmrdb");this.smilesUrlFormat=this.databases.get("nci")+"/file?format=sdf&get3d=True";this.nihResolverFormat=this.databases.get("nci");this.pubChemFormat=this.databases.get("pubchem");for(var c,g=0,e=J.constant.EnumCallback.values();g<
e.length&&((c=e[g])||1);g++)this.resetValue(c.name()+"Callback",a);this.setI("historyLevel",0);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);this.setS("hoverLabel","");this.setB("isKiosk",this.viewer.isKiosk());this.setS("logFile",this.viewer.getLogFileName());this.setI("logLevel",J.util.Logger.getLogLevel());this.setF("mouseWheelFactor",1.15);this.setF("mouseDragFactor",1);this.setI("navFps",10);this.setI("navigationDepth",0);this.setI("navigationSlab",0);
this.setI("navX",0);this.setI("navY",0);this.setI("navZ",0);this.setS("pathForAllFiles","");this.setI("perspectiveModel",11);this.setS("picking","identify");this.setS("pickingStyle","toggle");this.setB("refreshing",!0);this.setI("rotationRadius",0);this.setI("scaleAngstromsPerInch",0);this.setI("scriptReportingLevel",0);this.setB("selectionHalos",!1);this.setB("showaxes",!1);this.setB("showboundbox",!1);this.setB("showfrank",!1);this.setB("showUnitcell",!1);this.setI("slab",100);this.setB("slabEnabled",
!1);this.setF("slabrange",0);this.setI("spinX",0);this.setI("spinY",30);this.setI("spinZ",0);this.setI("spinFps",30);this.setI("stereoDegrees",-5);this.setI("stateversion",0);this.setB("syncScript",this.viewer.getStatusManager().syncingScripts);this.setB("syncMouse",this.viewer.getStatusManager().syncingMouse);this.setB("syncStereo",this.viewer.getStatusManager().stereoSync);this.setB("windowCentered",!0);this.setB("zoomEnabled",!0);this.setI("zDepth",0);this.setB("zShade",!1);this.setI("zSlab",50);
this.setI("_version",J.viewer.GlobalSettings.getJmolVersionInt());this.setB("axesWindow",!0);this.setB("axesMolecular",!1);this.setB("axesPosition",!1);this.setB("axesUnitcell",!1);this.setI("backgroundModel",0);this.setB("colorRasmol",!1);this.setS("currentLocalPath","");this.setS("defaultLattice","{0 0 0}");this.setS("defaultColorScheme","Jmol");this.setS("defaultDirectoryLocal","");this.setS("defaults","Jmol");this.setS("defaultVDW","Jmol");this.setS("exportDrivers","Idtf;Maya;Povray;Vrml;X3d;Tachyon;Obj");
this.setI("propertyAtomNumberColumnCount",0);this.setI("propertyAtomNumberField",0);this.setI("propertyDataColumnCount",0);this.setI("propertyDataField",0);this.setB("undo",!0);this.setB("allowEmbeddedScripts",this.allowEmbeddedScripts);this.setB("allowGestures",this.allowGestures);this.setB("allowKeyStrokes",this.allowKeyStrokes);this.setB("allowModelkit",this.allowModelkit);this.setB("allowMultiTouch",this.allowMultiTouch);this.setB("allowRotateSelected",this.allowRotateSelected);this.setB("allowMoveAtoms",
this.allowMoveAtoms);this.setI("ambientPercent",this.ambientPercent);this.setI("animationFps",this.animationFps);this.setB("antialiasImages",this.antialiasImages);this.setB("antialiasDisplay",this.antialiasDisplay);this.setB("antialiasTranslucent",this.antialiasTranslucent);this.setB("appendNew",this.appendNew);this.setS("appletProxy",this.appletProxy);this.setB("applySymmetryToBonds",this.applySymmetryToBonds);this.setB("atomPicking",this.atomPicking);this.setS("atomTypes",this.atomTypes);this.setB("autoBond",
this.autoBond);this.setB("autoFps",this.autoFps);this.setI("axesMode",this.axesMode.getCode());this.setF("axesScale",this.axesScale);this.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);this.setF("bondTolerance",this.bondTolerance);this.setF("cameraDepth",this.defaultCameraDepth);this.setB("cartoonBaseEdges",this.cartoonBaseEdges);this.setB("cartoonFancy",
this.cartoonFancy);this.setB("cartoonLadders",this.cartoonLadders);this.setB("cartoonRockets",this.cartoonRockets);this.setB("chainCaseSensitive",this.chainCaseSensitive);this.setB("celShading",this.celShading);this.setI("celShadingPower",this.celShadingPower);this.setS("dataSeparator",this.dataSeparator);this.setB("debugScript",this.debugScript);this.setS("defaultAngleLabel",this.defaultAngleLabel);this.setF("defaultDrawArrowScale",this.defaultDrawArrowScale);this.setS("defaultDirectory",this.defaultDirectory);
this.setS("defaultDistanceLabel",this.defaultDistanceLabel);this.setS("defaultDropScript",this.defaultDropScript);this.setS("defaultLabelPDB",this.defaultLabelPDB);this.setS("defaultLabelXYZ",this.defaultLabelXYZ);this.setS("defaultLoadFilter",this.defaultLoadFilter);this.setS("defaultLoadScript",this.defaultLoadScript);this.setB("defaultStructureDSSP",this.defaultStructureDSSP);this.setS("defaultTorsionLabel",this.defaultTorsionLabel);this.setF("defaultTranslucent",this.defaultTranslucent);this.setI("delayMaximumMs",
this.delayMaximumMs);this.setI("diffusePercent",this.diffusePercent);this.setF("dipoleScale",this.dipoleScale);this.setB("disablePopupMenu",this.disablePopupMenu);this.setB("displayCellParameters",this.displayCellParameters);this.setI("dotDensity",this.dotDensity);this.setI("dotScale",this.dotScale);this.setB("dotsSelectedOnly",this.dotsSelectedOnly);this.setB("dotSurface",this.dotSurface);this.setB("dragSelected",this.dragSelected);this.setB("drawHover",this.drawHover);this.setF("drawFontSize",this.drawFontSize);
this.setB("drawPicking",this.drawPicking);this.setB("dsspCalculateHydrogenAlways",this.dsspCalcHydrogen);this.setS("edsUrlFormat",this.edsUrlFormat);this.setS("edsUrlCutoff",this.edsUrlCutoff);this.setB("ellipsoidArcs",this.ellipsoidArcs);this.setB("ellipsoidArrows",this.ellipsoidArrows);this.setB("ellipsoidAxes",this.ellipsoidAxes);this.setF("ellipsoidAxisDiameter",this.ellipsoidAxisDiameter);this.setB("ellipsoidBall",this.ellipsoidBall);this.setI("ellipsoidDotCount",this.ellipsoidDotCount);this.setB("ellipsoidDots",
this.ellipsoidDots);this.setB("ellipsoidFill",this.ellipsoidFill);this.setS("energyUnits",this.energyUnits);this.setF("exportScale",this.exportScale);this.setB("fontScaling",this.fontScaling);this.setB("fontCaching",this.fontCaching);this.setB("forceAutoBond",this.forceAutoBond);this.setS("forceField",this.forceField);this.setB("fractionalRelative",this.fractionalRelative);this.setF("particleRadius",this.particleRadius);this.setB("greyscaleRendering",this.greyscaleRendering);this.setF("hbondsAngleMinimum",
this.hbondsAngleMinimum);this.setF("hbondsDistanceMaximum",this.hbondsDistanceMaximum);this.setB("hbondsBackbone",this.hbondsBackbone);this.setB("hbondsRasmol",this.hbondsRasmol);this.setB("hbondsSolid",this.hbondsSolid);this.setI("helixStep",this.helixStep);this.setS("helpPath",this.helpPath);this.setI("hermiteLevel",this.hermiteLevel);this.setB("hideNameInPopup",this.hideNameInPopup);this.setB("hideNavigationPoint",this.hideNavigationPoint);this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",
this.hoverDelayMs/1E3);this.setB("imageState",this.imageState);this.setB("isosurfaceKey",this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",this.legacyHAddition);this.setF("loadAtomDataTolerance",this.loadAtomDataTolerance);this.setS("loadFormat",
this.loadFormat);this.setS("loadLigandFormat",this.loadLigandFormat);this.setB("logCommands",this.logCommands);this.setB("logGestures",this.logGestures);this.setB("measureAllModels",this.measureAllModels);this.setB("measurementLabels",this.measurementLabels);this.setS("measurementUnits",this.measureDistanceUnits);this.setI("meshScale",this.meshScale);this.setB("messageStyleChime",this.messageStyleChime);this.setF("minBondDistance",this.minBondDistance);this.setI("minPixelSelRadius",this.minPixelSelRadius);
this.setI("minimizationSteps",this.minimizationSteps);this.setB("minimizationRefresh",this.minimizationRefresh);this.setB("minimizationSilent",this.minimizationSilent);this.setF("minimizationCriterion",this.minimizationCriterion);this.setB("modelKitMode",this.modelKitMode);this.setF("modulationScale",this.modulationScale);this.setB("monitorEnergy",this.monitorEnergy);this.setF("multipleBondRadiusFactor",this.multipleBondRadiusFactor);this.setF("multipleBondSpacing",this.multipleBondSpacing);this.setB("multiProcessor",
this.multiProcessor&&1<J.viewer.Viewer.nProcessors);this.setB("navigationMode",this.navigationMode);this.setB("navigationPeriodic",this.navigationPeriodic);this.setF("navigationSpeed",this.navigationSpeed);this.setS("nmrPredictFormat",this.nmrPredictFormat);this.setS("nmrUrlFormat",this.nmrUrlFormat);this.setB("partialDots",this.partialDots);this.setB("pdbAddHydrogens",this.pdbAddHydrogens);this.setB("pdbGetHeader",this.pdbGetHeader);this.setB("pdbSequential",this.pdbSequential);this.setB("perspectiveDepth",
this.defaultPerspectiveDepth);this.setI("percentVdwAtom",this.percentVdwAtom);this.setI("phongExponent",this.phongExponent);this.setI("pickingSpinRate",this.pickingSpinRate);this.setS("pickLabel",this.pickLabel);this.setI("platformSpeed",this.platformSpeed);this.setF("pointGroupLinearTolerance",this.pointGroupLinearTolerance);this.setF("pointGroupDistanceTolerance",this.pointGroupDistanceTolerance);this.setB("preserveState",this.preserveState);this.setS("propertyColorScheme",this.propertyColorScheme);
this.setS("quaternionFrame",this.quaternionFrame);this.setB("rangeSelected",this.rangeSelected);this.setI("repaintWaitMs",this.repaintWaitMs);this.setI("ribbonAspectRatio",this.ribbonAspectRatio);this.setB("ribbonBorder",this.ribbonBorder);this.setB("rocketBarrels",this.rocketBarrels);this.setB("saveProteinStructureState",this.saveProteinStructureState);this.setB("scriptqueue",this.useScriptQueue);this.setB("selectAllModels",this.selectAllModels);this.setB("selectHetero",this.rasmolHeteroSetting);
this.setB("selectHydrogen",this.rasmolHydrogenSetting);this.setF("sheetSmoothing",this.sheetSmoothing);this.setB("showHiddenSelectionHalos",this.showHiddenSelectionHalos);this.setB("showHydrogens",this.showHydrogens);this.setB("showKeyStrokes",this.showKeyStrokes);this.setB("showMeasurements",this.showMeasurements);this.setB("showMultipleBonds",this.showMultipleBonds);this.setB("showNavigationPointAlways",this.showNavigationPointAlways);this.setI("showScript",this.scriptDelay);this.setB("showtiming",
this.showTiming);this.setB("slabByMolecule",this.slabByMolecule);this.setB("slabByAtom",this.slabByAtom);this.setB("smartAromatic",this.smartAromatic);this.setI("smallMoleculeMaxAtoms",this.smallMoleculeMaxAtoms);this.setS("smilesUrlFormat",this.smilesUrlFormat);this.setS("nihResolverFormat",this.nihResolverFormat);this.setS("pubChemFormat",this.pubChemFormat);this.setB("solventProbe",this.solventOn);this.setF("solventProbeRadius",this.solventProbeRadius);this.setB("specular",this.specular);this.setI("specularExponent",
this.specularExponent);this.setI("specularPercent",this.specularPercent);this.setI("specularPower",this.specularPower);this.setB("ssbondsBackbone",this.ssbondsBackbone);this.setF("starScale",this.starScale);this.setB("statusReporting",this.statusReporting);this.setI("strandCount",this.strandCountForStrands);this.setI("strandCountForStrands",this.strandCountForStrands);this.setI("strandCountForMeshRibbon",this.strandCountForMeshRibbon);this.setF("strutDefaultRadius",this.strutDefaultRadius);this.setF("strutLengthMaximum",
this.strutLengthMaximum);this.setI("strutSpacing",this.strutSpacing);this.setB("strutsMultiple",this.strutsMultiple);this.setB("testFlag1",this.testFlag1);this.setB("testFlag2",this.testFlag2);this.setB("testFlag3",this.testFlag3);this.setB("testFlag4",this.testFlag4);this.setB("traceAlpha",this.traceAlpha);this.setB("translucent",this.translucent);this.setB("twistedSheets",this.twistedSheets);this.setB("useArcBall",this.useArcBall);this.setB("useMinimizationThread",this.useMinimizationThread);this.setB("useNumberLocalization",
this.useNumberLocalization);this.setF("vectorScale",this.vectorScale);this.setB("vectorSymmetry",this.vectorSymmetry);this.setF("vibrationPeriod",this.vibrationPeriod);this.setF("vibrationScale",this.vibrationScale);this.setF("visualRange",this.visualRange);this.setB("waitForMoveTo",this.waitForMoveTo);this.setB("wireframeRotation",this.wireframeRotation);this.setI("zDepth",this.zDepth);this.setB("zeroBasedXyzRasmol",this.zeroBasedXyzRasmol);this.setB("zoomHeight",this.zoomHeight);this.setB("zoomLarge",
this.zoomLarge);this.setI("zShadePower",this.zShadePower);this.setI("zSlab",this.zSlab)},"J.viewer.GlobalSettings,~B");c(c$,"setDefaultLattice",function(a){Float.isNaN(a.x+a.y+a.z)||this.ptDefaultLattice.setT(a)},"JU.P3");c(c$,"setUnits",function(a){var b=this.measureDistanceUnits,c=this.energyUnits;a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||a.equalsIgnoreCase("nm")?this.measureDistanceUnits="nanometers":a.equalsIgnoreCase("picometers")||
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0<this.bsSelection.length()?0:1;this.selectionChanged(!1)});c(c$,"excludeSelectionSet",function(a){null==a||1==this.empty||(this.bsSelection.andNot(a),this.empty=-1)},"JU.BS");c(c$,"getSelectionCount",function(){if(1==this.empty)return 0;this.empty=1;var a;null!=this.bsSubset?(this.bsTemp.clearAll(),this.bsTemp.or(this.bsSubset),this.bsTemp.and(this.bsSelection),a=this.bsTemp):a=this.bsSelection;a=a.cardinality();0<a&&(this.empty=0);return a});c(c$,"addListener",function(a){for(var b=this.listeners.length;0<=
--b;)if(this.listeners[b]===a){this.listeners[b]=null;break}for(var c=this.listeners.length,b=c;0<=--b;)if(null==this.listeners[b]){this.listeners[b]=a;return}this.listeners=0==this.listeners.length?Array(1):JU.AU.doubleLength(this.listeners);this.listeners[c]=a},"J.api.JmolSelectionListener");c(c$,"selectionChanged",function(a){this.hideNotSelected&&this.hide(this.viewer.getModelSet(),J.util.BSUtil.copyInvert(this.bsSelection,this.viewer.getAtomCount()),0,a);if(!(a||0==this.listeners.length))for(a=
this.listeners.length;0<=--a;)null!=this.listeners[a]&&this.listeners[a].selectionChanged(this.bsSelection)},"~B");c(c$,"deleteAtoms",function(a){var b=J.util.BSUtil.copy(a);null==this.bsDeleted?this.bsDeleted=b:(b.andNot(this.bsDeleted),this.bsDeleted.or(a));this.bsHidden.andNot(this.bsDeleted);this.bsSelection.andNot(this.bsDeleted);return b.cardinality()},"JU.BS");c(c$,"getDeletedAtoms",function(){return this.bsDeleted});c(c$,"getSelectionSet",function(a){if(a||null==this.bsDeleted&&null==this.bsSubset)return this.bsSelection;
a=new JU.BS;a.or(this.bsSelection);this.excludeAtoms(a,!1);return a},"~B");c(c$,"getSelectionSubset",function(){return this.bsSubset});c(c$,"excludeAtoms",function(a,b){null!=this.bsDeleted&&a.andNot(this.bsDeleted);!b&&null!=this.bsSubset&&a.and(this.bsSubset)},"JU.BS,~B");c(c$,"processDeletedModelAtoms",function(a){null!=this.bsDeleted&&J.util.BSUtil.deleteBits(this.bsDeleted,a);null!=this.bsSubset&&J.util.BSUtil.deleteBits(this.bsSubset,a);J.util.BSUtil.deleteBits(this.bsFixed,a);J.util.BSUtil.deleteBits(this.bsHidden,
a);var b=J.util.BSUtil.copy(this.bsSelection);J.util.BSUtil.deleteBits(b,a);this.setSelectionSet(b,0)},"JU.BS");c(c$,"setMotionFixedAtoms",function(a){this.bsFixed.clearAll();null!=a&&this.bsFixed.or(a)},"JU.BS");c(c$,"getMotionFixedAtoms",function(){return this.bsFixed});E(c$,"TRUE",1,"FALSE",0,"UNKNOWN",-1)}),p("J.viewer"),t(["JU.BS"],"J.viewer.ShapeManager","java.lang.Boolean java.util.Hashtable JU.P3 $.SB J.constant.EnumPalette $.EnumVdw J.modelset.Atom J.util.BSUtil $.Logger J.viewer.JC".split(" "),
function(){c$=w(function(){this.navigationCrossHairMinMax=this.bsRenderableAtoms=this.viewer=this.shapes=this.modelSet=this.gdata=null;u(this,arguments)},J.viewer,"ShapeManager");Q(c$,function(){this.bsRenderableAtoms=new JU.BS;this.navigationCrossHairMinMax=D(4,0)});A(c$,function(a){this.viewer=a;this.gdata=a.getGraphicsData()},"J.viewer.Viewer");c(c$,"findNearestShapeAtomIndex",function(a,b,c,g){if(null!=this.shapes)for(var e=0;e<this.shapes.length&&null==c[0];++e)null!=this.shapes[e]&&this.shapes[e].findNearestAtomIndex(a,
b,c,g)},"~N,~N,~A,JU.BS");c(c$,"getShapes",function(){return this.shapes});c(c$,"getShapePropertyIndex",function(a,b,c){if(null==this.shapes||null==this.shapes[a])return null;this.viewer.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,c);this.viewer.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(c$,"getShapePropertyData",function(a,b,c){if(null==this.shapes||null==this.shapes[a])return!1;this.viewer.setShapeErrorState(a,"get "+b);a=this.shapes[a].getPropertyData(b,c);this.viewer.setShapeErrorState(-1,
null);return a},"~N,~S,~A");c(c$,"getShapeIdFromObjectName",function(a){if(null!=this.shapes)for(var b=16;29>b;++b)if(null!=this.shapes[b]&&0<=this.shapes[b].getIndexFromName(a))return b;return-1},"~S");c(c$,"loadDefaultShapes",function(a){this.modelSet=a;if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].setModelSet(a);this.loadShape(0);this.loadShape(1)},"J.modelset.ModelSet");c(c$,"loadShape",function(a){if(null==this.shapes)return null;if(null!=this.shapes[a])return this.shapes[a];
if(2==a||3==a||4==a)return null;var b=J.viewer.JC.getShapeClassName(a,!1);try{var c=Class.forName(b).newInstance();this.viewer.setShapeErrorState(a,"allocate");c.initializeShape(this.viewer,this.gdata,this.modelSet,a);this.viewer.setShapeErrorState(-1,null);return this.shapes[a]=c}catch(g){if(C(g,Exception))return J.util.Logger.errorEx("Could not instantiate shape:"+b,g),null;throw g;}},"~N");c(c$,"refreshShapeTrajectories",function(a,b,c){var g=Integer.$valueOf(a);a=this.viewer.getModelUndeletedAtomsBitSet(a);
for(var e=0;36>e;e++)null!=this.shapes[e]&&this.setShapePropertyBs(e,"refreshTrajectories",[g,b,c],a)},"~N,JU.BS,JU.M4");c(c$,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");c(c$,"resetShapes",function(){this.viewer.noGraphicsAllowed()||(this.shapes=Array(36))});c(c$,"setShapeSizeBs",function(a,b,c,g){if(null!=this.shapes){if(null==g&&(1!=a||2147483647!=b))g=this.viewer.getSelectionSet(!1);null!=c&&(0!=c.value&&c.vdwType===J.constant.EnumVdw.TEMP)&&this.modelSet.getBfactor100Lo();
this.viewer.setShapeErrorState(a,"set size");(null==c?0!=b:0!=c.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,c,g);this.viewer.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(c$,"setLabel",function(a,b){if(null==a){if(null==this.shapes[5])return}else this.loadShape(5),this.setShapeSizeBs(5,0,null,b);this.setShapePropertyBs(5,"label",a,b)},"~S,JU.BS");c(c$,"setShapePropertyBs",function(a,b,c,g){null==this.shapes||null==this.shapes[a]||(null==g&&
(g=this.viewer.getSelectionSet(!1)),this.viewer.setShapeErrorState(a,"set "+b),this.shapes[a].setProperty(b.intern(),c,g),this.viewer.setShapeErrorState(-1,null))},"~N,~S,~O,JU.BS");c(c$,"checkFrankclicked",function(a,b){var c=this.shapes[35];return null!=c&&c.wasClicked(a,b)},"~N,~N");c(c$,"checkObjectClicked",function(a,b,c,g,e){var f,h=null;if(0!=c&&this.viewer.getBondPicking()&&null!=(h=this.shapes[1].checkObjectClicked(a,b,c,g,e)))return h;for(var k=0;k<J.viewer.ShapeManager.clickableMax;k++)if(null!=
(f=this.shapes[J.viewer.ShapeManager.hoverable[k]])&&null!=(h=f.checkObjectClicked(a,b,c,g,e)))return h;return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectDragged",function(a,b,c,g,e,f,h){for(var k=!1,l=0<h?h+1:36;!k&&h<l;++h)null!=this.shapes[h]&&(k=this.shapes[h].checkObjectDragged(a,b,c,g,e,f));return k},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,c,g){var e=this.shapes[1];if(g&&null!=e&&e.checkObjectHovered(a,b,c))return!0;for(g=0;g<J.viewer.ShapeManager.hoverable.length;g++)if(e=
this.shapes[J.viewer.ShapeManager.hoverable[g]],null!=e&&e.checkObjectHovered(a,b,c))return!0;return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var c=0;36>c;c++)null!=this.shapes[c]&&this.setShapePropertyBs(c,"deleteModelAtoms",a,b)},"~A,JU.BS");c(c$,"deleteVdwDependentShapes",function(a){null==a&&(a=this.viewer.getSelectionSet(!1));null!=this.shapes[24]&&this.shapes[24].setProperty("deleteVdw",null,a);null!=this.shapes[25]&&this.shapes[25].setProperty("deleteVdw",
null,a)},"JU.BS");c(c$,"getAtomShapeValue",function(a,b,c){a=J.viewer.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;c=this.shapes[a].getSize(c);if(0==c){if(0==(b.shapeVisibilityFlags&this.shapes[a].myVisibilityFlag))return 0;c=this.shapes[a].getSizeG(b)}return c/2E3},"~N,J.modelset.Group,~N");c(c$,"getObjectMap",function(a,b){if(null!=this.shapes)for(var c=Boolean.$valueOf(b),g=16;29>g;++g)this.getShapePropertyData(g,"getNames",[a,c])},"java.util.Map,~B");c(c$,"getProperty",function(a){return a.equals("getShapes")?
