ChemDoodleWeb.js

//
// ChemDoodle Web Components 7.0.1
//
// http://web.chemdoodle.com
//
// Copyright 2009-2015 iChemLabs, LLC.  All rights reserved.
//
// The ChemDoodle Web Components library is licensed under version 3
// of the GNU GENERAL PUBLIC LICENSE.
//
// You may redistribute it and/or modify it under the terms of the
// GNU General Public License as published by the Free Software Foundation,
// either version 3 of the License, or (at your option) any later version.
//
// As an exception to the GPL, you may distribute this packed form of
// the code without the copy of the GPL license normally required,
// provided you include this license notice and a URL through which
// recipients can access the corresponding unpacked source code. 
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// Please contact iChemLabs <http://www.ichemlabs.com/contact-us> for
// alternate licensing options.
//
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g,p,h,y,j,q,l,r,o,v;if(!d||c===d)return c[12]=c[0]*f+c[4]*e+c[8]*a+c[12],c[13]=c[1]*f+c[5]*e+c[9]*a+c[13],c[14]=c[2]*f+c[6]*e+c[10]*a+c[14],c[15]=c[3]*f+c[7]*e+c[11]*a+c[15],c;b=c[0];n=c[1];g=c[2];p=c[3];h=c[4];y=c[5];j=c[6];q=c[7];l=c[8];r=c[9];o=c[10];v=c[11];d[0]=b;d[1]=n;d[2]=g;d[3]=p;d[4]=h;d[5]=y;d[6]=j;d[7]=q;d[8]=l;d[9]=r;d[10]=o;d[11]=v;d[12]=b*f+h*e+l*a+c[12];d[13]=n*f+y*e+r*a+c[13];d[14]=g*f+j*e+o*a+c[14];d[15]=p*f+q*e+v*a+c[15];return d},scale:function(c,a,d){var f=a[0],e=a[1];a=a[2];
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p=Math.cos(a);h=1-p;a=c[0];n=c[1];y=c[2];j=c[3];q=c[4];l=c[5];r=c[6];o=c[7];v=c[8];A=c[9];t=c[10];u=c[11];w=e*e*h+p;x=b*e*h+d*g;B=d*e*h-b*g;ca=e*b*h-d*g;da=b*b*h+p;ea=d*b*h+e*g;Y=e*d*h+b*g;e=b*d*h-e*g;b=d*d*h+p;f?c!==f&&(f[12]=c[12],f[13]=c[13],f[14]=c[14],f[15]=c[15]):f=c;f[0]=a*w+q*x+v*B;f[1]=n*w+l*x+A*B;f[2]=y*w+r*x+t*B;f[3]=j*w+o*x+u*B;f[4]=a*ca+q*da+v*ea;f[5]=n*ca+l*da+A*ea;f[6]=y*ca+r*da+t*ea;f[7]=j*ca+o*da+u*ea;f[8]=a*Y+q*e+v*b;f[9]=n*Y+l*e+A*b;f[10]=y*Y+r*e+t*b;f[11]=j*Y+o*e+u*b;return f},
rotateX:function(c,a,d){var f=Math.sin(a);a=Math.cos(a);var e=c[4],b=c[5],n=c[6],g=c[7],p=c[8],h=c[9],y=c[10],j=c[11];d?c!==d&&(d[0]=c[0],d[1]=c[1],d[2]=c[2],d[3]=c[3],d[12]=c[12],d[13]=c[13],d[14]=c[14],d[15]=c[15]):d=c;d[4]=e*a+p*f;d[5]=b*a+h*f;d[6]=n*a+y*f;d[7]=g*a+j*f;d[8]=e*-f+p*a;d[9]=b*-f+h*a;d[10]=n*-f+y*a;d[11]=g*-f+j*a;return d},rotateY:function(c,a,d){var f=Math.sin(a);a=Math.cos(a);var e=c[0],b=c[1],n=c[2],g=c[3],p=c[8],h=c[9],y=c[10],j=c[11];d?c!==d&&(d[4]=c[4],d[5]=c[5],d[6]=c[6],d[7]=
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-f+j*a;return d},frustum:function(c,a,d,f,e,b,n){n||(n=r.create());var g=a-c,p=f-d,h=b-e;n[0]=2*e/g;n[1]=0;n[2]=0;n[3]=0;n[4]=0;n[5]=2*e/p;n[6]=0;n[7]=0;n[8]=(a+c)/g;n[9]=(f+d)/p;n[10]=-(b+e)/h;n[11]=-1;n[12]=0;n[13]=0;n[14]=-(2*b*e)/h;n[15]=0;return n},perspective:function(c,a,d,f,e){c=d*Math.tan(c*Math.PI/360);a*=c;return r.frustum(-a,a,-c,c,d,f,e)},ortho:function(c,a,d,f,e,b,n){n||(n=r.create());var g=a-c,p=f-d,h=b-e;n[0]=2/g;n[1]=0;n[2]=0;n[3]=0;n[4]=0;n[5]=2/p;n[6]=0;n[7]=0;n[8]=0;n[9]=0;n[10]=
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c[0]+", "+c[1]+", "+c[2]+", "+c[3]+", "+c[4]+", "+c[5]+", "+c[6]+", "+c[7]+", "+c[8]+", "+c[9]+", "+c[10]+", "+c[11]+", "+c[12]+", "+c[13]+", "+c[14]+", "+c[15]+"]"}},v={create:function(c){var a=new e(4);c?(a[0]=c[0],a[1]=c[1],a[2]=c[2],a[3]=c[3]):a[0]=a[1]=a[2]=a[3]=0;return a},createFrom:function(c,a,d,f){var b=new e(4);b[0]=c;b[1]=a;b[2]=d;b[3]=f;return b},set:function(c,a){a[0]=c[0];a[1]=c[1];a[2]=c[2];a[3]=c[3];return a},equal:function(c,a){return c===a||1E-6>Math.abs(c[0]-a[0])&&1E-6>Math.abs(c[1]-
a[1])&&1E-6>Math.abs(c[2]-a[2])&&1E-6>Math.abs(c[3]-a[3])},identity:function(c){c||(c=v.create());c[0]=0;c[1]=0;c[2]=0;c[3]=1;return c}},u=v.identity();v.calculateW=function(c,a){var d=c[0],f=c[1],e=c[2];if(!a||c===a)return c[3]=-Math.sqrt(Math.abs(1-d*d-f*f-e*e)),c;a[0]=d;a[1]=f;a[2]=e;a[3]=-Math.sqrt(Math.abs(1-d*d-f*f-e*e));return a};v.dot=function(c,a){return c[0]*a[0]+c[1]*a[1]+c[2]*a[2]+c[3]*a[3]};v.inverse=function(c,a){var d=c[0],f=c[1],e=c[2],b=c[3],d=(d=d*d+f*f+e*e+b*b)?1/d:0;if(!a||c===
a)return c[0]*=-d,c[1]*=-d,c[2]*=-d,c[3]*=d,c;a[0]=-c[0]*d;a[1]=-c[1]*d;a[2]=-c[2]*d;a[3]=c[3]*d;return a};v.conjugate=function(c,a){if(!a||c===a)return c[0]*=-1,c[1]*=-1,c[2]*=-1,c;a[0]=-c[0];a[1]=-c[1];a[2]=-c[2];a[3]=c[3];return a};v.length=function(c){var a=c[0],d=c[1],f=c[2];c=c[3];return Math.sqrt(a*a+d*d+f*f+c*c)};v.normalize=function(c,a){a||(a=c);var d=c[0],f=c[1],e=c[2],b=c[3],n=Math.sqrt(d*d+f*f+e*e+b*b);if(0===n)return a[0]=0,a[1]=0,a[2]=0,a[3]=0,a;n=1/n;a[0]=d*n;a[1]=f*n;a[2]=e*n;a[3]=
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a*e-n*f,f=-a*f-n*e-g*b;d[0]=p*c+f*-a+h*-g-y*-n;d[1]=h*c+f*-n+y*-a-p*-g;d[2]=y*c+f*-g+p*-n-h*-a;return d};v.scale=function(c,a,d){if(!d||c===d)return c[0]*=a,c[1]*=a,c[2]*=a,c[3]*=a,c;d[0]=c[0]*a;d[1]=c[1]*a;d[2]=c[2]*a;d[3]=c[3]*a;return d};v.toMat3=function(c,a){a||(a=A.create());var d=c[0],f=c[1],e=c[2],b=c[3],n=d+d,g=f+f,p=e+e,h=d*n,y=d*g,d=d*p,j=f*g,f=f*p,e=e*p,n=b*n,g=b*g,b=b*p;a[0]=1-(j+e);a[1]=y+b;a[2]=d-g;a[3]=y-b;a[4]=1-(h+e);a[5]=f+n;a[6]=d+g;a[7]=f-n;a[8]=1-(h+j);return a};v.toMat4=function(c,
a){a||(a=r.create());var d=c[0],f=c[1],e=c[2],b=c[3],n=d+d,g=f+f,p=e+e,h=d*n,y=d*g,d=d*p,j=f*g,f=f*p,e=e*p,n=b*n,g=b*g,b=b*p;a[0]=1-(j+e);a[1]=y+b;a[2]=d-g;a[3]=0;a[4]=y-b;a[5]=1-(h+e);a[6]=f+n;a[7]=0;a[8]=d+g;a[9]=f-n;a[10]=1-(h+j);a[11]=0;a[12]=0;a[13]=0;a[14]=0;a[15]=1;return a};v.slerp=function(c,a,d,f){f||(f=c);var e=c[0]*a[0]+c[1]*a[1]+c[2]*a[2]+c[3]*a[3],b,n;if(1<=Math.abs(e))return f!==c&&(f[0]=c[0],f[1]=c[1],f[2]=c[2],f[3]=c[3]),f;b=Math.acos(e);n=Math.sqrt(1-e*e);if(0.001>Math.abs(n))return f[0]=
0.5*c[0]+0.5*a[0],f[1]=0.5*c[1]+0.5*a[1],f[2]=0.5*c[2]+0.5*a[2],f[3]=0.5*c[3]+0.5*a[3],f;e=Math.sin((1-d)*b)/n;d=Math.sin(d*b)/n;f[0]=c[0]*e+a[0]*d;f[1]=c[1]*e+a[1]*d;f[2]=c[2]*e+a[2]*d;f[3]=c[3]*e+a[3]*d;return f};v.fromRotationMatrix=function(c,a){a||(a=v.create());var d=c[0]+c[4]+c[8],f;if(0<d)f=Math.sqrt(d+1),a[3]=0.5*f,f=0.5/f,a[0]=(c[7]-c[5])*f,a[1]=(c[2]-c[6])*f,a[2]=(c[3]-c[1])*f;else{f=v.fromRotationMatrix.s_iNext=v.fromRotationMatrix.s_iNext||[1,2,0];d=0;c[4]>c[0]&&(d=1);c[8]>c[3*d+d]&&
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this.x;b=this.y-b.y;for(var g=0,g=0===h?0===b?0:0<b?j.PI/2:3*j.PI/2:0===b?0<h?0:j.PI:0>h?j.atan(b/h)+j.PI:0>b?j.atan(b/h)+2*j.PI:j.atan(b/h);0>g;)g+=2*j.PI;return g%=2*j.PI}})(ChemDoodle.structures,Math);
(function(b,j){var o=/[ ,]+/,l=/\-+/,h=["Helvetica","Arial","Dialog"];j.Query=function(e){this.type=e;this.elements={v:[],not:!1};this.saturation=this.hydrogens=this.connectivityNoH=this.connectivity=this.chirality=this.charge=void 0;this.orders={v:[],not:!1};this.cache=this.ringCount=this.aromatic=this.stereo=void 0};j.Query.TYPE_ATOM=0;j.Query.TYPE_BOND=1;var g=j.Query.prototype;g.parseRange=function(e){var a=[];e=e.split(o);for(var d=0,b=e.length;d<b;d++){var f=e[d],g=!1,h=!1;"-"===f.charAt(0)&&
(g=!0,f=f.substring(1));-1!=f.indexOf("--")&&(h=!0);-1!=f.indexOf("-")?(f=f.split(l),g={x:parseInt(f[0])*(g?-1:1),y:parseInt(f[1])*(h?-1:1)},g.y<g.x&&(h=g.y,g.y=g.x,g.x=h),a.push(g)):a.push({x:parseInt(f)*(g?-1:1)})}return a};g.draw=function(e,a,d){this.cache||(this.cache=this.toString());var n=this.cache,f=void 0,g=n.indexOf("(");-1!=g&&(n=this.cache.substring(0,g),f=this.cache.substring(g,this.cache.length));e.textAlign="center";e.textBaseline="middle";e.font=b.getFontString(12,h,!0,!1);g=e.measureText(n).width;
e.fillStyle=a.backgroundColor;e.fillRect(d.x-g/2,d.y-6,g,12);e.fillStyle="black";e.fillText(n,d.x,d.y);f&&(e.font=b.getFontString(10,h,!1,!0),g=e.measureText(f).width,e.fillStyle=a.backgroundColor,e.fillRect(d.x-g/2,d.y+6,g,11),e.fillStyle="black",e.fillText(f,d.x,d.y+11))};g.outputRange=function(e){for(var a=!1,d=[],b=0,f=e.length;b<f;b++){a&&d.push(",");var a=!0,g=e[b];g.y?(d.push(g.x),d.push("-"),d.push(g.y)):d.push(g.x)}return d.join("")};g.toString=function(){var e=[],a=[];this.type===j.Query.TYPE_ATOM?
(!this.elements||0===this.elements.v.length?e.push("[a]"):(this.elements.not&&e.push("!"),e.push("["),e.push(this.elements.v.join(",")),e.push("]")),this.chirality&&a.push((this.chirality.not?"!":"")+"@\x3d"+this.chirality.v),this.aromatic&&a.push((this.aromatic.not?"!":"")+"A"),this.charge&&a.push((this.charge.not?"!":"")+"C\x3d"+this.outputRange(this.charge.v)),this.hydrogens&&a.push((this.hydrogens.not?"!":"")+"H\x3d"+this.outputRange(this.hydrogens.v)),this.ringCount&&a.push((this.ringCount.not?
"!":"")+"R\x3d"+this.outputRange(this.ringCount.v)),this.saturation&&a.push((this.saturation.not?"!":"")+"S"),this.connectivity&&a.push((this.connectivity.not?"!":"")+"X\x3d"+this.outputRange(this.connectivity.v)),this.connectivityNoH&&a.push((this.connectivityNoH.not?"!":"")+"x\x3d"+this.outputRange(this.connectivityNoH.v))):this.type===j.Query.TYPE_BOND&&(!this.orders||0===this.orders.v.length?e.push("[a]"):(this.orders.not&&e.push("!"),e.push("["),e.push(this.orders.v.join(",")),e.push("]")),this.stereo&&
a.push((this.stereo.not?"!":"")+"@\x3d"+this.stereo.v),this.aromatic&&a.push((this.aromatic.not?"!":"")+"A"),this.ringCount&&a.push((this.ringCount.not?"!":"")+"R\x3d"+this.outputRange(this.ringCount.v)));0<a.length&&(e.push("("),e.push(a.join(",")),e.push(")"));return e.join("")}})(ChemDoodle.extensions,ChemDoodle.structures,Math);
(function(b,j,o,l,h,g){l.Atom=function(e,a,d,n){this.label=e?e.replace(/\s/g,""):"C";b[this.label]||(this.label="C");this.x=a?a:0;this.y=d?d:0;this.z=n?n:0};l=l.Atom.prototype=new l.Point(0,0);l.charge=0;l.numLonePair=0;l.numRadical=0;l.mass=-1;l.coordinationNumber=0;l.bondNumber=0;l.angleOfLeastInterference=0;l.isHidden=!1;l.altLabel=void 0;l.isLone=!1;l.isHover=!1;l.isSelected=!1;l.add3D=function(e){this.x+=e.x;this.y+=e.y;this.z+=e.z};l.sub3D=function(e){this.x-=e.x;this.y-=e.y;this.z-=e.z};l.distance3D=
function(e){var a=e.x-this.x,d=e.y-this.y;e=e.z-this.z;return h.sqrt(a*a+d*d+e*e)};l.draw=function(e,a){if(this.isLassoed){var d=e.createRadialGradient(this.x-1,this.y-1,0,this.x,this.y,7);d.addColorStop(0,"rgba(212, 99, 0, 0)");d.addColorStop(0.7,"rgba(212, 99, 0, 0.8)");e.fillStyle=d;e.beginPath();e.arc(this.x,this.y,5,0,2*h.PI,!1);e.fill()}if(!this.query){this.textBounds=[];this.specs&&(a=this.specs);var b=j.getFontString(a.atoms_font_size_2D,a.atoms_font_families_2D,a.atoms_font_bold_2D,a.atoms_font_italic_2D);
e.font=b;e.fillStyle=this.getElementColor(a.atoms_useJMOLColors,a.atoms_usePYMOLColors,a.atoms_color,2);"H"===this.label&&a.atoms_HBlack_2D&&(e.fillStyle="black");var f;if(this.isLone&&!a.atoms_displayAllCarbonLabels_2D||a.atoms_circles_2D)e.beginPath(),e.arc(this.x,this.y,a.atoms_circleDiameter_2D/2,0,2*h.PI,!1),e.fill(),0<a.atoms_circleBorderWidth_2D&&(e.lineWidth=a.atoms_circleBorderWidth_2D,e.strokeStyle="black",e.stroke());else if(this.isLabelVisible(a))if(e.textAlign="center",e.textBaseline=
"middle",void 0!==this.altLabel){e.fillText(this.altLabel,this.x,this.y);var g=e.measureText(this.altLabel).width;this.textBounds.push({x:this.x-g/2,y:this.y-a.atoms_font_size_2D/2+1,w:g,h:a.atoms_font_size_2D-2})}else{e.fillText(this.label,this.x,this.y);g=e.measureText(this.label).width;this.textBounds.push({x:this.x-g/2,y:this.y-a.atoms_font_size_2D/2+1,w:g,h:a.atoms_font_size_2D-2});var p=0;-1!==this.mass&&(d=e.font,e.font=j.getFontString(0.7*a.atoms_font_size_2D,a.atoms_font_families_2D,a.atoms_font_bold_2D,
a.atoms_font_italic_2D),p=e.measureText(this.mass).width,e.fillText(this.mass,this.x-p-0.5,this.y-a.atoms_font_size_2D/2+1),this.textBounds.push({x:this.x-g/2-p-0.5,y:this.y-1.7*a.atoms_font_size_2D/2+1,w:p,h:a.atoms_font_size_2D/2-1}),e.font=d);var d=g/2,q=this.getImplicitHydrogenCount();if(a.atoms_implicitHydrogens_2D&&0<q){f=0;var l=e.measureText("H").width,r=!0;if(1<q){var v=g/2+l/2,u=0,t=j.getFontString(0.8*a.atoms_font_size_2D,a.atoms_font_families_2D,a.atoms_font_bold_2D,a.atoms_font_italic_2D);
e.font=t;var w=e.measureText(q).width;1===this.bondNumber?this.angleOfLeastInterference>h.PI/2&&this.angleOfLeastInterference<3*h.PI/2&&(v=-g/2-w-l/2-p/2,r=!1,f=h.PI):this.angleOfLeastInterference<=h.PI/4||(this.angleOfLeastInterference<3*h.PI/4?(v=0,u=0.9*-a.atoms_font_size_2D,0!==this.charge&&(u-=0.3*a.atoms_font_size_2D),r=!1,f=h.PI/2):this.angleOfLeastInterference<=5*h.PI/4?(v=-g/2-w-l/2-p/2,r=!1,f=h.PI):this.angleOfLeastInterference<7*h.PI/4&&(v=0,u=0.9*a.atoms_font_size_2D,r=!1,f=3*h.PI/2));
e.font=b;e.fillText("H",this.x+v,this.y+u);e.font=t;e.fillText(q,this.x+v+l/2+w/2,this.y+u+0.3*a.atoms_font_size_2D);this.textBounds.push({x:this.x+v-l/2,y:this.y+u-a.atoms_font_size_2D/2+1,w:l,h:a.atoms_font_size_2D-2});this.textBounds.push({x:this.x+v+l/2,y:this.y+u+0.3*a.atoms_font_size_2D-a.atoms_font_size_2D/2+1,w:w,h:0.8*a.atoms_font_size_2D-2})}else v=g/2+l/2,u=0,1===this.bondNumber?this.angleOfLeastInterference>h.PI/2&&this.angleOfLeastInterference<3*h.PI/2&&(v=-g/2-l/2-p/2,r=!1,f=h.PI):this.angleOfLeastInterference<=
h.PI/4||(this.angleOfLeastInterference<3*h.PI/4?(v=0,u=0.9*-a.atoms_font_size_2D,r=!1,f=h.PI/2):this.angleOfLeastInterference<=5*h.PI/4?(v=-g/2-l/2-p/2,r=!1,f=h.PI):this.angleOfLeastInterference<7*h.PI/4&&(v=0,u=0.9*a.atoms_font_size_2D,r=!1,f=3*h.PI/2)),e.fillText("H",this.x+v,this.y+u),this.textBounds.push({x:this.x+v-l/2,y:this.y+u-a.atoms_font_size_2D/2+1,w:l,h:a.atoms_font_size_2D-2});r&&(d+=l)}0!==this.charge&&(b=this.charge.toFixed(0),b="1"===b?"+":"-1"===b?"\u2013":j.stringStartsWith(b,"-")?
b.substring(1)+"\u2013":b+"+",g=e.measureText(b).width,d+=g/2,e.textAlign="center",e.textBaseline="middle",e.font=j.getFontString(h.floor(0.8*a.atoms_font_size_2D),a.atoms_font_families_2D,a.atoms_font_bold_2D,a.atoms_font_italic_2D),e.fillText(b,this.x+d-1,this.y-a.atoms_font_size_2D/2+1),this.textBounds.push({x:this.x+d-g/2-1,y:this.y-1.8*a.atoms_font_size_2D/2+5,w:g,h:a.atoms_font_size_2D/2-1}))}if(0<this.numLonePair||0<this.numRadical){e.fillStyle="black";q=this.angles.slice(0);d=this.angleOfLeastInterference;
b=this.largestAngle;void 0!==f&&(q.push(f),q.sort(),b=o.angleBetweenLargest(q),d=b.angle%(2*h.PI),b=b.largest);g=[];for(p=0;p<this.numLonePair;p++)g.push({t:2});for(p=0;p<this.numRadical;p++)g.push({t:1});if(void 0===f&&h.abs(b-2*h.PI/q.length)<h.PI/60){q=h.ceil(g.length/q.length);p=0;for(l=g.length;p<l;p+=q,d+=b)this.drawElectrons(e,a,g.slice(p,h.min(g.length,p+q)),d,b,f)}else this.drawElectrons(e,a,g,d,b,f)}}};l.drawElectrons=function(e,a,d,b,f,g){g=f/(d.length+(0===this.bonds.length&&void 0===
g?0:1));f=b-f/2+g;for(var j=0;j<d.length;j++){var q=d[j];b=f+j*g;var l=this.x+Math.cos(b)*a.atoms_lonePairDistance_2D,r=this.y-Math.sin(b)*a.atoms_lonePairDistance_2D;2===q.t?(q=b+Math.PI/2,b=Math.cos(q)*a.atoms_lonePairSpread_2D/2,q=-Math.sin(q)*a.atoms_lonePairSpread_2D/2,e.beginPath(),e.arc(l+b,r+q,a.atoms_lonePairDiameter_2D,0,2*h.PI,!1),e.fill(),e.beginPath(),e.arc(l-b,r-q,a.atoms_lonePairDiameter_2D,0,2*h.PI,!1),e.fill()):1===q.t&&(e.beginPath(),e.arc(l,r,a.atoms_lonePairDiameter_2D,0,2*h.PI,
!1),e.fill())}};l.drawDecorations=function(e){if(this.isHover||this.isSelected)e.strokeStyle=this.isHover?"#885110":"#0060B2",e.lineWidth=1.2,e.beginPath(),e.arc(this.x,this.y,this.isHover?7:15,0,2*h.PI,!1),e.stroke();this.isOverlap&&(e.strokeStyle="#C10000",e.lineWidth=1.2,e.beginPath(),e.arc(this.x,this.y,7,0,2*h.PI,!1),e.stroke())};l.render=function(e,a,d){this.specs&&(a=this.specs);var n=g.translate(e.modelViewMatrix,[this.x,this.y,this.z],[]),f=a.atoms_useVDWDiameters_3D?b[this.label].vdWRadius*
a.atoms_vdwMultiplier_3D:a.atoms_sphereDiameter_3D/2;0===f&&(f=1);g.scale(n,[f,f,f]);d||(d=a.atoms_color,a.atoms_useJMOLColors?d=b[this.label].jmolColor:a.atoms_usePYMOLColors&&(d=b[this.label].pymolColor),e.material.setDiffuseColor(d));e.setMatrixUniforms(n);e.drawElements(e.TRIANGLES,(this.renderAsStar?e.starBuffer:e.sphereBuffer).vertexIndexBuffer.numItems,e.UNSIGNED_SHORT,0)};l.renderHighlight=function(e,a){if(this.isSelected||this.isHover){this.specs&&(a=this.specs);var d=g.translate(e.modelViewMatrix,
[this.x,this.y,this.z],[]),n=a.atoms_useVDWDiameters_3D?b[this.label].vdWRadius*a.atoms_vdwMultiplier_3D:a.atoms_sphereDiameter_3D/2;0===n&&(n=1);n*=1.3;g.scale(d,[n,n,n]);e.setMatrixUniforms(d);e.material.setDiffuseColor(this.isHover?"#885110":"#0060B2");e.drawElements(e.TRIANGLES,(this.renderAsStar?e.starBuffer:e.sphereBuffer).vertexIndexBuffer.numItems,e.UNSIGNED_SHORT,0)}};l.isLabelVisible=function(e){return e.atoms_displayAllCarbonLabels_2D||"C"!==this.label||this.altLabel||(-1!==this.mass||
0!==this.charge)||e.atoms_showAttributedCarbons_2D&&(0!==this.numRadical||0!==this.numLonePair)||this.isHidden&&e.atoms_showHiddenCarbons_2D||e.atoms_displayTerminalCarbonLabels_2D&&1===this.bondNumber?!0:!1};l.getImplicitHydrogenCount=function(){if("H"===this.label||!b[this.label]||!b[this.label].addH)return 0;var e=b[this.label].valency,a=e-this.coordinationNumber;0<this.numRadical&&(a=h.max(0,a-this.numRadical));0<this.charge?(e=4-e,a=this.charge<=e?a+this.charge:4-this.coordinationNumber-this.charge+
e):a+=this.charge;return 0>a?0:h.floor(a)};l.getBounds=function(){var e=new o.Bounds;e.expand(this.x,this.y);if(this.textBounds)for(var a=0,d=this.textBounds.length;a<d;a++){var b=this.textBounds[a];e.expand(b.x,b.y,b.x+b.w,b.y+b.h)}return e};l.getBounds3D=function(){var e=new o.Bounds;e.expand3D(this.x,this.y,this.z);return e};l.getElementColor=function(e,a,d){e?d=b[this.label].jmolColor:a&&(d=b[this.label].pymolColor);return d}})(ChemDoodle.ELEMENT,ChemDoodle.extensions,ChemDoodle.math,ChemDoodle.structures,
Math,ChemDoodle.lib.mat4);
(function(b,j,o,l,h,g,e){o.Bond=function(a,d,e){this.a1=a;this.a2=d;this.bondOrder=void 0!==e?e:1};o.Bond.STEREO_NONE="none";o.Bond.STEREO_PROTRUDING="protruding";o.Bond.STEREO_RECESSED="recessed";o.Bond.STEREO_AMBIGUOUS="ambiguous";b=o.Bond.prototype;b.stereo=o.Bond.STEREO_NONE;b.isHover=!1;b.ring=void 0;b.getCenter=function(){return new o.Point((this.a1.x+this.a2.x)/2,(this.a1.y+this.a2.y)/2)};b.getLength=function(){return this.a1.distance(this.a2)};b.getLength3D=function(){return this.a1.distance3D(this.a2)};b.contains=
function(a){return a===this.a1||a===this.a2};b.getNeighbor=function(a){if(a===this.a1)return this.a2;if(a===this.a2)return this.a1};b.draw=function(a,d){if(!(this.a1.x===this.a2.x&&this.a1.y===this.a2.y)){this.specs&&(d=this.specs);var e=this.a1.x,f=this.a2.x,b=this.a1.y,g=this.a2.y,q=this.a1.distance(this.a2),A=f-e,r=g-b;if(this.a1.isLassoed&&this.a2.isLassoed){var v=a.createLinearGradient(e,b,f,g);v.addColorStop(0,"rgba(212, 99, 0, 0)");v.addColorStop(0.5,"rgba(212, 99, 0, 0.8)");v.addColorStop(1,
"rgba(212, 99, 0, 0)");var u=2.5,t=this.a1.angle(this.a2)+h.PI/2,w=h.cos(t),t=h.sin(t),x=e-w*u,B=b+t*u,c=e+w*u,k=b-t*u,C=f+w*u,D=g-t*u,w=f-w*u,t=g+t*u;a.fillStyle=v;a.beginPath();a.moveTo(x,B);a.lineTo(c,k);a.lineTo(C,D);a.lineTo(w,t);a.closePath();a.fill()}if(d.atoms_display&&!d.atoms_circles_2D&&this.a1.isLabelVisible(d)&&this.a1.textBounds){u=w=0;for(x=this.a1.textBounds.length;u<x;u++)w=Math.max(w,l.calculateDistanceInterior(this.a1,this.a2,this.a1.textBounds[u]));w+=d.bonds_atomLabelBuffer_2D;
w/=q;e+=A*w;b+=r*w}if(d.atoms_display&&!d.atoms_circles_2D&&this.a2.isLabelVisible(d)&&this.a2.textBounds){u=w=0;for(x=this.a2.textBounds.length;u<x;u++)w=Math.max(w,l.calculateDistanceInterior(this.a2,this.a1,this.a2.textBounds[u]));w+=d.bonds_atomLabelBuffer_2D;w/=q;f-=A*w;g-=r*w}d.bonds_clearOverlaps_2D&&(w=e+0.15*A,t=b+0.15*r,u=f-0.15*A,q=g-0.15*r,a.strokeStyle=d.backgroundColor,a.lineWidth=d.bonds_width_2D+2*d.bonds_overlapClearWidth_2D,a.lineCap="round",a.beginPath(),a.moveTo(w,t),a.lineTo(u,
q),a.closePath(),a.stroke());a.strokeStyle=d.bonds_color;a.fillStyle=d.bonds_color;a.lineWidth=d.bonds_width_2D;a.lineCap=d.bonds_ends_2D;if(d.bonds_useJMOLColors||d.bonds_usePYMOLColors)w=a.createLinearGradient(e,b,f,g),t=this.a1.getElementColor(d.bonds_useJMOLColors,d.bonds_usePYMOLColors,d.atoms_color,2),u=this.a2.getElementColor(d.bonds_useJMOLColors,d.bonds_usePYMOLColors,d.atoms_color,2),w.addColorStop(0,t),d.bonds_colorGradient||(w.addColorStop(0.5,t),w.addColorStop(0.51,u)),w.addColorStop(1,
u),a.strokeStyle=w,a.fillStyle=w;if(d.bonds_lewisStyle_2D&&0===this.bondOrder%1)this.drawLewisStyle(a,d,e,b,f,g);else switch(this.query?1:this.bondOrder){case 0:f-=e;g-=b;f=h.sqrt(f*f+g*g);g=h.floor(f/d.bonds_dotSize_2D);f=(f-(g-1)*d.bonds_dotSize_2D)/2;1===g%2?f+=d.bonds_dotSize_2D/4:(f-=d.bonds_dotSize_2D/4,g+=2);g/=2;r=this.a1.angle(this.a2);w=e+f*Math.cos(r);t=b-f*Math.sin(r);a.beginPath();for(u=0;u<g;u++)a.arc(w,t,d.bonds_dotSize_2D/2,0,2*h.PI,!1),w+=2*d.bonds_dotSize_2D*Math.cos(r),t-=2*d.bonds_dotSize_2D*
Math.sin(r);a.fill();break;case 0.5:a.beginPath();a.moveTo(e,b);j.contextHashTo(a,e,b,f,g,d.bonds_hashSpacing_2D,d.bonds_hashSpacing_2D);a.stroke();break;case 1:if(!this.query&&(this.stereo===o.Bond.STEREO_PROTRUDING||this.stereo===o.Bond.STEREO_RECESSED))r=d.bonds_width_2D/2,u=this.a1.distance(this.a2)*d.bonds_wedgeThickness_2D/2,t=this.a1.angle(this.a2)+h.PI/2,w=h.cos(t),t=h.sin(t),x=e-w*r,B=b+t*r,c=e+w*r,k=b-t*r,C=f+w*u,D=g-t*u,w=f-w*u,t=g+t*u,a.beginPath(),a.moveTo(x,B),a.lineTo(c,k),a.lineTo(C,
D),a.lineTo(w,t),a.closePath(),this.stereo===o.Bond.STEREO_PROTRUDING?a.fill():(a.save(),a.clip(),a.lineWidth=2*u,a.lineCap="butt",a.beginPath(),a.moveTo(e,b),j.contextHashTo(a,e,b,f,g,d.bonds_hashWidth_2D,d.bonds_hashSpacing_2D),a.stroke(),a.restore());else if(!this.query&&this.stereo===o.Bond.STEREO_AMBIGUOUS){a.beginPath();a.moveTo(e,b);f=h.floor(h.sqrt(A*A+r*r)/d.bonds_wavyLength_2D);t=this.a1.angle(this.a2)+h.PI/2;w=h.cos(t);t=h.sin(t);g=A/f;r/=f;u=0;for(x=f;u<x;u++)e+=g,b+=r,f=d.bonds_wavyLength_2D*
w+e-0.5*g,q=d.bonds_wavyLength_2D*-t+b-0.5*r,A=d.bonds_wavyLength_2D*-w+e-0.5*g,B=d.bonds_wavyLength_2D*t+b-0.5*r,0===u%2?a.quadraticCurveTo(f,q,e,b):a.quadraticCurveTo(A,B,e,b);a.stroke();break}else a.beginPath(),a.moveTo(e,b),a.lineTo(f,g),a.stroke(),this.query&&this.query.draw(a,d,this.getCenter());break;case 1.5:case 2:this.stereo===o.Bond.STEREO_AMBIGUOUS?(u=this.a1.distance(this.a2)*d.bonds_saturationWidth_2D/2,t=this.a1.angle(this.a2)+h.PI/2,w=h.cos(t),t=h.sin(t),x=e-w*u,B=b+t*u,c=e+w*u,k=
b-t*u,C=f+w*u,D=g-t*u,w=f-w*u,t=g+t*u,a.beginPath(),a.moveTo(x,B),a.lineTo(C,D),a.moveTo(c,k),a.lineTo(w,t),a.stroke()):!d.bonds_symmetrical_2D&&(this.ring||"C"===this.a1.label&&"C"===this.a2.label)?(a.beginPath(),a.moveTo(e,b),a.lineTo(f,g),w=0,q=this.a1.distance(this.a2),r=this.a1.angle(this.a2),t=r+h.PI/2,u=q*d.bonds_saturationWidth_2D,A=d.bonds_saturationAngle_2D,A<h.PI/2&&(w=-(u/h.tan(A))),h.abs(w)<q/2&&(A=e-h.cos(r)*w,e=f+h.cos(r)*w,f=b+h.sin(r)*w,b=g-h.sin(r)*w,w=h.cos(t),t=h.sin(t),x=A-w*
u,B=f+t*u,c=A+w*u,k=f-t*u,C=e-w*u,D=b+t*u,w=e+w*u,t=b-t*u,!this.ring||this.ring.center.angle(this.a1)>this.ring.center.angle(this.a2)&&!(this.ring.center.angle(this.a1)-this.ring.center.angle(this.a2)>h.PI)||this.ring.center.angle(this.a1)-this.ring.center.angle(this.a2)<-h.PI?(a.moveTo(x,B),2===this.bondOrder?a.lineTo(C,D):j.contextHashTo(a,x,B,C,D,d.bonds_hashSpacing_2D,d.bonds_hashSpacing_2D)):(a.moveTo(c,k),2===this.bondOrder?a.lineTo(w,t):j.contextHashTo(a,c,k,w,t,d.bonds_hashSpacing_2D,d.bonds_hashSpacing_2D)),
a.stroke())):(u=this.a1.distance(this.a2)*d.bonds_saturationWidth_2D/2,t=this.a1.angle(this.a2)+h.PI/2,w=h.cos(t),t=h.sin(t),x=e-w*u,B=b+t*u,c=e+w*u,k=b-t*u,C=f+w*u,D=g-t*u,w=f-w*u,t=g+t*u,a.beginPath(),a.moveTo(x,B),a.lineTo(w,t),a.moveTo(c,k),2===this.bondOrder?a.lineTo(C,D):j.contextHashTo(a,c,k,C,D,d.bonds_hashSpacing_2D,d.bonds_hashSpacing_2D),a.stroke());break;case 3:u=this.a1.distance(this.a2)*d.bonds_saturationWidth_2D,t=this.a1.angle(this.a2)+h.PI/2,w=h.cos(t),t=h.sin(t),x=e-w*u,B=b+t*u,
c=e+w*u,k=b-t*u,C=f+w*u,D=g-t*u,w=f-w*u,t=g+t*u,a.beginPath(),a.moveTo(x,B),a.lineTo(w,t),a.moveTo(c,k),a.lineTo(C,D),a.moveTo(e,b),a.lineTo(f,g),a.stroke()}}};b.drawDecorations=function(a){if(this.isHover||this.isSelected){var d=2*h.PI,e=(this.a1.angleForStupidCanvasArcs(this.a2)+h.PI/2)%d;a.strokeStyle=this.isHover?"#885110":"#0060B2";a.lineWidth=1.2;a.beginPath();var f=(e+h.PI)%d,f=f%(2*h.PI);a.arc(this.a1.x,this.a1.y,7,e,f,!1);a.stroke();a.beginPath();e+=h.PI;f=(e+h.PI)%d;a.arc(this.a2.x,this.a2.y,
7,e,f,!1);a.stroke()}};b.drawLewisStyle=function(a,d,e,f,b,g){var j=this.a1.angle(this.a2),l=j+h.PI/2;b-=e;g-=f;b=h.sqrt(b*b+g*g)/(this.bondOrder+1);g=b*h.cos(j);j=-b*h.sin(j);e+=g;f+=j;for(b=0;b<this.bondOrder;b++){var r=d.atoms_lonePairSpread_2D/2,o=e-h.cos(l)*r,u=f+h.sin(l)*r,t=e+h.cos(l)*r,r=f-h.sin(l)*r;a.beginPath();a.arc(o-d.atoms_lonePairDiameter_2D/2,u-d.atoms_lonePairDiameter_2D/2,d.atoms_lonePairDiameter_2D,0,2*h.PI,!1);a.fill();a.beginPath();a.arc(t-d.atoms_lonePairDiameter_2D/2,r-d.atoms_lonePairDiameter_2D/
2,d.atoms_lonePairDiameter_2D,0,2*h.PI,!1);a.fill();e+=g;f+=j}};b.render=function(a,d,b){this.specs&&(d=this.specs);var f=this.a1.distance3D(this.a2);if(0!==f){var y=d.bonds_cylinderDiameter_3D/2,p=d.bonds_color,q,l=g.translate(a.modelViewMatrix,[this.a1.x,this.a1.y,this.a1.z],[]),r,o=[this.a2.x-this.a1.x,this.a2.y-this.a1.y,this.a2.z-this.a1.z],u=[0,1,0],t=0;this.a1.x===this.a2.x&&this.a1.z===this.a2.z?(u=[0,0,1],this.a2.y<this.a1.y&&(t=h.PI)):(t=j.vec3AngleFrom(u,o),u=e.cross(u,o,[]));var w=d.bonds_useJMOLColors,
x=d.bonds_usePYMOLColors;if(w||x)p=this.a1.getElementColor(w,x,p),q=this.a2.getElementColor(w,x,d.bonds_color),p!=q&&(r=g.translate(a.modelViewMatrix,[this.a2.x,this.a2.y,this.a2.z],[]));var w=[0],B;if(b){d.bonds_showBondOrders_3D&&1<this.bondOrder&&(w=[d.bonds_cylinderDiameter_3D],B=[0,0,1],b=g.inverse(a.rotationMatrix,[]),g.multiplyVec3(b,B),B=e.cross(o,B,[]),e.normalize(B));var y=1,c=d.bonds_pillSpacing_3D,o=d.bonds_pillHeight_3D;0==this.bondOrder&&(d.bonds_renderAsLines_3D?o=c:(o=d.bonds_pillDiameter_3D,
o<d.bonds_cylinderDiameter_3D&&(o/=2),y=o/2,f/=y,c/=y/2));b=o+c;var x=h.floor(f/b),k=(c+d.bonds_pillDiameter_3D+(f-b*x))/2,C=x;r&&(C=h.floor(x/2));f=0;for(c=w.length;f<c;f++){var D=g.set(l,[]);0!==w[f]&&g.translate(D,e.scale(B,w[f],[]));0!==t&&g.rotate(D,t,u);1!=y&&g.scale(D,[y,y,y]);p&&a.material.setDiffuseColor(p);g.translate(D,[0,k,0]);for(var G=0;G<C;G++)d.bonds_renderAsLines_3D?0==this.bondOrder?(a.setMatrixUniforms(D),a.drawArrays(a.POINTS,0,1)):(g.scale(D,[1,o,1]),a.setMatrixUniforms(D),a.drawArrays(a.LINES,
0,a.lineBuffer.vertexPositionBuffer.numItems),g.scale(D,[1,1/o,1])):(a.setMatrixUniforms(D),0==this.bondOrder?a.drawElements(a.TRIANGLES,a.sphereBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0):a.drawElements(a.TRIANGLES,a.pillBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0)),g.translate(D,[0,b,0]);if(r){var E,H;d.bonds_renderAsLines_3D?(E=o,E/=2,H=0):(E=2/3,H=(1-E)/2);0!=x%2&&(g.scale(D,[1,E,1]),a.setMatrixUniforms(D),d.bonds_renderAsLines_3D?0==this.bondOrder?a.drawArrays(a.POINTS,0,1):
a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems):0==this.bondOrder?a.drawElements(a.TRIANGLES,a.sphereBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0):a.drawElements(a.TRIANGLES,a.pillBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0),g.translate(D,[0,b*(1+H),0]),g.scale(D,[1,1/E,1]));g.set(r,D);0!==w[f]&&g.translate(D,e.scale(B,w[f],[]));g.rotate(D,t+h.PI,u);1!=y&&g.scale(D,[y,y,y]);q&&a.material.setDiffuseColor(q);g.translate(D,[0,k,0]);for(G=0;G<C;G++)d.bonds_renderAsLines_3D?
