@datagrok/sequence-translator 1.4.1 → 1.4.3

package/.eslintrc.json

@@ -21,7 +21,7 @@
     ],
     "max-len": ["error", 120],
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-    "max-lines-per-function": ["warn", 100],
+    "max-lines-per-function": ["warn", 300],
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     "no-unused-vars": "off",
     "@typescript-eslint/no-unused-vars": "warn",

package/CHANGELOG.md

@@ -1,5 +1,25 @@
 # Sequence Translator changelog
 
+## 1.4.3 (2024-09-27)
+
+### Features
+
+* Add PolyTool convert reverse
+
+### Bug fixes
+
+* Add sample reaction rule aG + azG = GGaz, test data
+* Fix using MonomerLibHelper.loadMonomerLibForTests
+* Add test toAtomicLevel with overridden monomer lib
+* Fix PolyTool Enumerate for zero-based monomer position
+* Fix Chain.getHelm square brackets for multi char symbols
+
+## 1.4.2 (2024-09-24)
+
+### New features
+
+* Add PolyTool breadth enumerator
+
 ## 1.4.1 (2024-09-12)
 
 ### Bug fixes

package/dist/package-test.js

@@ -1,2 +1,2 @@
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Items"}(st||(st={}));new Uint32Array(65536);var it,rt,ot,at,lt,ct,ht,ut;(rt=it||(it={})).HAMMING="Hamming",rt.LEVENSHTEIN="Levenshtein",rt.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",rt.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",it.HAMMING,it.LEVENSHTEIN,it.NEEDLEMANN_WUNSCH,it.MONOMER_CHEMICAL_DISTANCE,Z.Tanimoto,Z.Dice,Z.Asymmetric,Z.BraunBlanquet,Z.Cosine,Z.Kulczynski,Z.McConnaughey,Z.RogotGoldberg,Z.Russel,Z.Sokal,Z.Hamming,Z.Euclidean,Z.Tanimoto,Z.Dice,Z.Asymmetric,Z.BraunBlanquet,Z.Cosine,Z.Kulczynski,Z.McConnaughey,Z.RogotGoldberg,Z.Russel,Z.Sokal,Z.Hamming,Z.Euclidean,Z.Tanimoto,Z.Dice,Z.Cosine,Z.Tanimoto,Z.Asymmetric,Z.Cosine,Z.Sokal,it.HAMMING,it.LEVENSHTEIN,it.MONOMER_CHEMICAL_DISTANCE,it.NEEDLEMANN_WUNSCH,new RegExp("[rd]\\((\\w)\\)p?","g");class ft{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}wu,(ut=ot||(ot={})).FASTA="fasta",ut.SEPARATOR="separator",ut.HELM="helm",(ht=at||(at={})).DNA="DNA",ht.RNA="RNA",ht.PT="PT",ht.UN="UN",(ct=lt||(lt={})).aligned="aligned",ct.alphabet="alphabet",ct.alphabetSize=".alphabetSize",ct.alphabetIsMultichar=".alphabetIsMultichar",ct.separator="separator",ct.isHelmCompatible=".isHelmCompatible",ct.positionNames=".positionNames",ct.positionLabels=".positionLabels",ct.regions=".regions";const gt=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 ft(at.PT,gt.fasta.peptide,.5),new ft(at.DNA,gt.fasta.dna,.55),new ft(at.RNA,gt.fasta.rna,.55);class dt{static makePalette(t,e=!1,n=dt){const s={};return t.forEach((t=>{const n=t[0],i=t[1];n.forEach(((t,n)=>{s[t]=this.colourPalette[i][e?0:n]}))})),new n(s)}constructor(t){this._palette=t}get(t){return this._palette[t]}}dt.undefinedColor="rgb(100,100,100)",dt.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 yt extends dt{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,yt)),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,yt)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new yt({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 yt.aaSynonyms?yt.aaSynonyms[t]:t;return super.get(e)}}yt.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class pt{static getPalette(t="grok"){switch(t){case"grok":return yt.GrokGroups;case"lesk":return yt.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",s="";for(const i of t)"("==i?e++:")"==i?e--:e?n+=i:s+=i;return isNaN(parseInt(n))?[s,n]:[s,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[s,i]=this.getInnerOuter(t);if(s=s.length>6?`${s.slice(0,3)}...