this.shapes:null},"~O");c(c$,"getRenderableBitSet",function(){return this.bsRenderableAtoms});c(c$,"getShape",function(a){return null==this.shapes?null:this.shapes[a]},"~N");c(c$,"getShapeInfo",function(){var a=new java.util.Hashtable,b=new JU.SB;if(null!=this.shapes)for(var c=0;36>c;++c){var g=this.shapes[c];if(null!=g){var e=J.viewer.JC.shapeClassBases[c],g=g.getShapeDetail();null!=g&&a.put(e,g)}}0<b.length()&&a.put("shapeCommands",b.toString());return a});c(c$,"mergeShapes",function(a){if(null!=
a)if(null==this.shapes)this.shapes=a;else for(var b=0;b<a.length;++b)null!=a[b]&&(null==this.shapes[b]&&this.loadShape(b),this.shapes[b].merge(a[b]))},"~A");c(c$,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.modelSet),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.constant.EnumPalette.NONE,a))},"JU.BS");c(c$,"setAtomLabel",function(a,b){null!=this.shapes&&
(this.loadShape(5),this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null))},"~S,~N");c(c$,"setModelVisibility",function(){if(!(null==this.shapes||null==this.shapes[0])){for(var a=this.viewer.getVisibleFramesBitSet(),b=1;36>b;b++)null!=this.shapes[b]&&this.shapes[b].setVisibilityFlags(a);this.shapes[0].setVisibilityFlags(a);for(b=0;36>b;++b)a=this.shapes[b],null!=a&&a.setModelClickability()}});c(c$,"finalizeAtoms",function(a,b){if(null!=a){var c=this.viewer.getAtomSetCenter(a),g=new JU.P3;
this.viewer.transformPt3f(c,g);g.add(b);this.viewer.unTransformPoint(g,g);g.sub(c);this.viewer.setAtomCoordsRelative(g,a);b.set(0,0,0)}this.bsRenderableAtoms.clearAll();c=this.modelSet.atoms;for(g=this.modelSet.getAtomCount();0<=--g;)0!=(c[g].getShapeVisibilityFlags()&1)&&this.bsRenderableAtoms.set(g)},"JU.BS,JU.P3");c(c$,"transformAtoms",function(){for(var a=this.modelSet.vibrations,b=this.modelSet.atoms,c=null!=a&&this.viewer.isVibrationOn(),g=this.bsRenderableAtoms.nextSetBit(0);0<=g;g=this.bsRenderableAtoms.nextSetBit(g+
1)){var e=b[g],f=c&&e.hasVibration()?this.viewer.transformPtVib(e,a[g]):this.viewer.transformPt(e);e.sX=f.x;e.sY=f.y;e.sZ=f.z;var h=Math.abs(e.madAtom);h==J.modelset.Atom.MAD_GLOBAL&&(h=y(2E3*this.viewer.getFloat(1141899265)));e.sD=oa(this.viewer.scaleToScreen(f.z,h))}if(this.viewer.getSlabEnabled()){g=this.viewer.getBoolean(603979940);a=this.viewer.getBoolean(603979938);c=this.gdata.getSlab();f=this.gdata.getDepth();if(g){e=this.modelSet.getMolecules();h=this.modelSet.getMoleculeCountInModel(-1);
for(g=0;g<h;g++){var k=e[g],l=0,m=k.firstAtomIndex;if(this.bsRenderableAtoms.get(m)){for(;l<k.atomCount&&!this.gdata.isClippedZ(b[m].sZ-(b[m].sD>>1));l++,m++);if(l!=k.atomCount){m=k.firstAtomIndex;for(l=0;l<k.atomCount;l++)this.bsRenderableAtoms.clear(m),b[m++].sZ=0}}}}for(g=this.bsRenderableAtoms.nextSetBit(0);0<=g;g=this.bsRenderableAtoms.nextSetBit(g+1))if(e=b[g],this.gdata.isClippedZ(e.sZ-(a?b[g].sD>>1:0)))e.setClickable(0),h=s((a?-1:1)*e.sD/2),(e.sZ+h<c||e.sZ-h>f||!this.gdata.isInDisplayRange(e.sX,
e.sY))&&this.bsRenderableAtoms.clear(g)}if(0==this.modelSet.getAtomCount()||!this.viewer.getShowNavigationPoint())return null;a=2147483647;c=-2147483648;f=2147483647;h=-2147483648;for(g=this.bsRenderableAtoms.nextSetBit(0);0<=g;g=this.bsRenderableAtoms.nextSetBit(g+1))e=b[g],e.sX<a&&(a=e.sX),e.sX>c&&(c=e.sX),e.sY<f&&(f=e.sY),e.sY>h&&(h=e.sY);this.navigationCrossHairMinMax[0]=a;this.navigationCrossHairMinMax[1]=c;this.navigationCrossHairMinMax[2]=f;this.navigationCrossHairMinMax[3]=h;return this.navigationCrossHairMinMax});
c(c$,"setModelSet",function(a){this.modelSet=this.viewer.modelSet=a},"J.modelset.ModelSet");c(c$,"checkInheritedShapes",function(){null!=this.shapes[24]&&this.setShapePropertyBs(24,"remapInherited",null,null)});c(c$,"restrictSelected",function(a,b){var c=J.util.BSUtil.copy(this.viewer.getSelectionSet(!0));if(b){this.viewer.invertSelection();var g=this.viewer.getSelectionSubset();null!=g&&(c=J.util.BSUtil.copy(this.viewer.getSelectionSet(!0)),c.and(g),this.viewer.select(c,!1,0,!0),J.util.BSUtil.invertInPlace(c,
this.viewer.getAtomCount()),c.and(g))}J.util.BSUtil.andNot(c,this.viewer.getDeletedAtoms());g=this.viewer.getBoolean(603979812);a||this.viewer.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var e=this.viewer.getSelectionSet(!1),f=21;0<=--f;)6!=f&&null!=this.getShape(f)&&this.setShapeSizeBs(f,0,null,e);null!=this.getShape(21)&&
this.setShapePropertyBs(21,"delete",e,null);this.setLabel(null,e);a||this.viewer.setBooleanProperty("bondModeOr",g);this.viewer.select(c,!1,0,!0)},"~B,~B");E(c$,"hoverable",[30,25,24,22,35]);c$.clickableMax=c$.prototype.clickableMax=J.viewer.ShapeManager.hoverable.length-1}),p("J.viewer"),t(["java.util.Hashtable"],"J.viewer.StateManager","java.util.Arrays JU.BS $.SB J.modelset.Orientation J.util.BSUtil J.viewer.GlobalSettings".split(" "),function(){c$=w(function(){this.saved=this.viewer=null;this.lastCoordinates=
this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastOrientation="";la("J.viewer.StateManager.Scene")||J.viewer.StateManager.$StateManager$Scene$();la("J.viewer.StateManager.Connections")||J.viewer.StateManager.$StateManager$Connections$();la("J.viewer.StateManager.Connection")||J.viewer.StateManager.$StateManager$Connection$();u(this,arguments)},J.viewer,"StateManager");Q(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",
function(a,b,c,g){var e=new JU.SB,f=0,h=Array(a.size()),k;for(a=a.entrySet().iterator();a.hasNext()&&((k=a.next())||1);){var l=k.getKey(),m=k.getValue();if((c||!l.startsWith("site_"))&&(!g||"@"==l.charAt(0)))h[f++]=l+("@"==l.charAt(0)?" "+m.asString():" = "+J.viewer.StateManager.varClip(l,m.escape(),b))}java.util.Arrays.sort(h,0,f);for(b=0;b<f;b++)null!=h[b]&&e.append("  ").append(h[b]).append(";\n");0==f&&!g&&e.append("# --no global user variables defined--;\n");return e.toString()},"java.util.Map,~N,~B,~B");
c$.getObjectIdFromName=c(c$,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());return 0>a?a:s(a/11)},"~S");c$.getObjectNameFromId=c(c$,"getObjectNameFromId",function(a){return 0>a||8<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*a,11*a+11).trim()},"~N");A(c$,function(a){this.viewer=a},"J.viewer.Viewer");c(c$,"getGlobalSettings",function(a,
b){this.saved.clear();return new J.viewer.GlobalSettings(this.viewer,a,b)},"J.viewer.GlobalSettings,~B");c(c$,"clear",function(a){this.viewer.setShowAxes(!1);this.viewer.setShowBbcage(!1);this.viewer.setShowUnitCell(!1);a.clear()},"J.viewer.GlobalSettings");c(c$,"setCrystallographicDefaults",function(){this.viewer.setAxesModeUnitCell(!0);this.viewer.setShowAxes(!0);this.viewer.setShowUnitCell(!0);this.viewer.setBooleanProperty("perspectiveDepth",!1)});c(c$,"setCommonDefaults",function(){this.viewer.setBooleanProperty("perspectiveDepth",
!0);this.viewer.setFloatProperty("bondTolerance",0.45);this.viewer.setFloatProperty("minBondDistance",0.4);this.viewer.setBooleanProperty("translucent",!0)});c(c$,"setJmolDefaults",function(){this.setCommonDefaults();this.viewer.setStringProperty("ColorScheme","Jmol");this.viewer.setBooleanProperty("axesOrientationRasmol",!1);this.viewer.setBooleanProperty("zeroBasedXyzRasmol",!1);this.viewer.setIntProperty("percentVdwAtom",23);this.viewer.setIntProperty("bondRadiusMilliAngstroms",150);this.viewer.setVdwStr("auto")});
c(c$,"setRasMolDefaults",function(){this.setCommonDefaults();this.viewer.setStringProperty("defaultColorScheme","RasMol");this.viewer.setBooleanProperty("axesOrientationRasmol",!0);this.viewer.setBooleanProperty("zeroBasedXyzRasmol",!0);this.viewer.setIntProperty("percentVdwAtom",0);this.viewer.setIntProperty("bondRadiusMilliAngstroms",1);this.viewer.setVdwStr("Rasmol")});c(c$,"setPyMOLDefaults",function(){this.setCommonDefaults();this.viewer.setStringProperty("measurementUnits","ANGSTROMS");this.viewer.setBooleanProperty("zoomHeight",
!0)});c$.getNoCase=c(c$,"getNoCase",function(a,b){for(var c,g=a.entrySet().iterator();g.hasNext()&&((c=g.next())||1);)if(c.getKey().equalsIgnoreCase(b))return c.getValue();return null},"java.util.Map,~S");c(c$,"listSavedStates",function(){for(var a="",b,c=this.saved.keySet().iterator();c.hasNext()&&((b=c.next())||1);)a+="\n"+b;return a});c(c$,"deleteSavedType",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&b.remove()},"~S");c(c$,"deleteSaved",function(a){this.saved.remove(a)},
"~S");c(c$,"saveSelection",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Selected_"):(a=this.lastSelected="Selected_"+a,this.saved.put(a,J.util.BSUtil.copy(b)))},"~S,JU.BS");c(c$,"restoreSelection",function(a){a=J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Selected_"+a:this.lastSelected);if(null==a)return this.viewer.select(new JU.BS,!1,0,!1),!1;this.viewer.select(a,!1,0,!1);return!0},"~S");c(c$,"saveState",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("State_"):
(a=this.lastState="State_"+a,this.saved.put(a,this.viewer.getStateInfo()))},"~S");c(c$,"getSavedState",function(a){a=J.viewer.StateManager.getNoCase(this.saved,0<a.length?"State_"+a:this.lastState);return null==a?"":a},"~S");c(c$,"saveStructure",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Shape_"):(a=this.lastShape="Shape_"+a,this.saved.put(a,this.viewer.getStructureState()))},"~S");c(c$,"getSavedStructure",function(a){a=J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Shape_"+
a:this.lastShape);return null==a?"":a},"~S");c(c$,"saveCoordinates",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Coordinates_"):(a=this.lastCoordinates="Coordinates_"+a,this.saved.put(a,this.viewer.getCoordinateState(b)))},"~S,JU.BS");c(c$,"getSavedCoordinates",function(a){a=J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Coordinates_"+a:this.lastCoordinates);return null==a?"":a},"~S");c(c$,"getOrientation",function(){return new J.modelset.Orientation(this.viewer,!1,null)});
c(c$,"getSavedOrientationText",function(a){var b;if(null!=a)return b=this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var c=this.saved.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(c$,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");else{var c=ka(J.viewer.StateManager.Scene,this,null,b);c.saveName=this.lastScene="Scene_"+
a;this.saved.put(c.saveName,c)}},"~S,java.util.Map");c(c$,"restoreScene",function(a,b){var c=this.getSceneFor(a);return null!=c&&c.restore(b)},"~S,~N");c(c$,"getSceneFor",function(a){return J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene)},"~S");c(c$,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var c=new J.modelset.Orientation(this.viewer,a.equalsIgnoreCase("default"),b);c.saveName=this.lastOrientation="Orientation_"+
a;this.saved.put(c.saveName,c)}},"~S,~A");c(c$,"restoreOrientation",function(a,b,c){a=this.getOrientationFor(a);return null!=a&&a.restore(b,c)},"~S,~N,~B");c(c$,"getOrientationFor",function(a){return J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Orientation_"+a:this.lastOrientation)},"~S");c(c$,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=ka(J.viewer.StateManager.Connections,this,null);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,
b)}},"~S");c(c$,"restoreBonds",function(a){a=J.viewer.StateManager.getNoCase(this.saved,0<a.length?"Bonds_"+a:this.lastConnections);return null!=a&&a.restore()},"~S");c$.varClip=c(c$,"varClip",function(a,b,c){0<c&&b.length>c&&(b=b.substring(0,c)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");c$.$StateManager$Scene$=function(){fa();c$=w(function(){ma(this,arguments);this.scene=this.saveName=null;u(this,arguments)},J.viewer.StateManager,"Scene");
A(c$,function(a){this.scene=a},"java.util.Map");c(c$,"restore",function(a){var b=this.scene.get("generator");null!=b&&b.generateScene(this.scene);b=this.scene.get("pymolView");return null!=b&&this.b$["J.viewer.StateManager"].viewer.movePyMOL(this.b$["J.viewer.StateManager"].viewer.eval,a,b)},"~N");c$=ea()};c$.$StateManager$Connections$=function(){fa();c$=w(function(){ma(this,arguments);this.saveName=null;this.bondCount=0;this.connections=null;u(this,arguments)},J.viewer.StateManager,"Connections");
A(c$,function(){var a=this.b$["J.viewer.StateManager"].viewer.getModelSet();if(null!=a){this.bondCount=a.bondCount;this.connections=Array(this.bondCount+1);for(var a=a.bonds,b=this.bondCount;0<=--b;){var c=a[b];this.connections[b]=ka(J.viewer.StateManager.Connection,this,null,c.getAtomIndex1(),c.getAtomIndex2(),c.mad,c.colix,c.order,c.getEnergy(),c.getShapeVisibilityFlags())}}});c(c$,"restore",function(){var a=this.b$["J.viewer.StateManager"].viewer.getModelSet();if(null==a)return!1;a.deleteAllBonds();
for(var b=this.bondCount;0<=--b;){var c=this.connections[b],g=a.getAtomCount();c.atomIndex1>=g||c.atomIndex2>=g||(g=a.bondAtoms(a.atoms[c.atomIndex1],a.atoms[c.atomIndex2],c.order,c.mad,null,c.energy,!1,!0),g.setColix(c.colix),g.setShapeVisibilityFlags(c.shapeVisibilityFlags))}for(c=this.bondCount;0<=--c;)a.getBondAt(c).setIndex(c);this.b$["J.viewer.StateManager"].viewer.setShapeProperty(1,"reportAll",null);return!0});c$=ea()};c$.$StateManager$Connection$=function(){fa();c$=w(function(){ma(this,arguments);
this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;u(this,arguments)},J.viewer.StateManager,"Connection");A(c$,function(a,b,c,g,e,f,h){this.atomIndex1=a;this.atomIndex2=b;this.mad=c;this.colix=g;this.order=e;this.energy=f;this.shapeVisibilityFlags=h},"~N,~N,~N,~N,~N,~N,~N");c$=ea()};E(c$,"OBJ_BACKGROUND",0,"OBJ_AXIS1",1,"OBJ_AXIS2",2,"OBJ_AXIS3",3,"OBJ_BOUNDBOX",4,"OBJ_UNITCELL",5,"OBJ_FRANK",6,"OBJ_MAX",8,"objectNameList","background axis1      axis2      axis3      boundbox   unitcell   frank      ")}),
p("J.viewer"),t(["java.util.Hashtable"],"J.viewer.StatusManager","java.lang.Boolean $.Float javajs.awt.Dimension JU.List $.PT J.api.Interface J.constant.EnumCallback J.util.Logger".split(" "),function(){c$=w(function(){this.jmolCallbackListener=this.jmolStatusListener=this.viewer=null;this.statusList="";this.allowStatusReporting=!1;this.messageQueue=null;this.statusPtr=0;this.jmolScriptCallbacks=null;this.minSyncRepeatMs=100;this.stereoSync=this.syncDisabled=this.isSynced=this.drivingSync=this.syncingMouse=
this.syncingScripts=!1;this.qualityPNG=this.qualityJPG=-1;this.imageType=null;u(this,arguments)},J.viewer,"StatusManager");Q(c$,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});A(c$,function(a){this.viewer=a},"J.viewer.Viewer");c(c$,"setAllowStatusReporting",function(a){this.allowStatusReporting=a},"~B");c(c$,"getStatusList",function(){return this.statusList});c(c$,"getMessageQueue",function(){return this.messageQueue});c(c$,"recordStatus",function(a){return this.allowStatusReporting&&
0<this.statusList.length&&(this.statusList.equals("all")||0<=this.statusList.indexOf(a))},"~S");c(c$,"setStatusChanged",function(a,b,c,g){if(this.recordStatus(a)){var e=new JU.List;e.addLast(Integer.$valueOf(++this.statusPtr));e.addLast(a);e.addLast(Integer.$valueOf(b));e.addLast(c);b=g?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.List):b.size()==J.viewer.StatusManager.MAXIMUM_QUEUE_LENGTH&&b.remove(0);b.addLast(e)}},"~S,~N,~O,~B");c(c$,"getStatusChanged",function(a){var b=
0<a.length&&"-"==a.charAt(0),c=0<a.length&&"+"==a.charAt(0),g=!1;b?this.statusList=JU.PT.simpleReplace(this.statusList,a.substring(1,a.length),""):(a=JU.PT.simpleReplace(a,"+",""),this.statusList.equals(a)||c&&0<=this.statusList.indexOf(a)?g=!0:(c||(this.statusList=""),this.statusList+=a,J.util.Logger.debugging&&J.util.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.List;if(g)for(var e,g=this.messageQueue.entrySet().iterator();g.hasNext()&&((e=g.next())||1);)a.addLast(e.getValue());
this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(c$,"setJmolStatusListener",function(a,b){this.jmolStatusListener=a;this.jmolCallbackListener=null==b?a:b},"J.api.JmolStatusListener,J.api.JmolCallbackListener");c(c$,"setJmolCallbackListener",function(a){this.jmolCallbackListener=a},"J.api.JmolCallbackListener");c(c$,"jmolScriptCallback",function(a){a=this.jmolScriptCallbacks.get(a);null!=a&&this.viewer.evalStringQuietSync(a,!0,!1);return a},"J.constant.EnumCallback");c(c$,"setCallbackFunction",
function(a,b){var c=J.constant.EnumCallback.getCallback(a);if(null!=c){var g=null==b?0:7<b.length&&0==b.toLowerCase().indexOf("script:")?7:11<b.length&&0==b.toLowerCase().indexOf("jmolscript:")?11:0;0==g?this.jmolScriptCallbacks.remove(c):this.jmolScriptCallbacks.put(c,b.substring(g).trim())}null!=this.jmolCallbackListener&&this.jmolCallbackListener.setCallbackFunction(a,b)},"~S,~S");c(c$,"notifyEnabled",function(a){return null!=this.jmolCallbackListener&&this.jmolCallbackListener.notifyEnabled(a)},
"J.constant.EnumCallback");c(c$,"setStatusAppletReady",function(a,b){var c=b?this.jmolScriptCallback(J.constant.EnumCallback.APPLETREADY):null;this.notifyEnabled(J.constant.EnumCallback.APPLETREADY)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.APPLETREADY,[c,a,Boolean.$valueOf(b),null])},"~S,~B");c(c$,"setStatusAtomMoved",function(a){var b=this.jmolScriptCallback(J.constant.EnumCallback.ATOMMOVED);this.setStatusChanged("atomMoved",-1,a,!1);this.notifyEnabled(J.constant.EnumCallback.ATOMMOVED)&&
this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.ATOMMOVED,[b,a])},"JU.BS");c(c$,"setStatusAtomPicked",function(a,b){var c=this.jmolScriptCallback(J.constant.EnumCallback.PICK);J.util.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",a,b,!1);this.notifyEnabled(J.constant.EnumCallback.PICK)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.PICK,[c,b,Integer.$valueOf(a)])},"~N,~S");c(c$,"setStatusClicked",function(a,b,c,g,e){var f=this.jmolScriptCallback(J.constant.EnumCallback.CLICK);
if(!this.notifyEnabled(J.constant.EnumCallback.CLICK))return c;e=[c,e];this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.CLICK,[f,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),Integer.$valueOf(g),e]);return e[0]},"~N,~N,~N,~N,~N");c(c$,"setStatusResized",function(a,b){var c=this.jmolScriptCallback(J.constant.EnumCallback.RESIZE);this.notifyEnabled(J.constant.EnumCallback.RESIZE)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.RESIZE,[c,Integer.$valueOf(a),
Integer.$valueOf(b)])},"~N,~N");c(c$,"setStatusAtomHovered",function(a,b){var c=this.jmolScriptCallback(J.constant.EnumCallback.HOVER);this.notifyEnabled(J.constant.EnumCallback.HOVER)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.HOVER,[c,b,Integer.$valueOf(a)])},"~N,~S");c(c$,"setStatusObjectHovered",function(a,b,c){var g=this.jmolScriptCallback(J.constant.EnumCallback.HOVER);this.notifyEnabled(J.constant.EnumCallback.HOVER)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.HOVER,
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(f=this.viewer.getParameter("_smilesString"),0!=f.length&&(b=f),this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.LOADSTRUCT,[k,a,b,c,g,Integer.$valueOf(e),this.viewer.getParameter("_modelNumber"),this.viewer.getModelNumberDotted(this.viewer.getModelCount()-1),h]))},"~S,~S,~S,~S,~N,~B,Boolean");c(c$,"setStatusFrameChanged",function(a,b,c,g,e,f,h){if(null!=this.viewer.getModelSet()){var k=this.viewer.isAnimationOn();this.setStatusChanged("frameChanged",a,0<=a?this.viewer.getModelNumberDotted(a):
"",!1);var l=this.jmolScriptCallback(J.constant.EnumCallback.ANIMFRAME);k&&(a=-2-a);this.notifyEnabled(J.constant.EnumCallback.ANIMFRAME)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.ANIMFRAME,[l,[a,b,c,g,e,f],h]);null!=this.viewer.jmolpopup&&!k&&this.viewer.jmolpopup.jpiUpdateComputedMenus()}},"~N,~N,~N,~N,~N,~N,~S");c(c$,"setScriptEcho",function(a,b){if(null!=a){this.setStatusChanged("scriptEcho",0,a,!1);var c=this.jmolScriptCallback(J.constant.EnumCallback.ECHO);this.notifyEnabled(J.constant.EnumCallback.ECHO)&&
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this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.MEASURE,[e,c,Integer.$valueOf(b),a,Float.$valueOf(g)])},"~S,~N,~S,~N");c(c$,"notifyError",function(a,b,c){var g=this.jmolScriptCallback(J.constant.EnumCallback.ERROR);this.notifyEnabled(J.constant.EnumCallback.ERROR)&&this.jmolCallbackListener.notifyCallback(J.constant.EnumCallback.ERROR,[g,a,b,this.viewer.getShapeErrorState(),c])},"~S,~S,~S");c(c$,"notifyMinimizationStatus",function(a,b,c,g,e){var f=this.jmolScriptCallback(J.constant.EnumCallback.MINIMIZATION);
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null!=this.viewer.appConsole&&0==b&&this.viewer.appConsole.sendConsoleMessage(null==a[1]?null:a[1].toString())},"~A");c(c$,"doSync",function(){return this.isSynced&&this.drivingSync&&!this.syncDisabled});c(c$,"setSync",function(a){this.syncingMouse?null!=a&&this.syncSend(a,"*",0):this.syncingScripts||this.syncSend("!"+this.viewer.getMoveToText(this.minSyncRepeatMs/1E3),"*",0)},"~S");c(c$,"setSyncDriver",function(a){this.stereoSync&&4!=a&&(this.syncSend("SET_GRAPHICS_OFF","*",0),this.stereoSync=!1);
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null;this.haveNotifiedNaN=!1;this.spinX=0;this.spinY=30;this.spinZ=0;this.spinFps=30;this.navZ=this.navY=this.navX=0;this.navFps=NaN;this.isSpinSelected=this.isSpinFixed=this.isSpinInternal=!1;this.rotationCenterDefault=this.perspectiveShiftXY=this.perspectiveOffset=this.fixedRotationCenter=this.fixedRotationOffset=null;this.rotationRadiusDefault=0;this.internalRotationCenter=this.internalTranslation=this.internalRotationAxis=this.fixedRotationAxis=null;this.internalRotationAngle=0;this.rotationAxis=
this.pointT2=this.vectorT2=this.vectorT=this.axisangleT=this.matrixTemp4=this.matrixTemp3=this.matrixRotate=null;this.rotationRate=0;this.cameraSetting=this.camera=this.fixedTranslation=this.arcBall0Rotation=this.arcBallAxis=this.arcBall1=this.arcBall0=null;this.yTranslationFraction=this.xTranslationFraction=0.5;this.previousY=this.previousX=this.prevZoomSetting=0;this.zoomEnabled=!0;this.zoomPercentSetting=this.zoomPercent=100;this.zoomRatio=0;this.zShadeEnabled=this.internalSlab=this.slabEnabled=
!1;this.depthPercentSetting=this.slabPercentSetting=0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=null;this.slabRange=this.zDepthValue=this.zSlabValue=this.depthValue=this.slabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRange=0;this.cameraDistance=1E3;this.scale3DAngstromsPerInch=this.scaleDefaultPixelsPerAngstrom=this.scalePixelsPerAngstrom=this.screenPixelCount=this.height=
this.width=0;this.zoomHeight=this.useZoomLarge=this.antialias=!1;this.screenHeight=this.screenWidth=0;this.ptVibTemp=this.point3iScreenTemp=this.point3fScreenTemp=this.matrixTransformInv=this.matrixTransform=null;this.navigating=!1;this.defaultMode=this.mode=0;this.motion=this.matrixTest=this.aaTest1=this.ptTest3=this.ptTest2=this.ptTest1=this.untransformedPoint=this.pointTsp=null;this.navOn=this.spinOn=!1;this.spinThread=null;this.vibrationOn=this.spinIsGesture=!1;this.vibrationScale=this.vibrationPeriodMs=
this.vibrationPeriod=0;this.stereoColors=this.stereoMode=this.vibrationThread=this.vibrationT=null;this.stereoDegrees=NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=!1;this.ptOffset=this.bsSelectedAtoms=this.frameOffset=this.frameOffsets=null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;u(this,arguments)},J.viewer,"TransformManager");Q(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=
new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;
this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.arcBall0=new JU.V3;this.arcBall1=new JU.V3;this.arcBallAxis=new JU.V3;this.arcBall0Rotation=new JU.M3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.point3fScreenTemp=new JU.P3;this.point3iScreenTemp=new JU.P3i;this.ptVibTemp=new J.util.Point3fi;this.pointTsp=new JU.P3;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=
new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.constant.EnumStereoMode.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});A(c$,function(a,b,c){this.setViewer(a,b,c)},"J.viewer.Viewer,~N,~N");c(c$,"setViewer",function(a,b,c){this.viewer=a;this.setScreenParameters(b,c,!0,!1,!0,!0)},"J.viewer.Viewer,~N,~N");c(c$,"homePosition",function(a){a&&this.setSpinOff();this.setNavOn(!1);this.navFps=