0==this.bondOrder?(a.setMatrixUniforms(D),a.drawArrays(a.POINTS,0,1)):(g.scale(D,[1,o,1]),a.setMatrixUniforms(D),a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems),g.scale(D,[1,1/o,1])):(a.setMatrixUniforms(D),0==this.bondOrder?a.drawElements(a.TRIANGLES,a.sphereBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0):a.drawElements(a.TRIANGLES,a.pillBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0)),g.translate(D,[0,b,0]);0!=x%2&&(g.scale(D,[1,E,1]),a.setMatrixUniforms(D),d.bonds_renderAsLines_3D?
0==this.bondOrder?a.drawArrays(a.POINTS,0,1):a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems):0==this.bondOrder?a.drawElements(a.TRIANGLES,a.sphereBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0):a.drawElements(a.TRIANGLES,a.pillBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0),g.translate(D,[0,b*(1+H),0]),g.scale(D,[1,1/E,1]))}}}else{if(d.bonds_showBondOrders_3D){switch(this.bondOrder){case 1.5:w=[-d.bonds_cylinderDiameter_3D];break;case 2:w=[-d.bonds_cylinderDiameter_3D,
d.bonds_cylinderDiameter_3D];break;case 3:w=[-1.2*d.bonds_cylinderDiameter_3D,0,1.2*d.bonds_cylinderDiameter_3D]}1<this.bondOrder&&(B=[0,0,1],b=g.inverse(a.rotationMatrix,[]),g.multiplyVec3(b,B),B=e.cross(o,B,[]),e.normalize(B))}else switch(this.bondOrder){case 0:y*=0.25;break;case 0.5:case 1.5:y*=0.5}r&&(f/=2);y=[y,f,y];f=0;for(c=w.length;f<c;f++)D=g.set(l,[]),0!==w[f]&&g.translate(D,e.scale(B,w[f],[])),0!==t&&g.rotate(D,t,u),g.scale(D,y),p&&a.material.setDiffuseColor(p),a.setMatrixUniforms(D),d.bonds_renderAsLines_3D?
a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems):a.drawArrays(a.TRIANGLE_STRIP,0,a.cylinderBuffer.vertexPositionBuffer.numItems),r&&(g.set(r,D),0!==w[f]&&g.translate(D,e.scale(B,w[f],[])),g.rotate(D,t+h.PI,u),g.scale(D,y),q&&a.material.setDiffuseColor(q),a.setMatrixUniforms(D),d.bonds_renderAsLines_3D?a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems):a.drawArrays(a.TRIANGLE_STRIP,0,a.cylinderBuffer.vertexPositionBuffer.numItems))}}};b.renderHighlight=function(a,
d){if(this.isSelected||this.isHover){this.specs&&(d=this.specs);this.specs&&(d=this.specs);var b=this.a1.distance3D(this.a2);if(0!==b){var f=d.bonds_cylinderDiameter_3D/1.2,y=g.translate(a.modelViewMatrix,[this.a1.x,this.a1.y,this.a1.z],[]),p=[this.a2.x-this.a1.x,this.a2.y-this.a1.y,this.a2.z-this.a1.z],q=[0,1,0],l=0;this.a1.x===this.a2.x&&this.a1.z===this.a2.z?(p=[0,0,1],this.a2.y<this.a1.y&&(l=h.PI)):(l=j.vec3AngleFrom(q,p),p=e.cross(q,p,[]));b=[f,b,f];0!==l&&g.rotate(y,l,p);g.scale(y,b);a.setMatrixUniforms(y);
a.material.setDiffuseColor(this.isHover?"#885110":"#0060B2");a.drawArrays(a.TRIANGLE_STRIP,0,a.cylinderBuffer.vertexPositionBuffer.numItems)}}};b.renderPicker=function(a,d){this.specs&&(d=this.specs);var b=this.a1.distance3D(this.a2);if(0!==b){var f=d.bonds_cylinderDiameter_3D/2,y=g.translate(a.modelViewMatrix,[this.a1.x,this.a1.y,this.a1.z],[]),p=[this.a2.x-this.a1.x,this.a2.y-this.a1.y,this.a2.z-this.a1.z],q=[0,1,0],l=0;this.a1.x===this.a2.x&&this.a1.z===this.a2.z?(q=[0,0,1],this.a2.y<this.a1.y&&
(l=h.PI)):(l=j.vec3AngleFrom(q,p),q=e.cross(q,p,[]));var o=[0],v;if(d.bonds_showBondOrders_3D)if(d.bonds_renderAsLines_3D){switch(this.bondOrder){case 1.5:case 2:o=[-d.bonds_cylinderDiameter_3D,d.bonds_cylinderDiameter_3D];break;case 3:o=[-1.2*d.bonds_cylinderDiameter_3D,0,1.2*d.bonds_cylinderDiameter_3D]}if(1<this.bondOrder){v=[0,0,1];var u=g.inverse(a.rotationMatrix,[]);g.multiplyVec3(u,v);v=e.cross(p,v,[]);e.normalize(v)}}else switch(this.bondOrder){case 1.5:case 2:f*=3;break;case 3:f*=3.4}else switch(this.bondOrder){case 0:f*=
0.25;break;case 0.5:case 1.5:f*=0.5}b=[f,b,f];f=0;for(p=o.length;f<p;f++)u=g.set(y,[]),0!==o[f]&&g.translate(u,e.scale(v,o[f],[])),0!==l&&g.rotate(u,l,q),g.scale(u,b),a.setMatrixUniforms(u),d.bonds_renderAsLines_3D?a.drawArrays(a.LINES,0,a.lineBuffer.vertexPositionBuffer.numItems):a.drawArrays(a.TRIANGLE_STRIP,0,a.cylinderBuffer.vertexPositionBuffer.numItems)}}})(ChemDoodle.ELEMENT,ChemDoodle.extensions,ChemDoodle.structures,ChemDoodle.math,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3);
(function(b,j){b.Ring=function(){this.atoms=[];this.bonds=[]};var o=b.Ring.prototype;o.center=void 0;o.setupBonds=function(){for(var b=0,h=this.bonds.length;b<h;b++)this.bonds[b].ring=this;this.center=this.getCenter()};o.getCenter=function(){for(var l=Infinity,h=Infinity,g=-Infinity,e=-Infinity,a=0,d=this.atoms.length;a<d;a++)l=j.min(this.atoms[a].x,l),h=j.min(this.atoms[a].y,h),g=j.max(this.atoms[a].x,g),e=j.max(this.atoms[a].y,e);return new b.Point((g+l)/2,(e+h)/2)}})(ChemDoodle.structures,Math);
(function(b,j,o,l,h){o.Molecule=function(){this.atoms=[];this.bonds=[];this.rings=[]};var g=o.Molecule.prototype;g.findRings=!0;g.draw=function(e,a){this.specs&&(a=this.specs);if(a.atoms_display&&!a.atoms_circles_2D)for(var d=0,b=this.atoms.length;d<b;d++)this.atoms[d].draw(e,a);if(a.bonds_display){d=0;for(b=this.bonds.length;d<b;d++)this.bonds[d].draw(e,a)}if(a.atoms_display){d=0;for(b=this.atoms.length;d<b;d++){var f=this.atoms[d];a.atoms_circles_2D&&f.draw(e,a);f.query&&f.query.draw(e,a,f)}}};
g.render=function(e,a){this.specs&&(a=this.specs);var d=0<this.atoms.length&&void 0!==this.atoms[0].hetatm;if(d){if(a.macro_displayBonds){0<this.bonds.length&&(a.bonds_renderAsLines_3D&&!this.residueSpecs||this.residueSpecs&&this.residueSpecs.bonds_renderAsLines_3D?(e.lineWidth(this.residueSpecs?this.residueSpecs.bonds_width_2D:a.bonds_width_2D),e.lineBuffer.bindBuffers(e)):e.cylinderBuffer.bindBuffers(e),e.material.setTempColors(a.bonds_materialAmbientColor_3D,void 0,a.bonds_materialSpecularColor_3D,
a.bonds_materialShininess_3D));for(var b=0,f=this.bonds.length;b<f;b++){var g=this.bonds[b];if(!g.a1.hetatm&&(-1===a.macro_atomToLigandDistance||void 0!==g.a1.closestDistance&&a.macro_atomToLigandDistance>=g.a1.closestDistance&&a.macro_atomToLigandDistance>=g.a2.closestDistance))g.render(e,this.residueSpecs?this.residueSpecs:a)}}if(a.macro_displayAtoms){0<this.atoms.length&&(e.sphereBuffer.bindBuffers(e),e.material.setTempColors(a.atoms_materialAmbientColor_3D,void 0,a.atoms_materialSpecularColor_3D,
a.atoms_materialShininess_3D));b=0;for(f=this.atoms.length;b<f;b++)if(g=this.atoms[b],!g.hetatm&&(-1===a.macro_atomToLigandDistance||void 0!==g.closestDistance&&a.macro_atomToLigandDistance>=g.closestDistance))g.render(e,this.residueSpecs?this.residueSpecs:a)}}if(a.bonds_display){var h=[],q=[];0<this.bonds.length&&(a.bonds_renderAsLines_3D?(e.lineWidth(a.bonds_width_2D),e.lineBuffer.bindBuffers(e)):e.cylinderBuffer.bindBuffers(e),e.material.setTempColors(a.bonds_materialAmbientColor_3D,void 0,a.bonds_materialSpecularColor_3D,
a.bonds_materialShininess_3D));b=0;for(f=this.bonds.length;b<f;b++)if(g=this.bonds[b],!d||g.a1.hetatm)a.bonds_showBondOrders_3D?0==g.bondOrder?q.push(g):0.5==g.bondOrder?h.push(g):(1.5==g.bondOrder&&h.push(g),g.render(e,a)):g.render(e,a);if(0<h.length){a.bonds_renderAsLines_3D||e.pillBuffer.bindBuffers(e);b=0;for(f=h.length;b<f;b++)h[b].render(e,a,!0)}if(0<q.length){a.bonds_renderAsLines_3D||e.sphereBuffer.bindBuffers(e);b=0;for(f=q.length;b<f;b++)q[b].render(e,a,!0)}}if(a.atoms_display){b=0;for(f=
this.atoms.length;b<f;b++)g=this.atoms[b],g.bondNumber=0,g.renderAsStar=!1;b=0;for(f=this.bonds.length;b<f;b++)g=this.bonds[b],g.a1.bondNumber++,g.a2.bondNumber++;0<this.atoms.length&&(e.sphereBuffer.bindBuffers(e),e.material.setTempColors(a.atoms_materialAmbientColor_3D,void 0,a.atoms_materialSpecularColor_3D,a.atoms_materialShininess_3D));h=[];b=0;for(f=this.atoms.length;b<f;b++)if(g=this.atoms[b],!d||g.hetatm&&(a.macro_showWater||!g.isWater))a.atoms_nonBondedAsStars_3D&&0===g.bondNumber?(g.renderAsStar=
!0,h.push(g)):g.render(e,a);if(0<h.length){e.starBuffer.bindBuffers(e);b=0;for(f=h.length;b<f;b++)h[b].render(e,a)}}if(this.chains){e.setMatrixUniforms(e.modelViewMatrix);if(a.proteins_displayRibbon){e.material.setTempColors(a.proteins_materialAmbientColor_3D,void 0,a.proteins_materialSpecularColor_3D,a.proteins_materialShininess_3D);g=a.proteins_ribbonCartoonize?this.cartoons:this.ribbons;d=0;for(h=g.length;d<h;d++)if(q=g[d],"none"!==a.proteins_residueColor){q.front.bindBuffers(e);for(var A="rainbow"===
a.proteins_residueColor,b=0,f=q.front.segments.length;b<f;b++)A&&e.material.setDiffuseColor(j.rainbowAt(b,f,a.macro_rainbowColors)),q.front.segments[b].render(e,a);q.back.bindBuffers(e);b=0;for(f=q.back.segments.length;b<f;b++)A&&e.material.setDiffuseColor(j.rainbowAt(b,f,a.macro_rainbowColors)),q.back.segments[b].render(e,a)}else q.front.render(e,a),q.back.render(e,a)}if(a.proteins_displayPipePlank){d=0;for(h=this.pipePlanks.length;d<h;d++)this.pipePlanks[d].render(e,a)}if(a.proteins_displayBackbone){if(!this.alphaCarbonTrace){this.alphaCarbonTrace=
{nodes:[],edges:[]};d=0;for(h=this.chains.length;d<h;d++)if(q=this.chains[d],!(2<q.length&&l[q[2].name]&&"#BEA06E"===l[q[2].name].aminoColor)&&0<q.length){b=0;for(f=q.length-2;b<f;b++)g=q[b].cp1,g.chainColor=q.chainColor,this.alphaCarbonTrace.nodes.push(g),g=new o.Bond(q[b].cp1,q[b+1].cp1),g.residueName=q[b].name,g.chainColor=q.chainColor,this.alphaCarbonTrace.edges.push(g),b===q.length-3&&(g=q[b+1].cp1,g.chainColor=q.chainColor,this.alphaCarbonTrace.nodes.push(g))}}if(0<this.alphaCarbonTrace.nodes.length){d=
new o.VisualSpecifications;d.atoms_display=!0;d.bonds_display=!0;d.atoms_sphereDiameter_3D=a.proteins_backboneThickness;d.bonds_cylinderDiameter_3D=a.proteins_backboneThickness;d.bonds_useJMOLColors=!1;d.atoms_color=a.proteins_backboneColor;d.bonds_color=a.proteins_backboneColor;d.atoms_useVDWDiameters_3D=!1;e.material.setTempColors(a.proteins_materialAmbientColor_3D,void 0,a.proteins_materialSpecularColor_3D,a.proteins_materialShininess_3D);e.material.setDiffuseColor(a.proteins_backboneColor);b=
0;for(f=this.alphaCarbonTrace.nodes.length;b<f;b++)g=this.alphaCarbonTrace.nodes[b],a.macro_colorByChain&&(d.atoms_color=g.chainColor),e.sphereBuffer.bindBuffers(e),g.render(e,d);b=0;for(f=this.alphaCarbonTrace.edges.length;b<f;b++){var g=this.alphaCarbonTrace.edges[b],r,h=l[g.residueName]?l[g.residueName]:l["*"];a.macro_colorByChain?r=g.chainColor:"shapely"===a.proteins_residueColor?r=h.shapelyColor:"amino"===a.proteins_residueColor?r=h.aminoColor:"polarity"===a.proteins_residueColor?r=h.polar?"#C10000":
"#FFFFFF":"acidity"===a.proteins_residueColor?r=1===h.acidity?"#0000FF":-1===h.acidity?"#FF0000":h.polar?"#FFFFFF":"#773300":"rainbow"===a.proteins_residueColor&&(r=j.rainbowAt(b,f,a.macro_rainbowColors));r&&(d.bonds_color=r);e.cylinderBuffer.bindBuffers(e);g.render(e,d)}}}if(a.nucleics_display){e.material.setTempColors(a.nucleics_materialAmbientColor_3D,void 0,a.nucleics_materialSpecularColor_3D,a.nucleics_materialShininess_3D);d=0;for(h=this.tubes.length;d<h;d++)e.setMatrixUniforms(e.modelViewMatrix),
q=this.tubes[d],q.render(e,a)}}if(a.atoms_display){r=!1;b=0;for(f=this.atoms.length;b<f;b++)if(g=this.atoms[b],g.isHover||g.isSelected){r=!0;break}if(!r){b=0;for(f=this.bonds.length;b<f;b++)if(g=this.bonds[b],g.isHover||g.isSelected){r=!0;break}}if(r){e.sphereBuffer.bindBuffers(e);e.blendFunc(e.SRC_ALPHA,e.ONE);e.material.setTempColors(a.atoms_materialAmbientColor_3D,void 0,"#000000",0);e.enable(e.BLEND);e.depthMask(!1);e.material.setAlpha(0.4);e.sphereBuffer.bindBuffers(e);b=0;for(f=this.atoms.length;b<
f;b++)g=this.atoms[b],(g.isHover||g.isSelected)&&g.renderHighlight(e,a);e.cylinderBuffer.bindBuffers(e);b=0;for(f=this.bonds.length;b<f;b++)g=this.bonds[b],(g.isHover||g.isSelected)&&g.renderHighlight(e,a);e.depthMask(!0);e.disable(e.BLEND);e.blendFuncSeparate(e.SRC_ALPHA,e.ONE_MINUS_SRC_ALPHA,e.ONE,e.ONE_MINUS_SRC_ALPHA)}}this.surface&&a.surfaces_display&&(e.setMatrixUniforms(e.modelViewMatrix),this.surface.bindBuffers(e),e.material.setTempColors(a.surfaces_materialAmbientColor_3D,a.surfaces_color,
a.surfaces_materialSpecularColor_3D,a.surfaces_materialShininess_3D),"Dot"===a.surfaces_style?e.drawArrays(e.POINTS,0,this.surface.vertexPositionBuffer.numItems):e.drawElements(e.TRIANGLES,this.surface.vertexIndexBuffer.numItems,e.UNSIGNED_SHORT,0))};g.renderPickFrame=function(e,a,d,b,f){this.specs&&(a=this.specs);var g=0<this.atoms.length&&void 0!==this.atoms[0].hetatm;if(f&&a.bonds_display){0<this.bonds.length&&(a.bonds_renderAsLines_3D?(e.lineWidth(a.bonds_width_2D),e.lineBuffer.bindBuffers(e)):
e.cylinderBuffer.bindBuffers(e));f=0;for(var h=this.bonds.length;f<h;f++){var q=this.bonds[f];if(!g||q.a1.hetatm)e.material.setDiffuseColor(j.idx2color(d.length)),q.renderPicker(e,a),d.push(q)}}if(b&&a.atoms_display){f=0;for(h=this.atoms.length;f<h;f++)b=this.atoms[f],b.bondNumber=0,b.renderAsStar=!1;f=0;for(h=this.bonds.length;f<h;f++)q=this.bonds[f],q.a1.bondNumber++,q.a2.bondNumber++;0<this.atoms.length&&e.sphereBuffer.bindBuffers(e);q=[];f=0;for(h=this.atoms.length;f<h;f++)if(b=this.atoms[f],
!g||b.hetatm&&(a.macro_showWater||!b.isWater))a.atoms_nonBondedAsStars_3D&&0===b.bondNumber?(b.renderAsStar=!0,q.push(b)):(e.material.setDiffuseColor(j.idx2color(d.length)),b.render(e,a,!0),d.push(b));if(0<q.length){e.starBuffer.bindBuffers(e);f=0;for(h=q.length;f<h;f++)b=q[f],e.material.setDiffuseColor(j.idx2color(d.length)),b.render(e,a,!0),d.push(b)}}};g.getCenter3D=function(){if(1===this.atoms.length)return new o.Atom("C",this.atoms[0].x,this.atoms[0].y,this.atoms[0].z);var e=Infinity,a=Infinity,
d=Infinity,b=-Infinity,f=-Infinity,g=-Infinity;if(this.chains)for(var j=0,q=this.chains.length;j<q;j++)for(var l=this.chains[j],r=0,v=l.length;r<v;r++)var u=l[r],e=h.min(u.cp1.x,u.cp2.x,e),a=h.min(u.cp1.y,u.cp2.y,a),d=h.min(u.cp1.z,u.cp2.z,d),b=h.max(u.cp1.x,u.cp2.x,b),f=h.max(u.cp1.y,u.cp2.y,f),g=h.max(u.cp1.z,u.cp2.z,g);j=0;for(q=this.atoms.length;j<q;j++)e=h.min(this.atoms[j].x,e),a=h.min(this.atoms[j].y,a),d=h.min(this.atoms[j].z,d),b=h.max(this.atoms[j].x,b),f=h.max(this.atoms[j].y,f),g=h.max(this.atoms[j].z,
g);return new o.Atom("C",(b+e)/2,(f+a)/2,(g+d)/2)};g.getCenter=function(){if(1===this.atoms.length)return new o.Point(this.atoms[0].x,this.atoms[0].y);for(var e=Infinity,a=Infinity,d=-Infinity,b=-Infinity,f=0,g=this.atoms.length;f<g;f++)e=h.min(this.atoms[f].x,e),a=h.min(this.atoms[f].y,a),d=h.max(this.atoms[f].x,d),b=h.max(this.atoms[f].y,b);return new o.Point((d+e)/2,(b+a)/2)};g.getDimension=function(){if(1===this.atoms.length)return new o.Point(0,0);var e=Infinity,a=Infinity,d=-Infinity,b=-Infinity;
if(this.chains){for(var f=0,g=this.chains.length;f<g;f++)for(var j=this.chains[f],q=0,l=j.length;q<l;q++)var r=j[q],e=h.min(r.cp1.x,r.cp2.x,e),a=h.min(r.cp1.y,r.cp2.y,a),d=h.max(r.cp1.x,r.cp2.x,d),b=h.max(r.cp1.y,r.cp2.y,b);e-=30;a-=30;d+=30;b+=30}f=0;for(g=this.atoms.length;f<g;f++)e=h.min(this.atoms[f].x,e),a=h.min(this.atoms[f].y,a),d=h.max(this.atoms[f].x,d),b=h.max(this.atoms[f].y,b);return new o.Point(d-e,b-a)};g.check=function(e){if(e&&this.doChecks){if(this.findRings)if(this.bonds.length-
this.atoms.length!==this.fjNumCache){this.rings=(new b.informatics.SSSRFinder(this)).rings;for(var a=0,d=this.bonds.length;a<d;a++)this.bonds[a].ring=void 0;a=0;for(d=this.rings.length;a<d;a++)this.rings[a].setupBonds()}else{a=0;for(d=this.rings.length;a<d;a++){var g=this.rings[a];g.center=g.getCenter()}}a=0;for(d=this.atoms.length;a<d;a++)if(this.atoms[a].isLone=!1,"C"===this.atoms[a].label){for(var f=g=0,h=this.bonds.length;f<h;f++)(this.bonds[f].a1===this.atoms[a]||this.bonds[f].a2===this.atoms[a])&&
g++;0===g&&(this.atoms[a].isLone=!0)}g=!1;a=0;for(d=this.atoms.length;a<d;a++)0!==this.atoms[a].z&&(g=!0);g&&(this.sortAtomsByZ(),this.sortBondsByZ());this.setupMetaData();this.atomNumCache=this.atoms.length;this.bondNumCache=this.bonds.length;this.fjNumCache=this.bonds.length-this.atoms.length}this.doChecks=!e};g.getAngles=function(e){for(var a=[],d=0,b=this.bonds.length;d<b;d++)this.bonds[d].contains(e)&&a.push(e.angle(this.bonds[d].getNeighbor(e)));a.sort();return a};g.getCoordinationNumber=function(e){for(var a=
0,d=0,b=e.length;d<b;d++)a+=e[d].bondOrder;return a};g.getBonds=function(e){for(var a=[],d=0,b=this.bonds.length;d<b;d++)this.bonds[d].contains(e)&&a.push(this.bonds[d]);return a};g.sortAtomsByZ=function(){for(var e=1,a=this.atoms.length;e<a;e++)for(var d=e;0<d&&this.atoms[d].z<this.atoms[d-1].z;){var b=this.atoms[d];this.atoms[d]=this.atoms[d-1];this.atoms[d-1]=b;d--}};g.sortBondsByZ=function(){for(var e=1,a=this.bonds.length;e<a;e++)for(var d=e;0<d&&this.bonds[d].a1.z+this.bonds[d].a2.z<this.bonds[d-
1].a1.z+this.bonds[d-1].a2.z;){var b=this.bonds[d];this.bonds[d]=this.bonds[d-1];this.bonds[d-1]=b;d--}};g.setupMetaData=function(){for(var e=this.getCenter(),a=0,d=this.atoms.length;a<d;a++){var b=this.atoms[a];b.bonds=this.getBonds(b);b.angles=this.getAngles(b);b.isHidden=2===b.bonds.length&&h.abs(h.abs(b.angles[1]-b.angles[0])-h.PI)<h.PI/30&&b.bonds[0].bondOrder===b.bonds[1].bondOrder;var f=j.angleBetweenLargest(b.angles);b.angleOfLeastInterference=f.angle%(2*h.PI);b.largestAngle=f.largest;b.coordinationNumber=
this.getCoordinationNumber(b.bonds);b.bondNumber=b.bonds.length;b.molCenter=e}a=0;for(d=this.bonds.length;a<d;a++)this.bonds[a].molCenter=e};g.scaleToAverageBondLength=function(e){var a=this.getAverageBondLength();if(0!==a){e/=a;for(var a=0,d=this.atoms.length;a<d;a++)this.atoms[a].x*=e,this.atoms[a].y*=e}};g.getAverageBondLength=function(){if(0===this.bonds.length)return 0;for(var e=0,a=0,d=this.bonds.length;a<d;a++)e+=this.bonds[a].getLength();return e/=this.bonds.length};g.getBounds=function(){for(var e=
new j.Bounds,a=0,d=this.atoms.length;a<d;a++)e.expand(this.atoms[a].getBounds());if(this.chains){a=0;for(d=this.chains.length;a<d;a++)for(var b=this.chains[a],f=0,g=b.length;f<g;f++){var h=b[f];e.expand(h.cp1.x,h.cp1.y);e.expand(h.cp2.x,h.cp2.y)}e.minX-=30;e.minY-=30;e.maxX+=30;e.maxY+=30}return e};g.getBounds3D=function(){for(var e=new j.Bounds,a=0,d=this.atoms.length;a<d;a++)e.expand(this.atoms[a].getBounds3D());if(this.chains){a=0;for(d=this.chains.length;a<d;a++)for(var b=this.chains[a],f=0,g=
b.length;f<g;f++){var h=b[f];e.expand3D(h.cp1.x,h.cp1.y,h.cp1.z);e.expand3D(h.cp2.x,h.cp2.y,h.cp2.z)}}return e}})(ChemDoodle,ChemDoodle.math,ChemDoodle.structures,ChemDoodle.RESIDUE,Math);
(function(b,j,o,l){var h,g=-1;b.Residue=function(a){this.resSeq=a};var e=b.Residue.prototype;e.setup=function(a,d){this.horizontalResolution=d;var e=[a.x-this.cp1.x,a.y-this.cp1.y,a.z-this.cp1.z],f=l.cross(e,[this.cp2.x-this.cp1.x,this.cp2.y-this.cp1.y,this.cp2.z-this.cp1.z],[]);this.D=l.cross(f,e,[]);l.normalize(f);l.normalize(this.D);this.guidePointsSmall=[];this.guidePointsLarge=[];e=[(a.x+this.cp1.x)/2,(a.y+this.cp1.y)/2,(a.z+this.cp1.z)/2];this.helix&&(l.scale(f,1.5),l.add(e,f));this.guidePointsSmall[0]=
new b.Atom("",e[0]-this.D[0]/2,e[1]-this.D[1]/2,e[2]-this.D[2]/2);for(f=1;f<d;f++)this.guidePointsSmall[f]=new b.Atom("",this.guidePointsSmall[0].x+this.D[0]*f/d,this.guidePointsSmall[0].y+this.D[1]*f/d,this.guidePointsSmall[0].z+this.D[2]*f/d);l.scale(this.D,4);this.guidePointsLarge[0]=new b.Atom("",e[0]-this.D[0]/2,e[1]-this.D[1]/2,e[2]-this.D[2]/2);for(f=1;f<d;f++)this.guidePointsLarge[f]=new b.Atom("",this.guidePointsLarge[0].x+this.D[0]*f/d,this.guidePointsLarge[0].y+this.D[1]*f/d,this.guidePointsLarge[0].z+
this.D[2]*f/d)};e.getGuidePointSet=function(a){if(0===a)return this.helix||this.sheet?this.guidePointsLarge:this.guidePointsSmall;if(1===a)return this.guidePointsSmall;if(2===a)return this.guidePointsLarge};e.computeLineSegments=function(a,d,e,f,b){this.setVerticalResolution(b);this.split=e.helix!==this.helix||e.sheet!==this.sheet;this.lineSegments=this.innerCompute(0,a,d,e,!1,b);f&&(this.lineSegmentsCartoon=this.innerCompute(this.helix||this.sheet?2:1,a,d,e,!0,b))};e.innerCompute=function(a,d,e,
f,g,p){var q=[],A=this.getGuidePointSet(a);d=d.getGuidePointSet(a);e=e.getGuidePointSet(a);for(var r=f.getGuidePointSet(a),v=0,u=A.length;v<u;v++){for(var t=o.multiply([d[v].x,d[v].y,d[v].z,1,e[v].x,e[v].y,e[v].z,1,A[v].x,A[v].y,A[v].z,1,r[v].x,r[v].y,r[v].z,1],h,[]),w=[],x=0;x<p;x++){for(a=3;0<a;a--)for(f=0;4>f;f++)t[4*a+f]+=t[4*(a-1)+f];w[x]=new b.Atom("",t[12]/t[15],t[13]/t[15],t[14]/t[15])}q[v]=w}if(g&&this.arrow)for(a=0;a<p;a++){g=1.5-1.3*a/p;A=j.floor(this.horizontalResolution/2);d=q[A];f=0;
for(e=q.length;f<e;f++)f!==A&&(r=d[a],v=q[f][a],u=[v.x-r.x,v.y-r.y,v.z-r.z],l.scale(u,g),v.x=r.x+u[0],v.y=r.y+u[1],v.z=r.z+u[2])}return q};e.setVerticalResolution=function(a){if(a!==g){var d=a*a,e=a*a*a;h=o.multiply([-1/6,0.5,-0.5,1/6,0.5,-1,0.5,0,-0.5,0,0.5,0,1/6,2/3,1/6,0],[6/e,0,0,0,6/e,2/d,0,0,1/e,1/d,1/a,0,0,0,0,1],[]);g=a}}})(ChemDoodle.structures,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3);
(function(b,j,o,l,h){j.Spectrum=function(){this.data=[];this.metadata=[];this.dataDisplay=[];this.memory={offsetTop:0,offsetLeft:0,offsetBottom:0,flipXAxis:!1,scale:1,width:0,height:0}};l=j.Spectrum.prototype;l.title=void 0;l.xUnit=void 0;l.yUnit=void 0;l.continuous=!0;l.integrationSensitivity=0.01;l.draw=function(g,e,a,d){this.specs&&(e=this.specs);var j=5,f=0,l=0;g.fillStyle=e.text_color;g.textAlign="center";g.textBaseline="alphabetic";g.font=b.getFontString(e.text_font_size,e.text_font_families);
this.xUnit&&(l+=e.text_font_size,g.fillText(this.xUnit,a/2,d-2));this.yUnit&&e.plots_showYAxis&&(f+=e.text_font_size,g.save(),g.translate(e.text_font_size,d/2),g.rotate(-h.PI/2),g.fillText(this.yUnit,0,0),g.restore());this.title&&(j+=e.text_font_size,g.fillText(this.title,a/2,e.text_font_size));g.lineCap="square";l+=5+e.text_font_size;e.plots_showYAxis&&(f+=5+g.measureText("1000").width);e.plots_showGrid&&(g.strokeStyle=e.plots_gridColor,g.lineWidth=e.plots_gridLineWidth,g.strokeRect(f,j,a-f,d-l-
j));g.textAlign="center";g.textBaseline="top";for(var p=this.maxX-this.minX,q=p/100,o=0.001;o<q||25<p/o;)o*=10;for(var r=0,v=e.plots_flipXAxis?a:0,p=h.round(this.minX/o)*o;p<=this.maxX;p+=o/2){var u=this.getTransformedX(p,e,a,f);if(u>f)if(g.strokeStyle="black",g.lineWidth=1,0===r%2){g.beginPath();g.moveTo(u,d-l);g.lineTo(u,d-l+2);g.stroke();for(q=p.toFixed(5);"0"===q.charAt(q.length-1);)q=q.substring(0,q.length-1);"."===q.charAt(q.length-1)&&(q=q.substring(0,q.length-1));var t=g.measureText(q).width;
e.plots_flipXAxis&&(t*=-1);var w=u-t/2;if(e.plots_flipXAxis?w<v:w>v)g.fillText(q,u,d-l+2),v=u+t/2;e.plots_showGrid&&(g.strokeStyle=e.plots_gridColor,g.lineWidth=e.plots_gridLineWidth,g.beginPath(),g.moveTo(u,d-l),g.lineTo(u,j),g.stroke())}else g.beginPath(),g.moveTo(u,d-l),g.lineTo(u,d-l+2),g.stroke();r++}if(e.plots_showYAxis||e.plots_showGrid){o=1/e.scale;g.textAlign="right";g.textBaseline="middle";for(p=0;10>=p;p++)if(q=o/10*p,r=j+(d-l-j)*(1-q*e.scale),e.plots_showGrid&&(g.strokeStyle=e.plots_gridColor,
g.lineWidth=e.plots_gridLineWidth,g.beginPath(),g.moveTo(f,r),g.lineTo(a,r),g.stroke()),e.plots_showYAxis){g.strokeStyle="black";g.lineWidth=1;g.beginPath();g.moveTo(f,r);g.lineTo(f-3,r);g.stroke();q*=100;v=h.max(0,3-h.floor(q).toString().length);q=q.toFixed(v);if(0<v)for(;"0"===q.charAt(q.length-1);)q=q.substring(0,q.length-1);"."===q.charAt(q.length-1)&&(q=q.substring(0,q.length-1));g.fillText(q,f-3,r)}}g.strokeStyle="black";g.lineWidth=1;g.beginPath();g.moveTo(a,d-l);g.lineTo(f,d-l);e.plots_showYAxis&&
g.lineTo(f,j);g.stroke();if(0<this.dataDisplay.length){g.textAlign="left";g.textBaseline="top";p=q=0;for(o=this.dataDisplay.length;p<o;p++)if(this.dataDisplay[p].value)g.fillText([this.dataDisplay[p].display,": ",this.dataDisplay[p].value].join(""),f+10,j+10+q*(e.text_font_size+5)),q++;else if(this.dataDisplay[p].tag){r=0;for(v=this.metadata.length;r<v;r++)if(b.stringStartsWith(this.metadata[r],this.dataDisplay[p].tag)){v=this.metadata[r];this.dataDisplay[p].display&&(v=this.metadata[r].indexOf("\x3d"),
v=[this.dataDisplay[p].display,": ",-1<v?this.metadata[r].substring(v+2):this.metadata[r]].join(""));g.fillText(v,f+10,j+10+q*(e.text_font_size+5));q++;break}}}this.drawPlot(g,e,a,d,j,f,l);this.memory.offsetTop=j;this.memory.offsetLeft=f;this.memory.offsetBottom=l;this.memory.flipXAxis=e.plots_flipXAxis;this.memory.scale=e.scale;this.memory.width=a;this.memory.height=d};l.drawPlot=function(b,e,a,d,n,f,l){this.specs&&(e=this.specs);b.strokeStyle=e.plots_color;b.lineWidth=e.plots_width;var p=[];b.save();
b.rect(f,n,a-f,d-l-n);b.clip();b.beginPath();if(this.continuous)for(var q=!1,o=0,r=!1,v=0,u=this.data.length;v<u;v++){var t=this.getTransformedX(this.data[v].x,e,a,f),w;v<u&&(!q&&this.data[v+1])&&(w=this.getTransformedX(this.data[v+1].x,e,a,f));if(t>=f&&t<a||void 0!==w&&w>=f&&w<a){var x=this.getTransformedY(this.data[v].y,e,d,l,n);e.plots_showIntegration&&h.abs(this.data[v].y)>this.integrationSensitivity&&p.push(new j.Point(this.data[v].x,this.data[v].y));q||(b.moveTo(t,x),q=!0);b.lineTo(t,x);o++;
0===o%1E3&&(b.stroke(),b.beginPath(),b.moveTo(t,x));if(r)break}else q&&(r=!0)}else{v=0;for(u=this.data.length;v<u;v++)t=this.getTransformedX(this.data[v].x,e,a,f),t>=f&&t<a&&(b.moveTo(t,d-l),b.lineTo(t,this.getTransformedY(this.data[v].y,e,d,l,n)))}b.stroke();if(e.plots_showIntegration&&1<p.length){b.strokeStyle=e.plots_integrationColor;b.lineWidth=e.plots_integrationLineWidth;b.beginPath();v=p[1].x>p[0].x;if(this.flipXAxis&&!v||!this.flipXAxis&&v){for(v=p.length-2;0<=v;v--)p[v].y+=p[v+1].y;q=p[0].y}else{v=
1;for(u=p.length;v<u;v++)p[v].y+=p[v-1].y;q=p[p.length-1].y}v=0;for(u=p.length;v<u;v++)t=this.getTransformedX(p[v].x,e,a,f),x=this.getTransformedY(p[v].y/e.scale/q,e,d,l,n),0===v?b.moveTo(t,x):b.lineTo(t,x);b.stroke()}b.restore()};l.getTransformedY=function(b,e,a,d,h){return h+(a-d-h)*(1-b*e.scale)};l.getInverseTransformedY=function(b){return 100*((1-(b-this.memory.offsetTop)/(this.memory.height-this.memory.offsetBottom-this.memory.offsetTop))/this.memory.scale)};l.getTransformedX=function(b,e,a,
d){b=d+(b-this.minX)/(this.maxX-this.minX)*(a-d);e.plots_flipXAxis&&(b=a+d-b);return b};l.getInverseTransformedX=function(b){this.memory.flipXAxis&&(b=this.memory.width+this.memory.offsetLeft-b);return(b-this.memory.offsetLeft)*(this.maxX-this.minX)/(this.memory.width-this.memory.offsetLeft)+this.minX};l.setup=function(){for(var b=Number.MAX_VALUE,e=Number.MIN_VALUE,a=Number.MIN_VALUE,d=0,j=this.data.length;d<j;d++)b=h.min(b,this.data[d].x),e=h.max(e,this.data[d].x),a=h.max(a,this.data[d].y);this.continuous?
