@datagrok/bio 2.22.5 → 2.22.6

package/dist/package.js

@@ -1,4 +1,4 @@
-var bio;(()=>{var t={8924:(t,e,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(t){const e=t in o.aaSynonyms?o.aaSynonyms[t]:t;return super.get(e)}}o.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class r{static getPalette(t="grok"){switch(t){case"grok":return o.GrokGroups;case"lesk":return o.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",i="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:i+=o;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[i,o]=this.getInnerOuter(t);if(i=i.length>6?`${i.slice(0,3)}...`:i,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,i,o,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,o,2]:[this.undefinedColor,i,o,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,o,3]:[this.undefinedColor,i,o,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,o,4]:[this.undefinedColor,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:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var i=n(6082);async function o(){const t=i.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},3599:(t,e,n)=>{"use strict";n.d(e,{o:()=>i.o});var i=n(6869)},9124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>r,fA:()=>s});var i=n(7389),o=n(6082);async function r(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}function s(t,e){if(!t)throw new Error("Argument 'a' of type Atom or HelmType is mandatory.");let n,i;const o=t;return"ATOM"===o.T?(n=o.biotype(),i=o.elem):(n=t,i=e),[n,i]}o.JsInputBase,Error,i.input.helmAsync=async function(t,e){return(await r()).createHelmInput(t,e)}},8438:(t,e,n)=>{"use strict";function i(t){return t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):t}n.d(e,{D:()=>i})},8123:(t,e,n)=>{"use strict";n.d(e,{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:(t,e,n)=>{"use strict";n.d(e,{Eu:()=>a,ub:()=>s});var i=n(4328);const o="Libraries";let r=Promise.resolve();async function s(){let t;return r=r.then((async()=>{const e=i.userSettings.getValue(o,"Settings",!0);t=e?JSON.parse(e):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],t.duplicateMonomerPreferences=t.duplicateMonomerPreferences instanceof Object?t.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await r,t}async function a(t){r=r.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),i.userSettings.add(o,"Settings",JSON.stringify(t),!0)})),await r}},5553:(t,e,n)=>{"use strict";n.d(e,{Qc:()=>A,WN:()=>S});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=(t,e,n,i)=>{"function"==typeof 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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},A={sugar:v,phosphate:w,seqLength:t.length,atomCount:c,bondCount:u},S=new o.Cg,x=[];let E,T=0;for(C.i=0;C.i<A.seqLength;++C.i){const n=t[C.i];if(n.symbol===s._S)continue;const i=(0,o.xb)(e,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});E=i.terminalR2Atom;const r=C.nodeShift,l=C.bondShift;b(i,g,y,C,A),i.stereoAtoms?.forEach((t=>x.push(t+T))),T+=i.atoms.x.length;const c=C.nodeShift-r,h=new Array(c);for(let t=0;t<c;++t)h[t]=r+t;const u=C.bondShift-l,d=new Array(u);for(let t=0;t<u;++t)d[t]=l+t;S.set(C.i,{biotype:n.biotype,symbol:n.symbol,atoms:h,bonds:d})}p&&function(t,e,n,o,r=i.u.OXYGEN){const s=n.nodeShift+1;t[o.atomCount]=i.u.V3K_BEGIN_DATA_LINE+s+" "+(r??i.u.OXYGEN)+" "+f(n.backbonePositionShift[0])+" "+n.flipFactor*f(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;e[o.bondCount]=i.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(g,y,C,A,E??i.u.OXYGEN);const M=i.u.V3K_BEGIN_COUNTS_LINE+c+" "+u+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,_+=M,_+=i.u.V3K_BEGIN_ATOM_BLOCK,_+=g.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(t){const e=[];let n=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let i=0;i<t.length;i++){const o=`${n} ${t[i]}`;o.length>76?(e.push(`${n} -\n`),n=`M  V30 ${t[i]}`):n=o,i===t.length-1&&e.push(`${n})\n`)}return`M  V30 BEGIN COLLECTION\n${e.join("")}M  V30 END COLLECTION\n`}(x)),_+=i.u.V3K_END_CTAB_BLOCK,_+=i.u.V3K_END,{molfile:_,monomers:S}}function h(t,e,n,i){i.flipFactor=(-1)**(i.i%2),u(t,e,n,i)}function u(t,e,n,o){!function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;e[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+t.atoms.atomTypes[o]+" "+f(n.backbonePositionShift[0]+t.atoms.x[o])+" "+f(n.backbonePositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}}(t,e,o),p(t,n,o),function(t,e,n){if(0!==n.backboneAttachNode){const o=n.bondShift,r=n.backboneAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[n.bondShift-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}}(t,n,o),null!==t.meta.branchShift&&t.meta.terminalNodes.length>2&&function(t,e){e.branchAttachNode=e.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)e.branchPositionShift[n]=e.backbonePositionShift[n]+t.meta.branchShift[n]}(t,o),function(t,e){e.backboneAttachNode=e.nodeShift+t.meta.terminalNodes[1],e.bondShift+=t.bonds.atomPairs.length+1,e.nodeShift+=t.atoms.atomTypes.length,e.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,e.backbonePositionShift[1]+=e.flipFactor*(t.meta.backboneShift?.[1]??0)}(t,o)}function d(t,e,n,o,r){if(0===o.i)u(r.sugar,e,n,o);else for(const t of[r.phosphate,r.sugar])u(t,e,n,o);!function(t,e,n,o){(function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;e[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+t.atoms.atomTypes[o]+" "+f(n.branchPositionShift[0]+t.atoms.x[o])+" "+f(n.branchPositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}})(t,e,o),p(t,n,o),function(t,e,n){const o=n.bondShift,r=n.branchAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[o-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}(t,n,o);const r=o.bondShift,s=o.branchAttachNode,a=t.meta.terminalNodes[0]+o.nodeShift;n[r-1]=i.u.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+a+"\n",o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length}(t,e,n,o)}function p(t,e,n){for(let o=0;o<t.bonds.atomPairs.length;++o){const r=n.bondShift+o+1,s=t.bonds.atomPairs[o][0]+n.nodeShift,a=t.bonds.atomPairs[o][1]+n.nodeShift;let l="";if(t.bonds.bondConfiguration.has(o)){let e=t.bonds.bondConfiguration.get(o);n.flipFactor<0&&(e=1===e?3:1),l=" CFG="+e}const c=t.bonds.kwargs.has(o)?" 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i=n(4328),o=n(6082),r=n(1991),s=n.n(r),a=n(439),l=n(3561),c=n(9235),h=n(294),u=n(9192),d=n(330),p=n(8123);async function m(t,e,n,r,l){if(e.