@datagrok/sequence-translator 1.2.5 → 1.2.6

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Files changed (6) hide show
  1. package/CHANGELOG.md +7 -0
  2. package/dist/package.js +1 -1
  3. package/dist/package.js.map +1 -1
  4. package/package.json +1 -1
  5. package/src/model/structure-app/mol-transformations.ts +2 -2
  6. package/src/model/structure-app/sequence-to-molfile.ts +1 -1
package/CHANGELOG.md CHANGED
@@ -1,5 +1,12 @@
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  # Sequence Translator changelog
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+ ## 1.2.6 (2024-01-29)
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+
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+ ### Bug fixes
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+
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+ * Fixed column input in Pattern
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+ * Fixed whitespaces in molfiles
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+
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  ## 1.2.0 (2023-10-27)
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  ### Features
package/dist/package.js CHANGED
@@ -1,2 +1,2 @@
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- var sequencetranslator;(()=>{"use strict";var t={622:(t,e,n)=>{n.d(e,{w:()=>r});class o{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const o=this.isWhitespace(n)?e:e-1;for(let t=0;t<o;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let o=0;o<t;o++)n=this.shiftIdxToAtomType(n),e[o]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let o=this.getAtomBlockIdx();for(let r=0;r<this.atomCount;r++){o=this.shiftIdxToXColumn(o);for(const i of[t,e,n])i[r]=this.parseFloatValue(o),o=this.getNextColumnIdx(o);o=this.getNextLineIdx(o)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const o=new Uint16Array(2);o[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),o[1]=this.parseIntValue(e),t[n]=o,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let o=0;o<t;o++)n=this.shiftIdxToBondType(n),e[o]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class r extends o{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let o=0;o<e;o++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}},577:(t,e,n)=>{n.d(e,{u:()=>r});var o=n(622);class r extends o.w{constructor(t){super(t),this.init(t)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static validate(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M 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l=Object.keys(s.Rv).concat([o.NI.HELM]);if(!t||-1!==e&&n!==o.NI.HELM)return{};if(!l.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const c=l.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),u=new i.I(t,n),d=Object.fromEntries(c.map((t=>{let e;try{e=u.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),h=function(t,e){const n=new RegExp("\\([^()]*\\)","g"),i=t.match(n);if(!i)return null;return i.map((t=>{const n=t.replace(/[\[\]()]/g,"");return o.mc.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||r.s8)).join("")}(n===o.NI.HELM?t:d[o.NI.HELM],a.A.getInstance());return h&&(d.Nucleotides=h),d}},456:(t,e,n)=>{n.d(e,{I:()=>u});var o=n(29),r=n(544),i=n(996);const s=(t,e)=>e.length-t.length;class a{constructor(){this.formats=this.getFormats()}formats;getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const o=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[o]?e[o]=[t]:e[o].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const o=n.sort(s);e[t]=o[0]})),e}(i.Rv[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=i.Rv[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(s)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(l(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=i.Rv[t],n=l(Array.from(new Set(Object.values(e[r.DD.LINKAGE]))).sort(s));return new RegExp(`${r.$3}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(i.Rv)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===o.NI.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(s)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(l(e)+"|\\([^()]*\\)|.","g")}}function l(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const c={LEFT:"RNA1{",RIGHT:"}$$$$"};class u{sequence;sourceFormat;constructor(t,e){this.sequence=t,this.sourceFormat=e}formats=new a;convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===o.NI.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===o.NI.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(l(Object.values(c)),"g");let o=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),s=this.formats.getTargetFormatHelmCodes(e),a=this.formats.getTargetFormatHelmCodesRegExp(e);return o=o.replace(a,(t=>s.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,r.s8).replace(/p\.|\./g,""),o=o.replace(/<empty>/g,""),o=o.replace(/\/\//g,"/"),o}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),o=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),s=this.formats.getPhosphateHelmCodesRegExp(e);let a=t.replace(i,(t=>o.includes(t)?n[t]+".":"?"));return a=a.replace(/\?+/g,`${r.s8}.`),a=a.slice(0,-1),a[a.length-1]===r.$3&&(a=a.slice(0,-1)),a=a.replace(s,((t,e)=>e)),a=a.replace(/<empty>/g,""),`${c.LEFT+a+c.RIGHT}`}}},593:(t,e,n)=>{n.r(e),n.d(e,{_package:()=>pe,demoOligoPattern:()=>Oe,demoOligoStructure:()=>Ie,demoTranslateSequence:()=>Ee,getCodeToWeightsMap:()=>Ce,getMolfileFromGcrsSequence:()=>we,initSequenceTranslatorLibData:()=>xe,linkStrands:()=>ye,oligoPatternApp:()=>Ae,oligoStructureApp:()=>ve,oligoToolkitApp:()=>ge,oligoTranslatorApp:()=>fe,translateOligonucleotideSequence:()=>Se,validateSequence:()=>be});var o=n(976),r=n(469);const i=ui,s=rxjs;var a=n(379),l=n.n(a),c=n(795),u=n.n(c),d=n(569),h=n.n(d),p=n(565),m=n.n(p),g=n(216),f=n.n(g),A=n(589),v=n.n(A),x=n(602),C={};C.styleTagTransform=v(),C.setAttributes=m(),C.insert=h().bind(null,"head"),C.domAPI=u(),C.insertStyleElement=f(),l()(x.Z,C),x.Z&&x.Z.locals&&x.Z.locals;var b=n(947),w=n(669),y=n(29),E=n(559),O=n(996);class I{sequence;constructor(t){this.sequence=t,this.libWrapper=E.A.getInstance(),this.formats=Object.keys(O.Rv)}libWrapper;formats;getFormat(){if(this.sequence.startsWith("RNA"))return y.NI.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=new b.b(this.sequence),n=Array(t.length).fill(0);for(let o=0;o<t.length;++o){const r=t[o];n[o]=e.getInvalidCodeIndex(r)}const o=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(o)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence;let e=[];for(const n of this.formats){let o=(0,w.xB)(this.libWrapper.getCodesByFormat(n)),r=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){r=e+1;break}o.some((e=>e===t.slice(r,r+e.length)))&&e.push(n)}return e}}const S=$;var T=n.n(S);function M(t){let e=0;const n=new I(t).getFormat();null!==n&&(e=new b.b(t).getInvalidCodeIndex(n));const o=e<0||""===t,r=i.span([]);T()(r).css("-webkit-text-fill-color","var(--grey-6)");const s=i.span([]);return T()(s).css("-webkit-text-fill-color","red"),o?r.innerHTML=t:(r.innerHTML=t.slice(0,e),s.innerHTML=t.slice(e)),[r,s]}var B=n(490),N={};N.styleTagTransform=v(),N.setAttributes=m(),N.insert=h().bind(null,"head"),N.domAPI=u(),N.insertStyleElement=f(),l()(B.Z,N),B.Z&&B.Z.locals&&B.Z.locals;class L{textInputBase;painter;constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,T()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{T()(this.textArea).css("height",0),T()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=i.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged((()=>this.colorize()))}highlights;get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}var D=n(900);class F{sequence;codeMap;constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,o)=>{const r=this.getSymbolForCode(n);o>0&&function(t){return O.iA.left.includes(t)}(r)&&e.pop(),e.push(r);const i=V(r),s=o===t.length-1,a=o+1<t.length&&V(this.getSymbolForCode(t[o+1]));i||function(t){return O.iA.right.includes(t)}(r)||a||s||e.push(D.$)})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??=t,e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const o=t.find((t=>t===this.sequence.substring(n,n+t.length)));e.push(o),n+=o.length}return e}getAllCodesOfFormat(){let t=Array.from(this.codeMap.keys());return(0,w.xB)(t)}}function V(t){return O.iA.phosphate.includes(t)}class k{invert;constructor(t,e=!1,n){this.invert=e,this.lib=E.A.getInstance();const o=this.lib.getCodeToSymbolMap(n);this.parser=new F(t,o)}parser;lib;convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const o=this.getMonomerMolfile(t,n);e.push(o)}));let n=this.getPolymerMolfile(e);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(t){const e=t.indexOf("M V30 BEGIN BOND"),n=t.indexOf("M V30 END BOND");let o=t.substring(e,n);return o=o.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${e}3`:"3"===n?`${e}1`:t)),t.substring(0,e)+o+t.substring(n)}getMonomerMolfile(t,e){const n=this.lib.getMolfileBySymbol(t);return this.lib.isModification(t)?0===e?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(t){return this.linkV3000(t)}reflect(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n),i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;for(let t=0;t<n;t++)e.x[t]=-e.x[t];const a=e.x[o];for(let t=0;t<n;t++)e.x[t]-=a;let l=t.indexOf("M V30 BEGIN ATOM");l=t.indexOf("\n",l);let c=l;for(let o=0;o<n;o++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,c=t.indexOf(" ",l)+1,c=t.indexOf(" ",c),l=(t=t.slice(0,l)+e.x[o]+" "+e.y[o]+t.slice(c)).indexOf("\n",l)+1;return t}extractAtomDataV3000(t){const e=this.extractAtomsBondsNumbersV3000(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let o=n;const r=Array(e.natom),i=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let l=0;l<e.natom;l++)n=t.indexOf("V30",n)+4,o=t.indexOf(" ",n),r[l]=parseInt(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),i[l]=t.substring(n,o),n=o+1,o=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,o)),n=t.