(this.minX=b,this.maxX=e):(this.minX=b-1,this.maxX=e+1);d=0;for(j=this.data.length;d<j;d++)this.data[d].y/=a};l.zoom=function(b,e,a,d){b=this.getInverseTransformedX(b);e=this.getInverseTransformedX(e);this.minX=h.min(b,e);this.maxX=h.max(b,e);if(d){d=Number.MIN_VALUE;e=0;for(b=this.data.length;e<b;e++)o.isBetween(this.data[e].x,this.minX,this.maxX)&&(d=h.max(d,this.data[e].y));return 1/d}};l.translate=function(b,e){var a=b/(e-this.memory.offsetLeft)*(this.maxX-this.minX)*(this.memory.flipXAxis?1:
-1);this.minX+=a;this.maxX+=a};l.alertMetadata=function(){alert(this.metadata.join("\n"))};l.getInternalCoordinates=function(b,e){return new ChemDoodle.structures.Point(this.getInverseTransformedX(b),this.getInverseTransformedY(e))};l.getClosestPlotInternalCoordinates=function(b){var e=this.getInverseTransformedX(b-1);b=this.getInverseTransformedX(b+1);if(e>b){var a=e,e=b;b=a}for(var a=-1,d=-Infinity,h=!1,f=0,j=this.data.length;f<j;f++){var p=this.data[f];if(o.isBetween(p.x,e,b))p.y>d&&(h=!0,d=p.y,
a=f);else if(h)break}if(-1!==a)return p=this.data[a],new ChemDoodle.structures.Point(p.x,100*p.y)};l.getClosestPeakInternalCoordinates=function(b){var e=this.getInverseTransformedX(b);b=0;for(var a=Infinity,d=0,j=this.data.length;d<j;d++){var f=h.abs(this.data[d].x-e);if(f<=a)a=f,b=d;else break}for(var a=e=b,f=this.data[b].y,l=this.data[b].y,d=b+1,j=this.data.length;d<j;d++)if(this.data[d].y+0.05>l)l=this.data[d].y,a=d;else break;for(d=b-1;0<=d;d--)if(this.data[d].y+0.05>f)f=this.data[d].y,e=d;else break;
b=this.data[e-b>a-b?a:e];return new ChemDoodle.structures.Point(b.x,100*b.y)}})(ChemDoodle.extensions,ChemDoodle.structures,ChemDoodle.math,ChemDoodle.lib.jQuery,Math);
(function(b,j,o){j._Shape=function(){};j=j._Shape.prototype;j.drawDecorations=function(b,h){if(this.isHover)for(var g=this.getPoints(),e=0,a=g.length;e<a;e++){var d=g[e];this.drawAnchor(b,h,d,d===this.hoverPoint)}};j.getBounds=function(){for(var j=new b.Bounds,h=this.getPoints(),g=0,e=h.length;g<e;g++){var a=h[g];j.expand(a.x,a.y)}return j};j.drawAnchor=function(b,h,g,e){b.save();b.translate(g.x,g.y);b.rotate(o.PI/4);b.scale(1/h.scale,1/h.scale);b.beginPath();b.moveTo(-4,-4);b.lineTo(4,-4);b.lineTo(4,
4);b.lineTo(-4,4);b.closePath();b.fillStyle=e?"#885110":"white";b.fill();b.beginPath();b.moveTo(-4,-2);b.lineTo(-4,-4);b.lineTo(-2,-4);b.moveTo(2,-4);b.lineTo(4,-4);b.lineTo(4,-2);b.moveTo(4,2);b.lineTo(4,4);b.lineTo(2,4);b.moveTo(-2,4);b.lineTo(-4,4);b.lineTo(-4,2);b.moveTo(-4,-2);b.strokeStyle="rgba(0,0,0,.2)";b.lineWidth=5;b.stroke();b.strokeStyle="blue";b.lineWidth=1;b.stroke();b.restore()}})(ChemDoodle.math,ChemDoodle.structures.d2,Math);
(function(b,j,o,l,h){l.Bracket=function(b,e){this.p1=b?b:new o.Point;this.p2=e?e:new o.Point};l=l.Bracket.prototype=new l._Shape;l.charge=0;l.mult=0;l.repeat=0;l.draw=function(g,e){var a=h.min(this.p1.x,this.p2.x),d=h.max(this.p1.x,this.p2.x),j=h.min(this.p1.y,this.p2.y),f=h.max(this.p1.y,this.p2.y),l=f-j,p=l/10;g.beginPath();g.moveTo(a+p,j);g.lineTo(a,j);g.lineTo(a,f);g.lineTo(a+p,f);g.moveTo(d-p,f);g.lineTo(d,f);g.lineTo(d,j);g.lineTo(d-p,j);this.isLassoed&&(p=g.createLinearGradient(this.p1.x,this.p1.y,
this.p2.x,this.p2.y),p.addColorStop(0,"rgba(212, 99, 0, 0)"),p.addColorStop(0.5,"rgba(212, 99, 0, 0.8)"),p.addColorStop(1,"rgba(212, 99, 0, 0)"),g.lineWidth=e.shapes_lineWidth+5,g.strokeStyle=p,g.lineJoin="miter",g.lineCap="square",g.stroke());g.strokeStyle=e.shapes_color;g.lineWidth=e.shapes_lineWidth;g.lineJoin="miter";g.lineCap="butt";g.stroke();0!==this.charge&&(g.fillStyle=e.text_color,g.textAlign="left",g.textBaseline="alphabetic",g.font=b.getFontString(e.text_font_size,e.text_font_families),
p=this.charge.toFixed(0),p="1"===p?"+":"-1"===p?"\u2013":b.stringStartsWith(p,"-")?p.substring(1)+"\u2013":p+"+",g.fillText(p,d+5,j+5));0!==this.mult&&(g.fillStyle=e.text_color,g.textAlign="right",g.textBaseline="middle",g.font=b.getFontString(e.text_font_size,e.text_font_families),g.fillText(this.mult.toFixed(0),a-5,j+l/2));0!==this.repeat&&(g.fillStyle=e.text_color,g.textAlign="left",g.textBaseline="top",g.font=b.getFontString(e.text_font_size,e.text_font_families),p=this.repeat.toFixed(0),g.fillText(p,
d+5,f-5))};l.getPoints=function(){return[this.p1,this.p2]};l.isOver=function(b){return j.isBetween(b.x,this.p1.x,this.p2.x)&&j.isBetween(b.y,this.p1.y,this.p2.y)}})(ChemDoodle.extensions,ChemDoodle.math,ChemDoodle.structures,ChemDoodle.structures.d2,Math);
(function(b,j,o,l){o.Line=function(b,e){this.p1=b?b:new j.Point;this.p2=e?e:new j.Point};o.Line.ARROW_SYNTHETIC="synthetic";o.Line.ARROW_RETROSYNTHETIC="retrosynthetic";o.Line.ARROW_RESONANCE="resonance";o.Line.ARROW_EQUILIBRIUM="equilibrium";var h=o.Line.prototype=new o._Shape;h.arrowType=void 0;h.topText=void 0;h.bottomText=void 0;h.draw=function(b,e){if(this.isLassoed){var a=b.createLinearGradient(this.p1.x,this.p1.y,this.p2.x,this.p2.y);a.addColorStop(0,"rgba(212, 99, 0, 0)");a.addColorStop(0.5,
"rgba(212, 99, 0, 0.8)");a.addColorStop(1,"rgba(212, 99, 0, 0)");var d=2.5,h=this.p1.angle(this.p2)+l.PI/2,f=l.cos(h),h=l.sin(h),j=this.p1.x-f*d,p=this.p1.y+h*d,q=this.p1.x+f*d,A=this.p1.y-h*d,r=this.p2.x+f*d,v=this.p2.y-h*d,u=this.p2.x-f*d,t=this.p2.y+h*d;b.fillStyle=a;b.beginPath();b.moveTo(j,p);b.lineTo(q,A);b.lineTo(r,v);b.lineTo(u,t);b.closePath();b.fill()}b.strokeStyle=e.shapes_color;b.fillStyle=e.shapes_color;b.lineWidth=e.shapes_lineWidth;b.lineJoin="miter";b.lineCap="butt";if(this.p1.x!==
this.p2.x||this.p1.y!==this.p2.y){if(this.arrowType===o.Line.ARROW_RETROSYNTHETIC){var a=2*l.sqrt(2),d=e.shapes_arrowLength_2D/a,f=this.p1.angle(this.p2),h=f+l.PI/2,a=e.shapes_arrowLength_2D/a,w=l.cos(f),x=l.sin(f),f=l.cos(h),h=l.sin(h),j=this.p1.x-f*d,p=this.p1.y+h*d,q=this.p1.x+f*d,A=this.p1.y-h*d,r=this.p2.x+f*d-w*a,v=this.p2.y-h*d+x*a,u=this.p2.x-f*d-w*a,t=this.p2.y+h*d+x*a,B=this.p2.x+2*f*d-2*w*a,c=this.p2.y-2*h*d+2*x*a,k=this.p2.x-2*f*d-2*w*a,d=this.p2.y+2*h*d+2*x*a;b.beginPath();b.moveTo(q,
A);b.lineTo(r,v);b.moveTo(B,c);b.lineTo(this.p2.x,this.p2.y);b.lineTo(k,d);b.moveTo(u,t);b.lineTo(j,p)}else this.arrowType===o.Line.ARROW_EQUILIBRIUM?(a=2*l.sqrt(2),d=e.shapes_arrowLength_2D/a/2,f=this.p1.angle(this.p2),h=f+l.PI/2,a=2*e.shapes_arrowLength_2D/l.sqrt(3),w=l.cos(f),x=l.sin(f),f=l.cos(h),h=l.sin(h),j=this.p1.x-f*d,p=this.p1.y+h*d,q=this.p1.x+f*d,A=this.p1.y-h*d,r=this.p2.x+f*d,v=this.p2.y-h*d,u=this.p2.x-f*d,t=this.p2.y+h*d,b.beginPath(),b.moveTo(q,A),b.lineTo(r,v),b.moveTo(u,t),b.lineTo(j,
p),b.stroke(),q=r-0.8*w*a,A=v+0.8*x*a,B=r+f*e.shapes_arrowLength_2D/3-w*a,c=v-h*e.shapes_arrowLength_2D/3+x*a,b.beginPath(),b.moveTo(r,v),b.lineTo(B,c),b.lineTo(q,A),b.closePath(),b.fill(),b.stroke(),q=j+0.8*w*a,A=p-0.8*x*a,B=j-f*e.shapes_arrowLength_2D/3+w*a,c=p+h*e.shapes_arrowLength_2D/3-x*a,b.beginPath(),b.moveTo(j,p),b.lineTo(B,c),b.lineTo(q,A),b.closePath(),b.fill()):this.arrowType===o.Line.ARROW_SYNTHETIC?(f=this.p1.angle(this.p2),h=f+l.PI/2,a=2*e.shapes_arrowLength_2D/l.sqrt(3),w=l.cos(f),
x=l.sin(f),f=l.cos(h),h=l.sin(h),b.beginPath(),b.moveTo(this.p1.x,this.p1.y),b.lineTo(this.p2.x-w*a/2,this.p2.y+x*a/2),b.stroke(),q=this.p2.x-0.8*w*a,A=this.p2.y+0.8*x*a,B=this.p2.x+f*e.shapes_arrowLength_2D/3-w*a,c=this.p2.y-h*e.shapes_arrowLength_2D/3+x*a,k=this.p2.x-f*e.shapes_arrowLength_2D/3-w*a,d=this.p2.y+h*e.shapes_arrowLength_2D/3+x*a,b.beginPath(),b.moveTo(this.p2.x,this.p2.y),b.lineTo(k,d),b.lineTo(q,A),b.lineTo(B,c),b.closePath(),b.fill()):this.arrowType===o.Line.ARROW_RESONANCE?(f=this.p1.angle(this.p2),
h=f+l.PI/2,a=2*e.shapes_arrowLength_2D/l.sqrt(3),w=l.cos(f),x=l.sin(f),f=l.cos(h),h=l.sin(h),b.beginPath(),b.moveTo(this.p1.x+w*a/2,this.p1.y-x*a/2),b.lineTo(this.p2.x-w*a/2,this.p2.y+x*a/2),b.stroke(),q=this.p2.x-0.8*w*a,A=this.p2.y+0.8*x*a,B=this.p2.x+f*e.shapes_arrowLength_2D/3-w*a,c=this.p2.y-h*e.shapes_arrowLength_2D/3+x*a,k=this.p2.x-f*e.shapes_arrowLength_2D/3-w*a,d=this.p2.y+h*e.shapes_arrowLength_2D/3+x*a,b.beginPath(),b.moveTo(this.p2.x,this.p2.y),b.lineTo(k,d),b.lineTo(q,A),b.lineTo(B,
c),b.closePath(),b.fill(),b.stroke(),q=this.p1.x+0.8*w*a,A=this.p1.y-0.8*x*a,B=this.p1.x-f*e.shapes_arrowLength_2D/3+w*a,c=this.p1.y+h*e.shapes_arrowLength_2D/3-x*a,k=this.p1.x+f*e.shapes_arrowLength_2D/3+w*a,d=this.p1.y-h*e.shapes_arrowLength_2D/3-x*a,b.beginPath(),b.moveTo(this.p1.x,this.p1.y),b.lineTo(k,d),b.lineTo(q,A),b.lineTo(B,c),b.closePath(),b.fill()):(b.beginPath(),b.moveTo(this.p1.x,this.p1.y),b.lineTo(this.p2.x,this.p2.y));b.stroke();this.topText&&(b.textAlign="center",b.textBaseline=
"bottom",b.fillText(this.topText,(this.p1.x+this.p2.x)/2,this.p1.y-5));this.bottomText&&(b.textAlign="center",b.textBaseline="top",b.fillText(this.bottomText,(this.p1.x+this.p2.x)/2,this.p1.y+5))}};h.getPoints=function(){return[this.p1,this.p2]};h.isOver=function(g,e){var a=b.distanceFromPointToLineInclusive(g,this.p1,this.p2);return-1!==a&&a<e}})(ChemDoodle.math,ChemDoodle.structures,ChemDoodle.structures.d2,Math);
(function(b,j,o,l,h){var g=function(a){var b=[];if(a instanceof o.Atom)if(0===a.bondNumber)b.push(h.PI);else{if(a.angles){if(1===a.angles.length)b.push(a.angles[0]+h.PI);else{for(var f=1,e=a.angles.length;f<e;f++)b.push(a.angles[f-1]+(a.angles[f]-a.angles[f-1])/2);f=a.angles[a.angles.length-1];b.push(f+(a.angles[0]+2*h.PI-f)/2)}a.largestAngle>h.PI&&(b=[a.angleOfLeastInterference]);if(a.bonds){f=0;for(e=a.bonds.length;f<e;f++){var g=a.bonds[f];if(2===g.bondOrder&&(g=g.getNeighbor(a),"O"===g.label)){b=
[g.angle(a)];break}}}}}else a=a.a1.angle(a.a2),b.push(a+h.PI/2),b.push(a+3*h.PI/2);f=0;for(e=b.length;f<e;f++){for(;b[f]>2*h.PI;)b[f]-=2*h.PI;for(;0>b[f];)b[f]+=2*h.PI}return b},e=function(a,b){var e=3;if(a instanceof o.Atom){if(a.isLabelVisible(b)&&(e=8),0!==a.charge||0!==a.numRadical||0!==a.numLonePair)e=13}else a instanceof o.Point?e=0:1<a.bondOrder&&(e=5);return e},a=function(a,b,f,g,j,q,l,r,v,u){var t=q.angle(j),w=l.angle(r),x=h.cos(t),t=h.sin(t),B=e(f,b);j.x-=x*B;j.y+=t*B;B=w+h.PI/2;f=2*b.shapes_arrowLength_2D/
h.sqrt(3);var x=h.cos(w),t=h.sin(w),c=h.cos(B),k=h.sin(B);r.x-=5*x;r.y+=5*t;w=new o.Point(r.x,r.y);B=e(g,b)/3;w.x-=x*B;w.y+=t*B;r.x-=x*(0.8*f+B);r.y+=t*(0.8*f+B);g=w.x-0.8*x*f;var B=w.y+0.8*t*f,C=new o.Point(w.x+c*b.shapes_arrowLength_2D/3-x*f,w.y-k*b.shapes_arrowLength_2D/3+t*f);b=new o.Point(w.x-c*b.shapes_arrowLength_2D/3-x*f,w.y+k*b.shapes_arrowLength_2D/3+t*f);t=x=!0;1===v&&(C.distance(q)>b.distance(q)?t=!1:x=!1);a.beginPath();a.moveTo(w.x,w.y);t&&a.lineTo(b.x,b.y);a.lineTo(g,B);x&&a.lineTo(C.x,
C.y);a.closePath();a.fill();a.stroke();a.beginPath();a.moveTo(j.x,j.y);a.bezierCurveTo(q.x,q.y,l.x,l.y,r.x,r.y);a.stroke();u.push([j,q,l,r])};l.Pusher=function(a,b,e){this.o1=a;this.o2=b;this.numElectron=e?e:1};l=l.Pusher.prototype=new l._Shape;l.drawDecorations=function(a,b){if(this.isHover)for(var e=this.o1 instanceof o.Atom?new o.Point(this.o1.x,this.o1.y):this.o1.getCenter(),g=this.o2 instanceof o.Atom?new o.Point(this.o2.x,this.o2.y):this.o2.getCenter(),e=[e,g],g=0,h=e.length;g<h;g++){var j=
e[g];this.drawAnchor(a,b,j,j===this.hoverPoint)}};l.draw=function(d,e){if(this.o1&&this.o2){d.strokeStyle=e.shapes_color;d.fillStyle=e.shapes_color;d.lineWidth=e.shapes_lineWidth;d.lineJoin="miter";d.lineCap="butt";for(var f=this.o1 instanceof o.Atom?new o.Point(this.o1.x,this.o1.y):this.o1.getCenter(),j=this.o2 instanceof o.Atom?new o.Point(this.o2.x,this.o2.y):this.o2.getCenter(),p=g(this.o1),q=g(this.o2),l,r,v=Infinity,u=0,t=p.length;u<t;u++)for(var w=0,x=q.length;w<x;w++){var B=new o.Point(f.x+
35*h.cos(p[u]),f.y-35*h.sin(p[u])),c=new o.Point(j.x+35*h.cos(q[w]),j.y-35*h.sin(q[w])),k=B.distance(c);k<v&&(v=k,l=B,r=c)}this.caches=[];-1===this.numElectron?(u=f.distance(j)/2,q=f.angle(j),p=q+h.PI/2,t=h.cos(q),w=h.sin(q),q=new o.Point(f.x+(u-1)*t,f.y-(u-1)*w),v=new o.Point(q.x+35*h.cos(p+h.PI/6),q.y-35*h.sin(p+h.PI/6)),u=new o.Point(f.x+(u+1)*t,f.y-(u+1)*w),p=new o.Point(u.x+35*h.cos(p-h.PI/6),u.y-35*h.sin(p-h.PI/6)),a(d,e,this.o1,q,f,l,v,q,1,this.caches),a(d,e,this.o2,u,j,r,p,u,1,this.caches)):
(b.intersectLines(f.x,f.y,l.x,l.y,j.x,j.y,r.x,r.y)&&(p=l,l=r,r=p),p=l.angle(f),q=r.angle(j),v=h.max(p,q)-h.min(p,q),0.001>h.abs(v-h.PI)&&this.o1.molCenter===this.o2.molCenter&&(p+=h.PI/2,q-=h.PI/2,l.x=f.x+35*h.cos(p+h.PI),l.y=f.y-35*h.sin(p+h.PI),r.x=j.x+35*h.cos(q+h.PI),r.y=j.y-35*h.sin(q+h.PI)),a(d,e,this.o1,this.o2,f,l,r,j,this.numElectron,this.caches))}};l.getPoints=function(){return[]};l.isOver=function(a,b){for(var e=0,g=this.caches.length;e<g;e++)if(j.distanceFromCurve(a,this.caches[e]).distance<
b)return!0;return!1}})(ChemDoodle.math,ChemDoodle.math.jsBezier,ChemDoodle.structures,ChemDoodle.structures.d2,Math);
(function(b){b._Mesh=function(){};b=b._Mesh.prototype;b.storeData=function(b,o,l){this.positionData=b;this.normalData=o;this.indexData=l};b.setupBuffers=function(b){this.vertexPositionBuffer=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,this.vertexPositionBuffer);b.bufferData(b.ARRAY_BUFFER,new Float32Array(this.positionData),b.STATIC_DRAW);this.vertexPositionBuffer.itemSize=3;this.vertexPositionBuffer.numItems=this.positionData.length/3;this.vertexNormalBuffer=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,
this.vertexNormalBuffer);b.bufferData(b.ARRAY_BUFFER,new Float32Array(this.normalData),b.STATIC_DRAW);this.vertexNormalBuffer.itemSize=3;this.vertexNormalBuffer.numItems=this.normalData.length/3;this.indexData&&(this.vertexIndexBuffer=b.createBuffer(),b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,this.vertexIndexBuffer),b.bufferData(b.ELEMENT_ARRAY_BUFFER,new Uint16Array(this.indexData),b.STATIC_DRAW),this.vertexIndexBuffer.itemSize=1,this.vertexIndexBuffer.numItems=this.indexData.length);if(this.partitions)for(var o=
0,l=this.partitions.length;o<l;o++){var h=this.partitions[o],g=this.generateBuffers(b,h.positionData,h.normalData,h.indexData);h.vertexPositionBuffer=g[0];h.vertexNormalBuffer=g[1];h.vertexIndexBuffer=g[2]}};b.generateBuffers=function(b,o,l,h){var g=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,g);b.bufferData(b.ARRAY_BUFFER,new Float32Array(o),b.STATIC_DRAW);g.itemSize=3;g.numItems=o.length/3;o=b.createBuffer();b.bindBuffer(b.ARRAY_BUFFER,o);b.bufferData(b.ARRAY_BUFFER,new Float32Array(l),b.STATIC_DRAW);
o.itemSize=3;o.numItems=l.length/3;var e;h&&(e=b.createBuffer(),b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,e),b.bufferData(b.ELEMENT_ARRAY_BUFFER,new Uint16Array(h),b.STATIC_DRAW),e.itemSize=1,e.numItems=h.length);return[g,o,e]};b.bindBuffers=function(b){this.vertexPositionBuffer||this.setupBuffers(b);b.bindBuffer(b.ARRAY_BUFFER,this.vertexPositionBuffer);b.vertexAttribPointer(b.shader.vertexPositionAttribute,this.vertexPositionBuffer.itemSize,b.FLOAT,!1,0,0);b.bindBuffer(b.ARRAY_BUFFER,this.vertexNormalBuffer);
b.vertexAttribPointer(b.shader.vertexNormalAttribute,this.vertexNormalBuffer.itemSize,b.FLOAT,!1,0,0);this.vertexIndexBuffer&&b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,this.vertexIndexBuffer)}})(ChemDoodle.structures.d3,Math);
(function(b){b._Measurement=function(){};(b._Measurement.prototype=new b._Mesh).render=function(b,o){b.setMatrixUniforms(b.modelViewMatrix);o.measurement_update_3D&&(this.text=this.vertexPositionBuffer=void 0);this.vertexPositionBuffer||this.calculateData(o);this.bindBuffers(b);b.material.setDiffuseColor(o.shapes_color);b.lineWidth(o.shapes_lineWidth);b.drawElements(b.LINES,this.vertexIndexBuffer.numItems,b.UNSIGNED_SHORT,0);if(o.measurement_displayText_3D){this.text||(this.text=this.getText(o));
var l={position:[],texCoord:[],translation:[]};b.textImage.pushVertexData(this.text.value,this.text.pos,1,l);b.textMesh.storeData(b,l.position,l.texCoord,l.translation);b.enable(b.BLEND);b.depthMask(!1);b.enableVertexAttribArray(b.shader.vertexTexCoordAttribute);b.textImage.useTexture(b);b.textMesh.render(b);b.disableVertexAttribArray(b.shader.vertexTexCoordAttribute);b.disable(b.BLEND);b.depthMask(!0)}}})(ChemDoodle.structures.d3);
(function(b,j,o,l,h,g,e){o.Angle=function(a,d,b){this.a1=a;this.a2=d;this.a3=b};b=o.Angle.prototype=new o._Measurement;b.calculateData=function(a){var d=[],b=[],f=[],g=this.a2.distance3D(this.a1),p=this.a2.distance3D(this.a3);this.distUse=h.min(g,p)/2;this.vec1=e.normalize([this.a1.x-this.a2.x,this.a1.y-this.a2.y,this.a1.z-this.a2.z]);this.vec2=e.normalize([this.a3.x-this.a2.x,this.a3.y-this.a2.y,this.a3.z-this.a2.z]);this.angle=j.vec3AngleFrom(this.vec1,this.vec2);g=e.normalize(e.cross(this.vec1,
this.vec2,[]));g=e.normalize(e.cross(g,this.vec1,[]));a=a.measurement_angleBands_3D;for(p=0;p<=a;++p){var l=this.angle*p/a,o=e.scale(this.vec1,h.cos(l),[]),l=e.scale(g,h.sin(l),[]),o=e.scale(e.normalize(e.add(o,l,[])),this.distUse);d.push(this.a2.x+o[0],this.a2.y+o[1],this.a2.z+o[2]);b.push(0,0,0);p<a&&f.push(p,p+1)}this.storeData(d,b,f)};b.getText=function(){var a=e.scale(e.normalize(e.add(this.vec1,this.vec2,[])),this.distUse+0.3);return{pos:[this.a2.x+a[0],this.a2.y+a[1],this.a2.z+a[2]],value:[l.angleBounds(this.angle,
!0).toFixed(2)," \u00b0"].join("")}}})(ChemDoodle.ELEMENT,ChemDoodle.extensions,ChemDoodle.structures.d3,ChemDoodle.math,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3);
(function(b,j){b.Arrow=function(b,l){for(var h=[],g=[],e=0;e<=l;e++){var a=2*e*j.PI/l,d=j.sin(a),a=j.cos(a);g.push(0,0,-1,0,0,-1,a,d,0,a,d,0,0,0,-1,0,0,-1,a,d,1,a,d,1);h.push(0,0,0,b*a,b*d,0,b*a,b*d,0,b*a,b*d,2,b*a,b*d,2,2*b*a,2*b*d,2,2*b*a,2*b*d,2,0,0,3)}e=[];for(d=0;d<l;d++)for(var a=8*d,n=0;7>n;n++){var f=n+a,y=f+7+2;e.push(f,y,f+1,y,f,y-1)}this.storeData(h,g,e)};b.Arrow.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math);
(function(b){b.Box=function(b,o,l){b/=2;l/=2;var h=[],g=[];h.push(b,o,-l);h.push(b,o,-l);h.push(-b,o,-l);h.push(b,o,l);h.push(-b,o,l);h.push(-b,o,l);for(var e=6;e--;g.push(0,1,0));h.push(-b,o,l);h.push(-b,o,l);h.push(-b,0,l);h.push(b,o,l);h.push(b,0,l);h.push(b,0,l);for(e=6;e--;g.push(0,0,1));h.push(b,o,l);h.push(b,o,l);h.push(b,0,l);h.push(b,o,-l);h.push(b,0,-l);h.push(b,0,-l);for(e=6;e--;g.push(1,0,0));h.push(b,o,-l);h.push(b,o,-l);h.push(b,0,-l);h.push(-b,o,-l);h.push(-b,0,-l);h.push(-b,0,-l);
for(e=6;e--;g.push(0,0,-1));h.push(-b,o,-l);h.push(-b,o,-l);h.push(-b,0,-l);h.push(-b,o,l);h.push(-b,0,l);h.push(-b,0,l);for(e=6;e--;g.push(-1,0,0));h.push(-b,0,l);h.push(-b,0,l);h.push(-b,0,-l);h.push(b,0,l);h.push(b,0,-l);h.push(b,0,-l);for(e=6;e--;g.push(0,-1,0));this.storeData(h,g)};b.Box.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math);
(function(b,j,o){b.LineArrow=function(){this.storeData([0,0,-3,0.1,0,-2.8,0,0,-3,-0.1,0,-2.8,0,0,-3,0,0,3,0,0,3,0.1,0,2.8,0,0,3,-0.1,0,2.8],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0])};b.LineArrow.prototype=new b._Mesh;b.Compass=function(h,g){this.textImage=new b.TextImage;this.textImage.init(h);this.textImage.updateFont(h,g.text_font_size,g.text_font_families,g.text_font_bold,g.text_font_italic,g.text_font_stroke_3D);this.textMesh=new b.TextMesh;this.textMesh.init(h);var e=3/(g.compass_size_3D/
h.canvas.clientHeight),a=j.tan(g.projectionPerspectiveVerticalFieldOfView_3D/360*j.PI),d=e/a,n=j.max(d-e,0.1),f=h.canvas.clientWidth/h.canvas.clientHeight,l,p;g.projectionPerspective_3D?(p=n,l=o.frustum):(p=d,l=o.ortho);var q=2*(p/h.canvas.clientHeight)*a,a=a*p;p=-a;var A=f*p,f=f*a;if(0===g.compass_type_3D){var r=(-(h.canvas.clientWidth-g.compass_size_3D)/2+this.textImage.charHeight)*q,q=(-(h.canvas.clientHeight-g.compass_size_3D)/2+this.textImage.charHeight)*q,A=A-r,f=f-r;p-=q;a-=q}this.projectionMatrix=
l(A,f,p,a,n,d+e);this.translationMatrix=o.translate(o.identity([]),[0,0,-d]);e={position:[],texCoord:[],translation:[]};this.textImage.pushVertexData("X",[3.5,0,0],0,e);this.textImage.pushVertexData("Y",[0,3.5,0],0,e);this.textImage.pushVertexData("Z",[0,0,3.5],0,e);this.textMesh.storeData(h,e.position,e.texCoord,e.translation)};var l=b.Compass.prototype;l.renderArrow=function(b,g,e,a){b.material.setDiffuseColor(e);b.setMatrixUniforms(a);1===g?b.drawArrays(b.LINES,0,b.lineArrowBuffer.vertexPositionBuffer.numItems):
b.drawElements(b.TRIANGLES,b.arrowBuffer.vertexIndexBuffer.numItems,b.UNSIGNED_SHORT,0)};l.render=function(b,g){1===g.compass_type_3D?b.lineArrowBuffer.bindBuffers(b):b.arrowBuffer.bindBuffers(b);b.material.setTempColors(g.bonds_materialAmbientColor_3D,void 0,g.bonds_materialSpecularColor_3D,g.bonds_materialShininess_3D);var e=o.multiply(this.translationMatrix,b.rotationMatrix,[]),a=j.PI/2;b.fogging.setMode(0);this.renderArrow(b,g.compass_type_3D,g.compass_axisXColor_3D,o.rotateY(e,a,[]));this.renderArrow(b,
g.compass_type_3D,g.compass_axisYColor_3D,o.rotateX(e,-a,[]));this.renderArrow(b,g.compass_type_3D,g.compass_axisZColor_3D,e)};l.renderAxis=function(b){var g=o.multiply(this.translationMatrix,b.rotationMatrix,[]);b.setMatrixUniforms(g);this.textImage.useTexture(b);this.textMesh.render(b)}})(ChemDoodle.structures.d3,Math,ChemDoodle.lib.mat4);
(function(b,j){b.Cylinder=function(b,l,h,g){var e=[],a=[];if(g){for(g=0;g<=h;g++){var d=2*(g%h)*j.PI/h,n=j.cos(d),d=j.sin(d);a.push(0,-1,0);e.push(0,0,0);a.push(0,-1,0);e.push(b*n,0,b*d)}for(g=0;g<=h;g++)d=2*(g%h)*j.PI/h,n=j.cos(d),d=j.sin(d),a.push(n,0,d),e.push(b*n,0,b*d),a.push(n,0,d),e.push(b*n,l,b*d);for(g=0;g<=h;g++)d=2*(g%h)*j.PI/h,n=j.cos(d),d=j.sin(d),a.push(0,1,0),e.push(b*n,l,b*d),a.push(0,1,0),e.push(0,l,0)}else{for(g=0;g<h;g++)d=2*g*j.PI/h,n=j.cos(d),d=j.sin(d),a.push(n,0,d),e.push(b*
n,0,b*d),a.push(n,0,d),e.push(b*n,l,b*d);a.push(1,0,0);e.push(b,0,0);a.push(1,0,0);e.push(b,l,0)}this.storeData(e,a)};b.Cylinder.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math);
(function(b,j,o,l){j.Distance=function(b,g,e,a){this.a1=b;this.a2=g;this.node=e;this.offset=a?a:0};j=j.Distance.prototype=new j._Measurement;j.calculateData=function(h){var g=[this.a1.x,this.a1.y,this.a1.z,this.a2.x,this.a2.y,this.a2.z];this.node&&(this.move=this.offset+o.max(h.atoms_useVDWDiameters_3D?b[this.a1.label].vdWRadius*h.atoms_vdwMultiplier_3D:h.atoms_sphereDiameter_3D/2,h.atoms_useVDWDiameters_3D?b[this.a2.label].vdWRadius*h.atoms_vdwMultiplier_3D:h.atoms_sphereDiameter_3D/2),this.displacement=
[(this.a1.x+this.a2.x)/2-this.node.x,(this.a1.y+this.a2.y)/2-this.node.y,(this.a1.z+this.a2.z)/2-this.node.z],l.normalize(this.displacement),h=l.scale(this.displacement,this.move,[]),g[0]+=h[0],g[1]+=h[1],g[2]+=h[2],g[3]+=h[0],g[4]+=h[1],g[5]+=h[2]);this.storeData(g,[0,0,0,0,0,0],[0,1])};j.getText=function(){var b=this.a1.distance3D(this.a2),g=[(this.a1.x+this.a2.x)/2,(this.a1.y+this.a2.y)/2,(this.a1.z+this.a2.z)/2];if(this.node){var e=l.scale(this.displacement,this.move+0.1,[]);g[0]+=e[0];g[1]+=
e[1];g[2]+=e[2]}return{pos:g,value:[b.toFixed(2)," \u212b"].join("")}}})(ChemDoodle.ELEMENT,ChemDoodle.structures.d3,Math,ChemDoodle.lib.vec3);
(function(b,j){j.Fog=function(b){this.gl=b;this.mUL=b.getUniformLocation(b.program,"u_fog_mode");this.cUL=b.getUniformLocation(b.program,"u_fog_color");this.sUL=b.getUniformLocation(b.program,"u_fog_start");this.eUL=b.getUniformLocation(b.program,"u_fog_end");this.dUL=b.getUniformLocation(b.program,"u_fog_density")};var o=j.Fog.prototype;o.setTempParameter=function(j,h,g,e){if(!this.cCache||this.cCache!==j)this.cCache=j,j=b.getRGB(j,1),this.gl.uniform3f(this.cUL,j[0],j[1],j[2]);if(!this.sCache||this.sCache!==
h)this.sCache=h,this.gl.uniform1f(this.sUL,h);if(!this.eCache||this.eCache!==g)this.eCache=g,this.gl.uniform1f(this.eUL,g);if(!this.dCache||this.dCache!==e)this.dCache=e,this.gl.uniform1f(this.dUL,e)};o.setMode=function(b){if(!this.mCache||this.mCache!==b)this.mCache=b,this.gl.uniform1i(this.mUL,b)}})(ChemDoodle.math,ChemDoodle.structures.d3,ChemDoodle.lib.vec3);
(function(b,j){j.Label=function(){this.textImage=new j.TextImage};var o=j.Label.prototype;o.init=function(b,h){this.textImage.init(b);this.textImage.updateFont(b,h.atoms_font_size_2D,h.atoms_font_families_2D,h.atoms_font_bold_2D,h.atoms_font_italic_2D,h.text_font_stroke_3D)};o.updateVerticesBuffer=function(j,h,g){for(var e=0,a=h.length;e<a;e++){for(var d=h[e],n=d.labelMesh,f=d.atoms,y=this.textImage,p={position:[],texCoord:[],translation:[]},q=0<f.length&&void 0!=f[0].hetatm,o=0,r=f.length;o<r;o++){var v=
f[o],u=v.label,t=0.05;g.atoms_useVDWDiameters_3D?(u=b[u].vdWRadius*g.atoms_vdwMultiplier_3D,0===u&&(u=1),t+=u):g.atoms_sphereDiameter_3D&&(t+=1.5*(g.atoms_sphereDiameter_3D/2));if(q)if(v.hetatm){if(v.isWater&&!g.macro_showWaters)continue}else if(!g.macro_displayAtoms)continue;y.pushVertexData(v.altLabel?v.altLabel:v.label,[v.x,v.y,v.z],t,p)}if((d=d.chains)&&(g.proteins_displayRibbon||g.proteins_displayBackbone)){o=0;for(r=d.length;o<r;o++){f=d[o];q=0;for(t=f.length;q<t;q++)u=f[q],u.name&&(v=u.cp1,
y.pushVertexData(u.name,[v.x,v.y,v.z],2,p))}}n.storeData(j,p.position,p.texCoord,p.translation,p.zDepth)}};o.render=function(b,h,g){b.setMatrixUniforms(b.modelViewMatrix);this.textImage.useTexture(b);h=0;for(var e=g.length;h<e;h++)g[h].labelMesh&&g[h].labelMesh.render(b)}})(ChemDoodle.ELEMENT,ChemDoodle.structures.d3);
(function(b,j){b.Sphere=function(b,l,h){for(var g=[],e=[],a=0;a<=l;a++)for(var d=a*j.PI/l,n=j.sin(d),f=j.cos(d),d=0;d<=h;d++){var y=2*d*j.PI/h,p=j.sin(y),y=j.cos(y)*n,q=f,p=p*n;e.push(y,q,p);g.push(b*y,b*q,b*p)}b=[];h+=1;for(a=0;a<l;a++)for(d=0;d<h;d++)n=a*h+d%h,f=n+h,b.push(n,n+1,f),d<h-1&&b.push(f,n+1,f+1);this.storeData(g,e,b)};b.Sphere.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math);
(function(b,j,o,l){function h(b,a,d,g){this.entire=b;this.name=a;this.indexes=d;this.pi=g}var g=h.prototype;g.getColor=function(e){return e.macro_colorByChain?this.entire.chainColor:this.name?this.getResidueColor(b[this.name]?this.name:"*",e):this.helix?this.entire.front?e.proteins_ribbonCartoonHelixPrimaryColor:e.proteins_ribbonCartoonHelixSecondaryColor:this.sheet?e.proteins_ribbonCartoonSheetColor:this.entire.front?e.proteins_primaryColor:e.proteins_secondaryColor};g.getResidueColor=function(e,
a){var d=b[e];if("shapely"===a.proteins_residueColor)return d.shapelyColor;if("amino"===a.proteins_residueColor)return d.aminoColor;if("polarity"===a.proteins_residueColor){if(d.polar)return"#C10000"}else if("acidity"===a.proteins_residueColor){if(1===d.acidity)return"#0000FF";if(-1===d.acidity)return"#FF0000";if(!d.polar)return"#773300"}return"#FFFFFF"};g.render=function(b,a,d){if(this.entire.partitions&&this.pi!==this.entire.partitions.lastRender){var g=this.entire.partitions[this.pi];b.bindBuffer(b.ARRAY_BUFFER,
g.vertexPositionBuffer);b.vertexAttribPointer(b.shader.vertexPositionAttribute,g.vertexPositionBuffer.itemSize,b.FLOAT,!1,0,0);b.bindBuffer(b.ARRAY_BUFFER,g.vertexNormalBuffer);b.vertexAttribPointer(b.shader.vertexNormalAttribute,g.vertexNormalBuffer.itemSize,b.FLOAT,!1,0,0);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,g.vertexIndexBuffer);this.entire.partitions.lastRender=this.pi}this.vertexIndexBuffer||(this.vertexIndexBuffer=b.createBuffer(),b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,this.vertexIndexBuffer),b.bufferData(b.ELEMENT_ARRAY_BUFFER,
new Uint16Array(this.indexes),b.STATIC_DRAW),this.vertexIndexBuffer.itemSize=1,this.vertexIndexBuffer.numItems=this.indexes.length);b.bindBuffer(b.ELEMENT_ARRAY_BUFFER,this.vertexIndexBuffer);!d&&"rainbow"!==a.proteins_residueColor&&b.material.setDiffuseColor(this.getColor(a));b.drawElements(b.TRIANGLES,this.vertexIndexBuffer.numItems,b.UNSIGNED_SHORT,0)};j.Ribbon=function(b,a,d){var g=b[0].lineSegments.length,f=b[0].lineSegments[0].length;this.partitions=[];this.partitions.lastRender=0;var j;this.front=