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${e.semType}'`]};let h=e;const p=r.getSeqHandler(e);let m,g;p.notation!==a.Hi.SEPARATOR&&(h=p.convert(a.Hi.SEPARATOR,"."),h.name=e.name);try{g=r.getSeqHandler(h).alphabet,m=(0,d.pz)(g)}catch(t){const[e,n]=(0,u.AP)(t);return{molCol:null,warnings:[e]}}const y=function(t,e){const n=t.length,o=new Array(n),r=e.getSeqHandler(t);let a=!1;const l=r.defaultBiotype;for(let t=0;t<n;++t){const e=r.getSplitted(t);a||(a=0===e.length),o[t]=s().count(0).take(e.length).filter((t=>!e.isGap(t))).map((t=>({position:t,biotype:l,symbol:e.getCanonical(t)}))).toArray()}return a&&i.shell.warning(`Some values in the "${t.name}" column are empty`),o}(h,r),b=f(y,m,g,n,l),v=h.length,w=await(0,c.R)(h,b,g,m,n,r,l);return w.warnings.length>.05*v&&i.shell.warning(`Molfile conversion resulted in ${w.warnings.length} errors`),w}function f(t,e,n,i,o){const r=(0,l.Hb)(i,e,n),s={},c={value:null};if("RNA"===e){const t=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of t)g(s,n.symbol,r,o,e,c)}for(let n=0;n<t.length;++n){const i=t[n];for(const t of i){const n=t.symbol;if(""!==n)try{if("RNA"===e&&3===n.split(/\(|\)/).filter((t=>!!t)).length){const t=n.split(/\(|\)/)[1];g(s,t,r,o,e,c),s[e]?.[t]&&(s[e][n]=s[e][t])}else g(s,n,r,o,e,c)}catch(t){const e=t instanceof Error?t.message:t.toString(),i=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${e}\n${i}`),new Error(`Can't get monomer '${n}' from library: ${e}`)}}}return s}function g(t,e,n,i,o,r){const s={polymerType:o,symbol:e};if(!(0,h.bq)(t,s)){const a=function(t,e,n,i,o){if(e.has(t)){const 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o=t.meta.terminalNodes[0]-1;const r=t.meta.rNodes[1]-1;T(t,-n[o],-i[o]);const s=A(n[t.meta.rNodes[2]-1],i[t.meta.rNodes[2]-1]);S(t.atoms,-s),n[t.meta.rNodes[0]-1]>n[t.meta.rNodes[1]-1]&&x(t);const a=A(n[r],i[r]);S(t.atoms,3*Math.PI/2-a),e.value=function(t){const e=t.atoms.x,n=t.atoms.y,i=t.meta.rNodes[2]-1,o=t.meta.terminalNodes[2]-1,r=e[i]-e[o],s=n[i]-n[o];return Math.atan2(r,s)}(t),o=t.meta.terminalNodes[0]-1,T(t,-n[o],-i[o])}(v,o):t===p.u.PHOSPHATE.symbol?function(t){const e=t.meta.rNodes[1]-1,n=t.meta.rNodes[0]-1,i=t.atoms.x,o=t.atoms.y;T(t,-i[e],-o[e]);const r=A(i[n],o[n]);S(t.atoms,Math.PI/2-r)}(v):function(t,e){const n=t.atoms.x,i=t.atoms.y,o=t.meta.terminalNodes[0]-1,r=t.meta.rNodes[0]-1;T(t,-n[o],-i[o]);const s=A(n[r],i[r]),a=e.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");S(t.atoms,Math.PI-s+a);const c=function(t,e){return(0,l.YN)(Math.sqrt((t.x-e.x)**2+(t.y-e.y)**2))}({x:n[t.meta.rNodes[0]-1],y:i[t.meta.rNodes[0]-1]},{x:n[t.meta.terminalNodes[0]-1],y:i[t.meta.terminalNodes[0]-1]});if(1!=c)for(let t=0;t<n.length;++t)n[t]=(0,l.YN)(n[t]/c),i[t]=(0,l.YN)(i[t]/c)}(v,o),function(t,e,n){if("PEPTIDE"===t){b(e,t);const n=w(e,e.meta.rNodes[1]);n?.removedAtom&&(e.terminalR2Atom=n.removedAtom)}else n===p.u.RIBOSE.symbol||n===p.u.DEOXYRIBOSE.symbol?(w(e,e.meta.rNodes[1]),e.meta.rNodes[1]=e.meta.terminalNodes[1],y(e.bonds,e.meta),b(e,t),w(e,e.meta.rNodes[1]),w(e,e.meta.rNodes[0]),w(e,e.meta.rNodes[2])):n===p.u.PHOSPHATE.symbol&&(e.meta.terminalNodes[0]=e.meta.rNodes[0],T(e,-e.atoms.x[e.meta.terminalNodes[0]-1],-e.atoms.y[e.meta.terminalNodes[0]-1]),b(e,t),w(e,e.meta.rNodes[1]))}(i,v,t),function(t){let e=0;for(;e<t.atoms.atomTypes.length;)t.atoms.atomTypes[e]===p.u.HYDROGEN&&(w(t,e+1),--e),++e}(v),function(t){let e=0;for(;e<t.atoms.atomTypes.length;)"oh"===t.atoms.atomTypes[e]?.toLowerCase()&&(t.atoms.atomTypes[e]="O"),"?"===t.atoms.atomTypes[e]&&(t.atoms.atomTypes[e]="H"),++e}(v),function(t){const e=" RGROUPS=(1 1)";for(let n=0;n<(t.atoms.kwargs?.length??0);n++){const i=t.atoms.kwargs[n];i&&i.includes(e)&&(t.atoms.kwargs[n]=i.replace(e,""))}}(v),v}var r;return null}(e,n,i,o,r);if(!a)throw new Error(`Monomer with symbol '${e}' is absent the monomer library`);(0,h.LQ)(t,s,a)}}function y(t,e){const n=e.rNodes;e.terminalNodes=new Array(n.length).fill(0);const i=e.terminalNodes,o=t.atomPairs;let r=0,s=0;for(;r<o.length&&s<i.length;){for(let t=0;t<i.length;++t)for(let e=0;e<2;++e)o[r][e]===n[t]&&(i[t]=o[r][(e+1)%2],n.length,++s);++r}}function b(t,e){t.meta.rNodes.length>1&&(t.meta.backboneShift=v(t,t.meta.rNodes[1]-1,t.meta.terminalNodes[0]-1)),"RNA"===e&&t.meta.rNodes.length>2&&(t.meta.branchShift=v(t,t.meta.rNodes[2]-1,t.meta.terminalNodes[0]-1))}function v(t,e,n){return[(0,l.YN)(t.atoms.x[e]-t.atoms.x[n]),(0,l.YN)(t.atoms.y[e]-t.atoms.y[n])]}function w(t,e){if(void 0!==e){const n=e-1,i=t.atoms,o=t.bonds,r=t.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 t=0;t<r.terminalNodes.length;++t)r.terminalNodes[t]>e?--r.terminalNodes[t]:r.terminalNodes[t]===e&&(r.terminalNodes[t]=-1);for(let t=0;t<r.rNodes.length;++t)r.rNodes[t]>e?--r.rNodes[t]:r.rNodes[t]===e&&(r.rNodes[t]=-1);let a=0;for(;a<o.atomPairs.length;){const t=o.atomPairs[a][0],n=o.atomPairs[a][1];t===e||n===e?(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]=t>e?t-1:t,o.atomPairs[a][1]=n>e?n-1:n),++a}let l=Array.from(o.bondConfiguration.keys());return l.forEach((t=>{if(o.bondConfiguration.has(t)&&t>n){const e=o.bondConfiguration.get(t);o.bondConfiguration.delete(t),o.bondConfiguration.set(t-1,e)}})),l=Array.from(o.kwargs.keys()),l.forEach((t=>{if(o.kwargs.has(t)&&t>n){const e=o.kwargs.get(t);o.kwargs.delete(t),o.kwargs.set(t-1,e)}})),s?{removedAtom:s}:void 0}}function C(t,e,n,i){const o=new t(e.length-i);let r=0,s=0;for(;r<e.length;)r===n&&(r+=i),o[s]=e[r],++s,++r;return o}function A(t,e){let n;if(0===t)n=e>0?0:Math.PI;else if(0===e)n=t>0?-Math.PI/2:Math.PI/2;else{const i=e/t,o=Math.atan(i);n=t<0?Math.PI/2+o:-Math.PI/2+o}return n}function S(t,e){if(0!==e){const n=t.x,i=t.y,o=Math.cos(e),r=Math.sin(e);for(let t=0;t<n.length;++t){const e=n[t];n[t]=(0,l.YN)(e*o-i[t]*r),i[t]=(0,l.YN)(e*r+i[t]*o)}}}function x(t){E(t,!1)}function E(t,e){if(e){const e=t.atoms.y;for(let t=0;t<e.length;t++)e[t]=-e[t]}else{const e=t.atoms.x;for(let t=0;t<e.length;t++)e[t]=-e[t]}const n=t.bonds.bondConfiguration;for(const[t,e]of n){const i=1===e?3:1;n.set(t,i)}}function T(t,e,n){const i=t.atoms.x,o=t.atoms.y;for(let t=0;t<i.length;++t)i[t]=(0,l.YN)(i[t]+e),void 0!==n&&(o[t]=(0,l.YN)(o[t]+n))}},294:(t,e,n)=>{"use strict";function i(t,e){return t[e.polymerType]?.[e.symbol]}function o(t,e){return!!t[e.polymerType]?.