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}extractAtomsBondsNumbersV3000(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const o=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:o,nbond:parseInt(t.substring(e,n))}}rotateNucleotidesV3000(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,o,r);const i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;let a=0;if(0===e.x[o])a=e.y[o]>e.y[r]?Math.PI/2:3*Math.PI/2;else if(0===e.y[o])a=e.x[o]>e.x[r]?Math.PI:0;else{const t=e.y[o]/e.x[o];a=t>0?e.x[o]>0?Math.PI-Math.atan(t):2*Math.PI-Math.atan(t):e.x[o]>0?-Math.PI-Math.atan(t):Math.atan(t)}const l=Math.cos(a),c=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*l-e.y[t]*c,e.y[t]=n*c+e.y[t]*l}const u=e.x[o];for(let t=0;t<n;t++)e.x[t]-=u;let d=t.indexOf("M V30 BEGIN ATOM");d=t.indexOf("\n",d);let h=d;for(let o=0;o<n;o++)d=t.indexOf("V30",d)+4,d=t.indexOf(" ",d)+1,d=t.indexOf(" ",d)+1,h=t.indexOf(" ",d)+1,h=t.indexOf(" ",h),d=(t=t.slice(0,d)+e.x[o]+" "+e.y[o]+t.slice(h)).indexOf("\n",d)+1;return t}linkV3000(t,e=!0){let n="\nDatagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let i=0;n&&(i=this.extractAtomDataV3000(t[e]).atomIndex.length),t[e]=t[e].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const u=this.extractAtomsBondsNumbersV3000(t[e]),d=this.extractAtomDataV3000(t[e]);let h=t[e].indexOf("M V30 BEGIN ATOM");h=t[e].indexOf("\n",h);let p=h,m=h;for(let o=0;o<u.natom;o++)if(1!==d.atomIndex[o]||0===e){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);let o=0;n?(o=parseInt(t[e].substring(p,m)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);const r=c-d.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(p,m))+r))/1e4;t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p),s=Math.round(1e4*parseFloat(t[e].substring(p,m)))/1e4,t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf("\n",p)+1}else p=t[e].indexOf("M V30",p)-1,m=t[e].indexOf("\n",p+1),t[e]=t[e].slice(0,p)+t[e].slice(m);const g=t[e].indexOf("M V30 END ATOM");o+=t[e].substring(h+1,g);let f=t[e].indexOf("M V30 BEGIN BOND");f=t[e].indexOf("\n",f),p=f,m=f;for(let o=0;o<u.nbond;o++){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);const o=parseInt(t[e].substring(p,m))+l;t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);let r=0;n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=Math.min(t[e].indexOf("\n",p),t[e].indexOf(" ",p)),r=0,n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf("\n",p)+1}const A=t[e].indexOf("M V30 END BOND");r+=t[e].substring(f+1,A);let v=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const n=t[e].indexOf(")",v);t[e].substring(v,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=n,v=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=u.natom-1,l+=u.nbond,c+=n?Math.max(...d.x):d.x[u.natom-1]-d.x[0]}const u=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<u;t++){i+="M V30 ";const e=t+1===u?s.length-4*(u-1):4;for(let n=0;n<e;n++)i+=n+1===e?t===u-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return a++,n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",e&&s.length>0?(n+="M V30 BEGIN COLLECTION\n",n+=i,n+="M V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M V30 END CTAB\n",n+="M END",n}fix5Prime(t,e,n){const o=e+1,r=t.x[o],i=t.y[o],s=t.x[n]-r,a=t.y[n]-i,l=t.x[e]-r,c=t.y[e]-i,u=l*Math.cos(2*Math.PI/3)-c*Math.sin(2*Math.PI/3),d=l*Math.sin(2*Math.PI/3)+c*Math.cos(2*Math.PI/3),h=l-s,p=c-a,m=u-s,g=d-a;Math.sqrt(g*g+m*m)>=Math.sqrt(p*p+h*h)&&(t.x[e]=u+r,t.y[e]=d+i)}}var P,H=n(864),_=n(622);!function(t){t.HEADER="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t.RGP_LINE="M RGP",t.A_LINE="A ",t.END="M END"}(P||(P={}));class R extends _.w{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(P.HEADER)&&-1!==t.indexOf(P.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,P.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<P.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,P.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,P.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+P.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=P.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}var j=n(577);class q{constructor(){}static getInstance(t){if(R.validate(t))return new R(t);if(j.u.validate(t))return new j.u(t);throw new Error("Malformed molfile")}}var G=n(604);const U=class extends Error{constructor(t){super(t)}};class W{constructor(t){this.molblock=t}_validMolBlock;get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof U&&(t="");const n=(0,G.O)(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new U("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(t){try{await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=(0,G.O)(t);console.error(e)}}getMoleculeDimensions(){const t=q.getInstance(this.molblock),e=Math.max(...t.x)-Math.min(...t.x);return{height:Math.max(...t.y)-Math.min(...t.y),width:e}}async zoomIn(){const t=i.dialog({title:"Molecule",showFooter:!1}),e=.7*T()(window).height(),n=this.getMoleculeDimensions(),o=e/n.height,r=e,s=n.width*o,a=i.canvas(s,r);await this.drawMolBlockOnCanvas(a);const l=i.block([a],{style:{overflowX:"scroll"}});t.add(l).showModal(!0),T()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),T()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),T()(t.root).find(".d4-dialog-contents").addClass("ui-box"),T()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const o=i.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);o.style.width=`${e}px`,o.style.height=`${n}px`,o.style.cursor="zoom-in",this.drawMolBlockOnCanvas(o),o.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(i.tooltip.bind(o,"Click to zoom"))}}var Y=n(713),z=n(511),X=n(456);class Z{constructor(){const t=Object.keys(O.Rv).concat(y.NI.HELM);this.moleculeImgDiv=i.div([]),this.moleculeImgDiv.className="mol-host",this.moleculeImgDiv.style.border="1px solid var(--grey-2)",this.moleculeImgDiv.style.borderRadius="1px",this.moleculeImgDiv.style.marginTop="12px",this.outputTableDiv=i.div([]),this.formatChoiceInput=i.choiceInput("",y.NI.HELM,t,(async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()})),this.sequenceInputBase=i.textInput("",z.T,(()=>{this.onInput.next()})),this.init(),o.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()}))}onInput=new s.Subject;moleculeImgDiv;outputTableDiv;formatChoiceInput;sequenceInputBase;molfile;sequence;format;async getHtmlElement(){const t=new L(this.sequenceInputBase,M),e=i.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=i.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),o=i.div([this.formatChoiceInput]),r=i.button(i.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));i.tooltip.bind(r,"Clear input");const s={format:o,textInput:t.root,clearBtn:r},a=i.table([s],(t=>[t.format,t.textInput,t.clearBtn]));a.classList.add("st-translator-input-table");const l=i.block([this.outputTableDiv,e,n]),c=i.box(i.panel([a,l,i.block([i.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),c}saveMolfile(){const t=new k(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";(0,w.LR)(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const t=o.chem.convert(this.molfile,o.chem.Notation.MolBlock,o.chem.Notation.Smiles);navigator.clipboard.writeText(t).then((()=>r.shell.info(Y.AU)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?new b.b(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,H.D)(this.sequence,t,this.format),n=[];for(const t of Object.keys(e)){const o="indexOfFirstInvalidChar"in 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K=n(753),Q={};Q.styleTagTransform=v(),Q.setAttributes=m(),Q.insert=h().bind(null,"head"),Q.domAPI=u(),Q.insertStyleElement=f(),l()(K.Z,Q),K.Z&&K.Z.locals&&K.Z.locals;var J=n(261);function tt(t,e){if(""===t)return"";const n=new I(t).getFormat();if(!n)return"";let o="";try{o=new k(t,e,n).convert()}catch(t){const e=(0,G.O)(t);console.error(e)}return o}function et(t,e,n,o){const r=[t,e,n].filter((t=>""!==t.strand));if(1===r.length)return tt(r[0].strand,r[0].invert);{const r=tt(t.strand,t.invert),i=[tt(e.strand,e.invert),tt(n.strand,n.invert)].filter((t=>""!==t));return(0,J.v5)({senseStrands:[r],antiStrands:i},o)}}const nt=["ss","as","as2"];class ot{constructor(){this.onInput=new s.Subject,this.onInvalidInput=new s.Subject,this.inputBase=Object.fromEntries(nt.map((t=>[t,i.textInput("","",(()=>{this.onInput.next()}))]))),this.useChiralInput=i.boolInput("Use chiral",!0),this.saveAllStrandsInput=i.boolInput("Save as one entity",!0),i.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(nt.map((t=>[t,!1]))),this.moleculeImgDiv=i.block([]),T()(this.moleculeImgDiv).addClass("st-structure-mol-img"),o.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),o.debounce(this.onInvalidInput,1e3).subscribe((async()=>{r.shell.warning("Insert Sense strand")}))}onInput;onInvalidInput;useChiralInput;saveAllStrandsInput;inputBase;directionInversion;moleculeImgDiv;async getHtmlDivElement(){const t=this.getTableInput(),e=this.getBoolInputsAndButton();await this.updateMoleculeImg();const n=i.divH([e,this.moleculeImgDiv]);T()(n).addClass("st-structure-bottom");const o=i.divV([t,n]);return T()(o).addClass("st-structure-body"),o}getBoolInputsAndButton(){const t=i.buttonsInput([i.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,o,i){const s=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===s.length||1===s.length&&""===t.strand)r.shell.warning("Enter SS and optionally AS/AS2 to save SDF");else{let a;if(i)a=et(t,e,n,o)+"\n$$$$\n";else{const d=tt(t.strand,t.invert),h=tt(e.strand,e.invert),p=tt(n.strand,n.invert);a=d+"\n> <Sequence>\nSense Strand\n$$$$\n",h&&(a+=h+"\n> <Sequence>\nAnti Sense\n$$$$\n"),p&&(a+=p+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}const u=l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds());(0,w.LR)(`SequenceTranslator-${u}.sdf`,encodeURIComponent(a))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=i.divV(e);for(const t of e)T()(t).addClass("st-structure-bool-button-block");return n}getTableInput(){const t=Object.fromEntries(nt.map((t=>[t,new L(this.inputBase[t],M)]))),e=Object.fromEntries(nt.