0<a;for(var p=0,q=b.length;p<q;p++){if(!j||65E3<j.positionData.length)0<this.partitions.length&&p--,j={count:0,positionData:[],normalData:[]},this.partitions.push(j);var A=b[p];j.count++;for(var r=0;r<g;r++)for(var v=d?A.lineSegmentsCartoon[r]:A.lineSegments[r],u=0===r,t=!1,w=0;w<f;w++){var x=v[w],B=p,c=w+1;p===b.length-1&&w===f-1?c--:w===f-1&&(B++,c=0);var c=d?b[B].lineSegmentsCartoon[r][c]:b[B].lineSegments[r][c],B=!1,k=r+1;r===g-1&&(k-=2,B=!0);var k=d?A.lineSegmentsCartoon[k][w]:A.lineSegments[k][w],
c=[c.x-x.x,c.y-x.y,c.z-x.z],k=[k.x-x.x,k.y-x.y,k.z-x.z],C=l.cross(c,k,[]);0===w&&(l.normalize(c),l.scale(c,-1),j.normalData.push(c[0],c[1],c[2]),j.positionData.push(x.x,x.y,x.z));u||t?(l.normalize(k),l.scale(k,-1),j.normalData.push(k[0],k[1],k[2]),j.positionData.push(x.x,x.y,x.z),u&&w===f-1&&(u=!1,w=-1)):(l.normalize(C),(B&&!this.front||!B&&this.front)&&l.scale(C,-1),j.normalData.push(C[0],C[1],C[2]),l.scale(C,o.abs(a)),j.positionData.push(x.x+C[0],x.y+C[1],x.z+C[2]),r===g-1&&w===f-1&&(t=!0,w=-1));
if(-1===w||w===f-1)l.normalize(c),j.normalData.push(c[0],c[1],c[2]),j.positionData.push(x.x,x.y,x.z)}}g+=2;f+=2;this.segments=[];this.partitionSegments=[];a=0;for(A=this.partitions.length;a<A;a++){j=this.partitions[a];v=[];p=0;for(q=j.count-1;p<q;p++){for(var D=p,r=0;r<a;r++)D+=this.partitions[r].count-1;D=b[D];u=p*g*f;j=[];r=0;for(t=g-1;r<t;r++){x=u+r*f;for(w=0;w<f;w++)B=1,p===q?B=0:w===f-1&&(B=g*f-w),B=[x+w,x+f+w,x+f+w+B,x+w,x+w+B,x+f+w+B],w!==f-1&&(this.front?j.push(B[0],B[1],B[2],B[3],B[5],B[4]):
j.push(B[0],B[2],B[1],B[3],B[4],B[5])),w===f-2&&p<q&&(c=g*f-w,B[2]+=c,B[4]+=c,B[5]+=c),this.front?v.push(B[0],B[1],B[2],B[3],B[5],B[4]):v.push(B[0],B[2],B[1],B[3],B[4],B[5])}d&&D.split&&(r=new h(this,void 0,v,a),r.helix=D.helix,r.sheet=D.sheet,this.partitionSegments.push(r),v=[]);this.segments.push(new h(this,D.name,j,a))}r=new h(this,void 0,v,a);r.helix=D.helix;r.sheet=D.sheet;this.partitionSegments.push(r)}this.storeData(this.partitions[0].positionData,this.partitions[0].normalData);1===this.partitions.length&&
(this.partitions=void 0)};(j.Ribbon.prototype=new j._Mesh).render=function(b,a){this.bindBuffers(b);var d=a.macro_colorByChain?this.chainColor:void 0;d||(d=this.front?a.proteins_primaryColor:a.proteins_secondaryColor);b.material.setDiffuseColor(d);for(var d=0,g=this.partitionSegments.length;d<g;d++)this.partitionSegments[d].render(b,a,!a.proteins_ribbonCartoonize)}})(ChemDoodle.RESIDUE,ChemDoodle.structures.d3,Math,ChemDoodle.lib.vec3);
(function(b,j,o){j.Light=function(j,h,g){this.diffuseRGB=b.getRGB(j,1);this.specularRGB=b.getRGB(h,1);this.direction=g};j.Light.prototype.lightScene=function(b){b.uniform3f(b.getUniformLocation(b.program,"u_light_diffuse_color"),this.diffuseRGB[0],this.diffuseRGB[1],this.diffuseRGB[2]);b.uniform3f(b.getUniformLocation(b.program,"u_light_specular_color"),this.specularRGB[0],this.specularRGB[1],this.specularRGB[2]);var h=o.create(this.direction);o.normalize(h);o.negate(h);b.uniform3f(b.getUniformLocation(b.program,
"u_light_direction"),h[0],h[1],h[2]);var g=[0,0,0],h=[g[0]+h[0],g[1]+h[1],g[2]+h[2]],g=o.length(h);0===g?h=[0,0,1]:o.scale(h,1/g);b.uniform3f(b.getUniformLocation(b.program,"u_light_half_vector"),h[0],h[1],h[2])}})(ChemDoodle.math,ChemDoodle.structures.d3,ChemDoodle.lib.vec3);(function(b){b.Line=function(){this.storeData([0,0,0,0,1,0],[0,0,0,0,0,0])};b.Line.prototype=new b._Mesh})(ChemDoodle.structures.d3);
(function(b,j){j.Material=function(b){this.gl=b;this.aUL=b.getUniformLocation(b.program,"u_material_ambient_color");this.dUL=b.getUniformLocation(b.program,"u_material_diffuse_color");this.sUL=b.getUniformLocation(b.program,"u_material_specular_color");this.snUL=b.getUniformLocation(b.program,"u_material_shininess");this.alUL=b.getUniformLocation(b.program,"u_material_alpha")};var o=j.Material.prototype;o.setTempColors=function(j,h,g,e){if(!this.aCache||this.aCache!==j)this.aCache=j,j=b.getRGB(j,
1),this.gl.uniform3f(this.aUL,j[0],j[1],j[2]);if(h&&(!this.dCache||this.dCache!==h))this.dCache=h,j=b.getRGB(h,1),this.gl.uniform3f(this.dUL,j[0],j[1],j[2]);if(!this.sCache||this.sCache!==g)this.sCache=g,j=b.getRGB(g,1),this.gl.uniform3f(this.sUL,j[0],j[1],j[2]);if(!this.snCache||this.snCache!==e)this.snCache=e,this.gl.uniform1f(this.snUL,e);this.alCache=1;this.gl.uniform1f(this.alUL,1)};o.setDiffuseColor=function(j){if(!this.dCache||this.dCache!==j)this.dCache=j,j=b.getRGB(j,1),this.gl.uniform3f(this.dUL,
j[0],j[1],j[2])};o.setAlpha=function(b){if(!this.alCache||this.alCache!==b)this.alCache=b,this.gl.uniform1f(this.alUL,b)}})(ChemDoodle.math,ChemDoodle.structures.d3);
(function(b,j,o,l){j.MolecularSurface=function(h,g,e,a,d){function j(a,c,d,b){var e=a.index;if(a.contained)for(var e=-1,f=Infinity,g=0,h=c.length;g<h;g++)for(var p=c[g],n=0,k=p.length;n<k;n++){var q=p[n];if(!q.contained&&q.index!==d&&q.index!==b){var l=q.distance3D(a);l<f&&(e=q.index,f=l)}}return e}for(var f=[],y=[],p=[],q=[],A=0;A<=g;A++)for(var r=A*l.PI/g,v=l.sin(r),u=l.cos(r),r=0;r<=e;r++){var t=2*r*l.PI/e;q.push(l.cos(t)*v,u,l.sin(t)*v)}v=[];A=0;for(r=h.atoms.length;A<r;A++){for(var u=[],w=h.atoms[A],
x=o[w.label][d]+a,B=[],t=0,c=h.atoms.length;t<c;t++)if(t!==A){var k=h.atoms[t];k.index=t;w.distance3D(k)<x+o[k.label][d]+a&&B.push(k)}t=0;for(c=q.length;t<c;t+=3){for(var C=new b.Atom("C",w.x+x*q[t],w.y+x*q[t+1],w.z+x*q[t+2]),D=0,G=B.length;D<G;D++)if(k=B[D],C.distance3D(k)<o[k.label][d]+a){C.contained=!0;break}u.push(C)}v.push(u)}h=[];e++;for(A=0;A<g;A++)for(r=0;r<e;r++)d=A*e+r%e,a=d+e,h.push(d),h.push(a),h.push(d+1),r<e-1&&(h.push(a),h.push(a+1),h.push(d+1));A=D=0;for(r=v.length;A<r;A++){u=v[A];
t=0;for(c=u.length;t<c;t++)C=u[t],C.contained||(C.index=D,D++,f.push(C.x,C.y,C.z),y.push(q[3*t],q[3*t+1],q[3*t+2]));t=0;for(c=h.length;t<c;t+=3)d=u[h[t]],a=u[h[t+1]],C=u[h[t+2]],!d.contained&&(!a.contained&&!C.contained)&&p.push(d.index,a.index,C.index)}q=[];A=0;for(r=v.length;A<r;A++){u=v[A];t=0;for(c=h.length;t<c;t+=3){d=u[h[t]];a=u[h[t+1]];C=u[h[t+2]];B=[];D=0;for(G=v.length;D<G;D++)D!==A&&B.push(v[D]);if((!d.contained||!a.contained||!C.contained)&&(d.contained||a.contained||C.contained))if(g=
j(d,B,-1,-1),e=j(a,B,g,-1),B=j(C,B,g,e),-1!==g&&-1!==e&&-1!==B){a=!1;D=0;for(G=q.length;D<G;D+=3)if(d=q[D],C=q[D+1],w=q[D+2],x=e===d||e===C||e===w,k=B===d||B===C||B===w,(g===d||g===C||g===w)&&x&&k){a=!0;break}a||q.push(g,e,B)}}}p=p.concat(q);this.storeData(f,y,p)};j.MolecularSurface.prototype=new j._Mesh})(ChemDoodle.structures,ChemDoodle.structures.d3,ChemDoodle.ELEMENT,Math);
(function(b){b.Picker=function(){};b=b.Picker.prototype;b.init=function(b){this.framebuffer=b.createFramebuffer();var o=b.createTexture(),l=b.createRenderbuffer();b.bindTexture(b.TEXTURE_2D,o);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_MAG_FILTER,b.NEAREST);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_MIN_FILTER,b.NEAREST);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_WRAP_S,b.CLAMP_TO_EDGE);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_WRAP_T,b.CLAMP_TO_EDGE);b.bindRenderbuffer(b.RENDERBUFFER,l);b.bindFramebuffer(b.FRAMEBUFFER,
this.framebuffer);b.framebufferTexture2D(b.FRAMEBUFFER,b.COLOR_ATTACHMENT0,b.TEXTURE_2D,o,0);b.framebufferRenderbuffer(b.FRAMEBUFFER,b.DEPTH_ATTACHMENT,b.RENDERBUFFER,l);b.bindTexture(b.TEXTURE_2D,null);b.bindRenderbuffer(b.RENDERBUFFER,null);b.bindFramebuffer(b.FRAMEBUFFER,null)};b.setDimension=function(b,o,l){b.bindFramebuffer(b.FRAMEBUFFER,this.framebuffer);var h=b.getFramebufferAttachmentParameter(b.FRAMEBUFFER,b.DEPTH_ATTACHMENT,b.FRAMEBUFFER_ATTACHMENT_OBJECT_NAME);b.isRenderbuffer(h)&&(b.bindRenderbuffer(b.RENDERBUFFER,
h),b.renderbufferStorage(b.RENDERBUFFER,b.DEPTH_COMPONENT16,o,l),b.bindRenderbuffer(b.RENDERBUFFER,null));h=b.getFramebufferAttachmentParameter(b.FRAMEBUFFER,b.COLOR_ATTACHMENT0,b.FRAMEBUFFER_ATTACHMENT_OBJECT_NAME);b.isTexture(h)&&(b.bindTexture(b.TEXTURE_2D,h),b.texImage2D(b.TEXTURE_2D,0,b.RGBA,o,l,0,b.RGBA,b.UNSIGNED_BYTE,null),b.bindTexture(b.TEXTURE_2D,null));b.bindFramebuffer(b.FRAMEBUFFER,null)};b.pick=function(b,o,l,h,g,e,a){var d=void 0,n=b.getParameter(b.COLOR_CLEAR_VALUE);b.bindFramebuffer(b.FRAMEBUFFER,
this.framebuffer);b.clearColor(1,1,1,0);b.clear(b.COLOR_BUFFER_BIT|b.DEPTH_BUFFER_BIT);b.fogging.setMode(0);b.disableVertexAttribArray(b.shader.vertexNormalAttribute);var f=[];b.material.setAlpha(255);for(var y=0,p=o.length;y<p;y++)o[y].renderPickFrame(b,l,f,e,a);b.flush();o=new Uint8Array(4);b.readPixels(h-2,g+2,1,1,b.RGBA,b.UNSIGNED_BYTE,o);0<o[3]&&(d=f[o[2]|o[1]<<8|o[0]<<16]);b.enableVertexAttribArray(b.shader.vertexNormalAttribute);b.fogging.setMode(l.fog_mode_3D);b.bindFramebuffer(b.FRAMEBUFFER,
null);b.clearColor(n[0],n[1],n[2],n[3]);return d}})(ChemDoodle.structures.d3,ChemDoodle.math,document);
(function(b,j){b.Pill=function(b,l,h,g){var e=1,a=2*b;l-=a;0>l?(e=0,l+=a):l<a&&(e=l/a,l=a);for(var a=[],d=[],n=0;n<=h;n++)for(var f=n*j.PI/h,y=j.sin(f),p=j.cos(f)*e,f=0;f<=g;f++){var q=2*f*j.PI/g,A=j.sin(q),q=j.cos(q)*y,r=p,A=A*y;d.push(q,r,A);a.push(b*q,b*r+(n<h/2?l:0),b*A)}b=[];g+=1;for(n=0;n<h;n++)for(f=0;f<g;f++)l=n*g+f%g,e=l+g,b.push(l,l+1,e),f<g-1&&b.push(e,l+1,e+1);this.storeData(a,d,b)};b.Pill.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math);
(function(b,j,o,l,h,g,e){function a(a,d,b){var e=new o.Residue(-1);e.cp1=e.cp2=new o.Atom("",a,d,b);return e}function d(a,d){this.a1=a;this.a2=d}function n(a,d,b){this.a1=a;this.a2=d;this.vx=b}j=d.prototype;j.render=function(a,d){var j=this.a1,n=this.a2,l=1.001*j.distance3D(n),r=d.proteins_cylinderHelixDiameter/2,l=[r,l,r],r=g.translate(a.modelViewMatrix,[j.x,j.y,j.z],[]),o=[0,1,0],u=0;j.x===n.x&&j.z===n.z?(o=[0,0,1],n.y<j.y&&(u=h.PI)):(j=[n.x-j.x,n.y-j.y,n.z-j.z],u=b.vec3AngleFrom(o,j),o=e.cross(o,
j,[]));0!==u&&g.rotate(r,u,o);g.scale(r,l);a.setMatrixUniforms(r);a.drawArrays(a.TRIANGLE_STRIP,0,a.cylinderClosedBuffer.vertexPositionBuffer.numItems)};j=n.prototype;j.render=function(a,d){this.specs&&(d=this.specs);var b=1.001*this.a1.distance3D(this.a2),h=[this.a2.x-this.a1.x,this.a2.y-this.a1.y,this.a2.z-this.a1.z],j=e.cross(h,this.vx,[]),n=e.cross(j,h,[]);e.normalize(n);e.normalize(h);e.normalize(j);b=[d.proteins_plankSheetWidth,b,d.proteins_tubeThickness];h=g.multiply(a.modelViewMatrix,[n[0],
n[1],n[2],0,h[0],h[1],h[2],0,j[0],j[1],j[2],0,this.a1.x,this.a1.y,this.a1.z,1],[]);g.scale(h,b);a.setMatrixUniforms(h);a.drawArrays(a.TRIANGLE_STRIP,0,a.boxBuffer.vertexPositionBuffer.numItems)};l.PipePlank=function(b,g){this.tubes=[];this.helixCylinders=[];this.sheetPlanks=[];this.chainColor=b.chainColor;var j=[],q=[],A=[],r=[];if(1<b.length){var v=b[0],u=b[1];u.helix?A.push(v):u.sheet?r.push(v):q.push(v)}v=1;for(u=b.length-1;v<=u;v++){var t=b[v];if(t.helix){if(A.push(t),t.arrow){var w=e.create(),
x=e.create();if(2==A.length)w=[A[0].cp1.x,A[0].cp1.y,A[0].cp1.z],x=[A[1].cp1.x,A[1].cp1.y,A[1].cp1.z];else{3==A.length&&A.unshift(b[h.max(v-3,0)]);for(var B=[],c=[],k=1,C=A.length-1;k<C;k++){var D=[A[k].cp1.x,A[k].cp1.y,A[k].cp1.z],G=[A[k-1].cp1.x,A[k-1].cp1.y,A[k-1].cp1.z],E=[A[k+1].cp1.x,A[k+1].cp1.y,A[k+1].cp1.z];e.subtract(G,D);e.subtract(E,D);var H=e.scale(G,e.length(E),[]),G=e.scale(E,e.length(G),[]),H=e.normalize(e.add(H,G,[]));B.push(D);c.push(H)}A=[];k=0;for(C=B.length-1;k<C;k++){var G=B[k],
E=c[k],D=B[k+1],H=c[k+1],I=e.normalize(e.cross(E,H,[])),M=e.subtract(D,G,[]),J=e.dot(M,I),I=e.scale(I,J,[]),I=e.length(I),M=e.length(M),M=-(I*I-M*M)/(2*e.dot(e.subtract(G,D,[]),H)),G=e.add(G,e.scale(E,M,[]),[]),D=e.add(D,e.scale(H,M,[]),[]);A.push([G,D])}k=A[0][0];C=A[0][1];C=e.subtract(k,C,[]);e.add(k,C,w);k=A[A.length-1][1];C=A[A.length-1][0];C=e.subtract(k,C,[]);e.add(k,C,x)}k=new o.Atom("",w[0],w[1],w[2]);C=new o.Atom("",x[0],x[1],x[2]);this.helixCylinders.push(new d(k,C));A=[];C=e.subtract(w,
x,[]);e.normalize(C);e.scale(C,0.5);0<q.length&&(k=e.add(w,C,[]),B=q[q.length-1].cp1,B=e.subtract([B.x,B.y,B.z],k,[]),e.normalize(B),e.scale(B,0.5),e.add(k,B),B=new o.Residue(-1),B.cp1=B.cp2=new o.Atom("",k[0],k[1],k[2]),q.push(B),B=a(w[0],w[1],w[2]),q.push(B),j.push(q));q=[];v<u&&(B=a(x[0],x[1],x[2]),q.push(B),w=b[v+1],w.sheet?(q.push(t),q.push(t),j.push(q),q=[],r.push(t)):(e.scale(C,-1),k=e.add(x,C,[]),t=w.cp1,t=e.subtract([t.x,t.y,t.z],k,[]),e.normalize(t),e.scale(t,0.5),e.add(k,t),B=a(k[0],k[1],
k[2]),q.push(B)))}}else if(t.sheet){if(r.push(t),t.arrow){x=[0,0,0];w=[0,0,0];k=0;for(C=r.length;k<C;k++)c=r[k].guidePointsLarge,B=c[0],c=c[c.length-1],e.add(x,[B.x,B.y,B.z]),e.add(w,[c.x,c.y,c.z]);e.scale(x,1/C);e.scale(w,1/C);w=e.subtract(x,w);x=r[r.length-1].guidePointsSmall[0];this.sheetPlanks.push(new n(r[0].guidePointsSmall[0],x,w));r=[];v<u&&(w=b[v+1],w.sheet?r.push(t):(B=a(x.x,x.y,x.z),q.push(B)))}}else q.push(t),v<u&&(w=b[v+1],w.sheet&&(c=t.guidePointsSmall[0],B=a(c.x,c.y,c.z),q.push(B),
j.push(q),q=[],r.push(t)))}1<q.length&&(2==q.length&&q.push(q[q.length-1]),j.push(q));q=[];r=0;for(t=j.length;r<t;r++){x=j[r];w=[];v=0;for(u=x.length-1;v<=u;v++)w.push(x[v].cp1);q.push(w)}v=0;for(u=q.length;v<u;v++)j=new l.CatmullTube(q[v],g.proteins_tubeThickness,g.proteins_tubeResolution_3D,g.proteins_horizontalResolution),j.chainColor=b.chainColor,this.tubes.push(j)};j=l.PipePlank.prototype=new l._Mesh;j.render=function(a,d){a.material.setTempColors(d.proteins_materialAmbientColor_3D,void 0,d.proteins_materialSpecularColor_3D,
d.proteins_materialShininess_3D);a.material.setDiffuseColor(d.macro_colorByChain?this.chainColor:d.proteins_tubeColor);for(var b=0,e=this.tubes.length;b<e;b++)a.setMatrixUniforms(a.modelViewMatrix),this.tubes[b].render(a,d);d.macro_colorByChain||a.material.setDiffuseColor(d.proteins_ribbonCartoonHelixSecondaryColor);a.cylinderClosedBuffer.bindBuffers(a);b=0;for(e=this.helixCylinders.length;b<e;b++)this.helixCylinders[b].render(a,d);d.macro_colorByChain||a.material.setDiffuseColor(d.proteins_ribbonCartoonSheetColor);
a.boxBuffer.bindBuffers(a);b=0;for(e=this.sheetPlanks.length;b<e;b++)this.sheetPlanks[b].render(a,d)}})(ChemDoodle.extensions,ChemDoodle.RESIDUE,ChemDoodle.structures,ChemDoodle.structures.d3,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3,ChemDoodle.math);
(function(b,j){b.Shader=function(){};var o=b.Shader.prototype;o.init=function(b){var h=this.getShader(b,"vertex-shader");h||(h=this.loadDefaultVertexShader(b));var g=this.getShader(b,"fragment-shader");g||(g=this.loadDefaultFragmentShader(b));b.attachShader(b.program,h);b.attachShader(b.program,g);this.vertexPositionAttribute=0;b.bindAttribLocation(b.program,this.vertexPositionAttribute,"a_vertex_position");b.linkProgram(b.program);b.getProgramParameter(b.program,b.LINK_STATUS)||alert("Could not initialize shaders: "+
b.getProgramInfoLog(b.program));b.useProgram(b.program);b.enableVertexAttribArray(this.vertexPositionAttribute);this.vertexTexCoordAttribute=b.getAttribLocation(b.program,"a_vertex_texcoord");this.vertexNormalAttribute=b.getAttribLocation(b.program,"a_vertex_normal");b.enableVertexAttribArray(this.vertexNormalAttribute);this.dimensionUniform=b.getUniformLocation(b.program,"u_dimension")};o.getShader=function(b,h){var g=j.getElementById(h);if(g){for(var e=[],a=g.firstChild;a;)3===a.nodeType&&e.push(a.textContent),
a=a.nextSibling;if("x-shader/x-fragment"===g.type)a=b.createShader(b.FRAGMENT_SHADER);else if("x-shader/x-vertex"===g.type)a=b.createShader(b.VERTEX_SHADER);else return;b.shaderSource(a,e.join(""));b.compileShader(a);if(b.getShaderParameter(a,b.COMPILE_STATUS))return a;alert(g.type+" "+b.getShaderInfoLog(a))}};o.loadDefaultVertexShader=function(b){var h=b.createShader(b.VERTEX_SHADER);b.shaderSource(h,"precision mediump float;attribute vec3 a_vertex_position;attribute vec3 a_vertex_normal;attribute vec2 a_vertex_texcoord;uniform vec3 u_light_diffuse_color;uniform vec3 u_material_ambient_color;uniform vec3 u_material_diffuse_color;uniform mat4 u_model_view_matrix;uniform mat4 u_projection_matrix;uniform mat3 u_normal_matrix;uniform vec2 u_dimension;varying vec2 v_texcoord;varying vec3 v_diffuse;varying vec4 v_ambient;varying vec3 v_normal;void main() {v_texcoord \x3d a_vertex_texcoord;if(length(a_vertex_texcoord) !\x3d 0.) {gl_Position \x3d u_model_view_matrix * vec4(a_vertex_position, 1.);vec4 depth_pos \x3d vec4(gl_Position);depth_pos.z +\x3d a_vertex_normal.z;gl_Position \x3d u_projection_matrix * gl_Position;depth_pos \x3d u_projection_matrix * depth_pos;gl_Position /\x3d gl_Position.w;gl_Position.xy +\x3d a_vertex_normal.xy / u_dimension * 2.;gl_Position.z \x3d depth_pos.z / depth_pos.w;} else {v_normal \x3d length(a_vertex_normal)\x3d\x3d0. ? a_vertex_normal : normalize(u_normal_matrix * a_vertex_normal);v_ambient \x3d vec4(u_material_ambient_color, 1.);v_diffuse \x3d u_material_diffuse_color * u_light_diffuse_color;gl_Position \x3d u_projection_matrix * u_model_view_matrix * vec4(a_vertex_position, 1.);gl_Position /\x3d gl_Position.w;}}");
b.compileShader(h);if(b.getShaderParameter(h,b.COMPILE_STATUS))return h;alert("Vertex shader failed to compile: "+b.getShaderInfoLog(h))};o.loadDefaultFragmentShader=function(b){var h=b.createShader(b.FRAGMENT_SHADER);b.shaderSource(h,"precision mediump float;\nuniform vec3 u_light_specular_color;uniform vec3 u_light_direction;uniform vec3 u_light_half_vector;uniform vec3 u_material_specular_color;uniform float u_material_shininess;uniform float u_material_alpha;uniform int u_fog_mode;uniform vec3 u_fog_color;uniform float u_fog_density;uniform float u_fog_start;uniform float u_fog_end;uniform sampler2D u_image;varying vec2 v_texcoord;varying vec3 v_diffuse;varying vec4 v_ambient;varying vec3 v_normal;void main(void){if(length(v_texcoord)!\x3d0.) {gl_FragColor \x3d texture2D(u_image, v_texcoord);return;}if(length(v_normal)\x3d\x3d0.){gl_FragColor \x3d vec4(v_diffuse, u_material_alpha);}else{float nDotL \x3d max(dot(v_normal, u_light_direction), 0.);vec4 color \x3d vec4(v_diffuse*nDotL, 1.);float nDotHV \x3d max(dot(v_normal, u_light_half_vector), 0.);vec3 specular \x3d u_material_specular_color * u_light_specular_color;color+\x3dvec4(specular * pow(nDotHV, u_material_shininess), 1.);gl_FragColor \x3d color+v_ambient;gl_FragColor.a*\x3du_material_alpha;}float fogCoord \x3d 1.-clamp((u_fog_end - gl_FragCoord.z/gl_FragCoord.w) / (u_fog_end - u_fog_start), 0., 1.);float fogFactor \x3d 1.;if(u_fog_mode \x3d\x3d 1){fogFactor \x3d 1.-fogCoord;}else if(u_fog_mode \x3d\x3d 2) {fogFactor \x3d clamp(exp(-u_fog_density*fogCoord), 0., 1.);}else if(u_fog_mode \x3d\x3d 3) {fogFactor \x3d clamp(exp(-pow(u_fog_density*fogCoord, 2.)), 0., 1.);}gl_FragColor \x3d mix(vec4(u_fog_color, 1.), gl_FragColor, fogFactor);}");
b.compileShader(h);if(b.getShaderParameter(h,b.COMPILE_STATUS))return h;alert("Fragment shader failed to compile: "+b.getShaderInfoLog(h))}})(ChemDoodle.structures.d3,document);
(function(b,j,o){j.Shape=function(j,h){for(var g=j.length,e=[],a=[],d=new b.Point,n=0,f=g;n<f;n++){var y=n+1;n===f-1&&(y=0);for(var p=j[n],y=j[y],q=o.cross([0,0,1],[y.x-p.x,y.y-p.y,0]),A=0;2>A;A++)e.push(p.x,p.y,h/2),e.push(p.x,p.y,-h/2),e.push(y.x,y.y,h/2),e.push(y.x,y.y,-h/2);for(A=0;4>A;A++)a.push(q[0],q[1],q[2]);a.push(0,0,1);a.push(0,0,-1);a.push(0,0,1);a.push(0,0,-1);d.add(p)}d.x/=g;d.y/=g;a.push(0,0,1);e.push(d.x,d.y,h/2);a.push(0,0,-1);e.push(d.x,d.y,-h/2);d=[];p=8*g;n=0;for(f=g;n<f;n++)g=
8*n,d.push(g),d.push(g+3),d.push(g+1),d.push(g),d.push(g+2),d.push(g+3),d.push(g+4),d.push(p),d.push(g+6),d.push(g+5),d.push(g+7),d.push(p+1);this.storeData(e,a,d)};j.Shape.prototype=new j._Mesh})(ChemDoodle.structures,ChemDoodle.structures.d3,ChemDoodle.lib.vec3);
(function(b,j,o){b.Star=function(){for(var b=[0.8944,0.4472,0,0.2764,0.4472,0.8506,0.2764,0.4472,-0.8506,-0.7236,0.4472,0.5257,-0.7236,0.4472,-0.5257,-0.3416,0.4472,0,-0.1056,0.4472,0.3249,-0.1056,0.4472,-0.3249,0.2764,0.4472,0.2008,0.2764,0.4472,-0.2008,-0.8944,-0.4472,0,-0.2764,-0.4472,0.8506,-0.2764,-0.4472,-0.8506,0.7236,-0.4472,0.5257,0.7236,-0.4472,-0.5257,0.3416,-0.4472,0,0.1056,-0.4472,0.3249,0.1056,-0.4472,-0.3249,-0.2764,-0.4472,0.2008,-0.2764,-0.4472,-0.2008,-0.5527,0.1058,0,-0.1708,0.1058,
0.5527,-0.1708,0.1058,-0.5527,0.4471,0.1058,0.3249,0.4471,0.1058,-0.3249,0.5527,-0.1058,0,0.1708,-0.1058,0.5527,0.1708,-0.1058,-0.5527,-0.4471,-0.1058,0.3249,-0.4471,-0.1058,-0.3249,0,1,0,0,-1,0],h=[0,9,8,2,7,9,4,5,7,3,6,5,1,8,6,0,8,23,30,6,8,3,21,6,11,26,21,13,23,26,2,9,24,30,8,9,1,23,8,13,25,23,14,24,25,4,7,22,30,9,7,0,24,9,14,27,24,12,22,27,3,5,20,30,7,5,2,22,7,12,29,22,10,20,29,1,6,21,30,5,6,4,20,5,10,28,20,11,21,28,10,19,18,12,17,19,14,15,17,13,16,15,11,18,16,31,19,17,14,17,27,2,27,22,4,22,29,
10,29,19,31,18,19,12,19,29,4,29,20,3,20,28,11,28,18,31,16,18,10,18,28,3,28,21,1,21,26,13,26,16,31,15,16,11,16,26,1,26,23,0,23,25,14,25,15,31,17,15,13,15,25,0,25,24,2,24,27,12,27,17],g=[],e=[],a=[],d=0,j=h.length;d<j;d+=3){var f=3*h[d],y=3*h[d+1],p=3*h[d+2],f=[b[f],b[f+1],b[f+2]],y=[b[y],b[y+1],b[y+2]],p=[b[p],b[p+1],b[p+2]],q=o.cross([p[0]-y[0],p[1]-y[1],p[2]-y[2]],[f[0]-y[0],f[1]-y[1],f[2]-y[2]],[]);o.normalize(q);g.push(f[0],f[1],f[2],y[0],y[1],y[2],p[0],p[1],p[2]);e.push(q[0],q[1],q[2],q[0],q[1],
q[2],q[0],q[1],q[2]);a.push(d,d+1,d+2)}this.storeData(g,e,a)};b.Star.prototype=new b._Mesh})(ChemDoodle.structures.d3,Math,ChemDoodle.lib.vec3);
(function(b,j,o,l){var h=1;l.devicePixelRatio&&(h=l.devicePixelRatio);b.TextImage=function(){this.ctx=o.createElement("canvas").getContext("2d");this.data=[];this.text="";this.charHeight=0};b=b.TextImage.prototype;b.init=function(b){this.textureImage=b.createTexture();b.bindTexture(b.TEXTURE_2D,this.textureImage);b.pixelStorei(b.UNPACK_FLIP_Y_WEBGL,!1);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_WRAP_S,b.CLAMP_TO_EDGE);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_WRAP_T,b.CLAMP_TO_EDGE);b.texParameteri(b.TEXTURE_2D,
b.TEXTURE_MIN_FILTER,b.NEAREST);b.texParameteri(b.TEXTURE_2D,b.TEXTURE_MAG_FILTER,b.NEAREST);b.bindTexture(b.TEXTURE_2D,null);this.updateFont(b,12,["Sans-serif"],!1,!1,!1)};b.charData=function(b){b=this.text.indexOf(b);return 0<=b?this.data[b]:null};b.updateFont=function(b,e,a,d,n,f){var l=this.ctx,p=this.ctx.canvas,q=[],o="";e*=h;n=j.getFontString(e,a,d,n);l.font=n;l.save();var r=0;e*=1.5;a=32;for(d=127;a<d;a++){var v=String.fromCharCode(a),u=l.measureText(v).width;q.push({text:v,width:u,height:e});
r+=2*u}var t=["\u00b0","\u212b","\u00ae"];a=0;for(d=t.length;a<d;a++)v=t[a],u=l.measureText(v).width,q.push({text:v,width:u,height:e}),r+=2*u;a=Math.sqrt(r*e);a=Math.ceil(a/e);r=Math.ceil(r/(a-1));p.width=r;p.height=a*e;l.font=n;l.textAlign="left";l.textBaseline="middle";l.strokeStyle="#000";l.lineWidth=1.4;l.fillStyle="#fff";a=v=n=0;for(d=q.length;a<d;a++){u=q[a];t=2*u.width;e=u.height;var w=u.text;v+t>r&&(n++,v=0);var x=n*e;f&&l.strokeText(w,v,x+e/2);l.fillText(w,v,x+e/2);u.x=v;u.y=x;o+=w;v+=t}this.text=
o;this.data=q;this.charHeight=e;b.bindTexture(b.TEXTURE_2D,this.textureImage);b.texImage2D(b.TEXTURE_2D,0,b.RGBA,b.RGBA,b.UNSIGNED_BYTE,p);b.bindTexture(b.TEXTURE_2D,null)};b.pushVertexData=function(b,e,a,d){var j=b.toString().split(""),f=this.getHeight(),l=this.getWidth();b=-this.textWidth(b)/2/h;for(var p=-this.charHeight/2/h,q=0,o=j.length;q<o;q++){var r=this.charData(j[q]),v=r.width,u=r.x/l,t=u+1.8*r.width/l,w=r.y/f,r=w+r.height/f,x=b+1.8*v/h,B=this.charHeight/2/h;d.position.push(e[0],e[1],e[2],
e[0],e[1],e[2],e[0],e[1],e[2],e[0],e[1],e[2],e[0],e[1],e[2],e[0],e[1],e[2]);d.texCoord.push(u,w,t,r,t,w,u,w,u,r,t,r);d.translation.push(b,B,a,x,p,a,x,B,a,b,B,a,b,p,a,x,p,a);b=x+(v-1.8*v)/h}};b.getCanvas=function(){return this.ctx.canvas};b.getHeight=function(){return this.getCanvas().height};b.getWidth=function(){return this.getCanvas().width};b.textWidth=function(b){return this.ctx.measureText(b).width};b.test=function(){o.body.appendChild(this.getCanvas())};b.useTexture=function(b){b.bindTexture(b.TEXTURE_2D,
this.textureImage)}})(ChemDoodle.structures.d3,ChemDoodle.extensions,document,window);
(function(b){b.TextMesh=function(){};b=b.TextMesh.prototype;b.init=function(b){this.vertexPositionBuffer=b.createBuffer();this.vertexTexCoordBuffer=b.createBuffer();this.vertexTranslationBuffer=b.createBuffer()};b.setVertexData=function(b,o,l,h){b.bindBuffer(b.ARRAY_BUFFER,o);b.bufferData(b.ARRAY_BUFFER,new Float32Array(l),b.STATIC_DRAW);o.itemSize=h;o.numItems=l.length/h};b.storeData=function(b,o,l,h){this.setVertexData(b,this.vertexPositionBuffer,o,3);this.setVertexData(b,this.vertexTexCoordBuffer,
l,2);this.setVertexData(b,this.vertexTranslationBuffer,h,3)};b.bindBuffers=function(b){b.bindBuffer(b.ARRAY_BUFFER,this.vertexPositionBuffer);b.vertexAttribPointer(b.shader.vertexPositionAttribute,this.vertexPositionBuffer.itemSize,b.FLOAT,!1,0,0);b.bindBuffer(b.ARRAY_BUFFER,this.vertexTexCoordBuffer);b.vertexAttribPointer(b.shader.vertexTexCoordAttribute,this.vertexTexCoordBuffer.itemSize,b.FLOAT,!1,0,0);b.bindBuffer(b.ARRAY_BUFFER,this.vertexTranslationBuffer);b.vertexAttribPointer(b.shader.vertexNormalAttribute,
this.vertexTranslationBuffer.itemSize,b.FLOAT,!1,0,0)};b.render=function(b){var o=this.vertexPositionBuffer.numItems;o&&(this.bindBuffers(b),b.drawArrays(b.TRIANGLES,0,o))}})(ChemDoodle.structures.d3,Math);
(function(b,j,o,l,h,g,e){l.Torsion=function(a,d,b,e){this.a1=a;this.a2=d;this.a3=b;this.a4=e};b=l.Torsion.prototype=new l._Measurement;b.calculateData=function(a){var d=[],b=[],f=[],g=this.a2.distance3D(this.a1),j=this.a2.distance3D(this.a3);this.distUse=h.min(g,j)/2;var j=[this.a2.x-this.a1.x,this.a2.y-this.a1.y,this.a2.z-this.a1.z],g=[this.a3.x-this.a2.x,this.a3.y-this.a2.y,this.a3.z-this.a2.z],q=[this.a4.x-this.a3.x,this.a4.y-this.a3.y,this.a4.z-this.a3.z],l=e.cross(j,g,[]),q=e.cross(g,q,[]);e.scale(j,
e.length(g));this.torsion=h.atan2(e.dot(j,q),e.dot(l,q));j=e.normalize(e.cross(l,g,[]));l=e.normalize(e.cross(g,j,[]));this.pos=e.add([this.a2.x,this.a2.y,this.a2.z],e.scale(e.normalize(g,[]),this.distUse));var q=[],o=a.measurement_angleBands_3D;for(a=0;a<=o;++a){var v=this.torsion*a/o,u=e.scale(j,h.cos(v),[]),v=e.scale(l,h.sin(v),[]),u=e.scale(e.normalize(e.add(u,v,[])),this.distUse);0==a&&(q=u);d.push(this.pos[0]+u[0],this.pos[1]+u[1],this.pos[2]+u[2]);b.push(0,0,0);a<o&&f.push(a,a+1)}this.vecText=
e.normalize(e.add(q,u,[]));g=e.normalize(g,[]);e.scale(g,0.0625);v=this.torsion-2*h.asin(0.125)*this.torsion/h.abs(this.torsion);u=e.scale(j,h.cos(v),[]);v=e.scale(l,h.sin(v),[]);u=e.scale(e.normalize(e.add(u,v,[])),this.distUse);d.push(this.pos[0]+g[0]+u[0],this.pos[1]+g[1]+u[1],this.pos[2]+g[2]+u[2]);b.push(0,0,0);d.push(this.pos[0]-g[0]+u[0],this.pos[1]-g[1]+u[1],this.pos[2]-g[2]+u[2]);b.push(0,0,0);f.push(--a,a+1,a,a+2);this.storeData(d,b,f)};b.getText=function(){e.add(this.pos,e.scale(this.vecText,
this.distUse+0.3,[]));return{pos:this.pos,value:[j.angleBounds(this.torsion,!0,!0).toFixed(2)," \u00b0"].join("")}}})(ChemDoodle.ELEMENT,ChemDoodle.math,ChemDoodle.extensions,ChemDoodle.structures.d3,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3);
(function(b,j,o,l,h,g,e,a){var d=function(a,d){a.bindBuffer(a.ARRAY_BUFFER,d.vertexPositionBuffer);a.vertexAttribPointer(a.shader.vertexPositionAttribute,d.vertexPositionBuffer.itemSize,a.FLOAT,!1,0,0);a.bindBuffer(a.ARRAY_BUFFER,d.vertexNormalBuffer);a.vertexAttribPointer(a.shader.vertexNormalAttribute,d.vertexNormalBuffer.itemSize,a.FLOAT,!1,0,0);a.bindBuffer(a.ELEMENT_ARRAY_BUFFER,d.vertexIndexBuffer)},n=function(a,d,b){var e=h.sqrt(d[1]*d[1]+d[2]*d[2]),j=[1,0,0,0,0,d[2]/e,-d[1]/e,0,0,d[1]/e,d[2]/
e,0,0,0,0,1],n=[1,0,0,0,0,d[2]/e,d[1]/e,0,0,-d[1]/e,d[2]/e,0,0,0,0,1],l=[e,0,-d[0],0,0,1,0,0,d[0],0,e,0,0,0,0,1];d=[e,0,d[0],0,0,1,0,0,-d[0],0,e,0,0,0,0,1];b=[h.cos(b),-h.sin(b),0,0,h.sin(b),h.cos(b),0,0,0,0,1,0,0,0,0,1];var o=g.multiply(j,g.multiply(l,g.multiply(b,g.multiply(d,n,[]))));this.rotate=function(){return g.multiplyVec3(o,a)}};l.Tube=function(f,l,p){var q=f[0].lineSegments[0].length;this.partitions=[];var A;this.ends=[];this.ends.push(f[0].lineSegments[0][0]);this.ends.push(f[f.length-
