@chemistry/mol3dview/dist/mol3dview.min.js

Crystal Structure Viewer

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e.toFixed(3)})+")"},e.prototype.set=function(e,y,t){if(e>4||e<0||y>4||y<0)throw new Error("Incorrect coeficients");this.elements[e+4*y]=t},e.prototype.get=function(e,y){if(e>4||e<0||y>4||y<0)throw new Error("Incorrect coeficients");return this.elements[e+4*y]},e.prototype.project=function(e){var y=this.elements[0]*e.x+this.elements[4]*e.y+this.elements[8]*e.z+this.elements[12],t=this.elements[1]*e.x+this.elements[5]*e.y+this.elements[9]*e.z+this.elements[13],x=this.elements[2]*e.x+this.elements[6]*e.y+this.elements[10]*e.z+this.elements[14];return new n.default(y,t,x)},e.prototype.rotate=function(y,t){var x=z.default.fromAxisAngle(y,t),n=e.fromQuaternion(x);return e.fromMultiplication(this,n)},e.prototype.translate=function(y){var t=this.elements;return new e([t[0],t[1],t[2],t[3],t[4],t[5],t[6],t[7],t[8],t[9],t[10],t[11],t[12]+y.x,t[13]+y.y,t[14]+y.z,t[15]])},e.prototype.extractTranslation=function(){return new n.default(this.elements[12],this.elements[13],this.elements[14])},e.prototype.extractScale=function(){var y=this.elements;return new e([y[0],y[1],y[2],y[3],y[4],y[5],y[6],y[7],y[8],y[9],y[10],y[11],0,0,0,1]).project(new n.default(1,1,1)).length/Math.sqrt(3)},e.prototype.inverse=function(){var y,t,x=new Array(16),z=this.elements;for(x[0]=z[5]*z[10]*z[15]-z[5]*z[14]*z[11]-z[6]*z[9]*z[15]+z[6]*z[13]*z[11]+z[7]*z[9]*z[14]-z[7]*z[13]*z[10],x[1]=-z[1]*z[10]*z[15]+z[1]*z[14]*z[11]+z[2]*z[9]*z[15]-z[2]*z[13]*z[11]-z[3]*z[9]*z[14]+z[3]*z[13]*z[10],x[2]=z[1]*z[6]*z[15]-z[1]*z[14]*z[7]-z[2]*z[5]*z[15]+z[2]*z[13]*z[7]+z[3]*z[5]*z[14]-z[3]*z[13]*z[6],x[3]=-z[1]*z[6]*z[11]+z[1]*z[10]*z[7]+z[2]*z[5]*z[11]-z[2]*z[9]*z[7]-z[3]*z[5]*z[10]+z[3]*z[9]*z[6],x[4]=-z[4]*z[10]*z[15]+z[4]*z[14]*z[11]+z[6]*z[8]*z[15]-z[6]*z[12]*z[11]-z[7]*z[8]*z[14]+z[7]*z[12]*z[10],x[5]=z[0]*z[10]*z[15]-z[0]*z[14]*z[11]-z[2]*z[8]*z[15]+z[2]*z[12]*z[11]+z[3]*z[8]*z[14]-z[3]*z[12]*z[10],x[6]=-z[0]*z[6]*z[15]+z[0]*z[14]*z[7]+z[2]*z[4]*z[15]-z[2]*z[12]*z[7]-z[3]*z[4]*z[14]+z[3]*z[12]*z[6],x[7]=z[0]*z[6]*z[11]-z[0]*z[10]*z[7]-z[2]*z[4]*z[11]+z[2]*z[8]*z[7]+z[3]*z[4]*z[10]-z[3]*z[8]*z[6],x[8]=z[4]*z[9]*z[15]-z[4]*z[13]*z[11]-z[5]*z[8]*z[15]+z[5]*z[12]*z[11]+z[7]*z[8]*z[13]-z[7]*z[12]*z[9],x[9]=-z[0]*z[9]*z[15]+z[0]*z[13]*z[11]+z[1]*z[8]*z[15]-z[1]*z[12]*z[11]-z[3]*z[8]*z[13]+z[3]*z[12]*z[9],x[10]=z[0]*z[5]*z[15]-z[0]*z[13]*z[7]-z[1]*z[4]*z[15]+z[1]*z[12]*z[7]+z[3]*z[4]*z[13]-z[3]*z[12]*z[5],x[11]=-z[0]*z[5]*z[11]+z[0]*z[9]*z[7]+z[1]*z[4]*z[11]-z[1]*z[8]*z[7]-z[3]*z[4]*z[9]+z[3]*z[8]*z[5],x[12]=-z[4]*z[9]*z[14]+z[4]*z[13]*z[10]+z[5]*z[8]*z[14]-z[5]*z[12]*z[10]-z[6]*z[8]*z[13]+z[6]*z[12]*z[9],x[13]=z[0]*z[9]*z[14]-z[0]*z[13]*z[10]-z[1]*z[8]*z[14]+z[1]*z[12]*z[10]+z[2]*z[8]*z[13]-z[2]*z[12]*z[9],x[14]=-z[0]*z[5]*z[14]+z[0]*z[13]*z[6]+z[1]*z[4]*z[14]-z[1]*z[12]*z[6]-z[2]*z[4]*z[13]+z[2]*z[12]*z[5],x[15]=z[0]*z[5]*z[10]-z[0]*z[9]*z[6]-z[1]*z[4]*z[10]+z[1]*z[8]*z[6]+z[2]*z[4]*z[9]-z[2]*z[8]*z[5],t=z[0]*x[0]+z[1]*x[4]+z[2]*x[8]+z[3]*x[12],y=0;y<16;y++)x[y]/=t;return