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3dmol

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Object oriented Javascript molecular visualization library

3dmol.csb.pitt.edu

dkoes/3Dmol.js

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1
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e;ne--,se+=ee[re++]<<le,le+=8}if(r.nlen=257+(31&se),se>>>=5,le-=5,r.ndist=1+(31&se),se>>>=5,le-=5,r.ncode=4+(15&se),se>>>=4,le-=4,r.nlen>286||r.ndist>30){e.msg="too many length or distance symbols",r.mode=Q;break}r.have=0,r.mode=V;case V:for(;r.have<r.ncode;){for(;le<3;){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}r.lens[_e[r.have++]]=7&se,se>>>=3,le-=3}for(;r.have<19;)r.lens[_e[r.have++]]=0;if(r.lencode=r.lendyn,r.lenbits=7,Ae={bits:r.lenbits},De=s(l,r.lens,0,19,r.lencode,0,r.work,Ae),r.lenbits=Ae.bits,De){e.msg="invalid code lengths set",r.mode=Q;break}r.have=0,r.mode=U;case U:for(;r.have<r.nlen+r.ndist;){for(;ve=(Ce=r.lencode[se&(1<<r.lenbits)-1])>>>16&255,ge=65535&Ce,!((pe=Ce>>>24)<=le);){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}if(ge<16)se>>>=pe,le-=pe,r.lens[r.have++]=ge;else{if(16===ge){for($e=pe+2;le<$e;){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}if(se>>>=pe,le-=pe,0===r.have){e.msg="invalid bit length 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j:for(;ve=(Ce=r.distcode[se&(1<<r.distbits)-1])>>>16&255,ge=65535&Ce,!((pe=Ce>>>24)<=le);){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}if(0==(240&ve)){for(ye=pe,be=ve,xe=ge;ve=(Ce=r.distcode[xe+((se&(1<<ye+be)-1)>>ye)])>>>16&255,ge=65535&Ce,!(ye+(pe=Ce>>>24)<=le);){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}se>>>=ye,le-=ye,r.back+=ye}if(se>>>=pe,le-=pe,r.back+=pe,64&ve){e.msg="invalid distance code",r.mode=Q;break}r.offset=ge,r.extra=15&ve,r.mode=H;case H:if(r.extra){for($e=r.extra;le<$e;){if(0===ne)break e;ne--,se+=ee[re++]<<le,le+=8}r.offset+=se&(1<<r.extra)-1,se>>>=r.extra,le-=r.extra,r.back+=r.extra}if(r.offset>r.dmax){e.msg="invalid distance too far back",r.mode=Q;break}r.mode=W;case W:if(0===ae)break e;if(ue=he-ae,r.offset>ue){if((ue=r.offset-ue)>r.whave&&r.sane){e.msg="invalid distance too far back",r.mode=Q;break}ue>r.wnext?(ue-=r.wnext,de=r.wsize-ue):de=r.wnext-ue,ue>r.length&&(ue=r.length),me=r.window}else 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o.Buf8(a.wsize)),i>=a.wsize?(o.arraySet(a.window,t,r-a.wsize,a.wsize,0),a.wnext=0,a.whave=a.wsize):((n=a.wsize-a.wnext)>i&&(n=i),o.arraySet(a.window,t,r-i,n,a.wnext),(i-=n)?(o.arraySet(a.window,t,r-i,i,0),a.wnext=i,a.whave=a.wsize):(a.wnext+=n,a.wnext===a.wsize&&(a.wnext=0),a.whave<a.wsize&&(a.whave+=n))),0}(e,e.output,e.next_out,he-e.avail_out)?(r.mode=K,b):(ce-=e.avail_in,he-=e.avail_out,e.total_in+=ce,e.total_out+=he,r.total+=he,r.wrap&&he&&(e.adler=r.check=r.flags?n(r.check,te,he,e.next_out-he):i(r.check,te,he,e.next_out-he)),e.data_type=r.bits+(r.last?64:0)+(r.mode===F?128:0)+(r.mode===N||r.mode===R?256:0),(0===ce&&0===he||t===u)&&De===m&&(De=x),De)},r.inflateEnd=function(e){if(!e||!e.state)return g;var t=e.state;return t.window&&(t.window=null),e.state=null,m},r.inflateGetHeader=function(e,t){var r;return e&&e.state?0==(2&(r=e.state).wrap)?g:(r.head=t,t.done=!1,m):g},r.inflateInfo="pako inflate (from Nodeca 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c[h++]=20971520,c[h++]=20971520,f.bits=1,0;for(C=1;C<S&&0===P[C];C++);for(_<C&&(_=C),L=1,A=1;A<=15;A++)if(L<<=1,(L-=P[A])<0)return-1;if(L>0&&(0===e||1!