1].lineSegments[0][0]);for(var r=[1,0,0],v=0,u=f.length;v<u;v++){if(!A||65E3<A.positionData.length)0<this.partitions.length&&v--,A={count:0,positionData:[],normalData:[],indexData:[]},this.partitions.push(A);var t=f[v];A.count++;for(var w=Infinity,x=new o.Atom("",f[v].cp1.x,f[v].cp1.y,f[v].cp1.z),B=0;B<q;B++){var c=t.lineSegments[0][B],k;k=B===q-1?v===f.length-1?t.lineSegments[0][B-1]:f[v+1].lineSegments[0][0]:t.lineSegments[0][B+1];k=[k.x-c.x,k.y-c.y,k.z-c.z];e.normalize(k);v===f.length-1&&B===q-
1&&e.scale(k,-1);var C=e.cross(k,r,[]);e.normalize(C);e.scale(C,l/2);C=new n(C,k,2*Math.PI/p);k=0;for(var D=p;k<D;k++){var G=C.rotate();k===h.floor(p/4)&&(r=[G[0],G[1],G[2]]);A.normalData.push(G[0],G[1],G[2]);A.positionData.push(c.x+G[0],c.y+G[1],c.z+G[2])}x&&(k=c.distance3D(x),k<w&&(w=k,f[v].pPoint=c))}}r=0;for(t=this.partitions.length;r<t;r++){A=this.partitions[r];v=0;for(u=A.count-1;v<u;v++){w=v*q*p;B=0;for(x=q;B<x;B++){c=w+B*p;for(k=0;k<p;k++)C=c+k,A.indexData.push(C),A.indexData.push(C+p),A.indexData.push(C+
p+1),A.indexData.push(C),A.indexData.push(C+p+1),A.indexData.push(C+1)}}}this.storeData(this.partitions[0].positionData,this.partitions[0].normalData,this.partitions[0].indexData);p=[new o.Point(2,0)];for(v=0;60>v;v++)q=v/60*h.PI,p.push(new o.Point(2*h.cos(q),-2*h.sin(q)));p.push(new o.Point(-2,0),new o.Point(-2,4),new o.Point(2,4));var E=new o.d3.Shape(p,1);this.render=function(c,n){this.bindBuffers(c);c.material.setDiffuseColor(n.macro_colorByChain?this.chainColor:n.nucleics_tubeColor);c.drawElements(c.TRIANGLES,
this.vertexIndexBuffer.numItems,c.UNSIGNED_SHORT,0);if(this.partitions)for(var k=1,p=this.partitions.length;k<p;k++){var q=this.partitions[k];d(c,q);c.drawElements(c.TRIANGLES,q.vertexIndexBuffer.numItems,c.UNSIGNED_SHORT,0)}c.sphereBuffer.bindBuffers(c);for(k=0;2>k;k++)q=this.ends[k],q=g.translate(c.modelViewMatrix,[q.x,q.y,q.z],[]),p=l/2,g.scale(q,[p,p,p]),c.setMatrixUniforms(q),c.drawElements(c.TRIANGLES,c.sphereBuffer.vertexIndexBuffer.numItems,c.UNSIGNED_SHORT,0);c.cylinderBuffer.bindBuffers(c);
k=0;for(p=f.length-1;k<p;k++){var r=f[k],v=r.pPoint,t=new o.Atom("",r.cp2.x,r.cp2.y,r.cp2.z),q=1.001*v.distance3D(t),r=[l/4,q,l/4],q=g.translate(c.modelViewMatrix,[v.x,v.y,v.z],[]),u=[0,1,0],A=0,w=[t.x-v.x,t.y-v.y,t.z-v.z];v.x===t.x&&v.z===t.z?(u=[0,0,1],v.y<v.y&&(A=h.PI)):(A=b.vec3AngleFrom(u,w),u=e.cross(u,w,[]));0!==A&&g.rotate(q,A,u);g.scale(q,r);c.setMatrixUniforms(q);c.drawArrays(c.TRIANGLE_STRIP,0,c.cylinderBuffer.vertexPositionBuffer.numItems)}E.bindBuffers(c);"none"===n.nucleics_residueColor&&
!n.macro_colorByChain&&c.material.setDiffuseColor(n.nucleics_baseColor);k=0;for(p=f.length-1;k<p;k++)r=f[k],t=r.cp2,q=g.translate(c.modelViewMatrix,[t.x,t.y,t.z],[]),u=[0,1,0],A=0,v=r.cp3,w=[v.x-t.x,v.y-t.y,v.z-t.z],t.x===v.x&&t.z===v.z?(u=[0,0,1],t.y<t.y&&(A=h.PI)):(A=b.vec3AngleFrom(u,w),u=e.cross(u,w,[])),0!==A&&g.rotate(q,A,u),t=[1,0,0],A=g.rotate(g.identity([]),A,u),g.multiplyVec3(A,t),A=r.cp4,v=r.cp5,A.y===v.y&&A.z===v.z||(A=[v.x-A.x,v.y-A.y,v.z-A.z],v=b.vec3AngleFrom(t,A),0>e.dot(w,e.cross(t,
A))&&(v*=-1),g.rotateY(q,v)),n.macro_colorByChain||("shapely"===n.nucleics_residueColor?j[r.name]?c.material.setDiffuseColor(j[r.name].shapelyColor):c.material.setDiffuseColor(j["*"].shapelyColor):"rainbow"===n.nucleics_residueColor&&c.material.setDiffuseColor(a.rainbowAt(k,p,n.macro_rainbowColors))),c.setMatrixUniforms(q),c.drawElements(c.TRIANGLES,E.vertexIndexBuffer.numItems,c.UNSIGNED_SHORT,0)}};l.Tube.prototype=new l._Mesh;l.CatmullTube=function(a,d,b,g){var j=[];a.push(a[a.length-1]);for(var l=
0,v=a.length-2;l<=v;l++){for(var u=a[0==l?0:l-1],t=a[l+0],w=a[l+1],x=a[l==v?l+1:l+2],B=[],c=0;c<g;c++){var k=c/g;l==v&&(k=c/(g-1));k=new o.Atom("C",0.5*(2*t.x+(w.x-u.x)*k+(2*u.x-5*t.x+4*w.x-x.x)*k*k+(3*t.x-u.x-3*w.x+x.x)*k*k*k),0.5*(2*t.y+(w.y-u.y)*k+(2*u.y-5*t.y+4*w.y-x.y)*k*k+(3*t.y-u.y-3*w.y+x.y)*k*k*k),0.5*(2*t.z+(w.z-u.z)*k+(2*u.z-5*t.z+4*w.z-x.z)*k*k+(3*t.z-u.z-3*w.z+x.z)*k*k*k));B.push(k)}j.push(B)}a=j[0].length;this.partitions=[];var C;this.ends=[];this.ends.push(j[0][0]);this.ends.push(j[j.length-
1][0]);u=[1,0,0];l=0;for(v=j.length;l<v;l++){if(!C||65E3<C.positionData.length)0<this.partitions.length&&l--,C={count:0,positionData:[],normalData:[],indexData:[]},this.partitions.push(C);t=j[l];C.count++;for(c=0;c<a;c++){w=t[c];g=c===a-1?l===j.length-1?t[c-1]:j[l+1][0]:t[c+1];g=[g.x-w.x,g.y-w.y,g.z-w.z];e.normalize(g);l===j.length-1&&c===a-1&&e.scale(g,-1);x=e.cross(g,u,[]);e.normalize(x);e.scale(x,d/2);x=new n(x,g,2*Math.PI/b);g=0;for(B=b;g<B;g++)k=x.rotate(),g===h.floor(b/4)&&(u=[k[0],k[1],k[2]]),
C.normalData.push(k[0],k[1],k[2]),C.positionData.push(w.x+k[0],w.y+k[1],w.z+k[2])}}d=0;for(j=this.partitions.length;d<j;d++){C=this.partitions[d];l=0;for(v=C.count-1;l<v;l++){u=l*a*b;c=0;for(t=a;c<t;c++){w=u+c*b;for(g=0;g<=b;g++)x=w+g%b,C.indexData.push(x,x+b)}}}this.storeData(this.partitions[0].positionData,this.partitions[0].normalData,this.partitions[0].indexData)};(l.CatmullTube.prototype=new l._Mesh).render=function(a,b){this.bindBuffers(a);for(var e=0,h=this.partitions.length;e<h;e++){var j=
this.partitions[e];d(a,j);a.drawElements(a.TRIANGLE_STRIP,j.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0)}a.sphereBuffer.bindBuffers(a);for(e=0;2>e;e++)j=this.ends[e],h=g.translate(a.modelViewMatrix,[j.x,j.y,j.z],[]),j=b.proteins_tubeThickness/2,g.scale(h,[j,j,j]),a.setMatrixUniforms(h),a.drawElements(a.TRIANGLES,a.sphereBuffer.vertexIndexBuffer.numItems,a.UNSIGNED_SHORT,0)}})(ChemDoodle.extensions,ChemDoodle.RESIDUE,ChemDoodle.structures,ChemDoodle.structures.d3,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3,
ChemDoodle.math);
(function(b){b.UnitCell=function(b){this.unitCell=b;var o=[],l=[],h=function(b,a,d,g){o.push(b[0],b[1],b[2]);o.push(a[0],a[1],a[2]);o.push(d[0],d[1],d[2]);o.push(g[0],g[1],g[2]);for(b=0;4>b;b++)l.push(0,0,0)};h(b.o,b.x,b.xy,b.y);h(b.o,b.y,b.yz,b.z);h(b.o,b.z,b.xz,b.x);h(b.yz,b.y,b.xy,b.xyz);h(b.xyz,b.xz,b.z,b.yz);h(b.xy,b.x,b.xz,b.xyz);b=[];for(h=0;6>h;h++){var g=4*h;b.push(g,g+1,g+1,g+2,g+2,g+3,g+3,g)}this.storeData(o,l,b)};(b.UnitCell.prototype=new b._Mesh).render=function(b,o){b.setMatrixUniforms(b.modelViewMatrix);this.bindBuffers(b);
b.material.setDiffuseColor(o.shapes_color);b.lineWidth(o.shapes_lineWidth);b.drawElements(b.LINES,this.vertexIndexBuffer.numItems,b.UNSIGNED_SHORT,0)}})(ChemDoodle.structures.d3,ChemDoodle.lib.vec3);
(function(b,j,o){b.Plate=function(b){this.lanes=Array(b);i=0;for(ii=b;i<ii;i++)this.lanes[i]=[]};var l=b.Plate.prototype;l.sort=function(){i=0;for(ii=this.lanes.length;i<ii;i++)this.lanes[i].sort(function(b,g){return b-g})};l.draw=function(b){var g=b.canvas.width,e=b.canvas.height;this.origin=9*e/10;this.front=e/10;this.laneLength=this.origin-this.front;b.strokeStyle="#000000";b.beginPath();b.moveTo(0,this.front);j.contextHashTo(b,0,this.front,g,this.front,3,3);b.closePath();b.stroke();b.beginPath();
b.moveTo(0,this.origin);b.lineTo(g,this.origin);b.closePath();b.stroke();i=0;for(ii=this.lanes.length;i<ii;i++){e=(i+1)*g/(ii+1);b.beginPath();b.moveTo(e,this.origin);b.lineTo(e,this.origin+3);b.closePath();b.stroke();s=0;for(ss=this.lanes[i].length;s<ss;s++){var a=this.origin-this.laneLength*this.lanes[i][s].rf;switch(this.lanes[i][s].type){case "compact":b.beginPath();b.arc(e,a,3,0,2*o.PI,!1);b.closePath();break;case "expanded":b.beginPath();b.arc(e,a,7,0,2*o.PI,!1);b.closePath();break;case "widened":j.contextOval(b,
e-18,a-10,36,10);break;case "cresent":b.beginPath(),b.arc(e,a,9,0,o.PI,!0),b.closePath()}switch(this.lanes[i][s].style){case "solid":b.fillStyle="#000000";b.fill();break;case "transparent":b.stroke()}}}};b.Plate.Spot=function(b,g,e){this.type=b;this.rf=g;this.style=e?e:"solid"}})(ChemDoodle.structures,ChemDoodle.extensions,Math);
(function(b,j,o){b.default_backgroundColor="#FFFFFF";b.default_scale=1;b.default_rotateAngle=0;b.default_bondLength_2D=20;b.default_angstromsPerBondLength=1.25;b.default_lightDirection_3D=[-0.1,-0.1,-1];b.default_lightDiffuseColor_3D="#FFFFFF";b.default_lightSpecularColor_3D="#FFFFFF";b.default_projectionPerspective_3D=!0;b.default_projectionPerspectiveVerticalFieldOfView_3D=45;b.default_projectionOrthoWidth_3D=40;b.default_projectionWidthHeightRatio_3D=void 0;b.default_projectionFrontCulling_3D=
0.1;b.default_projectionBackCulling_3D=1E4;b.default_cullBackFace_3D=!0;b.default_fog_mode_3D=0;b.default_fog_color_3D="#000000";b.default_fog_start_3D=0;b.default_fog_end_3D=1;b.default_fog_density_3D=1;b.default_atoms_display=!0;b.default_atoms_color="#000000";b.default_atoms_font_size_2D=12;b.default_atoms_font_families_2D=["Helvetica","Arial","Dialog"];b.default_atoms_font_bold_2D=!1;b.default_atoms_font_italic_2D=!1;b.default_atoms_circles_2D=!1;b.default_atoms_circleDiameter_2D=10;b.default_atoms_circleBorderWidth_2D=
1;b.default_atoms_lonePairDistance_2D=8;b.default_atoms_lonePairSpread_2D=4;b.default_atoms_lonePairDiameter_2D=1;b.default_atoms_useJMOLColors=!1;b.default_atoms_usePYMOLColors=!1;b.default_atoms_resolution_3D=60;b.default_atoms_sphereDiameter_3D=0.8;b.default_atoms_useVDWDiameters_3D=!1;b.default_atoms_vdwMultiplier_3D=1;b.default_atoms_materialAmbientColor_3D="#000000";b.default_atoms_materialSpecularColor_3D="#555555";b.default_atoms_materialShininess_3D=32;b.default_atoms_implicitHydrogens_2D=
!0;b.default_atoms_displayTerminalCarbonLabels_2D=!1;b.default_atoms_showHiddenCarbons_2D=!0;b.default_atoms_showAttributedCarbons_2D=!0;b.default_atoms_displayAllCarbonLabels_2D=!1;b.default_atoms_nonBondedAsStars_3D=!1;b.default_atoms_displayLabels_3D=!1;b.default_atoms_HBlack_2D=!0;b.default_bonds_display=!0;b.default_bonds_color="#000000";b.default_bonds_width_2D=1;b.default_bonds_saturationWidth_2D=0.2;b.default_bonds_ends_2D="round";b.default_bonds_useJMOLColors=!1;b.default_bonds_usePYMOLColors=
!1;b.default_bonds_colorGradient=!1;b.default_bonds_saturationAngle_2D=o.PI/3;b.default_bonds_symmetrical_2D=!1;b.default_bonds_clearOverlaps_2D=!1;b.default_bonds_overlapClearWidth_2D=0.5;b.default_bonds_atomLabelBuffer_2D=1;b.default_bonds_wedgeThickness_2D=0.22;b.default_bonds_hashWidth_2D=1;b.default_bonds_hashSpacing_2D=2.5;b.default_bonds_dotSize_2D=2;b.default_bonds_lewisStyle_2D=!1;b.default_bonds_showBondOrders_3D=!1;b.default_bonds_resolution_3D=60;b.default_bonds_renderAsLines_3D=!1;b.default_bonds_cylinderDiameter_3D=
0.3;b.default_bonds_pillLatitudeResolution_3D=10;b.default_bonds_pillLongitudeResolution_3D=20;b.default_bonds_pillHeight_3D=0.3;b.default_bonds_pillSpacing_3D=0.1;b.default_bonds_pillDiameter_3D=0.3;b.default_bonds_materialAmbientColor_3D="#222222";b.default_bonds_materialSpecularColor_3D="#555555";b.default_bonds_materialShininess_3D=32;b.default_proteins_displayRibbon=!0;b.default_proteins_displayBackbone=!1;b.default_proteins_backboneThickness=1.5;b.default_proteins_backboneColor="#CCCCCC";b.default_proteins_ribbonCartoonize=
!1;b.default_proteins_displayPipePlank=!1;b.default_proteins_residueColor="none";b.default_proteins_primaryColor="#FF0D0D";b.default_proteins_secondaryColor="#FFFF30";b.default_proteins_ribbonCartoonHelixPrimaryColor="#00E740";b.default_proteins_ribbonCartoonHelixSecondaryColor="#9905FF";b.default_proteins_ribbonCartoonSheetColor="#E8BB99";b.default_proteins_tubeColor="#FF0D0D";b.default_proteins_tubeResolution_3D=30;b.default_proteins_ribbonThickness=0.2;b.default_proteins_tubeThickness=0.5;b.default_proteins_plankSheetWidth=
3.5;b.default_proteins_cylinderHelixDiameter=4;b.default_proteins_verticalResolution=10;b.default_proteins_horizontalResolution=9;b.default_proteins_materialAmbientColor_3D="#222222";b.default_proteins_materialSpecularColor_3D="#555555";b.default_proteins_materialShininess_3D=32;b.default_nucleics_display=!0;b.default_nucleics_tubeColor="#CCCCCC";b.default_nucleics_baseColor="#C10000";b.default_nucleics_residueColor="none";b.default_nucleics_tubeThickness=1.5;b.default_nucleics_tubeResolution_3D=
60;b.default_nucleics_verticalResolution=10;b.default_nucleics_materialAmbientColor_3D="#222222";b.default_nucleics_materialSpecularColor_3D="#555555";b.default_nucleics_materialShininess_3D=32;b.default_macro_displayAtoms=!1;b.default_macro_displayBonds=!1;b.default_macro_atomToLigandDistance=-1;b.default_macro_showWater=!1;b.default_macro_colorByChain=!1;b.default_macro_rainbowColors=["#0000FF","#00FFFF","#00FF00","#FFFF00","#FF0000"];b.default_surfaces_display=!0;b.default_surfaces_style="Dot";
b.default_surfaces_color="#E9B862";b.default_surfaces_materialAmbientColor_3D="#000000";b.default_surfaces_materialSpecularColor_3D="#000000";b.default_surfaces_materialShininess_3D=32;b.default_plots_color="#000000";b.default_plots_width=1;b.default_plots_showIntegration=!1;b.default_plots_integrationColor="#c10000";b.default_plots_integrationLineWidth=1;b.default_plots_showGrid=!1;b.default_plots_gridColor="gray";b.default_plots_gridLineWidth=0.5;b.default_plots_showYAxis=!0;b.default_plots_flipXAxis=
!1;b.default_text_font_size=12;b.default_text_font_families=["Helvetica","Arial","Dialog"];b.default_text_font_bold=!0;b.default_text_font_italic=!1;b.default_text_font_stroke_3D=!0;b.default_text_color="#000000";b.default_shapes_color="#000000";b.default_shapes_lineWidth=1;b.default_shapes_arrowLength_2D=8;b.default_compass_display=!1;b.default_compass_axisXColor_3D="#FF0000";b.default_compass_axisYColor_3D="#00FF00";b.default_compass_axisZColor_3D="#0000FF";b.default_compass_size_3D=50;b.default_compass_resolution_3D=
10;b.default_compass_displayText_3D=!0;b.default_compass_type_3D=0;b.default_measurement_update_3D=!1;b.default_measurement_angleBands_3D=10;b.default_measurement_displayText_3D=!0;j.VisualSpecifications=function(){this.backgroundColor=b.default_backgroundColor;this.scale=b.default_scale;this.rotateAngle=b.default_rotateAngle;this.bondLength_2D=b.default_bondLength_2D;this.angstromsPerBondLength=b.default_angstromsPerBondLength;this.lightDirection_3D=b.default_lightDirection_3D.slice(0);this.lightDiffuseColor_3D=
b.default_lightDiffuseColor_3D;this.lightSpecularColor_3D=b.default_lightSpecularColor_3D;this.projectionPerspective_3D=b.default_projectionPerspective_3D;this.projectionPerspectiveVerticalFieldOfView_3D=b.default_projectionPerspectiveVerticalFieldOfView_3D;this.projectionOrthoWidth_3D=b.default_projectionOrthoWidth_3D;this.projectionWidthHeightRatio_3D=b.default_projectionWidthHeightRatio_3D;this.projectionFrontCulling_3D=b.default_projectionFrontCulling_3D;this.projectionBackCulling_3D=b.default_projectionBackCulling_3D;
this.cullBackFace_3D=b.default_cullBackFace_3D;this.fog_mode_3D=b.default_fog_mode_3D;this.fog_color_3D=b.default_fog_color_3D;this.fog_start_3D=b.default_fog_start_3D;this.fog_end_3D=b.default_fog_end_3D;this.fog_density_3D=b.default_fog_density_3D;this.atoms_display=b.default_atoms_display;this.atoms_color=b.default_atoms_color;this.atoms_font_size_2D=b.default_atoms_font_size_2D;this.atoms_font_families_2D=b.default_atoms_font_families_2D.slice(0);this.atoms_font_bold_2D=b.default_atoms_font_bold_2D;
this.atoms_font_italic_2D=b.default_atoms_font_italic_2D;this.atoms_circles_2D=b.default_atoms_circles_2D;this.atoms_circleDiameter_2D=b.default_atoms_circleDiameter_2D;this.atoms_circleBorderWidth_2D=b.default_atoms_circleBorderWidth_2D;this.atoms_lonePairDistance_2D=b.default_atoms_lonePairDistance_2D;this.atoms_lonePairSpread_2D=b.default_atoms_lonePairSpread_2D;this.atoms_lonePairDiameter_2D=b.default_atoms_lonePairDiameter_2D;this.atoms_useJMOLColors=b.default_atoms_useJMOLColors;this.atoms_usePYMOLColors=
b.default_atoms_usePYMOLColors;this.atoms_resolution_3D=b.default_atoms_resolution_3D;this.atoms_sphereDiameter_3D=b.default_atoms_sphereDiameter_3D;this.atoms_useVDWDiameters_3D=b.default_atoms_useVDWDiameters_3D;this.atoms_vdwMultiplier_3D=b.default_atoms_vdwMultiplier_3D;this.atoms_materialAmbientColor_3D=b.default_atoms_materialAmbientColor_3D;this.atoms_materialSpecularColor_3D=b.default_atoms_materialSpecularColor_3D;this.atoms_materialShininess_3D=b.default_atoms_materialShininess_3D;this.atoms_implicitHydrogens_2D=
b.default_atoms_implicitHydrogens_2D;this.atoms_displayTerminalCarbonLabels_2D=b.default_atoms_displayTerminalCarbonLabels_2D;this.atoms_showHiddenCarbons_2D=b.default_atoms_showHiddenCarbons_2D;this.atoms_showAttributedCarbons_2D=b.default_atoms_showAttributedCarbons_2D;this.atoms_displayAllCarbonLabels_2D=b.default_atoms_displayAllCarbonLabels_2D;this.atoms_nonBondedAsStars_3D=b.default_atoms_nonBondedAsStars_3D;this.atoms_displayLabels_3D=b.default_atoms_displayLabels_3D;this.atoms_HBlack_2D=b.default_atoms_HBlack_2D;
this.bonds_display=b.default_bonds_display;this.bonds_color=b.default_bonds_color;this.bonds_width_2D=b.default_bonds_width_2D;this.bonds_saturationWidth_2D=b.default_bonds_saturationWidth_2D;this.bonds_ends_2D=b.default_bonds_ends_2D;this.bonds_useJMOLColors=b.default_bonds_useJMOLColors;this.bonds_usePYMOLColors=b.default_bonds_usePYMOLColors;this.bonds_colorGradient=b.default_bonds_colorGradient;this.bonds_saturationAngle_2D=b.default_bonds_saturationAngle_2D;this.bonds_symmetrical_2D=b.default_bonds_symmetrical_2D;
this.bonds_clearOverlaps_2D=b.default_bonds_clearOverlaps_2D;this.bonds_overlapClearWidth_2D=b.default_bonds_overlapClearWidth_2D;this.bonds_atomLabelBuffer_2D=b.default_bonds_atomLabelBuffer_2D;this.bonds_wedgeThickness_2D=b.default_bonds_wedgeThickness_2D;this.bonds_hashWidth_2D=b.default_bonds_hashWidth_2D;this.bonds_hashSpacing_2D=b.default_bonds_hashSpacing_2D;this.bonds_dotSize_2D=b.default_bonds_dotSize_2D;this.bonds_lewisStyle_2D=b.default_bonds_lewisStyle_2D;this.bonds_showBondOrders_3D=
b.default_bonds_showBondOrders_3D;this.bonds_resolution_3D=b.default_bonds_resolution_3D;this.bonds_renderAsLines_3D=b.default_bonds_renderAsLines_3D;this.bonds_cylinderDiameter_3D=b.default_bonds_cylinderDiameter_3D;this.bonds_pillHeight_3D=b.default_bonds_pillHeight_3D;this.bonds_pillLatitudeResolution_3D=b.default_bonds_pillLatitudeResolution_3D;this.bonds_pillLongitudeResolution_3D=b.default_bonds_pillLongitudeResolution_3D;this.bonds_pillSpacing_3D=b.default_bonds_pillSpacing_3D;this.bonds_pillDiameter_3D=
b.default_bonds_pillDiameter_3D;this.bonds_materialAmbientColor_3D=b.default_bonds_materialAmbientColor_3D;this.bonds_materialSpecularColor_3D=b.default_bonds_materialSpecularColor_3D;this.bonds_materialShininess_3D=b.default_bonds_materialShininess_3D;this.proteins_displayRibbon=b.default_proteins_displayRibbon;this.proteins_displayBackbone=b.default_proteins_displayBackbone;this.proteins_backboneThickness=b.default_proteins_backboneThickness;this.proteins_backboneColor=b.default_proteins_backboneColor;
this.proteins_ribbonCartoonize=b.default_proteins_ribbonCartoonize;this.proteins_residueColor=b.default_proteins_residueColor;this.proteins_primaryColor=b.default_proteins_primaryColor;this.proteins_secondaryColor=b.default_proteins_secondaryColor;this.proteins_ribbonCartoonHelixPrimaryColor=b.default_proteins_ribbonCartoonHelixPrimaryColor;this.proteins_ribbonCartoonHelixSecondaryColor=b.default_proteins_ribbonCartoonHelixSecondaryColor;this.proteins_tubeColor=b.default_proteins_tubeColor;this.proteins_tubeResolution_3D=
b.default_proteins_tubeResolution_3D;this.proteins_displayPipePlank=b.default_proteins_displayPipePlank;this.proteins_ribbonCartoonSheetColor=b.default_proteins_ribbonCartoonSheetColor;this.proteins_ribbonThickness=b.default_proteins_ribbonThickness;this.proteins_tubeThickness=b.default_proteins_tubeThickness;this.proteins_plankSheetWidth=b.default_proteins_plankSheetWidth;this.proteins_cylinderHelixDiameter=b.default_proteins_cylinderHelixDiameter;this.proteins_verticalResolution=b.default_proteins_verticalResolution;
this.proteins_horizontalResolution=b.default_proteins_horizontalResolution;this.proteins_materialAmbientColor_3D=b.default_proteins_materialAmbientColor_3D;this.proteins_materialSpecularColor_3D=b.default_proteins_materialSpecularColor_3D;this.proteins_materialShininess_3D=b.default_proteins_materialShininess_3D;this.macro_displayAtoms=b.default_macro_displayAtoms;this.macro_displayBonds=b.default_macro_displayBonds;this.macro_atomToLigandDistance=b.default_macro_atomToLigandDistance;this.nucleics_display=
b.default_nucleics_display;this.nucleics_tubeColor=b.default_nucleics_tubeColor;this.nucleics_baseColor=b.default_nucleics_baseColor;this.nucleics_residueColor=b.default_nucleics_residueColor;this.nucleics_tubeThickness=b.default_nucleics_tubeThickness;this.nucleics_tubeResolution_3D=b.default_nucleics_tubeResolution_3D;this.nucleics_verticalResolution=b.default_nucleics_verticalResolution;this.nucleics_materialAmbientColor_3D=b.default_nucleics_materialAmbientColor_3D;this.nucleics_materialSpecularColor_3D=
b.default_nucleics_materialSpecularColor_3D;this.nucleics_materialShininess_3D=b.default_nucleics_materialShininess_3D;this.macro_showWater=b.default_macro_showWater;this.macro_colorByChain=b.default_macro_colorByChain;this.macro_rainbowColors=b.default_macro_rainbowColors.slice(0);this.surfaces_display=b.default_surfaces_display;this.surfaces_style=b.default_surfaces_style;this.surfaces_color=b.default_surfaces_color;this.surfaces_materialAmbientColor_3D=b.default_surfaces_materialAmbientColor_3D;
this.surfaces_materialSpecularColor_3D=b.default_surfaces_materialSpecularColor_3D;this.surfaces_materialShininess_3D=b.default_surfaces_materialShininess_3D;this.plots_color=b.default_plots_color;this.plots_width=b.default_plots_width;this.plots_showIntegration=b.default_plots_showIntegration;this.plots_integrationColor=b.default_plots_integrationColor;this.plots_integrationLineWidth=b.default_plots_integrationLineWidth;this.plots_showGrid=b.default_plots_showGrid;this.plots_gridColor=b.default_plots_gridColor;
this.plots_gridLineWidth=b.default_plots_gridLineWidth;this.plots_showYAxis=b.default_plots_showYAxis;this.plots_flipXAxis=b.default_plots_flipXAxis;this.text_font_size=b.default_text_font_size;this.text_font_families=b.default_text_font_families.slice(0);this.text_font_bold=b.default_text_font_bold;this.text_font_italic=b.default_text_font_italic;this.text_font_stroke_3D=b.default_text_font_stroke_3D;this.text_color=b.default_text_color;this.shapes_color=b.default_shapes_color;this.shapes_lineWidth=
b.default_shapes_lineWidth;this.shapes_arrowLength_2D=b.default_shapes_arrowLength_2D;this.compass_display=b.default_compass_display;this.compass_axisXColor_3D=b.default_compass_axisXColor_3D;this.compass_axisYColor_3D=b.default_compass_axisYColor_3D;this.compass_axisZColor_3D=b.default_compass_axisZColor_3D;this.compass_size_3D=b.default_compass_size_3D;this.compass_resolution_3D=b.default_compass_resolution_3D;this.compass_displayText_3D=b.default_compass_displayText_3D;this.compass_type_3D=b.default_compass_type_3D;
this.measurement_update_3D=b.default_measurement_update_3D;this.measurement_angleBands_3D=b.default_measurement_angleBands_3D;this.measurement_displayText_3D=b.default_measurement_displayText_3D};j.VisualSpecifications.prototype.set3DRepresentation=function(j){this.bonds_display=this.atoms_display=!0;this.bonds_color="#777777";this.bonds_showBondOrders_3D=this.bonds_useJMOLColors=this.atoms_useJMOLColors=this.atoms_useVDWDiameters_3D=!0;this.bonds_renderAsLines_3D=!1;"Ball and Stick"===j?(this.atoms_vdwMultiplier_3D=
0.3,this.bonds_useJMOLColors=!1,this.bonds_cylinderDiameter_3D=0.3,this.bonds_materialAmbientColor_3D=b.default_atoms_materialAmbientColor_3D,this.bonds_pillDiameter_3D=0.15):"van der Waals Spheres"===j?(this.bonds_display=!1,this.atoms_vdwMultiplier_3D=1):"Stick"===j?(this.bonds_showBondOrders_3D=this.atoms_useVDWDiameters_3D=!1,this.bonds_cylinderDiameter_3D=this.atoms_sphereDiameter_3D=0.8,this.bonds_materialAmbientColor_3D=this.atoms_materialAmbientColor_3D):"Wireframe"===j?(this.atoms_useVDWDiameters_3D=
!1,this.bonds_cylinderDiameter_3D=this.bonds_pillDiameter_3D=0.05,this.atoms_sphereDiameter_3D=0.15,this.bonds_materialAmbientColor_3D=b.default_atoms_materialAmbientColor_3D):"Line"===j?(this.atoms_display=!1,this.bonds_renderAsLines_3D=!0,this.bonds_width_2D=1,this.bonds_cylinderDiameter_3D=0.05):alert('"'+j+'" is not recognized. Use one of the following strings:\n\n1. Ball and Stick\n2. van der Waals Spheres\n3. Stick\n4. Wireframe\n5. Line\n')}})(ChemDoodle,ChemDoodle.structures,Math);
(function(b,j,o,l){o.getPointsPerAngstrom=function(){return b.default_bondLength_2D/b.default_angstromsPerBondLength};o.BondDeducer=function(){};var h=o.BondDeducer.prototype;h.margin=1.1;h.deduceCovalentBonds=function(b,e){var a=o.getPointsPerAngstrom();e&&(a=e);for(var d=0,h=b.atoms.length;d<h;d++)for(var f=d+1;f<h;f++){var y=b.atoms[d],p=b.atoms[f];y.distance3D(p)<(j[y.label].covalentRadius+j[p.label].covalentRadius)*a*this.margin&&b.bonds.push(new l.Bond(y,p,1))}}})(ChemDoodle,ChemDoodle.ELEMENT,
ChemDoodle.informatics,ChemDoodle.structures);
(function(b,j){b.HydrogenDeducer=function(){};b.HydrogenDeducer.prototype.removeHydrogens=function(b,l){for(var h=[],g=[],e=0,a=b.bonds.length;e<a;e++){var d=b.bonds[e],n="H"!==d.a1.label&&"H"!==d.a2.label;!n&&(!l&&d.stereo!==j.Bond.STEREO_NONE)&&(n=!0);n?(d.a1.tag=!0,g.push(d)):("H"===d.a1.label&&(d.a1.remove=!0),"H"===d.a2.label&&(d.a2.remove=!0))}e=0;for(a=b.atoms.length;e<a;e++)d=b.atoms[e],d.remove?d.remove=void 0:h.push(d);b.atoms=h;b.bonds=g}})(ChemDoodle.informatics,ChemDoodle.structures);
(function(b,j,o){j.MolecularSurfaceGenerator=function(){};j.MolecularSurfaceGenerator.prototype.generateSurface=function(b,h,g,e,a){return new o.MolecularSurface(b,h,g,e,a)}})(ChemDoodle,ChemDoodle.informatics,ChemDoodle.structures.d3);
(function(b,j){b.Splitter=function(){};b.Splitter.prototype.split=function(b){for(var l=[],h=0,g=b.atoms.length;h<g;h++)b.atoms[h].visited=!1;h=0;for(g=b.bonds.length;h<g;h++)b.bonds[h].visited=!1;h=0;for(g=b.atoms.length;h<g;h++){var e=b.atoms[h];if(!e.visited){var a=new j.Molecule;a.atoms.push(e);e.visited=!0;var d=new j.Queue;for(d.enqueue(e);!d.isEmpty();)for(var e=d.dequeue(),n=0,f=b.bonds.length;n<f;n++){var y=b.bonds[n];y.contains(e)&&!y.visited&&(y.visited=!0,a.bonds.push(y),y=y.getNeighbor(e),
y.visited||(y.visited=!0,a.atoms.push(y),d.enqueue(y)))}l.push(a)}}return l}})(ChemDoodle.informatics,ChemDoodle.structures);(function(b,j){b.StructureBuilder=function(){};b.StructureBuilder.prototype.copy=function(b){var l=new j.JSONInterpreter;return l.molFrom(l.molTo(b))}})(ChemDoodle.informatics,ChemDoodle.io,ChemDoodle.structures);
(function(b){b._Counter=function(){};b=b._Counter.prototype;b.value=0;b.molecule=void 0;b.setMolecule=function(b){this.value=0;this.molecule=b;this.innerCalculate&&this.innerCalculate()}})(ChemDoodle.informatics);(function(b){b.FrerejacqueNumberCounter=function(b){this.setMolecule(b)};(b.FrerejacqueNumberCounter.prototype=new b._Counter).innerCalculate=function(){this.value=this.molecule.bonds.length-this.molecule.atoms.length+(new b.NumberOfMoleculesCounter(this.molecule)).value}})(ChemDoodle.informatics);
(function(b,j){j.NumberOfMoleculesCounter=function(b){this.setMolecule(b)};(j.NumberOfMoleculesCounter.prototype=new j._Counter).innerCalculate=function(){for(var j=0,l=this.molecule.atoms.length;j<l;j++)this.molecule.atoms[j].visited=!1;j=0;for(l=this.molecule.atoms.length;j<l;j++)if(!this.molecule.atoms[j].visited){this.value++;var h=new b.Queue;this.molecule.atoms[j].visited=!0;for(h.enqueue(this.molecule.atoms[j]);!h.isEmpty();)for(var g=h.dequeue(),e=0,a=this.molecule.bonds.length;e<a;e++){var d=