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,i.choiceInput(`${t.toUpperCase()} direction`,n,["5′ → 3′","3′ → 5′"])]})));nt.forEach(((t,n)=>{e[t].onChanged((()=>{let o="3′ → 5′"===e[t].value;n>0&&(o=!o),this.directionInversion[t]=o,this.onInput.next()}))}));const n=["Sense Strand","Anti Sense","Anti Sense 2"],o=new Map(nt.map(((t,e)=>[t,n[e]]))),r=Object.fromEntries(nt.map((t=>[t,i.label(o.get(t))]))),s=Object.fromEntries(nt.map((e=>{const n=i.icons.delete((()=>{t[e].inputBase.value=""})),o=i.button(n,(()=>{}));return i.tooltip.bind(o,`Clear ${e.toUpperCase()}`),[e,n]}))),a=nt.map((n=>({label:r[n],textInput:t[n].root,clear:s[n],choiceInput:e[n].root}))),l=i.table(a,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));T()(l).css("margin-top","10px");for(const t of nt){let n=r[t].parentElement;n.classList.add("st-structure-input-form"),T()(n).css("padding-top","3px"),n=e[t].root.parentElement,n.classList.add("st-structure-input-form","st-structure-direction-choice"),n=this.inputBase[t].root.parentElement,n.classList.add("st-structure-text-input-td")}return l}getStrandData(){return Object.fromEntries(nt.map(((t,e)=>{let n=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:n}]})))}getMolfile(t,e,n){return et(t,e,n,this.useChiralInput.value)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=(0,G.O)(t);console.error(e)}const e=new W(t);await e.drawMolecule(this.moleculeImgDiv,650,150),T()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}const rt="SequenceTranslator",it="SS",st="AS",at=[it,st],lt={[it]:"Sense strand",[st]:"Anti sense"},ct="THREE_PRIME",ut="FIVE_PRIME",dt=[ct,ut],ht={[ct]:3,[ut]:5};function pt(t){return"(o)"===t.slice(-3)}function mt(t){let e=0;for(;e<t.length&&pt(t[e]);)e++;return e===t.length-1?0:e}function gt(t,e){const n=document.createElement("canvas").getContext("2d");return n.font=String(e),2*n.measureText(t).width}function ft(t,e){return pt(t[e])||!y.mc.includes(t[e])?"":t[e]}function At(t){const e=O.al[t].color.match(/\d+/g).map((t=>Number(t)));return.299*e[0]+.587*e[1]+.114*e[2]>186?"#33333":"#ffffff"}function vt(t){return O.al[t].color}const xt={xmlns:"http://www.w3.org/2000/svg",render:function(t,e){const n=document.createElementNS(this.xmlns,"svg");return n.setAttribute("id","mySvg"),n.setAttribute("width",String(t)),n.setAttribute("height",String(e)),n},circle:function(t,e,n,o){const r=document.createElementNS(this.xmlns,"circle");return r.setAttribute("cx",String(t)),r.setAttribute("cy",String(e)),r.setAttribute("r",String(n)),r.setAttribute("fill",o),r},text:function(t,e,n,o,r){const i=document.createElementNS(this.xmlns,"text");return i.setAttribute("x",String(e)),i.setAttribute("y",String(n)),i.setAttribute("font-size",String(o)),i.setAttribute("font-weight","normal"),i.setAttribute("font-family","Arial"),i.setAttribute("fill",r),i.innerHTML=t,i},star:function(t,e,n){const 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t(e){x[e].innerHTML="",C[e]=C[e].concat(Array(v[e]-b[e].length).fill(A)),b[e]=b[e].concat(Array(v[e]-b[e].length).fill(f));let o=0;for(let r=0;r<w[e].value;r++)C[e][r]=i.boolInput("",C[e][r].value,(()=>{s(),n()})),b[e][r]=i.choiceInput("",b[e][r].value,p,(e=>{g.includes(e)||(g.push(e),k.append(i.divText("",{style:{width:"25px"}}),i.boolInput(e,!0,(t=>{if(t)g.includes(e)||g.push(e);else{const t=g.indexOf(e,0);t>-1&&g.splice(t,1)}s()})).root)),t(st),s(),n()})),T()(b[e][r].root).addClass("st-pattern-choice-input"),pt(b[e][r].value)||o++,x[e].append(i.divH([i.div([i.label(pt(b[e][r].value)?"":String(o))],{style:{width:"20px"}}),i.block75([b[e][r].root]),i.div([C[e][r]])],{style:{alignItems:"center"}}))}function e(){Object.values(w).every((t=>t.value<35))?(at.forEach((e=>{w[e].value>v[e]&&(v[e]=w[e].value),t(e)})),s(),at.forEach((t=>{""===I[t].value&&(E[t].value=Ct(w[t].value,f.value))})),n()):i.dialog("Out of range").add(i.divText("Sequence length should be less than "+35..toString()+" due 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n}(n.asBases.concat(n.ssBases)),j.value=n.asBases.length>0,q.value=t;let o=["ssBases","asBases"];at.forEach(((t,e)=>{b[t]=[];const r=o[e];for(let e=0;e<n[r].length;e++)b[t].push(i.choiceInput("",n[r][e],p))})),o=["ssPtoLinkages","asPtoLinkages"],at.forEach(((t,e)=>{const r=o[e];S[t].value=n[r][0],C[t]=[];for(let e=1;e<n[r].length;e++)C[t].push(i.boolInput("",n[r][e]))})),o=["ssBases","asBases"],at.forEach(((t,e)=>{w[t].value=n[o[e]].length}));const r=[["ssThreeModification","ssFiveModification"],["asThreeModification","asFiveModification"]];at.forEach(((t,e)=>{dt.forEach(((o,i)=>{M[t][o].value=n[r[e][i]]}))})),$.value=n.comment})),e.close()}async function l(){const t=await async function(){return await r.dapi.users.current().then((t=>" (created by "+t.friendlyName+")"))}();return q.value=q.stringValue.includes("(created by 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pattern","",u,(t=>a(t))),o.root.append(l.input),o.root.append(o.input),o.input.style.maxWidth="120px",o.input.style.marginLeft="12px",o.setTooltip("Apply Existing Pattern"),F.innerHTML="",F.append(o.root),o.root.append(i.div([i.button(i.iconFA("trash-alt",(()=>{})),(async()=>{null===o.value?r.shell.warning("Choose pattern to delete"):await bt(q.value)?r.shell.warning("Cannot delete pattern, created by other user"):await r.dapi.userDataStorage.remove(rt,o.value,!1).then((()=>r.shell.info("Pattern '"+o.value+"' deleted"))),await c()}))],"ui-input-options"))}));l.input.style.maxWidth="142px",o.root.append(l.input),o.root.append(o.input),o.input.style.maxWidth="100px",o.setTooltip("Apply Existing Pattern"),F.innerHTML="",F.append(o.root),o.root.append(i.div([i.button(i.iconFA("trash-alt",(()=>{})),(async()=>{null===o.value?r.shell.warning("Choose pattern to delete"):await bt(q.value)?r.shell.warning("Cannot delete pattern, created by other user"):await r.dapi.userDataStorage.remove(rt,o.value,!1).then((()=>r.shell.info("Pattern '"+o.value+"' deleted"))),await c()}))],"ui-input-options"))}))}async function u(){await r.dapi.userDataStorage.get(rt,!1).then((t=>{if(Object.keys(t).includes(q.value)){const t=i.dialog("Pattern already exists");T()(t.getButton("OK")).hide(),t.add(i.divText("Pattern name '"+q.value+"' already exists.")).add(i.divText("Replace pattern?")).addButton("YES",(async()=>{await r.dapi.userDataStorage.remove(rt,q.value,!1).then((()=>l())),t.close()})).show()}else l()})),await c()}function d(t,e){const n=function(t){const e=H.value.getCol(t);let n=!0;for(let t=1;t<e.length;t++)if(e.get(t-1).length!==e.get(t).length&&0!==e.get(t).length){n=!1;break}if(!n){const n=i.dialog("Sequences lengths mismatch");T()(n.getButton("OK")).hide(),n.add(i.divText("The sequence length should match the number of Raw sequences in the input file")).add(i.divText("'ADD COLUMN' to see sequences lengths")).addButton("ADD COLUMN",(()=>{H.value.columns.addNewInt("Sequences lengths in "+t).init((t=>e.get(t).length)),r.shell.info("Column with lengths added to '"+H.value.name+"'"),n.close(),r.shell.v=r.shell.getTableView(H.value.name)})).show()}return e.get(0).length!==w[it].value&&i.dialog("Length was updated by value to from imported file").add(i.divText("Latest modifications may not take effect during translation")).onOK((()=>r.shell.info("Lengths changed"))).show(),n}(t),o=H.value.getCol(t).get(0);n&&o.length!==w[e].value&&(w[e].value=H.value.getCol(t).get(0).length),E[e].value=o}function h(t){const e=H.value.getCol(t);if(e.type!==o.TYPE.INT)r.shell.error("Column should contain integers only");else if(e.categories.filter((t=>""!==t)).length<e.toList().filter((t=>""!==t)).length){const t=(n=e.getRawData(),Array.from(new Set(n)).filter((t=>n.indexOf(t)!==n.lastIndexOf(t))));i.dialog("Non-unique IDs").add(i.divText("Press 'OK' to select rows with non-unique values")).onOK((()=>{H.value.selection.init((n=>t.indexOf(e.get(n))>-1)),r.shell.v=r.shell.getTableView(H.value.name),r.shell.info("Rows are selected in table '"+H.value.name+"'")})).show()}var n}const p=Object.keys(O.al),m=p[0],g=[m],f=i.choiceInput("Sequence basis",m,p,(t=>{var e;e=t,at.forEach((t=>{for(let n=0;n<b[t].length;n++)b[t][n].value=e})),s(),n()})),A=i.boolInput("Fully PTO",!0,(t=>{var e;at.forEach((e=>{S[e].value=t})),e=t,at.forEach((t=>{for(let n=0;n<C[t].length;n++)C[t][n].value=e})),s(),n()}));A.captionLabel.classList.add("ui-label-right"),A.captionLabel.style.textAlign="left",A.captionLabel.style.maxWidth="100px",A.captionLabel.style.maxWidth="100px",A.captionLabel.style.minWidth="40px",A.captionLabel.style.width="auto";const v=Object.fromEntries(at.map((t=>[t,23]))),x=Object.fromEntries(at.map((t=>[t,i.div([])]))),C=Object.fromEntries(at.map((t=>[t,Array(23).fill(i.boolInput("",!0))]))),b=Object.fromEntries(at.map((t=>[t,Array(23).fill(i.choiceInput("",m,p))]))),w=Object.fromEntries(at.map((t=>{const n=i.intInput(`${lt[t]} length`,23,(()=>e()));return n.setTooltip(`Length of ${lt[t].toLowerCase()}, including overhangs`),[t,n]}))),y=Object.fromEntries(at.map((t=>[t,""]))),E=Object.fromEntries(at.map((t=>[t,i.textInput("",Ct(w[t].value,f.value))]))),I=Object.fromEntries(at.map((t=>{const e=i.choiceInput(`${lt[t]} column`,"",[],(e=>{d(e,t),y[t]=e}));return[t,e]}))),S=Object.fromEntries(at.map((t=>{const e=i.boolInput(`First ${t} PTO`,A.value,(()=>s()));return e.setTooltip(`ps linkage before first nucleotide of ${lt[t].toLowerCase()}`),e.captionLabel.classList.add("ui-label-right"),e.captionLabel.style.textAlign="left",e.captionLabel.style.maxWidth="100px",e.captionLabel.style.minWidth="40px",e.captionLabel.style.width="auto",[t,e]}))),M=Object.fromEntries(at.map((t=>{const