new e(x)},e.prototype.determinant=function(){return this.get(0,3)*this.get(1,2)*this.get(2,1)*this.get(3,0)-this.get(0,1)*this.get(1,3)*this.get(2,1)*this.get(3,0)-this.get(0,3)*this.get(1,1)*this.get(2,2)*this.get(3,0)+this.get(0,1)*this.get(1,3)*this.get(2,2)*this.get(3,0)+this.get(0,1)*this.get(1,1)*this.get(2,3)*this.get(3,0)-this.get(0,1)*this.get(1,2)*this.get(2,3)*this.get(3,0)-this.get(0,3)*this.get(1,2)*this.get(2,0)*this.get(3,1)+this.get(0,1)*this.get(1,3)*this.get(2,0)*this.get(3,1)+this.get(0,3)*this.get(1,0)*this.get(2,2)*this.get(3,1)-this.get(0,0)*this.get(1,3)*this.get(2,2)*this.get(3,1)-this.get(0,1)*this.get(1,0)*this.get(2,3)*this.get(3,1)+this.get(0,0)*this.get(1,2)*this.get(2,3)*this.get(3,1)+this.get(0,3)*this.get(1,1)*this.get(2,0)*this.get(3,2)-this.get(0,1)*this.get(1,3)*this.get(2,0)*this.get(3,2)-this.get(0,3)*this.get(1,0)*this.get(2,1)*this.get(3,2)+this.get(0,0)*this.get(1,3)*this.get(2,1)*this.get(3,2)+this.get(0,1)*this.get(1,0)*this.get(2,3)*this.get(3,2)-this.get(0,0)*this.get(1,1)*this.get(2,3)*this.get(3,2)-this.get(0,1)*this.get(1,1)*this.get(2,0)*this.get(3,3)+this.get(0,1)*this.get(1,2)*this.get(2,0)*this.get(3,3)+this.get(0,1)*this.get(1,0)*this.get(2,1)*this.get(3,3)-this.get(0,0)*this.get(1,2)*this.get(2,1)*this.get(3,3)-this.get(0,1)*this.get(1,0)*this.get(2,2)*this.get(3,3)+this.get(0,0)*this.get(1,1)*this.get(2,2)*this.get(3,3)},e.prototype.clone=function(){return new e(this.elements)},e.prototype.equal=function(y){return e.equal(this,y)},e}();y.default=i},function(e,y,t){"use strict";Object.defineProperty(y,"__esModule",{value:!0});var x=function(){function e(e,y,t,x){this.data=[e,y,t,x]}return e.fromAxisAngle=function(y,t){var x=.5*t,z=y.scale(Math.sin(x));return new e(z.x,z.y,z.z,Math.cos(x))},e.prototype.X=function(){return this.data[0]},e.prototype.Y=function(){return this.data[1]},e.prototype.Z=function(){return this.data[2]},e.prototype.W=function(){return this.data[3]},e}();y.default=x}])})},function(e,y,t){"use strict";Object.defineProperty(y,"__esModule",{value:!0});var x=t(0),z=function(){function e(e,y,t,x,z,n,i){this.a=e,this.b=y,this.c=t,this.alpha=x,this.beta=z,this.gamma=n,this.spaceGroup=i,this.init()}return e.getMatrixFromSymetry=function(e){function y(e){for(var y=[0,0,0,0],x=e.split("+"),z=0,n=x;z<n.length;z++){var i=n[z],o=t(i);y[0]=y[0]+o[0],y[1]=y[1]+o[1],y[2]=y[2]+o[2],y[3]=y[3]+o[3]}return y}function t(e){for(var y=[0,0,0,0],t=e.split("-"),x=[0,0,0,0],n=0;n<t.length;n++)if(0!