this.molecule.bonds[e];d.contains(g)&&(d=d.getNeighbor(g),d.visited||(d.visited=!0,h.enqueue(d)))}}}})(ChemDoodle.structures,ChemDoodle.informatics);
(function(b){b._RingFinder=function(){};b=b._RingFinder.prototype;b.atoms=void 0;b.bonds=void 0;b.rings=void 0;b.reduce=function(b){for(var o=0,l=b.atoms.length;o<l;o++)b.atoms[o].visited=!1;o=0;for(l=b.bonds.length;o<l;o++)b.bonds[o].visited=!1;for(var h=!0;h;){h=!1;o=0;for(l=b.atoms.length;o<l;o++){for(var g=0,e,a=0,d=b.bonds.length;a<d;a++)if(b.bonds[a].contains(b.atoms[o])&&!b.bonds[a].visited){g++;if(2===g)break;e=b.bonds[a]}1===g&&(h=!0,e.visited=!0,b.atoms[o].visited=!0)}}o=0;for(l=b.atoms.length;o<
l;o++)b.atoms[o].visited||this.atoms.push(b.atoms[o]);o=0;for(l=b.bonds.length;o<l;o++)b.bonds[o].visited||this.bonds.push(b.bonds[o]);0===this.bonds.length&&0!==this.atoms.length&&(this.atoms=[])};b.setMolecule=function(b){this.atoms=[];this.bonds=[];this.rings=[];this.reduce(b);2<this.atoms.length&&this.innerGetRings&&this.innerGetRings()};b.fuse=function(){for(var b=0,o=this.rings.length;b<o;b++)for(var l=0,h=this.bonds.length;l<h;l++)-1!==this.rings[b].atoms.indexOf(this.bonds[l].a1)&&-1!==this.rings[b].atoms.indexOf(this.bonds[l].a2)&&
this.rings[b].bonds.push(this.bonds[l])}})(ChemDoodle.informatics);
(function(b,j){function o(b,g){this.atoms=[];if(g)for(var e=0,a=g.atoms.length;e<a;e++)this.atoms[e]=g.atoms[e];this.atoms.push(b)}var l=o.prototype;l.grow=function(b,g){for(var e=this.atoms[this.atoms.length-1],a=[],d=0,j=b.length;d<j;d++)if(b[d].contains(e)){var f=b[d].getNeighbor(e);-1===g.indexOf(f)&&a.push(f)}e=[];d=0;for(j=a.length;d<j;d++)e.push(new o(a[d],this));return e};l.check=function(b,g,e){for(var a=0,d=g.atoms.length-1;a<d;a++)if(-1!==this.atoms.indexOf(g.atoms[a]))return;var n;if(g.atoms[g.atoms.length-
1]===this.atoms[this.atoms.length-1]){n=new j.Ring;n.atoms[0]=e;a=0;for(d=this.atoms.length;a<d;a++)n.atoms.push(this.atoms[a]);for(a=g.atoms.length-2;0<=a;a--)n.atoms.push(g.atoms[a])}else{for(var f=[],a=0,d=b.length;a<d;a++)b[a].contains(g.atoms[g.atoms.length-1])&&f.push(b[a]);a=0;for(d=f.length;a<d;a++)if((1===g.atoms.length||!f[a].contains(g.atoms[g.atoms.length-2]))&&f[a].contains(this.atoms[this.atoms.length-1])){n=new j.Ring;n.atoms[0]=e;b=0;for(e=this.atoms.length;b<e;b++)n.atoms.push(this.atoms[b]);
for(b=g.atoms.length-1;0<=b;b--)n.atoms.push(g.atoms[b]);break}}return n};b.EulerFacetRingFinder=function(b){this.setMolecule(b)};l=b.EulerFacetRingFinder.prototype=new b._RingFinder;l.fingerBreak=5;l.innerGetRings=function(){for(var b=0,g=this.atoms.length;b<g;b++){for(var e=[],a=0,d=this.bonds.length;a<d;a++)this.bonds[a].contains(this.atoms[b])&&e.push(this.bonds[a].getNeighbor(this.atoms[b]));a=0;for(d=e.length;a<d;a++)for(var j=a+1;j<e.length;j++){var f=[];f[0]=new o(e[a]);f[1]=new o(e[j]);var l=
[];l[0]=this.atoms[b];for(var p=0,q=e.length;p<q;p++)p!==a&&p!==j&&l.push(e[p]);var A=[];for((p=f[0].check(this.bonds,f[1],this.atoms[b]))&&(A[0]=p);0===A.length&&0<f.length&&f[0].atoms.length<this.fingerBreak;){for(var r=[],p=0,q=f.length;p<q;p++)for(var v=f[p].grow(this.bonds,l),u=0,t=v.length;u<t;u++)r.push(v[u]);f=r;p=0;for(q=f.length;p<q;p++)for(u=p+1;u<q;u++)(t=f[p].check(this.bonds,f[u],this.atoms[b]))&&A.push(t);if(0===A.length){r=[];p=0;for(q=l.length;p<q;p++){u=0;for(t=this.bonds.length;u<
t;u++)this.bonds[u].contains(l[p])&&(e=this.bonds[u].getNeighbor(l[p]),-1===l.indexOf(e)&&-1===r.indexOf(e)&&r.push(e))}p=0;for(q=r.length;p<q;p++)l.push(r[p])}}if(0<A.length){f=void 0;p=0;for(q=A.length;p<q;p++)if(!f||f.atoms.length>A[p].atoms.length)f=A[p];A=!1;p=0;for(q=this.rings.length;p<q;p++){l=!0;u=0;for(t=f.atoms.length;u<t;u++)if(-1===this.rings[p].atoms.indexOf(f.atoms[u])){l=!1;break}if(l){A=!0;break}}A||this.rings.push(f)}}}this.fuse()}})(ChemDoodle.informatics,ChemDoodle.structures);
(function(b){b.SSSRFinder=function(j){this.rings=[];if(0<j.atoms.length){var o=(new b.FrerejacqueNumberCounter(j)).value,l=(new b.EulerFacetRingFinder(j)).rings;l.sort(function(a,b){return a.atoms.length-b.atoms.length});for(var h=0,g=j.bonds.length;h<g;h++)j.bonds[h].visited=!1;h=0;for(g=l.length;h<g;h++){j=!1;for(var e=0,a=l[h].bonds.length;e<a;e++)if(!l[h].bonds[e].visited){j=!0;break}if(j){e=0;for(a=l[h].bonds.length;e<a;e++)l[h].bonds[e].visited=!0;this.rings.push(l[h])}if(this.rings.length===
o)break}}}})(ChemDoodle.informatics);(function(b){b._Interpreter=function(){};b._Interpreter.prototype.fit=function(b,o,l){for(var h=b.length,g=[],e=0;e<o-h;e++)g.push(" ");return l?b+g.join(""):g.join("")+b}})(ChemDoodle.io);
(function(b,j,o,l,h,g,e){var a=/\s+/g,d=/\(|\)|\s+/g,n=/\'|\s+/g,f=/,|\'|\s+/g,y=/^\s+/,p=/[0-9]/g,q=/[0-9]|\+|\-/g,A=function(a){return 0!==a.length},r={P:[],A:[[0,0.5,0.5]],B:[[0.5,0,0.5]],C:[[0.5,0.5,0]],I:[[0.5,0.5,0.5]],R:[[2/3,1/3,1/3],[1/3,2/3,2/3]],S:[[1/3,1/3,2/3],[2/3,2/3,1/3]],T:[[1/3,2/3,1/3],[2/3,1/3,2/3]],F:[[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]},v=function(a){var b=0,d=0,e=0,c=0,f=a.indexOf("x"),g=a.indexOf("y"),h=a.indexOf("z");-1!==f&&(d++,0<f&&"+"!==a.charAt(f-1)&&(d*=-1));-1!==g&&
(e++,0<g&&"+"!==a.charAt(g-1)&&(e*=-1));-1!==h&&(c++,0<h&&"+"!==a.charAt(h-1)&&(c*=-1));if(2<a.length){f="+";g=0;for(h=a.length;g<h;g++){var j=a.charAt(g);if(("-"===j||"/"===j)&&(g===a.length-1||a.charAt(g+1).match(p)))f=j;j.match(p)&&("+"===f?b+=parseInt(j):"-"===f?b-=parseInt(j):"/"===f&&(b/=parseInt(j)))}}return[b,d,e,c]};o.CIFInterpreter=function(){};(o.CIFInterpreter.prototype=new o._Interpreter).read=function(p,o,u,B){o=o?o:1;u=u?u:1;B=B?B:1;var c=new l.Molecule;if(!p)return c;for(var k=p.split("\n"),
C=0,D=0,G=0,E=p=0,H=0,I="P",M,J,T,F,W=!0;0<k.length;)if(W?F=k.shift():W=!0,0<F.length)if(j.stringStartsWith(F,"_cell_length_a"))C=parseFloat(F.split(d)[1]);else if(j.stringStartsWith(F,"_cell_length_b"))D=parseFloat(F.split(d)[1]);else if(j.stringStartsWith(F,"_cell_length_c"))G=parseFloat(F.split(d)[1]);else if(j.stringStartsWith(F,"_cell_angle_alpha"))p=g.PI*parseFloat(F.split(d)[1])/180;else if(j.stringStartsWith(F,"_cell_angle_beta"))E=g.PI*parseFloat(F.split(d)[1])/180;else if(j.stringStartsWith(F,
"_cell_angle_gamma"))H=g.PI*parseFloat(F.split(d)[1])/180;else if(j.stringStartsWith(F,"_symmetry_space_group_name_H-M"))I=F.split(n)[1];else if(j.stringStartsWith(F,"loop_")){for(var R={fields:[],lines:[]},O=!1;void 0!==(F=k.shift())&&!j.stringStartsWith(F=F.replace(y,""),"loop_")&&0<F.length;)if(j.stringStartsWith(F,"_")){if(O)break;R.fields=R.fields.concat(F.split(a).filter(A))}else O=!0,R.lines.push(F);if(0!==k.length&&(j.stringStartsWith(F,"loop_")||j.stringStartsWith(F,"_")))W=!1;-1!==R.fields.indexOf("_symmetry_equiv_pos_as_xyz")||
-1!==R.fields.indexOf("_space_group_symop_operation_xyz")?M=R:-1!==R.fields.indexOf("_atom_site_label")?J=R:-1!==R.fields.indexOf("_geom_bond_atom_site_label_1")&&(T=R)}F=C;p=(g.cos(p)-g.cos(H)*g.cos(E))/g.sin(H);p=[F,0,0,0,D*g.cos(H),D*g.sin(H),0,0,G*g.cos(E),G*p,G*g.sqrt(1-g.pow(g.cos(E),2)-p*p),0,0,0,0,1];if(J){R=W=C=k=G=-1;H=0;for(E=J.fields.length;H<E;H++)F=J.fields[H],"_atom_site_type_symbol"===F?G=H:"_atom_site_label"===F?k=H:"_atom_site_fract_x"===F?C=H:"_atom_site_fract_y"===F?W=H:"_atom_site_fract_z"===
F&&(R=H);H=0;for(E=J.lines.length;H<E;H++)F=J.lines[H],D=F.split(a).filter(A),F=new l.Atom(D[-1===G?k:G].split(q)[0],parseFloat(D[C]),parseFloat(D[W]),parseFloat(D[R])),c.atoms.push(F),-1!==k&&(F.cifId=D[k],F.cifPart=0)}if(M&&!T){H=D=0;for(E=M.fields.length;H<E;H++)if(F=M.fields[H],"_symmetry_equiv_pos_as_xyz"===F||"_space_group_symop_operation_xyz"===F)D=H;W=r[I];k=[];H=0;for(E=M.lines.length;H<E;H++){F=M.lines[H].split(f).filter(A);for(var R=v(F[D]),O=v(F[D+1]),L=v(F[D+2]),I=0,C=c.atoms.length;I<
C;I++){F=c.atoms[I];var Z=F.x*R[1]+F.y*R[2]+F.z*R[3]+R[0],Da=F.x*O[1]+F.y*O[2]+F.z*O[3]+O[0],ka=F.x*L[1]+F.y*L[2]+F.z*L[3]+L[0];J=new l.Atom(F.label,Z,Da,ka);k.push(J);void 0!==F.cifId&&(J.cifId=F.cifId,J.cifPart=H+1);if(W){J=0;for(G=W.length;J<G;J++){var $=W[J],$=new l.Atom(F.label,Z+$[0],Da+$[1],ka+$[2]);k.push($);void 0!==F.cifId&&($.cifId=F.cifId,$.cifPart=H+1)}}}}H=0;for(E=k.length;H<E;H++){for(F=k[H];1<=F.x;)F.x--;for(;0>F.x;)F.x++;for(;1<=F.y;)F.y--;for(;0>F.y;)F.y++;for(;1<=F.z;)F.z--;for(;0>
F.z;)F.z++}J=[];H=0;for(E=k.length;H<E;H++){G=!1;F=k[H];I=0;for(C=c.atoms.length;I<C;I++)if(1E-4>c.atoms[I].distance3D(F)){G=!0;break}if(!G){I=0;for(C=J.length;I<C;I++)if(1E-4>J[I].distance3D(F)){G=!0;break}G||J.push(F)}}c.atoms=c.atoms.concat(J)}E=[];for(H=0;H<o;H++)for(I=0;I<u;I++)for(J=0;J<B;J++)if(!(0===H&&0===I&&0===J)){G=0;for(D=c.atoms.length;G<D;G++)F=c.atoms[G],k=new l.Atom(F.label,F.x+H,F.y+I,F.z+J),E.push(k),void 0!==F.cifId&&(k.cifId=F.cifId,k.cifPart=F.cifPart+(M?M.lines.length:0)+H+
10*I+100*J)}c.atoms=c.atoms.concat(E);H=0;for(E=c.atoms.length;H<E;H++)F=c.atoms[H],M=e.multiplyVec3(p,[F.x,F.y,F.z]),F.x=M[0],F.y=M[1],F.z=M[2];if(T){k=M=-1;H=0;for(E=T.fields.length;H<E;H++)F=T.fields[H],"_geom_bond_atom_site_label_1"===F?M=H:"_geom_bond_atom_site_label_2"===F&&(k=H);J=0;for(G=T.lines.length;J<G;J++){D=T.lines[J].split(a).filter(A);F=D[M];D=D[k];H=0;for(E=c.atoms.length;H<E;H++)for(I=H+1;I<E;I++){C=c.atoms[H];W=c.atoms[I];if(C.cifPart!==W.cifPart)break;(C.cifId===F&&W.cifId===D||
C.cifId===D&&W.cifId===F)&&c.bonds.push(new l.Bond(C,W))}}}else(new b.informatics.BondDeducer).deduceCovalentBonds(c,1);o=[-o/2,-u/2,-B/2];o={o:e.multiplyVec3(p,o,[]),x:e.multiplyVec3(p,[o[0]+1,o[1],o[2]]),y:e.multiplyVec3(p,[o[0],o[1]+1,o[2]]),z:e.multiplyVec3(p,[o[0],o[1],o[2]+1]),xy:e.multiplyVec3(p,[o[0]+1,o[1]+1,o[2]]),xz:e.multiplyVec3(p,[o[0]+1,o[1],o[2]+1]),yz:e.multiplyVec3(p,[o[0],o[1]+1,o[2]+1]),xyz:e.multiplyVec3(p,[o[0]+1,o[1]+1,o[2]+1])};return{molecule:c,unitCell:new h.UnitCell(o)}};
var u=new o.CIFInterpreter;b.readCIF=function(a,b,d,e){return u.read(a,b,d,e)}})(ChemDoodle,ChemDoodle.extensions,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.structures.d3,Math,ChemDoodle.lib.mat4,ChemDoodle.lib.vec3);
(function(b,j,o,l){j.CMLInterpreter=function(){};var h=j.CMLInterpreter.prototype=new j._Interpreter;h.read=function(b){var a=[];b=l.parseXML(b);b=l(b).find("cml");for(var d=0,g=b.length;d<g;d++)for(var f=l(b[d]).find("molecule"),h=0,j=f.length;h<j;h++){for(var q=a[h]=new o.Molecule,A=[],r=l(f[h]).find("atom"),v=0,u=r.length;v<u;v++){var t=l(r[v]),w=t.attr("elementType"),x,B,c;void 0==t.attr("x2")?(x=t.attr("x3"),B=t.attr("y3"),c=t.attr("z3")):(x=t.attr("x2"),B=t.attr("y2"),c=0);w=a[h].atoms[v]=new o.Atom(w,
x,B,c);A[v]=t.attr("id");void 0!=t.attr("formalCharge")&&(w.charge=t.attr("formalCharge"))}r=l(f[h]).find("bond");v=0;for(u=r.length;v<u;v++){t=l(r[v]);x=t.attr("atomRefs2").split(" ");w=q.atoms[l.inArray(x[0],A)];x=q.atoms[l.inArray(x[1],A)];switch(t.attr("order")){case "2":case "D":B=2;break;case "3":case "T":B=3;break;case "A":B=1.5;break;default:B=1}w=a[h].bonds[v]=new o.Bond(w,x,B);switch(t.find("bondStereo").text()){case "W":w.stereo=o.Bond.STEREO_PROTRUDING;break;case "H":w.stereo=o.Bond.STEREO_RECESSED}}}return a};
h.write=function(b){var a=[];a.push('\x3c?xml version\x3d"1.0" encoding\x3d"UTF-8"?\x3e\n');a.push('\x3ccml convention\x3d"conventions:molecular" xmlns\x3d"http://www.xml-cml.org/schema" xmlns:conventions\x3d"http://www.xml-cml.org/convention/" xmlns:dc\x3d"http://purl.org/dc/elements/1.1/"\x3e\n');for(var d=0,g=b.length;d<g;d++){a.push('\x3cmolecule id\x3d"m');a.push(d);a.push('"\x3e');a.push("\x3catomArray\x3e");for(var f=0,h=b[d].atoms.length;f<h;f++){var j=b[d].atoms[f];a.push('\x3catom elementType\x3d"');
a.push(j.label);a.push('" id\x3d"a');a.push(f);a.push('" ');a.push('x3\x3d"');a.push(j.x);a.push('" y3\x3d"');a.push(j.y);a.push('" z3\x3d"');a.push(j.z);a.push('" ');0!=j.charge&&(a.push('formalCharge\x3d"'),a.push(j.charge),a.push('" '));a.push("/\x3e")}a.push("\x3c/atomArray\x3e");a.push("\x3cbondArray\x3e");f=0;for(h=b[d].bonds.length;f<h;f++){j=b[d].bonds[f];a.push('\x3cbond atomRefs2\x3d"a');a.push(b[d].atoms.indexOf(j.a1));a.push(" a");a.push(b[d].atoms.indexOf(j.a2));a.push('" order\x3d"');
switch(j.bondOrder){case 1.5:a.push("A");break;case 1:case 2:case 3:a.push(j.bondOrder);break;default:a.push("S")}a.push('"/\x3e')}a.push("\x3c/bondArray\x3e");a.push("\x3c/molecule\x3e")}a.push("\x3c/cml\x3e");return a.join("")};var g=new j.CMLInterpreter;b.readCML=function(b){return g.read(b)};b.writeCML=function(b){return g.write(b)}})(ChemDoodle,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.lib.jQuery);
(function(b,j,o,l){o.MOLInterpreter=function(){};var h=o.MOLInterpreter.prototype=new o._Interpreter;h.read=function(e,a){a||(a=b.default_bondLength_2D);var d=new l.Molecule;if(!e)return d;for(var g=e.split("\n"),f=g[3],h=parseInt(f.substring(0,3)),f=parseInt(f.substring(3,6)),p=0;p<h;p++){var q=g[4+p];d.atoms[p]=new l.Atom(q.substring(31,34),parseFloat(q.substring(0,10))*a,(1===a?1:-1)*parseFloat(q.substring(10,20))*a,parseFloat(q.substring(20,30))*a);var o=parseInt(q.substring(34,36));0!==o&&j[d.atoms[p].label]&&
(d.atoms[p].mass=j[d.atoms[p].label].mass+o);switch(parseInt(q.substring(36,39))){case 1:d.atoms[p].charge=3;break;case 2:d.atoms[p].charge=2;break;case 3:d.atoms[p].charge=1;break;case 5:d.atoms[p].charge=-1;break;case 6:d.atoms[p].charge=-2;break;case 7:d.atoms[p].charge=-3}}for(p=0;p<f;p++){var q=g[4+h+p],r=parseInt(q.substring(6,9)),o=parseInt(q.substring(9,12));if(3<r)switch(r){case 4:r=1.5;break;default:r=1}q=new l.Bond(d.atoms[parseInt(q.substring(0,3))-1],d.atoms[parseInt(q.substring(3,6))-
1],r);switch(o){case 3:q.stereo=l.Bond.STEREO_AMBIGUOUS;break;case 1:q.stereo=l.Bond.STEREO_PROTRUDING;break;case 6:q.stereo=l.Bond.STEREO_RECESSED}d.bonds[p]=q}return d};h.write=function(e){var a=[];a.push("Molecule from ChemDoodle Web Components\n\nhttp://www.ichemlabs.com\n");a.push(this.fit(e.atoms.length.toString(),3));a.push(this.fit(e.bonds.length.toString(),3));a.push("  0  0  0  0            999 V2000\n");for(var d=e.getCenter(),g=0,f=e.atoms.length;g<f;g++){var h=e.atoms[g],p=" 0";if(-1!==
h.mass&&j[h.label]){var q=h.mass-j[h.label].mass;5>q&&-4<q&&(p=(-1<q?" ":"")+q)}q="  0";if(0!==h.charge)switch(h.charge){case 3:q="  1";break;case 2:q="  2";break;case 1:q="  3";break;case -1:q="  5";break;case -2:q="  6";break;case -3:q="  7"}a.push(this.fit(((h.x-d.x)/b.default_bondLength_2D).toFixed(4),10));a.push(this.fit((-(h.y-d.y)/b.default_bondLength_2D).toFixed(4),10));a.push(this.fit((h.z/b.default_bondLength_2D).toFixed(4),10));a.push(" ");a.push(this.fit(h.label,3,!0));a.push(p);a.push(q);
a.push("  0  0  0  0\n")}g=0;for(f=e.bonds.length;g<f;g++){h=e.bonds[g];d=0;h.stereo===l.Bond.STEREO_AMBIGUOUS?d=3:h.stereo===l.Bond.STEREO_PROTRUDING?d=1:h.stereo===l.Bond.STEREO_RECESSED&&(d=6);a.push(this.fit((e.atoms.indexOf(h.a1)+1).toString(),3));a.push(this.fit((e.atoms.indexOf(h.a2)+1).toString(),3));h=h.bondOrder;if(1.5==h)h=4;else if(3<h||0!=h%1)h=1;a.push(this.fit(h,3));a.push("  ");a.push(d);a.push("     0  0\n")}a.push("M  END");return a.join("")};var g=new o.MOLInterpreter;b.readMOL=
function(b,a){return g.read(b,a)};b.writeMOL=function(b){return g.write(b)}})(ChemDoodle,ChemDoodle.ELEMENT,ChemDoodle.io,ChemDoodle.structures);
(function(b,j,o,l,h,g,e){function a(a,b,d,e,g){for(var h=0,j=b.length;h<j;h++){var n=b[h];if(n.id===d&&e>=n.start&&e<=n.end){g?a.helix=!0:a.sheet=!0;e===n.end&&(a.arrow=!0);break}}}o.PDBInterpreter=function(){};var d=o.PDBInterpreter.prototype=new o._Interpreter;d.calculateRibbonDistances=!1;d.deduceResidueBonds=!1;d.read=function(d,n){var p=new l.Molecule;p.chains=[];if(!d)return p;var q=d.split("\n");n||(n=1);for(var o=[],r=[],v,u=[],t=[],w=[],x=0,B=q.length;x<B;x++){var c=q[x];if(j.stringStartsWith(c,
"HELIX"))o.push({id:c.substring(19,20),start:parseInt(c.substring(21,25)),end:parseInt(c.substring(33,37))});else if(j.stringStartsWith(c,"SHEET"))r.push({id:c.substring(21,22),start:parseInt(c.substring(22,26)),end:parseInt(c.substring(33,37))});else if(j.stringStartsWith(c,"ATOM")){var k=c.substring(16,17);if(" "===k||"A"===k){k=g(c.substring(76,78));if(0===k.length){var C=g(c.substring(12,14));"HD"===C?k="H":0<C.length&&(k=1<C.length?C.charAt(0)+C.substring(1).toLowerCase():C)}C=new l.Atom(k,parseFloat(c.substring(30,
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a(k,r,G,D,!1));c=g(c.substring(12,16));k=u[u.length-1];if("CA"===c||"P"===c||"O5'"===c)k.cp1||(k.cp1=C);else if("N3"===c&&("C"===k.name||"U"===k.name||"T"===k.name)||"N1"===c&&("A"===k.name||"G"===k.name))k.cp3=C;else if("C2"===c)k.cp4=C;else if("C4"===c&&("C"===k.name||"U"===k.name||"T"===k.name)||"C6"===c&&("A"===k.name||"G"===k.name))k.cp5=C;else if("O"===c||"C6"===c&&("C"===k.name||"U"===k.name||"T"===k.name)||"N9"===c){if(!u[u.length-1].cp2){if("C6"===c||"N9"===c)v=C;k.cp2=C}}else"C"===c&&(v=
C)}}else if(j.stringStartsWith(c,"HETATM"))k=g(c.substring(76,78)),0===k.length&&(k=g(c.substring(12,16))),1<k.length&&(k=k.substring(0,1)+k.substring(1).toLowerCase()),k=new l.Atom(k,parseFloat(c.substring(30,38))*n,parseFloat(c.substring(38,46))*n,parseFloat(c.substring(46,54))*n),k.hetatm=!0,"HOH"===g(c.substring(17,20))&&(k.isWater=!0),p.atoms.push(k),w[parseInt(g(c.substring(6,11)))]=k;else if(j.stringStartsWith(c,"CONECT")){if(k=parseInt(g(c.substring(6,11))),w[k]){C=w[k];for(D=0;4>D;D++)if(k=
g(c.substring(11+5*D,16+5*D)),0!==k.length&&(k=parseInt(k),w[k])){for(var G=w[k],E=!1,k=0,H=p.bonds.length;k<H;k++){var I=p.bonds[k];if(I.a1===C&&I.a2===G||I.a1===G&&I.a2===C){E=!0;break}}E||p.bonds.push(new l.Bond(C,G))}}}else if(j.stringStartsWith(c,"TER"))this.endChain(p,u,v,t),u=[];else if(j.stringStartsWith(c,"ENDMDL"))break}this.endChain(p,u,v,t);0===p.bonds.size&&(new b.informatics.BondDeducer).deduceCovalentBonds(p,n);if(this.deduceResidueBonds){x=0;for(B=t.length;x<B;x++){q=e.min(B,x+20);
for(k=x+1;k<q;k++)o=t[x],r=t[k],o.distance3D(r)<1.1*(h[o.label].covalentRadius+h[r.label].covalentRadius)&&p.bonds.push(new l.Bond(o,r,1))}}p.atoms=p.atoms.concat(t);this.calculateRibbonDistances&&this.calculateDistances(p,t);return p};d.endChain=function(a,b,d,e){if(0<b.length){var g=b[b.length-1];g.cp1||(g.cp1=e[e.length-2]);g.cp2||(g.cp2=e[e.length-1]);for(e=0;4>e;e++)g=new l.Residue(-1),g.cp1=d,g.cp2=b[b.length-1].cp2,b.push(g);a.chains.push(b)}};d.calculateDistances=function(a,b){for(var d=[],
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(function(b,j,o,l){var h={"@":0,A:1,B:2,C:3,D:4,E:5,F:6,G:7,H:8,I:9,a:-1,b:-2,c:-3,d:-4,e:-5,f:-6,g:-7,h:-8,i:-9},g={"%":0,J:1,K:2,L:3,M:4,N:5,O:6,P:7,Q:8,R:9,j:-1,k:-2,l:-3,m:-4,n:-5,o:-6,p:-7,q:-8,r:-9},e={S:1,T:2,U:3,V:4,W:5,X:6,Y:7,Z:8,s:9};o.JCAMPInterpreter=function(){};var a=o.JCAMPInterpreter.prototype=new o._Interpreter;a.convertHZ2PPM=!1;a.read=function(a){this.isBreak=function(a){return void 0!==h[a]||void 0!==g[a]||void 0!==e[a]||" "===a||"-"===a||"+"===a};this.getValue=function(a,b){var c=
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"##FIRSTY\x3d"))o=parseFloat(E.substring(9).trim());else if(j.stringStartsWith(E,"##NPOINTS\x3d"))r=parseFloat(E.substring(10).trim());else if(j.stringStartsWith(E,"##XFACTOR\x3d"))v=parseFloat(E.substring(10).trim());else if(j.stringStartsWith(E,"##YFACTOR\x3d"))u=parseFloat(E.substring(10).trim());else if(j.stringStartsWith(E,"##DELTAX\x3d"))w=parseFloat(E.substring(9).trim());else if(j.stringStartsWith(E,"##.OBSERVE FREQUENCY\x3d"))this.convertHZ2PPM&&(t=parseFloat(E.substring(21).trim()));else if(j.stringStartsWith(E,
"##.SHIFT REFERENCE\x3d"))this.convertHZ2PPM&&(B=E.substring(19).split(","),x=parseInt(B[2].trim()),B=parseFloat(B[3].trim()));else if(j.stringStartsWith(E,"##XYDATA\x3d")){k||(t=1);var H=c=!1,G=E.split("\n"),I=(p-q)/(r-1);if(-1!==w)for(var E=1,M=G.length;E<M;E++)if("|"===G[E].charAt(0)){I=w;break}for(var J=q-I,T=o,F=0,W,E=1,M=G.length;E<M;E++){for(var R=[],J=G[E].trim(),d=[],O=!1,L=0,Z=J.length;L<Z;L++)this.isBreak(J.charAt(L))?(0<d.length&&!(1===d.length&&" "===d[0])&&R.push(d.join("")),d=[J.charAt(L)]):
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x){G=B-b.data[x-1].x;C=0;for(D=b.data.length;C<D;C++)b.data[C].x+=G}}else if(j.stringStartsWith(E,"##PEAK TABLE\x3d")){c=!1;b.continuous=!1;for(var G=E.split("\n"),$=0,H=/[\s,]+/,E=1,M=G.length;E<M;E++){O=G[E].split(H);$+=O.length/2;L=0;for(Z=O.length;L+1<Z;L+=2)b.data.push(new l.Point(parseFloat(O[L].trim()),parseFloat(O[L+1].trim())))}}else if(j.stringStartsWith(E,"##ATOMLIST\x3d")){b.molecule=new l.Molecule;G=E.split("\n");H=/[\s]+/;E=1;for(M=G.length;E<M;E++)O=G[E].split(H),b.molecule.atoms.push(new l.Atom(O[1]))}else if(j.stringStartsWith(E,
"##BONDLIST\x3d")){G=E.split("\n");H=/[\s]+/;E=1;for(M=G.length;E<M;E++)O=G[E].split(H),L=1,"D"===O[2]?L=2:"T"===O[2]&&(L=3),b.molecule.bonds.push(new l.Bond(b.molecule.atoms[parseInt(O[0])-1],b.molecule.atoms[parseInt(O[1])-1],L))}else if(b.molecule&&j.stringStartsWith(E,"##XY_RASTER\x3d")){G=E.split("\n");H=/[\s]+/;E=1;for(M=G.length;E<M;E++)O=G[E].split(H),I=b.molecule.atoms[parseInt(O[0])-1],I.x=parseInt(O[1]),I.y=parseInt(O[2]),4==O.length&&(I.z=parseInt(O[3]));b.molecule.scaleToAverageBondLength(20)}else if(j.stringStartsWith(E,
"##PEAK ASSIGNMENTS\x3d")){G=E.split("\n");H=/[\s,()<>]+/;b.assignments=[];E=1;for(M=G.length;E<M;E++){O=G[E].split(H);F=parseFloat(O[1]);R=parseFloat(O[2]);I=b.molecule.atoms[parseInt(O[3])-1];O=!1;L=0;for(Z=b.assignments.length;L<Z;L++)if(J=b.assignments[L],J.x===F){J.as.push(I);I.assigned=J;O=!0;break}O||(J={x:F,y:R,as:[I]},I.assigned=J,b.assignments.push(J))}}}b.setup();return b};a.makeStructureSpectrumSet=function(a,d){this.convertHZ2PPM=!0;var e=this.read(d),g=new b.ViewerCanvas(a+"_molecule",
200,200);g.specs.atoms_displayTerminalCarbonLabels_2D=!0;g.specs.atoms_displayImplicitHydrogens_2D=!0;g.mouseout=function(){if(0!==this.molecules.length){for(var a=0,b=this.molecules[0].atoms.length;a<b;a++)this.molecules[0].atoms[a].isHover=!1;e.hovered=void 0;this.repaint();h.repaint()}};g.touchend=g.mouseout;g.mousemove=function(a){if(0!==this.molecules.length){for(var b=void 0,d=0,f=this.molecules[0].atoms.length;d<f;d++){var g=this.molecules[0].atoms[d];g.isHover=!1;if(g.assigned&&(void 0===
b||a.p.distance(g)<a.p.distance(b)))b=g}e.hovered=void 0;if(20>a.p.distance(b)){d=0;for(f=b.assigned.as.length;d<f;d++)b.assigned.as[d].isHover=!0;h.spectrum.hovered=b.assigned}this.repaint();h.repaint()}};g.touchmove=g.mousemove;g.drawChildExtras=function(a){if(0!==this.molecules.length)for(var b=0,d=this.molecules[0].atoms.length;b<d;b++)this.molecules[0].atoms[b].drawDecorations(a)};var h=new b.ObserverCanvas(a+"_spectrum",400,200);h.specs.plots_showYAxis=!1;h.specs.plots_flipXAxis=!0;h.mouseout=
function(){if(this.spectrum&&this.spectrum.assignments){for(var a=0,b=g.molecules[0].atoms.length;a<b;a++)g.molecules[0].atoms[a].isHover=!1;this.spectrum.hovered=void 0;g.repaint();this.repaint()}};h.touchend=h.mouseout;h.mousemove=function(a){if(this.spectrum&&this.spectrum.assignments){for(var b=void 0,d=0,e=g.molecules[0].atoms.length;d<e;d++)g.molecules[0].atoms[d].isHover=!1;this.spectrum.hovered=void 0;d=0;for(e=this.spectrum.assignments.length;d<e;d++){var f=this.spectrum.assignments[d];if(void 0===
b||Math.abs(this.spectrum.getTransformedX(f.x,this.specs,this.spectrum.memory.width,this.spectrum.memory.offsetLeft)-a.p.x)<Math.abs(this.spectrum.getTransformedX(b.x,this.specs,this.spectrum.memory.width,this.spectrum.memory.offsetLeft)-a.p.x))b=f}if(20>Math.abs(this.spectrum.getTransformedX(b.x,this.specs,this.spectrum.memory.width,this.spectrum.memory.offsetLeft)-a.p.x)){d=0;for(e=b.as.length;d<e;d++)b.as[d].isHover=!0;this.spectrum.hovered=b}g.repaint();this.repaint()}};h.touchmove=h.mousemove;
h.drawChildExtras=function(a){if(this.spectrum&&this.spectrum.hovered){var b=this.spectrum.getTransformedX(this.spectrum.hovered.x,h.specs,this.spectrum.memory.width,this.spectrum.memory.offsetLeft);b>=this.spectrum.memory.offsetLeft&&b<this.spectrum.memory.width&&(a.save(),a.strokeStyle="#885110",a.lineWidth=3,a.beginPath(),a.moveTo(b,this.spectrum.memory.height-this.spectrum.memory.offsetBottom),a.lineTo(b,this.spectrum.getTransformedY(this.spectrum.hovered.y,h.specs,this.spectrum.memory.height,
this.spectrum.memory.offsetBottom,this.spectrum.memory.offsetTop)),a.stroke(),a.restore())}};e&&(h.loadSpectrum(e),e.molecule&&g.loadMolecule(e.molecule));return[g,h]};var d=new o.JCAMPInterpreter;d.convertHZ2PPM=!0;b.readJCAMP=function(a){return d.read(a)}})(ChemDoodle,ChemDoodle.extensions,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.lib.jQuery);
(function(b,j,o,l,h,g){j.JSONInterpreter=function(){};var e=j.JSONInterpreter.prototype;e.contentTo=function(a,b){for(var e=0,g=0,h=0,j=a.length;h<j;h++){for(var l=a[h],o=0,v=l.atoms.length;o<v;o++)l.atoms[o].tmpid="a"+e++;o=0;for(v=l.bonds.length;o<v;o++)l.bonds[o].tmpid="b"+g++}h=e=0;for(j=b.length;h<j;h++)b[h].tmpid="s"+e++;e={};if(a&&0<a.length){e.m=[];h=0;for(j=a.length;h<j;h++)e.m.push(this.molTo(a[h]))}if(b&&0<b.length){e.s=[];h=0;for(j=b.length;h<j;h++)e.s.push(this.shapeTo(b[h]))}h=0;for(j=
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j;h++)a.atoms[h].tmpid=void 0;h=0;for(j=a.bonds.length;h<j;h++)a.bonds[h].tmpid=void 0}e=0;for(g=b.shapes.length;e<g;e++)b.shapes[e].tmpid=void 0;return b};e.queryTo=function(a){var b={},e=function(b,e,f,g){e&&(b[f]={v:g?a.outputRange(e.v):e.v,n:e.not})};a.type===o.Query.TYPE_ATOM?(e(b,a.elements,"as"),e(b,a.chirality,"@"),e(b,a.aromatic,"A"),e(b,a.charge,"C",!0),e(b,a.hydrogens,"H",!0),e(b,a.ringCount,"R",!0),e(b,a.saturation,"S"),e(b,a.connectivity,"X",!0),e(b,a.connectivityNoH,"x",!0)):(e(b,a.orders,
"bs"),e(b,a.stereo,"@"),e(b,a.aromatic,"A"),e(b,a.ringCount,"R",!0));return b};e.molTo=function(a){for(var b={a:[]},e=0,g=a.atoms.length;e<g;e++){var h=a.atoms[e],j={x:h.x,y:h.y};h.tmpid&&(j.i=h.tmpid);"C"!==h.label&&(j.l=h.label);0!==h.z&&(j.z=h.z);0!==h.charge&&(j.c=h.charge);-1!==h.mass&&(j.m=h.mass);0!==h.numRadical&&(j.r=h.numRadical);0!==h.numLonePair&&(j.p=h.numLonePair);h.query&&(j.q=this.queryTo(h.query));b.a.push(j)}if(0<a.bonds.length){b.b=[];e=0;for(g=a.bonds.length;e<g;e++)h=a.bonds[e],
j={b:a.atoms.indexOf(h.a1),e:a.atoms.indexOf(h.a2)},h.tmpid&&(j.i=h.tmpid),1!==h.bondOrder&&(j.o=h.bondOrder),h.stereo!==o.Bond.STEREO_NONE&&(j.s=h.stereo),h.query&&(j.q=this.queryTo(h.query)),b.b.push(j)}return b};e.queryFrom=function(a){var b=new o.Query(a.as?o.Query.TYPE_ATOM:o.Query.TYPE_BOND),e=function(a,b,d,e){b&&(a[d]={},a[d].v=e?a.parseRange(b.v):b.v,b.n&&(a[d].not=!0))};b.type===o.Query.TYPE_ATOM?(e(b,a.as,"elements"),e(b,a["@"],"chirality"),e(b,a.A,"aromatic"),e(b,a.C,"charge",!0),e(b,
a.H,"hydrogens",!0),e(b,a.R,"ringCount",!0),e(b,a.S,"saturation"),e(b,a.X,"connectivity",!0),e(b,a.x,"connectivityNoH",!0)):(e(b,a.bs,"orders"),e(b,a["@"],"stereo"),e(b,a.A,"aromatic"),e(b,a.R,"ringCount",!0));return b};e.molFrom=function(a){for(var b=new o.Molecule,e=0,g=a.a.length;e<g;e++){var h=a.a[e],j=new o.Atom(h.l?h.l:"C",h.x,h.y);h.i&&(j.tmpid=h.i);h.z&&(j.z=h.z);h.c&&(j.charge=h.c);h.m&&(j.mass=h.m);h.r&&(j.numRadical=h.r);h.p&&(j.numLonePair=h.p);h.q&&(j.query=this.queryFrom(h.q));void 0!==
h.p_h&&(j.hetatm=h.p_h);void 0!==h.p_w&&(j.isWater=h.p_w);void 0!==h.p_d&&(j.closestDistance=h.p_d);b.atoms.push(j)}if(a.b){e=0;for(g=a.b.length;e<g;e++)h=a.b[e],j=new o.Bond(b.atoms[h.b],b.atoms[h.e],void 0===h.o?1:h.o),h.i&&(j.tmpid=h.i),h.s&&(j.stereo=h.s),h.q&&(j.query=this.queryFrom(h.q)),b.bonds.push(j)}return b};e.shapeTo=function(a){var b={};a.tmpid&&(b.i=a.tmpid);if(a instanceof l.Line)b.t="Line",b.x1=a.p1.x,b.y1=a.p1.y,b.x2=a.p2.x,b.y2=a.p2.y,b.a=a.arrowType;else if(a instanceof l.Pusher)b.t=