`:s,i=i.length>6?`${i.slice(0,3)}...`:i,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,i,1]:[this.undefinedColor,s,i,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,i,2]:[this.undefinedColor,s,i,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,i,3]:[this.undefinedColor,s,i,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,i,4]:[this.undefinedColor,s,i,4]}return[this.undefinedColor,s,i,0]}}pt.SemType="Aminoacids",pt.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",pt.undefinedColor="rgb(100,100,100)",pt.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"},pt.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"},pt.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(*)*"},pt.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 Ct{}Ct.SemType="Nucleotides",Ct.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",Ct.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class mt{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 xt{}class bt extends xt{static buildPalette(){return[].concat(...Object.values(dt.colourPalette))}get(e){const n=mt.hashCode(e)%bt.palette.length;return function(e){if(null==e)return"rgb(100,100,100)";const n=t.Color.fromHtml(e),s=t.Color.g(n),i=t.Color.r(n),r=t.Color.b(n),o=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-s,2)+Math.pow(0-r,2));return o>210?`rgb(${i/o*210},${s/o*210},${r/o*210})`:t.Color.toRgb(n)}(bt.palette[n])}}async function At(){const e=t.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}bt.palette=bt.buildPalette(),new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},ot.FASTA,ot.SEPARATOR,ot.HELM;const Et="Libraries",vt={explicit:["HELMCoreLibrary.json","polytool-lib.json"],exclude:[],duplicateMonomerPreferences:{}};let Tt=Promise.resolve();async function Nt(){let t;return Tt=Tt.then((async()=>{const n=await e.dapi.userDataStorage.getValue(Et,"Settings",!0);t=n?JSON.parse(n):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],t.duplicateMonomerPreferences=t.duplicateMonomerPreferences instanceof Object?t.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await Tt,t}async function Pt(t){Tt=Tt.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),await e.dapi.userDataStorage.postValue(Et,"Settings",JSON.stringify(t),!0)})),await Tt}async function wt(){await Pt(vt)}class $t{constructor(t,e){this.linkages=e,this.monomers=t}static fromHelm(t){const e=t.split("$"),n=e[0].split("|"),s=e[1].split("|"),i=new Array(n.length),r=[];for(let t=0;t<n.length;t++){const e=n[t].indexOf("{"),s=n[t].indexOf("}");i[t]=n[t].slice(e+1,s).split(".")}for(let t=0;t<s.length;t++)if(""!==s[t]&&"V2.0"!==s[t]){const e=s[t].split(","),n=e[0].replace("PEPTIDE","")-1,i=e[1].replace("PEPTIDE","")-1,o=e[2].split("-"),a=o[0].split(":"),l=o[1].split(":");r.push({fChain:n,sChain:i,fMonomer:a[0],sMonomer:l[0],fR:a[1].replace("R",""),sR:l[1].replace("R","")})}return new $t(i,r)}static fromNotation(t,e){const n=e.heterodimerCode,s=e.homodimerCode,i=[],r=[],o=null!==n?t.split(`(${e.heterodimerCode})`):"";null!==n&&o.length>1?(r.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),i.push(o[1].replaceAll("{","").replaceAll("}","")),i.push(o[2].replaceAll("{","").replaceAll("}",""))):i.push(t);for(let t=0;t<i.length;t++)if(null!==s&&i[t].includes(`(${s})`)){const e=i.length;r.