[e.symbol]}function r(t,e,n){let i=t[e.polymerType];i||(i=t[e.polymerType]={}),i[e.symbol]=n}n.d(e,{Cg:()=>s,LQ:()=>r,bq:()=>o,vF:()=>a,xb:()=>i});class s extends Map{constructor(t){super(t)}}class a{constructor(t,e){this.molfile=t,this.monomers=e}static createEmpty(){return new a("",new s(null))}}},330:(t,e,n)=>{"use strict";n.d(e,{kA:()=>o,pz:()=>s,qj:()=>r,vG:()=>a});var i=n(2003);function o(t,e){return t?t.columns.getUnusedName(e):e}function r(t,e){return o(t,`molfile(${e})`)}function s(t){let e;if(t===i.YI.PT||t===i.YI.UN)e="PEPTIDE";else{if(t!==i.YI.RNA&&t!==i.YI.DNA)throw new Error(`Unexpected alphabet '${t}'.`);e="RNA"}return e}function a(t){const e=7===t.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(t):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(t);return e?[parseInt(e[1],16)/256,parseInt(e[2],16)/256,parseInt(e[3],16)/256,e.length>4?parseInt(e[4],16)/256:.3]:null}},1093:(t,e,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:(t,e,n)=>{"use strict";n.d(e,{e:()=>i});class i{static makePalette(t,e=!1,n=i){const o={};return t.forEach((t=>{const n=t[0],i=t[1];n.forEach(((t,n)=>{o[t]=this.colourPalette[i][e?0:n]}))})),new n(o)}constructor(t){this._palette=t}get(t,e){return this._palette[t]}}i.undefinedColor="rgb(100,100,100)",i.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 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180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]}},4574:(t,e,n)=>{"use strict";n.d(e,{O:()=>r,n:()=>o});var i=n(1858);class o{constructor(t,e=!0,n){return this.substructure=t,this.readOnly=e,this.logger=n,new Proxy(this,{set:(t,e,n)=>{if(this.logger?.debug(`BioFilterProps.set ${e.toString()}( '${n}' )`),this.readOnly)throw new Error("Properties are immutable.");return t[e]=n,!0}})}}class r{constructor(){this.onChanged=new i.Subject,this._props=null,this._propsChanging=!1}get props(){return this._props||(this._props=this.emptyProps),this._props}set props(t){this._propsChanging=!0;try{this._props=t,this.applyProps(),this.onChanged.next()}finally{this._propsChanging=!1}}saveProps(){const t={};for(const[e,n]of Object.entries(this.props))"_onChanged"!==e&&"logger"!==e&&(t[e]=this.props[e]);return t}async detach(){}get filterSummary(){return this.props.substructure}get isFiltering(){return""!==this.props.substructure}resetFilter(){this.props=this.emptyProps,this.onChanged.next()}}},4152:(t,e,n)=>{"use strict";var i=n(6082),o=n(7362),r=n(6718);function s(t,e=!0){if(null==t)return"rgb(100,100,100)";const n=i.Color.fromHtml(t);if(e){const t=i.Color.g(n),e=i.Color.r(n),o=i.Color.b(n),r=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-o,2));if(r>210)return`rgb(${e/r*210},${t/r*210},${o/r*210})`}return i.Color.toRgb(n)}class a{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class l{}class c extends l{static get palette(){return c._pallete||(c._pallete=c.buildPalette()),c._pallete}static buildPalette(){return(0,r.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{c.customMonomerColors={},c.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const i of n){const 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a{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++l.viewerCounter,this.errors=[],this._onRendered=new o.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((t=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(t){this.logger.error(t)}})))),this.tableCol&&this.subs.push(i.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(i.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const t of this.subs)t.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(t){this.invalidateGrid()}async awaitRendered(t=1e4,e=`${t} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,r.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),t,`${n}, ${e}`),this.errors.length>0){const t=this.errors[0];throw this.errors=[],t}this.logger.debug(`${n}, end`)}}l.viewerCounter=-1},673:(t,e,n)=>{"use strict";n.d(e,{s:()=>i});const i={true:"1",false:"0"}},6882:(t,e,n)=>{"use strict";n.d(e,{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),h=n(6718),u=n(9192),d=n(3856),p=n(673),m=n(3599),f=n(5553),g=n(9713);const y="rgb(100,100,100)";class b extends c.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(t,e,n,i,r){if(super(t,e,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 t=[l.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((e=>e.args.source===this.tableCol&&t.includes(e.args.key)))),200).subscribe((t=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((t=>t.args.source===this.tableCol&&t.args.key===l.gp.positionShift))),200).subscribe((t=>{this.reset()})))}}calculateFontBasedSpacing(t){const e=t.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const t=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof t||isNaN(t)||(n=Math.max(t,1))}return{lineHeight:Math.max(1.4*n,e.fontBoundingBoxAscent+e.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(t){return"true"===t.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(t,e,n,i,o,r){if(this.dirty)try{this.reset()}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(t),l=e-2*this.padding;let c=0;const h=[];if(i.length>0)for(let e=o;e<i.length;e++){const n=i.getOriginal(e),o=this.props.monomerToShort(n,r);h.push({text:o,posIdx:e}),c=Math.max(c,t.measureText(o).width)}if(0===h.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,f=Math.max(0,Math.floor(m/s)),g=[];let y=0;for(let t=0;t<f&&y<h.length;t++){const e=[];for(let t=0;t<p&&y<h.length;t++){const n=h[y],i=this.padding+t*(d+a);e.push({posIdx:n.posIdx,x:i,width:d,om:n.text,isSeparator:!1}),y++}g.push({lineIdx:t,elements:e})}return{lineLayouts:g,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,h.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}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(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=this.padding;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,r=Math.ceil(e/i)+o,s=n.splitter(t),a=Math.min(r,s.length),l=new Array(a-o);let c=0;for(let t=o;t<a;++t){const i=s.getOriginal(t),r=this.props.monomerToShort(i,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(l[t-o]=a,c+=a,c>e)break}return l}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/i)+e,r=n.getSplitted(t),s=Math.min(o,r.length);let a=this._monomerLengthList[t];if(null===a||a.length!