@datagrok/bio 2.22.7 → 2.22.8

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Files changed (7) hide show
  1. package/dist/package-test.js +1 -1
  2. package/dist/package-test.js.map +1 -1
  3. package/dist/package.js +1 -1
  4. package/dist/package.js.map +1 -1
  5. package/package.json +2 -2
  6. package/test-console-output-1.log +365 -366
  7. package/test-record-1.mp4 +0 -0
package/dist/package.js CHANGED
@@ -1,4 +1,4 @@
1
- var bio;(()=>{var e={8924:(e,t,n)=>{"use strict";var i=n(7362);class o extends i.e{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,o)),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,o)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new o({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 o.aaSynonyms?o.aaSynonyms[e]:e;return super.get(t)}}o.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class r{static getPalette(e="grok"){switch(e){case"grok":return o.GrokGroups;case"lesk":return o.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",i="";for(const o of e)"("==o?t++:")"==o?t--:t?n+=o:i+=o;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[i,o]=this.getInnerOuter(e);if(i=i.length>6?`${i.slice(0,3)}...`:i,o=o.length>6?`${o.slice(0,3)}...`:o,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,o,1]:[this.undefinedColor,i,o,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,o,2]:[this.undefinedColor,i,o,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,o,3]:[this.undefinedColor,i,o,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,o,4]:[this.undefinedColor,i,o,4]}return[this.undefinedColor,i,o,0]}}r.SemType="Aminoacids",r.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",r.undefinedColor="rgb(100,100,100)",r.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"},r.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"},r.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(*)*"},r.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"}},6717:(e,t,n)=>{"use strict";n.d(t,{j:()=>o});var i=n(6082);async function o(){const e=i.Func.find({package:"Chem",name:"getRdKitModule"});if(0===e.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await e[0].prepare().call()).getOutputParamValue()}},3599:(e,t,n)=>{"use strict";n.d(t,{o:()=>i.o});var i=n(6869)},9124:(e,t,n)=>{"use strict";n.d(t,{b2:()=>r,fA:()=>s});var i=n(7389),o=n(6082);async function r(){const e="Helm",t=o.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}function s(e,t){if(!e)throw new Error("Argument 'a' of type Atom or HelmType is mandatory.");let n,i;const o=e;return"ATOM"===o.T?(n=o.biotype(),i=o.elem):(n=e,i=t),[n,i]}o.JsInputBase,Error,i.input.helmAsync=async function(e,t){return(await r()).createHelmInput(e,t)}},8438:(e,t,n)=>{"use strict";function i(e){return e.startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e}n.d(t,{D:()=>i})},8123:(e,t,n)=>{"use strict";n.d(t,{u:()=>i});const i={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},4356:(e,t,n)=>{"use strict";n.d(t,{Eu:()=>a,ub:()=>s});var i=n(4328);const o="Libraries";let r=Promise.resolve();async function s(){let e;return r=r.then((async()=>{const t=i.userSettings.getValue(o,"Settings",!0);e=t?JSON.parse(t):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},e.exclude=e.exclude instanceof Array?e.exclude:[],e.explicit=e.explicit instanceof Array?e.explicit:[],e.duplicateMonomerPreferences=e.duplicateMonomerPreferences instanceof Object?e.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(e,void 0,2)}`)})),await r,e}async function a(e){r=r.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(e,void 0,2)}`),i.userSettings.add(o,"Settings",JSON.stringify(e),!0)})),await r}},5553:(e,t,n)=>{"use strict";n.d(t,{Qc:()=>S,WN:()=>A});var i=n(1991),o=n.n(i);const r="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,s=new Set,a="object"==typeof process&&process?process:{},l=(e,t,n,i)=>{"function"==typeof a.emitWarning?a.emitWarning(e,t,n,i):console.error(`[${n}] ${t}: ${e}`)};let c=globalThis.AbortController,u=globalThis.AbortSignal;if(void 0===c){u=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(e,t){this._onabort.push(t)}},c=class{constructor(){t()}signal=new u;abort(e){if(!this.signal.aborted){this.signal.reason=e,this.signal.aborted=!0;for(const t of this.signal._onabort)t(e);this.signal.onabort?.(e)}}};let e="1"!==a.env?.LRU_CACHE_IGNORE_AC_WARNING;const t=()=>{e&&(e=!1,l("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.","NO_ABORT_CONTROLLER","ENOTSUP",t))}}Symbol("type");const h=e=>e&&e===Math.floor(e)&&e>0&&isFinite(e),d=e=>h(e)?e<=Math.pow(2,8)?Uint8Array:e<=Math.pow(2,16)?Uint16Array:e<=Math.pow(2,32)?Uint32Array:e<=Number.MAX_SAFE_INTEGER?p:null:null;class p extends Array{constructor(e){super(e),this.fill(0)}}class m{heap;length;static#e=!1;static create(e){const t=d(e);if(!t)return[];m.#e=!0;const n=new m(e,t);return m.#e=!1,n}constructor(e,t){if(!m.#e)throw new TypeError("instantiate Stack using Stack.create(n)");this.heap=new t(e),this.length=0}push(e){this.heap[this.length++]=e}pop(){return this.heap[--this.length]}}class g{#t;#n;#i;#o;#r;#s;ttl;ttlResolution;ttlAutopurge;updateAgeOnGet;updateAgeOnHas;allowStale;noDisposeOnSet;noUpdateTTL;maxEntrySize;sizeCalculation;noDeleteOnFetchRejection;noDeleteOnStaleGet;allowStaleOnFetchAbort;allowStaleOnFetchRejection;ignoreFetchAbort;#a;#l;#c;#u;#h;#d;#p;#m;#g;#f;#y;#b;#v;#w;#C;#S;#A;static unsafeExposeInternals(e){return{starts:e.#v,ttls:e.#w,sizes:e.#b,keyMap:e.#c,keyList:e.#u,valList:e.#h,next:e.#d,prev:e.#p,get head(){return e.#m},get tail(){return e.#g},free:e.#f,isBackgroundFetch:t=>e.#x(t),backgroundFetch:(t,n,i,o)=>e.#M(t,n,i,o),moveToTail:t=>e.#E(t),indexes:t=>e.#T(t),rindexes:t=>e.#_(t),isStale:t=>e.#I(t)}}get max(){return this.#t}get maxSize(){return this.#n}get calculatedSize(){return this.#l}get size(){return this.#a}get fetchMethod(){return this.#r}get memoMethod(){return this.#s}get dispose(){return this.#i}get disposeAfter(){return 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r().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:v}))).toArray()})).toArray();for(let e=0;e<m;e++){const n=g[e],i=Math.floor(e*f),r=e===m-1?d:Math.floor((e+1)*f);y[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:w,monomersDict:t,alphabet:o,polymerType:l,start:i,end:r})}const C=[],S=[];await Promise.all(y).then((e=>{for(const t of e)C.push(...t.molfiles),S.push(...t.warnings)})),setTimeout((()=>{g.forEach((e=>{e.terminate()}))}),0);const A=(0,s.qj)(p,e.name),x=i.Column.fromType(i.COLUMN_TYPE.STRING,A,e.length).init((e=>C[e]?.molfile));return x.semType=i.SEMTYPE.MOLECULE,x.meta.units=i.UNITS.Molecule.MOLBLOCK,x.setTag(".sequence-src-col",e.name),{molCol:x,warnings:S}}function c(e,t){const n={},o={};for(const r of e){const e=t.getWebEditorMonomer(r.biotype,r.symbol).backgroundcolor,a=(0,s.vG)(e??i.Color.toRgb(i.Color.mouseOverRows))??[1,0,0,.7];for(const e of r.atoms)n[e]=a;for(const e of 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C={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},S={sugar:v,phosphate:w,seqLength:e.length,atomCount:c,bondCount:h},A=new o.Cg,x=[];let M,E=0;for(C.i=0;C.i<S.seqLength;++C.i){const n=e[C.i];if(n.symbol===s._S)continue;const i=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});M=i.terminalR2Atom;const r=C.nodeShift,l=C.bondShift;b(i,f,y,C,S),i.stereoAtoms?.forEach((e=>x.push(e+E))),E+=i.atoms.x.length;const c=C.nodeShift-r,u=new Array(c);for(let e=0;e<c;++e)u[e]=r+e;const h=C.bondShift-l,d=new Array(h);for(let e=0;e<h;++e)d[e]=l+e;A.set(C.i,{biotype:n.biotype,symbol:n.symbol,atoms:u,bonds:d})}p&&function(e,t,n,o,r=i.u.OXYGEN){const s=n.nodeShift+1;e[o.atomCount]=i.u.V3K_BEGIN_DATA_LINE+s+" "+(r??i.u.OXYGEN)+" "+g(n.backbonePositionShift[0])+" "+n.flipFactor*g(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;t[o.bondCount]=i.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(f,y,C,S,M??i.u.OXYGEN);const T=i.u.V3K_BEGIN_COUNTS_LINE+c+" "+h+i.u.V3K_COUNTS_LINE_ENDING;let _="";return _+=i.u.V3K_HEADER_FIRST_LINE,_+=i.u.V3K_HEADER_SECOND_LINE,_+=i.u.V3K_BEGIN_CTAB_BLOCK,_+=T,_+=i.u.V3K_BEGIN_ATOM_BLOCK,_+=f.join(""),_+=i.u.V3K_END_ATOM_BLOCK,_+=i.u.V3K_BEGIN_BOND_BLOCK,_+=y.join(""),_+=i.u.V3K_END_BOND_BLOCK,x.length>0&&(_+=function(e){const t=[];let n=`M V30 MDLV30/STEABS ATOMS=(${e.length}`;for(let i=0;i<e.length;i++){const o=`${n} ${e[i]}`;o.length>76?(t.push(`${n} -\n`),n=`M V30 ${e[i]}`):n=o,i===e.length-1&&t.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${t.join("")}M V30 END COLLECTION\n`}(x)),_+=i.u.V3K_END_CTAB_BLOCK,_+=i.u.V3K_END,{molfile:_,monomers:A}}function u(e,t,n,i){i.flipFactor=(-1)**(i.i%2),h(e,t,n,i)}function h(e,t,n,o){!function(e,t,n){for(let o=0;o<e.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;t[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.atoms.atomTypes[o]+" "+g(n.backbonePositionShift[0]+e.atoms.x[o])+" "+g(n.backbonePositionShift[1]+n.flipFactor*e.atoms.y[o])+" "+e.atoms.kwargs[o]}}(e,t,o),p(e,n,o),function(e,t,n){if(0!