Difference between revisions of "Template:Groningen/PV"

Revision as of 16:37, 17 October 2018 (view source)

MTadema (Talk | contribs)

Latest revision as of 16:38, 17 October 2018 (view source)

MTadema (Talk | contribs)

(One intermediate revision by the same user not shown)

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<html>

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/**

* PV - WebGL protein viewer v1.7.0dev

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},draw:function(a,b,c,d){if(this._O&&"normal"===d){var e=b.text;a.bind(e),this.bind();var f=this._c,g=a.upsamplingFactor();f.uniform1f(f.getUniformLocation(e,"xScale"),this._dp),f.uniform1f(f.getUniformLocation(e,"yScale"),this._do),f.uniform1f(f.getUniformLocation(e,"width"),2*g*this._k/a.viewportWidth()),f.uniform1f(f.getUniformLocation(e,"height"),2*g*this._m/a.viewportHeight()),f.uniform1i(f.getUniformLocation(e,"sampler"),0);var h=f.getAttribLocation(e,"attrCenter");f.enableVertexAttribArray(h),f.vertexAttribPointer(h,3,f.FLOAT,!1,20,0);var i=f.getAttribLocation(e,"attrCorner");f.vertexAttribPointer(i,2,f.FLOAT,!1,20,12),f.enableVertexAttribArray(i),f.enable(f.BLEND),f.blendFunc(f.SRC_ALPHA,f.ONE_MINUS_SRC_ALPHA),f.drawArrays(f.TRIANGLES,0,6),f.disableVertexAttribArray(h),f.disableVertexAttribArray(i),f.disable(f.BLEND)}}}),a}(),y=function(c){function e(){this._e=[],this._D=[],this._u=0}function f(a,b,d,f){Q.call(this,b),this._A=d,this._F=f,this._B=new e,this._dE=new c.ProtoSphere(8,8),this._dF=new c.ProtoCylinder(8),this._W=null,this._p=!1}function g(a,b,c){for(var d=0;c-1>d;++d)a.addTriangle(b,b+1+d,b+2+d);a.addTriangle(b,b+c,b+1)}function h(a,b,c){for(var d=b+c,e=0;c-1>e;++e)a.addTriangle(d,b+e+1,b+e);a.addTriangle(d,b,b+c-1)}var i=a.vec3,j=a.mat3,k=b.forceRGB;return e.prototype={numVerts:function(){return this._u},addVertex:function(a,b,c,d){this._u+=1,this._e.push(a[0],a[1],a[2],b[0],b[1],b[2],c[0],c[1],c[2],c[3],d)},addTriangle:function(a,b,c){this._D.push(a,b,c)},numIndices:function(){return this._D.length},indexData:function(){return this._D},vertData:function(){return this._e}},d.derive(f,Q,{updateProjectionIntervals:function(){},updateSquaredSphereRadius:function(a,b){return b},addTube:function(){var a=i.create(),b=i.create(),c=i.create(),d=i.create(),e=j.create();return function(f,j,m,n){n=n||{};var o=k(n.color||"white"),p=!0;void 0!==n.cap&&(p=n.cap),i.sub(d,j,f);var q=i.length(d);if(i.normalize(d,d),i.add(a,f,j),i.scale(a,a,.5),l.buildRotation(e,d,b,c,!1),p){var r=this._B.numVerts();this._B.addVertex(f,[-d[0],-d[1],-d[2]],o,0),g(this._B,r,8)}if(this._dF.addTransformed(this._B,a,q,m,e,o,o,0,0),p){var s=this._B.numVerts();this._B.addVertex(j,d,o,0),h(this._B,s-8,8)}this._p=!1}}(),addSphere:function(a,b,c){c=c||{};var d=k(c.color||"white");this._dE.addTransformed(this._B,a,b,d,0),this._p=!1},_dG:function(){this._p=!0,null!==this._W&&this._W.destroy(),this._W=new S(this._c,this._B.numVerts(),this._B.numIndices(),this._A,this._F),this._W.setIndexData(this._B.indexData()),this._W.setVertData(this._B.vertData())},draw:function(a,b,c,d){if(this._O){this._p||this._dG();var e=this.shaderForStyleAndPass(b,c,d);if(e){a.bind(e),this._c.uniform1i(e.symId,255);var f=this._W;f.bind(e),f.draw(),f.releaseAttribs(e)}}},shaderForStyleAndPass:function(a,b,c){if("normal"===c)return a.hemilight;if("select"===c)return null;if("outline"===c)return a.outline;var d=a[c];return void 0!==d?d:null}}),f}(m),z=function(){function b(a,b,c){this._cc=a,this._bO=b,this._bf=c,this._er=c,this._bl=Date.now(),this._cR=!1,this._ce=!1}function c(a,c,d){b.call(this,o.clone(a),o.clone(c),d),this._S=o.clone(a)}function e(a,c,d){var e=q.create(),f=q.create();q.fromMat4(e,a),q.fromMat4(f,c);var g=p.create(),h=p.create();p.fromMat3(g,e),p.fromMat3(h,f),this._S=q.create(),b.call(this,g,h,d)}function f(a,c){b.call(this,null,null,c),this._bM=o.clone(a),this.setLooping(!0),this._cI=0}function g(a,c){var d=1e3*(2*Math.PI/c);b.call(this,null,null,d),this._bM=o.clone(a),this.setLooping(!0),this._dz=c,this._cH=0}function h(){this._bi=[]}function i(a,b,d){return new c(a,b,d)}function j(a,b,c){return new e(a,b,c)}function k(a,c,d){return new b(a,c,d)}function m(a,b){return new g(a,b)}function n(){return new f([0,1,0],2e3)}var o=a.vec3,p=a.quat,q=a.mat3;return b.prototype={setLooping:function(a){this._cR=a},step:function(a){var 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e=this._R(d,c);e.color=e.color||b.byElement(),e.lineWidth=e.lineWidth||4;var f=l.lines(c,this._.gl(),e);return this.add(a,f)},points:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.byElement(),e.pointSize=e.pointSize||1;var f=l.points(c,this._.gl(),e);return this.add(a,f)},trace:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.uniform([1,0,0]),e.radius=e.radius||.3,e.arcDetail=2*(e.arcDetail||this.options("arcDetail")),e.sphereDetail=e.sphereDetail||this.options("sphereDetail");var f=l.trace(c,this._.gl(),e);return this.add(a,f)},fitTo:function(a){var b=this._d.mainAxes(),c=[new d.Range,new d.Range,new d.Range];if(a instanceof Q)a.updateProjectionIntervals(b[0],b[1],b[2],c[0],c[1],c[2]);else if(void 0!==a.eachAtom){a.eachAtom(function(a){for(var d=a.pos(),e=0;3>e;++e)c[e].update(v.dot(d,b[e]))});for(var e=0;3>e;++e)c[e].extend(1.5)}this._c9(b,c)},_c9:function(a,b){if(!