10;this.navX=this.navY=this.navZ=0;this.rotationCenterDefault.setT(this.viewer.getBoundBoxCenter());this.setFixedRotationCenter(this.rotationCenterDefault);this.rotationRadiusDefault=this.setRotationRadius(0,!0);this.windowCentered=!0;this.setRotationCenterAndRadiusXYZ(null,!0);this.matrixRotate.setIdentity();a=this.viewer.getModelSetAuxiliaryInfoValue("defaultOrientationMatrix");null!=a&&this.matrixRotate.setM(a);this.setZoomEnabled(!0);this.zoomToPercent(this.viewer.global.modelKitMode?50:100);
this.zoomPercent=this.zoomPercentSetting;this.slabReset();this.resetFitToScreen(!0);this.viewer.isJmolDataFrame()?this.fixedRotationCenter.set(0,0,0):this.viewer.global.axesOrientationRasmol&&this.rotateX(3.141592653589793);this.viewer.saveOrientation("default",null);1==this.mode&&this.setNavigationMode(!0)},"~B");c(c$,"clear",function(){this.clearVibration();this.clearSpin();this.stopMotion();this.fixedRotationCenter.set(0,0,0);this.navigating=!1;this.zSlabPoint=this.depthPlane=this.slabPlane=null;
this.resetNavigationPoint(!0)});c(c$,"setFixedRotationCenter",function(a){null!=a&&this.fixedRotationCenter.setT(a)},"JU.P3");c(c$,"setRotationPointXY",function(a){a=this.transformPoint(a);this.fixedTranslation.set(a.x,a.y,0)},"JU.P3");c(c$,"spinXYBy",function(a,b,c){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var g=JU.P3.newP(this.fixedRotationCenter),e=new JU.P3;this.transformPoint2(g,e);a=JU.P3.new3(-b,a,0);a.add(e);this.unTransformPoint(a,a);
this.viewer.setInMotion(!1);this.rotateAboutPointsInternal(null,a,g,10*c,NaN,!1,!0,null,!0,null,null,null)}},"~N,~N,~N");c(c$,"rotateArcBall",function(a,b,c){var g=(this.screenPixelCount>>2)*this.screenPixelCount;a-=this.fixedTranslation.x;b-=this.fixedTranslation.y;g=g-a*a-b*b;g=(0>g?-1:1)*Math.sqrt(Math.abs(g));0==c?(this.arcBall0Rotation.setM(this.matrixRotate),this.arcBall0.set(a,-b,g),Float.isNaN(g)||this.arcBall0.normalize()):!Float.isNaN(this.arcBall0.z)&&!Float.isNaN(g)&&(this.arcBall1.set(a,
-b,g),this.arcBall1.normalize(),this.arcBallAxis.cross(this.arcBall0,this.arcBall1),this.axisangleT.setVA(this.arcBallAxis,c*Math.acos(this.arcBall0.dot(this.arcBall1))),this.matrixRotate.setM(this.arcBall0Rotation),this.rotateAxisAngle2(this.axisangleT,null))},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b,c){this.rotateXRadians(0.017453292*b,c);this.rotateYRadians(0.017453292*a,c)},"~N,~N,JU.BS");c(c$,"rotateZBy",function(a,b,c){2147483647!=b&&2147483647!=c&&this.resetXYCenter(b,c);this.rotateZRadians(a/
57.29577951308232)},"~N,~N,~N");c(c$,"rotateFront",function(){this.matrixRotate.setIdentity()});c(c$,"rotateX",function(a){this.matrixRotate.rotX(a)},"~N");c(c$,"rotateY",function(a){this.matrixRotate.rotY(a)},"~N");c(c$,"rotateZ",function(a){this.matrixRotate.rotZ(a)},"~N");c(c$,"applyRotation",function(a,b,c,g,e){null==c?this.matrixRotate.mul2(a,this.matrixRotate):(this.viewer.moveAtoms(a,this.matrixRotate,g,this.internalRotationCenter,b,c,e),null!=g&&this.internalRotationCenter.add(g))},"JU.M3,~B,JU.BS,JU.V3,~B");
c(c$,"rotateXRadians",function(a,b){this.matrixTemp3.rotX(a);this.applyRotation(this.matrixTemp3,!1,b,null,!1)},"~N,JU.BS");c(c$,"rotateYRadians",function(a,b){this.matrixTemp3.rotY(a);this.applyRotation(this.matrixTemp3,!1,b,null,!1)},"~N,JU.BS");c(c$,"rotateZRadians",function(a){this.matrixTemp3.rotZ(a);this.applyRotation(this.matrixTemp3,!1,null,null,!1)},"~N");c(c$,"rotateAxisAngle",function(a,b){this.axisangleT.setVA(a,b);this.rotateAxisAngle2(this.axisangleT,null)},"JU.V3,~N");c(c$,"rotateAxisAngle2",
function(a,b){this.matrixTemp3.setAA(a);this.applyRotation(this.matrixTemp3,!1,b,null,!1)},"JU.A4,JU.BS");c(c$,"rotateAxisAngleAtCenter",function(a,b,c,g,e,f,h){null!=b&&this.moveRotationCenter(b,!0);this.setSpinOff();this.setNavOn(!1);if(this.viewer.isHeadless()){if(f&&3.4028235E38==e)return!1;f=!1}if(Float.isNaN(g)||0==g||0==e)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=g;if(f)return this.fixedRotationAxis.setVA(c,0.017453292*
g),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=h,this.setSpin(a,!0,e,null,null,h,!1),!1;a=0.017453292*e;this.fixedRotationAxis.setVA(c,e);this.rotateAxisAngleRadiansFixed(a,h);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,c,g,e,f,h,k,l,m,
n,q){this.setSpinOff();this.setNavOn(!1);if(this.viewer.isHeadless()){if(h&&3.4028235E38==e)return!1;h=!1}if(null==q&&(null==m||0.001>m.length())&&(!h||0==e||Float.isNaN(g)||0==g)&&(h||0==e))return!1;var p=null;null==q&&(p=JU.V3.newVsub(c,b),f&&p.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(p),this.internalTranslation=null==m?null:JU.V3.newV(m));b=null!=k;if(h)return null==q?(h=s(Math.abs(e)/Math.abs(g)*this.spinFps+0.5),Float.isNaN(e)?this.rotationRate=g:(this.rotationRate=
e/h*this.spinFps,null!=m&&this.internalTranslation.scale(1/h)),this.internalRotationAxis.setVA(p,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):e=g,this.setSpin(a,!0,e,n,q,k,l),null!=q||null!=k;a=0.017453292*e;this.internalRotationAxis.setVA(p,a);this.rotateAxisAngleRadiansInternal(a,k);return!1},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.List,~A");c(c$,"rotateAxisAngleRadiansInternal",function(a,
b){this.internalRotationAngle=a;this.vectorT.set(this.internalRotationAxis.x,this.internalRotationAxis.y,this.internalRotationAxis.z);this.matrixRotate.transform2(this.vectorT,this.vectorT2);this.axisangleT.setVA(this.vectorT2,a);this.matrixTemp3.setAA(this.axisangleT);this.applyRotation(this.matrixTemp3,!0,b,this.internalTranslation,1E6<a);null==b&&this.getNewFixedRotationCenter()},"~N,JU.BS");c(c$,"getNewFixedRotationCenter",function(){this.axisangleT.setAA(this.internalRotationAxis);this.axisangleT.angle=
-this.internalRotationAngle;this.matrixTemp4.setAA(this.axisangleT);this.vectorT.setT(this.internalRotationCenter);this.pointT2.sub2(this.fixedRotationCenter,this.vectorT);var a=new JU.P3;this.matrixTemp4.transform2(this.pointT2,a);a.add(this.vectorT);this.setRotationCenterAndRadiusXYZ(a,!1)});c(c$,"setTranslationFractions",function(){this.xTranslationFraction=this.fixedTranslation.x/this.width;this.yTranslationFraction=this.fixedTranslation.y/this.height});c(c$,"centerAt",function(a,b,c){null==c?
this.translateXYBy(a,b):(this.windowCentered&&this.viewer.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(c))},"~N,~N,JU.P3");c(c$,"percentToPixels",function(a,b){switch(a){case "x":return s(Math.floor(b/100*this.width));case "y":return s(Math.floor(b/100*this.height));case "z":return s(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return s(Math.floor(this.scalePixelsPerAngstrom*
a))},"~N");c(c$,"translateXYBy",function(a,b){this.fixedTranslation.x+=a;this.fixedTranslation.y+=b;this.setTranslationFractions()},"~N,~N");c(c$,"setCamera",function(a,b){this.cameraSetting.set(a,b,0==a&&0==b?0:1)},"~N,~N");c(c$,"translateToPercent",function(a,b){switch(a){case "x":this.xTranslationFraction=0.5+b/100;this.fixedTranslation.x=this.width*this.xTranslationFraction;break;case "y":this.yTranslationFraction=0.5+b/100;this.fixedTranslation.y=this.height*this.yTranslationFraction;break;case "z":1==
this.mode&&this.setNavigationDepthPercent(b)}},"~S,~N");c(c$,"getTranslationXPercent",function(){return 0==this.width?0:100*(this.fixedTranslation.x-this.width/2)/this.width});c(c$,"getTranslationYPercent",function(){return 0==this.height?0:100*(this.fixedTranslation.y-this.height/2)/this.height});c(c$,"getTranslationZPercent",function(){return 0});c(c$,"getTranslationScript",function(){var a="",b=this.getTranslationXPercent();0!=b&&(a+="translate x "+b+";");b=this.getTranslationYPercent();0!=b&&
(a+="translate y "+b+";");return a});c(c$,"getOrientationText",function(a){switch(a){case 4130:return this.getMoveToText(1,!1);case 1073742132:return this.getRotationQuaternion().toString();case 1073742178:return a=new JU.SB,J.viewer.TransformManager.truncate2(a,this.getTranslationXPercent()),J.viewer.TransformManager.truncate2(a,this.getTranslationYPercent()),a.toString();default:return this.getMoveToText(1,!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N");c(c$,"getOrientationInfo",function(){var a=
new java.util.Hashtable;a.put("moveTo",this.getMoveToText(1,!1));a.put("center","center "+this.getCenterText());a.put("centerPt",this.fixedRotationCenter);var b=new JU.A4;this.getAxisAngle(b);a.put("axisAngle",b);a.put("quaternion",J.util.Quaternion.newAA(b).toPoint4f());a.put("rotationMatrix",this.matrixRotate);a.put("rotateZYZ",this.getRotateZyzText(!1));a.put("rotateXYZ",this.getRotateXyzText());a.put("transXPercent",Float.$valueOf(this.getTranslationXPercent()));a.put("transYPercent",Float.$valueOf(this.getTranslationYPercent()));
a.put("zoom",Float.$valueOf(this.zoomPercent));a.put("modelRadius",Float.$valueOf(this.modelRadius));1==this.mode&&(a.put("navigationCenter","navigate center "+J.util.Escape.eP(this.navigationCenter)),a.put("navigationOffsetXPercent",Float.$valueOf(this.getNavigationOffsetPercent("X"))),a.put("navigationOffsetYPercent",Float.$valueOf(this.getNavigationOffsetPercent("Y"))),a.put("navigationDepthPercent",Float.$valueOf(this.getNavigationDepthPercent())));return a});c(c$,"getAxisAngle",function(a){a.setM(this.matrixRotate)},
"JU.A4");c(c$,"getTransformText",function(){return this.matrixRotate.toString()});c(c$,"getMatrixRotate",function(){return this.matrixRotate});c(c$,"setRotation",function(a){Float.isNaN(a.m00)||this.matrixRotate.setM(a)},"JU.M3");c(c$,"getRotation",function(a){a.setM(this.matrixRotate)},"JU.M3");c(c$,"zoomBy",function(a){20<a?a=20:-20>a&&(a=-20);var b=a*this.zoomPercentSetting/50;0==b&&(b=0<a?1:0>b?-1:0);this.zoomRatio=(b+this.zoomPercentSetting)/this.zoomPercentSetting;this.zoomPercentSetting+=b},
"~N");c(c$,"getZoomPercentFloat",function(){return this.zoomPercent});c(c$,"zoomToPercent",function(a){this.zoomPercentSetting=a;this.zoomRatio=0},"~N");c(c$,"translateZBy",function(a){a>=this.screenPixelCount||(a=this.scalePixelsPerAngstrom/(1-1*a/this.screenPixelCount),a>=this.screenPixelCount||(a=100*(a/this.scaleDefaultPixelsPerAngstrom),this.zoomRatio=a/this.zoomPercentSetting,this.zoomPercentSetting=a))},"~N");c(c$,"zoomByFactor0",function(a,b,c){!(0>=a)&&this.zoomEnabled&&(this.zoomRatio=a,
this.zoomPercentSetting*=a,this.resetXYCenter(b,c))},"~N,~N,~N");c(c$,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&this.viewer.setBooleanProperty("windowCentered",!1);var c=new JU.P3;this.transformPoint2(this.fixedRotationCenter,c);c.set(a,b,c.z);this.unTransformPoint(c,c);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(c)}},"~N,~N");c(c$,"zoomByPercent",function(a){var b=a*this.zoomPercentSetting/100;0==b&&(b=0>a?-1:1);this.zoomRatio=(b+this.zoomPercentSetting)/
this.zoomPercentSetting;this.zoomPercentSetting+=b},"~N");c(c$,"setScaleAngstromsPerInch",function(a){if(this.scale3D=0<a)this.scale3DAngstromsPerInch=a;this.perspectiveDepth=!this.scale3D},"~N");c(c$,"setZslabPoint",function(a){this.zSlabPoint=null==a?null:JU.P3.newP(a)},"JU.P3");c(c$,"getZShadeStart",function(){return this.zShadeEnabled?this.zDepthValue:0});c(c$,"setSlabRange",function(a){this.slabRange=a},"~N");c(c$,"setSlabEnabled",function(a){this.slabEnabled=a;this.viewer.global.setB("slabEnabled",
a)},"~B");c(c$,"setZShadeEnabled",function(a){this.zShadeEnabled=a;this.viewer.global.setB("zShade",a)},"~B");c(c$,"setZoomEnabled",function(a){this.zoomEnabled=a;this.viewer.global.setB("zoomEnabled",a)},"~B");c(c$,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1)});c(c$,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(c$,"slabByPercentagePoints",function(a){this.slabPlane=
null;this.slabPercentSetting+=a;this.slabDepthChanged();this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(c$,"slabDepthChanged",function(){this.viewer.global.setI("slab",this.slabPercentSetting);this.viewer.global.setI("depth",this.depthPercentSetting)});c(c$,"depthByPercentagePoints",function(a){this.depthPlane=null;this.depthPercentSetting+=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+
1);this.slabDepthChanged()},"~N");c(c$,"slabDepthByPercentagePoints",function(a){this.depthPlane=this.slabPlane=null;this.slabPercentSetting+=a;this.depthPercentSetting+=a;this.slabDepthChanged()},"~N");c(c$,"slabToPercent",function(a){this.viewer.setFloatProperty("slabRange",0);this.slabPercentSetting=a;this.slabPlane=null;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(c$,"depthToPercent",function(a){this.viewer.global.setI("depth",
a);this.depthPercentSetting=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(c$,"zSlabToPercent",function(a){this.zSlabPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zDepthPercentSetting=a)},"~N");c(c$,"zDepthToPercent",function(a){this.zDepthPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zSlabPercentSetting=a)},"~N");c(c$,"slabInternal",function(a,b){b?
(this.depthPlane=a,this.depthPercentSetting=0):(this.slabPlane=a,this.slabPercentSetting=100)},"JU.P4,~B");c(c$,"setSlabDepthInternal",function(a){this.finalizeTransformParameters();a?this.depthPlane=null:this.slabPlane=null;this.slabInternal(this.getSlabDepthPlane(a),a)},"~B");c(c$,"getSlabDepthPlane",function(a){if(a){if(null!=this.depthPlane)return this.depthPlane}else if(null!=this.slabPlane)return this.slabPlane;var b=this.matrixTransform;return JU.P4.new4(-b.m20,-b.m21,-b.m22,-b.m23+(a?this.depthValue:
this.slabValue))},"~B");c(c$,"getCameraFactors",function(){this.aperatureAngle=360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(s(this.screenWidth/2),s(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(s(this.screenWidth/2),s(this.screenHeight/2),0);this.viewer.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var c=JU.P3.new3(s(this.screenWidth/
2),s(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.viewer.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);return[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)]});c(c$,"getFrontPlane",function(){return y(this.cameraDistance)});c(c$,"setPerspectiveDepth",function(a){this.perspectiveDepth!=a&&(this.perspectiveDepth=a,this.viewer.global.setB("perspectiveDepth",a),this.resetFitToScreen(!1))},
"~B");c(c$,"getPerspectiveDepth",function(){return this.perspectiveDepth});c(c$,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);var c=0>a?-a/100:a;0!=c&&(this.cameraDepthSetting=c,this.viewer.global.setF("cameraDepth",this.cameraDepthSetting),1==this.mode&&(this.cameraDepth=NaN))},"~N,~B");c(c$,"getCameraDepth",function(){return this.cameraDepthSetting});c(c$,"setVisualRange",function(a){this.visualRange=a},"~N");c(c$,"getUnscaledTransformMatrix",function(){var a=JU.M4.newM(null);
this.vectorTemp.setT(this.fixedRotationCenter);this.matrixTemp.setZero();this.matrixTemp.setTranslation(this.vectorTemp);a.sub(this.matrixTemp);this.matrixTemp.setM3(this.matrixRotate);a.mul2(this.matrixTemp,a);return a});c(c$,"setScreenParameters0",function(a,b,c,g,e,f){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=g)?2*a:a,this.height=g?2*b:b,this.scaleFitToScreen(!1,c,e,f))},"~N,~N,~B,~B,~B,~B");c(c$,"setAntialias",function(a){var b=this.antialias!=
a;this.width=(this.antialias=a)?2*this.screenWidth:this.screenWidth;this.height=this.antialias?2*this.screenHeight:this.screenHeight;b&&this.scaleFitToScreen(!1,this.useZoomLarge,!1,!1)},"~B");c(c$,"defaultScaleToScreen",function(a){return this.screenPixelCount/2/a},"~N");c(c$,"resetFitToScreen",function(a){this.scaleFitToScreen(a,this.viewer.global.zoomLarge,!0,!0)},"~B");c(c$,"scaleFitToScreen",function(a,b,c,g){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*
(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),g&&this.resetNavigationPoint(c),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var c=this.scaleToPerspective(a,
b*this.scalePixelsPerAngstrom/1E3);return 0<c?c:1},"~N,~N");c(c$,"unscaleToScreen",function(a,b){var c=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?c/this.getPerspectiveFactor(a):c},"~N,~N");c(c$,"scaleToPerspective",function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(c$,"getMatrixtransform",function(){return this.matrixTransform});c(c$,"setNavigationMode",function(a){this.mode=a&&this.canNavigate()?1:this.defaultMode;this.resetNavigationPoint(!0)},
"~B");c(c$,"isNavigating",function(){return this.navigating||this.navOn});c(c$,"finalizeTransformParameters",function(){this.haveNotifiedNaN=!1;this.fixedRotationOffset.setT(this.fixedTranslation);this.camera.setT(this.cameraSetting);this.internalSlab=this.slabEnabled&&(null!=this.slabPlane||null!=this.depthPlane);var a=this.getZoomSetting();this.zoomPercent!=a&&(this.zoomPercent=a,this.viewer.global.fontCaching||this.viewer.getGraphicsData().clearFontCache());this.calcCameraFactors();this.calcTransformMatrix();
1==this.mode?this.calcNavigationPoint():this.calcSlabAndDepthValues()});c(c$,"getZoomSetting",function(){5>this.zoomPercentSetting&&(this.zoomPercentSetting=5);2E5<this.zoomPercentSetting&&(this.zoomPercentSetting=2E5);return this.zoomEnabled||1==this.mode?this.zoomPercentSetting:100});c(c$,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):s(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zoomPercentSetting/
100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPoint2(this.zSlabPoint,this.pointT2),this.zSlabValue=y(this.pointT2.z)}catch(a){if(!C(a,Exception))throw a;}this.viewer.global.setS("_slabPlane",
J.util.Escape.eP4(this.getSlabDepthPlane(!1)));this.viewer.global.setS("_depthPlane",J.util.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(c$,"zValueFromPercent",function(a){return s(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},"~N");c(c$,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.fixedRotationCenter,this.frameOffset);this.matrixTemp.setZero();this.matrixTemp.setTranslation(this.vectorTemp);
this.matrixTransform.sub(this.matrixTemp);this.matrixTemp.setM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=this.matrixTemp.m22=-this.scalePixelsPerAngstrom;this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.invertM(this.matrixTransform)}catch(a){if(C(a,
Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(c$,"rotatePoint",function(a,b){this.matrixRotate.transform2(a,b);b.y=-b.y},"JU.P3,JU.P3");c(c$,"transformPoints",function(a,b,c){for(;0<=--a;)c[a].setT(this.transformPoint(b[a]))},"~N,~A,~A");c(c$,"transformPointScr",function(a,b){b.setT(this.transformPoint(a))},"JU.P3,JU.P3i");c(c$,"transformPointNoClip",function(a,b){this.getTempScreenPt(a,null);b.setT(this.point3fScreenTemp)},"JU.P3,JU.P3");c(c$,"transformPoint",
function(a){return 3.4028235E38==a.z||-3.4028235E38==a.z?this.transformScreenPoint(a):this.getTempScreenPt(a,this.internalSlab?a:null)},"JU.P3");c(c$,"transformScreenPoint",function(a){-3.4028235E38==a.z?(this.point3iScreenTemp.x=s(Math.floor(a.x/100*this.screenWidth)),this.point3iScreenTemp.y=s(Math.floor((1-a.y/100)*this.screenHeight))):(this.point3iScreenTemp.x=y(a.x),this.point3iScreenTemp.y=this.screenHeight-y(a.y));this.antialias&&(this.point3iScreenTemp.x<<=1,this.point3iScreenTemp.y<<=1);
this.matrixTransform.transform2(this.fixedRotationCenter,this.pointTsp);this.point3iScreenTemp.z=y(this.pointTsp.z);return this.point3iScreenTemp},"JU.P3");c(c$,"transformPointVib",function(a,b){this.ptVibTemp.setT(a);return this.getTempScreenPt(this.getVibrationPoint(b,this.ptVibTemp),a)},"JU.P3,J.util.Vibration");c(c$,"getVibrationPoint",function(a,b){a.setTempPoint(b,this.vibrationT,this.vibrationScale,this.viewer.global.modulationScale);return b},"J.util.Vibration,J.util.Point3fi");c(c$,"transformPoint2",
function(a,b){this.getTempScreenPt(a,a);b.setT(this.point3fScreenTemp)},"JU.P3,JU.P3");c(c$,"transformVector",function(a,b){this.matrixTransform.rotate(a,b)},"JU.V3,JU.V3");c(c$,"move",function(a,b,c,g,e,f,h){var k=J.api.Interface.getOptionInterface("thread.MoveThread");k.setManager(this,this.viewer,[b,g,[c,e,f,h]]);0<f&&k.setEval(a);k.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"isInPosition",function(a,b){if(Float.isNaN(b))return!0;this.aaTest1.setVA(a,b/57.29577951308232);
this.ptTest1.set(4.321,1.23456,3.14159);this.getRotation(this.matrixTest);this.matrixTest.transform2(this.ptTest1,this.ptTest2);this.matrixTest.setAA(this.aaTest1);this.matrixTest.transform2(this.ptTest1,this.ptTest3);return 0.1>this.ptTest3.distance(this.ptTest2)},"JU.V3,~N");c(c$,"moveToPyMOL",function(a,b,c){var g=JU.M3.newA(c);g.invert();var e=c[9],f=-c[10],h=-c[11],k=JU.P3.new3(c[12],c[13],c[14]),l=c[15],m=c[16],n=c[17];this.setPerspectiveDepth(!(0<=n));var n=Math.abs(n)/2,q=Math.tan(3.141592653589793*
n/180),n=h*q,q=0.5/q-0.5,p=50/n;0<l&&(l=50+y((h-l)*p),h=50+y((h-m)*p),this.setSlabEnabled(!0),this.slabToPercent(l),this.depthToPercent(h),21==c.length&&(m=0!=c[18],p=0!=c[19],c=c[20],this.setZShadeEnabled(m),m&&(p?this.viewer.setIntProperty("zSlab",y(Math.min(100,l+c*(h-l)))):this.viewer.setIntProperty("zSlab",y((l+h)/2)),this.viewer.setIntProperty("zDepth",h))));this.moveTo(a,b,k,null,0,g,100,NaN,NaN,n,null,NaN,NaN,NaN,q,e,f)},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,c,g,e,
f,h,k,l,m,n,p,r,s,t,u,w){if(null==f)if(f=new JU.M3,g=JU.V3.newV(g),Float.isNaN(e))f.m00=NaN;else if(0.01>e&&-0.01<e)f.setIdentity();else{if(0==g.x&&0==g.y&&0==g.z)return;var y=new JU.A4;y.setVA(g,e/57.29577951308232);f.setAA(y)}u==this.cameraSetting.x&&(u=NaN);w==this.cameraSetting.y&&(w=NaN);t==this.cameraDepth&&(t=NaN);Float.isNaN(u)||(k=50*u/m/this.width*this.screenPixelCount);Float.isNaN(w)||(l=50*w/m/this.height*this.screenPixelCount);e=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(m);
if(0>=b)this.setAll(c,f,n,h,k,l,m,e,s,p,r,t,u,w),this.viewer.moveUpdate(b),this.viewer.finalizeTransformParameters();else try{null==this.motion&&(this.motion=J.api.Interface.getOptionInterface("thread.MoveToThread"));var z=this.motion.setManager(this,this.viewer,[c,f,n,[b,h,k,l,m,e,s,p,r,t,u,w]]);0>=z||this.viewer.global.waitForMoveTo?(0<z&&this.motion.setEval(a),this.motion.run(),this.viewer.isSingleThreaded||(this.motion=null)):this.motion.start()}catch(A){if(!C(A,Exception))throw A;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");
c(c$,"stopMotion",function(){this.motion=null});c(c$,"getRotationQuaternion",function(){return J.util.Quaternion.newM(this.matrixRotate)});c(c$,"getRotationText",function(){this.axisangleT.setM(this.matrixRotate);var a=57.29577951308232*this.axisangleT.angle,b=new JU.SB;this.vectorT.set(this.axisangleT.x,this.axisangleT.y,this.axisangleT.z);if(0.01>a)return"{0 0 1 0}";this.vectorT.normalize();this.vectorT.scale(1E3);b.append("{");J.viewer.TransformManager.truncate0(b,this.vectorT.x);J.viewer.TransformManager.truncate0(b,
this.vectorT.y);J.viewer.TransformManager.truncate0(b,this.vectorT.z);J.viewer.TransformManager.truncate2(b,a);b.append("}");return b.toString()});c(c$,"getMoveToText",function(a,b){this.finalizeTransformParameters();var c=new JU.SB;c.append("moveto ");b&&c.append("/* time, axisAngle */ ");c.appendF(a);c.append(" ").append(this.getRotationText());b&&c.append(" /* zoom, translation */ ");J.viewer.TransformManager.truncate2(c,this.zoomPercentSetting);J.viewer.TransformManager.truncate2(c,this.getTranslationXPercent());
J.viewer.TransformManager.truncate2(c,this.getTranslationYPercent());c.append(" ");b&&c.append(" /* center, rotationRadius */ ");c.append(this.getCenterText());c.append(" ").appendF(this.modelRadius);c.append(this.getNavigationText(b));b&&c.append(" /* cameraDepth, cameraX, cameraY */ ");J.viewer.TransformManager.truncate2(c,this.cameraDepth);J.viewer.TransformManager.truncate2(c,this.cameraSetting.x);J.viewer.TransformManager.truncate2(c,this.cameraSetting.y);c.append(";");return c.toString()},"~N,~B");