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=i[t].replace(`(${s})`,""),o=n.indexOf("{"),a=n.slice(0,o),l=n.replace(a,"").replaceAll("{","").replaceAll("}","");i[t]=a+l,i.push(l)}const a=new Array(i.length);for(let t=0;t<i.length;t++){const n=i[t].split("-"),s=this.getLinkedPositions(n,e.linkRules),[o,l,c,h,u]=this.getAllCycles(e.linkRules,n,s),f=new Array(o.length);for(let t=0;t<o.length;t++)f[t]=`[${o[t]}]`;for(let e=0;e<l.length;e++)r.push({fChain:t,sChain:t,fMonomer:l[e],sMonomer:c[e],fR:h[e],sR:u[e]});a[t]=f}return new $t(a,r)}getHelmChanged(t,e){let n=0,s=0,i=0;t:for(let e=0;e<this.monomers.length;e++)for(let r=0;r<this.monomers[e].length;r++){if(n==t){s=e,i=r;break t}n++}const r=this.monomers[s][i];this.monomers[s][i]=`[${e}]`;const o=this.getHelm();return this.monomers[s][i]=r,o}getHelm(){let t="";for(let e=0;e<this.monomers.length;e++){e>0&&(t+="|"),t+=`PEPTIDE${e+1}{`;for(let n=0;n<this.monomers[e].length;n++)n>0&&(t+="."),t+=this.monomers[e][n];t+="}"}t+="$";for(let e=0;e<this.linkages.length;e++)e>0&&(t+="|"),t+=`PEPTIDE${this.linkages[e].fChain+1},PEPTIDE${this.linkages[e].sChain+1},`,t+=`${this.linkages[e].fMonomer}:R${this.linkages[e].fR}-`,t+=`${this.linkages[e].sMonomer}:R${this.linkages[e].sR}`;return t+="$$$",t}static getLinkedPositions(t,e){const n=new Array(e.length);for(let s=0;s<e.length;s++){let i=!1,r=!1,o=!1,a=-1,l=-1;const c=`(${e[s].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(i){if(o&&t[n]==e[s].secondMonomer+c){r=!0,l=n;break}if(o||t[n]!=e[s].firstMonomer+c)continue;r=!0,l=n;break}if(t[n]==e[s].firstMonomer+c)i=!0,o=!0,a=n;else{if(t[n]!=e[s].secondMonomer+c)continue;i=!0,o=!1,a=n}}n[s]=i&&r?o?[a,l]:[l,a]:[-1,-1]}return n}static getAllCycles(t,e,n){const s=[],i=[],r=[],o=[],a=t.length;for(let l=0;l<a;l++){if(-1==n[l][0])continue;const 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t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,s=this.lengthInInts;for(let t=0;t<s;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,s=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(s)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,s=!0,o=!0){if(n&&o&&this.setAll(!e,!1),o)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(s)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return J.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return 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Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const s=this._length;this.setLength(this._length+e);for(let n=s-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let s=t;s<t+e;s++)this.setBit(s,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let 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Items"}(ot||(ot={}));new Uint32Array(65536);var rt,it,at,lt,ct,ht,ut,ft;(it=rt||(rt={})).HAMMING="Hamming",it.LEVENSHTEIN="Levenshtein",it.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",it.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",rt.HAMMING,rt.LEVENSHTEIN,rt.NEEDLEMANN_WUNSCH,rt.MONOMER_CHEMICAL_DISTANCE,tt.Tanimoto,tt.Dice,tt.Asymmetric,tt.BraunBlanquet,tt.Cosine,tt.Kulczynski,tt.McConnaughey,tt.RogotGoldberg,tt.Russel,tt.Sokal,tt.Hamming,tt.Euclidean,tt.Tanimoto,tt.Dice,tt.Asymmetric,tt.BraunBlanquet,tt.Cosine,tt.Kulczynski,tt.McConnaughey,tt.RogotGoldberg,tt.Russel,tt.Sokal,tt.Hamming,tt.Euclidean,tt.Tanimoto,tt.Dice,tt.Cosine,tt.Tanimoto,tt.Asymmetric,tt.Cosine,tt.Sokal,rt.HAMMING,rt.LEVENSHTEIN,rt.MONOMER_CHEMICAL_DISTANCE,rt.NEEDLEMANN_WUNSCH,new RegExp("[rd]\\((\\w)\\)p?","g"),wu;class gt{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}(ft=at||(at={})).FASTA="fasta",ft.SEPARATOR="separator",ft.HELM="helm",ft.CUSTOM="custom",(ut=lt||(lt={})).DNA="DNA",ut.RNA="RNA",ut.PT="PT",ut.UN="UN",(ht=ct||(ct={})).aligned="aligned",ht.alphabet="alphabet",ht.alphabetSize=".alphabetSize",ht.alphabetIsMultichar=".alphabetIsMultichar",ht.separator="separator",ht.isHelmCompatible=".isHelmCompatible",ht.positionNames=".positionNames",ht.positionLabels=".positionLabels",ht.regions=".regions";const