(b[0].empty()||b[1].empty()||b[2].empty())){var c=b[0].center(),d=b[1].center(),e=b[2].center(),f=[c*a[0][0]+d*a[1][0]+e*a[2][0],c*a[0][1]+d*a[1][1]+e*a[2][1],c*a[0][2]+d*a[1][2]+e*a[2][2]],g=this._d.fieldOfViewY(),h=this._d.aspectRatio(),i=b[0].length()/h,j=b[1].length(),k=.5*Math.max(i,j),l=k/Math.tan(.5*g),m=l+.5*b[2].length(),n=.5,o=Math.max(l-n,.1),p=2*n+l+b[2].length();this._d.setNearFar(o,p),this.setCamera(this._d.rotation(),f,m,this._b.animateTime),this.requestRedraw()}},autoZoom:function(){var a=this._d.mainAxes(),b=[new d.Range,new d.Range,new d.Range];this.forEach(function(c){c.visible()&&c.updateProjectionIntervals(a[0],a[1],a[2],b[0],b[1],b[2])}),this._c9(a,b)},slabInterval:function(){},autoSlab:function(){var a=this._b._eq.update(this._l,this._d);null!==a&&this._d.setNearFar(a.near,a.far),this.requestRedraw()},rockAndRoll:function(a){return void 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a=this._.gl();a.clearColor(0,0,0,0),a.disable(a.BLEND),a.clear(a.COLOR_BUFFER_BIT|a.DEPTH_BUFFER_BIT),a.clearColor(this._b.background[0],this._b.background[1],this._b.background[2],1),a.cullFace(a.FRONT),a.enable(a.CULL_FACE),this._ch("select")},pick:function(a){this._bW.bind(),this._d7();var b=new Uint8Array(4),c=this._.gl();c.readPixels(a.x,this._b.height-a.y,1,1,c.RGBA,c.UNSIGNED_BYTE,b),this._bW.release(),b.data&&(b=b.data);var d=b[0]|b[1]<<8|b[2]<<16,e=b[3],f=this._cL.objectForId(d);if(void 0===f)return null;var g=null;return 255!==e&&(g=f.geom.symWithIndex(e)),new r(f,255>e?e:null,g)},add:function(a,b){return b.name(a),this._l.push(b),this._l.sort(function(a,b){return a.order()-b.order()}),this.requestRedraw(),b},_c3:function(a){var b=a.replace(".","\\.").replace("*",".*");return new RegExp("^"+b+"$")},forEach:function(){var a,b="*";2===arguments.length?(a=arguments[1],b=arguments[0]):a=arguments[0];for(var c=this._c3(b),d=0;d<this._l.length;++d){var 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this._K.isHetatm()}}),{Atom:c,AtomView:e}}(),E=function(b){function c(){}function e(a,b,d,e){c.call(this),this._H=b,this._dL=d,this._dW=e,this._C=[],this._cz="C",this._J=a,this._cU=!1,this._cT=!1,this._b7=a.residues().length}function f(a,b){c.call(this),this._ea=a,this._C=[],this._t=b}var g=a.vec3,h=b.Atom,i=b.AtomView;return c.prototype={prop:function(a){return this[a]()},isWater:function(){return"HOH"===this.name()||"DOD"===this.name()},eachAtom:function(a,b){b|=0;for(var c=0;c<this._C.length;c+=1){if(a(this._C[c],b)===!1)return!1;b+=1}return b},qualifiedName:function(){var a=this.chain().name()+"."+this.name()+this.num();return"\x00"===this.insCode()?a:a+this.insCode()},atom:function(a){if("string"==typeof a){for(var b=0;b<this._C.length;++b)if(this._C[b].name()===a)return this._C[b];return null}return a>=this._C.length&&0>a?null:this._C[a]},centralAtom:function(){return this.isAminoacid()?this.atom("CA"):this.isNucleotide()?this.atom("C3'"):null},center:function(){var 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d.copy(a,this._s[b].centralAtom().pos()),a},normalAt:function(a,b){var c=this._s[b];return c.isAminoacid()&&d.sub(a,c.atom("O").pos(),c.atom("C").pos()),d.normalize(a,a),a},centralAtomAt:function(a){return this._s[a].centralAtom()},tangentAt:function(){var a=d.create(),b=d.create();return function(c,e){e>0?this.posAt(a,e-1):this.posAt(a,e),e<this._s.length-1?this.posAt(b,e+1):this.posAt(b,e),d.sub(c,b,a)}}(),fullTraceIndex:function(a){return a},subsets:function(a){for(var b=0,d=0,e=[];d<a.length&&b<this._s.length;){for(var f=a[d].full().index();this._s.length>b&&this._s[b].index()<f;)++b;if(b>=this._s.length)break;for(var g=this._s[b].index();a.length>d&&a[d].full().index()<g;)++d;if(d>=a.length)break;for(var h=b;a.length>d&&this._s.length>b&&a[d].full().index()===this._s[b].index();)++d,++b;var i=b;e.push(new c(this,h,i))}return e}},b.prototype.smoothPosAt=b.prototype.posAt,b.prototype.smoothNormalAt=b.prototype.normalAt,c.prototype={length:function(){return 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0!==b.rindexRange){for(d=b.rindexRange[0],e=Math.min(c.length-1,b.rindexRange[1]);e>=d;++d)f.push(c[d]);return f}if(b.rindices&&void 0!==b.rindices.length){for(f=[],d=0;d<b.rindices.length;++d)f.push(c[b.rindices[d]]);return f}return c}function f(f,g,h){var i=c(h),j=b(h),k=d(h);h.rindex&&(h.rindices=[h.rindex]);for(var l=0;l<f._j.length;++l){var m=f._j[l];if(a(m,k))for(var n=e(m,h),o=null,p=0;p<n.length;++p)if(a(n[p],i)){o||(o=g.addChain(m,!1));for(var q=null,r=n[p].atoms(),s=0;s<r.length;++s)a(r[s],j)&&(q||(q=o.addResidue(n[p],!1)),q.addAtom(r[s]))}}return g}return{dict:f}}(),J=U=function(b,c,e){function f(a){var b=q[a.toUpperCase()];return void 0!