=s-e){a=this._monomerLengthList[t]=new Array(r.length);let i=0;for(let t=e;t<s;++t){const o=r.getOriginal(t),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[t-e]=l,i+=l,i>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:i}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){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 t=n;t<i;t++){if(this._processedRows.get(t)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,s),i=Math.min(s,n.length);i-r>e.length&&e.push(...new Array(i-r-e.length).fill(o));let a=0;for(let t=r;t<i;++t){const i=n.getOriginal(t),o=this.props.monomerToShort(i,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(e[t-r]=Math.max(e[t-r]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(t,!0)}return e}getPosition(t,e,n,i){const[o,r]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e,n){if((n??0)>0&&e<(t[0]??0)+n)return-1;e-=n??0;let i,o=100,r=0,s=t.length-1;for(;r<=s;){if(i=Math.floor((s+r)/2),t[i]<=e&&e<t[i+1])return i;if(e<t[i]?s=i-1:r=i+1,--o<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(r,e,i)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}get positionShift(){const t=Number.parseInt(this.tableCol?.tags[l.gp.positionShift]??"0")??0;return isNaN(t)?0:Math.max(t,0)}render(t,e,n,i,r,a,c){const h=a.grid?.canvas===t.canvas;if(!this.seqHelper)return;const m=this.tableCol,f=this.positionShift;t.save();try{const c=this.seqHelper.getSeqHandler(m);let u=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const t=parseInt(m.getTag(d.gp.maxMonomerLength));u=!isNaN(t)&&t?t:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=u){let t=0;const e=8;t=m.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(u),this.setSeparatorWidth(c.isMsa()?e:t),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const g=a.cell.rowIndex,b=a.cell.value;h&&(i=v(a.grid,t,e,i,window.devicePixelRatio)),t.beginPath(),t.rect(e,n,i,r),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const w=m.meta.units,C=m.getTag(l.gp.aligned),A=m.getTag(l.gp.separator)??"",S=h?c.getSplitted(g):c.splitter(b);let x=d.yg.classic;C?.includes("MSA")&&w===l.Hi.SEPARATOR&&(x=d.yg.MSA);const E=m.temp["reference-sequence"],T=this.tableCol.temp["current-word"],M=(()=>{const t=(0,c.splitter)(null!=E&&""!==E?E:T??"");return s().count(0).take(t.length).slice(f).map((e=>t.getCanonical(e))).toArray()})(),_=Number.parseInt(m.getTag(l.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const s=[],l=this.calculateMultiLineLayoutDynamic(t,i,r,S,f,u);let h=n+this.padding;1===l.lineLayouts.length&&(h=n+(r-l.lineHeight)/2);for(const i of l.lineLayouts){const r=h+i.lineIdx*l.lineHeight;for(const h of i.elements){const u=e+h.x,p=h,g=p.posIdx,b=S.getCanonical(g);let v=y;const w=this.getMonomerLib();w&&(v=w.getMonomerTextColor(c.defaultBiotype,b));let C=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&M.length>0){const t=g-f;t>=0&&t<M.length&&b===M[t]&&(C=.7)}s.push({lineIdx:i.lineIdx,monomerIdx:g-f,bounds:new o.Rect(h.x,r-n,h.width,l.lineHeight),sequencePosition:g}),(0,d.oZ)(t,p.om,u,r,h.width,l.lineHeight,{color:v,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(_)||_<1?void 0:_,wordIdx:g})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,s)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(f)?t.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,i);h||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,i)));const s=this.props.separatorWidth+1*this.props.fontCharWidth,l=Math.min(S.length,Math.ceil(i/s)+f);for(let s=f;s<l;++s){const l=s<S.length?S.getOriginal(s):c.defaultGapOriginal,h=s<S.length?S.getCanonical(s):c.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(c.defaultBiotype,h));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:A,last:s===S.length-1,drawStyle:x,maxWord:o,wordIdx:s-f,gridCell:a,referenceSequence:M,maxLengthOfMonomer:u,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(_)||_<1?void 0:_-f};(0,d.oZ)(t,l,e+this.padding+this._leftThreeDotsPadding,n,i,r,m)}if(this.shouldRenderShiftedThreeDots(f)){const s={color:y,pivot:0,left:!0,transparencyRate:0,separator:A,last:!1,drawStyle:x,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:u,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,d.oZ)(t,"...",e+this.padding,n,i,r,s)}}}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}shouldRenderShiftedThreeDots(t){return t>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const o=this.positionShift,r=t.bounds,s=e.offsetX-t.gridColumn.left+(t.gridColumn.left-r.x),a=e.offsetY-r.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let c=null;const h=this._cellBounds.get(t.tableRowIndex);if(h){for(const t of h)if(t.bounds.contains(s,a)){c=t.monomerIdx;break}}else{const e=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;c=this.getPosition(t.tableRowIndex,s,r.width,e)}this.logger.debug(`${n}, argsX: ${s}, argsY: ${a}, left: ${c}`);const u=this.seqHelper.getSeqHandler(this.tableCol),d=u.getSplitted(t.tableRowIndex);if(null!==c&&c>=0&&c+o<d.length){const n=u.alphabet??l.YI.UN,r={position:c,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:d.getCanonical(c+o)},s=[];let a=this._monomerStructureMap[r.symbol];if(!a){const t=this.getMonomerLib();a=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}s.push(a),i.tooltip.show(i.divV(s),e.x+16,e.y+16),(0,f.WN)(t,r)}else-1===c?i.tooltip.show(i.divText(`${Math.min(o,d.length)} hidden monomers`),e.x+16,e.y+16):i.tooltip.hide(),(0,f.WN)(t,null)}}function v(t,e,n,i,o){return t?Math.max(Math.min(t.canvas.width/o-n,i)):Math.max(e.canvas.width/o-n,0)}},3856:(t,e,n)=>{"use strict";n.d(e,{Mn:()=>h,gp:()=>c,oZ:()=>p,yg:()=>u});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,h,u;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(c||(c={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(h||(h={})),function(t){t.MSA="MSA",t.classic="classic"}(u||(u={}));const d=new class{constructor(){this.color=r,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=u.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(t,e,n,o,c,h,p){var m,f,g;const y={...d,...p};if(y.isMultiLineContext){t.textBaseline="middle",t.textAlign="center";let i=e;null!=y.maxLengthOfMonomer&&(i=l(i,y.maxLengthOfMonomer));const s=Math.max(.1,1-(y.transparencyRate??0));t.globalAlpha=s;const u=t.measureText(i),d=u.fontBoundingBoxAscent+u.fontBoundingBoxDescent,p=o+(h-d)/2+u.fontBoundingBoxAscent;let m=y.color??r;return m&&m!==r||(m=a),t.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(t.save(),t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n,o,c,h),t.restore(),t.fillStyle=m),t.fillText(i,n+c/2,p),t.globalAlpha=1,t.textBaseline="top",t.textAlign="start",n+c}p.