e=Object.fromEntries(dt.map((e=>{const o=i.stringInput(`${t} ${ht[e]}' Modification`,"",(()=>{s(),n()}));return o.setTooltip(`Additional ${t} ${ht[e]}' Modification`),[e,o]})));return[t,e]}))),B=Object.fromEntries(at.map((t=>{const e=i.textInput("",yt(E[t].value,b[t],C[t],M[t][ct],M[t][ut],S[t].value));return e.input.style.minWidth="none",e.input.style.flexGrow="1",T()(e.root.lastChild).css("height","auto"),[t,e]}))),N=Object.fromEntries(at.map((t=>[t,i.block([i.h1(`${lt[t]}`),i.divH([i.div([i.divText("#")],{style:{width:"20px"}}),i.block75([i.divText("Modification")]),i.div([i.divText("PTO")])]),x[t]],{style:{paddingTop:"12px"}})])));at.forEach((t=>{E[t].input.style.resize="none",B[t].input.style.resize="none",E[t].input.style.minWidth="none",E[t].input.style.flexGrow="1",B[t].input.style.minWidth="none",B[t].input.style.flexGrow="1";let e=i.div([i.button(i.iconFA("copy",(()=>{})),(()=>{navigator.clipboard.writeText(B[t].value).then((()=>r.shell.info("Sequence was copied to clipboard")))}))],"ui-input-options");e.style.height="inherit",B[t].root.append(e)}));const L=i.div([]),D=i.div([],"ui-form ui-form-wide"),F=i.div([]),V=i.form([]),k=i.divH([i.boolInput(m,!0,(t=>{if(t)g.includes(m)||g.push(m);else{const t=g.indexOf(m,0);t>-1&&g.splice(t,1)}s(),n()})).root]),P=i.div([w[st].root]),H=function(t){const e=i.tableInput("Tables",t[0],t,(()=>{const t=e.value;if(null===t)return void console.warn("Table is null");const n=t.name;if(!r.shell.tableNames.includes(n)){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}const o=t.columns.names();at.forEach((t=>{const e=o[0];d(e,t),y[t]=e;const n=i.choiceInput(`${lt[t]} column`,e,o,(e=>{d(e,t),y[t]=e,console.log(`clicked ${t} var:`,y[t])}));T()(I[t].root).replaceWith(n.root)})),_=o[0];const s=i.choiceInput("ID column",o[0],o,(t=>{h(t),_=t}));T()(R.root).replaceWith(s.root)}));return e}([]);let _="";const R=i.choiceInput("ID column","",[],(t=>{h(t),_=t}));c();const j=i.boolInput("Anti sense strand",!0,(t=>{N[st].hidden=!t,I[st].root.hidden=!t,P.hidden=!t,V.hidden=!t,D.hidden=!t,S[st].root.hidden=!t,s()}));j.setTooltip("Create antisense strand sections on SVG and table to the right");const q=i.textInput("Save as","Pattern name",(()=>s()));q.setTooltip("Name Of New Pattern"),dt.forEach((t=>{V.append(M[st][t].root)}));const $=i.textInput("Comment","",(()=>s())),G=i.bigButton("Save",(()=>{if(""!==q.value)u().then((()=>r.shell.info("Pattern saved")));else{const t=i.stringInput("Enter name","");i.dialog("Pattern Name").add(t.root).onOK((()=>{q.value=t.value,u().then((()=>r.shell.info("Pattern saved")))})).show()}}));q.addOptions(G);const U=i.bigButton("Convert",(()=>{const t=[!0,j.value];if(console.log("strand vars:",Object.values(y)),at.some(((e,n)=>t[n]&&""===y[e])))r.shell.info("Please select table and columns on which to apply pattern");else if(at.some((t=>w[t].value!==E[t].value.length))){const t=i.dialog("Length Mismatch");T()(t.getButton("OK")).hide(),t.add(i.divText("Length of sequences in columns doesn't match entered length. Update length value?")).addButton("YES",(()=>{at.forEach((t=>{w[t].value=H.value.getCol(I[t].value).getString(0).length})),t.close()})).show()}else{""!==_&&function(t,e,n){const o="ID "+n,i=r.shell.table(t).columns;i.contains(o)&&i.remove(o);const s=i.byName(e);i.addNewString(o).init((t=>""===s.getString(t)?"":s.get(t)+"_"+n))}(H.value.name,_,wt(q.value));const t=[!0,j.value];at.forEach(((e,n)=>{t[n]&&function(t,e,n,o,i,s,a){const l="Axolabs "+e,c=r.shell.table(t).columns;c.contains(l)&&c.remove(l);const u=c.byName(e);c.addNewString(l).init((t=>""===u.getString(t)?"":yt(u.getString(t),n,o,i,s,a)))}(H.value.name,y[e],b[e],C[e],M[e][ut],M[e][ct],S[e].value)})),r.shell.v=r.shell.getTableView(H.value.name),r.shell.info((j.value?"Columns were":"Column was")+" added to table '"+H.value.name+"'"),n()}}));D.append(E[st].root),D.append(B[st].root),e(),i.div([i.h1("Conversion preview"),E[it].root,B[it].root,D],"ui-form ui-form-wide"),i.block50([i.h1("Convert options"),H.root,I[it].root,I[st].root,R.root,i.buttonsInput([U])]).classList.add("ui-form");const W=i.link("Download",(()=>Pt.saveSvgAsPng(document.getElementById("mySvg"),q.value,{backgroundColor:"white"})),"Download pattern as PNG image",""),Y=i.link("Edit pattern",(()=>{i.dialog("Edit pattern").add(i.divV([i.h1("PTO"),i.divH([A.root,S[it].root,S[st].root],{style:{gap:"12px"}})])).add(i.divH([N[it],N[st]],{style:{gap:"24px"}})).onOK((()=>{r.shell.info("Saved")})).show()}),"Edit pattern","");return w[it].addCaption("Length"),i.splitH([i.box(i.div([i.h1("Pattern"),j.root,w[it],w[st],f.root,$.root,F,q.root,i.h1("Convert"),H.root,I[it],I[st],R.root,i.buttonsInput([U])],"ui-form"),{style:{maxWidth:"450px"}}),i.panel([L,k,i.divH([W,Y],{style:{gap:"12px",marginTop:"12px"}}),i.divH([i.divV([i.h1("Sense strand"),E[it].root,B[it].root],"ui-block"),i.divV([i.h1("Anti sense"),E[st],B[st]],"ui-block")],{style:{gap:"24px",marginTop:"24px"}}),i.h1("Additional modifications"),i.form([M[it][ut],M[it][ct]]),V],{style:{overflowX:"scroll",padding:"12px 24px"}})],{},!0)}}async function _t(t){try{const e={overflowX:"scroll"},n=i.div([],{style:e}),o=(0,J.$U)(t),s=.7*T()(window).height(),a=Math.max(...o.x)-Math.min(...o.x),l=Math.max(...o.y)-Math.min(...o.y),c=s/l,u=c*a,d=c*l,h=i.canvas(u*window.devicePixelRatio,d*window.devicePixelRatio);h.style.width=`${u}px`,h.style.height=`${d}px`,await async function(t,e){await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:e,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,t),n.appendChild(h),i.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=(0,G.O)(t);console.error(e)}}class Rt{static async view(){const t=E.A.getInstance().getTableForViewer();t.name="Monomer Library";const e=r.shell.addTableView(t);e.grid.props.allowEdit=!1,e.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await _t(e)}))}}class jt{appName;parentAppName;constructor(t,e){this.appName=t,this.parentAppName=e}async createAppLayout(){const t=o.TaskBarProgressIndicator.create(`Loading ${this.appName}...`);let e=r.shell.v?.root;e&&i.setUpdateIndicator(e,!0),await(0,w.Y3)((async()=>{await this.addView()}),(()=>t.close())),e&&i.setUpdateIndicator(e,!1)}}class qt extends jt{constructor(t){super(t),this.view=o.View.create(),this.setupView()}view;async addView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;this.view.path=`/apps/${pe.name}/${t.replace(/\s/g,"")}/`,r.shell.addView(this.view)}async initView(){const t=await this.getHtml();this.view.append(t)}setupView(){this.view.box=!0,this.view.name=this.appName;const t=r.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}class $t extends jt{constructor(t){super("Oligo Toolkit"),this.externalViewFactories=t;const e=this.getViewFactories();this.multiView=new o.MultiView({viewFactories:e})}multiView;externalViewFactories;getViewFactories(){function t(t){const e=new t(o.View.create());return e.initView(),()=>e.getView()}let e={TRANSLATOR:t(Wt),PATTERN:t(Yt),STRUCTURE:t(zt)};return this.externalViewFactories&&(e=Object.assign({},e,this.externalViewFactories)),e}getPath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${pe.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getPath()}async addView(){this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),r.shell.addView(this.multiView)}}class Gt extends qt{constructor(t,e){super(t),this.layout=e}layout;getHtml(){return Promise.resolve(this.layout)}}class Ut{constructor(){}static getUI(t){switch(t){case"Oligo Translator":return new Wt;case"Oligo Pattern":return new Yt;case"Oligo Structure":return new zt;default:throw new Error(`Unknown app name: ${t}`)}}}class Wt extends qt{constructor(){super("Oligo Translator");const t=i.iconFA("book",Rt.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel]),this.ui=new Z}topPanel;ui;getHtml(){return this.ui.getHtmlElement()}}class Yt extends qt{constructor(){super("Oligo Pattern"),this.ui=new Ht}ui;getHtml(){return Promise.resolve(this.ui.htmlDivElement)}}class zt extends qt{constructor(){super("Oligo Structure"),this.ui=new ot}ui;getHtml(){return this.ui.getHtmlDivElement()}}var Xt,Zt,Kt=n(895);wu;class Qt{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}(Zt=Xt||(Xt={})).FASTA="fasta",Zt.SEPARATOR="separator",Zt.HELM="helm";const Jt=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};new Qt("PT",Jt.fasta.peptide,.5),new Qt("DNA",Jt.fasta.dna,.55),new Qt("RNA",Jt.fasta.rna,.55);class te extends Float32Array{}class ee{static makePalette(t,e=!1,n=ee){const o={};return t.forEach((t=>{const n=t[0],r=t[1];n.forEach(((t,n)=>{o[t]=this.colourPalette[r][e?0:n]}))})),new n(o)}constructor(t){this._palette=t}get(t){return this._palette[t]}}ee.undefinedColor="rgb(100,100,100)",ee.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class ne extends ee{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,ne)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,ne)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new ne({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in ne.aaSynonyms?ne.aaSynonyms[t]:t;return super.get(e)}}ne.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class oe{static getPalette(t="grok"){switch(t){case"grok":return ne.GrokGroups;case"lesk":return ne.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",o="";for(const r of t)"("==r?e++:")"==r?e--:e?n+=r:o+=r;return isNaN(parseInt(n))?[o,n]:[o,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[o,r]=this.getInnerOuter(t);if(o=o.length>6?`${o.slice(0,3)}...`:o,r=r.length>6?`${r.slice(0,3)}...`:r,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,r,1]:[this.undefinedColor,o,r,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,r,2]:[this.undefinedColor,o,r,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,r,3]:[this.undefinedColor,o,r,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,r,4]:[this.undefinedColor,o,r,4]}return[this.undefinedColor,o,r,0]}}oe.SemType="Aminoacids",oe.