mt=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 gt(lt.PT,mt.fasta.peptide,.5),new gt(lt.DNA,mt.fasta.dna,.55),new gt(lt.RNA,mt.fasta.rna,.55),at.FASTA,at.SEPARATOR,at.HELM;class dt{static makePalette(t,e=!1,n=dt){const s={};return t.forEach((t=>{const n=t[0],o=t[1];n.forEach(((t,n)=>{s[t]=this.colourPalette[o][e?0:n]}))})),new n(s)}constructor(t){this._palette=t}get(t,e){return this._palette[t]}}dt.undefinedColor="rgb(100,100,100)",dt.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 pt extends dt{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,pt)),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,pt)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new pt({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 pt.aaSynonyms?pt.aaSynonyms[t]:t;return super.get(e)}}pt.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class yt{static getPalette(t="grok"){switch(t){case"grok":return pt.GrokGroups;case"lesk":return pt.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",s="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:s+=o;return isNaN(parseInt(n))?[s,n]:[s,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[s,o]=this.getInnerOuter(t);if(s=s.length>6?`${s.slice(0,3)}...`:s,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,s,o,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,o,2]:[this.undefinedColor,s,o,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,o,3]:[this.undefinedColor,s,o,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,o,4]:[this.undefinedColor,s,o,4]}return[this.undefinedColor,s,o,0]}}yt.SemType="Aminoacids",yt.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",yt.undefinedColor="rgb(100,100,100)",yt.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"},yt.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"},yt.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(*)*"},yt.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 Ct{}function xt(e,n=!0){if(null==e)return"rgb(100,100,100)";const s=t.Color.fromHtml(e);if(n){const e=t.Color.g(s),n=t.Color.r(s),o=t.Color.b(s),r=Math.sqrt(Math.pow(0-n,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(r>210)return`rgb(${n/r*210},${e/r*210},${o/r*210})`}return t.Color.toRgb(s)}Ct.SemType="Nucleotides",Ct.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",Ct.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class Et{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 bt{}class At extends bt{static buildPalette(){return $t().then((t=>{t.awaitLoaded().then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{At.customMonomerColors={},At.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const s of n){const n=e.getMonomer(t,s);n?.meta?.colors?.default?.background&&(this.customMonomerColors[s]||(this.customMonomerColors[s]={}),this.customMonomerColors[s][t]=xt(n.meta.colors.default.background,!1))}}}))}))})),[].concat(...Object.values(dt.colourPalette))}get(t,e){const n=At.customMonomerColors[t],s=e??"PEPTIDE";if(n&&n[s])return n[s];const o=Et.hashCode(t)%At.palette.length;return xt(At.palette[o])}}async function $t(){const e=t.