@datagrok/helm 2.1.19 → 2.1.22

package/CHANGELOG.md

@@ -13,6 +13,8 @@
 * Prevent display tooltip by fallback cell renderer while WebEditor renders.
 * Reset monomer placer on monomer lib changed.
 * Fix Pistoia Helm WebEditor settings for case-sensitive monomer libs.
+* Fix cell renderer monomer tooltip for polymer type
+* Patch WebEditor hanging on getTextWidth
 
 ## 2.1.16 (2023-07-21)
 

package/dist/package-test.js

@@ -1,2 +1,2 @@
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e.forEach((e=>{const n=e[0],s=e[1];n.forEach(((e,n)=>{r[e]=this.colourPalette[s][t?0:n]}))})),new n(r)}constructor(e){this._palette=e}get(e){return this._palette[e]}}G.undefinedColor="rgb(100,100,100)",G.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 R extends G{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,R)),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,R)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new R({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(e){const t=e in R.aaSynonyms?R.aaSynonyms[e]:e;return super.get(t)}}R.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class D{static getPalette(e="grok"){switch(e){case"grok":return R.GrokGroups;case"lesk":return R.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",r="";for(const s of e)"("==s?t++:")"==s?t--:t?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[r,s]=this.getInnerOuter(e);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,s,1]:[this.undefinedColor,r,s,1]}if("d"==e[0]&&e[1]in n&&(2==e.length||"("==e[2])){const t=e[1]?.toUpperCase();return t in n?[n.get(t),t,s,2]:[this.undefinedColor,r,s,2]}if(e.substring(0,3)in this.AAFullNames&&(3==e.length||"("==e[3])){const t=this.AAFullNames[e.substring(0,3)];return t in n?[n.get(t),t,s,3]:[this.undefinedColor,r,s,3]}if(e[0]?.toLowerCase()==e[0]&&e.substring(1,3)in this.AAFullNames&&(4==e.length||"("==e[4])){const t=this.AAFullNames[e.substring(1,3)];return t in n?[n.get(t),t,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}D.SemType="Aminoacids",D.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",D.undefinedColor="rgb(100,100,100)",D.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"},D.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"},D.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(*)*"},D.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 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makePalette(t,e=!1,n=H){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]}}H.undefinedColor="rgb(100,100,100)",H.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 D extends H{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,D)),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,D)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new D({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 D.aaSynonyms?D.aaSynonyms[t]:t;return super.get(e)}}D.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class k{static getPalette(t="grok"){switch(t){case"grok":return D.GrokGroups;case"lesk":return D.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]}}k.SemType="Aminoacids",k.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",k.undefinedColor="rgb(100,100,100)",k.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"},k.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"},k.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(*)*"},k.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 F{}F.SemType="Nucleotides",F.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",F.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class R extends class{}{static buildPalette(){return[].concat(...Object.values(H.colourPalette))}get(t){const e=class{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}}.hashCode(t)%R.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=n.Color.fromHtml(t),s=n.Color.g(e),i=n.Color.r(e),o=n.Color.b(e),r=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-s,2)+Math.pow(0-o,2));return r>210?`rgb(${i/r*210},${s/r*210},${o/r*210})`:n.Color.toRgb(e)}(R.palette[e])}}R.palette=R.buildPalette();new Uint32Array(65536);var G,B;async function V(){const t=n.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}(B=G||(G={})).HAMMING="Hamming",B.LEVENSHTEIN="Levenshtein",B.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",B.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",G.HAMMING,G.LEVENSHTEIN,G.NEEDLEMANN_WUNSCH,G.MONOMER_CHEMICAL_DISTANCE,new class{constructor(){this.uhTemp=`units-handler.