c(c$,"getCenterText",function(){return J.util.Escape.eP(this.fixedRotationCenter)});c(c$,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,c=-(57.29577951308232*Math.asin(b)),g;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,this.matrixRotate.m11)),g=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),g=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");a.append(";center ").append(this.getCenterText());
0!=b&&(a.append("; rotate x"),J.viewer.TransformManager.truncate2(a,b));0!=c&&(a.append("; rotate y"),J.viewer.TransformManager.truncate2(a,c));0!=g&&(a.append("; rotate z"),J.viewer.TransformManager.truncate2(a,g));a.append(";");this.addZoomTranslationNavigationText(a);return a.toString()});c(c$,"addZoomTranslationNavigationText",function(a){100!=this.zoomPercent&&(a.append(" zoom"),J.viewer.TransformManager.truncate2(a,this.zoomPercent),a.append(";"));var b=this.getTranslationXPercent();0!=b&&(a.append(" translate x"),
J.viewer.TransformManager.truncate2(a,b),a.append(";"));b=this.getTranslationYPercent();0!=b&&(a.append(" translate y"),J.viewer.TransformManager.truncate2(a,b),a.append(";"));if(this.modelRadius!=this.rotationRadiusDefault||10==this.modelRadius)a.append(" set rotationRadius"),J.viewer.TransformManager.truncate2(a,this.modelRadius),a.append(";");1==this.mode&&(a.append("navigate 0 center ").append(J.util.Escape.eP(this.navigationCenter)),a.append(";navigate 0 translate"),J.viewer.TransformManager.truncate2(a,
this.getNavigationOffsetPercent("X")),J.viewer.TransformManager.truncate2(a,this.getNavigationOffsetPercent("Y")),a.append(";navigate 0 depth "),J.viewer.TransformManager.truncate2(a,this.getNavigationDepthPercent()),a.append(";"))},"JU.SB");c(c$,"getRotateZyzText",function(a){var b=new JU.SB,c=this.viewer.getModelSetAuxiliaryInfoValue("defaultOrientationMatrix");null==c?c=this.matrixRotate:(c=JU.M3.newM(c),c.invert(),c.mul2(this.matrixRotate,c));var g=c.m22,e=57.29577951308232*Math.acos(g);0.999<
g||-0.999>g?(g=57.29577951308232*Math.atan2(c.m10,c.m11),c=0):(g=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=g&&(0!=e&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=g&&(b.append("; rotate z"),J.viewer.TransformManager.truncate2(b,g));0!=e&&(b.append("; rotate y"),J.viewer.TransformManager.truncate2(b,e));0!=c&&(b.append("; rotate z"),J.viewer.TransformManager.truncate2(b,
c));b.append(";");this.addZoomTranslationNavigationText(b);return b.toString()},"~B");c$.truncate0=c(c$,"truncate0",function(a,b){a.appendC(" ");a.appendI(Math.round(b))},"JU.SB,~N");c$.truncate2=c(c$,"truncate2",function(a,b){a.appendC(" ");a.appendF(Math.round(100*b)/100)},"JU.SB,~N");c(c$,"setSpinXYZ",function(a,b,c){Float.isNaN(a)||(this.spinX=a);Float.isNaN(b)||(this.spinY=b);Float.isNaN(c)||(this.spinZ=c);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(c$,"setSpinFps",
function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(c$,"setNavXYZ",function(a,b,c){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(c)||(this.navZ=c)},"~N,~N,~N");c(c$,"clearSpin",function(){this.setSpinOff();this.setNavOn(!1);this.isSpinFixed=this.isSpinInternal=!1});c(c$,"getSpinOn",function(){return this.spinOn});c(c$,"getNavOn",function(){return this.navOn});c(c$,"setSpinOn",function(){this.setSpin(null,!0,3.4028235E38,null,null,null,!1)});c(c$,"setSpinOff",function(){this.setSpin(null,
!1,3.4028235E38,null,null,null,!1)});c(c$,"setSpin",function(a,b,c,g,e,f,h){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.viewer.global.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOptionInterface("thread.SpinThread"),this.spinThread.setManager(this,this.viewer,[Float.$valueOf(c),g,e,f,h?Boolean.TRUE:null]),this.spinIsGesture=h,null==f&&null==e?this.spinThread.start():(this.spinThread.setEval(a),this.spinThread.run())):null!=this.spinThread&&
(this.spinThread.reset(),this.spinThread=null))},"J.api.JmolScriptEvaluator,~B,~N,JU.List,~A,JU.BS,~B");c(c$,"setNavOn",function(a){if(!Float.isNaN(this.navFps)){var b=this.navOn;a&&this.spinOn&&this.setSpin(null,!1,0,null,null,null,!1);this.navOn=a;this.viewer.global.setB("_navigating",a);a||this.navInterrupt();a?(0==this.navX&&(0==this.navY&&0==this.navZ)&&(this.navZ=1),0==this.navFps&&(this.navFps=10),null==this.spinThread&&(this.spinThread=J.api.Interface.getOptionInterface("thread.SpinThread"),
this.spinThread.setManager(this,this.viewer,null),this.spinThread.start())):b&&null!=this.spinThread&&(this.spinThread.interrupt(),this.spinThread=null)}},"~B");c(c$,"setVibrationScale",function(a){this.vibrationScale=a},"~N");c(c$,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=y(1E3*this.vibrationPeriod);if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=
this.viewer.modelGetLastVibrationIndex(this.viewer.getCurrentModelIndex(),0))},"~N");c(c$,"setVibrationT",function(a){this.vibrationT.x=a;0==this.vibrationScale&&(this.vibrationScale=this.viewer.global.vibrationScale)},"~N");c(c$,"isVibrationOn",function(){return this.vibrationOn});c(c$,"setVibrationOn",function(a){a?1>this.viewer.getModelCount()?this.vibrationOn=!1:(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOptionInterface("thread.VibrationThread"),this.vibrationThread.setManager(this,
this.viewer,null),this.vibrationThread.start()),this.vibrationOn=!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=!1)},"~B");c(c$,"clearVibration",function(){this.setVibrationOn(!1);this.vibrationScale=0});c(c$,"setStereoMode2",function(a){this.stereoMode=J.constant.EnumStereoMode.CUSTOM;this.stereoColors=a},"~A");c(c$,"setStereoMode",function(a){this.stereoColors=null;this.stereoMode=a},"J.constant.EnumStereoMode");c(c$,"setStereoDegrees",
function(a){this.stereoDegrees=a;this.stereoRadians=0.017453292*a},"~N");c(c$,"getStereoRotationMatrix",function(a){this.stereoFrame=a;if(!a)return this.matrixRotate;this.matrixTemp3.rotY(-this.stereoRadians);this.matrixStereo.mul2(this.matrixTemp3,this.matrixRotate);return this.matrixStereo},"~B");c(c$,"isWindowCentered",function(){return this.windowCentered});c(c$,"setWindowCentered",function(a){this.windowCentered=a;this.resetNavigationPoint(!0)},"~B");c(c$,"getRotationCenter",function(){return this.fixedRotationCenter});
c(c$,"getRotationRadius",function(){return this.modelRadius});c(c$,"setRotationRadius",function(a,b){a=this.modelRadius=0>=a?this.viewer.calcRotationRadius(this.fixedRotationCenter):a;b&&this.viewer.setRotationRadius(a,!1);return a},"~N,~B");c(c$,"setRotationCenterAndRadiusXYZ",function(a,b){this.resetNavigationPoint(!1);null==a?(this.setFixedRotationCenter(this.rotationCenterDefault),this.modelRadius=this.rotationRadiusDefault):(this.setFixedRotationCenter(a),b&&this.windowCentered&&(this.modelRadius=
this.viewer.calcRotationRadius(this.fixedRotationCenter)))},"JU.P3,~B");c(c$,"setRotCenterRel",function(a,b){var c=JU.P3.newP(b);"average"===a?c.add(this.viewer.getAverageAtomPoint()):"boundbox"===a?c.add(this.viewer.getBoundBoxCenter()):"absolute"!==a&&c.setT(this.rotationCenterDefault);this.setRotationCenterAndRadiusXYZ(c,!0)},"~S,JU.P3");c(c$,"setNewRotationCenter",function(a,b){null==a&&(a=this.rotationCenterDefault);this.windowCentered?(this.translateToPercent("x",0),this.translateToPercent("y",
0),this.setRotationCenterAndRadiusXYZ(a,!0),b&&this.resetFitToScreen(!0)):this.moveRotationCenter(a,!0)},"JU.P3,~B");c(c$,"moveRotationCenter",function(a,b){this.setRotationCenterAndRadiusXYZ(a,!1);b&&this.setRotationPointXY(this.fixedRotationCenter)},"JU.P3,~B");c(c$,"setCenter",function(){this.setRotationCenterAndRadiusXYZ(this.fixedRotationCenter,!0)});c(c$,"setCenterAt",function(a,b){this.setRotCenterRel(a,b);this.resetFitToScreen(!0)},"~S,JU.P3");c(c$,"setFrameOffset",function(a){null==this.frameOffsets||
0>a||a>=this.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(c$,"setFrameOffsets",function(a){this.frameOffsets=a},"~A");c(c$,"setSelectedTranslation",function(a,b,c){this.bsSelectedAtoms=a;switch(b){case "X":case "x":this.ptOffset.x+=c;break;case "Y":case "y":this.ptOffset.y+=c;break;case "Z":case "z":this.ptOffset.z+=c}},"JU.BS,~S,~N");c(c$,"setNavFps",function(a){this.navFps=a},"~N");c(c$,"calcCameraFactors",function(){Float.isNaN(this.cameraDepth)&&
(this.cameraDepth=this.cameraDepthSetting,this.zoomFactor=3.4028235E38);this.cameraDistance=this.cameraDepth*this.screenPixelCount;this.referencePlaneOffset=this.cameraDistance+this.screenPixelCount/2;this.scalePixelsPerAngstrom=this.scale3D&&!this.perspectiveDepth&&1!=this.mode?72/this.scale3DAngstromsPerInch*(this.antialias?2:1):this.screenPixelCount/this.visualRange;1!=this.mode&&(this.mode=0==this.camera.z?0:2);this.perspectiveShiftXY.set(0==this.camera.z?0:100*(this.camera.x*this.scalePixelsPerAngstrom/
this.screenWidth),0==this.camera.z?0:100*(this.camera.y*this.scalePixelsPerAngstrom/this.screenHeight),0);this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom;var a=2*this.modelRadius/this.visualRange*this.referencePlaneOffset;if(1==this.mode)this.calcNavCameraFactors(a);else{this.zoomFactor=3.4028235E38;this.modelCenterOffset=this.referencePlaneOffset;if(!this.scale3D||this.perspectiveDepth)this.scalePixelsPerAngstrom*=this.modelCenterOffset/a*this.zoomPercent/100;this.modelRadiusPixels=
this.modelRadius*this.scalePixelsPerAngstrom}});c(c$,"calcNavCameraFactors",function(a){3.4028235E38==this.zoomFactor?(1E4<this.zoomPercent&&(this.zoomPercent=1E4),this.modelCenterOffset=100*a/this.zoomPercent):this.prevZoomSetting!=this.zoomPercentSetting&&(this.modelCenterOffset=0==this.zoomRatio?100*a/this.zoomPercentSetting:this.modelCenterOffset+(1-this.zoomRatio)*this.referencePlaneOffset,this.navMode=-1);this.prevZoomSetting=this.zoomPercentSetting;this.zoomFactor=this.modelCenterOffset/this.referencePlaneOffset;
this.zoomPercent=0==this.zoomFactor?1E4:100*(a/this.modelCenterOffset)},"~N");c(c$,"getPerspectiveFactor",function(a){return 0>=a?this.referencePlaneOffset:this.referencePlaneOffset/a},"~N");c(c$,"getTempScreenPt",function(a,b){this.matrixTransform.transform2(a,this.point3fScreenTemp);var c=this.point3fScreenTemp.z;Float.isNaN(c)?(!this.haveNotifiedNaN&&J.util.Logger.debugging&&J.util.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=!0,c=this.point3fScreenTemp.z=1):0>=c&&(c=this.point3fScreenTemp.z=
1);switch(this.mode){case 1:this.point3fScreenTemp.x-=this.navigationShiftXY.x;this.point3fScreenTemp.y-=this.navigationShiftXY.y;break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(c=this.getPerspectiveFactor(c),this.point3fScreenTemp.x*=c,this.point3fScreenTemp.y*=c);switch(this.mode){case 1:this.point3fScreenTemp.x+=this.navigationOffset.x;this.point3fScreenTemp.y+=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x-=
this.perspectiveShiftXY.x,this.point3fScreenTemp.y-=this.perspectiveShiftXY.y;case 0:this.point3fScreenTemp.x+=this.fixedRotationOffset.x,this.point3fScreenTemp.y+=this.fixedRotationOffset.y}Float.isNaN(this.point3fScreenTemp.x)&&!this.haveNotifiedNaN&&(J.util.Logger.debugging&&J.util.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.point3iScreenTemp.set(y(this.point3fScreenTemp.x),y(this.point3fScreenTemp.y),y(this.point3fScreenTemp.z));if(null!=b&&(null!=this.slabPlane&&
0<b.x*this.slabPlane.x+b.y*this.slabPlane.y+b.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>b.x*this.depthPlane.x+b.y*this.depthPlane.y+b.z*this.depthPlane.z+this.depthPlane.w))this.point3iScreenTemp.z=1;return this.point3iScreenTemp},"JU.P3,JU.P3");c(c$,"unTransformPoint",function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x+=
this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var c=this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=c;this.untransformedPoint.y/=c}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=
this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.transform2(this.untransformedPoint,b)},"JU.P3,JU.P3");c(c$,"canNavigate",function(){return!0});c(c$,"resetNavigationPoint",function(a){5>this.zoomPercent&&1!=this.mode?(this.perspectiveDepth=!0,this.mode=1):(1==this.mode?(this.navMode=1,this.slabPercentSetting=0,this.perspectiveDepth=!0):a&&(this.slabPercentSetting=100),this.viewer.setFloatProperty("slabRange",0),a&&this.setSlabEnabled(1==this.mode),
this.zoomFactor=3.4028235E38,this.zoomPercentSetting=this.zoomPercent)},"~B");c(c$,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();this.navigating=!1},"JU.P3");c(c$,"getNavigationCenter",function(){return this.navigationCenter});c(c$,"getNavigationDepthPercent",function(){return this.navigationDepth});c(c$,"setNavigationSlabOffsetPercent",function(a){this.viewer.global.setF("navigationSlab",a);this.calcCameraFactors();
this.navigationSlabOffset=a/50*this.modelRadiusPixels},"~N");c(c$,"getNavigationOffset",function(){this.transformPoint2(this.navigationCenter,this.navigationOffset);return this.navigationOffset});c(c$,"getNavPtHeight",function(){return this.height/2});c(c$,"getNavigationOffsetPercent",function(a){this.getNavigationOffset();return 0==this.width||0==this.height?0:"X"==a?100*(this.navigationOffset.x-this.width/2)/this.width:100*(this.navigationOffset.y-this.getNavPtHeight())/this.height},"~S");c(c$,
"getNavigationText",function(a){a=a?" /* navigation center, translation, depth */ ":" ";if(1!=this.mode)return a+"{0 0 0} 0 0 0";this.getNavigationOffset();return a+J.util.Escape.eP(this.navigationCenter)+" "+this.getNavigationOffsetPercent("X")+" "+this.getNavigationOffsetPercent("Y")+" "+this.getNavigationDepthPercent()},"~B");c(c$,"setScreenParameters",function(a,b,c,g,e,f){var h=1==this.mode?JU.P3.newP(this.navigationCenter):null,k=JU.P3.newP(this.navigationOffset);k.x/=this.width;k.y/=this.height;
this.setScreenParameters0(a,b,c,g,e,f);null!=h&&(this.navigationCenter.setT(h),this.navTranslatePercentOrTo(-1,k.x*this.width,k.y*this.height),this.setNavigatePt(h))},"~N,~N,~B,~B,~B,~B");c(c$,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(c$,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOptionInterface("navigate.Navigator");if(null==this.nav)return!1;this.nav.set(this,this.viewer);return!0});c(c$,"navigateList",function(a,b){this.getNav()&&this.nav.navigateList(a,
b)},"J.api.JmolScriptEvaluator,JU.List");c(c$,"navigateAxis",function(a,b){this.getNav()&&this.nav.navigateAxis(a,b)},"JU.V3,~N");c(c$,"zoomByFactor",function(a,b,c){1!=this.mode||!this.zoomEnabled||0>=a?this.zoomByFactor0(a,b,c):this.getNav()&&this.nav.zoomByFactor(a,b,c)},"~N,~N,~N");c(c$,"setNavigationOffsetRelative",function(){this.getNav()&&this.nav.setNavigationOffsetRelative()});c(c$,"navigateKey",function(a,b){this.getNav()&&this.nav.navigateKey(a,b)},"~N,~N");c(c$,"setNavigationDepthPercent",
function(a){this.getNav()&&this.nav.setNavigationDepthPercent(a)},"~N");c(c$,"navTranslatePercentOrTo",function(a,b,c){this.getNav()&&this.nav.navTranslatePercentOrTo(a,b,c)},"~N,~N,~N");c(c$,"calcNavigationPoint",function(){this.getNav()&&this.nav.calcNavigationPoint()});c(c$,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""});c(c$,"setZoomHeight",function(a,b){this.zoomHeight=a;this.scaleFitToScreen(!1,b,!1,!0)},"~B,~B");c(c$,"setAll",function(a,
b,c,g,e,f,h,k,l,m,n,p,r,s){this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=c&&1==this.mode&&this.navigationCenter.setT(c);Float.isNaN(p)||this.setCameraDepthPercent(p,!1);!Float.isNaN(r)&&!Float.isNaN(s)&&this.setCamera(r,s);Float.isNaN(g)||this.zoomToPercent(g);Float.isNaN(h)||(this.modelRadius=h);Float.isNaN(k)||(this.scaleDefaultPixelsPerAngstrom=k);!Float.isNaN(e)&&!Float.isNaN(f)&&(this.translateToPercent("x",e),this.translateToPercent("y",f));1==this.mode&&
(!Float.isNaN(m)&&!Float.isNaN(n)&&this.navTranslatePercentOrTo(0,m,n),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");E(c$,"degreesPerRadian",57.29577951308232,"DEFAULT_NAV_FPS",10,"DEFAULT_SPIN_Y",30,"DEFAULT_SPIN_FPS",30,"MAXIMUM_ZOOM_PERCENTAGE",2E5,"MAXIMUM_ZOOM_PERSPECTIVE_DEPTH",1E4,"MODE_STANDARD",0,"MODE_NAVIGATION",1,"MODE_PERSPECTIVE_PYMOL",2,"DEFAULT_PERSPECTIVE_MODEL",11,"NAV_MODE_IGNORE",-2,"NAV_MODE_ZOOMED",-1,"NAV_MODE_NONE",
0,"NAV_MODE_RESET",1,"NAV_MODE_NEWXY",2,"NAV_MODE_NEWXYZ",3,"NAV_MODE_NEWZ",4)}),p("J.viewer"),c$=M(J.viewer,"TransformManager11"),p("J.viewer"),t("java.lang.Enum javajs.api.PlatformViewer J.api.JmolViewer J.atomdata.AtomDataServer java.util.Hashtable javajs.awt.Dimension JU.List J.atomdata.RadiusData J.constant.EnumVdw J.i18n.GT J.util.CommandHistory".split(" "),"J.viewer.Viewer","java.io.Reader java.lang.Boolean $.Character $.Float JU.AU $.BS $.CU $.DF $.P3 $.P3i $.PT $.SB $.V3 J.adapter.smarter.SmarterJmolAdapter J.api.Interface $.JmolAppConsoleInterface J.constant.EnumAnimationMode $.EnumAxesMode $.EnumFileStatus $.EnumStereoMode J.io.CifDataReader $.JmolBinary J.modelset.Group J.script.SV $.T J.thread.TimeoutThread J.util.BSUtil $.C $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Measure $.Parser $.TempArray $.Txt J.viewer.ActionManager $.AnimationManager $.ColorManager $.FileManager $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager J.viewer.binding.Binding".split(" "),
function(){c$=w(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJS=this.haveDisplay=this.autoExit=!1;this.appletCodeBase=this.appletDocumentBase=this.fullName="";this.fileManager=this.modelSet=this.definedAtomSets=this.compiler=this.appletIdiomaBase=null;this.mustRender=this.listCommands=this.isSyntaxCheck=this.isSyntaxAndFileCheck=this.isJNLP=this.$isApplet=!1;this.insertedCommand=this.htmlName="";this.transformManager=this.statusManager=this.global=this.repaintManager=this.selectionManager=
this.shapeManager=this.dataManager=this.colorManager=this.animationManager=this.actionManager=this.applet=this.gdata=null;this.logFilePath=this.syncId="";this.useCommandThread=this.$noGraphicsAllowed=this.multiTouch=this.isSilent=this.isSignedAppletLocal=this.$isSignedApplet=this.isPrintOnly=this.allowScripting=!1;this.tempArray=this.eval=this.scriptManager=this.stateManager=this.modelManager=this.smilesMatcher=this.symmetry=this.commandHistory=this.access=this.modelAdapter=this.display=this.viewerOptions=
this.commandOptions=null;this.$isPreviewOnly=!1;this.mouse=null;this.mouseEnabled=!0;this.noneSelected=!1;this.frameOffsets=this.bsFrameOffsets=this.sc=this.ligandModelSet=this.ligandModels=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.dimScreen=null;this.maximumSize=2147483647;this.imageFontScaling=1;this.jsParams=this.captureParams=null;this.antialiasDisplay=!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverEnabled=!0;this.currentCursor=0;this.prevFrame=
-2147483648;this.haveJDX=!1;this.rd=this.language=this.jsv=null;this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkitPopup=this.jmolpopup=this.scriptEditor=this.appConsole=null;this.isTainted=!0;this.showSelected=this.movingSelected=!1;this.rotatePrev2=this.rotatePrev1=this.rotateBondIndex=-1;this.bsRotateBranch=null;this.creatingImage=!1;this.errorMessageUntranslated=this.errorMessage=this.defaultVdw=this.userVdwMars=this.userVdws=this.bsUserVdws=this.outputManager=
null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.privateKey=0;this.$isKiosk=!1;this.executor=this.minimizer=null;this.displayLoadErrors=!0;this.$isParallel=!1;this.actionStatesRedo=this.actionStates=null;this.stateScriptVersionInt=0;this.logFileName=this.nmrCalculation=this.chainList=this.chainMap=this.timeouts=this.htPdbBondInfo=this.jsExporter3D=null;u(this,arguments)},J.viewer,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,javajs.api.PlatformViewer]);Q(c$,
function(){this.commandHistory=new J.util.CommandHistory;this.dimScreen=new javajs.awt.Dimension(0,0);this.language=J.i18n.GT.getLanguage();this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.constant.EnumVdw.JMOL;this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.actionStates=new JU.List;this.actionStatesRedo=new JU.List;this.chainMap=new java.util.Hashtable;this.chainList=new JU.List});c(c$,"finalize",function(){J.util.Logger.debugging&&J.util.Logger.debug("viewer finalize "+
this);qa(this,J.viewer.Viewer,"finalize",[])});c(c$,"hasDisplay",function(){return this.haveDisplay});h(c$,"isApplet",function(){return this.$isApplet});c(c$,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");c(c$,"getActionManager",function(){return this.actionManager});c(c$,"getLogFilePath",function(){return this.logFilePath});c(c$,"isSignedApplet",function(){return this.$isSignedApplet});c$.getJmolVersion=h(c$,"getJmolVersion",function(){return null==J.viewer.Viewer.version_date?J.viewer.Viewer.version_date=
J.viewer.JC.version+"  "+J.viewer.JC.date:J.viewer.Viewer.version_date});c$.allocateViewer=c(c$,"allocateViewer",function(a,b,c,g,e,f,h,k){var l=new java.util.Hashtable;l.put("display",a);l.put("adapter",b);l.put("statusListener",h);l.put("platform",k);l.put("options",f);l.put("fullName",c);l.put("documentBase",g);l.put("codeBase",e);return new J.viewer.Viewer(l)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");A(c$,function(a){U(this,J.viewer.Viewer,
[]);this.setOptions(a)},"java.util.Map");c(c$,"getStatusManager",function(){return this.statusManager});c(c$,"haveAccess",function(a){return this.access===a},"J.viewer.Viewer.ACCESS");h(c$,"getModelAdapter",function(){null==this.modelAdapter&&(this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter);return this.modelAdapter});c(c$,"getSymmetry",function(){null==this.symmetry&&(this.symmetry=J.api.Interface.getOptionInterface("symmetry.Symmetry"));return this.symmetry});c(c$,"getSymmetryInfo",function(a,
b,c,g,e,f,h){return this.getPropertyManager().getSymmetryInfo(a,b,c,g,e,f,h)},"JU.BS,~S,~N,JU.P3,JU.P3,~S,~N");c(c$,"getSmilesMatcher",function(){null==this.smilesMatcher&&(this.smilesMatcher=J.api.Interface.getOptionInterface("smiles.SmilesMatcher"));return this.smilesMatcher});h(c$,"getSmartsMatch",function(a,b){null==b&&(b=this.getSelectionSet(!1));return this.getSmilesMatcher().getSubstructureSet(a,this.modelSet.atoms,this.getAtomCount(),b,!0,!1)},"~S,JU.BS");c(c$,"getViewerOptions",function(){return this.viewerOptions});
c(c$,"setOptions",function(a){this.viewerOptions=a;J.util.Logger.debugging&&J.util.Logger.debug("Viewer constructor "+this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==this.fullName&&(this.fullName="");var c=a.get("codePath");null==c&&(c="../java/");this.appletCodeBase=c.toString();this.appletIdiomaBase=this.appletCodeBase.substring(0,this.appletCodeBase.lastIndexOf("/",this.appletCodeBase.length-2)+1)+"idioma";c=a.get("documentBase");this.appletDocumentBase=
null==c?"":c.toString();c=a.get("options");this.commandOptions=null==c?"":c.toString();(a.containsKey("debug")||0<=this.commandOptions.indexOf("-debug"))&&J.util.Logger.setLogLevel(5);(this.isJNLP=this.checkOption2("isJNLP","-jnlp"))&&J.util.Logger.info("setting JNLP mode TRUE");this.$isApplet=(this.$isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet","-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");c=this.fullName.indexOf("__");
this.htmlName=0>c?this.fullName:this.fullName.substring(0,c);this.syncId=0>c?"":this.fullName.substring(c+2,this.fullName.length-2);this.$isApplet&&(self.Jmol&&(this.applet=Jmol._applets[this.htmlName.split("_object")[0]],this.strJavaVersion=J.viewer.Viewer.strJavaVersion=Jmol._version),a.containsKey("maximumSize")&&this.setMaximumSize(a.get("maximumSize").intValue()));this.access=this.checkOption2("access:READSPT","-r")?J.viewer.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?J.viewer.Viewer.ACCESS.NONE:
J.viewer.Viewer.ACCESS.ALL;(this.$isPreviewOnly=a.containsKey("previewOnly"))&&a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly","-p");var c=a.get("platform"),g="unknown";null==c&&(c=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");r(c,String)&&(g=c,this.isJS=(this.isWebGL=0<=g.indexOf(".awtjs."))||0<=g.indexOf(".awtjs2d."),c=J.api.Interface.getInterface(g));this.apiPlatform=c;this.display=a.get("display");