==n||""!==t[n]){var i=-1;0===n&&(i=1),x=z(t[n]),y[0]=y[0]+x[0]*i,y[1]=y[1]+x[1]*i,y[2]=y[2]+x[2]*i,y[3]=y[3]+x[3]*i}return y}function z(e){var y=[0,0,0,0];return e.indexOf("x")>=0?y[0]=i(e,"x"):e.indexOf("y")>=0?y[1]=i(e,"y"):e.indexOf("z")>=0?y[2]=i(e,"z"):y[3]=n(e),y}function n(e){var y;if(e.indexOf("/")>=0){var t=e.split("/");y=parseFloat(t[0])/parseFloat(t[1])}else{var x=e.replace(".",",");y=parseFloat(x)}return y}function i(e,y){var t=0;if(e.indexOf(y)>=0)if(e.indexOf("*")>=0){var x=e.split("*");if(t=n(x[0]),x[1]!==y)throw new Error("Incorect formula")}else{if(y===e)return 1;t=n(e.replace(y,""))}return t}var o=function(e,y,t){return e.replace(new RegExp(y.replace(/[-\/\\^$*+?.()|[\]{}]/g,"\\$&"),"g"),t)}(e.toLowerCase()," ",""),s=o.split(",");if(3!==s.length)throw new Error("can not parse symetry code : "+e);for(var r=y(s[0]),a=y(s[1]),h=y(s[2]),c=0;c<4;c++){var u="number"!=typeof 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x.Vec3(z.x,z.y,z.z),u=this.orthToFract(n),l=this.orthToFract(i),d=this.orthToFract(o),f=this.orthToFract(s),m=this.orthToFract(r),p=this.orthToFract(a),g=this.orthToFract(h),v=this.orthToFract(c),b=Math.floor(Math.min(u.x,l.x,d.x,f.x,m.x,p.x,g.x,v.x)),P=Math.floor(Math.min(u.y,l.y,d.y,f.y,m.y,p.y,g.y,v.y)),w=Math.floor(Math.min(u.z,l.z,d.z,f.z,m.z,p.z,g.z,v.z)),C=Math.ceil(Math.max(u.x,l.x,d.x,f.x,m.x,p.x,g.x,v.x)),M=Math.ceil(Math.max(u.y,l.y,d.y,f.y,m.y,p.y,g.y,v.y)),A=Math.ceil(Math.max(u.z,l.z,d.z,f.z,m.z,p.z,g.z,v.z)),I=[],T=b;T<C;T++)for(var F=P;F<M;F++)for(var E=w;E<A;E++)I.push(new x.Vec3(T,F,E));return I},e.prototype.init=function(){var y=.017453292519943295*this.alpha,t=.017453292519943295*this.beta,z=.017453292519943295*this.gamma,n=Math.sqrt(1-Math.cos(y)*Math.cos(y)-Math.cos(t)*Math.cos(t)-Math.cos(z)*Math.cos(z)+2*Math.cos(y)*Math.cos(t)*Math.cos(z)),i=(Math.sin(y),this.a,Math.sin(t),this.b,Math.sin(z)/this.c/n),o=Math.acos((Math.cos(t)*Math.cos(z)-Math.cos(y))/Math.sin(t)/Math.sin(z));Math.acos((Math.cos(y)*Math.cos(z)-Math.cos(t))/Math.sin(y)/Math.sin(z)),Math.acos((Math.cos(y)*Math.cos(t)-Math.cos(z))/Math.sin(y)/Math.sin(t));this.mOrthMatrix=new x.Matrix3x3,this.mOrthMatrix.set(0,0,this.a),this.mOrthMatrix.set(0,1,this.b*Math.cos(z)),this.mOrthMatrix.set(0,2,this.c*Math.cos(t)),this.mOrthMatrix.set(1,0,0),this.mOrthMatrix.set(1,1,this.b*Math.sin(z)),this.mOrthMatrix.set(1,2,-this.c*Math.sin(t)*Math.cos(o)),this.mOrthMatrix.set(2,0,0),this.mOrthMatrix.set(2,1,0),this.mOrthMatrix.set(2,2,1/i),this.mOrthMatrixInvert=x.Matrix3x3.inverse(this.mOrthMatrix),this.volume=n,this.symetryList=[];for(var s=0,r=this.spaceGroup.symetryList;s<r.length;s++){var a=r[s],h=e.getMatrixFromSymetry(a);this.symetryList.push(h)}},e}();y.UnitCell=z},function(e,y,t){"use