"Pusher",b.o1=a.o1.tmpid,b.o2=a.o2.tmpid,1!==a.numElectron&&(b.e=a.numElectron);else if(a instanceof l.Bracket)b.t="Bracket",b.x1=a.p1.x,b.y1=a.p1.y,b.x2=a.p2.x,b.y2=a.p2.y,0!==a.charge&&(b.c=a.charge),0!==a.mult&&(b.m=a.mult),0!==a.repeat&&(b.r=a.repeat);else if(a instanceof h.Distance)b.t="Distance",b.a1=a.a1.tmpid,b.a2=a.a2.tmpid,a.node&&(b.n=a.node,b.o=a.offset);else if(a instanceof h.Angle)b.t="Angle",b.a1=a.a1.tmpid,b.a2=a.a2.tmpid,b.a3=a.a3.tmpid;else if(a instanceof h.Torsion)b.t="Torsion",
b.a1=a.a1.tmpid,b.a2=a.a2.tmpid,b.a3=a.a3.tmpid,b.a4=a.a4.tmpid;else if(a instanceof h.UnitCell){b.t="UnitCell";for(var e in a.unitCell)b[e]=a.unitCell[e]}return b};e.shapeFrom=function(a,b){var e;if("Line"===a.t)e=new l.Line(new o.Point(a.x1,a.y1),new o.Point(a.x2,a.y2)),e.arrowType=a.a;else if("Pusher"===a.t){var g,j,q=0;for(e=b.length;q<e;q++){for(var A=b[q],r=0,v=A.atoms.length;r<v;r++){var u=A.atoms[r];u.tmpid===a.o1?g=u:u.tmpid===a.o2&&(j=u)}r=0;for(v=A.bonds.length;r<v;r++){var t=A.bonds[r];
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b[q];r=0;for(v=A.atoms.length;r<v;r++)u=A.atoms[r],u.tmpid===a.a1?t=u:u.tmpid===a.a2?w=u:u.tmpid===a.a3&&(x=u)}e=new h.Angle(t,w,x)}else if("Torsion"===a.t){var B,q=0;for(e=b.length;q<e;q++){A=b[q];r=0;for(v=A.atoms.length;r<v;r++)u=A.atoms[r],u.tmpid===a.a1?t=u:u.tmpid===a.a2?w=u:u.tmpid===a.a3?x=u:u.tmpid===a.a4&&(B=u)}e=new h.Torsion(t,w,x,B)}else if("UnitCell"===a.t){g={};for(q in a)g[q]=a[q];e=new h.UnitCell(g)}return e};e.pdbFrom=function(a){var b=this.molFrom(a.mol);b.findRings=!1;b.fromJSON=
!0;b.chains=this.chainsFrom(a.ribbons);return b};e.chainsFrom=function(a){for(var b=[],e=0,g=a.cs.length;e<g;e++){for(var h=a.cs[e],j=[],l=0,r=h.length;l<r;l++){var v=h[l],u=new o.Residue;u.name=v.n;u.cp1=new o.Atom("",v.x1,v.y1,v.z1);u.cp2=new o.Atom("",v.x2,v.y2,v.z2);v.x3&&(u.cp3=new o.Atom("",v.x3,v.y3,v.z3),u.cp4=new o.Atom("",v.x4,v.y4,v.z4),u.cp5=new o.Atom("",v.x5,v.y5,v.z5));u.helix=v.h;u.sheet=v.s;u.arrow=0<l&&h[l-1].a;j.push(u)}b.push(j)}return b};var a=new j.JSONInterpreter;b.readJSON=
function(b){var e;try{e=g.parse(b)}catch(f){return}if(e)return e.m||e.s?a.contentFrom(e):e.a?{molecules:[a.molFrom(e)],shapes:[]}:{molecules:[],shapes:[]}};b.writeJSON=function(b,e){return g.stringify(a.contentTo(b,e))}})(ChemDoodle,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.structures.d2,ChemDoodle.structures.d3,JSON);
(function(b,j,o){j.RXNInterpreter=function(){};var l=j.RXNInterpreter.prototype=new j._Interpreter;l.read=function(g,e){e||(e=b.default_bondLength_2D);var a=[],d;if(g){d=g.split("$MOL\n");for(var h=d[0].split("\n")[4],f=parseInt(h.substring(0,3)),h=parseInt(h.substring(3,6)),j=1,l=0,q=0,A=f+h;q<A;q++){a[q]=b.readMOL(d[j],e);var r=a[q].getBounds(),r=r.maxX-r.minX,l=l-(r+40);j++}q=0;for(A=f;q<A;q++){var r=a[q].getBounds(),r=r.maxX-r.minX,j=a[q].getCenter(),v=0;for(d=a[q].atoms.length;v<d;v++){var u=
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e){return h.read(b,e)};b.writeRXN=function(b,e){return h.write(b,e)}})(ChemDoodle,ChemDoodle.io,ChemDoodle.structures);
(function(b,j,o,l,h,g){l.XYZInterpreter=function(){};j=l.XYZInterpreter.prototype=new l._Interpreter;j.deduceCovalentBonds=!0;j.read=function(a){var d=new h.Molecule;if(!a)return d;a=a.split("\n");for(var e=parseInt(g(a[0])),f=0;f<e;f++){var j=a[f+2].split(/\s+/g);d.atoms[f]=new h.Atom(isNaN(j[0])?j[0]:o[parseInt(j[0])-1],parseFloat(j[1]),parseFloat(j[2]),parseFloat(j[3]))}this.deduceCovalentBonds&&(new b.informatics.BondDeducer).deduceCovalentBonds(d,1);return d};var e=new l.XYZInterpreter;b.readXYZ=
function(a){return e.read(a)}})(ChemDoodle,ChemDoodle.ELEMENT,ChemDoodle.SYMBOLS,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.lib.jQuery.trim);
ChemDoodle.monitor=function(b,j,o){var l={CANVAS_DRAGGING:void 0,CANVAS_OVER:void 0,ALT:!1,SHIFT:!1,META:!1};b.supports_touch()||j(o).ready(function(){j(o).mousemove(function(b){l.CANVAS_DRAGGING&&l.CANVAS_DRAGGING.drag&&(l.CANVAS_DRAGGING.prehandleEvent(b),l.CANVAS_DRAGGING.drag(b))});j(o).mouseup(function(b){l.CANVAS_DRAGGING&&l.CANVAS_DRAGGING!==l.CANVAS_OVER&&l.CANVAS_DRAGGING.mouseup&&(l.CANVAS_DRAGGING.prehandleEvent(b),l.CANVAS_DRAGGING.mouseup(b));l.CANVAS_DRAGGING=void 0});j(o).keydown(function(b){l.SHIFT=
b.shiftKey;l.ALT=b.altKey;l.META=b.metaKey||b.ctrlKey;var g=l.CANVAS_OVER;l.CANVAS_DRAGGING&&(g=l.CANVAS_DRAGGING);g&&g.keydown&&(g.prehandleEvent(b),g.keydown(b))});j(o).keypress(function(b){var g=l.CANVAS_OVER;l.CANVAS_DRAGGING&&(g=l.CANVAS_DRAGGING);g&&g.keypress&&(g.prehandleEvent(b),g.keypress(b))});j(o).keyup(function(b){l.SHIFT=b.shiftKey;l.ALT=b.altKey;l.META=b.metaKey||b.ctrlKey;var g=l.CANVAS_OVER;l.CANVAS_DRAGGING&&(g=l.CANVAS_DRAGGING);g&&g.keyup&&(g.prehandleEvent(b),g.keyup(b))})});
return l}(ChemDoodle.featureDetection,ChemDoodle.lib.jQuery,document);
(function(b,j,o,l,h,g,e,a,d,n){b._Canvas=function(){};var f=b._Canvas.prototype;f.molecules=void 0;f.shapes=void 0;f.emptyMessage=void 0;f.image=void 0;f.repaint=function(){if(!this.test){var b=a.getElementById(this.id);if(b.getContext){var d=b.getContext("2d");1!==this.pixelRatio&&b.width===this.width&&(b.width=this.width*this.pixelRatio,b.height=this.height*this.pixelRatio,d.scale(this.pixelRatio,this.pixelRatio));this.image?d.drawImage(this.image,0,0):(this.specs.backgroundColor&&this.bgCache!==
b.style.backgroundColor&&(b.style.backgroundColor=this.specs.backgroundColor,this.bgCache=b.style.backgroundColor),d.fillStyle=this.specs.backgroundColor,d.fillRect(0,0,this.width,this.height));if(this.innerRepaint)this.innerRepaint(d);else if(0!==this.molecules.length||0!==this.shapes.length){d.save();d.translate(this.width/2,this.height/2);d.rotate(this.specs.rotateAngle);d.scale(this.specs.scale,this.specs.scale);d.translate(-this.width/2,-this.height/2);for(var b=0,e=this.molecules.length;b<e;b++)this.molecules[b].check(!0),
this.molecules[b].draw(d,this.specs);b=0;for(e=this.shapes.length;b<e;b++)this.shapes[b].draw(d,this.specs);d.restore()}else this.emptyMessage&&(d.fillStyle="#737683",d.textAlign="center",d.textBaseline="middle",d.font="18px Helvetica, Verdana, Arial, Sans-serif",d.fillText(this.emptyMessage,this.width/2,this.height/2));this.drawChildExtras&&this.drawChildExtras(d)}}};f.resize=function(a,d){var e=g("#"+this.id);e.attr({width:a,height:d});e.css("width",a);e.css("height",d);this.width=a;this.height=
d;if(b._Canvas3D&&this instanceof b._Canvas3D){var e=a,f=d;1!==this.pixelRatio&&(e*=this.pixelRatio,f*=this.pixelRatio,this.gl.canvas.width=e,this.gl.canvas.height=f);this.gl.viewport(0,0,e,f);this.afterLoadContent()}else if(0<this.molecules.length){this.center();e=0;for(f=this.molecules.length;e<f;e++)this.molecules[e].check()}this.repaint()};f.setBackgroundImage=function(a){this.image=new Image;var b=this;this.image.onload=function(){b.repaint()};this.image.src=a};f.loadMolecule=function(a){this.clear();
this.molecules.push(a);this.center();b._Canvas3D&&this instanceof b._Canvas3D||a.check();this.afterLoadContent&&this.afterLoadContent();this.repaint()};f.loadContent=function(a,d){this.molecules=a?a:[];this.shapes=d?d:[];this.center();if(!(b._Canvas3D&&this instanceof b._Canvas3D))for(var e=0,f=this.molecules.length;e<f;e++)this.molecules[e].check();this.afterLoadContent&&this.afterLoadContent();this.repaint()};f.addMolecule=function(a){this.molecules.push(a);b._Canvas3D&&this instanceof b._Canvas3D||
a.check();this.repaint()};f.removeMolecule=function(a){this.molecules=g.grep(this.molecules,function(b){return b!==a});this.repaint()};f.getMolecule=function(){return 0<this.molecules.length?this.molecules[0]:void 0};f.getMolecules=function(){return this.molecules};f.addShape=function(a){this.shapes.push(a);this.repaint()};f.removeShape=function(a){this.shapes=g.grep(this.shapes,function(b){return b!==a});this.repaint()};f.getShapes=function(){return this.shapes};f.clear=function(){this.molecules=
[];this.shapes=[];this.specs.scale=1;this.repaint()};f.center=function(){for(var a=this.getContentBounds(),b=new h.Point((this.width-a.minX-a.maxX)/2,(this.height-a.minY-a.maxY)/2),d=0,f=this.molecules.length;d<f;d++)for(var g=this.molecules[d],j=0,l=g.atoms.length;j<l;j++)g.atoms[j].add(b);d=0;for(f=this.shapes.length;d<f;d++){g=this.shapes[d].getPoints();j=0;for(l=g.length;j<l;j++)g[j].add(b)}this.specs.scale=1;b=a.maxX-a.minX;a=a.maxY-a.minY;if(b>this.width||a>this.height)this.specs.scale=0.85*
e.min(this.width/b,this.height/a)};f.bondExists=function(a,b){for(var d=0,e=this.molecules.length;d<e;d++)for(var f=this.molecules[d],g=0,h=f.bonds.length;g<h;g++){var j=f.bonds[g];if(j.contains(a)&&j.contains(b))return!0}return!1};f.getBond=function(a,b){for(var d=0,e=this.molecules.length;d<e;d++)for(var f=this.molecules[d],g=0,h=f.bonds.length;g<h;g++){var j=f.bonds[g];if(j.contains(a)&&j.contains(b))return j}};f.getMoleculeByAtom=function(a){for(var b=0,d=this.molecules.length;b<d;b++){var e=
this.molecules[b];if(-1!==e.atoms.indexOf(a))return e}};f.getAllAtoms=function(){for(var a=[],b=0,d=this.molecules.length;b<d;b++)a=a.concat(this.molecules[b].atoms);return a};f.getAllPoints=function(){for(var a=[],b=0,d=this.molecules.length;b<d;b++)a=a.concat(this.molecules[b].atoms);b=0;for(d=this.shapes.length;b<d;b++)a=a.concat(this.shapes[b].getPoints());return a};f.getContentBounds=function(){for(var a=new o.Bounds,b=0,d=this.molecules.length;b<d;b++)a.expand(this.molecules[b].getBounds());
b=0;for(d=this.shapes.length;b<d;b++)a.expand(this.shapes[b].getBounds());return a};f.create=function(f,p,o){this.id=f;this.width=p;this.height=o;this.molecules=[];this.shapes=[];if(a.getElementById(f)){var A=g("#"+f);p?A.attr("width",p):this.width=A.attr("width");o?A.attr("height",o):this.height=A.attr("height");A.attr("class","ChemDoodleWebComponent")}else{if(!b.featureDetection.supports_canvas_text()&&-1!=n.indexOf("MSIE")){a.writeln('\x3cdiv style\x3d"border: 1px solid black;" width\x3d"'+p+'" height\x3d"'+
o+'"\x3ePlease install \x3ca href\x3d"http://code.google.com/chrome/chromeframe/"\x3eGoogle Chrome Frame\x3c/a\x3e, then restart Internet Explorer.\x3c/div\x3e');return}a.writeln('\x3ccanvas class\x3d"ChemDoodleWebComponent" id\x3d"'+f+'" width\x3d"'+p+'" height\x3d"'+o+'" alt\x3d"ChemDoodle Web Component"\x3eThis browser does not support HTML5/Canvas.\x3c/canvas\x3e')}f=g("#"+f);f.css("width",this.width);f.css("height",this.height);this.pixelRatio=d.devicePixelRatio?d.devicePixelRatio:1;this.specs=
new h.VisualSpecifications;var r=this;j.supports_touch()?(f.bind("touchstart",function(a){var b=(new Date).getTime();if(!j.supports_gesture()&&2===a.originalEvent.touches.length){var d=a.originalEvent.touches,e=new h.Point(d[0].pageX,d[0].pageY),d=new h.Point(d[1].pageX,d[1].pageY);r.implementedGestureDist=e.distance(d);r.implementedGestureAngle=e.angle(d);r.gesturestart&&(r.prehandleEvent(a),r.gesturestart(a))}r.lastTouch&&1===a.originalEvent.touches.length&&500>b-r.lastTouch?r.dbltap?(r.prehandleEvent(a),
r.dbltap(a)):r.dblclick?(r.prehandleEvent(a),r.dblclick(a)):r.touchstart?(r.prehandleEvent(a),r.touchstart(a)):r.mousedown&&(r.prehandleEvent(a),r.mousedown(a)):r.touchstart?(r.prehandleEvent(a),r.touchstart(a),this.hold&&clearTimeout(this.hold),this.touchhold&&(this.hold=setTimeout(function(){r.touchhold(a)},1E3))):r.mousedown&&(r.prehandleEvent(a),r.mousedown(a));r.lastTouch=b}),f.bind("touchmove",function(a){this.hold&&(clearTimeout(this.hold),this.hold=void 0);if(!j.supports_gesture()&&2===a.originalEvent.touches.length&&
r.gesturechange){var b=a.originalEvent.touches,d=new h.Point(b[0].pageX,b[0].pageY),f=new h.Point(b[1].pageX,b[1].pageY),b=d.distance(f),d=d.angle(f);a.originalEvent.scale=b/r.implementedGestureDist;a.originalEvent.rotation=180*(r.implementedGestureAngle-d)/e.PI;r.prehandleEvent(a);r.gesturechange(a)}if(1<a.originalEvent.touches.length&&r.multitouchmove){d=a.originalEvent.touches.length;r.prehandleEvent(a);b=new h.Point(-a.offset.left*d,-a.offset.top*d);for(f=0;f<d;f++)b.x+=a.originalEvent.changedTouches[f].pageX,
b.y+=a.originalEvent.changedTouches[f].pageY;b.x/=d;b.y/=d;a.p=b;r.multitouchmove(a,d)}else r.touchmove?(r.prehandleEvent(a),r.touchmove(a)):r.drag&&(r.prehandleEvent(a),r.drag(a))}),f.bind("touchend",function(a){this.hold&&(clearTimeout(this.hold),this.hold=void 0);!j.supports_gesture()&&r.implementedGestureDist&&(r.implementedGestureDist=void 0,r.implementedGestureAngle=void 0,r.gestureend&&(r.prehandleEvent(a),r.gestureend(a)));r.touchend?(r.prehandleEvent(a),r.touchend(a)):r.mouseup&&(r.prehandleEvent(a),
r.mouseup(a));250>(new Date).getTime()-r.lastTouch&&(r.tap?(r.prehandleEvent(a),r.tap(a)):r.click&&(r.prehandleEvent(a),r.click(a)))}),f.bind("gesturestart",function(a){r.gesturestart&&(r.prehandleEvent(a),r.gesturestart(a))}),f.bind("gesturechange",function(a){r.gesturechange&&(r.prehandleEvent(a),r.gesturechange(a))}),f.bind("gestureend",function(a){r.gestureend&&(r.prehandleEvent(a),r.gestureend(a))})):(f.click(function(a){switch(a.which){case 1:r.click&&(r.prehandleEvent(a),r.click(a));break;
case 2:r.middleclick&&(r.prehandleEvent(a),r.middleclick(a));break;case 3:r.rightclick&&(r.prehandleEvent(a),r.rightclick(a))}}),f.dblclick(function(a){r.dblclick&&(r.prehandleEvent(a),r.dblclick(a))}),f.mousedown(function(a){switch(a.which){case 1:l.CANVAS_DRAGGING=r;r.mousedown&&(r.prehandleEvent(a),r.mousedown(a));break;case 2:r.middlemousedown&&(r.prehandleEvent(a),r.middlemousedown(a));break;case 3:r.rightmousedown&&(r.prehandleEvent(a),r.rightmousedown(a))}}),f.mousemove(function(a){!l.CANVAS_DRAGGING&&
r.mousemove&&(r.prehandleEvent(a),r.mousemove(a))}),f.mouseout(function(a){l.CANVAS_OVER=void 0;r.mouseout&&(r.prehandleEvent(a),r.mouseout(a))}),f.mouseover(function(a){l.CANVAS_OVER=r;r.mouseover&&(r.prehandleEvent(a),r.mouseover(a))}),f.mouseup(function(a){switch(a.which){case 1:r.mouseup&&(r.prehandleEvent(a),r.mouseup(a));break;case 2:r.middlemouseup&&(r.prehandleEvent(a),r.middlemouseup(a));break;case 3:r.rightmouseup&&(r.prehandleEvent(a),r.rightmouseup(a))}}),f.mousewheel(function(a,b){r.mousewheel&&
(r.prehandleEvent(a),r.mousewheel(a,b))}));this.subCreate&&this.subCreate()};f.prehandleEvent=function(a){a.originalEvent.changedTouches&&(a.pageX=a.originalEvent.changedTouches[0].pageX,a.pageY=a.originalEvent.changedTouches[0].pageY);a.preventDefault();a.offset=g("#"+this.id).offset();a.p=new h.Point(a.pageX-a.offset.left,a.pageY-a.offset.top)}})(ChemDoodle,ChemDoodle.featureDetection,ChemDoodle.math,ChemDoodle.monitor,ChemDoodle.structures,ChemDoodle.lib.jQuery,Math,document,window,navigator.userAgent);
(function(b,j){b._AnimatorCanvas=function(b,h,g){b&&this.create(b,h,g)};var o=b._AnimatorCanvas.prototype=new b._Canvas;o.timeout=33;o.startAnimation=function(){this.stopAnimation();this.lastTime=(new Date).getTime();var b=this;this.nextFrame&&(this.handle=j.requestInterval(function(){var h=(new Date).getTime();b.nextFrame(h-b.lastTime);b.repaint();b.lastTime=h},this.timeout))};o.stopAnimation=function(){this.handle&&(j.clearRequestInterval(this.handle),this.handle=void 0)};o.isRunning=function(){return void 0!==
this.handle}})(ChemDoodle,ChemDoodle.animations);
(function(b,j){b.FileCanvas=function(b,l,h,g){b&&this.create(b,l,h);j.writeln('\x3cbr\x3e\x3cform name\x3d"FileForm" enctype\x3d"multipart/form-data" method\x3d"POST" action\x3d"'+g+'" target\x3d"HiddenFileFrame"\x3e\x3cinput type\x3d"file" name\x3d"f" /\x3e\x3cinput type\x3d"submit" name\x3d"submitbutton" value\x3d"Show File" /\x3e\x3c/form\x3e\x3ciframe id\x3d"HFF-'+b+'" name\x3d"HiddenFileFrame" height\x3d"0" width\x3d"0" style\x3d"display:none;" onLoad\x3d"GetMolFromFrame(\'HFF-'+b+"', "+b+')"\x3e\x3c/iframe\x3e');
this.emptyMessage="Click below to load file";this.repaint()};b.FileCanvas.prototype=new b._Canvas})(ChemDoodle,document);
(function(b){b.HyperlinkCanvas=function(b,o,l,h,g,e){b&&this.create(b,o,l);this.urlOrFunction=h;this.color=g?g:"blue";this.size=e?e:2};b=b.HyperlinkCanvas.prototype=new b._Canvas;b.openInNewWindow=!0;b.hoverImage=void 0;b.drawChildExtras=function(b){this.e&&(this.hoverImage?b.drawImage(this.hoverImage,0,0):(b.strokeStyle=this.color,b.lineWidth=2*this.size,b.strokeRect(0,0,this.width,this.height)))};b.setHoverImage=function(b){this.hoverImage=new Image;this.hoverImage.src=b};b.click=function(){this.e=
void 0;this.repaint();this.urlOrFunction instanceof Function?this.urlOrFunction():this.openInNewWindow?window.open(this.urlOrFunction):location.href=this.urlOrFunction};b.mouseout=function(){this.e=void 0;this.repaint()};b.mouseover=function(b){this.e=b;this.repaint()}})(ChemDoodle);
(function(b,j,o,l){b.MolGrabberCanvas=function(b,g,e){b&&this.create(b,g,e);g=[];g.push('\x3cbr\x3e\x3cinput type\x3d"text" id\x3d"');g.push(b);g.push('_query" size\x3d"32" value\x3d"" /\x3e');g.push("\x3cbr\x3e\x3cnobr\x3e");g.push('\x3cselect id\x3d"');g.push(b);g.push('_select"\x3e');g.push('\x3coption value\x3d"chemexper"\x3eChemExper');g.push('\x3coption value\x3d"chemspider"\x3eChemSpider');g.push('\x3coption value\x3d"pubchem" selected\x3ePubChem');g.push("\x3c/select\x3e");g.push('\x3cbutton id\x3d"');
g.push(b);g.push('_submit"\x3eShow Molecule\x3c/button\x3e');g.push("\x3c/nobr\x3e");l.getElementById(b);o("#"+b).after(g.join(""));var a=this;o("#"+b+"_submit").click(function(){a.search()});o("#"+b+"_query").keypress(function(b){13===b.which&&a.search()});this.emptyMessage="Enter search term below";this.repaint()};b=b.MolGrabberCanvas.prototype=new b._Canvas;b.setSearchTerm=function(b){o("#"+this.id+"_query").val(b);this.search()};b.search=function(){this.emptyMessage="Searching...";this.clear();
var b=this;j.getMoleculeFromDatabase(o("#"+this.id+"_query").val(),{database:o("#"+this.id+"_select").val()},function(g){b.loadMolecule(g)})}})(ChemDoodle,ChemDoodle.iChemLabs,ChemDoodle.lib.jQuery,document);
(function(b,j,o){var l=[],h=[1,0,0],g=[0,1,0],e=[0,0,1];b.RotatorCanvas=function(a,b,e,f){a&&this.create(a,b,e);this.rotate3D=f};b=b.RotatorCanvas.prototype=new b._AnimatorCanvas;j=j.PI/15;b.xIncrement=j;b.yIncrement=j;b.zIncrement=j;b.nextFrame=function(a){if(0===this.molecules.length&&0===this.shapes.length)this.stopAnimation();else if(a/=1E3,this.rotate3D){o.identity(l);o.rotate(l,this.xIncrement*a,h);o.rotate(l,this.yIncrement*a,g);o.rotate(l,this.zIncrement*a,e);a=0;for(var b=this.molecules.length;a<
b;a++){for(var j=this.molecules[a],f=0,y=j.atoms.length;f<y;f++){var p=j.atoms[f],q=[p.x-this.width/2,p.y-this.height/2,p.z];o.multiplyVec3(l,q);p.x=q[0]+this.width/2;p.y=q[1]+this.height/2;p.z=q[2]}f=0;for(y=j.rings.length;f<y;f++)j.rings[f].center=j.rings[f].getCenter();this.specs.atoms_display&&this.specs.atoms_circles_2D&&j.sortAtomsByZ();this.specs.bonds_display&&this.specs.bonds_clearOverlaps_2D&&j.sortBondsByZ()}a=0;for(b=this.shapes.length;a<b;a++){j=this.shapes[a].getPoints();f=0;for(y=j.length;f<
y;f++)p=j[f],q=[p.x-this.width/2,p.y-this.height/2,0],o.multiplyVec3(l,q),p.x=q[0]+this.width/2,p.y=q[1]+this.height/2}}else this.specs.rotateAngle+=this.zIncrement*a};b.dblclick=function(){this.isRunning()?this.stopAnimation():this.startAnimation()}})(ChemDoodle,Math,ChemDoodle.lib.mat4);
(function(b,j,o){b.SlideshowCanvas=function(b,h,g){b&&this.create(b,h,g)};b=b.SlideshowCanvas.prototype=new b._AnimatorCanvas;b.frames=[];b.curIndex=0;b.timeout=5E3;b.alpha=0;b.innerHandle=void 0;b.phase=0;b.drawChildExtras=function(b){var h=o.getRGB(this.specs.backgroundColor,255);b.fillStyle="rgba("+h[0]+", "+h[1]+", "+h[2]+", "+this.alpha+")";b.fillRect(0,0,this.width,this.height)};b.nextFrame=function(){if(0===this.frames.length)this.stopAnimation();else{this.phase=0;var b=this,h=1;this.innerHandle=
setInterval(function(){b.alpha=h/15;b.repaint();15===h&&b.breakInnerHandle();h++},33)}};b.breakInnerHandle=function(){this.innerHandle&&(clearInterval(this.innerHandle),this.innerHandle=void 0);if(0===this.phase){this.curIndex++;this.curIndex>this.frames.length-1&&(this.curIndex=0);this.alpha=1;var b=this.frames[this.curIndex];this.loadContent(b.mols,b.shapes);this.phase=1;var h=this,g=1;this.innerHandle=setInterval(function(){h.alpha=(15-g)/15;h.repaint();15===g&&h.breakInnerHandle();g++},33)}else 1===
this.phase&&(this.alpha=0,this.repaint())};b.addFrame=function(b,h){0===this.frames.length&&this.loadContent(b,h);this.frames.push({mols:b,shapes:h})}})(ChemDoodle,ChemDoodle.animations,ChemDoodle.math);
(function(b,j,o,l,h){b.TransformCanvas=function(b,e,a,d){b&&this.create(b,e,a);this.rotate3D=d};b=b.TransformCanvas.prototype=new b._Canvas;b.lastPoint=void 0;b.rotationMultMod=1.3;b.lastPinchScale=1;b.lastGestureRotate=0;b.mousedown=function(b){this.lastPoint=b.p};b.dblclick=function(){this.center();this.repaint()};b.drag=function(b){if(!this.lastPoint.multi){if(j.ALT){var e=new o.Point(b.p.x,b.p.y);e.sub(this.lastPoint);for(var a=0,d=this.molecules.length;a<d;a++){for(var n=this.molecules[a],f=
0,y=n.atoms.length;f<y;f++)n.atoms[f].add(e);n.check()}a=0;for(d=this.shapes.length;a<d;a++){n=this.shapes[a].getPoints();f=0;for(y=n.length;f<y;f++)n[f].add(e)}this.lastPoint=b.p}else if(!0===this.rotate3D){y=l.max(this.width/4,this.height/4);f=(b.p.x-this.lastPoint.x)/y*this.rotationMultMod;y=-(b.p.y-this.lastPoint.y)/y*this.rotationMultMod;e=[];h.identity(e);h.rotate(e,y,[1,0,0]);h.rotate(e,f,[0,1,0]);a=0;for(d=this.molecules.length;a<d;a++){n=this.molecules[a];f=0;for(y=n.atoms.length;f<y;f++)a=
n.atoms[f],d=[a.x-this.width/2,a.y-this.height/2,a.z],h.multiplyVec3(e,d),a.x=d[0]+this.width/2,a.y=d[1]+this.height/2,a.z=d[2];a=0;for(d=n.rings.length;a<d;a++)n.rings[a].center=n.rings[a].getCenter();this.lastPoint=b.p;this.specs.atoms_display&&this.specs.atoms_circles_2D&&n.sortAtomsByZ();this.specs.bonds_display&&this.specs.bonds_clearOverlaps_2D&&n.sortBondsByZ()}}else y=new o.Point(this.width/2,this.height/2),f=y.angle(this.lastPoint),y=y.angle(b.p),this.specs.rotateAngle-=y-f,this.lastPoint=
b.p;this.repaint()}};b.mousewheel=function(b,e){this.specs.scale+=e/50;0.01>this.specs.scale&&(this.specs.scale=0.01);this.repaint()};b.multitouchmove=function(b,e){if(2===e)if(this.lastPoint.multi){var a=new o.Point(b.p.x,b.p.y);a.sub(this.lastPoint);for(var d=0,h=this.molecules.length;d<h;d++){for(var f=this.molecules[d],j=0,l=f.atoms.length;j<l;j++)f.atoms[j].add(a);f.check()}d=0;for(h=this.shapes.length;d<h;d++){f=this.shapes[d].getPoints();j=0;for(l=f.length;j<l;j++)f[j].add(a)}this.lastPoint=
b.p;this.lastPoint.multi=!0;this.repaint()}else this.lastPoint=b.p,this.lastPoint.multi=!0};b.gesturechange=function(b){0!==b.originalEvent.scale-this.lastPinchScale&&(this.specs.scale*=b.originalEvent.scale/this.lastPinchScale,0.01>this.specs.scale&&(this.specs.scale=0.01),this.lastPinchScale=b.originalEvent.scale);if(0!==this.lastGestureRotate-b.originalEvent.rotation){for(var e=(this.lastGestureRotate-b.originalEvent.rotation)/180*l.PI,a=new o.Point(this.width/2,this.height/2),d=0,h=this.molecules.length;d<
h;d++){for(var f=this.molecules[d],j=0,p=f.atoms.length;j<p;j++){var q=f.atoms[j],A=a.distance(q),r=a.angle(q)+e;q.x=a.x+A*l.cos(r);q.y=a.y-A*l.sin(r)}f.check()}this.lastGestureRotate=b.originalEvent.rotation}this.repaint()};b.gestureend=function(){this.lastPinchScale=1;this.lastGestureRotate=0}})(ChemDoodle,ChemDoodle.monitor,ChemDoodle.structures,Math,ChemDoodle.lib.mat4);(function(b){b.ViewerCanvas=function(b,o,l){b&&this.create(b,o,l)};b.ViewerCanvas.prototype=new b._Canvas})(ChemDoodle);
(function(b){b._SpectrumCanvas=function(b,o,l){b&&this.create(b,o,l)};b=b._SpectrumCanvas.prototype=new b._Canvas;b.spectrum=void 0;b.emptyMessage="No Spectrum Loaded or Recognized";b.loadMolecule=void 0;b.getMolecule=void 0;b.innerRepaint=function(b){this.spectrum&&0<this.spectrum.data.length?this.spectrum.draw(b,this.specs,this.width,this.height):this.emptyMessage&&(b.fillStyle="#737683",b.textAlign="center",b.textBaseline="middle",b.font="18px Helvetica, Verdana, Arial, Sans-serif",b.fillText(this.emptyMessage,
this.width/2,this.height/2))};b.loadSpectrum=function(b){this.spectrum=b;this.repaint()};b.getSpectrum=function(){return this.spectrum};b.getSpectrumCoordinates=function(b,o){return spectrum.getInternalCoordinates(b,o,this.width,this.height)}})(ChemDoodle,document);(function(b){b.ObserverCanvas=function(b,o,l){b&&this.create(b,o,l)};b.ObserverCanvas.prototype=new b._SpectrumCanvas})(ChemDoodle);
(function(b){b.OverlayCanvas=function(b,o,l){b&&this.create(b,o,l)};b=b.OverlayCanvas.prototype=new b._SpectrumCanvas;b.overlaySpectra=[];b.superRepaint=b.innerRepaint;b.innerRepaint=function(b){this.superRepaint(b);if(this.spectrum&&0<this.spectrum.data.length)for(var o=0,l=this.overlaySpectra.length;o<l;o++){var h=this.overlaySpectra[o];h&&0<h.data.length&&(h.minX=this.spectrum.minX,h.maxX=this.spectrum.maxX,h.drawPlot(b,this.specs,this.width,this.height,this.spectrum.memory.offsetTop,this.spectrum.memory.offsetLeft,
this.spectrum.memory.offsetBottom))}};b.addSpectrum=function(b){this.spectrum?this.overlaySpectra.push(b):this.spectrum=b}})(ChemDoodle);
(function(b,j,o){b.PerspectiveCanvas=function(b,g,e){b&&this.create(b,g,e)};var l=b.PerspectiveCanvas.prototype=new b._SpectrumCanvas;l.dragRange=void 0;l.rescaleYAxisOnZoom=!0;l.lastPinchScale=1;l.mousedown=function(h){this.dragRange=new b.structures.Point(h.p.x,h.p.x)};l.mouseup=function(b){this.dragRange&&this.dragRange.x!==this.dragRange.y&&(this.dragRange.multi||(b=this.spectrum.zoom(this.dragRange.x,b.p.x,this.width,this.rescaleYAxisOnZoom),this.rescaleYAxisOnZoom&&(this.specs.scale=b)),this.dragRange=
void 0,this.repaint())};l.drag=function(b){this.dragRange&&(this.dragRange.multi?this.dragRange=void 0:(j.SHIFT&&(this.spectrum.translate(b.p.x-this.dragRange.x,this.width),this.dragRange.x=b.p.x),this.dragRange.y=b.p.x),this.repaint())};l.drawChildExtras=function(b){if(this.dragRange){var g=o.min(this.dragRange.x,this.dragRange.y),e=o.max(this.dragRange.x,this.dragRange.y);b.strokeStyle="gray";b.lineStyle=1;b.beginPath();for(b.moveTo(g,this.height/2);g<=e;g++)5>g%10?b.lineTo(g,o.round(this.height/
2)):b.moveTo(g,o.round(this.height/2));b.stroke()}};l.mousewheel=function(b,g){this.specs.scale+=g/10;0.01>this.specs.scale&&(this.specs.scale=0.01);this.repaint()};l.dblclick=function(){this.spectrum.setup();this.specs.scale=1;this.repaint()};l.multitouchmove=function(h,g){2===g&&(!this.dragRange||!this.dragRange.multi?(this.dragRange=new b.structures.Point(h.p.x,h.p.x),this.dragRange.multi=!0):(this.spectrum.translate(h.p.x-this.dragRange.x,this.width),this.dragRange.x=h.p.x,this.dragRange.y=h.p.x,
this.repaint()))};l.gesturechange=function(b){this.specs.scale*=b.originalEvent.scale/this.lastPinchScale;0.01>this.specs.scale&&(this.specs.scale=0.01);this.lastPinchScale=b.originalEvent.scale;this.repaint()};l.gestureend=function(){this.lastPinchScale=1}})(ChemDoodle,ChemDoodle.monitor,Math);
(function(b,j,o){b.SeekerCanvas=function(b,g,e,a){b&&this.create(b,g,e);this.seekType=a};var l=b.SeekerCanvas.prototype=new b._SpectrumCanvas;l.superRepaint=l.innerRepaint;l.innerRepaint=function(h){this.superRepaint(h);if(this.spectrum&&0<this.spectrum.data.length&&this.p){var g,e;if(this.seekType===b.SeekerCanvas.SEEK_POINTER)g=this.p,e=this.spectrum.getInternalCoordinates(g.x,g.y);else if(this.seekType===b.SeekerCanvas.SEEK_PLOT||this.seekType===b.SeekerCanvas.SEEK_PEAK){e=this.seekType===b.SeekerCanvas.SEEK_PLOT?