this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.$noGraphicsAllowed=this.checkOption2("noGraphics","-n");this.haveDisplay=this.isWebGL||null!=this.display&&!this.$noGraphicsAllowed&&!this.isHeadless()&&!this.checkOption2("isDataOnly","\x00");this.$noGraphicsAllowed=(new Boolean(this.$noGraphicsAllowed&null==this.display)).valueOf();this.haveDisplay?(this.mustRender=!0,this.multiTouch=this.checkOption2("multiTouch","-multitouch"),this.isWebGL||(this.display=document.getElementById(this.display))):
this.display=null;this.apiPlatform.setViewer(this,this.display);c=a.get("graphicsAdapter");null==c&&!this.isWebGL&&(c=J.api.Interface.getInterface("J.g3d.Graphics3D"));this.gdata=null==c?new J.util.GData:c;this.gdata.initialize(this.apiPlatform);this.stateManager=new J.viewer.StateManager(this);this.colorManager=new J.viewer.ColorManager(this,this.gdata);this.statusManager=new J.viewer.StatusManager(this);this.transformManager=new J.viewer.TransformManager(this,2147483647,0);this.selectionManager=
new J.viewer.SelectionManager(this);this.haveDisplay&&(this.actionManager=this.multiTouch?J.api.Interface.getOptionInterface("multitouch.ActionManagerMT"):new J.viewer.ActionManager,this.actionManager.setViewer(this,this.commandOptions+"-multitouch-"+a.get("multiTouch")),this.mouse=this.apiPlatform.getMouseManager(this.privateKey,this.display),this.multiTouch&&!this.checkOption2("-simulated","-simulated")&&this.apiPlatform.setTransparentCursor(this.display));this.modelManager=new J.viewer.ModelManager(this);
this.shapeManager=new J.viewer.ShapeManager(this);this.tempArray=new J.util.TempArray;this.animationManager=new J.viewer.AnimationManager(this);c=a.get("repaintManager");null==c&&(c=J.api.Interface.getOptionInterface("render.RepaintManager"));null!=c&&!c.equals("")&&(this.repaintManager=c).set(this,this.shapeManager);this.initialize(!0);this.fileManager=new J.viewer.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.$isApplet?(J.util.Logger.info("viewerOptions: \n"+
J.util.Escape.escapeMap(this.viewerOptions)),b=this.viewerOptions.get("documentLocation"),!this.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),J.util.Logger.info("setting current directory to "+b),this.cd(b)),b=this.appletDocumentBase,c=b.indexOf("#"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("?"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("/"),0<=c&&(b=b.substring(0,c)),J.viewer.Viewer.jsDocumentBase=b,this.fileManager.setAppletContext(this.appletDocumentBase),
b=a.get("appletProxy"),null!=b&&this.setStringProperty("appletProxy",b),this.$isSignedApplet?(this.logFilePath=JU.PT.simpleReplace(this.appletCodeBase,"file://",""),this.logFilePath=JU.PT.simpleReplace(this.logFilePath,"file:/",""),0<=this.logFilePath.indexOf("//")?this.logFilePath=null:this.isSignedAppletLocal=!0):this.isJS||(this.logFilePath=null)):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&J.util.Logger.setLogLevel(3),
this.isSyntaxCheck=(this.isSyntaxAndFileCheck=this.checkOption2("checkLoad","-C"))||this.checkOption2("check","-c"),this.listCommands=this.checkOption2("listCommands","-l"),this.autoExit=this.checkOption2("exit","-x"),this.cd("."),this.isHeadless()&&(this.headlessImageParams=a.get("headlessImage"),c=a.get("headlistMaxTimeMs"),null==c&&(c=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),c.intValue(),"exitJmol")));this.useCommandThread=!this.isHeadless()&&this.checkOption2("useCommandThread",
"-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",J.viewer.Viewer.nProcessors);c=a.get("menuFile");null!=c&&this.getProperty("DATA_API","setMenu",this.getFileAsString(c));this.isSilent||J.util.Logger.info("(C) 2012 Jmol Development\nJmol Version: "+J.viewer.Viewer.getJmolVersion()+"\njava.vendor: "+J.viewer.Viewer.strJavaVendor+"\njava.version: "+J.viewer.Viewer.strJavaVersion+"\nos.name: "+J.viewer.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getParameter("_memory")+
"\nprocessors available: "+J.viewer.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.$isApplet?"":"\nappletId:"+this.htmlName+(this.$isSignedApplet?" (signed)":"")));this.zap(!1,!0,!1);this.global.setS("language",J.i18n.GT.getLanguage());this.stateManager.setJmolDefaults()},"java.util.Map");c(c$,"setDisplay",function(a){this.display=a;this.apiPlatform.setViewer(this,a)},"~O");c(c$,"getDataManager",function(){return null==this.dataManager?this.dataManager=J.api.Interface.getOptionInterface("viewer.DataManager").set(this):
this.dataManager});c(c$,"getScriptManager",function(){this.allowScripting&&null==this.scriptManager&&(this.scriptManager=J.api.Interface.getOptionInterface("script.ScriptManager"),this.scriptManager.setViewer(this),this.eval=this.scriptManager.getEval(),this.useCommandThread&&this.scriptManager.startCommandWatcher(!0));return this.scriptManager});c(c$,"checkOption2",function(a,b){return this.viewerOptions.containsKey(a)||0<=this.commandOptions.indexOf(b)},"~S,~S");c(c$,"isPreviewOnly",function(){return this.$isPreviewOnly});
c(c$,"isHeadless",function(){return this.apiPlatform.isHeadless()});c(c$,"setStartupBooleans",function(){this.setBooleanProperty("_applet",this.$isApplet);this.setBooleanProperty("_jspecview",!1);this.setBooleanProperty("_signedApplet",this.$isSignedApplet);this.setBooleanProperty("_headless",this.apiPlatform.isHeadless());this.setStringProperty("_restrict",'"'+this.access+'"');this.setBooleanProperty("_useCommandThread",this.useCommandThread)});c(c$,"noGraphicsAllowed",function(){return this.$noGraphicsAllowed});
c(c$,"getExportDriverList",function(){return this.haveAccess(J.viewer.Viewer.ACCESS.ALL)?this.global.getParameter("exportDrivers"):""});c(c$,"getHtmlName",function(){return this.htmlName});h(c$,"getDisplay",function(){return this.display});c(c$,"clearMouse",function(){this.mouse.clear()});c(c$,"disposeMouse",function(){this.actionManager.dispose();this.mouse.dispose();this.mouse=null});h(c$,"processTwoPointGesture",function(a){this.mouse.processTwoPointGesture(a)},"~A");h(c$,"processMouseEvent",function(a,
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this.setObjectColor("background","black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.gdata.setAmbientPercent(this.global.ambientPercent);this.gdata.setDiffusePercent(this.global.diffusePercent);this.gdata.setSpecular(this.global.specular);this.gdata.setCel(this.global.celShading);this.gdata.setCelPower(this.global.celShadingPower);this.gdata.setSpecularPercent(this.global.specularPercent);this.gdata.setSpecularPower(-this.global.specularExponent);
this.gdata.setPhongExponent(this.global.phongExponent);this.gdata.setSpecularPower(this.global.specularPower);null!=this.modelSet&&this.animationManager.setAnimationOn(!1);this.animationManager.setAnimationFps(this.global.animationFps);this.statusManager.setAllowStatusReporting(this.global.statusReporting);this.setBooleanProperty("antialiasDisplay",this.global.antialiasDisplay);this.setTransformManagerDefaults()},"~B");c(c$,"listSavedStates",function(){return this.stateManager.listSavedStates()});
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NaN);break;case 12:this.transformManager.setNavXYZ(NaN,b,NaN);break;case 14:this.transformManager.setNavXYZ(NaN,NaN,b);break;case 16:this.transformManager.setNavFps(b)}this.global.setI((10>c?"spin":"nav")+a,b)}},"~S,~N");c(c$,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});c(c$,"setSpinOn",function(a){a?this.transformManager.setSpinOn():this.transformManager.setSpinOff()},"~B");c(c$,"getSpinOn",function(){return this.transformManager.getSpinOn()});c(c$,"setNavOn",function(a){this.transformManager.setNavOn(a)},
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"axis":b);if(!(0>g)){if(-2==c||-4==c){var e=c+3;c=this.getObjectMad(g);0==c&&(c=e)}this.global.setB("show"+b,0!=c);this.global.objStateOn[g]=0!=c;0!=c&&(this.global.objMad[g]=c,this.setShapeSize(a,c,null))}},"~N,~S,~N");c(c$,"getObjectMad",function(a){return this.global.objStateOn[a]?this.global.objMad[a]:0},"~N");c(c$,"setPropertyColorScheme",function(a,b,c){this.global.propertyColorScheme=a;a.startsWith("translucent ")&&(b=!0,a=a.substring(12).trim());this.colorManager.setPropertyColorScheme(a,
b,c)},"~S,~B,~B");c(c$,"getPropertyColorScheme",function(){return this.global.propertyColorScheme});c(c$,"getColixBackgroundContrast",function(){return this.colorManager.colixBackgroundContrast});c(c$,"getSpecularState",function(){return this.getStateCreator().getSpecularState()});c(c$,"getColixAtomPalette",function(a,b){return this.colorManager.getColixAtomPalette(a,b)},"J.modelset.Atom,~N");c(c$,"getColixBondPalette",function(a,b){return this.colorManager.getColixBondPalette(a,b)},"J.modelset.Bond,~N");
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a},"~B");c(c$,"getRefreshing",function(){return this.refreshing});h(c$,"pushHoldRepaint",function(){this.pushHoldRepaintWhy(null)});c(c$,"pushHoldRepaintWhy",function(a){null!=this.repaintManager&&this.repaintManager.pushHoldRepaint(a)},"~S");h(c$,"popHoldRepaint",function(a){null!=this.repaintManager&&this.repaintManager.popHoldRepaint(0>a.indexOf("\u0001## REPAINT_IGNORE ##"),a)},"~S");h(c$,"refresh",function(a,b){if(null!=this.repaintManager&&this.refreshing&&!(6==a&&this.getInMotion(!0))){if(this.isWebGL){if(2==
a||7==a){this.transformManager.finalizeTransformParameters();if(!self.Jmol)return;Jmol._refresh&&Jmol._refresh(this.applet,a,b,[this.transformManager.fixedRotationCenter,this.transformManager.getRotationQuaternion(),this.transformManager.xTranslationFraction,this.transformManager.yTranslationFraction,this.transformManager.scalePixelsPerAngstrom,this.transformManager.zoomPercent])}}else 0<a&&7!=a&&this.repaintManager.repaintIfReady("refresh "+a+" "+b);7!=a&&0!=a%3&&this.statusManager.doSync()&&this.statusManager.setSync(2==
a?b:null)}},"~N,~S");c(c$,"requestRepaintAndWait",function(a){this.haveDisplay&&null!=this.repaintManager&&(this.repaintManager.requestRepaintAndWait(a),this.setSync())},"~S");c(c$,"clearShapeRenderers",function(){this.clearRepaintManager(-1)});c(c$,"isRepaintPending",function(){return null==this.repaintManager?!1:this.repaintManager.isRepaintPending()});h(c$,"notifyViewerRepaintDone",function(){null!=this.repaintManager&&this.repaintManager.repaintDone();this.animationManager.repaintDone()});c(c$,
"areAxesTainted",function(){var a=this.axesAreTainted;this.axesAreTainted=!1;return a});c(c$,"setMaximumSize",function(a){this.maximumSize=Math.max(a,100)},"~N");h(c$,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.isStereoDouble()&&(a=s((a+1)/2));this.dimScreen.width==a&&this.dimScreen.height==b||this.resizeImage(a,b,!1,!1,!0)},"~N,~N");c(c$,"getImageFontScaling",function(){return this.imageFontScaling});c(c$,"resizeImage",function(a,b,c,g,e){if(c||
!this.creatingImage)!g&&!c&&this.setShapeProperty(5,"clearBoxes",null),this.antialiasDisplay=e?this.global.antialiasDisplay&&this.checkMotionRendering(603979786):c&&!g?this.global.antialiasImages:!1,this.imageFontScaling=(e||0>=a?1:s((this.global.zoomLarge==b>a?b:a)/this.getScreenDim()))*(this.antialiasDisplay?2:1),0<a?(this.dimScreen.width=a,this.dimScreen.height=b,c||(this.global.setI("_width",a),this.global.setI("_height",b),this.setStatusResized(a,b))):(a=0==this.dimScreen.width?this.dimScreen.width=
500:this.dimScreen.width,b=0==this.dimScreen.height?this.dimScreen.height=500:this.dimScreen.height),this.transformManager.setScreenParameters(a,b,c||e?this.global.zoomLarge:!1,this.antialiasDisplay,!1,!1),this.gdata.setWindowParameters(a,b,this.antialiasDisplay)},"~N,~N,~B,~B,~B");h(c$,"getScreenWidth",function(){return this.dimScreen.width});h(c$,"getScreenHeight",function(){return this.dimScreen.height});c(c$,"getScreenDim",function(){return this.global.zoomLarge==this.dimScreen.height>this.dimScreen.width?
this.dimScreen.height:this.dimScreen.width});h(c$,"generateOutputForExport",function(a){return this.$noGraphicsAllowed||null==this.repaintManager?null:this.getOutputManager().getOutputFromExport(a)},"java.util.Map");c(c$,"clearRepaintManager",function(a){null!=this.repaintManager&&this.repaintManager.clear(a)},"~N");h(c$,"renderScreenImageStereo",function(a,b,c,g){this.updateWindow(c,g)&&(null==b?this.getScreenImageBuffer(a,!1):(this.render1(b,this.getImage(!0,!1),0,0),this.render1(a,this.getImage(!1,
!1),0,0)));null!=this.captureParams&&Boolean.FALSE!==this.captureParams.get("captureEnabled")&&(System.currentTimeMillis()+50>this.captureParams.get("endTime").longValue()&&this.captureParams.put("captureMode",Integer.$valueOf(1150985)),this.processWriteOrCapture(this.captureParams));this.notifyViewerRepaintDone()},"~O,~O,~N,~N");h(c$,"updateJS",function(a,b){if(this.isWebGL)null==this.jsParams&&(this.jsParams=new java.util.Hashtable,this.jsParams.put("type","JS")),this.updateWindow(a,b)&&this.render(),
this.notifyViewerRepaintDone();else{var c=null,g=null;this.statusManager.jmolStatusListener.isStereoSlave||(c=this.apiPlatform.context,g=this.statusManager.jmolStatusListener.gright,this.renderScreenImageStereo(c,g,a,b))}},"~N,~N");c(c$,"updateWindow",function(a,b){if(!this.refreshing||this.creatingImage)return!1;(this.isTainted||this.getSlabEnabled())&&this.setModelVisibility();this.isTainted=!1;null!=this.repaintManager&&0!=a&&this.setScreenDimension(a,b);return!0},"~N,~N");c(c$,"renderScreenImage",
function(a,b,c){this.renderScreenImageStereo(a,null,b,c)},"~O,~N,~N");c(c$,"getImage",function(a,b){if(this.isWebGL)return null;var c=null;try{this.beginRendering(a,b),this.render(),this.gdata.endRendering(),c=this.gdata.getScreenImage(b)}catch(g){if(C(g,Error))this.gdata.getScreenImage(b),this.handleError(g,!1),this.setErrorMessage("Error during rendering: "+g,null);else throw g;}return c},"~B,~B");c(c$,"beginRendering",function(a,b){this.gdata.beginRendering(this.transformManager.getStereoRotationMatrix(a),
this.global.translucent,b,!this.checkMotionRendering(603979967))},"~B,~B");c(c$,"isAntialiased",function(){return this.antialiasDisplay});c(c$,"render",function(){if(!(null==this.modelSet||!this.mustRender||!this.refreshing&&!this.creatingImage||null==this.repaintManager)){var a=this.antialiasDisplay&&this.global.antialiasTranslucent;this.finalizeTransformParameters();this.shapeManager.finalizeAtoms(this.transformManager.bsSelectedAtoms,this.transformManager.ptOffset);var b=this.shapeManager.transformAtoms();
this.transformManager.bsSelectedAtoms=null;this.isWebGL?(this.repaintManager.renderExport(this.gdata,this.modelSet,this.jsParams),this.notifyViewerRepaintDone()):(this.repaintManager.render(this.gdata,this.modelSet,!0,b),this.gdata.setPass2(a)&&(this.transformManager.setAntialias(a),this.repaintManager.render(this.gdata,this.modelSet,!1,null),this.transformManager.setAntialias(this.antialiasDisplay)))}});c(c$,"render1",function(a,b,c,g){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,c,g,this.dimScreen.width,
this.dimScreen.height);this.gdata.releaseScreenImage()},"~O,~O,~N,~N");h(c$,"getScreenImageBuffer",function(a,b){if(this.isWebGL)return null;var c=null==a&&this.isStereoDouble(),g;this.transformManager.stereoMode.isBiColor()?(this.beginRendering(!0,b),this.render(),this.gdata.endRendering(),this.gdata.snapshotAnaglyphChannelBytes(),this.beginRendering(!1,b),this.render(),this.gdata.endRendering(),this.gdata.applyAnaglygh(this.transformManager.stereoMode,this.transformManager.stereoColors),g=this.gdata.getScreenImage(b)):
g=this.getImage(this.isStereoDouble(),b);var e=null;c&&(e=this.apiPlatform.newBufferedImage(g,this.dimScreen.width<<1,this.dimScreen.height),a=this.apiPlatform.getGraphics(e));null!=a&&(this.isStereoDouble()&&(this.render1(a,g,this.dimScreen.width,0),g=this.getImage(!1,!1)),this.render1(a,g,0,0));return c?e:g},"~O,~B");h(c$,"getImageAsBytes",function(a,b,c,g,e){return this.isWebGL?null:this.getOutputManager().getImageAsBytes(a,b,c,g,e)},"~S,~N,~N,~N,~A");h(c$,"releaseScreenImage",function(){this.gdata.releaseScreenImage()});
h(c$,"evalFile",function(a){if(!this.allowScripting)return null;var b=a.indexOf(" -noqueue");return 0<=b?this.evalStringWaitStatusQueued("String",a.substring(0,b),"",!0,!1,!1):this.getScriptManager().addScript(a,!0,!1)},"~S");c(c$,"getInsertedCommand",function(){var a=this.insertedCommand;this.insertedCommand="";J.util.Logger.debugging&&""!==a&&J.util.Logger.debug("inserting: "+a);return a});h(c$,"script",function(a){return this.evalStringQuietSync(a,!1,!0)},"~S");h(c$,"evalString",function(a){return this.evalStringQuietSync(a,
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b)},"~S,~B");h(c$,"scriptWait",function(a){return this.evalWait("JSON",a,"+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated")},"~S");h(c$,"scriptWaitStatus",function(a,b){return this.evalWait("object",a,b)},"~S,~S");c(c$,"evalWait",function(a,b,c){if(null==this.getScriptManager())return null;this.scriptManager.waitForQueue();var g=J.i18n.GT.setDoTranslate(!1);a=this.evalStringWaitStatusQueued(a,b,c,!1,!1,!1);J.i18n.GT.setDoTranslate(g);return a},"~S,~S,~S");c(c$,"evalStringWaitStatusQueued",
function(a,b,c,g,e,f){return 0==b.indexOf("JSCONSOLE")?(this.applet._showInfo(0>b.indexOf("CLOSE")),0<=b.indexOf("CLEAR")&&this.applet._clearConsole(),null):null==this.getScriptManager()?null:this.scriptManager.evalStringWaitStatusQueued(a,b,c,g,e,f)},"~S,~S,~S,~B,~B,~B");c(c$,"exitJmol",function(){if(!this.$isApplet||this.isJNLP){if(null!=this.headlessImageParams)try{this.isHeadless()&&this.outputToFile(this.headlessImageParams)}catch(a){if(!C(a,Exception))throw a;}J.util.Logger.debugging&&J.util.Logger.debug("exitJmol -- exiting");
System.out.flush();System.exit(0)}});c(c$,"scriptCheckRet",function(a,b){return null==this.getScriptManager()?null:this.scriptManager.scriptCheckRet(a,b)},"~S,~B");h(c$,"scriptCheck",function(a){return null==this.getScriptManager()?null:this.scriptCheckRet(a,!1)},"~S");h(c$,"isScriptExecuting",function(){return null!=this.eval&&this.eval.isExecuting()});h(c$,"haltScriptExecution",function(){null!=this.eval&&(this.eval.haltExecution(),this.eval.stopScriptThreads());this.setStringPropertyTok("pathForAllFiles",
545259571,"");this.clearTimeouts()});c(c$,"pauseScriptExecution",function(){null!=this.eval&&this.eval.pauseExecution(!0)});c(c$,"getDefaultLoadFilter",function(){return this.global.defaultLoadFilter});c(c$,"getDefaultLoadScript",function(){return this.global.defaultLoadScript});c(c$,"resolveDatabaseFormat",function(a){J.viewer.Viewer.hasDatabasePrefix(a)&&(a=this.setLoadFormat(a,a.charAt(0),!1));return a},"~S");c$.isDatabaseCode=c(c$,"isDatabaseCode",function(a){return"$"==a||"="==a||":"==a},"~S");
c$.hasDatabasePrefix=c(c$,"hasDatabasePrefix",function(a){return 0!=a.length&&J.viewer.Viewer.isDatabaseCode(a.charAt(0))},"~S");c(c$,"setLoadFormat",function(a,b,c){var g=a.substring(1);switch(b){case "=":if(a.startsWith("=="))g=g.substring(1),b="#";else if(0<g.indexOf("/"))try{var e=g.indexOf("/"),f=g.substring(0,e),g=this.global.resolveDataBase(f,g.substring(e+1));return null==g?a:g}catch(h){if(C(h,Exception))return a;throw h;}case "#":return c="="==b?this.global.loadFormat:this.global.loadLigandFormat,
0<g.indexOf(".")&&0<=c.indexOf("%FILE.")&&(c=c.substring(0,c.indexOf("%FILE")+5)),J.util.Txt.formatStringS(c,"FILE",g);case ":":a=this.global.pubChemFormat;c=g.toLowerCase();b=-2147483648;try{b=Integer.parseInt(g)}catch(k){if(!C(k,Exception))throw k;}-2147483648!=b?g="cid/"+b:c.startsWith("smiles:")?(a+="?POST?smiles="+g.substring(7),g="smiles"):c.startsWith("cid:")?g="cid/"+g.substring(4):(c.startsWith("name:")&&(g=g.substring(5)),c.startsWith("cas:")&&(g=g.substring(4)),g="name/"+JU.PT.escapeUrl(g));
return J.util.Txt.formatStringS(a,"FILE",g);case "$":if(a.startsWith("$$"))return g=g.substring(1),a=JU.PT.simpleReplace(this.global.smilesUrlFormat,"&get3d=True",""),J.util.Txt.formatStringS(a,"FILE",JU.PT.escapeUrl(g));case "N":case "2":case "I":case "K":case "/":g=JU.PT.escapeUrl(g);switch(b){case "N":a=this.global.nihResolverFormat+"/names";break;case "2":a=this.global.nihResolverFormat+"/image";break;case "I":a=this.global.nihResolverFormat+"/stdinchi";break;case "K":a=this.global.nihResolverFormat+
"/inchikey";break;case "/":a=this.global.nihResolverFormat+"/";break;default:a=this.global.smilesUrlFormat}return(c?"MOL3D::":"")+J.util.Txt.formatStringS(a,"FILE",g);case "_":return c=J.viewer.FileManager.fixFileNameVariables(this.global.edsUrlFormat,g),g=J.viewer.FileManager.fixFileNameVariables(this.global.edsUrlCutoff,g),[c,g]}return g},"~S,~S,~B");c(c$,"getElectronDensityLoadInfo",function(){return[this.global.edsUrlFormat,this.global.edsUrlCutoff,this.global.edsUrlOptions]});c(c$,"getStandardLabelFormat",
function(a){switch(a){default:case 0:return"%[identify]";case 1:return this.global.defaultLabelXYZ;case 2:return this.global.defaultLabelPDB}},"~N");c(c$,"getAdditionalHydrogens",function(a,b,c,g){null==a&&(a=this.getSelectionSet(!1));var e=D(1,0);a=this.modelSet.calculateHydrogens(a,e,b,c,g);e=Array(e[0]);for(c=b=0;b<a.length;b++)if(null!=a[b])for(g=0;g<a[b].length;g++)e[c++]=a[b][g];return e},"JU.BS,~B,~B,JU.List");h(c$,"setMarBond",function(a){this.global.bondRadiusMilliAngstroms=a;this.global.setI("bondRadiusMilliAngstroms",
a);this.setShapeSize(1,2*a,J.util.BSUtil.setAll(this.getAtomCount()))},"~N");c(c$,"setHoverLabel",function(a){this.loadShape(34);this.setShapeProperty(34,"label",a);(this.hoverEnabled=null!=a)||this.startHoverWatcher(!1)},"~S");c(c$,"hoverOn",function(a,b){this.setStatusAtomHovered(a,this.getAtomInfoXYZ(a,!1));if(this.hoverEnabled)if(this.global.modelKitMode)this.isAtomAssignable(a)&&this.highlight(J.util.BSUtil.newAndSetBit(a)),this.refresh(3,"hover on atom");else if(!(null!=this.eval&&this.isScriptExecuting()||
a==this.hoverAtomIndex||0==this.global.hoverDelayMs)&&this.isInSelectionSubset(a))this.loadShape(34),b&&this.modelSet.atoms[a].isShapeVisible(J.viewer.JC.getShapeVisibilityFlag(5))&&this.setShapeProperty(34,"specialLabel",J.i18n.GT._("Drag to move label")),this.setShapeProperty(34,"text",null),this.setShapeProperty(34,"target",Integer.$valueOf(a)),this.hoverText=null,this.hoverAtomIndex=a,this.refresh(3,"hover on atom")},"~N,~B");c(c$,"hoverOnPt",function(a,b,c,g,e){this.hoverEnabled&&!(null!=this.eval&&
this.isScriptExecuting())&&(this.loadShape(34),this.setShapeProperty(34,"xy",JU.P3i.new3(a,b,0)),this.setShapeProperty(34,"target",null),this.setShapeProperty(34,"specialLabel",null),this.setShapeProperty(34,"text",c),this.hoverAtomIndex=-1,this.hoverText=c,null!=g&&null!=e&&this.setStatusObjectHovered(g,c,e),this.refresh(3,"hover on point"))},"~N,~N,~S,~S,JU.P3");c(c$,"hoverOff",function(){try{if(this.global.modelKitMode&&this.highlight(null),this.hoverEnabled){var a=null!=this.hoverText||0<=this.hoverAtomIndex;
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a);null!=this.eval&&this.eval.setDebugging()},"~B");c(c$,"clearClickCount",function(){this.setTainted(!0)});c(c$,"getCursor",function(){return this.currentCursor});c(c$,"setCursor",function(a){if(!this.$isKiosk&&!(this.currentCursor==a||this.multiTouch||!this.haveDisplay))this.apiPlatform.setCursor(this.currentCursor=a,this.display)},"~N");c(c$,"setPickingMode",function(a,b){if(this.haveDisplay){this.showSelected=!1;var c=null;if(null!=a){var g=a.indexOf("_");0<=g&&(c=a.substring(g+1),a=a.substring(0,
g));b=J.viewer.ActionManager.getPickingMode(a)}0>b&&(b=1);this.actionManager.setPickingMode(b);this.global.setS("picking",J.viewer.ActionManager.getPickingModeName(this.actionManager.getAtomPickingMode()));if(!(null==c||0==c.length))switch(c=Character.toUpperCase(c.charAt(0))+(1==c.length?"":c.substring(1,2)),b){case 32:this.setAtomPickingOption(c);break;case 33:this.setBondPickingOption(c);break;default:J.util.Logger.error("Bad picking mode: "+a+"_"+c)}}},"~S,~N");c(c$,"getPickingMode",function(){return this.haveDisplay?