==b?b:1.5}function g(a,b,c){var d=b.atom("C"),e=c.atom("N");if(d&&e){var f=m.sqrDist(d.pos(),e.pos());1.6*1.6>f&&a.connect(e,d)}}function h(a,b,c){var d=b.atom("O3'"),e=c.atom("P");if(d&&e){var f=m.sqrDist(d.pos(),e.pos());1.7*1.7>f&&a.connect(d,e)}}function i(){}function j(){i.call(this),this._j=[],this._N=[],this._cM=0}function k(a){i.call(this),this._cO=a,this._j=[]}var m=a.vec3,n=b.Chain,o=b.ChainView,p=c.Bond,q={H:.31,HE:.28,LI:1.28,BE:.96,B:.84,C:.76,N:.71,O:.66,F:.57,NE:.58,NA:1.66,MG:1.41,AL:1.21,SI:1.11,P:1.07,S:1.05,CL:1.02,AR:1.06,K:2.03,CA:1.76,SC:1.7,TI:1.6,V:1.53,CR:1.39,MN:1.39,FE:1.32,CO:1.26,NI:1.24,CU:1.32,ZN:1.22,GA:1.22,GE:1.2,AS:1.19,SE:1.2,BR:1.2,KR:1.16,RB:2.2,SR:1.95,Y:1.9,ZR:1.75,NB:1.64,MO:1.54,TC:1.47,RU:1.46,RH:1.42,PD:1.39,AG:1.45,CD:1.44,IN:1.42,SN:1.39,SB:1.39,TE:1.38,I:1.39,XE:1.4,CS:2.44,BA:2.15,LA:2.07,CE:2.04,PR:2.03,ND:2.01,PM:1.99,SM:1.98,EU:1.98,GD:1.96,TB:1.94,DY:1.92,HO:1.92,ER:1.89,TM:1.9,YB:1.87,LU:1.87,HF:1.75,TA:1.7,W:1.62,RE:1.51,OS:1.44,IR:1.41,PT:1.36,AU:1.36,HG:1.32,TL:1.45,PB:1.46,BI:1.48,PO:1.4,AT:1.5,RN:1.5,FR:2.6,RA:2.21,AC:2.15,TH:2.06,PA:2,U:1.96,NP:1.9,PU:1.87,AM:1.8,CM:1.69};return i.prototype={eachResidue:function(a){for(var b=0;b<this._j.length;b+=1)if(this._j[b].eachResidue(a)===!1)return!1},eachAtom:function(a,b){b|=0;for(var c=0;c<this._j.length;c+=1)if(b=this._j[c].eachAtom(a,b),b===!1)return!1},residueCount:function(){for(var a=this.chains(),b=0,c=0;c<a.length;++c)b+=a[c].residues().length;return b},eachChain:function(a){for(var b=this.chains(),c=0;c<b.length;++c)if(a(b[c])===!1)return},atomCount:function(){for(var a=this.chains(),b=0,c=0;c<a.length;++c)b+=a[c].atomCount();return b},atoms:function(){var a=[];return this.eachAtom(function(b){a.push(b)}),a},atom:function(a){var b=a.split("."),c=this.chain(b[0]);if(null===c)return null;var d=c.residueByRnum(parseInt(b[1],10));return null===d?null:d.atom(b[2])},center:function(){var a=m.create(),b=0;return this.eachAtom(function(c){m.add(a,a,c.pos()),b+=1}),b&&m.scale(a,a,1/b),a},boundingSphere:function(){var a=this.center(),b=0;return this.eachAtom(function(c){b=Math.max(b,m.sqrDist(a,c.pos()))}),new l.Sphere(a,Math.sqrt(b))},backboneTraces:function(){for(var a=this.chains(),b=[],c=0;c<a.length;++c)Array.prototype.push.apply(b,a[c].backboneTraces());return b},select:function(a){return"protein"===a?this.residueSelect(function(a){return a.isAminoacid()}):"water"===a?this.residueSelect(function(a){return a.isWater()}):"ligand"===a?this.residueSelect(function(a){return!a.isAminoacid()&&!a.isWater()}):e.dict(this,new k(this),a||{})},residueSelect:function(a){for(var b=new k(this.full()),c=0;c<this._j.length;++c)for(var d=this._j[c],e=null,f=d.residues(),g=0;g<f.length;++g)a(f[g])&&(e||(e=b.addChain(d,!1)),e.addResidue(f[g],!0));return b},atomSelect:function(a){for(var b=new k(this.full()),c=0;c<this._j.length;++c)for(var d=this._j[c],e=null,f=d.residues(),g=0;g<f.length;++g)for(var h=null,i=f[g],j=i.atoms(),l=0;l<j.length;++l)a(j[l])&&(e||(e=b.addChain(d,!1)),h||(h=e.addResidue(i,!1)),h.addAtom(j[l]));return b},assembly:function(a){for(var b=this.assemblies(),c=0;c<b.length;++c)if(b[c].name()===a)return b[c];return null},chainsByName:function(a){for(var b={},c=this.chains(),d=0;d<c.length;++d)b[c[d].name()]=c[d];for(var e=[],f=0;f<a.length;++f){var g=b[a[f]];void 0!==g&&e.push(g)}return e},selectWithin:function(){var a=m.create();return function(b,c){c=c||{};var d=c.radius||4,e=d*d,f=!!c.matchResidues,g=[];b.eachAtom(function(a){g.push(a)});for(var h=new k(this.full()),i=null,j=null,l=this.chains(),n=!1,o=0;o<l.length;++o){var p=l[o].residues();j=null;for(var q=0;q<p.length;++q){i=null,n=!1;for(var r=p[q].atoms(),s=0;s<r.length&&!n;++s)for(var t=0;t<g.length;++t)if(m.sub(a,r[s].pos(),g[t].pos()),!(m.sqrLen(a)>e)){if(j||(j=h.addChain(l[o].full(),!1)),i||(i=j.addResidue(p[q].full(),f)),f){n=!0;break}i.addAtom(r[s].full());break}}}return h}}(),createEmptyView:function(){return new k(this.full())}},d.derive(j,i,{addAssembly:function(a){this._N.push(a)},setAssemblies:function(a){this._N=a},assemblies:function(){return this._N},chains:function(){return this._j},full:function(){return this},containsResidue:function(a){return a.full().structure()===this},chainByName:function(a){for(var b=0;b<this._j.length;++b)if(this._j[b].name()===a)return this._j[b];return null},chain:function(a){return this.chainByName(a)},nextAtomIndex:function(){var a=this._cM;return this._cM+=1,a},addChain:function(a){var b=new n(this,a);return this._j.push(b),b},connect:function(a,b){var c=new p(a,b);return a.addBond(c),b.addBond(c),c},deriveConnectivity:function(){var a=this,b=null;this.eachResidue(function(c){for(var d,e=c.atoms(),i=e.length,j=0;i>j;j+=1)for(var k=e[j],l=k.pos(),n=f(k.element()),o=0;j>o;o+=1){var p=e[o],q=f(p.element());d=m.sqrDist(l,p.pos());var r=n+q-.3,s=n+q+.3;s*s>d&&d>r*r&&a.connect(k,p)}c._d9(),null!==b&&(c.isAminoacid()&&b.isAminoacid()&&g(a,b,c),c.isNucleotide()&&b.isNucleotide()&&h(a,b,c)),b=c})}}),d.derive(k,i,{full:function(){return this._cO},assemblies:function(){return this._cO.assemblies()},addChain:function(a,b){var c=new o(this,a.full());if(this._j.push(c),b)for(var d=a.residues(),e=0;e<d.length;++e)c.addResidue(d[e],!0);return c},containsResidue:function(a){if(!a)return!1;var b=this.chain(a.chain().name());return b?b.containsResidue(a):!1},chains:function(){return this._j},chain:function(a){for(var b=0;b<this._j.length;++b)if(this._j[b].name()===a)return this._j[b];return null}}),{MolView:k,Mol:j}}(G,H,I),K=function(){function a(a){function b(a,b){return a=Math.abs(a),b=Math.abs(b),a>b?a*Math.sqrt(1+b*b/a/a):0==b?a:b*Math.sqrt(1+a*a/b/b)}var c,d=Math.pow(2,-52),e=1e-64/d,f=50,g=0,h=0,i=0,j=0,k=0,l=a,m=l.length,n=l[0].length;if(n>m)throw"Need more rows than columns";var o=new Array(n),p=new Array(n);for(h=0;n>h;h++)o[h]=p[h]=0;for(var q=[],h=0;n>h;++h){var r=[];q.push([]);for(var i=0;n>i;++i)r.push(0);q.push(r)}var s=0,t=0,u=0,v=0,w=0,x=0,y=0;for(h=0;n>h;h++){for(o[h]=t,y=0,k=h+1,i=h;m>i;i++)y+=l[i][h]*l[i][h];if(e>=y)t=0;else for(s=l[h][h],t=Math.sqrt(y),s>=0&&(t=-t),u=s*t-y,l[h][h]=s-t,i=k;n>i;i++){for(y=0,j=h;m>j;j++)y+=l[j][h]*l[j][i];for(s=y/u,j=h;m>j;j++)l[j][i]+=s*l[j][h]}for(p[h]=t,y=0,i=k;n>i;i++)y+=l[h][i]*l[h][i];if(e>=y)t=0;else{for(s=l[h][h+1],t=Math.sqrt(y),s>=0&&(t=-t),u=s*t-y,l[h][h+1]=s-t,i=k;n>i;i++)o[i]=l[h][i]/u;for(i=k;m>i;i++){for(y=0,j=k;n>j;j++)y+=l[i][j]*l[h][j];for(j=k;n>j;j++)l[i][j]+=y*o[j]}}w=Math.abs(p[h])+Math.abs(o[h]),w>v&&(v=w)}for(h=n-1;-1!