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}At.palette=At.buildPalette(),At.customMonomerColors={},At.polymerTypes=[],new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};const Pt="Libraries";let Tt=Promise.resolve();async function Nt(){let t;return Tt=Tt.then((async()=>{const n=await e.dapi.userDataStorage.getValue(Pt,"Settings",!0);t=n?JSON.parse(n):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],t.duplicateMonomerPreferences=t.duplicateMonomerPreferences instanceof Object?t.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await Tt,t}async function vt(t){Tt=Tt.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),await e.dapi.userDataStorage.postValue(Pt,"Settings",JSON.stringify(t),!0)})),await Tt}class wt{constructor(t,e){this.linkages=e,this.monomers=t}static fromHelm(t){const e=t.split("$"),n=e[0].split("|"),s=e[1].split("|"),o=new Array(n.length),r=[];for(let t=0;t<n.length;t++){const e=n[t].indexOf("{"),s=n[t].indexOf("}");o[t]=n[t].slice(e+1,s).split(".")}for(let t=0;t<s.length;t++)if(""!==s[t]&&"V2.0"!==s[t]){const e=s[t].split(","),n=e[0].replace("PEPTIDE","")-1,o=e[1].replace("PEPTIDE","")-1,i=e[2].split("-"),a=i[0].split(":"),l=i[1].split(":");r.push({fChain:n,sChain:o,fMonomer:a[0],sMonomer:l[0],fR:a[1].replace("R",""),sR:l[1].replace("R","")})}return new wt(o,r)}static fromNotation(t,e){const n=e.heterodimerCode,s=e.homodimerCode,o=[],r=[],i=null!==n?t.split(`(${e.heterodimerCode})`):"";null!==n&&i.length>1?(r.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),o.push(i[1].replaceAll("{","").replaceAll("}","")),o.push(i[2].replaceAll("{","").replaceAll("}",""))):o.push(t);for(let t=0;t<o.length;t++)if(null!==s&&o[t].includes(`(${s})`)){const e=o.length;r.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=o[t].replace(`(${s})`,""),i=n.indexOf("{"),a=n.slice(0,i),l=n.replace(a,"").replaceAll("{","").replaceAll("}","");o[t]=a+l,o.push(l)}for(let t=0;t<o.length;t++)if(null!==s&&o[t].includes(`(${s})`)){const e=o.length;r.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=o[t].replace(`(${s})`,""),i=n.indexOf("{"),a=n.slice(0,i),l=n.replace(a,"").replaceAll("{","").replaceAll("}","");o[t]=a+l,o.push(l)}const a=new Array(o.length);for(let t=0;t<o.length;t++){const n=o[t].split("-"),s=this.getLinkedPositions(n,e.linkRules),[i,l,c,h,u]=this.getAllCycles(e.linkRules,n,s);new Array(i.length);for(let e=0;e<l.length;e++)r.push({fChain:t,sChain:t,fMonomer:l[e],sMonomer:c[e],fR:h[e],sR:u[e]});a[t]=i}const l=[];for(let t=0;t<a.length;t++){const n=this.getLinkedPositions(a[t],e.reactionRules),[s,o,i,c]=this.getAllReactants(e.reactionRules,a[t],n);if(o.length>=1){const t=new Array(i[0]-1),n=new Array(s.length-i[0]);for(let e=0;e<i[0]-1;e++)t[e]=s[e];for(let t=i[0];t<s.length;t++)n[t-i[0]]=s[t];t[o[0]-1]=e.reactionRules[c[0]].name;for(let t=0;t<r.length;t++)r[t].fMonomer>i[0]&&(r[t].fMonomer-=i[0],r[t].fChain++),r[t].sMonomer>i[0]&&(r[t].sMonomer-=i[0],r[t].sChain++);r.push({fChain:0,sChain:0,fMonomer:o[0],sMonomer:i[0]-1,fR:3,sR:2}),r.push({fChain:0,sChain:1,fMonomer:o[0],sMonomer:1,fR:4,sR:1});const a=new Array(t.length);for(let e=0;e<t.length;e++)a[e]=`[${t[e]}]`;const h=new Array(n.length);for(let t=0;t<n.length;t++)h[t]=`[${n[t]}]`;l.push(t),l.push(n)}else l.push(a[t])}return new wt(l,r)}getHelmChanged(t,e){let n=0,s=0,o=0;t:for(let e=0;e<this.monomers.length;e++)for(let r=0;r<this.monomers[e].length;r++){if(n==t){s=e,o=r;break t}n++}const r=this.monomers[s][o];this.monomers[s][o]=`[${e}]`;const i=this.getHelm();return this.monomers[s][o]=r,i}getHelm(){let t="";for(let e=0;e<this.monomers.length;e++){e>0&&(t+="|"),t+=`PEPTIDE${e+1}{`;for(let n=0;n<this.monomers[e].length;n++){n>0&&(t+=".");const s=this.monomers[e][n];t+=s.length>1?