strict";Object.defineProperty(y,"__esModule",{value:!0});var x=t(3),z=t(5),n=t(17),i=t(19),o=t(25),s=function(){function e(e){this.options={bgcolor:e.bgcolor||"#2b303b",showLabels:!1,showMarkers:!0,showUnitCell:!1},this.initDone=!1,this.subscriptions=[],this.molecule=new z.Molecule3D}return e.prototype.append=function(e){var y=this;if(this.View||this.initDone)throw new Error("append or init were alredy done");this.View=$('<div class="jcmolview"><canvas></canvas></div>'),this.View.css({"background-color":this.options.bgcolor,dispaly:"block",height:"100%",position:"absolute",width:"100%"}),this.View.find("canvas").css({dispaly:"block"}),this.View.appendTo(e),this.canvasElement=this.View.find("canvas").get(0),this.context=this.canvasElement.getContext("2d"),this.painer=new n.Painter(this.context,this.options),this.camera=new x.Camera({element:this.canvasElement,onClick:function(e,t){if(y.options.showMarkers){var x=y.painer.uprojectToMarker({camera:y.camera,molecule:y.molecule,x:e,y:t});x&&(y.molecule.extendByMarker(x),y.redraw())}},onRedraw:function(){y.redraw()}}),this.contextMenu=new i.ContextMenu([new o.ContextMenuItem({command:function(){y.center()},title:"Center Molecule",type:"item"}),new o.ContextMenuItem({title:"----",type:"delimer"}),new o.ContextMenuItem({command:function(){y.options.showMarkers=!y.options.showMarkers,y.redraw()},isChecked:function(){return y.options.showMarkers},title:"Show Markers",type:"checkbox"}),new o.ContextMenuItem({command:function(){y.options.showUnitCell=!y.options.showUnitCell,y.redraw()},isChecked:function(){return y.options.showUnitCell},title:"Show Unit Cell",type:"checkbox"}),new o.ContextMenuItem({command:function(){y.options.showLabels=!y.options.showLabels,y.redraw()},isChecked:function(){return y.options.showLabels},title:"Show 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y=function(){e.resizeCanvas()};$(window).on("resize",y),this.subscriptions.push(function(){$(window).off("resize",y)}),setTimeout(function(){e.resizeCanvas()},0),this.contextMenu.onInit(this.View),this.initDone=!0},e.prototype.onDestroy=function(){this.camera.onDestroy(),this.subscriptions.forEach(function(e){e()})},e.prototype.redraw=function(){this.height&&this.width&&this.painer.draw(this.molecule,this.camera)},e.prototype.resizeCanvas=function(){var e=this.View.width(),y=this.View.height();e===this.width&&y===this.height||(this.width=e,this.height=y,this.canvasElement.width=this.width,this.canvasElement.height=this.height,this.redraw())},e}();y.Mol3DView=s},function(e,y,t){"use strict";Object.defineProperty(y,"__esModule",{value:!0});var x=t(0),z=t(4),n=function(){function e(e){this.element=e.element;var y=new 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 * Date: 2017-03-20T18:59Z
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