==n.backboneAttachNode){const o=n.bondShift,r=n.backboneAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[n.bondShift-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}}(e,n,o),null!==e.meta.branchShift&&e.meta.terminalNodes.length>2&&function(e,t){t.branchAttachNode=t.nodeShift+e.meta.terminalNodes[2];for(let n=0;n<2;++n)t.branchPositionShift[n]=t.backbonePositionShift[n]+e.meta.branchShift[n]}(e,o),function(e,t){t.backboneAttachNode=t.nodeShift+e.meta.terminalNodes[1],t.bondShift+=e.bonds.atomPairs.length+1,t.nodeShift+=e.atoms.atomTypes.length,t.backbonePositionShift[0]+=e.meta.backboneShift?.[0]??0,t.backbonePositionShift[1]+=t.flipFactor*(e.meta.backboneShift?.[1]??0)}(e,o)}function d(e,t,n,o,r){if(0===o.i)h(r.sugar,t,n,o);else for(const e of[r.phosphate,r.sugar])h(e,t,n,o);!function(e,t,n,o){(function(e,t,n){for(let o=0;o<e.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;t[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.atoms.atomTypes[o]+" "+g(n.branchPositionShift[0]+e.atoms.x[o])+" "+g(n.branchPositionShift[1]+n.flipFactor*e.atoms.y[o])+" "+e.atoms.kwargs[o]}})(e,t,o),p(e,n,o),function(e,t,n){const o=n.bondShift,r=n.branchAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[o-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}(e,n,o);const r=o.bondShift,s=o.branchAttachNode,a=e.meta.terminalNodes[0]+o.nodeShift;n[r-1]=i.u.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+a+"\n",o.bondShift+=e.bonds.atomPairs.length+1,o.nodeShift+=e.atoms.atomTypes.length}(e,t,n,o)}function p(e,t,n){for(let o=0;o<e.bonds.atomPairs.length;++o){const r=n.bondShift+o+1,s=e.bonds.atomPairs[o][0]+n.nodeShift,a=e.bonds.atomPairs[o][1]+n.nodeShift;let l="";if(e.bonds.bondConfiguration.has(o)){let t=e.bonds.bondConfiguration.get(o);n.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=e.bonds.kwargs.has(o)?" "+e.bonds.kwargs.get(o):"";t[n.bondShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.bonds.bondTypes[o]+" "+s+" "+a+l+c+"\n"}}function m(e,t,n,r){let l=0,c=0,u=0,h=!0,d=null;for(const n of e)if(n.symbol!==s._S){if("*"==n.symbol)throw new Error("Gap canonical symbol is '', not '*");d=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)}),l+=d.atoms.x.length,c+=d.bonds.bondTypes.length,u++}if("PEPTIDE"===r)l+=1,c+=u,u>0&&((d?.meta?.rNodes?.length??0)<2||d?.terminalR2Atom?.toLowerCase()===i.u.HYDROGEN.toLowerCase())&&(h=!1,l-=1,c-=1);else{const r=n===s.YI.DNA?(0,o.xb)(t,i.u.DEOXYRIBOSE):(0,o.xb)(t,i.u.RIBOSE),a=(0,o.xb)(t,i.u.PHOSPHATE);l+=(e.length-1)*a.atoms.x.length,l+=e.length*r.atoms.x.length,l+=1,c+=(e.length-1)*a.bonds.bondTypes.length,c+=e.length*r.bonds.bondTypes.length,c-=1,c+=3*e.length}return{atomCount:l,bondCount:c,needsCapping:h}}function g(e){return Math.round(i.u.PRECISION_FACTOR*e)/i.u.PRECISION_FACTOR}},6077:(e,t,n)=>{"use strict";n.d(t,{C4:()=>m,eM:()=>g});var i=n(4328),o=n(6082),r=n(1991),s=n.n(r),a=n(439),l=n(3561),c=n(9235),u=n(294),h=n(9192),d=n(330),p=n(8123);async function m(e,t,n,r,l){if(t.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let u=t;const p=r.getSeqHandler(t);let m,f;p.notation!==a.Hi.SEPARATOR&&(u=p.convert(a.Hi.SEPARATOR,"."),u.name=t.name);try{f=r.getSeqHandler(u).alphabet,m=(0,d.pz)(f)}catch(e){const[t,n]=(0,h.AP)(e);return{molCol:null,warnings:[t]}}const y=function(e,t){const n=e.length,o=new Array(n),r=t.getSeqHandler(e);let a=!1;const l=r.defaultBiotype;for(let e=0;e<n;++e){const t=r.getSplitted(e);a||(a=0===t.length),o[e]=s().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:l,symbol:t.getCanonical(e)}))).toArray()}return a&&i.shell.warning(`Some values in the "${e.name}" column are empty`),o}(u,r),b=g(y,m,f,n,l),v=u.length,w=await(0,c.R)(u,b,f,m,n,r,l);w.warnings.length>.05*v&&i.shell.warning(`Molfile conversion resulted in ${w.warnings.length} errors`);const C=o.Func.find({name:"convertToV3KViaOCL"})[0];if(C&&w.molCol)try{const e=w.molCol.toList(),t=await C.apply({mols:e});w.molCol.init((n=>t[n]?t[n]:e[n]))}catch(e){console.error(e)}return w}function g(e,t,n,i,o){const r=(0,l.Hb)(i,t,n),s={},c={value:null};if("RNA"===t){const e=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of e)f(s,n.symbol,r,o,t,c)}for(let n=0;n<e.length;++n){const i=e[n];for(const e of i){const n=e.symbol;if(""!==n)try{if("RNA"===t&&3===n.split(/\(|\)/).filter((e=>!!e)).length){const e=n.split(/\(|\)/)[1];f(s,e,r,o,t,c),s[t]?.[e]&&(s[t][n]=s[t][e])}else f(s,n,r,o,t,c)}catch(e){const t=e instanceof Error?e.message:e.toString(),i=e instanceof Error?e.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${t}\n${i}`),new Error(`Can't get monomer '${n}' from library: ${t}`)}}}return s}function f(e,t,n,i,o,r){const s={polymerType:o,symbol:t};if(!(0,u.bq)(e,s)){const a=function(e,t,n,i,o){if(t.has(e)){const s=t.get(e),a=function(e){const t=[];for(const n of e){let e=n.capGroupSmiles;e||(e=n.capGroupSMILES),e=e.replace(/(\[|\]|\*|:|\d)/g,"").replace("OH","O").replace("Oh","O"),t.push(e)}return t}(s.rgroups),c=(r=s.molfile).includes("V3000")?function(e){const t=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let i;for(;null!==(i=n.exec(e));)i.index===n.lastIndex&&n.lastIndex++,t.set(parseInt(i[1]),parseInt(i[3]));return t}(r):function(e){const t=new Map;let n=e.indexOf(p.u.V2K_A_LINE,0),i=n;for(;-1!==n;){i=e.indexOf("\n",n);const o=parseInt(e.substring(n,i).replace(/^A\s+/,""));n=e.indexOf("R",i),i=e.indexOf("\n",n);const r=parseInt(e.substring(n,i).replace(/^R/,""));t.set(o,r),n=e.indexOf(p.u.V2K_A_LINE,i)}for(n=e.indexOf(p.u.V2K_RGP_LINE,0),i=e.indexOf("\n",n);-1!==n;){n+=p.u.V2K_RGP_SHIFT,i=e.indexOf("\n",n);const o=e.substring(n,i).replaceAll(/\s+/g," ").split(" ").map((e=>parseInt(e))).slice(1);for(let e=0;e<o.length;e+=2){if(t.has(o[e])&&t.get(o[e])!==o[e+1])throw new Error(`r-group index ${o[e]} has already been added with a different value`);t.set(o[e],o[e+1])}n=e.indexOf(p.u.V2K_RGP_LINE,i)}return t}(r),u=s.molfile.includes("V3000")?s.molfile:function(e,t){const n=t.get_mol(function(e){return e.split("\n").map((e=>{const t=e.indexOf(" R# "),n=e.indexOf(" R ");if(-1===t&&-1===n)return e;const i=-1!==t?t:n,o=e.split("");for(let e=i+5;e<o.length;e++)" "!==o[e]&&(o[e]="0");return o.join("")})).join("\n")}(e)),i=n.get_v3Kmolblock();return n.delete(),i}(function(e){let t=e.indexOf(p.u.V2K_A_LINE,0);-1===t&&(t=e.indexOf(p.u.V2K_RGP_LINE));const n=e.indexOf(p.u.V3K_END,t);return e.substring(0,t)+e.substring(n)}(s.molfile),n),h=function(e){let t=(e=e.replaceAll("\r","")).indexOf(p.u.V3K_BEGIN_COUNTS_LINE)+p.u.V3K_COUNTS_SHIFT,n=e.indexOf(" ",t+1);const i=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(e.substring(t,n))}}(u),d=function(e,t){const n=new Array(t),i=new Float32Array(t),o=new Float32Array(t),r=new Array(t);let s=e.indexOf(p.u.V3K_BEGIN_ATOM_BLOCK);s=e.indexOf("\n",s);let a=s;for(let l=0;l<t;l++){s=e.indexOf(p.u.V3K_BEGIN_DATA_LINE,s)+p.u.V3K_IDX_SHIFT,a=e.indexOf(" ",s),s=a+1,a=e.indexOf(" ",s),n[l]=e.substring(s,a);const t=new Array(2);for(let n=0;n<2;++n)s=a+1,a=e.indexOf(" ",s),t[n]=parseFloat(e.substring(s,a));i[l]=t[0],o[l]=t[1],s=a,a=e.indexOf("\n",s)+1,r[l]=e.slice(s,a),s=a}return{atomTypes:n,x:i,y:o,kwargs:r}}(u,h.atomCount),m=function(e,t){const n=new Uint32Array(t),i=new Array(t),o=new Map,r=new Map;let s=e.indexOf(p.u.V3K_BEGIN_BOND_BLOCK);s=e.indexOf("\n",s);let a=s;for(let l=0;l<t;++l){const 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u=e.x.reduce(((t,n,i)=>{if(i===s)return t;if(i===c)return t;const o=e.y[i];return Math.sqrt((n-a)**2+(o-l)**2)>Math.sqrt((e.x[t]-a)**2+(e.y[t]-l)**2)?i:t}),-1);if(-1===u&&(u=e.x.length,e.x=new Float32Array([...e.x,-a]),e.y=new Float32Array([...e.y,-l]),e.atomTypes=[...e.atomTypes,"H"],e.kwargs=[...e.kwargs,""],t.atomPairs.push([c+1,u+1]),t.bondTypes=new Uint32Array([...t.bondTypes,1]),t.kwargs.set(t.atomPairs.length-1,"")),i.set(u+1,o),1===o)n.unshift(e.atomTypes[u]);else{if(2!==o)throw new Error(`Unexpected missing R-group: ${o}`);n.splice(1,0,e.atomTypes[u])}}return function(e,t,n){for(const[i,o]of n)e.atomTypes[i-1]=t[o-1]}(e,n,i),function(e,t){t.rNodes=Array.from(e.keys());for(let n=0;n<t.rNodes.length;n++)for(const i of[1,2])if(e.get(t.rNodes[n])===i){const e=t.rNodes[i-1];t.rNodes[i-1]=t.rNodes[n],t.rNodes[n]=e}}(i,o),y(t,o),o}(d,m,a,c),f=function(e){let t=[],n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const 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S(e,t)+Math.PI/2}(e.atoms.x[e.meta.terminalNodes[1]-1],e.atoms.y[e.meta.terminalNodes[1]-1])))}(e,s),function(e,t){const n=e.atoms.x;n[e.meta.rNodes[1]-1]>n[t-1]&&function(e,t,n){const i=t-1,o=n-1,r=e.atoms.x,s=e.atoms.y,a=r[i],l=s[i];r[i]=r[o],s[i]=s[o],r[o]=a,s[o]=l}(e,t,e.meta.rNodes[1])}(e,s))}(v):e===p.u.RIBOSE.symbol||e===p.u.DEOXYRIBOSE.symbol?function(e,t){const n=e.atoms.x,i=e.atoms.y;let o=e.meta.terminalNodes[0]-1;const r=e.meta.rNodes[1]-1;E(e,-n[o],-i[o]);const s=S(n[e.meta.rNodes[2]-1],i[e.meta.rNodes[2]-1]);A(e.atoms,-s),n[e.meta.rNodes[0]-1]>n[e.meta.rNodes[1]-1]&&x(e);const a=S(n[r],i[r]);A(e.atoms,3*Math.PI/2-a),t.value=function(e){const t=e.atoms.x,n=e.atoms.y,i=e.meta.rNodes[2]-1,o=e.meta.terminalNodes[2]-1,r=t[i]-t[o],s=n[i]-n[o];return Math.atan2(r,s)}(e),o=e.meta.terminalNodes[0]-1,E(e,-n[o],-i[o])}(v,o):e===p.u.PHOSPHATE.symbol?function(e){const t=e.meta.rNodes[1]-1,n=e.meta.rNodes[0]-1,i=e.atoms.x,o=e.atoms.y;E(e,-i[t],-o[t]);const r=S(i[n],o[n]);A(e.atoms,Math.PI/2-r)}(v):function(e,t){const n=e.atoms.x,i=e.atoms.y,o=e.meta.terminalNodes[0]-1,r=e.meta.rNodes[0]-1;E(e,-n[o],-i[o]);const s=S(n[r],i[r]),a=t.