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",oe.undefinedColor="rgb(100,100,100)",oe.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},oe.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},oe.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},oe.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class re{}re.SemType="Nucleotides",re.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",re.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class ie{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class se{}class ae extends se{static buildPalette(){return[].concat(...Object.values(ee.colourPalette))}get(t){const e=ie.hashCode(t)%ae.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=o.Color.fromHtml(t),n=o.Color.g(e),r=o.Color.r(e),i=o.Color.b(e),s=Math.sqrt(Math.pow(0-r,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return s>210?`rgb(${r/s*210},${n/s*210},${i/s*210})`:o.Color.toRgb(e)}(ae.palette[e])}}ae.palette=ae.buildPalette();new Uint32Array(65536);var le,ce;(ce=le||(le={})).HAMMING="Hamming",ce.LEVENSHTEIN="Levenshtein",ce.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",le.HAMMING,le.LEVENSHTEIN,le.NEEDLEMANN_WUNSCH,new 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t={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:de()}},e={};for(const[n,o]of Object.entries(t)){let t;try{t=await r.functions.call(n,o.parameters);const i=new Gt(o.tabName,t);i.initView(),e[o.tabName]=()=>i.getView()}catch(t){console.warn(`Plugin ${n} not loaded, reason:`,t);continue}}return e}();if(!t)throw new Error("External app view factories not loaded");const e=new $t(t);await e.createAppLayout()}async function fe(){await me("Oligo Translator")}async function Ae(){await me("Oligo Pattern")}async function ve(){await me("Oligo Structure")}async function xe(){await(0,O.VO)(),await pe.initMonomerLib()}function Ce(){const t=E.A.getInstance().getCodesToWeightsMap();return Object.fromEntries(t)}function be(t){const e=new b.b(t),n=new I(t).getFormat();return null!==n&&e.isValidSequence(n)}function we(t,e){return new k(t,e,"GCRS").convert()}function ye(t){return(0,J.v5)(t,!0)}async function Ee(){await async function(){await(0,w.Y3)((async()=>fe()))}()}async function Oe(){await async function(){await(0,w.Y3)((async()=>{async function t(t,n,o){await(0,ue.gw)(3e3);const r=document.querySelectorAll(".st-pattern-choice-input > select");e=r.length;const i=r[o(n)];i.value=t;const s=new Event("input");i.dispatchEvent(s)}let e;await Ae(),["DNA","invAb","Z-New"].forEach((async(e,n)=>{t(e,n,(t=>2*t))})),["2'-O-Methyl","2'-Fluoro","2'-O-MOE"].forEach((async(n,o)=>{t(n,o,(t=>e-2-2*t))}))}))}()}async function Ie(){await async function(){await(0,w.Y3)((async()=>{await ve(),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await(0,ue.gw)(500);const n=document.querySelectorAll(".colored-text-input > textarea")[t];n.value=e;const o=new Event("input");n.dispatchEvent(o)}(e,t)}))}))}()}async function Se(t,e,n){return await xe(),new X.I(t,e).convertTo(n)}},713:(t,e,n)=>{n.d(e,{AU:()=>o,wm:()=>r});const o="Copied",r="Copy sequence"},511:(t,e,n)=>{n.d(e,{T:()=>o});const o="Afcgacsu"},976:t=>{t.exports=DG},469:t=>{t.exports=grok}},e={};function n(o){var r=e[o];if(void 0!==r)return r.exports;var i=e[o]={id:o,exports:{}};return t[o](i,i.exports,n),i.exports}n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var o in e)n.o(e,o)&&!n.o(t,o)&&Object.defineProperty(t,o,{enumerable:!0,get:e[o]})},n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nc=void 0;var o=n(593);sequencetranslator=o})();
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+ var sequencetranslator;(()=>{"use strict";var t={622:(t,e,n)=>{n.d(e,{w:()=>r});class o{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return 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this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class r extends o{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let o=0;o<e;o++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}},577:(t,e,n)=>{n.d(e,{u:()=>r});var o=n(622);class r extends o.w{constructor(t){super(t),this.init(t)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static validate(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M 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e=0;e<m.length;e++){m[e]=m[e].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const n=i(m[e]),r=s(m[e]);if(e>=t.senseStrands.length?!1===p&&(p=!0,h=0):g=Math.min(g,Math.min(...r.y.filter((t=>t<0)))),p){const t=Math.min(...r.x)-h,e=Math.max(...r.y)+5;for(let e=0;e<r.x.length;e++)r.x[e]-=t;for(let t=0;t<r.y.length;t++)r.y[t]-=e-g}let l=m[e].indexOf("M V30 BEGIN ATOM");l=m[e].indexOf("\n",l);let f=l,A=l;for(let t=0;t<n.natom;t++){f=m[e].indexOf("V30",f)+4,A=m[e].indexOf(" ",f);const n=parseInt(m[e].substring(f,A))+u;m[e]=m[e].slice(0,f)+n+m[e].slice(A),f=m[e].indexOf(" ",f)+1,f=m[e].indexOf(" ",f)+1,A=m[e].indexOf(" ",f);let o=Math.round(1e4*r.x[t])/1e4;m[e]=m[e].slice(0,f)+o+m[e].slice(A),f=m[e].indexOf(" ",f)+1,A=m[e].indexOf(" ",f),o=Math.round(1e4*r.y[t])/1e4,m[e]=m[e].slice(0,f)+o+m[e].slice(A),f=m[e].indexOf("\n",f)+1}const v=m[e].indexOf("M V30 END ATOM");o+=m[e].substring(l+1,v);let x=m[e].indexOf("M V30 BEGIN BOND");x=m[e].indexOf("\n",x),f=x,A=x;for(let t=0;t<n.nbond;t++){f=m[e].indexOf("V30",f)+4,A=m[e].indexOf(" ",f);const t=parseInt(m[e].substring(f,A))+d;m[e]=m[e].slice(0,f)+t+m[e].slice(A),f=m[e].indexOf(" ",f)+1,f=m[e].indexOf(" ",f)+1,A=m[e].indexOf(" ",f);let n=parseInt(m[e].substring(f,A))+u;m[e]=m[e].slice(0,f)+n+m[e].slice(A),f=m[e].indexOf(" ",f)+1,A=Math.min(m[e].indexOf("\n",f),m[e].indexOf(" ",f)),n=parseInt(m[e].substring(f,A))+u,m[e]=m[e].slice(0,f)+n+m[e].slice(A),f=m[e].indexOf("\n",f)+1}const C=m[e].indexOf("M V30 END BOND");a+=m[e].substring(x+1,C);let b=m[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const t=m[e].indexOf(")",b);m[e].substring(b,t).split(" ").slice(1).forEach((t=>{c.push(parseInt(t)+u)})),b=t,b=m[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",b)}u+=n.natom,d+=n.nbond,h+=Math.max(...r.x)+5}const f=Math.ceil(c.length/4);l+="M V30 MDLV30/STEABS ATOMS=("+c.length+" -\n";for(let t=0;t<f;t++){l+="M V30 ";const e=t+1===f?c.length-4*(f-1):4;for(let n=0;n<e;n++)l+=n+1===e?t===f-1?c[4*t+n]+")\n":c[4*t+n]+" -\n":c[4*t+n]+" "}return n+="M V30 COUNTS "+u+" "+d+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=a,n+="M V30 END BOND\n",e&&c.length>0?(n+="M V30 BEGIN COLLECTION\n",n+=l,n+="M V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M V30 END CTAB\n",n+="M END",n}function r(t){const e=s(t),n=e.atomIndex.length,o=(Math.max(...e.x)+Math.min(...e.x))/2,r=(Math.max(...e.y)+Math.min(...e.y))/2;for(let t=0;t<n;t++)e.x[t]-=o,e.y[t]-=r;const i=Math.PI,a=Math.cos(i),l=Math.sin(i);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*a-e.y[t]*l,e.y[t]=n*l+e.y[t]*a}const c=Math.max(...e.y);for(let t=0;t<n;t++)e.x[t]+=o,e.y[t]-=c;let u=t.indexOf("M V30 BEGIN ATOM");u=t.indexOf("\n",u);let d=u;for(let o=0;o<n;o++)u=t.indexOf("V30",u)+4,u=t.indexOf(" ",u)+1,u=t.indexOf(" ",u)+1,d=t.indexOf(" ",u)+1,d=t.indexOf(" ",d),u=(t=t.slice(0,u)+e.x[o]+" "+e.y[o]+t.slice(d)).indexOf("\n",u)+1;return t}function i(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const o=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:o,nbond:parseInt(t.substring(e,n))}}function s(t){const e=i(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let o=n;const r=Array(e.natom),s=Array(e.natom),a=Array(e.natom),l=Array(e.natom);for(let i=0;i<e.natom;i++)n=t.indexOf("V30",n)+4,o=t.indexOf(" ",n),r[i]=parseInt(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),s[i]=t.substring(n,o),n=o+1,o=t.indexOf(" ",n),a[i]=parseFloat(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),l[i]=parseFloat(t.substring(n,o)),n=t.indexOf("\n",n)+1;return{atomIndex:r,atomType:s,x:a,y:l}}n.d(e,{$U:()=>s,v5:()=>o})},544:(t,e,n)=>{n.d(e,{$3:()=>r,DD:()=>o,s8:()=>i});const o={NUCLEOSIDE:"nucleoside",LINKAGE:"phosphateBackbone"},r="p",i="<?>"},864:(t,e,n)=>{n.d(e,{D:()=>l});var o=n(29),r=n(544),i=n(456),s=n(996),a=n(559);function l(t,e,n){const l=Object.keys(s.Rv).concat([o.NI.HELM]);if(!t||-1!==e&&n!==o.NI.HELM)return{};if(!l.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const c=l.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),u=new i.I(t,n),d=Object.fromEntries(c.map((t=>{let e;try{e=u.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),h=function(t,e){const n=new RegExp("\\([^()]*\\)","g"),i=t.match(n);if(!i)return null;return i.map((t=>{const n=t.replace(/[\[\]()]/g,"");return o.mc.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||r.s8)).join("")}(n===o.NI.HELM?t:d[o.NI.HELM],a.A.getInstance());return h&&(d.Nucleotides=h),d}},456:(t,e,n)=>{n.d(e,{I:()=>u});var o=n(29),r=n(544),i=n(996);const s=(t,e)=>e.length-t.length;class a{constructor(){this.formats=this.getFormats()}formats;getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const o=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[o]?e[o]=[t]:e[o].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const o=n.sort(s);e[t]=o[0]})),e}(i.Rv[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=i.Rv[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(s)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(l(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=i.Rv[t],n=l(Array.from(new Set(Object.values(e[r.DD.LINKAGE]))).sort(s));return new RegExp(`${r.$3}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(i.Rv)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===o.NI.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(s)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(l(e)+"|\\([^()]*\\)|.","g")}}function l(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const c={LEFT:"RNA1{",RIGHT:"}$$$$"};class u{sequence;sourceFormat;constructor(t,e){this.sequence=t,this.sourceFormat=e}formats=new a;convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===o.NI.