${n.SEMTYPE.MACROMOLECULE}`}},_.FASTA,_.SEPARATOR,_.HELM;const U="Libraries",W={explicit:["HELMCoreLibrary.json"],exclude:[]};let j=Promise.resolve();async function Y(){let t;return j=j.then((async()=>{const e=await s.dapi.userDataStorage.getValue(U,"Settings",!0);t=e?JSON.parse(e):{exclude:[],explicit:[]},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await j,t}async function Q(t){j=j.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),await s.dapi.userDataStorage.postValue(U,"Settings",JSON.stringify(t),!0)})),await j}async function z(){await Q(W)}var K=function(t,e,n,s){return new(n||(n=Promise))((function(i,o){function r(t){try{l(s.next(t))}catch(t){o(t)}}function a(t){try{l(s.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(r,a)}l((s=s.apply(t,e||[])).next())}))};A("findMonomers",(()=>{let t,e;y((()=>K(void 0,void 0,void 0,(function*(){t=yield V(),e=yield Y(),yield z(),yield t.loadLibraries(!0)})))),T((()=>K(void 0,void 0,void 0,(function*(){yield Q(e),yield t.loadLibraries(!0)}))));const n={withoutMissed:{test:"PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set},withMissed:{test:"PEPTIDE1{meI.missed2.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set(["missed2"])}};for(const[t,e]of Object.entries(n))C(t,(()=>K(void 0,void 0,void 0,(function*(){s(e.test,e.tgt)}))));function s(t,e){p(function(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],s=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{s.push(n[t][e].id)}));return new Set(t.filter((t=>!s.includes(t))))}(I(t)),e)}}));const J=$;var X,q=t.n(J),Z=function(t,e,n,s){return new(n||(n=Promise))((function(i,o){function r(t){try{l(s.next(t))}catch(t){o(t)}}function a(t){try{l(s.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(r,a)}l((s=s.apply(t,e||[])).next())}))};A("renderers",(()=>{C("missedInLib",(()=>Z(void 0,void 0,void 0,(function*(){yield function(){return Z(this,void 0,void 0,(function*(){const t=yield s.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),e=t.getCol("HELM"),o=s.shell.addTableView(t);yield function(t,e="Timeout exceeded",n=500,s=50){return i(this,void 0,void 0,(function*(){return new Promise(((i,o)=>{setTimeout((()=>{clearInterval(r),o(new Error(e))}),n);const r=setInterval((()=>{t()&&(clearInterval(r),i())}),s)}))}))}((()=>q()(o.root).find(".d4-grid canvas").length>0),"Table view canvas not found",100),f(e.semType,n.SEMTYPE.MACROMOLECULE),f(e.getTag(n.TAGS.UNITS),_.HELM),f(e.getTag(n.TAGS.CELL_RENDERER),"helm");const r=e.getTag(".cell-renderer.render.error");if(r){const t=JSON.parse(r),e=new Error(t.message);throw e.stack=t.stack,e}}))}()}))))}));class tt extends class{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 s=this.isWhitespace(n)?e:e-1;for(let t=0;t<s;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToAtomType(n),e[s]=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 s=this.getAtomBlockIdx();for(let i=0;i<this.atomCount;i++){s=this.shiftIdxToXColumn(s);for(const o of[t,e,n])o[i]=this.parseFloatValue(s),s=this.getNextColumnIdx(s);s=this.getNextLineIdx(s)}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 s=new Uint16Array(2);s[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),s[1]=this.parseIntValue(e),t[n]=s,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToBondType(n),e[s]=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))}}{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 s=0;s<e;s++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}!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"}(X||(X={}));class et extends tt{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(X.HEADER)&&-1!==t.indexOf(X.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,X.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<X.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,X.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,X.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+X.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=X.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class nt extends tt{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  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}var st=function(t,e,n,s){return new(n||(n=Promise))((function(i,o){function r(t){try{l(s.next(t))}catch(t){o(t)}}function a(t){try{l(s.