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");A(e.atoms,Math.PI-s+a);const c=function(e,t){return(0,l.YN)(Math.sqrt((e.x-t.x)**2+(e.y-t.y)**2))}({x:n[e.meta.rNodes[0]-1],y:i[e.meta.rNodes[0]-1]},{x:n[e.meta.terminalNodes[0]-1],y:i[e.meta.terminalNodes[0]-1]});if(1!=c)for(let e=0;e<n.length;++e)n[e]=(0,l.YN)(n[e]/c),i[e]=(0,l.YN)(i[e]/c)}(v,o),function(e,t,n){if("PEPTIDE"===e){b(t,e);const n=w(t,t.meta.rNodes[1]);n?.removedAtom&&(t.terminalR2Atom=n.removedAtom)}else n===p.u.RIBOSE.symbol||n===p.u.DEOXYRIBOSE.symbol?(w(t,t.meta.rNodes[1]),t.meta.rNodes[1]=t.meta.terminalNodes[1],y(t.bonds,t.meta),b(t,e),w(t,t.meta.rNodes[1]),w(t,t.meta.rNodes[0]),w(t,t.meta.rNodes[2])):n===p.u.PHOSPHATE.symbol&&(t.meta.terminalNodes[0]=t.meta.rNodes[0],E(t,-t.atoms.x[t.meta.terminalNodes[0]-1],-t.atoms.y[t.meta.terminalNodes[0]-1]),b(t,e),w(t,t.meta.rNodes[1]))}(i,v,e),function(e){let t=0;for(;t<e.atoms.atomTypes.length;)e.atoms.atomTypes[t]===p.u.HYDROGEN&&(w(e,t+1),--t),++t}(v),function(e){let t=0;for(;t<e.atoms.atomTypes.length;)"oh"===e.atoms.atomTypes[t]?.toLowerCase()&&(e.atoms.atomTypes[t]="O"),"?"===e.atoms.atomTypes[t]&&(e.atoms.atomTypes[t]="H"),++t}(v),function(e){const t=" RGROUPS=(1 1)";for(let n=0;n<(e.atoms.kwargs?.length??0);n++){const i=e.atoms.kwargs[n];i&&i.includes(t)&&(e.atoms.kwargs[n]=i.replace(t,""))}}(v),v}var r;return null}(t,n,i,o,r);if(!a)throw new Error(`Monomer with symbol '${t}' is absent the monomer library`);(0,u.LQ)(e,s,a)}}function y(e,t){const n=t.rNodes;t.terminalNodes=new Array(n.length).fill(0);const i=t.terminalNodes,o=e.atomPairs;let r=0,s=0;for(;r<o.length&&s<i.length;){for(let e=0;e<i.length;++e)for(let t=0;t<2;++t)o[r][t]===n[e]&&(i[e]=o[r][(t+1)%2],n.length,++s);++r}}function b(e,t){e.meta.rNodes.length>1&&(e.meta.backboneShift=v(e,e.meta.rNodes[1]-1,e.meta.terminalNodes[0]-1)),"RNA"===t&&e.meta.rNodes.length>2&&(e.meta.branchShift=v(e,e.meta.rNodes[2]-1,e.meta.terminalNodes[0]-1))}function v(e,t,n){return[(0,l.YN)(e.atoms.x[t]-e.atoms.x[n]),(0,l.YN)(e.atoms.y[t]-e.atoms.y[n])]}function w(e,t){if(void 0!==t){const n=t-1,i=e.atoms,o=e.bonds,r=e.meta,s=i.atomTypes.splice(n,1)[0];i.x=C(Float32Array,i.x,n,1),i.y=C(Float32Array,i.y,n,1),i.kwargs.splice(n,1);for(let e=0;e<r.terminalNodes.length;++e)r.terminalNodes[e]>t?--r.terminalNodes[e]:r.terminalNodes[e]===t&&(r.terminalNodes[e]=-1);for(let e=0;e<r.rNodes.length;++e)r.rNodes[e]>t?--r.rNodes[e]:r.rNodes[e]===t&&(r.rNodes[e]=-1);let a=0;for(;a<o.atomPairs.length;){const e=o.atomPairs[a][0],n=o.atomPairs[a][1];e===t||n===t?(o.atomPairs.splice(a,1),o.bondTypes=C(Uint32Array,o.bondTypes,a,1),o.bondConfiguration.has(a)&&o.bondConfiguration.delete(a),o.kwargs.has(a)&&o.kwargs.delete(a),--a):(o.atomPairs[a][0]=e>t?e-1:e,o.atomPairs[a][1]=n>t?n-1:n),++a}let l=Array.from(o.bondConfiguration.keys());return l.forEach((e=>{if(o.bondConfiguration.has(e)&&e>n){const t=o.bondConfiguration.get(e);o.bondConfiguration.delete(e),o.bondConfiguration.set(e-1,t)}})),l=Array.from(o.kwargs.keys()),l.forEach((e=>{if(o.kwargs.has(e)&&e>n){const t=o.kwargs.get(e);o.kwargs.delete(e),o.kwargs.set(e-1,t)}})),s?{removedAtom:s}:void 0}}function C(e,t,n,i){const o=new e(t.length-i);let r=0,s=0;for(;r<t.length;)r===n&&(r+=i),o[s]=t[r],++s,++r;return o}function S(e,t){let n;if(0===e)n=t>0?0:Math.PI;else if(0===t)n=e>0?-Math.PI/2:Math.PI/2;else{const i=t/e,o=Math.atan(i);n=e<0?Math.PI/2+o:-Math.PI/2+o}return n}function A(e,t){if(0!==t){const n=e.x,i=e.y,o=Math.cos(t),r=Math.sin(t);for(let e=0;e<n.length;++e){const t=n[e];n[e]=(0,l.YN)(t*o-i[e]*r),i[e]=(0,l.YN)(t*r+i[e]*o)}}}function x(e){M(e,!1)}function M(e,t){if(t){const t=e.atoms.y;for(let e=0;e<t.length;e++)t[e]=-t[e]}else{const t=e.atoms.x;for(let e=0;e<t.length;e++)t[e]=-t[e]}const n=e.bonds.bondConfiguration;for(const[e,t]of n){const i=1===t?3:1;n.set(e,i)}}function E(e,t,n){const i=e.atoms.x,o=e.atoms.y;for(let e=0;e<i.length;++e)i[e]=(0,l.YN)(i[e]+t),void 0!==n&&(o[e]=(0,l.YN)(o[e]+n))}},294:(e,t,n)=>{"use strict";function i(e,t){return e[t.polymerType]?.[t.symbol]}function o(e,t){return!!e[t.polymerType]?.[t.symbol]}function r(e,t,n){let i=e[t.polymerType];i||(i=e[t.polymerType]={}),i[t.symbol]=n}n.d(t,{Cg:()=>s,LQ:()=>r,bq:()=>o,vF:()=>a,xb:()=>i});class s extends Map{constructor(e){super(e)}}class a{constructor(e,t){this.molfile=e,this.monomers=t}static createEmpty(){return new a("",new s(null))}}},330:(e,t,n)=>{"use strict";n.d(t,{kA:()=>o,pz:()=>s,qj:()=>r,vG:()=>a});var i=n(2003);function o(e,t){return e?e.columns.getUnusedName(t):t}function r(e,t){return o(e,`molfile(${t})`)}function s(e){let t;if(e===i.YI.PT||e===i.YI.UN)t="PEPTIDE";else{if(e!==i.YI.RNA&&e!==i.YI.DNA)throw new Error(`Unexpected alphabet '${e}'.`);t="RNA"}return t}function a(e){const t=7===e.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e);return t?[parseInt(t[1],16)/256,parseInt(t[2],16)/256,parseInt(t[3],16)/256,t.length>4?parseInt(t[4],16)/256:.3]:null}},1093:(e,t,n)=>{"use strict";n(7362);class i{}i.SemType="Nucleotides",i.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",i.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"}},7362:(e,t,n)=>{"use strict";n.d(t,{e:()=>i});class i{static makePalette(e,t=!1,n=i){const o={};return e.forEach((e=>{const 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this._props||(this._props=this.emptyProps),this._props}set props(e){this._propsChanging=!0;try{this._props=e,this.applyProps(),this.onChanged.next()}finally{this._propsChanging=!1}}saveProps(){const e={};for(const[t,n]of Object.entries(this.props))"_onChanged"!==t&&"logger"!==t&&(e[t]=this.props[t]);return e}async detach(){}get filterSummary(){return this.props.substructure}get isFiltering(){return""!==this.props.substructure}resetFilter(){this.props=this.emptyProps,this.onChanged.next()}}},4152:(e,t,n)=>{"use strict";var i=n(6082),o=n(7362),r=n(6718);function s(e,t=!0){if(null==e)return"rgb(100,100,100)";const n=i.Color.fromHtml(e);if(t){const e=i.Color.g(n),t=i.Color.r(n),o=i.Color.b(n),r=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(r>210)return`rgb(${t/r*210},${e/r*210},${o/r*210})`}return i.Color.toRgb(n)}class a{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}class l{}class c extends l{static get palette(){return c._pallete||(c._pallete=c.buildPalette()),c._pallete}static buildPalette(){return(0,r.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{c.customMonomerColors={},c.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const i of n){const n=t.getMonomer(e,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][e]=s(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(o.e.colourPalette))}get(e,t){const n=c.palette.length,i=c.customMonomerColors[e],o=t??"PEPTIDE";if(i&&i[o])return i[o];const r=a.hashCode(e)%n;return s(c.palette[r])}}c._pallete=null,c.customMonomerColors={},c.polymerTypes=[]},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>s,sD:()=>l});var i=n(4328),o=n(1858),r=n(8070);function s(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const i=e.cell.column;if(t=t??(i?i.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,i,t]}class a{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class l extends a{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++l.viewerCounter,this.errors=[],this._onRendered=new o.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}})))),this.tableCol&&this.subs.push(i.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(i.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,r.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}l.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>i});const i={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Jy:()=>b,S$:()=>y,U0:()=>v});var i=n(7389),o=n(6082),r=n(1991),s=n.n(r),a=n(8312),l=n(2003),c=n(6642),u=n(6718),h=n(9192),d=n(3856),p=n(673),m=n(3599),g=n(5553),f=n(9713);const y="rgb(100,100,100)";class b extends c.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,i,r){if(super(e,t,n),this.monomerLengthLimit=i,this.propsProvider=r,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const e=[l.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(f.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(f.filter((e=>e.args.source===this.tableCol&&e.args.key===l.