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===o.NI.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(l(Object.values(c)),"g");let o=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),s=this.formats.getTargetFormatHelmCodes(e),a=this.formats.getTargetFormatHelmCodesRegExp(e);return o=o.replace(a,(t=>s.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,r.s8).replace(/p\.|\./g,""),o=o.replace(/<empty>/g,""),o=o.replace(/\/\//g,"/"),o}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),o=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),s=this.formats.getPhosphateHelmCodesRegExp(e);let a=t.replace(i,(t=>o.includes(t)?n[t]+".":"?"));return a=a.replace(/\?+/g,`${r.s8}.`),a=a.slice(0,-1),a[a.length-1]===r.$3&&(a=a.slice(0,-1)),a=a.replace(s,((t,e)=>e)),a=a.replace(/<empty>/g,""),`${c.LEFT+a+c.RIGHT}`}}},593:(t,e,n)=>{n.r(e),n.d(e,{_package:()=>pe,demoOligoPattern:()=>Oe,demoOligoStructure:()=>Ie,demoTranslateSequence:()=>Ee,getCodeToWeightsMap:()=>Ce,getMolfileFromGcrsSequence:()=>we,initSequenceTranslatorLibData:()=>xe,linkStrands:()=>ye,oligoPatternApp:()=>Ae,oligoStructureApp:()=>ve,oligoToolkitApp:()=>ge,oligoTranslatorApp:()=>fe,translateOligonucleotideSequence:()=>Se,validateSequence:()=>be});var o=n(976),r=n(469);const i=ui,s=rxjs;var a=n(379),l=n.n(a),c=n(795),u=n.n(c),d=n(569),h=n.n(d),p=n(565),m=n.n(p),g=n(216),f=n.n(g),A=n(589),v=n.n(A),x=n(602),C={};C.styleTagTransform=v(),C.setAttributes=m(),C.insert=h().bind(null,"head"),C.domAPI=u(),C.insertStyleElement=f(),l()(x.Z,C),x.Z&&x.Z.locals&&x.Z.locals;var b=n(947),w=n(669),y=n(29),E=n(559),O=n(996);class I{sequence;constructor(t){this.sequence=t,this.libWrapper=E.A.getInstance(),this.formats=Object.keys(O.Rv)}libWrapper;formats;getFormat(){if(this.sequence.startsWith("RNA"))return y.NI.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=new b.b(this.sequence),n=Array(t.length).fill(0);for(let o=0;o<t.length;++o){const r=t[o];n[o]=e.getInvalidCodeIndex(r)}const o=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(o)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence;let e=[];for(const n of this.formats){let o=(0,w.xB)(this.libWrapper.getCodesByFormat(n)),r=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){r=e+1;break}o.some((e=>e===t.slice(r,r+e.length)))&&e.push(n)}return e}}const S=$;var T=n.n(S);function M(t){let e=0;const n=new I(t).getFormat();null!==n&&(e=new b.b(t).getInvalidCodeIndex(n));const o=e<0||""===t,r=i.span([]);T()(r).css("-webkit-text-fill-color","var(--grey-6)");const s=i.span([]);return T()(s).css("-webkit-text-fill-color","red"),o?r.innerHTML=t:(r.innerHTML=t.slice(0,e),s.innerHTML=t.slice(e)),[r,s]}var B=n(490),N={};N.styleTagTransform=v(),N.setAttributes=m(),N.insert=h().bind(null,"head"),N.domAPI=u(),N.insertStyleElement=f(),l()(B.Z,N),B.Z&&B.Z.locals&&B.Z.locals;class L{textInputBase;painter;constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,T()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{T()(this.textArea).css("height",0),T()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=i.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged((()=>this.colorize()))}highlights;get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}var D=n(900);class F{sequence;codeMap;constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,o)=>{const r=this.getSymbolForCode(n);o>0&&function(t){return O.iA.left.includes(t)}(r)&&e.pop(),e.push(r);const i=V(r),s=o===t.length-1,a=o+1<t.length&&V(this.getSymbolForCode(t[o+1]));i||function(t){return O.iA.right.includes(t)}(r)||a||s||e.push(D.$)})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??=t,e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const o=t.find((t=>t===this.sequence.substring(n,n+t.length)));e.push(o),n+=o.length}return e}getAllCodesOfFormat(){let t=Array.from(this.codeMap.keys());return(0,w.xB)(t)}}function V(t){return O.iA.phosphate.includes(t)}class k{invert;constructor(t,e=!1,n){this.invert=e,this.lib=E.A.getInstance();const o=this.lib.getCodeToSymbolMap(n);this.parser=new F(t,o)}parser;lib;convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const o=this.getMonomerMolfile(t,n);e.push(o)}));let n=this.getPolymerMolfile(e);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(t){const e=t.indexOf("M V30 BEGIN BOND"),n=t.indexOf("M V30 END BOND");let o=t.substring(e,n);return o=o.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${e}3`:"3"===n?`${e}1`:t)),t.substring(0,e)+o+t.substring(n)}getMonomerMolfile(t,e){const n=this.lib.getMolfileBySymbol(t);return this.lib.isModification(t)?0===e?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(t){return this.linkV3000(t)}reflect(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n),i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;for(let t=0;t<n;t++)e.x[t]=-e.x[t];const a=e.x[o];for(let t=0;t<n;t++)e.x[t]-=a;let l=t.indexOf("M V30 BEGIN ATOM");l=t.indexOf("\n",l);let c=l;for(let o=0;o<n;o++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,c=t.indexOf(" ",l)+1,c=t.indexOf(" ",c),l=(t=t.slice(0,l)+e.x[o]+" "+e.y[o]+t.slice(c)).indexOf("\n",l)+1;return t}extractAtomDataV3000(t){const e=this.extractAtomsBondsNumbersV3000(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let o=n;const r=Array(e.natom),i=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let l=0;l<e.natom;l++)n=t.indexOf("V30",n)+4,o=t.indexOf(" ",n),r[l]=parseInt(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),i[l]=t.substring(n,o),n=o+1,o=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,o)),n=t.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}extractAtomsBondsNumbersV3000(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const o=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:o,nbond:parseInt(t.substring(e,n))}}rotateNucleotidesV3000(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,o,r);const i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;let a=0;if(0===e.x[o])a=e.y[o]>e.y[r]?Math.PI/2:3*Math.PI/2;else if(0===e.y[o])a=e.x[o]>e.x[r]?Math.PI:0;else{const t=e.y[o]/e.x[o];a=t>0?e.x[o]>0?Math.PI-Math.atan(t):2*Math.PI-Math.atan(t):e.x[o]>0?-Math.PI-Math.atan(t):Math.atan(t)}const l=Math.cos(a),c=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*l-e.y[t]*c,e.y[t]=n*c+e.y[t]*l}const u=e.x[o];for(let t=0;t<n;t++)e.x[t]-=u;let d=t.indexOf("M V30 BEGIN ATOM");d=t.indexOf("\n",d);let h=d;for(let o=0;o<n;o++)d=t.indexOf("V30",d)+4,d=t.indexOf(" ",d)+1,d=t.indexOf(" ",d)+1,h=t.indexOf(" ",d)+1,h=t.indexOf(" ",h),d=(t=t.slice(0,d)+e.x[o]+" "+e.y[o]+t.slice(h)).indexOf("\n",d)+1;return t}linkV3000(t,e=!0){let n="\n Datagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let i=0;n&&(i=this.extractAtomDataV3000(t[e]).atomIndex.length),t[e]=t[e].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const u=this.extractAtomsBondsNumbersV3000(t[e]),d=this.extractAtomDataV3000(t[e]);let h=t[e].indexOf("M V30 BEGIN ATOM");h=t[e].indexOf("\n",h);let p=h,m=h;for(let o=0;o<u.natom;o++)if(1!==d.atomIndex[o]||0===e){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);let o=0;n?(o=parseInt(t[e].substring(p,m)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);const r=c-d.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(p,m))+r))/1e4;t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p),s=Math.round(1e4*parseFloat(t[e].substring(p,m)))/1e4,t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf("\n",p)+1}else p=t[e].indexOf("M V30",p)-1,m=t[e].indexOf("\n",p+1),t[e]=t[e].slice(0,p)+t[e].slice(m);const g=t[e].indexOf("M V30 END ATOM");o+=t[e].substring(h+1,g);let f=t[e].indexOf("M V30 BEGIN BOND");f=t[e].indexOf("\n",f),p=f,m=f;for(let o=0;o<u.nbond;o++){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);const o=parseInt(t[e].substring(p,m))+l;t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);let r=0;n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=Math.min(t[e].indexOf("\n",p),t[e].indexOf(" ",p)),r=0,n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf("\n",p)+1}const A=t[e].indexOf("M V30 END BOND");r+=t[e].substring(f+1,A);let v=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const n=t[e].indexOf(")",v);t[e].substring(v,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=n,v=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=u.natom-1,l+=u.nbond,c+=n?Math.max(...d.x):d.x[u.natom-1]-d.x[0]}const u=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<u;t++){i+="M V30 ";const e=t+1===u?s.length-4*(u-1):4;for(let n=0;n<e;n++)i+=n+1===e?t===u-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return a++,n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",e&&s.length>0?(n+="M V30 BEGIN COLLECTION\n",n+=i,n+="M V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M V30 END CTAB\n",n+="M END",n}fix5Prime(t,e,n){const o=e+1,r=t.x[o],i=t.y[o],s=t.x[n]-r,a=t.y[n]-i,l=t.x[e]-r,c=t.y[e]-i,u=l*Math.cos(2*Math.PI/3)-c*Math.sin(2*Math.PI/3),d=l*Math.sin(2*Math.PI/3)+c*Math.cos(2*Math.PI/3),h=l-s,p=c-a,m=u-s,g=d-a;Math.sqrt(g*g+m*m)>=Math.sqrt(p*p+h*h)&&(t.x[e]=u+r,t.y[e]=d+i)}}var P,H=n(864),_=n(622);!function(t){t.HEADER="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t.RGP_LINE="M RGP",t.A_LINE="A ",t.END="M END"}(P||(P={}));class R extends _.w{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(P.HEADER)&&-1!==t.indexOf(P.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,P.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<P.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,P.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,P.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+P.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=P.