=h;h+=-1){if(0!=t){for(u=t*l[h][h+1],i=k;n>i;i++)q[i][h]=l[h][i]/u;for(i=k;n>i;i++){for(y=0,j=k;n>j;j++)y+=l[h][j]*q[j][i];for(j=k;n>j;j++)q[j][i]+=y*q[j][h]}}for(i=k;n>i;i++)q[h][i]=0,q[i][h]=0;q[h][h]=1,t=o[h],k=h}for(h=n-1;-1!=h;h+=-1){for(k=h+1,t=p[h],i=k;n>i;i++)l[h][i]=0;if(0!=t){for(u=l[h][h]*t,i=k;n>i;i++){for(y=0,j=k;m>j;j++)y+=l[j][h]*l[j][i];for(s=y/u,j=h;m>j;j++)l[j][i]+=s*l[j][h]}for(i=h;m>i;i++)l[i][h]=l[i][h]/t}else for(i=h;m>i;i++)l[i][h]=0;l[h][h]+=1}for(d*=v,j=n-1;-1!=j;j+=-1)for(var z=0;f>z;z++){var A=!1;for(k=j;-1!=k;k+=-1){if(Math.abs(o[k])<=d){A=!0;break}if(Math.abs(p[k-1])<=d)break}if(!A){g=0,y=1;var B=k-1;for(h=k;j+1>h&&(s=y*o[h],o[h]=g*o[h],!(Math.abs(s)<=d));h++)for(t=p[h],u=b(s,t),p[h]=u,g=t/u,y=-s/u,i=0;m>i;i++)w=l[i][B],x=l[i][h],l[i][B]=w*g+x*y,l[i][h]=-w*y+x*g}if(x=p[j],k==j){if(0>x)for(p[j]=-x,i=0;n>i;i++)q[i][j]=-q[i][j];break}if(z>=f-1)throw"Error: no convergence.";for(v=p[k],w=p[j-1],t=o[j-1],u=o[j],s=((w-x)*(w+x)+(t-u)*(t+u))/(2*u*w),t=b(s,1),s=0>s?((v-x)*(v+x)+u*(w/(s-t)-u))/v:((v-x)*(v+x)+u*(w/(s+t)-u))/v,g=1,y=1,h=k+1;j+1>h;h++){for(t=o[h],w=p[h],u=y*t,t=g*t,x=b(s,u),o[h-1]=x,g=s/x,y=u/x,s=v*g+t*y,t=-v*y+t*g,u=w*y,w*=g,i=0;n>i;i++)v=q[i][h-1],x=q[i][h],q[i][h-1]=v*g+x*y,q[i][h]=-v*y+x*g;for(x=b(s,u),p[h-1]=x,g=s/x,y=u/x,s=g*t+y*w,v=-y*t+g*w,i=0;m>i;i++)w=l[i][h-1],x=l[i][h],l[i][h-1]=w*g+x*y,l[i][h]=-w*y+x*g}o[k]=0,o[j]=s,p[j]=v}for(h=0;h<p.length;h++)p[h]<d&&(p[h]=0);for(h=0;n>h;h++)for(i=h-1;i>=0;i--)if(p[i]<p[h]){for(g=p[i],p[i]=p[h],p[h]=g,j=0;j<l.length;j++)c=l[j][h],l[j][h]=l[j][i],l[j][i]=c;for(j=0;j<q.length;j++)c=q[j][h],q[j][h]=q[j][i],q[j][i]=c;h=i}return{U:l,S:p,V:q}}return a}(),L=function(){function b(a){if(void 0===a||null===a||"all"===a)return null;if("backbone"===a)return{CA:!0,C:!0,O:!0,N:!0};if(void 0!==a.substr){for(var b={},c=a.split(","),d=0;d<c.length;++d)b[c[d].trim()]=!0;return b}for(var b={},d=0;d<a.length;++d)b[a[d]]=!0;return b}function c(a,b,c,d,e){for(var f=a.atoms(),g=b.atoms(),h=0;h<f.length;++h){var i=f[h];if(null===e||e[i.name()]===!0)for(var j=0;j<g.length;++j){var k=g[j];if(k.name()===i.name()){c.push(i),d.push(k);break}}}}function d(a,d,e,f){for(var g=a.full().createEmptyView(),h=d.full().createEmptyView(),i=Math.min(a.chains().length,d.chains().length),j=b(e),k=0;i>k;++k){var l=a.chains()[k],m=d.chains()[k],n=f(l,m),o=n[0],p=n[1];if(o.length!==p.length)return console.errors("chains",l.name()," and",m.name()," do not contain the same number of residues."),null;for(var q=g.addChain(l),r=h.addChain(m),s=0;s<o.length;++s){var t=o[s],u=p[s],v=[],w=[];if(c(t,u,v,w,j),0!==v.length)for(var x=q.addResidue(t),y=r.addResidue(u),z=0;z<v.length;++z)x.addAtom(v[z]),y.addAtom(w[z])}}return[g,h]}function e(a,b,c){return d(a,b,c,function(a,b){return[a.residues(),b.residues()]})}function f(a,b,c){return d(a,b,c,function(a,b){for(var c=[],d=[],e=a.residues(),f=0;f<e.length;++f){var g=b.residueByRnum(e[f].num());null!==g&&(c.push(e[f]),d.push(g))}return[c,d]})}var g=a.vec3,h=a.mat3,i=(a.quat,function(a,b){if(g.set(b,0,0,0),0!==a.length){for(var c=0;c<a.length;++c){var d=a[c];g.add(b,b,d.pos())}g.scale(b,b,1/a.length)}}),j=function(){var a=g.create(),b=g.create();return function(c,d,e,f,h){h[0]=0,h[1]=0,h[2]=0,h[3]=0,h[4]=0,h[5]=0,h[6]=0,h[7]=0,h[8]=0;for(var i=0;i<d.length;++i){g.sub(a,c[i].pos(),e),g.sub(b,d[i].pos(),f);var j=a,k=b;h[0]+=j[0]*k[0],h[1]+=j[0]*k[1],h[2]+=j[0]*k[2],h[3]+=j[1]*k[0],h[4]+=j[1]*k[1],h[5]+=j[1]*k[2],h[6]+=j[2]*k[0],h[7]+=j[2]*k[1],h[8]+=j[2]*k[2]}}}(),k=function(){var a=g.create(),b=g.create(),c=g.create(),d=h.create(),e=h.create(),f=h.create(),k=h.create(),l=h.create();return function(m,n){var o=m.atoms(),p=n.atoms();if(i(p,a),i(o,b),o.length!==p.length)return!1;if(o.length<3)return!1;j(o,p,b,a,e);var q=[[e[0],e[1],e[2]],[e[3],e[4],e[5]],[e[6],e[7],e[8]]],r=K(q);k[0]=r.U[0][0],k[1]=r.U[0][1],k[2]=r.U[0][2],k[3]=r.U[1][0],k[4]=r.U[1][1],k[5]=r.U[1][2],k[6]=r.U[2][0],k[7]=r.U[2][1],k[8]=r.U[2][2];var s=h.determinant(k);l[0]=r.V[0][0],l[1]=r.V[0][1],l[2]=r.V[0][2],l[3]=r.V[1][0],l[4]=r.V[1][1],l[5]=r.V[1][2],l[6]=r.V[2][0],l[7]=r.V[2][1],l[8]=r.V[2][2];var t=h.determinant(l);h.identity(f),0>s*t&&(f[8]=-1,h.mul(k,k,f)),h.mul(d,h.transpose(l,l),k),h.transpose(d,d);for(var u=m.full().atoms(),v=0;v<u.length;++v){var w=u[v];g.sub(c,w.pos(),b),g.transformMat3(c,c,d),g.add(c,a,c),w.setPos(c)}return!0}}();return{superpose:k,matchResiduesByNum:f,matchResiduesByIndex:e,parseAtomNames:b,addAtomsPresentInBoth:c}}(),M=U=function(b){function c(a){for(var b=0;b<a.length();++b)a.residueAt(b).setSS(g(a,b)?"H":h(a,b)?"E":"C")}function d(a){for(var b=a.chains(),d=0;d<b.length;++d){var e=b[d];e.eachBackboneTrace(c)}}var e=a.vec3,f=function(){var a=e.create(),b=e.create();return function(c,d,f,g){for(var h=Math.max(0,d-2);d>=h;++h)for(var i=2;5>i;++i)if(!