this.actionManager.getAtomPickingMode():0});c(c$,"setPickingStyle",function(a,b){this.haveDisplay&&(null!=a&&(b=J.viewer.ActionManager.getPickingStyleIndex(a)),0>b&&(b=0),this.actionManager.setPickingStyle(b),this.global.setS("pickingStyle",J.viewer.ActionManager.getPickingStyleName(this.actionManager.getPickingStyle())))},"~S,~N");c(c$,"getDrawHover",function(){return this.haveDisplay&&this.global.drawHover});h(c$,"getAtomInfo",function(a){return 0<=a?this.modelSet.getAtomInfo(a,null):this.shapeManager.getShapePropertyIndex(6,
"pointInfo",-a)},"~N");c(c$,"getAtomInfoXYZ",function(a,b){return this.modelSet.getAtomInfoXYZ(a,b)},"~N,~B");c(c$,"setSync",function(){this.statusManager.doSync()&&this.statusManager.setSync(null)});h(c$,"setJmolCallbackListener",function(a){this.statusManager.setJmolCallbackListener(a)},"J.api.JmolCallbackListener");h(c$,"setJmolStatusListener",function(a){this.statusManager.setJmolStatusListener(a,null)},"J.api.JmolStatusListener");c(c$,"getMessageQueue",function(){return this.statusManager.getMessageQueue()});
c(c$,"getStatusChanged",function(a){return null==a?null:this.statusManager.getStatusChanged(a)},"~S");c(c$,"menuEnabled",function(){return!this.global.disablePopupMenu&&null!=this.getPopupMenu()});c(c$,"popupMenu",function(a,b,c){if(this.haveDisplay&&this.refreshing&&!this.$isPreviewOnly&&!this.global.disablePopupMenu)switch(c){case "j":try{this.getPopupMenu(),this.jmolpopup.jpiShow(a,b)}catch(g){this.global.disablePopupMenu=!0}break;case "a":case "b":case "m":this.modelkitPopup=this.apiPlatform.getMenuPopup(null,
c),null!=this.modelkitPopup&&this.modelkitPopup.jpiShow(a,b)}},"~N,~N,~S");c(c$,"getMenu",function(a){this.getPopupMenu();return a.equals("\x00")?(this.popupMenu(this.dimScreen.width-120,0,"j"),"OK"):null==this.jmolpopup?"":this.jmolpopup.jpiGetMenuAsString("Jmol version "+J.viewer.Viewer.getJmolVersion()+"|_GET_MENU|"+a)},"~S");c(c$,"getPopupMenu",function(){return null==this.jmolpopup&&(this.jmolpopup=this.allowScripting?this.apiPlatform.getMenuPopup(this.menuStructure,"j"):null,null==this.jmolpopup)?
(this.global.disablePopupMenu=!0,null):this.jmolpopup.jpiGetMenuAsObject()});c(c$,"setMenu",function(a,b){b&&J.util.Logger.info("Setting menu "+(0==a.length?"to Jmol defaults":"from file "+a));0==a.length?a=null:b&&(a=this.getFileAsString(a));this.getProperty("DATA_API","setMenu",a);this.statusManager.setCallbackFunction("menu",a)},"~S,~B");c(c$,"setStatusFrameChanged",function(a){a&&(this.prevFrame=-2147483648);a=this.animationManager.getCurrentModelIndex();this.transformManager.setVibrationPeriod(NaN);
var b=this.animationManager.firstFrameIndex,c=this.animationManager.lastFrameIndex,g=this.isMovie(),e=this.animationManager.currentModelIndex;b==c&&!g&&(e=b);var f=this.getModelFileNumber(e),h=this.animationManager.getCurrentModelIndex(),k=f,l=f%1E6,m=g?b:this.getModelFileNumber(b),n=g?c:this.getModelFileNumber(c),p;g?p=""+(a+1):0==k?(p=this.getModelNumberDotted(b),b!=c&&(p+=" - "+this.getModelNumberDotted(c)),s(m/1E6)==s(n/1E6)&&(k=m)):p=this.getModelNumberDotted(e);0!=k&&(k=1E6>k?1:s(k/1E6));g||
(this.global.setI("_currentFileNumber",k),this.global.setI("_currentModelNumberInFile",l));this.global.setI("_currentFrame",h);this.global.setI("_morphCount",this.animationManager.morphCount);this.global.setF("_currentMorphFrame",this.animationManager.currentMorphModel);this.global.setI("_frameID",f);this.global.setS("_modelNumber",p);this.global.setS("_modelName",0>e?"":this.getModelName(e));b=0>e?"":this.getModelTitle(e);this.global.setS("_modelTitle",null==b?"":b);this.global.setS("_modelFile",
0>e?"":this.modelSet.getModelFileName(e));this.global.setS("_modelType",0>e?"":this.modelSet.getModelFileType(e));h!=this.prevFrame&&(this.prevFrame=h,g?g=""+(this.animationManager.getCurrentModelIndex()+1):(g=this.getModelName(a),b=""+this.getModelNumberDotted(a),g.equals(b)||(g=b+": "+g),50<g.length&&(g=g.substring(0,45)+"...")),this.statusManager.setStatusFrameChanged(a,k,l,0>this.animationManager.animationDirection?-m:m,0>this.animationManager.currentDirection?-n:n,h,g),this.doHaveJDX()&&this.getJSV().setModel(e))},
"~B,~B");c(c$,"doHaveJDX",function(){return this.haveJDX||(this.haveJDX=this.getBooleanProperty("_jspecview"))});c(c$,"getJSV",function(){null==this.jsv&&(this.jsv=J.api.Interface.getOptionInterface("viewer.JSpecView"),this.jsv.setViewer(this));return this.jsv});c(c$,"getJDXBaseModelIndex",function(a){return!this.doHaveJDX()?a:this.getJSV().getBaseModelIndex(a)},"~N");c(c$,"getJspecViewProperties",function(a){a=this.statusManager.getJspecViewProperties(""+a);null!=a&&(this.haveJDX=!0);return a},"~O");
c(c$,"scriptEcho",function(a){J.util.Logger.isActiveLevel(4)&&(System.out.println(a),this.statusManager.setScriptEcho(a,this.isScriptQueued()),this.listCommands&&(null!=a&&0==a.indexOf("$["))&&J.util.Logger.info(a))},"~S");c(c$,"isScriptQueued",function(){return null!=this.scriptManager&&this.scriptManager.isScriptQueued()});c(c$,"notifyError",function(a,b,c){this.global.setS("_errormessage",c);this.statusManager.notifyError(a,b,c)},"~S,~S,~S");c(c$,"jsEval",function(a){return this.statusManager.jsEval(a)},
"~S");c(c$,"setStatusAtomHovered",function(a,b){this.global.setI("_atomhovered",a);this.statusManager.setStatusAtomHovered(a,b)},"~N,~S");c(c$,"setStatusObjectHovered",function(a,b,c){this.global.setS("_objecthovered",a);this.statusManager.setStatusObjectHovered(a,b,c)},"~S,~S,JU.P3");c(c$,"setFileLoadStatus",function(a,b,c,g,e,f){this.setErrorMessage(e,null);this.global.setI("_loadPoint",a.getCode());var h=a!==J.constant.EnumFileStatus.CREATING_MODELSET;h&&this.setStatusFrameChanged(!1,!1);this.statusManager.setFileLoadStatus(b,
c,g,e,a.getCode(),h,f);h&&this.doHaveJDX()&&this.getJSV().setModel(this.getCurrentModelIndex())},"J.constant.EnumFileStatus,~S,~S,~S,~S,Boolean");c(c$,"getZapName",function(){return this.global.modelKitMode?"Jmol Model Kit":"zapped"});c(c$,"setStatusMeasuring",function(a,b,c,g){this.statusManager.setStatusMeasuring(a,b,c,g)},"~S,~N,~S,~N");c(c$,"notifyMinimizationStatus",function(){var a=this.getParameter("_minimizationStep"),b=this.getParameter("_minimizationForceField");this.statusManager.notifyMinimizationStatus(this.getParameter("_minimizationStatus"),
r(a,String)?Integer.$valueOf(0):a,this.getParameter("_minimizationEnergy"),a.toString().equals("0")?Float.$valueOf(0):this.getParameter("_minimizationEnergyDiff"),b)});c(c$,"setStatusAtomPicked",function(a,b){null==b&&(b=this.global.pickLabel,b=0==b.length?this.getAtomInfoXYZ(a,this.global.messageStyleChime):this.modelSet.getAtomInfo(a,b));this.global.setPicked(a);this.global.setS("_pickinfo",b);this.statusManager.setStatusAtomPicked(a,b);1==this.statusManager.getSyncMode()&&this.doHaveJDX()&&this.getJSV().atomPicked(a)},
"~N,~S");c(c$,"setStatusResized",function(a,b){this.statusManager.setStatusResized(a,b)},"~N,~N");c(c$,"scriptStatus",function(a){this.setScriptStatus(a,"",0,null)},"~S");c(c$,"scriptStatusMsg",function(a,b){this.setScriptStatus(a,b,0,null)},"~S,~S");c(c$,"setScriptStatus",function(a,b,c,g){this.statusManager.setScriptStatus(a,b,c,g)},"~S,~S,~N,~S");c(c$,"getModelTitle",function(a){return null==this.modelSet?null:this.modelSet.getModelTitle(a)},"~N");h(c$,"getModelFileName",function(a){return null==
this.modelSet?null:this.modelSet.getModelFileName(a)},"~N");c(c$,"dialogAsk",function(a,b){return prompt(a,b)},"~S,~S");h(c$,"showUrl",function(a){if(null!=a){if(0>a.indexOf(":")){var b=this.fileManager.getAppletDocumentBase();""===b&&(b=this.fileManager.getFullPathName(!1));0<=b.indexOf("/")?b=b.substring(0,b.lastIndexOf("/")+1):0<=b.indexOf("\\")&&(b=b.substring(0,b.lastIndexOf("\\")+1));a=b+a}J.util.Logger.info("showUrl:"+a);this.statusManager.showUrl(a)}},"~S");c(c$,"setMeshCreator",function(a){this.loadShape(24);
this.setShapeProperty(24,"meshCreator",a)},"~O");c(c$,"showConsole",function(a){if(this.haveDisplay)try{null==this.appConsole&&a&&this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.appConsole.setVisible(!0)}catch(b){}},"~B");c(c$,"clearConsole",function(){this.statusManager.clearConsole()});c(c$,"getParameterEscaped",function(a){return this.global.getParameterEscaped(a,0)},"~S");h(c$,"getParameter",function(a){return this.global.getParameter(a)},"~S");c(c$,"getOrSetNewVariable",function(a,
b){return this.global.getOrSetNewVariable(a,b)},"~S,~B");c(c$,"setUserVariable",function(a,b){return this.global.setUserVariable(a,b)},"~S,J.script.SV");c(c$,"unsetProperty",function(a){a=a.toLowerCase();(a.equals("all")||a.equals("variables"))&&this.fileManager.setPathForAllFiles("");this.global.unsetUserVariable(a)},"~S");c(c$,"getVariableList",function(){return this.global.getVariableList()});h(c$,"notifyStatusReady",function(a){System.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));
a||this.setModeMouse(-1);this.statusManager.setStatusAppletReady(this.fullName,a)},"~B");h(c$,"getBooleanProperty",function(a){a=a.toLowerCase();if(this.global.htBooleanParameterFlags.containsKey(a))return this.global.htBooleanParameterFlags.get(a).booleanValue();if(a.endsWith("p!")){if(null==this.actionManager)return!1;var b=this.actionManager.getPickingState().toLowerCase();a=a.substring(0,a.length-2)+";";return 0<=b.indexOf(a)}if(a.equalsIgnoreCase("executionPaused"))return null!=this.eval&&this.eval.isPaused();
if(a.equalsIgnoreCase("executionStepping"))return null!=this.eval&&this.eval.isStepping();if(a.equalsIgnoreCase("haveBFactors"))return null!=this.modelSet.getBFactors();if(a.equalsIgnoreCase("colorRasmol"))return this.colorManager.getDefaultColorRasmol();if(a.equalsIgnoreCase("frank"))return this.getShowFrank();if(a.equalsIgnoreCase("spinOn"))return this.getSpinOn();if(a.equalsIgnoreCase("isNavigating"))return this.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.modelSet.getSelectionHaloEnabled();
if(this.global.htUserVariables.containsKey(a)){b=this.global.getUserVariable(a);if(1048589==b.tok)return!0;if(1048588==b.tok)return!1}J.util.Logger.error("viewer.getBooleanProperty("+a+") - unrecognized");return!1},"~S");h(c$,"getInt",function(a){switch(a){case 553648132:return this.animationManager.animationFps;case 553648143:return this.global.dotDensity;case 553648144:return this.global.dotScale;case 553648146:return this.global.helixStep;case 553648151:return this.global.meshScale;case 553648153:return this.global.minPixelSelRadius;
case 553648154:return this.global.percentVdwAtom;case 553648157:return this.global.pickingSpinRate;case 553648158:return this.global.platformSpeed;case 553648166:return this.global.ribbonAspectRatio;case 536870922:return this.global.scriptDelay;case 553648170:return this.global.smallMoleculeMaxAtoms;case 553648184:return this.global.strutSpacing}J.util.Logger.error("viewer.getInt("+J.script.T.nameOf(a)+") - not listed");return 0},"~N");c(c$,"getDelayMaximumMs",function(){return this.haveDisplay?this.global.delayMaximumMs:
1});c(c$,"getHermiteLevel",function(){return this.getSpinOn()?0:this.global.hermiteLevel});c(c$,"getHoverDelay",function(){return this.global.modelKitMode?20:this.global.hoverDelayMs});h(c$,"getBoolean",function(a){switch(a){case 1074790662:return this.modelSet.getModelSetAuxiliaryInfoBoolean("isPDB");case 603979780:return this.global.allowGestures;case 603979784:return this.global.allowMultiTouch;case 603979785:return this.global.allowRotateSelected;case 603979792:return this.global.appendNew;case 603979794:return this.global.applySymmetryToBonds;
case 603979796:return this.global.atomPicking;case 603979798:return this.global.autoBond;case 603979800:return this.global.autoFps;case 603979806:return this.global.axesOrientationRasmol;case 603979812:return this.global.bondModeOr;case 603979817:return this.global.cartoonBaseEdges;case 603979819:return this.global.cartoonFancy;case 603979820:return this.global.cartoonLadders;case 603979818:return this.global.cartoonRockets;case 603979822:return this.global.chainCaseSensitive||0<this.chainList.size();
case 603979824:return this.global.debugScript;case 603979825:return this.global.defaultStructureDSSP;case 603979826:return this.global.disablePopupMenu;case 603979828:return this.global.displayCellParameters;case 603979830:return this.global.dotSurface;case 603979829:return this.global.dotsSelectedOnly;case 603979833:return this.global.drawPicking;case 603979844:return this.global.fontCaching;case 603979845:return this.global.fontScaling;case 603979846:return this.global.forceAutoBond;case 603979848:return this.global.fractionalRelative;
case 603979850:return this.global.greyscaleRendering;case 603979852:return this.global.hbondsBackbone;case 603979853:return this.global.hbondsRasmol;case 603979854:return this.global.hbondsSolid;case 1613758470:return this.global.rasmolHeteroSetting;case 603979858:return this.global.hideNameInPopup;case 603979864:return this.global.highResolutionFlag;case 1613758476:return this.global.rasmolHydrogenSetting;case 603979870:return this.global.isosurfaceKey;case 603979872:return this.global.justifyMeasurements;
case 603979874:return this.global.legacyAutoBonding;case 603979875:return this.global.legacyHAddition;case 603979877:return this.global.logGestures;case 603979878:return this.global.measureAllModels;case 603979879:return this.global.measurementLabels;case 603979880:return this.global.messageStyleChime;case 603979883:return this.global.modelKitMode;case 603979887:return this.global.navigationMode;case 603979888:return this.global.navigationPeriodic;case 603979889:return this.global.partialDots;case 603979892:return this.global.pdbSequential;
case 603979894:return this.global.preserveState;case 603979898:return this.global.ribbonBorder;case 603979900:return this.global.rocketBarrels;case 603979906:return this.global.selectAllModels;case 603979920:return this.global.showHiddenSelectionHalos;case 603979922:return this.global.showHydrogens;case 603979926:return this.global.showMeasurements;case 603979928:return this.global.showMultipleBonds;case 603979934:return this.global.showTiming;case 603979938:return this.global.slabByAtom;case 603979940:return this.global.slabByMolecule;
case 603979944:return this.global.smartAromatic;case 1613758488:return this.global.solventOn;case 603979952:return this.global.ssbondsBackbone;case 603979955:return this.global.strutsMultiple;case 603979966:return this.global.traceAlpha;case 603979967:return this.global.translucent;case 603979968:return this.global.twistedSheets;case 603979973:return this.global.vectorSymmetry;case 603979974:return this.global.waitForMoveTo;case 603979978:return this.global.zeroBasedXyzRasmol}J.util.Logger.error("viewer.getBoolean("+
J.script.T.nameOf(a)+") - not listed");return!1},"~N");c(c$,"allowEmbeddedScripts",function(){return this.global.allowEmbeddedScripts&&!this.$isPreviewOnly});c(c$,"getDragSelected",function(){return this.global.dragSelected&&!this.global.modelKitMode});c(c$,"getBondPicking",function(){return this.global.bondPicking||this.global.modelKitMode});c(c$,"useMinimizationThread",function(){return this.global.useMinimizationThread&&!this.autoExit});h(c$,"getFloat",function(a){switch(a){case 1141899265:return this.global.particleRadius;
case 570425346:return this.global.axesScale;case 570425348:return this.global.bondTolerance;case 570425354:return this.global.defaultTranslucent;case 570425352:return this.global.defaultDrawArrowScale;case 570425355:return this.global.dipoleScale;case 570425356:return this.global.drawFontSize;case 570425358:return this.global.exportScale;case 570425360:return this.global.hbondsAngleMinimum;case 570425361:return this.global.hbondsDistanceMaximum;case 570425363:return this.global.loadAtomDataTolerance;
case 570425364:return this.global.minBondDistance;case 1276121113:return this.global.modulationScale;case 570425370:return this.global.multipleBondSpacing;case 570425369:return this.global.multipleBondRadiusFactor;case 570425374:return this.global.navigationSpeed;case 570425382:return this.global.pointGroupDistanceTolerance;case 570425384:return this.global.pointGroupLinearTolerance;case 570425388:return this.transformManager.getRotationRadius();case 570425392:return this.global.sheetSmoothing;case 570425394:return this.global.solventProbeRadius;
case 570425403:return this.global.starScale;case 570425406:return this.global.strutDefaultRadius;case 570425408:return this.global.strutLengthMaximum;case 1649410049:return this.global.vectorScale;case 570425412:return this.global.vibrationPeriod}J.util.Logger.error("viewer.getFloat("+J.script.T.nameOf(a)+") - not listed");return 0},"~N");h(c$,"setStringProperty",function(a,b){if(null!=b)if("_"==a.charAt(0))this.global.setS(a,b);else{var c=J.script.T.getTokFromName(a);switch(J.script.T.getParamType(c)){case 603979776:this.setBooleanPropertyTok(a,
c,J.script.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,c,J.script.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,c,JU.PT.parseFloat(b));break;default:this.setStringPropertyTok(a,c,b)}}},"~S,~S");c(c$,"setStringPropertyTok",function(a,b,c){switch(b){case 545259521:this.setAnimationMode(c);return;case 545259569:this.global.nmrPredictFormat=c;break;case 545259548:this.global.defaultDropScript=c;break;case 545259571:c=this.fileManager.setPathForAllFiles(c);
break;case 545259558:this.setUnits(c,!1);return;case 545259560:this.global.forceField=c="UFF".equalsIgnoreCase(c)?"UFF":"MMFF";this.minimizer=null;break;case 545259570:this.global.nmrUrlFormat=c;break;case 545259568:this.setUnits(c,!0);return;case 545259566:this.global.loadLigandFormat=c;break;case 545259543:this.global.defaultLabelPDB=c;break;case 545259544:this.global.defaultLabelXYZ=c;break;case 545259549:this.global.defaultLoadFilter=c;break;case 545259567:c=this.getOutputManager().setLogFile(c);
if(null==c)return;break;case 545259559:break;case 545259524:this.global.atomTypes=c;break;case 545259538:break;case 545259576:this.global.pickLabel=c;break;case 545259580:this.global.quaternionFrame=2==c.length&&c.startsWith("R")?c.substring(0,2):""+(c.toLowerCase()+"p").charAt(0);JU.PT.isOneOf(this.global.quaternionFrame,"RC;RP;a;b;c;n;p;q;x;")||(this.global.quaternionFrame="p");this.modelSet.setHaveStraightness(!1);break;case 545259555:this.setVdwStr(c);return;case 545259564:new J.i18n.GT(this,
c);this.language=J.i18n.GT.getLanguage();this.modelkitPopup=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.statusManager.setCallbackFunction("language",this.language);c=J.i18n.GT.getLanguage();break;case 545259565:this.global.loadFormat=c;break;case 545259534:this.setObjectColor("background",c);return;case 545259528:this.setObjectColor("axis1",c);return;case 545259530:this.setObjectColor("axis2",c);return;case 545259532:this.setObjectColor("axis3",