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let b=e.substring(0),v=y.last?"":y.separator;y.drawStyle===u.MSA&&(v="");let w=!0,C=!0,A="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,A=y.gridCell.cell.column.temp["highlight-difference"]??"difference"),y.referenceSequence){const t=y.referenceSequence[y.wordIdx];C&&y.referenceSequence.length>0&&"difference"===A&&(y.transparencyRate=b==t?.7:y.transparencyRate),C&&y.referenceSequence.length>0&&"equal"===A&&(y.transparencyRate=b!=t?.7:y.transparencyRate)}null!=y.maxLengthOfMonomer&&(b=l(b,y.maxLengthOfMonomer));const S=b+v;(m=y.monomerTextSizeMap)[S]??(m[S]=t.measureText(S));let x=y.monomerTextSizeMap[S];(f=y.monomerTextSizeMap)[b]??(f[b]=t.measureText(b));let E=y.monomerTextSizeMap[b].width;const T=h/2-(x.fontBoundingBoxAscent+x.fontBoundingBoxDescent)/2+1;(g=y.monomerTextSizeMap)[v]??(g[v]=t.measureText(v));const M=y.monomerTextSizeMap[v].width;function _(e,r){let l=w?y.color:a;y.selectedPosition===y.wordIdx+1&&(t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n+e-4,o-5,y.monomerTextSizeMap[b].width+8,h+10),l=i.Color.toHtml(i.Color.setAlpha(i.Color.fromHtml(l),255))),t.fillStyle=l,t.globalAlpha=1-y.transparencyRate,y.drawStyle===u.classic&&(t.fillText(b,n+e,o+T),t.fillStyle=s,t.fillText(v,n+r,o+T)),y.drawStyle===u.MSA&&t.fillText(b,n+e,o+T),t.globalAlpha=1}x=x.width,y.drawStyle===u.MSA&&(E=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+E),n+I+E+M;{const t=(c-x)/2;return _(t,t+E),n+I+t+E}}},6307:(t,e,n)=>{"use strict";n.d(e,{F:()=>s});var i=n(7389),o=n(6082),r=n(439);function s(t,e,n){let s=0,a=null;for(const e of Object.values(t))s+=e,a=null===a?e:Math.max(a,e);const l=a/s,c=Object.assign({},...Array.from(Object.entries(t)).sort(((t,e)=>e[1]-t[1])).map((([t,a])=>{const c=a/s;let h;try{const i=n.getMonomerColors(e,t);h=i?.backgroundcolor||"#CCCCCC"}catch(e){console.warn(`Failed to get colors for monomer ${t}:`,e),h="#CCCCCC"}const u=i.div("",{classes:"macromolecule-cell-comp-analysis-bar"});u.style.width=50*c/l+"px",u.style.backgroundColor=h,r._S===t&&(u.style.borderWidth="1px",u.style.borderStyle="solid",u.style.borderColor=o.Color.toHtml(o.Color.lightGray));const d=r._S===t?"-":t,p=i.div(`${(100*c).toFixed(2)}%`),m=i.div([u,p],{classes:"macromolecule-cell-comp-analysis-value"});return{[d]:m}}))),h=i.tableFromMap(c);return Array.from(h.rows).forEach((t=>{const e=t.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;t.cells[0].style.color=e})),h}},3151:(t,e,n)=>{"use strict";n.d(e,{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)\\)${a}?`,"g")},9192:(t,e,n)=>{"use strict";function i(t){return"string"==typeof t||t instanceof String?t:"StateError"===t.constructor.name?t.message:"StateError"===t.constructor.name&&"$thrownJsError"in t?i(t.$thrownJsError):t instanceof Error?t.message:t.toString()}function o(t){return t instanceof Error?t.stack:"StateError"===t.constructor.name&&"$thrownJsError"in t?o(t.$thrownJsError):void 0}function r(t){return[i(t),o(t)]}n.d(e,{AP:()=>r})},3516:(t,e,n)=>{"use strict";n.d(e,{m:()=>r});var i=n(6082),o=n(439);class r{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(t,e){return this._fileContent.slice(t,e).split(/\s/).join("")}parseColumns(){const t=/^>(.*)$/gm;let e,n=0;for(;e=t.exec(this._fileContent);){const i=this._fileContent.substring(e.index+1,t.lastIndex);this._descriptionsArray.push(i),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,e.index)),n=t.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const t=i.Column.fromStrings("description",this.descriptionsArray),e=i.Column.fromStrings("sequence",this.sequencesArray);return e.semType=i.SEMTYPE.MACROMOLECULE,e.meta.units=o.Hi.FASTA,[i.DataFrame.fromColumns([t,e])]}constructor(t){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=t,this.parseColumns()}}},6873:(t,e,n)=>{"use strict";n.d(e,{Hx:()=>h,dW:()=>c});var i=n(6082),o=n(1991),r=n.n(o),s=n(2003),a=n(7278),l=n(439);function c(t=10**5){const e="meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe".repeat(Math.ceil(t/10)).slice(0,-1),n=i.Column.fromList(i.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(e));n.semType=i.SEMTYPE.MACROMOLECULE,n.meta.units=s.Hi.SEPARATOR,n.setTag(s.gp.separator,"/"),n.setTag(s.gp.alphabet,s.YI.UN),n.setTag(s.gp.alphabetIsMultichar,"true");const o=[];return o.push(n),o.push(i.Column.fromList(i.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),o}function h(t,e=s.Hi.SEPARATOR,n=s.YI.PT,o=(e===s.Hi.SEPARATOR?"-":void 0),c=void 0,h="seq",u=100,d=10**6){const p=n===s.YI.UN?c?.getMonomerSymbolsByType("PEPTIDE")??[]:Array.from((0,s.Qf)(n)),m=p.length,f=i.Column.fromType(i.COLUMN_TYPE.STRING,h,u);f.semType=i.SEMTYPE.MACROMOLECULE,f.meta.units=e,f.setTag(s.gp.alphabet,n),e==s.Hi.SEPARATOR&&f.setTag(s.gp.separator,o);const g=t.getSeqHandler(f);for(let t=0;t<u;t++){const n=r().count(0).take(d).map((t=>p[Math.floor(Math.random()*m)])).toArray(),i=g.joiner(new a.Mu(n,l.b9[e]));f.set(t,i)}return f}},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>l,Hi:()=>i,Vl:()=>c,YI:()=>o,_S:()=>u,b9:()=>d,gp:()=>r,ot:()=>p,q7:()=>h,z1:()=>a});var 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r.bonds)o[t]=a}return{atoms:Object.keys(n).map((t=>parseInt(t))),bonds:Object.keys(o).map((t=>parseInt(t))),highlightAtomColors:n,highlightBondColors:o}}},3561:(t,e,n)=>{"use strict";n.d(e,{Hb:()=>l,YN:()=>f,gU:()=>c});var i=n(8123),o=n(294),r=n(3151),s=n(439),a=n(6197);function l(t,e,n){const o=new Map;for(const a of t.getMonomerSymbolsByType(e)){const l=t.getMonomer(e,a);if("RNA"===e&&("Branch"===l.monomerType||n===s.YI.DNA&&l.symbol===i.u.DEOXYRIBOSE.symbol||n===s.YI.RNA&&l.symbol===i.u.RIBOSE.symbol||l.symbol===i.u.PHOSPHATE.symbol)||"PEPTIDE"===e&&"Branch"!==l.monomerType){const t={};r.f6.forEach((e=>{t[e]=l[e]})),o.set(l.symbol,t)}}return o}function c(t,e,n,r){if(0===t.length)return o.vF.createEmpty();const l=m,{atomCount:c,bondCount:u,needsCapping:p}=l(t,e,n,r),g=new Array(c),y=new Array(u);let b,v=null,w=null;"PEPTIDE"===r?b=h:(b=d,v=n===s.YI.DNA?(0,o.xb)(e,i.u.DEOXYRIBOSE):(0,o.xb)(e,i.u.RIBOSE),w=(0,o.xb)(e,i.u.PHOSPHATE));const 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a=n.backboneAttachNode,l=s;e[o.bondCount]=i.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(g,y,C,A,E??i.u.OXYGEN);const M=i.u.V3K_BEGIN_COUNTS_LINE+c+" "+u+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,_+=M,_+=i.u.V3K_BEGIN_ATOM_BLOCK,_+=g.