(h+i>=c.length())){var j=e.dist(c.posAt(a,h),c.posAt(b,h+i));if(Math.abs(j-f[i-2])>g)return!1}return!0}}(),g=function(a,b){var c=[5.45,5.18,6.37],d=2.1;return f(a,b,c,d)},h=function(a,b){var c=[6.1,10.4,13],d=1.42;return f(a,b,c,d)};return{Mol:U.Mol,MolView:U.MolView,assignHelixSheet:d,superpose:b.superpose,matchResiduesByIndex:b.matchResiduesByIndex,matchResiduesByNum:b.matchResiduesByNum}}(L),N=function(b){function c(){this._N={},this._S=null}function d(a){if(" "!==a[0]){var b=a.trim();if(4===b.length){for(var c=0,d=b.charCodeAt(c);4>c&&(65>d||d>122||d>90&&97>d);)++c,d=b.charCodeAt(c);return b[c]}var e=b.charCodeAt(0);return e>=48&&57>=e?b[1]:b.substr(0,2)}return a[1]}function e(a){this._b9=[],this._bQ=[],this._cn=[],this._bR={},this._i=new U.Mol,this._cF=new c,this._bL=null,this._br=null,this._et=null,this._b={},this._b.conectRecords=!!a.conectRecords}function f(a){return a.split(/\r\n|\r|\n/g)}function g(a,b){for(var 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b=this._b.slabMode.update(this._l,this._d);null!==b&&this._d.setNearFar(b.near,b.far),a.enable(a.CULL_FACE),this._b.outline&&(a.cullFace(a.BACK),a.enable(a.CULL_FACE),this._ch("outline")),a.cullFace(a.FRONT),a.enable(a.BLEND),a.blendFunc(a.SRC_ALPHA,a.ONE_MINUS_SRC_ALPHA),this._ch("normal")}},setCenter:function(a,b){return b|=0,0===b?void this._d.setCenter(a):(this._U.add(o.move(this._d.center(),v.clone(a),b)),void this.requestRedraw())},setZoom:function(a,b){return b|=0,0===b?void this._d.setZoom(a):(this._U.add(o.zoom(this._d.zoom(),a,b)),void this.requestRedraw())},centerOn:function(a,b){this.setCenter(a.center(),b)},clear:function(){for(var a=0;a<this._l.length;++a)this._l[a].destroy();this._l=[]},addListener:function(a,b){var c=this.listenerMap[a];if("undefined"==typeof c&&(c=[],this.listenerMap[a]=c),"center"===b){var e=d.bind(this._b1,this._b1._eb);c.push(e)}else c.push(b);this._bH&&"viewerReady"===a&&b(this,null)},_cj:function(a,b,c){var d=this.listenerMap[b];d&&d.forEach(function(b){b(c,a)})},RENDER_MODES:["sline","lines","trace","lineTrace","cartoon","tube","spheres","ballsAndSticks","points"],renderAs:function(a,b,c,d){for(var e=!1,f=0;f<this.RENDER_MODES.length;++f)if(this.RENDER_MODES[f]===c){e=!0;break}return e?this[c](a,b,d):void 0},_R:function(a,b){return a=this._ca(a),a.showRelated=a.showRelated||"asym",a.showRelated&&"asym"!==a.showRelated&&null===b.assembly(a.showRelated)&&(a.showRelated="asym"),a},_ca:function(a){return a=d.copy(a),a.float32Allocator=this._A,a.uint16Allocator=this._F,a.idPool=this._cL,a},lineTrace:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.uniform([1,0,1]),e.lineWidth=e.lineWidth||4;var f=l.lineTrace(c,this._.gl(),e);return this.add(a,f)},spheres:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.byElement(),e.sphereDetail=this.options("sphereDetail"),e.radiusMultiplier=e.radiusMultiplier||1;var f=l.spheres(c,this._.gl(),e);return this.add(a,f)},sline:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.uniform([1,0,1]),e.splineDetail=e.splineDetail||this.options("splineDetail"),e.strength=e.strength||1,e.lineWidth=e.lineWidth||4;var f=l.sline(c,this._.gl(),e);return this.add(a,f)},cartoon:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.bySS(),e.strength=e.strength||1,e.splineDetail=e.splineDetail||this.options("splineDetail"),e.arcDetail=e.arcDetail||this.options("arcDetail"),e.radius=e.radius||.3,e.forceTube=e.forceTube||!1;var f=l.cartoon(c,this._.gl(),e),g=this.add(a,f);return g},surface:function(a,b,c){var d=this._ca(c),e=l.surface(b,this._.gl(),d);return this.add(a,e)},tube:function(a,b,c){return c=c||{},c.forceTube=!0,this.cartoon(a,b,c)},ballsAndSticks:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.byElement(),e.radius=e.radius||.3,e.arcDetail=2*(e.arcDetail||this.options("arcDetail")),e.sphereDetail=e.sphereDetail||this.options("sphereDetail");var f=l.ballsAndSticks(c,this._.gl(),e);return this.add(a,f)},lines:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.byElement(),e.lineWidth=e.lineWidth||4;var f=l.lines(c,this._.gl(),e);return this.add(a,f)},points:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.byElement(),e.pointSize=e.pointSize||1;var f=l.points(c,this._.gl(),e);return this.add(a,f)},trace:function(a,c,d){var e=this._R(d,c);e.color=e.color||b.uniform([1,0,0]),e.radius=e.radius||.3,e.arcDetail=2*(e.arcDetail||this.options("arcDetail")),e.sphereDetail=e.sphereDetail||this.options("sphereDetail");var f=l.trace(c,this._.gl(),e);return this.add(a,f)},fitTo:function(a){var b=this._d.mainAxes(),c=[new d.Range,new d.Range,new d.Range];if(a instanceof Q)a.updateProjectionIntervals(b[0],b[1],b[2],c[0],c[1],c[2]);else if(void 0!==a.eachAtom){a.eachAtom(function(a){for(var d=a.pos(),e=0;3>e;++e)c[e].update(v.dot(d,b[e]))});for(var e=0;3>e;++e)c[e].extend(1.5)}this._c9(b,c)},_c9:function(a,b){if(!