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}var j=n(577);class q{constructor(){}static getInstance(t){if(R.validate(t))return new R(t);if(j.u.validate(t))return new j.u(t);throw new Error("Malformed molfile")}}var G=n(604);const U=class extends Error{constructor(t){super(t)}};class W{constructor(t){this.molblock=t}_validMolBlock;get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof U&&(t="");const n=(0,G.O)(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new U("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(t){try{await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=(0,G.O)(t);console.error(e)}}getMoleculeDimensions(){const t=q.getInstance(this.molblock),e=Math.max(...t.x)-Math.min(...t.x);return{height:Math.max(...t.y)-Math.min(...t.y),width:e}}async zoomIn(){const t=i.dialog({title:"Molecule",showFooter:!1}),e=.7*T()(window).height(),n=this.getMoleculeDimensions(),o=e/n.height,r=e,s=n.width*o,a=i.canvas(s,r);await this.drawMolBlockOnCanvas(a);const l=i.block([a],{style:{overflowX:"scroll"}});t.add(l).showModal(!0),T()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),T()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),T()(t.root).find(".d4-dialog-contents").addClass("ui-box"),T()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const o=i.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);o.style.width=`${e}px`,o.style.height=`${n}px`,o.style.cursor="zoom-in",this.drawMolBlockOnCanvas(o),o.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(i.tooltip.bind(o,"Click to zoom"))}}var Y=n(713),z=n(511),X=n(456);class Z{constructor(){const t=Object.keys(O.Rv).concat(y.NI.HELM);this.moleculeImgDiv=i.div([]),this.moleculeImgDiv.className="mol-host",this.moleculeImgDiv.style.border="1px solid var(--grey-2)",this.moleculeImgDiv.style.borderRadius="1px",this.moleculeImgDiv.style.marginTop="12px",this.outputTableDiv=i.div([]),this.formatChoiceInput=i.choiceInput("",y.NI.HELM,t,(async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()})),this.sequenceInputBase=i.textInput("",z.T,(()=>{this.onInput.next()})),this.init(),o.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()}))}onInput=new s.Subject;moleculeImgDiv;outputTableDiv;formatChoiceInput;sequenceInputBase;molfile;sequence;format;async getHtmlElement(){const t=new L(this.sequenceInputBase,M),e=i.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=i.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),o=i.div([this.formatChoiceInput]),r=i.button(i.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));i.tooltip.bind(r,"Clear input");const s={format:o,textInput:t.root,clearBtn:r},a=i.table([s],(t=>[t.format,t.textInput,t.clearBtn]));a.classList.add("st-translator-input-table");const l=i.block([this.outputTableDiv,e,n]),c=i.box(i.panel([a,l,i.block([i.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),c}saveMolfile(){const t=new k(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";(0,w.LR)(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const t=o.chem.convert(this.molfile,o.chem.Notation.MolBlock,o.chem.Notation.Smiles);navigator.clipboard.writeText(t).then((()=>r.shell.info(Y.AU)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?new b.b(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,H.D)(this.sequence,t,this.format),n=[];for(const t of Object.keys(e)){const o="indexOfFirstInvalidChar"in e?i.divH([]):i.link(e[t],(()=>navigator.clipboard.writeText(e[t]).then((()=>r.shell.info(Y.AU)))),Y.wm,"");n.push({format:t,sequence:o})}const o=i.table(n,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(o),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new W(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=new I(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===y.NI.HELM){const t=new X.I(this.sequence,this.format).convertTo(y.NI.AXOLABS);return new k(t,!1,y.NI.AXOLABS).convert()}return new k(this.sequence,!1,this.format).convert()}}var K=n(753),Q={};Q.styleTagTransform=v(),Q.setAttributes=m(),Q.insert=h().bind(null,"head"),Q.domAPI=u(),Q.insertStyleElement=f(),l()(K.Z,Q),K.Z&&K.Z.locals&&K.Z.locals;var J=n(261);function tt(t,e){if(""===t)return"";const n=new I(t).getFormat();if(!n)return"";let o="";try{o=new k(t,e,n).convert()}catch(t){const e=(0,G.O)(t);console.error(e)}return o}function et(t,e,n,o){const r=[t,e,n].filter((t=>""!==t.strand));if(1===r.length)return tt(r[0].strand,r[0].invert);{const r=tt(t.strand,t.invert),i=[tt(e.strand,e.invert),tt(n.strand,n.invert)].filter((t=>""!==t));return(0,J.v5)({senseStrands:[r],antiStrands:i},o)}}const nt=["ss","as","as2"];class ot{constructor(){this.onInput=new s.Subject,this.onInvalidInput=new s.Subject,this.inputBase=Object.fromEntries(nt.map((t=>[t,i.textInput("","",(()=>{this.onInput.next()}))]))),this.useChiralInput=i.boolInput("Use chiral",!0),this.saveAllStrandsInput=i.boolInput("Save as one entity",!0),i.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(nt.map((t=>[t,!1]))),this.moleculeImgDiv=i.block([]),T()(this.moleculeImgDiv).addClass("st-structure-mol-img"),o.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),o.debounce(this.onInvalidInput,1e3).subscribe((async()=>{r.shell.warning("Insert Sense strand")}))}onInput;onInvalidInput;useChiralInput;saveAllStrandsInput;inputBase;directionInversion;moleculeImgDiv;async getHtmlDivElement(){const t=this.getTableInput(),e=this.getBoolInputsAndButton();await this.updateMoleculeImg();const n=i.divH([e,this.moleculeImgDiv]);T()(n).addClass("st-structure-bottom");const o=i.divV([t,n]);return T()(o).addClass("st-structure-body"),o}getBoolInputsAndButton(){const t=i.buttonsInput([i.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,o,i){const s=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===s.length||1===s.length&&""===t.strand)r.shell.warning("Enter SS and optionally AS/AS2 to save SDF");else{let a;if(i)a=et(t,e,n,o)+"\n$$$$\n";else{const d=tt(t.strand,t.invert),h=tt(e.strand,e.invert),p=tt(n.strand,n.invert);a=d+"\n> <Sequence>\nSense Strand\n$$$$\n",h&&(a+=h+"\n> <Sequence>\nAnti Sense\n$$$$\n"),p&&(a+=p+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}const u=l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds());(0,w.LR)(`SequenceTranslator-${u}.sdf`,encodeURIComponent(a))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=i.divV(e);for(const t of e)T()(t).addClass("st-structure-bool-button-block");return n}getTableInput(){const t=Object.fromEntries(nt.map((t=>[t,new L(this.inputBase[t],M)]))),e=Object.fromEntries(nt.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,i.choiceInput(`${t.toUpperCase()} direction`,n,["5′ → 3′","3′ → 5′"])]})));nt.forEach(((t,n)=>{e[t].onChanged((()=>{let o="3′ → 5′"===e[t].value;n>0&&(o=!o),this.directionInversion[t]=o,this.onInput.next()}))}));const n=["Sense Strand","Anti Sense","Anti Sense 2"],o=new Map(nt.map(((t,e)=>[t,n[e]]))),r=Object.fromEntries(nt.map((t=>[t,i.label(o.get(t))]))),s=Object.fromEntries(nt.map((e=>{const n=i.icons.delete((()=>{t[e].inputBase.value=""})),o=i.button(n,(()=>{}));return i.tooltip.bind(o,`Clear ${e.toUpperCase()}`),[e,n]}))),a=nt.map((n=>({label:r[n],textInput:t[n].root,clear:s[n],choiceInput:e[n].root}))),l=i.table(a,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));T()(l).css("margin-top","10px");for(const t of nt){let n=r[t].parentElement;n.classList.add("st-structure-input-form"),T()(n).css("padding-top","3px"),n=e[t].root.parentElement,n.classList.add("st-structure-input-form","st-structure-direction-choice"),n=this.inputBase[t].root.parentElement,n.classList.add("st-structure-text-input-td")}return l}getStrandData(){return Object.fromEntries(nt.map(((t,e)=>{let n=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:n}]})))}getMolfile(t,e,n){return et(t,e,n,this.useChiralInput.value)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=(0,G.O)(t);console.error(e)}const e=new W(t);await e.drawMolecule(this.moleculeImgDiv,650,150),T()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}const rt="SequenceTranslator",it="SS",st="AS",at=[it,st],lt={[it]:"Sense strand",[st]:"Anti sense"},ct="THREE_PRIME",ut="FIVE_PRIME",dt=[ct,ut],ht={[ct]:3,[ut]:5};function pt(t){return"(o)"===t.slice(-3)}function mt(t){let e=0;for(;e<t.length&&pt(t[e]);)e++;return e===t.length-1?0:e}function gt(t,e){const n=document.createElement("canvas").getContext("2d");return n.font=String(e),2*n.measureText(t).width}function ft(t,e){return pt(t[e])||!y.mc.includes(t[e])?"":t[e]}function At(t){const e=O.al[t].color.match(/\d+/g).map((t=>Number(t)));return.299*e[0]+.587*e[1]+.114*e[2]>186?"#33333":"#ffffff"}function vt(t){return O.al[t].color}const xt={xmlns:"http://www.w3.org/2000/svg",render:function(t,e){const n=document.createElementNS(this.xmlns,"svg");return n.setAttribute("id","mySvg"),n.setAttribute("width",String(t)),n.setAttribute("height",String(e)),n},circle:function(t,e,n,o){const r=document.createElementNS(this.xmlns,"circle");return r.setAttribute("cx",String(t)),r.setAttribute("cy",String(e)),r.setAttribute("r",String(n)),r.setAttribute("fill",o),r},text:function(t,e,n,o,r){const i=document.createElementNS(this.xmlns,"text");return i.setAttribute("x",String(e)),i.setAttribute("y",String(n)),i.setAttribute("font-size",String(o)),i.setAttribute("font-weight","normal"),i.setAttribute("font-family","Arial"),i.setAttribute("fill",r),i.innerHTML=t,i},star:function(t,e,n){const 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Update length value?")).addButton("YES",(()=>{at.forEach((t=>{w[t].value=H.value.getCol(I[t].value).getString(0).length})),t.close()})).show()}else{""!