this.spectrum.getClosestPlotInternalCoordinates(this.p.x):this.spectrum.getClosestPeakInternalCoordinates(this.p.x);if(!e)return;g={x:this.spectrum.getTransformedX(e.x,this.specs,this.width,this.spectrum.memory.offsetLeft),y:this.spectrum.getTransformedY(e.y/100,this.specs,this.height,this.spectrum.memory.offsetBottom,this.spectrum.memory.offsetTop)}}h.fillStyle="white";h.strokeStyle=this.specs.plots_color;h.lineWidth=this.specs.plots_width;h.beginPath();h.arc(g.x,g.y,3,0,2*o.PI,!1);h.fill();h.stroke();
h.font=j.getFontString(this.specs.text_font_size,this.specs.text_font_families);h.textAlign="left";h.textBaseline="bottom";e="x:"+e.x.toFixed(3)+", y:"+e.y.toFixed(3);var a=g.x+3,d=h.measureText(e).width;a+d>this.width-2&&(a-=6+d);g=g.y;0>g-this.specs.text_font_size-2&&(g+=this.specs.text_font_size);h.fillRect(a,g-this.specs.text_font_size,d,this.specs.text_font_size);h.fillStyle="black";h.fillText(e,a,g)}};l.mouseout=function(){this.p=void 0;this.repaint()};l.mousemove=function(b){this.p={x:b.p.x-
2,y:b.p.y-3};this.repaint()};l.touchstart=function(b){this.mousemove(b)};l.touchmove=function(b){this.mousemove(b)};l.touchend=function(b){this.mouseout(b)};b.SeekerCanvas.SEEK_POINTER="pointer";b.SeekerCanvas.SEEK_PLOT="plot";b.SeekerCanvas.SEEK_PEAK="peak"})(ChemDoodle,ChemDoodle.extensions,Math);
(function(b,j,o,l,h,g,e,a,d,n,f,y){b._Canvas3D=function(a,b,d){a&&this.create(a,b,d)};var p=b._Canvas3D.prototype=new b._Canvas;p.rotationMatrix=void 0;p.translationMatrix=void 0;p.lastPoint=void 0;p.emptyMessage="WebGL is Unavailable!";p.lastPinchScale=1;p.lastGestureRotate=0;p.afterLoadContent=function(){for(var a=new o.Bounds,b=0,g=this.molecules.length;b<g;b++)a.expand(this.molecules[b].getBounds3D());var h=f.dist([a.maxX,a.maxY,a.maxZ],[a.minX,a.minY,a.minZ])/2+1.5;Infinity===h&&(h=10);b=45;
g=Math.tan(b/360*Math.PI)/0.8;this.depth=h/g;var g=e.max(this.depth-h,0.1),h=this.depth+h,j=this.gl.canvas.clientWidth/this.gl.canvas.clientHeight;1>j&&(b/=j);this.specs.projectionOrthoWidth_3D=2*(Math.tan(b/360*Math.PI)*this.depth)*j;this.specs.projectionPerspectiveVerticalFieldOfView_3D=b;this.specs.projectionFrontCulling_3D=g;this.specs.projectionBackCulling_3D=h;this.specs.projectionWidthHeightRatio_3D=j;this.translationMatrix=d.translate(d.identity([]),[0,0,-this.depth]);this.maxDimension=e.max(a.maxX-
a.minX,a.maxY-a.minY);this.setupScene()};p.setViewDistance=function(a){this.specs.projectionPerspectiveVerticalFieldOfView_3D=o.clamp(this.specs.projectionPerspectiveVerticalFieldOfView_3D/a,0.1,179.9);this.specs.projectionOrthoWidth_3D=2*(e.tan(this.specs.projectionPerspectiveVerticalFieldOfView_3D/360*Math.PI)*this.depth)*this.specs.projectionWidthHeightRatio_3D;this.updateScene()};p.repaint=function(){if(this.gl){this.gl.clear(this.gl.COLOR_BUFFER_BIT|this.gl.DEPTH_BUFFER_BIT);this.gl.modelViewMatrix=
d.multiply(this.translationMatrix,this.rotationMatrix,[]);this.gl.rotationMatrix=this.rotationMatrix;var a=this.gl.getUniformLocation(this.gl.program,"u_projection_matrix");this.gl.uniformMatrix4fv(a,!1,this.gl.projectionMatrix);this.gl.fogging.setMode(this.specs.fog_mode_3D);for(var b=0,e=this.molecules.length;b<e;b++)this.molecules[b].render(this.gl,this.specs);b=0;for(e=this.shapes.length;b<e;b++)this.shapes[b].render(this.gl,this.specs);this.specs.compass_display&&(this.gl.uniformMatrix4fv(a,
!1,this.compass.projectionMatrix),this.compass.render(this.gl,this.specs),this.gl.setMatrixUniforms(this.gl.modelViewMatrix),this.gl.uniformMatrix4fv(a,!1,this.gl.projectionMatrix));this.gl.enable(this.gl.BLEND);this.gl.depthMask(!1);this.gl.enableVertexAttribArray(this.gl.shader.vertexTexCoordAttribute);this.specs.atoms_displayLabels_3D&&this.label3D.render(this.gl,this.specs,this.getMolecules());this.specs.compass_display&&this.specs.compass_displayText_3D&&(this.gl.uniformMatrix4fv(a,!1,this.compass.projectionMatrix),
this.compass.renderAxis(this.gl),this.gl.setMatrixUniforms(this.gl.modelViewMatrix),this.gl.uniformMatrix4fv(a,!1,this.gl.projectionMatrix));this.gl.disableVertexAttribArray(this.gl.shader.vertexTexCoordAttribute);this.gl.disable(this.gl.BLEND);this.gl.depthMask(!0);this.gl.disable(this.gl.DEPTH_TEST);this.drawChildExtras&&this.drawChildExtras(this.gl);this.gl.enable(this.gl.DEPTH_TEST);this.gl.flush()}};p.pick=function(a,b,e,f){if(this.gl){d.multiply(this.translationMatrix,this.rotationMatrix,this.gl.modelViewMatrix);
this.gl.rotationMatrix=this.rotationMatrix;var g=this.gl.getUniformLocation(this.gl.program,"u_projection_matrix");this.gl.uniformMatrix4fv(g,!1,this.gl.projectionMatrix);b=this.height-b;1!==this.pixelRatio&&(a*=this.pixelRatio,b*=this.pixelRatio);return this.picker.pick(this.gl,this.molecules,this.specs,a,b,e,f)}};p.center=function(){for(var a=new l.Atom,b=0,d=this.molecules.length;b<d;b++){var e=this.molecules[b];a.add3D(e.getCenter3D())}a.x/=this.molecules.length;a.y/=this.molecules.length;b=0;
for(d=this.molecules.length;b<d;b++){for(var e=this.molecules[b],f=0,g=e.atoms.length;f<g;f++)e.atoms[f].sub3D(a);if(e.chains&&e.fromJSON){f=0;for(g=e.chains.length;f<g;f++)for(var h=e.chains[f],j=0,n=h.length;j<n;j++){var c=h[j];c.cp1.sub3D(a);c.cp2.sub3D(a);c.cp3&&(c.cp3.sub3D(a),c.cp4.sub3D(a),c.cp5.sub3D(a))}}}};p.subCreate=function(){try{var b=a.getElementById(this.id);this.gl=b.getContext("webgl");this.gl||(this.gl=b.getContext("experimental-webgl"))}catch(e){}this.gl?(1!==this.pixelRatio&&
this.gl.canvas.width===this.width&&(this.gl.canvas.style.width=this.width+"px",this.gl.canvas.style.height=this.height+"px",this.gl.canvas.width=this.width*this.pixelRatio,this.gl.canvas.height=this.height*this.pixelRatio),this.rotationMatrix=d.identity([]),this.translationMatrix=d.identity([]),this.gl.viewport(0,0,this.gl.canvas.width,this.gl.canvas.height),this.gl.program=this.gl.createProgram(),this.gl.shader=new h.Shader,this.gl.shader.init(this.gl),this.gl.programLabel=this.gl.createProgram(),
this.setupScene()):this.displayMessage()};b._Canvas.prototype.displayMessage=function(){var b=a.getElementById(this.id);b.getContext&&(b=b.getContext("2d"),this.specs.backgroundColor&&(b.fillStyle=this.specs.backgroundColor,b.fillRect(0,0,this.width,this.height)),this.emptyMessage&&(b.fillStyle="#737683",b.textAlign="center",b.textBaseline="middle",b.font="18px Helvetica, Verdana, Arial, Sans-serif",b.fillText(this.emptyMessage,this.width/2,this.height/2)))};p.renderText=function(a,b){if(this.gl){var d=
{position:[],texCoord:[],translation:[]};this.gl.textImage.pushVertexData(a,b,0,d);this.gl.textMesh.storeData(this.gl,d.position,d.texCoord,d.translation);this.gl.enable(this.gl.BLEND);this.gl.depthMask(!1);this.gl.enableVertexAttribArray(this.gl.shader.vertexTexCoordAttribute);this.gl.textImage.useTexture(this.gl);this.gl.textMesh.render(this.gl);this.gl.disableVertexAttribArray(this.gl.shader.vertexTexCoordAttribute);this.gl.disable(this.gl.BLEND);this.gl.depthMask(!0)}};p.setupScene=function(){if(this.gl){y("#"+
this.id).css("background-color",this.specs.backgroundColor);var a=o.getRGB(this.specs.backgroundColor,1);this.gl.clearColor(a[0],a[1],a[2],1);this.gl.clearDepth(1);this.gl.enable(this.gl.DEPTH_TEST);this.gl.depthFunc(this.gl.LEQUAL);this.gl.blendFuncSeparate(this.gl.SRC_ALPHA,this.gl.ONE_MINUS_SRC_ALPHA,this.gl.ONE,this.gl.ONE_MINUS_SRC_ALPHA);this.specs.cullBackFace_3D?this.gl.enable(this.gl.CULL_FACE):this.gl.disable(this.gl.CULL_FACE);this.gl.sphereBuffer=new h.Sphere(1,this.specs.atoms_resolution_3D,
this.specs.atoms_resolution_3D);this.gl.starBuffer=new h.Star;this.gl.cylinderBuffer=new h.Cylinder(1,1,this.specs.bonds_resolution_3D);this.gl.cylinderClosedBuffer=new h.Cylinder(1,1,this.specs.bonds_resolution_3D,!0);this.gl.boxBuffer=new h.Box(1,1,1);this.gl.pillBuffer=new h.Pill(this.specs.bonds_pillDiameter_3D/2,this.specs.bonds_pillHeight_3D,this.specs.bonds_pillLatitudeResolution_3D,this.specs.bonds_pillLongitudeResolution_3D);this.gl.lineBuffer=new h.Line;this.gl.lineArrowBuffer=new h.LineArrow;
this.gl.arrowBuffer=new h.Arrow(0.3,this.specs.compass_resolution_3D);this.gl.textMesh=new h.TextMesh;this.gl.textMesh.init(this.gl);this.gl.textImage=new h.TextImage;this.gl.textImage.init(this.gl);this.gl.textImage.updateFont(this.gl,this.specs.text_font_size,this.specs.text_font_families,this.specs.text_font_bold,this.specs.text_font_italic,this.specs.text_font_stroke_3D);this.label3D=new h.Label;this.label3D.init(this.gl,this.specs);for(var p=0,r=this.molecules.length;p<r;p++)if(a=this.molecules[p],
a.labelMesh instanceof h.TextMesh||(a.labelMesh=new h.TextMesh,a.labelMesh.init(this.gl)),a.chains){a.ribbons=[];a.cartoons=[];a.tubes=[];a.pipePlanks=[];for(var v=0,u=a.chains.length;v<u;v++){var t=a.chains[v],w=2<t.length&&g[t[2].name]&&"#BEA06E"===g[t[2].name].aminoColor;if(0<t.length&&!t[0].lineSegments){for(var x=0,B=t.length-1;x<B;x++)t[x].setup(t[x+1].cp1,w?1:this.specs.proteins_horizontalResolution);if(!w){x=1;for(B=t.length-1;x<B;x++)j.vec3AngleFrom(t[x-1].D,t[x].D)>e.PI/2&&(t[x].guidePointsSmall.reverse(),
t[x].guidePointsLarge.reverse(),f.scale(t[x].D,-1))}x=2;for(B=t.length-3;x<B;x++)t[x].computeLineSegments(t[x-2],t[x-1],t[x+1],!w,w?this.specs.nucleics_verticalResolution:this.specs.proteins_verticalResolution);t.pop();t.pop();t.pop();t.shift();t.shift()}x=o.hsl2rgb(1===u?0.5:v/u,1,0.5);x="rgb("+x[0]+","+x[1]+","+x[2]+")";t.chainColor=x;w?(w=new h.Tube(t,this.specs.nucleics_tubeThickness,this.specs.nucleics_tubeResolution_3D),w.chainColor=x,a.tubes.push(w)):(w=new h.PipePlank(t,this.specs),a.pipePlanks.push(w),
w=t.shift(),B={front:new h.Ribbon(t,this.specs.proteins_ribbonThickness,!1),back:new h.Ribbon(t,-this.specs.proteins_ribbonThickness,!1)},B.front.chainColor=x,B.back.chainColor=x,a.ribbons.push(B),B={front:new h.Ribbon(t,this.specs.proteins_ribbonThickness,!0),back:new h.Ribbon(t,-this.specs.proteins_ribbonThickness,!0)},B.front.chainColor=x,B.back.chainColor=x,a.cartoons.push(B),t.unshift(w))}}this.label3D.updateVerticesBuffer(this.gl,this.getMolecules(),this.specs);if(this instanceof b.MovieCanvas3D&&
this.frames){x=0;for(B=this.frames.length;x<B;x++){p=this.frames[x];v=0;for(u=p.mols.length;v<u;v++)a=p.mols[v],a.labelMesh instanceof l.d3.TextMesh||(a.labelMesh=new l.d3.TextMesh,a.labelMesh.init(this.gl));this.label3D.updateVerticesBuffer(this.gl,p.mols,this.specs)}}this.gl.lighting=new h.Light(this.specs.lightDiffuseColor_3D,this.specs.lightSpecularColor_3D,this.specs.lightDirection_3D);this.gl.lighting.lightScene(this.gl);this.gl.material=new h.Material(this.gl);this.gl.fogging=new h.Fog(this.gl);
this.gl.fogging.setTempParameter(this.specs.fog_color_3D||this.specs.backgroundColor,this.specs.fog_start_3D,this.specs.fog_end_3D,this.specs.fog_density_3D);this.compass=new h.Compass(this.gl,this.specs);a=this.width/this.height;this.specs.projectionWidthHeightRatio_3D&&(a=this.specs.projectionWidthHeightRatio_3D);this.gl.projectionMatrix=this.specs.projectionPerspective_3D?d.perspective(this.specs.projectionPerspectiveVerticalFieldOfView_3D,a,this.specs.projectionFrontCulling_3D,this.specs.projectionBackCulling_3D):
d.ortho(-this.specs.projectionOrthoWidth_3D/2,this.specs.projectionOrthoWidth_3D/2,-this.specs.projectionOrthoWidth_3D/2/a,this.specs.projectionOrthoWidth_3D/2/a,this.specs.projectionFrontCulling_3D,this.specs.projectionBackCulling_3D);a=this.gl.getUniformLocation(this.gl.program,"u_projection_matrix");this.gl.uniformMatrix4fv(a,!1,this.gl.projectionMatrix);var c=this.gl.getUniformLocation(this.gl.program,"u_model_view_matrix"),k=this.gl.getUniformLocation(this.gl.program,"u_normal_matrix");this.gl.setMatrixUniforms=
function(a){this.uniformMatrix4fv(c,!1,a);a=n.transpose(d.toInverseMat3(a,[]));this.uniformMatrix3fv(k,!1,a)};v=this.gl.getUniformLocation(this.gl.program,"u_dimension");this.gl.uniformMatrix4fv(a,!1,this.gl.projectionMatrix);this.gl.uniform2f(v,this.gl.canvas.clientWidth,this.gl.canvas.clientHeight);this.picker=new h.Picker;this.picker.init(this.gl);this.picker.setDimension(this.gl,this.gl.canvas.width,this.gl.canvas.height)}};p.updateScene=function(){this.gl.fogging.setTempParameter(this.specs.fog_color_3D||
this.specs.backgroundColor,this.specs.fog_start_3D,this.specs.fog_end_3D,this.specs.fog_density_3D);var a=this.width/this.height;this.specs.projectionWidthHeightRatio_3D&&(a=this.specs.projectionWidthHeightRatio_3D);this.gl.projectionMatrix=this.specs.projectionPerspective_3D?d.perspective(this.specs.projectionPerspectiveVerticalFieldOfView_3D,a,this.specs.projectionFrontCulling_3D,this.specs.projectionBackCulling_3D):d.ortho(-this.specs.projectionOrthoWidth_3D/2,this.specs.projectionOrthoWidth_3D/
2,-this.specs.projectionOrthoWidth_3D/2/a,this.specs.projectionOrthoWidth_3D/2/a,this.specs.projectionFrontCulling_3D,this.specs.projectionBackCulling_3D);this.repaint()};p.mousedown=function(a){this.lastPoint=a.p};p.mouseup=function(){this.lastPoint=void 0};p.rightmousedown=function(a){this.lastPoint=a.p};p.drag=function(a){if(this.lastPoint){if(b.monitor.ALT){var f=new l.Point(a.p.x,a.p.y);f.sub(this.lastPoint);var g=e.tan(this.specs.projectionPerspectiveVerticalFieldOfView_3D/360*e.PI),g=this.depth/
(this.height/2/g);d.translate(this.translationMatrix,[f.x*g,-f.y*g,0])}else g=a.p.x-this.lastPoint.x,f=a.p.y-this.lastPoint.y,g=d.rotate(d.identity([]),g*e.PI/180,[0,1,0]),d.rotate(g,f*e.PI/180,[1,0,0]),this.rotationMatrix=d.multiply(g,this.rotationMatrix);this.lastPoint=a.p;this.repaint()}};p.mousewheel=function(a,b){var d=this.specs.projectionPerspectiveVerticalFieldOfView_3D+b;this.specs.projectionPerspectiveVerticalFieldOfView_3D=0.1>d?0.1:179.9<d?179.9:d;this.specs.projectionOrthoWidth_3D=2*
(Math.tan(this.specs.projectionPerspectiveVerticalFieldOfView_3D/360*Math.PI)*this.depth)*this.specs.projectionWidthHeightRatio_3D;this.updateScene()};p.multitouchmove=function(a,b){if(2===b)if(this.lastPoint&&this.lastPoint.multi){var f=new l.Point(a.p.x,a.p.y);f.sub(this.lastPoint);var g=e.tan(this.specs.projectionPerspectiveVerticalFieldOfView_3D/360*e.PI),g=this.depth/(this.height/2/g);d.translate(this.translationMatrix,[f.x*g,-f.y*g,0]);this.lastPoint=a.p;this.repaint()}else this.lastPoint=a.p,
this.lastPoint.multi=!0};p.gesturechange=function(a){if(0!==a.originalEvent.scale-this.lastPinchScale){var b=30*-(a.originalEvent.scale/this.lastPinchScale-1);if(isNaN(b))return;b=this.specs.projectionPerspectiveVerticalFieldOfView_3D+b;this.specs.projectionPerspectiveVerticalFieldOfView_3D=0.1>b?0.1:179.9<b?179.9:b;this.specs.projectionOrthoWidth_3D=2*(Math.tan(this.specs.projectionPerspectiveVerticalFieldOfView_3D/360*Math.PI)*this.depth)*this.specs.projectionWidthHeightRatio_3D;this.updateScene();
this.lastPinchScale=a.originalEvent.scale}this.repaint()};p.gestureend=function(){this.lastPinchScale=1;this.lastGestureRotate=0}})(ChemDoodle,ChemDoodle.extensions,ChemDoodle.math,ChemDoodle.structures,ChemDoodle.structures.d3,ChemDoodle.RESIDUE,Math,document,ChemDoodle.lib.mat4,ChemDoodle.lib.mat3,ChemDoodle.lib.vec3,ChemDoodle.lib.jQuery,window);
(function(b,j,o,l){b.MolGrabberCanvas3D=function(b,g,e){b&&this.create(b,g,e);g=[];g.push('\x3cbr\x3e\x3cinput type\x3d"text" id\x3d"');g.push(b);g.push('_query" size\x3d"32" value\x3d"" /\x3e');g.push("\x3cbr\x3e\x3cnobr\x3e");g.push('\x3cselect id\x3d"');g.push(b);g.push('_select"\x3e');g.push('\x3coption value\x3d"pubchem" selected\x3ePubChem');g.push("\x3c/select\x3e");g.push('\x3cbutton id\x3d"');g.push(b);g.push('_submit"\x3eShow Molecule\x3c/button\x3e');g.push("\x3c/nobr\x3e");l.writeln(g.join(""));
var a=this;o("#"+b+"_submit").click(function(){a.search()});o("#"+b+"_query").keypress(function(b){13===b.which&&a.search()})};b=b.MolGrabberCanvas3D.prototype=new b._Canvas3D;b.setSearchTerm=function(b){o("#"+this.id+"_query").val(b);this.search()};b.search=function(){var b=this;j.getMoleculeFromDatabase(o("#"+this.id+"_query").val(),{database:o("#"+this.id+"_select").val(),dimension:3},function(g){b.loadMolecule(g)})}})(ChemDoodle,ChemDoodle.iChemLabs,ChemDoodle.lib.jQuery,document);
(function(b,j){b.MovieCanvas3D=function(b,h,g){b&&this.create(b,h,g);this.frames=[]};b.MovieCanvas3D.PLAY_ONCE=0;b.MovieCanvas3D.PLAY_LOOP=1;b.MovieCanvas3D.PLAY_SPRING=2;var o=b.MovieCanvas3D.prototype=new b._Canvas3D;o.timeout=50;o.frameNumber=0;o.playMode=2;o.reverse=!1;o.startAnimation=b._AnimatorCanvas.prototype.startAnimation;o.stopAnimation=b._AnimatorCanvas.prototype.stopAnimation;o.isRunning=b._AnimatorCanvas.prototype.isRunning;o.dblclick=b.RotatorCanvas.prototype.dblclick;o.nextFrame=function(){var b=
this.frames[this.frameNumber];this.molecules=b.mols;this.shapes=b.shapes;2===this.playMode&&this.reverse?(this.frameNumber--,0>this.frameNumber&&(this.frameNumber=1,this.reverse=!1)):(this.frameNumber++,this.frameNumber>=this.frames.length&&(2===this.playMode?(this.frameNumber-=2,this.reverse=!0):(this.frameNumber=0,0===this.playMode&&this.stopAnimation())))};o.center=function(){for(var b=new j.Atom,h=this.frames[0],g=0,e=h.mols.length;g<e;g++)b.add3D(h.mols[g].getCenter3D());b.x/=h.mols.length;b.y/=
h.mols.length;h=new j.Atom;h.sub3D(b);for(var b=0,a=this.frames.length;b<a;b++)for(var d=this.frames[b],g=0,e=d.mols.length;g<e;g++)for(var n=d.mols[g],f=0,o=n.atoms.length;f<o;f++)n.atoms[f].add3D(h)};o.addFrame=function(b,h){this.frames.push({mols:b,shapes:h})}})(ChemDoodle,ChemDoodle.structures);
(function(b,j,o){var l=[],h=[1,0,0],g=[0,1,0],e=[0,0,1];b.RotatorCanvas3D=function(a,b,e){a&&this.create(a,b,e)};var a=b.RotatorCanvas3D.prototype=new b._Canvas3D;a.timeout=33;j=j.PI/15;a.xIncrement=j;a.yIncrement=j;a.zIncrement=j;a.startAnimation=b._AnimatorCanvas.prototype.startAnimation;a.stopAnimation=b._AnimatorCanvas.prototype.stopAnimation;a.isRunning=b._AnimatorCanvas.prototype.isRunning;a.dblclick=b.RotatorCanvas.prototype.dblclick;a.mousedown=void 0;a.rightmousedown=void 0;a.drag=void 0;
a.mousewheel=void 0;a.nextFrame=function(a){0===this.molecules.length&&0===this.shapes.length?this.stopAnimation():(o.identity(l),a/=1E3,o.rotate(l,this.xIncrement*a,h),o.rotate(l,this.yIncrement*a,g),o.rotate(l,this.zIncrement*a,e),o.multiply(this.rotationMatrix,l))}})(ChemDoodle,Math,ChemDoodle.lib.mat4);(function(b){b.TransformCanvas3D=function(b,o,l){b&&this.create(b,o,l)};b.TransformCanvas3D.prototype=new b._Canvas3D})(ChemDoodle);
(function(b){b.ViewerCanvas3D=function(b,o,l){b&&this.create(b,o,l)};b=b.ViewerCanvas3D.prototype=new b._Canvas3D;b.mousedown=void 0;b.rightmousedown=void 0;b.drag=void 0;b.mousewheel=void 0})(ChemDoodle);
(function(b,j,o){function l(b,e,a,d){this.element=b;this.x=e;this.y=a;this.dimension=d;this.allowMultipleSelections=!1}b.PeriodicTableCanvas=function(b,e){this.padding=5;b&&this.create(b,18*e+2*this.padding,10*e+2*this.padding);this.cellDimension=e?e:20;this.setupTable();this.repaint()};var h=b.PeriodicTableCanvas.prototype=new b._Canvas;h.loadMolecule=void 0;h.getMolecule=void 0;h.getHoveredElement=function(){if(this.hovered)return this.hovered.element};h.innerRepaint=function(b){for(var e=0,a=this.cells.length;e<
a;e++)this.drawCell(b,this.specs,this.cells[e]);this.hovered&&this.drawCell(b,this.specs,this.hovered);this.selected&&this.drawCell(b,this.specs,this.selected)};h.setupTable=function(){this.cells=[];for(var g=this.padding,e=this.padding,a=0,d=0,h=b.SYMBOLS.length;d<h;d++){18===a&&(a=0,e+=this.cellDimension,g=this.padding);var f=b.ELEMENT[b.SYMBOLS[d]];if(2===f.atomicNumber)g+=16*this.cellDimension,a+=16;else if(5===f.atomicNumber||13===f.atomicNumber)g+=10*this.cellDimension,a+=10;if((58>f.atomicNumber||
71<f.atomicNumber&&90>f.atomicNumber||103<f.atomicNumber)&&113>f.atomicNumber)this.cells.push(new l(f,g,e,this.cellDimension)),g+=this.cellDimension,a++}e+=2*this.cellDimension;g=3*this.cellDimension+this.padding;for(d=57;104>d;d++)if(f=b.ELEMENT[b.SYMBOLS[d]],90===f.atomicNumber&&(e+=this.cellDimension,g=3*this.cellDimension+this.padding),58<=f.atomicNumber&&71>=f.atomicNumber||90<=f.atomicNumber&&103>=f.atomicNumber)this.cells.push(new l(f,g,e,this.cellDimension)),g+=this.cellDimension};h.drawCell=
function(b,e,a){var d=b.createRadialGradient(a.x+a.dimension/3,a.y+a.dimension/3,1.5*a.dimension,a.x+a.dimension/3,a.y+a.dimension/3,a.dimension/10);d.addColorStop(0,"#000000");d.addColorStop(0.7,a.element.jmolColor);d.addColorStop(1,"#FFFFFF");b.fillStyle=d;j.contextRoundRect(b,a.x,a.y,a.dimension,a.dimension,a.dimension/8);if(a===this.hovered||a===this.selected||a.selected)b.lineWidth=2,b.strokeStyle="#c10000",b.stroke(),b.fillStyle="white";b.fill();b.font=j.getFontString(e.text_font_size,e.text_font_families);
b.fillStyle=e.text_color;b.textAlign="center";b.textBaseline="middle";b.fillText(a.element.symbol,a.x+a.dimension/2,a.y+a.dimension/2)};h.click=function(){this.hovered&&(this.allowMultipleSelections?this.hovered.selected=!this.hovered.selected:this.selected=this.hovered,this.repaint())};h.touchstart=function(b){this.mousemove(b)};h.mousemove=function(b){var e=b.p.x;b=b.p.y;this.hovered=void 0;for(var a=0,d=this.cells.length;a<d;a++){var h=this.cells[a];if(o.isBetween(e,h.x,h.x+h.dimension)&&o.isBetween(b,
h.y,h.y+h.dimension)){this.hovered=h;break}}this.repaint()};h.mouseout=function(){this.hovered=void 0;this.repaint()}})(ChemDoodle,ChemDoodle.extensions,ChemDoodle.math,document);(function(b,j,o){b.png={};b.png.create=function(b){o.open(j.getElementById(b.id).toDataURL("image/png"))}})(ChemDoodle.io,document,window);(function(b,j){b.file={};b.file.content=function(b,l){j.get(b,"",l)}})(ChemDoodle.io,ChemDoodle.lib.jQuery);
(function(b,j,o,l,h,g){j.SERVER_URL="http://ichemlabs.cloud.chemdoodle.com/icl_cdc_v070000/WebHQ";j.inRelay=!1;j.asynchronous=!0;j.INFO={userAgent:navigator.userAgent,v_cwc:b.getVersion(),v_jQuery:h.version,v_jQuery_ui:h.ui?h.ui.version:"N/A"};var e=new o.JSONInterpreter,a=new l.Queue;j.useHTTPS=function(){j.SERVER_URL="https"+j.SERVER_URL.substr(4)};j._contactServer=function(b,e,f,g,l){this.inRelay?a.enqueue({call:b,content:e,options:f,callback:g,errorback:l}):(j.inRelay=!0,h.ajax({dataType:"text",
type:"POST",data:JSON.stringify({call:b,content:e,options:f,info:j.INFO}),url:this.SERVER_URL,success:function(b){b=JSON.parse(b);b.message&&alert(b.message);j.inRelay=!1;g&&(b.content&&!b.stop)&&g(b.content);b.stop&&l&&l();a.isEmpty()||(b=a.dequeue(),j.contactServer(b.call,b.content,b.options,b.callback,b.errorback))},error:function(){"checkForUpdates"!=b&&alert("Call failed. Please try again. If you continue to see this message, please contact iChemLabs customer support.");j.inRelay=!1;l&&l();if(!a.isEmpty()){var e=
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b,f,g){this._contactServer("generateImage",{mol:e.molTo(a)},b,function(a){f(a.link)},g)};j.generateIUPACName=function(a,b,f,g){this._contactServer("generateIUPACName",{mol:e.molTo(a)},b,function(a){f(a.iupac)},g)};j.getAd=function(a,b){this._contactServer("getAd",{},{},function(b){a(b.image_url,b.target_url)},b)};j.getMoleculeFromContent=function(a,b,f,g){this._contactServer("getMoleculeFromContent",{content:a},b,function(a){for(var b=!1,d=0,g=a.mol.a.length;d<g;d++)if(0!==a.mol.a[d].z){b=!0;break}if(b){d=
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h)};j.isSupergraphIsomorphism=function(a,b,f,g,h){this._contactServer("isSupergraphIsomorphism",{arrow:e.molTo(a),target:e.molTo(b)},f,function(a){g(a.value)},h)};j.getSimilarityMeasure=function(a,b,f,g,h){this._contactServer("getSimilarityMeasure",{first:e.molTo(a),second:e.molTo(b)},f,function(a){g(a.value)},h)};j.kekulize=function(a,b,f,g){this._contactServer("kekulize",{mol:e.molTo(a)},b,function(a){f(e.molFrom(a.mol))},g)};j.optimize=function(a,b,f,g){this._contactServer("optimize",{mol:e.molTo(a)},
b,function(g){g=e.molFrom(g.mol);if(2===b.dimension){for(var h=0,j=g.atoms.length;h<j;h++)a.atoms[h].x=g.atoms[h].x,a.atoms[h].y=g.atoms[h].y;f()}else if(3===b.dimension){h=0;for(j=g.atoms.length;h<j;h++)g.atoms[h].x/=20,g.atoms[h].y/=-20,g.atoms[h].z/=20;f(g)}},g)};j.readIUPACName=function(a,b,f,g){this._contactServer("readIUPACName",{iupac:a},b,function(a){f(e.molFrom(a.mol))},g)};j.readSMILES=function(a,b,f,g){this._contactServer("readSMILES",{smiles:a},b,function(a){f(e.molFrom(a.mol))},g)};j.saveFile=
function(a,b,f,g){this._contactServer("saveFile",{mol:e.molTo(a)},b,function(a){f(a.link)},g)};j.simulate13CNMR=function(a,g,f,h){g.nucleus="C";g.isotope=13;this._contactServer("simulateNMR",{mol:e.molTo(a)},g,function(a){f(b.readJCAMP(a.jcamp))},h)};j.simulate1HNMR=function(a,g,f,h){g.nucleus="H";g.isotope=1;this._contactServer("simulateNMR",{mol:e.molTo(a)},g,function(a){f(b.readJCAMP(a.jcamp))},h)};j.simulateMassParentPeak=function(a,g,f,h){this._contactServer("simulateMassParentPeak",{mol:e.molTo(a)},
g,function(a){f(b.readJCAMP(a.jcamp))},h)};j.writeSMILES=function(a,b,f,g){this._contactServer("writeSMILES",{mol:e.molTo(a)},b,function(a){f(a.smiles)},g)};j.version=function(a,b,e){this._contactServer("version",{},a,function(a){b(a.value)},e)};j.checkForUpdates=function(a){this._contactServer("checkForUpdates",{value:g.href},a,function(){},function(){})}})(ChemDoodle,ChemDoodle.iChemLabs,ChemDoodle.io,ChemDoodle.structures,ChemDoodle.lib.jQuery,location);