(b[0].empty()||b[1].empty()||b[2].empty())){var 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a=this._.gl();a.clearColor(0,0,0,0),a.disable(a.BLEND),a.clear(a.COLOR_BUFFER_BIT|a.DEPTH_BUFFER_BIT),a.clearColor(this._b.background[0],this._b.background[1],this._b.background[2],1),a.cullFace(a.FRONT),a.enable(a.CULL_FACE),this._ch("select")},pick:function(a){this._bW.bind(),this._d7();var b=new Uint8Array(4),c=this._.gl();c.readPixels(a.x,this._b.height-a.y,1,1,c.RGBA,c.UNSIGNED_BYTE,b),this._bW.release(),b.data&&(b=b.data);var d=b[0]|b[1]<<8|b[2]<<16,e=b[3],f=this._cL.objectForId(d);if(void 0===f)return null;var g=null;return 255!==e&&(g=f.geom.symWithIndex(e)),new r(f,255>e?e:null,g)},add:function(a,b){return b.name(a),this._l.push(b),this._l.sort(function(a,b){return a.order()-b.order()}),this.requestRedraw(),b},_c3:function(a){var b=a.replace(".","\\.").replace("*",".*");return new RegExp("^"+b+"$")},forEach:function(){var a,b="*";2===arguments.length?(a=arguments[1],b=arguments[0]):a=arguments[0];for(var c=this._c3(b),d=0;d<this._l.length;++d){var e=this._l[d];c.test(e.name())&&a(e,d)}},get:function(a){for(var b=0;b<this._l.length;++b)if(this._l[b].name()===a)return this._l[b];return null},hide:function(a){this.forEach(a,function(a){a.hide()})},show:function(a){this.forEach(a,function(a){a.show()})},rm:function(a){for(var b=[],c=this._c3(a),d=0;d<this._l.length;++d){var e=this._l[d];c.test(e.name())?e.destroy():b.push(e)}this._l=b},all:function(){return this._l},isWebGLSupported:function(){return this._.isWebGLSupported()},destroy:function(){this.clear(),this._.destroy(),this._=null}},s.prototype.on=s.prototype.addListener,{Viewer:function(a,b){return new s(a,b)},isWebGLSupported:e.isWebGLSupported}}(c,e,f,g,h,i,j,k,w,x,y,z),C=function(){function a(a,b){this._j=a||[],this._b2=b||[]}function b(a){this._H=a,this._cb=[]}return a.prototype={addChain:function(a){this._j.push(a)},chains:function(){return this._j},addMatrix:function(a){this._b2.push(a)},matrices:function(){return this._b2},matrix:function(a){return this._b2[a]}},b.prototype={name:function(){return this._H},generators:function(){return this._cb},generator:function(a){return this._cb[a]},addGenerator:function(a){this._cb.push(a)}},{SymGenerator:a,Assembly:b}}(),D=function(){function b(){}function c(a,c,d,e,f,g,h,i){b.call(this),this._t=a,this._cq=[],this._dU=!!g,this._H=c,this._bV=d,this._b7=f,this._be=e,this._dJ=void 0!==h?h:null,this._dx=void 0!==i?i:null}function e(a,c){b.call(this),this._dC=a,this._K=c,this._cq=[]}var f=a.vec3;return b.prototype={bondCount:function(){return this.bonds().length},eachBond:function(a){for(var b=this.bonds(),c=0,d=b.length;d>c;++c)a(b[c])},isConnectedTo:function(a){if(null===a)return!1;for(var b=a.full(),c=this.full(),d=this.bonds(),e=0,f=d.length;f>e;++e){var g=d[e];if(g.atom_one()===c&&g.atom_two()===b||g.atom_one()===b&&g.atom_two()===c)return!0}return!1}},d.derive(c,b,{addBond:function(a){this._cq.push(a)},name:function(){return this._H},bonds:function(){return this._cq},residue:function(){return this._t},structure:function(){return this._t.structure()},full:function(){return this},qualifiedName:function(){return this.residue().qualifiedName()+"."+this.name()},pos:function(){return this._bV},setPos:function(a){f.copy(this._bV,a)},element:function(){return this._be},index:function(){return this._b7},prop:function(a){return this[a]()},occupancy:function(){return this._dJ},tempFactor:function(){return this._dx},isHetatm:function(){return this._dU}}),d.derive(e,b,{full:function(){return this._K},name:function(){return this._K.name()},pos:function(){return this._K.pos()},element:function(){return this._K.element()},residue:function(){return this._dC},bonds:function(){return this._K.bonds()},index:function(){return this._K.index()},occupancy:function(){return this._K.occupancy()},tempFactor:function(){return this._K.tempFactor()},qualifiedName:function(){return this._K.qualifiedName()},isHetatm:function(){return this._K.isHetatm()}}),{Atom:c,AtomView:e}}(),E=function(b){function c(){}function e(a,b,d,e){c.call(this),this._H=b,this._dL=d,this._dW=e,this._C=[],this._cz="C",this._J=a,this._cU=!1,this._cT=!1,this._b7=a.residues().length}function f(a,b){c.call(this),this._ea=a,this._C=[],this._t=b}var g=a.vec3,h=b.Atom,i=b.AtomView;return c.prototype={prop:function(a){return this[a]()},isWater:function(){return"HOH"===this.name()||"DOD"===this.name()},eachAtom:function(a,b){b|=0;for(var c=0;c<this._C.length;c+=1){if(a(this._C[c],b)===!1)return!1;b+=1}return b},qualifiedName:function(){var a=this.chain().name()+"."+this.name()+this.num();return"\x00"===this.insCode()?a:a+this.insCode()},atom:function(a){if("string"==typeof a){for(var b=0;b<this._C.length;++b)if(this._C[b].name()===a)return this._C[b];return null}return a>=this._C.length&&0>a?null:this._C[a]},centralAtom:function(){return this.isAminoacid()?this.atom("CA"):this.isNucleotide()?this.atom("C3'"):null},center:function(){var a=0,b=g.create();return this.eachAtom(function(c){g.add(b,b,c.pos()),a+=1}),a>0&&g.scale(b,b,1/a),b},isAminoacid:function(){return this._cU},isNucleotide:function(){return this._cT}},d.derive(e,c,{_d9:function(){this._cT=null!==this.atom("P")&&null!==this.atom("C3'"),this._cU=null!==this.atom("N")&&null!==this.atom("CA")&&null!==this.atom("C")&&null!