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(t){const e=[];let n=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let i=0;i<t.length;i++){const o=`${n} ${t[i]}`;o.length>76?(e.push(`${n} -\n`),n=`M  V30 ${t[i]}`):n=o,i===t.length-1&&e.push(`${n})\n`)}return`M  V30 BEGIN COLLECTION\n${e.join("")}M  V30 END COLLECTION\n`}(x)),_+=i.u.V3K_END_CTAB_BLOCK,_+=i.u.V3K_END,{molfile:_,monomers:S}}function h(t,e,n,i){i.flipFactor=(-1)**(i.i%2),u(t,e,n,i)}function u(t,e,n,o){!function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;e[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+t.atoms.atomTypes[o]+" "+f(n.backbonePositionShift[0]+t.atoms.x[o])+" "+f(n.backbonePositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}}(t,e,o),p(t,n,o),function(t,e,n){if(0!==n.backboneAttachNode){const o=n.bondShift,r=n.backboneAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[n.bondShift-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}}(t,n,o),null!==t.meta.branchShift&&t.meta.terminalNodes.length>2&&function(t,e){e.branchAttachNode=e.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)e.branchPositionShift[n]=e.backbonePositionShift[n]+t.meta.branchShift[n]}(t,o),function(t,e){e.backboneAttachNode=e.nodeShift+t.meta.terminalNodes[1],e.bondShift+=t.bonds.atomPairs.length+1,e.nodeShift+=t.atoms.atomTypes.length,e.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,e.backbonePositionShift[1]+=e.flipFactor*(t.meta.backboneShift?.[1]??0)}(t,o)}function d(t,e,n,o,r){if(0===o.i)u(r.sugar,e,n,o);else for(const t of[r.phosphate,r.sugar])u(t,e,n,o);!function(t,e,n,o){(function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const r=n.nodeShift+o+1;e[n.nodeShift+o]=i.u.V3K_BEGIN_DATA_LINE+r+" "+t.atoms.atomTypes[o]+" "+f(n.branchPositionShift[0]+t.atoms.x[o])+" "+f(n.branchPositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}})(t,e,o),p(t,n,o),function(t,e,n){const o=n.bondShift,r=n.branchAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[o-1]=i.u.V3K_BEGIN_DATA_LINE+o+" 1 "+r+" "+s+"\n"}(t,n,o);const r=o.bondShift,s=o.branchAttachNode,a=t.meta.terminalNodes[0]+o.nodeShift;n[r-1]=i.u.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+a+"\n",o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length}(t,e,n,o)}function p(t,e,n){for(let o=0;o<t.bonds.atomPairs.length;++o){const r=n.bondShift+o+1,s=t.bonds.atomPairs[o][0]+n.nodeShift,a=t.bonds.atomPairs[o][1]+n.nodeShift;let l="";if(t.bonds.bondConfiguration.has(o)){let 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i=n(4328),o=n(6082),r=n(1991),s=n.n(r),a=n(439),l=n(3561),c=n(9235),h=n(294),u=n(9192),d=n(330),p=n(8123);async function m(t,e,n,r,l){if(e.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${e.semType}'`]};let h=e;const p=r.getSeqHandler(e);let m,g;p.notation!==a.Hi.SEPARATOR&&(h=p.convert(a.Hi.SEPARATOR,"."),h.name=e.name);try{g=r.getSeqHandler(h).alphabet,m=(0,d.pz)(g)}catch(t){const[e,n]=(0,u.AP)(t);return{molCol:null,warnings:[e]}}const y=function(t,e){const n=t.length,o=new Array(n),r=e.getSeqHandler(t);let a=!1;const l=r.defaultBiotype;for(let t=0;t<n;++t){const e=r.getSplitted(t);a||(a=0===e.length),o[t]=s().count(0).take(e.length).filter((t=>!e.isGap(t))).map((t=>({position:t,biotype:l,symbol:e.getCanonical(t)}))).toArray()}return a&&i.shell.warning(`Some values in the "${t.name}" column are empty`),o}(h,r),b=f(y,m,g,n,l),v=h.length,w=await(0,c.R)(h,b,g,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 t=w.molCol.toList(),e=await C.apply({mols:t});w.molCol.init((n=>e[n]?e[n]:t[n]))}catch(t){console.error(t)}return w}function f(t,e,n,i,o){const r=(0,l.Hb)(i,e,n),s={},c={value:null};if("RNA"===e){const t=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of t)g(s,n.symbol,r,o,e,c)}for(let n=0;n<t.length;++n){const i=t[n];for(const t of i){const n=t.symbol;if(""!==n)try{if("RNA"===e&&3===n.split(/\(|\)/).filter((t=>!!t)).length){const t=n.split(/\(|\)/)[1];g(s,t,r,o,e,c),s[e]?.[t]&&(s[e][n]=s[e][t])}else g(s,n,r,o,e,c)}catch(t){const e=t instanceof Error?t.message:t.toString(),i=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${e}\n${i}`),new 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t.substring(0,e)+t.substring(n)}(s.molfile),n),u=function(t){let e=(t=t.replaceAll("\r","")).indexOf(p.u.V3K_BEGIN_COUNTS_LINE)+p.u.V3K_COUNTS_SHIFT,n=t.indexOf(" ",e+1);const i=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e+1),{atomCount:i,bondCount:parseInt(t.substring(e,n))}}(h),d=function(t,e){const n=new Array(e),i=new Float32Array(e),o=new Float32Array(e),r=new Array(e);let s=t.indexOf(p.u.V3K_BEGIN_ATOM_BLOCK);s=t.indexOf("\n",s);let a=s;for(let l=0;l<e;l++){s=t.indexOf(p.u.V3K_BEGIN_DATA_LINE,s)+p.u.V3K_IDX_SHIFT,a=t.indexOf(" ",s),s=a+1,a=t.indexOf(" ",s),n[l]=t.substring(s,a);const e=new Array(2);for(let n=0;n<2;++n)s=a+1,a=t.indexOf(" ",s),e[n]=parseFloat(t.substring(s,a));i[l]=e[0],o[l]=e[1],s=a,a=t.indexOf("\n",s)+1,r[l]=t.slice(s,a),s=a}return{atomTypes:n,x:i,y:o,kwargs:r}}(h,u.atomCount),m=function(t,e){const n=new Uint32Array(e),i=new Array(e),o=new Map,r=new Map;let s=t.indexOf(p.u.V3K_BEGIN_BOND_BLOCK);s=t.indexOf("\n",s);let a=s;for(let l=0;l<e;++l){const 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r=A(i[n],o[n]);S(t.atoms,Math.PI/2-r)}(v):function(t,e){const n=t.atoms.x,i=t.atoms.y,o=t.meta.terminalNodes[0]-1,r=t.meta.rNodes[0]-1;T(t,-n[o],-i[o]);const s=A(n[r],i[r]),a=e.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");S(t.atoms,Math.PI-s+a);const c=function(t,e){return(0,l.YN)(Math.sqrt((t.x-e.x)**2+(t.y-e.y)**2))}({x:n[t.meta.rNodes[0]-1],y:i[t.meta.rNodes[0]-1]},{x:n[t.meta.terminalNodes[0]-1],y:i[t.meta.terminalNodes[0]-1]});if(1!=c)for(let t=0;t<n.length;++t)n[t]=(0,l.YN)(n[t]/c),i[t]=(0,l.YN)(i[t]/c)}(v,o),function(t,e,n){if("PEPTIDE"===t){b(e,t);const n=w(e,e.meta.rNodes[1]);n?.removedAtom&&(e.terminalR2Atom=n.removedAtom)}else 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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 t=[l.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((e=>e.args.source===this.tableCol&&t.includes(e.args.key)))),200).subscribe((t=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((t=>t.args.source===this.tableCol&&t.args.key===l.gp.positionShift))),200).subscribe((t=>{this.reset()})))}}calculateFontBasedSpacing(t){const e=t.