`[${s}]`:s}t+="}"}t+="$";for(let e=0;e<this.linkages.length;e++)e>0&&(t+="|"),t+=`PEPTIDE${this.linkages[e].fChain+1},PEPTIDE${this.linkages[e].sChain+1},`,t+=`${this.linkages[e].fMonomer}:R${this.linkages[e].fR}-`,t+=`${this.linkages[e].sMonomer}:R${this.linkages[e].sR}`;return t+="$$$",t}getNotation(t){return"not implemented"}static getLinkedPositions(t,e){const n=new Array(e.length);for(let s=0;s<e.length;s++){let o=!1,r=!1,i=!1,a=-1,l=-1;const c=`(${e[s].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(o){if(i&&t[n]==e[s].secondMonomer+c){r=!0,l=n;break}if(i||t[n]!=e[s].firstMonomer+c)continue;r=!0,l=n;break}if(t[n]==e[s].firstMonomer+c)o=!0,i=!0,a=n;else{if(t[n]!=e[s].secondMonomer+c)continue;o=!0,i=!1,a=n}}n[s]=o&&r?i?[a,l,s]:[l,a,s]:[-1,-1,-1]}return n}static getAllCycles(t,e,n){const s=[],o=[],r=[],i=[],a=t.length;for(let l=0;l<a;l++){if(-1==n[l][0])continue;const a=e[n[l][0]],c=e[n[l][1]];e[n[l][0]]=e[n[l][0]].replace(a,t[l].firstSubstitution),e[n[l][1]]=e[n[l][1]].replace(c,t[l].secondSubstitution),s.push(n[l][0]+1),o.push(n[l][1]+1),r.push(t[l].firstLinkingGroup),i.push(t[l].secondLinkingGroup)}return[e,s,o,r,i]}static getAllReactants(t,e,n){const s=[],o=[],r=[],i=t.length;for(let a=0;a<i;a++){if(-1==n[a][0])continue;const i=e[n[a][0]],l=e[n[a][1]];e[n[a][0]]=e[n[a][0]].replace(i,t[a].firstMonomer),e[n[a][1]]=e[n[a][1]].replace(l,t[a].secondMonomer),s.push(n[a][0]+1),o.push(n[a][1]+1),r.push(n[a][2])}return[e,s,o,r]}}function Ot(t,e){const n=new Array(t.length);for(let s=0;s<t.length;s++)if(null==t[s])n[s]="";else{const o=wt.fromNotation(t[s],e);n[s]=o.getHelm()}return n}const _t=ui,Lt="System:AppData/SequenceTranslator/polytool-rules/";async function It(n){const s=new t.FileSource(Lt),o=[],r=[],i={homodimerCode:null,heterodimerCode:null,linkRules:o,reactionRules:r};for(let t=0;t<n.length;t++){const a=await s.readAsText(n[t].replace(Lt,"")),l=JSON.parse(a);for(let t=0;t<l.length;t++)if(void 0!==l[t].type&&void 0!==l[t].code)switch(l[t].type){case"link":{const e=l[t].monomericSubstitution;e.code=l[t].code,o.push(e);break}case"reaction":{const e=l[t].monomericSubstitution;e.code=l[t].code,r.push(e);break}case"fragmentDuplication":i.homodimerCode&&e.shell.warning("PolyTool: homodimer code is duplicated in rules."),i.homodimerCode=l[t].code;break;case"differentFragments":i.heterodimerCode&&e.shell.warning("PolyTool: heterodimer code is duplicated in rules."),i.heterodimerCode=l[t].code;break;default:e.shell.warning(`PolyTool: Unexpected type - '${l[t]}'.`)}else e.shell.warning("Polytool: rules contain invalid rule")}return i}async function Rt(){const e="Helm",n=t.Func.find({package:e,name:"getHelmHelper"});if(0===n.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await n[0].prepare().call()).getOutputParamValue()}var Mt;function Dt(t,e,n,s){const o=new Array(s.length*(n-e+1));for(let r=0;r<s.length;++r){const i=n-e+1;for(let n=0;n<i;++n){const a=e+n,l=s[r],c=o[r*i+n]=t.clone(),h=c.atoms[a].elem;c.atoms[a].elem=l;const u=h?.length>1?`[${h}]`:h,f=l?.length>1?`[${l}]`:l;c.name=`${t.name}-${u}${a+1}${f}`}}return o}function Gt(t,e,n){const s=new JSDraw2.MolHandler,o=new org.helm.webeditor.Plugin(s);org.helm.webeditor.IO.parseHelm(o,t,new JSDraw2.Point(0,0),void 0);const r=s.m;r.name=e;let i=[];if(n.placeholders)switch(n.type){case Mt.Single:i=function(t,e){return e.map((e=>Dt(t,e.position,e.position,e.monomers))).reduce(((t,e)=>t.concat(e)),[])}(s.m,n.placeholders);break;case Mt.Matrix:i=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>Dt(e,t.position,t.position,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(s.m,n.placeholders)}let a=[];n.placeholdersBreadth&&(a=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>Dt(e,t.start,t.end,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(s.m,n.placeholdersBreadth)),i=i.concat(a),n.keepOriginal&&(i=[r,...i]);const l=i.