==this.atom("O")},name:function(){return this._H},insCode:function(){return this._dW},num:function(){return this._dL},full:function(){return this},addAtom:function(a,b,c,d,e,f){var g=new h(this,a,b,c,this.structure().nextAtomIndex(),d,e,f);return this._C.push(g),g},ss:function(){return this._cz},setSS:function(a){this._cz=a},index:function(){return this._b7},atoms:function(){return this._C},chain:function(){return this._J},structure:function(){return this._J.structure()}}),d.derive(f,c,{addAtom:function(a){var b=new i(this,a.full());this._C.push(b)},full:function(){return this._t},num:function(){return this._t.num()},insCode:function(){return this._t.insCode()},ss:function(){return this._t.ss()},index:function(){return this._t.index()},chain:function(){return this._ea},name:function(){return this._t.name()},atoms:function(){return this._C},qualifiedName:function(){return this._t.qualifiedName()},containsResidue:function(a){return this._t.full()===a.full()},isAminoacid:function(){return this._t.isAminoacid()},isNucleotide:function(){return this._t.isNucleotide()},isWater:function(){return this._t.isWater()}}),{ResidueView:f,Residue:e}}(D),F=function(){function b(){this._s=[]}function c(a,b,c){this._bI=a,this._2=b,this._c4=c,this._b4=0===this._2,this._b5=this._bI.length()===this._c4;var d=this._c4-this._2;this._b5||++d,this._b4||(++d,this._2-=1),this._b3=d}var d=a.vec3;return b.prototype={push:function(a){this._s.push(a)},length:function(){return this._s.length},residueAt:function(a){return this._s[a]},posAt:function(a,b){return d.copy(a,this._s[b].centralAtom().pos()),a},normalAt:function(a,b){var c=this._s[b];return c.isAminoacid()&&d.sub(a,c.atom("O").pos(),c.atom("C").pos()),d.normalize(a,a),a},centralAtomAt:function(a){return this._s[a].centralAtom()},tangentAt:function(){var a=d.create(),b=d.create();return function(c,e){e>0?this.posAt(a,e-1):this.posAt(a,e),e<this._s.length-1?this.posAt(b,e+1):this.posAt(b,e),d.sub(c,b,a)}}(),fullTraceIndex:function(a){return a},subsets:function(a){for(var b=0,d=0,e=[];d<a.length&&b<this._s.length;){for(var f=a[d].full().index();this._s.length>b&&this._s[b].index()<f;)++b;if(b>=this._s.length)break;for(var g=this._s[b].index();a.length>d&&a[d].full().index()<g;)++d;if(d>=a.length)break;for(var h=b;a.length>d&&this._s.length>b&&a[d].full().index()===this._s[b].index();)++d,++b;var i=b;e.push(new c(this,h,i))}return e}},b.prototype.smoothPosAt=b.prototype.posAt,b.prototype.smoothNormalAt=b.prototype.normalAt,c.prototype={length:function(){return this._b3},residueAt:function(a){return this._bI.residueAt(this._2+a)},_cV:function(){var a=d.create(),b=d.create();return function(c,e,f,g){return this.tangentAt(a,e),this.tangentAt(b,f),d.scale(a,a,g),d.scale(b,b,g),l.cubicHermiteInterpolate(c,this.centralAtomAt(e).pos(),a,this.centralAtomAt(f).pos(),b,.5,0),c}}(),smoothPosAt:function(){return function(a,b,c){if(0===b&&!this._b4)return this._cV(a,b,b+1,c);if(b===this._b3-1&&!this._b5)return this._cV(a,b-1,b,c);var e=this.centralAtomAt(b);return d.copy(a,e.pos()),a}}(),smoothNormalAt:function(){return function(a,b){return this._bI.normalAt(a,b+this._2),a}}(),posAt:function(a,b){var c=this.centralAtomAt(b),e=null;return d.copy(a,c.pos()),0!==b||this._b4||(e=this.centralAtomAt(b+1),d.add(a,a,e.pos()),d.scale(a,a,.5)),b!==this._b3-1||this._b5||(e=this.centralAtomAt(b-1),d.add(a,a,e.pos()),d.scale(a,a,.5)),a},centralAtomAt:function(a){return this.residueAt(a).centralAtom()},fullTraceIndex:function(a){return this._2+a},tangentAt:function(a,b){return this._bI.tangentAt(a,b+this._2)}},{TraceSubset:c,BackboneTrace:b}}(),G=function(b,c){function e(a,b){return a<<8|b.charCodeAt(0)}function f(a,b){return a.num()<b.num()}function g(a){return{num:function(){return a}}}function h(){}function i(a,b){h.call(this),this._i=a,this._H=b,this._bh=[],this._q=[],this._0=!0}function j(a,b,c){var d,e;if(a?(d=b.atom("C"),e=c.atom("N")):(d=b.atom("O3'"),e=c.atom("P")),d.isConnectedTo(e))return!1;var f=n.sqrDist(d.pos(),e.pos());return Math.abs(f-2.25)>1}function k(a,b){b.length()<2||a.push(b)}function l(a,b,c){if(0===a.length)return!0;if(!b)return!1;var d=e(c.num(),c.insCode()),f=a[a.length-1],g=e(f.num(),f.insCode());return d>g}function m(a,b){h.call(this),this._J=b,this._q=[],this._dS=a,this._cD={},this._0=!0}var n=a.vec3,o=b.Residue,p=b.ResidueView;return h.prototype={eachAtom:function(a,b){b|=0;for(var c=0;c<this._q.length;c+=1)if(b=this._q[c].eachAtom(a,b),b===!1)return!1;return b},atomCount:function(){for(var a=0,b=this.residues(),c=0;c<b.length;++c)a+=b[c].atoms().length;return a},eachResidue:function(a){for(var b=0;b<this._q.length;b+=1)if(a(this._q[b])===!1)return!1},residues:function(){return this._q},structure:function(){return this._i},asView:function(){var a=this.structure().createEmptyView();return a.addChain(this,!0),a},residueByRnum:function(a){var b=this.residues();if(this._0){var c=d.binarySearch(b,g(a),f);return-1===c?null:b[c]}for(var e=0;e<b.length;++e)if(b[e].num()===a)return b[e];return null},residuesInRnumRange:function(a,b){var c,e,h=[],i=this.residues();if(this._0===!0){var j=d.indexFirstLargerEqualThan(i,g(a),f);if(-1===j)return h;var k=d.indexLastSmallerEqualThan(i,g(b),f);if(-1===k)return h;for(c=j;k>=c;++c)h.push(this._q[c])}else for(c=0,e=i.length;c!