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const t=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof t||isNaN(t)||(n=Math.max(t,1))}return{lineHeight:Math.max(1.4*n,e.fontBoundingBoxAscent+e.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(t){return"true"===t.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(t,e,n,i,o,r){if(this.dirty)try{this.reset()}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(t),l=e-2*this.padding;let c=0;const h=[];if(i.length>0)for(let e=o;e<i.length;e++){const n=i.getOriginal(e),o=this.props.monomerToShort(n,r);h.push({text:o,posIdx:e}),c=Math.max(c,t.measureText(o).width)}if(0===h.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,f=Math.max(0,Math.floor(m/s)),g=[];let y=0;for(let t=0;t<f&&y<h.length;t++){const e=[];for(let t=0;t<p&&y<h.length;t++){const n=h[y],i=this.padding+t*(d+a);e.push({posIdx:n.posIdx,x:i,width:d,om:n.text,isSeparator:!1}),y++}g.push({lineIdx:t,elements:e})}return{lineLayouts:g,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,h.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}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(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=this.padding;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,r=Math.ceil(e/i)+o,s=n.splitter(t),a=Math.min(r,s.length),l=new Array(a-o);let c=0;for(let t=o;t<a;++t){const i=s.getOriginal(t),r=this.props.monomerToShort(i,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(l[t-o]=a,c+=a,c>e)break}return l}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/i)+e,r=n.getSplitted(t),s=Math.min(o,r.length);let a=this._monomerLengthList[t];if(null===a||a.length!=s-e){a=this._monomerLengthList[t]=new Array(r.length);let i=0;for(let t=e;t<s;++t){const o=r.getOriginal(t),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[t-e]=l,i+=l,i>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:i}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){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 t=n;t<i;t++){if(this._processedRows.get(t)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,s),i=Math.min(s,n.length);i-r>e.length&&e.push(...new Array(i-r-e.length).fill(o));let a=0;for(let t=r;t<i;++t){const i=n.getOriginal(t),o=this.props.monomerToShort(i,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(e[t-r]=Math.max(e[t-r]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(t,!0)}return e}getPosition(t,e,n,i){const[o,r]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e,n){if((n??0)>0&&e<(t[0]??0)+n)return-1;e-=n??0;let i,o=100,r=0,s=t.length-1;for(;r<=s;){if(i=Math.floor((s+r)/2),t[i]<=e&&e<t[i+1])return i;if(e<t[i]?s=i-1:r=i+1,--o<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(r,e,i)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}get positionShift(){const t=Number.parseInt(this.tableCol?.tags[l.gp.positionShift]??"0")??0;return isNaN(t)?0:Math.max(t,0)}render(t,e,n,i,r,a,c){const h=a.grid?.canvas===t.canvas;if(!this.seqHelper)return;const m=this.tableCol,f=this.positionShift;t.save();try{const c=this.seqHelper.getSeqHandler(m);let u=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const t=parseInt(m.getTag(d.gp.maxMonomerLength));u=!isNaN(t)&&t?t:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=u){let t=0;const e=8;t=m.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(u),this.setSeparatorWidth(c.isMsa()?e:t),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const g=a.cell.rowIndex,b=a.cell.value;h&&(i=v(a.grid,t,e,i,window.devicePixelRatio)),t.beginPath(),t.rect(e,n,i,r),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const w=m.meta.units,C=m.getTag(l.gp.aligned),A=m.getTag(l.gp.separator)??"",S=h?c.getSplitted(g):c.splitter(b);let x=d.yg.classic;C?.includes("MSA")&&w===l.Hi.SEPARATOR&&(x=d.yg.MSA);const E=m.temp["reference-sequence"],T=this.tableCol.temp["current-word"],M=(()=>{const t=(0,c.splitter)(null!=E&&""!==E?E:T??"");return s().count(0).take(t.length).slice(f).map((e=>t.getCanonical(e))).toArray()})(),_=Number.parseInt(m.getTag(l.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const s=[],l=this.calculateMultiLineLayoutDynamic(t,i,r,S,f,u);let h=n+this.padding;1===l.lineLayouts.length&&(h=n+(r-l.lineHeight)/2);for(const i of l.lineLayouts){const r=h+i.lineIdx*l.lineHeight;for(const h of i.elements){const u=e+h.x,p=h,g=p.posIdx,b=S.getCanonical(g);let v=y;const w=this.getMonomerLib();w&&(v=w.getMonomerTextColor(c.defaultBiotype,b));let C=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&M.length>0){const t=g-f;t>=0&&t<M.length&&b===M[t]&&(C=.7)}s.push({lineIdx:i.lineIdx,monomerIdx:g-f,bounds:new o.Rect(h.x,r-n,h.width,l.lineHeight),sequencePosition:g}),(0,d.oZ)(t,p.om,u,r,h.width,l.lineHeight,{color:v,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(_)||_<1?void 0:_,wordIdx:g})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,s)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(f)?t.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,i);h||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,i)));const s=this.props.separatorWidth+1*this.props.fontCharWidth,l=Math.min(S.length,Math.ceil(i/s)+f);for(let s=f;s<l;++s){const l=s<S.length?S.getOriginal(s):c.defaultGapOriginal,h=s<S.length?S.getCanonical(s):c.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(c.defaultBiotype,h));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:A,last:s===S.length-1,drawStyle:x,maxWord:o,wordIdx:s-f,gridCell:a,referenceSequence:M,maxLengthOfMonomer:u,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(_)||_<1?void 0:_-f};(0,d.oZ)(t,l,e+this.padding+this._leftThreeDotsPadding,n,i,r,m)}if(this.shouldRenderShiftedThreeDots(f)){const s={color:y,pivot:0,left:!0,transparencyRate:0,separator:A,last:!1,drawStyle:x,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:u,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,d.oZ)(t,"...",e+this.padding,n,i,r,s)}}}catch(t){const[e,n]=(0,u.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}shouldRenderShiftedThreeDots(t){return t>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const o=this.positionShift,r=t.bounds,s=e.offsetX-t.gridColumn.left+(t.gridColumn.left-r.x),a=e.offsetY-r.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let c=null;const h=this._cellBounds.get(t.tableRowIndex);if(h){for(const t of h)if(t.bounds.contains(s,a)){c=t.monomerIdx;break}}else{const e=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;c=this.getPosition(t.tableRowIndex,s,r.width,e)}this.logger.debug(`${n}, argsX: ${s}, argsY: ${a}, left: ${c}`);const u=this.seqHelper.getSeqHandler(this.tableCol),d=u.getSplitted(t.tableRowIndex);if(null!