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(r,a)}l((s=s.apply(t,e||[])).next())}))};A("getMolfiles",(()=>{let t,e;y((()=>st(void 0,void 0,void 0,(function*(){t=yield V(),e=yield Y(),yield z(),yield t.loadLibraries(!0)})))),T((()=>st(void 0,void 0,void 0,(function*(){yield Q(e),yield t.loadLibraries(!0)})))),C("linear1",(()=>st(void 0,void 0,void 0,(function*(){const t=n.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),e=t.getCol("Helm"),o=s.shell.addTableView(t),r=yield s.functions.call("Helm:getMolfiles",{col:e});yield N(100),yield function(t,e,n,s=0){return i(this,void 0,void 0,(function*(){let i;return new Promise(((o,r)=>{i=t.subscribe((t=>{try{e(t)}catch(t){r(t)}i.unsubscribe(),o("OK")})),setTimeout((()=>{i.unsubscribe(),r("timeout")}),s),n()}))}))}(o.grid.onAfterDrawContent,(()=>{}),(()=>{o.grid.invalidate()})),f(r.length,e.length);const a=r.toList().map((t=>class{constructor(){}static getInstance(t){if(et.validate(t))return new et(t);if(nt.validate(t))return new nt(t);throw new Error("Malformed molfile")}}.getInstance(t)));m(a.map((t=>t.atomCount)),t.getCol("atoms").toList()),m(a.map((t=>t.bondCount)),t.getCol("bonds").toList())}))))}));const it=new n.Package;function ot(t,e,o){return c=this,u=void 0,f=function*(){const c=yield function(t){var e,o,c,u,C;return i(this,void 0,void 0,(function*(){const f=null===(o=null===(e=s.functions.getCurrentCall())||void 0===e?void 0:e.func)||void 0===o?void 0:o.package;yield function(t,e){return i(this,void 0,void 0,(function*(){if(l[t])return;const e=r;if(void 0!==e["Auto Tests"]||Object.keys(e).find((t=>t.startsWith(a))))return void(l[t]=!0);const n=[],o=yield s.dapi.functions.filter(`package.id = "${t}"`).list(),c=new RegExp(/skip:\s*([^,\s]+)|wait:\s*(\d+)|cat:\s*([^,\s]+)/g);for(const t of o){const o=t.options.test;if(o&&Array.isArray(o)&&o.length)for(let r=0;r<o.length;r++){const l=o[r].matchAll(c),u={};Array.from(l).forEach((t=>{t[0].startsWith("skip")?u.skip=t[1]:t[0].startsWith("wait")?u.wait=parseInt(t[2]):t[0].startsWith("cat")&&(u.cat=t[3])}));const d=new h(a,1===o.length?t.name:`${t.name} ${r+1}`,(()=>i(this,void 0,void 0,(function*(){const e=yield s.functions.eval(E(o[r],t));if(u.wait&&(yield N(u.wait)),"boolean"==typeof e&&!e)throw`Failed: ${o[r]}, expected true, got ${e}`}))),{skipReason:u.skip});if(u.cat){const t="Auto Tests: "+u.cat;d.category=t,void 0===e[t]&&(e[t]={tests:[],clear:!0}),e[t].tests.push(d)}else n.push(d)}}l[t]=!0,n.length&&(e["Auto Tests"]={tests:n,clear:!0})}))}(f.id);const g=[];console.log("Running tests"),null!=t||(t={}),null!==(c=(C=t).testContext)&&void 0!==c||(C.testContext=new d),s.shell.lastError="";for(const[e,i]of Object.entries(r)){if(null!=(null==t?void 0:t.category)&&!e.toLowerCase().startsWith(null==t?void 0:t.category.toLowerCase()))continue;console.log(`Started ${e} category`);try{i.before&&(yield i.before())}catch(t){i.beforeStatus=t.toString()}const o=null!==(u=i.tests)&&void 0!==u?u:[],r=[];if(i.clear)for(let e=0;e<o.length;e++)r.push(yield b(o[e],null==t?void 0:t.test,i.timeout,f.name)),s.shell.closeAll(),n.Balloon.closeAll();else for(let e=0;e<o.length;e++)r.push(yield b(o[e],null==t?void 0:t.test,i.timeout,f.name));const a=(yield Promise.all(r)).filter((t=>"skipped"!=t.result));try{i.after&&(yield i.after())}catch(t){i.afterStatus=t.toString()}i.afterStatus&&a.push({category:e,name:"init",result:i.afterStatus,success:!1,ms:0,skipped:!1}),i.beforeStatus&&a.push({category:e,name:"init",result:i.beforeStatus,success:!1,ms:0,skipped:!1}),g.push(...a)}if(t.testContext.catchUnhandled&&(yield N(1e3),s.shell.lastError.length>0&&g.push({category:"Unhandled exceptions",name:"exceptions",result:s.shell.lastError,success:!1,ms:0,skipped:!1})),t.testContext.report){const t=new n.Logger,e=g.filter((t=>t.success)).length,s=g.filter((t=>t.skipped)).length,i=g.filter((t=>!t.success)),o="Package @package tested: @successful successful, @skipped skipped, @failed failed tests",r={successful:e,skipped:s,failed:i.length,package:f};for(const t of i)Object.assign(r,{[`${t.category} | ${t.name}`]:t.result});t.log(o,r,"package-tested")}return g}))}({category:t,test:e,testContext:o});return n.DataFrame.fromObjects(c)},new((C=void 0)||(C=Promise))((function(t,e){function n(t){try{i(f.next(t))}catch(t){e(t)}}function s(t){try{i(f.throw(t))}catch(t){e(t)}}function i(e){var i;e.done?t(e.value):(i=e.value,i instanceof C?i:new C((function(t){t(i)}))).then(n,s)}i((f=f.apply(c,u||[])).next())}));var c,u,C,f}helm_test=e})();
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