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return l}v("PolyTool: Convert",(()=>{let n,s;w((async()=>{n=await $t(),s=await Nt(),await n.loadMonomerLibForTests()})),O((async()=>{await vt(s),await n.loadMonomerLib(!0)}));const o={cyclized:{src:["R-F-C(1)-T-G-H-F-Y-P-C(1)-meI","C(1)-T-G-H-F-Y-P-C(1)-meI","R-F-C(1)-T-G-H-F-Y-P-C(1)","C(1)-T-G-H-F-H-P-C(1)","R-F-D(2)-T-G-H-F-Y-P-NH2(2)"],tgt:["PEPTIDE1{R.F.C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$","PEPTIDE1{C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$","PEPTIDE1{R.F.C.T.G.H.F.Y.P.C}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$","PEPTIDE1{C.T.G.H.F.H.P.C}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$","PEPTIDE1{R.F.D.T.G.H.F.Y.P.[NH2]}$PEPTIDE1,PEPTIDE1,10:R2-3:R3$$$"]}};for(const[t,e]of Object.entries(o))A(`${t}`,(async()=>{const t=await It(["rules_example.json"]);N(Ot(e.src,t),e.tgt)}));A("ui-col-wo-table",(async()=>{const n=Ht.name,s=t.Column.fromStrings("seq",o.cyclized.src),r=await e.functions.call(`${n}:polyToolConvert2`,{seqCol:s,generateHelm:!0,chiralityEngine:!0,rules:["rules_example.json"]});$(r.semType,t.SEMTYPE.MACROMOLECULE),$(r.meta.units,at.HELM),$(r.dataFrame,null)})),A("ui-col",(async()=>{const n=Ht.name,s=t.Column.fromStrings("seq",o.cyclized.src),i=t.DataFrame.fromColumns([s]),a=e.shell.addTableView(i),l=await e.functions.call(`${n}:polyToolConvert2`,{seqCol:s,generateHelm:!0,chiralityEngine:!0,rules:["rules_example.json"]});$(l.semType,t.SEMTYPE.MACROMOLECULE),$(l.meta.units,at.HELM),$(l.dataFrame.id,i.id),await function(t,e,n,s=0,o="timeout"){return r(this,void 0,void 0,(function*(){return new Promise(((r,i)=>{const a=t.subscribe((t=>{try{e(t),r("OK")}catch(t){i(t)}finally{a.unsubscribe(),clearTimeout(l)}})),l=setTimeout((()=>{a.unsubscribe(),i(o)}),s);n()}))}))}(a.grid.onAfterDrawContent,(()=>{}),(async()=>{a.grid.invalidate()}),15e3),$(l.getTag(t.TAGS.CELL_RENDERER),"helm")}))})),t.JsInputBase,Error,_t.input.helmAsync=async function(t,e){return(await Rt()).createHelmInput(t,e)},function(t){t.Single="single",t.Matrix="matrix"}(Mt||(Mt={})),v("PolyTool: Enumerate",(()=>{let t,e,n;w((async()=>{t=await Rt(),e=await $t(),n=await Nt(),await e.loadMonomerLibForTests()})),O((async()=>{await vt(n),await e.loadMonomerLib(!0)}));const 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e[0].prepare().call()).getOutputParamValue()}(),c=t.Column.fromList(t.COLUMN_TYPE.STRING,"helm",["PEPTIDE1{F.P.Y.[GGaz].H.A.A.G.G.A.C}|PEPTIDE2{A.A.A}$PEPTIDE1,PEPTIDE2,4:R4-1:R1|PEPTIDE1,PEPTIDE1,11:R2-4:R3$$$V2.0"]);c.semType=t.SEMTYPE.MACROMOLECULE,c.meta.units=at.HELM;const h=await l.helmToAtomicLevel(c,!1,!1,a);$(null!=h.molCol,!0,"Result molCol is null");const u=h.molCol.get(0);$(!!u,!0,"Molfile is empty");const f=s.get_mol(u);try{const t=f.get_inchi(),e=s.get_inchikey_for_inchi(t);$(f.get_num_bonds(),103),$(f.get_num_atoms(),98),$(e,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{f.delete()}}))}));const Ht=new k;async function St(e,n,s){const o=await I({category:e,test:n,testContext:s,verbose:!0});return t.DataFrame.fromObjects(o)}async function Ft(){await L(Ht,Ht.getModule("package-test.js"))}})(),sequencetranslator_test=s})();
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