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,i,o,r){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(e),l=t-2*this.padding;let c=0;const u=[];if(i.length>0)for(let t=o;t<i.length;t++){const n=i.getOriginal(t),o=this.props.monomerToShort(n,r);u.push({text:o,posIdx:t}),c=Math.max(c,e.measureText(o).width)}if(0===u.length)return{lineLayouts:[],lineHeight:s};const d=c;let p=Math.floor((l+a)/(d+a));p=Math.max(1,p);const m=n-2*this.padding,g=Math.max(0,Math.floor(m/s)),f=[];let y=0;for(let e=0;e<g&&y<u.length;e++){const t=[];for(let e=0;e<p&&y<u.length;e++){const n=u[y],i=this.padding+e*(d+a);t.push({posIdx:n.posIdx,x:i,width:d,om:n.text,isSeparator:!1}),y++}f.push({lineIdx:e,elements:t})}return{lineLayouts:f,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,u.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,r=Math.ceil(t/i)+o,s=n.splitter(e),a=Math.min(r,s.length),l=new Array(a-o);let c=0;for(let e=o;e<a;++e){const i=s.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(l[e-o]=a,c+=a,c>t)break}return l}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/i)+t,r=n.getSplitted(e),s=Math.min(o,r.length);let a=this._monomerLengthList[e];if(null===a||a.length!=s-t){a=this._monomerLengthList[e]=new Array(r.length);let i=0;for(let e=t;e<s;++e){const o=r.getOriginal(e),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[e-t]=l,i+=l,i>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:i}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=this.positionShift,s=Math.ceil(this.colWidth/o)+r;for(let e=n;e<i;e++){if(this._processedRows.get(e)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,s),i=Math.min(s,n.length);i-r>t.length&&t.push(...new Array(i-r-t.length).fill(o));let a=0;for(let e=r;e<i;++e){const i=n.getOriginal(e),o=this.props.monomerToShort(i,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(t[e-r]=Math.max(t[e-r]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,i){const[o,r]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let i,o=100,r=0,s=e.length-1;for(;r<=s;){if(i=Math.floor((s+r)/2),e[i]<=t&&t<e[i+1])return i;if(t<e[i]?s=i-1:r=i+1,--o<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(r,t,i)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[l.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,i,r,a,c){const u=a.grid?.canvas===e.canvas;if(!this.seqHelper)return;const m=this.tableCol,g=this.positionShift;e.save();try{const c=this.seqHelper.getSeqHandler(m);let h=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(d.gp.maxMonomerLength));h=!isNaN(e)&&e?e:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=h){let e=0;const t=8;e=m.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(h),this.setSeparatorWidth(c.isMsa()?t:e),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const f=a.cell.rowIndex,b=a.cell.value;u&&(i=v(a.grid,e,t,i,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,i,r),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const w=m.meta.units,C=m.getTag(l.gp.aligned),S=m.getTag(l.gp.separator)??"",A=u?c.getSplitted(f):c.splitter(b);let x=d.yg.classic;C?.includes("MSA")&&w===l.Hi.SEPARATOR&&(x=d.yg.MSA);const M=m.temp["reference-sequence"],E=this.tableCol.temp["current-word"],T=(()=>{const e=(0,c.splitter)(null!=M&&""!==M?M:E??"");return s().count(0).take(e.length).slice(g).map((t=>e.getCanonical(t))).toArray()})(),_=Number.parseInt(m.getTag(l.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const s=[],l=this.calculateMultiLineLayoutDynamic(e,i,r,A,g,h);let u=n+this.padding;1===l.lineLayouts.length&&(u=n+(r-l.lineHeight)/2);for(const i of l.lineLayouts){const r=u+i.lineIdx*l.lineHeight;for(const u of i.elements){const h=t+u.x,p=u,f=p.posIdx,b=A.getCanonical(f);let v=y;const w=this.getMonomerLib();w&&(v=w.getMonomerTextColor(c.defaultBiotype,b));let C=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&T.length>0){const e=f-g;e>=0&&e<T.length&&b===T[e]&&(C=.7)}s.push({lineIdx:i.lineIdx,monomerIdx:f-g,bounds:new o.Rect(u.x,r-n,u.width,l.lineHeight),sequencePosition:f}),(0,d.oZ)(e,p.om,h,r,u.width,l.lineHeight,{color:v,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(_)||_<1?void 0:_,wordIdx:f})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,s)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(g)?e.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,i);u||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,i)));const s=this.props.separatorWidth+1*this.props.fontCharWidth,l=Math.min(A.length,Math.ceil(i/s)+g);for(let s=g;s<l;++s){const l=s<A.length?A.getOriginal(s):c.defaultGapOriginal,u=s<A.length?A.getCanonical(s):c.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(c.defaultBiotype,u));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:S,last:s===A.length-1,drawStyle:x,maxWord:o,wordIdx:s-g,gridCell:a,referenceSequence:T,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(_)||_<1?void 0:_-g};(0,d.oZ)(e,l,t+this.padding+this._leftThreeDotsPadding,n,i,r,m)}if(this.shouldRenderShiftedThreeDots(g)){const s={color:y,pivot:0,left:!0,transparencyRate:0,separator:S,last:!1,drawStyle:x,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,d.oZ)(e,"...",t+this.padding,n,i,r,s)}}}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,r=e.bounds,s=t.offsetX-e.gridColumn.left+(e.gridColumn.left-r.x),a=t.offsetY-r.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let c=null;const u=this._cellBounds.get(e.tableRowIndex);if(u){for(const e of u)if(e.bounds.contains(s,a)){c=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;c=this.getPosition(e.tableRowIndex,s,r.width,t)}this.logger.debug(`${n}, argsX: ${s}, argsY: ${a}, left: ${c}`);const h=this.seqHelper.getSeqHandler(this.tableCol),d=h.getSplitted(e.tableRowIndex);if(null!==c&&c>=0&&c+o<d.length){const n=h.alphabet??l.YI.UN,r={position:c,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:d.getCanonical(c+o)},s=[];let a=this._monomerStructureMap[r.symbol];if(!a){const e=this.getMonomerLib();a=this._monomerStructureMap[r.symbol]=e?e.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}s.push(a),i.tooltip.show(i.divV(s),t.x+16,t.y+16),(0,g.WN)(e,r)}else-1===c?i.tooltip.show(i.divText(`${Math.min(o,d.length)} hidden monomers`),t.x+16,t.y+16):i.tooltip.hide(),(0,g.WN)(e,null)}}function v(e,t,n,i,o){return e?Math.max(Math.min(e.canvas.width/o-n,i)):Math.max(t.canvas.width/o-n,0)}},3856:(e,t,n)=>{"use strict";n.d(t,{Mn:()=>u,gp:()=>c,oZ:()=>p,yg:()=>h});var i=n(6082),o=n(7278);const r="rgb(100,100,100)",s="#808080",a="rgb(0,0,0)",l=o.zS;var c,u,h;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(c||(c={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(u||(u={})),function(e){e.MSA="MSA",e.classic="classic"}(h||(h={}));const d=new class{constructor(){this.color=r,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=h.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function p(e,t,n,o,c,u,p){var m,g,f;const y={...d,...p};if(y.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let i=t;null!=y.maxLengthOfMonomer&&(i=l(i,y.maxLengthOfMonomer));const s=Math.max(.1,1-(y.transparencyRate??0));e.globalAlpha=s;const h=e.measureText(i),d=h.fontBoundingBoxAscent+h.fontBoundingBoxDescent,p=o+(u-d)/2+h.fontBoundingBoxAscent;let m=y.color??r;return m&&m!==r||(m=a),e.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n,o,c,u),e.restore(),e.fillStyle=m),e.fillText(i,n+c/2,p),e.globalAlpha=1,e.textBaseline="top",e.textAlign="start",n+c}p.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let b=t.substring(0),v=y.last?"":y.separator;y.drawStyle===h.MSA&&(v="");let w=!0,C=!0,S="difference";if(null!=y.gridCell&&null!=y.gridCell.cell.column&&(w=y.gridCell.cell.column.temp["color-code"]??!0,C=y.gridCell.cell.column.temp["compare-with-current"]??!0,S=y.gridCell.cell.column.temp["highlight-difference"]??"difference"),y.referenceSequence){const e=y.referenceSequence[y.wordIdx];C&&y.referenceSequence.length>0&&"difference"===S&&(y.transparencyRate=b==e?.7:y.transparencyRate),C&&y.referenceSequence.length>0&&"equal"===S&&(y.transparencyRate=b!=e?.7:y.transparencyRate)}null!=y.maxLengthOfMonomer&&(b=l(b,y.maxLengthOfMonomer));const A=b+v;(m=y.monomerTextSizeMap)[A]??(m[A]=e.measureText(A));let x=y.monomerTextSizeMap[A];(g=y.monomerTextSizeMap)[b]??(g[b]=e.measureText(b));let M=y.monomerTextSizeMap[b].width;const E=u/2-(x.fontBoundingBoxAscent+x.fontBoundingBoxDescent)/2+1;(f=y.monomerTextSizeMap)[v]??(f[v]=e.measureText(v));const T=y.monomerTextSizeMap[v].width;function _(t,r){let l=w?y.color:a;y.selectedPosition===y.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,y.monomerTextSizeMap[b].width+8,u+10),l=i.Color.toHtml(i.Color.setAlpha(i.Color.fromHtml(l),255))),e.fillStyle=l,e.globalAlpha=1-y.transparencyRate,y.drawStyle===h.classic&&(e.fillText(b,n+t,o+E),e.fillStyle=s,e.fillText(v,n+r,o+E)),y.drawStyle===h.MSA&&e.fillText(b,n+t,o+E),e.globalAlpha=1}x=x.width,y.drawStyle===h.MSA&&(M=y.maxWord[y.wordIdx],x=y.maxWord[y.wordIdx]);const I=(y.maxWord[y.wordIdx]??0)-(y.maxWord[0]??0);if(y.left||x>c)return _(I,I+M),n+I+M+T;{const e=(c-x)/2;return _(e,e+M),n+I+e+M}}},6307:(e,t,n)=>{"use strict";n.d(t,{F:()=>s});var i=n(7389),o=n(6082),r=n(439);function s(e,t,n){let s=0,a=null;for(const t of Object.values(e))s+=t,a=null===a?t:Math.max(a,t);const l=a/s,c=Object.assign({},...Array.from(Object.entries(e)).sort(((e,t)=>t[1]-e[1])).map((([e,a])=>{const c=a/s;let u;try{const i=n.getMonomerColors(t,e);u=i?.backgroundcolor||"#CCCCCC"}catch(t){console.warn(`Failed to get colors for monomer ${e}:`,t),u="#CCCCCC"}const h=i.div("",{classes:"macromolecule-cell-comp-analysis-bar"});h.style.width=50*c/l+"px",h.style.backgroundColor=u,r._S===e&&(h.style.borderWidth="1px",h.style.borderStyle="solid",h.style.borderColor=o.Color.toHtml(o.Color.lightGray));const d=r._S===e?"