c);return;case 545259536:this.setObjectColor("boundbox",c);return;case 545259586:this.setObjectColor("unitcell",c);return;case 545259578:this.setPropertyColorScheme(c,!1,!1);break;case 545259562:this.setShapeProperty(34,"atomLabel",c);break;case 545259547:this.global.defaultDistanceLabel=c;break;case 545259542:this.global.defaultAngleLabel=c;break;case 545259554:this.global.defaultTorsionLabel=c;break;case 545259550:this.global.defaultLoadScript=c;break;case 545259522:this.fileManager.setAppletProxy(c);
break;case 545259546:null==c&&(c="");c=c.$replace("\\","/");this.global.defaultDirectory=c;break;case 545259561:this.global.helpPath=c;break;case 545259552:!c.equalsIgnoreCase("RasMol")&&!c.equalsIgnoreCase("PyMOL")&&(c="Jmol");this.setDefaultsType(c);break;case 545259545:this.setDefaultColors(c.equalsIgnoreCase("rasmol"));return;case 545259572:this.setPickingMode(c,0);return;case 545259574:this.setPickingStyle(c,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.statusManager.setCallbackFunction(a,
0==c.length||c.equalsIgnoreCase("none")?null:c);break}if(!this.global.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.global.setUserVariable(a,J.script.SV.newV(4,c));return}}this.global.setS(a,c)},"~S,~N,~S");h(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b))if("_"==a.charAt(0))this.global.setF(a,b);else{var c=J.script.T.getTokFromName(a);switch(J.script.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,
0!=b);break;case 553648128:this.setIntPropertyTok(a,c,y(b));break;default:this.setFloatPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,c){switch(b){case 570425366:this.modelSet.setModulation(null,!1,null,!1);this.global.modulationScale=Math.max(1,c);this.modelSet.setModulation(null,!0,null,!1);break;case 570425381:this.global.particleRadius=Math.abs(c);break;case 570425356:this.global.drawFontSize=c;break;case 570425358:this.global.exportScale=c;break;case 570425403:this.global.starScale=
c;break;case 570425369:this.global.multipleBondRadiusFactor=c;break;case 570425370:this.global.multipleBondSpacing=c;break;case 570425393:this.transformManager.setSlabRange(c);break;case 570425365:this.global.minimizationCriterion=c;break;case 570425359:this.haveDisplay&&this.actionManager.setGestureSwipeFactor(c);break;case 570425367:this.haveDisplay&&this.actionManager.setMouseDragFactor(c);break;case 570425368:this.haveDisplay&&this.actionManager.setMouseWheelFactor(c);break;case 570425408:this.global.strutLengthMaximum=
c;break;case 570425406:this.global.strutDefaultRadius=c;break;case 570425376:this.setSpin("X",y(c));break;case 570425378:this.setSpin("Y",y(c));break;case 570425380:this.setSpin("Z",y(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",y(c));break;case 570425363:this.global.loadAtomDataTolerance=c;break;case 570425360:this.global.hbondsAngleMinimum=c;break;case 570425361:this.global.hbondsDistanceMaximum=c;break;case 570425382:this.global.pointGroupDistanceTolerance=c;break;case 570425384:this.global.pointGroupLinearTolerance=
c;break;case 570425357:this.global.ellipsoidAxisDiameter=c;break;case 570425398:this.setSpin("x",y(c));break;case 570425400:this.setSpin("y",y(c));break;case 570425402:this.setSpin("z",y(c));break;case 570425396:this.setSpin("fps",y(c));break;case 570425352:this.global.defaultDrawArrowScale=c;break;case 570425354:this.global.defaultTranslucent=c;break;case 570425346:this.setAxesScale(c);break;case 570425416:this.transformManager.setVisualRange(c);this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(c);
break;case 570425374:this.global.navigationSpeed=c;break;case 570425373:this.transformManager.setNavigationSlabOffsetPercent(c);break;case 570425350:this.transformManager.setCameraDepthPercent(c,!1);this.refresh(1,"set cameraDepth");return;case 570425388:this.setRotationRadius(c,!0);return;case 570425362:this.global.hoverDelayMs=y(1E3*c);break;case 570425392:this.global.sheetSmoothing=c;break;case 570425355:c=J.viewer.Viewer.checkFloatRange(c,-10,10);this.global.dipoleScale=c;break;case 570425404:this.transformManager.setStereoDegrees(c);
break;case 1649410049:this.setVectorScale(c);return;case 570425412:this.setVibrationPeriod(c);return;case 570425414:this.setVibrationScale(c);return;case 570425348:this.setBondTolerance(c);return;case 570425364:this.setMinBondDistance(c);return;case 570425390:this.transformManager.setScaleAngstromsPerInch(c);break;case 570425394:c=J.viewer.Viewer.checkFloatRange(c,0,10);this.global.solventProbeRadius=c;break;default:if(!this.global.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.global.setUserVariable(a,
J.script.SV.newV(3,Float.$valueOf(c)));return}}this.global.setF(a,c)},"~S,~N,~N");h(c$,"setIntProperty",function(a,b){if(-2147483648!=b)if("_"==a.charAt(0))this.global.setI(a,b);else{var c=J.script.T.getTokFromName(a);switch(J.script.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 570425344:this.setFloatPropertyTok(a,c,b);break;default:this.setIntPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,
b,c){switch(b){case 553648137:this.global.celShadingPower=c;this.gdata.setCelPower(c);break;case 553648129:this.gdata.setAmbientOcclusion(c);break;case 553648158:this.global.platformSpeed=Math.min(Math.max(c,0),10);break;case 553648151:this.global.meshScale=c;break;case 553648153:this.global.minPixelSelRadius=c;break;case 553648149:this.global.isosurfacePropertySmoothingPower=c;break;case 553648165:this.global.repaintWaitMs=c;break;case 553648170:this.global.smallMoleculeMaxAtoms=c;break;case 553648152:this.global.minimizationSteps=
c;break;case 553648184:this.global.strutSpacing=c;break;case 553648156:c=J.viewer.Viewer.checkIntRange(c,0,1E3);this.gdata.setPhongExponent(c);break;case 553648146:this.global.helixStep=c;this.modelSet.setHaveStraightness(!1);break;case 553648144:this.global.dotScale=c;break;case 553648143:this.global.dotDensity=c;break;case 553648138:this.global.delayMaximumMs=c;break;case 553648150:J.util.Logger.setLogLevel(c);J.util.Logger.info("logging level set to "+c);this.global.setI("logLevel",c);null!=this.eval&&
this.eval.setDebugging();return;case 553648134:switch(J.constant.EnumAxesMode.getAxesMode(c)){case J.constant.EnumAxesMode.MOLECULAR:this.setAxesModeMolecular(!0);break;case J.constant.EnumAxesMode.BOUNDBOX:this.setAxesModeMolecular(!1);break;case J.constant.EnumAxesMode.UNITCELL:this.setAxesModeUnitCell(!0)}return;case 553648178:this.setStrandCount(0,c);return;case 553648182:this.setStrandCount(12,c);return;case 553648180:this.setStrandCount(13,c);return;case 553648155:return;case 536870922:this.global.scriptDelay=
c;break;case 553648176:c=0>c?J.viewer.Viewer.checkIntRange(c,-10,-1):J.viewer.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPower(c);break;case 553648172:c=J.viewer.Viewer.checkIntRange(-c,-10,-1);this.gdata.setSpecularPower(c);break;case 553648136:this.setMarBond(c);return;case 536870924:this.setBooleanPropertyTok(a,b,1==c);return;case 553648174:c=J.viewer.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPercent(c);break;case 553648142:c=J.viewer.Viewer.checkIntRange(c,0,100);this.gdata.setDiffusePercent(c);
break;case 553648130:c=J.viewer.Viewer.checkIntRange(c,0,100);this.gdata.setAmbientPercent(c);break;case 553648186:this.transformManager.zDepthToPercent(c);break;case 553648188:this.transformManager.zSlabToPercent(c);break;case 554176526:this.transformManager.depthToPercent(c);break;case 554176565:this.transformManager.slabToPercent(c);break;case 553648190:this.global.zShadePower=Math.max(c,1);break;case 553648166:this.global.ribbonAspectRatio=c;break;case 553648157:this.global.pickingSpinRate=1>
c?1:c;break;case 553648132:this.setAnimationFps(c);return;case 553648154:this.setPercentVdwAtom(c);break;case 553648147:this.global.hermiteLevel=c;break;case 553648145:case 553648148:case 553648160:case 553648159:case 553648162:case 553648164:break;default:if(!this.global.htNonbooleanParameterValues.containsKey(a)){this.global.setUserVariable(a,J.script.SV.newI(c));return}}this.global.setI(a,c)},"~S,~N,~N");c$.checkIntRange=c(c$,"checkIntRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");c$.checkFloatRange=
c(c$,"checkFloatRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");h(c$,"setBooleanProperty",function(a,b){if("_"==a.charAt(0))this.global.setB(a,b);else{var c=J.script.T.getTokFromName(a);switch(J.script.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,"");break;case 553648128:this.setIntPropertyTok(a,c,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,c,b?1:0);break;default:this.setBooleanPropertyTok(a,c,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",function(a,b,c){var g=
!0;switch(b){case 603979837:this.global.ellipsoidArrows=c;break;case 603979967:this.global.translucent=c;break;case 603979820:this.global.cartoonLadders=c;break;case 603979968:b=this.global.twistedSheets;this.global.twistedSheets=c;b!=c&&this.checkCoordinatesChanged();break;case 603979821:this.global.celShading=c;this.gdata.setCel(c);break;case 603979819:this.global.cartoonFancy=c;break;case 603979934:this.global.showTiming=c;break;case 603979973:this.global.vectorSymmetry=c;break;case 603979870:this.global.isosurfaceKey=
c;break;case 603979889:this.global.partialDots=c;break;case 603979874:this.global.legacyAutoBonding=c;break;case 603979825:this.global.defaultStructureDSSP=c;break;case 603979834:this.global.dsspCalcHydrogen=c;break;case 603979782:(this.global.allowModelkit=c)||this.setModelKitMode(!1);break;case 603979883:this.setModelKitMode(c);break;case 603979885:this.global.multiProcessor=c&&1<J.viewer.Viewer.nProcessors;break;case 603979884:this.global.monitorEnergy=c;break;case 603979853:this.global.hbondsRasmol=
c;break;case 603979881:this.global.minimizationRefresh=c;break;case 603979882:this.global.minimizationSilent=c;break;case 603979969:this.global.useArcBall=c;break;case 603979869:c&&(this.$isKiosk=!0,this.global.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979974:this.global.waitForMoveTo=c;break;case 603979876:this.global.logCommands=!0;break;case 603979877:this.global.logGestures=!0;break;case 603979784:this.global.allowMultiTouch=c;break;
case 603979894:this.global.preserveState=c;this.modelSet.setPreserveState(c);this.undoClear();break;case 603979955:this.global.strutsMultiple=c;break;case 603979842:break;case 603979938:this.global.slabByAtom=c;break;case 603979940:this.global.slabByMolecule=c;break;case 603979902:this.global.saveProteinStructureState=c;break;case 603979780:this.global.allowGestures=c;break;case 603979868:this.global.imageState=c;break;case 603979970:this.global.useMinimizationThread=c;break;case 603979781:this.global.disablePopupMenu&&
(c=!1);this.global.allowKeyStrokes=c;break;case 603979831:this.global.dragSelected=c;this.showSelected=!1;break;case 603979924:this.global.showKeyStrokes=c;break;case 603979844:this.global.fontCaching=c;break;case 603979796:this.global.atomPicking=c;break;case 603979814:this.highlight(null);this.global.bondPicking=c;break;case 603979906:this.global.selectAllModels=c;break;case 603979880:this.global.messageStyleChime=c;break;case 603979892:this.global.pdbSequential=c;break;case 603979890:this.global.pdbAddHydrogens=
c;break;case 603979891:this.global.pdbGetHeader=c;break;case 603979838:this.global.ellipsoidAxes=c;break;case 603979836:this.global.ellipsoidArcs=c;break;case 603979839:this.global.ellipsoidBall=c;break;case 603979840:this.global.ellipsoidDots=c;break;case 603979841:this.global.ellipsoidFill=c;break;case 603979845:this.global.fontScaling=c;break;case 603979956:this.setSyncTarget(0,c);break;case 603979958:this.setSyncTarget(1,c);break;case 603979976:this.global.wireframeRotation=c;break;case 603979871:this.global.isosurfacePropertySmoothing=
c;break;case 603979833:this.global.drawPicking=c;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,c);break;case 603979944:this.global.smartAromatic=c;break;case 603979794:this.setApplySymmetryToBonds(c);break;case 603979792:this.setAppendNew(c);break;case 603979800:this.global.autoFps=c;break;case 603979972:JU.DF.setUseNumberLocalization(this.global.useNumberLocalization=c);break;case 1611272202:a="showFrank";this.setFrankOn(c);break;case 603979918:this.setFrankOn(c);break;case 1613758488:a=
"solventProbe";this.global.solventOn=c;break;case 603979948:this.global.solventOn=c;break;case 603979785:this.global.allowRotateSelected=c;break;case 603979783:this.global.allowMoveAtoms=c;this.global.allowRotateSelected=c;this.global.dragSelected=c;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,c?1:0);return;case 603979778:this.global.allowEmbeddedScripts=c;break;case 603979888:this.global.navigationPeriodic=c;break;case 603979984:this.transformManager.setZShadeEnabled(c);
return;case 603979832:this.haveDisplay&&(this.global.drawHover=c);break;case 603979887:this.setNavigationMode(c);break;case 603979886:return;case 603979860:this.global.hideNavigationPoint=c;break;case 603979930:this.global.showNavigationPointAlways=c;break;case 603979896:this.setRefreshing(c);break;case 603979872:this.global.justifyMeasurements=c;break;case 603979952:this.global.ssbondsBackbone=c;break;case 603979852:this.global.hbondsBackbone=c;break;case 603979854:this.global.hbondsSolid=c;break;
case 536870924:this.gdata.setSpecular(c);break;case 603979942:this.transformManager.setSlabEnabled(c);return;case 603979980:this.transformManager.setZoomEnabled(c);return;case 603979864:this.global.highResolutionFlag=c;break;case 603979966:this.global.traceAlpha=c;break;case 603979983:this.global.zoomLarge=c;this.transformManager.setZoomHeight(this.global.zoomHeight,c);break;case 603979982:this.global.zoomHeight=c;this.transformManager.setZoomHeight(c,this.global.zoomLarge);break;case 603979873:J.i18n.GT.setDoTranslate(c);
break;case 603979862:this.selectionManager.setHideNotSelected(c);break;case 603979904:this.setScriptQueue(c);break;case 603979830:this.global.dotSurface=c;break;case 603979829:this.global.dotsSelectedOnly=c;break;case 1611141171:this.setSelectionHalos(c);break;case 603979910:this.global.rasmolHydrogenSetting=c;break;case 603979908:this.global.rasmolHeteroSetting=c;break;case 603979928:this.global.showMultipleBonds=c;break;case 603979920:this.global.showHiddenSelectionHalos=c;break;case 603979975:this.transformManager.setWindowCentered(c);
break;case 603979828:this.global.displayCellParameters=c;break;case 603979960:this.global.testFlag1=c;break;case 603979962:this.global.testFlag2=c;break;case 603979964:this.global.testFlag3=c;break;case 603979965:this.jmolTest();this.global.testFlag4=c;break;case 603979898:this.global.ribbonBorder=c;break;case 603979817:this.global.cartoonBaseEdges=c;break;case 603979818:this.global.cartoonRockets=c;break;case 603979900:this.global.rocketBarrels=c;break;case 603979850:this.gdata.setGreyscaleMode(this.global.greyscaleRendering=
c);break;case 603979879:this.global.measurementLabels=c;break;case 603979810:this.setAxesModeMolecular(!c);return;case 603979804:this.setAxesModeMolecular(c);return;case 603979808:this.setAxesModeUnitCell(c);return;case 603979806:this.setAxesOrientationRasmol(c);return;case 603979823:this.setStringPropertyTok("defaultcolorscheme",545259545,c?"rasmol":"jmol");return;case 603979824:this.setDebugScript(c);return;case 603979893:this.setPerspectiveDepth(c);return;case 603979798:this.setAutoBond(c);return;
case 603979914:this.setShowAxes(c);return;case 603979916:this.setShowBbcage(c);return;case 603979922:this.setShowHydrogens(c);return;case 603979926:this.setShowMeasurements(c);return;case 603979936:this.setShowUnitCell(c);return;case 603979812:g=!1;this.global.bondModeOr=c;break;case 603979978:g=!1;this.global.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979895:g=!1;this.global.rangeSelected=c;break;case 603979878:g=!1;this.global.measureAllModels=c;break;case 603979954:g=!1;this.statusManager.setAllowStatusReporting(c);
break;case 603979822:g=!1;this.global.chainCaseSensitive=c;break;case 603979858:g=!1;this.global.hideNameInPopup=c;break;case 603979826:g=!1;this.global.disablePopupMenu=c;break;case 603979846:g=!1;this.global.forceAutoBond=c;break;case 603979848:g=!1;this.global.fractionalRelative=c;break;default:if(!this.global.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.global.setUserVariable(a,J.script.SV.getBoolean(c));return}}this.global.setB(a,c);g&&this.setTainted(!0)},"~S,~N,~B");c(c$,"setModelKitMode",
function(a){if(null!=this.actionManager&&this.allowScripting){if(a||this.global.modelKitMode)this.setPickingMode(null,a?33:1),this.setPickingMode(null,a?32:1);var b=this.global.modelKitMode!=a;this.global.modelKitMode=a;this.highlight(null);a?(this.setNavigationMode(!1),this.selectAll(),this.setAtomPickingOption("C"),this.setBondPickingOption("p"),this.$isApplet||this.popupMenu(0,0,"m"),b&&this.statusManager.setCallbackFunction("modelkit","ON"),this.global.modelKitMode=!0,0==this.getAtomCount()&&
this.zap(!1,!0,!0)):(this.actionManager.setPickingMode(-1),this.setStringProperty("pickingStyle","toggle"),this.setBooleanProperty("bondPicking",!1),b&&this.statusManager.setCallbackFunction("modelkit","OFF"))}},"~B");c(c$,"getLanguage",function(){return this.language});c(c$,"setSmilesString",function(a){null==a?this.global.removeParam("_smilesString"):this.global.setS("_smilesString",a)},"~S");c(c$,"removeUserVariable",function(a){this.global.removeUserVariable(a);a.endsWith("callback")&&this.statusManager.setCallbackFunction(a,
null)},"~S");c(c$,"isJmolVariable",function(a){return this.global.isJmolVariable(a)},"~S");c(c$,"jmolTest",function(){});c(c$,"showParameter",function(a,b,c){c=""+this.global.getParameterEscaped(a,c);(b||0>c.indexOf("<not defined>"))&&this.showString(a+" = "+c,!1)},"~S,~B,~N");c(c$,"showString",function(a,b){this.isScriptQueued()&&((!this.isSilent||b)&&!this.isJS)&&J.util.Logger.warn(a);this.scriptEcho(a)},"~S,~B");c(c$,"getAllSettings",function(a){return this.getStateCreator().getAllSettings(a)},
"~S");c(c$,"getBindingInfo",function(a){return this.haveDisplay?this.actionManager.getBindingInfo(a):""},"~S");c(c$,"getIsosurfacePropertySmoothing",function(a){return a?this.global.isosurfacePropertySmoothingPower:this.global.isosurfacePropertySmoothing?1:0},"~B");c(c$,"setNavigationDepthPercent",function(a){this.transformManager.setNavigationDepthPercent(a);this.refresh(1,"set navigationDepth")},"~N");c(c$,"getShowNavigationPoint",function(){return!this.global.navigationMode||!this.transformManager.canNavigate()?