==c&&c>=0&&c+o<d.length){const n=u.alphabet??l.YI.UN,r={position:c,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:d.getCanonical(c+o)},s=[];let a=this._monomerStructureMap[r.symbol];if(!a){const t=this.getMonomerLib();a=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}s.push(a),i.tooltip.show(i.divV(s),e.x+16,e.y+16),(0,f.WN)(t,r)}else-1===c?i.tooltip.show(i.divText(`${Math.min(o,d.length)} hidden monomers`),e.x+16,e.y+16):i.tooltip.hide(),(0,f.WN)(t,null)}}function v(t,e,n,i,o){return t?Math.max(Math.min(t.canvas.width/o-n,i)):Math.max(e.canvas.width/o-n,0)}},3856:(t,e,n)=>{"use strict";n.d(e,{Mn:()=>h,gp:()=>c,oZ:()=>p,yg:()=>u});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,h,u;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(c||(c={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(h||(h={})),function(t){t.MSA="MSA",t.classic="classic"}(u||(u={}));const d=new class{constructor(){this.color=r,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=u.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(t,e,n,o,c,h,p){var m,f,g;const y={...d,...p};if(y.isMultiLineContext){t.textBaseline="middle",t.textAlign="center";let i=e;null!=y.maxLengthOfMonomer&&(i=l(i,y.maxLengthOfMonomer));const s=Math.max(.1,1-(y.transparencyRate??0));t.globalAlpha=s;const u=t.measureText(i),d=u.fontBoundingBoxAscent+u.fontBoundingBoxDescent,p=o+(h-d)/2+u.fontBoundingBoxAscent;let m=y.color??r;return m&&m!==r||(m=a),t.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(t.save(),t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n,o,c,h),t.restore(),t.fillStyle=m),t.fillText(i,n+c/2,p),t.globalAlpha=1,t.textBaseline="top",t.textAlign="start",n+c}p.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let b=e.substring(0),v=y.last?"":y.separator;y.drawStyle===u.MSA&&(v="");let w=!0,C=!0,A="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,A=y.gridCell.cell.column.temp["highlight-difference"]??"difference"),y.referenceSequence){const t=y.referenceSequence[y.wordIdx];C&&y.referenceSequence.length>0&&"difference"===A&&(y.transparencyRate=b==t?.7:y.transparencyRate),C&&y.referenceSequence.length>0&&"equal"===A&&(y.transparencyRate=b!=t?.7:y.transparencyRate)}null!=y.maxLengthOfMonomer&&(b=l(b,y.maxLengthOfMonomer));const S=b+v;(m=y.monomerTextSizeMap)[S]??(m[S]=t.measureText(S));let x=y.monomerTextSizeMap[S];(f=y.monomerTextSizeMap)[b]??(f[b]=t.measureText(b));let E=y.monomerTextSizeMap[b].width;const T=h/2-(x.fontBoundingBoxAscent+x.fontBoundingBoxDescent)/2+1;(g=y.monomerTextSizeMap)[v]??(g[v]=t.measureText(v));const M=y.monomerTextSizeMap[v].width;function _(e,r){let l=w?y.color:a;y.selectedPosition===y.wordIdx+1&&(t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n+e-4,o-5,y.monomerTextSizeMap[b].width+8,h+10),l=i.Color.toHtml(i.Color.setAlpha(i.Color.fromHtml(l),255))),t.fillStyle=l,t.globalAlpha=1-y.transparencyRate,y.drawStyle===u.classic&&(t.fillText(b,n+e,o+T),t.fillStyle=s,t.fillText(v,n+r,o+T)),y.drawStyle===u.MSA&&t.fillText(b,n+e,o+T),t.globalAlpha=1}x=x.width,y.drawStyle===u.MSA&&(E=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+E),n+I+E+M;{const t=(c-x)/2;return _(t,t+E),n+I+t+E}}},6307:(t,e,n)=>{"use strict";n.d(e,{F:()=>s});var i=n(7389),o=n(6082),r=n(439);function s(t,e,n){let s=0,a=null;for(const e of Object.values(t))s+=e,a=null===a?e:Math.max(a,e);const l=a/s,c=Object.assign({},...Array.from(Object.entries(t)).sort(((t,e)=>e[1]-t[1])).map((([t,a])=>{const c=a/s;let h;try{const i=n.getMonomerColors(e,t);h=i?.backgroundcolor||"#CCCCCC"}catch(e){console.warn(`Failed to get colors for monomer ${t}:`,e),h="#CCCCCC"}const u=i.div("",{classes:"macromolecule-cell-comp-analysis-bar"});u.style.width=50*c/l+"px",u.style.backgroundColor=h,r._S===t&&(u.style.borderWidth="1px",u.style.borderStyle="solid",u.style.borderColor=o.Color.toHtml(o.Color.lightGray));const d=r._S===t?"-":t,p=i.div(`${(100*c).toFixed(2)}%`),m=i.div([u,p],{classes:"macromolecule-cell-comp-analysis-value"});return{[d]:m}}))),h=i.tableFromMap(c);return Array.from(h.rows).forEach((t=>{const e=t.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;t.cells[0].style.color=e})),h}},3151:(t,e,n)=>{"use strict";n.d(e,{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)\\)${a}?`,"g")},9192:(t,e,n)=>{"use strict";function i(t){return"string"==typeof t||t instanceof String?t:"StateError"===t.constructor.name?t.message:"StateError"===t.constructor.name&&"$thrownJsError"in t?i(t.$thrownJsError):t instanceof Error?t.message:t.toString()}function o(t){return t instanceof Error?t.stack:"StateError"===t.constructor.name&&"$thrownJsError"in t?o(t.$thrownJsError):void 0}function r(t){return[i(t),o(t)]}n.d(e,{AP:()=>r})},3516:(t,e,n)=>{"use strict";n.d(e,{m:()=>r});var i=n(6082),o=n(439);class r{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(t,e){return this._fileContent.slice(t,e).split(/\s/).join("")}parseColumns(){const t=/^>(.*)$/gm;let e,n=0;for(;e=t.exec(this._fileContent);){const i=this._fileContent.substring(e.index+1,t.lastIndex);this._descriptionsArray.push(i),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,e.index)),n=t.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const t=i.Column.fromStrings("description",this.descriptionsArray),e=i.Column.fromStrings("sequence",this.sequencesArray);return e.semType=i.SEMTYPE.MACROMOLECULE,e.meta.units=o.Hi.FASTA,[i.DataFrame.fromColumns([t,e])]}constructor(t){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=t,this.parseColumns()}}},6873:(t,e,n)=>{"use strict";n.d(e,{Hx:()=>h,dW:()=>c});var i=n(6082),o=n(1991),r=n.n(o),s=n(2003),a=n(7278),l=n(439);function c(t=10**5){const e="meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe".repeat(Math.ceil(t/10)).slice(0,-1),n=i.Column.fromList(i.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(e));n.semType=i.SEMTYPE.MACROMOLECULE,n.meta.units=s.Hi.SEPARATOR,n.setTag(s.gp.separator,"/"),n.setTag(s.gp.alphabet,s.YI.UN),n.setTag(s.gp.alphabetIsMultichar,"true");const o=[];return o.push(n),o.push(i.Column.fromList(i.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),o}function h(t,e=s.Hi.SEPARATOR,n=s.YI.PT,o=(e===s.Hi.SEPARATOR?"-":void 0),c=void 0,h="seq",u=100,d=10**6){const 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