-":e,p=i.div(`${(100*c).toFixed(2)}%`),m=i.div([h,p],{classes:"macromolecule-cell-comp-analysis-value"});return{[d]:m}}))),u=i.tableFromMap(c);return Array.from(u.rows).forEach((e=>{const t=e.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;e.cells[0].style.color=t})),u}},3151:(e,t,n)=>{"use strict";n.d(t,{EK:()=>l,Ec:()=>r,f6:()=>i,pe:()=>s,q7:()=>a,yw:()=>o});const i=["symbol","molfile","rgroups","name"],o="MonomerName",r={monomerType:null,smiles:null,name:"Name",author:null,molfile:"molecule",naturalAnalog:"MonomerNaturalAnalogCode",rgroups:"MonomerCaps",createDate:null,id:null,polymerType:"MonomerType",symbol:"MonomerName"},s={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},a="p",l=new RegExp(`[rd]\\((\\w)\\)${a}?`,"g")},9192:(e,t,n)=>{"use strict";function i(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?i(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function o(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?o(e.$thrownJsError):void 0}function r(e){return[i(e),o(e)]}n.d(t,{AP:()=>r})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>r});var i=n(6082),o=n(439);class r{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(e,t){return this._fileContent.slice(e,t).split(/\s/).join("")}parseColumns(){const e=/^>(.*)$/gm;let t,n=0;for(;t=e.exec(this._fileContent);){const i=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(i),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=i.Column.fromStrings("description",this.descriptionsArray),t=i.Column.fromStrings("sequence",this.sequencesArray);return 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+ var bio;(()=>{var e={8924:(e,t,n)=>{"use strict";var i=n(7362);class o extends i.e{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,o)),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,o)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new o({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 o.aaSynonyms?o.aaSynonyms[e]:e;return super.get(t)}}o.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class r{static getPalette(e="grok"){switch(e){case"grok":return o.GrokGroups;case"lesk":return o.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",i="";for(const o of e)"("==o?t++:")"==o?t--:t?n+=o:i+=o;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[i,o]=this.getInnerOuter(e);if(i=i.length>6?`${i.slice(0,3)}...`:i,o=o.length>6?`${o.slice(0,3)}...`:o,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,o,1]:[this.undefinedColor,i,o,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,o,2]:[this.undefinedColor,i,o,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,o,3]:[this.undefinedColor,i,o,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,o,4]:[this.undefinedColor,i,o,4]}return[this.undefinedColor,i,o,0]}}r.SemType="Aminoacids",r.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",r.undefinedColor="rgb(100,100,100)",r.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic 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r().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:v}))).toArray()})).toArray();for(let e=0;e<m;e++){const n=g[e],i=Math.floor(e*f),r=e===m-1?d:Math.floor((e+1)*f);y[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:w,monomersDict:t,alphabet:o,polymerType:l,start:i,end:r})}const C=[],S=[];await Promise.all(y).then((e=>{for(const t of e)C.push(...t.molfiles),S.push(...t.warnings)})),setTimeout((()=>{g.forEach((e=>{e.terminate()}))}),0);const A=(0,s.qj)(p,e.name),x=i.Column.fromType(i.COLUMN_TYPE.STRING,A,e.length).init((e=>C[e]?.molfile));return x.semType=i.SEMTYPE.MOLECULE,x.meta.units=i.UNITS.Molecule.MOLBLOCK,x.setTag(".sequence-src-col",e.name),{molCol:x,warnings:S}}function c(e,t){const n={},o={};for(const r of e){const e=t.getWebEditorMonomer(r.biotype,r.symbol).backgroundcolor,a=(0,s.vG)(e??i.Color.toRgb(i.Color.mouseOverRows))??[1,0,0,.7];for(const e of r.atoms)n[e]=a;for(const e of 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C={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},S={sugar:v,phosphate:w,seqLength:e.length,atomCount:c,bondCount:h},A=new o.Cg,x=[];let M,E=0;for(C.i=0;C.i<S.seqLength;++C.i){const n=e[C.i];if(n.symbol===s._S)continue;const i=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});M=i.terminalR2Atom;const r=C.nodeShift,l=C.bondShift;b(i,f,y,C,S),i.stereoAtoms?.forEach((e=>x.push(e+E))),E+=i.atoms.x.length;const c=C.nodeShift-r,u=new Array(c);for(let e=0;e<c;++e)u[e]=r+e;const h=C.bondShift-l,d=new Array(h);for(let e=0;e<h;++e)d[e]=l+e;A.set(C.i,{biotype:n.biotype,symbol:n.symbol,atoms:u,bonds:d})}p&&function(e,t,n,o,r=i.u.OXYGEN){const s=n.nodeShift+1;e[o.atomCount]=i.u.V3K_BEGIN_DATA_LINE+s+" "+(r??i.u.OXYGEN)+" "+g(n.backbonePositionShift[0])+" "+n.flipFactor*g(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;t[o.bondCount]=i.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(f,y,C,S,M??i.u.OXYGEN);const T=i.u.V3K_BEGIN_COUNTS_LINE+c+" "+h+i.u.V3K_COUNTS_LINE_ENDING;let _="";return _+=i.u.V3K_HEADER_FIRST_LINE,_+=i.u.V3K_HEADER_SECOND_LINE,_+=i.u.V3K_BEGIN_CTAB_BLOCK,_+=T,_+=i.u.V3K_BEGIN_ATOM_BLOCK,_+=f.join(""),_+=i.u.V3K_END_ATOM_BLOCK,_+=i.u.V3K_BEGIN_BOND_BLOCK,_+=y.join(""),_+=i.u.V3K_END_BOND_BLOCK,x.length>0&&(_+=function(e){const t=[];let n=`M V30 MDLV30/STEABS ATOMS=(${e.length}`;for(let i=0;i<e.length;i++){const o=`${n} ${e[i]}`;o.length>76?(t.push(`${n} -\n`),n=`M V30 ${e[i]}`):n=o,i===e.length-1&&t.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${t.join("")}M V30 END COLLECTION\n`}(x)),_+=i.u.V3K_END_CTAB_BLOCK,_+=i.u.V3K_END,{molfile:_,monomers:A}}function u(e,t,n,i){i.flipFactor=(-1)**(i.i%2),h(e,t,n,i)}function h(e,t,n,o){!function(e,t,n){for(let o=0;o<e.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;t[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.atoms.atomTypes[o]+" "+g(n.backbonePositionShift[0]+e.atoms.x[o])+" "+g(n.backbonePositionShift[1]+n.flipFactor*e.atoms.y[o])+" "+e.atoms.kwargs[o]}}(e,t,o),p(e,n,o),function(e,t,n){if(0!==n.backboneAttachNode){const o=n.bondShift,r=n.backboneAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[n.bondShift-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}}(e,n,o),null!==e.meta.branchShift&&e.meta.terminalNodes.length>2&&function(e,t){t.branchAttachNode=t.nodeShift+e.meta.terminalNodes[2];for(let n=0;n<2;++n)t.branchPositionShift[n]=t.backbonePositionShift[n]+e.meta.branchShift[n]}(e,o),function(e,t){t.backboneAttachNode=t.nodeShift+e.meta.terminalNodes[1],t.bondShift+=e.bonds.atomPairs.length+1,t.nodeShift+=e.atoms.atomTypes.length,t.backbonePositionShift[0]+=e.meta.backboneShift?.[0]??0,t.backbonePositionShift[1]+=t.flipFactor*(e.meta.backboneShift?.[1]??0)}(e,o)}function d(e,t,n,o,r){if(0===o.i)h(r.sugar,t,n,o);else for(const e of[r.phosphate,r.sugar])h(e,t,n,o);!function(e,t,n,o){(function(e,t,n){for(let o=0;o<e.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;t[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.atoms.atomTypes[o]+" "+g(n.branchPositionShift[0]+e.atoms.x[o])+" "+g(n.branchPositionShift[1]+n.flipFactor*e.atoms.y[o])+" "+e.atoms.kwargs[o]}})(e,t,o),p(e,n,o),function(e,t,n){const o=n.bondShift,r=n.branchAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[o-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}(e,n,o);const r=o.bondShift,s=o.branchAttachNode,a=e.meta.terminalNodes[0]+o.nodeShift;n[r-1]=i.u.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+a+"\n",o.bondShift+=e.bonds.atomPairs.length+1,o.nodeShift+=e.atoms.atomTypes.length}(e,t,n,o)}function p(e,t,n){for(let o=0;o<e.bonds.atomPairs.length;++o){const r=n.bondShift+o+1,s=e.bonds.atomPairs[o][0]+n.nodeShift,a=e.bonds.atomPairs[o][1]+n.nodeShift;let l="";if(e.bonds.bondConfiguration.has(o)){let t=e.bonds.bondConfiguration.get(o);n.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=e.bonds.kwargs.has(o)?" "+e.bonds.kwargs.get(o):"";t[n.bondShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+e.bonds.bondTypes[o]+" "+s+" "+a+l+c+"\n"}}function m(e,t,n,r){let l=0,c=0,u=0,h=!0,d=null;for(const n of e)if(n.symbol!==s._S){if("*"==n.symbol)throw new Error("Gap canonical symbol is '', not '*");d=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)}),l+=d.atoms.x.length,c+=d.bonds.bondTypes.length,u++}if("PEPTIDE"===r)l+=1,c+=u,u>0&&((d?.meta?.rNodes?.length??0)<2||d?.terminalR2Atom?.toLowerCase()===i.u.HYDROGEN.toLowerCase())&&(h=!1,l-=1,c-=1);else{const r=n===s.YI.DNA?