==S))return-1;for(R[1]=0,A=1;A<15;A++)R[A+1]=R[A]+P[A];for($=0;$<l;$++)0!==t[r+$]&&(u[R[t[r+$]]++]=$);if(0===e?(F=O=u,y=19):1===e?(F=i,I-=257,O=n,k-=257,y=256):(F=a,O=s,y=-1),E=0,$=0,A=C,g=h,M=_,z=0,p=-1,v=(T=1<<_)-1,1===e&&T>852||2===e&&T>592)return 1;for(;;){0,b=A-z,u[$]<y?(x=0,w=u[$]):u[$]>y?(x=O[k+u[$]],w=F[I+u[$]]):(x=96,w=0),d=1<<A-z,C=m=1<<M;do{c[g+(E>>z)+(m-=d)]=b<<24|x<<16|w|0}while(0!==m);for(d=1<<A-1;E&d;)d>>=1;if(0!==d?(E&=d-1,E+=d):E=0,$++,0==--P[A]){if(A===S)break;A=t[r+u[$]]}if(A>_&&(E&v)!==p){for(0===z&&(z=_),g+=C,L=1<<(M=A-z);M+z<S&&!((L-=P[M+z])<=0);)M++,L<<=1;if(T+=1<<M,1===e&&T>852||2===e&&T>592)return 1;c[p=E&v]=_<<24|M<<16|g-h|0}}return 0!==E&&(c[g+E]=A-z<<24|64<<16|0),f.bits=_,0}},{"../utils/common":1}],10:[function(e,t,r){"use strict";t.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"}},{}],11:[function(e,t,r){"use strict";t.exports=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg="",this.state=null,this.data_type=2,this.adler=0}},{}],"/lib/inflate.js":[function(e,t,r){"use strict";var o=e("./zlib/inflate.js"),i=e("./utils/common"),n=e("./utils/strings"),a=e("./zlib/constants"),s=e("./zlib/messages"),l=e("./zlib/zstream"),c=e("./zlib/gzheader"),h=Object.prototype.toString,u=function(e){this.options=i.assign({chunkSize:16384,windowBits:0,to:""},e||{});var t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&0==(15&t.windowBits)&&(t.windowBits|=15),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new l,this.strm.avail_out=0;var r=o.inflateInit2(this.strm,t.windowBits);if(r!==a.Z_OK)throw new Error(s[r]);this.header=new c,o.inflateGetHeader(this.strm,this.header)};function f(e,t){var r=new u(t);if(r.push(e,!0),r.err)throw r.msg;return r.result}u.prototype.push=function(e,t){var r,s,l,c,u,f=this.strm,d=this.options.chunkSize;if(this.ended)return!1;s=t===~~t?t:!0===t?a.Z_FINISH:a.Z_NO_FLUSH,"string"==typeof e?f.input=n.binstring2buf(e):"[object ArrayBuffer]"===h.call(e)?f.input=new Uint8Array(e):f.input=e,f.next_in=0,f.avail_in=f.input.length;do{if(0===f.avail_out&&(f.output=new i.Buf8(d),f.next_out=0,f.avail_out=d),(r=o.inflate(f,a.Z_NO_FLUSH))!==a.Z_STREAM_END&&r!==a.Z_OK)return this.onEnd(r),this.ended=!0,!1;f.next_out&&(0!==f.avail_out&&r!==a.Z_STREAM_END&&(0!==f.avail_in||s!==a.Z_FINISH&&s!==a.Z_SYNC_FLUSH)||("string"===this.options.to?(l=n.utf8border(f.output,f.next_out),c=f.next_out-l,u=n.buf2string(f.output,l),f.next_out=c,f.avail_out=d-c,c&&i.arraySet(f.output,f.output,l,c,0),this.onData(u)):this.onData(i.shrinkBuf(f.output,f.next_out))))}while(f.avail_in>0&&r!==a.Z_STREAM_END);return r===a.Z_STREAM_END&&(s=a.Z_FINISH),s===a.Z_FINISH?(r=o.inflateEnd(this.strm),this.onEnd(r),this.ended=!0,r===a.Z_OK):s!==a.Z_SYNC_FLUSH||(this.onEnd(a.Z_OK),f.avail_out=0,!0)},u.prototype.onData=function(e){this.chunks.push(e)},u.prototype.onEnd=function(e){e===a.Z_OK&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=i.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg},r.Inflate=u,r.inflate=f,r.inflateRaw=function(e,t){return(t=t||{}).raw=!0,f(e,t)},r.ungzip=f},{"./utils/common":1,"./utils/strings":2,"./zlib/constants":4,"./zlib/gzheader":6,"./zlib/inflate.js":8,"./zlib/messages":10,"./zlib/zstream":11}]},{},[])("/lib/inflate.js")}),function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t():"function"==typeof define&&define.amd?define("netcdfjs",[],t):"object"==typeof exports?exports.netcdfjs=t():e.netcdfjs=t()}(this,function(){return function(e){var t={};function r(o){if(t[o])return t[o].exports;var i=t[o]={i:o,l:!1,exports:{}};return e[o].call(i.exports,i,i.exports,r),i.l=!0,i.exports}return r.m=e,r.c=t,r.i=function(e){return e},r.d=function(e,t,o){r.o(e,t)||Object.defineProperty(e,t,{configurable:!1,enumerable:!0,get:o})},r.