==e;++c){var l=i[c];l.num()>=a&&l.num()<=b&&h.push(l)}return h},prop:function(a){return this[a]()}},d.derive(i,h,{name:function(){return this._H},full:function(){return 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c=0;c<this._j.length;c+=1)if(b=this._j[c].eachAtom(a,b),b===!1)return!1},residueCount:function(){for(var a=this.chains(),b=0,c=0;c<a.length;++c)b+=a[c].residues().length;return b},eachChain:function(a){for(var b=this.chains(),c=0;c<b.length;++c)if(a(b[c])===!1)return},atomCount:function(){for(var a=this.chains(),b=0,c=0;c<a.length;++c)b+=a[c].atomCount();return b},atoms:function(){var a=[];return this.eachAtom(function(b){a.push(b)}),a},atom:function(a){var b=a.split("."),c=this.chain(b[0]);if(null===c)return null;var d=c.residueByRnum(parseInt(b[1],10));return null===d?null:d.atom(b[2])},center:function(){var a=m.create(),b=0;return this.eachAtom(function(c){m.add(a,a,c.pos()),b+=1}),b&&m.scale(a,a,1/b),a},boundingSphere:function(){var a=this.center(),b=0;return this.eachAtom(function(c){b=Math.max(b,m.sqrDist(a,c.pos()))}),new l.Sphere(a,Math.sqrt(b))},backboneTraces:function(){for(var a=this.chains(),b=[],c=0;c<a.length;++c)Array.prototype.push.apply(b,a[c].backboneTraces());return b},select:function(a){return"protein"===a?this.residueSelect(function(a){return a.isAminoacid()}):"water"===a?this.residueSelect(function(a){return a.isWater()}):"ligand"===a?this.residueSelect(function(a){return!a.isAminoacid()&&!a.isWater()}):e.dict(this,new k(this),a||{})},residueSelect:function(a){for(var b=new k(this.full()),c=0;c<this._j.length;++c)for(var d=this._j[c],e=null,f=d.residues(),g=0;g<f.length;++g)a(f[g])&&(e||(e=b.addChain(d,!1)),e.addResidue(f[g],!0));return b},atomSelect:function(a){for(var b=new k(this.full()),c=0;c<this._j.length;++c)for(var d=this._j[c],e=null,f=d.residues(),g=0;g<f.length;++g)for(var h=null,i=f[g],j=i.atoms(),l=0;l<j.length;++l)a(j[l])&&(e||(e=b.addChain(d,!1)),h||(h=e.addResidue(i,!1)),h.addAtom(j[l]));return b},assembly:function(a){for(var b=this.assemblies(),c=0;c<b.length;++c)if(b[c].name()===a)return b[c];return null},chainsByName:function(a){for(var b={},c=this.chains(),d=0;d<c.length;++d)b[c[d].name()]=c[d];for(var e=[],f=0;f<a.length;++f){var g=b[a[f]];void 0!==g&&e.push(g)}return e},selectWithin:function(){var a=m.create();return function(b,c){c=c||{};var d=c.radius||4,e=d*d,f=!!c.matchResidues,g=[];b.eachAtom(function(a){g.push(a)});for(var h=new k(this.full()),i=null,j=null,l=this.chains(),n=!1,o=0;o<l.length;++o){var p=l[o].residues();j=null;for(var q=0;q<p.length;++q){i=null,n=!1;for(var r=p[q].atoms(),s=0;s<r.length&&!n;++s)for(var t=0;t<g.length;++t)if(m.sub(a,r[s].pos(),g[t].pos()),!(m.sqrLen(a)>e)){if(j||(j=h.addChain(l[o].full(),!1)),i||(i=j.addResidue(p[q].full(),f)),f){n=!0;break}i.addAtom(r[s].full());break}}}return h}}(),createEmptyView:function(){return new k(this.full())}},d.derive(j,i,{addAssembly:function(a){this._N.push(a)},setAssemblies:function(a){this._N=a},assemblies:function(){return this._N},chains:function(){return this._j},full:function(){return this},containsResidue:function(a){return a.full().structure()===this},chainByName:function(a){for(var b=0;b<this._j.length;++b)if(this._j[b].name()===a)return this._j[b];return null},chain:function(a){return this.chainByName(a)},nextAtomIndex:function(){var a=this._cM;return this._cM+=1,a},addChain:function(a){var b=new n(this,a);return this._j.push(b),b},connect:function(a,b){var c=new p(a,b);return a.addBond(c),b.addBond(c),c},deriveConnectivity:function(){var a=this,b=null;this.eachResidue(function(c){for(var d,e=c.atoms(),i=e.length,j=0;i>j;j+=1)for(var k=e[j],l=k.pos(),n=f(k.element()),o=0;j>o;o+=1){var p=e[o],q=f(p.element());d=m.sqrDist(l,p.pos());var r=n+q-.3,s=n+q+.3;s*s>d&&d>r*r&&a.connect(k,p)}c._d9(),null!==b&&(c.isAminoacid()&&b.isAminoacid()&&g(a,b,c),c.isNucleotide()&&b.isNucleotide()&&h(a,b,c)),b=c})}}),d.derive(k,i,{full:function(){return this._cO},assemblies:function(){return this._cO.assemblies()},addChain:function(a,b){var c=new o(this,a.full());if(this._j.push(c),b)for(var d=a.residues(),e=0;e<d.length;++e)c.addResidue(d[e],!0);return c},containsResidue:function(a){if(!a)return!1;var b=this.chain(a.chain().name());return b?b.containsResidue(a):!1},chains:function(){return this._j},chain:function(a){for(var b=0;b<this._j.length;++b)if(this._j[b].name()===a)return this._j[b];return null}}),{MolView:k,Mol:j}}(G,H,I),K=function(){function a(a){function b(a,b){return a=Math.abs(a),b=Math.abs(b),a>b?a*Math.sqrt(1+b*b/a/a):0==b?a:b*Math.sqrt(1+a*a/b/b)}var c,d=Math.pow(2,-52),e=1e-64/d,f=50,g=0,h=0,i=0,j=0,k=0,l=a,m=l.length,n=l[0].length;if(n>m)throw"Need more rows than columns";var o=new Array(n),p=new Array(n);for(h=0;n>h;h++)o[h]=p[h]=0;for(var q=[],h=0;n>h;++h){var r=[];q.push([]);for(var i=0;n>i;++i)r.push(0);q.push(r)}var s=0,t=0,u=0,v=0,w=0,x=0,y=0;for(h=0;n>h;h++){for(o[h]=t,y=0,k=h+1,i=h;m>i;i++)y+=l[i][h]*l[i][h];if(e>=y)t=0;else 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A=!1;for(k=j;-1!=k;k+=-1){if(Math.abs(o[k])<=d){A=!0;break}if(Math.abs(p[k-1])<=d)break}if(!A){g=0,y=1;var B=k-1;for(h=k;j+1>h&&(s=y*o[h],o[h]=g*o[h],!(Math.abs(s)<=d));h++)for(t=p[h],u=b(s,t),p[h]=u,g=t/u,y=-s/u,i=0;m>i;i++)w=l[i][B],x=l[i][h],l[i][B]=w*g+x*y,l[i][h]=-w*y+x*g}if(x=p[j],k==j){if(0>x)for(p[j]=-x,i=0;n>i;i++)q[i][j]=-q[i][j];break}if(z>=f-1)throw"Error: no 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