(0,o.xb)(t,i.u.DEOXYRIBOSE):(0,o.xb)(t,i.u.RIBOSE),a=(0,o.xb)(t,i.u.PHOSPHATE);l+=(e.length-1)*a.atoms.x.length,l+=e.length*r.atoms.x.length,l+=1,c+=(e.length-1)*a.bonds.bondTypes.length,c+=e.length*r.bonds.bondTypes.length,c-=1,c+=3*e.length}return{atomCount:l,bondCount:c,needsCapping:h}}function g(e){return Math.round(i.u.PRECISION_FACTOR*e)/i.u.PRECISION_FACTOR}},6077:(e,t,n)=>{"use strict";n.d(t,{C4:()=>m,eM:()=>g});var i=n(4328),o=n(6082),r=n(1991),s=n.n(r),a=n(439),l=n(3561),c=n(9235),u=n(294),h=n(9192),d=n(330),p=n(8123);async function m(e,t,n,r,l){if(t.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let u=t;const p=r.getSeqHandler(t);let m,f;p.notation!==a.Hi.SEPARATOR&&(u=p.convert(a.Hi.SEPARATOR,"."),u.name=t.name);try{f=r.getSeqHandler(u).alphabet,m=(0,d.pz)(f)}catch(e){const[t,n]=(0,h.AP)(e);return{molCol:null,warnings:[t]}}const y=function(e,t){const n=e.length,o=new Array(n),r=t.getSeqHandler(e);let a=!1;const l=r.defaultBiotype;for(let e=0;e<n;++e){const t=r.getSplitted(e);a||(a=0===t.length),o[e]=s().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:l,symbol:t.getCanonical(e)}))).toArray()}return a&&i.shell.warning(`Some values in the "${e.name}" column are empty`),o}(u,r),b=g(y,m,f,n,l),v=u.length,w=await(0,c.R)(u,b,f,m,n,r,l);w.warnings.length>.05*v&&i.shell.warning(`Molfile conversion resulted in ${w.warnings.length} errors`);const C=o.Func.find({name:"convertToV3KViaOCL"})[0];if(C&&w.molCol)try{const e=w.molCol.toList(),t=await C.apply({mols:e});w.molCol.init((n=>t[n]?t[n]:e[n]))}catch(e){console.error(e)}return w}function g(e,t,n,i,o){const r=(0,l.Hb)(i,t,n),s={},c={value:null};if("RNA"===t){const e=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of e)f(s,n.symbol,r,o,t,c)}for(let n=0;n<e.length;++n){const i=e[n];for(const e of i){const n=e.symbol;if(""!==n)try{if("RNA"===t&&3===n.split(/\(|\)/).filter((e=>!!e)).length){const e=n.split(/\(|\)/)[1];f(s,e,r,o,t,c),s[t]?.[e]&&(s[t][n]=s[t][e])}else f(s,n,r,o,t,c)}catch(e){const t=e instanceof Error?e.message:e.toString(),i=e instanceof Error?e.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${t}\n${i}`),new Error(`Can't get monomer '${n}' from library: ${t}`)}}}return s}function f(e,t,n,i,o,r){const s={polymerType:o,symbol:t};if(!(0,u.bq)(e,s)){const a=function(e,t,n,i,o){if(t.has(e)){const s=t.get(e),a=function(e){const t=[];for(const n of e){let e=n.capGroupSmiles;e||(e=n.capGroupSMILES),e=e.replace(/(\[|\]|\*|:|\d)/g,"").replace("OH","O").replace("Oh","O"),t.push(e)}return t}(s.rgroups),c=(r=s.molfile).includes("V3000")?function(e){const t=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let i;for(;null!==(i=n.exec(e));)i.index===n.lastIndex&&n.lastIndex++,t.set(parseInt(i[1]),parseInt(i[3]));return t}(r):function(e){const t=new Map;let n=e.indexOf(p.u.V2K_A_LINE,0),i=n;for(;-1!==n;){i=e.indexOf("\n",n);const o=parseInt(e.substring(n,i).replace(/^A\s+/,""));n=e.indexOf("R",i),i=e.indexOf("\n",n);const r=parseInt(e.substring(n,i).replace(/^R/,""));t.set(o,r),n=e.indexOf(p.u.V2K_A_LINE,i)}for(n=e.indexOf(p.u.V2K_RGP_LINE,0),i=e.indexOf("\n",n);-1!==n;){n+=p.u.V2K_RGP_SHIFT,i=e.indexOf("\n",n);const o=e.substring(n,i).replaceAll(/\s+/g," ").split(" ").map((e=>parseInt(e))).slice(1);for(let e=0;e<o.length;e+=2){if(t.has(o[e])&&t.get(o[e])!==o[e+1])throw new Error(`r-group index ${o[e]} has already been added with a different value`);t.set(o[e],o[e+1])}n=e.indexOf(p.u.V2K_RGP_LINE,i)}return t}(r),u=s.molfile.includes("V3000")?s.molfile:function(e,t){const n=t.get_mol(function(e){return e.split("\n").map((e=>{const t=e.indexOf(" R# "),n=e.indexOf(" R ");if(-1===t&&-1===n)return e;const i=-1!==t?t:n,o=e.split("");for(let e=i+5;e<o.length;e++)" "!==o[e]&&(o[e]="0");return o.join("")})).join("\n")}(e)),i=n.get_v3Kmolblock();return n.delete(),i}(function(e){let t=e.indexOf(p.u.V2K_A_LINE,0);-1===t&&(t=e.indexOf(p.u.V2K_RGP_LINE));const n=e.indexOf(p.u.V3K_END,t);return e.substring(0,t)+e.substring(n)}(s.molfile),n),h=function(e){let t=(e=e.replaceAll("\r","")).indexOf(p.u.V3K_BEGIN_COUNTS_LINE)+p.u.V3K_COUNTS_SHIFT,n=e.indexOf(" ",t+1);const i=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(e.substring(t,n))}}(u),d=function(e,t){const n=new Array(t),i=new Float32Array(t),o=new Float32Array(t),r=new Array(t);let s=e.indexOf(p.u.V3K_BEGIN_ATOM_BLOCK);s=e.indexOf("\n",s);let a=s;for(let l=0;l<t;l++){s=e.indexOf(p.u.V3K_BEGIN_DATA_LINE,s)+p.u.V3K_IDX_SHIFT,a=e.indexOf(" ",s),s=a+1,a=e.indexOf(" ",s),n[l]=e.substring(s,a);const t=new Array(2);for(let n=0;n<2;++n)s=a+1,a=e.indexOf(" ",s),t[n]=parseFloat(e.substring(s,a));i[l]=t[0],o[l]=t[1],s=a,a=e.indexOf("\n",s)+1,r[l]=e.slice(s,a),s=a}return{atomTypes:n,x:i,y:o,kwargs:r}}(u,h.atomCount),m=function(e,t){const n=new Uint32Array(t),i=new Array(t),o=new Map,r=new Map;let s=e.indexOf(p.u.V3K_BEGIN_BOND_BLOCK);s=e.indexOf("\n",s);let a=s;for(let l=0;l<t;++l){const 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u=e.x.reduce(((t,n,i)=>{if(i===s)return t;if(i===c)return t;const o=e.y[i];return Math.sqrt((n-a)**2+(o-l)**2)>Math.sqrt((e.x[t]-a)**2+(e.y[t]-l)**2)?i:t}),-1);if(-1===u&&(u=e.x.length,e.x=new Float32Array([...e.x,-a]),e.y=new Float32Array([...e.y,-l]),e.atomTypes=[...e.atomTypes,"H"],e.kwargs=[...e.kwargs,""],t.atomPairs.push([c+1,u+1]),t.bondTypes=new Uint32Array([...t.bondTypes,1]),t.kwargs.set(t.atomPairs.length-1,"")),i.set(u+1,o),1===o)n.unshift(e.atomTypes[u]);else{if(2!==o)throw new Error(`Unexpected missing R-group: ${o}`);n.splice(1,0,e.atomTypes[u])}}return function(e,t,n){for(const[i,o]of n)e.atomTypes[i-1]=t[o-1]}(e,n,i),function(e,t){t.rNodes=Array.from(e.keys());for(let n=0;n<t.rNodes.length;n++)for(const i of[1,2])if(e.get(t.rNodes[n])===i){const e=t.rNodes[i-1];t.rNodes[i-1]=t.rNodes[n],t.rNodes[n]=e}}(i,o),y(t,o),o}(d,m,a,c),f=function(e){let t=[],n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const 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S(e,t)+Math.PI/2}(e.atoms.x[e.meta.terminalNodes[1]-1],e.atoms.y[e.meta.terminalNodes[1]-1])))}(e,s),function(e,t){const n=e.atoms.x;n[e.meta.rNodes[1]-1]>n[t-1]&&function(e,t,n){const i=t-1,o=n-1,r=e.atoms.x,s=e.atoms.y,a=r[i],l=s[i];r[i]=r[o],s[i]=s[o],r[o]=a,s[o]=l}(e,t,e.meta.rNodes[1])}(e,s))}(v):e===p.u.RIBOSE.symbol||e===p.u.DEOXYRIBOSE.symbol?function(e,t){const n=e.atoms.x,i=e.atoms.y;let o=e.meta.terminalNodes[0]-1;const r=e.meta.rNodes[1]-1;E(e,-n[o],-i[o]);const s=S(n[e.meta.rNodes[2]-1],i[e.meta.rNodes[2]-1]);A(e.atoms,-s),n[e.meta.rNodes[0]-1]>n[e.meta.rNodes[1]-1]&&x(e);const a=S(n[r],i[r]);A(e.atoms,3*Math.PI/2-a),t.value=function(e){const t=e.atoms.x,n=e.atoms.y,i=e.meta.rNodes[2]-1,o=e.meta.terminalNodes[2]-1,r=t[i]-t[o],s=n[i]-n[o];return Math.atan2(r,s)}(e),o=e.meta.terminalNodes[0]-1,E(e,-n[o],-i[o])}(v,o):e===p.u.PHOSPHATE.symbol?function(e){const t=e.meta.rNodes[1]-1,n=e.meta.rNodes[0]-1,i=e.atoms.x,o=e.atoms.y;E(e,-i[t],-o[t]);const r=S(i[n],o[n]);A(e.atoms,Math.PI/2-r)}(v):function(e,t){const n=e.atoms.x,i=e.atoms.y,o=e.meta.terminalNodes[0]-1,r=e.meta.rNodes[0]-1;E(e,-n[o],-i[o]);const s=S(n[r],i[r]),a=t.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");A(e.atoms,Math.PI-s+a);const c=function(e,t){return(0,l.YN)(Math.sqrt((e.x-t.x)**2+(e.y-t.y)**2))}({x:n[e.meta.rNodes[0]-1],y:i[e.meta.rNodes[0]-1]},{x:n[e.meta.terminalNodes[0]-1],y:i[e.meta.terminalNodes[0]-1]});if(1!=c)for(let e=0;e<n.length;++e)n[e]=(0,l.YN)(n[e]/c),i[e]=(0,l.YN)(i[e]/c)}(v,o),function(e,t,n){if("PEPTIDE"===e){b(t,e);const n=w(t,t.meta.rNodes[1]);n?.removedAtom&&(t.terminalR2Atom=n.removedAtom)}else n===p.u.RIBOSE.symbol||n===p.u.DEOXYRIBOSE.symbol?(w(t,t.meta.rNodes[1]),t.meta.rNodes[1]=t.meta.terminalNodes[1],y(t.bonds,t.meta),b(t,e),w(t,t.meta.rNodes[1]),w(t,t.meta.rNodes[0]),w(t,t.meta.rNodes[2])):n===p.u.PHOSPHATE.symbol&&(t.meta.terminalNodes[0]=t.meta.rNodes[0],E(t,-t.atoms.x[t.meta.terminalNodes[0]-1],-t.atoms.y[t.meta.terminalNodes[0]-1]),b(t,e),w(t,t.meta.rNodes[1]))}(i,v,e),function(e){let t=0;for(;t<e.atoms.atomTypes.length;)e.atoms.atomTypes[t]===p.u.HYDROGEN&&(w(e,t+1),--t),++t}(v),function(e){let t=0;for(;t<e.atoms.atomTypes.length;)"oh"===e.atoms.atomTypes[t]?.toLowerCase()&&(e.atoms.atomTypes[t]="O"),"?"===e.atoms.atomTypes[t]&&(e.atoms.atomTypes[t]="H"),++t}(v),function(e){const t=" RGROUPS=(1 1)";for(let n=0;n<(e.atoms.kwargs?.length??0);n++){const i=e.atoms.kwargs[n];i&&i.includes(t)&&(e.atoms.kwargs[n]=i.replace(t,""))}}(v),v}var r;return null}(t,n,i,o,r);if(!a)throw new Error(`Monomer with symbol '${t}' is absent the monomer library`);(0,u.LQ)(e,s,a)}}function y(e,t){const n=t.rNodes;t.terminalNodes=new Array(n.length).fill(0);const i=t.terminalNodes,o=e.atomPairs;let r=0,s=0;for(;r<o.length&&s<i.length;){for(let e=0;e<i.length;++e)for(let t=0;t<2;++t)o[r][t]===n[e]&&(i[e]=o[r][(t+1)%2],n.length,++s);++r}}function b(e,t){e.meta.rNodes.length>1&&(e.meta.backboneShift=v(e,e.meta.rNodes[1]-1,e.meta.terminalNodes[0]-1)),"RNA"===t&&e.meta.rNodes.length>2&&(e.meta.branchShift=v(e,e.meta.rNodes[2]-1,e.meta.terminalNodes[0]-1))}function v(e,t,n){return[(0,l.YN)(e.atoms.x[t]-e.atoms.x[n]),(0,l.YN)(e.atoms.y[t]-e.atoms.y[n])]}function w(e,t){if(void 0!