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return r.d(t,"a",t),t},r.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},r.p="",r(r.s=6)}([function(e,t,r){"use strict";function o(e){e.offset%4!=0&&e.skip(4-e.offset%4)}e.exports.notNetcdf=function(e,t){if(e)throw new TypeError("Not a valid NetCDF v3.x file: "+t)},e.exports.padding=o,e.exports.readName=function(e){var t=e.readUint32(),r=e.readChars(t);return o(e),r}},function(e,t,r){"use strict";const o=r(0).notNetcdf,i={BYTE:1,CHAR:2,SHORT:3,INT:4,FLOAT:5,DOUBLE:6};function n(e,t){if(1!==e){for(var r=new Array(e),o=0;o<e;o++)r[o]=t();return r}return t()}e.exports=i,e.exports.num2str=function(e){switch(Number(e)){case i.BYTE:return"byte";case i.CHAR:return"char";case i.SHORT:return"short";case i.INT:return"int";case i.FLOAT:return"float";case i.DOUBLE:return"double";default:return"undefined"}},e.exports.num2bytes=function(e){switch(Number(e)){case i.BYTE:case i.CHAR:return 1;case i.SHORT:return 2;case i.INT:case i.FLOAT:return 4;case i.DOUBLE:return 8;default:return-1}},e.exports.str2num=function(e){switch(String(e)){case"byte":return i.BYTE;case"char":return i.CHAR;case"short":return i.SHORT;case"int":return i.INT;case"float":return i.FLOAT;case"double":return i.DOUBLE;default:return-1}},e.exports.readType=function(e,t,r){switch(t){case i.BYTE:return e.readBytes(r);case i.CHAR:return 0===(a=e.readChars(r)).charCodeAt(a.length-1)?a.substring(0,a.length-1):a;case i.SHORT:return n(r,e.readInt16.bind(e));case i.INT:return n(r,e.readInt32.bind(e));case i.FLOAT:return n(r,e.readFloat32.bind(e));case i.DOUBLE:return n(r,e.readFloat64.bind(e));default:return void o(!0,"non valid type "+t)}var a}},function(e,t){var r;r=function(){return this}();try{r=r||Function("return this")()||(0,eval)("this")}catch(e){"object"==typeof window&&(r=window)}e.exports=r},function(e,t,r){"use strict";const o=r(1);e.exports.nonRecord=function(e,t){const r=o.str2num(t.type);for(var i=t.size/o.num2bytes(r),n=new Array(i),a=0;a<i;a++)n[a]=o.readType(e,r,1);return n},e.exports.record=function(e,t,r){const i=o.str2num(t.type),n=t.size?t.size/o.num2bytes(i):1;var a=r.length,s=new Array(a);const l=r.recordStep;for(var c=0;c<a;c++){var h=e.offset;s[c]=o.readType(e,i,n),e.seek(h+l)}return s}},function(e,t,r){"use strict";const o=r(0),i=r(1),n=0,a=10,s=11,l=12;function c(e){const t=e.readUint32();if(t===n)return o.notNetcdf(e.readUint32()!==n,"wrong empty tag for list of attributes"),[];{o.notNetcdf(t!==l,"wrong tag for list of attributes");const n=e.readUint32();for(var r=new Array(n),a=0;a<n;a++){var s=o.readName(e),c=e.readUint32();o.notNetcdf(c<1||c>6,"non valid type "+c);var h=e.readUint32(),u=i.readType(e,c,h);o.padding(e),r[a]={name:s,type:i.num2str(c),value:u}}}return r}e.exports=function(e,t){var r={recordDimension:{length:e.readUint32()}};r.version=t;var l=function(e){var t,r;const i=e.readUint32();if(i===n)return o.notNetcdf(e.readUint32()!==n,"wrong empty tag for list of dimensions"),[];{o.notNetcdf(i!