!1:this.isNavigating()&&!this.global.hideNavigationPoint||this.global.showNavigationPointAlways||this.getInMotion(!0)});c(c$,"getCurrentSolventProbeRadius",function(){return this.global.solventOn?this.global.solventProbeRadius:0});c(c$,"getTestFlag",function(a){switch(a){case 1:return this.global.testFlag1;case 2:return this.global.testFlag2;case 3:return this.global.testFlag3;case 4:return this.global.testFlag4}return!1},"~N");h(c$,"setPerspectiveDepth",function(a){this.transformManager.setPerspectiveDepth(a)},
"~B");h(c$,"setAxesOrientationRasmol",function(a){this.global.setB("axesOrientationRasmol",a);this.global.axesOrientationRasmol=a;this.reset(!0)},"~B");c(c$,"setAxesScale",function(a){a=J.viewer.Viewer.checkFloatRange(a,-100,100);this.global.axesScale=a;this.axesAreTainted=!0},"~N");c(c$,"getAxisPoints",function(){return 0==this.getObjectMad(1)||this.getAxesMode()!==J.constant.EnumAxesMode.UNITCELL||this.getShapeProperty(31,"axesTypeXY").booleanValue()||null!=this.getShapeProperty(31,"origin")?null:
this.getShapeProperty(31,"axisPoints")});c(c$,"resetError",function(){this.global.removeParam("_errormessage")});c(c$,"setAxesModeMolecular",function(a){this.global.axesMode=a?J.constant.EnumAxesMode.MOLECULAR:J.constant.EnumAxesMode.BOUNDBOX;this.axesAreTainted=!0;this.global.removeParam("axesunitcell");this.global.removeParam(a?"axeswindow":"axesmolecular");this.global.setI("axesMode",this.global.axesMode.getCode());this.global.setB(a?"axesMolecular":"axesWindow",!0)},"~B");c(c$,"setAxesModeUnitCell",
function(a){this.global.axesMode=a?J.constant.EnumAxesMode.UNITCELL:J.constant.EnumAxesMode.BOUNDBOX;this.axesAreTainted=!0;this.global.removeParam("axesmolecular");this.global.removeParam(a?"axeswindow":"axesunitcell");this.global.setB(a?"axesUnitcell":"axesWindow",!0);this.global.setI("axesMode",this.global.axesMode.getCode())},"~B");c(c$,"getAxesMode",function(){return this.global.axesMode});h(c$,"getPerspectiveDepth",function(){return this.transformManager.getPerspectiveDepth()});h(c$,"setSelectionHalos",
function(a){null==this.modelSet||a==this.modelSet.getSelectionHaloEnabled()||(this.global.setB("selectionHalos",a),this.loadShape(8),this.modelSet.setSelectionHaloEnabled(a))},"~B");c(c$,"getSelectionHaloEnabled",function(a){var b=this.modelSet.getSelectionHaloEnabled()||a&&this.showSelected;a&&(this.showSelected=!1);return b},"~B");c(c$,"setStrandCount",function(a,b){b=J.viewer.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.global.strandCountForStrands=b;break;case 13:this.global.strandCountForMeshRibbon=
b;break;default:this.global.strandCountForStrands=b,this.global.strandCountForMeshRibbon=b}this.global.setI("strandCount",b);this.global.setI("strandCountForStrands",this.global.strandCountForStrands);this.global.setI("strandCountForMeshRibbon",this.global.strandCountForMeshRibbon)},"~N,~N");c(c$,"getStrandCount",function(a){return 12==a?this.global.strandCountForStrands:this.global.strandCountForMeshRibbon},"~N");c(c$,"setNavigationMode",function(a){this.global.navigationMode=a;this.transformManager.setNavigationMode(a)},
"~B");c(c$,"setTransformManagerDefaults",function(){this.transformManager.setCameraDepthPercent(this.global.defaultCameraDepth,!0);this.transformManager.setPerspectiveDepth(this.global.defaultPerspectiveDepth);this.transformManager.setStereoDegrees(-5);this.transformManager.setVisualRange(this.global.visualRange);this.transformManager.setSpinOff();this.transformManager.setVibrationPeriod(0);this.transformManager.setFrameOffsets(this.frameOffsets)});c(c$,"getCameraFactors",function(){return this.transformManager.getCameraFactors()});
c(c$,"getCameraDepth",function(){return this.transformManager.getCameraDepth()});c(c$,"getLoadState",function(a){return this.getStateCreator().getLoadState(a)},"java.util.Map");h(c$,"setAutoBond",function(a){this.global.setB("autobond",a);this.global.autoBond=a},"~B");c(c$,"makeConnections",function(a,b,c,g,e,f,h,k,l,m){this.clearModelDependentObjects();this.clearMinimization();return this.modelSet.makeConnections(a,b,c,g,e,f,h,k,l,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");h(c$,"rebond",function(){this.rebondState(!1)});
c(c$,"rebondState",function(a){this.clearModelDependentObjects();this.modelSet.deleteAllBonds();a=a&&this.global.legacyAutoBonding;this.modelSet.autoBondBs4(null,null,null,null,this.getMadBond(),a);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":"connect;",!1,!0)},"~B");c(c$,"setPdbConectBonding",function(a,b){this.clearModelDependentObjects();this.modelSet.deleteAllBonds();var c=new JU.BS;this.modelSet.setPdbConectBonding(0,0,c);if(a){var g=b&&this.global.legacyAutoBonding;
this.modelSet.autoBondBs4(null,null,c,null,this.getMadBond(),g);this.addStateScript(g?"set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;":"connect PDB auto;",!1,!0)}else this.addStateScript("connect PDB;",!1,!0)},"~B,~B");h(c$,"setPercentVdwAtom",function(a){this.global.setI("percentVdwAtom",a);this.global.percentVdwAtom=a;this.rd.value=a/100;this.rd.factorType=J.atomdata.RadiusData.EnumType.FACTOR;this.rd.vdwType=J.constant.EnumVdw.AUTO;this.setShapeSizeRD(0,this.rd,null)},
"~N");c(c$,"getDefaultRadiusData",function(){return this.rd});h(c$,"getMadBond",function(){return 2*this.global.bondRadiusMilliAngstroms});c(c$,"getMarBond",function(){return this.global.bondRadiusMilliAngstroms});c(c$,"getModeMultipleBond",function(){return this.global.modeMultipleBond});h(c$,"setShowHydrogens",function(a){this.global.setB("showHydrogens",a);this.global.showHydrogens=a},"~B");h(c$,"setShowBbcage",function(a){this.setObjectMad(32,"boundbox",a?-4:0);this.global.setB("showBoundBox",
a)},"~B");h(c$,"getShowBbcage",function(){return 0!=this.getObjectMad(4)});c(c$,"setShowUnitCell",function(a){this.setObjectMad(33,"unitcell",a?-2:0);this.global.setB("showUnitCell",a)},"~B");c(c$,"getShowUnitCell",function(){return 0!=this.getObjectMad(5)});h(c$,"setShowAxes",function(a){this.setObjectMad(31,"axes",a?-2:0);this.global.setB("showAxes",a)},"~B");h(c$,"getShowAxes",function(){return 0!=this.getObjectMad(1)});h(c$,"setFrankOn",function(a){this.$isPreviewOnly&&(a=!1);this.frankOn=a;this.setObjectMad(35,
"frank",a?1:0)},"~B");c(c$,"getShowFrank",function(){return this.$isPreviewOnly||this.$isApplet&&this.creatingImage?!1:!this.isJS&&this.$isSignedApplet&&!this.isSignedAppletLocal||this.frankOn});h(c$,"setShowMeasurements",function(a){this.global.setB("showMeasurements",a);this.global.showMeasurements=a},"~B");c(c$,"setUnits",function(a,b){this.global.setUnits(a);b&&(this.global.setUnits(a),this.setShapeProperty(6,"reformatDistances",null))},"~S,~B");c(c$,"getMeasureDistanceUnits",function(){return this.global.measureDistanceUnits});
c(c$,"getEnergyUnits",function(){return this.global.energyUnits});c(c$,"setAppendNew",function(a){this.global.appendNew=a},"~B");h(c$,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});h(c$,"setJmolDefaults",function(){this.setDefaults()});c(c$,"setDefaultsType",function(a){a.equalsIgnoreCase("RasMol")?this.stateManager.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stateManager.setPyMOLDefaults():this.setDefaults()},"~S");c(c$,"setDefaults",function(){this.setShapeSizeRD(0,this.rd,
this.getAllAtoms())});c(c$,"setAntialias",function(a,b){switch(a){case 603979786:this.global.antialiasDisplay=b;break;case 603979790:this.global.antialiasTranslucent=b;break;case 603979788:this.global.antialiasImages=b;return}this.resizeImage(0,0,!1,!1,!0)},"~N,~B");c(c$,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(c$,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(c$,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},
"~N");c(c$,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},"~A");c(c$,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(c$,"freeTempEnum",function(a){this.tempArray.freeTempEnum(a)},"~A");c(c$,"getFont3D",function(a,b,c){return this.gdata.getFont3DFSS(a,b,c)},"~S,~S,~N");c(c$,"formatText",function(a){if(0>a.indexOf("@{")&&0>a.indexOf("%{"))return a;var b=a,c=0<=b.indexOf("\\");c&&(b=JU.PT.simpleReplace(b,"\\%","\u0001"),b=JU.PT.simpleReplace(b,"\\@","\u0002"),
c=!b.equals(a));for(var b=JU.PT.simpleReplace(b,"%{","@{"),g;0<=(a=b.indexOf("@{"));){a++;var e=a+1;g=b.length;a=J.util.Txt.ichMathTerminator(b,a,g);if(a>=g)return b;g=b.substring(e,a);if(0==g.length)return b;g=this.evaluateExpression(g);r(g,JU.P3)&&(g=J.util.Escape.eP(g));b=b.substring(0,e-2)+g.toString()+b.substring(a+1)}c&&(b=JU.PT.simpleReplace(b,"\u0002","@"),b=JU.PT.simpleReplace(b,"\u0001","%"));return b},"~S");c(c$,"getElementSymbol",function(a){return this.modelSet.getElementSymbol(a)},"~N");
c(c$,"getElementNumber",function(a){return this.modelSet.getElementNumber(a)},"~N");h(c$,"getAtomName",function(a){return this.modelSet.getAtomName(a)},"~N");h(c$,"getAtomNumber",function(a){return this.modelSet.getAtomNumber(a)},"~N");c(c$,"getAtomGroupQuaternions",function(a,b){return this.modelSet.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(c$,"getAtomQuaternion",function(a){return this.modelSet.getQuaternion(a,this.getQuaternionFrame())},"~N");h(c$,"getAtomPoint3f",function(a){return this.modelSet.atoms[a]},
"~N");c(c$,"getAtomPointVector",function(a){return this.modelSet.getAtomPointVector(a)},"JU.BS");h(c$,"getAtomRadius",function(a){return this.modelSet.getAtomRadius(a)},"~N");h(c$,"getAtomArgb",function(a){return this.gdata.getColorArgbOrGray(this.modelSet.getAtomColix(a))},"~N");h(c$,"getAtomModelIndex",function(a){return this.modelSet.atoms[a].modelIndex},"~N");h(c$,"getBondRadius",function(a){return this.modelSet.getBondRadius(a)},"~N");h(c$,"getBondOrder",function(a){return this.modelSet.getBondOrder(a)},
"~N");c(c$,"assignAromaticBonds",function(){this.modelSet.assignAromaticBonds()});c(c$,"resetAromatic",function(){this.modelSet.resetAromatic()});h(c$,"getBondArgb1",function(a){return this.gdata.getColorArgbOrGray(this.modelSet.getBondColix1(a))},"~N");h(c$,"getBondModelIndex",function(a){return this.modelSet.getBondModelIndex(a)},"~N");h(c$,"getBondArgb2",function(a){return this.gdata.getColorArgbOrGray(this.modelSet.getBondColix2(a))},"~N");h(c$,"getPolymerLeadMidPoints",function(a,b){return this.modelSet.getPolymerLeadMidPoints(a,
b)},"~N,~N");c(c$,"setStereoMode",function(a,b,c){this.setFloatProperty("stereoDegrees",c);this.setBooleanProperty("greyscaleRendering",b.isBiColor());null!=a?this.transformManager.setStereoMode2(a):this.transformManager.setStereoMode(b)},"~A,J.constant.EnumStereoMode,~N");c(c$,"isStereoDouble",function(){return this.transformManager.stereoMode===J.constant.EnumStereoMode.DOUBLE});h(c$,"getOperatingSystemName",function(){return J.viewer.Viewer.strOSName+(!this.isJS?"":this.isWebGL?"(WebGL)":"(HTML5)")});
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!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(c),null;case 60:return this.scriptEditorVisible=c.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:r(c,J.api.JmolAppConsoleInterface)?this.appConsole=c:null!=c&&!c.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=c&&c.booleanValue())&&(this.isJS&&(this.appConsole=J.api.Interface.getOptionInterface("consolejs.AppletConsole")),null!=this.appConsole&&this.appConsole.start(this)),
this.scriptEditor=this.isJS||null==this.appConsole?null:this.appConsole.getScriptEditor(),this.appConsole;case 100:return null==this.appConsole&&(null!=c&&c.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=c;case 140:return this.getSpaceGroupInfo(null);case 160:return this.global.disablePopupMenu=
!0,null;case 180:return this.global.defaultDirectory;case 200:return r(c,String)?this.getMenu(c):this.getPopupMenu();case 220:return this.shapeManager.getProperty(c)}J.util.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(c$,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},"~A");c(c$,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getOptionInterface("viewer.PropertyManager")).setViewer(this);
return this.pm});c(c$,"getModelExtract",function(a,b,c,g){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,c,g)},"~O,~B,~B,~S");c(c$,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(c$,"notifyMouseClicked",function(a,b,c,g){var e=J.viewer.binding.Binding.getButtonMods(c),f=J.viewer.binding.Binding.getClickCount(c);this.global.setI("_mouseX",a);this.global.setI("_mouseY",this.dimScreen.height-b);this.global.setI("_mouseAction",
c);this.global.setI("_mouseModifiers",e);this.global.setI("_clickCount",f);return this.statusManager.setStatusClicked(a,this.dimScreen.height-b,c,f,g)},"~N,~N,~N,~N");c(c$,"checkObjectClicked",function(a,b,c){return this.shapeManager.checkObjectClicked(a,b,c,this.getVisibleFramesBitSet(),this.global.drawPicking)},"~N,~N,~N");c(c$,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shapeManager&&this.shapeManager.checkObjectHovered(a,b,this.getVisibleFramesBitSet(),this.getBondPicking())},"~N,~N");
c(c$,"checkObjectDragged",function(a,b,c,g,e){var f=0;switch(this.getPickingMode()){case 2:f=5;break;case 4:f=22}this.shapeManager.checkObjectDragged(a,b,c,g,e,this.getVisibleFramesBitSet(),f)&&(this.refresh(1,"checkObjectDragged"),22==f&&this.scriptEcho(this.getShapeProperty(22,"command")))},"~N,~N,~N,~N,~N");c(c$,"rotateAxisAngleAtCenter",function(a,b,c,g,e,f,h){(a=this.transformManager.rotateAxisAngleAtCenter(a,b,c,g,e,f,h))&&this.refresh(-1,"rotateAxisAngleAtCenter");return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");
c(c$,"rotateAboutPointsInternal",function(a,b,c,g,e,f,h,k,l,m){(a=this.transformManager.rotateAboutPointsInternal(a,b,c,g,e,!1,f,h,!1,k,l,m))&&this.refresh(-1,"rotateAxisAboutPointsInternal");return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.List,~A");c(c$,"startSpinningAxis",function(a,b,c){this.getSpinOn()||this.getNavOn()?(this.setSpinOn(!1),this.setNavOn(!1)):this.transformManager.rotateAboutPointsInternal(null,a,b,this.global.pickingSpinRate,3.4028235E38,c,!0,null,!1,null,
null,null)},"JU.P3,JU.P3,~B");c(c$,"getModelDipole",function(){return this.modelSet.getModelDipole(this.animationManager.currentModelIndex)});c(c$,"calculateMolecularDipole",function(){return this.modelSet.calculateMolecularDipole(this.animationManager.currentModelIndex)});c(c$,"getAtomIdentityInfo",function(a,b){this.modelSet.getAtomIdentityInfo(a,b)},"~N,java.util.Map");c(c$,"setDefaultLattice",function(a){this.global.setDefaultLattice(a);this.global.setS("defaultLattice",J.util.Escape.eP(a))},
"JU.P3");c(c$,"getDefaultLattice",function(){return this.global.ptDefaultLattice});c(c$,"getTaintedAtoms",function(a){return this.modelSet.getTaintedAtoms(a)},"~N");c(c$,"setTaintedAtoms",function(a,b){this.modelSet.setTaintedAtoms(a,b)},"JU.BS,~N");c(c$,"getData",function(a,b){var c="";if(b.equalsIgnoreCase("MOL")||b.equalsIgnoreCase("SDF")||b.equalsIgnoreCase("V2000")||b.equalsIgnoreCase("V3000")||b.equalsIgnoreCase("XYZVIB")||b.equalsIgnoreCase("CD")||b.equalsIgnoreCase("JSON"))return this.getModelExtract(a,
!1,!1,b);if(0==b.toLowerCase().indexOf("property_"))c='{selected}.label("%{'+b+'}")';else{if(b.equalsIgnoreCase("CML"))return this.getModelCml(this.getAtomBitSet(a),2147483647,!0);c=b.equalsIgnoreCase("PDB")?'{selected and not hetero}.label("ATOM  %5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines+{selected and hetero}.label("HETATM%5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines':b.equalsIgnoreCase("XYZRN")?'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %8.3x %8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i").lines':
b.startsWith("USER:")?'{selected}.label("'+b.substring(5)+'").lines':'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %10.5x %10.5y %10.5z").lines'}a.equals("selected")||(c=JU.PT.simpleReplace(c,"selected",a));return this.evaluateExpression(c)},"~S,~S");c(c$,"getModelCml",function(a,b,c){return this.modelSet.getModelCml(a,b,c)},"JU.BS,~N,~B");c(c$,"getHelixData",function(a,b){return this.modelSet.getHelixData(a,b)},"JU.BS,~N");c(c$,"getPdbAtomData",function(a,b){return this.modelSet.getPdbAtomData(null==
a?this.getSelectionSet(!0):a,b)},"JU.BS,JU.OC");c(c$,"isJmolDataFrameForModel",function(a){return this.modelSet.isJmolDataFrameForModel(a)},"~N");c(c$,"isJmolDataFrame",function(){return this.modelSet.isJmolDataFrameForModel(this.animationManager.currentModelIndex)});c(c$,"getJmolDataFrameIndex",function(a,b){return this.modelSet.getJmolDataFrameIndex(a,b)},"~N,~S");c(c$,"setJmolDataFrame",function(a,b,c){this.modelSet.setJmolDataFrame(a,b,c)},"~S,~N,~N");c(c$,"setFrameTitle",function(a,b){this.modelSet.setFrameTitle(J.util.BSUtil.newAndSetBit(a),
b)},"~N,~S");c(c$,"setFrameTitleObj",function(a){this.loadShape(30);this.modelSet.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(c$,"getFrameTitle",function(){return this.modelSet.getFrameTitle(this.animationManager.currentModelIndex)});c(c$,"getJmolFrameType",function(a){return this.modelSet.getJmolFrameType(a)},"~N");c(c$,"getJmolDataSourceFrame",function(a){return this.modelSet.getJmolDataSourceFrame(a)},"~N");c(c$,"setAtomProperty",function(a,b,c,g,e,f,h){1649412120==b&&this.shapeManager.deleteVdwDependentShapes(a);
this.clearMinimization();this.modelSet.setAtomProperty(a,b,c,g,e,f,h);switch(b){case 1112541185:case 1112541186:case 1112541187:case 1112541188:case 1112541189:case 1112541190:case 1112539153:case 1112539154:case 1112539155:case 1087375365:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"checkCoordinatesChanged",function(){this.modelSet.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(c$,"setAtomCoord",function(a,b,c,g){this.modelSet.setAtomCoord(a,b,c,g)},
"~N,~N,~N,~N");c(c$,"setAtomCoordRelative",function(a,b,c,g){this.modelSet.setAtomCoordRelative(a,b,c,g)},"~N,~N,~N,~N");c(c$,"setAtomCoords",function(a,b,c){0!=a.cardinality()&&(this.modelSet.setAtomCoords(a,b,c),this.checkMinimization(),this.statusManager.setStatusAtomMoved(a))},"JU.BS,~N,~O");c(c$,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.getSelectionSet(!1));0!=b.cardinality()&&(this.modelSet.setAtomCoordsRelative(a,b),this.checkMinimization(),this.statusManager.setStatusAtomMoved(b))},
"JU.T3,JU.BS");c(c$,"invertAtomCoordPt",function(a,b){this.modelSet.invertSelected(a,null,-1,null,b);this.checkMinimization();this.statusManager.setStatusAtomMoved(b)},"JU.P3,JU.BS");c(c$,"invertAtomCoordPlane",function(a,b){this.modelSet.invertSelected(null,a,-1,null,b);this.checkMinimization();this.statusManager.setStatusAtomMoved(b)},"JU.P4,JU.BS");c(c$,"invertSelected",function(a,b,c,g){var e=this.getSelectionSet(!1);0!=e.cardinality()&&(this.modelSet.invertSelected(a,b,c,g,e),this.checkMinimization(),
this.statusManager.setStatusAtomMoved(e))},"JU.P3,JU.P4,~N,JU.BS");c(c$,"moveAtoms",function(a,b,c,g,e,f,h){0!=f.cardinality()&&(this.modelSet.moveAtoms(a,b,c,f,g,e,h),this.checkMinimization(),this.statusManager.setStatusAtomMoved(f))},"JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");c(c$,"moveSelected",function(a,b,c,g,e,f,h,k){0!=c&&(-2147483648==g&&(this.rotateBondIndex=-1),this.isJmolDataFrame()||(-2147483648==a?(this.showSelected=!0,this.loadShape(8),this.refresh(6,"moveSelected")):2147483647==a?this.showSelected&&
(this.showSelected=!1,this.refresh(6,"moveSelected")):this.movingSelected||(this.movingSelected=!0,this.stopMinimization(),0<=this.rotateBondIndex&&-2147483648!=g?this.actionRotateBond(a,b,g,e):(f=this.setMovableBitSet(f,!k),0!=f.cardinality()&&(h?(g=this.getAtomSetCenter(f),this.transformManager.finalizeTransformParameters(),e=this.global.antialiasDisplay?2:1,h=this.transformPt(g),a=-2147483648!=c?JU.P3.new3(h.x,h.y,h.z+c+0.5):JU.P3.new3(h.x+a*e+0.5,h.y+b*e+0.5,h.z),b=new JU.P3,this.unTransformPoint(a,
b),b.sub(g),this.setAtomCoordsRelative(b,f)):this.transformManager.rotateXYBy(a,b,f))),this.refresh(2,""),this.movingSelected=!1)))},"~N,~N,~N,~N,~N,JU.BS,~B,~B");c(c$,"highlightBond",function(a,b){if(!b||this.hoverEnabled){var c=null;if(0<=a){var g=this.modelSet.bonds[a],c=g.getAtomIndex2();if(!this.isAtomAssignable(c))return;c=J.util.BSUtil.newAndSetBit(c);c.set(g.getAtomIndex1())}this.highlight(c);this.refresh(3,"highlightBond")}},"~N,~B");c(c$,"highlight",function(a){null!=a&&this.loadShape(8);
this.setShapeProperty(8,"highlight",a)},"JU.BS");c(c$,"setRotateBondIndex",function(a){if(0<=this.rotateBondIndex||!(0>a))this.rotatePrev1=-1,this.bsRotateBranch=null,-2147483648!=a&&(this.rotateBondIndex=a,this.highlightBond(a,!1))},"~N");c(c$,"getRotateBondIndex",function(){return this.rotateBondIndex});c(c$,"actionRotateBond",function(a,b,c,g){if(!(0>this.rotateBondIndex)){var e=this.bsRotateBranch,f,h;if(null==e){h=this.modelSet.bonds[this.rotateBondIndex];f=h.getAtom1();h=h.getAtom2();this.undoMoveActionClear(f.index,
2,!0);c=JU.P3.new3(c,g,s((f.sZ+h.sZ)/2));this.transformManager.unTransformPoint(c,c);if(1==h.getCovalentBondCount()||c.distance(f)<c.distance(h)&&1!=f.getCovalentBondCount())g=f,f=h,h=g;if(90<J.util.Measure.computeAngleABC(c,f,h,!0)||90<J.util.Measure.computeAngleABC(c,h,f,!0))e=this.getBranchBitSet(h.index,f.index,!0);if(null!=e){c=0;for(g=f.getBonds().length;0<=--g;)if(e.get(f.getBondedAtomIndex(g))&&2==++c){e=null;break}}null==e&&(e=this.getMoleculeBitSet(f.index));this.bsRotateBranch=e;this.rotatePrev1=
f.index;this.rotatePrev2=h.index}else f=this.modelSet.atoms[this.rotatePrev1],h=this.modelSet.atoms[this.rotatePrev2];c=JU.V3.new3(h.sX-f.sX,h.sY-f.sY,0);a=JU.V3.new3(a,b,0);c.cross(c,a);a=(0<c.z?1:-1)*a.length();e=J.util.BSUtil.copy(e);e.andNot(this.selectionManager.getMotionFixedAtoms());this.rotateAboutPointsInternal(this.eval,f,h,0,a,!1,e,null,null,null)}},"~N,~N,~N,~N");c(c$,"refreshMeasures",function(a){this.setShapeProperty(6,"refresh",null);a&&this.stopMinimization()},"~B");c(c$,"functionXY",
function(a,b,c){var g=null;if(0==a.indexOf("file:"))g=this.getFileAsString(a.substring(5));else if(0!=a.indexOf("data2d_"))return this.statusManager.functionXY(a,b,c);b=Math.abs(b);c=Math.abs(c);if(null==g){a=this.getDataFloat2D(a);if(null!=a)return a;g=""}a=O(b,c,0);var e=O(b*c,0);J.util.Parser.parseStringInfestedFloatArray(g,null,e);for(var f=g=0;g<b;g++)for(var h=0;h<c;h++)a[g][h]=e[f++];return a},"~S,~N,~N");c(c$,"functionXYZ",function(a,b,c,g){var e=null;if(0==a.indexOf("file:"))e=this.getFileAsString(a.substring(5));
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!0,!1,"V2000")},"~S");c(c$,"getNMRPredict",function(a){var b=this.getModelExtract("selected",!0,!1,"V2000"),c=b.indexOf("\n"),b="Jmol "+J.viewer.Viewer.version_date+b.substring(c);return a?(this.$isApplet?this.showUrl(this.global.nmrUrlFormat+b):(this.syncScript("true","*",0),this.syncScript("JSpecView:",".",0)),null):this.getFileAsString(this.global.nmrPredictFormat+b)},"~B");c(c$,"getHelp",function(a){0>this.global.helpPath.indexOf("?")?(0<a.length&&0!=a.indexOf("?")&&(a="?search="+JU.PT.simpleReplace(a,
" ","%20")),a+=(0==a.length?"?ver=":"&ver=")+J.viewer.JC.version):a="&"+a;this.showUrl(this.global.helpPath+a)},"~S");c(c$,"show2D",function(a){this.showUrl(this.setLoadFormat("_"+a,"2",!1))},"~S");c(c$,"getChemicalInfo",function(a,b,c){a=this.setLoadFormat("_"+a,b,!1);"/"==b&&(a+=JU.PT.simpleReplace(c," ","%20"));return this.getFileAsString4(a,-1,!1,!1,!1)},"~S,~S,~S");c(c$,"addCommand",function(a){!this.autoExit&&(this.haveDisplay&&this.getPreserveState())&&this.commandHistory.addCommand(JU.PT.replaceAllCharacters(a,
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default:a=J.constant.EnumVdw.JMOL}a!==this.defaultVdw&&(a===J.constant.EnumVdw.USER&&null==this.bsUserVdws)&&this.setUserVdw(this.defaultVdw);this.defaultVdw=a;this.global.setS("defaultVDW",a.getVdwLabel())},"~S");c(c$,"setUserVdw",function(a){this.userVdwMars=D(J.util.Elements.elementNumberMax,0);this.userVdws=O(J.util.Elements.elementNumberMax,0);this.bsUserVdws=new JU.BS;a===J.constant.EnumVdw.USER&&(a=J.constant.EnumVdw.JMOL);for(var b=1;b<J.util.Elements.elementNumberMax;b++)this.userVdwMars[b]=
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var g=J.util.BSUtil.copy(this.getDeletedAtoms()),e=this.modelSet.deleteModels(a);this.selectionManager.processDeletedModelAtoms(e);this.setAnimationRange(0,0);null!=this.eval&&this.eval.deleteAtomsInVariables(e);this.clearRepaintManager(-1);this.animationManager.clear();this.animationManager.initializePointers(1);this.setCurrentModelIndexClear(1<this.getModelCount()?-1:0,1<this.getModelCount());this.hoverAtomIndex=-1;this.setFileLoadStatus(J.constant.EnumFileStatus.DELETED,null,null,null,null,null);
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" Energy = "+this.getParameter("_minimizationEnergy")))});c(c$,"minimize",function(a,b,c,g,e,f,h,k,l){var m=this.global.forceField,n=this.getModelUndeletedAtomsBitSetBs(this.getVisibleFramesBitSet());null==c?c=this.getModelUndeletedAtomsBitSet(this.getVisibleFramesBitSet().length()-1):c.and(n);0>=e&&(e=5);g=J.util.BSUtil.copy(null==g?this.selectionManager.getMotionFixedAtoms():g);var p=0<g.cardinality();p&&c.andNot(g);e=h?new JU.BS:this.getAtomsWithinRadius(e,c,!0,null);e.andNot(c);p?g.and(e):g=e;
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g=J.util.BSUtil.newAndSetBit(a);b=[b];var f=new JU.List;f.addLast(e);e=e.modelIndex;this.statusManager.modifySend(a,e,3);try{g=this.addHydrogensInline(g,f,b),a=g.nextSetBit(0),this.modelSet.assignAtom(a,c,!1)}catch(h){if(!C(h,Exception))throw h;}this.modelSet.setAtomNamesAndNumbers(a,-1,null);this.statusManager.modifySend(a,e,-3)}},"~N,JU.P3,~S");c(c$,"assignConnect",function(a,b){this.clearModelDependentObjects();var c=JU.AU.newFloat2(1);c[0]=[a,b];var g=this.modelSet.atoms[a].modelIndex;this.statusManager.modifySend(a,
g,2);this.modelSet.connect(c);this.modelSet.assignAtom(a,".",!0);this.modelSet.assignAtom(b,".",!0);this.statusManager.modifySend(a,g,-2);this.refresh(3,"assignConnect")},"~N,~N");c(c$,"moveAtomWithHydrogens",function(a,b,c,g,e){this.stopMinimization();if(null==e){var f=this.modelSet.atoms[a];e=J.util.BSUtil.newAndSetBit(a);a=f.getBonds();if(null!=a)for(var h=0;h<a.length;h++){var k=a[h].getOtherAtom(f);1==k.getElementNumber()&&e.set(k.index)}}this.moveSelected(b,c,g,-2147483648,-2147483648,e,!0,
!0)},"~N,~N,~N,~N,JU.BS");c(c$,"isAtomPDB",function(a){return this.modelSet.isAtomPDB(a)},"~N");c(c$,"isModelPDB",function(a){return this.modelSet.models[a].isBioModel},"~N");c(c$,"isAtomAssignable",function(a){return this.modelSet.isAtomAssignable(a)},"~N");h(c$,"deleteMeasurement",function(a){this.setShapeProperty(6,"delete",Integer.$valueOf(a))},"~N");c(c$,"haveModelKit",function(){return this.modelSet.haveModelKit()});c(c$,"getModelKitStateBitSet",function(a,b){return this.modelSet.getModelKitStateBitset(a,
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