==t){const n=t-1,i=e.atoms,o=e.bonds,r=e.meta,s=i.atomTypes.splice(n,1)[0];i.x=C(Float32Array,i.x,n,1),i.y=C(Float32Array,i.y,n,1),i.kwargs.splice(n,1);for(let e=0;e<r.terminalNodes.length;++e)r.terminalNodes[e]>t?--r.terminalNodes[e]:r.terminalNodes[e]===t&&(r.terminalNodes[e]=-1);for(let e=0;e<r.rNodes.length;++e)r.rNodes[e]>t?--r.rNodes[e]:r.rNodes[e]===t&&(r.rNodes[e]=-1);let a=0;for(;a<o.atomPairs.length;){const e=o.atomPairs[a][0],n=o.atomPairs[a][1];e===t||n===t?(o.atomPairs.splice(a,1),o.bondTypes=C(Uint32Array,o.bondTypes,a,1),o.bondConfiguration.has(a)&&o.bondConfiguration.delete(a),o.kwargs.has(a)&&o.kwargs.delete(a),--a):(o.atomPairs[a][0]=e>t?e-1:e,o.atomPairs[a][1]=n>t?n-1:n),++a}let l=Array.from(o.bondConfiguration.keys());return l.forEach((e=>{if(o.bondConfiguration.has(e)&&e>n){const t=o.bondConfiguration.get(e);o.bondConfiguration.delete(e),o.bondConfiguration.set(e-1,t)}})),l=Array.from(o.kwargs.keys()),l.forEach((e=>{if(o.kwargs.has(e)&&e>n){const t=o.kwargs.get(e);o.kwargs.delete(e),o.kwargs.set(e-1,t)}})),s?{removedAtom:s}:void 0}}function C(e,t,n,i){const o=new e(t.length-i);let r=0,s=0;for(;r<t.length;)r===n&&(r+=i),o[s]=t[r],++s,++r;return o}function S(e,t){let n;if(0===e)n=t>0?0:Math.PI;else if(0===t)n=e>0?-Math.PI/2:Math.PI/2;else{const i=t/e,o=Math.atan(i);n=e<0?Math.PI/2+o:-Math.PI/2+o}return n}function A(e,t){if(0!==t){const n=e.x,i=e.y,o=Math.cos(t),r=Math.sin(t);for(let e=0;e<n.length;++e){const t=n[e];n[e]=(0,l.YN)(t*o-i[e]*r),i[e]=(0,l.YN)(t*r+i[e]*o)}}}function x(e){M(e,!1)}function M(e,t){if(t){const t=e.atoms.y;for(let e=0;e<t.length;e++)t[e]=-t[e]}else{const t=e.atoms.x;for(let e=0;e<t.length;e++)t[e]=-t[e]}const n=e.bonds.bondConfiguration;for(const[e,t]of n){const i=1===t?3:1;n.set(e,i)}}function E(e,t,n){const i=e.atoms.x,o=e.atoms.y;for(let e=0;e<i.length;++e)i[e]=(0,l.YN)(i[e]+t),void 0!==n&&(o[e]=(0,l.YN)(o[e]+n))}},294:(e,t,n)=>{"use strict";function i(e,t){return e[t.polymerType]?.[t.symbol]}function o(e,t){return!!e[t.polymerType]?.[t.symbol]}function r(e,t,n){let i=e[t.polymerType];i||(i=e[t.polymerType]={}),i[t.symbol]=n}n.d(t,{Cg:()=>s,LQ:()=>r,bq:()=>o,vF:()=>a,xb:()=>i});class s extends Map{constructor(e){super(e)}}class a{constructor(e,t){this.molfile=e,this.monomers=t}static createEmpty(){return new a("",new s(null))}}},330:(e,t,n)=>{"use strict";n.d(t,{kA:()=>o,pz:()=>s,qj:()=>r,vG:()=>a});var i=n(2003);function o(e,t){return e?e.columns.getUnusedName(t):t}function r(e,t){return o(e,`molfile(${t})`)}function s(e){let t;if(e===i.YI.PT||e===i.YI.UN)t="PEPTIDE";else{if(e!==i.YI.RNA&&e!==i.YI.DNA)throw new Error(`Unexpected alphabet '${e}'.`);t="RNA"}return t}function a(e){const t=7===e.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e);return t?[parseInt(t[1],16)/256,parseInt(t[2],16)/256,parseInt(t[3],16)/256,t.length>4?parseInt(t[4],16)/256:.3]:null}},1093:(e,t,n)=>{"use strict";n(7362);class i{}i.SemType="Nucleotides",i.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",i.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"}},7362:(e,t,n)=>{"use strict";n.d(t,{e:()=>i});class i{static makePalette(e,t=!1,n=i){const o={};return e.forEach((e=>{const 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this._props||(this._props=this.emptyProps),this._props}set props(e){this._propsChanging=!0;try{this._props=e,this.applyProps(),this.onChanged.next()}finally{this._propsChanging=!1}}saveProps(){const e={};for(const[t,n]of Object.entries(this.props))"_onChanged"!==t&&"logger"!==t&&(e[t]=this.props[t]);return e}async detach(){}get filterSummary(){return this.props.substructure}get isFiltering(){return""!==this.props.substructure}resetFilter(){this.props=this.emptyProps,this.onChanged.next()}}},4152:(e,t,n)=>{"use strict";var i=n(6082),o=n(7362),r=n(6718);function s(e,t=!0){if(null==e)return"rgb(100,100,100)";const n=i.Color.fromHtml(e);if(t){const e=i.Color.g(n),t=i.Color.r(n),o=i.Color.b(n),r=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(r>210)return`rgb(${t/r*210},${e/r*210},${o/r*210})`}return i.Color.toRgb(n)}class a{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}class l{}class c extends l{static get palette(){return c._pallete||(c._pallete=c.buildPalette()),c._pallete}static buildPalette(){return(0,r.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{c.customMonomerColors={},c.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const i of n){const n=t.getMonomer(e,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][e]=s(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(o.e.colourPalette))}get(e,t){const n=c.palette.length,i=c.customMonomerColors[e],o=t??"PEPTIDE";if(i&&i[o])return i[o];const r=a.hashCode(e)%n;return s(c.palette[r])}}c._pallete=null,c.customMonomerColors={},c.polymerTypes=[]},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>s,sD:()=>l});var i=n(4328),o=n(1858),r=n(8070);function s(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const i=e.cell.column;if(t=t??(i?i.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,i,t]}class a{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class l extends a{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++l.viewerCounter,this.errors=[],this._onRendered=new o.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}})))),this.tableCol&&this.subs.push(i.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(i.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,r.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}l.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>i});const i={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Jy:()=>b,S$:()=>y,U0:()=>v});var i=n(7389),o=n(6082),r=n(1991),s=n.n(r),a=n(8312),l=n(2003),c=n(6642),u=n(6718),h=n(9192),d=n(3856),p=n(673),m=n(3599),g=n(5553),f=n(9713);const y="rgb(100,100,100)";class b extends c.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,i,r){if(super(e,t,n),this.monomerLengthLimit=i,this.propsProvider=r,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const e=[l.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(f.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(f.filter((e=>e.args.source===this.tableCol&&e.args.key===l.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,i,o,r){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(e),l=t-2*this.padding;let c=0;const u=[];if(i.length>0)for(let t=o;t<i.length;t++){const n=i.getOriginal(t),o=this.props.monomerToShort(n,r);u.push({text:o,posIdx:t}),c=Math.max(c,e.measureText(o).width)}if(0===u.length)return{lineLayouts:[],lineHeight:s};const d=c;let p=Math.floor((l+a)/(d+a));p=Math.max(1,p);const m=n-2*this.padding,g=Math.max(0,Math.floor(m/s)),f=[];let y=0;for(let e=0;e<g&&y<u.length;e++){const t=[];for(let e=0;e<p&&y<u.length;e++){const n=u[y],i=this.padding+e*(d+a);t.push({posIdx:n.posIdx,x:i,width:d,om:n.text,isSeparator:!1}),y++}f.push({lineIdx:e,elements:t})}return{lineLayouts:f,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,u.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,r=Math.ceil(t/i)+o,s=n.splitter(e),a=Math.min(r,s.length),l=new Array(a-o);let c=0;for(let e=o;e<a;++e){const i=s.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(l[e-o]=a,c+=a,c>t)break}return l}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/i)+t,r=n.getSplitted(e),s=Math.min(o,r.length);let a=this._monomerLengthList[e];if(null===a||a.length!=s-t){a=this._monomerLengthList[e]=new Array(r.length);let i=0;for(let e=t;e<s;++e){const o=r.getOriginal(e),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[e-t]=l,i+=l,i>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:i}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=this.positionShift,s=Math.ceil(this.colWidth/o)+r;for(let e=n;e<i;e++){if(this._processedRows.get(e)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,s),i=Math.min(s,n.length);i-r>t.length&&t.push(...new Array(i-r-t.length).fill(o));let a=0;for(let e=r;e<i;++e){const i=n.getOriginal(e),o=this.props.monomerToShort(i,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(t[e-r]=Math.max(t[e-r]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,i){const[o,r]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let i,o=100,r=0,s=e.length-1;for(;r<=s;){if(i=Math.floor((s+r)/2),e[i]<=t&&t<e[i+1])return i;if(t<e[i]?s=i-1:r=i+1,--o<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(r,t,i)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[l.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,i,r,a,c){const u=a.grid?.canvas===e.canvas;if(!this.seqHelper)return;const m=this.tableCol,g=this.positionShift;e.save();try{const c=this.seqHelper.getSeqHandler(m);let h=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(d.gp.maxMonomerLength));h=!isNaN(e)&&e?e:50}if(".mm.cellRenderer.maxMonomerLength"in m.temp){const e=m.temp[".mm.cellRenderer.maxMonomerLength"],t="number"==typeof e?e:parseInt(e);h=!isNaN(t)&&t?t:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=h){let e=0;const t=8;e=m.