==a,"wrong tag for list of dimensions");const n=e.readUint32();for(var s=new Array(n),l=0;l<n;l++){var c=o.readName(e);const i=e.readUint32();0===i&&(t=l,r=c),s[l]={name:c,size:i}}}return{dimensions:s,recordId:t,recordName:r}}(e);r.recordDimension.id=l.recordId,r.recordDimension.name=l.recordName,r.dimensions=l.dimensions,r.globalAttributes=c(e);var h=function(e,t,r){const a=e.readUint32();var l=0;if(a===n)return o.notNetcdf(e.readUint32()!==n,"wrong empty tag for list of variables"),[];{o.notNetcdf(a!==s,"wrong tag for list of variables");const n=e.readUint32();for(var h=new Array(n),u=0;u<n;u++){var f=o.readName(e);const n=e.readUint32();for(var d=new Array(n),m=0;m<n;m++)d[m]=e.readUint32();var p=c(e),v=e.readUint32();o.notNetcdf(v<1&&v>6,"non valid type "+v);const a=e.readUint32();var g=e.readUint32();2===r&&(o.notNetcdf(g>0,"offsets larger than 4GB not supported"),g=e.readUint32()),d[0]===t&&(l+=a),h[u]={name:f,dimensions:d,attributes:p,type:i.num2str(v),size:a,offset:g,record:d[0]===t}}}return{variables:h,recordStep:l}}(e,l.recordId,t);return r.variables=h.variables,r.recordDimension.recordStep=h.recordStep,r}},function(e,t,r){"use strict";(function(t){const o=r(11),i=8192,n=[];e.exports=class{constructor(e,t){t=t||{};var r=!1;void 0===e&&(e=i),"number"==typeof e?e=new ArrayBuffer(e):(r=!0,this._lastWrittenByte=e.byteLength);const o=t.offset?t.offset>>>0:0;let n=e.byteLength-o,a=o;e.buffer&&(e.byteLength!==e.buffer.byteLength&&(a=e.byteOffset+o),e=e.buffer),this._lastWrittenByte=r?n:0,this.buffer=e,this.length=n,this.byteLength=n,this.byteOffset=a,this.offset=0,this.littleEndian=!0,this._data=new 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t=this.readChars(e);return o.decode(t)}writeBoolean(e){return this.writeUint8(e?255:0),this}writeInt8(e){return this.ensureAvailable(1),this._data.setInt8(this.offset++,e),this._updateLastWrittenByte(),this}writeUint8(e){return this.ensureAvailable(1),this._data.setUint8(this.offset++,e),this._updateLastWrittenByte(),this}writeByte(e){return this.writeUint8(e)}writeBytes(e){this.ensureAvailable(e.length);for(var t=0;t<e.length;t++)this._data.setUint8(this.offset++,e[t]);return this._updateLastWrittenByte(),this}writeInt16(e){return this.ensureAvailable(2),this._data.setInt16(this.offset,e,this.littleEndian),this.offset+=2,this._updateLastWrittenByte(),this}writeUint16(e){return this.ensureAvailable(2),this._data.setUint16(this.offset,e,this.littleEndian),this.offset+=2,this._updateLastWrittenByte(),this}writeInt32(e){return this.ensureAvailable(4),this._data.setInt32(this.offset,e,this.littleEndian),this.offset+=4,this._updateLastWrittenByte(),this}writeUint32(e){return this.ensureAvailable(4),this._data.setUint32(this.offset,e,this.littleEndian),this.offset+=4,this._updateLastWrittenByte(),this}writeFloat32(e){return this.ensureAvailable(4),this._data.setFloat32(this.offset,e,this.littleEndian),this.offset+=4,this._updateLastWrittenByte(),this}writeFloat64(e){return this.ensureAvailable(8),this._data.setFloat64(this.offset,e,this.littleEndian),this.offset+=8,this._updateLastWrittenByte(),this}writeChar(e){return this.writeUint8(e.charCodeAt(0))}writeChars(e){for(var t=0;t<e.length;t++)this.writeUint8(e.charCodeAt(t));return this}writeUtf8(e){const t=o.encode(e);return this.writeChars(t)}toArray(){return new Uint8Array(this.buffer,this.byteOffset,this._lastWrittenByte)}getBuffer(){return void 0!==t?t.from(this.toArray()):this.toArray()}_updateLastWrittenByte(){this.offset>this._lastWrittenByte&&(this._lastWrittenByte=this.offset)}}}).call(t,r(8).Buffer)},function(e,t,r){"use strict";const 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