==_&&function(t,e,n){const o="ID "+n,i=r.shell.table(t).columns;i.contains(o)&&i.remove(o);const s=i.byName(e);i.addNewString(o).init((t=>""===s.getString(t)?"":s.get(t)+"_"+n))}(H.value.name,_,wt(q.value));const t=[!0,j.value];at.forEach(((e,n)=>{t[n]&&function(t,e,n,o,i,s,a){const l="Axolabs "+e,c=r.shell.table(t).columns;c.contains(l)&&c.remove(l);const u=c.byName(e);c.addNewString(l).init((t=>""===u.getString(t)?"":yt(u.getString(t),n,o,i,s,a)))}(H.value.name,y[e],b[e],C[e],M[e][ut],M[e][ct],S[e].value)})),r.shell.v=r.shell.getTableView(H.value.name),r.shell.info((j.value?"Columns were":"Column was")+" added to table '"+H.value.name+"'"),n()}}));D.append(E[st].root),D.append(B[st].root),e(),i.div([i.h1("Conversion preview"),E[it].root,B[it].root,D],"ui-form ui-form-wide"),i.block50([i.h1("Convert 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modifications"),i.form([M[it][ut],M[it][ct]]),V],{style:{overflowX:"scroll",padding:"12px 24px"}})],{},!0)}}async function _t(t){try{const e={overflowX:"scroll"},n=i.div([],{style:e}),o=(0,J.$U)(t),s=.7*T()(window).height(),a=Math.max(...o.x)-Math.min(...o.x),l=Math.max(...o.y)-Math.min(...o.y),c=s/l,u=c*a,d=c*l,h=i.canvas(u*window.devicePixelRatio,d*window.devicePixelRatio);h.style.width=`${u}px`,h.style.height=`${d}px`,await async function(t,e){await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:e,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,t),n.appendChild(h),i.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=(0,G.O)(t);console.error(e)}}class Rt{static async view(){const t=E.A.getInstance().getTableForViewer();t.name="Monomer Library";const e=r.shell.addTableView(t);e.grid.props.allowEdit=!1,e.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await _t(e)}))}}class jt{appName;parentAppName;constructor(t,e){this.appName=t,this.parentAppName=e}async createAppLayout(){const t=o.TaskBarProgressIndicator.create(`Loading ${this.appName}...`);let e=r.shell.v?.root;e&&i.setUpdateIndicator(e,!0),await(0,w.Y3)((async()=>{await this.addView()}),(()=>t.close())),e&&i.setUpdateIndicator(e,!1)}}class qt extends jt{constructor(t){super(t),this.view=o.View.create(),this.setupView()}view;async addView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;this.view.path=`/apps/${pe.name}/${t.replace(/\s/g,"")}/`,r.shell.addView(this.view)}async initView(){const t=await this.getHtml();this.view.append(t)}setupView(){this.view.box=!0,this.view.name=this.appName;const t=r.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}class $t extends jt{constructor(t){super("Oligo Toolkit"),this.externalViewFactories=t;const e=this.getViewFactories();this.multiView=new o.MultiView({viewFactories:e})}multiView;externalViewFactories;getViewFactories(){function t(t){const e=new t(o.View.create());return e.initView(),()=>e.getView()}let e={TRANSLATOR:t(Wt),PATTERN:t(Yt),STRUCTURE:t(zt)};return this.externalViewFactories&&(e=Object.assign({},e,this.externalViewFactories)),e}getPath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${pe.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getPath()}async addView(){this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),r.shell.addView(this.multiView)}}class Gt extends qt{constructor(t,e){super(t),this.layout=e}layout;getHtml(){return Promise.resolve(this.layout)}}class Ut{constructor(){}static getUI(t){switch(t){case"Oligo Translator":return new Wt;case"Oligo Pattern":return new Yt;case"Oligo Structure":return new zt;default:throw new Error(`Unknown app name: ${t}`)}}}class Wt extends qt{constructor(){super("Oligo Translator");const t=i.iconFA("book",Rt.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel]),this.ui=new Z}topPanel;ui;getHtml(){return this.ui.getHtmlElement()}}class Yt extends qt{constructor(){super("Oligo Pattern"),this.ui=new Ht}ui;getHtml(){return Promise.resolve(this.ui.htmlDivElement)}}class zt extends qt{constructor(){super("Oligo Structure"),this.ui=new ot}ui;getHtml(){return this.ui.getHtmlDivElement()}}var Xt,Zt,Kt=n(895);wu;class Qt{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}(Zt=Xt||(Xt={})).FASTA="fasta",Zt.SEPARATOR="separator",Zt.HELM="helm";const Jt=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};new Qt("PT",Jt.fasta.peptide,.5),new Qt("DNA",Jt.fasta.dna,.55),new Qt("RNA",Jt.fasta.rna,.55);class te extends Float32Array{}class ee{static makePalette(t,e=!1,n=ee){const o={};return t.forEach((t=>{const n=t[0],r=t[1];n.forEach(((t,n)=>{o[t]=this.colourPalette[r][e?0:n]}))})),new n(o)}constructor(t){this._palette=t}get(t){return this._palette[t]}}ee.undefinedColor="rgb(100,100,100)",ee.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class ne extends ee{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,ne)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,ne)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new ne({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in ne.aaSynonyms?ne.aaSynonyms[t]:t;return super.get(e)}}ne.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class oe{static getPalette(t="grok"){switch(t){case"grok":return ne.GrokGroups;case"lesk":return ne.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",o="";for(const r of t)"("==r?e++:")"==r?e--:e?n+=r:o+=r;return isNaN(parseInt(n))?[o,n]:[o,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[o,r]=this.getInnerOuter(t);if(o=o.length>6?`${o.slice(0,3)}...`:o,r=r.length>6?`${r.slice(0,3)}...`:r,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,r,1]:[this.undefinedColor,o,r,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,r,2]:[this.undefinedColor,o,r,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,r,3]:[this.undefinedColor,o,r,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,r,4]:[this.undefinedColor,o,r,4]}return[this.undefinedColor,o,r,0]}}oe.SemType="Aminoacids",oe.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",oe.undefinedColor="rgb(100,100,100)",oe.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},oe.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},oe.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},oe.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class re{}re.SemType="Nucleotides",re.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",re.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class ie{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class se{}class ae extends se{static buildPalette(){return[].concat(...Object.values(ee.colourPalette))}get(t){const e=ie.hashCode(t)%ae.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=o.Color.fromHtml(t),n=o.Color.g(e),r=o.Color.r(e),i=o.Color.b(e),s=Math.sqrt(Math.pow(0-r,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return s>210?`rgb(${r/s*210},${n/s*210},${i/s*210})`:o.Color.toRgb(e)}(ae.palette[e])}}ae.palette=ae.buildPalette();new Uint32Array(65536);var le,ce;(ce=le||(le={})).HAMMING="Hamming",ce.LEVENSHTEIN="Levenshtein",ce.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",le.HAMMING,le.LEVENSHTEIN,le.NEEDLEMANN_WUNSCH,new class{constructor(){this.uhTemp=`units-handler.${o.SEMTYPE.MACROMOLECULE}`}},Xt.FASTA,Xt.SEPARATOR,Xt.HELM;var ue=n(61);function de(){const t=i.textInput("","");return{coloredInput:new L(t,M),codes:O.BF}}class he extends o.Package{_monomerLib;get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}async initMonomerLib(){if(void 0!==this._monomerLib)return;const t=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");await(0,w.Y3)((async()=>{const t=await async function(){const t=o.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}();this._monomerLib=await t.readLibrary(Kt.BX,Kt.a_)}),(()=>t.close()))}}const pe=new he;async function me(t){await xe();const e=Ut.getUI(t);await e.createAppLayout()}async function ge(){await xe();const t=await async function(){const t={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:de()}},e={};for(const[n,o]of Object.entries(t)){let t;try{t=await r.functions.call(n,o.parameters);const i=new Gt(o.tabName,t);i.initView(),e[o.tabName]=()=>i.getView()}catch(t){console.warn(`Plugin ${n} not loaded, reason:`,t);continue}}return e}();if(!t)throw new Error("External app view factories not loaded");const e=new $t(t);await e.createAppLayout()}async function fe(){await me("Oligo Translator")}async function Ae(){await me("Oligo Pattern")}async function ve(){await me("Oligo Structure")}async function xe(){await(0,O.VO)(),await pe.initMonomerLib()}function Ce(){const t=E.A.getInstance().getCodesToWeightsMap();return Object.fromEntries(t)}function be(t){const e=new b.b(t),n=new I(t).getFormat();return null!==n&&e.isValidSequence(n)}function we(t,e){return new k(t,e,"GCRS").convert()}function ye(t){return(0,J.v5)(t,!0)}async function Ee(){await async function(){await(0,w.Y3)((async()=>fe()))}()}async function Oe(){await async function(){await(0,w.Y3)((async()=>{async function t(t,n,o){await(0,ue.gw)(3e3);const r=document.querySelectorAll(".st-pattern-choice-input > select");e=r.length;const i=r[o(n)];i.value=t;const s=new Event("input");i.dispatchEvent(s)}let e;await Ae(),["DNA","invAb","Z-New"].forEach((async(e,n)=>{t(e,n,(t=>2*t))})),["2'-O-Methyl","2'-Fluoro","2'-O-MOE"].forEach((async(n,o)=>{t(n,o,(t=>e-2-2*t))}))}))}()}async function Ie(){await async function(){await(0,w.Y3)((async()=>{await ve(),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await(0,ue.gw)(500);const n=document.querySelectorAll(".colored-text-input > textarea")[t];n.value=e;const o=new Event("input");n.dispatchEvent(o)}(e,t)}))}))}()}async function Se(t,e,n){return await xe(),new X.I(t,e).convertTo(n)}},713:(t,e,n)=>{n.d(e,{AU:()=>o,wm:()=>r});const o="Copied",r="Copy sequence"},511:(t,e,n)=>{n.d(e,{T:()=>o});const o="Afcgacsu"},976:t=>{t.exports=DG},469:t=>{t.exports=grok}},e={};function n(o){var r=e[o];if(void 0!==r)return r.exports;var i=e[o]={id:o,exports:{}};return t[o](i,i.exports,n),i.exports}n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var o in e)n.o(e,o)&&!n.o(t,o)&&Object.defineProperty(t,o,{enumerable:!0,get:e[o]})},n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nc=void 0;var o=n(593);sequencetranslator=o})();
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