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(h),this.setSeparatorWidth(c.isMsa()?t:e),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const f=a.cell.rowIndex,b=a.cell.value;u&&(i=v(a.grid,e,t,i,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,i,r),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const w=m.meta.units,C=m.getTag(l.gp.aligned),S=m.getTag(l.gp.separator)??"",A=u?c.getSplitted(f):c.splitter(b);let x=d.yg.classic;C?.includes("MSA")&&w===l.Hi.SEPARATOR&&(x=d.yg.MSA);const M=m.temp["reference-sequence"],E=this.tableCol.temp["current-word"],T=(()=>{const e=(0,c.splitter)(null!=M&&""!==M?M:E??"");return s().count(0).take(e.length).slice(g).map((t=>e.getCanonical(t))).toArray()})(),_=Number.parseInt(m.getTag(l.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const s=[],l=this.calculateMultiLineLayoutDynamic(e,i,r,A,g,h);let u=n+this.padding;1===l.lineLayouts.length&&(u=n+(r-l.lineHeight)/2);for(const i of l.lineLayouts){const r=u+i.lineIdx*l.lineHeight;for(const u of i.elements){const h=t+u.x,p=u,f=p.posIdx,b=A.getCanonical(f);let v=y;const w=this.getMonomerLib();w&&(v=w.getMonomerTextColor(c.defaultBiotype,b));let C=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&T.length>0){const e=f-g;e>=0&&e<T.length&&b===T[e]&&(C=.7)}s.push({lineIdx:i.lineIdx,monomerIdx:f-g,bounds:new o.Rect(u.x,r-n,u.width,l.lineHeight),sequencePosition:f}),(0,d.oZ)(e,p.om,h,r,u.width,l.lineHeight,{color:v,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(_)||_<1?void 0:_,wordIdx:f})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,s)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(g)?e.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,i);u||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,i)));const s=this.props.separatorWidth+1*this.props.fontCharWidth,l=Math.min(A.length,Math.ceil(i/s)+g);for(let s=g;s<l;++s){const l=s<A.length?A.getOriginal(s):c.defaultGapOriginal,u=s<A.length?A.getCanonical(s):c.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(c.defaultBiotype,u));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:S,last:s===A.length-1,drawStyle:x,maxWord:o,wordIdx:s-g,gridCell:a,referenceSequence:T,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(_)||_<1?void 0:_-g};(0,d.oZ)(e,l,t+this.padding+this._leftThreeDotsPadding,n,i,r,m)}if(this.shouldRenderShiftedThreeDots(g)){const s={color:y,pivot:0,left:!0,transparencyRate:0,separator:S,last:!1,drawStyle:x,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,d.oZ)(e,"...",t+this.padding,n,i,r,s)}}}catch(e){const[t,n]=(0,h.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,r=e.bounds,s=t.offsetX-e.gridColumn.left+(e.gridColumn.left-r.x),a=t.offsetY-r.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let c=null;const u=this._cellBounds.get(e.tableRowIndex);if(u){for(const e of u)if(e.bounds.contains(s,a)){c=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;c=this.getPosition(e.tableRowIndex,s,r.width,t)}this.logger.debug(`${n}, argsX: ${s}, argsY: ${a}, left: ${c}`);const h=this.seqHelper.getSeqHandler(this.tableCol),d=h.getSplitted(e.tableRowIndex);if(null!==c&&c>=0&&c+o<d.length){const n=h.alphabet??l.YI.UN,r={position:c,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:d.getCanonical(c+o)},s=[];let a=this._monomerStructureMap[r.symbol];if(!a){const e=this.getMonomerLib();a=this._monomerStructureMap[r.symbol]=e?e.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}s.push(a),i.tooltip.show(i.divV(s),t.x+16,t.y+16),(0,g.WN)(e,r)}else-1===c?i.tooltip.show(i.divText(`${Math.min(o,d.length)} hidden monomers`),t.x+16,t.y+16):i.tooltip.hide(),(0,g.WN)(e,null)}}function v(e,t,n,i,o){return e?Math.max(Math.min(e.canvas.width/o-n,i)):Math.max(t.canvas.width/o-n,0)}},3856:(e,t,n)=>{"use strict";n.d(t,{Mn:()=>u,gp:()=>c,oZ:()=>p,yg:()=>h});var i=n(6082),o=n(7278);const r="rgb(100,100,100)",s="#808080",a="rgb(0,0,0)",l=o.zS;var c,u,h;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(c||(c={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(u||(u={})),function(e){e.MSA="MSA",e.classic="classic"}(h||(h={}));const d=new class{constructor(){this.color=r,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=h.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function p(e,t,n,o,c,u,p){var m,g,f;const y={...d,...p};if(y.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let i=t;null!=y.maxLengthOfMonomer&&(i=l(i,y.maxLengthOfMonomer));const s=Math.max(.1,1-(y.transparencyRate??0));e.globalAlpha=s;const h=e.measureText(i),d=h.fontBoundingBoxAscent+h.fontBoundingBoxDescent,p=o+(u-d)/2+h.fontBoundingBoxAscent;let m=y.color??r;return m&&m!==r||(m=a),e.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n,o,c,u),e.restore(),e.fillStyle=m),e.fillText(i,n+c/2,p),e.globalAlpha=1,e.textBaseline="top",e.textAlign="start",n+c}p.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let b=t.substring(0),v=y.last?"":y.separator;y.drawStyle===h.MSA&&(v="");let w=!0,C=!0,S="difference";if(null!=y.gridCell&&null!=y.gridCell.cell.column&&(w=y.gridCell.cell.column.temp["color-code"]??!0,C=y.gridCell.cell.column.temp["compare-with-current"]??!0,S=y.gridCell.cell.column.temp["highlight-difference"]??"difference"),y.referenceSequence){const e=y.referenceSequence[y.wordIdx];C&&y.referenceSequence.length>0&&"difference"===S&&(y.transparencyRate=b==e?.7:y.transparencyRate),C&&y.referenceSequence.length>0&&"equal"===S&&(y.transparencyRate=b!=e?.7:y.transparencyRate)}null!=y.maxLengthOfMonomer&&(b=l(b,y.maxLengthOfMonomer));const A=b+v;(m=y.monomerTextSizeMap)[A]??(m[A]=e.measureText(A));let x=y.monomerTextSizeMap[A];(g=y.monomerTextSizeMap)[b]??(g[b]=e.measureText(b));let M=y.monomerTextSizeMap[b].width;const E=u/2-(x.fontBoundingBoxAscent+x.fontBoundingBoxDescent)/2+1;(f=y.monomerTextSizeMap)[v]??(f[v]=e.measureText(v));const T=y.monomerTextSizeMap[v].width;function _(t,r){let l=w?y.color:a;y.selectedPosition===y.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,y.monomerTextSizeMap[b].width+8,u+10),l=i.Color.toHtml(i.Color.setAlpha(i.Color.fromHtml(l),255))),e.fillStyle=l,e.globalAlpha=1-y.transparencyRate,y.drawStyle===h.classic&&(e.fillText(b,n+t,o+E),e.fillStyle=s,e.fillText(v,n+r,o+E)),y.drawStyle===h.MSA&&e.fillText(b,n+t,o+E),e.globalAlpha=1}x=x.width,y.drawStyle===h.MSA&&(M=y.maxWord[y.wordIdx],x=y.maxWord[y.wordIdx]);const I=(y.maxWord[y.wordIdx]??0)-(y.maxWord[0]??0);if(y.left||x>c)return _(I,I+M),n+I+M+T;{const e=(c-x)/2;return _(e,e+M),n+I+e+M}}},6307:(e,t,n)=>{"use strict";n.d(t,{F:()=>s});var i=n(7389),o=n(6082),r=n(439);function s(e,t,n){let s=0,a=null;for(const t of Object.values(e))s+=t,a=null===a?t:Math.max(a,t);const l=a/s,c=Object.assign({},...Array.from(Object.entries(e)).sort(((e,t)=>t[1]-e[1])).map((([e,a])=>{const c=a/s;let u;try{const i=n.getMonomerColors(t,e);u=i?.backgroundcolor||"#CCCCCC"}catch(t){console.warn(`Failed to get colors for monomer ${e}:`,t),u="#CCCCCC"}const h=i.div("",{classes:"macromolecule-cell-comp-analysis-bar"});h.style.width=50*c/l+"px",h.style.backgroundColor=u,r._S===e&&(h.style.borderWidth="1px",h.style.borderStyle="solid",h.style.borderColor=o.Color.toHtml(o.Color.lightGray));const d=r._S===e?"-":e,p=i.div(`${(100*c).toFixed(2)}%`),m=i.div([h,p],{classes:"macromolecule-cell-comp-analysis-value"});return{[d]:m}}))),u=i.tableFromMap(c);return Array.from(u.rows).forEach((e=>{const t=e.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;e.cells[0].style.color=t})),u}},3151:(e,t,n)=>{"use strict";n.d(t,{EK:()=>l,Ec:()=>r,f6:()=>i,pe:()=>s,q7:()=>a,yw:()=>o});const i=["symbol","molfile","rgroups","name"],o="MonomerName",r={monomerType:null,smiles:null,name:"Name",author:null,molfile:"molecule",naturalAnalog:"MonomerNaturalAnalogCode",rgroups:"MonomerCaps",createDate:null,id:null,polymerType:"MonomerType",symbol:"MonomerName"},s={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},a="p",l=new RegExp(`[rd]\\((\\w)\\)${a}?`,"g")},9192:(e,t,n)=>{"use strict";function i(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?i(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function o(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?o(e.$thrownJsError):void 0}function r(e){return[i(e),o(e)]}n.d(t,{AP:()=>r})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>r});var i=n(6082),o=n(439);class r{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(e,t){return this._fileContent.slice(e,t).split(/\s/).join("")}parseColumns(){const e=/^>(.*)$/gm;let t,n=0;for(;t=e.exec(this._fileContent);){const i=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(i),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=i.Column.fromStrings("description",this.descriptionsArray),t=i.Column.fromStrings("sequence",this.sequencesArray);return 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